title: Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 2]

city: Clayton

first: Yi-Cheng

last: Chang

address: 15 Innovation Walk

department: ARMI

institute: Monash University

summary: The vertebrate main-body axis is laid down during embryonic stages in an anterior-to-posterior (head-to-tail) direction, driven and supplied by posteriorly located progenitors. For the vertebral column, the process of axial progenitor cell expansion that drives axis elongation, and the process of segmentation which allocates these progenitors into repeating vertebral units, occurs seemingly uninterrupted from the first to the last vertebra. Nonetheless, there is clear developmental and evolutionary support for two discrete modules controlling processes within different axial regions: a trunk module and a tail module. The secreted signal Gdf11 has been identified as a principal regulator of timing the trunk-to-tail (T-to-T) transition, but has pleiotropic effects across much of the main body axis, highlighting the need to reveal intrinsic regulatory networks that function to exclusively control one or the other module. Here, we identify Nuclear receptor subfamily 6 group A member 1 (Nr6a1) as a master regulator of elongation, patterning and lineage allocation specifically within the trunk region of the mouse. Both gain- and loss-of-function in vivo analysis revealed that the precise level of Nr6a1 acts as a rheostat, expanding or contracting vertebral number of the trunk region autonomously from other axial regions. Moreover, the timely clearance of Nr6a1 observed at the T-to-T transition was essential in allowing the tail module to operate correctly. In parallel with these effects on vertebral number, we show that Nr6a1 controls the timely progression of global Hox signatures within axial progenitors, preventing the precocious expression of multiple posterior Hox genes as the trunk is being laid down and thus reinforcing that patterning and elongation are coordinated. Finally, our data  supports a crucial role for Nr6a1 in regulating gene regulatory networks that guide cell lineage choice of axial progenitors between neural and mesodermal fate. Collectively, our data reveals an axially-restricted role for Nr6a1 in all major cellular and tissue-level events required for vertebral column formation, supporting the view that modulation of Nr6a1 expression level or function may underpin evolutionary changes in axial formulae that exclusively alter the trunk region.

overall_design: RNA-seq of tailbud cells at E10.5 in wildtype and Nr6a1-overexpressed genomic backgrounds.

first: Ediwna

last: McGlinn


title: Elevated endogenous GDNF levels associate with schizophrenia in humans and mice

status: Public on Jan 03 2023

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

type: Expression profiling by high throughput sequencing

summary: Recent studies have identified presynaptic increase in striatal dopamine as the primary dopaminergic abnormality in schizophrenia, responsible for changes in cortical dopamine function in schizophrenic individuals. However, increased dopamine synthesis and release are not recapitulated in existing mouse models, limiting studies on disease progression and potential treatments. We found that the levels of glial cell line-derived neurotrophic factor (GDNF), a strong dopamine system modulator, are increased in the cerebrospinal fluid of first episode psychosis patients. Using a novel strategy to conditionally increase endogenous gene expression, we developed a mouse model with timed elevation of endogenous GDNF. Conditional ‘Knock Up’ of endogenous GDNF expression (GDNF cKU) in the central nervous system at midgestation resulted in an increase of dopamine levels in the presynaptic compartment of nigrostriatal dopamine neurons, hypodopaminergia in the prefrontal cortex (PFC) and schizophrenia-like behavioural deficits in the mouse. RNA sequencing from the PFC revealed gene expression changes similar to those previously found in schizophrenia patients, including downregulation of dopamine receptor 2 and adenosine A2a receptor (A2AR). Treatment of mice with A2AR antagonist istradefylline partially restored striatal and cortical dopamine levels, suggesting a potential therapeutic strategy to alleviate symptoms associated with schizophrenia. Taken together, our results demonstrate that timed increase in GDNF expression is sufficient to drive schizophrenia-like molecular and behavioural phenotypes, and represents a novel model for studying schizophrenia-associated pathologies in mice.

overall_design: Transcriptomics analysis from mouse brain. Prefrontal cortex, striatum and substantia nigra were dissected from 2-month-old Nestin-Cre x GDNF cKU mice or from GDNF cKU mice 2 months after striatal AAV-Cre delivery.

first: Kärt

last: Mätlik

first: Daniel

middle: R

last: Garton

first: Ana

last: Montaño-Rodríguez

first: Soophie

last: Olfat

first: Feride

last: Eren

first: Laoise

last: Casserly

first: Anne

last: Panhelainen

first: L

middle: L

last: Porokuokka

first: Jaakko

middle: J

last: Kopra

first: Giorgio

last: Turconi

first: Nadine

last: Schweizer

first: Erika

last: Bereczki

first: Fredrik

last: Piehl

first: Göran

last: Engberg

first: Simon

last: Cervenka

first: T

middle: P

last: Piepponen

first: Fu-Ping

last: Zhang

first: Petra

last: Sipilä

first: Johan

last: Jakobsson

first: Carl

middle: M

last: Sellgren

first: Sophie

last: Erhardt

first: Jaan-Olle

last: Andressoo


title: MicroRNA expression data from serum samples of adult atopic dermatitis and psoriasis patients and healthy controls

city: Tartu

first: Ana

last: Rebane

address: Ravila 14B

department: Institute of Biomedicine and Translational Medicine

country: Estonia

institute: University of Tartu

summary:
Atopic dermatitis (AD) and psoriasis vulgaris (PV) affect up to 3-5% of adults in developed countries and severely impair their quality of life thorough adulthood. MicroRNAs contribute to either the development or regulation of several diseases and are present in body fluids, such as serum or plasma, where their identification is of remarkable value as minimally invasive circulating markers of disease.
Although several miRNAs have been associated with AD, to our knowledge, no serum miRNA profiling of adult European AD patients has been published to date and no comparison of AD and PV has been performed.

overall_design: We conducted a miRNA profiling analysis of serum samples from adult AD and PV patients and control individuals.

first: Gemma

last: Carreras-Badosa


title: Whole-genome sequencing of chromatin in Hacat cells overexpressing WT1

city: Changsha

first: Liao

last: yuan

state: Hunan

address: 139 renmin zhong lu, furong district

department: dermatology department

country: China

institute: Second Xiang Ya Hospital of Central South University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of chip sequencing in the search  for target genes of transcription factor .Chip-seq efficiently detect genome-wide segments of DNA interacting with transcription factors.We overexpressed the transcription factor WT1 in hacat cells, and then performed chip experiments to collect the DNA fragments bound to WT1, which were then sequenced.Finally, we proved that interleukinin is the target gene of WT1, providing a new target for clinical research and treatment of skin diseases.

overall_design: Hacat cells overexpressing WT1 plasmid were sequenced and blank plasmid sets were established.


title: Differentially Expressed Genes in Males and Females with Ankylosing Spondylitis (AS): Discrete Effectors in IL-17-producing Cells of Patients with AS.

status: Public on Jan 02 2023

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

country: USA

institute: CWRU

summary: To compare differential effectors of IL-17 pathway between male and female patients with ankylosing spondylitis (AS)

overall_design: Isolated PBMCs from control and AS patients, stimulated with CytoSim for 4 hours, enriched the cells by IL-17, isolated total RNA, and ran the samples through RNA-seq

first: Chan-Mi

last: Lee

first: E

first: Darerian

last: Schueller

first: Maya

last: Breitman

first: Maricela

last: Haghiac

first: Marina

last: Magrey


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (CUT&RUN)

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

summary: Glucose is an important cellular energy source, however, glucose’s function as a second messenger remains relatively unexplored. Here, we find that glucose binds directly to DDX21 to regulate its function during epidermal differentiation. Specifically, glucose binds to the ATP-binding domain of DDX21 to induce a conformational change and inhibit helicase activity. Glucose binding inhibits the dimerization of DDX21 leading to re-localization from the nucleolus to the nucleoplasm and reassembly of DDX21 into larger protein complexes, increasing its association with splicing factors. This occurs during keratinocyte differentiation, where glucose accumulation is necessary, and results in DDX21 binding to RNA processing proteins and mRNA introns. Consequently, DDX21 regulates the splicing of key differentiation factors and promotes epidermal differentiation in a glucose-dependent manner. These findings reveal a novel mechanism of glucose regulation of cell signaling.

overall_design: CUT&RUN was performed on primary human keratinocytes from 4 unrelated donors using HA-tagged DDX21 (anti-HA, CST, #3724)  and one donor was assayed with antibodies to endogenous DDX21 (ProteinTech, 10528-1-AP)  in place of HA-DDX21. H3K27me3 and IgG controls were performed on the same donor tissue (antibodies: IgG, CST, #2729; anti-H3K27me3, Active Motif, 39055).

first: Weili

last: Miao

middle: F

first: Vanessa

last: Lopez-Pajares

first: Brian

last: Zarnegar

first: Yen-Yu

last: Yang

first: Ian

middle: D

last: Ferguson

first: Ryan

middle: A

last: Flynn

first: Jordan

last: Meyers

first: David

last: Reynolds

first: Muthukumar

last: Ramanathan

first: Audrey

middle: W

last: Hong

first: Shiying

last: Tao

first: Yinsheng

last: Wang

first: Paul

last: Khavari


title: Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

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

overall_design: Refer to individual Series


title: Delivery of a tissue derived extracellular matrix gel improves recovery following both acute and chronic disuse muscle injuries.

city: Fayetteville

first: Jeffrey

last: Wolchok

state: AR

address: 700 W. Research Blvd

department: Biomedical Engineering

institute: University of Arkansas

summary:
To evaluate decellularized skeletal muscle extracellular matrix hydrogel effectiveness in treating disuse atrophy using a mouse hindlimb suspension (HU) model. Male C57BL/6J mice were subjected to 5 days of hind limb unloading then received intramuscular matrix gel on the left TA.
We then performed gene expression profiling analysis using data obtained from RNA-seq from mouse TA muscles (n=4 for matrix gel treatment, n=4 for PBS control , and n=4 for uninjured control) at day 7 post matrix gel injection

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mouse Tibialis anterior muscle tissues between uninjured, Pbs and gel treatment

first: Tai

last: Huynh

first: Chris

last: Slaven


title: Microarray gene expression analyses of HCT116 parental and isogenic p53KO cell lines

city: Singapore

first: Chit Fang

last: Cheok

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*STAR

summary: Untreated cells were used for analysis of the basal gene expression levels in HCT116 parental and isogenic p53KO cell lines grown to confluency to elucidate the genes/pathways that are differentially regulated and dependent on the p53 pathway.

overall_design: Two hundred and fifty nanograms from RNA samples were label using Illumina TotalPrep RNA Amplification kit Lot # 1105025 (Ambion) as per amplification protocol. 750ng of cRNA generated from amplification and labeling were hybridized into 2 Human HT-12 v4.0 BeadChips


title: P-selectin identifies molecularly and functionally aged long-term hematopoietic stem cells in Mus musculus C57BL/6 female mice

city: Groningen

first: Leonid

last: Bystrykh

email: l.bystrykh@umcg.nl, l.bystrykh@rug.nl

address: Ant.Deusinglaan 1

department: ERIBA

country: Netherlands

institute: UMCG

summary: Aged hematopoietic stem cells (HSCs) display myeloid-biased differentiation and reduced regenerative potential. In this study, we uncover that P-selectin (Selp) marks a subset of aged HSCs with reduced repopulation capacity. This population of HSCs expresses a prominent aging transcriptome. Overexpression of Selp in young HSCs impaired long-term reconstitution potential and repressed erythropoiesis. We show that IL-1β is elevated in aged bone marrow and administration of IL-1β induces expression of Selp and other aging-associated genes in HSCs. Finally, we demonstrate that transplantation of aged HSCs into young recipients restores a young-like transcriptome, specifically by repressing pro-inflammatory pathways, highlighting the important role of the bone marrow microenvironment in HSC aging.

overall_design: Pre-transplant: 5000 Selp low HSCs (lineage negative, Sca-1+ c-Kit+ CD48- CD150+ Selp low) and 5000 Selp high HSCs (lineage negative, Sca-1+ c-Kit+ CD48- CD150+ Selp high), sorted from 4 old (>24 months) mice, were used for RNA-seq. Post-transplant: 1000 old Selp low and Selp high HSCs were transplanted to lethally irradiated young recipients (10-16 weeks), respectively. After 16 weeks, 5000 Selp low derived HSCs (CD45.2+ lineage negative, Sca-1+ c-Kit+ CD48- CD150+) and Selp high derived HSCs (CD45.2+ lineage negative, Sca-1+ c-Kit+ CD48- CD150+), sorted from recipients, were used for RNA-seq.

middle: V

first: Arthur

last: Svendsen

first: Daozheng


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (RNA-Seq III)

first: Douglas

last: Porter

overall_design: Two biological replicates of primary human foreskin keratinocytes were for RNA expression levels and splicing alterations caused by shDDX21 knock-down during differentiation.

first: Weili

last: Miao

first: Vanessa

last: Lopez-Pajares

first: Brian

last: Zarnegar

first: Yen-Yu

last: Yang

first: Ian


title: From phenotypical investigation to RNA-sequencing for gene expression analysis: a workflow for single and pooled rare cells

city: Meldola

first: Tania

last: Rossi

state: FC

address: Via Piero Maroncelli 40

department: Biosciences Laboratory

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

summary: Combining phenotypical and molecular characterization of rare cells is challenging due to their scarcity and difficult handling. In oncology, circulating tumor cells (CTCs) are considered among the most important rare cell populations. Their phenotypic and molecular characterization is necessary to define the molecular mechanisms underlying their metastatic potential. Several approaches that require cell fixation make difficult downstream molecular investigations on RNA. Conversely, the DEPArray technology allows phenotypic analysis and handling of both fixed and unfixed cells, enabling a wider range of applications. Here, we describe an experimental workflow that allows the transcriptomic investigation of single and pooled OE33 cells undergone to DEPArray analysis and recovery. In addition, cells were tested at different conditions (unfixed, CellSearch fixative (CSF)- and ethanol (EtOH)-fixed cells). In a forward-looking perspective, this workflow will pave the way for novel strategies to characterize gene expression profiles of rare cells, both single-cell and low-resolution input.

overall_design: In this study, we tested the ability of the QIAseq UPX 3’ Transcriptome kit (QIAGEN, Germantown, MD, USA) to provide valuable gene expression data on cells isolated using the DEPArray NxT platform (Menarini Silicon Biosystems, Castel Maggiore, Italy). In particular, samples were tested based on (i) condition (CellSearch fixative (CSF) and ethanol (EtOH)-fixed cells, unfixed cells) and (ii) type of sample (single cell, 10-cells pools, RNA).

first: Giulia

last: Gallerani

first: Davide

last: Angeli


title: Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 1]

first: Yi-Cheng

last: Chang

state: VIC

country: Australia

overall_design: RNA-seq of in vitro cultured cells along NMP differentation

first: Ediwna

last: McGlinn


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (CLIP-Seq II)

overall_design: HEK293T cells were infected with WT or mutant DDX21 to identify DDX21-bound RNAs by CLIP-seq. In addition, three biological replicates of primary human foreskin keratinocytes were used to identify DDX21-bound RNAs by CLIP-seq (easyCLIP variant) in progenitor (non-differentiating) cells in 2D culture. In both cases, cells were infected with lentivirus to express an HA-tagged DDX21 expression construct. CLIP-seq sequencing was performed on a Novaseq, PE150, with ~35 M reads for each sample.

last: Ferguson

first: Ryan

last: Flynn

first: Jordan

last: Meyers

first: David

last: Reynolds

first: Muthukumar

last: Ramanathan

first: Audrey

last: Hong

first: Shiying

last: Tao

first: Yinsheng

last: Wang

first: Paul

last: Khavari


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (RNA-Seq I)

first: Douglas

last: Porter

overall_design: 36 samples

first: Weili

last: Miao

first: Vanessa

last: Lopez-Pajares


title: Complex cellular differentiation in a haloarchaeon

city: Beijing

first: Zhenpeng

last: Zhang

address: 38 Life Science Park Road

institute: Beijing Proteome Research Center

summary:
Purpose: The goals of this study are to describe the morphological diversity of a novel archaea.
Methods: The aerial and substrate hyphae of wild strain, and the substrate hyphae of mutated strains were generated by deep sequencing, in triplicate, using Illumina HiSeq2000 system.
Results: Using an optimized data analysis workflow, we mapped about 1.7-4.4 million sequence reads per sample to wild and mutated hyphae samples by Bowti2 and RSeQC. Approximately half of the transcripts showed differential expression between the aerial and substrate hyphae, with a fold change ≥2.0 and p adjust <0.05.
Conclusions: Our study represents the first detailed analysis of wild and mutated hyphae transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: For wild aerial and substrate hyphae, 10^7 viable spores of YIM 93972 were spread on a layer of 0.20 μm BioTrace NT Nitrocellulose Transfer Membrane (Pall China, Beijing, China) covered on an ISP 4 medium containing 25% NaCl and 2% agar in 85 mm diameter Petri dish. The plates were cultured at 37 °C for 14 days. Totally, 96 culture plates were prepared, which were split into 6 groups as biological replicates. The aerial hyphae grown on nitrocellulose membrane, and the substrate hyphae below nitrocellulose membrane were recovered by scraping with a plain spatula, respectively. For two transitional and three bald mutants, the equal amounts of broken hyphae were spread on the same plates as described above. Totally 192 culture plates were prepared for each mutant strain, which were split into 6 groups as biological replicates. The substrate hyphae were recovered at 21 days. Totally, 6 pooled hyphae were collected for each strain, half of them were used for transcriptomic analysis.

first: Ping

last: Xu

first: Guo-ping

last: Zhao

first: Shukun

last: Tang


title: Nr6a1 controls Hox expression dynamics and is a master regulator of vertebrate trunk development

first: Yi-Cheng

last: Chang


title: Study on differentially expressed genes in the WT1 overexpressed group and the control group by RNA-seq

first: Liao

last: yuan

summary:
Purpose: The aim was to find the differentially expressed genes between the WT1 overexpressed group and the control group
Methods:Hacat cell was transfected with WT1 overexpressed plasmids and blank plasmids, then RNA from both groups of cells was sequenced.
The data obtained from the sequencing is called raw reads, and then the raw reads are subject to quality control QC. After the quality control is passed, the filtered clean reads are compared to the reference genome,
This was followed by gene Quantitative analysis, gene expression level based analyses, and more in depth mining analyses such as GO functional significance enrichment analysis and pathway significance enrichment analysis for the selected differentially expressed genes between samples.
Conclusions:Our study was the first to analyze the transcriptome of Hacat cells overexpressing WT1 generated by RNA-seq technique and to conduct biological replication. Six samples were measured using BGISEQ-500 platform, and the average output of each sample was 21.89 m. The average ratio of sample to genome was 94.81% . A total of 17,693 genes were detected. A total of 181 differentially expressed genes between the two groups were analyzed by GO and Kegg.


title: Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform [2D and 3D]

first: A

last: Bhutkar

summary: Lung cancer is the leading cause of cancer-related death worldwide. Lung adenocarcinoma (LUAD), the most common histological subtype, accounts for 40% of all cases. While existing genetically engineered mouse models (GEMMs) recapitulate the histological progression and transcriptional evolution of human LUAD, they are time-consuming and technically demanding. In contrast, cell line transplant models are fast and flexible, but these models fail to capture the full spectrum of disease progression. Organoid technologies provide a means to create next-generation cancer models that integrate the most advantageous features of autochthonous and transplant-based systems. However, robust and faithful LUAD organoid platforms are currently lacking. Here, we describe optimized conditions to continuously expand murine alveolar type 2 cells (AT2), a prominent cell-of-origin for LUAD, in organoid culture. These organoids display canonical features of AT2 cells, including marker gene expression, the presence of lamellar bodies, and an ability to differentiate into the AT1 lineage. We used this system to develop flexible and versatile immunocompetent organoid-based models of KRAS, BRAF, and ALK-mutant LUAD. Notably, organoid-based tumors display extensive burden and complete penetrance, and are histopathologically indistinguishable from their autochthonous counterparts. Altogether, this organoid platform is a powerful, versatile new model system to study LUAD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for eGFP+/- cells.

first: Santiago

last: Naranjo

first: Christina

last: Cabana

first: Lindsay

last: LaFave

first: Rodrigo

last: Romero

first: Sean

last: Shanahan

first: Arjun

first: Peter

last: Westcott

first: Jason

last: Schenkel

first: Arkopravo

last: Ghosh

first: Laura

middle: Z

last: Liao

first: Isabella

last: Del Priore

first: Dian

last: Yang

first: Tyler

last: Jacks


title: XBP1s cutnrun

city: Madison

first: Allan

last: brasier

state: WI

address: 715 HIghland

institute: University of Wisconsin-Madison

summary: Epithelial mesenchymal plasticity (EMP) is a complex cellular reprogramming event that plays a major role in tissue homeostasis to infections and injury.  Recently we elucidated a mechanism wherein the unfolded protein response (UPR) triggers EMP through the inositol-requiring protein 1 (IRE1α)–X-box-binding protein 1 (XBP1) axis, enhancing glucose shunting to protein N glycosylation producing ER stress.  To better the genomic targets for the IRE1-XBP1 pathway that activate compensatory metabolic changes in EMP, we systematically identified the genomic XBP1 targets using Cleavage Under Targets and Release Using Nuclease (CUT&RUN) of a FLAG-epitope tagged XBP1 in RSV infection.  CUT&RUN identified 7,086 enriched binding sites mapped to 4,827 genes; of these XBP1 binds to 2,119 sites within 1 kb of the transcription start sites.  Interestingly, XBP1 binds to 322 superenhancers associated with RHO GTPase signaling that were associated with largely inert gene expression.  By contrast, XBP1 binds to proximal promoters inducing coordinate mRNA expression of hexosamine biosynthetic enzymes encoding sequential steps in UDP-GlcNAc biosynthesis through AGCTCA motifs.  We demonstrate that IRE1-XBP1 signaling is necessary and sufficient to activate core HBP enzymatic pathway by recruiting transcriptional elongation-competent phospho-Ser2 CTD modified RNA Pol II (pSer-PolII).

overall_design: hSAECs were treated in triplicate replicates including FLAG-XBP1s transduced cells with or without RSV infection (MOI = 1.0, 24 h). Untransduced cells were negative control.  After trypsinization, 4 x 10^6 cells were aliquoted and incubated on ice for 10 minutes in 1 ml of nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine), the released nuclei were pelleted at 600x g, 5 minutes at 4 oC. A basic wash buffer (WB) consisting of 20 mM HEPES, pH7.5, 150 mM NaCl, 0.05% Triton X-1000, 0.1% BSA, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine was used throughout. Between incubation steps, the nuclei were pelleted at 600x g, 3 minutes at 4 oC. Prior to antibody binding, the isolated nuclei were incubated with nutation at 4 oC for 5 minutes in WB containing 2 mM EDTA, followed by nutation at 4 oC for 25 minutes in WB. The nuclei were resuspended in antibody buffer produced by diluting 5 mg of FLAG-M2 in 500 ml of Triton X-100-free WB, and incubated with nutation overnight at 4 oC.  After washing three times in 500 ml of WB on ice (10 minutes each time), the nuclei were incubated at 4 oC for 1 h in 50 ml of WB containing 2.5 ml of EpiCypher pAG-MNase 20x stock (EpiCypher, NC). Washing as above, targeted chromatin cleavage was then conducted by incubating the nuclei on ice for 1 h in 150 ml of BSA-free WB containing 2 mM CaCl2. The cleavage was terminated by adding 150 ml of stop buffer (300 mM NaCl, 20 mM EDTA, 4 mM EGTA and 0.5 ng of E. coli Spike-in DNA (EpiCypher, NC) per 150 ml).  The samples were further incubated with nutation at 4 oC for 1 h, centrifuged at 16,000x g for 5 min at 4 oC and the supernatant was collected. Phenol-chloroform DNA precipitation with 80 mg of glycogen was performed and the Cut&Run-enriched DNA was dissolved in 20 ml of 0.1x TE buffer. Following DNA quantitation by a Qubit fluorometer, Cut&Run DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, MA) per the manufacturer’s instruction, with modification in SPRI bead clearance of adaptor ligation and library amplification reactions to retain small-sized DNA fragments (down to ~170 bp in post-library amplification size). The quality of the resultant DNA libraries was confirmed by Agilent TapeStation HS DNA assay (Agilend, CA), and paired-end Illumina NGS was carried out on NovaSeq 6000 with 5 million reads per sample.

last: Brasier

first: Dianhua

last: Qiao


city: Aachen

first: Lars

last: Buschmann

address: Pauwelsstraße 30

department: Human Genetics

country: Germany

institute: RWTH University Hospital Aachen

summary: Genetic variants in sphingolipid metabolizing enzymes are known to cause neurodegenerative and metabolic diseases by altering the cellular sphingolipid composition. Dysfunction of delta4-dihydroceramide (dhCer) desaturase (DEGS1) has recently been associated with a rare human monogenic neurological disease affecting sphingolipid (SL) homeostasis. Patients with pathogenic DEGS1 variants show elevated levels of different dhCer species and develop a hypomyelinating leukodystrophy in early childhood. To better understand the human pathophysiology and mechanistic complexity of this severe and progressive disease, we here utilized human DEGS1-knockout (KO) HAP1 cells as a genetic KO model to comprehensively investigate the effects of elevated dihydroceramide species on various intracellular processes, like autophagy, apoptosis, ROS formation and ER Stress by using flow cytometry, Western Blot and fluorescence microscopy. DEGS1 KO cells show elevated ROS levels, enhanced autophagy and apoptosis, impaired lysosomal integrity and mild mitochondrial dysfunction. Furthermore, whole transcriptome analysis of DEGS1 KO cells by global RNA sequencing identified impaired processes associated to neuronal differentiation and synaptic function. Morphometric quantification of neuronal features in cultured primary neurons could substantiate RNA-seq results by showing a strong reduction of neuronal complexity 24 hours after Degs1-knockdown and thus impairment of neurodevelopment. In conclusion, we here demonstrate haploid DEGS1-KO cells as a valuable in vitro model for comprehensive mechanistic studies of inherited neurodegenerative diseases.

overall_design:
Transcriptomic analysis of HAP1 DEGS1 KO cells and their wildtype counterpart to determine cellular effects following DEGS1 KO.
Samples include 3 wildtype replicates and 3 DEGS1 KO replicates, with RNA isolated at the same stage

first: Natja

last: Haag


title: Unique transcriptome and gene expression analysis of rice seedling reveals different cadmium response regulatory mechanisms between Indica and Japonica rice

city: 南昌

first: Jianmin

last: Bian

state: 江西 (Jiāngxī)

address: 志敏大道1101

institute: 江西农业大学

summary: Purpose: The goal of this study is to compare the different genetic mechanisms between Indica and Japonica rice under cadmium stress.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: RNA-seq of two rice varieties with different sensitivity to cadmium. CH891 (Indica) is relatively more sensitive to cadmium stress than is 02428 (Japonica).

first: Yanning

last: Wang

first: Shan

last: Tong

first: Haohua

last: He


title: Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform (GFP)

first: A

last: Bhutkar

first: Santiago

last: Naranjo

first: Christina

last: Cabana

first: Lindsay

last: LaFave

first: Rodrigo

last: Romero

first: Sean

last: Shanahan


title: Short-term intensive fasting rejuvenates erythropoiesis

city: Suzhou

first: Jiawei

last: Qian

state: Jiangsu

address: Renai Road, No. 199 Suzhou University

institute: Cyrus Tang Medical Institute

summary: How erythropoiesis responds to fasting remains to be explored. Here, Xu et al. showed that short-term intensive fasting promotes the production of red blood cells and boosts their functions by regulating MS4A3-CDK2 module to enhance megakaryocyte-erythroid progenitor self-renewal and erythroid-biased differentiation.

overall_design: We sorted megakaryocyte–erythroid progenitor cell from the BM of 6h fasted mice and control mice for bulk RNA-seq to investigate the molecular influence which fasting poses on erythropoiesis.

first: Li

last: Xu

first: Wen

last: Wei


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (RNA-Seq II)

first: Douglas

last: Porter

overall_design: Two biological replicates of primary human foreskin keratinocytes were for RNA expression levels and splicing alterations caused by shDDX21 knock-down, differentiation, or glucose depletion.

first: Weili

last: Miao

first: Vanessa

last: Lopez-Pajares

first: Brian

last: Zarnegar

first: Yen-Yu

last: Yang

first: Ian

last: Ferguson

first: Ryan

last: Flynn

first: Jordan

last: Meyers

first: David

last: Reynolds

first: Muthukumar

last: Ramanathan

first: Audrey

last: Hong

first: Shiying

last: Tao

first: Yinsheng

first: Paul

last: Khavari


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (CLIP-Seq)

overall_design: Three biological replicates of primary human foreskin keratinocytes were used to identify DDX21-bound RNAs by CLIP-seq (easyCLIP variant) in differentiating cells under normal or low glucose conditions. Cells were infected with lentivirus to express an HA-tagged DDX21 expression construct. CLIP-seq sequencing was performed on a HiSeq X Ten, PE150, with ~35 M reads for each sample.

last: Wang


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation

overall_design: Refer to individual Series


title: Glioma epileptiform activity and progression are driven by IGSF3 mediated potassium dysregulation [mouse]

status: Public on Jan 01 2023

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Seizures are a pathophysiological feature of malignant glioma. Recent studies implicate peritumoral synaptic dysregulation as a driver of neuronal hyperactivity and tumor progression, however, the molecular mechanisms that govern these phenomena remain elusive. Using scRNA-seq and intraoperative patient ECoG recordings, we show that tumors from seizure patients are enriched for gene signatures regulating synapse formation. Employing a human-to-mouse in vivo functionalization pipeline to screen these gene sets, we identified IGSF3 as a mediator of glioma progression and dysregulated neural circuitry in the form of spreading depolarization (SD). Mechanistically, we discovered that IGSF3 interacts with Kir4.1 to suppress potassium buffering and found that seizure patients exhibit reduced expression of potassium handlers in proliferating tumor cells. In vivo imaging revealed dysregulated synaptic activity emanates from the tumor-neuron interface, which we confirmed in patients. Our studies reveal that tumor progression and seizures are enabled by ion dyshomeostasis and identify SD as a driver of disease.

overall_design: Single-celll RNA-sequencing of piggyBac in utero electroporation tumors

first: Curry

last: Naomi

first: Serin

middle: H

last: Akdes

first: Ganesh

last: Rao

first: Jeffery

last: Noebels

first: Deneen

last: Benjamin


title: The rise and fall of billionaire siRNAs during reproductive development in rice [sRNA-seq]

city: Nanjing

first: Lili

address: Weigang No.1

institute: Nanjing Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA polymerase IV-dependent siRNAs, usually 24 nt in length, function in the RNAdirected DNA methylation that is responsible for de novo methylation in plants. We analyzed 24 nt siRNAs in inflorescences and found that among the 20,200 24 nt siRNA clusters, the top 0.81% highly expressed clusters accounted for more than 68% of the 24 nt siRNA reads in inflorescences. We named the highly expressed siRNAs as billionaire siRNAs (bill-siRNAs) and the less-expressed siRNAs as pauper siRNAs (pau-siRNAs). The bill-siRNAs in inflorescences are mainly derived from the ovary. Female gametes produced more bill-siRNAs than male gametes. In embryos and seedlings developed from fertilized egg cells, the bill-siRNAs from gametes disappeared. The endosperm, which develops from the fertilized central cell, also contained no bill-siRNAs from gametes but did contain newly and highly expressed siRNAs produced in different regions. In contrast, bill-siRNAs from the ovaries were maintained in the seed coat. The biosynthesis of bill-siRNAs in various tissues and cells is dependent on OsRDR2 (RNA-dependent RNA polymerase 2) and Pol IV (DNA-dependent RNA polymerase IV). Similar to the pau-siRNAs, the first base of bill-siRNAs is enriched at adenine, and bill-siRNAs can direct DNA methylation in various tissues.

overall_design: small RNA sequencing data

first: Dong-Lei


title: Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (ChIP-Seq)

first: Douglas

last: Porter

overall_design: Two biological replicates of primary human foreskin keratinocytes were processed for DDX21 ChIP-seq. ChIP-seq sequencing was performed on a NovaSeq 6000, PE150, with ~40 M reads for each sample.

first: Weili

last: Miao

first: Vanessa

last: Lopez-Pajares

first: Brian

last: Zarnegar

first: Yen-Yu

first: Ian


title: Balancing of mitochondrial translation through METTL8-mediated m3C modification of mitochondrial tRNAs

city: Nashville

first: James

last: Marks

state: Tennessee

address: 638A Robinson Research Building

institute: NIAMS/NIH

summary: Mitochondria contain a specific translation machinery for the synthesis of respiratory chain components encoded on the mitochondrial genome. Mitochondrial tRNAs (mt-tRNAs) are also generated from the mitochondrial genome and, similar to their cytoplasmic counterparts, are modified at various positions. Here, we find that the RNA methyltransferase METTL8, is a mitochondrial protein that facilitates m3C methylation at position C32 of mt-tRNASer(UCN) and mt-tRNAThr. METTL8 knock out cells show reduced and over expressing cells enhanced respiratory chain activity. In pancreatic cancer, METTL8 levels are high, which correlates with patient survival. Indeed, METTL8 up regulation stimulates respiratory chain activity in these cells. Ribosome occupancy analysis using ribosome profiling revealed ribosome stalling on mt-tRNASer(UCN) and mt-tRNAThr codons and mass spectrometry analysis of native ribosomal subcomplexes unraveled reduced respiratory chain incorporation of the mitochondria encoded proteins ND6 and ND1. A well-balanced translation of mt-tRNASer(UCN) and mt-tRNAThr codons through METTL8-mediated C32 methylation might therefore provide optimal respiratory chain compositions and function.

overall_design: 4 mitoribosome profiling datasets of HEK293 cells. One control dataset, two biological replicates containing METTL8 knockouts, and one with a inducible METTL8 overexpression

first: Eva

last: Schöller

first: Virginie

last: Marchand

first: Astrid

last: Bruckman

first: Christopher

last: Powell

first: Markus

last: Reichold

first: Christian

last: Mutti

first: Robert

last: Hett

first: Katha

last: Dettmer-Wilde

first: Regina

last: Feederle

first: Stefan

last: Hüttelmeier

first: Mark

last: Helm

first: Richard

last: Warth

first: Peter

last: Oefner

first: Michal

last: Minczuk

first: Yuri

last: Motorin

last: Hafner

first: Gunter

last: Meister


title: The Rise and Fall of Billionaire siRNAs during Reproductive Development in Rice

first: Lili

last: Wang


title: Effect of the expression of viral SIRV2 gp21 on the gene expression profile of Saccharolobus islandicus LAL14/1

city: København N

first: Laura

last: Martínez Alvarez

state: Please select

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

summary: To identify putative target genes in S. islandicus LAL14/1 of the viral transcriptional regulator SIRV2 gp21

overall_design: RNAseq data of the gene expression changes in Sulfolobus islandicus LAL14/1 harboring a plasmid for the inducible expression of the ribbon-helix-helix transcriptional factor SIRV2gp21 at 0, 6 and 12 hours post-induction with 0.2% D-arabinose in comparison to Sulfolobus islandicus LAL14/1 cells harboring an empty plasmid as a control. Two independent biological replicates per time-point were analyzed

first: Xuyang

last: Li

first: Cristina

last: Madueño-Lozano

last: Martínez-Alvarez

first: Xu

last: Peng


first: Dong-Lei

last: Yang


title: Characterization of mu opioid receptor cells in a new Oprm1-cre mouse

city: Pensylvania

first: Julie A

last: Blendy

state: PA

address: 125 South 31st Street

department: Systems Pharmacology and Translational Therapeutics

institute: University of Pensylvania

summary:
we derived, validated, and applied a novel MOR-specific Cre mouse line, inserting a T2A cleavable peptide sequence and the Cre coding sequence into the MOR 3’UTR. Importantly, this line shows specificity and fidelity of MOR expression throughout the brain and with respect to function, there were no differences in behavioral responses to morphine when compared to wild type mice, nor are there any alterations in Oprm1 gene expression or receptor density.
To assess Cre recombinase activity, MOR-Cre mice were crossed with the floxed GFP-reporters, RosaLSLSun1-sfGFP or RosaLSL-GFP-L10a. The latter allowed for cell type specific RNA sequencing via TRAP (Translating Ribosome Affinity Purification) of striatal MOR+ neurons following opioid withdrawal.

overall_design: RNA was isolated from striatal cells expressing GFP-L10a by TRAP. Briefly, 24 hours after the last chronic morphine (100mg/kg) or saline dose,  Oprm1Cre/Cre; RosaLSL-GFP-L10a mice were euthanized via cervical dislocation, and striatum was isolated (both hemispheres, 2 brains pooled per sample), homogenized with lysis buffer, and incubated with magnetic beads that were pre-conjugated to anti-GFP antibodies (clones htz-GFP-19F and htz-GFP-19C8, Memorial Sloan-Kettering Monoclonal Antibody Facility, New York, New York, USA) to affinity purify RNA that was bound by GFP-L10a fusion protein.

first: Juliet

last: Mengaziol

first: Amelia

last: Dunn

first: Michelle

last: Ehrlich

first: Julie


title: Genetic deletion of translocator protein exacerbates post-sepsis syndrome with activation of the C1q pathway in septic mouse model

city: Minami-ku

first: Kazuya

last: Kikutani

state: Hiroshima

address: 1-2-3 Kasumi

department: Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences

country: Japan

institute: Hiroshima Univeristy

summary: To investigate the role of TSPO in the sequelae of sepsis induced by cecal ligation and puncture (CLP), hippocampal gene expression changes after CLP surgery were examined in wild-type and TSPO KO mice

overall_design: Animals were divided into three groups (i) Wiley type (WT) + sham, (ii) WT + CLP, and (iii) TSPO knockout + CLP, and hippocampal gene expression was examined on day 17 for each group

first: Hidenori

last: Aizawa


title: Postnatal neuronal Bace1 deletion impairs neuroblast and oligodendrocyte maturation

city: Farmington

first: Riqiang

last: Yan

address: 263 Farmington Ave

institute: Uconn Health

summary: We aim to understand the effect of postnatal neuronal deletion of Bace1 on the transcriptome of the hippocampus

overall_design: Single nuclei from P31 and P192 Bace1-fl/fl and Bace1-fl/fl;Thy1-cre mice were isolated from snap frozen hippocampii

first: Marc

last: Benoit

first: Xiangyou

last: Hu


title: The indispensable role of autophagy in lens morphogenesis

city: Baltimore

first: S. Amer

last: Riazuddin

address: 600 N. Wolfe street

institute: Johns Hopkins University

summary: FYVE and coiled-coil domain containing 1 (FYCO1) is expressed ubiquitously and is required for microtubule-dependent, plus-end-directed transport of autophagic vesicles. We previously reported loss of function mutations in FYCO1 responsible for cataractogenesis with no other ocular and/or extra-ocular phenotype. Here, we show that Fyco1-/- lenses recapitulated the cataract phenotype and exhibited diminished autophagy, consistent with a critical role of Fyco1 and autophagy in lens morphogenesis. Transcriptome coupled with proteome and metabolome profiling identified many differentially expressed, autophagy-related, genes, proteins, and lipids, respectively in Fyco1-/- lenses. Flow cytometry of FYCO1 (c.2206C>T) knock-in (KI) human lens epithelial (HLE) cell line confirmed reduced amounts of membrane-bound LC3B-II and autophagic vesicles resulting from the loss of FYCO1. Transmission electron microscopy showed persistent organelle mass in Fyco1-/-lenses and FYCO1 KI lens-like organoid structures, which were further confirmed through western blot analysis. In summary, our data show that the absence of FYCO1 causes diminished autophagy, delayed organelle degradation, and cataractogenesis. These data support the model of FYCO1 supplementing basal autophagy in the lens to meet the physiological necessity of high autophagy levels required during lens fiber cell differentiation and lack thereof results in delayed organelle removal.

overall_design: Next-generation (NG)-based whole transcriptome sequencing (RNA-Seq) was performed for wild-type (Wt) and Fyco1-/- lenses at postnatal day 0 (P0). Total RNA was subjected to RNA-Seq library preparation using NEB Next Ultra RNA Library Prep Kit. Six RNA-Seq bar-coded pooled libraries were sequenced (2 × 100 bp) on a HiSeq 2500. The raw reads (FASTQ) were processed and analyzed using combinations of algorithms (STAR, HTSeq, and DESeq2). The paired-end reads were aligned to the Mus musculus genome (GRCm38/mm10) using the STAR algorithm (Ver. 2.5). The HTSeq (Ver. 0.6.1) was used for the quantification of gene expression using mapped reads. The expression data were normalized by calculating the fragment per kilobase per million mapped reads (FPKM) values for each gene.  Differential gene expression analysis was performed using the DESeq2.

first: Shahid

middle: Y

last: Khan

first: S

last: Amer Riazuddin


title: Role of microRNAs in regulating the DNA damage response to ionizing radiation in Caenorhabditis elegans

city: Cologne

first: Bjoern

last: Schumacher

state: NRW

address: Joseph-Stelzmann-Strasse 26

department: Institute for Genome Stability in Ageing and Disease

institute: CECAD Cologne

summary: microRNAs fine-tune the regulation of numerous biological processes by mediating gene expression post-transcriptionally. Mature miRNAs associate with argonaute (AGO) proteins to form the RNA-induced silencing complex (RISC) that binds to and blocks translation of target mRNAs.  In our study, we address the function of miRNAs in regulating DNA damage responses in-vivo, by exploiting  the nematode model organism Caenorhabditis elegans. Using next-generation sequencing, we obtained miRNA expression profiles of WT worms as well as mutants harboring a loss-of-function deletion of the C. elegans AGO gene alg-2 that display abnormal cell death in response to genotoxic stress. 2.5 hours after exposure to ionizing irradiation, the miRNA transcriptomes of both WT and alg-2(ok304) mutant worms were only mildly altered in comparison to their respective untreated controls. However, irrespective of  treatment, alg-2(ok304) mutants exhibited noticeable dysregulation of several miRNA families with known physiological functions. Reduced levels of some of these miRNAs might explain the abnormal DNA damage response of alg-2-deficient C. elegans.

overall_design: miRNA expression profiles of adult N2 (WT) and alg-2(ok304) mutant C. elegans 2.5 hours after treatment with 90 Gy of ionizing radiation

first: Markus

last: Doll

first: Björn


first: Lili

last: Wang

overall_design: Transcriptome sequencing

first: Dong-Lei


title: Long non-coding RNAs associated with mitogen-activated protein kinase in pancreatic cancer cells.

city: Sendai

first: Tomohiko

last: Ishikawa

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Otolaryngology - Head and Neck Surgery

institute: Tohoku University Graduate School of Medicine

summary:
To investigate the long non-coding RNAs associated with mitogen-activated protein kinase in human pancreatic cancer, we isolated total RNA from three pancreatic cancer cell lines (MIAPaCa-2, AsPC-1, PCI-35) with or without 24h treatment of MAP2K inhibitor (U0126).
Total transcriptome sequencing analysis was performed in total 6 samples, and then we listed lncRNAs from the raw data.

overall_design: Comparative gene expression profiling analysis of long non-coding RNA-seq data for pancreatic cancer cell lines (MIAPaCa-2, AsPC-1, PCI-35) with or without MAP2K inhibitor (U0126).

first: Toru

last: Furukawa


title: Alternative splicing outcomes across an RNA-binding protein concentration gradient

city: Gainesville

first: Joseph

middle: Anthony

last: Ellis

state: FL

address: 1200 Newell Drive

department: Biochemistry and Molecular Biology

institute: University of Florida

summary: Alternative splicing (AS) is a dynamic RNA processing step that produces multiple RNA isoforms from a single pre-mRNA transcript and contributes to the complexity of the cellular transcriptome and proteome. This process is regulated through a network of cis-regulatory sequence elements and trans-acting factors, most-notably RNA binding proteins (RBPs).  The muscleblind-like (MBNL) and RNA binding fox-1 homolog (RBFOX) are two well characterized families of RBPs that regulate fetal to adult AS transitions critical for proper muscle, heart, and central nervous system development. To better understand how the concentration of these RBPs influences AS transcriptome wide, we engineered an MBNL1 and RBFOX1 inducible HEK-293 cell line. We found that induction of exogenous RBFOX1 modulated AS outcomes, despite significant levels of endogenous RBFOX1 and RBFOX2 expression. We characterized AS outcomes by RNAseq following dose-dependent MBNL1 induction to generate transcriptome wide dose-response curves of skipped exon events. Analysis of 43 validated splicing events by RT-PCR revealed a spectrum of dose-response splicing curves with a 2-fold range for EC50 values and slope values ranging from 4 to 10. Analysis of this data suggests that exclusion events, when compared to inclusion events, regulated by MBNL1, may require higher protein concentrations to regulate, and that multiple arrangements of YGCY motifs produce similar splicing outcomes. Together these data suggest that rather than a simple association between the configuration of RBP binding sites and a specific splicing outcome, that a complex network governs both AS inclusion and exclusion events that operates in an RBP dose-dependent manner.

overall_design: Alternative splicing analysis of RNAseq data using 6 difference concentrations of induced HA-MBNL1 protein in a HEK293 cell line

first: Melissa

last: Hale

first: Eric

middle: T

first: J

last: Berglund


title: TSPAN18 facilitates bone metastasis of prostate cancer by protecting STIM1 from TRIM32-mediated ubiquitination

city: Guangzhou

first: Qianghua

last: Zhou

address: Urology

institute: Sun yat-sen memorial hospital

summary: We demonstrated that TSPAN18 was overexpressed in prostate cancer (PCa) and markedly accelerated PCa cell migration and invasion in vitro and bone metastasis in vivo by inhibiting E3 ligase tripartite motif containing 32 (TRIM32)-mediated stromal interaction molecule ubiquitination and degradation. To further investigate the genes regulated by TSPAN18, we knockdown TSPAN18 by siRNA and performed high-throughput sequence. So we identify a series of genes regulated by TSPAN18.

overall_design: Prostate cancer cell line DU145 was transfected with the contol siRNA or TSPAN18 siRNA for 48h, respectively. The RNA of the treated cells was extracted and sequenced on Illumina HiSeq 2500 platform and 100-bp paired-end reads were generated.

first: Tianxin

last: Lin

first: Hai

last: Huang


title: Epigenetic centromere identity is precisely maintained through DNA replication but is uniquely specified among human cells

city: Pittsburgh

first: Megan

last: Mahlke

state: Pennsylvania

address: 5115 Centre Ave

institute: UPMC

summary: Centromere identity is defined and maintained epigenetically by the presence of the histone variant CENP-A. How centromeric CENP-A position is specified and precisely maintained through DNA replication is not fully understood. The recently released Telomere-to-Telomere (T2T-CHM13) genome assembly containing the first complete human centromere sequences provides a new resource for examining CENP-A position. Mapping CENP-A position in clones of the same cell line to T2T-CHM13 identified highly similar CENP-A position following multiple cell divisions. In contrast, centromeric CENP-A epialleles were evident at several centromeres of different human cell lines, demonstrating the location of CENP-A enrichment and site of kinetochore recruitment varies among human cells. Across the cell cycle, CENP-A molecules deposited in G1 phase are maintained at their precise position through DNA replication. Thus, despite CENP-A dilution during DNA replication, CENP-A is precisely reloaded onto the same sequences within the daughter centromeres, maintaining unique centromere identity among human cells.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variant CENP-A in PDNC4 cells.

first: Lior

last: Lumerman

first: Peter

last: Ly

first: Yael

last: Nechemia-Arbely


title: Glioma epileptiform activity and progression are driven by IGSF3 mediated potassium dysregulation

first: Akdes

last: Serin Harmanci

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Long non-coding RNA associated with mitogen-activated protein kinase in pancreatic cancer cells.

summary:
To investigate the genes associated with LINC00941, we isolated total RNA from AsPC-1 with or without the knockdown of LINC00941 using siRNA.
Total transcriptome sequencing analysis was performed in total 3 samples.

overall_design: Comparative gene expression profiling analysis of total RNA-seq data for AsPC-1 with or without knockdown of LINC00941 using siRNA.


title: Glioma epileptiform activity and progression are driven by IGSF3 mediated potassium dysregulation [human]

overall_design: Single-cell RNA-sequencing of human glioma

first: Curry

last: Naomi

first: Serin

last: Akdes

first: Ganesh

last: Rao

first: Jeffery

last: Noebels

first: Deneen

last: Benjamin


title: Gene expression profile at single cell level of haploid partenogenotes and androgenotes from pronuclear stage to four divisions [scRNA-seq]

city: Valencia

first: Pedro

last: de Castro

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

country: Spain

institute: IVI Foundation

summary: Partenogentoes and Androgenotes are constructs artificially conceived which are genetically composed of the unique genome corresponding to the original haploid germ cell used for their generation (oocyte pronucleus or sperm head). We used single cell RNA sequencing aproach to analyze the diversity of its blastomers along the first four cell divisions.

overall_design:
Single blastomers were isolated by lasser asisted embryo biopsy analyzed using RNAseq.
Please note that  each individual title corresponds to a different embryo and within each embryo there are different blastomeres (i.e. A3.2 (corresponds to cell cycle 3 of embryo number 2), A5-1, A5-2, A5-3, A5-4 (correspond to each of the 4 blastomeres that make up embryo A3.2)).

first: Xavier

last: Vendrell

first: Francisco

last: Dominguez

first: Maria

last: Escriba


title: CircPTK2/PABPC1/SETDB1 axis promotes EMT-mediated tumor metastasis and Gemcitabine resistance in bladder cancer

city: Wuhan

first: Li

last: weiquan

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: To elucidate the specific mechanism by which circPTK2 exerts oncogene functions, we screened the transcriptome by RNA-Seq, focusing on the differential expressed genes in UM-UC-3 and T24 cells with silenced circPTK2 compared to control cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bladder cancer cells (UMUC3,T24) and its KD derivatives (sh-circPTK2-UMUC3,sh-circPTK2-T24).

first: Xiangui

last: Meng

first: Wen

last: Xiao

first: Jiayin

last: Sun

first: Weiquan

last: Li

first: Hongwei

last: Yuan

first: Tiexi

last: Yu

first: Xiaoping

last: Zhang

first: Wei

last: Dong


title: Effect of depletion of SQLE on gene expression of B16F10 Melanoma cells in vivo

first: Xiaodong

last: Ma

state: Guangdong

address: No.55, West of ZhongShan Avenue, Tianhe District

institute: Department of Brain Science and Rehabilitation Medicine

summary:
To investigate the function SQLE in the regulation of tumor immune microenvironment, we established B16F10 cell lines in which target gene has been knocked down by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at same time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B16F10 cells and its KD derivatives (shSQLE).

first: X

first: Jun

last: Wu

first: Xun

first: Weibin

last: Hu


title: Del Nido Cardioplegia or Potassium Induces Nrf2 and Protects Cardiomyocytes Against Oxidative Stress

city: Tucson

first: Hongting

last: Diao

state: AZ

address: 1316 E 7th St

department: Medical Pharmacology

institute: University of Arizona

summary: Open heart surgery is often an unavoidable procedure for treatment of coronary artery disease.  The procedure associated reperfusion injury affects postoperative cardiac performance and long-term outcome.  We addressed here whether cardioplegia essential for cardiopulmonary bypass surgery activates Nrf2, a transcription factor regulating the expression of antioxidant and detoxification genes.  With commonly used cardioplegic solutions, High K+, Low K+, Del Nido (DN), histidine-tryptophan-ketoglutarate (HTK) and Celsior, we found that DN causes an increase of Nrf2 protein in AC16 human cardiomyocytes.  Tracing the ingredients in DN led to the discovery of KCl at the concentration above 5 mM capable of Nrf2 protein induction.  The Antioxidant Response Element luciferase reporter assay confirmed Nrf2 activation by DN or KCl.  Transcriptomic profiling using RNA-seq revealed that oxidation-reduction as a main gene ontology group affected by KCl.  KCl indeed elevated the expression of classical Nrf2 downstream targets, including TXNRD1, AKR1C, AKR1B1, SRXN1 and G6PD.  DN or KCl induced Nrf2 elevation is Ca2+ concentration dependent.  We found that KCl extended the half-life of Nrf2 from 17.8 to 25.1 mins, and decreased Nrf2 protein ubiquitination.  Knocking out Keap1 blocked Nrf2 induction by K+.  Nrf2 induction by DN or KCl protected against ROS generation or loss of viability by H2O2.  Our data support that high K+ concentration in DN cardioplegic solution can induce Nrf2 protein, which in turn mediates protection of cardiomyocytes

overall_design: AC16 cells were growing in 6-well plates and when the cell confluence reahed 90%, we treated cells with 26 mM KCl, incubated for 16 hours.  Total RNAs were extracted from control or 26 mM KCl treated AC16 cells at 16 hrs by RNeasy Kits (Qiagen).  Sample quality control, transcriptome library preparation, library quality control, sequencing, raw data output, data quality control and bioinformatics analysis were performed by BGI Americas Corporation (San Jose, CA) and validated by R-programming.

first: Wujing

last: Dai

first: Daniel

last: Wurm

first: Raymond

middle: K

last: Wong

first: Qin

last: Chen


title: High-Throughput Screening of the Saccharomyces cerevisiae Genome for 2-Amino-3-Methylimidazo [4,5-f] Quinoline Resistance Identifies Colon Cancer-Associated Genes

city: Albany

first: Michael

middle: Thomas

last: Fasullo

state: New York

address: 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

summary: 162 genes were identified as conferring resistance to 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 334 genes were identified as conferring resistance to bioactivated IQ.

overall_design: Two pooled diploid yeast deletion collections, one original and one expressing human CYP1A2 and NAT2, were exposed to either 400 μM IQ, 800 μM IQ, 2% methanol (+0.1% acetic acid), or nothing, for either 5 or 10 generations. Barcode DNA was extracted from pooled samples and differential abundance calculated for each strain in the collections to determine which deletion strains were sensitive to IQ and which were resistant.

last: Dolan


title: Activating MKL1/SRF pathway to target breast cancer metastasis

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

summary: To test whether activity of the mechano-sensitive transcription factor complex, MKL1/SRF, can be exploited to reduce breast cancer metastasis

overall_design: We performed bulk RNA-seq of control, MKL1 overexpressed (OE)  and caMKL1 OE in LM2 and 4T1 cell lines. We also performed bulk RNA-seq of control, low and high expression of LifeAct in LM2 cell line.

first: Jian

first: Xiao


title: The establishment of the anther somatic niche with single cell sequencing

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

institute: Stanford University

summary: Maize anthers ranging in size from 0.5mm to 3.0mm in increments of 0.25mm were dissected and their cells isolated using the FX-Cell protocol. scRNA-seq libraries were prepped using the CEL-Seq2 protocol and sequenced with 150bp PE reads with Illumina HiSeq or NovoSeq. The developmental trajectories of the somatic cell layers were investigated.

overall_design: Anthers were dissected from maize plants of the fertile inbred line W23. Anthers ranging in size from 0.5mm to 3.0mm in increments of 0.25mm were dissected, isolated using a Hana Cell Sorter (NamoCell) and used for scRNA-seq. At least two separate W23 plants provided anthers for each stage

first: D

middle: B

first: Virginia

last: Walbot


title: Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [RNA-seq]

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

summary: In this study, we showed chromatin accessibility-based epigenetic landscape in osteoclastogenesis. To reveal the affected genes by alteration in histone acetylation states after RANKL stimulation, we supplemented sodium acetate, which increased histone acetylation, to OC precursors. Then we conducted RNA-seq with BMM (D0), OC precursors (D1), and OC precursors treaed with sodium acetate (ACD1).

overall_design: Comparative gene expression profiling analysis of mRNA-seq data for BMMs (D0), OC precursors day1 (D1), and OC precursors day1 with sodium acetate (ACD1)

first: Sangyong

last: Lee

first: Jueng

middle: S

first: Myoung

middle: J

last: Kim

first: Seor

middle: I

last: Ahn


title: Transcriptomic profiling between attached and detached SAS cells

city: Toyoake

first: Kouhei

last: Sakurai

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Department of Joint Research Laboratory of Clinical Medicine, School of Medicine

institute: Fujita Health University

summary: Cancer cells acquire anchorage-independence to escape anoikis. This study aimed to evaluate the gene expression signature of SAS cells cultured at the standar plate and the low-attachment plate. Total RNAs were isolated from attached and detached SAS cells, and gene expression signatures were examined using gene expression microarray.

overall_design: Total RNA was isolated from attached SAS cells and detached SAS cells for gene expression profiling.


title: Adult mouse skin dendritic cells

city: San Francisco

first: Antonin

last: Weckel

state: CA

address: 513 Parnassus

institute: UCSF

summary: Early life establishment of tolerance to commensal bacteria at barrier surfaces carries enduring implications for immune health but remains poorly understood. Here we show that this process is controlled by microbial interaction with a specialized subset of antigen presenting cells. More particularly, we identify CD301b+ type 2 conventional dendritic cells (DC) as a subset in neonatal skin specifically capable of uptake, presentation and generation of regulatory T cells (Tregs) to commensal antigens. In early life, CD301b+ DC2 are enriched for programs of phagocytosis and maturation, while also expressing tolerogenic markers. In both human and murine skin, these signatures were reinforced by microbial uptake. In contrast to their adult counterparts or other early life DC subsets, neonatal CD301b+ DC2 highly expressed the retinoic acid-producing enzyme, RALDH2, deletion of which limited commensal-specific Tregs. Thus, synergistic interactions between bacteria and a specialized DC subset critically support early life tolerance at the cutaneous interface.

overall_design: We wanted to analyze by scRNAseq properties of adult skin dendritic cells and transcriptomics to compare to neonatal skin dendritic cells

first: Miqdad

middle: O

last: Dhariwala

first: Kevin

last: Ly

first: Oluwasunmisola

last: Ojewumi

first: Julianne

last: Riggs

first: Jeanmarie

middle: R

last: Gonzalez

first: Laura

last: Dwyer

first: Joy

middle: N

last: Okoro

first: John

middle: M

last: Leech

first: Margot

last: Bacino

first: Grace

last: Cho

first: Geil

last: Merana

first: Niroshana

last: Anandasabapathy

first: Yosuke

last: Kumamoto

first: Tiffany

middle: C

last: Scharschmidt


title: Serum response factor reduces gene expression noise and confers cell state stability (scRNA-Seq)

first: Shangqin

last: Guo

summary: To explore whether SRF controls cell state heterogeneity, SRF KO or wild type (WT) iPSCs cultured in serum containing medium.

overall_design: We performed bulk RNA-seq and single-cell RNA sequencing (scRNA-seq)of parallel SRF KO and WT iPSCs.

first: Jian

last: Zhang

first: Xiao

last: Hu


title: Serum response factor reduces gene expression noise and confers cell state stability (Bulk RNA-Seq)


title: Uninjured Mouse Liver Nuclei – Henderson Lab 1

city: Edinburgh

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

summary: Investigation of cell populations present in healthy mouse liver.

overall_design: Single nuclei were isolated from uninjured mouse liver (n=3 pooled).

first: Kylie

last: Matchett

first: Neil

last: Henderson


title: Histone lactylation drives endothelial activation-mediated lung injury in sepsis-associated ARDS via promoting ferroptosis

city: shanghai

first: Erzhen

last: Chen

address: ruijin hospital

institute: ruijin hospital

summary: The activation of pulmonary endothelial cells (ECs) triggers the occurrence of lung injury and is a hallmark of sepsis-associated acute respiratory distress syndrome(ARDS). Aberrant metabolism favoring glycolysis plays a pivotal role in the pathogenesis of sepsis-induced EC activation. Herein we demonstrate that glycolysis-related histone lactylation, represented by H3K14 lactylation (H3K14la), drives sepsis-associated EC activation and lung injury. Accordingly, H3K14la level is elevated in injured lung tissue and activated ECs. Inhibition of lactate production suppresses both H3K14la levels and EC activation in response to lipopolysaccharide (LPS). We also show that lactate-dependent H3K14la is enriched at the promoters of ferroptosis-related genes, thereby inducing ferroptosis in ECs, and inhibiting ferroptosis effectively ameliorates EC activation. Taken together, elevated lactate in sepsis modulates EC activation and lung injury via histone lactylation and manipulation of glycolysis/H3K14la/ferroptosis axis may provide novel therapeutic approaches for the treatment of sepsis-associated ARDS.

overall_design: Human umbilical vein endothelial cells (HUVEC)

first: Fangchen

last: Gong

first: Wen

last: Xu

first: Xiangtao

last: Zheng

first: Wenbin

last: Liu

first: Lei

last: Pei

first: Ming

last: Zhong

last: Shi

first: Hongping

last: Qu

first: EnQiang

last: Mao

first: Zhitao

last: Yang

first: Ying

first: Ranran

last: Li


title: Construction of ceRNA and m6A related-lncRNA networks associated with anti-inflammation of AdipoAI

city: GuangZhou

first: Yu

middle: Hong

last: Wen

state: GuangDong

address: No. 1023-1063, South Shatai Road, Baiyun District, Guangzhou City

institute: Southern Medical University

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

summary: Adiponectin (APN) is an endogenous adipokine secreted from adipocytes that exerts an anti-inflammation property. AdipoAI is an orally active adiponectin receptor agonist identified by our group, which can emulate APN's anti-inflammatory properties through mechanisms not fully understood. To explore AdipoAI function, we used lncRNA microarray and got differential lncRNA/mRNA expression medicated by AdipoAI. Identified as one kind of non-coding RNA with more than 200bp length, lncRNA has been demonstrated to have abundance biological functions, including anti-inflammatory response. In the current study, we performed an lncRNA microarray in LPS-induced Raw264.7 cells which pre-stimulated with AdipoAI, and screened 110 DElncRNAs and 190 DEmRNAs. Enrichment analyses were conducted to total mRNAs and DEmRNAs, including GSVA, ssGSEA, GO/KEGG, GSEA and PPI analysis. Among all these processes, endocytosis was significantly enriched. A co-expression analysis was built based on DElncRNAs and DEmRNAs. Then, using Targetscan and miRwalk to predict related microRNAs of DElncRNAs and DEmRNAs respectively, we established competing endogenous RNA (ceRNA) networks including 54 mRNAs from 8 GO items. Furthermore, 33 m6A methylation related marker genes were obtained from previous study and used for the construction of m6A related-lncRNA network using the co-expression analysis. We identified FTO as the hub gene of the network, and 14 lncRNAs that interacted with it. The expression levels of 10 lncRNAs selected from ceRNA and FTO- related lncRNAs networks were validated with qRT-PCR. Finally, Macrophage phenotype scores showed that AdipoAI could attenuate the M2b and M2c polarization of macrophage and correlate with the above lncRNAs. Our work reveals that lncRNA might involve in the anti-inflammation process of AdipoAI in LPS-induced macrophages through ceRNA network and epigenetic regulation of m6A. Mechanistically, these lncRNAs associated with AdipoAI might be related to endocytosis and polarization in macrophage, and provide new candidates for the anti-inflammatory application of APN and its receptor agonist.

overall_design: Raw264.7 cells were stimulated with AdipoAI for 24 h followed by  incubation with 100 ng/ml of LPS (E. coli 0111: B4, Sigma-Aldrich,   St. Louis, MO, USA) for an additional 6 h. Total RNA of cells was  extracted, and 5-μg total RNA from each cell sample was sent to  Arraystar Inc. (Rockville, MD, USA) for microarray analysis. Image  processing and data extraction and analysis also were performed by  Arraystar Inc. using their established protocols.

first: HongWen

last: Yu

first: Wei

last: Qiu


title: Tumor-derived oxidative stress triggers follicle loss in breast cancer

first: HUI

last: CHEN

address: Guangzhou Huangpu Road

department: medicine

institute: Jinan University School of Medicine

summary: Breast cancer is the common indication for ovarian cryopreservation. However, whether the grafting ovarian tissue meets the functional requirements and the need for additional interventions remains unclear. Here, we show abnormal serum hormones in breast cancer in human and tumor-bearing mice, and for the first time show that tumor induced loss of primordial and growing follicles and the number of follicles being lost to either growth or atresia. A gene signature of tumor-bearing mice demonstrates the disturbed regulatory network of steroidgenesis which link to mitochnondia dysfunction in oocytes and granulosa cells via PI3K signaling pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control female balb/c-nude mice and breast tumor bearing-mice.

first: Ping

first: Yongqi

last: Wu

first: Jieqiong

last: Huang

first: Hui


title: Lysine 117 Residue is Essential for the Function of the Hepatocyte nuclear factor 1α

city: Beijing

first: Yuan

last: Chu

address: No. 38, kexueyuan Road, Changping District

institute: Beijing Institute of Lifeomics

summary:
Hepatocyte nuclear factor 1α (HNF1α) play essential roles in controlling development and metabolism, its mutations are clearly linked to the occurrence of maturity-onset diabetes of the young (MODY3) in human. 117 lysine to glutamic acid (E117) mutation in the HNF1α gene was clinically associated with MOYD3, but no functional data on this variant is available. Here, we generated a knock-in mouse model in which the lysine 117 is replaced with glutamic acid in the endogenous murine HNF1α locus. The HNF1αE117/E117 mice reproduced HNF1-null phenotypes including dwarfism, hepatic dysfunction, renal Fanconi syndrome, diabetes and die from a progressive wasting syndrome, but no hyperphenylalaninemia. Moreover, HNF1αE117/E117 mice shared similar hepatic gene expression profiles with HNF1 deficient mice. In vitro  experiments showed that HNF1 mutants in which the lysine 117 residue were replaced by glutamic acid, arginine or glutamine residues, respectively, had a significant decreased in overall transactivation and DNA binding capacity. K117 mutants had no effect on its protein stabilities and nuclear localization, but significantly blocked its own association. Our results clearly demonstrate that the lysine 117 residue is essential for the function of the HNF1a, and prove important to identify the molecular basis for diseases associated with defects in HNF1α
We then performed gene expression profiling analysis using data obtained from RNA-seq of liver tissue of 3 WT mice and 3 KI mice.

overall_design: HNF1α K117E knock-in (HNF1αE117/+E117) mice, harboring the human pathogenic mutation (replacement of K with E) in the mouse ortholog, were generated using the CRISPR/Cas9 system on a C57/BL/6J background. Seven chimeras (HNF1αE117/+) were obtained and then backcrossed with wild-type(WT) C57BL/6J mice. We performed comparative transcriptome analysis by RNAseq of liver tissue from WT and KI mice

first: Long

last: Zhao

first: Xian

first: Chen

last: Chen

first: Song-Hui

last: Yao

first: Si-Cong

first: Shen-Si

last: Xiang

first: Xiao-Fang

last: Wang

first: Yue

last: Wan

first: Dian-Dian

last: Dong

first: Cang-Yan

first: Rong-Hua

last: Yin

first: Miao

first: Xiao-Ming


title: Effect of overexpression of WT-SOD2 and NLS-SOD2 on gene expression of MCF7 breast cancer cells

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: To investigate the demethylase function of SOD2 on gene expression in cells expressing a nuclear-targeted version of SOD2

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7, MCF7 overexpressing WT-SOD2 and MCF7 overexpressing NLS-SOD2 cells

first: Flavio

last: Palma


title: Gene expression profile at single cell level of splenocytes from wild-type and S100a9 knock-out mice ± repeated social defeat stress

city: Bryan

first: Adam

last: Case

state: TX

address: 8447 Riverside Pkwy

department: Psychiatry and Behavioral Sciences

institute: Texas A&M University

summary: Psychological trauma increases inflammation. In a mouse model of psychological trauma (repeated social defeat stress), we used single cell RNA sequencing to assess the gene expression in splenocytes ± psychological trauma as well as without S100a9 (gene of interest)

overall_design: 12 Mice (3 WT control, 3 KO control, 3 WT stress, 3 KO stress) underwent a standard 10 day repeated social defeat stress paradigm followed by 1 day of behavior testing. The following day (day 12), splenocytes were harvested and utilized for single cell RNA sequencing.


title: Mouse neonatal dendritic cells from uncolonized, and Staphylococcus epidermidis-zsgreen colonized mouse (loaded and non-loaded cells)

first: Antonin

last: Weckel

overall_design: We wanted to analyze by scRNAseq properties of neonatal skin dendritic cells and transcriptomics changes after phagocytosis of skin sommensals, here Staphylococcus epidermidis Tu3298

first: Miqdad

last: Dhariwala

first: Kevin

last: Ly

first: Oluwasunmisola

last: Ojewumi

first: Julianne

last: Riggs

first: Jeanmarie

last: Gonzalez

first: Laura

last: Dwyer

first: Joy

last: Okoro

first: John

last: Leech

first: Margot

last: Bacino

first: Grace

middle: D

last: Cho

first: Geil

last: Merana

first: Niroshana

last: Anandasabapathy

first: Yosuke

last: Kumamoto

first: Tiffany

last: Scharschmidt


title: Gene expression profile at single cell level of haploid partenogenotes and androgenotes from pronuclear stage to four divisions

first: Pedro

last: de Castro

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

institute: IVI Foundation

summary: Partenogentoes and Androgenotes are constructs artificially conceived which are genetically composed of the unique genome corresponding to the original haploid germ cell used for their generation (oocyte pronucleus or sperm head). We used single cell RNA sequencing aproach to analyze the diversity of its blastomers along the first four cell divisions.

overall_design: Single blastomers were isolated by lasser asisted embryo biopsy analyzed using RNAseq.

first: Xavier

last: Vendrell

first: Francisco

last: Dominguez

first: Maria

last: Escriba


title: Neonatal foreskin antigen presenting cells after colonization with Staphylococcus epidermidis

first: Antonin

last: Weckel

overall_design: We wanted to look at uptake of antigen presenting cells of commensal bacteria in neonatal human skin. Cells loaded with bacterial antigens will be compared to cells non-loaded with antigens to understand how phagocytosis of commensals affect cell polarization.

first: Miqdad

last: Dhariwala

first: Kevin

last: Ly

middle: T


title: Skin and Skin Draining lymph node dendritic cells from neonatal mouse colonized with a commensal or control

overall_design: We performed scRNAseq on neonatal mice colonized with S.epidermidis or S.aureus, and look at skin dendritic cells and skin draining lymph nodes migratory dendritic cells to understand specificities of neonatal DCs and uptake/carriage of bacterial antigens. CT-subpop corresponds to cells from uncolonized mice. SEneg-subpop corresponds to cells without bacteria from a mouse colonized with S.epidermis, SEpos-subpop corresponds to cells with bacteria from a mouse colonized with S.epidermis, SAneg-subpop corresponds to cells without bacteria from a mouse colonized with S.aureus, SApos-subpop corresponds to cells with bacteria from a mouse colonized with S.aureus. Cells were stained for ADT: CD103_ADT, CD301B_ADT, CD11B_ADT, EpCAM_ADT, PDL-1_ADT, CD86_ADT

first: Oluwasunmisola

last: Ojewumi

first: Julianne

last: Riggs

first: Jeanmarie

last: Gonzalez


title: NGS-Muscle of swine supplemented with cholecalciferol and 25(OH)D

city: Kraków

first: Alicja

last: Wierzbicka

address: ul. Sarego 2

country: Poland

institute: National Research Institute of Animal Produstion

summary: According to RNA-seq results, application of vitamin D in the form of 25(OH)D in swine diet can be beneficial for myogenesis, energy production and muscle fibre formation by influencing TOR signalling pathway. However, the use of vitamin D in the form of 25(OH)D may reduce muscle respiratory capacity.

overall_design: Effect of different doses of cholecalciferol and calcidiol on pork quality parameters and transcriptome profiles of skeletal muscle of swine. The vitamin D dosage of the groups was as follows : 1 group (control group) 2000 IU cholecalciferol (grower) and 1500 IU cholecalciferol/ kg feed (finisher)- 8 individuals, 2 group 3000IU cholecalciferol (grower) and 2500 IU cholecalciferol/ kg feed (finisher)- 10 individuals, 3 group 2000 IU cholecalciferol + 1000 IU 25(OH)D3 (grower) and 1500 IU cholecalciferol + 1000 IU 25(OH)D3/kg feed (finisher)- 8 individuals, 4 group 2000 IU 25(OH)D3 (grower) and 1500 IU 25(OH)D3/kg feed (finisher)- 8 individuals

last: Oczkowicz

first: Tomasz

last: Szmatoła


title: Staphylococcus aureus-derived factors promote Th9 cell polarization and strongly enhance a transcriptional program associated with inflammation and allergy

city: Stockholm

first: Isabella

last: Badolati

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

institute: Stockholm University

summary: T helper (Th) 9 cells, characterized by robust secretion of IL-9, have been increasingly associated with allergic disease. However, if and how Th9 cells are modulated by environmental stimuli remains poorly understood. In this study, we show that exposure of CD4 T-cells to Staphylococcus (S.) aureus-derived factors, including its toxins, potently enhances Th9 cell frequency and IL-9 secretion. Furthermore, S. aureus increases the expression of Th9-promoting factors at a transcriptional level, such as FOXO1, miR-155 and TNFRSF4. Addition of retinoic acid (RA) dampens the Th9 responses induced by S. aureus and substantially changes the transcriptional program induced by this bacterium, while also altering the expression of genes associated with allergic inflammation. Together, our results demonstrate a strong influence of microbial and dietary factors on Th9 cell polarization, which may be important in the context of allergy development and treatment.

overall_design: Human CD4 T-cells together with autologous monocytes were treated with S.aureus-derived factors, retinoic acid or the combination of the two and then polarized towards Th9 cells. An untreated control was also included. RNA-Seq analysis was performed to investigate the effect of the treatments on Th9 polarization at a transcriptional level.

first: Marieke

last: van der Heiden

first: David

last: Brodin

first: Marit

last: Zuurveld

first: Szilvia

last: Szilágyi

first: Sophia

last: Björkander

first: Eva

last: Sverremark-Ekström


title: A multi biomarker panel of miRNA-lncRNA interaction; a novel approach for early diagnosis of Acute coronary syndrome

city: Abbasia

first: Yahia

middle: Ahmad

last: Yahia

state: Cairo

address: Faculty of Medicine Ain Shams University

country: Egypt

institute: Faculty of Medicine Ain Shams Research Institute (MASRI)

summary: Acute coronary syndrome (ACS) is presented as a group of symptoms resulting from acute ischemia of the myocardium due to rupture of a coronary arterial plaque. It comprises different classes; unstable angina, STEMI and NSTEMI. The current cornerstones of ACS diagnosis are ECG, CK-MB and cardiac troponins however there are several limitations leading to evading early diagnosis and poor prognosis. This highlights the need for more sensitive and specific biomarkers for a better outcome. In this study,an initial screening set is RNA sequenced for retrieval of differentially expressed genes and miRNAs. Then, a microRNA-long non-coding RNA multi biomarker panel is retrieved via in silico data analysis related to PINK1/Parkin-induced mitophagy. This is followed by clinical validation of their expression in serum of ACS patients in comparison to non-cardiac chest pain patients and healthy volunteers via qRT-PCR.

overall_design: In this study, we have initially screened positive acute coronary syndrome cases for differentially expressed genes (DEG) and differentially expressed miRNAs(DEM) through RNA sequencing by targeted Next Generation sequencing(NGS). Then, this was followed by clinical validation through the implementation of a multi panel approach of four miRNAs that regulate mitophagy genes in addition to three lncRNAs suggested to regulate the selected miRNAs in turn via insilico analysis in addition to their implication in various cellular processes and signaling pathways involved in the pathogenesis of atherosclerosis, destabilization of arterial plaques and formation of blood clots and hence comprising a pattern of acute coronary syndrome

first: SARA

middle: H

last: AGWA

first: MARWA

last: MATBOLI

first: SHERIF

last: ELZAHWY

first: YAHIA

middle: A

last: YAHIA

first: NADINE

last: SHERIF


title: Epigenome analysis of normal and gastric cardia cancer samples

city: Shantou

first: Shuhui

last: Liu

address: No. 22, Xinling Road, Shantou, P.R. China

department: Department of Pathology

institute: Shantou University Medical College

summary: Genome wide DNA methylation profiling of normal and gastric cardia cancer samples. The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in normal and gastric cardia cancer samples. Samples included 8 normal -gastrica cardia cancer paired tissues.

overall_design: Bisulphite converted DNA from the 16 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip


title: Chromatin accessibility-based epigenetic landscape in osteoclastogenesis [ATAC-seq]

first: Jueng Soo

last: You

summary: In this study, we showed chromatin accessibility-based epigenetic landscape in osteoclastogenesis. To reveal chromatin accessibility landscape throughout osteoclastogenesis, we conducted Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) with BMM (D0), OC precursors day 1 (D1), OC precursor day 2 (D2), and OC (D3).

overall_design: Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) was conducted during osteoclastogenesis. We treated BMMs with RANKL for three days to differentiate them into osteoclasts (OCs). Cells in each day were subjected to ATAC-seq. Each sample was named as D0 (BMM), D1 (OC precursors day 1), D2 (OC precursor day 2), and D3 (OC), according to the day at which the cells were collected for the assay.

first: Sangyong

last: Lee

first: Jueng

first: Myoung

last: Kim

first: Seor

last: Ahn


title: A honeybee stinger inspired self-interlocking microneedle patch and its application in myocardial infarction treatment

city: Hang Zhou

first: Qiao

last: Jin

address: Sandun Town, Xihu District

department: College of Animal Sciences

institute: Zhe Jiang university

summary: Microneedle patches are widely employed in pain-free drug delivery, biosensing, and cosmetic applications. However, weak tissue adhesion remains a major challenge in clinical translation of microneedle patches. Here, mimicking the structural features of honeybee stingers, stiff polymeric microneedles with unidirectionally backward facing barbs were fabricated and embedded into various elastomer films to produce self-interlocking microneedle patches. The spirality of the barbing pattern was adjusted to increase interlocking efficiency. In the challenging working condition of animal hearts beat with large cyclic strains, the barbs provided 0.4 N interlocking force, which resulted in firm fixation of the bioinspired microneedle patch. In addition, the minimal bleeding caused by microneedle puncturing adhered the porous surface of the patch substrate between microneedles to the epicardium via coagulation. In the demonstrative application of myocardial infarction treatment, the microneedle patches significantly reduced cardiac wall stress and strain in the infarct and border zone, maintaining left ventricular function and morphology. In addition, the microneedle patch was minimally invasively implanted onto beating porcine heart free of sutures and adhesives, and the fixation step only took 2 minutes. Therefore, the honeybee stinger inspired microneedles could provide an adaptive and convenient means to adhere patches for various medical applications.

overall_design: Examination of the transcriptomes of rat heart tissue samples with the treatment below(n=6 MI,n=6,Sutured patch,n=6 Microneedle patch,n=6 Sham)

first: Yang

last: Zhu

first: Lenan

last: Zhuang

first: Yuwen

last: Lu


title: miRNA expression profiles of EVs from healthy control and MDS patients

city: Tokyo

first: Yasutaka

last: Hayashi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

institute: Institute of Medical Science, The University of Tokyo

summary: To investigated dysregulated miRNAs in human MDS patients, we performed miRNA-sequencing (miRNA-seq) of serum EVs from 38 MDS patients and 8 healthy subjects. The miRNA profile in EVs from MDS patients was distinctly clustered from that in healthy individuals. In addition, the miRNAs significantly upregulated in the MDS group target pathways linked to cell survival, proliferation, and MSC differentiation, indicating that they have remarkably similar properties to miRNAs in murine EVs from MDS cells. These results suggest that miRNAs play an essential role in the MSC impairment observed in MDS.

overall_design: Experiments using serum derived EVs from healthy control (n=8) and MDS patients (n=38).

first: Yusuke

last: Yoshioka

first: Tomofusa

last: Fukuyama

first: Kazuaki

last: Yokoyama

first: Tomoyuki

last: Uchida

first: Masao

last: Hagihara

first: Nobuhiro

last: Ohno

first: Kensuke

last: Usuki

first: Arinobu

last: Tojo

first: Susumu

last: Goyama

first: Daichi

last: Inoue

first: Takahiro

last: Ochiya

first: Toshio

last: Kitamura


title: Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

summary:
RNA-seq expression assays were done in larval Pimephales promelas (Fathead minnow, FHM) exposed to 10 chemicals (3 metals, 4 Neonicotinoids, and 3 pharmaceuticals) over a range of concentrations to derive relatively short term transcriptomics based points of departure (tPODs).
tPODs were compared to apical points of departures (aPODs) to investigate the potential  use of the FHM tPODS as part of a high throughput approach that might be used in a regulatory context.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data from exposed larval FHM; untreated controls vs. half-log dilution series of treatment concentrations (n=11) to estimate tPODs for ten chemicals (CuSO4, NiSO4, ZnSO4, Clothianidin, Flupyradifurone, Imidacloprid, Thiacloprid, Fluoxetine, Paroxetine and Sertraline).
For each treatment chemical, 96 well plate with individual 24 hour old FHM larva in each deep (1 mL) well. 8 replicates at each concentration, 24 hour static exposure, followed by phenotypic (survival, behavior) observation and subsequent homogenization and RNA sequencing of fish in doses that did not experience excessive mortality.

first: Daniel

middle: L

last: Villeneuve

first: Michelle

last: Le

first: Monique

last: Hazemi

first: Adam

last: Biales

first: David

last: Bencic

first: Kendra

last: Bush

first: Robert

last: Flick

first: Mackenzie

last: Morsehead

first: Kelvin

last: Rodriguez

first: Kelsey

last: Vitense

first: Kevin

last: Flynn


title: Genome-wide sequencing for mutp53 regulated network in NPC cell line

city: Houston

first: An

last: Xu

institute: UThealth Houston

summary: We report the application for high-throughput profiling of transcriptome, chromatin-associated proteins on a genome-wide level in NPC CNE2 cells.

overall_design: RNA-seq, ChIP-seq and m6Aseq are used to profile mutp53 NPC cell line

first: Haidan

last: Luo

first: Ruiying

last: Zhao

first: Huiling

last: Yang

first: Dung-Fang

last: Lee


title: Tamoxifen-induced Ghr deletion in SV40 C3(1) T-antigen mouse prostates

city: Madison

first: Paul

last: Marker

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin Madison

summary: Seven-month old tamoxifen-inducible Ghr recombination mice in T-antigen mouse model of prostate cancer (Ghrflox/flox;ROSA26Cre-ERT2+/0;SV40 C3(1) T-antigen+/0) or tamoxifen-control mice (Ghrflox/flox;SV40 C3(1) T-antigen+/0) were treated with 250 mg/kg tamoxifen for five straight days. The dorsolateral prostate of each mouse was collected one month after final treatment and RNA was collected. Samples include

overall_design: 5 samples. Two biological replicates of tamoxifen-control DLPs and three biological replicates of Ghr deletion DLPs.

first: Chris

last: Unterberger

first: Sean

last: McIlwain

first: Philippos

last: Tsourkas


title: Tamoxifen-induced Ghr deletion in WT mouse prostates

summary: Two-month old tamoxifen-inducible Ghr recombination mice (Ghrflox/flox;ROSA26Cre-ERT2+/0) or tamoxifen-control mice (Ghrflox/flox) were treated with 250 mg/kg tamoxifen for five straight days. The dorsolateral prostate of each mouse was collected one month after final treatment and RNA was collected. Samples include

overall_design: 5 samples. Three biological replicates of tamoxifen-control DLPs and two biological replicates of Ghr deletion DLPs.


title: Transcriptional profile of Pseudomonas aeruginosa infected cells

city: Barcelona

first: Marc

last: Torrent Burgas

address: Carrer de la Vall Moronta

institute: Universitat Autònoma de Barcelona

overall_design: Sequencing of NuLi-1 and CuFi-1 cells infected by two different Pseudomonas aeruginosa bacterial strains at 3 different post infection times

first: Nuria

last: Asensio

first: Javier

last: Rendón

first: Juan

middle: J

last: González López

first: María

last: Martín Gómez


title: Circular RNA profiling of left ventricles from cardiac-specific GRK-beta1AR transgenic and/or miR-150 transgenic mice treated with isoproterenol.

city: Indianapolis

first: Il-Man

last: Kim

state: IN

address: 635 Barnhill Drive, MS 346A

institute: INDIANA UNIVERSITY SCHOOL OF MEDICINE

summary: Genome-wide circular RNA profiling analyses in left ventricles (LVs) from cardiac-specific GRK-beta1AR transgenic (TG) and/or miR-150 TG mice treated with isoproterenol (ISO) were performed to identify novel circular RNAs regulated by beta-arrestin-mediated beta1AR signaling and miR-150 in the heart.

overall_design: The following 12 independent mouse LVs were used: three biological replicates for 4 groups (vehicle [Veh] GRK-beta1AR TG, ISO GRK-beta1AR TG, Veh GRK-beta1AR/miR-150 double TG [DTG] and ISO GRK-beta1AR/miR-150 DTG). LVs were harvested after 1 week of Veh or ISO injection.

first: Bruno

last: Moukette


title: Transcriptome profiling of left ventricles from cardiac-specific GRK-beta1AR transgenic and/or miR-150 transgenic mice treated with isoproterenol.

summary: Genome-wide transcriptomic analyses in left ventricles (LVs) from cardiac-specific GRK-beta1AR transgenic (TG) and/or miR-150 TG mice treated with isoproterenol (ISO) were performed to identify novel targets of beta-arrestin-mediated beta1AR signaling and miR-150 in the heart.

overall_design: The following 12 independent mouse LVs were used: three biological replicates for 4 groups (vehicle [Veh] GRK-beta1AR TG, ISO GRK-beta1AR TG, Veh GRK-beta1AR/miR-150 double TG [DTG] and ISO GRK-beta1AR/miR-150 DTG). LVs were harvested after 1 week of vehicle or ISO injection.


title: Transcriptome Sequencing of GLYR1-positive human pancreatic ductal adenocarcinoma.

city: Shanghai

first: Yan

last: Gu

address: 800 Xiangyin Road

department: Immunology

institute: Second Miilitary Medical University

summary: We performed transcriptome sequencing on GLYR1-positive and GLYR1-negative human pancreatic ductal adenocarcinoma (PDAC) to shed light on the transcriptional changes of GLYR1-positive PDAC.

overall_design: The specimens were prepared by laser capture microdissection (LCM). In brief, surgically removed tissues were sectioned for H&E staining and LCM (Life technologies) was performed. Tumor tissues (stroma were excluded) were used for RNA extraction, and sequencing. Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.Ribosomal RNA was removed from total RNA using Ribo-Zero rRNA removal beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

first: Yanfang

last: Liu