title: Efficacy of novel agents against cellular models of familial platelet disorder with myeloid malignancy (FPD-MM). [scRNA-Seq]

city: Houston

first: Xiaoping

last: Su

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: Germline, mono-allelic mutations in RUNX1 cause familial platelet disorder (RUNX1-FPD) that evolves into myeloid malignancy (FPD-MM): MDS or AML. FPD-MM commonly harbors co-mutations in the second RUNX1 allele and/or other epigenetic regulators. Here we utilized patient-derived (PD) FPD-MM cells and established the first FPD-MM AML cell line (GMR-AML1). GMR-AML1 cells exhibited active super-enhancers of MYB, MYC, BCL2 and CDK6, augmented expressions of c-Myc, c-Myb, EVI1 and PLK1 and surface markers of AML stem cells. In longitudinally studied bone marrow cells from a patient at FPD-MM vs RUNX1-FPD state, we confirmed increased chromatin accessibility and mRNA expressions of MYB, MECOM and BCL2 in FPD-MM cells. GMR-AML1 and PD FPD-MM cells were sensitive to homoharringtonine (HHT or omacetaxine) or mebendazole-induced lethality, associated with repression of c-Myc, EVI1, PLK1, CDK6 and MCL1. Co-treatment with MB and the PLK1 inhibitor volasertib exerted synergistic in vitro lethality in GMR-AML1 cells. In luciferase-expressing GMR-AML1 xenograft model, MB, omacetaxine or volasertib monotherapy, or co-treatment with MB and volasertib, significantly reduced AML burden and improved survival in the immune-depleted mice. These findings highlight the molecular features of FPD-MM progression and demonstrate HHT, MB and/or volasertib as effective agents against cellular models of FPD-MM.

overall_design: Single cell RNA Seq (scRNA-Seq) of a germline mutant Runx1 expressing AML treated with homoharringtonine for 16 hours.

first: Warren

last: Fiskus

first: Kapil

middle: N

last: Bhalla


title: Efficacy of novel agents against cellular models of familial platelet disorder with myeloid malignancy (FPD-MM). [ATAC-Seq]

status: Public on Feb 01 2024

state: Texas

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Paired end ATAC Seq of leukemia cell lines from germline mutant Runx1 expressing AML treated with homoharringtonine or mebendazole for 16/24 hours.


title: Efficacy of novel agents against cellular models of familial platelet disorder with myeloid malignancy (FPD-MM). [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27Ac in germline mutant Runx1 patient-derived AML cells.


title: Efficacy of novel agents against cellular models of familial platelet disorder with myeloid malignancy (FPD-MM).

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Infrapatellar fat pad adipose tissue-derived macrophages displays a predominant CD11c+CD206+ phenotype and expresses genotypes attributable to key features of OA pathogenesis

city: Bangkok

first: Rangsima

last: Reantragoon

address: 1873 Rama 4 Road

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

summary: In knee osteoarthritis (OA), macrophages are the most predominant immune cells that infiltrate synovial tissues and IPFPs. Both M1 and M2 macrophages have been described, but their role in OA have not been fully investigated. Therefore, we investigated macrophage subpopulations in IPFPs and synovial tissues of knee OA patients and their correlation with disease severity, examined their transcriptomics and tested for factors that influenced their polarization.

overall_design: 42 samples overall from knee OA patients were used to study the gene expression profile of macrophages. One pooled sample of macrophages isolated from an infrapatellar fat pad was obtained from 14 patients. Three pooled samples were utilized in this study.

first: Patchanika

last: Hengtrakool


title: Efficacy of novel agents against cellular models of familial platelet disorder with myeloid malignancy (FPD-MM). [Stranded mRNA-Seq]

overall_design: Paired end RNA-Seq of a leukemia cell line treated with homoharringtonine or mebendazole for 16/24 hours.


title: Fine tuning of CpG spatial distribution with DNA origami  for improved cancer vaccination

city: Boston

first: Yang

last: Zeng

address: 360 Longwood Avenue

institute: Dana Farber Cancer Institute

summary: Multivalent presentation of ligands often enhances receptor activation and downstream signaling. DNA origami offers precise nanoscale spacing of ligands, a potentially useful feature for therapeutic nanoparticles. Here, we use a square block DNA origami platform to explore the importance of spacing of CpG oligonucleotides. CpG engages Toll-like receptors and thereby acts to activate dendritic cells. Through in vitro cell-culture studies and in vivo tumor-treatment models, we demonstrate that square blocks induce Th1 immune polarization when CpG is spaced at 3.5 nm. We observe that this DNA origami vaccine enhances DC activation, antigen cross-presentation, CD8+ T cell activation, Th1-polarized CD4+ activation and natural killer cell activation. The vaccine also synergizes effectively with anti-PD-L1 for improved cancer immunotherapy in melanoma and lymphoma models and induces long-term T cell memory. Our results suggest that DNA origami may serve as a platform for controlling adjuvant spacing and co-delivering antigens in vaccines.

overall_design: The immature BMDCs were treated with different vaccines for 1 day and collected by TRIzol (Invitrogen). The samples were send to Genewiz for RNA sequencing.


title: Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (csRNA-seq)

city: Cerdanyola del Vallès

first: Julia

middle: I.

last: Qüesta

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

type: Non-coding RNA profiling by high throughput sequencing

summary: Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer  RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.

overall_design: Capped-small RNA sequencing (csRNA-seq) from seeds and early germinating Arabidopsis thaliana plants.

first: Benjamin

middle: J

last: Tremblay

first: Cristina

middle: P

last: Santini

first: Yajiao

last: Cheng

first: Xue

last: Zhang

first: Stefanie

last: Rosa

middle: I


title: Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (ATAC-seq)

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) from seeds and early germinating Arabidopsis thaliana plants.


title: RNA-seq analysis of S16 Schwann cells treated with siRNA for Nr2f1/Nr2f2 (CoupTFI/CoupTFII)

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: In a previous study, we had compared SOX10-bound regulatory elements in Schwann cells and oligodendrocytes, and we identified a specific enrichment for nuclear receptor motifs at SOX10 binding sites in Schwann cells. We initially focused on NR2F1 and NR2F2 (CoupTF1/CoupTF2) since they are expressed from neural crest through Schwann cell maturity, and found that knockdown of nuclear receptors Nr2f1 and Nr2f2 in primary Schwann cells downregulated genes such as Myelin Basic Protein (Mbp) and Desert Hedgehog (Dhh). In this study, we have elucidated a NR2F-regulated target gene network in Schwann cells, which revealed enrichment for non-myelinating Schwann cell genes. Cut&Run assays in S16 Schwann cells revealed novel, genome-wide binding sites of NR2F1/2 and downstream transcription factors, Retinoid X Receptor (RXRG) and TEA-Domain factor (TEAD1).

overall_design: RNA-seq analysis of S16 Schwann cells treated with control and Nr2f1/Nr2f2 siRNA

first: Raghu

last: Ramesh

first: Camila

last: Lopez-Anido


title: Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.


title: Optimization of Tissue Digestion Methods for Characterization of Photoaged Skin by Single Cell RNA Sequencing Reveals Preferential Enrichment of T Cell Subsets

city: Portland

first: Rosalyn

middle: M

last: Fey

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: Oregon Health & Science University

summary: Healthy human skin tissue is often used as a control for comparison to diseased skin in patients with skin pathologies, including skin cancers or other inflammatory conditions such as atopic dermatitis or psoriasis. Although non-affected skin from these patients is a more appropriate choice for comparison, there is a paucity of studies examining such tissue. This lack is exacerbated by the difficulty of processing skin tissue for experimental analysis. In addition, choosing a processing protocol for skin tissue which preserves cell viability and identity while sufficiently dissociating cells for single-cell analysis is not a trivial task. Here, we compare three digestion methods for human skin tissue, evaluating the cell yield and viability for each protocol. We find that the use of a sequential dissociation method with multiple enzymatic digestion steps produces the highest cell viability. Using single-cell sequencing, we show this method results in a relative increase in the proportion of non-antigen-presenting mast cells and CD8 T cells as well as a relative decrease in the proportion of antigen-presenting mast cells and KYNU+ CD4 T cells. Overall, our findings support the use of this sequential digestion method on freshly processed human skin samples for optimal cell yield and viability.

overall_design: Surgically resected human skin tissue for single-cell sequencing was digested using one of two protocols prior to bead column isolation of CD45+ cells, and CD45+ and CD45- fractions were analyzed by single-cell RNA sequencing and protein profiling.

first: Terri

last: Clister

first: Zachary

middle: R

last: Garrison

first: Cristian

middle: D

last: Valenzuela

first: Anna

last: Bar

first: Justin

last: Leitenberger

first: Rajan

last: Kulkarni


title: Function of CD44 in white adipose tissue

city: Nantong

first: Jinyu

last: Ma

address: 19 Qixiu Road, Nantong 226001, China.

country: China

institute: Nantong University

summary: Background CD44 is a transmembrane protein, which plays an essential role for transducing extracellular stimuli into intracellular signaling cascades especially in cancer cells. Recent studies have shown that CD44 may contribute to metabolic regulation. However, whether and how CD44 affects adipocyte differentiation in white adipose tissue (WAT) remain unclear. Wild type (WT) and CD44 knockout (KO) mice were fed with high-fat diet to induce obesity. eWAT from mice were then harvested for RNA-seq

first: Yuting

last: Wu

first: Runze

first: Cheng

last: Sun


title: Xist ribonucleoprotein particles promote female sex-biased autoimmunity.

city: Stanford

first: Diana

middle: Remy

last: Dou

state: CA

address: 269 Campus Drive, CCSR 2130

institute: Stanford University


title: Xist ribonucleoprotein particles promote female sex-biased autoimmunity [10X multi-ome]

summary: Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long noncoding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex, comprised of numerous autoantigenic components, is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multiorgan pathology in pristane-induced model of lupus than wild-type males. Xist expression in males reprogrammed T and B cell population and chromatin states to more resemble wild type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.

overall_design:
SJL/J WT or heterozygous for the transgene of a non-silencing, doxycycline-inducible mutant of Xist (tgXist) inserted on Chr11 were injected at 8-10 weeks of age with 0.5 mL pristane or PBS (injection control), fed water with or without doxycycline, and spleens harvested at 16 weeks.
Spleens were mechanically dissociated and isolated by FACS for viable (7-AAD-) CD45+ cells (SJL/J). The 10X genomics multiome ATAC+ gene expression kit was used to construct libraries from viably sorted cells.

first: Li

last: Rui

first: Howard

middle: Y

last: Chang


title: A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: The common oral microbe Fusobacterium nucleatum has recently gained attention when it was found to colonize tumors throughout the human body. Fusobacteria are also interesting in regard to bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. Here, to search for alternate sRNA-associated RBPs in F. nucleatum, we performed a systematic mass spectrometry analysis of proteins that copurified with 19 different sRNAs. Our approach recovered a 6S RNA-RNA polymerase complex in this species and discovered high enrichment of the KH domain proteins KhpA and KhpB with almost any tested sRNA, including the σE-dependent sRNA FoxI, a regulator of several envelope proteins. KhpA/B act as a dimer to bind sRNAs with low micromolar affinity and influence the cellular stability of several of their targets. RNA-seq analysis and cell biological assays suggest that KhpA/B have several physiological functions, including a strong requirement for ethanolamine utilization. Our RBP search and discovery of KhpA/B as major RBPs in F. nucleatum are important first steps in identifying key players of post-transcriptional control at the root of the bacterial phylogenetic tree.

sample_organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

overall_design: Gene expression was evaluated for F. nucleatum during the mid-exponential phase and stationary phase. For this the deletion strains of KhpA and KhpB were compared to the WT strain in triplicate. For RIP-seq, enriched RNA on either KhpA::FLAG or KhpB::FLAG were compared to the control strain in triplicate.

first: Yan

last: Zhu

first: Valentina

last: Cosi

first: Jörg

last: Vogel


title: Xist ribonucleoprotein particles promote female sex-biased autoimmunity [bulk RNA-seq]

overall_design:
C57BL6/J mice WT or heterozygous for the transgene of a non-silencing, doxycycline-inducible mutant of Xist (tgXist) inserted on Chr11 were injected at 12-14 weeks of age with 0.5 mL pristane or PBS (injection control), fed water with or without doxycycline, and spleens harvested at 52 weeks post-injection.
Spleens were mechanically dissociated and isolated by FACS for viably CD4+ T-cells (C57BL/6J) or CD45+ cells (SJL/J). Bulk OMNI ATAC-seq and RNA-seq were performed on the C57BL/6J cells while the 10X genomics multiome was used to construct libaries from SJL/J cells.


title: Anti-aging and Rejuvenating Effects and Potential Mechanism of Dead Sea Water in Skin

city: Shanghai

first: Xiaojuan

last: Yan

address: Guiping Road

institute: Fosun Jinmei Cosmetics

summary:
OBJECTIVE: External environmental stressors and internal factors significantly impact the skin by causing inflammation, aging, reduced immunity, and other adverse responses. Dead Sea Water (DSW) is well known for its dermatological benefits and has been widely used in dermatological therapy and skincare (e.g. psoriasis, atopic dermatitis and photoaging). However, the anti-aging and rejuvenating effects of DSW and the related biological pathways involved, which have attracted increasing attention, remain to be fully understood. The aim of this study is to investigate the anti-aging and rejuvenating effects and to probe to explore the related potential biological mechanisms of DSW under different environmental conditions.
METHODS: Using in vitro human dermal cells and reconstructed skin models, the effects of DSW treatment on the extracellular matrix (ECM) components and the morphological changes at the dermal-epidermal junction (DEJ) were investigated. RNA sequencing (RNA-seq) analysis of human dermal fibroblast models after DSW treatment was performed to explore the potential mechanisms of action of DSW under normal and UV stress conditions.
RESULTS: The novel findings in this work present the biological functions of DSW, including procollagen-1 and elastin secretion, hemidesmosome increase, and the epidermal basal cell regeneration. In addition, GO, KEGG, and Reactome analysis results reveal the activation of pathways related to ion transmembrane transporter activity, ECM component biosynthesis, senescence-associated secretory phenotype (SASP), DNA repair, and autophagy, which are associated with the anti-aging activities of DSW.
CONCLUSION: Our work provides new perspectives for understanding the anti-aging and rejuvenating effects and mechanisms of DSW. The new findings also provide a theoretical basis for further development of age-related strategies.

overall_design: non-UV group: Control , 0.02% Osmoter treatment, 0.06% Osmoter treatment; UV-group: Control , UV group, UV+0.02% Osmoter treatment, UV+0.06% Osmoter treatment.

first: Shujun

last: Cheng

first: Qian

last: Ba

first: Junzhuang

first: Kanghui

last: Zhou

first: Xijun

last: Bao

first: Xiufang


title: Mode of Action Studies on New Compounds with Leishmanicidal Activity, Through Functional Genomics Approach

city: Karachi

first: Ishtiaq

middle: Ahmad

last: Khan

state: SIndh

address: University Road

department: Dr. Panjwani Center for Molecular Medicine and Drug Research

country: Pakistan

institute: University of Karachi

summary: Leishmaniasis affects mainly the poorest population of the third world. Among visceral and cutaneous leishmaniasis (VL and CL, respectively), visceral leishmaniasis is the deadliest parasitic disease. There are no vaccines against leishmaniasis and the chemotherapeutic agents currently used are also insufficient. Pentavalent antimonials are being used for the effective treatment of Leishmaniasis.  In this study, we characterized compounds with leishmanicidal activity, and determined its mode of action through the whole transcriptome analyiss. The Lesihmania strains were treated with previously identified selected anti-leishmanial compounds in promastigotes cultures on M199 medium (supplemented with L-glutamine, 10% heat-inactivated fetal bovine serum, 0.25% hemin, 40 mM NaHCO3, 100μM adenine, 40 mM HEPES, 100 U/mL penicillin and 100μg/mL streptomycin). Following the total RNA isolation, RNA-seq was performed using the Illumina NextSeq500 system. The genes expression profiling in the treated and control samples were determined using the standard bioinormatics tools, and then compared statistically.

overall_design: To find the mode of action of our already reported anti-leishmanial compounds, we performed whole transcriptome analysis of the untreated promastigotes and treated promastigotes.


title: Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation

city: Atlanta

first: Anita

middle: H.

last: Corbett

state: Georgia

address: 1510 Clifton Road

department: Biology

institute: Emory University

summary: The RNA exosome is an evolutionarily conserved exoribonuclease complex that consists of a 3-subunit cap, a 6-subunit barrel-shaped core, and a catalytic base subunit. Missense mutations in genes encoding structural subunits of the RNA exosome cause a growing family of diseases with diverse pathologies, collectively termed RNA exosomopathies. The disease symptoms vary and can manifest as neurological defects or developmental disorders. The diversity of the RNA exosomopathy pathologies suggests that the different missense mutations in structural genes result in distinct in vivo consequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection of in vivo models using budding yeast by introducing pathogenic missense mutations in orthologous S. cerevisiae genes. We then performed a comparative RNA-seq analysis to assess broad transcriptomic changes in each mutant model. Three of the mutant models rrp4-G226D, rrp40-W195R and rrp46-L191H, which model mutations in the genes encoding structural subunits of the RNA exosome, EXOSC2, EXOSC3 and EXOSC5 showed the largest transcriptomic differences. Further analyses revealed shared increased transcripts enriched in translation or ribosomal RNA modification/processing pathways across the three mutant models. Studies of the impact of the mutations on translation revealed shared defects in ribosome biogenesis but distinct impacts on translation. Collectively, our results provide the first comparative analysis of several RNA exosomopathy mutant models and suggest that different RNA exosomopathy mutations result in in vivo consequences that are both unique and shared across each variant, providing more insight into the biology underlying each distinct pathology.

overall_design: RNA-seq analysis of biological triplicates of budding yeast RNA exosome mutant cells (rrp4-G226D, rrp40-S87A, rrp40-W195R, rrp45-I15P, rrp46-Q86I, rrp46-L127T, rrp46-L191H, rrp6∆) and budding yeast RNA exosome control cells (RRP4, RRP40, RRP45, RRP46, RRP6).

first: Maria

middle: C

last: Sterrett

first: Lauryn

middle: A

last: Cureton

first: Lauren

last: Cohen

first: Ambro

last: van Hoof

first: Sohail

last: Khoshnevis

first: Milo

middle: B

last: Fasken

middle: H

first: Homa

last: Ghalei


title: Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition (RNA-seq)

first: Julia

last: Qüesta

overall_design: RNA-seq from seeds and early germinating Arabidopsis thaliana plants.

first: Benjamin

last: Tremblay

first: Cristina

last: Santini

first: Yajiao

first: Xue

last: Zhang

first: Stefanie

last: Rosa


title: Umbrella Cells, Bladder Uroepithelial Cells that Exhibit Senescence Features Throughout the Mouse Lifespan, Are Not Depleted by Senolytics

city: Farmington

first: Dylan

last: Baker

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

summary: Lower urinary tract dysfunction (LUTD) increases with aging. Ensuing symptoms including incontinence greatly impact quality of life, isolation, depression, and nursing home admission. The aging bladder is hypothesized to be central to this decline, however, it remains difficult to pinpoint a singular strong driver of aging-related bladder dysfunction. Many molecular and cellular changes occur with aging, contributing to decreased resilience to internal and external stressors, affecting urinary control and exacerbating LUTD. In this study, we examined whether cellular senescence, a cell fate involved in the etiology of most aging diseases, contributes to LUTD. We found that umbrella cells (UCs), luminal barrier uroepithelial cells in the bladder, show senescence features over the mouse lifespan, identifying a novel non-aging related senescent cell population. While these senescent UCs may help maintain the blood-urine barrier, a novel example of beneficial senescence, they could also contribute to the generation of urothelial cancers and LUTD (antagonistic pleiotropy). These senescent UCs were not eliminated by the senolytic combination of Dasatinib and Quercetin, thus ensuring an intact blood-brain barrier when these agents are used in humans. We also tested the effect of a high fat diet and senescent cell transplantation on bladder function and showed that both models cause similar cystometric changes as natural aging in mice, with no effect of senolytics on HFD-induced changes. These findings illustrate the heterogeneity of cellular senescence in varied tissues, highlighting the importance of considering the safety of barrier cells in the bladder and possibly elsewhere during development and testing of future senolytics.

overall_design: RNAseq was done on whole mouse bladders from young (2 months), middle aged (10 months) and old (26 months) female C57BL/6 mice  and from old female mice treated with water, vehicle (60% Phosal 50 PG, 30% polyethylene glycol 400, 10% ethanol) , or D+Q (5mg/kg/day dasatinib and 50mg/kg/day quercetin)  once a month for 3 consecutive days from 21 to 26 months by oral gavage. Total RNA was extracted from whole bladders for RNAseq. 4-6 bladders per age/condition were run.

first: Iman

last: Al-Naggar

first: George

last: Kuchel

first: Ming

last: Xu


title: The renal capsule, a vibrant and adaptive cell environment of the kidney in homeostasis and aging

city: South San Francisco

first: Andrey

last: Shaw

state: California

address: 1 DNA Way

institute: Genentech


title: Development of serum cell-free miRNA panel for identification of girlish central precocious puberty and premature thelarche

city: Suzhou

first: Yihang

last: Shen

state: Jiangsu

address: 2666 Ludang Road

institute: Suzhou Ninth People's Hospital

summary: Seek and verify the effectiveness of a subset of cell-free miRNA to identify CPP and PT

overall_design: Total 88 subjects including 28 cases of CPP, 37 cases of PT, as well as 23 cases of normal control girls were enrolled as a training cohort. Serum cell-free miRNA was isolated and sequenced.


title: Xist ribonucleoprotein particles promote female sex-biased autoimmunity [bulk ATAC-seq]

first: Diana

last: Dou

overall_design:
C57BL6/J mice WT or heterozygous for the transgene of a non-silencing, doxycycline-inducible mutant of Xist (tgXist) inserted on Chr11 were injected at 12-14 weeks of age with 0.5 mL pristane or PBS (injection control), fed water with or without doxycycline, and spleens harvested at 52 weeks post-injection.
Spleens were mechanically dissociated and CD4+ cells were isolated from freshly dissociated mouse spleen using the EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, 19852). Freshly isolated CD4+ cells were prepared using the Omni-ATAC protocol to generate ATAC-seq libraries.

first: Howard

last: Chang


title: Transcriptome profiles of malignant peritoneal mesotheliomas of rats induced by multiwalled carbon nanotubes (MWCNTs)  and amosite asbestos

city: Hannover

first: Stella Marie

last: Reamon-Buettner

address: Nikolai-Fuchs Strasse1

department: Preclinical Pharmacology & In Vitro Toxicology

institute: Fraunhofer-ITEM

summary:
Malignant mesothelioma is an aggressive cancer that often originates in the pleural and peritoneal mesothelium. Exposure to asbestos is a frequent cause. But studies in rodents showed that certain multiwalled carbon nanotubes (MWCNTs) can induce malignant mesotheliomas. This study aimed to understand molecular pathways leading to the development of malignant mesotheliomas induced by MWCNTs and amosite asbestos in Wistar rats.
Using Affymetrix  microarrays, we carried out genome-wide transcriptome analysis on malignant peritoneal meosotheliomas induced by MWCNTs and amosite asbestos. The transcriptome  of MWCNTs and amosite asbestos-induced mesotheliomas exhibited commonalities, but also differences pertaining to differentially-expressed genes (DEGs), regulated canonical pathways, and molecular functions.

overall_design: Malignant mesotheliomas were induced by peritoneal treatments of MWCNTs and amosite asbestos in Wistar rats. Tumor and control peritoneal tissues were part of an in vivo study to determine carcinogenic effects of various MWCNTs (Rittinghausen et al 2014, Particle and fibre toxicology 11, 59). Genome-wide transcriptome analysis using Affymetrix microarrays was undertaken in n =11 tumors from different rats induced by MWCNTs and amosite asbestos, and n = 3 control peritoneal tissues.

first: Stella


title: Loss of alkyladenine DNA glycosylase alters gene expression in developing mouse brain and leads to reduced anxiety and increased exploratory behavior

city: Trondheim

first: Barbara

last: van Loon

address: Erling Skjalgsons gate 1

country: Norway

institute: Norwegian University of Science and Technology

summary: Neurodevelopment is a tightly coordinated process, in which genome is exposed to spectra of endogenous agents at different stages of differentiation. Increasing body of evidence suggests that DNA damage is an important feature of developing brain, tightly linked to gene expression programs and neuronal activity. Some of the most frequent DNA damage includes changes to DNA bases, recognized by DNA glycosylases and repaired through base excision repair (BER). The only mammalian DNA glycosylase able to remove frequent alkylated DNA based is alkyladenine DNA glycosylase (Aag, aka Mpg). Recently we showed that, besides participation in DNA repair, AAG affects expression of neurodevelopmental genes in human cells. Aag was further proposed to act as reader of epigenetic marks, including 5-hydroxymethylcytosine (5hmC), in the mouse brain. Despite the evidence of potential Aag involvement in the key brain processes, the impact of Aag loss on developing brain remains unknown. Here, by using Aag knockout (Aag-/-) mice, we show that Aag absence leads to reduced DNA damage levels, evident in lowered number of γH2AX foci in P5 hippocampi. This is accompanied by changes in 5hmC signal intensity in different hippocampal regions. Analysis of gene expression in hippocampus and prefrontal cortex, at multiple developmental stages, indicates that lack of Aag results in altered gene expression, primarily of genes involved in regulation of response to stress. One of the most prominent genes deregulated in Aag-dependent manner, at all tested developmental stages, is aldehyde dehydrogenase 2 (Aldh2). In line with the changes in hippocampal DNA damage levels and the gene expression, adult Aag-/- mice exhibit altered behavior, evident in decreased anxiety in the Elevated Zero Maze and increased alternations in the Elevated T Maze tests. Taken together these results suggests that Aag has functions in modulation of genome dynamics during brain development, important for animal behavior.

overall_design:
To characterize brain development in Aag-/- versus WT, mice at postnatal day five (P5), juvenile mice at six weeks (6W) and adult mice from four to six months (6M) were evaluated.
Hippocampus and pre-frontal cortex were isolated from P5, 6W and 6M male mice (4 animals per time point) for further RNA extraction.
Total RNA from hippocampus and pre-frontal cortex was then compared between the KO (Aag-/-) and WT genotypes in addition to comparisons at the 3 different time points.

middle: L

last: Bordin

first: Kayla

last: Grooms

first: Nicola

last: Montaldo

first: Sarah

last: Fordyce Martin

first: Pål

last: Sætrom

first: Leona

last: Samson

first: Magnar

last: Bjørås


title: ANXA1 promotes cell proliferation and drug-resistance in B cell acute lymphoblastic leukemia

city: Guiyang

first: Yunsheng

last: Ran

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

summary:
ANXA1 promoted cell proliferation, suppressed cell apoptosis induced cell cycle arrest in B-ALL cells by CCK8, Flow cytometry and RNA-seq Sequencing analysis. The in vivo results indicated that down-regulation of ANXA1 in B-ALL cells could significantly reduce leukemic cell burden.
We then performed gene expression profiling using data obtained from RNA-seq of B-ALL cells with the ANXA1 gene down-regulated in CCRF-SB.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CCRF-SB cells with its down-regulated ANXA1.

first: Ping

last: Liu

first: Dan

last: Ma


title: Antigen presentation by tumor-associated macrophages (TAM) mediates progenitor to terminal exhaustion transition in glioblastoma and other solid tumors

city: DURHAM

first: Jessica

last: Waibl Polania

state: NC

address: 303 Research Dr., RM 217

institute: Duke University

summary: While terminally exhausted T cells (Tex_term) retain important anti-tumor cytotoxic function, it is the relative preservation of renewable, stem-like progenitor exhaustion (Tex_prog) that better indicates immunotherapeutic responsivity. Although restraining the progression from Tex_prog to Tex_term thus takes on clinical significance, the cellular interactions in a tumor microenvironment (TME) governing such progression remain less established. Employing glioblastoma (GBM) and other solid tumors as models of severe exhaustion, we provide a detailed characterization of the progression from Tex_prog to Tex_term within the TME, where we observe a striking and disproportionate loss of Tex_prog over time, leading to a low progenitor exhaustion to terminal exhaustion ratio (PETER). We find exhaustion concentrated within tumor-specific T cell subsets, with cognate antigenic exposure requisite for acquisition of the Tex_term phenotype. However, we implicate tumor-associated macrophages (TAM), and not tumor cells, as the source of antigenic exposure governing the Tex_prog to Tex_term transition. Using cell – cell interaction analysis, we additionally highlight candidate receptor–ligand communications that may be specifically mediating the progression to Tex_term and resultant decline in PETER within the TME.

overall_design: CD3+CD4+ or CD3+CD8+ were sorted from D13 (n = 16) and D19 (n = 4) intracranial tumors. Four mice were pooled for each D13 replicate to achieve desired number of cells. 10X 5' Chromium chemistry was utilized. 10,000 total cells from each timepoint were targeted with an average read depth of 36,000 reads per cell for the gene expression library. Reads were sequenced on a NovaSeq S1 flow cell. For the TCR library, 9,000 reads per cell were targeted and sequenced on a NovaSeq SP.

first: Xanne

last: Hoyt-Miggelbrink

first: Wiliam

last: Tomaszweski

first: Lucas

last: Wachsmuth

first: Selena

last: Lorrey

first: Daniel

last: Wilkinson

first: Emily

last: Lerner

first: John

last: Finlay

first: Peter

last: Fecci


title: The renal capsule, a vibrant and adaptive cell environment of the kidney in homeostasis and aging [scRNA-seq]

first: Andrey

last: Shaw

summary: The kidney is a complex organ that governs many physiological parameters. It is roughly divided into three parts, the renal pelvis, medulla, and cortex. Covering the cortex is the renal capsule, a serosal tissue that provides protection and forms a barrier for the kidney. Serosal tissues of many organs have been recently shown to play a vital role in homeostasis and disease. Analyses of the cells that reside in these tissues have identified distinct cell types with unique phenotypes. Surprisingly, despite the importance of serosal tissues, little is known about cells of the renal capsule. Here, we characterized this niche and found that it is mainly comprised of fibroblasts and macrophages, but also includes many other diverse cell types. Characterizing renal capsule- associated macrophages, we found that they consist of a distinct subset (i.e., TLF+ macrophages) that is nearly absent in the kidney parenchyma. Injury, disease, and other changes within the kidney, affected the cell composition and phenotype of the renal capsule, indicating its dynamic and vibrant response to changes within the organ parenchyma. Lastly, we studied age-related changes in the renal capsule and found that aging affected the cell composition and pro- inflammatory phenotype of macrophages, increased CD8 T cells and other lymphocyte counts, and promoted a senescence-associated phenotype in fibroblasts. Taken together, our data illustrate the complexity and heterogeneity of the renal capsule and its underlying changes during aging and disease, improving our understanding of the kidney serosa that may be valuable for novel renal therapies.

overall_design: Renal capsules of young and old mice were dissected, dissociated, and analyzed using scRNA-seq

first: Ben

last: Korin

first: Shimrit

last: Avraham

first: Reuben

last: Moncada

first: Terence

last: Ho

first: Mayra

last: Tleugabulova

first: Hari

last: Menon

first: Spyros

last: Darmanis

first: Yuxin

last: Liang

first: Zora

last: Modrusan

first: Cecile

last: Chalouni

first: Charles

last: Victoria

first: Linda

last: Rangell

last: Havnar

first: Will

last: Ewart

last: Jones

first: Jian

last: Jiang

first: Debra

last: Dunlap

first: Monika

last: Dohse

first: Andrew

last: McKay

first: Joshua

last: Webster

first: Steffen

last: Durinck

middle: S


title: Sympathectomy effect on muscle clock

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

summary: Characterization of the effect of perturbation of sympathetic nervous system (SNS) on skeletal muscle rhythmic transcriptome.

overall_design: Mice were anesthetized with 2% inhaled isoflurane and for chemical sympathectomy, 6 (OH)DA, (Sigma # 162957) was intramuscularly injected (50 mg/kg) into tibialis muscle every two alternate days for 2 weeks. Before each injection, 6-OHDA was freshly dissolved in 0.3% ascorbic acid. Mice were than incubated for 2 weeks after treatment to recover from the effects of the sympathectomy and anesthesia, before the collection of final muscle samples. For sympathectomy not injected muscle was used as Sham.

first: Mireia

last: Vaca-Dempere

first: Arun

last: Kumar

first: Oleg

last: Deryagin

first: Pura

last: Munoz-Canoves


title: The renal capsule, a vibrant and adaptive cell environment of the kidney in homeostasis and aging [bulk RNA-seq]

first: Andrey

last: Shaw

overall_design: Renal capsules of young and old mice were dissected and either analyzed by bulk RNA-seq or further sorted by FACS for macrophages before performing bulk RNA-seq.

first: Ben

last: Korin

first: Shimrit

last: Avraham

first: Reuben

last: Moncada

first: Terence

last: Ho

first: Mayra

last: Tleugabulova

first: Hari

last: Menon

first: Spyros

last: Darmanis

first: Yuxin

last: Liang

last: Modrusan

last: Chalouni


title: Epigenome analysis of samples from  Alzheimer's disease patients and healthy controls with and without LOY (loss of chromosome Y)

city: Gdańsk

first: Marcin

last: Jakalski

address: Dębinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdańsk

summary: Samples from 43 AD patients and 30 age-matched normal controls were assayed using Illumina© Infinium MethylationEPIC BeadChip. The epigenome-wide association study (EWAS) was performed to evaluate the epigenetic differences using granulocyte and monocyte samples. LOY status of each individual was taken into account when performing differential methylation analyses.

first: Jakub

last: Mieczkowski


title: Adrenalectomy effect on muscle clock.

last: Perdiguero

summary: Characterisation the effect of removal of adreanl glands on skeletal muscle rhythmic transcriptome.

overall_design: Mice were anesthetized with 2% inhaled isoflurane and a midline incision were done in the abdominal cavity. The fat attached to the adrenal glands was pulled out of the cavity and after dissection of the adrenal gland, the fat was returned to the cavity, and the skin was sewn. The contralateral adrenal gland was similarly removed after two days. To compensate for the aldosterone loss, 0.9% of saline supplemented with 1 % glucose was provided. A sham-operated group was used as a control. Muscle samples were then taken from the animals after they had recovered for at least two weeks from the effects of the adrenalectomy and anesthesia. In order to treat adrenalectomized animals with exogenous hormones, an intraperitoneally (IP) injection of 5 mg/kg dexamethasone (Sigma # D1159) or 0.5 mg/kg adrenaline (Sigma #E4642) was given for 10 days at ZT12. Mice were than incubated for 2 weeks after treatment to recover from the effects of the adrenalectomy and anesthesia, before the collection of final muscle samples.

last: Vaca-Dempere


title: METTL1/WDR4-mediated tRNA m7G modification and mRNA translation control promotes oncogenesis and doxorubicin resistance in osteosarcoma

city: Canton

first: jieyi

last: Ma

state: Guangdong province

address: No.58 Zhong Shan Er Road

department: 1Department of Otolaryngology

institute: the First affiliated hospital of Sun Yat-sen University

summary: Osteosarcoma is the most common bone tumor that leads to high mortality in adolescents and children. The tRNA N7-methylguanosine methyltransferase METTL1 is located in chromosome 12q14.1, a region that is frequently amplified in osteosarcoma patients, while its functions and underlying mechanisms in regulation of osteosarcoma remain unknown. Herein we show that METTL1 and WDR4 are overexpressed in osteosarcoma and associated with poor patient prognosis. Knockdown of METTL1 or WDR4 causes decreased tRNA m7G modification level and impairs osteosarcoma progression in vitro and in vivo. Conversely, METTL1/WDR4 overexpression promotes osteosarcoma proliferation, migration and invasion capacities. tRNA methylation and mRNA translation profiling indicated that METTL1/WDR4 modified tRNAs enhance translation of mRNAs with more m7G tRNA-decoded codons, including extracellular matrix (ECM) remodeling effectors, which facilitates osteosarcoma progression and chemoresistance to doxorubicin.Our study demonstrates METTL1/WDR4 mediated tRNA m7G modification plays crucial oncogenic functions to enhance osteosarcoma progression and chemoresistance to doxorubicin via alteration of oncogenic mRNA translation, suggesting METTL1 inhibition combined with chemotherapy is a promising strategy for treatment of osteosarcoma patients.

overall_design: Polysome associated mRNAs of Control(shNC) and METTL1 knockdown(shM1-1,shM1-2) cells were isolated and sequenced.Each sample has 2 replicates.Corresponding total RNA(INPUT RNA) was used to normalize gene expression. TRAC-Seq were developed to identify the tRNA m7G methylome in OS cell line.

first: Zhaoyu

last: Wang

first: Shuibin

last: Lin


title: Changes in brain transcriptome and metabolome of juvenile crucian carp after chronic deltamethrin exposure

city: Changsha

first: Hao

last: Wu

address: Shuanghe Road 728, Kaifu District, Changsha

institute: Hunan Fisheries Science Institute

summary: Deltamethrin (Del) is a widely administered pyrethroid insecticide that is established as a common contaminant of the freshwater environment and can be detected in many freshwater ecosystems even at lower concentrations. In this study, we investigated the changes in brain transcriptome and metabolome of crucian carp after exposure to 0.6 μg/L Del for 28 days. Antioxidant system analysis revealed that Del exposure significantly increases MDA concentration, and the activity of SOD was significantly inhibited in the brain (p < 0.05). Moreover, a total of 70 differential metabolites (DMs) were identified by the liquid chromatography-mass spectrometry (LC-MS/MS) system analysis, including 32 upregulated and 38 downregulated DMs in the DG group. The DMs associated with chronic Del exposure were enriched in steroid hormone biosynthesis, fatty acid metabolism, and glycerophospholipid metabolisms, such as prostaglandin G2, 5-oxoeicosatetraenoic acid, progesterone, androsterone, etiocholanolone, and hydrocortisone. Simultaneously, transcriptomics analysis revealed that chronic Del exposure caused lipid metabolism disorder, endocrine disruption, and proinflammatory immune response by upregulating the pla2g4, cox2, log5, ptgis, lcn, and cbr gene expression. Importantly, the integrative analysis of transcriptomics and metabolomics indicated that the arachidonic acid (AA) metabolism pathway and steroid hormone biosynthesis were decisive pathways in the brain tissue of crucian carp after Del exposure. Further, Del exposure perturbed the tight junction, HIF-1 signaling pathway, and thyroid hormone signaling pathway. Overall, transcriptome and metabolome data in our study offer a new insight to assess the risk of chronic Del exposure in fish brains.

overall_design: During a 28-day exposure period，90 fish were divided into two treatment groups, one was a blank control group (CG), and another was an exposure group with 0.6 μg/L Del (DG),


title: Gene expression profile after freeze-thawing at single cell level of Innate Lymphoid Cells (ILCs), Natural Killer (NK) cells , and T cells from human tonsils

city: Huddinge

first: Christopher

middle: Thomas

last: Stamper

address: Alfred Nobels Allè 8

department: Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

summary: We used single cell RNA sequencing to investigate the diversity of ILCs, NKs, and T cells in the human tonsil and the impact of freeze-thawing on their expression profile

overall_design:
Tonsillar ILCs, NK cells, and T cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq after freeze-thawing to test the impact of freeze-thawing on their transcriptomic expression profiles.
*** Due to patient confidentiality concerns, Swedish law does not allow the raw data to be hosted outside of Sweden; contact submitter for more details. ***

middle: T

first: Jenny

last: Mjösberg


title: RBPJ::ALK : a novel fusion gene amplified in a metastatic sarcomatoid chromophobe renal cell carcinoma

city: nice

first: Ilaria

last: Di Mauro

address: 28 avenue de valombrose

country: France

institute: CHU de Nice

summary: Using Fluorescence in situ hybridization (FISH), Comparative genomic hybridization on array (aCGH) and Targeted RNA sequencing (RNASeq), we observed a novel fusion of ALK with RPBJ that was amplified and immunohistochemically overexpressed in both the small sarcomatoid component of a chromophobe renal cell carcinoma (chRCC) and in its lymph node metastasis. The amplified RBPJ::ALK  fusion was not detected in the chromophobe component of the primary tumour that harbored chRCC-typical losses of chromosomes 1, 2, 6, 10, 13 and 17. In contrast, the same mutations of PTEN, TP53 and TERT promoter were observed together in the three analyzed samples from chRCC, sarcomatoid component of the chRCC and metastasis.

overall_design: screening of 3 samples ofa chromophobe renal cell carcinoma by SNP array with affymetrix platform

first: Mounir

last: SERAG

first: Bérengère

last: DADONE-MONTAUDIE

last: MAURO

first: Séverine

last: CARPENTIER

first: Annie-Claude

last: PEYRON

first: Audrey

last: BAZIN

first: Bruno

last: VALENZA

first: Nicolas

last: WEINBRECK

first: Florence

last: PEDEUTOUR


title: Kidney Transcriptome and  Polycystic Kidney Disease Genes in Zebrafish

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Determine if there is sexual dimorphism at the transcriptomic level in zebrafish kidneys.

overall_design: Comparing gene expresion between male and female zebrafish kidneys, and identifying common genes in mouse PKD models

first: Mattew

last: Koslow

first: Ping

last: Zhu

first: Xueying

first: Xiaolei

last: Xu


title: Lungs from CYP1B1 knockout mice (or controls) fed a western diet for 10 weeks

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: Adult CYP1B1 knockout mice (constitutive) fed a high fat diet for 10 weeks, compared to WT mice on a high fat diet

overall_design: Examination of effect of loss of CYP1B1 in lungs in the context of a high fat diet

first: Xinping

last: Chen

first: Jingyuan

first: Eric

last: Austin


title: 5-hydroxymethylcytosines regulate gene expression as a passive DNA demethylation resisting epigenetic mark in proliferative somatic cells

city: Philadelphia

first: Hao

last: Wu

state: PA

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: 5-hydroxymethylcytosines regulate gene expression as a passive DNA demethylation resisting epigenetic mark in proliferative somatic cells [methylation]

summary: Enzymatic erasure of DNA methylation in mammals involves iterative 5-methylcytosine (5mC) oxidation by the ten-eleven translocation (TET) family of DNA dioxygenase proteins. As the most abundant form of oxidized 5mC, the prevailing model considers 5-hydroxymethylcytosine (5hmC) as a key nexus in active DNA demethylation that can either indirectly facilitate replication-dependent depletion of 5mC by inhibiting maintenance DNA methylation machinery (UHRF1/DNMT1), or directly be iteratively oxidized to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC) and restored to cytosine (C) through thymine DNA glycosylase (TDG)-mediated 5fC/5caC excision  repair. In proliferative somatic cells, to what extent TET-dependent removal of 5mC entails indirect DNA demethylation via 5hmC-induced replication-dependent dilution or direct iterative conversion of 5hmC to 5fC/5caC is unclear. Here we leverage a catalytic processivity stalling variant of human TET1 (TET1.var: T1662E) to decouple the stepwise generation of 5hmC from subsequent 5fC/5caC generation, excision and repair. By using a CRISPR/dCas9-based epigenome-editing platform, we demonstrate that 5fC/5caC excision repair (by wild-type TET1, TET1.wt), but not 5hmC generation alone (by TET1.var), is requisite for robust restoration of unmodified cytosines and reversal of somatic silencing of the methylation-sensitive, germline-specific RHOXF2B gene promoter. Furthermore, integrated whole-genome multi-modal epigenetic sequencing reveals that hemi-hydroxymethylated CpG dyads predominantly resist replication-dependent depletion of 5mC on the opposing strand in TET1.var-expressing cells. Notably, TET1.var-mediated 5hmC generation is sufficient to induce similar levels of differential gene expression (compared to TET1.wt) without inducing major changes in unmodified cytosine profiles across the genome. Our study suggests 5hmC alone plays a limited role in driving replication-dependent DNA demethylation in the presence of functional DNMT1/UHRF1 mechanisms, but can regulate gene expression as a bona fide epigenetic mark in proliferative somatic cells.

overall_design: Whole genome BS-seq and bACE-seq analyses of HEK293T cells

first: Alex

last: Wei

first: Hongjie

last: Zhang

first: Qi

last: Qiu

first: Emily

last: Fabyanic

first: Peng

last: Hu


title: CircAkt3 participates in bone cancer pain progression in rats by modulating MAPK signalling pathway

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

summary: CircRNA parent genes were mainly enriched in MAPK and neurodevelopmental signalling pathways. CircAkt3 and circMap4k1 were significantly up-regulated in the BCP group. CircaAkt3 may increase p-ERK expression by upregulating Col8a1, which may further activate the MAPK pathway.

overall_design: We established a BCP rat model. The top four differentially expressed circRNAs (DECs) in the model were validated by agarose gel electrophoresis and Sanger sequencing between the BCP group and sham group. A circRNA-miRNA-mRNA network was constructed based on the interactions among circRNAs, microRNA (miRNA), and mRNA, which were predicted by TargetScan. mRNA and circRNA expression levels were detected by quantitative RT-PCR. In addition, Western Blot was performed to identify the protein levels of p-ERK, ERK, and Col8a1.

first: Lvlv

first: Xiaoxia

first: Yuqi

last: Su

first: Yiwen


title: FASN inhibition in prostate cancer cells C4-2

city: New York

first: Caroline

last: Ribeiro

state: NY

address: 413 East 69th Street

department: Pathology

institute: Weill Cornell Medicine

summary: Fatty acid synthase (FASN) inhibition effect with IPI-9119 compound in prostate cancer cells C4-2

overall_design: Expression profiling by high throughput sequencing using C4-2 cells treated with 100 nM of IPI-9119 or control (DMSO) for 6 days, 3 replicates analyzed

middle: F

first: Silvia

last: Rodrigues

first: Massimo

last: Loda


title: Development of a prognostic index for predicting disease progression in non-muscle invasive bladder cancer

city: Daejeon

first: sungghwan

last: park

address: Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Although recent advances in high-throughput technology and data-driven approach have provided many insights into non-muscle invasive bladder cancer (NMIBC), previous studies are still limited in their ability to predict the clinical behavior of NMIBC including response to intravesical therapy. We aim to develop a prognostic index (PI) consisting of a small gene group that predicts the NMIBC progression and response to intravesical bacillus calmette-guérin (BCG) therapy. We analyzed progression-associated genes using Cox regression analysis and validated their predictive values using a fully connected neural network (FNN) algorithm. By applying a pathway enrichment analysis to these genes, a PI system consisting of small core genes for NMIBC progression was developed. Gene expression profiling in NMIBC patients identified a prognostic gene set for predicting NMIBC progression in multiple patient cohorts. Pathway enrichment analysis revealed a 23-gene signature. We incorporated these genes into the PI system, which was a significant prognostic indicator of NMIBC progression. The PI system was shown to be an independent risk factor by a multivariate analysis and subset stratification according to stage and grade. The subset analysis also revealed that the PI system could identify patients who would benefit from BCG immunotherapy. The 23-gene-based PI represents a promising diagnostic tool for identifying high-risk NMIBC patients who would display different clinical behaviors and response to BCG immunotherapy.

overall_design: We generated an RNA-seq data set of 49 samples with non-muscle-invasive bladder cancer. Total RNA was isolated from tissue using TRI-reagent based method. Total RNA (500 ng) was processed for preparing whole transcriptome sequencing library.  Enrichment of whole transcriptome RNA by depleting ribosomal RNA (rRNA) was processed for preparing whole transcriptome sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction. After the rRNA is depleted, the remaining RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved in the RT directional buffer, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.The double stranded library is quantified using QauntiFluor ONE dsDNA System (Promega) and equal 330 ng in a total volume of 60 ml or less. The library is cyclized at 37 °C for 60 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball (DNB), the library is incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system (MGI) with 150 bp paired-end reads.

first: Jung-Hwan

last: Kim

first: Seong-Hwan

last: Park

first: Jong-Lyul

first: Seon-Kyu

first: Seok

middle: J

last: Yun


title: 5-hydroxymethylcytosines regulate gene expression as a passive DNA demethylation resisting epigenetic mark in proliferative somatic cells [RNA-Seq]

first: Hao

overall_design: Total RNA analysis of HEK293T cells

first: Alex

first: Hongjie

first: Qi


title: Gene expression signature of three different fat depots of Monodelphis domestica of different ages

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

summary: Monodelphis domestica develops ex utero. Here, we have investigated the changes in the transcriptomics of adipose tissue during juvenile development to get further insights into the reprograming in marsupial mammals.

overall_design: Experiments were performed on laboratory bred gray short-tailed opossum (Monodelphis domestica). The animals were kept in type 4 cages with enrichment, at an ambient temperature of 26°C on a 12:12 hrs light:dark cycle with ad libitum access to food and water. In this study we used different aged animals (6 and 10 week old female and male animals, n=4-5).

first: Martin

last: Jastroch

first: Susanne

last: Keipert

first: Yiming

last: Cheng

first: José

middle: M

last: Monroy Kuhn


title: The latent HIV reservoir in the brain of people with HIV under antiretroviral therapy (scRNA-Seq)

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

institute: UCSD

summary: A growing body of data suggests that the human brain serves as a sanctuary for HIV persistence despite life-long antiretroviral therapy. Microglia, the innate immune cells of the brain parenchyma,  may serve as a reservoir for rebound of HIV infection. The extent of the latent brain reservoir and molecular phenotype of HIV infected microglia cells, however, are unknown. To address this major knowledge gap, we leveraged the ‘Last Gift’ rapid autopsy cohort to perform a multi-omics approach (single cell RNA-seq, single cell ATAC-seq, and H3K27ac ChIP-seq) of the myeloid compartment creating a gene expression and chromatin accessibility atlas of human microglia isolated from three male individuals with HIV on suppressive antiretroviral therapy.

overall_design: CD45+ cells were isolated from the frontal cortex (Brodman area 9) of individuals infected with HIV

first: Zhengyu

last: Ouyang


title: The latent HIV reservoir in the brain of people with HIV under antiretroviral therapy (scATAC-Seq)

first: Schlachetzki

last: Johannes

first: Ouyang

last: Zhengyu


title: ACOT1, ACOT2, and ACOT3 are involved in fatty acid metabolism and Cyp4a10, and Cyp4a14 are involved in the PPAR signaling pathway downregulated significantly after MSCs treatment in WD-induced NASH liver.

city: Shanghai

first: lan

last: Zhong

address: Jimo Road 150

institute: Shanghai East hospital

summary: To identify the therapeutic role of hUC-MSCs cell therapy in WD-induced NASH, we established a NASH mouse model.

overall_design: We evaluated the therapeutic efficacy of human umbilical cord-derived Mesenchymal Stromal Cells (MSCs) in NASH mice and investigated the potential mechanism.

first: Shan

last: Li

first: Jiali

last: Hu

first: Lan


title: The latent HIV reservoir in the brain of people with HIV under antiretroviral therapy


title: Single-nucleus RNA sequencing of the hippocampal formation from a genetically diverse Alzheimer's disease mouse model (AD-BXDs)

city: BAR HARBOR

first: Niran

last: Hadad

state: Maine

address: 5 Bloomfield Rd, Unit A

institute: The Jackson Laboratory

summary: Cognitive resilience describes a subset of the elderly population that present no cognitive decline despite harboring Alzheimer’s disease (AD) neuropathologies. We used single nucleus RNA-sequencing to profile the hippocampal formation of cognitively resilient and susceptible AD-BXD strains.

overall_design: Hippocampal formation was isolated from cognitively resilient and cognitively susceptible AD-BXD strains (5XFAD mutation carriers) and their nontransgenic counterparts at 6- and 14-months of age. Samples were flash-frozen and were used for snRNA-sequencing.


title: Maternal metabolic stress affects in vitro embryo's transcriptom pattern

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: This study aims to investigate the potential implication of epigenetic mechanisms in the transmission of maternal metabolic information to the embryo, in order to better understand how maternal metabolic stress influences fertility. To do this, we exposed the oocytes of 54 cows to different environments during maturation (24 hours). The treatments include normal glucose concentration (5.5 mM), low glucose concentration (2.75 mM) and low glucose concentration with supplementation of BHB (1.8 mM). BHB is a ketone body that accumulates in circulation during clinical ketosis due to an increased rate of fat mobilization. BHB can be metabolized by the embryo in addition to acting as an epigenetic regulator. Epigenetic modifications are a potential mechanism for transmitting maternal metabolic information from the oocyte to the embryo, given their heritability.  As a result, we observe normal oocyte maturation within each condition. On the other hand, we see significantly higher blastocyst rates in the BHB supplemented group compared to the low glucose group (p-value = 0.0318). By modulating the expression of several genes, some of which related to development and metabolism, glucose deprivation (low glucose) has a greater influence on the embryo transcriptome than the exposure to BHB during maturation. BHB appears to have a compensatory effect on blastocyst rates by minimizing the impact of glucose deprivation on developmental rates. This project elucidates how certain metabolic conditions, including clinical ketosis in dairy cows or obesity in women influences fertility and the health of offspring.

overall_design: Ovocytes are split into three groups and matured on three different media, one Control media and two stress media: Low Glucose and Low Glucose + BHB. Once mature, IVF is performed. The transcriptom of 8-days balstocystes are then extracted, sequenced and analyzed.

first: Julie-Pier

last: Robichaud

first: Isabelle

last: Laflamme

first: Helene

last: Martin

first: Meihong

last: Shi

first: Clement

last: Plessis


title: Effect of different genes expression with the development of peri-implantitis

city: Luzhou

first: Ke

last: Yu

address: 2, Jiangyang Nan Road, Luzhou, PR China

department: Implant Department

summary: To identify key lncRNAs and mRNAs and investigate the possible mechanisms associated with peri-implantitis, whole-transcriptome sequencing was performed based on 2 inflammatory tissues of peri-implantitis and 2 gingival tissues of healthy individuals

overall_design: Comparative gene expression profiling analysis of RNA-seq data for peri-implantitis and healthy individuals

first: Qiqi

last: Liu

first: Ruibin

last: Wang

first: Ziyang

last: Zheng


title: 5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma [KAS-Seq]

city: Chicago

first: Mark

last: Applebaum

state: IL

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary:
Purpose: Neuroblastoma is the most common extracranial solid tumor in childhood. We previously showed that circulating cell-free DNA (cfDNA) and tumor biopsy derived 5-hydroxymethylcytosime (5-hmC) profiles identified patients with neuroblastoma who experienced subsequent relapse. Here, we hypothesized that 5-hmC modifications selectively enriched in cfDNA compared with tumor biopsy samples would identify epigenetic changes associated with aggressive tumor behavior and identify novel biomarkers of outcome in patients with high- risk neuroblastoma.

Methods: 5-hmC profiles from cfDNA (n = 64) and tumor biopsies (n = 48) were compared. Two neuroblastoma cell lines underwent chromatin immunopre- cipitation followed by sequencing (ChIP-Seq) for H3K27me3, H3K4me3, and H3K27ac; kethoxal-associated single-stranded DNA sequencing; hmC-Seal for 5-hmC; and RNA-sequencing (RNA-Seq). Genes enriched for both H3K27me3 and H3K4me3 in the included cell lines were defined as bivalent. Using bivalent genes defined in vitro, a bivalent signature was established in three publicly available cohorts of patients with neuroblastoma through gene set variation analysis. Differences between tumors with high or low bivalent signatures were assessed by the Kaplan-Meier method and Cox proportional hazards models.

Results: In cfDNA compared with tumor biopsy derived 5-hmC profiles, we found in- creased 5-hmC deposition on Polycomb Repressive Complex 2 target genes, a finding previously described in the context of bivalent genes. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogeneous neuroblastoma cell lines. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in patients with high-risk neuroblastoma.

Conclusion: Low expression of bivalent genes is a biomarker of worse outcome in patients with high-risk neuroblastoma.

overall_design: Kethoxal-assisted single-stranded DNA sequencing (KAS-Seq) performed in 8 neuroblastoma cell lines

first: Mohansrinivas

last: Chennakesavalu

first: Kelley

last: Moore

first: Gepoliano

last: Chaves

first: Sahil

last: Veeravalli

first: Rachel

last: TerHaar

first: Tong

last: Wu

first: Ruitu

last: Lyu

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti


title: Single-cell RNA-seq characterization of acute lymphoblastic leukemia

first: Junfei Zhao

last: Zhao

address: 1130 St. Nicholas Ave

institute: Columbia University

summary: We investigated the nature and extent of transcriptional heterogeneity of acute lymphoblastic leukemia at the celluar level using 10x scRNAseq.

overall_design: We performed 10x scRNAseq on B/T-cell acute lymphoblastic leukemia samples including diagnosis, remission and relapse from 20 patients.

first: Junfei

first: Adolfo

last: Ferrando


title: The latent HIV reservoir in the brain of people with HIV under antiretroviral therapy (ChIP-Seq)

first: Johannes

last: Schlachetzki

first: Zhengyu

last: Ouyang


title: Direct Reprogramming of Human Astrocytes into Spinal Cord Organoids Facilitating Spinal Cord Regeneration

city: shanghai

first: zhicheng

last: shao

address: dongan road 130

institute: fudan

summary: Human astrocytes have reported to reprogram into neurons, but they have yet to be induced to three-dimensional (3D) neural tissue for neural organogenesis. Here, we demonstrate a remarkable strategy for 3D organoid generation by direct reprogramming human astrocytes. By combining overexpression OCT4, suppression p53 and small molecules CHIR99021, SB431542, RepSox and Y27632, termed as Op53-CSBRY, we successfully reprogramed human astrocytes into neural ectodermal cells and further induced human 3D-brain organoid. Those organoids can be finally induced into spinal cord organoids by activating FGF, SHH and BMP signaling. The grafts of Human astrocyte derived spinal cord organoids (hADSC-Organs) can survived, differentiated into spinal cord neurons, migrated long distance, formed synaptic connectivity with host neurons, bridged complete injury spinal cord tissue in mice. This method indicates that human astrocytes could be directly triggered neural organogenesis, and may hold a great promising to support local astrocytes in situ organogenesis after brain damages, such as stroke and spinal cord injury.

overall_design: Screen of molecular conbined with factors to direct reprogramming astrocyte into neuron progenitors cell and therapy for spinal cord injuy.

first: Jinhong

last: Xu

first: Shi

last: Fang

first: Suixin

last: Deng

first: Xiaoning

last: Lin


title: XX chromosome complement promotes, and w-3 fatty acid treatment prevents, adverse statin effects in mice

city: Los Angeles

first: Karen

last: Reue

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: RNA-sequening of livers from male and female C57BL/6J mice fed either chow diet or chow diet + simvastatin (0.1g/kg body weight) for 4 weeks.

overall_design: Male and female C57BL/6J mice were fed either chow diet or chow diet + simvastatin (0.1g/kg body weight) for 4 weeks. RNA was isolated from liver tissue and prepared for total RNA sequencing.

first: Peixiang

last: Zhang

first: Carrie

last: Wiese


title: 5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma [RNA-Seq]

first: Mark

last: Applebaum

overall_design: RNA-Seq performed in 8 neuroblastoma cell lines without any treatment. RNA-Seq performed in 2 neuroblastoma cell lines with and without tazemetostat treatment.

first: Mohansrinivas

last: Chennakesavalu

first: Kelley

last: Moore

first: Gepoliano

last: Chaves

first: Sahil

last: Veeravalli

first: Rachel

last: TerHaar

first: Tong

last: Wu

first: Ruitu


title: Heterozygous BRCA1 Deletion, but not Complete BRCA1 Loss, Confers Resistance to Androgen Deprivation Therapy in Prostate Cancer

city: Reno

first: Pier Paolo

last: Pandolfi

address: 75 Pringle Way

institute: Renown Institute for Cancer

summary: BRCA1 is biallelically deleted or mutated in at least 1.9% of prostate tumors, but whether BRCA1 deficiency influences resistance to androgen deprivation therapy (ADT) and prostate cancer development remains elusive. Here we surprisingly find that in human, BRCA1 heterozygous deletion is observed in approximately 13% of human prostate cancers, is more prevalent in neuroendocrine prostate tumors and predicts worse survival than BRCA1 homozygous deletion. In mice, we show that Brca1 heterozygosity (HET) but not Brca1 full inactivation (KO) accelerates early tumor development, invasion and resistance to ADT in Pten-null prostate tumors. Furthermore, pre-malignant tumors and organoids derived from Brca1 HET mice undergo neuroendocrine differentiation and exhibit elevated levels of the unfolded protein response potentially as a pro-survival mechanism, but not those of Brca1 KO. Our findings thus provide important insights into clinical management of prostate cancer patients, suggesting that patients heterozygous for Brca1 are prone to developing resistance to ADT and should be treated differently from patients with complete Brca1 loss.

overall_design: 24 samples were sequenced, including mouse prostate tissues and organoids of different genotypes and grown in different conditions. Samples can be grouped into biological replicates or triplicates

first: Tuan

last: Nguyen

first: Yulia

middle: V

last: Shulga

first: Maria

last: Sundvall

first: John

last: McElderry

first: Valerie

last: Maymi

first: Meredith

last: Omer

first: Sabina

last: Signoretti

middle: G

last: Clohessy

first: Pier

middle: P


title: 5-Hydroxymethylcytosine Profiling of Cell-Free DNA Identifies Bivalent Genes That Are Prognostic of Survival in High-Risk Neuroblastoma [ChIP-seq]

first: Mark

overall_design: ChIP-Seq (H3K27me3, H3K4me3, H3K27ac) experiments performed in 8 neuroblastoma cell lines. H3K27ac and H3K27me3 ChIP-Seq performed in neuroblastoma cell lines with and without tazemetostat treatment.

last: Lyu

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti


title: Influence of immunosuppressive drugs on NK cells in therapeutic drug exposure in liver transplantation

city: Hefei

first: Rongrong

last: Qin

address: Jinzhai Street

institute: University of Science and Technology of China

summary:
Natural killer (NK) cells are enriched in the liver and are main regulators in liver transplantation (LT) regarding rejection or tolerance, viral infection or tumor recurrence. Immunosuppression (IS) consists of a triple drug standard regimen, including Tacrolimus (TAC) and Corticosteroids (CS) with either Mycophenolate Mofetil (MMF) or Sirolimus (SIR)/Everolimus (EVE). In this study we simulated the immunosuppressive microenvironment in vitro.
Peripheral blood mononuclear cells (PBMC) were cultured at the clinically effective plasma concentration of each drug for 3 days. CS seriously impaired the killing function of NK cells, followed by MMF and SIR/EVE. CS and TAC/CSA significantly decreased the secretion of IFN-γ. NK cell function in liver transplant (LT) recipients was most pronouncedly inhibited by a triple immunosuppressive regimen, CS playing the most prominent role compared to the other drugs. The MMF containing regimen demonstrated a significant increase in the expression of suppressive genes, especially of the Siglec7/9 family. The SIR group had stronger NK cell activity compared with the MMF group, although liver transplantation patients have lower NK cell activity and function. In conclusion, despite an overall comparable immunosuppressive efficiency in terms of prevention of acute rejection, a mTORI including regimen might be considered as having less impact on NK cell function and thus retaining their function.

overall_design: The enriched NK cells from PBMC of healthy volunteers were cultured in the presence of rhIL-2 (100 U/mL) in culture medium (RPMI 1640 medium supplemented with penicillin -streptomycin (100 µL/mL) and 10% human fetal bovine serum (FBS)), in a 37◦C, 95% humidity, 5%CO2 incubator. In addition, NK cells were exposed to single immunosuppressants EVE, 5ng/ml (n=2); SIR, 5ng/ml (n=2); TAC, 5ng/ml (n=2); CSA, 125ng/ml (n=2); MMF, 15 µg/ml (n=2); CS, 0.5 µg/ml (n=2)) and combined immunosuppressants (Group 1: TAC, 5ng/ml + MMF, 15 µg/ml + CS, 0.5µg/ml (n=3); Group 2: TAC, 5ng/ml +SIR, 5ng/ml + CS, 0.5 µg/ml (n=3); Group 3: TAC, 5ng/ml + EVE, 5ng/ml + CS, 0.5 µg/ml (n=3)) for 3 days, the CTL (n=5) did not contain drugs, and RNA was extracted for transcriptome sequencing.

first: Björn

last: Nashan


title: CircRNA/mRNA expression data for the different phases of colitis-associated colorectal cancer in a mouse model

city: Soochow

first: Qiaoming

last: Zhi

address: No.188 Shizi Road

institute: Soochow university

summary: The causal relationships between inflammation and cancer are now widely recognized and discussed. Epidemiological and experimental studies have shown that patients with inflammatory bowel disease (IBD) are major risk factors for developing CRC than the general population. Approximately 18.4% of patients with IBD are reported to develop into colitis associated cancer (CAC) within 30 years after the onset of disease . CAC has become the major cause of death in IBD patients. While these mechanisms by which chronic inflammation promotes colonic carcinogenesis are being investigated, many unanswered questions remain. Circular RNA (CircRNA) is a newly discovered type of non-coding RNAs, which is involved in the colorectal cancer (CRC) development by diverse mechanisms. In our current study, we employed the widely used Dextran Sodium Sulfate (DSS)-induced acute colitis and Azoxymethane (AOM)/DSS-induced CAC models to screen the circRNA and mRNA expression profiles in inflammation and inflammation-associated cancer by the high throughput sequencing.

overall_design: 30 six-week-old male BALB/c mice (18-20g in weight) were divided into 3 groups: the blank control (NC, n=5), colitis (DSS, n=5) and CAC group (AOM/DSS, n=5). Mice of the NC group drank water for 75 days. Colitis was induced by replacing drinking water with 3.0% DSS (MW: 35,000-50,000, MP Biomedicals, Solon, USA) for 7 days. For the mouse CAC model, mice were intraperitoneally injected with 12.5 mg/kg azoxymethane (AOM, Sigma, USA). After 5 days, 3.0% DSS was included in the drinking water for 7 days, followed by 14 days of regular water. This cycle was repeated by three times. Upon sacrifice, the colon was excised from the ileocecal junction to the anus, cut open longitudinally, and prepared for subsequent experiments. Total RNA was extracted from the mice colons using the TRIzol® reagent (Life Technologies, USA). Then the quantity and integrity of total RNAs were measured by the NanoDrop™ ND-2000 (Thermo Fisher Scientifc, Scotts Valley, CA, USA) and Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) respectively. CircRNAs/mRNAs were quantitatively analyzed by Shanghai OE Biotech (Shanghai, China).

first: Q

first: D

last: Wan


title: Donor non-classical monocytes recruit recipient classical monocytes from the spleen by activating donor alveolar macrophages

first: Ankit

last: Bharat

address: 303 E. Chicago Ave

institute: Northwestern University

summary: Primary Graft Dysfunction (PGD) is the predominant cause of early graft loss following lung transplantation. We recently demonstrated that donor pulmonary intravascular non-classical monocytes (NCM) initiate neutrophil recruitment. Simultaneously, host-origin classical monocytes (CM) are mobilized from the spleen and, upon entry into the allograft, permeabilize the vascular endothelium to allow neutrophil extravasation necessary for PGD. Here, we show that CCL2-CCR2 axis is necessary for CM recruitment. Surprisingly, although intravital imaging and multichannel flow cytometry revealed that pharmacological or genetic depletion of donor NCM abrogated CM recruitment, single-cell RNAseq identified donor alveolar macrophages (AM) as predominant CCL2 secretors. Unbiased transcriptomic analysis of human and murine tissues combined with murine knockouts and chimeras indicated that while IL1β was secreted by multiple cell lineages, donor NCM were responsible for the early activation of AM and CCL2 release. IL1β production by NCM was NLRP3 inflammasome-dependent and inhibited by donor treatment using a clinically approved sulphonylurea, Glyburide. Production of CCL2 in the donor AM occurred through IL1R-dependent activation of PKC and NFκB-pathway. Accordingly, we show that IL1β-dependent paracrine interaction between donor NCM and AM leads to recruitment of host AM necessary for PGD. Since depletion of donor NCM, IL1β or IL1R antagonism, and inflammasome inhibition, abrogated recruitment of CM as well as PGD and are feasible using FDA-approved compounds, our findings have potential for immediate clinical translation.

overall_design: Single-cell RNAseq profiles of mouse naïve left lung and allograft after 24hr syngeneic transplantation.

first: Emilia

last: Lecuona

first: Wenbin

last: Yang

first: Ziyou

last: Ren


title: ChIP-seq genome-wide maps of nuclear receptor RORγ chromatin state in the liver of pig exposed to mycotoxin

city: Yangzhou

first: Demin

last: Cai

address: Daxue South Road 88

institute: Yangzhou University

summary: We show that RORγ functions as a master activator of the entire mevalonate pathway-cholesterol biosynthesis program in the porcine liver. RORγ genome-wide binding enrichments in the liver were significantly reduced in response to mycotoxin exposure.

overall_design: Liver samples were isolated from piglets with/without mycotoxin exposure and collected for ChIP-seq assay.

first: Yatian


title: Analysis of difference in transcriptome of Th2 cells derived from Gata3(fl/fl) and Klrg1Cre Gata3(fl/fl) mice

city: Bethesda

first: Jinfag

last: Zhu

state: MD

address: 10 Center Drive

department: Laboratory of Immune System Biology

institute: NIAID/NIH

summary:
Purpose: To analyze the transcriptome difference of Th2 cells derived from Gata3(fl/fl) and Klrg1Cre Gata3(fl/fl) mice
Method: Lung Th2 cells were used from mice chronically challenged with papain (40 µg/20 µl PBS, 6 subsequent papain challenges, day 0, 1, 2, 13, 14, and 15)

overall_design: Total RNA from lung Th2 cells (live CD4+ T1ST/2+) was used for RNA-seq library preparation

first: Rama

middle: K

last: Gurram

first: Xi

last: Chen

first: Keji

last: Zhao

first: Jinfang


title: Identification of gene related to stem cells from human exfoliated deciduous teeth (SHED) into epithelial-like differentiation using co-culture in epithelial microenvironment

city: Kubang Kerian

first: Ahmad

last: Azlina

state: Kelantan

address: Health Campus, Universiti Sains Malaysia

country: Malaysia

institute: School of Dental Sciences

summary: We employed microarray profiling to determine the gene(s) that control human exfoliated deciduous teeth (SHED) differentiation into epithelial-like cells. We introduced epithelial microenvironment using keratinocyte serum free medium (KSFM) and co-culture with human epithelial keratinocyte (HEK001) to promote epithelial-like differentiation.

overall_design: In this study, SHED was co-cultured with HEK001 in the keratinocyte serum free medium until day 7. Total RNA samples were harvested at day 5 and 7 for One-Step Real Time PCR for validation epithelial-like differentiation. SHED cultured in alpha-minimum essential medium (α-MEM) for 24-hours as a stem cell negative control, while HEK001 cultured in KSFM (24-hours) was a keratinocyte positive control. SHED cultured in KSFM for 7 days were used as SHED-epithelial differentiation control. This model set-up was used to investigate the SHED-epithelial differentiation processes, which also allowed researchers to investigate the secretome effect of keratinocyte on SHED. Experiments were done in triplicate.

first: Siti

middle: N

last: Hashim

first: Sarahani

last: Harun

last: Halim

first: Suzina

last: Hamid

first: Kannan

last: Ponnuraj

first: Khairul

last: Noordin

first: Nazia

last: Majid

first: Azlina

last: Ahmad


city: Hong Kong

first: Xiaodan

last: Zhang

address: No.5 Sassoon Road, Pokfulam,

institute: Hong Kong University

summary: Complete lncRNA and mRNA expression profile of ESCC KYSE150 cells and TPA-treatment KYSE150 cells

overall_design: One condition experiment, ESCC KYSE150 cells: TPA treatment vs. control, 3 TPA-treatment replicates and 3 control replicates

first: Wan

last: Lin

first: Liyan

last: Xu


title: Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [RNA-Seq WAT]

city: Heidelberg

first: Clarissa

last: Feuerstein-Akgoz

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: In the present study, we applied two whole-genome sequencing techniques (WGBS/oxBS and hMe-Seal) to detect 5hmC (and 5mC) changes during the differentiation of the human SGBS preadipocyte cell line to mature adipocytes. As technical and biological validation we performed BS and oxBS followed by 450k array analysis. RNA-seq data was performed in parallel to study transcriptional changes associated with differential hydroxymethylation.  In human white adipose tissue (WAT) hydroxymethylation (hME-Seal) was characterized in comparison with histone modifications and acNEIL1 binding (ACT-seq).

overall_design:
DNA and RNA of SGBS cells at different time points of differentiation (day 0, 1, 7, 11 (and 27)) were examined for DNA methylation and hydroxymethlyation and mRNA expression levels in two indepentent experiments (Exp.1 and 2). DNA, RNA and Nuclei of 3-5 white adipose tissue biopsies were examined for DNA hydroxymethylation, mRNA expresion levels and histone modifications and acNEIL1 binding.
Raw data not provided due to patient privacy concerns

first: Florian

last: Janke

first: Jessica

last: Heilmann

first: Linda

last: Kessler

last: Miehle

first: Anna

last: Artati

first: Dieter

last: Weichenhan

first: Daniela

last: Avilés-Huerta

first: Joschka

last: Hey

first: Reka

last: Toth

first: Kersten

last: Breuer

first: Annette

last: Weninger

first: Silvia

last: Garelli

first: Marianna

last: Farnè

first: Giampaolo

last: Ugolini

first: Giancarlo

last: Rosati

first: Luigi

last: Ricciardiello

first: Alessandra

last: Bordoni

first: Yassen

last: Assenov

first: Jerzy

last: Adamski

first: Holger

last: Sültmann

first: Christoph

last: Plass

last: Gerhauser


title: Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [ACT-Seq]

first: Clarissa

last: Feuerstein-Akgoz

first: Florian

last: Janke

first: Jessica

last: Heilmann

first: Linda

last: Kessler

last: Miehle

first: Anna

last: Artati

last: Weichenhan


title: Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [RNA-Seq exp1]

overall_design: DNA and RNA of SGBS cells at different time points of differentiation (day 0, 1, 7, 11 (and 27)) were examined for DNA methylation and hydroxymethlyation and mRNA expression levels in two indepentent experiments (Exp.1 and 2). DNA, RNA and Nuclei of 3-5 white adipose tissue biopsies were examined for DNA hydroxymethylation, mRNA expresion levels and histone modifications and acNEIL1 binding.

first: Dieter

first: Daniela

last: Avilés-Huerta

first: Joschka

last: Hey

first: Reka

last: Toth

first: Kersten

last: Breuer

last: Weninger

last: Garelli

last: Farnè


title: Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [hMe-Seal]

first: Annette

first: Silvia

first: Marianna

first: Giampaolo

last: Ugolini

first: Giancarlo

last: Rosati

last: Ricciardiello

last: Bordoni

last: Assenov

last: Adamski

last: Sültmann


title: Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [RNA-Seq exp2]

last: Feuerstein-Akgoz

last: Janke

last: Heilmann

last: Kessler

last: Miehle

first: Luigi

first: Alessandra

first: Yassen

first: Jerzy

first: Holger

last: Plass

last: Gerhauser


title: Ferroptosis as a senolytic target to clear primary and secondary senescent cells

city: Mountain View

first: Tesfahun

middle: Dessale

last: Admasu

state: CA

address: 110 pioneer way, ste. j

department: ApoptoSens

institute: SENS Research Foundation

summary:
Purpose: Next-generation sequencing (NGS) on senescent primary endothelial cells. The goals of this study was to compare NGS-derived transcriptome profiling (RNA-seq) of DPP4+ primary and secondary senescent endothelial cells isolated from multiple donors.
Methods: Gene expression profile of DPP4+ isolated primary and secondary senescent endothelial cells were generated by deep sequencing, in triplicate, using Illumina Hiseq4000. After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Results: After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison.
Conclusions: Our study represents the first detailed analysis of primary and secondary senescent cells  transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles of primary and secondary senescence. Our results show that primary and secondary senescent cells have distinct gene expression profile.

overall_design: senescence was induced for 7 days and DPP4+ senescent cells were isolated. Gene expression profiles of DPP4+ primary and secondary senescent endothelial cells were determined.

middle: D

first: Alexandra

last: Stolzing

first: Amit

last: Sharma


title: Small-molecule inhibition of PRMT5 activates p53 in erythropoiesis through perturbation of mRNA processing, transport and protein translation

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

summary: The protein arginine methyltransferase PRMT5 catalyzes symmetric di-methylation of numerous proteins involved in epigenetic gene regulation, mRNA splicing and DNA repair. Several small molecule inhibitors of PRMT5 are in clinical trials for acute myeloid leukemia, myelodysplasia, lymphoma and metastatic solid tumors. Here, we report the development of a new potent and specific small molecule inhibitor of PRMT5 (CTX-034) that binds and competes for the arginine substrate binding pocket. CTX-034 suppresses erythroid progenitor growth 30-fold more potently than myeloid progenitor growth through activation of p53. Using a combination of RNA-seq and proteomics, we show that PRMT5 binds and methylates numerous proteins required for protein translation including RNA transport (Heterogeneous Nuclear Ribonucleoprotein A1), initiation of translation (Poly(A) Binding Protein Cytoplasmic 1) and ribosomal assembly (Ribosomal Protein S10). Using an in vivo mouse model of JAK2V617F-driven Polycythemia Vera, CTX-034 suppresses the formation of immature erythroblasts as effectively as the JAK inhibitor Ruxolitinib.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 4 control and 4 treatment replicate mice and human CD34+ bone marrow samples.

first: Stefan

middle: E

last: Sonderegger

first: David

last: Curtis


title: Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers

first: Clarissa

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Metabolic changes during human adipocyte differentiation promote stable DNA hydroxymethylation and binding of acetylated NEIL1 to adipogenic enhancers [450k array]

first: Florian

first: Jessica

first: Linda

first: Anna

last: Artati

first: Dieter

last: Weichenhan

first: Daniela

last: Avilés-Huerta

first: Joschka

last: Hey

first: Reka

last: Toth

first: Kersten

last: Breuer

first: Annette

last: Weninger

last: Garelli

last: Farnè

last: Ugolini

last: Rosati

last: Ricciardiello

last: Bordoni

first: Christoph


title: 4E-BP1-dependent translation in microglia controls mechanical hypersensitivity

status: Public on Jan 31 2024

city: Montreal

first: Arkady

last: Khoutorsky

address: 3655 Promenade Sir-William-Osler

institute: McGill University

summary: Spinal microglia play a pivotal role in the development of neuropathic pain. Peripheral nerve injury induces changes in the transcriptional profile of microglia, including increased expression of components of translational machinery. Whether microglial protein synthesis is stimulated following nerve injury and has a functional role in mediating pain hypersensitivity is unknown. Here, we show that nascent protein synthesis is upregulated in spinal microglia following peripheral nerve injury. Stimulating mRNA translation in microglia, via selective ablation of the translational repressor, eukaryotic initiation factor 4E-binding protein 1 (4E-BP1), promoted the transition of microglia to a reactive state and induced mechanical hypersensitivity. Conversely, inhibiting microglial translation by expressing mutant 4E-BP1 in microglia attenuated their peripheral nerve injury-induced activation and alleviated neuropathic pain. Thus, the stimulation of 4E-BP1-dependent translation promotes microglia reactivity and mechanical hypersensitivity, whereas its inhibition alleviates neuropathic pain.

overall_design: Ablation of 4E-BP1 stimulates translation of eIF4E-sensitive mRNAs, which are involved in immune responses, modulation of extracellular matrix, cell survival and growth. To better understand how 4E-BP1 ablation affects microglial functions and induces mechanical pain hypersensitivity, we studied changes in the translational landscape in microglia lacking 4E-BP1. To identify the actively translating mRNAs in microglia, we employed a translating ribosome affinity purification (TRAP) approach . In TRAP, a ribosomal subunit L10a tagged with eGFP (L10a-eGFP) is expressed in a specific cell type. Immunoprecipitation (IP) with eGFP antibody captures the eGFP-tagged ribosomes and subsequent sequencing of immunoprecipitated ribosome-bound mRNAs allows the identification of actively translated mRNAs in the specific cell type.


title: Harnessing Crop Biodiversity and Genomics Assisted Pre-Breeding Approaches for Next Generation Climate-Smart Varieties

city: Shahin shar

first: Maryam

last: Salami

state: Mokhaberat

address: shahid beheshti

country: Iran

institute: Shiraz University

summary: Integration of genome wide association studies (GWAS), metabolomics and transcriptomics reveals phenolic acids and flavonoids associated genes and their regulatory elements under drought stress in rapeseed flowers

overall_design: Biochemical and metabolic processes help plants tolerate the adverse effects of drought. In plants accumulating bioactive compounds, understanding the genetic control of the biosynthesis of biochemical pathways helps the discovery of candidate gene–metabolite relationships.

first: Bahram

last: Heidari

first: Jacqueline

last: Batley

first: Jin

last: Wang

first: Xiaoli

last: Tan

first: Chris

last: Richards

first: Helin


title: Genetic background variation impacts microglial heterogeneity and disease progression in amyotrophic lateral sclerosis model mice

city: Nagoya

first: Okiru

last: Komine

state: Aichi

address: Furo-cho, Chikusa-ku

department: Neuroscience and Pathobiology

country: Japan

institute: Research Institute of Environmental Medicine, Nagoya University

summary: Recent single-cell analyses have revealed the complexity of microglial heterogeneity in brain development, aging, and neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Disease-associated microglia (DAMs) have been identified in ALS mice model, but their role in ALS pathology remains unclear. The effect of genetic background variations on microglial heterogeneity and functions remains unknown. Herein, we established and analyzed two mice models of ALS with distinct genetic backgrounds of C57BL/6 and BALB/c. We observed that the change in genetic background from C57BL/6 to BALB/c affected microglial heterogeneity and ALS pathology and its progression, likely due to the defective induction of neurotrophic factor-secreting DAMs and impaired microglial survival. Single-cell analyses of ALS mice revealed new markers for each microglial subtype and a possible association between microglial heterogeneity and systemic immune environments. Thus, we highlighted the role of microglia in ALS pathology and importance of genetic background variations in modulating microglial functions.

overall_design: We analyzed gene expressions in microglia isolated  from spinal cords of SOD1G93A mice carrying a low copy number of mutant SOD1 and having C57BL/6JJcl or BALB/cAJcl genetical backgrounds by magnetic-activated cell sorting (MACS) at end-stage of disease.

first: Yuichiro

last: Hara

first: Mayuko

last: Shimada

first: Tomoo

last: Ogi

first: Koji

last: Yamanaka


title: Neonatal monocytes in tracheal aspirates from infants at risk for Bronchopulmonary Dysplasia propagate IL-1 signaling in the first weeks of lung injury

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Sorted human monocytes, isolated from tracheal aspirates from intubated premature infants.

overall_design: We prospectively recruited premature infants who were born at less than 29 weeks gestation and who were intubated/ventilated for this study.  Tracheal aspirate samples were obtained at several time points (d0-3, 7-9, 14-17, 28-31) when possible.  Samples were delivered to BRI for analysis.  We used a 13-color panel of conjugated antibodies to identify T cells, B cells, NK cells, basophils, neutrophils, eosinophils, and 2 populations of monocyte/macrophages CD14+CD16+ (DP) and CD14 CD16- (SP) by flow cytometry.  Samples were sorted on the Aria II, and DP and SP cells were sorted into lysis buffer (Clontech/Takara RNA isolation kit).  Total RNA from these samples was isolated by us and delivered to the genomics core for cDNA synthesis with Smartseq

first: Laurie

last: Eldredge

first: Rane

last: Creasy

first: Scott

middle: R

last: Presnell

first: Jason

last: Debley

first: Sandra

last: Juul

first: Dennis

last: Mayock

first: Steven

last: Ziegler