title: Single cell sequencing of human primary LCs stimulated by TNF

status: Public on Jun 14 2021

city: Southampton

first: James

middle: David

last: Davies

state: Hampshire

address: LE57, Lab and Pathology block, Tremona Road

department: Clinical and Experimental Sciences

institute: University of Southampton

summary: Langerhans cells (LC) coordinate immune homeostasis at the human epidermis, proficent in initiating immunogenic and tolerogenic immune responses. To investigate the transcriptomic mediators of human LC immunogenic vs tolerogenic immune responses, we performed single cell RNA-sequencing of  migratory LCs extracted from epidermal sheets stimulated with or without TNF.

overall_design: Unstimulated and TNF-stimulated migrated human LC were subjected to single cell RNA-sequencing following encapsulation with Drop-seq. Migrated LC were extracted from 48 hour culture of epidermal sheets prior to stimulation.

first: Marta

middle: E

last: Polak

first: Sofia

last: Sirvent

first: Andres

middle: F

last: Vallejo


title: miRNA NGS of serum exosome in heat stroke patients

city: Guangzhou

first: Yue

last: Li

address: #111 Liuhua Road

country: China

institute: Department of Intensive Care Unit, General Hospital of Southern Theatre Command of PLA

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the differential expression of miRNA in serum exosome of heat strok patints. Compared with those from healthy volunteers, exosomes from patients with HS showed substantial changes in the expression of 202 exosomal miRNAs (154 upregulated and 48 downregulated miRNAs). The most upregulated miRNAs included miR-511-3p, miR-122-5p, miR-155-3p, miR-1290, and let7-5p, whereas the most downregulated ones included miR-150-3p, 146a-5p, and 151a-3p. Gene ontology enrichment of the miRNAs of patients with HS compared with control subjects were associated mostly with inflammatory response, including T cell activation, B cell receptor signaling, dendritic cell chemotaxis and leukocyte migration, and platelet activation and blood coagulation. The identified miRNAs were primarily enriched to the signal transduction pathways namely, T cell receptor signaling, Ras signaling, chemokine signaling, platelet activation, and leukocyte transendothelial migration, all of which are associated with inflammation and hemostasis. Multiple targeted mRNAs associated with the inflammatory response, blood coagulation, and platelet activation were further verified in serum exosomes. Exosomes from patients with HS convey miRNAs and mRNAs associated with pathogenic pathways, including inflammatory response and coagulation cascade. Exosomes may represent a novel mechanism for intercellular communication during HS.

overall_design: Blood samples were collected from three patients with HS at the time of admission to the intensive care unit; three healthy volunteers were selected as control. Exosomes were isolated using ultracentrifugation and their miRNA content was profiled using next-generation sequencing; mRNA content was evaluated using qPCR array.

first: Huasheng

last: Tong


title: Mechanistic Evaluation of Reduced Reproduction in Daphnia pulex Exposed to the Insensitive Munition, 1-methyl-3-nitro-1-nitroguanidine (MeNQ)

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

country: USA

institute: US Army ERDC

summary:
The US Department of Defense (DOD) is developing insensitive munitions (IMs) that are resistant to unintended detonation to protect warfighters.  To enable evaluation of the material life-cycle for the IM, 1-methyl-3-nitro-1-nitroguanidine (MeNQ), ecotoxicological impacts assessment was required.  A previous investigation of MeNQ exposures in Daphnia pulex revealed concentration-responsive decreases in reproduction relative to controls (0 mg/L) across a 174, 346, 709, 1385, and 2286 mg/L exposure range.  The present study used those exposures to conduct global transcriptomic expression analyses to establish hypothetical mechanisms underlying inhibited reproduction.  Changes in transcript expression tended to increase with increasing MeNQ concentration where hierarchical clustering analysis identified separation among the “low” (174 and 346 mg/L) and “high” (709, 1385, and 2286 mg/L) exposures.  The MeNQ exposures significantly decreased transcriptional expression for a vitellogenin precursor and juvenile hormone-inducible protein, each having plausible mechanistic connections to impaired reproductive physiology and reduced offspring production in Daphnia.  Further, MeNQ affected chorion peroxidase and high choriolytic enzyme transcriptional expression which are known to influence egg production / maturation processes in arthropods.  Additionally, MeNQ exposure caused dose-responsive decreases in transcriptional expression for a diverse set of cuticle proteins which requires closer examination regarding Daphnia embryo development and brood release.  Finally, canonical-pathway enrichment analysis identified significant effects on a broad array of energy metabolic processes in D. pulex which require consideration regarding potential shifts in homeostatic equilibrium that can have indirect costs on reproduction.  Overall, plausible mechanisms of inhibited D. pulex reproduction have been identified and should be tested in targeted bioassays.
see previous row.

overall_design: The present study was initiated using D. pulex sampled at the termination of the three-brood chronic reproduction assay described in Lotufo et al (2021) to conduct microarray-based global transcriptomic investigations.  In the Lotufo et al (2021) study, D. pulex were exposed to MeNQ at control (0 mg/L), 174, 346, 709, 1385, and 2286 mg/L (measured concentrations) as juveniles through three-broods of reproduction.   This three-brood reproduction experiment was executed using modified Zumwalt boxes which included 10 replicate D. pulex monitored for reproduction and reported in Lotufo et al (2021).  To increase the amount of D. pulex tissue available for transcriptomic analysis, the experiment size was doubled to 20 replicates per treatment, which were all run simultaneously.  The animals remaining at the termination of the assay were assigned to a set of 4 replicate groups of animals per treatment to serve as treatment replicates in the transcriptomic-expression experimental design (6 treatments x 4 replicates).    REFERENCE:  Lotufo GR, Ballentine ML, May LR, Moores LC, Gust KA, Chappell P. (2021) Multi-species aquatic toxicity assessment of 1-methyl-3-nitroguanidine (MeNQ). Arch Environ Contam Toxicol. In Press. PMID: 33386940 DOI: 10.1007/s00244-020-00796-x.

first: Guilherme

middle: R

last: Lotufo

first: Natalie

middle: D

last: Barker

first: Qing

last: Ji

first: Lauren

middle: K

last: May


title: Evalutation of DEGs by RNA-seq in thiaclopride exposed murine testis

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085

type: Expression profiling by high throughput sequencing

summary: Environmental factors such as pesticides could affect developmental processes and cause phenotypic changes. In this project we study whether the exposure to neonicotinoid pesticide, thiaclopride, during embryonic development, could cause gene expression deregulation in outbred Swiss mice. Mice were treated during embryonic development at dose 6mg/kg body weight/day. New-borns were grown until 35 days-old. RNA was extracted from testes of three different mice for each condition (control vs exposed) and stranded libraries were prepared.

overall_design: RNA was extracted from testes of 6 mice. Stranded libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according manufacturer's instructions. Testis_RNA_C1 : Library for control mouse 1 Testis_RNA_C2 : Library for control mouse 2 Testis_RNA_C3 : Library for control mouse 3 Testis_RNA_Th1 : Library for exposed mouse 1 Testis_RNA_Th2 : Library for exposed mouse 2 Testis_RNA_Th3 : Library for exposed mouse 3

last: Smagulova

first: Louis

last: Legoff


title: The H3.3K27M oncohistone antagonizes reprogramming in Drosophila

status: Public on Jun 15 2021

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Development proceeds by the activation of genes by transcription factors and the inactivation of others by chromatin-mediated gene silencing. In some cases development can be reversed or redirected by mis-expression of master regulator transcription factors. This must involve the activation of previously silenced genes, and such developmental aberrations are thought to underlie a variety of cancers. Here, we express the wing-specific Vestigial master regulator to reprogram the developing eye, and test the role of silencing in reprogramming using an H3.3K27M oncohistone mutation that dominantly inhibits histone H3K27 trimethylation. We find that expression of the oncohistone blocks eye-to-wing reprogramming. CUT&Tag chromatin profiling of mutant tissues shows that H3K27me3 domains are globally reduced with oncohistone expression, suggesting that previous developmental programs must be silenced for effective transformation. Strikingly, mis-expressed Vg and H3.3K27M synergize to stimulate overgrowth of eye tissue, a phenotype that resembles that of mutations in Polycomb Repressive Complex 1 components. Our results imply that growth dysregulation can result from the simple combination of crippled silencing and transcription factor mis-expression, an effect that may explain the origins of oncohistone-bearing cancers.

overall_design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.

first: Kami

last: Ahmad

first: Steven


title: Correct dosage of X chromosome transcription is controlled by a nuclear pore component

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We show that a nuclear pore component, Mtor, is involved in setting the correct levels of transcription from the male X chromosome. Using larval tissues, we demonstrate that depletion of Mtor results in selective upregulation at MSL targets of the male X, beyond the required two-fold. Mtor and MSL components interact genetically, and depletion of Mtor can rescue the male lethality phenotype of MSL components. Using RNA FISH analysis and nascent transcript sequencing, we find that Mtor’s effect is not due to defects in mRNA export, but occurs at the level of nascent transcription.

overall_design: RNA-seq of WT and Mtor KD in Drosophila 3rd instar larval salivary gland with duplicates or triplicates. TT-seq of control, Mtor KD and MOF KD in Drosophila S2 cells with duplicates or triplicates.

first: Jennifer

last: Aleman

first: Maya

last: Capelson


title: Secondary Resistance to Anti-EGFR Therapy by Transcriptional Reprogramming in Patient-Derived Colorectal Cancer Models

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

country: Germany

institute: Universitätsklinikum Tübingen

summary: 3' RNA-seq of patient derived colon cancer xenograft models (N=10)  showing initial disease control  under cetuximab treatment were collected.  All xenograft models were wildtype for KRAS, NRAS, BRAF and PIK3CA. All mice were treated with cetuximab (Merck Serono) by intra peritoneal (i.p.) injection twice per week and dosed at 25mg/kg to establish response characteristics. Tumors were chronically treated to establish cetuximab secondary resistant tumors .

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Three conditions were generated for comparisons: untreated control (K), 5 days cetuximab treatment (5dC) while pdx tumors were responsive to cetuximab  and cetuximab secondary resistant tumors (C) following chronic cetuximab treatment.

first: Stephan

last: Hahn


title: Longitudinal regulation over time of gene expression in mock infected and HIV-1 infected CD4+ T-cells

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

summary: HIV-1 infected cells can become a stable reservoir for the virus by harboring latent, but replication competent, viral genomes. Glycolytic metabolism has been identified as a major determinant of susceptibility to HIV-1 infection. We performed microarray analysis to analyze the regulation of transcriptional expression during the transition from productive to latent HIV-1 infection

overall_design: Primary CD4+ T-cells were isolated from total blood of two healthy donors. After isolation CD4+ T-cells were activated for 72 hours by adding the Dynabeads® Human T-Activator CD3/CD28 using a bead/cell ratio of 1:2. Following activation cells were divided in two groups and either infected with HIV-1 NL4-3 (2ng p24/million cells) or mock infected. Cells were cultured in RPMI 1640 supplemented with 20% fetal bovine serum (FBS), penicillin/streptomycin, and 10 ng/mL IL-2 and kept at a concentration between 1-2 million cells/mL. Cell pellets were collected at 7, 9 and 14 days post-infection and used for total RNA extraction and subsequent microarray analysis

first: Bojana

last: Lucic

first: Iart

middle: L

last: Shytaj

first: Silvio

last: Bicciato

first: Andrea

last: Savarino

first: Marina

last: Lusic


title: Gene expression data in Control, Doxorubicin-resistant, and Epirubicin-resistant breast cancer cells

city: Ottawa

first: Julie

last: St-Pierre

state: Ontario

address: 451 Smyth Road

department: Department of Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

summary: Development of chemotherapy resistance is a critical barrier in cancer treatment. Increased reliance on mitochondrial metabolism has been described as a distinctive characteristic of resistant cancers, however it is unknown whether enhanced oxidative metabolism is an intrinsic property or whether the metabolic signature of resistant cancers is dependent on the therapeutics. In this study, we used microarrays to detail the differences in global gene expression between anthracycline-resistant and -sensitive breast cancer cells. Taken together with metabolomics, bioenergetics, and functional experiments, we show that two anthracyclines (doxorubicin and epirubicin) elicit distinct metabolic adaptations in breast cancer and that interfering with global metabolic regulators can overcome resistance to different therapeutic agents by their ability to simultaneously interfere with numerous metabolic pathways.

overall_design: We obtained MCF-7 breast cancer cells selected in increasing doses of doxorubicin or epirubicin, previously described in PMID 18980695 and GSE12115. Cells were cultured using the same media and grown at similar densities. Control (sensitive) cells were maintained in 0.1% DMSO, DoxR (doxorubicin-resistant) cells in 98.1 nM doxorubicin, and EpiR (epirubicin-resistant) cells in 852 nM epirubicin at all times. Each condition has 3 biological replicates.

first: Shawn

last: McGuirk


title: Chaperone-like protein DAY plays critical roles in photomorphogenesis

status: Public on Jun 12 2021

city: Vienna

first: Ho-Seok

last: Lee

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: We found that the transcriptome of day RNAi seedlings significantly overlaps with that of the bri1-116 mutant, especially in the dark. These data indicate that DAY acts as a positive regulator of BR signaling.

overall_design: We compared the transcriptomes of day RNAi and bri1-116 seedlings grown in the dark or light.

first: Tak


title: Identification of genes whose expression is changed by the deletion of GPI7 in Candida albicans

status: Public on Jun 13 2021

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

summary: We compared the transcriptomes of C. albicans wild-type and the gpi7 knockout mutant, and identied genes that were up-regulated or down-regulated in the mutant.

overall_design: Both wild-type and the gpi7 knockout mutant were cultured under the same condition. Samples were collected and subjected to RNA extration and sequnecing.

first: Guisheng

last: Zeng

first: Jiaxin

last: Gao


title: High-Throughput 5’ UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies

status: Public on Jun 11 2021

city: Cambridge

first: Dianbo

last: Liu

state: Massachusetts

address: Building 32, MIT, cambridge .MA USA

institute: MIT

summary: Here, we develop a high-throughput strategy to design, screen, and optimize 5’ UTRs that enhance protein expression from a strong human cytomegalovirus (CMV) promoter. We first identify naturally occurring 5’ UTRs with high translation efficiencies and use this information with in silico genetic algorithms to generate synthetic 5’ UTRs. A total of ~12,000 5’ UTRs are then screened using a recombinase-mediated integration strategy that greatly enhances the sensitivity of high-throughput screens by eliminating copy number and position effects that limit lentiviral approaches. Using this approach, we identify three synthetic 5’ UTRs that outperform commonly used non-viral gene therapy plasmids in expressing protein payloads.

overall_design: Identify the 5'UTR sequences that are enriched in high GFP expression cells.

first: Jicong

last: Cao

first: Eva

middle: M

last: Novoa

first: Zhizhuo

last: Zhang


title: Overexpression of Gadd45b perturbs DNA methylation in mouse dopaminergic neurons

city: Paris

first: Julia

last: FUCHS SEBE

address: 11, Macelin Berthelot

department: CIRB

institute: Collège de France

type: Methylation profiling by high throughput sequencing

summary: Age is a major risk factor for neurodegenerative diseases like Parkinson disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation or Parkinson disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson disease.

overall_design: Examination of DNA methylation changes upon injection of a virus encoding Gadd45b compared tio a virus encoding mCherry as. a control into the mouse substantia nigra. DNA extraction after 14 and 90 days. RRBS-sequencing was perfomed in single-end mode, generating 50 bases reads (SE50) on an Illumina HiSeq 3000

first: Camille

last: Godreuil

last: Fuchs


title: Expression of the cancer-associated DNA polymerase epsilon P286R in fission yeast leads to translesion polymerase dependent hypermutation and defective DNA replication

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: Somatic mutations in the proofreading domain of the replicative DNA polymerase epsilon (POLE-exonuclease domain mutations, POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, microsatellite stability and a unique mutational signature, with predominance of C > A transversions in the context TCT. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrent POLE-EDM (POLE-P286R) in Schizosaccharomyces pombe. Whole-genome sequencing analysis revealed that the corresponding pol2-P287R also has a strong mutator effect in vivo, with high frequency of base substitutions and relatively few frameshift mutations. The mutations are equally distributed across different genomic regions, but they occur within an AT-rich context. The most abundant mutations are TCT > TAT transversions and, in contrast to human, TCG > TTG transitions are not elevated, likely due to the absence of cytosine methylation in fission yeast. The high mutation burden of pol2-P287R leads to increased sensitivity to elevated dNTP levels and DNA damaging agents and a phenotype that is exacerbated by depletion of the Pfh1 helicase. In addition, S phase is aberrant and RPA foci are elevated, suggestive of persistent ssDNA or DNA damage, and pol2-P287R shows synthetic lethality with rad3 deletion,  indicative of checkpoint activation. Significantly, deletion of translesion polymerases kappa and eta partially suppresses pol2-P287R hypermutation, indicating that both enzymes contribute to this phenotype.

overall_design: DNA-Seq of 8 S. pombe strains at 2 different time generations (G0 and G200) to detect somatic mutations that are incorporated.

first: Ignacio

last: Soriano

last: Vázquez

first: Nagore

last: de León

first: Sibyl

last: Bertrand

first: Ellen

last: Heitzer

first: Sophia

last: Toumazou

first: Chen-Chun

last: Pai

first: Timothy

last: Humphrey

first: Ian

last: Tomlinson

first: Sue

last: Cotterill

first: Stephen

last: Kearsey

first: Zhihan

last: Bo

first: Claire

last: Palles


title: Meniere's miRNA Expression Analysis

city: Kansas City

first: Hinrich

last: Staecker

state: KO

address: 3901 Rainbow Boulevard Mailstop 3010

department: Otolaryngology Head and Neck Surgery

institute: Kansas Unversity School of Medicine

summary: Serum was collected from patietns with bilateral Meniere's and aged matched controls.  miRNA analysis was performed to identify differential expression for potentital disease markers.

overall_design: Blood serum was collected for 5 patients with bilateral Meniere's disease and 5 patients blood serum was collected from age matched healthy controls.


title: Transcriptional profiling of mESC-derived tendon and fibrocartilage cell fate switch [scRNA-seq]

city: New York

first: Deepak

last: Kaji

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: We report a high-efficiency differentiation protocol to tendon and fibrocartilage perform molecular profiling of tendon and fibrocartilage fatse in relation to developmetnal in vivo analogues. We also the molecular induction of tendon and fibrocartilage by examining fate dependent and independent gene modules

overall_design: This experiment was designed to help understand the transcriptomic similarity of our ES derived tenocytes to their in vivo developmental analogues.

first: Roosheel

last: Patel

first: Angela

last: Montero

first: Alice

middle: H

last: Huang


title: Transcriptomic trajectory of the tendon and fibrocartilage fate switch

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

overall_design: Refer to individual Series


title: Ronin expression induces ataxia and cerebellar degeneration in a mouse model of ataxia

status: Public on Jun 10 2021

first: Thomas

last: Zwaka

address: 1425 Madison Ave

department: CDRB

institute: Icahn School of Medicine

summary: Gene expression studies in cerebella isolated from 5 week old wildtype or transgenic mice (C57BL/6) overexpressing Ronin in Purkinje cells were generated. RNA was isolated from cerebella of 3 transgenic animals at 5 weeks of agee and 3 wildtype litter mates.

overall_design: RNA was isolated from cerebella of 3 transgenic animals at 5 weeks of agee and 3 wildtype littermates.

middle: P

first: Marion

last: Dejosez


title: Transcriptomic trajectory of the tendon and fibrocartilage fate switch [bulk RNA seq]

summary: We report the transcriptomic profiling of tendon and fibrocartilage induction by day, examining both the fate dependent and independent modules

overall_design: Time course of murine tendon and fibrocartilage fate induction in vitro


title: Time-lapse super-resolution imaging reveals key principles for cis-limited Xist RNA localization (RNA-SPLIT)

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford


title: The clinical significance of regulatory variants at the GDF5 locus in joint disease

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

summary: Genetic variants in cis-regulatory regions of GDF5 can lead to common joint diseases with high degrees of joint specificity.

overall_design: Examination of open chromatin regions in multiple different growth plates (proximal vs distal femur, tibia) and acetabulum at E67

first: Daniel

last: Richard

first: Mariel

last: Young

first: Pushpanathan

last: Muthuirulan


title: Next Generation Sequencing identifies TAZ transcriptional targets in tumor derived isogenic cells

city: Buffalo

first: Jianmin

last: Zhang

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: To gain a broader perspective of the underlying biological processes used by TAZ-dependent (TAZDEP) and TAZ-independent (TAZIND) cells for the maintenance of their BCSC phenotypes, we performed an RNA-seq analysis.

overall_design: 4 replicates of each isogenic line

first: He

last: Shen

first: Yanmin

last: Chen

first: Yin

last: Wan

first: Tao

last: Liu

last: Wang

first: Yali

first: Lei

first: Qiang

last: Hu

first: Bo

last: Xu

first: Mikhail

last: Chernov

first: Costa

last: Frangou


title: Cellular expression of Ebola virus VP24 protein compromises the integrity of the nuclear envelope and induces a laminopathy-like cellular phenotype

first: Enrique

last: Vazquez de Luis

summary: Ebola virus VP24 protein is a minor matrix protein that inhibits interferon (IFN) gene expression and counteracts the IFN-mediated antiviral response by both direct interaction with STAT1 and binding to karyopherins to prevent them from transporting STAT1 to the nucleus. Proteomic studies to identify additional EBOV VP24 partners have pointed to the nuclear membrane component emerin as a potential element of the VP24 cellular interactome. Here, we have further studied this interaction and its impact on cell phenotype. We demonstrate that VP24 interacts with emerin but also with other components of the inner nuclear membrane such as lamin A/C and lamin B, and induces their displacement to the cytoplasm. We also show that VP24 diminishes the interaction between emerin and lamin A/C and compromises the integrity of the nuclear membrane, inducing nuclear morphological abnormalities, activating a DNA damage response, the activation of ERK and the induction of ISG15. Furthermore, expression of VP24 promoted cytoplasmic translocation and downmodulation of barrier to autointegration factor 1 (BANF1), a common interactor of lamin A/C and emerin, and repression of the BAF-regulated CSF1 gene. Importantly, some of the phenotypic characteristics induced by expressing VP24 were confirmed in EBOV infected cells. In summary, here we demonstrate that VP24 acts at the nuclear membrane causing morphological and functional changes in the cells that recapitulates some of the hallmarks of laminopathy diseases.

overall_design: We performed RNA sequencing using RNA from VERO cells co-transfected with VP24 or pcDNA together with GFP.

first: Vidal

last: Santiago

first: Maite

last: Sánchez-Aparicio

first: Rocío

last: Seoane

first: Ahmed

last: El Motiam

first: Sergio

last: Gómez-Medina

first: Yanis

last: Bouzaher

last: Baz-Martínez

last: Vázquez

first: Anxo

last: Vidal

first: Cesar

last: Muñoz-Fontela

first: Adolfo

last: García-Sastre

first: Carmen

last: Rivas


title: HDAC inhibitor chidamide  enhance the chemotaxis function of circulating PD-1(+) cells from patients with PTCL

first: chong

last: wei

address: Dongdan

institute: Peking Union Medical College Hospital

summary: Background: Peripheral T‐cell lymphomas (PTCLs) are a heterogeneous group of neoplasms characterized by a poor prognosis. Histone deacetylase (HDAC) inhibitors have emerged as novel therapeutic agents for PTCLs. In this study, we aimed to explore the immunomodulatory effect of the HDAC inhibitor chidamide on circulating PD-1(+) cells from patients with PTCL, as well as its correlation with treatment response. Methods: We enrolled newly diagnosed patients with PTCLs treated with a combination of chidamide and chemotherapy. Gene expression profile analysis was performed on peripheral blood PD-1(+) cells, both at baseline and at the end of treatment. A list of differentially expressed genes (DEGs) was identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the biological implications of the DEGs. A gene concept network was constructed to identify the key DEGs for further PCR verification. Results: A total of 302 DEGs were identified in the complete remission (CR) group, including 162 upregulated and 140 downregulated genes. In contrast, only 12 DEGs were identified in the non-CR group. GO analysis revealed that these upregulated DEGs were mainly involved in chemokine activity, cell chemotaxis, and cellular response to interleukin-1 and interferon-γ. Furthermore, KEGG pathway analysis showed that these DEGs were enriched in cytokine-cytokine receptor interaction and chemokine signaling pathways. The innate immune signaling pathways, including the Toll-like and NOD-like receptor signaling pathways, were also influenced. The gene concept network revealed that the key upregulated genes belonged to the C-C chemokine family.  Conclusion: Our results showed that chidamide treatment notably enhanced the expression of genes associated with chemokine activity and chemotaxis function of circulating PD-1(+) cells. By recruiting immune cells and improving the innate immune function of PD-1(+) cells, chidamide may reshape the tumor microenvironment to an anti-tumor phenotype and synergize with checkpoint inhibitors.

first: Chong

last: Wei

first: Shaoxuan

last: Hu

first: Mingjie

last: Luo

last: Chen

first: Wei

last: Wang

last: Zhang

first: Daobin

last: Zhou


title: Reconstitution of MSL2 binding in vtiro

city: Munich

first: Nikolas

last: Eggers

address: Grosshaderner Strasse 9

department: Molecular Biology

institute: LMU Munich

summary: Transcription factors distinguish functional response elements from a large excess of similar sequences in metazoan genomes. Faithful discrimination relies on DNA sequence and shape, but how shape is modulated by chromatin organisation is unclear. We explored binding site selection principles by blending unique biological and experimental systems. First, we assemble Drosophila genomes into physiological embryonic chromatin as a substrate for genome-wide binding assays. Secondly, we monitor binding site selection of a protein, MSL2, for which all functional elements reside on the X chromosome. We observe direct and nucleosome-mediated cooperativity between MSL2 and two other transcription factors and discover an extended DNA shape signature of functional elements that is read out in chromatin. Strikingly, the physiological binding profile is not achieved through intrinsic properties of MSL2 but is sculpted by an unrelated transcription factor, GAF, that occludes non-functional sites. Our results reveal novel aspects of target selection in a complex chromatin environment.

overall_design: Chip-Seq profiles of Msl2 Clamp Gaf and Nurf on in vitro assembled chromatin. Mnase-seq Profiles of in vitro chromatin before and after addition of Clamp or H1.


title: CD4 T cell transcriptomic response to HIV-1 infection: effects of time, viral strain, cell subtype, Vpr, and IFNa/b R2 blocking

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

summary: Analysis of gene expression in primary CD4 T cells of multiple donors, following in vitro HIV-1 infection. Gene expression was measured at 4.5, 8, 12, 24 and 48h post infection and compared to mock-infected and HIV-1 delta-Env infected cells to determine and categorise the temporal expression profiles of genes affected by HIV-1 infection. Additional experiments determined: 1) the degree to which the accessory viral protein Vpr is responsible for the observed transcriptomic changes, 2) the effect of varying the viral strain, 3) the effect on the transcriptome of specifically memory CD4 T cells, the primary target cell subtype of HIV-1, in comparison with bulk CD4 T cells, and 4) the effect of blocking the Interferon alpha/beta receptor 2 during HIV-1 infection.

overall_design: 13 experiments involving 147 samples, all measuring gene expression after HIV-1 (or mock) infection at particular time points; two experiments are time courses with additional time points; the others each vary an additional factor such as cell type or viral strain.

first: Caroline

last: Goujon

first: Helene

last: Bauby

first: Christopher

last: Ward

first: Rupert

last: Hugh-White

first: Chad

last: Swanson

first: Michael

last: Malim


title: Genetic Signatures from RNA sequencing of Pediatric Localized Scleroderma (LS) Skin

city: Pittsburgh

first: Kathryn

last: Torok

state: Pennsylvania

address: 530 45th St, Rangos 9161 Bay1

department: Peds Rheumatology

institute: University of Pittsburgh

summary: In this study, we explored the initial results of RNA transcriptomic expression between pediatric localized scleroderma skin tissue and healthy control skin, with a subanalyses of transcriptomic expression in different disease states. LS gene signatures compared to healthy controls showed a distinct expression of an inflammatory response gene signature (IRGS) composed of IFNγ, IFNα and TNFα associated genes.

overall_design: Comparision between localized scleroderma and healthy controls in bulk sequencing of the skin

first: Emily

last: Mirizio

last: Liu

first: Qi

last: Yan

first: Julia

last: Waltermire

first: Roosha

last: Mandel

first: Kaila

last: Schollaert

first: Liza

last: Konnikova

first: Xinjun

middle: S


title: Genome-wide maps of EED binding genes in WT and JARID2 KO human embryonic stem cells (hESCs)

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W. Walnut St.

department: Department of Pediatrics

institute: Indiana University School of Medicine

summary: We wanted to know whether JARID2 KO in hESCs could affect EED occupancy on chromatin.

overall_design: Examination of EED binding genes in hESCs

first: Juli


title: Host gene expression profiling of fungal (candidemia), bacterial, and viral infection, and non-infectious illness [discovery cohort]

status: Public on Jun 08 2021

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

summary: Improved diagnostics are necessary to differentiate between multipe potential etiologies of acute illness in a hospitalized patient. The peripheral blood host gene expression response can act as a supplementary diagnostic tool and better inform the full host immune response to a pathogen. We performed RNA sequencing on peripheral blood from 48 hospitalized patients with confirmed candidemia as well as patients with other acute viral, bacterial, and non-infectious illnesses and derived pathogen class-specific gene expression classifiers.

overall_design: 199 subjects were included in this analysis, including those with candidemia, bacterial and viral infection, noninfectious illness, and healthy controls. Samples were collected at enrollment for all samples. Additional serial samples were collected for candidemic subjects. Total RNA was extracted from human blood by PAXgene and RNA sequencing was performed.

first: Rachel

last: Myers

first: Micah

middle: T

last: McClain


title: LncRNA HBL1 Recruits Polycomb Repressive Complex 2 on Essential Cardiogenic Genes to Orchestrate Human Cardiogenesis


title: Genome-wide maps of JARID2 binding genes in WT and HBL1 KO human pluripotent stem cells (hPSCs).

summary: We reported loss of HBL1 lnRNA promoted cardiogenesis and the interaction of HBL1-JARID2 in hPSCs. Here we used specific JARID2 antibody to pull down their binding genomic DNAs in hPSCs, respectively, which let us know the potential genes regulated by HBL1-JARID2 during cardiogenesis. 1% Input samples were collected from the same samples after chromatin shearing.

overall_design: Examination of JARID2 binding genes in hiPSCs.


title: Genome-wide maps of EED and H3K27me3 binding genes in WT and HBL1 KO human induced pluripotent stem cells (hiPSCs).

summary: We reported loss of HBL1 lnRNA promoted cardiogenesis and the interaction of HBL1-EED in hiPSCs. Here we used specific EED and H3K27me3 antibodies to pull down their binding genomic DNAs in hiPSCs, respectively, which let us know the potential genes regulated by HBL1-EED-H3K27me3 during cardiogenesis. 1% Input samples were collected from the same samples after chromatin shearing.

overall_design: Examination of EED and H3K27me3 binding genes in hiPSCs.


title: Host gene expression profiling of fungal (candidemia), bacterial, and viral infection, and non-infectious illness [validation cohort]


title: Unique extracellular RNA profiles in different fractions of plasma

status: Public on Jun 07 2021

city: Tampa

first: Jing

last: Jia

state: Florida

address: 12902 Magnolia Drive

department: Tumor biology

institute: Moffitt cancer center

summary: Circulating extracellular RNAs (exRNAs) have great promise as novel clinically plasma-based biomarkers for cancer diagnosis and prognosis. knowledge of the difference or association between these different sources of exRNAs is very limited. We performed a sequential physical and biochemical precipitation to receive 4 plasma fractions (platelets and cell debris, Thrombin-treated fraction, extracellular vesicles and supernatant) from each plasma sample. After total RNA extraction, we made ligation-free libraries and performed RNA-seq to evaluate full spectrum of RNA abundance in each fraction. All RNAs were included without size selection during the library preparation. We utilized a successive stepwise alignment strategy to map the RNA sequences to different RNA categories. We found that each plasma fraction had its own unique distribution of RNA species. Hierarchical cluster analysis showed similarity in samples with same fraction and significant differences between different fractions. In addition, we also observed abundance difference of unique transcript. Furthermore, a considerable proportion of exogenous RNAs and novel predicted miRNAs in all plasma fractions were detected. These results demonstrate that thorough inspection of all plasma fractions is necessary for exRNA-based biomarker study and appropriate sampling processes is needed for illustrating the complexity of plasma-based EVs study.

overall_design: Total RNA extracted from each of the 4 fractions of 10 plasma samples. Sequencing data of all RNA species was generated by Illumina Hiseq sequencer.

first: Liang

last: Wang


title: Circulating pancreatic stellate cells: a new window into pancreatic cancer metastasis

city: Liverpool

first: Tony

last: Pang

state: NSW

address: 1 Campbell Street

department: South Western Sydney Clinical School

country: Australia

institute: University of New South Wales

summary: This study aims to identify and characterise circulating pancreatic stellate cells in an orthotopic mouse model of pancreatic cancer using single cell RNA sequencing.

overall_design: Two mice were orthotopically implanted with pancreatic cancer (10^6 AsPC-1 pancreatic cancer cell line cells + 10^6 human cancer-associated pancreatic stellate cells). The mice were allowed to progress for eight weeks. The mice were euthanased and samples from the primary tumour (MsPrim), metastasis (MsSec) and blood (MsBlood) were collected and pooled. Cultured cancer-associated human pancreatic stellate cells and AsPC-1 cells (Cult sample) - the source of implanted cells - were used for comparison. The paper is published in Cancers, 2021 (Pang et al, HGF/c-Met inhibition as adjuvant therapy improves outcomes in an orthotopic mouse model of pancreatic cancer, cancers, 2021).

first: Alpha

last: Mekapogu

first: Zhihong

last: Xu

first: Minoti

last: Apte


title: Che-1/AATF sustains cell growth and global transcription in Multiple Myeloma through the maintenance of open chromatin structure [ChIP-Seq]

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

institute: Italian National Cancer Institute "Regina Elena"

summary: Tumor transformation is the result of genetic modifications that alter gene transcription, thus producing a specific oncogenic program. However, in recent years, several exciting discoveries have shown that also aberrant epigenetic modifications play a major role in the genesis and progression of cancer. Multiple myeloma (MM) is a cancerous pathology resulting from the clonal expansion of plasma cells, and characterized by abnormal production and secretion of antibody proteins. This disease shows a great heterogeneity, caused by both genetic and epigenetic abnormalities, and despite the numerous therapeutic advances remains an incurable pathology. Here we show that the RNA Polymerase II binding protein, Che-1/AATF is required for MM cells growth by sustaining genome wide transcription and the recruitment of Pol II to the DNA. Notably, we found that Che-1 localizes on active chromatin and its depletion leads to accumulation of heterochromatin by a global decrease of histone acetylation. Moreover, we show that Che-1 directly interacts with histones and competes with HDAC class I members for histones binding. Strikingly, Che-1 downregulation decreases BRD4 chromatin accumulation and further sensitize MM cells to bromodomain and extra-terminal (BET) inhibitors. Overall, our findings identify an essential role of Che-1 in maintaining open chromatin required for sustaining MM growth, and support Che-1 as a possible target for MM therapy, alone or in combination with BET inhibitors.

overall_design: This series contains ChIP-seq data for Che-1, POL2 and histone modifications in the KMS-27 Multiple Myeloma cell line.

first: Tiziana

last: Bruno

first: Francesca

last: De Nicola

first: Frauke

last: Goeman

first: Simona

last: Iezzi

first: Maurizio

last: Fanciulli


title: Three-dimensional CRISPR screening reveals epigenetic interaction with anti-angiogenic therapy

status: Public on Jun 05 2021

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College St

institute: Princess Margaret Cancer Centre – University Health Network

summary: Angiogenesis underlies development, physiology and pathogenesis of cancer, eye and cardiovascular diseases. Inhibiting aberrant angiogenesis using anti-angiogenic therapy (AAT) has been successful in the clinical treatment of cancer and eye diseases. However, resistance to AAT inevitably occurs and its molecular basis remains poorly understood. Here, we identify novel molecular modifiers of the blood endothelial cell (EC) response to a widely used AAT bevacizumab by performing a pooled genetic screen using three-dimensional microcarrier-based cell culture and CRISPR–Cas9. Functional inhibition of the epigenetic reader BET family of proteins BRD2/3/4 shows unexpected mitigating effects on EC survival and/or proliferation upon VEGFA blockade. Moreover, transcriptomic and pathway analyses reveal an interaction between epigenetic regulation and anti-angiogenesis, which may affect chromosomal structure and activity in ECs via the cell cycle regulator CDC25B phosphatase. Collectively, our findings provide insight into epigenetic regulation of the EC response to VEGFA blockade and may facilitate development of quality biomarkers and strategies to overcome resistance to AAT.

overall_design: One cell line, six conditions, three biological replicates per condition.

first: Michael

last: He

first: Niko

last: Thio

first: Steven

last: Stacker


title: SmartSeq2 analysis of chemically-defined MiPs with and without valproic acid treatment

city: Leuven (3000)

first: Maurilio

last: Sampaolesi

address: herestraat, 49

department: Development and regeneration

country: Belgium

institute: KU Leuven

summary: We have optimized a protocol to generate chemically defined induced pluripotent stem cell-derived mesodermal progenitors. We demonstrate that these cells contribute to myotube formation that can be improved by the addition of valproic acid. Thanks to SmartSeq2 single cell RNAseq, we show that valproic acid treatment increase the number of myogenic progenitors. We also used gene set enrichment analysis to annotate the clusters further with correlations to the ARCHS4 Tissues database. In particular, we found that the gene expression profile of the VPA-treated single cell cluster correlated more to myoblasts compared to the untreated cells. Some key myogenic genes found to be differentially expressed were DESMIN and CD82, which were upregulated upon VPA supplementation.

overall_design: SmartSeq2 single cell analysis of  human chemically-defined MiPs with and without valproic acid treatment

first: Nefele

last: Giarratana

first: Natacha

last: Breuls


title: Genetic characterization of Slovenian indigenous goat breed Dreznica goat

city: Domžale

first: Neža

last: Pogorevc

address: Groblje 3

department: Department of Animal Science

country: Slovenia

institute: University of Ljubljana, Biotechnical Faculty

summary: Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia. Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps.

overall_design: For analysing genetic background of Dreznica goat, we genotyped 96 animals with the Illumina Goat SNP50 BeadChip. These genotyped animals capture a majority of farms/breeders (N=26), both production types (dairy and meat), and all main coat color patterns.

first: Simon

last: Horvat


title: Deep and accurate detection of m6A RNA modifications in human and mouse cells using miCLIP2 and m6Aboost machine learning

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

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

overall_design: Refer to individual Series


title: Single-cell transcriptome profiling of the branching epithelium of mouse salivary glands

status: Public on Jun 04 2021

city: Bethesda

first: Shaohe

last: Wang

state: Maryland

address: 9000 Rockville Pike, Bldg 30, Rm 403

department: DIR

institute: NIDCR, NIH

summary: To explore the molecular signatures of subtypes among epithelial cells of mouse embryonic submandibular salivary glands undergoing branching morphogenesis, we performed single-cell RNA-sequencing and profiled near 7,000 single-cell transcriptomes. These cells formed 7 main clusters that corresponded well to cells at distinct locations, based on known expression patterns of selective marker genes. This study revealed many additional genes with differential expressions among clusters or subtypes of epithelial cells. Those can be good candidates underlying the regulation of their distinct biophysical properties.

overall_design: Single-cell mRNA profiles of submandibular salivary gland epithelial rudiments from 13-day old wild type mouse embryos

first: Kenneth

last: Yamada


title: TIM-3 restrains anti-tumour immunity by regulating inflammasome activation.

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: Droplet-based massively parallel single-cell RNA sequencing (scRNAseq) was performed by encapsulating sorted live CD45+ tumour-infiltrating cells into droplets and libraries were prepared using Chromium Single Cell 5′ Reagent Kits v2 according to the manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using an Illumina HiSeq2500.

overall_design: Cells from each sample (tumour or dLN or ndLN from an individual mouse) was resuspended in PBS containing 2% FCS and stained with oligo tagged TotalSeq antibodies directed against CD45 for 30 min on ice. Cells were washed and pooled accordingly, centrifuged at 1,200 rcf for 5 min at 4 °C and resuspended in PBS + 2% FCS. For each 10X channel, 6 samples were combined: Havcr2fl/fl 1-Tumour, dLN, ndLN; KO1-Tumour, dLN, ndLN; Havcr2fl/fl 2-Tumour, dLN, ndLN; KO2- Tumour, dLN, ndLN.

first: Karen

last: Dixon


title: Listeria monocytogenes infected mouse liver RNA sequencing

status: Public on Jun 09 2021

city: Vienna

first: Thomas

last: Decker

state: Vienna

address: Dr Bohr Gasse 9

department: Microbiology, Immunobiology and Genetics

institute: University of Vienna, Max Perutz  Labs

summary: IFN-Is have a detrimental effect in the case of Listeria monocyteogenes (Lm) infection. Previously it has been shown that Ifnar-/- mice are protected from the infection induced death. However, we have found that IRF9, a downstream component of the IFNAR signalling, has a role in addition to the IFNAR signalling in protecting the mice from Lm infection. This is due to Irf9-/- mice being more protected than Ifnar-/- mice. Among other hypotheses, we think that the recently shown role of Irf9 in glucose metabolism can be effective in this additional protection. Furthermore, our metabolic screens point to similar direction. Therefore, we would like to measure the differential gene expression pattern in livers from uninfected and 1 day infected Wt, Irf9-/- and Ifnar-/- mice.

overall_design: RNA isolated from the livers of biological triplicates of  wt, Irf9-/-, Ifnar-/- mice kept uninfected and infected with Lm for 1 day

first: Duygu

last: Demiroz

first: Philipp

last: Fischer

last: Schuster


title: Integrated Transcriptome Profiling Revealed That Elevated Long Non- Coding RNA-AC007278.2 Expression Repressed CCR7 Transcription in Systemic Lupus Erythematosus

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Systemic lupus erythematosus (SLE) is a serious autoimmune disease whose molecular pathogenesis is not well understood, especially the functions long noncoding RNAs (lncRNAs) in SLE development. In this study, we integrated the transcriptome profiles (RNA-seq) of peripheral blood mononuclear cells (PMBCs) from SLE patients and two published RNA-seq datasets to explore the expression profile of lncRNAs. Bioinformatics analysis of these data revealed the dominant up-regulation of transcripts in SLE patients, including mRNAs and lncRNAs. Functional enrichment analysis also revealed the highly correlation between the up-regulated transcripts and disease. We constructed the lncRNA-mRNA regulatory networks by performing WGCNA analysis and found three modules that were highly related with SLE. We then focused on one lncRNA, AC007278.2, coming from a cytokine receptor genes locus in Chr2, with Th1 lineage specific expression pattern in previous study. We found it was with consistent higher expression level in SLE patients. Co-expression network revealed AC007278.2 participated in the innate immune response and inflammatory bowel disease pathways. By repressing the expression of AC007278.2, we clearly found it can regulates the expression of inflammatory and cytokine stimulus response related genes in trans-manner, including CCR7, AZU1, TNIP3, UCN, GNAO1, COL3A1, IL6ST, SKIL, and LIFR. We found AC007278.2 may extensively regulate autoimmunity and the progress of Tfh cell maturation by repressing CCR7 expression. In summary, our study indicated the important regulatory role of lncRNAs in SLE pathogenesis and development, and the novel functions of AC007278.2, which could provide novel biomarkers for SLE diagnosis, treatment and drug screening.

overall_design: Peripheral blood mononuclear cells from SLE patients and normal controls were used for RNA-seq experiment and analysis. Then we used Jurkat cells to knockdown AC007278.2 lncRNA with negative control. RNA-seq experiment was performed for Jurkat cells. Two biological replicates were performed for each experiment.

first: Yi

last: You


title: Auranofin prevents liver fibrosis by system Xc-mediated inhibition of NLRP3 inflammasome

city: Seoul

first: Jungwook

last: Hwang

address: 222, Wangsimni-ro, Seongdong-gu, Seoul, Republic of Korea

country: South Korea

institute: Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea

summary: Previous studies showed that the anti-rheumatic agent auranofin inhibits the NLRP3 inflammasome; thus, this study evaluate the anti-fibrotic effect of auranofin in vivo and explored the underlying molecular mechanism. The antifibrotic effect of auranofin is assessed in thioacetamide- and carbon tetrachloride-induced liver fibrosis models. In this study, we use RNA-sequencing in hepatic stellate cell (HSC), and bone marrow-derived macrophage (BMDM) to examine the underlying mechanism of auranofin.

overall_design: Examination of difference between Auranofin-treated group and un-treated group in activated hepatic stellate cell and bone marrow derived macrophage.

first: HyunYoung

last: Kim

first: YoungJae

last: Choi

first: SangKyum

first: Hyunsung

first: DaeWon

last: Jun

first: Kyungrok

last: Yoon

first: Nayoun

first: YoungMi

first: SungChul

last: Lim

first: KeonWook

last: Kang


title: Che-1/AATF sustains cell growth and global transcription in Multiple Myeloma through the maintenance of open chromatin structure

first: Matteo

last: Pallocca


title: A prenatal diagnosis case of partial duplication 21q21.1-q21.2 with normal phenotype maternally inherited

city: Taizhou

first: Chunyan

last: Jin

state: Jiangsu

address: 399 Hailin South Road

institute: Taizhou People's Hospital

summary:
Down syndrome is characterized by trisomy 21 or partial duplication of chromosome 21. There have been extensive studies focusing on the identification of the Down Syndrome Critical Region (DSCR). Our case aims in providing evidence that duplication of 21q21.1-q21.2 is not included in the DSCR and that it has no clinical consequences on the phenotype.
Due to missing the appropriate gestational age for serological screening, Non-Invasive Prenatal Testing (NIPT) analysis was performed for a pregnant woman with normal prenatal examinations at 22 weeks of gestation. The result of NIPT revealed a 5.8Mb maternally inherited duplication of 21q21.1-q21.2. To test whether the fetus also carried this duplication, ultrasound-guided amniocentesis was conducted and the result of chromosomal microarray analysis (CMA) with amniotic fluid showed a 6.7Mb duplication of 21q21.1-q21.2 (ranging from position 18,981,715 to 25,707,009) for the fetus. This partial duplication of 21q21.1-q21.2 for the fetus was maternally inherited. The pregnant woman and her family decided to continue the pregnancy after genetic counseling. This case clearly indicates that 21q21.1-q21.2 duplication is not included in the DSCR and most probably has no clinical consequences on the phenotype.

overall_design: Non-Invasive Prenatal Testing (NIPT) analysis was performed for a pregnant woman with normal prenatal examinations at 22 weeks of gestation due to missing the appropriate gestational age for serological screening. The result of NIPT revealed a 5.8Mb maternally inherited duplication of 21q21.1-q21.2. To test whether the fetus also carried this duplication, ultrasound-guided amniocentesis was conducted and the result of chromosomal microarray analysis (CMA) with amniotic fluid showed a 6.7Mb duplication of 21q21.1-q21.2 (ranging from position 18,981,715 to 25,707,009) for the fetus.

first: Tianhui

last: Xu


title: Reovirus low-density particles package viral and cellular RNA

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: Packaging of segmented, double-stranded RNA viral genomes requires coordination of multiple viral proteins and RNA segments. For mammalian orthoreovirus (reovirus), evidence suggests either all ten or zero viral RNA segments are simultaneously packaged in a highly coordinated process hypothesized to exclude host RNA. Accordingly, reovirus generates genome-containing virions and “genomeless” top component particles. However, despite ostensibly lacking the genome, top component particles maintain a low level of infectivity. Whether reovirus particles can package host RNA is unknown. To gain insight into reovirus packaging potential and mechanisms, we employed next-generation RNA-sequencing to define the viral and host RNA content of purified reovirus virions and top component particles. Reovirus top component particles contained double-stranded viral RNA segments in similar proportions but at reduced levels compared to virions. Top component particles also were enriched for numerous host RNAs, especially short, non-polyadenylated transcripts, that differed by reovirus strain, independent of the viral polymerase. In contrast, virions were enriched for very few host RNAs. Collectively, these findings indicate that genome packaging into reovirus virions is exquisitely selective, while incorporation of host RNAs into top component particles is more promiscuous or differentially selective and may contribute to or result from inefficient viral RNA packaging.

sample_organism:
Mus musculus
Mammalian orthoreovirus 1 Lang
Mammalian orthoreovirus 3 Dearing
blank sample

overall_design: Examination of RNA component in the Top component of reovirus

first: Timothy

middle: W

last: Thoner Jr

first: Kristen

last: Ogden


title: Validation of RelMtb as a target for Mycobacterium tuberculosis persisters

city: Baltimore

first: Noton

last: Dutta

state: MD

address: 1550 Orleans Street, Room 110

department: Medicine

institute: Johns Hopkins University

summary:
The lengthy and complicated multidrug therapy currently available to treat active tuberculosis (TB) infection has contributed to medical non-adherence and the emerging problems of multidrug-resistant (MDR)- and extensively drug-resistant (XDR)-TB, which are particularly deadly in the setting of HIV co-infection. The prolonged therapy required to eradicate TB infection is believed to reflect the ability of Mycobacterium tuberculosis (Mtb) to persist within host necrotic granulomas in a non-replicating state characterized by antibiotic tolerance to bactericidal drugs, which predominantly target actively dividing tubercle bacilli. The stringent response enzyme, RelMtb, is essential for Mtb survival under physiologically relevant stress conditions in vitro and in the lungs of mice and guinea pigs. A library of over 2 million compounds was screened in RelMtb-inhibition assays and whole-cell screens under conditions in which RelMtb is essential. A total of 178 RelMtb inhibitor candidates, representing 18 unique scaffolds, were identified and 39 compounds were tested against nutrient-starved wild-type Mtb. The antibiotic susceptibility of a relMtb deletion mutant (Δrel) was studied during nutrient starvation and chronic infection in mice, and isoniazid and RelMtb inhibitor candidates were tested for synergy against nutrient-starved wild-type Mtb and Δrel using checkerboard assays. The minimum bactericidal concentration of isoniazid was 500-fold lower against Δrel relative to wild type during nutrient starvation, and the potent bactericidal activity of isoniazid was maintained against Δrel during chronic infection in the lungs of mice. Inhibition of RelMtb appears to be a promising new approach to target Mtb persisters, with the potential to shorten the duration of treatment for drug-susceptible and drug-resistant TB.
We used microarray to characterize the transcriptomic profiles of the wild type and Δrel during nutrient starvation. The RelMtb inhibitor, (E)-4-(3-methyl-4-(2-(4-methylthiazol-5-yl)ethoxy)styryl)benzoic acid, killed wild-type Mtb and prevented isoniazid tolerance during nutrient starvation. Treatment of nutrient-starved wild-type with the RelMtb inhibitor led to downregulation of the RelMtb regulon. Transcriptomic analysis revealed an altered gene expression in Δrel and wild-type treated with RelMtb inhibitor during nutrient starvation.

overall_design: Microarrays were used to study the global gene expression profile of wild type Mtb exposed to the candidate Rel inhibitor (final concentration= 2µM) in 1x PBS and the transcriptional pattern was compared to that of ΔrelA in PBS at Day 1 and Day 7.

first: Petros

middle: C

last: Karakousis


title: Arginine methylation promotes siRNA-binding specificity for a spermatogenesis-specific isoform of the Argonaute protein CSR-1

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

state: CA

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

summary: CSR-1 is an essential Argonaute protein that binds to a subclass of 22G-RNAs targeting most germline-expressed genes. Here we show that the two isoforms of CSR-1 have distinct expression patterns; CSR-1B is ubiquitously expressed throughout the germline and during all stages of development while CSR-1A expression is restricted to germ cells undergoing spermatogenesis. Furthermore, CSR-1A associates preferentially with 22G-RNAs mapping to spermatogenesis-specific genes whereas CSR-1B-bound small RNAs map predominantly to oogenesis-specific genes. Interestingly, the exon unique to CSR-1A contains multiple dimethylarginine modifications, which are necessary for the preferential binding of CSR-1A to spermatogenesis-specific 22G-RNAs. Thus, we have discovered a regulatory mechanism for C. elegans Argonaute proteins that allows for specificity of small RNA binding between similar Argonaute proteins with overlapping temporal and spatial localization.

overall_design: 20 small-RNA seq libraries from immunoprecipitated samples (10 input, 10 IP) in either duplicate or triplicate, one small-RNA seq library from whole worm lysate in duplicate, and three mRNA-seq libraries in triplicate were generated and analyzed.

first: Dieu

last: Nguyen


title: Host gene expression profiling of fungal (candidemia), bacterial, and viral infection, and non-infectious illness

city: Durham

first: Julie

last: Steinbrink

address: 315 Trent Drive

institute: Duke University


title: Characterisation of DNA methylomic signatures of induced pluripotent stem cells during neuronal differentiation

status: Public on Jun 03 2021

city: Exeter

first: Jennifer

last: Imm

state: Devon

address: Barrack Road

department: College of Medicine and Health

institute: University of Exeter

summary: In development, inducing pluripotency and differentiation into different cell types results in global epigenetic changes, although the extent this occurs in induced pluripotent stem cell (iPSC)-based neuronal models has not been extensively characterized. We have differentiated iPSCs (33Qn1 cell line) into cortical neurons and assessed their DNA methylation profile at different time points during differentiation and maturation to identify DNA methylomic   trajectories of neuronal aging. Samples were collected at four different time points, these were at the iPSC, neuronal precursor (NPC) and two different terminally differentiated neuronal time points (day 37 and day 58). We have identified loci undergoing significant DNA methylation changes throughout differentiation, have created an epigenetic trajectory signature associated with differentiation/maturation and identified highly connected and influential loci using gene-gene interaction analysis.

overall_design: Samples were collected at four different time points during the differentiation and maturation of iPSCs into cortical neurons. Four replicates were collected for each time point apart from the iPSC stage where there are only two replicates.

first: Ehsan

last: Pishva

first: Ali

last: Muhammed

first: Talitha

last: Kerrigan

first: Aaron

last: Jeffries

first: Joe

last: Burrage

first: Enrico

last: Glaab

first: Emma

last: Cope

first: Kimberly

last: Jones

first: Nicholas

last: Allen

first: Katie

last: Lunnon


title: Single cell profiling of the cerebral organoids derived from Schinzel-Giedion syndrome cells and isogenic controls

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

summary: Schinzel-Giedion syndrome (SGS) is a developmental syndrome, due to SETBP1 gene mutations inducing the accumulation of the relative protein, which is fatal in early infancy. Here, we generated unpatterned cerebral organoids from both SGS iPSC line and isogenic control line (through CRISPR/Cas9 back correction). We showed that SEBP1 accumulation triggers the development of large and convoluted epithelial folds in SGS cerebral organoids. To thoroughly characterize the 3D organoids we used scRNAseq (10X platform) in which we evidences the presence of both neural progenitors and committed neural progenitors with aberrant gene signature in SGS organoids that possibly sustain the lateral increase of the neuroepithelium

overall_design: 1 organoid SEBP1 D686D (WT) and 1 organoid SEBP1 D686N (Mut)

first: Alessandro

last: Sessa

first: Edoardo

last: Bellini

first: Federica

last: Banfi

first: Vania

last: Broccoli


title: Molecular signature of Schinzel-Giedion syndrome in human neural progenitors

summary: Schinzel-Giedion syndrome (SGS) is a developmental syndrome, due to the accumulation of SETBP1 protein, which is fatal in early infancy. SGS has a multi-organ involvement with severe and persistent intellectual and physical problems. We produced a human SGS model that outlines disease-relevant phenotypes using patient-derived induced pluripotent stem cells and isogenic controls. Whole transcriptome profiling describes cancer-like alterations in SGS neural progenitors including deregulation of oncogenes and suppressors and enhanced proliferation. These findings demonstrated how SGS post-natal pathological traits mayhave developmental origin in the failure of controlling cell identity and homeostasis due to SETBP1 protein accumulation.

overall_design: 3x SETBP1 D868D NPCs, 3x SETBP1 D868N NPCs, 3x SETBP1 I871T NPCs


title: Patient-derived iPSC-cerebral organoid modeling of the 17q11.2 microdeletion syndrome establishes CRLF3 as a critical regulator of neurogenesis

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

summary: Neurodevelopmental disorders are often caused by chromosomal microdeletions encompassing numerous contiguous genes. One such microdeletion on chromosome 17q11.2, involving the NF1 gene and flanking regions ( NF1 total gene deletion; NF1 -TGD), occurs in a subset of Neurofibromatosis type 1 (NF1) patients with severe developmental delays and intellectual disability. Using patient-derived human induced pluripotent stem cell (hiPSC)-cerebral organoids (hCOs), we identified both neural stem cell (NSC) proliferation and neuronal maturation abnormalities in NF1 -TGD hCOs. While increased NSC proliferation resulted from decreased NF1 /RAS regulation, the neuronal defects (delayed neuronal differentiation, increased immature neuron apoptosis, and impaired dendrite maturation) were caused by reduced cytokine receptor-like factor 3 ( CRLF3 ) expression. Furthermore, we demonstrated a higher autistic trait burden in NF1 patients harboring a deleterious germline mutation in the CRLF3 gene (c.1166T>C, p.Leu389Pro). Collectively, these findings identify a new causative gene within the NF1 -TGD locus responsible for hCO neuronal abnormalities and autism in children with NF1.

overall_design: Examination of different transcript expression in human iPSC-neural progenitor cells harboring different types of microdeletion events or after CRLF3 gene knockdown

first: Michelle

last: Wegscheid

first: Corina

last: Anastasaki

first: Kelly

last: Hartigan

first: Jason

middle: B

last: Papke

middle: N

last: Traber

first: Stephanie

last: Morris

first: Olivia

last: Cobb


title: Che-1/AATF sustains cell growth and global transcription in Multiple Myeloma through the maintenance of open chromatin structure [ATAC-Seq]

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

institute: Italian National Cancer Institute "Regina Elena"

summary: Tumor transformation is the result of genetic modifications that alter gene transcription, thus producing a specific oncogenic program. However, in recent years, several exciting discoveries have shown that also aberrant epigenetic modifications play a major role in the genesis and progression of cancer. Multiple myeloma (MM) is a cancerous pathology resulting from the clonal expansion of plasma cells, and characterized by abnormal production and secretion of antibody proteins. This disease shows a great heterogeneity, caused by both genetic and epigenetic abnormalities, and despite the numerous therapeutic advances remains an incurable pathology. Here we show that the RNA Polymerase II binding protein, Che-1/AATF is required for MM cells growth by sustaining genome wide transcription and the recruitment of Pol II to the DNA. Notably, we found that Che-1 localizes on active chromatin and its depletion leads to accumulation of heterochromatin by a global decrease of histone acetylation. Moreover, we show that Che-1 directly interacts with histones and competes with HDAC class I members for histones binding. Strikingly, Che-1 downregulation decreases BRD4 chromatin accumulation and further sensitize MM cells to bromodomain and extra-terminal (BET) inhibitors. Overall, our findings identify an essential role of Che-1 in maintaining open chromatin required for sustaining MM growth, and support Che-1 as a possible target for MM therapy, alone or in combination with BET inhibitors.

overall_design: This series contains the ATAC-seq data for control and Che-1 silencing in the Multiple Myeloma KMS-27 cell line.

first: Tiziana

last: Bruno

first: Francesca

last: De Nicola

first: Frauke

last: Goeman

first: Simona

last: Iezzi

first: Maurizio

last: Fanciulli


title: Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation from Its Location in the Cytoplasm

status: Public on Jun 02 2021

city: WEST LAFAYETTE

first: Shaojun

last: Xie

address: 3135 Decatur Street

institute: Purdue University

summary: Agrobacterium effector protein VirE2 is important for plant transformation. VirE2 likely coats transferred DNA (T-DNA) in the plant cell and protects it from degradation. VirE2 localizes to the plant cytoplasm and interacts with several host proteins. Plant-expressed VirE2 can complement a virE2 mutant Agrobacterium strain to support transformation. We investigated whether VirE2 could facilitate transformation from a nuclear location by affixing to it a strong nuclear localization signal (NLS) sequence. Only cytoplasmic-, but not nuclear-localized, VirE2 could stimulate transformation. To investigate the ways VirE2 supports transformation, we generated transgenic Arabidopsis plants containing a virE2 gene under the control of an inducible promoter and performed RNA-seq and proteomic analyses before and after induction. Some differentially expressed plant genes were previously known to facilitate transformation. Knockout mutant lines of some other VirE2 differentially expressed genes showed altered transformation phenotypes. Levels of some proteins known to be important for transformation increased in response to VirE2 induction, but prior to or without induction of their corresponding mRNAs. Overexpression of some other genes whose proteins increased after VirE2 induction resulted in increased transformation susceptibility. We conclude that cytoplasmically-localized VirE2 modulates both plant RNA and protein levels to facilitate transformation.

overall_design: Examination of differentially expressed genes using RNAseq in transgenic Arabidopsis thaliana roots which inducibly express the Agrobacterium tumefaciens virulence protein VirE2 under induced and non-induced conditions in the presence of an avirulent Agrobacterium strain at 0, 3, and 12 hours post-treatment

first: Rachelle

last: Lapham

first: Lan-Ying

last: Lee

first: Eder

last: Xhako

first: Esteban

middle: G

last: Gómez

first: V

last: Nivya

first: Stanton

last: Gelvin


title: Total RNA-seq revealed function of HBL1 lncRNA during cardiac differentiation from hiPSCs.

city: Indianapolis

first: Lei

last: Yang

address: 1044 W. Walnut St.

institute: Indiana University School of Medicine

summary: We reported loss of HBL1 lncRNA promoted cardiogenesis. Here we wanted to know the genomewide gene expression profiles caused by HBL1 KO during cardiac differentiation.

overall_design: Gene expression profiles between WT and HBL1 KO hiPSCs (before and after cardiac differentiation)

first: Juli

last: Liu


title: Analysis of differentially expressed miRNA in cisplatin-resistant FaDu cell

city: Changsha

first: Wei

last: LI

state: Hunan

address: Tongzipo Road

department: Department of Otorhinolaryngology-head and neck surgery

institute: Third Xiangya hospital of Central South University

summary: Cisplatin is a common chemotherapeutic drug for hypopharyngeal cancer. But cisplatin-resistance of hypopharyngeal cancer is rarely explored. We cultured hypopharyngeal cancer cell (FaDu) and induced its cisplatin-resistant cell (FaDu/DDP4). The resistance index (RI) of FaDu/DDP4 was 2.828. Then we tested the differentially expressed genes (DEGs) between FaDu and FaDu/DDP4. DEGs contain 2388 lncRNAs, 1932 circRNAs, 745 mRNAs and 202 miRNAs. We used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyzed the DEGs. The differentially expressed 745 mRNAs were classified into 3 domains and 47 secondary GO terms. In KEGG pathway enrichment, “TNF signaling pathway”, “IL-17 signaling pathway” and “JAK-STAT signaling pathway” have greater enrich factors. And we drew the ceRNA networks of DEGs. 52 lncRNAs, 148 circRNAs, 155 mRNAs and 18 miRNAs were selected to draw the network. We noticed several potential targets (as miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1). At last, we chose 8 miRNAs and 6 mRNAs for qRT-PCR to verify our microarray. In them, miR-197-5p, miR-6808-5p, APOE, MMP1, S100A9 and CYP24A1 might be potential genes inducing resistance.

overall_design: Detect the expression of miRNA in FaDu and its cisplatin-resistant cell, FaDu/DDP4. Each cell strain was detected only once.

last: Li

first: Gehou

last: Zhang

first: Guolin

last: Tan


title: Analysis of differentially expressed miRNA, lncRNA, circRNA and mRNA between FaDu and cisplatin-resistant FaDu cell

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

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

overall_design: Refer to individual Series


title: Dasatinib enhances anti-tumor efficacy of chimeric antigen receptor T cells by inhibiting cell differentiation and exhaustion

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

summary: CD19-targeted Chimeric antigen receptor T cells (CART) cells have shown remarkable promise in various B cell malignancies. Sustained tonic signaling and antigen exposure drives CART cell differentiation and exhaustion, which limits the therapeutic potency and persistence of CART cells and is a major cause of CD19-expressing leukemia relapse after CD19-targeted CART cells treatment in ALL. Here, we systematically screened FDA approved tyrosine kinase inhibitors, and identified dasatinib as the best candidate to prevent or reverse both CD28/CART and 4-1BB/CART cells from differentiation and exhaustion during ex vivo expansion, which enhanced the therapeutic efficacy and in vivo persistence. Using RNA-seq, we identified the differentially expressed genes between dasatinib treated group and Nalm6 stimulated group, and found that memory-associated transcription factors TCF7 and naive/memory-associated cell surface marker CCR7 were upregulated, whereas exhaustion-related regulators (NR4A1, BATF3, ATF4 and FOS) and inhibitory receptors (PD1, LAG3) were down-regulated in dasatinib treated CAR T cells. Moreover, T cell activation associated signaling pathways (T cell receptor, Jak-STAT, MAPK and PI3K-Akt) which were upregulated in Nalm6 stimulated CART cells, showed fundamental downregulation in dasatinib treated CART cells. These findings imply that dasatinib played important roles in CART cell differentiation and exhaustion by inhibition of T cell activation pathways.

overall_design: For experiments of the impacts of dasatinib on differentiation and exhaustion of CART cells stimulated by Nalm6, GFP+ 4-1BB CART cells were sorted at 3-5 days after transfection and expanded for another 3-7 days, then treated with Nalm6 for 48 hours, and then dasatinib or imatinib was added for another 48 hours. The CART cells of each group were harvested and performed RNA-seq.

first: Hao

first: Yongxian

last: Hu

first: Mi

last: Shao

first: Xinyi

last: Teng

first: Penglei

last: Jiang

first: Xiujian

last: Wang

first: Hui

first: Jiazhen

last: Cui

first: Jian

last: Yu

first: Zuyu

first: Lijuan

last: Ding

first: Yingli

last: Han

first: Jieping

last: Wei

first: Yulin

last: Xu

first: Xiaoqin

last: Shan

first: Jimin

last: Shi

first: Yi

last: luo

first: Pengxu

last: Qian

first: He

last: Huang


title: SETBP1 accumulation induces P53 inhibition and genotoxic stress in neural progenitors underlying neurodegeneration in Schinzel-Giedion syndrome

first: Luca

last: Massimino


title: Astrocytic interleukin-3 programs microglia and limits Alzheimer’s disease

city: Boston

first: Cameron

last: McAlpine

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Communication within the glial cell ecosystem is essential for neuronal and brain health1–3. The influence of glial cells on the accumulation and clearance of β-amyloid (Aβ) and neurofibrillary tau in the brains of individuals with Alzheimer’s disease (AD) is poorly understood, despite growing awareness that these are therapeutically important interactions4,5. Here we show, in humans and mice, that astrocyte-sourced interleukin-3 (IL-3) programs microglia to ameliorate the pathology of AD. Upon recognition of Aβ deposits, microglia increase their expression of IL-3Rα—the specific receptor for IL-3 (also known as CD123)—making them responsive to IL-3. Astrocytes constitutively produce IL-3, which elicits transcriptional, morphological, and functional programming of microglia to endow them with an acute immune response program, enhanced motility, and the capacity to cluster and clear aggregates of Aβ and tau. These changes restrict AD pathology and cognitive decline. Our findings identify IL-3 as a key mediator of astrocyte–microglia cross-talk and a node for therapeutic intervention in AD.

overall_design: RNAseq analysis of 6 samples. 3 samples are from 5-month-old 5xFAD mice and 3 samples are from 5-month-old Il3-/-5xFAD mice (2 total groups). Each sample contains microlgia pooled from 2 male and 2 female age- and genotype-matched mice.

first: Filip

last: Swirski

first: Rudolph

middle: E

last: Tanzi


title: Transcriptional changes induced by Lamin A/C downregulation in the nuclei of E0771 breast cancer cells

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

summary: Major transcriptional changes (290 differentially expressed genes) take place upon downregulation of Lamin A/C in E0771 breast cancer cells

overall_design: Lamin A and lamin C expression in E0771 breast cancer cells were downregulated by stable introduction of a lamin A/C shRNA construct: MISSION® TRC2 pLKO.5-puro Empty Vector (shControl), Sigma-Aldrich Cat# SHC201 or MISSION® shRNA plasmid DNA Lamin A/C, Sigma-Aldrich TRC# TRCN0000317672 (shLmna), resulting in an expected increase in nuclear deformability and squeezing capacities in this breast cancer cell model. RNA was isolated from both shControl and shLmna E0771 cells for transcriptome analysis via MARS-seq sequencing and bioinformatics analysis.

first: Francesco

last: Roncato

first: Sara

last: Feigelson

first: Ronen

last: Alon


title: Reduced nuclear lamin A/C enhances cancer cell squeezing through rigid barriers, does not facilitate endothelial crossing, and impairs experimental metastasis


title: Transcriptional changes induced by Lamin A/C downregulation in the nuclei of B16F10 melanoma cells

summary: Major transcriptional changes (300 differentially expressed genes) take place upon downregulation of Lamin A/C in B16F10 melanoma cells

overall_design: Lamin A and lamin C expression in the nuclei of the B16F10 melanoma cells were downregulated by stable introduction of a lamin A/C shRNA construct., resulting in an expected increase in nuclear deformability and squeezing capacities in our melanoma cell model. RNA was isolated from both shControl and shLmna B16F10 cells for transcriptome analysis via MARS-seq sequencing and bioinformatics analysis.


title: 10X Genomics single-cell RNAseq combined with CRISPR tiling of Dot1l in mouse MLL-AF9 leukemia

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: High-density single-cell RNAseq and direct-capture Perturb-seq

overall_design: 602 sgRNAs targeting the coding exons of mouse Dot1l were cloned into a sgRNA vector with the CS1 capture sequence incorporated into the 3' end of the sgRNA backbone. The sgRNA library was transduced into mouse MLL-AF9 leukemia cells expressing Cas9 endonuclease. Single cells were isolated three days post-transduction using a 10X Chromium and 10X GEM v3.1 kit. Two sequencing libraries were derived from this single-cell sample (1) poly(T) captured mRNA library and (2) CS1 captured sgRNA library. Both libraries were sequenced using an Illumina HiSeq PE150.

first: Chen

last: Chun-Wei

first: Yang

last: Lu


title: The severity of infectious bursal disease in White Leghorn inbred chicken lines is associated with greater bursal inflammation in vivo and more rapid induction of pro-inflammatory responses following ex vivo stimulation of primary bursal cells.

city: London

first: Michael

middle: A

last: Skinner

address: St Mary's Campus, Norfolk Place

department: Faculty of Medicine, Section of Virology

institute: Imperial College London

summary:
Transcriptomics analysis reveals that severity of infectious bursal disease in White Leghorn inbred chicken lines is associated with greater bursal inflammation in vivo and more rapid induction of pro-inflammatory responses following ex vivo stimulation of primary bursal cells.
In order to better understand differences in the outcome of infectious bursal disease virus (IBDV) infection, we inoculated very virulent (vv) IBDV into White Leghorn chickens from inbred line W that previously had over 24% mortality, and three inbred lines (15I, C.B4 and O) that previously had 0% mortality. Within each experimental group, some individuals experienced more severe disease than others but line 15I birds experienced milder disease based on average clinical scores, percentage of birds with gross pathology, average bursal lesion scores and average peak bursal virus titre. RNA-Seq analysis revealed that more severe disease was associated with a significant up-regulation of pathways involved in inflammation, cytoskeletal regulation by Rho GTPase, nicotinic acetylcholine receptor signaling, and Wnt signaling in the bursa. Primary bursal cells cultured from line W birds and stimulated ex vivo with LPS had a more rapid up-regulation of pro-inflammatory gene expression than cells from line 15I birds, and line W birds had a significantly greater percentage of KUL01+ macrophage cells in the BF than line 15I birds.  We hypothesize that a more rapid induction of pro-inflammatory cytokine responses in line W birds causes excessive inflammation and clinical disease following IBDV infection compared to line 15I, and we suggest that pro-inflammatory pathways could be targeted to engineer more disease resistant birds in the future

overall_design: A comparison of the transcriptomic responses in the bursa of Fabricius from four birds from the "susceptible" White Leghorn inbred line W and six birds from the "resistant" line 15, following IBDV infection, and a comparison of the transcriptomic reponses in the bursa of Fabricius from six birds with a "high" clinical score (1 x line W, 1 x line 15, 2 x line C and 2 x line O) and six birds with a "low" clinical score  (1 x line W, 1 x line 15, 2 x line C and 2 x line O) following IBDV infection

first: Amin

last: Asfor

first: Salik

last: Nazki

first: Vishwanatha

last: Reddy

first: Elle

last: Campbell

first: Katherine

last: Dulwich

first: Efstathios

last: Giotis

first: Andrew

middle: J

last: Broadbent


title: RNA sequencing comparing in-vitro lentiviral CRISPR-Cas9 knockdown of Non-Canonical Polycomb Repressive Complex 1.6 members from a Kras G12D Trp53 -/- background mouse lung cancer cell line

status: Public on Jun 01 2021

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

summary: The goal of this study was to compare expression profiles of mouse Kras G12D Trp53 -/- lung cancer cells that have inactivated ncPRC1.6 components to a ncPRC1.6 wild type condition

overall_design:
Each condition (Empty vs sg_ncPRC1.6 member (either sgMga, sgL3mbtl2, sgPcgf6, or sgL3mbtl2+sgPcgf6 cotransduced) is represented in  1 control Empty line in biological triplicate, 1 sgMga line in biological triplicates, 1 sgL3mblt2 line in biological triplicate, 1sgPcgf6 in biological triplicate, and 1 sgL3mbtl2+sgPcg6 co-transduced line in biological triplicate.
ChiP-Seq comparing binding of various Non-Canonical Polycomb Repressive Complex 1.6 members and Pol II between WT MGA and MGA KO in cells derived from Kras G12D + Trp53 -/- mouse tumours.

first: Robert

last: Eisenman


title: Immature follicular origins and disrupted oocyte growth pathways contribute to decreased gamete quality during reproductive juvenescence in mice

city: Chicago,

first: Francesca

middle: E.

last: Duncan

state: IL

address: 303 E. Superior Street, Lurie 10-109

department: Department of Obstetrics and Gynecology

institute: Northwestern University

summary: Egg quality dictates fertility outcomes, and although there is a well-documented decline with advanced reproductive age, how it changes during puberty is less understood.  Such knowledge is critical, since advances in Assisted Reproductive Technologies are enabling pre- and peri-pubertal patients to preserve fertility in the medical setting.  Therefore, we investigated egg quality parameters in a mouse model of the pubertal transition or juvenescence (postnatal day; PND 11-40). Animal weight, vaginal opening, serum inhibin B levels, oocyte yield, oocyte diameter, and zona pellucida thickness increased with age. After PND 15, there was an age-associated ability of oocytes to resume meiosis and reach metaphase of meiosis II (MII) following in vitro maturation (IVM). However, eggs from the younger cohort (PND 16-20) had significantly more chromosome configuration abnormalities relative to the older cohorts and many were at telophase I instead of MII, indicative of a cell cycle delay. Oocytes from the youngest mouse cohorts originated from the smallest antral follicles with the fewest cumulus layers per oocyte, suggesting a more developmentally immature state. RNA Seq analysis of oocytes from mice at distinct ages revealed that the genes involved in cellular growth signaling pathways (PI3K, mTOR, and Hippo) were consistently repressed with meiotic competence, whereas genes involved in cellular communication were upregulated in oocytes with age.  Taken together, these data demonstrate that gametes harvested during the pubertal transition have low meiotic maturation potential and derive from immature follicular origins.

overall_design: Oocytes were collected from four cohorts of mice:  PND 13, PND 16 small, PND 16 large, and PND 40 mice.  For each cohort, pooled oocytes were snap frozen in three replicates. Each replicate had 18-45 oocytes. RNA was isolated using RNeasy Plus mini kit (Qiagen, Germany, 74134). cDNA synthesis was performed using NEB Next Ultra II directional RNA library prep kit (New England Biolabs, Ipswich, MA, E7760S) after rRNA depletion (NEB Next rRNA depletion kit, E6310S) for Illumina next generation sequencing (HiSeq-50bp).

first: Atsuko

last: Kusuhara

first: Elnur

last: Babayev

first: Luhan

last: Zhou

first: Vijay

last: Singh

first: Jennifer

last: Gerton


title: The gene expression in the kidney of  selenium-binding protein1 deficient and C57BL/6J mice under 20 hours fasting condition

city: Fukuoka

first: YUJI

last: ISHII

state: Fukuoka

address: Maidashi, 3-1-1, Higashiku

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Kyushu university

summary: Selenium-binding protein 1 (Selenbp1) is a 2,3,7,8-tetrechlorodibenzo-p-dioxin inducible protein whose function is yet to be comprehensively elucidated. As the highly homologous isoform, Selenbp2, is expressed at low levels in the kidney, it is worthwhile to compare wild-type C57BL mice and Selenbp1-deficient mice under dioxin-free conditions. In this study, we conducted a comprehensive analysis of Selenbp1-Knockout mice to elucidate the role of Selenbp1 in the kidneys of wild-type C57BL mice under non-dioxin-administered conditions. Data from DNA microarray analysis suggested that Selenbp1 is involved in lipid metabolism. The results of real-time RT-PCR confirmed that ablation of Selenbp1 alters lipid metabolism via the Ppara pathway.

overall_design: Total RNA were extracted from the kidney of wild-type and Selenbp1-KO mice at 8 weeks old under 20 hours fasting condition (each N=3) , and their cDNAs were applied to the analysis using Agilent -026655 Whole Mouse Genome Oligo DNA microarray (4X44K) version 2.

first: Yingxia

last: Song

first: Ren-shi

last: Li

first: Tomoki

last: Takeda

first: Yuji

last: Ishii


title: Next-Generation Standard RNA-Sequencing Analysis of human monocytes stimulated by HMGB1 with or without DMOG

city: Manhasset

first: Myoungsun

last: Son

state: NY

address: 350 Community Drive

department: Center for Autoimmune Musculoskeletal and Hematopoietic Diseases

institute: Feinstein Institute for Medical Research

summary: We report the application of standard RNA-sequencing technology for high-throughput profiling of differential gene expression in mammalian cells.  This study aims to compare differential gene expression in human monocytes in the absence or presence of HMGB1 and DMOG exposure would mimic hypoxia. Human monocytes (five million cells) from a healthy donor were divided into four groups in triplicate (control, DMOG, HMGB1 or HMGB1_DMOG). RNA isolation, RNA integrity check, library preparation and ~350M raw paired-end reads per lane (Illumina HISeq. 2x150 bp sequencing) were conducted at GENEWIZ, LLC.  We find that increased TNF signaling induced by HMGB1 and enhanced when DMOG was present, and reduced IFN signaling in DMOG in unstimulated and HMGB1-stimulated conditions.  We conclude that RNA-seq based UP and DOWN regulated genes/pathways characterization would confirm our results and expedite genetic network analyses.

overall_design: Examination of different gene expression/signaling pathways in human monocytes from four groups in triplicate (control, DMOG, HMGB1 or HMGB1_DMOG).

first: Travis

last: Peng


title: WGS data to conduct phylogenetic analysis in Trichinella

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

institute: Chinese Academy of Agricultural Sciences

summary: To reveal the correlation between epigenomic diversity and genomic SNVs, we first identified SNPs between T4 with other eleven Trichinella species. In total, we obtained 5,395,250 common SNVs across the twelve Trichinella species.

sample_organism:
Trichinella spiralis
Trichinella nativa
Trichinella nelsoni
Trichinella pseudospiralis
Trichinella britovi
Trichinella sp. T6
Trichinella sp. T8
Trichinella murrelli
Trichinella sp. T9
Trichinella papuae
Trichinella zimbabwensis
Trichinella patagoniensis

overall_design: Examination of SNVs in Trichinella.

first: Fei

last: Gao


title: Mouse RPE-Choroids mRNA profiles of 4-week subretinal injection of AAV-GFP/PDGF-D

city: Guangzhou

first: Zhen

last: Xiong

address: No.7 Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

summary: Wet age-related macular degeneration (AMD) is a progressive degenerative disease and a leading cause of blindness in elderly population. AMD pathogenesis initiated by several signals generates cellular and molecular cross-talk, including complement pathway-mediated inflammation, macrophage activation, and upregulation of angiogenic and cytokine/chemokine pathways. However, the mechanism by which the complement system is activated in AMD is not well understood, although its components are found in the neovascular lesions of wet AMD patients. Here, we show that increased PDGF-D expression engaged both classical and alternative complement pathways and markedly increased chemokine and cytokine responses to activate macrophages, thereby triggering neuroinflammatory milieu and exacerbating pathological neovascularization. Pharmacological targeting of the complement C3a receptor using SB290157 alleviated neuroinflammation by blocking macrophage polarization and by inhibiting pathological choroidal neovascularization (CNV). Our study thus suggests that therapeutic strategies targeting both PDGF-D and complement-mediated inflammatory signals may open up new possibilities for the treatment of neovascular diseases.

overall_design: RPE-specific expression of human PDGF-D/GFP was introduced into C57BL/6J mouse. RNA-sequencing analysis was carried out to compare the transcriptome profilings between the AAV-PDGF-D and AAV-GFP RPE-Choroids under the same condition.

first: Anil

last: Kumar

first: Jianing

last: Zhang

first: Xuri


title: Characterization of a key region involved in the NO stress response of Bacillus cereus

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

institute: INRAE

summary: Bacterial response to nitric oxide (NO) is of major importance for bacterial survival, as NO stress is a main actor of the eukaryote immune response. Several pathogenic bacteria have developed gene regulation systems involved in detoxification and in repairing the damages caused by NO. However, bacterial mechanisms of NO resistance are poorly described for Gram positive bacteria and especially Bacillus cereus. This food born and opportunistic pathogen does not have the common weapon against NO described in other pathogenic or non-pathogenic bacteria, such as the transcriptional regulators norR and nsrR, nor NO reductases.   Using a transcriptomic approach, we investigated the mechanisms used by B. cereus to fight against NO stress. A cluster of 6 genes was identified to be particularly overexpressed in the early response to NO stress. This cluster contains an iron-sulphur cluster repair enzyme, a nitrite reductase and three enzymes involved in siroheme biosynthesis. We show a co-expression and a close genetic localization implying a functional link between those genes. This cluster may play a pivotal role in the defence mechanisms used by B. cereus to fight against NO stress during infection.

overall_design: Impact of NO on B. cereus gene expression

first: Constance

last: Porrini

first: Rozenn

last: Dervyn

first: Pierre

last: Nicolas

first: Nalini

last: Ramarao