C6: A Monoclonal Antibody Specific for a Fibronectin Epitope Situated at the Interface between the Oncofoetal Extra-Domain B and the Repeat III8

Background

Fibronectin (FN) is a large multidomain molecule that is involved in many cellular processes. Different FN isoforms arise from alternative splicing of the pre-mRNA including, most notably, the FN isoform that contains the “extra-domain-B” (ED-B). The FN isoform containing ED-B (known as B-FN) is undetectable in healthy adult tissues but is present in large amounts in neoplastic and foetal tissues as well as on the blood vessels during angiogenesis. Thus, antibodies specific for B-FN can be useful for detecting and targeting neoplastic tissues in vivo. We previously characterised C6, a new monoclonal antibody specific for human B-FN and we suggested that it reacts with the B-C loop of the type III repeat 8 which is masked in FN isoforms lacking ED-B and that the insertion of ED-B in FN molecules unmasked it. Here we have now consolidated and refined the characterization of this B-FN specific antibody demonstrating that the epitope recognized by C6 also includes loop E-F of ED-B.

Methodology

We built the three dimensional model of the variable regions of the mAb C6 and of the FN fragment EDB-III8 and performed protein:protein docking simulation using the web server ClusPro2.0. To confirm the data obtained by protein:protein docking we generated mutant fragments of the recombinant FN fragment EDB-III8 and tested their reactivity with C6.

Conclusion

The monoclonal antibody C6 reacts with an epitope formed by the B-C loop of domain III8 and the E-F loop of ED-B. Both loops are required for an immunological reaction, thus this monoclonal is strictly specific for B-FN but the part of the epitope on III8 confers the human specificity.     

Alternative Splicing of the Fibronectin EIIIB Exon Depends on Specific TGCATG Repeats

The fibronectin EIIIB exon is alternatively spliced in a cell-type-specific manner, and TGCATG repeats in the intron downstream of EIIIB have been implicated in this regulation. Analysis of the intron sequence from several vertebrates shows that the pattern of repeats in the 3′ half of the intron is evolutionarily conserved. Point mutations in certain highly conserved repeats greatly reduce EIIIB inclusion, suggesting that a multicomponent complex may recognize the repeats. Expression of the SR protein SRp40, SRp20, or ASF/SF2 stimulates EIIIB inclusion. Studies of the interplay between mutations in the repeats and SRp40-stimulated inclusion suggest that the repeats are recognized in many, if not all, cell types, and that EIIIB inclusion may be regulated by quantitative changes in multiple factors.     

Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation

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Alternative Splicing of the RAGE Cytoplasmic Domain Regulates Cell Signaling and Function

The Receptor for Advanced Glycation End-products (RAGE) is a multi-ligand receptor present on most cell types. Upregulation of RAGE is seen in a number of pathological states including, inflammatory and vascular disease, dementia, diabetes and various cancers. We previously demonstrated that alternative splicing of the RAGE gene is an important mechanism which regulates RAGE signaling through the production of soluble ligand decoy isoforms. However, no studies have identified any alternative splice variants within the intracellular region of RAGE, a region critical for RAGE signaling. Herein, we have cloned and characterized a novel splice variant of RAGE that has a truncated intracellular domain (RAGEΔICD). RAGEΔICD is prevalent in both human and mouse tissues including lung, brain, heart and kidney. Expression of RAGEΔICD in C6 glioma cells impaired RAGE-ligand induced signaling through various MAP kinase pathways including ERK1/2, p38 and SAPK/JNK. Moreover, RAGEΔICD significantly affected tumor cell properties through altering cell migration, invasion, adhesion and viability in C6 glioma cells. Furthermore, C6 glioma cells expressing RAGEΔICD exhibited drastic inhibition on tumorigenesis in soft agar assays. Taken together, these data indicate that RAGEΔICD represents a novel endogenous mechanism to regulate RAGE signaling. Significantly, RAGEΔICD could play an important role in RAGE related disease states through down regulation of RAGE signaling.     

Alternative Splicing Modulates Autoinhibition and SH3 Accessibility in the Src Kinase Fyn

Src family kinases are central regulators of a large number of signaling pathways. To adapt to the idiosyncrasies of different cell types, these kinases may need a fine-tuning of their intrinsic molecular control mechanisms. Here, we describe on a molecular level how the Fyn kinase uses alternative splicing to adapt to different cellular environments. Using structural analysis, site-directed mutagenesis, and functional analysis, we show how the inclusion of either exon 7A or 7B affects the autoinhibition of Fyn and how this changes the SH3-dependent interaction and tyrosine phosphorylation of Sam68, with functional consequences for the Sam68-regulated survival of epithelial cells. Our results illustrate a novel mechanism of evolution that may contribute to the complexity of Src kinase regulation.The Src family of nonreceptor protein tyrosine kinases comprises nine members, including Src, Blk, Fgr, Fyn, Hck, Lyn, Lck, Yes, and Yrk. These kinases play crucial roles in a variety of cellular processes, such as cell cycle control, cell adhesion, cell motility, cell proliferation, and cell differentiation (41). Extensive studies indicate that the complexity of functional roles of Src kinases derives mainly from their ability to communicate with a large number of upstream receptors and downstream effectors, which vary by cell type (31). Given their critical role, diverse mechanisms of autoregulation have evolved, and their importance is highlighted by the implication of elevated Src expression levels and/or activity in epithelial cancers (for a review, see reference 48). The autoregulatory mechanisms depend on the composition and order of various domains and on posttranslational modification sites in the linker segments that connect the domains (35). From the N to C terminus, Src contains a myristoyl group attached to a unique domain, an Src homology 3 (SH3) domain that typically binds left-handed polyproline type II sequence motifs, an SH2 domain that binds to tyrosine-phosphorylated protein motifs, a protein-tyrosine kinase domain (SH1), and a C-terminal regulatory segment. Early biochemical studies suggested that these domains were critical for keeping Src catalytic activity under control (4, 23, 39, 40). The validation of the autoinhibitory role of these regulatory moieties came from the structures of Src and Hck kinases (36, 37, 43, 46, 47). The structures showed how interdomain interactions, stabilized by the binding of the SH2 domain to the tyrosine-phosphorylated C terminus (pTyr528), lock the molecule in a closed conformation. They further showed the unanticipated finding that residues in the linker region between the SH2 domain and the kinase domain, the SH2-kinase linker, make direct contact with the catalytic domain and adopts a polyproline type II helix conformation that docks onto the SH3 domain. This intramolecular interaction hinders the formation of a salt bridge that is crucial for the kinase activity, thereby eliciting an inhibitory effect. However, these interactions are suboptimal, and other phosphotyrosine- or polyproline-containing sequences can compete favorably with Src''s own sequences for SH2 or SH3 domain binding (3, 25). These binding events lead to the stimulation of Src kinase activity by disrupting the intramolecular constraints imposed on the kinase domain. Once released from the repressed state, the autophosphorylation of tyrosine residue Tyr416 (pTyr416) in the activation loop rapidly occurs, resulting in a conformational change that releases a fully active kinase.Remarkably, recent advances have highlighted the crucial role of linker regions in establishing the structural and functional assembly of multimodular proteins in signal transduction, and Src kinases are influential in our understanding of these mechanisms (13). The nine Src family members are very similar in terms of sequence identity, with, for example, the strong conservation of the SH3 binding surface and the cores of the kinase domain (44). Nevertheless, high sequence variability is noted in the SH2-kinase linker segment, except that the overall hydrophobicity is conserved. The interactions that this linker makes with both the SH3 domain and the back of the kinase domain probably result in a high-specificity binding. Indeed, the activities of chimeras in which the SH3 domain of Src kinases have been swapped show altered regulation (12, 14, 16). Furthermore, in contrast to deletion or point mutations in the SH3 domain, Src mutants in the linker segment or in the linker-interacting surface on the catalytic domain can transform fibroblast, suggesting specific function(s) (14).Src kinases originated by the duplication and diversification of the same ancestral gene with an original 10-intron structure before the separations of Teleostei from Tetrapoda (6). One of the Src-related kinases, Fyn, possesses two kinds of exon 7, exon 7A and exon 7B, essentially encoding for the SH2-kinase linker segment and the N terminus of the SH1 domain. The alternative splicing of exon 7A or 7B yields two major Fyn isoforms, FynB (exon 7A) and FynT (exon 7B) (7). Exon 7A shows a different evolutionary pattern from that of the other parts of the gene, suggesting that it is derived by a recombinatorial event with another gene (33). The newly captured exon, encoding FynB, was coopted by the central nervous system and possibly other tissues, while the ancestral isoform, encoding FynT, is expressed mainly in the hematopoietic system (7, 32). Whether this diversification process generated intrinsic biochemical functional novelty in addition to the differential tissue distribution and related functional divergence currently is unknown. Since the alternatively spliced exon that distinguishes the two isoforms essentially encodes for the SH2-kinase linker segment, it is possible that it confers distinct regulatory features. Thus, this evolutionary divergence in the SH2-linker segment of FynT and FynB, which maintain identical SH2, SH3, and kinase domains, offers the unique opportunity to explore the specific functions that this linker segment may impose on Src kinase function and/or regulation.Here, we have investigated how exons 7A and 7B affect the functional interaction of Fyn with the RNA-binding protein Sam68. Sam68 is known to activate Fyn by binding to its SH3 domain and also to serve as a substrate for phosphorylation by Fyn. We show that FynT and FynB display a distinct capacity to bind and phosphorylate Sam68. This differential interaction with a substrate is functionally relevant, because it allows the specific phosphorylation-mediated regulation of the Sam68-dependent alternative splicing of Bcl-x by FynT and results in the differential regulation of apoptosis in epithelial cells. Swapping experiments identify core residues of the exon 7A- or 7B-encoded SH2-kinase linker segment as both required and sufficient to confer this distinct function. In agreement with structural models, our data show that exon 7B reinforces the autoinhibitory lock that the SH2-linker region imposes onto the kinase domain and on SH3 domain accessibility. These results uncover a novel specific function that the SH2-kinase linker segment can play in Src biology and highlight the importance of alternative splicing for the acquisition of fine-tuning regulatory functions during evolution.     

CDO: An Oncogene-, Serum-, and Anchorage-regulated Member of the Ig/Fibronectin Type III Repeat Family

Cell adhesion molecules of the Ig superfamily are implicated in a wide variety of biological processes, including cell migration, axon guidance and fasciculation, and growth control and tumorigenesis. Expression of these proteins can be highly dynamic and cell type specific, but little is known of the signals that regulate such specificity. Reported here is the molecular cloning and characterization of rat CDO, a novel cell surface glycoprotein of the Ig superfamily that contains five Ig-like repeats, followed by three fibronectin type III–like repeats in its extracellular region, and a 256-amino acid intracellular region that does not resemble other known proteins. In rat embryo fibroblasts, cdo mRNA expression is maximal in confluent, quiescent cells. It is rapidly and transiently down-regulated by serum stimulation of such cells, and is constitutively down-regulated in oncogene-transformed derivatives of these cells. CDO protein levels are also dramatically regulated by cell–substratum adhesion, via a mechanism that is independent of cdo mRNA expression. The amount of CDO produced at the surface of a cell may therefore be governed by a complex balance of signals, including mitogenic stimuli that regulate cdo mRNA levels, and substratum-derived signals that regulate CDO protein production. cdo mRNA is expressed at low levels in most adult rat tissues. A closely related human gene maps to chromosome 11q23–24, a region that displays frequent loss of heterozygosity in human lung, breast, and ovarian tumors. Taken together, these data suggest that loss of CDO function could play a role in oncogenesis.     

Pressure-Overload Cardiac Hypertrophy Is Associated with Distinct Alternative Splicing Due to Altered Expression of Splicing Factors

Chronic pressure-overload cardiac hypertrophy is associated with an increased risk of morbidity/mortality, largely due to maladaptive remodeling and dilatation that progresses to dilated cardiomyopathy. Alternative splicing is an important biological mechanism that generates proteomic complexity and diversity. The recent development of next-generation RNA sequencing has improved our understanding of the qualitative signatures associated with alternative splicing in various biological conditions. However, the role of alternative splicing in cardiac hypertrophy is yet unknown. The present study employed RNA-Seq and a bioinformatic approach to detect the RNA splicing regulatory elements involved in alternative splicing during pressure-overload cardiac hypertrophy. We found GC-rich exonic motifs that regulate intron retention in 5′ UTRs and AT-rich exonic motifs that are involved in exclusion of the AT-rich elements that cause mRNA instability in 3′ UTRs. We also identified motifs in the intronic regions involved in exon exclusion and inclusion, which predicted splicing factors that bind to these motifs. We found, through Western blotting, that the expression levels of three splicing factors, ESRP1, PTB and SF2/ASF, were significantly altered during cardiac hypertrophy. Collectively, the present results suggest that chronic pressure-overload hypertrophy is closely associated with distinct alternative splicing due to altered expression of splicing factors.     

Sequences from the First Fibronectin Type III Repeat of the Neural Cell Adhesion Molecule Allow O-Glycan Polysialylation of an Adhesion Molecule Chimera

Polysialic acid is a developmentally regulated, anti-adhesive polymer that is added to N-glycans on the fifth immunoglobulin domain (Ig5) of the neural cell adhesion molecule (NCAM). We found that the first fibronectin type III repeat (FN1) of NCAM is required for the polysialylation of N-glycans on the adjacent Ig5 domain, and we proposed that the polysialyltransferases recognize specific sequences in FN1 to position themselves for Ig5 N-glycan polysialylation. Other studies identified a novel FN1 acidic surface patch and α-helix that play roles in NCAM polysialylation. Here, we characterize the contribution of two additional FN1 sequences, Pro⁵¹⁰-Tyr⁵¹¹-Ser⁵¹² (PYS) and Gln⁵¹⁶-Val⁵¹⁷-Gln⁵¹⁸ (QVQ). Replacing PYS or the acidic patch dramatically decreases the O-glycan polysialylation of a truncated NCAM protein, and replacing the α-helix or QVQ shifts polysialic acid to FN1 O-glycans in full-length NCAM. We also found that the FN1 domain of the olfactory cell adhesion molecule, a homologous but unpolysialylated protein, could partially replace NCAM FN1. Inserting Pro⁵¹⁰-Tyr⁵¹¹ eliminated N-glycan polysialylation and enhanced O-glycosylation of an NCAM- olfactory cell adhesion molecule chimera, and inserting other FN1 sequences unique to NCAM, predominantly the acidic patch, created a new polysialyltransferase recognition site. Taken together, our results highlight the role of the FN1 α-helix and QVQ sequences in N-glycan polysialylation and demonstrate that the acidic patch primarily functions in O-glycan polysialylation.     

Presence of a Fibronectin Type III Domain in a Plant Protein

A hidden Markov model (HMM) approach was used to identify potential candidates in sequence databases for fibronectin type III domains in plants, a kingdom heretofore bereft of these structures. Fortuitously, one of the proteins uncovered had already had a crystal structure published, allowing direct structural confirmation of the existence of this domain in plants. Received: 19 December 1997 / Accepted: 23 December 1997     

Deep Learning Deepens the Analysis of Alternative Splicing

The ever-increasing high-volume and high-dimensional geno-mics data on the one hand challenge traditional data analysis approaches,and on the other hand provide ample opportuni-ties for developing novel analytic strategies.