title: Defining the fetal gene program at single cell resolution in dilated cardiomyopathy.

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

institute: Murdoch Children's Research Institute

summary: It is hypothesized that the postnatal heart adopts a fetal-like transcriptional state in response to cardiac stress. Here, we analyse the transcriptome of 74,451 nuclei from fetal, non-diseased and early-onset DCM samples, which revealed 7 broad cell clusters across fetal, ND and DCM samples. We find that there are no statistically significant shifts in cellular composition between DCM and ND hearts. Also, pseudo-bulk profiling revealed that transcriptional pathways perturbed in DCM are predominantly associated with cardiomyocytes, fibroblasts and immune cells. We advance the hypothesis that only a small subset (<10%) of fetal genes is re-engaged in both cardiomyocyte and cardiac fibroblast of DCM. This study provides a framework to identify critical gene expression networks that underpin disease pathogenesis independent of genetic aetiology.

overall_design: 10x Chromium single nuclei sequencing (snRNA-seq) profiles of apical left ventricle tissue from fetal (19-20 weeks, n=3; 27,760 nuclei), non-diseased (ND; 4-14 years, n=3; 16,964 nuclei) and early-onset DCM samples (5-10 years, n=4; 32,712 nuclei)

first: Choon

last: Sim

first: Neda

last: Mehdiabadi


title: Single-cell RNA-seq of HeLa S3 cell line

status: Public on Oct 12 2022

city: beijing

first: Ying

last: Chen

state: chaoyang

address: No.1 West Beichen Road

country: China

institute: institute of genetics and developmental biology

type: Expression profiling by high throughput sequencing

summary: We performed single cell RNA-seq to obtain transcriptomes of cells through the cell cycle

overall_design: Generating single-cell RNA-seq of HeLa cells

first: Wenfeng

last: Qian


title: Microarray analysis of serum microRNAs for the detection of urothelial cancer and for the elucidation of cancer development mechanisms

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

summary: Selected 12 miRNAs have diagnostic performance of urothelial cancer.

overall_design: Serum microRNA profiles of 182 samples, which consist of 126 urothelial cancers (BCa: 106 samples; UTUC: 14 samples; UTUC with BCa: 6 samples) , 50 non-cancer control including 20 DM patients

first: Fumihiko

last: Urabe

first: Juntaro

last: Matsuzaki

first: Fumitaka

last: Takeshita

first: Takeshi

last: Kishida

first: Takahiro

last: Ochiya

first: Kotaro

last: Hirai


title: CRISPR/Cas9-induced structural variations expand in T lymphocytes in vivo

city: Beijing

first: Jinchun

last: Wu

address: No. 5, Yiheyuan street

institute: Peking University

summary: CRISPR/Cas9 has been adapted to disrupt endogenous genes in adoptive T-lymphocyte therapy to prevent graft-versus-host disease. However, genome editing also generates prevalent deleterious structural variations (SVs), including chromosomal translocations and large deletions, raising safety concerns about reinfused T cells. Here, we dynamically monitored the progression of SVs in a mouse model of T-cell receptor (TCR)-transgenic T-cell adoptive transfer, mimicking TCR T therapeutics. Remarkably, CRISPR/Cas9-induced SVs persist and undergo clonal expansion in vivo after three weeks or even two months, evidenced by high enrichment and low junctional diversity of identified SVs post infusion. Specifically, we detected 128 expanded translocations, with 20,615 as the highest number of amplicons. The identified SVs are stochastically selected among different individuals and show an inconspicuous locus preference. Moreover, viral DNA integrations are routinely detected in edited T cells and also undergo clonal expansion as SVs do. The persistent SVs and viral DNA integrations in the infused T cells may constantly threaten genome integrity, drawing immediate attention to the safety of CRISPR/Cas9-engineered T cells mediated immunotherapy.

overall_design: 26 Samples.

first: Ziye

last: Zou

first: Yang

last: Liu

first: Xuhao

first: Zhengrong

last: Zhangding

first: Mo

last: Xu

first: Jiazhi

last: Hu


title: The ColR/S two-component system is a conserved determinant of host association across Pseudomonas species

city: Vancouver

first: Chrisitna

middle: L

last: Wiesmann

state: British Columbia

address: 1365 - 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: The University of British Columbia

summary: Members of the bacterial genus Pseudomonas form associations with diverse hosts. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not host-specific, requirements for ColR-dependent genes.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas fluorescens

overall_design: P. fluorescens WCS365 and P. aeruginosa PAO1 wildtype and delta_colR mutants were grown in the rhizosphere or M9 minimal media. Comparative transcriptomics was performed to determine genotype and condition dependent tene expression.

first: Christina

first: Yue

last: Zhang


title: Endothelial senescence mediates hypoxia-induced vascular remodeling by modulating PDGFB expression

city: Milwaukee

first: Akiko

last: Mammoto

state: WI

address: 8701 Watertown Plank Road

country: USA

institute: Medical College of Wisconsin

summary: Uncontrolled accumulation of pulmonary artery smooth muscle cells (PASMC) to the non-muscularized distal pulmonary arterioles (PAs) is one of the major characteristics of pulmonary hypertension (PH). Cellular senescence contributes to aging and lung diseases associated with PH and links to PH progression. However, the mechanism by which cellular senescence controls vascular remodeling in PH is not fully understood. Here, we have demonstrated that endothelial senescence mediates PH pathology by increasing platelet-derived growth factor (PDGFB) expression. The levels of senescence markers p16INK4A and senescence-associated β-galactosidase (SA-β-gal) are higher in PA endothelial cells (ECs) isolated from IPAH patients compared to those from healthy individuals. Hypoxia-induced accumulation of α-smooth muscle actin (αSMA)-positive cells to the PAs is attenuated in p16INK4Afl/fl-Cdh5(PAC)-CreERT2 mice after tamoxifen induction. We have reported that endothelial TWIST1 mediates hypoxia-induced vascular remodeling by increasing PDGFB expression. Transcriptomic analyses of idiopathic pulmonary arterial hypertension (IPAH) patient lung ECs or hypoxia-induced mouse lung ECs reveal the alteration of senescence-related gene expression and interaction with TWIST1. Increases in the levels of PDGFB and TWIST1 in hypoxia-treated mouse lung ECs or IPAH patient lung ECs are attenuated by knocking down p16INK4A expression or treating with senolytic reagents. Knockdown of p16INK4A also suppresses accumulation of αSMA–positive cells to the supplemented ECs in the gel. Exosomes collected from hypoxia-treated mouse lung ECs stimulate SMC DNA synthesis and migration in vitro and in the gel implanted on the mouse lungs, while p16INK4A knockdown in ECs inhibits the effects. These results suggest that endothelial senescence controls αSMA–positive cell proliferation and migration in PH through TWIST1-PDGFB signaling.

overall_design: Mouse lung endothelial cells were isolated from C57Bl6J mouse lungs (8 week old male mice) 3 weeks after hypoxia and normoxia mouse lungs (n=3 per group, each n was pooled from 3 male mice) using anti-CD31 conjugated magnetic beads for transcriptome analysis.

first: Tadanori

first: Kathryn

last: Hendee

first: Priscilla

last: Kyi


title: Loss of the chromatin remodeler, ATRX, promotes aggressive features of osteosarcomas and activates NF-kB signaling and integrin receptor binding

city: Durham

first: Suzanne

middle: Bartholf

last: DeWitt

state: NC

address: 308 Research Dr.

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Osteosarcoma (OS) is a lethal disease with few known targeted therapies. Here we show that decreased ATRX expression is associated with more aggressive tumor cell phenotypes, including increased growth, migration, invasion, and metastasis.  These phenotypic changes correspond with activation of NF-κB signaling, extracellular matrix remodeling, increased integrin αvβ3 expression, and ETS family transcription factor binding.  However, this increased aggression substantially sensitizes ATRX-deficient OS cells to integrin signaling inhibition.  Thus, ATRX plays an important tumor suppression role in OS, and loss of function of this gene may underlie a new therapeutic vulnerability.  The relationship of ATRX expression with integrin binding, NF-κB activation, and ETS family transcription factor binding has not been noted in previous studies, but may impact other known diseases with ATRX loss, including other cancers and the ATR-X alpha thalassemia mental retardation syndrome.

overall_design: RNA-Seq and ATAC-Seq profiles of 143B human osteosarcomas cells stably transduced with either a non-silencing GFP shRNA or one of two independent shRNA constructs targeting ATRX.

middle: B

first: Sarah

middle: H

last: Plumlee

first: Hailey

last: Brighton

first: Dharshan

last: Sivaraj

first: E

middle: J

last: Martz

first: Maryam

last: Zand

first: Vardhman

last: Kumar

first: Maya

middle: U

last: Sheth

first: Warren

last: Floyd

first: Shyni

last: Varghese

first: Jianhua

last: Ruan

first: David

middle: G

last: Kirsch

first: Jason

middle: A

last: Somarelli

first: Ben

last: Alman

first: William

middle: C

last: Eward


title: Transcriptome analysis of Tregs (CD4+Foxp3+) and Tcons (CD4+Foxp3-) from spleen and CNS of naïve mice and at the peak of EAE

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

summary: Tregs and Tcons were isolated by flow cytometry from the spleen of naïve mice and from the spleen and central nervous system (brain + spinal cord) (CNS) of mice at the peak of experimental autoimmune encephalomyelitis (EAE) induced by immunization with MOG(35-55). Samples at EAE peak were collected at day 16-18 after immunization. Purity was >99.5%. Foxp3.eGFP mice (provided by A. Rudensky) were used to identify Tregs. A bin channel excluded CD11b+ cells during the sort. Mice were 6-10 weeks of age at the time of immunization. The goal was to identify genes differentially expressed between Tregs and Tcons from naive mice, and genes differentially expressed by these cells in the inflamed tissue (central nervous system) at the peak of the disease.

overall_design: The experiments include a total of 20 arrays, each corresponding to a distinct biological sample. There are 3 arrays (3 samples) for Tregs from the spleen of naïve mice, and 3 arrays (3 samples) for Tconvs from the spleen of naïve mice. There are 4 arrays (4 samples) for Tregs from the spleen of EAE mice, and 3 arrays (3 samples) for Tconvs from the spleen of EAE mice. There are 3 arrays (3 samples) for Tregs from the CNS of EAE mice, and 4 arrays (4 samples) for Tconvs from the CNS of EAE mice.

first: Simon

last: Fillatreau

first: Stephen

middle: M

last: Anderton

first: Richard

last: O'Connor

first: Luc

last: Jouneau


title: Sen1 and Rrm3 ensure permissive topological conditions for replication termination [ChIP-seq]

status: Public on Oct 11 2022

city: Milano

first: Mohamood Adhil

last: Mohammed Iqbal

state: Lombardia

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

summary: Replication forks terminate at TERs and telomeres. Forks that converge or encounter transcription generate topological stress. Combining genetic, genomic and imaging approaches we found that Rrm3hPif1 and Sen1hSenataxin helicases assist termination at TERs, Sen1 at telomeres.  rrm3 and sen1 are synthetic lethal, fail to terminate replication exhibiting lagging chromosomes and fragility at TERs and telomeres.  sen1 rrm3 build up RNA-DNA hybrids at TERs, sen1 accumulates RNPII at TERs and telomeres.  Double mutants exhibit X-shaped gapped or reversed converging forks. Rrm3 and Sen1 restrain Top1 and Top2 activities, preventing toxic accumulation of positive supercoil at TERs and telomeres. We suggest that Rrm3 and Sen1 coordinate the activities of fork-associated Top1 and Top2 with those of gene loop-associated Top1 and Top2 by preventing DNA and RNA polymerases slowing down when forks encounter transcription head-on or codirectionally, respectively. Hence Rrm3 and Sen1 are essential to generate permissive topological conditions for replication termination.

overall_design: RNA Pol II_Rpb1-ChIP-seq (S-phase)  and bTMP-seq

first: Ramveer

last: Choudhary

first: Mohamood

last: Adhil

first: Marco

last: Foiani


title: RNA-Seq in four pairs of human gastric cancer and matched adjacent normal tissue specimens

city: Nanjing

first: shouyu

last: wang

address: 22 Hankou Road

institute: Nanjing university medical school

type: Non-coding RNA profiling by high throughput sequencing

summary: Total RNA was extracted from human gastric cancer tissues (n=4) and matched adjacent normal tissues (n=4) . RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq 4000 platform was used to sequence the RNA samples for the subsequent generation of raw data. R package was utilized to select lncRNAs with significantly differential expression based on fold change  >2 or <1/2, p value <0.05 between human gastric cancer tissues and matched adjacent normal tissues, and the top 10 upregulated lncRNAs were selected for further study.

overall_design: LncRNA profiles of human gastric cancer and matched adjacent normal tissue specimens.

first: Shouyu

last: Wang


title: Characterization of the spectrum of trivalent VAV1 mutation-driven tumors using a gene-edited mouse model

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
VAV1 mutations have been recently found in peripheral T cell lymphoma and non-small cell lung cancer. To understand their pathogenic potential, we generated a gene-edited mouse model that expresses a Vav1 mutant protein that recapitulates the signaling alterations present the VAV1 mutant subclass most frequently found in tumors. We could not detect any overt tumorigenic process in those mice. However, the concurrent elimination of the Trp53 tumor suppressor gene in them drives T cell lymphomagenesis. This process represents an exacerbation of the normal functions that wild-type Vav1 plays in follicular helper T cells.
We also found that, in combination with an oncogenic Kras mutation, the Vav1 mutant version favors progression of non-small cell lung cancer. These data indicate that VAV1 mutations play critical, although highly cell typespecific roles in tumorigenesis. They also indicate that such functions are contingent on the mutational landscape of the tumors involved.

overall_design: Splenocytes from control (Trp53KI/KI) and lymphoma-bearing animals (Trp53KI/KI;Vav1DC/DC)

first: Javier

last: Robles-Valero

first: Lucía

last: Fernández-Nevado

first: Myriam

last: Cuadrado

first: L

middle: F

first: Isabel

last: Fernández-Pisonero

first: Antonio

last: Abad

first: Esther

last: Redín

first: Luis

last: Montuenga

first: Dionisio

last: Martín-Zanca

first: Anna

last: Bigas

first: Moises

last: Mallo

first: Mercedes

last: Dosil

first: Xosé

middle: R

last: Bustelo


title: Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear

city: La Jolla

first: Samuel

middle: Richard

last: Ward

state: CA

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

summary: Conditions affecting skeletal muscle, such as chronic rotator cuff tears, low back pain, dystrophies, and many others often share changes in muscle phenotype: intramuscular adipose and fibrotic tissue increase while contractile tissue is lost. The underlying changes in cell populations and cell ratios observed with these phenotypic changes complicate the interpretation of tissue-level transcriptional data. Novel single cell transcriptomics has limited capacity to address this problem because muscle fibers are too long to be engulfed in single cell droplets and single nuclei transcriptomics are complicated by muscle fibers’ multinucleation. Therefore, the goal of this project was to evaluate the potential and challenges of a spatial transcriptomics technology to add dimensionality to transcriptional data in an attempt to better understand regional cellular activity in heterogeneous skeletal muscle tissue.

overall_design: Fresh and 6 years old snapfrozen healthy and tenotomized rabbit supraspinatus muscle sections were mounted on 10x Visium slides

first: Severin

last: Ruoss

first: Mary

last: Esparza

first: Laura

middle: S

last: Vasquez-Bolanos

first: Chanond

last: Nasamran

first: Kathleen

last: Fisch

first: Adam

last: Engler


title: Fractionated irradiation of breast cancer cells rewires a gene regulatory circuit towards a treatment-resistant stemness phenotype

city: Antwerpen

first: Bart

last: Cuypers

state: Antwerp

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: Adrem Data Lab

summary: Radiotherapy is a potent component of the standard of care for breast cancer. However, surviving radioresistant cells can repopulate following treatment and provoke relapse. Better understanding of the molecular mechanisms of radiation resistance may help improve treatment of radioresistant tumours. To emulate radiation therapy at the cellular level, we exposed MCF7 breast cancer cells to daily radiation doses of 2 Gy up to an accumulated dose of 20 Gy. Fractionally irradiated cells (FIR20) displayed increased clonogenic survival and population doubling time as compared to age-matched sham-irradiated cells and untreated, parental MCF7 cells. RNA-sequencing revealed a core signature of 229 mRNAs and 7 circRNAs significantly altered in the FIR20 cells. The FIR20 cell transcriptome overlapped significantly with canonical radiation signatures, and demonstrated a remarkable commonality with radiation and endocrine therapy resistance expression profiles, suggesting crosstalk between both acquired resistance pathways. Using predictive analyses and functional enrichment, we identified a gene-regulatory network of circRNA and mRNA that promotes stemness and inflammatory signaling in FIR20 cells. We propose that these phenotypic traits render breast cancer cells more radioresistant and may therefore serve as potential modules for combination therapies.

overall_design: Linear and circular RNA profiles of Fractionally irraditated MCF7 culture cells compared to the parental and control lines.

first: Auchi

last: Inalegwu

first: Jürgen

last: Claesen

first: Ann

last: Janssen

first: Sarah

last: Baatout

first: Kris

last: Laukens

first: Winnok

last: De Vos

first: Roel

last: Quintens


title: Analysis of gene expression (RNAseq) from Tp53/Pten DKO and Pten KO  tumors 5 months post-castration

city: Chicago

first: Young

last: Yoo

state: IL

address: 303 E Superior St

institute: Northwestern University Feinberg School of Medicine

summary: The TP53 tumor suppressor is frequently altered in lethal, castration-resistant prostate cancer (CRPC). However, to date there are no effective treatments that specifically target TP53 alterations. Using transcriptomic and metabolomic analyses, we show here that TP53-altered prostate cancer (PCa) exhibits an increased dependency on asparagine and overexpresses asparagine synthetase (ASNS, the enzyme catalyzing the synthesis of asparagine). Mechanistically, loss/mutation of TP53 transcriptionally activate ASNS expression, directly as well as via ATF4, driving de novo asparagine biosynthesis to support CRPC growth. TP53-altered CRPC cells are sensitive to asparagine restriction by knockdown of ASNS and L-asparaginase treatment to deplete the intracellular and extracellular sources of asparagine respectively. This effect was rescued by asparagine addition. Notably, pharmacological inhibition of intracellular asparagine biosynthesis using a glutaminase (GLS) inhibitor and depletion of extracellular asparagine with L-asparaginase significantly reduced asparagine production and effectively impaired CRPC growth. This study highlights the significance of ASNS-mediated metabolic adaptation as a synthetic vulnerability in CRPC with TP53 alterations, providing a rationale for co-targeting intracellular and extracellular asparagine production to treat these lethal prostate cancers.

overall_design: Expression profiling by high throughput sequencing

first: Sarki

last: Abdulkadir


title: Screening of differentially expressed microRNAs and target genes in two potato varieties under nitrogen stress

city: Changchun

first: yue

last: lu

state: Jilin Province

address: Xincheng Street

department: College of Horticulture

institute: Jilin Agricultural University

summary:
Background: A reasonable supply of nitrogen (N) fertilizer is essential for obtaining high-quality, high-level, and stable potato yields, and an improvement in the N utilization efficiency can effectively reduce N fertilizer use. It is important to use accurate, straightforward, and efficient transgenic breeding techniques for the identification of genes that can improve nitrogen use efficiency, thus enabling us to achieve the ultimate goal of breeding N-efficient potato varieties. In recent years, some of the mechanisms of miRNAs have been elucidated via the analysis of the correlation between the expression levels of potato miRNA target genes and regulated genes under conditions of stress, but the role of miRNAs in the inhibition/expression of key genes regulating N metabolism under N stress is still unclear. Our study aimed to identify the role played by specific enzymes and miRNAs in the responses of plants to N stress.
Results: The roots and leaves of the N-efficient potato variety, Yanshu4 ("Y"), and N-inefficient potato variety, Atlantic ("D"), were collected at the seedling and budding stages after they were exposed to different N fertilizer treatments. The miRNAs expressed differentially under the two types of N stress and their corresponding target genes were first predicted using miRNA and degradome analysis. Then, quantitative polymerase chain reaction (qRT-PCR) was performed to verify the expression of differential miRNAs that were closely related to N metabolism. Finally, the shearing relationship between stu-miR396-5p and its target gene StNiR was determined by analyzing luciferase activity levels. The results showed that NiR activity increased significantly with an increase in the applied N levels from the seedling stage to the budding stage, and NiR responded significantly to different N treatments. miRNA sequencing enabled us to predict 48 families with conserved miRNAs that were mainly involved in N metabolism, carbon metabolism, and amino acid biosynthesis. The differences in the expression of the following miRNAs were identified via screening (high expression levels and P < 0.05): stu-miR396-5p, stu-miR408b-3p_R-1, stu-miR3627-3p, stu-miR482a-3p, stu-miR8036-3p, stu-miR482a-5p, stu-miR827-5p, stu-miR156a_L-1, stu-miR827-3p, stu-miR172b-5p, stu-miR6022-p3_7, stu-miR398a-5p, and stu-miR166c-5p_L-3. Degradome analysis showed that most miRNAs had many-to-many relationships with target genes. The main target genes involved in N metabolism were NiR, NiR1, NRT2.5, and NRT2.7. qRT-PCR analysis showed that there were significant differences in the expression levels of stu-miR396-5p, stu-miR8036-3p, and stu-miR482a-3p in the leaves and roots of the Yanshu4 and Atlantic varieties at the seedling and budding stages under conditions that involved no N and excessive N application; the expression of these miRNAs was induced in response to N stress. The correlation between the differential expression of stu-miR396-5p and its corresponding target gene NiR was further verified by determining the luciferase activity level and was found to be strongly negative.
Conclusion: The activity of NiR was significantly positively correlated with N application from the seedling to the budding stage. Differential miRNAs and target genes showed a many-to-many relationship with each other. The expression of stu-miR396-5p, stu-miR482a-3p, and stu-miR8036-3p in the roots and leaves of the Yanshu4 and Atlantic varieties at the seedling and budding stages was notably different under two types of N stress. Under two types of N stress, stu-miR396-5p was down-regulated in Yanshu4 in the seedling-stage and shoot-stage roots, and up-regulated in seedling-stage roots and shoot-stage leaves; stu-miR482a-3p was up-regulated in the seedling and shoot stages. The expression of stu-miR8036-3p was up-regulated in the leaves and roots at the seedling and budding stages, and down-regulated in roots under both types of N stress. The gene expressing the key enzyme involved in N metabolism, StNiR, and the stu-miR396-5p luciferase assay reporter gene had a strong regulatory relationship with each other. This study provides candidate miRNAs related to nitrogen metabolism and highlights that differential miRNAs play a key role in nitrogen stress in potato, providing insights for future research on miRNAs and their target genes in nitrogen metabolic pathways and breeding nitrogen-efficient potatoes.

overall_design: miRNA-sequencing analysis was performed on an Illumina Hiseq 2500 (LC Sciences, USA) following the vendor's recommended protocol

first: Yue

last: Lu

first: Zhijun

last: Han


title: Whole cell response to receptor stimulation involves many deep and distributed subcellular biochemical processes

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: To identify subcellular processes that enable a whole cell response, we stimulated Neuro 2A cells with the cannabinoid receptor agonist HU210 that triggers neurite outgrowth. After 4 different stimulation periods we harvest the cells and subjected them to bulk RNAseq. Differentially expressed genes after each stimulation time were subjected to dynamic and standard enrichment analysis using the Molecular Biology of the Cell Ontology. We predicted the involvement of multiple canonical subcellular processes (SCPs) . Using siRNA ablation experiments of representative SCP genes we documented the involvement of the predicted SCPs in neurite outgrowth.

overall_design: Neuro 2A cells were treated with HU210 or drug-free DMSO for 4 different timeperiods, yielding 8 different conditions. 2 to 3 independent experiments of each condition were pooled to generate 8 different samples.

first: Mustafa

last: Siddiq

first: Arjun

last: Yadaw

first: Rosa

middle: E

last: Tolentino

first: Vera

last: Rabinovich

first: Gomathi

last: Jayaraman

first: Mohit

last: Jain

first: Tong

last: Liu

first: Hong

last: Li

first: Yuguang

last: Xiong

first: Joseph

last: Goldfarb

first: Ravi

last: Iyengar


title: Sen1 and Rrm3 ensure permissive topological conditions for replication termination [ChIP-chip]

first: Mohamood Adhil

last: Mohammed Iqbal

type: Genome binding/occupancy profiling by genome tiling array

overall_design: G2/M arrested Yeast cells, BrdU-Chip data and DRIP-Chip (RNA-DNA hybrids) S-phase cell cycle

first: Ramveer

last: Choudhary

first: Mohamood

last: Adhil

first: Marco

last: Foiani


title: Sen1 and Rrm3 ensure permissive topological conditions for replication termination

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

overall_design: Refer to individual Series


title: Hypothalamus-specific NSCs derived from human brain organoids ameliorate age-associated dysfunction upon transplantation into aged mouse hypothalamus [human bulk RNAseq]

city: Seoul

first: Yanuar

middle: Alan

last: Sulistio

address: Wangsimni-ro 222

department: Biomedical Science

country: South Korea

institute: Hanyang University

summary: The hypothalamus is the brain region that regulates systemic body metabolism and multiple functions in other brain regions. In adult mice, the hypothalamus harbors neural stem/precursor cell (NSC)-like cells. Along with the dysregulation of body metabolism and physiology that occurs during aging, the NSC population in the hypothalamus declines with age. Here, we introduce a novel protocol that yields scalable and storable hypothalamus-specific NSCs (htNSCs) from hypothalamus-like organoids derived from human pluripotent stem cells (hPSCs). Implanting htNSCs into the medio-basal hypothalami of aged mice conspicuously ameliorated age-related declines in metabolic fitness, physical capacity, and cognitive function and produced corresponding histologic changes in various body tissues. Single transcriptome and immunohistochemical analyses of the grafted hypothalamic tissues showed that the anti-aging effects were attained by correcting glial NF-κB, TNFα, and NLRP3 inflammasome pathways. Collectively, our findings support the potential of anti- or healthy aging therapies that target htNSCs and hypothalamic inflammation.

overall_design: Comparing transcriptome of hPSC and hPSC-derived hypothalamic neural stem cell

first: Kelvin

last: Pieknell

first: Sang-Hun

last: Lee


title: EVI1 drives leukemogenesis through aberrant activation of ERG

city: Vienna

first: Florian

last: Andersch

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Institute of Molecular Pathology

summary: Chromosomal rearrangements involving EVI1 (MECOM) define a subtype of acute myeloid leukemia (AML) that is associated with a two-year survival rate of <10%. Gene regulatory functions of EVI1 are largely elusive and no targeted therapeutics exist. We developed experimentally tractable murine and human leukemia models that recapitulate phenotypic and transcriptional features of EVI1-rearranged AML and enable large-scale loss-of-function screens. We characterize EVI1-controlled transcriptional programs in cell culture and in vivo, perform CRISPR screens and identify the ETS-related transcription factor ERG as the only gene that is specifically required for EVI1-driven AML. ERG is transcriptionally activated by EVI1 and overexpressed in EVI1-rearranged AML patients. ERG suppression selectively induces terminal differentiation of leukemia cells. EVI1 becomes dispensable for leukemia cells upon ectopic expression of ERG, indicating that key functions of EVI1 are mediated through aberrant activation of ERG. Interfering with this regulatory axis may therefore provide new entry points for rational therapies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq of leukemia cells derived from mouse models driven by DOX-regulatable or constitutive RUNX1/EVI1, and NRAS(G12D) upon DOX treatment of mice (31848-31861). Quant-seq of in-vitro-cultured murine leukemia cells driven by constitutive RUNX1/EVI1  and NRAS(G12D) upon knockdown of RUNX1/EVI1 compared to ctrl (160665-160670). Quant-seq of in-vitro-cultured human AML cells (HNT-34) driven by EVI1 upon knockdown of EVI1 compared to ctrl (61648-61653). Quant-seq of in-vitro-cultured murine leukemia cells driven by constitutive RUNX1/EVI1, NRAS(G12D) upon knockdown of EVI1 in the presence or absence of ectopic ERG expression (160677-160688). ATAC-seq of murine leukemia cells driven by RUNX1/EVI1, NRAS(G12D) upon knockdown of RUNX1/EVI1 compared to ctrl (162167, 162169)

first: Johannes

last: Schmoellerl

first: Ines

last: Barbosa

first: Martina

last: Minnich

first: Leonie

last: Smeenk

first: Marije

last: Havermans

first: Thomas

last: Eder

first: Tobias

last: Neumann

first: Julian

last: Jude

first: Michaela

last: Fellner

first: Anja

last: Ebert

first: Monika

last: Steininger

first: Ruud

last: Delwel

last: Grebien

last: Zuber


title: Transcriptomic analysis of ETV2-overexpressing human dental pulp stem cells

city: Jinan

first: Jing

last: Li

address: No. 44-1 Wenhua Road West

institute: Shandong University

summary: To better understand the global responses of DPSCs to ETV2 overexpression after osteogenic induction, we performed a genome-wide transcriptome analysis by RNA-sequencing technology to determine the global changes on gene expression level

overall_design: DPSCs derived from the three different donors were infected with ETV2-overexpressing lentiviral particles or control lentiviral particles. RNA samples were harvested after 10 days of osteogenic differentiation.

first: Jianguang

last: Xu

first: Jun

last: Zhang


title: Muscle injury induces a transient senescence-like state that is required for myofiber growth during muscle regeneration

city: Halifax

first: Adam

last: Johnston

state: NS

address: 1344 Summer Street

department: Medical Neuroscience

institute: Dalhousie University

summary: Cellular senescence is the irreversible arrest of normally dividing cells and is driven by the cell cycle inhibitors Cdkn2a, Cdkn1a, and Trp53. Senescent cells are implicated in chronic diseases and tissue repair through their increased secretion of proinflammatory factors known as the senescence-associated secretory phenotype (SASP). Here, we use spatial transcriptomics and single-cell RNA sequencing (scRNAseq) to demonstrate that cells displaying senescent characteristics are “transiently" present within regenerating skeletal muscle and within the muscles of D2-mdx mice, a model of Muscular Dystrophy. Following injury, multiple cell types including macrophages and fibro-adipogenic progenitors (FAPs) upregulate senescent features such as senescence pathway genes, SASP factors, and senescence-associated beta-gal (SA-β-gal) activity. Importantly, when these cells  were removed with ABT-263, a senolytic compound, satellite cells are reduced, and muscle fibers were impaired in growth and myonuclear accretion.

overall_design: Tibialis anterior muscle were collected from C57BL/6 mice 5 days post-CTX or PBS injection (n = 5 mice for each group) and then pooled following dissociation into single cells. Single-cell RNA-sequencing (scRNA-seq) was performed using 10x Genomics Chromium Single Cell 3' platform (v3).

first: Laura

middle: V

last: Young

first: Griffen

last: Wakelin

middle: P


title: Loss of TGFβ signaling in the perichondrium drives longitudinal bone overgrowth in mice with Marfan syndrome

first: Jens

last: Hansen

summary: The goal of this study is to define the main tissue and mechanism implicated in the long bone overgrowth phenotype in mice with Marfan syndrome

overall_design: RNAsequencing of perichondrium microdissected from WT and Fbn1Scx-/- mice

first: Lauriane

last: Sedes

first: Elisa

last: Wondimu

first: Brittany

last: Crockett

first: Anna

last: Cantalupo

first: Keiichi

last: Asano

first: Ravi

last: Iyengar

first: Daniel

last: Rifkin

first: Silvia

last: Smaldone

first: Francesco

last: Ramirez


title: Long non-coding RNA ENSMUST00000197208 promotes a shift in the Th17/Treg ratio via the P2X7R-NLRP3 inflammasome axis in collagen-induced arthritis

first: Pan

last: Yuting

address: Guangzhou Road

institute: Children’s Hospital of Nanjing Medical University

summary: This study aims to define the role of long non-coding RNA ENSMUST00000197208 (lncRNA ENSMUST00000197208) and the P2X7R-NLRP3 inflammasome axis in Th17/Treg cell differentiation, then clarifying the pathological significance and regulatory mechanisms in collagen-induced arthritis (CIA). We then performed gene expression profiling analysis using data obtained from RNA-seq of spleen cells of CIA mice and healthy mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for spleen cells  of CIA mice and healthy mice.

first: Yuting

last: Pan

first: Yuying

last: Fang

first: Haiguo

last: Yu

first: Zhidan

last: Fan


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function [ATAC-seq_ESC_MUT]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Tight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We find major changes in chromatin compaction and localization of cardiac genes already in Lmna−/−ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate, accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal, and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. Importantly, we observe divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which has distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. Thus, disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.

overall_design:
Conrol , Lmna H222P Homo, Lmna G609G Het and Lmna G609G Homo  E14 Tg(Nkx2-5-EmGFP)  mESCs were maintained on mitomycin treated mouse embryonic fibroblasts (MEF) in DMEM high glucose  supplemented with 15% fetal bovine serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 4.5 mg/ml D-glucose, 1% penicillin-streptomycin and 1000 U/ml leukemia inhibitory factor and were collected for ATAC-seq.
Please note that each ESC_Lmna_*_ATAC_mer_RPKM_norm_mm10.bw file was generated from both replicates and is linked to the corresponding *Rep1 sample records.

first: Yinuo

last: Wang

first: Julio

last: Cordero

first: Haojie

last: Shi


title: The RNF26/CBX7 axis modulates the TNF signaling pathway to promote cell proliferation and regulate sensitivity to TKIs in ccRCC

city: Wuhan

first: Haixin

state: Hubei Province

address: 1277, Jiefang Avenue

institute: Wuhan union hospital

summary: We performed CBX7 knockdown in renal cancer cells along with RNA sequencing. The expression profiling showed TNF signaling as a potential CBX7 target and the conditions were also verified in clinical samples.

overall_design: Overall design: RNA sequencing in 786-O cell lines with sh-control or sh-CBX7

first: H

first: X

last: Jin


title: Class IIa HDACs reprogram mitochondrial metabolism to inhibit apoptosis and ferroptosis in response to lipotoxicity

city: Waurn Ponds

first: Sean

last: McGee

state: VIC

address: 75 Pigdons Rd

country: Australia

institute: Deakin University

summary: Lipotoxicity, the accumulation of lipids in non-adipose tissues, alters the metabolic transcriptome and mitochondrial metabolism in skeletal muscle. The mechanisms involved remain poorly understood. Here we show that lipotoxicity increased histone deacetylase 4 (HDAC4) and histone deacetylase 5 (HDAC5), which reduced the expression of metabolic genes and oxidative metabolism in skeletal muscle. This metabolic reprogramming was linked with reduced expression of p53-dependent genes that mediate apoptosis and ferroptosis, which preserved cell viability in response to lipotoxicity. Mechanistically, impaired mitochondrial metabolism reduced acetylation of p53 at K120, a modification required for transcriptional activation of apoptosis, while redox drivers of ferroptosis were also reduced. Overexpression of loss-of-function HDAC4 and HDAC5 mutants in skeletal muscle of obese db/db mice enhanced oxidative capacity, increased apoptosis and ferroptosis and reduced muscle mass. This study identifies HDAC4 and HDAC5 as repressors of the oxidative state of skeletal muscle, and that this metabolic reprogramming, considered deleterious for normal metabolism, is critical to preserve muscle integrity in response to lipotoxicity.

overall_design: gene expression profiling

middle: L

first: Sheree

middle: D

last: Martin

first: Timothy

last: Connor

first: Andrew

last: Sanigorski

first: Kevin

last: McEwen

first: Darren

last: Henstridge

first: Brunda

last: Nijagal

first: David

last: De Souza

first: Dedreia

last: Tull

first: Peter

last: Meikle

first: Greg

last: Kowalski

first: Clinton

last: Bruce

first: Paul

last: Gregorevic

first: Mark

last: Febbraio

first: Fiona

last: Collier

first: Ken

last: Walder


title: Interplay of stress responses underlying the development of LMNA cardiomyopathy

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Mutations in the LMNA gene encoding nuclear lamins A/C cause a diverse array of tissue-selective diseases, with the heart being the most commonly affected organ. Despite progress in understanding the molecular perturbations emanating from LMNA mutations, an integrative understanding of the pathogenesis leading to cardiac dysfunction remains elusive. Using a novel cell-type specific Lmna deletion mouse model capable of translatome profiling, we found that cardiomyocyte-specific Lmna deletion in adult mice led to rapid cardiomyopathy with pathological remodeling. Prior to the onset of cardiac dysfunction, lamin A/C-depleted cardiomyocytes displayed nuclear envelope deterioration, disruption of the ER-golgi interface, and ER stress. Translatome profiling identified upregulation of Med25, a transcriptional co-factor involved in unfolded protein responses. Culturing Lmna-deleted cardiomyocytes in stiff hydrogels recapitulated these pathological features, confirming that cardiomyocyte-extrinsic factors contribute to the pathogenesis. Pharmacological activation of autophagy or modulation of ER stress significantly improved the cardiac function. These studies support a unified hypothesis wherein cardiomyopathy develops from autophagic impairment that exacerbates ER stress emanating from nuclear envelope deterioration.

overall_design: RNA-seq experiment of cardiomyocytes under control (vehicle) or treated (Tamoxifen) conditions

first: Kunal

last: Sikder

first: Jason

last: Choi


title: Inhibition of the SRC-kinase HCK restricts pancreatic cancer development and metastasis

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

summary: Pancreatic cancer is an aggressive disease with a low 5-year survival rate and poor response to therapy. Here, we demonstrate that inhibition of the myeloid-specific SRC family-kinase HCK impairs pancreatic tumor growth and metastasis by enhancing the infiltration of cytotoxic effector cells, stimulating the activation of myeloid cells, and by reducing the desmoplastic microenvironment. Genetic ablation of HCK also maximizes the therapeutic efficacy of chemotherapy and immunotherapy, and improves progression-free survival in mice. Collectively, our results demonstrate that targeting HCK can overcome barriers that limit responses to therapy, and provide a compelling rationale for HCK to be considered as a drug target to improve the responsiveness of pancreatic tumors to chemotherapy and/or immune checkpoint blockade.

overall_design: We performed bulk RNA sequencing on PDAC liver tumors of wild-type (WT) and HCK knock-out mice (n=5 mice per group) 3 weeks following intraplenic injection of KPC pancreatic cancer cells.

first: Ashleigh

last: Poh

first: Megan

last: O’Brien

last: Chisanga

first: Hong

last: He

last: Baloyan

first: Jasmin

last: Traichel

first: Christine

last: Djikstra

first: Lachlan

last: Whitehead

first: Louis

last: Boon

last: Parkin

first: Clifford

last: Lowell

first: Marina

last: Pajic

first: Mehrdad

last: Nikfarjam

first: Matthias

last: Ernst


title: Sexual dimorphism of early transcriptional reprogramming in degenerating peripheral nerves

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

summary: Transcriptional changes are distinct in female and male mice in the time course of peripheral nerve injury response. Here, we present sexually dimorphic transcriptome profiles established in the space of 24 h period after sciatic nerve axotomy.

overall_design: Compare transcriptomes of female and male mice after sciatic nerve axotomy to identify sexually dimorphic molecular signatures, upstream regulators and signaling pathways.

first: Veronica

last: Shubayev


title: Investigation of the molecular mechanisms of the synergy between erdafitinib and quisinostat

city: New Haven

first: Karen

last: Anderson

state: CT

address: 333 Cedar Street

department: Pharmacology

institute: Yale University

summary: We first verified that erdafitinib is synergistic with quisinostat in vitro and confirmed that the combinational treatment can significantly enhance the inhibition of tumor growth and prolong the survival in vivo for bladder cancers with FGFR3 fusions. Next, in order to understand the underlying molecular mechanisms of this synergy, we performed RNA-seq analysis. We revealed that quisinostat can concomitantly inhibit FGFR signaling with erdafitinib by suppressing the translation of FGFR3 fusions. In addition, quisinostat can also sensitize bladder cancer cells to erdafitinib by downregulating HDGF, which is a second mechanism of the synergy independent of FGFR signaling.

overall_design: We have three bladder cancer cell lines with FGFR3 fusions: RT4, RT112, and SW780. We treated all three cells with quisinostat or DMSO control. And then we extracted mRNA and performed RNA-seq analysis.

first: Zechen

last: Wang


title: The prostate stromal transcriptome and aggressive and lethal prostate cancer

city: Boston

first: Yinglu

last: Zhou

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: RNA sequencing (Illumina TruSeq Exome Capture) of 272 tumor-adjacent and 120 benign-adjacent macrodissected prostate stromal samples from 293 men from the Health Professionals Follow-up Study and Physicians’ Health Study.

overall_design: 272 tumor-adjacent and 120 benign-adjacent macrodissected prostate stromal samples from 293 male patient, with other pathological information collected, such as Gleason scores, lethal level and cribriform

first: Svitlana

last: Tyekucheva

first: Kathryn

last: Penney


title: mRNA-seq analysis of Caenorhabditis elegans starved L1 larvae with and without AMA-1/Pol II degradation in the soma and germ line during L1 arrest

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

summary: Whole starved L1 larvae were collected with and without AMA-1 degradation by the auxin-inducible degron (AID) system in the soma and germ line between 36 and 132 hours of starvation along with controls.

overall_design: 4 strains each collected at 3 time points/conditions during L1 starvation: 36 hr, 132 hr with auxin, and 132 hr with ethanol. For auxin samples, auxin was added at 36 hr. 4 biological replicates were collected for each strain and time point (48 samples total).

first: Rojin

last: Chitrakar

first: L

last: Baugh


title: Nrf2 Mediates RNA Splicing Through Physical Association with the Survival Of Motor Neuron (SMN) Complex and Transcriptional Activation of the SMN1 Gene In Non-Small Cell Lung Cancer

city: HANGZHOU

first: XIUWEN

last: TANG

address: YUHANGTONG ROAD

department: BIOCHEMISTRY AND GENETICS

institute: ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE

summary: The nuclear factor erythroid 2-like 2 (NFE2L2; NRF2) signal pathway is frequently deregulated in human cancers. The critical functions of NRF2 other than transcriptional activation in cancers remain largely unknown. Here, we uncovered a previously unrecognized role of Nrf2 in RNA splicing via regulating survival of motor neuron protein (SMN). Here, we performed next-generation high throughput global RNA-sequencing of siNrf2-C27 and siGFP-C5, which are stable NRF2-knockdown and control cell lines derived from A549 NSCLC cells, respectively To investigate whether NRF2 plays any role in RNA splicing.

overall_design: We performed next-generation high throughput global RNA-sequencing of siNrf2-C27 and siGFP-C5, which are stable NRF2-knockdown and control cell lines derived from A549 NSCLC cells, respectively as well as HeLa cells, NRF2-knockdown HeLa cells (HeLa#B30CRNrf2 ), NRF2 overexpression of NRF2-knockdown HeLa cells (HeLa#B30CRNrf2-NRF2), and SMN overexpression of NRF2-knockdown HeLa cells (HeLa#B30CRNrf2-SMN).

first: Tang

last: Xiuwen

first: Ahmed

last: Hammad


title: Alternative somatic and germline gene-regulatory strategies during starvation-induced developmental arrest

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

overall_design: Refer to individual Series


title: mRNA-seq time series of Caenorhabditis elegans L1 starvation

summary: Whole starved L1 larvae were collected at twelve time points spanning from hatching to death.

overall_design: Four biological replicates were collected for each of 12 time points (-2, 0, 2, 4, 6, 9, 12, 24, 48, 96, 192, 288 hours) throughout L1 starvation.


title: TRH1/KUP4 is a coupler of auxin-mediated root system architecture responses in Arabidopsis

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

summary: TRH1, also classified as KUP4, belongs in the family of plant HAK/KUP/KT (High-Affinity K+/ K+ UPtake/ K+ Transporter) transporters, homologous to the bacterial KUP and fungal HAK transporters, which most likely as K+/H+ exchangers function as electrochemical potential-driven transporters. Arabidopsis contains 13 genes, classified into five major clades (Clades I-V). Members of Clade II, including TRH1, are associated with developmental processes. Targeted expression experiments demonstrated that K+ transporter TRH1 is a coupler of two auxin-mediated developmental processes that determine Root System Architecture, root hair morphogenesis and root gravitropism. Targeting TRH1 expression in central cylinder cells that coincide with the acropetal route of auxin transport, rescued trh1 root agravitropism, whereas positional TRH1 expression in peripheral cell layers that define the basipetal route of auxin transport, restored trh1 root hair defects. To dissect the two auxin-mediated developmental responses, a transcriptome analysis was performed identifying the differentially expressed genes involved in either root bending or root hair development.

overall_design: For the transcriptome studies, ~1 mm sections of root tips from trh1, pPIN1::TRH1-YFP and pPIN2::TRH1-YFP transgenic lines were collected for RNA-Seq analysis. Total RNA was extracted using the Direct-zol RNA Miniprep (Zymo research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis. RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on BGISEQ-500 platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample.

first: Dimitris

last: Templalexis


title: RNA Ligase RTCB-mediated mRNA Alternative Splicing is Required for Mouse Oocyte Development and Maintenance

status: Public on Oct 10 2022

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: Intron splicing of the pre-mRNA is usually coupled with the transcription elongation catalyzed by RNA polymerase. However, recent large-scale mRNA sequencing showed that introns are still retained in 5-10% of mRNA, these introns are named as exitrons. They are deleted in some special cells or conditions to deal with developmental transition or cellular stress response. The role of this mechanism in mammalian female reproduction is elusive so far. We found that RNA terminal phosphate cyclase B (RTCB) mainly regulated splicing of these transcripts related to p-CDK1, DNA methylation and DNA damage repair. On the one hand, it regulated the recovery of oocyte meiosis by affecting CDK1 activation. On the other hand, it also regulated the developmental potential of oocytes by influencing splicing of DNA methylation and DNA damage repair-related mRNA. In addition, it could also play a crucial role in follicular development. Rtcb deletion resulted in the accumulation of these maternal mRNAs containing unspliced introns, and the decline of the overall level of transcripts. As a result, Rtcb-/- female are sterile. Our study highlights the important role of RTCB-regulated non-canonical alternative splicing in female reproduction.

overall_design: A total of 6 samples were analyzed in this study, including WT and Rtcb knock-out oocytes from fully-grown GV stage. Each biological samples has three replicates.

first: Junchao

last: Jiang

first: Hua

last: Zhang

first: Yunwen

last: Wu

first: Hengyu


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function [ATAC-seq_ESC]

first: Gergana

last: Dobreva

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs  were maintained on mitomycin treated mouse embryonic fibroblasts (MEF) in DMEM high glucose  supplemented with 15% fetal bovine serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 4.5 mg/ml D-glucose, 1% penicillin-streptomycin and 1000 U/ml leukemia inhibitory factor and collected for ATAC-seq.

first: Yinuo

first: Julio

last: Cordero

first: Adel

last: Elsherbiny

first: Linda

last: Kessler


title: ATAC-seq of antigen-specific CD8+ T cells from tumor draining LNs of melanoma bearing mice II

city: Chongqing

first: lilin

last: ye

address: Gaotanyan Street, Shapingba District

department: Institute of Immunology

institute: Third Military Medical University

summary: CD8+ T cell-mediated immune response plays a pivotal role in controlling tumor growth.However, within the tumor microenvironment (TME), prolonged antigen exposure, as well as immunosuppressive factors, drive infiltrated tumor-specific CD8+ T cells into a hyporesponsive state known as “exhaustion”. Notably, our current understanding of tumor-specific CD8+ T cells mainly comes from experiments focusing on tumor infiltrated T cells, less is known about those in tumor draining LNs. Hence, we profiled the chromosome accessibilities of antigen-specific CD8+ T cells from tumor draining LNs of melanoma bearing mice in this project, aiming to draw a comprehensive immune-atlas of tumor-specific CD8+ T cells during tumorigenesis.

overall_design: We performed ATAC-Seq on antigen specific CD44+CD8+ T cells (P14)  originated from TdLNs (tumor draining lymph nodes) of melanoma tumor model  at indicated timepoints post P14 cell transfer. Cells were sorted as described in cell sorting strategy. 50,000 sorted cells were used for tagmentation and library construction.

first: Qizhao

last: Huang

first: Lifan

last: Xu

first: Xia

first: Zhiming

last: Wang

first: Xiangyu

last: Chen


title: UV-B and UV-C irradiation trigger both common and distinctive signal perceptions and transmissions in Pinus tabuliformis Carr.

city: beijing

first: xu

last: jie

state: beijing

address: No. 35 Qinghua East Road, Haidian District

institute: Beijing Forestry University

summary: In plants, ultraviolet (UV)-light is an important driver for their growth and natural distribution and is also a valuable tool for manipulating their productivity as well as their biotic interactions. Understanding plant responses to different UV radiation is sparse, especially from a systems biology perspective and particularly for conifers. Here, we evaluated the physiological and transcriptomic responses to the short-term application of high-irradiance UV-B and UV-C waves on Pinus tabuliformis Carr., a major conifer in Northern China. By undertaking time-ordered gene co-expression network analyses and network comparisons incorporating physiological traits and gene expression variation, we uncovered communalities but also differences in P. tabuliformis responses to UV-B and UV-C. Both types of spectral bands caused a significant inhibition of photosynthesis and conversely improvement of antioxidant capacity, flavonoid production and signaling pathways related to stress resistance, indicating a clear switch from predominantly primary metabolism to enhanced defensive metabolism in pine. We isolated distinct subnetworks for photoreceptor-mediated signal transduction, maximum quantum efficiency of photosystem II (Fv/Fm) regulation and flavonoid biosynthesis in response to UV-B and UV-C irradiation. From these subnetworks, we further identified phototropins as potential important elements in both UV-B and UV-C signaling and, for the first time, reveal peptide hormones possibly involved in promoting flavonoid biosynthesis against UV-B, while these hormones seem not to be implicated in defense against UV-C exposure. The present study employed an effective strategy for disentangling the complex physiological and genetic regulatory mechanisms in a non-model plant species, and thus, provides a suitable reference for future functional evaluations and artificial UV-light mediated growing strategies in plant production.

overall_design: Pinus tabuliformis Raw sequence reads from UV-B and UV-C irradiation experiment

first: Jie

first: Jian-Feng

last: Mao


title: scRNA-seq of antigen-specific CD8+ T cells from tumor draining LN, TIL and PBMC of melanoma bearing mice

summary: CD8+ T cell-mediated immune response plays a pivotal role in controlling tumor growth.However, within the tumor microenvironment (TME), prolonged antigen exposure, as well as immunosuppressive factors, drive infiltrated tumor-specific CD8+ T cells into a hyporesponsive state known as “exhaustion”. These Tex cells are mainly characterized by the sustained and elevated expression of a series of inhibitory receptors as well as the hierarchical loss of effector functions. Further, the impaired proliferative capacity of exhausted CD8+ T cells results in decreasing numbers of tumor-specific T cells, such that the residual CD8+ T cells within the TME can barely provide sufficient protective immunity against tumor progression.  Thus,  the maintenance or reinforcement of intratumoral antigen-specific CD8+ T cells is indispensable for tumor repression. Here, we profiled the transcriptional signatures of antigen-specific CD8+ T cells from tumor draining LN, TIL and PBMC of melanoma bearing mice at single-cell level, aiming to draw a comprehensive immune-atlas of tumor-specific CD8 T cells during tumorigenesis.

overall_design: We performed single-cell RNA-sequencing (scRNA-seq) on antigen specific CD8+ T cells (P14) originated from TdLNs, TIL and PBMC of melanoma tumor model at day 16 (D16) post P14 cell transfer and set memory (P14, D200) T cells from acute LCMV infection as control.

first: Wei

last: Dong


title: Inhibiting L-type calcium channel promotes cardiomyocyte proliferation through activating canonical Wnt signaling pathway

city: Shanghai

first: Mengying

last: Feng

address: no. 67 Chifeng road, Yangpu district

department: School of Life Sciences and Technology

institute: Tongji University

summary: We performed RNA-Seq analysis of neoatal rat ventricular cardiomyocytes (NRVCs) and human pluripotent stem cells derived cardiomyocytes (hPSC-CMs) which were treated with Nimodipine (NM) to investigate the moleclular mechanism of inhibiting L-type calcium channel (LTCC) to promote cardiomyocyte proliferation.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: RNA-Seq analysis of NM treated NRVCs and hPSC-CMs for 12 hours, 3 replicates per group.

first: Hongjie

first: Ke

last: Wei


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function[RNA-seq_CPC]

first: Gergana

summary: Tight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We find major changes in chromatin compaction and localization of cardiac genes already in Lmna−/−ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate, accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal, and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. Importantly, we observe divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which has distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. Thus, disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs were differentiated by hanging drop method. Day6 cardiac progenitor cells (CPCs) were  FACS-sorted by Nkx2-5+ GFP expression and performed RNA-seq.

first: Yinuo


title: Aplysia californica (California sea hare) RNA sequencing from multiple tissues

city: St Augustine

first: Leonid

last: Moroz

state: FL

address: 9505 Ocean Shore Blvd

institute: University of Florida

summary:
The marine opisthobranch mollusk, Aplysia californica, is a powerful experimental system in cellular, molecular, and behavioral neuroscience as well as cell and evolutionary biology because of the distinctive organization of its nervous system, which makes it advantageous for cellular and comparative analysis of a variety of behaviors and learning and memory. Aplysia's large neurons allow examination of neuronal architecture of instinctive and learned behaviors at the level of single characterized cells and defined cellular compartments (e.g., synapses). As a result, many fundamental problems in neurobiology can be analyzed more effectively in Aplysias than in Drosophila, C. elegans, and vertebrates. In a larger sense work on Aplysia is synergistic with these other experimental systems. Here, we are sequencing the genome of Aplysia both to gain access to genomic mechanisms of basic neuronal and other functions and to study these mechanisms in real physiological time with single-neuron resolution.
The distinction of Aplysia as a neurobiological and cellular model system is due to the following: (1) Its nervous system has a relatively small number of nerve cells. (2) Many of these cells are large (sometimes gigantic, up to 1 mm in diameter). (3) As a result of their size, pigmentation, and position in the nervous system, many cells can easily be uniquely identified at the single cell level and can be reliably linked to the animal's behavior. (4) The cells provide enough messenger RNA to generate cDNA libraries from single cells. (5) These neurons can be isolated and cultured in vitro and they form circuits which can be explored in detail at molecular and cellular levels. (6) The animal generates a variety of behaviors, many of which can be specified in terms of their underlying circuitry. (7) Some of these behaviors can be modified by different forms of learning.
Aplysia are easy to rear in the laboratory from fertilized ova to mature adults and it is possible to obtain an inbred stock of reproducing animals. In 1995, the NIH established a National Resource Center for Aplysia at the University of Miami to meet the growing needs of the biomedical community. This Center supplies over 20,000 cultured Aplysia at all developmental stages annually to the research community throughout the world. This community consists of more than 100 laboratories and over a thousand investigators with overall research budgets of tens of millions of dollars annually. In addition to its value to the neurobiological community, Aplysia is also of interest from a comparative biological perspective. Aplysia is a free-living representative of Mollusca, the second largest animal phylum (after Arthropoda). Members of this phylum have received relatively little genetic study, even though they are of considerable significance for evolutionary and developmental biology and for basic and applied biomedical studies. Aplysia has a stable diploid genome consisting of 17 haploid chromosomes with highly polyploid central neurons. The genome size of about 850 million base pairs is typical for many molluscan species.
Expressed sequence tags (ESTs) have already been sequenced, including more than 50,000 unique sequences representing several thousand genes, from the central nervous system of Aplysia – see Moroz et al (2006) . These ESTs have revealed many signaling molecules and pathways, including their key receptors, kinases and substrate proteins, but many rare yet key genes (e.g., ionic channels) have escaped detection so far. To achieve a complete understanding of the biologically important genes and their regulatory elements, a careful annotation and analysis of the sequenced genome is analysis is required.
The Aplysia genome project will serve two major functions. First, it will be important for neuroscience by providing a critical resource for facilitating: (a) identification of all genes and regulatory regions of this valuable organism, (b) assembling microarrays and cDNA libraries for global expression studies, including those based on single neurons and their processes, and (c) gene function analysis by RNA interference screens. Second, the Aplysia genome will be important for comparative, developmental and evolutionary biology. Aplysia will serve as a complementary invertebrate/molluscan genomic model from the most diverse and second largest clade of bilaterally symmetrical animals. The Aplysia genome will promote studies of metazoan evolution, developmental biology, neuroscience, and human health, including identifying and validating therapeutic targets for human disorders that are related to aging, cancer, the central nervous system, as well as learning and memory mechanisms.

overall_design: This project is highly collaborative. The genome as well as several transcriptomes has been sequenced at the Broad Institute as part of the Aplysia genome consortium. Here the transcriptomes were used in comparative analysis for BioProject; PRJNA77701, SRA project; SRP009481. In addition several of our public SRA data was also included from SRA; SRP001185, SRP007384, and SRP000986.

first: Andrea

middle: B

last: Kohn

first: Peter

last: Williams

first: Emily

last: Dabe

first: Gabrielle

last: Winters

first: Caleb

middle: J

last: Bostwick

first: Yelena

last: Bobkova

first: Tatiana


title: Antigen-specific CD8+ T cells from tumor draining of melanoma bearing mice

first: lilin

last: ye


title: ATAC-seq of antigen-specific CD8+ T cells from tumor draining LNs of melanoma bearing mice

overall_design: We performed ATAC-Seq on antigen specific CD8+ T cells (P14) originated from TdLNs (tumor draining lymph nodes) of melanoma tumor model at indicated time points post P14 cell transfer.

first: Qizhao

last: Huang

first: Lifan

first: Xia

last: Wu

first: Zhiming

first: Xiangyu


title: Histological subtypes drive distinct prognostic immune signatures in classical Hodgkin lymphoma.

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

summary: Classical Hodgkin lymphoma (cHL) is a highly curable disease, with about 80% of patients cured using standard first-line chemotherapy. However, outcomes for relapsed/refractory patients re-main unfavorable and there is a critical lack of predictive biomarkers for early identification of these patients who may benefit from new therapeutic strategies. Here we evaluated the dynamic expression of 571 immune-related genes in a cohort of 42 cHL using NanoString technology. We identified a 19-genes immune signature predictive of relapse at the time of diagnosis, which was found to be strongly dependent on histological subtype. Moreover, comparative analyses be-tween paired diagnostic/relapsed biopsies of nodular sclerosis cHL showed 134 differentially expressed genes, highlighting an immune contexture shift at relapse not found in the mixed-cellularity subtype. Overall, these results strongly suggest that the predictive value of immune signature in cHL is influenced by histological subtype, a criterion that should be con-sidered when assessing new immunotherapy strategies.

overall_design: Sixty-six formalin fixed paraffin embedded (FFPE) cHL biopsies at diagnosis and/or at relapse were obtained from a total of 42 patients, including 30 r/r cHL patients and 12 non-r/r cHL patients. Thirty-five FFPE samples were available at diagnosis (n= 12 non-r/r cHL and n=23 r/r cHL) and FFPE paired diagnosis and relapse biopsies were available for 22/30 r/r cHL patients. Nodular sclerosis subtype was the most represented histological subtype in our series (n=24/42, 57.1%) followed by the mixed-cellularity subtype (n=15/42, 35.7%). Only two patients presented a lymphocyte-rich pattern (4.8%), and one patient displayed a lymphocyte-depleted pattern (2.4%). The average age at diagnosis of r/r patients was 30 years (ranging from 15y to 83y) and that of non-r/r patients was 31 years (ranging from 23y to 58y). Less than 25% (n=9/39) of cases were Epstein-Barr virus (EBV) positive. EBV status was unknown for 3 cases. Thirty-two (78%) patients, including 20/30 r/r patients and 12/12 non-r/r patients, had extensive disease at diagnosis (Ann Arbor stage III-IV). Of the 40 assessable patients, 30.9% (n=13) were treated with bleomycin, etoposide, doxoru-bicin, cyclophosphamide, vincristine, procarbazine and prednisone (BEACOPP) and 57.1% (n=24) received doxorubicin, bleomycin, vinblastine and dacarbazine (ABVD). The 3 remaining patients received alternative chemotherapy

first: Claire

last: Lamaison

first: Charlotte

last: Syrykh


title: Adenoviral based-vaccine promotes neoantigen specific CD8+ T cell stemness and tumor rejection

city: Candiolo

first: Luigia

last: Pace

address: Strada Provinciale, 142 -KM 3.95

institute: Italian Institute for Genomic Medicine

summary: Upon chronic antigen exposure, CD8+ T cells become exhausted acquiring a dysfunctional state correlated with the inability to control infection or tumor. In contrast to exhausted T cells, stem-like CD8+ T progenitors maintain the ability to promote and sustain effective immunity. Adenovirus (Ad) vectored vaccines encoding tumor neoantigens have been shown to eradicate large tumors when combined with anti-Programmed cell death protein 1 (αPD-1) in murine models, however the mechanisms and translational potential have not yet been elucidated. Here, we show that gorilla Ad vaccine targeting tumor neoepitopes enhance responses to αPD-1 therapy, by improving immunogenicity and anti-tumor efficacy. Single cell RNA-seq demonstrated that the combination of Ad vaccine and αPD-1 increased the number of murine polyfunctional neoantigen specific CD8+ T cells over αPD-1 monotherapy, with an accumulation of Tcf1+ stem-like progenitors in draining lymph nodes and effector CD8+T cells in tumors. Combined TCR sequencing analysis highlighted a broader spectrum of neoantigen specific CD8+ T cells upon vaccination compared to αPD-1 monotherapy. The translational relevance of these data is supported by results obtained in the first 12 patients with metastatic deficient mismatch repair (dMMR) tumors vaccinated with an Ad vaccine encoding shared neoantigens.  Expansion and diversification of TCRs was observed in post-treatment biopsies of patients with clinical response, as well as an increase in tumor infiltrating T cells with an effector memory signature. These findings indicate a promising mechanism to overcome resistance to PD-1 blockade, by promoting immunogenicity and broadening the spectrum and magnitude of neoantigen-specific T cells infiltrating tumors.

overall_design: Comparative gene expression profiling analysis of MC38 cells from lymph nodes or tumors of C57BL/6J mice.

first: Nadia

last: Brasu

first: Carlo

last: De Intinis

first: Valentina

last: Russo


title: Extracellular vesicles carrying HIV-1 Nef induce long-term hyperreactivity of myeloid cells [ATAC-Seq]

status: Public on Oct 09 2022

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I street NW, Ross Hall, Suite 731

institute: George Washington University

summary: A possible explanation for chronic inflammation in HIV-infected individuals treated with anti-retroviral therapy is hyperreactivity of myeloid cells due to a phenomenon called ‘trained immunity’. Here, we demonstrate that human monocyte-derived macrophages originating from monocytes initially treated with extracellular vesicles containing HIV-1 protein Nef (exNef), but differentiating in the absence of exNef, released increased levels of pro-inflammatory cytokines after lipopolysaccharide stimulation. This effect was associated with epigenetic changes related to inflammation and cholesterol metabolism pathways, upregulation of the lipid rafts, and was blocked by methyl-beta-cyclodextrin, statin, and by an inhibitor of the lipid raft-associated receptor IGF1R. Bone marrow-derived macrophages from exNef-injected mice, as well as from mice transplanted with bone marrow from exNef-injected animals, produced elevated levels of TNFalpha upon stimulation. These phenomena are consistent with exNef-induced trained immunity that may contribute to persistent inflammation and associated co-morbidities in HIV-infected individuals with undetectable HIV load.

overall_design: All analyzed samples are from primary human monocytes treated in vitro with EVs carrying (experimental samples) or not carrying (control samples) HIV-1 Nef. Cells were then differentiated into MDM for 6 days without EVs. MDM wre either used for ATAC-seq analysis, or stimulated with LPS and used for RNA-seq analysis. Replicates are included for some RNA-seq samples, no replicates for ATAC-seq samples.

first: Larisa

last: Dubrovsky

first: Michael

last: Bukrinsky


title: Gene expression in Drosophila melanogaster adults.

city: Thibodaux

first: Himanshu

middle: Shekhar

last: Raje

state: Louisiana

address: 906 East First Street

department: Biological Sciences

institute: Nicholls State University

summary: We performed RNA-seq on total RNA isolated from Drosophila adults and analyzed the data for TAHRE gag and pol ORF transcripts.

overall_design: Gene expression analysis using RNA-seq on a total RNA sample isolated from Drosophila adults.

first: Adella

last: Guidroz

first: Rachael

last: Henning


title: lncRNA expression signatures for stroke mice

city: Shijiazhuang

first: Wen

last: Cao

state: China

address: 215 Hepingxi Road Shijiazhuang, Hebei,China

institute: Second Hospital of Hebei Medical University

summary: To identify the overall impact of permanent ischemia injury on lncRNAs, we profile diﬀerentially expressed lncRNAs using microarray analysis in mouse brains subjected to permenant focal ischemia via electrocoagulation. At 24h after dMCAO injury, the animals were executed for microarray analysis of lncRNA expression.

overall_design: 8 mice including 4 stroke mice and 4 sham control were used for lncRNA microarry analysis.


title: Extracellular vesicles carrying HIV-1 Nef induce long-term hyperreactivity of myeloid cells

overall_design: Refer to individual Series


title: Extracellular vesicles carrying HIV-1 Nef induce long-term hyperreactivity of myeloid cells [RNA-Seq]

overall_design: All analyzed samples are from primary human monocytes treated in vitro with EVs carrying (experimental samples) or not carrying (control samples) HIV-1 Nef. Replicates are included for some RNAseq samples, no replicates for ATACseq samples.


title: Cannabinoid signaling modulation through JZL184 restores key phenotypes of a mouse model for Williams- Beuren syndrome

city: Barcelona

first: Andrés

last: Ozaita

address: Dr Aiguader, 88

department: Department of Medicine and Life Sciences

institute: Universitat Pompeu Fabra

summary: JZL184 treatment restores neurological and cardiac phenotypes of a mouse model of Williams-Beuren syndrome

overall_design:
RNA-Seq was used to obtain mRNA profiles of wild-type and WBS-CD  mouse model, treated and non-treated with JZL184.
To analyze the basal differences, two wild-type non-treated replicates and three WBS-CD non-treated replicates were used.
To analyze the effect of the treatment, three biological replicates of wild-type and three biological replicates of WBS-CD treated with JZL184 were also analyzed.

first: Alba

last: Navarro-Romero

first: Lorena

last: Galera-López

first: Paula

last: Ortiz-Romero

first: Marina

last: Reixachs-Solé

first: Lucía

last: de los Reyes-Ramírez

first: Eduardo

last: Eyras

first: Victoria

last: Campuzano


title: RNA-seq analysis of pancreatic orthotopic tumor and primary tumor

city: Incheon

first: ENZHI

last: LUO

department: Pharmacy

institute: yonsei university

summary: The aim of this study is to evaluate data by comparing transcriptome profiling (RNA-seq) of pancreatic orthotopic tumor and primary tumor

overall_design: Patient pancreatic orthotopic tumor and primary tumor

first: Jung

last: Han

first: Junjeong

last: Choi

first: Seong

last: JPark

first: Enzhi

last: Luo


title: Endocardium-to-coronary artery differentiation during heart development and regeneration involves sequential roles of Bmp2 and Cxcl12/Cxcr4.

city: Palo Alto

first: Kristy

last: Red-Horse

address: 265 Campus Drive

department: Department of Biology and Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Endocardial cells lining the heart lumen are coronary vessel progenitors during embryogenesis. Re-igniting this developmental process in adults could regenerate blood vessels lost during cardiac injury, but this requires additional knowledge on molecular regulators. Here, we use mouse genetics and scRNAseq to identify novel regulators of endocardial angiogenesis and precisely assess the role of CXCL12/CXCR4 signaling. Time-specific lineage tracing demonstrated that endocardial cells differentiated in coronary endothelial cells primarily at mid-gestation. A new mouse line reporting CXCR4 activity—along with cell-specific gene deletions—revealed it was specifically required for artery morphogenesis rather than angiogenesis. Integrating scRNAseq data of endocardial-derived coronary vessels from mid- and late-gestation identified a Bmp2-expressing transitioning population specific to mid-gestation. Bmp2 stimulated endocardial angiogenesis in vitro and in injured neonatal mouse hearts. Our data shed light on how understanding the molecular mechanisms underlying endocardial angiogenesis can identify new potential therapeutic targets promoting revascularization of the injured heart.

overall_design: E17.5 BmxCreERT2;Rosa26tdTomato lineage-labeled hearts in which the Cxcr4flox allele was removed from endo cells at E9.5. FACS-sorted CD31+/tdTomato+ cells from Cxcr4 heterozygous (Cxcr4fl/+, control) and Cxcr4 knock-out (Cxcr4fl/fl, mutant) hearts were collected and processed using the 10X Genomics platform

first: Gaetano

last: D'Amato


title: RNA-seq of CAL-62 cells transfected with LINC00886 smart  silencer and negative control

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: We extracted total RNA samples for high-through RNA sequencing from CAL-62 cells transfected with LINC00886 smart silencer and negative control. Then RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.

first: Ben

last: Ma


title: Pancreatic β-cell specific Ets-1 inhibition treats type 2 diabetes via revitalized insulin production

city: Nanjing

first: shao

middle: yi

last: xue

address: LongMian street

institute: Nanjing Medical University

summary:
As a transcription factor, Ets1 (E26 transformation-specific-1 transcription factor) plays an important role in cell growth, development, differentiation, etc. Our research found that it plays an crucial role in β cell dysfunction induced by metabolic stress such as high glucose. In order to further clarify the downstream target molecules of Ets1 in β cells and the potential mechanism of regulating the mRNA level of target molecules, we transfected Min6(Mouse insulinoma cells) with control virus (Ad-GFP) and Ets-1 overexpression adenovirus (Ad-Ets-1) respectively. Through immunoprecipitation of Ets1 antibody, the DNA fragment specifically bound to Ets1 was obtained and used in high-throughput sequencing. By comparing the enriched DNA fragment with mouse genome (mm10) DNA, the downstream genes that Ets1 can bind to under physiological conditions and the differential peak related genes after overexpression of Ets1 were obtained. Through GO analysis and KFGG analysis of the above related genes, it was confirmed that there was an obvious regulatory relationship between Ets1 and β cell function related genes.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for E26 transformation-specific-1 transcription factor (Ets-1) in Min6 cells transfected Control virus (Ad-GFP) and Ets-1 overexpression adenovirus (Ad-Ets-1)

overall_design: Input and Ets1-IP DNA of Min6 cells transfected Control virus (Ad-GFP) and Ets-1 overexpression adenovirus (Ad-Ets-1)

first: Xiao

first: Fang

last: Chen

first: Tijun

last: Wu

first: Yixue

last: Shao


title: AgRP neurons regulate hematopoiesis and Treg generation through beta 3 adrenergic receptor-expressing stromal cells

city: Genova

first: Lorenzo

last: Ferrando

address: Viale Benedetto XV

department: Department of Internal Medicine

institute: University of Genoa

summary: Maturation of hematopoietic stem and progenitor cells (HSPC) in bone marrow (BM) and of T-lymphocytes in thymus occurs within stromal areas innervated by adrenergic fibers of the sympathetic nervous system (SNS). Here we have discovered that in experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis (MS), SNS signaling to specific  stromal cells expressing beta 3 adrenergic receptors (B3AR) promote differentiation and mobilization of hematopoietic precursors in BM and generation of regulatory T-lymphocytes (Treg)  in the thymus. We demonstrate that the functionality of B3AR on BM and thymic stromal cells is under control of hypothalamic neurons expressing Agouti-Related Protein (AgRP), which are activated in EAE. The finding that AgRP neuropeptide is increased in the serum of people with MS, supports that AgRP neurons might be activated also in MS.

overall_design: Lineage-/Sca1+/cKit+ cells isolated from the bone marrow of  3 naive C57BL/6 mice; 3 C57BL/6 mice 3 days after immunization for EAE; 3 C57BL/6 mice immunized for EAE and treated for 3  days with SR59230A, an antagonist of beta 3 adrenergic receptors.

first: Tiziana

last: Vigo


title: Expression data from MAT1 lncRNA knockdown UM cells (OCM1a)

first: hui

last: pan

address: Zhizaoju Road No.639, Huangpu District

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

summary: LncRNAs are key regulators of chromatin structure, however the mechanism of RNA-chromatin interactions are largely unclarified. Here we performed Chromatin Isolation by RNA Purification (ChIRP), using tiling oligonucleotides retrieve MAT1 lncRNA and bound DNA sequences are examined by high-throughout sequencing. ChIRP-seq enables the study of RNA regulation of chromatin and gene expression.

overall_design: Chromatin Isolation by RNA Purification (ChIRP) (ChIRP-seq) for MAT1 and lacZ in OCM1a cells.

first: H

last: Zhang

last: Pan

first: X

last: Fan


title: Typical Lung Carcinoids with Metastasis: Potential Role of MicroRNAs in the Regulation of Adaptive Immunity Associated with Disease: a Case Study

city: Botucatu

first: Ana

middle: Laura

last: Seneda

state: São Paulo

address: Prof. Mário Rubens Guimarães Montenegro, Avenue - UNESP - Campus de Botucatu

department: Surgery and Orthopedics

country: Brazil

institute: São Paulo State University (UNESP), Faculty of Medicine

summary:
Background/aims: Lung carcinoids are uncommon neuroendocrine tumours. Molecular features of lung carcinoids have been poorly defined. microRNAs (miRNAs) are potent gene expression regulators with important roles in cancer development and progression. However, little is known on the role of miRNAs in the pathogenesis of lung carcinoids. Our goals were to identify commonly deregulated miRNAs in a rare case of lung carcinoid of typical histology with metastasis, as well as map miRNA target genes in pathways potentially associated with disease development and progression.
Methods: miRNA expression profiles were assessed using the TaqMan Low Density Arrays, which is a platform including 384 miRNAs. miRNA profiles were generated in the tumor and its corresponding lymph node metastasis, compared to reference normal lung tissues. Furthermore, miRNA expression was validated in a separate, publicly available external dataset (n=19 typical lung carcinoids; 2/19 were metastatic tumors, compared to six normal lung tissues, GSE77380). Following this analysis, computational tools were applied for data interpretation. miRTarBase was used to determine miRNA-target genes, followed by ToppGene Suite analysis to identify pathways and biological functions. In addition, the expression of genes targeted by miRNAs was validated in a second, separate external dataset (n=13 tumour samples, GSE35679). GEO2R data analysis tool was used in both validation analyses (miRNAs and genes).
Results: We identified 15 commonly significantly downregulated miRNAs (fold change, FC≥2 and p<0.05) in the tumour and its paired metastasis, with further decreasing levels in the metastatic lesion. Downregulation of miR-126-3p and miR-146b-5p was validated in the external dataset GSE77380. In addition, SOX2 and TCF4 genes, targeted by miR-126-3p, were consistently overexpressed in a subset of six typical lung carcinoids from the external dataset GSE35679. Pathways analysis showed that miRNAs miR-126-3p and miR-146b-5p target genes with a role in the regulation of adaptive immune response.
Conclusion: Our results contribute to the identification of miRNA expression changes in a typical lung carcinoid and its corresponding lymph node metastasis. Down-regulated levels of miR-126-3p and miR-146b-5p and target gene over-expression could play a role in the progression of this case of primary typical lung carcinoid to regional metastasis. Identified miRNAs and target genes are potential candidates for validation in a larger number of cases.

overall_design: miRNA expression profiles were assessed using TaqMan Low Density Arrays (384 miRNAs) in a rare case of typical lung carcinoid and its corresponding lymph node metastasis, compared to reference normal lung tissues (N=9 samples). Our results were validated in a separate, external dataset (N=19 typical carcinoids compared to 6 normal lung tissues, GSE77380). Furthermore, computational analyses were performed to determine validated miRNA target genes and miRNA-modulated pathways.

first: Rainer

last: Lapa

first: Tainara

last: Felix

first: Iael

middle: W

last: Minutentag

first: Carolina

last: Campos

first: Rogério

middle: A

last: de Oliveira

first: Cristiano

middle: C

last: Oliveira

first: Érica

middle: N

last: Hasimoto

first: Daniele

last: Cataneo

first: Antonio

first: Julio

last: De Faveri

first: Sandra

last: Drigo

first: Luis

last: Mur

first: Patricia

last: Reis


title: DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis [BiSulfite-seq]

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

type: Methylation profiling by high throughput sequencing

summary: Meiotic recombination is initiated from the SPORULATION 11 (SPO11)-triggered formation of double strand breaks (DSBs) that usually occur in open chromatin with active transcriptional features in many eukaryotes. However, gene transcription at meiotic DSB sites appears to be detrimental for repair, and the mechanisms for gene silencing at DSB sites are largely undefined, especially in plants. Here, we demonstrate that the largest DNA polymerase epsilon subunit POL2A interacts with SU(VAR)3-9 homologs SUVH2 and SUVH9. N-SIM (Structured Illumination Microscopy) observation shows that the colocalization of SUVH2 with meiotic DSB marker γ- H2AX is dependent on POL2A. RNA-seq of male meiocytes identifies that POL2A and SUVH2 jointly repress the expression of 865 genes, which have several known characteristics associated with meiotic DSB sites. Bisulfite-seq and small RNA-seq of male meiocytes support the idea that the silencing of these genes by POL2A and SUVH2/9 is likely independent of CHH methylation or 24-nt siRNA accumulation. Consequently, pol2a suvh2 suvh9 triple mutants have more severe defects in meiotic recombination and fertility compared with either pol2a or suvh2 suvh9. Taken together, our results not only identify a new epigenetic regulatory mechanism for gene silencing in male meiocytes, but also reveal new roles for DNA polymerase and SUVH2/9 beyond their classic functions in mitosis.

overall_design: Examination of DNA methylation levels in meiocytes and seedlings of mutants, such as pol2a-1, suvh2 suvh9 etc, and wild type plants

first: Cong

last: Wang

first: Yingxiang


title: DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis [miRNA-seq]

overall_design: Examination of small RNA abundance in meiocytes and seedlings of mutants, such as pol2a-1, suvh2 suvh9 etc, and wild type plants


title: DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis

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


title: DUX4 expression activates JNK and p38 MAP kinases in myoblasts

city: Cambridge

first: Abby

middle: Shuman

last: Hill

address: 610 Main Street

department: Rare Disease Research Unit

institute: Pfizer

summary: Facioscapulohumoral muscular dystrophy (FSHD) is a progressive muscle wasting disease caused by misexpression of the DUX4 transcription factor. DUX4 expression in skeletal muscle cells results in a dramatic alteration in their transcriptional profile and cellular phenotype and subsequently, cell death. To gain insight into the kinetics of DUX4-induced stresses, we activated DUX4 expression in myoblasts and performed longitudinal RNA sequencing paired with proteomics and phosphoproteomics. This analysis revealed changes in cellular physiology such as DNA damage and altered mRNA splicing before detectable changes in protein levels. Implementation of phosphoproteomics uncovered that widespread changes in protein phosphorylation preceded changes in protein levels indicating that alterations in kinase signaling may play a role in DUX4-mediated stress and cell death. Here we demonstrate that two stress-responsive MAP kinase pathways, JNK and p38, are activated in response to DUX4 expression. Pharmacological inhibition of either of these pathways ameliorated DUX4-mediated cell death in myoblasts. These findings uncover JNK as a novel pathway involved in DUX4-mediated cell death, as well as provide additional insights into the role of the p38 pathway, a clinical target for the treatment of FSHD.

overall_design: Differential gene expression and splicing analysis of inducible DUX4 myoblasts treated with DMSO or at 2 hr, 6 hr, or 14 hr after doxycycline induction of DUX4 and WT myoblasts after 14 hr of doxycycline treatment or DMSO. N=4 culture wells per condition.

first: Christopher

last: Brennan

first: Vijaya

last: Madeti

first: Susanne

last: Breitkopf

first: Seth

last: Garren

first: Liang

last: Xue

first: Ramara

last: Gilbert

first: Angela

last: Hadjipanayis

first: Mara

last: Monetti

first: Charles

last: Emerson Jr

first: Robert

last: Moccia

first: Jane

last: Owens

first: Nicolas

last: Christoforou


title: Suppression of endogenous retroviral enhancers in somatic cell nuclear transfer embryos

status: Public on Oct 08 2022

city: Tsukuba

first: Inoue

last: Kimiko

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

summary: Endogenous retroviruses (ERVs) in the mammalian genome play diverse roles in embryonic development. These development-related ERVs are generally repressed in somatic cells and are therefore likely repressed in embryos derived from somatic cell nuclear transfer (SCNT). In this study, we sought to identify ERVs that are repressed in SCNT-derived morula embryos, which may consequently cause previously unexplained embryonic deaths shortly after implantation. Our transcriptome analysis revealed that, amongst ERV families, ERVK was specifically and strongly downregulated in SCNT embryos while other transposable elements including LINE and ERVL were unchanged. Among subfamilies of ERVK, RLTR45-int was most repressed in SCNT embryos despite its highest expression in control fertilized embryos. Interestingly, the nearby genes (within 5–50 kb, n = 19) of the repressed RLTR45-int loci were also repressed in SCNT embryos with a significant correlation between them. Furthermore, lysine H3K27 acetylation was enriched around the RLTR45-int loci. These findings indicate that RLTR45-int elements function as enhancers of nearby genes. Indeed, deletion of two sequential RLTR45-int loci on chromosome 4 or 18 resulted in downregulations of nearby genes at the morula stage. We also found that RLTR45-int loci, especially SCNT-low, enhancer-like loci, were strongly enriched with H3K9me3, a repressive histone mark. Importantly, these H3K9me3-enriched regions were resistant to histone demethylase Kdm4d in SCNT embryos. Thus, we identified ERVK subfamily RLTR45-int, putative enhancer elements, as a strong reprogramming barrier for SCNT. A large-scale downregulations of their regulating genes in SCNT morulae might cumulatively affect postimplantation development of SCNT embryos.

overall_design: Comparative analysis of the expression of genes and transposal elements in SCNT, IVF, RLTR45-int putative null, and RLTR45-int putative non-null embryos.

first: Daiki

last: Shikata

first: Shogo

last: Matoba

first: Kimiko

last: Inoue

first: Atsuo

last: Ogura


title: Molecular and clinicopathologic characteristics of CNS tumors with BCOR::EP300 gene fusions

city: BETHESDA

first: Zhichao

last: Wu

state: MD

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

summary: Genomewide DNA methylation array profiling of  37 BCOR altered tumors and 37 non-BCOR altered tumors to study the rare tumor entity of EP300::BCOR fusion in central nervous system. The raw methylation idat files and processed beta values were provided here.

overall_design: Bisulfite converted genomic DNA extracted from tumor samples was hybridized to Illumina Infinium EPIC Human DNA Methylation Beadchips

first: Kenneth

last: Aldape


title: RNA-seq data of 786-O cells transfected with control-sgRNA (Control) and PHF8-sgRNA (PHF8-KO)

city: Chongqing

first: Jun

last: Jiang

state: Chongqing

address: 10#, Changjiang Zhilu, Yuzhong District

department: Department of Urology

institute: Daping Hospital, Army Medical University

summary: RNA-seq analysis were applied to elucidate the transcriptional differences between 786-O cell lines transfected with control-sgRNA (Control) and PHF8-sgRNA (PHF8-KO). A total of 3575 differentially expressed genes (Fold Change > 2, or Fold Change＜0.5; FDR < 0.05) with 2097 down- and 1478 up-regulated genes were identified in PHF8-KO 786-O cells

overall_design: Total RNA was extracted from either PHF8 wild type or PHF8 knockout 786-O cells using Trizol reagent (CWBIO). After quality controlling and RNA library preparing, triplicate samples were subjected to sequence by Shanghai NovelBio Bio-Pharm Technology Co., Ltd (Shanghai, China). RNA-Seq reads were filtered and mapped to human genome (GRCh38, NCBI) utilizing HISAT2. HTSeq was used to calculate the gene count. Differentially expressed genes analysis was applied utilizing DESeq2 under following criteria: Fold Change > 2, or Fold Change＜0.5; FDR < 0.05.

first: Song

last: Peng

first: QiuLi

last: Liu


title: Regulation of cohesin-mediated chromosome structure by PDS5 in mammals [RNA-seq]

city: Shanghai

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

summary: Cohesin regulates sister chromatids cohesion but also contributes to chromosome folding by promoting the formation of chromatin loops, a process proposed to be mediated by loop extrusion. PDS5 plays a crucial role in regulating the cohesin dynamic on chromatin, mainly through WAPL-mediated release activity and the opponent ESCO1/2-sororin dependent pathway. However, the exact function of PDS5 on cohesin-mediated chromatin looping remains ambiguous. Two versions of PDS5 exist in vertebrates, PDS5A and PDS5B. Here, we construct cells for rapid PDS5A or PDS5B degradation in PLC/PRF/5 cell line with the FKBP12F36V-dTAG degron system to perform loss of function studies. Combining Hi-C, ChIP-seq for cohesin regulators, and RNA-seq data, we describe the redundant and discrete roles of PDS5A and PDS5B in three-dimensional genome organization and gene expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells mocked depleted or depleted of PDS5A/B

first: Dingdang

last: Yu