title: ChIP-seq analysis for TP73 protein in TL-Om1 cells

summary: ChIP-seq analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze DNA bindings of TP73 in TL-Om1 cells.

overall_design: TL-Om1 cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by DNBseq.  A sample of whole cell extract (WCE) was sequenced and used as the background (input) to determine enrichment.  ChIP was performed using an antibody against TP73 Antibody (ab14430).

first: Regina

last: Wong


title: Reduced synaptic activity and dysregulated extracellular matrix pathways in midbrain neurons from Parkinson’s disease patient

status: Public on Nov 20 2023

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

type: Expression profiling by high throughput sequencing

summary:
Several mutations that cause Parkinson’s disease (PD) have been identified over the past decade. These account for 15-25% of PD cases; the rest of the cases are considered sporadic. Currently, it is accepted that PD is not a single monolithic disease but rather a constellation of diseases with some common phenotypes. While rodent models exist for some of the PD-causing mutations, research on the sporadic forms of PD is lagging due to a lack of cellular models. In our study, we differentiated PD patient-derived dopaminergic (DA) neurons from the induced pluripotent stem cells (iPSCs) of several PD-causing mutations as well as from sporadic PD patients. Strikingly, we observed a common neurophysiological phenotype: neurons derived from PD patients had a severe reduction in the rate of synaptic currents compared to those derived from healthy controls. While the relationship between mutations in genes such as the SNCA and LRRK2 and a reduction in synaptic transmission has been investigated before, here we show evidence that the pathogenesis of the synapses in neurons is a general phenotype in PD. Analysis of RNA sequencing results displayed changes in gene expression in different synaptic mechanisms as well as other affected pathways such as extracellular matrix-related pathways. Some of these dysregulated pathways are common to all PD patients (monogenic or idiopathic). Our data, therefore, show changes that are central and convergent to PD and suggest a strong involvement of the tetra-partite synapse in PD pathophysiology.
RNA sequencing

overall_design: Shani Stern

first: Shong

last: Lau

first: Fred

last: Gage


title: RNA sequencing of IL-17A and IL-17F producing cells

city: Slough

first: Andrew

middle: James

last: Skelton

address: 208 Bath Road

department: Translational Bioinformatics

country: United Kingdom

institute: UCB

summary: IL-17A has emerged as a pivotal driver of tissue pathology in many immune-mediated inflammatory diseases. Despite sharing 50% sequence homology and the same signalling pathway, the role of IL-17F remains less clear. RNA sequencing of human IL-17 popualtions isolated using a cytokine capture technique identified clear transcriptional differences in IL-17A and IL-17F producing cells, with IL-17A producing cells showing enrichment for cytokine signaling and IL-17F producing cells showing enrichment for cellular replication.

overall_design: Memory CD4+ T cells were isolated from PBMCs and activated with anti-CD3/CD28, IL-1b and IL-23 for 72 hours from n=6 individual donors. IL-17 secreting cells were captured using bispecific antibodies: CD45/IL-17A or CD45/IL-17F. Live cells were then washed and stained with fluorochrome conjugated antibodies towards IL-17A or IL-17F and FACS sorted.

first: Suzanne

last: Cole

middle: J

first: Ash

last: Maroof


title: H3K27ac HiChIP analysis in TL-Om1 cells

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

summary: H3K27ac HiChIP analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze active chromatin-chromatin interactions in TL-Om1 cells.

overall_design: TL-Om1 cells were crosslinked with formaldehyde for 10 min.  DNA was enriched by chromatin-immunoprecipitation (ChIP), tagmented with Tn5 and analyzed by DNBseq.  HiChIP was performed using an antibody against H3K27ac Antibody  (ab4729).

first: Jolynn

middle: L

last: Ong

first: Rui

last: Yokomori

first: Tze

middle: K

first: Takaomi

last: Sanda


title: Requirement for TP73 in cancer cell maintenance and genetic alterations originating from its intragenic super-enhancer

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq analysis after genetic overexpression or knockdown of TP73 in TL-Om1 cells

summary: RNA-seq analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze gene expression changes after genetic overexpression or knockdown of TP73.

overall_design: For overexpression study, lentiviral infection was carried out on TL-Om1 cells to overexpress TAp73 or ∆Np73 under doxycycline (dox)-inducible system.  For knockdown study, lentiviral infection was carried out on TL-Om1 cells to stably express dCas9 and dox-inducible sgRNA targeting TP73 locus. Total RNA was harvested 3 days after dox induction and RNA-seq analysis was performed.


title: Pyruvate is effective in restoring cataracts formed by galactose-induced cataract models.

status: Public on Nov 18 2023

city: Fukui

first: Fuga

last: Masuda

state: Fukui

address: 3-9-1 Bunkyo

department: Applied Chemistry & Biotechnology

country: Japan

institute: University of Fukui

summary:
The addition of Pyruvate to the lens induced by galactose eliminated the white clouding formed and showed a therapeutic effect.
Genes regulated by pyruvate addition were identified by microarray analysis. A total of seven samples were used in this analysis: two samples without galactose (control), three samples with galactose (galactose) and two samples with Pyruvate (Pyruvate).

overall_design: Genes that increased in galactose-treated lenses and reverted with Pyruvate were extracted.

first: Mayumi

last: Inami

first: Yoshihiro

last: Takamura

first: Masaru

last: Inatani

first: Masaya

last: Oki


title: Effects of iron overload on primary hepatocyte of WT and Fxr-/- mice

city: Tianjin

first: Lei

last: Cao

address: 92 Weijin Road

country: China

institute: The School of Pharmaceutical Science and Technology (SPST)

summary: WT and Fxr-/- mouse primary hepatocytes were treated with FAC or AC for 24 h. The transcriptome profiling (RNA-seq) analysis revealed that FXR plays critical roles in regulating iron homeostasis.

overall_design: Liver-derived WT and Fxr-/- mouse primary hepatocytes were cultured in 10% FBS containing DMEM and treated with FAC (100μM) or AC(100μM)  for 24 h. Total RNA was subjected to RNA sequencing.

first: Youcai

last: Zhang

first: Hui

last: Xiong


title: The TGF-β/SMAD pathway upregulates SRC

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The non-receptor tyrosine kinase SRC is upregulated in various human cancers and plays crucial roles in cancer progression by promoting invasion and metastasis. We show that the transforming growth factor beta (TGF-β/SMAD pathway directly upregulates SRC during the epithelial-mesenchymal transition. In human epithelial MCF10A cells, TGF-β1 treatment markedly upregulated mRNA expression of SRC. Knockout of SMAD4 suppressed upregulation of SRC by TGF-β1. ChIP-sequencing analysis revealed that SRC was transcribed from the SRC1A promoter, which interacted with SMAD2 and SMAD4, in response to TGF-β1. These findings demonstrate that a direct interaction of the activated SMAD complex with the SRC1A promoter directly upregulates SRC and suggest that TGF-β contributes to SRC upregulation in the tumor microenvironment, where TGF-β-mediated tumor progression takes place.

overall_design: MCF10A cells were treated with or without TGF-β1 (10 ng/ml) for 48 h. Fixed lysates were subjected to ChIP using an anti-RNA polymerase II antibody

first: Yuki

last: Kubo

first: Masato

last: Okada


title: Strategies for the Enhanced Expression of Porcine RSAD2 against Pseudorabies Virus Infection

status: Public on Nov 19 2023

city: Chang Chun

first: Feng

last: Li

address: xi an street

institute: Jilin University

summary: To further investigate the effect of RSAD2 on global gene expression levels in pigs, transcriptome sequencing analysis of lungs between WT and RSAD2 knock-in pigs were performed.

overall_design: Compair gene expression of lungs between WT and RSAD2 knock-in pigs

first: Zicong

last: Xie

first: Hao

last: Yu

first: DaXin

last: Pang


title: The OsSRO1c-OsDREB2B complex senses low temperatures to confer cold tolerance via direct regulation of COLD1 in rice

city: Wuhan

first: Dan

last: Hu

address: Shizishanjie NO.1

institute: Huazhong Agricultural University

summary: Cold stress is one of the major abiotic stress factors affecting rice growth and development, leading to great yield loss in the context of global climate change. Exploring superior natural variants that confer cold resistance and the underlying molecular mechanism is the major strategy to breed cold tolerant rice varieties. Here, we identified natural variations of a SIMILAR to RCD ONE (SRO) gene OsSRO1c that confers cold tolerance in rice at both seedling and booting stages. OsSRO1c interacts with transcription factor OsDREB2B and promotes its transcriptional activity by concentrating OsDREB2B into biomolecular condensates in the nucleus. The OsSRO1c-OsDREB2B complex directly sense cold stress through dynamic phase transitions in vivo and in vitro and regulate key cold response gene COLD1. Introgression of an elite haplotype of OsSRO1c into a cold susceptible indica rice can significantly increase its cold resistance ability. Thus, our work revealed a novel cold stress sensing module and provided a promising gene resource for breeding cold tolerant rice varieties.

overall_design: To search for downstream target genes of OsSRO1c-OsDREB2B complex under cold stress, we performed RNA-Seq analysis using ossro1c mutants, osdreb2b mutants and wild type ZH11 plants. Those genes down-regulated in both ossro1c mutants and osdreb2b mutants are candidates for OsSRO1c-OsDREB2B complex regulation under cold stress.


title: A helicase-independent role of DHX15 promotes MYC stability and acute leukemia cell survival

city: Hubei

first: Qilong

address: Donghu road

institute: Wuhan university

summary: DHX15 has been implicated in RNA splicing and ribosome biogenesis, primarily functioning as an RNA helicase. To systematically assess the cellular role of DHX15, we conducted proteomic analysis to investigate the landscape of DHX15 interactome, and identified MYC as a binding partner. DHX15 co-localizes with MYC in cells and directly interacts with MYC in vitro. Importantly, DHX15 contributes to MYC protein stability at the post-translational level and independent of its RNA binding capacity. Mechanistic investigation reveals that DHX15 interferes the interaction between MYC and FBXW7, thereby preventing MYC polyubiquitylation and proteasomal degradation. Consequently, abrogation of DHX15 drastically inhibits MYC-mediated transcriptional output. While DHX15 depletion blocks T-cell development and leukemia cell survival as we recently reported, overexpression of MYC significantly rescues the phenotypic defects. These findings shed light on the essential role of DHX15 in mammalian cells and suggest that maintaining sufficient MYC expression is a significant contributor to DHX15-mediated cellular functions.

overall_design: To confirm the pivotal role of MYC as a significant downstream target of DHX15, we performed the transcriptome analysis in DHX15-depleted KOPTK1 cells while MYC was restored.

last: Guo

first: Jin

last: Xu

first: Xinlu

first: Donghai

last: Wang

first: Ying

first: Guoliang

last: Qing

first: Pieter

last: Van Vlierberghe

first: Hudan

last: Liu


title: IGFBP6 knokdown in MDA-MB-231 cell line

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

summary: Breast cancer line MDA-MB-231 was cultured in complete culture medium containing high glucose DMEM (4.5 g/L) supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1% antibiotic-antimycotic solution ( Gibco) in an MCO-18AC incubator (Sanyo, Japan) at 37ºC and 5% CO2 concentration in the air. Cell reseeding was carried out every 2-3 days according to the standard protocol. The protocol for obtaining the MDA-MB-231 cell line with stable knockdown of IGFBP6 was described previously (Nikulin et al., 2021).

overall_design: The RNA extraction was performed using the miRNeasy Micro Kit (Qiagen, Germany). RNA samples were treated for ribosomal RNA removal using the MGIEasy rRNA Depletion Kit (MGI, China), and the purified RNA library was prepared for NGS using MGIEasy Directional Library Prep Set (MGI, China). Libraries were sequenced on the DNBSEQ-G50 sequencing platform (MGI, China) with High-throughput Sequencing Set (FCL, SE100).

first: Sergey

last: Nikulin


title: RNA-seq analysis of transcriptomes of WT and Foxp3∆2 Treg cells in colon lamina propria

city: Beijing

first: Gu

last: Qianchong

address: No. 3, yard 1, Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sicences

summary:
We performed RNA-seq analysis of Tregs isolated from Foxp3RFP/∆2Foxp3GFP-cre female mice. CD4+GFP+RFP+ (WT Tregs) and CD4+GFP+RFP- (Foxp3∆2 Tregs) cells were sorted from colon lamina propria to a typical purity of >95%. In order to obtain enough RNA for sequencing, we combined the cells sortd from the cLP of three mice for library construction.
Genes that were upregulated (532 genes) and downregulated (497 genes) in Foxp3∆2 Tregs

overall_design: Transcriptional profiles of WT and Foxp3∆2 Treg cells in  colon lamina propria

first: Qianchong

last: Gu

first: Xuyu

last: Zhou


title: The splicing isoform Foxp3∆2 differentially regulates tTregs and pTregs homeostasis

summary: Foxp3 is the master transcription factor for the regulatory T cells (Tregs). Alternative splicing of human Foxp3 results in the expression of two isoforms: the full-length and an exon 2-deleted protein. Here, AlphaFold2 predictions and in vitro experiments demonstrate that the N-terminal domain of Foxp3 inhibits DNA binding by moving toward the C-terminus and that this movement is mediated by exon 2. Consequently, we find Foxp3∆2-bearing tTregs in the peripheral lymphoid organ are less sensitive to TCR due to the enhanced binding of Foxp3∆2 to the Batf promoter and are unsusceptible to IL-2. In contrast, among RORγt+ pTregs in the large intestine, Foxp3∆2 pTregs express much more RORγt-related genes conferring a competitive advantage. Together, our results reveal that alternative splicing of exon 2 generates a constitutively active form of Foxp3, which plays a differential role in regulating tTregs and pTregs homeostasis.

overall_design: Lymphocytes were isolated from the spleen and lymph nodes of 6- to 8-week-old Foxp3RFP/∆2Foxp3GFP-creR26YFP female mice and enriched for CD4+ T cells using magnetic beads. Then, CD4+YFP+RFP+ (WT Tregs) and CD4+YFP+RFP- (Foxp3∆2 tTregs) cells were sorted to a typical purity of >95%. CUT&Tag libraries were generated with the Hyperactive In-Situ ChIP Library Prep Kit for Illumina Kit (Vazyme Biotech, TD901). Briefly, 50,000 cells for each CUT&Tag library were incubated with 10 μl balanced concanavalin A-coated magnetic beads at RT for 10 min. The bead-bound cells were resuspended with 50 μl of antibody buffer. In all, 1 μg anti-Foxp3 antibody (Abcam, ab150743) was then added to the bead-bound cells. After 2-h incubation at RT, the primary antibody was discarded carefully and 0.5 μl goat anti-rabbit IgG (Vazyme, Ab206-10-AA) diluted with 50 μl Dig-wash buffer was added to the cells. The cells were then incubated at RT for 1 h. Afterward, samples were washed gently with 800 μl Dig-wash buffer, and 0.58 μl pG–Tn5 together with 100 μl Dig-300 buffer was added to the samples. After 1-h incubation at RT, samples were washed gently with 800 μl Dig-300 buffer. In all, 300 μl tagmentation buffer was then added to each sample and the samples were incubated at 37 °C for 1 h. The interactions were quenched by adding 10 μl 0.5 M EDTA, 3 μl 10% SDS, and 2.5 μl 20 mg/ml Proteinase K and incubating the samples at 50 °C for 1 h. Phenol–chloroform and ethanol precipitation, as well as PCR and size selection, were performed as described in Hi-C library construction. All CUT&Tag libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode subsequently.


title: Effect of monomethylarsonous acid (MMAIII) on primary fibroblasts in vitro derived from Diversity Outbred (DO) mice aged 4-6 weeks

city: Bar Harbor

first: Callan

last: O'Connor

state: Maine

address: 87 Pine Heath Rd

institute: The Jackson Laboratory

summary: Genetically diverse cell populations derived from mice are powerful tools for studying gene-environment interactions. Using fibroblasts derived from Diversity Outbred (DO) mice, we performed a high-content screen (HCS) of cell morphology changes to the oxidative stress and DNA damage-inducing arsenic metabolite monomethylarsonous acid (MMAIII). We show that fibroblast morphological changes in response to increasing MMAIII exposure can be modeled using dose-response modeling. We use dose-response model parameters (i.e., EC50) as traits to map cell morphology quantitative trait loci (QTL) in response to MMAIII exposure. We find that dose-response cmQTLs overlap many known genes associated with arsenic susceptibility, including Abcc4 and Txnrd1, and also represent novel targets, including Xrcc2. Moreover, we show that the cmQTL effects are reproducible and how mouse genetics can be leveraged in a systems toxicological approach to find candidate genes and support experimental validation. In summary, our work demonstrates that cmQTLs reflect the key molecular events that are known to occur during acute arsenic exposure, which are adaptable across chemicals and cell culture models.

overall_design: To assess transcription changes in genetically diverse muring fibroblasts exposed to MMAIII, we selected 16 fibroblasts line from DO mice based on their haplotype at mouse chromosome 10:82.9 Mbp (GRCm38). We performed gene expression analysis obtained from RNA-seq of these 16 fibroblast lines in unexposed and 0.75 uM MMAIII exposed culture conditions. These dtaa were used for differential expression analysis and gene set enrichment analyss, in addition to supporting gene candidates within cmQTL intervals based on overall expression and differences in expression following MMAIII exposure.

first: O'Connor

last: Callan

first: Reinholdt

last: Laura G.


title: Effect of SJQYD alleviate Sjögren’s Syndrome on gene expression of NOD/LTJ mice

city: Hangzhou

first: Sun

last: Peng

address: 260 Baichuan Street

institute: Zhejiang chinese medical University

summary: We conducted experiments on SJQYD against Sjögren's Syndrome in NOD/LTJ mice. We used RNA sequencing to analyze the potential pathways of SJQYD.

overall_design: We isolated submandibular glands from different groups of mice for RNA sequencing analysis.

first: Qin

last: Luping


title: The Unique Function of Runx1 in Skeletal Muscle Differentiation and Regeneration is Mediated by an ETS Interaction Domain

status: Public on Nov 17 2023

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center


title: The Unique Function of Runx1 in Skeletal Muscle Differentiation and Regeneration is Mediated by an ETS Interaction Domain (RNA-Seq)

summary: The conserved Runt-related (RUNX) transcription factor family are well-known master regulators of developmental and regenerative processes. Both Runx1 and Runx2 are expressed in satellite cells (SC) and skeletal myotubes. Conditional deletion of Runx1 in adult SC negatively impacted self-renewal, and skeletal muscle maintenance was impaired; Runx1-deficient SC cannot support muscle regeneration in response to injury. To determine the unique molecular functions of Runx1 that cannot be compensated by Runx2 we deleted Runx1 in C2C12 that retain Runx2 expression and established that myoblasts differentiation was blocked in vitro due in part to ectopic expression of Mef2c, a target repressed by Runx1. Structure-function analysis demonstrated that the Ets-interacting MID/EID region of Runx1 absent from Runx2 is critical to regulating myoblasts proliferation, differentiation, and fusion. Analysis of in-house and published ChIP-seq datasets from Runx1 (T-cells, muscle) versus Runx2 (preosteoblasts) dependent tissue identified enrichment for a Ets:Runx composite site in Runx1-dependent tissues. Comparing ATACseq datasets from WT and Runx1KO C2C12 cells showed that the Ets:Runx composite motif was enriched in peaks open exclusively in WT cells compared to peaks unique to Runx1KO cells. Thus, engagement of a set of targets by the RUNX1/ETS complex define the non-redundant functions of Runx1

overall_design: RNA was collected from control and Runx1KO C2C12 cells in triplicate in growth media (20% FBS) or during differentiation in low serum (2% horse serum) media at 1 day , 3 days or 5 days. Differential gene expression was determined comparing control vs Runx1KO in growth media or at each timepoint. Additionally, gene expression during differentiation was determined by comparing gene expression of the timepoint versus growth media.

first: Matthew

middle: R

last: Hass

first: Meng

last: Yu

first: Xinhua

last: Lin

first: Raphael

last: Kopan


title: Identification and profiling of microRNAs in the developmental transitions of Spodoptera frugiperda

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are endogenous small noncoding RNAs (18–25 nt) that are involved in many physiological processes including development, cancer, immunity, apoptosis and host-microbe interactions through posttranscriptional regulation of gene expression. In this study, we measured the profile of small RNAs over the developmental transitions of Spodoptera frugiperda from egg to adult. We identified 741 miRNAs, including 493 known and 248 novel miRNAs. In addition, we identified the miRNAs differentially expressed over the developmental transitions via weighted gene co-expression network analysis (WGCNA). This study identified critical miRNAs involved in the transitions of this important pest insect S. frugiperda from egg to adult, thus providing a useful resource for exploring the regulatory role of miRNAs during insect post-embryonic development.

overall_design: The microRNAs expression profile from egg to adult in Spodoptera frugiperda


title: A BMP-controlled metabolic-epigenetic signaling cascade directs midfacial morphogenesis

first: Lingxin

last: Zhu

state: Hubei

address: 237 Luoyu Road, Hongshan District, School and Hospital of Stomatology, Wuhan University

institute: Wuhan University

summary: To begin identifying potential downstream of BMP signaling involved in midline facial development, we conducted a transcriptome analysis comparing the expression profiles of control versus ca-Acvr1(A11);P0-Cre nasal process tissues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E11.5 control and ca-Acvr1(A11) nasal process tissues.

first: Jingwen

last: Yang

first: Yuji

last: Mishina


title: Transcriptome sequencing of rabbit cornea after different illumination

first: Ye

last: Shen

state: Zhejiang

address: Qingchun Road 79th

institute: zhejiang university

summary: This study aimed to investigate the effects of long-term pollution from different wavelengths of light on the corneal epithelium (CE) and identify potential biomarkers. Rabbits were exposed to red, green, blue, white, and environmental light for 6 weeks. The CE was assessed using various techniques such as fluorescein sodium staining, transcriptome sequencing, electron microscopy, and molecular assays. In human corneal epithelial cells (hCECs), the downregulation of vascular cell adhesion molecular 1 (VCAM1) in response to blue light (BL) pollution was observed.  This downregulation of VCAM1 inhibited hCEC migration and increased reactive oxygen species (ROS) levels, apoptosis, and inhibited the AKT/p70S6K cascade. Animal experiments confirmed that BL pollution caused similar effects on the rabbit cornea, including increased ROS production, apoptosis, delayed wound healing, and decreased VCAM1 expression. In conclusion, BL-induced VCAM1 downregulation may impair CE and wound healing, and promotes ROS and apoptosis in vitro and in vivo.

overall_design: 12 samples from rabbit cornea

first: Kuangqi

last: Chen

first: Le

last: Jin

first: Yingying

last: Wen

first: Qianjie

first: Xiang

last: Li

first: Liyue

last: Zhang

first: Liyin

last: Wang

first: Yutong

last: Xia

first: Zhitong

first: Chen

last: Xie

first: Jianping

last: Tong


title: Comparison of Transcriptome-wide N6-methyladenosine profiles from healthy trio families reveals regulator-mediated methylation alterations.

first: Lijia

last: Ma

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

type: Methylation profiling by high throughput sequencing

summary: By performing methylated RNA immunoprecipitation sequencing (MeRIP-seq) to profile a transcriptome-wide N6-methyladenine modification in lymphoblastoid cell lines (LCLs) of 18 individuals from 6 YRI families. We found that that more than 70% of m6A peaks are shared by children and their parents, but the difference between patients and children is higher than that between families. The group-specific peaks in children are primarily enriched in cell cycle control, while those in parents are mainly enriched in chromatin/histone modifications. Moreover, the protein-protein interaction(PPI) network showed that seven significantly m6A regulators were closely interact with age-related genes, APOE and CEBPA, . In addition, we found that more SNPs are enriched around m6A peaks, and both parents-derived SNVs and de novo mutations could contribute to m6A methylation levels.

overall_design: Transcriptome-wide profile of m6A RNA modification between parents and their child in six healthy trio families.

first: Yini

first: hang

last: liu


title: Mixed-Lineage Leukemia 1 Inhibition Enhances the Differentiation Potential of Bovine Embryonic Stem Cells by Increasing H3K4 Mono-Methylation at Active Promoters.

city: Hohhot

first: jing

last: wang

state: Nei Mongol

address: Zhaojun Road

institute: Inner Mongolia University

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

overall_design: Refer to individual Series


title: Exposure to low-oxygen environment cause implantation failure and changes in transcriptome of uterus and ovary

city: Nagoya

first: Hossam

middle: Hassan

last: Shawki

state: Aichi

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

institute: Nagoya City University

summary: Hypoxia is a condition in which tissues of the body do not receive sufficient amounts of oxygen supply. The current study aimed to clarify the impact of a forced low-oxygen environment on the early pregnancy by exposing mice to low-oxygen conditions for 72 hours after fertilization. The treatment resulted in a complete failure of blastocyst implantation accompanied by vascular hypermeability in the uterus. The transcriptome analysis of uterus and ovary revealed remarkable alterations in gene expression between the control normoxic and hypoxic treatment groups. These alterations were encompassed a number of genes categorized to the immune responses and oxidative demethylation process.

overall_design:
To explore the effect of forced low oxygen on the implantation window. Pregnant mice exposed to low oxogen 72 hours after fertilization the then were sacrificied at E3.5, Uterine and ovarian samples were collected.
Total RNA were wxtracted for each treatment group (hypoxia and normoxia), three samples were pooled, and RNA sequencing libraries were constructed.
Differentially expressed genes (DEGs) were identified based on a Log2-fold change (FC) threshold of ≥ 2.

first: Asmaa

middle: Y

last: Ammar

middle: H

first: Hisashi

last: Oishi


title: Single-cell multi-omics sequencing revealed cytoskeleton defects led to human embryonic arrest characterized with zygotic genome activation

city: GuangZhou

first: Teng

address: jingxiStreet

institute: Southern Medical University

summary: Human in vitro-fertilized (IVF) embryos exhibit low developmental capabilities. However, the mechanisms underlying human embryonic arrest remain unclear. Here, using single-cell multi-omics sequencing approach, we simultaneously dissected the alteration of transcriptome, chromatin accessibility and DNA methylome in human early embryos arrested for unexplained reasons. Human arrested embryos displayed transcriptome disorders, including distorted microtubule cytoskeleton, increased genomic instability and impaired glycolysis, which were coordinated with multiple epigenetic reprogramming defects. Moreover, we identified Aurora A kinase (AURKA) repression was a reason for human embryonic arrest. Mechanistically, human arrested embryos from AURKA inhibited group resembled the reprogramming abnormalties of clinically arrested embryos in terms of transcriptome, DNA methylome, chromatin accessibility and H3K4me3. Through mitosis-independent sequential activation of zygotic genome in human arrested embryos, we found YY1 contributed to human major zygotic genome activation (ZGA). Collectively, our study decodes the reprogramming abnormalities and mechanisms for human embryonic arrest and key regulators of human ZGA.

overall_design:
We collected human arrested zygote, 2-cell, 4-cell and 8-cell embryos that were with no further development for another two days, followed by performing single-cell multi-omics sequencing including transcriptome, DNA methylome and chromatin accessibility. Additionally, we performed single-embryo multi-omics sequencing of human 8-cell embryos (3PN) from YY1 knockdown group and control group, single-embryo RNA sequencing of human 8-cell embryos (3PN) from KDOAM25 treated group and control group, single-cell multi-omics sequencing of human arrested zygote (3PN) from AURKA inhibited group and control zygotes, and single-cell RNA sequencing of mouse arrested zygote from AURKA inhibited group and control embryos (raw sequencing data of mouse embryos have been deposited in Genome Sequence Archive (GSA) database with the accession number CRA012505; processed data for mouse samples are available in the OMIX database (China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences) with accession number OMIX004867).

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Due to the relevant regulation from China's Ministry of Science and Technology related to the export of genetic information and materials, all raw sequencing data of human embryos reported in this study have been deposited in Genome Sequence Archive (GSA) for human database with the accession number HRA003366.
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first: Lin

first: Lei

first: Junhua

last: Peng

first: Jiaqi

last: Fan


title: SPINDOC promotes genome-wide redistribution of Spindlin1

first: Fan

last: Zhao

address: 1 Qinghuayuan

institute: Tsinghua University

summary: Spindlin1 is a histone reader with three Tudor-like domains and its reader activity of histone methylation could be attenuated by SPINDOC. To validate such a role in cellular context, we performed ChIP-Seq in HEK293 cell with SPINDOC overexpressed cell line and control cell line.

overall_design: Flag-Spindlin1 stably expressed HEK293 cells were transiently transfected with HA-SPINDOC. Essentially, cells were crosslinked with formaldehyde. After chromatin sonification and centrifugation, the supernatant was aliquoted and subjected to immunoprecipitation using ChIP-grade Flag beads, 4 μg of H3K4me3 and H3K9me3 antibody respectively. Immune complexes were purified by Protein A/G agarose. After reverse crosslinking, the resultant DNA was eluted and purified for sequencing.

first: Yan

last: Yan

first: Juntao

last: Gao

first: Haitao


title: Lipin-1 inhibition alters the transcriptome and lipidome of castration-resistant prostate cancer cells

city: Athens

first: Brian

middle: Scott

last: Cummings

state: Georgia

address: 302 College of Pharmacy South, Pharmaceutical and Biomedical Sciences

institute: University of Georgia

summary: The lipin family consists of three members (lipin-1, lipin-2 and lipin-3) that are phosphatidate phosphatases. Lipins facilitate lipid synthesis and remodeling through the conversion of phosphatidic acid to diacylglycerol. Lipin-1 and lipin-2 are also transcriptional co-regulators of peroxisome proliferator-activated receptors (PPARs). Our previous studies showed differential lipin-1 expression in numerous prostate cancer cell lines, and the lipin-1 expression was higher in cells representing advanced prostate cancer. However, the role of lipin-1 in prostate cancer cell growth is not fully understood. This study addressed the role of lipin-1 in prostate cancer cell function by performing RNA sequencing and qualitative LC-MS/MS analysis in PC-3 cells in which the gene for lipin-1 (LPIN1) was genetically inhibited. Transcriptomic and lipidomic analyses of LPIN1 knockdown PC-3 cells demonstrated alterations in the expression of numerous genes and the peak intensities of several lipids. The genes and lipids aligned with pathways that mediate focal adhesion, glycerophospholipid metabolism (GM), and PPAR signaling. Additionally, treatment of PC-3 cells with curcumin, a suggested inhibitor of lipin, decreased lipin-1 and lipin-3 expression, with no effect on lipin-2 expression. Bioinformatic analysis of prostate cancer patients demonstrated a correlation between LPIN3 mRNA expression and higher Gleason scores (8-10). These data show the novel findings that lipin-1 mediates the lipidome of castration-resistant prostate cancer cells and identified several pathways that it regulates, beyond GM and PPAR. Additionally, these data suggest that curcumin may be used to treat advanced prostate cancer that overexpresses lipin-3.

overall_design:
To investigate the role of lipin-1 in the progression of prostate cancer, we established PC-3 cell lines in which each target LPIN1 gene sequence has been knocked down by shRNA lentiviral particles.
We then performed gene expression profiling analysis using data obtained from RNA-seq of five different passages of the PC-3 cell line transfected with either a blank/control sequence (shRNA control) or part of the sequence for the LPIN1 gene (Targets A and B) to knockdown the gene.

first: Morgan

middle: C

last: Finnerty

first: Franklin

middle: E

last: Leach III

first: Naomi

last: Kramer

middle: S


title: Tumor cells obtain and overexpress AT2 cell marker

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

summary:
Background: The tobacco carcinogen urethane causes lung adenocarcinomas (LUAD) in mice. They show high similarity to human LUAD of smokers, including driver KrasQ61R mutations. However, the time line of KRASQ61R mutation acquisition as well as the affected cell lineages are still obscure.
Objectives: With this study we aim to identify which cells of the lung gain KrasQ61R mutations and when they occur in response to urethane treatment.
Methods: Airway and alveolar GFP-lineage-marked mice received single urethane hits (1 g/Kg). Lungs were harvested at 0, 1, 2, 4, and 8 weeks and LUAD tumors were collected at 16, 24, and 32 weeks post-urethane. The DNA was subjected to digital droplet PCR interrogating the coexistence of GFP and KrasQ61R in the same DNA copy. RNA of tumors was submitted to sequencing for gene expression analysis.
Results: Starting from even 1 week post-urethane, both airway and alveolar lineages suffered KrasQ61R mutations (2.57% of copies examined). In airway-labelled cells KrasQ61R mutations increased by 4.06% and 2.55% at 4 and 32 weeks post-urethane, respectively. In contrast, in alveolar-labelled cells KrasQ61R mutations declined by 5.92% and 6.12%. Strikingly, gene expression analysis on tumors revealed an over expression of alveolar markers whereas expression of airway marker genes decreased.
Conclusion: After pulmonary tumor initiation by urethane, airway cells accumulate KrasQ61R mutations over time, whereas alveolar cells tend to lose them. However, tumor cells are over expressing alveolar cell markers and lose airway markers. Altogether, these results indicate that smoking-induced LUAD develops from club cells which acquire alveolar cell characteristics. These data provide further insights into the mechanisms underlying LUAD evolution in patients.

overall_design: Comparison of differential gene expression between control mouse lungs and urethane induced lung tumors; triplicates are used for each group

first: Georgia

middle: A

last: Giotopoulou

first: Sabine

last: Behrend


title: Host chromatin architecture constrains the cis-regulatory effect of HPV integrations in cervical tumors.

city: Bangalore

first: Anurag

middle: Kumar

last: Singh

address: GKVK, Bellary Road

country: India

institute: National Centre for Biological Sciences

summary: By using HeLa as our model system, which has integration in the most recurrently integrated TAD in the cervical tumors i.e. TAD3189, we show most of the interactions of integrated HPV18 DNA is constrained within the TAD with integration. Similarly, TAD3189 also showed very high and most significant allele specific expression among all the TADs on chr8, in HeLa. The integrated HPV18 DNA also showed strong chromatin looping interactions with the oncogenes present in the TAD3189 which were ~500kb away from the integration. These oncogenes in the TAD3189 further showed high allele specific expression from the haplotype with HPV18 integration, possibly representing the cis-regulatory potential of integrated HPV DNA.

overall_design: 4C-seq in HeLa, using the integrated HPV18 DNA as the bait region.

first: Kaivalya

last: Walavalkar

first: Sabarinathan

last: Radhakrishnan


title: ATM inhibition enhances cancer immunotherapy by promoting mtDNA leakage/cGAS-STING activation

city: Durham

first: Chuan-Yuan

last: Li

state: NC

address: 905 S. Lasalle St

institute: Duke University Medical Center


title: VSIG4 inhibits RANKL-induced osteoclastogenesis by suppressing Nrf2-mediated reactive oxygen species production

city: wenzhou

first: Jiansen

last: Miao

state: zhejiang province

address: No. 1111, East Section of Wenzhou Avenue, Longwan District

department: Orthopaedics

institute: The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University

summary: Osteoporosis is a common systemic skeletal disorder especially in postmenopausal women due to excessive production and activation of osteoclasts. However, current anti-osteoporotic drugs used in clinical practice may cause some side effects. Thus, it is necessary to further explore the potential mechanisms regulating the differentiation of osteoclast and develop novel targets for the treatment of osteoporosis. In our study, we found that VSIG4 exhibited the most significant decline among VSIG family members. Overexpression of VSIG4 significantly inhibited RANKL-induced osteoclastogenesis and bone resorption function. Mechanismly, the western blot and immunofluorescence results also showed that overexpression of VSIG4 attenuated the expression of osteoclast marker genes and the activation of MAPK and NF-κB signaling pathways. We found that overexpression of VSIG4 could suppress the generation of reactive oxygen species (ROS) and activate the expression of Nrf2 and its downstream antioxidant enzymes. ML385, a potent Nrf2 inhibitor, was found to reverse the inhibitory impact of VSIG4 on osteoclast differentiation. Consistently, overexpression of VSIG4 also rescued OVX-induced bone loss and attenuated the activation of osteoclasts in vivo. Taken together, our results indicated that VSIG4 could be an novel target to address postmenopausal osteoporosis by suppressing osteoclast formation via regulation of Nrf 2-mediated ROS generation.

overall_design: To investigate the expression changes of VSIG4 during RANKL-induced osteoclastogenesis, bone marrow monocytes(BMMs) were treated with RANKL(50ng/ml) for 0 or 5 days. we then performed gene expression profiling analysis using data obtained from RNA-seq of BMMs at two time points.

first: Haiming

last: Jin


title: ATM inhibition enhances cancer immunotherapy by promoting mtDNA leakage/cGAS-STING activation [B16 vivo]

summary: Novel approaches are needed to boost the efficacy of immune checkpoint blockade (ICB) therapy.  Ataxia Telangiectasia Mutated (ATM) protein plays a central role in sensing DNA double strand  breaks and coordinating their repair. Recent data indicated that ATM might be a promising target  to enhance immune checkpoint blockade (ICB) therapy. However, the molecular mechanism  involved is not clearly elucidated. Here we show that ATM inhibition could potentiate ICB therapy  by promoting cytoplasmic leakage of mitochondrial DNA and activation of the cGAS/STING  pathway. Genetic depletion of ATM in murine cancer cells significantly delayed tumor growth in  syngeneic mouse hosts in a T-cell dependent manner. Furthermore, chemical inhibition of ATM  significantly potentiated anti-PD1 therapy of mouse tumors. ATM inhibition potently activated the  cGAS/STING pathway and enhanced lymphocyte infiltration into the tumor microenvironment by  downregulating TFAM, which led to mitochondrial DNA leakage into the cytoplasm. Moreover,  our analysis of data from a large patient cohort indicated that ATM mutations, especially nonsense  mutations, predicted for clinical benefits for ICB therapy. Our study therefore provides strong  evidence that ATM may serve both as a therapeutic target and a biomarker to enable ICB therapy.

overall_design: mRNA profiles of vector control and ATM KO B16 murine in vivo melanomas

first: Mengjie

last: Hu

first: Xuhui

last: Bao


title: Increased HRD score in cisplatin resistant penile cancer cells

city: Frankfurt am Main

first: Ria

last: Winkelmann

address: Theodor-Stern-Kai 7

institute: Dr. Senckenberg Institute of Pathology Frankfurt am Main

summary: HRD Score was generated from a penile carcinoma cell line resistant to 5FU and CDDP as well as cross resistant cell line.

overall_design:
Array-based genome-wide copy-number analysis was conducted using OncoScan FFPE Microarrays (Affymetrix, Santa Clara, California, USA). For the assay, an input amount of 79.2 ng DNA was used.  The OncoScan® assay utilizes the molecular inversion probe technology (MIP), which is optimized for highly degraded FFPE samples, for the identification of copy number (CN) alterations, loss of heterozygosity (LOH) and somatic mutations (SMs). MIP probes in the OncoScan® assay capture the alleles of over 220,000 SNPs within ~900 cancer genes. Furthermore, the MIP probes also enable detection of 74 frequently tested somatic mutations in nine genes implicated in cancer (BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS and TP53). The molecular inversion probe processing was done according to the OncoScan FFPE Assay Kit Protocol (Affymetrix, Santa Clara, California, USA).  At the end of the hybridization period, arrays were stained and washed using the GeneChip® Fluidics Station 450 and loaded into the GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara, California, USA) where array fluorescence intensity was scanned to generate array images (DAT file). Array fluorescence intensity (CEL) files were automatically generated from DAT files by the Affymetrix® GeneChip® Command Console® (AGCC) Software version 4.0. Resulting data files (CEL files) were processed and viewed by using Chromosome Analysis Suite (ChAS) software version 4.2.0.80.
Copy number analysis of Affymetrix 100K and 500K SNP arrays was performed for penile carcinoma cell lines from one patient resistant against 5FU and CDDP as well as both agents.

first: Claudia

last: Doering


title: ATM inhibition enhances cancer immunotherapy by promoting mtDNA leakage/cGAS-STING activation [4T1 in vitro]

overall_design: mRNA profiles of vector control and ATM KO 4T1 murine breast cancer cells

first: Min

last: Zhou


title: Novel biomarkers for contrast-induced acute kidney injury identified from RNA sequencing data

city: Fuzhou

first: Kaiyang

last: Lin

state: Please Select

address: No. 134, East Street, Gulou District

institute: Fujian province hospital

summary: Contrast-induced acute kidney injury (CI-AKI) is a serious complication of percutaneous coronary intervention (PCI). Emerging evidence suggests that messengerRNAs (mRNAs) and long non-coding RNAs (lncRNAs) could serve as biomarkers for various diseases.

overall_design: 4 patients with postoperative CI-AKI (case group) and 4 patients without CI-AKI (control group) were enrolled among the patients hospitalized in our department undergoing elective PCI. The groups were matched in terms of age, sex, and comorbidities (diabetes, heart failure).

first: Yansong

last: Guo

first: Xueqin


title: Identification and characterization of small molecule inhibitors of the LINE-1 retrotransposon endonuclease

city: Providence

first: John

last: Sedivy

address: 70 Ship St

institute: Brown University

summary: The long interspersed nuclear element-1 (LINE-1 or L1) retrotransposon is the only active autonomously replicating retrotransposon in the human genome. L1 harms the cell by inserting new copies, generating DNA damage, and triggering inflammation. Therefore, L1 inhibition could be used to treat many diseases associated with these processes. Previous research has focused on inhibition of the L1 reverse transcriptase due to the prevalence of well-characterized inhibitors of related viral enzymes. Here we present the L1 endonuclease as another target for reducing L1 activity. We have characterized structurally diverse small molecule endonuclease inhibitors using computational, biochemical, and biophysical methods. We also show that these inhibitors reduce L1 retrotransposition, L1-induced DNA damage, and inflammation reinforced by L1 in senescent cells. These inhibitors could be further used to better understand the life cycle of this element and its impact on human health.

overall_design: Human normal diploid lung fibroblast cells were passaged into replicative senescence, the irreversible exit of cells from the cell cycle. Samples were treated in triplicate with vehicle, L1 reverse transcriptase inhibitor 3TC, or L1 endonuclease inhibitor AD12. The gene expression changes of inflammation markers were analyzed in response to inhibitor treatment.

first: Alexandra

middle: M

last: D'Ordine


title: 10x single-cell RNA sequencing of microglia from wild-type C57BL/6 and P301S mice

city: Rochester

first: Cheng

last: Zhang

state: MN

address: 200 1st street SW

institute: Mayo Clinic

summary: The existence and contribution of microglia with senescent-like alterations in the pathogenesis of age-related neurodegenerative disease have been suggested in recent years. However, the identification of this distinct microglial population in vivo has proven challenging, largely due to overlaps in the inflammatory phenotype of activated and senescent microglia. Furthermore, attempts at recapitulating senescence in microglia in vitro are limited. To overcome these challenges, we analyzed the RNA expression patterns of individual microglia from normal mice and the pathogenic tau P301S PS19 mouse model. We have previously demonstrated that p16-expressing senescent microglia occur in these mice when neurodegeneration has occurred. Here we identify a subset of disease-associated microglia with senescent features, notably characterized by the expression of Ccl4. This signature overlaps with established markers of senescence from other cell types. Our characterization of senescent microglia can be used to better understand the role of senescent microglia in various age-related contexts, including whether clearance of senescent microglia represents a viable therapeutic option.

overall_design: P301S and C57BL/6 mice of 9.5 months of age were perfused and cortices and hippocampi isolated. Cortices and hippocampi were incubated with accutase for single-cell dissociation, before myelin removal and CD11b selection.

first: Pei

last: Ng

first: Li

first: Darren

last: Baker


title: Next Generation Sequencing Analysis on Grafts with Macrosteatosis for Liver Transplantation in rats

city: hangzhou

first: zhengtao

last: liu

address: 8 shuren street

institute: zhejiang shuren university

summary: We reported the transcriptomic expression profile of the MaS/non-MaS graft samples from rats before/after liver transplantation and long-term surviving rats.

overall_design: Transcriptomics analysis on 12 pre-transplant samples, 12 post-transplant samples, and 8 samples from long-term survivors

first: Zhengtao

last: Liu


title: Early to Sustained Impacts of Lethal Radiation on Circulating miRNAs in a Minipig Model

status: Public on Nov 16 2023

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Early diagnosis of lethal radiation is imperative since its intervention time windows are considerably short. Hence, ideal diagnostic candidates of radiation should be easily accessible, enable to inform about the stress history and objectively triage subjects in a time-efficient manner. Therefore, the small molecules such as metabolites and microRNAs (miRNAs) from plasma are legitimate biomarker candidate for lethal radiation. Our objectives were to comprehend the radiation-driven molecular pathogenesis and thereby determine biomarkers of translational potential. We investigated an established minipig model of LD70/45 total body irradiation (TBI). In this pilot study, plasma was collected pre-TBI and at multiple time points, post-TBI. The majority of differentially expressed miRNAs and metabolites were perturbed immediately after TBI that potentially underlined the severity of its acute impact. The integrative network analysis of miRNA and metabolites showed a cohesive response; the early and consistent perturbations of networks were linked to cancer and the shift in musculoskeletal atrophy synchronized with the comorbidity-networks associated with inflammation and bioenergy synthesis. Subsequent comparative pipeline delivered 92 miRNAs, which demonstrated sequential homology between human and minipig, and potentially similar responses to lethal radiation across these two species. This panel promised to retrospectively inform the time since the radiation occurred; thereby could facilitate knowledge-driven intervention.

overall_design: 30 pigs at different time points after radiation.

first: Nabarun

last: Chakraborty

first: Gregory

middle: P

last: Holmes-Hampton

first: Raina

last: Kumar

first: Bernadette

last: Hritzo

first: Betre

last: Legessa

first: George

last: Dimitrov

first: Sanchita

last: Ghosh

first: Rasha

last: Hammamieh


title: MST2 Methylation by PRMT5 Inhibits Hippo Signaling and Promotes Pancreatic Cancer Progression

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

summary: As a classic tumor suppressor pathway, Hippo signaling axis is activated by various extra-pathway factors to regulate cell differentiation and organ development. However, recent studies have reported that the activation of Hippo signaling pathway may be more dependent on the autophosphorylation of its core kinase cassette. Here, we demonstrate that protein arginine methyltransferase 5 (PRMT5) is involved in inducing the inactivation of Hippo signaling pathway in pancreatic cancer. Our study shows that the initiator serine/threonine kinase 3 (STK3, also known as MST2) of Hippo signaling pathway can be symmetrically di-methylated at arginine-461 (R461) and arginine-467 (R467) in the SARAH domain by PRMT5, and the methylated MST2 suppresses its autophosphorylation and kinase activity by blocking the formation of homodimer, thereby inactivating Hippo signaling pathway in pancreatic cancer. Moreover, we also discover that the specific PRMT5 inhibitor GSK3326595 re-activates the dysregulated Hippo signaling pathway and inhibits the growth of human-derived pancreatic cancer xenografts in immunodeficient mice, which provides a theoretical foundation for the clinical application of PRMT5 inhibitor in pancreatic cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the pancreatic cancer cells after kncokdown of PRMT5.

first: Xin

last: Jin


title: GLIDR-mediated Regulation of Tumor Malignancy and Cisplatin Resistance in Non-Small Cell Lung Cancer via the miR-342-5p/PPARGC1A Axis

first: Ruihua

address: No.24 Zhaogun Road

summary: LncRNAs play a crucial role in regulating the progression of NSCLC, making them potential targets for cancer diagnosis and treatment. Therefore, identifying new lncRNAs as therapeutic target and comprehending their underlying regulatory mechanisms are crucial for treating NSCLC. In this study, we found that glioblastoma down-regulated RNA (GLIDR) was increased in non-response NSCLC patients with the primary treatment, and GLIDR was also highly expressed in NSCLC patients. We used bioinformatic analysis and luciferase assays to identify that microRNA-342-5p (miR-342-5p) directly targets GLIDR. MiR-342-5p overexpression inhibits NSCLC cell proliferation, migration, and invasion, whereas miR-342-5p inhibition promotes NSCLC malignancy, which can be rescued by suppressing GLIDR. Peroxisome proliferator-activated receptor-gamma coactivator-1alpha (PPARGC1A) was identified as a downstream target of miR-342-5p. PPARGC1A inhibition significantly suppresses NSCLC malignancy, whereas overexpression promotes it. The results also revealed that GLIDR overexpression reduced PPARGC1A inhibition by miR-342-5p, and increased PPARGC1A expression reversed the inhibition of NSCLC malignancies caused by decreased GLIDR. To the best of our knowledge, we are the first to discover that GLIDR promotes NSCLC progression by sponging miR-342-5p to regulate PPARGC1A expression, presenting that GLIDR act as a potential therapeutic target in NSCLC.

overall_design: To investigate the abnormality expressed lncRNA in NSCLC, we performed a whole-transcriptome sequencing compared lncRNA expression in the normal lung epithelium cell line (HEB) and the lung adenocarcinoma cell line (A549). Then the differentially expressed genes (DEGs) were analyzed using data obtained from the RNA sequencing.

first: Ruhua

first: Jiemin

last: Wang

first: Shu

first: Haiquan

last: Yu


title: ROS-induced translation impairment underlies ZAK-mediated metabolic decline in obesity and aging

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

summary: The ribotoxic stress response (RSR) denotes a signaling pathway in which the p38 and JNK-activating MAP3 kinase ZAKalpha senses stalling and/or collision of ribosomes with unknown physiological implications. Here, we show that reactive oxygen species (ROS)-generating agents robustly trigger translational impairment and ZAKalpha activation. As a testament to the physiological importance of this signaling pathway, zebrafish larvae deficient for the ZAKalpha kinase are protected from ROS-induced pathology and death. Furthermore, livers of mice fed a ROS-generating and obesogenic diet accrue ZAKalpha-activating and antioxidant-reversed ribosomal stalls and collisions. Highlighting a role for the RSR in metabolic regulation, ZAK knockout (KO) mice are protected from developing insulin resistance and liver steatosis under these conditions. Finally, aged chow-fed ZAK KO mice do not display the normal hallmarks of metabolic aging. In sum, our work highlights ROS-induced translational impairment as a physiological activation signal for ZAKalpha that underlies metabolic adaptation in obesity and aging.

overall_design: Comparative ribosome footprint of RIBO-seq data of 12-week-old male C57BL/6J mice fed chow or high fat high sugar (HFHS) diet and optionally supplemented with 2 g/l N-acetylcysteine (NAC) in the drinking water for 8 weeks

first: Goda

last: Snieckute

first: Laura

last: Ryder

first: Anna

last: Vind

first: Zhenzhen

last: Wu

first: Frederic

last: Schrøder Arendrup

first: Mark

last: Stoneley

first: Sébastien

last: Chamois

first: René

first: Alexander

last: Russell

first: Aitana

middle: V

last: Genzor

first: Astrid

last: Linde Basse

first: Morten

last: Dall

first: Lucile

last: Dollet

first: Melanie

last: Blasius

first: Anne

last: Willis

first: Anders

last: Lund

first: Jonas

last: Thue Treebak

first: Steen

last: Seier Poulsen

first: Betsy

last: Pownall

first: Christoffer

last: Clemmensen

first: Zach

last: Gerhart-Hines

first: David

last: Gatfield

first: Simon

last: Bekker-Jensen


title: The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish

city: Guangzhou

first: zhujuan

last: huang

address: No. 382, east waihuan road, panyu district, GuangZhou city, GuangDong province Medical college of south China university of technology, panyu university town, Guangzhou city

institute: South China University of Technology

summary: Neutrophils and erythrocytes are vital to the immune system and oxygen transport, respectively. However, the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research, zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study, we showed that erythrocytes predominantly reside inside the blood vessels of the CHT, while neutrophils stay outside. Ectopic vascular endothelium, induced by Bone Morphogenetic Protein 2b(Bmp2b) overexpression, attracts both cell types, with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta (VDA) but severely affects definitive erythrocytes from the same source. Bulk RNA-sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter, which is specifically expressed in vein, lymphatic vessels and CHT vein endothelial cells, rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils.

overall_design: We then performed gene expression profiling analysis using data obtained from BULK RNA-seq of 5dpf vein endothelium cells and endothelium cells.

first: Zhujuan

last: Huang

first: Jiahao

last: Chen

first: Yongtai

last: Xu


title: Functional dissection of human cardiac enhancers with hiPSC-CMs and lentiMPRA

city: Jamaica Plain

first: Xiaoran

last: Zhang

state: MA

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

summary: To assess human cardiac enhancer activity, 400 bp candidate cardiac enhancers and controls were tested in iPSC-CMs using lentiMPRA.

overall_design: We applied lentiMPRA to measure the enhancer activity of 2891 candidate human cardiac enhancers and 859 negative controls. iPSC-CMs were transfected with the lentiMPRA library at day 10 or 17 of iPSC-CM differentiation, and cells were collected 7 days later. A region of the 3’UTR of the reporter gene containing the candidate CREs was amplified from RNA and genomic DNA and sequenced.

first: Feng

last: Xiao

first: Sarah

middle: U

last: Morton

first: Christine

last: Seidman

first: Jonathan

middle: G

first: William

last: Pu


title: DNA methylation of insulin signalling pathways in human primary muscle stem cells is associated with HOMA2-IR in older adults

city: Southampton

first: Matthew

last: Hewitt

state: Hampshire

address: Institute of developmental sciences, 216 Tremona Road

department: Human Development and Health

institute: University of Southampton

summary: Context: While ageing is associated with increased insulin resistance (IR), the molecular mechanisms underlying increased IR in muscle, the primary organ for glucose clearance, have yet to be elucidated in older individuals. As epigenetic processes are suggested to contribute to development of ageing-associated diseases, in human primary muscle stem cells (myoblasts) from community dwelling older individuals we investigated whether differential DNA methylation was associated with IR.  Methods: We measured DNA methylation (Infinium HumanMethylationEPIC BeadChip) in myoblast cultures from vastus lateralis biopsies (119 male/females, mean age 78.24 years) from the Hertfordshire Sarcopenia Study extension (HSSe) and examined differentially methylated Cytosine phosphate Guanine (CpG) sites (dmCpG), regions (DMRs) and gene pathways associated with HOMA2-IR (derived from fasting insulin/glucose) and HbA1c.   Results:  38 dmCpGs (false discovery rate (FDR)<0.05), and 8 DMRs (Stouffer<0.05) were associated with HOMA2-IR; 6 dmCpGs and 3 DMRs were robust to adjustment for BMI, including DMRs within T-box transcription factor (TBX1) and nuclear receptor subfamily-2 group F member-2 (NR2F2). HOMA2-IR associated dmCpGs were enriched in genes linked with skeletal muscle development and insulin signalling. 49 dmCpGs were associated with HbA1c, with 48 robust to adjustment for BMI. The only dmCpG associated with both HOMA2-IR and HbA1c was cg13451048, located within Exoribonuclease Family Member 3 (ERI3). HOMA2-IR and HbA1c dmCpGs were not associated with accelerated epigenetic ageing.   Conclusions: These findings suggest differential DNA methylation in muscle stem cells may contribute to age-related decline in glycaemic control. The identification of dmCpGs, associated genes and pathways may provide novel targets for pharmacological intervention.

overall_design: A total of 145 samples had sufficient DNA for methylation analysis. This included 7 technical inter-chip and intra-chip replicates. Replicates were removed after normalization but before inference (the replicate with the lowest MAD score was removed). Nineteen samples showed aberrant methylation densities and MAD scores lower than -5 were removed from subsequent analysis. This resulted in 119 samples which were taken forward for further analysis. A total of 7 inter-chip and intra-chip replicates were included in the analysis.

first: Mark

last: Burton

first: Emma

last: Garratt

middle: O

first: Hannan

last: Sharkh

first: Elie

last: Antoun

first: Leo

middle: D

last: Westbury

first: Elaine

last: Dennison

first: Nicholas

last: Harvey

first: Cyrus

last: Cooper

first: Harnish

last: Patel

first: Keith

last: Godfrey

first: Karen

last: Lillycrop


title: Analysis of human iPSC-derived cardiomyocytes

first: Xiaoran

last: Zhang

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

overall_design: Refer to individual Series


title: Functional analysis of human cardiac enhancers by tiling mutagenesis

summary: To further determine the sequence features of active cardiac enhancers, 123 cardiac enhancers were functionally dissected by 10 bp tiling deletion-based mutagenesis MPRA in iPSC-CMs.

overall_design: We performed systematic, tiling mutagenesis MPRA of 123 cardiac enhancers identified by 400 bp lentiMPRA. Each 400 bp region was represented as three fragments (F1, F2, F3), each containing 171 bp of genomic sequence. Each of these wild type sequences was tiled with 17 10 bp deletions.

first: Feng

last: Xiao

first: Sarah


title: The deletion of the Williams-Beuren Syndrome critical region dysregulate the expression of miR379-410 miRNA members in human isogenic iNeurons

status: Public on Nov 15 2023

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

institute: ETH Zürich

summary: While psychiatric disorders (e.g., schizophrenia) and autism spectrum disorders (ASD) are typically associated with a deficit in social behavior, the opposite trait of hypersociability is exhibited by individuals with specific neurodevelopmental disorders, e.g., Angelman Syndrome (AS) and Williams-Beuren Syndrome (WBS). We have recently reported that the deletion of the miR379-410 cluster in mice led to hypersocial behavior. To study the roles of this miRNA cluster in the context of WBS, we sent for smallRNA sequencing RNA isolated from isogenic human iPSC-derived neurons harboring a deletion present in Williams-Beuren-Syndrome patients (7q11.23). Specifically, we found that members of the miR379-410 cluster were strikingly overrepresented among downregulated miRNAs in iNeurons harboring a deletion of the WBS critical region. Thus, we obtained the first evidence for the pathophysiological significance of the miR379-410 miRNA cluster in the context of WBS. We conclude that targeting this novel pathway could have therapeutic potential for WBS and other neurodevelopmental conditions characterized by social impairments.

overall_design: The generation of the isogenic iPSCs and their Ngn2-driven differentiation to iNeurons was described in https://doi.org/10.1101/2022.10.10.511483 .  We then performed a smallRNA sequencing in samples obtained from 3 control iNeurons and 2 iNeurons containing the WBS deletion.

first: Marija

last: Mihailovich

first: Pierre-Luc

last: Germain

first: Prakruti

last: Nanda

first: Giuseppe

last: Testa


title: Analysis of CHD non-coding DNVs for their impact on cardiac cis-regulatory element activity

summary: 6761 CHD non-coding DNVs were prioritized from 749 unexplained CHD trios and functionally assessed in iPSC-CMs using lentiMPRA.

overall_design: We synthesized 6761 reference (REF) and variant (ALT) pairs, comprising 171 bp of genomic sequence centered on the DNVs. The CHD MPRA library also included 865 negative controls (ATAC-seq peaks in iPSCs and not iPSC-CMs) and 613 additional oligos derived from the 18 enhancers with the most subregion activity in the mutagenesis MPRA. The 15000 pooled oligos were synthesized following the same barcoded design as used for tiling mutagenesis.

last: Morton

first: Christine

last: Seidman

first: Jonathan

first: William

last: Pu


title: Trancriptome profiling of genome-edited 16HBE cells on the receptor tyrosine kinase MET in response to HGF

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Effect of MET exon 14 skipping on gene expression stimulated or not by its ligand Hepatocyte Growth Factor (HGF) in pulmonary epithelial 16HBE cell line which undergone genome-editing by CRISPR-Cas9 technology.

overall_design: Comparisons of genes regulated by MET WT or MET Ex14 receptor in response to HGF in pulmonary epithelial 16HBE cell line

first: Marie

last: Fernandes

first: David

last: Tulasnes

first: Zoulika

last: Kherrouche


title: Profiling T cell repertoires and RNA sequencing from mouse CT-26 tumor model by TRJL

city: wuhan

first: zaiqiao

last: sun

institute: wuhan university

summary: we provide a novel immune repertoire and RNA-seq joint library construction method (IRJL), we used IRJL protocol to compare the transcriptomic and immune repertoire of CT-26 tumor model and normal mouse spleen. Overall, IRJL offers a greatly simplified, shortcut and cost-effective protocol with RNA-seq and immune repertoire.


title: Activation of the integrated stress response rewires cardiac metabolism in Barth syndrome

city: Würzburg

first: Jan

last: Dudek

address: Am Schwarzenberg 15

department: Department of Translational Research, Comprehensive Heart Failure Center

institute: University Clinic Würzburg

summary: Barth Syndrome (BTHS) is an inherited cardiomyopathy caused by defects in the mitochondrial transacylase TAFAZZIN (Taz), required for the synthesis of the phospholipid cardiolipin. BTHS is characterized by heart failure, increased propensity for arrhythmias and a blunted inotropic reserve. Defects in Ca2+-induced Krebs cycle activation contribute to these functional defects, but despite oxidation of pyridine nucleotides, no oxidative stress developed in the heart. Here, we investigated how retrograde signaling pathways orchestrate metabolic rewiring to compensate for mitochondrial defects. In mice with an inducible knockdown (KD) of TAFAZZIN, mitochondrial uptake and oxidation of fatty acids was strongly decreased, while glucose uptake was increased. Unbiased transcriptomic analyses revealed that the activation of the eIF2/ATF4 axis of the integrated stress response upregulates one-carbon metabolism, which diverts glycolytic intermediates towards the biosynthesis of serine and fuels the biosynthesis of glutathione. In addition, strong upregulation of the glutamate/cystine antiporter xCT increases cardiac cystine import required for glutathione synthesis. Increased glutamate uptake facilitates anaplerotic replenishment of the Krebs cycle, sustaining energy production and antioxidative pathways. These data indicate that ATF4-driven rewiring of metabolism compensates for defects in mitochondrial uptake of fatty acids to sustain energy production and antioxidation.

overall_design:
Heart tissue and skeletal muscle from a mouse model with a systemic reduction of Tafazzin (Taz) gene expression at an age of 20 weeks are compared to control. Deficiency in Taz gene expression causes mitochondrial dysfunction and cardiomyopathy and relates to Barth syndrome (BTHS).
To profile the whole transcriptome expression changes between Taz-KD and WT mice,  Illumina PE RNA-seq were performed using total RNAs extracted from cardiac tissue and skelecal muscle of Taz-KD and WT mice. 10 cardiac tissue are from WT and Taz-KD mice; 10 skeletal muscle from WT and Taz-KD mice.

first: Ke

first: Christoph

last: Maack


title: Transcriptional changes in human pluripotent stem cell-derived cardiomyocytes induced by apilimod, remdesivir, ritonavir, and lopinavir treatment

first: Ying

last: Zhang

state: Guangdong

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

summary: The rapid development of safe and effective treatments for COVID-19 had become a top priority to fight against this spreading pandemic worldwide in 2019. 20%–30% of COVID-19 patients experience severe cardiovascular damage, patients with pre-existing heart complications are more likely to develop severe illness and have higher risk of death compared with patients without co-morbidities. In such a context, whether the repurposed drugs are at risk of inducing heart damage to COVID-19 patients remains unclear. Here, we demonstrated that four antiviral drugs, including apilimod, remdesivir, ritonavir, and lopinavir, exhibit cardiotoxicity at clinically relevant doses. RNA-seq analysis revealed that human pluripotent stem cell-derived cardiomyocytes (hCMs) treated by each drug had significantly different expression profiles when compared with the untreated control. The expression of genes that regulate cardiomyocyte function, such as sarcomere organization and ion hemostasis, was significantly altered after drug treatment. These results not only warrant caution and careful monitoring when prescribing the above-mentioned drugs in patients, but also provide a valuable platform for understanding the molecular mechanism underlined the toxic effects of these prospective drugs and for protective agent discovery.

overall_design: To identify the transcriptomic basis of the cardiotoxic effect of the four drugs, we performed comparative gene expression profiling analysis using data from RNA-seq of hCMs with or without drug treatment.

last: Cao

first: He

last: Xu

first: Ge

last: Liu

first: Jixing

last: Gong

first: Shanshan

last: Gu


title: Integrated transcriptomic and proteomic analysis revealed the inhibition mechanism of a natural luvangetin from Zanthoxylum avicennae against Fusarium verticillioides

city: yangzhou

first: yuchen

last: zhou

address: daxue southern road

institute: yangzhou university

summary: (i) To determine the inhibitory effect of Luvangetin against Fusarium verticillioides and fumonisins production in vitro and in vivo, and (ii) to investigate the mode of action of Luvangetin against Fusarium verticillioides by transcriptomics and proteomics analysis.

overall_design: Two experimental groups were set up, one was coumarin-treated and one was untreated, and each group had three replicates

first: Jiahuan

last: Chen

first: Yuchen

last: Zhou

first: Duxuan

first: Haoyu


first: Xiaoran

summary: Bulk RNA-seq of human iPSC-derived cardiomyocytes was performed to analyze transcription factors expressed in iPSC-CMs.

overall_design: WTC-Cas9 iPSCs were differentiated into cardiomyocytes using CHIR99021 and IWP2/XAV933. At differentiation day 10, iPSC-CMs were replated into 6-well plates. Lactate selection was performed between day 12 and day 14. After lactate selection, iPSC-CMs were cultured with RPMI/B27 medium and harvested at day 17.

first: Feng

last: Xiao

first: William

last: Pu


title: A Pancreas Organoids-based Screen Identifies a Specific KRAS Mutation Inhibitor that Attenuating Cholesterol Biosynthesis Pathway in Pancreatic Cancer

city: New York

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: we reported a high-content drug screening platform of a series of pancreas organoids which contain common mutations found in human pancreatic cancer, wide type (WT), KC (KRASG12D), KPC (KRASG12D; Tp53R172H), KSC (KRASG12D; SMAD4-/-) and KPSC (KRASG12D; Tp53R172H and SMAD4-/-). Based on this platform, we screened about 6000 compounds and identified Perhexiline, which can inhibit the growth of pancreas organoids with KRAS mutation in vitro and in vivo. Single cell RNA-seq data shows that the cholesterol synthesis pathway is activated specifically caused by KRAS in mutated organoid lines. The key cholesterol synthesis regulator of SREBP2 and its downstream genes are activated in KRAS mutated organoids compared with WT. Interestingly, Perhexiline can reverse the metabolism changes in pancreas organoids with KRAS through downregulating SREBP2 at transcription level. Finally, we further validated targeting SREBP2 can attenuate tumor growth significantly with chemical inhibitor and genetic perturbation. These findings boost further understanding of KRAS in PDAC and provide a valuable resource for targeting KRAS therapeutics development.

overall_design: Five kinds of pancreas organoids, wide type (WT), KC (KRASG12D), KPC (KRASG12D; Tp53R172H), KSC (KRASG12D; SMAD4-/-) and KPSC (KRASG12D; Tp53R172H and SMAD4-/-) were treated with or without perhexiline. Ten samples were barcoded by 10 CMOs, respectively. And then, 10 samples were pooled for library preparation and sequence.

first: Xiaohua

last: Duan

first: Xing

last: Wang

first: Tuo


title: Ascites exosomal lncRNA PLADE enhances platinum sensitivity by inducing R-loop in ovarian cancer

city: Hefei

first: Hanyuan

address: Huangshan Road

institute: University of Science and Technology of China

summary: To investigate functional lncRNAs in ovarian cancer ascites exosomes, we performed high-throughput RNA sequencing (RNA-seq) of ascites-derived exosomes from 3 cisplatin-sensitive and 7 cisplatin-resistant HGSOC patients

overall_design: We performed ribosomal RNA (rRNA) depleted RNA sequencing (RNA-seq) of ascites-derived exosomes from the cisplatin-sensitive or -resistant HGSOC patients.

first: Ying


title: Combined anti-inflammatory and regenerative therapies rescue skeletal muscle after IRI through multi-pathway activation

city: Shanghai

first: chen

last: xingxing

address: nanchen road 381

institute: Shanghai University

summary: Ten-week-old C57BL/6J mice were subjected to unilateral hind limb ischemia-reperfusion (I/R) injury by postural suspension method for 4 hours, and then treated with aspirin anti-inflammatory group and peptide functionalized hydrogel drug. RNA-seq analysis was then performed.

overall_design: All mice were subjected to hindlimb suspension ischemia model. Then, three c57b6l mice were treated with aspirin for anti-inflammation(Asp group), three c57b6l mice were treated with peptide hydrogel combined with aspirin(Asp+Pep group), and three c57b6l mice were left untreated as controls(Ctrl group).

first: Xingxing

first: Jia

last: Jia


title: Rna_seq analysis of aorta in young and aging mice

first: fei

last: sun

state: Shanghai

address: Laboratory of Biotechnology, School of Life Science, Baoshan Campus, Shanghai University, Dachang Town, Baoshan District, Shanghai

summary: Analyzing the aortic transcriptome of young and aged mice can help reveal the differences in vascular transcriptome during aging in mice. Moreover, this dataset can provide a basis for cross-species transcriptome comparison

overall_design: Three 6-week-old c57b6l and three 6-month-old c57b6l mice

first: Fei

last: Sun

first: Yanwen

last: Ge


title: Transcriptomic profiling of the acute mucosal response to local food injections in adults with eosinophilic esophagitis

city: Utrecht

first: Mirelle

last: Kleuskens

address: Universiteitsweg 99

country: Netherlands

institute: Utrecht University

summary: Background: Exposure of the esophageal mucosa to food allergens can cause acute mucosal responses in patients with eosinophilic esophagitis (EoE), but the underlying local immune mechanisms driving these acute responses are not well understood. Objective: To gain insight into the early transcriptomic changes that occur during an acute mucosal response to food allergens in EoE. Methods: Bulk RNA-sequencing was performed on esophageal biopsies from adult EoE patients (n = 5) collected before and 20 minutes after intramucosal injection of various food extracts in the esophagus. Baseline biopsies from non-EoE controls (n = 5) were also included. Results: At baseline, the transcriptome of the EoE patients showed increased expression of genes related to an EoE signature. After local food injection, we identified 40 genes with a potential role in the early immune response to food allergens (most notably CEBPB, IL1B, TNFSF18, PHLDA2, and SLC15A3). These 40 genes were enriched in processes related to immune activation, such as the acute phase response, cellular responses to external stimuli, and cell population proliferation. TNFSF18 (also called GITRL), a member of the TNF superfamily that is best studied for its co-stimulatory effect on T cells, was the most dysregulated early EoE gene showing a 12-fold increase compared with baseline and an 18-fold increase compared with a negative visual response. Further experiments showed that the esophageal epithelium may be an important source of TNFSF18 in EoE, which was rapidly induced by stimulating differentiated esophageal epithelial cells with the key EoE cytokine interleukin-13. Conclusion: Our data provide unprecedented insight into the transcriptomic changes that mediate the acute mucosal immune response to food allergens in EoE, and suggests that TNFSF18 may be an important effector molecule in this response.

first: Maria

middle: L

last: Haasnoot

first: Johan

last: Garssen

first: Albert

middle: J

last: Bredenoord

first: Betty

last: van Esch

first: Frank

last: Redegeld


title: HSP27 (Heat Shock Protein 27, HSPB1) overexpression effect on bleomycin-induced PF (Pulmonary fibrosis) mice model

city: Seoul

first: Yun-Sil

last: Lee

address: 52, Ewhayeodae-gil, Seodaemun-gu

department: College of Pharmacy

country: South Korea

institute: Ewha Womans University

summary: To analyze the role of HSP27 in bleomycin (BLM)-induced pulmonary fibrosis in vivo, we used TG mice that conventionally overexpressed HSP27. Our previously reported that HSP27 plays an important role in pulmonary fibrosis. In mice overexpressing HSPB1, BLM-induced fibrotic regions and collagen deposits were increased compared with those in control BL6 mice. Following intratracheal treatment of BLM, the HSP25 TG mice showed an abundance of mononuclear and neutrophils cells in the alveoli, greater destruction of alveolar septa, intra-alveolar hyaline membrane formation, and a marked increase in collagen deposition compared with control BL6 mice.

overall_design: In the analysis of the study, the mice were intratracheally injected with BLM (1.25mg/kg). Mice were sacrificed at 2 weeks after BLM treatment.

first: YoungJo

last: Yoo

first: Seulgi

last: Jeon

first: Hee

last: Jin


title: MAPK-DLK signaling coupled with DNA damage promotes  intrinsic neurotoxicity associated with non-mutated tau

city: Houston

first: Wei

last: Cao

state: Texas

address: 6431 Fannin Street

institute: The University of Texas Health Science Center at Houston

summary: Alzheimer’s disease (AD) is the most prevalent form of neurodegeneration. Despite the well-established link between tau aggregation and clinical progression, the major pathways driven by this protein to intrinsically damage neurons are incompletely understood. To model AD-relevant neurodegeneration driven by tau, we overexpressed non-mutated human tau in primary mouse neurons and observed substantial axonal degeneration and cell death, a process accompanied by activated caspase 3. Mechanistically, we detected deformation of the nuclear envelope and increased DNA damage response in tau-expressing neurons. Gene profiling analysis further revealed significant alterations in the mitogen-activated protein kinase (MAPK) pathway; moreover, inhibitors of dual leucine zipper kinase (DLK) and c-Jun N-terminal kinase (JNK) were effective in alleviating wild-type human tau-induced neurodegeneration. In contrast, mutant P301L human tau was less toxic to neurons, despite causing comparable DNA damage. Axonal DLK activation induced by wild-type tau potentiated the impact of DNA damage response, resulting in overt neurotoxicity. In summary, we have established a cellular tauopathy model highly relevant to AD and identified a functional synergy between the MAPK-DLK axis and DNA damage response in the neuronal degenerative process.

overall_design: Primary cultured mouse cortical and hippocampal neurons were infected with/without AAV1-Control, WT tau or P301L. At day 7 after infection, we performed gene expression profiling analysis.

first: Sanming

last: Li


title: STAT3 phosphorylation at serine 727 activates specific genetic programs and promotes clear cell renal cell carcinoma (ccRCC) aggressiveness

city: Barcelona

first: Anna

last: Meseguer

address: Paseo Vall d'Hebron 119-129

country: Spain

institute: VHIR

summary:
The signal transducer and activator of transcription 3 (STAT3) is a transcription factor mainly activated by phosphorylation in either tyrosine 705 (Y705) or serine 727 (S727) residues that regulates essential processes such as cell differentiation, apoptosis inhibition, or cell survival.
we used microarrays to evaluate the effects of the STAT3 phosphomutants on global gene expression and identify the genes and pathways regulated by different STAT3 phosphorylation states in the 769-P cell line.

overall_design: we have generated human-derived ccRCC cell lines carrying STAT3 Y705 and S727 phosphomutants to identify genes and pathways regulated by pS727 that could be distinguished from those regulated by pY705 or by the combination of both. First, 769-P cells were depleted of endogenous STAT3 using shRNA and STAT3 WT form was then rescued. On this rescued STAT3 gene backbone, Y705 and S727 STAT3 phosphomutants were generated by introducing structurally similar amino acids that prevent (phosphoablative) or mimic (phosphomimetic) phosphorylation for each residue. A phosphomimetic substitution for Y705, however, was not possible since tyrosine is an aromatic amino acid and neither aspartic nor glutamic acid resembles the structure or charge density of a phosphotyrosine. To overcome this, we used interleukin-6 (IL6), a classic activator of the JAK/STAT3 pathway via pY705.

first: Jazmine

last: Arevalo


title: Identify proinsulin regulators using CRISPR screen and mouse genetics

city: Cleveland

first: Sisi

last: Lai

state: Ohio

address: 10900 Euclid Avenue, BRB 609A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identify proinsulin regulators using CRISPR screen and mouse genetics [CRISPR screen]

summary: Proinsulin is the precursor of insulin in pancreatic beta cells. Altered proinsulin and proinsulin to insulin ratio mark beta cell dysfunction, predictuing disease progression into type 1 and type 2 diabetes. Of essential role for beta cell function, knowledge about proinsulin production and its role in disease are currently very limited. Using genome wide CRISPR screen, we identified 84 proinsulin regulators including classical protein convertases Pcsk1 and Cpe, and novel factors like Pdia6. Among the list 29 proinsulin regulators were trajectory genes involved in disease progression in obesity and type 2 diabetes in humans. In vivo mouse genetics study revealed unique genetic architecture and quantitative trait loci (QTLs) modulating plasma proinsulin levels. Integrative analyzing and mapping of the QTL signals directly pinpointed to proinsulin regulators identified from the CRISPR screen, which in return greatly improved resolution of the mouse genetic study. 4 out of 5 overlapped genes can be individually validated. Knocking down the leading hits Pdia6 leads to decreased proinsulin content and remarkable loss of proinsulin granules in beta cells. Consequently, proinsulin secretion was greatly decreased. Mechanistically, protein translation rate was greatly impaired after knocking down Pdia6. Our study demonstrated the power of combining in vitro functional genomics with in vivo mouse genetics study to identify proinsulin regulatory network in pancreatic beta cells.

overall_design: MIN6 cells transfected with the GeCKOv2 library were stained with proinsulin and insulin antibodies. Cells were assigned and sorted into "proinsulin high" and "proinsulin low" populations. Genomic DNA of each cell population were extracted using the Dneasy Blood & Tissue kit (Qiagen) and the sgRNA regions were PCR amplified by Herculase II (Agilent) polymerase using indicated primers. The PCR products were purified with Aline PCR Clean DX magnetic beads and processed into Truseq libraries followed by NGS analysis.

first: Chen

last: Weng

first: Yan


title: Identify proinsulin regulators using CRISPR screen and mouse genetics [RNA-Seq]

overall_design: RNA-seq of MIN6 and EndoC-bH3 cells in the context of non-targeting control and shRNA (MIN6) or siRNA (EndoC-bH3) mediated Pdia6 knocking down.

first: Weng

last: Chen

first: Shanshan

last: Zhang

first: Peidong

last: Gao


title: Transcriptomic analysis of the HIF-1α impact on the gene expression profile of chicken fibroblasts under hypoxia

first: qijun

last: wu

address: shizishan street

institute: huazhong agriculture university

summary: Hypoxia-inducible factor 1 (HIF-1) is a transcriptional regulator that mediates cellular adaptive responses to hypoxia. Hypoxia-inducible factor 1α (HIF-1α) is involved in the development of ascites syndrome (AS) in broiler chickens. Therefore, studying the effect of HIF-1α on the cellular transcriptome under hypoxic conditions will help to better understand the mechanism of HIF-1α in the development of AS in broilers. In this study, we analyzed the gene expression profile of the DF-1 cell line under hypoxic conditions by RNA-seq. Additionally, we constructed the HIF-1α knockdown DF-1 cell line by using the RNAi method and analyzed the gene expression profile under hypoxic conditions. The results showed that exposure to hypoxia for 48 hours had a significant impact on the expression of genes in the DF-1 cell line, which related to cell proliferation, stress response, and apoptosis. In addition, after HIF-1α knockdown more differential expression genes appeared than in wild-type cells, and the expression of most hypoxia-related genes was either down-regulated or remained unchanged. Pathway analysis results showed that differentially expressed genes were mainly enriched in pathways related to cell proliferation, apoptosis, and oxidative phosphorylation. Our study obtained transcriptomic data from chicken fibroblasts at different hypoxic times and identified the potential regulatory network associated with HIF-1α. This data provides valuable support for understanding the transcriptional regulatory mechanism of HIF-1α in the development of AS in broilers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DF-1 cells and HIF1A knock-down cell line .

first: Aikebaier

last: Reheman

first: Qijun

last: Wu

first: Jianing

last: Xu

first: Jiang

last: He

first: Meng

last: Qi

first: Kai

first: Gang

first: Xinwei

last: Feng


title: Transcriptomics profile of human bronchial epithelial cells exposed to influenza virus (H3N2) and ambient fine particles

city: XinXiang

first: WeiDong

address: JinSuiStreet

institute: XinXiangMedicalUniversity

summary: Fine particulate matter (PM2.5) pollution remains a major threat to public health. As the physical barrier against inhaled air pollutants, airway epithelium is a primary target for PM2.5 and influenza viruses, two major environmental insults. Recent studies have shown that PM2.5 and influenza viruses may interact to aggravate airway inflammation, an essential event in the pathogenesis of diverse pulmonary diseases. Airway epithelium plays a critical role in lung health and disorders. Thus far, the mechanisms for the interactive effect of PM2.5 and the influenza virus on gene transcription of airway epithelial cells have not been fully uncovered. In this present pilot study, the transcriptome sequencing approach was introduced to identify responsive genes following individual and co-exposure to PM2.5 and influenza A (H3N2) viruses in a human bronchial epithelial cell line (BEAS-2B). Enrichment analysis revealed the function of differentially expressed genes (DEGs). Specifically, the DEGs enriched in the xenobiotic metabolism by the cytochrome P450 pathway were linked to PM2.5 exposure. In contrast, the DEGs enriched in environmental information processing and human diseases, such as viral protein interaction with cytokines and cytokine receptors and epithelial cell signaling in bacterial infection, were significantly related to H3N2 exposure. Meanwhile, this study found that co-exposure to PM2.5 and H3N2 may affect G protein-coupled receptors on the cell surface by modulating Ca2+. Thus, the results from this study provides insights into PM2.5- and influenza virus-induced airway inflammation and potential mechanisms

overall_design:
The transcriptome sequencing approach was introduced to identify responsive genes following individual and co-exposure to PM2.5 and influenza A (H3N2) viruses in a human bronchial epithelial cell line (BEAS-2B).
The cells were subjected to the following treatments: serum-free medium (control group, mock), PM2.5 (12.5 μg/mL), H3N2 (MOI=1), or co-exposure of PM2.5 (12.5 μg/mL) and H3N2 (MOI=1).

first: Yuan

last: Liu

first: Yinbiao

last: Wang

first: Rui

first: Weidong


title: iPSC-derived microglia export cholesterol to neuronal cells in human brain organoids and promote their maturation

city: 1 Fusionopolis Way, #20-10 Connexis North Tower

first: nicholas

last: ang

institute: SIgN

summary: Microglia are specialised brain-resident macrophages that arise from primitive macrophages colonising the embryonic brain. Microglia contribute to multiple aspects of brain development, but their precise roles in early human brain remain poorly understood due to limited access to relevant tissues. The generation of brain organoids from induced human pluripotent stem cells (iPSC) recapitulates some key features of human embryonic brain development, but current approaches do not incorporate microglia and thus are lacking. Here, we generated microgliasufficient brain organoids by co-culturing brain organoids with primitive-like macrophages generated from the same human iPSC (iMac). In organoid co-cultures, iMac differentiated into cells with microglia-like phenotypes and functions (iMicro), and modulated neuronal progenitor cell (NPC) differentiation, limiting NPC proliferation and promoting axonogenesis. Mechanistically, iMicro contained high levels of PLIN2+ lipid droplets that exported cholesterol and its esters which weretaken up by NPC in the organoids. We also detected PLIN2+ lipid droplet-loaded microglia in mouse and human embryonic brain. Overall, our approach significantly advances current human brain organoid approaches by incorporating microglial

overall_design: 6 samples,  hiMacs and hiMicros co-cultured with cortical neurons (on day 12 of co-culture), with 3 independent replicates, respectively

first: Dong

last: Park

first: Tatsuya

last: Kozaki

first: Kaibo

last: Duan

first: Florent

last: Ginhoux


title: Identification of chromatin accessibility during the early stage of pig SCNT embryo reprogramming by ATAC-seq

city: Nanjing

first: Xue

state: Jiangsu

address: 1 Weigang

institute: Nanjing Agricultural University

summary: Somatic cell nuclear transplantation (SCNT) can transform highly differentiated donor nuclei into pluripotent nuclei through the large-scale reprogramming of chromatin. The reprogramming of chromatin has been documented to take place in the first few hours after SCNT embryo activation. Thus, studies that characterize dynamic changes in chromatin during the first few hours after embryo activation could provide insight into the mechanism and significance of genome-wide reprogramming. However, few studies have examined the epigenetic remodeling of reconstructed embryos during the early stage of reprogramming. Here, we conducted ATAC-seq on 50 porcine SCNT-HMC embryos and 50 parthenogenetic activation (PA) embryos 10 h after activation. Along with pig embryonic fibroblast (PEF) ATAC-seq data, we found low levels of chromatin accessibility and gene transcription in SCNT and PA embryos. Moreover, PEF genes and the X chromosome became inaccessible during embryo reprogramming. GO enrichment analysis revealed that the molecular functions related to accessible chromatin in embryos primarily included transcriptional regulatory activity and SMAD binding. The differentially accessible chromatin sites between SCNT and PEF were primarily related to transcriptional activity and histone modification. These results indicated that despite the tight chromatin structure during the early stage of embryo reprogramming, some accessible chromatin sites, which were primarily distributed in the intergenic region, were still detected. Dynamic changes in chromatin accessibility during reprogramming were primarily related to transcriptional activity and histone modification. Generally, this study provided new insight into the dynamics and importance of chromatin accessibility during the early stages of embryo reprogramming.

overall_design: ATAC-seq were applied on porcine oocytes at GV stage, SCNT-HMC embryos and parthenogenetic activation embryos 10 hr after activation. Two replicates were performed for each group.

first: Juan

last: Li

first: Honglin


title: Epithelial Yap/Taz are required for functional alveolar regeneration following acute lung injury

city: Nashville

first: Jonathan

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

summary: A hallmark of idiopathic pulmonary fibrosis (IPF) and other interstitial lung diseases is dysregulated repair of the alveolar epithelium. The Hippo pathway effector transcription factors YAP and TAZ are implicated as essential for type 1 and type 2 alveolar epithelial cell (AT1 and AT2) differentiation in the developing lung, yet aberrant activation of YAP/TAZ is a prominent feature of the dysregulated alveolar epithelium in IPF. In these studies, we sought to define the functional role of YAP/TAZ activity during alveolar regeneration. We demonstrated that Yap and Taz are normally activated in AT2 cells shortly after injury, and deletion of Yap/Taz in AT2 cells led to pathologic alveolar remodeling, failure of AT2 to AT1 cell differentiation, increased collagen deposition, exaggerated neutrophilic inflammation, and increased mortality following injury induced by a single dose of bleomycin. Loss of Yap/Taz activity prior to a LPS injury prevented AT1 cell regeneration, led to intra-alveolar collagen deposition, and resulted in persistent innate inflammation. Together these findings established that AT2 cell Yap/Taz activity is essential for functional alveolar epithelial repair and prevention of fibrotic remodeling.

overall_design:
Lung single-cell suspensions were generated with MACS-column-based downsampling of Cd45+ cells from tamxifen-treated  WT and SPC-CreERT2 Yap f/f; Taz f/f mice at day 28 after intratracheal bleomycin or PBS. ScRNA-seq was performed using the Parse Biosciences Evercode system.

Please note that eight paired sets of FASTQ files are sub-libraries (represented as GSMnnnn records), each of which contain cells from all of the 19 individual samples. The post-demultiplexing counts files for each sample (along with each sample information file, metadata_19samples.txt) are linked as Series supplementary files.

first: Kropski

last: Jonathan

first: Gokey

last: Jason