Differences in articular hip cartilage gene expression between femoroacetabular impingement (FAI) and end-stage hip osteoarthritis

Objectives: The morphological deformities in Femoroacetabular Impingement (FAI) have been associated with hip osteoarthritis (OA), however the molecular mechanisms for OA initiation and progression are poorly understood. The purpose of this study was to use whole genome RNA sequencing to characterize differences in gene expression articular cartilage samples isolated from patients undergoing surgery for FAI and idiopathic OA. We hypothesized that there would be significant differences in genes expression in pathways related to inflammation as well as cartilage and bone turnover. Methods: 20 patients undergoing either hip arthroscopy for FAI (5 male, 5 female) or total hip arthroplasty (5 male, 5 female) for end-stage osteoarthritis were included in the study. FAI patients required a Cam deformity with an Alpha Angle greater than 55 while patients with dysplasia (LCEA<25) or prior hip surgery were excluded. Exclusion criteria for the THA cohort included dysplasia, and post-traumatic OA or inflammatory OA. Cartilage samples were obtained over the Cam deformity prior to femoroplasty in the FAI group or over anterosuperior femoral head-neck junction in the OA group following extraction of the femoral head. Following RNA isolation, Next Generation RNA sequencing was performed to evaluate gene expression. Differential expression data was incorporated into the Ingenuity Pathway Analysis (IPA) platform to identify differences in canonical signaling pathways associated with osteoarthritis. Results: There were 3531 genes that were significantly differentially expressed between the FAI and OA cohorts. Of these, there were 27 genes that were upregulated by a greater than 2 log-fold change in the OA cohort and 524 genes that were upregulated by a greater than 2 log-fold change in the FAI cohort. There was significant differential expression in genes related to cartilage metabolism (Table 1) and canonical osteoarthritis pathways involving BMP, TGFβ, and Wnt signaling. (Table 2). Additionally, FAI samples had significant upregulation of EGF-ERBB mediated signaling which compared to osteoarthritic tissue. Conclusion: The results of the present study support our hypothesis that there are significant differences in gene expression between FAI and OA samples in multiple pathways that are implicated in osteoarthritis. Osteoarthritis samples had increased expression of cartilage breakdown and inflammation while femoroacetabular impingement samples had greater expression of chondroprotective genes. Further study of cartilage samples from FAI patients may provide insight into the molecular mechanisms of osteoarthritis progression. [Table: see text][Table: see text]

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Comparative analysis of molecular aberration in different genders for identification of key pathways in hepatocellular carcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e23192 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e23192-e23192

Author(s):

Li Yu ◽

Feng Tieshan ◽

Lifeng Li ◽

Shifu Chen ◽

Liu Xiaoliang

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Differential Expression ◽

Mutation Frequency ◽

Molecular Mechanisms ◽

Rho Gtpase ◽

Enrichment Analysis ◽

Fold Change ◽

P Value ◽

Males And Females

e23192 Background: The incidence rate of hepatocellular carcinoma (HCC) varies significantly between genders, being higher in men than in women. While the molecular mechanisms remain unexplored, we systematically analyzed the gene expression and SNV signature to identify key molecular aberrations and pathways. Methods: Gene expression and simple nucleotide variation data of 407 HCC patients with HCC including 140 females and 267 males were collected. We identified genes with differential mutation frequency in two cohorts using Fisher’s exact test (p-value < 0.05), and Deseq2 to identify differential expression genes (FDR < 0.05 and fold change > 2). Enrichment analysis was applied using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Reactome database (p adjust < 0.05). Results: In total, 103 genes with differential mutation frequency in two cohorts were identified. Of these genes, 57 genes were differentially expressed, and the number of up-regulated genes in males and females were 21 and 36, respectively. The genes that show significant up-regulation in males are KDM5D and ANKFN1 which have the log2(fold change) of 7.49 and 4.45. The genes that show significant up-regulation in females are SYT13 and SCD5 which have the log2(fold change) of 2.33 and 2.29. The result of enrichment analysis showed that the up-regulated genes in males and females were involved in different biological pathways. In males, the up-regulated genes mainly participated in the PPAR signaling pathway. In females, the up-regulated genes mainly participated in the Rho GTPase cycle, regulation of insulin secretion and integration of energy metabolism. Conclusions: In this study, 57 genes with differential mutation frequency and differential expression between males and females with HCC were identified based on TCGA dataset. Enrichment analysis result indicated that these genes are mainly involved in signaling pathways relevant to carcinogenesis and metabolism.

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Transcriptomic Modification in the Cerebral Cortex following Noninvasive Brain Stimulation: RNA-Sequencing Approach

Neural Plasticity ◽

10.1155/2016/5942980 ◽

2016 ◽

Vol 2016 ◽

pp. 1-15 ◽

Cited By ~ 2

Author(s):

Ben Holmes ◽

Seung Ho Jung ◽

Jing Lu ◽

Jessica A. Wagner ◽

Liudmilla Rubbi ◽

...

Keyword(s):

Gene Expression ◽

Cerebral Cortex ◽

Rna Sequencing ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Current Intensity ◽

Beneficial Effects ◽

Group A ◽

The Impact

Transcranial direct current stimulation (tDCS) has been shown to modulate neuroplasticity. Beneficial effects are observed in patients with psychiatric disorders and enhancement of brain performance in healthy individuals has been observed following tDCS. However, few studies have attempted to elucidate the underlying molecular mechanisms of tDCS in the brain. This study was conducted to assess the impact of tDCS on gene expression within the rat cerebral cortex. Anodal tDCS was applied at 3 different intensities followed by RNA-sequencing and analysis. In each current intensity, approximately 1,000 genes demonstrated statistically significant differences compared to the sham group. A variety of functional pathways, biological processes, and molecular categories were found to be modified by tDCS. The impact of tDCS on gene expression was dependent on current intensity. Results show that inflammatory pathways, antidepressant-related pathways (GTP signaling, calcium ion binding, and transmembrane/signal peptide pathways), and receptor signaling pathways (serotonergic, adrenergic, GABAergic, dopaminergic, and glutamate) were most affected. Of the gene expression profiles induced by tDCS, some changes were observed across multiple current intensities while other changes were unique to a single stimulation intensity. This study demonstrates that tDCS can modify the expression profile of various genes in the cerebral cortex and that these tDCS-induced alterations are dependent on the current intensity applied.

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The Western Diet Regulates Hippocampal Microvascular Gene Expression: An Integrated Genomic Analyses in Female Mice

Scientific Reports ◽

10.1038/s41598-019-55533-9 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Saivageethi Nuthikattu ◽

Dragan Milenkovic ◽

John Rutledge ◽

Amparo Villablanca

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Differential Expression ◽

Differential Gene Expression ◽

Gene Networks ◽

Molecular Mechanisms ◽

Western Diet ◽

Protein Coding ◽

Female Mice ◽

Differential Gene

AbstractHyperlipidemia is a risk factor for dementia, and chronic consumption of a Western Diet (WD) is associated with cognitive impairment. However, the molecular mechanisms underlying the development of microvascular disease in the memory centers of the brain are poorly understood. This pilot study investigated the nutrigenomic pathways by which the WD regulates gene expression in hippocampal brain microvessels of female mice. Five-week-old female low-density lipoprotein receptor deficient (LDL-R−/−) and C57BL/6J wild type (WT) mice were fed a chow or WD for 8 weeks. Metabolics for lipids, glucose and insulin were determined. Differential gene expression, gene networks and pathways, transcription factors, and non-protein coding RNAs were evaluated by genome-wide microarray and bioinformatics analysis of laser captured hippocampal microvessels. The WD resulted in differential expression of 2,412 genes. The majority of differential gene expression was attributable to differential regulation of cell signaling proteins and their transcription factors, approximately 7% was attributable to differential expression of miRNAs, and a lesser proportion was due to other non-protein coding RNAs, primarily long non-coding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs) not previously described to be modified by the WD in females. Our findings revealed that chronic consumption of the WD resulted in integrated multilevel molecular regulation of the hippocampal microvasculature of female mice and may provide one of the mechanisms underlying vascular dementia.

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Experimental Design & Analysis of Protein Array Data: Applying Methods from cDNA Arrays.

Blood ◽

10.1182/blood.v104.11.4280.4280 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4280-4280

Author(s):

Jeanette E. Eckel ◽

Antje Hoering ◽

Irene Ghobrial

Keyword(s):

Gene Expression ◽

Experimental Design ◽

Differential Expression ◽

Protein Microarray ◽

Random Noise ◽

Reference Sample ◽

Fold Change ◽

Protein Array ◽

Microarray Technology ◽

Cdna Arrays

Abstract It appears that a number of recent manuscripts using protein microarray technology are using equivalent analysis procedures that the gene-expression microarray community implemented in their infancy. That is, utilizing a classic reference design such that the ratio of the sample of interest to a reference sample is the response of interest and assessing fold change to determine differential expression. For example, recent publications have concluded that proteins with a fold change less than 0.7 or greater than 1.3 demonstrate significant down- or up-regulated differential expression, respectively. However, fold change is an unreliable measure of differential expression and statistical models that distinguish true signal from random noise should be utilized instead of fold changes. Over the last half decade a tremendous amount of research has been devoted to gene-expression microarrays to vastly improve on the areas of experimental design, normalization and statistical analyses to assess differential expression and classification and these methods are directly applicable to protein microarray technology. Thus, the objective is to review the statistical methodology that has been developed for two-color cDNA arrays that is directly applicable to protein arrays. Examples are provided from a mantle-cell lymphoma protein-array experiment.

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RNA sequencing of Stentor cell fragments reveals key processes underlying cellular regeneration

10.1101/232363 ◽

2017 ◽

Cited By ~ 1

Author(s):

Henning Onsbring Gustafson ◽

Mahwash Jamy ◽

Thijs J. G. Ettema

Keyword(s):

Differential Expression ◽

Rna Sequencing ◽

Molecular Mechanisms ◽

Anterior Part ◽

Differential Expression Analysis ◽

Biological Studies ◽

Ability To Regenerate ◽

Cellular Regeneration ◽

A Cell ◽

Cell Fragments

SummaryWhile ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast. Altogether, differential expression analysis of both posterior and anterior S. polymorphus cell fragments for four different post-split time points revealed over 10,000 up-regulated genes throughout the regeneration process. Among these, genes involved in cell signaling, microtubule-based movement and cell cycle regulation seemed to be particularly important during cellular regeneration. We identified roughly nine times as many up-regulated genes in regenerating S. polymorphus posterior fragments as compared to anterior fragments, indicating that regeneration of the anterior oral apparatus is a complex process that involves many genes. Our analyses identified several expanded groups of genes such as dual-specific tyrosine-(Y)-phosphorylation regulated kinases and MORN domain containing proteins that seemingly act as key-regulators of cellular regeneration. In agreement with earlier morphological and cell biological studies, our differential expression analyses indicate that cellular regeneration and vegetative division share many similarities.

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Single nucleus RNA-sequencing reveals altered intercellular communication and dendritic cell activation in nonobstructive hypertrophic cardiomyopathy

10.1101/2021.12.20.21267954 ◽

2021 ◽

Author(s):

Christina J Codden ◽

Amy Larson ◽

Junya Awata ◽

Gayani Perera ◽

Michael T Chin

Keyword(s):

Gene Expression ◽

Extracellular Matrix ◽

Hypertrophic Cardiomyopathy ◽

Growth Factor ◽

Rna Sequencing ◽

Intercellular Communication ◽

Inhibitor Activity ◽

Factor Binding ◽

Single Nucleus ◽

End Stage

End stage, nonobstructive hypertrophic cardiomyopathy (HCM) is an intractable condition with no disease-specific therapies. To gain insights into the pathogenesis of nonobstructive HCM, we performed single nucleus RNA-sequencing (snRNA-seq) on human HCM hearts explanted at the time of cardiac transplantation and organ donor hearts serving as controls. Differential gene expression analysis revealed 64 differentially expressed genes linked to specific cell types and molecular functions. Analysis of ligand-receptor pair gene expression to delineate potential intercellular communication revealed significant reductions in expressed ligand-receptor pairs affecting the extracellular matrix, growth factor binding, peptidase regulator activity, platelet-derived growth factor binding and protease binding in the HCM tissue. Changes in Integrin-beta1 receptor expression were responsible for many changes related to extracellular matrix interactions, by increasing in dendritic, smooth muscle and pericyte cells while decreasing in endothelial and fibroblast cells, suggesting potential mechanisms for fibrosis and microvascular disease in HCM and a potential role for dendritic cells. In contrast, there was an increase in ligand-receptor pair expression associated with adenylate cyclase binding, calcium channel molecular functions, channel inhibitor activity, ion channel inhibitor activity, phosphatase activator activity, protein kinase activator activity and titin binding, suggesting important shifts in various signaling cascades in nonobstructive, end stage HCM.

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Sex differences in the human brain transcriptome of cases with schizophrenia

10.1101/2020.10.05.326405 ◽

2020 ◽

Author(s):

Gabriel E. Hoffman ◽

Yixuan Ma ◽

Kelsey S. Montgomery ◽

Jaroslav Bendl ◽

Manoj Kumar Jaiswal ◽

...

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Differential Expression ◽

Large Scale ◽

Molecular Mechanisms ◽

Age Of Onset ◽

Differential Expression Analysis ◽

Gene Expression Signature ◽

Synaptic Organization ◽

Expression Signature

AbstractWhile schizophrenia differs between males and females in age of onset, symptomatology and the course of the disease, the molecular mechanisms underlying these differences remain uncharacterized. In order to address questions about the sex-specific effects of schizophrenia, we performed a large-scale transcriptome analysis of RNA-seq data from 437 controls and 341 cases from two distinct cohorts from the CommonMind Consortium. Analysis across the cohorts identifies a reproducible gene expression signature of schizophrenia that is highly concordant with previous work. Differential expression across sex is reproducible across cohorts and identifies X- and Y-linked genes, as well as those involved in dosage compensation. Intriguingly, the sex expression signature is also enriched for genes involved in neurexin family protein binding and synaptic organization. Differential expression analysis testing a sex-by-diagnosis interaction effect did not identify any genome-wide signature after multiple testing corrections. Gene coexpression network analysis was performed to reduce dimensionality and elucidate interactions among genes. We found enrichment of co-expression modules for sex-by-diagnosis differential expression signatures, which were highly reproducible across the two cohorts and involve a number of diverse pathways, including neural nucleus development, neuron projection morphogenesis, and regulation of neural precursor cell proliferation. Overall, our results indicate that the effect size of sex differences in schizophrenia gene expression signatures is small and underscore the challenge of identifying robust sex-by-diagnosis signatures, which will require future analyses in larger cohorts.

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A guide to creating design matrices for gene expression experiments

F1000Research ◽

10.12688/f1000research.27893.1 ◽

2020 ◽

Vol 9 ◽

pp. 1444

Author(s):

Charity W. Law ◽

Kathleen Zeglinski ◽

Xueyi Dong ◽

Monther Alhamdoosh ◽

Gordon K. Smyth ◽

...

Keyword(s):

Gene Expression ◽

Data Analysis ◽

Differential Expression ◽

Rna Sequencing ◽

Expression Analysis ◽

Graphical Representation ◽

Differential Expression Analysis ◽

Data Types ◽

Software Packages ◽

Set Up

Differential expression analysis of genomic data types, such as RNA-sequencing experiments, use linear models to determine the size and direction of the changes in gene expression. For RNA-sequencing, there are several established software packages for this purpose accompanied with analysis pipelines that are well described. However, there are two crucial steps in the analysis process that can be a stumbling block for many -- the set up an appropriate model via design matrices and the set up of comparisons of interest via contrast matrices. These steps are particularly troublesome because an extensive catalogue for design and contrast matrices does not currently exist. One would usually search for example case studies across different platforms and mix and match the advice from those sources to suit the dataset they have at hand. This article guides the reader through the basics of how to set up design and contrast matrices. We take a practical approach by providing code and graphical representation of each case study, starting with simpler examples (e.g. models with a single explanatory variable) and move onto more complex ones (e.g. interaction models, mixed effects models, higher order time series and cyclical models). Although our work has been written specifically with a limma-style pipeline in mind, most of it is also applicable to other software packages for differential expression analysis, and the ideas covered can be adapted to data analysis of other high-throughput technologies. Where appropriate, we explain the interpretation and differences between models to aid readers in their own model choices. Unnecessary jargon and theory is omitted where possible so that our work is accessible to a wide audience of readers, from beginners to those with experience in genomics data analysis.

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Age-related differences in gene expression in colorectal cancer (CRC).

Journal of Clinical Oncology ◽

10.1200/jco.2018.36.4_suppl.654 ◽

2018 ◽

Vol 36 (4_suppl) ◽

pp. 654-654

Author(s):

Raphael M Byrne ◽

Rebecca Ruhl ◽

Christian Lanciault ◽

Sudarshan Anand ◽

Abhinav Nellore ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Rna Sequencing ◽

Young Patients ◽

Young Group ◽

Fold Change ◽

Differentially Expressed ◽

Mouse Tumor ◽

Sequencing Data ◽

Old Patients

654 Background: Colorectal cancer (CRC) in young patients is increasing in incidence and is associated with worse outcomes than CRC in older patients. While distinct molecular subtypes of CRC have been recently characterized, it is unclear whether there are molecular differences between the tumors of young and old patients. We sought to identify differences in gene expression of CRC between these two groups. Our discovery analysis identified a gene signature of several differentially expressed RNAs, from which we validated PEG10. The PEG10 gene on chromosome 7q21.3 has been implicated in liver, gallbladder, thyroid, and blood cancers, and is thought to play a role in cancer cell survival and regulation of apoptosis. In hepatocellular carcinoma, increased PEG10 expression has been associated with younger patient age. Methods: RNA sequencing data was obtained from The Cancer Genome Atlas (TCGA) and analyzed for differences in gene expression between patients ≤ 45 years old and those ≥ 65 years old. The identified differentially expressed genes were then validated with qPCR using human CRC tissue from patients ≤ 45 years old and those ≥ 65 years old. Results: RNA sequencing data from patients ≤ 45 years old (n = 29) and patients ≥ 65 years old (n = 299) identified seven genes with increased expression in younger patients: ZNF334 (log2 [fold change] = 2.30), DSC3 (1.78), PEG10 (1.67), CACNA1I (1.54), PKIA (1.33), MAP9 (1.27), and EPHX3 (1.17) (p < 0.07). Validation with qPCR for PEG10 was most promising, and was performed on both young (n = 10, mean age = 39) and old patient samples ( n= 8, mean age = 72). Two cancers (20%) in the young group received radiation treatment and five (50%) received chemotherapy. One cancer (12.5%) in the old group received radiation and two (25%) received chemotherapy. PEG10 had increased expression in the young group with log2 [fold change] = 3.16 (p < 0.02). Conclusions: We have identified a potentially unique gene expression signature for CRC in young patients, which includes PEG10. Functional analysis of PEG10 and other genes is underway using in vitro cell culture, archived human tumor tissue, and mouse tumor models.

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RNA Sequencing Analysis to Capture the Transcriptome Landscape during Tenderization in Sea Cucumber Apostichopus japonicus

Molecules ◽

10.3390/molecules24050998 ◽

2019 ◽

Vol 24 (5) ◽

pp. 998 ◽

Cited By ~ 1

Author(s):

Xiufang Dong ◽

Hang Qi ◽

Baoyu He ◽

Di Jiang ◽

Beiwei Zhu

Keyword(s):

Gene Expression ◽

Rna Sequencing ◽

Sea Cucumber ◽

Molecular Mechanisms ◽

Apostichopus Japonicus ◽

Expression Profiles ◽

Textural Properties ◽

Sequencing Analysis ◽

Type Iv Collagenase ◽

Illumina Hiseq

Sea cucumber (Apostichopus japonicus) is an economically significant species in China having great commercial value. It is challenging to maintain the textural properties during thermal processing due to the distinctive physiochemical structure of the A. japonicus body wall (AJBW). In this study, the gene expression profiles associated with tenderization in AJBW were determined at 0 h (CON), 1 h (T_1h), and 3 h (T_3h) after treatment at 37 °C using Illumina HiSeq™ 4000 platform. Seven-hundred-and-twenty-one and 806 differentially expressed genes (DEGs) were identified in comparisons of T_1h vs. CON and T_3h vs. CON, respectively. Among these DEGs, we found that two endogenous proteases—72 kDa type IV collagenase and matrix metalloproteinase 16 precursor—were significantly upregulated that could directly affect the tenderness of AJBW. In addition, 92 genes controlled four types of physiological and biochemical processes such as oxidative stress response (3), immune system process (55), apoptosis (4), and reorganization of the cytoskeleton and extracellular matrix (30). Further, the RT-qPCR results confirmed the accuracy of RNA-sequencing analysis. Our results showed the dynamic changes in global gene expression during tenderization and provided a series of candidate genes that contributed to tenderization in AJBW. This can help further studies on the genetics/molecular mechanisms associated with tenderization.

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