Defects of type I procollagen metabolism correlated with decrease of prolidase activity in a case of lethal osteogenesis imperfecta

ClearF++: Improved Supervised Feature Scoring Using Feature Clustering in Class-Wise Embedding and Reconstruction

Feature selection methods are essential for accurate disease classification and identifying informative biomarkers. While information-theoretic methods have been widely used, they often exhibit limitations such as high computational costs. Our previously proposed method, ClearF, addresses these issues by using reconstruction error from low-dimensional embeddings as a proxy for the entropy term in the mutual information. However, ClearF still has limitations, including a nontransparent bottleneck layer selection process, which can result in unstable feature selection. To address these limitations, we propose ClearF++, which simplifies the bottleneck layer selection and incorporates feature-wise clustering to enhance biomarker detection. We compare its performance with other commonly used methods such as MultiSURF and IFS, as well as ClearF, across multiple benchmark datasets. Our results demonstrate that ClearF++ consistently outperforms these methods in terms of prediction accuracy and stability, even with limited samples. We also observe that employing the Deep Embedded Clustering (DEC) algorithm for feature-wise clustering improves performance, indicating its suitability for handling complex data structures with limited samples. ClearF++ offers an improved biomarker prioritization approach with enhanced prediction performance and faster execution. Its stability and effectiveness with limited samples make it particularly valuable for biomedical data analysis.

NSAIDs Induce Proline Dehydrogenase/Proline Oxidase-Dependent and Independent Apoptosis in MCF7 Breast Cancer Cells

Non-steroidal anti-inflammatory drugs (NSAIDs) are considered in cancer therapy for their inhibitory effect on cyclooxygenase-2 (COX-2), which is overexpressed in most cancers. However, we found that NSAIDs as ligands of peroxisome proliferator-activated receptor-γ (PPARγ)-induced apoptosis independent of the COX-2 inhibition, and the process was mediated through activation of proline dehydrogenase/proline oxidase (PRODH/POX)-dependent generation of reactive oxygen species (ROS). This mitochondrial enzyme converts proline to ∆1-pyrroline-5-carboxylate (P5C) during which ATP or ROS is generated. To confirm the role of PRODH/POX in the mechanism of NSAID-induced apoptosis we obtained an MCF7 CRISPR/Cas9 PRODH/POX knockout breast cancer cell model (MCF7^POK-KO). Interestingly, the studied NSAIDs (indomethacin and diclofenac) in MCF7^POK-KO cells contributed to a more pronounced pro-apoptotic phenotype of the cells than in PRODH/POX-expressing MCF7 cells. The observed effect was independent of ROS generation, but it was related to the energetic disturbances in the cells as shown by an increase in the expression of AMPKα (sensor of cell energy status), GLUD1/2 (proline producing enzyme from glutamate), prolidase (proline releasing enzyme), PPARδ (growth supporting transcription factor) and a decrease in the expression of proline cycle enzymes (PYCR1, PYCRL), mammalian target of rapamycin (mTOR), and collagen biosynthesis (the main proline utilizing process). The data provide evidence that the studied NSAIDs induce PRODH/POX-dependent and independent apoptosis in MCF7 breast cancer cells.

Extracellular Prolidase (PEPD) Induces Anabolic Processes through EGFR, β1-integrin, and IGF-1R Signaling Pathways in an Experimental Model of Wounded Fibroblasts

The role of prolidase (PEPD) as a ligand of the epidermal growth factor receptor (EGFR) was studied in an experimental model of wound healing in cultured fibroblasts. The cells were treated with PEPD (1-100 nM) and analysis of cell viability, proliferation, migration, collagen biosynthesis, PEPD activity, and the expressions of EGFR, insulin-like growth factor 1 (IGF-1), and β₁-integrin receptor including downstream signaling proteins were performed. It has been found that PEPD stimulated proliferation and migration of fibroblasts via activation of the EGFR-downstream PI3K/Akt/mTOR signaling pathway. Simultaneously, PEPD stimulated the expression of β₁-integrin and IGF-1 receptors and proteins downstream to these receptors such as FAK, Grb2, and ERK1/2. Collagen biosynthesis was increased in control and "wounded" fibroblasts under PEPD treatment. The data suggest that PEPD-induced EGFR signaling may serve as a new attempt to therapy wound healing.

PROLIDASE: A Review from Discovery to its Role in Health and Disease

Prolidase (peptidase D), encoded by the PEPD gene, is a ubiquitously expressed cytosolic metalloproteinase, the only enzyme capable of cleaving imidodipeptides containing C-terminal proline or hydroxyproline. Prolidase catalyzes the rate-limiting step during collagen recycling and is essential in protein metabolism, collagen turnover, and matrix remodeling. Prolidase, therefore plays a crucial role in several physiological processes such as wound healing, inflammation, angiogenesis, cell proliferation, and carcinogenesis. Accordingly, mutations leading to loss of prolidase catalytic activity result in prolidase deficiency a rare autosomal recessive metabolic disorder characterized by defective wound healing. In addition, alterations in prolidase enzyme activity have been documented in numerous pathological conditions, making prolidase a useful biochemical marker to measure disease severity. Furthermore, recent studies underscore the importance of a non-enzymatic role of prolidase in cell regulation and infectious disease. This review aims to provide comprehensive information on prolidase, from its discovery to its role in health and disease, while addressing the current knowledge gaps.

A novel plausible mechanism of NSAIDs-induced apoptosis in cancer cells: the implication of proline oxidase and peroxisome proliferator-activated receptor

Although pharmaco-epidemiological studies provided evidence for the anticancer potential of non-steroidal anti-inflammatory drugs (NSAIDs), the mechanism of their anti-cancer activity is not known. Several lines of evidence suggest that proline dehydrogenase/proline oxidase (PRODH/POX) may represent a target for NSAIDs-dependent anti-cancer activity. PRODH/POX catalyzes conversion of proline into Δ1-pyrroline-5-carboxylate releasing ATP or reactive oxygen species for autophagy/apoptosis. Since NSAIDs are ligands of peroxisome proliferator-activated receptor (PPARs) and PPARs are implicated in PRODH/POX-dependent apoptosis we provided a hypothesis on the mechanism of NSAIDs-induced apoptosis in cancer cells.

Proline-dependent regulation of collagen metabolism

This review is focused on recent data on the role of proline (Pro) in collagen biosynthesis and cellular metabolism. It seems obvious that one of the main substrates for collagen biosynthesis Pro is required to form collagen molecule. The question raised in this review is whether the Pro for collagen biosynthesis is synthesized "de novo", comes directly from degraded proteins or it is converted from other amino acids. Recent data provided evidence that extracellular Pro (added to culture medium) had significant, but relatively little impact on collagen biosynthesis in fibroblasts (the main collagen synthesized cells) cultured in the presence of glutamine (Gln). However, extracellular Pro drastically increased collagen biosynthesis in the cells cultured in Gln-free medium. It suggests that Pro availability determines the rate of collagen biosynthesis and demand for Pro in fibroblasts is predominantly met by conversion from Gln. The potential mechanism of this process as well as possible implication of this knowledge in pharmacotherapy of connective tissue diseases is discussed in this review.

Prolidase-proline dehydrogenase/proline oxidase-collagen biosynthesis axis as a potential interface of apoptosis/autophagy

Prolidase is a cytosolic imidodipeptidase that specifically splits imidodipeptides with C-terminal proline or hydroxyproline. The enzyme plays an important role in the recycling of proline from imidodipeptides for resynthesis of collagen and other proline-containing proteins. The mechanism of prolidase-dependent regulation of collagen biosynthesis was found at both transcriptional and post-transcriptional level. The increase in the enzyme activity is due to its phosphorylation on serine/threonine residues. Prolidase-dependent transcriptional regulation of collagen biosynthesis was found at the level of NF-κB, known inhibitor of type I collagen gene expression. Proline dehydrogenase/proline oxidase (PRODH/POX) is flavin-dependent enzyme associated with the inner mitochondrial membrane. The enzyme catalyzes conversion of proline into Δ(1) -pyrroline-5-carboxylate (P5C), during which reactive oxygen species (ROS) are produced, inducing intrinsic and extrinsic apoptotic pathways. Alternatively, under low glucose stress, PRODH/POX activation produces ATP for energy supply and survival. Of special interest is that PRODH/POX gene is induced by P53 and peroxisome proliferator-activated gamma receptor (PPARγ). Among down-regulators of PRODH/POX is an oncogenic transcription factor c-MYC and miR-23b*. On the other hand, PRODH/POX suppresses HIF-1α transcriptional activity, the MAPK pathway, cyclooxygenase-2, epidermal growth factor receptor and Wnt/b-catenin signaling. PRODH/POX expression is often down-regulated in various tumors, limiting mitochondrial proline utilization to P5C. It is accompanied by increased cytoplasmic level of proline. Proline availability for PRODH/POX-dependent ATP or ROS generation depends on activity of prolidase and utilization of proline in process of collagen biosynthesis. Therefore, Prolidase-PRODH/POX-Collagen Biosynthesis axis may represent potential interface that regulate apoptosis and survival. © 2016 BioFactors, 42(4):341-348, 2016.

Enalapril stimulates collagen biosynthesis through prolidase-dependent mechanism in cultured fibroblasts

The mechanism of a lower incidence of dermatological manifestations in patients treated with enalapril compared to patients treated with other ACE-inhibitors, e.g., captopril, is not known. The finding that prolidase plays an important role in collagen biosynthesis and that some angiotensin-converting enzyme inhibitors affect prolidase activity led us to evaluate its effect on collagen biosynthesis in cultured human skin fibroblasts. Since insulin-like growth factor (IGF-I) and transforming growth factor beta 1 (TGF-β1) are the most potent stimulators of both collagen biosynthesis and prolidase activity, and prolidase is regulated by β₁ integrin signaling, the effect of enalapril and enalaprilat on IGF-IR, TGF-β1, and β₁ integrin receptor expressions was evaluated. Cells were treated with milimolar concentrations (0.3 and 0.5 mM) of enalapril and enalaprilat for 24 h. The activity of prolidase was determined by colorimetic assay. Collagen biosynthesis was evaluated by radiometric assay. Expression of signaling proteins was evaluated using Western blot. It was found that enalapril- and enalaprilat-dependent increase in prolidase activity and expression was accompanied by parallel increase in collagen biosynthesis. The exposure of the cells to 0.5 mM enalapril and enalaprilat contributed to increase in IGF-IR and α₂β₁ integrin receptor as well as TGF-β1 and NF-κB p65 expressions. Enalapril- and enalaprilat-dependent increase of collagen biosynthesis in fibroblasts results from increase of prolidase activity and expression, which may undergo through activation of α₂β₁ integrin and IGF-IR signaling as well as upregulation of TGF-β1 and NF-κB p65, the inhibitor of collagen gene expression.

Lack of prolidase causes a bone phenotype both in human and in mouse

The degradation of the main fibrillar collagens, collagens I and II, is a crucial process for skeletal development. The most abundant dipeptides generated from the catabolism of collagens contain proline and hydroxyproline. In humans, prolidase is the only enzyme able to hydrolyze dipeptides containing these amino acids at their C-terminal end, thus being a key player in collagen synthesis and turnover. Mutations in the prolidase gene cause prolidase deficiency (PD), a rare recessive disorder. Here we describe 12 PD patients, 9 of whom were molecularly characterized in this study. Following a retrospective analysis of all of them a skeletal phenotype associated with short stature, hypertelorism, nose abnormalities, microcephaly, osteopenia and genu valgum, independent of both the type of mutation and the presence of the mutant protein was identified. In order to understand the molecular basis of the bone phenotype associated with PD, we analyzed a recently identified mouse model for the disease, the dark-like (dal) mutant. The dal/dal mice showed a short snout, they were smaller than controls, their femurs were significantly shorter and pQCT and μCT analyses of long bones revealed compromised bone properties at the cortical and at the trabecular level in both male and female animals. The differences were more pronounce at 1 month being the most parameters normalized by 2 months of age. A delay in the formation of the second ossification center was evident at postnatal day 10. Our work reveals that reduced bone growth was due to impaired chondrocyte proliferation and increased apoptosis rate in the proliferative zone associated with reduced hyperthrophic zone height. These data suggest that lack of prolidase, a cytosolic enzyme involved in the final stage of protein catabolism, is required for normal skeletogenesis especially at early age when the requirement for collagen synthesis and degradation is the highest.

Serum prolidase activity in benign joint hypermobility syndrome

BACKGROUND

Moderate joint laxity is widespread in many joints of the body, and this condition is considered to be caused by an abnormality in the collagen structure. This study was carried out to determine the serum prolidase activity in female patients with benign joint hypermobility syndrome (BJHS), and to evaluate its correlation with their clinical features.

METHODS

A total of 45 patients with BJHS and 40 healthy controls were included in the study. All of the patients with BJHS met the Beighton diagnostic criteria. All the patients and the control group underwent a comprehensive examination of the locomotor system and took the New York Posture Rating Test. The examination and test results were recorded. Serum prolidase activity was measured in both the groups.

RESULTS

Prolidase activity was significantly lower in patients with BJHS (479.52 ± 126.50) compared to the healthy controls (555.97 ± 128.77) (p = 0.007). We found no correlation between serum prolidase activity and Beighton scores or New York rating test scores. On the other hand, mean prolidase activity was significantly lower in patients with pes planus or hyperlordosis compared to those without (p = 0.05, p = 0.03, respectively). We did not find such a correlation with the other clinical features.

CONCLUSIONS

Significantly lower prolidase activity in patients with BJHS suggests that prolidase may affect the collagen metabolism and cause hyperlaxity.

Serum prolidase activity and oxidative-antioxidative status in Legg-Calve-Perthes disease

We aimed to find out that whether collagen turnover is altered in the context of Legg-Calve-Perthes disease (LCPD) by evaluating serum prolidase activity. We also investigated the correlation between collagen turnover and oxidative-antioxidative status in LCPD. Plasma prolidase activity, total oxidant status (TOS), total antioxidant capacity, and oxidative stress index (OSI) were determined for 39 patients with LCPD and 40 healthy controls. Serum prolidase activity, TOS, and OSI were higher, but TAC was lower in patients with LCPD compared with controls. Prolidase activity was positively correlated with TOS and OSI levels. Serum prolidase activity is significantly associated with LCPD.

Biotechnological applications of recombinant microbial prolidases

Prolidase is a metallopeptidase that is ubiquitous in nature and has been isolated from mammals, bacteria and archaea. Prolidase specifically hydrolyzes dipeptides with a prolyl residue in the carboxy terminus (NH(2)-X-/-Pro-COOH). Currently, the only solved structure of prolidase is from the hyperthermophilic archaeon Pyrococcus furiosus. This enzyme is of particular interest because it can be used in many biotechnological applications. Prolidase is able to degrade toxic organophosphorus (OP) compounds, namely, by cleaving the P-F and P-O bonds in the nerve agents, sarin and soman. Applications using prolidase to detoxify OP nerve agents include its incorporation into fire-fighting foams and as biosensors for OP compound detection. Prolidases are also employed in the cheese-ripening process to improve cheese taste and texture. In humans, prolidase deficiency (PD) is a rare autosomal recessive disorder that affects the connective tissue. Symptoms of PD include skin lesions, mental retardation and recurrent respiratory infections. Enzyme replacement therapies are currently being studied in an effort to optimize enzyme delivery and stability for this application. Previously, prolidase has been linked to collagen metabolism and more recently is being associated with melanoma. Increased prolidase activity in melanoma cell lines has lead investigators to create cancer prodrugs targeting this enzyme. Thus, there are many biotechnological applications using recombinant and native forms of prolidase and this review will describe the biochemical and structural properties of prolidases as well as discuss their most current applications.

Prolidase-dependent regulation of collagen biosynthesis

Prolidase [EC.3.4.13.9] is a cytosolic imidodipeptidase, which specifically splits imidodipeptides with C-terminal proline or hydroxyproline. The enzyme plays an important role in the recycling of proline from imidodipeptides (mostly derived from degradation products of collagen) for resynthesis of collagen and other proline-containing proteins. The enzyme activity is up-regulated by beta(1)-integrin receptor stimulation. The increase in the enzyme activity is due to its phosphorylation on serine/threonine residues. Collagen is not only structural component of extracellular matrix. It has been recognized as a ligand for integrin receptors, which play an important role in signaling that regulate ion transport, lipid metabolism, kinase activation and gene expression. Therefore, changes in the quantity, structure and distribution of collagens in tissues may affect cell signaling, metabolism and function. Several line of evidence suggests that prolidase activity may be a step-limiting factor in the regulation of collagen biosynthesis. It has been shown in different physiologic and pathologic conditions. It is of great importance during wound healing, inflammation, aging, tissue fibrosis and possibly skeletal abnormalities seen in Osteogenesis Imperfecta. The mechanism of prolidase-dependent regulation of collagen biosynthesis was found at both transcriptional and post-transcriptional levels. In this study, we provide evidence for prolidase-dependent transcriptional regulation of collagen biosynthesis. The mechanism was found at the level of NF-kB, known inhibitor of type I collagen gene expression. Modulation of integrin-dependent signaling by stimulatory (i.e. thrombin) or inhibitory (i.e. echistatin) beta(1)-integrin ligands or by nitric oxide donors (i.e. DETA/NO) affect prolidase at post-transcriptional level. All those factors may represent novel approach to pharmacotherapy of connective tissue disorders.

Cord blood prolidase activity correlates with gestational age and birth weight

BACKGROUND

Prolidase, a specific iminopeptidase involved in collagen turnover, is especially active in growing tissues.

OBJECTIVES

To investigate the relationship between cord blood prolidase activity and both birth weight and gestational age.

METHODS

Cord blood was collected consecutively from 50 healthy newborns (35 term, 15 preterm). Prolidase activity was measured in the samples using standard methods.

RESULTS

Themean +/- SD cord blood prolidase activity was 41.4 +/- 6.9 U/l in term infants and 35.2 +/- 8.0 U/l in preterm infants and these were significantly different (p < 0.01). There were positive correlations between cord blood prolidase and both birth weight (r = 0.533, p < 0.01) and gestational age (r = 0.806, p < 0.01).

CONCLUSION

Cord blood prolidase activity may be a good indicator of fetal maturation and gestational age.

Correlations of serum prolidase activity between bone turnover markers and mineral density in postmenopausal osteoporosis

Prolidase is a specific imidodipeptidase involved in collagen degradation. The increase in the enzyme activity is believed to be correlated with the increased intensity of collagen degradation. The aim of this study was to evaluate the serum prolidase activity and its relationship between bone turnover markers and bone mineral density (BMD) in postmenopausal osteoporosis. The study included 45 postmenopausal osteoporotic, 55 postmenopausal nonosteoporotic and 38 premenopausal healthy women. BMD was measured at the femoral neck and lumbar spine with DEXA. T score was more than 2.5 SD below the normal at the lumbar spine or femoral neck in postmenopausal osteoporotic patients. Serum levels of prolidase, C-terminal telopeptide of type I collagen (C-telopeptide), total alkaline phosphatase (ALP), osteocalcin (OC), urinary deoxypyridinoline (Dpd) and urinary creatinine were also assayed. C-telopeptide, total ALP, OC, urinary Dpd levels were significantly higher in postmenopausal osteoporotic group compared with premenopausal women. However, there was no statistical difference in serum prolidase activity between the three groups. There were also no significant correlations between serum prolidase and any biomarkers of bone turnover as well as BMD. To conclude, in postmenopausal osteoporotic women with increased bone turnover, serum prolidase concentration was not correlated with the biomarkers of bone formation or bone resorption and with BMD.

The role of emerging techniques in the investigation of prolidase deficiency: From diagnosis to the development of a possible therapeutical approach

The aim of the present article is to review the efforts performed in the past two decades by numerous research groups for the development of methods that allow a correct diagnosis of prolidase deficiency (PD), a rare autosomal recessive disorder and for the rationalization of a possible therapeutic intervention on these patients. In particular, the interest of the reader is focused on the application of capillary electrophoresis (i) for the detection of biological markers that reflect the pathological feature of the disease and (ii) for the determination of the efficiency of a carrier system in delivering prolidase inside cells in a possible therapy based on enzyme replacement.

Fasting-induced inhibition of collagen biosynthesis in rat skin. A possible role for phosphoenolpyruvate in this process

Fasting is accompanied by a decrease in collagen biosynthesis. The mechanism of this phenomenon involves inhibition of prolidase activity, an enzyme that plays a key role in upregulation of collagen metabolism. The mechanism of fasting-induced inhibition of prolidase activity is not known. Phosphoenolpyruvate (PEP) is known as a strong inhibitor of prolidase activity. It exerts this effect by inhibition of the enzyme phosphorylation. Unphosphorylated prolidase is inactive. One may expect that fasting-associated increase in posphoenolpyruvate content in animal tissues may be a factor which inactivates prolidase and makes it inactive in collagen biosynthesis. We measured the levels of phosphoenolpyruvate, pyruvate, and pyruvate kinase in the skin of control and fasted rats and correlated these parameters with prolidase expression, prolidase activity and collagen biosynthesis in this tissue. Significant increase of PEP concentration (about 30%) was found in the skin of fasted rats. In the same time prolidase activity and collagen biosynthesis decreased by about 50% and 30%, respectively, compared to controls. It is known that phosphoenolpyruvate is converted to pyruvate by the action of pyruvate kinase. Since fasting significantly decreases the activity of this enzyme, one may suggest that the accumulation of PEP is caused by a reduced utilisation of this metabolite. As demonstrated by Western immunoblot analysis the decrease in prolidase activity was not accompanied by a decrease in the amount of the enzyme protein. Instead, a decrease in the enzyme phosphorylation was observed. The reduction in phosphorylation seems to be responsible for the decrease in prolidase activity. These data suggest that fasting-evoked accumulation of PEP reduces the activity of prolidase, providing a mechanism for inhibition of collagen biosynthesis in the skin.

Collagen content and growth factor immunoexpression in uterine lower segment of type IA osteogenesis imperfecta: Relationship with recurrent uterine rupture in pregnancy

OBJECTIVE

The purpose of this study was to evaluate collagen content and platelet-derived growth factor, vascular endothelial growth factor, and connective tissue growth factor expression in the myometrium of the uterine lower segment from a patient with type IA osteogenesis imperfecta with recurrent uterine rupture and to evaluate the existence of a relationship between the rare recurrent uterine rupture and the tissue disorders of type IA osteogenesis imperfecta.

STUDY DESIGN

Collagen content and platelet-derived growth factor, vascular endothelial growth factor, and connective tissue growth factor expression in the uterine lower segment were assessed in the patient with type IA osteogenesis imperfecta and in eight otherwise healthy ("control") patients.

RESULTS

Type IA osteogenesis imperfecta contained less total collagen amount, with no difference in type III collagen expression and showed increased levels of platelet-derived growth factor and vascular endothelial growth factor in myometrial smooth muscle cells. No difference was observed in connective tissue growth factor expression.

CONCLUSION

These findings confirm the diminished collagen amount in myometrium from osteogenesis imperfecta and show the presence of additional pathogenetic mechanisms. A relationship is hypothesized between the underlying myometrial biochemical modifications and the recurrent uterine rupture.

Gly511 to Ser substitution in the COL1A1 gene in osteogenesis imperfecta type III patient with increased turnover of collagen

Osteogenesis imperfecta (OI) is a result of heterozygous mutations in the COL1A1 or COL1A2 genes, encoding type I procollagen chains. Here we described the molecular and biochemical defects detected in a case of severe type III OI. Cultured skin fibroblasts from the proband produced both normal and mutant type I collagen which was secreted into the medium. The mutation site was localized in alpha 1(I)-CB3 by CNBr cleavage of collagen chains. Subsequent reverse transcription-PCR amplification and direct sequencing of single-stranded PCR product led to identification of G to A transition in the COL1A1 gene, resulting in Gly511Ser substitution in the a1 chain of type I collagen. The new mutation conforms to the chain-specific non-lethal microdomain of Gly to Ser substitutions in the genotype-phenotype map. We have found that biosynthesis of collagen was increased in OI cells to about 160% of the control value. However, the amount of collagen deposed to the insoluble matrix was decreased as compared to the control. This suggests increased degradation of collagen, since the collagenolytic activity of OI cells was increased. Furthermore, the activity of prolidase, which is a marker of collagen turnover, was increased in OI cells. In regulation of activity of the enzyme are involved beta1 integrin and insulin-like growth factor (IGF) receptors. Western immunoblot analysis showed that the expressions of both receptors were markedly increased in OI cells. These results suggest that increase in activity of prolidase can be associated with increase in intensity of collagen metabolism in type III OI patient with identified new G511S mutation.