title: Estrogenic activity of fermented soymilk extracts and soy compounds

city: Fukuoka

first: Kentaro

last: Nishi

address: 2-3-1 Matsukadai Higashi-ku

department: Life Science

country: Japan

institute: Kyushu sangyo university

summary: To understand the complex mechanism of estrogen action, multiple assays based on different biological principles is important. Here, multiple assays based on cell, protein and transcription assays were used to evaluate estrogenic activity of soymilk extracts before and after fermentation, and four soy compounds, genistein and daidzein, and their glycosides, genistin and daidzin, respectively. The data obtained by a transcription assay, RNA-sequencing (RNA-seq), was further examined by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis to understand cell functions, i.e. biological processes and metabolic pathways. Among the cell functions identified, the sets of genes for cell division/cell cycle and DNA replication/DNA repair are significantly up-regulated, whereas those for autophagy are significantly down-regulated, which explains well the enhanced activity of cell proliferation by these materials. The applications of estrogenic activity of soymilk extracts and soy flavonoids, and the contribution of fermentation, include pharmacological benefits, such as bone protection/bone regeneration, cancer chemoprevention, neuroprotection and the treatment of menopausal syndromes.

overall_design: MCF-7 cells at a density of 1.0×106 cells per well were cultured in RPMI1640 supplemented with 10% DCC-FBS for 3 days under the  conditions of 37°C in 5% CO2. The cells were treated in RPMI1640 supplemented with 10 nM E2, 10 µg/ml unfermented soymilk extracts (Yellow or Black Soybean), 10 µg/ml fermented soymilk extracts (Yellow or Black Soybean), 10 µM genistin, 10 µM genistein, 10 µM daidzin, 10 µM daidzein or 0.1% DMSO (vehicle)  for 3 more days.

first: Ikumi

last: Imamura

first: Takuya

last: Takemoto

first: Kazuhiro

last: Iga

first: Ryoiti

last: Kiyama


title: Differentially expressed mRNA in biological premature ovarian insufficiency (bPOI)

status: Public on Oct 31 2023

city: Shanghai

first: Liu

last: Dan

address: 2699 Gaoke West Road, Pudong District

country: China

institute: Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University

type: Expression profiling by high throughput sequencing

summary:
The aim of this study is to identify the expression profile of mRNA in granulosa cells of POI
We performed gene expression profiling analysis using data obtained from RNA-seq of the GCs in 6 POI patients and 5 control patients.This study provides a better understanding of molecular mechanism of POI and identifies the possible biomarkers of POI.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of GCs from 6 POI patients and 5 control patients.

first: Dan

last: Liu

first: Kunming

last: Li


title: Gene expression data in MIO-M1-CTG(648) and MIO-MI-CTG(0) cells before and after doxycycline induction.

city: Mexico City

first: Oscar

last: Hernández-Hernández

state: Mexico City

address: Calz. México Xochimilco 289

department: Genetics

country: Mexico

institute: Instituto Nacional de Rehabilitación

summary:
Myotonic dystrophy type 1 (DM1), the most frequent inherited muscular dystrophy in adults, is caused by the CTG repeat expansion in the 3’UTR of the DMPK gene. Mutant DMPK RNA accumulates in nuclear foci altering diverse cellular functions including alternative splicing regulation. DM1 is a multisystemic condition, with debilitating central nervous system alterations. Although a defective neuroglia communication has been described as a contributor of the brain pathology in DM1, the specific cellular and molecular events potentially affected in glia cells have not been totally recognized. Thus, to study the effects of DM1 mutation on glial physiology, in this work we have established an inducible DM1 model derived from the MIO-M1 cell line expressing 648 CUG repeats. This new model recreated the molecular hallmarks of DM1 elicited by a toxic RNA gain-of-function mechanism: accumulation of RNA foci colocalized with MBNL proteins and dysregulation of alternative splicing. By applying a microarray whole-transcriptome approach, we identified several gene changes associated with DM1 mutation in MIO-M1 cells, including the immune mediators CXCL10, CCL5, CXCL8, TNFAIP3, and TNFRSF9, as well as the microRNAs miR-222, miR-448, among others, as potential regulators. A gene ontology enrichment analyses revealed that inflammation and immune response emerged as major cellular deregulated processes in the MIO-M1 DM1 cells. Our findings indicate the involvement of an altered immune response in glia cells, opening new windows for the study of glia as potential contributor of the CNS symptoms in DM1.
In this dataset, we include the expression data obtained from MIO-M1-CTG(648) and MIO-M1-CTG(0) with and witouth Doxycycline treatment (1µg/ml) by 8 days . These data are used to obtain genes that are differentially expressed in response to mutant (CUG expanded) DMPK RNA expression.

overall_design: 12 Total samples were analyzed. 3 Biological replicates were used for each of the following condition: MIO-M1-CTG(0) in the absence of Dox, MIO-M1-CTG(0) in the presence of Dox, MIO-M1-CTG(648) in the absence of Dox and, MIO-M1-CTG(648) in the presence of Dox. We determined the gene expression differences between Dox-induced MIO-M1-CTG(648) and non-induced MIO-M1-CTG(648) cells (contrast A). To do that, we first compared the gene expression profile between MIO-M1-CTG(0) Dox-treated cells and MIO-M1-CTG(0) non-induced cells, in order to remove those genes dysregulated by the Dox treatment.  In parallel, a second contrast (Contrast B) was analyzed. In this case we compared the transcriptome of Dox-induced MIO-M1-CTG(648) cells versus that of Dox-induced MIO-M1-CTG(0) cells. Gene changes derived from gene insertion site were first identified contrasting gene profiles of MIO-M1-CTG(648) vs MIO-M1-CTG(0) both non-induced (-Dox) cells, and subsequently discharged from this data set .Contrast A led us to identify 316 differentially expressed genes, while contrast B 790. A total of 111 differential expressed genes were overlapped in both contrasts A and B. Differentially expressed genes were considered as log fold change (FC) >0.5 and P val < 0.005

first: Cuauhtli

middle: N

last: Azotla-Vilchis

first: Daniel

last: Sanchez-Celis

first: Luis

middle: E

last: Agonizantes-Juárez

first: Rocío

last: Suárez-Sánchez

first: J

middle: M

first: Jorge

last: Peña

first: Karla

last: Vázquez-Santillán

first: Norberto

last: Leyva-García

first: Arturo

last: Ortega

first: Vilma

last: Maldonado

first: Claudia

last: Rangel

first: Jonathan

middle: J

last: Magaña

first: Bulmaro

last: Cisneros


title: Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding

status: Public on Oct 30 2023

city: Grand Forks

first: Sergei

last: Nechaev

state: North Dakota

address: Columbia Hall Room 1733c, 501 North Columbia Road Stop 9061

department: Biomedical Sciences

country: USA

institute: University of North Dakota

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background.  The Heat Shock Response (HSR) is an evolutionarily conserved mechanism that helps cells adapt to environmental stresses. Heat Shock Factor 1 (HSF1) is a master HSR transcription factor that is long known to bind at promoters of its target HSP genes to rapidly activate their transcription. However, recent genome-wide studies revealed HSF1 binding at thousands of sites outside of heat-shock responsive gene promoters, implying a broader role of HSF1 in HSR.   Results.  We asked how the widespread HSF1 binding is established and to what extent it may be related to transcription activation. To answer these questions, we examined responses of two different human cancer cell lines to two stimuli that induce HSR, exposure to 42C and inorganic arsenic at the ambient temperature, by manually integrating ChIP-sequencing against HSF1, RNA Pol II, H3K4Me3 with nascent RNA- and ATAC-sequencing datasets in cells before and during HSR induced by these two stimuli. We show that widespread HSF1 binding is a temperature-agnostic hallmark of HSR whose genome-wide patterns combine cell type specificity with robustness to the nature of a stimulus and magnitude of activation. Mechanistically, HSR involves amplification of pre-existing low level HSF1 binding with few changes in accessible chromatin. HSF1 binding patterns show more stability than transcriptionally activated genes both between conditions and between cell lines.  Conclusions.  Comparing responses of distant cell lines to two HSR-inducing stimuli allowed us to define several features of HSR. Genome-wide HSF1 binding is a sensitive readout of HSR whose genome-wide patterns retain cell type identity across a broad dynamic range. The pre-existing genomic architecture is retained during HSR down to individual loci. Context-specific transcription involving common HSF1 binding favors a model of regulation by combinatory interplay of rigid transcription factor patterns.

overall_design: Control cells, cells treated with heat shock at 42'C for 60 minutes, and cells treated with 500micromolar sodium metaarsenite for 60 minutes were subjected to ChIP-seq against total RNA pol II, histone H3 Lysine 4 trimethylation and total HSF1, ATAC-seq, and Precision Run-on sequencing (PRO-seq). Unless indicated, all treatments involve two independent biological replicates.

first: Sayantani

middle: G

last: Dastidar

first: Bony

last: De Kumar

first: Bo

last: Lauckner

first: Damien

last: Parrello

first: Danielle

last: Perley

first: Maria

last: Vlasenok

first: Antariksh

last: Tyagi

first: Nii

middle: K

last: Koney

first: Ata

last: Abbas


overall_design: Control cells, cells treated with heat shock at 42'C for 60 minutes, and cells treated with 500micromolar sodium metaarsenite for 60 minutes were subjected to ChIP-seq against total RNA pol II, histone H3 Lysine 4 trimethylation and total HSF1, ATAC-seq, and Precision Run-on sequencing (PRO-seq). Unless indicated otherwise, all treatments involve two independent biological replicates.


title: Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC)

status: Public on Oct 29 2023

city: Montreal

first: Tho-Alfakar

last: Al-Aubodah

state: Quebec

address: 1001 boulevard Decarie

country: Canada

institute: McGill University

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

overall_design: Refer to individual Series


title: Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [RTXrel_vs_RTXrem]

summary: An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Here, we performed single-cell RNA-sequencing (scRNAseq) on B cells isolated from peripheral blood mononuclear cells (PBMC) collected from four children with INS during the B cell recovery phase of a previous RTX treamtent while in remission or relapse (paired relapse-remisison samples). We show that the post-RTX B cell landscape is overwhelmingly antigen-inexperienced with minimal transcriptomic differences between relapse and remission. However, post-RTX relapses were associated with an early resurgence of an extrafollicular B cell population expressing genes associated with marginal zone B cells (MZB1, CD24, IGHM, CD1C, TNFRSF13B, GPR183). Together, our study provides evidence for an extrafollicular origin for humoral immunity in active INS.

overall_design: PBMC were isolated from the blood of four children with INS during the B cell recovery phase of previous RTX treatments during relapse and remission. Live B cells were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq).

first: Ciriaco

middle: A

last: Piccirillo

first: Tomoko

last: Takano


title: Translatome analysis of Tuberous Sclerosis Complex 1 patient-derived isogenic neural progenitor cells reveal rapamycin-dependent and independent alterations

status: Public on Oct 27 2023

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

summary: Tuberous sclerosis complex (TSC) is an inherited multi-system disorder caused by mutations in the TSC1 or TSC2 gene. TSC patients are often diagnosed with a range of neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD), intellectual disability (ID), anxiety and mood disorders. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) kinase signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using neural progenitor cells (NPCs) from patient-derived induced pluripotent stem cells (iPSCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in CRISPR-modified TSC1-null NPCs, which were unaffected by mTORC1 inhibition by rapamycin,the only approved therapy for TSC1. Here, to assess TSC1-dependent gene expression programs in NPCs, we used polysome-profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level. In addition to changes in mRNA abundance, this revealed numerous TSC1-dependent alterations in translational efficiencies. To assess the relevance of these gene expression alterations we performed polysome-profiling in post-mortem brains originating from ASD donors and matched controls. Strikingly, TSC1-dependent alterations in mRNA translation observed in NPCs were largely recapitulated in human brains. Furthermore, although polysome-profiling revealed a partial reversal of TSC1-associated gene expression alterations following rapamycin treatment, most genes related to neural activity/synaptic regulation or ASD that showed TSC1-dependent translation were rapamycin-insensitive. Therefore, we also examined whether early ND rapamycin-insensitive phenotypes in TSC1-null NPCs could be rescued by a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272 (Revolution Medicines, Inc.). Unlike rapamycin, RMC-6272 strongly inhibited translation and reversed TSC1-associated proliferation and neurite outgrowth phenotypes. In summary, we reveal ample translational alterations in TSC1 patient-derived NPCs recapitulating human brain expression profiles and potential implications for treatment of TAND.

overall_design: Analysis of total and polysomal mRNA samples of NPCs derived from a female TSC1 patient, including TSC1-null (-/-) and CRISPR-corrected TSC1-WT (+/+), treated with DMSO or rapamycin in triplicates.

first: Inci

middle: S

last: Aksoylu

first: Pauline

last: Martin

first: Francis

last: Robert

first: Nicholas

last: Redmond

first: Shan

last: Chen

first: Roberta

middle: L

last: Beauchamp

first: Irene

last: Nobeli

first: Jerry

last: Pelletier

first: Ola

last: Larsson

first: Vijaya

last: Ramesh


first: Sergei

last: Nechaev


title: Translatome analysis in postmortem brain-derived samples from Autism Spectrum Disorder affected individuals

summary: Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic link, but no single well-established cause. This suggests that perturbed regulatory network may better explain its heterogeneity of phenotypes and multiple gene associations. Consistently, our previous study provided evidence of abnormal alternative polyadenylation in transcripts from distinct brain regions suggesting a potential imbalance in the protein synthesis in the postsynaptic density. To test this hypothesis, we studied transcriptome-wide alterations of mRNA translation in post-mortem brain samples from neurotypical and ASD-affected young males subjects. To this end, we employed an optimised polysome profiling technique amendable for small tissue samples and analyzed changes in the translatome using the anota2seq algorithm. The analysis revealed bolstered translation of mRNAs whose translational efficiency was previously reported to be sensitive to eIF4E, a key factor for synaptic protein synthesis modulated by Ras/ERK and PI3K/mTOR signaling pathways. This observation is consistent with previous findings linking hyperactive eIF4E to increased translation of neuroligins, a disturbed excitation/inhibition ratio in synapses and autistic-like phenotypes in mice. In summary, we reveal a link between eIF4E-dependent translation and human autism, indicating a potential pharmacy-therapeutical target for the prevention of behavioral impairments in ASD.

overall_design: 10 brain samples were collected post-mortem from neurotypical and ASD-affected donors (NIH NeuroBioBank). To minimize study bias, the donors were matched for age (4-9 years old) and sex (male); and samples only originated from Brodmann Area 19.


title: Discordance between chromatin accessibility and transcriptional activity during the human primed-to-naïve pluripotency transition process

status: Public on Oct 28 2023

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

summary: Our results revealed critical chromatin remodeling events and highlight the discordance between chromatin accessibility and transcriptional activity. We further demonstrate that the differential epigenetic modifications and transcription factor (TF) activities may play a critical role in regulating gene expression, and account for the observed variations in gene expression despite similar chromatin landscapes.

overall_design: Analyzing histone modication profiles of transitioning intermediates during primed-to-naive transition process.

first: Zhifen

last: Tu

first: Yan

last: Bi


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [scRNA-Seq]

status: Public on Oct 25 2023

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

summary: Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.

overall_design: 10X Genomics 3prime v3


title: Gene expression profiles of peripheral blood mononuclear cells (PBMC) from children with active idiopathic nephrotic syndrome (INS) and healthy controls (HC) [HC_vs_INS]

first: Tho-Alfakar

last: Al-Aubodah

summary: An autoimmune B cell origin for childhood idiopathic nephrotic syndrome (INS) is predicted based on the efficacy of rituximab (RTX) at maintaining long-term remission from proteinuria. Knowledge regarding the nature of the culprit B cell response is very limited. In particular, no transcriptomics work has been performed to evaluate the B cell response in INS. Using single-cell RNA-sequencing (scRNAseq) on peripheral blood mononuclear cells (PBMC) isolated from four affected children with active INS and four age/sex-matched health controls (HC), we demonstrate that a B cell transcriptional program poised for effector functions represents the major immune perturbation in the blood of children with active INS. We show that this nephrotic B cell signature is conferred by the engagement of memory B cells through an extrafollicular developmental route defined by expression of the interfollicular-homing gene GPR183 and the expansion of atypical B cells and marginal zone-like B cells. Moreover, we show that genes involved in APRIL signaling, which promotes extrafollicular antibody-secreting cell development, were substantially upregulated in B cells, monocytes, and dendritic cells from INS children. Collectively, our study provides evidence for an extrafollicular origin for humoral immunity in active INS.

overall_design: PBMC were isolated from the blood of four children at either first onset or relapse of INS and four healthy age-matched controls. Live lymphocytes and monocytes were sorted by fluorescence-activated cell sorting (FACS) and analyzed by single-cell RNA-sequencing (scRNAseq).

first: Ciriaco

last: Piccirillo

first: Tomoko

last: Takano


title: IL-21 Producing Effector Tfh Cells Promote B Cell Alloimmunity in Lymph Nodes and Kidney Allografts

status: Public on Oct 23 2023

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

summary: Follicular helper T (Tfh) cells have been implicated in controlling rejection after allogeneic kidney transplantation, but the precise subsets, origins and functions of Tfh cells in this process have not been fully characterized. Here we show that a subset of effector Tfh cell marked by previous IL- 21 production is potently induced during allogeneic kidney transplantation and is inhibited by immunosuppressive agents. Single-cell RNAseq revealed that these lymph node effector Tfh cells have transcriptional and clonal overlap with IL-21 producing kidney infiltrating Tfh cells, implicating common origins and developmental trajectories. To investigate the precise functions of IL-21 producing effector Tfh cells in lymph nodes and allografts, we used a mouse model to selectively eliminate these cells and assessed allogeneic B cell clonal dynamics using a single B cell culture system. We found that IL-21 producing effector Tfh cells were essential for transplant rejection by regulating donor-specific germinal center B cell clonal dynamics both systemically in the draining lymph node and locally within kidney grafts. Thus, IL-21 producing effector Tfh cells have multifaceted roles in antibody-mediated rejection after kidney transplantation by promoting B cell alloimmunity.

overall_design: Lymph node and graft T follicular helper cells and lymph node Tcon all in duplicate

middle: T

first: Hengcheng

last: Zhang


title: IgG Autoantigen Array using sera from primary Sjogren's syndrome patients and non-Sjogren's syndrome controls

status: Public on Oct 24 2023

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: Sera were acquired from the Sjogren's International Collaborative Clinical Alliance (SICCA) biorepository and were assayed for IgG autoantibodies. The autoantigen array was performed to identify the specific autoantibodies that were enriched in pSS patients.

overall_design: Sera from 15 pSS patients and 15 non-SS controls were assayed. All subjects were females and were matched according to age and ethnicity. Samples were stored at -80 C and shipped to UT Southwestern for autoantigen array analysis.

first: Jill

last: Kramer


title: Eye lens organoids going simple: characterization of a new model

city: Rennes

first: Luc

last: Paillard

state: Brittany

address: 2 Ave Leon Bernard

department: IGDR (UMR6290)

country: France

institute: Univ Rennes

summary: To characterized a new model for lens development, a 3’ end RNA-seq was perform on the cell in 2D culture, on the all organoids (3D) and on the external and internal part of the organoids obtain with laser microdissection follow by RNA-extraction

overall_design: Differential Gene Expression analysis of RNA-seq data from cell (21EM15) on  2D culture, on the all organoids (3D) and on the external and internal part of the organoids was performed

first: Matthieu

last: Duot

first: David

last: Reboutier

first: Justine

last: Viet

first: Carole

last: Gautier-Courteille


title: Impact of diffused vs vasculature targeted DNA damage on the heart of mice depleted of the telomeric factor Ft1

city: Rome

first: Isabella

last: Saggio

address: p.le Aldo Moro, 5

department: Biology and Biotechnologies Charles Darwin

country: Italy

institute: Sapienza, University of Rome

summary: DNA damage is emerging as driver of heart disease, however, the cascade of events, its timing and the cell types involved are yet to be fully clarified. In this context, the implication of cardiomyocytes has been highlighted, while that of vasculature smooth muscle cells has been suggested, but not explored exhaustively. In our previous work we characterized a factor named Ft1 in mice and AKTIP in humans whose depletion generates telomere instability and DNA damage. Here, we explored the effect of the reduction of Ft1 on the heart with the goal of comparatively defining the impact of DNA damage targeted to smooth muscle cells to that of diffused damage. Using two newly generated mouse models, Ft1 constitutively knocked out (Ft1ko) mice, and mice in which we targeted the Ft1 depletion to the smooth muscle cells (Ft1sm22ko), we show that both genetic models display cardiac defects but with differences. Both Ft1ko and Ft1sm22ko mice display hypertrophy and fibrosis, while only Ft1ko mice display a robust DNA damage response and cardiac left ventricle alterations. Interestingly, Ft1sm22ko mice have early pathological traits that become manifest with age. Significantly, the defects of Ft1ko mice, including the alteration of the left ventricle, are rescued by the depletion of the DNA damage sensor p53. These results point to Ft1 deficiency as a driver of cardiac disease and show that Ft1 deficiency targeted to vasculature smooth muscle cells generates a pre-pathological profile exacerbated by age.

overall_design: Comparative gene expression profiling analysis of RNAseq data of cardiac tissue derived from WT, Ft1ko, Ft1sm22ko animals of 1 week of age.


title: Identification of tumor-intrinsic drivers of immune exclusion in acral melanoma

status: Public on Oct 20 2023

city: Rochester

middle: Christian

last: Augustin

state: MN

address: 200 1st St SW

department: Oncology

institute: Mayo Clinic

summary: Background:Acral melanoma (AM) has distinct characteristics as compared to cutaneous melanoma and exhibits poor response to immune checkpoint inhibitors (ICI). Tumor-intrinsic mechanisms of immune exclusion have been identified in many cancers but less studied in AM. Methods: We characterized clinically annotated tumors from patients diagnosed with AM at our institution in correlation with ICI response using whole transcriptome RNAseq, whole exome sequencing, CD8 immunohistochemistry, and multispectral immunofluorescence imaging. A defined interferon-γ-associated T cell-inflamed gene signature was used to categorize tumors into non-T cell-inflamed and T cell-inflamed phenotypes. In combination with AM tumors from two published studies, we systematically assessed the immune landscape of AM and detected differential gene expression and pathway activation in a non-T cell-inflamed tumor microenvironment (TME). Two single-cell(sc) RNAseq AM cohorts and 11 bulk RNAseq cohorts of various tumor types were used for independent validation on pathways associated with lack of ICI response. In total, 892 specimens were included in this study. Results: 72.5% of AM tumors showed low expression of the T cell-inflamed gene signature, with 23.9% of total tumors categorized as the non-T cell-inflamed phenotype. Patients of low CD3 + CD8 + PD1 + intratumoral T cell density showed poor prognosis. We identified 11 oncogenic pathways significantly upregulated in non-T cell-inflamed relative to T cell-inflamed TME shared across all three acral cohorts (MYC, HGF, MITF, VEGF, EGFR, SP1, ERBB2, TFEB, SREBF1, SOX2, and CCND1). scRNAseq analysis revealed that tumor cell-expressing pathway scores were significantly higher in low vs high T cell-infiltrated AM tumors. We further demonstrated that the 11 pathways were enriched in ICI non-responders compared to responders across cancers, including acral melanoma, cutaneous melanoma, triple-negative breast cancer, and non-small cell lung cancer. Pathway activation was associated with low expression of interferon stimulated genes, suggesting suppression of antigen presentation. Across the 11 pathways, fatty acid synthase and CXCL8 were unifying downstream target molecules suggesting potential nodes for therapeutic intervention. Conclusions: A unique set of pathways is associated with immune exclusion and ICI resistance in AM. These data may inform immunotherapy combinations for immediate clinical translation.

overall_design:
We used a validated T cell-inflamed gene signature to cluster acral tumor samples into non T cell-inflamed versus inflamed samples using bulk RNAseq data. We then identified differentially expressed genes between the two groups which were subsequently validated in additional previously published bulk and single-cell RNAseq datasets. T cell-inflamed status was compared against repsonse to immune checkpoint inhibitors provided in metadata.

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<

first: Riyue

last: Bao


title: Autoantibodies secreted by TLR7-stimulated B cell subsets from mice with primary Sjogren's syndrome

summary:
Spleens (n = 2-3)  were harvested from mice with primary Sjogren's syndrome (NOD.B10) and cells were sort-purified. Follicular B cells (FO) (6 million), Marginal zone B cells (4.5 million) and age-associated B cells (500,000) were sorted. Cells were cultured in 200 uL of complete RPMI media containing 62.5 ng/mL of imiquimod, a TLR7 agonist.
Cells were cultured for 6 days, and the supernatants were harvested and stored at -20 C. Samples were shipped to UT Southwestern for autoantigen array analysis.

overall_design: 5 samples were analyzed for each subset. Each sample was derived from 2-3 pooled spleens from aged NOD.B10 females. Cells were sort-purified using the following markers: FO: B220+, CD23+, CD21lo/-, MZ: B220+, CD23-, CD21+, ABC: B220+, CD11c+, CD11b+.


title: An API for dynamic estimation of reference intervals for functional abundances of gut microbiota

city: izmir

first: leman

last: binokay

address: Mithatpaşa

country: Turkey

institute: İzmir Biyomedicine and Genom Instıtute

summary: This study demonstrates the usefulness of the API by generating a baseline gut microbiota profile of a healthy population and estimating reference intervals for the functional abundance of manually selected KEGG pathways. API facilitates microbiome research by providing dynamic and customizable tools for estimating reference intervals for gut microbiota functional abundances. Through the API, researchers can rapidly generate gut microbiota functional profiles of healthy populations to use as a baseline for comparison. The API also allows users to manually select specific KEGG pathways and estimate reference intervals for the functional abundance of those pathways. By generating these customized reference intervals, researchers can better understand the expected range of gut microbiota functions in healthy individuals. API enables microbiome studies to go beyond simple taxonomic profiling and delve deeper into the functional potential of gut microbiome communities. In summary, API represents a valuable tool for microbiome researchers that enhances the ability to elucidate connections between gut microbial functions and human health.

overall_design: The overall design of the microbiome study utilizing the API for gut microbiota functional profiles in a healthy cohort. 57 Participants were recruited from the general population using inclusion-exclusion criteria to select healthy adults. Stool samples were collected from each participant and microbial DNA was extracted. The DNA was sequenced with iSeq100 and analyzed using the Kraken2 and picrust2 tools to generate microbiota taxonomic and functional profiles. Sequences were mapped to KEGG orthologs and pathways. The API can rapidly estimate reference intervals for these pathways in the healthy cohort by using the refineR algorithm. Researchers can then conduct analyses to identify functional features of the gut microbiome associated with health. Furthermore, the customized reference intervals can serve as a baseline for comparison in future microbiome studies related to disease states. The rapid generation of functional profiles and reference intervals represents a major advantage of the API over traditional microbiome analysis pipelines. Overall, the API provides an efficient tool to gain a deeper understanding of gut microbiota functional patterns tied to human physiology.

first: Leman

last: Binokay

first: Yavuz

last: Oktay

first: Gökhan

last: Karakülah


title: Synergistic roles of tristetraprolin family members in myeloid cells in controlling inflammation

city: Durham

first: Brittany

last: Snyder

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS


title: Differential Gene Expression and mRNA decay in Wild-Type and Myeloid-specific TTP Knock-out macrophages using RNA-Seq

summary: Members of the tristetraprolin (TTP) family of RNA-binding proteins can bind to and promote the decay of specific transcripts containing AU-rich motifs.  ZFP36 (TTP) is best known for regulating cytokine expression in myeloid cells; however, the mammalian paralogues ZFP36L1 and ZFP36L2 have not been viewed as important in controlling inflammation.  To study potential functional overlaps of these three TTP family proteins in myeloid cells, we developed myeloid-specific knock-out (M-KO) mice of these genes, singly and together.  M-Zfp36-KO mice exhibited a mild inflammatory syndrome late in life, while M-Zfp36l1-KO and M-Zfp36l2-KO mice had no apparent spontaneous phenotypes.  Mice with simultaneous deficiency of all three TTP family members in myeloid cells developed a severe, spontaneous, inflammatory phenotype, with a median survival of 8 weeks.  Macrophages derived from these mice contained many more stabilized transcripts than cells from M-Zfp36-KO mice, many encoding pro-inflammatory cytokines and chemokines.  Our findings emphasize the importance of all three family members, acting in concert, in myeloid cell function.

overall_design: We generated mRNA profiles of wild-type (WT) and M-TTP knock-out (KO) bone marrow-derived macrophages at 8 different timepoints in quadruplicate, using RNA-Seq.  The first goal of this study was to compare transcriptome-wide gene expression in wild-type (WT) and myeloid-specific TTP (M-TTP) knock-out (KO) macrophages before and after lipopolysaccharide (LPS) treatment.  The second goal of this study was to compare mRNA decay rates in WT and M-TTP KO macrophages after LPS and Actinomycin D (ActD) treatment.

first: Adam

middle: B

last: Burkholder

first: Perry

last: Blackshear


title: FUS-NLS mutation causes neurodevelopmental and systemic metabolic alterations

status: Public on Oct 19 2023

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

country: Spain

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

summary: Mutations in the ubiquitously expressed DNA/RNA binding protein FUS cause aggressive juvenile forms of amyotrophic lateral sclerosis (ALS). While most FUS mutation studies have focused on motor neuron degeneration, little is known about wider systemic or developmental effects. We studied pleiotropic phenotypes in a physiological knock-in mouse model carrying the pathogenic FUSDelta14 mutation in homozygosity. RNA sequencing of multiple organs aimed to identify pathways altered by the mutant protein in the systemic transcriptome, including metabolic tissues given the link between ALS-FTD and altered metabolism.

overall_design: To investigate pleiotropic phenotypes in a physiological knock-in mouse model carrying the pathogenic FUSDelta14 mutation in homozygosity 6 tissues (frontal cortex, spinal cord, tibialis anterior, liver, iWAT and BAT) from wild type and FusΔ14/Δ14 male mice at 9.5 weeks of age (n=4)

first: Zeinab

last: Ali

first: Juan

last: Godoy-Corchuelo

first: Irene

last: Garcia-Toledo

first: Luis

middle: C

last: Fernández-Beltrán

first: Elizabeth

last: Fisher

first: Thomas

last: Cunningham


title: Transcriptional Reprogramming of Brain Cells Under Anesthesia in wt and Alzheimer's Disease mouse model

city: Jerusalem

first: Miriam

last: Adam

state: Israel

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: In this study, we addressed the following questions: Which brain cell types are transcriptionally reprogrammed under anesthesia? What is the cell-type specific response to anesthesia? And how does the response change between WT and AD in mouse models? We profiled by single nucleus RNA-sequencing (snRNA-seq) of hippocampus brain region samples from awake and anesthetized wild-type (WT) and APP/PS1 AD mouse model. We found a strong and robust transcriptional switch in all glial cell types in the anesthetized mice and in specific neuronal sub-types. Comparing WT to AD mice uncovered an AD-specific transcriptional response to anesthesia in glial cells and in specific neuronal sub-types. These findings provide new insights on the molecular changes occurring in the anesthetized brain and how they are altered in AD.

overall_design:
The study included sNuc-seq profiles of 20 mice hippocampus tissue (n=20; WT-Awake=5, WT-ISO=4, WT-KETA=2, AD-Awake=4, AD-ISO=3, AD-KETA=2)
contributor: naomi.habib@mail.huji.ac.il


title: Ikaros is a principal regulator of Aire+ mTEC homeostasis, thymic mimetic cell diversity, and central tolerance

city: San Francisco

first: Jun Hyung

last: Sin

state: CA

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: Differential Gene Expression and mRNA decay in Wild-Type and Myeloid-specific TTP Family Member Triple (M-Triple) Knock-out macrophages using RNA-Seq

overall_design: We generated mRNA profiles of wild-type (WT) and M-triple knock-out (KO) bone marrow-derived macrophages at 8 different timepoints in quadruplicate, using RNA-Seq. The first goal of this study was to compare transcriptome-wide gene expression in wild-type (WT) and M-triple knock-out (KO) macrophages before and after lipopolysaccharide (LPS) treatment.  The second goal of this study was to compare mRNA decay rates in WT and M-triple KO macrophages after LPS and Actinomycin D (ActD) treatment.


title: The root-colonizing endophyte Piriformospora indica supports nitrogen-starved Arabidopsis seedlings with N metabolites

city: Jena

first: Ralf

last: Oelmüller

address: Dornburger Str. 159

department: Plant Physiology

country: Germany

institute: Friedrich-Schiller-University Jena

summary: The root-colonizing endophytic fungus Piriformospora indica promotes root and shoot growth of its host plants. We show that growth promotion of Arabidopsis leaves is abolished when the seedlings are grown on media with nitrogen (N) limitation. The fungus neither stimulated the total N content nor did it promote 15NO3- uptake from agar plates to the leaves of the host under N-sufficient or N-limiting conditions. However, when the roots were co-cultivated with 15N-labelled P. indica, more label can be detected in the leaves of N-starved host plants, but not of plants supplied with sufficient N. Amino acid and primary metabolite profiles, as well as expression analyses of N metabolite transporter genes suggest that the fungus alleviates the adaptation of its host to the N limitation condition. P. indica alters the expression of transporter genes which participate in relocation of NO3-, NH4+ and N metabolites from the roots to the leaves under N limitation. We propose that P. indica participates in the plant´s metabolomic adaptation to N limitation by delivering reduced N metabolites to the host, alleviating metabolic N starvation responses, and reprogramming the expression of N-metabolism related genes.

overall_design: The Arabidopsis thaliana host plants were in vitro cultivated under full N conditions and under N-limited conditions, each in the presence or absence of the endophytic fungus P. indica. The plants were pre-grown on N-limited MGRL media for 10 days, then they were transferred to plates with PNM co-culture medium (+N or -N), where the fungus was pre-grown for 7 days. Samples for RNAseq were taken after 4 days.

first: Sandra

last: Scholz

first: Emanuel

last: Barth

first: Gilles

last: Clement

first: Anne

last: Marmagne

first: Jutta

last: Ludwig-Müller

first: Hitoshi

last: Sakakibara

first: Takatoshi

last: Kiba

first: Jesús

last: Vicente-Carbajosa

first: Stephan

last: Pollmann

last: Krapp


title: Genes regulated by p16KO stem cell activation

city: Udine

first: Simone

last: Scalabrin

state: UD

address: via Jacopo Linussio 51

institute: IGA Technology Services

summary: Neural stem cells divide throughout adulthood in neurogenic niches - the dentate gyrus of the hippocampus and the subventricular zone (SVZ) - producing progenitor cells and new neurons. Moreover, stem cells self-renew, thus preserving their pool. The number of stem/progenitor cells in the neurogenic niches declines with age. We have previously demonstrated that the cyclin-dependent kinase inhibitor p16Ink4a maintains, in aged mice, the pool of dentate gyrus stem cells by preventing their activation after a neurogenic stimulus such as exercise (running). We showed that, although p16Ink4a ablation by itself does not activate stem/progenitor cells, exercise strongly induced stem cell proliferation in p16Ink4a knockout dentate gyrus, but not in wild-type. As p16Ink4a regulates stem cell self-renewal during aging, we sought to profile the dentate gyrus transcriptome from p16Ink4a wild-type and knockout aged mice, either sedentary or running for 12 days. By pairwise comparisons of differentially expressed genes and by correlative analyses through the DESeq2 software, we identified genes regulated by p16Ink4a deletion, either without stimulus (running) added, or following running. The p16Ink4a knockout basic gene signature, i.e. in sedentary mice, involves up-regulation of apoptotic, neuroinflammation- and synaptic activity-associated genes, suggesting a reactive cellular state. Conversely, another set of 106 genes we identified, whose differential expression specifically reflects the pattern of proliferative response of p16 knockout stem cells to running, are involved in processes regulating stem cells activation, i.e., synaptic function, neurotransmitter metabolism, stem cell proliferation control, and regulation of ROS levels. Moreover, we analyzed the regulation of these stem cell-specific genes after a second running stimulus. Surprisingly, the second running neither activated stem cell proliferation in the p16Ink4a knockout dentate gyrus nor changed the expression of these genes, confirming that they are correlated to the stem cell reactivity to stimulus.

overall_design: Samples: RNAs from dentate grus of one-year-old p16Ink4a knockout or p16 wild-type mice , either undergoing 12 days of running or sedentary. 4 groups analyzed:1) WT Contro;l 2) KO control; 3) WT Running; 4) KO Running. Four replicates per condition.

first: Laura

last: Micheli

first: Giorgio

last: D'Andrea

first: Teresa

last: Creanza

first: Daniel

last: Volpe

first: Nicola

last: Ancona

first: Raffaella

last: Scardigli

first: Felice

last: Tirone


title: Analyzing the immune cell population changes in the brain and the gut of PD mice

city: Wuerzburg

first: Rhonda

last: McFleder

address: Josef-schneider-strasse 11

institute: Neurologische Klinik und Poliklinik des Universitaetsklinikum Wuerzburg

summary: In this study we compare the CD4, CD8, and CD11c cell changes in the brain, ileum, and spleen of Parkinson's (PD) animals. A mouse model of PD was created as previously described by stereotactically injecting an AAV-expressing the human A53T-mutated form of a-Synuclein into the Substantia Nigra of adult mice, while controle mice were injected with an empty vector (EV). These mice exhibit neurodegneration and PD-like motor dysfunction. Five weeks after injection immune cells were isolated from the brain, spleen, and ileum of five mice per group. Similar organs from the same group were pooled and sorted for CD45+CD4+, CD45+CD8+, and CD45+CD11c+ cells. Twenty-thousand cells from the same group and organ were pooled and subjected to single cell sequencing. By comparing the cells from the different organs we were able to identify both T cell and CD11c+ cell populations that are shared between the brain and the gut and differentially regulated in PD.

overall_design: Each sample represents a pool of 20,000 CD4, CD8, and CD11c+ cells from either the brain, spleen, or ileum of 5 EV or PD mice.

first: Chi

middle: W

last: Ip

first: Fabian

last: Imdahl

first: Antoine-Emmanuel

last: Saliba

first: Jörg

last: Vogel


title: Essential role of Helicobacter pylori apolipoprotein N-acyltransferase (Lnt) in stomach colonization

status: Public on Oct 17 2023

city: NASHVILLE

first: Mark

last: McClain

state: Tennessee

address: 1161 21st Ave South, A2321 Medical Center North

institute: Vanderbilt University Medical Cente

summary: Deleting lnt changes the number of acyl chains on lipoproteins and the number of acyl chains on lipoproteins impacts the innate immune response through TLR2 signaling. We treated primary human gastric epithelial cells with a purified lipoprotein from wild-type or lnt mutant H. pylori and performed RNAseq. Differential gene expression analysis indicated lipoprotein from the lnt mutant induced a more robust TLR2 response.

overall_design: Deidentified primary human gastric epithelial cells were left untreated or treated with purified triacylated Lpp20-HA, diacylated Lpp20-HA, Pam3-CSK4, or Pam2-CSK4 for 4 hours

first: Matthew

last: Jung

first: Holly

last: Algood

first: Blanca

last: Piazuelo

first: Lee

last: Brackman


title: An adaptive stress response that confers cellular resilience to decreased ubiquitination

status: Public on Oct 18 2023

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Ubiquitination is a post-translational modification that regulates protein function and turnover. E2 ubiquitin-conjugating enzymes are key for ubiquitination but it remains uncharted what fraction of the proteome is E2-modulated. Here, we utilized deep-coverage TMT mass spectrometry to determine how protein abundance is modulated by E2s. Analysis of human cells with ~25% reduction in ubiquitination and with individual E2 knockdown indicates that 48% of the proteome is modulated by partial E2 loss, and that this rewires organelle and metabolic functions by reducing the turnover of E2-sensitive targets. In particular, several peroxins are upregulated by UBA1/E2 RNAi, and this promotes peroxisomal protein import and rewires cellular metabolism. Altogether, this study provides a framework for understanding how moderate reduction in E2 function rewires the proteome and cellular function.

overall_design: 116 RNA-seq samples from human HEK293T cells treated with siRNAs targetingUBA1 and E2 ubiquitin-conjugating enzymes compared to control treatment with non-targeting (NT) siRNAs

first: Liam

last: Hunt

first: Vishwajeeth

last: Pagala

first: Anna

last: Stephan

first: Boer

last: Xie

first: Kiran

last: Kodali

first: Kanisha

last: Kavdia

first: Abbas

last: Shirinifard

first: Michelle

last: Curley

first: Yingxue

last: Fu

first: Suresh

last: Poudel

first: Yuxin

last: Li

first: Haiyan

last: Tan

first: Junmin

last: Peng

first: Fabio

last: Demontis


title: Blastomeres of 8-cell mouse embryos differ in their ability to generate embryonic stem cells and produce lines with different transcriptional signatures.

city: Bellaterra (Cerdanyola del Vallès)

first: Sandra

middle: Alonso

last: Alonso

state: Barcelona

address: Carrer de la Val Moronta, Unitat de Biologia Cel·lular, Facultat de Biociències, UAB

department: Departament de Biologia Cel·lular, Fisiologia i Immunologia

institute: Universitat Autònoma de Barcelona

summary: The ability of sister blastomeres of 8-cell mouse embryos to produce ESC lines was measured, and the transcriptome of the Bm-mESCs lines generated was analyzed by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for embryonic stem cells generated from single blastomeres (Bm-mESCs) of the same 8-cell mouse embryo. Three biological replicates: embryo 1 (5 Bm-mESC lines), embryo 2 (7 Bm-mESC lines), and embryo 3 (7 Bm-mESC lines). (19 Bm-mESCs lines in total).

first: S

last: Alonso-Alonso

first: A

last: Esteve

first: B

last: Martin

first: L

last: Álvarez-González

last: Ruiz-Herrera

first: J

last: Santaló

first: E

last: Ibáñez


title: Epigenetic regulation of beta-endorphin synthesis in hypothalamic arcuate nucleus neurons modulates neuropathic pain in a rodent pain model

city: Suzhou

first: Jin

last: Tao

state: Jiangsu

address: 199 Ren-Ai Road

department: Physiology and Neurobiology

institute: Soochow University

type: Non-coding RNA profiling by high throughput sequencing

summary: Beta-endorphinergic neurons in the hypothalamic arcuate nucleus (ARC) synthesize beta-endorphin (β-EP) to alleviate nociceptive behaviors, although the underlying regulatory mechanisms remain unknown. Here, we elucidated a novel epigenetic pathway driven by microRNA regulation of beta-endorphin synthesis in ARC neurons to control neuropathic pain. In pain-injured rats miR-203a-3p was the most highly upregulated miRNA in the ARC. A similar increase was identified in the cerebrospinal fluid of trigeminal neuralgia patients. Mechanistically, histone deacetylase 9 downregulation increased acetylation of histone H3 lysine-18, facilitating the binding of NR4A2 transcription factor to the miR-203a-3p gene promoter increasing miR-203a-3p expression following nerve injury. Further, increased miR-203a-3p was found to maintain neuropathic pain by targeting proprotein convertase 1, an endopeptidase necessary for the cleavage of proopiomelanocortin, the precursor of β-EP. Our findings highlight an epigenetic regulatory pathway for β-EP synthesis that contributes to neuropathic pain development and maintenance mechanisms providing for new therapeutic targets for neuropathic pain treatment.

overall_design: Hypothalamic arcuate nucleus miRNA profiles in rat ARC tissue on day 14 after CCI-ION (n=3) or sham operation (n=3)

first: Yu


title: Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2 complexes

city: Fukushima

first: Miwako

middle: Kato

last: Homma

department: Biomolecular Sciences

institute: Fukushima Medcial University Sch Medicine

summary: Protein kinase CK2 is a conserved serine/threonine kinase that participates in various cellular processes. Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2alpha to the active gene locus, more abundantly in late G1 phase than in early G1. Notably, we confirmed the presence of CK2alpha at transcriptional start sites of core histone genes, growth stimulus-associated genes, and ribosomal RNAs. This study suggests that nuclear CK2alpha complexes, uniquely constituted during cell cycle progression, are essential for cell proliferation, by activating histone genes, triggering ribosome biogenesis, and synthesizing components necessary for cell division, specified in the nucleus and nucleolus.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CK2 as well as the histone modifications H3K4me3, H3K27ac, Pol II, Pol IISerP2 in RPE cells versus CK2alpha-CRISPR/Cas9 knockout cells as a control.

first: Ryuichiro

last: Nakato

first: Atsushi

last: Niita

first: Masashige

last: Bando

first: Katsunori

last: Fujiki

first: Naoko

last: Yokota

first: So

last: Yamamoto

first: Takeshi

last: Shibata

first: Motoki

last: Takagi

first: Junko

last: Yamaki

first: Hiroko

last: Kozuka-Hata

first: Masaaki

last: Oyama

first: Katsuhiko

last: Shirahige

first: Yoshimi


title: Precision pharmacological reversal of strain-specific diet-induced metabolic syndrome in mice informed by epigenetic and transcriptional regulation

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

type: Methylation profiling by high throughput sequencing

summary: We exposed three mouse strains to a high-fat high-carbohydrate diet, leading to varying degrees of metabolic syndrome. Comprehensive methylation and transcriptomic analysis found overlapping but also highly divergent changes in DNA methylation and gene expression, with pathway analysis suggesting a strategy for strain-specific targeted pharmacologic intervention of upstream regulators. Administeration of the drug GW4064 to target one of these genotype-dependent networks, the farnesoid X receptor pathway resulted in genotype-specific protection against dietary effects in BL6 as predicted by our epigenetic analysis.

overall_design: WGBS and RNA-Seq was performed on BL6, A/J, and NOD mice fed Standard or American diets. Some mice were also administered DMSO vehicle or the FXR agonist GW4064.

first: Adam

last: Davidovich

first: Anna

last: Salvador

first: Gabrielle

last: Manno

first: M

middle: N

last: Huda

first: Brian

last: Bennett

first: L

last: Adam

first: Kasper

middle: D

last: Hansen

first: David

last: Threadgill

first: Andrew

middle: P

last: Feinberg


title: Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2 complexes [array]

first: Miwako

last: Homma

summary: Protein kinase CK2 is a conserved serine/threonine kinase that participates in various cellular processes. Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2α to the active gene locus, more abundantly in late G1 phase than in early G1. We analyzed the transcriptome of RPE wt and CK2α-ko cells, both arrested in early and late G1 during progression of the cell cycle. This study suggests that nuclear CK2α complexes, uniquely constituted during cell cycle progression, are essential for cell proliferation, by activating genes and synthesizing components necessary for cell division, specified in the nucleus and nucleolus.

overall_design: Comprehensive gene expression analysis was performed using microarray in RPE wild-type cells versus CK2α-CRISPR/Cas9 knockout cells as a control.

first: Ryuichiro

last: Nakato

first: Atsushi

last: Niita

first: Masashige

last: Bando

first: Katsunori

last: Fujiki

first: Naoko

last: Yokota

first: So

last: Yamamoto

first: Takeshi


title: In vitro human H9 ESC-derived microglia scRNA seq

status: Public on Oct 16 2023

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

summary: Given that the γ-secretase substrate proteome identified in H9MG reveals its central role in microglial signaling-regulatory events, we reasoned that investigating the overall profile of the transcriptomes of the microglia would provide a good integrated read-out for the overall context-dependent effect of blocking the processing of >85 γ-secretase substrates. Although the alteration in tonic signaling caused by γ-secretase inhibition does not change the overall cell state, i.e. the cells with γ-secretase deficiency do not cluster dramatically differently in the UMAP plots (Figure 4E-F and J-K), the tonic signaling is robust as it remains discernible in the background of a strong LPS-induced response (Figure 4H and M).

overall_design: We analyzed the single-cell transcriptome of in vitro microglia in the presence and absence of the γ-secretase inhibitor Semagacestat to see how the inhibition of the processing of these proteins affect gene expression.  We performed a second experiment in parallel asking whether a strong γ-secretase independent signal could overcome the predicted tonic signaling. To this end, we treated cell cultures for 6 hours with lipopolysaccharide (LPS). Therefore, a total 12 samples in 4 experimental conditions (Ctrl, LPS, Sema, SemaLPS, with 3 biological replicates in each condition) were labeled with unique Hashtag antibodies and equally pooled. The pooled cells were then equally devided into 2 libraries (GEO samples) for scRNA seq.

first: Pengfei

last: Hou

first: Magdalena

last: Zielonka

first: Lutgarde

last: Serneels

last: Martinez-Muriana

first: Nicola

last: Fattorelli

first: Leen

last: Wolfs

first: Suresh

last: Poovathingal

first: Dries

last: T'Syen

first: Sriram

last: Balusu

first: Tom

last: Theys

first: Mark

last: Fiers

first: Renzo

last: Mancuso

middle: J

last: Howden

last: De Strooper


title: A SOX9-B7x axis safeguards dedifferentiated tumor cells from immune surveillance to drive breast cancer progression

city: New York

first: Wenjun

last: Guo

state: NY

address: 1301 Morris Park

department: Cell Biology

institute: Albert Einstein College of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: In vivo mouse microglia scRNA seq

summary: To address the question of whether γ-secretase deficiency affects the tonic signaling in microglia in vivo as well, we analyzed the single-cell transcriptomes of the γ-secretase deficient microglia from WT and AD mouse models at 3 ,6 and 7 months of age. Like the in vitro observations, genetic knockout of γ-secretase induced mild changes to the transcriptomes of in vivo microglia in the WT mice and also AD mice at 3 months. However, The relative proportions of DAM, CRM and TRM were significantly reduced in AppNL-G-F-GSiΔMG mice compared to AppNL-G-F-GSWT mice at 7 months, whereas HM and tCRM were significantly increased. Thus γ-secretase has a crucial role in the microglial transition from the homeostatic to the full DAM phenotype in AD.

overall_design: Mice were treated with tamoxifen or vehicle at 1 month of age and were sacrificed at 3, 6 or 7 months for single-cell transcriptomics analysis. To evaluate the potential effects of tamoxifen, we treated the Aph1-floxed mice (WT background and APPNLGF background) with or without tamoxifen and performed single-cell RNA sequencing to evaluate the transcriptional microglia cell states in these mice. N = 4 mice in each condition.

first: Anna

first: Andrew


title: Alternations in gut microbiota and host transcriptome of patients with coronary artery disease [16S_rRNA]

status: Public on Oct 15 2023

city: WenZhou

first: Zheng

last: GongWei

address: OuHai ChaShan

institute: WenZhou Medical University

summary: Coronary artery disease (CAD) is a widespread heart condition caused by atherosclerosis and influences millions of people worldwide. Early detection of CAD is challenging due to the lack of specific biomarkers. The gut microbiota and host-microbiota interactions have been well documented to affect human health. However, investigation that reveals the role of gut microbes in CAD is still limited. This study aims to uncover the synergistic effects of host genes and gut microbes associated with CAD through integrative genomic analyses.

overall_design: We collected fecal and blood samples from CAD patients and matched controls,uncover the synergistic effects of host genes and gut microbes associated with CAD through integrative genomic analyses.


title: Alternations in gut microbiota and host transcriptome of patients with coronary artery disease [RNA-seq]


title: Neuronal membrane proteasome-derived peptides modulate neuronal signaling

city: Baltimore

first: Fulya

last: Turker

state: MD

address: 725 N. Wolfe Street

department: Biological Chemistry

institute: Johns Hopkins School of Medicine

summary: The novel neuroproteasome is localized to the neuronal plasma membrane to degrade intracellular proteins into peptides that are released to the extracellular space. Selective inhibition of this neuronal membrane proteasome (NMP) complex ceased the release of peptides and rapidly attenuated neuronal transmission. Based on these findings, we hypothesize that these neuron-specific peptides mediate a novel form of communication through unique peptide-receptor interactions to promote intracellular signaling cascades relevant to neuronal development and function. Our work indicates that NMP peptides can rapidly induce N-methyl-D-aspartate receptor (NMDAR)-dependent calcium influx from dendrites to the soma, leading to rapid and sustained phosphorylation of the well-defined activity-dependent transcription factor cAMP response element-binding protein (CREB). We also determined that the gene expression program drastically changes upon NMP peptide treatment of neurons with an increase in expression of immediate early genes (e.g., Fos, Npas4, Egr4) known to have critical neuroregulatory roles. These data support our current thinking that NMP peptides are endogenous and selective activators of synaptic NMDA receptors and are critical for promoting activity-dependent gene expression. This pathway is orthogonal to the classic neurotransmitters previously described to activate NMDARs and points to NMP and its resulting peptides as key contributors to the development and function of the nervous system. However, the unique peptide sequences leading to neuronal activation are still poorly understood. Here, we show that the NMP peptides have tremendous sequence diversity through an unbiased peptidomic approach, and the current ongoing effort is to identify unique active peptide sequences with distinct receptor specificity. Elucidating the mechanism of the NMP and its active peptide products is crucial to understanding the role of this novel signaling process in the nervous system.

overall_design: Mouse primary cortical neurons were cultured and treated with 4 different drugs/compounds plus a DMSO control at DIV12.  There were 14 samples with 3 biological replicates.

last: Türker

first: Seth

last: Margolis


title: Merging short and stranded long reads improves transcript assembly

status: Public on Oct 14 2023

city: Chicago

first: Alexander

last: Ruthenburg

state: IL

address: 920 E. 58th Street

department: Molecular Genetics and Cell Biology

institute: University of Chicago

summary: New tools for improved long-read transcript assembly and coalescence with its short-read counterpart are required. Using our short- and long-read measurements from different cell lines with spiked-in standards, we systematically compared key parameters and biases in the read alignment and assembly of transcripts. We report a cDNA synthesis artifact in long-read datasets that impacts the identity and quantitation of assembled transcripts. We developed a computational pipeline to strand long-read cDNA libraries that markedly improves assembly of transcripts from long-reads. Incorporating stranded long-reads in a new hybrid assembly approach, we demonstrate its efficacy for improved characterization of challenging lncRNA transcripts. Our workflow can be applied to a wide range of transcriptomics datasets for superior demarcation of transcript ends and refined isoform structure, which can enable better differential gene expression analyses and molecular manipulations of transcripts.

overall_design: Nuclei from HL1 cells were isolated by detergent lysis, fractionated, then three chromatin and three nucleplasm RNA samples were converted to cDNA using NEBNext Ultra II Directional library kit, and sequenced on Illumina HiSeq 4000. In parallel, chromatin fraction RNA from two replicates were converted to cDNA using Oxford Nanopore direct cDNA sequencing kit and sequenced on MinION flowcell.

first: Amoldeep

last: Kainth

first: Gabriela

last: Haddad

first: Johnathon

middle: M

last: Hall


overall_design: Nuclei from HAP1 cells were isolated by detergent lysis, fractionated, then three chromatin and three nucleplasm RNA samples were converted to cDNA using NEBNext Ultra II Directional library kit, and sequenced on Illumina HiSeq 4000. In parallel, chromatin fraction RNA from two replicates were converted to cDNA using Oxford Nanopore direct cDNA sequencing kit and sequenced on MinION flowcell.

middle: A


title: ABIN1 (Q478) is required to prevent hematopoietic deficiencies through regulating type I IFNs expression

city: shanghai

first: xuanhui

last: wu

state: shanghai

address: yueyang road 320

department: Institute of Nutrition

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: A20-binding inhibitor of NF-κB activation (ABIN1) is a polyubiquitin-binding protein that regulates cell death and immune responses. Although Abin1 (Tnip1) is located on chromosome 5q in the region commonly deleted in patients with 5q minus syndrome, the most distinct of the myelodysplastic syndromes (MDSs), the precise role of ABIN1 in MDSs remains unknown. In this study, we generated mice with a mutation that disrupts the polyubiquitin-binding site (Abin1Q478H/Q478H). These mice developed MDS-like diseases characterized by anemia, thrombocytopenia, and megakaryocyte dysplasia. Extramedullary hematopoiesis and bone marrow failure are also observed in Abin1Q478H/Q478H mice.  t Notably, higher levels of type I interferon (IFN-I) expression were observed in the bone marrow cells of Abin1Q478H/Q478H mice than in those of wild-type mice. Consistently, blocking type I IFN signaling through the co-deletion of Ifnar1 greatly ameliorated anemia, thrombocytopenia, and splenomegaly in Abin1Q478H/Q478H mice. Taken together, these results demonstrated that ABIN1 (Q478) prevents the development of hematopoietic deficiencies by regulating type I IFN expression.

overall_design: Isolate and amplify bone marrow HSPC cells from mice including HPC-1, HPC-2, MPP, and LT-HSC, and then perform transcriptome sequencing.

first: Xuanhui

last: Wu

first: Haibing

last: Zhang


title: Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive

institute: Duke University

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

overall_design: Refer to individual Series


title: Inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills tumours by inducing readthrough transcription [RNA-seq]

status: Public on Oct 13 2023

city: Solna

first: Vladislav

last: Kuzin

state: Stockholm

address: Solnavägen 9

department: Cell and Molecular Biology

institute: Karolinska Institute

summary: Transcription inhibition has become an attractive strategy for anticancer therapy because many cancers arise from dysregulated transcription programs. Topoisomerase 1 (TOP1) and bromodomain containing protein 4 (BRD4) coordinate each other to regulate transcriptional elongation. Using a collection of patient-derived xenograft mouse models of pancreatic cancer we show that the combined inhibition of TOP1 and BRD4 is synergistic in arresting tumor growth. We link this effect to the ability of TOP1 and BRD4 to control pause-release, a rate-limiting step in early elongation. By comparing nascent transcripts with the recruitment of elongation and termination factors along genes, we found that combined inhibition of TOP1 and BRD4, while globally impairing RNA production, also disturbs the recruitment of proteins involved in termination. Thus, RNA polymerases stay engaged with the DNA downstream of polyadenylation sites for hundreds of kilobases leading to readthrough-transcription. Because this pervasive transcription occurs also during replication, it perturbs replisome progression leading to increased DNA damage and cell cycle arrest. The synergistic effect of TOP1 and BRD4 inhibition is specific for the tumor cells as negligible transcriptional defects are observed in non-tumor cells. This work provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors in the treatment of highly transcription- and replication-driven tumors.

overall_design: RNA-seq of extracts from patient-derived xenografts of pancreactic tumors (B099, neuroendochrine tumor(panNEC); Bo103, pancreatic ductal adenocarcinoma(PDAC)). Mice with one tumor implanted on either side were either treated for 5 days with the indicated drug combinations (or DMSO for control) or subjected to zero, one or two cycles (C1, C2, C3) of Irinotecan + JQ1 treatment and tumor recovery before harvest at set time points after the last treatment.

first: Jan

last: Grosser

first: Evanthia

last: Iliopoulou

first: Donald

last: Cameron

first: Anika

last: Wiegard

first: Laura

last: Baranello


title: Inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills tumours by inducing readthrough transcription [CAD-seq]

overall_design: Covalent adduct detection coupled to sequencing (CAD-seq) in bo103 cells for Topoisomerase1 (TOP1) in duplicates.


title: Inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills tumours by inducing readthrough transcription


title: Spatial transcriptomics map of the embryonic mouse brain: a tool to explore neurogenesis

status: Public on Oct 12 2023

city: Heidelberg

first: Javier

last: Vázquez-Marín

state: Baden-Württemberg

address: Im Neuenheimer Feld 230, 5th floor

department: Centre for Organismal Studies (COS)

institute: Heidelberg University

summary: The developing brain has a complex and well-organized anatomical structure comprising different types of neural and non-neural cells. Stem cells, progenitors, and newborn neurons tightly interact with their neighbouring cells and tissue microenvironment, and this intricate interplay ultimately shapes the output of neurogenesis. Given the relevance of spatial cues during brain development, we acknowledge the necessity for a transcriptomics atlas within the tissue context accessible to the neurodevelopmental community. To fulfil this need, we offer an open-access spatial gene expression browser of the embryonic mouse brain at the peak of neurogenesis. Using 10x Visium technology, we generated spatially-resolved RNAseq data from E13.5 embryonic brain sections. Unsupervised clustering reliably defined specific cell type populations of diverse lineages and maturational states. Differential expression analysis revealed unique transcriptional signatures across specific embryonic brain areas, uncovering novel features inherent to particular anatomical domains. Furthermore, we integrated single-cell RNAseq data from E13.5 mouse brains into our Spatial Transcriptomics data, adding tissue context to single-cell resolution. In summary, we provide a valuable tool that enables the exploration and discovery of unforeseen molecular players involved in neurogenesis, particularly in the crosstalk between different cell types.

overall_design: Four sections from four different WT mouse embryonic heads (stage E13.5) were extracted for spatial transcriptomics using the 10x Genomics Visium platform in order to identify areas of the embryonic brain with different cell lineages and maturation states at the peak of neurogenesis.

first: Barbara

last: Di Marco

first: Hannah

last: Monyer

first: Lázaro

last: Centanin

first: Julieta

last: Alfonso


title: Inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills tumours by inducing readthrough transcription [SLAM-seq]

overall_design: RNA-seq with extracts from Bo103 cells.


title: Effect of volume overload on gene expression of right atrium during postnatal heart development

city: Shanghai

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

summary: To investigate the effect of volume overload (VO) during postnatal right atrium (RA) development, we established the RA VO model by conducting the fistula between abdominal aorta and inferior vena cava (ACF) on postnatal day 7(P7)  C57/BL6 mice. We then performed gene expression analysis using data obtained from RNA-seq of RA from VO and sham-operated mice at postnatal day 21 (P21).

overall_design: Comparative gene expression profiling analysis of RNA-seq  data for right atrium free wall myocardium in volume overload and sham-operated C57/BL6 mice on postnatal day21.

first: Debao

last: Li

first: Lincai

last: Ye

first: Fen


title: Inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills tumours by inducing readthrough transcription [ChIP-seq]

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in Bo103 cells for H3K27ac, H3K36me3, BRD4, RNAPII-ser2P and Cstf64 in duplicates.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in Bo103 cells for RNAPII and TOP1 in duplicates.


title: Effect of  PDGF, TGF-β and miR-221 on gene expression during proliferation and differentiation of human aortic smooth muscle cells

first: wu

last: hao

address: No. 650 Xin Songjiang Road

department: Precision Research Center for Refractory Diseases, Institute for Clinical Research

institute: Shanghai General Hospital

summary: To investigate the key molecular and mechanism during the proliferation and differentiation of human aortic smooth muscle cells, we treated HASMC cell lines  with  PDGF, TGF-β and miR-221.We then performed gene expression profiling analysis using data obtained from ONT long-read RNA-seq of 4 different treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control HASMC cells and 3 different treatments (PDGF, TGF-β and miR-221).

first: Shengli

first: Deping

last: Kong

first: Zhiqian

last: Lv

first: Yicheng

first: Hao

last: Wu


title: Inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills tumours by inducing readthrough transcription [Repli-seq]

first: Vladislav

last: Kuzin

overall_design: Repli-seq in bo103 cells.

first: Jan

last: Grosser

first: Evanthia

first: Donald

first: Anika


title: Spatial Transcriptomics Suggests That Alterations 4 Occur in the Preneoplastic Breast Microenvironment of 5 Q2 BRCA1/2 Mutation Carriers

status: Public on Oct 11 2023

city: Cleveland

first: Peter

last: Bazeley

state: OH

address: 9500 Euclid Avenue

department: Lerner Research Institute

institute: Cleveland Clinic

summary: Breast cancer is the most common cancer in females, affecting one in every eight women and accounting for the majority of cancer-related deaths in women worldwide. Germline mutations in the BRCA1 and BRCA2 genes are significant risk factors for specific subtypes of breast cancer. BRCA1 mutations are associated with basal-like breast cancers, whereas BRCA2 mutations are associated with luminal-like disease. Defects in mammary epithelial cell differentiation have been previously recognized in germline BRCA1/2 mutation carriers even before cancer incidence. However, the underlying mechanism is largely unknown. Here, we employ spatial transcriptomics to investigate defects in mammary epithelial cell differentiation accompanied by distinct microenvironmental alterations in preneoplastic breast tissues from BRCA1/2 mutation carriers and normal breast tissues from non-carrier controls. We uncovered spatially defined receptor-ligand interactions in these tissues for the investigation of autocrine and paracrine signaling. We discovered that β1-integrin-mediated autocrine signaling in BRCA2-deficient mammary epithelial cells may differ from BRCA1-deficient mammary epithelial cells. In addition, we found that the epithelial-to-stromal paracrine signaling in the breast tissues of BRCA1/2 mutation carriers is greater than in control tissues. More integrin-ligand pairs were differentially correlated in BRCA1/2-mutant breast tissues than non-carrier breast tissues with more integrin receptor-expressing stromal cells. Implications: These results suggest alterations in the communication between mammary epithelial cells and the microenvironment in BRCA1 and BRCA2 mutation carriers, laying the foundation for designing innovative breast cancer chemo-prevention strategies for high-risk patients.

overall_design: 12 patients, 3 genotypes, 4 patients per genotype, 11-15 ROI per patient

first: Antony

last: Caputo

first: Kavya

last: Vipparthi

first: Erinn

last: Downs-Kelly

first: Patrick

last: McIntire

first: Ying

last: Ni

first: Bo

first: Ruth

last: Keri

first: Mihriban

last: Karaayvaz


title: Landscape of enhancer disruption and functional screen in melanoma [HiChIP]

city: Tianjin

first: Mulin

middle: Jun

state: Tianjin

address: 22 Qixiangtai Road, Tianjin, Tianjin, China

department: Department of Epidemiology and Biostatistics

institute: Tianjin Medical University

summary: The high mutation rate across the whole melanoma genome provides a major challenge in stratifying true driver events from the background mutations. Many non-coding recurrent events, such as those occurred in enhancer, can shape tumor evolution, emphasizing the importance in systematically deciphering enhancer disruptions in melanoma. Here, we leveraged 297 melanoma whole-genome sequencing (WGS) samples to prioritize highly recurrent regions (HRRs). By performing a genome-scale CRISPR interference (CRISPRi) screen on HRR-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers revealed many known and hidden mechanisms underlying melanoma development. We demonstrated that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A and another distal enhancer was able to sustain PTEN tumor-suppressive potential via long-range interaction. Our study established a catalogue of crucial enhancers and their target genes in melanoma development and progression, which illuminates the identification of novel mechanism of dysregulation for melanoma driver genes and new therapeutic targeting strategy.

overall_design: To delineate the potential target genes for functional enhancers, we performed in situ Hi-C followed by chromatin immunoprecipitation (HiChIP) of enhancer mark H3K27ac on A375 cells.

first: Zhao

last: Wang

first: Menghan

last: Luo

first: Qian

last: Liang

first: Wei


title: RNA-Seq analysis of Candida glabrata wild-type, Δckb1 and Δckb2 mutant in the presence and absence of methyl methanesulfonate (MMS).

first: Xianwei

address: No.725 South Wanping Road

department: Institute of Respiratory Diseases

institute: Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

summary:
To obtain a better understanding of molecular mechanisms underlying the DNA damage response in Δckb1 and Δckb2 mutants, transcriptome analyses were performed between WT, Δckb1, and Δckb2 strains.
Comparative transcriptome analysis of Δckb1 and Δckb2 mutants showed similar transcriptional profiles in the presence and absence of MMS. The data also indicated that compared with WT, about 200 genes were up or downregulated in Δckb1 and Δckb2 strains with or without treatment with 0.01% MMS. GO analysis highlighted that the differentially expressed genes in Δckb1 and Δckb2 were significantly enriched in the processes related to the programmed formation of DNA double-strand breaks (DSBs), recombination, and DNA repair coordination of the meiotic cell cycle.

overall_design: The study was designed to profile the transcriptomes of C. glabrata wild-type, Δckb1 and Δckb2 mutant grown under normal (YPD medium) and DNA damage stress (0.01% MMS treatment for 1h) conditions via RNA-Sequencing approach. The experiment was performed with three biological replicates.

first: Qi

first: Tongxuan

last: Su

first: Cen

last: Jiang

first: Danfeng

last: Dong

first: Daosheng

last: Chen

first: Yingchao

last: Cui

first: Yibing

last: Peng


title: Landscape of enhancer disruption and functional screen in melanoma [4C-seq]

last: Li

overall_design: We performed the circularized chromosome conformation capture (4C) assay on the A375 cell line to evaluate the spatial proximity between enhancer E_349 (GRCh37/hg19: Chr15: 99,982,353–99,983,277) and MEF2A, and between enhancer E_156 (GRCh37/hg19 chr10:89,986,509-89,987,396) and PTEN.


title: Gene expression of MC38 tumor tissues from PBS, VNP20009 and HCS1-treated mice.

status: Public on Oct 10 2023

city: Changsha

first: yujie

last: sun

address: Juzizhou street

institute: Hunan University

summary: To investigate the different functions between VNP20009 and HCS1 in Salmonella-mediated cancer therapy.

overall_design: Gene expression profiling analysis using data obtained from RNA-seq of 4 different tumor tissues after 1 day treatment.

first: Yujie

last: Sun

first: Yanxia

last: Guo

first: Xiaoqing

last: Liu

first: Jinling


title: In Vivo Investigation of the Effect of Dietary Acrylamide and Evaluation of its Clinical Relevance in Colon Cancer

city: Egkomi

first: Panagiotis

last: Papageorgis

state: Nicosia

address: 6 Diogenous street

department: Life Sciences

country: Cyprus

institute: European University Cyprus

summary: Dietary exposure to Acrylamide (AA) has been linked with carcinogenicity in the gastrointestinal (GI) tract. However, epidemiologic data on AA intake in relation to cancer risk are limited and contradicting, while the potential cancer-inducing molecular pathways following AA exposure remain elusive. In this study, we collected mechanistic information regarding the induction of carcinogenesis by dietary AA in the colon, using an established animal model. Male Balb/c mice orally received AA (0.1 mg/kg/day) daily for 4 weeks. RNA was extracted from colon tissue samples, followed by RNA sequencing. Comparative transcriptomic analysis between AA and mock-treated groups revealed a set of differentially expressed genes (DEGs) that were further processed using different databases through the STRING-DB portal, to reveal deregulated protein-protein interaction networks. We found that genes implicated in RNA metabolism, processing and formation of the ribosomal subunits and protein translation and metabolism are upregulated in AA-exposed colon tissue; these genes were also overexpressed in human colon adenocarcinoma samples and were negatively correlated with patient overall survival (OS), based on publicly available datasets. Further investigation of the potential role of these genes during the early stages of colon carcinogenesis may shed light into the underlying mechanisms induced by dietary AA exposure.

overall_design: To investigate the effects in colon gene expression patterns of dietary exposure to acrylamide in vivo using mouse models.  Male Balb/c mice (n=5 per group) orally received AA (0.1 mg/kg/day) or PBS daily for 4 weeks. RNA was extracted from colon tissue samples, followed by RNA sequencing.

first: Maria-Ioanna

last: Christodoulou

first: Christiana

last: Neophytou


title: STAT1 deficiency underlies a proinflammatory imprint of naive CD4+ T cells in spondyloarthritis [RNA-Seq]

city: Montigny-le-Bretonneux

first: Frédéric

last: Crémazy

address: 2 avenue de la source de la Bièvre

institute: UVSQ/INSERM

summary: In spondyloarthritis (SpA), an increased type 3 immune response, including T helper cells (Th) 17 excess, is observed in both human and SpA animal models, such as the HLA-B27/human β2-microglobulin transgenic rat (B27-rat). To investigate this unexplained Th17-biased differentiation, we focused on understanding the immunobiology of B27-rat naive CD4+ T cells (Tn). We observed that neutrally stimulated B27-rat Tn developed heightened Th17 profile even before disease onset, suggesting an intrinsic proinflammatory predisposition. In parallel with this observation, transcriptomic and epigenomic analysis showed that B27-rat Tn exhibited a decreased expression of Interferon/Th1- and increased expression of Th17-related genes. This molecular signature was predicted to be related to an imbalance of STAT1/STAT3 transcription factors activity. Stat1 mRNA and STAT1 protein expression were decreased before disease onset in Tn, even in their thymic precursors, whereas Stat3/STAT3 expression increased upon disease establishment. Confirming the relevance of these results, STAT1 mRNA expression was also decreased in Tn from SpA patients, as compared with healthy controls and rheumatoid arthritis patients. Finally, stimulation of B27-rat Tn with a selective STAT1 activator abolished this preferential IL-17A expression, suggesting that STAT1 altered activity in B27-rats allows Th17 differentiation. Altogether, B27-rat Tn harbor a STAT1 deficiency preceding disease onset, that may occur during their thymic differentiation, secondarily associated with a persistent Th17 bias, which is imprinted at the epigenomic level. This early molecular phenomenon might lead to the persistent proinflammatory skew of CD4+ T cells in SpA patients, thus offering new clues to better understand and treat SpA.

overall_design: RNA-sequencing, performed on naive CD4+ T cells total RNA, sorted from mesenteric lymph nodes. Comparison of non transgenic and B27-transgenic rats, premorbid or sick. Whole-genome sequencing. Analysis: differential gene expression (DESeq2) including batch effect.

first: Bilade

last: Cherqaoui

first: Marc

last: Lauraine

first: Ghazal

last: Shammas

first: Roula

last: Said Nahal

first: Hendrick

last: Mambu Mambueni

first: Félicie

last: Costantino

first: Marine

last: Fourmont

first: Audrey

last: Hulot

first: Henri-Jean

last: Garchon

first: Simon

last: Glatigny

first: Luiza

last: Araujo

first: Maxime

last: Breban


title: Regulatory T cell adoptive transfer alters uterine macrophage populations, increasing a novel MHC-II-low macrophage associated with healthy pregnancy.

status: Public on Oct 09 2023

first: Emma

last: Lewis

state: PA

address: 3400 Spruce Street

department: Obstetrics and Gynecology

institute: University of Pennsylvania

summary: To investigate local immune mechanisms of intrauterine fetal demise (IUFD), we used the CBA mouse strain, which naturally has mid-late gestation fetal loss. We performed a Treg adoptive transfer and interrogated both pregnancy outcomes and the impact of systemic maternal Tregs on mucosal immune populations at the maternal-fetal interface. Treg transfer prevented fetal loss and increased an MHC-IIlow population of uterine macrophages. Single-cell RNA-sequencing was utilized to precisely evaluate the impact of systemic Tregs on uterine myeloid populations. A population of C1q+, Trem2+, MHC-IIlow uterine macrophages were increased in Treg-recipient mice. The transcriptional signature of this novel uterine macrophage subtype is enriched in multiple studies of human healthy decidual macrophages, suggesting a conserved role for these macrophages in preventing fetal loss.

overall_design: Timed-pregnant CBA mice received Treg adoptive transfer or PBS injections on embryonic day 2 (E2) (N=3 mice/group). Uteri from these mice were harvested and processed at E15. Fluorescence activated cell sorting (FACS) was used to isolate myeloid cells gated on live, singlet, CD45+, CD11b+ cells from the uteri to use for single cell RNA-sequencing.

first: Erin

middle: R

last: Reichenberger

first: Paige

last: Porrett

first: Michal

last: Elovitz


title: A hormone-activated mobile RNAi pathway defends plant stem cells from virus infection

city: Vienna

first: Ruben

last: Gutzat

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute GmbH

summary: Study on the role of Arabidopsis thaliana RDR1 and other RNAi factors in the exclusion of RNA viruses from the shoot apical meristem stem cells

overall_design: WT and rdr1-1 Arabidopsis plants (Col-0  ecotype) were inoculated with TuMV-6K2:Scarlet at approx. 3.5 weeks of age. Mock inoculation with buffer only was performed as control. 16 days after inoculation, inflorescences from systemically infected flowers (terminal 1mm apex, inflorescence meristem and flower buds <1mm diameter) were harvested. Each sample (biological replicate) consists of tissue from five plants. Two biological replicates per genotype/condition were harvested. RNA was extracted with standard Trizol protocol.

first: Marco

last: Incarbone

first: Vu

middle: H

last: Nguyen


title: Salicylic acid and RNA interference mediate antiviral immunity of plant stem cells (Previous preprint title: A hormone-activated mobile RNAi pathway defends plant stem cells from virus infection)

city: Potsdam

address: 1 Am Muehlenberg

institute: Max Planck Institute of Molecular Plant Physiology


title: Landscape of enhancer disruption and functional screen in melanoma

first: Mulin

last: Li

summary: Here, we leveraged 297 melanoma whole-genome sequencing (WGS) samples to prioritize highly recurrent regions (HRRs). By performing a genome-scale CRISPR interference (CRISPRi) screen on HRR-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers revealed many known and hidden mechanisms underlying melanoma growth. Utilizing extensive functional validation experiments, we demonstrated that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A and another distal enhancer was able to sustain PTEN tumor-suppressive potential via long-range interaction.

overall_design: Refer to individual Series


title: Landscape of enhancer disruption and functional screen in melanoma [CRISPRi]

overall_design: To systematically inspect the functional consequence of enhancer disruption within melanoma HRRs, we performed a CRISPR interference (CRISPRi) screen on the A375 human melanoma cell line by employing the dCas9-KRAB system and tiling dispersedly tiled sgRNAs for each of selected HRR-associated enhancers.

first: Zhao

last: Wang

first: Menghan

last: Luo

first: Qian

last: Liang

first: Wei


title: Profound DNA methylomic differences between single- and multi-fraction alpha irradiations of lung fibroblasts

city: Chalk River

first: Richard

middle: B.

last: Richardson

state: Ontario

address: 286 Plant Rd

department: Radiobiology and Health

institute: Canadian Nuclear Laboratories

summary: Alpha (α)-radiation is a ubiquitous environmental agent with epigenotoxic effects. Human exposure to α-radiation at potentially harmful levels can occur repetitively over the long term via inhalation of naturally occurring radon gas that accumulates in enclosed spaces, or as a result of a single exposure from a nuclear accident. Alterations in epigenetic DNA methylation (DNAm) have been implicated in normal aging and cancer pathogenesis. Nevertheless, the effects of aberrations in the methylome of human lung cells following exposure to single or multiple α-radiation events on these processes remain unexplored. Here, we performed genome-wide DNAm profiling of human embryonic lung fibroblasts from control and irradiated cells using americium-241 α-sources. Cells were α-irradiated in quadruplicates to seven doses using two exposure regimens, a single-fraction (SF) where the total dose was given at once, and a multi-fraction (MF) method, where the total dose was equally distributed over 14 consecutive days. Our results revealed that SF irradiations were prone to a decrease in methylation levels, while MF irradiations mostly increased methylation. The analysis also showed that the gene body (i.e. exons and introns) was the region mostly altered by both the SF hypomethylation and the MF hypermethylation. Additionally, the MF irradiations induced the highest number of differentially methylated regions in genes associated with DNAm biomarkers of aging, carcinogenesis, and cardiovascular disease. The DNAm profile of the oncogenes and tumour suppressor genes suggested that the fibroblasts elicited a defensive response to the MF α-irradiation. Key DNAm events of ionizing radiation exposure including changes in methyl levels in mitochondria dysfunction-related genes were mainly identified in the MF groups. However, these alterations were under-represented, indicating that the mitochondria undergo adaptive mechanisms, aside from methylation, in response to radiation-induced oxidative stress. In this study, we identified a contrasting methylomic profile in the lung fibroblasts α-irradiated to SF compared with MF exposures. These findings demonstrate that the methylome response of the lung cells to α-radiation is highly dependent on both the total dose and the exposure regimen. They also provide novel insights into potential biomarkers of α-radiation which may lead to the development of innovative approaches to detect, prevent and treat α-particle related diseases.

overall_design: We first irradiated primary lung fibroblast cells to seven doses of americium-241 α-sources ranging from 2.0 to 2,200 mGy using two exposure regimens, a single-fraction where the total dose was given at once, and a multi-fraction method, where the total dose was equally distributed over 14 consecutive days. The irradiation per dose for each regimen was independently conducted in 4 biological replicates. We then performed Methylated DNA immunoprecipitation (MeDIP) coupled with sequencing.

first: Marilyn

last: Vera-Chang

first: John

last: Danforth

first: Marilyne

last: Stuart

first: Aaron

middle: G

last: Goodarzi

first: Marjorie

last: Brand


title: L-Arginine enhances oral keratinocyte proliferation under high glucose conditions through upregulation of CYP1A1, SKP2, and SRSF5

first: Trevor

last: Leonardo

state: Illinois

address: 801 South Paulina Street

department: Medicine

institute: University of Illinois at Chicago

summary: L-Arginine promotes oral keratinocyte proliferation under high glucose conditions. The treatment leads to changes in a substantial number of gene transcripts related to cell cycle, cell proliferation, and spliceosome GO terms as well as signaling pathways. Among these top-upregulated genes, CYP1A1, SKP2, and SRSF5 are of particular significance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human gingival keratinocytes (TIGK) cultured under high glucose conditions (48mM) treated with 500uM L-Arginine.

first: Junhe

last: Shi

first: Chen

last: Han

first: Hiba

middle: I

last: Bangash

first: Dandan

last: Chen

first: Harsh

last: Trivedi

first: Lin


title: Effect of silencing of p53 on gene expression in MDA-MB 231 TNBC cell line. [sip53]

status: Public on Oct 06 2023

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary:
Mutant p53 can acquires oncogenic properties supporting tumor growth, metastases and chemoresistance, by reprogramming cancer cell transcriptome, proteome and metabolome. To investigate what is the gene expression network regulated by mutant p53, we silenced its expression in MDA-MB-231 Triple Negative Breast Cancer (TNBC) cell line.
We then performed gene expression profiling analysis using data obtained from RNA-seq of MDA-MB 231.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MDA-MB 231 cells transfected with Control or p53 siRNAs, each in triplicate.

first: Camilla

last: Tombari

first: Alessandro

last: Zannini

first: Giannino

last: Del Sal


title: STAT1 deficiency underlies a proinflammatory imprint of naive CD4+ T cells in spondyloarthritis

first: Frédéric

last: Crémazy

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


title: STAT1 deficiency underlies a proinflammatory imprint of naive CD4+ T cells in spondyloarthritis [ChIP-Seq]

overall_design: Activating histone mark ChIP-seq, performed on naive CD4+ T cells chromatin, sorted from mesenteric lymph nodes. Comparison of non transgenic and B27-transgenic rats, premorbid or sick. H3K4Me3 and H3K27Ac Abs immunoprecipitation and IgG control. Whole genome sequencing. Analysis: Peak calling (MACS2); differential peaks enrichment (DiffBind); superenhancers (ROSE); transcription factors binding motif (HOMER).

first: Bilade

last: Cherqaoui

first: Marc

last: Lauraine

first: Ghazal

last: Shammas

first: Roula

last: Said Nahal

first: Hendrick

last: Mambu Mambueni

first: Félicie

last: Costantino

first: Marine

last: Fourmont

first: Audrey

last: Hulot

first: Henri-Jean

last: Garchon

first: Simon

last: Glatigny

first: Luiza

last: Araujo

first: Maxime

last: Breban