Leukocyte and fibroblast interferon genes are located on human chromosome 9

Cloning of human Type I interferon cDNAs

In the late 1970s, crude interferon samples were found to exhibit anti-tumour activity. This discovery led to the interferon as a "magic drug" for cancer patients. Many groups, including those in Tokyo, Zürich, and San Francisco, attempted to identify human interferon cDNAs. Tadatsugu Taniguchi was the first to announce the cloning of human interferon-β cDNA in the December 1979 issue of Proc. Jpn. Acad. Ser. B. This was followed by the cloning of human interferon-α by a Zürich group and interferon-γ by a group in Genentech in San Francisco. Recombinant interferon proteins were produced on a large scale, and interferon-α was widely used to treat C-type hepatitis patients. The biological functions of interferons were quickly elucidated with the purified recombinant interferons. The molecular mechanisms underlying virus-induced interferon gene expression were also examined using cloned chromosomal genes. The background that led to interferon gene cloning and its impact on cytokine gene hunting is described herein.

N-glycosylation of murine IFN-beta in a putative receptor-binding region

Human and mouse genomes contain more than 20 related genes encoding diverse type I interferons (IFNs- alpha/beta), cytokines that are crucial for resistance of organisms against viral infections. Although the amino acid sequences of various IFN-alpha/beta subtypes differ markedly, they are all considered to share a common three-dimensional structure and to bind the same heterodimeric receptor, composed of the IFNAR-1 and IFNAR-2 subunits. Analysis of available mammalian IFN-beta sequences showed that they all carry 1 to 5 predicted N-glycosylation sites. Murine IFN-beta contains three predicted N-glycosylation sites (Asn29, Asn69, Asn76), one of which (Asn29) is located in the AB loop, in a region predicted to interact with the type I IFN receptor. The aim of this work was to test if this site is indeed N-glycosylated and if this glycosylation would affect IFN antiviral activity. We showed that all three N-glycosylation sites predicted from the sequence, including Asn29, carry N-linked sugars. Mutation of individual N-glycosylation sites had a weak negative influence on IFN antiviral activity. In contrast, the complete loss of glycosylation dramatically decreased activity. Our data suggest that interaction of murine IFN-beta with the IFNAR could locally differ from that of human IFN-alpha2 and human IFN-beta.

Multiple calmodulin genes in fish

In mammals, identical calmodulin (CaM) proteins are encoded by three nonallelic genes that differ in their promoter regions and untranslated regions (UTRs). The UTRs of each of these three genes are specific for each gene and are highly conserved. In this study, sequences obtained from the GenBank and EST databases and sequencing were examined for several species of fish to ascertain whether this multi-gene one protein system exhibited in mammals extends to other vertebrates. Three genes in zebrafish (Danio rerio) designated alpha, beta, and gamma were identified. As in mammals, these genes differ in the 3'-UTR region but encode completely identical CaMs. PCR primers spanning the coding and the 3'-UTR regions were designed based on the assembled sequences and used to confirm the presence of each gene in the cDNA library. Other species of fish were also found to contain homologous genes that were closely related as indicated by phylogenetic analysis. The 3'-UTR of the alpha, beta and particularly the gamma CaM gene of fish were not found to be as conserved as the corresponding genes of mammalian species possibly due to the span of evolutionary time. Only a few short elements in the 3'-UTR were observed to be similar in fish and mammals. These short regions of identity are shared primarily between the mammalian CaM II and CaM I and the alpha gene and beta gene of fish, respectively. Thus, the multi-gene one protein system occurs among fish as well as among mammals.

Linkage of high-density lipoprotein-cholesterol concentrations to a locus on chromosome 9p in Mexican Americans

High-density lipoproteins (HDLs) are anti-atherogenic lipoproteins that have a major role in transporting cholesterol from peripheral tissues to the liver, where it is removed. Epidemiologic studies have shown that low levels of high-density lipoprotein-cholesterol (HDL-C) are associated with an increased incidence of coronary heart disease and an increased mortality rate, indicating a protective role of high concentrations of HDL-C against atherogenesis and the development of coronary heart disease. HDL-C level is influenced by several genetic and nongenetic factors. Nongenetic factors include smoking, which has been shown to decrease the HDL-C level. Exercise and alcohol have been shown to increase HDL-C levels. Decreased HDL-C is often associated with other coronary heart disease risk factors such as obesity, hyperinsulinemia and insulin resistance, hypertriglyceridemia and hypertension. Although several genes have been identified for rare forms of dyslipidemia, the genes accounting for major variation in HDL-C levels have yet to be identified. Using a multipoint variance components linkage approach, we found strong evidence of linkage (lod score=3.4; P=0.00004) of a quantitative trait locus (QTL) for HDL-C level to a genetic location between markers D9S925 and D9S741 on chromosome 9p in Mexican Americans. A replication study in an independent set of Mexican American families confirmed the existence of a QTL on chromosome 9p.

Comparative pathology of recombinant murine interferon-gamma in mice and recombinant human interferon-gamma in cynomolgus monkeys

Interferon-gamma is a highly species-specific cytokine and has the most restricted host range of activity of the interferons. Recombinant human IFN-gamma was one of the first species-specific recombinant proteins to be thoroughly assessed in conventional safety models used for xenobiotics. Acute single-dose intravenous toxicity studies with rHuIFN-gamma were performed in rats, marmosets, and squirrel monkeys with no indications of toxicity. A complete series of subchronic toxicity studies and segment I and II reproductive studies in the rat revealed no evidence of toxicity at any of the doses tested. These results suggested that studies conducted in pharmacologically nonresponsive species may not be predictive of clinical toxicity. Human IFN-gamma is active on nonhuman primate cells, though not at the same level as on human cells. Multidose studies in cynomolgus monkeys with rHuIFN-gamma for 28 or 90 days were predictive of many of the dose-limiting clinical toxicities. Qualitative similarity was observed between toxicity studies employing rHuIFN-gamma in the cynomolgus monkey and rMuIFN-gamma in the mouse. The adverse effects seen in toxicity studies with cytokines and growth factors are often exaggerated pharmacological effects of the molecules, and therefore can only be studied in a responsive species. In situations in which a high degree of species specificity is encountered, studies employing a recombinant protein in a homologous species may provide a useful test system for preclinical safety assessment.

New chromosomal mapping assignments for argininosuccinate synthetase pseudogene 1, interferon-beta 3 gene, and the diazepam binding inhibitor gene

Argininosuccinate synthetase pseudogene 1 (ASSP1), interferon-beta 3 (IFNB3) gene, and diazepam binding inhibitor (DBI) gene have previously been mapped to human chromosome 2. Their nucleotide sequences, recorded in the GENBANK data base, were used to generate DNA primers to amplify specific sequences using the polymerase chain reaction (PCR). These primers failed to amplify DNA sequences when used to analyze microcell hybrid clones containing human chromosome 2. In order to map these genes, a panel of somatic cell hybrids was analyzed by PCR with these primer sets. The results of these experiments place ASSP1 sequences on human chromosome 6, IFNB3 on human chromosome 8, and DBI on human chromosome 6.

Interferon-alpha but not -beta genes require de novo protein synthesis for efficient expression in human monocytes

Monocytes produce interferon-alpha (IFN)-alpha) and -beta when human peripheral blood mononuclear cells (PBMCs) are stimulated in vitro by Sendai virus (SV). We found that about 70% of the IFN-producing cells (IPCs) expressed both IFN-alpha and -beta mRNA; the rest expressed only IFN-beta mRNA. In the presence of the protein synthesis inhibitor cycloheximide (CHX), the frequency of IFN-alpha mRNA-containing cells, measured after 6h, was decreased by 85-90%. Results of nuclear run-on transcription assays showed that CHX inhibited IFN-alpha gene expression. The frequency of IFN-beta mRNA-containing cells was not reduced by CHX. Actually, a threefold increase was observed at the lower CHX concentrations. Studies on the kinetics of IFN-alpha/beta mRNA induction showed that CHX accelerated the appearance of IFN-beta mRNA-containing cells, increased IFN-beta mRNA levels, and delayed the normally occurring post-inductional decrease of IFN-beta mRNA. Unexpectedly, an initially normal or even accelerated IFN-alpha mRNA response was seen in the presence of CHX during the first 3-4 h after SV stimulation. This occurred in a small proportion of the potential IPCs. However, CHX prevented the subsequent marked increase of IFN-alpha mRNA levels. Preincubation of PBMCs for 6 h in conditioned medium (CM) containing IFN and other cytokines prevented the CHX-mediated inhibition of IFN-alpha mRNA. Without preincubation this was not seen. The preincubation in CM caused an accelerated appearance of IFN-alpha mRNA, resembling that of IFN-beta mRNA. The results suggest that IFN-alpha and -beta genes are differentially regulated in the same monocytes, the former requiring de novo synthesis of intracellular protein(s) for efficient expression.

De novo protein synthesis is essential to human interferon gamma gene expression by the stimulation with polyI:polyC

Transcription of human interferon (IFN) gamma gene is induced in human peripheral lymphocyte nylon-nonadherent cells (NNA cells) by double strand RNA poly I:poly C [(1985) J. Interferon Res. 5, 77-84]. In this report, the necessity of de novo protein synthesis in an early stage of IFN gamma gene expression is described. For induction of IFN gamma gene expression, only initial 4 h treatment of poly I:poly C to NNA cells is sufficient. Addition of inhibitor of protein synthesis, cycloheximide (CHX), at an early stage of induction periods (0-4 h) inhibits the IFN gamma induction by poly I:poly C. Cell free translation assay using RNAs isolated from NNA cells which are induced by poly I:poly C in the presence of CHX reveals that in these RNAs, IFN gamma mRNA does not exist. These results demonstrate that CHX inhibits de novo synthesis of a certain protein (or proteins) and for lack of the protein(s), IFN gamma mRNA cannot be transcribed. The evidence is also described in this report which suggests that the essential protein(s) might be that (those) involved in protein kinase C (pkC) activation.

Lymphokines and cytokines as cancer treatment. Immunotherapy realized

Human proteins with identified effects on host responses to malignant cells have been established as effective therapeutic techniques in cancer. Lymphokines, products of activated cells of the immune system, have pleiotropic biochemical and cellular effects. These include stimulation of immune effector cell proliferation, augmentation of cytotoxicity of immune effector cells for tumor cell targets, enhancement in antigen-recognition potential by monocytes, and modulation of tumor-associated antigen expression on neoplastic cells. Interferons (IFN) and interleukin-2 (IL-2), purified to homogeneity, can induce regression of metastatic malignancy. Recombinant DNA technology has facilitated large-scale production of these and other lymphokines and cytokines. It has also made possible analyses of physical structures of the molecules themselves and has enabled creation of mutated molecules with specific, desired substitutions in their amino acid sequence. Monoclonal antibodies, directed at tumor-associated antigens, can augment antibody-dependent cell-mediated cytotoxicity and can selectively deliver cytotoxic techniques to malignant cells. Molecules that modify the host resistance to malignant disease also have potential to augment effectiveness of other cancer treatment techniques. Lymphokines, cytokines, and monoclonal antibodies, all products of biotechnology, have resulted in fulfillment of the promise of the immune system for inhibition of growth of human malignancy.

Identification of a functional allele of a human interferon-alpha gene previously characterized as a pseudogene

Three recombinant phage lambda L47 clones containing 4 alpha interferon (IFN) genes have been isolated from a newly constructed human genomic library. Each gene is an allele of a previously described IFN gene, three being only minor variants. The fourth gene SMTIII.1A is a functional allele of the psi LeIF-L gene which previously has been described only as a pseudogene. Therefore, it appears likely that other variant alleles may remain to be described and that the IFN system may be able to tolerate some degeneracy as a consequence of the large number of members of the family.

Mapping of mutation causing Friedreich's ataxia to human chromosome 9

Friedreich's ataxia is an autosomal recessive disease with progressive degeneration of the central and peripheral nervous system. The biochemical abnormality underlying the disorder has not been identified. Prompted by the success in localizing the mutations causing Duchenne muscular dystrophy, Huntington's disease and cystic fibrosis, we have undertaken molecular genetic linkage studies to determine the chromosomal site of the Friedreich's ataxia mutation as an initial step towards the isolation and characterization of the defective gene. We report the assignment of the gene mutation for this disorder to chromosome 9p22-CEN by genetic linkage to an anonymous DNA marker MCT112 and the interferon-beta gene probe. In contrast to the clinical variation seen for the disorder, no evidence of genetic heterogeneity is observed.

Human fibroblast but not lymphoid cells have unusually long polyadenylated interferon-beta 1 mRNAs

The transcription unit of human interferon-beta 1 (IFN-beta 1) mRNA was examined by chain elongation of nascent RNA in isolated nuclei of human fibroblasts and lymphoid cells induced to produce IFN. In fibroblasts, transcription proceeds beyond 2,400 nucleotides downstream from the poly(A) site of mature mRNA and appears to terminate in the region rich in Alu sequences. Northern hybridization showed the presence of a minor polyadenylated RNA species, about 3,200 nucleotides long, that hybridized to the probes derived from 3'-flanking regions of IFN-beta 1 mRNA. S1 nuclease analysis established that this long polyadenylated transcript represents a mixture of three RNA molecules with defined 3' termini. In all three mRNAs, as in mature IFN-beta 1 mRNA, the polyadenylation site was located within a few nucleotides downstream from the AAUAAA hexanucleotide consensus sequence. Surprisingly, in Namalva lymphoblastoid cells no transcription beyond the polyadenylation site of mature IFN-beta 1 mRNA could be detected either in isolated nuclei or total RNA.

Detection of human leukocyte interferon-alpha A and -alpha 2 genes in genomic DNAs by the use of deoxyoctadecyloligonucleotide probes

Two deoxyoctadecyloligonucleotides complementary to the sequence spanning a single base substitution between human leukocyte interferon (HuIFN) alpha A and alpha 2 genes were efficiently used as probes to distinguish between HuIFN-alpha A and -alpha 2 genes. At 37 degrees C or 42 degrees C under aqueous conditions (0.9 M NaCl), hybridization between both probes and the alpha A and alpha 2 genes without any mismatch was strong, whereas the hybridization with one base mismatch (alpha A probe-alpha 2 gene and alpha 2 probe-alpha A gene) was very weak or negligible. Because the single base substitution of G in the alpha 2 gene for A in the alpha A gene provides an extra HinfI site in the alpha 2 gene at the center of the sequence hybridizing to the alpha 2 probe, digestion with HinfI restriction endonuclease caused complete loss of the hybridization between the alpha 2 probe and the alpha 2 gene. PvuII digestion provides 298-bp fragments hybridizing to the probes only from the alpha A and alpha 2 genes among the known HuIFN-alpha genes. Thus, with the use of these oligonucleotide probes in combination with PvuII and PvuII-HinfI restriction endonuclease digestion, the existence of the sequences corresponding to both IFN-alpha A and IFN-alpha 2 genes in human genomic DNAs was demonstrated. The results also surprisingly indicate that these genes, formerly considered alleles because of their essential identity (1 base pair difference in the coding sequence), are not likely to be alleles, but represent closely related distinct genes.

Anti-beta-interferon antibodies inhibit the increased expression of HLA-B7 mRNA in tumor necrosis factor-treated human fibroblasts: structural studies of the beta 2 interferon involved

Recombinant Escherichia coli-derived human tumor necrosis factor (TNF) induces the 1.3-kilobase beta 2 interferon (IFN-beta 2) mRNA in human diploid fibroblasts (FS-4 strain). IFN-beta 2 is serologically related to the well-characterized IFN-beta 1 (respective antisera cross-neutralize the heterologous protein). Polyclonal and monoclonal anti-IFN-beta antibodies inhibit the increase in class I HLA gene expression (HLA-B7 mRNA) in TNF-treated FS-4 cells suggesting that TNF-induced IFN-beta 2 mediates the enhancing effect of TNF on HLA gene expression in human fibroblasts. The structure of this autocrine human interferon has been determined. A cDNA library was prepared from polyadenylylated RNA extracted from TNF-induced FS-4 cells, and eight IFN-beta 2 cDNA clones were isolated using a 21-nucleotide synthetic oligonucleotide probe. The 1128-nucleotide sequence of IFN-beta 2 mRNA and the 212-amino acid sequence of the IFN-beta 2 protein were deduced from these cDNA clones. The amino acid sequences of the serologically related human IFN-beta 1 and -beta 2 were compared using the Sellers TT metric algorithm for locating similarities and using the pattern scoring method for evaluating the observed similarities. IFN-beta 1 and -beta 2 each contain a segment that is approximately 100 amino acids including 39 amino acids that are aligned and identical in the two proteins. The hydropathic index plots across these segments in the two proteins are also strikingly similar. The region of similarity between IFN-beta 1 and -beta 2 includes a section that is also highly conserved in all IFN-alpha species sequenced. Thus IFN-beta 2 shares structural similarities with other human interferons that also preferentially increase class I HLA gene expression.

Molecular cloning and sequencing of a gene encoding biologically active porcine alpha-interferon

Nine distinct genomic clones containing human alpha 1-interferon (IFN-alpha 1) related sequences were isolated from a porcine genomic library constructed in phage lambda. Restriction mapping and Southern blot analysis revealed that these clones contained a total of 10 potential porcine IFN-alpha genes or pseudogenes belonging to a multigene family of at least 12 members. One of these genes was subcloned in plasmid pUC8 and the recombinant plasmid obtained was shown to direct the synthesis of a low but detectable IFN-alpha activity in Escherichia coli JM103. The sequence of this porcine IFN-alpha gene (Po IFN-alpha 1) was determined. As expected, it contained no introns and encoded a 189-amino-acid-long preprotein with a putative signal peptide of 23 residues. The homology to human (Hu)IFN-alpha 1 was 78.5% at the nucleotide level and 64% at the amino acid level.

Human chromosome 7 carries the beta 2 interferon gene

A cDNA clone (pAE20-4) corresponding to the 1.3-kilobase human beta 2 interferon mRNA was used as a probe in blot-hybridization experiments of DNA from a panel of human-rodent somatic cell hybrids containing overlapping subsets of human chromosomes. The DNA hybridization experiments showed that the human beta 2 interferon gene is located on human chromosome 7. This assignment is consistent with previous experimental data in which the expression of the translationally active 1.3-kilobase beta 2 interferon mRNA was assayed in various somatic cell hybrids. Blot-hybridization experiments using DNA from different human cell strains and cell lines reveal distinct EcoRI restriction fragment length polymorphisms of the human beta 2 interferon gene.

Interferon structural genes do not participate in quantitative regulation of interferon production by If loci as shown in C57BL/6 mice that are congenic with BALB/c mice at the alpha interferon gene cluster

Previous studies have shown that serum interferon (IFN) production in mice is quantitatively influenced by If loci, whose alleles determine high or low production. Although different loci influence IFN production in response to different inducers, such as Newcastle disease virus, Sendai virus, herpes simplex virus type 1, and polyriboinosinic-polyribocytidylic acid, BALB/c mice are in every instance low producers. It was therefore possible that, in addition to If loci, some feature of the BALB/c structural IFN genes contributed to low production. This was examined in the present work, in which IFN production was measured in two strains of C57BL/6 mice congenic with BALB/c at the murine alpha IFN (IFN-alpha) gene cluster on chromosome 4. One line, HW13 (B6.C-H-15c-H-16c-H-20c-H-21c/By) has a BALB/c fragment on chromosome 4 of at least 35 centimorgans which includes the BALB/c IFN-alpha gene cluster and four loci of the brown histocompatibility complex; the other line, HW13J (B6.C-H-15c/By), has a much shorter fragment (about 15 centimorgans), but it also comprises the BALB/c IFN-alpha gene cluster. We show that these mice, carrying the BALB/c IFN-alpha structural genes on a C57BL/6 background, are high IFN producers when stimulated by Newcastle disease virus, Sendai virus, herpes simplex virus type 1, or polyriboinosinic-polyribocytidylic acid. Thus, the low IFN production of BALB/c mice is not directly due to some feature of the IFN-alpha structural genes but is mainly the result of different alleles at If loci.

Assignment of two mouse genes coinduced with interferon to chromosomes 12 and X

Two murine cDNAs (pMIF20/11 and pMIF3/10) coinduced with interferon in mouse cells infected with Newcastle disease virus (NDV) were identified previously. By genomic Southern blot analysis of hamster/mouse somatic cell hybrids, the gene hybridizing with pMIF20/11 has been localized on chromosome 12 and the gene hybridizing with pMIF3/10 on chromosome X.

The gene for the human immune interferon receptor is located on chromosome 6

When 32P-labeled human recombinant immune interferon gamma (Hu-[32P]IFN-gamma) is crosslinked to human cells with disuccinimidyl suberate, a complex with a molecular size of approximately equal to 117,000 Da was identified by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The formation of this complex is inhibited when the binding is performed in the presence of excess unlabeled Hu-IFN-gamma. The specific formation of the 117,000-Da complex is not observed in mouse L cells or Chinese hamster ovary cells. This complex shows all of the criteria that identify it as the Hu-IFN-gamma receptor or its binding subunit. The same complex can be formed following binding and covalent crosslinking of Hu-[32P]IFN-gamma to some hamster-human or mouse-human somatic cell hybrids. The presence of human chromosome 6 in the hybrids is necessary and sufficient for the formation of this complex. More specifically, the long arm of chromosome 6 seems sufficient. Therefore, we have localized the gene for the Hu-IFN-gamma receptor (or its binding subunit) to the long arm of human chromosome 6. The presence of this chromosome in the somatic cell hybrids is not adequate, however, to confer antiviral resistance to the hybrids in the presence of Hu-IFN-gamma.

Segregation of restriction fragment length polymorphism in an interspecies cross of laboratory and wild mice indicates tight linkage of the murine IFN-beta gene to the murine IFN-alpha genes

Southern blot analysis with murine (Mu) interferon (IFN)-alpha cDNA of restricted genomic DNA of three inbred strains of mice belonging to the species Mus musculus domesticus (BALB/c, C57BL/6, and DBA/2) revealed only a limited degree of polymorphism. For example, with HindIII there were only two polymorphic bands out of 14 hybridizing fragments. With Mu IFN-beta cDNA there was no polymorphism at all between BALB/c and C57BL/6 in DNA restricted with seven different enzymes. In contrast, HindIII-restricted DNA of an inbred strain of wild mice (M. spretus Lataste) hybridized with the IFN-alpha probe displayed a high degree of polymorphism compared with the three strains of laboratory mice and was also polymorphic when probed with IFN-beta cDNA. Although M. musculus domesticus and M. spretus Lataste represent different species, certain interspecies crosses are possible in the laboratory. This enabled us to follow segregation of restriction fragment length polymorphism in HindIII-restricted DNA obtained from 18 backcross progeny of a (DBA/2 X M. spretus)F1 X DBA/2 interspecies cross. There was complete coincidence between the segregation of parental (DBA/2) and (DBA/2 X M. spretus)F1-type IFN-beta and IFN-alpha restriction fragment length polymorphism, indicating tight linkage of the IFN-beta and IFN-alpha genes. In addition, in 15 of 18 progeny the segregation coincided with that of the brown locus on chromosome 4, in accord with previous results obtained with the IFN-alpha probe in strains derived from crosses between BALB/c and C57BL/6 mice. Thus, the Mu IFN-beta gene is tightly linked to the Mu IFN-alpha gene cluster on chromosome 4 near the brown locus.

Human lymphotoxin and tumor necrosis factor genes: structure, homology and chromosomal localization

Human Tumor Necrosis Factor and Lymphotoxin are cytotoxic proteins which have similar biological activities and share 30 percent amino acid homology. The single copy genes which encode these proteins share several structural features: each gene is approximately three kilobase pairs in length and is interrupted by three introns. In addition, these genes are closely linked and have been mapped to human chromosome 6. However, only the last exons of both genes, which code for more than 80 percent of each secreted protein, are significantly homologous (56 percent).

Interferon-beta-related DNA on human chromosome 4

A DNA subclone (pPE-4000) derived from the lambda B4 interferon-beta-related human genomic DNA clone was used as a probe in blot-hybridization experiments of DNA from a panel of human-rodent somatic cell hybrids containing overlapping subsets of human chromosomes. The DNA hybridization experiments showed that the lambda B4 IFN-beta locus is localized to human chromosome 4. A provisional regional assignment to 4q12-qter was also obtained. Thus available hybridization data implicate human chromosomes 2, 4, and 9 in the human IFN-beta system while the available biological data also implicated human chromosome 5.

Two distinct families of human and bovine interferon-alpha genes are coordinately expressed and encode functional polypeptides

The classical human interferon-alpha (HuIFN-alpha) gene family is estimated to consist of 15 or more nonallelic members which encode proteins sharing greater than 77% amino acid sequence homology. Low-stringency hybridization with a HuIFN-alpha cDNA probe permitted the isolation of two distinct classes of bovine IFN-alpha genes. The first subfamily (class I) is more closely related to the known HuIFN-alpha genes than to the second subfamily (class II) of bovine IFN-alpha genes. Extensive analysis of the human genome has revealed a HuIFN-alpha gene subfamily corresponding to the class II bovine IFN-alpha genes. The class I human and bovine IFN-alpha genes encode mature IFN polypeptides of 165 to 166 amino acids, whereas the class II IFN-alpha genes encode 172 amino acid proteins. Expression in Escherichia coli of members of both gene subfamilies results in polypeptides having potent antiviral activity. In contrast to previous studies which found no evidence of class II IFN-alpha protein or mRNA expression, we demonstrate that the class I and class II IFN-alpha genes are coordinately induced in response to viral infection.

Family of human alpha-interferon-like sequences

An interferon-alpha-like sequence was isolated from a human genomic library by hybridization with a 15-base oligonucleotide. The sequence also showed homology to alpha-interferon and was most closely related to the leukocyte interferon-M gene fragment. The original isolate cross-hybridized to a family of sequences, 10 of which were isolated as clones. Some of these sequences were located within a few kilobases of alpha-interferon genes, consistent with our assignment of several members of the family to human chromosome 9 which also has the beta 1- and alpha-interferon genes.

Significance of similarities in patterns: an application to beta interferon-related DNA on human chromosome 2

The nucleotide sequence of a 14-kilobase (kb) region of the human beta interferon (IFN-beta)-related DNA locus on chromosome 2 (genomic DNA clone lambda B3) was determined and compared to that of the IFN-beta 1 gene by using the Sellers TT algorithm. This algorithm aligns segments of one sequence with similar segments in a second sequence. A strategy was developed for assessing the significance of similarities between DNA sequences based on a scheme that recognizes patterns or runs of identities within an alignment. The pattern score (II) thus obtained is an entropy-like measure. Numerically it is a reflection of the length of the second longest run of identity in an alignment plus a correction factor due to the other shorter identity runs in the alignment. When the IFN-beta 1 gene is compared to a random nucleotide sequence, the distribution of II scores in such comparisons fits a Gaussian function. This strategy has been used to identify seven segments along one strand of lambda B3 DNA that are related to segments in IFN-beta 1; these seven alignments have II scores greater than or equal to 3 standard deviations above the mean score obtained in comparisons between IFN-beta 1 and random nucleotide sequences. One of these alignments (section 7) has a II score 8.02 standard deviations above this mean score. The likelihood of finding an alignment statement as good as that in section 7 in a random sequence the length of the human genome is approximately 10(-7). Furthermore, the lambda B3 DNA sequence in section 7 selects the human IFN-beta 1 gene as the most significant alignment in computer searches of mammalian nucleotide sequence data bases.

The effect of murine interferon-alpha/beta on an established Rauscher murine leukemia virus-induced erythroleukemia in BALB/c mice

Rauscher murine leukemia virus (R-MuLV) induces a rapidly developing erythroleukemia in BALB/c mice. Previously, we have shown that mouse interferon-alpha/beta (Mu IFN-alpha/beta) applied shortly after virus inoculation efficiently inhibits the leukemic process (Hekman et al., 1981). Here we describe the effect of Mu IFN-alpha/beta on an established leukemia. Varying doses of Mu IFN-alpha/beta were injected over 3 days, starting 8 to 12 days after virus inoculation. The effect of Mu IFN-alpha/beta on the leukemic process was monitored by measuring the spleen weight, reverse transcriptase activity in the serum and, in selected experiments, by microscopic examination of sections of the spleen using standard histological and immunological staining techniques. Depending on the spleen weight at the start of its application (maximal about 450 mg), Mu IFN-alpha/beta caused a dramatic reduction in the number of virus-infected erythroleukemic cells in the spleen. Also, R-MuLV disappeared from the serum within 3 days. If Mu IFN-alpha/beta was injected into R-MuLV-infected mice with an already 10-fold enlarged spleen, it could only stop further development of leukemia. Results obtained with crude Mu IFN-alpha/beta preparations were confirmed with absolutely pure Mu IFN-beta.

Two distinct families of human and bovine interferon-alpha genes are coordinately expressed and encode functional polypeptides

The classical human interferon-alpha (HuIFN-alpha) gene family is estimated to consist of 15 or more nonallelic members which encode proteins sharing greater than 77% amino acid sequence homology. Low-stringency hybridization with a HuIFN-alpha cDNA probe permitted the isolation of two distinct classes of bovine IFN-alpha genes. The first subfamily (class I) is more closely related to the known HuIFN-alpha genes than to the second subfamily (class II) of bovine IFN-alpha genes. Extensive analysis of the human genome has revealed a HuIFN-alpha gene subfamily corresponding to the class II bovine IFN-alpha genes. The class I human and bovine IFN-alpha genes encode mature IFN polypeptides of 165 to 166 amino acids, whereas the class II IFN-alpha genes encode 172 amino acid proteins. Expression in Escherichia coli of members of both gene subfamilies results in polypeptides having potent antiviral activity. In contrast to previous studies which found no evidence of class II IFN-alpha protein or mRNA expression, we demonstrate that the class I and class II IFN-alpha genes are coordinately induced in response to viral infection.

Isolation of a cDNA clone corresponding to an X-linked gene family (XLR) closely linked to the murine immunodeficiency disorder xid

The striking number of human and murine immunodeficiency disorders which map to the X chromosome suggests that genes localized on this chromosome must have important roles in lymphocyte development. At least seven distinct disorders in the human and two in the mouse disrupt lymphocyte maturation, particularly that of B cells, at characteristic stages. As functional genes mapping to the X chromosome in one mammal are found on the X chromosome in all other mammals, the same genes regulating lymphocyte development are expected to be found on the X chromosome in mouse and man. Investigations into the possible mechanisms of these X-linked disorders have been hampered by the lack of molecular probes for the genes or gene products affected; because of this, and the possibility of correlating one or more of the several hundred B- or T-cell-specific genes with a specific mutation, we surveyed 15 different B- and T-cell-specific cDNA clones for localization to the X chromosome. We report here the characterization of one of these murine cDNA clones, which hybridizes with a large, X-linked gene family, designated XLR (X-linked, lymphocyte-regulated). We show that the XLR gene family is closely linked to the X-linked immunodeficiency described in the CBA/N mouse strain (xid), by restriction fragment length polymorphism (RFLP) analysis of DNA from mice congeneic for xid. This finding, together with data on the expression of the XLR locus in B cells, indicates that this gene family either includes the locus defined by the xid mutation or is adjacent to it in a gene complex which may be important in lymphocyte differentiation.

Family of human alpha-interferon-like sequences

An interferon-alpha-like sequence was isolated from a human genomic library by hybridization with a 15-base oligonucleotide. The sequence also showed homology to alpha-interferon and was most closely related to the leukocyte interferon-M gene fragment. The original isolate cross-hybridized to a family of sequences, 10 of which were isolated as clones. Some of these sequences were located within a few kilobases of alpha-interferon genes, consistent with our assignment of several members of the family to human chromosome 9 which also has the beta 1- and alpha-interferon genes.

Characterization of a mouse interferon gene locus I. Isolation of a cluster of four alpha interferon genes

A BALB/c mouse genomic library was screened with a murine interferon alpha 2 (MuIFN-alpha 2) cDNA coding region fragment. Eight clones were isolated which contain different mouse chromosomal segments related to the MuIFN-alpha 2 probe and a 28 kilobase (kb) region of mouse genomic DNA containing four different MuIFN-alpha genes (alpha 1, alpha 4, alpha 5 and alpha 6) was identified and characterized; an intergenic 1000 nucleotide long conserved sequence was found to be associated with three of these four alpha genes, indicating that this alpha-IFN gene cluster evolved through tandem duplications. Sequence analysis revealed the absence of a polyadenylation site in the 3' untranslated region of MuIFN-alpha 1, and showed that one of the genes (alpha 4) contains an internal deletion of 5 amino acids in the coding region.

Organization, structure and expression of murine interferon alpha genes

Using a human interferon-alpha probe we have isolated recombinant phages containing murine interferon-alpha (Mu IFN-alpha) genes from a genomic library. One of these phages contained two complete Mu IFN-alpha genes and part of a third gene. The insert of a second phage held two IFN genes. This indicates that the Mu IFN-alpha genes are clustered in the genome as is the case for the analogous human genes. The nucleotide sequences of these 5 genes were determined. They show that the genes are all different, albeit highly homologous. The deduced amino acid sequences show that four of the five genes contain a putative glycosylation site. Three genes were transiently expressed in COS cells and they gave rise to protein products showing antiviral properties. The expression of the five Mu IFN-alpha genes and the Mu IFN-beta gene was studied in virus-induced mouse L cells. The individual mRNAs were visualized in a nuclease S1 experiment, using a specific probe for each gene. In RNA preparations from induced cells mRNAs for each of the five alpha genes and the beta gene were present. However, substantial differences in the amounts of the individual mRNAs were observed.

Localization of the mouse interferon-beta 1 gene to chromosome 4

Using Southern blot analysis of genomic DNA isolated from hamster/mouse somatic cell hybrids, we have mapped the mouse interferon-beta 1 gene to chromosome 4. Thus, as in humans, both the alpha- and beta-interferon genes are localized on the same chromosome in mouse.

Differential regulation of interferon synthesis in lymphoblastoid cells

We have examined the molecular mechanisms involved in the induction and regulation of expression of alpha and beta 1 human interferons (HuIFN) in Namalva cells. Cloned IFN-alpha and -beta 1 cDNAs, and antisera to purified IFN-alpha and -beta 1 were used as specific probes to determine the expression of HuIFN genes both on the RNA and protein levels. The rates of gene transcription were correlated with the relative levels of HuIFN mRNA present in induced cells and with the amounts of HuIFN peptides synthesized by these cells. The comparative rate of transcription of HuIFN-alpha and -beta 1 genes was measured in nuclei isolated from Namalva cells before and after induction. No transcription of HuIFN-alpha and -beta 1 genes was detected in nuclei isolated from the uninduced cells. The correspondence in the rate of HuIFN-alpha and -beta 1 genes transcription after virus infection with the relative levels of HuIFN mRNA in the induced cells indicates that the stimulation of HuIFN synthesis by viral infection results from the activation of the transcription of HuIFN genes. The relative levels of alpha and beta 1 induced transcripts were the same in spite of the differences in the number of copies of HuIFN-alpha and -beta 1 genes indicating that the beta 1 gene is transcribed more efficiently than the alpha genes. The steady-state levels of HuIFN-alpha and -beta 1 mRNAs in induced Namalva cells are comparable, however, the overall amount of HuIFN-beta 1 synthesized (as determined by radioimmunoassay and biological activity) is approximately 10-fold lower than that of IFN-alpha. No evidence has been found that would indicate that HuIFN-beta 1 mRNA induced in Namalva cells is different from that induced in human fibroblasts. The data indicate, however, that in Namalva cells, the IFN-beta 1 polypeptide has a higher turnover rate and slower rate of release into medium than the HuIFN-alpha polypeptides, indicating that the observed difference in the overall amounts of these two types of interferons present in the medium is due to regulation on posttranslational level.

[Interferons--research, effects and importance]

Interferons are a family of proteins synthesized by the cells of higher organisms as a first reaction to viral infections, preceding the immune response. They are also involved in the regulation of the immune system and therefore included among the lymphokines. Since they had been shown to have antitumor activity in vitro and in experimental animals, they were suggested to be powerful drugs in cancer therapy.

The gene for human fibroblast interferon (IFB) maps to 9p21

The interferons have been classified into alpha, beta, and gamma (leukocyte, fibroblast, and immune). We used a human genomic clone for beta 1 interferon IFB to determine the gene copy number in two patients with unbalanced rearrangements of 9p. Our results provide evidence for regional assignment of this gene to 9p21.

Linkage analysis of the murine interferon-alpha locus on chromosome 4

Southern blot analysis with a murine interferon-alpha2 (MuIFN-alpha2) cDNA probe revealed restriction fragment polymorphism of EcoRI- and HindIII-digested C57BL/6 and BALB/cDNA. The inheritance pattern of this polymorphism was examined using DNA from each of the seven recombinant inbred strains derived from C57BL/6 and BALB/c; the strain distribution pattern suggests linkage of INF-alpha genes to two histocompatibility loci on chromosome 4. Southern blot analysis of DNA from six bilinear congenic strains carrying different fragments of the BALB/c chromosome 4 on a C57BL/6 background showed linkage of IFN-alpha genes to the histocompatibility locus H-15. It can therefore be concluded that the IFN-alpha gene cluster is situated on chromosome 4 near the H-15 locus, between loci Mup-1 and b.

Chromosomal assignments of human genes for serine proteases trypsin, chymotrypsin B, and elastase

The genes for the serine proteases trypsin, chymotrypsin B, and elastase were chromosomally assigned in man using cDNA probes that have been isolated from a rat pancreatic cDNA library. DNA from human X rodent somatic cell hybrids was cleaved with BamHI or EcoRI and analyzed by Southern filter hybridization methods for the segregation of the genes for trypsin-1 (TRY1), chymotrypsin B (CTRB), and elastase-1 (ELA1). TRY1 was assigned to human chromosome 7q22----qter, CTRB to chromosome 16, and ELA1 to chromosome 12. Although the three genes are members of the same gene family, they are dispersed over different chromosomes.

Novel Human Leukocyte Interferon Subtype and Structural Comparison of Alpha Interferon Genes

In the cDNA library of virus-induced human leukocytes a novel subtype of IFN-alpha gene has been identified and sequenced, named IFN-alpha-N. A comparison of nucleotide sequences within the genes coding for different subtypes of human leukocyte interferon (IFN-alpha) has revealed the natural hybrid structure of individual alpha-IFNs-H,B,F, and N. Certain regions of the genes for IFN-alpha-H,B,F,N show a homology with one of the two structurally distinct groups of leukocyte interferons--either IFN-alpha-A,D or IFN-alpha-C,C1 utilized as reference standards.

The production of interferon-alpha and -beta by cloned human lymphoblastoid cells. Brief report

In our previous study we found that the ARH 77 human B lymphoblastoid cell line, originating from a patient with multiple myeloma, produced both human interferon-alpha (HuIFN-alpha) and HuIFN-beta after induction with Sendai virus. In order to examine whether IFN-alpha-producing ARH 77 cell clones can be separated from IFN-beta-producing ones, the ARH 77 line was cloned by the soft agar method. Twelve clones chosen at random were examined for IFN production and the antigenic types of IFN produced were determined. All examined clones simultaneously produced both HuIFN-alpha and HuIFN-beta, although the ratio of HuIFN-alpha to HuIFN-beta production was variable among the clones. This result suggests that one lymphoblastoid cell can produce both HuIFN-alpha and HuIFN-beta.

The tumor phenotype and the human gene map

The tumor phenotype is associated with the rearrangement of genetic information and the altered expression of many gene products. In this review, genes associated with the tumor phenotype have been arranged on the human gene map and indicate the extent to which the tumor phenotype involves the human genome. Nonrandom chromosomal aberrations that are frequently observed in tumors are presented. Altered metabolic demands of the tumor cell are reflected in altered gene expressions of a wide range of enzymes and other proteins, and these changed enzyme patterns are described. The study of oncogenes increasingly suggests that they may be significant in certain cancers, and the assignment of these genes has been tabulated. The biochemical and metabolic changes observed in tumors are complex; studying the patterns and interactions of these changes will aid our genetic understanding of the origins and development of tumors.