Elliptocytosis in patients with C-terminal domain mutations of protein 4.1 correlates with encoded messenger RNA levels rather than with alterations in primary protein structure

Cytoskeletal Protein 4.1R in Health and Diseases

The protein 4.1R is an essential component of the erythrocyte membrane skeleton, serving as a key structural element and contributing to the regulation of the membrane's physical properties, including mechanical stability and deformability, through its interaction with spectrin-actin. Recent research has uncovered additional roles of 4.1R beyond its function as a linker between the plasma membrane and the membrane skeleton. It has been found to play a crucial role in various biological processes, such as cell fate determination, cell cycle regulation, cell proliferation, and cell motility. Additionally, 4.1R has been implicated in cancer, with numerous studies demonstrating its potential as a diagnostic and prognostic biomarker for tumors. In this review, we provide an updated overview of the gene and protein structure of 4.1R, as well as its cellular functions in both physiological and pathological contexts.

cis Elements that Mediate RNA Polymerase II Pausing Regulate Human Gene Expression

Aberrant gene expression underlies many human diseases. RNA polymerase II (Pol II) pausing is a key regulatory step in transcription. Here, we mapped the locations of RNA Pol II in normal human cells and found that RNA Pol II pauses in a consistent manner across individuals and cell types. At more than 1,000 genes including MYO1E and SESN2, RNA Pol II pauses at precise nucleotide locations. Characterization of these sites shows that RNA Pol II pauses at GC-rich regions that are marked by a sequence motif. Sixty-five percent of the pause sites are cytosines. By differential allelic gene expression analysis, we showed in our samples and a population dataset from the Genotype-Tissue Expression (GTEx) consortium that genes with more paused polymerase have lower expression levels. Furthermore, mutagenesis of the pause sites led to a significant increase in promoter activities. Thus, our data uncover that RNA Pol II pauses precisely at sites with distinct sequence features that in turn regulate gene expression.

RNA splicing during terminal erythropoiesis

PURPOSE OF REVIEW

Erythroid progenitors must accurately and efficiently splice thousands of pre-mRNAs as the cells undergo extensive changes in gene expression and cellular remodeling during terminal erythropoiesis. Alternative splicing choices are governed by interactions between RNA binding proteins and cis-regulatory binding motifs in the RNA. This review will focus on recent studies that define the genome-wide scope of splicing in erythroblasts and discuss what is known about its regulation.

RECENT FINDINGS

RNA-seq analysis of highly purified erythroblast populations has revealed an extensive program of alternative splicing of both exons and introns. During normal erythropoiesis, stage-specific splicing transitions alter the structure and abundance of protein isoforms required for optimized red cell production. Mutation or deficiency of splicing regulators underlies hematopoietic disease in myelopdysplasia syndrome patients via disrupting the splicing program.

SUMMARY

Erythroid progenitors execute an elaborate alternative splicing program that modulates gene expression posttranscriptionally, ultimately regulating the structure and function of the proteome in a differentiation stage-specific manner during terminal erythropoiesis. This program helps drive differentiation and ensure synthesis of the proper protein isoforms required to produce mechanically stable red cells. Mutation or deficiency of key splicing regulatory proteins disrupts the splicing program to cause disease.

Novel mutations in patients with hereditary red blood cell membrane disorders using next-generation sequencing

To diagnose and investigate the genotype-phenotype relationship in intractable hereditary red blood cell (RBC) membrane cases, we have utilized next-generation sequencing (NGS) to develop a high-throughput, highly sensitive assay. Three unrelated families including 15 individuals were analysed with a panel interrogating 600 genes related to haematopathy disorders. Where possible, inheritance patterns of pathogenic mutations were determined by sequencing the relatives. We identified 2 novel mutations in ANK1 (Y216X and E142X) responsible for hereditary spherocytosis (HS) that were stop-gain single nucleotide variants (SNVs). Furthermore, a novel SPTA1 mutation (H54P) was identified; it is a nonsynonymous SNV and is associated with hereditary elliptocytosis (HE). In addition, patients who also carried erythropoiesis gene mutations showed more severe disease phenotype. The NGS panel provides a fast and accurate method for molecular diagnosis in patients with intractable hereditary RBC membrane disorders. An approach integrating medical history, clinical and molecular testing, and pedigree analysis is beneficial for these patients and families.

ICSH guidelines for the laboratory diagnosis of nonimmune hereditary red cell membrane disorders

INTRODUCTION

Hereditary spherocytosis (HS), hereditary elliptocytosis (HE), and hereditary stomatocytosis (HSt) are inherited red cell disorders caused by defects in various membrane proteins. The heterogeneous clinical presentation, biochemical and genetic abnormalities in HS and HE have been well documented. The need to raise the awareness of HSt, albeit its much lower prevalence than HS, is due to the undesirable outcome of splenectomy in these patients.

METHODS

The scope of this guideline is to identify the characteristic clinical features, the red cell parameters (including red cell morphology) for these red cell disorders associated, respectively, with defective cytoskeleton (HS and HE) and abnormal cation permeability in the lipid bilayer (HSt) of the red cell. The current screening tests for HS are described, and their limitations are highlighted.

RESULTS

An appropriate diagnosis can often be made when the screening test result(s) is reviewed together with the patient's clinical/family history, blood count results, reticulocyte count, red cell morphology, and chemistry results. SDS-polyacrylamide gel electrophoresis of erythrocyte membrane proteins, monovalent cation flux measurement, and molecular analysis of membrane protein genes are specialist tests for further investigation.

CONCLUSION

Specialist tests provide additional evidence in supporting the diagnosis and that will facilitate the management of the patient. In the case of a patient's clinical phenotype being more severe than the affected members within the immediate family, molecular testing of all family members is useful for confirming the diagnosis and allows an insight into the molecular basis of the abnormality such as a recessive mode of inheritance or a de novo mutation.

The Protein 4.1 family: hub proteins in animals for organizing membrane proteins

Proteins of the 4.1 family are characteristic of eumetazoan organisms. Invertebrates contain single 4.1 genes and the Drosophila model suggests that 4.1 is essential for animal life. Vertebrates have four paralogues, known as 4.1R, 4.1N, 4.1G and 4.1B, which are additionally duplicated in the ray-finned fish. Protein 4.1R was the first to be discovered: it is a major mammalian erythrocyte cytoskeletal protein, essential to the mechanochemical properties of red cell membranes because it promotes the interaction between spectrin and actin in the membrane cytoskeleton. 4.1R also binds certain phospholipids and is required for the stable cell surface accumulation of a number of erythrocyte transmembrane proteins that span multiple functional classes; these include cell adhesion molecules, transporters and a chemokine receptor. The vertebrate 4.1 proteins are expressed in most tissues, and they are required for the correct cell surface accumulation of a very wide variety of membrane proteins including G-Protein coupled receptors, voltage-gated and ligand-gated channels, as well as the classes identified in erythrocytes. Indeed, such large numbers of protein interactions have been mapped for mammalian 4.1 proteins, most especially 4.1R, that it appears that they can act as hubs for membrane protein organization. The range of critical interactions of 4.1 proteins is reflected in disease relationships that include hereditary anaemias, tumour suppression, control of heartbeat and nervous system function. The 4.1 proteins are defined by their domain structure: apart from the spectrin/actin-binding domain they have FERM and FERM-adjacent domains and a unique C-terminal domain. Both the FERM and C-terminal domains can bind transmembrane proteins, thus they have the potential to be cross-linkers for membrane proteins. The activity of the FERM domain is subject to multiple modes of regulation via binding of regulatory ligands, phosphorylation of the FERM associated domain and differential mRNA splicing. Finally, the spectrum of interactions of the 4.1 proteins overlaps with that of another membrane-cytoskeleton linker, ankyrin. Both ankyrin and 4.1 link to the actin cytoskeleton via spectrin, and we hypothesize that differential regulation of 4.1 proteins and ankyrins allows highly selective control of cell surface protein accumulation and, hence, function. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé

Nonsense-mediated mRNA decay (NMD) blockage promotes nonsense mRNA stabilization in protein 4.1R deficient cells carrying the 4.1R Coimbra variant of hereditary elliptocytosis

We describe a new approach to stabilize nonsense mRNA, based on the inhibition of the NMD mechanism, by combining cycloheximide-mediated inhibition of translation, and caffeine-mediated inhibition of UPF1 phosphorylation. This approach aimed to identify the impact of a 4.1R splicing mutation. This mutation is involved in a partial deficiency of 4.1R in the homozygous state in a patient with hereditary elliptocytosis and a moderated hemolytic anemia. We show that, in addition to two known minor shortened and stable spliceoforms, the mutation activates an intronic cryptic splice site, which results in a nonsense mRNA major isoform, targeted to degradation in intact cells by NMD. This accounts for the main cause of 4.1R partial deficiency. In a general perspective, blocking the NMD mechanism would help to identify a missing isoform, and pave the path for a molecular targeting strategy to circumvent a deleterious splicing pathway in favor of a therapeutic splicing pathway.

Cryptic splicing sites are differentially utilized in vivo

It has long been considered that cryptic splice sites are ignored by the splicing machinery in the context of intact genuine splice sites. In the present study, it is shown that cryptic splice sites are utilized in all circumstances, when the authentic site is intact, partially functional or completely abolished. Their use would therefore contribute to a background lack of fidelity in the context of the wild-type sequence. We also found that a mutation at the 5' splice site of beta-globin intron 1 accommodates multiple cryptic splicing pathways, including three previously reported pathways. Focusing on the two major cryptic 5' splice sites within beta-globin exon 1, we show that cryptic splice site selection ex vivo varies depending upon: (a) the cell stage of development during terminal erythroid differentiation; (b) the nature of the mutation at the authentic 5' splice site; and (c) the nature of the promoter. Finally, we found that the two major cryptic 5' splice sites are utilized with differential efficiencies in two siblings sharing the same beta-globin chromosome haplotype in the homozygous state. Collectively, these data suggest that intrinsic, sequence specific factors and cell genetic background factors both contribute to promote a subtle differential use of cryptic splice sites in vivo.

LAMA2 mRNA processing alterations generate a complete deficiency of laminin-alpha2 protein and a severe congenital muscular dystrophy

An increasing number of genomic variations are no more regarded as harmless changes in protein coding sequences or as genetic polymorphisms. Studying the impact of these variations on mRNA metabolism became a central issue to better understand the biological significance of disease. We describe here a severe congenital muscular dystrophy (CMD) with lumbar scoliosis and respiratory complications in a patient, who died at the age of 10. Despite a poor linkage to any form of CMD, total deficiency of laminin-alpha2 rather suggested the occurrence of an MDC1A form. Extensive analysis of LAMA2 gene revealed two novel mutations: a (8007delT) frameshift deletion in exon 57, and a de novo 7nt deletion in intron 17. Using an ex vivo approach, we provided strong evidence that the intron mutation is responsible for complete exon 17 skipping. The mutations are in trans and they each generate a nonsense mRNA potentially elicited to degradation by NMD. We further discuss the impact of mRNA alterations on the subtle phenotypic discrepancies.

The molecular basis of hereditary red cell membrane disorders

The red cell membrane is one of the best known membranes in terms of structure, function and genetic disorders. As any plasma membrane it mediates transport functions. It also provides the erythrocytes with their resilience and deformability. Many of the proteins and the genes performing these functions are known in great detail, although some disease-responsible genes are yet to be elucidated. Basic knowledge has shed light on important groups of genetic disorders. The latter include (i) the disorders of the red cell mechanics: hereditary spherocytosis, hereditary elliptocytosis and poikilocytosis, and (ii) the disorders of the passive flux of the monovalent cations across the membrane: the stomacytoses and allied conditions. Reciprocally, many information have come from genetics abnormalities. We will review the mutation-disease relationship. A number of points will be underscored: widespread weak alleles modulate the expression of the SPTA1 gene, encoding the alpha-chain of spectrin; mutations in the anion exchanger can give rise to an array of distinct nosological entities, including a renal condition; splenectomy is banned in the stomatocytoses; a variety of stomatocyosis is part of a pleiotropic syndrome that may includes perinatal fetal liquid effusions. The diagnosis, follow-up and treatment of the involved diseases have gradually improved.

Protein 4.1R expression in normal and dystrophic skeletal muscle

4.1R pre-mRNA alternative splicing results in multiple mRNA and protein isoforms that are expressed in virtually all tissues. More specifically, isoforms containing the alternative exon 17a, are exclusively expressed in muscle tissues. In this report, we show that these isoforms are preferentially present in the myoplasm of fast myofibres. 4.1R epitopes are also found at the sarcolemma of both slow and fast myofibres in normal muscle. Interestingly, they are absent from dystrophin-deficient sarcolemma of DMD muscle, and colocalize with partially expressed dystrophin in BMD muscle. We also show that alternative splicing of exons 16 and 17a is regulated during muscle differentiation in an asynchronous fashion, with an early inclusion of exon 16 in forming myotubes, and a late inclusion of exon 17a. Consistently, Western blot analysis led to characterize mainly an approximately 96/98-kDa doublet bearing exons 16-17a-encoding peptide, exclusively occurring in the differentiated muscle.

Different impacts of alleles alphaLEPRA and alphaLELY as assessed versus a novel, virtually null allele of the SPTA1 gene in trans

The family of two siblings with severe hereditary spherocytosis was investigated. The decrease was evident on both the alpha- and the beta-chains. The parents were haematologically normal. The mother was heterozygous for the low-expression polymorphic allele alphaLEPRA. The father was heterozygous for a novel combination in which one allele showed the alpha-spectrin low expression polymorphic allele alphaLELY, while his other allele showed the alphaLELY polymorphism in cis with a G-->A substitution, named Bicêtre, found at the extreme 3' end of exon 51. This combination was designated alpha(LELY-Bicêtre). The children were compound heterozygotes for alleles alphaLEPRA and alpha(LELY-Bicêtre). Reverse transcription polymerase chain reaction detected only trace amounts of the mRNA coding for alpha(LELY-Bicêtre). Mutation is therefore an essentially null mutation with no functional protein product. The lack of disease in the alphaLELY/(LELY-Bicêtre) father compared with the marked haemolysis in the alphaLEPRA/alpha(LELY-Bicêtre) children showed that expression of allele alphaLELY is not low enough to expose null alpha-spectrin alleles on the other chromosome. Quantitative estimations from these findings suggest that, to evoke spherocytosis, it is necessary that alpha-spectrin expression must be reduced to less than 25% of normal, while a reduction to 8% is sufficient.

Hereditary elliptocytosis: spectrin and protein 4.1R

Hereditary elliptocytosis (HE) is a common disorder of erythrocyte shape, occurring especially in individuals of African and Mediterranean ancestry, presumably because elliptocytes confer some resistance to malaria. The principle lesion in HE is mechanical weakness or fragility of the erythrocyte membrane skeleton due to defects in alpha-spectrin, beta-spectrin, or protein 4.1. Numerous mutations have been described in the genes encoding these proteins, including point mutations, gene deletions and insertions, and mRNA processing defects. Several mutations have been identified in a number of individuals on the same genetic background, suggesting a "founder effect." The majority of HE patients are asymptomatic, but some may experience hemolytic anemia, splenomegaly, and intermittent jaundice.

Multiple cis elements regulate an alternative splicing event at 4.1R pre-mRNA during erythroid differentiation

The inclusion of exon 16 in the mature protein 4.1R messenger RNA (mRNA) is a critical event in red blood cell membrane biogenesis. It occurs during late erythroid development and results in inclusion of the 10-kd domain needed for stabilization of the spectrin/actin lattice. In this study, an experimental model was established in murine erythroleukemia cells that reproduces the endogenous exon 16 splicing patterns from a transfected minigene. Exon 16 was excluded in predifferentiated and predominantly included after induction. This suggests that the minigene contained exon and abutting intronic sequences sufficient for splicing regulation. A systematic analysis of the cis-acting regulatory sequences that reside within the exon and flanking introns was performed. Results showed that (1) the upstream intron of 4.1R pre-mRNA is required for exon recognition and it displays 2 enhancer elements, a distal element acting in differentiating cells and a proximal constitutive enhancer that resides within the 25 nucleotides preceding the acceptor site; (2) the exon itself contains a strong constitutive splicing silencer; (3) the exon has a weak 5' splice site; and (4) the downstream intron contains at least 2 splicing enhancer elements acting in differentiating cells, a proximal element at the vicinity of the 5' splice site, and a distal element containing 3 copies of the UGCAUG motif. These results suggest that the interplay between negative and positive elements may determine the inclusion or exclusion of exon 16. The activation of the enhancer elements in late erythroid differentiation may play an important role in the retention of exon 16.

Spectrin and ankyrin-based pathways: metazoan inventions for integrating cells into tissues

The spectrin-based membrane skeleton of the humble mammalian erythrocyte has provided biologists with a set of interacting proteins with diverse roles in organization and survival of cells in metazoan organisms. This review deals with the molecular physiology of spectrin, ankyrin, which links spectrin to the anion exchanger, and two spectrin-associated proteins that promote spectrin interactions with actin: adducin and protein 4.1. The lack of essential functions for these proteins in generic cells grown in culture and the absence of their genes in the yeast genome have, until recently, limited advances in understanding their roles outside of erythrocytes. However, completion of the genomes of simple metazoans and application of homologous recombination in mice now are providing the first glimpses of the full scope of physiological roles for spectrin, ankyrin, and their associated proteins. These functions now include targeting of ion channels and cell adhesion molecules to specialized compartments within the plasma membrane and endoplasmic reticulum of striated muscle and the nervous system, mechanical stabilization at the tissue level based on transcellular protein assemblies, participation in epithelial morphogenesis, and orientation of mitotic spindles in asymmetric cell divisions. These studies, in addition to stretching the erythrocyte paradigm beyond recognition, also are revealing novel cellular pathways essential for metazoan life. Examples are ankyrin-dependent targeting of proteins to excitable membrane domains in the plasma membrane and the Ca(2+) homeostasis compartment of the endoplasmic reticulum. Exciting questions for the future relate to the molecular basis for these pathways and their roles in a clinical context, either as the basis for disease or more positively as therapeutic targets.

Regulation of alternative pre-mRNA splicing during erythroid differentiation

Although the mature enucleated erythrocyte is no longer active in nuclear processes such as pre-mRNA splicing, the function of many of its major structural proteins is dependent on alternative splicing choices made during the earlier stages of erythropoiesis. These splicing decisions fundamentally regulate many aspects of protein structure and function by governing the inclusion or exclusion of exons that encode protein interaction domains, regulatory signals, or translation initiation or termination sites. Alternative splicing events may be partially or entirely erythroid-specific, ie, distinct from the splicing patterns imposed on the same transcripts in nonerythroid cells. Moreover, differentiation stage-specific splicing "switches" may alter the structure and function of erythroid proteins in physiologically important ways as the cell is morphologically and functionally remodeled during normal differentiation. Derangements in the splicing of individual mutated pre-mRNAs can produce synthesis of truncated or unstable proteins that are responsible for numerous erythrocyte disorders. This review will summarize the salient features of regulated alternative splicing in general, review existing information concerning the widespread extent of alternative splicing among erythroid genes, and describe recent studies that are beginning to uncover the mechanisms that regulate an erythroid splicing switch in the protein 4.1R gene.