title: Sex-Specific DNA Methylation and Gene Expression Changes in Mouse Placentas After Early Preimplantation Alcohol Exposure[RNA-Seq]

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

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

summary: Preimplantation alcohol exposure can negatively impact embryonic development through disruption of molecular profiles and lead to fetal alcohol spectrum disorder (FASD). Despite the central role of the placenta in proper embryonic development and successful pregnancy, studies on the placenta in a FASD context are markedly lacking. Here, preimplantation binge-like alcohol exposure was implemented on pregnant C57BL/6 female mice through subcutaneous injection with two doses of either 2.5 g/kg 50% ethanol or an equivalent volume of saline at 2-h intervals on embryonic day 2.5 corresponding to the 8-cell stage. The placental morphology, DNA methylation and gene expression patterns in male and female late-gestation (E18.5) placentas were assessed. While overall placental morphology was not affected, we found a significant decrease in male ethanol-exposed embryo weights. When looking at molecular profiles, we uncovered numerous differentially methylated regions (DMRs ≥10% difference; 991 in males; 1309 in females) and differentially expressed genes (DEGs; 1046 in males; 340 in females) in the placentas. Remarkably, only 21 DMRs and 54 DEGs were common to both sexes, which were enriched for genes involved in growth factor response pathways. Preimplantation alcohol exposure had a greater impact on imprinted genes expression in male placentas (imprinted DEGs: 18 in males; 1 in females). Finally, by using L1-regularized linear regression, we were able to precisely discriminate control and ethanol-exposed placentas based on their specific DNA methylation patterns. This is the first study demonstrating that preimplantation alcohol exposure alters the DNA methylation and transcriptomic profiles of late-gestation placentas in a sex-specific manner. Importantly, it reveals a placental DNA methylation signature that can detect prenatal alcohol exposure in early life in order to provide appropriate support to attenuate and prevent eventual impact.

overall_design: To investigate the impact of prenatal alcohol exposure during preimplantaton on the DNA methylation and gene expression landscape of late-gestation placenta

first: Lisa-Marie

last: Legault

first: Mélanie

last: Breton-Larrivée

first: Fannie

last: Filion-Bienvenue

first: Anthony

last: Lemieux

first: Alexandra

last: Langford-Avelar

first: Thomas

last: Dupas


title: Sex-Specific DNA Methylation and Gene Expression Changes in Mouse Placentas After Early Preimplantation Alcohol Exposure[Methyl-Seq]

status: Public on Feb 07 2024

country: Canada

type: Methylation profiling by high throughput sequencing


title: X inactivation regulates lymphocyte induced cardiac remodeling

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

country: USA

institute: Medical University of South Carolina

type: Expression profiling by high throughput sequencing

summary: After menopause, women lose the protective effect of female hormones and experience increased risk of adverse cardiac remodeling following myocardial infarction (MI). This may be due in part to the deleterious effects of genes encoded on the X chromosome. On average, 15% of genes located on the X chromosome escape inactivation in women, resulting in over expression. We hypothesize that with age T-cells escape X-chromosome inactivation (XCI), thus exacerbating the inflammatory response and resulting in adverse post-MI remodeling in women. We will use 2 aims to delineate a mechanism defining age effects on XCI and how this in turn influences T-cell mediated post-MI remodeling. Aim 1 will test the hypothesis that older females have an increased number of T-cells that escape XCI and exacerbate monocyte recruitment and activation post-MI. Aim 2 will test the hypothesis that female mice with T-cells that have escaped XCI will have adverse remodeling and decreased post-MI survival. Our understanding of sex differences especially the influence of sex chromosomes during post-MI remodeling and development of heart failure is lacking. The information obtained from the proposed experiments will have direct implications for medical management of women post-MI.

overall_design: Myocardial infarction as induced in C57Bl6/J female mice by permanent occlusion of the left anterior descending artery ligation. At post-MI Day 5, cells were isolated from the infarct zone of young (3-5 months) and old (15-17 months old) and run for scRNA sequencing.

first: Bryan

last: Granger

first: Kristine

last: Deleon-Pennell


title: Next generation sequencing to identify GPT1 regulating signaling pathway in CRC

city: Guangzhou

first: Li

last: Xiong

state: Guangdong

address: 58 Zhongshan Road 2

department: Department of Endocrinology

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: We performed next generation sequencing between control CRC cells and CRC cells with GPT1 overexpression to identify GPT1 regulating signaling pathway

first: Zhenxing

last: Liang

first: Huashan

last: Liu


title: Interactions of erythromycin and an antibiotic-mixture to the gut microbiome of juvenile rainbow trout

city: Duluth

first: Phillip

last: Ankley

state: MN

address: 6201 Congdon Blvd

institute: U.S. EPA

summary: Erythromycin (ERY) is a commonly used antibiotic that can be found in wastewater effluents globally. Due to the mechanisms by which they kill and prevent bacterial growth, antibiotics can have significant unwanted impacts on the fish gut microbiome. The overall objective of this project was to assess the effects of erythromycin and an antibiotic mixture on fish gut microbiomes. The project was split into two experiments to assess gut microbiome in response to exposure with ERY alone or in mixture with other common antibiotics. The objectives of experiment 1 were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7 d uptake followed by a 7 d depuration period using three concentrations of ERY. Furthermore, throughout the study changes in gut microbiome response were assessed. In experiment 2, a follow-up study was conducted using an identical experimental design to assess the impacts of an antibiotic-mixture (ERY, ampicillin, metronidazole, and ciprofloxacin at 100 µg/g each). Here, three matrices were analyzed, with gut collected for 16s metabarcoding, plasma for untargeted metabolomics, and brain for mRNA-seq analysis. ERY was depurated from the fish relatively quickly and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7 d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing temporality compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. Brain transcriptome revealed only slight alterations due to antibiotic exposure. The results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics in fish feed and the environment, with implications for host health.

overall_design: Five RBT were exposed in each of six replicate 20-L tanks for each treatment in a dilutor system to regulate temperature (12°C) and light (14 h: 10 h light: dark). To maintain optimal water quality and consistency of the water microbiome, fish were housed under flow-through conditions with three complete renewals of cold, filtered facility water every 24 h. During experiments, water quality was assessed every 3 days. RBT were exposed via diet to two treatments of antibiotics, including 1,000 µg ERY/g and a mixture of antibiotics (ant-mix) containing nominal concentrations of 100 µg/g each of ampicillin, metronidazole, ciprofloxacin, and ERY, and one solvent control (MeOH). The 7-d exposure was followed by a 7-d depuration, during which food containing antibiotics was replaced with solvent control food. Brain mRNAseq was ran to assess effects of antibiotics on the transcriptome of the brain. Briefly, flash-frozen brain tissue was extracted for high-quality RNA using RNeasy Plus Universal Mini Kit with QIAzol Lysis Reagent (Qiagen, Germany). Two samples of whole brain collected from each tank after 7 d, were extracted and pooled at equimolar amounts with measurement using Qubit RNA HS Assay Kit (Thermo Fisher, USA). Extracted RNA was assessed for RNA integrity number (RIN) using Agilent RNA 6000 Nano kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) with all values being ≥ 6.5 with a mean ± standard deviation of 7.84 ± 0.875. Samples were then shipped on dry ice to Genome Quebec Innovation Centre for paired-end sequencing (2x100), using an Illumina NovaSeq 6000. Quality control of resulting sequence output was conducted using FastQC, and reads were assessed for quality, then trimmed to a minimum Phred score of 20 and a minimum length of 35 bases using Trimmomatic (Bolger et al., 2014). The abundance of transcripts was estimated using Salmon (version 1.10.2) with the reference RBT transcriptome USDA_OmykA_1.1 (GenBank Acc. no. GCA_013265735.3) (Patro et al., 2017) and mapped to genes using GenomicFeatures (version 1.52.1) (Lawrence et al., 2013) and corresponding gtf file (Oncorhynchus_mykiss.USDA_OmykA_1.1.110.gtf).

first: Jonathan

last: Challis

first: Pu

last: Xia

first: Yufeng

last: Gong

first: Yutong

last: Zhou

first: Markus

last: Hecker

first: John

last: Giesy

last: Brinkmann


title: Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

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

overall_design: Refer to individual Series


title: Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING (RNA-Seq)

summary: The transforming growth factor-β (TGF-ꞵ) family member activin A (hereafter Activin-A) is overexpressed in many cancer types, often correlating with cancer-associated cachexia and poor prognosis. Activin-A secretion by melanoma cells indirectly impedes CD8+ T cell-mediated anti-tumor immunity and promotes resistance to immunotherapies, even though Activin-A can be proinflammatory in other contexts. To identify underlying mechanisms, we here analyzed the effect of Activin-A on syngeneic grafts of Braf mutant YUMM3.3 mouse melanoma cells and on their microenvironment using single-cell RNA sequencing. We found that the Activin-A-induced immune evasion was accompanied by a proinflammatory interferon signature across multiple cell types, and that the associated increase in tumor growth depended at least in part on pernicious STING activity within the melanoma cells. Besides corroborating a role for proinflammatory signals in facilitating immune evasion, our results suggest that STING holds considerable potential as a therapeutic target to mitigate tumor-promoting Activin-A signaling at least in melanoma.

overall_design: To assess how crosstalk of Activin-A with IFN-γ influences gene expression in the absence of the TME, mRNA from YUMM3.3 cells that were treated in quadriplicates with IFN-γ and Activin-A individually or together for 4 or 12 hrs was analyzed by Bulk RNA Barcoding and Sequencing (BRB-seq)

first: Katarina

last: Pinjusic

first: Joao

last: Lourenco

first: Nadine

last: Fournier

first: Christian

last: Iseli

first: Nicolas

last: Geux

first: Olga

last: Egorova

first: Sina

last: Nassiri

first: Daniel

middle: B

last: Constam


title: Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING (scRNA-Seq)

overall_design: To assess activin-induced changes in melanoma and in their TME, YUMM3.3 mouse melanoma grafts expressing lentiviral INHBA (βA) or empty control lentivirus (Ctrl) were analyzed by single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform. The YUMM3.3-Ctrl and -βA melanoma cells were transduced with a lentiviral green fluorescent protein (GFP) expression vector to distinguish stromal and cancerous cells. Tumors were digested and single cells were separated into GFPhi tumor cells and GFPint/low stromal cells and then mixed at a 1:9 ratio to enrich the library for stromal cells. Triplicate Ctrl and ꞵA samples consisting of each of two tumors were collected on day 13 post-injection when tumor sizes were not yet significantly enlarged by Activin-A.


title: Fusobacterium nucleatum infection modulates the transcriptome and epigenome of colon cancer cells in an oxygen-dependent manner

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

type: Genome binding/occupancy profiling by high throughput sequencing


title: Fusobacterium nucleatum infection modulates the transcriptome and epigenome of colon cancer cells in an oxygen-dependent manner [ChIP-seq]

summary: We studied how Fusobacterium nucleatum infection under hypoxia regulated the epigenome and transcriptome of colon cancer cells. The six datasets that are described in this study are labeled as follows: (a) Normoxia - No Bacteria (NN), (b) Normoxia - infection with Fnn (NF), (c) Normoxia - infection with E. coli (NE),  (d) Hypoxia - No Bacteria (HN), (e) Hypoxia - infection with Fnn (HF), and (f) Hypoxia - infection with E. coli (HE).

overall_design: We split HCT116 cells into two sets of flasks and conditioned them to hypoxic and normoxic environments. One set of cells continued to proliferate in normoxia (18% oxygen) while the other half was exposed to hypoxia (1% oxygen) for 24 hours. After the initial exposure to the oxygen environment, the conditioned cells were infected with Fnn for 4 hours in their respective oxygen environments in pre-equilibrated media. Infection with non-invasive E. coli with otherwise identical conditions was used as a control to validate host cell response. The cells were further incubated for 24 hours in their respective oxygen environments with pre-equilibrated media before they were extracted for analysis.

first: Zirui


title: The P-body protein 4E-T regulates the balance between cell genesis and establishment of the postnatal neural stem cell pool by repressing mRNA translation

status: Public on Feb 08 2024

city: Toronto

first: Adelaida

last: Kolaj

state: Ontario

address: 27 King's College Circle

institute: University of Toronto


title: Fusobacterium nucleatum infection modulates the transcriptome and epigenome of colon cancer cells in an oxygen-dependent manner [RNA-seq]


title: Transcriptome analysis of Control and FBXO38 knockdown B16-F10 tumor issue

city: shanghai

first: Yijia

last: Wu

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: shanghai jiaotong university

summary: F-box only protein 38 (FBXO38), which belongs to SKP1-CUL1-F-box protein (SCF) family, exhibits the ability to mediate Lys48-linked poly-ubiquitination and subsequent proteasome degradations of PD-1.To investigate the effect of FBXO38 knockdown on transcription in tumor, we performed RNA-seq in control and FBXO38 knockdown B16-F10 tumor issue.

overall_design: We constructed control and FBXO38 knockdown  by shRNA in B16-F10 cell lines. Tumor cells were then injected subcutaneously into C57BL/6 mice. After 16 days of culture, the mice were sacrificed by cervical dislocation, tumors were isolated, and RNA-Seq sequencing was performed on the tumor tissue.

first: Jianfeng

last: Shen


title: Volatile communication in plants relies on a KAI2-mediated signaling pathway

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

summary: Plants are targets of volatile organic compounds (VOCs) released as a part of plant-plant communication, within-plant self-signaling and plant-microbe interactions. Therefore, understanding VOC perception and downstream signaling is vital for unraveling the mechanisms behind information exchange in plants, which remain largely unexplored. Using the hormone-like function of volatile terpenoids in reproductive organ development as a system with a visual marker for communication, we demonstrated that among the four petunia karrikin-insensitive receptors, PhKAI2ia stereo-specifically perceives the (-)-germacrene D signal, triggering a karrikin-like signaling cascade. This study provides new insights into plant olfaction, uncovers the role(s) of the unique intermediate clade of KAI2 receptors, illuminates the involvement of KAI2ia-dependent signaling pathway in volatile communication and gives insight into the long-standing question about the nature of potential endogenous karrikin-like ligand(s).

overall_design: Total RNA was extracted from wild type and PhTPS1 RNAi mutant pistils on day -1 and +1 postanthesis for RNA-Seq of Petunia hybrida cv. Mitchell samples.

middle: M

first: Shannon

last: Stirling

first: Benoît

last: Boachon

first: Natalia

last: Dudareva


title: Folate depletion induces erythroid differentiation through perturbation of de novo purine synthesis

city: Boston

first: Naama

last: Kanarek

state: Massachusetts

address: 61 Binney St Rm 1126, Enders Building

department: Pathology

institute: Boston Children's Hospital

summary: Folate, an essential vitamin, is a one-carbon acceptor and donor in key metabolic reactions. Erythroid cells harbor a unique sensitivity to folate deprivation, as revealed by the primary pathological manifestation of nutritional folate deprivation: megaloblastic anemia. To study this metabolic sensitivity, we applied mild folate depletion to human and mouse erythroid cell lines, and primary murine erythroid progenitors. We show that folate depletion induces early blockade of purine synthesis and accumulation of the purine synthesis intermediate and signaling molecule, AICAR, followed by enhanced heme metabolism, hemoglobin synthesis, and erythroid differentiation. This is phenocopied by inhibition of folate metabolism using the SHMT1/2 inhibitor - SHIN1, and by AICAR supplementation. Mechanistically, the metabolically-driven differentiation is independent of nucleotide sensing through mTORC1 and AMPK, and is instead mediated by protein kinase C (PKC). Our findings suggest that folate deprivation-induced premature differentiation of erythroid progenitor cells is a molecular etiology to folate-deficiency induced anemia.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We investigated the impact of folate depletion and one-carbon metabolism inhibiton on K562 and MEL cells. We cultured K562 and MEL cells in 2,000 nM folic acid or 100 nM folic acid, and in the presence of SHIN1 (1.25 uM) or AICAR (500 nM). We performed gene expression profiling analysis following 72 hours of culture in the indicated  treatment conditions.

first: Maynard

middle: G

last: Adam

first: Wong

middle: L

last: Alan

first: Kanarek

last: Naama


title: Sex-Specific DNA Methylation and Gene Expression Changes in Mouse Placentas After Early Preimplantation Alcohol Exposure

first: Serge

last: McGraw


title: Targeting focal adhesion kinase boosts immune response in KRAS/LKB1 co-mutated lung adenocarcinoma via remodeling the tumor microenvironment

city: Shanghai

first: Meng

last: Qiao

address: No.507 Zhengmin Road, Yangpu District

institute: Shanghai Pulmonary Hospital

summary: Background: KRAS mutation is one of the most common oncogenic drivers in NSCLC, however, the response to immunotherapy is heterogeneous owing to the distinct co-occurring genomic alterations. KRAS/LKB1 co-mutated lung adenocarcinoma displays poor response to PD-1 blockade whereas the mechanism remains undetermined. Methods: We explored the specific characteristics of tumor microenvironment (TME) in KL tumors using syngeneic KRASG12DLKB1-/-(KL) and KRASG12DTP53-/- (KP) lung cancer mouse models. The impact of focal adhesion kinase (FAK) inhibitor on KL lung tumors was investigated in vitro and in vivo through evaluation of both KL cell lines and KL lung cancer mouse models. Results: We identified KL tumors as “immune-cold” tumors with excessive extracellular matrix (ECM) collagen deposition that formed a physical barrier to block the infiltration of CD8+T cells. Mechanistically, abundant activated cancer-associated fibroblasts (CAFs) resulted from FAK activation contributed to the formation of the unique TME of KL tumors. FAK inhibition with a small molecular inhibitor could remodel the TME by inhibiting CAFs activation, decreasing collagen deposition and further facilitating the infiltration of anti-tumor immune cells, including CD8+ T cells, DC cells and M1-like macrophages into tumors, hence, converting “immune-cold” KL tumors into “immune-hot” tumors. The combined FAK inhibitor and PD-1 blockade therapy synergistically retarded primary and metastatic tumor growth of KL tumors.Conclusions: Our study identified FAK as a promising intervention target for KL tumors and provided basis for the combination of FAK inhibitor with PD-1 blockade in the management of KL lung cancers.

overall_design: To investigate the characteristics of TME in KP and KL tumors, in vivo tumor formation assay was performed. A total of 2 × 106 KP or KL cells were suspended in 200 μL PBS and then injected subcutaneously into 6 week old male C57BL/6 mice in the right flank. The tumor volumes were measured by caliper and calculated with a formula of π/6 × long diameter × short diameter × short diameter. Mice were sacrificed when tumor volume reached 700-800mm3. ce were sacrificed when tumor volume reached 700-800mm3. Tumors from KP or KL cell-bearing mice were excised for further analysis.

first: Caicun

last: Zhou


title: Altered gene expression linked to germline dysfunction following exposure to environmentally relevant level of DEET

first: VICTOR

last: BARRERA BURGOS

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

summary: N,N-Diethyl-meta-toluamide (DEET) is a synthetic insect repellent invented in 1946 by the US Department of Agriculture for use by military personnel and now used worldwide as evidenced by its detection at various levels in human urine, serum, semen, and cord serum (1–5). While the neurological effects of DEET have been widely investigated (6–8), its effects on the germline and reproductive health are less understood. Here we used the nematode Caenorhabditis elegans, a genetically and cytologically tractable model system that shares a high degree of conservation of its genes and biochemical pathways with humans and is highly predictive of mammalian reprotoxicity, to study how DEET affects the germline (9–12). We found that exposure to environmentally relevant levels of DEET causes activation of p53/CEP-1-dependent germ cell apoptosis and alters recombination by inducing elevated levels of meiotic DNA double-strand breaks (DSBs) and crossovers (COs) resulting in chromosome abnormalities and missegregation. RNA sequencing (RNA-seq) analysis links DEET induced alterations in the expression of genes related to oxidation and reduction (redox) processes and chromatin structure to reduced mitochondrial function, altered DSB repair progression, and impaired early embryonic cell division. Our work shows that exposure to environmentally relevant levels of DEET interferes with gene expression, leading to increased oxidative stress and altered chromatin structure resulting in detectable germline effects that can pose a risk to reproductive health.

overall_design: To examine the effects of exposure to DEET on gene expression in C. elegans we compared  col-121 worms exposed for 24 hours to either vehicle alone (0.1% DMSO) or to DEET (0.1M). Analysis was done on whole worm samples (4 independent biological repeats) where worms were picked at late L4 stage and exposed for 24 hours.

first: Nara

last: Shin

first: Laura

middle: I

last: Lascarez-Lagunas

first: Rajendiran

last: Karthikraj

first: Shannan

last: Ho Sui

first: Kurunthachalam

last: Kannan

first: Monica

middle: P

last: Colaiacovo

first: Martinez-Garcia

last: Marina

first: Victor

last: Barrera


title: Relative quantification of the recA gene for antibiotic susceptibility testing in response to ciprofloxacin for pathogens of concern

city: Frederick

first: Christopher

middle: Patrick

last: Stefan

state: MD

address: 1425 Porter Street

institute: USAMRIID

summary: Antibiotic resistance (AR) is one of the greatest threats to global health and is associated with higher treatment costs, longer hospital stays, and increased mortality. Current gold standard antibiotic susceptibility tests (AST) are dependent on organism growth rates resulting in prolonged diagnostic answers for slow growing organisms. Changes in the cellular transcriptome can be instantaneous in the presence of stressors such as antibiotic pressure. Here, we demonstrate that relative quantification of the recA gene in response to breakpoint concentrations of ciprofloxacin is an indicator of pathogen susceptibly. For this purpose, we developed seven duplex RT-qPCR assays targeting the recA and 16S rRNA gene, as response and housekeeping genes respectively, for biothreat and ESKAPE pathogens. Surrogate biothreat agents Y. pestis and B. anthracis saw increases in relative recA gene expression, independent of growth rate after 15 minutes of exposure to ciprofloxacin with maximal expression seen after 60 minutes. Treatment with doxycycline also demonstrated an increase in relative recA fold changes compared to no treatment controls. Final evaluation of all seven duplex assays tested across 125 strains, including Tier 1 pathogens, from broth culture demonstrated an overall categorical agreement compared to gold standard microbroth dilution of 97.56% with major error (ME) rates of 1.59% and very major error (VME) rates of 3.23%. Testing on pathogen strains commonly associated with urinary tract infections in contrived clinical sample sets demonstrated an overall categorical agreement of 95.8% with a ME rate of 0.0% and VME rate of 7.69%. These data indicate that relative quantification of a single highly conserved gene accurately predicts susceptibility for multiple bacterial species in response to ciprofloxacin.

sample_organism:
Yersinia pestis
Bacillus anthracis

platform_organism:
Yersinia pestis
Bacillus anthracis

overall_design: RNA sequencing was performed on bacterial samples exposed to breakpoint concentrations of ciprofloxacin across time. RNA sequencing analysis was compared between resistant and suceptable strains as well as compared across multple organisms including B. anthracis and Y. pestis.


title: Inhibition of protein arginine methyltransferase 6 (PRMT6) activates interferon signaling and induces apoptosis in endometrial cancer cells via histone modification [RNA-seq]

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

summary: Histone modification, a major epigenetic mechanism which regulates gene expression by chromatin remodeling, introduces dynamic changes in chromatin architecture. Protein arginine methyltransferase 6 (PRMT6) is overexpressed in various types of cancers. Epigenome regulates the expression of endogenous retrovirus (ERV), which activates interferon signaling related to cancer. We investigated the antitumor effects of PRMT6 inhibition and the role of PRMT6 in endometrial cancer (EC), using epigenome multi-omics analysis including assay for chromatin immunoprecipitation sequencing (ChIP-seq) and ribonucleic acid sequencing (RNA-seq). The expression of PRMT6 in EC was analyzed using real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC). The prognostic impact of PRMT6 expression was evaluated using IHC. We investigated the effects of PRMT6-knockdown (KD) using cell viability and apoptosis assays, as well as its effects on the epigenome using ChIP-seq of H3K27ac antibodies and RNA-seq. Finally, we evaluated the downstream targets identified by multi-omics analysis. PRMT6 was overexpressed in EC and associated with a poor prognosis. PRMT6-KD induced histone hypomethylation, while suppressing cell growth and apoptosis. ChIP-seq revealed that PRMT6 regulated genomic regions related to interferons and apoptosis through histone modifications. RNA-seq data showed altered interferon-related pathways and increased expression of tumor suppressor genes, such as NKX6-1 and PIK3R1, after PRMT6-KD. RT-qPCR showed that eight ERV genes which activated interferon signaling were upregulated by PRMT6-KD. Our data suggested that PRMT6 inhibition induced apoptosis through interferon signaling activated by ERV. PRMT6 regulated tumor suppressor genes and may be a novel therapeutic target in EC.

overall_design: PRMT6 knockdown in HEC1B endometrial cancer cell line

first: Futaba

last: Inoue

first: Kenbun

last: Sone

first: Reo

last: Maruyama


title: Effect of depletion or overexpression of EGR1 on gene expression in HCC cells (deletion in MHCC97H cells, overexpression in PLC/PRF5 cells)

city: chongqing

first: Pan

last: Mingang

address: No. 1, Medical College Road, Yuzhong District, Chongqing

institute: ChongQing Medical University

summary: To investigate the function of EGR1 in HCC growth, we established EGR1 knock out MHCC97H cells by CRISPR/Cas9 system and EGR1-overexpressing PLC/PRF5 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of EGR1 knock out MHCC97H cells and parental MHCC97H cells, EGR1-overexpressing PLC/PRF5 cells and control PLC/PRF5 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EGR1 knock out MHCC97H cells and parental MHCC97H cells (EGR1_KO, Mock), EGR1-overexpressing PLC/PRF5 cells and control PLC/PRF5 cells (EGR1, Vector).

first: Mingang

last: Pan

first: Jie

last: Xia


title: CD73 contributes to the pathogenesis of Fusion-Negative Rhabdomyosarcoma through the purinergic signaling pathway

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: We performed RNA-seq to evaluated the transcriptional changes of CD73 knockdown in RD cells, a Fusion Negative Rhabdomyosarcoma cell line. We used a Dox-inducible shRNA targetting the 3'UTR of CD73 to knockdown this gene. Cells with No-Dox were used as control.

overall_design: Comparative gene expression profiling of RNA-seq data from the human derived RD cell line upon CD73 knockdown with Dox, or No-Dox as control.

first: Lin

last: Xu

first: Akansha

last: Shah

middle: A

last: Lopez

first: Vincent

middle: S

last: Tagliabracci

first: Kenian

last: Chen

first: Rhonda

last: Bassel-Duby

first: Eric

middle: N

last: Olson

first: Ning

last: Liu


title: Inhibition of protein arginine methyltransferase 6 (PRMT6) activates interferon signaling and induces apoptosis in endometrial cancer cells via histone modification


title: MAGEA antigens as immunotherapeutic targets for advanced osteosarcoma

city: Leiden

first: Debora

last: Meijer

address: Albinusdreef 2

country: Netherlands

institute: Leiden University Medical Center

summary: Osteosarcoma is the most common primary bone sarcoma. About 50% of patients develop metastatic disease and their 5-year survival lingers at around 20-30%. T cell checkpoint blockade immunotherapies have revolutionized cancer treatment in the last decade, but their impact remains limited in osteosarcoma. In order to reveal potentially novel immunotherapeutic strategies for advanced osteosarcoma, we conducted an immunogenomic characterization of a unique sample set comprising multiple osteosarcoma samples from seven patients, collected throughout the progression of the disease. We performed RNA-sequencing and imaging mass cytometry analysis on those samples to reveal the immunological landscape during osteosarcoma progression. Transcriptional and phenotypical hallmarks of cytotoxic T cell-driven anti-cancer immunity were enriched in metastatic lesions as compared to primary tumors. In parallel, we found a pronounced increase in the expression of cancer testis antigens, particularly MAGEA-related antigens, in osteosarcoma metastases. Their overexpression in metastatic lesions was confirmed at protein level and positive expression of MAGEA3 in primary tumors showed a significant association with metastasis free survival. Importantly, we demonstrated the presentation of MAGE-derived peptides in three osteosarcoma cell lines. These findings indicate a concurrent augmentation of cytotoxic anti-tumor immune responses and expression of MAGEA antigens from primary to metastatic osteosarcoma. This observation warrants the exploration of MAGEA antigens as potential targets for immunotherapy in the treatment of advanced osteosarcoma.

overall_design: To investigate transcriptome of osteosarcoma during the disease progression. For this, Primary tumors, recurrences and metastases of 7 patiens were collected

first: Noel

middle: F

last: de Miranda

first: Judith

middle: V

last: Bovee


title: Effect of SET knock down on human osteosarcoma cell line HOS gene expression

city: Yamaguchi

first: Naoki

last: Kohyanagi

address: 1677-1, Yoshida

institute: The univercity of Yamaguchi

summary: SE translocation (SET) functions as an inhibitory protein of protein phosphatase 2A (PP2A), an important tumor suppressor, and contributes to the maintenance of stemness in various cancers. In the present study, we used the Tet on system to suppress SET expression in the osteosarcoma cell line HOS in a doxycycline-dependent manner and analyzed its effect on gene expression. The results revealed that SET is involved in mammalian target of rapamycin complex 1 (mTORC1) and B-lymphoma Moloney murine leukemia virus insertion region-1 (Bmi-1).

overall_design: HOS cells expressing pTRIPZ non target shRNA (shNT) , SET target shRNA (shSET) were treated with doxycycline (500 ng/ml) for 2 days and then RNA was extracted with TRIzol Reagent for RNA seq.

first: Nao

last: Kitamura

first: Shunta

last: Ikeda

first: Shusaku

last: Shibutani

first: Koichi

last: Sato

first: Takashi

last: Ohama


title: Targeting FBXO22 enhances radiosensitivity of non-small cell lung cancer by inhibiting FOXM1/Rad51 axis

city: Wuhan

first: Yunshang

address: No. 1277 Jiefang Avenue

institute: Wuhan Union Hospital

summary: FBXO22 is the substrate recognition subunit of SCF E3 ubiquitin ligase, which plays an important role in the occurrence, development and therapeutic response of solid tumors.At present, the relationship between FBXO22 and radiosensitivity of lung cancer has not been fully elucidated.Here we present evidence to prove that abnormally expressed FBXO22 in lung cancer promotes transcriptional activation of homologous recombination enzyme Rad51 by up-regulating transcription factor FOXM1, which in turn induces radioresistance in lung cancer.By comparing with the reference data set of cMap database, Deguelin was identified as a small molecular inhibitor of FBXO22.Deguelin increases the radiosensitivity of lung cancer cells in vitro and in vivo in a FBXO22-dependent manner and is safely tolerated.This study revealed the identity of a novel radioresistance biomarker of FBXO22 and provided preclinical evidence for the clinical transformation of this target by screening small molecular inhibitors.

overall_design: A549 cells transfected with Scrambled or SiRNAs targeting FBXO22 for 48 hours were analyzed by RNA-seq.

first: Xiaohua

last: Jie

first: Gang

last: Wu


title: Inhibition of protein arginine methyltransferase 6 (PRMT6) activates interferon signaling and induces apoptosis in endometrial cancer cells via histone modification [ChIP-seq]

first: Kohei

last: Kumegawa

first: Futaba

last: Inoue

first: Kenbun

last: Sone

first: Reo

last: Maruyama


title: Nervous system injury establishes a microenvironment sufficient for brain tumor formation

city: Saint Louis

first: David

last: Gutmann

state: MO

address: Box 8111, 660 S Euclid Ave

department: Neurology

institute: Washington University in St. Louis School of Medicine

summary: To investigate the mechanism by which optic nerve crush induces microglia Ccl5 production, we performed bulk RNA sequencing on isolated optic nerves from crush- and sham-treatedNf1flox/flox;hGFAP-Cre miceat 3 months of age.

overall_design: Comparative gene expression analysis using buk RNA-seq data from optic nerves of 3 crush-treated mice vs 3 sham-treated (control) mice

first: Jit

last: Chatterjee

first: Lucy

last: Boggs


title: Magnesium promotes vascularized osseointegration in diabetic states

city: chengdu

first: linfeng

last: liu

address: wuhou

institute: sichuan university

summary: The poor osseointegration of dental implants in diabetic patients has become a long-standing clinical problem. Magnesium has been proved to promote bone healing under normal conditions. Here, we elucidate the mechanism by which Mg2+ promotes vascularized osseointegration in diabetic status. We generated a diabetic mice model and demonstrated the alveolar bone healing was compromised, with significantly decreased angiogenesis. We then developed Mg-coating implants with hydrothermal synthesis. These implants sucessfully improved the vascularization and osseointegration in diabetic status. Mechanically, Mg2+ promoted the degradation of Kelch-like ECH associated protein 1 (Keap1) and the nucleation of nuclear factor erythroid 2-related factor 2 (Nrf2) by up-regulating the expression of sestrin 2 (SESN2) in endothelial cells, thus reducing the elevated levels of oxidative stress in mitochondria and relieving endothelial cell dysfunction under hyperglycemia. Altogether, our data proved that Mg2+ promoted vascularized osseointegration in diabetic mice by regulating endothelial mitochondrial metabolism.

overall_design: HUVEC were cultured in three different conditions: high glucose (HG, 35mM), and HG+Mg2+ (MgSO4, MACKLIN).HUVECs were treated with HG medium or HG medium containing 5mM Mg2+ for 48h (n = 3 in each group) for RNA-Sequencing .Then we performed analysis and compared gene expression.

first: Linfeng

last: Liu


title: YTHDF2 accelerates brain aging process via trapping mitochondrial morphology associated genes

city: Hefei

first: Ding

middle: feng

last: Li

address: Huang shan road 443

institute: USTC

summary: We report the high-throughput sequencing of RNA expression in YTHDF-RIP, YTHDF1+2 overexpression and  insoluble fraction of 22 months mice

overall_design: Examination of RNA expression pattern in YTHDF-RIP, YTHDF1+2 overexpression and  insoluble fraction of 22 months mice

first: Qiang

first: Juan

last: Zhang

first: Dingfeng


title: Loss of NSD2 causes dysregulation of synaptic genes and altered H3K36 dimethylation in mice [ChIP-seq]

city: Setagaya

first: Shiori

last: Kinoshita

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: Epigenetic disruptions have been implicated in neurodevelopmental disorders. NSD2 is associated with developmental delay/ intellectual disability; however, its role in brain development and function remains unclear. We performed transcriptomic and epigenetic analyses using Nsd2 knockout mice to better understand the role of NSD2 in the brain. Transcriptomic analysis revealed that the loss of NSD2 caused dysregulation of genes related to synaptic transmission and formation. By analyzing changes in H3 lysine 36 dimethylation (H3K36me2), NSD2-mediated H3K36me2 mainly marked quiescent state regions and the redistribution of H3K36me2 occurred at transcribed genes and enhancers. By integrating transcriptomic and epigenetic data, we observed that H3K36me2 changes in a subset of dysregulated genes related to synaptic transmission and formation. These results suggest that NSD2 is involved in the regulation of genes important for neural function through H3K36me2. Our findings provide insights into the role of NSD2 and improve our understanding of epigenetic regulation in the brain.

overall_design: ChIP-seq was performed for H3K36me2 in WT and Nsd2 KO E15.5 brain.


title: A non-canonical Hippo pathway represses the expression of deltaNp63

city: NEW YORK

first: Ana Maria

last: Low Calle

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciencies

institute: Columbia University

summary: Regulation of p63 expression occurs by a non-canonical version of the Hippo pathway in mammary epithelial, breast carcinoma and head and neck squamous carcinoma cells

overall_design: MCF10A cells (3x105 cells per well) were seeded in 6 well plates. Next day cells were transfected with 11 nM of two different siRNAs sets against YAP and TAZ or 22 nM of control siRNA; 48 h post transfection fresh media with DMSO or 5 µM of XMU-MP1 (MST1/2 inhibitor) was added and cells were harvested 6 h later. Total RNA was isolated using TRIzol reagent (Thermofisher, 15596026) following the manufacturer’s instructions

first: Ana

last: Low-Calle

first: Hana

last: Ghoneima

first: Nicholas

last: Ortega

first: Adriana

last: Cuibus

first: Chen

last: Katz

last: Tong

first: Carol

last: Prives

first: Ron

last: Prywes


title: Loss of NSD2 causes dysregulation of synaptic genes and altered H3K36 dimethylation in mice

overall_design: RNA-seq and H3K36me2 ChIP-seq were performed in WT and Nsd2 KO E15.5 brain.


title: Single-cell sequencing reveals the cardio-protective role of overexpressing Cox7B in hypertrophic cardiomyopathy

city: Tianjin

first: Kui

last: Wang

address: Weijin Road 94

department: School of Statistics and Data Science

institute: Nankai University

summary: Hypertrophic cardiomyopathy (HCM) is an important cause leading to heart failure. Preserving cardiac function particularly in cardiomyocytes (CMs) is essential for improving prognosis in HCM patients. Therefore, understanding single-cell transcriptome characteristics of CMs in HCM would be indispensable to investigate potential therapeutic targets. We applied single-cell tagged reverse transcription (STRT-seq) approach and obtained 338 CM transcriptomes. The human heart samples were collected from HCM patients who had extended septal myectomy and healthy donors. Our results revealed that in nonfailing HCM heart CMs could be categorized into three subsets: high energy synthesis cluster, high cellular metabolism cluster and intermediate cluster. The expression of mitochondrial and electron transport chain (ETC) was up-regulated in larger-sized CMs from high energy synthesis cluster. Of note, we found the expression of Cytochrome c oxidase subunit 7B (Cox7B), a subunit of Complex IV in ETC was positively correlated with CMs size. Further, after assessing Cox7B expression in HCM patients, we speculated that Cox7B was compensatory up-regulated at early-stage but down-regulated at end-stage of HCM. To test the hypothesis that Cox7B might play a cardioprotective role in the early-stage of HCM, we used adeno associated virus 9 (AAV9) to mediate the expression of Cox7B in pressure overload-induced mice. Mice in vivo data supported that knockdown of Cox7B would accelerate heart failure progression and Cox7B overexpression could restore partial cardiac function in hypertrophy.

overall_design: Primary cardiocytes were isolated from human heart of HCM patients. We applied single-cell tagged reverse transcription (STRT-seq) approach and obtained 338 CM transcriptome.

first: Jingyu

first: Shi

last: Chen


title: Identification of PSMB4 and PSMD4 as novel target correlated with 1q21 amp in patients with smoldering myeloma and multiple myeloma.

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Multiple myeloma (MM) is a malignant plasma cell (PC) dyscrasia characterized by heterogeneous biological features and genetic alterations, resulting in a wide range of disease courses. Despite all the therapeutic strategies developed in the last three decades, MM is still incurable, and almost all patients will inevitably experience disease progression and eventually relapse.   Among all the genetic abnormalities, the amplification of the 1q21 region is one of the most frequent lesions occurring in malignant PCs and it has become a new prognostic factor in MM patients.  Furthermore, the incidence of gain and/or amplification of the 1q21 locus (1q21+) increases with disease progression. It can be detected in around 30-45% of patients with smoldering MM (SMM) and newly diagnosed MM (NDMM), and in around 70% of relapsed/refractory MM patients. Moreover, the impact of 1q21 on disease progression at an early stage has not been widely investigated. Few studies have suggested that the acquisition of extra 1q21 copies may play a role in disease progression. In fact, SMM patients with 1q21+ may be more likely to progress to MM than patients without 1q21+. Recent studies have demonstrated that the 1q21 copy number has a different impact on the responsiveness to MM treatments, especially proteasome inhibitors (PIs). Throughout the years, the implementation of PIs drugs as part of standard MM therapy has continued to improve the quality of life and clinical outcomes of MM patients. However, innate and acquired resistance to PIs limits their long-term clinical utility. Furthermore, additional copies of 1q21 have been associated with PI resistance and recurrence of the disease in patients with 1q21+. Several genes are known to be deregulated upon the amplification of the 1q21 locus, however, the pathogenic mechanism of how those genes drive disease progression and contribute to the poor outcome in patients with 1q21+ and their possible role as druggable targets is not fully understood. In this study, we analyzed purified CD138+ bone marrow PCs from 11 SMM and 18 NDMM patients to identify genes whose expressions are deregulated in patients with 1q21+ in correlation with the number of copies and their putative role in drug response.

overall_design: Total RNA samples from highly purified plasma cells of 29 cases (11 SMM and 18 MM). The expression profile was compared between the patients with or without Chr1 1q21 amplification and was correlated with the number of copies of 1q21 region in each patients.

first: Jessica

last: Burroughs Garcia

first: Paola

last: Storti

first: Nicolas

middle: T

last: Iannozzi

first: Valentina

last: Marchica

first: Denise

last: Toscani

last: Franceschi

first: Giannalisa

last: Todaro

first: Gabriella

last: Sammarelli

first: Laura

last: Notarfranchi

first: Matteo

last: Scita

first: Benedetta

last: Dalla Palma

first: Vincenzo

last: Raimondi

first: Oxana

last: Lungu

first: Giancarlo

last: Pruneri

first: Gaetano

last: Donofrio

first: Nicola

last: Giuliani


title: Circ-Phkb promote LPS-induced acute lung injury via the TLR4/MyD88/NF-κB /CCL2 axis

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

type: Non-coding RNA profiling by high throughput sequencing

summary: Our results showed that both circRNA and mRNA profiles are different from those of the sham group. A significant upregulation of circ-Phkb was observed in NR8383 cells and rats exposed to LPS. When circ-Phkb expression was reduced in NR8383 cells, apoptosis and inflammation were greatly reduced, and cell proliferation was increased, while overexpression of circ-Phkb have the opposite effect. In terms of mechanism, circ-Phkb suppression inhibits CCL2 expression via TLR4/MyD88/NF-κB pathway.

overall_design: In this study, we obtained differential circRNA and mRNA expression profiles and possible ceRNA networks through circRNA sequencing, mRNA sequencing and bioinformatics analysis of lung tissues from an LPS-induced ALI rat model. Furthermore, qRT-PCR assays were performed to screen for circ-Phkb in ALI rat lung tissues, alveolar macrophages and LPS-induced NR8383 cells. Induction with or without LPS was then conducted with circ-Phkb siRNA and overexpression lentivirus in NR8383. Proliferation was detected by CCK8 and Edu staining, and apoptosis was detected by TUNEL assay and cytometry. Inflammatory factors were detected using ELISA. Finally, WB was used to detect the apoptosis-related proteins and the activation of the TLR4/MyD88/NF-κB pathway.

first: Xuxia

last: Wei

first: Xiaomeng

last: Yi

first: Jianrong

last: Liu

first: Huimin


title: Mutation of PAX3 gene impairs otic vesicles via inhibiting the Wnt1/β-catenin signaling pathway in inner ear organoids of Waardenburg syndrome type I

city: Changsha

first: sijun

last: li

state: Hunan

address: 87 Xiangya Road

department: ENT

institute: Xiangya Hospital, Central South University

summary: To investigate pathogenic mechnism of hearing loss in inner ear organoids in PAX3 gene mutation of WS1 patient in vitro , we established the iPSCs line from one WS1 patient carrying a heterozygous mutation in the PAX3 gene and one healthy control. We also constructed  the iPSCs line from isogenic CRISPR/Cas9 corrected iPSCs of PAX3 gene mutation. These iPSCs were differentiated into inner ear organoid-like structure with otic vesicles-specific marker.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of four different cells at two time points in their respective iPSCs and inner ear organoids.

first: Sijun

last: Li

first: Jian

last: Song

first: Lingyun

last: Mei

first: Yong

last: Feng


title: Loss of NSD2 causes dysregulation of synaptic genes and altered H3K36 dimethylation in mice [RNA-seq]

first: Shiori

last: Kinoshita

overall_design: RNA-seq was performed in WT and Nsd2 KO E15.5 brain.


title: Developing biomarkers incorporating high throughput RNA, DNA, small RNA sequencing and protein expression in Inflammatory Bowel Disease using formalin-fixed, paraffin-embedded (FFPE) tissue samples.

city: Chapel Hill

first: Terrence

last: Furey

state: NC

address: 7320 Medical Biomolecular Research Building, CB# 7032, 111 Mason Farm Road

department: Center for Gastrointestinal Biology and Disease

institute: University of North Carolina at Chapel Hill

summary: This dataset includes RNA-seq data from ileal and colonic biopsies at time of diagnosis for treatment-naive, uncomplicated Crohn's disease (CD) patients and matched controls. This is includes 56 CD patients each for ileal and colonic tissue and for controls, 46 colonic samples and 45 ileal samples. Clinical characteristics such as development of complications, disease remission, or progression to surgery were recorded with a mean follow-up of 6 years.

overall_design:
RNA-seq data was generated from biopsies at time of diagnosis. Retrospective chart review was used to obtain clinical characteristics. Gene expression was compared and modeled between diseased and non-diseased cases and complicated and uncomplicated cases.
NOTE FROM SUBMITTER: Due to patient privacy concerns, we plan to upload raw fastq files to dbGaP.

first: Shehzad

last: Sheikh


title: Comparative gene expressions profiling of brain and muscle across ruminants

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

summary: To describe the gene expression profile of brain and muscle across ruminants, we performed gene expression analysis of brain and muscle using RNA-seq data for three ruminants.

sample_organism:
Bos taurus
Capra hircus
Ovis aries

platform_organism:
Bos taurus
Capra hircus
Ovis aries

overall_design: Comparative gene expression profiling of RNA-seq data for three ruminants.

first: Ying

last: Yu


title: Comparative epigenomic analyses of DNA methylomes and gene expression during ruminant evolution

summary: This study is the first to report a genome-wide comparative DNA methylation map in three ruminants using WGBS technology.

overall_design: Investigate DNA methylomes using WGBS and analyze DNA methylation variation during ruminant evolution


title: Transcriptome analysis of Control and FBXO38 knockdown in HCT116 and Hela cell lines

city: Shanghai

first: Nestor

last: Zhang

address: Dongchuan Road

institute: Shanghai Jiao Tong University

summary: F-box only protein 38 (FBXO38), which belongs to SKP1-CUL1-F-box protein (SCF) family, exhibits the ability to mediate Lys48-linked poly-ubiquitination and subsequent proteasome degradations of PD-1.To investigate the effect of FBXO38 knockdown on transcription in tumor, we constructed control and FBXO38 knockdown  by shRNA in Hela and HCT116 cell lines. We found that FBXO38 may interact with the immune pathway in the tumor.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq with control (shscramble) and FBXO38 knockdown (shFBXO38) HCT116 and Hela cells at two times.

first: Jianfeng

last: Shen

first: Zhe


title: Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue

city: Bethesda

first: Joshua

last: Stone

state: Maryland

address: 37 Convent Drive Room 3050

institute: NIH

summary: Rates of esophageal adenocarcinoma are rising globally, with risk factors including a range of genetic and environmental factors, including obesity, tobacco smoking, TP53 mutations, and Barrett’s esophagus, a proinflammatory condition which often occurs prior to developing adenocarcinoma. Interestingly, these factors also modulate the gastrointestinal microbiome.    To better understand the linkage between the microbiome, inflammation, and development of esophageal adenocarcinoma, we integrated 16S and RNA sequencing data. We found several microbial taxa enriched in tumor samples which were correlated with predicted immune cell infiltration from RNA-seq data, including a decrease in megakaryocyte-erythroid progenitor cells with a concomitant increase in platelets. These data suggest dysbiosis of the intratumoral microbiome promotes development and production of platelets, which reveal alterations in the immune microenvironment of esophageal adenocarcinoma and suggest novel therapeutic targets.

overall_design: 49 esophageal normal and adenocarcinoma tissues

first: Curtis

middle: C

last: Harris

middle: K

first: K

last: Greathouse


title: TBCRC 039: A phase II study of preoperative ruxolitinib with or without paclitaxel for triple-negative inflammatory breast cancer

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We conducted a randomized phase II study with nested window-of-opportunity in patients with TN-IBC. Patients were randomized to receive a 7-day run-in of ruxolitinib (RUX) alone or ruxolitinib plus paclitaxel (RUX+PAC) in a 1:2 ratio, followed by 12 weeks of neoadjuvant paclitaxel alone or in combination with ruxolitinib in a 1:2 ratio. All patients subsequently received 4 cycles of doxorubicin plus cyclophosphamide, followed by modified radical mastectomy. Patients provided tumor tissue from research biopsies performed at baseline (pre-run-in) and after the completion of run-in therapy. Tumor tissue was evaluated for phosphorylated STAT3 (pSTAT3) using immunohistochemistry (IHC) and immunofluorescence, and a subset of cases were also analyze by RNA-seq. The primary objective was to evaluate the percent of patients whose tumors were pSTAT3-positive at baseline, and which subsequently became pSTAT3-negative after run-in therapy. Secondary endpoints included pathologic complete response (pCR), residual tumor burden (RCB) and event-free survival (EFS) from the date of surgery. There were 23 patients enrolled, 11 in RUX and 12 in RUX+PAC combination. The most common adverse events were fatigue and nausea. Two patients achieved pCR and 21 completed pre-operative therapy. We detected a decrease in pSTAT3 and IL6/JAK/STAT3 signaling pathways in post-run-in biopsies of RUX-treated samples, but this did not correlate with pCR, while RUX+PAC upregulated IL6/JAK/STAT3 signaling. Both treatments decreased GZM+ T cells implying immune suppression, which might have contributed to lack of efficacy.

overall_design: We performed RNA-seq on paired pre- and post-run-in tumor biopsy samples from 5 patients who received run-in ruxolitinib (only pre-run-in sample was available for one patient) and 4 patients who received run-in ruxolitinib plus paclitaxel. The eight patients with paried specimens were subjected into downstream analysis.

first: Filipa

last: Lynce

first: Laura

last: Stevens

first: Zheqi


title: Bispecific dendritic-T Cell Engager potentiates anti-tumor immunity

status: Public on Feb 06 2024

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Immune checkpoint inhibition treatment using aPD-1 monoclonal antibodies is a promising cancer immunotherapy approach. However, its effect on tumor immunity is narrow, as most patients do not respond to the treatment or suffer from recurrence. We show that the crosstalk between conventional type I dendritic cells (cDC1) and T cells is essential for an effective aPD-1-mediated anti-tumor response. Accordingly, we developed a Bispecific DC-T Cell Engager (BiCE), a reagent that facilitates physical interactions between PD-1+ T-cells and cDC1. BiCE treatment promoted the formation of active dendritic/T cell crosstalk in the tumor and tumor-draining lymph nodes. In vivo, single cell and physical interacting cell analysis demonstrated the distinct and superior immune reprogramming of the tumors and tumor-draining lymph nodes treated with BiCE, as compared to conventional aPD-1 treatment. BiCE introduces a new concept in immunotherapy, bridging of immune cells to potentiate cell circuits and communication pathways needed for effective anti-tumor immunity.

overall_design: Dissecting the effect of BiCE on tumor immune microenvironment using single-cell RNA sequencing. Mice were inoculated with B16 cells and treated with either BiCE,aPD1/Synagis,aPD1 mAb mIg or untreated. Immune cells were harvested from tumors in early and late different time-points and underwent scRNAseq.

first: Yuval

last: Shapir-Itai

first: Oren

last: Barboy

first: Ran

last: Salomon

first: Akhiad

last: Bercovich

first: Ken

last: Xie

first: Eitan

last: Winter

first: Tamar

last: Shami

first: Ziv

last: Porat

first: Erez

last: Neta

first: Amos

last: Tanay

first: Rony

last: Dahan


title: Effect of deficiency of TAS1R3 on testicular gene expression in male mice

city: Seoul

first: Hobin

last: Seong

state: KOREA, REPUBLIC OF

address: Gwanak-ro 1, Seoul National University

country: South Korea

institute: Seoul National University

summary: Many studies have reported that taste receptor TAS1R3 is highly expressed in male reproductive tract, but the role of TAS1R3 in male reproduction and underlying molecular mechanisms remain unknown. To investigate the role of taste receptor TAS1R3 in the male reproduction, we performed RNA-sequenceing analysis on testes from C57BL/6 male mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for testes from Tas1r3+/+ and Tas1r3-/- mice.

first: Woo-Jeong

last: Shon

first: Dong-Mi

last: Shin


title: ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [scRNA-seq]

city: New Haven

first: Bomiao

last: Hu

state: CT

address: 310 Cedar Street

institute: Yale University

summary: The majority of EGFR mutant lung adenocarcinomas respond well to EGFR tyrosine kinase inhibitors (TKIs). However, most of these responses are partial with drug tolerant residual disease remaining even at the time of maximal response. This residual disease ultimately leads to relapses which eventually develop in most patients. To investigate the cellular and molecular properties of residual tumor cells in vivo, we leveraged patient-derived models of EGFR mutant lung cancer. Subcutaneous EGFR mutant PDXs were treated with the 3rd generation TKI osimertinib until maximal tumor regression. Residual tissue inevitably harbored tumor cells that were transcriptionally, but not mutationally, distinct from bulk pre-treatment tumor. Using single cell transcriptional profiling we found evidence of cells matching the profiles of drug-tolerant cells present in the pre-treatment tumor. In one of the PDXs analyzed, osimertinib treatment caused dramatic transcriptomic changes that featured upregulation of the neuroendocrine lineage transcription factor ASCL1. Mechanistically, we found that ASCL1 confers drug tolerance by initiating an epithelial-to-mesenchymal gene expression program in permissive cellular contexts. Our study reveals fundamental insights into the biology of drug tolerance, the plasticity of cells through TKI treatment and explains why specific phenotypes are only observed in certain tumors.

overall_design: To investigate the cellular heterogeneity in the PDXs and its relationship with drug tolerance, untreated and residual tumor tissues were analyzed with scRNA-seq.

first: Dejian

last: Zhao

first: Lok-Hei

last: Chan

first: Mary

last: Melnick

first: Anna

last: Wurtz

first: Qin

last: Yan

first: Katerina

last: Politi


title: ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [Cell Line RNA-seq]

overall_design: Human lung cancer cell lines stably transfected with EV or dox-inducible ASCL1 were treated with vehicle or osimertinib for different length of time. The gene expression of the resulting cells were profiled by RNA-seq.


title: Understanding differential heat tolerance of the threatened mountainous star coral Orbicella faveolata from inshore and offshore reef sites in the Florida Keys using gene network analysis

city: Miammi

first: Catalina

last: Aguilar

state: Florida

address: 4600 Rickenbacker Causeway

department: Rosenstiel School of Marine, Atmospheric & Earth Science

institute: University of Miami

summary: We subjected three inshore and four offshore genotypes of the coral Orbicella faveolata to 30, 31, 32, or 33ºC for 31 days and measured photochemical efficiency (Fv/Fm), the types and relative abundance of dinoflagellate endosymbionts, and gene expression of the host and symbiont. All inshore coral genotypes, regardless of symbiont type, were significantly more thermotolerant than offshore genotypes based on declines in Fv/Fm. The most heat-tolerant inshore genotype (In1) was dominated by Durusdinium trenchii; all other genotypes were Breviolum-dominated, suggesting local adaptation or acclimatization contributes to the heat tolerance of inshore genotypes. After 31 days of heat stress, all coral genotypes (except In2) had lost most of their Breviolum and became dominated by D. trenchii. Host genotype In1 presented unique expression patterns of genes involved in heat shock response, immunity, and protein degradation. There were few changes in the symbiont transcriptomes of inshore corals under heat stress, but significant changes in symbiont gene expression from the offshore colonies, including increases in ribosomal and photosynthetic proteins. These data show that the differential thermotolerance between inshore and offshore O. faveolata in the Florida Keys is associated with statistically significant differences in both host and symbiont gene expression that provide insights into the mechanisms underlying holobiont heat tolerance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the coral Orbicella faveolata at different temperature treatments.

first: Ian

last: Enochs

first: Kami

last: Cohen

first: Leah

last: Chomiak

first: Graham

last: Kolodziej

first: Andrew

last: Baker

first: Derek

last: Manzello


title: FABP7 drives an inflammatory response in human astrocytes

city: Madison

first: Marcelo

last: Vargas

state: WI

address: 600 Highland Avenue

institute: UW-Madison

summary: To investigate the effect of FABP7 over-expression in human iPCS-derived astrocytes.

overall_design: Differential gene expression analysis of RNA-seq data from control and FABP7 over-expressing human iPCS-derived astrocytes

first: Mariana

last: Pehar


title: Comparison of iTurbo domain and native cytokine receptor signaling by RNASeq analysis

city: South San Francisco

first: Regina

middle: Junhui

last: Lin

state: CA

address: 210 E Grand Ave

institute: Allogene Therapeutics, Inc.

summary: While cytokine support can enhance CAR T cell function, co-administering cytokines or engineering CAR T cells to secrete cytokines can result in toxicities. To mitigate these safety risks, we engineered iTurboCARTM T cells that coexpress a novel inducible Turbo (iTurbo) cytokine signaling domain. Being modular, iTurbo domains are customizable with a variety of cytokine signaling outputs, which can be multiplexed to generate combinatorial signaling outcomes. Unlike most canonical cytokine receptors that signal as heterodimers, iTurbo domains leverage a homodimeric design that minimizes viral vector cargo. Using an iTurbo domain activatable by the clinically-validated dimerizer, AP1903, the ability of homodimeric iTurbo domains to elicit signaling mimicking that of the heterodimeric parental cytokine receptor was examined. We find that iTurbo domains phenocopy and activate transcriptional programs highly similar to native cytokine receptors

overall_design: RNASeq of AP1903- or vehicle control-treated iTurboCAR T cells

middle: J

middle: R

last: Nager


title: Genome-wide comparative methylation analysis reveals the fate of germ stem cells after surrogate production in teleost

city: Vodnany

first: Rigolin

last: Nayak

state: South Bohemia

address: Zátiší 728/II

department: Faculty of Fisheries and Protection of Waters

country: Czech Republic

institute: University of South Bohemia in Ceske Budejovice

summary: Surrogate production technologies in fish by germ stem cell transplantation into the sterile recipient is becoming popular but lacks epigenetic information of the donor-derived gametes. In our study, we have thoroughly investigated and compared the genome-wide DNA methylation pattern of donor-derived gametes, and the progeny derived from them in two different types of chimera (interspecific and intraspecific) with the donor strain.

overall_design: We have performed whole genome bisulfite sequencing of genomic DNA from sperm and whole larvae from three groups

first: Roman

last: Franěk

first: Audrey

last: Laurent

first: Martin

last: Pšenička


title: Metabolic and transcriptional response to the induction of a heterologous poly-3-hydroxybutyrate pathway in Phaeodactylum tricornutum

city: Sydney, Chippendale

first: Matthias

last: Windhagauer

state: NSW

address: 745 Harris St

country: Australia

institute: University of Technology Sydney

summary: The marine diatom Phaeodactylum tricornutum is an emerging host for metabolic engineering, but little is known about how introduced pathways are integrated into the existing metabolic framework of the host and how this influences trans- and native-gene expression. In this study we used episomal vectors to express the heterologous poly-3-hydroxybutyrate (PHB) pathway in diatoms, which produces precursors for polymeric bioplastics from acetyl coenzyme-A (AcCoA). By experimentally perturbing cultivation conditions, we gained insight into the regulation of the endogenous metabolism in transgenic lines under various environmental scenarios. Biosynthesis of PHB led to distinct shifts in the metabolome of the host, and further analysis revealed a condition-dependent relationship between endogenous and transgenic metabolic pathways. Under N-limitation, which induced a significant increase in neutral lipid content, both metabolic and transcriptomic data suggest that AcCoA was preferentially shunted into the endogenous metabolism over the transgenic PHB pathway. In contrast, supply of organic carbon in the form of glycerol supported both fatty acid and PHB biosynthesis, suggesting cross-talk between cytosolic and plastidial AcCoA precursors. This is the first study to investigate the transcriptomic and metabolomic response of diatom cell lines expressing a heterologous multi-gene pathway under different environmental conditions, providing useful insights for future engineering attempts for pathways based on the precursor AcCoA.

overall_design: RNA-seq

first: Raffaela

middle: M

last: Abbriano

first: Brandon

last: Signal

first: Martina

last: Doblin


title: Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult

status: Public on Feb 05 2024

city: Stockholm

first: Stephen

last: Malin

address: Bioclinicum J8:20, Visionsgatan 4

country: Sweden

institute: Karolinska Institutet

summary: Apolipoprotein-B (APOB)-containing lipoproteins cause atherosclerosis. Whether the vasculature is initially responding site, or if atherogenic-dyslipidemia affects other organs simultaneously, is unknown. Here we show that the liver responds to a dyslipidemic insult based on inducible models of familial hypercholesterolemia and APOB tracing. An acute transition to atherogenic APOB-lipoprotein levels resulted in uptake by Kupffer cells and rapid accumulation of triglycerides and cholesterol in the liver. Bulk and single-cell RNA-seq revealed an Kupffer cell-specific transcriptional program that was not activated by a high-fat diet alone, or detected in standard liver function or pathological assays, even in the presence of fulminant atherosclerosis. Depletion of Kupffer cells altered the dynamic of plasma and liver lipid concentrations, indicating that these liver macrophages help restrain and buffer atherogenic lipoproteins, whilst simultaneously secreting atherosclerosis-modulating factors into plasma. Our results place Kupffer cells as key sentinels in organizing systemic responses to lipoproteins at the initiation of atherosclerosis.

overall_design: Liver samples from APOE cKO and D374Y mice and respective littermate controls. Biological replicates are indicated by the number at the end of each sample number. Mice were maintained on a choe diet for 10 days, or on a high fat diet for 4,8,12 or 20 weeks as indicated.


title: High throughput sequencing identifies chilling responsive genes in sweetpotato (Ipomoea batatas Lam.) during storage

city: Xuzhou

first: Jiahao

last: Zhu

address: Shanghai Road 101

institute: Jiangsu Normal University

summary: Sweetpotato (Ipomoea batatas L.) is a globally important economic food crop. It belongs to Convolvulaceae family and origins in the tropics; however, sweetpotato is sensitive to cold stress during storage. In this study, we performed transcriptome sequencing to investigate the sweetpotato response to chilling stress during storage. A total of 110,110 unigenes were generated via high-throughput sequencing. Differentially expressed genes (DEGs) analysis showed that 18,681 genes were up-regulated and 21,983 genes were down-regulated in low temperature condition. Many DEGs were related to the cell membrane system, antioxidant enzymes, carbohydrate metabolism, and hormone metabolism, which are potentially associated with sweetpotato resistance to low temperature. The existence of DEGs suggests a molecular basis for the biochemical and physiological consequences of sweetpotato in low temperature storage conditions. Our analysis will provide a new target for enhancement of sweetpotato cold stress tolerance in postharvest storage through genetic manipulation.

overall_design:
Sweetpotato cultivar Xushu 18 (I. batatas L. cv. Xushu 18) was kindly provided by the Chinese Academy of Agricultural Science.The sweetpotato were randomly divided into two groups, which were stored at 4 °C (LTC) or 14 °C (ATC) and with a relative humidity of 85%, respectively. Each group had the same number of samples. Sweetpotato not stored at the abovementioned specific conditions were considered members of the not stored condition group (CK). Sample tissues were collected every other week while in storage, immediately frozen in liquid nitrogen, and then stored at -80 °C prior to analysis. To minimize variations, seven sweetpotato tuberous roots were pooled into one biological replicate, and three biological replicates were assessed at each time point.
To screen genes associated with root tuber response to low temperature, transcriptome sequencing of sweetpotato roots in different temperature (CK, ATC and LTC) was performed.


title: A highly reproducible and efficient method for retinal organoid differentiation from human pluripotent stem cells

city: Indianapolis

first: Chi

last: Zhang

state: IN

address: 410 W. 10th Street, Suite 5000

institute: Indiana University School of Medicine

summary: Human pluripotent stem cell (hPSC)-derived retinal organoids are three-dimensional cellular aggregates that differentiate and self-organize to closely mimic the spatial and temporal patterning of the developing human retina. Retinal organoid models serve as reliable tools for studying human retinogenesis, yet limitations in the efficiency and reproducibility of current retinal organoid differentiation protocols have limited the use of these models for more high throughput applications such as disease modelling and drug screening. To address these shortcomings, the current study aimed to standardize prior differentiation protocols to yield a highly reproducible and efficient method for generating retinal organoids. Results demonstrated that through regulation of organoid size and shape using quick reaggregation methods, retinal organoids were highly reproducible compared to more traditional methods. Additionally, the timed activation of BMP signaling within developing cells generated pure populations of retinal organoids at 100% efficiency from multiple widely used cell lines, with the default forebrain fate resulting from the inhibition of BMP signaling. Furthermore, given the ability to direct retinal or forebrain fates at complete purity, mRNA-seq analyses were then utilized to identify some of the earliest transcriptional changes that occur during the specification of these two lineages from a common progenitor. These improved methods also yielded retinal organoids with expedited differentiation timelines when compared to traditional methods. Taken together, the results of this study demonstrates the development of a novel, highly reproducible and minimally variable method for generating retinal organoids suitable for analyzing the earliest stages of human retinal/forebrain cell fate specification.

overall_design: To assess the transcriptional profile of cells at the earliest stages of retinal fate specification, hPSC aggregates were differentiated as described above for the first 6 days of the protocol, and then split into 3 conditions: Day 6 baseline, Day 8 BMP4 (treated from days 6-8) and Day 8 LDN treated (treated from days 6-8).

first: Jason

last: Meyer


title: Comprehensive analysis of differentially expressed mRNA, circRNA and miRNA and their ceRNA networks in testis of cattle-yak, yak and cattle

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. The DEGs of cattle-yak, cattle and yak were mainly enriched in biological processes such as spermatogenesis, male gamete generation and sexual reproduction. At the same time, GO and KEGG analysis suggested that DECs host genes and DEMs source genes were also involved in the regulation of spermatogenesis. The construction of potential ceRNA networks found that some differentially expressed ncRNAs may be involved in the regulation of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, miR-15b, etc., as well as unreported miR-6123, miR-1306 and some miRNA and circRNA interaction pairs. This study provides a reference for further study on the mechanism of male sterility in cattle-yak.

sample_organism:
Bos taurus
Bos grunniens
Bos grunniens x Bos taurus

overall_design: Testes of adult cattle, yaks and cattle-yaks were sequenced by whole-transcription

first: Mengli

last: Cao

first: Shaoke

last: Guo

first: Jie

last: Pei

first: Xian


title: Construction of a dorsal-ventral patterned neural tube organoid from pluripotent stem cells.

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary:
Purpose: Characterization of cell types in wild-type and TCTN2 KO human neural tube organoids (hNTOs).
Methods:  Wild-type and TCTN2 KO hNTOs were harvested at day11. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 (10x Genomics, Cat# PN-1000121) according to the manufacturer’s protocol for 10000 cells recovery.
Results: 13 neural progenitor cells were detected in wild-type hNTOs, and TCTN2 deficiency led to reduction of ventral progenitors cells.
Conclusions: A well-organized nueral tube organoid was constructed by applying BMP and SHH morphogen gradients.

overall_design:
Wild-type and TCTN2 KO hNTOs  were harvested at day 11 for scRNA-seq.
TCTN2_vko refers to the hNTO in which TCTN2 was knocked out specifically in ventral aggregates. On the other hand, TCTN2_dko represents the hNTOs where TCTN2 was knocked out in both ventral and intermediate aggregates.

last: Cheng

last: Luo

first: Cong

last: Liu


title: Single-cell sequencing of testis from mice on a high-fat diet

city: Changchun

first: guitian

last: he

institute: jilin university

summary: the extent of testicular impairment caused by HFD was assessed using the scRNA-seq technique.

overall_design: Assessment of transcriptomic data for various cell types in the testis of normal and high-fat diet mice

last: Wang


title: Dental Lighting Environment Induces Disruption of the Blood-Retinal Barrier

city: Chengdu

first: Shuhuai

last: Meng

address: Huaxi

institute: Huaxi

summary: Excessive lighting is integral to dentists' daily routines but can impair their vision, affecting personal and professional performance. Most studies focus on acute photodamage, neglecting chronic photoinjury from dental lighting and its impact on the blood-retinal barrier homeostasis. An epidemiological survey involving 14,523 individuals reveals dentists have a higher prevalence of vision-related issues compared to other occupations. Subsequently, chronic photodamage models in rats were created to accurately simulate dental working conditions. Using systematic imaging and gene analysis, including OCT, tissue clearing technology and RNA-sequencing, dental lighting was found to disrupted both inner and outer blood-retinal barriers, reduced retinal blood vessels, and promoted perivascular macrophage recruitment. Moreover, the activation of inflammatory-related pathways such as NF-κB signalling resulted in the damage of vision-related functional structures in the retina. Notably, among the three commonly used dental lighting sources, low-intensity halogen light possessed a minimal impact on the retina, while blue and white LEDs have remarkable negative effects on blood-retinal barrier homeostasis. This study explored the potential mechanism of dental lighting environment inducing the disruption of blood-retinal barrier homeostasis, and provided essential guidance for dental professionals in selecting light sources, which is conducive to reducing the risk of occupational ocular diseases among dentists.

overall_design: After 6 months of exposure to light, extract rat retina tissues from different light groups, including Control, Halogen 200, Halogen 1000, Blue 200, Blue 1000, White 200, White 1000, a total of seven groups, each with three samples, for RNA transcriptome sequencing

first: Haiyang

last: Sun

first: Qianbing

last: Wan

first: Junyu

last: Chen


title: The ALOG domain defines a new family of plant-specific transcription factors acting during Arabidopsis flower development

city: Grenoble

first: Jérémy

last: LUCAS

address: 17 avenue des Martyrs

country: France

institute: CNRS

summary: The ALOGs (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1) are Transcription Factors (TFs) from an evolutionarily conserved plant-specific family shown to play critical roles in meristem identity, inflorescence architecture and organ boundaries in diverse species from mosses to higher flowering plants. However, the DNA binding-specificity and molecular determinants of protein-DNA interactions of this family were uncharacterized. Using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato and rice. In order to determine the amino acids responsible for DNA-binding specificity, we solved the 2.1Å structure of the ALOG DNA binding domain in complex with its cognate DNA. The ALOG DBD is an all-alpha helical domain with a structural zinc ribbon insertion and an N-terminal disordered NLS. The NLS sequence forms an integral part of the DNA binding domain and contributes to direct base read-out. To define the function of a group of redundant ALOG proteins in the model plant Arabidopsis thaliana, we generated a series of alog mutants and uncovered their participation in a gene regulatory network involving the other floral regulators LEAFY, BLADE-ON-PETIOLE and PUCHI, all active in defining boundary regions between reproductive meristems and repressing bracts development. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in defining organ boundaries in Arabidopsis.

overall_design: ampDAP-seq experiments with tagged ALOG proteins were done on 2-weeks old Arabidopsis thaliana seedlings. ALOG tagged proteins were first mixed together with DNA prior to affinity purification. Three replicates were done and only consensus peaks in all three were retained.

first: Philippe

last: Rieu

last: Lucas

first: François

last: Parcy

first: Chloé

last: Zubieta


title: Morc2a variants cause hydroxyl radical-mediated neuropathy and are rescued by GHKL ATPase gene therapy

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

summary: Mutations in the Microrchidia CW-Type Zinc Finger 2 (MORC2) GHKL ATPase module cause Charcot Marie Tooth type 2Z or a broad range of neuropathy, but etiology and therapeutic strategy are not fully defined. Previously, we reported that the Morc2a p.S87L mouse model led to neuropathy and muscular dysfunction through DNA damage accumulation. This study revealed that Morc2a p.S87L caused a protein synthesis defect, resulting in the loss of function of Morc2a and weakening its function of maintaining DNA integrity and hydroxyl radical scavenging in the GHKL ATPase domain. Morc2a GHKL ATPase domain was considered a therapeutic target based on its function of simultaneously complementing hydroxyl radical scavenging and ATPase activity. Adeno-associated virus PHP.eB serotype that has high central nervous system transduction efficiency was applied to express Morc2a or Morc2a GHKL ATPase domain protein in vivo. AAV gene therapy improved neuropathy and muscular dysfunction with single-time treatment. The loss of function characteristics due to protein synthesis defect in Morc2a p.S87L was also observed in human MORC2 p.S87L or p.R252W variant, suggesting a relevance between mouse and human pathogenesis. Here, we demonstrate Morc2a p.S87L variant causes hydroxyl radical-mediated neuropathy and could be rescued through AAV-based gene therapy.

overall_design: RNA sequencing of spinal cord (SC) and mouse fetal fibroblast (MEF) of wild-type (WT) or Morc2a p.S87L heterozygote (S87L) mice (n=3 for WT-SC, S87L-SC, and WT-MEF; n=2 for S87L-MEF)

first: Su

last: Yeom

first: Daehee

last: Hwang


title: The investigation of genes among normal tenocytes and inflammtory tenocytes

city: shanghai

first: zengguang

last: wang

address: No. 639 Zhizaoju Road, Shanghai 200001

institute: Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Tendinopathy is a common disease of the musculoskeletal system, however, the mechanism of tendinopathy has not yet been elucidated, and there are no clear conclusions about the changes in gene expression within tendinopathy. In order to better investigate the mechanisms inherent to the development of tendinopathy, we performed RNA sequencing on normal tendon cells and inflammatory tendon cells

overall_design: In the present study,  tendon cells were used for the assay, no stimulation was added to the control tendon cells(50ng/ml), and IL-1β was added to the experimental cells, and the stimulation duration was 24 hours.

first: zhenglin

last: dong

first: yaokai

last: gan


title: Gene expression analysis of murine wt and Nbeal2 -/- bone marrow derived mast cells (BMMCs) w/o IL-33 treatment

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

summary: The Neurobeachin-like 2 (Nbeal2) protein is a BEACH (beige and chediak-higashi) family member. Loss of function mutations of the human NBEAL2 gene result in development of the gray platelet syndrome (GPS) a bleeding disorder characterized by macrothrombocytopenia, splenomegaly, and paucity of Î±-granules in megakaryocytes, platelets, mast cells (MCs), neutrophils and NK cells. We found that Nbeal2 deficiency in MCs leads to an enhanced resistance to growth factor deprivation, dysregulated distribution of c-Kit and of the multidrug resistant protein-1 (ABCB1), as well as to a pro-inflammatory MC-phenotype. These characteristics are caused by a defective protein degradation machinery resulting in accumulation of RSK and ribosomal proteins (RPS). These data demonstrate that Nbeal2 prevents oncogenic transformation by controlling protein homeostasis (proteostasis) in MCs.

overall_design: 16 samples in four groups: Nbeal2 -/- w/o IL-33: 4 samples; Nbeal2 -/- with IL-33: 4 samples; wildtype w/o IL-33: 4 samples; wildtype with IL-33: 4 samples.

first: Sebastian

last: Drube

first: Nico

last: Andreas


title: ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts [Cell Line ATAC-seq]

first: Bomiao

last: Hu

summary: The majority of EGFR mutant lung adenocarcinomas respond well to EGFR tyrosine kinase inhibitors (TKIs). However, most of these responses are partial with drug tolerant residual disease remaining even at the time of maximal response. This residual disease ultimately leads to relapses which eventually develop in most patients. To investigate the cellular and molecular properties of residual tumor cells in vivo, we leveraged patient-derived models of EGFR mutant lung cancer. Subcutaneous EGFR mutant PDXs were treated with the 3rd generation TKI osimertinib until maximal tumor regression. Residual tissue inevitably harbored tumor cells that were transcriptionally, but not mutationally, distinct from bulk pre-treatment tumor. Using single cell transcriptional profiling we found evidence of cells matching the profiles of drug-tolerant cells present in the pre-treatment tumor. In one of the PDXs analyzed, osimertinib treatment caused dramatic transcriptomic changes that featured upregulation of the neuroendocrine lineage transcription factor ASCL1. Mechanistically, we found that ASCL1 confers drug tolerance by initiating an epithelial-to-mesenchymal gene expression program in permissive cellular contexts. Our study reveals fundamental insights into the biology of drug tolerance, the plasticity of cells through TKI treatment and explains why specific phenotypes are only observed in certain tumors.

overall_design: Human lung cancer cell lines stably transfected with EV or dox-inducible ASCL1 were treated with vehicle or osimertinib for different length of time. The chromatin accessibility of the resulting cells were profiled by ATAC-seq.

first: Fernando

last: de Miguel

first: Katerina

last: Politi


title: Spatiotemporal Patterns of Gene Expression Around Implanted Silicon Electrode Arrays

city: EAST LANSING

first: Erin

last: Purcell

state: MI

address: 775 WOODLOT DRIVE

department: Biomedical Engineering

institute: MICHIGAN STATE UNIVERSITY

summary: Objective. Intracortical brain interfaces are an ever evolving technology with growing potential for clinical and research applications. The chronic tissue response to these devices traditionally has been characterized by glial scarring, inflammation, oxidative stress, neuronal loss, and blood-brain barrier disruptions. The full complexity of the tissue response to implanted devices is still under investigation. Approach. In this study, we have utilized RNA-sequencing to identify the spatiotemporal gene expression patterns in interfacial (within 100 µm) and distal (500 µm from implant) brain tissue around implanted silicon microelectrode arrays. Naïve, unimplanted tissue served as a control. Main results. The data revealed significant overall differential expression (DE) in contrasts comparing interfacial tissue vs naïve (157 DE genes), interfacial vs distal (94 DE genes), and distal vs naïve tissues (21 DE genes). Our results captured previously characterized mechanisms of the foreign body response, such as astroglial encapsulation, as well as novel mechanisms which have not yet been characterized in the context of indwelling neurotechnologies. In particular, we have observed perturbations in multiple neuron-associated genes which potentially impact the intrinsic function and structure of neurons at the device interface. In addition to neuron-associated genes, the results presented in this study identified significant DE in genes which are associated with oligodendrocyte, microglia, and astrocyte involvement in the chronic tissue response. Significance. The results of this study increase the fundamental understanding of the complexity of tissue response in the brain and provide an expanded toolkit for future investigation into the bio-integration of implanted electronics with tissues in the central nervous system.

overall_design: Comparative gene expression profiling of interfacial tissue (within100um of implant), distal tissue (500um from implant), and naïve tissue (no-implant) at 24hours, 1-week, and 6-weeks post-implantation of electrode.

first: Cort

middle: H

last: Thompson

first: Akash

last: Saxena

first: Nicholas

last: Heelan

first: Joseph

last: Salatino


title: G-quadruplex DNA structure is a positive regulator of MYC transcription

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

summary: DNA structure can regulate genome function. Four-stranded DNA G-quadruplex (G4) structures have been implicated in transcriptional regulation; however, previous studies have not directly addressed the role of an individual G4 within its endogenous cellular context. Using CRISPR to genetically abrogate endogenous G4 structure folding, we directly interrogate the G4 found within the upstream regulatory region of the critical human MYC oncogene. G4 loss leads to suppression of MYC transcription from the P1 promoter that is mediated by the deposition of a de novo nucleosome alongside alterations in RNA polymerase recruitment. We also show that replacement of the endogenous MYC G4 with a different G4 structure from the KRAS oncogene restores G4 folding and MYC transcription. Moreover, we demonstrate that the MYC G4 structure itself, rather than its sequence, recruits transcription factors and histone modifiers. Overall, our work establishes that G4 structures are important features of transcriptional regulation that coordinate recruitment of key chromatin proteins and the transcriptional machinery through interactions with DNA secondary structure, rather than primary sequence.

overall_design: Expression profiling by high throughput sequencing. Genome binding/occupancy profiling by high throughput sequencing

first: Isabel

last: Esain-Garcia

first: Angie

last: Kirchner

first: Rafael

middle: D

last: Araujo Tavares

first: Somdutta

last: Dhir

first: Angela

last: Simeone

first: Zutao

last: Yu

first: Sarah

last: Madden

first: Regina

last: Hermann

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult (scRNA-Seq)

first: Stephen

last: Malin

overall_design: Liver sample from  D374YmCherry-APOB mice. Mice were maintained on a chow diet for 10 days after tamoxifen.


title: Reactive astrocytes promote tumor progression via up-regulating tumor PCDH1 expression in lung cancer brain metastasis

city: Dalian

first: Mengyi

last: Tang

address: 467 Zhongshan Road

institute: the Second Affiliated Hospital of Dalian Medical University

summary: To investigate the function of PCDH1 in the lung cancer brain metastasis cells, we established PC9-BrM3 cells in which PCDH1 has been knocked down by shRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  PC9-BrM3 cells with or without PCDH1 knockdown.

first: Kun

last: Liang

first: Wenwen

last: Liu

first: QI

last: Wang


title: Neural activity recorded in breast tumors originates from the sympathetic nervous

city: CLEVELAND

first: Haidong

last: Huang

state: OH

address: 9500 EUCLID AVE RK-15

department: Cancer Biology

institute: Cleveland Clinic Foundation

summary: The autonomic nervous system (ANS) is a regulator of major pathological events in the tumor microenvironment (TME) of solid carcinomas where the branches of ANS have antagonistic effects on tumor growth and metastasis. Neural activity recorded from breast tumors may be associated with autonomic system function. To test this hypothesis, we performed in vivo chronic electrical recordings from murine mammary tumors of triple negative breast cancers (TNBC) following complete sub-diaphragmatic vagotomy and chemical sympathectomy. In addition to TNBC mammary tumors, we also obtained daily electrical recordings from mammary tumors overexpressing human epidermal growth factor receptor-2 (HER2) following chemical sympathectomy. Our results show that tumoral neural activity is partially blocked in vagotomized animals while it is completely absent in the sympathectomized subjects. These studies indicate that neural activity in TNBC and HER2+ tumors is predominantly generated by peripheral nor-adrenergic sympathetic nerves and provide evidence of a strong active link between the brain and tumor through the autonomic nervous system. The results implicate a new and as yet unexplored mechanism to investigate the potential role of the sympathetic nervous system in the regulation of tumor growth and metastasis.

overall_design: To analyze the transcriptomic change in the onset of neural activity, we collected tumors before and at the day of the first peak to extract RNAs.

first: Jay

last: Shiralkar


title: Transcription bodies regulate gene expression by sequestering CDK9

city: Lausanne

first: Martino

last: Ugolini

state: Vaud

address: Genopode

department: CIG

institute: UNIL

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

overall_design: Refer to individual Series


title: Detect accessible chromatin using ATAC sequencing in the Kasumi-1 cell line transfected with PHF19 shRNA or scrambled control shRNA

city: Beijing

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

summary: To investigate the function of PHF19 in the regulation of chromatin accessibility in t(8;21) AML, we established Kasumi-1 cell line in which PHF19 gene has been knocked down by shRNA. We then performed chromatin accessibility analysis using data obtained from ATAC-seq of the PHF19 knockdown cells and the scrambled control cells.

overall_design: Stable silencing of the PHF19 gene in Kasumi-1 cells was achieved through a lentiviral vector-based system for RNAi (GV493/hU6-MCS-CBh-gcGFP-IRES-puromycin) constructed by GeneChem Technologies (China). Transfection of lentivirus was conducted according to the manufacturer's instruction. Kasumi-1 cells were seeded into 6-well plates overnight before transfection and the medium was changed approximately 12 to 16 hours after transfection. Forty-eight hours after shRNA transfection, cells were selected with puromycin (2 microgram per milliliter) for at least 24 hours before further investigations.

first: Xiao-Ning