Nonsense-associated altered splicing of MAP3K1 in two siblings with 46,XY disorders of sex development

Defects in mRNA splicing and implications for infertility: a comprehensive review and in silico analysis

BACKGROUND

mRNA splicing is a fundamental process in the reproductive system, playing a pivotal role in reproductive development and endocrine function, and ensuring the proper execution of meiosis, mitosis, and gamete function. Trans-acting factors and cis-acting elements are key players in mRNA splicing whose dysfunction can potentially lead to male and female infertility. Although hundreds of trans-acting factors have been implicated in mRNA splicing, the mechanisms by which these factors influence reproductive processes are fully understood for only a subset. Furthermore, the clinical impact of variations in cis-acting elements on human infertility has not been comprehensively characterized, leading to probable omissions of pathogenic variants in standard genetic analyses.

OBJECTIVE AND RATIONALE

This review aimed to summarize our current understanding of the factors involved in mRNA splicing regulation and their association with infertility disorders. We introduced methods for prioritizing and functionally validating splicing variants associated with human infertility. Additionally, we explored corresponding abnormal splicing therapies that could potentially provide insight into treating human infertility.

SEARCH METHODS

Systematic literature searches of human and model organisms were performed in the PubMed database between May 1977 and July 2024. To identify mRNA splicing-related genes and pathogenic variants in infertility, the search terms 'splice', 'splicing', 'variant', and 'mutation' were combined with azoospermia, oligozoospermia, asthenozoospermia, multiple morphological abnormalities of the sperm flagella, acephalic spermatozoa, disorders of sex development, early embryonic arrest, reproductive endocrine disorders, oocyte maturation arrest, premature ovarian failure, primary ovarian insufficiency, zona pellucida, fertilization defects, infertile, fertile, infertility, fertility, reproduction, and reproductive.

OUTCOMES

Our search identified 5014 publications, of which 291 were included in the final analysis. This review provided a comprehensive overview of the biological mechanisms of mRNA splicing, with a focus on the roles of trans-acting factors and cis-acting elements. We highlighted the disruption of 52 trans-acting proteins involved in spliceosome assembly and catalytic activity and recognized splicing regulatory regions and epigenetic regulation associated with infertility. The 73 functionally validated splicing variants in the cis-acting elements of 54 genes have been reported in 20 types of human infertility; 27 of them were located outside the canonical splice sites and potentially overlooked in standard genetic analysis due to likely benign or of uncertain significance. The in silico prediction of splicing can prioritize potential splicing abnormalities that may be true pathogenic mechanisms. We also summarize the methods for prioritizing splicing variants and strategies for functional validation and review splicing therapy approaches for other diseases, providing a reference for abnormal reproduction treatment.

WIDER IMPLICATIONS

Our comprehensive review of trans-acting factors and cis-acting elements in mRNA splicing will further promote a more thorough understanding of reproductive regulatory processes, leading to improved pathogenic variant identification and potential treatments for human infertility.

REGISTRATION NUMBER

N/A.

Androgen insensitivity and the evolving genetic heterogeneity

Androgen Insensitivity Syndrome (AIS) is a 46,XY difference of sex development (DSD) classically caused by mutations in the androgen receptor (AR) gene, leading to variable androgen resistance and a broad phenotypic spectrum traditionally classified as complete, partial, or mild. Phenotypic variability can occur even with identical AR mutations, particularly those within the ligand-binding domain of the AR. Emerging evidence implicates non-coding regulatory variants, deep intronic mutations, AR co-regulator dysfunction, and oligogenic inheritance in the aetiology of AIS. The molecular diagnostic workflow should incorporate either targeted AR sequencing or whole-exome sequencing, depending on the clinical context. Biochemical and functional assays remain clinically useful, especially when AR variants are not detected or when variants of unknown significance (VUS) are identified. Advances in patient-derived hiPSC models and testicular organoids provide new insights into AR function and therapeutic strategies. Expanding genomic and epigenetic research will refine diagnostic accuracy, and personalized care, ultimately optimizing patient outcomes in AIS.

PTPN11 and FLNA variants in a boy with ambiguous genitalia, short stature, and non-specific dysmorphic features

Noonan syndrome is a congenital disorder characterized by distinctive facial appearance, congenital heart defects, short stature, and skeletal dysplasia. Although boys with Noonan syndrome frequently exhibit cryptorchidism, a mild form of 46,XY disorders of sex development (DSD), they barely manifest more severe genital abnormalities. Here, we report a boy with ambiguous genitalia, short stature, and non-specific dysmorphic features. He had no cardiac abnormalities or skeletal dysplasia. His score in the Noonan syndrome diagnostic criteria (36 of 157 points, 23%) was lower than the cutoff for diagnosis (50%). Whole-exome sequencing identified a de novo heterozygous variant (c.922A>G: p.Asn308Asp) in PTPN11 and a maternally inherited hemizygous variant (c.1439C>T: p.Pro480Leu) in FLNA. The PTPN11 variant was a known causative mutation for Noonan syndrome. FLNA is a causative gene for neurodevelopmental and skeletal abnormalities and has also been implicated in 46,XY DSD. The p.Pro480Leu variant of FLNA was assessed as deleterious by in silico analyses. These results provide evidence that whole-exome sequencing is a powerful tool for diagnosing patients with atypical disease manifestations. Furthermore, our data suggest a possible role of digenic mutations as phenotypic modifiers of Noonan syndrome.

Escaping from CRISPR-Cas-mediated knockout: the facts, mechanisms, and applications

Clustered regularly interspaced short palindromic repeats and associated Cas protein (CRISPR-Cas), a powerful genome editing tool, has revolutionized gene function investigation and exhibits huge potential for clinical applications. CRISPR-Cas-mediated gene knockout has already become a routine method in research laboratories. However, in the last few years, accumulating evidences have demonstrated that genes knocked out by CRISPR-Cas may not be truly silenced. Functional residual proteins could be generated in such knockout organisms to compensate the putative loss of function, termed herein knockout escaping. In line with this, several CRISPR-Cas-mediated knockout screenings have discovered much less abnormal phenotypes than expected. How does knockout escaping happen and how often does it happen have not been systematically reviewed yet. Without knowing this, knockout results could easily be misinterpreted. In this review, we summarize these evidences and propose two main mechanisms allowing knockout escaping. To avoid the confusion caused by knockout escaping, several strategies are discussed as well as their advantages and disadvantages. On the other hand, knockout escaping also provides convenient tools for studying essential genes and treating monogenic disorders such as Duchenne muscular dystrophy, which are discussed in the end.

Pathogenic Variants in MAP3K1 Cause 46,XY Gonadal Dysgenesis: A Review

Pathogenic variants in the MAP3K1 gene are an important cause of 46,XY non-syndromic partial and complete gonadal dysgenesis, accounting for at least 4% of cases. Inheritance occurs in a sex-limited, autosomal dominant fashion with virtually complete penetrance in 46,XY individuals. 46,XX carriers appear to have normal fertility and no developmental abnormalities. Pathogenic variants occur almost exclusively within known domains of the MAP3K1 protein, facilitating annotation when identified. Where studied, these variants have been modeled to alter the local MAP3K1 folding and surface domains and have been shown to alter interactions with known binding partners. The net effect of these variants is to increase phosphorylation of downstream targets ERK1, ERK2, and p38, resulting in multiple gain-of-function effects interfering with testis determination and enabling ovarian determination.

MAP3K1 Variant Causes Hyperactivation of Wnt4/β-Catenin/FOXL2 Signaling Contributing to 46,XY Disorders/Differences of Sex Development

Background: 46,XY disorders/differences of sex development (46,XY DSD) are congenital conditions that result from abnormal gonadal development (gonadal dysgenesis) or abnormalities in androgen synthesis or action. During early embryonic development, several genes are involved in regulating the initiation and maintenance of testicular or ovarian-specific pathways. Recent reports have shown that MAP3K1 genes mediate the development of the 46,XY DSD, which present as complete or partial gonadal dysgenesis. Previous functional studies have demonstrated that some MAP3K1 variants result in the gain of protein function. However, data on possible mechanisms of MAP3K1 genes in modulating protein functions remain scant.

Methods: This study identified a Han Chinese family with the 46,XY DSD. To assess the history and clinical manifestations for the 46,XY DSD patients, the physical, operational, ultra-sonographical, pathological, and other examinations were performed for family members. Variant analysis was conducted using both trio whole-exome sequencing (trio WES) and Sanger sequencing. On the other hand, we generated transiently transfected testicular teratoma cells (NT2/D1) and ovary-derived granular cells (KGN), with mutant or wild-type MAP3K1 gene. We then performed functional assays such as determination of steady-state levels of gender related factors, protein interaction and luciferase assay system.

Results: Two affected siblings were diagnosed with 46,XY DSD. Our analysis showed a missense c.556A > G/p.R186G variant in the MAP3K1 gene. Functional assays demonstrated that the MAP3K1^R186G variant was associated with significantly decreased affinity to ubiquitin (Ub; 43–49%) and increased affinity to RhoA, which was 3.19 ± 0.18 fold, compared to MAP3K1. The MAP3K1^R186G led to hyperphosphorylation of p38 and GSK3β, and promoted hyperactivation of the Wnt4/β-catenin signaling. In addition, there was increased recruitment of β-catenin into the nucleus, which enhanced the expression of pro-ovarian transcription factor FOXL2 gene, thus contributing to the 46,XY DSD.

Conclusion: Our study identified a missense MAP3K1 variant associated with 46,XY DSD. We demonstrated that MAP3K1^R186G variant enhances binding to the RhoA and improves its own stability, resulting in the activation of the Wnt4/β-catenin/FOXL2 pathway. Taken together, these findings provide novel insights into the molecular mechanisms of 46,XY DSD and promotes better clinical evaluation.

Genetic Control of MAP3K1 in Eye Development and Sex Differentiation

The MAP3K1 is responsible for transmitting signals to activate specific MAP2K-MAPK cascades. Following the initial biochemical characterization, genetic mouse models have taken center stage to elucidate how MAP3K1 regulates biological functions. To that end, mice were generated with the ablation of the entire Map3k1 gene, the kinase domain coding sequences, or ubiquitin ligase domain mutations. Analyses of the mutants identify diverse roles that MAP3K1 plays in embryonic survival, maturation of T/B cells, and development of sensory organs, including eye and ear. Specifically in eye development, Map3k1 loss-of-function was found to be autosomal recessive for congenital eye abnormalities, but became autosomal dominant in combination with Jnk and RhoA mutations. Additionally, Map3k1 mutation increased eye defects with an exposure to environmental agents such as dioxin. Data from eye developmental models reveal the nexus role of MAP3K1 in integrating genetic and environmental signals to control developmental activities. Here, we focus the discussions on recent advances in understanding the signaling mechanisms of MAP3K1 in eye development in mice and in sex differentiation from human genomics findings. The research works featured here lead to a deeper understanding of the in vivo signaling network, the mechanisms of gene-environment interactions, and the relevance of this multifaceted protein kinase in disease etiology and pathogenesis.

The Lipocalin Apolipoprotein D Functional Portrait: A Systematic Review

Apolipoprotein D is a chordate gene early originated in the Lipocalin protein family. Among other features, regulation of its expression in a wide variety of disease conditions in humans, as apparently unrelated as neurodegeneration or breast cancer, have called for attention on this gene. Also, its presence in different tissues, from blood to brain, and different subcellular locations, from HDL lipoparticles to the interior of lysosomes or the surface of extracellular vesicles, poses an interesting challenge in deciphering its physiological function: Is ApoD a moonlighting protein, serving different roles in different cellular compartments, tissues, or organisms? Or does it have a unique biochemical mechanism of action that accounts for such apparently diverse roles in different physiological situations? To answer these questions, we have performed a systematic review of all primary publications where ApoD properties have been investigated in chordates. We conclude that ApoD ligand binding in the Lipocalin pocket, combined with an antioxidant activity performed at the rim of the pocket are properties sufficient to explain ApoD association with different lipid-based structures, where its physiological function is better described as lipid-management than by long-range lipid-transport. Controlling the redox state of these lipid structures in particular subcellular locations or extracellular structures, ApoD is able to modulate an enormous array of apparently diverse processes in the organism, both in health and disease. The new picture emerging from these data should help to put the physiological role of ApoD in new contexts and to inspire well-focused future research.