title: Differential transcription profiling of the phage LUZ19 infection process in different growth media

status: Public on Nov 28 2020

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

institute: KU Leuven

summary: RNA sequencing (RNA-seq) of phage infected bacterial cultures offers a snapshot of transcriptional events occurring during the infection process, providing insights into the phage transcriptional organization as well as the bacterial response. To better mimic real environmental contexts, we performed RNA-seq of P. aeruginosa PAO1 cultures infected with phage LUZ19 in a mammalian cell culture medium (MCCM) to better simulate a phage therapy event, and the data were compared to LB medium. Regardless of the media, phage LUZ19 induces significant transcriptional changes in the bacterial host over time, particularly during early infection (t= 5 min) and gradually shuts down bacterial transcription. In a common response in both media, 56 P. aeruginosa PAO1 genes are differentially transcribed and clustered into several functional categories such as metabolism, translation and transcription. Our data allowed us to tease apart a medium-specific response during infection from the identified infection-associated responses. This reinforces the concept that phages overtake bacterial transcriptome in a strict manner to gain control of the bacterial machinery and reallocate resources for infection, in this case overcoming the nutritional limitations of the mammalian cell culture medium. From a phage therapy perspective, this study contributes towards a better understanding of phage-host interaction in human physiological conditions and demonstrates the versatility of phage LUZ19 to adapt to different environments.

sample_organism:
Pseudomonas aeruginosa PAO1
Pseudomonas phage LUZ19

overall_design: Study of transcriptome from P. aeruginosa PAO1 infected with LUZ19 phage in LB and MCCM media at time points 0, 5, 10 and 15 min post-infection. Foe each time point there was triplicates. Control samples correspond to time point 0 min (uninfected cultures).

first: Ana

last: Brandão

first: Diana

last: Pires

first: Lucas

last: Coppens

first: Marleen

last: Voet

first: Joana

last: Azeredo


title: RNAseq Analysis of wild type and nrt1.13 in normal or low nitrate condition

city: Taipei

first: Yi-Fang

last: Tsay

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

type: Expression profiling by high throughput sequencing

summary: We report the nitrate-dependent regulation of gene-expression that resulted in the late flowering phenotype. This work studies the impact of NRT1.13 in the nitrate-dependent control of flowering.

overall_design: Wild type and nrt1.13 were grown in hydroponic medium with  2 (normal) or 0.2 (low)  mM potasium nitrate. The shoot were harvested at 16 or 25-day after germination for RNA extraction. Three replicates of samples were analyzed.

first: Hui-Yu

last: Chen

first: Shan-Hua

last: Lin

first: Ling-Hsin

last: Cheng

first: Jeng-Jong

last: Wu

first: Yi-Chen


title: Fine-tuning Mybl2 levels are required for proper MET process during somatic reprogramming [ChIP-Seq]

status: Public on Nov 29 2020

city: Birmingham

first: Carl

last: Ward

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome wide data investigating the role of Mybl2 in reprogramming

overall_design:
ChIP-seq of Mybl2 in MEF.

This dataset is not included in PMID 30089261.

first: Paloma

last: Garcia


title: Pediatric MDS-Associated Germline Mutations in SAMD9 and SAMD9L Impair Multiple Pathways in Primary Hematopoietic Cells

status: Public on Nov 30 2020

city: Memphis

first: Jeffery

last: Klco

state: Tennessee

address: 262 Danny Thomas Place, D4047B

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

summary: Here, we used a lentiviral over-expression approach to assess the functional impact and underlying cellular processes of wild-type and mutant SAMD9 or SAMD9L in primary mouse or human hematopoietic stem and progenitor cells (HSPC). Using a combination of protein interactome analyses, transcriptional profiling and functional validation, we found that SAMD9 and SAMD9L are multifunctional proteins that cause profound alterations in cell cycle, protein translation, and proliferation of HSPCs. Importantly, our molecular and functional studies also demonstrated that expression of these genes and their mutations leads to a toxic cellular environment that promotes DNA-damage repair defects and ultimately lead to apoptosis in hematopoietic cells. This study provides novel functional insights into SAMD9 and SAMD9L and how their mutations can potentially alter hematopoietic function and lead to bone marrow hypocellularity, a hallmark of pediatric MDS.

overall_design: mRNA from human cord blood-derived CD34+cells expressing wild-type and mutant SAMD9 and SAMD9L

first: Melvin

middle: E

last: Thomas III

first: Sherif

last: Abdelhamed

first: Ryan

last: Hiltenbrand

first: Jason

middle: R

last: Schwartz

first: Michael

last: Walsh

first: Guangchun

last: Song

first: Jing

last: Ma

middle: M


title: Inducible mechanisms of disease tolerance provide an alternative strategy of acquired immunity to malaria.

status: Public on Nov 26 2020

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary:
Disease tolerance is an important alternative strategy for rapidly acquired immunity to malaria. We show that tolerance is induced by a single malaria episode - in the absence of parasite clearance.
Inflammatory spleen monocytes from C57Bl6/J mice with memory of malaria infection dramatically change their transcriptional response to a second infection; instead of driving emergency inflammation they promote stress and tissue tolerance (RNAseq data available in GEO series GSE150047).
This unique functional profile is not underpinned by alterations in the epigenetic landscape of inflammatory monocytes before their release from the bone marrow (ChIPseq data available in GEO series GSE150478) - tolerance is therefore imprinted within the spleen (microarray data available in GEO series GSE149894).
Hosts thus acquire long-lasting mechanisms that control inflammation (reducing collateral tissue damage) and learn to actively promote stress tolerance (protecting tissues against toxic products and processes) after one malaria episode.

overall_design: Refer to individual Series


title: Tissue printing: splenic red pulp macrophages of once-malaria infected mice are transcriptionally identical to prenatally seeded red pulp macrophages from uninfected mice.

summary: Acute malaria infection with P. chabaudi obliterates embryonically seeded tissue-resident red pulp macrophages in the spleen of C57Bl/6J mice - regardless of whether the infection is mild (mosquito transmitted P. chabaudi AS - no hyperparasitaemia, no measurable clinical manifestations of disease other than low-grade anaemia) or severe (mosquito transmitted P. chabaudi AJ - acute hyperparasitaemia, severe anaemia, hypothermia and prostration). Red pulp macrophages return 100 days later, once mice cleared parasitaemia. We then flow sorted 10,000 red pulp macrophages (lineage-, autofluorescent, F4/80+, B220-, CD11bint, CD11cint) directly into Trizol, extracted total RNA and analysed their transciptome using the affymetrix mouse exon 1.0 ST array.  Red pulp macrophages from mice once infected with mild AS or severe AJ P. chabaudi parasites were compared to uninfected age-matched mice.  We uncover that red pulp macrophages isolated from the spleens of once-malaria infected mice are transcriptionally identical to prenatally seeded red pulp macrophages from uninfected mice. The spleen tissue niche thus imprints an identical functional profile onto these cells - regardless of their origin.

overall_design:
C57Bl/6J mice were bred and housed in individually ventilated cages under specific pathogen free conditions (22°C, 50% humidity) at the University of Edinburgh, UK. Malaria infections were initiated when mice were approximately 9 weeks of age by intravenous injection of 200 sporozoites (according to our previously published protocol: Spence, P.J., et al., Mosquito transmission of the rodent malaria parasite Plasmodium chabaudi. Malar J, 2012. 11: p. 407). We mosquito transmitted two distinct Plasmodium chabaudi chabaudi clones, which we obtained from the European Malaria Reagent Repository (malariaresearch.eu) at the University of Edinburgh: P. chabaudi AS (28AS11) and P. chabaudi AJ (96AJ15). Anopheles stephensi mosquitoes (strain SD500) were reared in house at the University of Edinburgh. We initiated all experimental infections with sporozoites, since we have previously shown that mosquito transmission resets expression of the large sub-telomeric multi-gene families that control parasite virulence, and in turn shapes the host immune response during the pathogenic blood-stage of malaria infection (Spence, P.J., et al., Vector transmission regulates immune control of Plasmodium virulence. Nature, 2013. 498(7453): p. 228-31).
100 days after infection, once mice had cleared parasitaemia, red pulp macrophages were flow sorted from the spleens of mice once-infected with P. chabaudi AS (mild acute infection, n = 4) or P. chabaudi AJ (severe acute infection, n = 3) and their transcriptome compared to red pulp macrophages isolated from age-matched uninfected mice (n = 5).

first: Wiebke

last: Nahrendorf

middle: C

first: Philip

middle: J

last: Spence


title: Genetic dissection of a super enhancer controlling the Nppa-Nppb locus in the heart (CUT&RUN)

status: Public on Nov 25 2020

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: CUT&RUN H3K27ac PCM-1 sorted left ventricle of Nppa-Nppb double-knockout

overall_design: CUT&RUN H3K27ac PCM-1 sorted left ventricle of 8-12 wks old Nppa-Nppb double-knockout

first: Joyce

last: Man

first: K

last: van Duijvenboden


title: Expression array data from human gastric cancer cell lines

status: Public on Nov 27 2020

city: Itabashi-Ku

first: Yu

last: Takahashi

state: Tokyo

department: gastroenterology

country: Japan

institute: Nihon University

summary:
We used microarrays to identify the gene expression accompanied with growth arrest caused by the transduction of CDX1 or CDX2.
Ectopic expression of CDXs causes intestinal metaplasia, which is thought to be precancerous legion of gastric cancer. On the contrary, there were some studies reported that CDX2 positive gastric cancers showed better prognosis or tumor suppressive activity. To evaluate the effect of exogenous CDX expression in  gastric cancer cells, we  transducted CDX1 or CDX2 in two   CDX negative expression cell lines, MKN7 and TMK1.

overall_design: Two CDX negative expression gastric cancer cell lines, MKN7 and TMK1, were transducted CDX1, CDX2 and/or Puromycin resistant gene by retrovirus vector. Both of them showed marked cell growth suppression and morphological change and lead eventually to cell death To clalify the mechanism of this growth arerst, extraction of RNA were performed at post infection day 7, which is the day after complete selection but before cell death. As a control, we used not infected cells and only puromycin resistant gene transducted cells.

first: Chiemi

last: Nakayama

first: Nobutake

last: Yamamichi


title: Transcriptional response in ileum tissue from wild-type and Fat1+/- male mice

status: Public on Nov 24 2020

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Males were placed onto an all liquid diet with gradually increasing amounts of ethanol as follows:  no ethanol for 2 days, 1% (v/v) for 2 days, 2% for 2 days, 4% for 1 week, 5% for 1 week, and 6% for 3 weeks.  At the end of the experiment, one group from each genotype was injected with 5 mg/kg LPS.  Mice were then euthanized 24 hours later.

overall_design: For the initial sequencing, a total of four conditions, with 3-5 replicates in each condition, were studied, including: Wild-type, pair-fed (WT-PF); Fat1+/-, pair-fed (Fat1+/- -PF); Wild-type, Ethanol-Fed (WT-EtOH); and Fat1+/-, Ethanol-Fed (Fat1+/- - EtOH).

first: Irina

middle: A

last: Kirpich

first: Dennis

last: Warner


title: Genetic dissection of a super enhancer controlling the Nppa-Nppb locus in the heart (RNA-Seq)

summary: Whole transcriptome expression analysis of RE1-deficient mice

overall_design: RNA-seq on left ventricle of 8-12 wks old RE1-deficient mice

middle: K


title: Short and mid-term effects on performance, health and qualitative behavioural assessment in Romane lambs in different milk feeding conditions

status: Public on Nov 23 2020

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

summary: The common practise of artificially rearing some lambs from prolific meat breeds of sheep constitutes a welfare issue due to increased mortality rates and negative health issues. In this multidisciplinary study, we investigated the possible short and mid-term advantages of artificially feeding fresh ewe’s milk instead of commercial milk replacer on lambs’ growth, health and welfare. Romane lambs were either separated from their mothers on D3 and fed with Lacaune ewes’ milk (LAC, n=13) or milk replacer (REP, N=15), or they were reared by their mothers (MOT, n=15). On D45, they were weaned, gathered in single sex groups until the end of the study on D150. Lamb performance and biomarkers of overall health were assessed by measuring: growth, dirtiness of the perianal area, enteric pathogens in the faeces, total antioxidant status and redox status assessed by plasma reduced (GSH)/oxidized (GSSG) glutathione ratio, and immune response after vaccination against chlamydiosis. As an exploratory approach, blood cell transcriptomic profiles were also investigated. Last, Qualitative Behaviour Assessment was performed as an integrated welfare criteria. LAC and REP never differed in their average daily gain but grew less than MOT lambs in the early suckling period and just after weaning. No effect was detected afterwards. On D30, LAC and REP lambs had lower total antioxidant and higher redox status than MOT lambs but did not differ among themselves. LAC and MOT had a cleaner perianal area than REP lambs on D21, while faecal pathogen infection did not vary between the treatment groups. After vaccination, LAC also had a stronger immune response on D90 compared to REP lambs. Transcriptome analysis performed on D150 showed differential gene expression, mainly in relation to inflammatory, immune and cell cycle response, between male lambs of the LAC group and those of the MOT and REP groups. Based on Qualitative Behaviour Assessment, LAC lambs never differed from MOT lambs in their general activity and varied from REP only on D21; REP lambs were always more agitated than MOT lambs. In conclusion, artificial milk feeding impaired early growth rate, health, and emotional state mainly during the milk feeding period and at weaning. Feeding artificially reared lambs with fresh ewe's milk partly mitigated some of the negative effects induced by milk replacer but without achieving the full benefit of being reared by the mother.

overall_design: A flock of 32 ewes gave birth within a week under 24/24h supervision mainly to twins and triplets. On day 3 (D3), lambs were randomly allocated by sex and birth weight (minimum 2.5 kg) into 3 groups. In 2 of them, lambs were separated from their mother and artificially fed with either a milk replacer (REP group) or fresh ewes’ milk (lacaune milk, LAC group). In the third group, lambs remained with their dam (natural rearing, MOT group). Transcriptomic analyses were performed on 6 males and 4 females of the MOT group, 4 males and 7 females of the LAC group and 6 males and 5 females of the REP group. All animals were sampled at D150.

first: M

last: Mialon

first: X

last: Boivin

first: D

last: Durand

first: A

last: Boissy

first: E

last: Delval

middle: S

last: Bage

first: C

last: Clanet

first: F

last: Cornilleau

last: Parias

last: Foury

middle: P

last: Moisan

first: T

last: Fassier

last: Marcon

first: L

last: Guilloteau

first: R

last: Nowak


title: Bone marrow monocytes from once-malaria infected mice have no epigenetic memory of the infection.

first: Alasdair

last: Ivens

summary:
Disease tolerance is an alternative strategy for acquired immunity to malaria and can be rapidly induced after a single malaria episode - in the absence of improved parasite clearance. Memory of a first malaria episode dampens the inflammatory profile of spleen monocytes and induces mechanisms of stress tolerance to minimise tissue damage. This begs the question how monocytes are instructed to respond in a different way to second compared to first malaria infection. We asked if malaria alters the epigenetic landscape of inflammatory monocytes before their release from the bone marrow - thus testing the compelling innate memory hypothesis. We compared the genome-wide distribution of histone modifications on flow-sorted bone marrow monocytes from mice with memory of severe mosquito transmitted P. chabaudi AJ infection (30 days after drug cure) and drug treated uninfected age-matched controls using ChIPseq. Specifically, we tested whether once-infected mice have long-lived modifications in i) transcription start sites marked with H3K27ac to activate transcription ii) enhancers or superenhancers marked with H3K4me1 to promote gene expression and iii) in H3K9me3 to condense DNA into heterochromatin thereby silencing gene expression.
We found no meaningful differences in the histone modification profiles of 2848 genes that define monocyte function in first and second malaria infection using the motif discovery software HOMER. Furthermore, when calling differentially modified regions (DMR) between once-infected mice and uninfected mice to ask whether there were any measurable differences in the epigenetic landscapes of these genes, we found 95% had no detectable modifications. In those rare cases where a DMR was called, HOMER assigned a low peak score, indicating low confidence and minimal biological relevance. Epigenetic reprogramming does therefore not underpin the functional specialisation of inflammatory monocytes in tolerised hosts. Innate memory is thus not induced by malaria infection in vivo. Instead, altered monocyte function and fate are imprinted within the spleen (link to GEO microarray) to promote disease tolerance.

overall_design: C57Bl6/J mice were infected with mosquito transmitted P. chabaudi AJ, leading to an acute severe malaria episode and persisting chronic infection, which was drug treated using chloroquine after 40 days. 30 days after the start of drug treatment we assessed the enrichment of three histone modifications (H3K27ac, H3K4me1 and H3K9me3) in flow-sorted bone marrow monocytes relative to non-immunoprecipitated input. Histone modification profiles of genes that could promote or silence malaria responsive gene expression, and thus impart innate memory in once-infected mice, were compared to age-matched uninfected mice receiving an identical chloroquine regimen.

first: Wiebke

last: Nahrendorf

first: Philip

last: Spence


title: Fully defined human PSC-derived microglia and tri-culture system reveals cell type specific potentiation of complement C3 production in a model of Alzheimer’s disease [smarter-seq]

status: Public on Nov 22 2020

city: New York

first: Sudha

last: Guttikonda

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: MSKCC

summary: Aberrant inflammation in the central nervous system (CNS) has been implicated as a major player in the pathogenesis of human neurodegenerative disease. However, the specific contribution of each cell type to the neuroinflammatory axis in vivo remains unclear with species-specific differences in key signaling pathways further complicating the challenge. To assemble a fully human platform to study neuroinflammation, we first developed a novel approach to derive microglia from human pluripotent stem cells (hPSCs) that faithfully recapitulates microglial ontogeny as validated by single cell RNA-sequencing and stage-specific mapping onto datasets of developing mouse microglia. Using these cells, we build the first defined and completely hPSC-derived tri-culture system containing pure populations of hPSC-derived microglia, astrocytes, and neurons to dissect cellular crosstalk along the neuroinflammatory axis in vitro. We next used the tri-culture system to model neuroinflammation in Alzheimer’s Disease using hPSCs harboring the APPSWE+/+ mutation and their isogenic control. Our data reveal that production of complement C3, a protein that is increased under inflammatory conditions and implicated in synaptic loss, is potentiated under tri-culture conditions, and is further enhanced in APPSWE+/+ tri-cultures. Using cell type-specific ablation studies, we report that C3 potentiation is due to the presence of a neuroinflammatory loop in which microglia are the key initiators that activate reciprocal signaling with astrocytes to produce excess C3. Our study defines the major cellular players contributing to increased C3 in AD and presents a broadly applicable platform to study neuroinflammation in human disease.

overall_design: hPSC-derived microglia derived from 2 different methods are compared to primary human microglia, in triplicate, using 3 different lines. hPSC-derived neurons sorted from co-cultured samples serve as a negative control.

first: Lisa

last: Sikkema

first: Jason

last: Tchieu

first: Nathalie

last: Saurat

first: Ryan

last: Walsh

first: Gabriele

last: Ciceri

first: Marjolein

last: Sneeboer

first: Linas

last: Mazutis

first: Manu

last: Setty

first: Lot

middle: D

last: de Witte

first: Dana

last: Pe'er

first: Lorenz

last: Studer


title: Transcriptome Effects of the knockout of Intraflagellar Transport 88 gene in mice Mitral leaflets

status: Public on Nov 20 2020

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: The gene Ift88 is a gene critical for primary cilium biogenesis, the objective this study was to determine the transcriptome changes in Mitral leaflets in the absence of the gene.

overall_design: Examination of transcriptome changes in an in vivo model organism knockout of the gene Ift88.

first: Katelynn

last: Toomer

first: Mengyao

last: Yu

first: Diana

last: Fulmer

first: Lilong

last: Guo

first: Neal

last: Peterson

first: Alex

last: Drohan

first: Breiona

last: Catching

first: Andy

last: Wessels

first: Joshua

last: Lipschutz

first: Francesca

middle: N

last: Delling

first: Xavier

last: Jeunmaitre

first: Christian

last: Dina

last: Collins

first: Harrison

last: Brand

first: Mike

last: Talkowski

first: Rupak

last: Mukherjee

first: Simon

last: Body

first: Willian

last: da Silveira

first: Baolin

last: Wang

first: Maire

last: Leyne

first: Ronen

last: Durst

first: Roger

last: Markwald

first: Solena

last: Le Scouranec

first: Albert

last: Hagege

first: David

last: Milan

first: Jean-Jacques

last: Schott

first: Thierry

last: Le Tourneau

first: Robert

last: Levine

first: Nabila

last: Bouatia-Naji

first: Susan

last: Slaugenhaupt

first: Russell

last: Norris


title: A single malaria episode induces mechanisms that minimise inflammation and promote tolerance in spleen inflammatory monocytes.

first: Alasdair

last: Ivens

summary:
Disease tolerance is an important alternative strategy for rapidly acquired immunity to malaria. We show that tolerance is induced by a single malaria episode - in the absence of parasite clearance. Inflammatory spleen monocytes from C57Bl6/J mice respond with interferon-stimulated inflammation to acute first Plasmodium chabaudi infection and are destined to differentiate into inflammatory macrophages. This dramatic transcriptional response is tolerised during persisting chronic infection (with parasite densities up to 1000 parasites per µl), since the fitness costs of maintaining an emergency inflammatory response for several months would not be compatible with survival. However, spleen monocytes from chronically infected mice are not in a permanent refractory state, since their inflammatory response is identical to monocytes from uninfected mice when removed from the spleen and stimulated with LPS in vitro.
Using a newly developed reinfection model to closely match parasitaemia between first and second P. chabaudi infection, we further uncover that memory of first malaria infection (30 days after drug treatment of chronic infection) dramatically changes the transcriptional response of inflammatory spleen monocytes to second infection. They now minimise inflammation and instead promote stress and tissue tolerance. This unique functional profile is not underpinned by alterations in the epigenetic landscape of inflammatory monocytes before their release from the bone marrow (link to GEO ChIPseq) - tolerance is therefore imprinted within the spleen. Hosts thus acquire long-lasting mechanisms that control inflammation (reducing collateral tissue damage) and learn to actively promote stress tolerance (protecting tissues against toxic products and processes) after one malaria episode.

overall_design: Transcriptional response of inflammatory spleen monocytes from C57Bl/6J mice to i) acute (mild P. chaubaudi AS & severe P. chabaudi AJ) and ii) chronic mosquito transmitted P. chabaudi infection. iii) the response of spleen monocytes from chronically malaria infected mice to restimulation with LPS in vitro. iv) their memory response 30 days after drug treatment of chronic P. chabaudi infection. v) spleen inflammatory monocyte response to second infection in our novel reinfection model with identical parasite densities between first and second infection.

first: Wiebke

last: Nahrendorf

first: Philip

last: Spence


title: Relationship between insulin sensitivity and gene expression in human skeletal muscle (Study B)

status: Public on Nov 19 2020

city: Tampa

first: Hemang

middle: Mahendrakumar

last: Parikh

state: FL

address: 3650 Spectrum Blvd.

department: Health Informatics Institute

institute: University of South Florida

summary: We studied 9 healthy young non-diabetic men without any family history of diabetes. The mean age and body mass index (BMI) were 25.33 ± 0.33 years and 24.57 ± 0.62 kg/m2, respectively, and the mean 1/ homeostatic model assessment of insulin resistance (HOMA-IR) was 1.17 ± 0.12. We included baseline gene expression profile data (i.e. only before bed rest)

overall_design: The aim of this study was to investigate molecular mechanisms associated with insulin sensitivity in skeletal muscle by relating global skeletal muscle gene expression with a surrogate measure of insulin sensitivity, i.e. homeostatic model assessment of insulin resistance (HOMA-IR)


title: Relationship between insulin sensitivity and gene expression in human skeletal muscle

summary:
The aim of this study was therefore to investigate molecular mechanisms associated with insulin sensitivity in skeletal muscle by relating global skeletal muscle gene expression with a surrogate measure of insulin sensitivity, i.e. homeostatic model assessment of insulin resistance (HOMA-IR). To identify genes with skeletal muscle expression related to insulin sensitivity, we obtained muscle biopsies from 38 non-diabetic participants in study A. We then profiled muscle gene expression using Affymetrix oligonucleotide microarrays (Affymetrix Custom Array NuGO-Hs1a520180 GeneChip). To replicate the findings from study A, we included 9 non-diabetic participants from study B. We performed skeletal muscle gene expression profiling from these participants using the Agilent oligonucleotide microarrays (Agilent-G4112F (Feature Number version)). Insulin sensitivity was estimated using the 1/HOMA-IR method calculated from the oral glucose tolerance test (OGTT) values.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
The aim of this study was therefore to investigate molecular mechanisms associated with insulin sensitivity in skeletal muscle by relating global skeletal muscle gene expression with a surrogate measure of insulin sensitivity, i.e. homeostatic model assessment of insulin resistance (HOMA-IR).

Refer to individual Series


title: Relationship between insulin sensitivity and gene expression in human skeletal muscle (Study A)

summary: To identify genes correlated to insulin sensitivity in skeletal muscle, we studied 38 non-diabetic men from Malmö, Sweden. Briefly, the Malmö Exercise Intervention cohort consists of sedentary but otherwise healthy male subjects from southern Sweden. They all have European ancestry and 18 of them have a first-degree family member with T2D. The mean age and body mass index (BMI) were 37.71 ± 0.71 years and 28.47 ± 0.48 kg/m2, respectively, and the mean 1/the homeostatic model assessment-insulin resistance (HOMA-IR) was 0.69 ± 0.04


title: Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure

city: Potsdam

first: Heinrich

last: Bente

address: Am Muehlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

type: Non-coding RNA profiling by high throughput sequencing

summary: A role for sRNAs in paramuation is emerging, but their nature and mode of action remain elusive. Paramutation between genetically identical epialleles in Arabidopsis allowed the analysis of associated sRNAs (the data deposited here) and revealed differences connected with gene expression, tissue type, and ploidy.

overall_design: Six sRNA libraries prepared from total RNA of seedlings and 14  libraries with sRNAs enriched from flower buds;  using diploid or tetraploid Arabidopsis thaliana plants with active or silent epialleles.

first: Andrea

last: Foerster

first: Nicole

last: Lettner

first: Ortrun

last: Scheid


title: OXPHOS deficiency activates global adaptation pathways to maintain mitochondrial membrane potential

city: Beijing

first: Hui

last: Jiang

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences

summary: Reduction of mitochondrial membrane potential is a hallmark of mitochondrial dysfunction. It activates adaptive responses in organisms from yeast to human to rewire metabolism, remove depolarized mitochondria, and degrade unimported precursor proteins. It remains unclear how cells maintain mitochondrial membrane potential, which is critical for maintaining iron-sulfur cluster (ISC) synthesis, an indispensable function of mitochondria. Here we show that yeast oxidative phosphorylation mutants deficient in complex III, IV, V, and mtDNA respectively, have graded reduction of mitochondrial membrane potential and proliferation rates. Extensive omics analyses of these mutants show that accompanying mitochondrial membrane potential reduction, these mutants progressively activate adaptive responses, including transcriptional downregulation of ATP synthase inhibitor Inh1 and OXPHOS subunits, Puf3-mediated upregulation of import receptor Mia40 and global mitochondrial biogenesis, Snf1/AMPK-mediated upregulation of glycolysis and repression of ribosome biogenesis, and transcriptional upregulation of cytoplasmic chaperones. These adaptations disinhibit mitochondrial ATP hydrolysis, remodel mitochondrial proteome, and optimize ATP supply to mitochondria to convergently maintain mitochondrial membrane potential, ISC biosynthesis, and cell proliferation.

overall_design:
1. Differential expression analysis between OXPHOS mutants and WT cells.
2. Examination of gene expression upon PUF3 deletion in WT, atp7D and r0 cells.
3. Examination of gene expression upon blocking Puf3 hyperphosphorylation in WT and r0 cells.
4. Examination of gene expression upon SNF1 deletion in WT and r0 cells.
5. Examination of gene expression upon INH1 overexpression in r0 cells.
6. Examination of gene expression upon MIG1 deletion in snf1 r0 cells.
7. Analysis of ribosome footprints in WT, puf3D, r0, puf3D r0 cells.
Three biological replicates were prepared for mRNA profiles, and two biological replicates were prepared for ribosome profiling.

first: Siqi

last: Liu

first: Shanshan

first: Baiyu

last: He

first: Lanlan

last: Li

first: Jiawen

last: Wang

first: Tao

last: Cai

first: She

last: Chen


title: Expression profile of the 22Rv1 cells overexpressing ABHD5

city: Detroit

first: Jian

state: MI

address: 6135 Woodward Ave

institute: Wayne State University School of Medicine

summary: ABHD5 is a crucial metabolic regulator of cancer cells. The goal of this study is to identify the regulation of gene expression by ABHD5 in prostate cancer cells using RNA-seq.

overall_design: We utilized a 22Rv1 cell line engineered to overexpress a doxycycline-inducible ABHD5 transgene stably. The cells were grown in the absence or presence of doxycycline for 48 h and then harvested for transcriptome profiling.

first: Guohua


title: Response of E. coli to m-Tyrosine

city: Los Angeles

first: Beth

last: Lazazzera

state: CA

address: 405 Hilgard Ave.

department: MIMG

institute: UCLA

summary: To ensure faithful translation of the genetic code, some aminoacyl-tRNA synthetases have a quality control (QC) mechanism that allows them to remove similarly shaped, non-protein amino acids (NPAs) from a mischarged tRNA.  In E. coli, the QC function of phenyalanyl-tRNA synthetase (PheRS) is required for resistantce to the toxic NPA, meta-Tyrosine (m-Tyr).  Here, we sought to understand the mechanism of m-Tyr toxicity. Using RNA-seq, we observed >500 genes were differential expressed after the addition of m-Tyr. The most strongly up-regulated genes are involved in unfolded-protein stress response, and cells exposed to m-Tyr contained large, electron-dense protein aggregates, indicating that m-Tyr destabilized a large fraction of the proteome.  Additionally, we observed that amino acid biosynthesis and transport regulons, controlled by ArgR, TrpR, and TyrR, and the stringent-response regulon, controlled by DksA/ppGpp, were differentially expressed. m-Tyr resistant mutants were isolated and found to have altered a promoter to increase expression of the enzymes for Phe production or to have altered transporters, which likely result in less uptake or increased efflux of m-Tyr. These findings indicate that QC by PheRS is the critical point for resisting the toxic effects of m-Tyr, when m-Tyr has passed the QC checkpoint and enters the proteome, it is sequestered in protein aggregates that are eventually lost through cell division.

overall_design: A 5 ml LB culture was inoculated from a single colony of BAL4703 (pheT(G318W)) strain and grown until it reached mid-log phase (OD600 0.4-0.6).  A 1 ml sample of the cells were then washed in 0.9% NaCl and used to inoculate a 100 ml, M9 minimal media culture in a 500 ml flask to an OD600 of 0.001. The M9 culture was allowed to grow with shaking at 37°C until it reached an OD600 of 0.5.  A sample of cells was taken at this time (t=0) for RNA purification and CFU/ml determination.  A m-Tyr solution was then added to the culture to 0.5 mM.  The culture was then allowed to continue growing at 37C with shaking.  Additional sampling for RNA purification and CFU/ml measurements was done at 30, 60, and 120 minutes after m-Tyr addition.  This protocol was repeated for a total of three biological replicates.


title: RNA sequencing and gene analysis of unstimulated and stimulated MRSA cultures

city: Padova

first: PAOLA

last: BRUN

state: PD

address: via Gabelli

department: Molecular Medicine

country: Italy

institute: Università di Padova

summary: Aim: the goal of this study is to compare Quorum sensing related gene expression in MRSA cultures incubated with an aza-derivative

overall_design:
Methods: 1x10^6 CFU/ml bacteria were grown for 16 hours in the presence or absence of an aza-derivative (100 microM) or vehicle (DMSO 0,05%). The bacterial RNA was purified using the GRS Total RNA Kit – Bacteria (#GK16.0100, GRISP Research Solution) following the manufacturer’s instructions. Integrity was evaluated both by agarose gel electrophoresis and BioAnalyzer analysis before RNA-seq analysis was carried out.  RNA-seq libraries were prepared with the TruSeq RNASample Prep kit (Illumina, San Diego, CA). The total RNA samples were subjected to poly(A) enrichment, and 100 nucleotides of sequence was determined from both ends of each cDNA fragment using the HiSeq platform (Illumina). Sequencing reads were annotated and aligned to the USA300 MRSA reference genome using TopHat. Comparisons were made between MRSA vehicle (DMSO 0,05%) and MRSA treated with the aza-derivative.
Result: a set of genes known to be functionally related to agr QS system were selected a priori by retrieving all the genes that were used to construct a Boolean network describing quorum sensing in Staphylococcus aureus.  The genes were divided into four categories: virulence, metabolism, membrane, and gene expression.

first: G

last: Bernabè

first: I

last: Castagliuolo

first: P

last: Brun


title: CD14+ Bovine Milk Macrophage Challenge with Streptococcus uberis

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

institute: University of Nottingham

summary: CD14+ Macrophage were challenged with Wildtype (WT), or S1154-deletion mutant (Del), and sequenced at timepoints zero hours (T0) and twenty-four hours (T24). To generate DEGs T0 and T24 timepoints were compared, a multifactor DESEQ2 run comparing T0 and T24 in both Wildtype and Deletion strains, and a direct comparison of T24 timepoints in Mutant and Deletion were generated.

overall_design: Three replicates of each of: WT T0; WT T24; Del T0; Del T24 were generated using the Quantseq-3' FWD protocol, with the additional of the optional UMI during second strand synthesis. After sequencing across four lanes of a Nextseq 500 high yield run, the data was demulitplexed using BCL2FASTQ with the --no-lane-splitting option enabled. UMIs were used to correct for any PCR amplification errors during alignment using the standard Quantseq-3' FWD-UMI pipeline. For final analysis, (UMI-corrected) read counts were read into R studio and differential expression analysis carried out with DESEQ2. The various plots were generated in graphpad prism or R studio using the enhanced volcano and ggplot2 libraries.

first: James

last: Leigh

first: Tracey

last: Coffey

first: Sharon

last: Egan


title: Isosorbide di-(linoleate/oleate) stimulates pro-differentiation gene expression to restore the epidermal barrier and improve skin hydration

status: Public on Nov 16 2020

city: Ann Arbor

first: William

last: Swindell

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

summary: The breakdown of epidermal barrier and consequent loss of skin hydration is a feature of skin aging and eczematous dermatitis. Few treatments, however, resolve these underlying processes to provide full symptomatic relief. In this study, we generated a novel compound, isosorbide di-(linoleate/oleate) (IDL), by esterifying isosorbide with sunflower fatty acids. Topical effects of IDL in skin were compared to those of ethyl linoleate/oleate (EL), which has previously been shown to improve skin barrier function. Both IDL and EL down-regulated inflammatory gene expression, but IDL more effectively up-regulated the expression of genes associated with keratinocyte differentiation (e.g., KRT1, GRHL2, SPRR4). Consistent with this, IDL increased abundance of epidermal barrier proteins (filaggrin and involucrin) and prevented cytokine-mediated stratum corneum degradation. IDL also down-regulated expression of “unhealthy skin signature” genes linked to loss of epidermal homeostasis and uniquely repressed an interferon-inducible co-expression module activated in multiple skin diseases including psoriasis. In a double-blind placebo-controlled trial enrolling females with dry skin, 2% IDL lotion applied over 2 weeks significantly improved skin hydration and decreased transepidermal water loss (NCT04253704). These results demonstrate mechanisms by which IDL improves skin hydration and epidermal barrier function, supporting IDL as an effective intervention for treatment of xerotic pruritic skin.

overall_design: Total RNA obtained from EpiDermFT skin substitutes treated with 0.1% DMSO (control, CTL), ethyl linoleate/oleate (EL, 50 µg/ml) or isosorbide di-(linoleate/oleate) (IDL, 50 µg/ml) for 48 hours (n = 2 replicates per treatment).

first: Krzysztof

last: Bojanowski

first: Shyla

last: Cantor

first: Ratan

last: Chaudhuri


title: Targeted single-cell RNA-seq identifies minority cell types of kidney distal nephron & A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse

status: Public on Nov 18 2020

city: Bethesda

first: Lihe

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary: Characterization of gene expression for each renal cell type is essential for identifying mechanisms underlying kidney physiology and pathophysiology. Here, we built a transcriptome landscape mouse renal epithelial cells by deep sequencing of all 14 mouse renal segments, upon which we developed an enrichment protocol to characterize distal nephron cells by single-cell RNA-seq. Our renal tubule expression atlas provided landscapes of gene expression and alternative splicing along the renal tubule segments.  We identified, and integrated segment-specific genes with human gene nomenclature to understand the gene function and conservation. We further developed an enrichment strategy for single-cell analysis of distal nephron cells. The analysis revealed heterogeneous gene expression in DCT1-DCT2-CNT. Moreover, we identified two mosaic cell types in thick ascending limb and verified their presence in mouse kidney tissue. Our data provides a rich resource for kidney research and we provide our data user-friendly at https://esbl.nhlbi.nih.gov/MRECA/Nephron/ and https://esbl.nhlbi.nih.gov/MRECA/DCT/.

overall_design:
To quantify the gene expression, we carried out ultra-low input RNA-Seq in each of the 14 renal tubule segments plus glomerulus from male mouse kidneys. Samples were collected from at least 3 mice (6- to 8-week-old). In total, we analyzed 93 samples from 53 mice (87 renal tubules plus 6 glomeruli).   For single-cell RNA-seq, we dissociated the mouse renal cortical tissue into single-cell suspensions using a cold-active protease followed by cell enrichment for scRNA-seq on 10X Chromium platform. We carried out 3 independent runs with 3000-6000 cells each as input

Definitions:
PTS1, initial segment of the proximal convoluted tubule
PTS2, proximal straight tubule in cortical medullary rays
PTS3, last segment of the proximal straight tubule in outer stripe of outer medulla
DTL1, short descending limb of the loop of Henle
DTL2, long descending limb of the loop of Henle in the outer medulla
DTL3, long descending limb of the loop of Henle in the inner medulla
ATL, thin ascending limb of the loop of Henle
MTAL, medullary thick ascending limb of the loop of Henle
CTAL, cortical thick ascending limb of the loop of Henle
DCT, distal convoluted tubule
CNT, connecting tubule
CCD, cortical collecting duct
OMCD, outer medullary collecting duct
IMCD, inner medullary collecting duct

first: Chun-Lin

last: Chou

first: Mark

last: Knepper


title: Identification of exosomal circRNAs as potential biomarkers for postmenopausal osteoporosis

status: Public on Nov 13 2020

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

institute: Third Affiliated Hospital of Soochow University

summary: Background: Osteoporosis is one of the most common chronic diseases around the world, especially in postmenopausal women. Circular RNAs (circRNAs) are emerging as important regulators in human disease. The aim of the present study was to analyze circRNA expression profiles in osteoporosis and to explore the clinical significance.  Methods: The serum samples were collected from osteoporosis patients and healthy people. The circRNA array was performed to screen for differentially expressed circRNAs. The mRNA expression levels of target genes were analyzed by quantitative real-time PCR (qRT-PCR).   Results: Hsa_circ_0006859 was identified as one of the most upregulated circRNAs in the microarray analysis. Hsa_circ_0006859 in exosome was upregulated in osteoporosis patients compared with healthy controls. Hsa_circ_0006859 could differentiate osteopenia or osteoporosis patients from healthy controls with high sensitivity and specificity.  Conclusion: Exosomal hsa_circ_0006859 is a potential biomarker for postmenopausal osteoporosis.

overall_design: The circRNA expression profiles of exosomes isolated from osteoporosis patients (N=3) and healthy controls (N=3) were examined by circRNA microarray.

first: Fei

last: Hua


title: Silencing ZNF180, ZNF347 and PPP1R2 in SkMEL147 cells

first: Won-Min

last: Song

address: One Gustave L. Levy Place, Box 1123

institute: Icahn school of medicine at Mount Sinai

summary: ZNF180, ZNF347 and PPP1R2 were silenced by respective siRNA in SkMEL147 cells, in conjunction with non-transfected controls.

overall_design: 3 biological replicates were generated per siRNA.

first: Praveen

last: Agrawal

first: Bin

last: Zhang

first: Eva

last: Hernando


title: Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders

city: Brisbane

first: Marta

middle: Filipa

last: Nabais

state: Queensland

address: 306 Carmody Rd, St. Lucia

department: Institute for Molecular Biosciences

country: Australia

institute: University of Queensland

summary: People with neurodegenerative disorders have diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) is a widely studied chemical modification to DNA, and increasing evidence suggests that DNAm alterations play an important role in neurodegenerative disorders. In this study we aimed to identify shared blood DNAm differences between 471-1,522 controls and people with Alzheimer’s disease (N = 161), amyotrophic lateral sclerosis (N = 3,032) and Parkinson’s disease (N = 1,132). We used a mixed-linear model method (MOMENT) that has been shown to account for the effect of (un)known confounders, to test for association of each DNAm site with each disorder. A fixed-effects meta-analysis of Alzheimer’s disease, amyotrophic lateral sclerosis, and Parkinson’s disease results identified 12 differentially methylated positions passing a genome-wide significant threshold. Predicted immune cell-type proportions were disrupted across all neurodegenerative disorders, as well as schizophrenia and rheumatoid arthritis. Protein inflammatory markers were correlated with profile sum-scores derived from disease-associated immune cell-type proportions in a healthy ageing cohort. In contrast, they were not correlated with MOMENT DNAm-derived profile sum-scores, calculated using effect sizes of the 12 differentially methylated positions as weights. We have identified shared differentially methylated positions in whole blood between neurodegenerative disorders that point to shared pathogenic mechanisms. These shared differentially methylated positions may reflect causes or consequences of disease, but they are unlikely to reflect cell-type proportion differences.

overall_design:
161 Alzheimer's disease patients, 471 healthy individuals and 94 mild cognitive impairment patients, from the AIBL cohort (https://aibl.csiro.au/). All the other accession number from publicly available data used in this study have been properly cited in the accompanying manuscript.

For data access questions please contact Prof. Simon Laws at: s.laws@ecu.edu.au

middle: F

first: Simon

last: Laws

first: Naomi

last: Wray

first: Allan

last: McRae

first: Anjali

last: Henders

first: Leanne

last: Wallace


title: Distal regulation of c-myb expression in human myeloid leukemia cells

city: Shanghai

first: Mengjia

last: Li

address: 999 Hucheng Ring Road

department: College of Fisheries and Life Science

institute: Shanghai Ocean University

summary: The transcription factor c-Myb a key regulator in proliferation and differentiation of hematopoietic progenitor cells, is precisely regulated during essential cellular processes. Overexpression and rearrangement of c-myb has been reported in human tumors including myeloid leukemia, but exact regulatory mechanisms have remained elusive. Here, we identified, using 4C assay with the c-myb promoter as an anchor, the interaction site at -34k region upstream of c-myb gene that are involved in c-myb expression.  Furthermore, we found that the long-range interactions changed with c-myb being down-regulated on differentiation progress in human myeloid leukemia cell lines. Taken together, our date revealed that a potential c-myb enhancer-promoter interactions may be a particularly important regulatory mechanism for c-myb gene expression in human myeloid leukemia cells.

overall_design: We used human myeloid leukemia cell lines K562, U937 and HL60 to carry out 4C-seq experiments, as a control, we carried out parallel 4C measurements in HeLa cells, the c-myb promoter fragment served as a bait fragment to detect the long-range interactions. To validate the presence of potential enhancers in Hbs1l-Myb intergenic region that regulate c-myb transcription by physically interacting with the c-myb promoter via chromatin looping, 4C-Seq was subsequently carried out using the c-myb promoter as viewpoint in K562, U937 and HL60 cells before and after differentiation, representing stages of high and low c-myb expression, respectively.

first: Penglei

last: Jiang

first: Bingshe

last: Han

first: Junfang


title: Phenotypic characterization of Adig null mice suggests roles for adipogenin in the regulation of fat mass accrual and leptin secretion

status: Public on Nov 11 2020

city: Cambridge

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

institute: WT-MRC Institute of Metabolic Science

summary:
Adipogenin (Adig) is an adipocyte-enriched transmembrane protein. Its expression is induced during adipogenesis in rodent cells and a recent genome wide association study associated BMI-adjusted leptin levels with the ADIG locus.
In order to begin to understand the biological function of adipogenin, we studied adipogenesis in Adig deficient cultured adipocytes and phenotyped Adig null (Adig-/-) mice. Data from Adig deficient cells showed that Adig is required for adipogenesis.
In vivo, Adig-/- mice were leaner than wildtype mice when fed a high-fat diet and when crossed with Ob/Ob hyperphagic mice.
In addition to the impact on adipogenesis and fat mass accrual, Adig deficiency also reduced fat mass adjusted plasma leptin levels and impaired leptin secretion from adipose explants, suggesting an additional direct impact on the regulation of leptin secretion.

overall_design: Two genotypes (Wild type and Adig-/-) were studied under the Chow Diet dietary condition. For each sample, 5 replicates were considered.

first: Anna

last: Alvarez Guaita


title: Next Generation Sequencing Facilitates Quantitative Analysis of The Transcriptome of Microbiota-Specific Memory CD4 Cells With vs Without CAMCI Treatment

status: Public on Nov 12 2020

city: Birmingham

first: Charles

middle: O

last: Elson

state: Alabama

address: 1825 University Blvd

department: Gastroenterology - Medicine

institute: University of Alabama at Birmingham

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the transcriptomes of microbiota-specific memory CD4 T cells that were treated with vs without the combination of cell activation and metabolic checkpoint inhibition (CAMCI) strategy in vivo.
Methods: mRNA profiles of donor-derived CBir1 TCR Tg CD4+ cells were generated by deep sequencing, with cells from 3-4 mice polling together per group, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed with DESeq2 for gene expression comparisons between groups of samples. The Wald test was used to generate p-values and log2 fold changes.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (GRCm38). Depending on the groups that were compared, a range from 17-2868 transcripts showed differential expression, with an absolute log2 fold change >1 and an adjusted p value <0.01. Differentially expressed genes (DEGs) were used to generate a heatmap, a principle component analysis plot, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.

overall_design: Comparison of donor-derived CBir1 TCR Tg CD4+ cells isolated from No treatment, MEP1+CMC treatment, MEP1+Metformin treatment, MEP1+Rapamycin treatment, and MEP1+Metformin+Rapamycin treatment groups.

first: Qing

last: Zhao

first: Fengyuan

last: Huang


title: RNA sequencing of CHBP- and CHBP+ monocyte myeloid-derived suppressor cells

status: Public on Nov 05 2020

first: Jiawei

address: 180 Fenglin Road

institute: Fudan University Zhongshan Hospital

summary: MDSC (myeloid-derived suppressor cells) can be divided into two subsets: granulocytic MDSC (G-MDSC) and monocyte MDSC (M-MDSC).We found that CHBP induced M-MDSC have stronger immunosuppressive function. To identify the specific role of CHBP induced M-MDSC, we used RNA squencing to compare the M-MDSC with CHBP induced M-MDSC. We analyzed the differential expressed genes between these two groups.

overall_design: We first used GM-CSF and CHBP to induce MDSC from bone marrow in vitro. Then, total RNA was isolated from M-MDSC after flow cytometry.

first: Cheng

last: Yang

first: Ruiming

last: Rong


title: The effect of mouse cathelicidin (mCRAMP) on gene expression in CD4+ T cells cultured under Th17-driving conditions

status: Public on Nov 04 2020

city: Edinburgh

first: Emily

last: Gwyer Findlay

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: We have shown that cathelicidin amplifies Th17 differentiation. To determine the mechanism through which this host defence peptide acts, we performed multiplex gene expression analysis (NanoString) to identify the effects of mouse cathelicidin (mCRAMP) on murine CD4+ T cells cultured under Th17-driving conditions.

overall_design: In the study presented here, whole single cell splenic suspensions were cultured under Th17-driving conditions, with or without mCRAMP (2.5 uM) for 24 hours. CD4+ T cells were isolated by FACS and the RNA extracted for NanoString analysis (mouse Immunology panel). We compared the gene expression profiles of untreated (UT) and mCRAMP-treated cells.

first: Danielle

last: Minns


title: Comparison of young and senescent human endometrial stromal cells by their ability for tissue-specific decidual differentiation [RNA-Seq]

city: Saint-Petersburg

first: Aleksandra

last: Borodkina

address: Tikhoretsky ave. 4

country: Russia

institute: Institute of Cytology RAS

summary: The goal of the analysis is to reveal molecular basis underlying an impairement of decidual reaction of human endometrial stromal cells (ESCs) following senescence progression. For senescence induction the model of oxidative stress induced premature senescence was applied. Young cells are non-stressed, proliferating primary ESCs of passage 8. Senescent ones — exposed to 200 µM of H2O2 for 1 hour in serum-free media and then cultured for 14 days in the complete media for senescence stabilization. Decidualization of the cells was induced by  differentiation media containig 0.3 mM dibutyryl cAMP, 1 µM medroxyprogesterone 17-acetate and 10 nM β-estradiol. Full description of the experimental procedures can be found in the relevant article.

overall_design: Genome-wide transcriptome analysis of non-differentiated young (CTR) and senescent (SEN) ESCs and differentiated ones at days 4 and 8 since decidualization induction. All 6 groups contain 4 biological replicates.

first: Pavel

last: Deryabin


title: RNA-sequencing of C3H/10T1/2 mesenchymal stem cells expressing H2B mutant histones

city: New York City

first: Agata

middle: Lemiesz

last: Patriotis

address: 1230 York ave

institute: Rockefeller University

summary: Purpose of study is to assess changes in gene expression profiles of mesenchymal stem cell upon expression of H2BE71K/Q, H2BE76K/Q and H2BE113K/Q

overall_design: Examination of 3 independent biological replicates of C3H/10T1/2

middle: L

first: Thomas

last: Carroll

last: Allis


title: Single cell RNA sequencing reveals functional heterogeneity and sex differences of glioma-associated brain macrophages

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

summary: Single cell RNA-seq analysis of CD11b+ cells sorted from murine syngeneic gliomas, indicating distinct activity of microglia, infiltrating monocytes/macrophages and CNS border associated macrophages. It demonstrates a molecular heterogeneity in the innate immune response in gliomas. Differently expressed genes were identified in activated microglia from glioma-bearing mice of different sex, and profound overexpression of the MHCII genes was observed in male microglial cells.

overall_design: Single cell RNA sequencing analysis of 4 groups: female control (2 samples), female tumor (14 days post implantation, 2 samples), male control (2 samples), male tumor (14 days post implantation, 2 samples).

first: Natalia

last: Ochocka

first: Pawel

last: Segit

first: Kacper

last: Walentynowicz

first: Kamil

last: Wojnicki

first: Salwador

last: Cyranowski

first: Julian

last: Swatler

first: Bozena

last: Kaminska


title: Overcoming TKI resistance in a lung xenograft model

status: Public on Nov 17 2020

city: Rehovot

first: Yosef

last: Yarden

address: Herzl St 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

summary: Bulk RNA-Seq of PC9 xenograft tumors in different stages of response and resistance to Erlotinib treatment. A combination treatment is proposed in order to overcome Erlotinib drug resistance.

overall_design: PC9 cells (3X106/mouse) were subcutaneously injected in the flanks of 13 CD1-nu/nu mice. When tumors reached 500 mm3, mice were treated daily with erlotinib (50 mg/kg). Once started relapsing and reached 800 mm3, we switched to a combination of 2XmAbs (Cetuximab + Trastuzumab) plus erlotinib (50 mg/kg)

first: Diana

last: Drago

first: Yossi

middle: Y

first: Ilaria

last: Marrocco


title: RNA-Seq of whole Drosophila larval central nervous systems (mid-3rd instar stage, central brain + ventral nerve cord) with panneuronal ISWI knockdown and controls

status: Public on Nov 02 2020

city: Philadelphia

first: Matthew

last: Kayser

state: PA

address: 320 Clinical Research Building

institute: University of Pennsylvania

summary: Sleep disruptions are among the most commonly-reported symptoms across neurodevelopmental disorders (NDDs), but mechanisms linking brain development to normal sleep are largely unknown. From a Drosophila screen of human NDD-associated risk genes, we identified the chromatin remodeler Imitation SWItch/SNF (ISWI) to be required for adult fly sleep. To better understand the mechanisms by which ISWI regulates sleep, we performed RNA-Seq analysis on mid-3rd instar larval central nervous systems (central brain + ventral nerve cord)  in the setting of pan-neuronal ISWI knockdown (elav-GAL4>UAS-ISWI RNAi) compared to controls (elav-GAL4;+). We chose mid-3rd instar because temporal mapping revealed ISWI knockdown during this pre-adult developmental stage led to adult fly sleep deficits.

overall_design: Experimental: elav-GAL4>UAS-ISWI RNAi (4 replicates) versus controls: elav-GAL4; + (3 replicates). All samples were from 4 days post-egg lay (the mid-3rd instar larval stage), with at least 40 CNS per replicate.

first: Naihua

last: Gong

first: Leela

middle: C

last: Dilley


title: Myeloma-modified 3T3-L1 adipocytes exhibit aberrant gene expression profiles [experiment 2]

status: Public on Nov 01 2020

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

department: Biology

institute: Norwich University

summary:
Herein we compare mouse 3T3-L1 adipocyte gene expression after 7 days of adipogenic differentiation with and without exposure to MM.1S myeloma cells.
Microarray analysis was used to compare adipogenic gene expression either following exposure to MM.1S cells prior to differentiation (48h) or after differentiation (72h).

overall_design: Total RNA from 10 3T3-L1 adipocyte samples was extracted via Qiagen RNeasy Kit and run on Affymetrix® ClariomTM S Arrays. This dataset includes the 5 samples in the mature exposure experiment.

last: Campbell

first: Michaela

last: Reagan


title: Myeloma-modified 3T3-L1 adipocytes exhibit aberrant gene expression profiles

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

overall_design: Refer to individual Series


title: eEF3 promotes late stages of tRNA translocation on the ribosome

status: Public on Oct 28 2020

city: Frederick

first: Colin

last: Wu

department: RNA Biology Laboratory

institute: NCI

summary: In addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the A and E sites, its exact mechanism of action is unclear. Here we show that eEF3 acts at the mRNA–tRNA translocation step by promoting the dissociation of the tRNA from the E site, but independent of aminoacyl-tRNA recruitment to the A site. Depletion of eEF3 in vivo leads to a general slow-down in translation elongation due to accumulation of ribosomes with an occupied A site. Cryo-EM analysis of native eEF3-ribosome complexes shows that eEF3 facilitates late steps of translocation by favoring non-rotated ribosomal states as well as by opening the L1 stalk to release the E-site tRNA. Additionally, our analysis provides structural insights into novel translation elongation states, enabling presentation of a revised yeast translation elongation cycle.

overall_design: 5 biological samples are included for ribosome profiling libaries prepared with CHX+TIG or CHX+ANS in the lysis buffer.

first: Rachel

last: Green


title: Human Cerebrospinal Fluid modulates pathways promoting Glioblastoma malignancy

city: Jacksonville

first: Yan

middle: W.

last: Asmann

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: Glioblastoma (GBM) is the most common and devastating primary cancer of the central nervous system in adults. High grade gliomas are able to modify and respond to the brain microenvironment. When GBM tumors infiltrate the Subventricular zone (SVZ) they have a more aggressive clinical presentation than SVZ-distal tumors. We suggest that cerebrospinal fluid (CSF) contact contributes to enhance GBM malignant characteristics in these tumors.  We evaluated the impact of human CSF on GBM, performing a transcriptome analysis on human primary GBM cells exposed to CSF of cancer and non cancer origin to measure changes in gene expression profile associated with increased malignancy and their clinical relevance on disease outcome.

overall_design: Microarray gene expression analysis was conducted from 2 primary GBM cells lines exposed to CSF of cancer and non cancer origin for 24 hours. 3 replicates per conditions

first: Anna

last: Carrano

first: Natanael

last: Zarco

first: Jordan

last: Phillipps

first: Montserrat

last: Lara-Velasquez

first: Paola

last: Suarez-Meade

first: Emily

last: Norton

first: Kaisorn

last: Chaichana

first: Alfredo

last: Quiñones-Hinojosa

middle: W

first: Hugo

last: Guerrero-Cázares


title: Insulin fused to apolipoprotein A-I

status: Public on Oct 27 2020

city: Pamplona

first: Pedro

last: Berraondo

address: Avenida Pio XII 55

department: Program of Immunology and Immunotherapy

country: Spain

institute: Cima Universidad de Navarra

summary: In order to evaluate the in vivo properties of insulin fused to apolipoprotein A-I, we compared the pharmacodynamic properties in the liver to other insulin derivatives with long half-life in circulation: the fusion protein of albumin and insulin (Albulin) [30]. We administered subcutaneously saline, Albulin or Insulin-Apo to wild type mice, and 6 hours later, livers were extracted and homogenized. RNA was obtained and used to analyze the gene expression profile induced by the different insulin modifications.

overall_design: We administered subcutaneously saline, Albulin (55nmol/kg), Insulin-Apo (55nmol/kg) or insulin glargine (55nmol/kg) to wild type mice, and 6 hours later, livers were extracted and homogenized. RNA was obtained and used to analyze the gene expression profile induced by the different insulin modifications using Affymetrix Mouse Gene 1.0 ST array.


title: Maternal Brown Fat Thermogenesis Programs Glucose Tolerance in the Male Offspring

status: Public on Nov 09 2020

city: Lübeck

first: Rebecca

last: Oelkrug

address: Ratzeburger Allee 160

institute: University of Lübeck

summary:
We tested if minor changes in maternal non-shivering thermogenesis during pregnancy can severely alter the phenotype of the offspring already in the next generation. Therefore, male offspring of dams lacking the uncoupling protein 1 (UCP1-KO) in the thermogenic brown adipose tissue were analysed. Genome-wide expression profiling identified several alterations in the hepatic transcriptomic landscape, demonstrating that even minor differences in the demand for maternal thermogenesis profoundly and permanently alter hepatic gene activity in the adult offspring.

Liver gene expression data of offspring from WT and UCP1-KO dams.

overall_design: Six adult male mice per maternal condition (WT and UCP1-KO) were analysed (2 group comparison).

first: Jens

last: Mittag


title: Human bile cholangiocyte organoids originate from the extrahepatic bile duct and can repair bile duct scaffolds in vitro

city: Guangzhou

first: Haoyu

address: Kai Yuan Avenue 190

institute: GIBH

summary: Cholangiocyte organoids provide a powerful tool for characterizing bile duct epithelium and expanding cholangiocytes for tissue engineering purposes. However, this involves invasively obtained tissue-biopsies via surgery which is not preferential and limits the patient-specific capacities of these cultures. To overcome this, organoid culture were initiated from minimal invasive bile-samples obtained during routine clinical procedures. Characterization revealed that these bile-cholangiocyte organoids originate from the extrahepatic bile duct and are capable to repopulate human extrahepatic bile duct scaffolds. With this, bile duct tissue engineering as well as personalized disease modelling is in sight.

overall_design:
mRNA profiles of BCO, ERCP, ECO and ICO samples with three biological replicates
mRNA profiles of ERCP samples cultured in BME and human ductal scaffolds with three biological replicates.

first: Floris

last: Roos

first: Monique

last: Verstegen

first: Luc

last: van der Laan


title: Proteome-wide analysis reveals substrates of E3 ligase RNF146 targeted for degradation

city: Houston

first: Litong

last: Nie

state: Texas

address: 6565 MD Anderson Blvd Unit, Desk Z6.2026

department: ERO

institute: The University of Texas MD Anderson Cancer Center

summary: To check whether mRNA level change for the changed proteins in protein level.

overall_design: Whole mRNA profile for RNF146KO, 293A, TP53TNKS1/2TKO and TP53KO cells

first: Chao

last: Wang

first: Junjie

last: Chen


title: Drug-induced mitochondrial oxidative stress is responsible for various effects of the survivin inhibitor Sepantronium Bromide (YM155) in triple negative breast cancer cells

status: Public on Oct 24 2020

city: Greater Noida

first: Anindita

last: Chakrabarty

state: UP

address: NH91 Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar University

summary: Sepantronium bromide (YM155), a transcriptional inhibitor of anti-apoptotic protein survivin, is considered as a potential drug candidate for triple negative breast cancers (TNBC). Regardless of its excellent performance in pre-clinical models of TNBC,  in patients, this drug was unable to outperform the standard chemotherapy docetaxel. The goal of this study was to identify the pathways/molecules affected by YM155 in TNBC cell lines. Detailed biochemical analysis of the paired YM155-sensitive and resistant cell lines indicates that induction of mitochondrial oxidative stress is a first-line response to the drug, ultimately leading to growth inhibition and induction of cell death. Multiple pathways involved in dampening oxidative stress-induced damages are differentially regulated in YM155-resistant cells. Furthermore, the emergence of YM155 resistance is associated with an extensive transcriptional reprogramming and alteration of many more biological pathways in addition to those identified by biochemical assays. Molecules associated with these biological pathways will potentially serve as biomarkers predicting YM155 sensitivity in TNBC cells.

overall_design: Two biological replicates were analyzed for each of samples (Sensitive and Resistant)

first: Tasaduq

middle: H

last: Wani

first: Goutam

last: Chowdhury


title: Plasma circulating MiRNAs: a new potential biomarker for prostate cancer diagnosis.

city: rome

first: simona

last: giglio

state: rome

address: via di grottarossa

department: clinical and molecolar medicine

institute: Sapienza university

summary:
Purpose: PCa is the second most commonly diagnosed malignancy in men. PCa Diagnosis are based on biopsy sampling that is an invasive, expensive procedure and does not accurately represent multifocal disease. It is desirable to have an easily accessible, minimally invasive way to accurately determine the molecular signature of patient’s tumor that can aid in diagnosis and risk stratification.

Methods:we enrolled a total of 70 patients underwent 12-core transrectal ultrasound (TRUS) biopsy of which 48% had cancer in the diagnosis.  The mean age at diagnosis was 67.15 (IR 55/75), the mean PSA (ng/ml) at diagnosis was 7.8 (IR 4.1/13.4) and the mean TRUS Volume (ml) was 53.5 (IR 29/86). The cancer biopsy presented 73.1% of positive core. Among all cancer patients, 57% showed a High grade of cancer status (Grade 3). Controls are patients with Benign Prostate Hyperplasia (BPH). MicroRNA-expression profiling (NGS analysis) was performed  to identify tumor-related microRNAs (miRs) and determine their association with clinicopathological characteristics.

Results: The expression of miRs -4732-3p, let7a, 26b-5p, 98-5p, 30c-5p and 21-5p may identified Prostate Cancer in plasma samples. Higher expression of mir-4732-3p is associated with a high grade tumor

Conclusions: miRs signature discriminate Prostate cancer in plasma better to PSA values and is associated with high grade tumor status

overall_design: Evaluation of MiRNome in plasma samples from patients with diagnosis of prostate adenocarcinoma or benign hyperplasia prostatitis in the biopsy.

first: Simona

last: Giglio

first: Andrea

last: Vecchione


title: Medication for acromegaly reduces expression of MUC16, MACC1 and GRHL2 in pituitary neuroendocrine tumour tissue

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

summary:
Acromegaly is a disease mainly caused by pituitary neuroendocrine tumours (PitNETs) overproducing growth hormone. First-line medication for this condition is the use of somatostatin analogues (SSAs), that decrease tumour mass and induce antiproliferative effects on PitNET cells. Dopamine agonists (DAs) can also be used, if SSA treatment is not effective. This study aimed to determine differences in transcriptome signatures induced by SSA/DA therapy in PitNET tissue.
We selected tumour tissue from twelve patients with somatotrophinomas, with half of the patients receiving SSA/DA treatment before surgery, and the other half treatment naive. Transcriptome sequencing was then carried out to identify differentially expressed genes (DEGs) and their protein-protein interactions, using pathway analyses.
We found 34 upregulated and six downregulated DEGs in patients with SSA/DA treatment. Three tumour development promoting factors MUC16, MACC1 and GRHL2, were significantly downregulated in therapy administered PitNET tissue. Protein-protein interactions and pathway analyses revealed extracellular matrix involvement in the antiproliferative effects of this type of the drug treatment, with pronounced alterations in collagen regulation.
Here, we have demonstrated that somatotrophinomas can be distinguished based on their transcriptional profiles following SSA/DA therapy, and SSA/DA treatment does indeed cause changes in gene expression. Treatment with SSA/DA, significantly downregulated several factors involved in tumourigenesis, including MUC16, MACC1 and GRHL2. Genes that were upregulated, however, did not have a direct influence on antiproliferative function in the PitNET cells. These findings suggested that SSA/DA treatment acted in a tumour suppressive manner and furthermore, collagen related interactions and pathways were enriched, implicating extracellular matrix involvement in this anti-tumour effect of drug treatment.

overall_design:
PitNET RNA profiles in treated and untreated acromegaly patients
Please note that the 'PitNET06' and 'PitNET07' samples are outliers by their treatment.

first: Rihards

last: Saksis

first: Ivars

last: Silamikelis

first: Pola

last: Laksa

first: Kaspars

last: Megnis

first: Inga

last: Balcere

first: Ilze

last: Konrade

first: Liva

last: Steina

first: Janis

last: Stukens

first: Jelizaveta

last: Sokolovska

first: Valdis

last: Pirags

last: Klovins

first: Vita

last: Rovite


title: Efficient transcription-coupled chromatin accessibility mapping in situ

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. In the popular ATAC-seq method, Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here we show that by simply modifying the tagmentation conditions for histone H3K4me2/3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce accessible DNA maps that are indistinguishable from the best ATAC-seq maps. Thus, DNA accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Steven

first: Hatice

last: Kaya-Okur

first: Kami

last: Ahmad


title: Evolution and molecular basis of caste differentiation in bees

city: Orebro

first: Anders

middle: M.

last: Wirén

address: Sodra Grev Rosengatan 42b

department: Clinical research centre

country: Sweden

institute: Region Orebro lan

summary: Our aim was to identify the genes that are responsible for caste differentiation in the primitively eusocial bumble bee, Bombus terrestris. To do this we extracted RNA from both queen- and worker-destined larvae. We extracted RNA from three key stages during bumble bee development (before, during, and after their caste becomes fixed), and then sent the sequencing to the Earlham Institute. They used mRNAseq to isolate the RNA from each developmental stage and caste pathway.

overall_design: We used mRNAseq to identify the RNA profiles in queen and worker-destined larvae in the bumble bee Bombus terrestris, the RNA was extracted from three developmental stages in each caste pathway.

first: David

last: Collins

first: Marjorie

last: Labédan

first: Irina-Ioana

last: Mohorianu

first: Tamas

last: Dalmay

first: Andrew

last: Bourke


title: Genome-wide expression analysis of overexpressing Ctrl and PRLR-SF AsPC-1 cells

city: Shanghai

first: PeiQi

last: Huang

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: The study is to explore differentially expressed genes in AsPC-1 cells overexpressing Ctrl or PRLR-SF.

overall_design: The genome-wide cDNA microarrays were performed to investigate the differentially expressed genes in PRLR-SF-overexpressed AsPC-1 cells compared to control cells estabilished by our own lab using Affymetrix U133 Plus 2.0 whole-genome chips.Each group contains three biological replicates.

first: Huizhen

last: Nie


title: RNA-seq analysis of regulatory T cells in thymus, placenta, spleen and white adipose tissue of pregnant mice

status: Public on Oct 21 2020

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: In this study we performed RNA sequencing to determine and compare the transcriptome of regulatory T cells (Tregs) present in the thymus, placenta, spleen and white adipose tissue (FAT) of pregnant mice. We further assessed how the expression of the receptor Rank in the thymic medullary epithelia affects the transcriptional program of these Treg populations. For the isolation of viable and bona fide Tregs, we first generated RankWt (wild type control mice) and RankΔFoxn1 (which lack expression of Rank in the thymic epithelia) and further crossed them to mice that express GFP from the Foxp3 promoter. Neuropilin1 was used to mark the thymic origin of the Tregs. Equal numbers of Tregs (280 cells) were sorted as CD45-CD8-CD4+GFP+Neuropilin1High cells from the thymus and placenta of RankWtFoxp3GFP/GFP and RankΔFoxn1Foxp3GFP/GFP pregnant females at E17.5 (both samples from the same female; n=4 females per genotype). Thymus Tregs from non-pregnant littermate female mice for each genotype cohort were also studied. To increase robustness, the 280 placental Tregs were purified from 5 individual placentas per pregnant female (56 Tregs/placenta). Our study is the first one to determine the transcriptome of thymus and placenta Tregs during pregnancy and reveals that, partially dependent on Rank expression in the thymic epithelia, placental-resident Tregs are molecularly distinct from thymic Tregs. In a separate experiment with different pregnant mice than those used for thymus and placenta analysis, VAT Tregs (20-30 cells) and splenic Tregs (150 cells) were sorted (both samples from the same female) by using the same mouse lines (Rank Wt and RankΔFoxn1), embryological days of analysis (E17.5) and sorting strategies.

overall_design:
RNA-seq analysis of small, FACS-sorted cell pools.

Affiliation: Magdalena Paolino, IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences

Affiliation: Josef M. Penninger, IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences

first: Magdalena

last: Paolino

first: Josef

middle: M

last: Penninger


title: The role of Arid4b in mESC lineage commitment (ChIP-Seq)

status: Public on Oct 20 2020

city: Boston

first: Jialiang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Distinct cell types emerge from embryonic stem cells through a precise and coordinated execution of gene expression programs during lineage commitment. This is established by the action of lineage specific transcription factors along with chromatin complexes. Numerous studies focused on epigenetic factors that affect ESC self-renewal and pluripotency. However, the contribution of chromatin to lineage decisions at the exit from pluripotency has not been studied extensively. We have set out to identify chromatin related factors critical for differentiation towards mesodermal and endodermal lineages. Our results reveal a critical role for chromatin protein, Arid4b. Arid4b deficient mESCs are similar to wild-type mESCs in the expression of pluripotency factors and their self-renewal. However, we found that Arid4b loss results in defects in upregulation of meso/endodermal gene expression program. Arid4b is in the Sin3a complex along with Hdac1 and Hdac2. We identified a physical and functional interaction of Arid4b with Hdac1 rather than Hdac2. Arid4b deficiency leads to changes in the overall chromatin environment. Most notably, a subset of the genomic loci was found to gain H3K27Ac whereas several of the key developmental genes instead have increased H3K27me3 levels. Accordingly, the super-enhancers associated with meso/endoderm commitment were selectively reduced in arid4b∆ cells.

overall_design: arid4b∆  vs. wild type

first: Nihal

middle: T

last: Cizmecioglu

first: Stuart

last: Orkin


title: The role of Arid4b in mESC lineage commitment


title: Circular RNA expression profile in human primary multiple intracranial aneurysms

city: Longyan

first: YAN

middle: MING

last: HUANG

state: Fujian

address: 105 Jiuyi North Road, Xinluo

department: Neurosurgery

institute: Longyan First Hospital Affiliated to Fujian Medical University

summary: Primary multiple intracranial aneurysms (MIA) is a vascular disease that often leads to fatal vascular rupture and subarachnoid hemorrhage. However, little is known about the epigenetic regulation of MIA. Circular RNAs (circRNAs) serve important roles in cardiovascular diseases; however, they have received little research attention regarding their association with MIA. The present study initially aimed to explore novel mechanisms of MIA through circRNA expression profiles. Comprehensive circRNA expression profiles were detected by RNA sequencing (RNA-Seq) in human peripheral blood mononuclear cells. The RNA-Seq results were validated by reverse transcription-quantitative PCR. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses suggested the functions of these circRNAs. Among the 3,328 differentially expressed circRNAs between the MIA and matched groups, 60 exhibited marked expression changes (|log2 fold change|≥2; P<0.05). Among the 60 circRNAs that exhibited significant changes, 20 were upregulated, while the other 40 were downregulated. The circRNAs hsa_circ_0135895, hsa_circ_0000682 and hsa_circ_0000690 could regulate protein tyrosine kinase 2, protein kinase Cβ and integrin subunit αL, respectively. To the best of our knowledge, the present study was the first to perform circRNA sequencing analysis of MIA. Furthermore, the results specifically predicted the regulatory role of circRNAs in MIA pathogenesis.

overall_design: Circular RNA expression profile of three pairs of matched patients with primary MIA and healthy individuals

first: H

last: Cao

first: J

last: Chen

first: X

last: Lai

first: T

last: Liu

first: P

last: Qiu

first: S

last: Que

first: Y


title: The Longevity Gene mIndy (I’m Not Dead, Yet) Affects Blood Pressure Through Sympathoadrenal Mechanisms

status: Public on Oct 19 2020

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Reduced expression of the plasma-membrane citrate-transporter INDY (acronym I’m Not Dead, Yet) extends life span in lower organisms. Deletion of the mammalian Indy (mIndy) gene in rodents improves metabolism via mechanisms akin to caloric restriction, known to lower blood pressure (BP) by sympathoadrenal inhibition. We hypothesized that mIndy deletion attenuates sympathoadrenal support of BP. mINDY-knockout (KO) mice were monitored using radiotelemetry; autonomic cardiovascular control was assessed by pharmacological testing, spectral analysis, urine catecholamines and adrenal transcriptome analysis. In vivo echocardiography, vascular function and steroid hormones were assessed. Continuous arterial BP and heart rate (HR) were reduced in mINDY-KO mice compared to littermate controls. Urinary catecholamines were reduced and the decreases in BP and HR by mIndy deletion were attenuated after autonomic ganglionic blockade. Catecholamine biosynthesis pathways were reduced in mINDY-KO adrenals using unbiased microarray analysis. Citrate, the main mINDY substrate, increased catecholamine content in pheochromocytoma cells, while pharmacological inhibition of citrate uptake blunted the effect. Adrenal size, histological structure and cardiac function  were not affected. Our data suggest that deletion of mIndy reduces sympathoadrenal support of BP and HR by attenuating catecholamine biosynthesis. mIndy deletion recapitulates beneficial cardiovascular and metabolic responses to caloric restriction making it an attractive therapeutic target.

overall_design: Transcriptional changes in mINDY knock-out (KO) versus WT littermate adrenals were assayed (N=5 biological repeats per condition) using gene expression microarray analysis.

first: Diana

last: Willmes

first: Martin

middle: A

last: Daniels

first: Stefanie

last: Lieske

first: Nicole

last: Bechmann

first: Tina

last: Schumann

first: Christine

last: Henke

first: Anica

last: Kurzbach

first: Nermeen

last: ElAgroudy

first: Andrey

last: DaCosta Goncalvez

first: Mirko

last: Peitzsch

first: Anja

last: Hofmann

first: Waldemar

last: Kanczkowski

first: Kristin

last: Kräker

first: Dominik

middle: N

last: Müller

first: Henning

last: Morawietz

first: Andreas

last: Deussen

first: Michael

last: Wagner

first: Ali

last: El-Armouche

first: Stephen

last: Helfand

first: Stephan

middle: R

last: Bornstein

first: Rafael

last: de Cabo

first: Michel

last: Bernier

first: Graeme

last: Eisenhofer

first: Jens

last: Tank

last: Jordan

last: Birkenfeld


title: The role of Arid4b in mESC lineage commitment (RNA-Seq)

first: Jialiang

last: Huang

first: Nihal

last: Cizmecioglu

first: Stuart

last: Orkin


title: An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants

status: Public on Oct 18 2020

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry.  Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape.  Here, we directly test this hypothesis.  Using deep mutagenesis, we find that the ACE2-binding surface of the SARS-CoV-2 spike tolerates high mutational diversity, which may act as a source for resistance to therapeutics.  However, saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor.  We conclude that resistance to engineered decoys will be rare.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: A human codon optimized gene for full-length SARS-CoV-2 S (GenBank YP_009724390.1) with an N-terminal c-myc tag was diversified by site-saturation mutagenesis across the RBD (a.a. C336-L517).  Degenerate NNK codons were introduced at each residue position to provide a library that scans the RBD sequence of S. The library was expressed in Expi293F cells that were then sorted by FACS in two different ways.  First, the library was incubated with wild type sACE2, and cells were collected that both expressed myc-tagged S and either bound sACE2 at high or low levels, referred to as the ACE2-High and ACE2-Low sorts, respectively.  Second, the library was incubated with competing wild type sACE2 and engineered sACE2.v2.4, which binds the SARS-CoV-2 spike with high affinity.  Now, cells were collected where binding signals were shifted to favor the binding of wild type or engineered receptors, referred to as the WT-specific and v2.4-specific sorts.  The specificity selections were replicated in an independent experiment.  RNA was extracted from the sorted cell populations and Illumina sequenced. Transcript frequencies for all substitutions within the RBD were compared to their respective frequencies in the naive plasmid library to calculate an enrichment ratio.


title: scRNAseq analysis from mixed cell culture from rat optic nerve

status: Public on Oct 14 2020

city: Pittsburgh

first: Sayan

last: Ghosh

address: 4401 Penn Avenue

department: Ophthalmology

institute: University of Pittsburgh

overall_design: Optic nerve was harvested from rats of different genotypes, digested and single cell suspension was prepared and the cells were anlyased with the Illumina Nextseq 550

first: Debasish

last: Sinha


title: mRNA and microRNA profiles in KC (Kupffer cells) after partial hepatoctomy

status: Public on Oct 08 2020

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

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

overall_design: Refer to individual Series


title: Molecular mechanisms of Enterobacter sp. SA187 induced thermotolerance in Arabidopsis thaliana

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: Global warming and heat stress belong to the most critical environmental challenges to agriculture worldwide, causing severe losses of major crop yields. In present study we report that the endophytic bacterium Enterobacter sp. SA187 protects Arabidopsis thaliana to heat stress. To understand the mechanisms at molecular level we performed RNA-seq

overall_design: mRNA seq to elucidate the SA187 mediated thermotolerance in Arabidopsis thaliana inoculated with entrobacter sp SA187

first: Kirti

last: Shekhawat

first: Heribert

last: Hirt

first: Kiruthiga

last: Mariappan


title: microRNA profiles in KC (Kupffer cells) after partial hepatoctomy

summary: The 70% resection promotes migration of Ly6C+CD11b+ monocytes/macrophages to the remnant liver accompanied by a reduction in its CD206+ macrophage content. mRNA and microRNA expression profiles were studied by NanoString technology and verified by a reverse transcription-based qPCR assay. Corresponding  microtranscriptomic profiles cannot be unambiguously defined as pro- or anti-inflammatory. Their typical features include elevated expression of leukocyte chemoattractant factors, and many of the differentially expressed sequences are related to the control of cell growth and metabolic processes in the liver.

overall_design: In the study presented here, KC samples obtained after partial hepatoctomy  was used to acquire microRNA profiles of a total of 577 mouse miRNA. For each sample, sorted cells from 5(?) mice were pooled.

first: Maria

last: Nikitina

first: Andrey

last: Elchaninov


title: Fully defined human PSC-derived microglia and tri-culture system reveals cell type specific potentiation of complement C3 production in a model of Alzheimer’s disease [scRNA-seq]

status: Public on Nov 22 2020

city: New York

first: Sudha

last: Guttikonda

state: New York

address: 430 E 67th St

department: Developmental Biology

country: USA

institute: MSKCC

summary: Aberrant inflammation in the central nervous system (CNS) has been implicated as a major player in the pathogenesis of human neurodegenerative disease. However, the specific contribution of each cell type to the neuroinflammatory axis in vivo remains unclear with species-specific differences in key signaling pathways further complicating the challenge. To assemble a fully human platform to study neuroinflammation, we first developed a novel approach to derive microglia from human pluripotent stem cells (hPSCs) that faithfully recapitulates microglial ontogeny as validated by single cell RNA-sequencing and stage-specific mapping onto datasets of developing mouse microglia. Using these cells, we build the first defined and completely hPSC-derived tri-culture system containing pure populations of hPSC-derived microglia, astrocytes, and neurons to dissect cellular crosstalk along the neuroinflammatory axis in vitro. We next used the tri-culture system to model neuroinflammation in Alzheimer’s Disease using hPSCs harboring the APPSWE+/+ mutation and their isogenic control. Our data reveal that production of complement C3, a protein that is increased under inflammatory conditions and implicated in synaptic loss, is potentiated under tri-culture conditions, and is further enhanced in APPSWE+/+ tri-cultures. Using cell type-specific ablation studies, we report that C3 potentiation is due to the presence of a neuroinflammatory loop in which microglia are the key initiators that activate reciprocal signaling with astrocytes to produce excess C3. Our study defines the major cellular players contributing to increased C3 in AD and presents a broadly applicable platform to study neuroinflammation in human disease.

overall_design: Cell heterogeneity was assessed at timepoints during in vitro human primitive hematopoiesis using single-cell RNA-sequencing to identify the early trajectories of differentiating microglial cells.

first: Lisa

last: Sikkema

first: Jason

last: Tchieu

first: Nathalie

last: Saurat

first: Ryan

last: Walsh

first: Gabriele

last: Ciceri

first: Marjolein

last: Sneeboer

first: Linas

last: Mazutis

first: Manu

last: Setty

first: Lot

middle: D

last: de Witte

first: Dana

last: Pe'er

first: Lorenz

last: Studer


title: Transcriptional effects of YAP/TAZ knockout in mouse gliomaspheres

status: Public on Oct 02 2020

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: We compared the transcriptomes of control and YAP/TAZ knockout gliomaspheres derived from mouse newborn astrocytes transformed with KRAS/shp53. We wanted to evaluate the effects of YAP/TAZ depletion on gliomaspheres transcriptional program.

overall_design: Gliomaspheres were obtained by transforming R26CagCreER;Yapf/f;Tazf/f mouse astrocyte with KRasG12V/shp53. Spheres were treated with 4OH TAM to promote YAP/TAZ knockout or left untreated. After 1 week, gliomaspheres were harvested for RNA extraction; RNA was then used for polyA RNA-sequencing.

first: Oriana

last: Romano

first: Martina

last: Castellan

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Differential expression of genes associated with inflammation in KC (Kupffer cells) after partial hepatoctomy

first: Polina

last: Vishnyakova

summary: The 70% resection promotes migration of Ly6C+CD11b+ monocytes/macrophages to the remnant liver accompanied by a reduction in its CD206+ macrophage content. Macrophage proliferation within the liver reaches maximum on day 3 after the surgery. Transcriptomic profiles of macrophages isolated from the regenerating livers reveal chemokine signaling signatures in combination with indications of the involvement in specific metabolic pathways rather than inflammatory effects or morphogenesis.

overall_design: In the study presented here, KC samples obtained after partial hepatoctomy were used to generate expression profiles of a total of 248 unique genes associated with inflammation. For each sample, sorted cells from 5 (?) Mice were pooled.

first: Maria

last: Nikitina

first: Andrey

last: Elchaninov


title: Transcriptional effects of YAP/TAZ depletion in astrocytes, gliomaspheres, and glioblastoma cell lines

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptional profiling of Kras/shp53-induced gliomaspheres and tumors

summary: We compared the transcriptome of gliomaspheres and of a subcutaneous tumor from Kras/shp53-transformed mouse newborn astrocytes.

overall_design:
Gliomaspheres were obtained by transforming R26CagCreER;Yapf/f;Tazf/f mouse astrocyte with KRasG12V/shp53. The subcutaneous tumor derived from Kras/shp53-induced gliomaspheres injected in the flank of an immunocompromised mouse.
The experiment includes 3 samples of control mouse astroglial cells, 2 sample of tumor Kras/shp53 with YTwt, and 1 sample of tumor Kras/shp53 with YTKO.


title: Transcriptional effects of YAP/TAZ depletion during oncogene-mediated transformation in mouse astrocyte

summary: To understand the role of YAP/TAZ during gliomagenesis, we compared the transcriptomes of control and YAP/TAZ knockout astrocytes derived from newborn mice, transformed with oncogenic HER2.

overall_design: Yapf/f;Tazf/f mouse astrocyte were expanded and transduced with lentiviral particles encoding for doxy-inducible version of HER2CA, rtTA and CreERT2. Cells were also treated with DMSO (control) or TAM to promote YAP/TAZ knockout during the oncogene transformation. Not transformed astrocytes were used as control. Fully formed P1 Gliomaspheres were also profiled as comparison. After 15 days, cells were harvested for RNA extraction. Gliomaspheres were harvested for RNA extraction 3 weeks after the beginning of the experiment; RNA was then used for polyA RNA-sequencing.