Natural Splice Research Articles

Gene Dosage of F5 c.3481C>T Stop-Codon (p.R1161Ter) Switches the Clinical Phenotype from Severe Thrombosis to Recurrent Haemorrhage: Novel Hypotheses for Readthrough Strategy.

Inherited defects in the genes of blood coagulation essentially express the severity of the clinical phenotype that is directly correlated to the number of mutated alleles of the candidate leader gene (e.g., heterozygote vs. homozygote) and of possible additional coinherited traits. The F5 gene, which codes for coagulation factor V (FV), plays a two-faced role in the coagulation cascade, exhibiting both procoagulant and anticoagulant functions. Thus, defects in this gene can be predisposed to either bleeding or thrombosis. A Sanger sequence analysis detected a premature stop-codon in exon 13 of the F5 gene (c.3481C>T; p.R1161Ter) in several members of a family characterised by low circulating FV levels and contrasting clinical phenotypes. The propositus, a 29 y.o. male affected by recurrent haemorrhages, was homozygous for the F5 stop-codon and for the F5 c.1691G>A (p.R506Q; FV-Leiden) inherited from the heterozygous parents, which is suggestive of combined cis-segregation. The homozygous condition of the stop-codon completely abolished the F5 gene expression in the propositus (FV:Ag < 1%; FV:C < 1%; assessed by ELISA and PT-based one-stage clotting assay respectively), removing, in turn, any chance for FV-Leiden to act as a prothrombotic molecule. His father (57 y.o.), characterised by severe recurrent venous thromboses, underwent a complete molecular thrombophilic screening, revealing a heterozygous F2 G20210A defect, while his mother (56 y.o.), who was negative for further common coagulation defects, reported fully asymptomatic anamnesis. To dissect these conflicting phenotypes, we performed the ProC®Global (Siemens Helthineers) coagulation test aimed at assessing the global pro- and anticoagulant balance of each family member, investigating the responses to the activated protein C (APC) by means of an APC-sensitivity ratio (APC-sr). The propositus had an unexpectedly poor response to APC (APC-sr: 1.09; n.v. > 2.25), and his father and mother had an APC-sr of 1.5 and 2.0, respectively. Although ProC®Global prevalently detects the anticoagulant side of FV, the exceptionally low APC-sr of the propositus and his discordant severe-moderate haemorrhagic phenotype could suggest a residual expression of mutated FV p.506QQ through a natural readthrough or possible alternative splicing mechanisms. The coagulation pathway may be physiologically rebalanced through natural and induced strategies, and the described insights might be able to track the design of novel treatment approaches and rebalancing molecules.

Abstract 36: The discovery of a novel CD19xCD22 dual-targeting CAR for the development of an IPSC-derived cell therapy

Abstract Dual-targeting cell therapies to address CD19 antigen loss in heme malignancies are being explored by Century Therapeutics and others for unmet clinical need in hematological malignancies. CD22 chimeric antigen receptor (CAR) T-cell therapies have shown promising efficacy in relapsed or refractory B-lineage acute lymphoblastic leukemia (B-ALL) alone and in combination with CD19 CAR-T cell therapies (1,2). CD22 is a multi-domain glycoprotein expressed on B-cells. Natural splice variants of CD22 can exclude domains near the N-terminus, allowing for therapeutic resistance when these domains are targeted. We identified novel single domain antibodies (VHH) to CD22 that bind to multiple epitopes on different domains of CD22, including membrane proximal binders. The VHHs were affinity matured to enhance cell-based binding and formatted as CARs in monovalent and tandem, bivalent formats. Our data demonstrates the best efficacy against CD22+ tumor cells with a biparatopic, tandem VHH CAR format. Through additional engineering, bispecific CARs that combined three CD22-binding VHH and the anti-CD19 scFv, FMC63, in a loop CAR configuration were designed and tested. This CD19xCD22 bispecific, CD22 biparatopic CAR was engineered into primary T-cells and demonstrated cytotoxicity activity against CD19 and CD22 positive tumor cells as well as CD19 knockout and CD22 knockout cell lines. CD19xCD22 bispecific primary CAR-T cells were efficacious in controlling tumors in mouse xenograft models. This novel CAR is being tested in IPSC-derived iT and iNK cells for off-the-shelf allogeneic cell therapy to expand patient access beyond CD19 CAR-T cell therapies. Ref: 1. Nat Med. 2018;24(1):20-28. doi: 10.1038/nm.4441. 2. Blood. 2018;132(suppl 1). Abstract 27 Citation Format: Jill M. Carton, John Wheeler, Chris Dower, Liam Campion, Hillary J. Millar, Marilda Beqiri, Barry Morse, Buddha Gurung, Rebecca Genovese, Steven DeLuca, Charles Dominick, Michael Naso, Hy Levitsky. The discovery of a novel CD19xCD22 dual-targeting CAR for the development of an IPSC-derived cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 36.

The cytokine receptor CRLF3 is a human neuroprotective EV-3 (Epo) receptor.

The evolutionary conserved orphan cytokine receptor-like factor 3 (CRLF3) has been implicated in human disease, vertebrate hematopoiesis and insect neuroprotection. While its specific functions are elusive, experimental evidence points toward a general role in cell homeostasis. Erythropoietin (Epo) is a major regulator of vertebrate hematopoiesis and a general cytoprotective cytokine. Erythropoietic functions mediated by classical Epo receptor are understood in great detail whereas Epo-mediated cytoprotective mechanisms are more complex due to involvement of additional Epo receptors and a non-erythropoietic splice variant with selectivity for certain receptors. In the present study, we show that the human CRLF3 mediates neuroprotection upon activation with the natural Epo splice variant EV-3. We generated CRLF3 knock-out iPSC lines and differentiated them toward the neuronal lineage. While apoptotic death of rotenone-challenged wild type iPSC-derived neurons was prevented by EV-3, EV-3-mediated neuroprotection was absent in CRLF3 knock-out neurons. Rotenone-induced apoptosis and EV-3-mediated neuroprotection were associated with differential expression of pro-and anti-apoptotic genes. Our data characterize human CRLF3 as a receptor involved in Epo-mediated neuroprotection and identify CRLF3 as the first known receptor for EV-3.

PMON270 Coexistence of 46, XX Testicular Disorder of Sex Development and 11β-Hydroxylase Deficiency: In Vivo and In Vitro Studies

Abstract Background 46, XX testicular disorder of sex development and 11β-hydroxylase deficiency (11β-OHD) are two extremely rare types of disorder of sex development (DSD). No coexistence has been reported yet. Clinical Case A 22-year-old male showed small testes (volume=4ml) and gynecomastia for 2 years. At the age of 3.5, he was diagnosed as simple virilizing type of 21-hydroxylase deficiency (21-OHD) for the manifestations of the enlarged penis (length=7.5cm), hyperpigmentation, and normal blood pressure. Adrenal ultrasound suggested bilateral adrenal hyperplasia (both length * width = 2.4*0.9cm) and X-ray showed accelerated bone age (12.5 years old). Irregular cortisone acetate 6.25mg per day was administrated since then. At the age of 18, he was sent to emergency for aortic aneurysm rupture and heart failure, and hypertension urgency was diagnosed. Sanger sequencing revealed that he carried compound heterozygous variants in CYP11B1 gene: NM_000497.3: c.905_907delinsTT and NM_000497.3: c.954+7C&amp;gt;T, which were respectively inherited from his father and mother. Pathogenesis of the novel intron variant (c.954+7C&amp;gt;T) was further verified in COS7, CHO, and 273T cell lines by transfecting wild-type and mutant-type minigene, extracting RNA of cells, reversing RNA into cDNA, PCR, and Sanger sequencing. The result showed that the c.954+7C&amp;gt;T variant introduced a cryptic donor splice site at a site 5 bp downstream of the 3' natural splice donor site of exon 5. The level of adrenal steroids detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was consistent with the characteristics of 11β-OHD. The patient was treated by neoplasty of thoracic aortic aneurysm and added anti-hypertension drugs in addition to glucocorticoid after surgery. Unexpectedly, the abnormalities of male characteristics including small testes and gynecomastia appeared since adolescence. Laboratory tests showed an elevated level of FSH and LH and azoospermia. Scrotum Ultrasound showed bilateral testicular dysplasia (right: 1.9*1.4*0.8cm, left: 1.9*1.3*0.8cm). To figure out the unexplainable results, whole-exome sequencing was performed and revealed two copy number variants: the duplication of Xp22.33-q28 which spans 151.32Mb, and the deletion of Yp11.2-q11.23 which spans 23.34Mb. Meanwhile, the karyotype test by culturing blood lymphocytes showed 46, XX (100/100), which confirmed the diagnosis of 46, XX testicular DSD. Fluorescence in situ hybridization (FISH) revealed the presence of the SRY gene, which is translocated into the short arm of the X chromosome. Testosterone replacement is unnecessary for the normal level of testosterone (T) (4.44ng/ml, N: 1.75-7.81ng/ml), which is the result of the combined action of 11β-OHD with adrenal T accumulation and 46, XX testicular DSD with testicular T deficiency. Assisted reproduction consulting should start early. Conclusion This is the first case demonstrating the possibility of coexistence of 46, XX testicular DSD and 11β-OHD and hinting at the significance of a combination of clinical and molecular diagnostic methods. Presentation: Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.

Functional Characterization of Two Variants at the Intron 6—Exon 7 Boundary of the KCNQ2 Potassium Channel Gene Causing Distinct Epileptic Phenotypes

Pathogenic variants in KCNQ2 encoding for Kv7.2 potassium channel subunits have been found in patients affected by widely diverging epileptic phenotypes, ranging from Self-Limiting Familial Neonatal Epilepsy (SLFNE) to severe Developmental and Epileptic Encephalopathy (DEE). Thus, understanding the pathogenic molecular mechanisms of KCNQ2 variants and their correlation with clinical phenotypes has a relevant impact on the clinical management of these patients. In the present study, the genetic, biochemical, and functional effects prompted by two variants, each found in a non-familial SLNE or a DEE patient but both affecting nucleotides at the KCNQ2 intron 6-exon 7 boundary, have been investigated to test whether and how they affected the splicing process and to clarify whether such mechanism might play a pathogenetic role in these patients. Analysis of KCNQ2 mRNA splicing in patient-derived lymphoblasts revealed that the SLNE-causing intronic variant (c.928-1G > C) impeded the use of the natural splice site, but lead to a 10-aa Kv7.2 in frame deletion (Kv7.2 p.G310Δ10); by contrast, the DEE-causing exonic variant (c.928G > A) only had subtle effects on the splicing process at this site, thus leading to the synthesis of a full-length subunit carrying the G310S missense variant (Kv7.2 p.G310S). Patch-clamp recordings in transiently-transfected CHO cells and primary neurons revealed that both variants fully impeded Kv7.2 channel function, and exerted strong dominant-negative effects when co-expressed with Kv7.2 and/or Kv7.3 subunits. Notably, Kv7.2 p.G310S, but not Kv7.2 p.G310Δ10, currents were recovered upon overexpression of the PIP2-synthesizing enzyme PIP5K, and/or CaM; moreover, currents from heteromeric Kv7.2/Kv7.3 channels incorporating either Kv7.2 mutant subunits were differentially regulated by changes in PIP2 availability, with Kv7.2/Kv7.2 G310S/Kv7.3 currents showing a greater sensitivity to PIP2 depletion when compared to those from Kv7.2/Kv7.2 G310Δ10/Kv7.3 channels. Altogether, these results suggest that the two variants investigated differentially affected the splicing process at the intron 6-exon 7 boundary, and led to the synthesis of Kv7.2 subunits showing a differential sensitivity to PIP2 and CaM regulation; more studies are needed to clarify how such different functional properties contribute to the widely-divergent clinical phenotypes.

A hydrophobic patch (PLVIVG; 1481–1486) in the B‐domain of factor V‐short is crucial for its synergistic TFPIα‐cofactor activity with protein S and for the formation of the FXa‐inhibitory complex comprising FV‐short, TFPIα, and protein S

BackgroundFactor V‐short (FV756‐1458) is a natural splice variant functioning in synergy with protein S as tissue factor pathway inhibitor alpha (TFPIα)–cofactor in inhibition of factor Xa (FXa). An exposed acid region (AR2; 1493–1537) in the B domain binds TFPIα. The preAR2 (1458–1492) is crucial for the synergistic TFPIα–cofactor activity between FV‐short and protein S and for assembly of a trimolecular FXa‐inhibitory complex among FV‐short, protein S, and TFPIα. ObjectiveTo identify which part of preAR2 is required for the synergistic TFPIα–cofactor activity between FV‐short and protein S. MethodsA FXa‐inhibition assay was used to test the synergistic TFPIα cofactor activity between protein S and new FV‐short variants FV709‐1476, FV712‐1478, FV712‐1481, FV712‐1484, FV712‐1487, and FV712‐1490. A microtiter‐based assay analyzed binding among FV‐short variants, protein S, and TFPIα. ResultsFV709‐1476, FV712‐1478, and FV712‐1481 were fully active as synergistic TFPIα cofactors with protein S; FV712‐1484 showed intermediate activity; and FV712‐1487 and FV712‐1490 were inactive. TFPIα interacted with all variants in the absence of protein S but FV712‐1478 and FV712‐1481 bound TFPIα with highest affinity. None of the FV‐short variants bound directly to protein S in the absence of TFPIα. In the presence of TFPIα, efficient cooperative binding was demonstrated between protein S, TFPIα, and FV709‐1476, FV712‐1478, or FV712‐1481. In contrast, no cooperativity among TFPIα, protein S, and FV712‐1484, FV712‐1487, or FV712‐1490 was seen. ConclusionA short hydrophobic patch in preAR2 (PLVIVG, 1481–1486) in FV‐short is crucial for the synergistic TFPIα‐cofactor activity between FV‐short and protein S and for the assembly of a trimolecular FXa‐inhibitory complex among FV‐short, protein S, and TFPIα.

Molecular mechanisms by which splice modulator GEX1A inhibits leukaemia development and progression.

Splice modulators have been assessed clinically in treating haematologic malignancies exhibiting splice factor mutations and acute myeloid leukaemia. However, the mechanisms by which such modulators repress leukaemia remain to be elucidated. The primary goal of this assessment was to assess the molecular mechanism by which the natural splice modulator GEX1A kills leukaemic cells in vitro and within in vivo mouse models. Using human leukaemic cell lines, we assessed the overall sensitivity these cells have to GEX1A via EC50 analysis. We subsequently analysed its effects using in vivo xenograft mouse models and examined whether cell sensitivities were correlated to genetic characteristics or protein expression levels. We also utilised RT-PCR and RNAseq analyses to determine splice change and RNA expression level differences between sensitive and resistant leukaemic cell lines. We found that, in vitro, GEX1A induced an MCL-1 isoform shift to pro-apoptotic MCL-1S in all leukaemic cell types, though sensitivity to GEX1A-induced apoptosis was negatively associated with BCL-xL expression. In BCL-2-expressing leukaemic cells, GEX1A induced BCL-2-dependent apoptosis by converting pro-survival BCL-2 into a cell killer. Thus, GEX1A + selective BCL-xL inhibition induced synergism in killing leukaemic cells, while GEX1A + BCL-2 inhibition showed antagonism in BCL-2-expressing leukaemic cells. In addition, GEX1A sensitised FLT3-ITD+ leukaemic cells to apoptosis by inducing aberrant splicing and repressing the expression of FLT3-ITD. Consistently, in in vivo xenografts, GEX1A killed the bulk of leukaemic cells via apoptosis when combined with BCL-xL inhibition. Furthermore, GEX1A repressed leukaemia development by targeting leukaemia stem cells through inhibiting FASTK mitochondrial isoform expression across sensitive and non-sensitive leukaemia types. Our study suggests that GEX1A is a potent anti-leukaemic agent in combination with BCL-xL inhibitors, which targets leukaemic blasts and leukaemia stem cells through distinct mechanisms.

The preAR2 region (1458–1492) in factor V‐Short is crucial for the synergistic TFPIα‐cofactor activity with protein S and the assembly of a trimolecular factor Xa‐inhibitory complex comprising FV‐Short, protein S, and TFPIα

BackgroundFactor V‐Short (FV756‐1458) is a natural splice variant in which 702 residues are deleted from the B domain. It exposes an acid region (AR2; 1493–1537) that binds tissue factor pathway inhibitor alpha (TFPIα). Protein S also interacts with TFPIα and serves as TFPIα‐cofactor in factor Xa (FXa) inhibition. FV‐Short and protein S function as synergistic TFPIα‐cofactors in inhibition of FXa. FV810‐1492 is an artificial FV‐Short variant that cannot synergize with protein S as TFPIα cofactor even though it contains AR2 and binds TFPIα. ObjectiveTo elucidate the mechanisms for the synergism between FV756‐1458 and protein S as TFPIα cofactors. MethodsFour FV‐Short variants were created, FV756‐1458 and FV712‐1458 contained the preAR2 region (1458–1492), whereas FV810‐1492 and FV713‐1492 lacked this region. The synergistic TFPIα cofactor activity between FV‐Short variants and protein S was analyzed by FXa‐inhibition. A microtiter‐based assay tested binding between FV‐Short variants, protein S, and TFPIα. ResultsThe two preAR2‐containing FV‐Short variants were active as synergistic TFPIα cofactors, whereas the other two were inactive. All variants bound to TFPIα. None of the FV‐Short variants bound directly to protein S. The combination of TFPIα and preAR2‐containing FV‐Short variants bound protein S, whereas TFPIα together with the preAR2‐minus variants did not. Protein S potentiated TFPIα‐binding to the preAR2‐containing variants and binding between TFPIα and protein S was stimulated only by the preAR2‐containing variants. ConclusionThe preAR2 region is demonstrated to be crucial for the synergistic TFPIα‐cofactor activity between FV‐Short and protein S and for the assembly of a trimolecular FXa‐inhibitory complex comprising FV‐Short, protein S, and TFPIα.

Cryptic splicing events result in unexpected protein products from calpain-10 (CAPN10) cDNA

Calpain-10 (CAPN10) belongs to the calpain superfamily. Genetic polymorphisms of the CAPN10 gene are associated with susceptibility to develop type 2 diabetes mellitus. Although the role of CAPN10 in the pathophysiology of diabetes has been extensively investigated, its biochemical properties are largely unknown. In this report, we made the surprising discovery that CAPN10 cDNA transcripts are subject to cryptic splicing and unexpected protein products were expressed. The same set of splicing products was reproducibly detected in four types of cultured cells including the primary culture of mouse myoblast. At least, one of the products was identical to a natural splicing variant. Sequence analysis of the splicing potential of CAPN10 cDNA, together with mutagenesis studies, resulted in the identification of a powerful splicing acceptor site at the junction of the sequences encoded by exons 9 and 10. We successfully extended the analysis to create expression construct resistant to splicing for both human and mouse CAPN10. The construct allowed us to analyze two major CAPN10 isoforms and reveal their difference in substrate proteolysis and potential cell functions.These results demonstrate that proteins produced from cDNA do not necessarily reflect the original nucleotide sequence. We provide insight into the property of recombinantly expressed CAPN10 proteins in cultured cells circumventing unexpected protein products.

Novel variations in spermatogenic transcription regulators RFX2 and TAF7 increase risk of azoospermia.

Genetic etiology of idiopathic male infertility is enigmatic owing to involvement of multiple gene regulatory networks in spermatogenesis process. Any change in optimal function of the transcription factors involved in this process owing to polymorphisms/mutations may increase the risk of infertility. We investigated polymorphisms/mutations of spermatogenic transcription regulators TAF7 and RFX2 and analysed their association with incidence of azoospermia among the men from West Bengal, India. Genotyping was carried by Sanger's dideoxy sequencing of 130 azoospermic men who were detected negative in Y chromosome microdeletion screening and 140 healthy controls. Association study was done by suitable statistical methods. In silico analysis was performed to infer the intuitive damaging effects of detected variants at transcripts and protein level. We found significant association of TAF7 C16T (MW827584 G > A), RFX2 562delT (MZ560629delA), rs11547633 A > C, rs17606721 A > G, MW827583 C > T, and MZ379836 C > T variants with the incidence of azoospermia. In silico analysis predicted that the variants either alter the natural splice junctions of the transcript or cause probable damage in the structure of proteins of respective genes. Polymorphisms/mutations of TAF7 and RFX2 genes increase risk of male infertility in Bengali population. The novel variants may be used as markers for male infertility screening in ART practise.

Short tail stories: the hirudin-like factors HLF6 and HLF7 of the Asian medicinal leech, Hirudinaria manillensis

The leech-derived hirudins and hirudin-like factors (HLFs) share a common molecule structure: a short N-terminus, a central globular domain, and an elongated C-terminal tail. All parts are important for function. HLF6 and HLF7 were identified in the Asian medicinal leech, Hirudinaria manillensis. The genes of both factors encode putative splice variants that differ in length and composition of their respective C-terminal tails. In either case, the tails are considerably shorter compared to hirudins. Here we describe the functional analyses of the natural splice variants and of synthetic variants that comprise an altered N-terminus and/or a modified central globular domain. All natural splice variants of HLF6 and HLF7 display no detectable thrombin-inhibitory potency. In contrast, some synthetic variants effectively inhibit thrombin, even with tails as short as six amino acid residues in length. Our data indicate that size and composition of the C-terminal tail of hirudins and HLFs can vary in a great extent, yet the full protein may still retain the ability to inhibit thrombin.

A Novel Splice Variant of the Inhibitor of Growth 3 Lacks the Plant Homeodomain and Regulates Epithelial-Mesenchymal Transition in Prostate Cancer Cells.

Inhibitor of growth 3 (ING3) is one of five members of the ING tumour suppressor family, characterized by a highly conserved plant homeodomain (PHD) as a reader of the histone mark H3K4me3. ING3 was reported to act as a tumour suppressor in many different cancer types to regulate apoptosis. On the other hand, ING3 levels positively correlate with poor survival prognosis of prostate cancer (PCa) patients. In PCa cells, ING3 acts rather as an androgen receptor (AR) co-activator and harbours oncogenic properties in PCa. Here, we show the identification of a novel ING3 splice variant in both the human PCa cell line LNCaP and in human PCa patient specimen. The novel ING3 splice variant lacks exon 11, ING3∆ex11, which results in deletion of the PHD, providing a unique opportunity to analyse functionally the PHD of ING3 by a natural splice variant. Functionally, overexpression of ING3Δex11 induced morphological changes of LNCaP-derived 3D spheroids with generation of lumen and pore-like structures within spheroids. Since these structures are an indicator of epithelial–mesenchymal transition (EMT), key regulatory factors and markers for EMT were analysed. The data suggest that in contrast to ING3, ING3Δex11 specifically modulates the expression of key EMT-regulating upstream transcription factors and induces the expression of EMT markers, indicating that the PHD of ING3 inhibits EMT. In line with this, ING3 knockdown also induced the expression of EMT markers, confirming the impact of ING3 on EMT regulation. Further, ING3 knockdown induced cellular senescence via a pathway leading to cell cycle arrest, indicating an oncogenic role for ING3 in PCa. Thus, the data suggest that the ING3Δex11 splice variant lacking functional PHD exhibits oncogenic characteristics through triggering EMT in PCa cells.

A Severe Case of Spondylometaphyseal Dysplasia Algerian Type with Two Mutations in COL2A1.

Spondylometaphyseal dysplasia Algerian type (MIM no.: 184253) is an uncommon autosomal dominant skeletal dysplasia caused by heterozygous mutations in the COL2A1 gene (MIM no.: 120140). In this case based review, we reported a 5-year-old boy with short stature, severe dorsolumbar scoliosis, lumbar hyperlordosis, short trunk, and severe genu valgum . Radiological examination showed platyspondyly, irregular metaphyseal radiolucencies intermingled with radiodensities, and corner fractures. The patient has a c.3275G > A; p.Gly1092Asp mutation in exon 47 of the COL2A1 gene and a variant of unknown significance in c.1366-13C > A in intron 21. This latter sequence variant could partially or completely disrupt the natural splice acceptor site of intron 21/exon 22 in the COL2A1 gene leading to a potential modification of the phenotypic severity.

Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity

APOBEC3A (A3A) and APOBEC3B (A3B) enzymes drive APOBEC-mediated mutagenesis. Identification of factors affecting the activity of these enzymes could help modulate mutagenesis and associated clinical outcomes. Here, we show that canonical and alternatively spliced A3A and A3B isoforms produce corresponding mutagenic and non-mutagenic enzymes. Increased expression of the mutagenic A3B isoform predicted shorter progression-free survival in bladder cancer. We demonstrate that the production of mutagenic vs. non-mutagenic A3B protein isoforms was considerably affected by inclusion/skipping of exon 5 in A3B. Furthermore, exon 5 skipping, resulting in lower levels of mutagenic A3B enzyme, could be increased in vitro. Specifically, we showed the effects of treatment with an SF3B1 inhibitor affecting spliceosome interaction with a branch point site in intron 4, or with splice-switching oligonucleotides targeting exon 5 of A3B. Our results underscore the clinical role of A3B and implicate alternative splicing of A3B as a mechanism that could be targeted to restrict APOBEC-mediated mutagenesis.

Synthesizing Long and Repetitive Proteins Via a “Loopable Translator” System

The expression of long proteins with repetitive amino acid sequences often presents a challenge in recombinant systems. To overcome this obstacle, we present a system that generates circular mRNA in vivo by circularly permuting the self-splicing thymidylate synthase (TD) intron from T4 bacteriophage, resulting in “loopable” translation. In this system, the order of exons and intron are rearranged such that the identical natural RNA splicing events result in a circular mRNA. The self-splicing group I intron was selected because it does not require an enzyme for its activity. We demonstrated that circularization successfully occurs in vivo, and under the optimal conditions (identified to date) the looping construct achieves 15% of the GFP production relative to the positive control. Successful mRNA circularization was confirmed by SDS-PAGE gel electrophoresis. The data suggest that protein yield may be limited by inefficient initiation, though ribosomes can perform many transits on a circular mRNA template per initiation event. This circularizing translation system may contribute to the production of protein-based polymers with diverse applications.

A Generic Assay to Detect Aberrant ARSB Splicing and mRNA Degradation for the Molecular Diagnosis of MPS VI

Identification and characterization of disease-associated variants in monogenic disorders is an important aspect of diagnosis, genetic counseling, prediction of disease severity, and development of therapy. However, the effects of disease-associated variants on pre-mRNA splicing and mRNA degradation are difficult to predict and often missed. Here we present a generic assay for unbiased identification and quantification of arylsulfatase B (ARSB) mRNA for molecular diagnosis of patients with mucopolysaccharidosis VI (MPS VI). We found that healthy control individuals have inefficient ARSB splicing because of natural skipping of exon 5 and inclusion of two pseudoexons in introns 5 and 6. Analyses of 12 MPS VI patients with 10 different genotypes resulted in identification of a 151-bp intron inclusion caused by the c.1142+2T>C variant and detection of low ARSB expression from alleles with the c.629A>G variant. A special case showed skipping of exon 4 and low ARSB expression. Although no disease-associated DNA variant could be identified in this patient, the molecular diagnosis could be made based on RNA. These results highlight the relevance of RNA-based analyses to establish a molecular diagnosis of MPS VI. We speculate that inefficient natural splicing of ARSB may be a target for therapy based on promotion of canonical splicing.

Antisense oligonucleotide modulation of non-productive alternative splicing upregulates gene expression

While most monogenic diseases are caused by loss or reduction of protein function, the need for technologies that can selectively increase levels of protein in native tissues remains. Here we demonstrate that antisense-mediated modulation of pre-mRNA splicing can increase endogenous expression of full-length protein by preventing naturally occurring non-productive alternative splicing and promoting generation of productive mRNA. Bioinformatics analysis of RNA sequencing data identifies non-productive splicing events in 7,757 protein-coding human genes, of which 1,246 are disease-associated. Antisense oligonucleotides targeting multiple types of non-productive splicing events lead to increases in productive mRNA and protein in a dose-dependent manner in vitro. Moreover, intracerebroventricular injection of two antisense oligonucleotides in wild-type mice leads to a dose-dependent increase in productive mRNA and protein in the brain. The targeting of natural non-productive alternative splicing to upregulate expression from wild-type or hypomorphic alleles provides a unique approach to treating genetic diseases.

Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing.

Splice isoform structure and abundance can be affected by either noncoding or masquerading coding variants that alter the structure or abundance of transcripts. When these variants are common in the population, these nonconstitutive transcripts are sufficiently frequent so as to resemble naturally occurring, alternative mRNA splicing. Prediction of the effects of such variants has been shown to be accurate using information theory-based methods. Single nucleotide polymorphisms (SNPs) predicted to significantly alter natural and/or cryptic splice site strength were shown to affect gene expression. Splicing changes for known SNP genotypes were confirmed in HapMap lymphoblastoid cell lines with gene expression microarrays and custom designed q-RT-PCR or TaqMan assays. The majority of these SNPs (15 of 22) as well as an independent set of 24 variants were then subjected to RNAseq analysis using the ValidSpliceMut web beacon (http://validsplicemut.cytognomix.com), which is based on data from the Cancer Genome Atlas and International Cancer Genome Consortium. SNPs from different genes analyzed with gene expression microarray and q-RT-PCR exhibited significant changes in affected splice site use. Thirteen SNPs directly affected exon inclusion and 10 altered cryptic site use. Homozygous SNP genotypes resulting in stronger splice sites exhibited higher levels of processed mRNA than alleles associated with weaker sites. Four SNPs exhibited variable expression among individuals with the same genotypes, masking statistically significant expression differences between alleles. Genome-wide information theory and expression analyses (RNAseq) in tumor exomes and genomes confirmed splicing effects for 7 of the HapMap SNP and 14 SNPs identified from tumor genomes. q-RT-PCR resolved rare splice isoforms with read abundance too low for statistical significance in ValidSpliceMut. Nevertheless, the web-beacon provides evidence of unanticipated splicing outcomes, for example, intron retention due to compromised recognition of constitutive splice sites. Thus, ValidSpliceMut and q-RT-PCR represent complementary resources for identification of allele-specific, alternative splicing.

Pan-cancer repository of validated natural and cryptic mRNA splicing mutations.

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. An algorithm was developed to classify variants into splicing molecular phenotypes that integrates germline heterozygosity, degree of information change and impact on expression. The classification thresholds were calibrated against the ClinVar clinical database phenotypic assignments. Variants are partitioned into allele-specific alternative splicing, likely aberrant and aberrant splicing phenotypes.Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon "Validated Splicing Mutations" either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website.The website provides additional information, such as a visual representation of supporting RNAseq results, gene expression in the corresponding normal tissues, and splicing molecular phenotypes.

Pan-cancer repository of validated natural and cryptic mRNA splicing mutations.

We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon "Validated Splicing Mutations" either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website.