Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged

Alternative splicing of mRNA precursors is a nearly ubiquitous and extremely flexible point of gene control in humans. It provides cells with the opportunity to create protein isoforms of differing, even opposing, functions from a single gene. Cancer cells often take advantage of this flexibility to produce proteins that promote growth and survival. Many of the isoforms produced in this manner are developmentally regulated and are preferentially re-expressed in tumors. Emerging insights into this process indicate that pathways that are frequently deregulated in cancer often play important roles in promoting aberrant splicing, which in turn contributes to all aspects of tumor biology.     

Molecular characterization of a novel fission yeast gene spUAP2 that interacts with the splicing factor spU2AF59

A protein essential for pre-mRNA splicing, the U2 auxiliary factor (U2AF), is composed of a large and small subunit. Previously we cloned and characterized both subunits, spU2AF⁵⁹ and spU2AF²³, from fission yeast. We now report a novel U2AF-associated-protein, spUAP2, which interacts with both subunits. SpUAP2 contains a classical and a degenerate RNA recognition motif (RRM), both of which are required for interaction with spU2AF⁵⁹. Interaction also requires the arginine/serine-rich region and the first RRM of spU2AF⁵⁹. A null allele of the gene for spUAP2 is lethal. Received: 23 May / Accepted: 6 August 1997     

Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer

Splicing of the Drosophila P-element third intron (IVS3) is repressed in somatic tissues due to the function of an exonic splicing silencer (ESS) complex present on the 5′ exon RNA. To comprehensively characterize the mechanisms of this alternative splicing regulation, we used biochemical fractionation and affinity purification to isolate the silencer complex assembled in vitro and identify the constituent proteins by mass spectrometry. Functional assays using splicing reporter minigenes identified the proteins hrp36 and hrp38 and the cytoplasmic poly(A)-binding protein PABPC1 as novel functional components of the splicing silencer. hrp48, PSI, and PABPC1 have high-affinity RNA-binding sites on the P-element IVS3 5′ exon, whereas hrp36 and hrp38 proteins bind with low affinity to the P-element silencer RNA. RNA pull-down and immobilized protein assays showed that hrp48 protein binding to the silencer RNA can recruit hrp36 and hrp38. These studies identified additional components that function at the P-element ESS and indicated that proteins with low-affinity RNA-binding sites can be recruited in a functional manner through interactions with a protein bound to RNA at a high-affinity binding site. These studies have implications for the role of heterogeneous nuclear ribonucleoproteins (hnRNPs) in the control of alternative splicing at cis-acting regulatory sites.     

Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes

A large fraction of sequence variants of unknown significance (VUS) of the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2 may induce splicing defects. We analyzed 53 VUSs of BRCA1 or BRCA2, detected in consecutive molecular screenings, by using five splicing prediction programs, and we classified them into two groups according to the strength of the predictions. In parallel, we tested them by using functional splicing assays. A total of 10 VUSs were predicted by two or more programs to induce a significant reduction of splice site strength or activation of cryptic splice sites or generation of new splice sites. Minigene-based splicing assays confirmed four of these predictions. Five additional VUSs, all at internal exon positions, were not predicted to induce alterations of splice sites, but revealed variable levels of exon skipping, most likely induced by the modification of exonic splicing regulatory elements. We provide new data in favor of the pathogenic nature of the variants BRCA1 c.212+3A>G and BRCA1 c.5194−12G>A, which induced aberrant out-of-frame mRNA forms. Moreover, the novel variant BRCA2 c.7977−7C>G induced in frame inclusion of 6 nt from the 3′ end of intron 17. The novel variants BRCA2 c.520C>T and BRCA2 c.7992T>A induced incomplete skipping of exons 7 and 18, respectively. This work highlights the contribution of splicing minigene assays to the assessment of pathogenicity, not only when patient RNA is not available, but also as a tool to improve the accuracy of bioinformatics predictions.     

Splice site selection and ribonucleoprotein complex assembly during in vitro pre-mRNA splicing

To study the determinants of splice site selection, we have inserted synthetic 5' and 3' splice sites at different positions within beta-globin genes and analyzed the resultant RNA substrates for in vitro splicing, factor binding, and complex assembly. We show that consensus 5' and 3' splice site sequences are insufficient to determine splice site utilization; in the presence or absence of the authentic site, the synthetic sites are variably active in a position-dependent manner. However, regardless of position or utilization, the synthetic 5' and 3' splice sites are bound by the appropriate splicing factors. Thus, binding of splicing factors is necessary but not sufficient for splice site utilization. Finally, we demonstrate that a block to efficient splicing can occur at multiple steps in the pathway of normal splicing complex assembly.     

Ex vivo splicing assays of mutations at noncanonical positions of splice sites in USHER genes

Molecular diagnosis in Usher syndrome type 1 and 2 patients led to the identification of 21 sequence variations located in noncanonical positions of splice sites in MYO7A, CDH23, USH1C, and USH2A genes. To establish experimentally the splicing pattern of these substitutions, whose impact on splicing is not always predictable by available softwares, ex vivo splicing assays were performed. The branch‐point mapping strategy was also used to investigate further a putative branch‐point mutation in USH2A intron 43. Aberrant splicing was demonstrated for 16 of the 21 (76.2%) tested sequence variations. The mutations resulted more frequently in activation of a nearby cryptic splice site or use of a de novo splice site than exon skipping (37.5%). This study allowed the reclassification as splicing mutations of one silent (c.7872G>A (p.Glu2624Glu) in CDH23) and four missense mutations (c.2993G>A (p.Arg998Lys) in USH2A, c.592G>A (p.Ala198Thr), c.3503G>C [p.Arg1168Pro], c.5944G>A (p.Gly1982Arg) in MYO7A), whereas it provided clues about a role in structure/function in four other cases: c.802G>A (p.Gly268Arg), c.653T>A (p.Val218Glu) (USH2A), and c.397C>T (p.His133Tyr), c.3502C>T (p.Arg1168Trp) (MYO7A). Our data provide insights into the contribution of splicing mutations in Usher genes and illustrate the need to define accurately their splicing outcome for diagnostic purposes. Hum Mutat 31:1–9, 2010. © 2010 Wiley‐Liss, Inc.     

胃癌细胞中RHAMM基因表达的对比分析

目的 分析胃癌发生中透明质酸（ｈｙａｌｕｒｏｎｉｃ ａｃｉｄ,ＨＡ）介导的细胞游走受体（ｒｅｃｅｐｔｏｒ ｏｆ ＨＡ ｍｅｄｉａｔｅｄ ｍｏｔｉｌｉｔｙ,ＲＨＡＭＭ）的表达形式以及ＨＡ对其表达的影响。方法 采用免疫组织化学和Ｗｅｓｔｅｒｎ印迹杂交方法,分析ＲＨＡＭＭ蛋白在１０例萎缩性胃炎、１２例肠上皮化生、２０例Ⅲ度非典型增生、７４例各类型胃癌／２析胃癌细胞系以及３６例非癌粘膜临床标本中的表达形式     

CM-DIL和DAPI标记的骨髓间充质干细胞

背景：在有关“细胞移植”的实验研究中,细胞标记技术被广泛应用。CM-DIL与DAPI是细胞标记实验中常用的荧光染料,目前两者的对比研究报道较少。 目的：从体外实验与体内实验两方面,探讨两种荧光染料CM-DIL与DAPI在标记大鼠骨髓间充质干细胞方面的差异。 方法：用贴壁培养法获取、培养、扩增大鼠骨髓间充质干细胞,分别用CM-DIL与DAPI进行标记,锥虫蓝计数检测骨髓间充质干细胞的活力;MTS法检测骨髓间充质干细胞的增殖能力并绘制增殖曲线;倒置相差荧光显微镜下动态观察标记后1,2,3代骨髓间充质干细胞的荧光衰减情况。结扎SD大鼠冠状动脉前降支致心肌梗死。1周后于心肌梗死边缘处注射CM-DIL与DAPI标记的细胞,细胞移植后3 d取材观察骨髓间充质干细胞的分布情况。 结果与结论：体外实验中,CM-DIL与DAPI标记的骨髓间充质干细胞两者的早期增殖能力均低于对照组;两种染料标记后的第1代细胞的荧光阳性率均为100%,但DAPI标记后的第3代细胞的荧光强度明显减弱。体内实验中,CM-DIL组与DAPI组心肌组织冰冻与石蜡切片均检测到集中分布的荧光;CM-DIL组冰冻切片红色荧光比DAPI组的蓝色荧光边界清晰并且背景低;CM-DIL组还可以通过含细胞核染色的封片剂封片排除荧光假阳性。可见,CM-DIL染料比DAPI更适合对骨髓间充质干细胞进行体内示踪。     

Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A

Spliceostatin A (SSA) is a stabilized derivative of a Pseudomonas bacterial fermentation product that displays potent anti-proliferative and anti-tumor activities in cancer cells and animal models. The drug inhibits pre-mRNA splicing in vitro and in vivo and binds SF3b, a protein subcomplex of U2 small nuclear ribonucleoprotein (snRNP), which is essential for recognition of the pre-mRNA branch point. We report that SSA prevents interaction of an SF3b 155-kDa subunit with the pre-mRNA, concomitant with nonproductive recruitment of U2 snRNP to sequences 5' of the branch point. Differences in base-pairing potential with U2 snRNA in this region lead to different sensitivity of 3' splice sites to SSA, and to SSA-induced changes in alternative splicing. Indeed, rather than general splicing inhibition, splicing-sensitive microarray analyses reveal specific alternative splicing changes induced by the drug that significantly overlap with those induced by knockdown of SF3b 155. These changes lead to down-regulation of genes important for cell division, including cyclin A2 and Aurora A kinase, thus providing an explanation for the anti-proliferative effects of SSA. Our results reveal a mechanism that prevents nonproductive base-pairing interactions in the spliceosome, and highlight the regulatory and cancer therapeutic potential of perturbing the fidelity of splice site recognition.     

Multiple genetic and biochemical interactions of Brr2, Prp8, Prp31, Prp1 and Prp4 kinase suggest a function in the control of the activation of spliceosomes in Schizosaccharomyces pombe

The spliceosomal component Prp1 (U5-102 kD) is found in Schizosaccharomyces pombe, a physiological substrate of Prp4 kinase. Here, we identify, spp41-1, a previously isolated extragenic suppressor of Prp4 kinase. The gene encodes an ATP-dependent RNA helicase homologous to the splicing factor Brr2 of Saccharomyces cerevisiae and U5-200 kD of mammalia. The suppressor allele, spp41-1, interacts genetically with alleles of prp1. We show that Prp1 and Brr2 are complexed in vivo with spliceosomal particles containing the five snRNAs U1, U2, U5, and base-paired U4/U6. Prp1 was found exclusively in small ribonucleoprotein particle (snRNP) complexes sedimenting in the range of 30S–60S, whereas Brr2 was also found sedimenting lower than 30S and free of snRNAs. Moreover, we find that the splicing factor Prp31 is complexed with Prp1 in the same spliceosomal particles containing the five snRNAs. These data indicate that in fission yeast spliceosomal particles larger than 30S exist, which can be considered as pre-catalytic spliceosomes. In addition, we show that S. pombe cells lacking Prp1 still contain these large pre-catalytic spliceosomal particles associated with Prp31. These data are consistent with the notion that in fission yeast phosphorylation of Prp1 by Prp4 kinase is involved in the activation of pre-catalytic spliceosomes. Electronic Supplementary Material Supplementary material is available for this article at