title: Co-occurrence of Beckwith–Wiedemann Syndrome and colorectal cancer in a young woman

status: Public on Apr 01 2023

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

summary: Beckwith-Wiedemann Spectrum (BWSp) is a disorder predisposing to tumors of embryonic origin that arise during childhood. Little is known concerning the tumor risk and histotype prevalence in adult BWSp patients. However, several studies report cases of co-occurrence of BWSp and tumors in early adulthood, suggesting that the cancer risk in BWSp could be relevant also later than childhood. Here, we report for the first time a case of co-occurrence of BWSp and early-onset colorectal cancer (EO-CRC). The results disclosed genetic and epigenetic molecular lesions of the patient at both somatic and germline levels, providing support to the hypothesis that epigenetic changes contribute to cancer initiation in tissues where a genetic insult is already present, acting in a cooperative manner to stimulate tumorigenesis.

overall_design: DNA samples extracted from peripheral blood were subjected to methylation profile analysis using Infinium MethylationEPIC 850K Bead Chip and pyrosequencing. 8 Controls from the same batch were downloaded from GSE195873 (GSM5855510 to GSM5855517).  The GSM is also reported as colname in the Matrix_processed_blood file.

first: Laura

last: Pignata

first: Bruno

last: Hay Mele

first: Abu

last: Saadat

first: Orazio

last: Palumbo

first: Pietro

first: Massimo

last: Carella

first: Gioacchino

last: Scarano

first: Giovanni

last: Rossi

first: Claudia

last: Angelini

first: Angela

last: Sparago

first: Flavia

last: Cerrato

first: Andrea

last: Riccio


title: Effect of repeated optogenetic stimulation on gene expression and chromatin accessibility in the mouse dentate gyrus

status: Public on Mar 31 2023

city: Toyoake

first: Tomoyuki

last: Murano

address: 1-98 Dengakugakubo, Kutsukake-cho

country: Japan

institute: Fujita Health University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Visium Spatial transcriptomics analysis of human primary colorectal cancer

status: Public on Mar 14 2023

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

country: South Korea

institute: Ajou University School of Medicine

summary: To reveal the spatial distribution and the difference gene expression pattern of cancer cells in colorectal cancer, Visium spatial transcriptomics of four CRC patients was applied

overall_design: Visium analysis of four CRC patients

first: Soon

middle: S

first: Young-Kyeong

last: Lee

first: So-Hyun

first: Young

middle: H

last: Kim

first: Jun

last: Shin

first: Yong

middle: W

last: Choi

first: Jang-Hee

first: Tae

middle: J


title: Blood cells with trisomy 21 overreact to heat shock stress [ATAC-seq]

status: Public on Apr 21 2023

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

country: USA

institute: University of Colorado

summary: Lymphoblastoid cells trisomic for chromosome 21 activate the heat shock response more robustly than disomic cells.

overall_design: D21 and T21 lymphoblastoid cells derived from EBV infection of B cells from two brothers were assayed before and after heat shock using ATAC-seq, PRO-seq and scRNA-seq. Heat shock was 42C for 1 hour. This dataset includes the ATAC-seq data.

first: Joseph

last: Cardiello

first: Robin

last: Dowell


title: Single-cell RNA sequencing shows the heterogeneity of cancer-associated fibroblast in HBV-related hepatocellular carcinoma

status: Public on Mar 13 2023

city: shanghai

first: Gui-Qi

last: zhu

address: shanghai

country: China

institute: zhongshan hospital

summary: We identified 5 distinct fibroblast subsets by sequencing 74957 single cells derived from 7 HBV-related HCC tissues, of which the CD36+ CAFs were highlighted, with enriched lipid metabolism and secreting high levels of macrophage migration inhibitory factor (MIF). CD36+ CAFs had tight interactions with CD33+ MDSCs through MIF/CD74 axis.

overall_design: We performed scRNA-seq derived from 7 HBV-related HCC tissues and 4 adjacent liver tissues

first: Gui-qi

last: Zhu

first: Wei-Ren

last: Liu

first: Ying-Hong

last: Shi

first: Jia

last: Fan


title: mRNA expression profile of control and senescent human colorectal cancer cell line SW620

first: Soon Sang

summary: To reveal the difference in mRNA expression profile between non-senescent cancer cells and senescent cancer cells in colorectal cancer, CRC cell line SW620 was treated with hydrogen peroxide to induce senescent.

overall_design: control SW620 and 150mM H2O2 -treated SW620 were compared


title: Gene expression profile of pDC like cells

status: Public on Feb 24 2023

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel


title: Single-cell RNA sequencing analysis of mouse normal brain and GBM tumors

status: Public on Feb 17 2023

city: Philadelphia

first: Yi

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

summary: To investigate the transcriotome in glioblastoma tumor and normal brain on a single cell level, we performed RNA sequcening analysis with single cells derived from mouse normal brain tissue or GBM tumor tissue. Particularly, vascular endothelial cells (ECs) were traced using a Cdh5-Cre;LSL-tdTomato system.

overall_design: Chicken DF-1 fibroblasts were transfected with RCAS-PDGF-B and RCAS-Cre plasmids to produce retrovirus, followed by orthotopic injection into Ntv-a;Ink4a-Arf-/-;Ptenfl/fl;LSL-luc mice to induce GBM. Tumors were isolated and subjected to mechanical dissociation with a gentleMACS Dissociator and enzymatic digestion using collagenase II and dispase II to obtain single-cell suspensions. Tumor-derived single-cell suspensions were cultured with NeuroCult mouse stem cell medium. Attached cells were discarded to remove tumor stromal cells, and non-adherent sphere-forming tumor cells were injected into Cdh5-Cre;LSL-tdTomato mouse brains.

first: Zhang

last: Duo

first: Huang

last: Menggui

first: Fan

last: Yi


title: Effects of PHGDH CRISPR knockout on gene expression in glioblastoma-associated endothelial cells

summary: PHGDH was knocked out in human glioblastoma (GBM)-associated endothelial cells (ECs) using CRISPR-Cas9/gRNA. RNA was isolated and analyzed by RNAseq. The effects of PHGDH knockout on gene expression were determined.

overall_design: ECs were isolated from GBM tumors and transduced with the lenvirus expressing PHGDH sgRNA or control sgRNA, followed by cell selection by incubation with medium containing 2 µg/ml puromycin. RNA was isolated and analyzed by RNAseq.

first: Hu

last: Guanghui


title: Gene expression profile for sort purified CD11c+ cells derived from C57BL/6 or Klf4fl/fl ItgaxCre+ spleens, sLNs and mLNs at single cell level [scRNA-Seq]

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CD11c+ cells  in spleen, skin draining lymph nodes and mesenteric lymphnodes. We have compared the cells derived from C57BL/6 or Klf4fl/fl ItgaxCre+ mice.

overall_design: Mouse CD11c+ cells derived from C57BL/6 or Klf4fl/fl ItgaxCre+ spleens, sLNs and mLNs were analysed using scRNASeq

first: Patrick

middle: F

last: Rodrigues

first: Robert

last: Ivanek

first: Roxane

last: Tussiwand


title: Transcriptome analysis of tumor and normal brain endothelial cells

summary: The global RNA expression was assayed with endothelial cells (ECs) derived from human glioblastoma and normal brains using RNAseq.

overall_design: GBM tumor-derived single-cell suspensions were prepared by the tissue bank at Department of Neurosurgery of the Hospital of the University of Pennsylvania. Cell suspensions were subjected to magnetic activating cell sorting (MACS) with anti-CD31 antibody-conjugated magnetic beads. Sorted ECs were verified by Dil-Ac-LDL absorption and vWF staining. Normal human brain-derived ECs were used as controls. RNA was isolated and analyzed by RNAseq.


title: Single-cell epigenomics and high-density genetic variation resolve the architecture of the Treg regulatory network [scATAC-seq]

status: Public on Feb 01 2023

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: To systematically examine the transcription factors and cis-regulatory elements that shape diverse Treg regulatory programs, we used single-cell Assay for Transposase-Accessible Chromatin with high-throughput sequencing (scATAC-seq) to generate chromatin accessibility profiles of mouse regulatory and conventional T cells from different organs and genetic backgrounds.

overall_design: T regulatory (Treg) and conventional (Tconv) cells were sorted from either different organs (spleen, colon), genetic backgrounds (B6, B6/Cast F1), or different transcription factor knockouts (FoxP3, Gata3) for analysis by scATAC-seq

first: Kaitavjeet

last: Chowdhary

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Functional implications of polygenic risk for schizophrenia in human neurons

city: New York

first: Kayla

last: Townsley

state: New York

address: 240 E. 89th Street, Apt. #1C

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: We predicted that eGenes linked to schizophrenia would share substantial downstream transcriptomic changes with a common direction of effect (termed “convergence”). Although convergence has been described in the context of loss-of-function autism spectrum disorder risk genes, these rare mutations almost never co-occur in the same individual. The convergent impact of common variants which are frequently inherited together, and the impacts of which are apparent only in aggregate remain unknown. We targeted twenty-one schizophrenia eGenes in iGLUTs using pooled and arrayed CRISPR-based approaches, significantly perturbing seventeen (CALN1, CLCN3, DOC2A, FES, FURIN, GATAD2A, NAGA, PCCB, PLCL1, THOC7, TMEM219, SF3B1, SNAP91, SNCA, UBE2Q2L, ZNF823, ZNF804A), and resolving convergent impacts robust to experimental and donor effects. To test if convergence influenced the outcome when eGenes were inherited in combination (i.e. if eGene effects sum linearly according to the additive model), we compared manipulation of eGenes one at a time and in groups defined by annotated functions at the synapse (“synaptic”: SNAP91, CLCN3, PLCL1, DOC2A, SNCA), or regulating transcription (“regulatory”: ZNF823, INO80E, SF3B1, THOC7, GATAD2A), or with un-related non-synaptic, non-regulatory biology (“multi-function”: CALN1, CUL9, TMEM219, PCCB, FURIN), and random combinations thereof. Altogether, with broad relevance across complex polygenic disease our work begins to experimentally determine answers to the long-standing question of how risk variants interact in human neurons.

overall_design:
Pooled CRISPR screening combined single-cell RNA sequencing readouts and direct detection of sgRNAs. Two independently designed, constructed, and validated pooled CRISPRa libraries were transduced into iGLUTs from two donors in independent experiments at unique developmental time-points (DIV7 or DIV21). To identify groups of genes with similar expression patterns across eGene perturbations we define “convergent networks” as relationships between genes that are co-regulated by shared biological mechanisms. To study the strength and composition of convergent networks, we define “network convergence” as the sum of the network connectivity score (i.e., networks with fewer nodes and more interconnectedness have increased convergence). We endeavored to identify the biological factors (e.g., number of eGenes, functional similarity of eGenes, and eGene co-expression) that influenced network convergence. eGene number tested the number of eGenes used to generate a convergent network.  Functional similarity (i.e., the degree of shared biological functions amongst eGenes) was calculated two ways: Gene Ontology semantic similarity scoring (within biological pathway, cellular component, and molecular function), and synaptic/signaling score (proportion of eGenes with annotated function as either “signaling” for pooled or “synaptic” for arrayed)

We next manipulated eGenes in combination to approximate the polygenic nature of schizophrenia and test if convergence between eGenes influences observed effects. Given that genes implicated in synaptic biology and epigenetic/transcriptional regulation are enriched for the schizophrenia risk we sought to generate three groups of eGenes, linked to synaptic biology, gene regulation, or neither (Fig. 1A, arrayed experiment). Unconstrained by the unidirectionality of pooled CRISPR screens, we did not restrict our list to eGenes with a single direction of effect. From the 18 coding genes prioritized by the intersection of transcriptomic imputation and colocalization, eGenes were separated into discrete functional categories based on gene ontology annotations. Our final gene list included five synaptic genes (SNAP91, CLCN3, PLCL1, DOC2A, SNCA), five regulatory genes (ZNF823, INO80E, SF3B1, THOC7, GATAD2A), and five genes with non-synaptic, non-regulatory functions, termed “multi-function” (CALN1, CUL9, TMEM219, PCCB, FURIN).
We then applied an arrayed design (i.e., distinct conditions in each well) to manipulate schizophrenia eGenes alone and in combination, allowing us to capture cell autonomous and non-cell autonomous effects in a manner not possible in the pooled design. Three to five vectors per gene were tested in 7-day-old (D7) iGLUTs, identifying the single vector that best achieved the level of significant perturbation predicted by eQTL analyses as confirmed by qPCR. Each eGene was perturbed in 21-day-old (D21) iGLUTs for 72 hours, individually and jointly, including appropriate vector and scrambled controls, from two neurotypical donors with average polygenic risk scores (one experimental batch per donor). Three groups of five random genes, one group of ten random genes, and one group of all fifteen genes were also included. Significant (p<0.05) changes in eGene expression in iGLUTs were confirmed by RNAseq in 13/15 eGenes (SNAP91, CLCN3, PLCL1, DOC2A, SNCA, ZNF823, SF3B1, THOC7, GATAD2A, CALN1, TMEM219, PCCB, FURIN) (SI Fig. 1G, SI Fig. 19A); we validated the magnitude and direction of experimental eGene perturbation relative to the dosage effects of the top predicted causal SNPs (e.g. eQTL effect size) and predicted eGene expression changes.

middle: G

last: Retallick-Townsley

first: Peter

middle: M

last: Deans

first: Aiqun

last: Li

first: Carina

last: Seah

first: Jessica

last: Johnson

first: Judit

last: Garcia Gonzalez

first: Sam

last: Cartwright

first: Georgios

last: Voloudakis

first: Wen

last: Zhang

first: Minghui

last: Wang

first: John

last: Fullard

first: Kiran

last: Girdhar

first: Eli

last: Stahl

first: Panos

last: Roussos

first: Schahram

last: Akbarian

first: Bin

first: Paul

last: O'Reilly

first: Laura

last: Huckins

first: Kristen

last: Brennand

first: Nadine

last: Schrode

first: Evan

last: Cao


title: A discrete 'early-responder' stromal-cell subtype orchestrates immunocyte recruitment to injured tissue, thereby promoting regeneration [RNA-seq]

status: Public on Dec 31 2022

first: CBDM

last: Lab

summary: Following acute injury, stromal cells promote tissue regeneration by diverse mechanisms. Time-resolved single-cell RNA sequencing of muscle mesenchymal stromal cells (MmSCs) responding to cardiotoxin (CTX)-induced injury identified an “early-responder” subtype that spiked on day 1 and expressed a striking array of transcripts encoding immunomodulators. IL-1b, TNFa and oncostatin M, primarily produced by myeloid cells, each strongly and rapidly induced MmSCs transcribing most of these immunomodulators. Transfer of the inflammatory MmSC subtype, tagged with a unique surface marker, into healthy hindlimb muscle induced inflammation primarily driven by neutrophils and macrophages. Among the abundant inflammatory transcripts produced by this subtype, Cxcl5 was stroma-specific and highly upregulated with injury. Depletion of this chemokine early after injury revealed a non-redundant impact on recruitment of neutrophils, a prolongation of inflammation at later times, and ineffectual tissue regeneration. MmSC subtypes expressing a comparable inflammatory program were found in a mouse model of muscular dystrophy and in several other tissues and pathologies in both mice and humans. These “early-responder” MmSCs, already in place, permit rapid and coordinated mobilization and amplification of critical cell collaborators during tissue regeneration.

overall_design:
To study the impact of different cytokines on MmSCs in vivo, we intraperitoneally (i.p.) co-injected four cytokines (Il-1b, TNFa, oncostatin M, and Il-17A) into uninjured mice, and flow-cytometrically double-sorted MmSCs from the hindlimb muscles 2, 4 and 8 hrs later for population-level RNA-seq. 2 hrs was selected as the ideal timepoint. To deconvolute the significance of the individual cytokines, we repeated the experiment using the 2 hrs timepoint but injected cytokines individually and as pairs. In these experiments, MmSCs from mice i.p. injected with PBS was used as the control.

To assess the transcriptional inductions in the major muscle-cell compartments with CTX-induced injury, we flow-cytometrically double-sorted CD31+, CD45+, MmSCs, and satellite cells (MuSCs) at homeostasis and 1 day after injury for population-level RNAseq.

To validate that the IL-6 reporter/depleter system tagged MmSCs enriched for inflammatory transcripts, we flow-cytometrically double-sorted Thy1.1+ and Thy1.1- MmSCs 12 hrs following CTX-induced injury and performed population-level RNA-seq.

To assess tissue-level transcriptional changes in muscle at 7 days following CTX-induced injury in mice depleted of Cxcl5 (via i.p. anti-Cxcl5 antibody injections), whole muscle RNA was isolated and submitted for RNAseq. Muscle tissue isolated at the same timepoint from mice i.p. injected with IgG was used as the control.

To survey MmSCs at different disease stages of a muscular dystrophy mouse model, we flow-cytometrically double-sorted MmSCs from the hindlimb muscles of 2.5-, 7- and 12.5-wk-old mdx mice and performed population-level RNA-seq.

To determine the importance of Il-1b in the induction of inflammatory transcripts in MmSCs in vivo, we flow-cytometrically double-sorted MmSCs from Il-1b KO or Il-1b WT littermates at 1 day after CTX-induced injury for population-level RNAseq.

first: Omar

middle: K

last: Yaghi

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: A20 attenuate oxidized self-DNA mediated inflammasome activation through promoting NEK7 ubiquitination in AKI

status: Public on Dec 20 2022

city: 成都

first: Hanwen

last: Li

state: 四川

address: 四川省成都市武侯区人民南路四川大学华西校区

institute: 四川大学华西口腔医学院


title: A discrete 'early-responder' stromal-cell subtype orchestrates immunocyte recruitment to injured tissue, thereby promoting regeneration.


title: Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted by metastasis

status: Public on Mar 01 2023

city: San Francisco

first: Matthew

last: Spitzer

state: CA

address: 513 Parnassus Ave.

institute: University of California, San Francicso

summary: CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment (TME), recent studies in mice identified responses in lymph nodes (LN) as essential; however, the role of LN in human cancer patients remains unknown. Here, we examined CD8+ T cells in human head and neck squamous cell carcinomas (HNSCC) and regional lymph node (LN) using single-cell genomics. We identified progenitor exhausted CD8+ T cells (TCF7 Exhausted) that were clonally related to terminally exhausted CD8 T cells in the TME. Our results identify an important role for the LN as a reservoir of more functional CD8+ T cells for anti-tumor immune responses in humans.

overall_design: We performed scRNA sequencing to understand how the tissue compartment (lymph node versus tumor) affects T cell phenotype in the context of head and neck squamous cell carcinoma (HNSCC). We used a combination of scRNA-sequencing + scTCR-sequencing and CITE-sequencing, which obtains measurements at both the protein and transcriptome level for a subset of samples, + scTCR-sequencing to obtain TCR sequences to identify and phenotype shared clones in the tissue compartments.

first: Maha

last: Rahim

first: Trine

last: Okholm

first: Kyle

middle: B

last: Jones

first: Elizabeth

middle: E

last: McCarthy

first: Candace

middle: C

last: Liu

first: Jacqueline

middle: L

last: Yee

first: Stanley

last: Tamaki

first: Diana

last: Marquez

first: Iliana

last: Tenvooren

first: Katherine

last: Wai

first: Alexander

last: Cheung

first: Brittany

middle: R

last: Davidson

first: Vrinda

last: Johri

first: Bushra

last: Samad

first: William

last: O'Gorman

last: Krummel

first: Alexis

last: Combes

first: Michael

last: Angelo

first: Lawrence

last: Fong

first: Alain

middle: P

last: Algazi

first: Patrick

last: Ha


title: A discrete 'early-responder' stromal-cell subtype orchestrates immunocyte recruitment to injured tissue, thereby promoting regeneration [scRNA-seq]

first: CBDM

last: Lab

summary: Following acute injury, stromal cells promote tissue regeneration by diverse mechanisms. Time-resolved single-cell RNA sequencing of muscle mesenchymal stromal cells (MmSCs) responding to cardiotoxin(CTX)-induced injury identified an “early-responder” subtype that spiked on day 1 and expressed a striking array of transcripts encoding immunomodulators. IL-1b, TNFa and oncostatin M, primarily produced by myeloid cells, each strongly and rapidly induced MmSCs transcribing most of these immunomodulators. Transfer of the inflammatory MmSC subtype, tagged with a unique surface marker, into healthy hindlimb muscle induced inflammation primarily driven by neutrophils and macrophages. Among the abundant inflammatory transcripts produced by this subtype, Cxcl5 was stroma-specific and highly upregulated with injury. Depletion of this chemokine early after injury revealed a non-redundant impact on recruitment of neutrophils, a prolongation of inflammation at later times, and ineffectual tissue regeneration. MmSC subtypes expressing a comparable inflammatory program were found in a mouse model of muscular dystrophy and in several other tissues and pathologies in both mice and humans. These “early-responder” MmSCs, already in place, permit rapid and coordinated mobilization and amplification of critical cell collaborators during tissue regeneration.

overall_design: We investigated the transcriptional heterogeneity of flow-cytometrically sorted MmSCs from hindlimb muscles (tibialis anterior, gastrocnemius and quadriceps) of 6- to 8-wk-old male Foxp3GFP mice at homeostasis and at day 0.5, 1, 3, 7 and 14 following CTX-induced injury; 2.5-, 5- and 12.5-wk-old male Dmdmdx mice; or 2.5- and 12.5-wk-old male DBA/2J mice. Cells were encapsulated using the Chromium Single Cell 5′ v3 platform (10x Genomics). For sequencing of MmSCs from Dmdmdx and DBA/2J mice, individual samples were tagged (hashed) with DNA-coded anti-biotin antibodies (Biolegend).

first: Omar

last: Yaghi

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Identifying potential hepatic genes regulating the ovine response to gastrointestinal nematodes using RNA-Sequencing

status: Public on Feb 10 2023

city: Guelph

first: Samantha

last: Dixon

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

country: Canada

institute: University of Guelph

summary: Gastrointestinal nematode (GIN) infections are considered the most important disease of grazing sheep. Due to increasing anthelmintic resistance, chemical control alone is inadequate. Resistance to GIN infection is a heritable trait, and through natural selection many sheep breeds have higher resistance. Studying the transcriptome from GIN-exposed and GIN-unexposed sheep using RNA-Sequencing technology can provide measurements of transcript levels associated with the host response to GIN infection, and these transcripts may harbor genetic markers that can be used in selective breeding programs to enhance disease resistance. The objective of this study was to compare liver transcriptomes of sheep naturally exposed to GINs, with either high or low parasite burdens, to GIN-unexposed control sheep in order to identify key regulator genes and biological processes associated with GIN infection. Differential gene expression analysis revealed no significant differentially expressed genes (DEG) between sheep with a high or low parasite burden (P-value ≤ 0.01; False Discovery Rate (FDR) ≤ 0.05; and Fold-Change (FC) of > 2). However, when compared to the control group, low parasite burden sheep showed 159 DEG, and high parasite burden sheep showed 146 DEG (P-value ≤ 0.01; FDR ≤ 0.05; and FC of > 2). Among these two lists of significant DEG, 86 DEG were found in common between the two parasite burden groups compared to the control (GIN-unexposed sheep). Functional analysis of these significant 86 DEG found upregulated genes involved in immune response and downregulated genes involved in lipid metabolism. Results of this study offer insight into the liver transcriptome during natural GIN exposure that helps provide a better understanding of the key regulator genes involved in GIN infection in sheep.

overall_design: Compare liver transcriptomes of sheep naturally exposed to GINs, with either high (n=6) or low (n=5) parasite burdens, to GIN-unexposed control sheep (n=4).

first: Niel

middle: A

last: Karrow

first: Emma

last: Borkowski

first: Aroa

last: Suarez-Vega

first: Paula

middle: I

last: Menzies

first: Delma

last: Kennedy

first: Andrew

last: Peregrine

first: Bonnie

last: Mallard

first: Ángela

last: Cánovas


title: Bioinformatic Investigation of the Zic1/2 binding reveals novel co-factors in Zic-mediated gene regulation in the cerebellum

city: Durham

first: Anne

last: West

state: NC

address: 311 Research Dr

department: Neurobiology

institute: Duke University

summary: The family of Zic transcription factors (TFs) are required for cerebellar development, and their binding is highly enriched at developmentally regulated enhancers active in cerebellar granule neurons at the progenitor stage around postnatal day 7 (P7) and the mature adult stage at P60 in the mouse cerebellum. Interestingly, Zic1/2 ChIP-seq data reveal that the Zics change their binding profile over time. To characterize these differences in Zic targeting between early and late cerebellar maturation, we compared the sequence underlying Zic Peaks, their relationship with active chromatin and gene expression at P7 and P60. From this we found Zic peaks tend to be large and bind open-active chromatin. Strikingly, Zic peaks shift from binding at promoter proximal regions at P7 to distal enhancer regions at P60. We hypothesize that other TFs collaborate with the Zic TFs to change their binding targets and affect their regulatory activity. A multi-tiered approach was used to predict TF binding at those Zic ChIP sites. We assessed motif enrichment (HOMER) and in-vivo TF binding profiles (BART) to determine putative TFs collaborating with Zic to drive this regulation. We then validated the presence of the predicted TFs in granule neurons using gene expression. This workflow identified known and novel distinct collaborators of Zic between early and late development. Early collaborates of Zic includes bHLH factors and chromatin remodelers whereas late collaborators of Zic are activity regulated TFs which are markers of synaptic maturation. To identify Zic’s developmental gene targets in cerebellar maturation, we used H3K4me3 PLAC-seq data, which captures promoter-enhancer loops from the adult mouse cerebellum and Hi-C data from the young mouse cerebellum to map genes to Zic bound enhancers. This revealed Zic as a transcriptional activator of late developmental genes in the cerebellum. Using this same approach with in vitro Zic KD, we were able to identify Zic dependent developmental gene targets which have functions in axonogenesis, axon guidance, and ion channel signaling, which are integral in proper maturation of a neuron. These integrated analyses reveal how Zic and other TFs regulate temporal expression of CGN developmental genes and provides information that will enhance our understanding of the molecular mechanisms that regulate the mode of TF function at enhancers.

overall_design: Zic1/2 CUT&RUN-seq performed on cerebellar granule neurons harvested after 1, 3, 5 and 7 days in vitro. (n=3 biological replicates)

first: Melyssa

last: Minto

first: Jesus Emiliano

last: Sotelo-Fonseca

first: Vijyendra

last: Ramesh


title: TP53-mediated clonal hematopoiesis confers increased risk for incident peripheral artery disease

status: Public on Nov 29 2022

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary:
Background: Somatic mutations in blood indicative of clonal hematopoiesis of indeterminate potential (CHIP), particularly in DNMT3A, TET2, and JAK2, are associated with an increased risk of hematologic malignancy, coronary artery disease, and all-cause mortality. However, whether CHIP is associated with increased risk of peripheral artery disease (PAD) remains unknown. In addition, chemotherapy frequently causes mutations in DNA Damage Repair (DDR) genes TP53 and PPM1D, and whether CHIP caused by somatic mutations in DDR genes results in increased risk of atherosclerosis is unclear. We sought to test whether CHIP, and CHIP caused by DDR genes, associates with incident peripheral artery disease (PAD) and atherosclerosis.
Methods: We identified CHIP among 50,122 exome sequences in individuals from UK and Mass General Brigham Biobanks and tested CHIP status (N=2,851) with incident PAD and atherosclerosis across multiple arterial beds. To mimic the human scenario of clonal hematopoiesis and test whether the expansion of p53-deficient hematopoietic cells contributes to atherosclerosis, a competitive bone marrow transplantation (BMT) strategy was used to generate atherosclerosis-prone Ldlr-/- chimeric mice carrying 20% Trp53-/- hematopoietic cells (20% KO-BMT mice). We then evaluated aortic plaque burden and plaque macrophage accumulation 12 weeks after grafting.
Results: CHIP associated with incident PAD (HR 1.7; P=2.2x10-5) and atherosclerosis in multiple beds (HR 1.3; P=9.7x10-5), with increased risk among individuals with DDR CHIP (HR 2.0; P=0.0084). Among atherosclerosis-prone Ldlr null mice, the p53 -/- 20% KO-BMT mice demonstrated increased aortic plaque size (p=0.013) and accumulation of p53-/- plaque macrophages (P<0.001), driven by an abundance of p53-deficient plaque macrophages. The expansion of p53-deficient cells did not affect the expression of the pro-inflammatory cytokines IL-6 and IL-1β in the atherosclerotic aortic wall.
Conclusions: Our findings highlight the role of CHIP as a broad driver of atherosclerosis across the entire arterial system, with evidence of increased plaque among p53 -/- 20% KO-BMT mice via expansion of plaque macrophages. These observations provide new insight into the link between CHIP and cardiovascular disease, and lend human genetic support to the concept that post-cytotoxic chemotherapy patients may benefit from surveillance for atherosclerotic conditions in addition to therapy-related myeloid neoplasms.

overall_design: Bone marrow-derived macrophages (BMDM), p53 wt and p53 ko.

first: María

last: Zuriaga

first: Nuria

last: Matesanz

first: Roberta

last: Carriero

first: Paolo

last: Kunderfranco

first: Carolina

last: Greco

first: José

last: Fuster


title: Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity

status: Public on Dec 01 2022

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

summary: It is increasingly appreciated that long non-coding RNAs (lncRNAs) carry out important functions in mammalian cells, but how these are encoded in their sequences, and manifested in their structures remains largely unknown. Some lncRNAs bind to and modulate the availability of RNA binding proteins, but the structural principles that underlie this mode of regulation are underexplored. Here, we focused on the NORAD lncRNA, which binds Pumilio proteins and modulates their ability to repress hundreds of mRNA targets. We probed the RNA structure and long-range RNA-RNA interactions formed by NORAD inside cells, under different stressful conditions. We discovered that NORAD structure is highly modular, and consists of well-defined domains that contribute independently to NORAD function. The structure adopted by NORAD spatially clusters the Pumilio binding sites along NORAD in a manner that contributes to de-repression of Pumilio target proteins. Following arsenite stress, the majority of NORAD structure undergoes relaxation and forms inter-molecular interactions with RNAs that are targeted to stress granules. NORAD sequence thus dictates elaborated structural domain organisation that facilitates its function on multiple levels, and which helps explain the extensive evolutionary sequence conservation of NORAD regions that are not predicted to directly bind Pumilio proteins.

overall_design:
Examination of NORAD RNA structure in: untreated cells (3 biological replicates and 3 paired controls); cells under DNA damage stress (2 biological replicates and 2 paired controls; and cells under Arsenite stress (3 biological replicates and 3 paired controls)
DMS-seq for a region comprising NRU7-8 in NORAD

first: Omer

last: Ziv

first: Svetlana

last: Farberov

first: Jian

middle: Y

last: Lau

first: Eric

last: Miska

first: Igor

last: Ulitsky


title: Dual oxic-anoxic co-culture enables direct study of host-anaerobe interactions at the airway epithelial interface

status: Public on Nov 19 2022

city: Minneapolis

first: Ryan

last: Hunter

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

summary: To understand the physiological response of Calu-3 cells to dual oxic-anoxic culture

overall_design: We used bulk RNAseq to compare gene expression under mixed oxic conditions to culture under normoxia

first: Patrick

last: Moore

first: Talia

last: Wiggen


title: A20 attenuate oxidized self-DNA mediated inflammasome activation  in AKI [AA-DNA]

first: Hanwen

last: Li

address: 四川省成都市武侯区人民南路四川大学华西校区

summary:
To seek out the target of restricting the exaggerated inflammation results from ox-self-DNA, we treated BMDMs  with self-dsDNA from kidney of acute kidney injury mice model.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different groups of BMDMs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDMs treated with AA-DNA(AA-DNA 1,2,3) or empty vector(Lipo3000 1,2,3)

first: Jiayun

last: Yu

first: Yongyao

last: Wu

first: Min

last: Luo

first: Siyuan

last: Chen

first: Weimin

last: Lin

first: Zhan

first: Yang

last: Yang

first: Aiping

last: Tong

first: Guobo

last: Shen

first: Xiawei

last: Wei

first: Bin

last: Shao


title: Inhibition of LIFR blocks adiposity driven endometrioid endometrial cancer growth

status: Public on Nov 16 2022

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We examined the mechanisms by which adiposity regulates EEC progression. EEC cells were incubated with or without adipocyte conditioned medium (ADP-CM), and total RNA was isolated for RNA-seq analysis. Our results demonstrated that ADP-CM stimulated EEC cells showed upregulation of several LIF/LIFR modulated pathways including Jak/STAT and cytokine pathways.

overall_design: Total RNA from RL95-2 control, and ADP-CM cells were isolated using RNeasy mini kit (Qiagen). For whole-genome transcriptome profiling, 2 libraries (3 replicates from each group) were generated using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 50 base-pair single-read (50SR) sequencing module.

first: Ratna

last: Vadlamudi

first: Suryavathi

last: Viswanadhapalli

first: Yidong

first: Zhao

last: Lai


title: Haptoglobin Gene Expression and Anthracycline-related Cardiomyopathy in Childhood Cancer Survivors

status: Public on Jan 31 2023

city: Birmingham

first: Smita

last: Bhatia

state: AL

address: 1600 7th Avenue South Lowder 500

department: Pediatrics

institute: University of Alabama at Birmingham

summary: In this study RNA-Seq was performed in anthracycline- exposed childhood cancer survivors who had cardiomyopathy (cases) matched to those without cardiomyopathy (controls) to understand the pathogenesis of anthrcaycline-related cardiomyopathy

overall_design: Peripheral whole blood transcriptome assessed by RNA-Seq on Illumina HiSeq in 40 cases and 64 matched controls


title: A20 attenuate oxidized self-DNA mediated inflammasome activation through promoting NEK7 ubiquitination in AKI [ox-dsDNA90]

first: Hanwen

address: 四川省成都市武侯区人民南路四川大学华西校区

summary:
To seek out the target of restricting the exaggerated inflammation results from ox-dsDNA90, we treated BMDMs  with ox-dsDNA90 from kidney of acute kidney injury mice model.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different groups of BMDMs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDMs treated with ox-dsDNA90(ox-dsDNA90 1,2,3) or empty vector(Lipo3000 1,2,3)

first: Jiayun


title: Single-nucleus transcriptional profiling of Gad2-positive neurons from the mouse lateral habenula with distinct expression of neurotransmitter-related genes

status: Public on Nov 08 2022

city: durham

first: Anne

last: West

address: 311 research drive

summary:
Glutamatergic projection neurons of the lateral habenula (LHb) effect behavioral statemodulation by regulating the activity of midbrain monoaminergic neurons. Identifying circuit mechanisms that control LHb output is of interest for understanding motivated behaviors. A small population of neurons within the medial subnucleus of the mouse LHb express the GABAergic synthesizing enzyme GAD2 and are capable of inhibiting nearby LHb projection neurons. However, these neurons lack most markers of classic inhibitory interneurons, and they
co-express the vesicular glutamate transporter VGLUT2. To determine the molecular phenotype of these neurons, we genetically tagged the nuclei of GAD2-positive cells and used fluorescence-activated nuclear sorting followed by single nuclear RNA sequencing (FANS-snRNAseq) to determine the full transcriptional profile of GAD2+ neurons isolated from LHb. Our data demonstrate that LHb GAD2+ neurons co-express markers of both glutamatergic and GABAergic transmission and that they are transcriptionally distinct from GABAergic
interneurons or habenular glutamatergic neurons. We show sex-specific differences in gene expression in this neuronal population and find that these gene sets are enriched for genes involved in depression. Finally, we identify the Ntng2 gene encoding the cell adhesion protein Netrin-G2 as a selective marker of LHb GAD2+ neurons that may contribute to their target projections. These data show the value of using genetic enrichment of rare cell types for transcriptome studies, and they advance understanding of the molecular composition of a functionally important class of neurons in the LHb.

overall_design: Single sample run on 4 lanes for sequencing using NextSeq 500 mid output. Tissue was mixed from 6 male and 3 female mice.

first: Matthew

last: Green

first: David

last: Gallegos

first: Luke

last: Bartelt


title: Epiregulin is a dendritic cell-derived EGFR ligand that maintains skin and lung fibrosis

status: Public on Dec 09 2022

city: New Haven

first: Ian

last: Odell

state: CT

address: 330 Cedar St. LMP-5040

department: Dermatology

institute: Yale University

summary: Immune cells are fundamental regulators of extracellular matrix (ECM) production by fibroblasts and have important roles in determining extent of fibrosis in response to inflammation. Although much is known about fibroblast signaling in fibrosis, the molecular signals between immune cells and fibroblasts that drive its persistence are poorly understood. We therefore analyzed skin and lung samples of patients with diffuse cutaneous systemic sclerosis, an autoimmune disease that causes debilitating fibrosis of the skin and internal organs. Here we define a critical role of epiregulin – EGFR signaling between dendritic cells and fibroblasts to maintain elevated ECM production and accumulation in fibrotic tissue. Mechanistic studies demonstrate that epiregulin expression marks an inducible state of DC3 dendritic cells triggered by type I interferon. DC3-derived epiregulin activates EGFR on fibroblasts, which drives a positive feedback loop through NOTCH signaling. In well-established mouse models of skin and lung fibrosis, epiregulin was essential for persistence of fibrosis in both tissues, which could be abrogated by epiregulin genetic deficiency or a neutralizing antibody. Notably, therapeutic administration of epiregulin antibody reversed fibrosis in patient skin and lung explants, identifying it as a novel biologic drug target. Our findings reveal epiregulin as a crucial immune signal that maintains skin and lung fibrosis in multiple diseases and is a highly promising antifibrotic target.

overall_design: Skin biopsies from 5 patients with scleroderma (SSc1-5) and 6 healthy controls (Normal1-6) were analyzed using 10x genomics platform

middle: D


title: RNA Sequencing in LXR agonist fed Atp7b-/- mice (Wilson disease)

status: Public on Oct 26 2022

city: Baltimore

first: Som

last: Dev

state: MD

address: 725 N, Wolfe St

department: Physiology, School of Medicine

institute: Johns Hopkins University

summary: The goal of the study was find the gene expression of diverse signaling pathways altered in Atp7b-/- mice (murine WD)  liver as compared to control  mice and how LXR agonist treatment will improve/ameliorate WD phenotype in Atp7b-/- mice.  Activation of LXR/RXR using synthetic LXR agonist ameliorates liver inflammation and fibrosis in murine WD by changing gene expression.

overall_design:
Examination of gene expression in Het (control) and Atp7b-/- mice and LXR agonist fed Atp7b-/- mice
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Authors indicate that they have lost the raw sequences, "I contacted the company server,  unfortunately they have deleted the data from the server after 3 months."

first: Svetlana

last: Lutsenko

first: James

last: Hamilton


title: Expression analysis of WT, dnmt3bb.2-/- and dnmt3aa-/-

status: Public on Oct 24 2022

city: Obu

first: Nobuyoshi

last: Shimoda

state: Aichi

address: Morioka 7-430

department: Research Core Facility

institute: National Institute for Geriatrics and Gerontology

summary: To investigate the effects of gene expression by dnmt3bb.2 and dnmt3aa mutations in zebrafish, expression array analyses were performed.

overall_design: Analyzing gene expression by microarray in WT, dnmt3bb.2-/- and dnmt3aa-/-.  Three independent experiments were performed at following developmental stages; 1~2-cell, shield, 5-somite, 1 dpf, and 2 dpf.

first: Hayato

last: Yokoi

first: Kazuya

last: Sakaguchi

first: Masaki

last: Shirai

last: Takayama

first: Haruko

last: Takahashi

first: Yutaka

last: Kikuchi


title: Single cell RNA-sequencing reveals five subtypes of olfactory bulb-derived olfactory ensheathing cells that secrete Reelin

status: Public on Oct 13 2022

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Olfactory ensheathing cells (OECs) are the only glial cells that support the olfactory sensory neurons which undergo adult neurogenesis and continually project their axons to glomeruli in the olfactory bulbs. We used single cell RNA sequencing to study the gene expression programs of OECs and to determine the diversity of purified OECs previously shown to promote spinal cord injury repair. Our analyses revealed five subtypes of OECs, each expressing unique marker genes and pathways indicative of progenitor, axonal regeneration, migration, or microglia-like functions. As expected, we found substantial overlap of OEC genes with those of Schwann cells, but also with astrocytes, oligodendrocytes and microglia. We experimentally confirmed the classic marker genes of the OEC subtypes and provide evidence that Reelin and Connective Tissue Growth Factors are secreted by multiple OEC subtypes. Our results support that adult OECs are a hybrid glia including some with progenitor characteristics and that they likely carry out diverse functions related to injury repair and axonal regeneration.

overall_design: Olfactory bulbs were collected from 8-10 weeks old GFP-labeled Sprague-Dawley rats. Primary cultures were generated from both olfactory bulbs from each rodent. Immunopurification was carried out using anti-GFRp75. Flasks with purified OECs and leftover cells were rinsed with HBSS and dissociated with trypsin-EDTA as above. Cells were washed in D/F-FBS-P/S medium and further resuspended with silconized pipettes. Media and cells  were washed and centrifuged at 365 g for 10 min, and resuspended. After the final wash, cells for sequencing were resuspended in PBS+BSA in volumes of 1200 cells/µL. 4 flasks of cells (2 purified OECs and 2 ‘leftovers’) were generated on each of 2 different culture dates for scRNA-seq, yielding 8 samples in total (4 purified OECs and 4 ‘leftovers’)

first: Patricia

last: Phelps

first: Sung

last: Ha


title: A novel small molecule targeting oncogenic PELP1 demonstrates anti-tumor activity in wild type and mutant estrogen receptor alpha-positive breast cancer

status: Public on Nov 02 2022

first: YI

last: ZOU

summary: RNA-seq analyses showed SMIP34 treatment altered the expression of genes associated withEstrogen Response, Cell Cycle and Apoptosis pathways

overall_design: Total RNA from ZR-75 cells treated with or with out SMIP34  was isolated using RNeasy mini kit (Qiagen). For whole-genome transcriptome profiling, 2 libraries (3 replicates each for SMIP34 and control) were generated using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.).

first: Ratna

last: Vadlamudi

first: Kristin

last: Altwegg

first: Suryavathi

last: Viswanadhapalli

first: Yidong

last: Chen

first: Zhao

last: Lai


title: 3D chromatin organizations of human pancreatic cells reveal cell-type specific regulatory architectures of diabetes risk

status: Public on Sep 06 2022

city: Philadelphia

first: Chun

last: Su

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: To understand the cell-type specific regulatory architectures of diabetes risk, we generated transcriptomic and 3D epigenomic profiles from sorted human pancreatic acinar, alpha, and beta cells using Arima Hi-C.

overall_design: We performed Arima Hi-C on FACS-sorted human pancreatic acinar, alpha and beta cells. Two biological replicates pooled from 5 healthy donors were sequenced for each cell type.

last: Pippin

first: Klaus

last: Kaestner

first: Struan

last: Grant

first: Andrew

last: Wells


title: CircRNA study in MLL::AF4 rearranged acute lymphoblastic leukemia

status: Public on Sep 22 2022

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: An Adaptive Response through N6-Methyladenosine in Fetal Offspring following Gestational Nano-TiO2 Inhalation Exposure

status: Public on Aug 24 2022

city: Morgantown

first: Quincy

middle: Alexander

last: Hathaway

state: WV

address: 1 Medical Center Drive

institute: West Virginia University


title: An Adaptive Response through N6-Methyladenosine in Fetal Offspring following Gestational Nano-TiO2 Inhalation Exposure II

summary: Background: N6-methyladenosine (m6A) is the most prominent epitranscriptomic modification to RNA in eukaryotes, but it’s role in adaptive changes within the gestational environment are poorly understood. Nano titanium dioxide (TiO2) exposure is common during pregnancy, though the impact fetal progeny is not entirely understood. We propose that gestational exposure to nano-TiO2 contributes to cardiac m6A methylation in fetal offspring and indirectly contributes to mitochondrial dysfunction.

overall_design: Results: 10-week-old pregnant female FVB/NJ wild type mice (n=14) on gestational day (GD) 5 underwent 6 non-consecutive days of whole-body inhalation exposure. Mice were exposed to filtered room air or nano-TiO2 with a target aerosol mass concentration of 12 mg/m3. At GD 15 mice were sacrificed and cardiac RNA and mitochondrial proteins extracted. There were no differences in maternal or fetal pup weights, number of pups, or pup heart weight between exposure and control groups. Immunoprecipitation with m6A antibodies was performed followed by sequencing of immunoprecipitant (m6A) and input (mRNA) on the Illumina NextSeq 2000.

first: Amina

last: Kunovac


title: RNA sequencing of CD11b+ cells isolated from human gut mucosal biopsies of IBD patients

status: Public on Aug 23 2022

city: Miami

first: Maria

middle: T

last: Abreu

state: Florida

address: 1475 NW 12th Ave floor 1

department: Gastroenterology

institute: University of Miami

summary: CD11b+ cells isolated from IBD patient biopsies have distinct transcriptomic signatures based on their location along the GI tract, inflammation status, IBD type, and medication response. These cells also respond to JAK inhibitors by decreasing cytokine output.

overall_design: Total RNA sequencing of 58 samples

first: Gillian

last: Jacobsen

first: Irina

last: Fernandez

last: Quintero

first: Ana

last: Santander

first: Judith

last: Pignac-Kobinger

first: Oriana

last: Damas

first: Amar

last: Deshpande

first: David

middle: H

last: Kerman

first: Yuguang

last: Ban

first: Zhen

last: Gao

first: Tiago

last: Silva

first: Lily

last: Wang

first: Ashley

last: Beecham

first: Jacob

last: McCauley

first: Juan

last: Burgueno


title: Whole blood transcriptomic analysis in BoHV-1 experimentally challenged dairy calves and comparison to a Bovine Respiratory Syncytial Virus (BRSV) challenge

status: Public on Aug 19 2022

city: Grange, Dunsany

first: Stephanie

last: O'Donoghue

state: Meath

address: Animal Bioscience Research Centre

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

summary: Bovine Herpesvirus 1 (BoHV-1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the whole blood mRNA transcriptomic response to an experimental challenge with BoHV-1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily until euthanasia at day 6 post-challenge. Total RNA was extracted and sequenced from whole blood (100 bp paired-end). Sequence reads were aligned to the ARS-UCD1.2 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BoHV-1 challenged and control calves based on the gene expression changes in whole blood. There were 488 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BoHV-1 challenged and control calves.

overall_design: Examination of a single tissue type (whole blood) in two different treatment groups, BoHV-1 challenged calves (n=12) and control calves (n=6)

first: Dayle

last: Johnston

first: Bernadette

last: Earley

first: Matthew

middle: S

last: McCabe

first: JaeWoo

last: Kim

first: Jeremy

middle: F

last: Taylor

first: Ken

last: Lemon

first: Catherine

last: Duffy

first: Michael

last: McMenamy

first: S

last: Cosby

first: Derek

middle: W

last: Morris

first: Sinead

last: Waters


title: An Adaptive Response through N6-Methyladenosine in Fetal Offspring following Gestational Nano-TiO2 Inhalation Exposure I

first: Quincy

last: Hathaway

first: Amina

last: Kunovac


title: Single cell transcriptomics of Atlantic salmon (Salmo salar L.) liver reveals cellular heterogeneity and immunological responses to challenge by Aeromonas salmonicida

status: Public on Aug 16 2022

first: Richard

middle: Sydney

state: Midlothian

address: The University of Edinburgh, Easter Bush Campus

department: Roslin Institute

summary: The liver is a multitasking organ with essential functions for vertebrate health spanning metabolism and immunity. To explore the multifaceted role played by liver cells in response to bacterial infection in fishes, we generated a transcriptomic atlas of nuclei isolated from the liver of Atlantic salmon (Salmo salar L.), contrasting control fish with those challenged with a pathogenic strain of Aeromonas salmonici. We found a dominant hepatocyte population that radically remodels its transcriptome following infection to activate the acute phase response and other defense functions, while repressing routine functions such as metabolism. In addition, we discover numerous cell specific responses to infection within the immune cell compartments, and identify  many novel cell-specific marker genes to empower future studies of this organ in fishes.

overall_design: Twenty Atlantic salmon were  anaesthetized and given an intraperitoneal injection of either PBS  (n=10), or the pathogenic Hooke strain of A. salmonicida (n=10). Sampling was performed 24 h post-injection and control (n=2) and infected (n=2) fish were selected based on immune response validated with qPCR. Single nucleus libraries were constructed according using the 10x Genomics Chromium platform.

first: R

last: Daniels

last: Dobie

last: Naseer

first: Thomas

last: Clark

first: Neil

last: Henderson

first: P

last: Boudinot

first: Samuel

last: Martin

first: D

middle: J

last: Macqueen


title: Decrypting the role of HSP90α and β isoforms to overcome resistance in BCR-ABL1+ leukemia

status: Public on Jul 19 2022

city: Düsseldorf

first: Julian

last: Schliehe-Diecks

address: Moorenstr. 5

country: Germany

institute: Uniklinik Düsseldorf

summary: BCR-ABL1+ leukemia entity still is associated with poor prognosis and new therapies are urgently needed. Heat shock proteins of 90 kDa (HSP90) have been widely studied due to their chaperone function, implicated in stabilizing various oncoproteins, including BCR-ABL1 kinase. However, HSP90 inhibitors (HSP90i) have not entered routinely in clinics, primarily due to the associated resistance via heat shock response (HSR) induction and dose limiting toxicity. Accordingly to study complications coupled with HSP90i, with aim to develop a novel strategy for therapy-refractory BCR-ABL1+ leukemia, genetic knockout (KO) models of cytosolic HSP90α/β isoforms were generated. Notably, β-KO cells displayed augmented HSR, whereas, α-KO cells revealed higher abundance of BCR-ABL1-foci and related hyperactive downstream pro-survival signaling. Although there is a strong compensatory behavior reported among HSP90α and β isoforms in their chaperoning their client proteins, global multi-omics profiling of α- vs. β-KO cells revealed a distinctive phenotype of the regulated signaling networks. Whereas in vivo engraftment of BCR-ABL1+ cells was found significantly reduced upon α-KO, validated by the prolonged overall survival of the mice. Later to investigate the acquired resistance evoked upon pharmacological targeting of HSP90, resistant cells were generated by chronic exposure of distinct HSP90i. Strikingly, clinically advanced (HSP90i) PU-H71-resistant cells acquired amplification and a distinctive mutation (S164F) in the HSP90AA1 locus, with concomitant elevation of HSP90α and ALDH1A1 expression, via activating ribosomal protein S6 kinase. Moreover BCR-ABL1+ cells displayed hypersensitivity toward CDK7i upon α-KO or when applied in combination with HSP90i, noticeably due to elevated CDK7 and androgen receptor (AR) signaling.

overall_design: Triplicates of K562 HSP90 alpha / HSP90 beta knock outs were compared to an empty vector controll & PUH71 resistant K562 were compared to a DMSO treated controll

first: Melina

last: Vogt

first: Niklas

last: Dienstbier

first: Sanil

last: Bhatia


title: Single-nucleus resolution of the adult C. elegans and its application to the mapping of inter-generational response to alcohol exposure [scRNA-seq]

status: Public on Jul 21 2022

first: Yen-Wei

last: Chen

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

summary: Single-cell RNA sequencing technologies have significantly contributed to our understanding of tissue heterogeneity as well as developmental and cell differentiation trajectories. They also provide an opportunity to map an organism’s response to environmental cues with high resolution and identify sensitive tissues and cell types. However, the requirement for cellular integrity during extraction has limited the examination of organs that are syncytial or of cell types, such as neurons, that have significant cellular projections. We developed a mechanical method for single nucleus extraction in C. elegans that, combined with snRNA-seq, identifies a remarkable number of cell types in the adult nematode. Clustering analysis recapitulated established morphological and functional categories as well as the differentiation trajectory of the syncytial germline. Our approach also uncovered novel features of C. elegans biology, such as previously uncharacterized intestinal subpopulations and the up-regulation of X-linked transcripts in the somatic compartment of the hermaphrodite spermatheca. We applied this method to identify the impact of intergenerational exposure to a human-relevant dose of alcohol. We show that parental ethanol exposure causes a highly cell type-specific response in the adult F1 with oocytes, motor neurons, mechanosensory neurons, and neuronal support cells displaying the highest number of differentially expressed genes, the majority of which were downregulated. Cluster-level GO analysis revealed pathways previously not known to be altered by ethanol such as sister chromatid dynamics in the oocyte and autophagy in the uterine epithelium. Together, snRNA-seq provides a powerful approach for the detailed examination of an adult organism physiology.

overall_design: 31 single nuclei C. elegans datasets were generated, divided into 5 batchs, four treatment group (normal, water, 0.5% ethanol, 0.05% ethanol) and two generations (F1 and F3)

first: Patrick

last: Allard

first: Lisa

last: Truong

first: Rio

last: Barrere-Cain


title: Mammalian Methylation Consortium

status: Public on Aug 05 2023

first: Steve

last: Horvath

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

department: Human Genetics

summary: The Mammalian Methylation Consortium aimed to characterize the relationship between cytosine methylation levels and a) species characteristics such as maximum lifespan and b) individual sample characteristics such as age, sex, tissue type. Both supervised machine learning approaches and unsupervised machine learning approaches were applied to the data as described in the citations. To facilitate comparative analyses across species, the mammalian methylation consortium applied a single measurement platform (the mammalian methylation array, GPL28271) to n=15216 DNA samples derived from 70 tissue types of 348 different mammalian species (331 eutherian-, 15 marsupial-, and 2 monotreme species). Most of the CpGs are located in highly conserved stretches of DNA but not all CpGs apply to all species as detailed in the description of the platform, GPL28271 and on https://github.com/shorvath/MammalianMethylationConsortium/.

sample_organism:
Ornithorhynchus anatinus
Tachyglossus aculeatus
Didelphis virginiana
Didelphis marsupialis
Sarcophilus harrisii
Notamacropus agilis
Notamacropus eugenii
Macropus fuliginosus
Macropus giganteus
Osphranter robustus
Osphranter rufus
Tamandua mexicana
Bradypus variegatus
Choloepus hoffmanni
Dasypus novemcinctus
Erinaceus europaeus
Atelerix albiventris
Echinops telfairi
Suncus murinus
Sorex hoyi
Blarina brevicauda
Amblysomus hottentotus
Pteropus poliocephalus
Pteropus hypomelanus
Rousettus aegyptiacus
Artibeus jamaicensis
Phyllostomus hastatus
Desmodus rotundus
Tadarida brasiliensis
Antrozous pallidus
Lemur catta
Varecia variegata
Cheirogaleus medius
Otolemur crassicaudatus
Loris tardigradus
Nycticebus coucang
Perodicticus potto
Callithrix jacchus
Macaca mulatta
Papio hamadryas
Gorilla gorilla
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Canis latrans
Canis lupus familiaris
Lycaon pictus
Vulpes vulpes
Ursus americanus
Martes americana
Mustela putorius furo
Crocuta crocuta
Felis catus
Panthera leo
Panthera tigris
Puma concolor
Zalophus californianus
Odobenus rosmarus divergens
Phoca vitulina
Delphinus delphis
Orcinus orca
Tursiops truncatus
Phocoena phocoena
Delphinapterus leucas
Physeter macrocephalus
Balaenoptera borealis
Balaenoptera musculus
Megaptera novaeangliae
Trichechus manatus
Elephas maximus
Loxodonta africana
Equus grevyi
Equus caballus
Diceros bicornis
Rhinoceros unicornis
Procavia capensis
Orycteropus afer
Sus scrofa
Sus scrofa domesticus
Capreolus capreolus
Cervus elaphus
Odocoileus virginianus
Muntiacus vaginalis
Giraffa camelopardalis
Aepyceros melampus
Bos taurus
Capra hircus
Ovis aries
Tragelaphus oryx
Tragelaphus strepsiceros
Tragelaphus imberbis
Ochotona princeps
Oryctolagus cuniculus
Sylvilagus floridanus
Marmota monax
Tamiasciurus hudsonicus
Cricetulus griseus
Cricetulus longicaudatus
Mesocricetus auratus
Peromyscus leucopus
Peromyscus maniculatus
Meriones unguiculatus
Microtus pennsylvanicus
Ondatra zibethicus
Acomys cahirinus
Cricetomys gambianus
Mus musculus
Mus minutoides
Rattus norvegicus
Rattus rattus
Apodemus sylvaticus
Hystrix cristata
Cavia porcellus
Galea musteloides
Hydrochoerus hydrochaeris
Myocastor coypus
Bathyergus janetta
Bathyergus suillus
Cryptomys hottentotus
Georychus capensis
Heterocephalus glaber
Eulemur coronatus
Eulemur fulvus
Hapalemur griseus
Monodelphis domestica
Nanger granti
Balaena mysticetus
Lagenorhynchus albirostris
Molossus molossus
Nycticeius humeralis
Choloepus didactylus
Elephantulus edwardii
Eptesicus fuscus
Chaetophractus villosus
Macroscelides proboscideus
Vombatus ursinus
Vicugna pacos
Sylvilagus audubonii
Propithecus tattersalli
Eulemur macaco
Microcebus murinus
Galago moholi
Nannospalax ehrenbergi
Sciurus carolinensis
Daubentonia madagascariensis
Acinonyx jubatus
Dromiciops gliroides
Eulemur mongoz
Eulemur rubriventer
Chinchilla lanigera
Erethizon dorsatum
Sciurus niger
Oreamnos americanus
Enhydra lutris
Eumetopias jubatus
Sorex cinereus
Suricata suricatta
Hippotragus equinus
Hippotragus niger
Tupaia belangeri
Cavia aperea
Caenolestes fuliginosus
Globicephala macrorhynchus
Phascolarctos cinereus
Apodemus agrarius
Phoca groenlandica
Carollia perspicillata
Ochotona rufescens
Peromyscus eremicus
Peromyscus polionotus
Peromyscus californicus
Ictidomys tridecemlineatus
Tamias striatus
Glaucomys sabrinus
Steno bredanensis
Sorex palustris
Eulemur fulvus collaris
Phodopus campbelli
Lepus americanus
Lepus californicus
Mesoplodon bidens
Tamandua tetradactyla
Cabassous unicinctus
Hylomys suillus
Sylvilagus nuttallii
Urocitellus columbianus
Talpa occidentalis
Myotis myotis
Nyctalus noctula
Jaculus jaculus
Castor canadensis
Aplodontia rufa
Callithrix geoffroyi
Trachypithecus francoisi
Cynopterus brachyotis
Myotis lucifugus
Pipistrellus pipistrellus
Rhinolophus ferrumequinum
Saccopteryx bilineata
Addax nasomaculatus
Antidorcas marsupialis
Kobus megaceros
Chlorocebus sabaeus
Arvicanthis niloticus
Lynx rufus
Plecotus auritus
Ctenomys lewisi
Ctenomys opimus
Ctenomys steinbachi
Sorex minutissimus
Sorex caecutiens
Sorex isodon
Neomys fodiens
Sorex tundrensis
Sorex roboratus
Sorex vagrans
Sorex trowbridgii
Tamias amoenus
Tragelaphus angasii
Nanger dama
Chrysocyon brachyurus
Tragelaphus eurycerus
Tragelaphus spekii
Gazella leptoceros
Nanger soemmerringii
Eudorcas thomsonii
Litocranius walleri
Tupaia tana
Scalopus aquaticus
Equus asinus somalicus
Ceratotherium simum simum
Dipus sagitta
Callospermophilus lateralis
Eidolon helvum
Pteropus rodricensis
Microtus ochrogaster
Tursiops aduncus
Propithecus diadema
Cyclopes didactylus
Okapia johnstoni
Eulemur flavifrons
Equus quagga
Phyllostomus discolor
Mustela altaica
Marmota flaviventris
Parascalops breweri
Tenrec ecaudatus
Callospermophilus saturatus
Alexandromys fortis
Xanthonycticebus pygmaeus
Connochaetes taurinus albojubatus
Napaeozapus insignis
Eozapus setchuanus
Cephalorhynchus commersonii
Neotoma cinerea
Apodemus peninsulae
Cuniculus paca
Myotis brandtii
Myotis nattereri
Phodopus roborovskii
Microtus richardsoni
Elephantulus myurus
Rhabdomys pumilio
Eulemur sanfordi
Tamias townsendii
Rhinopoma hardwickii
Ochotona alpina
Ochotona dauurica
Ochotona hyperborea
Ochotona pallasi
Pteropus vampyrus
Apodemus uralensis
Cavia tschudii
Condylura cristata
Tamiasciurus douglasii
Myotis thysanodes
Myotis yumanensis
Pteropus pumilus
Neophoca cinerea
Zapus princeps
Scapanus orarius
Neurotrichus gibbsii
Tolypeutes matacus
Rhombomys opimus
Hemiechinus auritus
Myotis vivesi
Orientallactaga sibirica
Mops pumilus
Tupaia longipes
Rhynchonycteris naso
Rhinolophus alcyone
Myotis evotis
Paraechinus aethiopicus
Microtus guentheri
Gerbillus nanus
Meriones rex
Meriones libycus
Smutsia temminckii
Hemicentetes semispinosus
Setifer setosus
Tupaia gracilis
Ellobius talpinus
Cricetulus barabensis
Microgale cowani
Mirza zaza
Alticola semicanus
Dendrohyrax arboreus
Suncus varilla
Sylvilagus bachmani
Propithecus coquereli
Lasiopodomys mandarinus
Alticola barakshin
Lasiopodomys brandtii
Aonyx cinereus
Neogale vison
Crocidura cyanea
Hipposideros ruber
Alexandromys maximowiczii
Micaelamys namaquensis
Clethrionomys gapperi
Galeopterus variegatus
Sylvilagus brasiliensis
Varecia rubra
Asellia tridens
Galea musteloides leucoblephara
Leptonycteris yerbabuenae
Alexandromys mongolicus
Eulemur rufus
Fukomys damarensis
Nannospalax galili
Cephalorhynchus hectori hectori
Eulemur albifrons
Cephalorhynchus hectori maui
Paraechinus hypomelas
Gerbillus cheesmani
Microgale thomasi
Cervus canadensis
Microgale drouhardi
Notamacropus rufogriseus
Alexandromys oeconomus
Nesogale talazaci
Myodes rufocanus
Nothocricetulus migratorius
Neogale frenata
Sagmatias obliquidens
Stenocranius gregalis

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Cytosine methylation data from the following species and tissues. Subsets of these data are available in other accession numbers: GSE174758, GSE184211, GSE184213, GSE184215, GSE184216, GSE184218, GSE184220, GSE184221, GSE184224, GSE190660, GSE190661, GSE190662, GSE190663, GSE190664, GSE174544, GSE190665, GSE174767, GSE184222, GSE184223, GSE174777, GSE174778, GSE173330, GSE164127, GSE147002,GSE147003, GSE147004.


title: Therapeutic Targeting of Ovarian Cancer Stem Cells Using Estrogen Receptor Beta Agonist

status: Public on Jul 13 2022

first: YI

last: ZOU

summary: We examined the transcriptional changes altered by ERβ agonist LY500307 treatment in ovarian cancer stem cells (OCSCs) by performing global transcriptome analysis. SKOV3-ALDH+ OCSCs were treated with vehicle or LY500307 (5 µM) for 24 h and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that the top pathways altered by LY500307 were related to cell cycle and apoptosis. Functional enrichment using GSEA analysis showed that LY500307-regulated genes showed positive enrichment in the p53 pathway, oxidative phosphorylation, apoptosis and estrogen late response genes, and negative correlation with E2F targets, G2/M checkpoint and mitotic spindle.

overall_design: SKOV3-ALDH+ OCSCs were treated with vehicle or LY500307 (5 µM) for 24 h and the total RNA was isolated using RNeasy Mini Kit (Qiagen, Valencia, CA). Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Yidong


title: CXCL10 promotes vascular permeability upon TNF-induced release from pericytes

status: Public on Jul 01 2022

city: Rotterdam

first: Rutger

middle: Wubbe Willem

last: Brouwer

address: Wytemaweg 80

department: Center for Biomics

country: Netherlands

institute: Erasmus MC

summary: Tumor necrosis factor alpha induces vascular permeability, playing an important role in inflammation. Also, TNF-induced vascular leakage is involved in the increased extravasation of nanoparticle formulated chemotherapeutics improving drug delivery and subsequently tumor response, and we found a positive correlation between the presence of pericytes in the tumor-associated vasculature and TNF-induced leakage. RNA sequencing and pathway analysis of TNF-stimulated versus non-stimulated pericytes and endothelial cells show significant upregulation of several pathways involving interferon regulating pathways with a high expression of CXCL10, also known as Interferon gamma-inducible protein 10 (IP-10) in TNF-stimulated pericytes. In addition, CXCL10 protein production was significantly increased in conditioned medium from TNF-exposed pericytes compared to the other conditions. In our animal studies, we observed that tumor types with high pericyte covered vessels show enhanced permeability when exposed to TNF, which can be blocked with a neutralizing CXCL10 antibody. Vice versa, tumors with vessels low in pericyte number do not respond to TNF, i.e., do not express elevated permeability. Importantly, this lack of pericyte coverage can be compensated by co-administration of CXCL10. Our finding reveals a mechanism where TNF induces CXCL10 release from pericytes, being at the basis of increased permeability and thus vascular leakage.

overall_design: We performed RNA sequencing on TNF- or non-stimulated endothelial cells and pericytes. Differentially regulated genes were determined by comparison of time controlled (12, 24, 72 hours) gene expression in TNF-stimulated pericytes versus the other conditions (i.e. non-stimulated pericytes, TNF-stimulated endothelial cells and non-stimulated endothelial cells).

first: A

last: Seynhaeve

first: H

last: Liu

first: M

last: Priester

last: Valentijn

first: J

last: Van Holten-Neelen

first: R

last: van Brakel

first: W

last: Dik

last: van Ijcken

last: Debets

first: T

last: ten Hagen


title: Identification of Mettl3-dependent m6A-modified mRNAs upon DNA-damage

status: Public on Jul 07 2022

city: Stanford

first: Nitin

last: Raj

address: 269 Campus Drive, CCSR-South, Rm 1240, MC5152

department: Radiation Oncology

institute: Stanford University

summary: The goal of the study was to identify those mRNAs that are m6A-modified in a Mettl3-dependent manner under DNA-damage condition in oncogene-expressing mouse embryonic fibroblasts

overall_design: We performed m6A-eCLIP-seq to identify those Mettl3-dependent m6A RNA modifications occurring after DNA-damage. We utilized oncogene-expressing fibroblasts expressing control shRNAs or shRNAs directed against Mettl3 to acutely knockdown Mettl3, and we treated cells for 6 hours with o,2 ug/ml of doxorubicin before performing m6A-eCLIP-seq.

first: Laura

last: Attardi


title: Single-cell Miniaturized Total RNA-seq (STORM-seq) in cell lines and primary tissues

status: Public on Aug 05 2022

city: Grand Rapids

first: Benjamin

middle: K

last: Johnson

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

summary: Here we introduce STORM-seq, a standardized and generally available approach to profiling total RNA in single cells by miniaturization of the Takara SMART-seq Stranded (SSS) kit. The use of nanoliter-scale reaction volumes allows STORM-seq to efficiently scale to hundreds of high-complexity single cell libraries per run, from dissociated tissues and non-adherent cells, with greater than 99% per cell/library success. The use of ribosomal RNA depletion and random hexamer priming, rather than oligo-dT (poly-A) selection, allows comprehensive, whole-transcriptome analysis in each individual cell. STORM-seq recovers both coding and non-coding transcripts at an equal or greater rate to full volume reactions. Applying the method to cultured K562 cells and primary human fallopian tube epithelial (FTE) cells results in equivalent or better gene detection than manual preparation. Across all transcript biotypes, additional mRNA and lncRNA transcripts are detected beyond SSS or SMART-seq2. STORM-seq libraries from primary human FTE reveal intermediate cell types not observed by other technologies, with clear transitional significance visible upon data integration.  STORM-seq provides a scalable, efficient protocol to recover deep whole transcriptomes from individual cells while minimizing costs.

overall_design:
Optimizing and increasing the throughput of ribo-reduced total single-cell RNA-seq to investigate cellular heterogeneity and the differentiation trajectory in human fallopian tube epithelium
Please note that the raw data files for the primary tissue samples are being uploaded to dbGaP.

first: Mary

last: Rhodes

first: Marc

last: Wegener

first: Pamela

last: Himadewi

first: Kelly

last: Foy

first: Joshua

last: Schipper

first: Rebecca

last: Siwicki

first: Larissa

last: Rossell

first: Emily

last: Siegwald

first: Dave

last: Chesla

first: Rachael

last: Sheridan

first: Marie

last: Adams

first: Hui

last: Shen

first: Timothy

last: Triche Jr


title: sequencing data in multiple cell lines

status: Public on Jun 17 2022

city: Changsha

first: Jiankang

last: Wang

state: Hunan

address: Lushan

institute: School of biology

summary: Here the sequencing data in different cell line.

overall_design: sequencing in multiple cell lines


title: Novel genetic variants of KHDC3L and other members of the subcortical maternal complex associated with Beckwith-Wiedemann syndrome or Pseudohypoparathyroidism 1B and multi-locus imprinting disturbances

status: Public on Jun 02 2022

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

institute: University of Campania "Luigi Vanvitelli"

type: Methylation profiling by genome tiling array

summary:
Beckwith–Wiedemann syndrome (BWS) and Pseudohypoparathyroidism type 1B (PHP1B) are imprinting disorders (ID) caused by deregulation of the imprinted gene clusters located at 11p15.5 and 20q13.32, respectively. In both of these diseases a subset of the patients is affected by multi-locus imprinting disturbances (MLID). In several families, MLID is associated with damaging variants of maternal-effect genes encoding protein components of the subcortical maternal complex (SCMC).
However, frequency, penetrance and recurrence risks of these variants are still undefined. In this study, we screened two cohorts of BWS patients and one cohort of PHP1B patients for the presence of MLID, and analysed the positive cases for the presence of maternal variants in the SCMC genes by whole exome-sequencing and in silico functional studies.
We identified 10 new cases of MLID associated with the clinical features of either BWS or PHP1B, in which segregate 13 maternal putatively damaging missense variants of the SCMC genes.
The affected genes also included KHDC3L that has not been associated with MLID to date.
Moreover, we highlight the possible relevance of relatively common variants in the aetiology of MLID.
Our data further add to the list of the SCMC components and maternal variants that are involved in MLID, as well as of the associated clinical phenotypes.
Also, we propose that in addition to rare variants, common variants may play a role in the aetiology of MLID and imprinting disorders by exerting an additive effect in combination with rarer putatively damaging variants. These findings provide useful information for the molecular diagnosis and recurrence risk evaluation of MLID-associated IDs in genetic counselling.

overall_design: DNA samples extracted from peripheral blood were subjected to methylation profile analysis using Infinium MethylationEPIC 850K Bead Chip and pyrosequencing. We also included 12 individuals as control samples.

last: Pignata

first: Ankit

last: Verma

first: Bruno

last: Mele

first: Maria

last: Monticelli

first: Basilia

last: Acurzio

first: Carlo

last: Giaccari

first: Angela

last: Sparago

middle: V

last: Cubellis

first: Andrea

last: Riccio

first: Flavia

last: Cerrato


title: A subset of late infiltrating neutrophils have a unique transcriptome of alternative activation associated with their pro-regenerative capacity

status: Public on Jun 01 2022

city: Columbus

first: Andrew

last: Sas

state: OH

address: 395 W 12th Ave 7th Floor

department: Neurology

institute: Ohio State University

summary: Recent studies using advanced techniques such as single cell RNA sequencing (scRNAseq), high parameter flow cytometry, and proteomics have revealed that neutrophils are more heterogeneous than previously thought. Unique subsets have been identified in the context of bacterial and parasitic infections, cancer and tissue injury and repair. The diversity of subsets that predominate the neutrophil infiltrate in each of these conditions appears dependent on the type of injury and timing of neutrophil involvement in the disease state. We previously described a subpopulation of immature Ly6Glow neutrophils that accumulate in the peritoneal cavity 3 days following intraperitoneal (i.p.) administration of the fungal cell wall extract, zymosan. In contrast, conventional, mature Ly6Ghi neutrophils dominate the peritoneal infiltrate 4 hours following i.p. zymosan injection. The 3 day Ly6Glow, but not 4 hour Ly6Ghi, neutrophils induce neurite outgrowth of explanted neurons in vitro. Furthermore, they drive axon regeneration in the optic nerve (ON) and spinal cord (SC) when adoptively transferred in proximity to the eye after ON crush injury or SC dorsal column transection, respectively. These pro-regenerative effects are mediated in part, by the production of the growth factors insulin-like growth factor-1 (IGF-1) and nerve growth factor (NGF). In the current study, we expand upon on our previous observations by performing an in-depth characterization of the zymosan-modulated neutrophil subsets through scRNAseq and high parameter flow cytometry. Circulating neutrophils, harvested from unmanipulated mice, were analyzed in parallel as a control. We found that each of the unfractionated neutrophil populations is diverse, composed of multiple distinct clusters. Zymosanmodulated 3-day Ly6Glow neutrophils contain a cluster that expresses neuroprotective growth factors in association with markers of alternative activation. Furthermore, the unfractionated neutrophil populations were analyzed by liquid chromatography/ mass spectrometry for proteomic analysis. This new proteomic data identified a wide variety of proteins and pathways that contribute to the alternative activation state of these pro-regenerative 3 day Ly6Glow neutrophils. Collectively, the data generated by the current study constitute another step towards pinpointing the identity and mechanisms of action of pro-regenerative, neuroprotective neutrophil subsets.

overall_design: 10x Genomics single cell sequencing of mouse Ly6G+ neutrophils isolated 4 hours or 3 days after mice were subjected to i.p zymosan injection as well as whole blood PBMCs from naive mice.

first: A

last: Jerome

first: J

last: Atkinson

last: McVey Moffatt

last: Sepeda

first: B

last: Segal


title: CDK5 inhibition abrogates TNBC stem-cell property and enhances anti-PD-1 therapy

status: Public on Jun 18 2022

city: Nanjing

first: Yuncheng

last: Bei

state: Jiangsu

address: Zhongshan Road No.321

department: Oncology

institute: Nanjing Drum Tower Hospital

summary: Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer that shows high infiltration of cancer stem cells (CSCs), which correlates with poor clinical outcome. Here, we have demonstrated that an aberrant activation of CDK5/pho-PPARg axis associated with TNBC progression closely. CDK5 blockade sufficiently abrogates stemness transformation of TNBC cells, resulting in a significant inhibition of tumor metastatic progression. Moreover, CDK5 inhibitor Rosc attenuates CD44v+ BCSCs, hereby reversing immunosuppressive microenvironment and enhancing anti-PD-1 effects on TNBC. Mechanistically, CDK5/pho-PPARgaxis modulates the ESRP1 degradation via E3 ligase-like activity, leading to CD44 variant (CD44v) expression. Our finding indicates that CDK5 blockade could be a potent strategy to target CSCs in TNBC, and to increase the response to PD-1 blockade in TNBC therapy.

overall_design: mRNA profiles of 4T1 mouse TNBC cells with or without treatment of CDK5 inhibitor, Rosc, were generated by deep sequencing, in triplicate.

last: Cheng

first: Ting

last: Chen

first: Yuxin

last: Shu

first: Ye

last: Yang

first: Nanfei

first: Xinyu

last: Zhou

first: Baorui

last: Liu

first: Jia

last: Wei

first: Qin

first: Wei

last: Zheng

first: Wenlong

last: Zhang

first: Huifang

last: Su

first: Weiguo

last: Zhu

first: Jianguo

last: Ji

first: Pingping

last: Shen


title: Global genomic and proteomic analysis of TNBC cells identifies the critical role of PELP1 in ribosome biogenesis

status: Public on Mar 03 2022

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We examined the mechanisms by which PELP1 regulates TNBC progression. MDA-MB-231 cells were stably transfected with control non-targeted shRNA or PELP1 shRNA, and total RNA was isolated for RNA-seq analysis. Our results demonstrated that PELP1 regulates the expression of Myc, E2F and mTOR targets in TNBC.

overall_design: Total RNA from MDA-MB-231 control-shRNA and PELP1-shRNA cells were isolated using RNeasy mini kit (Qiagen). For whole-genome transcriptome profiling, 2 libraries (3 replicates each for knockdown and control) were generated using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 50 base-pair single-read (50SR) sequencing module.

first: Ratna

last: Vadlamudi

first: Suryavathi

last: Viswanadhapalli

first: Yidong

first: Zhao

last: Lai


title: Epigenetic profiles of chimeric antigen receptor T cells with knockout of PRDM1

status: Public on May 17 2022

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary: Persistence of infused antitumor T cells is one of the essential factors for durable therapeutic response. T cells undergo genome-wide alterations in epigenetic architecture upon repeated antigen encounter, which is inevitably accompanied by progressive T cell differentiation and loss of longevity. In this study, we explored key epigenetic factors associated with terminal T cell differentiation using CRISPR/Cas9-mediated knockout of epigenetic genes in chimeric antigen receptor (CAR)-engineered human T cells and identified PRDM1 as one of the key epigenetic genes regulating T cell differentiation. We compared epigenetic profiles of control and PRDM1-knockout CAR-T cells by ATAC-sequencing analysis.

overall_design: Human CD8+ T cells derived from two different healthy donors were retrovirally transduced with an anti-CD19 CAR gene (FMC63-28z) and the disrupted with PRDM1 using the CRISPR/Cas9 system. The control or PRDM1-knockout CAR-T cells were then stimulated with the CD19+ B-cell acute lymphoblastic leukemia cell line NALM-6 for three times. CD8+ CAR-T cells were isolated after the third stimulation, and epigenetic profiles were analyzed by ATAC sequencing.


title: Transcriptomic profiling of the normal mammalian olfactory mucosa and olfactory neuroblastoma

status: Public on May 05 2022

city: Boston

first: Matthew

middle: Joseph

last: Zunitch

state: MA

address: 150 Harrison Ave

institute: Tufts University

summary: Characterizing olfactory neuroblastoma with respect to normal olfactory mucosal tissue and cell types

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell transcriptomics of the murine olfactory mucosa, single cell transcriptomics of olfactory neuroblastoma, bulk tissue transcriptomics of olfactory neuroblastoma biopsies, and bulk tissue transcriptomics of normal human olfactory mucosal biopsies.


title: Gene expression profiles of chimeric antigen receptor T cells with knockout of epigenetic genes

summary: Persistence of infused antitumor T cells is one of the essential factors for durable therapeutic response. T cells undergo genome-wide alterations in epigenetic architecture upon repeated antigen encounter, which is inevitably accompanied by progressive T cell differentiation and loss of longevity. In this study, we explored key epigenetic factors associated with terminal T cell differentiation using CRISPR/Cas9-mediated knockout of epigenetic genes in chimeric antigen receptor (CAR)-engineered human T cells and identified multiple key epigenetic genes. We analyzed gene expression profiles of CAR-T cells that were knocked out with the specific epigenetic genes by RNA-sequencing.

overall_design: Human CD8+ T cells derived from three different healthy donors were retrovirally transduced with an anti-CD19 CAR gene (FMC63-28z) and stimulated with the CD19+ B-cell acute lymphoblastic leukemia cell line NALM-6 for three times. RNA was collected after the third stimulation, and gene expression profiles were analyzed by RNA sequencing.


title: Transcriptional profile of tumor associated macrophages in High fat diet mouse models

status: Public on Feb 16 2022

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

institute: IRCCS Humanitas Research Hospital

summary: Tumor associated macrophages (TAMs) are correlated with the progression of prostatic adenocarcinoma (PCa) but are still poorly described in this context. Here we applied high dimensional single-cell RNA-seq to profile the transcriptional landscape of TAMs in PCa. We identified a subset of tumor infiltrating macrophages that shows a dysregulation in transcriptional pathways associated with lipid metabolism. In human and mouse models of PCa this subset of macrophages expresses the scavenger receptor MARCO and is characterized by accumulation of lipid droplets. We identified a gene signature derived from MARCO-expressing TAMs that correlates with PCa progression and is associated with shorter disease-free survival.  Mechanistically, we observed that lipid accumulation in TAMs is promoted by the secretome of cancer cells. Lipid-loading confers on tumor-conditioned macrophages the capability to promote cancer cell migration mediated by CCL6. Importantly, administration of high fat diet to tumor-bearing mice raises lipid accumulation in TAMs and affects their transcriptional profile. Finally, we demonstrate that the accumulation of lipids in macrophages is dependent on MARCO expression and we show that MARCO blockade hinders tumor growth and invasiveness in models of advanced PCa. Our findings provide evidence that lipid-loaded TAMs represent a new therapeutic target in PCa.

overall_design: Tota RNA-seq of tumor associated macrophage sorted by prostate tissue in mouse models of high fat diet

first: R

last: Carriero

first: M

last: Masetti

first: D

last: Di Mitri


title: Tumor immunogenomic features determine outcomes in metastatic colorectal cancer patients treated with standard-of-care combinations of bevacizumab and cetuximab

city: Chapel Hill

first: Federico

last: Innocenti

state: North Carolina

address: 120 Mason Farm  Road, CB7361

department: Eshelman School of Pharmacy

institute: University of North Carolina at Chapel Hill

summary: CALGB/SWOG 80405 was a randomized phase III trial in first-line mCRC patients treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on OS. Primary tumors (N=554) were profiled by RNAseq. Immune signatures of macrophages, lymphocytes, TGF-β, INF-γ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8+ T cells, resting and activated memory CD4+ T cells, M0 and M2 macrophages, and activated mast cells were measured. Increased M2 macrophage score (HR 6.30, 95% CI 3.0-12.15) and TGF-β signature expression (HR 1.35, 95% CI 1.05-1.77) were associated with shorter OS. Increased scores of plasma cells (HR 0.55, 95% CI 0.38-0.87) and activated memory CD4+ T cells (HR 0.34, 95% CI 0.16-0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0-1 beneficial features associated with longer OS, and the median (95% CI) OS decreased from 42.5 (35.8-47.8), to 31.0 (28.8-34.4), 25.2 (20.6-27.9), and 17.7 (13.5-20.4) months respectively (p-value 3.48e-11). New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.

overall_design: RNA-seq of 469 primary mCRC tumors, metastatic samples, or tumors of unknown origin

first: Akram

last: Yazdani

first: Naim

last: Rashid

first: Xueping

last: Qu

first: Fang-Shu

last: Ou

first: Scott

last: Van Buren

first: Monica

last: Bertagnolli

first: Omar

last: Kabbarah

first: Charles

last: Blanke

first: Alan

middle: P

last: Venook

first: Heinz-Josef

last: Lenz

first: Benjamin

middle: G

last: Vincent


title: scRNAseq muscle stem cells

status: Public on Mar 14 2022

city: West Lafayette

first: Shihuan

last: Kuang

state: IN

address: 270 S. Russell Street

institute: Purdue University

summary: Single-cell RNA sequencing muscle stem cells from non-injured, 5, and 10 days post injury

overall_design: Muscle stem cells were isolated from non-injured, 5 and 10 day post injury skeleta tibalis anterios mucsle using fluroescence activated cell sorting. n=3 male mice combined per sample; Pax7GkCre;sfGFP mice

first: Stephanie

middle: N

last: Oprescu

first: Feng

last: Yue


title: investigation of methylation level change of Endothelial cells and Magnesium-based alloy treated Endothelial cells

status: Public on Feb 27 2022

city: Chengdu

first: hongchi

last: Yu

state: Sichuan

address: No.24 South Section 1, Yihuan Road

institute: Sichuan University

summary: We have completed the Arraystar Human m6A-mRNA&lncRNA Epitranscriptomic microarray analysis of the samples to validate the modulating role of Magnesium-based alloy on methylation of inflammatory genes.

overall_design:
two samples. Endothelial cells used as control and Magnesium-based alloy treated Endothelial cells
Please note that the experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as though they are single channel (Cy3 and Cy5 signals are calculated). Thus, two sample records were created for each experiment and the raw data file is linked to the corresponding IP_Cy5 sample records.

first: Hongchi

first: Rifang

last: Luo


title: Single-cell transcriptome sequencing of macrophages in acute kidney injury

status: Public on Feb 09 2022

city: Beijing

first: Weijian

last: YAO

state: Beijing

address: No. 8 Xishiku Street, Xicheng District

department: Renal division

institute: Peking university first hospital

summary: We uesd single-cell transcriptome sequencing technology to sequence the mononuclear phagocytes in the mice kidney, blood and spleen after acute kidney injury, and comprehensively describe characteristics of mononuclear phagocytes.

overall_design: We used a unilateral ischemia-reperfusion renal injury (uIRI) 45minAKI model. The mouse kidney, spleen, and peripheral blood were taken 1 and 3 days after surgery, and the kidney, spleen and peripheral blood of normal mice were used as controls.  Mononuclear phagocytic cells were sorted by  FACS  and then performed single cell  transcriptome sequencing. 6 mice at each time point.

last: Yao

first: Ying

last: Chen

first: Zehua

last: Li

first: Li

last: Yang


title: Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism [WGS]

status: Public on Jan 16 2022

city: Davis

first: Janine

last: LaSalle

state: CA

address: Medical Microbiology and Immunology

institute: UC Davis

summary: Most autism spectrum disorder (ASD) cases involve complex genetics interacting with perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. Here we used whole genome bisulfite sequencing (WGBS) in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene in a co-methylated block at 22q13.33. Differentially methylated region (DMR) analysis identified 139 DMRs common to ASD in placental samples, including a high-confidence 118 kb hypomethylated block at 22q13.33 that replicated in two additional cohorts and identified the novel transcript NHIP as neuronal hypoxia inducible, placenta associated (gene name approved by HGNC). NHIP characterized by high expression in brain, increased expression following neuronal differentiation or hypoxia in vitro, and minimal expression in ASD placenta. Transient NHIP overexpression in cell lines increased cellular proliferation and altered expression of genes regulating synapses and neurogenesis in response to hypoxia, significantly overlapping with NHIP-associated transcript levels in ASD brain and known ASD risk genes. A common Alu insert near a fetal brain enhancer correlated with NHIP placental and brain expression levels and ASD risk, demonstrating a common genetic influence on DNA methylation levels. Together, these results demonstrate a novel environmentally-responsive ASD risk gene relevant to brain development in a hitherto uncharacterized region of the human genome.

overall_design: WGBS, WGS, RNAseq on brain, and cell

first: Yihui

last: Zhu


title: Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism [WGBS]

type: Methylation profiling by high throughput sequencing


title: Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism [RNA-seq]


title: Differential LncRNA/mRNA expression profiling and functional network analyses in BMP2 deletion of mouse dental papilla cells

status: Public on Jan 12 2022

first: YI

last: ZOU

state: TX

summary: We examined the transcriptional changes of the dental papilla mesenchymal cells of Bmp2 floxed/floxed and knock out mice by performing global transcriptome analysis. Total RNAs were isolated from the Bmp2 floxed/floxed and knock out cells for 8h, 48h and 72h and were utilized for RNA-seq. Our results showed that different gene expression of coding RNAs and non-coding RNAs was observed and involved in cell cycle, transcriptional regulation and developmentally relevant signaling pathways.

overall_design: Total RNAs were isolated from the Bmp2 floxed/floxed and knock out mouse dental papilla cells cultured for 8h, 24h, 48h and 72h. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000. The combined raw reads were aligned to UCSC mm9 by Tophat2. Genes and Long_noncoding regions were annotated and quantified by HTSeq-DESeq pipeline.

first: Shuo

first: Yi

last: Zou

last: Wang


title: Gene expression changes in Laccaria bicolor mycelium grown under different nutritional conditions

status: Public on Dec 15 2021

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

summary: Illumina  technology was used to generate mRNA profiles of Laccaria bicolor mycelium grown under different nutrien conditions.  Total RNA was extracted.TruSeq mRNA Stranded libraries were constructed and   and  sequenced (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France).    Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and   aligned to the L. bicolor v2 reference transcripts available at   the JGI database  https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8.

overall_design: mRNA profiles of Laccaria bicolor grown under different nutrient conditions were generated  by Illumina HiSeq 3000 (2x150bp). Three biological replicates were sequenced.

first: Joske

last: Ruytinx

first: Sebastian

last: Wittulsky

first: Maíra

last: de Freitas Pereira

first: Francis

last: Martin