The cartilage-specific lectin C-type lectin domain family 3 member A (CLEC3A) enhances tissue plasminogen activator-mediated plasminogen activation

Transcriptomic Profiles of Pectoralis major Muscles Affected by Spaghetti Meat and Woody Breast in Broiler Chickens

Spaghetti meat (SM) and woody breast (WB) are breast muscle myopathies of broiler chickens, characterized by separation of myofibers and by fibrosis, respectively. This study sought to investigate the transcriptomic profiles of breast muscles affected by SM and WB. Targeted sampling was conducted on a flock to obtain 10 WB, 10 SM, and 10 Normal Pectoralis major muscle samples from 37-day-old male chickens. Total RNA was extracted, cDNA was used for pair-end sequencing, and differentially expressed genes (DEGs) were determined by a false discovery rate of <0.1 and a >1.5-fold change. Principal component and heatmap cluster analyses showed that the SM and WB samples clustered together. No DEGs were observed between SM and WB fillets, while a total of 4018 and 2323 DEGs were found when comparing SM and WB, respectively, against Normal samples. In both the SM and WB samples, Gene Ontology terms associated with extracellular environment and immune response were enriched. The KEGG analysis showed enrichment of cytokine-cytokine receptor interaction and extracellular matrix-receptor interaction pathways in both myopathies. Although SM and WB are macroscopically different, the similar transcriptomic profiles suggest that these conditions may share a common pathogenesis. This is the first study to compare the transcriptomes of SM and WB, and it showed that, while both myopathies had profiles different from the normal breast muscle, SM and WB were similar, with comparable enriched metabolic pathways and processes despite presenting markedly different macroscopic features.

C-type lectin domain-containing protein CLEC3A regulates proliferation, regeneration and maintenance of nucleus pulposus cells

It is widely assumed that as connective tissue, the intervertebral disc (IVD) plays a crucial role in providing flexibility for the spinal column. The disc is comprised of three distinct tissues: the nucleus pulposus (NP), ligamentous annulus fibrous (AF) that surrounds the NP, and the hyaline cartilaginous endplates (CEP). Nucleus pulposus, composed of chondrocyte-like NP cells and its secreted gelatinous matrix, is critical for disc health and function. The NP matrix underwent dehydration accompanied by increasing fibrosis with age. The degeneration of matrix is almost impossible to repair, with the consequence of matrix stiffness and senescence of NP cells and intervertebral disc, suggesting the value of glycoproteins in extracellular matrix (ECM). Here, via database excavation and biological function screening, we investigated a C-type lectin protein, CLEC3A, which could support differentiation of chondrocytes as well as maintenance of NP cells and was essential to intervertebral disc homeostasis. Furthermore, mechanistic analysis revealed that CLEC3A could stimulate PI3K-AKT pathway to accelerate cell proliferation to further play part in NP cell regeneration.

Can Scoliotic Discs Be Controls for Molecular Studies in Intervertebral Disc Research? Insights From Proteomics

STUDY DESIGN

Proteomic analysis of human intervertebral discs.

OBJECTIVES

To compare the characters of scoliotic discs and discs from magnetic resonance imaging (MRI)-normal voluntary organ donors controls used in disc research employing proteomics and establish "true controls" that can be utilized for future intervertebral disc (IVD) research.

METHODS

Eight MRI-normal discs from 8 brain-dead voluntary organ donors (ND) and 8 scoliotic discs (SD) from 3 patients who underwent anterior surgery for adolescent idiopathic scoliosis were subjected to tandem mass spectrometry, and further analysis was performed.

RESULTS

Mass spectrometry identified a total of 235 proteins in ND and 438 proteins in the SD group. Proteins involved in extracellular matrix integrity (Versican, keratins KRT6A, KRT14, KRT5, and KRT 13A1, A-kinase anchor protein 13, coagulation factor XIII A chain, proteoglycan 4) and proteins involved in transcription and DNA repair (Von Willebrand factor A domain-containing 3B, eukaryotic initiation factor 2B, histone H4, leukocyte cell-derived chemotaxin 2) were found to be downregulated in SD. Inflammatory proteins (C3, C1S), and oxidative stress response proteins (peroxiredoxin-2,6, catalase, myeloperoxidase, apolipoprotein E) were found to be upregulated in SD. These changes were reflected at the pathway level also.

CONCLUSION

Findings of our study confirm that scoliotic discs have an abundance of inflammatory, oxidative stress response proteins, which are either absent or downregulated in the ND group indicating that scoliotic discs are not pathologically inert. Furthermore, this study has established MRI-normal discs from voluntary organ donors as the "true" control for molecular studies in IVD research.

Comparison of Gene Expression Patterns in Articular Cartilage and Xiphoid Cartilage

Cartilage is a resilient and smooth connective tissue that is found throughout the body. Among the three major types of cartilage, namely hyaline cartilage, elastic cartilage, and fibrocartilage, hyaline cartilage is the most widespread type of cartilage predominantly located in the joint surfaces (articular cartilage, AC). It remains a huge challenge for orthopedic surgeons to deal with AC damage since it has limited capacity for self-repair. Xiphoid cartilage (XC) is a vestigial cartilage located in the distal end of the sternum. XC-derived chondrocytes exhibit strong chondrogenic differentiation capacity. Thus, XC could become a potential donor site of chondrocytes for cartilage repair and regeneration. However, the underlying gene expression patterns between AC and XC are still largely unknown. In the present study, we used state-of-the-art RNA-seq technology combined with validation method to investigate the gene expression patterns between AC and XC, and identified a series of differentially expressed genes (DEGs) involved in chondrocyte commitment and differentiation including growth factors, transcription factors, and extracellular matrices. We demonstrated that the majority of significantly up-regulated DEGs (XC vs. AC) in XC were involved in regulating cartilage regeneration and repair, whereas the majority of significantly up-regulated DEGs (XC vs. AC) in AC were involved in regulating chondrocyte differentiation and maturation. This study has increased our knowledge of transcriptional networks in hyaline cartilage and elastic cartilage. It also supports the use of XC-derived chondrocytes as a potential cell resource for cartilage regeneration and repair.

Senescent cells suppress innate smooth muscle cell repair functions in atherosclerosis

Senescent cells (SNCs) degenerate the fibrous cap that normally prevents atherogenic plaque rupture, a leading cause of myocardial infarction and stroke. Here we explored the underlying mechanism using pharmacological or transgenic approaches to clear SNCs in the Ldlr ^-/- mouse model of atherosclerosis. SNC clearance reinforced fully deteriorated fibrous caps in highly advanced lesions, as evidenced by restored vascular smooth muscle cell (VSMC) numbers, elastin content, and overall cap thickness. We found that SNCs inhibit VSMC promigratory phenotype switching in the first interfiber space of the arterial wall directly beneath atherosclerotic plaque, thereby limiting lesion entry of medial VSMCs for fibrous cap assembly or reinforcement. SNCs do so by antagonizing IGF-1 through the secretion of insulin-like growth factor-binding protein 3 (Igfbp3). These data indicate that the intermittent use of senolytic agents or IGFBP-3 inhibition in combination with lipid lowering drugs may provide therapeutic benefit in atherosclerosis.

Investigation of chitosan-g-PEG grafted nanoparticles as a half-life enhancer carrier for tissue plasminogen activator delivery

Tissue plasminogen activator (tPA) a thrombolytic agent is commonly used for digesting the blood clot. tPA half-life is low (4-6 min) and its administration needs a prolonged continuous infusion. Improving tPA half-life could reduce enzyme dosage and enhance patient compliance. Nano-carries could be used as delivery systems for the protection of enzymes physically, enhancing half-life and increasing the stability of them. In this study, chitosan (CS) and polyethylene glycol (PEG) were used for the preparation of CS-g-PEG/tPA nanoparticles (NPs) via the ion gelation method. Particles' size and loading capacity were optimised by central composite design. Then, NPs cytotoxicity, release profile, enzyme activity and in vivo half-life and coagulation time were investigated. The results showed that NPs does not have significant cytotoxicity. Release study revealed that a burst effect happened in the first 5 min and resulted in releasing 30% of tPA. Loading tPA in NPs could decrease 25% of its activity but the half-life of it increases in comparison to free tPA in vivo. Also, blood coagulation time has significantly affected (p-value = 0.041) by encapsulated tPA in comparison to free tPA. So, CS-g-PEG/tPA could increase enzyme half-life during the time and could be used as a non-toxic candidate delivery system for tPA.

DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics

The spatiotemporal proteome of the intervertebral disc (IVD) underpins its integrity and function. We present DIPPER, a deep and comprehensive IVD proteomic resource comprising 94 genome-wide profiles from 17 individuals. To begin with, protein modules defining key directional trends spanning the lateral and anteroposterior axes were derived from high-resolution spatial proteomes of intact young cadaveric lumbar IVDs. They revealed novel region-specific profiles of regulatory activities and displayed potential paths of deconstruction in the level- and location-matched aged cadaveric discs. Machine learning methods predicted a ‘hydration matrisome’ that connects extracellular matrix with MRI intensity. Importantly, the static proteome used as point-references can be integrated with dynamic proteome (SILAC/degradome) and transcriptome data from multiple clinical samples, enhancing robustness and clinical relevance. The data, findings, and methodology, available on a web interface (http://www.sbms.hku.hk/dclab/DIPPER/), will be valuable references in the field of IVD biology and proteomic analytics.

The backbone of vertebrate animals consists of a series of bones called vertebrae that are joined together by disc-like structures that allow the back to move and distribute forces to protect it during daily activities. It is common for these intervertebral discs to degenerate with age, resulting in back pain and severely reducing quality of life.

The mechanical features of intervertebral discs are the result of their proteins. These include extracellular matrix proteins, which form the external scaffolding that binds cells together in a tissue, and signaling proteins, which allow cells to communicate. However, how the levels of different proteins in each region of the disc vary with time has not been fully examined.

To establish how protein composition changes with age, Tam, Chen et al. quantified the protein levels and gene activity (which leads to protein production) of intervertebral discs from young and old deceased individuals. They found that the position of different mixtures of proteins in the intervertebral disc changes with age, and that young people have high levels of extracellular matrix proteins and signaling proteins. Levels of these proteins decreased as people got older, as did the amount of proteins produced.

To determine which region of the intervertebral disc different proteins were in, Tam, Chen et al. also performed magnetic resonance imaging (MRI) of the samples to correlate image intensity (which represents water content) with the corresponding protein signature. The data obtained provides a high-quality map of how the location of different proteins changes with age, and is available online under the name DIPPER. This database is an informative resource for research into skeletal biology, and it will likely advance the understanding of intervertebral disc degeneration in humans and animals, potentially leading to the development of new treatment strategies for this condition.

Suppression of CLEC3A inhibits osteosarcoma cell proliferation and promotes their chemosensitivity through the AKT1/mTOR/HIF1α signaling pathway

Osteosarcoma (OS) is a primary malignant tumor that occurs in bone, and mainly affects children and adolescents. C-type lectin domain family 3 member A (CLEC3A) is a member of the C-type lectin superfamily, which regulates various biological functions of cells. The present study aimed to identify the effects and related mechanisms of CLEC3A in the proliferation and chemosensitivity of OS cells. The expression of CLEC3A in OS was analyzed using the Gene Expression Omnibus data profile GSE99671, and its expression in OS samples was verified using reverse transcription-quantitative PCR (RT-qPCR) and immunohistochemical staining. The relationship between the expression of CLEC3A and clinical traits in patients with OS was also analyzed, including age, tumor size, TNM stage and lymph node metastasis. Cell Counting Kit-8 assays, colony formation assays and cell cycle distribution analysis were used to determine the roles of CLEC3A in the proliferation and chemosensitivity of OS cells. Finally, RT-qPCR and western blotting were used to demonstrate the relationship between CLEC3A and the AKT1/mTOR/hypoxia-inducible factor 1-α (HIF1α) pathway. Both the mRNA and protein expression levels of CLEC3A were increased in OS tissues compared with adjacent non-tumor tissues, and this was positively associated with TNM stage and lymph node metastasis. The genetic knockdown of CLEC3A with small interfering RNA decreased OS cell proliferation and colony formation, and induced G1 phase arrest, whereas the overexpression of CLEC3A increased OS cell proliferation and colony formation, and alleviated G1 phase arrest. The suppression of CLEC3A also promoted enhanced the chemosensitivity of OS cells to doxorubicin (DOX) and cisplatin (CDDP); it also inhibited the expression of AKT1, mTOR and HIF1α, further to the nuclear localization of HIF1α, and HIF1α target gene expression levels, including VEGF, GLUT1 and MCL1 were also decreased. Furthermore, treatment with the AKT activator SC79 blocked the inhibitory effects of CLEC3A silencing in OS cells. In conclusion, these findings suggested that CLEC3A may function as an oncogene in OS, and that the suppression of CLEC3A may inhibit OS cell proliferation and promote chemosensitivity through the AKT1/mTOR/HIF1α signaling pathway.

Progression of acute-to-chronic atopic dermatitis is associated with quantitative rather than qualitative changes in cytokine responses

BACKGROUND

Although multiple studies have assessed molecular changes in chronic atopic dermatitis (AD) lesions, little is known about the transition from acute to chronic disease stages, and the factors and mechanisms that shape chronic inflammatory activity.

OBJECTIVES

We sought to assess the global transcriptome changes that characterize the progression from acute to chronic stages of AD.

METHODS

We analyzed transcriptome changes in paired nonlesional skin, acute and chronic AD lesions from 11 patients and 38 healthy controls by RNA-sequencing, and conducted in vivo and histological assays to evaluate findings.

RESULTS

Our data demonstrate that approximately 74% of the genes dysregulated in acute lesions remain or are further dysregulated in chronic lesions, whereas only 34% of the genes dysregulated in chronic lesions are altered already in the acute stage. Nonlesional AD skin exhibited enrichment of TNF, T_H1, T_H2, and T_H17 response genes. Acute lesions showed marked dendritic-cell signatures and a prominent enrichment of T_H1, T_H2, and T_H17 responses, along with increased IL-36 and thymic stromal lymphopoietin expression, which were further heightened in chronic lesions. In addition, genes involved in skin barrier repair, keratinocyte proliferation, wound healing, and negative regulation of T-cell activation showed a significant dysregulation in the chronic versus acute comparison. Furthermore, our data show progressive changes in vasculature and maturation of dendritic-cell subsets with chronicity, with FOXK1 acting as immune regulator.

CONCLUSIONS

Our results show that the changes accompanying the transition from nonlesional to acute to chronic inflammation in AD are quantitative rather than qualitative, with chronic AD having heightened T_H2, T_H1, T_H17, and IL36 responses and skin barrier repair mechanisms. These findings provide novel insights and highlight underappreciated pathways in AD pathogenesis that may be amenable to therapeutic targeting.

Antimicrobial peptides derived from the cartilage.-specific C-type Lectin Domain Family 3 Member A (CLEC3A) - potential in the prevention and treatment of septic arthritis

OBJECTIVE

To investigate the antimicrobial activity of peptides derived from C-type Lectin Domain Family 3 Member A (CLEC3A), shed light on the mechanism of antimicrobial activity and assess their potential application in prevention and treatment of septic arthritis.

DESIGN

We performed immunoblot to detect CLEC3A peptides in human cartilage extracts. To investigate their antimicrobial activity, we designed peptides and recombinantly expressed CLEC3A domains and used them to perform viable count assays using E.coli, P.aeruginosa and S.aureus. We investigated the mechanism of their antimicrobial activity by fluorescence and scanning electron microscopy, performed ELISA-style immunoassays and transmission electron microscopy to test for lipopolysaccharide binding and surface plasmon resonance to test for lipoteichoic acid (LTA) binding. We coated CLEC3A peptides on titanium, a commonly used prosthetic material, and performed fluorescence microscopy to quantify bacterial adhesion. Moreover, we assessed the peptides' cytotoxicity against primary human chondrocytes using MTT cell viability assays.

RESULTS

CLEC3A fragments were detected in human cartilage extracts. Moreover, bacterial supernatants lead to fragmentation of recombinant and cartilage-derived CLEC3A. CLEC3A-derived peptides killed E.coli, P.aeruginosa and S.aureus, permeabilized bacterial membranes and bound lipopolysaccharide and LTA. Coating CLEC3A antimicrobial peptides (AMPs) on titanium lead to significantly reduced bacterial adhesion to the material. In addition, microbicidal concentrations of CLEC3A peptides in vitro displayed no direct cytotoxicity against primary human chondrocytes.

CONCLUSIONS

We identify cartilage-specific AMPs originating from CLEC3A, resolve the mechanism of their antimicrobial activity and point to a novel approach in the prevention and treatment of septic arthritis using potent, non-toxic, AMPs.

Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients

Background

Presently, a 50-gene expression model (PAM50) serves as a breast cancer (BC) subtype classifier that is insufficient to distinguish, within each single PAM50-classified subtype, patient subpopulations having different prognosis. There is a pressing need for inexpensive and minimally invasive biomarker tests to easily and accurately predict individuals’ clinical outcomes and response to treatments. Although quantitative proteomic approaches have been developed to identify/profile proteins secreted (secretome) from various cancer cell lines in vitro, missing are the clinicopathological relevance and the associated prognostic value of these secretomic identifications.

Methods

To discover biomarkers to predict individualized prognosis we introduce a new multi-omics (secreto-transcriptomics) method that identifies, in their oncogenically secreted states, candidate markers of BC subtypes whose genes bear patient-specific mRNA expression alterations of prognostic significance. First, we used label-free quantitative (LFQ) proteomics to identify the proteins showing BC-subtypic secretion from a series of BC cell lines representing major BC-subtypes. To determine and externally validate the prognostic value of these secreted proteins, we developed a secreto-transcriptomic approach that discovered a PAM50-subtypic Secretion-Correlated mRNA Expression Pattern (SeCEP) wherein the PAM50-subtypic secretion of select proteins statistically correlated with cis-mRNA expression of their encoding genes in patients of the corresponding PAM50-subtypes. Kaplan-Meier analysis of SeCEP genes was used to identify new liquid biopsy biomarkers for predicting individualized prognosis.

Results

The mRNA expression-to-secretion correlation (SeCEP) pinpointed multiple genes that are fully translated into the oncogenically active secretome in a PAM50-subtypic manner. Further, multiple SeCEP genes in distinct combinations or panels of multiple SeCEP genes were identified as ‘systems prognostic markers’ that showed mRNA co-overexpression patterns in the distinct subpopulations of PAM50-subtypic patients with poor prognosis or high-risk of relapse. Thus, our secreto-transcriptomic approach statistically linked BC subtypic secretome genes with patient-specific information about their mRNA expression alterations and significantly improved the sensitivity and specificity in patient stratification in the context of clinical outcomes or prognosis.

Conclusions

By combining LFQ secretome screening with proteo-transcriptomic retrospective analysis of patient data our integrated multi-omics approach bypasses costly, tedious, genome-wide fishing and predictive modeling that are commonly required to distinguish a few prognostically altered genes from thousands of other non-BC related genes in a genome.

Electronic supplementary material

The online version of this article (10.1186/s12920-019-0530-7) contains supplementary material, which is available to authorized users.

Identification of antibodies against extracellular matrix proteins in human osteoarthritis

We investigated the presence of autoantibodies against the extracellular matrix proteins thrombospondin-4 (TSP-4), cartilage oligomeric matrix protein (COMP), C-type lectin domain family 3 member A (CLEC3A), collagen II, collagen VI, matrilin-3, and fibrillin-2 in the serum of osteoarthritis (OA) patients. We compared those results with the presence of such antibodies in rheumatoid arthritis (RA) patients and in healthy donors (HD). Our study examines whether antibodies against extracellular proteins can be used as potential biomarkers to support the clinical diagnosis of OA. 10 OA, 10 RA patients and 10 HD were enrolled in this explorative cross-sectional study. SDS-PAGE and immunoblot were used to investigate the presence of antibodies against extracellular matrix proteins. The serum of 5/10 OA patients but 0/10 HD exhibited TSP-4 IgG isotype antibodies (P = 0.033). The serum of 8/10 OA patients but only 1/10 HD exhibited IgG isotype antibodies against TSP-4 or COMP (P = 0.005). The serum of 9/10 OA patients but only 1/10 HD exhibited IgG isotype antibodies against TSP-4, COMP or CLEC3A (P = 0.005). We found strong evidence for the presence of IgG isotype autoantibodies against the cartilage extracellular matrix proteins TSP-4, COMP and CLEC3A in OA. The detection of IgG isotype autoantibodies against TSP-4, COMP and CLEC3A may support the clinical diagnosis of OA. OA with autoantibodies against cartilage extracellular matrix proteins defines a new OA subgroup suggesting that patients with high concentrations of autoantibodies may benefit from an immune suppressive therapy.

Overexpression of CLEC3A promotes tumor progression and poor prognosis in breast invasive ductal cancer

Introduction

The aim of this study was to evaluate the expression of C-type lectin domain family 3 member A (CLEC3A) and its clinical significance in breast invasive ductal cancer (IDC) as well as its effect on breast cancer (BC) cell proliferation and metastasis. In this study, the level of CLEC3A expression in The Cancer Genome Atlas (TCGA) datasets was analyzed.

Materials and methods

Clinical collected samples and BC cells were measured using quantitative reverse transcription polymerase chain reaction. Its correlations with patients’ clinicopathological characteristics were analyzed by Pearson’s chi-squared test. Overall survival (OS) analysis was performed by the Kaplan–Meier method and Cox’s proportional-hazards model. BC cell proliferation, migration, and invasion by CLEC3A knockdown were assessed using Cell Counting Kit-8 and colony formation assay, wound healing model and transwell assay, respectively, in BT474 cell line. Activities of survival factors and phosphatidylinositol-3-kinase (PI3K)/protein kinase B (AKT) signaling were measured by testing key molecules using Western blot assay.

Results

CLEC3A expression was markedly higher in breast IDC tissues than normal breast tissues or adjacent normal tissue. Patients with high CLEC3A expression related to higher lymph node and poorer OS of breast IDC. CLEC3A knockdown by siRNA could inhibit the BC cells BT474 proliferation, migration, and invasion, together with a decrease in expression of key proteins in survival factors and PI3K/AKT signaling pathway.

Conclusion

Elevated CLEC3A expression may correlate with breast IDC metastatic potential and indicated a poor prognosis in breast IDC. CLEC3A knockdown inhibited BC cell growth and metastasis might be through suppressing PI3K/AKT signaling activity. These findings unravel that CLEC3A is a promising therapeutic target for BC in the future.