Periodic Reporting for period 1 - DisCo-I (Discovering Collagen I degradation process in chronic diseases with fibrotic component)
Reporting period: 2022-09-01 to 2024-08-31
DisCo-I addresses chronic diseases (CDs) with a fibrotic component, such as chronic kidney disease (CKD), heart failure (HF), and liver diseases (LD), being among the leading global causes of morbidity and mortality. Fibrosis, resulting from abnormal tissue repair, plays a central role in the progression of these diseases. It is characterized by an imbalance in extracellular matrix (ECM) homeostasis, leading to the excessive accumulation of ECM components, particularly type I collagen (COL1).
The scientific goal of DisCo-I is to improve the understanding of the molecular mechanisms involved in COL1 degradation in major fibrotic CDs and to investigate a disruptive hypothesis: that attenuated COL1 degradation is a key driver of fibrosis and a major contributor to the onset and progression of CDs. Through that, DisCo-I addresses the development of biomarkers and better therapeutics for major diseases affecting the EU and beyond, which may ultimately lead to reducing the disease burden. To achieve this, six doctoral candidates (DCs) have been recruited. Through multi-disciplinary and inter-sectoral training, the DCs have already produced significant scientific outputs while gaining expertise in cutting-edge technologies, clinical aspects of CDs, and industrial applications. They have participated in workshops, secondments, and collaborative research, preparing them for leadership roles in academia and industry.
The scientific goal of DisCo-I is to improve the understanding of the molecular mechanisms involved in COL1 degradation in major fibrotic CDs and to investigate a disruptive hypothesis: that attenuated COL1 degradation is a key driver of fibrosis and a major contributor to the onset and progression of CDs. Through that, DisCo-I addresses the development of biomarkers and better therapeutics for major diseases affecting the EU and beyond, which may ultimately lead to reducing the disease burden. To achieve this, six doctoral candidates (DCs) have been recruited. Through multi-disciplinary and inter-sectoral training, the DCs have already produced significant scientific outputs while gaining expertise in cutting-edge technologies, clinical aspects of CDs, and industrial applications. They have participated in workshops, secondments, and collaborative research, preparing them for leadership roles in academia and industry.
Progress has been made in understanding COL1 degradation in CDs, focusing on gene expression (transcriptomics), translation (proteomics, ELISA), post-translational modifications (PTMs), and protein degradation (peptidomics, ELISA).
DC1's study of urinary peptide changes in CDs (CKD, HF and LD) identified 111 COL1 degradation products with consistent regulation trends across these conditions, the majority containing hydroxylated proline, a modification introduced during COL1 biosynthesis. A support vector machine (SVM) model using these peptides detected fibrotic CDs with an Area Under Curve of 0.865 in an independent cohort. Further analysis highlighted the complexity of COL1 degradation as a multi-step process involving endopeptidases in the early stages and exopeptidases later (Mina IK et al. Proteomics. 2024). DC4 explored the biological effects of urinary COL1 degradation products on endothelial cell migration, revealing that while COL1 promoted migration, a specific COL1 peptide inhibited it via integrin α2β1, suggesting a regulatory role in ECM and fibrosis.
Given the associations of urinary peptides with CDs, DC6 developed an SVM model based on 189 peptides to predict non-response to treatment/progression in diabetic kidney disease (Jaimes Campos MA et al. Nephrol Dial Transplant. 2024). In silico analyses simulated intervention impacts, enabling personalized therapeutic recommendations (Jaimes Campos MA et al. Pharmaceuticals. 2023). Moreover, DC1 identified 90 sex-associated urinary peptides, and comparison with transcriptomic data suggested that, while many differences in the abundance of non-collagen peptides reflected sex-biased gene expression, changes in collagen peptides indicated sex-biased collagen degradation (Mina IK et al. Proteomics. 2024). To facilitate future omics studies, Gaussian copulas were used to generate synthetic datasets, which preserved clinical and molecular data correlations while ensuring confidentiality (Jaimes Campos MA et al. medRxiv 2024).
DC2 assessed COL1 turnover (synthesis and degradation) in circulation using ELISA. Multiple peptides were evaluated: elevated C1M levels in type 2 diabetes were linked to mortality, while C1M and CTX-I were elevated in Autosomal Dominant Polycystic Kidney Disease, indicating a degradation-driven phenotype. C1M and C1SIG levels increased after ST-elevation myocardial infarction, predicting mortality at 30 days and one year. In cirrhosis, increased C1M and C1SIG reflected elevated COL1 degradation. Novel immunoassays (C1SIG, C1-CKD) were developed, with C1-CKD correlating with kidney function. These results are part of manuscripts that have not yet been published.
DC4 studied tissue proteomes. Together with DC5, initial ECM enrichment efforts using decellularization protocols (Frattini T, Devos H et al. Proteomics. 2024) showed misrepresentation of the native ECM composition, leading to its exclusion from further analysis. DC4 synthesized existing knowledge on COL1A regulators (Devos H et al. Int J Mol Sci. 2023) and conducted proteomic analysis of existing HF, LD, and kidney tissue datasets, revealing significant protein changes associated with fibrosis that are currently further investigated. Transcriptomics analysis by DC6 from public repositories identified 497 differentially expressed genes with the same expression trend across HF, CKD and LD, significant in at least one condition. Pathway analysis linked fibrosis to ECM organization, immune response, and metabolism.
Animal models (DC3- rat, DC5- mouse) were used to investigate fibrosis. SNx rats developed kidney and heart fibrosis, high-fat diet rats showed liver fibrosis and steatosis, and UUO/Alport mice exhibited significant kidney fibrosis. Proteomic analysis of SNx tissues revealed changes in ECM proteins. Sexual dimorphism in antifibrotic DMAPT efficacy was observed in female Col4α3-KO mice, emphasizing the importance of sex as a biological variable. Urinary peptide analysis in UUO models identified 942 collagen fragments with different regulations between bladder and pelvis. Ex vivo experiments with precision-cut kidney slices showed limited overlap between peptides released from tissues and those detected in urine, requiring further investigation.
DC1's study of urinary peptide changes in CDs (CKD, HF and LD) identified 111 COL1 degradation products with consistent regulation trends across these conditions, the majority containing hydroxylated proline, a modification introduced during COL1 biosynthesis. A support vector machine (SVM) model using these peptides detected fibrotic CDs with an Area Under Curve of 0.865 in an independent cohort. Further analysis highlighted the complexity of COL1 degradation as a multi-step process involving endopeptidases in the early stages and exopeptidases later (Mina IK et al. Proteomics. 2024). DC4 explored the biological effects of urinary COL1 degradation products on endothelial cell migration, revealing that while COL1 promoted migration, a specific COL1 peptide inhibited it via integrin α2β1, suggesting a regulatory role in ECM and fibrosis.
Given the associations of urinary peptides with CDs, DC6 developed an SVM model based on 189 peptides to predict non-response to treatment/progression in diabetic kidney disease (Jaimes Campos MA et al. Nephrol Dial Transplant. 2024). In silico analyses simulated intervention impacts, enabling personalized therapeutic recommendations (Jaimes Campos MA et al. Pharmaceuticals. 2023). Moreover, DC1 identified 90 sex-associated urinary peptides, and comparison with transcriptomic data suggested that, while many differences in the abundance of non-collagen peptides reflected sex-biased gene expression, changes in collagen peptides indicated sex-biased collagen degradation (Mina IK et al. Proteomics. 2024). To facilitate future omics studies, Gaussian copulas were used to generate synthetic datasets, which preserved clinical and molecular data correlations while ensuring confidentiality (Jaimes Campos MA et al. medRxiv 2024).
DC2 assessed COL1 turnover (synthesis and degradation) in circulation using ELISA. Multiple peptides were evaluated: elevated C1M levels in type 2 diabetes were linked to mortality, while C1M and CTX-I were elevated in Autosomal Dominant Polycystic Kidney Disease, indicating a degradation-driven phenotype. C1M and C1SIG levels increased after ST-elevation myocardial infarction, predicting mortality at 30 days and one year. In cirrhosis, increased C1M and C1SIG reflected elevated COL1 degradation. Novel immunoassays (C1SIG, C1-CKD) were developed, with C1-CKD correlating with kidney function. These results are part of manuscripts that have not yet been published.
DC4 studied tissue proteomes. Together with DC5, initial ECM enrichment efforts using decellularization protocols (Frattini T, Devos H et al. Proteomics. 2024) showed misrepresentation of the native ECM composition, leading to its exclusion from further analysis. DC4 synthesized existing knowledge on COL1A regulators (Devos H et al. Int J Mol Sci. 2023) and conducted proteomic analysis of existing HF, LD, and kidney tissue datasets, revealing significant protein changes associated with fibrosis that are currently further investigated. Transcriptomics analysis by DC6 from public repositories identified 497 differentially expressed genes with the same expression trend across HF, CKD and LD, significant in at least one condition. Pathway analysis linked fibrosis to ECM organization, immune response, and metabolism.
Animal models (DC3- rat, DC5- mouse) were used to investigate fibrosis. SNx rats developed kidney and heart fibrosis, high-fat diet rats showed liver fibrosis and steatosis, and UUO/Alport mice exhibited significant kidney fibrosis. Proteomic analysis of SNx tissues revealed changes in ECM proteins. Sexual dimorphism in antifibrotic DMAPT efficacy was observed in female Col4α3-KO mice, emphasizing the importance of sex as a biological variable. Urinary peptide analysis in UUO models identified 942 collagen fragments with different regulations between bladder and pelvis. Ex vivo experiments with precision-cut kidney slices showed limited overlap between peptides released from tissues and those detected in urine, requiring further investigation.
By combining cutting-edge research with multidisciplinary and intersectoral training, DisCo-I will contribute to European research excellence and innovation, potentially delivering health, health care, and economic benefits in the long term. DisCo-I is on track to achieving these impacts while training translational researchers, enhancing their career prospects and employability, sustaining its impact after the project ends. Scientific impact through publications has already been achieved and will be expanded, including advancing knowledge of COL1 degradation and fibrosis, and developing biomarkers, paving the way for innovative diagnostic tools and therapies. Economically, the project’s outcomes may reduce healthcare costs by improving the management of CDs. Societally, DisCo-I is very active in reaching the general public through social media and informing on research towards improved detection of CDs and intervention guidance as a means to enhance patient outcomes and improve quality of life.