title: Gene expression analysis in canine epitheliotropic lymphoma - validation cohort

overall_design:
Gene expression was analyzed using the Canine IO NanoString probeset to analyze 6 canine EL biopsies compared to 8 interface dermatitis (ID) biopsies.
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Authors state, There are no processed data files, as I am providing raw count data and RCC files.

first: Cheryl

last: London

first: Kelly

middle: L

last: Hughes


title: Gene expression analysis in canine epitheliotropic lymphoma

status: Public on Oct 25 2023

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

country: USA

institute: Tufts Cummings School of Veterinary Medicine

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

overall_design: Refer to individual Series


title: Hypoxia-induced circPLOD2a/b promote migration and invasion of GBM cells via suppressing XIRP1 through binding to HuR

status: Public on Oct 23 2023

city: Wuhan

first: Yiqi

last: Wang

state: State...

address: Shizishan Street

country: China

institute: Huazhong Agricultural University, China

type: Expression profiling by high throughput sequencing


title: Hypoxia-induced circPLOD2a/b promote migration and invasion of GBM cells via suppressing XIRP1 through binding to HuR [1]

summary: Background. Glioblastoma (GBM) is the most lethal form of brain tumors in human adults, and hypoxia is a common microenvironment in this disease. Circular RNAs (circRNAs) are identified as regulators in cancers including GBM. However, the specific roles of circRNAs in GBM under hypoxic condition remains elusive. Methods. RNA-seq was employed to investigate the expression profile of circRNAs in U87 cells under normoxia and hypoxia. Two circRNAs spliced from the same parental gene, named as circPLOD2a and circPLOD2b, were identified as hypoxia-responsive circRNAs, whose circular structures were verified by, qRT-PCR, RNase R digesting and Sanger sequencing in U87. Knockdown and overexpression of circPLOD2a/b in GBM cells were used to investigate the biological functions of these two circRNAs on tumor progression. Fluorescence in situ hybridization, RNA-pull down, mass spectrometry and RNA immunoprecipitation assays were conducted to explore the interactions between circPLOD2a/b, human antigen R (HuR), xin actin binding repeat containing 1 (XIRP1). Results. CircPLOD2a/b were significantly up-regulated in hypoxic GBM cells and directly induced by HIF1α under hypoxia. Overexpression of circPLOD2a/b enhance GBM cell invasion and migration, which could be inhibited by circPOD2a/b knockdown. Mechanistically, circPLOD2a/b competitively bind to HuR, inhibiting the interaction between HuR and XIRP1, thus promoting the tumor aggressiveness in GBM both in vitro and in vivo through down-regulating XIRP1.  Conclusions. Hypoxia-induced circPLOD2a/b were identified as key regulators of migration and invasion in GBM cells, and act as oncogenic circRNAs to attenuate the interaction between HuR and XIRP1, which may be potential therapeutic strategy for GBM treatment.

overall_design: U87 cells knockingdown of circPLOD2a and circPLD2b were planted in 6-cm dish respectively,and treated in normoxia  (21% O2, 74% N2 and 5% CO2) condition. 48 hours later, the DMEM medium was removed, and 1mL PBS buffer was added into each dish to wash medium residue. Remove all the PBS buffer from the dishes and add 1mL Trizol buffer. Solution from each dish was collected into 1.5mL EP tube, and stored in liguid nitrogon for further analysis.


title: Dissecting telomerase RNA structural heterogeneity in living human cells with DMS-MaPseq

status: Public on Oct 20 2023

city: Santa Cruz

first: Michael

last: Stone

state: CA

address: 1156 High Street

institute: University of California Santa Cruz

summary: Telomerase is a specialized reverse transcriptase that uses an intrinsic RNA subunit as the template for telomeric DNA synthesis. Biogenesis of human telomerase requires its RNA subunit (hTR) to fold into a multi-domain architecture that includes the template-containing pseudoknot (t/PK) and the three-way junction (CR4/5). These two hTR domains bind the telomerase reverse transcriptase (hTERT) protein and are thus essential for telomerase catalytic activity. Here, we probe the structure of hTR in living cells using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and ensemble deconvolution analysis. Unexpectedly, approximately 15% of the steady state population of hTR has a CR4/5 conformation lacking features required for hTERT binding. Mutagenesis demonstrates that stabilization of the alternative CR4/5 conformation is detrimental to telomerase assembly and activity. We propose that this misfolded portion of the cellular hTR pool is either slowly refolded or degraded. Thus, kinetic traps for RNA folding that have been so well-studied in vitro may also present barriers for assembly of ribonucleoprotein complexes in vivo.

overall_design: HeLa cells were treated with dimethyl sulfate (DMS) and total RNA harvested. Amplicon libraries of endogenous human telomerase RNA (hTR) or transfected overexpressed mutant hTR constructs were prepared by reverse transcription with TGIRT-III and sequences on an Illumina iSeq100 system. Reads were size selected and trimmed with TrimGalore, then mapped to the hTR reference sequence with Bowtie2. Mutations were quantified with DREEM, and normalized mutation frequencies were used as psuedoenergy constraints in RNAstructure. The predicted hTR secondary structures were visualized with VARNA.

first: Nicholas

last: Forino

first: Jia

middle: Z

last: Woo

first: Arthur

middle: J

last: Zaug

first: Arcelia

middle: G

last: Jimenez

first: Thomas

middle: R

last: Cech

first: Silvi

last: Rouskin

middle: D


title: Lung mesenchymal cells from wild-type mouse lungs

status: Public on Oct 03 2023

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

country: Japan

institute: Hamamatsu University School of Medicine

summary: Lung fibroblasts include several subpopulations. We used single cell RNA sequencing (scRNAseq) to analyze the heterogeneity of lung fibroblasts.

overall_design: Lung fibroblasts of three wild-type mice (12wks, male) were isolated by FACS using negative selection of lineage markers (CD45, CD31, E-cadherin, CD146, LYVE-1, TER119).

first: Atsuki

last: Fukada

first: Toshihide

last: Iwashita


title: Hypoxia-induced circPLOD2a/b promote migration and invasion of GBM cells via suppressing XIRP1 through binding to HuR [2]

overall_design: Human GBM cell U87-wt were planted in six 6-cm dish. Three dishes of cells were cultured in hypoxia (1% O2, 94% N2 and 5% CO2) and another three dishes treated in normoxia  (21% O2, 74% N2 and 5% CO2) respectively. 24 hours later, the DMEM medium was removed, and 1mL PBS buffer was added into each dish to wash medium residue. Remove all the PBS buffer from the dishes and add 1mL Trizol buffer. Solution from each dish was collected into 1.5mL EP tube, and stored in liguid nitrogon for further analysis.


title: Bone marrow derived macrophages RNA-Seq (WT vs SIRPa KO)

status: Public on Oct 02 2023

city: Montreal

first: André

last: Veillette

state: QC

address: 110 Des Pins Ouest Rm1065

department: Molecular Oncology

country: Canada

institute: IRCM

summary: RNA transcriptome difference between WT and SIRPa knockout (KO) bone marrow derived macrophages (BMDMs). To understand how SIRPa inhibits the phagocytotic capacity of macrophages, a mouse lacking SIRPa was generated, and the transcriptional profiles of BMDMs from wild-type and SIRPa KO mice were compared, using RNA sequencing.

overall_design: BMDMs from WT and SIRPa KO mice were generated by growing freshly isolated bone marrow cells for 7 days in medium supplemented with 30% (vol/vol) L929 cell-conditioned medium. Total RNA was isolated from WT and SIRPa KO macrophage using the RNeasy Plus Mini Kit (Cat# 74134, Qiagen). RNA-Seq library preparation was performed using the Illumina TruSeq Stranded mRNA Kit, according to manufacturer’s instructions, and sequenced with Illumina HiSeq 2000 Sequencer. Read quality was confirmed using FastQC v0.10.1 before alignment using TopHat v2.0.10 on the mouse GRCm38/mm10 genome.

first: Z

last: Tang

first: A


title: Multimodal probing of T cell sensitivity with hexapod heterostructures

status: Public on Oct 07 2023

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

summary: Studies employing antigen-presenting systems at the ensemble or single cell level can provide complementary insights into T-cell activation and signaling. However, synthetic material toolkits that probe T cells at both levels are lacking, although they would be essential in advancing basic immunology and immunotherapy. Here, we develop a biomimetic antigen-presenting system (bAPS) using hexapod heterostructures (i.e., a sub-micrometer hematite core, and nanostructured silica branches with diverse surface modifications) for single-cell, single-molecule stimulation and ensemble modulation of T-cell signaling. We report with single molecule resolution of: T-cell sensing/activation by a single agonist peptide-major histocompatibility complex; distinct T-cell receptor (TCR) responses to discriminate structurally similar peptides that differ by just one amino acid; and the superior sensitivity of TCR antigen recognition compared to chimeric antigen receptors (CARs). We also show that magnetic field-induced piconewton×micrometer-level torques on the hexapods amplify immune responses in suspension T and CAR-T cells. Furthermore, by using our bAPS, we have developed a reliable and high-throughput new method for identifying neoantigen-specific TCRs at the single-cell level. The multimodal hexapod bAPS presents an unexplored, nanotechnology-based biointerface tool for investigating recognition, signaling, and the biochemical/mechanical dual sensitivity of T cells and beyond.

overall_design: Examination of paired single-cell RNA-seq and single-cell TCR-seq in CD4 and CD8 T cells obtained from in vitro hexapod-stimulatation of mixed 1% target and 99% wildtype cells and sorting for TNF-alhpa or IL2 positive populations

first: Bozhi

last: Tian

first: Guoshuai

last: Cao

first: Xiaodan


title: Whole Blood miRNA Seq of Children with Asthma in Costa Rica

status: Public on Oct 01 2023

city: Boston

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Mass General Brigham

type: Non-coding RNA profiling by high throughput sequencing

summary: Rationale: MicroRNAs have emerged as crucial post-transcriptional and network regulators in inflammatory diseases, including asthma. We hypothesized that peripheral blood miRNA would be associated with airflow obstruction in children with asthma, and that some of these effects would also be observable in adults with COPD. Methods: We analyzed small RNA-Seq data from 365 peripheral blood samples from the Genetics of Asthma in Costa Rica Study (GACRS). GACRS comprised children from the Central Valley of Costa Rica age 6-14 years with physician-diagnosed asthma and ≥2 respiratory symptoms or asthma attacks in the prior year. FEV1/FVC percent-predicted was dichotomized at 100%, splitting the cohort into those with and without evidence of airflow obstruction and used as our primary outcome. Differentially expressed (DE) miRs were identified using the DESeq2 package in R with a 10% FDR and adjustment for age, gender, and inhaled corticosteroid (ICS) use. We attempted to replicate the top airflow obstruction-associated microRNAs from the GACRS study in the COPDGene study, in which blood microRNA data were available in 439 current and former smoking adults with and without airflow obstruction (defined as raw FEV1/FVC < 0.7).  Results: After QC, we had 361 samples and 649 miRs for DE analysis. Of the 361 samples, 220 and 141 were from subjects without and with airflow obstruction, respectively. We found 1 upregulated (let-7e-5p p=0.0004) and 2 downregulated (miR-342-3p p=0.0002; miR-671-5p p=0.0001) miRs in subjects with airflow obstruction compared to those without airflow obstruction. These three miRNAs were then tested for association with airflow obstruction in the COPDGene study, in which let-7e-5p was upregulated (p = 0.064) and miR-342-3p (p =0.085) was downregulated in participants with FEV1/FVC < 0.7 (n=196) compared to those with FEV1/FVC > 0.7 (n=243). Differentially expressed miR’s target genes were enriched for PI3K-Akt, Hippo, WNT, MAPK, and focal adhesion signaling pathways. We also separately considered the targets of only the two miRNAs that were also associated with FEV1/FVC in the adult current and former smokers, where PI3K-Akt, MAPK and Hippo signaling pathways were among the top five most enriched pathways. Conclusion: Three DE miRs were linked to airflow obstruction in children with asthma. Two miRs were associated with FEV1/FVC in current and former smoking adults. These miRs were involved in asthma and COPD-related pathways: PI3K-Akt, Hippo, MAPK, and focal adhesion signaling pathways. Together these findings provide important evidence that these two disorders may share genetic regulatory systems that contribute to airflow obstruction.

first: Anshul

last: Tiwari

first: Michael

last: McGeachie


title: Interleukin 11 therapy causes acute heart failure and its use in patients should be reconsidered

status: Public on Sep 30 2023

city: London

first: Mark

last: Sweeney

address: Du Cane Road

department: London Institute of Medical Science

country: United Kingdom

institute: Imperial College London

summary: Background: Interleukin-11 (IL11) was initially identified as a fibroblast secreted factor that supports haematopoietic cell function. This led to its development as a drug to increase platelet counts in patients with thrombocytopenia. However, IL11 was later found redundant for hematopoiesis and its use in humans causes severe and unexplained cardiac side effects. Here we identify and dissect mechanisms underlying previously unappreciated cardiac toxicities associated with IL11 therapy. Methods: We injected recombinant mouse lL11 (rmIl11) at clinically relevant doses to study its effects on myocardial signalling using immunoblotting and genomic variation using qRT-PCR, RNA-seq and ATAC-seq. The physiological impact of Il11 was assessed by echocardiography in vivo and cardiomyocyte contractility assays in vitro. To determine the specific activity of IL11 in cardiomyocytes we generated two distinct cardiomyocyte-specific IL11 receptor knockout (CMKO) mouse models using either AAV9-mediated, Tnnt2-restricted (vCMKO) or mhy6 (m6CMKO) Cre expression in an Il11ra1 floxed mouse strain. In pharmacologic studies, we studied the effects of JAK/STAT inhibition following rmIl11 injection to mice.Results: Injection of rmIl11 to mice caused dose-dependent impairment of left ventricular ejection fraction (LVEF: saline, 64.2%±1.62; rmIl11 (50 mg/kg), 31.6±2.0; p<0.0001). RNA-seq of hearts one and three hours following rmIl11 injection revealed strong upregulation of the TNF, NFkB and JAK/STAT pathways as well as increased Nppa and Rrad levels. vCMKO mice were protected from rmIl11-induced STAT3 activation, Rrad upregulation and LV impairment. Similarly, m6CMKO mice of both sexes, were protected from the molecular, cellular and whole organ cardiac toxicities associated with Il11. Administration of JAK inhibitors prevented rmIl11-induced STAT3 activation and preserved cardiac function. Conclusions: Here we show that Il11 injection to mice is strongly proinflammatory in the heart. Furthermore, Il11 has profound negative inotropic effects that are mediated via its on-target activation of JAK/STAT3 signalling  in cardiomyocytes. Our data explain the cardiac side effects associated with IL11 therapy and question its continued use in patients.

overall_design: RNA-seq analysis of the hearts of male C57BL6/J mice injected with recombinant mouse IL11 at basline, 1 ,3 and 6 hours after injection.

first: Stuart

last: Cook

last: Lee


title: Matrix electrical stimulation regulates CD8+ T cell fate

city: Beijing

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: We next applied scRNA-seq to examine the status of CD8+ T lymphocytes cultured on ferroelectric nanocomposite membrane.

overall_design: Study of CD8+ T lymphocytes with or without matrix electrical stimulation using 10x scRNA-seq technologies.

first: Xuliang

last: Deng

first: Xin

last: Zhang


title: Unveiling the Impact of Arsenic Toxicity on Immune Cells in Atherosclerotic Plaques: Insights from Single-Cell Multi-Omics Profiling

city: Jinan

first: Yang

last: Xiuhui

state: Shandong

address: NO.1500,ShunHua Road

department: School of Software

institute: Shandong University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Arsenic exposure is a global health problem and is correlated with adverse atherosclerotic outcomes in humans and in mouse models. However, the mechanisms of action are unclear. Since an atherosclerotic plaque is an amalgam of diverse immune and non-immune cells working in consortium, we set out to understand the mechanisms of arsenic-enhanced atherosclerosis in the CD45+ immune cells of atherosclerotic plaques in apoE-/- mouse model. To do this, we employ single-cell RNA- and single-cell-ATAC sequencings to understand both the genomic and epigenomic landscapes of these plaques.

overall_design: 5-week-old apoe-/- male mice were started on a high-fat diet and either left as control or given 200 ppb arsenic (which is a concentration known to exacerbate atherosclerosis in these mice) for 13 weeks. At the end of the timepoint, mice were injected intravenously with anti-CD45 antibody to stain circulating leucocytes. Within 10/15 minutes of this injection, mice were asphyxiated, blood was drawn through cardiac puncture, followed by a cardiac perfusion with ice-cold PBS. At this point, most of the blood should be removed from the heart and aorta and what remains should be stained with the CD45 antibody. Next, the plaques from the aortic arch and the aortic sinus were harvested, minced and then chemically digested with an enzyme cocktail at 37 degrees for 1 hour. Then the sample was stained with CD45 antibody conjugated with a fluorophore different from the one used for IV injection and a L/D stain. Lastly, the live CD45 plaque-resident cells were sorted to eliminate circulating leucocytes and were sent for single-cell sequencing.

first: Makhani

last: Kiran

first: Ding

last: Jun

first: Mann

last: Koren


title: Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome

status: Public on Sep 12 2023

city: Boulder

first: Meaghan

last: Courvan

state: CO

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

summary: Individuals with Down syndrome have a increased likelihood of suffering from inflammatory and autoimmune conditions, due to the presence of four interferon receptors on chromosome 21. Transcription of genes plays a key role in the interferon response, and the Mediator kinases, CDK8 and CDK19, are essential in potentiating this transcription. Given the role CDK8/19 play in the interferon response, and the fact that selective inhibitors of these kinases exist (such as Cortistatin A), it is possible that targetting Mediator kinase activity may alleviate symptoms of chronic inflammation in Down syndrome.

overall_design: Examination of effects of Mediator kinase inhibition (through treatment with selective inhibitor Cortistatin A) and interferon gamma stimulation on transcription (through RNA-seq) in cell lines from a pair of siblings, one with Down syndrome and one without

first: Kira

middle: A

last: Cozzolino

first: Benjamin

last: Erickson

first: David

last: Bentley


title: Il-6 signaling exacerbates hallmarks of tendon lesions by stimulating progenitor proliferation & migration to damage.

status: Public on Sep 13 2023

city: Zurich

first: Tino

last: Stauber

address: Lengghalde 5

country: Switzerland

institute: ETH Zurich

summary: We leveraged an explant-based, tissue engineered model of tendon damage to study cross-compartmental interactions between the tendon core and extrinsic progenitors, as well as between the tendon core and extrinsic macrophages. We suspected IL-6 signaling to play a major role in this crosstalk, so we also incorporated core explants from IL-6 knock-out mice.

overall_design: 1) Comparative gene expression profiling analysis of RNA-seq data for wildtype core explants or IL-6 knock-out core explants surrounded by a cell-free hydrogel, one filled with extrinsic progenitors, or one filled with macrophages. 2) Comparative gene expression profiling analysis of RNA-seq data for extrinsic progenitors surrounding a wildtype or a knock-out core.

first: Greta

last: Moschini

first: Amro

last: Hussien

first: Patrick

middle: K

last: Jaeger

first: Katrien

last: De Bock

first: Jess

last: Snedeker


title: Single cell RNA-seq of mouse leptomeninges cells

status: Public on Sep 28 2023

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

summary: We performed single-cell RNA sequencing (scRNA-seq) for isolated leptomeninges cells

overall_design: Mouse leptomeninges was manually carefully peeled off from cerebral hemispheres of 3 months old Pdgfra-H2BGFP males and females, digested into single-cell suspensions and subjected to droplet-based ScRNAseq

first: Johanna

last: Andrae

first: Christer

last: Betsholtz


title: Endocan-PDGFRα mediated signaling drives glioblastoma spatial heterogeneity and influences tumor vasculature/radioresistance [RNA-seq]

status: Public on Sep 01 2023

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: The goal of this project was to study the difference in GBM tumors formed in ESM1 Knockout vs. WT mice.

overall_design: ESM1 Knockout and WT mice were injected intracranially with mG7080 (Murine GBM tumor cell line). Mice were monitored for tumor formation. Once these mice formed tumor, n=3 per group were sacrificed and tumor was resected and immediately processed for RNA-extraction.

first: Soniya

last: Bastola

first: Yasmin

last: Ghochani

first: Sree

last: Muthukrishnan

first: Marat

middle: S

last: Pavlyukov

first: Yue

last: Qin

first: Harley

middle: I

last: Kornblum

first: Ichiro

last: Nakano


title: Endocan-PDGFRα mediated signaling drives glioblastoma spatial heterogeneity and influences tumor vasculature/radioresistance


title: Endocan-PDGFRα mediated signaling drives glioblastoma spatial heterogeneity and influences tumor vasculature/radioresistance [ATAC-seq]

overall_design: ESM1 Knockout and WT mice were injected intracranially with mG7080 (Murine GBM tumor cell line). Mice were monitored for tumor formation. Once these mice formed tumor, n=2 per group were sacrificed and tumor was resected and immediately processed for ATAC-seq.


title: Sleeping Beauty transposon mutagenesis identified genes involved in colorectal cancer development in the inflammatory microenvironment

status: Public on Aug 31 2023

city: Chuo-ku

first: Haruna

last: Takeda

state: Tokyo

address: 5-1-1 Tsukiji,

institute: National Cancer Center Japan


title: Sleeping Beauty transposon mutagenesis identified genes involved in colorectal cancer development in the inflammatory microenvironment [DSS]

summary: To identify genes and molecular pathways involved in colorectal cancer (CRC) that developed in an inflammatory microenvironment, we performed Sleeping Beauty (SB) transposon mutagenesis screening in Dextran Sodium Sulfate treated-mice. We have shown that cell cycle-related genes and TGFb pathway-related genes are frequently mutated in inflammation-related tumors. We have demonstrated that TNFa can promote dedifferentiation of colonic epithelial cells via epigenomic reprogramming, and activate both Cdkn2a-p53 signaling and CycD-Cdk4/6, creating advantageous conditions for selecting cells carrying mutations in the Cdkn2a-p53 pathway genes.  We have also showed that Cdk4/6 inhibitors are effective against colorectal tumors in an inflammatory microenvironment using the SB mouse model, presenting a potential new therapeutic strategy. Thus, SB screening is not only powerful in identifying genes involved in cancers that develop in specific microenvironments, but also helpful in validating the efficacy of drugs.

overall_design: Mouse colonic organoids were established from 3 wt mice and 3 DSS-treated wt mice (Day 14 after DSS treatment), and RNA was collected at Day 4 from establishement to perform RNA-seq.

first: Kana

last: Shimomura

first: Daichi

last: Narushima

first: Mamoru

last: Kato


title: Sleeping Beauty transposon mutagenesis identified genes involved in colorectal cancer development in the inflammatory microenvironment [wtvsTNF_KrasvsTNF]

overall_design: wt colonic organoids and KrasG12D colonic organoids were treated with TNFa (40 ng/ml) for 3 wks.


title: Identification of YTHDC2 knockout regulated mRNA

status: Public on Aug 29 2023

city: 上海

first: 建港

last: 郭

address: 浦江智谷25号楼

institute: 欧易生物

summary: In order to identify YTHDC2 downstream genes, we performed RNA-seq in WT and YTHDC2 knockout H1975 cells and analyzed the changed mRNAs.

overall_design: The WT group had three repetitions, and the YTHDC2 knockout group had three repetitions

first: Xiao

last: Zhang

first: Zhixin

last: Yin


title: Photoperiodic transcriptional responses in Ostreococcus tauri

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

country: Spain

institute: University of Sevilla

summary: Although it is well established the seasonal effect of the photoperiod over the transcriptional expression patterns in plants, this effect has not been studied in microalgae. Here we fill the gap using the model microalgae Ostreococcus tauri.

overall_design: Ostreococcus tauri sequenced strain RCC4221 was cultivated in 1.8L column photochemostats operating in continous mode at 20ºC and pH 8 with air bubbling to enable culture homogenization. Media was added at a dilution rate of 0.4 day-1. After four weeks entrainment under long day conditions (16h light : 8 hours dark) or short day conditions (8h light: 16 hours dark) samples were collected every four hours during three days. Subsequently, samples were collected for two days every four hours under free running conditions consisting in continous light. The growth media was prepared using Artificial Sea Water (24.55g NaCl, 0.75g KCl, 4.07g MgCl2·6H2O, 1.47g CaCl2 ·2H2O, 6.04g MgSO4·7H2O and 0.21g NaHCO3 per 1L distilled water) supplemented with 1 mL of Solution I (100g NaNO3 in 250mL distilled water), 1mL of Solution II (700mg  Na2HPO4 and 2.5g K2HPO4 in 250mL distilled water) and 1mL of Solution III with trace metals (2.68g NH4Cl, 5.2g Fe-EDTA, 37.2g Na2 -EDTA, 23mg ZnSO4, 14mg CoSO4 , 7.89mg Na2 MoO4 ·2H2O, 2.5mg CuSO4 , 1.7mg H2SeO3 and 180mg MnCl2·4H2O in 500mL distilled water).

first: Mercedes

last: García-González

first: Ana

last: Belen Romero-Losada

first: Christina

last: Arvanitidou


title: Developmental pyrethroid exposure disrupts molecular pathways for MAP kinase and circadian rhythms in mouse brain

status: Public on Aug 28 2023

city: Toledo

first: Jennifer

last: Nguyen

state: OH

address: 3000 Arlington Ave

department: Neuroscience

institute: University of Toledo

summary: Neurodevelopmental disorders (NDDs) are a category of pervasive disorders of the developing nervous system with few or no recognized biomarkers. A significant portion of the risk for NDDs, including attention deficit hyperactivity disorder (ADHD), is contributed by the environment, and exposure to pyrethroid pesticides during pregnancy has been identified as a potential risk factor for NDD in the unborn child. We recently showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice causes male-biased changes to ADHD- and NDD-relevant behaviors as well as the striatal dopamine system. Here, we used an integrated multiomics approach to determine the broadest possible set of biological changes in the mouse brain caused by developmental pyrethroid exposure (DPE). Using a litter-based, split-sample design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood, euthanized them, and pulverized and divided whole brain samples for split-sample transcriptomics, kinomics and multiomics integration. Transcriptome analysis revealed alterations to multiple canonical clock genes, and kinome analysis revealed changes in the activity of multiple kinases involved in synaptic plasticity, including the mitogen-activated protein (MAP) kinase ERK. Multiomics integration revealed a dysregulated protein-protein interaction network containing primary clusters for MAP kinase cascades, regulation of apoptosis, and synaptic function. These results demonstrate that DPE causes a multi-modal biophenotype in the brain relevant to ADHD and identifies new potential mechanisms of action.

overall_design: Here, we used split-sample transcriptomics and kinomics to explore, in a hypothesis-free way, the effects of developmental deltamethrin exposure on mouse brain as previously described at the level of gene transcription and protein activity.

middle: H

first: Melissa

last: Curtis

first: Ali

last: Imami

first: William

last: Ryan

first: Khaled

last: Alganem

first: Kari

last: Neifer

first: N

last: Saferin

first: Charlotte

middle: N

last: Nawor

first: Brian

middle: P

last: Kistler

first: Gary

middle: W

last: Miller

first: Rammohan

last: Shukla

first: Robert

middle: E

last: McCullumsmith

first: James

last: Burkett


title: A Bioengineered Platform for Enhanced Observability of Patterned Gastrointestinal Organoid Monolayers with Bilateral Access

status: Public on Aug 21 2023

city: Lausanne

first: Matthias

last: Lutolf

address: Route Cantonale

institute: EPFL

summary: Studying the physiology and pathology of gastrointestinal (GI) tissues requires tools that can accurately mimic their complex architecture and functionality in vitro. Organoids have emerged as one such promising tool, though their closed structures with poorly accessible lumen and limited observability makes readouts challenging. In this study, we introduce a bioengineered organoid platform that generates bilaterally accessible 3D tissue models, allowing independent manipulation of both the apical and basal sides of patterned epithelial monolayers. We successfully constructed gastric, small intestinal, caecal, and colonic epithelial models that faithfully reproduced tissue-respective geometries and exhibited high physiological relevance, evidenced by the regionalization of stem cells and transcriptional resemblance to real epithelia. The gained observability allowed single-cell tracking over time and studies into the motility of cells in immersion and air-liquid interface cultures. Additionally, this model recapitulated Trichuris muris infection of the caecum epithelium, allowing the first live imaging of syncytial tunnel formation. Overall, this platform offers accessible organoids with improved observability, making it a valuable tool for investigating the dynamics of GI epithelial cells and their interactions with pathogens.

overall_design: RNA-Seq

first: Moritz

last: Hofer

first: Maria

last: Duque-Correa


title: Dual Inhibition of DNA methylation and PARP Increases Anti-tumor Efficacy in SETD2 Deficient Kidney Cancer

first: Xinyi

last: Zhou

address: 1441 Eastlake Ave.

institute: Keck School of Medicine

summary: Purpose: SETD2 deficiency, a driving force of depleted levels of H3K36me3 due to impaired methyltransferase activity, plays an important role in diverse forms of cancer, most notably in aggressive and metastatic clear cell renal cell carcinomas (ccRCC). Developing novel treatment schema targeting SETD2-compromised cancer cells are urgently needed.   Methods: Human kidney cancer cell lines with or without SETD2 deficiency were treated with a DNA Hypomethylating Agent (HMA), a poly(ADP-ribose) polymerase inhibitor (PARPi), and both (HMA + PARPi) in combination in both in vitro and in vivo settings. Cell inhibition, Comet, flow cytometry, western blot, and RNA-sequencing (RNA-seq) gene expression assays as well as bioinformatic analyses were performed to explore the underlying mechanism action.   Results: By taking advantage of involvement of SETD2 in DNA methylation and DNA repair, we found the combination treatment of an HMA (5-Aza-CdR/DAC) and a PARPi (Talazoparib/BMN-673) generated increased cytotoxicity in in vitro SETD2-deficient RCC cell lines than in SETD2-proficient cell lines. Furthermore, our results also demonstrate synergetic anti-tumor effects in SETD2 deficiency RCC cell lines when treated with DAC and BMN-673 that include apoptotic induction, increased DNA damage, insufficient DNA damage repair, upregulation of immune responses by STING and transposable elements (TEs), as well as increased genomic instability. Finally, the combination treatment for SETD2-deficient RCCs was also validated using in vivo mouse models.   Conclusion: SETD2 deficiency creates a vulnerable epigenetic status to generate efficacious anti-tumor effects via the combination treatment of DAC and BMN-673 in human and mouse RCC systems, making it a precise medicine-based approach for SETD2-compromised cancers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 786-0 SETD2 WT/KO cells upon DAC, BMN763 and Combination (DAC+BMN673) treatment

first: Yohei

last: Sekino

first: Guanghou

last: Fu

first: Hong-Tao

last: Li

first: Zhi

last: Yang

first: Shuqing

last: Zhao

first: Hemant

last: Gujar

first: Xiongbing

last: Zu

first: Daniel

last: Weisenberger

first: Inderbir

last: Gill

first: David

last: Quinn

first: Bo

last: Han

first: Gangning

last: Liang


title: Regulation of TROP2 expression in breast cancer

city: Houston

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary: Expression of genes highly correlated with TACSTD2 expression in breast tumors and corresponding patient-derived xenografts (PDXs) and found that 29 genes were overlapping between in 18 breast cancer samples and matching PDXs.  Among these genes, TACSTD2 expression strongly correlated with expression of epithelial marker CDH1 (E-Cadherin) (r2=0.823; p<0.001).  Expression of TACSTD2 was then compared to expression of CDH1 in breast cancer cell lines from The Cancer Cell Line Encyclopedia (CCLE) (N = 51) and The Library of Integrated Network-Based Cellular Signatures (LINCS) (N = 35).  There was also a significant correlation between TACSTD2 and CDH1 in both CCLE (r2=0.564, p < 0.001) and LINCS (r2= 0.755; p < 0.001).

overall_design: Comparision of gene expression between PDX and tumors.

first: Kurt

last: Evans

first: Ming

first: Erkan

last: Yuca


title: Impact of bacterial derived microvesicles on gene expression of Caco2 cells.

status: Public on Aug 19 2023

city: Ottawa

first: Basit

last: Yousuf

state: ON

address: 2035, Othello Avenue, Ottawa

institute: University of Ottawa

summary: Microvesicles (MEVs) were added on the Caco2 cells grown for 21 days on the insert until monolayer confluence. Triplicate samples for the MEVs treated (T1, T2, T3) and Triplicate samples for non-treated samples (C1, C2, C3) were processed for RNA extraction using Trizol method. Finally, RNA samples were DNase treated and cleaned with RNeasy MinElute Cleanup Kit (Qiagen) samples. Purified RNA was sequenced at Genome Québec (Montreal, Canada) and sequencing was performed using an Illumina NovaSeq PE100 sequencer.

overall_design: MEVs were addred to the Caco2 monolayer after 21 days of growth on an insert and were allowed to be in communication with Caco2 for 24 hours. Following incubation, triplicate RNA samples for the MEVs treated (T1, T2, T3) and Triplicate samples for non-treated samples (C1, C2, C3) were sequence. C3 and T1 Samples are not included in the submission as the samples were not sequenced due to low quality RNA.

first: Tamer

last: Ahmed

first: Riadh

last: Hammami


title: Three-dimensional molecular architecture of mouse organogenesis

status: Public on Aug 09 2023

city: Guangzhou

first: Guangdun

last: Peng

state: Guang dong

address: Building 3, KaiYuan Road, Huangpu District

department: Center for Cell Lineage and Atlas

institute: Bioland Laboratory

summary: Mammalian embryos exhibits sophisticated cell organizations that are intricately orchestrated at both molecular and cellular level. It has recently become apparent that cells within the animal body display significant heterogeneity, both in terms of their cellular properties and their spatial distributions. However, current spatial transcriptomics profiling either lack three-dimensional representation or are limited in their ability to capture the complexity of embryonic tissues and organs. Here, we present a represented spatial transcriptome atlas of all major organs at embryonic day 13.5 (E13.5) in the mouse embryo, and provide a three- dimensional rendering of molecular regulation for embryonic patterning with stacked sections. By integrating this spatial transcriptome data with corresponding single-cell transcriptome data, we offer a detailed molecular annotation of the dynamic nature of organ development, spatial cellular interaction, embryonic axes and divergence of cell fates underlying mammalian development, which would pave the way for precise organ engineering and stem cell-based regenerative medicine.

overall_design: Organogenesis stage (embryonic day 13.5, E13.5) embryos were collected of C57BL/6 mice, and embryos images were taken for recording and conformation of developmental staging. Collected embryos were embedded in Tissue freezing medium and stored at -80°C until sectioning. The whole embryo tissue was serially cryo-sectioned along craniocaudal axis at 10μm, and about 1000 sections were harvested. Considering the morphology and uniform sampling, 10 sections from a male embryo and 4 sections from a female embryo were selected for spatial transcriptomic analysis by 10x Genomics Visium platform.

first: Fangfang

last: Qu

first: Wenjia

first: Jian

last: Xu


title: Time-course gene expression profiles to understand compositional changes of the E. coli K-12 MG1655 transcriptiome during the transition from the exponential growth to the stationary phase

status: Public on Aug 07 2023

city: San Diego

first: Bernhard

middle: O.

last: Palsson

state: California

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

overall_design: Ribosomal RNA removed RNA prepared from cell cultures of E. coli K-12 MG1655

first: Hyun

last: Lim

middle: O


title: Hepatic transcriptome analysis of PRDX1fl/fl and Alb-Cre；PRDX1fl/fl mice on MCD

status: Public on Aug 14 2023

city: TIANJIN

first: Yin

last: Wen

state: TIANJIN

address: Address:No.6 North Huanrui Rd, Beichen District, Tianjin, P.R China

department: NHC Key Laboratory of Hormones and Development

institute: Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University

summary: The etiology of non-alcoholic steatohepatitis (NASH) has been complicated. An increasing body of literature has indicated that hepatic oxidative stress exerts a causal role in driving NASH. Nevertheless, how the anti-oxidant defense system guards against oxidative stress and NASH remains unclear. In this study, we sought to investigate how the peroxidase peroxiredoxin 1 protects against NASH. To this end, we fed WT and hepatic PRDX1 knockout (Alb-Cre;Prdx1fl/fl) a methionine and choline deficient diet (MCD) for 5 weeks and collected liver samples for RNA sequencing analysis. As revealed by gene-set enrichment analysis (GSEA) and KEGG pathway enrichment analysis, there was an enrichment of genes involved in JAK-STAT signaling. Further, we observed that the expression of many genes involved in JAK-STAT signaling such as Pdgfb and Pdgfra was significantly increased in Alb-Cre;Prdx1fl/fl mice. Collectively, these results suggest that increased JAK-STAT signaling accounts for the deteriorated NASH phenotypes in Alb-Cre;Prdx1fl/fl mice.

overall_design: We fed 8-week-old male mice a MCD for 5 weeks and collected their liver samples for RNA sequencing. 3 mice per genotype (PRDX1fl/fl or Alb-Cre；PRDX1fl/fl) were used.

first: Wen

last: Yin

first: Rui

last: Liu


title: How host-like signals drive gene expression and gene expression drives capsule growth in Cryptococcus neoformans [ep_pert]

status: Public on Aug 02 2023

city: St Louis

first: Michael

last: Brent

state: Missouri

address: 4515 McKinley Ave

institute: Washington University

summary: Cryptococcus neoformans is a fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew wild-type cells and cells lacking components of the cAMP pathway: Pde1, Pde2, Pkr1. We also took samples for RNA-Seq at 30, 90, 180, 1440 minutes and carried out RNA-Seq in quadruplicate. We also measured capsule thickness at 1440 min.

overall_design: After growth in YPD at 30C, WT cells and cells lacking PDE1, PDE2, or PKR1 were washed in PBS and transferred to RPMI medium at 30C. Samples were taken for RNA-Seq at 0, 30, 90, 180, 1440 minutes after transfer. We aimed for at least four replicates of each concentration at each time point. Replicates were grown and library-prepped on separate days to account for day-to-day variability. On each growth and library prep date, we included cells from between the PBS wash and innocoulation into the planned growth conditions, as a constant control and an initial timepoint. These PBS samples are labeled as time 0. However, they turned out to have much more variability in their RNA-Seq data than other conditions, so we did not use them in our analysis.

first: Tamara

middle: L

last: Doering


title: Dose-dependent transcriptome expression of alcohol on oligodendrocytes

status: Public on Sep 24 2023

city: Austin

first: Esther

last: Melamed

address: 1601 Trinity St bldg b

department: Department of Neurology, Dell Medical School

institute: The University of Texas at Austin

summary: Oligodendrocytes (OLs) are glial cells within the central nervous system (CNS) that produce myelin, which coats neuronal axons and enhances fast propagation of neuronal signals. OLs are known to be severely affected by alcohol in fetal alcohol spectrum disorder (FASD) and alcohol use disorder (AUD). In FASD, oligodendrocyte precursor cells have been reported to be highly affected by any dose of alcohol. In AUD, high doses of alcohol can lead to demyelinating complications such as Wernicke-Korsakoff sybdrome. However, relatively little is known about how alcohol at low and high doses affects mature OLs (mOLs). To better understand the impact of concentration-dependent alcohol exposure on mOLs, we isolated and differentiated immature murine OLs into mOLs and exposed them to a moderate or high concentration of alcohol in vitro. RNA was then isolated from the cultures and sequenced using 3’-Tag RNA sequencing. Differential expression across alcohol concentration and control groups was calculated, which was used for gene set enrichment analysis to identify KEGG and GO terms that were significantly changed as a result of alcohol treatment. We found concentration dependent changes in biological pathways related to cell cycle regulation, translation initiation, integrin signaling, FGF2 signaling, inflammation, and myelination. Further, we found that the moderate and high concentrations of alcohol elicited distinct changes in gene expression, indicating that concentration is a critical factor when determining the effects of alcohol on transcriptomic changes.

overall_design: Differentiated oligodendrocytes were grown in culture and exposed to alcohol at two different concentrations across two experiments. In the first, 6 wells each of control (no alcohol) and high concentration (30mM) ethanol-exposed oligodendrocytes were lysed and RNA was extracted for 3'-Tag sequencing. In the second experiment, 6 wells each of control and moderate concentration (10mM) ethanol-exposed oligodendrocytes were lysed and RNA was extracted for 3'-Tag sequencing. The cells were isolated from P5-7 mouse pups and differentiated for three days in culture. On the third day, alcohol was added to the culture and allowed to incubate for an additional three days before cells were lysed.

first: Sam

last: Bazzi

first: Cole

last: Maguire


title: How host-like signals drive gene expression and gene expression drives capsule growth in Cryptococcus neoformans

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

relation:
SuperSeries of: GSE226255
SuperSeries of: GSE226637
SuperSeries of: GSE226651

overall_design: Refer to individual Series


title: How host-like signals drive gene expression and gene expression drives capsule growth in Cryptococcus neoformans [ep_titration]

summary: Cryptococcus neoformans is a fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew cells wild-type KN99 cells with either no added cyclic AMP (cAMP), 1.1 mM, 1.8 mM, 3.3 mM, 11 mM, or 20 mM cAMP. capsule thickness at 1440 min. We also took samples for RNA-Seq at 30, 90, 180, 1440 minutes and carried out RNA-Seq in quadruplicate. We also measured capsule thickness at 1440 min.

overall_design: After growth in YPD at 30C, cells were washed in PBS and transferred to RPMI medium at 30C and incubated in an atmosphere of room air (no added CO2) with either no added cyclic AMP (cAMP), 1.1 mM, 1.8 mM, 3.3 mM, 11 mM, or 20 mM cAMP. Samples were taken for RNA-Seq at 0, 30, 90, 180, 1440 minutes after transfer. We aimed for at least four replicates of each concentration at each time point. Replicates were grown and library-prepped on separate days to account for day-to-day variability. On each growth and library prep date, we included cells from between the PBS wash and innocoulation into the planned growth conditions, as a constant control and an initial timepoint. These PBS samples are labeled as time 0. However, they turned out to have much more variability in their RNA-Seq data than other conditions, so we did not use them in our analysis.


title: mRNA transcriptome data of bovine granulosa cells cultured under DMSO and 50µM PD98059 treatments

status: Public on Aug 01 2023

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

country: Germany

institute: Leibniz institute for farm animal biology

summary: Ovarian follicular luteal transformation is associated with induction of mitogen activated kinase (MAPK3/1) signaling. Here we investigated the genome wide changes induced by MAPK3/1 signaling in primary granulosa cell cultures treated with control (DMSO) and MAPK3/1 a.k.a ERK1/2 inhibitor PD98059.

overall_design: RNA from DMSO (3n) and PD98059 (3n) treated granulosa cells were processed for microarray analysis

first: Vijay

first: Jens

last: Vanselow


title: mRNA changes during primary human keratinocyte differentiation

status: Public on Jul 21 2023

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

summary: RNA sequencing (RNAseq) of primary neonatal human keratinocytes under non-differentiated or differentiated conditions

overall_design: mRNA levels were compared between keratinocytes at different stages of differentiation vs non-differentiated keratinocytes (Basal). In addition, keratinocytes were cultured in media without epinephrine for two passages (Basal_NoEpi) and compared with keratinocytes in full media (Basal).


title: How host-like signals drive gene expression and gene expression drives capsule growth in Cryptococcus neoformans [ep_wt]

summary: Cryptococcus neoformans is a fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew cells with and without all combinations of 5 signals suspected of affecting capsule size: Tissue-culture medium (DMEM or RPMI), temperature (37°C), CO2 (5%), and the addition of HEPES buffer. For each combination of conditions, we grew cultures with or without exogenous cAMP, and sampled cells for RNA-Seq at 0, 30, 90, 180, 1440 minutes and for measurement of capsule thickness at 1440 min. We also took samples for RNA-Seq at 30, 90, 180, 1440 minutes and carried out RNA-Seq in quadruplicate.

overall_design: After growth in YPD at 30C, cells were washed in PBS and transferred to one of 48 growth conditions, representing all combinations of 3 media (YPD, DMEM, or RPMI), 2 atmospheres (room air or 5% CO2), 2 temperatures (30C or 37C), +/- 20 mM cAMP, +/- 25 mM HEPES buffer at pH 7.0. Samples were taken for RNA-Seq at 0, 30, 90, 180, 1440 minutes after transfer. We aimed for at least four replicates of each condition at each time point. Replicates were grown and library-prepped on separate days to account for day-to-day variability. On each growth and library prep date, we included cells from between the PBS wash and inoculation into the planned growth conditions, as a constant control and an initial time point. These PBS samples are labeled as time 0. However, they turned out to have much more variability in their RNA-Seq data than other conditions, so we did not use them in our analysis. On 10 dates, we also have controls from just before the PBS wash, which are listed as “medium: YPD, temperature: 30, time: 1440”. We used these as baselines in our time series analyses.


title: Cholinergic neuro-epithelial interactions and gap junctions spread Ca2+ across the intestinal epithelium to promote homeostasis after injury

status: Public on Jul 18 2023

city: Boston

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: How a tissue returns to homeostasis following injury remains enigmatic. Here, we show that elevated Ca2+ dynamics among enterocytes (ECs) mediated by nAchRs (nicotinic Acetylcholine (Ach) Receptor) in the adult Drosophila midgut, are essential for the epithelium to return to homeostasis after injury. This bioelectric signal is controlled by 1) changes in EC-responsiveness to Ach; 2) enteric neuro-EC interactions; and 3) epithelial gap junctions. Our findings demonstrate how a bioelectric signal during regeneration, initiated by local neuro-epithelial communication and propagated by gap junctions, is coupling the epithelium into a unified response that promotes return to homeostasis.

overall_design: 10x single-nuclei RNA-sequencing of adult Drosophila gut

first: Afroditi

last: Petsakou

first: Yifang

first: Norbert

last: Perrimon


title: Knockdown of LTB4R, HCAR3, GPR153, and GPR137 in primary human keratinocytes

summary: RNA sequencing (RNAseq) of primary neonatal human keratinocytes transduced with pooled siRNAs targeting LTB4R, HCAR3, GPR153, and GPR137, or non-targeting control siRNA (siCon)

overall_design: Comparison of primary keratinocytes transduced with siRNAs with control cells. Data is from two different sequencing batches designated as EXPA and EXPB, each treatment was analyzed in triplicate

first: Pilar

middle: M

last: Pedro

first: Ting

last: Chen


title: Expression of piRNAs and miRNAs in embryonic mouse ovary cells: dysregulation and apoptosis by exposure to Vinclozolin and MEHP

status: Public on Jul 17 2023

city: Madrid

first: Odei

last: Barreñada

address: C/ Ramiro de Maeztu 9

institute: CIB Margarita Salas - CSIC

summary: The early stages of embryonic development are critical for the proper formation of primordial germ cells. This process is tightly regulated by different cellular signals. Among others, small non-coding RNAs (sncRNAs) are involved in the regulation of these signals to carry out the embryonic development of germ cell linage. We analyzed the expression profiles of piRNAs and miRNAs after maternal exposure of embryos, during the first 13.5 days post-coitum, to two different endocrine disruptors (EDs) chemicals: vinclozolin and the main metabolite of phthalates (MEHP), in three successive generations after exposure only in the first generation. Our results indicate clear alterations in the expression of both piRNAs and miRNAs (including mitochondrial-related), concomitant with an increase in apoptotic cells in the female early folliculogenesis during this stage of development. However, the most drastic changes occur when the effect is generated by the exposure through both paternal and maternal pathways, rather than exclusively through the maternal exposure. Based on these findings, we hypothesize the existence of an "ovarian filtering" mechanism triggered by disruptor exposure and mediated by apoptotic mechanisms regulated by sncRNAs. This system, present only in the female germ cell lineage, could render a decrease in the follicle reserve in the adult life and would function as a defense mechanism to prevent the transmission of deleterious effects to subsequent generations.

overall_design: Briefly, a first generation of mice has been crossed, which are considered generation F0. When a successful mating is detected, they are randomly assigned to Control, VZN or MEHP group. From this moment on, they are exposed during the first 13.5 days of gestation to the endocrine disruptor or control. One part of these pregnant female mice was sacrificed at 13.5 dpc to obtain the fetal ovaries by dissection and differentiation of the sexes by gonadal morphology evident at this date of development, the other part of pregnant female mice was withdrawn from exposure to ED and allowed to finish gestation and birth, to analyze the effects of exposure to ED in the following generations, obtaining embryonic ovaries also at 13.5 dpc in each subsequent generation. This process was repeated two more generations to study both the F1 generation (directly exposed during their embryonic period to DEs) and the F2 and F3 (both indirectly exposed to DEs, since only their first- and second-degree female progenitors, respectively, have been exposed). Furthermore, an additional group was made ("-Sy" group or "paternal effect -PA- group")  evaluating the additive effect of the both progenitros (exposed to the same DE and dose).

first: Miguel

last: Brieño-Enriquez

first: Jesús

last: del Mazo


title: Gene expression analysis in untreated adult zebrafish livers (~1 year older): wild-type TAB14 compared to as3mt-/- mutants

status: Public on Jul 07 2023

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to compare the changes in basal gene expression in livers of ~1 year old  zebrafish adults in response to whole body mutation of the arsenite methyltransferase gene (as3mt) - 8 bp deletion in exon 3 resulting in a loss of function.

overall_design: The Sadler lab generated a whole body knockout of as3mt in zebrafish using CRISPR. This line a missense mutaion with a premature stopcodon (8 bp deletion in exon 3). This experiment was conducted by dissecting livers from 2 males and 2 females of WT-TAB14 (DOB: March 15, 2022) or as3mt mutant (DOB: January 19, 2022)fish. Livers were dissect under the steroscope and immediately placed in TRIzol on ice. RNA from was extracted per standard TRIzol/Chloroform method and concentrated and concentreated and DNAse treated (RNase-Free DNase Set; Qiagen) using RNeasy Mini Spin column kit (Qiagen) and resuspended in 30 uL of DNase/RNase free water (Thermo Fisher Scientifc). For library preparation, high quality of total RNA was QCed using a bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA was then quantified by Qubit flurometer. Next, RNA quality was measured on a Bioanalyzer (Agilent) and the only RNA with RIN score >7 were used for library preparation.mRNA library was prepared using Illumina TruSeq V2 RNA sample Prep Kit (San Diego, CA) according to the manufacturer’s protocol. Briefly, 100 ng of total mRNA was poly-A purified, fragmented, and first-strand cDNA reverse transcribed using random primers. Following second-strand cDNA synthesis, end repair, addition of a single A base, TrueSeq adapter-index was ligated to cDNA libraries, and PCR amplification of 12 cycles was done for enrichment, producing a 350-400 bp fragment including adapters. The fragment sizes and purity of the libraries were confirmed by analyzing on a Bioanalyzer 2100 (Agilent Technologies). The quantities of the libraries required for RNA-seq were determined by real-time qPCR using a KAPA library quantification kit for the NEBNext Ultra II Directional RNA Library Prep kit for Poly A. Enriched cDNA libraries were sequenced using the Illumina NextSeq550 (Illumina). Note:wttab14_female_liver2 was excluded from analyses

first: Patrice

last: Delaney

last: Edepli


title: Tumor-derived biomarkers beyond antigen expression enhance efficacy of CD276/B7H3 antibody-drug conjugate in metastatic prostate cancer

status: Public on Jul 11 2023

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Antibody-drug conjugates(ADCs) are promising targeted cancer therapy; however, patient selection based solely on target antigen expression without consideration for cytotoxic payload vulnerabilities has plateaued clinical benefits. Biomarkers to capture patients who might benefit from specific ADCs have not been systematically determined for any cancer. We present a comprehensive therapeutic and biomarker analysis of a B7H3-ADC with pyrrolobenzodiazepine(PBD) payload in 26 treatment-resistant, metastatic prostate cancer(mPC) models. B7H3 is a tumor-specific surface protein widely expressed in mPC, and PBD is a DNA cross-linking agent. B7H3 expression was necessary but not sufficient for B7H3-PBD-ADC responsiveness. RB1 deficiency and/or replication stress, characteristics of poor prognosis, conferred sensitivity and were associated with complete tumor regression in both neuroendocrine (NEPC) and androgen receptor positive(ARPC) prostate cancer models, even with low B7H3 levels. Non-ARPC models, which are currently lacking efficacious treatment, demonstrated the highest replication stress and were most sensitive to treatment. In RB1 wild-type ARPC tumors, SLFN11 expression or select DNA repair mutations in SLFN11 non-expressors governed response. Significantly, wild-type TP53 predicted non-responsiveness (7/8 models). Overall, biomarker-focused selection of models led to high efficacy of in vivo treatment. These data enable a paradigm shift to biomarker-driven trial designs for maximizing clinical benefit of ADC therapies.

overall_design:
The objective of this study was to evaluate B7H3 expression and treatment efficacy of the B7H3 ADC armed with a pyrrolobenzodiazepine warhead (SG3315) in a diverse spectrum of PDX/organoid preclinical models of mPC.
An additional objective was to identify predictive biomarkers of B7H3-PBD response.
In total, 37 mPC organoid models were evaluated for B7H3 expression.
mPC organoids were evaluated by RNA-seq by at 1-5 replicates each.
**Raw data for these Samples are being submitted to dbGAP (accession ID phs001587.v2.p1)

first: Supreet

last: Agarwal

first: Brian

middle: J

last: Capaldo

middle: G

first: Kathleen

last: Kelly


title: Endothelial Cell CD36 Regulates Membrane Ceramide Formation, Exosome Fatty Acid Delivery to Tissues and Circulating Fatty Acid Levels

status: Public on Jul 02 2023

first: Nada

last: Abumrad

address: 660 S. Euclid

summary: Endothelial cell (EC) CD36 controls tissue fatty acid (FA) uptake. Here we examined how ECs transfer FAs. FA interaction with apical membrane CD36 induced Src phosphorylation of caveolin-1 tyrosine-14 (Cav-1Y14) and ceramide generation in caveolae. Fission of the caveolae yielded vesicles containing FAs, CD36 and ceramide that were secreted basolaterally as small (80-100nm) exosome-like extracellular vesicles (sEVs). We visualized EC transfer of FAs in sEVs to underlying myotubes in transwells. In mice with EC-expression of the exosome marker emeraldGFP-CD63, muscle fibers accumulated circulating FAs in emGFP-labeled puncta. The FA-sEV pathway was mapped through its suppression by CD36 depletion, blocking actin-remodeling, Src inhibition, Cav-1Y14 mutation, and neutral sphingomyelinase 2 inhibition. Suppression of sEV formation in mice reduced muscle FA uptake, raised circulating FAs, which remained in blood vessels, and lowered glucose, mimicking prominent Cd36-/- phenotypes. The findings show that FA uptake influences membrane ceramide, endocytosis, and EC communication with parenchymal cells.

overall_design: Gene expression analyses was conducted using RNASeq on control or CD36 knockdown human dermal microvascular cells

first: Vivek

last: Peche

first: Terri

last: Pietka


title: Mechanism of Nootkatone in U251

city: Hangzhou

first: Wang

last: Qian

state: Zhejiang

address: 2318 Yuhangtang Road

institute: Hangzhou Normal University

summary: Nootkatone can induce the changes of gene expression in U251 cells

overall_design: The cells were treated with 200μ nootkatone in the experimental group and compared with the control group.


title: LIPG regulates goat intramuscular preadipocyte proliferation and lipid deposition through PPARα signaling pathway

status: Public on Jun 17 2023

city: chengdu

first: Yinggui

last: Wang

state: sichuan

address: 2-31, Jingwenyuan, South District, Airport Campus, Southwest University for Nationalities, Chengdu, Sichuan

institute: Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province

summary: LIPG has an important role in the maintenance of lipid homeostasis.To reveal the potential molecular mechanisms by which LIPG regulates lipid deposition and proliferation in goat intramuscular preadipocytes by constructing a transcriptional profile of knockdown LIPG gene.This work extends the regulatory network of IMF deposition.

overall_design: The sequencing samples were goat intramuscular preadipocytes. The samples transfected with LIPG silencing RNA (siRNA) were the experimental group and the samples transfected with negative control RNA (NC) were the control group (n=3).

first: Jiangjiang

last: Zhu

first: Lian

last: Huang

first: Wenyang

last: Zhang


title: Single-cell transcriptome characterization of the livers from patients with alcoholic liver disease

status: Public on Jul 03 2023

city: Jinan

first: Yuan

last: Detian

email: yuandt@sdu.edu.cn, lishiyang@sdu.edu.cn

address: Wenhuaxi Road 44

institute: Shandong University

summary: The immunological mechanisms involved in the pathogenesis of alcohol-related liver disease (ALD) are still not fully understood. Here, we conducted an analysis of the transcriptome of liver immune cells using single-cell RNA sequencing. This study utilized single-cell data from liver samples of 5 ALD human cases. The study provides insights into the cellular diversity of liver immune cell populations in the pathogenesis of ALD and may offer potential foundations for tailored therapies in the future.

overall_design: Performing single-cell transcriptomic sequencing on liver tissue from 5 patients with alcoholic liver disease.

first: Detian

last: Yuan

first: Shiyan

last: Li

first: Peng

last: zhang

first: Chao

last: Gao


title: Single-cell Transcriptomic Architecture Reveals Dynamic Heterogeneity and Intracellular Crosstalk Features Which Triggers Liver Mallory-Denk Bodies Pathogenesis

status: Public on Jun 21 2023

first: Hui

last: Liu

address: Xinzao Road No.1

institute: Guangzhou Medical University

summary: Liver cell injury causes balloon hepatocytes and Mallory-Denk Bodies (MDBs) formation impeding liver parenchymal regeneration. MDBs are an intracellular deposition of misfolded protein and typical features of distinct chronic liver disease. Therefore, a comprehensive understanding of cellular heterogeneity and intercellular signaling of MDBs formation is essential to elucidate the mechanisms driving MDBs formation and chronic liver disease progression and to develop therapeutic approaches.

overall_design: Herein, we performed single-nucleus RNA-sequencing (snRNA-seq) to illustrate the comprehensive transcriptomic landscape and intercellular ligand-receptor signaling on the fractionations isolated from healthy and MDB-forming mouse livers induced following DDC. In addition, we applied an MDB-forming cell model induced by cytokines combined clinical hepatocellular carcinoma specimen which had formed MDBs to further verify the potential MDB-forming markers. The results of the analyses were validated using typical MDB-related immunofluorescence staining, bulk transcriptomic datasets, and functional experiments in vitro and in vivo.

first: Rong

first: Menghua

last: He

first: Bei

last: Zhong

first: Jun

last: Dong

first: Xinyu

last: Yang

first: Jiangtao

last: Jia

first: Zixuan

last: Fang

first: Jiayi

last: Pan

first: Wuyi

last: Zeng

first: Jiashan

first: Xinghua


title: Genome-wide maps of transcription in PNPO overexpression(OE) and empty vector(EV) cells in RAW264.7

status: Public on Jun 15 2023

city: Jiangsu Nanjing

first: Deng

middle: Zhen

address: Xianlin Roud 138

institute: Nanjing University of Chinese Medicine

summary: We found different genes change between EV and PNPO-OE RAW264.7 cells.

overall_design: Examination of 2 different genes changes in RAW264.7 cell.

first: Zhendong

last: Deng


title: SnRNA-seq reveals heterogeneity of mouse cholangiocyte in liver Mallory-Denk bodies formation

summary: Mallory-Denk bodies (MDBs) are misfolded protein aggregates that include hepatocytes present in liver diseases, and are considered a typical feature of chronic liver diseases. Cholangiocytes are an epithelial cell type constituting the hepatic parenchyma, and play a role in liver regeneration if hepatocyte regeneration is compromised. UbD, which is overexpressed in hepatocellular carcinoma (HCC) plays an important role in immune regulation and MDB pathogenesis. In this study, we conducted the first comprehensive study on cholangiocyte heterogeneity to demonstrate the pathogenesis of MDBs formation using single-nucleus RNA sequencing (snRNA-seq) from fractionations of normal and DDC-treated mouse livers. We found that cholangiocytes in the MDB-forming groups were significantly expanded, and the enrichment pathways of differentially expressed genes (DEGs) were markedly involved in metabolic processes, neurodegenerative diseases, autophagy, and ubiquitin-mediated proteolysis. We proposed a cellular-state landscape for cholangiocytes using uniform manifold approximation and projection (UMAP) analysis, which includes numerous cell subpopulations, referred to as Clusters0 through 7, with Cluster1 being the sole subpopulation made up entirely of DDC-treated cells. UbD was highly expressed in Cluster4 and colocalized with the cholangiocyte marker gene cytokeratin 19 (Krt19), implying that cholangiocytes function as facultative liver progenitor cells (LPCs) to supply damaged hepatocytes to promote MDBs formation. In summary, we revealed, for the first time, the heterogeneity of cholangiocytes and provided a novel viewpoint for understanding the mechanism of MDBs formation as well as chronic liver disease progression.

overall_design: SnRNA-seq was performed on two groups (Control vs. DDC), and each group independent sample consisted of liver tissues from three mice. Biological functions of cholangiocyte differentially expressed genes (DEGs) were well identified by the comparison between Control group and DDC group at the single-cell level. Gene ontology (GO) term, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway and Gene set enrichment analysis (GSEA) software were used to reveal cholangiocytes heterogeneity. qRT-PCR and immunohistochemistry staining were used to evaluate the expression of signature genes in cholangiocytes. Finally, FISH analysis was used to assess the colocalization.

first: Yi

last: Shi

first: Ailin

last: Tao


title: RIF1 regulates replication origin activity and early replication timing in B cells [RNA-seq]

status: Public on Jun 13 2023

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin, regulates early origin firing and promotes early replication. However, RIF1 has a minor role in gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal a new layer of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.

overall_design: RNA-Seq LacZ and Mcm infected CH12 and Rif -/-  CH12 cells

first: Daniel

last: Malzl

first: Mihaela

last: Peycheva

first: Ali

last: Rahjouei

first: Stefano

last: Gnan

first: Kyle

last: Klein

first: Mariia

last: Nazarova

first: Ursula

last: Schoeberl

first: David

last: Gilbert

first: Sara

middle: C

last: Buonomo

first: Michela

last: Di Virgilio

first: Rushad

last: Pavri


title: RIF1 regulates replication origin activity and early replication timing in B cells [SNS-seq]

overall_design: SNS-seq inLacZ and Mcm infected CH12 and Rif -/- cells


title: RIF1 regulates replication origin activity and early replication timing in B cells [PRO-seq]

overall_design: PRO-seq of priB and CH12 WT cells


title: RIF1 regulates replication origin activity and early replication timing in B cells [HI-C]

overall_design: HiC in LacZ and Mcm infected CH12 Rif1KO cells


title: RIF1 regulates early replication timing in murine B cells.

summary: The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating murine B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin and promotes early replication, but plays a minor role in regulating replication origin activity, gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal new layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.

overall_design: Refer to individual Series


title: Lurbinectedin is an effective therapeutic target for de novo and transformed small cell lung cancer and modulates EMT and NOTCH signaling pathways.

status: Public on Jun 08 2023

city: New York

first: Triparna

last: Sen

state: New York

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Small cell lung cancer (SCLC) is a high-grade neuroendocrine tumor with a dismal prognosis and limited treatment options. Lurbinectedin, approved as a second-line treatment for metastatic SCLC, showed only a partial response in clinical trials highlighting the need to develop improved mechanistic insight and predictive biomarkers of response. In this study, we determine the preclinical efficacy of lurbinectedin in a comprehensive panel of SCLC cell lines and patient-derived xenografts of SCLC. Furthermore, we demonstrate that lurbinectedin, either as a single agent or in combination with osimertinib, causes remarkable anti-tumor response in multiple models of SCLC transformation. Transcriptomic analysis identified induction of apoptosis, repression EMT and modulation of PI3K/AKT, NOTCH signalling pathway being associated with lurbinectedin response in de novo and transformed SCLC models. We provide a mechanistic insight of lurbinectedin response in SCLC and is the first demonstration that lurbinectedin is a potential therapeutic target after SCLC transformation.

overall_design: RNA.seq analysis data of small cell lung cancer  of 3 patient derived xenograft models of de-novo small cell lung cancer (LX110, LX33 and LX1322) in lurbinectedin treated and vehicle treated group. Data also include RNA seq analysis of 2 patient derived xenograft models of transformed SCLC , LX1042 and LX831b comparing vehicle, only osimertinib, only lurbinectedin and lurbinectedin+osimertinib combination treatment groups.

first: Dan

last: Hasson

first: Subhamoy

last: Chakraborty

first: Deniz

last: Demircioglu

first: Charles

last: Coleman


title: Age associated epigenome changes in human mammary epithelial cells

status: Public on Jun 09 2023

city: Duarte

first: Parijat

last: Senapati

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

type: Methylation profiling by high throughput sequencing

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


title: Age associated epigenome changes in human mammary epithelial cells (ATAC-Seq)

summary: ATAC-seq profiling of luminal epithelial cells obtained from reduction mammoplasty tissue from young (<30 year) and old (>55 year) individuals.

overall_design: We performed ATAC-seq on mammary luminal epithelial cells from young and old individuals.

first: Mark

middle: A

last: LaBarge

first: Dustin

last: Schones


title: Identification of pan-phylum conserved parasitic nematode proteins that activate immunity

city: St. Louis

first: Bruce

last: Rosa

state: MO

address: 4444 Forest Park Ave

department: Medicine

institute: Washington University in St Louis

summary: A cocktail of five bioinformatically and experimentally prioritized recombinant proteins was used immunize pigs and test for active antibody responses.

overall_design: This antibody-protein array of putative immunogenic proteins was developed using bioinformatic, experimental, and literature-based parasite protein targets. Screening the array with sera and ileal fluid samples from immunized pigs suggested cross-reactivity among homologous proteins and general immunity activation. Overall immune responses were significantly altered by immunization, but not by direct worm challenge.

first: Dante

middle: S

last: Zarlenga

first: Valsin

last: Fournet

first: Ethiopia

last: Beshah

first: Dolores

last: Hill

first: Alexander

first: Angela

last: Yee

first: Xiaowu

last: Liang

first: Adam

middle: D

last: Shandling

first: Amit

last: Oberai

first: Joseph

middle: F

last: Urban Jr

first: Makedonka

last: Mitreva


title: A microglia-CD4+ T cell partnership generates protective anti-tumor immunity to glioblastoma [RNAseq-2]

status: Public on Jun 06 2023

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

summary: The aim of the study is to analyze and compare the transcriptional profiles of tumor-infiltrating Microglia from glioma brearing brain tissues treated with anti-CTLA4 in the presence or absence of CD4 T cells .

overall_design: RNA of in vitro cultured Glioma-005 cell lines was performed before transfer.

first: Dan

last: Chen

first: Siva

middle: K

last: Varanasi

first: Susan

last: Kaech


title: RIF1 regulates replication origin activity and early replication timing in B cells [Repli-Seq]

first: Tobias

last: Neumann

overall_design: Repli-seq in LacZ and Mcm infected CH12 and Rif-/- CH12 cells cells

first: Daniel

last: Malzl

first: Mihaela

last: Peycheva

first: Ali

last: Rahjouei

first: Stefano

last: Gnan

first: Kyle

middle: N

last: Klein

first: Mariia

last: Nazarova

first: Ursula

last: Schoeberl

first: David

last: Gilbert

first: Sara

last: Buonomo

first: Michela

last: Di Virgilio

first: Rushad

last: Pavri


title: A microglia-CD4+ T cell partnership generates protective anti-tumor immunity to glioblastoma [scRNA/TCR seq]

status: Public on Jun 01 2023

summary: The aim of the study is to analyze and compare the transcriptional profiles at a single cell resolution of tumor-infiltrating immune cells from healthy mouse brain as well as glioma brearing brain tissues treated with anti-CTLA4 in the presence or absence of CD4 T cells .

overall_design: 10x Chromium Single cell 5’ + VDJ Library; Single-cell RNA of all immune cells from healthy brain and Glioma-005 glioblastoma tumors treated with IgG, anti_CTLA4 and combination of anti_CTLA4 and anti_CD4 (depletion) were performed at Day 35 post implantation. Each sample is a pool of 3 tumor samples.


title: A microglia-CD4+ T cell partnership generates protective anti-tumor immunity to glioblastoma [scRNA-seq]

overall_design: Single-cell RNA of all immune cells from healthy brain and Glioma-005 glioblastoma tumors treated with IgG, anti_CTLA4 and combination of anti_CTLA4 and anti_CD4 (depletion) were performed at Day 35 post implantation. Each sample is a pool of 3 tumor samples.


title: Combination of triciribine and p38 inhibitors enhances the differentiation effect on myeloid leukemia cells

status: Public on Jun 27 2023

city: Sendai-shi

first: Susumu

last: Suzuki

institute: Tohoku Medical and Pharmaceutical University

summary: Differentiation therapy with all-trans retinoic acid (ATRA) is well established for acute promyelocytic leukemia (APL). However, the narrow application and tolerance development of ATRA remain to be improved. A number of kinase inhibitors have been reported to induce differentiation. In this study, we challenged several combinations of these kinase inhibitors. As a result, we found that the combination of Akt inhibitor Triciribine (TCN) and several p38 MAPK inhibitors have profound effect for differentiation in several myeloid cell lines. To reveal the molecular mechanisms involved in TCN and p38 MAPK inhibitor induced differentiation, we performed microarray analysis.

overall_design: We use 4 samples. As a control, we used DMSO sample. The other samples are Triciribine (TCN), PD169316 and TCN+PD169316. All samples were exposed to reagents for 72 hours.

first: Shinichiro

last: Takahashi


title: A microglia-CD4+ T cell partnership generates protective anti-tumor immunity to glioblastoma [RNA-seq]

status: Public on Jun 02 2023

first: Kathryn

last: Lande

overall_design: RNA of all Microglia from Glioma-005 glioblastoma tumors treated with IgG, anti_CTLA4 and combination of anti_CTLA4 and anti_CD4 (depletion) were performed at Day 35 post implantation.

first: Dan

last: Chen


title: RNAseq of SARS-CoV-2-infected mice

status: Public on Jun 05 2023

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

summary: SARS-CoV-2 infected animals and controls were treated with antiviral peptides

overall_design: Animals were untreated or pretreated with either dimer or PEG-24 lipopeptide, followed by SARS-2 infection. Lungs were collected two days post infection

first: Alexander

last: Greninger

first: Branka

last: Horvat


title: A microglia-CD4+ T cell partnership generates protective anti-tumor immunity to glioblastoma.


title: Single-cell transcriptomics reveal hyperacute cytokine and immune checkpoint axis in patients with poor neurological outcomes after cardiac arrest.

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

institute: University of Alabama at Birmingham


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada


title: Single-cell transcriptomics reveal hyperacute cytokine and immune checkpoint axis in patients with poor neurological outcomes after cardiac arrest [BRI]

summary: Neurological injury is a major driver for mortality among patients hospitalized after cardiac arrest (CA). The early systemic inflammatory response after CA is associated with neurological injury and mortality but remains poorly defined. We determine the innate immune network induced by clinical CA at single-cell resolution. Immune cell states diverge as early as 6h post-arrest between patients with good or poor neurological outcomes at hospital discharge. Nectin-2+ monocytes and Tim-3+ natural killer (NK) cell subpopulations associate with poor outcomes, and interactome analysis highlight their cross-talk via cytokines and immune checkpoints. Ex vivo studies on peripheral blood cells from CA patients demonstrate that immune checkpoints are a compensatory mechanism for the resolution of inflammation after CA. IFNγ/IL-10 induce Nectin-2 on monocytes; in a negative feedback loop, Nectin-2 suppresses IFNγ production by NK cells. The initial hours after CA may represent a window for therapeutic intervention in the resolution of inflammation via  immune checkpoints.

overall_design: PBMC from 11 post-OHCA patients and 3 healthy subjects were used for 10X single-cell RNA-sequencing. Sorted PBMC were processed for bulk RNA sequencing.

first: Edy

middle: Y

last: Kim

first: Tomoyoshi

last: Tamura

first: Xiang


title: Rigidity of cell fate and function among monocytes (RNA-Seq)

middle: T

last: Scadden

state: MA

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH

summary: Here, we used an inducible and reversible system to pause myeloid differentiation at a self-renewing state. These cells were clonally isolated and allowed to differentiate to test whether function was clone-specific and clonally restricted.  We found that monocytic subsets exist with inherent, restricted capabilities which differ in their capacity to perform traditional monocytic functions.

overall_design: We performed high-throughput RNA-sequencing on both progenitors and monocyte ER-Hoxb8 clones, clonally paired as progenitors and mature cells. In addition, we performed RNA-sequencing on primary monocytes as well.


title: Rigidity of cell fate and function among monocytes (ATAC-Seq)

overall_design: We performed high-throughput ATAC-sequencing on both progenitors and monocyte ER-Hoxb8 clones, clonally paired as progenitors and mature cells.


title: Global gene expression of human malaria parasite liver stages throughout intrahepatocytic development

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

summary:
To investigate the poorly characterized asymptomatic liver stages (LS) of plasmodium faciparum, we analyzed isoloated LS RNA which is the first comprehensive gene expression profile during in vivo intrahepatocytic development.
We identified LS-specific processes such as cell cycle, metabolism, and host-parasite interaction pathways, and, interestingly, var gene transcipts.

sample_organism:
Plasmodium falciparum
Plasmodium vivax

platform_organism:
Plasmodium falciparum
Plasmodium vivax

overall_design: Differential gene expression profiling analysis of RNA-seq data for plasmodium falciparum in the early liver stage and comparative analysis with plasmodium vivax.

first: Gigliola

last: Zanghi

first: Hardik

last: Patel

first: Nelly

last: Camargo

first: Jenny

last: Smith

first: Yeji

last: Bae

first: Erika

last: Flannery

first: Vorada

last: Chuenchob

first: Wanlapa

last: Roobsoong

first: Jetsumon

last: Sattabongkot

first: Kiera

last: Hayes

first: Ashley

last: Vaughan

first: Stefan

middle: H

last: Kappe


title: RIF1 regulates replication origin activity and early replication timing in B cells [ChIP-seq]

first: Tobias

last: Neumann

overall_design: ChIP-seq for Rif1-FH in primary B cells

first: Daniel

last: Malzl

first: Mihaela

last: Peycheva

first: Ali

last: Rahjouei

first: Stefano

last: Gnan

first: Kyle

last: Klein

first: Mariia

last: Nazarova

first: Ursula

middle: E

last: Schoeberl

first: David

middle: M

last: Gilbert

first: Sara

last: Buonomo

first: Michela

last: Di Virgilio

first: Rushad

last: Pavri


title: Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer

status: Public on May 31 2023

city: Daegu

first: Incheol

last: Seo

address: 680 gukchaebosang-ro, Jung-gu

country: South Korea

institute: KYUNGPOOK NATIONAL UNIVERSITY INDUSTRY-ACADEMIC COOPERATION FOUNDATION

summary: Neoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC. We analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets. Gene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature. Taken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.

overall_design: Formalin-fixed paraffin-embedded (FFPE) block specimens from preoperative biopsy via sigmoidoscopy and surgical resection of the primary tumor were obtained from the 11 pairs of human locally advanced rectal cancer. Total RNA was extracted using TRIzol RNA Isolation Reagent (Life Technologies) from the samples. The quantity and quality of the total RNA were evaluated using an Agilent 2100 bioanalyzer RNA kit. The isolated total RNA was processed for preparation of an RNA-seq library using an Illumina TruSeq Stranded mRNA Sample Preparation kit according to the manufacturer’s protocol. The quality and size of libraries were assessed using an Agilent 2100 bioanalyzer DNA kit. All libraries were quantified by quantitative real-time PCR using a CFX96 Real Time System and sequenced on NextSeq500 sequencers with a paired-end 76 bp plus single 6 bp index read run. For quality control, low-quality bases and adapter sequences were trimmed from the raw sequencing reads using Trimmomatic software with default parameters, except that the minimum length of reads to be dropped was 38 bp. Trimmed sequencing reads were mapped to the hg38 human reference genome using STAR aligner with default parameters. Reads per gene was counted simultaneously by STAR using the ‘--quantMode GeneCounts’ parameter. Count normalization were performed DESeq2.

first: HyeWon

last: Lee

first: SangJun

last: Byun

first: JeeYoung

last: Park

first: Hyeonj

last: Min

first: SungHwan

first: Ju-Seog

first: Shin

last: Kim

first: SungUk

last: Bae


title: scRNA-seq analysis of SHH medulloblastomas in Gfap-Cre/SmoM2 mice treated with CT-179 or Pox-resiquimod

status: Public on May 30 2023

city: Atlanta

first: Timothy

last: Gershon

state: Georgia

address: 201 Dowman Dr

institute: Emory University

summary: Our parallel studies have shown that the OLIG2 inhibitor CT-179 and the TLR7/8 agonist resiquimod delivered in polyoxazoline nanoparticle (Pox-resiquimod) produce significant anti tumor effects when administered to mice with SHH medulloblastoma. To gain insight into the cellular events set in motion by each treatment, we compared sets of replicate mice with SHH medulloblastomas treated with either CT-179 or POx-resiquimod to a common set of untreated control mice with SHH medulloblastoma.

overall_design: We generated replicate mice that developed medulloblastoma by breeding hGfap-Cre and SmoM2 mouse lines to generate Gfap-Cre/SmoM2 mouse pups. We then treated one group of 4 replicates with CT-179 and another group of 3 replicates wih POx-resiquimod, and another 4 replicates served as untreated controls. All mice were harvested at P15 and tumros were dissociated and subjected to scRNA-seq using the Split-Seq-based Parse 1.0 WT kit (Parse Biosciences) and then sequenced on an Illumina S2 flow cell.

middle: R

first: Daniel

last: Malawsky


title: Intravenous BCG induces primed immune signaling that correlates with protection against tuberculosis

city: Cambridge

first: Bryan

middle: B

last: Bryson

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

summary: We profiled rested and PPD-stimulated bronchoalveolar lavages to understand immune features of protection.

overall_design: Rested and PPD-stimulated bronchoalveolar lavages (BALs) from vaccinated and naïve rhesus macaques were profiled using Seq-Well

first: Joshua

last: Peters

first: Tricia

last: Darrah


title: Hepatic niche leads to aggressive NK-cell leukemia proliferation

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

summary: We report the transcriptomic profiles of liver-tropic and spleen-tropic ANKL cells obtained from patient-derived xenograft (PDX) mouse. We also report the transcriptomic profiles of liver niche collected from healthy mice or PDX mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profiles of ANKL cells and mouse liver niche

first: Kazuaki

last: Kameda

first: Ai

last: Kotani


title: Rigidity of cell fate and function among monocytes

city: Boston

first: David

last: Scadden

overall_design: Refer to individual Series


title: Synapse related gene expression is downregulated in SPG7 patient induced pluripotent stem cell derived cortical neurons

city: Sydney

first: Gautam

last: Wali

address: Randwick

country: Australia

institute: Neuroscience Research Australia

summary: To understand the disease mechanism of SPG7 hereditary spastic paraplegia, we generated and evaluated patient and control induced pluripotent stem cell derived cortical neurons. We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression pathway enrichment analysis analysis of RNA-seq data for of 3 SPG7 patient and 3 controls.

first: Carolyn

last: Sue


title: Symmetric self-renewal and dormancy define functional fetal liver hematopoietic stem cells at single cell resolution

status: Public on May 24 2023

first: Brandon

last: Hadland

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Center

summary: Our study disclosed previously unrecognized heterogeneity in fetal liver (FL) hematopoietic stem cells (HSC), highlighting biosynthetic dormancy as a key to symmetric self-renewal of engraftable HSC and supports recent studies demonstrating distinct developmental origins for multipotent progenitors and HSC in definitive hematopoiesis.

overall_design: single cell RNA-sequencing (10X Genomics platform) of murine E12 FL-derived cultured endothelial cells expressing mAkt (FL-EC) used as stroma to support HSC developemnt/expansion ex vivo; and murine E13.5 FL-derived FACS-isolated VEcadherin-/low,CD45+,Gra1-F4/80-,Sca1+,EPCR+  cells enriched for HSCs (primary cells and progeny following co-culture with FL-EC). Sample 4 also included CD11b-ESAM expression in sorting.

first: Hadland

last: Brandon


title: Bulk and single cell sequencing of peripheral nervous system tumors in neurofibromatosis

status: Public on May 22 2023

city: San Francisco

first: Harish

last: Vasudevan

address: 1450 3rd street

institute: UCSF

summary: Peripheral nervous system tumors in neurofibromatosis

overall_design: Bulk and single cel RNA-sequencing of human tumors, patient derived cell lines, and mouse xenografts

last: Raleigh

first: Frank

last: McCormick


title: The single-cell atlas of the heart reveals an unexpected erythrocyte-like cardiomyocyte

status: Public on May 20 2023

city: Shanghai

first: junwei

last: shen

state: Shanghai

address: No.1239 Siping Road

institute: Tongji University

summary:
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) is widely used in cancer research and organ development since its powerful ability to analyze cellular heterogeneity. However, its application in cardiomyocytes is rare mainly because the cardiomyocytes are too large and fragile to withstand traditional single-cell approaches.
METHODS: Through designing the isolation procedure of neonatal mouse cardiac cells, we perform scRNA-seq with samples from 27 neonatal mice. Individual cell transcriptomes were subsequently clustered based on transcriptional profiles of highly variable genes. Then these clusters were used as the basis for between-cluster differential gene expression analyses and between-cluster interaction analyses. At last, we analyzed the intersection of these clusters with genetic and pharmacologic data.
RESULTS: We provide detailed cellular atlases of the heart at single-cell resolution across four different stages after birth. We have luckily obtained tens of thousands of cardiomyocytes, to our knowledge, the most extensive reference framework so far. Moreover, we have discovered unexpected erythrocytes-like cardiomyocyte-terminal cardiomyocytes, comprising more than a third of all the cardiomyocytes. Only a few genes are highly expressed in these cardiomyocytes. They are highly differentiated cardiomyocytes that function as contraction pump. In addition, we have identified two cardiomyocyte-like conducting cells, lending support to the theory that the sinoatrial node pacemaker cells are specialized cardiomyocytes. Furthermore, we provide a substantial blueprint for comprehensive interactions between cardiomyocytes and other cardiac cells. We linked specific cell types to adverse drug reactions and congenital heart diseases and analyzed the roles of cell subtypes in adverse drug reactions and cardiac diseases.
CONCLUSIONS: This mouse cardiac cell atlas improves our understanding of the heart and provides a valuable reference in response to varying physiological conditions and diseases.

overall_design: We collected ~50000 single cells from the entire hearts of neonatal C57BL/6 mice (Day1, Day2, Day4, and Day6 after birth) and performed single-cell RNA-seq sequencing.

first: Junwei

last: Shen

first: Linlin

last: Ma

first: Jing

last: Hu

first: Yanfei

last: Li


title: Peripheral nervous system tumors in neurofibromatosis

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