Adverse effects of Alport syndrome-related Gly missense mutations on collagen type IV: Insights from molecular simulations and experiments

A Deeper Insight into COL4A3, COL4A4, and COL4A5 Variants and Genotype-Phenotype Correlation of a Turkish Cohort with Alport Syndrome

Introduction

Alport syndrome (AS) is an inherited, rare, progressive kidney disease that affects the eye and ear physiology. Pathogenic variants of COL4A5 account for 85% of all cases, while COL4A3 and COL4A4 account for the remaining 15%.

Methods

Targeted next-generation sequencing of the COL4A3, COL4A4, and COL4A5 genes was performed in 125 Turkish patients with AS. The patients were compared to 45 controls and open-access population data.

Results

The incidence of AS variants in patients was found as 21.6%. 27 variants were identified as pathogenic/likely pathogenic, 28 as variant of uncertain significance, and 52 as benign/likely benign. We also found 31 novel variants (14 in COL4A3, 6 in COL4A4, and 11 in COL4A5) of which 27 were classified as pathogenic/likely pathogenic. Pathogenic/likely Pathogenic variants were most commonly found in the COL4A5 gene, consistent with the literature. This study contributed novel variants associated with AS to the literature.

Conclusion

Genetic testing is a crucial part for the diagnosis and management of AS. Studies on the genetic etiology of AS are limited for the Turkish population. We believe that this study will contribute to the literature and the clinical decision-making process of patients with AS and emphasize the importance of genetic counseling.

Designing collagens to shed light on the multi-scale structure-function mapping of matrix disorders

Collagens are the most abundant structural proteins in the extracellular matrix of animals and play crucial roles in maintaining the structural integrity and mechanical properties of tissues and organs while mediating important biological processes. Fibrillar collagens have a unique triple helix structure with a characteristic repeating sequence of (Gly-X-Y)n. Variations within the repetitive sequence can cause misfolding of the triple helix, resulting in heritable connective tissue disorders. The most common variations are single-point missense mutations that lead to the substitution of a glycine residue with a bulkier amino acid (Gly → X). In this review, we will first discuss the importance of collagen's triple helix structure and how single Gly substitutions can impact its folding, structure, secretion, assembly into higher-order structures, and biological functions. We will review the role of "designer collagens," i.e., synthetic collagen-mimetic peptides and recombinant bacterial collagen as model systems to include Gly → X substitutions observed in collagen disorders and investigate their impact on structure and function utilizing in vitro studies. Lastly, we will explore how computational modeling of collagen peptides, especially molecular and steered molecular dynamics, has been instrumental in probing the effects of Gly substitutions on structure, receptor binding, and mechanical stability across multiple length scales.

Novel Digenic Variants in COL4A4 and COL4A5 Causing X-Linked Alport Syndrome: A Case Report

Introduction

Alport syndrome (AS) is a hereditary, progressive kidney disease characterized by structural abnormalities and dysfunction of the glomerular basement membrane (GBM). AS is classified as X-linked, autosomal, and digenic. The number of cases of digenic AS has increased, but the genotype-phenotype correlation of patient with digenic AS is still unclear. Here, we present a case of digenic AS with novel digenic missense variants in COL4A4 (c.827G>C, p.Gly276Ala) and COL4A5 (c.4369G>C, p.Gly1457Arg).

Case Presentation

The patient was a 29-year-old Japanese man suffering from persistent microscopic hematuria and proteinuria without kidney function impairment. Kidney biopsy showed focal interstitial foam cell infiltration, global and segmental glomerulosclerosis. Immunofluorescence staining for collagen IV α5 was almost negative in the GBM and Bowman's capsule. Electron microscopy revealed irregular thickening with lamellation and segmental thinning of the GBM. Clinical and pathological findings were consistent with AS. Comprehensive next-generation sequencing revealed a heterozygous missense variant in COL4A4 (c.827G>C, p.Gly276Ala) in exon 1 and a hemizygous missense variant in COL4A5 (c.4369G>C, p.Gly1457Arg) in exon 49 on the patient's paternal and maternal alleles, respectively. The same digenic variants were detected in his sister, and she also showed a similar phenotype. After treatment with angiotensin-converting enzyme inhibitors, proteinuria decreased from 2.3 to 1.1 g/g creatinine, but occult blood persisted. During follow-up, kidney function has been preserved.

Conclusion

The novel genotype of our case provides more information on the genotype-phenotype correlation of digenic XLAS, although long-term follow-up is required. The findings in the present case also indicate the importance of genetic tests for family members of a patient diagnosed with digenic AS.

Case report: A case report of Alport syndrome caused by a novel mutation of COL4A5

Alport syndrome (#308940) is an X-linked genetic disease with clinical manifestations, such as hematuria, proteinuria, renal insufficiency, and end-stage renal disease. The disease is characterized by the thinning of the glomerular basement membrane in the early stages and the thickening of the glomerular basement membrane in the late stages and may be associated with ocular lesions and varying degrees of sensorineural deafness. Herein, we report a case of Alport syndrome caused by a de novo mutation in COL4A5. The patient was a young male with clinical manifestations of hematuria and massive proteinuria who was diagnosed with Alport syndrome based on renal pathology and genetic testing.

Purification of recombinant bacterial collagens containing structural perturbations

Streptococcus pyogenes-derived recombinant bacterial collagen-like proteins (CLPs) are emerging as a potential biomaterial for biomedical research and applications. Bacterial CLPs form stable triple helices and lack specific interactions with human cell surface receptors, thus enabling the design of novel biomaterials with specific functional attributes. Bacterial collagens have been instrumental in understanding collagen structure and function in normal and pathological conditions. These proteins can be readily produced in E. coli, purified using affinity chromatography, and subsequently isolated after cleavage of the affinity tag. Trypsin is a widely used protease during this purification step since the triple helix structure is resistant to trypsin digestion. However, the introduction of Gly→X mutations or natural interruptions within CLPs can perturb the triple helix structure, making them susceptible to trypsin digestion. Consequently, removing the affinity tag and isolating collagen-like (CL) domains containing mutations is impossible without degradation of the product. We present an alternative method to isolate CL domains containing Gly→X mutations utilizing a TEV protease cleavage site. Protein expression and purification conditions were optimized for designed protein constructs to achieve high yield and purity. Enzymatic digestion assays demonstrated that CL domains from wild-type CLPs could be isolated by digestion with either trypsin or TEV protease. In contrast, CLPs containing Gly→Arg mutations are readily digested by trypsin while digestion with TEV protease cleaved the His6-tag, enabling the isolation of mutant CL domains. The developed method can be adapted to CLPs containing various new biological sequences to develop multifunctional biomaterials for tissue engineering applications.

Macrophages Rapidly Seal off the Punctured Zebrafish Larval Brain through a Vital Honeycomb Network Structure

There is accumulating evidence that macrophages play additional important roles in tissue damage besides their typical phagocytosis. Although the aggregation of macrophages on injured sites has long been observed, few researchers have focused on the role of the overall structure of macrophage aggregation. In this study, we developed a standardized traumatic brain injury (TBI) model in zebrafish larvae to mimic edema and brain tissue spillage symptoms after severe brain trauma. Using time-lapse imaging, we showed that macrophages/microglia in zebrafish larvae responded rapidly and dominated the surface of injured tissue, forming a meaningful honeycomb network structure through their compact aggregation and connection. Disrupting this structure led to fatal edema-like symptoms with severe loss of brain tissue. Using the RNA-Seq, together with the manipulation of in vitro cell lines, we found that collagen IV was indispensable to the formation of honeycomb network structures. Our study thus revealed a novel perspective regarding macrophages forming a protective compact structure with collagen IV. This honeycomb network structure acted as a physical barrier to prevent tissue loss and maintain brain homeostasis after TBI. This study may provide new evidence of macrophages’ function for the rapid protection of brain tissue after brain injury.

Monogenic focal segmental glomerulosclerosis: A conceptual framework for identification and management of a heterogeneous disease

Focal segmental glomerulosclerosis (FSGS) is not a disease, rather a pattern of histological injury occurring from a variety of causes. The exact pathogenesis has yet to be fully elucidated but is likely varied based on the type of injury and the primary target of that injury. However, the approach to treatment is often based on the degree of podocyte foot process effacement and clinical presentation without sufficient attention paid to etiology. In this regard, there are many monogenic causes of FSGS with variable presentation from nephrotic syndrome with histological features of primary podocytopathy to more modest degrees of proteinuria with limited evidence of podocyte foot process injury. It is likely that genetic causes are largely underdiagnosed, as the role and the timing of genetic testing in FSGS is not established and genetic counseling, testing options, and interpretation of genotype in the context of phenotype may be outside the scope of practice for both nephrologists and geneticists. Yet most clinicians believe that a genetic diagnosis can lead to targeted therapy, limit the use of high-dose corticosteroids as a therapeutic trial, and allow the prediction of the natural history and risk for recurrence in the transplanted kidney. In this manuscript, we emphasize that genetic FSGS is not monolithic in its presentation, opine on the importance of genetic testing and provide an algorithmic approach to deployment of genetic testing in a timely fashion when faced with a patient with FSGS.

Case Report: Identification of a Novel Heterozygous Missense Mutation in COL4A3 Gene Causing Variable Phenotypes in an Autosomal-Dominant Alport Syndrome Family

Alport syndrome (AS) is a genetic kidney disease of basement membrane collagen disorder accounting for approximately 2% of ESRD patients. Next-generation and whole-exome sequencing methods are increasingly frequently used as an efficient tool not only for the diagnosis of AS but also for the establishment of genotype–phenotype correlation. We herein report the identification of a novel heterozygous missense mutation in COL4A3 gene (c.G3566A: p.G1189E) causing variable phenotypes in an ADAS Family based on the combination of clinical, histologic, pedigree, and genetic sequencing information. The proband is a 48-year-old Chinese woman suffering from persistent subnephrotic proteinuria and intermittent hematuria without renal function impairment over a 10-year time-span. Renal biopsy showed diffuse thin basement membrane and focal interstitial foam cell infiltration. The proband’s mother progressed to end-stage renal failure and the proband’s sister presented with subnephrotic proteinuria and intermittent hematuria as well. AS was highly suspected and confirmed by exome sequencing which revealed a novel heterozygous missense mutation in COL4A3 gene (c.G3566A: p.G1189E) in all the affected family members, although their current medical conditions vary significantly. Our present finding emphasizes the significance of next-generation sequencing technology for genetic screening which gives us an accurate clinical diagnosis of ADAS patients. The identification of c.G3566A as a new ADAS-related mutation contributes to both genetic diagnosis of ADAS and further functional study of COL4A3. The variable phenotypes from the same genotype of our case also provide more information to genotype–phenotype correlation study.

Identification of a novel pathogenic COL4A3 gene mutation in a Chinese family with autosomal dominant Alport syndrome: A case report

Alport syndrome (AS) is a genetic disease with various manifestations, including hematuria, proteinuria, impaired renal function and potential ocular or auditory abnormalities. Mutations in the collagen type IV α 3 chain (COL4A3), collagen type IV α 4 chain and collagen type IV α 5 chain genes encoding the α3, α4 and α5 chains of type IV collagen may undermine glomerular basement membrane (GBM) integrity and cause persistent renal deterioration. In the present study, the case of a Chinese family diagnosed with AS was examined. Pedigree investigations and whole exome sequencing (WES) revealed the presence of two heterozygous mutations (c.2603G>A; p.G868E, and c.583G>A; p.G195S) in the COL4A3 gene. p.G868E was identified as the 'culprit' mutation, whereas p.G195S was identified as an 'auxiliary' mutation for AS with regards to the manifestations observed in the patients carrying each of the gene mutations. In conclusion, these findings suggested that c.2603G>A may be a novel overt pathogenic mutation site for autosomal dominant AS. In addition, WES may be effective for the early diagnosis and medical intervention of AS, and may be widely used for AS prognosis prediction and pre-implantation genetic diagnosis.

Sequence-dependent mechanics of collagen reflect its structural and functional organization

Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen proteins. In particular, network-forming collagen IV, an integral component of basement membranes, has been far less studied than fibril-forming collagens. A key feature of collagen IV is the presence of interruptions in the triple-helix-defining (Gly-X-Y) sequence along its collagenous domain. Here, we used atomic force microscopy to determine the impact of sequence heterogeneity on the local flexibility of collagen IV and of the fibril-forming collagen III. Our extracted flexibility profile of collagen IV reveals that it possesses highly heterogeneous mechanics, ranging from semiflexible regions as found for fibril-forming collagens to a lengthy region of high flexibility toward its N-terminus. A simple model in which flexibility is dictated only by the presence of interruptions fit the extracted profile reasonably well, providing insight into the alignment of chains and demonstrating that interruptions, particularly when coinciding in multiple chains, significantly enhance local flexibility. To a lesser extent, sequence variations within the triple helix lead to variable flexibility, as seen along the continuously triple-helical collagen III. We found this fibril-forming collagen to possess a high-flexibility region around its matrix-metalloprotease binding site, suggesting a unique mechanical fingerprint of this region that is key for matrix remodeling. Surprisingly, proline content did not correlate with local flexibility in either collagen type. We also found that physiologically relevant changes in pH and chloride concentration did not alter the flexibility of collagen IV, indicating such environmental changes are unlikely to control its compaction during secretion. Although extracellular chloride ions play a role in triggering collagen IV network formation, they do not appear to modulate the structure of its collagenous domain.

Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria

The recent Chandos House meeting of the Alport Variant Collaborative extended the indications for screening for pathogenic variants in the COL4A5, COL4A3 and COL4A4 genes beyond the classical Alport phenotype (haematuria, renal failure; family history of haematuria or renal failure) to include persistent proteinuria, steroid-resistant nephrotic syndrome, focal and segmental glomerulosclerosis (FSGS), familial IgA glomerulonephritis and end-stage kidney failure without an obvious cause. The meeting refined the ACMG criteria for variant assessment for the Alport genes (COL4A3-5). It identified 'mutational hotspots' (PM1) in the collagen IV α5, α3 and α4 chains including position 1 Glycine residues in the Gly-X-Y repeats in the intermediate collagenous domains; and Cysteine residues in the carboxy non-collagenous domain (PP3). It considered that 'well-established' functional assays (PS3, BS3) were still mainly research tools but sequencing and minigene assays were commonly used to confirm splicing variants. It was not possible to define the Minor Allele Frequency (MAF) threshold above which variants were considered Benign (BA1, BS1), because of the different modes of inheritances of Alport syndrome, and the occurrence of hypomorphic variants (often Glycine adjacent to a non-collagenous interruption) and local founder effects. Heterozygous COL4A3 and COL4A4 variants were common 'incidental' findings also present in normal reference databases. The recognition and interpretation of hypomorphic variants in the COL4A3-COL4A5 genes remains a challenge.

Structure-Property Relationships of Elastin-like Polypeptides: A Review of Experimental and Computational Studies

Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor tropoelastin, a 60-72 kDa water-soluble and temperature-responsive protein that coacervates at physiological temperature, undergoing a phenomenon termed lower critical solution temperature (LCST). Inspired by this behavior, many scientists and engineers are developing recombinantly produced elastin-inspired biopolymers, usually termed elastin-like polypeptides (ELPs). These ELPs are generally comprised of repetitive motifs with the sequence VPGXG, which corresponds to repeats of a small part of the tropoelastin sequence, X being any amino acid except proline. ELPs display LCST and mechanical properties similar to tropoelastin, which renders them promising candidates for the development of elastic and stimuli-responsive protein-based materials. Unveiling the structure-property relationships of ELPs can aid in the development of these materials by establishing the connections between the ELP amino acid sequence and the macroscopic properties of the materials. Here we present a review of the structure-property relationships of ELPs and ELP-based materials, with a focus on LCST and mechanical properties and how experimental and computational studies have aided in their understanding.

Understanding Plant Biomass via Computational Modeling

Plant biomass, especially wood, has been used for structural materials since ancient times. It is also showing great potential for new structural materials and it is the major feedstock for the emerging biorefineries for building a sustainable society. The plant cell wall is a hierarchical matrix of mainly cellulose, hemicellulose, and lignin. Herein, the structure, properties, and reactions of cellulose, lignin, and wood cell walls, studied using density functional theory (DFT) and molecular dynamics (MD), which are the widely used computational modeling approaches, are reviewed. Computational modeling, which has played a crucial role in understanding the structure and properties of plant biomass and its nanomaterials, may serve a leading role on developing new hierarchical materials from biomass in the future.

Current Insights on the Diverse Structures and Functions in Bacterial Collagen-like Proteins

The dearth of knowledge on the diverse structures and functions in bacterial collagen-like proteins is in stark contrast to the deep grasp of structures and functions in mammalian collagen, the ubiquitous triple-helical scleroprotein that plays a central role in tissue architecture, extracellular matrix organization, and signal transduction. To fill and highlight existing gaps due to the general paucity of data on bacterial CLPs, we comprehensively reviewed the latest insight into their functional and structural diversity from multiple perspectives of biology, computational simulations, and materials engineering. The origins and discovery of bacterial CLPs were explored. Their genetic distribution and molecular architecture were analyzed, and their structural and functional diversity in various bacterial genera was examined. The principal roles of computational techniques in understanding bacterial CLPs' structural stability, mechanical properties, and biological functions were also considered. This review serves to drive further interest and development of bacterial CLPs, not only for addressing fundamental biological problems in collagen but also for engineering novel biomaterials. Hence, both biology and materials communities will greatly benefit from intensified research into the diverse structures and functions in bacterial collagen-like proteins.

Birefringent Silk Fibroin Hydrogel Constructed via Binary Solvent-Exchange-Induced Self-Assembly

Birefringent hydrogels have a strong potential for applications in biomedicine and optics as they can modulate the optical and mechanical anisotropy in confined two-dimensional geometries. However, production of birefringent hydrogels with hierarchical structures, mechanical properties, and biorelated behavior that are analogous to biological tissues is still challenging. Starting from the silk fibroin (SF)-ionic liquid solution system, this study aimed to rationally design a "binary solvent-exchange-induced self-assembly (BSEISA)" strategy to produce birefringent SF hydrogels (SFHs). In this method, the conformational transition rate of SF can be effectively controlled by the exchange rate of the binary solvents. Therefore, this method provides the possibility of controlling the conformation and orientation of SF. Molecular simulations confirmed that methanol is more effective in driving β-sheet formation than other often used solvents, such as formic acid and water. The formed β-sheets act as the physical cross-links that connect disparate protein chains, thereby forming continuous and stable three-dimensional (3D) hydrogel networks. The resultant BSEISA-SFHs are transparent and birefringent with mechanical characteristics similar to those of soft biological tissues, such as lens and cartilage. Interestingly, our results revealed that the evolution of experimental birefringent fringes perfectly matched the changes in stress distribution predicted using finite element analysis. Owing to the unique birefringence of BSEISA-SFHs, together with the advantages in mechanical performance, these hydrogels are anticipated to act as good tissue surrogates for understanding the mechanical response of biological tissues.

A glycine substitution in the collagenous domain of Col4a3 in mice recapitulates late onset Alport syndrome

Alport syndrome (AS) is a severe inherited glomerulopathy caused by mutations in the genes encoding the α-chains of type-IV collagen, the most abundant component of the extracellular glomerular basement membrane (GBM). Currently most AS mouse models are knockout models for one of the collagen-IV genes. In contrast, about half of AS patients have missense mutations, with single aminoacid substitutions of glycine being the most common. The only mouse model for AS with a homozygous knockin missense mutation, Col4a3-p.Gly1332Glu, was partly described before by our group. Here, a detailed in-depth description of the same mouse is presented, along with another compound heterozygous mouse that carries the glycine substitution in trans with a knockout allele. Both mice recapitulate essential features of AS, including shorten lifespan by 30–35%, increased proteinuria, increased serum urea and creatinine, pathognomonic alternate GBM thinning and thickening, and podocyte foot process effacement. Notably, glomeruli and tubuli respond differently to mutant collagen-IV protomers, with reduced expression in tubules but apparently normal in glomeruli. However, equally important is the fact that in the glomeruli the mutant α3-chain as well as the normal α4/α5 chains seem to undergo a cleavage at, or near the point of the mutation, possibly by the metalloproteinase MMP-9, producing a 35 kDa C-terminal fragment. These mouse models represent a good tool for better understanding the spectrum of molecular mechanisms governing collagen-IV nephropathies and could be used for pre-clinical studies aimed at better treatments for AS.

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Two mouse models were generated that recapitulate essential features of AS patients.

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Glomeruli and tubuli respond differently to mutant collagen IV protomers.

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The mutant colIV protomers in glomeruli probably undergo a cleavage process by MMP9.

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The two AS mouse models represent a good tool for studying collagen-IV nephropathies.

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These models could be used for pre-clinical studies aimed at better treatments.