title: Affymetrix CytoScan HD data on neuroblastoma cell lines

city: Gothenburg

first: Susanne

middle: Marie

last: Fransson

address: Medicinaregatan 3

department: Laboratory medicine

country: Sweden

institute: Gothenburg University

summary: Neuroblastomas are characterized by recurrent segmental and/or numerical chromosomal abberations such as MYCN-amplification or 11q-deletion. To further elucidate recurrent chromosomal alterations, 16 neuroblastoma cell lines were investigated.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell lines cultured under standard condition

first: Tommy

last: Martinsson


title: Transcriptomic profiling of adult zebrafish photoreceptors

status: Public on Nov 10 2022

city: Bethesda

first: Juan

last: Angueyra

state: MD

address: 35 Convent Drive

department: Unit of Retinal Neurophysiology

country: USA

institute: National Eye Institute

type: Expression profiling by high throughput sequencing

summary: Identifying the transcription factors required to specify photoreceptor subtypes is critical to understand the normal development of the retina and to inform cell-replacement therapies to restore vision. RNA-seq is a powerful way to identify novel genes expressed in particular cell subtypes. Although RNA-seq approaches have been used to identify genes differentially expressed between photoreceptor subtypes in many species, the limited transcriptome depth derived from single-cell techniques constitutes a barrier in the reliable detection of transcription factors. To obtain a deep, high-quality RNA-seq dataset from zebrafish photoreceptors, we manually collected pools of photoreceptors of a single subtype.

overall_design: We identified photoreceptors using well-characterized transgenic lines that express fluorescent proteins in each subtype with high specificity, including rods—Tg(xOPS:GFP), UV cones—Tg(opn1sw1:GFP), S cones—Tg(opn1sw2:GFP), M cones—Tg(opn1mw2:GFP) and L cones—Tg(thrb:tdTomato). We manually collected pools of 20 dissociated but healthy photoreceptors of a single subtype for each of our samples, while actively avoiding cellular debris and other contaminants.

first: Vincent

middle: P

last: Kunze

first: Wei

last: Li

first: Katherine

middle: S

last: Kindt

first: Laura

middle: K

last: Patak


title: Effect of Ptpn2 KO and IFNγ on axon regeneration

city: Hong Kong

first: Xu

last: Wang

state: New Territories

address: HKUST

department: LIFS

country: Hong Kong

institute: HKUST

summary: To investigate the function of Ptpn2, IFNγ and cGAS on axon regeneration, we performed gene transcription profiling of dorsal root ganglion neurons from 5 groups (WT, cKO, WT injured, cKO injured, RU521 injured) and retinal ganglion cells from 4 groups (WT, IFNγ, cKO, IFNγ+cKO).

overall_design:
For DRG experiment, cGAS inhibitor RU521 was injected to the sciatic nerve of wildtype mice. Nerve samples were collected 3 days after injury and RNA was extracted for sequencing.
For RGC experiment, AAV-Cre or GFP was injected to the eyes of Ptpn2 flox mice 2 weeks before optic nerve injury. IFNγ was injected to the eyes right after injury. Retinal ganglion cells (WT,IFNγ,cKO,cKO+IFNγ) were collected 3 days after injury and RNA was extracted for sequencing.

first: Kai

last: Liu


title: Genome Editing Is Induced in a Binary Manner in Single Human Cells

status: Public on Nov 09 2022

city: Setagaya-ku

first: Gou

last: Takahashi

state: Tokyo

address: 2-1-6 Kamikitazawa

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

type: Genome variation profiling by genome tiling array

summary: Even when precise nucleotide manipulations are intended, the outcomes of genome editing can be diverse, often including random insertions and deletions. The combinations and frequencies of these different outcomes in single cells are critical not only in the generation of genetically modified cell lines but also in the evaluation of the clinical effects of genome editing therapies. However, current methods only analyze cell populations, not single cells. Here, we utilized the Single Particle isolation System (SPiS) for the efficient isolation of single cells to systematically analyze genome editing results in individual human cultured cells. As a result, we discovered that genome editing induction has a binary nature, that is, the target alleles of cells tend to be all edited or not edited at all. This study enhances our understanding of the induction mechanism of genome editing and provides a new strategy to analyze genome editing outcomes in single cells.

overall_design: To determine gene copy number in HEK293T, HeLa and PC9 cells, we compared them to iPS (WTC11) cells, which are diploid cells.

first: Yuichiro

last: Miyaoka

first: Nishito

last: Yasumasa


title: Novel EGFR-Mutant Mouse Models of Lung Adenocarcinoma Reveal Adaptive Immunity Requirement for Durable Osimertinib Response

city: Aurora

first: Lynn

last: Heasley

state: CO

department: Craniofacial Biology

institute: University of Colorado, Anschutz Medical Campus

summary: Lung cancers bearing oncogenically-mutated EGFR represent a significant fraction of lung adenocarcinomas (LUADs) for which EGFR-targeting tyrosine kinase inhibitors (TKIs) provide a highly effective therapeutic approach. However, these lung cancers eventually acquire resistance and undergo progression within a characteristically broad treatment duration range. Our previous study of EGFR mutant lung cancer biopsies highlighted the positive association of a TKI-induced interferon g transcriptional response with increased time to treatment progression. Herein, we demonstrate that two additional gene expression signatures predictive of immunotherapy response also associate with longer duration of TKI treatment response, despite lack of efficacy of immunotherapy in EGFR mutant lung cancers. To test the hypothesis that host immunity contributes to the TKI  response, we developed novel genetically-engineered mouse models of EGFR mutant lung cancer bearing exon 19 deletions (del19) or the L860R missense mutation. Both oncogenic EGFR mouse models developed multifocal LUADs from which transplantable cancer cell lines sensitive to the EGFR-specific TKIs, gefitinib and osimertinib, were derived. When propagated orthotopically in the left lungs of syngeneic C57BL/6 mice, deep and durable shrinkage of the cell line-derived tumors was observed in response to daily treatment with osimertinib. By contrast, orthotopic tumors propagated in immune deficient nu/nu mice exhibited modest tumor shrinkage followed by rapid progression on continuous osimertinib treatment. Osimertinib treatment significantly increased intratumoral CD3+ T cell content relative to diluent treatment. The findings provide strong evidence supporting the requirement for adaptive immunity in the durable therapeutic control of EGFR mutant lung cancer.

overall_design: In Vitro RNA was collected from novel EGFR-mutant lung adenocarcinoma cell lines treated for 1, 2, 4, 6 days with DMSO or 100nM Osimertinib and submitted to RNAseq

first: Emily

last: Kleczko

first: Anh

middle: T

last: Le

first: Trista

last: Hinz

first: Teresa

last: Nguyen

first: Andre

last: Navarro

first: Cheng-Jun

last: Hu

first: Eric

last: Clambey

first: Daniel

last: Merrick

first: Mary

last: Weiser-Evans

first: Raphael

middle: A

last: Nemenoff

middle: E


title: Effect of antibiotic perturbation of gut microbiota on liver gene expression

city: Charleston

first: Matthew

last: Carson

state: South Carolina

address: 171 Ashley Avenue, basic science building room 241

institute: Medical University of South Carolina

summary: To discern the impact of minocycline therapy on liver gene expression during pubertal/postpubertal development in mice.

overall_design: Mice were treated from age 6-12 weeks with 100 mg/L minocycline or vehicle-control. Animals were euthanized at age 12 weeks and age 18 weeks to assess immediate and sustained antibiotic treatment effects.

first: Chad

last: Novince


title: Loss of SUV420H2-dependent chromatin compaction drives right-sided colon cancer progression [CGH]

city: Frankfurt am Main

first: Mohammed

middle: Hossameldin

last: Mosa

state: Hessen

address: Paul-Ehrlich Str. 42-44

country: Germany

summary: Epigenetic processes regulating gene expression contribute markedly to epithelial cell plasticity in colorectal carcinogenesis. The lysine methyltransferase SUV420H2 comprises an important regulator of epithelial plasticity and is primarily responsible for trimethylation of H4K20 (H4K20me3). Loss of H4K20me3 has been suggested as a hallmark of human cancer due to its interaction with DNMT1. However, the role of Suv4-20h2 in colorectal cancer is unknown.

overall_design: Molecular function of Suv4-20h2 was analysed in APT organoids. Suv4-20h2 expression was depleted in APT mouse organoids using two shrot hairpin RNAs targeting to different exons: exon4 (clone#1) and exon9 (clone#2).

first: Verawan

last: Boonsanay

middle: H

first: Mario

last: Looso

first: Dieter

last: Weichenhan

first: Fatih

last: Ceteci

first: Lorenz

last: Pudelko

first: André

last: Lechel

first: Christian

last: Michel

first: Carsten

last: Künne

first: Henner

middle: F

last: Farin

first: Christoph

last: Plass

first: Florian

middle: R

last: Greten


title: Loss of SUV420H2-dependent chromatin compaction drives right-sided colon cancer progression [RNA-seq]


title: Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma [EPIC]

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

type: Methylation profiling by genome tiling array

summary: MYC-driven medulloblastoma (MB) is an aggressive pediatric brain tumor characterized by therapy resistance and disease recurrence. Here we integrated data from unbiased genetic screening and metabolomic profiling to identify multiple cancer-selective metabolic vulnerabilities in MYC-driven MB tumor cells, which are amenable to therapeutic targeting. Among these targets, dihydroorotate dehydrogenase (DHODH), an enzyme that catalyzes de novo pyrimidine biosynthesis, emerged as a favorable candidate for therapeutic targeting. Mechanistically, DHODH inhibition acts on-target leading to uridine metabolite scarcity and hyperlipidemia, accompanied by reduced protein O-GlcNAcylation and c-Myc degradation. Pyrimidine starvation evokes a metabolic stress response that leads to cell cycle arrest and apoptosis. We further show that an orally available small molecule DHODH inhibitor demonstrates potent mono-therapeutic efficacy against patient-derived MB xenografts in vivo. The reprogramming of pyrimidine metabolism in MYC-driven medulloblastoma represents an unappreciated therapeutic strategy and a potential new class of treatments with stronger cancer selectivity and fewer neurotoxic sequelae.

overall_design: SU_MB002 cells were treated with DMSO or BAY (IC50) and collected at 48h and 72h (2 technical replicates per condition). gDNA was extracted using Puregene Cell and Tissue kit (Qiagen) as per manufacturer’s instructions and quantified using spectrophotometry. Illumina Human Infinium MethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) array was performed at The Centre for Applied Genomics, The Hospital for Sick Children (Toronto) using the manufacturer’s standard protocol.

first: William

middle: D

last: Gwynne

first: Yujin

last: Suk

first: Stefan

last: Custers

first: Nicholas

last: Mikolajewicz

first: Jeremy

last: Chan

first: Zsolt

last: Zador

first: Shawn

last: Chafe

first: Kui

last: Zhai

first: Laura

last: Escudero

first: Cunjie

last: Zhang

first: Olga

last: Zaslaver

first: Chirayu

last: Chokshi

first: Muhammad

middle: V

last: Shaikh

first: David

last: Bakhshinyan

first: Ian

last: Burns

first: Iqra

last: Chaudhry

first: Omri

last: Nachmani

first: Daniel

last: Mobilio

last: Maich

first: Patricia

last: Mero

first: Kevin

last: Brown

first: Andrew

last: Quaile

first: Chitra

last: Venugopal

first: Jason

last: Moffat

first: Rafael

last: Montenegro-Burke


title: Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia

city: Madison

first: Ayken

last: Askapuli

state: WI

address: 250 North Mills Street

department: Integrative Biology

institute: University of Wisconsin-Madison

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex population history. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. In addition, our analyses indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.

overall_design:
mtDNA data of 200 individuals from four Kazak populations in Jetisuu, Kazakstan were analyzed. 80 out of 200 samples were analyzed via GenoChip (Geno 2.0) microarray under the framework of Genographic Project, the Naional Geographic Society, USA.

>>>Raw data are not available for this series because the samples were genotyped via GenoChip under the framework of the Genographic Project, the National Geographic Society, USA. Submitter states that they do not have access to the raw data files<<<

first: Miguel

middle: G

last: Vilar


title: Cancer-selective metabolic vulnerabilities in MYC-amplified medulloblastoma [RNA-seq]

first: Sheila

last: Singh

overall_design: Total RNA was isolated from 200,000-300,000 viable tumor cells (three replicates of DHODH-KO and AAVS1-KO SU-MB002 cells (at day 8 post-transduction)) and then sequenced using Illumina HiSeq.

first: William

last: Gwynne

first: Yujin

last: Suk

first: Stefan

last: Custers

first: Nicholas

last: Mikolajewicz

first: Jeremy

last: Chan

first: Zsolt

last: Zador

first: Shawn

last: Chafe

first: Kui

last: Zhai

first: Laura

last: Escudero

first: Cunjie

last: Zhang

last: Zaslaver


title: Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee (RNA-Seq).

city: London

first: Paul

last: Hurd

address: Mile End Road

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

summary: Using the assay for  transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome-  wide maps of chromatin accessibility across all three adult honey bee phenotypes. We  identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the  vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq  and ChIP-seq data, we show a positive correlation between chromatin accessibility at  introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA  transcript. Importantly, we find that these regulatory regions are enriched in transcription  factor binding motifs and using ATAC-seq footprinting we identify queen, worker and drone -  specific occupancy and uncover novel transcription factor networks.

overall_design: RNA-seq in brains of newly-eclosed adult Q, W and D honey bees

first: Robert

last: Lowe


title: Integrated omics reveal time-resolved insights into T4 phage infection of E. coli on proteome and transcriptome level

city: Marburg

first: Katharina

last: Höfer

address: Karl-von-Frisch-Str. 14

institute: Max-Planck-Institute for terrestrial Microbiology

summary: Bacteriophages are highly abundant viruses of bacteria. The major role of phages in shaping bacterial communities and their emerging medical potential as antibacterial agents has trig-gered a rebirth of phage research. To understand the molecular mechanisms by which phages hijack their host, omics technologies can provide novel insights into the organization of tran-scriptional and translational events occurring during the infection process. In this study, we ap-ply transcriptomics and proteomics to characterize the temporal patterns of transcription and protein synthesis during T4 phage infection of E. coli. We investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying degradation of E. coli transcripts and preservation of the host proteome. Moreover, the correlation of the phage transcriptome and proteome reveals specific T4 phage mRNAs and proteins that are temporally decoupled, suggesting post-transcriptional and translational regulation mechanisms. This study provides the first comprehensive insights into the molecular takeover of E. coli by bacteriophage T4. This data set represents a valuable resource for future studies seeking to study molecular and regulatory events during infection. We created a user-friendly online tool, POTATO4, available to the scientific community to access gene expression patterns for E. coli and T4 genes.

overall_design: Exponentially growing E. coli were infected with T4 phage and RNA was isolated after 1, 4, 7 and 20 min of infection. RNA from uninfected E. coli was isolated to monitor the E. coli transcriptome immediately before infection (control/reference sample). The isolated total RNA was depleted from rRNA and sequenced by RNA-Seq. Thereby, expression of T4 phage and E. coli genes throughout infection can be monitored.

first: Maik

last: Wolfram-Schauerte

first: David

last: Ibberson


title: Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee (ATAC-Seq).

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in brains of newly-eclosed adult Q, W and D honey bees


title: Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee (ChIP-Seq).

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications (H3K27me3, H3K27ac, H3K4me1, H3K4me3) in brains of newly-eclosed adult Q, W and D honey bees


title: Loss of SUV420H2-dependent chromatin compaction drives right-sided colon cancer progression

first: Mohammed

last: Mosa

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

overall_design: Refer to individual Series


title: An in vitro study of the development of resistance to FGFR inhibition in two urothelial carcinoma cell lines

city: Leeds

first: Margaret

last: Knowles

address: Beckett Street

institute: University of Leeds

summary:
Expression array data was used to compare parental FGFR3-TACC3 fusion-driven urothelial cell lines with their FGFR inhibitor-resistant derivatives.
In this dataset, we include RT112 and RT4 parental cells, RT112 cells acutely treated with PD173074 (24 h), RT112 and RT4 resistant derivatives cultured with drug and their resistant derivatives cultured for four to six passages out of drug.

overall_design: 11 cell lines were analysed on the Affymetrix HTA 2.0 platform: RT112 and RT4 parental cells (RT112 parental no PD; RT4 parental no PD), RT112 cells acutely treated with PD173074 (24 h) (RT112 parental PD), RT112 and RT4 resistant derivatives cultured with drug (RT112 R1 PD; RT112 R2 PD; RT112 R3 PD; RT4 R1 PD) and their resistant derivatives cultured for four to six passages out of drug (RT112 R1 no PD; RT112 R2 no PD; RT112 R3 no PD; RT4 R1 no PD). Each cell line was analysed in triplicate (33 samples in total).

first: Geoffrey

last: Pettitt

first: Julie

last: Burns

first: Carolyn

last: Hurst


title: Endosperm cellularization failure induces a dehydration stress response leading to embryo arrest

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

summary: The endosperm is a nutritive tissue supporting embryo growth in flowering plants. Most commonly, the endosperm initially develops as a coenocyte (multinucleate cell) and then cellularizes. This process of cellularization is frequently disrupted in hybrid seeds generated by crosses between different flowering plant species or plants that differ in ploidy, resulting in embryo arrest and seed lethality. The reason for embryo arrest upon cellularization failure remains unclear. In this study, we show that triploid Arabidopsis thaliana embryos surrounded by uncellularized endosperm mount an osmotic stress response that is connected to increased levels of abscisic acid (ABA) and enhanced ABA responses. Impairing ABA biosynthesis and signalling aggravated triploid seed abortion, while increasing endogenous ABA levels as well as the exogenous application of ABA induced endosperm cellularization and suppressed embryo growth arrest. Taking these results together, we propose that endosperm cellularization is required to establish dehydration tolerance in the developing embryo, ensuring its survival during seed maturation.

overall_design: Embryos were dissected from developing seeds of Arabidopsis thaliana and their transcriptome profiles were analyzed. Firstly, by comparing three replicates of the triploid wild-type embryos derived from crosses (2x wt × 4x wt) against three replicates of the diploid wild-type embryos derived from crosses (2x wt × 2x wt). Secondly, by comparing three replicates of the triploid nrpd1 embryos derived from crosses (2x wt × 4x nrpd1) against three replicates of the triploid wild-type embryos.

first: Wenjia

last: Xu

first: Hikaru

last: Sato

first: Heinrich

last: Bente

first: Claudia

last: Köhler


title: Up-regulation of ATF4-LAMP3 axis by ORF45 facilitate lytic replication of Kaposi’s sarcoma-associated herpesvirus

city: Guangzhou

first: Ersheng

last: Kuang

state: Guangdong

address: 74 Zhongshan 2nd Rd

department: Zhongshan School of Medicine

country: China

institute: Sun Yat-Sen University

summary: To investigate the regulation of ER stress-related gene expression by KSHV-ORF45 during lytic replication, we performed RNA-sequencing analysis of iSLK-BAC16 vs. iSLK-STOP45 cells under lytic induction for 72h. When the differentially expressed genes were filtered and analyzed, we found that ER stress-related gene expression was much low in iSLK-STOP45 cells compared with iSLK-BAC16 cells, indicating that ORF45 expression is required for induction of ER stress.To further reveal the signal transduction of LAMP3 in KSHV lytic replication, RNA-sequencing analysis was performed to identify the differentially expressed genes (DEGs) in normal vs. LAMP3-silenced cells under lytic replication. A total of 35372 raw read targets were obtained and all DEG clusters were filtered and analyzed by KEGG pathway enrichment analysis. Eleven pathway were significantly enriched over 10 fold in LAMP3-depleted cells compared with control cells, including PI3K-Akt signaling pathway.Given that Akt and ERK activation play the important roles in KSHV lytic replication, we conclude that LAMP3 might promote Akt and ERK activation and then consequently facilitate KSHV lytic replication.

overall_design: mRNA profiles of iSLK-BAC16 vs. iSLK-STOP45 cells under lytic induction for 72h

first: Qinqin

last: Sun

first: Fan

last: Wang

first: Qingyang

last: Chen

first: Ronit

last: Sarid

first: Xiaojuan

last: Li


title: The ATAC analysis for Usp18 heterozygous depletion in established AML1/ETO 9a leukemia mouse model

city: La Jolla

first: Kei-ichiro

last: Arimoto

state: CA

address: 3855 Health Sciences Dr

institute: UCSD Moores Cancer Center

summary: Type I IFN induces IFN stimulated genes (ISGs) and exert varieties of immunomoduratory functions. However, it is not well characterized how ISGs are regulated by negative regulators of IFN signaling. Here, we analyzed the chromatin accessibility when combined with depletion of USP18, one of major negative regulators for IFN signaling.

overall_design: Usp18+/f UBCER-Cre  AML1/ETO 9a leukemia cells were transplanted into recipient mice. After mice become sick, oil or tamoxifen were injected to heterozygously deplete Usp18. Three days after first injection, Lin- c-kit+ AML cells were sorted from mouse splenocytes. Then performed RNA-sequencing of control (Oil) and USP18KD (Tam) RNA. For RNA-sequencing, 3 biological replicates were prepared for each condition.  ATAC-sequencing of Usp18+/f and Usp18+/∆  AE9a cells.  Same biological replicates were processed to RNA-seq as well.

first: Ty

last: Troutman

first: Dong-Er

last: Zhang


title: The transcriptomic analysis for Usp18 heterozygous depletion in established AML1/ETO 9a leukemia mouse model [AE9a_RNA-seq II]

summary: Usp18 is a potent negative reguator of type I IFN signaling. However, it is not well characterized how Usp18 affects IFN stimulated genes (ISGs) induction in AML in mouse model. Here, we analyzed the transcriptomic data when combined with heterozygous depletion of USP18, which phenotypicaly reduce AE9a leukemia progression.

overall_design: Usp18+/f UBCER-Cre  AML1/ETO 9a leukemia cells were transplanted into recipient mice. After mice become sick, oil or tamoxifen were injected to heterozygously deplete Usp18. Three days after first injection, Lin- c-kit+ AML cells were sorted from mouse splenocytes. Then performed RNA-sequencing of control (Oil) and USP18KD (Tam) RNA. For RNA-sequencing, 3 biological replicates were prepared for each condition.  This biological replicates were also processed for ATAC-seq. This RNA-seq is the another batch of same setting RNA-seq (GSE165424).


title: The transcriptomic analysis for Usp18 homozygous depletion in established AML1/ETO 9a leukemia mouse model [AE9a_scRNA-seq II]

summary: Usp18 is a potent negative reguator of type I IFN signaling. However, it is not well characterized how Usp18 affects IFN stimulated genes (ISGs) induction in AML in mouse model. Here, we analyzed the transcriptomic data when combined with homozygous depletion of USP18, which phenotypicaly reduce AE9a leukemia progression.

overall_design: Usp18f/f UBCER-Cre  AE9a leukemia cells were transplanted into recipient mice. After mice become sick, oil or tamoxifen were injected to heterozygously deplete Usp18. Three days after first injection, Lin- c-kit+ AML cells were sorted from mouse splenocytes. Then performed RNA-sequencing of control (Oil) and USP18KD (Tam). For scRNA-sequencing,  approximately 8,000 cells from each group (3 mice each) (GFP+Lin-c-Kit+ Usp18f/f and Usp18∆/∆ leukemia cells) were pooled.


title: Type I interferon (IFN) response in USP18 knockout in MDA-MB-231 breast cancer cells [RNA-seq]

summary: Type I IFN induces IFN stimulated genes (ISGs) and exert varieties of immunomoduratory functions. However, it is not well characterized how ISGs are regulated by negative regulators of IFN signaling. Here, we analyzed the transcriptomic change when combined with depletion of USP18, one of major negative regulators for IFN signaling.

overall_design: RNA-sequencing of control and USP18KO MDA-MB-231 cells with or without IFN treatment for 6 hours. For RNA-sequencing, 3 biological replicates were prepared for each condition.


title: Type I interferon (IFN) response in USP18 knockout in THP-1 AML cells [ChIP-seq]

summary: Type I IFN induces IFN stimulated genes (ISGs) and exert varieties of immunomoduratory functions. However, it is not well characterized how ISGs are regulated by negative regulators of IFN signaling. Here, we analyzed the chromatin activity using H3K27Ac ChIP when combined with depletion of USP18, one of major negative regulators for IFN signaling.

overall_design: ChIP-sequencing of control and USP18KO THP-1 cells with or without IFN treatment for 6 hours. For ChIP-sequencing, 2 biological replicates were prepared for each condition.


title: High-throughput discovery of human antimicrobial peptide activators of Salmonella Typhimurium PhoPQ

city: Houston

first: Jeffrey

middle: J.

last: Tabor

state: TX

address: 6100 Main Street

department: Bioengineering

institute: Rice University

summary: We developed a surface-displayed library of 117 human antimicrobial peptides (AMPs) and over 3000 human AMP variants in a laboratory E. coli strain expressing PhoP and PhoQ from Salmonella Typhimurium. We used sort-seq (fluorescence-activated cell sorting followed by next-generation sequencing) to characterize PhoPQ activation by these surface-displayed AMPs.

overall_design: Initial assessment of library diversity, sort-seq characterization

first: Kathryn

last: Brink

middle: J


title: Type I interferon (IFN) response in USP18 knockout in THP-1 AML cells [RNA-seq]

summary: Type I IFN induces IFN stimulated genes (ISGs) and exert varieties of immunomoduratory functions. However, it is not well characterized how ISGs are regulated by negative regulators of IFN signaling. Here, we analyzed the transcriptomic data when combined with depletion of USP18, one of major negative regulators for IFN signaling.

overall_design: RNA-sequencing of control and USP18KO THP-1 cells with or without IFN treatment for 6 hours. For RNA-sequencing, 3 biological replicates were prepared for each condition.

first: Arimoto

last: Kei-ichiro

first: Zhang

last: Dong-Er


title: Type I interferon (IFN) response in USP18 knockout in THP-1 AML cells [ATAC-seq]

overall_design: ATAC-sequencing of control and USP18KO THP-1 cells with or without IFN treatment for 6 hours. For ATAC-sequencing, 2 biological replicates were prepared for each condition.


title: The transcriptomic analysis for Usp18 heterozygous depletion in established AML1/ETO 9a leukemia mouse model [AE9a_scRNA-seq]

overall_design: Usp18+/f UBCER-Cre  AE9a leukemia cells were transplanted into recipient mice. After mice become sick, oil or tamoxifen were injected to heterozygously deplete Usp18. Three days after first injection, Lin- c-kit+ AML cells were sorted from mouse splenocytes. Then performed RNA-sequencing of control (Oil) and USP18KD (Tam). For scRNA-sequencing,  approximately 8,000 cells from each group (3 mice each) (GFP+Lin-c-Kit+ Usp18+/f and Usp18+/D leukemia cells) were pooled.


title: The transcriptomic analysis for Usp18 heterozygous depletion in established AML1/ETO 9a leukemia mouse model [AE9a_RNA-seq]

overall_design: Usp18+/f UBCER-Cre  AML1/ETO 9a leukemia cells were transplanted into recipient mice. After mice become sick, oil or tamoxifen were injected to heterozygously deplete Usp18. Three days after first injection, Lin- c-kit+ AML cells were sorted from mouse splenocytes. Then performed RNA-sequencing of control (Oil) and USP18KD (Tam) RNA. For RNA-sequencing, 3 biological replicates were prepared for each condition.


title: Rpb4 and Puf3

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet


title: Rpb4 and Puf3 imprint and post-transcriptionally control stability of a common set of mRNAs in yeast

summary: Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, a crosstalk where mRNA decay machinery impacts transcription and transcription machinery influences mRNA stability. Rpb4, and likely the dimer Rpb4/7 seem to be the central components of the RNA pol II governing these processes. In this work we unravel more precisely the molecular mechanisms participated by Rpb4 that mediates the posttranscriptional events regulating mRNA imprinting and stability. We analysed genome-wide, by RIP-seq, the association of Rpb4 with mRNAs and demonstrated that it targets a broad population of about 1400 transcripts. A group of mRNAs are also targets of the RPB, Puf3. We demonstrated that Rpb4 and Puf3, physically, genetically and functionally interact and cooperate to imprint and regulate stability of this group of mRNA. We also demonstrated, by the first time, that Puf3 associates with the chromatin, in an Rpb4-dependent manner. Our data also point to Rpb4 as the key element of the RNA pol II that interplay mRNA synthesis, imprinting and stability, in cooperation with RBPs.

overall_design: We performed 2 biologically independent RIP-Seq experiments.

first: Ana

middle: I

last: Garrido-Godino

first: Ishaan

last: Gupta

first: Francisco

last: Gutierrez-Santiago

middle: B

last: Martinez-Padilla

first: Alisa

last: Alekseenko

first: Lars

middle: M

last: Steinmetz

first: Jose

last: Perez-Ortin

last: Navarro


title: Potential modulation of Puf3 chromatin association mediated by Rpb4

summary: Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, a crosstalk where mRNA decay machinery impacts transcription and transcription machinery influences mRNA stability. Rpb4, and likely the dimer Rpb4/7 seem to be the central components of the RNA pol II governing these processes. Here we investigate the effect of ∆rrp4 on the potential chromatin association of the RNA binding protein Puf3 to chromatin in S. cerevisiae.

overall_design: ChIP-seq was performed for 8 samples: 3 biological replicates for PUF3-TAP WT and PUF3-TAP Δrpb4 strains, and 2 biological replicates for the WT strain. For each sample, input was also sequenced.


title: comprehensive miRNA analysis of human atopic plasma

status: Public on Nov 08 2022

city: Kyoto City

first: Hiromi

last: Nishigaki

address: 465 Kajii-Cyo, Hirokouji, Kawaramachi doori, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary:
miRNAs are kown to be deeply involved in the progression of chronic inflammatory diseases. We comprehensively analyzed miRNAs in human plasma from AD(atopic dermatitis) and ACD(allergic conjunctival disease) patients.
We performed a comprehensive human plasma miRNA analysis and identified significantly up-regulated miRNAs in both AD (atopic dermatitis) and ACD (allergic conjunctival disease).

overall_design: Total RNA in human plasma was extracted, and comprehensive miRNA RNA analysis was performed in three groups: healthy control, AD without ACD, and AD with ACD.

first: Mayumi

last: Ueta


title: Global gene expression analysis of THP-1 cells (a monocytic cell line) transfected with hsa-let-7a-5p mimics.

summary:
In our previous study, HAS-Let-7A-5P was significantly upregulated in the plasma of atopic patients.
To study the function of hsa-let-7a-5p, which is significantly upregulated in the plasma of atopic patients, we performed mimic-transfected THP-1 cells, a mononuclear cell line, and performed comprehensive genetic analysis.

overall_design: THP-1 cells were transfected with let-7a-5p mimics or negative controls and RNA was extracted. The RNA was then used for hybridization on Affymetrix microarrays.


title: Equilibrative Nucleoside Transporter 3 is an IFN-stimulated Gene that Facilitates Viral Genome Release

city: Taipei

first: Chia-Lin

last: Hsu

address: R309, Biomedical Building, NYCU, No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of Microbiology and Immunology

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: An increasing body of evidence emphasizes the role of metabolic reprogramming in immune cells to fight off infections. However, little is known about the regulation of metabolite transporters that facilitate and support metabolic demands. In this study, we found that the expression of Equilibrative Nucleoside Transporter 3 (ENT3, encoded by SoLute Carrier family 29 member 3, Slc29a3) is part of the innate immune response which is rapidly upregulated upon pathogen insults. The transcription of Slc29a3 is directly under the regulation of IFN-induced signaling, positioning this metabolite transporter as an Interferon-stimulated gene (ISG). Suprisingly, we unveil that several viruses, including SARS-CoV2, require ENT3 to facilitate their entry into the cytoplasm. The removal or suppression of ENT3 expression is sufficient to significantly decrease viral replication in vitro and in vivo. Our study reveals that ENT3 is a pro-viral ISG co-opted by some viruses for a survival advantage.

overall_design: Bone marrow-derived macrophages generated from C57BL wild type and ENT3-/- mice were treated with or without 1000 U/mL IFN-β for 4 hr, then harvested for RNA extraction. Each sample represents a biological replicate. The library was prepared by using Illumina TruSeq Stranded mRNA Sample Prep Kit and sequenced by Illumina NextSeq High Output Kit v2.5-75 cycles on the NextSeq 550 platform. The sequence was annotated according to Mus musculus GRCm38 mm10.

first: Yu

last: Hsieh

first: Tsung

middle: L

last: Tsai

first: Chia


title: CyclinD2-mediated regulation of neurogenic output from the retinal ciliary margin  is perturbed in albinism

city: New York

first: Revathi

last: Balasubramanian

state: NY

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

summary: Ciliary margin zone cells have differential neurogenic potential in albino and pigmented eyes. We used single cell RNA sequencing (scRNA-seq) of albino and pigmented eyes to determine transcriptomic changes underlying differential RGC genesis.

overall_design: Peripheral retina cells containing ciliary margin zone was isloated using a-Cre;Td mice on albino and pigmented backgrounds. Cells were isolated by Fluorescence-activated cell sorting (FACS) according to the presence TdTomato signal and analyzed using scRNAseq.

first: Slavi

last: Nefeli

first: Balasubramanian

last: Revathi

first: Mason

last: Carol


title: Transcriptomics indicate nuclear division and cell adhesion not recapitulated in MCF7 and MCF10A compared to luminal A breast tumours

city: Singapore

first: Keng Hwee

last: Chiam

address: 30 Biopolis Street

country: Singapore

institute: Bioinformatics Institute

summary: To better understand the tumour-modelling efficacy of cell lines, we performed RNA-seq analyses on 2D and 3D cultures of tumourigenic MCF7 and non-tumourigenic MCF10A and augmented our data with published datasets. To our knowledge, this was the first RNA-seq dataset comprising 2D and 3D cultures of MCF7 and MCF10A within the same experiment. We then compared tumourigenesis within cell lines (MCF7-vs-MCF10A) and tumourigenesis within clinical tissues (Luminal A-vs-Normal) from the TCGA-BRCA dataset and considered whether the same cancer-related processes could be observed.

overall_design: Comparative gene expression profiling analysis for 3D MCF10A, 2D MCF10A, 3D MCF7, 2D MCF7.

first: Keng-Hwee

first: Corinna

last: Goh

first: Jeremy

first: Qian Wei

last: Lim

first: Songjing

last: Zhang

first: Cheng-Gee

last: Koh


title: RNA-sequencing of THP-1 derived macrophages with and without ASAP2 knockdown

city: Shushan District

first: Ming

last: Lu

state: ANHUI SHENG

address: No.81 Meishan Road

department: Immunology

institute: Anhui Medical University

summary: To explore the potential functions of ASAP2 in macrophage, we established ASAP2 stable knockdown THP-1 cells and differentiated them into macrophages with PMA (50 ng/ml, 48 hours). Then we performed RNA-sequencing on the macrophages derived from THP-1 with (shASAP2) or without ASAP2 knockdown (shNC) to analyze the enriched functions by ASAP2-correlated genes and differentially expressed genes.

overall_design: THP-1 derived macrophage (THP-1 cells were differentiated into macrophage in a 6 cm dish by 50 ng/ml PMA for 48 hours). Total RNA was extracted from shNC (n=3) and shASAP2 (n=3) THP-1 macrophage. Illumina novaseq 6000 platform was used to sequence the RNA samples for the subsequent generation of raw data.

first: Hui

last: Shi

first: Jiangling

last: Duan

first: Jiayu

last: Wang

first: Haohao

last: Li

first: Zhiheng

last: Wu

first: Shuaideng

first: Xueyan


title: Aberrant L-Fucose accumulation and increased core fucosylation are specific metabolic liabilities in mesenchymal glioblastoma

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary:
Dysregulated metabolism in glioblastoma (GBM), the deadliest brain tumor of adults, offers an opportunity to deploy metabolic interventions as precise therapeutic strategies. To identify the molecular drivers and the modalities by which different molecular subgroups of GBM exploit metabolic rewiring to sustain tumor progression, we interrogated the transcriptome, the metabolome and the glycoproteome of human subgroup-specific GBM stem cells (GSCs).
Here we report that L-Fucose abundance and core fucosylation activation are more highly enhanced in mesenchymal (MES) than in proneural (PN) GSCs; this pattern is retained in subgroup-specific xenografts and, most significantly, retrieved in subgroup-affiliated human patients’ samples. Genetic and pharmacological inhibition of core fucosylation in MES GBM preclinical models results in significant reduction in tumor burden. LC/MS-based glycoproteomic screening indicates that most MES-restricted core fucosylated proteins are involved in therapeutically relevant GBM pathological processes, such as extracellular matrix interaction, cell adhesion and integrin-mediated signaling. Notably, selective L-Fucose accumulation in MES GBMs is demonstrated by pre-clinical minimally-invasive positron emission tomography (PET), implying this metabolite as a potential subgroup-restricted biomarker.
Overall, these findings indicate that L-Fucose pathway activation in MES GBM offers subgroup-specific, GSC-restricted dependencies to be exploited as diagnostic markers and actionable therapeutic targets.

overall_design: Gene expression profiles of proneural (PN) and mesenchymal (MES) glioblastoma (GBM) stem cells (GSCs) were compared to identify differentially expressed genes

first: Valentina

last: Pieri

first: Rossella

last: Galli


title: Polycomb group protein BMI1 prevents neuroblastoma cells from DNA-damage-induced apoptotic cell death

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: BMI1 is a polycomb protein and its overexpression has been correlated with cancer development and aggressiveness. We previously reported that v-myc avian myelocytomatosis viral oncogene neuroblastoma-derived homolog (MYCN)-induced BMI1 positively regulated neuroblastoma (NB) cell proliferation via the transcriptional suppression of tumor suppressors in NB cells. In order to evaluate the potential of BMI1 as a new target for NB therapy, we herein examined the effects of BMI1 reductions on NB cell differentiation and apoptotic NB cell death. BMI1 knockdown (KD) up to 7 days in NB cells significantly induced their differentiation. BMI1 depletion up to 14 days significantly induced apoptotic NB cell death along with the activation of p53, increases in p73, and induction of p53 family downstream molecules. BMI1 depletion in vivo markedly suppressed NB xenograft tumor growth. A pathological analysis using the TUNEL assay indicated the induction of apoptotic cell death. BMI1 reductions activated ATM and increased γ-H2AX in NB cells. Importantly, these DNA damage signals and apoptotic cell death were not canceled by transduction of polycomb group molecules EZH2 and RING1B. Further, EZH2 or RING1B knockdown could not induce apoptotic NB cell death at the same level of BMI1 KD. Together, BMI1 appears to be a promising target of molecular therapy for NB tumors and our report clarified, for the first time, the shared role of PcG proteins in DNA damage response of NB cells.

overall_design: RNA was extracted at 8-14 days after shBMI1-expressing lentiviral infection, and a microarray analysis was performed using the HG-U133 plus 2.0 arrays were used to deteremine the genes perturbed by knockdown of BMI1.

first: Nobuhiro

last: Akita

first: Ryu

last: Okada

first: Kyosuke

last: Mukae

first: Ryuichi

middle: P

last: Sugino

first: Koji

last: Chikaraishi

first: Hidemasa

last: Ochiai

first: Yohko

last: Yamaguchi

first: Miki

last: Ohira

first: Haruhiko

last: Koseki

first: Takehiko

last: Kamijo


title: PolyA RNA-seq from iPSCs and differentiated iPSCs treated with Nutlin-3

city: Aurora

first: Matthew

last: Galbraith

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Analysis of steady-state mRNA levels in induced pluripotent stem cells (iPSCs), iPSCs differentiated for 5 days with retinoic acid (RA) (5d-RAI), and iPSCs differentiated to cardiomyocytes (CM), and treated with DMSO (vehicle) or the p53 inhibitor Nutlin-3.

overall_design: Three independent cell lines each for iPSCs, RA-differentiated iPSCs, and cardiomyocyte-differentiated iPSCs treated with DMSO or 2.5µM Nutlin-3.

first: Roubina

last: Tatavosian

first: Joaquin

last: Espinosa


title: PolyA RNA-seq from retinoic acid-differentiated iPSCs treated with GSK343, 5-aza, or Combo (GSK343 & 5-aza)

summary: Analysis of steady-state mRNA levels in induced pluripotent stem cells (iPSCs) differentiated for 5 days with retinoic acid (RA) and treated for final 48 hrs with GSK343 (EZH2 inhibitor), 5-azacytidine (5-aza, DNA methyltransferase inhibitor), or their combination (Combo).

overall_design: Two independent biological replicates each of RA-differentiated iPSCs treated with 4µM GSK343, 5µM 5-azacytidine (5-aza), or Combo (4µMGSK343 & 5µM 5-aza).


title: KMT2D deficiency drives lung squamous cell carcinoma and hypersensitivity to RTK-RAS inhibition

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: To investigate the role of KMT2D in the lung squamous cell carcinoma (LUSC), we established the Kmt2d WT and Kmt2d Mut cells

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Kmt2d KO Kmt2d WT cells
Comparative gene expression profiling analysis of RNA-seq data Kmt2d KO and Kmt2d WT organoids and tumors
Profiling the histone modification H3K4me1 and H3K4me3 in Kmt2d KO and Kmt2d WT cells
Profiling the histone modification H3K27ac in Kmt2d KO and Kmt2d WT cells
Profiling the chromatin accessibility using ATAC-seq in Kmt2d KO and Kmt2d WT cells

first: Yuanwang

last: Pan

first: Kwok-King

last: Wong


title: PolyA RNA-seq from differentiated iPSCs

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

overall_design: Refer to individual Series


title: Unscheduled DNA replication in G1 causes genome instability and damage signatures indicative of replication collisions [mRNA-seq]

city: Martinsried

first: Karl-Uwe

last: Reusswig

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

summary: DNA replicates once per cell cycle. Interfering with the regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineered genetic systems in budding yeast to induce unscheduled replication in the G1-phase of the cell cycle. Unscheduled G1 replication initiated at canonical S-phase origins. We quantified the composition of replisomes in G1- and S-phase and identified firing factors, polymerase alpha, and histone supply as factors that limit replication outside S-phase. G1 replication per se did not trigger cellular checkpoints. Subsequent replication during S-phase, however, resulted in over-replication and led to chromosome breaks and chromosome-wide, strand-biased occurrence of RPA-bound single-stranded DNA indicating head-to-tail replication collisions as a key mechanism generating genome instability upon G1 replication. Low-level, sporadic induction of G1 replication induced an identical response, indicating findings from synthetic systems are applicable to naturally occurring scenarios of unscheduled replication initiation.

overall_design: RNA-seq after polyA-enrichment of wild-type cells in S-phase or cells that were induced to initiate DNA replication in G1 (expression of Dbf4, Dpb11, sld2-T84D). G1-arrested wild-type undergoing the same treatment are included as a control. n=4 replicates for each experimental condition.

first: Julia

last: Bittmann

first: Martina

last: Peritore

first: Michael

last: Wierer

first: Matthias

last: Mann

first: Boris

last: Pfander


title: Dynamic DNA methylation reveals novel cis-regulatory elements in murine hematopoiesis

city: Heidelberg

first: Maximilian

last: Schönung

address: Im Neuenheimer Feld 280

department: Division Translational Medical Oncology

institute: German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg

summary: Genome wide DNA methylation profiling of 9 different cell types of the murine hematopoietic system. The samples comprise FACS-sorted biological triplicates of hematopoietic stem and progenitor cells (LSK, CMP, GMP, MEP) and terminally differentiated immune cells (monocytes, neutrophils, CD4+ T-cells, CD8+ T-cells, B-cells). Additionally, bone marrow of CD45.1 (B6.SJL-Ptprca Pepcb/BoyCrl) and CD45.2 (C57BL/6J) mice as well as JAK2-V617F mutant mice was analyzed. The Illumina Infinium Mouse Methylation BeadChip was used to generate DNA methylation profiles across approximately 285,000 CpGs in these samples.

overall_design: DNA methylation profiles were generated from 9 different FACS-sorted murine hematopoietic cell types isolated from bone marrow of two congenic mouse strains (CD45.1, CD45.2) and of JAK2-V617F mutant mice. DNA methylation data was generated using the Illumina Infinium Mouse Methylation BeadChip array.

first: Daniel

last: Lipka


title: Effect of LEF1 overexpression on gene expression of human Natural Killer T cells

status: Public on Nov 07 2022

first: Leonid

middle: S

last: Metelitsa

address: 1102 Bates Avenue

institute: Baylor College of Medicine

summary: Vα24-invariant natural killer T cells (NKTs) possess innate antitumor properties that can be exploited for cancer immunotherapy. We have shown that the CD62L+ central memory-like subset drives NKT in vivo anti-tumor activity, but molecular mediators of NKT central memory differentiation remain unknown. Here, we demonstrate that CD62L+ NKTs express Wnt/β-catenin transcription factor LEF1 and maintain active Wnt/β-catenin signaling. CRISPR/Cas9-mediated LEF1 knockout reduced CD62L+ frequency after antigenic stimulation, while Wnt/β-catenin activator Wnt3a ligand increased CD62L+ frequency. LEF1 overexpression promoted NKT expansion and limited exhaustion following serial tumor challenge and was sufficient to induce a central memory-like transcriptional program in NKTs. In mice, NKTs expressing a GD2-specific chimeric antigen receptor (CAR) with LEF1 demonstrated superior control of neuroblastoma xenograft tumors compared to CAR-NKTs. These results identify LEF1 as a transcriptional activator of the NKT central memory program and advance development of NKT cell-based immunotherapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NKTs with LEF1 overexpression versus control luciferase overexpression

first: Ho

last: Ngai

first: Julien

last: Balzeau

first: Chunchao

last: Zhang


title: Distinct B-Cell Specific Transcriptional Contexts of the BCL2 Oncogene Impact Pre-Malignant Development in Mouse Models [scRNA-Seq]

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

country: France

institute: Université Rennes

summary: We designed two different BCL2 deregulation models in transgenic mice, whereby the oncogene was either associated with the IgH3′RR superenhancer, as in t(14;18), or inserted into the kappa light chain locus. We compared the impact of these models on B-cell fate and lymphoid tissues. Linkage to the IgH superenhancer showed a quite specific impact on germinal center B cell popu-lations. The Ig kappa model was much less specific and strongly boosted the plasma cell in-flow and the accumulation of long-lived plasma cells.

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data, made from sorted splenocytes from immunized mice

first: Michel

last: Cogné


title: Corticosterone induces obesity via promoting intestinal cell proliferation and survival

city: Shanghai

first: Guanhao

last: Wang

address: Siping Road

institute: Tongji University

summary: A vicious cycle ensues whereby prolonged exposure to social stress causes increased production of glucocorticoids, leading to obesity even further. Understanding the role of glucocorticoids, the key element in the vicious circle, might be helpful to break the vicious circle. However, the mechanism by which glucocorticoids induce obesity remains elusive. Herein we find that administration of corticosterone (CORT) to mice promotes the proliferation and survival of intestinal cells, which might contribute to the longer small intestines and the elongated intestinal villi, thus leading to increased nutrient absorption and obesity in mice. RNA-seq was performed to analyze transcriptional alterations in small intestines and livers after CORT-treatment, indicating differentially expressed genes (DEGs) were enriched in several cell growth/death-associated signaling pathways. This study would provide novel therapeutic clues for stress or glucocorticoids-related obesity.

overall_design: Comparative gene expression profiling of RNA-seq data from livers and intestines from CORT and Veh mice

first: Jianfeng

last: Lu


title: Single-cell RNA-Seq of young, old and metformin-treated mouse muscle and adipose

city: North Chicago

first: Ameya

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

summary: Here we investigate the nature of cellular heterogeneity in the gene expression of aging and characterize the changes that metformin causes in mouse adipose and muscle at the single-cell resolution. The single cell transcriptomes of ~13,000 cells were captured using single-cell RNA-sequencing, resulting in gene expression data for 13 cell types from the visceral adipose tissue stromal-vascular fraction and ~5,000 cells from 12 cell types from the gastrocnemius muscle. The study design featured three groups of male C57BL/6J mice that corresponded to three-month-old controls (young), 18-month-old controls (old), and 18-month-olds treated with 1000 ppm (0.1% w/w) metformin for 6 weeks (treated). Our analyses demonstrate that metformin’s age-associated changes results in the modulation of an old to young expression profile via a cell type-specific manner. This reversion is demonstrated by significant changes observed in cell-type proportions and the degree of cell-cell heterogeneity. Additionally, metformin is known to restore the dysregulation due to age in autophagy and immune response in adipose, hypoxia in muscle, and inflammatory responses in both tissues. In our data, we detect evidence of these processes at play where endothelial cells, macrophages, and stem/progenitor cells respond most effectively to metformin’s gerotherapeutic response compared to other cell types. We further characterize metformin’s role in reverting age-associated cell-type-specific shifts in the transcriptional space by investigating changes in gene expression distributions and gene regulatory network dynamics.

overall_design: Gastrocnemius muscle and visceral adipose tissues were collected from 12 C57BL/6J mice belonging to 3 groups: young, old and metformin-treated (4 mice/group). Single-cells were captured from each of the tissues and scRNA-Seq was conducted in 13 cell types from adipose stromal vascular fraction and 12 cell types from muscle using the 10x Genomics Chromium platform.

first: Nir

last: Barzilai

first: Jessica

last: Mar


title: Control of cranial ectomesenchyme fate by Nr2f nuclear receptors

city: Cincinnati

first: Lindsey

last: Barske

state: OH

address: 3333 Burnet Ave MLC 7016

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: Certain cranial neural crest cells are uniquely endowed with the ability to make skeletal cell types otherwise only derived from mesoderm. As these cells migrate into the pharyngeal arches, they downregulate neural crest specifier genes and upregulate so-called ectomesenchyme genes characteristic of skeletal progenitors. While both external and cell-autonomous factors have been proposed as triggers of this transition, the details remain obscure. Here we report the Nr2f nuclear receptors as novel intrinsic activators of the ectomesenchyme program: zebrafish nr2f5 and nr2f2; nr2f5 mutants show a marked delay in upregulation of ectomesenchyme genes such as dlx2a, prrx1a/b, sox9a, twist1a, and fli1a, and in downregulation of the non-ectomesenchyme specifier sox10. Depending on genotype, mutants partially or fully recover, likely via functional redundancy with other Nr2f genes. Loss of sox10 fully rescued skeletal development in nr2f5 single but not nr2f2; nr2f5 double mutants, while the ectomesenchyme defect persisted in both. Sox10 perdurance thus antagonizes the recovery rather than causing the initial aberration. Unraveling the mechanics of Nr2f function will help solve the enduring puzzle of how cranial neural crest acquire skeletal potency.

overall_design: Bulk RNA-seq was performed on FACS-purified zebrafish neural crest cells expressing sox10:DsRed from 20 hpf nr2f2[unknown]; nr2f5[mutant] embryos (2 replicates: n = 88 & 35) and wild-type control embryos (2 replicates: n = 110 & 120).

first: Chukwuebuka

last: Okeke

first: David

last: Paulding

first: Alexa

last: Riedel

first: Sandhya

last: Paudel

first: Conrad

last: Phelan

first: Camilla

last: Teng


title: mTOR inhibition amplifies the anti-lymphoma effect of PI3Kβ/δ blockage in diffuse large B-cell lymphoma

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous diagnostic category that can be stratified in molecular subtypes based on gene expression profiles and genetic alterations. As roughly one-third of DLBCL patients do not sustainably respond to the current standard chemo-immunotherapy, novel treatment options targeting oncogenic pathways might improve their outcome. Chronic B-cell receptor signaling or PTEN deficiency drive the constitutive activation of the phosphoinositide 3-kinase (PI3K). Since pan-PI3K inhibitors cause severe side effects, we investigated the anti-lymphoma efficacy of the specific PI3Kβ/δ inhibitor AZD8186. We identified a subset of DLBCL models within activated B cell-like (ABC) and germinal center B cell-like (GCB) DLBCL that were sensitive to AZD8186 treatment. On the molecular level, PI3Kβ/δ inhibition decreased the pro-survival nuclear factor kappa-B (NF-κB) and activator protein 1 (AP-1) activity or led to downregulation of the oncogenic transcription factor MYC. In AZD8186-resistant models, we detected a feedback activation of the PI3K/AKT/mTOR pathway following PI3Kβ/δ inhibition. The combined treatment with AZD8186 and the mTOR inhibitor AZD2014 overcame resistance to PI3Kβ/δ inhibition and completely prevented outgrowth of lymphoma cells in vivo in cell line- and patient-derived xenograft mouse models. Collectively, our study reveals that subsets of DLBCLs are addicted to PI3Kβ/δ signaling and thus identifies a previously unappreciated role of the PI3Kβ isoform in DLBCL survival. Furthermore, our data demonstrate that combined targeting of PI3Kβ/δ and mTOR is effective in all major DLBCL subtypes supporting the evaluation of this strategy in a clinical trial setting.

overall_design: For gene expression profiling, we performed RNA-sequencing of two AZD8186-sensitive ABC DLBCL cell lines (OCI-Ly10 and TMD8) and two sensitive GCB DBLCL cell lines (HT and K422) after 6, 12 (not TMD8), 18, and 24 hours of AZD8186 treatment, compared to untreated controls. Each time point was measured once, resulting in 30 samples in total. Statistics were computed over all time points and the two cell lines of the same DLBCL subtype.

first: Georg

last: Lenz


title: Effect of deletion of trkA on gene expression of Porphyromonas gingivalis W83

city: chengdu

first: renjie

last: zou

state: Sichuan

address: Chengdu City, Sichuan Province, Wuhou District people's South Road, three 17

institute: sichuan university

summary: To investigate the comprehensive function of trkA in Porphyromonas gingivalis W83, we established isogenic trkA deletion strain via homologous recombination and compared the transcriptional alteration between mutant and wild type group through RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Porphyromonas gingivalis W83 wild type and isogenic trkA mutant. Each group contains 3 samples.

first: Renjie

last: Zou

first: Daonan

last: Shen

first: Yafei

last: Wu


title: Effect of laminin adhesion on basal human mammary epithelial cells

city: Helsinki

first: Pekka

last: Katajisto

state: helsinki

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

summary: Mammary epithelium is composed by luminal and basal epithelial cells, which are adhere to the basement membrane (BM). To dissect how basal cell functions are regulated by  BM laminin adhesion, we performed RNA sequencing of basal human mammary epithelial cells adhered on laminin-111, -421 or -521 coated cell culture plates for 48 hours.

overall_design: Investigating the differences in transcriptome of human mammary epithelial cell line HMEC-FL2 grown on laminin substrates.

first: Johanna

last: Englund

first: Fredrik

last: Fagerström-Billai

first: Anastasius

last: Damdimopoulos


title: HISTONE DEACETYLASES 1 AND 2 TARGET GENE REGULATORY NETWORKS OF NEPHRON PROGENITORS TO CONTROL NEPHROGENESIS [RNA-seq]

city: New Orleans

first: Hongbing

last: Liu

address: 1430 Tulane Ave

institute: Tulane University

summary: Our studies demonstrated the critical role of Histone deacetylases (HDACs) in the regulation of nephrogenesis. To better understand the key pathways regulated by HDAC1/2 in early nephrogenesis, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) of Hdac1/2 on isolated nephron progenitor cells (NPCs) from mouse E16.5 kidneys. Our analysis revealed that 11802 (40.4%) of Hdac1 peaks overlap with Hdac2 peaks, further demonstrates the redundant role of Hdac1 and Hdac2 during nephrogenesis. Common Hdac1/2 peaks are densely concentrated close to the transcriptional start site (TSS). GREAT Gene Ontology analysis of overlapping Hdac1/2 peaks reveals that Hdac1/2 are associated with metanephric nephron morphogenesis, chromatin assembly or disassembly, as well as other DNA checkpoints. Pathway analysis shows that negative regulation of Wnt signaling pathway is one of Hdac1/2’s most significant function in NPCs. Known motif analysis indicated that Hdac1 is enriched in motifs for Six2, Hox family, and Tcf family members, which are essential for self-renewal and differentiation of nephron progenitors. Interestingly, we found the enrichment of HDAC1/2 at the enhancer and promoter regions of actively transcribed genes, especially those concerned with NPC self-renewal. Hdac1/2 simultaneously activate or repress the expression of different genes to maintain the cellular state of nephron progenitors. We used the Integrative Genomics Viewer to visualize these target genes associated with each function and found that Hdac1/2 co-bound to the enhancers or/and promoters of genes associated with nephron morphogenesis, differentiation, and cell cycle control. Taken together, our ChIP-Seq analysis demonstrates that Hdac1/2 directly regulate the molecular cascades essential for nephrogenesis.

overall_design: Transcriptomic profiling of Hdac1 and Hdac2 conditional mutant cap mesenchyme cells at E16.5.


title: Epigenomic analysis of Ink4a-/- HA JICD1 cells identifies that SOX2 acts as a regulator of the oncogenic function of JICD1

city: Seoul

first: Jung Yun

last: Kim

address: 145 Anam-ro, Seungbuk-gu

country: South Korea

institute: Korea University

summary: To identify transcription factor associated with JICD1 transcriptional complex, transcription factor binding motifs that interact with JICD1 were defined by chromatin immunoprecipitation sequencing (ChIP-seq) analysis. Further, the activated transcription-associated DNA motifs were detected by H3K9 acetylation. We verified JICD1 associated and activated transcription-associated DNA motif in Sox2 promoter. Transcription factors binding these motifs are SMAD3 (SMAD Family Member 3), TGIF1 (TGFB induced factor homeobox 1), and TGIF2 (TGFB induced factor homeobox 2).

overall_design: Examination of HA-JICD1 binding sequence and histone modification in Ink4a/Arf-/- astrocytes.

first: Eun-Jung

first: Jung

middle: Y


title: Targeting SNX9 rescues CD28-mediated T cell exhaustion for cancer immunotherapy

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Long-lasting effect of jasmonic acid (JA) seedling treatment on the transcriptional response to JA challenge of five-week-old Arabidopsis thaliana (ecotype Col-0).

city: Sheffield

first: Jurriaan

last: Ton

state: South Yorkshire

address: Western Bank

department: Animal and Plant Sciences

institute: University of Sheffield

summary: Treatment of Arabidopsis thaliana (ecotype Col-0) seedlings with jasmonic acid (JA) elicits long-term induced resistance (IR) against the chewing herbivore Spodoptera littoralis. We used RNA-seq to profile the transcriptional changes associated with this long-lasting JA-IR.

overall_design: mRNA profiles for the leaves of 5-week-old plants treated 4 hours previously with water or JA. Plants were from 2-week-old seedlings treated with water or JA. A total of 16 RNA-seq samples, 4 biological replicates for each of the 4 treatment groups.

first: Samuel

middle: W

last: Wilkinson

first: Adam

last: Hannan Parker

first: Amos

last: Muench

first: Robert

last: Wilson

first: Kourosh

last: Hooshmand

middle: A

last: Henderson

first: Emma

middle: K

last: Moffat

first: Pedro

last: Rocha

first: Helen

last: Hipperson

first: Joost

last: Stassen

first: Ana

last: López Sánchez

first: Inge

last: Fomsgaard

first: Paal

last: Krokene

first: Melissa

last: Mageroy


title: Prediction of tissue-of-origin of early-stage cancers using serum miRNomes

status: Public on Nov 12 2022

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

summary: Large-scale serum miRNomics in combination with machine learning could lead to the development of a blood-based cancer classification system.

overall_design: Serum microRNA profiles of 9,921 patients with 13 types of human solid cancers [breast (BR; n = 675), bladder (BL; n = 399), biliary tract (BT; n = 402), colorectal (CR; n = 1,596), esophageal squamous cell (ES; n = 566), lung (LU; n = 1,699), gastric (GA; n = 1,418), hepatocellular (HC; n = 348), pancreatic (PA; n = 851), prostate (PR; n = 1,027), ovarian (OV; n = 400), bone and soft tissue sarcomas (SA; n = 299), and intraparenchymal brain tumors (gliomas, primary central nervous system lymphomas, and metastatic tumors) (GL; n = 241)] ,626 non-cancer conditions [benign disease in the breast (BR_N; n = 31), extraparenchymal brain tumor and benign disease in the brain (GL_N; n = 24), benign disease in the ovary (OV_N; n = 28), benign disease in the prostate (PR_N; n = 230), or benign disease in the bone and soft tissue (SA_N; n = 313)], and 5,643 non-cancer controls.

first: Juntaro

last: Matsuzaki

first: Ken

last: Kato

first: Kenta

last: Oono

first: Naoto

last: Tsuchiya

first: Kazuki

last: Sudo

first: Akihiko

last: Shimomura

first: Kenji

last: Tamura

first: Sho

last: Shiino

first: Takayuki

last: Kinoshita

first: Hiroyuki

last: Daiko

first: Takeyuki

last: Wada

first: Hitoshi

last: Katai

first: Hiroki

last: Ochiai

first: Yukihide

last: Kanemitsu

last: Takamaru

first: Seiichiro

last: Abe

first: Yutaka

last: Saito

first: Narikazu

last: Boku

first: Shunsuke

last: Kondo

first: Hideki

last: Ueno

first: Takuji

last: Okusaka

first: Kazuaki

last: Shimada

first: Yuichiro

last: Ohe

first: Keisuke

last: Asakura

first: Yukihiro

last: Yoshida

first: Shun-ichi

last: Watanabe

first: Naofumi

last: Asano

first: Akira

last: Kawai

first: Makoto

last: Ohno

first: Yoshitaka

last: Narita

first: Mitsuya

last: Ishikawa

first: Tomoyasu

last: Fujimoto

first: Shumpei

last: Niida

first: Hiromi

last: Sakamoto

first: Takuya

last: Akiba

first: Daisuke

last: Okanohara

first: Kouya

last: Shiraishi

first: Takashi

last: Kohno

first: Fumitaka

last: Takeshita

last: Nakagama

first: Nobuyuki

last: Ota

first: Takahiro

last: Ochiya


title: Identification of genes regulated by rpoH in Pseudomonas aeruginosa

status: Public on Nov 06 2022

city: Bozeman

first: Michael

last: Franklin

state: MT

address: 109 Lewis Hall

department: Microbiology and Cell Biology

institute: Montana State University

summary:
The bacterial heat-shock response is regulated by the alternative sigma factor sigma 32 (RpoH), which responds to misfolded protein stress and directs the RNA polymerase to the promoterss for genes required for protein refolding or degradation. In P. aeruginosa, RpoH is essential for viability under laboratory growth conditions. Here, we used a transcriptomics approach to identify the genes of the RpoH regulon, including RpoH-regulated genes that are essential for P. aeruginosa. We placed the rpoH gene under control of the arabinose inducible PBAD promoter, then deleted the chromosomal rpoH allele. This allowed transcriptomic analysis of the RpoH regulon following a short up-shift in the cellular concentration of RpoH by arabinose addition, in the absence of a sudden increase in temperature. The P. aeruginosa ∆rpoH (PBAD-rpoH) strain grew in the absence of arabinose, indicating that some rpoH expression occurs without arabinose-induction.  When arabinose was added, the rpoH mRNA abundance of P. aeruginosa ∆rpoH (PBAD-rpoH) measured by RT-qPCR increased fivefold within 15 min of arabinose addition. Whole genome transcriptome results showed that P. aeruginosa genes required for protein repair or degradation are induced by increased RpoH levels, and that many of the genes induced by RpoH are essential for P. aeruginosa growth. Other stress response genes induced by RpoH are involved in nucleic acid damage and repair and in amino acid metabolism. Annotation of the hypothetical proteins under RpoH control included proteins that may play a role in antibiotic resistances and in non-ribosomal peptide synthesis.  The P. aeruginosa ∆rpoH (PBAD-rpoH) strain is impaired in its ability to survive during starvation compared to the wild-type strain.  P. aeruginosa ∆rpoH (PBAD-rpoH) also has increased sensitivity to aminoglycoside antibiotics, but not to other classes of antibiotics, whether cultured planktonically or in biofilms. The enhanced aminoglycoside resistance of the mutant strain may be due to indirect effects, such as the build-up of toxic misfolded proteins, or to the direct effect of genes such as aminoglycoside acetyl transferases that are regulated by RpoH.  Overall, the results demonstrate that RpoH regulates genes that are essential for viability of P. aeruginosa, that it protects P. aeruginosa from damage from aminoglycoside antibiotics, and that it is required for survival during nutrient limiting conditions.
We used Affymetrix microarrays to characterize the RpoH regulon in P. aeruginosa. Using the P. aeruginosa ∆rpoH strain with rpoH under control of the PBAD promoter, we were able to perform transcriptomic analysis of genes induced by a sudden increase (15 min) in the cellular concentration of RpoH, independent from a sudden increase in temperature.

overall_design: For untreated control samples, P. aeruginosa ∆rpoH (PBAD-rpoH) cells were cultured plantonically for 8 hours in Biofilm Minimal Medium. For induced test samples, P. aeruginosa ∆rpoH (PBAD-rpoH) cells were cultured planktonically for 7.75 hours in Biofilm Minimal Medium, and then rpoH was induced for 15 minutes with 0.1% arabinose. For control and test samples, cells were collected at 8 hours and RNA was extracted for transcriptomic studies.

first: Kerry

last: Williamson

first: Mensur

last: Dlakić

first: Tatsuya

last: Akiyama


title: Whole genome bisulfite sequencing of five-week-old Arabidopsis thaliana (ecotype Col-0) plants from water and jasmonic acid treated seedlings.

first: Jurriaan

last: Ton

type: Methylation profiling by high throughput sequencing

summary: Treatment of Arabidopsis thaliana (ecotype Col-0) seedlings with jasmonic acid (JA) elicits long-term induced resistance (IR) against the chewing herbivore Spodoptera littoralis. We used whole genome bisulfite-seq to profile the methylome associated with this long-lasting JA-IR.

overall_design: Genome-wide cytosine methylation profiles for the leaves of 5-week-old plants, from 2-week-old seedlings treated with water (control) or 1 mM JA. A total of 6 Bisulfite-seq samples, 3 biological replicates per seedling treatment groups.

first: Samuel

last: Wilkinson

first: Adam

last: Hannan Parker

first: Amos

last: Muench

first: Robert

last: Wilson

first: Kourosh

last: Hooshmand

last: Henderson

first: Emma

last: Moffat

first: Pedro

last: Rocha

first: Helen

last: Hipperson

first: Joost

middle: H

last: Stassen

first: Ana

last: López Sánchez

first: Inge

last: Fomsgaard

first: Paal

last: Krokene

first: Melissa

last: Mageroy


title: RNA-seq of iNKT cells in the skin and spleen of CCR10+/EGFP mice

city: San Antonio

last: Xiong

state: Texas

address: 7703 Floyd Curl Drive

department: MIMG

institute: UTHSCSA

summary: To compare transcriptomic profiles between skin and spleen iNKT cells, the analysis of global gene expressions in iNKT cells was performed using RNA-seq data obtained from iNKT cells purified from skin and spleen of CCR10+/EGFP mice.

overall_design: Total RNA of  iNKT cells were isolated. RNA-sequencing was done for the transcriptomic analysis of skin and spleen iNKT cells.

first: Wang

last: Wei-Bei

first: Xiong


title: Targeted immunosuppression enhances repeated gene delivery

city: Houston

first: H. Courtney

last: Hodges

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

summary: Immune system responses against adeno-associated virus (AAV) vectors are potentiated after the first administration, which has prevented the clinical use of repeated administration of AAV-based gene therapies. Here, we quantify the contributions of multiple immune system components towards AAV response in mice. We identify B-cell-mediated immunity, specifically the generation of IgM antibodies, as a critical component preventing vector re-administration.

overall_design: Single-cell 5' RNA-seq (scRNA-seq) of spleens from C57BL/6 mice that recieved a single-, double- or control AAV injection. All samples are pooled from 3 independent mice in the same condition and processed using 10x Chromium NextGEM Single Cell Immune Profiling Solution 5’v2 according to the manufacturer's instructions.

first: Maria

last: Chen

first: Boram

last: Kim

first: H

first: Omid

last: Veiseh


title: Neutrophil profiles of pediatric COVID-19 and multisystem inflammatory syndrome in children

status: Public on Nov 05 2022

city: Cambridge

first: Thomas

middle: James

last: LaSalle

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Multisystem Inflammatory Syndrome in Children (MIS-C) is a delayed-onset, COVID-19-related hyperinflammatory illness characterized by SARS-CoV-2 antigenemia, cytokine storm, and immune dysregulation. In severe COVID-19, neutrophil activation is central to hyperinflammatory complications, yet the role of neutrophils in MIS-C is undefined. Here, we collect blood from 152 children: 31 cases of MIS-C, 43 cases of acute pediatric COVID-19, and 78 pediatric controls. We find that MIS-C neutrophils display a granulocytic myeloid-derived suppressor cell (G-MDSC) signature with highly altered metabolism, distinct from the neutrophil interferon-stimulated gene (ISG) response we observe in pediatric COVID-19. Moreover, we observe extensive spontaneous neutrophil extracellular trap (NET) formation in MIS-C, and we identify neutrophil activation and degranulation signatures. Mechanistically, we determine that SARS-CoV-2 immune complexes are sufficient to trigger NETosis. Our findings suggest that the hyperinflammatory presentation during MIS-C could be mechanistically linked to persistent SARS-CoV-2 antigenemia, driven by uncontrolled neutrophil activation and NET release in the vasculature.

overall_design: Gene expression profiling analysis using bulk RNA-seq data of neutrophils enriched from fresh whole blood of 19 children with acute COVID-19, 17 children with MIS-C, and 12 pediatric controls.

first: Brittany

last: Boribong

first: Moshe

last: Sade-Feldman

first: Lael

last: Yonker


title: RNA-seq of skin tissues from WT and Cd1d KO B6 mice

summary: To investigate the effect of iNKT deficiency in the skin, the analysis of global gene expression in the skin tissues from WT and Cd1d KO mice were performed using RNA-seq data obtained from these samples.

overall_design: Total RNA of ear skin tissues were isolated. RNA-sequencing was done for the transcriptomic analysis of skin from WT and Cd1d KO mice.


title: Differential expression profiles of circRNA  in mice with traumatic heterotopic ossification

city: Wuhan

first: Zheng

last: Wang

state: China

address: Zhongnan Hospital, Wuhan University

institute: Zhongnan Hospital, Wuhan University

summary: To investigate whether circRNAs could participate in the pathological osteogenesis of traumatic heterotopic ossification (HO). RNA sequencing was performed to analyze the circRNA expression profile in mice HO tissues and to investigate the relevant mechanisms. We found that 491 circRNAs were significantly differentially expressed in mouse HO tissues by a fold-change ≥2 and p-value ≤0.05. Among these, 168 circRNAs were upregulated, while 323 were downregulated.

overall_design: A mice traumatic HO model was established by Achilles tenotomy and burn injury. The mice in control were only subjected to a longitudinal skin incision. At 9 weeks after surgery, tissues were harvested for RNA sequencing for analyzing the circRNA expression profile from the tendon insertion into the calcaneus to the distal gastrocnemius in both groups.

first: Xinzeyu

last: Yi

first: Zonghuan

last: Li

first: Aixi

last: Yu


title: HISTONE DEACETYLASES 1 AND 2 TARGET GENE REGULATORY NETWORKS OF NEPHRON PROGENITORS TO CONTROL NEPHROGENESIS.

first: Hongbing

last: Liu

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

overall_design: Refer to individual Series


title: Gene expression in BMDM treated with GW4064

status: Public on Nov 04 2022

city: Tokushima

first: Hideki

last: Arimochi

address: 3-18-15 Kuramoto

institute: Tokushima University

summary: We have employed whole genome microarray expression profiling with the samplaes prepared by treating BMDM with GW4064, an fxr agonist. Some genes upregulated in GW4064 treated sample were used for qPCR to confirm the change of expression level.

overall_design: C57BL6 mouse was used to prepare BMDMs, and they were treated with 10 micro M GW4064 or DMSO for 24h

first: Koji

last: Yasutomo


title: Effects of 17-DMAG treatment on transcription in 4T1 cells populations resistant and non-resistant to 17-DMAG

city: Buffalo

first: Andrei

last: Gudkov

address: Elm and Carlton Streets

department: Department of Cell Stress Biology

institute: Roswell Park Comprehensive Cancer Center

summary: Activation of endogenous retrotransposons frequently occurs in cancer cells and contributes to tumor genomic instability. To test whether inhibition of retrotranspositions has an anticancer effect, we used treatment with the nucleoside reverse transcriptase inhibitor (NRTI) stavudine in mouse cancer models, MMTV-HER2/Neu and Th-MYCN, that spontaneously develop breast cancer and neuroblastoma, respectively. In both cases, stavudine in drinking water did not affect tumor incidence nor demonstrate any direct antitumor effects. However, stavudine dramatically extended progression-free survival in both models following an initial complete response to chemotherapy. To approach the mechanism underlying this phenomenon, we analyzed the effect of NRTI on the selection of treatment-resistant variants in tumor cells in culture. Cultivation of mouse breast carcinoma 4T1 in the presence of stavudine dramatically reduced the frequency of cells capable of surviving treatment with anticancer drugs. Global transcriptome analysis demonstrated that the acquisition of drug resistance by 4T1 cells was accompanied by an increase in the constitutive activity of interferon type I and NF-ϰB pathways and an elevated expression of LINE-1 elements, which are known to induce inflammatory responses via their products of reverse transcription. Treatment with NRTI reduced NF-ϰB activity and reverted drug resistance. Furthermore, the inducible expression of LINE-1 stimulated inflammatory response and increased the frequency of drug resistant variants in a tumor cell population. These results indicate a new mechanism by which retrotransposon desilencing can stimulate tumor cell survival during treatment and suggest reverse transcriptase inhibition as a potential new therapeutic approach for targeting the development of drug resistant cancers.

overall_design: RNA isolation was performed from subconfluent cultures. Independently generated cell populations resistant to treatment with HSP90 inhibitor 17-DMAG (4T1R1 and 4T1R2) were obtained by several cycles of exposure of the initial population of 4T1 cells to 1 ug/ml of 17-DMAG for 24 hours following the expansion of surviving cells in 17-DMAG-free medium. RNA was isolated from untreated cells ("untreated") and 2 hours following 17-DMAG treatment ("DMAG-treated") in three biological replicas ("Rep 1-3").

first: Ksenia

last: Novototskaya-Vlasova

first: Nickolay

last: Neznanov

first: Ivan

last: Molodtsov


title: Pseudomonas aeruginosa promotes persistence of Stenotrophomonas maltophilia via increased adherence to depolarized respiratory epithelium

city: Birmingham

first: Melissa

middle: Skye

last: McDaniel

state: AL

address: 845 19th St S BBRB 744

department: Microbiology

institute: University of Alabama at Birmingham

summary: In this study, we used host and bacterial RNA sequencing to evaluate the impact of dual species infections with S. maltophilia and P. aeruginosa on CF disease progression. To evaluate S. maltophilia transcript profiles we used a recently described method for selective capture of bacterial mRNA transcripts with strain specific RNA probes.

sample_organism:
Mus musculus
Stenotrophomonas maltophilia

overall_design: RNA-sequencing of tanscriptome from mouse lung infected with Stenotrophomonas maltophilia, Pseudomonas aerugionsa, or both.

first: Natalie

last: Lindgren

first: Caitlin

last: Billiot

first: Kristina

last: Valladares

first: Nicholas

last: Sumpter

first: Edward

last: Swords


title: Functions of four members of PHR1 family in plant responses to phosphate starvation

city: Beijing

first: Dong

state: Select Region

address: School Of Life Sciences

institute: Tsinghua University

summary: We analyzed the RNA expression profiles of the mutants of four memebrs of Arabidopsis PHR1 family to understand their roles in regulating plant responses to phosphate starvation

overall_design: Total RNAs were extracted from the roots of 8-day-old seedlings grown under Pi sufficiency and deficiency. All RNA samples were subjected to sequencing using next generation sequencing technology. Three biological replicates were used for all genotypes.

first: Zhen

last: Wang

first: Zai

last: Zheng

first: Yuming

last: Zhu


title: Inflammatory response to retrotransposons drives tumor drug resistance that can be prevented by reverse transcriptase inhibitors

state: NY


title: Brief treatment in-vitro with Dasatinib does not appreciably alter gene expression by CD8+ T cells

city: Sydney

first: Moumita

last: Paul

state: New South Wales

address: Level 5 East 59, Charles Perkins Centre D17, The University of Sydney

country: Australia

institute: The University of Sydney

summary: Pre-incubation of T cells with the protein kinase inhibitor dasatinib prevents internalisation of T cell receptors upon binding by peptide-MHC multimers and enhances multimer staining. If used with downstream sc-RNAseq of sorted T cells, there is a possibility that this treatment could influence gene expression. No significant changes in gene expression were detected between dasatinib-treated and untreated cells.

overall_design: To assess the effect of dasatinib, we combined mouse liver leukocytes from 3 male B10.BR individuals (H-2k) following a prime-boost against H-2Kb, and separated them into two pools. One was incubated with dasatinib (50nM) for 30 minutes at ambient temperature prior to staining with a panel of antibodies, the other was pre-incubated with staining buffer only. Treated and untreated cells were sorted into 3 populations of CD8+ T cells each (activated, virtual-central memory and naïve) using the BD Influx cytometer, followed by Sample Tag labelling. The tagged samples were pooled prior to capture on a BD Rhapsody instrument, and library preparation using the Rhapsody Whole Transcriptome Analysis kit, according to the manufacturer’s instructions. Libraries were sequenced using an Illumina NextSeq 1000 with subsequent processing via Seven Bridges.

last: Paul-Heng

first: Alexandra

last: Sharland

first: Taeyoung

middle: E

last: Son


title: Oxidized thioredoxin-1 restrains the NLRP1 inflammasome.

city: New York

first: Daniel

middle: Parker

last: Ball

state: New York

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center


title: Transcription profiling of primary and reccurent spontaneous mammary gland tumors in female MMTV-HER2/neu mice in response to varying 17-DMAG/Stavudine treatment regiments

first: Andrei

last: Gudkov

summary: Activation of endogenous retrotransposons frequently occurs in cancer cells and contributes to tumor genomic instability. To test whether inhibition of retrotranspositions has an anticancer effect, we used treatment with the nucleoside reverse transcriptase inhibitor (NRTI) stavudine in mouse cancer models, MMTV-HER2/Neu and Th-MYCN, that spontaneously develop breast cancer and neuroblastoma, respectively. In both cases, stavudine in drinking water did not affect tumor incidence nor demonstrate any direct antitumor effects. However, stavudine dramatically extended progression-free survival in both models following an initial complete response to chemotherapy. To approach the mechanism underlying this phenomenon, we analyzed the effect of NRTI on the selection of treatment-resistant variants in tumor cells in culture. Cultivation of mouse breast carcinoma 4T1 in the presence of stavudine dramatically reduced the frequency of cells capable of surviving treatment with anticancer drugs. Global transcriptome analysis demonstrated that the acquisition of drug resistance by 4T1 cells was accompanied by an increase in the constitutive activity of interferon type I and NF-B pathways and an elevated expression of LINE-1 elements, which are known to induce inflammatory responses via their products of reverse transcription. Treatment with NRTI reduced NF-B activity and reverted drug resistance. Furthermore, the inducible expression of LINE-1 stimulated inflammatory response and increased the frequency of drug resistant variants in a tumor cell population. These results indicate a new mechanism by which retrotransposon desilencing can stimulate tumor cell survival during treatment and suggest reverse transcriptase inhibition as a potential new therapeutic approach for targeting the development of drug resistant cancers.

overall_design: Total RNA was isolated from individual spontaneous mammary gland tumors ("tumor") representing several experimental groups and from cancer-free mammary glands ("mammary gland"; "untreated") of female MMTV-HER2/neu mice . Samples marked as "untreated" represent RNAs from tumor that developed in control untreated mice. Samples marked as "STV" represent tumors that developed in mice that received reverse transcriptase inhibitor stavudine in drinking water. Samples marked as "DMAG" represent RNAs from recurrent tumors that regrew following initial complete response following treatment with HSP90 inhibitor 17-DMAG. Samples marked as "DMAG+STV" represent RNAs from recurrent tumors that regrew following initial complete response following treatment with HSP90 inhibitor 17-DMAG under constitutive treatment with stavudine in drinking water.

first: Ksenia

last: Novototskaya-Vlasova


title: Effects of LINE-1 induction on transcription in 4T1 cells carrying transgenic recombinant cassette with doxycyclin-inducible LINE-1 with a downstream Gaussia luciferase

overall_design: RNA isolation was performed from subconfluent cultures of 4T1-tetL1(GLucAI) cells carrying transgenic recombinant cassette with doxycyclin (DOX)-inducible LINE-1 with a downstream Gaussia luciferase (Gluc) gene controlled by SV40 promoter, both in opposite (antisense) orientation. Gluc has an intron sequence in sense orientation. This cassette enables DOX-regulated activation of LINE-1 expression and detection of retrotranspositions by the appearance of a Cluc signal indicative of restoration of Gluc open reading frame following RNA splicing and cDNA synthesis in the process of reverse transcription. The idea of experiment is to characterize the effect of LINE-1 induction of global transciption profile.

first: Nickolay

last: Neznanov

first: Ivan

last: Molodtsov


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [Promoter capture HiC]

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Acute myeloid leukaemia (AML) is a heterogeneous haematological malignancy caused by mutations in genes encoding transcriptional and epigenetic regulators together with signalling genes. It is characterised by a disturbance of differentiation and abnormal proliferation of hematopoietic progenitors. We have previously shown that each AML subtype establishes its own core gene regulatory network, consisting of transcription factors binding to their target genes and imposing a specific gene expression pattern that is required for AML maintenance. In the study presented here, we integrate gene expression, open chromatin and ChIP data, with promoter-capture HiC data to define a refined core gene regulatory network common to all patients with one CEBPA N-terminal mutation plus one C- terminal mutation that each disrupt the structure of a major regulator of myelopoiesis (CEBPAN/C AML). We identify the binding sites of mutated C/EBPα proteins in primary cells, we show that the C/EBP family, AP-1 factors and RUNX1 colocalise and are all required for AML maintenance, and we employ single cell experiments to link important network nodes to the specific differentiation trajectory from leukemic stem to blast cells. Taken together, our study provides an important resource which predicts the specific therapeutic vulnerabilities of this AML sub-type in human cells.

overall_design: Promoter capture HiC of an Acute Myeloid Leukemia patient with double CEBPA mutations

first: Assunta

last: Adamo

first: Paulynn

last: Chin

first: Salam

last: Assi

first: Sandeep

last: Potluri

first: Sophie

middle: G

last: Kellaway

last: Coleman

first: Anetta

last: Ptasinska

first: H

middle: R

last: Delwel

middle: N

last: Cockerill

first: Constanze

last: Bonifer


title: Oxidized thioredoxin-1 restrains the NLRP1 inflammasome [NTERT-1]

summary: The danger signals that activate the NLRP1 inflammasome have yet to be firmly established. NLRP1 undergoes autoproteolysis to generate N-terminal (NT) and C-terminal (CT) fragment, which importantly, is a necessary step for its check-point regulation by the DPP9 ternary complex and the mechanistic activation of NLRP1 through functional degradation. Here, we report an added layer of regulatory complexity to NLRP1 activity, in the form of a repressive interaction that NLRP1 forms with the  oxidized, but not reduced, form of thioredoxin-1 (TRX1). Loss of TRX1 destabilizes the NT fragment of NLRP1 and promotes enhanced inflammasome activation. The TRX1 interaction occurs through the NACHT-LRR of NLRP1 and requires nucleotide binding in its ATPase domain. In addition, we found that several patient-derived and ATPase-inactivating mutations in the NACHT-LRR region hyperactive the inflammasome by destabilize protein folding and are also shown to abrogate TRX1 binding. Thus, NLRP1 appears to detect intracellular reductive stress through a decrease in the fraction of intracellular oxidized TRX1, which enhances protein disorder, leading to inflammasome signaling. These findings  link the cellular redox environment to NLRP1-mediated innate immunity.

overall_design: Total RNA content from N/TERT-1 keratinocyte cells is analyzed by RNASeq following electroporation with either Control or TXN1 sgRNA:Cas9 RNP particles to compromise protein translation of TRX1. Experiment was performed in triplicate, and the differential gene expression analysis was used to determine the impact of TRX1 protein loss on the expression of NLRP1 inflammasome genes.

last: Bachovchin


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [Patient DNase1-seq]

overall_design: Open chromatin profiling (DNaseI-Seq) of of sorted CD34+ CEBPA double-mutant primary cells


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [KO52 RNA-seq]

overall_design: Gene Expression profiling (RNA-Seq) of KO52 cell line transfected with dnFOS, dnCEBP or empty vector


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [Patient ATAC-seq]

type: Genome variation profiling by high throughput sequencing

overall_design: Open chromatin profiling (ATAC-Seq) of sorted CD34+ CEBPA double-mutant primary cells


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [KO52 ATAC-seq]

overall_design: Open chromatin profiling (ATAC-Seq) of KO52 cell line transfected with dnFOS, dnCEBP or empty vector


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [Patient ChIP-seq]

overall_design: ChIP-Seq of sorted CD34+ CEBPA double-mutant primary cells or KO52 cell line targeting CEBPA, RUNX1 or cFOS


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [ID216 scRNA-seq]

overall_design: Single cell gene Expression profiling (scRNA-Seq) of sorted LSC and Blast populations from a CEBPA double-mutant patient


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [ID216 RNA-seq]

overall_design: Gene Expression profiling (RNA-Seq) of sorted LSC and Blast populations from a CEBPA double-mutant patient


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [ID216 ATAC-seq]

overall_design: Chromatin accessibility profiling (ATAC-Seq) of sorted LSC and Blast populations from a CEBPA double-mutant patient


title: Oxidized thioredoxin-1 restrains the NLRP1 inflammasome [mBMDM]

last: Ball

overall_design: Total RNA content from wild-type and Txn1 KO C57BL/6J mouse BMDMs is analyzed by RNASeq. Experiment was performed in triplicate, and the differential gene expression analysis was used to determine the impact of TRX1 protein loss on the expression of NLRP1 inflammasome genes.


title: Identification and interrogation of the gene regulatory network of CEBPA double mutant Acute Myeloid Leukaemia [Patient RNA-seq]

overall_design: Gene expression profiling (RNA-Seq) of sorted CD34+ CEBPA double-mutant primary cells