Loss Of Heterozygosity For Markers Research Articles

MON-321 Metastatic Melanoma with Unknown Primary Site in a Patient with Multiple Endocrine Neoplasia Type 1

Background: MEN1 is a rare hereditary tumor syndrome caused by germline inactivating mutations of the tumor suppressor gene MEN1 and is characterized by a predisposition to endocrine tumors primarily of parathyroid, enteropancreatic, and anterior pituitary origin, as well as nonendocrine neoplasms. Cutaneous manifestations mainly include lipomas, angiofibromas, and collagenomas. Melanoma has been observed in MEN1 with 9 cases described in the literature, including 2 cases with unknown primary site (Nord et al. 2000; Baldauf et al. 2009; Brown et al. 2015). Clinical Case: A 45 year old man with MEN1 syndrome manifesting as primary hyperparathyroidism, metastatic pancreatic neuroendocrine tumor (NET), Zollinger-Ellison syndrome, nonfunctional pituitary microadenoma, anterior mediastinal mass and skin angiofibromas presented with a left neck mass that developed over 1 year. CT neck confirmed a 2.2 cm left lateral neck level V mass. Further evaluation revealed stable NET disease with the exception of an enlarging 1.3 cm anterior mediastinal nodule. 18F-FDG PET/CT demonstrated more activity in the left neck mass and mediastinal mass than 68Ga-DOTATATE PET/CT. Biopsy of the left neck mass revealed a high grade malignant neoplasm with epithelioid features and markedly elevated MIB1. Tumor cells were positive for CD56, SOX-10 and S-100 protein, but negative for CD20, CD3, CD5, chromogranin, synaptophysin, AE1/AE3, CAM5.2, C-Kit and p53. Molecular analysis showed pathogenic variants in BRAF, TERT, PIK3C, and RB1, a likely pathogenic variant in FBXW7, and a variant of uncertain significance in PMS2. Given these histologic and molecular findings, the diagnosis of metastatic melanoma was favored. Ophthalmological evaluation, skin examination and biopsy of suspicious cutaneous lesions did not reveal the primary site of melanoma. PCR did not reveal MEN1 loss of heterozygosity (LOH) of the neck mass, though there was insufficient material to evaluate for large MEN1 deletions. Conclusion: Of the 9 cases of melanoma previously reported in MEN1, only 1 was evaluated for MEN1 LOH, which was not demonstrated. MEN1 LOH has been described in sporadic melanoma and in vitro and in vivo studies in mice suggest a role for MEN1 as a tumor suppressor gene in melanoma (Gao et al. 2011, Fang et al. 2013). Whether melanoma in MEN1 is related to the germline MEN1 mutation or is sporadic is still unclear. Evaluation of melanomas for MEN1 LOH initially with targeted sequencing of the germline mutation followed by LOH for markers in and near the MEN1 gene at 11q13, may help further elucidate the role of MEN1 in melanoma.

Template switching during break-induced replication

DNA double-strand breaks (DSBs) are potentially lethal lesions that arise spontaneously during normal cellular metabolism, as a consequence of environmental genotoxins or radiation, or during programmed recombination processes. Repair of DSBs by homologous recombination generally occurs by gene conversion resulting from transfer of information from an intact donor duplex to both ends of the break site of the broken chromosome. In mitotic cells, gene conversion is rarely associated with reciprocal exchange and thus limits loss of heterozygosity for markers downstream of the site of repair and restricts potentially deleterious chromosome rearrangements. DSBs that arise by replication fork collapse or by erosion of uncapped telomeres have only one free end and are thought to repair by strand invasion into a homologous duplex DNA followed by replication to the chromosome end (break-induced replication, BIR). BIR from one of the two ends of a DSB would result in loss of heterozygosity, suggesting that BIR is suppressed when DSBs have two ends so that repair occurs by the more conservative gene conversion mechanism. Here we show that BIR can occur by several rounds of strand invasion, DNA synthesis and dissociation. We further show that chromosome rearrangements can occur during BIR if dissociation and reinvasion occur within dispersed repeated sequences. This dynamic process could function to promote gene conversion by capture of the displaced invading strand at two-ended DSBs to prevent BIR.

Deletion of chromosome 1, but not mutation of MEN-1, predicts prognosis in sporadic pancreatic endocrine tumors.

Pancreatic endocrine tumors (PETs) may be sporadic or inherited in the multiple endocrine neoplasia type 1 (MEN-1) syndrome. The inherited form is caused by mutations of the MEN-1 gene, which functions as a tumor suppressor gene and maps to chromosome 11q13. These tumors tend to have a better prognosis than their sporadic counterparts, which often have mutations of the MEN-1 gene. Previous molecular analyses of sporadic PETs suggest a high frequency of loss of heterozygosity (LOH) at chromosome 1 as well as mutation of MEN-1. In this study we correlate abnormalities of MEN-1 and chromosome 1 LOH with the biological behavior of sporadic PETs. Loss of heterozygosity for markers at chromosome 11q13 and mutation of MEN-1 were equally frequent in tumors with or without liver metastases. Mutation of MEN-1 is more frequent in gastrinomas than in non-gastrinomas. Loss of heterozygosity for markers on chromosome 1 is more frequent in PETs with liver metastases. These results suggest a molecular tumor model in which there is a dichotomy in the development of benign and malignant PETs.

Somatic Mutations in the STK11/LKB1 Gene Are Uncommon in Rare Gynecological Tumor Types Associated with Peutz-Jegher's Syndrome

Peutz-Jegher's syndrome (PJS) is a rare autosomal dominant disorder characterized by mucocutaneous pigmentation, hamartomatous polyposis, and predisposition to benign and malignant tumors of the gastrointestinal tract, breast, ovary, uterine cervix, and testis. Germline-inactivating mutations in one allele of the STK11/LKB1 gene at chromosome 19p13.3 have been found in most PJS patients. Although ovarian sex cord tumors with annular tubules (SCTATs) and minimal deviation adenocarcinomas (MDAs) of the uterine cervix are very rare in the general population, both tumor types occur with increased frequency in women with PJS. An earlier report indicated that the 19p13.3 region containing the STK11 gene was affected by loss of heterozygosity (LOH) in nearly 50% of MDAs of the uterine cervix. We investigated the role of STK11 mutations and LOH of the 19p13.3 region in two PJS-associated SCTATs and in five SCTATs and eight MDAs of the uterine cervix, which occurred in patients lacking features of PJS (referred to here as "sporadic" cases). Germline mutations in the STK11 gene, accompanied by LOH of markers near the wild-type STK11 allele, were found in the two PJS-associated SCTATs. Somatic mutations in the coding region of STK11 were not found in any of the sporadic SCTATs or MDAs studied, although LOH of the 19p13.3 region was seen in three of eight MDAs. Our findings indicate that STK11, like other tumor suppressor genes, is affected by biallelic inactivation in gynecological tumors of PJS patients. In addition, although LOH of the 19p13.3 region was seen in sporadic MDAs, somatic STK11 mutations are rare. A yet-to-be-defined tumor suppressor gene in the 19p13.3 region may be the specific target of inactivation in these tumors.

Construction of a High-Resolution Physical Map of the ∼ 1-Mb Region of Human Chromosome 7q31.1–q31.2 Harboring a Putative Tumor Suppressor Gene

Reports of frequent loss of heterozygosity (LOH) of markers on human chromosome 7q in malignant myeloid disorders as well as breast, prostate, ovarian, colon, head and neck, gastric, pancreatic, and renal cell carcinomas suggest the presence of a tumor suppressor gene (TSG). Functional assays have demonstrated that the introduction of an intact copy of human chro- mosome 7 (hchr7) can restore senescence to immortalized human fibroblast cell lines having LOH of markers within 7q31-q32 and can inhibit the tumorigenic phenotype of a murine squamous cell carcinoma cell line. To facilitate the cloning of the putative TSG, we have constructed a high-resolution physical map of this region of hchr7, specifically that encompassing the markers D7S522 and D7S677 within 7q31.1-q31.2. By using a lower resolution yeast artificial chromosome-based map as a starting framework, we established complete clone coverage of the implicated critical region in bacterial-artificial chromosomes (BACs) and P1-derived artificial chromosomes (PACs). The resulting BAC/PAC-based contig map has provided suitable clones for the systematic sequencing of the entire interval. In addition, we have already identified 29 clusters of overlapping expressed-sequence tags (ESTs) and 4 known genes contained within these clones. Together, the physical map reported here coupled with the evolving sequence and gene maps should hasten the identification of the putative TSG residing within this region of hchr7.

Frequent Loss of Heterozygosity for Chromosome 10 in Uterine Leiomyosarcoma in Contrast to Leiomyoma

Distinction of malignant uterine leiomyosarcomas from benign leiomyomas by morphological criteria is not always possible. Leiomyosarcomas typically have complex cytogenetic abnormalities; in contrast, leiomyomas have simple or no cytogenetic abnormalities. To understand better the biological distinction(s) between these tumors, we analyzed two other potential markers of genomic instability, loss of heterozygosity (LOH) and microsatellite instability. We examined archival materials from 16 leiomyosarcomas and 13 benign leiomyomas by polymerase chain reaction for 26 microsatellite polymorphisms. Markers were selected based on previous reports of cytogenetic or molecular genetic abnormalities in leiomyosarcomas or leiomyomas and surveyed chromosomes 7, 9, 10, 11, 12, 14, 15, 16, 18, 21, and X. LOH for markers on chromosomes 15, 18, 21, and X was infrequent in leiomyosarcomas (1 of 6 tumors for each chromosome) and not observed for markers on chromosomes 7, 9, 11, 12, 14, or 16. Interestingly, 8 of 14 (57.2%) informative leiomyosarcomas had LOH for at least one marker on chromosome 10 and involved both chromosomal arms in 45.5% (5 of 11). In contrast to leiomyosarcomas, LOH for chromosome 10 was not found in 13 benign leiomyomas. Microsatellite instability was found infrequently in leiomyosarcomas and not detected in leiomyoma. Clinicopathological features (eg, atypia, necrosis, and clinical outcome) did not appear to correlate with LOH for chromosome 10. In contrast to other chromosomes studied, LOH on chromosome 10 was frequent in leiomyosarcomas and absent in benign leiomyomas.

Chromosome loss with concomitant duplication and recombination both contribute most to loss of heterozygosity in vitro.

Loss of heterozygosity (LOH) plays an important role in the expression of recessive mutations in mammalian cells. To gain insight into the rate and mechanisms of LOH the autosomal HLA-A gene was used as a model system. Spontaneous HLA-A2 mutants originated with a rate of respectively 4.1 x 10(-6) and 6.9 x 10(-6) per cell per generation in TK6 and WI-L2-NS, two isogenic lymphoblastoid cell lines which differ in TP53 status. The rate of loss of HLA-A2 is 10-50 times higher compared to the mutation rate of the X-linked HPRT gene. The homozygous TP53 mutation in WI-L2-NS had no effect on the rate of HLA-A2 loss or the spectrum of these mutations. Microsatellite analysis of most of the HLA-A2 mutants (84%) showed LOH for multiple markers on chromosome arm 6p telomeric of a recombination breakpoint, LOH for all 6p markers, or LOH for markers on both the 6p- and 6q-arms. Cytogenetic analysis showed that these mechanisms gave mutant cells which harbored two intact chromosomes 6 and which were indistinguishable from non-mutant cells. Therefore, loss of HLA-A2 is mainly caused by somatic recombination (33-50%) or chromosome loss with duplication of the remaining chromosome (34-40%). These findings correspond to the mechanisms behind loss of the wild-type RBI allele in retinoblastoma and suggest that both somatic recombination and chromosome loss followed by duplication contribute to tumorigenesis.

Loss of heterozygosity of chromosome 14q in low- and high-grade meningiomas

Abnormalities of chromosome 22q have been well studied as a major molecular genetic event in meningiomas. Chromosome 14q loss has also been shown to be a common phenomenon. However, only a few studies have reported molecular genetic changes of this chromosome in meningioma. In this study, we examined 41 sporadic meningiomas of different histological subtypes and grades with 15 polymorphic microsatellite markers covering a wide region on chromosome 14q. Overall, 37% (15 of 41) of cases showed loss of heterozygosity for one or more allelic markers. Thirty percent (10 of 33) of benign tumors showed allelic losses, whereas 62.5% (5 of 8) of high-grade meningiomas showed loss of heterozygosity. There were altogether eight cases of partial deletions and seven cases of probable monosomy of 14q. Allelic losses of 14q were also commonly seen in recurrent tumors (3 of 3, 100%), parasagittal tumors (4 of 7, 57%), and tumors with transitional subtype (7 of 14, 50%). Among the tumors with allelic losses of 14q, all except one concurrently showed loss of heterozygosity for markers on 22q by our previous study. Of the eight cases with partial deletions, one showed losses on 14q11.1-31, two showed deletions on 14q24.3-31, three showed losses at 14q32.1-32.2, and the remaining two showed deletions at 14q24.3-32.2. We therefore defined two cluster regions of deletion on chromosome 14q: 14q24.3-31 and 14q32.1-32.2. Our studies suggested that more than one tumor suppressor gene(s) residing on distinct regions of chromosome 14q are important in the development and atypical or anaplastic changes in meningiomas.

Role of genomic instability in meningioma progression.

Microsatellite length instability, probably resulting from defective DNA mismatch repair mechanisms, has been described in a variety of cancers. Such genetic instability may play a significant role in tumor formation and progression. To investigate the role of microsatellite alterations in meningioma tumorigenesis and progression, we examined 33 microsatellite markers on nine chromosomes for abnormalities in 18 benign, 15 atypical, and 11 malignant meningiomas. In each tumor, at least 15 markers were investigated. Microsatellite instability was not detected in any of the cases examined. However, loss of heterozygosity for markers from various chromosomes was seen frequently among atypical and malignant meningiomas. Although some of these chromosomal losses might represent random events, our data also indicate a role for specific loci on chromosome arms 14q, 1p, 10q, and possibly 9p in the development of malignancy in meningiomas. Our results argue against a significant role for a generalized microsatellite instability phenotype in meningiomas, but they suggest that genomic instability resulting in frequent allelic deletions may contribute to meningioma progression.

Allelotyping in Wilms Tumors Identifies a Putative Third Tumor Suppressor Gene on Chromosome 11

An analysis of loss of heterozygosity for markers on both the short and the long arm of chromosome 11 was performed in 24 sporadic Wilms tumors. Six cases (25%) showed allelic losses involving the entire chromosome. In one case (4%) the loss was restricted solely to the WT1 gene on band p13. Two cases (8%) displayed allelic losses for WT1 and for markers on band p15.5, where the putative tumor suppressor gene WT2 has been mapped, but retained heterozygosity for markers on the long arm. In three tumors (13%) the loss of heterozygosity involved markers mapped to chromosomal regions p15.5 and q23.3-qter, but did not affect WT1 and markers on q12-q13. Altogether, the proportion of cases showing allelic losses at the distal region of 11q (37%) was comparable to that of cases with LOH affecting the WT1 (37%) or the WT2 (46%) loci, thus suggesting the existence of a third chromosome 11 tumor suppressor gene involved in the pathogenesis of Wilms tumors.

Loss of Alleles in Vestibular Schwannomas: Use of Microsatellite Markers on Chromosome 22

Using highly informative microsatellite markers flanking the neurofibromatosis type 2 gene, we determined the frequency of chromosome 22 allele loss in vestibular schwannomas. Peripheral lymphocyte/vestibular schwannoma DNA pairs were analyzed with five different microsatellite markers on chromosome 22. Samples were taken from 32 patients (17 females and 15 males). Twenty-seven tumors occurred sporadically, and five were from patients with neurofibromatosis type 2. Using the microsatellite markers D22S351, CRYB2, D22S268, D22S304, and interleukin type 2RP3, we found loss of heterozygosity for at least two markers in 12 tumors. Ten tumors showed loss of heterozygosity for markers flanking the neurofibromatosis type 2 gene. Although microsatellite markers require little DNA for analysis and are highly informative, allele patterns may be difficult to interpret in some cases. Loss of heterozygosity of chromosome 22 alleles was a frequent event in vestibular schwannomas. In 10 tumors, heterozygosity was lost for centromeric and telomeric markers indicating likely monosomy 22. However, 63% of tumors did not reveal a detectable chromosomal loss. Unless a second vestibular schwannoma locus exists, these tumors likely harbor point mutations in the neurofibromatosis type 2 gene or deletions below the level of resolution of the markers used in this study.

A case of transitional cell carcinoma of the bladder with a del(9)(q11q21.2)

Monosomy for chromosome 9, as well as loss of heterozygosity for markers on this chromosome, has been detected in a high percentage of transitional cell carcinomas (TCC) of the bladder. We report a case of a TCC of the bladder with an interstitial del(9)(q11q21.2) that could be indicative of the presence of a putative tumor-suppressor gene related to bladder tumor progression. To elucidate the role of chromosome 9 in bladder tumors, it would be interesting to study a possible loss of heterozygosity in this chromosome region.

Chromosome 22 heterozygosity is retained in most hyperdiploid and pseudodiploid meningiomas

Hyperdiploid or pseudodiploid modal chromosome numbers were found characterizing six human meningiomas, and all six tumors were disomic for chromosome 22. The scarce previous reports on the subject suggest that, in these cytogenetic subgroups of meningiomas, duplication of the retained chromosome 22 occurs after the loss of the other member of the pair, thus correlating well with the main characteristic of meningiomas, that is, losses of 22. To verify this question, molecular genetic analyses were performed on DNA pairs from blood and tumoral samples of all six cases, using polymorphic markers for chromosome 22. Restriction fragment length polymorphism studies failed to show any loss of heterozygosity for markers located on this chromosome in all six cases, suggesting that a different mechanism to that previously proposed might take place in the hyperdiploid or pseudodiploid meningiomas; perhaps a submicroscopic involvement (microdeletions or inactivating mutations) of the meningioma locus (both alleles) may result in an effect similar to that produced by monosomy 22 (which probably unmasks recessive mutations on the retained allele), enhancing the development of meningiomas.

Search for putative suppressor genes in meningioma: significance of chromosome 22.

Cytogenetic and molecular studies of various solid tumors have indicated that a series of different chromosomal regions may be deleted in the tumor genome. Usually, losses of heterozygosity are observed and, from this finding, the presence of specific genes acting as tumor suppressors has been deduced. In particular tumors, however, only a single chromosome site appears to be affected. Therefore, we have carried out a study of human meningioma, investigating 7 such putative suppressor regions by applying twelve site-specific DNA markers. In 6 out of 19 tumors, we exclusively found loss of heterozygosity for markers of the long arm of chromosome 22; none of the tumors showed statistically significant additional allelic losses for the regions 1p, 3p, 5p, 5q, 11p, 13q, 17p. Our data support the long-standing observation that only losses of or within chromosome 22 are associated with the development of meningiomas. Other suppressor regions are apparently not involved.

Loss of chromosome 22 alleles in human sporadic spinal schwannomas

Acoustic neuromas occur either as sporadic solitary tumors in the general population or as inherited bilateral tumors typically in patients with neurofibromatosis type 2. Loss of heterozygosity for markers on the long arm of chromosome 22 has been reported in both instances, and neurofibromatosis type 2 has been genetically linked to a marker on the long arm of this autosome, suggesting that a unique locus on chromosome 22 is implicated in tumorigenesis of both sporadic and inherited acoustic neuromas. To determine whether the locus for neurofibromatosis type 2 might also be responsible for tumorigenesis of those schwannomas distinct from acoustic neuromas in people without neurofibromatosis type 2, we studied the DNA content of three sporadic spinal schwannomas. In all three, we found loss of heterozygosity for at least three markers on the long arm of chromosome 22, indicating a partial or total monosomy 22 in the tumor. Our results suggest that a locus on chromosome 22 is responsible for tumorigenesis in schwann cells regardless of their location in the central nervous system, and that some other mechanism (genetic or nongenetic) might account for the relative high proportion of schwannomas developing from the eighth cranial nerve.