title: The Gut Microbe-Derived Metabolite Trimethylamine is a Biomarker of and Therapeutic Target in Alcohol-Associated Liver Disease

status: Public on Mar 31 2021

city: Cleveland

first: Chase

last: Neumann

state: OH

address: 99089 Carnegie Ave

institute: CCF

summary: BACKGROUND & AIMS: There is mounting evidence that microbes resident in the human intestine contribute to diverse alcohol-associated liver diseases (ALD) including the most deadly form known as alcoholic hepatitis (AH). However, mechanisms by which gut microbiota synergize with excessive alcohol intake to promote liver injury are poorly understood. Furthermore, whether drugs that selectively target gut microbial metabolism can improve ALD has never been tested.  METHODS: We used liquid chromatography tandem mass spectrometry to quantify the levels of microbe and host choline co-metabolites in healthy controls and AH patients, and identified the metabolite trimethylamine (TMA) as a gut microbe-derived biomarker of AH. In subsequent studies, we treated mice with non-lethal mechanism-based bacterial choline TMA lyase inhibitors to blunt gut microbe-dependent production of TMA in the context of chronic ethanol administration. Indices of liver injury were quantified by complementary RNA sequencing, biochemical, and histological approaches. In addition, we examined the impact of ethanol consumption and TMA lyase inhibition on gut microbiome structure via 16S rRNA sequencing. RESULTS: We show the gut microbial choline metabolite trimethylamine (TMA) is elevated in AH patients, which is correlated with reduced hepatic expression of the TMA oxygenase flavin-containing monooxygenase 3 (FMO3). Provocatively, we find that small molecule inhibition of gut microbial choline TMA lyase activity protects mice from ethanol-induced liver injury. TMA lyase inhibitor-driven improvement in ethanol-induced liver injury is associated with distinct reorganization of the gut microbiome community and host liver transcriptome.        CONCLUSIONS: The microbial metabolite TMA is a biomarker of AH, and blocking TMA production from gut microbes can blunt ALD in mice.

overall_design: All animals were on a Pair Diet or Lieber-DeCarli Chronic Ethanol Diet. One group (n=4) was maintained as pair diet-vehicle cohort. The second group (n=4) was maintained on pair diet-IMC (specific inhibitor of choline conversion to TMA). The third group was maintained on chronic ethanol diet and vehicle (n=4). The fourth group was maintained on chronic ethanol diet and IMC (n=4). All samples were run as pair-end 100bp library construction.

middle: M

last: Brown

first: Rober

last: Helsley

first: Anagha

last: Kadam


title: A Pig BodyMap Transcriptome Reveals Diverse Tissue Physiologies and Evolutionary Dynamics of Transcription [RNA-Seq pig]

status: Public on Apr 20 2021

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Comprehensive transcriptomic survey of the pig (Sus scrofa) may lead to a better understanding of mechanisms of tissue specialization that underlie economic traits of this species and accelerate its use as a biomedical model. Here, we characterized four distinct transcript types (lncRNAs, TUCPs, miRNAs and circRNAs) in 31 adult pig tissues and two cell lines, together with protein-coding genes. We dissected their distinct structural and transcriptional features and uncovered transcriptome variability as related to tissue physiology. We discovered extraordinary diversity among 47 anatomically distinct skeletal muscle types, as well as among six adipose depots, which are linked to their diverse origins, metabolic features, cell composition, physical activity and mitochondrial pathways. In particular, transcription of HOX genes across skeletal muscles exhibited a position-dominant pattern, revealing a similar developmental history of these tissues within the same body part. Transcriptional patterns across adipose depots demonstrated a metabolically protective role of subcutaneous adipose tissue and the association of visceral adipose tissue with metabolic dysfunction. Comparative analysis of the transcriptomes of seven tissues of the pig and nine other vertebrates revealed insights into evolutionary divergence of transcription that contributes to lineage-specific tissue biology. We also analyzed long-range regulation of promoters by their enhancers with downstream transcription in subcutaneous adipose tissues of six mammals, showing that evolutionary stability of transcription can mainly be attributed to multiple enhancers buffering gene expression patterns against genetic perturbations, thereby conferring robustness during speciation. Collectively, this study offers a resource for the accelerated use of the pig as a biomedical model for human biology and disease and uncovers molecular bases of its diverse economic traits.

overall_design: We generated RNA  sequencing (RNA-seq) data of pig tissues of 1-3 replicates.

first: Long

last: Jin

first: Silu

last: Hu

first: Mingzhou

last: Li

first: Qianzi

last: Tang


title: T3-Dependent Transcriptional Programming by TR-beta Requires SWI/SNF Chromatin Remodelers

status: Public on Apr 01 2021

city: Minneapolis

first: Noelle

middle: E

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

country: USA

institute: University of Minnesota

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Whole transcriptome analysis of brain hippocampal tissue from SAMP8 mice and rat primary neurons treated with the Alzheimer’s disease drug candidate CAD031

status: Public on Apr 21 2021

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Alzheimer’s disease (AD) drug discovery has rarely been addressed in the context of aging even though sporadic AD accounts for 99% of the cases. Phenotypic screens based upon old age-associated brain toxicities were used to develop the potent AD drug candidate CAD031. The aim of this project was to investigate whether CAD031 prevented the progression of dementia in SAMP8 mice when administered at advanced stages of disease, and the possible mechanism of this prevention effect. These transcriptomic data are part of an integrative multi-omics approach that also investigated protein expression, metabolite levels as well as cognition. In addition, in order to further investigate the effect of the drugs in in vitro neuronal cultures, rat primary neurons were treated with the compound and the transcriptome sequenced.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Six nine-month old female SAMP8 mice were fed with vehicle diet and with CAD031 (200ppm). Diet treatment lasted for four months until mice reached thirteen months of age. Mice were then sacrificed and RNA extracted from the brain hippocampus. Five eight-month old male SAMP8 mice were used as the baseline control group  (included in previous GEO accession GSE101112). For the in vitro experiments, Primary cortical neurons were prepared from day seventeen rat embryos and allowed to differentiate in culture. At seven days in vitro, neurons were treated with 1μM of the compound for 24h, and RNA purified.


title: Multimodal Analysis for Human ex vivo Studies Shows Extensive Molecular Changes from Delays in Blood Processing

status: Public on Mar 29 2021

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The importance of these platforms in clinical and translational studies led us to investigate the impact of delayed blood processing on the numbers and state of peripheral blood mononuclear cells (PBMC) and on the plasma proteome. Similar to previous studies, we show minimal effects of delayed processing on the numbers and general phenotype of PBMCs up to 18 hours. In contrast, profound changes in the single-cell transcriptome and composition of the plasma proteome become evident as early as 6 hours after blood draw. These reflect patterns of cellular activation across diverse cell types that lead to progressive distancing of the gene expression state and plasma proteome from native in vivo biology. Differences accumulating during an overnight rest (18 hours) could confound relevant biologic variance related to many underlying disease states.

overall_design:
To study the effects of delays in PBMC processing from whole blood we performed two similar but independent experiments. In Experiment 1, we isolated PBMC from whole blood at 2, 4, 6, 8, and 18 hours after blood draw from healthy donors (n=3) or those diagnosed with systemic lupus erythematosus (SLE, n=3). In Experiment 2, we assayed PBMC isolated from only healthy donors (n=4) starting at 2, 4, 6, 10, 14, and 18 hours after blood draw. In both experiments, the whole blood was held in the dark at room temperature prior to PBMC isolation by Ficoll gradient separation. PBMC were assayed after freeze/thaw by 10x Genomics single-cell RNA-sequencing.

>>> Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns. dbGap: phs002280<<<

first: Adam

middle: K

last: Savage

first: Miriam

middle: V

last: Gutschow

first: Tony

last: Chiang

first: Kathy

middle: F

last: Henderson

first: Richard

last: Green

first: Monica

last: Chaudhari

first: Elliot

last: Swanson

first: Alexander

middle: T

last: Heubeck

first: Nina

last: Kondza

first: Kelli

middle: C

last: Burley

first: Palak

last: Genge

first: Cara

last: Lord

first: Tanja

last: Smith

first: Zachary

last: Thomson

first: Aldan

last: Beaubien

first: Ed

last: Johnson

first: Jeff

last: Goldy

first: Hamid

last: Bolouri

first: Jane

middle: H

last: Buckner

first: Paul

last: Meijer

first: Ernest

last: Coffey

first: Peter

middle: J

last: Skene

first: Troy

middle: R

last: Torgerson

first: Xiao-jun

first: Thomas

last: Bumol


title: T3-Dependent Transcriptional Programming by TR-beta Requires SWI/SNF Chromatin Remodelers (CUT&RUN)

first: Noelle

last: Gillis

summary: We used an integrated genomics approach to profile and characterize the cistrome of TR-beta, map changes in chromatin accessibility, and capture the transcriptomic changes in response to T3 in a normal thyroid cell line. Our data demonstrates that T3 promotes significant shifts in TR-beta genomic occupancy, which are associated with differential chromatin accessibility, and differential recruitment of SWI/SNF chromatin remodelers.

overall_design: Epigenetic and transcriptomic anlaysis a of thyroid hormone receptor beta binding and regulation of chormatin accessibility in normal thyroid cells in the presence and absence of thyroid hormone.

first: Seth

last: Frietze

first: Frances

last: Carr


title: RNA-Sequencing Characterisation of the Renal Cortical Response to Roux-en-Y Gastric Bypass Surgery Alone and Combined Roux-en-Y Gastric Bypass Surgery and Medical Therapy in the Zucker Diabetic Sprague Dawley Rat Model of Diabetic Kidney Disease

status: Public on Mar 17 2021

city: Dublin

first: William

middle: P.

last: Martin

state: - Select State/Province -

address: Diabetes Complications Research Centre, Conway Institute, University College Dublin

country: Ireland

institute: University College Dublin

summary: We report results from renal cortical transcriptomic analysis of responses to RYGB surgery alone and the combination of RYGB surgery and medical therapy in the Zucker Diabetic Sprague Dawley (ZDSD) rat model of diabetic kidney disease.

overall_design:
Healthy controls: Sprague Dawley rats.
Disease controls: SHAM-operated Zucker Diabetic Sprague Dawley (ZDSD) rats (laparotomy).
RYGB-operated ZDSD rats.
ZDSD rats treated with RYGB surgery plus medical therapy (ramipril, metformin, rosuvastatin, fenofibrate).

middle: P

first: Carel

middle: W

last: le Roux

first: Neil

middle: G

last: Docherty


title: T3-Dependent Transcriptional Programming by TR-beta Requires SWI/SNF Chromatin Remodelers (ATAC-Seq)


title: Single Cell Atlas of Injured Sciatic Nerve Tissue

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

summary: Sciatic nerve crush (SNC) triggers sterile inflammation within the distal nerve and de-afferented dorsal root ganglia (DRGs). In the nerve, neutrophils and pro-inflammatory Ly6Chigh monocytes appear first and rapidly give way to Ly6Clow resolving macrophages. Transcriptional profiling of injured nerve tissue identifies six macrophage subpopulations, repair Schwann cells and mesenchymal cells as the main cell types.  Macrophages at the nerve crush site are distinct from macrophages associated with degenerating nerve fibers. Monocytes and macrophages in the injured nerve “eat” apoptotic cell corpses of leukocytes and thereby contribute to an anti-inflammatory milieu. Studies with chimeric mice show that following SNC few blood-derived immune cells enter DRGs. Myeloid cells in the injured nerve, but not DRGs, express the receptor for the chemokine GM-CSF. In the absence of GM-CSF, conditioning-lesion induced regeneration of DRG neuron central projections is abrogated. Thus, a carefully orchestrated immune response in the nerve is required for conditioning-lesion induced neurorepair.

overall_design: scRNAseq analysis, 3 days post sciatic nerve crush, for 3 WT mice

first: Roman

last: Giger

first: Ashley

middle: L

last: Kalinski

first: Choya

last: Yoon

first: Lucas

middle: D

last: Huffman

first: Patrick

last: Duncker

first: Craig

middle: N


title: Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions

status: Public on Mar 23 2021

city: Berkeley

first: Iswar

middle: Krishna

last: Hariharan

state: CA

address: Weill Hall

department: Molecular & Cell Biology

institute: University of California, Berkeley

summary: In both vertebrates and invertebrates, generating a functional appendage requires interactions between ectoderm-derived epithelia and mesoderm-derived cells. To investigate such interactions, we used single-cell transcriptomics to generate a temporal cell atlas of the Drosophila wing disc from two developmental time points. Using these data, we visualized gene expression using a multi-layered model of the wing disc and catalogued ligand-receptor pairs that could mediate signaling between epithelial cells and adult muscle precursors (AMPs). We found that localized expression of the FGF ligands, Thisbe and Pyramus, in the disc epithelium regulates the number and location of the AMPs. In addition, Hedgehog ligand from the epithelium activates a specific transcriptional program within adjacent AMP cells, defined by AMP-specific targets Neurotactin and midline, that is critical for proper formation of direct flight muscles. More generally, our annotated temporal cell atlas provides an organ-wide view of potential cell-cell interactions between epithelial and myogenic cells.

overall_design: Cells were dissociated from Drosophila melanogaster (Oregon R strain) wing-imaginal discs, barcoded using the 10x Chromium single-cell RNA sequencing platform, and sequenced on an Illumina NovaSeq. Wing disc samples were collected from two developmental time points, 96 and 120 hours after egg lay. For each time point, two replicates were collected, for a total of 4 sequencing runs.

first: Nicholas

last: Everetts

first: Melanie

middle: I

last: Worley

first: Riku

last: Yasutomi

first: Nir

last: Yosef


title: Elevated Expression of Two Circulating LncRNAs Predicts Poor Prognosis for Acute Cerebral Infarction

status: Public on Mar 18 2021

city: shanghai

first: tian

last: chunou

address: 168 changhai road

department: Neurosurgery Department

institute: Changhai Hospital, Second Military Medical University, China

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: Poor prognosis for acute cerebral infarction (ACI) was suggested to be predicted using the high expression of some novel molecular markers, for example long non-coding RNAs (lncRNAs). Differentially expressed lncRNAs in peripheral whole blood from the ACI patients and healthy volunteers(HVT) were identified using microarray and further verified by qRT-PCR. The clinical outcome evaluated by 3-month modified Rankin Score (mRS), stroke stratification classified by OCSP criteria, and the expression characteristics of specific lncRNAs were analyzed in ACI patients. Among 5686 differentially expressed lncRNAs screened out by the microarray, nine were verified by qRT-PCR. Particularly, the expression of NR_120420 and  lnc-GCH1-2:3 in the ACI group were significantly higher than the HVT group. ROC analysis showed that the sensitivity and specificity of NR_120420 were 85.7% and 84.6% in patients with total anterior circulation infarction (TACI) respectively(area under curve，AUC=0.861), while the sensitivity and specificity of lnc-GCH1-2:3 were 85.7% and 82.1% in patients with TACI respectively(AUC=0.802). Multivariate logistic regression showed that NR_120420 was a significantly independent diagnostic factor for ACI. The elevated expression levels of NR_120420 and lnc-GCH1-2:3 were associated with the TACI stroke classification and the poor prognosis of ACI. Our study clearly illustrated that the elevated expression levels of circulating NR_120420 and lnc-GCH1-2:3 could predict the TACI stroke classification with high sensitivity and specificity and the poor prognosis of patients with ACI.

overall_design: Peripheral whole blood from patients with acute cerebral infarction (ACI) (n=6) and healthy controls (HVT) (n=3) were screened by microarray to find differentially expressed lncRNAs.Time duration from stroke onset to admission was less than 6 hours.

first: Chunou

last: Tian

first: Bo

last: Hong


title: Impairing one sensory modality enhances another by reprogramming peptidergic circuits in Caenorhabditis elegans.

status: Public on Mar 10 2021

city: Klosterneuburg

first: Giulio

last: Valperga

address: Am Campus 1

country: Austria

institute: IST Austria

summary: Abstract: Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. To probe these mechanisms, we perform a forward genetic screen for mutants with enhanced O2 perception in C. elegans. Multiple mutants exhibiting increased responsiveness to O2 concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL chemosensory neurons. We find that ADL’s responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1 and other sensory defective mutants resulting in an enhanced neurosecretion. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling of ADL neurons indicates its acquired O2-evoked neurosecretion is the result of a transcriptional reprogramming that up-regulates neuropeptide signalling. We show that the conserved neuropeptide receptor NPR-22 is necessary and sufficient in ADL to enhance its neurosecretion levels. Sensory loss can thus confer cross-modal plasticity by re-wiring peptidergic circuits.

overall_design: In this dataset we compare the transcriptome of ADL sensory neurons between wild types and qui-1 mutants. To isolate ADL sensory neurons we dissociate animals where ADL neurons are markered by a fluorescent protein (mKate2) expressed under the control of an ADL-specific promoter (srh-220p). Sample size: N= 6 (WT), N=4 (qui-1).

first: Fabian

last: Amman

first: Mario

last: de Bono


title: RNA-sequencing in liver of rats exposed to glyphosate, MON 52276, and a mixture of pesticides

status: Public on Apr 12 2021

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

summary: Human health effects from chronic exposure to pesticide residues are little investigated. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in an in vivo subchronic toxicity test of a glyphosate, its formulated product MON 52276, and mixture of six pesticide active ingredients frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole). Sprague-Dawley rats were administered with the pesticide mixture with each ingredient at its regulatory permitted acceptable daily intake.

overall_design: Evaluation of transcriptome in liver of rats exposed to glyphosate, MON 52276, and a mixture of pesticides

first: Charles

middle: A

last: Mein


title: Insights into Epithelial Cell Senescence from Transcriptome and Secretome Analysis of Human Oral Keratinocytes [RNA-seq]

first: April

middle: Elizabeth

last: Williams

summary: Senescent cells are one source of the chronic inflammation that contributes to the diseases and debilities of aging.  Whereas cellular senescence in fibroblasts is well documented, how this process is orchestrated in epithelial cells, the origin of human carcinomas, is much less understood.  We used normal primary human oral keratinocytes (NOKs) to elucidate senescence programs in a prototype mucosal epithelial cell that undergoes senescence spontaneously.  We employed widely-accepted assays to characterize senescence phenotypes in these cells and found that p21WAF1/CIP1 is not a reliable marker of senescence for NOKs, as it is for fibroblasts.  We performed transcriptome analysis by RNA-seq and proteomic analysis of secreted proteins, both non-vesicular and those associated with extracellular vesicles (EVs).  NOKs, while sharing with fibroblasts certain important aspects of inflammation, such as upregulation of the NF-κB, interferon, and p38MAPK pathways, also exhibit novel senescence associated characteristics.  In two of the donors, we observed an expected repression of DNA repair genes, correlating with downregulation of E2F1 mRNA and protein, but saw a divergent result for the third donor. We were able to highlight potential senolytic targets.  Our secretome analysis led us to propose additions to the senescence associated secretory phenotype, including HSP60, which we found on the surface of EVs.  Moreover, EVs from senescent NOKs can create inflammation by stimulating interferon pathway signaling in THP-1 monocytes in culture.  Our results highlight important senescence changes in epithelial cells in terms of how these cells contribute to chronic inflammation, aging, and age-related diseases.

overall_design: RNA-seq analysis of cellular senescence in normal human oral keratinocytes

first: Rachael

middle: E

last: Schwartz

first: Maxim

last: Shokhirev

first: Gerald

middle: S

last: Shadel


title: PolyA RNA-seq from whole blood of Sars-COV2-negative and -positive subjects

status: Public on Feb 26 2021

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Analysis of steady-state mRNA levels during COVID19.

overall_design: Comparison of hospitalized subjects: 30 Sars-COV2-negative versus 65 Sars-COV2-positive

first: Keith

last: Smith

first: Kelly

last: Sullivan

first: Joaquin

middle: M

last: Espinosa


title: scRNAseq of Aging Drosophila ISCs [NGS1910]

status: Public on Apr 02 2021

city: Warsaw

first: Michal

last: Pawlak

address: Domaniewska 39 B

country: Poland

institute: Roche Polska Sp. z o.o.

summary: Tissue homeostasis requires long-term lineage fidelity of somatic stem cells. Whether and how age-related changes in somatic stem cells impact the faithful execution of lineage decisions remains largely unknown. Here, we address this question using genome-wide chromatin accessibility and transcriptome analysis as well as single cell RNA-seq to explore stem cell intrinsic changes in the aging Drosophila intestine. These studies indicate that in stem cells of old flies, promoters of Polycomb (Pc) target genes become differentially accessible, resulting in the increased expression of enteroendocrine (EE) cell specification genes. Consistently, we find age related changes in the composition of the EE progenitor cell population in aging intestines, as well as a significant increase in the proportion of EE-specified ISCs and progenitors in aging flies. We further confirm that Pc-mediated chromatin regulation is a critical determinant of EE cell specification in the Drosophila intestine. Pc is required to maintain expression of stem cell genes while ensuring repression of differentiation and specification genes. Our results identify Pc group proteins as central regulators of lineage identity in the intestinal epithelium and highlight the impact of age-related decline in chromatin regulation on tissue homeostasis.

overall_design: For the scRNA-seq experiments, we used the wild-type WDah fly line and dissected whole midguts at young (~7d), mid-age (~30d) and old time-points (~60d). In total, we had two young, one mid age and two old samples. The cell density and viability of single-cell suspension were determined by Vi-CELL XR cell counter (Beckman Coulter). All of the processed samples had very high percentage of viable cells (>90%). The cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~6,000 cells per sample. cDNAs and libraries were prepared following manufacturer’s user guide (10x Genomics). Libraries were profiled on 2100 Bioanalyzer (Agilent Technologies) using High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems). Each library was sequenced in one lane of HiSeq4000 (Illumina) following manufacturer’s sequencing specification (10x Genomics).

first: Helen

last: Tauc

first: Imilce

last: Rodriguez-Fernandez

first: Jason

last: Hackney

first: Tal

last: Oron

first: Jerome

last: Korzelius

first: Hagar

middle: F

last: Moussa

first: Subhra

last: Chaudhuri

first: Zora

last: Modrusan

first: Bruce

last: Edgar

first: Heinrich

last: Jasper


title: Placental uptake and metabolism as determinants of pregnancy vitamin D status [RNA-seq]

status: Public on Feb 25 2021

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

summary: Pregnancy 25-hydroxyvitamin D (25(OH)D) concentrations are associated with maternal and fetal health outcomes, but the underlying mechanisms have not been elucidated. Using physiological human placental perfusion approaches and intact villous explants we demonstrate a role for the placenta in regulating the relationships between maternal 25(OH)D concentrations and fetal physiology. Here, we demonstrate active placental uptake of 25(OH)D3 by endocytosis and placental metabolism of 25(OH)D3 into 24,25-dihydroxyvitamin D3 and active 1,25-dihydroxyvitamin D [1,25(OH)2D3], with subsequent release of these metabolites into both the fetal and maternal circulations. Active placental transport of 25(OH)D3 and synthesis of 1,25(OH)2D3 demonstrate that fetal supply is dependent on placental function rather than solely the availability of maternal 25(OH)D3. We demonstrate that 25(OH)D3 exposure induces rapid effects on the placental transcriptome and proteome. These map to multiple pathways central to placental function and thereby fetal development, independent of vitamin D transfer, including transcriptional activation and inflammatory responses. Our data suggest that the underlying epigenetic landscape helps dictate the transcriptional response to vitamin D treatment. This is the first quantitative study demonstrating vitamin D transfer and metabolism by the human placenta; with widespread effects on the placenta itself. These data show complex and synergistic interplay between vitamin D and the placenta, and inform possible interventions to optimise placental function to better support fetal growth and the maternal adaptations to pregnancy.

overall_design: Villous fragments from eight fresh term human placenta were treated for 8 hours with 20µM 25-hydroxyvitamin D (25(OH)D) and processed for RNA-seq together with controls.

first: Brogan

last: Ashley

first: Claire

last: Simner

first: Antigoni

last: Manousopoulou

first: Carl

last: Jenkinson

first: Felicity

last: Hey

first: Jennifer

last: Frost

first: Faisal

last: Rezwan

first: Cory

middle: H

last: White

first: Emma

last: Lofthouse

first: Emily

last: Hyde

first: Sarah

last: Crozier

first: Hazel

last: Inskip

last: Godfrey

first: John

last: Holloway

first: Cyrus

last: Cooper

first: Kerry

last: Jones

first: Rohan

last: Lewis

first: Martin

last: Hewison

first: Spiros

last: Garbis

first: Nicholas

middle: C

last: Harvey

first: Jane

middle: K

last: Cleal


title: Placental uptake and metabolism as determinants of pregnancy vitamin D status  [Array]

first: Miguel

last: Branco

type: Methylation profiling by genome tiling array

overall_design: Villous fragments from eight fresh term human placenta were treated for 8 hours with 20µM 25-hydroxyvitamin D (25(OH)D) and compared to paired controls.

first: Brogan

last: Ashley

first: Claire

last: Simner

first: Antigoni

last: Manousopoulou

first: Carl

last: Jenkinson

last: Hey

first: Keith

middle: W


title: Gene expression profile in mouse skeletal muscle after 4F induction

status: Public on Mar 22 2021

first: April

last: Williams

summary: Analysis of soleus (SOL) and extensor digitorum longus (EDL) muscles isolated from Acta1-Cre+/4Fhet (as treatment) and Acta1-Cre-/4Fhet (as control) mice. Results provide unbiased gene expression profile of SOL and EDL muscles after 4F induction.

overall_design: Myofiber-specific 4F mice (Acta1-Cre/4Fhet) were generated to investigate the effect of 4F on extrinsic modulators of SCs. In this mouse model, LoxP-STOP-LoxP cassette is excised by Cre, resulting in restricted rtTA induction to induce 4F expression in myofibers upon doxycycline (Dox) administration. Two-month-old Acta1-Cre+/4Fhet (as treatment) and Acta1-Cre-/4Fhet mice (as control) were fed with water containing Dox (1 mg/ml) for 2.5, 5.5 or 8.5-days to induce 4F overexpression, and the EDL muscles and the SOL muscles were isolated for whole muscle RNA-seq analysis (N=2 per condition). Day 5.5 samples were assessed as outliers and removed from downstream analysis.

first: Chao

last: Wang

first: Juan

last: Izpisua Belmonte

first: Maxim

last: Shokhirev

first: Ling

last: Huang


title: Increased IL-6 and altered inflammatory response in bipolar disorder patient-derived astrocytes

status: Public on Mar 19 2021

summary:
The goals of this study are to examine responses to inflammation in astrocytes from  induced pluripotent stem cells derived from healthy controls and bipolar disorder patients. We examine the transcriptomic inflmmatory signature of generated astrocytes following Il1Beta exposure in BD vs. control
Results: BD-patient astrocytes show a unique inflammatory response with differentially regulated genes.

overall_design: Human induced pluripotent stem cells (hiPSC)-derived astrocytes were treated with Il1beta and compared to vehicle treated controls from four healthy invididuals and five bipolar disorder patient individuals (run in duplicate).

first: Krishna

last: Vadodaria

first: Carol

last: Marchetto

first: Fred

last: Gage


title: Primary hepatocyte transcriptional response to Fis1 and Drp1 over-expression by adenovirus

status: Public on Mar 26 2021

city: Boston

first: Yae-Huei

last: Liou

state: MA

address: 665 Huntington Ave.

department: MET

institute: Harvard School of Public health

summary: RNA-seq analysis of Ad-LacZ, Ad-Fis1 and Ad-Drp1 infected primary hepatocyte.

overall_design: Differential expression of mRNA from Ad-LacZ, Ad-Fis12 and Ad-Drp1 infected primary hepatocyte. 4 samples from each groups was analyzed.

first: Chih-Hao

last: Lee


title: RNA-seq in QGY-7703 cell line before and after PRMT7 knockdown

city: Guangzhou

first: Haitao

last: Chen

state: Guangdong

address: 1838 North Guangzhou Ave

institute: Southern medical university

summary: To explore the mechanism by which PRMT7 regulates HCC cell malignant phenotypes, we performed RNA-seq in QGY-7703 cells before and after PRMT7 knockdown to identify the affected signaling pathways. 296 differentially expressed genes were identified in PRMT7-downregulated cells (Figure 6A) and these genes were enriched in cancer-related pathways including MAPK signaling pathway, p53 signaling pathway, and FoxO signaling pathway (Figure 6B), as revealed by DAVID KEGG analysis.

overall_design: RNA-seq was constructed in QGY-7703 cells without PRMT7 knockdown and cells with PRMT7 knockdown  by two short hairpin RNA (shRNA), shRNA1 and shRNA2, respectively.

first: Ting

last: Shen


title: Placental uptake and metabolism as determinants of pregnancy vitamin D status

first: Miguel

last: Branco

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

overall_design: Refer to individual Series


title: Modified Hypoxia-Inducible Factor Expression in CD8+ T Cells Increases Antitumor Efficacy [HIF2 Dataset]

status: Public on Feb 16 2021

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

institute: University of Cambridge

summary:
Adoptive transfer of anti-tumor cytotoxic T cells is a novel form of cancer immunotherapy, and a key challenge is to ensure the survival and function of the transferred T cells. Immune cell survival requires adaptation to different micro-environments, and particularly to the hypoxic milieu of solid tumors. The hypoxia-inducible factor (HIF) transcription factors are an essential aspect of this adaptation, and we undertook experiments to define structural determinants of HIF that would potentiate anti-tumor efficacy in cytotoxic T cells. We created retroviral vectors to deliver ectopic expression of HIF-1ɑ and HIF-2ɑ in mouse CD8+ T cells, together or individually, and with or without sensitivity to their oxygen-dependent inhibitors Von Hippel-Lindau (VHL) and Factor Inhibiting HIF (FIH). We found that HIF-2ɑ, but not HIF-1ɑ, drives broad transcriptional changes in CD8+ T cells, resulting in increased cytotoxic differentiation and cytolytic function against tumor targets. We further found that a specific mutation replacing the hydroxyl group acceptor site for FIH in the HIF-2ɑ isoform gives rise to the most effective anti-tumor T cells after adoptive transfer in vivo. Lastly, we show that co-delivering an FIH-insensitive form of HIF-2ɑ with an anti-CD19 chimeric antigen receptor greatly enhances cytolytic function of human CD8+ T cells against lymphoma cells both in vitro and in a xenograft adoptive transfer model. These experiments provide a means to increase the anti-tumor efficacy of therapeutic CD8+ T cells via ectopic expression of the HIF transcription factor.
Method: OT-I CD8+ T cells were activated with 100 ng/ml OVA for 24 hours before retroviral transducton with with mouse HIF1 or mouse HIF2-expressing vectors, expanded in IL-2 for 5 days before being sorted on Thy-1.1 surface expression on a BD FACSAria Fusion cell sorter (BD Biosciences) directly into RLT Plus lysis buffer (Qiagen, #1053393). Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing the Illumina TruSeq Stranded mRNA Sample preparation protocol, which includes cDNA synthesis, ligation of adapters and amplification of indexed libraries, was used (Illumina, #20020594). The yield and quality of the amplified libraries were analysed using Qubit by Thermo Fisher and the Agilent Tapestation. The indexed cDNA libraries were normalised and combined and the pools were sequenced on the Nextseq 550 for a 50-cycle v2.5 sequencing run generating 75 bp single-end reads. Basecalling and demultiplexing was performed using CASAVA software with default settings generating Fastq files for further downstream mapping and analysis.

overall_design: Mouse OT-I CD8+ T cells were retrovirally transduced to ectopically express mouse HIF2 (Epas1). Each HIF was transduced with its hydroxylation accepting sites in native form (P404, P530, N851: PPN) or in mutated forms (P404, P530, A851" PPA), (A404, A530, N851: AAN) or (A404, A530, A851: AAA). All vectors encoded  Thy-1.1 as a surface transduction marker. A Thy-1.1 only vector control was also included. Transduced OT-I cells were cultured for  5 days before Thy-1.1 purification using FACS. Each vector (VC; HIF2_PPN; HIF2_PPA; HIF2_AAN; HIF2_AAA) was independently transduced into OT-I cells from 3 or 4 individual mice (A, B, C, D).

first: Pedro

last: Velica

middle: P

last: Cunha

first: Nikola

last: Vojnovic

first: Iosifina

last: Foskolou

first: Milos

last: Gojkovic

first: Helene

last: Rundqvist

first: Randall

last: Johnson


title: Sphingolipids Control Dermal Fibroblast Heterogeneity

status: Public on Feb 23 2021

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

country: Switzerland

institute: EPFL

summary: Human cells produce thousands of lipids that impact biological processes in ways we are only starting to characterize. The cellular composition in lipids changes during differentiation and also varies across individual cells of the same type. Yet, whether and how cell-to-cell differences in lipid composition affect cell phenotypes remain unknown. Here we have measured the lipidomes and transcriptomes of individual human dermal fibroblasts by coupling high-resolution mass spectrometry imaging to single-cell transcriptomics. We find that the cell-to-cell variation of specific lipid metabolic pathways contributes to the establishment of cell states involved in the organization of skin architecture. In fact, sphingolipid composition defines fibroblast subpopulations and its metabolic rewiring drives cell state transitions. These data uncover a role for cell-to-cell lipid heterogeneity in the determination of cell states and reveal a new regulatory component to the self-organization of multicellular systems.

overall_design:
Dermal human fibroblasts were grown in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS), 4.5 g/l glucose, 2 mM L-glutamine, 1 U/ml penicillin/streptomycin. The cell lines were grown under a controlled atmosphere in the presence of 5% CO2 at 37 °C. Cells were grown in a flask until 90% confluence. The medium was removed and trypsin-EDTA solution (0.05% trypsin, 0.02% EDTA) was added for 3-5 min. Then, the medium was added back to block the protease action, and the cells were collected into a plastic tube. After centrifugation for 5 min at 1200 rpm, the cell pellet was resuspended in fresh medium, gently mixed, and placed in a new plastic flask with fresh growth medium.

Bulk RNA sequencing was performed on the following FACS sorted populations of dHFs: Cholera Toxin positive (n=2), ChTxB/ShTxB1a/ShTxB2e positive (n=2), ShTxB1a/ShTxB2e positive (n=3) and ShTxB2e positive (n=1) and to a control unsorted population (n=2). Total RNA was isolated from FACS sorted dHFs populations using Rneasy Mini kits (Qiagen, Germany) according to the manufacturer instructions. The yield and the integrity of the RNA were determined using a spectrophotometer (NanoDrop ND-1000; Thermo Scientific, USA). Total RNA (10ng-1mg, depending on the different population) were submitted for RNA-seq with GENEWIZ, NJ. Libraries were prepared using Illumina HiSeq platform with ultra-low input configuration and sequenced with 2× 150 bp sequencing configuration to a depth of 350 million reads (GENEWIZ, NJ). Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.

scRNA-seq experiments were performed using 10X Genomics Chromium cRNA-seq kit v3.1. following provider instructions to obtain 3500 cells per replicate. Libraries were sequenced at the depth of 300 million reads corresponding to an average of 80k reads per cell. Data was pre-processed using cellranger and velocyto v0.17 and then analyzed using scanpy.

first: Laura

last: Capolupo

first: Irina

last: Khven

first: Alex

last: Lederer

first: Luigi

last: Mazzeo

first: Galina

last: Glousker

first: Sylvia

last: Ho

first: Francesco

last: Russo

first: Jonathan

last: Paz Montoya

first: Dhaka

last: Bhandari

first: Andrew

last: Bowman

first: Shane

last: Ellis

first: Romain

last: Guiet

first: Olivier

last: Burri

first: Johanna

last: Detzner

first: Johannes

last: Muthing

first: Krisztian

last: Homicsko

first: Francois

last: Kuonen

first: Michel

last: Gilliet

first: Bernhard

last: Spengler

first: Ron

last: A Heeren

first: Gian Paolo

last: Dotto

first: Giovanni

last: D’Angelo


title: Sciatic Nerve Injury Triggered Inflammation: Insights into Conditioning-Lesion Induced Axon Regeneration

first: Michigan

middle: CDB

last: Bioinformatics


title: Endoplasmic Reticulum (ER) Chaperones Are Effector Genes Mediating Long-Term Memory Consolidation

status: Public on Mar 01 2021

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

summary:
Purpose: We investigated Nr4a effector genes following a hippocampus dependent learning task using a dominant mouse model of Nr4a.
Method: We performed total RNA sequencing after training for hippocampus-dependent memory from Nr4ADN and control littermates
Results: Using an unbiased analysis of gene expression after training for hippocampus-dependent memory, we found that Nr4a transcription factors regulate expression of specific effector genes encoding endoplasmic reticulum (ER) chaperones that drive protein folding, enabling membrane proteins to more efficiently traffic to the cell surface.
Conclusion: This study identified the effector genes of Nr4a transcription factors involved in learning and memory.

overall_design: Dorsal hippocampus mRNA profiles of 2-4 months old male Nr4ADN and control littermates

first: Snehajyoti

last: Chatterjee

first: Utsav

last: Mukherjee

first: Emily

last: Walsh

first: Mahesh

last: Shetty

first: Amy

last: Yan

first: Yann

last: Vanrobaeys

first: Joseph

last: Lederman

first: Peter

last: Giese

first: Jacob

middle: J

last: Michaelson

first: Ted

last: Abel


title: Modified Hypoxia-Inducible Factor Expression in CD8+ T Cells Increases Antitumor Efficacy [HIF1 Dataset]

first: David

last: Bargiela

overall_design: Mouse OT-I CD8+ T cells were retrovirally transduced to ectopically express mouse HIF1 (Hif1a). Each HIF was transduced with its hydroxylation accepting sites in native form (P402, P577, N813: PPN) or in mutated forms (P402, P577, A813: PPA), (A402, A577, N813: AAN) or (A402, A577, A813: AAA). All vectors encoded  Thy-1.1 as a surface transduction marker. A Thy-1.1 only vector control was also included. Transduced OT-I cells were cultured for  5 days before Thy-1.1 purification using FACS. Each vector (VC; HIF1_PPN; HIF1_PPA; HIF1_AAN; HIF1_AAA) was independently transduced into OT-I cells from 3 individual mice (A, B, C,).

first: Pedro

last: Velica

last: Cunha

first: Nikola

last: Vojnovic

first: Iosifina

last: Foskolou

first: Milos

last: Gojkovic

first: Helene

last: Rundqvist

first: Randall

last: Johnson


title: Modified Hypoxia-Inducible Factor Expression in CD8+ T Cells Increases Antitumor Efficacy


title: Stabilized Epithelial Phenotype of Cancer Cells in Primary Tumors Leads to Increased Colonization of Liver Metastasis in Pancreatic Cancer

status: Public on Feb 11 2021

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

summary: Single-cell RNA-sequencing analyses were performed on unfractionated live cell mixtures or YFP sorted cancer cells from pancreatic tumors or liver mets of KPC;YFP control mice and KPC;SnailKO;TwistKO;YFP mice, so as to investigate the Epithelial-to-Mesenchymal Transition (EMT) of cancer cells in primary tumors and metastases. The effect of cancer-specific knockout of EMT transcription factor Snail and Twist on cancer cell EMT was studied by comparing KPC;YFP control mice and KPC;SnailKO;TwistKO;YFP mice. Each sample was in an individual folder containing the related fastq raw data files.

overall_design: Unfractionated live cell mixtures or YFP sorted cancer cells from pancreatic tumors or liver mets of KPC;YFP control mice and KPC;SnailKO;TwistKO;YFP mice were analyzed by 10x single-cell RNA-sequencing

first: Sujuan

last: Yang

first: Julienne

last: Carstens

first: Raghu

last: Kalluri


title: Placental uptake and metabolism as determinants of pregnancy vitamin D status [ChIP-seq]

first: Miguel

last: Branco

overall_design: Cytotrophoblast cells were treated for 24 hours with 20 µM 25-hydroxyvitamin D (25(OH)D) and processed for H3K27ac and H3K4me3 ChIP-seq together with controls.

first: Brogan

last: Ashley

first: Claire

last: Simner

first: Antigoni

last: Manousopoulou

first: Carl

last: Jenkinson

first: Felicity

last: Hey

first: Jennifer

last: Frost

first: Faisal

last: Rezwan

first: Cory

last: White

first: Emma

last: Lofthouse

first: Emily

last: Hyde

first: Sarah

last: Crozier

first: Hazel

last: Inskip

first: Keith

last: Godfrey

first: John

last: Holloway

first: Cyrus

last: Cooper

first: Kerry

last: Jones

first: Rohan

last: Lewis

first: Martin

last: Hewison

first: Spiros

middle: D

last: Garbis

first: Nicholas

last: Harvey

first: Jane

last: Cleal


title: Absence of Batf3 reveals a new dimension of phenotypic cell state plasticity within conventional dendritic cells

status: Public on Feb 24 2021

city: Woolloongabba

first: Chenhao

last: Zhou

state: QLD

address: 37 Kent Street

country: Australia

institute: The University of Queensland Frazer Institute

summary: Conventional dendritic cells (cDCs) are traditionally subdivided into cDC1 and cDC2 lineages. Batf3 is a cDC1-required transcription factor, and we observed that Batf3-/- mice harbor a population of cDC1-like cells co-expressing cDC2-associated surface molecules. Using single cell RNA sequencing with integrated cell surface protein expression (CITE-seq), we found that Batf3-/- mitotic immature cDC1-like cells showed reduced expression of cDC1 features and increased levels of cDC2 features. In wildtype, we also observed a proportion of mature cDC1 cells expressing surface features characteristic to cDC2, and found that overall cDC cell state heterogeneity was mainly driven by developmental stage, proliferation and maturity. We detected population diversity within Sirpa+ cDC2 cells, including a Cd33+ cell state expressing high levels of Sox4 and lineage-mixed features characteristic to cDC1, cDC2,  pDCs and monocytes. In conclusion, these data suggest that multiple cDC cell states can co-express  lineage-overlapping  features, revealing a level of previously unappreciated cDC plasticity.

overall_design: CITE-seq of live MHCII+CD11c+ cells sorted from T and B cell depleted splenocytes from C57BL/6 and Batf3-/- mice

first: Samuel

last: Lukowski

first: Inga

last: Rodahl

last: Kelly

first: Meihua

last: Yu

first: Susan

last: Millard

first: Stacey

middle: B

last: Andersen

first: Angelika

middle: N

last: Christ

first: Gabrielle

last: Belz

first: Ian

last: Frazer

first: Janin

last: Chandra


title: Dual tumor and normal biopsies from various cancer patients

status: Public on Mar 11 2021

city: Villejuif

first: Shai

last: Magidi

address: rue Guy Moquet

country: France

institute: WIN Consortium

summary: Transcriptomic profiling of cancer patients from tumor tissue and organ-matched normal tissue as reference which were taken as part of the WINTHER clinical trial. The organ-matched normal tissues were used in order to eliminate host gene expression variability while discarding most genetic variability between individuals. The goal was to develop an algorithm, Digital Display Precision Predictor (DDPP), which aims to identify transcriptomic predictors of treatment outcome, which were recorded in the trial.

overall_design: Dual biopsies experiment - Tumor tissue vs. organ-matched normal tissue. 23 Samples were collected along with the outcomes under treatments, which was individualized based on the cancer type and individual status. Hybridizations were performed as dual-dye-swapped (direct and inversed labeling) experiments

first: Vladimir

last: Lazar


title: Transcriptional and protein-level profiling of engraftable human fetal liver (fl)-derived hematopoietic stem cells (HSCS)

status: Public on Feb 08 2021

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: We provide an in-depth characterization of engraftable fetal liver (FL) HSCs as these have been shown to possess superior engraftment potential compared to cord blood (CB) and bone marrow (BM) HSCs. We have single cell profiled 26,407 FL cells, of which 7,235 highly-enriched functional FL HSCs, both at the transcriptional and protein level to uncover the detailed molecular signature of engraftment potential.

overall_design: Following dissociation of human FL, cells were divided into either CD34+-enriched cells or CD34- flowthrough cells via magnetic bead separation. The CD34- live cell fraction was further subdivided into GYPA+ and GYPA- via fluorescence activated cell sorting (FACS). From the CD34+-enriched fraction live CD34+ cells were sorted (CD34+bulk). In a separate sample, we further enriched this population using FACS based on GPI-80 expression (GPI-80+), a marker tightly linked to engraftment potential to focus our analysis on HSCs capable of long-term engraftment. Prior to sorting, cells were stained with a panel of oligo-tagged antibodies so that the antibody-derived tags (ADTs) corresponding to the cell surface markers present on each cell would also be captured in the sequencing data.

first: Kim

last: Vanuytsel

first: Jonathan

last: Lindstrom-Vautrin

first: George

last: Murphy


title: Differential microRNA Expression in USP8-Mutated and Wild-Type Corticotroph Pituitary Tumors Reflect the Difference in Protein Ubiquitination Processes

status: Public on Feb 06 2021

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

summary: Background: USP8 mutations are the most common driver changes in corticotroph pituitary  tumors. They have direct effect on cells’ proteome through disturbance of ubiquitination process and  also influence gene expression. The aim of this study was to compare microRNA profiles in USP8-  mutated and wild-type tumors and determine the probable role of differential microRNA expression  by integrative microRNA and mRNA analysis. Methods: Patients with Cushing’s disease (n = 28)  and silent corticotroph tumors (n = 20) were included. USP8 mutations were identified with Sanger  sequencing. MicroRNA and gene expression was determined with next-generation sequencing.  Results: USP8-mutated patients with Cushing’s disease showed higher rate of clinical remission  and trend towards lower tumor volume than wild-type patients. Comparison of microRNA profiles  of USP8-mutated and wild-type tumors revealed 68 differentially expressed microRNAs. Their  target genes were determined by in silico prediction and microRNA/mRNA correlation analysis.  GeneSet Enrichment analysis of putative targets showed that the most significantly overrepresented  genes are involved in protein ubiquitination-related processes. Only few microRNAs influence  the expression of genes differentially expressed between USP8-mutated and wild-type tumors.  Conclusions: Differences in microRNA expression in corticotropinomas stratified according to  USP8 status reflect disturbed ubiquitination processes, but do not correspond to differences in gene  expression between these tumors.

overall_design: Pituitary tumor samples were collected during transsphenoidal surgery and fixed in formalin for routine diagnostic procedures, including immunohistochemical and ultrastruc- tural evaluation. Archival formalin-fixed paraffin-embedded (FFPE) tissue samples from 48 patients, including 28 samples from patients with Cushing’s disease and 20 samples from patients with SCA, were included.

first: Paulina

last: Kober

first: Joanna

last: Boresowicz

first: Natalia

last: Rusetska

last: Zeber-Lubecka

first: Agnieszka

last: Paziewska

first: Monika

last: Pekul

first: Grzegorz

last: Zielinski

first: Andrzej

last: Styk

first: Jacek

last: Kunicki

first: Jerzy

last: Ostrowski

first: Janusz

middle: A

last: Siedlecki

first: Maria

last: Maksymowicz


title: NAP1L2 Drives Mesenchymal Stem Cell Senescence and Suppresses Osteogenic Differentiation [RNA-Seq]

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

summary: Changes in these genes are probably a consequence of aging, and the real regulators governing BMSC senescence and osteogenesis are still unclear.In the current study, we report that nucleosome assembly-related protein NAP1L2 serves as an important regulator of both the senescence and osteogenic differentiation of BMSCs through inhibition of NF-κB signaling and recruitment of SIRT1 to deacetylate the H3K14ac level on promoters of osteogenic genes. Thus, targeting NAP1L2 using an aging antagonist such as NMN would benefit aging-related disease.

overall_design: Non-target control and knockdown Nap1l2 C3H10T1/2 cells were divided into the following four groups depending on whether osteogenesis induction for 7days is performed: NC, KD-Nap1l2, NC-7day, KD-Nap1l2-7day.And cells were harvested for gene expression profiling. Two replicates were performed.

first: MeiLin

last: Hu


title: Differential gene expression analysis in eosinophilic and mixed granulomatous lung inflammation

status: Public on Feb 03 2021

city: Auburn

first: Amarjit

last: Mishra

state: AL

address: 1130 Wire Road, 264 Greene Hall

department: Pathobiology

institute: Auburn University

summary:
Alteration in the gene expression level in the lungs are thought to play a crucial role during the development of asthma and airway hyperresponsiveness. House dust mite induced allergic asthma is a Th2-lymphocyte driven inflammation characterized by airway hyperresponsiveness and eosinophilia while c-di-GMP, which is a potent mucosal adjuvant, induces a Th1-Th17 response accompanied by neutrophilia along with a low Th2 response.
We aimed to identify changes in the expression of genes important in asthma pathology via targeted gene expression arrays.

overall_design: Mice lungs from asthma (Th2 and Th1-Th17-driven) and control were selected for RNA extraction and hybridization on GeneChip whole transcriptome microarrays. We sought to obtain the comparative lung gene expression profile data from the samples of saline, eosinophilic and mixed granulomatous inflammation, to identify disease associated changes in the asthmatic lungs.

first: A

last: Jaiswal

last: Mitra


title: Microglia use TAM receptors to detect and engulf amyloid beta plaques

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Two microglial TAM receptor tyrosine kinases - Axl and Mer - have been linked to Alzheimer’s disease, but their roles in disease have not been tested experimentally. We find that in Alzheimer’s disease and its mouse models, induced expression of Axl and Mer in amyloid plaque-associated microglia is coupled to induced plaque decoration by the TAM ligand Gas6 and its co-ligand phosphatidylserine. In the APP/PS1 mouse model of Alzheimer’s disease, sIngle cell RNAseq analysis comparing wild type microglia with those with Axl and Mer deficiency reveals a similar disease state transitional program of microglia but a dampened differential expression of numerous AD siganture genes in microglia lacking TAM receptors. In line with the transcriptomic data, using two-photon microscopy, we show that genetic ablation of Axl and Mer results in microglia that are unable to normally detect, respond to, organize, or phagocytose amyloid beta plaques. These major deficits notwithstanding, and contrary to expectation, TAM-deficient APP/PS1 mice develop fewer dense-core plaques than APP/PS1 mice with normal microglia. Our findings reveal that the TAM system is an essential mediator of microglial recognition and engulfment of amyloid plaques, and that TAM-driven microglial phagocytosis does not constrain, but rather promotes, plaque development.

overall_design: Immune cells were isolated and sorted from pooled cortices (2 per sample) from 18 month old APP/PS1 (AD) and age-matched APP/PS1 Axl-/- Mertk-/- mice (ADAM), 2 biological replicates per group in total of 4 samples.

first: Youtong

last: Huang

first: Kaisa

last: Happonen

first: Greg

last: Lemke

first: Ling

first: Axel

last: Nimmerjahn

first: Patrick

last: Burrola


title: Transcriptome analysis of SARS-CoV-2 infected H522 human lung adenocarcinoma cells

status: Public on Jan 31 2021

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

summary:
Purpose:  The goal of this study is to define the transcriptional response of H522 cells to SARS-CoV-2 infection.
Methods:H522 cells were infected with SARS-CoV-2 at varying multiplicities of infection and samples processed for RNA-seq at 4, 24, 48, 72 and 96 hours post-infection.
Results: We provide the transcriptomic and translatomic landscape of SARS-CoV-2-infected H522 cells from multiple RNA-seq libraries. We found that the robust transcriptional upregulation of numerous type I interferon and cell cycle associated genes in SARS-CoV-2-infected cells.
Conclusions: Our study represents the detailed analysis of transcriptional responses of H522 cells to SARS-CoV-2 and demonstrates upregulation of key pathways that may paly a role in disease pathogenesis.


title: NAP1L2 Drives Mesenchymal Stem Cell Senescence and Suppresses Osteogenic Differentiation


title: Evolution of core archetypal phenotypes in high-grade serous ovarian cancer (HGSOC)

status: Public on Feb 09 2021

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: 24 malignant fluid samples were collected from 9 high-grade ovarian cancer patients at various time points over the course of chemotherapy. Additionally, an independent cohort of 8 malignant fluid samples were collected from pre-treatment patients and 7 samples from post-treatment patients. Single-cell RNA sequencing (scRNA-seq) was performed using 10X or iCell8 technologies.

overall_design:
Single-cell RNA sequencing of 39 malignant fluid samples from ovarian cancer patients.
---------------------------------------------
Submitters state "we cannot upload the raw data to GEO due to patient privacy issues".  Thus, this dataset is incomplete.

first: Aritro

last: Nath

last: Cosgrove

first: Benjamin

last: Copeland

first: Hoda

last: Mirsafian

first: Elizabeth

last: Christie

first: Lance

last: Pflieger

first: Sumana

last: Majumdar

first: Mihaela

last: Cristea

first: Earnest

middle: S

last: Han

first: Stephen

last: Lee

first: Edward

last: Wang

first: Theresa

last: Werner

first: Adam

middle: L

last: Cohen

first: Sian

last: Fereday

first: Nadia

last: Traficante

first: Phillip

last: Moos

middle: T

first: David

last: Bowtell

first: Andrea

last: Bild


title: Understanding BRCA1 function in INK4-RB deficient tumors

status: Public on Jan 27 2021

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
Most BRCA1-deficient BLBCs carry a dysfunctional INK4-RB pathway.
Thus, we have created genetically engineered mice with Brca1 loss and deletion of p16INK4A, or separately p18INK4C, to model the deficient INK4-RB signaling in human BLBC. By using these mutant mice and human BRCA1 deficient and proficient breast cancer tissues and cells, we tested if there exists a druggable target in BRCA1 deficient breast cancers.

overall_design: Gene expression microarray analysis of mouse mammary tumors.

middle: M

first: Daniel

last: Hollern


title: NAP1L2 Drives Mesenchymal Stem Cell Senescence and Suppresses Osteogenic Differentiation [ChIP-Seq]

first: Liu

last: Zhiqiang

overall_design: Examination of histone modification in non-target control and knockdown Nap1l2 C3H10T1/2 cells

first: MeiLin

last: Hu


title: Gene expression in the adult zebrafish intestine during starvation and refeeding

city: Durham

first: John

last: Rawls

address: 323 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University

summary: In this RNA-Seq dataset, we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA-Seq data revealed starvation-induced alterations in transcript levels for many genes, including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days after starvation was sufficient to restore most transcripts to their baseline pre-starvation levels. These host RNA-Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding.

overall_design: This study consists of two treatment groups of adult zebrafish (81dpf, days post-fertilization) that were separately housed. One treatment group (control) was continuously fed throughout the study, while the experimental group was starved for up to 21 days and then refed. At each timepoint (3dpS = 3 days post-starvation; 21dpS = 21 days post-starvation; 3dpR = 3 days post-refeeding), 4 zebrafish were taken from each treatment group, euthanized, and dissected to remove the whole intestine for RNA extraction and RNA-Seq analysis.

first: Jayanth

last: Jawahar


title: ZFP57 dictates allelic expression switch of target imprinted genes

city: Shanghai

first: weijun

last: jiang

address: Haike Road, 230

institute: Shanghaitech University

type: Methylation profiling by high throughput sequencing

summary: We did RNA-seq analysis to compare gene expression profiles in mouse embryos with or without ZFP57. We also perfromed whole-genome bisulfite sequencing analysis (WGBS) for the Zfp57 mutant mouse embryos and control heterozygous embryos. We analyzed DNA methylation at the imprinting control regions (ICRs), differentially methylation regions (DMRs) and repetitive elements including LINE-1, LINE-2, SINE, LTR and IAP.

overall_design: RNA-seq analysis was used to find the target genes of Zfp57 in mouse embryos. WGBS was applied to examine the effects of ZFP57 on DNA methylation at the ICRs, DMRs and some repetitive elements.

first: Weijun

last: Jiang

first: Yu

last: Zhang

first: Qiu

first: Xiajun

last: Li


title: RNA-seq analysis of CARIP knockout mice

status: Public on Jan 01 2021

city: Heidelberg

first: Tang

last: Yiheng

address: Im Neuenheimer Feld 224

department: Department of Neuropathology

country: Germany

institute: Heidelberg University Hospital

summary: CARIP is a lncRNA highly expressed in mouse brain. In order to better understand functions of the lncRNA, we performed RNA-seq analysis on three types of brain tissues of CARIP-/- (KO) and wild type (WT) mice, and profiled differentially expressed genes between the two groups.

overall_design: A total of 7 samples from CARIP KO mice were analyzed, including 3 cerebellar, 2 cerebral and 2 hippocampal samples. Correspondingly, 7 WT samples were used as control.

first: Erzhong

last: Wu

first: Yiheng

last: Tang

first: Jianjun

last: Luo

first: Runsheng

last: Chen


title: RNA-seq study on mouse bone marrow HSPC cells isolated from Arid2 conditional knockout and control mice.

status: Public on Jan 08 2021

city: Milwaukee

last: Zhu

state: WI

address: 8733 W Watertown Plank Rd

institute: Versiti Blood Research Institute Milwaukee

summary: We isolated lineage negative, cKit+, Sca1+ hematopoietic stem and progenitor cells from mouse bone marrow from Arid2fl/fl:MxCre+ (knockout) and MxCre+ (control) mice. Mice were injected with pIpC 6 weeks prior to isolation of LSK cells. Total RNA was isolated followed by mRNA selection. cDNA libraries were generated and NextGen Sequencing was performed.

overall_design: We performed RNA-seq in mouse LSK cells (lineage negative, cKit+, Sca1+) isolated from Arid2fl/fl:MxCre+ (knockout) and MxCre+ (control) mice 6 weeks post pIpC injection.

first: Robert

last: Burns

first: Shikan

last: Zheng

first: Theresa

last: Bluemn


title: Long-read RNA sequencing of cattle, pig, and chicken tissues

city: Fort Collins

first: Michelle

last: Halstead

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

summary: Long-read Nanopore cDNA sequencing of polyA-enriched RNA was implemented in a range of adult tissues isolated from cattle, pig, and chicken. These data were used to identify and characterize the expression patterns of full-length transcript isoforms.

sample_organism:
Gallus gallus
Sus scrofa
Bos taurus

platform_organism:
Gallus gallus
Sus scrofa
Bos taurus

overall_design:
RNA was extracted from a total of 189 biological samples, corresponding to 93 cattle samples (32 tissues from two males and two females; represented as one 'Cattle_tissues_mixed' sample), 28 pig samples (17 tissues from two males), and 68 chicken samples (19 tissues from four males and two females). Raw data were procured from two lanes of PromethION sequencing: one lane for pooled cattle libraries, and one lane for pooled pig and chicken libraries.

Please note that 'Cattle_tissues_mixed' sample represents non-demultiplexed cattle samples.

first: Pablo

last: Ross


title: A transcriptomic atlas of mouse cerebellar cortex reveals novel cell types

status: Public on Jan 22 2021

first: Evan

last: Macosko

address: 75 Ames St, Broad Institute

institute: Broad Institute

summary: The cerebellar cortex is a well-studied brain structure with diverse roles in motor learning, coordination, cognition, and autonomic regulation.  Nonetheless, a complete inventory of cerebellar cell types is presently lacking.  We used high-throughput transcriptional profiling to profile more than 600,000 nuclei and molecularly define cell types across individual lobules of the adult mouse cerebellum.  Purkinje neurons showed considerable regional specialization, with the greatest diversity occurring in the posterior lobules.  For multiple types of cerebellar interneurons, the molecular variation within each type was more continuous, rather than discrete.  For the unipolar brush cells (UBCs)—an interneuron population previously subdivided into discrete populations—the continuous variation in gene expression was associated with a graded continuum of electrophysiological properties.  Most surprisingly, we found that molecular layer interneurons (MLIs) were composed of two molecularly and functionally distinct types.  Both show a continuum of morphological variation through the thickness of the molecular layer, but electrophysiological recordings revealed marked differences between the two types in spontaneous firing, excitability, and electrical coupling.  Together, these findings provide the first comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological, and physiological ontologies for defining brain cell types.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Characterization and annotation of single nuclei transcriptomes from adult and developing mouse cerebella. Nuclei suspensions for adult mouse cerebellum profiles were generated from 2 female and 4 male adult mice (60 days old), from individual dissections across 16 regions. Nuclei suspensions for developing mouse cerebellum profiles were generated from 2 E18 mice, 2 P0 (newborn) mice, 2 P4 (4 days old) mice, 2 P8, 2 male P12 and 2 male P16 mice.

>>>Raw data are unavailable for human samples due to patient privacy concerns<<<

first: Velina

last: Kozareva

first: Caroline

last: Martin

first: Tomas

last: Osorno

first: Stephanie

last: Rudolph

first: Chong

last: Guo

first: Charles

last: Vanderburg

first: Naeem

last: Nadaf

first: Aviv

last: Regev

first: Wade

last: Regehr


title: Chemical Genetics of Regeneration: Contrasting Temporal Effects of CoCl2 on Axolotl Tail Regeneration

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

summary: The Mexican axolotl provides a powerful model to investigate mechanisms of tissue regeneration. A recent chemical screen found that HDAC inhibitor romidepsin, administered for only 1-minute post amputation (1 MPA), blocks axolotl tail regeneration. Here, we tested the potential for cobalt chloride (CoCl2), a chemical stabilizer of HIF1a and inducer of hypoxia, to rescue romidepsin-inhibition of tail regeneration. Tail regeneration was partially rescued when embryos with amputated tails were co-treated with romidepsin and CoCl2. However, extending the CoCl2 dosage window either inhibited regeneration (CoCl2:0-30 MPA) or was lethal (CoCl2:0-24 hours post amputation; HPA). CoCl2:0-30 MPA caused tissue damage, tissue loss, and cell death at the distal tail tip, and blocked regeneration. In contrast, CoCl2 treatment of non-amputated embryos or CoCl2:60-90 MPA treatment of amputated embryos did not affect wound healing or inhibit tail regeneration. To further investigate the contrasting effects of CoCl2, microarray analysis was performed to identify differentially expressed genes at 3 HPA. CoCl2-romidepsin:1 MPA treatment significantly increased the expression of transcription factors associated with appendage regeneration, while CoCl2:0-30 MPA significantly increased expression of hemoglobin and platelet-specific transcripts, consistent with hemorrhage and an impaired hemostatic response. Also, CoCl2:0-30 MPA significantly increased expression of hypoxia inducible genes, including genes that encode Hif1a interacting proteins and heat shock proteins (HSP); in contrast, genes encoding TGFB signaling components were significantly downregulated. Using additional chemical inhibitors of tail regeneration, we identified transcriptional responses associated with HSP90 activity and TGFB signaling. Notably, geldanamcin decreased transcription of matrix metalloproteinases and sustained muscle-specific gene expression, suggesting a role for HSP90 in regulating extracellular matrix remodeling and muscle dedifferentiation. Our study shows the power of using chemical tools to precisely identify temporal windows within which critical biological processes are enacted during tissue regeneration.

overall_design: A microarray experiment was performed to determine the effect of 7.5 mM CoCl2 treatment on axolotl embryo gene expression at 3 hours post amputation. For each treatment tested (0-30 MPA CoCl2, 60-90 MPACoCl2, 10 uM romidepsin and CoCl2, Control), tail amputations were performed on 36 embryos (2 mm removed from distal tip with a razor blade) and then embryos were placed into microtiter plates containing rearing water (Control) or rearing water with chemicals. Exactly 1 mm of the distal tail tip was removed from embryos at 3 HPA. Tissues from 12 embryos were pooled into a 1.5 ml tubes with 0.5 ml of RNA-later (Qiagen) to obtain three replicate pools per treatment. In addition, a microarray experiment was performed to determine the effect of 1 um geldanamycin and 10 uM SB505124 on axolotl embryo gene expression at 24 hours post amputation. For each treatment tested (geldanamycin vs control, SB505124 vs control), tail amputations were performed on 48 embryos (2 mm removed from distal tip with a razor blade) and then embryos were placed into microtiter plates containing rearing water or rearing water (Control) with chemical. Exactly 1 mm of the distal tail tip was removed from embryos at 3 HPA. Tissues from 12 embryos were pooled into a 1.5 ml tubes with 0.5 ml of RNA-later (Qiagen) to obtain four replicate pools per treatment.

first: S

middle: R

last: Voss


title: Identification of CaMKIIβ binding lncRNAs in mouse hippocampus via RIP-seq

status: Public on Dec 27 2020

first: Tang

last: Yiheng

summary: In order to screen for CaMKIIβ binding lncRNAs, we performed a RIP-seq analysis on mouse hippocampus. Potential CaMKIIβ binding RNAs are identified through differential expression analysis between CaMKIIβ RIP-seq results and the control groups, IgG and input. Differentially expressed genes are subsequently filtered by biotype and expression level.

overall_design: RIP assay is performed with CaMKIIβ (Cell Signaling Technology, 12716) and IgG (Cell Signaling Technology, I8140) antibodies. The resulting RNA is extracted and deep-sequenced. The data include three CaMKIIβ replicates, three IgG replicates and two replicates of input RNA expression levels.

first: Erzhong

last: Wu

first: Yiheng

last: Tang

first: Jianjun

last: Luo

first: Runsheng

last: Chen


title: Whole genome sequencing of T and ITNK cells

status: Public on Dec 31 2020

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

summary: Compare mutation locus in T and ITNK cells

first: Zhiwu

last: Jiang

first: Peng

last: Li


title: Expression profiling of microRNAs during osteogenic differentiation of human MSCs

city: St. Louis

first: Jinsheng

last: Yu

address: 660 S. Euclid Ave.

department: Genetics

summary: The goal of this study was to determine expression profiles of microRNAs (miRNAs) in whole cell extracts of human bone marrow-derived mesenchymal stem/stromal cells (MSCs) as well as in MSCs during osteogenic differentiation. MicroRNAs are epigenetic regulators that commonly function by targeting specific mRNAs resulting in suppression of protein expression and modulation of a number of cellular pathways. This experiment is part of a larger study analyzing the expression of mitochondria-associated miRNAs in MSCs during osteogenesis that we recently submitted to GEO (Series GSE134946). Here, the same three human MSC lines were used in this study, under the same osteogenic induction conditions, to generate expression profiles of miRNAs present in whole cell extracts.  A standard in vitro osteogenesis assay system was used to differentiate MSCs toward the osteoblast lineage.Purified whole cell extracts were obtained from MSCs or from MSCs at specific time points of osteogenic induction. RNA was isolated from whole cell extracts and then biotin-labeled in preparation for microRNA array (Affymetrix miRNA array 4.0). Array data was analyzed to generate information on most abundantly-expressed miRNAs in non-induced MSCs as well as in MSCs at set time points (day 3, 7, or 14) of osteogenic induction. Information on significantly differentially-expressed miRNAs during osteogenesis (comparing day 0 with either day 3, 7 or 14) was also obtained.

overall_design: In this study, 3 independent human bone marrow-derived MSC cell lines were used. Each MSC cell line was differentiated toward the osteoblast lineage and RNA was isolated from MSCs at day 3, 7, or 14 of differentiation. As a control, RNA from non-induced MSCs (day 0) was also collected, Therefore, 12 samples in total were analyzed.

first: Audrey

last: McAlinden

first: Hongjun

last: Zheng


title: Long-term expansion using IL-7 and IL-15 increases T cell yield with preserved Tcm/Tscm properties suitable for adoptive T cell therapy

status: Public on Jan 28 2021

city: Berlin

first: Il-Kang

address: Augustenburger Platz 1

institute: Charité- Universitätsmedizin Berlin

summary: Adoptive T cell therapy (ATT) requires activation, expansion and, for certain indications, gene-modification of T cells. Sufficient numbers of T cells and the characteristics of the final T cell product decisively determine the success of treatment. In this study, we addressed the question if prolonged expansion by simply using the cytokine combination IL-7/IL-15 could enhance the T cell yield without sacrifying T cell functionality. Prolonged expansion resulted in a 50-fold increase of CD8+ central memory T cells (Tcm). RNA sequencing and differential analysis of short-term expanded (ST) and long-term expanded (LT) murine CD8+ and CD4+ Tcm revealed that LT T cells retain a gene expression profile related to Tcm/stem central memory T cells (Tscm). Upon anti-CD3/CD28 stimulation, ST and LT T cells proliferated and underwent apoptosis comparably. IL-2 and INF- production was higher for LT T cells. Engraftment, persistence and anti-tumor capacities of LT murine T cells were preserved after in vivo administration. We confirmed our in vitro findings for human T cells. Our study demonstrates the feasibility of manufacturing an increased number of favorable T cells with Tcm/Tscm properties for ATT by a prolonged, minimally manipulative expansion protocol using the cytokines IL-7 and IL-15.

overall_design: transcriptome profiling of long-term T-cell cultures

first: Stefanie

last: Herda

first: Andreas

last: Heimann

first: Benedikt

last: Obermayer

last: Althoff

first: Josefine

last: Ruß

first: Lars

last: Bullinger

first: Antonio

last: Pezzutto

first: Thomas

last: Blankenstein

first: Dieter

last: Beule


title: Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker

status: Public on Dec 23 2020

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Macrophages are the most common infiltrating immune cells in glioblastoma (GBM), and play a wide variety of pro-tumor and anti-tumor roles. However, the different subpopulations of macrophages and their effects on the tumor microenvironment remain poorly understood. Here, we combine new and previously-published single-cell RNA-seq data from 86,279 single cells from a total of 63 gliomas to profile 17,774 individual macrophages. Unsupervised clustering revealed an anti-inflammatory subpopulation of macrophages characterized by expression of MARCO (macrophage receptor with collagenous structure), a gene which has not been previously well-characterized in gliomas. MARCO is almost exclusively expressed in macrophages of IDH1-wildtype GBM rather than IDH1-mutated GBM or lower-grade gliomas. Previous studies have implicated MARCO as an unfavorable marker in melanoma and non-small-cell lung cancer; here, we find that bulk MARCO expression is associated with worse prognosis in TCGA glioblastomas, and associates with the mesenchymal expression subtype. Our single-cell analysis shows that this previously-reported mesenchymal signature primarily arises from MARCO-expressing macrophages. These MARCO-expressing macrophages differentially over-express gene sets related to hypoxia and the epithelial-mesenchymal transition, and under-express gene sets related to inflammation and antigen presentation. We show evidence that MARCO-expressing macrophages are recruited from the blood (as opposed to being resident microglia), and paired single-cell analysis of tumor and myeloid cells demonstrate that this recruitment may be driven by known chemoattractant factors. Furthermore, MARCO expression is significantly altered over the course of treatment with PD1 checkpoint inhibitors. These findings illustrate a novel myeloid subpopulation that drives tumor progression in glioblastomas, and suggest potential therapeutic targets to prevent their recruitment glioblastoma.

overall_design: Performed single cell RNA-seq on human glioma surgical specimens.

first: Andrew

first: Wenting

last: Zhou

first: Jinzhou

last: Yuan

first: Raul

last: Rabadan


title: Transcriptome Analysis of Plasmodium ΔCSP stable expressing or control HepG2 cells

city: Chongqing

first: Hong

address: 30 Gaotanyan Street

institute: Army Medical University (Third Military Medical University)

summary:
Purpose:To understand the change in transcriptome for the overxepression of ΔCSP in HepG2 cells.
Methods:Total RNAs of ΔCSP stable expressing or control HepG2  cells were extracted using TRIzol (Invitrogen), following the manufacturer's instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Sangon Bio Ltd. Briefly, sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech, Nanjing, China) following manufacturer's recommendations and were sequenced on HiSeq XTen sequencers (Illumina, San Diego, CA). Raw reads in FASTQ format were subjected to quality control using FastQC. RNA-seq reads were aligned to the reference genome using Bowtie. Uniquely mapped reads were used for further analysis. Gene expression levels are expressed as TPM (Transcripts per million reads) and differences in gene expression were calculated with rSeq.
Results:There were 492 genes differentially expressed in ΔCSP-overexpressing HepG2 cells compare to the control group respectively (fold change >2 or < 0.5).

overall_design: mRNA profiles of ΔCSP stable expressing or control HepG2 cells were generated by deep sequencing in triplicate, using illumina HiSeq XTen platform.

first: Xiao

last: Lu

first: Kai

last: Li

first: Feng

last: Zhu

first: Chenhao

last: Zhao

first: Taiping

last: Liu

first: Yan

last: Ding

first: Yong

last: Fu

first: Jigang

last: Dai

first: Yuzhang

last: Wu

first: Wenyue

last: Xu


title: Glucose-6-Phosphate Dehydrogenase as a Prognostic Predictor Correlates with the Tumor Immune Activity Including Programmed Death Ligand-1 Expression in Merkel Cell Carcinoma

status: Public on Dec 13 2020

city: Nagoya

first: Motoki

last: Nakamura

state: Aichi

address: 1-Kawasumi, Mizuho-ku, Mizuho-cho

department: Department of Geriatric and Environmental Dermatology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary:
Purpose: Merkel cell carcinoma (MCC) is a rare but highly malignant skin cancer. However, it is well known that some cases have a good prognosis including spontaneously regression. To precise such a different patient’s outcome, reported prognostic markers, e.g. Merkel cell polyoma virus infection or programmed death ligand-1 (PD-L1) expression, are still insufficient. Here we performed RNA sequencing to evaluate immune response and comprehensively estimate prognostic values of immunogenic factors in MCC.
Experimental Design: We collected 90 specimens from 71 patients and 53 blood serum samples from 21 patients with MCC from 9 facilities. mRNA was extracted from formalin fixed paraffin embedded (FFPE) tissues. Analyses of next generation sequencing data, immunohistochemical staining and blood serum tests were performed.
Results:  Next generation sequencing revealed that MCC samples could be divided into two types. “immune active type” showed better clinical outcomes than “cell division type”. Glucose-6-Phosphate Dehydrogenase (G6PD) was one of the most significantly up-regulated gene in “cell division type”. G6PD expression correlated with the presence or absence of lymph node or distant metastases during the course and negatively correlated with high or low of PD-L1 expression with the top significance in 395 genes both. Immunohistochemical staining of G6PD was also correlated with disease specific survival and showed less heterogeneity compared with PD-L1 expression. G6PD activity was measurable by the blood serum test and detection values significantly increased as the cancer stage progression and significantly decreased after treatment.
Conclusion: G6PD expression was an immunohistochemically and serum-detectable prognostic marker and negatively correlated with immune activity including PD-L1 associate with the prediction of immunotherapy response.

overall_design:
RNA sequencing of 41samples of MCC to evaluate immune response and comprehensively estimate prognostic values of immunogenic factors
Targeted RNA seq panel of 474 genes

last: Nakmaura

first: Maki

last: Yoshimitsu

first: Tetsuya

last: Magara

first: Yuka

last: Nojiri

first: Hiroshi

last: Kato

first: Kotaro

last: Nagase

first: Akimichi

last: Morita


title: Cell-free DNA methylome profiling by MBD-seq with ultra-low input

city: Tampa

first: Jinyong

last: Huang

state: Florida

address: 12902 USF Magnolia Drive

department: Tumor biology

institute: Moffitt Cancer Center

summary: Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions of cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data showed that cfMBD-seq performs equally to the standard MBD-seq (>1000 ng input) even when using 1 ng DNA as the input. cfMBD-seq demonstrated equivalent sequencing data quality as well as similar methylation profile when compared to cfMeDIP-seq. We showed that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulfite-free ultra-low input methylation profiling technology has a great potential in non-invasive and cost-effective cancer detection and classification.

overall_design: Different conditions of cfMBD-seq

first: Alex

middle: C

last: Soupir


title: Transcriptomic changes of Synechocystis sp. PCC 6803 upon surface contact after 4 and 8 h

status: Public on Dec 17 2020

city: Freiburg i. Br.

first: Sabrina

last: Oeser

address: Schänzlestraße 1

department: Institute of Biology III

institute: University of Freiburg

summary: Microarray analysis demonstrated that the expression levels of minor pilin genes change in response to surface contact. A total of 120 genes were determined to have altered transcription between planktonic and surface growth in this analysis. Among these genes, 13 are located on the pSYSM plasmid, and some are newly predicted minor pilin genes.

overall_design: Transcriptional changes of Synechocystis sp. PCC 6803 cells upon surface contact were measured. Therefore, samples were taken from a planktonic and a sessile culture after 4 and 8 h. For each condition, duplicates were analyzed.

first: Viktoria

last: Reimann

first: Annegret

last: Wilde


title: Distal nephron plasticity allows the induction of ureteric tip and stalk for the modelling of collecting duct disease

status: Public on Jan 15 2021

city: Parkville

first: Sean

last: Wilson

state: Victoria

address: 50 Flemington Road

institute: MCRI

summary: During development, distinct progenitors contribute to the nephrons versus the ureteric epithelium of the kidney. Indeed, previous pluripotent stem cell-derived models of kidney tissue either contain nephrons or pattern specifically to the ureteric epithelium. By reanalysing the transcriptional distinction between distal nephron and ureteric epithelium in human fetal kidney, we show here that while existing nephron-containing kidney organoids contain distal nephron epithelium and no ureteric epithelium, this distal nephron segment alone displays significant in vitro plasticity and can adopt a ureteric epithelial tip identity when isolated and cultured in defined conditions. “Induced” ureteric epithelium cultures can be cryopreserved, serially passaged without loss of identity and transitioned towards a collecting duct fate. Indeed, cultures harbouring loss-of-function mutations in PKHD1 recapitulate the cystic phenotype associated with autosomal recessive polycystic kidney disease.

overall_design: All bulk sequenced samples were analyzed in triplicate. Two single cell RNA sequencing datasets were generated from different cell lines.

first: Sara

last: Howden

first: Melissa

last: Little


title: Interdependence between histone marks and steps in Pol II transcription [Danko.submission]

status: Public on Dec 12 2020

city: Ithaca

first: Charles

middle: G

last: Danko

address: Hungerford Hill Rd

institute: Baker Institute

summary: We trained sensitive machine learning models that decompose maps of primary transcription into ChIP-seq profiles representing 9 distinct histone modifications. We show that transcription measured using precision run-on and sequencing (PRO-seq)  can recover the pattern of active histone modifications at nucleosome resolution and with an accuracy that rivals the correlation between independent ChIP-seq experiments in holdout cell types. To define the nature of the causal relationship between histone modifications and transcription, we perturbed transcription and examined the genomic distribution of four active and one repressive histone modification: H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K27me3.

overall_design: Examination of four active and one repressive histone modification: H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K27me3 by ChIP-seq. Observation of chromatin accessibility by ATAC-seq and H3 CUT&RUN, and transcription by ChRO-seq.

first: Alexandra

last: Chivu

first: Edward

last: Rice

first: John

last: Lis


title: microarray analysis of lung SPC/GFP+ EpCAM+ cells from different smoke exposure mice

status: Public on Dec 10 2020

city: Tokyo

first: Hidehiro

last: Irie

address: 35 Shinanomachi Shinjuku-ku

institute: Keio University

summary:
We extracted RNA of sorted lung SPC/GFP+ EpCAM+ cells and performed microarray analyses. Total RNA was extracted from sorted Ep-CAMhigh/GFPhigh cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. The RNA integrity was examined on an Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA). Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using the GeneChip WT PLUS Reagent Kit User Manual (Affymetrix/Thermo Fisher Scientific). Fragmented and labeled ss-cDNA were hybridized on a GeneChip Clariom S Array (Affymetrix/Thermo Fisher Scientific) (n =3/group).
We used microarrays to detail the global gene expression of SPC/GFP+ EpCAM+ cells from the control mice(G37-1_(Clariom_S_Mouse)), 3 week continuous smoke mice (G37-2_(Clariom_S_Mouse)) and 3 weeks intermittent smoke mice(G37-3_(Clariom_S_Mouse)), and identified distinct classes of up-regulated genes during this process.

overall_design: Lung SPC/GFP+ EpCAM+ cells from the control mice, 3 week continuous smoke mice, and 3 week intermittent smoke mice were sorted, RNA extraction from these cells was hybridized on Affymetrix microarrays.


title: Interdependence between histone marks and steps in Pol II transcription

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

sample_organism:
Homo sapiens
Equus caballus

platform_organism:
Homo sapiens
Equus caballus

overall_design: Refer to individual Series


title: SWI/SNF complex mutations promote thyroid tumor progression and resistance to redifferentiation therapy [RNA-seq]

status: Public on Dec 02 2020

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: Recurrent mutations in genes encoding subunits of the SWI/SNF chromatin remodeling complex occur commonly in human cancers of different lineages, including advanced thyroid cancers. Thyroid-specific loss of Arid1a, Arid2 or Smarcb1 in mouse BrafV600E-mutant tumors promotes disease progression and decreased survival, associated with lesion-specific effects on chromatin accessibility and differentiation. Swi/Snf loss leads to a repressive chromatin state at thyroid lineage transcription factors and their target binding sites, resulting in impaired expression of genes required for thyroid hormone biosynthesis. Thyroid differentiation and response to radioiodine therapy is restored by MAPK inhibitors in mouse BrafV600E-mutant thyroid cancers, which is abrogated in the context of Swi/Snf loss. MAPK inhibitors also failed to restore thyroid differentiation and radioiodide incorporation in patients with BRAFV600E or RAS-mutant tumors with SWI/SNF mutations. SWI/SNF complexes are central to the maintenance of differentiated thyroid function, and their loss confers RAI refractoriness and resistance to MAPK inhibitor-based redifferentiation therapies.

overall_design: RNA-seq of Braf-V600E thyroid tumor cell lines with SWI/SNF KO or WT treated with MEK inhibitor CH5126766 (CKI) or control

first: Mahesh

last: Saqcena

middle: P

first: James

last: Fagin


title: Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids

status: Public on Dec 07 2020

city: Pittsburgh

first: Mo

last: Ebrahimkhani

state: PA

address: A809B Scaife Hall, 3550 Terrace Street

department: Pathology

institute: University of Pittsburgh

summary: Pluripotent stem cell (PSC)-derived organoids are emerging as novel human-based microphysiological models but display immature phenotypes with limited subsets of endothelial or stromal cells. Here we demonstrate that in vitro manipulation of gene regulatory networks (GRNs) in PSC-derived liver organoids selected either through computational analysis or targeted tissue design can advance tissue maturation in vitro. Through an unbiased comparison with the genetic signature of mature livers, we identify downregulated GRNs in fetal liver organoids compared to adult livers. We demonstrate that overexpression of PROX1 and ATF5, together with targeted CRISPR-based transcriptional activation of endogenous CYP3A4, drives maturation in vitro. Single cell analyses reveal hepatobiliary-, endothelial-, and stellate-like cell populations. The engineered organoids demonstrate enhanced vasculogenesis, capture native liver characteristics (e.g.  FXR signaling, CYP3A4 activity), and exhibit therapeutic potential in mice. Collectively, our approach provides a genetically guided framework for engineering developmentally advanced multilineage tissues from hiPSCs.

overall_design: Bulk RNA sequencing of iPSC fetal liver organoid (FeLO), and designer liver organoids (DesLO) at different stages of development and different engineering conditions. Single cell RNA sequencing of time matched FeLO and DesLO. ATAC sequencing of iPSC, FeLO and DesLO


title: SWI/SNF complex mutations promote thyroid tumor progression and resistance to redifferentiation therapy [ATAC-seq]

overall_design: ATAC-seq of Braf-V600E thyroid tumor cell lines with SWI/SNF KO or WT treated with MEK inhibitor CH5126766 (CKI) or control


title: SWI/SNF complex mutations promote thyroid tumor progression and resistance to redifferentiation therapy [ChIP-seq]

overall_design: ChIP-seq of histone modifications from Braf-V600E thyroid tumor cell lines with SWI/SNF KO or WT


title: SWI/SNF complex mutations promote thyroid tumor progression and resistance to redifferentiation therapy (ATAC-seq, Fig3)

overall_design: ATAC-seq of Braf-V600E thyroid tissue with SWI/SNF KO or WT treated with MEK inhibitor CH5126766 (CKI) or control


title: Single Cell Sequencing Reveals Artifactual Gene Expression in Microglia in Response to Experimental Variability

status: Public on Dec 01 2020

city: Boston

first: Beth

last: Stevens

state: Massachusetts

address: 3 Blackfan Circle, 12220 Center for Life Sciences

institute: Boston Children's Hospital

summary: Single Cell Sequencing of FACS purified microglia/myeloid cells isolated with cold mechanical dounce homogenization (24 hrs post tail vein PBS injection)

overall_design: 4 animals,  P90

first: Samuel

middle: E

last: Marsh


title: SWI/SNF complex mutations promote thyroid tumor progression and resistance to redifferentiation therapy (RNA-seq, Fig3)

overall_design: RNA-seq of Braf-V600E thyroid tissue with SWI/SNF KO or WT treated with MEK inhibitor CH5126766 (CKI) or control


title: SWI/SNF complex mutations promote thyroid tumor progression and resistance to redifferentiation therapy


title: SWI/SNF complex mutations promote thyroid tumor progression and resistance to redifferentiation therapy (RNA-seq, Fig2)

overall_design: RNA-seq of SWI/SNF KO and WT thyroid tissue


title: Dissection of artificial and confounding glial signatures by single cell sequencing of mouse and human brain


title: Study of transcriptional changes in MCM7-depleted and G1/S-arrested A549 and A375 cells

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: We tested if the changes in cell invasion and migration observed after MCM7 depletion manifested in an altered gene expression profile. For this purpose, we performed RNAseq analysis after MCM7 knock-down in A549 and A375 cells expressing a Dox-inducible shMCM7. As controls, we used shMCM7 cells that had not been induced with Dox, as well as the parental A549 and A375 cell lines grown in the presence or absence of Dox. To exclude possible effects caused by changes in cell cycle progression, all RNA samples were extracted from double thymidine synchronized cell populations, in which >98% cells were arrested at the G1/S phase boundary.

overall_design: RNAseq analysis after MCM7 knock-down in A549 and A375 cells expressing a Dox-inducible shMCM7. As controls, we used shMCM7 cells that had not been induced with Dox, as well as the parental A549 and A375 cell lines grown in the presence or absence of Dox. Three biological replicates for each condition were analyzed.

first: Michael

last: Walser

first: Patrizia

last: Widmer

first: Alex

last: Hajnal