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Detection and consequences of recombinant protein isoforms: implications for biological potency.

Protein isoforms commonly occur in nature and in products produced by recombinant DNA technologies. Some isoforms may be generated as a consequence of the manufacturing process. Bioassay methods may not be sufficiently sensitive enough or specific enough to determine the biological effect of having a new or increased level of a particular isoform. Sophisticated analytical techniques exist for the structural characterization of protein isoforms. The biological implications of these isoforms are not easy to determine. Additional "Biological Characterization" work may need to be done to evaluate the biological consequences of isoforms. An understanding of the product's mechanism of action and the disease mechanism of action is essential for a thorough evaluation.

Electrophoresis, Polyacrylamide Gel↗

Cloning and characterization of Cbl-associated protein splicing isoforms.

Cbl-associated protein (CAP) is an adaptor protein that plays important roles in both signal transduction and cytoskeleton rearrangement. Alternative splicing of the gene SORBS1 results in multiple isoforms of CAP protein. We report here the cloning of 3 new CAP isoforms, CAP2, CAP3, and CAP4, from mouse adipose tissue. RT-PCR analyses reveal that the isoform mRNAs are differentially expressed. CAP2, CAP3, and CAP4 contain a coiled-coil domain. In addition, CAP4 contains a proline-rich region, part of which exists in CAP3. Coimmunoprecipitation experiments show that CAP4 forms a homodimeric complex. While these new isoforms similarly interact with Cbl, they exhibit varied binding specificity toward vinculin. In contrast to CAP1 and CAP2, CAP4 does not interact with vinculin, and CAP3 binds with low affinity. Immunofluorescence analysis demonstrates differential subcellular localization of Myc-tagged CAP isoforms in 3T3-L1 adipocytes. These results suggest that these new isoforms of CAP might play different signaling roles.

3T3 Cells↗

Expression of a MYCN-interacting isoform of the tumor suppressor BIN1 is reduced in neuroblastomas with unfavorable biological features.

PURPOSE: Amplification of the MYCN proto-oncogene is strongly correlated with poor outcome in neuroblastoma (NB), although deregulated MYCN is a potent inducer of apoptosis. BIN1 (2q14) encodes multiple isoforms of a Myc-interacting adaptor protein that has features of a tumor suppressor, including the ability to inhibit Myc-mediated cell transformation and to promote apoptosis. We hypothesized that BIN1 may function as a suppressor gene in NB, because Bin1 is highly expressed in neural tissues and binds the Myc Box motifs that are conserved in MycN. EXPERMENTAL DESIGN: Expression of MYCN, total BIN1, and BIN1 isoforms were determined in 56 primary NBs using the real-time PCR. Expression was correlated with biological and genetic features. To determine the functional significance of BIN1 expression we ectopically expressed BIN1 isoforms in NB cell lines with and without MYCN amplification, and assessed clonogenic growth. RESULTS: Four predominant BIN1 isoforms resulting from alternative splicing of exon 12A (a neural tissue-specific exon) and exon 13 (a Myc-binding domain encoding exon) were variably expressed in the 56 primary NBs. Expression of BIN1 was lower in: NBs with MYCN amplification (n = 10) compared with those without, P < 0.03; in International Neuroblastoma Risk Group high-risk NB (n = 19) compared with low- or intermediate-risk NB, P < 0.01; and in metastatic NB (n = 21) compared with localized NB, P < 0.06. BIN1 inactivation by deletion or genomic rearrangement was identified infrequently. Forced expression of BIN1 isoforms containing the Myc-binding domain (with or without exon 12A) inhibited colony formation in NB cell lines with MYCN amplification (P < 0.01) but not in those without. Forced expression of BIN1 isoforms with a MBD deletion did not inhibit colony formation in any cell line assessed. CONCLUSIONS: These data support that reduced BIN1 expression contributes to the malignant phenotype of childhood NB. As we reported previously, BIN1 may function to circumvent MycN-mediated apoptosis in NBs with MYCN amplification.

Adaptor Proteins, Signal Transducing↗

[Expression of androgen receptor isoforms in normal human prostate].

OBJECTIVE: To investigate the expression of androgen receptor (AR) isoforms in normal human prostate. METHODS: Fourteen normal prostatic specimens from donors, aged 25 on average (21-28 yr), were analyzed by high resolution isoelectric focusing (IEF). The expression of AR isoforms was demonstrated in all 14 normal human prostatic tissues. RESULTS: Four types of AR isoforms were detected with isoelectric point value at 6.5, 6.0, 5.8 and 5.3 in 14 prostatic specimens. Binding of 3H-dihydrotestosterone (DHT) to these four AR isoforms was inhibited by the addition of 100-fold excess of DHT and testosterone. No effect of progesterone, estradiol and diethylstilbestrol on tritiated hormone binding was observed. CONCLUSIONS: There are four AR isoforms in normal human prostate. The expression of AR isoforms is different from one another.

Adult↗

Differential expression and splicing isoform analysis of human Tcf-4 transcription factor in brain tumors.

Tcf family transcription factors are the downstream effectors of the Wnt signal transduction pathway that regulates developmental and oncogenetic processes among species. The alternative splicing of consecutive exons in the 3' part of the Tcf-4 gene and an error-prone A9 repeat in exon 17 have recently been examined in several tumors. To further understand the roles played by differential expression and splicing isoforms of human Tcf-4 in brain tumorigenesis, the expression of the 3' part of the Tcf-4 gene (exons 10-17) was analyzed by RT-PCR, nested RT-PCR and DNA sequencing. The results showed that at least 13 of the Tcf-4 alternative splicing isoforms were found and most of them were overexpressed in various brain tumors. L3 isoform was particularly dominant in metastasis. Several novel splicing isoforms were identified. One that contains different combinations of exon 16 (10-11-12-16-17, S5) was found in normal brain and pituitary adenoma but not in astrocytoma, meningioma or metastasis, whereas the other that contains part of intron 16, designated exon-16', was found in metastasis. Overall 23% of sequencing analysis in brain tumors exhibited frameshift mutations in an A9 repeat region of exon 17. These mutants exhibited 2-base or 1-base deletion (A7, A8) and 1-base insertion (A10). Nonetheless, in vitro functional assay showed that these mutants did not affect the transactivity of Tcf-4 comparing to wild-type Tcf-4. Collectively, our data suggest that a large number of alternative splicing isoforms may together with variable mutations of A9 repeat region maintain balanced pools of Tcf-4 isoforms during brain tumorigenesis.

Adenoma↗

[Clinical significance of PML/RARalpha isoforms in adult patients with acute promyelocytic leukemia].

To evaluate the relation of PML/RARalpha isoforms in adult APL patients to clinical therapy and prognosis, the picture of blood and bone marrow aspirates for 71 APL patients treated by induction therapy were peridically examined and the different transcripts of PML/RARalpha were assayed by nested RT-PCR. The results showed that the median WBC count (x 10(9)/L) in the patients with the short (S) and variable (V) isoform were significantly higher than that in long (L) isoform. So, the serious bleeding complications early occurred. Relapse risk for patients with S and variable isoforms were higher than that with L isoform. In conclusion, PML/RARalpha isoforms in patients with APL may be the independent prognostic factor.

Adolescent↗

Characterization of multiple isoforms of protein 4.1R expressed during erythroid terminal differentiation.

In erythrocytes, 80-kD protein 4.1R regulates critical membrane properties of deformability and mechanical strength. However, previously obtained data suggest that multiple isoforms of protein 4. 1, generated by alternative pre-mRNA splicing, are expressed during erythroid differentiation. Erythroid precursors use two splice acceptor sites at the 5' end of exon 2, thereby generating two populations of 4.1 RNA: one that includes an upstream AUG-1 in exon 2' and encodes high molecular weight isoforms, and another that skips AUG-1 in exon 2' and encodes 4.1 by initiation at a downstream AUG-2 in exon 4. To begin an analysis of the complex picture of protein 4.1R expression and function during erythropoiesis, we determined the number and primary structure of 4.1R isoforms expressed in erythroblasts. We used reverse-transcription polymerase chain reaction to amplify and clone full-length coding domains from the population of 4.1R cDNA containing AUG-1 and the population excluding AUG-1. We observed an impressive repertoire of 4.1R isoforms that included 7 major and 11 minor splice variants, thus providing the first definitive characterization of 4.1R primary structures in a single-cell lineage. 4.1R isoforms, transfected into COS-7 cells, distributed to the nucleus, cytoplasm, plasma membrane, and apparent centrosome. We confirmed previous studies showing that inclusion of exon 16 was essential for efficient nuclear localization. Unexpectedly, immunochemical analysis of COS-7 cells transfected with an isoform lacking both AUG-1 and AUG-2 documented that a previously unidentified downstream translation initiation codon located in exon 8 can regulate expression of 4.1R. We speculate that the repertoire of primary structure of 4.1R dictates its distinct binding partners and functions during erythropoiesis.

Alternative Splicing↗

Expression of cardiac troponin T isoforms in skeletal muscle of renal disease patients will not cause false-positive serum results by the second generation cardiac troponin T assay.

The purpose of this study was to determine whether the two monoclonal anti-cardiac troponin T (cTnT) antibodies used in the second generation cTnT assay (capture Ab, M11.7; detection Ab, M7) would detect expression of cTnT isoforms in skeletal muscle from chronic renal disease patients. Skeletal muscle biopsies obtained from 45 chronic renal disease patients (as well as human heart muscles and normal human skeletal muscles) were prepared for Western blot analysis and blotted with the following anti-cTnT antibodies: M 11.7; M7; JS-2, Lakeland Biomedical; 13-11, Duke University) and anti-cTnI antibody JS-1. Using the M11.7 Ab, 20 of 45 renal skeletal muscles demonstrated one to three cTnT isoforms, MW34 39 kDa. These findings were confirmed by both the Lakeland and Duke antibodies. However the BM M7 antibody detected, in two of 45 muscles, only a protein with a MW of approximately 39 kDa. All four antibodies demonstrated equivalence in detection the 39 kDa cTnT isoform expressed in heart muscle. None detected any isoforms in normal skeletal muscle. A single cTnI isoform, MW 25 kDa, was detected by JS-1 only in normal adult myocardium. Based on the antibody configuration of the second generation cTnT assay, we conclude that while cTnT isoforms are expressed in human skeletal muscle obtained from chronic renal disease patients, if released into the circulation, they would not be detected.

Adult↗

Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues.

Cell and tissue functions arise from complex interactions among numerous genes, and a systematic understanding of these functions requires isoform-resolved transcriptomic analysis of single cells with high spatial resolution. Here, we introduce an in situ RNA amplification method and its integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) to detect short RNA sequences and enable whole-transcriptome-scale, isoform-resolved spatial transcriptomics of individual cells in intact tissues. Using this approach, we imaged &#x223c;33,000 distinct RNAs-including &#x223c;23,000 genes and &#x223c;10,000 isoforms-in the mouse brain. Our data enabled systematic analyses of region- and cell-type-specific gene programs and ligand-receptor-based cell-cell communications. These data further revealed rich spatial diversity and cell-type specificity in isoform usage across numerous genes, as well as brain structures particularly rich in isoform specificity. We anticipate broad application of this method for characterizing the molecular and cellular basis of tissue functions, unlocking previously inaccessible discoveries in cell and organismal biology.

Animals↗

GABAergic axon terminals at perisomatic and dendritic inhibitory sites show different immunoreactivities against two GAD isoforms, GAD67 and GAD65, in the mouse hippocampus: a digitized quantitative analysis.

Glutamic acid decarboxylase (GAD), the gamma-aminobutyric acid (GABA)-synthetic enzyme, consists of two isoforms, GAD67 and GAD65. Although distributions of the two GAD isoforms at the somatic level are known to be heterogeneous among different subpopulations of GABAergic neurons, those at the synaptic level have not been investigated. In order to analyze quantitatively the two GAD-isoform immunoreactivities in axon terminals, we combined confocal laser scanning microscopy with digitized image analysis to measure the gray levels of immunofluorescent signals for the two GAD isoforms in a large number of individual boutons in each hippocampal and dentate layer of the mouse. Synaptic boutons exhibited lamina-specific immunoreactivities against the GAD isoforms. Boutons in the principal cell layers (stratum pyramidale of the hippocampus proper and the granule cell layer of the dentate gyrus) showed more intense immunoreactivity against GAD67 than those in the dendritic layers (strata lacunosum-moleculare, radiatum, and oriens of the hippocampus proper and the molecular layer of the dentate gyrus). By contrast, boutons in the dendritic layers showed more intense immunoreactivity against GAD65 than those in the principal cell layers. Such differential distributions could be correlated to the GAD-isoform immunoreactivities in the axon terminals originating from parvalbumin-containing neurons, a particular subpopulation of hippocampal GABAergic neurons mainly innervating the perisomatic domain of principal neurons. In addition to previously reported physiological and pharmacological differences between the GABAergic synapses on perisomatic domain and those on distal dendrites, the present results suggest a functional differentiation of GABAergic synapses between these two inhibitory sites.

Animals↗

Differential expression of C-protein isoforms in the developing heart of normal and cardiac lethal mutant axolotls (Ambystoma mexicanum).

Regulated assembly of contractile proteins into sarcomeric structures, such as A- and I-bands, is still currently being defined. The presence of distinct isoforms of several muscle proteins suggests a possible mechanism by which myocytes regulate assembly during myofibrillogenesis. Of several muscle isoforms located within the A-band, myosin binding proteins (MyBP) are reported to be involved in the regulation and stabilization of thick filaments during sarcomere assembly. The present confocal study characterizes the expression of one of these myosin binding proteins, C-protein (MyBP-C) in wild-type and cardiac lethal mutant embryos of the axolotl, Ambystoma mexicanum. C-protein isoforms are also detected in distinct temporal patterns in whole-mounted heart tubes and thoracic skeletal muscles. Confocal analysis of axolotl embryos shows both cardiac and skeletal muscles to regulate the expression of C-protein isoforms over a specific developmental window. Although the CPROAxslow isoform is present during the initial heartbeat stage, its expression is not retained in the adult heart. C-protein isoforms are simultaneously expressed in both cardiac and skeletal muscle during embryogenesis.

Ambystoma↗

Preferential expression of novel MUC1 tumor antigen isoforms in human epithelial tumors and their tumor-potentiating function.

The human MUC1 gene expresses at least 2 type 1 membrane proteins: MUC1/REP, a polymorphic high m.w. MUC1 glycoprotein often highly expressed in breast cancer tissues and containing a variable number of tandem 20 amino acid repeat units, and the MUC1/Y protein, which lacks this repeat array and, therefore, is not polymorphic. Despite their documented importance in signal transduction processes, the relative expression of the 2 isoforms in epithelial tumors is unknown. Using antibody reagents which recognize different MUC1 domains, the expression of these isoforms in malignant epithelial cells has been evaluated. A comparison of the amounts of the 2 isoforms revealed preferential expression of the novel MUC1/Y protein in breast cancer tissue samples. Furthermore, although the MUC1/REP protein is almost undetectable in HeLa cervical adenocarcinoma epithelial cells, the MUC1/Y isoform is extensively expressed in these cells. The presence of the MUC1/Y sequence as well as that of an additional tandem-repeat-array-lacking isoform, designated MUC1/X, were demonstrated by reverse transcriptase PCR amplification of RNA extracted from HeLa and ovarian carcinoma cells. It has been shown previously that the MUC1 cytoplasmic domain interacts with the SH2 domain containing GRB2 protein, which transduces signals to ras, a protein which in its activated form can lead to cell transformation. We present here data demonstrating that MUC1/Y isoform expression increases the tumorigenic potential of DA3 mouse mammary epithelial cells; in contrast, potentiation of tumorigenicity is not observed with MUC1/REP expression. Our studies thus demonstrate that expression of the MUC1 gene in epithelial tumors can give rise to substantial levels of MUC1 proteins devoid of the tandem repeat array, which are generated by alternative splicing mechanisms.

Amino Acid Sequence↗

Role of protein kinase C isoforms in locomotion of Walker 256 carcinosarcoma cells.

Treatment with low (nanomolar) concentrations of phorbol-12-myristate-13-acetate (PMA) for 5 to 30 min suppresses locomotion of Walker 256 carcinosarcoma cells, suggesting that activation of protein kinase C (PKC) is a stop signal for tumor cell locomotion. We have compared the effects of PMA on cell shape and motility with down-regulation of specific PKC isoforms. Using specific antibodies, we show that Walker carcinosarcoma cells express PKC isoforms alpha, betaI, betaII, gamma, lambda, mu, eta and zeta. Short-term incubation with PMA induced a marked shift of isoforms alpha, betaI, betaII, gamma and eta to the particulate fraction. Long-term incubation with PMA (0.1 microM, 6 hr) resulted in significant reduction of expression of conventional PKCs alpha, betaI, betaII and gamma and of the novel PKC eta to 10% to 26% of controls. Down-regulation of PKC alpha, betaI and betaII by long-term incubation with PMA was reversible after removal of PMA, whereas that of isoforms gamma and eta was not. The motile properties of cells after down-regulation of PKC isoforms were investigated. Concomitant with down-regulation of PKC isoforms, long-term incubation of cells with PMA resulted in recovery of the polar shape and the ability to migrate. Motility and polarized shape of the down-regulated cells were no longer susceptible to short-term treatment with PMA, showing that active PKC is indeed responsible for the inhibitory effects of PMA. Effects of long-term incubation with PMA on cell shape and motility were reversible. Our findings strongly suggest that PKCs alpha, betaI and betaII activated by PMA are involved in stopping Walker carcinosarcoma cell locomotion.

Animals↗

Differential intracellular sorting of the myelin-associated glycoprotein isoforms.

Myelin-associated glycoprotein (MAG), a myelin-specific protein, is expressed as two isoforms, designated as L-MAG and S-MAG. Both share identical extracellular and transmembrane domains but differ in their cytoplasmic domains. L-MAG is expressed earlier during myelination than S-MAG. These features, as well as others, suggest that the isoforms have different functions. To confirm this hypothesis, both isoforms were expressed transiently and stably in Madin-Darby canine kidney (MDCK) epithelial cells, and the localization of the isoforms was studied. In both transiently and stably transfected cells, L-MAG sorted primarily to the basolateral membrane. In single transfected cells, S-MAG sorted primarily to the apical membrane. When groups of adjacent cells became transiently transfected, S-MAG accumulated at areas of cell-cell contact within the basolateral membrane. In stably transfected cells S-MAG sorted to the basolateral membrane. The data suggest that L-MAG contains an invariable basolateral sorting signal, but that the sorting of S-MAG is dependent upon extrinsic factors, such as coexpression by adjacent (contacting) cells. As MDCK cells sort the MAG isoforms differently, these data support the hypothesis that the MAG isoforms do perform different functions.

Animals↗

Differential expression of rab3 isoforms in oligodendrocytes and astrocytes.

The small GTP-binding protein Rab3a is involved in regulated secretory pathways and is enriched in synaptic and neuroendocrine secretory vesicles. We have reported previously the developmental regulation of Rab3a in oligodendrocytes in culture and purified central nervous system myelin (Huber et al.: FEBS Lett 347: 273-278, 1994). Since multiple rab3 isoforms exist in the brain and may be associated with different secretory pathways, we have investigated the differential expression of the rab3 isoforms in oligodendrocytes, astrocytes, and Schwann cell line RT4-D6P2T. The expression of specific rab3 isoforms (rab3a-c) was detected by polymerase chain reaction (PCR) amplification and confirmed by sequence analyses. These data show that in addition to the previously reported expression in neurons, the two macroglial populations, astrocytes and oligodendrocytes, also express rab3 isoforms. Rab3b was preferentially amplified from purified, cultured astrocytes, while rab3a and rab3c were preferentially amplified from highly enriched populations of both cultured oligodendrocytes and those isolated directly from the brain by immunopanning. No novel rab3 isoform was detected in glia. These results indicate that glial cells in the brain express specific isoforms of the vesicular trafficking Rab3 protein family.

Amino Acid Sequence↗

Multiple isoforms of neuregulin are expressed in developing rat dorsal root ganglia.

Accumulating evidence suggests that neuregulin (NRG) plays special roles in the development of the mammalian nervous system. We have already identified NRG as a survival factor for Schwann cells during development. In this report, we have studied all possible NRG isoforms and expression of NRG in the developing rat dorsal root ganglia (DRG) and compared them with those of brain and spinal cord. Neural NRG isoforms comprise common immunoglobulin and epidermal growth factor domains. Various different transcripts were characterized, which arose by alternative splicing in several regions: N-terminal (exon 1 or 2), spacer (exon 5), juxtamembrane (exon 9 or 10), and cytoplasmic (exon 12, 13, or 14) domains. At least 13 novel isoforms among 16 splice variants were identified. The transmembrane isoforms of NRG are dominant forms in developing rat DRG. The mRNA expression of NRG isoforms in DRG is similar to that in spinal cord, while in brain the expression is much less. The mRNA in DRG was found at similar levels from birth to postnatal day 7 of the premyelinating stage, and it decreased afterward. Our results suggest that several NRGs, including isoforms not reported before, play a role as survival factors for Schwann cells in the premyelinating stage.

Aging↗

Rat skeletal muscle in culture expresses the alpha1 but not the alpha2 protein subunit isoform of the Na+/K+ pump.

Studies from this laboratory have shown that the physiological expression of the Na+/K+ pump in primary cultures of rat skeletal muscle increases with development. The molecular mechanisms underlying these changes are not known. Therefore, we have examined the expression of alpha and beta subunits of the Na+/K+ pump at both the protein and mRNA levels during myogenesis of primary skeletal muscle cell cultures obtained from newborn rats. Protein isoforms were identified by Western blotting techniques with specific monoclonal and polyclonal antibodies and subunit mRNA was studied with specific cDNA probes. Freshly isolated skeletal muscle from newborn rats expressed both alpha1 and alpha2 protein subunits. From day 1 after plating, primary cultures expressed only the alpha1 protein isoform. In contrast, both beta1 and beta2 isoforms were expressed in freshly isolated muscle and in primary cultures, with beta1 expression being stronger in both preparations. Studies on RNA expression showed that mRNA for alpha1, alpha2, beta1, and beta2 isoforms was identified both in freshly isolated muscle and after plating of cells in culture. These findings indicate that the lack of alpha2 protein expression in primary muscle cell cultures reflects a form of posttranscriptional regulation. There did not appear to be a quantitative difference in isoform expression as a function of age or of fusion in spite of developmental increases in Na+/K+ pump activity and its dependence on cell fusion. The lack of expression of the alpha2 subunit isoform suggests that the developmental changes in physiological expression of the Na+/K+ pump in primary cultures of skeletal muscle may be attributable either to the changes in activity of the alpha1 subunit or to differential activities of alphabeta complexes involving either of the beta subunits.

Animals↗

Coordinate changes of myosin light and heavy chain isoforms during forced fiber type transitions in rabbit muscle.

Skeletal muscle fibers are versatile entities, capable of changing their phenotype in response to altered functional demands. In the present study, fast-to-slow fiber type transitions were induced in rabbit tibialis anterior (fA) muscles by chronic low-frequency stimulation (CLFS). The time course of changes in relative protein concentrations of fast and slow myosin light chain (MLC) isoforms and changes in their relative synthesis rates by in vivo labeling with [35S]methionine were followed during stimulation periods of up to 60 days. Generally, relative synthesis rates and protein concentrations changed in parallel; i.e., fast isoforms decreased and slow isoforms increased. MLC3f, however, which turns over at a higher rate than the other light chains, exhibited a conspicuous discrepancy between a markedly reduced relative synthesis but only a moderate decrease in protein amount during the initial 2 weeks of CLFS. Apparently, MLC3f is regulated independent of MLC1f, with protein degradation playing an important role in its regulation. The exchange of fast MLC isoforms with their slow counterparts seemed to correspond to the ultimate fast-to-slow (MHCIIa-->MHCI) transition at the MHC level. However, due to an earlier onset of the fast-to-slow transition of the regulatory light chain and the delayed fast-to-slow exchange of the alkali light chains, a spectrum of hybrid isomyosins composed of fast and slow light and heavy chains must have existed transiently in transforming fibers. Such hybrid isomyosins appeared to be restricted to MHCIIa- and MHCI-based combinations. In conclusion, fiber type specific programs that normally coordinate the expression of myofibrillar protein isoforms seem to be maintained during fiber type transitions. Possible differences in post-transcriptional regulation may result in the transient accumulation of atypical combinations of fast and slow MLC and MHC isoforms, giving rise to the appearance of hybrid fibers under the conditions of forced fiber type conversion.

Adaptation, Physiological↗