title: In vivo and in vitro matured oocytes from mice of advanced reproductive age exhibit alternative splicing processes for mitochondrial oxidative phosphorylation

city: Beijing

first: Hao

last: Qin

address: 49 North Garden Rd.,Haidian District

institute: Peking University Third Hospital

summary: The mean age of women seeking infertility treatment has gradually increased over recent years. This has coincided with the emergence of in vitro maturation (IVM), a method used in assisted reproductive technology for patients with special requirements. However, when compared with conventional in vitro fertilization, IVM is associated with poor embryonic development potential and low live birth rates, thus limiting the widespread application of this technique. In this study, we performed RNA-sequencing transcriptomic assays and identified a total of 2,627 significant differentially expressed genes (DEGs) between IVM oocytes and in vivo matured oocytes from mice of advanced reproductive age. Next, Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to identify the potential functions of the DEGs. The most significantly enriched pathway was oxidative phosphorylation (OXPHOS). In addition, we constructed a protein-protein interaction network to identify key genes and determined that most of the hub genes were mtDNA-encoded subunits of respiratory chain complex I. Antioxidant supplementation lead to an increase in ATP production and reduced the gene expression profile of the OXPHOS pathway in the IVM group. Moreover, alternative splicing (AS) events were identified during in vivo or in vitro oocyte maturation; data showed that skipped exons were the most frequent type of AS event. A number of genes associated with the OXPHOS pathway exhibited alterations in AS events, including Ndufa7, Ndufs7, Cox6a2, Ndufs5, Ndufb1, and Uqcrh. Furthermore, the process of IVO promoted the skipping of exon 2 in Ndufa7 and exon 3 in Ndufs7 compared with the IVM oocytes, as determined by semi‑quantitative RT‑PCR. Collectively, these findings provide potential new therapeutic targets for improving IVM of aged women who undergo infertility treatment.

overall_design:
We used ICR mice at the age of 42-45 weeks (a reproductive advanced age) that were near to the end of their reproductive lifespan and exhibited a decline in oocyte quality, as described in previous studies (Li et al., 2020). These mice are commonly regarded as a natural aging model and were used as donors for IVM and IVO oocytes so that we could carry out RNA sequencing. First, we used cDNA to generate libraries for IVM and IVO oocytes, which were then sequenced by the Illumina NovaSeq 6000 platform (three biological replicates per group).
Li, C., He, X., Huang, Z., Han, L., Wu, X., Li, L., Xin, Y., Ge, J., Sha, J., Yin, Z., and Wang, Q. (2020). Melatonin ameliorates the advanced maternal age-associated meiotic defects in oocytes through the SIRT2-dependent H4K16 deacetylation pathway. Aging (Albany NY) 12, 1610-1623.

first: Yi

last: Qu

first: Rong

last: Li

first: Jie

last: Qiao


title: Single cell Ig VDJ sequencing (10X Genomics) of human blood B cells from SLE pateints and healthy controls

status: Public on Jan 26 2022

city: Aurora

first: Roberta

last: Pelanda

state: CO

address: 12800 East 19th Avenue

department: Immunology&Microbiology

country: USA

institute: University of Colorado Anschutz Medical Campus

summary: B cells positive for Ig kappa and Ig lambda are observed by flow cytometry in one fourth of patients with Systemic Lupus Erythematosus (SLE). Single cell Ig VDJ sequencing (10X Genomics) reveals that kappa/lambda B cells are at the same frequency (about 1.5%) in these SLE patients as in healthy controls. Cells observed by flow cytometry are instead decorated with VH4-34 IgM (kappa or lambda) autoantibodies that are present in some but not all SLE patients.

overall_design: B cells were enriched by magnetic cell sorting from PBMCs of 3 SLE adult patients (ABA-07; ABA-15; ABA-19) and 3 healthy controls (ABCtr-07; ABCtr-15; ABCtr-19); cells were processed for Ig VDJ libraries (10X Genomics).

first: Jacob

middle: N

last: Peterson

first: Sophina

middle: H

last: Taitano

first: Allison

last: Sang

first: Margot

last: Kelly

first: Julie

last: Lang

first: Jeremy

middle: T

last: Rahkola

first: Anjelica

middle: M

last: Miranda

first: Ryan

last: Sheridan

first: V

middle: K

last: Rao

first: Joshua

last: Thurman

first: Raul

last: Torres

first: Susan

middle: A

last: Boackle


title: GATA3 truncation mutants alter EMT related gene expression via partial motif recognition in luminal breast cancer cell

status: Public on Jan 15 2022

city: Grand Forks

first: Motoki

last: Takaku

state: North Dakota

address: 501 N Columbia Road,

institute: University of North Dakota

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: GATA3 is one of the most frequently mutated genes in breast cancer. The roles of GATA3 mutations remain elusive. In this study, we characterized newly established luminal breast cancer cell lines that stably express different GATA3 patient-derived mutants (Splice site deletion, C321 frame-shift, and A333 frame-shift mutants). The expression of these mutants lead to altered expression of  EMT related genes as well as redistribution of GATA3.

overall_design: Genome-wide mapping of chromatin localization of GATA3 and transcriptome analysis in GATA3 mutant cells

first: Deepak

middle: B

last: Poduval


title: Association of epigenetic differences nominated by monozygotic twins discordant for attention-deficit hyperactivity disorder with their brain structures

status: Public on Jan 12 2022

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

summary: The present study examined the relationship between genome-wide methylation differences and variations in brain structures involved in the development of attention-deficit hyperactivity disorder (ADHD). We used monozygotic twins discordant for ADHD to identify candidate DNA methylation sites involved in the development of ADHD. Two pairs of MZ twins discordant for ADHD were recruited from the Department of Child and Adolescent Psychological Medicine at the University of Fukui Hospital. The twins were 9-year-old males (pair 1) and 16-year-old females (pair 2). Genomic DNA was collected from saliva samples, and the DNA was then whole-genome amplified, fragmented, and hybridized to the Human MethylationEPIC BeadChip.

overall_design: Bisulphite converted saliva DNA from the 4 samples (2 monozygotic twins discordant for ADHD) were hybridized to the Illumina Infinium Methylation EPIC Kit array

first: Takashi

middle: X

last: Fujisawa

first: Akemi

last: Tomoda


title: RB1 loss promotes a noncanonical activator function of LSD1 and sensitizes castration-resistant prostate cancer to LSD1 inhibition

status: Public on Jan 14 2022

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

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

overall_design: Refer to individual Series


title: eIF3 and its mRNA-entry-channel arm contribute to the recruitment of mRNAs with long 5'-untranslated regions

status: Public on Jan 11 2022

city: Poughkeepsie

first: Colin Echeverría

last: Aitken

state: NY

address: 124 Raymond Ave., Box 731

institute: Vassar College

summary: Translation initiation in eukaryotes is multi-step pathway and the most regulated phase of translation. Eukaryotic initiation factor 3 is the largest and most complex of the translation initiation factors, and it contributes to events throughout the initiation pathway. In particular, eIF3 appears to play critical roles in mRNA recruitment. More recently, eIF3 has been implicated in driving the selective translation of specific classes of mRNAs. However, unraveling the mechanism of these diverse contributions — and disentangling the roles of the individual subunits of the eIF3 complex — remains challenging. We employed ribosome profiling of budding yeast cells expressing two distinct mutations targeting the eIF3 complex. These mutations either disrupt the entire complex or subunits positioned near the mRNA-entry channel of the ribosome which appear to relocate during or in response to mRNA binding and start-codon recognition. Disruption of either the entire eIF3 complex or specific targeting of these subunits affects mRNAs with long 5’-untranslated regions and whose translation is more dependent on eIF4A, eIF4B, and Ded1 but less dependent on eIF4G, eIF4E, and PABP. Disruption of the entire eIF3 complex further affects mRNAs involved in mitochondrial processes and with structured 5’-untranslated regions. Comparison of the suite of mRNAs most sensitive to both mutations with those uniquely sensitive to disruption of the entire complex sheds new light on the specific roles of individual subunits of the eIF3 complex.

overall_design: We investigated the effects of disruption of the entire eIF3 complex or its mRNA-entry-channel arm on the translational efficiency (TE) of individual mRNAs across the transcriptome. This study includes 16 samples: 8 mRNA-seq samples and 8 ribosome footprint profiling samples, obtained from biological replicates of S. cerevisiae strains expressing either temperature-sensitive degron alleles of eIF3a and eIF3ab (eIF3a/b Degron) or a specific mutation of the eIF3i subunit (eIF3i DDKK), as well as isogenic wild-type strains for each. All strains were grown initially under permissive conditions prior to shifting to restrictive conditions for a duration resulting in approximately 80-90% reduction in global translational levels in each mutant strain.

first: Andrei

last: Stanciu

first: Juncheng

last: Luo

first: Lucy

last: Funes

first: Shanya

last: Galbokke Hewage

first: Colin

last: Echeverría Aitken


title: Deciphering the role of 3D genome organization in breast cancer susceptibility

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N Orchard St

department: Wisconsin Institute For Discovery

institute: University of Wisconsin-Madison


title: Gene expression profile in prostate cancer xenograft tumors after FGFRL1 knockdown

city: Turku

first: Pirkko

last: Härkönen

state: Finland

address: Medisiina D, 5th floor, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: FGFRs regulate PCa development and progression, but the role of the recently found FGFR-like 1 (FGFRL1) remains unclear. The data consists of gene expression profiles of mouse subcutanous xenograft tumors generated of human PC3M prostate cancer cells with stable knockdown of FGFRL1 gene and of the control xenografts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Control PC3M cells with scrambled sh-RNA tarnsfection or with FGFRL1 knock-down by sh-RNA were inoculated subcutaneously to athymic nu/nu mice. Tumors wer harvested at day 45. The RNAseq samples include RNAs from five control tumors (derived from ctrl-sh8 cells)  and five tumors with FGFRL1 knockdown (derived from FGFRL1-sh11 cells).

first: Lan

last: Yu

first: Mervi

last: Toriseva

first: Syeda

last: Afshan

first: Mario

last: Cangiano

first: Vidal

last: Fey

first: Inès

middle: J

last: Beumer

first: Matthias

last: Nees


title: Deciphering the role of 3D genome organization in breast cancer susceptibility (RNA-Seq)

summary: Cancer risk by environmental exposure is modulated by an individual’s genetics and age at exposure. This age-specific period of susceptibility is referred to as a “Window of Susceptibility” (WOS). Radiation exposures poses a high breast cancer risk for women between the early childhood and young adult stage and is reduced in the mid-30s. Rats have a similar WOS for developing breast cancer. Previous studies have identified a looping interaction between a genomic region in the mammary carcinoma susceptibility Mcs5c locus and a known cancer gene, PAPPA. However, the global role of three-dimensional organization in the WOS is not known. Therefore, we generated Hi-C and RNA-seq data in rat mammary epithelial cells within and outside WOS. We compared the temporal changes in chromosomal looping to those in expression and find that interactions that have significantly higher counts within WOS are significantly enriched for genes upregulated in WOS. To systematically identify higher-order changes in 3D genome organization, we developed an approach that combines network enhancement to smooth the Hi-C matrices followed by multitask non-negative matrix factorization (NMF) to identify clusters of interacting loci. We found that large-scale topological re-organizations are enriched for differential interactions within and outside the WOS timepoints. Finally, we mapped previously published breast-cancer associated human GWAS variants to rat loci and identified the corresponding rat ortholog gene interacting with the loci. Many of the associated rat genes participate in differential interactions, recapitulate the human SNP- gene interactions and are associated with breast cancer. Our results suggest that WOS-specific changes in 3D genome organization are linked to transcriptional changes that may increase susceptibility to breast cancer.

overall_design: RNASeq to characterize gene expression differences in 6wk old (n=6) and 10wk old (n=7) rat mammary epithelial cells

first: Brittany

last: Baur

first: Jill

last: Haag

first: Da-Inn

last: Lee


title: Broad deregulation of fibroblast activation and wound healing genes within Ezh2 cKO decidua.

city: San Francisco

first: Ivan

last: Osokine

state: California

address: 513 Parnassus Avenue S1058

department: Laboratory Medicine

institute: University of California, San Francisco

summary:
Our objective was to identify genes differentially expressed between control and Ezh2 cKO decidua, and to compare this set of genes with a previously identified gene set of H3K27me3-marked decidual genes that are putatively silenced by EZH2/PRC2 (Nancy et al. JCI. 2018).
RNA was isolated from whole tissue decidua and myometrium of control and Ezh2 cKO mice. Sequencing provided was 731 million total reads with an average of 84.5% of these reads aligning uniquely to the mouse genome. Reads uniquely mapped to known mRNAs were used to identify gene expression changes between housing conditions using DESeq2.
We found that 2530 protein-coding genes were differentially expressed within the decidua and 521 were differentially expressed in the myometrium (FDR<0.05, excluding genes whose normalized read counts were less than 30 averaged across samples). Hypergeometric analysis revealed a strong enrichment for previously identified H3K27me3 targets within genes overexpressed in Ezh2 cKO decidua.

overall_design: RNA was prepared from whole tissue myometrium and decidua of control (n=4) and Ezh2 cKO (n=3) and E7.5 of pregnancy. One control myometrial sample was excluded due to failed QC. Decidua was the tissue of primary interest, with myometrium serving as reference tissue. Next generation sequencing was performed using Illumina HiSeq 4000.

first: Damon

last: Rideaux

first: Stephany

last: Ma

first: Adrian

last: Erlebacher


title: Deciphering the role of 3D genome organization in breast cancer susceptibility (Hi-C)

overall_design: Hi-C data from mammary epithelial cells for 3 6wk old rats and 3 12wk old rats


title: Notch signaling rapidly regulates the expression of the small GTPase RND1 and a diverse endothelial transcriptome

city: Chicago

first: Jan

last: Kitajewski

state: Illinois

address: 909 South Wolcott Avenue

department: Department of Physiology and Biophysics

institute: University of Illinois, Chicago

summary: Endothelial Notch signaling regulates transcription of many downstream effectors controlling sprouting, migration, proliferation, barrier formation, and other phenotypes. However, endothelial-relevant Notch targets are largely uncharacterized. Few are studied in depth, and many transient, early response Notch targets are yet to be described. We therefore determined the Notch early response transcriptional profile in several experimentally relevant in vivo and in vitro contexts: ligand-specific or EGTA-induced Notch activation in different primary endothelial cells, and gamma secretase-mediated Notch inhibition in neonatal brain endothelium in a RiboTag mouse model. The intersection of these profiles reveals a core set of early Notch-responsive targets.  Among these are effectors in GPCR signaling, not previously implicated downstream of Notch signaling. We demonstrate the Rho GTPase RND1 is a direct Notch transcriptional target and required for Notch control of sprouting angiogenesis, endothelial migration and Ras activity.

overall_design: RNAseq screens from in-vitro activation of Endothelial Cells by tethered DLL4 (6h) or EGTA (1.5h) or EGTA in combination with CpE (1.5h) or in-vivo RiboTagEC mice treated with CpE (6h).

first: Bhairavi

last: Swaminathan

first: Seock-Won

last: Youn

first: Naiche

middle: L

last: Adler

first: Jing

last: Du

first: Stephanie

middle: R

last: Niemczyk

first: Jordan

last: Metz

first: Huijin

last: Feng

first: Chaolin

last: Zhang

first: Raphael

last: Kopan

first: Peter

last: Sims


title: A Mediator-cohesin axis controls heterochromatin domain formation [RNA-seq]

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: The genome consists of regions of transcriptionally active euchromatin and more silent heterochromatin. We reveal that the formation of heterochromatin domains requires cohesin turnover on DNA. Stabilization of cohesin on DNA through depletion of its release factor WAPL leads to a near-complete loss of heterochromatin domains. The Mediator CDK module controls heterochromatin in an opposing manner. Loss of this module leads to an almost binary partition of the genome into dense H3K9me3 domains, and regions devoid of H3K9me3 spanning the rest of the genome. By restricting the degree of heterochromatinization, the Mediator CDK module creates a transcription-permissive context that enables gene expression within heterochromatin domains. WAPL deficiency prevents the formation of heterochromatin domains, thus allowing for gene expression even in the absence of the Mediator CDK module. We propose that heterochromatin is controlled by two opposing activities, in which the Mediator CDK module and cohesin turnover must be balanced to enable the correct distribution of epigenetic marks to ensure proper gene expression.

overall_design: RNA-seq

first: Robin

first: Elzo

last: de Wit


title: Pre-clinical and clinical studies on the role of RBM3 in muscle-invasive bladder cancer: longitudinal expression, transcriptome-level effects and modulation of chemosensitivity

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

summary:
Background: The response to neoadjuvant cisplatin-based chemotherapy (NAC) in muscle-invasive bladder cancer (MIBC) is impaired in up to 50% of patients due to chemoresistance, with no predictive biomarkers in clinical use. RNA-binding motif protein 3 (RBM3) has emerged as a putative modulator of chemotherapy response but has a hitherto unrecognized role in MIBC.
Methods: Tumour-specific RBM3 protein expression was assessed via immunohistochemistry in paired transurethral resection of the bladder (TURB) specimens, cystectomy specimens and lymph node metastases from 145 patients. The effect of RBM3 suppression on chemosensitivity was examined in RT4 and T24 cells in vitro. RNA-sequencing was applied to compare gene expression profiles between siRBM3-treated and control cells.
Findings: RBM3 protein expression was significantly higher in TURB compared to cystectomy specimens but showed consistency between primary tumours and lymph node metastases. High tumour-specific RBM3 expression was significantly associated with a reduced risk of recurrence in NAC treated patients. In T24 cells, which displayed higher RBM3 levels than RT4 cells, RBM3 silencing conferred a decreased sensitivity to cisplatin and gemcitabine. RNA-sequencing revealed potential involvement of RBM3 in facilitating cell cycle progression, in particular G1/S-phase transition, and initiation of DNA replication.
Interpretation: The presented data highlight the predictive value of RBM3 in MIBC, which could, if prospectively validated, improve treatment stratification of patients with this aggressive disease.

overall_design: n = 3 T24 control vs. n = 3 T24 siRNA targetting RBM3.

first: Sara

last: Wahlin

first: Karin

last: Jirström


title: A Mediator-cohesin axis controls heterochromatin domain formation.


title: Competition but not cross-competition controls T cell proliferation in transplant patients following cytomegalovirus reactivation

status: Public on Jan 18 2022

city: Seattle

first: Martin

last: Prlic

state: WA

address: 1100 Fairview Ave, Mail stop E5-110

institute: Fred Hutch

summary: Competition between antigen-specific T cells for peptide:MHC (p:MHC) complexes shapes the ensuing T cell response. T cells also compete for access to antigen presenting cells (APCs), which results in competition between T cells of different antigen specificities and is referred to as cross-competition. When both mechanisms are in place, a memory T cell population specific for just a single epitope can effectively limit de novo antigen-specific T cell responses. Whether human cytomegalovirus (CMV)-specific T cell responses prevent other de novo T cell responses is unknown, but of interest in a transplant context as well as the development of CMV-based vaccines. We assessed the extent of T cell competition and cross-competition in a cohort of non-myeloablative hematopoietic stem cell transplant (nmHSCT) patients. In our cohort, HSCT donors and recipients were CMV-seronegative and -positive, respectively, thus providing genetically distinct memory and naïve T cell populations. We used single-cell transcriptomics to track donor versus recipient-derived T cell clones. We found that recipient-derived CMV-specific memory T cells outcompeted donor-derived responses of identical specificity; however, expansion of other donor-derived T cell clones still occurred averaging 24 rounds of cell division. The transcriptional programs between expanding donor and recipient-derived cells were largely congruent and consistent with an effector T cell response. Our data further indicated that the composition of the T cell compartment changed due to expanding and contracting clones in the first 90 days post-nmHSCT. Overall, our data suggest that CMV-specific memory T cells compete for p:MHC but not APC access during CMV reactivation.

overall_design: CD8+ T cells were isolated from cryopreserved PBMCs collected longitudinally post non-myeloablative hematopeotic stem cell transplant. These cells were then process for transcriptional profiling and/or V(D)J sequencing using either 3' or 5' whole transcriptomic approaches (10x)

first: Jami

last: Erickson


title: Phenotypic spectrum and molecular basis in a Chinese cohort of osteogenesis imperfecta with mutations in type I collagen

status: Public on Jan 10 2022

city: Shenzhen

first: Peikai

last: Chen

address: 1 Haiyuan Rd

country: China

institute: The University of Hong Kong - Shenzhen Hospital

summary: Osteogenesis imperfecta (OI) is a rare inherited connective tissue dysplasia characterized with skeletal fragility, recurrent fractures and bone deformity, predominantly caused by mutations in the genes COL1A1 or COL1A2 that encode the chains of type I collagen. In the present study, clinical manifestations and genetic variants were analysed from 188 Chinese OI patients, majority of which are of southern China origin. By targeted sequencing, 64 and 58 OI patients were found carrying mutations in COL1A1 and COL1A2 respectively, including 12 novel COL1A1 and 8 novel COL1A2 variants. We identified a COL1A1 hotspot (c.G2461A; p.G821S) in 8 patients and validated two novel splicing mutations. A diverse mutational and phenotypic spectrum was observed, coupling with heterogeneity observed in the transcriptomic data (n=6) derived from osteoblasts of our cohort. Missense mutations were significantly associated (χ2 p=0.0096) with a cluster of patients with more severe clinical phenotypes. Additionally, the severity of OI was more correlated with the quality of bones, rather than the bone mineral density. Bone density is most responsive to bisphosphonate (BP) treatment during the juvenile stage (10-15 y/o). In contrast, height is not responsive to bisphosphonate treatment. Our findings expand the mutational spectrum of type I collagen genes and the genotype-phenotype correlation in Chinese OI patients. The observation of effective BP treatment in an age-specific manner may help to improve OI patient management.

overall_design: We conducted bulk transcriptomic profiling on osteoblasts derived from 6 OI individuals with Collagen 1 mutations and two non-OI samples

first: Tan

last: Zhijia

first: Michael

last: To


title: Overactivation of wound healing-associated TGF-beta responses in EZH2-deficient decidual stromal cells.

first: Ivan

last: Osokine

summary:
Our objective was to identify genes upregulated by TGF-beta in control and Ezh2 cKO decidual stromal cells (DSCs), and to compare this set of genes with a previously identified gene set of H3K27me3-marked decidual genes that are putatively silenced by EZH2/PRC2 (Nancy et al. JCI. 2018). We also wanted to assess baseline (BL) gene expression in control and Ezh2 cKO DSCs, and compare it to an RNA-seq analysis of differential gene expression in whole tissue Ezh2 cKO and control decidua.
RNA was isolated from untreated and TGF-beta treated decidual stromal cells from control and Ezh2 cKO mice. Sequencing provided was 706 million total reads with an average of 82.2% of these reads aligning uniquely to the mouse genome. Reads uniquely mapped to known mRNAs were used to identify gene expression changes between housing conditions using DESeq2.
TGF-beta induced 638 protein-coding genes in EZH2-deficient DSCs versus 480 in control DSCs (with a 295 gene overlap), demonstrating that EZH2-deficient DSCs are transcriptionally more responsive to TGF- (P=0.0025, Fisher’s exact test). Within the 638 genes, activated fibroblast signature genes were highly over-represented. TGF-target genes were 2.7-fold over-represented within the set of genes with higher expression in EZH2-deficient DSCs at baseline (BL; i.e., when neither EZH2-deficient nor control DSCs were treated with TGF-beta; P<1x10-20) . 741 genes were overexpressed in Ezh2 cKO DSCs compared to control DSCs, and 904 genes were underexpressed. Moreover, by comparing to our laboratory's previous CHIP-Seq analysis (Nancy et al. JCI 2018), we noted that  genes overexpressed in cKO mice were enriched in previously identified H3K27me3-marked genes (P<1x10-26).

overall_design: Decidual stromal cells (DSCs) were isolated from control or Ezh2 cKO decidual tissue at E7.5 of pregnancy. Each biological isolate was split into two replicates, one of which was cultured without treatment, and one of which was cultured with 2 ng/mL of TGF-beta. Samples were cultured for 24 hours. RNA was subsequently prepared.  Next generation sequencing was performed using Illumina HiSeq 4000.

first: Damon

last: Rideaux

first: Stephany

last: Ma

first: Adrian

last: Erlebacher


title: Comparison of wild-type and ctbp-1(lf) AIA neuron transcriptional profiles in L4 larval stage C. elegans

city: Cambridge

first: Joshua

last: Saul

department: Biology

institute: MIT

summary: ctbp-1 mutant C. elegans display a number of late-onset defects in their AIA neurons including (so far only a few identified) changes in their transcriptional profile. We sought to better characterize the gene expression changes occuring in these neurons by conducting a single, exploratory single cell RNA-seq experiment comparing wild-type and ctbp-1(lf) mutant gene expression profiles. Our main focus was on changes occurring specifically in the AIA neurons, though we decided to sequence the whole of the C. elegans nervous system so as to have to possibility of analyzing data detailing changes in other cell types should we so choose

overall_design: Single cell RNA-seq experiment performed on neurons from wild-type (control) and ctbp-1(lf) mutant C. elegans. Animals carrying a pan-neuronal GFP reporter were grown to the L4 larval stage, dissociated into single cell suspensions, FACS sorted for GFP+ living neurons, and prepped using 10X Genomics' library prep kits. A single replicate of each was performed. Single cell transcriptional profiles were processed and specific, desired cell type profiles were identified and analyzed for transcriptional changes between mutant and wild-type worms. Identified changes in gene expression were validated afterwards

first: Josh

first: H

last: Horvitz


title: Analysis of accessible chromatin regions in response to microgravity in C2C12 mouse myotubes

status: Public on Jan 13 2022

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

summary: We analyzed the accessible chromatin regions globally in response to microgravity in C2C12 mouse myotubes.

overall_design: ATAC-seq profiling of effects of microgravity in C2C12 myotubes.

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: Development of novel in vitro human alveolar epithelial cell models to study distal lung biology and disease.

city: Los Angeles

first: Evelyn

last: Tran

state: CA

address: 1441 Eastlake Ave

department: Biochemistry/Surgery

institute: University of Southern California


title: A Mediator-cohesin axis controls heterochromatin domain formation

first: Robin H.

last: van der Weide

overall_design: Hi-C

first: Robin

first: Elzo

last: de Wit


title: A Mediator-cohesin axis controls heterochromatin domain formation [ChIP-seq]

overall_design: ChIP-seq


title: Genome-wide MNase-ChIP profile of transfected Strep-LIN9 in WT and LIN37-/- HCT116 cells

city: Santa Cruz

first: Seth

last: Rubin

address: 1156 High Street

department: Chemistry

institute: UC Santa Cruz

summary: We performed MNase-ChIP seq with deep digestion to identify the MuvB associated nucleosomes in WT and LIN37 -/- HCT116 cells in G1 arrested and cycling cells. Strep-LIN9 as well as a mutant of the protein (Strep-4xLIN9: R174A/R175A/F180A/F181A) which is unable to associate with LIN37 or RbAP48 were transiently transfected in WT and LIN37 -/- HCT116 cells. At 24 hours after transfection, cells were treated with Nutlin-3a to induce G1 arrest; cells were harvested 48 hours following treatment. For several samples, Nutlin-3a treatment was omitted to maintain cycling conditions. Cells were then cross-linked with formaldehyde, lysed and treated with micrococcal nuclease. Chromatin fragments were precipitated with Streptactin-XT magnetic beads after which DNA was purified and libraries were prepared and sequenced using NovaSeq 6000 platform in 150bp paired-end mode. We find that LIN9 precipitates to +1 nucleosomes of target genes in arrested HCT116 and LIN37 -/- cells. The precipitation of this nucleosome is diminished in cycling cells as well as in arrested cells transfected with the Strep-4xLIN9 mutant.

overall_design: MNase-ChIP seq profiles of transiently transfected Strep-LIN9 proteins and a LIN9 mutant in HCT116 WT and HCT116 LIN37 -/- in cycling and arrested conditions

first: Anushweta

last: Asthana

first: Gerd

last: Müller


title: Development of novel in vitro human alveolar epithelial cell models to study distal lung biology and disease [scRNA-seq]

summary: To address the need for human alveolar epithelial cell (AEC)-derived lines to more suitably model distal lung diseases, we have generated and characterized novel immortalized cell lines derived from human AECs. We used a combination of the ROCK inhibitor, Y-27632, and lentiviral transduction of SV40 Large T antigen of previously cryopreserved isolated human alveolar epithelial type 2 (AT2) cells to generate immortalized AECs. These AEC lines proliferate well on standard tissue culture dishes forming an epithelial monolayer and express lung progenitor markers SOX9 and SOX2. When grown in 3D culture with lung fibroblasts, the cells form NKX2-1+ organoids expressing more mature alveolar lung markers, AQP5 and GPRC5A. Single cell RNA-sequencing of one AEC line comparing cells in 2D versus 3D revealed increased cellular heterogeneity and an induction of cytokine and lipoprotein signaling in 3D culture, reflecting interactions with the microenvironment during organoid formation. Taken together, these data show our novel progenitor-like AEC lines retain a genetic and structural memory of their alveolar cell lineage despite long-term expansion, providing a valuable new system to model the distal lung in vitro.

overall_design: We compared cells of the SV40 Large T antigen-immortalized AEC line, AEC-ON, grown in 2D monolayer versus 3D organoids by single cell RNA-sequencing.

first: Tuo

last: Shi

first: Xiuwen

last: Li

first: Adnan

middle: Y

last: Chowdhury

first: Du

last: Jiang

first: Yixin

last: Liu

first: Hongjun

last: Wang

first: Chunli

last: Yan

first: William

middle: D

last: Wallace

first: Rong

last: Lu

first: Amy

last: Ryan

first: Crystal

last: Marconett

first: Beiyun

last: Zhou

first: Zea

last: Borok

first: Ite

last: Offringa


title: Screening of genes differentiating transcriptional profiles of CIA rats at different NAMPT expression statuses

status: Public on Jan 09 2022

city: wuhu

first: qing

middle: meng

last: tao

address: Wenchang road

institute: Wannan Medical College

summary: We screened out differentially expressed genes between CIA rats and healthy controls at both NAMPT++ (CIA1) and NAMPT+ (CIA2) statuses.It was obvious that that high expression of NAMPT is linked to acute inflammation, as TLRs and its downstream MAPKs and NF-κB were identified as the most affected pathways in NAMPT++ samples compared with normal control. However, by the decrease of NAMPT expression, the pathological situation was not eased but became even more complicated. Energy metabolism (mainly lipid metabolism) was significantly altered at this status. Interestingly, many RA-related pathways emerged, such as TGF-β, IL-17, PI3K-AKT and osteoclast differentiation pathways. These results solidly support the hypothesis that NAMPT overexpression is an early event in CIA and directly affects the innate rather than adaptive immunity.

overall_design: Screened out differentially expressed genes between CIA rats and healthy controls at both NAMPT++ and NAMPT+ statuses

first: Ming

last: Lei

first: Meng-Qing

last: Tao

first: Jian

last: Zuo


title: Surgical trauma in mice modifies the content of circulating extracellular vesicles

status: Public on Jan 08 2022

city: Stockholm

first: Souren

last: Mkrtchian

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary:
Purpose: Aseptic tissue injuries including major surgeries are associated with structural and functional changes in the brain suggesting the existence of periphery-to-brain communication. However, the nature of the carriers of such signaling remains largely unknown. Analyzis of the miRNAome and proteome of circulating extracellular vesicles (EVs) to evaluate their potential contribution to the periphery-to-brain signaling.
Methods: EVs were isolated from the serum of the mice subjected to a tibia surgery after 6, 24, and 72 h, using Exoquick ULTRA commercial ki. Proteome and miRNAome were mapped using mass spectrometry and RNA-seq approaches.
Results: Next-generation sequencing of small RNA libraries prepared from the total RNA isolated from the mouse serum EVs detected 252 miRNAs. Differential expression analysis using DESeq2 statistical package revealed 50 dysregulated miRNAs in the 24 h post-surgery EVs. The surgery effect declines after 72 h as judged by the lower number of dysregulated miRNAs. The differentially expressed miRNAs were examined by the DIANA-miRPath online tool that predicted dysregulation of several KEGG pathways including pathways involved in the lipid metabolism, ECM-receptor interaction, gap junction, various signal transduction pathways.
Conclusions: The main question of the current project, is the surgery capable of modifying the expression of cargo molecules in circulating EVs, can be answered positively. Moreover, differential expression of a specific set of miRNAs in the “surgical” EVs suggests that they can be involved in the regulation of several metabolic pathways, such as ECM-receptor interaction and lipid metabolism in the recipient tissues, which is consistent with our data on hippocampal metabolic and functional dysregulation after surgery  We conclude that surgery alters the EV composition in the blood, which paves the way for further studies on the functional effects of these EVs on the brain.

overall_design: Analysis of miRNAs from 24 serum EV samples isolated from control, 6 h, 24 h, 72 h post-surgery mice (6 biological replicates in each group).

first: Marta

last: Gómez-Galán


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in Tbx2 depleted melanoma cells

status: Public on Jan 07 2022

city: Oxford

first: Sizhu

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford branch

summary: Mouse melanoma B16 cells were transfected with either siCtrl of siTbx2 for 48 h, then RNA extracted and use in library preparation and following sequencing.

overall_design: mRNA profiles of untransfected or siCtrl or siTbx2 transfected melanoma cells

first: Colin

last: Goding

first: Pakavarin

last: Louphrasitthiphol


title: Gene expression profile in prostate cancer cells after FGF13 or FGFRL1 knockdown

first: Pirkko

last: Härkönen

summary: FGFRs regulate PCa development and progression, but the role of the recently found FGFR-like 1 (FGFRL1, FGFR5) remains unclear. The data consists of gene expression profiles of FGF13 and FGFRL1 knock-down PC3M prostate cancer cells compared to control cells.

overall_design: RNA sequencing was performed from two replicate samples of two different PC3M control clones (transfected with scrambled sh-RNA, sh5 and sh8), two replicate samples of three FGF13 knock-down PC3M clones (sh9, sh19, sh21) and two biological replicates of FGFRL1 knock-down PC3M cell clone (sh11). The RNA samples were harvested from actively proliferating cells cultured in the presence of 10% iFBS.

first: Lan

last: Yu

first: Mervi

last: Toriseva

first: Syeda

last: Afshan

first: Vidal

last: Fey

first: Matthias

last: Nees


title: Development of novel in vitro human alveolar epithelial cell models to study distal lung biology and disease [bulk RNA-seq]

first: Evelyn

last: Tran

overall_design: We compared our novel AEC lines transcriptomically  to 12 primary AECs (AT2 and AT1-like cells), 3 lung fibroblasts, fetal lung tissue, and 18 lung adenocarcinoma (LUAD) cell lines. The LUAD cell data were downloaded from the publicly available resource DBTSS. Two of the 3 lung fibroblast samples and the fetal lung tissue were downloaded from ENCODE. Four of the primary AEC data were previously published. We profiled 7 human AEC lines generated in the study (one cell line sequenced with a replicate), 1 human lung fibroblast cell line, purified human AT2 cells from two lung donors, purified human AT2 cells from the same two donors transdifferentiated on Transwell filters for 2, 4, and 6 days into alveolar type 1 (AT1)-like cells. The remaining samples used in the entire analyses were taken from previously published work and publicly available datasets, as discussed in the paper.

first: Tuo

last: Shi

first: Xiuwen

last: Li

first: Adnan

last: Chowdhury

first: Du

last: Jiang

first: Yixin

last: Liu

first: Hongjun

last: Wang

first: Chunli

last: Yan

first: William

last: Wallace

first: Rong

last: Lu

first: Amy

last: Ryan

first: Crystal

last: Marconett

first: Beiyun

last: Zhou

first: Zea


title: Expression data of shDIDO1  and shCtrl HUVEC cell lines

city: Kunming

first: Shen

last: Zhenglei

state: Yunnan

address: No.519, Kunzhou Road, Xishan District

institute: The third Affiliated Hospital of Kunming Medical University

summary:
DIDO1(Death inducer-obliterator) gene localizes in the nucleus and cytosol, which is required in the early steps during the tumor progression and metastasis.
We analyzed the GeneChip expression profiles of human umbilical vein endothelial cells transfected by RNAi lentiviral vectors, shDIDO1 cell line and shCtrl cell lines

overall_design:
Firstly, we identified the DEGs between HUVEC cell lines (GSM4742969-GSM4742972) and the K562-HUVEC co-cultivated cell lines (GSM4742973-GSM4742976) by Human GeneChip primeview (Affymetrix, 901838). Four biological repeats were taken.
DIDO1 was identified as a key candidate gene, so we construct DIDO1-RNAi vector and transfected HUVEC cell lines. The DEGs between shDIDO1 cell lines (GSM4742963-GSM4742965) and the controls (shCtrl) (GSM4742966-GSM4742968) were analyzed by GeneChip. Three biological repeats were taken.

first: Zhenglei

last: Shen

first: Honghua

last: Cao


title: Gene expression after liver transplantation

status: Public on Jan 05 2022

city: Rotterdam

first: Aafke

last: Duizendstra

address: Doctor Molewaterplein 40

institute: Erasmus Medical Center

summary:
The purpose of this study was to validate differentially expressed immune system related genes described in previous studies that identified tolerant LTx recipients after immunosuppressive drug (IS) weaning. Blood was collected of tolerant LTx recipients (TOL), a control group of LTx recipients with regular IS regimen (CTRL), a group of LTx recipients with minimal IS regimen (MIN) and healthy controls (HC), and groups were matched on age, sex, primary disease, time after LTx, and cytomegalovirus serostatus after LTx.
Quantitative Polymerase Chain Reaction was used to determine expression of twenty selected genes and transcript variants in PBMCs. In conclusion, we found confounding effects of IS regimen and prior cytomegalovirus infection, on peripheral blood expression of several selected genes that were described as tolerance-associated genes by previous studies.

overall_design: 4 study groups; in total 52 study samples analyzed in triplicate


title: Klf9 regulates neural stem cell activation and expansion in the adult hippocampus

status: Public on Jan 06 2022

city: Boston

first: Lai Ping

last: Wong

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Experience governs neurogenesis from radial-glial neural stem cells (RGLs) in the adult hippocampus to support memory. Transcription factors in RGLs integrate physiological signals to dictate quiescence-activation decisions and self-renewal divisions. Whereas asymmetric RGL self-renewal drives neurogenesis during favorable conditions, symmetric divisions prevent premature neurogenesis during unfavorable conditions while amplifying RGLs to anticipate neurogenic demands when conditions become favorable.  Here, we show that the transcription factor Kruppel-like factor 9 (Klf9) is enriched in quiescent RGLs and inducible, bidirectional modulation of Klf9 biases RGL quiescence-activation decisions. Clonal lineage tracing and longitudinal intravital two-photon imaging of RGLs following cell-autonomous Klf9 deletion directly demonstrated increased symmetric self-renewal. In vivo translational profiling of RGLs identified a Klf9-dependent blueprint for genetic and metabolic programs instructing RGL quiescence and expansion. Thus, experience dependent regulation of Klf9 in RGLs may ensure self-preservation of neural stem cells while anticipating future demands for neurogenesis and astrogenesis to support hippocampal functions.

overall_design: Analysis of WT and Klf9 CKO (Gli1+ RGls)

first: Amar

last: Sahay


title: miR-3607 controls Wnt/bCat pathway to regulate cerebral cortex development

city: San Joan d'Alacant

first: Jose

middle: P

last: Lopez-Atalaya

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias

country: Spain

institute: CSIC-UMH

summary: We report that miR3607 controls the embryonic cerebral cortex development by regulating neurogenesis, neuron migration and axon growth in a bCatenin signaling pathway dependent manner.

overall_design: To dissect the effects of miR3607 overexpression on gene expression profiles in cortical progenitors, we in utero electroporated cortices of brain embryos (E14.5) with miR3607-GFP or scrambled-GFP constructs. 24h after electroporation (E15.5), GFP positive cells were FACS sorted and mRNA expression profiles were analysed by RNA sequencing (RNA-seq).

first: Angel

last: Marquez-Galera

first: Kaviya

last: Chinnappa

first: Victor

last: Borrell


title: Transcriptomic analysis of the interaction between FLOWERING LOCUS T induction and photoperiodic signaling in response to spaceflight

city: Shanghai

first: 丽华

last: 王

state: 上海

address: 300 Fenglin Road

institute: Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS)

summary: Spaceflight has an impact on growth and development of higher plants at both vegetative stage and reproductive stage. A great deal of information has been available on the vegetative stage in space, but relatively little is known about the influence of spaceflight on plants at the reproductive stage. In this study, we constructed a transgenic Arabidopsis thaliana plants expressing flowering control gene, FLOWERING LOCUS T (FT), together with green fluorescent protein gene(GFP) under control of a heat shock-inducible promoter (HSP17.4), by which we induced FT expression inflight through remote controlling heating shock (HS) treatment. Inflight photography data showed that induction of FT expression in plants in space under short-day condition could eliminated the difference of stem length between spaceflight and ground control . Whole-genome microarray analysis of gene expression changes in leaves of wild-type and these transgenic plants grown under the long-day and short-day  photoperiod conditions in space indicated that the function of the photoperiod-related spaceflight responsive genes are mainly involved in protein synthesis and post-translation protein modulation, notably protein phosphorylation. In addition, changes of circadian component gene expression in response to spaceflight under different photoperiod indicated that roles of circadian oscillator could act as integrators of spaceflight response and photoperiodic signals in Arabidopsis plants grown in space.

overall_design: Arabidopsis thaliana Columbia (Col-0) ecotype was used as the wild-type (WT) and a transgenic plant expressing FLOWERING LOCUS T (FT) and the reporter gene green fluorescent protein (GFP) under control of a heat shock-inducible promoter (HSP17.4) (pHSP::FT, pHSP::GFP, FG) was constructed. Plants were germinated and grown under long-day (16h light /8h dark, LD) or the short-day (16 h dark/ 8h light, SD) for 20 days prior to flight, then transferred to plant culture box (PCB) flighted with Chinese SJ-10 satellite for 12 days and 15h (launch: 1:38, April 6, 2016; landing: 16:30, April 18, 2016) or keep on ground as control. Temperatures were 22±2°C, relative humidity was between 90% and 100%. The photosynthetically active photon flux density produced by LED lamps was 120 umol.m-2.s-1. Total RNA was extracted from rosette leaves of WT under LD (LW) and under SD (SW) and FG under LD(LG) and under SD (SG) in space (S) and on ground (C), respectively. Each treatment have four rosette leaves and two biological repeat (i.e. S4a, S4b, C4a and C4b).

first: Lihua

last: Wang

first: Junyan

last: Xie

first: Chenghong

last: Mou

first: Yuwei

last: Jiao

first: Yanhui

last: Dou

first: Huiqiong

last: Zheng


title: MicroRNA analyses of serum samples for early detection of colorectal cancers

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
MiRNA analyses of serum samples from 7 patients with colorectal cancers and 7 matched controls
MiRNAs were extracted from serum by using QIAGEN miRNeasy filter column

overall_design: MiRNA expression analyses based on matched case-control samples

first: Asahi

last: Hishida

first: Hiroya

last: Yamada


title: RNA-Seq of miR-29cb2 ko vs WT

first: Yun

last: Liao

address: Xianxia

institute: Shanghai Jiao Tong University School of Medicine

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived bone transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Bone mRNA profiles of 16-weeks old wild type (WT) and29cb2-/- mice

first: Xuanyong

last: Liu

first: Jun

last: Ma

first: Liping

last: Ouyang

first: Yingxiao

last: Sun

first: Dan

last: Lv

first: Xiaochun

last: Peng

first: Xiaoming

first: Lei

last: Ci

first: Guoning

last: Zhang

first: Bo

last: Yuan

first: Ling

last: Li

first: Jian

last: Fei


title: Next generation sequencing compares CNS-infiltrating CD4 cells versus draining lymph node effector CD4 cells in experimental autoimmune encephalomyelitis

status: Public on Jan 04 2022

first: Lifei

last: Hou

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: The immunology has been advanced mostly by studying peripheral blood in human and peripheral immune organ in mouse. However, a long standing problem in develop therapeutics treating autoimmune diseases is that we are short of knowledge about inflammatory-tissue infiltraing CD4 cells, which are terminally differentiated effector that exactly mediate the tissue damage. Thus, to address this issue, we induced experimental autoimmune encephalomyelitis (EAE) in mouse and sorted out both CNS infiltrating CD4 cells and draining lymph node effector CD4 cells at disease onset, and compared their transcriptome

overall_design: Cells were FACS-sort purified and subjected to RNA isolation, mRNA profiles were generated by deep sequencing, in duplicates

first: Eileen

last: Remold-O‘Donnell


title: The immunological comparison of control PDA tumors and Krt19-edited PDA tumors

city: Cold Spring Harbor

first: Ran

last: Yan

state: New York

address: 1 Bungtown Rd

institute: CSHL

summary: Our studies indicate that cancer cells of carcinomas are coated with CXCL12 chemokine in covalent conjugation with keratin-19 (KRT19). Murine pancreatic ductal adenocarcinomas (PDA) formed with Krt19-edited cancer cells lack the CXCL12-coating and are infiltrated with T cells, compared to tumors formed with control sgScramble PDA cells. To probe the immunological role of this CXCL12-coating thoroughly, bulk RNA sequencing of subcutaneous (s/c) murine sgScramble PDA tumors and Krt19-edited PDA tumors were conducted. As comparison, an immunogenic tumor model was also assessed. To do so, s/c sgScramble PDA tumors and PDA tumors formed with sgScramble cells exppressing doxcycline-inducible ovalbumin (icOVA) were harvested and processed for bulk RNA sequencing.

overall_design: sgScramble PDA tumors vs sgScramble-icOVA tumors

first: Zhikai

last: Wang

first: Douglas

last: Fearon


title: NFAM1 promotes pro-inflammatory cytokine production in mouse and human monocytes.

status: Public on Jan 03 2022

city: Ridgefield

first: Li

state: Connecticut

address: PO Box 368

institute: Boehringer Ingelheim Pharmaceuticals, Inc.

summary: NFAM1 is an ITAM bearing-transmembrane receptor. Based on overexpression studies, NFAM1 is reported to play a role in B cell signaling and development. We performed expression analysis of NFAM1 in publicly available gene expression data sets and discovered that NFAM1 expression is significantly induced in intestinal biopsies from Crohn’s disease (CD) and ulcerative colitis (UC) patients. At the cellular level, we observed high expression of NFAM1 in monocytes and neutrophils, in addition to expression in B and T cells.  To explore the role of NFAM1 in multiple immune cells and its potential role in IBD, we generated NFAM1-/- mice. Contrary to previous reports using NFAM1-transgenic mice, NFAM1-/- mice have no obvious defects in immune cell development, or in T cell-dependent or independent B cell responses. Interestingly, NFAM1-/- monocytes produce reduced levels of TNF-α in response to activation by multiple IBD-relevant stimuli, including CD40L, TLR ligands and MDP.  Collectively, these findings indicate that NFAM1 promotes pro-inflammatory monocyte development, thereby amplifying the response to diverse stimuli. These findings are not mouse-specific, as we found that deletion of NFAM1 in human monocytes also reduced expression of CD40L-induced CCL4.

overall_design: To better understand the impact of NFAM1 deletion of monocyte activation, monocytes isolated from human PBMCs were nucleofected with CRISPR ribonucleoprotein (RNP) complexes using an Amaxa 4D nucleofection system according to manufacturer’s instructions (Lonza). Knockout efficiency was assessed by western blot detection of NFAM1 protein or sanger sequencing of PCR amplified target genomic loci. We performed whole transcriptome analysis on monocytes that were cultured in the presence or absence of IFN-γ plus CD40L for 6 and 24 hours. NFAM1+/+ and NFAM1-/- monocytes were left unstimulated, or stimulated with IFN-γ plus 1 ug/mL MegaCD40L. 6 or 24 hours later, supernatant was removed, cells were resuspended in RNAlater, and RNA was isolated using an RNeasy Plus Mini kit. Library construction and sequencing were performed at Beijing Genomics Institute as follows. RNA was then fragmented and cDNA was synthesized using the Illumina Truseq polyA mRNA library preparation protocol (non-stranded). RNA-sequencing was performed on an Illumina HiSeq2000 sequencer to generate 101x2 pair-end reads.

first: Kathryn

last: Juchem


title: Knockdown of YBX1 impairs alternative splicing and maternal mRNA decay during pre-implantation development

status: Public on Jan 01 2022

city: Nanjing

first: Mingtian

last: Deng

state: Jiangsu

address: Weigang No.1

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

summary: In mammals, maternal gene products decay and zygotic genome activation (ZGA) onsets during maternal to zygotic transition (MZT). Y-box binding protein YBX1 plays vital roles in RNA stabilization and transcriptional regulation, but its roles in pre-implantation development remain to be elucidated. In the present study, we aim to investigate the role of YBX1 during goat MZT and further explore the molecular mechanisms. The expression of YBX1 was increased during MZT in goat, bovine, human, and mice. We successfully knocked down YBX1 by microinjection of siRNA against YBX1, and the embryo development was impaired when YBX1 was knocked down. Using RNA-seq, we identified 1623 up-regulated and 3531 down-regulated genes in the 8-cell stage YBX1 knockdown embryos. GO/KEGG/GSEA enrichment analysis revealed that the down-regulated genes were enriched in regulation of RNA/mRNA stability and spliceosome, suggesting that YBX1 might medicate pre-implantation development by alternative splicing and maternal mRNA decay. To this end, we identified 3284 differential alternative splicing events and 1322 differentially expressed maternal mRNAs at the 8-cell stage YBX1 knockdown embryos compared to the controls. Moreover, the splicing factors and mRNA decay related genes were aberrantly expressed. Lastly, knockdown of YBX1 impaired transcriptional activity during ZGA in goat and mice as revealed by 5-EU staining. Our results identify that YBX1 serves an important role in maternal mRNA decay, alternative splicing, and the transcriptional activity required for early embryogenesis, which will broaden the current understanding of YBX1 functions during the stochastic reprogramming events.

overall_design: In this study, the 8-cell stage YBX1 knockdown embryos and the controls was directly lysed for RNA-seq and immunofluorescence staining. Bioinformatic analysis was performed to identified differentially expressed genes and alternative splicing events.

first: Feng


title: Genome-wide distribution of ZHX3 in human fibroblast cells.

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

institute: Tokyo Women's Medical University

summary: ChIP-seq analysis of ZHX3 in IMR-90 cells. We found that ZHX3 is enriched at the promoter site of target genes.

overall_design: Examination of ZHX3-DNA interaction in IMR-90 cells in growing condition.

first: Tomoka

last: Igata

first: Mitsuyoshi

last: Nakao


title: YAP/TAZ drives cell proliferation and tumour growth via a polyamine-eIF5A hypusination-LSD1 axis (RNA-Seq)

city: Dallas

first: Hongde

state: Texas

address: 6001 Forest Park Road, Department of Physiology, ND13-510

institute: UT Southwestern Medical Center

summary: Here using mouse genetic models and human cancer cells, we show that YAP/TAZ reprogram polyamine metabolism to promote cell proliferation and tumor growth. Mechanistically, YAP/TAZ increases polyamine synthesis mainly through direct upregulation of the major rate-limiting enzyme ornithine decarboxylase 1. We further demonstrate that the polyamine spermidine sustains eukaryotic translation factor 5A (eIF5A) hypusination to support efficient translation of histone demethylase LSD1 that maintains a favored epigenetic status for YAP/TAZ-induced cell proliferation. Furthermore, inhibiting either polyamine synthesis or LSD1 can suppress YAP/TAZ-induced cell proliferation in mouse liver and human cancer cells. Thus our study identifies a YAP/TAZ-polyamine-eIF5A hypusination-LSD1 axis as required for YAP/TAZ-induced cell proliferation and tumor growth and suggests LSD1 as a critical target of polyamine in tumorigenesis.

overall_design: Examination of the transcriptional alterations caused by YAP/LSD1 in mouse livers.

first: Duojia

last: Pan


title: RNA sequencing of early extracellular vesicles derived from human monocytes in presence of C. albicans

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: 75 high abudance human miRNA were found to be transported by extracellular vesicles from human monocytes in presence of C. albicans

overall_design: Blood derived monocytes were incubated with C. albcians for 1 h, followed by isolation of extracellular vesicle and the cargo RNA. RNA from 8 donors were combined and sequenced

first: Luke

last: Halder

first: Christine

last: Skerka

middle: G


title: Human Nasal Epithelial Cells sustain persistent SARS-CoV-2 infection in vitro, despite eliciting a prolonged antiviral response.

city: Singapore

first: Wharton

middle: O Y

last: Chan

state: Singapore

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke-NUS Medical School

summary: Single Cell Sequencing of SARS-CoV2 Infected Human Nasal Epithelial Cells

overall_design: Uninfected, D3 and D28 post infection

first: Akshamal

last: Gamage

first: Kai

middle: S

last: Tan

middle: O

first: Zhe

middle: Z

last: Lew

first: De

first: Lin-Fa


title: Single-cell transcriptomics analysis of the tumor microenvironment from murine MC38 xenografts upon SHP099 treatment

first: Dijun

last: Chen

address: Xianlin

department: Life Sciences

institute: Nanjing University

summary: Colorectal cancer (CRC), a malignant tumor worldwide consists of microsatellite instability (MSI) and microsatellite stable (MSS) phenotypes. Although SHP2 is a potential target for cancer therapy, its relationship with innate immunosuppression remains elusive. To address that, single-cell RNA sequencing was performed to explore the role of SHP2 in all cell types of tumor microenvironment (TME) from murine MC38 xenografts.

overall_design: SHP2i-remodeled TME revealed by scRNA-seq

first: Yang

last: Sun

first: Jian

last: Gao

first: Zhigui

last: Wu


title: Functional characterization of the transcription programs underlying phase transition in the BSL3 pathogen Coccidioides immitis

city: La Jolla

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Coccidioidomycosis (Valley Fever) is an emerging endemic fungal infection with a rising incidence and an expanding geographic range. It is caused by Coccidiodes, which are thermally dimorphic fungi that grow as mycelia in soil but transition in the lung to form pathogenic spherules. The regulatory mechanisms underlying this transition are not understood. Exploiting capped small (cs)RNA-seq, which identifies   actively initiated stable and unstable transcripts and thereby detects acute changes in gene regulation with remarkable sensitivity, here we report the changes in architectural organization and key sequence features underlying phase transition of this highly pathogenic fungus. Spherule transition was accompanied by large-scale transcriptional reprogramming, functional changes in transcript isoforms, and a massive increase in promoter-distal transcription of ncRNAs. Analysis of spherule-activated regulatory elements revealed a motif predicted to recruit a WOPR family transcription factor, which are known regulators of virulence in other fungi.  We identify CIMG_02671 as a C. immitis WOPR homologue and show that it activates transcription in a WOPR motif-dependent manner, suggesting it is an important regulator of pathogenic phase transition. Collectively, this also highlights csRNA-seq as a powerful means to identify transcriptional mechanisms that control pathogenesis.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Agaricus bisporus
Coccidioides immitis

overall_design: Decoding Gene Regulatory Features of C. immitis phase transition

first: Sascha

middle: H

last: Duttke

first: Aaron

middle: F

last: Carlin


title: Mycobacterium leprae transcriptome during in vivo growth and ex vivo stationary phases.

city: Albany

first: Olabisi

last: Ojo

state: GA

address: 504 College Dr

department: Natural Sciences

institute: Albany State University

summary: Mycobacterium leprae, the causative agent of leprosy, an obligate intracellular pathogen has the ability to survive and grow for extended periods within phagocytes and Schwann cells. M. leprae genome analysis predicts a highly degraded genome resulting in a significant loss of its genomic coding capacity. Detailed dynamics of carbon sources for energy utilization and growth of M. leprae is unclear. This study, therefore, presents M. leprae transcriptome during in vivo growth and ex vivo stationary phases, and explores metabolic pathways relevant to its growth from global gene expression data. This report provides a glimpse of some of M. leprae nutritional requirements for growth, which most likely, needs to be supplemented, in an axenic growth media.

overall_design: RNA Sequencing of M. leprae invivo and and in axenic medium

first: Diana

last: Williams

first: Ramanuj

last: Lahiri


title: YAP/TAZ drives cell proliferation and tumour growth via a polyamine-eIF5A hypusination-LSD1 axis

first: Hongde

last: Li

overall_design: Examination of 2 different histone modifications and LSD1 binding site in mouse livers.

first: Mohammed

last: Kanchwala

first: Chao

last: Xing

first: Duojia

last: Pan


title: Integrative analysis of lncRNAs, mRNAs and miRNAs indicates the neurodevelopmental dysfunction in the hippocampus of gut microbiota-dysbiosis mice

status: Public on Dec 31 2021

city: Chongqing

first: Anna

last: Liu

address: 1 Youyi Road, Yuzhong Dist.

institute: Chongqing Medical University

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Integrative analysis of lncRNAs, mRNAs and miRNAs indicates the neurodevelopmental dysfunction in the hippocampus of gut microbiota-dysbiosis mice [lncRNA-mRNA]

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

summary: Major depressive disorder is caused by gene-environment interactions and the gut microbiota plays a pivotal role in the development of depression. However, the mechanisms by which the gut microbiota modulates depression remain elusive. Herein, we detected the differentially expressed hippocampal long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs) and microRNAs (miRNAs) between mice inoculated with gut microbiota from major depressive disorder patients or healthy controls, to identify the effects of gut microbiota-dysbiosis on gene regulation patterns at the transcriptome level. We also performed functional analysis to explore the microbial-regulated pathological mechanisms of depression. Two hundred mRNAs, 358 lncRNAs and 4 miRNAs were differentially expressed between the two groups. Functional analysis of these differentially expressed mRNAs indicated dysregulated inflammatory response to be the primary pathological change. Intersecting the differentially expressed mRNAs with targets of differentially expressed miRNAs identified 47 intersected mRNAs, which were mainly related to neurodevelopment. Additionally, we constructed a microbial-regulated lncRNA-miRNA-mRNA network based on RNA-RNA interactions. According to the competitive endogenous RNA hypothesis, two neurodevelopmental ceRNA sub-networks implicating in depression were identified. This study provides new understanding of the pathogenesis of depression induced by gut microbiota-dysbiosis and may act as a theoretical basis for the development of gut microbiota-based antidepressants.

overall_design: We performed lncRNA, mRNA and miRNA expression profiling in the hippocampus of mice that had been inoculated with “depression microbiota” (microbiota from fecal samples of MDD patients) or “healthy microbiota” (microbiota from fecal samples of healthy controls)

first: Lanxiang

first: Haiyang

last: Wang


title: Genome-wide maps of Tbx2-binding sites in mouse melanoma cells

city: Oxford

first: Sizhu

last: Lu

address: Old Road Campus Research Building (off Roosevelt Drive)

institute: Ludwig Institute for Cancer Research, Oxford branch

summary: We report the high-throughput profiling of Tbx2 binding sites in mouse melanoma B16 cells. We generated B16 clones that have endogenous Tbx2 tagged with 3xHA, and used HA antibody for immunoprecipitation. This study provides a high-quality genome-wide Tbx2 binding profile and helps further understand Tbx2 role in melanoma progression

overall_design: Examination of Tbx2 binding sites in 2 clones of B16-Tbx2-3xHA.

first: Colin

last: Goding

first: Pakavarin

last: Louphrasitthiphol


title: RNA sequencing in 12-week old orbital frontal cortex in circHomer1/Homer1b knockdown and control mice

city: Albuquerque

first: Nikolaos

last: Mellios

state: NM

address: 915 Camino De Salud NE

department: Neuroscience

institute: University of New Mexico

summary: These are RNA sequencing data from 12 week old orbital frontal cortex from mice who received a shRNA targeting circHomer1 and Homer1b (double knockdown) or control shRNA (scramble)

overall_design: Examination of mRNA expression in 4 circHomer1/Homer1b knockdown and 4 control samples

first: Mellios

last: Nikolaos


title: Drosophila photoreceptor transcriptome landscape upon disruption of Clock activity [Rh1-ClkDN_RNA]

city: West Lafayette

first: Vikki

middle: M

last: Weake

state: Indiana

address: 175 S University St

department: Biochemistry

institute: Purdue University

summary: We report the transcriptome landscape of Drosophila photoreceptor neurons obtained using a tissue-specific approach at different time points after eclosion upon expression of a Clock dominant negative mutant

overall_design: Photoreceptor neuron-specific transcritpome profiling at day 2 and 10

first: Juan

last: Jauregui-Lozano


title: Integrative analysis of lncRNAs, mRNAs and miRNAs indicates the neurodevelopmental dysfunction in the hippocampus of gut microbiota-dysbiosis mice [miRNA]

overall_design: we performed lncRNA, mRNA and miRNA expression profiling in the hippocampus of mice that had been inoculated with “depression microbiota” (microbiota from fecal samples of MDD patients) or “healthy microbiota” (microbiota from fecal samples of healthy controls)


title: Drosophila photoreceptor chromatin accessibility landscape upon disruption of Clock activity [ClkATACseq]

summary: We report the chromatin accessibility landscape of Drosophila photoreceptor neurons obtained using a tissue-specific approach at different time points after eclosion upon expression of a Clock dominant negative mutant

overall_design: Photoreceptor neuron-specific chromatin accessibility profiling at day 2 and 10


title: Reciprocal epigenetic remodeling mediated by polycomb and DNMT3B control testicular cancer hypersensitivity and resistance to 5-aza and cisplatin

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

summary: We undertook a pharmacogenomic approach in order to better understand mechanisms of hypomethylating agent hypersensitivity of TGCTs by generating a panel of acquired 5-aza resistant TGCT cells and contrasting these to previously generated acquired cisplatin resistance cells from the same parent.  Interestingly, there was a reciprocal relationship between cisplatin and 5-aza sensitivity, with cisplatin resistance associated with increased sensitivity to 5-aza and 5-aza resistance associated with increased sensitivity to cisplatin.  Unbiased transcriptome analysis revealed 5-aza resistant cells strongly downregulated polycomb target gene expression, the exact opposite of the finding for cisplatin resistant cells which upregulated polycomb target genes. This was associate with a dramatic increase in H3K27me3 and substantial decrease in DNMT3B levels in 5-aza resistant cells, the exact opposite changes seen in cisplatin resistant cells.

overall_design: gene expression of parental and Aza resistant cell lines in biological triplicate were analysed

first: Zeeshan

last: Fazal


title: Reciprocal epigenetic remodeling mediated by polycomb and DNMT3B control testicular cancer hypersensitivity and resistance to 5-aza and cisplatin [DNMT3B Knockdown]

overall_design: gene expression of DNMT3B and control knockdown in cells derived from  2102EP


title: 3'mRNA sequencing of hepatic RNA (MACE) at the time points 24h/48h after acetaminophen (APAP) (300mg/kg) administration

city: Frankfurt

first: Malte

last: Bachmann

address: Theodor Stern Kai 7

department: General Pharmacology

institute: University Hospital Frankfurt

summary: Hepatic RNA specimens from mice (C57BL/6) of the 4 groups (vehicle-treated at 24h/48h, n=6; acetaminophen (APAP)-treated (300mg/kg) at 24h/48h, n=7) were pooled at equal shares. Thereafter, pooled RNA underwent analysis by 3'mRNA sequencing (MACE, GenXPro, Frankurt, Germany).

overall_design: Examination of acetaminophen (APAP) induced liver injury at two timepoints

first: Sina

last: Gonther

first: Heiko

last: Mühl


title: Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation

first: Tatjana

last: Sauka-spengler

address: Headley Way, Headington

department: Radcliffe Dept of Medicine

institute: University of Oxford

summary: The epiblast of vertebrate embryos is comprised of neural and non-neural ectoderm, with the border territory at their intersection harbouring neural crest and cranial placode progenitors. Here we profile avian epiblast cells as a function of time using single-cell RNA-seq to define transcriptional changes in the emerging ‘neural plate border’. The results reveal gradual establishment of heterogeneous neural plate border signatures, including novel genes that we validate by fluorescent in situ hybridization. Developmental trajectory analysis shows that segregation of neural plate border lineages only commences at early neurulation, rather than at gastrulation as previously predicted. We find that cells expressing the prospective neural crest marker Pax7 contribute to multiple lineages, and a subset of premigratory neural crest cells shares a transcriptional signature with their border precursors. Together, our results suggest that cells at the neural plate border remain heterogeneous until early neurulation, at which time progenitors become progressively allocated toward defined lineages.

overall_design: 10X based single-cell RNA-seq across multiple timepoints of early chick embryo development

first: Ruth

last: Williams

first: Martyna

last: Lukoseviciute

last: Sauka-Spengler

first: Marianne

last: Bronner


title: The volume regulated anion channel LRRC8C suppresses T cell function by regulating cyclic dinucleotide transport and STING-p53 signaling

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: The volume-regulated anion channel (VRAC) is a hexameric complex formed by LRRC8 proteins. VRACs are responsible for the regulatory volume decrease (RVD) after hypotonic cell swelling by mediating the efflux of chloride. Besides chloride, LRRC8 proteins transport other molecules including immunomodulatory cyclic dinucleotides (CDNs) such as 2’3’cGAMP. Here we identify LRRC8C as a critical component of VRACs in T cells, where its deletion abolishes VRAC currents and RVD. We find that LRRC8C mediates the transport of 2’3’cGAMP in T cells. T cells of Lrrc8c-/- mice have increased cell cycle progression, proliferation, survival, Ca2+ influx and cytokine production in vitro and enhanced T cell mediated immunity in vivo. We used RNA sequencing of CD4+ T cells from wild-type (WT) and Lrrc8c-/- mice to determine the effects of impaired cGAMP signaling in T cells. T cells of Lrrc8c-/- mice had impaired p53 signaling which was associated with decreased p53 expression. We found that uptake of 2’3’cGAMP and other CDNs via LRRC8C results in STING activation and p53 accumulation. Inhibition of STING in WT T cells recapitulates the phenotype of LRRC8C-deficient T cells whereas overexpression of p53 inhibits enhanced T cell function in the absence of LRRC8C. These findings establish cGAMP uptake through LRRC8C and subsequent STING-p53 signaling as a novel inhibitory signaling pathway in T cells and adaptive immunity.

overall_design: Purified CD4+ T cells from WT and Lrrc8c-/- mice were isolated from the spleen and left unstimulated or stimulated with plate-bound anti-CD3 and anti-CD28 antibodies in 12-well plates for 24h and 48h. Additionally, WT CD4+ T cells were stimulated in the presence of 20 micromolar DCPIB (VRAC inhibitor). A total of 24 samples were analyzed by RNASeq.

first: Axel

last: Concepcion

first: Stefan

last: Feske


title: Gene expression in human recurrent glioblastoma before and after inoculation with the oncolytic herpes simplex virus G207

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital


title: Gene expression in human recurrent glioblastoma before and after inoculation with the oncolytic herpes simplex virus G207 using NanoString pancancer immune profiling gene expression panel

summary: We have previously developed the use of genetically engineered herpes simplex virus type 1 (G207) for the experimental treatment of malignant glioma (PMID: 18957964). We demonstrated that G207 propagates in and kills nervous system tumor cells with little to no evidence of viral encephalitis. Here, six adult patients with recurrent glioblastoma  were recruited onto a phase 1b clinical trial to test safety and efficacy of G207 in anti-tumor response. We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to gene expression profiling using NanoString Pancancer Immune panel. Our data indicate in the post-G207 samples that interferon immune response and the subsequent recruitment of an adaptive immune response strongly associated with overall survival after inoculation with oncolytic virus G207 in patients with recurrent malignant glioma.

overall_design: Gene expression panel analysis of recurrent glioblastoma before and after inoculation with oncolytic herpes simplex virus G207

first: James

last: Markert

first: Kevin

middle: A

last: Cassady

first: Elaine

last: Mardis


title: RNA-sequencing of human glioblastoma resected tissue before and after inoculation with G207, an oncolytic herpes simplex virus; tissues from a Phase Ib clinical trial

summary: We have previously developed the use of genetically engineered herpes simplex virus type 1 ("G207") for the experimental treatment of malignant glioma (PMID: 18957964). We demonstrated that G207 propagates in and kills nervous system tumor cells with little to no evidence of viral encephalitis. Here, six adult patients with recurrent glioblastoma were recruited onto a phase Ib clinical trial to test G207 safety and efficacy in anti-tumor response. We obtained resected tumor tissue before and after (within 2-5 days) inoculation with G207. RNA was extracted from all tissues and subject to library preparation for RNA sequencing on Illumina instrumentation.

overall_design: Gene expression analysis of recurrent glioblastoma before and after inoculation with oncolytic herpes simplex virus G207.


title: Gene-expression profiling on a HPV-related head and neck cancer patient with idiopathic CD4 lymphocytopenia and complete remission to checkpoint inhibitors

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: PD-L1 immunohistochemical staining has been not always enough reliable to accurately predict the response to immunotherapy; thus, and other biomarkers are required. In this context qualitative and quantitative multiparametric analyses seems promising. Data on the activity of nivolumab in challenging populations (e.g patients with autoimmune disorders; post-organ transplant; chronic viral infections; ongoing immunosuppressant use; elderly) are scant, mainly due to their underrepresentation in clinical trials. Nonetheless, it has been demonstrated that the use of ICI is safe and effective in HIV oncologic patients. Herein, we analyzed a metastatic HNSCC patient with an idiopathic CD4 lymphocytopenia who, after a recovery from a progressive multifocal leukoencephalopaty received 10 courses of nivolumab and obtained a complete remission maintaining  the response  two years after PD-1 blockade withdrawn.

overall_design: A 64 year-old man, active smoker, was referred to the Fondazione IRCCS Istituto Nazionale Tumori (Milan, Italy).  A contrast head and neck MRI demonstrated a large lesion of the right infratemporal fossa.  Fine needle aspiration biopsy of the largest neck node (25 mm) demonstrated a poorly differentiated carcinoma. Tumor was staged as an oropharynx cancer, p16 positive, high-risk HPV-DNA positive, cT4 N1 according to AJCC VIII classification. Immunohistochemical analysis showed high PD-L1 expression both in tumour cells (40%) and  infiltrating cells (20%) with a CPS of 60. Moreover, we observed an enrichment (80%) of tumor-infiltrating lymphocytes (TILs). RNA was extracted from 10 frozen blood buffycoat (QIAGEN RNeasy Lipid Tissue Mini Kik,Qiagen): 5 samples were collected from the “case” patient; 5 samples were collected from 5 HNSCC patients tumor-free after first line treatment, used as “controls”.


title: Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation [H2AK9ac ChIP-seq]

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Histone proteolysis is a poorly understood phenomena by which the N-terminal tail of histones are irreversible cleaved by intracellular proteases. During development histone PTMs are known orchestrate gene expression and ultimately cell fate decision, therefore it will be key to decipher underlying mechanisms that lead to proteolysis during cellular differentiation. Previous reports have found that histone H2A is cleaved at the C-terminus, and here we found that the N-terminal is also proteolytically clipped and removed by the lysosomal protease Cathepsin L. Using quantitative mass spectrometry (MS), we identified L23 to be the primary site for this protease, with this clipped H2A (cH2A) form representing ~1% of the total H2A reaching a maximum after 4 days of differentiation. Using Chip-seq, we found reduced proteolysis, lead to increase acetylated H2A at promoter regions in differentiated ES cells.  We also report novel readers of acetylated H2A during in pluripotency as we identified members of the pBAF complex to recognize different forms of H2A acetylation. Moreover, our data showed that this recognition is abolished upon proteolysis. All in, our data suggest that proteolysis serve as a quick mechanism to silence genes involve in pluripotency and destabilize the nucleosome core particle as indicated by protein degradation studies.

overall_design: H2AK9ac ChIP-seq in mESCs differentiation with CTSL KD.

first: Mariel

last: Coradin

first: Benjamin

last: Garcia


title: Differential gene expression of intermittent compressive force treated mouse gingival fibrpblast derived induced pluripiotent stem cells

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

summary: Mechanical force regulates various biological responses in many cell types. Here, the retinoic acid treated mouse gingival fibroblast derived induced pluripotent stem cells were treated with intermittent compressive for 24 h and gene expression profiling was evaluated using RNA sequencing technique. Results indicated that intermittent compressive stress regulated various pathways in these cells including p53 signaling and other metabolic pathways.

overall_design: Mouse gingival fibroblast derived induced pluripotent stem cells were cultured in low attachment plate to form embryoid bodies and subsequently treated with retinoic acid. Retinoic acid treated embryoid bodies were then transfer to gelatin coated dishes. The intermittent compressive stress was treated in serum free culture condition with 1.5 g/cm2 with the loading frequency of 0.23 Hz. Total RNA was collected at 24 h after loading and prepared for gene expression analysis using RNA sequencing technique.

first: Jeeranan

last: Manokawinchoke

first: Prasit

last: Pavasant

first: Hiroshi

last: Egusa


title: Oncogenic HPV E7 promotes the expression of a long noncoding RNA lnc-FANCI-2 via YY1 and miR-29a

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

summary: Long noncoding RNAs (lncRNA) play diverse roles in biological processes, but their expression profiles and functions in cervical carcinogenesis remains unknown. By RNA-seq analyses of 18 clinical samples and validated by RT-qPCR analyses of 72 clinical samples, we provide the first evidence in this report that 194 lncRNAs are differentially regulated by high-risk HPV infection along with cervical lesion progression. One such lncRNA, lnc-FANCI-2, induced by high-risk HPV infection was carefully analyzed because it is expressed from the same chr 15q26.1 region of FANCI gene encoding an important DNA repair factor. We found a mutual regulation of lnc-FANCI-2 and FANCI in cervical cancer cells and high-risk E6 and mainly E7 for this upregulation independent of p53 and pRb/E2F1. In HPV16-positive CaSki cells, lnc-FANCI-2, primarily in the cytoplasm in ~10 copies per cell, is transcribed from two alternative promoters and polyadenylated at two alternative poly(A) sites. Alternative RNA splicing of lnc-FANCI-2 transcripts leads to produce 14 detectable RNA isoforms. YY1 interacts with viral E7 and transactivates the transcription by binding to two YY1-binding motifs in the lnc-FANCI-2 promoter. Knockdown of either YY1 or E7 expression led to significant reduction of lnc-FANCI-2 expression. The 3’ untranslational region of YY-1 RNA contains a consensus seed match to miR-29a and is sensitive to miR-29a-mediated inhibition of YY1 expression. High-risk HPV infections were found to induce YY1 expression in HPV18-infected HFKs by reduction of host miR-29a expression. Together, our data have provided novel insights into mechanisms of how high-risk HPVs contribute to cervical carcinogenesis.

overall_design: LncRNA expression patterns of cervical tissues were compared between normal, CIN 2-3 and cancer tissues by two different RNA-seq platforms. Additional 72 clinical samples and HPV-infected keratinocytes were analyzed by RT-qPCR to verify the HPV-infection altered gene expression.

first: Haibin

last: Liu

first: Junfen

last: Xu

first: Xiaohong

last: Wang

first: Ethan

last: Wu

first: Vladimir

last: Majerciak

first: Renske

last: Steenbergen

first: Hsu-Kun

first: Nilam

last: Banerjee

first: Yang

last: Li

first: Weiguo

last: Lu

first: Craig

last: Meyers

first: Jun

last: Zhu

first: Xing

last: Xie

first: Louise

last: Chow

first: Zhi-Ming

last: Zheng


title: ATAD3A has a scaffolding role regulating mitochondria inner membrane structure and protein assembly

status: Public on Dec 30 2021

city: Miami

first: Tania

last: Arguello

state: Florida

address: 1420 NW 9TH AVE

department: Neurology

institute: University of Miami

summary: The ATPase Family AAA Domain Containing 3A (ATAD3A) is a mitochondrial inner membrane protein conserved in metazoans. ATAD3A has been associated with several mitochondrial functions, including nucleoid organization, cholesterol metabolism, and mitochondrial translation. To address its primary role, we generated a neuronal-specific conditional knockout (Atad3 nKO) mouse model, which developed a severe encephalopathy by 5 months of age. Pre-symptomatic mice showed aberrant mitochondrial cristae morphogenesis in the cortex as early as 2 months. Using a multi-omics approach in the CNS of 2-3-month-old mice, we found early alterations in the organelle membrane structure. We also showed that human ATAD3A associates with different components of the inner membrane, including: OXPHOS complex I, Letm1 and prohibitin complexes. Stochastic Optical Reconstruction Microscopy (STORM) showed that ATAD3A is regularly distributed along the inner mitochondrial membrane, suggesting a critical structural role in inner mitochondrial membrane and its organization, most likely in an ATPase-dependent manner.

overall_design: Total RNA from cortex tissues of 2.5-month-old Atad3 nKO male mice and control littermates (5 biological replates per group).


title: Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define growth physiology

city: Uppsala

first: Ankita

last: Pal

address: Husargatan 3

department: Medical Biochemistry and Microbiology

institute: Uppsala University

summary: We report high-throughput RNA sequencing of Δcrp and five adaptively evolved mutants of Δcrp in the batch exponential phase, IG116-Δcrp in batch exponential phase and  Δcrp and two adaptively evolved mutants of Δcrp in chemostat cultivations

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA was extracted from two biological replicates of WT, Δcrp , five adaptively evolved mutants of Δcrp and IG116- Δcrp in the batch exponential phase grown in glucose minimal media conditions. For glucose-limited chemostat cultivations, RNA was extracted from two biological replicates of WT, Δcrp , two adaptively evolved mutants of Δcrp after 3-5 residence times at steady state. RNA sequencing was done using Illumina Hi-Seq 2500 (Rapid Mode) platform.

first: Mahesh

last: Iyer

first: Sumana

last: Srinivasan

first: Aswin

last: Seshasayee

first: K

middle: V

last: Venkatesh


title: High throughput characterization of human glioblastoma multiforme cell response to Type 1 interferons

status: Public on Dec 29 2021

city: Moscow

first: Irina

last: Tarasova

address: Pogodinskaya 10-8

country: Russia

institute: Orekhovich Institute of Biomedical Chemistry

summary: Oncolytic virus therapy is a promising direction for cancer treatment. Numerous oncolytic viruses are under development or examined in clinical trials, there are examples of FDA approved virus vaccines. Although evident progress exists, oncolytic viruses still suffer low efficiency and the mechanisms of their action remain poorly understood. Defects in antiviral mechanisms that include type I interferon (IFN) signaling, contribute to sensitivity of malignant cells to oncolytic viruses, however, this sensitivity significantly differs for different malignant cells. In this project, we present a collection of representative transcriptomics and proteomics data for primary glioblastoma multiforme (GBM) cell cultures with established sensitivity to type I IFNs and the comprehensive characterization of GBM responses at both protein and RNA levels. Analysis demonstrated that GBM cells can respond to treatment by extreme upregulation of IFN-induced genes that is very similar to classic response in normal human cells. GBM cultures can significantly differ from each other by a value of transcriptome and proteome changes that are well correlated with sensitivity tests. In our data, upregulation of IFIT1/2/3, OAS1/2/3/L, MX1/2 among the others, was a reproducible marker for the developed resistance of GBM cells to vesicular stomatitis virus (VSV).

overall_design:
Primary cell cultures derived from adult glioblastoma multiforme were treated with IFN α-2b and compared to the untreated controls.
*** Submitter declares that raw data are irretrievably lost.

first: Anastasia

last: Lipatova

first: Alesya

last: Soboleva

first: Vladimir

last: Gorshkov

first: Julia

last: Bubis

first: Elizaveta

last: Solovyeva

first: Dmitry

last: Kochetkov

first: Pavel

last: Vorobyev

first: Sergey

last: Moshkovskii

first: Frank

last: Kjeldsen

first: Mikhail

first: Peter

last: Chumakov


title: RNA-Seq in retinoblastoma 1 (RB1) knock out IMR-90 cells

city: Stanford

first: Ashby

middle: J

last: Morrison

state: CA

address: 371 Serra Mall Gilbert Bldg, Room 326

department: Biology

institute: Stanford University

summary: Total RNA-seq with rRNA depletion in retinoblastoma protein 1 knockout (RB1 KO) IMR-90

overall_design: Isolation of total RNA, followed by rRNA depletion and library preparation.

first: Ka

last: Wong


title: ChIP-Seq, CPD-Seq and RNA-Seq in retinoblastoma 1 (RB1) knock out cells

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

overall_design: Refer to individual Series


title: Single-cell resolution of MET- and EMT-like programs in osteoblasts during zebrafish fin regeneration

status: Public on Dec 27 2021

city: Seattle

first: Weishene

middle: Joyce

last: Tang

address: 850 Republican Street

department: Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine

institute: University of Washington

summary: We performed single-cell RNA-sequencing (scRNA-seq) to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with epithelial-to-mesenchymal transition (EMT) and its reverse, mesenchymal-to-epithelial transition (MET). Trajectory analyses indicate osteoblastic cells solely expressed EMT components, or transiently expressed components for MET before EMT. We provide evidence that the EMT markers cdh11 and twist2 are co-expressed in dedifferentiating cells at the amputation stump, and in differentiating osteoblastic cells in the regenerate, the latter of which are enriched in EMT signatures. We also show that esrp1, a regulator of alternative splicing in epithelial cells that is associated with MET, is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration, and supports the contribution of MET- and EMT-associated components to this process.

overall_design: Single-cell RNA profiling of regenerating zebrafish caudal fin tissue at multiple timepoints using sci-RNA-seq3

first: W

first: Claire

last: Watson

first: Theresa

last: Olmstead

first: Christopher

last: Allan

first: Ronald

middle: Y

last: Kwon


title: Necrotic debris and STING exert therapeutically relevant effects on tumor cholesterol homeostasis

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

summary: Necrosis is a common feature of most solid malignant tumors and a major consequence of chemotherapy. The debris released by necrotic cells includes many damage/danger-associated molecular patterns (DAMPs) that stimulate cell surface and intracellular pattern recognition receptors (PRRs) activation. Treatment of Ewing’s sarcoma with conventional chemotherapy has reached a plateau in efficacy. The inability to target the fusion protein responsible for its pathogenesis warrants the quest for alternative therapeutic strategies. We have shown that DAMPs released by necrotic cells can stimulate the growth of EwS cells cultured in 3D and that of the related tumors in vivo. In stark contrast, we observed that STING, a signaling platform that responds to nucleic acids released from damaged nuclei, opposed the effect of DAMPs on EwS cell growth in vitro and tumor growth in vivo, maintaining cholesterol homeostasis. Our observations suggest that STING activation in conjunction with cholesterol-reducing agents may offer an unsuspected approach to control EwS growth.

overall_design: Total Two samples of primary Ewing sarcomas, plus A673 cell line in spherogenic and adherent cultures: cGAMP, shRNA, DAMPs treatments.

first: Sampath

middle: K

last: Katakam

first: Ivan

last: Stamenkovic

first: Santosh

last: Anand


title: Translational profiling of zebrafish retina cells using translating ribosome affinity purification methods

city: Sevilla

first: Jorge

last: Corbacho

address: Universidad Pablo de Olavide. Ctra. de Utrera Km.1

institute: CABD

summary: Translating ribosome affinity purification (TRAP) methods allow cell-specific recovery of polyribosome-associated RNAs by genetic tagging of ribosomes in selected cell populations. In this study, we purified and analysed the polyribosome-associated RNA fraction of zebrafish embryo´s retinas at 22 hours post-fertilization. To this aim, we generated a transgenic strain in which the tagged ribosomes expression is restricted to the retina cells due to the activity of a specific promoter.

overall_design: Analysis of ribosome-associated mRNAs in zebrafish retina cells

first: Estefanía

last: Sanabria-Reinoso

first: Lorena

last: Buono

first: Ana

last: Fernández-Miñán

first: Juan-Ramón

last: Morales


title: Expression data from HUVEC treated with combinations of IL-1 plus P. santalinus extract

status: Public on Dec 28 2021

city: Vienna

first: Rainer

last: de Martin

address: Schwarzspanierstr. 17

department: Vascular Biology

country: Austria

institute: Medical University of Vienna

summary:
HUVEC respond to pro-inflammatory stimuli such as IL-1 by expressing several hundreds of genes including cytokines, chemokines, cell adhesion molecules, and those involved in coagulation, survival/apoptosis, and metabolism.
Extract of P. santalinus inhibited the expression of certain genes, while leaving other unaffected; therby a set of responsive and non-responsive genes could be defined, to be further analyzed by bioinformatics.

overall_design: Post-confluent HUVEC were pre-treated with 50micrograms/mL of P. santalinus extract, then stimulated with 5 ng/mL IL-1 for 2 hours, mRNA analyzed by Clariom S arrays.

first: Priscilla

last: Natalia


title: Nanostring ncounter NHP Immunology V2 panel

status: Public on Dec 25 2021

city: Chapel Hill

first: Kristina

last: De Paris

state: North Carolina

address: Mary Ellen Jones Building , 116 manning Drive

department: Department of Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

summary: The gene expression analysis of the RNA samples were analyzed with NanoString Non Human Primate immunology panel comprised of 754 immune related gene

overall_design: The study compared the RNA expression profile of a 3M-052-SE adjuvanted HIV Env protein to a regimen combining the adjuvanted ENV protein with simulataneous administration of Modified Vaccinia Ankara virus

first: Kristin

last: DeParis


title: H3K9me3 and H3K27me3 ChIP-Seq in retinoblastoma 1 (RB1) knock out cells

first: Ashby

last: Morrison

summary: Comparative analysis of H3K9me3 and H3K27me3 in RB1 KO and wild type IMR-90 cells

overall_design: Examination of 2 histone modifications in RB1 KO and wild type IMR-90 cells

first: Ka

last: Wong