title: A circulating risk score, based on combination of exo-miR130a-3p and fibrinopeptide A, as predictive biomarker of relapse in early stage non-small cell lung cancer patients [Nanostring]

first: simona

last: coco

summary: To date, the 5-year overall survival of early stage non-small cell lung cancer (NSCLC) is still unsatisfactory at 59.8%. Therefore, reliable prognostic factors are needed. Growing evidence shows that cancer progression may depend on a double interconnection between cancer cells and the surrounding tumor microenvironment, and circulating molecules may represent promising markers of cancer recurrence. Here, we performed in-depth analysis of circolome-derived markers, including Exo-miRnome and peptidome in 67 radically resected NSCLCs, to identify a prognostic score. The miRnome profile selected exo-miR130a-3p as the most overexpressed in patients with relapse. Peptidome analysis identified 4 fibrinopeptide A (fpA), which were depleted in progressing patients. Notably, the combination of exo-miR130a-3p and the greatest fpA (2-16) built a score where high-risk patients had 24 months of disease-free survival. Moreover, in vitro transfections showed that higher levels of exo-miR-130a-3p lead to a deregulation of some pathways involved in metastasis, in angiogenesis, such as in coagulation which could be linked to the FpA reduction. In conclusion, the identified risk score integrating circulating markers can help clinicians predict early-stage NSCLC patients who are more likely to relapse after initial surgery.

overall_design:
A549 cells treated with miR130a-3p or miR17-5p.
A total of 67 resected NSCLC samples were analyzed to define a miRNA signature capable to predict patients who experience progression of the disease (PD).

first: Simona

last: Coco

first: Giuseppa

last: De Luca

first: Mariella

last: Dono

first: Michela

last: Croce

first: Silvia

last: Marconi

first: Angela

last: Alama


title: Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids

status: Public on Apr 30 2022

city: Utrecht

first: Maria

last: Alieva

state: Netherlands

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

type: Expression profiling by high throughput sequencing

summary: Cellular immunotherapies are rapidly gaining clinical importance, yet predictive platforms for modeling their mode of action are lacking. Here, we unravel the behavioral and underlying molecular mechanisms that govern breast cancer targeting by an emerging cancer metabolome-sensing immunotherapy:  T cells engineered to express a V9/V2 T cell receptor (TEGs). Using a dynamic immuno-organoid 3D imaging-transcriptomics platform, BEHAV3D, we first demonstrate that TEGs kill organoids of multiple breast cancer subtypes, yet with varying sensitivity between individual patient-derived organoids (PDOs) and even among individual PDOs derived from the same patient. Furthermore, live-tracking of over 120,000 TEGs revealed a diverse behavioral landscape and identified a ‘super-engager’ cluster with serial killing capability. Inference of single-cell behavior with transcriptomics unraveled gene signatures linked to specific behaviors. The most notable gene signature identified ‘super engager’ killer TEGs and contained multiple genes previously unstudied in T cells. Furthermore, guided by a dynamic type 1 interferon (IFN-I) signaling module specifically induced by the highest TEG-sensitive organoid culture, we show that IFN-I can prime resistant organoids for¬ TEG-mediated killing. Thus, BEHAV3D characterizes behavioral-phenotypic heterogeneity of cellular immunotherapies and holds promise for improving solid tumor-targeting in a patient-specific manner.

overall_design: Patient derived breast cancer organoids, that are known to have different responsiveness to the same engeneered T cells (TEGs) (Inez Johanna  et al 2019, J Immunother Cancer) were subjected to RNA seq. TEGs were isolated at different stages of targeting from the co-culture with 2 types of breast cancer organoids and subjected to scRNAseq.

first: Johanna

middle: F

last: Dekkers

first: Astrid

last: Cleven

first: Farid

last: Keramati

first: Peter

last: Brazda

first: Heggert

middle: G

last: Rebel

first: Amber

middle: K

last: Wezenaar

first: Maj-Britt

last: Buchholz

first: Mario

last: Barrera Román

first: Inez

last: Johanna

first: Angelo

middle: D

last: Meringa

first: Domenico

last: Fasci

first: Maarten

middle: H

last: Geurts

first: Hendrikus

middle: C

last: Ariese

first: Esmée

middle: J

last: van Vliet

first: Ravian

middle: L

last: van Ineveld

first: Effrosyni

last: Karaiskaki

first: Oded

last: Kopper

first: Yotam

middle: E

last: Bar-Ephraim

first: Kai

last: Kretzschmar

first: Ellen

last: Wehrens

first: Henk

last: Stunnenberg

first: Hans

last: Clevers

first: Jürgen

last: Kuball

first: Zsolt

last: Sebestyen

first: Anne

last: Rios

first: Sam

last: de Blank

first: Annelisa

middle: M

last: Cornel

first: Else

last: Driehuis

first: Rosemary

last: Millen

first: Trudy

last: Straetemans

first: Mara

last: Nicolasen

first: Tineke

last: Aarts-Riemens

first: Hannah

middle: R

last: Johnson

first: Stefan

last: Nierkens

first: Alexander

last: Eggermont


title: Age-related demyelination and neurodegeneration susceptibility associates with meningeal neutrophil accumulation in a murine model of multiple sclerosis

status: Public on Apr 29 2022

city: Toronto

first: Michelle

last: Zuo

state: ON

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

summary: People living with multiple sclerosis (MS) experience episodic central nervous system (CNS) white matter lesions instigated by autoreactive T cells. With age, MS patients show evidence of grey matter demyelination and experience devastating non-remitting symptomology. What drives progression is unclear and has been hampered by the lack of suitable animal models. Here we show that passive experimental autoimmune encephalomyelitis (EAE) induced by an adoptive transfer of young Th17 cells induces a non-remitting clinical phenotype that is associated with persistent leptomeningeal inflammation and cortical pathology in old, but not young SJL/J mice.  While the quantity and quality of T cells did not differ in the brains of old vs young EAE mice, an increase in neutrophils and a decrease in B cells was observed in the brains of old mice.  Neutrophils were also found in the leptomeninges of a subset of progressive MS patient brains that showed evidence of leptomeningeal inflammation and subpial cortical demyelination. Taken together, our data show that while Th17 cells initiate CNS inflammation, subsequent clinical symptoms and grey matter pathology are dictated by age and associated with other immune cells such as neutrophils.

overall_design:
We performed scRNAseq (CITE-seq) to understand transcriptional states of immune cells in the meninges of young and old SJL/J mice at D11 post induction of EAE.
Naïve SJL/J Young mouse: TotalSeq B Hashtag 1    ACCCACCAGTAAGAC
Naïve SJL/J Old mouse: TotalSeq B Hashtag 2    GGTCGAGAGCATTCA
EAE SJL/J Young mouse: TotalSeq B Hashtag 3    CTTGCCGCATGTCAT
EAE SJL/J Old mouse: TotalSeq B Hashtag 4    AAAGCATTCTTCACG
All mice: Anti-PE barcode TGACCAGTTCCGCAT

first: Naomi

last: Fettig

first: Valeria

last: Ramaglia

first: Jennifer

last: Gommerman


title: Transcriptome diversity in human medullary thymic epithelial cells - RNAseq

city: Cold Spring Harbor

middle: Verena

last: Meyer

state: New York

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

summary: The induction of central T-cell tolerance in the thymus depends on the  presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs), enabled by a process known as promiscuous gene expression (pGE). Transcriptome diversity generated during pGE has many contributors, including non-canonical transcription initiation, alternative splicing and expression of endogenous retroelements (EREs). However, their significance and regulation are poorly understood in the healthy human thymus. Here, we mapped the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5'Cap and RNA sequencing. Overall, 96\% of protein coding genes were represented across five human mTEC samples, with mature mTECs showing increased rates of global transcript mis-initiation. Both mTEC populations have increased splicing entropy, which appears to be driven by expression of peripheral splicing factors. Furthermore, EREs enriched in long terminal repeat retrotransposons are up-regulated during mTEC maturation and enriched in genomic proximity to differentially expressed genes. We provide an interactive interface to explore the transcriptome diversity we uncovered at http://transcriptomediversity.cshl.edu/. Our findings represent an important first step towards the generation of a comprehensive map of transcriptome diversity in the healthy human thymus. Ultimately, a complete map of thymic expression diversity will allow for the identification of epitopes that contribute to the pathogenesis of auto-immunity and that drive immune recognition of tumor antigens.

overall_design: Gene expression profiling analysis of RNA-seq data for human mature (MHCII high) and immature (MHCII) medullary thymic epithelial cells

middle: V

first: Jason

middle: A

last: Carter


title: The role of endogenous Smad7 in regulating macrophage phenotype following myocardial infarction [JunLi_MyS7KOinvitro]

city: Bronx

first: Silvia

last: Hernandez

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

summary: Induction of the inhibitory Smad, Smad7 serves as a negative feedback mechanism that restrains TGF-b-mediated actions in injured tissues. In inflammatory cells, Smad7 has been suggested to exert both pro-inflammatory actions attributed to inhibition of TGF-b-induced suppression of inflammation, and anti-inflammatory effects due to disruption of the TAK-1/NF-kB system. Myocardial infarction triggers a macrophage-driven inflammatory response that plays a central role in cardiac repair, but also contributes to adverse remodeling and fibrosis. We hypothesized that Smad7 upregulation in infarct macrophages may play a modulatory role in cardiac repair, by restraining effects of TGF-b. To test the hypothesis, we investigated the response of Myeloid cell-specific Smad7 knockout mice (MyS7KO) following myocardial infarction protocols, and we examined the in vitro effects of Smad7 in isolated macrophages. Smad7 was upregulated in a subset of infarct macrophages, peaking 7 days after infarction. Myeloid cell-specific Smad7 loss did not affect baseline macrophage gene expression and had no significant effects on homeostatic functions. Although RNA-seq analysis predicted that, in the absence of Smad7, infarct macrophages may have attenuated activation of inflammatory pathways and suppressed TREM1 signaling, myeloid cell-specific Smad7 loss had no significant effects on ventricular dysfunction, adverse remodeling, scar remodeling and collagen deposition after myocardial infarction. In isolated macrophages, TGF-b attenuated pro-inflammatory cytokine and chemokine expression, modulated synthesis of matrix remodeling genes, and had profound effects on macrophage profile, inducing genes associated with activation of sphingosine-1 phosphate and integrin signaling pathways, and inhibiting cholesterol biosynthesis genes. However, RNA-seq and PCR array experiments showed that Smad7 loss has minimal effects on TGF-b-mediated macrophage responses, restraining synthesis of only a small fraction of TGF-b-induced genes, such as Itga5, Olfml3 and Fabp7. Smad7 absence did not affect the anti-inflammatory actions of TGF-b in TNF-stimulated cells. In conclusion, our findings suggest a limited role for macrophage Smad7 in regulation of post-infarction inflammation and repair, and demonstrate that the anti-inflammatory effects of TGF-b in macrophages are not restrained by endogenous Smad7 induction.

overall_design:
In order to study the role of Smad7 in myeloid cells in vitro, we generated mice with inducible global loss of Smad7 (S7KO). We used a transgenic mouse line in which Cre recombinase is driven by CAGG promoter (Jackson Laboratory, stock No: 004682). CAGGCre-ER mice were bred with Smad7fl/fl mice (Jackson Laboratory, stock No: 017008) to generate CAGGCre-ER;Smad7fl/fl animals (S7KO) and corresponding Smad7fl/fl control littermates. For the experiment, both, control mice (Smad7 fl/fl) and global inducible S7KO mice (CAGGCre-ER;Smad7fl/fl), were injected with tamoxifen (20 mg/kg). Tamoxifen was administered intraperitoneally once for 5 consecutive days to 1 month old mice. Mice were sacrificed 2 weeks after tamoxifen injection and Bone marrow macrophages were isolated and culture in the presence or absence of 10ng/ml TGF- β1. The loss of Smad7 in S7KO macrophages has been documented by qPCR and western blot.
>>> Raw data are no longer available. <<<

first: Jun

last: Li

first: Ruoshui

first: Izabela

last: Tuleta

first: Claudio

last: Humeres

first: Anis

last: Hanna

first: Bijun

last: Chen

first: Nikolaos

last: Frangogiannis


title: N1-methyladenosine modification in mitochondrial tRNAs is associated with Alzheimer’s disease

city: Atlanta

first: Andrew

last: Shafik

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: Here we used the newly developed m1A-quant-seq appraoch to map m1A modification transcriptome wide on the cortex of 6 month old BL6 mice and 5XFAD mice (Alzheimer's mouse model).

overall_design: RNA was extracted from the cortex in biologcial triplicates. m1A-quant-seq was performed as described in Zhou et al., 2019. Nat Methods.

first: Peng

last: Jin


title: Multi-Dimensional Profiling Reveals a Molecularly Distinct Injury-Responsive Population of Regulatory T Cells [scRNA-seq]

status: Public on May 01 2022

city: Boston

first: James

last: Lederer

state: MA

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

summary: CD4+ regulatory T cells (Tregs) activate and expand in response to many different types of injuries, suggesting that they play a critical role in controlling the host response to tissue damage. Here we use multi-dimensional profiling techniques to comprehensively characterize injury responsive Tregs in mice.  CD44high Tregs expand in response to injury and are more suppressive than CD44low Tregs. T cell receptor (TCR) analysis reveal that CD44high Tregs undergo TCRαβ clonal expansion and increased CDR3 diversity in response to injury. Bulk and single-cell RNA sequencing with paired TCR clonotype analysis demonstrate that important Treg-associated genes were significantly differentially expressed in both CD44high and CD44low Tregs with expanded TCR clonotypes. CyTOF analysis verified protein expression of these genes on CD44high Tregs, with increases in Helios, Galectin-3 and PYCARD expression following injury. Collectively, these data provide new insights into CD44high Tregs, an important subset in the response to injury to tissue damage.

overall_design: FACS sorted viable lymph node FoxP3 GFP+ cells from Foxp3DTR mice, uninjured or at 7 days after injury

first: Fei

last: Guo


title: An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]

city: Cambridge

first: Yrjö

last: Helariutta

address: 47 Bateman Street,

department: Sainsbury Laboratory

country: United Kingdom

institute: University of Cambridge

summary: Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome by sorting cells with specific markers, to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

overall_design: RNA-sequencing of root meristems comparing wild type and double mutant papl1-1papl2 (aka cog1-6cdf4)

first: Sofia

last: Otero

first: Iris

last: Sevilem

first: Pawel

last: Roszak

first: Lu

last: Yipeng

first: Valerio

last: Di Vittori

first: Matthieu

last: Bourdon

first: Lothar

last: Kalmbach

first: Bernhard

last: Blob

first: Jung-ok

last: Heo

first: Federico

last: Peruzzo

first: Thomas

last: Laux

first: Alisdair

last: Fernie

first: Hugo

last: Tavares


title: An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

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

overall_design: Refer to individual Series


title: RNA-seq data of esophageal cancer cell Kyse510 after inhibition or silencing of LSD1 and G9a

city: Hangzhou

first: Hongxiao

last: wang

state: zhejiang

address: kaixuan road

country: China

institute: Zhejiang University

summary: The goals of this study are to compare transcriptome profiling (mRNA level) and signaling pathways between the control and ablating LSD1, the control and ablating G9a, the control and co-ablating LSD1 and G9a. We found pathways in apoptosis, endoplasmic reticulum stress and unfolded protein response were obviously changed in these groups, which are important for esophageal cancer therapy.

overall_design: For inhibition of LSD1 and G9a, Kyse510 esophageal cancer cells were treated with vehicle, 7uM SP2509, 7uM UNC0642 and the combination for 2 days, then whole RNA was extracted and RNA-seq analysis was performed. For silencing of LSD1/G9a, Kyse510 esophageal cancer cells were transfected with sh-LSD1 or sh-G9a and screened 14 days for stable clones through puromycin. Then doxycycline was used to silence LSD1 and G9a for 2 days, then whole RNA was extracted and RNA-seq analysis was performed.

last: Wang

first: Fudi

first: Junxia

last: Min


title: Gene expression (GeneChip) data from scramble- and CRMP2A siRNA-treated A549 cells.

city: Edmonton

first: Evangelos

middle: D.

last: Michelakis

state: Alberta

department: Medicine

institute: University of Alberta

summary:
We sought to assess how temporary loss of the microtubule-associated protein CRMP2A could affect global gene expression in the A549 lung cancer cells.
We used microarrays to identify differentially regulated genes when CRMP2A is temporarily removed from A549 cells using siRNA.

overall_design: Scramble-treated and CRMP2A siRNA-treated A549 cells were cultured under identical conditions for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare the gene expression profiles between the two cell lines and correlate it with other in vitro and in vivo findings.

first: Aristeidis

last: Boukouris


title: Fate mapping reveals two pathways of native thrombopoiesis (bulk RNA sequencing)

status: Public on Apr 28 2022

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

country: Germany

institute: Medical Faculty TU Dresden

summary: Bulk transcriptomes of Megakaryocyte progenitor cells  isolated from bone marrow of WT mice; the following cell types were sorted:  CD48high Megakaryocyte Progenitor (MkP): lineage- Sca-1- c-kit+ CD41+ CD150+ CD48hi; CD48-/low Megakaryocyte Progenitor (MkP): lineage- Sca-1- c-kit+ CD41+ CD150+ CD48lo

overall_design: 4000-20000 CD48hi (n=4) or CD48-/lo (n=3) MkP from WT mice were sorted and subjected to bulk transcriptome analysis.


title: Fate mapping reveals two pathways of native thrombopoiesis (scRNA sequencing)

summary: Transcriptomes of 1141 single cells isolated from bone marrow of induced R26rtTA/rtTA/Col1A1H2B-GFP/H2B-GFP mice; the following cell types were sorted: Megakaryocyte Progenitor (MkP): lineage- Sca-1- c-kit+ CD41+ CD150+; Multipotent Progenitor (MPP): lineage- Sca-1+ c-kit+ CD48- CD150- ; Hematopoietic Stem Cell (HSC):lineage- Sca-1+ c-kit+ CD48- CD150+; E34 HSC: lineage- Sca-1+ c-kit+ CD48- CD150+ CD201hi CD34-/lo; Restricted hematopoietic progenitor 1 (HPC-1): lineage- Sca-1+ c-kit+ CD48+ CD150-; lineage- kit+ CD41- CD150- cells; lineage- kit+ CD150+ cells.

overall_design: Single hematopoietic stem and progenitor cells were isolated from R26rtTA/rtTA/Col1A1H2B-GFP/H2B-GFP mice (n=6); all mice were induced with doxycycline for 35 days and followed by 75 days of chase prior to analysis.


title: Differential effects of Smad2 and Smad3 in regulation of macrophage phenotype and function in the infarcted myocardium

first: Silvia

last: Hernandez

summary: TGF-βs regulate macrophage responses, by activating Smad2/3. We have previously demonstrated that macrophage-specific Smad3 stimulates phagocytosis and mediates anti-inflammatory macrophage transition in the infarcted heart. However, the role of macrophage Smad2 signaling in myocardial infarction remains unknown. We studied the role of macrophage-specific Smad2 signaling in the healing infarct, and we explored the basis for the distinct effects of Smad2 and Smad3. Infarct macrophages exhibited both Smad2 and Smad3 activation. In contrast to the effects of Smad3 loss, myeloid cell-specific Smad2 disruption had no effects on mortality, ventricular dysfunction and adverse remodeling, after myocardial infarction. Phagocytic removal of dead cells, macrophage and myofibroblast infiltration, collagen deposition, angiogenesis and scar remodeling were not affected by macrophage Smad2 loss. In isolated macrophages, TGF-β1, -β2 and -β3, activated both Smad2 and Smad3, whereas BMP6 triggered only Smad3 activation. Smad2 and Smad3 had similar patterns of nuclear translocation in response to TGF-β1. Smad3, and not Smad2, was the main mediator of transcriptional effects of TGF-β on macrophages and Smad3 loss resulted in enrichment of genes associated with RAR/RXR signaling, cholesterol biosynthesis and lipid metabolism. In conclusion, the in vivo and in vitro effects of TGF-β on macrophage function involve Smad3, and not Smad2.

overall_design: This study is designed to compare gene expression profiles between Smad2fl/fl and MyS2KO (Smad2fl/fl + LyzMCre), and Smad3fl/fl and MyS3KO (Smad3fl/fl + LyzMCre) bone marrow derived macrophages in the presence or absence of 10 ng/ml TGF-β1. The loss of Smad2 and Smad3 in MyS2KO, MyS3KO macrophages has been documented by qPCR and western blot.

first: Bijun

last: Chen

first: Ruoshui

last: Li

first: Anis

last: Hanna

first: Kai

last: Su

first: Arti

last: Shinde

first: Nikolaus

last: Frangogiannis


title: MPST sulfurtransferase maintains mitochondrial protein import and cellular bioenergetics to attenuate obesity

status: Public on Apr 26 2022

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

summary: To gain insight into the biological processes altered by Mpst deletion, RNA-sequencing  was performed using inguinal fat from WT and Mpst-/- mice maintained on high fat diet (HFD).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for inguinal adipode tissue of WT HFD and Mpst knockout HFD mice

first: Antonia

last: Katsouda

middle: S


title: Transcriptomic responses to phosphate limitation in maize lines with different breeding history

status: Public on Apr 23 2022

city: Montpellier

first: Christophe

last: Maurel

address: 2 place Pierre Viala

department: Water, signaling and hydraulic architecture

country: France

institute: Institute for Plant Sciences of Montpellier (IPSiM)

summary: Plants cope with low phosphorus availability by adjusting growth and metabolism through transcriptomic adaptations. We hypothesize that selected genotypes with distinct P use efficiency covering the breeding history of European heterotic pool allow us to reveal general and genotype-specific molecular responses correlated with low phosphate induced traits.

overall_design:
Nine pre-selected genotypes were cultured under high P and low P conditions. 3 replicates of roots samples were sequenced in each genotype and P treatment. Comparative gene expression profiling analysis of RNA-seq data for each genotype between high P and low P treatments.
Pleaese note that the records have been updated with additional samples on May 4, 2022.

first: Xuelian

first: Melissa

last: Mang

first: Uwe

last: Ludewig


title: m7G-MeRIP-sequencing of mRNA in drug-resistant acute myeloid leukemia

city: jinan

first: bing

last: zhang

address: 107 Wenhua Xilu

institute: Qilu Hospital of Shandong University

type: Methylation profiling by high throughput sequencing

summary: m7G-MeRIP-sequencing for AML cells(HL-60) and drug-resistant AML Cells(HL60/MX2).

overall_design: Compare the transcriptom profiling  of m7G methylation modification in AML cells(HL-60) and drug-resistant AML Cells(HL60/MX2).

first: Bing

last: Zhang

first: Dong

first: Ran

last: Wang


title: Transcriptomic analysis of lipid biosynthesis pathways for HBV cure

status: Public on Apr 22 2022

city: Foster City

first: Ricardo

last: Ramirez

state: CA

address: 333 Lakeside Drive

institute: Gilead Sciences

summary: RNAseq analysis of liver tissue samples from uninfected (n=5) and HBV-infected (n=5) humanized chimeric liver (uPA/SCID) mice was performed to identify potential new host factors and pathways modulated by HBV infection

overall_design: Human liver-chimeric uPA/SCID mice were generated by PhoenixBio Co., Ltd. (Higashi-Hiroshima, Japan). Human hepatocytes were derived from donor BD195 (BD Biosciences, Woburn, MA). Mice containing human hepatocytes with a mean estimated replacement index of 86% (range 83-90%), calculated based on the blood concentration of human albumin [h-Alb]), were infected with 1x105 copies/mouse of HBV genotype C and followed for eight weeks to establish persistent infection of the human hepatocytes in the chimeric liver. At baseline (day 0 post-infection), mean body weights across all randomized mice were 18.0 g (19.0 - 21.1 g) with average serum levels of h-Alb of 10.0 mg/mL (9.2 - 11.9 mg/mL). Throughout the infection, all mice maintained a body weight of more than 90% of the initial level (HBV-inoculated group ranged from 90% (17.6 g) to 110% (21.6 g) to that in the control group) and an average blood h-Alb concentration of more than 10 mg/mL (HBV-inoculated group ranged from 90% (9.7 mg/mL) to 110% (11.9 mg/mL) to that in the control group).

first: Anastasia

last: Hyrina

first: Dara

last: Burdette

first: Meghan

last: Holdorf


title: Genes regulated by Yki play roles in the cell cycle, cell migration and cell adhesion in Drosophila

first: Yue

last: Li

state: Zhejiang

address: The College of Medicine Keyan C-161, Zijingang Campus, Zhejiang University, Yuhangtang Rd. 866

department: School of medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In order to investigate the underlying molecular mechanism of Yki-regulated tracheal progenitor migration and proliferation, genomic chromatin immunoprecipitation (ChIP-seq) was performed to identify loci bound by Yki in trachea.The peaks we observed included multiple Yki binding sites in the promoter and intronic regions of expanded (ex) and Diap1, which are well-characterized direct target genes of Yki. Other Yki targets are regulators in cell migration, cell cycle, and cell adhesion, and include hnt, which is a regulator of cell cycle in follicle cells.Yki occupancy was also pronounced in the promoter region of two heparan sulfate proteoglycans (HSPGs), Dally and Dally-like protein (Dlp) , which together with Ex and Diap1 belong to the cell migration GO cluster. Significant ChIP-seq peaks were observed in the region of N-cadherin (Ncad), a cell adhesion molecule that promotes cell migration and Matrix metalloproteinase-1 (MMP-1), a component of the extracellular matrix. Together, these results suggest that Yki activates various targets that function in cell cycle, cell migration and cell adhesion.

overall_design: Identify the targets of Yki using ChIP-seq in the white pupae of Drosophila

first: Pengzhen

last: Dong

first: Tianyu

last: Guo

first: Hai

last: Huang


title: Porphyromonas gingivalis tyrosine kinase is a fitness determinant in polymicrobial infections

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

summary: Tn-Seq was used to identify P. gingivalis genes that confer fitness during cooperative growth with S. gordonii or F. nucleatum in a murine abscess model.

overall_design: After generating a saturating Porphyromonas gingivalis transposon library using Mariner-based transposon mutagenesis, this library was inoculated either alone (Pg) or in conjunction with Streptococuus gordonii (Sg) or with Fusobacterium nucleatum (Fn) subcutaneously into BALB/cJ mice. Bacteria recovered from developed abscesses were cultured in vitro for two passages and genomic DNA was isolated. Genomic DNA was also isolated from the P. gingivalis transposon library (Input) and was not used to infect mice and used as a control.

first: John

last: Perpich

first: Lan

last: Yakoumatos

first: Kendall

last: Stocke


title: An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [10x scRNA-seq]

first: Yrjö

last: Helariutta

overall_design: Single-cell sequencing (10x Chromium) of FACS-sorted cells using fluorescent reporters expressed in the protophloem and metaphloem sieve elements, companion cells and phloem pole pericycle of Arabidopsis roots.

first: Sofia

last: Otero

first: Iris

last: Sevilem

first: Pawel

last: Roszak

first: Lu

last: Yipeng

first: Valerio

last: Di Vittori

first: Matthieu

last: Bourdon

first: Lothar

last: Kalmbach

first: Bernhard

last: Blob

first: Jung-ok

last: Heo

first: Federico

last: Peruzzo

first: Thomas

last: Laux

first: Alisdair

last: Fernie

first: Hugo

last: Tavares


title: Single-cell response to LPS of wild-type and cohesin-deficient macrophages.

status: Public on Apr 17 2022

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Transcription is an intermittent process that occurs in bursts. The frequency and the number of messenger RNA (mRNA) produced by these bursts determine expression levels and shape cell-to-cell variability. Productive encounters between enhancers and promoters control burst dynamics, which the cohesin complex can facilitate through loop extrusion. Cohesin is a ring-shaped complex involved in enhancer-promoter interactions. Without cohesin, bone-marrow-derived macrophages' transcriptional response to LPS is severely impaired (Cuartero et al., 2018). Single-cell RNA sequencing (scRNAseq) showed that the frequency of cells expressing inducible transcripts (as defined in Bhatt et al., 2012) was reduced in cohesion-deficient macrophages before and after LPS stimulation.  In contrast, when considering only cells expressing LPS-inducible transcripts, cohesin-deficient macrophages showed reduced mean expression at baseline and late LPS-response (8h) but not in the early response (2h). These results support a model where cohesin is implicated in the control of burst frequencies upon LPS.

overall_design: scRNAseq data of untreated and LPS-stimulated WT and Rad21-/- primary mouse macrophages.

first: Sergi

last: Cuartero

first: Gustavo

last: Rodríguez

first: Elisabetta

last: Mereu


title: Integrated Genomics Approaches Identify Mediators of Transcriptional and Epigenetic Responses to Afghan Desert Particulate Matter in Small Airway Epithelial Cells (ATAC-Seq)

status: Public on Apr 27 2022

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

institute: National Jewish Health

summary: New respiratory diseases in personnel deployed to Southwest Asia after September 11th raise major concerns about the impacts of airborne particulate matter. Although regulations exist, the knowledge about how particulates influence disease states is limited, precluding the appropriate recognition, prevention and treatment of deployment-related lung diseases. We applied two genomics assays, Precision Run-on sequencing (PRO-seq) and the assay for transposase accessible chromatin with sequencing (ATAC-seq), to characterize the small airway epithelial cell response to Afghan desert particulate matter (APM).

overall_design: The Omni method for the Assay for transposase-accessible chromatin by sequencing (Omni-ATAC-seq) was performed in primary small airway epithelial cells exposed to Afghan desert particulate matter at 50 ug/cm2 or WSP at 1 mg/ml for 20 hours. All samples were sequenced in duplicate.

first: Sarah

last: Sasse

first: Reena

last: Berman

first: Margaret

last: Gruca

first: Robin

last: Dowell

first: Hong

middle: W

last: Chu

first: Gregory

middle: P

last: Downey

first: Anthony

middle: N

last: Gerber


title: Integrated Genomics Approaches Identify Mediators of Transcriptional and Epigenetic Responses to Afghan Desert Particulate Matter in Small Airway Epithelial Cells (PRO-Seq)

overall_design: Deep sequencing of nascent transcripts was performed using Precision Run-on sequencing (PRO-seq) in small airway epithelial cells following exposure to Afghan Desert Particulate matter. All samples were sequenced in duplicate.

middle: K


title: Cancer-Selective Mechanistic Targets of Diallyl Trisulfide (DATS) in Human Breast Cancer Cells Identified by RNA-seq Analysis

status: Public on Apr 20 2022

city: Pittsburgh

first: Shivendra

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: We report differentially expressed genes by DATS exposure in MCF-10A human epithelial cell line and SK-BR-3 human breast cancer cell line

overall_design: Examination of DATS-regulated transcriptome in MCF-10A and SK-BR-3 cells


title: TNFR2 is critical for TNF-induced rheumatoid arthritis fibroblast-like synoviocyte inflammation

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna

summary:
Objectives: TNF-induced activation of fibroblast-like synoviocytes (FLS) is a critical determinant for synovial inflammation and joint destruction in rheumatoid arthritis (RA). The detrimental role of TNF-receptor 1 (TNFR1) has thoroughly been characterized. The contributions of TNFR2, however, are largely unknown. This study was performed to delineate the role of TNFR2 in human FLS activation.
Methods: TNFR2 expression in synovial tissue samples was determined by immunohistochemistry. Expression of TNFR2 was silenced using RNAi or CRISPR/Cas9 technologies. Global transcriptional changes were determined by RNA-seq. QPCR, ELISA and immunoblotting were used to validate RNA-seq results and to uncover pathways operating downstream of TNFR2 in FLS.
Results. TNFR2 expression was increased in RA when compared to OA synovial tissues. In particular, RA-FLS demonstrated higher levels of TNFR2 when compared to OA-FLS. TNFR2 expression in RA-FLS correlated with RA disease activity, synovial T- and B-cell infiltration. TNF and IL1 were identified as inflammatory mediators that upregulate TNFR2 in RA-FLS. Silencing of TNFR2 in RA-FLS markedly diminished the TNF-induced expression of inflammatory cytokines and chemokines, including CXCR3-binding chemokines and the B-cell activating factor TNFSF13B. Immunobiochemical analyses revealed that TNFR2-mediated expression of inflammatory mediators critically depends on STAT1.
Conclusion: Our results define a critical role for TNFR2 in FLS-driven inflammation and unfold its participation in the unresolved course of synovial inflammation in RA.

overall_design: Examining the effect of TNFR2 knockdown on gene expression in TNF-stimulated fibroblast-like synoviocytes (FLS)

last: Karonitsch


title: Molecular landscape of immature neurons in the human hippocampus across the lifespan

status: Public on Apr 19 2022

city: Philadelphia

first: Yijing

last: Su

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

summary: Immature neurons arising from adult neurogenesis contribute to plasticity and unique functionsinthe adult mammalian brain. Whether immature dentate granule cells (imGCs) exist in the adult human hippocampusis under debate. Herewe performedsingle-nucleus transcriptomicanalysis aided by a validated machinelearning approach to quantify the abundance of imGCs in the 5postnatal human hippocampus and to investigate their molecular properties. We show the sustained presence of human imGCs through prenatal, infant, child, adolescent, adult,andaging stages andreveal their shared and differentmolecular characteristicsacross agesandspecies. Furthermore, we directly demonstrate the capacity for neurogenesis in the postnatal human hippocampus using surgical specimensin culture. Together, these resultsprovide novel insights10into molecular propertiesof imGCs in humans across the lifespan.

overall_design: single nucleus RNA-seq on human hippocampus


title: Integrated Genomics Approaches Identify Mediators of Transcriptional and Epigenetic Responses to Afghan Desert Particulate Matter in Small Airway Epithelial Cells

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

overall_design: Refer to individual Series


title: Skeletal muscle unloading affects muscle progenitor cells functional activity

status: Public on Apr 25 2022

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

summary: In this work we employed classic skeletal muscle unloading rat model to determine how hindlimb suspension (HS) affects functional activity of skeletal muscle progenitor cells (SMPC).  We have purified SMPC from m. soleus from control rats and after 1, 3, 7 and 14 days of exposure (HS1, HS3, HS7, HS14).

overall_design:
Libraries were prepared with TruSeq Stranded mRNA kit, samples were RNA-sequenced on Illumina NextSeq 2000, read length 51 bp.
Project was supported by RSF grant №20-75-10080.

middle: Y

last: Komarova

first: Oksana

last: Ivanova

first: Renata

middle: I

last: Dmitrieva

first: Boris

last: Shenkman

first: Natalia

last: Vilchinskaya


title: M1 macrophages induce an inflammatory phenotype in melanoma cells via TNFR-NF-κB signaling

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: Tumor microenvironment with distinctive cell types and a complex extracellular matrix has a tremendous effect on cancer progression. In the present study we investigated the effects of proinflammatory (M1) and immunosuppressive (M2) macrophages on melanoma cell hyaluronan (HA) metabolism and inflammatory response. M1 macrophages stimulated the formation of a thick pericellular HA matrix in melanoma cells, and the overall HA synthesis was increased due to upregulation of HA synthases (HAS) 1 and 2. HAS2 silencing reversed the effect of M1 CM (conditioned medium) on pericellular HA coat formation, similarly as the chemical inhibitors for TNFR (R-7050), IKK2 (IKK16) and MEK (U0126). RNA sequencing analysis indicated that several inflammation related genes (IL1, IL6, CXCL6) were highly upregulated in M1 CM treated melanoma cells. Gene set enrichment analysis identified that genes related to inflammatory response and TNFα signaling via NF-κB are enriched in M1 CM treated cells. Our results indicate that the activation of MEK and TNFR-NF-κB signaling leads to HAS2 upregulation, while MEK signaling pathway is not involved in cytokine upregulation. Furthermore, HAS2 silencing downmodulated the M1 CM-induced cytokine expression. Our results indicate that proinflammatory macrophages induce an inflammatory response in melanoma cells, where HAS2 upregulation associates with a protumor inflammatory gene signature.

overall_design: MV3 human melanoma cells were exposed to three types of conditioned RMPI media from THP-1 monocyte cell line: THP-1 cells differentiated to M0 macrophages using PMA (M0) that were thereafter polarized to either M1 macrophages using LPS and IFNγ (M1) or M2 macrophages using IL4 and IL13 (M2). Fresh, unconditioned RMPI medium served as a control. Total RNA was extracted from the cells and subjected to RNA-seq (N=3 per group). The main statistical analysis focused on identifying differences in gene expression between the M0, M1 and M2 groups.

first: Sanna

last: Pasonen-Seppänen

first: Kirsi

last: Kainulainen


title: Global evolution of the tumor microenvironment associated with progression from preinvasive/minimally invasive to invasive human lung adenocarcinoma

status: Public on Apr 10 2022

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

summary: To investigate changes in the tumor microenvironment (TME) during lung cancer progression, we interrogate tumors from two computer tomography (CT) defined groups. Pure non-solid (pNS) CT density nodules contain preinvasive/minimally invasive cancers and solid density nodules invasive cancers. Profiling data reveal a dynamic interaction between the tumor and its TME throughout progression. Alterations in genes regulating the extracellular matrix and genes regulating fibroblasts are central at the preinvasive state.  T cell-mediated immune suppression is initiated in preinvasive nodules and sustained with rising intensity through progression to invasive tumors. Reduced T cell infiltration of the cancer cell nests is more frequently associated with preinvasive cancers, possibly until tumor evolution leads to a durable, viable invasive phenotype accompanied by more varied and robust immune suppression. Upregulation of immune checkpoints occurs only in the invasive nodules. Throughout progression an effector immune response is present but is effectively thwarted by the immune-suppressive elements.

overall_design: Normal lung, pure non-solid CT scan density adenocarcinoma nodules and solid density nodules were profiles by RNAseq to reveal transcriptome differences associated with progression from normal lung to preinvasive/minimally invasive to invasive lung cancer.

first: Nasser

last: Altorki

first: Alain

middle: C

last: Borczuk

first: Bhavneet

last: Bhinder

first: Sebron

last: Harrison

first: Lauren

last: Groner

first: Vivek

last: Mittal

first: Timothy

last: McGraw


title: Isolevuglandins disrupt PU.1 mediated C1q expression and promote autoimmunity and hypertension in systemic lupus erythematosus

status: Public on Apr 13 2022

city: Nashville

first: David

last: Patrick

state: TN

address: 2213 Garland Avenue

institute: Vanderbilt University Medical Center

summary:
To determine the gene expression of profile of dendritic cells (DCs) from lupus prone mice we sorted CD11c+ cells from 4 7 week old female C57Bl/6 mice and 4 7 week old B6.SLE123 mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq from DCs of these 8 animals.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DCs from 7 week old female C57BL/6 mice vs B6.SLE123 mice

first: Shilin

last: Zhao


title: RNA-sequencing analysis of innate lymphoid cell progenitors from wild-type and circTmem241-deficient mice

status: Public on Apr 24 2022

city: Beijing

first: Nian

last: LIU

address: #15 Datun Road, Chaoyang District

institute: Institute of Biophysics,CAS

summary: To explore the role of circular RNA,circTmem241, on ILC3 commitment, we isolated ILCPs from wild-type or circTmem241-deficient mice.

overall_design:
Then RNA-sequencing analysis were performed and differentially expressed transcriptional factors were identified.
Total RNAs were extracted from ILCPs and subjected to RNA-sequencing analysis  through BGISEQ-500 platform

last: Liu

first: Zusen

last: Fan


title: Multistage  Transcriptomics Data Set of Zymomonas mobilis 2032 During Fermentation in 6% and 9% Glucan-Loading AFEX-Pretreated Corn Stover Hydrolysates and 7% Glucan-Loading AFEX-Pretreated Switchgrass Hydrolysate

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: The fermentation of Zymomonas mobilis 2032 was conducted in 6% and 9% glucan-loading AFEX-pretreated corn stover hydrolysates, as well as in 7% glucan-loading AFEX-pretreated switchgrass hydrolysate, and RNA samples were collected at both glucose and xylose growth stages. Here we present a comprehensive RNA-Seq data set at both growth stages.

overall_design: Here, we explored the differences in gene expression based on different hydrolysates. A total of 25 samples were used:  5 biological replicates during the glucose phase in 6% ACSH, 4 biological replicates during the xylose phase in 6% ACSH, 3 biological replicates during the glucose phase in 7% ASGH, 3 biological replicates during the xylose phase in 7% ASH, 5 biological replicates during the glucose phase in 9% ACSH, and 5 biological replicates during the xylose phase in 9% ACSH. Comparison of the 7% ASGH and 9% ASCH to 6% ACSH during glucose or xylose growth will reveal interesting patterns of gene expression that change in response to different glucan-loading hydrolysates.

first: Yaoping

last: Zhang

first: Michael

last: Place

first: Jose

last: Serate

first: Dan

last: Xie

first: Edward

last: Pohlmann

first: Alex

last: LaReau

first: Trey

last: Sato

first: Robert

last: Landick


title: In vitro methylation studies in human fibroblasts from progeria cases

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

institute: University of California, Los Angeles

summary: An Infinium microarray platform (GPL23976, Illumina Infinium HumanMethylation850 BeadChip) was used to generate DNA methylation data from fibroblasts from human progeria cases. Treatment: Antisense oligonucleotide for Line 1 elements.

overall_design: n=16 samples. Fibroblasts from Hutchinson Gilford Progeria and Werner syndrome. Treatment takes 3 values: 1) Antisense Oligonucleotides for Line 1 elements, 2) Scrambled, 3) None.

first: Pradeep

last: Reddy


title: Drug-resistant acute myeloid leukemia

first: bing

last: zhang


title: Transcriptome Analaysis of humanized lungs in COVID-19

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptome analysis of virgin and mated Anopheles gambiae and Anopheles albimanus

city: Boston

first: Flaminia

last: Catteruccia

address: 655 huntington ave

institute: Harvard University

summary: We custom-built a bioinformatics pipeline to search for 20E-modifying enzymes in the accessory glands of Anopheles gambiae males, searching for ecdysteroid kinases (EcK), ecdysone oxidases (EO), and ecdysteroid-phosphate phosphatases (EPP). To this end, we generated RNAseq datasets of different An. gambiae tissues dissected from virgin and mated females and males, and produced similar datasets for Anopheles albimanus, a South American species that does not synthetize and transfer ecdysteroids during mating. These analyses led to the identification of one candidate EPP and two potential EcKs (EcK1 and EcK2), which we demonstrated are involved in the activity of a male-specific oxidized ecdysteroid (3D20E). We further determined that 3D20E is specifically produced by the An. gambiae male accessory glands and is transferred to females during copulation, where it triggers a series of post-mating responses.

sample_organism:
Anopheles gambiae
Anopheles albimanus

platform_organism:
Anopheles gambiae
Anopheles albimanus

overall_design: RNAseq datasets of different Anopheles gambiae and Anopheles albimanus tissues dissected from virgin and mated females and males. Tissues analyzed included: male accessory glands and rest of the body (for males); atria, head, spermatheca and rest of body (for females).

first: Evdoxia

middle: G

last: Kakani

first: Sara

last: Mitchell

first: Duo

last: Peng

first: W

last: Shaw


title: Next Generation Sequencing of Beauvericin/LPS/Beauvericin with LPS treated GM-CSF-cultured bone marrow derived cells.

status: Public on Apr 08 2022

city: Dusseldorf

first: Xiaoli

last: Yang

address: Moorenstr. 5

institute: Heinrich Heine University

summary:
Purpose: The goals of this study are to compare NGS-derived GM-CSF-cultured bone marrow derived cells transcriptome profiling (RNA-seq) normalized counts and differential expression of genes between different stimulations (untreated, Beauvericin, LPS or Beauvericin with LPS).
Methods: mRNA profiles of  GM-CSF-cultured bone marrow derived FACS purified MHCII high CD11c+ cells from wild-type C57BL/6N mice that were left untreated or stimulated with Beauvericin, LPS or Beauvericin with LPS for 4h were generated by deep sequencing, in quadruplicate, using the Illumina NextSeq550 system. DNase digested total RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific) and quality measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’
Results: The reads of all probes were adapter trimmed (Illumina TruSeq). Mapping was done against the Mus musculus (mm39; GRCm39) (June 24, 2020) genome sequence. After grouping of samples (four biological replicates each) according to their respective experimental condition, multi-group comparisons were made and statistically determined using DESeq2. The Resulting P values were corrected for multiple testing by FDR. A P value of <0.05 was considered significant.
Conclusions: Our study represents the first detailed analysis of untreated and Beauvericin stimulated GM-CSF-cultured bone marrow derived cells transcriptomes.Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within GM-CSF-cultured bone marrow derived cells. We conclude that Beauvericin activates GM-CSF-cultured bone marrow derived cells inducing inflammatory cytokine,chemokine and Type I IFN production via a TLR4 dependent signaling pathway, but induces a gene expression profile different from LPS.

overall_design: mRNA profiles of GM-CSF-cultured bone marrow derived  FACS purified MHCII high CD11c+ cells from wild-type C57BL/6N mice that were left untreated or stimulated with Beauvericin, LPS or Beauvericin with LPS for 4 hours.

first: Shafaqat

last: Ali

first: Stefanie

last: Scheu


title: Polysome profiling quantified by RNA sequencing in PANC1 cells treated with MNK2 inhibitors or DMSO

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Regenerating pancreatic b-cells is a potential curative approach for diabetes. We previously identified the small molecule CID661578 as a potent inducer of b-cell regeneration but its target and mechanism of action have remained unknown. We now screened 257 million yeast clones and determined that CID661578 targets MAP kinase-interacting serine/threonine kinase 2 (MNK2), an interaction that was genetically validated in vivo. CID661578 increased b-cell neogenesis from ductal cells in zebrafish, neonatal pig islet aggregates and human pancreatic ductal organoids. Mechanistically, we found that CID661578 boosts protein synthesis and regeneration by blocking MNK2 from binding EIF4G in the translation initiation complex at the mRNA cap. This blocking activity augmented the interaction between EIF4E and EIF4G, which is necessary for both hypertranslation and b-cell regeneration. Taken together, our findings demonstrate a targetable role of MNK2-controlled translation in b-cell regeneration, a role that warrants further investigation in diabetes.

overall_design: Four replicated of polysome profiling were performed on PANC1 cells treated with MNK2 inhibitors (CID661578 [40uM], and cercosporamide [5uM]) or DMSO for 6 hours. Total cytosolic RNA, and polysome-associated mRNA (mRNA associated with > 3 ribosomes) were quantified using RNA sequencing.

first: Kathleen

last: Watt

first: Olov

last: Andersson


title: Investigation of genetic compensation in tdp1-/- zebrafish embryos

city: Sheffield

first: Sherif

last: El-Khamisy

state: South Yorkshire

address: Firth Court, Western Bank

department: Department of Molecular Biology and Biotechnology

institute: The University of Sheffield

summary:
Tdp1, tyrosyl-DNA phosphodiesterase 1, is an enzyme responsible for the repair of DNA breaks resulting from aberrant topoisomerase 1 activity, called Top1 cleavage complexes (Top1-CCs). Mutation of Tdp1 leads to a progressive neurodegenerative disorder spinocerebellar ataxia with axonal neuropathy 1 (SCAN1). We have generated tdp1-/- zebrafish as a model for SCAN1. The adult fish have a behavioral defect and hypersensitivity to camptothecin (CPT), a Top1 poison. Strikingly, the embryos do not show increased sensitivity to CPT, unlike any other reported vertebrate models, suggesting genetic compensation is at play at this stage.
We thus carried out microarray analysis in CPT-treated zebrafish embryos to compare the gene expression profiles of tdp1WT and tdp1-/- genotypes. Gene expression analysis revealed 1,8111 genes that were differentially expressed: 1,071 were upregulated and 740 were downregulated. Sprtn and neil1, two potential compensation candidates were upregulated in the tdp1-/- embryos.

overall_design: Gene expression profiling utilized total RNA extracted from whole zebrafish embryo lysate from 5 dpf tdp1WT and tdp1-/- embryos, treated with 500 nM CPT for 16h 4-5dpf.

first: Ringaile

last: Zaksauskaite

first: Paul

last: Heath

first: Freek

last: van Eeden


title: Projection neuron subtypes establish microglia sub-states and regulate neuroimmune interactions

city: Cambridge

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

summary: Microglia are the resident immune cells of the brain, and have critical roles in circuit development and plasticity. During embryonic and postnatal development, microglia exist in multiple transcriptional states. However, it is still poorly understood how these states are established, and whether they are influenced by their cellular environment. Here we show that in the juvenile neocortex, microglia exist in multiple states whose identity and laminar distribution is instructed by the neuronal class identity of local pyramidal neurons. Using single-cell RNA sequencing, we unveil molecular signatures of distinct microglia sub-states, and show that they can be divided into layer-restricted or broadly-distributed states. Strikingly, conversion of deep-layer pyramidal neurons to an alternate class identity reconfigures both the density and molecular state of local layer-restricted microglia to correspond to the new neuronal niche, thus identifying specific populations of microglia that are sensitive to pyramidal neuron subtypes. Ligand-receptor interactomes for individual neuronal subtype-microglia pairings uncovers two categories of neuron-to-microglia communication: one associated with neuronal class identity and one associated with microglial state. Our findings highlight the fundamental role that neuronal identity and neuronal niches play in locally controlling the transcriptional status of postnatal microglia.

overall_design: Examination of Mg states from different neuronal niches of the cerebral cortex.

first: Jeffrey

last: Stogsdill

first: Kwanho

last: Kim

first: Loïc

last: Binan

first: Samouil

middle: L

last: Farhi

first: Joshua

middle: Z

last: Levin


title: Isolevuglandins modify immune function in hypertension in systemic lupus erythematosus

status: Public on Apr 16 2022

first: David

last: Patrick

summary: Single cell sequencing was performed on splenocytes after depletion of CD3+ T-cells.

overall_design: Single cell sequencing was peformed from splenocytes of male C57Bl/6 mice treated with sham, angiotensin II, and angiotensionII + 2hydroxybenzylamine. Additionally, female C57Bl/6 mice, B6.SLE123 mice, and B6.SLE123 mice treated with 2hydroxybenzylamine were also included.


title: Single-Cell immunoprofiling after immunotherapy for allergic rhinitis reveals functional suppression of pathogenic Th2 cells and clonal conversion

status: Public on Apr 07 2022

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

summary: Background: Allergic rhinitis is a growing problem worldwide and the only treatment that modifies the cause of the disease is antigen-specific immunotherapy; however, its mechanism(s) of action are not fully understood.   Objective: Here, we comprehensively investigated the role and changes of antigen-specific T cells before and after sublingual immunotherapy (SLIT) for Japanese cedar pollinosis (JCP).   Methods: We cultured PBMCs obtained both before and at one-year after initiating SLIT and used a combination of single-cell RNA sequence and repertoire sequencing. To investigate biomarkers, we used PBMCs from patients participating a phase II/III trial of SLIT tablets for JCP and PBMCs from good and poor responders in outpatients.   Results: Antigen-stimulated culturing after SLIT led to clonal expansion of Th2 and Treg cells, and most of these CD4+ T cells retained their CDR3 regions before and after treatment, indicating antigen-specific clonal responses and differentiation secondary to SLIT. However, SLIT reduced the number of clonal functional Th2 cells but increased the Trans-type Th2 cell population that expresses musculin (MSC), TGF-β, and IL-2. Trajectory analysis suggested that SLIT induced clonal differentiation of the Trans-type Th2 cells differentiated into Treg cells. By using real-time PCR, we found that MSC levels increased after 1 year of treatment in the active SLIT group and good responders.   Conclusion: The combination of single-cell RNA sequencing and repertoire analysis helped reveal a part of the underlying mechanism— that SLIT promotes the expression of MSC on pathogenic Th2 cells and suppresses their function, and that MSC may be a potential biomarker of SLIT for allergic rhinitis.    Clinical implications  MSC expression was higher in the group of active patients who were responsive to SLIT, indicating that these molecules may be potential biomarkers of SLIT efficacy.

overall_design: scRNA-seq and scVDJ-seq of 14 PBMC samples collected from 7 patients suffering from Japanese cedar pollinosis before and 1 year after SLIT treatment.

first: Tomohisa

last: Iinuma

first: Kiyoshi

last: Hirahara

first: Junya

last: Kurita

first: Kota

last: Kokubo

first: Hiroyuki

last: Yagyu

first: Riyo

last: Yoneda

first: Tomoyuki

last: Arai

first: Yuri

last: Sonobe

first: Masaki

last: Fukuyo

first: Atsushi

last: Kaneda

first: Syuji

last: Yonekura

first: Toshinori

last: Nakayama

first: Yoshitaka

last: Okamoto

first: Toyoyuki

last: Hanazawa


title: Lactational delivery of Triclosan promotes non-alcoholic fatty liver disease in newborn mice

status: Public on Apr 15 2022

city: San Diego

first: Andre

middle: Alberto

last: Weber

address: 9500 Gilman Dr. La Jolla

institute: UCSD

summary: To investigate the hepatic effects of lactational deliver of Triclosan in neonatal mice we performed a gene expression profiling analtsis  RNA-Seq of liver using data obtained from RNA-seq of Triclosan treated mice and control group (N=3/group)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Triclosan treated group and control group.

first: Robert

middle: H

last: Tukey

first: Kristen

last: Jepsen


title: RNA-Seq in hippocampus of control and Jade2-KO mice

status: Public on Apr 11 2022

first: yongqing

last: liu

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

institute: Peking University Health Science Center

summary: Impairment of synaptic plasticity is involved in a range of pathological conditions such as cognitive deficits. However, how synaptic efficacy is regulated is not fully understood. Here, we report that the epigenetic factor Jade family PHD finger 2 (JADE2), which is upregulated by neuronal activities, is critically involved in the maintenance of hippocampal synaptic plasticity and cognitive functions in mice. Knockdown or genetic deletion of JADE2 in hippocampal CA1 results in impaired structural and functional synaptic plasticity, leading to memory impairment, whereas overexpression of JADE2 in CA1 neurons facilitates hippocampal-dependent learning and memory. Mechanistically, we show that JADE2 modulates synaptic functions mainly by transcriptional activation of cytoskeletal protein RAC1, and this activity is dependent on its interaction with histone acetyltransferase HBO1. Together, our findings suggest JADE2 is a critical player for experience-dependent gene regulation in controlling synaptic plasticity and cognitive functions.

overall_design: Hippocampal tissues mRNA profiles of 8-week old Control (wild type) and Jade2-KO mice were generated by deep sequencing, using Illumina NovaSeq 6000

first: Yongqing

last: Liu

first: Minghua

last: Fan


title: Epitranscriptomic map of N6-methyladenosine circular RNAs in the spinal cord of morphine-tolerant rats

status: Public on Apr 05 2022

city: Changsha

first: Manyu

last: Xing

state: Hunan

address: 87 Xiangya Road

institute: Xiangya hospital, Central South University

summary: Morphine tolerance is a tricky problem, the mechanism of it is still unclear. Circular RNAs (CircRNAs) play important roles in biological process of central nervous system. N6-methyladenosine (m6A) as a key post-transcriptional modification of RNA can regulate the metabolism and functions of circRNAs. Here we conducted this research to explore the patterns of m6A-methylation of circRNAs in the spinal cords of 4 morphine tolerated rats and 4 normal rats.

overall_design: The adult male SD rats were randomly divided into normal saline group (NS group) and morphine tolerance group (MT group). Rats in the MT group were administrated morphine hydrochloride injection 10 μg/10 μl intrathecally through the tube inserted into the sheath at 8:00 a.m. and 20:00 p.m. for 7 consecutive days, the NS group was given 10 μl of normal saline at the same time point.

first: Meiling

last: Deng

first: Yufei

last: Shi

first: Jiajia

last: Dai

first: Tong

last: Ding

first: Zongbin

last: Song

first: Wangyuan

last: Zou


title: Autophagy regulated by the HIF/REDD1/mTORC1 signaling is progressively increased during erythroid differentiation under hypoxia

status: Public on Apr 04 2022

first: Cheng

last: Quan

state: Beijing

address: Beijing Taiping Road No.27

institute: Beijing Institute of Radiation Medicine

summary: For hematopoietic stem and progenitor cells (HSPCs), hypoxia is a specific microenvironment known as the hypoxic niche. The role of hypoxia in maintaining quiescence, self-renewal and proliferation of HSPCs has been more elaborated. What remains unclear is the regulation of hypoxia on HSPC differentiation, especially on the differentiation of HSPCs into erythrocytes. In this study, we show that hypoxia evidently accelerates erythroid differentiation, and in this process effectively enhances autophagy which rapidly supplies cellular components through degradation of organelles or proteins to meet the needs of cell stress or development. In order to ascertain whether autophagy mediates the erythroid differentiation promoted by hypoxia, we analyze the perturbation of erythroid differentiation after pharmacological and genetic interference with autophagy, and address that autophagy is required for hypoxia-accelerated erythroid differentiation. Transcriptomics reveals HIF-1 and mTORC1 pathways may function as the upstream of autophagy to regulate erythroid differentiation under hypoxia. We further determine that mTORC1 signaling is suppressed by hypoxia to relieve its inhibition of autophagy. In addition, we also discover a new regulatory pattern that with the process of erythroid differentiation, mTORC1 activity gradually decreases and autophagy activity increases concomitantly. Moreover, we provide evidence that HIF-1 target gene REDD1, which inhibits mTORC1 activity, is dramatically upregulated under hypoxia. Silencing REDD1 expression activates mTORC1 signaling and impairs the enhanced autophagy and the accelerated erythroid differentiation under hypoxia. Together, our study reveals that hypoxia is conductive to accelerating erythroid differentiation, in which autophagy induced by the HIF-1/REDD1/mTORC1 pathway plays a pivotal role.

overall_design: K562 or CD34+ HSC  exposed to normoxia or hypoxia during erythroid differentiation.

first: Jian

last: Li

first: Li-Ying

last: Wu


title: Temporal retinal transcriptome analysis in Staphylococcus aureus endophthalmitis

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: 615 Michael Street, Whitehead Biomedical Research Building

department: Department of Pediatrics

institute: Emory University

summary:
Bacterial endophthalmitis remains a devastating inflammatory disease associated with permanent vision loss. The mechanisms regulating inflammation to protect the eye remain elusive. Therefore, assessing the host immune response in bacterial endophthalmitis may provide new therapeutic targets.
We used microarrays to determine the global profiling of up-regulated and downregulated gene expression in bacterial endophthalmitis.

overall_design: In the current study, we used a mouse model of S. aureus endophthalmitis to understand the transcriptomic changes. Briefly, endophthalmitis was induced in C57BL/6 mice by intravitreal injection of S. aureus (SA, RN6390 ~5000CFU/eye). In the Pam3 treatment group, Pam3 (0.1 μ g) was injected 24 h prior to SA injections. In the control group, the eyes were left either uninjected (control) or injected with sterile PBS (Veh control). The retinas were harvested at 3, 6, 12, and 24h post-infection. RNA was isolated using the RNeasy Mini Kit (Qiagen) and microarray was performed to determine the comprehensive transcriptomic changes with respect to control/veh. control.

first: Deepa

last: Rajamani

first: Pawan

last: Singh

first: Bruce

last: Rottmann

first: Natasha

first: Ashok

last: Kumar


title: Expression data from MAT1 lncRNA knockdown UM cells

status: Public on Mar 31 2022

city: Shanghai

first: hui

last: pan

address: Zhizaoju Road No.639, Huangpu District

department: Department of Ophthalmology

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

summary: The role of lncRNA in uveal melanoma (UM) is not well studied. We used microarrays to identify the downstream targets of MAT1 lncRNA to invesitgate the mechanism of lncRNA in UM oncogenesis

overall_design:
MAT1 was knockdown in uveal melanoma cell line OCM1a and OM431.RNA extraction from cells was used to be hybridized on Affymetrix microarrays.

**Please note that the records have been updated with new sample records on Aug 9, 2022 (as the previous sample records were incorrect).

first: H

last: Pan

first: X

last: Zhang


title: Single-cell RNA-sequencing of human vascular and tissue innate lymphoid cells (ILCs) in the spleen of MISTRG humanized mice

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

summary: The migratory properties of human ILCs are poorly understood. In this study, we mapped at single-cell resolution the heterogeneity and spatial compartmentalization of human ILCs in the spleen, using an in-vivo model (MISTRG humanized mice) for human ILCs.

overall_design:
We used intravascular cell labeling in combination with single-cell RNA-sequencing to define the gene signatures of human ILCs in the vascular and tissue compartment of MISTRG mice engrafted with human CD34+ hematopoietic stem and progenitor cells (HSPCs).

**As Swedish legislation and GDPR prevent unrestricted distribution of raw sequencing data, raw sequence data cannot be provided, including through controlled access databases.***

first: Daryl

last: Boey

first: Yu

last: Gao

first: Arlisa

last: Alisjahbana

first: Imran

last: Mohammad


title: Heterogeneity of circulating CD4+CD8+ double-positive T cells characterized by scRNA-seq analysis and trajectory inference

status: Public on Mar 30 2022

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: We subdivided circulating CD4+CD8+ double positive T cells, known to be associated with various disease environments, into several subtypes through single-cell RNA sequencing, and analyzed transition in transcriptome using trajectory analysis.

overall_design: Heterogeneous subsets of circulating CD4+CD8+ double positive T cells were analyzed by scRNA-seq after labeling CD4 and CD8 feature barcodes, characterized their characteristic with CD4, CD8 coreceptor expresion levels.

first: Jae

first: Sung

middle: M

last: Choi


title: Transcriptional profiling of multiple system atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease [cohort 2]

status: Public on Apr 03 2022

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

summary: Multiple system atrophy (MSA) is a rare adult-onset neurodegenerative disease of unknown cause, with no effective therapeutic options, and no cure. Limited work to date has attempted to characterize the transcriptional changes associated with the disease, which presents as either predominating parkinsonian (MSA-P) or cerebellar (MSC-C) symptoms. We report here the results of RNA expression profiling of cerebellar white matter (CWM) tissue from two independent cohorts of MSA patients (n = 66) and healthy controls (HC; n = 66). RNA samples from bulk brain tissue and from oligodendrocytes obtained by laser capture microdissection (LCM) were sequenced. Differentially expressed genes (DEGs) were obtained and were examined before and after stratifying by MSA clinical sub-type.    We detected the highest number of DEGs in the MSA-C group (n = 747) while only one gene was noted in MSA-P, highlighting the larger dysregulation of the transcriptome in the MSA-C CWM. Results from both bulk tissue and LCM analysis showed a downregulation of oligodendrocyte genes and an enrichment for myelination processes with a key role noted for the QKI gene. Additionally, we observed a significant upregulation of neuron-specific gene expression in MSA-C and enrichment for synaptic processes. A third cluster of genes was associated with the upregulation of astrocyte and endothelial genes, two cell types with a key role in inflammation processes. Finally, network analysis in MSA-C showed enrichment for β-amyloid related functional classes, including the known Alzheimer’s disease (AD) genes, APP and PSEN1.    This is the largest RNA profiling study ever conducted on post-mortem brain tissue from MSA patients. We were able to define specific gene expression signatures for MSA-C highlighting the different stages of the complex neurodegenerative cascade of the disease that included alterations in several cell-specific transcriptional programs. Finally, several results suggest a common transcriptional dysregulation between MSA and AD-related genes despite the clinical and neuropathological distinctions between the two diseases.

overall_design: RNA sequencing case-control study between MSA patients and controls (samples from cohort 2 as indicated in the manuscript)

first: Christiane

last: Bleul

first: Isabelle

last: Schrauwen

first: Joshua

last: Talboom

first: Llorida

last: Llaci

first: Matthew

middle: D

last: DeBoth

first: Marcus

last: Naymik

first: Glenda

last: Halliday

first: Conceicao

last: Bettencourt

first: Janice

last: Holton

first: Geidy

middle: E

last: Serrano

first: Lucia

last: Sue

first: Thomas

last: Beach

first: Nadia

last: Stefanova

middle: J

last: Huentelman


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [HiChIP2]

status: Public on Apr 02 2022

city: Stanford

first: Jan-Renier

last: Moonen

address: 269 Campus Drive, CCSR 1220

department: Pediatrics

institute: Stanford University

summary: Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote this beneficial response. We show that under LSS, KLF4 interacts with the SWI/SNF nucleosome remodeling complex to increase accessibility at enhancer sites that promote expression of homeostatic endothelial genes. By combining molecular and computational approaches we discovered enhancers that loop to promoters of known and novel KLF4- and LSS-responsive genes that stabilize endothelial cells and suppress inflammation, such as BMPR2 and DUSP5. By linking enhancers to genes that they regulate under physiologic LSS, our work establishes a foundation for interpreting how non-coding DNA variants in these regions might disrupt protective gene expression to influence vascular disease.

overall_design: PAEC were transfected with siRNA targeting KLF2 and KLF4 (siKLF), or non targeting controls (siC), followed by 24 h of exposure to 15 dyne/cm2 of LSS. HiChIP was performed as previously described (Mumbach et al. Nat Methods. 2016) using 1000,000 cells.

first: J

middle: R

last: Chappell

first: M

last: Snyder

last: Rabinovitch


title: Ventral hippocampal transcriptome analysis after acute corticosterone exposure.

status: Public on Mar 28 2022

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

institute: Leiden University Medical Center

summary:
Aim: We investigated the effect of acute corticosterone exposure 3 hours after subcutaneous injection on the ventral hippocampus transcriptome.
Methods: Adult male mice were used in the experiment. Mice were sacrificed 3 hours after corticosterone (3mg/kg) of vehicle injection and the ventral hippocampus was dissected and snap-frozen. Subsequently, total RNA was isolated and send for 100bp paired-end sequencing by BGI.

overall_design: Ventral hippocampal mRNA profiles of male mice studying corticosterone effects.

first: Eva

last: Viho

first: Onno

last: Meijer


title: Partitioned Usage of Chromatin Remodelers by Nucleosome Displacing Factors

status: Public on Apr 06 2022

city: UNIVERSITY PARK

first: Lu

last: Bai

address: 406 South Frear

institute: Penn State University

summary: Nucleosome-displacing factors (NDFs) in yeast, similar to pioneer factors in higher eukaryotes, cause opening of closed chromatin and formation of nucleosome-depleted regions (NDRs). NDRs in yeast are also affected by ATP-dependent chromatin remodelers (CRs). However, how NDFs and CRs coordinate in nucleosome invasion and NDR formation is still unclear. Here, we designed a high-throughput method to systematically study the interplay between NDFs and CRs. By combining integrated synthetic oligonucleotide library with DNA methyltransferase-based, single-molecule nucleosome mapping, we measured the impact of CRs on NDRs generated by individual NDFs. We found that CRs were dispensable for nucleosome invasion by NDFs, and they function downstream of NDF binding to modulate the NDR length. A few CRs show high specificity towards certain NDFs; however, in most cases, CRs are recruited in a factor-nonspecific and length-dependent manner.  Overall, our study represents a novel framework to investigate how NDFs and CRs cooperate to generate desired pattern of chromatin opening.

overall_design: Study of NDR change on synthetic oligo libraries in four remodeler depletion yeast strains and one WT yeast strain. Each sample contains 2-3 replicates.

first: Chen

last: Hengye

first: Bai

last: Lu

first: Michael

last: Kladde

first: Archana

last: Dhasarathy


title: Inhibition of lncRNA TCONS_00077866 ameliorates the high stearic acid diet-induced mouse pancreatic β-cell inflammatory response by increasing miR-297b-5p to downregulate SAA3 expression

city: Harbin

first: Huimin

state: Heilongjiang

address: 157 Baojian Road

department: Nutrition and Food Hygiene

institute: Harbin Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Long-term high-fat diet feeding increases the circulating concentration of stearic acid (SA), which has a potent toxic effect on β-cells, but the underlying molecular mechanisms have not been fully elucidated. Here, we evaluated the role of lncRNA TCONS_00077866 (lncRNA-866) in SA-induced β-cell inflammation. lncRNA-866 was selected for study because it demonstrated the largest fold-difference in expression of five lncRNAs that were affected by SA treatment using lncRNA High-throughput Sequencing analysis. Knockdown of lncRNA-866 by virus-mediated shRNA expression in mice or Smart Silencer in β-TC6 cells significantly inhibited the SA-induced reduction in insulin secretion and β-cell inflammation. lncRNA-866 directly bound to miR-297b-5p, thereby preventing it from reducing the expression of its target serum amyloid A3 (SAA3), according to lncRNA-miRNA-mRNA co-expression network analysis and luciferase reporter assay. Furthermore, overexpression of miR-297b-5p or inhibition of SAA3 also had marked protective effects against the deleterious effects of SA in β-TC6 cells and mouse islets. In conclusion, lncRNA-866 silencing ameliorates SA-induced β-cell inflammation by targeting the miR-297b-5p/SAA3 axis. lncRNA-866 inhibition may represent a new strategy to protect β-cells against the effects of SA during the development of type 2 diabetes.

overall_design: LncRNA profiles of nine samples from β-TC6 cells (three control, three stearic acid-treated, and three palmitic acid-treated samples

first: Rui

last: Guo

first: Changhao

last: Sun


title: Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology

city: xinxiang

first: jing

last: li

state: henan

address: No. 46, Jianshe East Road

institute: henan normal university

summary:
Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals, for example, flatworms, newts, salamanders, and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately, the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues, and even cause serious loss of function or death. However, the research on regeneration mechanisms is limited and incomplete so far. Here, we investigated the biological mechanisms of zebrafish caudal fin regeneration.
Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d, 3d, and 7d after caudal fin removal, and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome.
Results: We observed that the amputated caudal fin went through a complex genetic change, especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa (blastema outgrowth stage) were dramatically enriched in 20 Biological Processes (FDR < 0.05), three of which were cell cycle (GO:0007049), mitotic cell cycle (GO:0000278), and cell cycle process (GO:0022402), one was response to wounding (GO:0009611), etc.
Conclusion: Taken together, the results revealed that the DEGs were enriched in numerous biological processes, molecular function, cellular component, and signaling pathways, suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism.

overall_design: Caudal fin RNA profiles of  test and control samples were generated by deep sequencing, using Illumina HiSeq 4000.

first: Jing

last: Li

first: Xiaoyu


title: Type 2 cytokines in the thymus activate Sirpa+ dendritic cells to promote clonal deletion

status: Public on Mar 23 2022

city: Minneapolis

first: Matous

last: Voboril

state: Minnesota

address: 2101 6th Street SE

department: Department of Lab Medicine & Pathology

institute: University of Minnesota

summary: The thymus contains a diversity of dendritic cells (DC) that exist in defined locations and have different antigen processing and presenting features. This suggests that they play non-redundant roles in mediating thymocyte selection. In an effort to eliminate SIRP+ cDC2, we discovered that a substantial proportion expresses the surface lectin, CD301b, in the thymus. These cells resemble the CD301b+ type 2 immune response promoting DC that are present in the skin draining lymph nodes. Transcriptional and phenotypic comparison to other DC subsets in the thymus revealed that thymic CD301b+ cDC represent an activated state that exhibits enhanced antigen processing and presentation. Furthermore, CD301b+ cDC2 demonstrated a type 2 cytokine signature and required steady state IL-4 receptor signaling. Selective ablation of CD301b+ cDC2 impaired clonal deletion without affecting regulatory T cells. TCR alpha repertoire sequencing confirmed that cDC2 promote deletion of conventional T cells with minimal effect on regulatory T cell selection. Together, these findings suggest that cytokine-induced activation of DC in the thymus substantially enforces central tolerance.

overall_design: Sorted dendritic cell populations from the thymus of 3 C57BL/6 mice at 8weeks of age

first: Elise

last: Breed

first: Matouš

last: Vobořil

first: Katharine

last: Ashby

first: Ryan

last: Martinez

first: Lily

last: Qian

first: Haiguang

last: Wang

first: Oscar

last: Salgado

first: Christine

last: O'Connor

first: Kristin

middle: A

last: Hogquist


title: Transcriptional profiling of multiple system atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease [Oligodendrocytes LCM data]

first: Ignazio

last: Piras

overall_design: RNA sequencing case-control study between MSA patients and controls (Oligodendrocytes LCM data)

middle: S

first: Christiane

last: Bleul

first: Isabelle

last: Schrauwen

first: Joshua

last: Talboom

first: Llorida

last: Llaci

first: Matthew

last: DeBoth

first: Marcus

last: Naymik

first: Glenda

last: Halliday

first: Conceicao

last: Bettencourt

first: Janice

last: Holton

first: Geidy

last: Serrano

first: Lucia

last: Sue

first: Thomas

last: Beach

first: Nadia

last: Stefanova

last: Huentelman


title: RNA sequencing of Pseudomonas aeruginosa phoenix colonies, viable but non-culturable colonies (VBNCs), and control samples

status: Public on Mar 27 2022

city: Columbus

first: Devin

last: Sindeldecker

state: OH

department: MI&I

institute: The Ohio State University

summary: We report RNA sequencing data for mRNA transcripts obtained from tobramycin exposed phoenix colonies, VBNCs, and various controls (untreated lawn, edge of the zone of clearance of tobramycin, treated outer background lawn). Extracted mRNA was sequenced using an Illumina HiSeq 4000, mapped to a Pseudomonas aeruginosa PAO1 reference genome, and processed to obtain counts for all gene transcripts for each sample. This is the first sequencing data generated for Pseudomonas aeruginosa phoenix colonies and VBNCs.

overall_design: mRNA transcription profiles of phoenix colonies, VBNCs, and various control samples

first: Paul

last: Stoodley


title: Transcriptomes of crypt intestinal epithelial cells from Apln-/- mice

status: Public on Mar 29 2022

city: Geneva

last: Dupanloup

address: Rue Michel-Servet, 1

institute: University of Geneva

summary: We used bulk RNAseq to analyze crypt intestinal epithelial gene expression changes between wild-type and Apln-/- adult mice

overall_design: Small intestines from 13 week old, male, wild-type control (C57Bl/6) or Apln-/- mice were harvested and digested with Liberase TL and crypt epithelial cells were sorted as single, live, CD31neg, CD45neg, EpCAM+, CD44+ cells. RNA was reverse transcribed, amplified and sequenced.

first: J

last: Bernier-Latmani

first: I

first: M

last: Delorenzi

first: T

middle: V

last: Petrova


title: Transcriptomes of intestinal blood endothelial cells (BEC) from mice with acute epithelial Apc deletion.

first: Isabelle

summary:
APC is mutated in the majority of colorectal cancers. Inducible deletion of Apc in intestinal epithelial cells in Apcfl//fl; Villin-CreERT2 mice recapitulates this tumor-initiating mutation resulting in expanded intestinal crypts, including stem cells.
We used microarrays to analyze BEC gene expression changes during the early stages of intestinal tumorigenesis.

overall_design: Adult wild-type control (Apcfl//fl) or Apcfl//fl; Villin-CreERT2 (KO) mice were daily injected subcutaneously with tamoxifen for 5 days. At day 6 the intestine was harvested and digested with Collagenase IV and BECs were sorted as single, live, CD45neg, EpCAMneg, gp38neg, CD31+ cells. RNA was amplified and hybridized on Affymetrix Mouse Gene 2.0 ST arrays.

first: S

last: Nassiri


title: Combined fiber atrophy and decreased muscle regeneration capacity driven by mitochondrial DNA alterations underlie the development of sarcopenia

status: Public on Mar 26 2022

city: Angers

first: Olivier

middle: R.

last: Baris

address: 4 rue Larrey

department: CHU Angers, IBS

institute: UMR 6015 CNRS / 1083 INSERM

summary: Mitochondrial dysfunction caused by mitochondrial (mtDNA) deletions have been associated with skeletal muscle atrophy and myofiber loss. However, whether such defects occurring in myofibers cause sarcopenia is unclear. Also, the contribution of mtDNA alterations in muscle stem cells (MuSCs) to sarcopenia remain to be investigated. We expressed a dominant-negative variant of the mitochondrial helicase, which induces mtDNA alterations, specifically in differentiated myofibers (K320Eskm mice) and MuSCs (K320Emsc mice), respectively, and investigated their impact on muscle structure and function by immunohistochemistry, analysis of mtDNA and respiratory chain content, muscle transcriptome and functional tests. K320Eskm mice at 24 months of age had higher levels of mtDNA deletions compared to controls in soleus (SOL, 0.07673 % vs 0.00015 %, p=0.0167), extensor digitorium longi (EDL, 0.0649 vs 0.000925, p= 0.0015) and gastrocnemius (GAS, 0.09353 vs 0.000425, p=0.0004). K320Eskm mice revealed a progressive increase in the proportion of cytochrome c oxidase deficient fibers (COX-) in cross sections, reaching a maximum of 3.03%, 4.36%, 13.58% and 17.08% in EDL, SOL, tibialis anterior (TA) and GAS, respectively. However, mice did not show accelerated loss of muscle mass, muscle strength or physical performance. Histological analyses revealed ragged red fibers but also stimulated regeneration, indicating activation of MuSCs. RNAseq demonstrated enhanced expression of genes associated with protein synthesis, but also degradation, as well as muscle fiber differentiation and cell proliferation. In contrast, 7 days after destruction by cardiotoxin, regenerating TA of K320Emsc mice showed 30% of COX- fibers. Notably, regenerated muscle showed dystrophic changes, increased fibrosis (2.5% vs 1.6%, p=0.0003), increased abundance of fat cells (2.76% vs 0.23%, p=0.0144) and reduced muscle mass (regenerated TA: 40.0mg vs 60.2mg, p=0.0171). In contrast to muscles from K320Eskm mice, freshly isolated MuSCs from aged K320Emsc mice were completely devoid of mtDNA alterations. However, after passaging, mtDNA copy number as well as respiratory chain subunits and p62 levels gradually decreased.Taken together, accumulation of large-scale mtDNA alterations in myofibers alone is not sufficient to cause sarcopenia. Expression of K320E is tolerated in quiescent MuSCs, but progressively leads to mtDNA and respiratory chain depletion upon activation, in vivo and in vitro, possibly caused by an increased mitochondrial removal. Altogether, our results suggest that the accumulation of mtDNA alterations in myofibers activates regeneration during aging, which leads to sarcopenia if such alterations have expanded in MuSCs as well.

overall_design: RNA sequencing profile of 24 month-old Tibialis anterior muscle from K320E-skm and wild-type mice

first: Sammy

last: Kimoloï

first: David

last: Pla-Martin

first: Rudolf

last: Wiesner


title: Effect of disturbance of vagal- or COX- dependent route of neuroimmune communication on the hypotalamic transcriptome

status: Public on Mar 24 2022

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

summary: This is data from studies on mechanisms compensating for disturbances in the activity of neuronal or humoral neuroimmune communication pathways in the model of intraperitoneal inflammation.

overall_design: Experiments were performed on 3-month-old male Wistar rats (300 g ± 25 g). Animals belonging to group CNT were not subjected to any procedures. Groups “NaCl”, “CEL”, “SC560”, “INDOM” were subcutaneously injected for 10 days with NaCl, celecoxib, SC-560 or indometacin, respectively. Groups “vagotomy” and “sham_operation” were subjected to either subdiaphragmatic vagotomy or sham operation performed in analogous way to the vagotomy, with exception of cutting the nerves. Next, animals were allowed to recover from surgery for 30 days. On the day following the end of the treatment (11th day for “NaCl”, “CEL”, “SC560”, “INDOM” and 31th day for “vagotomy” and “sham_operation”groups), the animals received a single intraperitoneal injection of either 10 µg lipopolysaccharide dissolved in 100 μl 0.9% NaCl (groups named “-I”) or the same volume of saline (groups named “-III”). Animals were decaptitated 120 minutes after injection. Immediately after decapitation, hypothalamus samples, restricted mainly to the medial part containing the paraventricular nucleus, were disected.

first: Anna

last: Kobrzycka

first: Joanna

last: Goscik

first: Monika

last: Gora

first: Beata

last: Burzynska

first: Roksana

last: Iwanicka-Nowicka

first: Krystyna

last: Pierzchala-Koziec

first: Marek

last: Wieczorek

first: Pawel

last: Napora


title: Antagonistic action of a synthetic androgen ligand mediates chromatin remodeling in a human prostate cancer cell line

city: Iwaki

first: Takahiro

last: Sawada

state: Fukushima

address: Jobankamiyunagayamachi Kaminodai57

institute: Research Institute of Innovative Medicine

summary: Androgen receptor (AR) antagonists have been clinically applied with success to the prostate cancer patients and draw remission of androgen-dependent tumors. However, a couple of years after the treatments, transit of the tumors into in androgen-independent state is often observed with altered gene expression profiles, but the molecular basis is barely known. Since the AR antagonists trigger the transition, we tested in the present study if the AR antagonists are potent to induce chromatin reorganization in an androgen-dependent prostate cancer cell line (LNCaP cells).

overall_design: Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) by LNCaP cells treated MeOH (control), DHT (10 nM) and bicalutamide (10 µM) for 5 h or 120 h.

first: Y

last: Kanemoto

first: R

last: Amano

first: A

last: Hayakawa

last: Kurokawa

first: J

last: Mori

last: Kato


title: JMJD6 is a possible epigenetic regulator of PD-L1 expression and an independent favorable prognostic factor of intrahepatic cholangiocarcinoma

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Association of Jumonji domain-containing 6 (JMJD6) with outcomes of various cancers has been shown, however the impact on intrahepatic cholangiocarcinoma (ICC) has never been reported yet. The aim of this study is to clarify the role of JMJD6 in the clinical settings and the impact on the outcomes of ICC. The resected liver specimens of 53 patients who underwent surgery for ICC were analyzed for JMJD6 expression by immunohistochemistry staining. The relationship between clinicopathological factors and the JMJD6 expression was investigated. Commercial culture cell lines derived from primary ICC were incubated with siRNA to decrease the expression of JMJD6. The RNA and protein were extracted to analyze the downstream gene expression with RNA-sequence and western blotting. The relationship between JMJD6 expression and tumor immunological factors were evaluated. Low expression of JMJD6 was significantly associated with poor overall survival (OS, p=0.0024). The further analyses revealed that the higher expression of JMJD6 was one of the independent better prognostic factors. ICC cells with JMJD6 knockdown revealed significantly higher programmed death-ligand 1 (PD-L1) expression (p=0.0410) in RNA-seq. The western blotting showed the result matching with the RNA-seq. H3K4me3 histone protein expression was also upregulated under the knockdown of JMJD6. A higher CD8+ T cell count combined with high expression of JMJD6 was one of the significant indicators of better prognosis both in PFS and OS. In vitro experiments proved that JMJD6 regulated the expression of PD-L1 and the paired evaluation of JMJD6 and the immune status was one of the useful factors to stratify the prognosis of ICC. Our results suggest that JMJD6 could influence the prognosis of ICC through the epigenetic regulation of PD-L1 expression.

overall_design: To explore more of the importance of JMJD6 in ICC, SSP-25 cells knocked down for JMJD6 were analyzed by RNA-sequencing.

first: Yukiko

last: Kosai-Fujimoto

first: Takasuke

last: Fukuhara


title: Single-cell RNA sequencing on peripheral blood cells of patients with giant cell arteritis

status: Public on Mar 22 2022

city: Groningen

first: Rosanne

last: Reitsema

address: Hanzeplein 1

institute: University Medical Center Groningen

summary: Vasculitis is characterized by the inflammation of blood vessels. In patients with giant cell arteritis (GCA) large- to medium-sized vessels are affected. Single-cell RNA sequencing was performed on GCA patients and healthy controls (HC) to study the transcriptome of peripheral blood mononuclear cells of patients and controls.

overall_design: Peripheral blood mononuclear cells (PBMCs) were obtained from patients with GCA and age- and sex-matched healthy controls. Patient samples were obtained before start of treatment.

first: Kornelis

last: van der Geest

first: Maria

last: Sandovici

first: William

middle: F

last: Jiemy

first: Jacoba

middle: C

last: Graver

first: Wayel

last: Abdulahad

first: Annemieke

last: Boots

first: Peter

last: Heeringa

first: Elisabeth

last: Brouwer


first: Isabelle

last: Dupanloup

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

overall_design: Refer to individual Series