Pathogenic signal peptide variants in the human genome

Protein targeting to the ER membrane: multiple pathways and shared machinery

The endoplasmic reticulum (ER) serves as a central hub for protein production and sorting in eukaryotic cells, processing approximately one-third of the cellular proteome. Protein targeting to the ER occurs through multiple pathways that operate both during and independent of translation. The classical translation-dependent pathway, mediated by cytosolic factors like signal recognition particle, recognizes signal peptides or transmembrane helices in nascent proteins, while translation-independent mechanisms utilize RNA-based targeting through specific sequence elements and RNA-binding proteins. At the core of these processes lies the Sec61 complex, which undergoes dynamic conformational changes and coordinates with numerous accessory factors to facilitate protein translocation and membrane insertion across and into the endoplasmic reticulum membrane. This review focuses on the molecular mechanisms of protein targeting to the ER, from the initial recognition of targeting signals to the dynamics of the translocation machinery, highlighting recent discoveries that have revealed unprecedented complexity in these cellular trafficking pathways.

Molecular puzzle of insulin: structural assembly pathways and their role in diabetes

Properly folded proteins are essential for virtually all cellular processes including enzyme catalysis, signal transduction, and structural support. The cells have evolved intricate mechanisms of control, such as the assistance of chaperones and proteostasis networks, to ensure that proteins mature and fold correctly and maintain their functional conformations. Here, we review the mechanisms governing the folding of key hormonal regulators or glucose homeostasis. The insulin synthesis in pancreatic β-cells begins with preproinsulin production. During translation, the insulin precursor involves components of the endoplasmic reticulum (ER) translocation machinery, which are essential for proper orientation, translocation, and cleavage of the signal peptide of preproinsulin. These steps are critical to initiate the correct folding of proinsulin. Proinsulin foldability is optimized in the ER, an environment evolved to support the folding process and the formation of disulfide bonds while minimizing misfolding. This environment is intricately linked to ER stress response pathways, which have both beneficial and potentially harmful effects on pancreatic β-cells. Proinsulin misfolding can result from excessive biosynthetic ER load, proinsulin gene mutations, or genetic predispositions affecting the ER folding environment. Misfolded proinsulin leads to deficient insulin production and contributes to diabetes pathogenesis. Understanding the mechanisms of protein folding is critical for addressing diabetes and other protein misfolding-related diseases.

Multiplex, multimodal mapping of variant effects in secreted proteins

Despite widespread advances in DNA sequencing, the functional consequences of most genetic variants remain poorly understood. Multiplexed Assays of Variant Effect (MAVEs) can measure the function of variants at scale, and are beginning to address this problem. However, MAVEs cannot readily be applied to the ~10% of human genes encoding secreted proteins. We developed a flexible, scalable human cell surface display method, Multiplexed Surface Tethering of Extracellular Proteins (MultiSTEP), to measure secreted protein variant effects. We used MultiSTEP to study the consequences of missense variation in coagulation factor IX (FIX), a serine protease where genetic variation can cause hemophilia B. We combined MultiSTEP with a panel of antibodies to detect FIX secretion and post-translational modification, measuring a total of 44,816 effects for 436 synonymous variants and 8,528 of the 8,759 possible missense variants. 49.6% of possible F9 missense variants impacted secretion, post-translational modification, or both. We also identified functional constraints on secretion within the signal peptide and for nearly all variants that caused gain or loss of cysteine. Secretion scores correlated strongly with FIX levels in hemophilia B and revealed that loss of secretion variants are particularly likely to cause severe disease. Integration of the secretion and post-translational modification scores enabled reclassification of 63.1% of F9 variants of uncertain significance in the My Life, Our Future hemophilia genotyping project. Lastly, we showed that MultiSTEP can be applied to a wide variety of secreted proteins. Thus, MultiSTEP is a multiplexed, multimodal, and generalizable method for systematically assessing variant effects in secreted proteins at scale.

Signal Peptides and Their Fragments in Post-Translation: Novel Insights of Signal Peptides

Signal peptides (SPs), peptide sequences located at the N-terminus of newly synthesized proteins, are primarily known for their role in targeting proteins to the endoplasmic reticulum (ER). It has traditionally been assumed that cleaved SPs are rapidly degraded and digested near the ER. However, recent evidence has demonstrated that cleaved SP fragments can be detected in extracellular fluids such as blood flow, where they exhibit bioactivity. In addition, SP fragments are delivered to extracellular fluids via extracellular vesicles such as exosomes and microvesicles, which are important mediators of intercellular communication. These findings suggest that SPs and their fragments may have physiological roles beyond their classical function. This review aims to provide a comprehensive overview of these novel roles and offer new insights into the potential functions of SPs and their fragments in post-translational regulation and intercellular communication.

A monoallelic variant in CCN2 causes an autosomal dominant spondyloepimetaphyseal dysplasia with low bone mass

Cellular communication network factor 2 (CCN2) is a secreted extracellular matrix-associated protein, and its aberrantly increased expression has been implicated in a diversity of diseases involving pathological processes of fibrosis, chronic inflammation, or tissue injury, which has promoted the evaluation of CCN2 as therapeutic targets for multiple disorders. However, human phenotypes associated with CCN2 deficiency have remained enigmatic; variants in CCN2 have not yet been associated with a human phenotype. Here, we collected families diagnosed with spondyloepimetaphyseal dysplasia (SEMD), and screened candidate pathogenic genes for families without known genetic causes using next-generation sequencing. We identified a monoallelic variant in signal peptide of CCN2 (NM_001901.2: c.65 G > C [p.Arg22Pro]) as the cause of SEMD in 14 subjects presenting with different degree of short stature, premature osteoarthritis, and osteoporosis. Affected subjects showed decreased serum CCN2 levels. Cell lines harboring the variant displayed decreased amount of CCN2 proteins in culture medium and an increased intracellular retention, indicating impaired protein secretion. And the variant weakened the stimulation effect of CCN2 on osteogenesis of bone marrow mesenchymal stem cells. Zebrafish ccn2a knockout model and osteoblast lineage-specific Ccn2-deficient mice (Ccn2fl/fl;Prx1Cre) partially recapitulated the phenotypes including low bone mass observed in affected subjects. Pathological mechanism implicated in the skeletal abnormality in Ccn2fl/fl;Prx1Cre mice involved decreased bone formation, increased bone resorption, and abnormal growth plate formation. Collectively, our study indicate that monoallelic variants in CCN2 lead to a human inherited skeletal dysplasia, and highlight the critical role of CCN2 in osteogenesis in human.

Molecular Origins of the Mendelian Rare Diseases Reviewed by Orpha.net: A Structural Bioinformatics Investigation

The study of rare diseases is important not only for the individuals affected but also for the advancement of medical knowledge and a deeper understanding of human biology and genetics. The wide repertoire of structural information now available from reliable and accurate prediction methods provides the opportunity to investigate the molecular origins of most of the rare diseases reviewed in the Orpha.net database. Thus, it has been possible to analyze the topology of the pathogenic missense variants found in the 2515 proteins involved in Mendelian rare diseases (MRDs), which form the database for our structural bioinformatics study. The amino acid substitutions responsible for MRDs showed different mutation site distributions at different three-dimensional protein depths. We then highlighted the depth-dependent effects of pathogenic variants for the 20,061 pathogenic variants that are present in our database. The results of this structural bioinformatics investigation are relevant, as they provide additional clues to mitigate the damage caused by MRD.

A new mRNA structure prediction based approach to identifying improved signal peptides for bone morphogenetic protein 2

BACKGROUND

Signal peptide (SP) engineering has proven able to improve production of many proteins yet is a laborious process that still relies on trial and error. mRNA structure around the translational start site is important in translation initiation and has rarely been considered in this context, with recent improvements in in silico mRNA structure potentially rendering it a useful predictive tool for SP selection. Here we attempt to create a method to systematically screen candidate signal peptide sequences in silico based on both their nucleotide and amino acid sequences. Several recently released computational tools were used to predict signal peptide activity (SignalP), localization target (DeepLoc) and predicted mRNA structure (MXFold2). The method was tested with Bone Morphogenetic Protein 2 (BMP2), an osteogenic growth factor used clinically for bone regeneration. It was hoped more effective BMP2 SPs could improve BMP2-based gene therapies and reduce the cost of recombinant BMP2 production.

RESULTS

Amino acid sequence analysis indicated 2,611 SPs from the TGF-β superfamily were predicted to function when attached to BMP2. mRNA structure prediction indicated structures at the translational start site were likely highly variable. The five sequences with the most accessible translational start sites, a codon optimized BMP2 SP variant and the well-established hIL2 SP sequence were taken forward to in vitro testing. The top five candidates showed non-significant improvements in BMP2 secretion in HEK293T cells. All showed reductions in secretion versus the native sequence in C2C12 cells, with several showing large and significant decreases. None of the tested sequences were able to increase alkaline phosphatase activity above background in C2C12s. The codon optimized control sequence and hIL2 SP showed reasonable activity in HEK293T but very poor activity in C2C12.

CONCLUSIONS

These results support the use of peptide sequence based in silico tools for basic predictions around signal peptide activity in a synthetic biology context. However, mRNA structure prediction requires improvement before it can produce reliable predictions for this application. The poor activity of the codon optimized BMP2 SP variant in C2C12 emphasizes the importance of codon choice, mRNA structure, and cellular context for SP activity.

SignalP: The Evolution of a Web Server

SignalP ( https://services.healthtech.dtu.dk/services/SignalP-6.0/ ) is a very popular prediction method for signal peptides, the intrinsic signals that make proteins secretory. The SignalP web server has existed since 1995 and is now in its sixth major version. In this historical account, we (three authors who have taken part in the entire journey plus the first author of the latest version) describe the differences between the versions and discuss the various decisions taken along the way.