title: Gene expression analysis following overexpression of L2 delta13 in C57BL/6J mice

city: Shantou

first: Xiu-Hui

last: Zhan

address: 22, Xinling Road

institute: Shantou University

summary: High level expression of LOXL2 has been shown to be associated with tumor metastasis and poor clinical outcome in several types of cancers. We have previously identified a natural LOXL2 splice variant, called L2 delta13, in human esophageal squamous cell carcinoma cells. Unlike extracellular full-length LOXL2, L2 delta13 lacks amine oxidase activity and fails to be secreted from cells. To determine which genes are regulated by L2 delta13 in vivo, next generation RNA sequencing was performed to compare the RNA expression profile of liver tissues excised from L2 delta13-overexpressing and wild-type mice.

overall_design: RNA-sequencing of overexpression of L2 delta13 and wild type mice were performed by the BGISEQ-500 platform.

first: Ji-Wei

last: Jiao

first: En-Min


title: A hypermethylated ALOX12 gene is highly susceptible to 5-azacytidine treatment in myelodysplastic syndromes

status: Public on May 31 2023

city: Kurume

first: Taichi

last: Matsumoto

state: Fukuoka

address: 422, Tsubuku-honmachi

department: Basic Medical Science Unit

country: Japan

institute: St. Mary's Research Center

summary: 5-azacytidine (AZA) is widely used for treatment of myelodysplastic syndromes (MDS). However, identifying predictive factors for response to AZA remains challenging. The aim in present study was to identify the genes which are susceptible to AZA in MDS and investigate the possibility of the gene for predictor for response to AZA therapy. To identify AZA-susceptible genes, we compared the gene expression changes by AZA in MDS-L cells (AZA-sensitive) with those in MDS-L/CDA cells (AZA-resistant) in culture. Of 438 AZA-susceptible genes, we searched the genes which are hypermethylated in MDS patients as compared to healthy controls by analyzing public dataset GSE152710, and found ALOX12 gene. Analysis of public dataset GSE145733 and GSE58831 revealed that ALOX12 expression was suppressed in MDS classes with excess blasts but not in other classes, and were negatively and positively correlated with bone marrow blast counts and survival, respectively, in MDS patients. Analysis of public dataset GSE152710 revealed that the methylation level of ALOX12 gene was decreased in MDS patients with complete remission but not in those with partial response and progression disease after AZA therapy. Our retrospective clinical study in which nine AZA-treated patients were enrolled suggested that ALOX12 expression was increased in patients with favorable response, while decreased in patient with poor response after AZA therapy. In conclusion, ALOX12 gene could be tumor suppressive and promising marker for predicting the response to AZA therapy in MDS.

overall_design: MDS-L and MDS-L/CDA cells were treated with either vehicle (0.1% DMSO) or 1 mM 5-azacytidine (AZA) for 72 h.

first: Yuichi

last: Murakami


title: Detailed Survey of an in-vitro Intestinal Epithelium Model by Single-Cell Transcriptomics

city: Cleveland

first: Douglas

last: Brubaker

state: OH

address: 10900 Euclid Ave

country: USA

institute: Case Western Reserve University

type: Expression profiling by high throughput sequencing

summary: The gut plays a critical role in maintaining human health by facilitating the absorption of nutrients, regulating metabolism, and interacting with the immune system and gut microbiota. The co-culture of two human colorectal cancer cell lines, Caco-2 and HT29, on Transwell is commonly used as an in vitro gut mimic in studies of intestine absorption pharmacokinetic, gut mechanics, and gut-microbes interplay given the similar morphology, expression of transporters and enzymes, and barrier function. However, to sufficiently evaluate the translatability of insights from such a system to human physiological contexts, a detailed survey of cell type heterogeneity in the system and a holistic comparison with human physiology needs to be conducted rather than by the presence of a few well-studied proteins. Single-cell RNA sequencing provides high-resolution expression profiles of cells in the co-culture, enabling the heterogeneity to be characterized and the similarity to human epithelial cells to be evaluated. 16019 genes transcriptional profile in 13784 cells were acquired and compared to human epithelial cells (GSE185224). We identified the intestinal stem cell, transit amplifying, enterocyte, goblet cell, and enteroendocrine-like cells together with differentiating HT29 cells in the system based on the expression of canonical markers in healthy adult human epithelial cells. The epithelium-like co-culture was fetal intestine-like, with less variety of gene expression compared to the human gut. Transporters for major types of substance (lipid, amino acid, ion, water, etc.) were found transcribed in the majority of the enterocytes-like cells in the system. However, some of the well-studied transporters were absent. Toll-like receptors were not highly expressed in the sample, yet the treatment of LPS still caused a mild change in TEER and gene expression, possibly by the interaction with CD14. Overall, the Caco-2/HT29 co-culture is a cost-effective epithelium model for drug permeability testing or mechanical simulation, but its discrepancy with the real epithelium phenotype-wise is not negligible. As a result, its response to biological factors might not provide transferrable knowledge to the study of human gut physiology, especially the innate immune aspect.

overall_design: We cultured Caco-2 (ATCC, passage no. 8) and HT29 (ATCC, passage no.13) separately at 1x105 cells/ cm2 and seeded them together into the apical chamber of three Transwells (Corning Inc, Costar, USA) with a ratio of 9:1 on day 0. Two Transwells were used as controls, where cells were co-cultured and harvested on day 23. The other Transwell was treated with 1 ng/ml Escherichia coli O111:B4 lipopolysaccharides on day 22 and harvested on day 23. Then all samples were prepared for single-cell RNA sequencing per the manufacturer's instruction (10X genomics). Cell morphology agreed with the previous description of the Caco-2/HT29 monolayers. The TEER values reported from control treatments were within range values reported by Hoffmann et aL, indicating the established Caco-2/HT29 co-culture systems possesses comparable properties as other reported cases.

first: Javier

last: Munoz

first: Smrutiti

last: Jena

first: Ran

last: Ran

middle: K


title: Modifications in the T arm of tRNA globally determine tRNA function and cellular fitness

city: Chicago

first: Christopher

middle: Daniel

last: Katanski

state: IL

institute: University of Chicago

summary: Abstract: tRNAs are highly modified in the elbow region and harbor 5-methyluridine at position 54 and pseudouridine at position 55 in the T arm, which are generated by the enzymes TrmA and TruB, respectively. Although all elongator tRNAs contain these modifications across all domains of life, the cellular relevance of these modifications and their corresponding modifying enzymes remains elusive. In addition to modifying every tRNA, Escherichia coli TrmA and TruB have both been shown to fold tRNA independently of its modification activity acting as tRNA chaperones, and strains lacking trmA or truB are outcompeted by wildtype. To identify how TrmA and TruB contribute to cellular fitness, we have systematically assessed the effects of deleting trmA and/or trmB in E. coli. Since tRNA folding is a pre-requisite for tRNA aminoacylation, we determined cellular aminoacylation levels revealing a global decrease in aminoacylation for all tRNAs in ΔtrmA and ΔtruB. Moreover, the absence of 5-methyluridine 54 or pseudouridine 55 alters tRNA modification at other positions: whereas acp3U47 is decreased, thiouridine levels are increased. Understanding the importance of TrmA and TruB for tRNA aminoacylation and modification, we then analyzed how these global tRNA changes in ΔtrmA and ΔtruB strains affect translation. Whereas global protein synthesis is not significantly changed in ΔtrmA and ΔtruB, the abundances of many specific proteins are altered, and transcriptomics experiments suggest that the dysregulation of many proteins is controlled at the translational level. In conclusion, we demonstrate that universally conserved modifications of the tRNA elbow are critical for global tRNA function by enhancing other tRNA modifications, tRNA folding, tRNA aminoacylation and translation of specific genes thereby contributing to cellular fitness.

overall_design: In order to compare the fraction of aminoacylated tRNA between ΔtrmA, ΔtruB, and ΔtrmAΔtruB Escherichia coli strains and the parental strain, E. coli BW25113, tRNA-seq was performed following β-elimination of the 3ʹ-A from uncharged tRNAs.

first: Sarah

last: Schultz

middle: D

first: Richard

last: Fahlman

first: Tao

last: Pan

first: Ute

last: Kothe


title: microRNA-132 regulates gene expression programs involved in microglial homeostasis

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

summary: microRNA-132 (miR-132), a known neuronal regulator, is one of the most robustly downregulated microRNAs (miRNAs) in the brain of Alzheimer’s disease (AD) patients. Increasing miR-132 in AD mouse brain ameliorates amyloid and Tau pathologies, and also restores adult hippocampal neurogenesis and memory deficits. However, the functional pleiotropy of miRNAs requires in-depth analysis of the effects of miR-132 supplementation before it can be moved forward for AD therapy. We employ here miR-132 loss- and gain-of-function approaches using single-cell transcriptomics, proteomics and in silico AGO-CLIP datasets to identify molecular pathways targeted by miR-132 in mouse hippocampus. We find that miR-132 modulation significantly affects the transition of microglia from a disease-associated to a homeostatic cell state. We confirm the regulatory role of miR-132 in shifting microglial cell states using human microglial cultures derived from induced pluripotent stem cells.

overall_design: Cells from the right hippocampus of mice treated with miR-132 antagomiR/scrambled control and miR-132 mimic/negative control were isolated by Fluorescence-activated cell sorting (FACS) based on viability (e780, replicates 1 and 3) and in addition for the presence or absence of YFP signal (neurons) or CD11b and ACSA-2 (astrocytes) (replicates 2, 4 and 5) and analyzed using scRNAseq.

first: Hannah

last: Walgrave

first: Amber

last: Penning

first: Giorgia

last: Tosoni

last: Snoeck

first: Emma

last: Davis

first: Leen

last: Wolfs

first: Annerieke

last: Sierksma

first: Mayte

last: Mars

first: Taofeng

last: Bu

first: Nicola

last: Thrupp

first: Lujia

last: Zhou

first: Diederik

last: Moechars

first: Renzo

last: Mancuso

first: Mark

last: Fiers

first: Andrew

middle: J

last: Howden

first: Bart

last: De Strooper

first: Evgenia

last: Salta


title: Patient-derived tumor xenograft study with CDK4/6 inhibitor plus AKT inhibitor for management of metastatic castrate resistant prostate cancer

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

type: Genome variation profiling by genome tiling array

summary: We applied DNA content flow cytometry to a series of prostate cancer (PC) patient derived tumor xenografts (PDTXs). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) analyses. These identified a variety of somatic genomic lesions targeting  genes and cellular pathways in PC. Of significant interest are lesions that may affect responses to therapies.  Guided by the genomic alterations in these models and interrelated mechanisms between androgen signaling axis, the cell cycle, and AKT pathway, we identified and investigated the combination of CDK4/6 inhibitors with AKT inhibitors as a potential therapy for patients with mCRPC. Using 3-D spheroid drug assays followed by in vivo experiments in three unique PDTX models, these preclinical results highlight the potential use of CDK4/6 inhibitor with AKT inhibitors for the treatment of mCRPC who have intact retinoblastoma pathway, thereby, providing the experimental data support and rationale for future clinical investigation

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from prostate tumor patient derived tumor xenografts (PDTXs). We coupled this strategy with oligonucleotide array CGH (aCGH) thereby obtaining high definition genomic profiles of clonal populations from each tumor. Response to CDK4/6 and AKT inhibition was assesed with organoid models derived from the PDTXs.

first: Adam

last: Kase

first: Justyna

last: Gleba

first: James

middle: L

last: Miller

first: Erin

first: Joachim

last: Petit

first: Yumei

middle: T

first: Ephraim

middle: E

last: Parent

first: Hancheng

last: Cai

first: Josh

last: Knight

first: Jacob

last: Orme

first: Jordan

last: Reynolds

first: William

middle: F

last: Durham

first: Thomas

middle: M

last: Metz

first: Nathalie

last: Meurice

first: Brandy

last: Edenfield

first: Aylin

middle: A

last: Demirer

first: Ahmet

last: Bilgili

first: Peyton

middle: G

last: Hickman

first: Matthew

last: Pawlush

first: Daniel

last: Wickland

first: Winston

last: Tan

first: John

last: Copland III


title: Gene expression changes in lung cancer cells upon TIGD1 knockdown

city: Xi'an

first: Yiqun

last: Wei

address: No. 157, Xiwu Road, Xi'an, Shaanxi, 710004, China

country: China

institute: the Second Affiliated Hospital of Xi'an Jiaotong University

summary: To explore the function of TIGD1 in lung cancer cells, we performed microarray to analyze the expression pattern changes by knockdown of TIGD1 in A549 cells.

overall_design: Microarray was preformed in lung cancer A549 cells transfected with control or TIGD1-specific small-hairpin RNA (shRNA) .

first: Runmiao

last: Wu

first: Shuanying

last: Yang

first: Yanfei

last: Cao

first: Jing

last: Li

first: Huihui

last: Ma

first: Junfang

first: Jinjin

last: Duan

first: Shumei


title: Immune stimulation recruits a subset of pro-regenerative macrophages to the retina that promotes axonal regrowth of injured neurons

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

institute: Vrije Universiteit Brussel - VIB

summary: The multifaceted nature of neuroinflammation is highlighted by its ability to both aggravate and promote neuronal health. While in mammals retinal ganglion cells (RGCs) are unable to regenerate following injury, acute inflammation can induce axonal regrowth. However, the nature of the cells, cellular states and signalling pathways that drive this inflammation-induced regeneration have remained elusive. Here, we investigated the functional significance of macrophages during RGC de- and regeneration, by characterizing the inflammatory cascade evoked by optic nerve crush (ONC) injury, with or without local inflammatory stimulation in the vitreous. By combining single-cell RNA sequencing and fate mapping approaches, we elucidated the response of retinal microglia and recruited monocyte-derived macrophages (MDMs) to RGC injury. Importantly, inflammatory stimulation recruited large numbers of MDMs to the retina, which exhibited long-term engraftment and promoted axonal regrowth. Ligand-receptor analysis highlighted a subset of recruited macrophages that exhibited expression of pro-regenerative secreted factors, which were able to promote axon regrowth via paracrine signalling. Our work reveals how inflammation may promote CNS regeneration by modulating innate immune responses, providing a rationale for macrophage-centred strategies for driving neuronal repair following injury and disease.

overall_design: CD11b+ CD45+ cells were isolated from retina samples of naive mice, mice after optic nerve crush injury (injured retinas) and mice 4 days or 8 days after optic nerve crush and inflammatory stimulation (stimulated retinas).

first: Lien

last: Andries

first: Luca

last: Masin

first: Isabelle

last: Scheyltjens

first: Hannah

last: Van Hove

first: Karen

last: De Vlaminck

first: Steven

last: Bergmans

first: Marie

last: Claes

first: Lies

last: De Groef

first: Lieve

last: Moons

first: Kiavash

last: Movahedi


title: Single-cell Profiling Identified Tdgf1 as a Regulator of the Second Lineage Specification in Mouse Preimplantation Embryos

status: Public on Jun 01 2023

city: Taian

first: Qingqing

last: Wei

state: Shandong

address: 61 Daizong Street

institute: Shandong Agricultural University

summary: We have analyzed changes of gene expression in mouse morula, early blastocyst and late blastocyst after siRNA injection (negative control and Tdgf1 target) to illustrate the mechanism of Tdgf1.

overall_design: mRNA profile of  mouse morula, early blastocyst and late blastocyst after siRNA injection (negative control and Tdgf1 target) by deep sequencing.

first: Liang

last: Zhong


title: Porcine circovirus modulates swine influenza virus replication in pig trachea epithelial cells and porcine alveolar macrophages [iPAM]

city: Saint-Hyacinthe

first: Yaima

last: Burgher Pulgaron

state: Québec

address: 3200 Sicotte

country: Canada

institute: Faculté de médecine vétérinaire, Université de Montréal

summary: The pathogenesis of porcine circovirus type 2b (PCV2b) and swine influenza A virus (SwIV) during co-infection in swine respiratory cells is poorly understood. To elucidate the impact of PCV2b/SwIV co-infection, newborn porcine tracheal epithelial cells (NPTr) and immortalized porcine alveolar macrophages (iPAM 3D4/21) were co-infected with PCV2b and SwIV (H1N1 or H3N2 genotype). Viral replication, cell viability and cytokine mRNA expression were determined and compared between single-infected and co-infected cells. Finally, 3’mRNA sequencing was performed to identify the modulation of gene expression and cellular pathways in co-infected cells. It was found that PCV2b significantly decreased and improved SwIV replication, in co-infected NPTr and iPAM 3D4/21 cells respectively, compared to single infected cells. Interestingly, PCV2b/SwIV co-infection synergistically up-regulated IFN expression in NPTr cells whereas in iPAM 3D4/21 cells, PCV2b impaired the SwIV IFN induced response, both correlating with SwIV replication modulation. RNA-sequencing analyses revealed that the modulation of gene expression and enriched cellular pathways during PCV2b/SwIV H1N1 co-infection is regulated in a cell type-dependent-manner. This study revealed different outcomes of PCV2b/SwIV co-infection in porcine epithelial cells and macrophages and provides new insights on porcine viral co-infections pathogenesis.

overall_design: Total RNA was purified from different types of infections. The samples were PCV2b-infected cells, SwIV H1N1-infected cells and PCV2b/SwIV H1N1-infected cells. Mock infected cells were used as control. Three biological replicates were included for each type of infection.

first: Chantale

last: Provost

first: Marie-Jeanne

last: Pesant

first: Carl

last: Gagnon


title: Porcine circovirus modulates swine influenza virus replication in pig trachea epithelial cells and porcine alveolar macrophages [NPTr]


title: PD-1 prevents pathogenicity of effector CD8 T cells that infiltrate skin under homeostatic conditions

city: New Haven

first: Nikhil

last: Joshi

state: CT

address: 300 Cedar St, PO Box 208011

department: Immunobiology

institute: Yale University

summary: Self-reactive T cells are part of the peripheral T cell repertoire in healthy individuals. Checkpoint receptors like PD-1 allow the establishment of peripheral tolerance by inducing deletion or anergy of self-reactive CD8 T cells, however the high frequency of immune-related Adverse Events (irAEs) among cancer patients receiving checkpoint receptor inhibitor (CPI) immunotherapy led us to question how checkpoint receptors are involved in peripheral T cell tolerance. We developed a novel mouse model for studying peripheral T cell tolerance in the skin where skin-specific expression of T cell antigens (Ags) caused local infiltration of Ag-specific CD8 T cells with effector capacity. In this setting, PD-1 was required for maintaining local tolerance by allowing the co-existence of Ag-expressing cells and Ag-specific effector CD8 T cells in skin without tissue pathology, while CD8 T cell-mediated elimination of Ag-expressing cells and consequent tissue pathology developed in the absence of PD-1-mediated regulation. In this model, PD-1 allowed maintenance of skin tolerance by preventing tissue-infiltrating Ag-specific effector CD8 T cells from 1) acquiring a fully functional, pathogenic differentiation state, 2) secreting significant amounts of effector molecules, and 3) gaining access to Ag-expressing cells in the epidermis. Transcriptomic analysis of skin biopsies from two patients with cutaneous lichenoid irAEs showed presence of clonally expanded effector CD8 T cells in both lesional and non-lesional skin. Thus, our data support a model of peripheral T cell tolerance where PD-1 allows Ag-specific effector CD8 T cells to persist in a tissue where their cognate Ag is expressed without causing pathology.

overall_design: Skin biopsies from patients with lichenoid cutaneous immune-related adverse events (lesional skin LS1-2, nonlesional skin NLS1-2) and healthy control patients (NS1-2) were analyzed using single-cell RNA sequencing on the 10X Genomics platform.

first: Noah

middle: I

last: Hornick

first: Martina

last: Damo

middle: S


title: Novel microRNAs modulating ecto-5′-nucleotidase expression [MaMel]

city: Greifswald

first: Theresa

last: Kordaß

state: Mecklenburg-Vorpommern

address: Ferdinand-Sauerbruch Straße DZ7 5.05

department: Surgical Research Laboratory

country: Germany

institute: Univserity Medicine Greifswald

summary: the effect of NT5E enhancing miRNAs was studied by gene expression profiling to unterstand mechanism of observed NT5E upregulation.

overall_design: Gene expression profiling of tumor cell lines transfected with miRNAs enhancing NT5E expression was performed as follows: MaMel-02  cells were transfected with 50 nM miRNA, including a non-targeting control miRNA (control-1/ath-miR-416) in a 12 well plate format, performing triplicates for each format. After 48 h, cells were harvested for RNA isolation using an RNAeasy kit (Qiagen, Hilden, Germany). Microarrays were performed by DKFZ-Genomics and Proteomics Core Facility using an Affymetrix Clariom S human chip for all samples. Raw data processing was also performed using the Core Facility. Differential gene expression was calculated by comparing miRNA-induced gene expression levels to the respective gene expression levels following mimic control-1 transfection.

first: Tsu-Yang

last: Chao


title: Novel microRNAs modulating ecto-5′-nucleotidase expression

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

overall_design: Refer to individual Series


title: Novel microRNAs modulating ecto-5′-nucleotidase expression [SK-Mel-28]

overall_design: Gene expression profiling of tumor cell lines transfected with miRNAs enhancing NT5E expression was performed as follows: SK-Mel-28  cells were transfected with 50 nM miRNA, including a non-targeting control miRNA (control-1/ath-miR-416) in a 12 well plate format, performing triplicates for each format. After 48 h, cells were harvested for RNA isolation using an RNAeasy kit (Qiagen, Hilden, Germany). Microarrays were performed by DKFZ-Genomics and Proteomics Core Facility using an Affymetrix Clariom S human chip for all samples. Raw data processing was also performed using the Core Facility. Differential gene expression was calculated by comparing miRNA-induced gene expression levels to the respective gene expression levels following mimic control-1 transfection.


title: Regulation of lung EC transcriptome by leene in mouse

city: Duarte

first: Zhen

last: Chen

state: CA

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

summary: Vascular endothelial cells play a pivotal role in whole-body homeostasis. To test the function of LEENE in vivo, particularly in the context of hypertension, we subjected WT and leene-KO mice to an Angiotensin II-induced hypertension model. We then profiled the transcriptomic changes in the EC-enriched fractions of the lung.

overall_design: PolyA-enriched RNA-seq in lung endothelial cells of leene WT and KO mice supplemented with AngII implantation

first: Xiaofang

last: Tang

first: Chih-Hung

last: Lai

first: Yingjun

last: Luo

first: Dongqiang

last: Yuan

first: Riccardo

last: Calandrelli

middle: B


title: Porcine circovirus modulates swine influenza virus replication in pig trachea epithelial cells and porcine alveolar macrophages


title: Novel microRNAs modulating ecto-5′-nucleotidase expression [MDA-MB-231]

overall_design: Gene expression profiling of tumor cell lines transfected with miRNAs enhancing NT5E expression was performed as follows: MDA-MB-231 cells were transfected with 50 nM miRNA, including a non-targeting control miRNA (control-1/ath-miR-416) in a 12 well plate format, performing triplicates for each format. After 48 h, cells were harvested for RNA isolation using an RNAeasy kit (Qiagen, Hilden, Germany). Microarrays were performed by DKFZ-Genomics and Proteomics Core Facility using an Affymetrix Clariom S human chip for all samples. Raw data processing was also performed using the Core Facility. Differential gene expression was calculated by comparing miRNA-induced gene expression levels to the respective gene expression levels following mimic control-1 transfection.


title: Abcg2 expressing VESC in adult heart

city: New York

first: Yang

last: Lin

state: NY

address: 455 Main Street 06W

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Abcg2 expressing vascular endothelial stem cells (AbcVESC) in adult murine heart promote vessel regeneration after cardiac infarction injury. Here we compared H3.3 K4Me3, K27Me3 modifications between AbcVESC and mature EC

overall_design: AbcVESC in adult Abcg2creERT;ROSATdtomato (Abcg2TT) mice were labeled by TdTomato 1 day after 50mg/kg tamoxifen injection. H3.3 K4Me3, K27Me3 CHIP-Seq were performed in TdTomato+ AbcVESC and TdTomato- mature EC from adult Abcg2TT mouse heart.

first: Chang-Hyun

last: Gil

first: Kimihiko

last: Banno

first: Ying

last: Liu

first: Shahin

last: Rafii

first: Mervin

middle: C

last: Yoder


title: Periodontitis-induced inflammation: impacts of hyperglycemic microenvironment

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 bd Laurier

institute: Université Laval

summary: Dysbiosis of subgingival microbiome promotes the growth of periodontopathogens and the development of periodontitis, an irreversible chronic inflammatory disease. Untreated periodontitis leads to the destruction of connective tissues, alveolar bone resorption and ultimately to tooth loss. Periodontitis has been associated with inflammatory metabolic diseases such as type 2 diabetes. While periodontitis-induced inflammation is a key player in both, the development of subgingival microbiome dysbiosis and in the host-microbiome interaction, the effects of hyperglycemia on the regulation of the host genes controlling the inflammatory response and the host-microbiome interaction are still scarce. We investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and gene expression of a gingival fibroblasts-macrophages coculture model stimulated with dysbiotic subgingival microbiomes.     A coculture model composed of immortalized human gingival fibroblasts overlaid with U937 macrophages-likes cells were stimulated with subgingival microbiome collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinase were measured by a Luminex assay while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed by using an advanced multi-omics bioinformatic data integration model.     Our results showed that krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key correlated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment.      To conclude, our multi-omics integration analysis unveiled unique differentially interrelated bacterial genera, genes and pro-inflammatory cytokines involved in the regulation of the inflammatory response in a hyperglycemic microenvironment. These data also highlight the importance of considering hyperglycemic conditions in the development of new drugs or treatments for periodontal disease in link with type 2 diabetes.

overall_design: 4 samples with periodontitis co-cultured with low glucose level, 4 samples with periodontitis co-cultured with high glucose level, 4 healthy samples co-cultured with low glucose level, 4 healthy samples co-cultured with high glucose level, 2 negative control samples.

first: Sarah

last: Lafleur

last: Bodein

first: Joanna

last: Malaïka Mutombo

first: Alban

last: Mathieu

first: Charles

last: Beauparlant

first: Xavier

last: Minne

first: Fatiha

last: Chandad

first: Arnaud

last: Droit

first: Vanessa

middle: P

last: Houde


title: Significant increase of high-risk chromosome 1q gain and 6q loss at recurrence in posterior fossa group A ependymoma: a multicenter study

city: Aurora

first: Andrew

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus


title: Expression data from urinary exosome of diabetic and non-diabetic rats

city: Lucknow

first: Swasti

last: Tiwari

state: Uttar Pradesh

address: Raibareli Road

department: Molecular Medicine and Biotechnology

country: India

institute: Sanjay Gandhi Postgraduate Institute of Medical Sciences

summary:
We performed microarray miRNA expression profiling of diabetes induced rat via intraperitoneal (I.P) administration of streptozotocin (STZ).
Rats were considered diabetic when their blood glucose exceeded 200 mg/dL (11 mmol/L).

overall_design: Microarray analysis was performed using N=2 diabetic rats versus N=2 controls


title: Effect of SF3B4 depletion on gene expression of A549 lung cancer cell

city: Jinan City

first: Tao

last: Li

address: No. 107, Wenhua West Road, Lixia District

institute: Qilu Hospital of Shandong University

summary: To investigate the  function SF3B4 during the progression of lung cancer, A549 cells with either SF3B4 siRNA or scramble siRNA were used for RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 cells transfected with either SF3B4 siRNA or scramble siRNA


title: Differential Expression Profiles and Function Predictions for tRFs & tiRNAs in BALB/c mice with atopic dermatitis

city: Shanghai

first: Qinyu

last: Tang

address: 389 Xincun Road, Putuo District, Shanghai, China

institute: Tongji University

summary: Purpose: To explore the expression and biological functions of tRFs & tiRNAs in BALB/c mice with AD.  Method: tRFs/tiRNAs profiles of control mice skin and 2,4-dinitrochlorobenzene(DNCB)- induced mice skin were generated by the Arraystar Mouse Small RNA Arrays. qRT–PCR validation was performed using SYBR Green assays.  Results: There were 676 tRFs/tiRNAs that were aberrantly expressed in BALB/c mice with AD; 298 were upregulated and 378 were downregulated. tRF5-20-GluCTC-1, 5'tiRNA-33-ProTGG-4, 5'tRF-GluTTC, and mt-tRF3a-ProTGG were significantly expressed and confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the Small RNA microarray technology.   Conclusion: The pathogenesis of AD may be related with the differential expression of tRFs/tiRNAs. These findings may provide new perspectives for elucidating the molecular mechanisms and future treatments for AD.

overall_design: The DNCB-treated group (six mice) was challenged by application of 200 µL and 20 μL of 1% DNCB [acetone/olive oil (4:1)] on the back skin from days 1 to 10, for four times in total; and 0.5% DNCB from days 15 to 27, for five times in total. The normal control group (six mice) received a mixture of acetone and olive oil at the same time. tRFs/tiRNAs profiles of 3 normal skin samples and 3 atopic dermatitis skin samples in BALB/c mice.

first: Chen

last: Liang

first: Liangliang

last: Shen


title: The Chd4 helicase regulates chromatin accessibility and gene expression critical for β-cell function in vivo [ATAC-seq]

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

institute: Indiana University

summary: To establish the role of Chd4 on controlling gene expression programs in the beta cell, we generated a tamoxifen-inducible, beta-cell-specific knockout mouse model; control (MIP-CreERT; Chd4flox/+;R26RtdTomato) and Chd4Db (MIP-CreERT; Chd4flox/flox;R26RtdTomato.

overall_design: Dispersed islets from tamoxifen treated control and Chd4Db mice were flow-sorted, and ATAC-Seq performed.

first: Rebecca

last: Davidson


title: Enhanced STAT5a activation opposes Tox and rewires exhausted CD8 T cells towards a hybrid durable effector-like state during chronic stimulation [scRNA-seq_PostInfection]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: Here, we discovered a reciprocal antagonism between Stat5a and Tox in TEX cells. Stat5a antagonized the Tox-mediated exhaustion program to achieve a durable and protective hybrid effector/NK-like differentiation state in settings that typically drive exhaustion. Stat5 also drove TEX progenitors to differentiate into the effector-like TEXint subset, a key developmental step for PD-1 blockade responsiveness.

overall_design: P14 CD8 Tcells post infection were assayed using 10x scRNAseq

first: Jean

last: Beltra

last: Wherry


title: Genome-wide binding of TrmB in Haloarcula hispanica

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) from TrmB in the halophilic archaeon Haloarcula hispanica in the presence and absense of glucose.

overall_design: ChIP-Seq

first: Rylee

last: Hackley


title: Effect of ARID1A deficiency on transcriptome regulation during pancreatic cancer development and progression

city: Goettingen

first: Zhe

last: Zhang

state: Niedersachsen

address: Robert-Koch-Strasse 40

department: Department of Gastroenterology & GI oncology

institute: University Medical Center, Goettingen

summary: In order to investigate the funcational and mechanistic role of ARID1A in regulating PDAC development and progression, we generated mRNA expression profiles from human pancreatic cancer cell line L3.6pl, which underwent ARID1A-depletion by CRISPR-Cas9 technology. The same-processed L3.6pl parental cell line was used as control.

overall_design: mRNA expression profiles of human pancreatic cancer cell line L3.6pl in the context of ARID1A deficiency and treatment-naïve contidion.

first: Xin

last: Wang

first: Shilpa

last: Patil

first: Elisabeth

last: Hessmann


title: The effect of LncRNA FAS-AS1 on gene expression of nasopharyngeal carcinoma

city: Changsha

first: Zhen

last: Guo

state: hunan

address: Changsha Medical University, LeiFeng Avenue NO.1501

institute: Changsha Medical University

summary: This study investigates the function of FAS-AS1 in the regulation of nasopharyngeal carcinoma. GSEA analysis of RNA-seq data suggested FAS-AS1 participate in mitochondria regulation and mRNA alternative splicing

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HNE1 cells transfected with FAS-AS1 overexpression vector or control vector for 24 h.

first: BinSheng

last: He


title: RNA-seq dissects incomplete activation of glyceollin biosynthesis by soybean transcription factors GmMYB29A2 and GmNAC42-1

city: Toronto

first: Jie

last: Lin

state: Ontario

address: 4700 keele street

department: Biology

institute: York University

summary: RNA-seq was conducted on overexpressed GmMYB29A2 hairy roots of Williams 82 (W82)

overall_design: Overexpressing GmMYB29A2 hairy roots of W82 were treated with H2O (mock) for 24 hours, total RNA was extratced for RNAseq.

first: Nik

last: Kovinich

first: Sajjad

last: Ahmed

first: Ivan

last: Monsalvo


title: Enhanced STAT5a activation opposes Tox and rewires exhausted CD8 T cells towards a hybrid durable effector-like state during chronic stimulation [CITE-seq_PostInfection]

overall_design: CITE-seq was done on 2 samples for quantifying gene expression and protein, WT and STAT5 KO cells


title: Enhanced STAT5a activation opposes Tox and rewires exhausted CD8 T cells towards a hybrid durable effector-like state during chronic stimulation [ATAC-postInfection]

summary:
Here, we discovered a reciprocal antagonism between Stat5a and Tox in TEX cells. Stat5a antagonized the Tox-mediated exhaustion program to achieve a durable and protective hybrid effector/NK-like differentiation state in settings that typically drive exhaustion. Stat5 also drove TEX progenitors to differentiate into the effector-like TEXint subset, a key developmental step for PD-1 blockade responsiveness.
Therapeutic enhancement of Stat5 activity in TEX cells using an orthogonal IL-2/IL2Rb pair system fostered TEXint cell accumulation and synergized with PD-L1 blockade. Finally, targeted delivery of Stat5-signals in TEX progenitors achieved partial epigenetic rewiring of these cells towards the effector/memory lineage and revived polyfunctionality. Together, these data highlight therapeutic opportunities of targeting Stat5 to antagonize the Tox-dependent epigenetic programming of TEX and provoke a hybrid program that exploits effector biology and durability for optimal therapeutic potential

overall_design: CD8 Tcells from naïve mice,P14 CD8 T cells from LCMV Armstrong infected mice at D8p.i,P14 CD8 T cells transduced with an Empty (control) retrovirus and isolated from LCMV Cl13 infected mice at D8p.i,P14 CD8 T cells transduced with a retrovirius encoding STAT5CA and isolated from LCMV Cl13 infected mice at D8p.i. were assayed using ATACseq assay using DNA from three or 4 biological replicates.


title: Gene expression profiling of N87 and OE19 gastric cancer cell lines grown in 3D or 2D condition

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: A great deal of evidence indicates that solid and hematological tumors are driven and maintained by a minor cell compartment with stem cell properties. In this context, gastric cancer stem cells (GCSCs) are implicated in tumor aggressiveness, invasion, metastasis and therapy resistance. HER2 amplification/overexpression (HER2+) is found in about 20% of GCs. Although the anti-HER2 antibody trastuzumab has improved the outcomes of patients with HER2+ advanced disease, its benefits are usually transitory because of high HER2 heterogeneity and frequent co-existence of other oncogenic drivers associated with primary/acquired resistance. To identify potential drivers of trastuzumab resistance in GCSCs, we compare the gene expression profile of OE19 and N87 HER2+ GC cell lines cultured as gastrospheres, peculiar 3D cell cultures that allow detecting the in vitro enrichment of CSCs, versus their matched adherent cell (2D) counterparts.  Comparison of the transcriptomic profiles of HER2+ GC cells cultured in 2D versus 3D conditions evidenced a significant enrichment of Fatty Acid Synthase (FASN) transcript among the genes upmodulated in 3D cell cultures. We found that the pharmacological blockade of HER2 and FASN targets CSCs and decreases tumor growth of HER2-positive GC models

overall_design: Gastrospheres were derived from OE19 and N87 HER2+ GC cell lines. Gene expression profiles of these cells were compared with the profiles of the same cells cultured in adherent conditions (2D). (n=3 biological replicates)

first: Serenella

last: Pupa

first: Lorenzo

last: Castagnoli

first: Loris

last: De Cecco


title: Enhanced STAT5a activation opposes Tox and rewires exhausted CD8 T cells towards a hybrid durable effector-like state during chronic stimulation [ATAC-postChallenge]

first: E

last: WHERRY

overall_design: ATAC-postChallenge, LCMV Armstrong

first: Jean

last: Beltra

last: Wherry


title: A single-cell multi-modal ATAC + gene expression sequencing in tendinopathy

city: Chongqing

first: JUNFENG

last: GUO

state: Chongqing

address: No. 30, Gaotan Yanzheng Street,

department: Department of Orthopedics/Sports Medicine Center

institute: Southwest Hospital, Third Military Medical University

summary: As people become more motivated to exercise regularly and stay healthy, tendinopathy is a common problem in both active athletes and inactive individuals, which imposes a considerable social and economic burden. Here we provide a single-cell multi-modal ATAC + gene expression sequencing in tendinopathy. We have identified pathways and genes regulated in tendinopathy samples that will help contribute to further investigation into the development and molecular hallmarks of tendinopathy.

overall_design: Single-cell multi-modal ATAC + gene expression sequencing of human tendinopathy

first: Junfeng

first: Taotao

last: Liang

first: Kanglai

last: Tang


title: Overactivation of notch1 signaling in uterine epithelium

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

summary:
We show that the overexpression of N1ICD in the epithelium also results in infertility as a consequence of abnormal differentiation between luminal epithelium (LE) and glandular epithelium (GE), including excessive proliferation in LE and increased response to estrogen in GE.
These findings provide insight into the effects of Notch signaling on both types of epithelium.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ctrl-LE, Ctrl-GE, EOEX-LE, E-OEX-GE.

first: Qixin

last: Xu

first: Renwei


title: IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression [mouse miRNA-Seq]

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

summary: Chromosome 17q gain is an independent prognostic marker in neuroblastoma, harboring several potential oncogenes including IGF2BP1 and BIRC5. IGF2BP1 was shown to be upregulated in unfavorable neuroblastoma and correlates with poor patient survival. Here, we report that overexpression of IGF2BP1 in a transgenic mouse model induces neuroblastoma with all characteristics known for human neuroblastoma, including MYCN upregulation and genomic aberrations. Furthermore, we demonstrate that genes located at chromosome 17q have an exceptionally high potential as therapeutic targets in addition to a combined inhibition of IGF2BP1 and BIRC5 resulting in additive effects.

overall_design: Non-coding RNA profiling by high throughput sequencing of neuroblastoma mouse tumor samples

first: Sven

last: Hagemann

first: Stefan

last: Hüttelmaier


title: LSD1 inhibition disrupts super-enhancer activities in CRPC

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

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

overall_design: Refer to individual Series


title: A genome-wide CRISPR screen identifies ZNF251 critical for resistance to PARP inhibitors

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

summary: The poly (ADP-ribose) polymerases (PARPs) inhibitors are an exciting new class of agents that have shown efficacy in treating various cancers, especially these harboring BRCA1/2 mutations. The cancer associated BRCA1/2 mutations disrupt DNA double strand break (DSB) repair by homologous recombination (HR). PARP inhibitors (PARPi) have been applied to trigger synthetic lethality in BRCA1/2-mutated cancer cells by promoting accumulation of toxic DSBs. Unfortunately, PARP inhibitor (PARPi) resistance is common and develops through multiple mechanisms. Restoration of HR and/or stabilizing replication forks are two major mechanisms of PARPi resistance in BRCA1/2-mutated cells. To further understand the mechanisms of drug resistance to PARPi, we undertook an unbiased approach with a CRISPR-pooled library to screen new genes whose loss-of-function confers resistance to PARPi olaparib. We identified ZNF251, a transcription factor, and confirmed its loss-of-function led to the PARPi resistance in BRCA1-mutated breast and ovarian cancer lines. Elevated activities of both HR and non-homologous end joining (NHEJ) repair were detected in cancer cells harboring BRCA1 mutation and ZNF251 deletion (BRCA1mut+ZNF251del) and were associated with enhanced expression of RAD51 and Ku70/Ku80, respectively. Furthermore, we showed that DNA-PKcs inhibitor restored sensitivity of BRCA1mut+ZNF251del cells to PARPi. Taken together, our study identified a novel gene whose loss of function conferred resistance to PARPi, providing new insight into signaling pathways that contribute to acquired resistance in BRCA1-mutated breast and ovarian cancers.

overall_design: GeCKO CRISPR library was purchased from Addgene (#1000000048), amplified, and packaged as lentivirus based on the instructions on Addgene website. The CRISPR screen was performed as described previously(Hou et al. Cancer research 2017). In brief, MDA-MB-436 cells were transduced with lentivirus carrying GeCKO library, and puromycin selection was performed for 2 days. Then we treated transduced MDA-MB-436 cells with olaparib for 14 days and the survived cells were harvested. The genomic DNA was extracted, and PCR was carried out before deep sequencing of sgRNA sequence in the survived cells genome.

first: Jian

last: Huang


title: Pervasive environmental chemicals impair oligodendrocyte development

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Exposure to environmental chemicals can impair neurodevelopment. Oligodendrocytes that wrap around axons to boost neurotransmission may be particularly vulnerable to chemical toxicity as they develop throughout fetal development and into adulthood. However, few environmental chemicals have been assessed for potential risks to oligodendrocyte development. Here, we utilized a high-throughput developmental screen and human cortical brain organoids, which revealed environmental chemicals in two classes that disrupt oligodendrocyte development. Quaternary compounds, ubiquitous in disinfecting agents, hair conditioners, and fabric softeners, were potently and selectively cytotoxic to developing oligodendrocytes through activation of the integrated stress response. Organophosphate flame retardants, commonly found in household items such as furniture and electronics, were non-cytotoxic but prematurely arrested oligodendrocyte maturation. Chemicals from each of the two classes impaired human oligodendrocyte development in a 3D organoid model of prenatal cortical development. In analysis of epidemiological data from the CDC’s National Health and Nutrition Examination Survey, adverse neurodevelopmental outcomes were associated with childhood exposure to the top organophosphate flame retardant identified in our oligodendrocyte toxicity platform. Collectively, our work identifies toxicological vulnerabilities specific to oligodendrocyte development and highlights common household chemicals with high exposure risk to children that warrant deeper scrutiny for their impact on human health.

overall_design: Mouse iPSC-derived OPCs were plated in 6-well plates coated with poly-L-ornithine (Sigma, P3655) and laminin (Sigma, L2020) in OPC medium (Fisher Scientific, 14-832-11) and allowed to attach for one hour. OPCs were incubated with methyltrioctylammonium chloride (Tox1) and tributyltetradecylphosphonium chloride (Tox2) at their approximate IC90 concentrations for 4 hours. OPCs were then lysed in TRIzol (Invitrogen, 15596018) and RNA was extracted by phenol-chloroform extraction and purified using the RNeasy Mini Kit (Qiagen, 74104). Samples were sent to Novogene for library preparation and mRNA sequencing. Libraries were generated according to protocols from the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L) and then evenly pooled and sequenced on the Illumina NovaSeq with 150bp paired-end reads and a read dept of at least 20 million reads per sample.

first: Erin

last: Cohn


title: Single-Cell Characterization of the Frizzled 5 (Fz5) Mutant Mouse and Human Persistent Fetal Vasculature (PFV)

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

summary: During early development, a transitory fetal vasculature of the vitreous hyaloid vessels (HV) provides temporary nutrients for the developing lens and retina. HV regresses when the intraretinal vasculature develops to replace its function. Failure in regression of the HV leads to persistent fetal vasculature (PFV), a pathological condition accounting for 4.8% children blindness in the USA. To date, the HV formation and regression as well as the related PFV pathogenesis are largely unknown. In this study, by single-cell RNA sequencing (scRNA-seq) the vitreous cells derived from normal and the Fzd5 mutant mice at two time points, postnatal day 3 (P3) and P6, we collectively defined 10 major cell types, present in both wild type and mutant developing vitreous but with much higher numbers of endothelial cells, macrophages, erythroid-like cells, pericytes, smooth muscle cells, fibroblasts and melanocytes in the P3 mutants. Both mutant and wild type cell types declined to similar sizes at P6 with varied compositions of sub clusters. We further compared gene expression profiles of residual major sub clusters at P6, and showed altered metabolic activities of the mutant cells. Additionally, two macrophage clusters expressed markers for hyalocytes supporting the notion that these cells are of macrophage origin. The melanocytes predominantly existed in the Fzd5 mutants expressing neural crest markers including Pax3 and Sox10, similar to that of choroidal pigment cells. Taken together, these data revealed cell features of normal and pathological hyaloid tissues, which has not been known precedentially.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Illumina BCL files were converted to fastq files by using 10X Genomics Cell Ranger pipeline mkfastq function (https://support.10xgenomics.com/). Next, cellranger count function was used to generate Gene-Barcode matrices from the fastq files, which uses the STAR algorithm to map high-quality reads to the mouse reference genome (mm10), followed by UMI counting.

Human scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. UMI-tools was applied for Single Cell Transcriptome Analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to human genome (Ensemble version 100) utilizing STAR mapping with customized parameter from UMI-tools standard pipeline to obtain the UMIs counts of each sample. Cells contained over 200 expressed genes and mitochondria UMI rate below 40% passed the cell quality filtering and mitochondria genes were removed in the expression table.

Raw data (for human sample) will be available through GSA (controlled access) due to patient privacy concerns.

first: Chunqiao

last: Liu

first: Zhi

last: Xie

first: Yuanyuan

last: Chen


title: Genome-wide single nucleotide polymorphism analysis identifies DNA variations predictive of R-CHOP efficacy in diffuse large B-cell lymphoma

city: Firenze

first: Stefania

last: Nobili

address: viale Pieraccini 6

department: Health Sciences

institute: University of Florence

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: R-CHOP standard chemotherapy is successful in about 60% of patients with diffuse large B-cell lymphoma (DLBCL). Patients who do not benefit from it, due to tumor drug resistance, have a poor prognosis. To date, the available predictive biomarkers mainly relate to prognosis. We conducted the first prospective GWAS clinical study appositely designed to identify constitutional biomarkers predictive of R-CHOP efficacy and toxicity. Overall, 217 any stage chemonaive DLBCL patients candidate to R-CHOP were enrolled. ~800000 SNPs were analysed by the UK Biobank Axiom Array. Median age of eligible pts was 59.2 years, women were 49.7%. 45.4% of pts were in stage I-II. According to the revised IPI (R-IPI), 14.1%, 56.8% and 29.2% were in the very good (0), good (1-2) and poor (3-5) prognosis groups, respectively. 85.9% of pts obtained CR to R-CHOP. Based on the results obtained, we were able to build a seven-SNP score by summing the number of deleterious alleles from the SNPs for which highly significant associations with PFS were achieved. Wild-type patients showed a prolonged PFS compared with patients carrying 1 deleterious allele or 2+ deleterious alleles (p<0.001). When the score was applied to patients stratified according to R-IPI, wild-type patients classified as R-IPI 1-2 and R-IPI 3-5 showed a prolonged PFS compared with patients with the same respective R-IPI score carrying 1 deleterious allele or 2+ deleterious alleles (p<0.001). After a proper validation in an independent cohort of patients, the seven-SNP risk score could be proposed to select patients to whom offer a more aggressive treatment as well as an additional factor to those currently included in the R-IPI that could successfully contribute to predict response to R-CHOP.

overall_design: Affymetrix SNP arrays were performed on 187 constitutional DNA samples from adult DLBCL patients (two samples did not pass the quality control of genotypic data). Overall, 185 samples are provided.

first: Gabriele

last: Perrone

first: Luigi

last: Rigacci

first: Sara

last: Urru

first: Sofia

last: Kovalchuk

first: Marco

last: Brugia

first: Alberto

last: Fabbri

first: Lorenzo

last: Iovino

first: Benedetta

last: Puccini

first: Emanuele

last: Cencini

first: Enrico

last: Orciuolo

first: Silvia

last: Birtolo

first: Alessandro

last: Melosi

first: Simone

last: Santini

first: Ida

last: Landini

first: Giandomenico

last: Roviello

first: Giovanna

last: Chiorino

last: Bosi

first: Monica

last: Bocchia

first: Mario

last: Petrini

last: Mini


title: BACH1 Deficiency Prevents Neointima Formation and Maintains the Differentiated Phenotype of Vascular Smooth Muscle Cell by Regulating Chromatin Accessibility

first: Jieyu

last: Guo

address: 138 Yixueyuan Rd,

institute: fudan university

summary: Chromatin accessibility is important for cell fate determination in differentiation and multiple pathophysiological processes. Here, we report a transcription factor BACH1, facilitates the recruitment of G9a and YAP, maintains the state of H3K9me2 and decreases the chromatin accessibility at the promoter of VSMC marker genes, thereby repressing their expression and contributing to dedifferentiated VSMC phenotype. Moreover, VSMC-specific loss of BACH1 in mice inhibited the transformation of VSMC from contractile to synthetic phenotype and VSMC proliferation and attenuated the neointimal hyperplasia in wire-injured femoral arteries.

first: D

last: Meng

first: J


title: IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression [mouse RNA-seq]

first: Danny

last: Misiak

overall_design: PolyA enriched RNA-sequencing of neuroblastoma mouse tumor samples.

first: Sven

last: Hagemann

first: Stefan

last: Hüttelmaier


title: IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression [mouse sWGS]

type: Genome variation profiling by high throughput sequencing

overall_design: Low coverage (~0.9X) shallow whole genome sequencing (sWGS) of neuroblastoma mouse tumor samples.


title: Impact of phage predation on bacterial transcriptome under simulated human airway conditions

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

institute: KU Leuven

summary: Phage therapy is a promising adjunct therapeutic approach against bacterial multidrug-resistant infections, including Pseudomonas aeruginosa-derived infections. Nevertheless, the current knowledge about the phage-bacteria interaction within a human environment is limited. In this work, we performed a transcriptome analysis of phage-infected P. aeruginosa adhered to a human epithelium (Nuli-1 ATCC® CRL-4011™). To this end, we performed RNA-sequencing from a complex mixture comprising phage–bacteria–human cells at early, middle, and late infection and compared it to uninfected adhered bacteria. Overall, we demonstrated that phage genome transcription is unaltered by bacterial growth and phage employs a core strategy of predation through upregulation of prophage-associated genes, a shutdown of bacterial surface receptors, and motility inhibition. In addition, specific responses were captured under lung-simulating conditions, with the expression of genes related to spermidine syntheses, sulfate acquisition, spermidine syntheses, biofilm formation (both alginate and polysaccharide syntheses), lipopolysaccharide (LPS) modification, pyochelin expression, and downregulation of virulence regulators. These responses should be carefully studied in detail to better discern phage-induced changes from bacterial responses against phage. Our results establish the relevance of using complex settings that mimics in vivo conditions to study phage-bacteria interplay, being obvious the phage versatility on bacterial cell invasion.

overall_design: Total transcriptome of Pseudomonas LUZ19 phage-infected bacteria (P. aeruginosa PAO1) when adhered to a monolayer of Nuli-1 cell line (ATCC® CRL-4011™) from normal human airway epithelium.

first: Ana

last: Brandão

first: Leena

last: Putzeys

first: Diana

last: Pires

first: Marleen

last: Voet

first: Jan

last: Paeshuyse

first: Joana

last: Azeredo


title: IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression [human sWGS]

overall_design: Low coverage (~0.7X) shallow whole genome sequencing (sWGS) of primary neuroblastoma tumor samples.


title: Transcriptomic profiling of differentially expressed mRNA, lncRNA and circRNA in atorvastatin-treated human endothelial cells

city: Hefei

first: Zhenghong

last: Liu

address: 443 Huangshan road

institute: University of Science and Technology of China

type: Non-coding RNA profiling by high throughput sequencing

summary: Statins are competitive inhibitors of (3-hydroxy-3-methylglutaryl coenzyme A) HMG-CoA reductase. The primary mechanism of statins is the lowering of serum cholesterol through inhibiting hepatic cholesterol biosynthesis. Statins exert pleiotropic vasoprotective and atheroprotective effects in the vasculature, with its mechanism of action being incompletely understood.To depict the statin-regulated mRNA,long non-coding RNA (lncRNA) and circular RNA (circRNA) in human endothelial cells, we performed transcriptomic profiling of human umbilical vein endothelial cells (HUVECs) with atorvastatin treatment.Differentially expressed mRNA, lncRNA and circRNA may represent novel therapeutic targets against cardiovascular diseases.

overall_design: Human umbilical vein endothelial cells (HUVECs) were seeded in 0.2% gelatin-coated dishes the day before experiment. The next day, cells were treated with DMSO or atorvastatin (10μM) for 24 hours. After treatment, total RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN). RNA libraries were prepared for sequencing using rRNA Removal Library Construction Protocol. Briefly, take a certain amount of total RNA samples, and remove rRNA by using RNase H or Ribo-Zero method, then fragment the RNA. Obtain the first and second strands of cDNA by reverse transcription. Then add adapters at both ends of the cDNA for PCR amplification to obtain the cDNA library. The library was amplified with phi29 to make DNA nanoball (DNB) which have more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS). The sequencing data was filtered with SOAPnuke (v1.5.2), afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).  Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), then expression level of gene was calculated by RSEM (v1.2.12).

first: Jianping

last: Weng

first: Suowen

last: Xu


title: IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression [human RNA-seq]

overall_design: RNA sequencing of primary neuroblastoma tumor samples.


title: Chemo-immonotherapeutic effects of  PD-L1-targeted antibody-catalyst conjugate plus DOX prodrug in a mouse model of colon cancer

first: Xinyu

last: Wang

address: Zhongshan 2nd Road

department: Department of Immunology

institute: Sun-yat sen University

summary:
We designed a study to investiagate chemo-immunotheraputic effect using a mouse model of colon cancer.
To investigate the anti-tumor effect of the combination therapy, the in vivo antitumor activities of different mono- and combinational therapy were subsequently evaluated using a C57BL/6J mouse model bearing MC38 tumors. Subcutaneous injection of 1×106 of MC38 cells in the right flank of a mouse was performed 9 days before therapy. The Ru-PD-L1 was administrated by intraperitoneal injection, while the DPD or DOX was given by peritumoral injection. For combinational treatment, each mouse was treated with 14 µg DPD or DOX (0.56 mg/kg) 6 hours after administering 20 ug Ru-PD-L1 (0.80mg/kg). For monotherapy, each mouse was treated with Ru-PD-L1, DPD, or DOX alone.  On the 20th day, the mice were sacrificed for tumor collection. The results highlighted that the combination of ACC and DOX prodrug synergistically enhanced immune response and higher antitumor activity compared to the ACC and DOX combination.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for (1) Control; (2) DOX; (3) DPD; (4) Ru-PD-L1; (5) Ru-PD-L1+DOX; (6) Ru-PD-L1+DPD treated tumor bearing mice.

first: Zong-Wan

last: Mao

first: Wei

last: Xia

first: Jun

last: Chen

first: Zhennan

last: Zhao

first: Jinhui

first: Yiyi

last: Li

first: Kai

last: Lu

first: Wenkai

last: Lin


title: Bulk RNA-seq of Human Platelets Before and After Flu Vaccination

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

summary: The goal of this study was to examine differential gene expression in human platelets, focusing on it's relationship to flu vaccine response and how it may vary with age.

overall_design: A total of 82 subjects were sequenced. Samples were taken prior to flu vaccination, then again at two, seven or 28 days post-vaccination.

first: Anthony

last: Melillo

first: Anna

last: Konstorum

first: Albert

last: Shaw


title: Transcriptome analysis of murine primary pancreatic acinar cells in the context of Arid1a deficiency

first: Zhe

last: Zhang

address: Robert-Koch-Strasse 40

institute: University Medical Center, Goettingen

summary: mRNA expression profiles were generated from primary pancreatic acinar cells of Arid1a-deficient and Arid1a-wildtype mice. Arid1a depletion leads to transcription activation to the majority of genes.

overall_design: Primary acinar cells were isolated from the pancreas of Arid1a-knockout mice and their control cohorts and subjected to RNA-sequencing.

first: Xin

first: Shilpa

last: Patil

first: Elisabeth

last: Hessmann


title: NFATc1 is a central mediator of EGFR-induced ARID1A chromatin dissociation during acinar cell reprogramming


title: Analysis of chromatin accessibility in Arid1a-deficient murine primary pancreatic acinar cells using ATAC-seq

summary: To gain insight into how the loss of SWI/SNF component ARID1A affects the chromatin accessibility, primary acinar cells were isolated from Arid1a-knockout and control mice and subjected to ATAC-sequencing.

overall_design: Primary acinar cells were isolated from Arid1a-knockout and control mice in triplicates and processed individualy for ATAC-seq.

first: Feda

last: Hamdan


title: Genome-wide maps of H3K27ac ocupancy on chromatin in murine acinar cell line upon EGF treatment and Arid1a silencing

summary: Chromatin Immunoprecipitation-based sequencing (ChIP-seq) of H3K27ac was conduced in murine Kras-mutant acinar cell line 266-6 in the context of Arid1a-knockdown and/or EGF treatment. We found EGFR signaling activation as well as Arid1a silencing leads to additional increase of H3K27ac level genome-widely. And the maximal H3K27ac was achieved by the combined- EGF treatment and Arid1a knockdown.

overall_design: Examination of H3K27ac of Arid1a-intact- and knockdown cells with or without 8-hour EGF treatment.


title: Genome-wide occupancy profile of ARID1A in the presence and absence of epidermal growth factor stimulation  in murine acinar cell line 266-6 (ChIP-seq)

summary: We identified the genome binding profile of SWI/SNF complex component ARID1A in pancreatic acinar cells. By comparing the genomic occupancy profiles, we found that EGF strikingly diminished ARID1A genome-wide affinity to the chromatin.

overall_design: Examination of ARID1A genomic binding profiles of EGF-treated or ctrl murine 266-6 cells.

first: Madhobi

last: Sen


title: Interplay of EGFR signaling and ARID1A in regulating transcriptome of celllular-plasticity genes

summary: mRNA expression profiles of Arid1a-wildtype and Arid1a-knockdown murine 266-6 cells were generated, in the presence or absence of EGF. We found that EGFR signaling activation and Arid1a loss cooperatively upregulate a subset of genes which are involved in cellular palsticity regulation.

overall_design: mRNA pexpression profiles of murine acinar cell line 266-6 in the context of Arid1a-knockdown (48h) and/or EGF treatment (8h).

last: Wang


title: FUS facilitates gene body export from nuclear condensates

status: Public on May 30 2023

city: Ithaca

first: Hojoong

last: Kwak

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: Membraneless nuclear condensates are an emerging model of transcriptional regulation that involves spatially clustered enhancers and genes forming transcription condensates (TCs). We used a physical isolation approach and DNA/nascent RNA analysis to investigate the global organization of the genome in TCs. Comparative analysis of the two revealed the dynamic nature of the genome, with stable localization of promoters, dynamic recruitment of enhancers, and dynamic export of gene bodies out of TCs upon gene activation. Our findings also suggest that the RNA binding protein FUS undergoes decondensation upon nascent RNA binding, facilitating gene body export out of TCs.

overall_design: Nascent RNA sequencing and DNA sequencing of whole nuclear vs nuclear condensate compartments, with biological replicates in HeLa cells and FUS overexpressed vs wild type HEK293 cells

first: Seungha

last: Lee

first: Emily

last: Uh


title: Effect of RT-MPs treatment on gene expression of stem-like Lewis cells

city: Wuhan, China

first: Xiao

last: Yang

state: 湖北省

address: 武汉市江汉区马场路109号协和医院肿瘤中心

institute: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

summary:
To further elucidate the mechanism underlying the RT-MPs killing effect on SLTCs, we performed RNA-seq on stem-like Lewis cells and RT-MP-treated stem-like Lewis cells
We then performed gene expression profiling analysis using data obtained from RNA-seq of stem-like Lewis cells untreated or treated with RT-MPs for 48 h

overall_design: Comparative gene expression profiling analysis of RNA-seq data for stem-like Lewis cells and RT-MP-treated stem-like Lewis cells.

first: Yajie

last: Sun

first: Yan

last: Hu


title: Contribution of IGCR1 and 3' CBE Super Anchor to Developmental Regulation of Igh V(D)J Recombination [GRO_Seq]

first: Frederick

last: Alt

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital / Harvard Medical School

summary: Immunoglobulin heavy chain variable region exons are assembled in progenitor-B cells, from VH, D, and JH gene segments located in separate clusters across the Igh locus.  RAG endonuclease orchestrates V(D)J recombination from a JH-based recombination center (RC). Cohesin-mediated extrusion of upstream chromatin past RC-bound RAG presents Ds for joining to JHs to form a DJHRC, from which RAG scans upstream for VHs to assemble VHDJH exons in an ordered recombination process.  Cohesin-mediated chromatin loop extrusion is impeded by CTCF-bound elements (CBEs), with extrusion between two CBEs, particularly if convergently-oriented, forming chromatin-contact loops genome-wide.  Igh has provocative CBE organization, with two divergently-oriented CBEs (CBE1 and CBE2) in the IGCR1 element between the VH and D/JH domains, dozens of VH domain CBEs convergent to CBE1, and 10 3'Igh-CBEs convergent to CBE2. IGCR1 CBEs segregate D/JH and VH domains by impeding RAG-scanning.  After DJH formation, down-regulation of WAPL, a cohesin unloader, neutralizes IGCR1 and VH-domain CBEs, allowing RAG to scan the VH domain.  To elucidate potential mechanisms underlying the developmental transition from D-to-JH to VH-to-DJH recombination and potential roles of IGCR1-based CBEs and 3'Igh-CBEs in regulating RAG-scanning, we tested effects of deleting or inverting IGCR1 or 3'Igh-CBEs in mice and/or progenitor-B cell lines. These studies revealed that normal IGCR1 CBE orientation augments its RAG-scanning impediment activity and that the 3'Igh-CBEs reinforce RC activity as a dynamic loop extrusion impediment, thereby, increasing its ability to support V(D)J recombination.  Finally, our findings implicate a mechanism by which developmental WAPL down-regulation contributes to ordered V(D)J recombination.

overall_design: We performed GRO_Seq to determine the roles of IGCR1 and 3'Igh CBEs in v-abl cells, pro-B cells.

first: Zhuoyi

last: Liang

middle: W


title: Contribution of IGCR1 and 3' CBE Super Anchor to Developmental Regulation of Igh V(D)J Recombination [3C_HTGTS_Seq]

overall_design: We performed 3C_HTGTS_Seq to determine the roles of IGCR1 and 3'Igh CBEs in v-abl cells, pro-B cells.


title: Contribution of IGCR1 and 3' CBE Super Anchor to Developmental Regulation of Igh V(D)J Recombination [HTGTS_VDJ_Seq]

overall_design: We performed HTGTS-VDJ-Seq to determine the roles of IGCR1 and 3'Igh CBEs in v-abl cells, pro-B cells.


title: Contribution of IGCR1 and 3' CBE Super Anchor to Developmental Regulation of Igh V(D)J Recombination

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

overall_design: Refer to individual Series


title: Infant Pain Vs. Pain with Parental Suppression: Immediate and Enduring Impact on Brain, Pain and Affect

city: Philadelphia

first: Gordon

middle: Alfred

last: Barr

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Anesthesiology

institute: CHOP

summary:
Pain experienced within a social context impacts infant neurobehavioral responses and initiates an altered developmental trajectory of pain and affect processing that diverges from experiencing pain alone.
We used microarrays to detail the  gene expression following pain with and without the mother at different preweaning ages

overall_design: Pups at PN 8 or PN12 were given very mild tail shocks or were controls with or without the mother and the amygdala dissected at assayed for gene expression

first: Maya

last: Opendak

first: Rosemarie

last: Perry

first: Emma

last: Sarro

first: Regina

last: Sullivan


title: Effect of ectopic expression of EtROP2 kinase on gene expression of avian epithelial cells (Clec213)

status: Public on May 26 2023

city: Nouzilly

first: Anne

last: SILVESTRE

department: Animal Health

country: France

institute: INRAE

summary: EtROP2 is a virulence determinant produced by Eimeria tenella in host cells, during and early after cell invasion. We compared transcriptomic analyses of avian cells transfected either by control plasmid or by plasmid allowing EtROP2 expression. We used an avian epithelial cell model developed in our lab (Clec213). Transfected avian cells were FACS sorted by fluorescent marker in order to reduce background noise from non-transfected cells. This analysis allowed us to assess EtROP2 effect on host cell transcription and possibly identify host signalling pathways modified by the parasite. These signalling pathways will pave the way to the identification of potential host protein targeted by parasite virulence factors.

overall_design: Two samples, four replicates. Clec213 cells transfected either with pcDNA-EGFP or with pcDNA-EtROP2-YFP-FLAG. Transfected cells were FACS sorted.

last: Silvestre

first: Adeline

last: Ribeiro E Silva


title: PD-1 prevents pathogenicity of effector CD8 T cells that infiltrate skin under homeostatic conditions

status: Public on May 27 2023

first: Martina

last: Damo

state: CT

address: 300 Cedar St

department: Immunobiology

summary: All healthy individuals have autoreactive T cells in their peripheral T cell pool, but peripheral tolerance mechanisms prevent these T cells from causing autoimmunity. Two primary mechanisms of peripheral tolerance are T cell anergy and clonal deletion, which occur after tolerogenic priming of T cells by dendritic cells (DCs). Induction of anergy and deletion are impaired in the absence of checkpoint receptors (like PD-1), but, once established, they are not reversed by blockade of checkpoint receptors. Thus, the occurrence of immune-related Adverse Events (irAEs) in up to 70% of patients treated with checkpoint inhibitor (CPI) immunotherapy has raised questions about how checkpoint receptors are functioning to maintain peripheral tolerance of autoreactive T cells under homeostatic conditions. To address this, we developed a novel mouse model for studying peripheral T cell tolerance in the skin in which the development of localized autoimmune-like pathology was dependent on skin-infiltrating CD8 T cells following skin-specific expression of T cell antigens (Ags) and administration of PD-1 blocking antibodies. Interestingly, Ag-specific CD8 T cells were found to infiltrate Ag-expressing skin even in the absence of PD-1 blockade, however they did not cause disease and in fact co-existed with the skin cells expressing their cognate Ag. At the protein level, non-pathogenic skin-infiltrating CD8 T cells produced lower amounts of many T cell effector proteins compared to their pathogenic counterparts, explaining the lack of cutaneous pathology, but non-pathogenic T cells were functional because they remodeled the local myeloid cell compartment. Moreover, and unlike in other models of tolerance, non-pathogenic and pathogenic skin-infiltrating CD8 T cells were nearly identical at the transcriptional level, indicating that both T cell populations were differentiating towards the same effector state. In this context, checkpoint receptors prevented the majority of the non-pathogenic CD8 T cells from reaching their terminal, fully effector and pathogenic state, thus maintaining tolerance in the skin. Finally, analysis of skin biopsies from two patients with cutaneous lichenoid irAEs showed presence of clonally expanded effector CD8 T cells with comparable transcriptional profiles in both lesional and non-lesional skin. Thus, our data are in line with a model of peripheral T cell tolerance where PD-1 allows peripheral Ag-specific effector CD8 T cells to co-exist in a tissue where their cognate Ag is expressed without causing pathology and provide a mechanism for the development of cutaneous lichenoid irAEs upon administration of CPI immunotherapy.

overall_design: Prepared single cell suspensions from the 4-OH-Tam-treated skin area of for each mouse  and performed Chromium scRNAseq via 10x Genomics. A total of 21178 cells were sequenced  from the six experimental samples (two Ag OFF mice, two Ag ON mice, and 2 Ag ON/CPI mice)

first: Noah

last: Hornick

first: Aarthi

last: Venkat

first: Ivana

last: William

first: Darwin

last: Kwok

first: Kathryn

last: Clulo

first: Can

last: Cui

first: Srividhya

last: Venkatesan

first: Jiaming

last: He

first: Eric

last: Fagerberg

first: Jennifer

last: Loza

first: Jessica

last: Buck

first: Aya

last: Tal

first: Jaiveer

last: Singh

first: William

last: Damsky

first: Jonatahn

last: Leventhal

first: Smita

last: Krishnaswamy

first: Nikhil

last: Joshi


title: Interplay between PML NBs and HIRA for H3.3 deposition on transcriptionally active interferon-stimulated genes

status: Public on May 25 2023

city: Lyon

first: Armelle

last: Corpet

address: 8 avenue Rockefeller

department: Laboratoire Physiopathologie et Génétique du Neurone et du Muscle

institute: Institut NeuroMyoGene

summary: Promyelocytic Leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. Here, by using specific siRNAs and protein Affimers, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. In addition, we demonstrate that HIRA localization in the nuclear bodies is intimately linked to the presence of a soluble pool of H3.3-H4 dimers inside PML NBs,  that is not found in cancer cells. Transcription inhibition prevents HIRA accumulation in PML NBs underscoring the importance of transcriptional activity to drive HIRA through PML NBs. Finally, in the context of inflammatory responses, HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of interferon-stimulated genes (ISGs), well beyond the peak of transcription. We thus propose that HIRA partitioning in PML NBs is essential to regulate H3.3 deposition on transcriptionally active regions.

overall_design:
H3.3 ChIP-seq on human primary BJ cells treated with siLuc, sILuc+IFN, siHIRA+IFN or siPML+IFN
GSE233298 and GSE186937 (biorxiv accession) are indeed identical.

first: Kleijwegt

last: Constance

first: Corpet

last: Armelle

first: Lomonte

last: Patrick

first: Simonet

last: Thomas


title: The metallic compound promotes primordial follicle activation and ameliorates fertility deficits in aged mice

first: Lincheng

last: Han

address: Guangzhou Higher Education Mega Center

institute: South China University of Technology

summary: We found MnCl2 and ZnSO4 promoted the activation of mouse primordial follicles through glycosis-dependent mTOR pathway in granulosa cells and PI3K/Akt pathway in oocytes. We further analyzed the transcriptome changes in the ovaries after MnCl2 and ZnSO4 treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the 1-day cultured ovaries between the control group (Ct) and the MnCl2 (Mn) or ZnSO4 (Zn) group.

first: Yingying

last: Huang

first: Biao

last: Li

first: Weiyong

last: Wang

first: Yan-li

last: Sun

first: Xiaodan

last: Zhang

first: Wenbo

first: Shuang

last: Liu

first: Wenjun

last: Zhou

first: Wei

last: Xia

first: Meijia


title: Gene expression in self-activating CAR-T cells with CD28 or 4-1BB costimulatory domains.

status: Public on May 28 2023

city: Yokohama

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

institute: Kanagawa Cancer Center Research Institute

summary: We observed self-activation of SKM-CAR-T cells which target novel mesothelioma antigen. CAR-T with CD28 costimulatory domain showed signs of exhaustion while those with 4-1BB costimulatory domain did not. Changes in the gene expression by substituting CD28 co-stimulatory domain to 4-1BB co-stimulatory domain was investigated.

overall_design: We performed RNA-seq analysis of SKM-CAR-T cells with CD28 or 4-1BB together with T cells without transducing CAR.

first: Tetsuro

last: Sasada


title: CD4+ T-cell-induced inflammatory killing controls immune evasive tumors

status: Public on May 24 2023

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Most clinically applied cancer immunotherapies rely on the ability of CD8+ cytolytic T-cells to directly recognise and kill tumor cells. These strategies are limited by the emergence of MHC-deficient tumor cells and the development of an immunosuppressive tumor microenvironment. The ability of CD4+ effector cells to contribute to anti-tumor immunity independently of CD8+ T-cells is increasingly recognised, but strategies to unleash their full potential remain to be identified. Here, we describe a mechanism through which a small number of CD4+ T-cells is sufficient to eradicate MHC-deficient tumors that escape direct CD8+ T-cell targeting. The CD4+ effector T-cells preferentially cluster at tumor invasive margins where they interact with MHC-II+CD11c+ antigen-presenting cells. We show that Th1-directed CD4+ T-cells and innate immune stimulation reprogram the tumor-associated myeloid cell network towards IFN-activated antigen-presenting and iNOS-expressing tumoricidal effector phenotypes. Together, CD4+ T-cells and tumoricidal myeloid cells orchestrate a remote inflammatory cell death process that indirectly eradicates IFN-unresponsive and MHC-deficient tumors. These results warrant to clinically exploit the ability of CD4+ T-cells and innate immune stimulators as a strategy to complement the direct cytolytic activity of CD8+ T- and NK-cells and advance cancer immunotherapies.

overall_design: Myeloid immune cells were isolated by FACS from HCmel12 melanomas in C57BL/6 mice treated with TRP-1 TCRtg CD4+ T-cells or left untreated and analyzed using scRNAseq.

first: T

last: Tueting

first: A

middle: D

last: Braun

first: R

middle: J

last: Müller


title: Acellular Ex Vivo Lung Perfusion Silences Pro-Inflammatory Signaling in Human Lung Endothelial and Epithelial Cells

city: Toronto

first: Jamie

middle: E.

last: Jeon

address: 101 College St.

department: Physiology

institute: University of Toronto

summary: Ischemia reperfusion (IR) injury is a key complication following lung transplantation, and it remains to be fully resolved. Ex vivo lung perfusion (EVLP) has shown its significance as a platform to assess and repair marginal donor lungs prior to transplants with good clinical outcomes. Recently, it has been shown that Glutamax supplementation to Steen solution can improve basic cellular function as well as porcine EVLP duration with stable lung quality. To better understand the molecular mechanisms of IR injury, acellular EVLP, and Glutamax supplementation during EVLP, transcriptomic changes in cell culture models simulating IR and EVLP have been investigated. Briefly, human pulmonary microvascular endothelial cells (HPMEC) and human lung epithelial cells (BEAS-2B) were cultured in DMEM+10%FBS, then were perfused with Perfadex at 4°C for 18H to simulate cold ischemic time (CIT). Subsequently, the cells were perfused in either DMEM+10%FBS (IR model) or in Steen solution or Steen with 4mM Glutamax (EVLP models) for 4H. RNA samples were collected for CIT, IR, and two EVLP conditions, and sequencing data were analyzed for differentially expressed genes and pathways. HPMEC and BEAS-2B cells showed significant changes in gene expressions for IR and EVLP models. In pathway analyses, IR models of both cell types had up-regulated pro-inflammatory responses and down-regulated cell metabolism, and there was up-regulation of epithelial process and/or vascular activation. Steen alone EVLP models exhibited down-regulation of cell metabolism, with an absence of inflammatory and vascular or epithelial signals, while Steen with Glutamax exhibited similar down-regulation of cell metabolism as well as down-regulated inflammatory and vascular process. The commonly used EVLP perfusate, acellular Steen solution, can silence the activation of pro-inflammatory signaling in HPMEC and BEAS-2B cell culture models. This finding may yield insights into how acellular EVLP has been successful in safe preservation of the donor lungs during organ evaluation and repair prior to lung transplantation.

overall_design: Human pulmonary microvascular endothelial cells (HPMEC) and human lung epithelial cells (BEAS-2B) RNA samples are analyzed. There were 4 groups for each cell line: cold ischemic time 18h, reperfusion 4h, Steen 4h, and Steen with Glutamax 4h. With 4 samples per group, the total number of samples analyzed was 32.

first: Lei

first: Zhiyuan

last: Zhu

first: Aaron

last: Wong

first: Shaf

last: Keshavjee

first: Mingyao


title: Single -cell transcriptomic profiling of stem cell derived retinal pigment epithelial cell monolayers after subretinal transplantation

status: Public on May 22 2023

city: Singapore

first: Paul

last: Blakeley

address: 61 Biopolis Dr, Proteos, Singapore 138673

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

summary: Transplantation of stem cell derived retinal pigment epithelial (RPE) cells can potentially restore vision in patients with age-related macular degeneration (AMD). Several landmark Phase I/II clinical trials have demonstrated safety and tolerability of RPE transplants in AMD patients, albeit with limited efficacy. Currently, there is limited understanding of how the recipient retina regulates the survival, maturation and fate specification of transplanted RPE cells. To address this, we transplanted stem cell derived RPE into the subretinal space of immunocompetent rabbits for one month and conducted single-cell RNA sequencing analyses on the explanted RPE monolayers, compared to their age-matched in vitro counterparts. We observed an unequivocal retention of RPE identity, and a trajectory inferred survival of all in vitro RPE populations after transplantation. Furthermore, there was a unidirectional maturation trajectory towards the native adult human RPE state in all transplanted RPE cells, regardless of stem cell resource. Using adult human RPE cells as a reference, we reconstructed the gene regulatory networks in our transplanted stem cell derived RPE, and identified tripartite transcription factors (MAFF, JUND and FOS), known to modulate a broad array of RPE functions in vivo. This includes regulation of canonical RPE signature genes known to support host photoreceptors, and pro-survival genes required for adaptation to the host subretinal microenvironment. These findings shed insights into the transcriptional landscape of RPE cells after subretinal transplantation, with important implications for cell-based therapy for AMD.

overall_design: Two pluripotent stem cell sources, ESC and skin-derived iPSCs, were differentiated to RPE generated ESC-RPE and iPSC-RPE. They were further matured in vitro to day 60. Condition 1: At day 60, n=3 ESC-RPE and n=3 iPSC-RPE monolayers were were transplanted into the subretinal region of immunocompetent rabbits and follow-up for 30 days to day 90. Condition 2: At day 60, n=1 ESC-RPE and n=1 iPSC-RPE were further matured in vitro to day 90 and served as age-matched controls for transplanted RPE. Upon reaching day 90, both conditions were harvest and dissociated to single cells for single-cell RNA sequencing experiments.

first: Bhav

middle: H

last: Parikh

first: Tim

last: Hu

first: Xinyi

last: Su


title: Whole transcriptome profiling of glioma tissue with PDX model

status: Public on May 20 2023

city: ChangSha

first: Yongwei

state: Hunan

address: No.87,  Xiangya Street

institute: CSU Xiangya hospital

summary: A mouse model of patient-derived glioma tissue was used to explore the relationship between transcriptome alterations and tissue stiffness.

overall_design: Female NOD scid gamma /J#5557 immunodeficient mice were used for xenograft experiment.The mice were housed on aseptic condition at The Centre for Phenogenomics (TCP) in Toronto. 4 mice were subjected to intracranial orthotopic implantation of human GBM stem cell line (G411). Each mouse was injected with 10000 G411 cells. After 11 day, tumor was dissociated and we performed tissue stiffness measurement by micropipette aspiration right away.

first: Xi

last: Huang

first: Xuejun

last: Li

first: Siyi

last: Wanggou

first: Hongyu

last: Zhao


title: Transcriptome of ΔPfPRMT5 parasite

status: Public on May 19 2023

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida


title: Genetic perturbation of AMP biosynthesis extends lifespan and restores metabolic health in a naturally short-lived vertebrate

status: Public on May 23 2023

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: During aging, the loss of metabolic homeostasis drives a myriad of pathologies. A central regulator of cellular energy, the AMP-activated protein kinase (AMPK), orchestrates organismal metabolism. However, direct genetic manipulations of the AMPK complex in mice have, so far, produced detrimental phenotypes. Here, as an alternative approach, we alter energy homeostasis by manipulating the upstream nucleotide pool. Using the turquoise killifish, we mutate APRT, a key enzyme in AMP biosynthesis, and extend the lifespan of heterozygous males. Next, applying an integrated omics approach identify that metabolic functions are rejuvenated in old mutants, which also display a fasting-like metabolic profile and resistance to high-fat diet. On the cellular level, heterozygous cells exhibit enhanced nutrient sensitivity, reduced ATP levels, and AMPK ¬activation. Finally, lifelong intermittent fasting abolishes the longevity benefits. Our findings suggest that perturbing AMP biosynthesis may modulate vertebrate lifespan, and propose APRT as a promising target for promoting metabolic health.

overall_design: Samples of livers and muscle of the Nothobranchius furzeri at different experimental conditions, including Age: 6.5 weeks-old (young) and 15 weeks-old (old); Genotype: wild-type (WT) and APRT heterozygous (Het); Feeding condition: fully fed (full) and starved 24h (fasted); and Sex: males (M) and females (F). The muscles and livers were extracted from the same fish.

first: Gwendoline

last: Astre

first: Tehila

last: Atlan

first: Uri

last: Goshtchevsky

first: Adi

last: Oron-Gottesman

first: Margarita

last: Smirnov

first: Kobi

last: Shapira

first: Ariel

last: Velan

first: Joris

last: Deelen

first: Tomer

last: Levy

first: Erez

middle: Y

last: Levanon


title: Alterations in microbiome composition and metabolic byproducts drive behavioral and transcriptional responses to morphine

status: Public on May 18 2023

city: Winston-Salem

first: Drew

last: Kiraly

address: 115 South Chestnut Street

department: Physiology, Pharmacology, Psychiatry

institute: Wake Forest University School of Medicine

summary: Recent evidence has demonstrated that the gut microbiome has marked effects on neuronal function and behavior. Disturbances to microbial populations within the gut have been linked to myriad models of neuropsychiatric disorders. However, the role of the microbiome in substance use disorders remains understudied. Here we show that male mice with their gut microbiome depleted by nonabsorbable antibiotics (Abx) exhibit decreased formation of morphine conditioned place preference across a range of doses (2.5-15 mg/kg), have decreased locomotor sensitization to morphine, and demonstrate marked changes in gene expression within the nucleus accumbens (NAc) in response to high-dose morphine (20 mg/kg × 7 days). Replacement of short-chain fatty acid (SCFA) metabolites, which are reduced by microbiome knockdown, reversed the behavioral and transcriptional effects of microbiome depletion. This identifies SCFA as the crucial mediators of microbiome-brain communication responsible for the effects on morphine reward caused by microbiome knockdown. These studies add important new behavioral, molecular, and mechanistic insight to the role of gut-brain signaling in substance use disorders

overall_design: RNA-seq profiling of Nac from male mice with their gut microbiome depleted by nonabsorbable antibiotics (Abx) and treated with morphine.

first: Rebecca

last: Hofford

first: Nicholas

middle: L

last: Mervosh

first: Tanner

last: Euston

first: Katherine

middle: R

last: Meckel

first: Amon

middle: T

last: Orr


title: Zymoseptoria tritici suppresses the host immune response and facilitates the success of avirulent strains in mixed infections

status: Public on May 15 2023

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

summary: Wheat (Chisenese Spring) transcriptome analyses during single and mixed infections by an avirulent and a virulent strains of Z. tritici.

overall_design: We performed a comparative transcriptomic approach to of wheatresponses to i) a virulent strain ST99CH_3D7, ii) an avirulent strain ST99CH_1E4, iii) and 1:1 ratio mix of the two strains infection at early stages of 3 and 6 days post-inoculation, and iv) mock inoculation with water that we used as negative control. All treatments were done in triplicates.

first: Alessio

last: Bernasconi

first: Andrea

last: Sánchez-Vallet


title: c-Myc supports polyploidy and prevents senescence in the murine placenta [scRNA-Seq]

status: Public on May 12 2023

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

summary: Placenta is essential for reproductive success and placental abnormalities are the leading cause of low birth weight and preterm birth. The placenta includes polyploid cells that are crucial for its function. Polyploidy occurs broadly in nature but the regulators that enable polyploidy to arise in a spatiotemporally regulated manner in the placenta are unknown. We used scRNA seq to understand molecular regulators of polyploidy.

overall_design: 14.5 dpc placenta was isolated in D-PBS (Thermo Fisher Scientific (#14287072) and adult brain dissociation kit (#130-107-677) was used to make single cell suspension as per manufacturer instructions. Each 14.5 dpc placenta was cut into four small pieces using scalpel blades. Placental pieces were transferred in gentleMACS™ C tube (Miltenyi Biotec- #130-093-237) and 1950 l of Enzyme mix 1 (Buffer Z 1900 l + Enzyme P 50 l) was added. Further 30 l of Enzyme mix 2 (Buffer Y 20 l + Enzyme A 10 l) to the same tube was added. 37C_ABDK_01 program of gentleMACS was used and once program is completed, cells were centrifuged at 300Xg for 5 minutes. Pellet was resuspended in cold 10 ml D-PBS and filtered it through 70 m MACS SmartStrainer (Miltenyi Biotec- #130-098-462) using 50 mL falcon tube. C tube was washed again with 10 ml cold D-PBS and filter with the same SmartStrainer. MACS SmartStrainer was discarded and cell suspension was centrifuged at 300Xg for 10 minutes at 4°C. Supernatant was removed and pellet was resuspended in cold 1550 l D-PBS and transferred it to 15 mL falcon tube. 450 l of debris removal solution was added and mixed well. Gently 2 mL of cold D-PBS was overlayed, and tube was centrifuged at 4°C and 3000Xg for 10 minutes. Three phases were formed after centrifugation. Top two layers were discarded, and tube was filled with 10 mL cold D-PBS. Tube was gently mixed and centrifuged at 4°C and 1000Xg for 10 minutes. Pellet was resuspended in 0.5 mL of 1X red blood cell removal solution and incubated for 10 minutes at 4°C. 5 mL of cold -DPBS was added and centrifuged at 4°C and 300Xg for 10 minutes. Pellet was resuspended in 0.5 ml of cold PBS and acridine orange (AO)/ propidium iodide (PI) method was used to cell viability. Samples with viability above 87% were used for further sequencing. Chromium Next GEM Single Cell 3' Reagent Kits v3.1 was used for making cDNA library using 10X Genomic reagents (Next GEM Chip G Single Cell Kit #1000120, Next GEM Single Cell 3' Gel Bead Kit v3.1 #1000122,  Single Cell 3' Gel Beads v3.1#2000164, Next GEM Single Cell 3' GEM Kit v3.1 #1000123, Next GEM Single Cell 3' Library Kit v3.1 #1000157, i7 Multiplex Kit #120262, DynaBead - MyOne Silane Beads #2000048 and SPRIselect Beads #17201600).  Sequencing was performed using Illumina Nova-Seq-SP.

first: Vijay

last: Singh

first: Jennifer

last: Gerton