title: Quantitative Proteomic Profiling of Murine Embryonic Heart Development Reveals a Role for the Mevalonate Pathway in Cardiomyocyte Proliferation [Cardiomyocytes_Statins_RNASeq]

city: Chapel Hill

first: Whitney

last: Edwards

state: NC

address: 133 North Medical Drive

department: Biology

institute: University of North Carolina Chapel Hill

summary:
Purpose: The goals of this study are to characterize and analyze the transcriptome (RNA-seq) of emrbyonic day 12.5 cultured cardiomyocytes treated with simvastatin
Methods: mRNA profiles of control and simvastatin treated E12.5 cardiomocyteswere generated by deep sequencing, n=4 for each condition, using Illumina HiSeq2500.
Results: Using an optimized data analysis workflow, we mapped at least 34 million sequence reads per sample to the mouse genome (build mm10) and identified approximately 16,000 transcripts.

overall_design: Embryonic day 12.5 (E12.5) cardiomyocytes were isolated from C57/Bl6 mice and treated in culture with control or media containing 10 micromolar simvastatin.

first: Frank

last: Conlon


title: Quantitative Proteomic Profiling of Murine Embryonic Heart Development Reveals a Role for the Mevalonate Pathway in Cardiomyocyte Proliferation

status: Public on Apr 07 2023

country: USA

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Spatially defined gene signatures uncover the association of extracellular matrix genes with immunotherapy resistance in head and neck squamous cell carcinoma

city: New Haven

first: Niki

last: Gavrielatou

address: 310 Cedar Street

institute: Yale University School of Medicine

summary: Background: Immune-checkpoint inhibition (ICI) only benefits a subgroup of patients with head and neck squamous cell carcinoma (HNSCC). Several molecular and cellular components of the tumor microenvironment (TME) have been hypothesized to drive either response or resistance. Here, spatially defined whole transcriptome data were analysed in search of associations of compartment-specific gene-signatures with HNSCC immunotherapy outcomes.         Methods: Pre-treatment biopsy samples from 50 immunotherapy-treated recurrent or metastatic HNSCC patients as well as 12 matched post-treatment biopsies obtained after 4 weeks of treatment, constructed in tissue microarray format (YTMA496), were included in the study. The GeoMx Human Whole Transcriptome Atlas (NanoString Technologies) assay was performed on samples to allow RNA quantification of 18,677 protein encoding genes, using in situ hybridization, in three molecularly defined tissue compartments; tumor (CK), leukocyte (CD45), macrophage (CD68). Differentially expressed genes (DEGs) (P<0.05) between pre- and post-treatment biopsies in each of the tissue compartments were identified. Next, these DEGs were used as a “biological” filter for the initial 18,677 gene set and analysed using LASSO logistic regression models with the aim to obtain pre-treatment gene expression signatures for best overall response (RECIST 1.1.). The performance of each compartment signature was evaluated using the receiver operating characteristic (ROC) curve and AUCs were calculated for Best Overall Response (BOR) to ICI.   Results: A six-gene signature (DDX4, COL17A1, HBA1, MMP1, GPNMB, TTN) in the CD45 compartment presented the highest AUC (0.83), followed by signatures in the CK and CD68 compartments (AUC: 0.72 and 0.68, respectively). Cross-testing of the CD45 signature in the other two compartments, as well as in a third, artificially generated “pseudo-bulk” compartment (all compartments combined), showed poor performance, indicating spatial specificity. Interestingly, the CD45 signature included three extracellular-matrix protein-encoding genes (MMP1, COL17A1, TTN), all associated with resistance (negative coefficients in the BOR model) to ICI. Fibroblast and dendritic cell populations, characterized using the CIBERSORTx gene matrix, were the immune phenotypes most closely associated with the CD45 signature.  Conclusions: Our results indicate that CD45 molecular tissue compartment gene expression demonstrates increased association with ICI resistance in HNSCC. Extracellular matrix genes rather than immune-cell related genes dominated the CD45 compartment signature, highlighting the importance of non-immune stromal components within the TME and the importance of the use of spatial information in the understanding of ICI resistance.

overall_design: This dataset comprises gene expression data from 50 pre-treatment tissue samples of anti-PD-1 treated head and neck squamous cell carcinoma patients in three molecularly defined compartments; tumor (defined by CK), leukocyte (defined by CD45) and macrophage (defined by CD68). Samples were constructed in tissue microarray format and experiments were performed on slides from two separate paraffin blocks (2-fold redundancy), each containing a non-adjacent tissue core from each patient-biopsy.  Nanostring GeoMx Digital Spatial Profiling (DSP) Whole Transcriptome Atlas (WTA) Panel (>18,677 target genes) was used per manufacturer’s protocol.  240 ROIs corresponding to 240 AOIs were collected and analysed.

first: David

middle: L

last: Rimm


title: Quantitative Proteomic Profiling of Murine Embryonic Heart Development Reveals a Role for the Mevalonate Pathway in Cardiomyocyte Proliferation [Heart_RNAseq]

summary:
Purpose: The goals of this study are to characterize and analyze the emrbyonic heart transcriptome profiling (RNA-seq) at E9.5, E10.5, E12.5, E14.5 and E16.5.
Methods: mRNA profiles of E9.5, E10.5, E12.5, E14.5 and E16.5 C57/Bl6 mouse embryonic hearts were generated by deep sequencing, n=3 or 4 for each age, using Illumina HiSeq2500.
Results: Using an optimized data analysis workflow, we mapped at least 36 million sequence reads per sample to the mouse genome (build mm10) and identified 17,537 transcripts in the mouse hearts.

overall_design: E9.5. E10.5, E12.5, E14.5, E16.5 C57/Bl6 mouse embryonic hearts RNAseq


title: Gene expression profile of Arabidopsis root tip cells exposed to 2 hours of 50µM jasmonate

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the response to jasmonate treatment in root tips at the single cell level.

overall_design: protoplast were generated from root tips then cells were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of DAPI signal and analyzed using scRNAseq.

first: Andrés

last: Ritter

first: Alain

last: Goossens


title: Transcriptional specification of early cardiac precursor cells at single cell resolution

city: San Francisco

first: Alexis

middle: Leigh

last: Krup

state: CA

address: 1650 Owens Street

department: Gladstone Institutes of Cardiovascular Disease

institute: Gladstone Institutes

summary: Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood due in part to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single cell transcriptomic time course of mouse embryos to identify emerging CPCs and describe their transcriptional profiles. Mesp1, a transiently-expressed mesodermal transcription factor (TF), is canonically described as an early regulator of cardiac specification. However, we observed perdurance of CPC transgene-expressing cells in Mesp1 mutants, albeit mis-localized, prompting us to investigate the scope of Mesp1’s role in CPC emergence and differentiation. Mesp1 mutant CPCs failed to robustly activate markers of cardiomyocyte maturity and critical cardiac TFs, yet they exhibited transcriptional profiles resembling cardiac mesoderm progressing towards cardiomyocyte fates. Single cell chromatin accessibility analysis defined a Mesp1-dependent developmental breakpoint in cardiac lineage progression at a shift from mesendoderm transcriptional networks to those necessary for cardiac patterning and morphogenesis. These results reveal Mesp1-independent aspects of early CPC specification and underscore a Mesp1-dependent regulatory landscape required for progression through cardiogenesis.

overall_design: Single cell RNA sequencing profiling transcriptional profiles of control and Mesp1 KO cells harvested from whole embryos in a time course of murine gastrulation stages E6.0-E7.75.

first: Benoit

middle: G

last: Bruneau


title: Chromatin accessibility profiles of early cardiac precursor cells at single cell resolution

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Single cell ATAC sequencing investigating chromatin accessibility profiles of cells harvested from control and Mesp1 KO whole embryos ages E7.5 and E7.75.


title: Nonpathological inflammation drives the development of an avian flight adaptation

city: Clemson

first: Joseph

middle: Robert

last: Sheheen

state: SC

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

summary: Bird tails transitioned during the Mesozoic from long to shortened and distally fused. Fusion of the distalmost vertebrae manifests as the bony pygostyle, a trait retained in extant avians that contributes to flight aerodynamics. Here, we investigate the mechanism responsible for pygostyle formation. Transcriptomic profiling and histology reveal that the immune system is responsible for this important adaptation in avian evolutionary history. Pygostyle formation commences with cell death in the intervertebral discs, within the nucleus pulposus and annulus fibrosus. The nucleus pulposus, observed for the first time in birds, forms differently in fused versus unfused regions of the tail, and its deterioration in the pygostyle is crucial to the cascade of events that eventually lead to ankylosis. The Complement cascade, vasculogenesis, neutrophil-like cell function, involvement of both the innate and adaptive immune systems and multiple additional events mirror those observed during bone fracture healing. The key common denominator in both processes that differentiates them from general endochondral ossification is an inflammatory response. These studies suggest that a universal mechanism for bone repair has been co-opted in avian evolution for the formation of a flight-adapted tail structure.

overall_design: 8-10 week old chicken Intervertebral disc RNA samples. 4 samples from degenerating pygostyle ivds and 4 from permanent ivds.

first: Susan

last: Chapman

first: Dana

last: Rashid


title: TLE3 CUT&Tag-Seq to characterize TLE3-binding sites in colonic macrophages

city: Beijing

first: Xiaoyu

last: Li

address: Tsinghua University, Haidian District

department: School of Medicine

country: China

institute: Tsinghua University

summary: We found that TLE3 in colonic macrophages mainly occupied distal intergenic regions (48%) and gene body regions (47%) with limited occupancy at the gene proximal regions (5%).

overall_design: Colonic macrophages were sorted from untreated WT mice. TLE3-binding sites were analyzed by TLE3 CUT&Tag-Seq.


title: Selective inhibition of HDAC6 promotes bladder cancer radiosensitization without inducing CXCL1 signalling

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary:
Although bladder-preserving trimodality therapy is recognized for patients with muscle-invasive bladder cancer (MIBC), chemotherapy can have toxic effects. Inhibitors to histone deacetylases (HDACis) have been identified as an effective strategy to enhance the radiotherapy (RT) effect, and several of them have clinical efficacy in BC.  However, little is known about how a specific HDAC6 inhibitor (HDAC6i) acts in concert with RT. Knockdown of HDAC6 enhanced the radiosensitization of BC cells and increased γH2AX accumulation, similar to the effect of panobinostat, a pan-HDACi. Applying tubacin, a selective HDAC6i, to T24 cells induced H3K9ac and α-tubulin acetylation, and significantly decreased clonogenic cell survival when combined with RT. Further transcriptomic analysis of shHDAC6-transduced T24 cells under irradiation showed that genes that were highly downregulated compared to the levels in response to RT alone were significantly enriched in the inflammatory response.
Moreover, HDAC6 knockdown counteracted the RT-induced mRNA expression of CXCL1, SERPINE1, SDC1 and SDC2. Importantly, tubacin suppressed RT-promoted invaded/migrated T24 cells, whereas panobinostat elevated RT-induced CXCL1 expression and invasion/migration abilities. This phenotype was significantly abrogated by the CXCL1 antibody, indicating that RT-induced CXCL1 is the key regulator contributing to BC malignancy. Immunohistochemical evaluation of tumours from BC patients supported the correlation between CXCL1 overexpression and poor prognosis. Unlike the pan-HDACi, the selective HDAC6i tubacin can enhance BC radiosensitization and suppress RT-induced oncogenic CXCL1-Snail signalling, thus further advancing the therapeutic potential of tubacin with RT.

overall_design: RNAs were extracted from T24 cell line and profiled by RNA-seq

first: Y

middle: C

last: Tsai

first: S

middle: F

last: Su


title: ATAC-Seq to profile the chromatin accessibility in colonic macrophages from Tle4KO (Tle4fl/fl, Lyz2-Cre) and WT (Lyz2-Cre) mice

summary: We found that TLE4 maintained overall chromatin accessibility in colonic macrophages.

overall_design: Colonic macrophages were sorted from untreated WT and myeloid cell-specic Tle4KO mice. Differential chromatin accessibility was analyzed by ATAC-Seq.

first: Bin

last: Zhang


title: Human motor neurons are rare in the spinal cord and can be transcriptomically divided into known subtypes divided into known subtypes.

status: Public on Apr 06 2023

city: Stanford

first: Jacob

last: Blum

address: 279 Campus Dr

institute: Stanford University

summary: Motor neurons are a rare neuronal subtype in the adult spinal cord. We performed single-nucleus RNA sequencing on nuclei extracted from adult human spinal cord and describe the transcriptional heterogeneity.

overall_design: Nuclei from the cervical spinal cord of a neurologically healthy control patient were isolated, homogenized, and stained with antibodies against neuronal marker NeuN. Nuclei were sorted by FANS and transcriptomes captured using 10x V3.1 3' kits.

first: Olivia

last: Gautier

first: James

last: Maksymetz

first: Derek

last: Chen

first: Christopher

last: Schweingruber

first: Irene

last: Mei

first: Anita

last: Hermann

last: Hackos

first: Eva

last: Hedlund

first: John

last: Ravits

first: Aaron

last: Gitler


title: Repurposing the antipsychotic drug amisulpride for targeting synovial fibroblast activation in arthritis

city: Vari

first: George

last: Kollias

state: Attica

address: 34 Fleming Street

department: Institute for Bioinnovation/ Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/ National and Kapodistrian University of Athens


title: RNA-Seq to profile transcriptomes in colonic macrophages from Tle3KO (Tle3fl/fl, Lyz2-Cre), Tle4KO (Tle4fl/fl, Lyz2-Cre) and WT (Lyz2-Cre) mice

last: Li

summary: We identified TLE3- and TLE4-regulated transcriptomes in colonic macrophages.

overall_design: Colonic macrophages were sorted from untreated WT, myeloid cell-specic Tle3KO, and myeloid cell-specic Tle4KO mice. RNA was extracted and used for RNA-Seq analysis.


title: Insights into the Formation and Diversification of a Novel Chiropteran Wing Membrane from Embryonic Development

city: Los Angeles

first: Karen

last: Sears

address: 612 Charles E Young Drive

institute: UCLA

summary: Background: Through the evolution of novel wing structures, bats (Order Chiroptera) became the only mammalian group to achieve powered flight. This achievement preceded the massive adaptive radiation of bats into diverse ecological niches. We investigate here some of the developmental processes that underlie the origin and subsequent diversification of one of the novel membranes of the bat wing: the plagiopatagium, which connects the fore- and hind limb in all bat species. Results: Our results suggest that the plagiopatagium initially arises through novel outgrowths from the body flank that subsequently merge to the limbs to generate the wing airfoil. Our findings further suggest that this merging process, which is highly conserved across bats, occurs through modulation of the programs controlling the development of the periderm of the epidermal epithelium. Finally, our results suggest that the shape of the plagiopatagium begins to diversify in bats only after this merging has occurred. Conclusions: This study demonstrates how a focus on the evolution of cellular processes can inform an understanding of the developmental factors shaping evolution of novel, highly adaptive structures.

sample_organism:
Pteronotus quadridens
Erophylla sezekorni

overall_design: Samples include RNAseq data for individuals for forelimb, heart, plagiopatagial, and uropatagial  tissues from Erophylla sezekorni (3 samples for each tissue for Cretekos Stage 14 and 3 samples for each tissue for Cretekos Stage 16) and Pteronotus quadridens (3 samples for each tissue for Cretekos Stage 14 and 3 samples for each tissue for Cretekos Stage 16)

middle: E

first: Daniel

middle: J

last: Urban

first: Neal

last: Anthwal


title: A comparative gene expression matrix in Apoe-deficient mice identifies unique and atherosclerotic disease stage-specific gene regulation patterns in monocytes and macrophages

city: Freiburg

first: Ingo

last: Hilgendorf

address: Hugstetter Straße 55

department: Department of Cardiology and Angiology

country: Germany

institute: UNIVERSITY HOSPITAL FREIBURG University Heart Center Freiburg-Bad Krozingen

summary: Atherosclerosis is a systemic and chronic inflammatory disease propagated by monocytes and macrophages. Yet, our knowledge on how transcriptional profiles of these cells evolve in time and space is limited. We aimed at characterizing gene expression changes in site-specific macrophages, i.e. atherosclerotic aorta versus remote peritoneal cavity, and in circulating monocytes during the course of atherosclerosis initiation and progression in Apoe deficient mice. Constructing a comparative directory of cell type- and disease stage-specific whole transcriptome information, we identified a distinctive gene regulation profile of aortic macrophages. Overall 1149 differentially expressed genes (DEG) were involved in the biological modulation of aortic macrophages, and they were further categorized into regulated early, late, and transitorily throughout the disease course. The commonality of gene regulation was surprisingly low among the three investigated cell types. Through complementary interrogation of murine and human single cell RNA sequencing datasets, we showcased the practicality of our directory, using the selected gene, Glycoprotein Nmb (Gpnmb), whose expression in aortic macrophages, and a subset of foamy macrophages in particular, strongly correlated with disease advancement during atherosclerosis initiation and progression. Our study provides a unique toolset to explore gene regulation of macrophage-related biological processes in and outside the atheromatous plaque at early and advanced disease stages for pathomechanistic insight and therapeutic target screening.

overall_design: We acquired three cell types (circulating monocytes, peritoneal macrophages, aortic macrophages) from atherosclerotic mice with different disease severity (baseline, early atheroma, advanced atheroma). Atheroma formation was controled by feeding Apoe-deficient mice high cholesterol diet for different durations (chow diet, 1 month feeding, 6 month feeding). The study aimed to investigate gene regulation changes of systemic and lesional monocytes/macrophages during atheroma initiation and progression. There were four replicates for each cell type and each disease stage.

first: Carmen

last: Haerdtner

first: Tsai-sang

last: Dederichs


title: Effects of prenatal pesticide exposure on the fetal brain and placenta transcriptomes in  a rodent model

city: New York

first: Corina

last: Lesseur

state: New York

address: 1428 Madison Ave

department: Environmental Medicine & Public Health

institute: Icahn School of Medicine at Mount Sinai

summary: Organophosphate and pyrethroid pesticides are among the most extensively used insecticides worldwide. Prenatal exposures to both classes of pesticides have been linked to a wide range of neurobehavioral deficits in the offspring. The placenta is a neuroendocrine organ and the crucial regulator of the intrauterine environment; early-life toxicant exposures could impact neurobehavior by disrupting placental processes. Female C57BL/6J mice were exposed via oral gavage to an organophosphate, chlorpyrifos (CPF) at 5 mg/kg, a pyrethroid, deltamethrin (DM), at 3 mg/kg, or vehicle only control (CTL). Exposure began two weeks before breeding and continued every three days until euthanasia at gestational day 17. The transcriptomes of fetal brain (CTL n=18, CPF n= 6, DM n=8) and placenta (CTL n=19, CPF n= 16, DM n=12) were obtained through RNA sequencing, and resulting data was evaluated using weighted gene co-expression networks, differential expression, and pathway analyses. Fourteen brain gene co-expression modules were identified; CPF exposure disrupted the module related to ribosome and oxidative phosphorylation, whereas DM disrupted the modules related to extracellular matrix and calcium signaling. In the placenta, network analyses revealed 12 gene co-expression modules. While CPF exposure disrupted modules related to endocytosis, Notch and Mapk signaling, DM exposure dysregulated modules linked to spliceosome, lysosome and Mapk signaling pathways. Overall, in both tissues, CPF exposure impacted oxidative phosphorylation, while DM was linked to genes involved in spliceosome and cell cycle. The transcription factor Max involved in cell proliferation was overexpressed by both pesticides in both tissues.  In summary, gestational exposure to two different classes of pesticide can induce similar pathway-level transcriptome changes in the placenta and the brain; further studies should investigate if these changes are linked to neurobehavioral impairments.

overall_design: Analyses of the effects of gestational exposure to pesticides (groups: corn oil control, chlorpyrifos or deltamethrin on the gene co-expression networks of fetal brain and placenta tissue of mouse pups at gestational day 17.  C57BL/6J Dams were exposed via oral gavage every 3 days beginning 2 weeks prior to breeding continuing until gestational day 17 (GD17) and were euthanized on GD 17.

first: Jia

last: Marsit

first: Ke

last: Hao

first: William

middle: M

last: Caudle


title: The imbalance of excitatory/inhibitory neuron differentiation in neurodevelopmental disorders with an NR2F1 point mutation (The Third Replicate)

city: Shanghai

last: Zhang

address: No.320 Yueyang Road

institute: SIBCB

summary: Recent studies have revealed an essential role for embryonic cortical development in the pathophysiology of neurodevelopmental disorders, including autism spectrum disorder (ASD). However, the genetic basis and underlying mechanisms remain unclear. Here, we generate mutant human embryonic stem cell lines (Mut hESCs) carrying an NR2F1-R112K mutation that has been identified in a patient with ASD features, and investigate their neurodevelopmental alterations. Mut hESCs overproduce ventral telencephalic neuron progenitors (ventral NPCs) and inhibitory neurons, and underproduce dorsal NPCs and excitatory neurons. These alterations can be mainly attributed to the aberrantly activated Hedgehog signaling pathway. Moreover, the corresponding Nr2f1 point mutant mice display a similar excitatory/inhibitory neuron imbalance and abnormal behaviors. Antagonizing the increased inhibitory synaptic transmission partially alleviates their behavioral deficits. Together, our results suggest that the NR2F1-dependent imbalance of excitatory/inhibitory neuron differentiation caused by the activated Hedgehog pathway is one precursor of neurodevelopmental disorders and may enlighten the therapeutic approaches.

overall_design: WT and Mut human NPCs were subjected into transcriptome analysis (The third replicates).


title: Expression data from syngeneic Hepa1-6 model in C57Bl/6J mice

city: Barcelona

first: Laura

last: Torrens

state: Barcelona

address: Esther Koplowitz Center, 3rd Floor. C/ Rosselló 149-153

country: Spain

institute: IDIBAPS, Hospital Clínic Barcelona

summary:
Lenvatinib is an effective drug in advanced hepatocellular carcinoma (HCC). Its combination with the anti-PD1 immune checkpoint inhibitor pembrolizumab has achieved encouraging results in phase Ib and is currently being tested in phase III trials. Here, we aimed at exploring the molecular and immunomodulatory effects of lenvatinib alone or in combination with anti-PD1.
We generated a syngeneic model of HCC in C57BL/6J mice and randomized the animals to receive placebo, lenvatinib, anti-PD1 or combination treatment. Transcriptomic analysis were performed to assess the expression profile of tumors from mice receiving each treatment strategy.

overall_design: Tumors were collected 13 days post-randomization. Animals were euthanized 1 day after the last anti-PD1 dose and 2h after the last lenvatinib dose in accordance with pharmacodynamic studies (n=21). Gene expression analyses were conducted using the Clariom S Mouse Array (Affymetrix).

first: Josep

last: Llovet


title: Genetic differences in conditioned medium through adding PTN on neural stem progenitor cells (NSPCs).

city: Guangzhou

first: Li

last: Xu

address: TianHe road 600#

institute: the third affiliated hospital of SYSU

summary:
To investigate the genetic differencesin conditioned medium beteen PTN group and control group, we established NSPCs line.
We then performed gene expression profiling analysis using data obtained from RNA-seq after 24h with stimulation with PTN and PBS (Control).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PTN groups and control groups.

first: Changyong

last: Tang


title: Repurposing the antipsychotic drug amisulpride for targeting synovial fibroblast activation in arthritis II

last: Kollias

summary: Amisulpride, a known antipsychotic drug, was identified to target synovial fibroblasts activation in arthritis through novel identified targets.

overall_design: 3’ RNA-Seq (QuantSeq) profiling of isolated hTNFtg primary mouse joint synovial fibroblasts and hTNFtg synovial fibroblasts treated with Amisulpride for 48h. 3 replicates per group.

first: Dimitra

last: Papadopoulou

first: Fani

last: Roumelioti

first: Christos

last: Tzaferis

first: Panagiotis

last: Chouvardas

first: Anna-Kathrine

last: Pedersen

first: Filippos

last: Charalampous

first: Eleni

last: Christodoulou-Vafeiadou

first: Lydia

last: Ntari

first: Niki

last: Karagianni

first: Maria

last: Denis

first: Jesper

middle: V

last: Olsen

first: Alexis

middle: N

last: Matralis


title: Repurposing the antipsychotic drug amisulpride for targeting synovial fibroblast activation in arthritis I

first: George

overall_design: 3’ RNA-Seq (QuantSeq) profiling of isolated WT, hTNFtg  primary mouse joint synovial fibroblasts and hTNFtg synovial fibroblasts treated with Infliximab (Remicade) for 48h. 3 replicates per group.


title: Mechanistic connections among epithelial plasticity, skin barrier, inflammation, and whole-body metabolism

city: Irvine

first: Morgan

last: Dragan

address: D288 Medical Sciences I

department: Biological Chemistry

institute: UC Irvine

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

overall_design: Refer to individual Series


title: Transcriptional analysis of human IL-23R mediated apoptosis in human cervical cancer cells in vitro

first: Xiaomei

last: Yuan

state: Beijing

address: Three No. 5, Dongdan, Dongcheng District, Beijing

department: Department of Pathogen Biology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, PUMC

summary: We found that IL-23R mediated HeLa cell apoptosis by characterizing the functional domains responsible for this event. For exploring apoptotic pathways activated by IL-23R, the altered transcriptomic profiles in responding to IL-23R over-expression was also revealed by RNAseq analysis.

overall_design: HeLa cells were transiently transfected with either empty vector pCMV-Myc or pCMV-Myc-IL-23R group. RNA of the transfected cells was extracted and used for transcriptome analysis.

first: Hu

last: Zhang

last: Liu


title: The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8 T cells in chronic viral infection (RNA-Seq II)

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: T-cell factor 1 (Tcf-1) expressing CD8 T cells exhibit stem-like self-renewing capacity rendering them key for immune defense against chronic viral infection and cancer. Yet, the signals that promote the formation and maintenance of these memory-like CD8 T cell (CD8ML) remain poorly defined.  Studying CD8 T cell differentiation in mice with chronic viral infection we identify the alarmin interleukin-33 (IL-33) as pivotal for the expansion and stem-like functioning of CD8ML as well as for virus control. IL-33 receptor- (ST2-) deficient CD8 T cells exhibit biased end-differentiation and premature loss of Tcf-1. Intriguingly, ST2-deficient CD8ML responses are restored by blockade of type I interferon signaling, suggesting that opposing IFN-I and IL-33 effects control CD8ML formation in chronic infection. IL-33 signals broadly augment chromatin accessibility in CD8ML and determine these cells’ re-expansion potential.   Our study identifies the IL-33 – ST2 axis as an important CD8ML-promoting pathway in the context of chronic viral infection.

overall_design: RNA expression profile of P14 WT and P14 ST2ko cells on day 6 after LCMV Cl13 high dose infection.

first: Anna-Friederiek

last: Marx

first: Florian

last: Geier

first: Daniel

last: Pinschewer


title: The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8 T cells in chronic viral infection (ATAC-Seq)

overall_design: ATAC-seq analysis of P14 WT Tcf7gpf+ cells and of P14 ST2-/- Tcf7gpf+ cells on day 4 after LCMV infection


title: The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8 T cells in chronic viral infection


title: Transcriptomic data of liver endothelial cells from Alk1-(alias Acvrl1) knockout mice II

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Hereditary hemorrhagic telangiectasia (HHT, alias Rendu-Osler-Weber syndrome) is an autosomal dominant genetic disease that causes vascular malformations in multiple organs. Malformations and shunts in the liver are relevant for the long-term prognosis as they can lead to heart failure. Moreover, the role of ALK-1 in the hepatic vascular niche remains elusive.  In this project, we aimed to establish a novel HHT model covering hepatic involvement by the disease and to investigate the role of ALK-1 in the hepatic vascular niche.  We crossed Stab2-icre mice (MGI: 6741034) with Acvrl1-floxed mice (MGI: 4398901) to generate constitutive hepatic endothelial Acvrl1 knockout (Acvrl1-HEC-KO, alias Alk1-HEC-KO) mice. To dissect microvascular transcriptomic alterations, we performed RNA sequencing of freshly isolated hepatic endothelial cells from 3 months old mice.  Transcriptomic analyses revealed an arterialization of hepatic vessels accompanied by loss of LYVE-1 and induction of Endomucin. The loss of endothelial Wnt2, Wnt9b, and Rspo3 led to a disruption of hepatic metabolic zonation with a dominance of periportal genes in Alk1-HEC-KO mice and HHT patients. Furthermore, we identified PRND (alias Doppel) and placenta growth factor (PlGF) as novel candidates of HHT pathogenesis in mice.  ALK-1 controls hepatic metabolic zonation via Wnt signaling and suppresses PRND and PlGF that represent novel candidates in HHT pathogenesis.

overall_design: 5 Alk1-Knockout samples vs. 5 control samples

first: Christian

middle: D

last: Schmid

first: Manuel

last: Reinhart


title: Transcriptomic data of liver endothelial cells from Alk1-(alias Acvrl1) knockout mice


title: Transcriptomic data of whole liver from Alk1-(alias Acvrl1) knockout mice I

summary: Hereditary hemorrhagic telangiectasia (HHT, alias Rendu-Osler-Weber syndrome) is an autosomal dominant genetic disease that causes vascular malformations in multiple organs. Malformations and shunts in the liver are relevant for the long-term prognosis as they can lead to heart failure. Moreover, the role of ALK-1 in the hepatic vascular niche remains elusive.  In this project, we aimed to establish a novel HHT model covering hepatic involvement by the disease and to investigate the role of ALK-1 in the hepatic vascular niche.  We crossed Stab2-icre mice (MGI: 6741034) with Acvrl1-floxed mice (MGI: 4398901) to generate constitutive hepatic endothelial Acvrl1 knockout (Acvrl1-HEC-KO, alias Alk1-HEC-KO) mice. To dissect hepatic transcriptomic alterations, we performed RNA sequencing of freshly isolated whole liver cells from 3 months old mice.  Transcriptomic analyses revealed an arterialization of hepatic vessels accompanied by loss of LYVE-1 and induction of Endomucin. The loss of endothelial Wnt2, Wnt9b, and Rspo3 led to a disruption of hepatic metabolic zonation with a dominance of periportal genes in Alk1-HEC-KO mice and HHT patients. Furthermore, we identified PRND (alias Doppel) and placenta growth factor (PlGF) as novel candidates of HHT pathogenesis in mice.  ALK-1 controls hepatic metabolic zonation via Wnt signaling and suppresses PRND and PlGF that represent novel candidates in HHT pathogenesis.


title: The alarmin interleukin-33 promotes the expansion and preserves the stemness of Tcf-1+ CD8 T cells in chronic viral infection (RNA-Seq I)

overall_design: RNA expression profile of Tcf7gfp pos and Tcf7gfp neg WT/ST2ko P14 T cells on day 4 after LCMV Cl13 high dose infection.


title: Sex-specific differences in the pulmonary epigenome in neonatal hyperoxic lung injury

city: Houston

first: Krithika

last: Lingappan

address: 6621 Fannin

institute: Baylor College of Medicine

summary: Changes in the H3K27Ac mark in male and female mice on PND7 and PND21 exposed to room air or hyperoxia

overall_design: Examination of the effect of hyperoxia on the lung epigenome (H3K27Ac mark) and sex-specific differences

first: Coarfa

last: Cristian


title: RNASeq analysis of murine bone marrow derived macrophages (BMDMs)

city: Biberach

first: karim

last: el kasmi

address: Birkendorferstr 65

department: Immunology & Respiratory

institute: Boehringer Ingelheim Pharma GmbH & CO. KG

summary: Macrophages can adapt and change various activation states. Pro-inflammatory macrophages are induced by stimulation with LPS or IFNy whereas repair macrophages are induced by stimulation with IL4/IL13. However, due to their plasticity macrophages might adapt several activation states including inflammatory- and repair-like activation states as well as intermediate activation states which are associated with distinct gene expression patterns.

overall_design: Here we analyse murine bone marrow derived macrophages (BMDMs) which have been untreated, treated with IL4/IL13, or IL4/IL13+TNFa. For each treatment condition we analyzed six replicates for a total of 18 samples by bulk RNASeq.

first: Karim

last: El Kasmi

first: Carolin

middle: K

last: Koss

first: Michèl

last: Przibilla

first: Carmen

last: Lerner

first: Katrin

last: Fundel-Clemens

first: Coralie

last: Viollet

first: Matthew

last: Thomas

first: Fidel

last: Ramirez

first: Peter

last: Murray


title: Effects of nintedanib on unstimulated and stimulated macrophages from human monocytes in single culture and in co-culture with fibroblasts.

summary: Macrophages have emerged as important cells in both promoting and resolving tissue fibrosis. It is thought that macrophages can execute these functionally opposing phenotypes as a result of their ability to dynamically respond to signals in their microenvironment. One approved antifibrotic drug for the treatment of lung fibrosis is nintedanib. Nintedanibs effect has largely been attributed to its inhibitory effect on tyrosine kinases resulting in inhibition of fibroblast proliferation with only very few studies investigating its effects on macrophage phenotypes. This study was carried out to address the anti-fibrotic effect of NTB on macrophage phenotypes in the context of fibroblasts to approximate the tissue environment.

overall_design: Analysis of bulk RNA-Seq samples from human monocyte derived macrophages which have been cultured in either single culture (SiCu_MDM) or co-culture with fibroblasts (CoCu_MDM). Macrophages were obtained from 6 human donors, Fibroblasts were obtained from one donor. The following conditions were evaluated: Untreated +/- Nintedanib (NTB), IL4/IL13 + TNF +/- Nintedanib. All conditions were applied to Macrophages in single culture as well as Macrophages that have been cultured in indirect co-culture with fibroblasts, with six replicates for a total of 48 RNA-Seq samples.

first: Heinrich

last: Huber


title: Harnessing matrix stiffness to engineer a bone marrow niche for hematopoietic stem cell rejuvenation

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

summary:
RNA and ATAC sequencing data of primary sorting CD45-Ter119-CD31-Scf; GFP+Cxcl12; DsRed+ bone marrow stromal cells ,2D cultured bone marrow stromal cells and 3D cultured bone marrow stromal cells. RNA sequencing data of sorted primary and 3D cocultured Lin-Sca1+C-kit+CD150+CD48+ hematopoietic stem cells from 8-12 weeks and 12-13 months old mice.

RNA and ATAC sequencing data of primary sorting CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells from young (8 wks), middle aged (12 months) and aged (22-24 months) Lepr-Cre;td-Tomato mice.

overall_design:
Total RNA from 3 biological replicates of CD45-Ter119-CD31-Scf; GFP+Cxcl12; DsRed+ bone marrow stromal cells,2D cultured bone marrow stromal cells and 3D cultured bone marrow stromal cells. Paired-end sequencing 150bp reads Novaseq (Illumina). ATAC-seq of 3 biological replicates of CD45-Ter119-CD31-Scf; GFP+Cxcl12; DsRed+ bone marrow stromal cells,2D cultured bone marrow stromal cells and 3D cultured bone marrow stromal cells.Paired-end sequencing 150bp reads HiSeq X Ten system (Illumina). RNA-seq of 3 biological replicates of sorted primary and 3D cocultured Lin-Sca1+C-kit+CD150+CD48+ hematopoietic stem cells from 8-12 weeks and 12-13 months old mice.Paired-end sequencing 150bp reads HiSeq X Ten system (Illumina).

Total RNA from 3 biological replicates of CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells from young (8 wks), middle aged (12 months) and aged (22-24 months) Lepr-Cre;td-Tomato mice. Paired-end sequencing 150bp reads Novaseq (Illumina). ATAC-seq of 3 biological replicates of CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells from young (8 wks), middle aged (12 months) and aged (22-24 months) Lepr-Cre;td-Tomato mice. Paired-end sequencing 150bp reads (Illumina).

first: Rui

last: Yue

first: Xiaoying

last: Zhang

first: Liting

last: Xu


title: Protectin DX as a therapeutic strategy against frailty in mice

status: Public on Apr 05 2023

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Frailty in aging is driven by the dysregulation of multiple biological pathways. Protectin DX (PDX) is a docosahexaenoic acid (DHA)-derived molecule that alleviates many chronic inflammatory disorders, but its potential effects on frailty remain unknown. Our goal is to identify age-related impairments in metabolic systems and to evaluate the therapeutic potential of PDX on frailty, physical performance, and health parameters. A set of 22-month-old C57BL/6 male and female mice were assigned to vehicle (Old) or PDX daily gavage treatment for 8 weeks, whereas 6-monthold (Adult) mice received only vehicle. Forelimb and hindlimb strength, endurance, voluntary wheel activity and walking speed determined physical performance and were combined with a frailty index score and body weight loss to determine frailty status. Our data shows that old vehicle-treated mice from both sexes had body weight loss paralleling visceromegaly, and old females also had impaired insulin clearance as compared to the Adult group. Aging was associated with physical performance decline together with higher odds of frailty development. There was also age-driven mesangial expansion and glomerular hypertrophy as well as bone mineral density loss. All of the in vivo and in vitro impairments observed with aging co-occurred with upregulation of inflammatory pathways and Myc signaling as well as downregulation of genes related to adipogenesis and oxidative phosphorylation in liver. PDX attenuated the age-driven physical performance (strength, exhaustion, walking speed) decline, promoted robustness, prevented bone losses and partially reversed changes in hepatic expression of Myc targets and metabolic genes. In conclusion, our data provides evidence of the beneficial therapeutic effect of PDX against features of frailty in mice. Further studies are warranted to investigate the mechanisms of action and the potential for human translation.

overall_design: A set of 22-month-old C57BL/6 male and female mice were assigned to vehicle (Old) or PDX daily gavage treatment for 8 weeks, whereas 6-month-old (Adult) mice received only vehicle.  RNA was extracted from the liver of 15 female mice, five from each experimental group, and sequenced in order to assess the transcriptional consequences of aging and PDX treatment.

first: Lais

last: Perazza

first: LaDora

last: Thompson


title: Full-length, single cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity

city: Washington

first: Marcel

middle: O

last: Schmidt

state: DC

address: 3970 Reservoir Road, N.W.,  NRB #E311

department: Oncology

institute: Georgetown University

summary: Here, we investigate the extent to which individual cells within the total bone marrow (tot-BM) and the lineage negative (Lin-neg) populations exhibit this isoform diversity and whether distinct subpopulations in tot-BM and Lin-neg cells intersect based on transcript isoform usage. We extracted healthy donor human bone marrow tissues from discarded harvesting filters. From this total bone marrow cell preparation (tot-BM) we enriched for lineage-negative progenitor cells (Lin-neg) by magnetic selection as described earlier (Deslattes Mays et al. 2019). We then analyzed total and Lin-neg cell populations by droplet-based single cell RNA sequencing (10xGenomics). In order to increase the number of mRNA molecules detectable per cell we reduced the cell input to approximately 500 cells for each experiment. After single-cell selection, the barcoded cDNA libraries were equally divided and each pool was analyzed in parallel by short-read sequencing (Illumina) and by single-molecule real-time (SMRT) full-length RNA sequencing (Pacific Biosciences).

overall_design: Single cell short-read and full-length RNA sequencing

first: Anton

last: Wellstein


title: High-throughput Drug Screening Identifies Fluoxetine as a Potential Therapeutic Agent for Neuroendocrine Prostate Cancer

first: Qi

last: Wang

state: Shanghai

address: Shanghai Pu Dong district, Dongfang Rd. No.1630

institute: Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine

summary: Here, we performed a high-throughput drug screening and identified fluoxetine, originally an FDA-approved antidepressant, as candidate therapeutic agent for NEPC. In vitro experiments revealed that fluoxetine effectively curbed the neuroendocrine differentiation and inhibited the cell viability by targeting the AKT pathway. Altogether, this work repurposed fluoxetine for antitumor application, and supported its clinical development for NEPC therapy, which may provide a promising therapeutic strategy.

overall_design: mRNA profiles of LASCPC-01 cells treated with PBS or Fluoxetine

first: Lei

last: Chen

first: Yiyi

last: Ji

first: Ang

last: Li

first: Wei

last: Xue

first: Yinjie

last: Zhu


title: Cigarette Smoke Alters CircRNA Expression in Human T-Cells

city: Erie

first: Ashley

last: Russell

state: PA

address: 4205 College Dr.

department: Department of Biology

institute: Penn State Erie School of Science, The Behrend College

summary: Circular RNAs, once thought to be a result of splicing errors, have been found to be involved in various molecular processes and in pathology of various diseases, including cancer and neurodegenerative disease. Additionally, circRNA expression was found to be altered by lifestyle habits, such as smoking cigarettes. Past studies have revealed that the rate of smoking remains high in the HIV-positive population. In this study, we isolated total RNA from uninfected T-cells that have been exposed to cigarette smoke and compared the expression levels of circRNAs to those of T-cells that were not exposed to cigarette smoke. We identified certain circRNAs that were upregulated or downregulated in T-cells when exposed to cigarette smoke. These data indicate that the study of circRNAs is warranted within the context of HIV infection.

overall_design: 3 replicates of human lymphocytic T-cells were exposed to 50% cigarette smoke exposure media and 3 additional replicates were exposed to 0% cigarette smoke exposure media for 24 hours. The isolated total intracellular RNA were then sent to Arraystar to assess the effect of cigarette smoke on circRNA levels.

first: So

last: Hong

first: Ahley

first: Kenneth

middle: W

last: Witwer

first: Zhaohao

last: Liao


title: Chronic administration of non-constitutive proteasome inhibitor modulates plasticity in hippocampus following tetanic stimulation, but not short theta-burst stimulation.

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

summary: Proteasomes degrade most intracellular proteins. Several different forms of proteasomes are known. Proteasome inhibitors targeting different proteasome forms are used in clinical practice and were shown to modulate long-term potentiation (LTP) in hippocampal slices of untreated animals. Here we studied the effect of chronic administration of non-constitutive proteasome inhibitor ONX-0914 on the LTP induced by two different protocols: tetanic stimulation and theta-burst stimulation (TBS). Excitatory postsynaptic potentials (fEPSPs) in hippocampal slices from control animals and animals treated with DMSO or ONX-0914 were compared. The TBS stimulation did not change LTP kinetics in hippocampal slices, however chronic administration of ONX-0914 led to the decrease in fEPSP slopes after tetanic stimulation. Observed effects correlated with differential expression of genes involved in synaptic plasticity, glutaminergic synapse and synaptic signaling. Obtained results indicate that non-constitutive proteasomes are likely involved in the tetanus-evoked LTP but not the LTP occurring after TBS, supporting the relevance and complexity of the role of proteasomes in the synaptic plasticity.

overall_design: deep RNA sequencing of hyppocampus tissues of mice treated with immunoproteasome inhibitor ONX-0914

first: A

middle: P

first: S

middle: Y

last: Funikov

last: Morozov

last: Burov


title: Noncoding RNA-mediated DNA methylation directs nucleosome positioning

city: Ann Arbor

first: Shriya

last: Sethuraman

state: MI

address: 5164 Biological Sciences Building, 1105 N. University Ave.

department: Bioinformatics

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing.

overall_design:
14 samples of MNase-H3-ChIP-Seq with 6 different genotypes and 2 replicates of each (Col-0, nrpe1, swi3b, drm2, cmt3, met1-3)
6 samples of WGBS with 3 different genotypes and 2 replicates of each (Col-0, nrpe1, swi3b)
Please note that as processed data was generated from multiple samples (as indicated in the corresponding sample description field) and is linked to the Series records.

first: Hafiz

last: Rothi

first: Andrzej

last: Wierzbicki


title: Systematic comparison of culture media uncovers phenotypic shift of primary human microglia defined by reduced reliance to CSF1R signaling

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: Efforts to understand microglia function in health and diseases have been hindered by the lack of culture models that recapitulate in situ cellular properties. In recent years, the use of serum-free media with brain-derived growth factors (CSF1R ligands and TGF-b1/2) have been favored for the maintenance of rodent microglia as they promote morphological features observed in situ. Here we study the functional and transcriptomic impacts of such media on human microglia. Media formulation had little impact on microglia transcriptome assessed by RNA sequencing which was sufficient to significantly alter microglia capacity to phagocytose myelin debris and to elicit an inflammatory response to lipopolysaccharide. When compared to immediately ex vivo microglia from the same donors, the addition of fetal bovine serum to culture media, but not growth factors, was found to aid in the maintenance of key signature genes including those involved in phagocytic processes. A phenotypic shift characterized by CSF1R downregulation in culture correlated with a lack of reliance on CSF1R signaling for survival. Consequently, no improvement in cell survival was observed following culture supplementation with CSF1R ligands. Our study provides better understanding of human microglia in culture, with observations that diverge from those previously made in rodent microglia.

overall_design: Transcriptomic analysis of human mciroglia maintained in various culture media for six days

first: Marie-France

last: Dorion

first: Moein

last: Yaqubi

first: Hunter

last: Murdoch

first: Jeffrey

last: Hall

first: Roy

last: Dudley

first: Jack

last: Antel

first: Thomas

last: Durcan

first: Luke

last: Healy


title: Dysregulated miRNAs modulate tumor microenvironment associated signaling networks in pancreatic ductal adenocarcinoma

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goals of this study are to investigate the role of miRNAs in regulating pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) and PDAC progress.
Methods: Total RNA-seq and miRNA-seq were performed on PDAC tumor and adjacent benigh tissues, and the miRNA profile was also investigated from the patient and healthy subject plasma. Single-cell RNA-seq was performed on one PDAC tissue, using 10x Genomics 5 prime gene expression technology.
Results: The RNA-seq and miRNA-seq libraries were sequenced on Illumina NextSeq 550 or HiSeq 4000 (Illumina, San Diego, CA). All sequencing data were demultiplexed and converted into fastq files by Illumina bcl2fastq2 v2.17.14. Filtered sequence reads were mapped to reference genome GRCh38 using STAR (RNA-seq) or Botwie (miRNA-seq) with default settings. Single cell data was mapped and counted uisng Cellranger (v5.0).
Conclusions: We identifed 322 and 49 differentially expressed miRNAs in PDAC tissue and patient plasma, respectively. We also identify 1,445 differentially expressed genes from PDAC tissue and paired the DEGs with their regualtory miRNAs through miRNA functional prediction.

overall_design: Tumor and adjacent benign tissues were obtained during surgical resections from PDAC patients. Plasma was obtained from peripheral blood of PDAC patients and healthy control subjects. Total RNA was extracted with Qiagen Allprep DNA/RNA/miRNA kit. RNA-seq libraries were constructed using Tecan Universal NuQuant kit and miRNA-seq libraries were constructed using QIAseq miRNA library kit.

first: Tiantian

last: Liu

first: Zhong

last: Chen


title: Transcriptomic profiles reveal differences between remote and ischemic myocardium after acute myocardial infarction in swine model

city: Cáceres

first: Esther

last: López Nieto

state: Cáceres

address: Carretera Nacional 521, Km 41.8 - 10071

department: Stem Cells Therapy

institute: jesús usón minimally invasive surgery centre

summary: The purpose of this study was to unravel the differences in the molecular profile between ischemic and remote myocardium after AMI.

overall_design: Four healthy pigs were subjected to a 90 minutes balloon occlusion of the mid-left anterior descending coronary artery. Seven days after model induction, animals were euthanized and myocardial tissue from ischemic and remote ventricle zones was collected for omics techniques.

first: María

last: Pulido

last: Ángeles de Pedro

last: López


title: H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [ChIP-seq]

city: guangzhou

first: Xinjie

last: Li

address: gongming street 66

institute: sun yat-sen university

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for  LSD1 as well as histone modifications H3K4me1, H3K4me3 and H3K27me3 in WT OG2 mESC cells and its KO derivatives (Eed-KO and Suz12-KO ).

overall_design: Comparative LSD1 and histone modifications distribution pattern analysis of ChIP-sep data for WT OG2 mESC cells and its KO derivatives (Eed-KO and Suz12-KO ).

first: Yue

last: Yu


title: The utility of circulating CX3CR1+ CD8+ T cells as a predictive correlate of response to chemo-immunotherapy in patients with non-small cell lung cancer

city: Buffalo

first: Mark

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Lack of reliable predictive biomarkers is a major limitation of combination therapy with chemotherapy and anti-PD-1 therapy (chemo-immunotherapy). The increase of peripheral blood (PB) CD8+ T cells expressing CX3CR1, a marker of differentiation, correlates with response to anti-PD-1 therapy; however, the predictive and prognostic value of T-cell CX3CR1 expression during chemo-immunotherapy remains elusive. Here, we evaluated the utility of PB CX3CR1+CD8+ T cells as a predictive correlate of response to chemo-immunotherapy in non-small cell lung cancer (NSCLC) patients. At least 10% increase of the CX3CR1+ subset in circulating CD8+ T cells from baseline (CX3CR1 score) was associated with response to chemo-immunotherapy at 6 weeks (p = 0.0382) and 9 weeks (p = 0.0045). Sensitivity, specificity, positive and negative predictive value of at least 10% increase of the CX3CR1 score was 83.3%, 88.2%, 83.3% and 88.2%, respectively with 86.2% overall accuracy of predicting response at 9 weeks. Furthermore, at least 10% increase of the CX3CR1 score correlated with improved overall (p = 0.0105) and progression-free survival (p = 0.0265). Combined T-cell receptor (TCR) sequencing of tumor tissue and single-cell RNA/TCR sequencing of longitudinal PB samples from a patient who received a long-term benefit from chemo-immunotherapy demonstrated that circulating clonally expanded CD8+ T cells were terminal effector T cells expressing high levels of CX3CR1, and contained frequent tumor-infiltrating T-cell colonotypes early-on post treatment. Collectively, these findings suggest the potential utility of T-cell CX3CR1 expression as a dynamic blood-based biomarker during the course of chemo-immunotherapy and a marker to identify frequent tumor-infiltrating lymphocyte repertoires.

overall_design: Single live CD45+CD19–CD3+CD56– cells were enriched from cryopreserved PBMC samples obtained pre-treatment and on-treatment at 3, 6, 9 weeks by flow cytometry sorting using a BD FACSAria II (BD Biosciences). Cells were counted, hashed with TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253 and TotalSeq-C0254 anti-human antibodies, BioLegend) and pooled. The pooled cells were then counted again and immediately loaded onto the chromium chip G using the standard protocol for the Chromium single-cell 5’ kit v2 (10x Genomics, Inc). Following Gel Bead-in Emulsion (GEM) generation, samples were processed using the standard manufacturer’s protocol. Once sequencing libraries passed standard quality control metrics, the libraries were sequenced on Illumina NovaSeq6000 S1 100cycle v1.5 kits with the following read structure: read1: 28, read2: 90, index 1: 10, index 2:10. Libraries were sequenced to obtain a read depth greater than 16,000 reads/cell for the gene-expression (GEX) libraries and greater than 4,000 reads/cell for the V(D)J-enriched T Cell libraries.

first: Long

last: Mark

first: Ito

last: Fumito


title: Fasting-mimicking diet synergizes with ferroptosis against quiescent, chemotherapy-resistant cells

first: Xiaoxia

state: Guangdong

address: 26 Yuancun Erheng Road

department: The Sixth Affiliated Hospital

institute: Sun Yat-sen University

summary: To investigate the molecular mechanisms of Nutrient-restricted conditions (Fasting), 5 Fluorouracil+oxaliplatin, and their combination in CRC cell line RKO

overall_design: We have treated CRC cell line RKO with fasting-cultures, 10 µM of 5-FU/oxaliplatin, and their combination for 48 hours. Then we performed RNA sequencing.

first: Yanxin

last: Luo

first: Shaoyong

last: Peng

first: Yumo

last: Xie


title: Next Generation Sequencing facilitates to identify the differential expression genes of liver tissue from with liver injury(AST>40) or without liver injury(AST<40) from HBV-infected patients.

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

summary: We obtained HBV-infected liver tissues from liver surgery(AST<40) and liver transplantation(AST>40) to perform next-generation sequencing (NGS). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results,  we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).

overall_design: Differential gene expression between liver tissue (AST<40 and AST>40).

first: Xiufang

last: Weng


title: H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development.

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

overall_design: Refer to individual Series


title: Characterization of E13.5 forelimb gene expression after Hic1 knockout

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

institute: University of British Columbia

summary: To investigate the effect of the mesenchymal quiescence regulator, Hic1, on forelimb development, we collected forelimbs from conventional Hic1 knockout animals to animals with a limb specific Hic1 knockout driven by the proposed limb mesenchyme specific Prrx1-Cre line.

overall_design:
We then homogenized the forelimbs for RNAseq analysis and normalized by FPKM.
Comparative gene expression profiling analysis of RNA-seq data from animals using two knockout strategies to delete Hic1.

first: Martin

last: Arostegui

first: Wilder

last: Scott

first: T


title: WGBS-seq and oxWGBS-seq Atlas for Oral Squamous Cell Carcinoma

city: Hengyang

first: Zhengqing

last: Wan

address: 28 West Changsheng Road

institute: University of South China

summary: Whole genome bisulfite sequencing (WGBS‑seq) and whole-genome oxidative bisulfite sequencing (oxWGBS‑seq) in four paired OSCC tumor and its NAT were performed to obtain precise, genome-wide, single-base resolution maps of 5mC and 5hmC. Based on these maps, the genomic content of 5mC and 5hmC in these paired samples were observed, as well as the distributions of 5mC and 5hmC in genic regions and histone-marked gene regulatory regions.

overall_design: WGBS-seq and oxWGBS-seq profiles of four paired samples of OSCC and NAT

first: Danling

last: Wang


title: ALDOC- and ENO2- driven glucose metabolism sustains 3D tumor spheroids growth regardless of nutrient environmental conditions: a multi-omics analysis

city: Rome, RM

first: Alice

last: Massacci

address: Via Elio Chianesi, 53, 00128 Rome RM

country: Italy

institute: IRCSS Regina Elena National Cancer Institute, Rome

summary: Investigation of lung adenocarcinoma (LUAD) and breast cancer cells cultured in either a nutrient-rich or -restricted culture conditions trough a multi-omics approach, including transcriptomics, to explore the molecular changes underlying the transition from 2D to 3D cultures.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 2D to 3D cultures of H460 and MCF7 cells

first: Rita

last: Mancini

first: Claudia

last: De Vitis

first: Sara

last: Bruschini

first: Andrea

last: Vecchione

first: Francesca

last: Ascenzi

first: Francesco

last: Costanzo

first: Flavia

last: Biamonte

first: Gianluca

last: Santamaria

first: Anna

last: Battaglia

first: Marco

last: Gaspari

first: Giovanni

last: Cuda

first: Alessandro

last: Sacco

first: Antonella

last: Esposito

first: Rosy

last: Cavaliere

first: Maria

last: Mimmi

first: Cristina

last: Cereda

first: Ferdinando

last: Chiaradonna

first: Gennaro

last: Ciliberto

first: Giulia

last: Ricci

first: Matteo

last: Pallocca

first: Eleonora

last: Sperandio

last: De Nicola

first: Maurizio

last: Fanciulli

first: Valentina

last: Salvati

first: Alberto


title: KIT D816V mast cells derived from induced pluripotent stem cells recapitulate systemic mastocytosis transcriptional profile

city: Aachen

first: Mirle

last: Schemionek

state: NRW

address: Pauwelsstr. 30

department: Hematology, Oncology, Hemostaseology and SCT

institute: University Hospital RWTH Aachen

summary: Mast cells (MC) represent a population of hematopoietic cells with a key role in innate and adaptive immunity and are well known for their detrimental role in allergic responses. Yet, MC occur in low abundance which hampers their detailed molecular analysis. Here, we capitalized on the potential of induced pluripotent stem (iPS) cells to give rise to all cells of the body and established a robust protocol for human iPS cell differentiation towards MC. Relying on a panel of systemic mastocytosis (SM) patient-specific iPS cell lines carrying the KIT D816V mutation, we generated functional MC that recapitulate SM disease features: increased number of MC, abnormal maturation kinetics and activated phenotype, CD2 and CD30 surface expression and a transcriptional signature characterized by upregulated expression of innate and inflammatory response genes. Therefore, human iPS cell-derived MC are a reliable and close-to-human tool for disease modeling and pharmacological screening to explore novel MC therapeutics.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KIT D816V mast cells and WT mast cells

first: Marcelo

middle: A

last: Toledo

first: Tiago

last: Maié

first: Ivan

middle: G

last: Costa

first: Martin

last: Zenke


title: Study on tolerance of Vibrio splendidus to tetracycline and coelomic fluid of sea cucumber

city: Nibong

first: Li

middle: Ya

address: 818 Fenghua Road

institute: Ningbo university

summary: It was found that Vibrio splendidus could survive under high concentration of tetracycline, and the coelomic fluid of sea cucumber increased the tolerance of Vibrio splendidus to tetracycline. Therefore, the transcriptome was determined to find the cause of drug resistance in Vibrio splendidus.

overall_design: Vibrio splendidus at three culture stages included OD600=0.6,1.2,2.0. Tetracycline was treated with 10 times minimum inhibitory concentration at 28 ° C for 4 hours. For the coelomic fluid, it was pretreated for 1 h and then exposed to tetracycline for 4 h at 28 ° C


title: Next Generation Sequencing facilitates identification of differentially expressed genes in circulating and hepatic CD161+CD8+T cells (CD161P), CD161-CD8+T cells (CD161N) and MAIT cells from healthy donors(HD) and HBV-infected patients

first: xiufang

last: weng

summary: We enriched circulating and hepatic CD161N, CD161P and MAIT cells through flow sorting from heathy donors and HBV-infected patients to perform next-generation sequencing (NGS). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina novaseq 6000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results, we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of CD161N,CD161P and MAITcells from healthy donors and HBV-infected patients.

overall_design: Differential gene expression between circulating and hepatic CD161N, CD161P and MAIT cells from healthy donors and HBV-infected patients

first: Xiufang

last: Weng


title: Monocyte subpopulations display disease-specific miRNA signatures depending on the subform of Spondyloarthropathy

city: Kraków

first: Marcin

last: Czepiel

address: Anny 12

department: Clinical Immunology

country: Poland

institute: Jagiellonian University Medical College

summary:
Our data indicate for the first time that in different SpA subtypes, monocyte subpopulations bear disease-specific miRNA signatures that could be relevant for SpA diagnosis/differentiation process and may help to understand SpA etiopathology in the context of already known functions of monocyte subpopulations
The aim of the study was to investigate the micro-RNA (miRNA) profiles in monocyte subpopulations (classical, intermediate and non-classical subpopulations) acquired from SpA patients or healthy individuals in search for prospective disease specific and/or disease subtype differentiating miRNA markers

overall_design: Monocyte subpopulations were isolated from peripheral blood mononuclear cells (PBMC) obtained from SpA patients or healthy donors. PBMC were isolated from EDTA-treated whole peripheral blood by the standard Pancoll human (Panbiotech, Aidenbach, Germany) density gradient centrifugation. PBMC were washed in PBS (Sigma-Aldrich, Saint Louis, USA) and then monocyte subsets (classical - CD14++CD16-, intermediate - CD14++CD16+ and non-classical - CD14+CD16++) were isolated using flow cytometry cell sorting

first: Małgorzata

last: Stec

first: Mariusz

last: Korkosz

first: Maciej

last: Siedlar


title: IRX5 promotes DNA damage repair and activation of hair follicle stem cells (hfsc)

city: Irvine

first: Jefferson

last: Chen

address: UC Irvine

institute: UC Irvine

summary: Here, we identify the transcription factor IRX5 as a promoter of HFSC activation. Irx5-/- mice display delayed onset of first postnatal anagen, with increased DNA damage and diminished HFSC proliferation. Through transcriptomic and epigenetic analysis, we discover the formation of open chromatin regions near key cell cycle progression- and DNA damage repair genes in Irx5-/- HFSC. We also identify DNA damage repair factors BRCA1 and BARD1 as IRX5 downstream targets. Inhibition of FGF18 kinase signaling partially rescues the anagen delay in Irx5-/- mice, indicating that the Irx5-/- HFSC quiescent phenotype is in part due to failure to suppress Fgf18 expression. Our findings identify IRX5 as a required promoter of DNA damage repair in HFSC activation and hair cycle initiation.

overall_design: P18 and P20 back skin was dissected and incubated in 0.25% trypsin (Invitrogen 1505-065) for 2hrs at 34C. The epidermal side was mechanically separated and resuspended in 2% FBS PBS. Debris was removed with 40uM and 70uM mesh filters. Whole epidermis samples were processed for bulk RNA-seq. For HFSC bulk RNAseq, cells were labeled with CD45f (eBioscience 12-0495), Ly-6A/E (eBioscience 45-5981-82), CD34 (eBioscience 50-0341-82), and DAPI.  Ly-6A/E- CD34+ CD45f+ HFSC were isolated for bulk RNAseq

first: Bogi

last: Andersen


title: Role of adipose tissue Na/K ATPase signaling in uremic cardiomyopathy

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: The objective of the present study is to explore the role of human MSC derived adipocytes transduced with/without lenti adipo-NaKtide or lenti adipo-scrambled NaKtide in experimental uremic cardiomyopathy. We investigated the pathophysiological changes in recipient mice that underwent partial nephrectomy surgery, as a model of uremic cardiomyopathy, and implanted with NaKtide transfected human MSC derived adipocytes. We aimed to demonstrate that adipocyte specific NaKtide reprograms the adipocyte phenotype and transplantation of these metabolically healthy adipocytes in diseased condition exhibits improved systemic and cardiovascular function, through intra-organ crosstalk.

overall_design: RNA was extracted from Heart, Kidney and Visceral adipose tissues of SCID mice (12 weeks old, male) in each group; SCID-Sham, SCID-PNx, SCID-ControlCells-PNx, SCID-Lenti-NaKtideCells-PNx, SCID-Scrambled-NaKtideCells-PNx,  and sequenced in a 2x50 base-pair design on an Illumina 1500 sequencer.

first: Komal

last: Sodhi

first: Sneha

middle: S

last: Pillai

first: Hari

last: Lakhani

first: Mishghan

last: Zehra

first: Duane

last: Pereira

first: Muhammad

last: Chaudhary

first: Xiaoliang

last: Wang

first: Yiliang

first: Jiang

last: Liu

first: Khew-Voon

last: Chin

first: Joseph

middle: I

last: Shapiro


title: Comparison of germ free and colonized mouse livers at baseline and 3 hours post partial hepatectomy

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

institute: University of Bern

summary: The microbiota is known to exert substantial effects on shaping an organism's immune system and immune composition of organs. Here we questioned the effect of the microbiota on the transcriptional signature of mouse liver tissue at baseline and during regeneration.

overall_design: A two-thirds surgical partial hepatectomy was performed in germ free (GF) mice and mice colonized with altered scaedler flora (ASF). Mouse liver tissue was analyzed 3 hours post resection by RNA seq.

first: Guido

last: Beldi

first: Deborah

last: Stroka

last: Sanchez-Taltavul

first: Thomas

last: Malinka


title: Reversal of post-hepatectomy liver failure using a bioartifical liver supporting system implanted with clinical-grade human induced hepatocytes

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: Here, we developed a clinical-grade bioartificial liver (BAL) device by implanting with directly reprogrammed human hepatocytes (hiHep) manufactured and cryopreserved under current good manufacturing practice (cGMP) conditions. Notably, in a porcine PHLF model induced by 85% hepatectomy, hiHep-BAL treatment showed a remarkable survival benefit, as well as improvements of liver metabolic gene expression, ammonia detoxification, and liver regeneration. Furthermore, an investigator-initiated study in seven patients with extended liver resection (NCT05035108) demonstrated that hiHep-BAL treatment was well tolerated without complications and associated with ameliorative liver function and remarkable liver regeneration, meeting the primary outcome of safety and feasibility. These encouraging results warrant the further efficacy testing of hiHep-BAL for PHLF followed by the future broadening the patients eligible for liver resection in clinics.

overall_design: To determine the therapeutic mechanism of hiHep-BAL on PHLF,we performed a whole-genome RNA-sequencing analysis of PHLF livers from the No-BAL group versus normal liver to determine PHLF-associated genes.  Expression profile of hiHep-BAL-treated livers on day 4 and 8 were then compared to identify the reverted PHLF genes, as potential hiHep-BAL-regulated genes. Empty-BAL group was used as a control to exclude the effect of blood.

first: Yifan

first: Qiang

last: Zheng

first: Zhen

last: Sun

first: Ludi

last: Zhang

first: Xiujun

last: Cai


title: Low dose interleukin-2 treatment selectively expands circulating regulatory T cells but fails to promote their trafficking into the liver and the induction of liver transplant tolerance

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Low dose interleukin-2 (LDIL-2) can effectively expand endogenous circulating regulatory T-cells (Tregs) in vivo, but its role in promoting allograft tolerance in humans has not been investigated. We conducted a clinical trial in stable liver transplant recipients to determine the capacity of LDIL-2 to suppress allospecific immune responses and allow the complete discontinuation of maintenance immunosuppression (clinicaltrials.gov NCT02949492). LDIL-2 treatment achieved a marked and sustained increase in circulating Tregs in all patients. However, this was not associated with the preferential expansion of donor-reactive Tregs, did not promote the accumulation of Tregs within the liver allograft, failed to induce tolerance and primed the allograft for rejection even before immunosuppression weaning was initiated.

overall_design: PBMC and Liver biopsies were extracted from six subjects treated with LDIL-2 at baseline and four weeks.

first: T

last: Lim

first: A

last: Sanchez-Fueyo

first: Martinez-L

last: Lordella

first: J

middle: J

first: E

last: Perpiñan

first: M

middle: C

last: Londoño

first: R

last: Miquel


title: Impact of circadian time, feeding-fasting rhythm and the autonomous clock on chromatin accessibility

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: Using an "omics"-based approach, we investigated the interaction between the autonomous liver clock and feeding-fasting rhythm. Transcriptomic analysis and subsequent quantification of exonic and intronic reads revealed that transcriptional mechanisms mediate, at least in part, the integration of feeding signals by the liver clock to drive mRNA oscillations. Therefore, we performed ATAC-seq to probe the state of chromatin accessibility genome-wide. While most open chromatin regions are unchanged across genotype, time and feeding status, transcription factor (TFs) footprints showed altered activity of certain TFs in Liver-RE AL vs NF. For example, CEBPB activity is altered in Liver-RE AL and restored in NF, an observation accompanied by restored CEBPB and BMAL1 common target gene oscillations. Finally, metabolomics analysis illustrated the partial rescue of hepatic metabolism in Liver-RE NF compared to AL (extensive carbohydrate pathway oscillations), and made clear that extra-hepatic clocks contribute significantly to metabolic oscillations in the liver, particularly for pathways involving lipids. Please see the associated reference for full results.

overall_design: 8-12 week old male wild type (WT), Bmal1-KO (Bmal1 stop-Fl; KO) and Bmal1 Liver-reconstituted (Bmal1 stop-Fl, AlfP cre +/-; Liver-RE) mice were subjected to ad libitum feeding (AL) or feeding restricted to the nighttime (NF, ZT12-24) of normal chow for 2 weeks under a standard 12 hr light - 12 hr dark cycle. Livers were collected at ZT8 and ZT20 and prepared for ATAC-sequencing.

first: Kevin

middle: B

last: Koronowski

first: Paolo

last: Sassone-Corsi

first: Carolina

middle: M

last: Greco

first: Jacob

last: Smith


title: RRBS analysis of Braf-activated MEFs

city: Worcester

first: Ichiro

last: Onoyama

address: 364 Plantation St

institute: University of Massachusetts Medical School

summary: We investigated DNA methylation status by RRBS method after oncogenic Braf activation using MEFs isolated from Braf knockin mice. Window-based analysis made it clear that the regions <500 bp from TSS were hypermethylated after Braf activation, whereas those >5000 bp from TSS were less methylated after Braf activation compared with wild-type MEFs. A hallmark of human cancer genomes is global DNA hypomethylation accompanied by focal DNA hypermethylation. Although factors and pathways that mediate DNA hypermethylation in cancer cells have been described, the basis of DNA hypomethylation remains to be determined. Here we show that expression of an activated BRAF oncoprotein, BRAFV600E, is sufficient to promote global DNA hypomethylation in mouse embryonic fibroblasts (MEFs). Conversion of 5-methylcytosine (5-mC) to its oxidation product 5-hydroxymethylcytosine (5-hmC) is thought to be the first step in a pathway leading to complete DNA demethylation. We find that BRAFV600E-directed global DNA hypomethylation occurs through conversion of 5-mC to 5-hmC by TET3, a member of the ten-eleven translocation (TET) family of proteins. In normal cells, TET3 is maintained at low levels resulting from ubiquitination by a SKP1–CUL1–F-box (SCF)-type ubiquitin ligase containing the F-box protein FBXW7, a known tumor suppressor, and subsequent proteasome-mediated degradation. BRAFV600E increases TET3 levels through inhibition of glycogen synthase kinase-3b (GSK3b), a protein kinase that phosphorylates TET3 and is required for SCFFBXW7-mediated ubiquitination. Consistent with these cell culture results, we find increased levels of TET3 and 5-hmC in experimentally induced mouse lung adenomas and patient-derived human colorectal adenomas that contain BRAFV600E. Moreover, we show that RNAi-mediated knockdown of Tet3 results in decreased BRAFV600E-induced tumorigenesis. Finally, to test the generality of our findings, we repeated several key experiments using a KRASG12D oncoprotein rather than BRAFV600E and obtained similar results. Collectively, our results elucidate a mechanism of global DNA hypomethylation promoted by oncogenic BRAF and KRAS, and establish an essential role for TET3 at an early stage of oncogenesis.

overall_design: Rosa26-CreERT2; Braf+/+ female MEFs (Control) and Rosa26-CreERT2; Braf+/LSL female MEFs were treated with 4-OHT to induce Cre recombinase. MEFs were harvested 0 or 21 days after 4-OHT treatments. We repeated the experiments 3 times with different clones. Total samples are 12.

first: Shoichiro

last: Takeishi

first: W

middle: R

last: Hardy

first: Lihua

last: Zhu

first: Lloyd

last: Hutchinson

first: Jianhong

last: Ou

first: Leyuan

last: Ma

first: Ching-Man

last: Virbasius

first: Keiichi

last: Nakayama

first: Michael

last: Green


title: H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development [RNA-seq]

first: Xinjie

last: Li

address: gongming street 66

institute: sun yat-sen university

summary: To investigate the differential expression pattern between wild type mESC cells and PRC2-deficient cells. We established Eed-KO and Suz12-KO cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq of these different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT OG2 mESC cells and its KO derivatives (Eed-KO and Suz12-KO ).

first: Yue

last: Yu


title: A landscape of circular RNAs expression in the castration-resistant prostate cancer

city: Guangzhou

first: wen

last: tao

address: Tianhe Road 600

institute: The Third Affiliated Hospital, Sun Yat-sen University

summary: Prostate cancer is one of the major cancers that seriously affect men's health. It has high morbidity and high mortality, but there is still no ideal molecular markers for the diagnosis and prognosis of prostate cancer. Castration-resistant prostate cancer is associated with wide variations in survival. To determine whether differentially expressed circRNAs in plasma exosomes can be used as a novel biomarker for castration-resistant prostate cancer prognosis, we performed high-throughput circRNA sequencing on 15 pairs of plasma exosomes from 30 metastatic castration-resistant prostate cancer patients, with or without early progression, to screen differentially expressed circRNAs.

overall_design: We performed deep RNA-sequencing on ribosomal-depleted RNA isolated from 15 pairs of plasma exosomes from 30 independent patients with castration-resistant prostate cancer, with or without the presence of metastases, using Illumina X Ten.  Patients were paired according to their age and clinical indicators.

first: Liao-Yuan

first: Wen

last: Tao


title: RNA-seq analysis of HeLa cells in nutrient-rich and nutrient-deprived media

city: Tel Aviv

first: Karen

last: Avraham

country: Israel

institute: TAU

summary: RNA-seq analysis was applied in two independent batches, each one in triplicate samples of HeLa cells in nutrient-rich and nutrient-deprived media

overall_design: Transcriptome analysis of HeLa cells in nutrient-rich and nutrient-deprived (starved) media in two independent batches/sets, each one in three biological repeats

first: Margarita

last: Galves

first: Michal

last: Sperber

first: Fatima

last: Amer-Sarsour

first: Ran

last: Elkon

first: Avraham

last: Ashkenazi


title: Gene expression profiling of Fah- and Hgd-deficient mouse livers upon short-term nitisinone discontinuation

status: Public on Apr 04 2023

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology & Dermato-cosmetology (IVTD)

institute: Vrije Universiteit Brussel

summary:
Hereditary tyrosinemia type 1 (HT1) is a severe genetic disorder that affects the liver due to a defective fumarylacetoacetate hydrolase (Fah) enzyme in hepatocytes. The drug nitisinone (NTBC) has offered a life-saving treatment for HT1 patients by inhibiting the upstream enzyme 4-hydroxyphenylpyruvate dioxygenase (HPD).
We used microarray analyses to to identify changes in molecular pathways associated to the development and progression of the liver pathogenesis of HT1 that remain uncorrected under NTBC therapy by using gene expression profiling of Fah-deficient mouse livers subjected to continuous NTBC therapy and after seven days of NTBC therapy discontinuation. As a control of a TIMD without hepatic manifestation, we used the Hgd-deficient mouse model of AKU, also under continuous NTBC treatment and after seven days of NTBC therapy discontinuation. Consequently, we identified a set of 25 genes that discriminates HT1 livers from AKU livers, even under continuous NTBC therapy, as such representing remnants of an HT1-driven residual uncorrected liver disease phenotype.

overall_design: FAH5981SB mice (C57Bl/6J background) bear a mutation that is a G-to-A transition at the last base of VEGA exon OTTMUSE00000329891 leading to the splicing out of this exon, which results in a frameshift and subsequently the introduction of a premature stop codon at amino acid position 303, ultimately leading to formation of truncated, unstable and degraded Fah protein and served thereby as experimental model for HT1. The homozygous Hgd knockout-first allele mouse (Hgd tm1a-/-) (C57Bl/6J  background), is an animal model of human AKU. Hgd tm1a-/- mice contain an IRES:LacZ gene trap cassette and a promoter-driven neo cassette inserted into the fifth Hgd intron with the sixth exon flanked by loxP sequences. Homozygous Hgd tm1a-/- mice therefore show an AKU phenotype based on Hgd gene disruption. Hgd tm1a-/- mice develop specific symptoms of AKU including blackening of urine and progressive osteoarthritis when NTBC is not administered. Fah- and Hgd-deficient mice were either continuously treated with 8 mg/L NTBC through their drinking water or deprived from NTBC therapy for seven consecutive days. Withdrawal samples were collected seven days after NTBC discontinuation.

first: Jessie

last: Neuckermans

first: Haaike

last: Colemonts-Vroninks

first: Paul

last: Claes

first: Anja

last: Heymans

first: Geert

last: Martens

first: Tamara

last: Vanhaecke


title: Interaction between the microbiome and the severity of diversion colitis after low anterior resection of rectal cancer

first: Yunjie

last: Shi

address: No.800 Xiangyin Road

institute: Naval Medical University

summary: Background:Diversion colitis (DC) is a non-specific inflammation in the intestinal mucosa with colonic dysfunction after low anterior resection of rectal cancer. It is newly proposed in recent years. With the gradual prolongation time of the ileostomy status, the condition of DC may become increasingly severe. However, the corresponding pathogenesis of DC has not been clarified yet.  Methods:Clinical information were collected from patients with low rectal cancer admitted to the Department of Anorectal Surgery, Changzheng Hospital, from April 2017 to April 2019. All patients were underwent laparoscopic low anterior resection combined with terminal ileum enterostomy (dual-chamber). After 3-6 months, selective enterostomy closure surgeries were conducted. Retrospective data were divided into mild and severe groups based on the scores of electronic colonoscopy  made during follow-up. We then used chi-square test to comparethe clinical baseline information, clinical symptoms, and endoscopic characteristics between the two groups of patients. The multivariate Cox proportional hazards regression model was applied for estimating the odds ratio (OR) and corresponding 95% confidence interval (CI) to identify potential significant factors affecting severity of DC severity. After that, we recruited 40 patients with low rectal cancer after surgery (enterostomy status) and 40 patients were further classified into mild and severe groups according to the scores of endoscopic examinations. The following indexes were tested in the above two groups patients: calprotectin in intestinal lavage fluid, inflammatory factors in tissue and plasma, and lipopolysaccharide levels in plasma. Moreover, 16s-rDNA sequencing was carried out to analyze the diversity and and differences of microbiome in theintestinal lavage fluid of the two groups.  Results:According to the endoscopic scores, there were 52 cases in the mild group and 58 cases in the severe group. We found that the age, BMI, history of diabetes , and the incidence of DC-related clinical symptoms (including abdominal pain, mucus, bloody stool, etc.) were significantly different between the two groups. (P＜0.05). Logistic multi-factor regression analysis results showed that age, BMI, history of diabetes, and symptoms associated with the state of the stoma are the independent risk factors that affect DC severity (P＜0.05). After enterostomy closure surgeries, compared with mild group, patients in the severe group showed much more clinical signs, such as abdominal pain, bloody stools, tenesmus, and anal pain andthe daily number of diarrhea, the time to return to normal stool and the level of CRP in plasma were significantly higher (P＜0.05). Results also showed that age, BMI, history of diabetes, and endoscopic scores were the independent risk factors affecting diarrhea severity after enterostomy closure surgery (P＜0.05). Of the 40 patients with low rectal cancer recruited, 23 were in the mild group and 17 in the severe group.In particular, the levels of calprotectin in the intestinal lavage fluid, TNF-α, IL-1β, IL-6 and IL-17 in mucosal /plasma, and the plasma LPS level of severe group were significantly higher than that of mild group (P＜0.05). .   The results of 16s-rDNA sequencing showed that micromicrobiome with high enrichment values primarily consisted of Bifidobacteriales and Prevotella in mild group, whereas that in the severe group consisted of Providencia and Dorea. The functional predictions on such two types of microbiome were mainly focused on lipid synthesis, glycan synthesis, metabolism, and amino acid metabolism pathways.

overall_design: Clinical information were collected from patients with low rectal cancer admitted to the Department of Anorectal Surgery, Changzheng Hospital, from April 2017 to April 2019. All patients were underwent laparoscopic low anterior resection combined with terminal ileum enterostomy (dual-chamber). After 3-6 months, selective enterostomy closure surgeries were conducted. Retrospective data were divided into mild and severe groups based on the scores of electronic colonoscopy  made during follow-up. We then used chi-square test to comparethe clinical baseline information, clinical symptoms, and endoscopic characteristics between the two groups of patients. The multivariate Cox proportional hazards regression model was applied for estimating the odds ratio (OR) and corresponding 95% confidence interval (CI) to identify potential significant factors affecting severity of DC severity. After that, we recruited 40 patients with low rectal cancer after surgery (enterostomy status) and 40 patients were further classified into mild and severe groups according to the scores of endoscopic examinations. The following indexes were tested in the above two groups patients:calprotectin in intestinal lavage fluid, inflammatory factors in tissue and plasma, and lipopolysaccharide levels in plasma. Moreover, 16s-rDNA sequencing was carried out to analyze the diversity and and differences of microbiome in theintestinal lavage fluid of the two groups.

first: Qiang

last: Sun

first: Xiaoben

last: Liang

first: Xinxing

last: Li


title: Expression data from regulatory T cells of lymph nodes from NOD and NOD.Drak2-/- mice

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary:
Drak2-deficient (Drak2-/-) mice are resistant to autoimmune disease, yet maintain the ability to effectively eliminate pathogens and tumors. Thus, DRAK2 is an ideal target to treat autoimmune disease. However, the mechanisms by which DRAK2 regulates autoimmune disease development, particularly in type 1 diabetes (T1D), remain unresolved.
We demonstrate that the resistance to T1D in non-obese diabetic (NOD) mice was due to the absence of Drak2 in T cells and required the presence of regulatory T cells (Tregs).

overall_design: Regulatory T cells (CD4+ CD8- CD25+ CD45RBlo) sorted from lymph nodes of NOD and NOD.Drak2-/- mice were sorted for RNA extraction and microarray analysis.

first: Aleandra

middle: H

last: Mandarano

first: Meenu

last: Pillai

first: Sarah

last: Mullen

first: Maureen

last: McGargill


title: Canagliflozin impairs T-cell effector function via metabolic suppression in autoimmunity [Autoimmune Profiling]

city: Swansea

first: Benjamin

middle: James

last: Jenkins

address: Singleton Park

country: United Kingdom

institute: Swansea University

summary: Augmented T-cell function leading to host damage in autoimmunity is supported by metabolic dysregulation. Targeting immunometabolism for the treatment of autoimmunity by repurposing clinically approved metabolic modulators, such as those used to treat people with type 2 diabetes (T2D), is therefore an attractive avenue. Canagliflozin, a class of the newest type of T2D drug – sodium glucose co-transporter 2 (SGLT2) inhibitors – has known off-target effects including mitochondrial glutamate dehydrogenase (GDH) and complex I inhibition. To date, the effects of SGLT2 inhibitors on human T-cell function are extremely limited. Here, we analysed 784 genes using the Nanostring nCounter® Autoimmune Profiling Panel and discovered 42 genes that were differentially regulated between canagliflozin-treated (cana, C; n = 6) and DMSO vehicle control (V; n = 6) T-cells. Of these genes, 39 were downregulated, including IL2, CSF2 and CCL20; whilst 3 were upregulated, including SELL. Dapagliflozin was used as another control, as this SGLT2 inhibitor does not exhibit any known off-target effects like canagliflozin. Here, there were no differentially expressed genes between dapagliflozin-treated (dapa, D; n = 4) and DMSO vehicle control (V; n = 4) T-cells. These analyses allowed a greater understanding of the global changes in T-cell function that occur in response to treatment with SGLT2 inhibitors.

overall_design: Three treatment conditions - DMSO vehicle control, canagliflozin-treated and dapagliflozin-treated

first: Julianna

last: Blagih

first: Fernando

last: Ponce-Garcia

first: Mary

last: Canavan

first: Nancy

last: Gudgeon

first: Simon

last: Eastham

first: David

last: Hill

first: Megan

last: Hanlon

first: Eric

last: Ma

first: Emma

middle: L

last: Bishop

first: April

last: Rees

first: James

last: Cronin

first: Elizabeth

last: Jury

middle: K

last: Dimeloe

first: Douglas

last: Veale

first: Catherine

last: Thornton

first: Karen

last: Vousden

last: Finlay

first: Ursula

last: Fearon

first: Gareth

middle: W

last: Jones

first: Linda

middle: V

last: Sinclair

middle: E

last: Vincent

first: Nicholas


title: Effect of knockout and overexpression of the Streptococcus pneumoniae topoisomerase I regulator StaR on gene expression.

city: Madrid

first: Pablo

last: Hernandez

state: Madrid

address: Ramiro de Maeztu 9

department: Cellular and Molecular Biology

institute: Centro de Investigaciones Biologicas (CSIC)

summary: Strain ∆staRPZnstaR was obtained to investigate genome-wide differential gene expresion when staR gene is reppressed or overexpressed by adding Zn to the culture medium.  In addition, gene expression profile alterations produced upon inhibition of gyrase with Novobiocin were studied in the absence and presence of StaR.

overall_design: Cultures were grown to OD620nm = 0.2, diluted 50-fold in medium either without ZnSO4 (staR repressed) or with 150 µM ZnSO4 (staR activated) and grown to OD620nm = 0.4. Samples were taken at this point for the comparative gene expression profiling analysis of RNA-seq when staR was repressed or over-expressed (two biological replicates). Then, novobiocin was added to the cultures and they were grown for 30 additional min, while the same ZnSO4 concentration was maintained. Samples were taken at this point for the comparative gene expression profiling analysis of RNA-seq when gyrase is inhibited with novobiocin in the absence or in the presence of StaR. Two biological replicates were analyzed.

first: Antonio

middle: A

last: de Vasconcelos Jr

first: Jose

last: Tirado-Vélez

last: Martín-Galiano

first: Diego

last: Megías

first: María-José

last: Ferrándiz

last: Hernández

first: Mónica

last: Ambla

first: Adela

middle: G

last: de la Campa


title: Transcriptional and chromatin accessibility profiling of neural stem cells differentiating into astrocytes reveal dynamic signatures under homeostatic and inflammatory conditions

city: New Delhi

first: Kartikeya

last: Singh

address: Outer Ring road

country: India

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

overall_design: Refer to individual Series