Protein modeling to assess the pathogenicity of rare variants of SERPINA1 in patients suspected of having Alpha 1 Antitrypsin Deficiency

Computational Tools to Assist in Analyzing Effects of the SERPINA1 Gene Variation on Alpha-1 Antitrypsin (AAT)

In the rapidly advancing field of bioinformatics, the development and application of computational tools to predict the effects of single nucleotide variants (SNVs) are shedding light on the molecular mechanisms underlying disorders. Also, they hold promise for guiding therapeutic interventions and personalized medicine strategies in the future. A comprehensive understanding of the impact of SNVs in the SERPINA1 gene on alpha-1 antitrypsin (AAT) protein structure and function requires integrating bioinformatic approaches. Here, we provide a guide for clinicians to navigate through the field of computational analyses which can be applied to describe a novel genetic variant. Predicting the clinical significance of SERPINA1 variation allows clinicians to tailor treatment options for individuals with alpha-1 antitrypsin deficiency (AATD) and related conditions, ultimately improving the patient's outcome and quality of life. This paper explores the various bioinformatic methodologies and cutting-edge approaches dedicated to the assessment of molecular variants of genes and their product proteins using SERPINA1 and AAT as an example.

Rare variants in alpha 1 antitrypsin deficiency: a systematic literature review

BACKGROUND

Alpha 1 Antitrypsin Deficiency (AATD) is a largely underrecognized genetic condition characterized by low Alpha 1 Antitrypsin (AAT) serum levels, resulting from variations in SERPINA1. Many individuals affected by AATD are thought to be undiagnosed, leading to poor patient outcomes. The Z (c.1096G > A; p.Glu366Lys) and S (c.863A > T; p.Glu288Val) deficiency variants are the most frequently found variants in AATD, with the Z variant present in most individuals diagnosed with AATD. However, there are many other less frequent variants known to contribute to lung and/or liver disease in AATD. To identify the most common rare variants associated with AATD, we conducted a systematic literature review with the aim of assessing AATD variation patterns across the world.

METHODS

A systematic literature search was performed to identify published studies reporting AATD/SERPINA1 variants. Study eligibility was assessed for the potential to contain relevant information, with quality assessment and data extraction performed on studies meeting all eligibility criteria. AATD variants were grouped by variant type and linked to the geographical region identified from the reporting article.

RESULTS

Of the 4945 articles identified by the search string, 864 contained useful information for this study. Most articles came from the United States, followed by the United Kingdom, Germany, Spain, and Italy. Collectively, the articles identified a total of 7631 rare variants and 216 types of rare variant across 80 counties. The F (c.739C > T; p.Arg247Cys) variant was identified 1,281 times and was the most reported known rare variant worldwide, followed by the I (c.187C > T; p.Arg63Cys) variant. Worldwide, there were 1492 Null/rare variants that were unidentified at the time of source article publication and 75 rare novel variants reported only once.

CONCLUSION

AATD goes far beyond the Z and S variants, suggesting there may be widespread underdiagnosis of patients with the condition. Each geographical region has its own distinctive variety of AATD variants and, therefore, comprehensive testing is needed to fully understand the true number and type of variants that exist. Comprehensive testing is also needed to ensure accurate diagnosis, optimize treatment strategies, and improve outcomes for patients with AATD.

Protein modeling and in silico analysis to assess pathogenicity of ABCA4 variants in patients with inherited retinal disease

Purpose

The retina-specific ABCA transporter, ABCA4, plays an essential role in translocating retinoids required by the visual cycle. ABCA4 genetic variants are known to cause a wide range of inherited retinal disorders, including Stargardt disease and cone-rod dystrophy. More than 1,400 ABCA4 missense variants have been identified; however, more than half of these remain variants of uncertain significance (VUS). The purpose of this study was to employ a predictive strategy to assess the pathogenicity of ABCA4 variants in inherited retinal diseases using protein modeling and computational approaches.

Methods

We studied 13 clinically well-defined patients with ABCA4 retinopathies and identified the presence of 10 missense variants, including one novel variant in the ABCA4 gene, by next-generation sequencing (NGS). All variants were structurally analyzed using AlphaFold2 models and existing experimental structures of human ABCA4 protein. The results of these analyses were compared with patient clinical presentations to test the effectiveness of the methods employed in predicting variant pathogenicity.

Results

We conducted a phenotype-genotype comparison of 13 genetically and phenotypically well-defined retinal disease patients. The in silico protein structure analyses we employed successfully detected the deleterious effect of missense variants found in this affected patient cohort. Our study provides American College of Medical Genetics and Genomics (ACMG)-defined supporting evidence of the pathogenicity of nine missense ABCA4 variants, aligning with the observed clinical phenotypes in this cohort.

Conclusions

In this report, we describe a systematic approach to predicting the pathogenicity of ABCA4 variants by means of three-dimensional (3D) protein modeling and in silico structure analysis. Our results demonstrate concordance between disease severity and structural changes in protein models induced by genetic variations. Furthermore, the present study suggests that in silico protein structure analysis can be used as a predictor of pathogenicity and may facilitate the assessment of genetic VUS.

Alu RNA induces NLRP3 expression through TLR7 activation in α-1-antitrypsin-deficient macrophages

α-1 antitrypsin (AAT) is a serine protease inhibitor that plays a pivotal role in maintaining lung homeostasis. The most common AAT allele associated with AAT deficiency (AATD) is PiZ. Z-AAT accumulates in cells due to misfolding, causing severe AATD. The major function of AAT is to neutralize neutrophil elastase in the lung. It is generally accepted that loss of antiprotease function is a major cause of COPD in individuals with AATD. However, it is now being recognized that the toxic gain-of-function effect of Z-AAT in macrophage likely contributes to lung disease. In the present study, we determined that TLR7 signaling is activated in Z-MDMs, and the expression level of NLRP3, one of the targets of TLR7 signaling, is significantly higher in Z- compared with M-MDMs. We also determined that the level of endosomal Alu RNA is significantly higher in Z-compared with M-MDMs. Alu RNA is a known endogenous ligand that activates TLR7 signaling. Z-AAT likely induces the expression of Alu elements in MDMs and accelerates monocyte death, leading to the higher level of endosomal Alu RNA in Z-MDMs. Taken together,this study identifies a mechanism responsible for the toxic gain of function of Z-AAT macrophages.

Frequency of alleles and genotypes associated with alpha-1 antitrypsin deficiency in clinical and general populations: Revelations about underdiagnosis

BACKGROUND AND OBJECTIVE

Alpha-1 antitrypsin deficiency (AATD) is an underdiagnosed hereditary condition that promotes the development of lung and liver diseases, and the most common potentially life-threatening genetic condition in Caucasian adults. In this study, the clinical and genetic profile of pulmonary patients from a single center in La Palma Island (Canary Islands, Spain) was assessed to predict how to increase AATD diagnosis.

METHODS

AATD was tested in 1,493 pulmonary outpatients without regard to respiratory symptoms and 465 newborns. Variants of the SERPINA1 gene were characterised by real-time PCR, DNA sequencing, molecular haplotyping and phenotyping (AAT isoelectric focusing). Different respiratory pathologies were diagnosed in patients and their levels of serum AAT were measured by nephelometry.

RESULTS

The prevalence of pneumological patients with AATD alleles was 30.5%, including PI*S, PI*Z and 6 rare genetic variants. Certain deficiency genotypes were unevenly distributed among patients diagnosed with respiratory diseases: PI*ZZ (71.4%) and PI*SS (34.8%) genotypes were more represented in patients with chronic obstructive pulmonary disease (COPD), whereas PI*MZ (27.7%) and PI*SZ (34.5%) genotypes were more abundant in patients with bronchial asthma. The estimated frequency of PI*S and PI*Z alleles in the general population was 8.2% and 2.1%, respectively. A very significant enrichment (p< 0.01) of PI*S allele, independent of the PI*Z allele, was detected in the clinical population.

CONCLUSIONS

AATD diagnosis would improve if both the COPD and the asthmatic patients were included to screening programs. The prevalence of PI*ZZ genotype in La Palma (1/2,162) was relatively high within Spain (average 1/3,344).

New variants of alpha-1-antitrypsin: structural simulations and clinical expression

BACKGROUND

Alpha-1 antitrypsin deficiency (AATD) is characterized by reduced serum levels of the AAT protein and predisposes to liver and lung disease. The characterization at structural level of novel pathogenic SERPINA1 mutants coding for circulating AAT could provide novel insights into the mechanisms of AAT misfolding. The present study aimed to provide a practical framework for the identification and analysis of new AAT mutations, combining structural simulations and clinical data.

METHODS

We analysed a total of five mutations (four not previously described) in a total of six subjects presenting moderate to severe AATD: Gly95Alafs*18, Val210Glu, Asn247Ser, Pi*S + Asp341His and Pi*S + Leu383Phe + Lys394Ile. Clinical data, genotyping and phenotyping assays, structural mapping, and conformational characterization through molecular dynamic (MD) simulations were developed and combined.

RESULTS

Newly discovered AAT missense variants were localized both on the interaction surface and the hydrophobic core of the protein. Distribution of mutations across the structure revealed Val210Glu at the solvent exposed s4C strand and close to the "Gate" region. Asn247Ser was located on the accessible surface, which is important for glycan attachment. On the other hand, Asp341His, Leu383Phe were mapped close to the "breach" and "shutter" regions. MD analysis revealed the reshaping of local interactions around the investigated substitutions that have varying effects on AAT conformational flexibility, hydrophobic packing, and electronic surface properties. The most severe structural changes were observed in the double- and triple-mutant (Pi*S + Asp341His and Pi*S + Leu383Phe + Lys394Ile) molecular models. The two carriers presented impaired lung function.

CONCLUSIONS

The results characterize five variants, four of them previously unknown, of the SERPINA1 gene, which define new alleles contributing to the deficiency of AAT. Rare variants might be more frequent than expected, and therefore, in discordant cases, standardized screening of the S and Z alleles needs complementation with gene sequencing and structural approaches. The utility of computational modelling for providing supporting evidence of the pathogenicity of rare single nucleotide variations is discussed.

Molecular characterization of PI * S hangzhou , a SERPINA1 allele from continental China encoding a defective alpha-1-antitrypsin

Alpha-1-antitrypsin deficiency (AATD) is a heritable condition that predisposes to respiratory and hepatic complications. Screenings in East Asia human populations for the AATD alleles most commonly found among Caucasians have yielded poor outcomes. Serum alpha-1-antitrypsin (AAT) levels, AAT phenotypes, and sequences of SERPINA1 gene were examined in a Chinese child with a moderate deficit of serum AAT, who had suffered several episodes of liver disease, as well as in his first-order relatives. Results allowed the identification of PI ^* S _hangzhou , a novel SERPINA1 defective allele, which has been characterized by a L276R substitution, found in a SERPINA1-M3 genetic background. Moreover, potential effects of PI ^* S _hangzhou mutation over the AAT structure were studied by 3D homology modeling. The presence of an arginine residue at position 276 could destabilize the tertiary structure of AAT, since it occurs at a highly conserved hydrophobic cavity in the protein surface, and very close to two positively-charged lysine residues. Attending to the frequency of R276 variant reported in databases for individuals of East Asian ancestry, the PI ^* S _hangzhou allele may explain the global prevalence of the PiS phenotype observed in China.

The Mechanism of Mitochondrial Injury in Alpha-1 Antitrypsin Deficiency Mediated Liver Disease

Alpha-1 antitrypsin deficiency (AATD) is caused by a single mutation in the SERPINA1 gene, which culminates in the accumulation of misfolded alpha-1 antitrypsin (ZAAT) within the endoplasmic reticulum (ER) of hepatocytes. AATD is associated with liver disease resulting from hepatocyte injury due to ZAAT-mediated toxic gain-of-function and ER stress. There is evidence of mitochondrial damage in AATD-mediated liver disease; however, the mechanism by which hepatocyte retention of aggregated ZAAT leads to mitochondrial injury is unknown. Previous studies have shown that ER stress is associated with both high concentrations of fatty acids and mitochondrial dysfunction in hepatocytes. Using a human AAT transgenic mouse model and hepatocyte cell lines, we show abnormal mitochondrial morphology and function, and dysregulated lipid metabolism, which are associated with hepatic expression and accumulation of ZAAT. We also describe a novel mechanism of ZAAT-mediated mitochondrial dysfunction. We provide evidence that misfolded ZAAT translocates to the mitochondria for degradation. Furthermore, inhibition of ZAAT expression restores the mitochondrial function in ZAAT-expressing hepatocytes. Altogether, our results show that ZAAT aggregation in hepatocytes leads to mitochondrial dysfunction. Our findings suggest a plausible model for AATD liver injury and the possibility of mechanism-based therapeutic interventions for AATD liver disease.

Variants of SERPINA1 and the increasing complexity of testing for alpha-1 antitrypsin deficiency

Alpha-1 antitrypsin deficiency (AATD) is caused by mutations in the SERPINA1 gene, which encodes the alpha-1 antitrypsin (AAT) protein. Currently, over 200 SERPINA1 variants have been identified, many of which cause the quantitative and/or qualitative changes in AAT responsible for AATD-associated lung and liver disease. The types of these pathogenic mutations are varied, often resulting in misfolding, or truncating of the AAT amino acid sequence, and improvements in sequencing technology are helping to identify known and novel genetic variants. However, due to the diversity and novelty of rare variants, the clinical significance of many is largely unknown. There is, therefore, a lack of guidance on how patients should be monitored and treated when the clinical significance of their variant combination is unclear or variable. Nevertheless, it is important that physicians understand the advantages and disadvantages of the different testing methodologies available to diagnose AATD. Owing to the autosomal inheritance of the genetic mutations responsible for AATD, genetic testing should be offered not only to patients at increased AATD risk (e.g. patients with chronic obstructive pulmonary disease), but also to relatives of those with an abnormal result. Genetic counseling may help patients and family members understand the possible outcomes of testing and the implications for the family. While stress/anxiety can arise from genetic diagnosis or confirmation of carrier status, there can be positive consequences to genetic testing, including improved lifestyle choices, directed medical care, and empowered family planning. As genetic testing technology grows and becomes more popular, testing without physician referral is becoming more prevalent, irrespective of the availability of genetic counseling. Therefore, the Alpha-1 Foundation offers genetic counseling, as well as other support and educational material, for patients with AATD, as well as their families and physicians, to help improve the understanding of potential benefits and consequences of genetic testing.

Clinical presentations of four patients with rare Alpha 1 Antitrypsin variants identified in a single US center

Alpha 1 Antitrypsin Deficiency (AATD) is a rare condition primarily associated with lung complications and liver disease. As disease symptoms are similar to those in other respiratory conditions, patients generally experience long delays before receiving an accurate diagnosis and treatment. AATD results from mutations in the SERPINA1 gene that encodes Alpha 1 Antitrypsin (AAT). Over 500 single-nucleotide variants have been reported in mutation databases; however, there is increasing interest in the clinical significance of rare and novel SERPINA1 variants. In this case series of four patients from a single US center, next-generation sequencing (NGS) was used to guide AATD diagnosis. Four distinct rare variants of SERPINA1 (P289S; I50N; E204K; H262Y) were identified, three of which were found in patients with advanced chronic obstructive pulmonary disease (COPD)/emphysema. Computational modeling predicted these mutations to have potentially deleterious effects, a finding supported by AAT levels that were comparable with those seen in individuals heterozygous for the most common deficiency allele (PI*MZ). The remaining mutation (E204K) was found in a patient with a cerebral aneurysm; potential links between SERPINA1 variants and neurological conditions, such as cerebral aneurysm and arterial dissections, have been previously reported in individuals with heterozygous AATD phenotypes (PI*MS and PI*MZ). Novel and rare variants, often not detected by basic AATD diagnostic tests, have the potential to contribute to the development of COPD and emphysema. Detection of these variants can be enhanced by NGS, and modeling techniques can help determine if variants are pathogenic, thereby enabling a quicker, more accurate AATD diagnosis.

PredictAAT: Accounting for Inflammation in the Diagnosis of Alpha 1 Antitrypsin Deficiency

Alpha 1 antitrypsin deficiency (AATD) is a rarely diagnosed hereditary condition characterized by low alpha 1 antitrypsin (AAT) levels, which can lead to early-onset emphysema due to accelerated degradation of lung tissue. Similar to C-reactive protein (CRP), AAT is an acute phase reactant, meaning that blood levels rise in response to inflammation, injury or infection. Testing AAT levels is essential in the diagnosis of AATD; however, the presence of inflammation at the time of AATD testing can provide a false 'normal' level reading of the patient's baseline AAT levels. Researchers from a US-wide screening program for AATD found that a large number of individuals with AATD variants (particularly with the PI*MZ genotype) presented with elevated CRP levels (≥5 mg/L), suggesting the presence of inflammation. Using a series of calculations, the relationship between AAT and CRP levels was characterized and found to be genotype specific. We have developed a publicly available, easy-to-use online calculator (PredictAAT) that enables the instant calculation of predicted baseline AAT levels in patients exhibiting elevated CRP levels that accounts for specific AATD genotype. There is a need to raise awareness of the importance of simultaneous determination of AAT and CRP levels to aid the accurate diagnosis of patients with AATD. The PredictAAT calculator is therefore a valuable tool for physicians to enhance early disease diagnosis and individualize treatment.

New Patient-Centric Approaches to the Management of Alpha-1 Antitrypsin Deficiency

Alpha-1 antitrypsin deficiency (AATD) is a rare and underdiagnosed genetic predisposition for COPD and emphysema and other conditions, including liver disease. Although there have been improvements in terms of awareness of AATD and understanding of its treatment in recent years, current challenges center on optimizing detection and management of patients with AATD, and improving access to intravenous (IV) AAT therapy – the only available pharmacological intervention that can slow disease progression. However, as an orphan disease with geographically dispersed patients, international cooperation is essential to address these issues. To achieve this, new European initiatives in the form of the European Reference Network for Rare Lung Diseases (ERN-LUNG) and the European Alpha-1 Research Collaboration (EARCO) have been established. These organizations are striving to address the current challenges in AATD, and provide a new platform for future research efforts in AATD. The first objectives of ERN-LUNG are to establish a quality control program for European AATD laboratories and create a disease management program for AATD, following the success of such programs in the United States. The main purpose of EARCO is to create a pan-European registry, with the aim of understanding the natural history of the disease and supporting the development of new treatment modalities in AATD and access to AAT therapy. Going further, other patient-centric initiatives involve improving the convenience of intravenous AAT therapy infusions through extended-interval dosing and self-administration. The present review will discuss the implementation of these initiatives and their potential contribution to the optimization of patient care in AATD.

Leveraging Population Genomics for Individualized Correction of the Hallmarks of Alpha-1 Antitrypsin Deficiency

Deep medicine is rapidly moving towards a high-definition approach for therapeutic management of the patient as an individual given the rapid progress of genome sequencing technologies and machine learning algorithms. While considered a monogenic disease, alpha-1 antitrypsin (AAT) deficiency (AATD) patients present with complex and variable phenotypes we refer to as the "hallmarks of AATD" that involve distinct molecular mechanisms in the liver, plasma and lung tissues, likely due to both coding and non-coding variation as well as genetic and environmental modifiers in different individuals. Herein, we briefly review the current therapeutic strategies for the management of AATD. To embrace genetic diversity in the management of AATD, we provide an overview of the disease phenotypes of AATD patients harboring different AAT variants. Linking genotypic diversity to phenotypic diversity illustrates the potential for sequence-specific regions of AAT protein fold design to play very different roles during nascent synthesis in the liver and/or function in post-liver plasma and lung environments. We illustrate how to manage diversity with recently developed machine learning (ML) approaches that bridge sequence-to-function-to-structure knowledge gaps based on the principle of spatial covariance (SCV). SCV relationships provide a deep understanding of the genotype to phenotype transformation initiated by AAT variation in the population to address the role of genetic and environmental modifiers in the individual. Embracing the complexity of AATD in the population is critical for risk management and therapeutic intervention to generate a high definition medicine approach for the patient.