Genomewide analysis of bull sperm quality and fertility traits.

Because the priority of AI industry is to identify subfertile bulls, a predictive model that allowed for the prediction of 91% bulls of low fertility was implemented based on seminological (motility) parameters and DNA status assessed both as DNA fragmentation index (DFI) and by TUNEL assay using sperm of 105 Holstein-Friesian bulls (four batches per bull) selected based on in vivo estimated relative conception rates (ERCR). Thereafter, sperm quality and male fertility traits of bulls were explored by GWAS using a high-density (777K) Illumina chip. After data editing, 85 bulls and 591,988 SNPs were retained for GWAS. Of 12 SNPs with false discovery rate <0.2, four SNPs located on BTA28 and BTA18 were significantly associated (LD-adjusted Bonferroni <0.05) with the non-compensatory sperm parameters DFI and TUNEL. Other SNPs of interest for potential association with TUNEL were found on BTA3, in the same chromosome where associations with non-compensatory in vivo bull fertility were already reported. Further suggestive SNPs for sperm membrane integrity were located on BTA28, the chromosome where QTL studies previously reported associations with sperm quality traits. Suggestive SNPs for ERCR were found on BTA18 in the vicinity of a site already associated with in vivo bull fertility. Additional SNPs associated with ERCR and sperm kinetic parameters were also identified. In contrast to other, but very few GWAS on fertility traits in bovine spermatozoa, which reported significant SNPs located on BTX, we have not identified SNPs of interest in this sexual chromosome.

Endometrial polyps with predominant stromal component are characterized by a t(6;14)(p21;q24) translocation.

Cytogenetic investigation of endometrial polyps revealed the presence of a t(6;14)(p21;q24) as the sole abnormality in three cases. All tumors showed a histopathological pattern of predominant stromal hyperplasia with scarce representation of glandular elements, suggesting that a cytogenetic subgroup characterized by the t(6;14) translocation can be associated with endometrial polyps with a preponderant component of mesenchymal origin.

Four cytogenetic subgroups can be identified in endometrial polyps.

We have cytogenetically investigated a total of 33 simple benign endometrial polyps, 7 of which have been reported previously. Clonal chromosome rearrangements are found in 19 of 33 lesions (57%). Three major cytogenetically abnormal subgroups can be distinguished: (a) those with rearrangements in the 6p21-p22 region; (b) those with rearrangements of the 12q13-15 region; (c) those with rearrangements of the 7q22 region. A normal karyotype is found in a fourth subgroup. Recombinations of the 6p21-22 region with 2q35 and 10q22, as well as rearrangements of 7q22, have not been described before. It can be concluded that endometrial polyps, like several other types of benign mesenchymal tumors, present several cytogenetically different subgroups despite a seemingly identical clinical and morphological appearance. It is mandatory, therefore, to look for a common denominator of these tumors at the molecular level.

Cytogenetic analysis of subcutaneous angiolipoma: further evidence supporting its difference from ordinary pure lipomas: a report of the CHAMP Study Group.

Subcutaneous angiolipomas are benign soft-tissue lesions consisting of two mesenchymal elements (i.e., adipose tissue and blood vessels) and having distinct clinical features. They usually are multiple, with an obvious male predominance, and hereditary occurrence has been described. Twenty subcutaneous angiolipomas from 10 patients with typical clinical and morphologic features were reviewed. All lesions had a normal karyotype. This finding is in striking contrast with ordinary lipomas, spindle-cell and pleomorphic lipomas, lipoblastomas, and hibernomas, most of which have characteristic clonal chromosomal aberrations. The normal karyotype of subcutaneous angiolipoma as well as its distinct clinical and morphologic features suggest a different pathogenesis from pure lipomas.

Combined morphologic and karyotypic study of 59 atypical lipomatous tumors. Evaluation of their relationship and differential diagnosis with other adipose tissue tumors (a report of the CHAMP Study Group).

Fifty-nine cases of atypical lipomatous tumors (ALT) of soft tissue (atypical lipomas, well-differentiated liposarcomas) were studied morphologically and cytogenetically as part of an international collaborative study. Forty-nine cases were deeply seated (including retroperitoneum), and 10 were superficial. Clonal chromosomal abnormalities were found in 55 cases (93%). Supernumerary ring or giant marker chromosomes (RGCs), the sole consistent alteration, were found in 37 ALTs (63%). They were more common in tumors that were large (p < 0.001), deeply seated (p < 0.005), that contained lipoblasts (p < 0.05), and that had marked cytologic atypia (p < 0.05). In a relatively short follow-up period (average, 3 years), only three of 59 cases recurred, one resulting in the patient's death. All three cases had RGCs. Also, five of the six cases that underwent dedifferentiation had RGCs, indicating that RGCs are associated not only with low-grade malignant behavior (in the form of local recurrence) but also with the potential for tumor progression. When the karyotypic profile of ALT was compared with that of 233 other types of adipose tissue tumors similarly analyzed by the authors, a statistically highly significant correlation (p < 0.0001) was found between ALT and RGCs. These results support the existence of ALT as a distinct tumor subtype that is different from ordinary lipoma and from spindle or pleomorphic lipoma, albeit histogenetically closely related to them. It also supports the proposed pathogenetic link between ALT and dedifferentiated liposarcoma. The association between chromosomal and morphologic findings indicates the potential role of karyotypic analysis in the differential diagnosis of ALT with ordinary lipoma, spindle or pleomorphic lipoma, hibernoma, and myxoid liposarcoma.

Combined morphologic and karyotypic study of 28 myxoid liposarcomas. Implications for a revised morphologic typing, (a report from the CHAMP Group).

Cytogenetic analysis carried out in 28 adipose tissue tumors diagnosed microscopically as myxoid liposarcoma (ML) revealed a t(12;16)(q13:p11) chromosomal translocation in 26 of the 28 cases. Morphologically, these tumors were subclassified into the following categories: well-differentiated, six cases: poorly differentiated round cell type, 17 cases: poorly differentiated spindle cell type, five cases. Poorly differentiated ML behaved in a more aggressive fashion than the well-differentiated tumors. The results of this study confirm the consistency and specificity of the t(12;16)(q13:p11) translocation as the genetic marker of ML, support the contention that liposarcomas with round cells belong to the ML category, and confirm Stout's proposal for the existence of a poorly differentiated ML composed of spindle cells. Cytogenetic analysis may be helpful in the differential diagnosis of ML with atypical lipomatous tumors, which is characteristically associated with ring and giant marker chromosomes, and of ML with lipoblastoma, which is typically associated with 8q alterations. The existence of a mixed ML-atypical lipomatous tumor remains questionable. The genetic events associated with the greater aggressiveness of the poorly differentiated types of ML remain to be determined.

Selective digestion of human metaphase chromosomes by Alu I restriction endonuclease.

Human cytological preparations have been digested with Alu I restriction endonuclease (Endo R Alu I) and subsequently stained with acridine orange. Metaphase chromosomes treated in this way revealed a clear-cut bright/ dull longitudinal differentiation. It has been postulated that these cytological findings could be related to the selective digestion, by Alu I, of all DNA with the exception of some heterochromatic, possibly satellite, fractions.

Clonal cytogenetic changes in atherosclerotic plaques including trisomy 20.

To examine the possible implications of chromosomal changes in the etiology of atherosclerotic plaques, we cytogenetically investigated cultured cells from atheromata at different sites of six patients. Fixed metaphase chromosomes from short-term cultures of cells obtained from atherosclerotic plaques were examined by GTG banding. One case, characterized by the presence of two abnormal related clones, showed numerical and structural karyotypic changes. This observation, confirms the presence of chromosome abnormalities in cells from atherosclerotic plaques, and contributes to the debate on the origin of this cell neoproliferation.

Translocation (8;12)(q13;q15) in a pediatric tumour.

A reciprocal translocation, t(8;12)(q13;q15), was found to be the sole karyotypic change in a deep-seated lipogenic tumour in a 3-year-old child. Judging from recent data on the cytogenetic characterization of adipose tumours, this finding seems to support the histopathologic diagnosis of lipoma in spite of foci of atypical cells observed at the histologic examination.

A case of dermatofibrosarcoma protuberans of the vulva with a COL1A1/PDGFB fusion identical to a case of giant cell fibroblastoma.

Dermatofibrosarcoma protuberans (DFSP) is a highly recurrent low-grade soft tissue sarcoma, which is usually located on the trunk. Presentation in the vulva is rare, with only 13 cases being reported to date, none of which have been investigated at the cytogenetic or molecular level. Specific cytogenetic abnormalities, involving chromosomes 17 and 22, are characteristic features of DFSP and giant cell fibroblastoma (GCF), a tumor closely related to DFSP. These chromosomal rearrangements result in the fusion of the COL1A1 and PDGFB genes in both lesions and show wide variation in the position of the fusion point in COL1A1. Here, we describe a case of DFSP of the vulva with a typical monotonous storiform pattern, with no foci of multinucleated giant cells. Cytogenetic analysis showed a 47,XX,+r karyotype in 50% of the cells, and molecular investigation disclosed the presence of a transcript fusing COL1A1 exon 37 to PDGFB exon 2. This is the first case of DFSP showing such a fusion point, which is intriguingly identical to that found in a GCF case, indicating that the COL1A1/PDGFB fusion point position does not seem to affect tumor morphology. This finding further underlines the very close relationship between these two morphologically distinct entities.

Uterine leiomyoma cytogenetics. II. Report of forty cases.

Chromosome analysis of 40 cultured uterine leiomyomas revealed the presence of clonal changes in 32.5% of them, confirming the cytogenetic heterogeneity within this type of tumor, mostly referable to a few cytogenetic subgroups. Preferential involvement of 12q14-15 and 14q23-24 bands in reciprocal and complex translocations was most commonly observed. Deletions of chromosome 7 and changes of chromosomes 1, 2, and to a lesser extent, chromosomes 19 and 22 were also found. Constitutional karyotype of patients bearing tumors with karyotypic abnormalities was examined. In one patient, two cells were found with t(12;14)(q14-15;q23-24) translocation and two with del(14)(q13q23-24). The latter rearrangement was also present as a clonal change in the tumor.

Deletion 7q in uterine leiomyoma: fluorescence in situ hybridization characterization on primary cytogenetic preparations.

Deletions of the long arm of chromosome 7 constitute one of the most common clonal chromosomal changes associated with uterine leiomyoma cells. Recently, the molecular cytogenetic refinement of 7q deletions in two myoma-derived cell lines, with the use of a panel of 39 ordered 7q DNA probes corresponding to 87 genetic markers, showed results in line with those obtained by loss of heterozygosity (LOH) analysis. Referring to this panel, we extended fluorescence in situ hybridization (FISH) analysis on primary cytogenetic preparations from three myomas with del(7q), thereby avoiding cell passages. This was fundamental in the maintenance of cells with del(7q) in the two cases showing mosaicism (i.e., the presence of an extra normal clone), which are prone to lose the abnormal clone in the very early passages. The data obtained, together with previously published findings on the two leiomyoma-derived cell lines, indicated a commonly deleted region of 11 cM. If the fact that the presence of normal cells may interfere with LOH analysis is taken into account, the FISH approach seems to be a reliable complementing tool for refining the deletion and analyzing the smallest overlapping region in cases with both normal and del(7q) cells.

Uterine leiomyoma cytogenetics. I. Rearrangements of chromosome 12.

Cytogenetic investigation on 19 benign tumors of uterine smooth muscle was carried out after short-term cultures. Clonal chromosome abnormalities were present in four cases; 15 had normal karyotypes. All four cases with abnormal karyotype showed changes of chromosome 12. In three cases, chromosome 12 was involved in structural rearrangements with chromosome X, 1, and 4, respectively. Breakpoints on this chromosome occurred in different regions. The fourth case had trisomy 12 and an extra deleted chromosome 2, del(2)(p22). These findings confirm the involvement of chromosome 12 in uterine leiomyoma.

Chromosomal changes in dysplastic nevi.

The dysplastic nevus is considered to be a precursor lesion of melanoma, representing one of the first steps in the progressive transformation from normal melanocyte to melanoma. Various risk degrees of developing cutaneous melanoma in patients with dysplastic nevi have been advanced, based on the presence of dysplastic nevi or melanoma or both in members of the patient's family. We report on the cytogenetic study of three nevi in a young patient with a family history of melanoma. Each nevus showed a simple clonal chromosome change. The t(6;15)(q13;q21) translocation found in one of them seems of particular significance in view of the fact that a similar one, with breakpoint at 6q13 was reported both in an acquired nevus from a patient with a family history of melanoma and in a case of cutaneous metastatic melanoma. These observations seem to support the hypothesis of the existence of a biological continuum between normal melanocyte and melanoma. Furthermore, the finding of chromosome changes similar to those associated with melanoma reinforces the need for a careful follow-up of patients with dysplastic nevi.

Chromosome changes in nonneoplastic tissue. Numerical and structural abnormalities in nasal polyps with atypical stromal cells.

Cytogenetic investigation on short-term cultures of 13 nasal polyps disclosed the presence of chromosome aberrations in three cases: one (a recurrence) showed numerical changes; the other two had structural abnormalities, an inv(12)(q15q22) in one case, a der(6)t(6;12)(q22;q15) in the other. The three cases were characterized histologically by the presence of frequent atypical stromal cells, and were positive for vimentin and smooth muscle actin. Of the remaining 10 cases, three were not analyzable, and seven had normal karyotypes, although random structural changes were seen in two of them.

Derivative 11 marker chromosome in bladder carcinoma.

Cytogenetic studies on bladder carcinomas from two patients were carried out on preparations obtained by a direct method. The chromosome mode was 49 and 55, respectively. Several karyotypic changes were found in the tumors. Moreover, the analysis of Q-banded chromosomes revealed the presence in both cases of a chromosome 11p+. These rearranged chromosomes showed a very similar banding pattern. The finding of a der(11) chromosome marker in two patients is intriguing, and suggests the possibility of nonrandom chromosome changes in bladder carcinoma, as already found in other kinds of tumors. The occurrence of chromosome #11 aberrations in tumors of the urinary tract is discussed in connection with the current theories on oncogenesis.

Cytogenetic investigation on 30 bladder carcinomas.

Cytogenetic study of 30 bladder carcinomas confirmed the heterogeneity and the complexity of the karyotypic picture in this type of tumor. Presence of numerical and/or structural chromosome aberrations was observed in all tumors. Clonal abnormalities were found in 19 cases. Chromosomes most frequently involved in changes were chromosome #1, #3 and #11(36.6%, 26.6%, and 20% of the cases respectively). Trisomy 7 and monosomy 9 were the sole abnormalities in one case each.

Uterine leiomyoma cytogenetics. III. Interphase cytogenetic analysis of karyotypically normal uterine leiomyoma excludes possibility of undetected trisomy 12.

Uterine leiomyoma, a benign tumor that histopathologically is rather homogeneous, was recently characterized cytogenetically. About 40% of the investigated tumors are associated with clonal chromosome abnormalities and five different subgroups have been identified, characterized by trisomy 12, t(12;14)(q14-15;q23-24), del(7q), t(1;2)(p36;p24), and 6p rearrangements. In our survey of 76 cases, trisomy 12 was observed in 10% of the abnormal cases. To exclude a possible underscoring of this abnormality, we reexamined 15 of the cases with normal karyotype by interphase cytogenetics using a chromosome 12 alphoid DNA probe.

Endometrial polyp: another benign tumor characterized by 12q13-q15 changes.

Clustering of aberrations to specific chromosome regions of benign tumors may indicate the location of genes related to the proliferative process. Although few endometrial polyps have been cytogenetically investigated, 6p21 band appears to be involved consistently in the chromosome changes. We report two cases of this type of benign tumor with chromosome rearrangements in 12q14-15, allowing identification of a second cytogenetic subgroup in endometrial polyps.

Comprehensive conventional and molecular cytogenetic characterization of B-CPAP, a human papillary thyroid carcinoma-derived cell line.

Cell lines derived from different thyroid tumor histotypes are useful for the in vitro study of both the phenotypic and genetic features of these cancers. Although karyotypic changes are known to be associated with thyroid lesions, the chromosome patterns of only a few cell lines have been published. Herein, we report an extensive conventional and molecular cytogenetic investigation of the human papillary thyroid carcinoma derived cell line B-CPAP. Morphological studies and expression of tumor markers in this cell line have been reported previously, but no detailed characterization on the origin of the chromosome markers is available. B-CPAP cells have a rather stable hypertriploid karyotype, with chromosome polysomies and structural chromosome abnormalities featuring whole chromosome arm imbalances. Chromosome banding revealed a main clone with nine chromosome markers, and fluorescence in situ hybridization (FISH) with whole chromosome paint (wcp), partial chromosome paint (pcp), and centromeric probes clarified their origin. The use of centromeric probes provided accurate refinement of the rearrangements classified as whole-arm translocations by banding and FISH with wcp probes. Both chromosomal and array-based comparative genomic hybridization experiments confirmed the cytogenetic characterization of this cell line. Moreover, the use of fluorescence immunophenotyping and interphase cytogenetics as a tool for the investigation of neoplasms (FICTION) technique, which simultaneously shows nuclear ploidy and cytoplasmic immunofluorescence, detailed the oncocytic feature of the cells. Intriguingly, despite their origin, they lack most of the features expressed in papillary thyroid tumor cells and have a chromosomal pattern reminiscent of that of a subgroup of oncocytic malignant thyroid tumors.