title: NG2/CSPG4 regulates the transcriptional profile of mandibular fibrochondrocytes during serum starvation [RNAseq-primary cells]

status: Public on Nov 30 2023

city: Chicago

first: David

middle: A

last: Reed

state: IL

address: 801 South Paulina Street

department: Department of Oral Biology

country: USA

institute: University of Illinois at Chicago

type: Expression profiling by high throughput sequencing

summary: Changes in the mechanical homeostasis of the temporomandibular joint (TMJ) can lead to the initiation and progression of degenerative arthropathies such as osteoarthritis (OA). Cells sense and engage with their mechanical microenvironment through interactions with the extracellular matrix. In the mandibular condylar cartilage, the pericellular microenvironment is composed of type VI collagen. NG2/CSPG4 is a transmembrane proteoglycan that binds with type VI collagen, and has been implicated in the cell stress response. The objective of this study is to define the role of NG2/CSPG4 in the cell stress response during serum starvation. To evaluate the role of the NG2/CSPG4, primary mandibular fibrochondrocytes from c57 BL/6 J and NG2/CSPG4 knockout mice (mixed sex) were cultured in normal and serum starvation conditions. To evaluate the role of the NG2/CSPG4 ectodomain, primary mandibular fibrochondrocytes were immortalized using hTERT. CRSIPR/Cas9 was used to truncate the NG2/CSPG4 ectodomain by targeting the type VI collagen binding region. Normal culture conditions were AMEM growth media supplemented with 10% FBS, penicillin, L-Glut, and plasmocin.  Serum starvation conditions were Optimem media with no FBS, supplemented with penicillin, L-Glut, and plasmocin. Serum starvation was induced for 24 hours. RNA from the cells was isolated using the RNeasy kit (Qiagen). poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system. Sequencing was done by LC Sciences. These data illustrate that in serum starvation conditions, NG2/CSPG4 knockout mandibular fibrochondrocytes and targeted truncation of the NG2/CSPG4 ectodomain alters the transcriptional profile of the cell, promoting biological processes associated with cell stress, migration, and ossiciation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data comparing c57/BL6J and NG2/CSPG4 knockout primary mandibular fibrochondrocytes collected from 10-14 day old pups in normal and serum starvation conditions and immortalized primary mandibular fibrochondrocytes with and without genetic truncation of the ectodomain in normal and serum starvation conditions.


title: Balance macrophage polarization via cell synthesis of apoptotic bodies in hydrogel microspheres

city: Shanghai

first: Jiayi

last: Mao

address: Zhi Zao Ju road

country: China

institute: shanghai ninth people's hospital

summary: Maintaining the homeostasis of immune ecological niches such as macrophages is essential for skin regeneration. In this study, apoptotic bodies (ABs) with intact bioactive substances of ADSC were constructed by biosynthesis. Further, injectable apoptotic bodies-GelMA microspheres (ABs@GMS) were constructed by microfluidics to maintain the homeostasis of the immune ecological niche in trauma, and inhibit the secretion of argininosuccinate synthetase 1 (ASS1) by ABs-induced downregulated JAK/STAT1 signaling pathway. Consequently, the macrophages’ polarization and inflammatory response were balanced in the wound with promoted angiogenesis. This ABs-functionalized microsphere slowly released biosynthetic apoptotic vesicles that expressed C1q, C3b and other surface "eat me" signals. These vesicles can be directly recognized, phagocytosed and degraded by macrophages, and allow scavenger cells to give meaning to cell death. In vitro, ABs@GMS balanced the JAK/STAT signaling pathway in a form of positive communication from dead to living cells via apoptotic vesicles. In vivo, ABs@GMS balanced the polarization of macrophages and increased the expression of α-smooth muscle actin. In conclusion, ABs synthesized by ADSC can balance traumatic immune disorders and restore homeostasis of the wound immune microenvironment, which would be a highly promising material for macrophage-mediated wound repair.

overall_design: RNA-seq of THP-1 cells stimulated with PMA and treated with LPS or ABS.

first: Shutong

last: Qian

first: Qiuyu

last: Zhao

first: Binfan

first: Zhimo

last: Liu

first: Bolun

last: Lu

first: Fei

last: Wang

first: Yawei

last: Du

first: Liucheng

last: Zhang

first: Xiyuan

first: Yuguang

first: Wenguo

last: Cui

first: Xiaoming

last: Sun


title: Neu5Gc intake increases the expression of colorectal cancer-related genes in the APCMin+ mouse

city: Chengdu

first: yuan

last: teng

address: huimin road 211

institute: Sichuan Agricultural University

summary: Clinical cohort data suggest that high consumption of red meat containing N-glycolylneuraminic acid (Neu5Gc) may increase colorectal prevalence, therefore, we investigated the effect of high Neu5Gc intake on colon cancer using the APCMin/+ mouse model . Ten APCMin/+ male mice were divided into two groups and fed normal (control group: 0.0507 mg per mouse per day) and high concentrations (treatment group: 1.014 mg per mouse per day) of Neu5Gc to mimic Normal and excessive consumption of red meat in humans, respectively. After two weeks of feeding, colorectal and liver were collected for histopathological diagnosis and transcriptome analysis.

overall_design: Eight-week-old male APCMin/+ mice were divided into two groups, 6 mice in the control group and 4 mice in the treatment group. The control group drank low-concentration Neu5Gc water (0.0127mg/ml), and the treatment group drank high-concentration Neu5Gc water (0.2535mg/ml) for 14 consecutive days. Intestinal and liver tissues were collected after sacrifice, followed by histopathological diagnosis, intestinal and liver transcriptome analysis.

first: Teng

last: Yuan

first: Anjing


title: Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation (Dianthus caryophyllus L.)

city: Wu han

first: feng

last: shan

address: Shizishan Street

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, involvement of histone methylation in regulating petal senescence is still largely unknown. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during the ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). The H3K4me3 levels are positively associated with the expression of transcription factor DcWRKY75, ethylene biosynthetic genes DcACS1 and DcACO1, and senescence associated genes (SAGs) DcSAG12 and DcSAG29. Further, we identified that carnation DcATX1 (ARABIDOPSIS HOMOLOG OF TRITHORAX1) encodes a histone lysine methyltransferase which can methylate H3K4. Knockdown of DcATX1 delays ethylene induced petal senescence in carnation, which is associated with the downregulated expression of DcWRKY75, DcACO1 and DcSAG12. While overexpression of DcATX1 exhibits the opposite effects. DcATX1 promotes the transcription of DcWRKY75, DcACO1 and DcSAG12 by targeting to their promoters to elevate the H3K4me3 levels. Overall, our results demonstrate that DcATX1 is a H3K4 methyltransferase that promotes the expression of DcWRKY75, DcACO1, DcSAG12 and maybe other downstream target genes by regulating H3K4me3 levels, thereby accelerating ethylene induced petal senescence in carnation. This study further indicates that epigenetic regulation is important for plant senescence process.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K4me3 in carnation petals.

first: Shan

last: Feng

first: Xinyu

last: Jiang

first: Ruiming

first: Hualiang

last: Tan

first: Linlin

last: Zhong

first: Yunjiang

last: Cheng

first: Manzhu

last: Bao

first: Hong

last: Qiao

first: Fan


title: The effect of WB436B or siRNA towards STAT3 on the whole-transcriptome analysis with total RNA sequencing (RNA-Seq) in BxPC3 cells

first: Huang

last: Chen

address: Road of Dongchuan  500

institute: East China Normal University

summary: To examine the effect of WB436B or siRNA towards STAT3 on the whole-transcriptome analysis with total RNA sequencing (RNA-Seq) in BxPC3 cells.

overall_design: RNA-seq results of BxPC3-Vehicle, BxPC3-siRNASTAT3, and BxPC3-WB436B-0.1μM.

first: Chen

last: Huang

first: Yizheng

last: Fang


title: Clostridioides difficile: R20291_pMTL84151 transconjugant (C) vs.  R20291_pMTL84151-03890 (T1)

city: Tainan

first: JunJia

last: Gong

address: University Rd, No. 1

department: Institute of Basic Medical Sciences

country: Taiwan

institute: National Cheng Kung University

summary: Gene expression level of Clostridioides difficile (C. difficile) strain R20291 comparing control C. difficile carring pMTL84151 as vector plasmid with C. difficile conjugated with a pMTL84151-03890 gene. Goal was to determine the effects of 03890 gene conjugation on C. difficile strain R20291 gene expression.

overall_design: Two-condition experiment, C. difficile strain R20291_V vs. C. difficile strain R20291_T1. Biological replicates: 3 conjugated control replicates, 3 conjugated test-1 replicates.

first: Jenn-Wei

first: Si-Xuan

last: Xie


title: Improved Cardiac Function in Post-Ischemic Rats Using an Optimized Cardiac Reprogramming Cocktail Delivered in a Single Novel AAV

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

summary:
BACKGROUND: Cardiac reprogramming is a technique to directly convert non-myocytes into myocardial cells using genes and/or small molecules. This intervention provides functional benefit to the rodent heart when delivered at the time of myocardial infarction or activated transgenically up to 4 weeks after myocardial infarction. Yet, several hurdles have prevented the advancement of cardiac reprogramming for clinical use.
METHODS: Through a combination of screening and rational design, we identified a cardiac reprogramming cocktail that can be encoded in a single AAV. We also created a novel AAV capsid that can transduce cardiac fibroblasts more efficiently than available parental serotypes by mutating post-translationally modified capsid residues. Since a constitutive promoter was needed to drive high expression of these cell-fate altering reprogramming factors, we included binding sites to a cardiomyocyte-restricted microRNA within the 3’ UTR of the expression cassette that limits expression to non-myocytes. After optimizing this expression cassette to reprogram human cardiac fibroblasts into induced cardiomyocyte-like cells in vitro, we also tested the ability of this capsid / cassette combination to confer functional benefit in acute mouse myocardial infarction and chronic rat myocardial infarction models.
RESULTS: We demonstrated sustained, dose-dependent improvement in cardiac function when treating a rat model two weeks after MI, showing that cardiac reprogramming, when delivered in a single, clinically relevant AAV vector, can support functional improvement in the post-remodeled heart. This benefit was not observed with GFP or a hepatocyte reprogramming cocktail and was achieved even in the presence of immunosuppression, supporting myocyte formation as the underlying mechanism.
CONCLUSION: Collectively, these results advance the application of cardiac reprogramming gene therapy as a viable therapeutic approach to treat chronic heart failure resulting from ischemic injury.

overall_design: RNA sequencing on 3 control hiPSC-CM samples, one mixture of cFB and CM (9/1 ratio), as well as 15 other human cFB cell lines treated with either GFP cassette, MyA cassette, or MyD3 cassette

first: Huanyu

last: Zhou

first: Jin

last: Yang

first: Chetan

last: Srinath

first: Aliya

last: Zeng

first: Iris

last: Wu

first: Elena

middle: C

last: Leon

first: Tawny

last: Neal Qureshi

first: Christopher

last: Reid

first: Emily

middle: R

last: Nettesheim

first: Emma

last: Xu

first: Zoe

last: Duclos

first: Tamer

middle: M

last: Mohamed

first: Anthony

last: Fejes

first: Jun

last: Liu

first: Samantha

last: Jones

first: Charles

last: Feathers

first: Tae

middle: W

last: Chung

first: Frank

last: Jing

first: William

middle: S

last: Prince

first: JianMin

last: Lin

first: Pengzhi

last: Yu

first: Deepak

last: Srivastava

first: Timothy

last: Hoey

first: Kathryn

middle: N

last: Ivey

first: Laura

last: Lombardi


title: Med12 ablation promotes anti-tumor function by enhancing tumor intrinsic immunogenicity in Pancreatic ductal adenocarcinoma [ATAC-seq]

first: JIng

last: Xue

address: No.1630 dongfang road, pudong new district, Shanghai

institute: Renji Hospital, School of Medicine,Shanghai Jiaotong University

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with limited treatment options, including checkpoint blockade (ICB) immunotherapy. Epigenetic dysregulation is a defining feature of tumorigenesis and contributes to immune escape. However, little is known about whether and how epigenetic regulators evade immune surveillance in PDAC. Here, we identified Med12, a subunit of RNA polymerase II, as a mediator of immune escape in PDAC with in vivo CRISPR-Cas9 Screening. In murine PDAC models, Med12 loss effectively promoted infiltration and cytotoxicity of CD8+ T cells and NK cells，thereby sensitized to ICB and led to a marked extension of survival. Mechanistically, Med12 loss derepressed endogenous retroelements via impairing H3K9me3 and increasing H3K27Ac modification, triggering cytosolic RNA-sensing and DNA-sensing pathways as well as the type I interferon pathways. Moreover, Med12 depletion induced H3K27Ac gain in the Med12-binding domains, further enhanced the interferon-related genes transcription. Our results demonstrated the role of Med12 in suppressing tumor-intrinsic immunogenicity, thus provided a potential target or marker for immunotherapy of PDAC.

overall_design: To investigate the function of Med12 regulating tumor instrinsic immunogenicity, wo conducted Med12 KO and WT cell lines. Then, we performed ATAC-seq sequencing to combine with RNAseq to  analyse how Med12 regulates retroelements inhibition.

first: Yingying

last: Tang

first: Jing


title: Multi-tissue expression profiling of TALLYHO/Jng and C57BL/6J Mice under high-fat and chow diets

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: In order to identify gene expression patterns that vary with diet, genetics, and their interaction, we performed expression profiling by RNA-Seq across four different tissues (liver, gonadal fat, soleus muscle, and pancreas) of TALLYHO/Jng (TH) and C57BL/6J (B6) male (M) and female (F) mice, fed either a chow or high fat (HF) diet at 5 weeks and 20 weeks of age.

overall_design: Expression profiling by RNA-Seq was performed on fat, liver, pancreas, and soleus muscle samples from male (M) and female (F) TALLYHO (TH) and C57BL/6J (B6) mice fed either a chow or high-fat (HF) diet. Samples were taken from mice aged 5 weeks and 20 weeks.

last: Fan

first: Kristiana

last: Sklioutovskaya-Lopez

first: Don

last: Primerano

first: Jung

middle: H

last: Kim


title: Zebrafish fbln1 mutant (ulg075) larvae at 10dpf versus AB wt

city: Liège

first: Marc

last: Muller

address: B34 Sart Tilman

department: Life Sciences

country: Belgium

institute: Université de Liège

summary: We generated a 16 nucleotide deletion mutant in the zebrafish fbln1 gene and we compared the whole larvae transcriptome to wt siblings in 10dpf larvae.

overall_design: fbln1+/- parents were crossed, wt and fbln1-/- homozygous mutants were selected in three independant batches (about 20 individuals/sample) for extracting RNA and performing RNA-Seq. Each mutant batch was compared to its wt siblings.

first: Ratis

last: Raman


title: YTHDF2 mediates the action of BDNF stimulating proliferation of porcine follicle granulosa cells

city: Changchun

first: kening

last: liu

state: jilin

address: Xian road

institute: jilin university

summary: Total RNA of porcine follicle granulosa cells from different groups was extracted and RNA purity and quality control were performed.

overall_design: the control group, transfection negative control; the siYTHDF2 group, transfection interference YTHDF2 group.

first: Chunjin

last: Li

first: Xu

last: Zhou


title: Oxaliplatin-Induced Upregulation of Exosomal miR-424-3p Derived from Human Bone Marrow Mesenchymal Stem Cells Attenuates Progression of Gastric Cancer Cells

city: Zhengzhou

first: Wei

last: Shen

state: Henan

address: 127 Dongming Road

department: Department of Medical Oncology

institute: The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Introduction Chemotherapy, particularly with oxaliplatin, is a key treatment for advanced gastric cancer (GC), and exosomes derived from human bone marrow mesenchymal stem cells (hBM-MSCs) play a vital role in the tumor microenvironment.
Objectives The study aims to elucidate the previously unexplored role of exosomes derived from hBM-MSCs in GC tumorigenesis, especially under the influence of chemotherapy.
Methods We conducted an integrated study, utilizing miRNA sequencing and biological experiments, to analyze the tumorigenicity of exosomal miR-424-3p secreted by hBM-MSCs and its target gene RHOXF2 in GC cell lines. The results were confirmed through experimentation using a xenograft mouse model.
Results This study demonstrated the role of hBM-MSCs in the GC microenvironment, focusing on their Epithelial-Mesenchymal Transition (EMT) facilitation through exosomes, which led to enhanced tumorigenicity of in GC cells. Intriguingly, this pro-tumor effect was abrogated when hBM-MSCs were treated with oxaliplatin. Exosomal miRNA sequencing revealed that oxaliplatin can upregulate the levels of miR-424-3p in exosomes secreted by hBM-MSCs, thereby inhibiting the EMT process in GC cells. Furthermore, miR-424-3p was identified to target and downregulate RHOXF2 expression, impeding the malignant behavior of GC cells both in vitro and in the mouse model.
Conclusions These findings uncover a potential hidden mechanism of oxaliplatin's anti-tumor action and propose the delivery of miR-424-3p via exosomes as a promising avenue for anti-tumor therapy.

overall_design: hBM-MSCs that were exposed to PBS or oxaliplatin (0.25uM) were cultured in a serum-free culture system for 48 hours and then centrifuged at 1 200 g for 25 min at 4 °C to remove the cell debris and dead cells. Exosomes were isolated by using differential centrifugal speeds. The cells were filtered through a 0.2 mm filter, followed by ultracentrifugation at 4 ° C and 20 000 g for 30 min to remove the large cell blisters. The collected supernatant was filtered through a 0.22-μm filter and centrifuged again at 4°C and 100 000 g for 90 min. After removing the supernatant, the white sedimentation from the tube bottom was suspended in 500 μL of PBS and stored at −80 °C for future experiments.

first: Suxia

last: Luo

first: Chen

last: Wei

first: Ning

first: Xinyi

last: Yang

first: Wenyue

last: Yu


title: Single-cell RNA sequence of postnatal 3 days ovarian tissues treaed with melatonin

city: Qingdao

first: Jun-Jie

last: Wang

state: Shandong

address: Changcheng 700

department: Qingdao Agricultural University

institute: College of Life Sciences

summary: In the present study, a pregnant mouse model exposed to di(2-ethylhexyl) phthalate (DEHP, one of the most common plasticizers) during primordial follicle formation was established. The single-cell transcriptome technology was applied to investigate the roles of melatonin in ovarian cells against DEHP exposure. .

overall_design: In the current investigation, scRNA-seq was applied to investigate the rescue effect of MLT on ovaries of offspring with maternal DEHP exposure during primordial follicle formation (from E16.5 to PD3).

first: Xiao-Yuan

last: Zhang


title: Gene expression profile of Wild Type (WT) and P2x7 knockout (P2X7-KO) leukemia leukemia-initiating cells Transcriptomes

first: Xiaoxiao

last: He

state: Shanghai

address: 280 South Chongqing Road, Shanghai 200025

department: Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Faculty of Basic Medicine

institute: Shanghai Jiao Tong University School of Medicine

summary: To determine the underlying molecular mechanisms that control the homing and self-renewal activities of P2x7-null Mac-1+c-Kit+ LICs, WT and P2x7-null LICs were WT and P2x7-KO  were sorted by flow cytometry, followed by the extraction of total RNA and subjected to the RNA-sequencing.

overall_design: Wild Type (WT) and P2x7 knockout (P2X7-KO) two population AML leukemia leukemia-initiating cells from bone marrow were sorted to measure gene expression.

first: Junke

last: Zheng


title: Qing-Zhi-Tiao-Gan-Tang (QZTGT) prevents nonalcoholic steatohepatitis (NASH) by expression pattern correction.

city: Nanjing

first: Hang

last: Chu

address: No.24, Tongjiaxiang

institute: China Pharmacuetical University

summary: To investigate the molecular composition of TCM and the possible molecular mechanism of TCM to improve NASH phenotypes.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 different livers of mice which  fed with vehicle or QZTGT

first: Peng

first: Ke

first: Yan

last: Tan


title: A novel lncRNA FUAT1/TNS4 axis confers chemoresistance by suppressing ROS-mediated apoptosis in gastric cancer

city: Jining

first: Mingliang

last: Liu

address: Affiliated Hospital of Jining Medical College, Jining 272007, China

institute: Affiliated Hospital of Jining Medical University

summary: Reactive oxygen species (ROS) play a vital role in conveying the cytotoxicity and resistance of  most chemo-drugs. Thus, a better understanding of the detailed activities against oxidative stress in cancer cells may provide novel insights into the discovery of common mechanisms underlying chemoresistance. In this study, taking advantage of a customized screening strategy based on transcriptome sequencing (RNA-Seq) technology, we identified a novel lncRNA, designated FUAT1, as a key non-genetic player that participates in ROS-mediated intrinsic chemoresistance in gastric cancer (GC) cells. The role of the FUAT1 regulatory axis in chemoresistance was further explored by using a series of in vitro and in vivo assays, including gain/loss-of-function and rescue experiments. Mechanistically, FUAT1 could upregulate TNS4 by sponging miR-140-5p, allowing GC cells to survive upon chemotherapy via inhibition of ROS-mediated apoptosis. Clinically, the FUAT1/TNS4 regulatory axis is negatively associated with overall and progression-free survival in gastric and colon cancer patients treated with 5-FU adjuvant chemotherapy. Our findings touch on a fundamental adaptive mechanism for the survival of cancer cells upon chemotherapy, providing a novel insight into the development of strategies to overcome chemoresistance.

overall_design: To identify the critical player in ROS-mediated chemoresistance,we established untreated(control),   5-FU(7.69uM) and H2O2(80uM)-induced SNU16 cell lines for 24h.We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different treated cells with three replicates.Comparative gene expression profiling analysis of RNA-seq data for control cells and treated cells(5-FU or H2O2).

first: Liren

first: Hehe

first: Xiaoling


title: Neuronal A2A receptor exacerbates synapse loss and memory deficits in APP/PS1 mice

city: Lille

first: David

last: Blum

state: Cedex

address: 1 place de Verdun

department: Lille Neurosience & Cognition

country: France

institute: Inserm

summary: Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by a progressive cognitive decline. Epidemiological studies have suggested a protective role of caffeine consumption against age-related cognitive impairments and the risk of developing AD. Effects of caffeine have been particularly ascribed to its ability to block adenosine A2A receptors (A2ARs). Early pathological upregulation of these receptors by neurons is thought to be involved in the development of synaptic and memory deficits in AD but this remains ill-defined. To tackle this question, we employed a novel transgenic mouse model allowing to promote a neuronal upregulation of A2AR in the hippocampus of APP/PS1 mice, developing AD-like amyloidogenesis. This new model was used to determine the impact of an early upregulation of A2AR on the progression of neuropathological lesions, associated behavior and underlying mechanisms in APP/PS1 mice. Our findings revealed that the early upregulation of A2AR in the presence of an ongoing amyloid pathology exacerbates memory impairments of APP/PS1 mice. These behavioral changes were not linked to major change in the development of amyloid pathology but rather associate with an increased p-tau at neuritic plaques. Moreover, proteomic and transcriptomic analysis coupled to quantitative immunofluorescence studies indicated that neuronal impairment of the receptor promoted both neuronal- and non-neuronal autonomous alterations i.e. loss of excitatory synapses and neuroinflammatory response, respectively, both presumably accounting for the detrimental effect on memory. Overall, our results provide compelling evidence that neuronal A2AR dysfunction as seen in the brain of patients contributes to AD pathogenesis, favoring synaptic deficits promoted by both amyloid (this study) and tau lesions (our previous study). In addition to provide new insights into the complex pathophysiology of AD, the present findings underscore the potential of A2AR as a relevant therapeutic target for mitigating early synaptic loss in this neurodegenerative disorder.

overall_design: Heterozygous APPswe/PS1dE9 mice (herein referred to as APP/PS1, C57Bl6/J background) were crossed with an in-house developed TRE-A2A transgenic strain (in which the mouse A2AR cDNA is under the control of a Tet-responsive element). Four genotypic heterozygous groups were therefore obtained: WT, TRE-A2A (or A2A), APP/PS1 and APP/PS1 TRE-A2A (or APP/PS1 A2A). We used females in our experiments. To achieve upregulation of neuronal A2AR in TRE-A2A mice, a tTA transactivator protein needs to bind the Tet-Responsive Element (TRE) promoter. To this end, all mice were thus bi-laterally injected into the CA1 region of the dorsal hippocampus with a serotype 5 adeno-associated viral (AAV2/5) vector allowing neuronal tropism, encoding the tTA transactivator under the control of the chicken beta-actin (CBA) promoter (AVV2/5-CBA-tTA-WPRE-bGH). The tTA protein expressed in the hippocampus then binds to the TRE, driving the expression of the murine A2AR in the TRE-A2A and APP/PS1 TRE-A2A groups only. Control animals, referred as WT and APP/PS1, were injected with the same viral vector but do not express the A2AR. All mice were injected at 3 months of age and sacrificed at 6 months of age, hippocampus dissected out and frozen before RNA extraction an sequencing.

first: Victoria

last: Gomez-Murcia

first: Agathe

last: Launay

first: Kévin

last: Carvalho

first: Céine

last: Mériaux

first: Raphaëlle

last: Caillierez

first: Sabiha

last: Eddarkaoui

first: Devrim

last: Kilinc

first: Dolores

last: Siedlecki

first: Mélanie

last: Besegher

first: Séverine

last: Bégard

first: Claire

last: Montmasson

first: Alexis-Pierre

last: Bemelmans

first: Malika

last: Hamdane

first: Thibaud

last: Lebouvier

first: Didier

last: Vieau

first: Isabelle

last: Fournier

first: Luc

last: Buée

first: Sabine

last: Lévi

first: Luisa

middle: V

last: Lopes

first: Emilie

last: Faivre


title: Type I IFN signaling pathway promotes osteoblast differentiation through targeting Sox9.

city: beijing

first: lei

last: zhang

address: xueyuan road 38th

department: heath science center

institute: peking university

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Type I IFN signaling pathway promotes osteoblast differentiation through targeting Sox9 [RNA-seq]

summary: Ossification of the posterior longitudinal ligament (OPLL) is a progressive ectopic bone formation of ligaments and may lead to severe neurological symptoms. However, in addition to conservative therapy for neurological symptoms or surgical management, effective pharmacotherapy and preventive intervention for OPLL remains absent. Here, to reveal the potential therapeutic target we generate single-cell maps of T-OPLL patients. We found that type I IFN signaling pathway is significantly activated during the progression of ossification. Further, stimulation of IFN β obviously promoted the calcium deposition of murine MC3T3-E1 preosteoblasts. We profiled the transcriptome in MC3T3-E1 cells after osteogenic induction, and found that IFN β promoted the expression of Sox9 and SPP1. STAT1 positively regulated the expression of Sox9 and phosphorylated STAT1 occupied on the promoter of Sox9. We also observed the localization of Sox9 in the ossificated region of ligament from OPLL patients. Thus, Sox9 is a target gene of type I IFN pathway during osteogenic induction. Furthermore, blockage of IFNAR1 by anti-IFNAR1 neutralizing antibody significantly impeded osteoblast differentiation induced by IFN β and display efficacy against ossification. Together, these results demonstrated that type I IFN signaling pathway promotes osteoblast differentiation. Anti-IFNAR1 neutralizing antibody could be used as a potential therapy for OPLL by blocking type I IFN signaling pathway.

overall_design: To investigate type I IFN signaling in osteoblast, we established M3T3-E1 cell lines in which treated with mouse IFN beta.

first: Xiao

last: Liu

first: Lei

last: Zhang

first: Ge

last: Wang

first: Wei

last: Zhao

first: Chen

last: Liang

first: Youzhi

last: Tang

first: Yenan

last: Fu

first: Bo

first: Jing

first: Xiaoguang

first: Hongquan

first: Yu

last: Yu


title: Impact of CD4+ T cell help on CD8+ CAR T cell gene expression during ex-vivo manufacturing

city: Seattle

first: Brian

last: Till

state: WA

address: 1100 Fairview Ave N, D3-100

institute: Fred Hutchinson Cancer Center

summary: Cell culture conditions impact the clinical efficacy of chimeric antigen receptor (CAR) T cell products, but the optimal approach remains unknown. Separate CD4+ and CD8+ cultures offer a potential advantage but complicate manufacturing and may affect cell expansion and function. We evaluated the co-culture of CD4+ and CD8+ cells at a defined ratio at culture initiation. We observed that the presence of CD4+ cells markedly improves expansion of CD8+ CAR T cells, and CD8+ cells cultured in isolation exhibit a hypofunctional phenotype and transcriptional signature compared with those co-cultured with CD4+ cells. Mixed-culture CAR T cells also confer superior anti-tumor activity in vivo compared with separately expanded, co-infused cells. CD4+ cell effects on CD8+ cells are mediated through both cytokines and direct cell contact, including CD40L-CD40 and CD70-CD27 interactions.

overall_design: We analyzed transcriptional profiles of CD8+ CAR T cells from 6 subjects (a mix of healthy donors and patients with B-cell lymphoma) expanded in mixed cultures with CD4+ cells compared with those in separate CD8-only cell cultures. Total RNA was isolated from FACS-sorted CD8+ T cells expressing a 3rd generation CD20-targeted chimeric antigen receptor (CAR) containing CD28 and 41BB costimulatory domains, at either day 8 (without restimulation) or day 14 (after restimulation with CD20+ lymphoblastoid cells at day 7).

first: Sang

middle: Y

last: Lee

first: Dong

last: Sun

first: Francisco

last: Cervantes-Contreras

first: Ryan

last: Basom

first: Feinan

last: Wu

first: Si

first: Richa

last: Rai

first: Hamid

last: Mirzaei

first: Shyril

last: O'Steen

first: Damian

last: Green

first: Mazyar

last: Shadman


title: To investigate gene expression differences between wild-type and tpcn2 mutant zebrafish embryos during trunk development

city: Hong Kong

first: Andrew

last: Miller

address: Division of LIFS, HKUST, Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: To investigate gene expression differences between wild-type and tpcn2 mutant zebrafish embryos during notochord and muscle development.

overall_design: Gene expression analysis using RNA-seq data from wild-type zebrafish embryos and the tpcn2 mutant, each with five biological replicates.

middle: L


title: miRNA sequencing detecting miRNA cargo from PRP derived exosomes isolated from young donors and old donors

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

summary: We detected and compared the miRNAs contained in Y-PRP-exos or O-PRP-exos. The results showed that most miRNAs (38) can be identified in both Y-PRP-exos and O-PRP-exos. In addition, hsa-let-7f-5p, hsa-miR-16-5p and hsa-miR-126-3p were top 3 enriched miRNAs in PRP-exos of all donors. These results indicated the heterogeneity of miRNAs in PRP-exos was small, regardless of age. However, the abundance of miRNAs in Y-PRP-exos and O-PRP-exos was quite different, especially in high-ranking miRNAs. The expression of hsa-miR-16-5p and has-let-7f-5p in O-PRP-exos in two old donors was only approximately 1/4-1/2 of that in Y-PRP-exos in two young donors

overall_design: To investigate the miRNAs in PRP-exosomes that could regulate adipogenesis and proliferation of Pdgfrα+ progenitors and fatty infiltration in muscle injury, we isolated PRP exosomes derived from two young donors and two old donors, respectively, and compared the enriched miRNAs.

first: Jin

last: Qian


title: Effect of depletion of YAP and TAZ on gene expression of LX2 cells

city: Durham

first: KUO

last: DU

state: NC

address: 905 SOUTH LASALLE STREET, Room 1063

department: Medicine

institute: Duke Universty

summary: To investigate how YAP and TAZ affect the HSC biology, we depleted YAP and TAZ in LX2 cells using siRNA for 7 days.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 biological replicate samples in each group (siNT, siYAP, siNT).

first: Kuo

last: Du

first: Anna

last: Diehl

first: Tianyi

last: Chen


title: Osteoblasts isolated from sp7-GFP transgenics by FACS sorting of 4dpf zebrafish larvae

first: Marc

last: Muller

summary: The transgenic zebrafish line Tg(sp7:sp7-GFP) (ulg071 Tg) was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence, P2 displaying high fluorescence. Cells were collected and sumitted to RNA-Seq

overall_design:
A Tg(sp7:sp7-GFP) heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non-transgenic offspring. Two populations with low (P1) and high (P2) fluorescence were separated.   The collected cells from populations P1 and P2 (about 30-50000 cells) were immediately lysed in 0.5% Triton X-100 containing 2U/µl RNAsin and stored at -80°C. cDNAs were prepared from these lysed cells according to the SMART-Seq 2.0 protocol (Illumina, San Diego, CA, USA) for low input RNA sequencing, while libraries were prepared using the Nextera XT DNA library kit.

Third-party re-analysis:
Table_P2_Sanger_P1_Sanger_P1_P2.csv  (our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2_Sanger;log2FoldChange P2_Sanger;padj P2_Sanger;Sanger_baseMean;P2_baseMean;ID;gene;baseMean P1_Sanger;log2FoldChange P1_Sanger;padj P1_Sanger;Sanger_baseMean;P1_baseMean;ID;gene;baseMean;log2FoldChange P1_P2;padj P1_P2;P2_baseMean;P1_baseMean).
Table_Counts_P1_P2_Sanger.csv  (the counts table complete with the Sanger data).

first: Ratish

last: Raman


title: Human iPSC-derived renal collecting duct organoids model cystogenesis in ADPKD

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: Here, establishing expansion cultures of hiPSC-derived ureteric bud tip cells, an embryonic precursor that gives rise to collecting ducts, we succeeded in advancing the developmental stage of collecting duct organoids and showed that all collecting duct organoids derived from PKD1-/- hiPSCs spontaneously develop multiple cysts, clarifying the initiation mechanisms of cystogenesis.

overall_design: RNA sequencing analysis for PKD1+/+ and PKD1-/- ureteric bud tip cells cultured for 6 weeks.

first: Kenji

last: Osafune

first: Shin-Ichi

last: Mae


title: The miRNA expression profile in the progression of the gastric cancer

city: JiangSu

first: An

last: Fangmei

address: NO. 299, QingYang Road, Wuxi, Jiangsu

institute: Wuxi Public Hospital

summary: To study the miRNA expression profiles and explore the underlying roles of Helicobacter pylori (H. pylori), miR-196a/b-5p, and IFG2BP1 in the carcinogenesis of gastric mucosa.

overall_design: miRNA-seq was applied to investigate the miRNA expression profiles during the progression of gastric carcinogenesis in the patients with H. Pylori infection

first: Qiang

last: Zhan

first: Fangmei

last: An


title: Microsecond pulsed electric fields induce myocardial ablation by damaging mitochondria

city: Hangzhou City

first: Ruoshi

state: Zhejiang

address: No. 79 Qingchun Road

institute: Zhejiang University

summary: Catheter ablation is an effective treatment to prevent recurrence of Atrial fibrillation (AF) and can be used to maintain sinus rhythm and improve symptoms of AF, but to some extent it can cause a range of adverse effects associated with catheter ablation. Pulsed electric field is a newer treatment modality to replace catheter ablation for atrial fibrillation due to its fewer side effects. Different from radiofrequency ablation, which destroys diseased myocardial tissue by thermal energy, pulsed electric field ablation achieves the purpose of atrial fibrillation ablation by inducing damage to diseased myocardial cells through irreversible electroporation. However, some experimental parameters and mechanism of pulsed electric fields remain unclear.

overall_design: we analyzed the effects of microsecond pulsed electric field on cardiomyocyte apoptosis and cardiac activity in vitro and in vivo, and explored its mechanism by transcriptome study.

first: Shengjun

last: Wu

first: Mingqian

last: Li

first: Peng

last: Teng


title: Extracellular phosphate is involved in the virulence regulation of Streptococcus pneumoniae

city: LuZhou

first: Zhikun

last: Zhang

state: Sichuan

address: Xianglin Road 1#

institute: Southwest Medical University

summary: The gene expression of S. pneumoniae cultured in medium with different concentration of phosphate were detected, aiming to analyze the role of reduced extracellular phosphate in virluence regulation of S. pneumoniae.

overall_design: ATCC495619 cells culture in Brain heart infusion broth of 12mM phosphate were applied in transcriptome sequencing, using normal brain heart infusion broth as control

first: Yingshun

last: Zhou


title: Higher colonic proliferation and tumor prevalence amongst azoxymethane treated A/J mice receiving fecal microbiota transplants from old mice compared to recipients of young mice

city: Boston

first: Samuel

last: Beck

state: MA

address: 609 Albany st.

department: Dermatology

institute: Boston University School of Medicine

sample_organism:
Mus musculus
feces metagenome

platform_organism:
Mus musculus
feces metagenome


title: Tumor-driven stromal reprogramming in the pre-metastatic lymph node

status: Public on Nov 29 2023

city: Cambridge

first: Michelle

last: Piquet

address: 250 Massachusetts Ave,

institute: Novartis Institutes for BioMedical Research

summary: Metastatic dissemination is critically reliant on the formation of a receptive niche, a process which is thought to rely on signals derived from the primary tumor. Lymph nodes are continuously exposed to such signals through the flow of afferent lymph, allowing the potential reprograming of lymphoid tissue stroma in support of metastases or immunosuppression. We utilize single cell RNA sequencing to profile reprograming of the stromal support network within the pre-metastatic lymph node. Transcriptomic changes of the tumor-draining LN are compared against those of the contralateral non-draining LN. Additionally, we include experimental conditions for comparison in which LNs are exposed to fixed tumor cells, mimicking antigenic challenge without active tumor growth, thereby allowing us to distinguish between active tumor-elicited reprograming and general immune responses to tumor antigen.

overall_design: Single Cell RNA sequencing was performed on enriched PDPN+ stromal cells isolated from enzymatically dissociated lymph nodes. Tumor-draining and non-draining inguinal lymph nodes were harvested from mice bearing subcutaneous MC38 tumors. Draining and non-draining inguinal lymph nodes were also harvested from mice inoculated with fixed (non-viable) MC38 cancer cells. For both conditions, 5 x 105 cells were implanted subcutaneously on the animal’s lower-right flank. Mice were euthanized and LNs were collected on day 12 after treatment.

first: David

last: Ruddy

first: Viviana

last: Cremasco

first: Jonathan

last: Chang


title: Spatial Gene Expression in the Adult Rat Patellar Tendon

city: Davis

first: Michael

middle: J.

last: Mienaltowski

address: One Shields Ave

department: Animal Science

institute: University of California Davis

summary: Tendons are dense connective tissues with relatively few cells which makes studying the molecular profile of the tissue challenging. There is not a consensus on the spatial location of various cell types within a tendon, nor the accompanying transcriptional profile. In the present study, we used two male rat patellar tendon samples for sequencing-based spatial transcriptomics to determine the gene expression profile. We integrated our data with a single cell dataset to predict the cell type composition of the patellar tendon as a function of location within the tissue. The spatial location of the predicated cell types suggested that there were two populations of tendon fibroblasts, one located in the tendon midsubstance, while the other localized with red blood cells, pericytes, and immune cells to the tendon peripheral connective tissue. Of the highest expressed spatially variable genes, there were multiple genes with known function in tendon: Col1a1, Col1a2, Dcn, Fmod, Sparc, and Comp. Further, a novel spatially regulated gene (AABR07000398.1) with no known function was identified. The spatial gene expression of tendon associated genes (Scx, Thbs4, Tnmd, Can, Bgn, Lum, Adamts2, Lox, Ppib, Col2a1, Col3a1, Col6a2) was also visualized. Both patellar tendon samples had similar expression patterns for all these genes. This dataset provides new spatial insights into gene expression in a healthy tendon.

overall_design: tissue sections from two male rat patellar tendons

first: Danielle

last: Steffen

middle: J

first: Keith

last: Baar


title: Single-cell transcriptome profiling reveals developmental trajectory and regulatory networks of mouse maxillary prominence [RNA-seq]

city: Shanghai

first: Jian

last: Sun

address: Quxi Road No.500

institute: Shanghai Ninth People's Hospital

summary: The formation of maxillary prominence in vertebrates involves precisely coordinated migration and differentiation of neural crest cells. However, the regulatory factors and networks underpinning such an intricate process has not been fully elucidated. Here we combined bulk and single-cell RNA-Seq to comprehensively characterize the transcriptome dynamics during mouse maxillary development from embryonic day (E) 10.5 to 12.5, a critical period when a multitude of facial tissues start to emerge.  We identified multiple cell populations that represent different developmental transition states and inferred the developmental trajectory of maxillary mesenchyme, revealing that a developmental bifurcation toward either an osteochondrogenic fate or a non-osteochondrogenic fate occurs at E11.5. We further deduced the core transcriptional regulators and gene regulatory networks associated with the maxillary cell fate transitions. Moreover, we revealed transcriptional regulators that are linked to dynamic changes in chromatin accessibility during maxillary development. Collectively, our study for the first time characterized the maxillary developmental process at single cell resolution, providing rich resources and important insights for achieving a systems level understanding of craniofacial morphogenesis and abnormality.

overall_design: Bulk RNA sequencing of E10.5, E11.5, E12.5, E14.5 mouse embryonic maxillary prominence tissue. Three biological replicates per group

first: Qian

last: Bian

first: Xudong

last: Wang

first: Nayoung

last: Ha


title: Conservation and contrast in cell states of echinoderm ovaries

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

summary: In contrast to women, echinoderms have the amazing ability to keep producing functional gametes throughout their lifespan, in some cases exceeding 200 years. The histology and ultrastructure of echinoderm ovaries has been described but how these ovaries function and maintain the production of high-quality gametes is still a mystery. Here, we present the first single cell RNA sequencing (scRNAseq) datasets of two sea urchin species (Strongylocentrotus purpuratus and Lytechinus variegatus) and one sea star species (Patiria miniata). We find 14 cell states in the Sp ovary, 16 cell states in the Lv ovary and 13 cell states in the ovary of the sea star. This resource is essential to understand the structure and functional biology of the ovary in echinoderms, and better informs decisions in the utilization of in situ RNA hybridization probes selective for various cell types. We link key genes with cell clusters of the feature plots in validation of this approach. This resource also aids in the identification of the stem cells for prolonged and continuous gamete production, is a foundation for testing changes in the annual reproductive cycle, and is essential for understanding the evolution of reproduction of this important phylum. Highly selective gene expression revealed by this dataset also divulges gene targets of highest priority for interrogating gene activities by Cas9-targeted gene knock-out and knock-in approaches and in dissociated ovarian cell cultures to test the function of each cell type identified.

sample_organism:
Lytechinus variegatus
Strongylocentrotus purpuratus
Patiria miniata

overall_design: Adult Strongylocentrotus purpuratus were obtained from Pete Halmay of Pt. Loma Marine Invertebrate Lab (Lakeside, CA, e-mail: peterhalmay@gmail.com) and housed in aquaria with artificial seawater (ASW) at 16°C (Coral Life Scientific Grade Marine Salt; Carson, CA). Adult Lytechinus variegatus were obtained from the Pelagic Corporation (pelagiccorp@bellsouth.net). They were housed in aquaria with ASW at room temperature (Coral Life Scientific Grade Marine Salt; Carson, CA). Adults Patiria miniata were collected by Josh Ross (South Coast Bio-Marine) off the Californian coast housed in aquaria with artificial seawater (ASW) at 16°C. Ovaries were collected from adult echinoderms and washed twice with calcium-free seawater (For 1 L: NaCl 26.5 gm; KCl 0.7 gm; MgSO4-7H2O 11.9 gm; NaHCO3 0.5 gm; pH to 8.0, salinity should be 34 ppt; McClay, 2004), and then suspended in hyalin-extraction media (HEM, for 1 L: NaCl 18.5 gm; KCl 0.7 gm; MgSO4-7H2O 11.9 gm; glycine 22.5 gm; Tris base 1.21 gm; EGTA 0.76 gm; pH to 8.0; 56) for 15 min. When cells were beginning to dissociate, the ovaries were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40 micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the scRNA-seq protocol.

first: Shumpei

last: Morita

first: Stephany

last: Foster

first: Gary

last: Wessel


title: Single-cell transcriptome profiling reveals developmental trajectory and regulatory networks of mouse maxillary prominence


title: LEO1 Is Required for Efficient Entry into Quiescence, Control of H3K9 methylation and Gene Expression in Human Fibroblasts

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute


title: LEO1 Is Required for Efficient Entry into Quiescence, Control of H3K9 methylation and Gene Expression in Human Fibroblasts [RNA-Seq]

summary: Abstract: (1) Background: The LEO1 (Left open reading frame 1) protein is a conserved subunit of the PAF1C complex (RNA polymerase II associated factor 1 complex). PAF1C has well-established mechanistic functions in elongation of transcription and RNA processing. We have previously shown, in fission yeast, that LEO1 is controlling histone H3K9 methylation levels by affecting the turnover of histone H3 in chromatin, and that it is essential for proper regulation of gene expression during cellular quiescence. Human fibroblasts enter a reversible quiescence state upon serum deprivation in the growth media. Here we investigate the function of LEO1 in human fibroblasts. (2) Methods: We knocked out the LEO1 gene using CRISPR/Cas9 methodology in human fibroblasts and verified that the LEO1 protein was undetectable by Western blot. We characterized the phenotype of the DLEO1 knockout cells with FACS analysis and cell growth assays. We used RNA-sequencing using spike-in controls to measure gene expression and spike-in controlled ChIP-sequencing experiments to measure the histone modification H3K9me2 genome-wide. (3) Results: Gene expression levels are altered in quiescent cells, however factors controlling chromatin and gene expression changes in quiescent human cells are largely unknown. The DLEO1 knockout fibroblasts are viable but have reduced metabolic activity compared to wild type cells. DLEO1 cells showed a slower entry into quiescence and a different morphology compared to wild type cells. Gene expression was generally reduced in quiescent wild type cells. The downregulated genes included genes involved in cell proliferation. A small number of genes were upregulated in quiescent wild type cells including several genes involved in ERK1/ERK2 and Wnt signaling. In quiescent DLEO1 cells many genes were mis-regulated compared to wild type cells. This included genes involved in Calcium ion transport and cell morphogenesis. Finally, spike-in controlled ChIP-sequencing experiments demonstrated that the histone modification H3K9me2 levels are globally increased in quiescent DLEO1 cells.   (4) Conclusions: Thus, LEO1 is important for proper entry into cellular quiescence, control H3K9me2 levels and gene expression in human fibroblasts.

first: Marc

last: Laurent

first: Lina

last: Cordeddu

first: Yasaman

last: Zahedi

first: Karl

last: Ekwall


title: Genetic separation of Brca1 functions reveal mutation-dependent Pol theta vulnerabilities

city: St Louis

first: John

last: Krais

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University School of Medicine

summary: We report DNA resection length after induced double stranded breaks in specific genomic loci with the expression of the AsisI restriction enzyme

overall_design: Exponentially AsiSI-expressing MEFs with different Brca1 alleles with and without 53bp1 KO were treated with 1uM doxocyclin (DOX) for 24 hours with tamoxifen for the last 5h, resulting in the nuclear translocation of AsiSI  BRCA1 alleles used in this study: CC: Deletion 4287 to 4295 Del 11: Deletion 874 to 4188

first: J

first: N

last: Johnson


title: Sedanolide ameliorates hydrogen peroxide-induced apoptotic cell death via activation of KEAP1-NRF2 pathway

city: Takamatsu

first: Yosuke

last: Tabei

state: Kagawa

institute: National Institute of Advanced Industrial Science and Technology

summary: Sedanolide is a bioactive compound with anti-inflammatory and antitumor activities. Although it has been recently suggested that sedanolide activates the nuclear factor E2-related factor 2 (NRF2) pathway, there is little research on its effects on cellular resistance to oxidative stress. The objective of the present study was to investigate the function of sedanolide in suppressing hydrogen peroxide (H2O2)-induced oxidative damage and the underlying molecular mechanisms in human hepatoblastoma cell line HepG2 cells. We found that sedanolide activated the antioxidant response element (ARE)-dependent transcription mediated by the nuclear translocation of NRF2. Pathway enrichment analysis of RNA sequencing data revealed that sedanolide upregulated the transcription of antioxidant enzymes involved in the NRF2 pathway and glutathione metabolism. Then, we further investigated whether sedanolide exerts cytoprotective effects against H2O2-induced cell death. We showed that sedanolide significantly attenuated cytosolic and mitochondrial reactive oxygen species (ROS) generation induced by exposure to H2O2. Furthermore, we demonstrated that pretreatment with sedanolide conferred a significant cytoprotective effect against H2O2-induced cell death by preventing the decrease of the mitochondrial membrane potential and the increase of caspase-3/7 activity. Our study demonstrated that sedanolide enhanced cellular resistance to oxidative damage via the activation of the Keich-like ECH-associated protein 1 (KEAP1)–NRF2 pathway.

overall_design: To investigate the biological effects of sedanolide, we analyzed the transcriptomic changes of luciferases-expressing HepG2 cells treated with sedanolide for 24 h and compared them with those of control cells.

first: Hiroko

last: Abe

first: Shingo

last: Suzuki

first: Nobuaki

last: Takeda

first: Jun-ichiro

last: Arai

first: Yoshihiro

last: Nakajima


title: DNA methylation activated full-length EMX1 facilitates metastasis through EMX1-EGFR-ERK axis in hepatocellular carcinoma

city: Guangzhou

first: Dongsheng

last: Wen

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

summary: Altered DNA methylation is a crucial epigenetic event in hepatocellular carcinoma (HCC) development and progression. Through methylation-transcriptomic analysis, we identified a set of sixty potential DNA methylation-based epidriver genes. This set of genes focuses on the hypermethylation of EMX1, which is frequently observed in hepatobiliary tumors. Despite of its frequent occurrence, the function of EMX1 remains largely unknown. By utilizing bisulfite-next-generation sequencing, we have detected EMX1 DNA hypermethylation on the gene body, which is positively correlated with EMX1 mRNA expression. Further analysis revealed that EMX1 mRNA terminal exon splicing in HCC generated two protein isoforms: EMX1 full length (EMX1-FL) and alternative terminal exon splicing isoform (EMX1-X1). Cellular functional assays demonstrated that gain-of-function EMX1-FL, but not EMX1-X1, induced HCC cells migration and invasion while silencing EMX1-FL inhibited HCC cells motility. This result was further validated by in vivo tumor metastasis models. Mechanistically, EMX1-FL bound to EGFR promoter, promoting EGFR transcription and activating EGFR-ERK signaling to trigger tumor metastasis. Therefore, EGFR may be a potential therapeutic target for EMX1-high expression HCC. Our work illuminated the crucial role of gene body hypermethylation-activated EMX1-FL in promoting tumorigenesis and metastasis in HCC. These findings pave the way for targeting the EMX1-EGFR axis in HCC tumorigenicity and metastasis.

overall_design: To investigate the function of EMX1-FL and EMX1-X1 in HCC, we established SNU-398 cell line that stably overexpressed EMX1-FL or EMX1-X1 through lentiviral transfection.

first: Li-chang

last: Huang

first: Xiao-yun

last: Bu


title: Gene expression in Mon-Mac-6 cells treated with METTL3 PROTAC, WD6305 and inhibitor, UZH2

city: shanghai

first: huang

last: yuting

address: 555 Zu Chong Road

institute: Shanghai Jiaotong University

summary: N6-methyladenosine (m6A) methylation is the most prevalent RNA modification, which plays a critical role in various bioprocesses.1 This modification is predominantly catalyzed by the m6A methyltransferase complex (MTC), consisting of core subunits such as methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14), along with cofactors like Wilms tumor 1-associated protein (WTAP). We described the development of a first-in-class potent and selective METTL3-targeted degrader, WD6305, which can effectively degrade both METTL3 and its partner protein METTL14. WD6305 showed superior antiproliferative effects in multiple AML cell lines compared to its parent inhibitor, UZH2. Here, we want to compare the changes in genes between the two.

overall_design: In order to detect the gene expresion changes of Mon-Mac-6 after treatment with WD6305 and UZH2, we sequenced Mon-Mac-6 cells after treatment with 500nM DMSO, WD6305, and UZH2 for 48h.

first: Xun

first: Jian

last: Ding

first: Shilin

last: Xu

first: Yuting


title: Single-cell transcriptome profiling reveals developmental trajectory and regulatory networks of mouse maxillary prominence [ATAC-seq]

last: Sun

overall_design: ATAC-seq of E10.5, E11.5, E12.5 mouse embryonic maxillary process mesenchymal cells. Three biological replicates per group

first: Qian

last: Bian

first: Xudong

last: Wang

first: Nayoung

last: Ha


title: Single-cell sequencing of 12 PBMC samples to study the different immune response after SARS-CoV-2 vaccines injection

first: Xiaoyu

last: Liu

address: 639 Manufacturing Board Road

summary: The effectiveness of SARS-CoV-2 vaccines varies among individuals. In the COVID-19 global pandemic, it showed a significant Th1 characteristics, suggesting that the immune disorder and production of SARS-CoV-2 antibodies may be related to Th1/Th2 bias. However, the molecular mechanisms of how Th1/Th2 bias affects the differences in host immune responses to viruses remain unclear. A total of 3 subjects with elevated antibody (E) and 3 without changes (C) were recruited. We collected peripheral blood and performed single-cell sequencing before and after the third dose of SARS-CoV-2 vaccine. The changes of T cell clusters were analyzed and differential analysis of T cells between the two groups was performed.

overall_design:
Six subjects with different antibody levels after vaccination (three with markedly elevated vs. three without) were enrolled in this study. All subjects were vaccinated with inactivated SARS-CoV-2 vaccine. Peripheral blood samples were collected before and after the third dose of the vaccine. In total, 12 peripheral blood samples (3 pre-injection samples in the elevated group (E), 3 post-injection samples in E group, 3 pre-injection samples in the control group (C), 3 post-injection samples in C group) were sequenced.

***************************************************************
Submitter states that missing raw data are being made available for controlled access in the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa/).
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first: Junyong

last: Han

first: Renjie

last: Cui

first: Meifang

last: Peng

first: Huaidong

last: Song

first: Rui

last: Li

first: Gang

last: Chen


title: RAB7 deficiency impairs pulmonary artery endothelial function and promotes pulmonary hypertension

city: Columbus

first: Laszlo

last: Farkas

state: OH

address: 473 W 12th Avenue

institute: The Ohio State University

summary: Pulmonary arterial hypertension (PAH) is a devastating and progressive disease with limited treatment options. Endothelial dysfunction plays a central role in development and progression of PAH, yet the underlying mechanisms are incompletely understood. The endosome-lysosome system is important to maintain cellular health and the small GTPase RAB7 regulates many functions of this system. Here, we explored the role of RAB7 in endothelial cell (EC) function and lung vascular homeostasis. We found reduced expression of RAB7 in ECs from PAH patients. Endothelial haploinsufficiency of RAB7 caused spontaneous PH in mice. Silencing of RAB7 in ECs induced broad changes in gene expression revealed via RNA sequencing and RAB7 silenced ECs showed impaired angiogenesis, expansion of a senescent cell fraction, combined with impaired endolysosomal trafficking and degradation, which suggests inhibition of autophagy at the pre-degradation level.

overall_design: Human primary PAECs were cultured in complete EGM-2MV media (Lonza CC-3162) in a cell culture incubator at 37°C with 5% CO2 and 100% humidity. For siRNA-mediated knockdown of RAB7, PAECs were transfected with 50 nM RAB7 or control siRNA using GenMute Reagent (SL100568, SignaGen). The following siRNAs were used: RAB7 siRNA (IDT, NM_004637 13.2), control siRNA (IDT, 51-01-14-04). After 24h, siRNA was removed, and RNA was isolated  48h after transfection.

first: Piper

last: Bryce

first: Srimathi

last: Bogamuwa

first: Pearlly

last: Yan


title: Global transcriptomic changes elicited by sodB deletion and menadione exposure in Aspergillus nidulans

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Manganese superoxide dismutases (MnSODs) play a pivotal role in the preservation of mitochondrial integrity and function in fungi under various endogenous and exogenous stresses. Deletion of Aspergillus nidulans mnSOD/sodB increased oxidative stress sensitivity and apoptotic cell death rates as well as affected antioxidant enzyme and sterigmatocystin productions, respiration, conidiation and the stress tolerance of conidiospores. The physiological consequences of the lack of sodB were more pronounced during carbon-starvation than in the presence of glucose. Lack of SodB also affected the changes in the transcriptome, recorded by high-throughput RNA sequencing, in menadione sodium bisulfite (MSB)-exposed, submerged cultures supplemented with glucose. Surprisingly, the difference between the global transcriptional changes of the ΔsodB mutant and the control strain was relatively small indicating that the SodB-dependent maintenance of mitochondrial integrity was not essential under these experimental conditions. Owing to the outstanding physiological flexibility of the Aspergilli, certain antioxidant enzymes and endogenous antioxidants together with the reduction in mitochondrial functions well compensated for the lack of SodB. The lack of sodB reduced the growth of surface cultures more than submerged culture, which should be considered in future development of fungal disinfection methods.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mycelia of Aspergillus nidulans reference strain, and DsodB mutant under menadione (MSB) treated and untreated conditions with three biological replicates.

first: Klaudia

last: Pákozdi

first: Tamás

first: Károly

last: Antal

first: István

last: Pócsi


title: A novel B cell-driven EAE mouse model reveals the impact of B cell-derived cytokines on CNS autoimmunity

city: Planegg-Martinsried

first: Anneli

last: Peters

address: Großhaderner Str. 9

department: Clinical Neuroimmunology

country: Germany

institute: LMU Hospital

summary: We developed an adjuvant-free co-transfer EAE mouse model, in which highly activated, MOG-specific induced germinal center B (iGB) cells provide the critical stimulus for disease development. As our model allows for B cell manipulation prior to transfer, we found that overexpression of IL-6 leads to an accelerated EAE onset accompanied by activation/expansion of the myeloid compartment even in mice that received non-specific polyclonal iGB cells. To analyze the effects of IL-6 overexpression on the myeloid compartment, we compared CD11b+ cells from mice that received polyclonal WT iGB cells overexpressing IL-6 (WT iGB6) and mice that received MOG-specific B cells transduced with an empty vector (IgHMOG iGBGFP) by RNAseq.

overall_design: RNAseq from CD11b+ cells isolated from WT iGB6 recipients vs. CD11b+ cells from IgHMOG iGBGFP recipients (n=3 mice/group).

first: Thomann

last: Anna S.

first: McQuade

last: Courtney A.

first: Pinjušić

last: Katarina

first: Kolz

last: Anna

first: Schmitz

last: Rosa

first: Kitamura

last: Daisuke

first: Wekerle

last: Hartmut

first: Peters

last: Anneli


title: PSI photoinhibition alters iron homeostasis in chloroplasts and initiates retrograde signaling regulating nuclear gene expression

city: Turku

first: Mehmet

last: Kilic

address: FI-20014 TURUN YLIOPISTO

department: Molecular Plant Biology

country: Finland

institute: University of Turku

summary: Photosystem I (PSI) is a critical component of the photosynthetic machinery in plants. Under conditions of environmental stress, PSI becomes photoinhibited, leading to redox imbalance in the chloroplast. PSI photoinhibition is caused by an increase in electron pressure within PSI, which damages the iron-sulfur centers. In this study, we investigated the effect of PSI electron acceptors on the susceptibility of PSI to photoinhibition at different CO2 concentrations in the plant environment. We also analyzed the global gene expression in plants exposed to PSI photoinhibition. PSI was photoinhibited using a specific illumination technique that inhibited PSI with minimal effect on PSII. CO2 levels neither increased nor decreased the likelihood of PSI photodamage. PSI photoinhibition, independent of CO2 levels, upregulated the genes involved in the response to iron excess in plants and downregulated the genes involved in iron deficiency. It also induced the genes of photosynthetic proteins that act as electron acceptors for PSI. We propose that PSI photoinhibition causes a release of iron from iron-sulfur centers, which initiates a retrograde signal from the chloroplast to the nucleus to modify gene expression. In addition, deprivation of CO2 from the air initiated a signal that induced flavonoid biosynthesis genes, probably via jasmonate production.

overall_design: Arabidopsis thaliana plants were exposed to  growth light (GL; control) and PSI photoinhibition treatment (PSI-PI) under 0, 100, 400 and 1000 ppm CO2 to study gene expression in response to PSI photoinhibiton.

first: Eevi

last: Rintamäki


title: LEO1 Is Required for Efficient Entry into Quiescence, Control of H3K9 methylation and Gene Expression in Human Fibroblasts [ChIP-Seq]

first: Anastasios

last: Damdimopoulos

overall_design: We knocked out the LEO1 gene using CRISPR/Cas9 methodology in human fibroblasts and verified that the LEO1 protein was undetectable by Western blot. We characterized the phenotype of the DLEO1 knockout cells with FACS analysis and cell growth assays. We used RNA-sequencing using spike-in controls to measure gene expression and spike-in controlled ChIP-sequencing experiments to measure the histone modification H3K9me2 genome-wide.

first: Marc

last: Laurent

first: Lina

last: Cordeddu

first: Yasaman

last: Zahedi

first: Karl

last: Ekwall


title: ZNF643/ZFP69B exerts oncogenic properties and associates with cell adhesion and immune processes [RNA-seq]

city: Poznan

first: Marta

last: Machnik

state: Wielkopolska

address: Rokietnicka 8

department: Chair of Medical Biotechnology

country: Poland

institute: Poznan University of Medical Sciences

summary: The global cancer burden remains high; thus, it is crucial to entangle molecular mechanisms driving carcinogenesis to improve current prevention and treatment options. We previously detected the ZNF643/ZFP69B gene upregulated in multiple tumors, and we speculated it may play a role in tumor biology. To test this hypothesis, we employed TCGA-centered databases to correlate ZNF643 status with various clinicopathological parameters. We also performed RNA-seq analysis, in vitro studies assessing cancer cell phenotype, and searched for ZNF643-bound genomic loci. Our data indicated higher levels of ZNF643 in most analyzed tumors compared to normal samples, possibly due to copy number variations. ZNF643 mRNA correlated with diverse molecular and immune subtypes and clinicopathological features (tumor stage, grade, patient survival). RNA-seq analysis revealed that ZNF643 silencing triggers the deregulation of the genes implicated in various cancer-related processes, such as growth, adhesion, and the immune system. Moreover, we observed that ZNF643 positively influences cell proliferation, cell cycle, migration, and invasion in a cell type-dependent manner. Finally, our ChIP-seq analysis indicated that the genes associated with ZNF643 binding are linked to adhesion and immune signaling. In conclusion, our data confirm the oncogenic properties of ZNF643 and pinpoint its impact on cell adhesion and immune processes.

overall_design: We analyzed 6 samples from two different lung cancer cell lines in biological triplicates (total 18 samples). For each cell line (H2073 and SKMES) we analyzed unmodified cells (WT), cells with knocked-down expression of ZNF643 (shZNF643) and cells carrying control shRNA sequence (shLUC). Pair-end RNA sequencing was performed for all samples on a NovaSeq 6000 Sequencing System (Illumina). DEG (Differentially Expressed Genes) analysis was performed on two different comparison pairs (sh643 vs. two control samples WT and shLUC separately) using edgeR.

first: Urszula

last: Oleksiewicz


title: Gene expression in Mon-Mac-6 cells treated with METTL3 PROTAC, WD6305

first: huang

last: yuting

summary: We developed a new METTL3 PROTAC, WD6305, which, unlike inhibitors, can reduce the expression of METTL3 protein. Here, we tested the gene expression after dosing by RNA-seq.

overall_design: In order to detect the gene expression changes of Mon-Mac-6 after treatment with WD6305, we sequenced Mon-Mac-6 cells after treatment with 500nM DMSO and WD6305 for 48h.

first: Yuting

last: Huang


title: ZNF643/ZFP69B exerts oncogenic properties and associates with cell adhesion and immune processes [ChIP-seq]

city: Poznań

state: Greater Poland

address: Rokietnicka 8, Medical Biology Center

overall_design: Chromatin immunoprecipitation coupled with next generation seqencing (ChIP-seq) with anti-HA antibody in wild-type (WT) and HA-tagged ZNF643 overexpressing SKMES lung cancer cell line.


title: ZNF643/ZFP69B exerts oncogenic properties and associates with cell adhesion and immune processes

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

overall_design: Refer to individual Series


title: The Heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

summary: Analyzing differences in transcriptome profile of Mto3DhbhA in 7H9 and Sauton's media compared to control Mto3.

overall_design: Mto3∆hbhA was inoculated at 0.05 OD, in 7H9 and Sauton's media. At 0.8  OD total RNA was islolated and RNA seq was performed.

first: Saba

last: Naz

first: Priyadarshini

last: Sanyal

middle: K

first: Divya

middle: T

last: Sowpati

first: Vinay

last: Nandicoori


title: RNAseq analysis on liver from pigs treated with testosterone and nandrolone esters: identification and field validation of transcriptional biomarkers

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: The use of anabolic steroid hormones as growth promoters in farm animals is banned in the European Union. However, among anabolic compounds, testosterone and nandrolone are still illegally administered to fattening pigs in the form of synthetic steroid esters. To tackle steroid misuse alternative approaches based on biological methods, able to investigate perturbations induced by these compounds at level of proteins, transcripts, metabolites is becoming recommendable. The aim of this work was to characterize by RNAseq coding mRNAs perturbations related to illicit administration of testosterone and nandrolone esters in fattening pigs. Twenty-seven clinically healthy 90-day-old pigs were randomly assigned to test (18 animals) and control (9 animals) groups. Nine of the eighteen animals from the test group were treated with an i.m. injections of 4 mg/kg b.w. of Sustanon (250 mg/ml). The other nine animals of the test group undergo i.m. injections of 5 mg/kg b.w. of Myodine (25 mg/ml). The animals were injected on day 4 after the start of the experiment and were euthanized on day 114 of the experiment. Liver samples were collected and stored in RNAlater solution for gene expression studies.

overall_design: Sustanon treatment (8 animals), Myodin treatment (8 animals), untreated (8 animals)

first: Benedetto

last: Alessandro

first: Kamil

last: Stastny

first: Nunzia

last: Giaccio

first: Marturella

last: Marianna

first: Biasibetti

last: Elena

first: Maddalena

last: Arigoni

first: Gili

last: Marilena

first: Pezzolato

last: Marzia

first: Martin

last: Faldyna

first: Bozzetta


title: Clostridioides difficile toxins deregulate tight junction proteins.

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: The Clostridioides difficile toxins TcdA and TcdB are responsible for diarrhea and colitis. The aim of this project was to explore the effects of the toxins on epithelial barrier function and the molecular mechanisms for diarrhea and inflammation. RNA-seq of toxin-treated intestinal cell monolayers was performed to describe the C. difficile-mediated effects. mRNA profiles from intestinale epithelial cells were generated by deep sequencing using Illumina NovaSeq 6000. This data provide the basis for subsequent upstream regulator analysis.

overall_design: mRNA profiles from 3 TcdA-treated, 3 TcdB-treated and 3 control cell monolayers were generated by paired-end sequencing using Illumina NovaSeq 6000.

first: Martina

last: Schneemann

first: Lucas

last: Heils

first: Verena

last: Moos

first: Dieter

last: Beule

first: Ralf

last: Gerhard

first: Jörg-Dieter

last: Schulzke

first: Roland

last: Bücker


title: ATAC sequencing of control siRNA and Zmiz1 siRNA treated Human dermal lymphatic endothelial cell (HDLECs)

city: new orleans

first: Rajan

last: K C

state: LA

address: 6602 Freret St

department: Cell and Molecular Biology

institute: Tulane University

summary:
Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profileepigenetic changes upon Zmiz1 knockdown using siRNA.
Methods: ATAC sequencing library was prepared as per manufacturer instruction (Active Motif, 53150). Briefly, intact nuclei were isolated from control and Zmiz1 siRNA transfected HDLECs. Samples were treated with a hyperactive Tn5 transposase which tag the target DNA with sequencing adapters and fragment the DNA simultaneously. Library was then quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA High Sensitivity Assay Kit (Agilent, 5067-4626). Validated samples were sequenced using the NextSeq1000/2000 P2 Reagents (100 Cycles) v3 (Illumina, 20046811) on a Nextseq1000/2000. Resulting sequencing data were analyzed using basepairtech ATAC-Seq pipeline (www.basepairtech.com). Briefly, sequenced reads were aligned to the human (hg19) reference genome using Bowtie2. ATAC-Seq peaks and differentially accessible regions were quantified using MACS2 and DESeq2.
Results: ATAC seq peaks analysis using MACS2 identified 576 peaks of which are mostly located in intergenic regions followed by introns. We found significantly reduced open chromatin near Prox1 loci upol loss of Zmiz1.
Conclusions: We identify Zmiz1 regulates chromatin accessibility near Prox1 genomic loci in lymphatic endothelial cells

overall_design: Control siRNA and Zmiz1 siRNA treated Human dermal lymphatic endothelial cell (HDLECs) followed by ATAC sequencing

first: Stryder

last: Meadows


title: RNA sequencing of control siRNA and Zmiz1 siRNA treated Human dermal lymphatic endothelial cell (HDLECs)

summary:
Purpose: Zinc Finger MIZ-Type Containing 1 (Zmiz1) is a member of the PIAS family of protein and function as a transcriptional coactivator of Notch, Androgen Receptor (AR), p53, Estrogen Receptor (ER), and Smad3/4 . Despite Zmiz1 critical role in angiogenesis, its role in lymphatic vasculature is unknown. Here, we use HDLECs cell line to profile transcriptional changes upon Zmiz1 knockdown using siRNA.
Methods: Total RNA was extracted from control and Zmiz1 siRNA transfected HDLECs using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732) following the manufacturer instructions. RNA concentration and RNA integrity (RIN) number were determined using Qubit RNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32852) and Bioanalyzer RNA 6000 Nano assay kit (Agilent, 5067-1511) respectively. RNA library was prepared using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505). Verified samples were sequenced using the NextSeq1000/2000 P2 Reagents (200 Cycles) v3 (Illumina, 20046812) on a Nextseq1000/2000. Sequenced reads were aligned to the human (hg19) reference genome with RNA-Seq alignment tool (STAR aligner). The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-Seq Differential Expression tool (version 1.0.1). Both alignment and differential expression analysis were performed using the tools in the illumina BaseSpace Sequence Hub.
Results: We found 2,228 differentially expressed genes of which 1,115 genes were upregulated while 1,113 genes were downregulated. Downregulated genes were enriched in biological processes such as lymph vessel development, cell migration and heart valve development.
Conclusions: We identify Zmiz1 regulates Prox1 in lymphatic endothelial cells

overall_design: Control siRNA and Zmiz1 siRNA treated Human dermal lymphatic endothelial cell (HDLECs) RNA sequencing

last: KC


title: Survival of E. coli O104:H4 Strain C227/11Φcu in a Soil Microenvironment is Associated with a Broad Time-Dependent Τranscriptional Activity of Metabolic Genes

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: Plant-associated outbreaks with enterohemorrhagic E. coli (EHEC) increased worldwide during the last decades. Agricultural soil is an important contamination source for edible plants. Thus, the survival of pathogenic E. coli in agricultural soil samples was analyzed in previous studies. Thereby, the influence of environmental factors and biotic factors was investigated. In the current study, genetic factors that influence the survival of enterohemorrhagic/enteroaggregative E. coli (EHEC/EAEC) O104:H4 strain C227/11Φcu in agricultural soil microenvironments was investigated. The strain was incubated in alluvial loam (AL) for up to 4 weeks and total RNA was prepared from samples taken immediately after inoculation (time point 0), after 1 week and after 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes. The two lists of differentially expressed genes were then subject to gene set enrichment of Gene ontology terms. After 1 week of incubation 36 gene sets were significantly enriched while only 38 gene sets were found to be enriched for the genes that were differentially expressed after 4 weeks. Especially stress response genes and genes of the primary metabolism such as carbohydrate and amino acid metabolism were concerned for both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment

overall_design: Comparative gene expression profiling analysis of RNA-seq data as a time series with  biological replicates

first: Jonathan

last: Währer

first: Katharina

last: Detert

first: Herbert

last: Schmidt


title: Gene expression profile at single cell level of CD45+ tumor-infiltrating immune cells in lung adenocarcinoma patients

city: Tokushima

first: atsushi

last: mitsuhashi

address: 3-18-15 Kuramoto-cho

department: Department of Respiratory Medicine and Rheumatology

institute: Tokushima university

summary: Fibrocytes are bone marrow-derived cells expressing fibroblast markers. We used single cell RNA sequencing (scRNA-seq) to analyze the tumor-infiltrating fibrocytes in the lung adenocarcinoma patients

overall_design: Tumor-infiltrating immune cells of lung adenocarcinoma patients were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of PE-Cy7-conjugated CD45 antibody and analyzed using scRNAseq.

first: Atsushi

last: Mitsuhashi

first: Kazuya

last: Koyama

first: Yasuhiko

last: Nishioka


title: MYC enhancer invasion promotes prognostic cancer type-specific gene programs through an epigenetic switch [ATAC-seq]

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC enhancer binding directly promotes cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNAPII, rather than regulating RNAPII pause-release as is the case at promoters. This is mediated by MYC-induced H3K9 demethylation by KDM3A and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. Thus, we propose that MYC drives prognostic cancer type-specific gene programs by promoting RNAPII recruitment to enhancers through induction of an epigenetic switch.

overall_design: ATAC-seq during MYC inhibition using KJ-PYR-9 in BT549 triple negative breast cancer cells

first: Rikke

last: Jensen

first: Tina

last: Ravnsborg

first: Christian

middle: D

last: Vaagenso

first: Maria

last: Madsen

first: Robin

last: Andersson

first: Ole

first: Rasmus

last: Siersbæk


title: MYC enhancer invasion promotes prognostic cancer type-specific gene programs through an epigenetic switch [CAGE-seq]

overall_design: CAGE-seq during MYC inhibition using KJ-PYR-9 in BT549 triple negative breast cancer cells


title: MYC enhancer invasion promotes prognostic cancer type-specific gene programs through an epigenetic switch [RNA-seq]

overall_design: RNA-seq during MYC inhibition using KJ-PYR-9 and MYC KD in BT549 triple negative breast cancer cells. RNA-seq during GCN5 inhibition using MB-3  in BT549 triple negative breast cancer cells.


title: Expression data from bronchial epithelial cell obtained before and after bronchial thermoplasty treatment in severe asthma

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

institute: University Hospital of Montpellier, Inserm

summary:
Biological mechanisms explaining asthma control improvement following bronchial thermoplasty are still not well understood.
We used a large-scale transcriptomic approach to evaluate the transcriptome of bronchial epithelial cell (BEC) obtained before and after bronchial thermoplasty treatment (BT).

overall_design: We compared gene expression profile from six bronchial epithelial cell obtained before and after bronchial thermoplasty treatment in severe asthma. Total RNA was extracted using the RNeasy mini kit (Qiagen) following the supplier’s recommendations. RNA concentration was measured using a Nanodrop and their integrity by using the Agilent 2100 Bioanalyzer (Agilent Technologies). Microarray analysis was performed on 500ng RNA samples with Affymetrix human ClariomTM S assay containing 280,809 probes (Affymetrix, Santa Clara, CA) at the McGill University and Genome Quebec Innovation Centre. RNA processing steps (RNA extraction, cDNA synthesis, cDNA fragmentation and labeling, and chip hybridization) were performed in parallel for each pair of epithelial samples to minimize technical variability. The raw image files (CEL format) generated from the analysis of the scanned image were used for the statistical analysis

first: Jamila

last: Chakir

first: Catherine

last: Laprise


title: Activation and presentation of SIINFEKL:Kb by lung CD11b+ and CD103+ DCs after intranasal SIIN-Q11.

city: Chicago

first: Anita

last: Chong

state: IL

address: 5841 South Maryland Avenue

institute: The University of Chicago

summary: To investigate whether differentially expressed genes induced by SIIN-Q11 were shared between lung CD11b+ and CD103+ DCs, we performed gene expression profiling analysis of lung CD11b+ and CD103+ DCs after intranasal SIIN-Q11.

overall_design: Comparative gene expression profiling analysis of lung CD11b+ and CD103+ DCs at 18 hours after I.N. SIIN-Q11

first: Youhui

last: Si

first: Yihan

last: Wang


title: Intranasal SIIN-Q11 induces shared transcriptional profiles in LN CD103+ and CD11b+ DCs

summary: To gain insights into the activation of LN DCs by intranasal SIIN-Q11, we conducted a transcriptional analysis on flow-sorted LN CD11b+ and CD103+ DCs

overall_design: Comparative gene expression profiling analysis of CD11b+ and CD103+ DCs isolated from mediastinal LN at 48 h after I.N. SIIN-Q11


title: Adenosine induced gene expression

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

summary: HCT116 cells are treated by adenosine (4 mM) for 6 hours and then using total RNA for sequencing analysis to evaluate adenosine induced gene expression.

overall_design: Genome-wide expression profiling of induced by adenosine treatment

first: Cheng'e

last: Tu


title: Effect of incubation in red, blue, and green monochromatic lights on gene expression in a species of Ostreococcus; RCC809

city: Umeå

first: Elizabeth

last: Sands

state: Västerbotten

address: Stipendiegränd 4B 0302

department: EMG

institute: Umea University

summary: To investigate responses to light quality in this eukaryotic phytoplankton species, replicates were incubated for 72 hours in monochromatic light at 4umol photons m-2 s-1. We then performed gene expression profiling analysis using data obtained from RNA-seq of biological replicates in three light quality conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ostreococcus RCC809 in red, green, and blue monochromatic lights

first: Sian

last: Davies

first: Isabelle

last: Carre


title: MDA5 guards against infection by surveying cellular RNA homeostasis [II]

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: MDA5 is an innate immune RNA sensor that detects a range of viruses. MDA5’s RNA agonists are not well defined. We used individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to study its ligands. Surprisingly, upon infection with SARS-CoV-2 or encephalomyocarditis virus (EMCV), MDA5 bound overwhelmingly to cellular RNAs. Many binding sites were intronic and proximal to Alu elements. MDA5-bound RNA was enriched in Poly(A) and Poly(U) motifs, some of which may form double-stranded RNA. In EMCV-infected cells, cytoplasmic levels of intron-containing unspliced transcripts were increased, suggesting dysregulation of splicing. Concomitantly, MDA5 iCLIP peaks were enriched in introns accumulating in the cytoplasm of infected cells. Moreover, rescue of splicing abrogated MDA5 activation. Finally, depletion of viral RNA from RNA extracted from infected cells did not diminish its MDA5-stimulatory potential. Taken together, MDA5 surveys RNA processing fidelity and detects splicing perturbation during infection, establishing a paradigm of innate immune ‘guarding’ for RNA sensors.

overall_design: Calu-3 cells were either left untreated, infected with SARS-CoV-2 (MOI = 0.1, 48 hr), or treated with human IFN beta (100 IU/ml, 6 hr) and cytoplasmic RNA was extracted to examine exon- and intron-level gene expression by RNA sequencing.

first: Natalia

middle: G

last: Sampaio

first: Linden

first: Paul

last: Hertzog

first: Jan

last: Rehwinkel


title: Gene expression profile at single cell level of primary human aortic endothelial cells (HAECs) under stimulation of pathophysiologic flows and antiproliferative therapies (rapamycin, paclitaxel)

city: Cambridge

first: Antonio Gabino

last: Salazar Martin

state: Massachusetts

address: 400 Main Street, Building E25-449

institute: Massachusetts Institute of Technology

summary: Endothelial cells (ECs) are by definition plastic and multipotent. EC plasticity was evaluated by stimulating EC to physiological and pathological stress coupled with antiproliferative therapies.

overall_design: HAECs were stimulated with unimodal stress (physiologic flow, 30 dynes/cm2; and pathologic/altered flow, 2.5dynes/cm2) for 72 hours. Also, HAECs were stimulated with bimodal stress: after 24 hours with either physiologic or pathologic flows, paclitaxel or rapamycin were added to flow systems. Cells were harvested and analyzed 48 hours after chemical stimulation.

first: Antonio

last: Salazar-Martin

first: Aditya

last: Kalluri

first: Travis

last: Hughes

first: Martin

last: Villanueva

first: Marc

last: Wadsworth II

first: Tyler

last: Dao

first: Mercedes

last: Balcells

first: Alex

last: Shalek

first: Elazer

middle: R

last: Edelman


title: Transcriptional profiling by RNA-seq in Dbx2-overexpressing cultures of adult neural progenitors

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: In selected tissutal niches of the adult mouse brain, such as the subventricular zone (SVZ) underlying the lateral ventricles, neurogenesis persists thanks to a population of quiescent neural stem cells, which can be activated (aNSCs) by extrinsic stimuli to initiate proliferation and generate a neurogenic lineage consisting of transit amplifying progenitors (TAPs), neuroblasts (NBs) and newborn neurons. This process is markedly reduced during aging, which might contribute to the cognitive decline of elderly subjects. Recent studies suggest that the aged niche environment may decrease the pool of proliferating neural/stem progenitor cells (NSPCs), and hence adult neurogenesis, by causing transcriptomic changes that favour NSC quiescence over activation. The transcription factors that mediate these changes, however, remain largely unclear. We previously found that the homeobox gene Dbx2 is upregulated in NSPCs of the aged mouse SVZ and can inhibit the growth of young adult NSPC cultures. Here, we show that Dbx2 expression is downregulated by Epidermal Growth Factor Receptor signalling, which promotes NSPC proliferation and decreases in the aged SVZ. By means of transgenic NSPC lines, we also show that Dbx2 inhibits NSPC proliferation by hindering the G1/S and the G2/M transition. Furthermore, we exploit RNA sequencing of transgenic NSPCs to elucidate the transcriptional networks modulated by Dbx2. Among the top hits, we report the downregulation of several gene categories implicated in cell cycle progression. Accordingly, we find that Dbx2 function is negatively correlated with the transcriptional signatures of proliferative NSPCs (aNSCs, TAPs and early NBs). Altogether, these results point to Dbx2 as a potential molecular node relaying the extracellular anti-neurogenic input of the aged niche to the NSPC transcriptome.

overall_design: mRNA profiles of transgenic NSPC lines with constitutive expression of a Dbx2 transgene, eight biological replicates for each experimental group.

first: Andrea

last: Giuliani

first: Paola

middle: S

last: Nisi

first: Mario

last: Fiore

first: Stefano

last: Biagioni

first: Rodolfo

last: Negri

first: Peter

last: Rugg-Gunn

first: Emanuele

last: Cacci

first: Giuseppe

last: Lupo


title: A primate-specific ELOA3 gene cluster augments sensitivity to BET bromodomain inhibition

last: Morgan

address: 303 East Superior St, SQI 7-511

institute: Northwestern University

summary: We have identified a cluster of ELOA3 gene homologs that are activated upon treatment with BET bromodomain inhibitors and mediate sensitivity to BET inhibition.

overall_design: We have performed ChIP-seq for ELOA3, RNA polymerase II (RNAPII) and other transcription elongation factors. In addition we have performed RNA-sequencing in ELOA3 loss-of-function and gain-of-function experiments.

first: Ali

last: Shilatifard


title: MDA5 guards against infection by surveying cellular RNA homeostasis [I]

first: Jamie

last: Gearing

overall_design: THP-1 cells (IRF3 knock out) were treated with 10 ng/ml PMA for 24 hr, and either left untreated, infected with EMCV (MOI = 2, 20 hr), or treated with human IFN beta (100 IU/ml, 6 hr) and cytoplasmic RNA was extracted to examine exon- and intron-level gene expression by RNA sequencing.

first: Natalia

last: Sampaio

first: Linden

first: Paul

last: Hertzog

first: Jan

last: Rehwinkel


title: Function of YAP in glucose deprivation-induced gene expression

city: shanghai

first: Yongfeng

last: Liu

summary: Knockdown of YAP in HCT116 cells by lentivirus-mediated shRNA, and after glucose deprivation treatment using total RNA for sequencing analysis to evaluate the function of YAP in glucose deprivation induced gene expression.

overall_design: Genome-wide expression profiling of induced by glucose deprivation with or without YAP interference

first: Cheng'e

last: Tu