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PubMed2024

Directed evolution of engineered virus-like particles with improved production and transduction efficiencies.

Engineered virus-like particles (eVLPs) are promising vehicles for transient delivery of proteins and RNAs, including gene editing agents. We report a system for the laboratory evolution of eVLPs that enables the discovery of eVLP variants with improved properties. The system uses barcoded guide RNAs loaded within DNA-free eVLP-packaged cargos to uniquely label each eVLP variant in a library, enabling the identification of desired variants following selections for desired properties. We applied this system to mutate and select eVLP capsids with improved eVLP production properties or transduction efficiencies in human cells. By combining beneficial capsid mutations, we developed fifth-generation (v5) eVLPs, which exhibit a 2-4-fold increase in cultured mammalian cell delivery potency compared to previous-best v4 eVLPs. Analyses of v5 eVLPs suggest that these capsid mutations optimize packaging and delivery of desired ribonucleoprotein cargos rather than native viral genomes and substantially alter eVLP capsid structure. These findings suggest the potential of barcoded eVLP evolution to support the development of improved eVLPs.

Humans↗
PubMed1998

Analysis of the uncoupling protein-1 (UCP1) gene in obese and lean subjects: identification of four amino acid variants.

Uncoupling protein-1 (UCP1) is uniquely expressed in brown adipose tissue (BAT) and of major importance for the tissues thermogenic capacity. This study was undertaken to detect variants in the UCP1 gene by single strand conformational polymorphism (SSCP) analysis and subsequent sequencing, and determine their potential association with obesity. Four variants predicting for amino acid substitutions were detected, of which Arg40Trp (exon 1) and Lys257Arg (exon 5) were rare mutations. In contrast, the allele frequency of a polymorphism in exon 2 predicting for an Ala64Thr substitution was 8.2% in a cohort of 293 obese children and adolescents compared to 4.1% in 134 lean individuals, while the allele frequency of a Met229Leu variant (exon 5) was not markedly different between the obese (10.4%) and lean (12.0%) study groups. Although one of the identified polymorphisms tends to have a higher frequency in obese than in lean subjects, variants of the UCP1 gene do not seem to contribute significantly to the development of early-onset obesity in the German population.

Adolescent↗
PubMed2004

Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment.

Several databases have been published to predict alternative splicing of mRNAs by analysing the exon linkage relationship by alignment of expressed sequence tags (ESTs) to the genome sequence; however, little effort has been made to investigate the relationship between cancers and alternative splicing. We developed a program, Alternative Splicing Assembler (ASA), to look for splicing variants of human gene transcripts by genome-wide ESTs alignment. Using ASA, we constructed the biosino alternative splicing database (BASD), which predicted splicing variants for reference sequences from the reference sequence database (RefSeq) and presented them in both graph and text formats. EST clusters that differ from the reference sequences in at least one splicing site were counted as splicing variants. Of 4322 genes screened, 3490 (81%) were observed with at least one alternative splicing variants. To discover the variants associated with cancers, tissue sources of EST sequences were extracted from the UniLib database and ESTs from the same tissue type were counted. These were regarded as the indicators for gene expression level. Using Fisher's exact test, alternative splicing variants, of which EST counts were significantly different between cancer tissues and their counterpart normal tissues, were identified. It was predicted that 2149 variants, or 383 variants after Bonferroni correction, of 26 812 variants were likely tumor-associated. By reverse transcription-PCR, 11 of 13 novel alternative splicing variants and eight of nine variants' tissue specificity were confirmed in hepatocellular carcinoma and in lung cancer. The possible involvement of alternative splicing in cancer is discussed.

Alternative Splicing↗
PubMed2005

Identification of novel RARbeta2 transcript variants with short 5'-UTRs in normal and cancerous breast epithelial cells.

Functional significance of RARbeta2 as a putative tumor suppressor gene has been studied in breast cancer and other tumors. The long 5'-untranslated region (5'-UTR) of its transcript with multiple open-reading frames (uORFs) is considered as a regulatory unit for translation. Here, for the first time we identified RARbeta2 transcript variants with short 5'-UTRs in both normal and malignant breast epithelial cells. The 5'-RACE analysis of RARbeta2 mRNA in these cells demonstrated the existence of short RARbeta2 transcript variants that are identical to the sequence of known RARbeta2, but lack all the uORFs present in the full-length 5'-UTR. By RT-PCR analysis, we found that the expression of both transcripts with short and full-length 5'-UTR is mediated by retinoic acid, while cellular sensitivity is preferentially correlated to upregulation of short RARbeta2 transcript variants in response to retinoic acid. The transfection and in vitro translation assay indicated that the short 5'-UTR has no inhibitory effects on translation, while the presence of full-length 5'-UTR inhibited translation by 60%. In addition, no promoter activity was detectable in RARbeta2 full-length 5'-UTR region. Our data suggest that the RARbeta2 transcript variants with short 5'-UTR may serve as major transcripts for RARbeta2 protein translation as well as potential targets for retinoids in breast cancer prevention and therapy studies.

5' Untranslated Regions↗
PubMed2006

Identification of a novel splice variant of AML1b in ovarian cancer patients conferring loss of wild-type tumor suppressive functions.

Acute myeloid leukemia (AML) 1 is often disrupted by chromosomal translocations generating oncogenic fusions in human leukemias. However, its role in epithelial cancers has not been extensively investigated. Herein, we show a marked accumulation of AML1 transcripts including a high frequency of a novel alternatively spliced AML1b transcript lacking exon 6 (AML1b(Del179-242)) in ovarian cancer patients. The increases in RNA transcripts for total wild-type AML1 and AML1b(Del179-242) are associated with poor patient outcomes. We have shown that although both wild-type AML1b and AML1b(Del179-242) are localized to nuclear speckles, AML1b(Del179-242) was observed to have dramatically reduced transactivation potential with the plasminogen activator inhibitor-1 promoters and behaved as a weak dominant negative of wild-type AML1b. Wild-type AML1b was found to inhibit the growth of immortalized ovarian epithelial cells (T29) decreasing colony-forming ability. Moreover, we have identified a novel function of AML1b where it inhibits ovarian cell migration. In contrast, AML1b(Del179-242) has lost the ability to inhibit both ovarian cell proliferation and migration indicating that the functional effects observed with wild-type AML1b are dependent on amino acids 179-242. Collectively, these studies suggest that deregulated alternative splicing of AML1b transcripts may potentially contribute to the pathophysiology of ovarian cancers.

Alternative Splicing↗
PubMed1997

Simultaneous SIL-TAL1 RT-PCR detection of all tal(d) deletions and identification of novel tal(d) variants.

Site-specific deletions of the 5' part of the TAL1 gene (tal(d)) are among the most frequent non-random genetic abnormalities in T-cell acute lymphoblastic leukaemia (T-ALL). They are usually detected by PCR from DNA with several primer pairs or by Southern blot analysis. Since tal(d) lead to expression of a SIL-TAL1 fusion transcript, irrespective of the genomic breakpoint, we have used a single monoplex RT-PCR reaction to screen 55 T-ALL patients at diagnosis. SIL-TAL1 transcripts were demonstrated in 12 (22%) cases, including 7/27 (26%) children <15 years of age, 2/8 (25%) adolescents and 2/17 (12%) adults aged >20 years. SIL-TAL1 RT-PCR was preferrable to tal(d) DNA PCR since it allowed the simultaneous detection of tal(d), tal(d2) and two previously undescribed tal(d) variants. SIL-TAL1 RT-PCR screening should therefore increase the detection rate of tal(d) by approximately 15-20%, with an at least comparable sensitivity to tal(d) genomic PCR, and represents a more practical and economic alternative to multiple DNA PCRs or Southern blotting when incorporated into molecular screening for multiple transcripts at diagnosis.

Adolescent↗
PubMedDate not supplied

The characterization of pregnancy associated plasma protein-E and the identification of an alternative splice variant.

We have performed differential display and bioinformatic database mining of the placenta, in an attempt to find novel diagnostic markers of pathological pregnancies. We have identified a full-length cDNA encoding the preproprotein of pregnancy associated plasma protein-E (PAPP-E); a putative metalloprotease, of 1790-residues with a putative 21-residue signal peptide. An alternatively spliced mRNA was found to encode an 826-residue precursor protein corresponding to the N-terminus of PAPP-E. Both PAPP-E variants were found to be co-expressed abundantly in the placenta and non-pregnant mammary gland with low expression in the kidney, foetal brain and pancreas. Analysis of the predicted proteins suggests that the longer variant be targeted to the nucleus while the shorter variant is secreted extracellularly. Gene structure analysis revealed that PAPP-E was encoded on 23 exons on chromosome 1 and its splice variant on the first five same exons. The discovery of the PAPP-E variants will help in the deciphering of the physiology of this new family of metzincins in not only the placenta during pregnancy but also the mammary gland in breast cancer. The new PAPP-E variants could have the potential for the diagnosis of pathological pregnancies including trisomies such as Down's syndrome.

Alternative Splicing↗
PubMed2001

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

Synovial sarcoma (SS) is cytogenetically characterized by the translocation t(X;18)(p11.2-q11.2) generating a fusion between the SYT gene on chromosome 18 and one member of the SSX family gene (SSX1; SSX2; SSX4) on chromosome X. Here, we report for the first time that 2 forms of SYT mRNA are present in both normal tissues and SSs. By amplifying the full-length SYT cDNA of two SSs, we detected 2 bands, here designated N-SYT and I-SYT. The latter, previously undescribed, contains an in-frame insertion of 93 bp. Its sequencing revealed a 100% homology with the mouse SYT gene. These two SYT forms were present, although in different amounts, in all human normal tissues examined, including kidney, stomach, lung, colon, liver and synovia. Coexistence of N-SYT and I-SYT (both fused with SSX) was detected in a series of 59 SSs (35 monophasic and 24 biphasic) and in a SS cell line. A preliminary analysis of the differential expression levels of N-SYT and I-SYT in SSs revealed that the latter was consistently overexpressed, suggesting a role in SS pathogenesis.

Alternative Splicing↗
PubMed2005

Adaptive evolution of heparanase in hypoxia-tolerant Spalax: gene cloning and identification of a unique splice variant.

Heparan sulfate (HS) side chains of HS proteoglycans bind to and assemble extracellular matrix proteins and play important roles in cell-cell and cell-extracellular matrix interactions. HS chains bind a multitude of bioactive molecules and thereby function in the control of multiple normal and pathological processes. Enzymatic degradation of HS by heparanase, a mammalian endoglycosidase, affects the integrity and functional state of tissues and is involved in, among other processes, inflammation, angiogenesis, and cancer metastasis. Here, we report the cloning of heparanase from four Israeli species of the blind subterranean mole rat (Spalax ehrenbergi superspecies), 85% homologous to the human enzyme. Unlike its limited expression in human tissues, heparanase is highly expressed in diverse Spalax tissues. Moreover, we have identified a unique splice variant of the Spalax enzyme lacking 16 aa encoded by exon 7. This deletion resulted in a major defect in trafficking and processing of the heparanase protein, leading to a loss of its enzymatic activity. Interspecies variation was noted in the sequence and in the expression of the splice variant of the heparanase gene in blind mole rats living under different ecogeographical stresses, indicating a possible role in adaptation to stress in Spalax evolution.

Alternative Splicing↗
PubMed2002

A Drosophila dopamine 2-like receptor: Molecular characterization and identification of multiple alternatively spliced variants.

Dopamine is an important neurotransmitter in the central nervous system of both Drosophila and mammals. Despite the evolutionary distance, functional parallels exist between the fly and mammalian dopaminergic systems, with both playing roles in modulating locomotor activity, sexual function, and the response to drugs of abuse. In mammals, dopamine exerts its effects through either dopamine 1-like (D1-like) or D2-like G protein-coupled receptors. Although pharmacologic data suggest the presence of both receptor subtypes in insects, only cDNAs encoding D1-like proteins have been isolated previously. Here we report the cloning and characterization of a newly discovered Drosophila dopamine receptor. Sequence analysis reveals that this putative protein shares highest homology with known mammalian dopamine 2-like receptors. Eight isoforms of the Drosophila D2-like receptor (DD2R) transcript have been identified, each the result of alternative splicing. The encoded heptahelical receptors range in size from 461 to 606 aa, with variability in the length and sequence of the third intracellular loop. Pharmacologic assessment of three DD2R isoforms, DD2R-606, DD2R-506, and DD2R-461, revealed that among the endogenous biogenic amines, dopamine is most potent at each receptor. As established for mammalian D2-like receptors, stimulation of the Drosophila homologs with dopamine triggers pertussis toxin-sensitive Gi/o-mediated signaling. The D2-like receptor agonist, bromocriptine, has nanomolar potency at DD2R-606, -506, and -461, whereas multiple D2-like receptor antagonists (as established with mammalian receptors) have markedly reduced if any affinity when assessed at the fly receptor isoforms. The isolation of cDNAs encoding Drosophila D2-like receptors extends the range of apparent parallels between the dopaminergic system in flies and mammals. Pharmacologic and genetic manipulation of the DD2Rs will provide the opportunity to better define the physiologic role of these proteins in vivo and further explore the utility of invertebrates as a model system for understanding dopaminergic function in higher organisms.

Alternative Splicing↗
PubMed1999

The pre-transmembrane 1 domain of acid-sensing ion channels participates in the ion pore.

The acid-sensing ion channel (ASIC) subunits ASIC1, ASIC2, and ASIC3 are members of the amiloride-sensitive Na+ channel/degenerin family of ion channels. They form proton-gated channels that are expressed in the central nervous system and in sensory neurons, where they are thought to play an important role in pain accompanying tissue acidosis. A splice variant of ASIC2, ASIC2b, is not active on its own but modifies the properties of ASIC3. In particular, whereas most members of the amiloride-sensitive Na+ channel/degenerin family are highly selective for Na+ over K+, ASIC3/ASIC2b heteromultimers show a nonselective component. Chimeras of the two splice variants allowed identification of a 9-amino acid region preceding the first transmembrane (TM) domain (pre-TM1) of ASIC2 that is involved in ion permeation and is critical for Na+ selectivity. Three amino acids in this region (Ile-19, Phe-20, and Thr-25) appear to be particularly important, because channels mutated at these residues discriminate poorly between Na+ and K+. In addition, the pH dependences of the activity of the F20S and T25K mutants are changed as compared with that of wild-type ASIC2. A corresponding ASIC3 mutant (T26K) also has modified Na+ selectivity. Our results suggest that the pre-TM1 region of ASICs participates in the ion pore.

Alternative Splicing↗
PubMed2000

Identification of novel, functional genetic variants in the human matrix metalloproteinase-2 gene: role of Sp1 in allele-specific transcriptional regulation.

Matrix metalloproteinase-2 (MMP-2) is an enzyme with proteolytic activity against matrix and nonmatrix proteins, particularly basement membrane constituents. Thus, any naturally occurring genetic variants that directly affect gene expression and/or protein function would be expected to impact on progression of pathological processes involving tissue remodeling. We scanned a 2-kilobase pair promoter region and all 13 exons of the human MMP-2 gene, from a panel of 32 individuals, and we identified the position, nature, and relative allele frequencies of 15 variant loci as follows: 6 in the promoter, 1 in the 5'-untranslated region, 6 in the coding region, 1 in intronic sequence, and 1 in the 3'-untranslated region. The majority of coding region polymorphisms resulted in synonymous substitutions, whereas three promoter variants (at -1306, -790, and +220) mapped onto cis-acting elements. We functionally characterized all promoter variants by transient transfection experiments with 293, RAW264.7, and A10 cells. The common C --> T transition at -1306 (allele frequency 0.26), which disrupts an Sp1-type promoter site (CCACC box), displayed a strikingly lower promoter activity with the T allele. Electrophoretic mobility shift assays confirmed that these differences in allelic expression were attributable to abolition of Sp1 binding. These data suggest that this common functional genetic variant influences MMP-2 gene transcription in an allele-specific manner and is therefore an important candidate to test for association in a wide spectrum of pathologies for which a role for MMP-2 is implicated, including atherogenesis and tumor invasion and metastasis.

3' Untranslated Regions↗
PubMed2001

Identification of a novel structural variant of the alpha 6 integrin.

The alpha(6) integrin is a 140-kDa (nonreduced) laminin receptor. We have identified a novel 70-kDa (nonreduced) form of the alpha(6) integrin called alpha(6)p for the latin word parvus, meaning small. The variant was immunoprecipitated from human cells using four different alpha(6)-specific monoclonal antibodies but not with alpha(3) or alpha(5) antibodies. The alpha(6)p integrin contained identical amino acid sequences within exons 13--25, corresponding to the extracellular "stalk region" and the cytoplasmic tail of the alpha(6) integrin. The light chains of alpha(6) and alpha(6)p were identical as judged by alpha(6)A-specific antibodies and electrophoretic properties. The alpha(6)p variant paired with either beta(1) or beta(4) subunits and was retained on the cell surface three times longer than alpha(6). Reverse transcription/polymerase chain reaction analysis revealed a single polymerase chain reaction product. The alpha(6)p variant was found in human prostate (DU145H, LnCaP, PC3) and colon (SW480) cancer cell lines but not in normal prostate (PrEC), breast cancer (MCF-7), or lung cancer (H69) cell lines or a variant of a prostate carcinoma cell line (PC3-N). Protein levels of alpha(6)p increased 3-fold during calcium-induced terminal differentiation in a normal mouse keratinocyte model system. A novel form of the alpha(6) integrin exists on cell surfaces that contains a dramatically altered extracellular domain.

Amino Acid Sequence↗
PubMed2003

Identification of novel alternative splice variants of APOBEC-1 complementation factor with different capacities to support apolipoprotein B mRNA editing.

Two novel mRNA transcripts have been identified that result from species- and tissue-specific, alternative polyadenylation and splicing of the pre-mRNA encoding the apolipoprotein B (apoB) editing catalytic subunit 1 (APOBEC-1) complementation factor (ACF) family of related proteins. The alternatively processed mRNAs encode 43- and 45-kDa proteins that are components of the previously identified p44 cluster of apoB RNA binding, editosomal proteins. Recombinant ACF45 displaced ACF64 and ACF43 in mooring sequence RNA binding but did not demonstrate strong binding to APOBEC-1. In contrast, ACF43 bound strongly to APOBEC-1 but demonstrated weak binding to mooring sequence RNA. Consequently ACF45/43 complemented APOBEC-1 in apoB mRNA editing with less efficiency than full-length ACF64. These data, together with the finding that all ACF variants were co-expressed in rat liver nuclei (the site of apoB mRNA editing), suggested that ACF variants might compete with one another for APOBEC-1 and apoB mRNA binding and thereby contribute to the regulation of apoB mRNA editing. In support for this hypothesis, the ratio of nuclear ACF65/64 to ACF45/43 decreased when hepatic editing was inhibited by fasting and increased when editing was re-stimulated by refeeding. These findings suggested a new model for the regulation of apoB mRNA editing in which the catalytic potential of editosomes is modulated at the level of their assembly by alterations in the relative abundance of multiple related RNA-binding auxiliary proteins and the expression level of APOBEC-1.

APOBEC-1 Deaminase↗
PubMed2004

Identification of strain-specific variants of mouse Adamts13 gene encoding von Willebrand factor-cleaving protease.

Human ADAMTS13 was recently identified as a gene encoding von Willebrand factor-cleaving protease, hADAMTS13. Both congenital and acquired defects in this enzyme can cause thrombotic thrombocytopenic purpura. hADAMTS13 consists of 1,427 amino acid residues and is composed of multiple structural domains including thrombospondin type 1 motifs and CUB domains. To analyze the functional roles of these domains in vivo, we determined the cDNA sequence of the mouse ortholog, mADAMTS13. Unexpectedly, two forms of the mouse Adamts13 gene were isolated that differed in the insertion of an intracisternal A particle (IAP) retrotransposon including a premature stop codon. The IAP insertion was found in BALB/c, C3H/He, C57BL/6, and DBA/2 strains but not in the 129/Sv strain. The outbred ICR strain had either the IAP-free or IAP-inserted allele or both. IAP-free Adamts13 encoded mADAMTS13L, a protein of 1,426 amino acid residues with the same domain organization as hADAMTS13. In contrast, IAP-inserted Adamts13 encoded a C-terminally truncated enzyme, mADAMTS13S, that is comprised of only 1,037 amino acid residues and lacking the C-terminal two thrombospondin type 1 motifs and two CUB domains. Strain specificity was also confirmed by reverse transcription-PCR and Northern blot analyses. Both recombinant mADAMTS13L and mADAMTS13S exhibited von Willebrand factor cleaving activities in vitro. The natural variation in mouse ADAMTS13 should allow for the determination of hitherto unknown functions of its C-terminal domains in vivo.

ADAM Proteins↗
PubMed2005

Identification of an alternatively spliced variant of Ca2+-promoted Ras inactivator as a possible regulator of RANKL shedding.

The receptor activator of NF-kappaB ligand (RANKL), a critical regulator of osteoclastogenesis, is synthesized as a membrane-anchored protein and cleaved into a soluble form by ectodomain shedding. We developed an assay system to identify molecules regulating the RANKL shedding. Using this system, we found that a splice variant of Ca2+-promoted Ras inactivator (CAPRI), deltaCAPRI, which is expressed in primary osteoblasts, promoted the RANKL shedding. The wild type CAPRI is a member of the Ras GTPase-activating protein (GAP) family and suppresses Ca2+-dependent Ras activation, whereas deltaCAPRI, which lacks one exon in the GAP-related domain, activated the Ras pathway. Overexpression of deltaCAPRI or a constitutive active form of Ras up-regulated the expression level of matrix-metalloproteinase 14 (MMP14), which directly cleaves the ectodomain of RANKL, whereas Erk activation by expressing the constitutive active Mek1 did not affect the MMP14 expression or RANKL shedding. These results suggest that deltaCAPRI is a possible regulator of RANKL shedding by modulating MMP14 expression through Ras signaling cascades other than the Erk pathway.

Alkaline Phosphatase↗