Domain-encoding Exons Research Articles

SCAF4 variants are associated with epilepsy with neurodevelopmental disorders.

The genetic causes of epilepsy with unknown etiology in most patients remain unknown. The aim of this study was to elucidate the phenotype of SCAF4-related epilepsy. Trio-based whole-exome sequencing was performed in patients with epilepsy. Silico programs and protein modeling were employed to predict the damaging of variants. Previously reported SCAF4 variants were systematically reviewed to analyze the genotype-phenotype correlations. Three heterozygous variants in the SCAF4 were detected in three cases, including one missense variant and two frameshift variants. All variants were de novo. None of these variants is present in gnomAD controls. The missense variant was predicted to be damaging in silico tools. Protein modeling showed that two frameshift variants resulted in loss of domains, and the missense variant may disrupt a nearby phosphorylation site and alter the hydrogen bonds around 54C and the stability of the SCAF4 protein. Intellectual development was mildly delayed for all patients except for one with whom contact was lost. All probands experienced epilepsy as infrequent seizures, responded well to antiseizure drugs, and had a median [IQR] seizure onset age of 4 [1.75, 7.5] years. The variants in the domain-encoding exons and upstream exons exhibited a strong association with epilepsy. SCAF4 is a potential causative gene of epilepsy with neurodevelopmental disorders.

Uterine Inflammatory Myofibroblastic Tumors Frequently Harbor ALK Fusions With IGFBP5 and THBS1.

Inflammatory myofibroblastic tumor (IMT) can occur in a number of anatomic sites, including the uterus. Like its soft tissue counterpart, uterine IMT frequently expresses ALK and harbors ALK genetic rearrangements. The aim of this study is to fully characterize the genetic fusions that occur in uterine IMT. We studied 11 uterine IMTs with typical histology and 8 uterine myxoid smooth muscle tumors (5 leiomyomas, 1 smooth muscle tumor of uncertain malignant potential, and 2 leiomyosarcomas) in which the differential of IMT was considered, using a RNA-sequencing-based fusion assay to detect genetic fusions involving ALK, ROS1, RET, NTRK1/3, and other genes. ALK was expressed in 10 of 11 IMTs and 1 tumor initially categorized as a myxoid leiomyoma (granular cytoplasmic staining with paranuclear accentuation). Fusion transcripts involving ALK were identified in 9 of 10 ALK immunopositive IMTs, with 3 harboring IGFBP5-ALK, 3 harboring THBS1-ALK, 2 harboring FN1-ALK, and 1 harboring TIMP3-ALK. Among the smooth muscle tumors, IGFBP5-ALK fusion transcript was identified in only 1 ALK immunopositive case. Further review revealed that although a diagnosis of IMT was considered for the ALK immunopositive myxoid leiomyoma, this diagnosis was not initially rendered only because fluorescence in situ hybridization analysis was interpreted as negative for ALK genetic rearrangement; this case is best reclassified as an IMT. Notably, all the ALK fusions identified in our study included the transmembrane domain-encoding exon 19 of ALK. Our findings confirm the high frequency of ALK fusions in uterine IMT, with an enrichment of novel 5' ALK fusion partners (IGFBP5, THBS1, and TIMP3) and exon 19-containing ALK fusion. Given that IGFBP5 and FN1 are both situated on the same chromosome as ALK, fluorescence in situ hybridization analysis for ALK rearrangement may not be reliable and a negative result should not exclude a diagnosis of uterine IMT if the histologic features and ALK immunostaining findings are supportive.

Domain-Focused CRISPR Screening Identifies Potential Drug Targets.

Targeting protein domain-encoding exons in CRISPR-Cas9 screens can reveal genetic dependencies.

Interleukin 7 Up-regulates CD95 Protein on CD4+ T Cells by Affecting mRNA Alternative Splicing: PRIMING FOR A SYNERGISTIC EFFECT ON HIV-1 RESERVOIR MAINTENANCE

Interleukin-7 (IL-7) has been used as an immunoregulatory and latency-reversing agent in human immunodeficiency virus type 1 (HIV-1) infection. Although IL-7 can restore circulating CD4(+) T cell counts in HIV-1-infected patients, the anti-apoptotic and proliferative effects of IL-7 appear to benefit survival and expansion of HIV-1-latently infected memory CD4(+) T lymphocytes. IL-7 has been shown to elevate CD95 on CD4(+) T cells in HIV-1-infected individuals and prime CD4(+) T lymphocytes to CD95-mediated proliferative or apoptotic signals. Here we observed that through increasing microRNA-124, IL-7 down-regulates the splicing regulator polypyrimidine tract binding protein (PTB), leading to inclusion of the transmembrane domain-encoding exon 6 of CD95 mRNA and, subsequently, elevation of CD95 on memory CD4(+) T cells. Moreover, IL-7 up-regulates cellular FLICE-like inhibitory protein (c-FLIP) and stimulates c-Jun N-terminal kinase (JNK) phosphorylation, which switches CD95 signaling to survival mode in memory CD4(+) T lymphocytes. As a result, co-stimulation through IL-7/IL-7R and FasL/CD95 signal pathways augments IL-7-mediated survival and expansion of HIV-1-latently infected memory CD4(+) T lymphocytes. Collectively, we have demonstrated a novel mechanism for IL-7-mediated maintenance of HIV-1 reservoir.

Tissue- and Ligand-Specific Sensing of Gram-Negative Infection in Drosophila by PGRP-LC Isoforms and PGRP-LE

The Drosophila antimicrobial response is one of the best characterized systems of pattern recognition receptor-mediated defense in metazoans. Drosophila senses Gram-negative bacteria via two peptidoglycan recognition proteins (PGRPs), membrane-bound PGRP-LC and secreted/cytosolic PGRP-LE, which relay diaminopimelic acid (DAP)-type peptidoglycan sensing to the Imd signaling pathway. In the case of PGRP-LC, differential splicing of PGRP domain-encoding exons to a common intracellular domain-encoding exon generates three receptor isoforms, which differ in their peptidoglycan binding specificities. In this study, we used Phi31-mediated recombineering to generate fly lines expressing specific isoforms of PGRP-LC and assessed the tissue-specific roles of PGRP-LC isoforms and PGRP-LE in the antibacterial response. Our in vivo studies demonstrate the key role of PGRP-LCx in sensing DAP-type peptidoglycan-containing Gram-negative bacteria or Gram-positive bacilli during systemic infection. We also highlight the contribution of PGRP-LCa/x heterodimers to the systemic immune response to Gram-negative bacteria through sensing of tracheal cytotoxin (TCT), whereas PGRP-LCy may have a minor role in antagonizing the immune response. Our results reveal that both PGRP-LC and PGRP-LE contribute to the intestinal immune response, with a predominant role of cytosolic PGRP-LE in the midgut, the central section of endodermal origin where PGRP-LE is enriched. Our in vivo model also definitively establishes TCT as the long-distance elicitor of systemic immune responses to intestinal bacteria observed in a loss-of-tolerance model. In conclusion, our study delineates how a combination of extracellular sensing by PGRP-LC isoforms and intracellular sensing through PGRP-LE provides sophisticated mechanisms to detect and differentiate between infections by different DAP-type bacteria in Drosophila.

The novel RUNX3/p33 isoform is induced upon monocyte-derived dendritic cell maturation and downregulates IL-8 expression

RUNX proteins are heterodimeric factors that play crucial roles during development and differentiation of cells of the immune system. The RUNX3 transcription factor controls lineage decisions during thymopoiesis and T-cell differentiation, and modulates myeloid cell effector functions. We now report the characterization of the human RUNX3/p33 isoform, generated by splicing out a Runt DNA-binding domain-encoding exon, and whose transcriptional activities differ from those of the prototypic RUNX3/p44 molecule. Unlike RUNX3/p44, RUNX3/p33 is induced upon maturation of monocyte-derived dendritic cells (MDDC), and is unable to transactivate the regulatory regions of the CD11a, CD11c and CD49e integrin genes. Overexpression of RUNX3/p33 in myeloid cell lines led to diminished expression of genes involved in inflammatory responses. Moreover, overexpression of RUNX3/p33 down-modulated the basal level of IL-8 production from immature monocyte-derived dendritic cells (MDDC). Besides, siRNA-mediated knock-down of RUNX3 led to diminished levels of IL-8 RNA in immature MDDC, and modulated the neutrophil-recruiting capacity of myeloid cell line supernatants. Since IL-8 promotes neutrophil chemotaxis and degranulation during inflammatory responses, and exerts mitogenic and angiogenic actions within tumor microenvironment, our results imply that myeloid RUNX3 expression regulates the recruitment of leukocytes towards inflammatory foci and might also contribute to human cancer progression.

Abstract 2712: Heterogeneous nuclear ribonucleoprotein H1 confers transcription and transactivation of androgen receptor: Implications for prostate cancer progression in African American men

Abstract Caucasian American (CA) and other ethnic minority groups. The causes of this ethnic disparity in clinical manifestation and outcome of the disease are not well understood. Here we identified, by employing a combined approach of laser capture microdissected (LCM), suppressive subtractive hybridization (SSH), and custom race-based CaP cDNA microarray on fresh specimens, selective expression of heterogeneous nuclear ribonucleoprotein H1 (hnRNPH1) in prostate tumor cells of AA men in comparison to CA men. An ethnicity-based tissue microarray (TMA) analysis revealed selective nuclear accumulation of hnRNPH1 in tumor cells compared to adjacent normal epithelium and benign prostatic hyperplasia (BPH). We also show that hnRNPH1 up-regulates transcription, physically interact with, and confers hormone-dependent (HD) and independent (HI) transactivation of androgen receptor (AR) in CaP cells. Further, our reporter, ChIP, and EMSA analyses demonstrate hnRNPH1 binds to androgen response elements (AREs) on promoter and enhancer element of PSA gene and the ligand binding domain-encoding exons D, E and H of the AR gene, suggesting it acts as a coactivator of AR in CaP cells. Interestingly, siRNA silencing of hnRNPH1caused growth arrest and enhanced cytotoxicty of Bicalutamide in AR-expressing CaP cells. These findings support a model in which hnRNP H1 is an exclusive auxiliary factor for AR to elicit androgen-specific transcriptional regulation of androgen-regulated genes and drug resistance. Given heterogeneity of CaP and that AR is implicated in androgen independent progression of CaP, the results demonstrate a previously uncharacterized mechanism for AR-hnRNPH1 axis in disease progression and hormone refractory via enhancing HD and HI mediated transcription and transactivation of AR in a subset of prostate tumor cells in AA men. The results not only reveal racial differences in the biology of CaP, but also provide, for the first time, a new frontier for the development of diagnostic, preventive, and/or targeted therapeutic strategies to circumvent disease progression in AA men. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2712.

Structural Requirements for Multimerization of the Pathogen Receptor Dendritic Cell-specific ICAM3-grabbing Non-integrin (CD209) on the Cell Surface

The myeloid C-type lectin dendritic cell-specific ICAM3-grabbing non-integrin (DC-SIGN, CD209) recognizes oligosaccharide ligands on clinically relevant pathogens (HIV, Mycobacterium, and Aspergillus). Alternative splicing and genomic polymorphism generate DC-SIGN mRNA variants, which have been detected at sites of pathogen entrance and transmission. We present evidence that DC-SIGN neck variants are expressed on dendritic and myeloid cells at the RNA and protein levels. Structural analysis revealed that multimerization of DC-SIGN within a cellular context depends on the lectin domain and the number and arrangement of the repeats within the neck region, whose glycosylation negatively affects oligomer formation. Naturally occurring DC-SIGN neck variants differ in multimerization competence in the cell membrane, exhibit altered sugar binding ability, and retain pathogen-interacting capacity, implying that pathogen-induced cluster formation predominates over the basal multimerization capability. Analysis of DC-SIGN neck polymorphisms indicated that the number of allelic variants is higher than previously thought and that multimerization of the prototypic molecule is modulated in the presence of allelic variants with a different neck structure. Our results demonstrate that the presence of allelic variants or a high level of expression of neck domain splicing isoforms might influence the presence and stability of DC-SIGN multimers on the cell surface, thus providing a molecular explanation for the correlation between DC-SIGN polymorphisms and altered susceptibility to HIV-1 and other pathogens.

Immunoglobulin heavy chain constant region of five Acipenseridae: cDNA sequence and evolutionary relationship

The immunoglobulin M (IgM) heavy chain constant region genes of Russian sturgeon ( Acipenser gueldenstaedtii), Sterlte sturgeon ( Acipenser ruthenus), Amur sturgeon ( Acipenser schrenckii), Chinese sturgeon ( Acipenser sinensis) and Great sturgeon ( Huso huso) were cloned and analyzed with molecular biology and bioinformatics methods. We cloned IGH nucleic acid sequences by RT-PCR using the specific primer, then determined the characteristics and functions of the amino acid sequences. The gene contains four constant region domain-encoding exons (CH1–4), of which CH4 sub-regions were the most conserved in IgM heavy chain constant region domain and had the highest identity within all the experimental species. According to the analysis of the phylogenetic tree, the variation expectation value ( K aa), and species differentiation time ( T) in the CH4 sub-region, we found that Chinese sturgeon and the other five sturgeon form one whole bifurcation of the tree, while, among the five left, Amur sturgeon and Huso sturgeon, Russian sturgeon and Siberian sturgeon (data from GenBank), Sterlte itself forms three other bifurcations. This result can clearly explain the relations of taxonomic status, geographical distribution and evolution among the species studied.

Denaturing- HPLC and HR-1 Melter-Based Detection of ABL Mutations in Patients with Chronic Myelogenous Leukemia (CML).

Imatinib mesylate is the first line of drug for CML since its ability to induce durable remissions in most patients with Philadelphia-positive leukemias and cytogenetic responses in most patients with chronic-phase CML. Although Imatinib mesylate has revolutionized current chronic myeloid leukemia therapy the phenomenon of relapse because of the emergence of resistance were observed. There were well-known mutations in kinase domain that confer resistance despite continued Imatinib mesylate chemotherapy and number of resistance-conferring mutation is increasing. In this study we systematically scanned kinase domain-encoding exon 5, 7, 8, 9, 10 and 11 from genomic DNA of 79 patients with CML to identify novel mutation using denaturing high-performance liquid chromatography (dHPLC) and HR-1 melter (Idaho Technology). In total 15 mutations in the regions were identified and three mutations are found to be novel and two were located in the catalytic domain region (F359I and E374K). Since these two mutations were identified in patients with primary and secondary resistance respectively, it might be classified into resistance-conferring mutation conditional on further functional evaluation. Also we found P499L mutation in the C-terminus and interestingly we detected E478Q in six patients with CML. Analysis with dHPLC and HR-1 screening after PCR amplification proved to be accurate and effective methods to isolate mutation. In addition dHPLC and HR-1 more sensitive compared to PCR direct sequencing methods since two mutations which were not detected by direct sequencing were confirmed only after subcloning of PCR products and sequencing. Taken together, we designed six PCR amplicons encompassing the kinase domain of abl kinase and screened for novel mutations patients with CML. Out of fourteen mutations identified two novel mutations in the catalytic domain need further investigation to understand if they contribute to the acquirance of imatinib mesylate resistance

The Relationship Between Domain Duplication and Recombination

Protein domains represent the basic evolutionary units that form proteins. Domain duplication and shuffling by recombination are probably the most important forces driving protein evolution and hence the complexity of the proteome. While the duplication of whole genes as well as domain-encoding exons increases the abundance of domains in the proteome, domain shuffling increases versatility, i.e. the number of distinct contexts in which a domain can occur. Here, we describe a comprehensive, genome-wide analysis of the relationship between these two processes. We observe a strong and robust correlation between domain versatility and abundance: domains that occur more often also have many different combination partners. This supports the view that domain recombination occurs in a random way. However, we do not observe all the different combinations that are expected from a simple random recombination scenario, and this is due to frequent duplication of specific domain combinations. When we simulate the evolution of the protein repertoire considering stochastic recombination of domains followed by extensive duplication of the combinations, we approximate the observed data well. Our analyses are consistent with a stochastic process that governs domain recombination and thus protein divergence with respect to domains within a polypeptide chain. At the same time, they support a scenario in which domain combinations are formed only once during the evolution of the protein repertoire, and are then duplicated to various extents. The extent of duplication of different combinations varies widely and, in nature, will depend on selection for the domain combination based on its function. Some of the pair-wise domain combinations that are highly duplicated also recur frequently with other partner domains, and thus represent evolutionary units larger than single protein domains, which we term "supra-domains".

Structures of two major histocompatibility complex class I genes of the rainbow trout (Oncorhynchus mykiss).

Here we describe two rainbow trout major histocompatibility complex (MHC) class I genes characterized from lambda phage genomic clones prepared from a single fish. Clone GC71 contains all exons except a leader peptide-encoding exon. An open reading frame is maintained, and thus the gene MhcOnmy-U71 could be expressed in this individual. The class I gene found on clone GC41 lacks exons encoding the leader peptide and cytoplasmic domain. This gene, MhcOnmy-U41p, is a pseudogene due to a deletion in the alpha(2) domain-encoding exon causing premature termination. Both the Onmy-U71 and Onmy-U41p genes are distinguished by long introns between the exons encoding the alpha(1) and alpha(2) domains. Clone GC41 also contains the 3' exons of the LMP7/ PSMB8 gene encoding the gamma-interferon-induced proteosome subunit of rainbow trout.

Exon structure of the nuclear factor I DNA-binding domain from C. elegans to mammals.

The Nuclear Factor I (NFI) family of DNA-binding proteins is essential for adenovirus DNA replication and the transcription of many cellular genes. Mammals have four genes encoding NFI proteins, C. elegans has only a single NFI gene, and prokaryotes have none. To assess the relationship between members of this unusually small family of transcription/replication factors, we mapped the chromosomal locations of the four murine NFI genes and analyzed the exons encoding the DNA-binding domains of the mouse, Amphioxus, and C. elegans NFI genes. The four murine NFI genes are on Chrs 4 (Nfia and Nfib), 8 (Nfix), and 10 (Nfic), suggesting early duplication of the genes and dispersal throughout the genome. The DNA-binding domains of all four NFI genes are encoded by large (532 bp) exons with identical splice acceptor and donor sites in each. In contrast, the C. elegans nfi-1 gene has four phased introns interrupting this DNA-binding, domain-encoding exon, and the last exon extends 213 bp past the splice site used in all four murine genes. In addition, the introns present in C. elegans nfi-1 are missing from the NFI genes of Amphioxus and all mammalian genomes examined. This analysis of the exon structure of the C. elegans and murine NFI genes indicates that the murine genes were probably generated by duplication of a C. elegans-like ancestral gene, but that significant changes have occurred in the genomic organization of either the C. elegans or murine NFI genes during evolution.

Characterization of the gene for the membrane and secretory form of the IgM heavy‐chain constant region gene (Cμ) of the cow (Bos taurus)

Our present understanding of the evolution of immunoglobulins is derived from a few vertebrate species. In order to obtain additional information on the development of the humoral immune system, we cloned and determined the nucleotide sequence of the bovine cDNA and genomic IgM heavy-chain constant region gene (C mu). The gene contains four constant region domain-encoding exons (CH1 to CH4) and two exons encoding the transmembrane domain (TM1, TM2), expressed in the membrane-bound receptor form of the IgM. The sequence of a cDNA clone encoding the 3' portion of the membrane form of the mu-chain revealed that the TM1 exon is spliced to the CH4 exon, as occurs in other mammals. Comparison of deduced amino acid sequence data from different vertebrates revealed a high similarity to sheep C mu (88%) and a lower degree of similarity to pig (62%), rat (62%), rabbit (58%) human (56%), hamster (55%), mouse (54%), chicken (28%) and horned shark (22%) C mu.

Characterization of the bovine epsilon gene.

Immunoglobulin E is quantitatively a minor immunoglobulin class in serum, but nevertheless the major class of antibody mediating type I hypersensitivity reactions and hence, type I allergic phenomena. The bovine epsilon gene is one of the as yet uncharacterized mammalian immunoglobulin genes. We have therefore cloned and determined the cDNA sequence and genomic organization of the gene. It contains four constant region domain-encoding exons (CH1 to CH4) with a high homology to sheep C epsilon (87%) and to a lower degree to dog (62%), horse (58%), chimpanzee, orangutan, human (55%), mouse (52%) and rat (52%) C epsilon genes. Southern blot analysis of bovine genomic DNA, revealed the existence of a single C epsilon gene with a presence of allelic restriction fragment length polymorphism (RFLP).

Soluble Fcγ Receptor, FcγRIIa2, is Present in Two Forms in Human Serum and is Increased in Patients: With Stage C Chronic Lymphocytic Leukemia

Human Fcγ receptor type II (FcγRII/CD32) can be produced in a soluble form, termed FcγRIIa2, which contains the extra- and intracellular regions of the receptor, due to an alternative splicing of the transmembrane domain-encoding exon. We show that human sera contain two forms of FcγRIIa2. A full-length secreted protein, which has a 32 kDa backbone, can be detected only in some sera while all sera contain a C-terminal truncated form, lacking part of the intracytoplasmic tail, and exhibiting a 24 kDa protein backbone. The 24 kDa form is significantly increased in sera from stage C patients with B chronic lymphocytic leukemia, compared to healthy donors, stage A and B CLL patients, or CLL patients in complete remission.

Exon-intron organization of fish major histocompatibility complex class II B genes.

Major histocompatibility complex (Mhc) molecules bind self and foreign peptides and present them to lymphocytes for recognition. Activation of lymphocytes by Mhc-bound foreign peptides leads to specific immune response against parasites. The Mhc genes have been studied extensively in mammals and birds but much less in other vertebrate classes. In this communication we provide the first description of the exon-intron organization of class II beta-chain-encoding genes from the teleost fish Aulonocara hansbaenschi, family Cichlidae. Each of the genes consists of six exons, E1 through E6, encoding the leader peptide (E1), beta 1 domain (E1+E2), beta 2 domain (E3+E4), connecting peptide (E5), transmembrane region (E5), cytoplasmic domain (E5+E6), and the 3' untranslated region (E6). The exons are separated by relatively short introns, the length of the longest intron being 1.3 kilobase pairs. An important difference between these and all other known class II B genes is that the beta 2 domain-encoding exon is split by an intron 97 base pairs in length. The intron is absent in other teleost fishes such as Brachydanio rerio. A change in the 3' splice site of intron 4 in some of the genes of A. hansbaenschi and of another cichlid fish, Cyphotilapia frontosa, has produced two extra codons at the 5' end of exon 5. Comparison of the A. hansbaenschi coding sequences with those of C. frontosa has revealed a concentration of variability in exon 2 and part of exon 3. Taken together, these observations provide evidence for the existence in cichlid fishes of at least two class II B loci which are functionally equivalent to the corresponding loci in mammals. The exon-intron organization and sequence similarities indicate that the two loci arose by duplication from a common ancestral gene.

The immunoglobulin M heavy chain constant region gene of the channel catfish,Ictalurus punctatus:an unusual mRNA splice pattern produces the membrane form of the molecule

The immunoglobulin (IgM) heavy chain constant region gene of the channel catfish, Ictalurus punctatus, has been cloned and characterized. The gene contains four constant region domain-encoding exons (CH1 to CH4) expressed in the secreted form of the immunoglobulin, and two exons encoding the transmembrane (TM) domain utilized in the lymphocyte membrane receptor form of the immunoglobulin. The sequence of a cDNA clone encoding the 3' region of the message for the membrane receptor form of the mu chain indicates that the TM1 exon is spliced directly to the CH3 exon, and not into a site within the CH4 exon, as occurs in the mammals, a shark and an amphibian. This unusual pattern of splicing, which produces a membrane heavy chain that is characteristically smaller than the secreted heavy chain, may be common to all teleost fish.

Evolution, Expression, and Chromosomal Location of a Novel Receptor Tyrosine Kinase Gene, eph

Partial sequence analysis of the genomic eph locus revealed that the splicing points of kinase domain-encoding exons were completely distinct from those of the other protein tyrosine kinase members reported, suggesting that this is the earliest evolutionary split within this family. In Northern (RNA) blot analysis, the eph gene was expressed in liver, lung, kidney, and testis of rat, and screening of 25 human cancers of various cell types showed preferential expression in cells of epithelial origin. Overexpression of eph mRNA was found in a hepatoma and a lung cancer without gene amplification. Comparison of cDNA sequences derived from a normal liver and a hepatoma that overproduces eph mRNA demonstrated that two of them were completely identical throughout the transmembrane to the carboxy-terminal portions. Southern blot analysis of DNAs from human-mouse hybrid clones with an eph probe showed that this gene was present on human chromosome 7.

Evolution, expression, and chromosomal location of a novel receptor tyrosine kinase gene, eph.

Partial sequence analysis of the genomic eph locus revealed that the splicing points of kinase domain-encoding exons were completely distinct from those of the other protein tyrosine kinase members reported, suggesting that this is the earliest evolutionary split within this family. In Northern (RNA) blot analysis, the eph gene was expressed in liver, lung, kidney, and testis of rat, and screening of 25 human cancers of various cell types showed preferential expression in cells of epithelial origin. Overexpression of eph mRNA was found in a hepatoma and a lung cancer without gene amplification. Comparison of cDNA sequences derived from a normal liver and a hepatoma that overproduces eph mRNA demonstrated that two of them were completely identical throughout the transmembrane to the carboxy-terminal portions. Southern blot analysis of DNAs from human-mouse hybrid clones with an eph probe showed that this gene was present on human chromosome 7.