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.

Would a morphomolecular approach help in defining pseudosarcomatous myofibroblastic proliferations? A study of a heart polypoid lesion.

Many cardiac neoplasms lack pathognomonic clinical features, and this leads to controversial interpretations. As genomic changes may correlate with these malignancies and possibly aid in diagnosis, fluorescence in situ hybridisation (FISH) was used to study a polypoid lesion found incidentally at autopsy on the septal wall of the left ventricle of a 75-year-old man who had died from a heart attack. Histology and immunohistochemistry disclosed atypical stromal cells with irregular voluminous nuclei positive for vimentin and smooth muscle actin; these cells were reminiscent of those previously reported in a subset of nasal polyps showing aneuploidy. The scarce lymphoplasmocytic infiltrate hindering the diagnosis of inflammatory myofibroblastic tumours (IMT), and the presence of atypical cells, prompted the use of FISH: lack of ALK gene rearrangement and aneuploidy were observed in the irregular nuclei, supporting the diagnosis of a pseudosarcomatous myofibroblastic proliferation (PMP). These results stress that IMT and PMP may represent variants within a spectrum of myofibroblastic proliferations/tumours.

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.

Recurrent chromosome aberrations in fibrous dysplasia of the bone: a report of the CHAMP study group. CHromosomes And MorPhology.

The nosologic status of fibrous dysplasia (FD), a well-known and relatively common bone lesion, is controversial. Information collected by the CHromosomes And MorPhology (CHAMP) study group on published and unpublished cases of fibrous dysplasia shows the presence of clonal chromosome changes in at least a proportion of these lesions. The chromosome aberrations found in FD lesions have been quite variable and have included both structural and numerical changes. Two of the three cases investigated at the study group had trisomy 2 as the sole acquired anomaly. Combined with previously published data, +2 and rearrangements involving chromosome band 12p13 have each been detected in 3 of 8 cases with abnormal karyotype of 11 in which chromosomal analysis has been performed, suggesting that FD is a neoplastic lesion rather than a "dysplastic" process, as has been generally believed and as implied by its very name.

Cytogenetic-morphologic correlations in aneurysmal bone cyst, giant cell tumor of bone and combined lesions. A report from the CHAMP study group.

Aneurysmal bone cyst and giant cell tumor of bone are relatively rare bone tumors that sometimes coexist. We examined the karyotypes of 3 aneurysmal bone cysts, 12 giant cell tumors, and 3 combined lesions. All aneurysmal bone cysts showed involvement of chromosome segments 17p11-13 and/or 16q22. In addition, in 1 of the 3 giant cell tumors with secondary aneurysmal bone cyst, both chromosome bands were rearranged as well, albeit not in a balanced translocation. Seven out of 12 giant cell tumors were characterized by telomeric associations. One giant cell tumor showed a dup(16)(q13q22), suggesting the presence of a (minor) secondary aneurysmal bone cyst component, despite the absence of histological proof. Our results, combined with literature data further substantiate that segments 16q22 and 17p11-13 are nonrandomly involved in at least some aneurysmal bone cysts, irrespective of subtype (primary, secondary, intra/extraosseous, solid or classic). These findings strongly suggest that some aneurysmal bone cysts are true neoplasms. In addition, telomeric associations are the most frequent chromosomal aberrations in giant cell tumor of bone, the significance of which remains elusive. In combined giant cell tumor/aneurysmal bone cyst each component seems to retain its own karyotypic abnormality.

Cytogenetic, clinical, and morphologic correlations in 78 cases of fibromatosis: a report from the CHAMP Study Group. CHromosomes And Morphology.

Whether fibromatoses are neoplastic or reactive lesions has long been controversial and the relationship, if any, between the superficial and deep forms (desmoid tumors) are poorly understood. Clinical, pathologic, and cytogenetic data of 78 cases of fibromatosis were analyzed and correlated with each other. The results demonstrate that clonal chromosome aberrations are a common feature of this entity, being present in 46% of desmoid tumors, although less frequent in the superficial types (10%). In the deep-seated extra-abdominal fibromatoses, trisomies 8 and 20 and loss of 5q material were the only recurrent features. No correlation between +8 and local recurrence was found. Our findings provide additional evidence for the neoplastic nature of fibromatoses.

Cytogenetic evidence of clonality in cutaneous benign fibrous histiocytomas: a report of the CHAMP study group.

AIMS: Cutaneous benign fibrohistiocytic tumours are among the most common soft tissue lesions. Their biological nature, in particular whether they are neoplastic or reactive, has long been disputed. Some morphological subtypes can be confused with sarcoma. Since available karyotypic data in these lesions are scarce, this study was undertaken to determine whether their cytogenetic analysis might demonstrate clonality and might help in differential diagnosis. METHODS AND RESULTS: Thirteen karyotyped benign cutaneous fibrous histiocytomas (BFH) were morphologically reassessed and classified as ordinary BFH (eight cases), cellular BFH (four cases), and one ankle-type lesion. Five cases (38%) showed clonal cytogenetic changes, although the aberrations varied and did not correlate with histological subtypes. Karyotypic aberrations were more common in cellular BFH (3/4) than in the ordinary BFH (2/8). CONCLUSIONS: The demonstration of clonal chromosome abnormalities, in at least some cases, supports the neoplastic nature of cutaneous BFH. The karyotypic changes identified are different from those in dermatofibrosarcoma, with which cellular BFH is often confused histologically.

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.

HMGI-C and HMGI(Y) immunoreactivity correlates with cytogenetic abnormalities in lipomas, pulmonary chondroid hamartomas, endometrial polyps, and uterine leiomyomas and is compatible with rearrangement of the HMGI-C and HMGI(Y) genes.

High-mobility group (HMG) proteins are nonhistone nuclear proteins that play an important role in the regulation of chromatin structure and function. HMGI-C and HMGI(Y) are members of the HMGI family of HMG proteins, and their expression in adult tissues generally correlates with malignant tumor phenotypes. However, HMGI-C and HMGI(Y) dysregulation as a result of specific rearrangements involving 12q15 and 6p21, the respective chromosomal sites in which the HMGI-C and HMGI(Y) genes are located, is also identified in a variety of common benign mesenchymal tumors, such as lipomas and uterine leiomyomata. The general prevalence of HMGI-C and HMGI(Y) protein expression and its correlation with chromosomal alterations in these benign tumors are unknown. We analyzed 95 human tumors (20 lipomas, 21 pulmonary chondroid hamartomas, 26 uterine leiomyomata, and 28 endometrial polyps) representing a selection of the benign lesions in which karyotypic alterations involving the chromosomal regions 12q15 and 6p21 are frequently detected. All cases were successfully karyotyped and some of them analyzed by fluorescent in situ hybridization with probes spanning the HMGI-C and HMGI(Y) genes. The results of this study demonstrate that expression of HMGI-C or HMGI(Y) is a common occurrence in lipomas, pulmonary chondroid hamartomas, leiomyomata, and endometrial polyps; that it correlates with 12q15 and 6p21 chromosomal alterations (p < 0.001); and that it is compatible with rearrangement of the HMGI-C and HMGI(Y) genes. The expression pattern and cellular localization of the immunoreactivity support the view that in biphasic lesions composed of a mixture of both stromal and epithelial cells, such as pulmonary chondroid hamartoma and endometrial polyps, the mesenchymal component is the site of the HMGI genetic alterations.

Comparative cytogenetic study of spindle cell and pleomorphic leiomyosarcomas of soft tissues: a report from the CHAMP Study Group.

Leiomyosarcomas (LMS) of soft tissues frequently show complex karyotypic changes, and no specific aberration has been identified. The aim of this study was to search for recurrent chromosome aberrations in soft tissue LMSs and to correlate these, if present, with morphological and clinical parameters. From a series of soft tissue sarcomas thoroughly reexamined cytogenetically and histopathologically, 45 LMSs were retrieved; 35 were classified microscopically as spindle cell, 3 as epithelioid, and 7 as pleomorphic. Clonal chromosome changes were present in 14, 3, and 3 cases, respectively. This series was combined with 11 previously published, karyotypically abnormal pleomorphic LMSs for cytogenetic-clinico-histopathological correlations. The breakpoints were widely scattered, with no predilection of any of the recurrent breakpoints and losses to any of the morphologic subtypes. Combining numerical and unbalanced structural changes, the most frequently lost segments were 3p21-p23 (11 cases), 8p21-pter, 13q12-q13, 13q32-qter (10 cases each), 1q42-qter, 2p15-pter, 18p11 (9 cases each), 1p36, 11q23-qter (8 cases each), and 10q23-qter (7 cases). The most frequent gain was 1q12-q31 (6 cases). There was a greater frequency of losses in 1p and 8p and a lower frequency of losses in 10q and 13q in tumors that had metastasized than in localized tumors. We conclude that LMSs with clonal abnormalities display highly complex karyotypic changes and extensive heterogeneity. No significant correlation exists between these changes and age and sex of the patients, or with depth of tumor, topography, microscopic subtype, or tumor grade. Losses in 1p36 and 8p21-pter may be associated with increased risk of metastases. Comparison of our findings in soft tissue LMS with those previously reported in LMS in other locations suggest that the karyotypic profile is more dependent on site of origin than on microscopic features.

Cytogenetic characterization of peripheral nerve sheath tumours: a report of the CHAMP study group.

The findings of characteristic, sometimes pathognomonic, chromosome aberrations in several types of soft tissue tumours have not only added to our understanding of the mechanisms behind the genesis of these tumours, but have also revealed the importance of cytogenetic analysis as a diagnostic tool. For many soft tissue tumours, including peripheral nerve sheath tumours, the number of analysed cases is, however, still very low, precluding evaluations of the clinical or biological significance of different chromosomal patterns. As part of an ongoing project aiming at identifying clinical-histopathological-cytogenetic correlations among soft tissue tumours, a series of 46 benign, the vast majority of which were located in the extremities, and 20 malignant peripheral nerve sheath tumours (BPNSTs and MPNSTs, respectively) that had been successfully analysed by chromosome banding techniques were evaluated with regard to clinical, morphological, and cytogenetic features. Clonal chromosome aberrations were found in 20 BPNSTs, with abnormal karyotypes being significantly more frequent among Schwannomas than among neurofibromas. Recurrent aberrations, all of which were confined to the Schwannoma subtypes, included loss of 22q material, loss of a sex chromosome, and trisomy 7. The results show that the cytogenetic features of Schwannomas are not dependent on the site of origin. The MPNSTs, all of which had clonal chromosome aberrations, displayed complex karyotypes with numerous structural and numerical changes, except in two cases showing +7 and -22, respectively, as the sole changes. None of the recurrent imbalances was restricted to either NF1-associated or sporadic MPNST, nor was any of the imbalances significantly associated with clinical outcome. The presence of a triploid or tetraploid clone was, however, associated with grade 3 tumours and a poor prognosis. The cytogenetic findings in peripheral nerve sheath tumours show that the karyotype is a good discriminator between BPNSTs and MPNSTs, and that the pattern of aberrations among the latter may add prognostic information.

Expression of HMGIY in three uterine leiomyomata with complex rearrangements of chromosome 6.

Uterine leiomyomata (UL) are a major public health problem, yet little is known about their etiology. Genetic factors likely influence UL development and growth; for example, approximately 40% of UL have chromosomal abnormalities detectable by conventional cytogenetic analysis, including t(12;14)(q15;q23-24), rearrangements involving the short arm of chromosome 6 and interstitial deletions of the long arm of chromosome 7. Two high-mobility group (HMG) protein genes, HMGIC and HMGIY, located at 12q15 and 6p21.3, respectively, are involved in rearrangements in various mesenchymal tumors including UL. In this study, we investigated HMGIY expression in three UL with complex cytogenetic rearrangements of 6p21.3 by reverse transcriptase-polymerase chain reaction (RT-PCR) and electrophoretic shift assay (EMSA). Our findings suggest that there are multiple mechanisms for HMGIY dysregulation, which may include post-translational modification of the hmgiy protein and dysregulation due to different translocation partners. Furthermore, the mechanism dysregulating HMGIY in UL with 6p21.3 and 14q23-24 rearrangements may be similar to the mechanism dysregulating HMGIC in UL characterized as t(12;14)(q15;q23-24), because of the common involvement of an HMG gene and a gene at 14q23-24.

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.

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.

Analysis of 35 cases of localized and diffuse tenosynovial giant cell tumor: a report from the Chromosomes and Morphology (CHAMP) study group.

The karyotypes of 44 specimens from 35 patients with localized (n = 19) or diffuse (n = 16) tenosynovial giant cell tumors were studied. The majority of cases in both categories (11 of 19 localized; 12 of 16 diffuse) displayed clonal chromosomal aberrations, with a complex karyotype in three cases and a simple chromosomal aberration in the others. No difference in the distribution of karyotypic abnormalities was found between the localized and diffuse form except for trisomies (usually of chromosomes 5 and/or 7), which were more frequent in the diffuse type. The short arm of chromosome 1 (1p11-13) was most frequently rearranged, with 7 of 11 localized and 7 of 12 diffuse lesions affected. These findings indicate that the localized and diffuse forms of tenosynovial giant cell tumor might represent two morphologic manifestations of the same entity. The high frequency of clonal chromosomal abnormalities, with a clustering of structural rearrangements to 1p11-13, suggests that this disease is most likely neoplastic in nature and paves the way to search for gene(s) that might be involved in its development.

Correlation between clinicopathological features and karyotype in spindle cell sarcomas. A report of 130 cases from the CHAMP study group.

Soft-tissue tumors have proved to be a fruitful area for the identification of reproducible cytogenetic aberrations, especially among pediatric round-cell sarcomas and lipomatous tumors. Thus far, however, data regarding sarcomas of monomorphic spindle cell type have been limited and somewhat disappointing, with the notable exception of synovial sarcoma. As part of an ongoing international collaborative study, 130 karyotyped spindle-cell sarcomas were reviewed and classified histologically, without knowledge of the clinical and karyotypic data, with the aim of identifying objective correlations between morphology, karyotype, and clinical parameters. Clonal chromosomal abnormalities were identified in 82 cases studied (63%), but only in the group of synovial sarcomas was there clear correlation between the cytogenetic findings, in the form of a consistent t(X;18)(p11;q11), and morphology. Among leiomyosarcomas (41 cases) and malignant peripheral nerve sheath tumors (MPNSTs; 27 cases) as well as in individual examples of rarer entities, there was a general tendency for karyotypic complexity associated with frequent loss or rearrangement of chromosome arms 1p, 10p, 11q, 12q, 17p, and 22q. Rearrangements of 17q (the region of the NF1 gene) were seen in 9/27 (33%) of MPNSTs. Among nine cases of solitary fibrous tumor (in which previous cytogenetic data are very limited) no consistent aberrations were identified. We conclude that, with the exception of synovial sarcoma, most spindle-cell sarcomas share with pleomorphic sarcomas the tendency for karyotypic complexity. There was no indication (in most of these lesions) that detectable cytogenetic aberrations could either facilitate their diagnosis or help to determine prognosis. There is a clear need to further study and understand the significance of multiple chromosomal abnormalities in this group of mesenchymal neoplasms with the particular goal of determining their role in the process of tumor development.

Establishment and characterization of a human neuroectodermal cell line (TB) from a cerebrospinal fluid specimen.

We have established a cell line (TB) from a cerebrospinal fluid (CSF) specimen of a patient with a primary leptomeningeal melanomatosis. TB cell line was immunoreactive with the antibodies for low molecular weight neurofilament protein, vimentin, neuron-specific enolase, chromogranin, synaptophysin and HMB-45 (an antibody sensitive and specific for melanoma). When TB cells were transplanted into nude mice, the same immunohistochemical pattern present in cultured cells was found but surprisingly, a positive staining for desmin was observed. Significant amounts of serotonin and its metabolite were detectable. Retinoic acid but not nerve growth factor was able to induce differentiation towards a neuronal phenotype. In summary, TB cells represent primitive neuroectodermal cells having the potential for neuronal, myoblastic and possibly melanoblastic differentiation.