title: Injectable natural polymer hybrid hydrogel targeting aseptic loosening due to wear particle induced osteolysis

status: Public on Jun 17 2023

city: Erlangen

first: Xi

last: Chen

address: Universitätsstraße 42-44, 91054 Erlangen

department: Department of Internal Medicine 3 - Rheumatology and Immunology

institute: Friedrich-Alexander University Erlangen-Nuremberg (FAU) and Universitätsklinikum Erlangen

summary: Aseptic loosening represents a significant factor contributing to joint replacement failure, primarily associated with diminished bone formation and heightened osteoclast-induced osteolysis. Here, a natural polymer-based injectable hydrogel that encapsulates irisin protein (referred to as I-OG hydrogel) is reported. The hierarchical cross-linked structure of the I-OG hydrogel confers favorable mechanical properties, desirable self-healing ability, and acceptable injectability and, more importantly, sustains continuous release of the protein at the interface between the bone and implant prosthesis. The I-OG hydrogel effectively fills the gap between the titanium pin and bone tissue, successfully inhibiting aseptic loosening induced by titanium particles, which outcome confirms the occurrence of irisin protein's slow-release process and its inhibitory effect on osteolysis. Mechanistically, our in vitro experiments demonstrated that irisin released from the I-OG hydrogel upregulates the Wnt/β-catenin signaling pathway in bone marrow stromal cells (BMSCs) through integrin αV, while concurrently downregulating the NF-κB (P65) signaling pathway in osteoblasts. These molecular events ultimately promote osteogenic differentiation and inhibit osteoclast activation. Collectively, our findings establish that the I-OG hydrogel effectively counteracts aseptic loosening by resisting osteolysis caused by titanium particles and enhancing periprosthetic bone formation, and offers promising prospects for the treatment of aseptic loosening in prosthetic implants.

overall_design: Irisin is thought to be produced by muscles as an actin. This project was undertaken by synthesising a natural polymer based injectable hydrogel encapsulating Irisin, called I OG hydrogel, and injecting it into the tibiae of aseptic loose mice. After 5 weeks of treatment, we analysed differential mRNA expression in tibiae between each group. It was demonstrated that I OG hydrogel inhibited the development of aseptic loosening by modulating integrin pathway, Wnt pathway and inflammatory pathway.


title: Molecular signatures of CD45+ cells from brain and spleen after intracerebral hemorrhage

status: Public on Jun 07 2023

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

type: Expression profiling by high throughput sequencing

summary: Leukocyte infiltration accelerates brain injury following intracerebral hemorrhage (ICH). But the involvement of T lymphocytes in this process has not been fully elucidated.To further depict the landscape of the composition and functional states of brain-infiltrating immune cells following ICH, single-cell RNA sequencing was performed to compare  the molecular characteristics of CD45+ cells from brain and spleen tissues in ICH and control mice.Our results revealed that brain-infiltrating T cells exhibited enhanced pro-inflammatory and pro-apoptotic signatures.

overall_design: CD45+ cells were sorted from the spleen and brain of ICH mice or sham controls at day 3, and were subjected to single-cell RNA sequencing. And to obtain enough CD4+ T cells in sham brains for sub-clustering and data processing, we optimized the FACS-sorting to enrich CD45hi cells. Data were pooled from 15 mice in each group.

first: Samuel

middle: X

last: Shi

first: Yuwen

last: Xiu

first: Yan

last: Li

first: Kaibin

first: Meng

last: Yuan

first: Qiang

last: Liu

first: Xiaoying

last: Wang

first: Weina


title: RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

status: Public on Jun 08 2023

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene expression in murine T cells from Ebi3-WT or Ebi3-KO mice

status: Public on May 31 2023

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

summary: mRNA profiles of T cells from 8-week-old wild-type (Foxp3 YFP/cre) or Ebi3-KO (Foxp3 YFP/cre Ebi3-/-) mice were generated by 3'-sequencing, in triplicate.

overall_design: mRNA profiles from T cells activated in vitro (anti-CD3, anti-CD28, IL-2)

first: Jerome

last: Paggetti


title: Effects of gut microbiota on gene expression in the choroid plexus

status: Public on Jun 05 2023

city: Zwijnaarde

first: Roosmarijn

middle: E.

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

country: Belgium

institute: VIB-UGent

summary: Accumulating evidence indicates that gut microbiota dysbiosis is associated with increased blood-brain barrier (BBB) permeability and contributes to Alzheimer’s disease (AD) pathogenesis. In contrast, the influence of gut microbiota on the blood-cerebrospinal fluid (CSF) barrier has not yet been studied. Here, RNA-seq analysis of choroid plexus tissues of normal colonized specific pathogen-free (SPF) versus decolonized antibiotics-treated mice revealed that the barrier function of choroid plexus is affected by the absence of gut microbiota in the AB mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from Choroid Plexus of SPF, SPF Reconstituted, Germ-Free, Germ-Free Reconstituted, AB-treated and AB-treated Reconstituted mice

first: Junhua

last: Xie

first: Arnout

last: Bruggeman

first: Clint

last: De Nolf


title: Imbalanced Unfolded Protein Response Signaling Contributes to 1-Deoxysphingolipid Retinal Toxicity

status: Public on May 30 2023

city: La Jolla

first: R.

middle: Luke

last: Wiseman

address: 10550 N Torrey Pines Rd

department: Dept. of Molecular Medicine

country: USA

institute: The Scripps Research Institute

summary: 1-deoxysphinganine accumulation is associated with retinal toxicity. We used single nucelus and bulk sequencing to profile transcriptional remodeling following treatment with 1-dexoysphnganine in human iPSC-derived retinal organoids.

overall_design: Human iPSC-derived retinal organoids were incubated with 1-dSA for either 2 days, 3 days or 4 days. At four days, organoids were treated with 1-dSA  in the presence or absence of the ISRIB or AA147.

first: Jessica

middle: D

last: Rosarda

first: Sarah

last: Giles

last: Harkins-Perry

first: Elizabeth

last: Mills

first: Martin

last: Friedlander

first: R

middle: L

first: Kevin

middle: T

last: Eade


title: 2-hydroxypropyl-beta-cyclodextrin treatment induces modest immune activation in healthy rhesus macaques [ATAC-seq]

status: Public on Jun 12 2023

city: Bethesda

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

summary: Experimental SIV infection of Asian macaques is an excellent model for HIV disease progression and therapeutic development. Recent coformulations of nucleoside analogs and an integrase inhibitor have been used for parenteral antiretroviral (ARV) administration in SIV-infected macaques, successfully resulting in undetectable plasma SIV RNA. In a cohort of SIVmac239-infected macaques, we recently observed that administration of co-formulated ARVs resulted in an unexpected increase in plasma levels of soluble CD14 (sCD14), associated with stimulation of myeloid cells. We hypothesized that the coformulation solubilizing agentKleptoseTM(2-hydroxypropyl-beta-cyclodextrin; HPβCD) may induce inflammation with myeloid cell activation and the release of sCD14. Herein, we stimulated peripheral blood mononuclear cells (PBMCs) from healthy macaques with HPβCD from different commercial sources and evaluated inflammatory cytokine productionin vitro.Treatment of PBMCs resulted in increased sCD14 release and myeloid cell IL-1bproduction - with stimulation varyingsignificantlyby HPβCD source - and destabilized lymphocyte CCR5 surface expression.We further treated healthy macaques withKleptosealone.In vivo, we observed modestly increased myeloid cell activation in response to Kleptose treatment without significant perturbation of the immunological transcriptome or epigenome.Our resultsdemonstrate a need for vehicle-only controls and highlight immunological perturbations that can occur when using HPβCD in pharmaceutical co-formulations.

overall_design: Samples were obtained before or after treating animals with 2-hydroxypropyl-beta-cyclodextrin at 15% (w/w) Kleptose(TM) HBP parenteral grade (Roquette #346111109D) subcutaneously at 1 ml/kg/day for up to 120 days.

first: Alexandra

middle: M

last: Ortiz

first: Andrew

middle: R

last: Rahmberg

first: Tovah

middle: E

last: Markowitz


title: Costs of reproduction and their effect on age-related gene expression in Bombus terrestris queens

status: Public on Jun 06 2023

city: Norwich

first: David

middle: C.

last: Prince

address: Norwich Research Park

country: United Kingdom

institute: University of East Anglia

summary: Our two main aims were 1) to isolate age-related changes in gene expression in queens of the eusocial bumble bee, Bombus terrestris; and 2) to determine whether experimentally increasing the costs of reproduction (by removing eggs) caused changes in age-related gene expression in these queens. To address these aims we extracted RNA from three key tissues (brain, fat body and ovary) from queens at two time points (10% and 60% mortality phases). Each of these queens had experienced one of two treatments: an egg removal (R) treatment (to increase the costs of reproduction) and an egg removal and replacement (C) treatment (to control for the effects of disturbance caused by egg removal).

overall_design: We used mRNA-seq to identify the RNA profiles in three tissue types (brain, fat body and ovary) in two time points (after 10% cohort death (TP1) and 60% cohort death (TP2)) for two treatments (egg removal (R) and egg removal and replacement (C)), with up to six biological replicates per tissue/time point/treatment combination. Each sample was sequenced on two lanes (L1 and L2) of the sequencing machine in order to generate sufficient numbers of reads while controlling for between lane variability.

middle: H

last: Collins

middle: C

first: Jenny

last: Donelan

first: Tracey

last: Chapman

middle: F

last: Bourke


title: Perturbation of protein homeostasis brings plastids at the crossroad between repairment and dismantling

status: Public on May 26 2023

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

summary: In this study, we have addressed the complex regulatory chloroplast quality-control pathway by modulating the expression of two nuclear genes encoding the plastid ribosomal proteins PRPS1 and PRPL4.

overall_design: Comparative RNA-Seq analyses of Arabidopsis indPRPS1 and indPRPL4 dexamethasone-inducible lines overexpressing genes encoding the plastid ribosomal subunit S1 and the plastid ribosomal subunit L4, respectively.

first: Luca

last: Tadini

first: Nicolaj

last: Jeran

first: Paolo

last: Pesaresi


title: Directed differentiation of human hindbrain neuroepithelial stem cells recapitulates cerebellar granule neurogenesis.

status: Public on May 29 2023

city: Toronto

first: Biren

last: Dave

state: Ontario

address: 686 Bay Street

country: Canada

institute: University of Toronto


title: RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ChIP-Seq]

first: Mayra

last: Furlan-Magaril

summary: Chicken erythrocytes are nucleated cells often referred to as transcriptionally inactive, although the epigenetic changes and chromatin remodeling that mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here we characterized the changes in gene expression, chromatin accessibility, genome organization, and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and found a complex chromatin reorganization at different genomic scales. We identified a robust decrease in transcription in erythrocytes. Nevertheless, a set of genes maintains their expression in erythrocytes, including genes involved in RNA pol II promoter-proximal pausing. Erythrocytes exhibit an inverted nuclear architecture and reposition euchromatin towards the nuclear periphery together with the paused RNA polymerase. In erythrocytes, chromatin domains are partially lost genome-wide except at mini domains retained around paused promoters. Our results suggest that promoter-proximal pausing of the RNA pol II participates in the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.

overall_design: ChIP-seq for the RNA Polymerase II phosphorylated on the serine 5 of the CTD-terminal repeat experiments on HD3 Erythroblasts cell line, chicken primary embryonic (Embryonic day 10; eRBC) or adult red blood cells (aRBC). Two biological replicates for cell type are included.

first: Andrés

last: Penagos-Puig

first: Sherlyn

last: Claudio-Galeana

first: Aura

last: Stephenson-Gussinye

first: Karina

last: Jácome-López

first: Amaury

last: Aguilar-Lomas

first: Rosario

last: Pérez-Molina


title: Infectivity, pathogenicity, and immune protection of the pangolin-origin SARS-CoV-2 related coronavirus

status: Public on May 25 2023

city: Suzhou

first: Hang-Yu

last: Zhou

state: Jiangsu

address: 100 Chongwen Road

institute: Institute of Systems Medicine, Chinese Academy of Systems Medicine

summary: The natural host of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains elusive. A panel of SARS-CoV-2-related coronaviruses have been identified in pangolins, while the infectivity and pathogenicity of these pangolin-origin coronaviruses (pCoV) to human remains largely unknown. Herein, we comprehensively characterized the infectivity and pathogenicity of pCoV-GD01, the most closest pCoV to SARS-CoV-2, in human cells, human tracheal epithelium organoids, and established animal models in comparision with. The results show that pCoV-GD01 showed similar infectivity to SARS-CoV-2 in human cells and organoids. Remarkably, intranasal inoculation of pCoV-GD01 caused severe lung pathological damage in hACE2 mice, and could establish efficient transmission among co-caged hamsters. Interestingly, in-depth antigenic analysis and animal heterologous challenge experiments demonstrate that pre-existing immunity induced by SARS-CoV-2 infection or vaccination was sufficient to provide cross-protection against pCoV-GD01 challenge. These collective results highlight the potential risk of persistent spillover from animal hosts like the pangolin, and the COVID-19 pandemic and massive vaccination have reduced the possibility of pCoVs circulation in mankind.

overall_design: Human airway epithelium primary cells were induced to generate 2D airway organoids.  Then, SARS-CoV-2 and pCoV-GD01 used to infect the organoids. Samples were harvested for transcriptome sequencing.

first: Xing-Yao

last: Huang

first: Qi

last: Chen

first: MengXu

last: Sun


title: Gene expression profile of Aggressive NK cell Leukemia (ANKL) cells in liver and spleen microenvironments

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

summary: In patient-derived xenograft (PDX) mouse, ANKL cells actively proliferate in liver, compared with spleen. We use single cell RNA sequencing (scRNA-seq) to analyze  the diversity of ANKL cells in liver and spleen

overall_design: Human-CD45+ ANKL cells were isolated from liver and spleen of ANKL-PDX mice by magnetic cell sorting (MACS), and analyzed using scRNAseq.

first: Kazuaki

last: Kameda

first: Ai

last: Kotani


title: SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity [scRNA-Seq 1]

status: Public on May 24 2023

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Cancer cells evade T-cell-mediated killing through poorly understood mechanisms of tumour–immune interactions. Dendritic cells (DCs), especially type-1 conventional DCs (cDC1), mediate T-cell priming and therapeutic efficacy against tumours. Besides pattern recognition receptors (PRRs), how DC functions are shaped by other environmental cues remains incompletely defined. Nutrients are emerging mediators of adaptive immunity, but whether nutrients impact DC function or innate–adaptive cell communication is largely unresolved. Here, we establish glutamine as an intercellular metabolic checkpoint to mediate tumour–cDC1 crosstalk and license cDC1 functionality for activating cytotoxic T cells. Intratumoral glutamine supplementation inhibits tumour growth by augmenting cDC1-mediated CD8+ T-cell immunity, and also overcomes therapeutic resistance to checkpoint blockade and T-cell-mediated immunotherapies. Mechanistically, tumour cells and cDC1 compete for glutamine uptake via transporter SLC38A2 to tune anti-tumour immunity. Nutrient screening and integrative analyses show that glutamine is the dominant amino acid for promoting cDC1 function, by signalling via FLCN to impinge upon TFEB function. Loss of FLCN in DCs selectively impairs cDC1 function in vivo in a TFEB-dependent manner, and phenocopies SLC38A2 deficiency by abrogating anti-tumour therapeutic effect of glutamine supplementation. Our findings establish glutamine-mediated intercellular metabolic crosstalk between tumour cells and cDC1 that underpins tumour immunoevasion, and reveal glutamine acquisition and signalling in cDC1 as limiting events for DC activation and putative targets for cancer treatment.

overall_design: wild-type and Flcn∆DC mice (n = 2 per genotype) were challenged with MC38 cells. CD45+ cells and DC (CD45+CD64−CD11c+MHC-II+) in the tumour tissues were sorted at 15 d after tumour challenge and mixed at a 2:1 ratio.

first: Chuansheng

last: Guo

first: Yu

first: Hao

last: Shi


title: SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity [array]

overall_design: We used microarrays to compare the global transcription profiles of splenic cDC1 cells from naïve WT (n =2 ) and  Flcn∆DC mice (n = 3)

first: Xingrong

last: Du

first: Yogesh

last: Dhungana


title: SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity


title: RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [RNA-seq]

first: Mayra

last: Furlan-Magaril

overall_design: Total stranded RNAseq on chicken primary fibroblasts, HD3 Erythroblasts cell line, primary embryonic (Embryonic day 10; eRBC) and adult red blood cells (aRBC). Three replicates per cell types are included.

first: Andrés

last: Penagos-Puig

first: Sherlyn

last: Claudio-Galeana

first: Aura


title: Basic helix-loop-helix transcription factors MYC-MAX and CLOCK-BMAL1 associate with histones for E-box access

status: Public on May 23 2023

city: Munich

first: Nikolas

last: Eggers

address: Grosshaderner Strasse 9

department: Molecular Biology

country: Germany

institute: LMU Munich

summary: Basic helix-loop-helix (bHLH) transcription factors (TF) recognize E-boxes (CANNTG) and include over 100 members. Here we investigated how chromatinised E-boxes are engaged by two structurally diverse bHLH family members; the proto-oncogene MYC-MAX and the circadian TF, CLOCK-BMAL1. Both bind E-boxes preferentially near the nucleosomal entry/exit sites. Structural studies with artificial or endogenous nucleosome sequences illustrate that MYC-MAX/CLOCK-BMAL1 trigger DNA release from histones to gain access. The CLOCK-BMAL1 PAS dimerization domains engage the histone-octamer disc atop the H2A/H2B acidic patch, an interaction critical for circadian cycling. Binding of tandem E-boxes at endogenous DNA sequences is similarly achieved through direct interactions between two CLOCK-BMAL1 protomers and histones. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B/H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerisation domain jointly determine the histone contact, the affinity, and the degree of competition/cooperativity with other nucleosome-bound factors.

overall_design: ChiP-seq profiles of MYC:MAX and CLOCK:BMAL1 on in vitro reconstituted chromatin.


title: RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ATAC-seq]

overall_design: ATAC-seq experiments on chicken primary fibroblasts, HD3 Erythroblasts cell line, primary embryonic (Embryonic day 10; eRBC) and adult red blood cells (aRBC). Two biological replicates for cell type are included.

last: Stephenson-Gussinye

first: Karina

last: Jácome-López

first: Amaury

last: Aguilar-Lomas

first: Rosario

last: Pérez-Molina


title: A cytochrome P450 CYP87A4 imparts sterol side-chain cleavage in digoxin biosynthesis

city: BUFFALO

first: BARADWAJ

last: RAVI GOPAL

state: NEW YORK

address: 653 Cooke Hall

department: BIOLOGICAL SCIENCES

institute: STATE UNIVERSITY OF NEW YORK AT BUFFALO

summary: Identifying the foxglove P450scc through differential transcriptomic analysis.

overall_design: Leaf and root tissues from three different seedlings were used to prepare the Illumina sequence library in duplicate. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Germantown, MD, USA). The sequencing library was prepared from total RNA using the TrueSeq Ribo-Zero Plant RNA library prep kit (Illumina, San Diego, CA, USA) that removes ribosomal RNA. A quality check of the library was carried out with an Agilent 2100 bioanalyzer. The library was sequenced using Illumina HiSeq 2500 to generate 100 bp paired-end raw reads.

first: Carroll

last: Emily

first: Ravi Gopal

last: Baradwaj

first: Raghavan

last: Indu

first: Wang

middle: Q

last: Zhen


title: SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity [ATAC-Seq]

first: Hongbo

last: Chi

overall_design: We performed ATAC seq analysis with 8 splenic cDC1 samples from naïve WT and Flcn∆DC mice (n = 4 per genotype)

first: Chuansheng

last: Guo

first: Yu

last: Sun


title: Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex func-tion during cellular differentiation

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

summary: The Nucleosome Remodeling and Deacetylation (NuRD) complex is a crucial regulator of cellular differentiation. Two members of the Methyl-CpG-binding domain (MBD) protein family, MBD2 and MBD3, are known to be integral, but mutually exclusive subunits of the NuRD complex. Several MBD2 and MBD3 isoforms are present in mammalian cells, resulting in distinct MBD-NuRD complexes. Whether these different complexes serve distinct functional activities during differentiation is not fully explored. Based on the essential role of MBD3 in lineage commitment, we systematically investigated a diverse set of MBD2 and MBD3 variants for their potential to rescue the differentiation block observed for mouse embryonic stem cells (ESCs) lacking MBD3. While MBD3 is indeed crucial for ESC differentiation to neuronal cells, it functions independently of its MBD domain. We further identify that MBD2 isoforms can replace MBD3 during lineage commitment, however with different potential. Full-length MBD2a only partially rescues the differentiation block, while MBD2b, an isoform lacking an N-terminal GR-rich repeat, fully rescues the Mbd3 KO phenotype. In case of MBD2a, we further show that removing the methylated DNA binding capacity or the GR-rich repeat enables full redundancy to MBD3, highlighting the synergistic requirements for these domains in diversifying NuRD complex function.

overall_design: Examination of gene expression in wild type, MBD3-KO, and MBD3-KO expressing various MBD2 or MBD3 proteins in neuronal progenitors. Chromatin Immunoprecipitation using biotin-tagged MBD2 variants in ES cells.

first: Nina

last: Schmolka


title: mPFC DUSP1 mediates adolescent cocaine exposure-induced higher sensitivity to drug in adulthood

status: Public on May 20 2023

city: Nanjing

last: Fan

address: Xianlin 138 Road

institute: Nanjing University of Chinese Medicine

summary:
Adolescent cocaine abuse increases the risk for developing addiction
in later life, but the underlying molecular mechanism remains
poorly understood. Here, we establish adolescent cocaine-exposed
(ACE) male mouse models. A subthreshold dose of cocaine (sdC)
treatment, insufficient to produce conditioned place preference
(CPP) in adolescent mice, induces CPP in ACE mice during adulthood,
along with more activated CaMKII-positive neurons, higher
dual specificity protein kinase phosphatase-1 (Dusp1) mRNA, lower
DUSP1 activity, and lower DUSP1 expression in CaMKII-positive
neurons in the medial prefrontal cortex (mPFC). Overexpressing
DUSP1 in CaMKII-positive neurons suppresses neuron activity and
blocks sdC-induced CPP in ACE mice during adulthood. On the
contrary, depleting DUSP1 in CaMKII-positive neurons activates
more neurons and further enhances sdC-induced behavior in ACE
mice during adulthood. Also, ERK1/2 might be a downstream
signal of DUSP1 in the process. Our findings reveal a role of mPFC
DUSP1 in ACE-induced higher sensitivity to the drug in adult mice.
DUSP1 might be a potential pharmacological target to predict or
treat the susceptibility to addictive drugs caused by adolescent
substance use.

overall_design: Adolescent cocaine-exposed (ACE) male mice models were established by administrating cocaine during adolescent period.

first: Xiaoyan

last: Wei

first: Jiasong

last: Chang

first: Zhen

last: Cheng

first: Wenwen

last: Chen

first: Hao

first: Zhaoyu

last: Liu

first: Yuning

last: Mai

first: Tao

last: Hu

first: Yuanyuan

last: Zhang

first: Qinglong

last: Cai

first: Feifei

last: Ge

first: Xiaowei

last: Guan


title: RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [Hi-C]

first: Mayra

last: Furlan-Magaril

overall_design: Hi-C Experiments experiments on chicken primary fibroblasts, HD3 Erythroblasts cell line, primary embryonic (Embryonic day 10; eRBC) and adult red blood cells (aRBC). Two biological replicates per cell type are included.

first: Andrés

last: Penagos-Puig

first: Sherlyn

last: Claudio-Galeana

first: Aura

last: Stephenson-Gussinye

first: Karina

last: Jácome-López

first: Amaury

last: Aguilar-Lomas

first: Rosario

last: Pérez-Molina


title: ASH1L methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair [ChIP-Seq ASH1L-CTD]

city: Zurich

first: Michelle

last: Yancoskie

address: Winterthurerstr. 260

department: Vetsuisse Faculty

country: Switzerland

institute: Institute of Veterinary Pharmacology and Toxicology, University of Zurich

summary: To recognize DNA damage, nucleotide excision repair (NER) deploys a multipart mechanism by which the XPC sensor detects helical distortions followed by engagement of TFIIH for lesion verification. Accessory players ensure that this factor handover takes place on chromatin where DNA is wrapped around histones. We show that the histone methyltransferase ASH1L, once activated by MRG15, accelerates global-genome NER activity. Upon UV irradiation, ASH1L deposits H3K4me3 marks all over the genome (except in gene promoters), thus priming chromatin for relocations of XPC from native to damaged DNA. ASH1L further recruits the histone chaperone FACT to UV lesions. In the absence of ASH1L, MRG15 or FACT, XPC persists on damaged DNA without being able to deliver lesions to the TFIIH verifier. We conclude that ASH1L implements repair hotspots whose H3K4me3 and FACT occupancy confers an active promoter-like code and organization of histones that make DNA damage verifiable by the NER machinery.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for histone mark H3K36me2 in wildtype U2OS cells and for ASH1L-CTD (or, as an input control, empty vector) transfected into ASH1L knockout U2OS cells. Wildtype and ASH1L knockout cells were either not exposed to UV or assayed 3 hours post UV.

first: Corina

last: Maritz

middle: N

first: Sarah

last: Diethelm

first: Reihaneh

last: Khaleghi

first: Sonja

last: Brülisauer

first: Natalia

middle: S

last: Ferreira

first: Yang

last: Jiang

first: Shana

middle: J

last: Sturla

first: Hanspeter

last: Naegeli


title: RNA-seq of SCD2-deficient murine bone marrow-derived macrophages

status: Public on May 19 2023

city: Saint Louis

first: Joseph

middle: B

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

summary: We evaluated the effect of Scd2 ablation on the transcriptome of bone marrow-derived macrophages prepared from mice.

overall_design: We obtained mice with floxed Scd2 alleles from Hide Tsukamoto (Keck School of Medicine from the University of Southern California). We crossed these mice with mice carrying the lysozyme M-Cre transgene to generate mice with myelomonocyte-specific deletion of Scd2. We prepared macrophages from bone marrow. To isolate bone marrow from mice, we sacrificed mice using CO2 euthanasia, dissected out both tibias and femurs, and passed 8 ml of ice-cold DMEM through each bone's medullary cavity. We filtered the bone marrow aspirates through a 40 micrometer nylon mesh strainer, pelleted the cells, and re-suspended the pellet in macrophage differentiation media consisting of DMEM with 10% FBS, 10% CMG-conditioned media, 1% P/S, and 1% L-glut. We replenished differentiation media 3 days after initial plating. After differentiation for 5-6 days, macrophages were maintained in mature macrophage media consisting of DMEM with 10% FBS, 2% CMG-conditioned media, 1% P/S, and 1% L-glut.

first: Rajendra

last: Apte


title: DNA sequences at integration sites in primary mammary tumors and lung metastases from a sleeping-beauty transposon-mediated mutagenesis screen on Rb-deficient background

status: Public on May 17 2023

first: Eldad

last: Zacksenhaus

address: 101 College Street

institute: University Health Network

summary: This deposition describes DNA sequences at integration sites in primary tumors and lung metastases from a sleeping-beauty transposon-mediated mutagenesis screen on Rb-deficient background in the mammary gland in MMTV-Cre:Rbf/f:T2/Onc3a:R26lsl_SB11 and MMTV-Cre:Rbf/f:T2/Onc3b:R26lsl_SB11  female mice. In these mice, Rb floxed (Rbf/f) alleles and a SB11 transposase, knocked into the ROSA26 locus (R26lsl_SB11), are mobilized via MMTV-Cre.  Two different transgenic transposon concatemers, T2/Onc3a and T2/Onc3b, containing 11 and 28 copies on chromosomes 9 and 12 were used so that local hoping in the respective chromosomes can be discarded.  These mice developed large primary tumors and macroscopic lung metastases; biopsies from the primary tumors and entire lung metastases were used to extract DNA. The DNA was subjected to sonication, ligation-mediated PCR with 79 bar coded primers, followed by next-generation DNA sequencing.  We identified Primary-specific and lung Metastasis-specific gene-centric Common Integration Sites (gCIS) as well as shared gCIS, observed in both primary mammary tumors and lung metastases.  Using sequence analysis of integration sites, we were able to demonstrate in multiple cases clonal relationship between primary lesions and metastases. The metastatic gCIS form specific hubs that may be prioritized for targeted therapy. For details, see reference below.

overall_design: Sleeping Beauty (SB) screens in Rb-deficient model of breast cancer

first: Zhe

first: Patryk

last: Skowron

first: Jiao

last: Zhang

first: Michael

last: Taylor


title: Definition and prognostic impact of Ph-like and IKZF1plus features in children with Down Syndrome Acute Lymphoblastic Leukaemia

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
Background
Children with Down Syndrome have an augmented risk for B-cell acute lymphoblastic leukaemia (DS-ALL), which is associated with a survival lower than in non-DS ALL, due to increased chemotherapy-related toxicity and a higher relapse rate, thus demanding new tailored therapeutic strategies.
Cytogenetic abnormalities common in childhood ALL are less frequent in DS-ALL, while alterations in CRLF2 and IKZF1 genes are increased.
Aim of the study was to evaluate in DS-ALL children the incidence and prognostic value of the Philadelphia Chromosome-Like (Ph-like) status and the “IKZF1plus” profile, both associated with poor outcome in non-DS ALL and therefore introduced in current therapeutic protocols for BCP-ALL.
Method
Seventy DS-ALL patients at diagnosis treated in Italian centres from 2000 to 2014 were evaluated for their cytogenetic status, including the Ph-like ALL profile, while the IKZF1plus feature was investigated in a larger cohort of 134 patients treated in Italian and German centres from 2000 to 2011.
Findings
Forty-six out of 70 (65•7%) AIEOP DS-ALL patients displayed the Ph-like ALL gene expression signature, mostly characterized by CRLF2 (n=33) and IKZF1 (n=16) alterations (13 had both alterations); only one case was positive for an ABL-class and one for a PAX5 fusion gene. In the Italian and German joint cohort, we observed 35•6% patients positive for P2RY8::CRLF2 fusion, 24•8% for IKZF1 deletion and 18% for IKZF1plus feature. Unexpectedly, a higher IKZF1 expression and activity were observed in IKZF1plus than IKZF1 wt DS-ALL patients. Ph-like signature and IKZF1 deletion were associated with poor outcome, which further worsens when IKZF1 deletion was co-occurring with P2RY8::CRLF2, qualifying for the IKZF1plus definition.
Interpretation
These subgroups, which for the most part are not associated with other high risk features, need new and tailored therapeutic strategies, not only focussed on the use of drugs that restore IKZF1 function.

overall_design: Gene expression was measured using Affymetrix platform in DownSyndrome BCP-ALL pediatric patients at diagnosis

first: Silvia

last: Bresolin

first: Chiara

last: Palmi


title: UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma [CRISPR_screen]

city: San Francisco

first: Alex

middle: G

last: Lee

state: CA

address: 1550 4th Street

institute: UCSF

summary: We performed a focused CRISPR in KRAS mutant lung cancer cells (A549) using a minipool sgRNA library targeting 80 lung cancer specific tumor suppressor genes and 12 control genes. This screen identified tumor suppressor genes regulated by Uhrf1 in KRAS mutant lung cancer.

overall_design: KRAS mutant A549 cells expressing Cas9 were infected with the minipool sgRNA library containing 483 sgRNAs targeting 92 protein coding genes and 26 negative "safe" sgRNAs. Following puromycin selection the cells were transfected either with a negative sgRNA or sgRNA targeting UHRF1. Cells were expanded for 4-5 days and then split. At this point the cells were also collected for T0. After 18 days of passaging cells were collected for DNA extraction (T1).

first: Marta

last: Moreno

first: Kaja

last: Kostyrko

first: Alejandro

last: Sweet-Cordero


title: The EZH2-PRC2-H3K27me3 axis governing the endometrial cell cycle and differentiation for successful blastocyst invasion

status: Public on May 15 2023

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

summary: Ezh2-catalyzing H3K27 trimethylation regulates uterine epithelial and stromal differentiation and blastocyst invasion, contributing to successful pregnancy outcomes.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq analysis using uteri from Ezh2-floxed control mice and uterine-specific KO mice of Ezh2 (Ezh2 uKO); RNA-seq analysis using uteri from Ezh2-floxed control mice and uterine-specific KO mice of Ezh2; RNA-seq analysis using endometrial tissues from human patients with or without recurrent implantation failure (RIF)

first: Yamato

last: Fukui

first: Akihiko

last: Sakashita

first: Yasushi

last: Hirota


title: SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity [scRNA-Seq 2]

first: Hongbo

last: Chi

overall_design: Wild-type mice were challenged with MC38 colon adenocarcinoma cells, and treated with PBS or glutamine daily starting from day 5. Anti-PD-1 antibody or rat IgG2b isotype control was injected intraperitoneally three times on day 7, 10 and 13. CD45− tumour cells, macrophages (CD45+CD64+), CD45+   non-macrophage immune cells (CD45+CD64−), and dendritic cells (CD45+CD64−CD11c+MHC-II+) in the tumour tissues were sorted at 15 d after tumour challenge and mixed at a 1:1:4:5 ratio (n = 2 biological replicates per group).

first: Chuansheng

last: Guo

first: Yu

last: Sun

first: Hao

last: Shi


title: UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma [epic_methyl]

summary: Methylation array was performed to understand the role of UHRF1 in DNA methylation in KRAS mutant lung cancer cell lines. Knock-down of UHRF1 leads to significant changes in global DNA methylation in both cell lines.

overall_design: Two KRAS mutant lung cancer cell lines were used (A549, H358). Each cell line was treated with control siRNA (siNeg), anti-KRAS siRNA (siKRAS) or anti-UHRF1 siRNA (siUHRF1) in 2 (siNeg) or 3 (siUHRF1, siKRAS) biological replicates.


title: UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma [RNA-seq]

summary: RNA sequening was performed to understand the role of UHRF1 in regulation of gene expression in KRAS mutant lung cancer cell lines. Knock-down of both UHRF1 and KRAS leads to significant and overlapping changes in gene expression in both cell lines.

overall_design: Two KRAS mutant lung cancer cell lines were used (A549, H358). Each cell line was treated with control siRNA (siNeg), anti-KRAS siRNA (siKRAS) or anti-UHRF1 siRNA (siUHRF1) in 3 biological replicates.

first: Kostyrko

last: Kaja

first: Sweet-Cordero

last: Alejandro

first: Lee

last: Alex


title: Histone demethylase KDM5D upregulation drives sex differences in colon cancer [ChIP-Seq]

status: Public on May 13 2023

city: Houston

first: Jiexi

last: Li

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: Sex exerts a profound impact on cancer incidence, spectrum and outcomes, yet the molecular genetic bases of such sex differences are ill-defined and presumptively ascribed to X-chromosome genes and sex hormones. Such sex differences are particularly prominent in colorectal cancer (CRC) where men experience higher metastases and mortality. A murine CRC model, engineered with an inducible transgene encoding oncogenic mutant KRASG12D and conditional null alleles of Apc and Trp53 tumor suppressors (designated iKAP), revealed higher metastases and worse outcomes specifically in males with oncogenic mutant KRAS (KRAS*) CRC. Integrated cross-species molecular and transcriptomic analyses identified Y-chromosome gene histone demethylase KDM5D as a transcriptionally up-regulated gene driven by KRAS*-mediated activation of the STAT4 transcription factor. KDM5D-dependent chromatin mark and transcriptome changes showed repression of regulators of the epithelial cell tight junction and MHC class I complex components. Deletion of Kdm5d in iKAP cancer cells increased tight junction integrity, decreased cell invasiveness, and enhanced cancer cell killing by CD8+ T cells. Conversely, iAP mice engineered with a Kdm5d transgene to provide constitutive Kdm5d expression specifically in iAP cancer cells exhibited an increased propensity for more invasive tumors in vivo. Thus, KRAS*-STAT4-mediated upregulation of Y chromosome KDM5D contributes significantly to the sex differences in KRAS* CRC via its disruption of cancer cell adhesion properties and tumor immunity, providing an actionable therapeutic strategy for metastasis risk reduction for men afflicted with KRAS* CRC.

overall_design: Profiling of histone modification and STAT4 binding in iKAP CRC cancer cells


title: Histone demethylase KDM5D upregulation drives sex differences in colon cancer [HiChIP]


title: Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis

status: Public on May 11 2023

city: Hangzhou

first: jianpeng

last: sheng

address: No. 79 Qingchun Street

institute: Zhejiang University School of Medicine

summary: Ulcerative colitis (UC) is a chronic inflammatory bowel disorder with cellular heterogeneity. To understand the composition and spatial changes of the UC ecosystem, we use imaging mass cytometry (IMC) and single-cell RNA sequencing (scRNA-seq) to depict the single-cell landscape of the human colon ecosystem. We find tissue topological changes featured with macrophage disappearance reaction (MDR) in the UC region, occurring only for tissue-resident macrophages. Reactive oxygen species (ROS) levels are higher in the UC region, but ROS scavenging enzyme SOD2 is barely detected in resident macrophages, resulting in distinct ROS vulnerability for inflammatory macrophages and resident macrophages. Inflammatory macrophages replace resident macrophages and cause a spatial shift of TNF-α production during UC via a cytokine production network formed with T and B cells. Our study discovers the mechanism of MDR of resident macrophages, providing novel mechanistic hints for MDR in other inflammation or infection situations.

overall_design: Four healthy control subjects and 4 UC patients were enrolled. 4 pinch biopsy specimens from the healthy volunteers served as healthy control (HC group). For each of the 4 patients, 1 pinch biopsy specimen was collected from the inflamed colon region as the UC group, and 1 pinch biopsy specimen from the normal ascending colon of patients served as self-control (UCSC group).

first: Juan

last: Du

first: Junlei

last: Zhang

first: Lin

last: Wang

first: Xiaocang

last: Cao

first: Xun

first: Xueli

last: Bai

first: Xinjuan

last: Liu

first: Wei

last: Shao

first: Jianpeng

last: Sheng


title: Targeting the ADPKD methylome using nanoparticle-mediated combination therapy

status: Public on May 10 2023

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

type: Methylation profiling by high throughput sequencing

summary: DNA methylation aberrancies are found in autosomal dominant polycystic kidney disease (ADPKD) which suggest the methylome to be a promising therapeutic target. However, the impact of combining DNA methylation inhibitors (DNMTi) and ADPKD drugs in treating ADPKD and on disease-associated methylation patterns has not been fully explored. To test this, ADPKD drugs, metformin and tolvaptan (MT), were delivered in combination with DNMTi 5-aza-2’-deoxycytidine (Aza) to 2D or 3D cystic Pkd1 heterozygous renal epithelial cells (PKD1-Het cells) as free drugs or within nanoparticles to enable direct delivery for future in vivo applications. We found Aza synergizes with MT to reduce cell viability and cystic growth. Reduced representation bisulfite sequencing (RRBS) was performed across 4 groups: PBS, Free-Aza (Aza), Free-Aza+MT (F-MTAza), and Nanoparticle-Aza+MT (NP-MTAza). Global methylation patterns showed that while Aza alone induces a unimodal intermediate methylation landscape, Aza+MT recovers the bimodality reminiscent of somatic methylomes. Importantly, site-specific methylation changes associated with F-MTAza and NP-MTAza were largely conserved including hypomethylation at ADPKD-associated genes. Notably, we report hypomethylation of cancer-associated genes implicated in ADPKD pathogenesis as well as new target genes that may provide additional therapeutic effects. Overall, this study motivates future work to further elucidate the regulatory mechanisms of observed drug synergy and apply these combination therapies in vivo.

overall_design: Reduced-Representation Bisulfite Sequencing (RRBS) on Pkd1 heterozygous renal epithelial cells (PKD1-Het cells) treated for 24h with a PBS control (PBS, n=3), 50 µM Aza (Aza, n=3), and a drug combination consisting of 50 µM Aza, 300 µM metformin, and 10 µM tolvaptan delivered as free molecules (F-MTAza, n=3), or the aforementioned drug combination delivered in micelle formulation (NP-MTAza, n=3).

first: Yi

last: Huang

first: Hanjuan

first: Aparna

last: Ram

first: Julien

last: Morival

first: Jonathan

first: Eun

last: Chung

first: Timothy

last: Downing


title: Histone demethylase KDM5D upregulation drives sex differences in colon cancer [RNA-Seq]

first: Jiexi

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iKAP cells


title: Analysis of differential gene expression in the choroid plexus (ChP) of P60 mice at 9am and 9pm

city: Boston

first: Maria

last: Lehtinen

state: MA

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

summary: 3 mice per timepoint (9am and 9pm) with FoxJ1-Cre x TRAP-BAC-EGFP:L10a dissected choroid plexus. Transmission and secretion of signals via the choroid plexus (ChP) brain barrier can modulate brain states via regulation of cerebrospinal fluid (CSF) composition. Here, we developed a platform to analyze diurnal variations in male mouse ChP and CSF. Ribosome profiling of ChP epithelial cells revealed diurnal translatome differences in metabolic machinery, secreted proteins, and barrier components. Using ChP and CSF metabolomics and blood-CSF barrier analyses, we observed diurnal changes in metabolites and cellular junctions. We then focused on transthyretin (TTR), a diurnally regulated thyroid hormone chaperone secreted by the ChP. Diurnal variation in ChP TTR depended on Bmal1 clock gene expression. We achieved real-time tracking of CSF-TTR in awake TtrmNeonGreen mice via multi-day intracerebroventricular fiber photometry. Diurnal changes in ChP and CSF TTR levels correlated with CSF thyroid hormone levels. These datasets highlight an integrated platform for investigating diurnal control of brain states by the ChP and CSF.

overall_design: TRAP mRNAs were isolated and sequenced from the choroid plexus (ChP) of P60 mice

middle: K

first: Ryann

last: Fame

first: Myriam

last: Heiman

first: Amanda

last: Vernon

first: Fan

last: Gao


title: Genome-wide maps of chromatin state in mouse perinatal testes [scATAC-seq]

city: Hong Kong

first: Tin-Lap

last: Lee

address: LKSIBSB, CUHK, Shatin, Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We report the application of single-cell ATAC-seq to reconstruct the epigenetic program and identify key transcription factors and cis-regulatory elements during the perinatal testiscular develpment. First, we constructed sequencing libraries from testes collected from E18.5, PND0, PND3 and PND6 mice. The cell clusters identidied from scATAC-seq were assigned to known testicular cell types, including germ cells, Sertoli cells, Leydig cells, peritubular myoid cells, stromal cells, endothelial cells and blood cells. We then constructed pseudotime developmental trajectories and identified transcription factor regulators for each cell type. Lastly, we identified cis-regulatory elements such peak-to-gene linkages across testis.

overall_design: Chromatin accessibility profiles of mouse testicular cells at E18.5, PND0.5, PND3 and PND6.

first: Jinyue

last: Liao

first: Hoi Ching

last: Suen


title: UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma [shRNA]

first: Alex

summary: Using pooled shRNA libraries we performed a focused screen of 115 genes in 3D ex vivo cultures of primary murine lung tumor cells and 2D cultures of murine LKR10 cells. These screens identify Uhrf1 as gene selectively important for the 3D growth of primary lung cancer spheroids.

overall_design: We analyze shRNA abundance at two different timepoints in primary tumor cells grown in 3D ex vivo cultures (5 sample pools x 6 replicates) and compare these results to a murine NSCLC cell line (LKR10) grown in 2D culture (5 sample pools x 6 replicates). The analysis compares T1 vs T0 groups.

first: David

last: Simpson

first: Alejandro

last: Sweet-Cordero


title: Changes in the Coexpression of Innate Immunity Genes During Persistent Islet Autoimmunity Are Associated With Progression of Islet Autoimmunity:  Diabetes Autoimmunity Study in the Young (DAISY)

status: Public on May 01 2023

city: Aurora

first: Lauren

last: Vanderlinden

state: Colorado

address: 13001 E. 17th Place, Mail Stop B119

department: Department of Biostatistics and Informatics

institute: Colorado School of Public Health

summary: Longitudinal changes in gene expression during islet autoimmunity (IA) may provide insight into biological processes that explain progression to type 1 diabetes (T1D). We identified individuals from Diabetes Autoimmunity Study in the Young (DAISY) who developed IA, autoantibodies present on two or more visits. Illumina's NovaSeq 6000 was used to quantify gene expression in whole blood. With linear mixed models we tested for changes in expression after IA that differed across individuals who progressed to T1D (progressors) (n = 25), reverted to an autoantibody-negative stage (reverters) (n = 47), or maintained IA positivity but did not develop T1D (maintainers) (n = 66). Weighted gene coexpression network analysis was used to identify coexpression modules. Gene Ontology pathway analysis of the top 150 differentially expressed genes (nominal P < 0.01) identified significantly enriched pathways including leukocyte activation involved in immune response, innate immune response, and regulation of immune response. We identified a module of 14 coexpressed genes with roles in the innate immunity. The hub gene, LTF, is known to have immunomodulatory properties. Another gene within the module, CAMP, is potentially relevant based on its role in promoting β-cell survival in a murine model. Overall, results provide evidence of alterations in expression of innate immune genes prior to onset of T1D.

overall_design: We identified individuals who developed IA between February 1994 and February 2019 in DAISY and underwent autoantibody testing at two or more visits (n = 214).  We divided individuals into three IA progression phenotypes. The reverter group was defined as individuals who reverted for all autoantibodies (two or more consecutive visits in which no autoantibodies were detected), did not develop T1D, and were autoantibody negative for all autoantibodies at their last DAISY visit (n = 47). The maintainer group was defined as individuals who continued to test positive for autoantibodies and did not develop T1D during follow-up (n = 66). The progressor group was defined as individuals who developed T1D (n = 25). We selected venous blood samples from two visits (termed IA-1 and IA-2) that occurred after the onset of IA for mRNA sequencing. The IA-1 visit was selected as the first available visit after the onset of IA for all groups. In the progressor group, the visit that preceded clinical onset of T1D was selected as the IA-2 visit. In the maintainer and reverter groups, the IA-2 visit was selected as the visit where age was closest to median age in the progressor group at the IA-2 visit.  We also included 12 control samples and 12 technical replicates.


title: ATAC-seq of isogenicHIV-1 infected Jurkat T cell lines

city: New Haven

first: Ya-Chi

last: Ho

state: Connecticut

address: 295 Congress Avenue,BCMM 354E

institute: Yale University

summary: HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin. We postulate that the integrated provirus serves as an ectopic enhancer that recruits additional transcriptional factors to the integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both retroviral and host gene expression. We used 4 well-characterized HIV-1-infected cell line clones having unique integration sites and low to high levels of HIV-1 expression. Using single-cell DOGMA-seq, which captured the heterogeneity of HIV-1 expression and host chromatin accessibility, we found that HIV-1 transcription correlated with HIV-1 accessibility and host chromatin accessibility. HIV-1 integration increased local host chromatin accessibility within ~5–30 kb distance. CRISPRa and CRISPRi-mediated HIV-1 promoter activation and inhibition confirmed integration site-dependent HIV-1-driven changes of host chromatin accessibility. HIV-1 did not drive chromatin confirmation changes at the genomic level (by Hi-C) or the enhancer connectome (by H3K27Ac HiChIP). Using 4C-seq to interrogate HIV-1-chromatin interactions, we found that HIV-1 interacted with host chromatin ~100–300 kb from the integration site. By identifying chromatin regions having both increased transcription factor activity (by ATAC-seq) and HIV-1-chromtain interaction (by 4C-seq), we identified enrichment of ETS, RUNT, STAT, and ZNF transcription factor binding that may mediate HIV-1-host chromatin interactions. Our study found that HIV-1 promoter activity increased host chromatin accessibility, increased HIV-1-host chromatin interactions in an integration site dependent manner, within the existing chromatin boundaries without impacting broader host chromatin structure.

overall_design: Unstimulated Jurkat CD4+ T cells with or without an HIV-1 provirus were profiled.

first: Jack

last: Collora


title: HIV-1 LTR targeting 4C-seq


title: Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary:
In Mycobacterium tuberculosis, the PhoPR two-component regulatory system controls production and secretion of proteins and lipid virulence effectors.
Several mutations, present in phoR of Mycobacterium canettii relative to M. tuberculosis, impact the expression of the PhoP regulon and the pathogenicity of the strains.
Here, we analyse by RNA-seq the expression profile of PhoP-regulated genes between the two M. tuberculosis strains H37Rv and HN878 and the two M. canettii isolates STB-Ks and STB-Kr.

sample_organism:
Mycobacterium tuberculosis
Mycobacterium canetti

overall_design: Gene expression profiling by RNA-seq of M. tuberculosis H37Rv and HN878 strains and M. canettii STB-Ks and STB-Kr isolates cultured in normal growth condition

first: Eva

last: Meunier

first: Alexandre

last: Pawlik

first: Elodie

last: Turc

first: Marc

last: Monot

first: Roland

last: Brosch

first: Christophe

last: Guilhot


title: Ectopic expression of FvVND4c promotes secondary cell wall thickening and flavonoid accumulation in Fragaria vesca

city: Fuzhou

first: Bei

last: Zhang

address: 15 Shangxia Dian Road

institute: Fujian Agriculture and Forestry University

summary: Secondary cell wall thickening (SCW) has a significant effect in the growth and development of plants, as well as in the resistance to various biotic and abiotic stresses. It is regulated by a multilevel transcriptional regulatory network, in which VASCULAR-RELATED NAC-DOMAINs (VNDs) act as key regulators. Lignin is an important component of SCW, it has a cooperative regulation with the biosynthesis of flavonoids which also originate from phenylpropanoid pathway. However, there are few studies on SCW thickening and flavonoid biosynthesis in flesh fruits. We want to investigate the role of FvVNDs on cell wall and fruit color development in Fragaria vesca.

overall_design: We characterized three VNDs in Fragaria vesca , and  transient overexpression of FvVND4c  and its candidate downstream factor FvMYB46 induced SCW thickening in diploid strawberry fruits . We then performed transcriptome analysis of FvVND4c and FvMYB46 overexpressed plants to investigate which metabolic pathways they are involved in.

first: Xiaofei

last: Dang

first: Hao

last: Chen

first: Tian

last: Li

first: Fangjie

last: Zhu

first: Shingo

last: Nagawa


title: SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity [ATAC-seq]

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

summary: Spalt-Like Transcription Factor 1 (Sall1) is a critical regulator of organogenesis and microglia identity. Despite its known biological importance, mechanisms that specify the cell-specific expression of Sall1 and its transcriptional functions remain poorly understood. Here, we demonstrate that targeted deletion of a conserved microglia-specific super enhancer interacting with the Sall1 promoter results in complete and specific loss of Sall1 expression in microglia, thereby identifying an essential regulatory element that transduces brain environmental signals required for microglia-specific gene expression.  By determining the genomic binding sites of SALL1 and leveraging Sall1 enhancer knock out (EKO) mice to probe how SALL1 shapes the regulatory landscape of microglia, we provide evidence that SALL1 functions to both directly activate microglia-specific genes and repress genes that are associated with inflammation and aging. Unexpectedly, motifs for SMAD proteins that mediate transcriptional effects of TGFb signaling were enriched within the set of enhancers predicted to be directly activated by SALL1, suggesting that collaborative interactions between SALL1 and SMADs are required to establish microglia-specific gene expression.  To test this hypothesis, we determined the transcriptional consequences of a conditional knockout of the common co-SMAD Smad4 and defined the genome-wide locations of SMAD4 in wild type and EKO microglia.  These studies revealed two layers of functional interdependence.  First, we found that SMAD4 binds directly to the Sall1 super enhancer and is required for Sall1 expression, consistent with the requirement of the TGFb and SMAD homologues Dpp and Mad for cell-specific expression of Spalt in the Drosophila wing.  Second, we extend this paradigm by demonstrating that SALL1 in turn promotes binding and function of SMAD4 at microglia-specific enhancers while simultaneously suppressing binding of SMAD4 to enhancers of genes that become inappropriately activated in EKO microglia. Collectively, these results suggest molecular mechanisms by which SALL1 enforces microglia-specific functions of the TGFb-SMAD signaling axis that may be relevant to roles of SALL1 in other developmental contexts.

overall_design: Poly-A RNA-seq, ATAC-seq, and H3K27ac-ChIP-seq of whole cell microglia or PU.1-positive nuclei isolated from mouse brains (Control, SALL1-Enhancer knockout, SMAD4 knockout).

first: Bethany

last: Fixsen

first: Claudia

middle: Z

last: Han

first: Nathan

last: Spann

first: Payam

last: Saisan

first: Zeyang

last: Shen

first: Mashito

last: Sakai

first: Isidoro

last: Cobo

first: Inge

last: Holtman

first: Anna

last: Warden

first: Gabriela

last: Ramirez

last: Balak

first: Jana

last: Collier

first: Martina

middle: P

last: Pasillas

first: Miao

last: Yu

first: Rong

last: Hu

first: Bin

first: Sarah

last: Belhocine

first: David

last: Gosselin

first: Nicole

last: Coufal

first: Bing

last: Ren


title: High-throughput Oligopaint screen identifies druggable 3D genome regulators

status: Public on May 05 2023

city: Philadelphia

first: Daniel

middle: Sungjoo

last: Park

state: PA

address: 415 Curie Blvd

department: Genetics

institute: University of Pennsylvania

summary: Although the molecular rules governing chromatin folding are being quickly elucidated, relatively few proteins regulating genome organization have been identified. To address this, we developed HiDRO (high-throughput labeling of DNA or RNA with optimized Oligopaint probes). Combined with automated image analysis, we used HiDRO to conduct a novel FISH-based screen of ~3,000 druggable genes that alter inter-TAD interactions. We isolated several enzymes that alter the integrity of architectural boundaries, including our top hit Glycogen synthase kinase alpha (GSK3A). We demonstrated using chemical and genetic inhibition that this ubiquitously expressed kinase enhances chromatin looping by regulating the chromatin binding of cohesin regulators.  Finally, our data demonstrate that a GSK3A inhibitor can rescue both chromatin misfolding and gene misexpression at a sensitive locus after partial cohesin loss. These results illustrate a noncanonical role for GSK3A in cohesin regulation and highlight the broader utility of HiDRO-based screening to identify novel genome organizing factors.

overall_design: RAD21and CTCF ChIP-seq was performed for three biological replicates each of control siRNA or GSK3A siRNA treated HCT-116 cells. After input normalization, bigwig files from each replicate as well as a bigwig file subsampled from all three replicates were produced. Bed files of peaks were generated from each bigwig. In situ Hi-C was performed for two biological replicate each of control siRNA, GSK3A siRNA, WAPL siRNA or PDS5A siRNA treated HCT-116 cells.

first: Son

last: Nguyen

first: Eric

last: Joyce


title: SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity [ChIP-seq]

first: Christopher

last: Glass

first: Bethany

last: Fixsen

first: Claudia

last: Han

first: Nathan

last: Spann

first: Payam

last: Saisan

first: Zeyang

last: Shen

first: Mashito

last: Sakai

last: Li


title: SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity [3D]

first: Isidoro

last: Cobo

first: Inge

last: Holtman

first: Anna

last: Warden

first: Gabriela

last: Ramirez

last: Balak

first: Jana

last: Collier

first: Martina

last: Pasillas

first: Miao

last: Yu


title: Single-cell RNAseq data from mouse intrinsically-photosensitive retinal ganglion cells

city: Baltimore

first: Alex

last: Kolodkin

state: Maryland

address: 725 N Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

summary: The goal of this study was to characterize the transcriptomes of intrinsically-photosenstive retinal ganglion cells that innervate different retinorecipient target regions in the brain

overall_design: Each sample contains sequenced mRNA from a single intrinsically-photosensitive retinal ganlgion cell (ipRGC). Cells were taken at P1 and P5.

first: John

middle: L

last: Hunyara

first: K

middle: M

last: Daly

first: Katherine

last: Torres

first: Ruchi

last: Komal

first: Samer

last: Hattar


title: Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies.

city: Shanghai

first: Yibo

last: Lu

address: No.1678, Dongfang Road, Shanghai

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University

summary: We analyzed lncRNAs located in CNV loci associated with congenital anomalies of the kidney and urinary tract (CAKUT). HSALNG0134318 at CNV 22q11 was identified as CAKUT related lncRNA, which was coexpressed with multiple known CAKUT associated genes. To validate our findings, we performed knockdown experiments in HEK293 cell line to characterize the trascriptomic profiles regulated by HSALNG0134318 in human embryonic kidney cells.

overall_design: RNA-seq of lncRNA HSALNG0134318 knockdown human embryonic kidney cells (HEK293) and the negative control cells. Three biological replicates were obtained for each sample.

first: Yiyang

last: Zhou

first: Bo

last: Wang


title: Gene expression signatures in EGFR-deleted oral squamous cell carcinoma (OSCC) cell lines

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of EGFR disruption on gene expression, we generated EGFR-knockout (EGFR-KO) cell clones using CRISPR/Cas9 system with OSCC cell lines HSC-2 and HSC-3 cells. The OSCC cells were incubated for 48 h in vitro.

overall_design: HSC-2 and HSC-3 cells were maintained in RPMI 1640 supplemented with 5% FBS at 37 ℃ in 5% CO2 humidified atmosphere.

first: Maho

last: Onda

first: Sivasundaram

last: Karnan


title: QIAGEN RT2 profiler Rabbit Wound Healing

city: CPH

first: Constance

middle: E

last: Grandjean

address: Blegdamsvej 3

department: Cluster for Molecular Imaging

country: Denmark

institute: University of Copenhagen

summary: Examining controls and atherosclerotic rabbits gene expression

overall_design: Abdonimal aortas were extracted from rabbits, and qPCR were performed on the tissue in order to determined gene expression differences in the developement of athreosclerosis compared with healthy controls

first: Tina

last: Binderup


title: Histone demethylase KDM5D upregulation drives sex differences in colon cancer

status: Public on May 12 2023

first: Jiexi

last: Li

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

overall_design: Refer to individual Series


title: Continuous muscle, glial, epithelial, neuronal, and hemocyte cell lines for Drosophila research

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Expression of activated Ras, RasV12, provides Drosophila cultured cells with a proliferation and survival advantage that simplifies the generation of continuous cell lines. Here we used restricted RasV12 expression to generate continuous cell lines of muscle, glial, and epithelial cell type. Cell lines with neuronal and hemocyte characteristics were isolated by cloning from cell cultures established with broad RasV12 expression. Differentiation with the hormone ecdysone caused maturation of cells from mesoderm lines into active muscle tissue and enhanced dendritic features in neuronal-like lines. Transcriptome analysis showed expression of key cell-type specific genes and the expected alignment with single cell sequencing data in several cases. Overall, the technique has produced in vitro cell models with characteristics of glia, epithelium, muscle, nerve, and hemocyte. The cells and associated data are available from the Drosophila Genomic Resource Center.

overall_design: Making tissue specific fly cell lines and the transcriptome analysis

first: Daniel

last: Mariyappa

first: Arthur

last: Luhur

first: Andrew

last: Zelhof

first: Amanda

last: Simcox


title: Influence of sulfide on diazotrophic growth of the methanogen Methanococcus maripaludis and its implications for the origin of nitrogenase

city: Bozeman

first: Rachel

middle: L.

last: Spietz

state: MT

institute: Montana State University

summary: Methanogens inhabit euxinic (sulfide-rich) or ferruginous (iron-rich) environments that promote the precipitation of transition metals as metal sulfides, such as pyrite, reducing metal or sulfur availability. Such environments have been common throughout Earth’s history raising the question as to how anaerobes obtain(ed) these elements for the synthesis of enzyme cofactors. Here, we show a methanogen can synthesize molybdenum nitrogenase metallocofactors from pyrite as the source of iron and sulfur, enabling nitrogen fixation. Pyrite-grown, nitrogen-fixing cells grow faster and require 25-fold less molybdenum than cells grown under euxinic conditions. Growth yields are 3 to 8 times higher in cultures grown under ferruginous relative to euxinic conditions. Physiological, transcriptomic, and geochemical data indicate these observations are due to sulfide-promoted metal limitation, in particular molybdenum. These findings suggest that molybdenum nitrogenase may have originated in a ferruginous environment that titrated sulfide to form pyrite, facilitating the availability of sufficient iron, sulfur, and molybdenum for cofactor biosynthesis.

overall_design: Differential expression analysis of Methanococcus maripaludis strain S2 cells grown with different iron and sulfur sources (FeS2 vs Fe(II)/HS-) and with or without a fixed nitrogen source (NH3). Three replicate cultures were grown for each of the following growth conditions: 1. Fe(II)/HS N2-fixing, 2. Fe(II)/HS NH3-amended, 3. FeS2 N2-fixing, and 4. FeS2 NH3-amended.

first: Devon

last: Payne

first: Eric

last: Boyd


title: Transcriptome for alfalfa roots under alkaline stress

status: Public on May 08 2023

city: Beijing

first: Lin

last: Chen

state: Haidian

address: Beijing, Haidian, West Road 2 yuanmingyuan.

institute: Chinese Academy of Agricultural Sciences

summary: Abstract: In order to clarify the response mechanism of alfalfa under alkali stress, the transcriptome of roots was sequenced at different time points after stress and the expression patterns of all genes were analyzed.

overall_design: RNA-seq data for alfalfa roots under normal conditions and alkaline (50 mmol/L NaHCO3) stress


title: Gene expression profiling of human neuroblastoma cell line SMS-KCNR treated with DMSO, simvastatin at 5 µM or simvastatin at 5 µM plus mevalonate at 2 mM for 30 hours

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

institute: University of Alabama at Birmingham

summary: Microarray gene expression profiling reveals that simvastatin regulates the expression of M phase cell cycle genes and mevalonate metabolism

overall_design: Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent samples of SMS-KCNR cells treated with DMSO, simvastatin at 5 µM or simvastatin at 5 µM plus mevalonate at 2 mM for 30 hours

first: Jane


title: Comprehensive sequence-based DNA methylation analysis suggests that PanIN lesions are acinar-derived and epigenetically primed for carcinogenesis

first: Emily

last: Lo

state: MD

address: 733 N Broadway

institute: Johns Hopkins

summary: Pancreatic ductal adenocarcinoma (PDAC) is believed to arise from the accumulation of a series of somatic mutations and is also frequently associated with pancreatic intraepithelial neoplasia (PanIN) lesions. However, there is still debate as to whether the cell-type-of-origin of PanINs and PDACs is acinar or ductal. As cell type identity is maintained epigenetically, DNA methylation changes during pancreatic neoplasia can provide a compelling perspective to examine this question, but DNA methylation sequencing has not yet been performed genome-wide on purified exocrine and neoplastic cell types in the pancreas. Thus, we performed genome-wide DNA methylation sequencing on acini, non-neoplastic ducts, PanIN lesions, and PDAC lesions. We found that: 1) both global methylation profiles and block DMRs clearly implicate an acinar origin for PanINs; 2) at the gene level, PanIN lesions exhibit an intermediate acinar-ductal phenotype resembling acinar-to-ductal metaplasia (ADM); and 3) PanINs are epigenetically primed to progress to PDAC. Thus, epigenomic analysis complements histopathology to define molecular progression toward PDAC.

overall_design: Here, we performed laser-capture microdissection on surgically resected specimens from 18 patients to isolate, with high purity, DNA from four relevant cell types: acini (n=8), non-neoplastic ducts (n=7), PanIN lesions (n=14), and PDAC lesions (n=6). We then performed whole-genome bisulfite sequencing and identified differentially methylated regions (DMRs) using two complementary analytical approaches: bsseq, which identifies any DMRs but is particularly useful for large block-like DMRs; and informME which profiles the potential energy landscape across the genome and is particularly useful for identifying differential methylation entropy.

first: Brian

last: Mears

first: H

last: Maurer

first: Adrian

last: Idrizi

first: Kasper

middle: D

last: Hansen

first: Elizabeth

last: Thompson

first: Ralph

middle: H

last: Hruban

first: Kenneth

last: Olive

last: Feinberg


title: Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [RNA-seq 2]

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary:
Studying the role of circular RNAs in cancer initiation by profiling the interaction of circRNAs with DNA in human cells. The first step of oncogenesis is the acquisition of a repertoire of genetic mutations to initiate and sustain the malignancy. An important example of this initiation phase in leukaemia is the formation of a potent oncogene by chromosomal translocations between the histone methyltransferase Mixed Lineage Leukaemia (MLL) gene and one of over 100 translocation partner genes. Here we show that circular RNAs (circRNAs) - which are a family of covalently-closed, alternatively-spliced RNA molecules - bind DNA, forming circRNA:DNA hybrids (circR-loops) at their cognate loci, and promote transcriptional pausing and DNA breaks. The MLL recombinome concentrates these circR-loops and by overexpressing circRNAs from MLL in human cells we could generate de novo chromosomal translocations, mimicking the MLL recombinome. We anticipate our findings will illuminate this critical phase in cancer initiation and provide a framework to investigate the action of endogenous RNA molecules underlying various genetic aberrations through a process of Endogenous RNA-Directed DNA Damage (ER3D).
Biological triplicates of each cell line, or individual representatives from tumour cells purified from mouse xenograft experiments (labeled tumour) underwent mRNA sequencing

overall_design: John Toubia

first: Shashikanth

last: Marri


title: Enhancers of the PAIR4 regulatory module promote distal VH gene recombination at the Igh locus

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: While extended loop extrusion across the entire Igh locus controls VH-DJH recombination, local regulatory sequences, such as the PAIR elements, may also activate VH gene recombination in pro-B-cells. Here we show that PAIR-associated VH8 genes contain a conserved putative regulatory element (V8E) in their downstream sequences. To investigate the function of PAIR4 and its V8.7E, we deleted all 14 PAIRs in the Igh 5’-region, which reduced distal VH gene recombination over a 100-kb distance on either side of the 890-kb deletion. Reconstitution by insertion of PAIR4-V8.7E strongly activated distal VH gene recombination. PAIR4 alone resulted in lower induction of recombination, indicating that PAIR4 and V8.7E function as one regulatory unit. The pro-B-cell-specific activity of PAIR4 depends on CTCF, as mutation of its CTCF-binding site led to sustained PAIR4 activity in pre-B and immature B-cells and in PAIR4 activation in T-cells. Notably, insertion of V8.8E was sufficient to activate VH gene recombination. Hence, enhancers of the PAIR4-V8.7E module and V8.8E element activate distal VH gene recombination and thus contribute to the diversification of the BCR repertoire in addition to loop extrusion.

overall_design: VDJ-Seq: Nine experimental conditions, with three biological replicates each, associated with control samples (Igh(+/+)). RNA-Seq: two control (Igh(_delta_890/+) and two experimental (Igh(P4V/P4V)) samples. total RNA-Seq: two control samples. ChIP-Seq: Four control samples, single replcates.

first: Louisa

last: Hill

first: Markus

last: Jaritz

first: Karina

last: Schindler

first: Hiromi

last: Tagoh

first: Daniela

last: Kostanova-Poliakova

first: Qiong

last: Sun

first: Tanja

middle: A

last: Schwickert

first: Martin

last: Leeb

first: William

middle: C

last: Skarnes

first: Meinrad

last: Busslinger


title: Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [ATAC-Seq]

summary:
Studying the role of circular RNAs in cancer initiation by profiling the interaction of circRNAs with DNA in human cells. The first step of oncogenesis is the acquisition of a repertoire of genetic mutations to initiate and sustain the malignancy. An important example of this initiation phase in leukaemia is the formation of a potent oncogene by chromosomal translocations between the histone methyltransferase Mixed Lineage Leukaemia (MLL) gene and one of over 100 translocation partner genes. Here we show that circular RNAs (circRNAs) - which are a family of covalently-closed, alternatively-spliced RNA molecules - bind DNA, forming circRNA:DNA hybrids (circR-loops) at their cognate loci, and promote transcriptional pausing and DNA breaks. The MLL recombinome concentrates these circR-loops and by overexpressing circRNAs from MLL in human cells we could generate de novo chromosomal translocations, mimicking the MLL recombinome. We anticipate our findings will illuminate this critical phase in cancer initiation and provide a framework to investigate the action of endogenous RNA molecules underlying various genetic aberrations through a process of Endogenous RNA-Directed DNA Damage (ER3D).
Single replicates of each cell line underwent ATAC-seq


title: SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity [RNA-seq]

first: Christopher

last: Glass

first: Bethany

middle: R

last: Fixsen

first: Claudia

last: Han

first: Nathan

last: Spann

first: Payam

last: Saisan

first: Zeyang

last: Shen

first: Mashito

last: Sakai

first: Isidoro

last: Cobo

first: Inge

last: Holtman

first: Anna

last: Warden

first: Gabriela

last: Ramirez

last: Balak

first: Jana

last: Collier

first: Martina

last: Pasillas

first: Miao

last: Yu

first: Rong

last: Hu

first: Bin

last: Li

first: Sarah

last: Belhocine

first: David

last: Gosselin

first: Nicole

last: Coufal

first: Bing

last: Ren


title: SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity

first: Christopher

last: Glass


title: Effect of IFNg on gene expression of CD90pos and CD90neg PyMT tumors

city: Lausanne

first: Laurent

last: Beziaud

address: Route Cantonale

institute: EPFL

summary: To investigate effect of IFNg in the plasticity of PyMT, we treated PyMT with IFNg for 24h then FACS sorted the CD90pos and CD90neg PyMT. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different PyMT cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PyMT tumor cells treated with IFNg

first: Joerg

last: Huelsken


title: Nono deficiency impedes the proliferation and adhesion of H9c2 cardiomyocytes through Pi3k/Akt signaling pathway [ATAC-seq]

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: Purpose: Congenital heart disease (CHD) is the most common type of birth defect and the main noninfectious cause of death during the neonatal stage. Currently, hemizygous loss-of-function variants in NONO(The non-POU domain containing, octamer-binding) gene have been described as the cause of congenital heart defects in males. However, the effects of NONO on cardiac development have not been fully elucidated.

overall_design: Rat cardiomyocytes H9c2 mRNA profiles and chromatin accessibility across the genome in wild type group and Nono gene knockout group

first: Yuqing

last: Lei

first: Hua

last: Cao


title: Nono deficiency impedes the proliferation and adhesion of H9c2 cardiomyocytes through Pi3k/Akt signaling pathway


title: Nono deficiency impedes the proliferation and adhesion of H9c2 cardiomyocytes through Pi3k/Akt signaling pathway [RNA-seq


title: Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice

city: Wuhan

first: wu

last: bi

state: Hubei

address: wuhan hzau

institute: hzau

summary: One-step and two-step pathways are proposed to synthesize cytokinin. One-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for two-step pathway has not been identified yet. Here, we show that a QTL GY3 boosts grain yield by more than 20% via manipulating two-step pathway. GY3 encodes a LOG protein that acts as a 5’-ribonucleotide phosphohydrolase by excessive consuming the cytokinin precursors, which contrasts with the activity of canonical LOG members as phosphoribohydrolases in a one-step pathway. The residue S41 of GY3 is crucial for the dephosphorylation of iPRMP. A solo-LTR insertion within the promoter of GY3 suppressed its expression and resulted in a higher content of active cytokinins in young panicles. Introgression of GY302428 increased grain yield per plot by 7.4% to 16.3% in all investigated indica backgrounds both under long-day and short-day conditions, which demonstrates the great value of GY302428 in indica rice production.

overall_design: eChip-seq of panicle with two replicates

first: Bi

last: Wu

first: Jianghu

last: Meng

first: Hongbo

last: Liu

first: Donghai

last: Mao

first: Huanran

last: Yin

first: Zhanyi

last: Zhang

first: Xiangchun

last: Zhou

first: Bo

first: Ahmed

last: Sherif

first: Haiyang

first: Xianghua

first: Jinghua

last: Xiao

first: Wenhao

last: Yan

first: Lei

first: Xingwang

first: Wei

last: Chen

first: Weibo

last: Xie

first: Ping

first: Qifa

first: Yongzhong

last: Xing


title: 4C analysis with circular RNA overexpression

first: Simon

last: Conn

summary: Assessing impact on the chromosome conformation by manipulating the expressino of a single circRNA

overall_design: 4 samples sequenced using HEK293T cells. Two replicates for controls (empty vector, pcDNA3.1) and 2 circular RNA overexpression (circMLLe9-10)

first: Vanessa

first: Shashikanth

last: Marri


title: Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding

first: Yuejun

state: Shanghai

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

summary: A fundamental interest in developmental neuroscience is to map the complete single-cell lineages within the brain. We developed a CRISPR editing-based lineage specific tracing (CREST) method for clonal tracing in Cre mice. We combined two complementary strategies to map the comprehensive single-cell lineage landscape in developing mouse brain. Applying snapCREST (snapshotting CREST) in mouse ventral midbrain (vMB), we constructed a spatiotemporal lineage landscape spanning the major developmental stage of vMB. Specifically, we identified six progenitor archetypes that could represent principal clonal fate of individual vMB progenitors, whose progenies showed restricted and graded distribution along the dorsal-ventral axis. We uncovered subregion-specific relationship between glutamatergic and GABAergic neurons and identified three distinct clonal lineages in the floor plate that specified glutamatergic neurons, dopaminergic neurons, or both neuronal types. We further created pandaCREST (progenitor and derivative associating CREST) by combining CREST, ex vivo organoid culture, and clonal splitting strategy to associate the transcriptome of progenitor cells in vivo with their differentiation potentials. Using pandaCREST, we identified multiple developmental origins of dopaminergic neurons and demonstrated that the fate potential of a transcriptome-defined progenitor type reflects the composite potentials of individual progenitors, each with distinct clonal fate and molecular signatures. Thus, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.

overall_design: We performed scRNA-seq at different time points to investigate single-cell lineage in developing mouse ventral midbrain. CREST barcodes from mouse embryonic  fibroblasts and different mouse tissues were enriched from genomic DNA or scRNA-seq cDNA libraries for CREST characterization and lineage analyses.

first: Lianshun

first: Hengxin

first: Zhiwen

last: You

first: Luyue

last: Wang

first: Xinyue

first: Tingli

last: Yuan

first: Ziyan

first: Wenping

last: Zheng

first: Man

last: Xiong

first: Wu

last: Wei


title: Effect of deletion of all0854 on gene expression of  Nostoc sp. PCC 7120

first: Zi-Qian

address: NO.1 Beichen West  Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary:
To investigate the function of All0854, we constructed the all0854 deletion mutant Mall0854, in which all0854 was  knocked out by CRISPER-cpf1.
We then performed gene expression profiling analysis using data obtained from RNA-seq of wide type Nostoc sp. PCC 7120 and Mall0854.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wide type Nostoc sp. PCC 7120 and its derivative Mall0854.

first: Ziqian

first: Yiling

last: Yang

first: Juyuan

first: Xiaoli

last: Zeng

first: Chengcai


title: Serum miRNAs as potential biomarkers for exposure to embedded military-relevant metals

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

type: Non-coding RNA profiling by high throughput sequencing

summary: Many veterans live with military grade heavy metal fragments retained in soft tissue. Retained heavy metal fragments may negatively impact health in various organ systems and can manifest as gastrointestinal, neurocognitive, pulmonary and renal disturbances. As such, a better understanding of the long-term effects of retained metals and identification of biomarkers indicative of detrimental health outcomes would benefit clinical decision making. In this study, we analyzed serum microRNAs from rats with military-relevant pure metals implanted in the gastrocnemius muscle for 1, 3, 6, and 12 months in order to identify potential microRNA biomarkers that are indicative of exposure to one or more metals.

overall_design: Three month old, male, Sprague-Dawley rats (n=8/group) were surgically implanted with one of eight metals of interest (W, Ni, Co, Fe, Cu, Al, Pb, and DU) or tantalum (Ta); Ta, serves as a surgical procedure control because it has been shown to be inert when embedded in skeletal muscle. Serum was collected from each rat at 1, 3, 6, and 12 months after surgically implanting two metal pellets (1 mm diameter x 2 mm length) into each gastrocnemius muscle. Small RNA sequencing was performed on RNA isolated from serum samples.

first: Charlotte

last: Peterson

first: John

last: McCarthy


title: Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [RNA-seq]

first: Simon

summary: Studying the role of circular RNAs in cancer initiation by profiling the interaction of circRNAs with DNA in human cells. The first step of oncogenesis is the acquisition of a repertoire of genetic mutations to initiate and sustain the malignancy. An important example of this initiation phase in leukaemia is the formation of a potent oncogene by chromosomal translocations between the histone methyltransferase Mixed Lineage Leukaemia (MLL) gene and one of over 100 translocation partner genes. Here we show that circular RNAs (circRNAs) - which are a family of covalently-closed, alternatively-spliced RNA molecules - bind DNA, forming circRNA:DNA hybrids (circR-loops) at their cognate loci, and promote transcriptional pausing and DNA breaks. The MLL recombinome concentrates these circR-loops and by overexpressing circRNAs from MLL in human cells we could generate de novo chromosomal translocations, mimicking the MLL recombinome. We anticipate our findings will illuminate this critical phase in cancer initiation and provide a framework to investigate the action of endogenous RNA molecules underlying various genetic aberrations through a process of Endogenous RNA-Directed DNA Damage (ER3D).

overall_design: Biological duplicates of each sample type were sequenced to identify circular RNAs in total RNA and subcellular localisation (nucleus/cytosol)

last: Toubia

first: Shashikanth


title: TF ChIP-seq from HepG2 (ENCSR998LUY)

status: Public on Apr 30 2023

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

institute: University of Wisconsin

summary: All organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These pathways must be properly coordinated to elicit the appropriate response to an ever-changing environment. While individual pathways have been well studied in a variety of model systems, there remains much to uncover about how they are integrated to produce global changes in a cell. Past work from our lab, focused on engineering the budding yeast Saccharomyces cerevisiae for fermentation of the non-native pentose sugar xylose, discovered that hyperactivation of the RAS/Protein Kinase A (PKA) pathway was needed for rapid anaerobic xylose fermentation. Interestingly, the mechanism of PKA hyperactivation has a dramatic impact on growth and metabolism on xylose; deletion of the RAS inhibitor IRA2 permits rapid growth and fermentation, while deletion of the PKA regulatory subunit BCY1 allows for fermentation without growth on xylose. To understand how a single deletion in the PKA pathway can decouple growth and metabolism, we performed transcriptomic analysis of these strains, predicting that altered PKA activity would impact global gene expression and identify pathways important for growth and metabolism coordination. Notably, we found enriched differential expression of lipid metabolism genes, targets of the phospholipid biosynthetic gene transcription factor Ino4, and genes containing the Aft1/2 consensus motif. These results suggested that dysfunctional lipid homeostasis may be responsible for decoupling growth and metabolism in the bcy1∆ strain. In parallel work, we also directly evolved the bcy1∆ strain to grow anaerobically on xylose and found point mutations in TPK1, OPI1, RIM8, and TOA1 permitted growth. Interestingly, Opi1 is the inhibitor of Ino4, further supporting the role of lipid homeostasis in growth and metabolism coordination. This work shows that a single genetic change can have dramatic impacts on multiple aspects of cellular physiology.

overall_design: Comparative gene expression analyzing response to shift from anaerobic glucose to anaerobic xylose in yeast strains with different mutations in the PKA pathway.

first: Ellen

last: Wagner

first: Nicole

last: Nightingale

first: Annie

last: Jen

first: Katherine

last: Overmyer

first: Mick

last: McGee

first: Joshua

last: Coon


title: TF ChIP-seq from WTC11 (ENCSR989LMJ)

summary:
ChIP-Seq on WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from WTC11 (ENCSR987FPY)


title: TF ChIP-seq from K562 (ENCSR980ZWE)

summary:
ChIP-Seq on K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptomic analysis of cultured myotonic dystrophy type 1 myoblasts treated with blocking or gapmer AONs

city: Nijmegen

first: Leontien

last: van der Bent

address: Geert Grooteplein 26-28

department: Cell Biology

institute: Radboudumc

summary: Antisense oligonucleotides (AONs) have gained momentum as therapeutics for neuromuscular disorders with the clinical approval of nusinersen and eteplirsen. For microsatellite repeat expansion disorders, AONs have not reached the clinic yet. Oligonucleotide therapies in such disorders are based on preventing translation of expanded repeats or sequestration of RNA-binding proteins. This can be achieved both by steric hindrance and by degradation of the transcript, and it is unknown which approach is superior. Here, we directly compared blocking AONs with RNase H-recruiting gapmers in a myotonic dystrophy type 1 cell model. Two target sequences were selected: the triplet repeat, which offers many identical binding sites, and a unique sequence upstream of the repeat. We  performed RNA sequencing to investigate both on- and off-target effects on a transcriptome-wide level.

overall_design: Immortalized DM1 patient-derived myoblasts (DM11) were treated with (CAG)5 repeat blocking AONs, (CAG)6 repeat gapmer AONs, or DMPK-specific gapmer AONs. As negative controls, non-targeting (GAC)5 blocking, (GAC)6 gapmer AONs and untreated cells were included. As positive reference, untreated healthy control myoblasts (C25) were included. The negative controls were grouped for the analysis to exclude non-specific effects of AON treatment.

first: M

first: R

last: Brock

first: D

last: Wansink


title: TF ChIP-seq from HepG2 (ENCSR992KMO)


title: Transcriptome analysis following an acute loading-induced skeletal muscle growth stimulus in mice yields tools for discerning global and MYC regulatory networks

first: Yuan

summary: We investigated global, actively transcribed, stable, and myonucleus-specific transcriptomes following an acute hypertrophic stimulus in mouse plantaris. With these datasets we define global and Myc-specific dynamics at the onset of rapid loading-induced muscle fiber growth.

overall_design: Experiment 1 defines the global transcriptome using RNA-sequencing (RNA-seq) during 72 hours of plantaris muscle mechanical overload in the mouse. Experiments 2 and 3 used the tissue from Experiment 1 to provide information on the contribution of active transcription versus mRNA stability to global gene expression with overload (i.e. transcriptional dynamics). Experiment 4 details the myonucleus-specific transcriptome during overload to identify muscle-fiber enriched genes, which is further informed by Experiments 2 and 3. Myonuclei only comprise ~30% of all nuclei after short-term mechanical overload, so defining the transcriptome specifically in myonuclei is critical to understanding muscle fiber adaptation. The transcriptional regulation and localization of Myc and its impact on muscle gene expression was explored using data from Experiments 1-4. Experiment 5 utilized a doxycycline-inducible muscle fiber-specific in vivo Myc pulse in the plantaris to understand what genes Myc controls within muscle fibers, and how this relates to myonuclear gene expression during overload (Experiment 4).

first: Kevin

last: Murach

first: Ferdinand

last: von Walden


title: TF ChIP-seq from HepG2 (ENCSR979KHU)


title: TF ChIP-seq from WTC11 (ENCSR963CCJ)


title: TF ChIP-seq from HepG2 (ENCSR243OKN)


title: TF ChIP-seq from HepG2 (ENCSR978DQT)


title: TF ChIP-seq from HepG2 (ENCSR976KGR)


title: TF ChIP-seq from HepG2 (ENCSR965SHB)


title: TF ChIP-seq from K562 (ENCSR976MXN)


title: TF ChIP-seq from HepG2 (ENCSR977FRK)