title: A cerebrospinal fluid microRNA analysis of progressive supranuclear palsy.

status: Public on Dec 05 2021

city: Kamakura

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The cerebrospinal fluid miRNAs expression was markedly altered in  the patients with progressive supranuclear palsy and controls.

overall_design: We analyzed the expression levels of 2632 human miRNA probes in the cerebrospinal fluid of patients with progressive supranuclear palsy and controls. The patients were divided into two groups based on disease stage (early onset and advanced).

first: N

last: Wakako

first: T

last: Masaki


title: Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival

status: Public on Dec 06 2021

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Expression profiling by high throughput sequencing

summary: Zygotic Genome Activation (ZGA) represents the initiation of transcription following fertilization. Despite its importance in shifting developmental control from primarily maternal stores in the oocyte to the embryo proper, we know little of the molecular events that initiate ZGA in vivo. Recent in vitro studies in mouse embryonic stem cells (ESCs) have revealed Developmental Pluripotency Associated 2 and 4 (Dppa2/4) as key regulators of ZGA-associated transcription. However, their roles in initiating ZGA in vivo remain unexplored. We reveal Dppa2/4 proteins are present in the nucleus at all stages of preimplantation development and associate with mitotic chromatin. We generated single and double maternal knockout mouse models to deplete maternal stores of Dppa2/4. Importantly, while fertile, Dppa2/4 maternal knockout mice had reduced litter sizes, indicating decreased offspring survival. Immunofluorescence and transcriptome analyses of 2-cell embryos revealed while ZGA took place there were subtle defects in embryos lacking maternal Dppa2/4. Strikingly, heterozygous offspring that inherited the null allele maternally had higher preweaning lethality than those that inherited the null allele paternally. Together our results show that while Dppa2/4 are dispensable for ZGA transcription, maternal stores have an important role in offspring survival, potentially via epigenetic priming of developmental genes.

overall_design: Embryos were collected from 2x each mating (2x cKO x WT; 2x cKO x HET; 2x Ctrl x WT), denoted mating1 and mating2 in each file name; For the HET genotypes (included in each sample name) HET1= embryos from cKO x WT male mating (100% HET), and HET2= embryos from cKO x HET male mating (50% should be HET and 50% HOMs, according to the Mendelian ratio)

first: Oana

last: Kubinyecz

first: Fatima

last: Santos

first: Deborah

last: Drage

first: Wolf

last: Reik

first: Melanie

middle: A

last: Eckersley-Maslin


title: scATAC-seq of innate immune cells from mice treated with the adjuvant 3M052

city: Stanford

first: Madeleine

last: Scott

state: CA

address: 729 Lagunita Dr

country: USA

institute: Stanford

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: to explore the epigenomic landscape of innate immune cells stimulated with a novel adjuvant, 3M052
Methods: Mice were injected with 3M052. Draining lymph nodes were negatively selected for CD19+ and CD3+, then flow sorted into four populations: Dendritic cells (DCs), Double positive cells (DP, CD11b+BST1+), Ly6c+ cells (Ly6c), and plasmacytoid dendritic cells (pDCs). Lymph nodes were harvested at baseline (D0), 24 hours post-treatment (D1) or 28 days post-treatment (D28).

overall_design: single cell ATAC seq of innate immune cells in the lymph nodes of mice after treatment with 3M052

first: Audrey

last: Lee


title: A small set of accessible enhancers enables breast cancer cell response to  physiological progestin concentrations

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary: Here, we report that in T47D breast cancer cells 50pM progestin is sufficient to activate cell cycle entry and the progesterone gene expression program in breast cancer cells. At this concentration, equivalent to the progesterone blood levels found around the menopause, PR binds only to 2,800 genomic sites, which are accessible to ATAC cleavage prior to hormone. These Highly-Accessible PR Binding sites (HAPRBs) are surrounded by well-organized nucleosomes and exhibit breast enhancer features, including higher estrogen receptor (ERa), FOXA1 and BRD4 occupancy. Although, HAPRBs are enriched in RAD21 and CTCF, PR binding is the driving force for the most robust interactions with hormone-regulated genes. HAPRBs show higher frequency of 3D contacts among themselves than with other PRBs, indicating co-localization in similar compartment. Gene regulation   via   HAPRBs is independent of classical co-regulators and ATP-activated remodelers, relaying mainly on MAP kinase activation that enables PR nuclear engagement.  HAPRBs are also preferentially occupied by PR and ERa in breast cancer xenografts derived from MCF-7 cells as well as from patients (PDXs), indicating their usefulness as potential targets for therapeutic intervention.

overall_design: HiChIP, ChiP-seq, RNA-seq, ATAC-seq

first: Roser

last: Zaurin

first: A

middle: S

last: Nacht

first: Jose

last: Carbonell

first: Francois

last: Le Dily

first: Jofre

last: Font-Mateu

first: Lara

middle: I

last: de Llobet Cucalon

first: Enrique

last: Vidal

first: Antonios

last: Lioutas

first: Miguel

last: Beato

first: Guillermo

middle: P

last: Vicent


title: Genome-wide maps of histone PTMs and co-factors in pluripotent mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs)

city: Copenhagen

first: Aditya

last: Sankar

email: cnj376@ku.dk, aditya.sankar@embl.de

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

summary: We report here the genome wide mapping of histone PTMs and chromatin bound factors in pluripotent control and H3K27R base edited mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs) using ChIP-Seq technology. We have deposited results from chromatin immunoprecipitations done using antibodies against Rpb1 (Pol-II), Med1,H3.3, H3K27me1, H3K27me2, H3K27me3 and H3K27ac (rabbit and mouse monoclonal antibodies). We show the loss of all H3K27 from H3.1/2/3 results in loss of associated K27 methylation and acetylation as expected. In such cells, there are only modest changes to MED1 or RNA Pol-II binding or activity that correlate with transcriptional status, suggesting that H3K27ac is not required to initiate or maintain transcription of genes, while loss of H3K27me3 associates with derepression of Polycomb target genes.

overall_design:
100 ug, 200 ug and 1 mg were input chromatin amounts used for histone PTM, Rpb1 (Pol-II) and Med1 ChIPs. 5% Drosophila chromatin was spiked in during immunoprecipitations for IP normalization in addition to standard FPKM normalization. Comparisons were performed between control mESCs (ABE) and two independent clones that were either mutant for only canonical H3K27 (cK27R) or all H3K27 (pK27R). In addition, we sequenced one input sample from control mESCs and EpiLCs to represent the different input chromatin amounts during immunoprecipitation.
ChIP signal intensities quantified across enhancers and non-redundant genes are deposited. The non-redundant UCSC genes regionset is used from Sankar et al., Nature Cell Biology 2020 (PMID: 32231309). The enhancers defined in mouse ESCs from Whyte et al., Cell 2013 (PMID: 23582322) and in EpiLCs (H3K27ac+, H3K4me1+ and p300+ peaks) from Buecker et al., Cell Stem Cell 2014 (PMID: 24905168) were lifted over to corresponding mm10 genomic co-ordinates prior to downstream global analysis.

first: Faizaan

last: Mohammad


title: Single Cell RNA-seq of the draining lymph nodes of mice treated with either 3M052 or Yellow Fever Vaccine (YF)

summary:
Purpose: To understand the innate immune response to an adjuvant, 3M052, and yellow fever vaccine, YFV
Methods: Draining lymph nodes were negatively selected for CD19+ and CD3+, then flow sorted into four populations: Dendritic cells (DCs), Double positive cells (DP, CD11b+BST1+), Ly6c+ cells (Ly6c), and plasmacytoid dendritic cells (pDCs). Lymph nodes were harvested at baseline (D0), 24 hours post-treatment (D1) or 28 days post-treatment (D28).
Results: TBD
Conclusions: TBD

overall_design: scRNA of murine lymph nodes after treatment with the adjuvant 3M052 or Yellow Fever vaccine.

middle: K


title: Quantitative Analysis of erythroblast cells Transcriptomes treated with cholesterol or not

city: Jinan

first: Zhiyuan

last: Lu

state: Shandong

address: 6699 Qingdao road

department: School of Pharmaceutical Sciences & Institute of Materia Medica

country: China

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: In our work, we explored the dynamics of cholesterol homeostasis during terminal erythropoiesis. Interestingly, we found differential requirements of cholesterol during terminal erythropoiesis, with that cholesterol is essential for the early stage erythroblasts proliferation, while the downregulation of cholesterol biosynthesis is required for late stage cell cycle exit and final enucleation. To reveal the role of cholesterol in the the early stage erythroblasts proliferation and the detail mechanisms of erythroblasts late stage cell cycle exit, we performed RNA sequencing to analyze the gene expression profiles change between untreated and cholesterol treated erythroblasts.

overall_design: TER119-negative fetal liver erythroblasts were purified and cultured in Epo containing medium for 30 h supplemented with or without cholesterol (40 μM), and total RNA was extracted using the TRIzol reagent. RNA sequencing was conducted using the BGIseq500 platform (Shenzhen, China) in triplicate.

first: Baobing

last: Zhao


title: MicroRNAs Mediate Insecticide Tolerance in Spodoptera frugiperda

status: Public on Dec 04 2021

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Spodoptera frugiperda is the world’s major agricultural pests, and has the distinctive features of high fecundity, strong migratory capacity and high resistance to most insecticides. At present, the control of S. frugiperda in China relies mainly on the spraying of chemical insecticides. MicroRNAs (miRNAs) are a class of small, single-stranded, non-coding RNAs, and play crucial regulatory roles in various physiological processes, including the insecticide resistance in insects. However, little is known about the regulatory roles of miRNAs on the resistance of S. frugiperda to insecticides. In the present research, the miRNAs that were differentially expressed after cyantraniliprole, spinetoram, emamectin benzoate and tetraniliprole treatment were analyzed by RNA-Seq. A total of 504 miRNAs were systematically identified from S. frugiperda, and 24, 22, 31 and 30 miRNAs were differentially expressed after treatments of cyantraniliprole, spinetoram, emamectin benzoate and tetraniliprole. GO and KEGG enrichment analyses were used to predict the function of differentially expressed miRNAs’ target genes. Importantly, ten miRNAs were significantly differentially expressed among the treatments of three insecticides. MiR-278-5p, miR-13b-3p, miR-10485-5p and miR-10483-5p were significantly down-regulated among the treatments of three insecticides by RT-qPCR. Furthermore, overexpression of miR-278-5p, miR-13b-3p, miR-10485-5p and miR-10483-5p significantly increased the mortality of S. frugiperda to cyantraniliprole and emamectin benzoate. The mortality was significantly increased with spinetoram treatment after overexpression of miR-13b-3p, miR-10485-5p and miR-10483-5p. These results suggest that miRNAs, which are differentially expressed in response to insecticides, may play a key regulatory role in the insecticide resistance in S. frugiperda.

overall_design: The miRNAs that were differentially expressed after cyantraniliprole, spinetoram, emamectin benzoate and tetraniliprole treatment were analyzed in Spodoptera frugiperda.

first: Jianhua

last: Zhang

first: Yuanxue

last: Yang

first: Yun


title: Progesterone differentially affects the transcriptomic profiles of cow endometrial cell types

status: Public on Dec 03 2021

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

country: France

institute: INRAE

summary: In this study, whole transcriptome changes induced by P4 were analysed by RNAseq following laser capture microdissection (LCM) of endometrial biopsies to isolate LE, GE and ST cells. The study was performed in cows without any sign of uterine disease (as assessed by uterine cytology). At 45 days postpartum, the presence of a Corpus Luteum (CL) assessed by ultrasonography and plasma P4 concentrations were used to categorise healthy cows at 45 days postpartum determine if cows were in luteal phase (CL, P4 concentrations ≥1 ng/ml; n=4) or not (no CL, P4 concentrations < 1ng/ml; n=9). Overall, endometrial LE, GE, and ST cells shown specific transcriptomic profiles with different proportions and type of genes expressed over 10 tpm. Most of the genes differentially expressed (DEGs) in response to P4 were cell type-specific (93.9%). Genes involved in cell cycle and nuclear division were under-expressed in presence of P4 in GE and LE, highlighting the anti-proliferative action of P4 in epithelial cells. Elevated P4 concentrations were also associated with the under-expression of estrogen receptor 1 (ESR1) in GE and of oxytocin receptor (OXTR) in GE and ST. In ST, transcription factors such as SOX17 and FOXA2 , as well as interferon related genes which are known to regulate uterine epithelial–stromal crosstalk conveying to endometrial receptivity for embryo implantation, were over-expressed under P4. The results from this study show that progesterone regulates endometrial function in a cell type specific way, which looks independent of the expression of its main receptor PGR. These novel insights into uterine physiology, stand the cell compartment, rather than the whole tissue, as a physiological unit.

overall_design: High-yielding dairy cows from Holstein herd were submitted to uterine biopsy at 44 ± 0.7 days postpartum (DPP). The uterine status of all the cows included in this study (n = 13) was assessed as healthy, with no clinical signs of endometritis. The cut-off value used to define cows with elevated P4 concentrations was 1 ng/mL. The three endometrial cell types: luminal (LE), glandular (GE) epithelium and stroma (ST) were collected by laser microdissection from endometrial biopsies.

first: Gonçalo

last: Pereira

first: Yongzhi

last: Guo

first: Elisabete

last: Silva

first: Claudia

last: Bevilacqua

first: Gilles

last: Charpigny

first: Luís

last: Lopes-da-Costa

first: Patrice

last: Humblot


title: Tumor-derived exosomal miR-181a-5p activates hepatic stellate cells to promote liver metastasis of colorectal cancer

city: Shanghai

first: Senlin

address: 270 Dong An Road

department: Colorectal Surgery

institute: Cancer Hospital, Fudan University

summary:
A previous study suggested that the expression of miR181a-5p was higher in CRC tissues, but whether CRC cell-derived exosomes regulate the activation of HSCs through secreting miR181a-5p and promoting CRLM warrants further investigation.
We compared the miRNA expression profiles between exosomes from highly metastatic CRC cells (RKO and SW620) and those from weakly-metastatic CRC cells (HT29 and SW480).

overall_design: The Agilent Human miRNA Microarray Kit, Release 21.0, 8x60K (DesignID: 070156) experiment and data analysis were performed in exosomes from two highly metastatic CRC cells (RKO and SW620) and two weakly-metastatic CRC cells (HT29 and SW480). The microarray contains 2570 probes for mature miRNA. Three independent experiments were performed.

first: Yushuai

last: Mi

first: Binbin

last: Zheng

first: Ping

last: Wei

first: Yanzi

last: Gu

first: Ye

last: Xu

first: Sanjun

last: Cai

first: Xinxiang

last: Li

first: Dawei


title: Molecular properties of epimutation hotspots

status: Public on Dec 02 2021

city: Freising

first: Rashmi

middle: Rekha

last: Hazarika

address: Liesel Beckmann-Str-2

country: Germany

institute: Technical University of Munich

type: Methylation profiling by high throughput sequencing

summary: Mistakes in the maintenance of CG methylation is a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harboring localized “epimutation hotspots”. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states (CS) that map to sub-regions of gene body methylation genes. Although these regions comprise only ~12% of all CGs in the genome, they account for ~63% of all epimutation events per unit time. Molecular profiling revealed that these regions contain unique sequence features, harbor steady-state intermediate methylation levels, and act as putative targets of antagonistic DNA methylation pathways. We further demonstrate that experimentally-induced shifts in steady-state methylation in these hotspot regions are sufficient to significantly alter local epimutation intensities. Our work thus lays foundation for dissecting the molecular mechanisms of epimutation hotspots in plants.

overall_design: We created two mutant lineages of MA_cmt3, and MA_suvh4/5/6 mutation accumluation lines from Col-0 that were propagated by single seed descent growth for the indicated number of generations (G#).

first: R

middle: J

last: Schmitz

first: F

last: Johannes


title: High-pressure sprayed siRNAs influence the efficiency but not the profile of transitive silencing

status: Public on Dec 01 2021

city: Neustadt-Mußbach

first: Veli Vural

last: Uslu

state: DEUTSCHLAND

address: Epigenetics, Breitenweg 71

department: Epigenetics

institute: AgroScience GmbH AlPlanta-Institute for Plant Research

summary: In plants, small interfering RNAs (siRNAs) are a quintessential class of RNA interference (RNAi)-inducing molecules produced by the endonucleolytic cleavage of double stranded RNAs (dsRNAs). In order to ensure robust RNAi, siRNAs are amplified through a positive feedback mechanism called transitivity. Transitivity relies on RNA-DIRECTED-RNA POLYMERASE 6 (RDR6)-mediated dsRNA synthesis using siRNA-targeted RNA. The newly synthesized dsRNA is subsequently cleaved into secondary siRNAs by DICER-LIKE (DCL) endonucleases. Just like primary siRNAs, secondary siRNAs are also loaded into ARGONAUTE proteins (AGOs) to form an RNA-induced silencing complex (RISC) reinforcing the cleavage of the target RNA. Although the molecular players underlying transitivity are well established, the mode of action of transitivity remains elusive. In this study, we investigated the influence of primary target sites on transgene silencing and transitivity using the GFP-expressing Nicotiana benthamiana 16C line, high pressure spraying protocol (HPSP), and synthetic 22-nucleotide (nt) long siRNAs. We found that the 22-nt siRNA targeting the 3’ of the GFP transgene was less efficient in inducing silencing when compared to the siRNAs targeting the 5’ and middle region of the GFP. Moreover, sRNA sequencing of locally silenced leaves showed that the amount but not the profile of secondary RNAs is shaped by the occupancy of the primary siRNA triggers on the target RNA. Our findings suggest that RDR6-mediated dsRNA synthesis is not primed by primary siRNAs and that dsRNA synthesis appears to be generally initiated at the 3’ end of the target RNA.

overall_design: siRNAs are exogenously applied on Nicotiana benthamiana via High Pressure Spraying Protocol and the transitive silencing phenotype is evaluated by sRNA-seq

first: Veli

last: Vural Uslu

first: Athanasios

last: Dalakouras

first: Victor

last: Steffens

first: Gabi

last: Krczal

first: Michael

last: Wassenegger


title: Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae

city: Berkeley

first: Molly

last: Brothers

address: UC Berkeley 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

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

overall_design: Refer to individual Series


title: Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. Here we show that without histone H1, RdDM enters heterochromatin, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically required for small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.

overall_design: Bisulfite and RNA sequencing was performed using h1cmt2, h1cmt2shh1, h1cmt2cmt3 plants (1-2 replicates) to examine the effect of H1, non-CG DNA methylation and SHH1 on RNA-directed DNA methylation activity. sRNA-seq was performed using wt, h1, ddm1, h1ddm1, cmt2cmt3, h1cmt2cmt3, met1, and h1met1 plants (3 replicates, except for met1 and h1met1) to examine the effect of H1, non-CG DNA methylation on 24 nt sRNA expression. To explore H3K9me1 and H3K9me2 distribution in wt, h1, ddm1, h1ddm1, cmt2cmt3, and h1cmt2cmt3, antibody against H3K9me1 and H3K9me2 were used to enrich chromatin bound to modified histones.

first: David

middle: B

last: Lyons


title: BET inhibitors enhance the expression of fetal and embryonic hemoglobin genes

city: Chicago

first: Lucy

last: Godley

state: IL

address: 5841 S. Maryland Ave. MC 2115

institute: University of Chicago


title: The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II

city: Montpellier FRANCE

first: Julie

last: Carnesecchi

address: 1919, route de Mende team JCL team JCL

department: IGMM

institute: CNRS

summary: Transcription Factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. Our results demonstrate a new RNA-binding ability of Ubx. We find that the N51 amino acid of the DNA-binding Homeodomain is non-essential for RNA interaction in vitro, but is required for RNA interaction in vivo and Ubx splicing activity. Moreover, mutation of the N51 amino acid weakens the interaction between Ubx and active RNA Polymerase II (Pol II). Our results reveal that Ubx regulates elongation-coupled splicing, which could be coordinated by a dynamic interplay with active Pol II on chromatin. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.

overall_design: Total RNAs were extracted from four independent replicates from Drosophila S2R+ cells expressing GFPnls, myc-UbxWT, or myc-UbxN51A (Gal4-UAS, actin promoter) using Qiagen RNA extraction kit (RNeasy). RNA quality was assessed using BioAnalyzer 2100TM (Agilent Technologies). Material handling and mRNA-Seq directional libraries were performed with the Deep-Sequencing facility in Heidelberg (Cell Networks) with TruSeq kit and poly(A) selection according to the manufacturer’s protocol (Illumina). Sequencing was performed with NextSeq500 High-Output with a read-length of 75bp and single-end strands. Replicates were validated by FastQC report and 3 replicates for each sample were further selected according to Principle Component Analysis (PCA) analysis for the study.

first: Panagiotis

last: Boumpas

first: Patrick

last: van Nierop y Sanchez

first: Katrin

last: Domsch

first: Hugo

middle: D

last: Pinto

first: Pedro

first: Ingrid

last: Lohmann


title: A Phase 2 Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma

city: Newton

first: Christopher

last: Walker

state: MA

address: 85 Wells Ave

institute: Karyopharm Therapeutics, Inc

summary: In a post-hoc exploratory analysis of the KING trial to seek molecular markers of outcome, RNAseq was performed on resected tumor specimens at the time of diagnostic surgery before the recurrence from 57 study patients from all arms with adequate selinexor exposure and evidence of either clinical benefit or resistance defined above. RNAseq data were used to infer the activity for 6,203 master regulator proteins using the VIPER algorithm.

overall_design: The sequenced specimens were split into a discovery set of 7 clear responders (BOD of CR or PR) compared to 23 resistors (BOR of PD) and a validation set of 11 with other evidence of clinical benefit (BOR of durable SD >140 days) and 11 non-responders (BOR of PD, or BOR non-durable SD <100 days). An ensemble of five different machine learning algorithms was used to generate an integrated predictive model for selinexor response in GBM. This model was based on the VIPER-inferred activity for three proteins that were activated in the responders compared to the non-responders in the discovery set, ZC3H12A (false discovery rate P-value [FDR]=6.45 x 10^-11), RAB43 (FDR=3.81 x 10^-10), and SOCS3 (FDR=3.16 x 10^-9). The model achieved an integrated area under the receiver operating characteristic (ROC) curve of 0.88 (p<0.05, permutation test) for a Leave-one-out cross-validation analysis in the discovery set and correctly predicted 9 of 11 patients classified as experiencing clinical benefit and 7 of 11 patients classified as non-responders in the validation set (ROC-AUC = 0.67).

first: Mariano

last: Alvarez

first: Andrea

last: Califano

first: Yosef

last: Landesman


title: BET inhibitors enhance the expression of fetal and embryonic hemoglobin genes [K562]

summary: We performed RNA-sequencing on erythroid cell lines treated with DMSO or JQ1. We found that JQ1 induces erythropoiesis and specifically upregulated fetal and embryonic globin genes at the beta globin locus.

overall_design: RNA was extracted from cultured cells treated with JQ1 or DMSO (control) collected at day 3 or 5 and submitted for deep sequencing

first: John

middle: Z

last: Cao

first: Bigelow

last: Kristina

first: Amittha

last: Wickrema


title: BET inhibitors enhance the expression of fetal and embryonic hemoglobin genes [TF-1]

overall_design: RNA was extracted from cultured cells treated with JQ1 or DMSO (control) collected at day 3 and submitted for deep sequencing


title: Ovol1 regulates psoriasis-like skin inflammation and epidermal hyperplasia

city: Irvine

first: Remy

last: Vu

address: D288 Med Sci I Health Sciences Rd

institute: University of California, Irvine

summary: Psoriasis is a common inflammatory skin disease characterized by aberrant inflammation and epidermal hyperplasia. Molecular mechanisms that regulate psoriasis-like skin inflammation remain to be fully understood.  Here we show that the expression of Ovol1 transcription factor is upregulated in psoriatic skin, and its deletion results in aggravated psoriasis-like skin symptoms following stimulation with imiquimod (IMQ). Using bulk and single-cell RNA-sequencing, we identify molecular changes in the epidermal, fibroblast and immune cells of Ovol1-deficient skin that reflect altered course of epidermal differentiation and enhanced inflammatory responses. Furthermore, we provide evidence for excessive full-length IL-1 signaling in the microenvironment of IMQ-treated Ovol1-deficient skin that functionally contributes to immune cell infiltration and epidermal hyperplasia. Collectively, our study uncovers a protective role for Ovol1 in curtailing psoriasis-like inflammation and the associated skin pathology

overall_design: Droplet-based single cell RNA-seq experiments were performed to identify molecular differences between control and Ovol1 null in untreated and imiquimod (IMQ) treated adult murine back skin.

first: Xing

last: Dai

first: Peng

last: Sun

first: Guadalupe

last: Gutierrez


title: Transcriptome Profile of Natural Product Deoxyshikonin Induced Gene Expression in IPEC-J2

status: Public on Nov 30 2021

city: Beijing

first: Jing

last: Wang

address: Shuguanghuayuan middle road #9, Haidian district

department: Institute of Animal Husbandry and Veterinary Medicine

institute: Beijing Academy of Agriculture and Forestry Sciences

summary: To understand the immunomodulatory effects  of deoxyshikonin (a natural derivative of well-known Chinese medicine shikonin) on porcine intestinal epithelium cells, the transcriptome analysis was performed to explore the transcriptional profile of porcine IPEC-J2 cells after deoxyshikonin treatment.

overall_design: The IPEC-J2 cells were exposed to deoxyshikonin at 5 μmol/L in triplicate. Non-treated cells served as a control (n=3).

first: Wei

last: Zhang

first: Xu

last: Chu


title: Coordinated mis-splicing of TMEM14C and ABCB7 causes ring sideroblast formation in SF3B1-mutant myelodysplastic syndrome

status: Public on Nov 29 2021

city: Seattle

first: Courtnee

last: Clough

state: Washington

address: 1959 Pacific St

department: Hematology

institute: University of Washington

summary:
Purpose: Mutant SF3B1 is near universally associated with MDS-RS but the exact mechanism of how mutant-SF3B1 induces ring sideroblast formation is unclear.
Methods: iPSC samples were differentiated from 5F-HPC derived from MDS-RS patient iPSCs. CD34+ progenitors were isolated using the CD34 enrichment kit (Miltenyi). CD34-CD71+GlyA- pro-erythroblasts were isolated by flow sorting on day 4. CD71+GlyA+ erythroblasts were isolated by flow sorting on day 9. Libraries with DNA fragments of ~300bp were selected using AMPure XP bead purification. Purified libraries were sequenced on an Illumina HiSeq 2000 using paired-end, 50 bp reads. Mis-splicing analysis was performed as described in Inoue et al. 2019.
Results: Mis-splicing analysis reveals ~100 genes that are strongly mis-spliced (>40%) by mutant SF3B1 during erythroid differentiation. We identify that mis-splicing of TMEM14C and ABCB7 contribute to RS formation in mutant SF3B1 cells.
Conclusion: Our iPS derived mutant SF3B1MDS-RS in vitro model is the first demonstration of a cell line that recapitulates mis-splicing, erythroid differentiation, and ring sideroblast formation.

overall_design: RNA sequencing profiles of CD34+ progenitors, CD34-CD71+GlyA- proerythroblasts, and CD34-CD71+GlyA+ erythroblasts derived from SF3B1 G742D/+  and SF3B1 +/+ iPS lines, and RNA profiles from SF3B1 K700E/+ and SF3B1 +/+ K562 cells.

first: Joseph

last: Pangallo

first: Martina

last: Sarchi

first: Janine

middle: O

last: Ilagan

first: Khrystyna

last: North

first: Rochelle

last: Bergantinos

first: Massiel

middle: C

last: Stolla

first: Jasmine

last: Naru

first: Patrick

last: Nugent

first: Eunhee

last: Kim

first: Derek

middle: L

last: Stirewalt

first: Arvind

middle: R

last: Subramaniam

first: Omar

last: Abdel-Wahab

first: Janis

last: Abkowitz

first: Robert

last: Bradley

first: Sergei

last: Doulatov


title: Transcriptomic analyis of isotype specific bone marrow and siLP IgA and IgAKO plasma cells as well as follicular and MZ B cells

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary: Plasma cell gene expression is driven both by isotype and tissue location.  In this series we examine gene expression of bone marrow IgA, IgM and IgG plasma cells as well as IgA plasma cells from small intestine lamina propria.  To validate tissue specific gene expression we also include gene expression from lamina propria IgA-/- plasma cells.  All plasma cell samples are from Blimp1+/GFP reporter animals and splenic follicular and marginal zone B cell gene expression have been added as reference populations.

overall_design: Samples are double sorted IgM+, IgA+ and IgM/A- BM PCs, IgA+ siLP PCs and PCs from IgAKO siLP as well as splenic follicular and marginal zone B cells. cDNA was prepared from RNA with 3' polyA capture method.  Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.

first: David

last: Allman

first: Joel

last: Wilmore

middle: T


title: Gene expression data from very early stage lesions (T1) of colorectal cancer

city: Belfast

first: Philip

middle: D.

last: Dunne

address: 97 Lisburn Road

department: The Patrick G Johnston Centre for Cancer Research

institute: Queen's University Belfast

summary: There are ~1.4 million cases of colorectal cancer (CRC) annually worldwide. Due to recent implementation of bowel cancer screening (BCS), incidence of diagnosis with stage I (T1/2, N0, M0) CRC has increased nearly four-fold; from approximately 12% pre-screening to approximately 42-45%. While survival rates for patients diagnosed with stage I CRC remains above 95%, and identification of patients at this early stage provides the best opportunity to improve in cancer survival rates, recent data has provided quantitative evidence that metastatic seeding can occur from disseminated cells at the very earliest stage of CRC development. The aim of study was to give an insight into aggressive “born-to-be-bad” biology through generation and transcriptional profiling of a novel case-controlled retrospective T1 CRC discovery cohort. We performed transcriptional and histological profiling to identify molecular pathology features of the high-risk metastatic phenotypes, discriminating between relapse and non-relapse T1 lesions and found that a cohort of aggressive early disseminating stage 1 CRC is associated with high cell intrinsic TGFB signalling and not stromal signalling.

overall_design:
Following pathological verification of T1 status (pT1), Almac Diagnostics Xcel Array platform was used to generate transcriptional profiling of a novel case-controlled retrospective T1 CRC discovery cohort (n=27 patients, to discriminate between T1 lesions with the high-risk of disease progression (Relapse; distant relapse and/or cancer specific death; n=10 patients) from those T1 lesions with low-risk of progression (Non-relapse; cured by surgery alone; n=17) following primary surgery.

** Submitter states they are not allowed to release the relapse status of the patients. To access relapse status data, please contact authors **


title: Dysregulation of miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

address: 1 University of New Mexico

institute: University of New Mexico

summary: In this study, we elucidated the role of miRNA dysregulation in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats. Male Sprague-Dawley rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced by carbohydrate. After 5 weeks, locked nucleic acid (LNA)-modified oligo antisense to miR-21 (AM21, Exiqon) was used to inhibit miRNA in vivo, and rats were subjected to 70% PHx. Liver samples were collected at 6 h, 24 h and 72 h after the surgery. The excised liver samples at t=0 served as within-animal controls.NanoString rat miRNA panel was used to obtain miRNA expression profile from 48 liver samples.

overall_design: miRNA expression was profiled in chronic ethanol-fed (EtOH) and carbohydrate control pair-fed (CHO) rat liver prior to (control, t=0) and 6 h, 24 h and 72 h after 70% partial hepatectomy (PHx), or at 0 h and 24 h with AM21 treatmemt.

first: Austin

last: Parrish

first: Ankita

last: Srivastava

first: Egle

last: Juskeviciute

first: Jan

last: Hoek


title: Single-cell profiling of human subventricular zone progenitors identifies SFRP1 as a target for stimulating progenitor activation.

city: Amsterdam

first: Vanessa

last: Donega

address: Boelelaan 1108

department: Anatomy and Neuroscience

country: Netherlands

institute: Amsterdam UMC

summary: Following the decline of neurogenesis at birth, progenitors of the subventricular zone (SVZ) remain mostly in a quiescent state in the adult human brain. The mechanisms that regulate this quiescent state are still unclear. Here, we isolated CD271+ progenitors from the aged human SVZ for single-cell RNA sequencing analysis. Our transcriptome data revealed the identity of progenitors of the aged human SVZ as late oligodendrocyte progenitor cells. We identified the Wnt pathway antagonist SFRP1 as a possible signal that promotes quiescence of progenitors from the aged human SVZ. Administration of WAY-316606, a small molecule that inhibits SFRP1 function, stimulates activation of neural stem cells both in vitro and in vivo under homeostatic conditions. Our data unravel a possible mechanism through which progenitors of the adult human SVZ are maintained in a quiescent state and a potential target for stimulating progenitors to re-activate.

overall_design: Single-cell transcriptome data from the aged human SVZ. Progenitors, astrocytes, and microglia were isolated by FACS. Sort-seq was run on single-cells as described in Muraro et al., 2016.

first: Astrid

last: van der Geest

first: Jacqueline

middle: A

last: Sluijs

first: Roland

middle: E

last: van Dijk

first: ChiChiu

last: Wang

first: Onur

last: Basak

first: Jeroen

last: Pasterkamp

first: Elly

middle: M

last: Hol


title: Differential interferon-α immune signatures prevent SARS-CoV-2 infection

status: Public on Nov 28 2021

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

summary: Type 1 interferons (IFN-I) exert pleiotropic biological effects during viral infections, balancing virus control and immune-mediated pathology and have been successfully employed for the treatment of viral diseases. In humans, there are twelve IFN-alpha (α) subtypes, which activate downstream signalling cascades and result in a distinct pattern of immune responses and differential antiviral responses. In this project, we analysed the antiviral activity of IFNα subtypes towards SARS-CoV-2 to identify the underlying immune signatures and explore their therapeutic potential. Pre-treatment of primary human airway epithelial cells (hAEC) cells with different human IFN-α subtypes demonstrated distinct antiviral activities against SARS-CoV-2. We identified IFNα5 as one of the strongest antiviral acting IFNs against SARS-CoV-2 infection in this study. Dose-dependency studies displayed an additive effect when co-administered with the broad antiviral drug remdesivir in cell culture. Bulk transcriptomics of pre-treated hAEC revealed differentially expressed gene signatures, with IFNα subtype-specific distinct, intersecting and common genes. Proteomic analysis confirmed the expression of distinct interferon effectors for the subset of highly antiviral IFNα5. Therefore, our data elucidate molecular antiviral host responses upon treatment with type I IFNs on several levels, knowledge which could aid in the development of novel therapeutic approaches.

overall_design: Primary human airway epithelial cells (hAEC) of four different donors were pre-treated with IFNalpha subtypes. Sixteen hours port stimulaiton, cells were lysed and total RNA was sequenced.   In addition, untreated cells were infected with SARS-CoV-2

first: Jonas

last: Schuhenn

first: Toni

last: Meister

first: Thilo

last: Bracht

first: Karin

last: Schork

first: Jean-Noël

last: Billaud

first: Carina

last: Elsner

first: Zehra

last: Karakoese

first: Sybille

last: Haid

first: Sriram

last: Kumar

first: Linda

last: Brunotte

first: Martin

last: Eisenacher

first: Thomas

last: Pietschmann

first: Bettina

last: Wiegmann

first: Hendrik

last: Beckert

first: Christian

last: Taube

first: Kerry

last: Lavender

first: Vu

last: Le-Trilling

first: Mirko

last: Trilling

first: Adalbert

last: Krawczyk

first: Stefan

last: Ludwig

first: Eike

last: Steimann

first: Ulf

last: Dittmer

first: Beate

last: Sodeik

first: Kathrin

last: Sutter

first: Stephanie

last: Pfaender


title: Comprehensive gene expression analysis in liver tissue following forced activation of Notch1 and Notch2 signaling.

city: Tokyo

first: Yasuhiro

last: Nakano

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University (TMDU)

summary: We compared the effects of Notch1 and Notch2 signaling induced by AAV8-mediated forced expression of Notch1 intracellular domain (NICD1) and Notch2 intracellular domain (NICD2), respectively, in the liver. Eight-week-old wild-type male mice were injected intraperitoneally with an NICD1- and/or NICD2-overexpressing AAV8 vector. Efficient AAV8-mediated gene transfer was confirmed by co-expressed green fluorescent protein (GFP) fluorescence in hepatocytes. A comprehensive gene expression analysis using DNA microarray indicated that the expression levels of 1704 and 1325 genes were altered by overexpressing NICD1 and NICD2, respectively, compared with the control group expressing only GFP.

overall_design: C57Bl6/J male mice were injected intraperitoneally with adeno-associated virus 8 (AAV8) expressing control GFP (6 × 10^11 vg/mouse), NICD1 and GFP (3 × 10^11 vg each/mouse), NICD2 and GFP (3 × 10^11 vg each//mouse), or NICD1&NICD2 (3 × 10^11 vg each/ mouse). Five days later, total RNA was isolated from excised liver tissues and subjected to expression microarray analysis.

first: Yutaka

last: Inagaki


title: Sexual dimorphism of early transcriptional reprogramming in dorsal root ganglia after peripheral nerve injury

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: Peripheral nerve injury induces genome-wide transcriptional reprogramming of first-order neurons and auxiliary cells of dorsal root ganglia (DRG). Accumulating experimental evidence suggests that onset and mechanistic principles of post-nerve injury processes are sexually dimorphic. We examined largely understudied aspects of early transcriptional events in DRG within 24 h after sciatic nerve axotomy in mice of both sexes. Using high-depth RNA sequencing (>50 million reads/sample) to pinpoint sexually dimorphic changes related to regeneration, immune response, bioenergy, and sensory functions, we identified a higher number of transcriptional changes in male relative to female DRG. In males, the induction of innate immune cascades via TLR, chemokine, and Csf1-receptor axis, robust regenerative programs driven by Sox, Twist1/2, Pax5/9 transcription factors were accompanied by a decline in ion channel transcripts. Females demonstrated nerve injury-specific transcriptional co-activation of the actinin 2 networks. The predicted upstream regulators and interactive networks highlighted the role of novel epigenetic factors and genetic linkage to sex chromosomes as hallmarks of gene regulation post-PNI. We implicated epigenetic X chromosome inactivation in the regulation of immune response activity uniquely in females. Sexually dimorphic regulation of MMP/ADAMTS metalloproteinases and their intrinsic X-linked regulator Timp1 contributes to extracellular matrix remodeling integrated with pro-regenerative and immune functions. Lexis1 noncoding RNA involved in LXR-mediated lipid metabolism was identified as a novel nerve injury marker. Together, our data identified unique early response triggers of sex-specific peripheral nerve injury regulation to gain mechanistic insights into the origin of female- and male-prevalent sensory neuropathies.

overall_design: Compare DRG transcriptomes of female and male mice after sciatic nerve axotomy to identify sexually dimorphic molecular signatures, upstream regulators and signaling pathways.

middle: V

first: Veronica

middle: I

last: Shubayev


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for advanced gastric cancer with different tumour-stroma-scores

city: Harbin

first: Yingwei

last: Xue

address: 150, Haping St, Nangang District

department: Department of Gastrointestinal Oncology

institute: Harbin Medical University Cancer Hospital

summary: Gastric cancer is one of the leading causes of cancer mortality worldwide. We compared transcriptomic profiles of  advanced gastric cancer with different tumour-stroma-scores to identify the prognostic significance of tumour-stroma-score in advanced gastric cancer.

overall_design: High-throughput sequence profiles from 38 gastric tumors and paired normal 38 gastric tissues from gastric cancer patients


title: Total RNA sequencing in neuroprogenitors after SMG6 deletion

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: Identification of transcriptome changes in neuroprogenitor cells deficient for SMG6 mediated nonsence mediated mRNA decay with the aim to identify specific pathways or single genes causing the observed phenotype. Nestin-cre mediated Smg6 inactivation caused perinatal lethality and defective late cortical neurogenesis due to reduced renewal and survival of the cortical neuroprogenitor cells. However the Emx1-cre mediated deletion only in cortical and hippocampal progenitors did not cause comparable phenotypes. RNAseq identified mainly cell cycle and DNA damage response pathways modulating the transcriptome. FOXM1 was identified as possible upstream regulator of interneuron progenitor fate.

overall_design: Transcriptome comparison of neural stem cells isolated from E13.5 embryo brains. The analysis of in vitro cultures was performed 6 days after the start of 4-OHT treatment (Smg6-iKO). 3 sample groups were evaluated, 1 mutant ("Smg6-iKO") and 2 control groups while the latter two were used to evaluate the effect of 4-OHT: In the mutant Smg6-iKO cells, Smg6 was deleted after 4-OHT treatment (i.e., induced knock-out). The first control group ("control") contains the same cells as in Smg6-iKO but was not treated with 4-OHT. The second group ("control with 4-OHT") contains cells that were treated with 4-OHT but cannot induce Smg6 deletion due to the genotype of the cells.

first: Paulius

last: Grigaravicius

first: Marco

last: Groth

first: Gabriela

last: Guerra

first: Zhao-Qi

last: Wang


title: scRNAseq analysis of mouse WT and Fmr1KO dorsal root ganglions

status: Public on Nov 27 2021

city: Athens

first: Oshri

last: Avraham

state: GA

address: 120 Cedar St

department: Cellular Biology

institute: University of Georgia

summary: Sensory hypersensitivity and somatosensory deficits represent the core symptoms of Fragile X syndrome (FXS).These alterations are believed to arise from changes in cortical sensory processing, while potential deficits in the function of peripheral sensory neurons or surrounding satellite glial cells (SGCs) residing in dorsal root ganglia remain unexplored. We found that cultured peripheral sensory neurons exhibit pronounced hyperexcitability in Fmr1 KO mice evident in markedly increased firing rate and decreased spike threshold. These alterations were caused primarily by increased input resistance, which aroused from decreased HCN channel-mediated current Ih. EM analyses also revealed major structural defects in neuron-SGC association. Single-cell RNAseq demonstrated extensive transcriptional changes in both neurons and SGCs indicative of defects in neuronal maturation/differentiation and neuron-SGC communication. These results reveal a hyper-excitable state of peripheral sensory neurons in Fmr1 KO mice with contributions from intrinsic alterations and from disrupted neuron-glia association and communication.

overall_design: We have applied the high-throughput single-cell mRNA sequencing technique, using the Chromium Single Cell Gene Expression Solution (10x Genomics) to mouse DRG, 2 biological replicates for each sample.

first: Valeria

last: Cavalli


title: Genetic studies of human-chimpanzee divergence using stem cell fusions

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

summary: Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human-chimpanzee divergence, we have generated human and chimpanzee auto-tetraploids and allo-tetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. The resulting tetraploid iPSCs can be stably maintained and retain the ability to differentiate along ectoderm, mesoderm, and endoderm lineages. RNA sequencing identifies thousands of genes whose expression differs between humans and chimpanzees when assessed in single-species diploid or auto-tetraploid iPSCs. Analysis of gene expression patterns in inter-specific allo-tetraploid iPSCs shows that human-chimpanzee expression differences arise from substantial contributions of both cis-acting changes linked to the genes themselves, and trans-acting changes elsewhere in the genome. To enable further genetic mapping of species differences, we tested chemical treatments for stimulating genome-wide mitotic recombination between human and chimpanzee chromosomes, and CRISPR methods for inducing species-specific changes on particular chromosomes in allo-tetraploid cells. We successfully generated derivative cells with nested deletions or inter-specific recombination on the X chromosome. These studies identify a long distance cis-regulatory domain of the Fragile X-associated gene (FMR1), confirm an important role for the X chromosome in trans-regulation of other expression differences, and illustrate the potential of this system for more detailed mapping of the molecular basis of human and chimpanzee evolution.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Bulk RNA sequencing of human and chimpanzee diploid, auto-tetraploid, and allo-tetraploid iPSC lines

middle: H

first: Rachel

last: Grant

last: Behrens

first: Marek

last: Kucka

first: Garrett

last: Roberts Kingman

first: Volker

last: Soltys

first: Yingguang

middle: F

last: Chan

first: David

last: Kingsley


title: Minimal Genomic Instability and Increased Immune Activity Differentiate EBV-positive PTCL from ENKTL and PTCL NOS

city: Singapore

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level  3

department: Department of Pathology

country: Singapore

institute: National University Health System, Singapore

type:
Genome variation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis[RNA-seq]

city: beijing

first: Danhua

last: Jiang

address: No. 1 West Beichen Road, Chaoyang District

institute: Chinese Academy of Sciences

summary: Global warming imposes a major threat to plant growth and crop production. In some plants including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments, termed thermomorphogenesis to facilitate plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermo-responsive genes, resulting in their activation. However, the mechanisms that regulate H2A.Z eviction and subsequent transcription activation are largely unknown. Here, we show that the ino80 chromatin-remodeling complex (ino80-C) promotes thermomorphogenesis and activates the expression of thermo-responsive and auxin-related genes. ino80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator in thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, ino80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification Histone H3 lysine 4 trimethylation (H3K4me3) and RNA Polymerase II (RNA Pol II) elongation, leading to the thermal induction of transcription. Notably, transcription elongation factors are required for the eviction of H2A.Z at PIF4 targets, suggesting the cooperation of ino80-C and transcription elongation in H2A.Z removal. Our results demonstrate that the (PIF4)-(ino80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, and establish a link between H2A.Z eviction and active transcription.

overall_design: Examination of transcriptome in ino80 mutant.

first: Huairen

last: Zhang

first: Mande

last: Xue


title: Minimal Genomic Instability and Increased Immune Activity Differentiate EBV-positive PTCL from ENKTL and PTCL NOS [GEP]

summary:
The molecular biology of the primary nodal EBV-positive variant of PTCL (PTCL-EBV) and its relationship with extranodal NK/T-cell lymphoma (ENKTL) and peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) remains poorly understood.
In this study, we assessed the relationship between the three diseases using gene and EBV miRNA expression profiling, and copy number aberration (CNA) analyses and attempted to characterize the degree of genomic instability (GI).  This series is the GEP data of 84 cases of FFPE NKTL samples and 4 cases of Lymph node controls.

overall_design: We used a combinational approach involving gene expression profiling (GEP), copy number alterations (CNA) analyses and EBV miRNA expression profiling in a large cohort of adult patients

first: Shangying

last: Chen


title: The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis


title: Minimal Genomic Instability and Increased Immune Activity Differentiate EBV-positive PTCL from ENKTL and PTCL NOS [CNA]

summary:
The molecular biology of the primary nodal EBV-positive variant of PTCL (PTCL-EBV) and its relationship with extranodal NK/T-cell lymphoma (ENKTL) and peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) remains poorly understood.
In this study, we assessed the relationship between the three diseases using gene and EBV miRNA expression profiling, and copy number aberration (CNA) analyses and attempted to characterize the degree of genomic instability (GI).  This series is the oncoscan CNA data of 77 NKTL samples.


title: FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression [HiChIP]

status: Public on Nov 26 2021

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We applied proximity-ligation with chromatin immunoprecipitation (HiChIP) in Treg and closely related conventional CD4+ T cells (Tconv) to map the H3K27Ac, FoxP3 and Yy1 chromatin structures.

overall_design: For analyses in FoxP3 proficient mice, splenic CD4 T cells from FoxP3-Thy1.1 hemizygous male mice were first enriched using CD4 untouched kit (Miltenyi), followed by secondary purification with anti-CD90.1 microbeads (Miltenyi) according to manufacturer’s instructions. Tconv (FoxP3-Thy1.1-Tcrb+CD4+CD45+CD19-CD8-CD11b-CD11c-) and Treg cells (FoxP3-Thy1.1+Tcrb+CD4+, CD45+CD19-CD8-CD11b-CD11c-) were sorted on a FACS-Aria to 96% and 94% purity, respectively. For experiments in FoxP3-deficient Tregs (Fig. 3), CD4+ T cells from spleen and peripheral lymph nodes from 6 week-old heterozygous females were first enriched as above by negative magnetic selection (Stem Cell), and Treg-like cells sorted as CD19-TCRβ+CD4+Thy1.1-GFP+ on a Moflo Astrios (Beckman Coulter).

first: Ricardo

last: Ramirez

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Interleukin-22 (IL-22) regulates B3GNT7 expression to induce intestinal fucosylation of O-linked glycans

city: Dallas

first: Jennifer

last: Kohler

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Interleukin (IL) - 22 is a cytokine that plays a critical role in the maintenance of intestinal epithelial homeostasis. Its downstream functions are mediated through ligation of its heterodimeric receptor comprised of IL-22 receptor subunit alpha 1 (IL-22Ra1) and IL-10R2, and subsequent activation of signal transducer and activator of transcription 3 (STAT3). IL-22 signaling can induce genes necessary for intestinal epithelial cell proliferation, tissue regeneration, tight junction fortification, and production of antimicrobials. Emerging studies have also implicated IL-22 signaling in the regulation of intestinal epithelial fucosylation in mice. However, whether IL-22 regulates intestinal fucosylation in human intestinal epithelial cells and the molecular mechanisms that govern this process are unknown. Here, we show that IL-22 signaling regulates expression of the B3GNT7 transcript, which encodes a β1-3-N-acetylglucosaminyltransferase that can participate in the synthesis of poly-N-acetyllactosamine (LacNAc) chains. Additionally, we show that IL-22 signaling regulates levels of the a1-3-fucosylated Lewis X (Lex) blood group antigen and this glycan epitope is primarily displayed on heavily O-glycosylated intestinal epithelial glycoproteins. The IL-22-mediated increase in Lex antigen levels requires B3GNT7, as disruption of B3GNT7 expression moderated the IL-22-dependent increase in Lex antigen levels. Moreover, we show that increased expression of B3GNT7 alone is sufficient to promote increased display of Lex-decorated carbohydrate glycan structures primarily on O-glycosylated intestinal epithelial glycoproteins. Together, the data presented here identify B3GNT7 as a critical intermediary in IL-22-dependent induction of intestinal fucosylation of O-linked glycans and uncover a novel role for B3GNT7 in intestinal glycosylation.

overall_design: Differentiated Caco-2 BBe1 cells were treated with 10 ng/mL rhIL-22 for 4 h and RNA was isolated for RNA-seq analysis. A no treatment control was used for comparision. Six samples were analyized, which included three biological replicates for each group (no treatment versus IL-22 treated group.

first: Daniela

middle: J

last: Carroll

first: Lynda

last: Mottram

first: Daniel

last: Propheter

first: Gabrielle

last: Lessen

first: Ashwani

last: Kumar

first: Chao

last: Xing

first: Lora

last: Hooper

first: Ulf

last: Yrlid

first: Mary

middle: W

last: Burns


title: An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element

city: Dunedin

first: Benjamin

last: Perry

state: Otago

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC can represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently-coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.

overall_design: Differential gene expression analysis of R7A and R7A* (a derivative of R7A with an epigenetic change)

first: Joshua

middle: P

last: Ramsay

first: Tahlia

last: Bastholm

first: Callum

last: Verdonk

first: Dinah

middle: D

last: Tambalo

first: John

last: Sullivan

first: Liam

middle: K

last: Harold

first: Beatrice

last: Panganiban

first: Elena

last: Colombi

first: William

last: Jowsey

first: Calum

last: Morris

first: Michael

last: Hynes

first: Charles

middle: S

last: Bond

first: Andrew

last: Cameron

first: Christopher

last: Yost

first: Clive

last: Ronson


title: A 37 kb region upstream of Brachyury comprising a notochord enhancer is essential for notochord and tail development

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

summary: Genetic dissection of the mouse Brachyury locus identified a notochord enhancer and predicts additional control elements essential for trunk and tail development of the mouse embryo.

overall_design: In order to indentify autoregulatory enhancers controlling Brachyury (T) expression in the notochord, we assesed the binding profile of T in in vitro generated notochord cells.

first: Dennis

last: Schifferl

first: Manuela

last: Scholze-Wittler

first: Lars

last: Wittler

first: Jesse

last: Veenvliet

first: Bernhard

middle: G

last: Herrmann


title: Single-cell transcriptomic outlook of human dental pulp in health and disease

city: Bangkok

first: Varodom

last: Charoensawan

address: 272 Rama VI Road, Ratchathewi District

department: Biochemistry

country: Thailand

institute: Mahidol university

summary: We present a collection of single-cell transcriptomic profiles of 6,810 pulpal cells isolated from a sound human maxillary third molars and carious teeth at different stages. We showed that the presence of deep, but not enamel caries, altered the immune cell compositions of the dental pulp. Differential expression analysis further revealed that the pro-inflammatory, anti-inflammatory and mineralization-related genes were upregulated in immune and stromal cells in deep dental caries. Cell-cell interaction prediction showed potential interactions between immune and stromal cells during homeostasis, and enhanced interactions between different cell types with macrophage during deep dental caries. Taken together, our study serves as a comprehensive survey of human pulpal cell heterogeneity, as well as provides novel molecular insights into dental pulps in health and disease.

overall_design: The single-cell transcriptomic profiles from cells residing in dental pulp from a sound tooth, enamel caries and deep dental caries were compared. Cell type frequency and differential gene expression were analyzed. Cell-cell interactions were predicted from the expression level of ligands and receptors.

first: Anunya

last: Opasawatchai

first: Sarintip

last: Nguantad

first: Benjamaporn

last: Sriwilai

first: Ponpan

last: Matangkasombut

first: Oranat

first: Ratchapin

last: Srisatjalak


title: The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis[ChIP-seq]

first: Danhua

last: Jiang

overall_design: Examination of H2A.Z enrichment in ino80 mutant.

first: Huairen

last: Zhang

first: Mande

last: Xue


title: Gene expession profle of melanoma subtypes selected by reflectance confocal microscopy

city: Modena

first: Marika

last: Quadri

state: Modena

address: Via del Pozzo 71

institute: University of Modena and Reggio Emilia

summary: Melanoma is the deadliest type of skin cancer, characterized by high cellular heterogeneity which contributes to therapy resistance and unpredictable disease outcome. Recently, by correlating Reflectance-Confocal-Microscopy (RCM) morphology with histopathological type, we identified four distinct melanoma-subtypes: dendritic-cell (DC), round-cell (RC), dermal-nest (DN), and combined-type (CT) melanomas. Our results demontsrate that each melanoma subtypes has a distinct biological and gene expression profile, related to tumor aggressiveness, confirming that RCM can be a dependable tool for in vivo detecting different types of melanoma and for early diagnostic screening

overall_design: In the study preseted here, 32 patients (9 samples for DC melaomas, 6 samples for RC melanomas,  7 samples for DN melanoma and 10 samples for CT melanomas) were analysed. NanoString nCounter technology was performed by PharmaDiagen team (Pordenone, Italy) and the analysis was focused on 770 genes (nCounter PanCancer Progression Panel).

first: Alessandra

last: Marconi

first: Elisabetta

last: Palazzo

first: Pellacani

last: Giovanni


title: Intersection of Regulatory Pathways Controlling Hemostasis and Hemochorial Placentation

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center


title: p53 pro-apoptotic activity is regulated by the G2/M promoting factor Cdk1 in response to DNA damage.

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

summary: Exposure to genotoxic stress promotes cell-cycle arrest and DNA repair or apoptosis. These “life” or “death” cell fate decisions often rely on the activity of the tumor suppressor gene p53. Therefore, how p53 activity is precisely regulated is essential to maintain tissue homeostasis and to prevent cancer development. Here we demonstrate that Drosophila p53 pro-apoptotic activity is regulated by the G2/M kinase Cdk1. We find that cell cycle arrested or endocycle-induced cells are refractory to ionizing radiation induced apoptosis. We show that the p53 protein is not able to bind to the p53 responding elements of the pro-apoptotic genes and to activate their expression in experimentally arrested cells. Our results indicate that p53 genetically and physically interacts with Cdk1 and that p53 pro-apoptotic role is regulated by the cell cycle status of the cell. We propose a model in which cell cycle progression and p53 pro-apoptotic activity are molecularly connected to coordinate the appropriate response after DNA damage.

overall_design: ATACseq experiments in Drosophila melanogaster wing imaginal discs in different conditions

first: Mireya

last: Ruiz-Losada

first: Raul

last: González

first: Ana

last: Peropadre

first: Alejandro

last: Gil-Gálvez

first: Antonio

last: Baonza

first: Carlos

last: Estella


title: Translational implications of Th17-skewed inflammation due to genetic deficiency of a cadherin stress sensor III

status: Public on Nov 25 2021

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: Desmoglein 1 (Dsg1) is a cadherin restricted to stratified tissues of terrestrial vertebrates, which serve as essential physical and immune barriers. Dsg1 loss-of-function mutations in humans result in skin lesions, multiple allergies, and isolated patient keratinocytes exhibit increased pro-allergic cytokine expression. However, the mechanism by which genetic deficiency of Dsg1 causes chronic inflammation is unknown. To determine the systemic response to Dsg1 loss, we deleted the three tandem Dsg1 genes in mice. Whole transcriptome analysis of embryonic Dsg1-/- skin showed a delay in expression of adhesion/differentiation/keratinization genes at E17.5, a subset of which recovered or increased by E18.5. Comparing epidermal transcriptomes from Dsg1-deficient mice and humans revealed a shared IL-17-skewed inflammatory signature. Although the impaired intercellular adhesion observed in Dsg1-/- mice resembles that resulting from anti-Dsg1 pemphigus foliaceus antibodies, pemphigus skin lesions exhibit a weaker IL-17 signature. Consistent with the clinical importance of these findings, treatment of two Dsg1-deficient patients with an IL-12/IL-23 antagonist originally developed for psoriasis resulted in improvement of skin lesions. Thus, beyond impairing the physical barrier, loss of Dsg1 function through gene mutation results in a psoriatic-like inflammatory signature before birth and treatment with a targeted therapy significantly improved skin lesions in patients.

overall_design: Examination of whole transcriptome in  patients with Severe Dermatitis, Multiple Allergies, and Metabolic Wasting (SAM) Syndrome

first: Kathleen

last: Green

first: Quinn

middle: R

last: Roth-Carter

middle: C


title: Actin binding proteins expression levels when modifying the actin sequence

city: Marseille

first: Thomas

last: Vannier

address: Campus de Luminy, 163 Av. de Luminy

institute: Aix-Marseille University

summary: We modified the actin gene in budding yeast and analyzed the cellular phenotypes of this modification. One important control is to verify the expression of actin binding proteins in these strains.

overall_design: The mRNA sequencing  of 8 Saccharomyces cerevisiae strains that express different actins were generated by deep sequencing, in triplicate, using Hiseq 4000 sequencing 1x50 bases. 5 haploid strains : Sc[Ca], Sc[Sp], Sc[At], N2 and Ca. 1 wild type haploid strain : ScNI. 1 diploid strain N2/Ca and 1 diploid wild type strain Sc/Sc.

first: Micaela

last: Boiero Sanders

first: Alphée

last: Michelot


title: RNA-seq of neuroblastoma syngeneic mouse models treated with anlotinib

city: tianjin

first: Yudong

last: Su

address: Huanhuxi Road

institute: Tianjin Medical University Cancer Institute and Hospital

summary: We utilized murine neuroblastoma (NB) cell lines 975A2 and 9464D. Both cell lines were derived from spontaneous NB in the adrenal glands of TH-MYCN transgenic mice on a C57BL/6 background. 975A2 (2 x 106) and 9464D (1 x 106) tumor cells were subcutaneously implanted into the right back of 6-week-old C57BL/6 mice. When the mean tumor volume reached 30-50 mm3, the mice were randomized into individual treatment groups. After 9 days of anlotinib (6mg/kg) treatment, 3 mice from the treatment group and the vehicle group were sacrificed, and the tumors were snap-frozen with liquid nitrogen immediately after resection. Sequencing was performed at Beijing Novogene Co., Ltd., and the differentially expressed genes (DEGs) were subjected to enrichment analysis. The results showed that anlotinib treatment significantly upregulated immune-related pathways such as adaptive immune response, T cell activation, regulation of INF-γ production, lymphocyte chemotaxis, migration and adhesion, and cytokine receptor activity and significantly downregulated angiogenesis-related pathways such as cellular response to vascular endothelial growth factor stimulus and blood vessel endothelial cell proliferation involved in sprouting angiogenesis.

overall_design: Gene expression analysis of murine neuroblastoma tumors treated with anlotinib

first: Qiang

last: Zhao

first: Long

last: Li


title: Translational implications of Th17-skewed inflammation due to genetic deficiency of a cadherin stress sensor I

overall_design: Skin transcriptional profiles from E18.5 wildtype, Dsg1+/-, and Dsg1-/- mice


title: Translational implications of Th17-skewed inflammation due to genetic deficiency of a cadherin stress sensor II

overall_design: Skin transcriptional profiles from E15.5-E18.5 wildtype, Dsg1+/-, and Dsg1-/- mice


title: Nuclear Poly(A) Binding Protein 1 (PABPN1) Mediates Zygotic Genome Activation-dependent Maternal mRNA Clearance During Mouse Early Embryonic Development

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: An embryo starts its life with maternal mRNA clearance, which is crucial for embryonic development. The elimination of maternal transcripts occurs by the joint action of two pathways: the first is a maternally encoded mRNA decay pathway (M-decay), while the second is zygotic genome activation (ZGA)-dependent pathway (Z-decay). However, the zygotic factors triggering maternal mRNA decay in early mammalian embryos remain largely unknown. In this study, we identify the zygotically encoded nuclear poly(A) binding protein 1 (PABPN1) as a factor required for maternal mRNA turnover, with an unpredictable cytoplasmic function. Cytoplasmic PABPN1 docks on 3ʹ-uridylated transcripts, downstream of terminal uridylyl transferases TUT4 and TUT7, and recruits 3ʹ-5ʹ exoribonuclease DIS3L2 to its targets, facilitating the decay of maternal mRNA. Pabpn1-knockout in mice resulted in preimplantation-stage mortality, due to early developmental arrest at the morula stage. This study characterizes the presence of a zygotic destabilizer of maternal mRNA and helps in elucidating the Z-decay process mechanisms, which potentially contribute to human fertility.

overall_design: Zygotes,  2-cell, and 8-cell embryos of WT and Pabpn1 knockdown for replicates are performed RNA sequencing. 2-cell embryos of control and Dis3l2 knockdown for replicates are performed RNA sequencing.

first: Long-Wen

first: Ye-Zhang

last: Zhu

first: Yun-Wen

last: Wu

first: Shuai-Bo

last: Pi

first: Li

last: Shen

first: Heng-Yu


title: Depicting human endothelial to hematopoietic transition and the effects of modulating pyruvate catabolism on blood formation

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: Hematopoietic stem cell (HSC) quiescence, maintenance and differentiation are closely linked to changes in metabolism. However, the role of metabolism during the first emergence of HSCs from hemogenic endothelium (HE) is still unknown. In this study, we focus on the implication of energetic metabolic pathways during endothelial to hematopoietic transition (EHT). EHT is accompanied by a metabolic switch, with concomitant increases in glycolysis and oxidative phosphorylation (OXPHOS). Inhibiting glycolysis in HE cells leads to a block in hematopoietic lineage specification. An OXPHOS fuel, glutamine, is essential for HSC emergence and provides distinct intermediates to mediate differentiation towards the two major hematopoietic lineages, GPA+ and CD45+ cells. Strikingly, shifting the fate of pyruvate from glycolysis to the TCA cycle redirects HE specification towards CD45+ cells at the expense of GPA+ cells and vice versa. As such, our findings reveal the plasticity of hematopoietic lineage specification during EHT which can be modulated by metabolism.

overall_design:
Transcriptomic analysis of hiPSC-derived HE, EHT, HSC-like cells and cord blood CD34+ cells. Comparison of control HE cells with UK5099- or DCA-treated HE cells.

***Raw data not provided due to patient privacy concerns***

first: Els

last: Mansell

first: Isaac

last: Canals

first: Carolina

last: Guibentif

first: Niels-Bjarne

last: Woods

first: Leal

last: Oburoglu


title: Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae [I]

status: Public on Nov 24 2021

city: Berkeley

first: Molly

last: Brothers

state: CA

address: UC Berkeley 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. For the following datasets, we created a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, with or without a 3xV5 epitope at the C-terminus. We performed ChIP-seq experiments (immunoprecipitated Sir3-M.EcoGII-3xV5) and MeDIP-seq experiments (immunoprecipitated m6A methylated DNA). We also used a temperature-sensitive allele of SIR3 (sir3-8) fused to M.ECOGII to induce m6A methylation for MeDIP-seq.

overall_design: 32 samples total (24 in initial submission, 8 more in resubmission). Input and IP data for each experiment are included.

first: Jasper

last: Rine


title: miRNAs' functions in ADHD

city: Kaohsiung

first: Sung-Chou

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary:
In our previous study, we found that WBC miRNA may serve as ADHD prediction biomarkers. Therefore, we wonder whether these biomarkers miRNAs may regulate the neuron cells.
We had Human Cortical Neuronal cells (HCN-2) transfected with miR-126-5p, miR-140-3p or Scrambled control mimics, followed by observing the differentiation of HCN-2 cells. We found that miR-126-5p and miR-140-3p promoted HCN-2 differentiation.

overall_design: To understand why these two miRNAs promoted HCN-2 differentiation. We collected total RNA samples of these three sets and examined gene expression with Human Clariom D microarray assay.

first: Liang-Jen

last: Wang

first: Ho-Chang

last: Kuo


title: Small RNA-seq analysis of serum miRNAs in patients with severe COVID-19

city: Ancona

first: Jacopo

last: Sabbatinelli

state: AN

address: Via Tronto 10/A

department: Department of Clinical and Molecular Sciences

institute: Università Politecnica delle Marche

summary: The clinical course of Coronavirus disease 2019 (COVID-19) displays a wide variability, ranging from completely asymptomatic forms to diseases associated with severe clinical outcomes. To reduce the incidence COVID-19 severe outcomes, innovative molecular biomarkers are needed to improve the stratification of patients at the highest risk of mortality and to better customize therapeutic strategies.  MicroRNAs associated with COVID-19 outcomes could allow quantifying the risk of severe outcomes and developing models for predicting outcomes, thus helping to customize the most aggressive therapeutic strategies for each patient. Here, we analyzed the circulating miRNA profiles in a set of 12 hospitalized patients with severe COVID-19, with the aim to identify miRNAs associated with in-hospital mortality.

overall_design: MicroRNA expression profile obtained from small RNA-sequencing of serum samples of 12 COVID-19 patients (6 survivors, 6 deceased) with multifocal interstitial pneumonia and requiring oxygen therapy.

first: Fabiola

last: Olivieri

first: Angelica

last: Giuliani

first: Giulia

last: Matacchione

first: Deborah

last: Ramini


title: Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function [ChIPseq]

city: Cambridge

first: Matthew

last: Brown

address: 75 Ames St

institute: Broad Institute

summary: Circadian rhythm disruption (CD) is associated with dysregulation of glucose homeostasis and Type 2 diabetes mellitus (T2DM). While the link between CD and T2DM remains unclear, there is accumulating evidence that disruption of fasting/feeding cycles mediates CD-induced metabolic dysfunction. Herein we utilized an approach encompassing analysis of behavioral, physiological, transcriptomic, and single-cell epigenomic effects of CD and consequences of restoration of fasting/feeding cycles through time-restricted feeding (tRF) in mice. Results show that CD perturbs glucose homeostasis through disruption of pancreatic β-cell function and loss of circadian β-cell transcriptional and epigenetic control. In contrast, restoration of fasting/feeding cycle prevented CD-mediated metabolic dysfunction by reestablishing circadian regulation of glucose tolerance, β-cell function, β-cell transcriptional profile, and reestablishment of proline and acidic amino acid-rich basic leucine zipper (PAR-bZIP) transcription factor activity in β-cells. This study provides mechanistic insights into beneficial effects of tRF and its role in prevention of β-cell failure in T2DM.

overall_design: Examination of DBP binding in INS1 832/13 pancreatic beta cells

first: Satish

last: Sen

first: Amelia

last: Mazzone

first: Tracy

last: Her

first: Yuning

last: Xiong

first: Jeong-Heon

last: Lee

first: Naureen

last: Javeed

first: Christopher

last: Colwell

first: Kuntol

last: Rakshit

first: Nathan

last: Lebrasseur

first: Alexandre

last: Gaspar-Maia

first: Tamas

last: Ordog

first: Aleksey

last: Matveyenko


title: Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function [ATACseq]

overall_design: Examination of open chromatin regions at circadian time 4 and 16 in pancreatic islets in mice exposed to either control, circadian disruption, or circadian disruption plus 8h time-restricted feeding


title: Beta-cell specific insulin resistance promotes glucose-stimulated insulin hypersecretion

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

summary: Insulin receptor (Insr) protein can be found at higher levels in pancreatic b-cells than in most other cell types, but the consequences of b-cell insulin resistance remain enigmatic. Ins1cre allele was used to delete Insr specifically in b-cells of both female and male mice which were compared to Ins1cre-containing littermate controls at multiple ages and on multiple diets. RNA-seq of recombined b-cells revealed significant differences in multiple pathways previously implicated in insulin secretion and cellular fate, including rewired Ras and NFkB signaling. Male, but not female, bInsrKO mice had reduced oxygen consumption rate, while action potential and calcium oscillation frequencies were increased in Insr knockout b-cells from female, but not male mice. Female bInsrKO and bInsrHET mice exhibited elevated insulin release in perifusion experiments, during hyperglycemic clamps, and following i.p. glucose challenge. Deletion of Insr did not reduce b-cell mass up to 9 months of age, nor did it impair hyperglycemia-induced proliferation. Based on our data, we adapted a mathematical model to include b-cell insulin resistance, which predicted that b-cell Insr knockout would improve glucose tolerance depending on the degree of whole-body insulin resistance. Indeed, glucose tolerance was significantly improved in female bInsrKO and bInsrHET mice when compared to controls at 9, 21 and 39 weeks. We did not observe improved glucose tolerance in adult male mice or in high fat diet-fed mice, corroborating the prediction that global insulin resistance obscures the effects of b-cell specific insulin resistance. We further validated our in vivo findings using the Ins1-CreERT transgenic line and found improved glucose tolerance 4 weeks after tamoxifen-mediated Insr deletion. Collectively, our data show that loss of b-cell Insr alone is sufficient to drive glucose-induced hyperinsulinemia, thereby improving glucose homeostasis in otherwise insulin sensitive dietary and age contexts.

overall_design: Study of beta cells in mouse islets with three different genotypes for the Insr gene (WT, KO, HET) and both sexes, with between 5 and 8 replicates per genotype-sex combination.

first: Søs

last: Skovsø

first: James

last: Johnson


title: PDGF promotes skin fibrosis via a novel mechanism mediated by signaling through MCHR1

city: Charleston

first: Carol

last: Feghali-Bostwick

state: SC

address: 96 Johnathan Lucas St Suite 816 MSC 637

department: Medicine - Rheumatology

institute: Medical University of South Carolina

summary: We identified several differentially expressed genes in dermal fibroblasts from patients with SSc compared to their healthy twins, including the upregulation of MCHR1 in SSc fibroblasts. We also uncovered MCHR1 as a hub gene with the highest centrality degree in the network analysis, suggesting important biological role. We identified PDGF as the pro-fibrotic growth factor that increases MCHR1 levels. We further determine that PDGF induction of dermal fibroblast activation and pro-fibrotic factor production is mediating by MCHR1 using silencing and chemical inhibition of MCHR1.

overall_design: Compare the expression profiling of primary human skin fibroblasts from healthy donors transfected with siRNA to silence MCHR1 with PDGFBB or vehicle treatment

first: Naoko

last: Takamura

first: Ludivine

last: Renaud

first: Willian

last: da Silveira


title: Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function [scATAC-seq]

first: Matthew

last: Brown

overall_design: Examination of open chromatin regions at circadian time 4 and 16 in single pancreatic islet cells in mice exposed to either control, circadian disruption, or circadian disruption plus 8h time-restricted feeding

first: Satish

last: Sen

first: Amelia

last: Mazzone

first: Tracy

last: Her


title: WNT signals inhibit paracrine induction of senescence in human multipotent stromal cells

city: Rotterdam

first: Derk

last: ten Berge

state: Zuid-Holland

address: Postbus 2040

department: Cell Biology

institute: Erasmus MC

summary: Senescence, the irreversible cell cycle arrest of damaged cells, is accompanied by a deleterious pro-inflammatory senescence-associated secretory phenotype (SASP). Senescence and the SASP are major factors in aging, cancer, and degenerative diseases, and interfere with the expansion of adult cells in vitro, yet little is known about how to counteract their induction and deleterious effects. Paracrine signals are increasingly recognized as important senescence triggers and understanding their regulation and mode of action may provide novel opportunities to reduce senescence-induced inflammation and improve cell-based therapies. Here, we show that the signalling protein WNT3A counteracts senescence in cultured human adult multipotent stromal cells (MSCs) by limiting paracrine senescence. We find that entry into senescence in a small subpopulation of MSCs triggers a secretome that causes a feed-forward signalling cascade that with increasing speed induces healthy cells into senescence. WNT signals interrupt this cascade by repressing cytokines that mediate this induction of senescence. Inhibition of those mediators by interference with NF-kB or interleukin 6 signalling reduced paracrine senescence in absence of WNT3A and promoted the expansion of MSCs. Our work reveals how WNT signals can antagonize senescence and has relevance not only for expansion of adult cells but can also provide new insights into senescence-associated inflammatory and degenerative diseases. //  The RNAseq data in particular focusses on the transcriptome changes in MSCs occuring in vitro culture over four passages in presence or absence of growth factors WNT3A and FGF2.

overall_design: RNA sequencing of 18 human bone marrow derived multipotent stromal cell cultures from three bone marrow donors (female, post-menopause age) [6 per donor]; cells were harvested at two different time points (passages): passage 1 after six hours culture with either: FGF2 and WNT3A, FGF2 and CHAPS (vehicle for WNT3A), WNT3A only (FGF2 was dissolved in cell culture medium, thus no vehicle), CHAPS only; passage 4 after culture since passage 1 in either: FGF2 and WNT3A or FGF2 and CHAPS

first: Johannes

last: Lehmann

first: Roberto

last: Narcisi

first: Natasja

last: Franceschini

first: Danai

last: Chatzivasileiou

first: Cindy

last: Boer

first: Wendy

last: Koevoet

first: Diana

last: Putavet

first: Dubravka

last: Drabek

first: Rien

last: van Haperen

first: Peter

middle: L

last: de Keizer

first: Gerjo

last: van Osch


title: 5C Chromatin interactions in the Igh locus in resting splenic B cells

status: Public on Nov 23 2021

city: Chicago

first: Amy

last: Kenter

state: Illinois

address: 835 S Wolcott Ave

institute: University of Illinois at Chicago

summary: These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme. The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells. The cells are then lysed and chromatin is digested with the Hind III restriction enzyme. The digested fragments are ligated under dilute conditions to promote intra-molecular ligation. A genome-wide interaction library of ligation products corresponding to all possible chromatin interactions is produced by this method. In 5C assays, over 12,000 potential ligation products specific to the Igh locus are detected by PCR using multiplexed primer pairs. Here we focused on the 3’ end of the Igh locus to evaluate the status of the constant region domain of the locus in LPS+IL4 activated splenic B cells.  We observe that the configuration of the 3’ end of the Igh locus spanning the CH region genes assumes a developmental stage specific configuration in B lineage B cells. We find that the interaction frequency and activation state of the 3’ enhancer increases as B cells mature.

overall_design: The aim of this study was to create a comprehensive map of chromatin interactions spanning the entire 2.9 Mb Igh locus inunstimulated resting splenic B cells. 5C primers follow an alternating pattern and were designed at HindIII restriction sites using the 5C primer design tools that are available online (http://my5C.umassmed.edu) (Lajoie et al., 2009) and were previously reported (Kumar et al., 2013).  In this experiment, 112 forward primers and 113 reverse primers were designed for all possible HindIII restriction fragments. This design allowed for the interrogation of many (but not all) restriction fragments, thus an unbiased interaction map across the locus and for potentially identifying new regulatory elements. An alternating scheme of forward and reverse primers was also included for a gene desert on chromosome 5 using 24 forward and 25 reverse 5C primers for a total of 525 potential cis interactions. Primers settings were: U-BLAST: 3; S-BLAST: 80: 15-MER: 800; MIN_FSIZE: 1000; MAX_FSIZE: 15,000; OPT_TM: 65; OPT_PSIZE: 30. Several primers with somewhat relaxed parameters were included to provide a more complete coverage of the Igh locus. Currently, data for two biological replicates have been generated for unstimulated resting splenic B cells spanning the murine Igh locus and a gene desert on chromosome 5 using high-throughput paired-end sequencing in the Illumina GAII platform. The 5C looping interactions that are detected in both the biological replicates are considered significant.  These samples are part of a series of 5C analyses which were previously published (Montefiori et al. Cell Rep 2016 Feb 2;14(4):896-906).

first: Robert

last: Wuerffel


title: 5C Chromatin interactions in the Igh locus in activated splenic B cells

overall_design: The aim of this study was to create a comprehensive map of chromatin interactions spanning the entire 2.9 Mb Igh locus in LPS+IL4 activated splenic B cells. 5C primers follow an alternating pattern and were designed at HindIII restriction sites using the 5C primer design tools that are available online (http://my5C.umassmed.edu) (Lajoie et al., 2009) and were previously reported (Kumar et al., 2013).  In this experiment, 112 forward primers and 113 reverse primers were designed for all possible HindIII restriction fragments. This design allowed for the interrogation of many (but not all) restriction fragments, thus an unbiased interaction map across the locus and for potentially identifying new regulatory elements. An alternating scheme of forward and reverse primers was also included for a gene desert on chromosome 5 using 24 forward and 25 reverse 5C primers for a total of 525 potential cis interactions. Primers settings were: U-BLAST: 3; S-BLAST: 80: 15-MER: 800; MIN_FSIZE: 1000; MAX_FSIZE: 15,000; OPT_TM: 65; OPT_PSIZE: 30. Several primers with somewhat relaxed parameters were included to provide a more complete coverage of the Igh locus. Currently, data for two biological replicates have been generated for LPS+IL4 activated splenic B cells spanning the murine Igh locus and a gene desert on chromosome 5 using high-throughput paired-end sequencing in the Illumina GAII platform. The 5C looping interactions that are detected in both the biological replicates are considered significant.  These samples are part of a series of 5C analyses which were previously published (Montefiori et al. Cell Rep 2016 Feb 2;14(4):896-906).


title: Administration of aerosolized SARS-CoV-2 to K18-hACE2 mice uncouples respiratory infection from fatal neuroinvasion

city: Milano

first: Chiara

last: Laura

address: Via Olgettina 58

institute: San Raffaele Scientific Institute

summary: The development of tractable animal models that faithfully reproduce COVID-19 pathogenesis would arguably be a major benefit. Infection of transgenic mice expressing the human version of the SARS-CoV-2 receptor (hACE2) by intranasal instillation of a liquid SARS-CoV-2 suspension under deep anesthesia results in disproportionate high CNS infection leading to fatal encephalitis, which is rarely observed in humans and severely limits this model’s usefulness. Here, we describe the characterization of a novel COVID-19 mouse model based on an inhalation tower system that allows to expose unanesthetized mice to aerosolized virus under controlled conditions. Aerosol exposure of K18-hACE2 transgenic mice to SARS-CoV-2 resulted in robust viral replication in the respiratory tract, anosmia, and airway obstruction, but did not lead to fatal viral neuroinvasion. When compared to intranasal inoculation, aerosol infection resulted in a more pronounced lung pathology including increased immune infiltration, fibrin deposition and a transcriptional signature comparable to that observed in humans. This model may prove useful for studies of viral transmission, disease pathogenesis (including long-term consequences of SARS-CoV-2 infection) and therapeutic interventions.

overall_design: Bulk RNA-seq of lung homogenates 6 days after SARS-CoV-2 infection. Comparison between intranasal- (n=3) and aerosol- (n=4) infected mice, 2 PBS-treated mice are added as control

first: Valeria

last: Fumagalli

first: Micol

last: Ravà

first: Davide

last: Marotta

first: José

last: Garcia-Manteiga

first: Luca

last: Guidotti

first: Matteo

last: Iannacone


title: Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function [RNAseq]

first: Matthew

last: Brown

state: MA

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Examination of gene expression in: (1) Pancreatic islets from mice exposed to either control, circadian disruption, or circadian disruption plus 8h time-restricted feeding; (2) INS-1 832/13 cells transfected with scramble or Dbp siRNA

first: Satish

last: Sen

first: Amelia

last: Mazzone

first: Tracy

last: Her

first: Yuning

last: Xiong

first: Jeong-Heon

last: Lee

first: Naureen

last: Javeed

first: Christopher

last: Colwell

first: Kuntol

last: Rakshit

first: Nathan

last: Lebrasseur

first: Alexandre

last: Gaspar-Maia

first: Tamas

last: Ordog

first: Aleksey

last: Matveyenko