title: Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment [ChIP-seq]

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

summary: How constitutive allelic methylation at imprinting control regions (ICRs) interacts with other levels of regulation to drive timely parental allele-specific expression along large imprinted domains remains partially understood at most imprinted loci. To gain insight into the regulation of the Peg13-KcnK9 domain, an imprinted domain with important brain functions, during neural commitment, we performed a detailed integrative analysis of the epigenetic, transcriptomic and cis-spatial organisation in an allele-specific manner in a mouse stem cell-based model of corticogenesis that recapitulates the control of imprinted gene expression in the embryonic brain. We have evidence that despite an allelic higher order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts can occur on both alleles, although they are only productive on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side, and suggests a more nuanced role for allelic CTCF binding at the ICR of this locus.

overall_design: ChIP-seq  for H3K4me3 and H3K4me2 were generated on ES and NP cells for B6 x JF1  genetic backgrounds.

first: Jil

last: Cercy

first: Franck

last: Court

first: Philippe

last: Arnaud


title: PHF19 shRNA or scrambled control shRNA

status: Public on Feb 05 2024

city: Beijing

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

country: China

institute: Chinese PLA General Hospital

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment [RNA-seq]

country: France

overall_design: RNA-seq  generated on ES and NP cells for B6 x JF1 and JF1 x B6 genetic backgrounds.


title: High-throughput identification of the spatial origins of Drosophila optic lobe neurons using single-cell mRNA-sequencing

city: New York

first: Felix

last: Simon

state: New York

address: 24 Waverly Place

department: Biology

country: USA

institute: NYU

summary: The medulla is the largest neuropil of the Drosophila optic lobe. It contains about 100 neuronal types that have been comprehensively characterized morphologically and molecularly. These neuronal types are specified from a larval neuroepithelium called the Outer Proliferation Center (OPC) via the integration of temporal, spatial, and Notch-driven mechanisms. Although we recently characterized the temporal windows of origin of all medulla neurons, as well as their Notch status, their spatial origins remained unknown. Here, we isolated cells from different OPC spatial domains and performed single-cell mRNA-sequencing to identify the neuronal types produced in these domains. This allowed us to characterize in a high-throughput manner the spatial origins of all medulla neurons.

overall_design:
We drove the expression of nuclear GFP in cells produced from the various mOPC spatial domains using spatial region-specific Gal4 drivers. We isolated the labeled cells by Fluorescence-Activated Cell Sorting, performed scRNA-seq on the sorted cells, and annotated the cells from each population using a neural network classifier.

Optix: nuclear GFP positive optic lobe cells from the Optix-TS-MC>GFP line
dOptix: nuclear GFP positive optic lobe cells from the dOptix>GFP line
vOptix: nuclear GFP positive optic lobe cells from the vOptix-MC>GFP line
hh: nuclear GFP positive optic lobe cells from the hh-TS-MC>GFP line
dpp: nuclear GFP positive optic lobe cells from the dpp>GFP line
pxb: nuclear GFP positive optic lobe cells from the pxb-MC>GFP line

first: Félix

first: Isabel

last: Holguera

first: Yen-Chung

last: Chen

first: Jennifer

last: Malin

first: Priscilla

last: Valentino

first: Ted

last: Erclik

first: Claude

last: Desplan


title: Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment [Cut&Run]

overall_design: Cut & Run experiments for H3K27me3, CTCF, ZFP57 were generated on ES and NP cells for B6 x JF1 or JF1 x B6 genetic backgrounds.

first: Sophie

last: Perillous


title: Effect of knockdown Tbl1xr1 on gene expression after 2/3 hepatectomy

city: Guangzhou

first: Yiwei

last: Lai

state: Guangdong

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: Our spatiotemporal data confirmed activation of Tbl1xr1 in hepatocytes after 2/3 hepatectomy. TBL1XR1 is a transcriptional cofactor inducing ubiquitination and degradation of NCoR/SMRT co-repressors and NCoR is a negative regulator of hepatocyte proliferation acting through histone deacetylases (HDACs). We have examined the role of TBL1XR1 in liver regeneration through in vivo shRNA knockdown using adeno-associated viruses (shNC and shTbl1xr1) specifically targeting hepatocytes. The knockdown of Tbl1xr1 results in impair hepatocyte proliferation.To investigate the downstream targets of TBL1XR1 during liver regenration, we here perform the bulk RNA-seq for shNC and shTbl1xr1 at D2 after hepatectomy. Our data show demonstrated that Tbl1xr1 knockdown not only led to reduced cell cycle genes but also to impaired fatty acid β-oxidation as the most obviously affected liver function.

overall_design: To examine the role of TBL1XR1 in liver regeneration, we performed in vivo shRNA knockdown (shNC and shTbl1xr1) using adeno-associated viruses specifically targeting hepatocytes. Four weeks post-infection we performed PHx and extracted the liver at D2 for bulk RNA-seq.


title: RNAseq analysis of normal childhood brain tissue

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

summary: Normal brain RNAseq data provides a critical comparitor for evaluation of gene expression changes in childhood brain tumors.

overall_design: We performed RNAseq on "normal" brain samples obtained from either autopsy or routine epilepsy surgery for use in differentially gene expressed studies of childhood brain tumors. Samples were snap frozen at the time of collection and RNA was later collected using a Qiagen RNA extraction kit.


title: Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment [4C-seq]

overall_design: 4C-seq for Peg13 DMR, Kcnk9 promoter and a putative enhancer in Trappc9 gene were generated on ES and NP cells for B6 x JF1 or JF1 x B6 genetic backgrounds.

first: Cecilia

last: Rengifo Rojas


title: RNA sequencing in the Kasumi-1 cell line transfected with PHF19 shRNA or scrambled control shRNA

summary: To investigate the fuctional role of PHF19 in the regulation of cell cycle progression in t(8;21) AML, we established Kasumi-1 cell line in which PHF19 gene has been knocked down by shRNA. We then performed bulk RNA sequencing  to analyze the changes of gene expression profiling in the PHF19 knockdown cells as compared with the scrambled control cells.

overall_design: Stable silencing of the PHF19 gene in Kasumi-1 cells was achieved through a lentiviral vector-based system for RNAi (GV493/hU6-MCS-CBh-gcGFP-IRES-puromycin) constructed by GeneChem Technologies (China). Transfection of lentivirus was conducted according to the manufacturer's instruction. Kasumi-1 cells were seeded into 6-well plates overnight before transfection and the medium was changed approximately 12 to 16 hours after transfection. Forty-eight hours after shRNA transfection, cells were selected with puromycin (2 microgram per milliliter) for at least 24 hours before further investigations.

first: Xiao-Ning


title: Multi-omics study identifies unique metabolic responses to high glycemic diet in liver and retina

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: High glycemic index (HGI) diet induces hyperglycemia, an etiologic risk factor in major diseases affecting multiple organ systems. We hypothesized that adaptation to dietary glycemic exposure is tissue-specific and depends on the length of intake. We therefore evaluated transcriptomic responses to HGI diet after one or 12-months in the liver and retina of C57BL/6J wild-type mice. In the liver, the genes associated with inflammation and fatty acid metabolism were altered within one-month of HGI diet, whereas 12-month HGI diet-fed group showed dysregulated expression of multiple cytochrome P450 genes and overexpression of key lipogenic factors including Srebf1 and Elovl5. In contrast, retinal transcriptomes exhibited fewer HGI-related changes after one-month, and notable alterations in energy metabolism genes were apparent after 12-months of HGI diet. Fatty acid profiles of liver samples corroborated transcriptomic trends and revealed elevated levels of monounsaturated fatty acid in the HGI group. Conversely, saturated fatty acids and polyunsaturated fatty acids were lower in livers of HGI fed animals, regardless of length of exposure. HGI also resulted in a significant increase in blood low-density lipoprotein (LDL) and overall cholesterol levels. We also uncovered diet-aging interactions affecting expression of mitochondrial oxidative phosphorylation genes in the liver, and inherited disease-associated genes in the retina. Our findings provide new insights into tissue-specific adaptive mechanisms, focusing on the liver and the retina, to dietary hyperglycemia.

overall_design: Male C57BL/6J mice at either 6 or 12 months (M) of age were fed a high glycemic index (HGI) or low glycemic index (LGI) diet for 1 or 12 months, respectively.  The LGI diet consisted of 70% amylose and 30% amylopectin and the HGI diet consisted of 100% amylopectin.  Mice were pair-fed to ensure equal consumption in both HGI and LGI diet groups.  At experimental endpoint, mice were fasted for 6 hours and euthanized.  Tissues were collected and snap frozen in liquid nitrogen.  Total RNA was isolated from samples using a RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen).  Whole retinas or 100mg of liver tissue were homogenized and RNA-seq libraries were prepared using a TruSeq Stranded mRNA Sample Prep Kit (Illumina).  Libraries were pair-end sequenced to 101 bases on an Illumina HiSeq 2500 system.  Raw fastq files from the Illumina HiSeq 2500 System were quality checked and aligned to the v104 Mus musculus Ensembl gene annotation.  The gene counts matrix was then normalized and expressed in counts per million (CPM) using the edgeR package from Bioconductor.  To remove lowly expressed genes, a filter was used to select for genes with an average expression of greater than 1 CPM in any experimental group. Due to sequencing liver and retina samples on the same lane, 29 highly expressed retinal genes, which comprised the highest loading score values from principal component analysis, were removed from the liver samples.  Differential expression analysis comparing HGI relative to LGI groups was conducted using the voom function on the normalized, filtered counts and fitted to a linear model with the limma Bioconductor package.

first: Anupam

middle: K

last: Mondal

first: Daniel

middle: C

last: Brock

first: Sheldon

last: Rowan

first: Zhi-Hong

last: Yang

first: Krishna

middle: V

last: Rojulpote

first: Kelsey

last: Smith

first: Sarah

middle: G

last: Francisco

first: Eloy

last: Bejarano

first: Milton

last: English

first: Amy

last: Deik

last: Jeanfavre

first: Clary

middle: B

last: Clish

first: Alan

middle: T

last: Remaley

first: Allen

last: Taylor

first: Anand

last: Swaroop


title: Transcriptome profiling of lesional skin from neonate Spink5 constitutive knock-out mice

city: Paris

first: Evgeniya

last: Petrova

address: 24 Boulevard du Montparnasse

department: Imagine Institute

institute: INSERM UMR1163

summary:
Spink5 constitituve knock-out mice mimic the disease features of Netherton syndrome but die within several hours after birth due to severe skin barrier defect.
To characterize the skin barrier and skin inflammation phenotype of this mouse model at the molecular level, we collected back skin samples from mice shortly after their birth.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Spink5 constitutive knock-out newborn mice (n=4) and control (wild-type) newborn mice (n=4).

first: Jesus

last: Lopez-Gay

first: Matthias

last: Fahrner

first: Florent

last: Leturcq

first: Jean-Pierre

last: de Villartay

first: Claire

last: Barbieux

first: Patrick

last: Gonschoreck

first: Lam

last: Tsoi

first: Johann

last: Gudjonsson

first: Oliver

last: Schilling

first: Alain

last: Hovnanian


title: Neural control of fluid homeostasis is engaged below 10°C in hibernation

city: New Haven

first: Madeleine

last: Junkins

state: Connecticut

address: 333 Cedar Street

department: Cellular & Molecular Physiology; Neuroscience

institute: Yale University

summary: Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) hibernate for several months each winter without access to water, but the mechanisms that maintain fluid homeostasis during hibernation are poorly understood. In torpor, when body temperature (TB) reaches 4°C, squirrels decrease metabolism, slow heart rate, and reduce plasma levels of the antidiuretic hormones arginine vasopressin (AVP) and oxytocin (OXT). Squirrels spontaneously undergo interbout arousal (IBA) every 2 weeks, temporarily recovering an active-like metabolism and a TB of 37°C for up to 48 h. Despite the low levels of AVP and OXT during torpor, profound increases in blood pressure and heart rate during the torpor-IBA transition are not associated with massive fluid loss, suggesting the existence of a mechanism that protects against diuresis at a low TB. Here, we demonstrate that the antidiuretic hormone release pathway is activated by hypothalamic supraoptic nucleus (SON) neurons early in the torpor-arousal transition. SON neuron activity, dense-core vesicle release from the posterior pituitary, and plasma hormone levels all begin to increase before TB reaches 10°C. In vivo fiber photometry of SON neurons from hibernating squirrels, together with RNA sequencing and c-FOS immunohistochemistry, confirms that SON is electrically, transcriptionally, and translationally active to monitor blood osmolality throughout the dynamic torpor-arousal transition. Our work emphasizes the importance of the antidiuretic pathway during the torpor-arousal transition and reveals that the neurophysiological mechanism that coordinates the hormonal response to retain fluid is active at an extremely low TB, which is prohibitive for these processes in non-hibernators.

overall_design: Gene expression analysis and differential transcriptomics of the supraoptic nucleus of the hypothalamus (n = 5 biological replicates) across active (non-hibernating), torpid (hibernating) and interbout arousal (IBA) (hibernating) states in thirteen-lined ground squirrel.

middle: S

first: Ni

middle: Y

last: Feng

first: Sviatoslav

middle: N

last: Bagriantsev

first: Elena

middle: O

last: Gracheva


title: Transcription bodies regulate gene expression by sequestering CDK9 [SLAM-seq I]

city: Lausanne

first: Martino

last: Ugolini

state: Vaud

address: Genopode

department: CIG

country: Switzerland

institute: UNIL

summary: The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. It remains unclear, however, if and how they affect gene expression. Here, we disrupted the formation of two prominent endogenous transcription bodies that mark the onset of zygotic transcription in zebrafish embryos and analysed the effect on gene expression using enriched SLAM-Seq and live-cell imaging. We find that the disruption of transcription bodies results in downregulation of hundreds of genes, providing experimental support for a model in which transcription bodies increase the efficiency of transcription. We also find that a significant number of genes are upregulated, counter to the suggested stimulatory effect of transcription bodies. These upregulated genes have accessible chromatin and are poised to be transcribed in the presence of the two transcription bodies, but they do not go into elongation. Live-cell imaging shows that the disruption of the two large transcription bodies enables these poised genes to be transcribed in ectopic transcription bodies, suggesting that the large transcription bodies sequester a pause release factor. Supporting this hypothesis, we find that CDK9, the kinase that releases paused polymerase II, is highly enriched in the two large transcription bodies. Importantly, overexpression of CDK9 in wild type embryos results in the formation of ectopic transcription bodies and thus phenocopies the removal of the two large transcription bodies. Taken together, our results show that transcription bodies regulate transcription genome-wide: the accumulation of transcriptional machinery creates a favourable environment for transcription locally, while depriving genes elsewhere in the nucleus from the same machinery.

overall_design: To investigate the role of Zygotic genome activation (ZGA) in zebrafish of the loss of two major transcription bodies, we performed enriched SLAM-Seq on wild type and mir430-/- + inj. Mir430 embryos at 4 stages of ZGA, in biological triplicates.

first: Ksenia

last: Kuznetsova

first: Haruka

last: Oda

first: Hiroshi

last: Kimura

first: Nadine

middle: L

last: Vastenhouw


title: Transcription bodies regulate gene expression by sequestering CDK9 [SLAM-seq II]

overall_design: To investigate the role of Zygotic genome activation (ZGA) in zebrafish of the loss of two major transcription bodies, we performed enriched SLAM-Seq on wild type embryos that were untreated, injected with MiR430 microRNA or injected with cdk9 mRNA to cause a CDK9 overexpression. Embryos in these 3 conditions were collected at 2 stages of ZGA, in biological triplicates.


title: Transcriptome profiling of lesional skin from 3-week-old Tg.hKLK5 mice

first: Evgeniya

last: Petrova

summary:
Transgenic mice over-experssing human KLK5 (Tg.hKLK5) in the epidermis develop an inflammatory skin phenotype resembling Netherton syndrome.
To characterize the skin inflammation phenotype of this mouse model at the molecular level, we collected back skin samples from young mice at three weeks of age, when the skin phenotype is most severe.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Tg.hKLK5 mice (n=5) and control (wild-type) mice (n=5).

first: Jesus

last: Lopez-Gay

first: Matthias

last: Fahrner

first: Florent

last: Leturcq


title: Adipose-tissue regulatory T cells are a consortium of subtypes that evolves with age and diet

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Foxp3+CD4+ regulatory T (Treg) cells found within tissues regulate local immunity, inflammation and homeostasis. Tregs in epididymal visceral adipose tissue (eVAT) are critical regulators of local and systemic inflammation and metabolism. During aging and under obesogenic conditions, eVAT Tregs undergo transcriptional and phenotypic changes and are important for containing inflammation and normalizing metabolic indices. We have employed single-cell RNA sequencing, single-cell Tra and Trb sequencing, adoptive transfers, photoconvertible mice, cellular interaction analyses and in vitro cultures to dissect the evolving heterogeneity of eVAT Tregs with aging and obesity. Distinct Treg subtypes with distinguishable gene-expression profiles and functional roles were enriched at differing ages and with differing diets. Like those in lean mice, eVAT Tregs in obese mice were not primarily recruited from the circulation but instead underwent local expansion and had a distinct and diversified T cell receptor repertoire. The different eVAT-Treg subtypes specialized in different functions; for example, the subtypes enriched in lean, but not obese, mice suppressed adipogenesis. The existence of functionally divergent eVAT-Treg subtypes in response to obesogenic conditions presents possibilities for precision therapeutics in the context of obesity.

overall_design: We investigated how the heterogeneity of the eVAT SVF and Treg compartments evolved with aging and obesity. 14-wk-old Foxp3-GFP mice were placed on a low-fat or high-fat diet for 16 weeks. For scRNA-seq, the total SVF and Tregs sorted from eVAT of the mice, hashed by individual groups, and encapsulated with the Chromium 3' v3 platform. For joint scRNA-seq and scTra/b-seq, Tregs sorted from eVAT and spleen of lean and obese mice were encapsulated using the Chromium Single Cell 5' v2 and V(D)J platform (10X Genomics). Data from two independent experiments.

first: Andrés

middle: R

last: Muñoz-Rojas

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Single-Cell Analysis of Placenta Accreta Spectrum: Novel Contribution of Endothelial Cells to the Pathogenesis of Disease

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: This study utilizes advances in single-cell RNA-sequencing to generate transcriptomes from placenta accreta and control specimens.

overall_design: For each of 3 accreta placentas, a biopsy was taken at the site of deepest invasion, AI (accreta invasive), and a site opposite of AI in the same placenta where it was attached normally, AO (accreta opposite). AI and AO from three accreta participants were compared to placental biopsies from three control (C) participants.

first: Ophelia

last: Yin

first: Christine

last: Jang

first: Deanna

last: Wong

first: Yalda

last: Afshar

first: Anhyo

last: Jeong

first: Yazhen

last: Zhu


title: Transcriptome profiling of lymph nodes from Spink5 conditional knock-out mice.

summary:
We generated a viable mouse model of Netherton syndrome by conditional ablation of Spink5 gene in the epidermis.
To study the systemic inflammation phenotype of this mouse model at the molecular level, we induced Spink5 deletion in the skin of young adult mice and collected inguinal lymph nodes for transcriptome analyses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for inguinal lymph nodes of Spink5 conditional knock-out mice (n=5) and control (wild-type) mice (n=5).

first: Jean-Pierre

last: de Villartay

first: Claire

last: Barbieux

first: Patrick

last: Gonschoreck

first: Lam

last: Tsoi

first: Johann

last: Gudjonsson

first: Oliver

last: Schilling

first: Alain

last: Hovnanian


title: Transcriptome profiling of lesional skin from Spink5 conditional knock-out mice

first: Evgeniya

last: Petrova

summary:
We generated a viable mouse model of Netherton syndrome by conditional ablation of Spink5 gene in the epidermis.
To characterize this model at the molecular level, we induced Spink5 deletion in young adult mice and collected lesional skin samples for transcriptome analyses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Spink5 conditional knock-out mice (n=5) and control (wild-type) mice (n=5).

first: Jesus

last: Lopez-Gay

first: Matthias

last: Fahrner

first: Florent

last: Leturcq


title: APP and its intracellular domain modulate Alzheimer’s disease risk gene networks in transgenic APPsw and PSEN1M146I porcine models

status: Public on Feb 04 2024

city: Aarhus c

first: Per

last: Qvist

state: Danmark

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

overall_design: Refer to individual Series


title: APP and its intracellular domain modulate Alzheimer’s disease risk gene networks in transgenic APPsw and PSEN1M146I porcine models [fibroblasts]

summary: Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most frequent cause of dementia. The disease has a substantial genetic component comprising both highly penetrant familial mutations (APP, PSEN1 and PSEN2) and sporadic cases with complex genetic etiology. Mutations in APP and PSEN1/2 alter the proteolytic processing of APP to its metabolites, including Ab and APP Intracellular Domain (AICD). In this study, we use transgenic porcine models carrying the human APPsw and PSEN1M146I transgenes to demonstrate the pathobiological relevance of transcriptional regulation facilitated by APP and its AICD domain. Through molecular characterization of hippocampal tissue, we describe the differential expression of gene sets that cluster in molecular pathways with translational relevance to AD. We further identify phosphorylated and unphosphorylated AICD in differential complexes with proteins implicated in signal transduction and transcriptional regulation. Integrative genomic analysis of transcriptional changes in somatic cell cultures derived from pigs treated with g-secretase inhibitor demonstrates the importance of g-secretase APP processing in transcriptional regulation. Collectively, our data supports a model in which APP, and in particular its AICD domain, modulates gene networks associated with AD pathobiology through interaction with signaling proteins.

overall_design: Fibroblasts derived from wild type (WT) and transgenic Göttingen minipigs, carrying  copies of human APP695 cDNA with the Lys670Asn/Met671Leu (APP) double-mutation and/or one copy of human PSEN1 cDNA with the Met146Ile (genotype PS1) mutation were subjected to transcriptomic profiling using RNAseq. Fibroblasts were treated with 50M  LY294002 (in DMSO; Cell Signaling) or 2L-685-458 (secretase inhibitor in DMSO; Merck Millipore),-Secretase Inhibitor IV(in DMSO; Merck Millipore),orDMSO (Sigma Aldrich) for 24hrs.

first: Mette

last: Habekost


title: APP and its intracellular domain modulate Alzheimer’s disease risk gene networks in transgenic APPsw and PSEN1M146I porcine models [hippocampus]

overall_design: Hippocampal tissue samples from wild type (WT) and transgenic Göttingen minipigs, carrying  copies of human APP695 cDNA with the Lys670Asn/Met671Leu (APP) double-mutation and/or one copy of human PSEN1 cDNA with the Met146Ile (genotype PS1) mutation was included in study (4x APP/PS1, 4x PS1 and 4X WT). Library construction, sequencing and initial data filtering including adaptor removal were performed by BGI Europe Genome Center. Total RNA was subjected to oligo dT based mRNA enrichment. 100 bp paired-end read sequencing was performed on DNBseq platform (hippocampal tissues). More than 20 million clean reads were obtained per sample. Reads were aligned to the porcine genome build Sscrofa11.1 (Ensemble release 92) using HISAT2 aligner (v2.1.0). Transcript quantification was performed using htseq-count (v0.9.1) and the read counts were normalized for effective gene length, and sequencing depth to yield Transcripts Per Kilobase Million (TPM). Differentially expressed genes were determined from count tables using DEseq2 (v2.11.40.6)


title: Single-cell sequencing Unveils Age-Dependent Differential Impacts of Mxra7 Knockout on Mouse Bone Marrow Immune Cell Development and Function

city: Suzhou

first: Yiqiang

last: Wang

address: 111 Ren’ai Road

institute: Xi’an Jiaotong-Liverpool University

summary: Matrix remodeling associated 7 (Mxra7) belongs to the matrix remodeling-related gene family and is implicated in inflammatory neovascularization, liver injury, and autoimmune skin diseases. To elucidate the composition and transcriptional changes of bone marrow cells in Mxra7 knockout mice, we conducted single-cell RNA sequencing (scRNA-seq) in two-month-old and two-year-old mice. Our investigation revealed that Mxra7 knockout influences early B cell development and normal cell cycle functioning, impacting processes such as chromosome segregation and cell mitosis. Additionally, bone marrow B cells from knockout mice exhibited heightened differentiation potential compared to wild-type counterparts in aged mice. Mxra7 knockout initially suppressed basophil development at two months of age, only to yield an increased basophil proportation in two-year-old mice. Moreover, knockout mice exhibited elevated basophil numbers within bone marrow granulocytes. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated alterations in neurological disease-related functions in Mxra7 knockout bone marrow granulocytes. Cell communication analysis highlighted heightened quantity and quality of cellular interactions within bone marrow cells of knockout mice, notably enriching three inflammation-regulating signaling pathways. These findings underscore the pivotal role of Mxra7 in bone marrow immune cell development, with age-dependent effects on immune and inflammatory responses.

overall_design: Comprehensive analysis of single-cell RNA-seq data revealed differences between two-month-old and two-year-old wild-type (WT) and Mxra7 knockout (KO) mice.

first: Yihan

last: Chen

first: Yudan

last: Zheng


title: Biallelic non-productive enhancer-promoter interaction precedes imprinted expression of KcnK9 during mouse neural commitment

first: franck

last: court


title: The effect of MEL-6 on gene expression in LNCaP cells

city: Leuven

first: Christine

last: Helsen

address: Herestraat 49

department: Cellular and Molecular Medicine

country: Belgium

institute: KU Leuven

summary: Prostate cancer patients benefit from treatment with androgen receptor signaling inhibitors such as AR antagonists. The emergence of resistance to the clinically applied AR antagonists opens up the need for development of alternative AR antagonists. We show here the development of a novel AR antagonists that is structurally different from enzalutamide. Moreover, MEL-6 remains active in the presence of several AR mutations (T877A, W741C and F876L) that are found in patients resistant to hydroxyflutamide, bicalutamide and enzalutamide.  To validate the androgen receptor (AR) as the target of our experimental AR antagonist, MEL-6, we investigated the effect of MEL-6 treatment on the prostate cancer cell line, LNCaP.

overall_design: To identify the androgen receptor as the target of MEL-6 we performed RNASeq analysis. LNCaP cells were plated in medium with 5% dextran-coated charcoal (DCC) treated FCS at a density of 1 million cells/well in 6-well plates. After 24 hours of steroid starvation the cells were treated with vehicle (DMSO), 1 nM of the androgen R1881 or 1 nM R1881 supplemented with 10 µM of MEL-6 for 18 hours. The list of differentially expressed genes of the R1881 + MEL-6 vs R1881 comparison was consequently analyzed using Gene set enrichment analysis.

first: Frank

last: Claessens

first: Lien

last: Spans


title: RNA-sequencing of Zdhhc5 knockout oligodendrocytes

city: Xiamen

first: Yanchen

last: Ma

state: Fujian

address: Xiang'an south road

institute: Xiamen University

summary: Myelin sheath is an important structure to maintain normal functions of the nerves in central nervous system. Protein palmitoylation has been established as a sorting determinant for the transport of myelin-forming proteins to the myelin membrane. However, its function in the regulation of oligodendrocyte development remains unknown. Here, we show that an Asp-His-His-Cys (DHHC) motif-containing palmitoyl acyltransferases, DHHC5, is involved in the control of oligodendrocyte development. Loss of Zdhhc5 in oligodendrocytes inhibits myelination and remyelination by a reduction on total myelinating oligodendrocyte population. STAT3 is the primary substrate for DHHC5 palmitoylation in oligodendrocytes. Zdhhc5 ablation reduces STAT3 palmitoylation, and then suppresses STAT3 phosphorylation and activation. As a result of the decreased STAT3 transactivity, the transcription of the myelin-related and anti-apoptosis genes is therefore inhibited, leading to suppressed oligodendrocyte development and myelination. Our findings demonstrate the key role DHHC5 in the control of myelinogenesis.

overall_design: Comparison of mRNA profiles of wild type (WT) and Zdhhc5 knockout oligodendrocytes.

first: Huiqing

last: Liu

first: Zhimin

last: Ou

first: Rui

last: Xing


title: RNA-sequencing and ChIP-sequencing of STAT3 in Zdhhc5 knockout oligodendrocytes

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


title: Comparative rhythmic transcriptome profiling of human and mouse striatal subregions

status: Public on Feb 03 2024

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

state: PA

address: 450 Technology Drive

institute: University of Pittsburgh

summary: The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). In mice, this roughly corresponds to the dorsal medial striatum (DMS), dorsal lateral striatum (DLS), and ventral striatum (NAc). Each of these structures have some overlapping and distinct functions related to motor control, cognitive processing, motivation, and reward. Previously, we used a “time-of-death” approach to identify diurnal rhythms in RNA transcripts in these three human striatal subregions. Here, we identify molecular rhythms across similar striatal subregions collected from C57BL/6J mice across 6 times of day and compare results to the human striatum. Pathway analysis indicates a large degree of overlap between species in rhythmic transcripts involved in processes like cellular stress, energy metabolism, and translation. Notably, a striking finding in humans is that small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs) are among the most highly rhythmic transcripts in the NAc and this is not conserved in mice, suggesting the rhythmicity of RNA processing in this region could be uniquely human. Furthermore, the peak timing of overlapping rhythmic genes is altered between species, but not consistently in one direction. Taken together, these studies reveal conserved as well as distinct transcriptome rhythms across the human and mouse striatum and are an important step in understanding the normal function of diurnal rhythms in humans and model organisms in these regions and how disruption could lead to pathology.

overall_design: Adult male and female C57BL/6J mice (Jax stock no: 000664) (~10 wks old) were maintained on a 12:12 light/dark schedule (lights on at 7 AM (zeitgeber time 0 (ZT0)) and off at 7 PM) and were provided with food and water ad libitum. All animal use was conducted in accordance with the National Institute of Health guidelines and approved by the Institutional Animal Care and Use Committees of the University of Pittsburgh.Mice were sacrificed across 6 times of day, 4 h apart (ZT 2, 6, 10, 14, 18, and 22; n=5–6 mice/sex/timepoint). Bilateral 1-mm punches were taken centered over the NAc, DMS, and DLS. Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent), respectively. Libraries were prepared using the Smartseq stranded total RNA ultra-low input sample preparation kits (Illumina). Paired-end dual-indexed sequencing (75bp) was performed using NextSeq 500 platform (Illumina) at the University of Pittsburgh Health Sciences Sequencing Core at UPMC Children’s Hospital of Pittsburgh. A total of 40 million reads per sample was targeted. After quality control, HISAT2 (HISAT2v2.1.0) was used to align reads to the reference (Mus musculus Ensembl GRCm38) using default parameters. The resulting bam files were converted to expression count data using HTSeq (HTSeq v0.10.0) with default union mode. Filtering and normal- ization were performed separately for NAc, DMS, and DLS samples. After filtering, 11,867, 12,101, and 11,395 genes remained for NAc, DMS, and DLS samples, respectively. DESeq2 was then used to normalize for sequencing depth and RNA composition followed by a log2 transformation.

first: Kaitlyn

middle: A

last: Petersen

first: Wei

last: Zong

first: George

last: Tseng


title: Lysosomal protein transmembrane 5 driving senescence in tubular epithelial cells accelerates chronic kidney disease progression.

city: JiNan

first: Liu

middle: Xiao

last: Han

address: Baotu Spring Street

institute: Shandong University

summary: Cellular senescence is associated with the progression of chronic kidney disease (CKD), and accelerated tubular cell senescence promotes the pathogenesis of renal fibrosis. We established three animal models related to Chronic Kidney Disease, including aristolochic acid nephropathy (AAN), bilateral ischemia/reperfusion injury (BIRI) and unilateral ureter obstruction (UUO).  By RNA sequencing analysis in AAN, BIRI and UUO mice, we observed significant changes of  senescence and fibrosis related genes.

overall_design: The gene expression of 4 samples from the AAN mice was compared to 4 sham samples by RNA sequencing. The gene expression of 3 samples from the BIRI mice was compared to 3 sham samples by RNA sequencing.  The gene expression of 4 samples from the UUO mice was compared to 4 sham samples by RNA sequencing.

first: Xiaohan

first: Min


title: Differential expressed genes in WT and SCRN1 KO HepG2 cells.

city: Shanghai

first: Yijie

last: Tao

state: 上海

address: 800 Xiangyin Road

institute: Naval Medical University

summary: To functionally identify the role of SCRN1 in HCC, the stable SCRN1-knockout  HepG2 cells were generated.

overall_design: SCRN1 KO HepG2 cell was generated by using Crispr-cas9.


title: Differential gene expression in Lithium chloride (LiCl) treated Scleroderma (SSc) skin fibroblasts

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Human scleroderma skin derived fibroblast were treated with LiCL. This is a study of differential gene expression between LiCl treated SSc group and untreated SSc group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SSc fibroblast and treated with LiCl

first: Priyanka

last: Verma

first: Swati

last: Bhattacharyya

first: John

last: Varga

first: Dibyendu


title: RNA seq data of sorafenib resistant HepG2 cells

summary: To investigate the molecular mechanism of ferroptosis resistance in HCC, we applied sorafenib, one of the class I ferroptosis inducers (FINs), to generate HepG2 sorafenib resistant (SR) cells.

overall_design: Sorafenib-resistant cell line were constructed using the hepatocellular carcinoma cell line HepG2. Cells were treated with 2.5 μM sorafenib as the initial concentration, each increase was 0.5μM when the cells tolerated. The final concentration is 7μM and the cells can proliferate normally.


title: Machine-learning model based on glycosyltransferase expression predicts multiple cancer types, subtypes and survival probability

city: Thuwal

first: Jing

last: Kai

address: King Abdullah University of Science and Techonology

department: Biological and Environmental Science and Engineering Division

country: Saudi Arabia

summary: Whereas current tools for diagnosing cancer focus on identifying markers in limited types of the disease, such as the PAM50 kit known primarily for subtyping breast cancer, our research reveals that 27 different cancers have a unique glycosyltransferase (GT) fingerprint that can be detected using a single test, with 93.7% accuracy in external validation. Four models were built on the expression patterns of 71 GTs that are universally influential in inducing the formation of cancer cells and giving them the impetus to metastasize. The first differentiates cancer tissue from normal tissue, the second distinguishes cancer types, and the third and fourth models differentiate between subtypes of cancer, in particular breast cancer and glioma. Data from the Cancer Genome Atlas database were used for deriving the models, while independent publicly available databases and newly collected patient samples were used for validation. Running these models against external databases showed just how powerful they are, producing results that were highly comparable to those achieved in internal testing. Furthermore, the breast cancer classifier differentiated between breast cancer subtypes with an average of 81% accuracy in external testing, far surpassing the industry-standard PAM50’s accuracy ratio of 43%. Meanwhile, a separate prognostic model designed to predict the probability of survival among glioma patients achieved high accuracy by zooming in on four GT genes that are strongly related to prognosis. Taken together, the models demonstrate the revolutionary potential of focusing on GT genes to simplify cancer diagnostics.

overall_design:
To establish the reproducibility and verify the effectiveness of our models, we sought external validation using collected patient tissues.
We isolated the mRNA from 57 fresh and frozen patient tissue samples, both with and without cancer across six different tissue types: breast tissues (23), colon/rectum tissues (10), kidney tissues (8), brain tissues (7), liver tissues (6), and uterine tissues (3).
RNA-seq data of patient samples were used to test the clinical values of our models

first: Jasmeen

last: Merzaban

first: Abdulghani

last: Nafisah

first: AlFadel

middle: M

last: AlShaibani

first: Ali

last: Alzahrani


title: Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC


summary: The p65/RelA factor of NF-κB plays a pivotal role in coordinating gene expression in response to diverse stimuli, including viral infections. At the chromatin level, p65/RelA governs gene transcription and alternative splicing (AS) through promoter enrichment and genomic exon occupancy, respectively. However, the mechanisms underlying the coordination of these processes remain elusive. In this study, we employed the HTLV-1 Tax viral oncoprotein, a potent activator of NF-κB, to investigate the integrative relationship between 3D chromatin architecture and NF-κB-regulated AS. Our analysis revealed that Tax induces a significant reorganization of the 3D genome, resulting in the formation of multigene complexes that comprise genes co-regulated in transcription and in AS. Notably, we found that the Tax-induced gene-gene contact between the two master genes NFKBIA and RELA is associated with their differential regulation in gene expression and alternative splicing, respectively. Through dCas9-mediated approaches, we demonstrated that NFKBIA-RELA interaction is required for alternative splicing regulation and is caused by an intragenic enrichment of p65/RelA on RELA. Via this mechanism, Tax promotes the expression of the splice isoform RELAE6 that exhibits specific gene transactivation capacity at the protein level. Our findings shed light on new regulatory mechanisms upon HTLV-1 Tax and underscore the crucial role of p65/RelA in coordinated regulation of NF-κB-responsive genes at both transcriptional and alternative splicing levels in the context of the 3D genome.

overall_design: 4C-seq experiments on 293 HEK cells expressing or not the HTLV-1 TAX protein

first: Paul

last: Marie

first: Julien

last: Ladet

first: Matéo

last: Bazire

first: Lamya

last: Ameur

first: Sanjay

last: Chahar

first: Nicolas

last: Fontrodona

first: Tom

last: Sexton

first: Didier

last: Auboeuf

first: Cyril

middle: F

last: Bourgeois

first: Franck

last: Mortreux


title: Chromatin landscape of budding yeast acquiring H3K9 methylation and its reader molecule HP1 [ATAC-Seq]

city: Saitama

first: Taiki

last: Shimizu

country: Japan

institute: RIKEN

summary: Histone H3 lysine 9 (H3K9) methylation and heterochromatin protein 1 (HP1) are well conserved epigenetic silencing mark and its reader molecule, and crucial for heterochromatin formation. However, the details of the importance of H3K9 methylation and HP1 in heterochromatin formation still remain unclear. One of the reason is the redundancy problem, as there are multiple reader molecules for H3K9 methylation, including HP1, and HP1 itself functions as a hub that recruits various effector molecules. To overcome the redundancy issue, we took synthetic biology approach and introduced H3K9 methylation and HP1 into budding yeast Saccharomyces cerevisiae, which does not have this system, and examined its impact on transcription and chromatin compaction. We observed that mammalian H3K9 methyltransferase can induce genome wide H3K9 di- and tri-methylation (H3K9me2,3) in budding yeast, and that HP1 accumulates over the H3K9 methylated regions. However, H3K9 methylation occurred mainly in the gene body region of the genes and excluded around TSS where H3K9ac pre-exists. Correspondingly, expression of H3K9 methyltransferase and HP1 did not affect transcription in budding yeast, including repression. ATAC-seq analysis also showed no impact on chromatin accessibility, and Hi-C-seq analysis of chromatin 3D structure revealed no significant differences. These results suggest that even though H3K9 methylation and recruitment of HP1 play essential roles in epigenetic regulation of heterochromatin, they are not sufficient to build up heterochromatin, at least at gene body regions, and further participation of effector molecules, including downstream factors of HP1, is required.

overall_design: mSUV39H1 and HP1 were expressed in S. Cerevisiae, and the genome accessibility was analyzed by ATAC-seq.

first: Kei

last: Fukuda

first: Jun-ichi

last: Nakayama

first: Masaya

last: Oki

first: Yoichi

last: Shinkai


title: Chromatin landscape of budding yeast acquiring H3K9 methylation and its reader molecule HP1


title: Chromatin landscape of budding yeast acquiring H3K9 methylation and its reader molecule HP1 [ChIP-Seq]

overall_design: mSUV39H1 and HP1 were expressed in S. Cerevisiae, and the H3K9 methylated regions and the localization of HP1 were analyzed by ChIP-seq.


title: Chromatin landscape of budding yeast acquiring H3K9 methylation and its reader molecule HP1 [RNA-Seq]

overall_design: The effect of mSUV39H1 and HP1 expression on gene expression in S. Cerevisiae were analyzed by RNA-seq.


title: Chromatin landscape of budding yeast acquiring H3K9 methylation and its reader molecule HP1 [Micro-C XL]

overall_design: mSUV39H1 and HP1 were expressed in S. Cerevisiae, and the chromatin conformation was analyzed by Micro-C XL.


title: Transcriptome analysis of a potent Small-Molecule immunomodulator

city: Edmonton

first: Yasser

last: Tabana

state: AB

address: 87 Avenue and 114 Street

department: Pharmacy

country: Canada

institute: University of Alberta

summary: To elucidate the signalling pathways that result in activation of PBMCs following the addition of Compound B

overall_design: PBMC was treated with 12h and 24 h with either DMSO or Compound B

first: Shima

last: Shahbaz

first: Shokrollah

last: Elahi

first: Khaled

last: Barakat


title: Ribosome footprinting of wild-type Col-0 and rlmnl3 mutant

city: Beijing

first: Guifang

last: Jia

address: college of chemistry and molecular engineering, Peking University

institute: Peking University

summary: In the present study, we discover the presence of m2A in chloroplast rRNA and tRNA, as well as cytosolic tRNA, in multiple plant species. We identify six m2A-modified chloroplast tRNAs and two m2A-modified cytosolic tRNAs across different plants. Furthermore, we characterize three Arabidopsis m2A methyltransferases—RLMNL1, RLMNL2, and RLMNL3—which methylate chloroplast rRNA, chloroplast tRNA, and cytosolic tRNA, respectively. Our findings demonstrate that m2A37 promotes a relaxed conformation of tRNA, enhancing translation efficiency in chloroplast and cytosol by facilitating decoding of tandem m2A-tRNA-dependent codons. This study provides insights into the molecular function and biological significance of m2A, uncovering a layer of translation regulation in plants.

overall_design: Translation efficiency was down-regulated in rlmnl3 mutant

first: Hong-Chao

last: Duan

first: Chi

last: Zhang


title: Pharmacologic targeting of SUMOylation drives mitochondrial dysfunction and metabolic alterations in B cell Malignancies

status: Public on Feb 02 2024

city: Duarte

first: Alexey

last: Danilov

state: California

address: 1500 E duarte rd

institute: City of Hope

summary: Sumoylation is a post-translational modification process that is deregulated in cancer. We foundthat sumoylation machinery was overexpressed in diffuse large B-cell lymphoma (DLBCL).Treatment with TAK-981, a SUMO-activating enzyme (SAE) inhibitor, induced desumoylationof cytoplasmic and mitochondrial proteins, restricting growth of DLBCL and mantle celllymphoma (MCL) cell lines and primary cells. DLBCL cells treated with TAK-981 exhibitedDNA damage, G2 arrest and downregulation of DNA repair, MYC and OxPhos pathways. SAEinhibition disrupted mitochondrial integrity and function, accompanied by mitophagy and rapidaccumulation of ROS. Metabolomic profiling revealed decreases in Krebs cycle substrates, andSeahorse respirometry confirmed dramatic reduction in OxPhos upon SAE inhibition. CRISPR-Cas9 loss-of-function library screens implicated NFκB, TP53, DNA damage andcentromere/telomere gene pathways in resistance to SAE inhibition; knockout of TP53 or BAXrescued DLBCL cells from TAK-981-induced apoptosis. Treatment with TAK-981 prolongedsurvival of mice xenografted with DLBCL and MCL PDX tumors. Thus, sumoylation is apromising target in lymphoid malignancies.

overall_design: To investigate the impact of TAK981 in B cell malignancies, cultured cell lines (OCI-LY3, OCI-LY19, U2932, SU-DHL4) were treated with TAK981 at corresponding time points and collected for RNA sequencing and ATAC sequencing and compared against a 0 hr timepoint.

first: Vi

last: Lam

first: Nur

last: Bruss

first: Tingting

last: Liu


title: RNA-seq of miR-146a-5p overexpressing T24 human bladder cancer cells

city: 南京

first: li

last: meiqian

address: 学府路12号

institute: 南京大学

summary: We established  stable miR-146a-5p overexpression T24 cells, then performed transcriptome profiling of miR-146a-5p overexpressing cells compared to control T24 cells to detect the molecular mechanisms of the miR-146a-5p’s effect on bladder cancer cells.

overall_design: T24 human bladder cells were transfected with a scramble control or with a mimic for the tumor suppressor miRNA, miR-146a-5p and following validation of miRNA expression, were subjected to gene expression profiling

first: Meiqian

last: Li

first: Jun

last: Yan


title: ChIP-sequencing of STAT3 in Zdhhc5 knockout oligodendrocytes

first: Yanchen

last: Ma

overall_design: Examination of the differences of STAT3 DNA binding in wildtype (WT) and Zdhhc5 knockout oligodendrocytes.

first: Huiqing

first: Zhimin

last: Ou

first: Rui

last: Xing


title: RELATIVE ABUNDANCE OF phyla ACTINOBACTERIA AND VITAMIN C CONSUMPTION ARE ASSOCIATED WITH DNA METHYLATION.

city: São Paulo

first: Isabella

middle: Harumi Yonehara

last: Noma

state: Please select

address: Av Prof. Lineu Prestes, 580 - Bloco15

country: Brazil

institute: Universidade de São Paulo

summary:
Background: Intestinal microbiota is an emerging field and is related to health and disease. There is an emerging body of evidence that Vitamin C consumption can modulate microbiota abundance and can also impact DNA methylation of the host and this could be a link between diet, microbiota, and immune response.
Objective: It was to evaluate common CpG sites associated both vitamin C and microbiota phyla abundance.

overall_design: Methods: Six healthy women participated in this cohort study. They were divided into two groups, according to the amount of ingested Vitamin C. Ingestion was evaluated using the 24 h-recall method. Illumina 450k Beadchip was used to evaluate DNA methylation. Singular Value Decomposition analyses were used to evaluate the principal components of this dataset. Associations were evaluated using the Differentially Methylated Positions function from the Champ package for R Studio. The Shapiro-Wilk test was used to verify normality, t-tests were used to verify differences between groups, and Spearman's correlation was done between Vitamin C and phyla.

first: Carla

last: Nonino


title: Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling

city: Berkeley

first: Joseph

middle: Heimlich

last: Lobel

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

institute: UC berkeley

summary: Disordered regions within RNA binding proteins are required to control mRNA decay and protein synthesis. To understand how these disordered regions modulate gene expression, we surveyed regulatory activity across the entire disordered proteome using a high-throughput functional assay. We identified hundreds of regulatory sequences within intrinsically disordered regions and demonstrate how these elements cooperate with core mRNA decay machinery to promote transcript turnover. Coupling high-throughput functional profiling with mutational scanning revealed diverse molecular features, ranging from defined motifs to overall sequence composition, underlying the regulatory effects of disordered peptides. Machine learning analysis implicated aromatic residues in particular contexts as critical determinants of repressor activity, consistent with their roles in forming protein-protein interactions with downstream effectors. Our results define the molecular principles and biochemical mechanisms that govern post-transcriptional gene regulation by disordered regions and exemplify the encoding of diverse yet specific functions in the absence of well-defined structure.

overall_design: We measured the post-transcriptional regulatory activity of thousands of disordered peptides using a Sort-Seq style approach in budding yeast

middle: H

first: Nicholas

last: Ingolia


title: Exploring the expression pattern of circRNA in the aortic valve

city: Guanzghou

first: Gaopeng

last: Xian

address: No. 1838, Baiyun Avenue North

institute: Nanfang Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Calcific Aortic Valve Disease (CAVD) is a common heart valve condition, often characterized by severe narrowing of the aortic valve. It lacks pharmaceutical treatments and typically requires aortic valve replacement surgery, imposing a significant burden on healthcare resources.This study reports the expression profile of circRNAs in the aortic valve tissues of CAVD patients and a normal control group (non-CAVD). We collected aortic valve tissue samples from three CAVD patients who underwent aortic valve replacement surgery due to severe aortic valve stenosis, as well as aortic valve samples from non-CAVD patients who either received heart transplant surgery (recipient heart) or had their aortic valve removed due to aortic dissection. Overall, our research reveals the significant role of circRNAs in the progression of CAVD. CircRNAs, a class of circular non-coding RNA molecules, are actively studied for their functions and regulatory mechanisms within cells. These findings contribute to a deeper understanding of the molecular mechanisms underlying CAVD, particularly the potential involvement of circRNAs in this disease.

overall_design:
High-throughput sequencing was conducted on aortic valve tissues from three patients with Calcific Aortic Valve Disease (CAVD) and from four patients who had their non-calcified aortic valves removed due to heart transplant or aortic dissection. Detected circRNAs were annotated using circBase.

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first: Qingchun

last: Zeng

first: Jiaying

first: Dingli

last: Xu


title: Exploring Genes Regulated by circHIPK3 in Aortic Valve Interstitial Cells

summary: Aortic valve calcific disease (CAVD) is a common heart valve condition typically characterized by severe narrowing of the aortic valve. Our previous research has shown that circHIPK3 is downregulated in calcified aortic valve tissues and plays a role in regulating the progression of CAVD. To further investigate how circHIPK3 exerts its inhibitory effects on aortic valve calcification, we overexpressed circHIPK3 in aortic valve interstitial cells and conducted RNA-seq analysis, revealing that circHIPK3 regulates key factors in the Wnt signaling pathway. These findings contribute to a deeper understanding of the molecular mechanisms underlying CAVD, particularly the potential involvement of circRNAs in this disease.

overall_design: We separately transfected circHIPK3 overexpression plasmids and empty vectors into aortic valve interstitial cells, followed by RNA-seq analysis.

first: Rong

last: Huang


first: franck

last: mortreux

overall_design: Hi-C experiments on 293 HEK cells expressing or not the HTLV-1 TAX protein

first: Paul

last: Marie

first: Julien

last: Ladet

first: Matéo

last: Bazire

first: Lamya

last: Ameur

first: Sanjay

last: Chahar

first: Nicolas

last: Fontrodona

first: Tom

last: Sexton

first: Didier

last: Auboeuf

first: Cyril

last: Bourgeois

first: Franck

last: Mortreux


title: DOK6 Selectively Docks the Neurotrophic Signaling Transduction to Restrain Peripheral Neuropathy

first: Yan

last: Guo

address: DongDan santiao 5th

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

summary: The appropriate and specific response of nerve cells to various external cues is essential for the establishment and maintenance of neural circuits, and this process requires the proper recruitment of adaptor molecules to selectively activate downstream pathways. Here, we identified that DOK6 is required for the maintenance of peripheral axons, and loss of Dok6 can cause typical peripheral neuropathy symptoms in mice, manifested as impaired sensory, abnormal posture, paws deformities, blocked nerve conduction, and dysmyelination. Furthermore, genetic deletion of Dok6 in peripheral neurons led to axonal degeneration and hindered retrograde axonal transport. Specifically, DOK6 acts as an adaptor protein for selectivity-mediated neurotrophic signal transduction and retrograde transport for TrkC and Ret but not TrkA and TrkB. DOK6 interacts with certain proteins in the trafficking machinery and controls their phosphorylation, including MAP1B, Tau and Dynein for axonal transport, and specifically activates the downstream ERK1/2 kinase pathway to maintain axonal survival and homeostasis. This finding provides new clues to potential insights into the pathogenesis and treatment of hereditary peripheral neuropathies or other degenerative diseases.

overall_design: Look insight into if the expression of myelination-related genes is altered in Dok6 mutant sciatic nerves

first: Pan

last: Xiang


title: RNA Pol II transcription antagonises mitotic chromosome assembly and segregation by condensin

city: Lyon

first: Léonard

last: Colin

address: 9, rue du Vercors

department: LBMC

institute: ENS de Lyon

summary: Condensin drives mitotic chromosome assembly by folding chromatin into loops and is enriched in the vicinity of highly expressed genes, but the significance of such proximity with respect to condensin activity has remained unclear. Here, by modulating the occupancy of RNA Pol II in vivo, we show that transcription plays no role in the steady state association of condensin with DNA. Rather, transcription stalls and even displaces condensin, hindering its ability to fold chromatin and to support chromosome segregation. Our results highlight a key aspect of the integrated functioning of condensin and suggest that a tight control of transcription underlies mitotic chromosome assembly.

overall_design: calibrated chromatin immunoprecipitation (calChIPseq) experiment against GFP-tagged kleisin Cnd2 (A111-22 antibody) from the condensin SMC complex and Hi-C experiments in Dhp1-3xsAID (XRN2 5\222xoribonuclease) and Rpb1-3xsAID (RPB1 large subunit of RNAPII) degron tagged strains treated with or without auxin. calibrated chromatin immunoprecipitation was performed against Rpb1 (8WG16 antibody) as control in Rpb1-3xsAID strains. Calibrated chromatin immunoprecipitation (calChIPseq) experiment against Rpb1 using 8WG16 antibody in Dhp1-3xsAID cells treated with NaOH or 5-adamantyl-IAA and Hi-C experiments in wild-type and Cut14-3xsAID cells treated with 5-adamantyl-IAA.

first: Lebreton

last: Jérémy

first: Colin

last: Léonard

first: Chatre

last: Elodie

first: Bernard

last: Pascal


title: Pre-osteoclast, as an another mechano-sensing cell, has a critical role in mechano-shaping of skeleton

city: Seoul

first: Jinman

last: Kim

address: 88, Olympic-ro 43-gil, Songpa-gu

country: South Korea

institute: Asan medical center

summary: It is unclear that osteoclast lineages can sense mechanical stimuli, mainly by lack of information about the presence or absence of mechano-sensing organelles in these cells. Primary cilium is a microtubule-based organelle, which can translate mechanical loading signals into biochemical and transcriptional responses. We first identified the presence of primary cilia in tartrate-resistant acid phosphatase (TRAP)-positive mononuclear cells (preosteoclasts) prior to form TRAP-positive multinuclear cells (osteoclasts), suggesting that preosteoclasts can sense mechanical stimuli. To understand a role of primary cilia in preosteoclasts, we generated osteoclast-specific Ift88 or Kif3a knockout Cathepsin K-Cre transgenic mice. Deletion of Ift88 or Kif3a reduced the number of cilia in preosteoclasts. Micro-CT analysis display that mice with conditional deletion of Ift88 or Kif3a in osteoclast lineages led to a decrease in femoral cortical bone tissue area and bone marrow area under exercise conditions, implying that disruption of primary cilia in preosteoclasts/osteoclasts narrowed the femoral cortical bone shape. In contrast, the trabecular and cortical bone mass was not altered in these mice. Mechanistic studies showed that shear stress suppressed osteoclastogenesis by c-fos degradation. Also, shear stress increased periostin levels in conditioned media from preosteoclasts, resulting in increased differentiation and bone nodule formation of osteoblasts through activation of LRP6/-catenin. All shear stress-induced changes were near completely blocked by knock-downs of Ift88 and Kif3a in preosteoclasts. These findings first suggest that preosteoclasts may sense mechanical stimuli with a primary cilium, and that mechanical stress-mediated primary cilia activation of preosteoclasts may play an important role in controlling bone modeling and shaping by modulating both bone resorption and formation.

overall_design: We investigated the role of Ift88 in osteoclast-lineage cells upon shear stress stimulation. We generated TRAP positive mononucleated cells (pre-osteoclasts) by knockdown with Ift88 shRNA and then treating the cells with MCSF and RANKL for 2 days. Then, we applied orbital shear stress stimulation to TRAP positive mononucleated cells and analyzed the gene expression regulated compared to control through RNA-seq. In addition, gene expression regulated after orbital shear stress stimulation in Ift88 knockdown cells were also obtained through RNA-seq analysis.

first: Jung-Min

last: Koh


title: NEUROD1 efficiently converts peripheral blood cells into neurons with partial reprogramming by pluripotency factors

city: Shinjuku-ku

first: Mitsuru

last: Ishikawa

state: Tokyo

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

summary: The direct reprogramming of cells has tremendous potential in in vitro neurological studies. Previous attempts to convert blood cells into induced neurons have presented several challenges, necessitating the development of a less invasive, efficient, rapid, and convenient approach. The current study introduces an optimized method for converting somatic cells into neurons using a nonsurgical approach that employs peripheral blood cells instead of fibroblasts. We have demonstrated the efficacy of a unique combination of transcription factors, including NEUROD1, and four Yamanaka reprogramming factors (OCT3/4, SOX2, KLF4, and c-MYC), in generating glutamatergic neurons within a three-week period. This approach, which requires only five pivotal factors (NEUROD1, OCT3/4, SOX2, KLF4, and c-MYC), has the potential to create functional neurons and circumvents the need for induced pluripotent stem cell (iPSC) intermediates, as evidenced by gene expression and single-cell RNA sequencing (RNA-seq) analyses. Our method presents a rapid solution for modeling neuronal diseases with significant implications for drug discovery and personalized medicine and offers a patient-friendly alternative to traditional fibroblast reprogramming techniques.

overall_design: Human T cell-derive induced-neuron. Two different induction method. Each three replicate.

first: Yoichi

last: Saito


title: Regulation of Spermatogenesis by Different Alternative Splicing Events of MEI1 Gene in Mongolian Horse

city: 呼和浩特市

first: 代玲

last: 宋

state: 内蒙古自治区

address: 内蒙古自治区呼和浩特市昭乌达路306号内蒙古农业大学新区

institute: lnner Mongolia Key Laboratory of Equine Science Research and Technology Innovation

summary: The Mongolian horse has the characteristics of cold resistance, rough feeding resistance, good endurance, strong disease resistance and strong gregariousness. The normal production of sperm in male mammals is the basis of reproduction, and spermatogenesis includes a mitosis, meiosis twice and metamorphosis of sperm cells. The MEI1 gene is involved in the meiosis cycle and is required for normal meiosis chromosome association. Previous studies have shown that alternative splicing of MEI1 gene can promote spermatogenesis in Mongolian horses. In this study, the expression of MEI1 gene was determined by immunofluorescence in the third generation Mongolian horse testicular sertoli cells. Two overexpressed lentiviral vectors with MXE and SE events of MEI1 gene were constructed and successfully infected into sertoli cells. CCK-8 was used to detect the proliferation and activity of infected cells, transcripomics and metabolomics were used to screen and annotate differential genes and differential metabolites in the two sertoli cells with MXE and SE events. After 72 h of virus infection, 193 differentially expressed genes and 11360 differentially expressed metabolites were screened, 109 up-regulated genes including MEI1 and 84 down-regulated genes, 7494 up-regulated metabolites and 3866 down-regulated metabolites. Differential genes and differential metabolites were mainly enriched in several pathways related to spermatogenesis. Differential genes such as IL31RA, ATP2B3, CASQ2 were highly expressed in SE events, IL11, PRLR, CCR7 were highly expressed in MXE events. Metabolites such as folic acid and spermine were highly expressed in SE events, citric acid and glutathione were highly expressed in MXE events. This suggested that both MXE and SE events of MEI1 gene can promote the activity of spermatogenesis signaling pathway, and the gene influences spermatogenesis by regulating the expression of metabolites. In summary, MXE and SE events of MEI1 gene can promote the expression of spermatogen-related genes and metabolites, and genes affect spermatogenesis by regulating the expression of metabolites. The results of this study laid a theoretical foundation for exploring the regulatory mechanism of different alternative splicing events on spermatogenesis in Mongolian horse.

overall_design: In this study, we constructed a MEI1 gene overexpression lentiviral vector with MXE and SE events and transfected it into supporting cells, respectively. With MXE group as the control group, CCK-8 was used to detect the proliferation and activity of infected cells. Transcriptomics and metabolomics were used to screen and annotate the differential genes and differential metabolites of the two supporting cells of MXE and SE events.

first: Dailing

last: Song

first: Yajuan

last: Weng

first: Baterin

last: Terigele

first: Guoqing

last: Wang

first: Dugarjaviin

last: Manglai

first: Bei

last: Li


title: Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions

city: Boston

first: Stuart

last: Orkin

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Childrens Hospital

summary: Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. Upon acute depletion of Matr3, gains in chromatin accessibility and MyoD binding were observed, prior to widespread loss in the steady-state Matr3-knockout. These initial changes correlated with gene expression changes later in development. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected in close proximity to enhancer and promoter regions, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.

overall_design: In order to track chromatin accessiblity and transcription factor binding in absence of Matr3 in myoblasts derived from the skeletal muscle line C2C12, we have designed an inducible targeted degradation system to target Matr3 protein expression. We performed ATAC-seq at 4 hrs., 8 hrs. post Matr3 depletion (by the addition of dTAG treatment) and compared those with DMSO-treated cells. We also performed MyoD CUT&RUN at the 4hr and 8hr post Matr3 depletion, and CTCF, Rad21, and YY1 CUT&RUN in the same time points. We measured the gene expression by RNAseq and SLAMseq at 4hr and steady state. This dataset contains the ATACseq, CUT&RUN, RNAseq portion. A separate dataset contains the HiC portion of the experiments.

first: Tianxin

last: Liu

first: Qian

last: Zhu


title: Inhalation of panaxadiol alleviates lung inflammation via inhibiting TNFA/TNFAR and IL7/IL7R signalling [Mouse]

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

summary: Background: There are no highly effective medications for treating pneumonia. Ginseng and its derivatives have anti-inflammatory properties, but their unstable physicochemical and metabolic properties prevent them from being used to treat pneumonia. The aforementioned issues may be resolved by inhalation, but the precise mechanism of action must be investigated.  Methods: In order to study the effects and mechanisms of PD inhalation drug delivery, models of LPS-induced murine holistic pneumonia, isolated macrophage inflammation, and epithelial cell co-culture are utilized. For the evaluation of efficacy, pathology and molecular assays have been utilized. Mechanisms of action and targets were screened and validated by molecular means using transcriptome sequencing. Efficacy and mechanism of action were ultimately validated using human BALF cell models. Also studied were pharmacokinetic parameters of inhaled PD.  Results: Inhalation of PD dose-dependently reduced LPS-induced lung inflammation in mice, including inflammatory cell infiltration, lung histopathology, and inflammatory factor expression. Oral PD had the same anti-inflammatory effect as inhalation, but inhalation was more effective at the same dose. It could be a result of its increased bioavailability and improved pharmacokinetic parameters. Using transcriptome analysis and validation of macrophage and epithelial cell experiments, we discovered that PD may inhibit TNFA/TFNAR and IL7/IL7R signaling to inhibit macrophage inflammatory factor-induced epithelial cell apoptosis and promote value-added initiation. Human alveolar lavage cell experimentation confirmed this result.  Conclusion: PD inhalation alleviates lung inflammation and pathology by inhibiting TNFA/TFNAR and IL7/IL7R signaling. PD may be a novel drug for the clinical treatment of lung inflammation.

overall_design: Animals were randomly divided into 3 groups (n = 6 in each group): control (sterile saline [0.9% NaCl]), model (LPS 50 μg/mouse), E (LPS+PD (10 mg/mL, inhalation [ih.])).  For the inhaled group, mice were put into an inhalation box connect with a aerosol device (PARIBOY SX, Germany) .


title: The therapeutic effect of extracellular vesicles isolated from tonsil-derived mesenchymal stem cells for the treatment of retinal degenerative disease

city: Seongnam

first: Seung Woo

last: Choi

state: Gyeonggi

address: 82, Gumi-ro 173beon-gil, Bundang-gu

institute: Seoul National University Bundang Hospital

summary: To evaluate the differences in gene expression on RPE-1 cells under various culture conditions including stressful environment, we added the extracellular vesicles ± all-trans-retinal to the cells.

overall_design: After RNA extraction from RPE-1 cells, transcriptome sequencing, k-means clustering, and enrichment analysis were performed using the iDEP web application.

first: Seung

middle: W

first: Sooin

last: Seo

first: Hye

middle: K

last: Hong

first: So

middle: J

last: Yoon

first: Minah

first: Sunghyun

last: Moon

first: Joo

last: Lee

first: Jaeseung

last: Lim

first: Jong

first: Se

last: Woo


title: Inhalation of panaxadiol alleviates lung inflammation via inhibiting TNFA/TNFAR and IL7/IL7R signalling [Human]

summary: In order to study the effects and mechanisms of PD inhalation drug delivery, models of LPS-induced murine holistic pneumonia, isolated macrophage inflammation, and epithelial cell co-culture are utilized. For the evaluation of efficacy, pathology and molecular assays have been utilized. Mechanisms of action and targets were screened and validated by molecular means using transcriptome sequencing. Efficacy and mechanism of action were ultimately validated using human BALF cell models. Also studied were pharmacokinetic parameters of inhaled PD.

overall_design: Human monocytic THP-1 and A549 were obtained from the Shanghai Institute of Cell Biology (Shanghai, China). THP-1 cells were cultured in RPMI 1640 (GIBCO, Grand Island, NY) containing 10% FBS (GIBCO, Grand Island, NY) in 5% CO2 at 37 °C. Before further treatment, THP-1 cells (1×106 cells/mL) were inoculated into 6-well plates and treated with 500 nM PMA for 4 h to induce macrophage differentiation. Next, cells were washed 3 times with phosphate-buffered saline (PBS) and incubated for 24 h to exclude PMA interference. THP-1 cells treatment was divided into 3 groups: a control group with no treatment, a model group with LPS at 1 μg/mL, a PD group with 1 μg/mL of LPS and 10 μM of PD.


title: Inhalation of panaxadiol alleviates lung inflammation via inhibiting TNFA/TNFAR and IL7/IL7R signalling

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: PI3Kγ maintains the self-renewal of acute myeloid leukemia stem cell through regulation of the pentose phosphate pathway

first: Jean

last: Zhao

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Leukemia stem cells (LSCs) are responsible for the initiation, progression, and recurrence of leukemia. Targeting LSCs is thought as an effective way to cure leukemia, for which it is pivotal to identify novel therapeutic targets. The phosphoinositide 3-kinase (PI3K)/Akt signaling pathway is frequently activated in acute myeloid leukemia (AML) and strongly contributes to survival and proliferation of leukemia cells. Herein, we revealed that the p110γ isoform of PI3K was highly expressed in both mouse and human LSCs. Leukemogenesis was drastically delayed upon Pik3cg deletion during serial transplantations in murine acute myeloid leukemia models. Knockout of Pik3cg resulted in a remarkably impaired self-renewal, enhanced differentiation, and 32-fold reduced number of mouse acute myeloid LSCs. Interestingly, Pik3cg deficiency did not alter the functions of mouse hematopoietic stem cells. Mechanistically, PIK3CG/AKT/NRF2/PGD signaling axis controlled the pentose phosphate pathway to regulate redox metabolism and support nucleotide synthesis to maintain LSC fates. PIK3CG knockdown also led to a significant extended survival of recipients transplanted with human AML cells. Pharmaceutical inhibition of PIK3CG could efficiently restrain the progression of AML. PIK3CG may serve as a potential therapeutic target for the elimination of LSCs without influencing normal hematopoiesis.

overall_design: Transcriptome analyses were performed on wild type and Pik3cg-knockout mouse Lin-CD127-Sca-1-c-Kit+CD34+CD16/32+ L-GMP cells in MLL-AF9+ AML model, and in vivo vehicle- or IPI-549-treated Lin-CD34+CD38- AML patient-derived xenograft (PDX) cells sorted from PDX mouse models.

first: Hao

last: Gu

first: Shaozhen


title: Spatial transcriptomics reveals functional compartmentalization of estrogen receptor positive (ER+) breast cancer

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: Intratumor heterogeneity is one of the hallmarks of cancers, including breast cancers. We performed spatial transcriptomics to profile heterogeneous cell populations within ER+ breast cancers as well as to determine their importance for estrogen-dependent tumor growth. Our analysis has revealed the key functional compartments for developing targeted therapeutic strategies against ER+ breast cancers.

overall_design: Two ER+ breast cancer patient-derived xenografts (PDXs) with opposite estrogen responses for tumor growths were used for the analysis: estrogen-suppressed GS3 and estrogen-dependent SC31 models. GS3 and SC31 tumors treated with placebo or 17β-estradiol (E2) were analyzed using spatial transcriptomics.

first: Ryohei

last: Yoshitake

first: Hitomi

last: Mori


title: RNA-sequencing of brain mural cells differentiated from human pluripotent stem cell-derived neural crest via Notch3 activation

city: La Jolla

first: Benjamin

middle: D

last: Gastfriend

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Molecular mechanisms underlying the differentiation of brain mural cells from neural crest are poorly understood. We found that activation of Notch3 signaling in human pluripotent stem cell-derived neural crest (using lentiviral overexpression of the human Notch3 intracellular domain, N3ICD) was sufficient to direct the differentiation of mural cells.

overall_design: RNA-seq was performed on cells from the DF19-9-11T, H9, IMR90-4, and WTC11 hPSC lines. For each line, differentiation-matched samples of neural crest cells, and GFP-negative and GFP-positive cells isolated via FACS 6 days after transduction of neural crest with N3ICD-GFP lentivirus, were analyzed.

first: Sean

middle: P

last: Palecek

first: Eric

middle: V

last: Shusta


title: Genes expression in ci-score3 renal allograft

city: Changchun

first: Yang-He

last: Zhang

state: Jilin

address: 126 Xinmin street

institute: Jilin university

summary: To investigate the expression of genes in fibrotic renal allograft.

overall_design: We conducted spatial transcriptome detection,and then performed gene expression profiling analysis.


title: Brain mural cells differentiated from human pluripotent stem cell-derived neural crest via Notch3 activation


title: Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

type: Genome binding/occupancy profiling by genome tiling array


title: Notch3 ChIP-sequencing of brain mural cells differentiated from human pluripotent stem cell-derived neural crest via Notch3 activation

summary: Molecular mechanisms underlying the differentiation of brain mural cells from neural crest are poorly understood. We found that activation of Notch3 signaling in human pluripotent stem cell-derived neural crest (using lentiviral overexpression of the human Notch3 intracellular domain, N3ICD) was sufficient to direct the differentiation of mural cells. We used Notch3 ChIP-sequencing to identify cis-regulatory elements directly bound by the Notch3 transcriptional activation complex in this system.

overall_design: Notch3 ChIP-seq was performed on cells from three independent differentiations of the H9 hPSC line. Neural crest cells were transduced with GFP or N3ICD-GFP lentiviruses and analyzed 6 days after transduction.


title: Characterization of a luminal breast cancer patient-derived xenograft (PDX) via single-cell RNA-sequencing (scRNA-seq)

summary: Luminal breast cancers are characterized by estrogen-regulated gene profiles. We performed scRNA-seq on a luminal breast cancer PDX named GS1 to profile the gene expression of the cells constituting GS1 tumor and to investigate the effect of estrogen on the individual populations.

overall_design: GS1 has shown a luminal-B like feature with low estrogen receptor (ER) expression (5%). Because the growth of this tumor can be partly promoted by the addition of estrogen but also grow without estrogen, GS1 has been defined as an estrogen-accelerating luminal breast cancer model. GS1 tumors from control, 17β-estradiol (E2), and E2 + ICI 182, 780 (ER antagonist; ICI) groups were analyzed using scRNA-seq.

first: Hyun-Jeong

last: Shim


title: Sex-specific nociceptor modulation of apical periodontitis transcriptome

status: Public on Feb 01 2024

city: San Antonio

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Apical periodontitis (AP) is a painful disease that develops quickly following dental infections and is primarily characterized by robust inflammation surrounding the tissues of the affected tooth, resulting in disruption of bone homeostasis and periradicular bone loss. Moreover, there are distinct clinical presentations, symptoms, and responses to AP treatment between males and females, creating a desperate need to further understand the sex-specific mechanisms of AP. With the growing evidence that nociceptors modulate AP development, we utilized RNA sequencing in nociceptor-ablated (Nav1.8 cre+/-, Diphtheria Toxin Alox+/-) transgenic mice to study nociceptor regulation of the periapical lesion transcriptome using a rodent model of AP in female mice over 14 days. Overall, we found that female mice exhibit unique patterns of differentially expressed genes throughout AP infection compared to male mice, and that the expression of these genes is regulated by nociceptors. Additionally, nociceptor-ablation results in a more significant enrichment of biological processes related to immune responses earlier compared to cre-control (Nav1.8 cre+/-) females as well as greater expression of genes involved in inflammatory processes and osteolytic activity. Therefore, while nociceptor-ablation augments inflammatory and bone resorption responses in both males and females in a mouse model of AP, transcriptomic analyses demonstrate the mechanisms through which nociceptors modulate AP are distinct between sexes. These studies will provide the foundation needed to study further mechanisms of sex differences in AP, an area with a desperate need for investigation to treat current AP patients. Understanding these mechanisms can ultimately inform treatment options to alleviate suffering for millions of patients suffering from AP.

overall_design: For each time point (Day 0, Day 7, and Day 14), we used 3-4 female mice, approximately 8 weeks old, from each strain. These strains included Nav1.8cre+ (control) and Nav1.8cre+/DTA+ (nociceptor-ablated), amounting to a total of 20 samples.

first: Anibal

last: Diogenes

first: Katherine

last: Lillis

first: Zhao

last: Lai


title: Genomic characteristics of RARRES1 wild type and knockout mice lung tissues

city: Goyang-si

first: Kyungtae

last: Kim

state: Gyeonggi-do

address: 323 Ilsan-ro

institute: National Cancer Center

summary:
Purpose: RARRES1 is proposed as tumor suppressor gene but its function is not clear yet. To elucidate RARRES1 function in carcinogenesis, we examine phenotype and genetic characteristics of the RARRES1 genetically knockout mice lung.
Methods: Genetic profiles of RARRES1 wild type and knockout mouse lung tissues of embryonic day 19.5, 10-month-old, and 18-month-old mice were analyzed by whole genome and RNA sequencing in triplicate, using Illumina Hiseq X ten. Additionally, three lung tumors originated from RARRES1 knockout mice also examine using same platform.
Results: RARRES1 knockout accelerate spontaneous lung carcinogenesis, with pluripotency of stem cells, Hippo signaling pathway, Wnt signaling pathway, and cell cycle related genes are significantly activated including Nanog, CDK1, Cyclin E. In addition, RARRES1 knockout induced lung cancer had rare oncogenic mutations, on the contrary, lung tissue progenitor cell, lung bipotent progenitor cell and AT2 type cell popularity increased.
Conclusions: RARRES1 knockout accelerate spontaneous lung carcinogenesis through organ stem cell population enhancement with various stemness related gene set activation beside rare mutational driving.

overall_design: Lung whole genome and RNA profiles of triplicated embryonic day 19.5, 10-month-old, and 18-month-old wild type and RARRES1 knockout mice. Additionally, three RARRES1 knockout mice originated lung tumor were analyzed by Illumina Hiseq X ten.

first: Eun-Kyung

last: Yoon

first: Su

last: Lee

first: Doyeong

last: Yu

first: Ho

first: Charny

last: Park


title: Effect of knockdown ACOX1 on gene expression in HK-2 cells

summary: To investigate the role of ACOX1, we knocked down ACOX1 by shRNA in HK-2 cell lines and detected differential genes. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control HK-2 cells and its KD derivative (shACOX1).


title: Identification of lineage-specific epigenetic regulators FOXA1 and GRHL2 through chromatin accessibility profiling in breast cancer cell lines [RNA-seq]

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

summary: Breast cancer is a heterogeneous disease, and breast cancer cell lines are invaluable for studying this heterogeneity. However, the epigenetic diversity across these cell lines remains poorly understood. In this study, we performed genome-wide chromatin accessibility analysis on 23 breast cancer cell lines, including 2 estrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative (ER+/HER2−), 3 ER+/HER2+, 2 HER2+, and 15 triple-negative breast cancer (TNBC) lines. These cell lines were classified into three groups based on their chromatin accessibility: the receptor-positive group (Group-P), TNBC basal group (Group-B), and TNBC mesenchymal group (Group-M). Motif enrichment analysis revealed that only Group-P exhibited coenrichment of forkhead box A1 (FOXA1) and grainyhead-like 2 (GRHL2) motifs, whereas Group-B was characterized by the presence of the GRHL2 motif without FOXA1. Notably, Group-M did not show enrichment of either FOXA1 or GRHL2 motifs. Furthermore, gene ontology analysis suggested that group-specific accessible regions were associated with their unique lineage characteristics. To investigate the epigenetic landscape regulatory roles of FOXA1 and GRHL2, we performed knockdown experiments targeting FOXA1 and GRHL2, followed by assay for transposase-accessible chromatin sequencing analysis. The findings revealed that FOXA1 maintains Group-P–specific regions while suppressing Group-B–specific regions in Group-P cells. In contrast, GRHL2 preserves commonly accessible regions shared between Group-P and Group-B in Group-B cells, suggesting that FOXA1 and GRHL2 play a pivotal role in preserving distinct chromatin accessibility patterns for each group. Specifically, FOXA1 distinguishes between receptor-positive and TNBC cell lines, whereas GRHL2 distinguishes between basal-like and mesenchymal subtypes in TNBC lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T47D and HCC38 and their KD derivatives (siFOXA1 or siGRHL2).

first: Liying

last: Yang

first: Reo

last: Maruyama


title: Identification of lineage-specific epigenetic regulators FOXA1 and GRHL2 through chromatin accessibility profiling in breast cancer cell lines [ATAC-seq]

overall_design: chromatin accessibility profile of breast cancer cell lines using ATAC-seq


title: Cyclosporin ameliorates right ventricular remodeling of postnatal mice with volume overload.

city: Shanghai

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

summary: We reported the RNAseq analyses of right ventricular free wall of myocardium in three groups of mice（3 in each group）at postnatal day 14 (P14). The mice in volume overload (VO) group underwent an abdominal surgery by puncture from aorta to inferior vena cava at P7, mice in Sham group underwent the same surgery except for the puncture. The mice in CsA group were VO mice who were also injected with cyclosporin A(CsA) for seven days. The results revealed that there were differentially expressed genes between VO and sham group at P14, Inhibiting the immune response with CsA caused the gene expression profile of VO mice to shift towards that of sham mice.

overall_design: RNAseq analyses of right ventricular myocardium  in volume overload, CsA treated and sham-operated postnatal mice.

first: Sijuan

last: Sun

first: Lincai

last: Ye


title: Batf3-Dependent Orchestration of the Robust Th1 Responses and Fungal Control during Cryptococcal Infection, the role of cDC1.

city: Ann Arbor

first: Jintao

last: Xu

address: 2215 Fuller Rd

institute: University of Michigan Hospital

summary: We investigated the role of the cDC1 subset in a fungus-restricting mouse model of cryptococcal infection.

overall_design: Immune cells from Naïve and infected brains of C57Bl6/J mice at different time points were isolated and analyzed using the 10x Genomics' Chromium Single Cell 3' solution

first: Rylan

last: Hissong

first: Rachel

last: Bareis

first: Arianna

last: Creech

first: Kristie

last: Goughenour

first: Christine

last: Freeman

first: Michal

last: Olszewski


title: Single-cell RNA-seq analysis of orbitofrontal cortex in rodent model of Methamphetamine-induced sensitization

city: Ningbo

first: Qiong

state: Zhejiang

address: Kongpu

institute: Ningbo University

summary: Due to the complexity and diversity of the cellular changes, our understanding of the exact molecular and cellular mechanisms underpinning behavioral sensitization remains incomplete, particularly, the role of non-neuronal cells. Therefore, the present study explored the single-cell transcriptional changes in the orbitofrontal cortex (OFC) - a region implicated in decision-making and reward-related behaviors in a rodent model of methamphetamine-induced sensitization. Our study provides insights into the molecular mechanisms underlying dysfunction of microglial cells associated with the development of drug addiction.

overall_design: Animals included in current study were all 8-week-old male Sprague-Dawley rats. Rats were treated with 1 mg/kg METH or saline (intraperitoneal) for 7 days in the METH and saline groups, respectively. Then all rats were deeply anesthetized with pentobarbital (60 mg/kg, i.p.) and sacrificed, and the OFCs of four per group were rapidly removed and prepared for single nucleus isolation on ice. The nucleus-barcoded 3’ gene expression libraries were sequenced on an Illumina NovaSeq6000 system.


title: Hippo signaling-controlled MHC-I antigen processing and presentation pathway potentiates antitumor immunity

city: Nanjing

first: linyuan

last: peng

address: #639 Longmian Dadao, Jiangning District,Nanjing

institute: China Pharmaceutical University

summary: MHC class I (MHC-I)-mediated tumor antigen processing and presentation (APP) pathway is essential for recruitment and activation of cytotoxic CD8+ T lymphocytes (CD8+ CTLs). However, this pathway is frequently dysregulated in many cancers, thus leading to a failure of immunotherapy. Here, we reported that activation of the tumoral intrinsic Hippo pathway positively correlated with the expression of MHC-I APP genes and the abundance of CD8+ CTLs in mouse tumors and patients. Blocking the Hippo pathway effector YAP/TEAD potently improved antitumor immunity. Mechanistically, the YAP/TEAD complex cooperated with the NuRD complex to repress the NLRC5 transcription. The upregulation of NLRC5 by YAP/TEAD depletion or pharmacological inhibition increased the expression of MHC-I APP genes and enhanced CD8+ CTLmediated killing of cancer cells. Collectively, our results suggest a novel tumorpromoting function of YAP depending on NLRC5 to impair MHC-I APP pathway and provide a rationale for inhibiting YAP activity in immunotherapy for cancer.

overall_design: To elucidate the potential mechanism of Yap in breast cancer, RNA-seq analysis was performed in 4T1 cells to analyze differential expressed genes after Yap knockdown.RNA libraries were prepared for sequencing using standard Illumina protocols.

first: Zhongyuan

last: Wang

first: Minxian

last: Qian

first: Desheng

last: Lu


title: RNA sequencing of PART1 knockdown by siRNA in ovarian cancer cells

city: Jinan, Shandong

first: Huan

last: Wu

state: Asia

address: 107 West Wenhua Road

department: Obstetrics and Gynecology

institute: Qilu Hospital

summary: The expression of lncRNA PART1 was found to be significantly upregulated in platinum-sensitive patients with ovarian cancer, and this upregulation was positively correlated with a favorable prognosis. Cellular experiments demonstrated that inhibition of PART1 led to cellular senescence and increased resistance to cisplatin and PARP inhibitors. Thus, LncRNA PART1 is a novel target for overcoming resistance to PARP inhibitors in ovarian cancer.

overall_design: To investigate the comprehensive function of lncRNA PART1 in the regulation of PARP inhibitor sensitivity, we established A2780 cell lines in which PART1 has been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression profiling analysis of RNA-seg data for A2780 cells and its KD derivatives.


title: Transcriptional response of Gemmatimonas phototrophica to changing light regimes [AP64_HighLight]

city: Trebon

first: Karel

middle: Vaclav

last: Kopejtka

address: Novohradska

department: Centre Algatech

country: Czech Republic

institute: Institute of Microbiology Czech Acad. Sci.

summary: In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.

overall_design: G. phototrophica AP64T (= DSM 29774) was grown in an optimized liquid medium described earlier (Shivaramu et al., 2023) at 25°C. At the beginning of each experiment, the inoculum (approx. OD600 = 0.2) was diluted in 100 mL of a fresh medium to approx. OD600 = 0.03. Cultures were grown in triplicates aerobically in the dark until reaching approx. OD600 = 0.2. Then cultures were illuminated with photon flux density of 200 µmol photons m-2 s-1. Sampling was done 2, 4, and 8 hours after the light was switched on. Control cultures were kept in dark and sampled for each time point as a reference.

first: Jürgen

last: Tomasch

first: Sahana

last: Shivaranu

first: Mohit

last: Saini

first: David

last: Kaftan

last: Koblížek