Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model

McCoy, Annette M.; Kemper, Ann M.; Boyce, M.; Brown, M. P.; Trumble, Troy N.

doi:10.1186/s12864-020-07228-z

Cited by 10 publications

(17 citation statements)

References 56 publications

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“…The 8 DEGs that were represented in at least 2 studies were: MMP1, MMP2, MMP13, APOD, TNFAIP6, IL6, FCER1G, and IGF1. Three of the overlapping DEGs, APOD, TNFAIP6, and IL6 are all genes that have been found to regulate the pro-inflammatory pathway ( Li and Zheng 2020 ; McCoy et al, 2020 ; Steinberg et al, 2021 ; Huang et al, 2022 ). IL6 was differently expressed in 3 of the 5 studies and is a key contributor to modulating inflammation in both acute and chronic inflammation ( McCoy et al, 2020 ; Steinberg et al, 2021 ; Huang et al, 2022 ; Safran et al, 2022 ).…”

Section: Resultsmentioning

confidence: 99%

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RNAseq of Osteoarthritic Synovial Tissues: Systematic Literary Review

2022

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Osteoarthritis (OA) is one of the most common causes of disability in aged people, and it is defined as a degenerative arthropathy, characterized by the disruption in joint tissue. The synovium plays a vital role in maintaining the health of the joint by supplying the nutrients to the surrounding tissues and the lubrication for joint movement. While it is well known that all the joint tissues are communicating and working together to provide a functioning joint, most studies on OA have been focused on bone and cartilage but much less about synovium have been reported. The purpose of this review was to investigate the current literature focused on RNA sequencing (RNAseq) of osteoarthritic synovial tissues to further understand the dynamic transcriptome changes occurring in this pivotal joint tissue. A total of 3 electronic databases (PubMed, CINHAL Complete, and Academic Complete) were systematically searched following PRISMA guidelines. The following criteria was used for inclusion: English language, free full text, between the period 2011–2022, size of sample (n > 10), study design being either retrospective or prospective, and RNAseq data of synovial tissue from OA subjects. From the initial search, 174 articles, 5 met all of our criteria and were selected for this review. The RNAseq analysis revealed several differentially expressed genes (DEGs) in synovial tissue. These genes are related to the inflammatory pathway and regulation of the extracellular matrix. The MMP family, particularly MMP13 was identified by three of the studies, indicating its important role in OA. IL6, a key contributor in the inflammation pathway, was also identified in 3 studies. There was a total of 8 DEGs, MMP13, MMP1, MMP2, APOD, IL6, TNFAIP6, FCER1G, and IGF1 that overlapped in 4 out of the 5 studies. One study focused on microbial RNA in the synovial tissue found that the microbes were differentially expressed in OA subjects too. These differentially expressed microbes have also been linked to the inflammatory pathway. Further investigation with more clinical gene profiling in synovial tissue of OA subjects is required to reveal the causation and progression, as well as aid in the development of new treatments.

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Section: Resultsmentioning

confidence: 99%

“…IGF1 was shown to be highly expressed having a role in the inflammation resolving pathway, as well as having a role in enhanced extracellular matrix production and inhibition of apoptosis in chondrocytes. ( McCoy et al, 2020 ; Wen et al, 2021 ; Huang et al, 2022 ). The gene MMP13 was represented in 3 of the 5 studies included.…”

Section: Resultsmentioning

confidence: 99%

RNAseq of Osteoarthritic Synovial Tissues: Systematic Literary Review

2022

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“…However, osteoarthritis can sometimes result from trauma or injury to joints (Lacourt et al, 2012;Rickey et al, 2012;Boyce et al, 2013;Jiménez et al, 2018). In humans and horses, the rate at which osteoarthritis progresses can vary greatly among individuals: in some cases, it may take several years before individuals develop severe forms of the disease; in other cases, rapid deterioration may occur in less than a year (Pivec et al, 2013;Driban et al, 2014;McCoy et al, 2020). The rate at which osteoarthritis progresses in moose may be similarly variable.…”

Section: Study Systemmentioning

confidence: 99%

“…To ensure that individuals were assessed for osteoarthritis in a consistent manner, the severity of osteoarthritis was determined by the same observer (ROP) throughout the entire study period. It was not possible to determine how long individuals might have had osteoarthritis prior to death because the rate at which osteoarthritis progresses is known to be highly variable (Pivec et al, 2013;Driban et al, 2014;McCoy et al, 2020).…”

Section: Data Collectionmentioning

confidence: 99%

The Role of Wolves in Regulating a Chronic Non-communicable Disease, Osteoarthritis, in Prey Populations

2022

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It is widely accepted that predators disproportionately prey on individuals that are old, weak, diseased or injured. By selectively removing individuals with diseases, predators may play an important role in regulating the overall health of prey populations. However, that idea is seldom tested empirically. Here we assess the extent that wolves (Canis lupus) select adult moose (Alces alces) in Isle Royale National Park on the basis of age-class and osteoarthritis, a chronic, non-communicable disease. We also assess how temporal variation in kill rates (on moose by wolves) were associated with the subsequent incidence of osteoarthritis in the moose population over a 33-year period (1975–2007). Wolves showed strong selection for senescent moose and tended to avoid prime-aged adults. However, the presence of severe osteoarthritis, but not mild or moderate osteoarthritis, appeared to increase the vulnerability of prime-aged moose to predation. There was weak evidence to suggest that senescent moose with osteoarthritis maybe more vulnerable to wolves, compared to senescent moose without the disease. The incidence of osteoarthritis declined following years with higher kill rates–which is plausibly due to the selective removal of individuals with osteoarthritis. Together those results suggest that selective predation plays an important role in regulating the health of prey populations. Additionally, because osteoarthritis is influenced by genetic factors, these results highlight how wolf predation may act as a selective force against genes associated with developing severe osteoarthritis as a prime-aged adult. Our findings highlight one benefits of allowing predators to naturally regulate prey populations. The evidence we present for predation’s influence on the health of prey populations is also relevant for policy-related arguments about refraining from intensively hunting wolf populations.

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“…At present, the clinical methods for the diagnosis of liver metastasis of colorectal cancer mainly include abdominal enhanced CT, serum CEA, CA19-9 examination, pathological staging [19,31,32], liver MRI examination and other equipment examination. Because there are certain differences in the genes of each person, doctors can analyze the gene expression of patients.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Co-Expression Module of Liver Metastasis Genes in Colorectal Cancer and Mining of Potential High-Expression Biomarkers

Wang¹,

Nie²,

Wang³

et al. 2021

Preprint

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AimsThe Hub genes highly related to the disease were found from the gene co-expression module, and the potential high expression genes were analyzed to predict the liver metastasis of colorectal cancer, so as to provide reference for subsequent targeted therapy.MethodsIn this study, we used the public data set of GEO database (GSE50760) to analyze the gene co-expression of liver metastasis of colon cancer, primary colon cancer and normal colon tissue (54 cases) and 50 cases of clinical cases. The functional annotations based on GO database are enriched, and the functional annotations of five gene modules are obtained through the enrichment of biological processes. Then the data mining is carried out to find the sub-networks with high adjacency in the gene co-expression network. At the same time, these sub-networks are annotated to find oncogenes related to liver metastasis of colorectal cancer.ResultsThis experiment found that KRAS, APC, FBXW7, PIK3CA, TP53 were highly correlated with liver metastasis of colorectal cancer. Finally, two protein genes STAT1 and MAPK1 were found by MCODE, which may be highly correlated with liver metastasis of colorectal cancer. Two new genes with high expression proteins found in this experiment have potential cancer, which has not been reflected in previous studies.ConclusionAccording to clinical data, KRAS, APC, FBXW7, PIK3CA, TP53 are related to colorectal cancer liver metastasis, and the analysis of the data set shows that STAT1 and MAPK1 are not only related to colorectal cancer liver metastasis oncogene but also related to clinically obtained genes.

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Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model

Cited by 10 publications

References 56 publications

RNAseq of Osteoarthritic Synovial Tissues: Systematic Literary Review

RNAseq of Osteoarthritic Synovial Tissues: Systematic Literary Review

The Role of Wolves in Regulating a Chronic Non-communicable Disease, Osteoarthritis, in Prey Populations

Analysis of Co-Expression Module of Liver Metastasis Genes in Colorectal Cancer and Mining of Potential High-Expression Biomarkers

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