title: Performance comparison of small RNA-Seq library preparation methods for biofluid samples

status: Public on Dec 31 2020

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

summary:
We report performance of six different protocols for small RNAseq library preparation and of a method utilizing sequencing of probes targeting microRNAs (HTG EdgeSeq).

Recently, small RNA sequencing (small RNA-seq) has been introduced as a method for quantifying circulating microRNAs (miRNAs) and enabling their global profiling without prior knowledge of target sequences. Despite its great promise, small RNA-seq has not delivered the expected outcomes, particularly due to ligation and PCR bias introduced within the workflow. In this study, we assessed the performance of all existing approaches to the small RNA-seq of miRNAs in plasma samples: original two adapter ligation approach; single adapter ligation with subsequent circularization; polyadenylation; use of randomized adapters; and use of unique molecular identifiers (UMI). Using comprehensive set of metrics, we evaluated each protocol in terms of yield, precision, accuracy, sensitivity, and ability to detect isomiRs. Moreover, we assessed performance of targeted RNA-seq method utilizing hybridization probes across relevant metrics and together with RT-qPCR we used it as a reference for accuracy evaluation. The best results were delivered by targeted RNA-seq outperforming other methods in all relevant parameters. The protocols using randomized adapters or UMIs showed consistent good performance across all of the assessed metrics. In contrast, the polyadenylation approach generated a high percentage of discarded reads and impeded the analysis of isomiRs. The single adapter ligation with subsequent circularization failed to prevent ligation bias and the traditional two adapter ligation approach achieved the worse scores in the majority of tested metrics. To sum, we provide a comprehensive comparison that can serve as a guide for new users interested in analysis of circulating miRNAs and as a reference for further comparative studies.

sample_organism:
Homo sapiens
synthetic RNA

platform_organism:
Homo sapiens
synthetic RNA

overall_design: All seven protocols were used to sequence two types of samples - human plasma and equimolar pool of synthetic miRNAs (miRXplore Miltenyi Biotec) - in two technical replicates.

first: Peter

last: Androvic

first: Sarka

last: Benesova

last: Valihrach


title: Gene expression analysis by mRNAseq in Fusarium graminearum WT and a DNMT mutant

status: Public on Mar 03 2021

city: Ottawa

first: Christopher

middle: Thomas

last: Bonner

state: Ontario

address: 960 Carling

country: Canada

institute: Agriculture Canada

type: Expression profiling by high throughput sequencing

summary: Identifying the role of two DNA methyltransferase enzymes in Fusarium graminearum isolate NRRL29169 by high-throughput mRNA sequencing under 2 environmental conditions.

overall_design: Two strains of F. graminearum (WT and a DNMT mutant, ∆FgDim-2/∆FgRid) under 2 environmental conditions (24h Preferred nutrient (PN) and 24h Non-preferred nutrient (NPN)) in triplicate.

middle: T

first: Rajagopal

last: Subramaniam


title: The Nab2 RNA binding protein promotes sex-specific splicing of Sex lethal in Drosophila neuronal tissue

status: Public on Dec 02 2020

city: Atlanta

first: Ken

last: Moberg

state: Georgia

address: 615 Michael Street

department: Cell Biology

country: USA

institute: Emory University School of Medicine

summary: The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls axon projection, locomotion, and memory. Here we define an unexpectedly specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and link the most prominent of these, female retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl), to a role in m6A-dependent mRNA splicing. Genetic evidence indicates that aberrant Sxl splicing underlies multiple phenotypes in Nab2 mutant females. At a molecular level, Nab2 associates with Sxl pre-mRNA and ensures proper female-specific splicing by preventing m6A hypermethylation by Mettl3 methyltransferase. Consistent with these results, reducing Mettl3 expression rescues developmental, behavioral and neuroanatomical phenotypes in Nab2 mutants. Overall these data identify Nab2 as a required regulator of m6A-regulated Sxl splicing and imply a broader link between Nab2 and Mettl3-regulated brain RNAs.

overall_design: Profiling effects of Nab2 loss by RNA sequencing on total, rRNA-depleted RNA isolated from adult Drosophila melanogaster heads. Samples consisted of 3 biological replicates each of 4 sample categories, or 12 samples in total. Sample categories were female wild type (Nab2pex41), female Nab2 null (Nab2ex3), male wild type (Nab2pex41), and male Nab2 null (Nab2ex3).

first: Binta

last: Jalloh

first: John

middle: C

last: Rounds

first: Kenneth

middle: H


title: The effect of CDK6 expression on the murine transcriptome

status: Public on Nov 24 2020

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

summary: We performed RNA-seq analyses in BCR-ABL+ cells either expressing or lacking CDK6. 3 replicates per group were analysed.

overall_design: 3 BCR-ABL+/CDK6wt cell lines, 3 BCR-ABL+/CDK6-/- cell lines.

first: Veronika

last: Sexl


title: scRNAseq of orthotopic mismatch repair deficient (dMMR) or chromosomally instable (CIN) colorectal cancer

status: Public on Jul 19 2021

city: Edmonton

first: Kristi

last: Baker

state: AB

address: 11560 University Ave NW, Room 2308

institute: University of Alberta

summary: Colorectal cancers (CRCs) deficient in DNA mismatch repair (dMMR) contain abundant CD8+ tumor infiltrating lymphocytes (TILs) responding to the abundant neoantigens from their unstable genomes. Priming of such tumor-targeted TILs first requires recruitment of CD8+ T cells into the tumors, implying that this is an essential prerequisite of successful dMMR anti-tumor immunity. We have discovered that selective recruitment and activation of systemic CD8+ T cells into dMMR CRCs strictly depends on overexpression of CCL5 and CXCL10 due to endogenous activation of cGAS/STING and IFN signaling by damaged DNA. TIL infiltration into orthotopic dMMR CRCs is neoantigen-independent and followed by induction of a resident memory-like phenotype key to the anti-tumor response. CCL5 and CXCL10 could be upregulated by common chemotherapies in all CRCs, indicating that facilitating CD8+ T cell recruitment underlies their efficacy. Induction of CCL5 and CXCL10 thus represents a tractable therapeutic strategy to induce TIL recruitment into CRCs where local priming can be maximized even in neoantigen-poor CRCs.

overall_design: Orthotopic CRC experiments were performed by injecting 1.5x105 dMMR or CIN MC38 CRC cells (containing targeted mutations in Mlh1 or Kras, respectively) in 50 µl PBS into the wall of the descending colon using a flexible needle inserted through the working channel of an endoscope and visualized via the ColoView imaging system. Orthotopic tumour growth was monitored by endoscopy and tumours were harvested after 14-21 days and dissociated by digestion in an enzyme cocktail (RPMI containing 0.5 mg/ml collagenase IV (SigmaAldrich), 10 µg/ml DNaseI (SigmanAldrich), 10% FBS, 1% penicillin-streptomycin and 1% HEPES buffer) for 30 minutes at 37˚C in a shaking incubator at 200 rpm. Dead cells were removed using the EasySep Dead Cell Removal Kit (StemCell). CD45+ cells were purified using magnetic beads (StemCell) and then mixed at a 5:1 ratio of CD45+ cells to tumor cells. Samples were submitted to the University of Alberta High Content Analysis Core for processing with a Single Cell Immune Profiling kit (10X Genomics) and sequenced by Novogene. The data were first processed using the Cell Ranger v5.0 pipeline (10X Genomics) and then further analyzed using the Seurat package for R (v3.0) as described previously (Stuart et al., 2019; Wang et al., 2019).

first: Courtney

last: Mowat

first: Shayla

middle: R

last: Mosley

first: Afshin

last: Namdar

first: Daniel

last: Schiller


title: The effect of CDK6 expression on DNA methylation and DNMT3B regulation

type: Methylation profiling by high throughput sequencing

summary: We performed methylation analyses in BCR-ABL+ cells either expressing or lacking CDK6 using the next-generation sequencing approach RRBS and identified DNA methylation changes towards both hyper- and hypomethylation. CDK6 mediated methylation changes are largely reverted by CDK6 re-expression in this experimental system.

overall_design: 3 BCR-ABL+/CDK6wt cell lines, 3 BCR-ABL+/CDK6-/- cell lines, 3 BCR-ABL+/CDK6-/-+Cdk6 cell lines.


title: RNA-Seq experiment on Arabidopsis seedlings regarding SLIM1 and EIL1 function at low S

status: Public on Nov 19 2020

city: Cologne

first: Stanislav

last: Kopriva

address: Zülpicher Str. 47 B

department: Institute for Plant Sciences

country: Germany

institute: University of Cologne

summary: Purpose: To obtain insights into the global transcription networks regulated by SLIM1 and EIL1, as well as their functional overlaps, we utilized RNAseq. For this RNA was isolated from shoots and roots of the four genotypes Col-0, eil1, eil3, and eil3 eil1 grown at normal and low sulfur conditions.

overall_design: Leaf and root mRNA of 18-days old Arabidopsis seedlings (WT (Col-0), eil1, eil3, and eil3 eil1) at either +S or -S conditions

first: Christof

last: Dietzen

first: Anna

last: Koprivova

first: Sarah

middle: J

last: Whitcomb

first: Gregor

last: Langen

first: Timothy

middle: O

last: Jobe

first: Rainer

last: Hoefgen


title: RNA sequencing of human marcrophages treated with lipopolysaccharide (LPS) for 8 hours, with or without BCAT1 inhibitor (ERG240)

status: Public on Nov 23 2020

city: London, United Kingdom

first: Norzawani

middle: Binti

last: Buang

state: London

address: 9N15 Commonwealth Buidling, Ducane Road

country: United Kingdom

institute: Imperial College London

summary: Branched-chain aminotransferases (BCAT) are enzymes that initiate the catabolism of  branched-chain amino acids (BCAA), such as leucine, thereby providing macromolecule  precursors. In order to study the effect of BCAT1 inhibitor (ERG240) on LPS-polarized macrophage transcriptome, we stimulated monocyte derived macrophages (MDMs) with LPS for 8 hours, with or without the presence of  ERG240. We then performed whole-genome transcriptome sequencing by RNA-sequencing  (RNA-seq).

overall_design: Macrophages from 3 healthy donors were either treated LPS (100 ng/ml, 8 hours) with ERG240 (designated as LPS + ERG) or without (LPS).  RNA-seq was performed on Illumina Hiseq 2500

first: Jacques

middle: V

last: Behmoaras


title: Gene expression of optic nerve head astrocytes in aged and glaucomatous mouse

status: Public on Oct 29 2020

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

institute: Massachusetts Eye and Ear Infirmary

summary: Microbeads (experimental glaucoma) or saline solution (controls) were injected into right anterior chamber of young adult mice to induce high intraocular pressure in glaucoma group. In addition, 13 week old and 40 week old naïve C57bl/6 mice were also examined.

overall_design: optic nerve head total RNA profiles of 13 week-young, 40-week old naïve mice, saline injected, and microbeads induced ocular hypertension young adult mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Ying

last: Zhu


title: Time-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19

status: Public on Feb 10 2021

city: New Haven

first: Andrew

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

institute: Yale School of Medicine

summary: COVID-19 exhibits extensive clinical heterogeneity ranging from asymptomatic infection to death. Unraveling the basis of immune response differences across individuals is critical for developing effective therapeutics and prophylactics. We longitudinally assessed 192 surface protein markers, the transcriptome, and T-cell receptor sequence profiles simultaneously in single peripheral immune cells from COVID-19 patients, and compared to age-matched healthy control samples.

overall_design: Peripheral blood mononuclear cells from 33 COVID19 patients and 14 age-matched healthy controls were profiled using multi-modal single cell RNAseq (surface protein staining (Biolegend TotalSeq-C lyophilized panel), mRNA, and T cell recpetor VDJ regions) using the 10x Genomics Chromium system. Individual patients samples, in some cases with multiple samples per donor from different timepoints during disease, were combined and ran together in several lanes of the 10x system, and assignment of the individual cells to a donor and timepoint was done using a combination of SNP and antibody hashtags. SNP calls per donor were determined from bulk level RNAseq data of the individual samples. A single sample, CHI014, was included across the three batches as a technical control, but not used in further analysis. Additionally, a healthy control donor, SHD8, was excluded from further analysis upon finding lymphoma-like B cells in this sample; the HDML_bc and HDVO_bc samples were included to test an alternate cell freezing protocol, and also not used in further analysis.

first: Can

last: Liu

first: William

middle: W

last: Lau

first: Nicholas

last: Rachmaninoff

first: Jinguo

last: Chen

first: Luisa

last: Imberti

first: Darius

last: Mostaghimi

first: Danielle

middle: L

last: Fink

first: Peter

middle: D

last: Burbelo

first: Kerry

last: Dobbs

first: Ottavia

middle: M

last: Delmonte

first: Neha

last: Bansal

first: Laura

last: Failla

first: Alessandra

last: Sottini

first: Eugenia

last: Quiros-Roldan

first: Kyu

last: Han

first: Brian

middle: A

last: Sellers

first: Foo

last: Cheung

first: Rachel

last: Sparks

first: Tae-Wook

last: Chun

first: Susan

last: Moir

last: Lionakis

first: Camillo

last: Rossi

last: NIAID-COVID-Consortium

last: COVID-Clinicians

first: Helen

last: Su

first: Douglas

middle: B

last: Kuhns

first: Luigi

last: Notarangelo

first: John

middle: S

last: Tsang


title: Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

status: Public on Nov 17 2020

city: New York

first: Anoushka

last: Joglekar

state: NY

address: 413 E 69th St

department: Dept. of Neurogenetics

institute: Weill Cornell Medicine

summary: Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown. Here we present the first single-cell investigation of differential isoform expression (DIE) between brain regions, by performing single cell long-read transcriptome sequencing in the mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7. Using isoform tests for brain-region specific DIE, which outperform exon-based tests, we detect hundreds of brain-region specific DIE events traceable to specific cell-types. Many DIE events correspond to functionally distinct protein isoforms, some with just a 6-nucleotide exon variant. In most instances, one cell type is responsible for brain-region specific DIE. Cell types indigenous to only one anatomic structure display distinctive DIE, where for example, the choroid plexus epithelium manifest unique transcription start sites. However, for some genes, multiple cell-types are responsible for DIE in bulk data, indicating that regional identity can, although less frequently, override cell-type specificity. We validated our findings with spatial transcriptomics and long-read sequencing, yielding the first spatially resolved splicing map in the postnatal mouse brain (www.isoformAtlas.com). Our methods are highly generalizable. They provide a robust means of quantifying isoform expression with cell-type and spatial resolution, and reveal how the brain integrates molecular and cellular complexity to serve function.

overall_design: 10X single-cell sequencing done on two replicates of Hippocampus and Prefrontal Cortex (PFC) samples. PacBio sequencing done on the same cDNA to get long read expression data in single cells. Spatial sequencing was conducted using 10X visium sequencing on brain slices, followed by PacBio and Oxford Nanopore sequencing on the same cDNA

first: Paul

last: Collier

first: Hagen

last: Tilgner


title: Evolution of CpH methylation in vertebrate brains

status: Public on Oct 26 2020

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

summary: The brain requires complex mechanisms of genome regulation to encode and store behavioural information. In mammals, DNA methylation deposited at non-CG dinucleotides characterises brain epigenomes. However, it is unclear to what extent this non-canonical form of DNA methylation is evolutionarily conserved. To test this we profile brain cytosine methylation across the major vertebrate lineages, amphioxus, honeybee and octopus, finding that non-CG methylation in adult brain methylomes is restricted to vertebrates. In vertebrates, the genomic patterns of non-CG do not recapitulate those of CG methylation, yet both patterns are deeply conserved. Whereas low levels of gene body CG methylation demarcate a set of developmental transcription factors across tissues and species, a distinct set of neurodevelopmental genes accumulate non-CG methylation in neural tissues. We further show that the establishment of this methylation context coincides with the origin of the “writer” of non-CG methylation, the methyltransferase DNMT3A, and the “reader”, the methyl-CpG binding protein 2 (MeCP2), fuelled by the ancestral whole genome duplication in vertebrates. Surprisingly, MeCP2 evolved in a stepwise process, from an ancestral MBD4 protein with a dual role in transcriptional regulation and DNA repair in chordates. In sum, we show how a novel neural epigenomic layer assembled at the root of vertebrates and gained new regulatory roles partly independent from CG methylation, which could have fostered the sophisticated cognitive repertoires found in the vertebrate lineage.

sample_organism:
Apis mellifera
Branchiostoma lanceolatum
Callorhinchus milii
Danio rerio
Gallus gallus
Ornithorhynchus anatinus
Monodelphis domestica
Octopus bimaculoides
Lethenteron camtschaticum

overall_design: Profiling of cytosine methylation for brain samples from Monodelphis domestica, Ornithorhynchus anatinus, Gallus gallus, Callorhinchus milii, Lethenteron camtschaticum, Apis mellifera, Octopus bimaculoides, and Branchiostoma lanceolatum.

first: Alex

last: de Mendoza

first: Daniel

last: Poppe

first: Sam

last: Buckberry

first: Jahnvi

last: Pflueger

first: Ozren

last: Bogdanovic


title: Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

summary: Different cell isolation techniques exist for transcriptomic and proteotype profiling of brain cells. Here, we provide a systematic investigation of the influence of different cell isolation protocols on transcriptional and proteotype profiles in mouse brain tissue by taking into account single-cell transcriptomics of brain cells, proteotypes of microglia and astrocytes, and flow cytometric analysis of microglia. We show that standard enzymatic digestion of brain tissue at 37°C induces profound and consistent alterations in the transcriptome and proteotype of neuronal and glial cells, as compared to an optimized mechanical dissociation protocol at 4°C. These findings emphasize the risk of introducing technical biases and biological artefacts when implementing enzymatic digestion-based isolation methods for brain cell analyses.

overall_design: Adult male mice hippocampi where dissociated via either enzymatic digestion for 30 min at 37°C or via mechanical dissociation at 4°C. The resulting cell suspensions were analysed via 10X Genomics single cell sequencing.

first: Daniele

last: Mattei

first: Andranik

last: Ivanov

first: Marc

last: van Oostrum

first: Stanislav

last: Pantelyushin

first: Juliet

last: Richetto

first: Flavia

last: Mueller

first: Michal

last: Beffinger

first: Linda

last: Schellhammer

first: Johannes

last: vom Berg

first: Bernd

last: Wollscheid

first: Dieter

last: Beule

first: Rosa

last: Paolicelli

first: Urs

last: Meyer


title: Single-cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue

status: Public on Oct 01 2020

city: Houston

first: Yanming

last: Li

state: TX

address: One Baylor Plaza

department: Michael E. DeBakey Department of Surgery

institute: Baylor College of Medicine

summary:
BACKGROUND: Ascending thoracic aortic aneurysm (ATAA) is caused by the progressive weakening and dilatation of the aortic wall and can lead to aortic dissection, rupture, and other life-threatening complications. To improve our understanding of ATAA pathogenesis, we sought to comprehensively characterize the cellular composition of the ascending aortic wall and to identify molecular alterations in each cell population of human ATAA tissues.
METHODS: We performed single-cell RNA sequencing (sc-RNAseq) analysis of ascending aortic tissues from 11 study participants, including 8 patients with ATAA (4 women and 4 men) and 3 controls (2 women and 1 man). Cells extracted from aortic tissue were analyzed and categorized by using sc-RNAseq data to perform cluster identification. ATAA-related changes were then examined by comparing the proportions of each cell type and the gene expression profiles between ATAA and control tissues. We also examined which genes may be critical for ATAA by performing the integrative analysis of our sc-RNAseq data with publicly available data from genome-wide association studies (GWAS).
RESULTS: We identified 11 major cell types in human ascending aortic tissue; the high-resolution reclustering of these cells further divided them into 40 subtypes. Multiple subtypes were observed for smooth muscle cells, macrophages, and T lymphocytes, suggesting that these cells have multiple functional populations in the aortic wall. Generally, ATAA tissues had fewer nonimmune cells and more immune cells, especially T lymphocytes, than did control tissues. Differential gene expression data suggested the presence of extensive mitochondrial dysfunction in ATAA tissues. In addition, integrative analysis of our sc-RNAseq data with public GWAS data and promoter capture Hi-C data suggested that ERG (ETS [erythroblast transformation-specific] related gene) exerts an important role in maintaining normal aortic wall function.
CONCLUSIONS: Our study provides a comprehensive evaluation of the cellular composition of the ascending aortic wall and reveals how the gene expression landscape is altered in human ATAA tissue. The information from this study makes important contributions to our understanding of ATAA formation and progression.

overall_design: mRNA profiles of 3 control and 8 ATAA human aortic tissue at single cell level

first: Ying

last: Shen

first: Scott

last: LeMaire


title: Time-resolved single-cell RNAseq profiling identifies   a novel Fabp5-expressing subpopulation of   inflammatory myeloid cells in chronic spinal cord injury

status: Public on Oct 23 2020

city: Cambridge

first: Regan

last: Hamel

address: Cambridge Biosciences Campus, Hills Rd

department: Clinical Neurosciences

institute: University of Cambridge

summary:
Traumatic spinal cord injury (SCI) is a debilitating central nervous system (CNS) pathology that lacks effective restorative treatments. The mechanisms of tissue recovery after SCI are dysregulated in comparison to normal wound healing, leading to a chronic wound state, rather than a return to homeostasis. While this state is characterized by persistent inflammation driven by CNS resident microglia (MG) and infiltrating myeloid cells, the precise roles of myeloid cell subsets after SCI remains unclear. In particular, upon crossing the blood-brain barrier, tissue infiltrating monocyte-derived macrophages (MCd) take on the morphology of MG, and upregulate canonical MG markers2, making the two populations practically indistinguishable.
Here, we first employed a Cx3cr1-CreERT2 mouse model to label Cx3cr1+ cells for FACS isolation. Then we utilized fate-mapping approach (see methods) to investigate the ontology and temporal dynamics of Cx3cr1+ spinal cord MG (RFP+/YFP+) and Cx3cr1+ infiltrating myeloid cells (RFP-/YFP+) via FACS isolation and single-cell RNA sequencing (scRNAseq) in a mouse model of thoracic contusion SCI.
Useful Links: Github repository (https://github.com/regan-hamel/SCI_2020)

overall_design: 30,958 cells isolated via FACS from the lesion epicentre. Collected at 1, 3, 10, and 21 days post-SCI and laminectomy-only controls. Each sample comprises tissue from 1-3 mice.


title: Differences in tissue populations following hematopoietic stem cell transplantation in Crohn’s disease patients

status: Public on Oct 22 2020

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

summary: Treatment of severely refractory Crohn’s disease (CD) patients remains a clinical challenge. Recent studies show the efficacy of autologous hematopoietic stem cell transplant (HSCT) in these severely compromised patients. HSCT is thought to eliminate auto-reactive cells; however, no specific studies of immune reconstitution in CD patients are available. We studied a group of CD patients (n=18) receiving autologous HSCT and non-IBD patients (n=19) to elucidate the mechanism of interaction with the microorganisms.

overall_design: Biopsy mRNA profiles of CD patients undergoing HSCT were generated by deep sequencing, using HiSeq4000 platform (Illumina, San Diego, CA)

first: Ana

last: Corraliza

first: Lluís

last: Revilla Sancho


title: Single-cell RNA sequencing on human bone marrow-derived mesenchymal stem cells

status: Public on Sep 28 2020

city: New Orleans

first: Hong-Wen

last: Deng

state: Louisiana

address: 1324 Tulane Ave

institute: Tulane

summary: To investigate the transcriptional diversity of BM-MSCs, we performed single-cell RNA sequencing (scRNA-seq) on freshly isolated CD271+ BM-derived mononuclear cells (BM-MNCs) from two human subjects. We successfully identified LEPRhiCD45low BM-MSCs in the CD271+ BM-MNC population, and further classified the BM-MSCs into distinct subpopulations corresponding to the osteogenic, chondrogenic, and adipogenic differentiation trajectories, as well as terminal-stage quiescent cells. This study provides a systematic dissection of human BM-MSCs at the single-cell resolution, offering novel insights into the extent of their cellular heterogeneity and importance for bone homeostasis.

overall_design: We conducted scRNA-seq on freshly isolated CD271+ BM-MNCs from the femur head of two human subjects (one with osteoporosis and one with osteoarthritis). Cells were isolated by positive selection of CD271 using magnetic microbeads, and mRNA libraries were prepared and sequenced using the 10x Genomics Chromium system. To investigate the cellular heterogeneity within BM-MSCs, we extracted LEPR+CD45- cells (clusters C and D) from the original dataset for further analysis.

first: Zun

last: Wang

first: Yun

last: Gong


title: The effect of CDK6 expression on DNA methylation, DNMT3B regulation, and the transcriptome

first: Gerwin

last: Heller

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

overall_design: Refer to individual Series


title: Skin-resident innate lymphoid cells converge on a pathogenic effector state

status: Public on Dec 14 2020

first: Elena

last: Torlai Triglia

address: 415 Main Street

institute: Broad Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tissue-resident innate lymphoid cells (ILCs) help sustain barrier function and respond to local signals. ILCs are traditionally classified as ILC1, ILC2 or ILC3 on the basis of their expression of specific transcription factors and cytokines1. In the skin, disease-specific production of ILC3-associated cytokines interleukin (IL)-17 and IL-22 in response to IL-23 signalling contributes to dermal inflammation in psoriasis. However, it is not known whether this response is initiated by pre-committed ILCs or by cell-state transitions. Here we show that the induction of psoriasis in mice by IL-23 or imiquimod reconfigures a spectrum of skin ILCs, which converge on a pathogenic ILC3-like state. Tissue-resident ILCs were necessary and sufficient, in the absence of circulatory ILCs, to drive pathology. Single-cell RNA-sequencing (scRNA-seq) profiles of skin ILCs along a time course of psoriatic inflammation formed a dense transcriptional continuum—even at steady state—reflecting fluid ILC states, including a naive or quiescent-like state and an ILC2 effector state. Upon disease induction, the continuum shifted rapidly to span a mixed, ILC3-like subset also expressing cytokines characteristic of ILC2s, which we inferred as arising through multiple trajectories. We confirmed the transition potential of quiescent-like and ILC2 states using in vitro experiments, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and in vivo fate mapping. Our results highlight the range and flexibility of skin ILC responses, suggesting that immune activities primed in healthy tissues dynamically adapt to provocations and, left unchecked, drive pathological remodelling.

overall_design: scRNA-seq profiles of mouse skin ILCs collected every 24h along a time course from healthy (day0) to psoriasis (day4). scATAC-seq profiles of ILC from healthy skin (day0) to psoriasis (day4).

first: Piotr

last: Bielecki

first: Samantha

last: Riesenfeld

first: Jan-Christian

middle: K

last: Hütter

first: Monika

last: Kowalczyk

first: Roberto

last: Ricardo-Gonzalez

first: Maria

last: Amezcua Vesely

first: Lina

last: Kroehling

first: Michal

last: Slyper

first: Christoph

last: Muus

first: Leif

last: Ludwig

last: Christian

first: Liming

last: Tao

first: Amanda

last: Kedaigle

first: Holly

last: Steach

first: Autumn

middle: G

last: York

first: Mathias

last: Skadow

first: Parastou

last: Yaghoubi

first: Danielle

last: Dionne

first: Abigail

last: Jarret

first: Heather

last: McGee

first: Caroline

last: Porter

first: Paula

last: Licona-Limón

first: Will

last: Bailis

first: Ruaidhri

middle: P

last: Jackson

first: Nicola

last: Gagliani

first: Mi

last: Lian

first: Hao

last: Xu

first: Georg

last: Gasteiger

first: Richard

last: Locksley

first: Aviv

last: Regev

last: Flavell


title: Blood RNA-seq of mice after influenza infection

status: Public on Oct 27 2020

first: Andrew

last: Martins

summary: Many previous attempts to derive survival models in whole blood transcriptomics data have failed. Statistical corrections of blood transcriptomics data are needed for multiple comparisons. However, these corrections reduce sensitivity and therefore can constrain discovery. Additionally, signals of inflammation in deep organs may be very weak and hard to detect in the blood, since the blood is not the site of perturbation. On the other hand, although signals in affected tissue are likely much stronger, deep tissues are much less accessible than peripheral blood. To overcome these limitations and allow discovery in peripheral blood, we hypothesized that transcriptional signatures from affected tissues can aid in blood transcriptomics analysis. The aim was to predict death in mice infected with lethal vs. non-lethal doses of influenza virus by examining gene expression in peripheral blood.

overall_design: 3 mice were infected with high dose PR8 and 3 mice were treated with PBS (vehicle/mock) on day 0. Two days later (day 2), blood was taken for RNA-seq analysis.

first: Pedro

last: Milanez-Almeida

first: John

last: Tsang

first: Ronald

middle: N

last: Germain


title: Transcriptome Profiling of Neutrophils from Patients Infected with IAV using RNA-seq

status: Public on Sep 11 2020

city: Beijing

first: Lihui

last: Liu

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

summary:
Purpose: To explore the roles of host lncRNAs during IAV infection
Methods:profiling whole transcriptional alterations using RNA-seq in neutrophil samples from 3 patients infected with IAV in the acute stage and their matched recovery-stage samples
Results:We identified a total of 404 differentially expressed genes (FC>2, p<0.05), including 234 up-regulated and 170 down-regulated genes,in each patient sample
Conclusion:Our study is the first profile of the transcriptome of IAV-infected patients' neutrophils

overall_design: The transcriptome profile of IAV-infected patients' neutrophils in the acute stage and recovery stage were generated by deep sequencing using Illumina Illumina HiSeq 2000

first: Chengcai

last: Lai

first: Keyu

last: Wang

first: Qinghua

first: Lili

last: Zhang


title: Knockouts of both Vitamin D receptor (VDR) and its coactivator Med1 enhance epidermal permeability barrier function

status: Public on Sep 14 2020

city: Hong Kong

first: Jing

address: 11 Yuk Choi Rd, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Vitamin D receptor (VDR) is crucial for formation of epidermal permeability barrier and ceramide production, while mediator complex subunit 1 (Med1), a coactivator of VDR, mediates the action of VDR. VDR deficiency compromises epidermal permeability barrier in mice. Hence, we are investigating the dual role of VDR and Med1 in epidermal permeability barrier. Mice with VDR and Med1 specifically deleted in Keratin 14 expressing keratinocytes (DKO) by Cre-lox strategy are utilized. The mice with both floxed VDR and Med1 but no Cre serve as control. The data showed here that knockouts of both VDR and Med1 enhanced epidermal permeability barrier in mice, accompanied by increased expression levels of mRNA for keratinocyte differentiation marker-related proteins, fatty acid and ceramide productions, which all are required for formation of epidermal permeability barrier. Moreover, expression levels of mRNA for ceramide transporter (ABCA12) were also elevated in DKO mice vs. knockout of either VDR or Med1 alone. Collectively, these results demonstrate that knockouts of both VDR and Med1 enhance epidermal permeability barrier function via upregulating expression levels of mRNA for epidermal differentiation marker-related proteins and lipid synthetic enzymes, suggesting additional signaling pathway(s) involve regulatory role of VDR/Med1 in epidermal function.

overall_design: Epidermal mRNA profiles of P36 and 6-month-old VDR and Med1 double knockout and control mice

first: Lizhi

last: Hu


title: Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer

status: Public on Sep 01 2020

city: Shanghai

first: Jia

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

summary: Neuroendocrine prostate cancer (NEPC) is a subset of castration-resistant prostate cancer (CRPC) and is thought to derive from prostate adenocarcinoma. However, the cellular basis responsible for Neuroendocrine differentiation (NED) is still under debate. Here, we characterized the tumor cell diversity of 6 CRPC patients using single cell RNA sequencing (scRNA-seq) and detected NED in four patients.

overall_design: Single cell mRNA profiles of 6 CRPC patients were generated by 10X Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina)

first: Wei-Qiang

last: Gao


title: scRNASeq data of CD45+CD3-CD19- and keratinocytes in normal and HS skin

status: Public on Aug 27 2020

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

summary: Hidradenitis suppurativa (HS) is a highly prevalent, morbid inflammatory skin disease with limited treatment options. The major cell types and inflammatory pathways in skin of HS patients are poorly understood. We profiled via scRNASeq myeloid cells and keratinocytes sort-purified from two healthy skin samples and two samples with HS pathology to determine major cell types and transcriptional pathways altered in HS.

overall_design: scRNASeq of myeloid immune cells and keratinocytes profiled in healthy appearing skin versus skin with hidradenitis suppurativa pathology

first: Michael

last: Rosenblum


title: RNA-seq of mouse sperm samples from different treatment groups

status: Public on Sep 30 2020

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: The goal of this project was to explore the effect of NH3 and/or H2S effect on the mouse sperm RNA expression and the transgenerational effects. RNA-seq of mouse sperm samples from different groups (NH3 and or H2S treatment) in different generations was done to search for transgenerational effects on RNA expression.

overall_design: RNA-seq of mouse sperm samples from different groups in different generations to search for transgenerational effects of NH3 and/or H2S treatment. First, three weeks of age ICR male mice were treated with NH3 and H2S for 5 weeks (F0 mice). Then the mice (F0) mated with normal ICR female mice. After delivery, F1 male mice were raised normally (without any treatments). At the 8 weeks of age, F1 male mice mated with normal female mice. The F2 male mice were raised normally without any treatment. The semen was collected for F0, F1, F2 mice for the RNA-seq to search for the transgenerational effects of NH3, H2S.

first: Bohui

last: Xiong

first: Cong

first: Hongfu


title: Single cell atlas of the human midbrain reveals cell state specific to Parkinson’s disease

status: Public on Sep 17 2020

city: Berlin

first: Malte

last: Spielmann

address: Ihnestraße 63

institute: Max Planck Institute for Molecular Genetics

summary: Using single-nucleus RNA sequencing, we profiled postmortem midbrain tissue from Idiopathic Parkinson’s Disease patients and matched controls.

overall_design: Single-cell transcriptomics of postmortem midbrain of six control and five idiopathic Parkinson's disease cases

first: Cesar

last: Prada-Medina

first: Semra

last: Smajić

first: Carola

last: Dietrich

first: Christopher

last: Morris

first: Bernd

last: Timmermann

first: Anne

last: Grünewald


title: WGBS analysis of various colon cancer cell lines

status: Public on Jul 21 2020

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

summary: We profiled genome-wide DNA methylation in four cancer cell line, ie SW480-lenti SW480-TET2CD, SW620--lenti and SW620-TET2CD.

overall_design: TET2 encodes a protein that catalyzes the conversion of the modified DNA base methylcytosine to 5-hydroxymethylcytosine. We compare the function of DNA demethylation of different cancer  cell lines.

first: Hui

last: Zheng

first: Changpeng

last: Li


title: Transcriptome-wide gene expression analysis of prostate cancer (PCa) tissue specimen I

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary:
We assessed transcriptome-wide gene expression in tissue specimens of PCa patients who underwent radical prostatectomy by next-generation sequencing (HiSeq 2000). We applied Cox proportional hazard models to the cohorts from different platforms and specimen types and combined the evidence from these by fixed effect meta-analysis to identify genes predictive for time to DoD (death of disease). Genes were combined by a weighted median approach into a prognostic score.
We stratified PCa patients according to seven clinical risk groups based on Gleason Score (GS), the presence of regional lymph node metastases (pN) and the occurrence of death of disease (DoD): (i) very low  risk (group V: GS<7, pN0), (ii) low risk (group L: GS=7, pN0), (iii) medium risk (group M: GS<=7, pN1), (iv) high risk survivors without lymph node infiltration (group H-s: GS>7, pN0), (v) high risk non-survivors without lymph node infiltration (group H-d: GS>7, pN0, DoD), (vi) high risk survivors with lymph node infiltration (group H+s: GS>7, pN1), (vii) high risk non-survivors with lymph node infiltration (group H+d: GS>7, pN1, DoD). For high risk groups adjacent tumor-free prostate tissue samples were obtained (groups H+sf, H-sf, H+df, H+df).
Information on the course of the disease, survival of the patients and the cause of death were obtained from the general practitioners or treating urologists or from records of the regional tumor registry. Clinicopathological parameters were obtained by routine histopathological examination of the surgical specimens. Serum levels of the prostate-specific antigen (PSA) were determined preoperatively (Abbott, Wiesbaden, Germany).
Frozen tissue samples were embedded in Tissue-Tek OCT-compound (Sakura Finetek GmbH, Staufen im Breisgau, Germany) and fixed on metal indenters by freezing. Cryo-sections were prepared using a cryo-microtome (Leica Biosystems, Nußloch, Germany) equipped with a microtome blade C35 cooled to -28 °C. For every tissue three stacks of consecutive cryo-sections (10 µm) were generated, each bordered/flanked by HE-stained cryo-sections (4 µm), which were evaluated by a pathologist with regard to tumor and stroma cell content. PCa tissue stacks had to be flanked on either side by sections containing at least 50 % tumor cells to be used for further analyses. Sections of the tissue stacks were immediately transferred to 1 ml Qiazol (Qiagen, Hilden, Germany) and stored at -80 °C until RNA isolation.

overall_design:
Total RNA of RPE-derived freshly frozen tissue of 40 PCa patients was assessed for gene expression profiling by strand-specific total RNASeq.
------------------------------------------------
Raw data not submitted to GEO due to patient privacy issues

first: Gustavo

last: Baretton

first: Sophie

last: Bartsch

first: Catharina

last: Bertram

first: Conny

last: Blumert

first: Tilo

last: Buschmann

first: Sabina

last: Christ

first: Kati

last: Erdmann

first: Maik

last: Friedrich

last: Froehner

first: Susanne

last: Fuessel

first: Joerg

last: Hackermueller

first: Friedemann

last: Horn

first: Markus

last: Kreuz

first: Dennis

last: Loeffler

last: Muders

first: Dominik

last: Otto

first: Sven-Holger

last: Puppel

last: Rade

first: Stephan

last: Schreiber

last: Specht

first: Marieta

middle: I

last: Toma

first: Karolin

last: Wiedemann

first: Manfred

last: Wirth


title: RNA-seq analysis of various colon cancer cell lines with TET2 overexpression

status: Public on Jul 12 2020

city: guangzhou

first: Li

last: Changpeng

address: kai yuan road

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Three cancer cell line, ie SW480, SW620 and Caco-2, were treated with TET2, TET2CD and control vector lentivirus. The expression of  TET2 was validated using qPCR. Then the total RNA of these samples were extracted and sequenced with Illumina Nextseq 500.

overall_design: TET2 encodes a protein that catalyzes the conversion of the modified DNA base methylcytosine to 5-hydroxymethylcytosine. We overexpressed TET2 in colon cancer cell lines to illustrate the function of DNA demethylation in colon cancer progrossion.

first: Changpeng

last: Li

first: Hui

last: Zheng


title: Identifying blood transcriptome biomarkers of Alzheimer’s disease using transgenic mice

status: Public on Aug 23 2020

city: Toon

first: Junichi

last: Iga

state: Ehime

address: Shitsukawa 454

department: Neuropsychiatry

country: Japan

institute: Ehime University

summary: In the present study, we used 3xTg-AD mice and collected brain and blood at the same time to identify novel blood transcriptome biomarkers of AD and to validate our previous biomarkers.

overall_design: The 3xTg-AD male mice (n=8 at 12 w.o.a; n=8 at 52 w.o.a) and age-matched B6129SF2 WT male mice (n=8 at 12 w.o.a; n=8 at 52 w.o.a) were killed and  gene expression profiles of their hippocampi and bloods were compared.


title: The effect of circadian rhythm on gene expression in human skin II

status: Public on Jul 20 2020

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary:
Skin is the largest organ in the body and serves important barrier, regulatory, and sensory functions. Like other tissues, skin is subject to temporal fluctuations in physiological responses under both homeostatic and stressed states. To gain insight into these fluctuations, we investigated the role of the circadian clock in the transcriptional regulation of skin
The purpose of this study was to gain insight into the evolutionarily-conserved rhythmic patterns of the circadian transcriptome in human skin and how it relates to published transcriptomes from other human tissues.

overall_design: Twenty healthy male subjects aged 21-49 years (median age = 24.5 years) were enrolled in an overnight, time-ordered study. Four 2mm punch biopsies from the forearm were collected from each subject over the course of 24 hours (12pm, 6pm, 12am, and 6am the following day). In a separate unordered study, punch biopsies were taken from the face (cheek), forearm, and buttocks from approximately 150 females between 20-80 years old to 1) determine circadian phase, and 2) compare circadian phase across body sites. All samples were processed for RNA extraction and hybridized on the Affymetrix U219 GeneTitan array. Laser capure microdissection was performed to isolate the dermal compartments for subsequent gene expression profiling.

first: Kevin

last: Mills

first: John

last: Oblong


title: Gene expression profiles in children under treatment for a malignancy presenting with neutropenic fever

status: Public on Aug 26 2020

city: Solna

first: Anna

last: Berggren

address: Avdelning för Infektion, Broliden/Färnert gruppVisionsgatan 4J7:20

department: Medicine

country: Sweden

institute: Karolinska Institutet

summary: By studying differently expressed immune genes with gene expression profiling in immune competent children researchers have been able to distinguish between children with asymptomatic viral infection and those with symptomatic viral infection as well as patients with bacterial infection. In this study we asked if gene expression profiling is feasible as a diagnostic tool in febrile neutropenia.  We included children under treatment for a malignancy presenting with febrile neutropenia. Clinical data regarding the infectious episode was prospectively collected and children grouped based on microbiological agent detected into virus, bacteria, co-infection and unknown aetiology. Fourty three episodes had sufficient RNA for RNA-sequencing, 15 with respiratory tract virus, 22 with unknown etiology, 4 with co-infection and 2 with bacteria. No pathogen specific host-innate immune expression profile was seen in the group with virus, bacteria nor unknown aetiology probably due to the low white blood cell account (WBC). In the co-infection group with higher WBC but lower absolute neutrophil count (ANC)  compared to the other groups, a downregulated innate response were detected. We conclude that gene expression profiling in children presenting with neutropenic fever is not a feasible diagnostic tool for febrile neutropenia in children with cancer due the low WBC.:

overall_design: RNA-sequencing of 43 episodes with febrile neutropenia grouped based on  microbiological agent detected and 12 controls.

first: Martina

last: Wahlund

first: Indranil

last: Sinha

first: Kristina

last: Broliden

first: Shanie

last: S-Hedengren

last: Nilsson


title: The effect of circadian rhythm on gene expression in human skin.


title: RNA-seq analysis of various colon cancer cell lines treated with TGFb1 and repsox

status: Public on Jul 18 2020

first: Hao

last: Sun

summary: Four cancer cell line, ie SW480-Vector, SW480-TET2, SW620-Vector and SW620-TET2 were treated with tgfb1, repsox and control. Then the total RNA of these samples were extracted and sequenced with Illumina Nextseq 500.

overall_design: TET2 encodes a protein that catalyzes the conversion of the modified DNA base methylcytosine to 5-hydroxymethylcytosine. We treated cells with tgfb1 and repsox to illustrate the function of DNA demethylation in the process of EMT.


title: Effect of antiretroviral prophylaxis on gene expression in the ectocervix

status: Public on Jul 07 2020

city: Seattle

first: Sean

last: Hughes

address: 850 Republican St

institute: University of Washington

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used ectocervical biopsies from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).

overall_design: Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation.

first: Florian

last: Hladik

first: Claire

last: Levy


title: Effect of antiretroviral prophylaxis on gene expression in the cervicovaginal tract and the blood

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

overall_design: Refer to individual Series


title: Effect of antiretroviral prophylaxis on gene expression in PBMCs

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used peripheral blood mononuclear cells from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).


title: Effect of antiretroviral prophylaxis on gene expression in the vagina

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used vaginal biopsies from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).


title: Effect of antiretroviral prophylaxis on gene expression in the endocervix

summary:
It is important to understand how, if at all, antiretroviral prophylaxis with tenofovir disoproxil fumarate (TDF) alone or TDF in conjunction with emtricitabine (FTC) affects gene expression.  To ask this question, we used cervicovaginal biopsies from women enrolled in the Genital Mucosal Substudy (GMS) [1] of the Partners PrEP Study (NCT02621242) [2]. Partners PrEP was a randomized Phase III trial of oral TDF or TDF/FTC compared to placebo, which showed that either active drug was effective at protecting against HIV-1 infection. Samples were taken after 24-36 months of oral treatment with placebo, TDF, or TDF/FTC or two months after discontinuation. Treatment adherence was based on plasma TDF concentrations. The samples in this series are thought to be endocervical biopsies on the basis of their gene expression.
Covariates included Nugent scores (for bacterial vaginosis), HSV-2 serology, age, and birth control method. Levels of natural and synthetic hormones (medroxyprogesterone acetate [MPA], estradiol [E2], ethinyl estradiol [EE2], levonorgestrel [LNG], etonogestrel [ENG], progesterone [P4], and norethisterone enanthate [NET-EN]) were measured in the serum.
1. Lund, J. M. et al. HIV-1-Neutralizing IgA Detected in Genital Secretions of Highly HIV-1-Exposed Seronegative Women on Oral Preexposure Prophylaxis. J. Virol. 90, 9855–9861 (2016).
2. Baeten, J. M. et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N. Engl. J. Med. 367, 399–410 (2012).


title: Single-cell RNA-sequencing of vein grafts in mouse models

status: Public on Jul 06 2020

city: London

first: Zhichao

last: Ni

address: 125 Coldharbour Lane, James Black Centre, King's College London

institute: King's College London

summary: We reported the transcriptional profiling of cells in a mouse model of vein grafts by single-cell RNA sequencing.

overall_design: This entry contains 10X Single-cell RNA-seq data of cells of  4-week vein grafts.

first: Ni

last: Zhichao

first: Deng

last: Jiacheng

first: Gu

last: Wenduo

first: Xu

last: Qingbo


title: Transcriptional profiling of ribociclib-treated sensitive and ribociclib resistant CAMA-1 cells

status: Public on Jun 22 2020

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: We report transcriptional response to ribociclib treatment in resistant and sensitive CAMA-1 cells using RNA sequencing. Acquired ribociclib resistant cells were generated by treating CAMA-1 cells over a period of 5 month. Cells were then treated with ribociclib or DMSO control and processed for RNA sequencing.

overall_design: Examination of transcriptional response to ribociclib in sensitive and resistant CAMA-1 cells. In total, 12 samples (2 cell lines with 2 treatments, 3 replicates) were analyzed.

first: Vince

last: Grolmusz

first: Jinfeng

last: Chen

first: Rena

last: Emond

first: Aritro

last: Nath

first: Patrick

last: Cosgrove

first: Lance

last: Pflieger

first: Phillip

last: Moos

first: Andrea

middle: H

last: Bild


title: Expression data from Patient-derived tumor models (PDX) establish from bone metastases and match human breast primary tumor.

status: Public on Jun 29 2020

city: Paris

first: Elisabetta

last: Marangoni

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary:
A significant proportion of patients with oestrogen receptor (ER) positive breast cancers (BC) develop resistance to endocrine treatments (ET) and relapse with metastatic disease. Bone is the most common metastatic site in ER+ patients, however bone metastases are technically challenging to biopsy and analyse. Difficulties concern both tumour tissue acquisition and techniques for analysis and RNA extractions. Patient-derived xenografts (PDX) of BC bone metastases have not been reported yet. For the first time we established PDX models from bone metastatic biopsies of patients progressing on ET and treated by vertebroplasty. PDX models were analysed at transcriptomic level and compared to patient’s early primary tumours to identify new therapeutic targets associated with endocrine resistance in the metastatic setting.
Identification of activated signalling pathways in bone metastasis by comparative transcriptomic analyses of the bone metastasis derived PDX compared to the patients' primary breast tumor.

overall_design: Microarrays of 8 PDX of bone metastasis samples and 4 matched patients’ breast tumor samples. No replicate.

first: E

last: Montaudon

first: Z

last: Tariq


title: RNA-seq testis

status: Public on Jul 05 2020

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

department: Biology

institute: University of North Carolina Greensboro

summary: medaka testies transcriptome were sequenced using RNA-seq

overall_design: Three biological replicates for each treatment and three testis samples for each biological replicate


title: Combined targeting of the BRD4-NUT-p300 axis in NUT midline carcinoma by dual selective bromodomain inhibitor, NEO2734

status: Public on Jun 19 2020

city: BOSTON

first: Chevaun

last: Morrison-Smith

address: 77 AVENUE LOUIS PASTEUR, NRB 652

department: Pathology

institute: Brigham and Women's Hospital

summary: NUT midline carcinoma (NMC) is a rare, aggressive subtype of squamous carcinoma that is driven by the BRD4-NUT fusion oncoprotein. BRD4, a BET protein, binds to chromatin through its two bromodomains, and NUT recruits the p300 histone acetyltransferse (HAT) to activate transcription of oncogenic target genes. BET selective bromodomain inhibitors have demonstrated on-target activity in NMC patients, but with limited efficacy. P300, like BRD4, contains a bromodomain. We show that combining selective p300/CBP and BET bromodomain inhibitors, GNE-781 and OTX015, respectively, induces synergistic inhibition of NMC growth. Treatment of NMC cells with the novel dual p300/CBP and BET bromodomain selective inhibitor, NEO2734, potently inhibits growth and induces differentiation of NMC cells in vitro; findings that correspond with potentiated transcriptional effects from combined BET and p300 bromodomain inhibition. In three disseminated NMC xenograft models, NEO2734 provided greater growth inhibition, with tumor regression and significant survival benefit seen in two of three models, compared with a lead clinical BET inhibitor or 'standard' chemotherapy.

overall_design: High throughput analysis of ribosomal RNA depleted total RNA

first: Christopher

last: French


title: Aberrant Clonal Hematopoiesis following Lentiviral Vector Transduction of HSPCs in a Rhesus Macaque

status: Public on Jun 25 2020

city: Bethesda

first: Cynthia

middle: E

last: Dunbar

state: Maryland

address: 10 Center Drive

department: Translational Stem Cell Biology Branch

institute: National Heart Lung Blood Institute

summary: Lentiviral vectors (LVs) are used for delivery of genes into hematopoietic stem and progenitor cells (HSPCs) in clinical trials worldwide. LVs, in contrast to retroviral vectors, are not associated with insertion site-associated malignant clonal expansions and, thus, are considered safer. Here, however, we present a case of markedly abnormal dysplastic clonal hematopoiesis affecting the erythroid, myeloid, and megakaryocytic lineages in a rhesus macaque transplanted with HSPCs that were transduced with a LV containing a strong retroviral murine stem cell virus (MSCV) constitutive promoter-enhancer in the LTR. Nine insertions were mapped in the abnormal clone, resulting in overexpression and aberrant splicing of several genes of interest, including the cytokine stem cell factor and the transcription factor PLAG1. This case represents the first clear link between lentiviral insertion-induced clonal expansion and a clinically abnormal transformed phenotype following transduction of normal primate or human HSPCs, which is concerning, and suggests that strong constitutive promoters should not be included in LVs.

overall_design: Hi-throughput sequencing to detect genetic barcodes from cells of the hematopoietic lineage. 38 samples from the rhesus macaque ZL34.

first: Diego

last: Espinoza

first: Xing

last: Fan

first: Di

last: Yang

first: Stefan

middle: F

last: Cordes

first: Lauren

last: Truitt

first: Katherine

middle: R

last: Calvo

first: Idalia

last: Yabe

first: Selami

last: Demirci

first: Kristin

middle: J

last: Hope

first: So

last: Hong

first: Allen

last: Krouse

first: Mark

last: Metzger

first: Aylin

last: Bonifacino

first: Rong

last: Lu

first: Naoya

last: Uchida

first: John

last: Tisdale

first: Xiaolin

last: Wu

first: Suk

last: Deravin

first: Harry

last: Malech

first: Robert

last: Donahue

first: Chuanfeng


title: Immunohistochemical Investigation for Renal Tubules in Adaptive and Maladaptive Repair Process after Renal Tubular Injury in the Kidney of Rats

status: Public on Jun 01 2020

city: Kawasaki City

first: Kohei

last: Matsushita

state: Kanagawa

address: 3-25-26 Tonomachi, Kawasaki-ku

institute: National Institute of Health Sciences

summary: Acute kidney injury (AKI) have been thought to be reversible condition, however, emerging evidence demonstrated association between AKI and subsequent development of irreversible fibrosis and chronic kidney disease. In the present study, since recovery of AKI depends on renal tubular regeneration, factors expressing in renal tubules in adaptive or maladaptive repair process were investigated to predict reversibility of kidney injury. In the kidney of female F344 rats subjected to ischemia/reperfusion (I/R), regenerative tubules and dilated tubules were observed at 3 and 7 days after I/R. In fibrotic areas of the kidney of male SD rats subjected to I/R, renal tubules were dilated or atrophied. From microarray data of regenerative tubules, survivin, sex-determining region Y (SRY)-box 9 (SOX9), and CD44 were extracted as factors possibly relating to tubular regeneration or fibrosis. Immunohistochmical analysis demonstrated that survivin and SOX9 expressed in regenerative tubules, while SOX9 also expressed in renal tubules in fibrotic area, indicating that survivin and SOX9 contribute renal tubular regeneration, but sustained SOX9 expression may lead fibrosis. CD44 expressed in dilated tubules at day 3 and 7, and tubules in fibrotic area, suggesting that CD44 expressed in maladaptive tubules. These information will be helpful to consider reversibility of kidney injury.

overall_design: Ten-weeks-old female F344 rats were performed to unilateral ischemia reperfusion injury in left kidney and sacrificed at 3 and 7 days after operation (n=4, respectively). Control Sham group were performed to sham operation and sacrificed at 7 days after operation (n=4).　Left kidneys of all rats were supplied for mRNA microarray analysis.


title: Differential gene expression analysis by assessing transcriptome-wide expression variation between tissue specimen of prostate cancer (PCa) and benign prostate hyperplasia (BPH)

status: Public on Jun 17 2020

last: Reiche

summary:
We assessed differential gene expression in tissue specimens of PCa and BPH patients who underwent radical prostatectomy by next-generation sequencing (HiSeq 2000).
We stratified PCa patients according to seven clinical risk groups based on Gleason Score (GS), the presence of regional lymph node metastases (pN) and the occurrence of death of disease (DoD): (i) very low  risk (group V: GS<7, pN0), (ii) low risk (group L: GS=7, pN0), (iii) medium risk (group M: GS<=7, pN1), (iv) high risk survivors without lymph node infiltration (group H-s: GS>7, pN0), (v) high risk non-survivors without lymph node infiltration (group H-d: GS>7, pN0, DoD), (vi) high risk survivors with lymph node infiltration (group H+s: GS>7, pN1), (vii) high risk non-survivors with lymph node infiltration (group H+d: GS>7, pN1, DoD). For high risk groups adjacent tumor-free prostate tissue samples were obtained (groups H+sf, H-sf, H+df, H+df). The control group contained patients with benign prostate hyperplasia (group C).
Information on the course of the disease, survival of the patients and the cause of death were obtained from the general practitioners or treating urologists or from records of the regional tumor registry. Clinicopathological parameters were obtained by routine histopathological examination of the surgical specimens. Serum levels of the prostate-specific antigen (PSA) were determined preoperatively (Abbott, Wiesbaden, Germany).
Frozen tissue samples were embedded in Tissue-Tek OCT-compound (Sakura Finetek GmbH, Staufen im Breisgau, Germany) and fixed on metal indenters by freezing. Cryo-sections were prepared using a cryo-microtome (Leica Biosystems, Nußloch, Germany) equipped with a microtome blade C35 cooled to   -28 °C. For every tissue three stacks of consecutive cryo-sections (10 µm) were generated, each bordered/flanked by HE-stained cryo-sections (4 µm), which were evaluated by a pathologist with regard to tumor and stroma cell content. PCa tissue stacks had to be flanked on either side by sections containing at least 50 % tumor cells to be used for further analyses. Sections of the tissue stacks were immediately transferred to 1 ml Qiazol (Qiagen, Hilden, Germany) and stored at -80 °C until RNA isolation.

overall_design:
Total RNA of RPE-derived freshly frozen tissue of 40 PCa and 8 BPH patients was assessed for gene expression profiling by strand-specific total RNASeq. For 16 of the high risk PCa patients adjacent tumor-free prostate tissue samples were additionally analysed.

Raw data not submitted to GEO due to patient privacy issues

first: Gustavo

last: Baretton

first: Sophie

last: Bartsch

first: Catharina

last: Bertram

first: Conny

last: Blumert

first: Tilo

last: Buschmann

first: Sabina

last: Christ

first: Kati

last: Erdmann

first: Maik

last: Friedrich

first: Michael

last: Froehner

first: Susanne

last: Fuessel

first: Joerg

last: Hackermueller

first: Friedemann

last: Horn

first: Markus

last: Kreuz

first: Dennis

last: Loeffler

last: Muders

first: Dominik

last: Otto

first: Sven-Holger

last: Puppel

last: Rade

first: Stephan

last: Schreiber

last: Specht

first: Marieta

last: Toma

first: Karolin

last: Wiedemann

first: Manfred

last: Wirth


title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [Human SCLC biopsy]

status: Public on May 28 2020

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

summary: Small cell lung cancer (SCLC) is a neuroendocrine tumor treated clinically as a single disease with poor outcomes. Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. We developed an in vitro model of MYC-driven SCLC tumor cell progression, and performed a time-series analysis of single-cell transcriptome profiling to reveal that MYC drives the dynamic evolution of SCLC subtypes. Analyses of these single-cell RNA seq data reveal that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Additional single-cell RNA sequencing of 4RPM tumors reveal individual tumors to consist of cells at nearly every stage of RPM tumor evolution modeled in vitro. With the single-cell RNA sequencing of this human SCLC liver biopsy, along with IHC on a panel of 21 human biopsies, we show that human SCLC exhibits intratumoral SCLC subtype heterogeneity, suggesting this dynamic evolution occurs in patient tumors. Together, these single-cell RNA sequencing data support our conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

overall_design: Single-cell RNA sequencing from a single human SCLC  biopsy from the liver.

first: Siddhartha

last: Devarakonda

first: Abbie

last: Ireland


title: FXR isoform selective DNA binding in mouse liver organoids

status: Public on Jul 27 2020

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

institute: University of Innsbruck

summary: The farnesoid X receptor (FXR) is a nuclear receptor activated by bile acids that regulates metabolic processes. FXR is expressed as four isoforms (α1-4), and their relative abundance is specific to tissue and bio-energetic conditions (Correia JC et al. 2015). Depending on the FXR isoform expressed, there is a degree of selectivity in target-genes activation. However, there is currently no data on how isoform-linked target selectivity is achieved. In this study we investigate the DNA binding profile of FXR isoforms on mouse liver organoids treated briefly with the FXR agonist obeticholic acid (OCA). From this analysis we concluded that FXR isoforms α2 and α4 binds to additional DNA regions, enriched for a specific discriminating binding motif. This binding led to isoform-selective gene regulation. Therefore, DNA binding selectivity therefore plays a defining role in FXR isoform-specific effects.

overall_design: FXR -/- mouse liver organoids were transduced with mouse FXR isoforms α1, α2, α3, α4 or H2b-NeonGreen(ko) using lentiviral vectors (pLV IRES PuroR). After selection, the organoids were differentiated into the hepatocyte lineage before fixation and  processing

first: Jose

first: Saskia

middle: W

last: van Mil


title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [WGS data]

summary: Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. To study transcriptional dynamics of MYC-driven tumor evolution and compare transcriptional states to human SCLC tumors, we performed bulk and single-cell RNA-sequencing on various timepoints of Rb1/Trp53/MycT58A (RPM) tumor cells (from Ad-Cgrp-Cre infected mice) as they progress in culture, and on RPM bulk tumors. Here, to complement these analyses we performed ~30X whole-genome sequencing (WGS) of early (day 4) and late (day 23) time-point RPM tumor cells from culture, along with a matching normal blood control to confirm complete loss of expected regions of Rb1 and Trp53. WGS analyses revealed no detectable copy number variations (CNVs), and SNV analysis suggests that minimal clonal and subclonal evolution occurs in vitro. Together, these data ultimately reveal that MYC drives the dynamic evolution of SCLC subtypes. We find that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. These findings support our overall conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

overall_design: ~30X WGS data was collected from Day 4 and Day 23 tumor samples, as well as from a blood sample from RPM mice as the normal control.

first: Yi

last: Qiao

first: Xiaomeng

last: Huang

first: Szabolcs

last: Tarapcsak

first: Gabor

last: Marth


title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [Bulk RNA-seq of RPM time-series cells]

summary: Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. To study transcriptional dynamics of MYC-driven tumor evolution and compare transcriptional states to human SCLC tumors, we performed bulk RNA-sequencing on various timepoints of Rb1/Trp53/MycT58A (RPM) tumor cells (from Ad-Cgrp-Cre infected mice) as they progress in culture. These bulk RNA-seq data of the RPM time-series cells complement time-series analysis of single-cell transcriptome profiling of similar timepoints and ultimately reveal that MYC drives the dynamic evolution of SCLC subtypes. We find that MYC promotes a temporal shift from an ASCL1-to-NEUROD1-to-YAP1+ state from a neuroendocrine cell of origin. MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. These findings support our overall conclusions that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

overall_design: We performed bulk RNA-sequencing of eight time points, days 3, 5, 7, 10, 12, 14, 19, and 21 during the RPM transition spanning 21 days in tissue culture. Day 0 is the first day mouse lung is digested and cells are placed in tissue culture.


title: Methylation data from healthy, adjacent normal and tumor colon cells

status: Public on May 10 2020

city: L'Hospitalet de Llobregat

first: Victor

last: Moreno

state: Barcelona

address: Granvia 199

department: Oncology Data Analytics Program

institute: Catalan Institute of Oncology

type: Methylation profiling by genome tiling array

summary: Methylation profiles of paired normal adjacent mucosa and tumor samples from 96 individuals and 48 healthy colon mucosae, were obtained through Illumina Infinium Human Methylation 450K BeadChip. This dataset is in the context of the COLONOMICS project and to query additional information you can visit the project website www.colonomics.org.

overall_design: Colon tumor and adjacent paired normal mucosa tissues samples used in this study were selected from a series of cases with a new diagnosis of colorectal adenocarcinoma histologically confirmed. Included cases were from a homogenous series of patients with more than three years of follow up, early stage (II), without neoadjuvant chemotherapy and microsatellite stable colon cancer. Additionally, samples of colon mucosa from 48 healthy donors without colonic lesions were obtained during colonoscopy.

first: Anna

last: Díez-Villanueva

first: Rebeca

last: Sanz-Pamplona

first: Robert

last: Carreras-Torres

first: Ferran

last: Moratalla

first: Henar

last: Alonso

first: Susanna

last: Aussó

first: Laia

last: Paré-Brunet

first: Toni

last: Berenguer

first: Miquel

last: Peinado

first: Maria

last: Berdasco


title: Potential Therapeutic Targets for Donor Lung Repair During Human Ex Vivo Lung Perfusion Prior to Transplantation

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

institute: University Health Network

type:
Expression profiling by array
Third-party reanalysis

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


title: Expression data of the Cerebral cortex in Tyr-Trp treated AD model mouse

status: Public on Apr 30 2020

city: Fukuoka

first: Takashi

last: Ichinose

address: 744 Motooka,Nishi-ku

institute: Kyushu University

summary:
Scope: As a result of population ageing, the number of Alzheimer’s disease (AD) patients has rapidly increased. There are many hypothesises on the pathogenesis of AD, but its detailed molecular mechanism is still unknown, and so no effective preventive or therapeutic measures have been established. Some reports showed a decrease in levels of norepinephrine (NE) has been suspected to be involved in the decline of cognitive function in AD patients and NE concentrations were decreased in postmortem AD patient brains. Tyr-Trp was identified as being the most effective dipeptide in enhancing norepinephrine (NE) synthesis and metabolism. And Tyr-Trp treatment ameliorated the short-term memory dysfunction in AD model mice caused by amyloid beta (Aβ) 25-35. So, the purpose of this study was to investigate the preventive or/and protective effects of Tyr-Trp administration in AD model mice.
Methods and results: ddY mice were fed normal diet. After 7 days of feeding, mice were divided into 3 groups (n=10 per group) as follows: the sham group, which received saline administration and distilled water injection; the Aβ group, which received saline administration and Aβ peptides 25–35 injection; and the Aβ+YW group, which received Tyr-Trp administration and Aβ peptides 25–35 injection. Tyr-Trp was orally administered Tyr-Trp (100 mg kg-1 day-1, twice a day), starting 7 days before Aβ peptides injection. The other groups received oral administration of saline (5 mL kg-1). After Aβ peptides injection or sham operation, each groups received every oral administration. DAN microarray showed that Tyrosine hydroxylase, dopa decarboxylase and dopamine receptor D2 mRNA expressions which were downregulated in Aβ group comparing with sham group were upregulated in Aβ+YW group comparing with Aβ group. In addition, quinoid dihydropteridine reductase mRNA expression which wasn’t changed in Aβ group comparing with sham group was upregulated in Aβ+YW group comparing with Aβ group. Conclusions: These results suggest that Tyr-Trp administration might ameliorate the short-term memory dysfunction in AD model mice because of enhancing norepinephrine (NE) synthesis and metabolism through metabolism of both Tyr and Trp.

overall_design: Male ddY mice at 10 weeks of age (SLC, Inc., Shizuoka, Japan) were housed in a room with controlled lighting (12 h light/12 h dark), and constant temperature (25°C), and provided with moderate fat diet (Oriental Yeast Co., Ltd., Tokyo, Japan) and water ad libitum. Mice were divided into 3 groups (n=10 per group) as follows: the sham group, which received saline administration and distilled water injection; the amyloid beta (Aβ) group, which received saline administration and Aβ peptides 25–35 injection; and the Aβ+YW group, which received Tyr-Trp administration and Aβ peptides 25–35 injection. Tyr-Trp was orally administered Tyr-Trp (100 mg kg-1 day-1, twice a day), starting 7 days before Aβ peptides injection. The other groups received oral administration of saline (5 mL kg-1). After 7 days of Aβ peptides injection or sham operation, behavioral test was conducted and Cx samples were collected. DNA microarray analysis was performed on Cx samples from a total of fourteen mice (sham group: n=4, Aβgroup; n=5, Aβ+YW group; n=5) by choosing average individuals from each group on the basis of their behavioral test score.

first: Hiroyasu

last: Murasawa

first: Tomoko

last: Ishijima

first: Shinji

last: Okada

first: Keiko

last: Abe

first: Saki

last: Matsumoto

first: Toshiro

last: Matsui

first: Shigeki

last: Furuya


title: Inhibition of Grb14, a negative modulator of insulin signaling,  improves glucose homeostasis without causing cardiac dysfunction

status: Public on Apr 14 2020

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary: Insulin resistance increases patient’s risk of developing type 2 diabetes (T2D), nonalcoholic  steatohepatitis (NASH) and a host of other comorbidities including  cardiovascular disease and cancer. At the molecular level, insulin exerts its function  through the insulin receptor (IR), a transmembrane receptor tyrosine kinase. Data from  human genetic studies have shown that Grb14 functions as a negative modulator of IR  activity, and germline Grb14-knockout (KO) mice have improved insulin signaling in liver  and muscle tissues. Here, we show that Grb14 knockdown in the liver and the heart with  an AAV-shRNA (Grb14-shRNA) improves glucose homeostasis in diet-induced obese (DIO)  mice. A previous report has shown that germline deletion of Grb14 in mice results in  cardiac hypertrophy and decreased systolic function, effects that could severely limit the  therapeutic potential of targeting Grb14. In this report, we demonstrate that there are  no significant changes in hemodynamic function as measured by echocardiography in DIO  Grb14 and DIO sham mice for a period of four months. While additional studies are  needed to further establish efficacy and to de-risk potential negative cardiac effects in  pre-clinical heart failure models, our data support inhibiting Grb14 to treat diabetes and  related conditions.

overall_design: We compared 1) Metabolically healthy obese (MHO, n=15) vs metabolically unhealthy obese (MUO, n=15) people, and 2) before vs. after weight loss (n=10).

first: Xunshan

last: Ding

first: Rugmani

last: Iyer

first: Christopher

last: Novotny

first: Daniel

last: Metzger

first: Heather

last: Zhou

first: Gordon

last: Smith

first: Mihoko

first: Samuel

last: Klein

first: Gayathri

last: Swaminath

first: Saswata

last: Talukdar

first: Yingjiang


title: Combination of host immune metabolic biomarkers for the PD-1 blockade cancer immunotherapy

status: Public on Apr 07 2020

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

summary:
Background. Current clinical biomarkers for the PD-1 blockade therapy are insufficient because they rely only on the tumor properties such as PD-L1 expression frequency and the amount of tumor mutation burden. Identifying reliable responsive biomarkers based on the host immunity is necessary to improve the predictive values.
Methods. We investigated the levels of plasma metabolites and T cell properties including energy metabolism markers in the blood of patients with non-small cell lung cancer before and after treatment with nivolumab (N=53). Predictive value of combination markers statistically selected were evaluated by cross validation and linear discriminant analysis on discovery and validation cohorts, respectively. Correlation between plasma metabolites and T cell markers were investigated.
Results. The four metabolites derived from microbiome (hippuric acid), fatty acid oxidation (butyrylcarnitine) and redox (cystine and glutathione disulfide) provided high response probability (AUC=0.91). Similarly, a combination of four T cell markers, those related to mitochondrial activation (PGC-1 expression and reactive oxygen species), and the frequencies of CD8+ PD-1high and CD4+ T cells demonstrated even higher prediction value (AUC=0.96). Among the pool of all selected markers, the four T cell markers were exclusively selected as the highest predictive combination probably due to their linkage to the above mentioned metabolite markers. In a prospective validation set (N=24) these four cellular markers showed a high accuracy rate for the clinical responses of the patients (AUC= 0.92).
Conclusion. Combination of biomarkers reflecting host immune activity is quite valuable for the responder prediction.

overall_design: 74 samples, compared with cellular markers measured by FACS.

first: Ryusuke

last: Hatae

first: Young

last: Hak Kim

first: Kazuhiro

last: Sonomura

first: Kei

last: Taneishi

first: Shuji

last: Kawaguchi

first: Hironori

last: Yoshida

first: Hiroaki

last: Ozasa

first: Yuichi

last: Sakamori

first: Maryam

last: Akrami

first: Sidonia

last: Fagarasan

first: Izuru

last: Masuda

first: Yasushi

last: Okuno

first: Fumihiko

last: Matsuda

first: Toyohiro

last: Hirai

first: Tasuku

last: Honjo


title: Epigenetic regulator genes direct the fate of multipotent precursor cell of origin in lineage switched MLL-AF4 leukaemia [DNase-Seq]

status: Public on Apr 21 2020

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: Malignant transformation in a multipotential precursor has recently been shown to underlie mixed phenotype acute leukaemias. In contrast, and despite the conclusive demonstration that MLL-AF4 infant ALL arises in utero.  In order to address this we purified haematopoietic stem/progenitor cell (HSPC) populations from four non-lineage switching presentation infant ALL cases and one ALL presentation which went on to lineage switch at relapse.  The specific MLL-AF4 fusion event was determined in unsorted samples by LDI-PCR and identified in purified populations by nested PCR.  In three cases where non-lineage restricted populations were able to be purified, MLL-AF4 was identified in the CD34+CD38-CD45RA+ population (LK228, LK230, LS01), the CD34+CD38-CD45RA-CD90- multipotential progenitor population (MPP, LS01) and even a candidate CD34+CD38-CD45RA-CD90+ haematopoietic stem cell (HSC) population (LK228) Interestingly, in a single non-switched MLL-AF9 case analysed for external comparison, the fusion was only identified in CD19+ blast/B cell populations, not in any HSPC population. Unexpectedly, we were also able to identify the presence of the MLL-AF4 fusion in apparently normally differentiated CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells from the peripheral blood/bone marrow of 4/5 cases examined. This finding was further supported by single cell analysis of LS01PALL which identified the fusion in 2/22 CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells analysed. Furthermore, the matched AML sample (LS01RAML) also contained MLL-AF4 positive mature T lymphoid cells.  These data imply that MLL-AF4 does not impose a complete block on normal haematopoietic differentiation, and raise the question of what additional factors contribute to leukaemic lineage determination in the setting of the MLL-AF4 translocation. To examine the functional capacity of MLL-AF4 transformed precursor cells we generated a patient-derived xenograft model using NOD-scid/IL2Rγ-/- (NSG) mice.  Serial xenotransplantation identified an MLL-AF4 positive clone persisting within the human CD34+CD38-CD45RA-CD90+ compartment across four generations of mice, confirming self-renewal of this population. Together these data identify an early multipotent progenitor or HSC as the putative cell of origin for MLL-AF4 ALL. Furthermore, they demonstrate that MLL-AF4, uniquely amongst MLL fusion genes, imposes a profound lymphoid bias on the developing leukemia but without completely abolishing broader, non-malignant, haematopoietic differentiation.

overall_design: High depth DNase-Seq analysis of an peripheral mononuclear cells from a pediatric ALL patient relapsing as AML

first: Ricky

last: Tirtakusuma

first: Paul

last: Milne

first: Anetta

last: Ptasinska

first: Claus

last: Meyer

first: Sirintra

last: Nakjang

first: Alexander

last: Komkov

first: Dan

last: Williamson

first: Salam

last: Assi

first: Helen

last: Blair

first: Maria

last: Imperato

first: Fotini

last: Vogiatzi

first: Shan

last: Lin

last: Evans

first: Hesta

last: McNeill

first: Alex

last: Elder

first: Natalia

last: Martinez-Soria

first: Sarah

last: Fordham

first: Yuzhe

last: Shi

first: Lisa

last: Russell

first: Deepali

last: Pal

last: Smith

first: Jean-Baptiste

last: Cazier

first: Zoya

last: Kingsbury

first: Jennifer

last: Becq

first: Cornelia

last: Eckert

first: Oskar

last: Haas

first: Peter

last: Carey

first: Simon

last: Bailey

first: Roderick

last: Skinner

last: Miakova

first: Matthew

last: Collin

first: Venetia

last: Bigley

first: Muzlifa

last: Haniffa

first: Rolf

last: Marschalek

first: Christine

last: Harrison

first: Catherine

last: Cargo

first: Denis

last: Schewe

first: Elena

last: Zerkalenkova

first: Yulia

last: Olshanskaya

first: Michael

last: Thirman

first: James

middle: C

last: Mulloy

first: Josef


title: Epigenetic regulator genes direct the fate of multipotent precursor cell of origin in lineage switched MLL-AF4 leukaemia [RNA-Seq]

first: Pierre

last: Cauchy

summary: Malignant transformation in a multipotential precursor has recently been shown to underlie mixed phenotype acute leukaemias. In contrast, and despite the conclusive demonstration that MLL-AF4 infant ALL arises in utero. In order to address this we purified haematopoietic stem/progenitor cell (HSPC) populations from four non-lineage switching presentation infant ALL cases and one ALL presentation which went on to lineage switch at relapse. The specific MLL-AF4 fusion event was determined in unsorted samples by LDI-PCR and identified in purified populations by nested PCR. In three cases where non-lineage restricted populations were able to be purified, MLL-AF4 was identified in the CD34+CD38-CD45RA+ population (LK228, LK230, LS01), the CD34+CD38-CD45RA-CD90- multipotential progenitor population (MPP, LS01) and even a candidate CD34+CD38-CD45RA-CD90+ haematopoietic stem cell (HSC) population (LK228) Interestingly, in a single non-switched MLL-AF9 case analysed for external comparison, the fusion was only identified in CD19+ blast/B cell populations, not in any HSPC population. Unexpectedly, we were also able to identify the presence of the MLL-AF4 fusion in apparently normally differentiated CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells from the peripheral blood/bone marrow of 4/5 cases examined. This finding was further supported by single cell analysis of LS01PALL which identified the fusion in 2/22 CD34-CD19/3-HLA-DR+CD14/11c+ monocytes/dendritic cells analysed. Furthermore, the matched AML sample (LS01RAML) also contained MLL-AF4 positive mature T lymphoid cells. These data imply that MLL-AF4 does not impose a complete block on normal haematopoietic differentiation, and raise the question of what additional factors contribute to leukaemic lineage determination in the setting of the MLL-AF4 translocation. To examine the functional capacity of MLL-AF4 transformed precursor cells we generated a patient-derived xenograft model using NOD-scid/IL2Rγ-/- (NSG) mice. Serial xenotransplantation identified an MLL-AF4 positive clone persisting within the human CD34+CD38-CD45RA-CD90+ compartment across four generations of mice, confirming self-renewal of this population. Together these data identify an early multipotent progenitor or HSC as the putative cell of origin for MLL-AF4 ALL. Furthermore, they demonstrate that MLL-AF4, uniquely amongst MLL fusion genes, imposes a profound lymphoid bias on the developing leukemia but without completely abolishing broader, non-malignant, haematopoietic differentiation.

overall_design: RNA-Seq analysis of an peripheral mononuclear cells from pediatric ALL patient relapsing as AML

first: Ricky

last: Tirtakusuma

first: Paul

last: Milne

first: Anetta

last: Ptasinska

first: Claus

last: Meyer

first: Sirintra

last: Nakjang

first: Alexander

last: Komkov

first: Dan

last: Williamson

first: Salam

last: Assi

first: Helen

last: Blair

first: Maria

last: Imperato

first: Fotini

last: Vogiatzi

first: Shan

last: Lin

last: Evans

first: Hesta

last: McNeill

first: Alex

last: Elder

first: Natalia

last: Martinez-Soria

first: Sarah

last: Fordham

first: Yuzhe

last: Shi

first: Lisa

last: Russell

first: Deepali

last: Pal

last: Smith

first: Jean-Baptiste

last: Cazier

first: Zoya

last: Kingsbury

first: Jennifer

last: Becq

first: Cornelia

last: Eckert

middle: A


title: Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation

status: Public on Mar 13 2020

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Cells rely on a diverse repertoire of genes for maintaining homeostasis, but the transcriptional networks underlying their expression remain poorly understood. The MOF acetyltransferase-containing Non-Specific Lethal (NSL) complex is a broad transcription regulator. It is essential in Drosophila and haploinsufficiency of the human KANSL1 subunit results in the Koolen-de Vries syndrome. Here, we perform a genome-wide RNAi screen and identify the BET protein BRD4 as evolutionary conserved co-factor of the NSL complex. Using Drosophila and mouse embryonic stem cells, we characterise a recruitment hierarchy, where NSL-deposited histone acetylation induces BRD4 recruitment for transcription of constitutively active genes. Transcriptome analyses in Koolen-de Vries patient-derived fibroblasts reveals perturbations with a cellular homeostasis signature that are evoked by the NSL complex/BRD4-axis. We propose that BRD4 represents a conserved bridge between the NSL complex and transcription activation and provide a new perspective in the understanding of their functions in healthy and diseased states.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

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


overall_design: Expression analysis following depletion of NSL complex members and dBRD4 by RNAi, or BET inhibitor treatments in Drosophila melanogaster cells (S2 cells)

first: Aline

last: Gaub


overall_design:
ChIP-seq profiles of Biotin-tagged dBRD4,endogenous dBRD4, H4K16ac, H3 and Rpb3 from Drosophila melanogaster cells (S2 cells)

Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.


title: Transcriptome changes in patients with severely impaired spermatogenesis

status: Public on Feb 19 2020

city: Ljubljana

first: Alenka

last: Hodžić

address: Šlajmerjeva 3

department: Centre for Mendelian Genomics

country: Slovenia

institute: Clinical Institute of Medical Genetics University Medical Centre Ljubljana

summary: Aiming to identify gene expression signatures underlying the pathogenesis of infertility, we performed global gene expression profiling on testis samples in patients with severely impaired and normal spermatogenesis.

overall_design: The study included 20 samples (10 showing obstructive azoospermia and 10 samples  showing non obstructive azoospermia). Differential gene expression was measured in  relation to the Agilent’s Universal Human Reference RNA and each experimental sample  was hybridized against this common reference sample.

first: Aleš

last: Maver

first: Borut

last: Peterlin


overall_design: Compartive expression analysis of Koolen-de-Vries patient and healthy control fibroblast cell lines


title: LncRNA/mRNA expression  in  Triple negative breast cancer(TNBC) and matched non-tumor tissues

status: Public on Feb 04 2020

city: nanjing

first: tang

last: li

address: No. 42 Baiziting Road,

department: Laboratory department

institute: Jiangsu Cancer Hospital

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

summary: To determine the lncRNA and mRNA expression profile in TNBC and matched non-tumor tissues, we uesed lncRNA microArray analysis form Arraystar to examine the expression of lncRNAs and mRNAs in TNBC and matched non-tumor tissues.

overall_design: human tissues from TNBC surgery were distributed into two experimental groups: tumor tissue group and matched non-tumor tissues group, then perform lncRNAs chips by Arraystar Human lncRNAs chip (Arraystar)

first: Li

last: TANG


title: MYC drives temporal evolution of small cell lung cancer subtypes by reprogramming neuroendocrine fate [Single Cell RNA seq on RPM time-series cells and 4 RPM bulk tumors]

first: Trudy

last: Oliver

summary: Small cell lung cancer (SCLC) is a neuroendocrine tumor treated clinically as a single disease with poor outcomes. Distinct SCLC molecular subtypes have been defined based on expression of lineage-related transcription factors: ASCL1, NEUROD1, POU2F3 or YAP1, but their origins remain unknown. Here, we develop an in vitro model of MYC-driven SCLC tumor cell progression and perform a time-series analysis of single-cell transcriptome profiling to reveal that MYC drives the dynamic evolution of SCLC subtypes. Analyses of these single-cell RNA seq data reveal that MYC promotes a temporal shift from an Ascl1-to-Neurod1-to-Yap1+ state from a neuroendocrine cell of origin. They also support our findings that MYC activates Notch signaling to dedifferentiate tumor cells to non-neuroendocrine fates. Additional single-cell RNA sequencing of 4 bulk Rb1/Trp53/MycT58A (RPM) tumors reveal individual tumors to consist of cells at nearly every stage of RPM tumor evolution modeled in vitro. Together, these single-cell RNA sequencing data place 3 of 4 SCLC subtypes on a defined trajectory and suggest that genetics, cell of origin, and tumor cell plasticity determine SCLC subtype.

overall_design: Live RPM time-series transition cells underwent library preparation directly from cell culture at days 4 (n = 2 of the same sample), 7, 11, 14, 17, and 21 post-digestion for a total of 6 distinct transition timepoints. Additionally, we performed single-cell RNA sequencing of 4 bulk RPM tumors.

first: Abbie

last: Ireland