title: Potentiating radiation-induced T1IFN and the anti-tumoral immune response with the ATM inhibitor AZD1390 in pancreatic cancer

first: Meredith

last: Morgan

state: Michigan

address: 1301 Catherin St

department: Radiation Oncology

summary: Radiotherapy induces a Type I interferon (TIFIN)-mediated anti-tumoral immune response that we hypothesized could be potentiated by a first-in-class ATM inhibitor leading to enhanced innate immune signaling. T1IFN expression, and sensitization to immunotherapy in pancreatic cancer. We evaluated the effects of AZD1390 or a structurally related compound AZD0156 on innate immune signaling and found that both inhibitors enhanced radiation-induced  T1IFN expression via the POLIII/RIG-I/MAVS pathway. In immunocompetent syngeneic mouse models of pancreatic cancer, ATM inhibitor enhanced radiation-induced anti-tumoral immune responses and sensitized to anti-PD-L1, producing immunogenic memory and durable tumor control. Therapeutic responses were associated with increased CD8+ T cell frequency and effector function. Tumor control was dependent on CD8+ T cells as therapeutic efficacy was blunted in immunodeficient or CD8+ T cell-depleted mice. Adaptive immune responses to combination therapy provided systemic control of contralateral tumors outside of the radiation field. Taken together, we show that a clinical candidate ATM inhibitor enhances radiation-induced T1IFN leading to both innate and subsequent adaptive immune response and sensitization of otherwise resistant pancreatic cancer to immunotherapy.

overall_design: 6-8 week old C57/Bl6 mice with subcutaneous mT4 tumors were treated with AZD1390 (20mg/kg) for 5 days starting on day 0, 1 dose of radiation (8Gy) on day 0, and 3 doses of anti-PD-L1 blocking antibody (100µg) once every three days starting on day -1. 6-8 tumors were harvested for each of the following treatment groups: IgG/control, AZD1390, RT+anti-PD-L1, and AZD1390+RT+anti-PD-L1. Tumors were harvested on day 5 and digested in a collagenase digest buffer, and filtered through 40µm mesh filter. Samples were depleted of dying cells twice using Dead Cell Removal Kit from Miltenyi. Cells were then seperated based on CD45 status, and mixed back in equal parts CD45+ and CD45- to enrich immune cells present in the samples. Samples were diluted to a final concentraiotn of 700-1000 cells/ul. Single cell sequencing was performed by the University of Michigan Advanced Genomics Core Research Facility. Library generation was performed on the 10x Genomica Chromium Controller following manufacturers protocol for the 3'v3.1 chemistry with NextGEM Chip G reagents. Library quality was assess by LabChip GXII HT and quantified by Qubit. Pooled libraries were subjected to 150 base pair, paired-end sequencing according to manufacturer protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software was used to de-multiplex fastq files and CellRanger v7 Pipeline was used to align reads and generate count matrices.

first: Qiang

last: Zhang

first: Long

last: Jiang

first: Weiwei

first: Amanda

last: Huber

first: Victoria

last: Valvo

first: Kassidy

last: Jungles

first: Erin

middle: A

last: Holcomb

first: Ashley

middle: N

last: Pearson

first: Stephanie

last: The

first: Zhuwen

first: Leslie

last: Parsels

first: Joshua

first: Daniel

last: Wahl

first: Arvind

last: Rao

first: Vaibhav

last: Sahai

first: Theodore

last: Lawrence

first: Michael

last: Green


title: RNA sequencing comparison of B7-H3.TMIGD2 and B7-H3.CD28.4-1BB CAR-T cells in vitro

status: Public on May 08 2024

city: Bronx

first: Christopher

last: Nishimura

state: NY

address: 1300 Morris Park Avenue

country: USA

institute: Albert Einstein College of Medicine

type: Expression profiling by high throughput sequencing

summary: CAR-T cell costimualtory domains can alter CAR-T cell phenotypes. We therefore performed RNA sequencing to understand the effect of TMIGD2 vs CD28.4-1BB comstimulation in B7-H3 CAR-T cells after in vitro coculture.

overall_design: We cocultured CAR-T cells and HCC827 tumor cells for 72 hours. After isolation of T cells and T cell RNA, we performed RNA sequencing

middle: D

first: Xiang

middle: Y

last: Zheng

first: Deyou

first: XingXing

last: Zang


title: Novel FOXM1 Inhibitor STL001 sensitizes different human cancers to broad spectrum of anticancer drugs

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

summary: We sought to investigate the anticancer effects of the novel FOXM1 inhibitor, STL001 in a variety of human cancers from solid tumors including ovarian cancer, colorectal cancer, breast cancer, and prostate cancers. Here, the capacity of the novel compounds STL001 as FOXM1 inhibitor was verified in human cancer cell lines from solid tumors. Further, we showed here that FOXM1 inhibitor STL001 treatment resulted in sensitization of cancer cells to apoptotic death by multiple chemotherapeutic agents. STL001 was studied further to verify its direct target engagement with FOXM1. We have also provided Transcriptome-supported evidence that STL001 exhibits selectivity toward suppressing FOXM1-controlled regulatory pathways. This study verify and characterize a novel FOXM1 inhibitor STL001 that effectively antagonize FOXM1 activity and sensitize a variety of human cancer cells to traditionally used chemotherapy agents, and may be suitable for further clinical evaluation in targeting chemotherapy resistance human cancers.

overall_design: RNA-seq of FLO-1 and OVCAR-8 cancel cell lines with and without STL001 treatment.

first: S

last: Raghuwanshi

first: X

first: Z

last: Arbieva

first: I

last: Khan

last: Wang

first: A

last: Domling

first: C

last: Camacho

middle: L

last: Gartel


title: Low serum apolipoprotein A1 impairs antitumor immunity of CD8+ T cells via the HIF-1α-glycolysis pathway

city: Shanghai

first: Qiaoying

last: Lv

address: No. 419, Fangxie Road

country: China

institute: Obstetrics & Gynecology Hospital of Fudan University

summary: An immunosuppressive microenvironment plays a major role in the occurrence and development of tumors. Low apolipoprotein A1 (ApoA1) is closely related to tumor development, but the underlying mechanisms are unclear. This study investigated the association between the serum ApoA1 level and immune microenvironment in endometrial, ovarian, and lung cancers. The serum ApoA1 level was decreased significantly in patients with endometrial and ovarian cancers compared with healthy controls. In endometrial cancer tissues, the low serum ApoA1 group showed increased CD163+ macrophages and decreased CD8+ T cell infiltration compared with the normal serum ApoA1 group. Compromised tumor-infiltrating CD8+ T cell functions and decreased CD8+ T cell infiltration were also found in tumor-bearing ApoA1-knockout mice. CD8+ T cell depletion experiments confirmed that ApoA1 exerted its antitumor activity in a CD8+ T cell-dependent manner. In vitro experiments showed that ApoA1 mimetic peptide L-4F directly potentiated the antitumor activity of CD8+ T cells via the HIF-1α-mediated glycolysis pathway. Mechanistically, ApoA1 suppressed the ubiquitin-mediated degradation pathway of HIF-1α protein by downregulating HIF-1α subunit α inhibitor, which maintained the stability of HIF-1α protein and HIF-1α signal activation. Tumor-bearing ApoA1 transgenic mice showed an increased response to anti-PD-1 therapy with inhibited tumor growth and increased tumor necrosis. Here, the data demonstrate the critical roles of ApoA1 in enhancing CD8+ T cell immune functions via HIF-1α-mediated glycolysis, which supports clinical investigation of combined ApoA1 supplementation and anti-PD-1 therapy for tumors.

overall_design: To determine how ApoA1 affects CD8+ T cell immune functions, L-4F-treated and untreated CD8+ T cells were analyzed by RNA-seq.


title: Effect of treatment by BAY1217389 for 48 hr on H1944

city: Tokyo

first: Shunsuke

last: Kitajima

department: Department of Cell Biology

country: Japan

institute: Japanese Foundation for Cancer Research

summary: We reported that MPS-1 inhibitors activate cGAS-STING pathway in tumor cells by forming micronuclei and inducing cytokine secretion such as type I interferon, CCL5, and CXCL10, thereby promoting immune cell migration and inducing tumor cell shrinkage.　In the present study, we performed RNA -seq to search for negative regulators of STING pathway by forcibly activating it in H1944 cells with MPS-1 inhibitors, BAY1217389 and found that the administration of BAY1217389 for 48-hour treatment increased downstream factors of STING pathway and genes involved in antigen presentation, while we found elevation of negative regulators such as TREX1.

overall_design: To investigate negative regulators of STING pathway, BAY1217389 or DMSO was administered to the lung cancer cell line H1944 for 48 hours, followed by medium exchange and RNA collection 24 hours later.

first: Kei

last: Mizuno

first: Tetsuo

last: Tani

first: David

last: Barbie


title: Epithelial-derived IL-23 promotes oral mucosal immunopathology

city: Bethesda

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

summary: At mucosal surfaces, epithelial cells provide a structural barrier and an immune defense system. However, dysregulated epithelial responses can contribute to disease states. Here, we demonstrate that epithelial intrinsic production of IL-23 triggers an inflammatory loop in the prevalent oral disease, periodontitis.  Epithelial IL-23 expression localized to areas proximal to the disease-associated microbiome, is evident both in experimental models and in patients with common and genetic forms of disease. Mechanistically, flagellated microbial species of the periodontitis microbiome, trigger epithelial IL-23 induction in a TLR5-dependent manner. Intriguingly, unlike other Th17-driven diseases, here non-hematopoietic cell-derived IL-23 serves as an initiator of pathogenic inflammation.  Beyond periodontitis, analysis of publicly available datasets reveals expression of epithelial IL-23 in settings of infection, malignancy, and autoimmunity, suggesting a broader role for epithelial-intrinsic IL-23 in human disease.  Collectively, this work highlights an unappreciated role for the barrier epithelium in the induction of IL-23-mediated inflammation.

overall_design:
Examine the changes in the transcriptom in human oral mucosal tissues from Healthy controls, chronic pariodontiits and LAD1-periodontitis.
contributor: NIDCD/NIDCR Genomics and Computational Biology Core

first: Tae

middle: S

last: Kim

first: Tomoko

last: Ikeuch

first: Vasileios

middle: I

last: Theofilou

first: Drake

middle: W

last: Williams

first: Teresa

last: Greenwell-Wild

first: Armond

last: June

first: Lu

last: Li

first: Loreto

last: Abusleme

first: Nicolas

last: Dutzan

first: Yao

last: Yuan

first: Laurie

last: Brenchley

last: Bouladoux

first: Yosuke

last: Sakamachi

first: Robert

middle: J

last: Palmer

first: Ramiro

last: Iglesias-Bartolome

first: Giorgio

last: Trinchieri

first: Stavros

last: Garantziotis

first: Yasmine

last: Belkaid

first: Alex

middle: M

last: Valm

first: Patricia

last: Diaz

first: Steven

last: Holland


title: Exploring the impact of PDGFD in osteosarcoma metastasis through single-cell sequencing analysis

status: Public on May 09 2024

first: Yujing

last: Huang

address: 600 Yishan Road, Xuhui District

department: Department of Oncology

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Purpose: The overall survival rate for metastatic osteosarcoma hovers around 20%. Responses to second-line chemotherapy, targeted therapies, and immunotherapies have demonstrated limited efficacy in metastatic osteosarcoma. Our objective is to validate differentially expressed genes and signaling pathways between non-metastatic and metastatic osteosarcoma, employing single-cell RNA sequencing (scRNA-Seq) and additional functional investigations. We aim to enhance comprehension of metastatic mechanisms and potentially unveil a therapeutic target. Methods: scRNA-Seq was performed on two primary osteosarcoma lesions (1 non-metastatic and 1 metastatic). Uniform manifold approximation and projection (UMAP) facilitated dimensionality reduction and cluster identification. Copy number variation (CNV) was predicted using InferCNV. CellChat characterized ligand-receptor-based intercellular communication networks. Differentially expressed genes underwent GO function enrichment analysis and GSEA. Validation was achieved through the GSE 52048 dataset, which identified PDGFD-PDGFRB as a common ligand-receptor pair with significant contribution. Immunohistochemistry assessed PDGFD and PDGFRB expression, while multicolor immunofluorescence and flow cytometry provided insight into spatial relationships and the tumor immune microenvironment. Kaplan-Meier survival analysis compared metastasis-free survival and overall survival between high and low levels of PDGFD and PDGFRB. Manipulation of PDGFD expression in primary osteosarcoma cells examined invasion abilities and related markers. Results: Ten clusters encompassing osteoblasts, osteoclasts, osteocytes, fibroblasts, pericytes, endothelial cells, myeloid cells, T cells, B cells, and proliferating cells were identified. Osteoblasts, osteoclasts, and osteocytes exhibited heightened CNV levels. Ligand-receptor-based communication networks exposed significant fibroblast crosstalk with other cell types, and the PDGF signaling pathway was activated in non-metastatic osteosarcoma primary lesions. These results were corroborated by the GSE 52048 dataset, confirming the prominence of PDGFD-PDGFRB as a common ligand-receptor pair. Immunohistochemistry demonstrated considerably greater PDGFD expression in non-metastatic osteosarcoma tissue and organoids, correlating with extended metastasis-free and overall survival. PDGFRB expression showed no significant variation between non-metastatic and metastatic osteosarcoma, nor strong correlations with survival times. Multicolor immunofluorescence suggested co-localization of PDGFD with PDGFRB. Flow cytometry unveiled a highly immunosuppressive microenvironment in metastatic osteosarcoma. Manipulating PDGFD expression demonstrated altered invasive abilities and marker expressions in primary osteosarcoma cells from both non-metastatic and metastatic lesions. Conclusions: scRNA-Seq illuminated the activation of the PDGF signaling pathway in primary lesions of non-metastatic osteosarcoma. PDGFD displayed an inhibitory effect on osteosarcoma metastasis, likely through the suppression of the EMT signaling pathway.

overall_design:
scRNA-seq was performed on two primary osteosarcoma lesions (1 Non-metastasis and 1 Metastasis)

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Dongyan

last: Cao

first: Daliu

last: Min

first: Aina

last: He


title: Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA processing is a fundamental mode of gene regulation that is perturbed in a variety of diseases including cancer and neurodegenerative disorders. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale without purifying individual RBPs. By deploying the exoribonuclease XRN1, ePRINT allows precise mapping of the 5’ end of the RBP binding site and uncovers direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, including neural progenitor differentiation into neurons. Given its versatility, ePRINT has vast application potential as an investigative tool for RNA regulation in development, health and disease.

overall_design: The following are sequencing data for an enhanced crosslinking immunoprecipitation-seq experiments. The sets contain the RNAs directly crosslinked to FUS with a size-matched control used as an input.

first: Sophie

last: Hawkins

first: Alexandre

last: Mondaini

first: Seema

middle: C

last: Namboori

first: Grady

middle: G

last: Nguyen

first: Gene

last: Yeo

first: Asif

last: Javed

first: Akshay

last: Bhinge


title: Essential role of macrophages in contact hypersensitivity-induced hair regeneration [DPCP vs control]

city: Taipei

first: Kai-Rong

address: No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan

department: Biomedical Engineering

country: Taiwan

institute: National Taiwan University

summary: This work demonstrates that contact hypersensitivity exerts a direct stimulatory effect on hair follicles to fasten anagen entry. The stimulatory effect on hair growth is mediated by macrophages.

overall_design: For our analysis on the differences in gene expression under DPCP treatment, we utilized whole skin samples from day 2. We conducted a comparative gene expression profiling using RNA-seq analysis for DPCP and control samples

first: Sabrina

last: Fan

first: Kang-Yu

last: Tai

first: Sung-Jan

last: Lin


title: Mycoplasma feriruminatoris transcriptome

city: Barcelona

first: Ludovica

last: Ciampi

state: Choose a State or Province

address: Carrer del Doctor Aiguader 88

country: Spain

institute: Centre for Genomic Regulation

summary: The goal of this experiment is to determine the overall relative strength of promoter sequences in Mycoplasma feriruminatoris. For this, 2 replicates were grown in parallel in Hayflick media and the RNA wa extracted at exponential growth phase (20 hours). With this data, new promoter sequences could be designed and further validated by the use of RT-qPCR and reporter assays.

overall_design: The cultures were started at 1:1000 proportion (10 µl in 10 ml of growth media). They were left to grow for 20 hours and collected at exponential phase. The cells were separated and washed via centrifugation. The cellular pellet was then extracted using a standard RNA extraction method using the RNeasy kit from Qiagen. The stage of exponential growth phase was confirmed via CFU/ml counting.

first: Javier

last: de Miguel

first: Irene

middle: R

last: Arce

first: Luis

last: Serrano


title: RGS4 controls airway hyperresponsiveness through GAP-independent mechanisms

first: Kirk

middle: M.

last: Druey

state: MD

address: 10 Center Drive Room 11N238A

department: NIAID

institute: National Institutes of Health

summary: Regulators of G protein signaling (RGS proteins) constrain G protein-coupled receptor (GPCR)-mediated and other responses throughout the body primarily, but not exclusively, through their GTPase activating (GAP) activity. Asthma is a highly prevalent condition characterized by airway hyper-responsiveness (AHR) to environmental stimuli resulting in part from amplified GPCR-mediated airway smooth muscle (ASM) contractility. Rgs2 or Rgs5 gene deletion in mice enhances AHR and ASM contraction whereas RGS4 knockout (KO) mice unexpectedly have decreased AHR due to increased production of the bronchodilator prostaglandin E2 (PGE2) by lung epithelial cells. Here we found that knockin mice harboring Rgs4 alleles encoding a point mutation (N128A) that sharply curtails RGS4 GAP activity had increased AHR, reduced airway PGE2 levels, and augmented GPCR-induced bronchial contraction compared to either RGS4 KO mice or WT controls. RGS4 interacted with the p85a subunit of PI3 kinase (PI3K) and inhibited PI3K-dependent PGE2 secretion elicited by TGFb in airway epithelial cells. Together these findings suggest that RGS4 affects asthma severity in part by regulating the airway inflammatory milieu in a G protein-independent manner.

overall_design: RGS4 knockout mice were generated to examine the role of RGS4 in asthma. These RGS4 KO mice were compared to WT, under exposure to Aspergillus fumigatus and control exposure to PBS. Poly A mRNAseq was performed.

first: Ilin

middle: V

last: Joshi

first: Eunice

last: Chan

first: Justin

middle: B

last: Lack

first: Chengyu

last: Liu


title: Combination therapy with low dose ruxolitinib and cyclosporine in murine immune bone marrow failure

first: Shouguo

last: Gao

address: 9000 Rockville Pike

department: NHLBI

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

overall_design: Refer to individual Series


title: Toxicicty of ruxolitinib in normal mice

summary:
Background and methods: Ruxolitinib (RUX), a Jak1/2 inhibitor, has been reported to attenuate murine bone marrow failure recently. Its potential toxocicty of anemia and thrombocytopenia in human remains a concern. We tested the toxicity of ruxolitinib on hematopoiesis in normal mice by feeding the mice with RUX chow for 3 months. Bone marrow Lin-CD117+ cells were sorted from treated or untreated mice. RNA-Seq and analysis was performed using SMART-Seq mRNA LP Kit (Takara) and the Illumina Novaseq6000, according to the Institute's protocols.
Results: Ruxolitinib reduced RBC and lymphocytes, but did not affect NEU and PLT in normal mice. RNA sequencing demonstrated that HSPCs from RUX-treated and untreated mice had overlapped transcriptome distribution in multiple dimentional scalling plot, indicating overall similarity at molecular level.
Conclusion: Our results demonstrate that ruxolitinib has minimal toxicity on hematopoiesis in normal mice.

overall_design:
We compared transcriptomes of HSPCs from the mice treated with and without ruxolitinib, and described differentially expressed genes of these cells.
Lin-CD117+ cells were FACS-sorted from bone marrow of ruxolitinib-treated and untreated mice. To get enough cells for RNA extraction, Lin-CD117+ cells from every 2-3 mice in the same group were pooled together, we obtained 3 pools/group.

first: Xingmin

last: Feng


title: Essential role of macrophages in contact hypersensitivity-induced hair regeneration

last: Huang


title: miRNA levels during mammary gland development

city: Laval

first: Isabelle

last: Plante

state: Québec

address: 531 boul Des prairies

department: Armand-Frappier Santé Biotechnologie

country: Canada

institute: INRS

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim of the project was to analyse the levels of miRNA at different stages of mammary gland development in mice, and to determine miRNAs differentially expresssed between stages.

overall_design: Inguinal mammary gland were sampled from C57/BL6 mouse mammary glands at stages of adulthood (week 10), pregnancy (day 18), lactation (day 3) and involution (day 7) and snap frozen. Tissues were reduced to powder in liquid nitrogen, and small ARN were extracted using the mirVana miRNA isolation kit following the manufacturer’s instructions (Thermo Fisher Scientific).

first: Plante

last: Isabelle

first: Confuorti

last: Cameron

first: Jaramillo

last: Maritza


title: FOXO1 enhances CAR T cell stemness, metabolic fitness and efficacy [human_FOXO1_scRNAseq]

city: Melbourne

first: Kevin

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

summary: gene expression profile of human FOXO1overexpressing α-lewisY CAR T cells on single cell level

overall_design: Human anti-Lewis Y CAR T cells overexpressing  mCherry (control) or FOXO1  were generated from healthy donor peripheral blood mononuclear cells (PBMC). Control or  FOXO1  overexpressing CD8+ CAR T cells were non-stimulated or stimulated with MCF7 tumour cells for 24 hours and assessed by scRNA-Sequencing

first: Paul

last: Beavis

first: Phil

last: Darcy

last: Sek

first: Christina

last: Scheffler

last: Munoz

first: Yu-Kuan


title: Interrogation of RNA-protein interaction dynamics in bacterial growth

city: Cambridge

first: Mie

last: Monti

email: miemtir@gmail.com, mm2073@cam.ac.uk

address: MRC Toxicology Unit, Tennis Ct Rd, Cambridge CB2 1QR

country: United Kingdom

institute: MRC Toxicology Unit

summary: RNA-protein interactions are fundamental for bacterial homeostasis. However, we lack a system-wide understanding of their dynamics upon environmental perturbation. In this study, we have characterised the dynamics of 91% of the Escherichia coli proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and reveal novel RBP functions for proteins like the chaperone HtpG, a new tRNA-binding protein. Moreover, we characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mainly present in Proteobacteria, two of them have human orthologs in the form of mitochondrial proteins associated with rare metabolic disorders. Altogether, we provide the first dynamic RBPome of a bacterium, showcasing how this approach can reveal the function of uncharacterised proteins, and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.

overall_design: Individual-nucleotide resolution UV cross-linking and immunoprecipitation-sequencing (iCLIP-seq) for candidate RBPs HtpG and YfiF in E. coli. Proteins of interest were N-terminal his-tagged and transformed into WT E. colis trains. Untransformed WT strain was negative control as well as non-cross-linked samples.

first: Reyme

last: Herman

first: Karen

last: Davey

first: Charlotte

last: Dawson

first: Ule

last: Jernej

first: Gavin

middle: H

last: Thomas

first: Anne

middle: E

last: Willis

first: Kathryn

last: Lilley

first: Eneko

last: Villanueva


title: RNA sequencing comparison of B7-H3.TMIGD2 and B7-H3.CD28.4-1BB CAR-T cells in vivo.

first: Christopher

last: Nishimura

summary: The tumor microenvironment can significantly alter CAR-T cell phenotypes. We therefore performed RNA sequencing to understand the effect of TMIGD2 vs CD28.4-1BB comstimulation in B7-H3 CAR-T cells after intravenous administration to tumor-bearing mice in vivo.

overall_design: We injected CAR-T cells intravenously in HCC827 lung tumor-bearing-mice. We isolated lung-infiltrating T cells, isolated T cell RNA, and finally performed RNA sequencing.

first: Xiang

last: Zheng

first: Deyou

first: XingXing

last: Zang


title: Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair [RNAseq_siRNA_MAPKi]

city: Lyon

first: Nicolas

last: Fontrodona

address: 46 allée d'Italie

country: France

institute: ENS de Lyon

summary: The translation-dependent effect of amino acid bioavailability on the nature of proteins that cells express could have major consequences on their phenotype. We report that the intracellular concentration decrease of amino acids like aspartate and glutamate in a melanoma cell line exposed to anti-cancer MAPK inhibitors (MAPKi) triggers ribosomal peaks in mRNA regions enriched in codons corresponding to these amino acids and in the translation-dependent degradation of mRNAs encoding proteins enriched in these amino acids. Since aspartate- and glutamate-rich proteins are involved in cell proliferation and DNA repair, we propose that MAPKi surviving cells degrade aspartate and glutamate to generate energy which simultaneously decreases their needs through the downregulation of gene products involved in cell proliferation. Moreover, the expression level decrease of aspartate- and glutamate-rich proteins involved in DNA repair increases as a side effect the probability of DNA damages and consequently the emergence of mutated cells in response to MAPKi.

overall_design: Differential expression analysis from triplicate RNA-seq data of A375 cells treated with MAPK inhibitors, DMSO or grown in a medium with or without glutamine.  Cells were transfected with siRNAs targeting either GL2, EPRS1 or CTU2 genes and harvested 48h later. During the last 24h, medium was replaced with a fresh medium containing (DMSO or MAPKi), or a (medium control or a medium without glutamine). Reference samples for cells treated with MAPK inhibitors are cells treated with DMSO. Reference samples for cells grown without glunamine are cells grown in glutamine (CTRL) medium.

first: Fabien

last: Aubé

first: Didier

last: Auboeuf


title: Effect of the exosomes from cardiopulmonary progenitors on gene expression of H9C2 cells

city: Guangzhou

first: Yingying

last: Xiao

state: Guangdong

address: A2-652, Guangzhou Medical University, Xinzao Road, Panyu District, Guangzhou

department: the School of Pharmaceutical Sciences

institute: Guangzhou Medical University

summary: To investigate the function of exosomes from cardiopulmonary progenitors in the regulation of gene expression in endothelial cells.We performed gene expression profiling analysis using data obtained from RNA-seq of H9C2 treated with or without CPPs exosomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H9C2 cells with or without treatment with exosomes from cardiopulmonary progenitors.

first: Luoxing

last: Xia


title: Adult onset cataract formation following loss of miR-26 results from deregulated inflammation and loss of epithelial homeostasis

city: OXFORD

first: Anil

last: Upreti

state: OH

address: 501 E High St, Oxford, OH 45056

department: Biology

institute: Miami University

summary: Despite strong evidence that normal lens development and function requires regulation governed by miRNAs, the role of specific miRNAs in mammalian lens FEV development and homeostasis remains largely unexplored. Here we undertook a comprehensive RNA-seq analysis of miRNA transcripts in the newborn mouse lens, exploring both differential expression between lens epithelial cells and lens fiber cells and overall miRNA abundance. We then selected the three most abundant lens miRNAs: miR-184, miR-1 and miR-26 for functional analysis. Of these three miRNAs, only miR-1, which was highly expressed in lens fiber cells, exhibited significant differential expression. Mouse lenses lacking miR-184, or both copies of miR-1, or all three copies of miR-26 exhibited morphologically normal prenatal lens development. However, mice lacking all three copies of miR-26 (miR-26KO) developed postnatal cataracts at approximately 4-6 weeks of age. RNA-seq analysis of neonatal lenses from miR-26KO mice demonstrated a deregulation of the complement pathway, inflammation and epithelial to mesenchymal transition

overall_design: Comparative microRNAs expression profiling was done on lens epithelial cells and lens fiber cells for newborn FVB/N mice (Lens Epithelium (E1,E2,E3) and Lens Fiber cells (F1,F2,F3)). Analyzing the newborn highly expressed miRNAs data, miR-26 was one of the highest expressed miRNAs. Therefore, miR-26 was knocked out in FVB/N strain mice followed by phenotypic and transcriptomic analysis. Comparative gene expression profiling analysis of RNA-seq data between miR-26 knockout mice (miR26) and wildtype (FVB) samples at postnatal five days (FVB_P5, miR26_P5), twenty-week wildtype (FVN_W20), twenty-week miR-26 knockout mice with cataract (miR26_C_W20), and twenty-week miR-26 knockout mice without cataract (miR26_NC_W20). Biological replicates were collected in triplicate.

first: Michael

last: Robinson

first: Jared

middle: A

last: Tangeman

first: Thanh

last: Hoang


title: Effect of the exosomes from cardiopulmonary progenitors on gene expression of HMEC-1 cells

summary: To investigate the function of exosomes from cardiopulmonary progenitors in the regulation of gene expressions in endothelial cells.We performed gene expression profiling analysis using data obtained from RNA-seq of HMEC-1 treated with or without CPPs exosomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HMEC-1 cells with or without treated by exosomes from cardiopulmonary progenitors.


title: miR-765 induces angiogenesis by inhibiting dipeptidyl peptidase 4 and increasing fibroblast growth factor 2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Given that extracellular vesicles (EVs) secreted from stem cells contain angiogenic microRNAs (miRNAs), these EVs show equivalent angiogenic therapeutic effect to cell transplantation. This study aimed to identify the angiogenic miRNAs from several miRNAs involved in EVs secreted from stem cells. In human dental pulp stem cells (hDPSCs) under hypoxic culture, vascular endothelial growth factor (VEGF) involved in EVs increased. We hypothesized that angiogenic miRNAs increase in EVs that are secreted from hDPSCs under hypoxic culture compared with those under normoxic culture. In the first screening, the expression levels of miRNAs involved in EVs that were secreted from hDPSCs cultured under hypoxic and normoxic conditions were analyzed using miRNA array. In the second screening, 12 miRNAs were individually involved in EVs, and the growth of human aortic endothelial cells was assayed. In the third screening, miRNA-encapsulated EVs were injected in BALB/c mouse hindlimb ischemia model, followed by angiogenesis evaluation by blood flow analysis. Results showed that miR-765 is an angiogenic miRNA, targeting the 3′ untranslated region of dipeptidyl peptidase 4 (DPP4) and upregulating fibroblast growth factor 2 (FGF2) in vitro and in vivo. In conclusion, as an angiogenesis mechanism, miR-765 increased FGF2 expression levels by inhibiting DPP4.

overall_design: To  compare the expression levels of miRNAs in EVs isolated from the conditioned medium under normoxic conditions and hypoxic conditions and then analyzed the expression levels of miRNAs encapsulated in EVs by array analysis. Human dental pulp stem cells (hDPSCs) (2 × 105 cells/10 mL) were seeded into 10 cm dish  in KBM ADSC-4 (#16030044; Kohjin Bio Co., Ltd.) and cultured 10 dishes of each for 7 days under normoxic and hypoxic conditions. The conditioned medium was concentrated using Amicon Ultra-15(#UFC901024, Merck Millipore Ltd.). Using the total exosome isolation reagent (from cell culture media)(#4478359, ThermoFisherScientific), we made pellets from the concentrated liquid of the conditioned medium. Next, microRNAs were isolated from the pellets by using the miRNeasy Mini Kit (#217004, Qiagen). The miRNA expression levels were analyzed using 3D-Gene® miRNA oligochips (Toray Industries, Inc.)

first: Koji

last: Ueno

first: Ryo

last: Suzuki

first: Hiroshi

last: Kurazumi

first: Takahiro

last: Mizoguchi

first: Toshiki

last: Tanaka

first: Kimikazu

last: Hamano


title: Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair


title: Gene expression profiling of ST-HSCs and MPP2 cells conditionally expressing MLL-ENL by RNA-seq

city: Tsu

first: Ryoichi

last: Ono

address: 2-174 Edobashi

department: Department of Microbiology

institute: Mie University Graduate School of Medicine

summary: To investigate the molecular mechanism of leukemic transformation by MLL-ENL in HSCs and immature progenitors, we preliminarily performed comprehensive gene expression profiling of ST-HSCs and MPP2 cells by RNA-seq using a mouse model enabling to conditionally express MLL-ENL at an endogenous-like expression level.

overall_design: ST-HSCs and MPP2 cells from our model mouse were treated with 4OHT conditionally inducing expression of MLL-ENL, or with ethanol as a vehicle control.Total RNA was extracted from 4 kinds of samples, respectively, and analyzed by RNA-seq. The induced cells were compared with the individual contorols.

first: Akihide

last: Nakamura

first: Tetsuya

last: Nosaka


title: Gene expression profile at single cell level of cells from the heart region of E9.5 mouse embryos (P0) and the cultured cells from P0 in vitro (P6).

summary: Cardiopulmonary progenitors (CPPs) are a population of cells that still in study. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cells isolated from in the mouse embryo heart, and CPPs we cultured in vitro.

overall_design: The cells isolated from E9.5 mouse embryos and cultured in vitro are analyzed using scRNAseq.


title: Essential role of macrophages in contact hypersensitivity-induced hair regeneration [Clod vs Encap]

first: Kai-Rong

last: Huang

overall_design: For our analysis on the differences in gene expression under DPCP treatment, we utilized whole skin samples from day 2. We conducted a comparative gene expression profiling using RNA-seq analysis for DPCP treated with clodrosome and DPCP treated with encapsosome

first: Sabrina

last: Fan

first: Kang-Yu

last: Tai

first: Sung-Jan

last: Lin


title: Low dose ruxolitinib plus cyclosporine to treat murine immune-mediated bone marrow failure

first: Shouguo

last: Gao

summary:
Background and methods: Ruxolitinib (RUX), a Jak1/2 inhibitor, has been reported to attenuate murine bone marrow failure recently. Its potential toxocicty of anemia and thrombocytopenia in human remains a concern. To minimize its potential toxoxicity, we tested therapeutic effectsof low dose ruxolitinib plus cyclosporine in murine model of immune-mediated bone marrow failure. Bone marrow CD8 and CD4 T cells were sorted from treated or untreated bone marrow failure mice. RNA-Seq and analysis was performed using SMART-Seq mRNA LP Kit (Takara) and the Illumina Novaseq6000, according to the Institute's protocols.
Results: low dose of ruxolitinib plus cyclosporine improved pancytopenia and BM cellularity and decreased BM T cell infiltration in bone marrow failure mice. RNA sequencing demonstrated that low dose of ruxolitinib plus cyclosporine suppressed immune-related pathways in bone marrow infiltrated CD8 T cells and MHC-II expression in CD4 T cells compared with untreated mice.
Conclusion: Our results demonstrate that low dose of ruxolitinib plus cyclosporine remains the efficacy in attenuation of disease and extending survival of immune-mediated bone marrow failure mice.

overall_design:
We compared transcriptomes of CD8 and CD4 T cells in the bone marrow failure mice treated with and without low dose of ruxolitinib plus cyclosporine, and described differentially expressed genes of these cells.
CD8+ and CD4+ T cells were isolated from bone marrow cells of low dose of ruxolitinib plus cyclosporine-treated and control BMF mice by FACS-sorting. To get enough cells for RNA extraction, CD8+ and CD4+ T cells from every 2-3 mice in the same group were pooled together, we obtained 3 pools/group.

first: Xingmin

last: Feng


title: Responders to immune checkpoint therapy display early clonal expansion of tumour-infiltrating lymphocytes

city: Crawley

first: Jonathan

last: Chee

state: WA

address: M503, 35 Stirling Highway

institute: University of Western Australia

summary: Using murine models that exclude variation in host genetics, environmental factors and tumour mutation burden, limiting variation between animals to naturally diverse TCRβ repertoires, we applied bulk TCRseq to study TCRβ repertoire dynamics in ICT responders and non-responders

overall_design: Bulk TCRβseq of tumor infiltrating lymphocytes at different timepoints prior to and during anti-CTLA-4 and anti-PD-L1 treatment, responders and non-responders. Each sample represents an individual biological replicate (i.e. no duplicate samples from the same mouse).

first: Joel

last: Kidman


title: The NADase CD38 is a central regulator in gouty inflammation and a novel druggable therapeutic target

city: San Diego

first: Paulo

middle: VG

last: Alabarse

address: 9500 Gilman Drive

department: Rheumatology

institute: University of California, San Diego

summary: Objectives: In gout, flares of severely painful inflammatory arthritis intersect with metabolism, circadian rhythm, and macrophage activation. NAD+ is a necessary cofactor and key metabolite in cellular bioenergy homeostasis, and NAD+ suppresses the NLRP3 inflammasome and inflammation. However, cellular NAD+ declines in inflammatory states, associated with increased activity of the leukocyte-expressed NADase CD38. Gouty arthritis is principally prevented and treated with nonselective and frequently toxic drugs (colchicine, NSAIDs, corticosteroids). Hence, we tested the potential role of therapeutically targeting CD38 and NAD+ in gout. Methods: We studied cultured mouse wild type and CD38 knockout (KO) murine bone marrow derived macrophages (BMDMs) stimulated by monosodium urate (MSU) crystals, and the air pouch gout synovitis model. Results: MSU crystals induced CD38 in BMDMs in vitro, associated with NAD+ depletion, and IL-1b and CXCL1 release, effects reversed by pharmacologic CD38 inhibitors (apigenin, 78c). Mouse air pouch inflammatory responses to MSU crystals were blunted by CD38 KO and apigenin. Pharmacologic CD38 inhibition suppressed MSU crystal-induced NLRP3 inflammasome activation and increased anti-inflammatory SIRT3-SOD2 in macrophages. BMDM RNA-seq analysis of 176 differentially expressed genes (DEGs) revealed CD38 control of multiple MSU crystal-modulated inflammation pathways. The top DEGs included the circadian rhythm modulator GRP176, and the metalloreductase STEAP4 that mediates iron homeostasis, and promotes oxidative stress and NF-kB activation when it is overexpressed. Conclusion: CD38 and NAD+ depletion are druggable targets controlling the MSU crystal- induced inflammation program. Targeting CD38 and NAD+ are potentially novel selective molecular approaches to limit gouty arthritis.

overall_design: After GM-CSF treatment for 24 hours, WT BMDMs in the presence or absence of apigenin and CD38KO BMDMs were stimulated with MSU crystals for 6 hours.

first: Particia

last: Oliveira

first: Huaping

last: Qin

first: Tiffany

last: Yan

first: Marie

last: Migaud

first: Robert

last: Terkeltaub

first: Ru

last: Liu-Bryan


title: Inhibition of Caspase-1 limits CD4+ T cell loss and restores host anti-retroviral function in HIV-1 infected humanized mice with augmented lymphoid tissue

city: Galveston

first: Steven

last: Widen

state: Texas

address: 301 University Blvd

department: BMB

institute: University of Texas Medical Branch

summary: The study of HIV infection and pathogenicity in physical reservoirs requires a biologically relevant model which resembles the human immune system and physiology. The human immune system (HIS) mouse is an established model of HIV infection1–3, but defects in immune tissue reconstitution remain a challenge for examining pathology in tissues1,3–7. Herein we show that exogenous injection of the human cytokine FLT-3L into the hematopoietic stem cell (HSC) cord blood HIS mouse model significantly expanded the total area of axillary lymph nodes and the absolute number of circulating  human T cells, thus enabling us to visualize and quantify HIV infectivity in the secondary lymphoid tissues of the spleen and axillary node. Further, we detected cell death and human T cell depletion in tissues, consistent with HIV pathogenesis. Treatment with the Caspase-1 inhibitor VX-765 restored CD4+ T donor cells and decreased plasma viral load as measured by gag qPCR, and apoptosis in the spleen. In situ hybridization further demonstrated a decrease in viral RNA in both the spleen and axillary lymph nodes.  Transcriptomic analysis revealed that in vivo inhibition of caspase-1 led to an upregulation in host HIV restriction factors including APOBR, SAMHD1 and APOBEC3A (study design depicted in graphical abstract). These findings demonstrate that exogenous rFLT-3L as a mechanism to enhance human immune system characteristics in HIS mice. These enhancements will support investigations of HIV pathogenesis and immune outcomes in tissue compartments. Targeting inflammasome pathways with VX-765 in HIS mice treated with rFLT-3L preserved T cell populations and decreased viral load after HIV infection.

overall_design: 9 NOD/SCID/γcnil/nil female mice at 3 weeks of age were irradiated at which point mixed donor human cord blood CD34+ stem cells were injected for the generation of humanized mice. There were 3 animals per group, in 3 groups total. Recombinant human FLT-3 ligand (rFLT-3L) N=3, rFLT-3L+HIV N=2, rFLT-3L+HIV+VX-765 N=3. Splenic tissues were harvested from euthanized animals on day 14. mRNA  was examined by Next Generation Sequence (NGS) analysis.

first: Alex

last: Holloway

first: Tais

last: Saito

first: Kubra

middle: F

last: Naqvi

first: Xiuzhen

first: Joshua

last: Lisinicchia

first: Benjamin

last: Gelman

first: Janice

last: Endsley

first: Mark

first: Matthew

last: Huante


title: Mapping genotypes to chromatin accessibility profiles in single cells

city: New York

first: Franco

last: Izzo

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mapping genotypes to chromatin accessibility profiles in single cells  [Genotyping GoT-ChA amplicon]

summary: Processed scATAC-seq sequencing data from myelofibrosis patients and raw sequencing data from scATAC-seq cell mixing experiments

overall_design: We performed two cell line mixing studies to determine the accuracy and cell recovery of the GoT-ChA genotyping method. Cells with distinct genotypes and cell types of origin were mixed in a 1:1 ratio and subjected to GoT-ChA. For myeloproliferative neoplasm (MPN) patients, cells were isolated and FACS-sorted with CD34+ DAPI- gating followed by processing via the GoT-ChA single cell ATAC-seq and genotyping protocol.

last: Myers

first: Dan

last: Landau


title: Mapping genotypes to chromatin accessibility profiles in single cells [scATAC-seq; Pt01-19;Pt-02 DOGMAseq]

overall_design:
We performed two cell line mixing studies to determine the accuracy and cell recovery of the GoT-ChA genotyping method. Cells with distinct genotypes and cell types of origin were mixed in a 1:1 ratio and subjected to GoT-ChA. For myeloproliferative neoplasm (MPN) patients, cells were isolated and FACS-sorted with CD34+ DAPI- gating followed by processing via the GoT-ChA single cell ATAC-seq and genotyping protocol.
***Raw data for patients are being submitted to the European Genome-Phenome Archive (EGA) due to patient privacy concerns***


title: miRNA expression data from exosomes of cardiopulmonary progenitors (CPPs) isolated and cultured in vitro

first: Yingying

last: Xiao

summary: Cardiopulmonary progenitors (CPPs)  derived from mouse embryos have multi-directional differentiation potential. Their exosomes are not be investigated yet.

overall_design: Exosomes from cardiopulmonary progenitors (CPPs) were isolated from the supernants, and RNA was extraction and non-coding RNAs were sequenced.

first: Luoxing

last: Xia


title: Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair [QuantSeq_BRAF]

first: Nicolas

last: Fontrodona

overall_design: QuanSeq data of A375 cells treated with MAPK inhibitors or DMSO for 18 hours then grown for 0, 1, 3 or 5 hours in a medium containing either DMSO, tryptolide (T), cycloheximid (CHX) or tryptolide and cycloheximid (TCHX). Cells grown for 0h corresponds to cell immediately harvested after DMSO, tryptolide, cycloheximid or tryptolide and cycloheximid treatment.

first: Fabien

last: Aubé

first: Didier

last: Auboeuf


title: Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair [QuantSeq_Q_siCTU2]

overall_design: QuanSeq data of A375 cells transfected with a siRNA targetting GL2 or CTU2 or grown in a middle with or without glutamine and then grown for 0, 3 or 5 hours in a medium containing either tryptolide (T), cycloheximid (CHX) or tryptolide and cycloheximid (TCHX). 0h samples correspond to cells immediately harvested after tryptolide/cycloheximid treatment.


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas [Nanostring_sample1]

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

summary: A 122-epigenetic gene signature distinguished low- versus high-risk early stage melanomas. We sought to validate the signature, examined clinical correlates in a cohort of primary melanomas of the skin, and studied the underlying transcriptomic aberrations and changes in chromatin in cell lines representing these two groups.

overall_design: We analyzed 229 human melanoma patient samples and 12 human primary melanoma cell lines using a custom Nanostring codeset.

first: Karen

last: Mendelson


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas [RPPA]

overall_design: We analyzed 5 human primary cutaneous melanoma cell lines (3 biological replicates per cell line) using a RPPA.


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas [nanotstring_sample2]


title: Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair [RNA-seq]

overall_design: Differential expression analysis from triplicate RNA-seq data of A375 cells treated with MAPK inhibitors, DMSO or grown in a medium with or without glutamine.  Reference samples for cells treated with MAPK inhibitors are cells treated with DMSO. Reference samples for cells grown without glunamine are grown in glutamine (CTRL) medium.


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas [YUCHIME]

overall_design: mRNA profiles of YUCHIME metatastic  human melanoma cell lines  with siRNA scramble and   YUCHIME metatastic  human melanoma cell lines  with siRNA ITGA3 were generated by deep sequencing, in triplicate, using Illumina NextSeq500.


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas [SKMel147]

overall_design: mRNA profiles of SKMel147 metatastic  human melanoma cell lines  with siRNA scramble (n=3) and  were generated by deep sequencing, in triplicate, using Illumina NextSeq500.


title: Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair [glutamine]

overall_design: Triplicate Ribo-seq data of A375 cells treated with MAPK inhibitors, DMSO or grown in a medium with or without glutamine.  Reference samples for cells treated with MAPK inhibitors are cells treated with DMSO. Reference samples for cells grown without glunamine are grown in glutamine (CTRL) medium.


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas [ChIP-seq]

summary:
A 122-epigenetic gene signature distinguished low- versus high-risk early stage melanomas. We sought to validate the signature, examined clinical correlates in a cohort of primary melanomas of the skin, and studied the underlying transcriptomic aberrations and changes in chromatin in cell lines representing these two groups.
H3K27Ac ChipSeq profiles of primary human melanoma cell lines (n=4) as well as corresponding input samples were generated by deep sequencing using Illumina NextSeq500.
Purpose: The goals of this study are to identify H3K27Ac differential peak expression between two groups of melanoma cell lines (Epgn1 and Epgn3) and relate this data to RNASeq.
Methods: H3K27Ac ChipSeq was performed on 4 melanoma cell lines by deep sequencing 75bp single end reads using Illumina NextSeq500. Reads were aligned and counts called using____. The sequence reads that passed quality filters were analyzed.
Results: Using an optimized data analysis workflow, we mapped about 40 million reads per Chip sample and 60 million reads per input sample to the human genome (build _____).
Conclusions: Our study allowed us to identify differentially expressed peaks between two classes of melanoma cell lines and relate this information to differential gene expression. Further in vitro and in vivo assays using some of the candidate genes identified will allow us to more fully understand primary melanoma progression.

first: Cristie

last: Nguyen


title: HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

summary: The packaging of DNA into chromatin and its compaction within cells renders the underlying DNA template un-accessible for processes like transcription, replication and repair. Active mechanisms as chromatin modifying activities or the association with non-coding RNAs can de-condense chromatin, rendering it accessible for the DNA dependent processes. High mobility group proteins (HMG) are small architectural chromatin proteins that were shown to contribute to the regulation of chromatin accessibility and condensation. Here we show that HMGN5, a member of the HMGN family is capable to de-compact chromatin and to activate gene expression. We identified and characterized a novel RNA binding domain within HMGN5 that overlaps with its nucleosome binding domain (NBD). HMGN5 binds exclusively to nucleosomes or RNA, suggesting a switching mechanism and different functionalities depending on its binding partner. For this we show that HMGN5 is bound to regulatory regions of the genes that it tends to activate and also is found on the primary transcript of these genes. The results suggest that HMGN5 is switching from the chromatin binding to the RNA binding state after gene activation, potentially improving RNA synthesis. Furthermore, HMGN5 co-localizes and directly interacts with CTCF, suggesting a cooperative role of both proteins in organizing higher order structures of chromatin and active chromatin domains.


title: HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [CLIP-seq]

summary: HMGN5 is a member of the HMGN family that de-compacts chromatin and regulates gene expression. Chromatin-associated RNAs are known to play a major role in controlling gene expression and chromatin architecture. We recently showed that RNA is required to open chromatin structure in Drosophila. A potential involvement of RNA in the HMGN5-dependent opening of chromatin has not been studied so far. Here we revealed that HMGN5 has a novel and specific RNA binding activity, which is extended to the HMGN family. HMGN5 is associated preferentially with active regulatory regions and binds co-transcriptionally to the nascent RNA. Additionally, we showed that HMGN5 co-localizes and interacts with CTCF, which suggests a cooperative role of both proteins in organizing higher order structures of chromatin. We showed that HMGN5 forms mutually exclusive complexes with chromatin and RNA in vitro, altogether suggesting a dual role for HMGN5 in gene regulation, switching from nucleosome to RNA binding during gene activation.

overall_design: This serie includes CLIP-seq  data from cells overexpresiong HMGN5-GFP (3 replicates),  and the control cell line overexpressing GFP (2 replicates)

first: Ingrid

last: Araya

first: Ivo

last: Carrasco

first: Uwe

last: Schwartz

first: Axel

last: Imhof

first: Martin

last: Montecino

first: Gernot

last: Längst


title: Next Generation Sequencing of Primary Melanocytes, Epgn1, and Epgn3 Melanoma Cell lines [RNA-seq]

summary:
Purpose: The goals of this study are to identify differentially expressed genes between two groups of melanoma cell lines (Epgn1 and Epgn3) as compared to control melanocytes.
Methods: Melanoma cell line profiles of control melanocytes and primary human cell lines were generated by deep sequencing 75bp paired end reads, in triplicate, using Illumina NextSeq500. Reads were aligned and counts called using STAR. The sequence reads that passed quality filters were analyzed at the transcript isoform level.
Results: Using an optimized data analysis workflow, we mapped about 35 million reads per sample to the human genome (build hg37). We identified 4566 transcripts which showed differential expression between groups Epgn1 and Epgn2, with a log fold change ≥2 and p value <=0.005. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to melanoma progression.
Conclusions: Our study allowed us to identify differentially expressed genes between two classes of melanoma cell lines as well as control melanocytes. Further in vitro and in vivo assays using some of the candidate genes identified will allow us to more fully understand primary melanoma progression.

overall_design: mRNA profiles of control primary human melanocytes (n=2) and primary human melanoma cell lines (n=6) were generated by deep sequencing, in triplicate, using Illumina NextSeq500.


title: HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [RNA-seq]

overall_design: RNA-seq data from cells overexpresiong HMGN5,  after HMGN5 knockdown and non-treated control cells.  2 replicates each


title: Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair [MAPK inhibitors]

summary: The translation-dependent effect of amino acid bioavailability on the nature of proteins that cells express could have major consequences on their phenotype. We report that the intracellular concentration decrease of amino acids like aspartate and glutamate in a melanoma cell line exposed to anti-cancer MAPK inhibitors (MAPKi) triggers ribosomal peaks in mRNA regions enriched in codons corresponding to these amino acids and in the translation-dependent degradation of mRNAs encoding proteins enriched in these amino acids. Since aspartate- and glutamate-rich proteins are involved in cell proliferation and DNA repair, we propose that MAPKi surviving cells degrade aspartate and glutamate to generate energy which simultaneously decreases their needs through the downregulation of gene products involved in cell proliferation. Moreover, the expression level decrease of aspartate- and glutamate-rich proteins involved in DNA repair increases as a side effect the probability of DNA damages and consequently the emergence of mutated cells in response to MAPKi.

overall_design: Differential expression analysis from triplicate RNA-seq data of A375 cells treated with DMSO or MAPK inhibitors for 3 days and then harvested (for DMSO and MAPK inhibitors treatment) or grown 2 or 9 days in DMEM for recovery (for MAPK inhibitors treatment only).


title: Echinatin alleviates inflammation and pyroptosis in hypoxic-ischemic brain damage by inhibiting TLR4/ NF-κB pathway

status: Public on May 07 2024

city: wenzhou

first: xiaoyue

last: tao

state: zhejiang

address: puxieshi road, Wenzhou, China

institute: wenzhou medical university

summary: Hypoxic ischemic encephalopathy (HIE) is a primary cause of neonatal death and disabilities resulting from perinatal hypoxia. The progression of HI injury is closely associated with neuroinflammation. Therefore, suppressing inflammatory pathways is a promising therapeutic strategy for treating HIE. Echinatin (Ech) is a principal active component of glycyrrhiza, with anti-inflammatory and anti-oxidative effects, often combined with other herbs to exert effects of clearing heat and detoxifying.  This study aimed to investigate the anti-inflammatory and neuroprotective effects of Ech on neonatal rats with hypoxic-ischemic brain damage and on PC12 cells induced by oxygen-glucose deprivation (OGD).

overall_design: Seven-day-old SD rats were subjected to 2.5 hours of ischemia-hypoxia for transcriptome sequencing. The results showed that inflammatory genes were enriched in HI rats compared with normal rats, the results were verified by PCR and wb, and TLR4, MyD88 and NF-κB were identified as the key regulators.. In vitro, Ech reduced TLR4-related protein levels, inhibited nuclear translocation of NF-κB, reduced the expression of downstream inflammatory cytokines, and prevented pyroptosis and cell membrane destruction. These results suggest that Ech can reduce neuroinflammation and pyroptosis in HI injury by inhibiting the TLR4/NF-κB pathway, which is expected to be a potential candidate for the treatment of HIE.

first: Xiaoyue

last: Tao


title: HMGN5, an RNA and Nucleosome binding protein required for chromatin de-condensation and gene activation [ChIP-seq]

overall_design: This serie includes ChIP-seq  data from  HMGN5-GFP cells with or without induction,  and the GFP-FlpIn induced cells as control


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas [Nanostring_sample3]


title: pooled clone sequencing from DNA cloning sample (ENCSR889TWE)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: pooled clone sequencing from DNA cloning sample (ENCSR915INT)


title: pooled clone sequencing from DNA cloning sample (ENCSR836ULU)


title: pooled clone sequencing from DNA cloning sample (ENCSR830AFA)


title: An epigenetic gene signature underlies phenotype switching in early stage melanomas.

overall_design: Refer to individual Series


title: pooled clone sequencing from DNA cloning sample (ENCSR798QUP)


title: pooled clone sequencing from DNA cloning sample (ENCSR866ZYZ)


title: pooled clone sequencing from DNA cloning sample (ENCSR744FBH)


title: pooled clone sequencing from DNA cloning sample (ENCSR772FAR)


title: pooled clone sequencing from DNA cloning sample (ENCSR721WTZ)


title: pooled clone sequencing from DNA cloning sample (ENCSR798ALS)


title: pooled clone sequencing from DNA cloning sample (ENCSR732JTP)


title: pooled clone sequencing from DNA cloning sample (ENCSR738NIX)


title: pooled clone sequencing from DNA cloning sample (ENCSR701FXI)


title: pooled clone sequencing from DNA cloning sample (ENCSR720LEA)


title: pooled clone sequencing from DNA cloning sample (ENCSR686UKL)


title: pooled clone sequencing from DNA cloning sample (ENCSR691FFI)


title: pooled clone sequencing from DNA cloning sample (ENCSR652NKB)


title: pooled clone sequencing from DNA cloning sample (ENCSR645FSB)


title: pooled clone sequencing from DNA cloning sample (ENCSR633PMZ)


title: pooled clone sequencing from DNA cloning sample (ENCSR620BYE)


title: pooled clone sequencing from DNA cloning sample (ENCSR607LDI)


title: pooled clone sequencing from DNA cloning sample (ENCSR992PQH)


title: Hepatic BMAL1 and HIF1a regulate a time-dependent hypoxic response and their absence leads to Hepatopulmonary Syndrome

city: Rehovot

first: Vaishnavi

last: Dandavate

address: 26B Arthur Ruppin street

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary: The transcriptional response to hypoxia is temporally regulated yet the molecular underpinnings and physiological implications are unknown. We examined herein the roles of hepatic Bmal1 and Hif1a in the circadian response to hypoxia in mice. We found that the majority of the transcriptional response to hypoxia is dependent on Bmal1 or Hif1a, through shared and distinct roles that are daytime determined. We further show that HIF1a accumulation upon hypoxia is temporally regulated and Bmal1-dependent. Unexpectedly, mice lacking both hepatic Bmal1 and Hif1a are hypoxemic and exhibit increased mortality upon hypoxic exposure in a daytime-dependent manner. These mice display mild liver dysfunction with pulmonary vasodilation likely due to ERK activation, endothelial nitric oxide synthase and nitric oxide accumulation in lungs, suggestive of hepatopulmonary syndrome. Our findings indicate that hepatic BMAL1 and HIF1a are key time-dependent regulators of the response to hypoxia and provide molecular insight on the pathophysiology of hepatopulmonary syndrome.

overall_design: RNA-sequencing on lungs of AlbCRE or BHLKO mice at CT16. Lights were turned off at the transition of dark to light regiment on the day of the experiment, following regular LD regimen.

first: Marina

last: Golik

first: Gad

last: Asher


title: pooled clone sequencing from DNA cloning sample (ENCSR471OZH)


title: pooled clone sequencing from DNA cloning sample (ENCSR813IVZ)


title: pooled clone sequencing from DNA cloning sample (ENCSR466AMS)


title: pooled clone sequencing from DNA cloning sample (ENCSR845WYW)


title: pooled clone sequencing from DNA cloning sample (ENCSR448FBS)


title: pooled clone sequencing from DNA cloning sample (ENCSR517VAN)


title: pooled clone sequencing from DNA cloning sample (ENCSR482UPX)


title: pooled clone sequencing from DNA cloning sample (ENCSR631SLY)


title: pooled clone sequencing from DNA cloning sample (ENCSR441MQR)


title: pooled clone sequencing from DNA cloning sample (ENCSR556IED)


title: pooled clone sequencing from DNA cloning sample (ENCSR335RIS)


title: pooled clone sequencing from DNA cloning sample (ENCSR273YHW)


title: pooled clone sequencing from DNA cloning sample (ENCSR367WAO)


title: pooled clone sequencing from DNA cloning sample (ENCSR332LAV)


title: pooled clone sequencing from DNA cloning sample (ENCSR393KCY)


title: pooled clone sequencing from DNA cloning sample (ENCSR437KIU)


title: pooled clone sequencing from DNA cloning sample (ENCSR271KLC)


title: pooled clone sequencing from DNA cloning sample (ENCSR152PLX)


title: pooled clone sequencing from DNA cloning sample (ENCSR020JTL)


title: MPRA from K562 (ENCSR971BEX)


title: pooled clone sequencing from DNA cloning sample (ENCSR205HWY)


title: MPRA from HepG2 (ENCSR979TSK)


title: MPRA from GM12878 (ENCSR918IAV)


title: MPRA from K562 (ENCSR997GVD)


title: MPRA from SK-N-SH (ENCSR959NUX)


title: MPRA from K562 (ENCSR971PLA)


title: MPRA from HepG2 (ENCSR885ULM)


title: MPRA from A549 (ENCSR888DPV)


title: MPRA from GM12878 (ENCSR812PWW)


title: MPRA from HCT116 (ENCSR873QHK)


title: MPRA from K562 (ENCSR917SFD)


title: MPRA from HepG2 (ENCSR847SNQ)


title: MPRA from HepG2 (ENCSR843APF)


title: MPRA from SK-N-SH (ENCSR833GXJ)


title: MPRA from SK-N-SH (ENCSR856SQG)


title: MPRA from HepG2 (ENCSR811QES)


title: MPRA from A549 (ENCSR729IRS)


title: MPRA from HepG2 (ENCSR712VZT)


title: MPRA from HepG2 (ENCSR833BYO)


title: MPRA from A549 (ENCSR793OLW)


title: MPRA from HEK293 (ENCSR781PSG)


title: MPRA from K562 (ENCSR753ZRI)


title: MPRA from K562 (ENCSR697PNZ)


title: MPRA from HepG2 (ENCSR736XUK)


title: MPRA from HepG2 (ENCSR694VUM)


title: MPRA from A549 (ENCSR653QXW)


title: MPRA from GM12878 (ENCSR645CIP)


title: MPRA from GM12878 (ENCSR587IBO)


title: MPRA from K562 (ENCSR653LWA)


title: MPRA from mammary epithelial cell (ENCSR616NNF)


title: MPRA from A549 (ENCSR645XWQ)


title: MPRA from SK-N-SH (ENCSR579QGV)


title: MPRA from SK-N-SH (ENCSR563TTU)


title: MPRA from SK-N-SH (ENCSR574GPT)


title: MPRA from SK-N-SH (ENCSR623DJZ)


title: MPRA from SK-N-SH (ENCSR562GGR)


title: MPRA from SK-N-SH (ENCSR541FWB)


title: MPRA from HepG2 (ENCSR554UKK)


title: MPRA from SK-N-SH (ENCSR742AAP)


title: MPRA from GM12878 (ENCSR560QIE)


title: MPRA from A549 (ENCSR523VYM)


title: MPRA from SK-N-SH (ENCSR505LQA)


title: MPRA from HEK293 (ENCSR481QRH)


title: MPRA from HCT116 (ENCSR443ZPY)


title: MPRA from GM12878 (ENCSR410EJE)


title: MPRA from HepG2 (ENCSR463DWN)


title: MPRA from SK-N-SH (ENCSR386XIB)


title: MPRA from HepG2 (ENCSR447RLV)


title: MPRA from GM12878 (ENCSR368PIO)


title: MPRA from K562 (ENCSR326HQU)


title: MPRA from K562 (ENCSR394HXI)


title: MPRA from K562 (ENCSR274WZF)


title: MPRA from K562 (ENCSR363XER)


title: MPRA from HepG2 (ENCSR354FXV)


title: MPRA from K562 (ENCSR341GVP)


title: MPRA from A549 (ENCSR273YGD)


title: MPRA from K562 (ENCSR857JFG)


title: MPRA from Jurkat (ENCSR247RPW)


title: MPRA from SK-N-SH (ENCSR181PJG)


title: MPRA from HepG2 (ENCSR167HAR)


title: MPRA from GM12878 (ENCSR248ZDI)


title: MPRA from SK-N-SH (ENCSR087VPA)


title: MPRA from K562 (ENCSR147BIK)


title: MPRA from HepG2 (ENCSR222QJT)


title: MPRA from K562 (ENCSR003TJR)


title: lncRNA profile of PANC-1 treated with CAFs derived EVs

first: Shangyou

last: Zheng

address: Guangzhou

institute: Guangdong Provincial People's Hospital

summary: Perineural invasion (PNI) is a unique biological feature of pancreatic cancer and is a key cause of pancreatic cancer metastasis, recurrence and poor postoperative survival, but its mechanism is largely unclarified. Clinical sample analysis and endoscopic ultrasonographic elasticity scoring indicated that cancer-associated fibroblasts (CAFs) are closely related to the occurrence of PNI. Furthermore, CAF-derived extracellular vesicles played an extremely important role in PNI in a dorsal root ganglion (DRG) coculture model and sciatic nerve model. To explore the lncRNA packaged in CAFs EVs transmitted to PANC-1, we conducted the lncRNA profile of PAN-1 treated with CAFs derived EVs.

overall_design: CAFs were isolated from pancreatic cancer and conditional medium were collected for EVs isolation. PANC-1 were treated with CAF-derived EVs and then the RNA were  extracted for lncRNA-seq.

first: Chonghui

last: Hu

first: Ting

last: Ting

first: Rufu

last: Chen


title: MPRA from HepG2 (ENCSR045VPN)


title: MPRA from A549 (ENCSR213UGS)


title: NR4A1 transcriptionally regulates the differentiation of stem-like CD8+ T cells in the tumor microenvironment

city: Shanghai

first: Jing

last: Hao

address: South Chongqing Road 227, Huangpu District

department: Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital

institute: Shanghai Immune Therapy Institute


title: MPRA from K562 (ENCSR135MRI)


title: RNA seq in IPSCs derived dopaminergic neurons comparison of SNORD116MD versus control

city: TOULOUSE

first: Juliette

last: SALLES

address: CHU Purpan - BP 3028

institute: INSERM

summary: Introduction: A microdeletion including the SNORD116 gene (SNORD116 MD) has been shown to drive the Prader-Willi syndrome (PWS) phenotype. PWS is a neurodevelopmental disorder resulting from hypothalamic dysfunction implicating oxytocin (OXT) circuits. It is clinically characterized by early severe obesity, endocrine impairment, intellectual disability and psychiatric symptoms such as a lack of emotional regulation, impulsivity, and intense temper tantrums with outbursts. In addition, this syndrome is associated with a nutritional trajectory characterized by addiction-like behavior around food in adulthood. PWS is related to the genetic loss of expression of a minimal region of chromosome 15 encompassing the SNORD116 gene, encoding for a long noncoding RNA that plays a potential role in epigenetic regulation. Nevertheless, the role of the SNORD116 MD in DNA methylation, as well as the impact of OXT on it, have never been investigated in human neurons. Methods: We studied the methylation marks in dopaminergic neurons issued from induced pluripotent stem neuronsscells (iPSC) carrying a SNORD116 MD in comparison with those from an age-matched adult healthy control. We also performed identical neurons differentiation in the presence of OXT. We performed a genome-wide DNA methylation analysis from iPSC-derived dopaminergic neurons by reduced-representation bisulfite sequencing. In addition, we performed RNA sequencing analysis in the iPSC-derived dopaminergic neurons differentiated with or without OXT. Results: The analysis revealed that among the differentially methylated genes, we determined a list of gene also differentially expressed. Enrichment analysis of this list encompassed dopaminergic system with COMT and SLC6A3.RT-qPCR attested significant over expression of SLC6A3 in SNORD116 MD neuronss. Moreover, the expression of this gene was significantly decreased in case of OXT adjunction during the differentiation. . Conclusion: SNORD116 MD dopaminergic neurons display differential methylation and expression in genes related to dopaminergic clearance  .

overall_design: Four differentiations were performed with SNORD116MD and control cell lines (no treatment) and two with oxytocin adjunction from day14 of the cell culture

last: Salles

first: Maithé

last: Tauber

first: Sanaa

last: Eddiry

first: Jean


title: DAPK1 acts as a positive regulator of hypertension via induction of vasoconstriction

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The objective of this research is to compare the differentially expressed genes in the vascular tissues of DAPK1 wild-type (WT) and DAPK1 knockout (KO) mice after being induced with or without Ang II. WT (n=10) mice were randomly divided into two groups: WT+NS group and WT+Ang II group (n=5 for each group). KO (n=10) mice were also randomly divided into two groups: KO+NS group and KO+Ang II group (n=5 for each group). Then the vascular  tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with vascular tissues of mice in 4 groups: WT+NS , WT+Ang II, KO+NS ，KO+Ang II to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Yao

last: Lin

first: Xiuli

last: Zhang


title: MPRA from GM12878 (ENCSR015VGW)

first: ENCODE

last: DCC


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing I

city: Zürich

first: Giulia

middle: Arianna

last: Moro

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

summary: Many scRNAseq-based methods suffer from a high number of non-detects and a bias towards the 3' or 5' end of transcripts. We developed a method termed RoCK and ROI to address these two biases. RoCK and ROI leads to the enrichment of the transcriptome profile of cells with information on transcripts of interest

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RoCK and ROI is based on barcoded beads of the BD Rhapsody platform. For RoCKseq specific capture, TSO oligos on BD Rhapsody beads are modified with a/ multiple capture sequence(s) specific to transcripts of interest. ROIseq, on the other hand, is based on specific primers which are spiked in during library generation, directing reads to regions of interest (ROIs). Multiple scRNAseq experiments were performed on several biological samples to validate RoCK and ROI. To validate RoCK and ROI library generation, scRNAseq experiments were performed on a mix of murine and human cell lines expressing eGFP or tdTomato respectively. As a further validation of RoCK and ROI, epithelial and mesenchymal cells from a transgenic mouse strain (B6.129S4-Pdgfratm11(EGFP)Sor/J) were used.

first: Izaskun

last: Mallona

first: Mark

middle: D

last: Robinson

first: Erich

last: Brunner

first: Konrad

last: Basler


title: The brittle star genome illuminates the genetic basis of animal appendage regeneration

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

institute: University College London

summary: Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited available genomic resources. Here, we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star displays the most rearranged genome amongst echinoderms sequenced to date, featuring a reorganised Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression throughout brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, notably during the proliferative phase of regeneration. Our findings emphasise the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.

overall_design: RNA-seq samples of brittle star arm regeneration timecoure (8 samples) and explant experiments to compare regeneration and wound healing

first: Elise

last: Parey

first: Olga

last: Ortega-Martinez

first: Paola

last: Oliveri


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing III


title: A microfluidics workflow for spatial analysis of microenvironmental gradient impact on cancer cell phenotypes

city: Copenhagen

first: Yifan

last: Dai

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: Copenhagen University

summary: Despite the physiological and pathophysiological significance of microenvironmental gradients, tools for generating such gradients and analysing their impact on cellular phenotypes are lacking. Here we present an integrated microfluidics-based workflow for mimicking extracellular pH gradients characteristic of solid tumors, and studying their multifactorial impact on cancer cells. Our microfluidics device generates a pH gradient across cancer cell 3D cultures in an extracellular matrix. The gradient, validated using pH-sensitive fluorophores can be rapidly controlled to represent spatiotemporal microenvironmental changes, and the device allows high resolution live imaging of, e.g., cell motility and chemotaxis. The device can be reopened, allowing immunofluorescence analysis of phenotypes and spatially resolved analysis of gene expression changes across the pH gradient. The workflow is easily adaptable for other gradients and multiple cell types, making it broadly applicable for integrated analysis of roles of microenvironmental gradients in biology.

overall_design: MDA-MB-231 cells grown in a microfluidics device generating a ph gradient from 6.0 to 7.4, in triplicates (one per library)

first: Jamie

last: Auxillos

first: Roxane

last: Crouigneau

first: Yanfang

last: Li

first: Arnaud

last: Stigliani

first: Isabella

last: Tavernaro

first: Ute

last: Resch-Genger

first: Albin

last: Sandelin

first: Rodolphe

last: Marie

first: Stine

last: Pedersen


title: RoCK and ROI: a single-cell RNA-sequencing method with enhanced transcriptome information via targeted enrichment of transcripts and preselected, region-specific sequencing  II

first: Giulia

last: Moro

first: Izaskun

last: Mallona

first: Mark

last: Robinson


title: Clinical and Immunological Responses to Combined JAK Inhibition and PD-1 immunotherapy for Lung Cancer Patients

city: Philadelphia

first: Andy

last: Minn

state: Philadelphia

address: 421 Curie  Blvd

institute: University of Pennsylvania

summary: Persistent inflammation driven by cytokines like type-one interferon (IFN-I) can cause immunosuppression. We show that administration of the JAK1 inhibitor itacitinib after anti-PD1 immunotherapy improves immune function and anti-tumor responses in mice, and results in high response rates (67%) in a phase-2 clinical trial for metastatic non-small cell lung cancer. Patients who failed to respond to initial anti-PD1 immunotherapy but responded after addition of itacitinib had multiple features of poor immune function to anti-PD1 alone that improved after JAK inhibition. Itacitinib promoted CD8 T cell plasticity and therapeutic responses of exhausted- and effector-memory-like T cell clonotypes. Patients with persistent inflammation refractory to itacitinib showed progressive CD8 T cell terminal differentiation and progressive disease. Thus, JAK inhibition may improve the efficacy of anti-PD1 immunotherapy by pivoting T cell differentiation dynamics.

overall_design: Live CD8+ cells or Live CD45+ cells were sorted from PBMCs of Patients with NSCLC treated with anti-PD1 and JAKi or anti-PD1 alone during select timeponts in treatment

first: Divij

last: Mathew


title: STAG2 mutations and 3D genome organization, chromatin loops, and polycomb signaling in glioblastoma multiforme

city: Boston

first: Wanying

last: Xu

state: MA

address: Karp Family Research Building

department: Hematology

institute: Boston Children's Hospital & Broad Institute

summary: Inactivating mutations of genes encoding the cohesin complex are common in a wide range of human cancers. STAG2 is the most commonly mutated subunit. Here we report the impact of stable correction of endogenous, naturally occurring STAG2 mutations on gene expression, 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme. Correction of mutant STAG2 significantly altered the expression of ~10% of all expressed genes. The genes most highly regulated by STAG2 (e.g. FGF7, c-KIT, MAGE tumor antigens) were virtually all upregulated in STAG2-mutant cells. Hi-C revealed that ~3% of A/B compartments switched after STAG2 correction, and confirmed prior findings that STAG2 is dispensable for maintenance of Topologically Associating Domains (TADs). The size and strength of thousands of chromatin loops were altered by STAG2 correction, a subset of which controlled the expression of adjacent genes. Loops specific to STAG2-mutant cells and tumors were very large, supporting prior findings that STAG1-containing cohesin complexes have greater loop extrusion processivity than STAG2-containing cohesin complexes, and suggesting that long loops may be a generalizable feature of STAG2-mutant cancers. Finally, STAG2-regulated chromatin loops were enriched for the H3K27me3 Polycomb epigenetic mark, revealing that inactivation of STAG2 can activate Polycomb signaling in GBM. Together these findings illuminate the landscape of STAG2-regulated genes, A/B compartments, chromatin loops, and pathways in GBM, providing important clues into the still mysterious mechanism of STAG2 tumor suppression in human cancer.

overall_design:
Hi-C of 4 cell lines
RNA-seq of 4 cell lines

first: Jung-Sik

last: Kim

first: Tianyi

last: Yang

first: Lisa

last: Sadzewicz

first: Luke

last: Tallon

first: Jann

last: Sarkaria

first: Fulai

last: Jin

first: Todd

last: Waldman


title: Chronic inflammatory activation of arterial endothelial cells in mice under normal lipoprotein/cholesterol levels and on normal diet.

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

summary: Inflammatory activation of endothelial cells is considered to be the first step in the development of atherosclerosis. Here, we determined changes of aortic gene expression after chronic inflammatory activation of arterial endothelial cells in genetically modified mice.

overall_design: We established a conditional transgenic mouse model, expressing a tamoxifen-inducible, constitutively active form of IKK2 exclusively in arterial endothelial cells (caIKK2EC mice) using BMX-CreERT2 mice in comparison to Cre-negative littermate controls. Ad libitum-fed male and female mice were used in this study at ∼6-8 weeks of age. mRNA profiles of whole aortas were generated by deep sequencing, using Illumina HiSeq3000/4000 instrument.

first: Marion

last: Mussbacher

first: José

last: Basílio

last: A Schmid


title: ENL reads histone β-hydroxybutyrylation to modulate gene transcription (CUT&Tag)

status: Public on May 06 2024

city: Tianjin

first: 爱源

last: 王

state: —Please choose an option—

address: No. 22, Meteorological Observatory Road, Heping District, Tianjin

department: Department of Biochemistry and Molecular Biology

institute: TianjinMedical University

summary: Histone modifications are typically recognized by chromatin-binding protein modules (referred to as “readers”) to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap must be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent photoaffinity probes to capture binders of the mark and identified ENL as a novel target of H3K9bhb. Biochemical studies and CUT&Tag analysis further suggested that ENL favorably binds to H3K9bhb, and co-localizes with it on promoter regions to modulate gene expression. Notably, disrupting the interaction between H3K9bhb and ENL via structure-based mutation leads to the suppressed expression of the gene like MYC that drives cell proliferation.

overall_design: We  implemented CUT&Tag assays in HepG2 cells to test whether ENL links H3K9bhb in the native chromatin context. The cells stably expressing Flag-tagged ENL were immunoprecipitated using Flag antibodies or H3K9bhb antibodies, respectively, followed by high-throughput sequencing.


title: Small RNA-seq analysis of E10.5 Tbx18-expressing peri-wolffian duct stroma

city: New York City

first: Dr. Yu Leng

last: Phua

state: New York

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

summary: The overall goal of this project is to characterize the repertoire of miRNAs in E10.5 Tbx18-expressing peri-wolffian duct stroma cells during development. To achieve this, E10.5 peri-wolffian ducts were dissected from timed-mated Tbx18-Cre;CAG-tdTomato embryos, followed by FACS sorting based on RFP expression to enrich for Tbx18-expressing cells.

overall_design: 1X75 bp standard RNA-seq was performed using an Illumina NextSeq platform.

first: Yu

middle: L


title: The role of macrophage VCAM-1 in atherosclerosis and inflammation

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

summary: VCAM-1 is known to be expressed by endothelial cells. We showed that this is also expressed by atherosclerotic plaque macrophages. However, the merit of this adhesion molecule is now known in atherosclerosis. In this RNA sequencing experiment, we analyzed VCAM-1+ vs. - atherosclerotic plaque macrophages. Additionally, we sorted macrophages from atherosclerotic plaques of mice after mitochondrial biogenesis gene Cmpk2 silencing in macrophages in vivo.

overall_design: We sorted VCAM-1+ and - macrophages from atherosclerotic plaques of Apoe KO mice fed with an atherogenic diet for four months. Moreover, we collected total atherosclerotic plaque macrophages from ApoeKO mice fed with an atherogenic diet for four months and treated with control and Cmpk2 siRNA formulated in lipidoid nanoparticles for a month. For the spatial transcriptomics experiment, we performed bone marrow transplantation in Ldlr KO mice with bone marrow from WT or myeloid Vcam1-deficient mice. The mice were placed on high fat diet a week later. The aortic roots were harvested after four months, spatial RNA seq using the Slide Seq technology was employed.

first: Niranjana

last: Natarajan

first: Jishnu

last: Das


title: IRF2BP2 counteracts the ATF7/JDP2 heterodimer to prevent inflammatory overactivation in AML cells [RNA-seq]

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

summary: Acute myeloid leukemia (AML) is a hematological malignancy characterized by abnormal proliferation and accumulation of immature myeloid cells in the bone marrow. Inflammation plays a crucial role in AML progression, but excessive activation of cell-intrinsic inflammatory pathways can also trigger cell death. IRF2BP2 is a chromatin regulator implicated in AML pathogenesis, although its precise role in this disease is not fully understood. In this study, we demonstrate that IRF2BP2 interacts with the AP-1 heterodimer ATF7/JDP2, which is involved in activating inflammatory pathways in AML cells. We show that IRF2BP2 is recruited by the ATF7/JDP2 dimer to chromatin and counteracts its gene-activating function. Loss of IRF2BP2 leads to overactivation of inflammatory pathways, resulting in strongly reduced proliferation. Our research indicates that a precise equilibrium between activating and repressive transcriptional mechanisms creates a pro-oncogenic inflammatory environment in AML cells. The ATF7/JDP2-IRF2BP2 regulatory axis is likely a key regulator of this process and may, therefore, represent a promising therapeutic vulnerability for AML. Thus, our study provides new insights into the molecular mechanisms underlying AML pathogenesis and identifies a potential therapeutic target for AML treatment.

overall_design: RNA-Seq in THP1 cells. Experiments were performed in Control cells, IRF2BP2 knockdown, ATF7 knockout, and JDP2 knockout cells

first: Sabrina

last: Fischer

first: Bastian

last: Stielow

first: Andrea

last: Nist


title: ENL reads histone β-hydroxybutyrylation to modulate gene transcription (RNA-Seq)

overall_design: we performed RNA-Seq by ectopically expressing WT-ENL or Mutant-ENL in cells


title: Single Cell Analysis of Lung Lymphatic Endothelial Cells and Lymphatic Responses during Influenza Infection

city: New York

first: Jian

last: Ge

institute: Columbia University

summary: Tissue lymphatic vessels network plays critical roles in immune surveillance and tissue homeostasis in response to pathogen invasion, but how lymphatic system per se is remolded during infection is less understood. Here, we observed that influenza infection induces a significant increase of lymphatic vessel numbers in the lung, accompanied with extensive proliferation of lymphatic endothelial cells (LECs). Single-cell RNA sequencing illustrated the heterogeneity of LECs, identifying a novel PD-L1+ subpopulation that is present during viral infection but not at steady state. Specific deletion of Pd-l1 in LECs elevated the expansion of lymphatic vessel numbers during viral infection. Together these findings elucidate a dramatic expansion of lung lymphatic network in response to viral infection, and reveal a PD-L1+ LEC subpopulation that potentially modulates lymphatic vessel remolding.


title: Necroptosis enhances “Don’t eat me” signal and induces macrophage extracellular traps to promote pancreatic cancer liver metastasis [scRNA-seq]

first: Chengyu

last: Liao

state: Fujain

address: 134, east road

department: Shengli Clinical Medical College

institute: Fujian Medical University

summary: We delved into the consequences of C57BL/6 orthotopic model injected with KPC cells with Vector/MLKL overexpression

overall_design: Pancreatic orthotpic tumors of C57BL/6 mice injected with KPC-OE-Vector cells and KPC-OE-MLKL cells

first: Fengping

last: Kang

first: Zuwei

last: Wang

first: Shi

last: Chen


title: Therapeutic radiation drives leptomeningeal dissemination of medulloblastoma [bulkRNA-seq]

city: Toronto

first: Carolina

last: Nor

state: Ontario

address: 686 Bay St

department: Developmental & Stem Cell Biology

institute: The Hospital for Sick Children

summary: In this study, we examine the effect of radiation on the transcriptional profile of medulloblastoma tumor cells and its microenvironment that could potentially be leading to metastatic dissemination.

overall_design: Cerebellar tumors from SmoA1 and Ptc het mice treated with radiation (1Gy) or sham radiation were collected at 5h after treatment and compared to normal cerebellum from C57BL/6 mice treated with radiation (1Gy) or sham-radiated controls by bulk cell RNA sequencing

first: Michael

last: Taylor


title: Therapeutic radiation drives leptomeningeal dissemination of medulloblastoma [scRNA-seq]

overall_design: Cerebellar tumors from SmoA1 mice treated with radiation (1Gy) were collected at 5h and 24h after treatment and compared to sham-radiated controls by single cell RNA sequencing


title: N6-Methyladenosine RNA Modification Regulates the Differential Muscle Development in Large White and Ningxiang Pigs

city: wuhan

first: gu

last: hao

address: 29 Nanhu Avenue, Shizishan Street

institute: Hubei Academy of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most common modification in eukaryotic RNAs. Accumulating evidence has shown that m6A methylation plays a vital role in various biological processes. However, research on the role of m6A modifications in regulation of porcine muscle growth is lacking. In this study, we identified differentially expressed genes in the early stages of muscle development between Large White (LW) and NingXiang (NX) pigs and further reported m6A methylation patterns via MeRIP-seq. We found that m6A modification regulates muscle cell development, myofibrils, cell cycle, and phosphatase regulator activity during the neonatal phase of muscle development. Interestingly, differentially expressed genes in LW and NX pigs were mainly enriched in pathways involved in protein synthesis. Furthermore, we performed a conjoint analysis of MeRIP-seq and RNA-seq data, and identified 27 differentially expressed and m6A-modified genes.

overall_design: To gain insight into the identity of m6A-modified mRNAs involved in muscle development in LW and NX pigs, we performed m6A RNA immunoprecipitation followed by sequencing (meRIP-seq) of the longissimus dorsi of 5-day-old LW and NX pigs

first: Hao

last: Gu


title: Pien Tze Huang enhances the killing effect of autologous T cells in colorectal cancer by inhibiting PD-L1, stem cell markers, and STAT3.

first: Zhiyun

last: Cao

state: 福建Fujian

address: 1# Qiu Yang Road

institute: Fujian university

summary: Aim: The aim of this study is to explore the impact of Pien Tze Huang (PZH) on enhancing T cell cytotoxicity by modulating colorectal cancer stem cell (CRC-CSC) markers, programmed death protein ligand-1 (PD-L1), and the transcription factor signal transducer and activator of transcription 3 (STAT3) protein expression in vivo, ex vivo, and in vitro. Methods: HCT116, HCT15, and SW480 cell lines were subjected to treatment with PZH, followed by assessment of cell viability and stemness through CCK8 and spheroid formation assays. Western blot and immunofluorescence techniques were employed to evaluate the expression levels of stem cell markers (DCLK1, CD133, CD44, MET, and LGR5), PD-L1, and STAT3 across three CRC cell lines and five patient-derived organoids (PDOs). Flow cytometry and western blot analyses were utilized to validate T cell expansion from both donors and CRC patients. CRC cells and CRC-PDOs, pre-treated with PZH, were co-cultured with expanded T cells from both donor and autologous peripheral blood mononuclear cells (PBMCs) respectively. The viability of CRC cells and PDOs was evaluated through Calcein-AM staining to measure fluorescence intensity and cell count following co-culture. In the syngeneic MC38 C57BL/6 xenograft model, tumor growth curve and body weight were monitored subsequent to treatment with PZH, anti-PD-1, and PZH combined with anti-PD-1. Immunohistochemistry was performed to assess protein levels of CD133, CD44, STAT3, PD-L1, CD8, and IL-6R in tumor tissue. Results: The effectiveness of PZH in reducing CRC cell viability and suppressing stemness markers, such as LGR5, CD44, MET, DCLK1, and CD133, is evident. PZH also displayed inhibitory effects on tumorigenesis in five CRC-PDOs, with varying sensitivity across cases (3 sensitive and 2 less sensitive). Moreover, PZH enhanced the cytotoxicity of donor T cells against CRC cells and rectified the cytotoxic deficiency or bolstered the cytotoxicity of autologous T cells against CRC-PDOs by downregulating PD-L1 and STAT3 protein expressi Conclusion: PZH enhances T cell-mediated killing effect by inhibiting CRC stem cell markers, PD-L1, and STAT3. Key Words: Pien Tze Huang, patient-derived organoid, colorectal cancer stem cells, programmed death protein ligand-1, signal transducer and activator of transcription 3

overall_design: CRC cell line MC38 were inoculated subcutaneously into C57 mice and treated with PZH for two weeks and then performed RNA-Sequencing (RNA-Seq) by sequencing company.

first: Qin

last: Lu

first: Zhuqing

last: Zhang

first: Sihan

last: Liu


title: Necroptosis enhances 'Don’t eat me' signal and induces macrophage extracellular traps to promote pancreatic cancer liver metastasis [THP1-derived macrophages]

summary: We delved into the consequences of macrophages that co-cultured with PDAC cells with Vector/MLKL overexpression. We treated THP1 derived macrophages with PANC1 cells with Vector/MLKL overexpression.

overall_design: THP1-derived macrophages cells co-cultured with Panc1-oe-Vector and THP1-derived macrophages cells co-cultured with Panc1-oe-Vector


title: FBXO32 drives pancreatic cancer progression

city: Beijing

first: Dan

last: Su

address: No. 1 Shuaifuyuan, Wangfujing Street, Beijing

department: Department of General Surgery

institute: Peking Union Medical college hospital

summary: In order to profile the translation events that were regulated by FBXO32, Ribo-seq was performed on PANC-1 cells which was used to generate FBXO32 stably depleted pancreatic cancer cells.

overall_design: FBXO32-depleted or control PANC-1 cells were collected for ribosome profiling analysis to uncover potential downstream genes regulated by FBXO32 at the translational level. There were two bioreplicates for each group.

first: Taiping