Identification of differentially expressed genes in spontaneously regressing melanoma using the MeLiM swine model.

Partial and some few cases of complete spontaneous regression have been observed in cutaneous melanoma patients but little is known about the molecular mechanisms involved. The Melanoblastoma-bearing Libechov Minipig (MeLiM) is a suitable animal model to study the phenomenon of spontaneous regression because MeLiM pigs exhibit naturally occurring melanomas which regress completely 6 months after birth. In this study, we used suppression subtractive hybridization (SSH) to identify molecular determinants of melanoma regression within swine melanoma tissues and melanoma cell cultures. Several markers involved in cell-adhesion, -communication, -motility, signal transduction, negative regulation of cell proliferation, transport and immune response were identified that correlated with melanoma regression whereas the main genes involved in melanin synthesis showed a strong downregulation. For the most differentially expressed genes, we validated the results obtained by SSH with qRT-PCR and with immunohistochemistry for some of them (CD9, MITF, RARRES1). Most notable, for the first time in melanoma, we identified the retinoic acid responder 1 gene (RARRES1) as a main actor of the regression process in melanoma. This first gene expression study in swine melanoma regression, may contribute to the finding of new therapeutic targets for human melanoma treatment.

Antifibrotic action of Cu/Zn SOD is mediated by TGF-beta1 repression and phenotypic reversion of myofibroblasts.

Skin fibrosis is characterized by the proliferation and accumulation of activated fibroblasts called myofibroblasts. They exhibit specific cytoskeletal differentiation, overexpress the fibrogenic cytokine TGF-beta1, synthesize excess extracellular matrix compounds and exhibit a depleted antioxidant metabolism. Recently, SOD was successfully used as an antifibrotic agent in vivo, thus challenging the postulate of established fibrosis irreversibility. We postulated that myofibroblasts could be a direct target for this therapeutic effect. To test this hypothesis, we used three-dimensional co-culture models of skin, in which specific phenotypes of normal fibroblasts versus myofibroblasts are retained. These 3-D models were treated with liposomal and carrier-free Cu/Zn SOD, and examined for their effects on cell number, cell death, and phenotypic differentiation. The results show that SOD did not induce myofibroblast cell death, whereas it significantly reduced TGF-beta1 expression, thus demonstrating that SOD might be proposed as a potent antagonist of this major fibrogenic growth factor. We also found that SOD significantly lowered the levels of the myofibroblast marker alpha-sm actin, of beta-actin, and of the extracellular matrix components alpha1(I) collagen and tenascin-C. In conclusion, our results suggest that SOD antifibrotic action occurred in vitro through the reversion of myofibroblasts into normal fibroblasts.

Opposite regulation of tenascin-C and tenascin-X in MeLiM swine heritable cutaneous malignant melanoma.

Interactions between tumour cells and surrounding extracellular matrix (ECM) influence the growth of tumour cells and their ability to metastasise. It is thus interesting to compare ECM composition in tumours and healthy tissues. Using the recently described MeLiM miniature pig model of heritable cutaneous malignant melanoma, we studied the expression of two ECM glycoproteins, the tenascin-C (TN-C) and tenascin-X (TN-X), in normal skin and melanoma. Using semiquantitative RT-PCR, we observed a 3.6-fold mean increase of TN-C RNAs in melanoma compared to normal skin. Both stromal and tumour cells synthesise TN-C. On the contrary, TN-X RNAs decreased 30-fold on average in melanoma. This opposite regulation of TN-C and TN-X RNAs was confirmed at the protein level by indirect immunofluorescence. Whereas pig normal skin displayed a discrete TN-C signal at the dermo-epidermal junction, around blood vessels and hair bulbs, the swine tumour showed enhanced expression of TN-C in these areas and around stromal and tumour cells. In contrast, normal skin showed a strong TN-X staining at the dermo-epidermal junction and in the dermis, whereas this signal almost completely disappeared in the tumour. The results presented here describe a dramatic alteration of the ECM composition in swine malignant melanoma which might have a large influence on tumourigenesis or invasion and metastasis of melanoma cells.

Identification and mapping of swine cyclin-dependent kinase inhibitor CDKN2A and CDKN2B exon 2 sequences.

We have isolated the swine homologs of human CDKN2A and CDKN2B exon 2 sequences. As in the human and mouse genomes, the exon 2 sequences of these two genes present a high level of sequence homology and are tightly linked. Using fluorescence in situ hybridization, we have mapped swine CDKN2A and CDKN2B to chromosome 1q25. This confirms the comparative mapping data among man, mouse, and swine, showing a conserved synteny among chromosome segments 9p21, 4C3-C6, and 1q25, respectively.

Unlike tenascin-X, tenascin-C is highly up-regulated in pig cutaneous and underlying muscle tissue developing fibrosis after necrosis induced by very high-dose gamma radiation.

Fibrosis is characterized by proliferation of fibroblasts and deposition of extracellular matrix (ECM). As alterations in the composition of ECM may account for its chronic extension, we studied the expression of the tenascin-C (TN-C) and tenascin-X (TN-X) ECM glycoproteins in our pig model of the effects of accidental exposures to radiation, in which cutaneous and muscle fibrosis developed after the induction of necrosis after a high single dose (160 Gy at the skin surface) of gamma rays. We found that, in the healed fibrotic dermis and underlying muscle fibrosis, the amount of TN-C mRNA was increased up to 18- and 39-fold, respectively, compared to normal dermis, whereas the level of TN-X mRNA remained almost unchanged. In analyses by Western blotting, the two main TN-C isoforms of 235-240 and 190-200 kDa increased up to 45- and 105-fold in fibrotic tissues, respectively. The large isoform was expressed more strongly than the smaller, although in healed fibrotic scar tissues their ratio was lower in protein than in RNA. Compared to unirradiated skin, an immunohistological study revealed stronger TN-C staining at the dermo-epidermal junction and in areas of remodeling in healed skin. An intense extracellular staining was observed around myofibroblasts in muscle fibrosis. Therefore, the gene encoding TN-C is highly up-regulated in fibrotic tissues, and mechanisms regulating the levels of TN-C variants occur at both the RNA and protein levels. Each isoform might play a distinct role in the chronic activation of fibrosis by differentially regulating mechanisms like cell adhesion, migration or proliferation.

Swine cytosolic malic enzyme: cDNA cloning, sequencing, and localization.

A highly significant genetic association has been found between some alleles of the swine Major Histocompatibility Complex SLA (Swine Leukocyte Antigen genetic complex) and the cytosolic malic enzymatic activity level in muscles. The aim of this study was to find out whether this genetic association was due to a close linkage of the SLA region and the gene coding for the enzyme. Since no swine cytosolic malic enzyme sequence (ME1) was available, we isolated several overlapping fragments that spanned the almost entire malic enzyme transcript both by screening of a swine cDNA library and by RT-PCR. The results indicated the existence of two transcripts of 2. 0 and 3.1 kb, which probably correspond to two alternative forms of one gene. The sequence of the transcript was highly similar to the other published mammalian cytosolic NADP+-dependent malic enzyme cDNA, especially within the four functional domains. Two major bands at 3.7 and 2.4 kb were detected on Northern blots containing the RNA from 25 tissues from fetuses and adult pigs. A high expression level was found in the adrenal gland, muscle, liver, and peripheral nerves. The analysis of malic enzyme RFLPs in five SLA informative families revealed an independent segregation of the ME1 gene from the SLA region. In situ hybridization results localized the cytosolic malic enzyme on the swine Chromosome (Chr) 1p1.2, except that the association between SLA and the malic enzyme activity level was due to a physical genetic linkage. Thus, the mechanisms underlying this association remain to be elucidated.

Distinct tissue distribution in pigs of tenascin-X and tenascin-C transcripts.

Tenascin-X and tenascin-C glycoproteins are phylogenetically conserved components of the extracellular matrix, although their specific roles remain to be determined. cDNA probes were produced from pig tenascin-X and tenascin-C genes and were used to examine the tissue distribution of the transcripts in 28 tissues from Large-White pigs, 4.5-42-months old (called adults) and 17 tissues from 87-day-old fetuses. The hybridization of Northern blots with tenascin-X probes revealed, in most tissues, a complex pattern of bands including a major band of about 13 kb, assumed to correspond to the main tenascin-X transcript. Hybridization with the tenascin-C probe showed two transcripts of 6.8 kb and 8.2 kb. The data from the ribonuclease-protection technique showed that both genes displayed large variations in the transcription levels among the tissues analysed. Overall, the tenascin-X gene was significantly expressed in two thirds of the tissues, and the tenascin-C gene in about 50% of them. The highest tenascin-X signals were observed in tendons, ligaments and, unexpectedly, in peripheral nerves. Other tissues, including colon, dermis, skin, heart, uterus, stomach, jejunum, placentae, aorta, lung, mammary and adrenal glands also exhibited significant signal intensities. In fetuses, mainly testes and skeletal muscle showed higher transcription levels than the adult counterparts. The tenascin-C gene was predominantly transcribed in the ligament, tendon, adrenal gland and colon, and more weakly in the stomach, jejunum, lung and spinal cord. In fetuses, the tenascin-C signal in the brain was higher than the signal in the brain of adult, whereas the reverse was true for the adrenal gland and the colon. Within a given tissue, the level of tenascin-X and tenascin-C transcripts varied greatly, indicating independent tenascin-X and tenascin-C transcription regulation mechanisms; this was particularly obvious in adult and fetal nerves but also in the dermis, skin, heart, uterus, placentae and aorta, where tenascin-X RNA molecules were much more abundant than those of tenascin-C. In addition, similar differences were observed in the skeletal muscle and adrenal gland of fetuses. In contrast, the amount of tenascin-C transcripts in the fetal brain and adult spinal cord was higher than those for tenascin-X. Our results draw attention to a possible specific role of tenascin-X in the peripheral nerve physiology.

The BAT1 gene in the MHC encodes an evolutionarily conserved putative nuclear RNA helicase of the DEAD family.

The BAT1 gene has previously been identified about 30 kb upstream from the tumor necrosis factor (TNF) locus and close to a NF kappa b-related gene of the nuclear factor family in the major histocompatibility complex (MHC) of human, mouse, and pig. We now show that the BAT1 translation product is the homolog of the rat p47 nuclear protein, the WM6 Drosophila gene product, and probably also Ce08102 of Caenorhabditis elegans, all members of the DEAD protein family of ATP-dependent RNA helicases. This family has more than 40 members, including the eukaryotic translation initiation factor-4A (eIF-4A), the human nuclear protein p68, and the Drosophila oocyte polar granule component vasa. BAT1 spans about 10 kb, is split into 10 exons of varying length, and encodes a protein of 428 amino acids (approximately 48 kDa). Human and pig BAT1 cDNAs display 95.6% identity in the coding region and 80% identity in the 5' and 3' noncoding regions. Several repeat sequences of different types were identified in introns of the porcine BAT1 gene. Three different mRNAs, 4.1, 1.7, and 0.9 kb, respectively, were detected in all tissues analyzed upon hybridization with porcine BAT1 cDNA. Transfection and expression of human BAT1 cDNA after tagging with a heterologous antibody recognition epitope revealed a nuclear localization of the hybrid protein. An MspI RFLP was detected in an SLA class I typed family, confirming the localization of the BAT1 gene in the porcine MHC. BAT1 thus encodes a putative nuclear ATP-dependent RNA helicase and is likely to have an indispensable function.

Sequences of the swine 21-hydroxylase gene (CYP21) and a portion of the opposite-strand overlapping gene of unknown function previously described in human.

We sequenced a 4.8 kb BamHI swine genomic fragment comprising the entire 21-hydroxylase gene (CYP21) and its 5' and 3' flanking segments. The CYP21 coding sequence spanned 3050 bp and as in other species, comprised 10 exons separated by the corresponding introns. The deduced protein corresponded to 492 amino acid residues, 8 of which differed from a previously sequenced swine CYP21 enzyme. The 5' flanking region displayed several putative cis-acting elements which may be involved in either constitutive or cyclic adenosine 3',5'-monophosphate (cAMP) dependent transcriptional expression. We also characterized within the 5' region a 139 bp repetitive element of the short interspersed nucleotide element (SINE) family located on the opposite strand. In addition, we characterized the last five exons of a human-like opposite strand gene (OSG/X) located in the swine at the 3' end of CYP21. The sequenced part of this OSG/X displayed a very strong homology with its human counterpart.

Marked genetic polymorphism of the swine steroid 21-hydroxylase gene, and its location between the SLA class I and class II regions.

Restriction fragment length polymorphism (RFLP) analysis of the swine 21-hydroxylase (CYP21) region was conducted on 31 unrelated SLA class I typed pigs, mainly Large Whites, including 15 haplotypes. Ten haplotypes were from SLA genotypic homozygotes and five were from SLA class I phenotypic homozygotes. DNA digestion with Hin dIII, TaqI and PstI, and hybridization to a 4.5-kb swine CYP21 genomic probe yielded respectively two, four and three RFLP patterns. Six patterns were identified with combined RFLP. In addition, analysis of the CYP21 region in families comprising several SLA recombinants demonstrated that the CYP21 gene lies in the DNA segment between the SLA class I and class II regions. These overall results reinforce our previous conclusion about the existence in the pig of a single 21-hydroxylase gene. The characterization of at least six CYP21 allelic patterns provides a new tool for studying the associations between the SLA region and zootechnical traits.

The swine steroid 21-hydroxylase gene (CYP21): cloning and mapping within the swine leucocyte antigen complex.

A swine genomic cosmid library constructed from a genotypically SLA homozygous Large White individual was screened with a murine genomic 21-hydroxylase probe. A clone which contained a pig 21-hydroxylase gene was isolated and after subcloning, the 5' region of the gene was sequenced. The deduced amino acid sequence corresponded almost exactly to the NH2 terminal portion of the steroid 21-hydroxylase from porcine adrenal microsomes. Comparison of the first 99 amino acid residues of both sequences revealed three substitutions comprising two leucine residues in positions 10 and 13, and one arginine residue in position 55 for our sequence, instead of threonine in position 10 and lysine in position 13 and 55 for the isolated enzyme. A swine homologous probe was derived from the isolated 21-hydroxylase gene and used for gene assignment by RFLP studies in two swine leucocyte antigen (SLA) informative families. The results demonstrate that the swine 21-hydroxylase gene is located within or close to the swine MHC. Taken together, the present results suggest the existence of a single 21-hydroxylase gene per haploid genome.

Molecular genetic analysis of the major histocompatibility complex in an ELA typed horse family.

Restriction fragment length polymorphism was studied in an ELA typed horse family which included a stallion, a mare with two full-sibs, another mare with three full-sibs and, in addition, three paternal half-sibs. DNA samples from all individuals were investigated by Southern blot analysis using three restriction enzymes (EcoRI, HindIII or TaqI) and human cDNA class I, class II (DR beta) and class III (C4) probes. In addition, a genomic class II DQ alpha probe was used. Fragments hybridized with the various probes revealed the existence of DNA sequences homologous to HLA class I, DR beta, DQ alpha and C4 genes in the horse. Polymorphic fragments were found when DNA was hybridized with class I and class II probes irrespective of the enzyme used; but hybridization with the C4 probe did not reveal variability. All polymorphic fragments segregated according to the ELA serological specificities, thus indicating a close linkage between the different revealed subregions. Banding patterns suggest that the horse possesses about 20-30 class I genes, probably more than one DR beta and DQ alpha genes and possibly only one C4 gene. The high degree of polymorphism observed suggests that molecular DNA typing may represent a potentially powerful aid to decision in parentage control determination.

Swine chromosomes: flow sorting and spot blot hybridization.

Flow cytometry analysis was applied to swine chromosomes prepared from phytohemagglutinin (PHA) stimulated peripheral blood lymphocytes. Flow karyotypes from both sexes and from t(3;7) translocation carrier females were obtained. A certain number of chromosome pairs could be assigned to various peaks. In fact, 13 peaks were observed for 18 autosomal pairs plus X and Y. Moreover, abnormalities owing to the t(3;7) translocation were readily observable. The number of base pairs for chromosomes associated with the various peaks was estimated by comparison with human flow karyotypes. The following four peaks were thus sorted: the peak assumed to represent the translocated chromosome 7 plus the normals associated with it; the corresponding peak from a normal swine; the peak assumed to contain among others the normal chromosome 7; and finally the peak corresponding to swine chromosome 1. Chromosomes of each peak were collected on Pall Biodyne membrane. Following appropriate denaturation and prehybridization, the four samples were hybridized with a human leucocyte antigen (HLA) class I 32P-labelled cDNA probe, representing most of the coding sequence of the HLA B7 gene. The results confirmed previous data from other techniques that assigned the swine MHC(SLA) to chromosome 7. Subsequently, sorted samples were hybridized with a porcine genomic Interferon alpha probe in order to confirm the mapping of this gene family on porcine chromosome 1.

Molecular genetic analyses of the major histocompatibility complex in pig families and recombinants.

Five HLA probes, one corresponding to class I genes, two corresponding to distinct class II light chain genes, DR beta and DQ beta, and two to class II heavy chain genes, DR alpha and DQ alpha, were used to analyse the genomic DNA of the pig. Three informative SLA typed families and four SLA recombinants were studied by Southern blot analysis. About 16 restriction fragments, generated by EcoR1 or Hind III endonucleases, were revealed for each individual, either with the class I probe or the DR beta probe. The number of restriction fragments which hybridized with the other probes was generally lower. Several restriction fragment-length polymorphisms were found and these segregated with SLA haplotypes. The studies on SLA recombinants showed that SLA DR beta- and DQ alpha-like genes are probably tightly clustered within the SLA-D-MLR region.

Restriction fragment length polymorphism of the major histocompatibility complex of the pig.

Human HLA cDNA probes were used to analyze the restriction fragment length polymorphism (RFLP) of the SLA major histocompatibility complex in swine. Cellular genomic DNA from 19 SLA homozygous pigs representing 13 different haplotypes was digested with restriction endonucleases Eco R1, Hind III, or Bam H1, separated by electrophoresis, and transferred onto diazobenzyloxymethyl paper by the Southern blot technique. The blots were probed with 32P-labeled class I or beta-DR class II cDNA. Depending on the haplotypes and the endonucleases used, seven to ten restriction fragments hybridized with the class I probe, and five to seven with the beta-DR probe. Their sizes ranged from 3.4 to 22 kilobase-pairs. Few bands were common to all 13 haplotypes. With all but one haplotype, identical autoradiogram patterns were obtained from unrelated, but phenotypically SLA-identical pigs, suggesting that most of the RFLP revealed were controlled by the SLA region. Further polymorphism was found in a group of seven unrelated pigs which typed serologically as SLA A15 C1 B18 homozygotes but could be divided into two subgroups, with five animals in one subgroup and two in the other, when the genomic DNA was hybridized with the class I probe. When the class II beta-DR probe was tested on the same seven pigs, another subdivision was seen, and this correlated with MLR data. These results demonstrate that HLA class I and class II probes can be used to identify certain well-established SLA haplotypes and to identify subclasses within at least one SLA haplotype.

Analysis of the sheep MHC using HLA class I, II, and C4 cDNA probes.

Four cDNA probes for the human major histocompatibility complex (MHC) were used to investigate the sheep MHC, in conjunction with serological typing for ovine lymphocyte antigen (OLA). Lymphocytes from a family (two parents and five offspring) of Romanov sheep were subjected to genomic DNA digestion by the restriction endonuclease Eco RI, followed by gel electrophoresis. A single Southern blot representing all seven individuals was then consecutively hybridized with the class I, alpha-DC, beta-DR, and C4 probes, which were originally designed to identify HLA class I, class II (DC and DR), and C4 products, respectively. Using each of the three class I/class II probes, several bands showing DNA polymorphism were detected. The segregation of these bands in the five offspring exactly paralleled the OLA haplotype segregation established by serological typing. A further eight individuals carrying haplotypes which were phenotypically identical to those in the above-mentioned family showed bands in the corresponding positions when tested with the same three probes. Using the C4 probe, no polymorphism was detected in these fifteen individuals.

Assignment of MHC in swine to chromosome 7 by in situ hybridization and serological typing.

Mapping of the MHC in swine (SLA) was achieved by direct in situ hybridization to chromosome preparations. We took advantage of the fact that the cDNA probe coding for class I HLA-B7 antigen cross-hybridizes with swine genomic DNA. By nick-translation, 35S nucleotides were incorporated to a specific activity of 2,7 10(7) cpm/ug. Analysis of 91 randomly selected labeled metaphases revealed highly significant labeling on chromosome 7. The SLA complex is most probably located at the proximal half of the long arm, as indicated in families carrying a modified chromosome 7 and heterozygous for SLA. The abnormal chromosome was always inherited with a specific haplotype whereas the other parental haplotypes were found in association with the normal 7.