GENOME-WIDE SCREENING OF LOSS OF HETEROZYGOSITY IN HUMAN MIDGUT CARCINOID TUMORS WITH FLUORESCENT TECHNIQUERuth Mari Caroline Löllgen Vorwort891.1.1.1.2.1.3.1.4.2.102.1.2.2.2.3.2.4.3.113.1.12133.1.1.3.1.1.1.3.1.1.2.3.1.2.3.1.2.1.143.1.2.2.3.2.153.3.3.3.1.163.3.2.3.3.3.173.4.3.4.1.3.4.1.1.3.4.1.2.3.4.2.183.4.3.3.4.4.3.4.5.3.4.6.3.4.7.3.5.193.6.3.6.1.203.7.3.7.1.4.214.1.4.2.22234.3.4.4.244.5.5.5.1.255.2.5.3.6.267.278.8.1.288.2.298.3.308.4.313233614#7329.343510.363738 REFERENCES394041424344454647Abbreviations Acknowledgements49 Lebenslauf505152 Eidestattliche Erklärung53enTable of contentsHelp RESULTS

For the genome-wide LOH analysis two primary tumors and six metastases with relatively low amount of contaminating fibroblasts were chosen from the collection of metastatic midgut carcinoid tumors at the Department of Surgical Sciences, Endocrine Unit, University Hospital, Uppsala, Sweden (Table 3.). The microsatellite markers used in the analysis are listed in Figure 1. and the LOH results of our midgut carcinoids are shown in Table 4..

A tumor was scored positive for LOH on one arm when at least one of the markers that define that region showed allelic loss. To investigate if a limited region of loss could be revealed by using denser genetic mapping we studied additional nearby microsatellites for all chromosomes with more frequent deletions and for chromosomes with a single LOH event to reconfirm our findings.

In total, 298 out of 312 examined chromosomal arms (96%) presented with at least one infor-mative marker. 45 different markers were lost and a various percentage of tumors was affected by LOH on the respective chromosomal arms, from 12,5 to 83%. Deletions were found on 11 chromosomes. LOH was found for a contiguous set of markers on chromosome 18 in all tumors except 5807. Two tumors (5216 and 5807) had lost parts of eight and seven chromosomes (chromosomes 4, 5, 7, 9, 12, 14, 18, 20 and 3, 4, 5, 7, 14, 19, 20 respectively) and tumor 2762 had deletions on chromosomes 9, 16, and 18. With exeption of tumor 5216, similar levels of allele retention were detected on both chromosomal arms. Fractional allelic loss (FAL) per tumor is defined as the number of markers displaying LOH per total number of informative microsatellites. The FAL was ranging from 1,4 to 35,% for all tumors. The highest number of deletions was found in tumors 5216 and 5807, with a FAL of 28,6% and 35,4% respectively. Tumor 5216 showed allelic retention levels differing from 11-25% (chromosomes 5, 9 and 18) to 46-60% (chromosomes 4, 7, 12, 14 and 20) whereas all other tumors revealed similar retention levels in all their chromosomes (Table 4). Tumors without LOH had retention levels of 88-100%.

No correlation between malignant features and number of allelic deletions was revealed, all tumors had metastasized to the liver and the levels of LOH were greatly differing.

LOH on chromosome 18.

Chromosome 18 showed the most significant rate of LOH with allelic loss in seven of eight tumors (88%). In six of these lesions the deletions spanned all informative markers on both the short and long arm of chromomsome 18. Tumour 2762 displayed LOH for microsatellite marker D18S541 and D18S844 at 18q21 while retaining D18S858 mapped more centromerically to 18q21 and all informative markers on 18p. This tumor, with a limited deletion on chromosome 18, also displayed LOH on chromosomal arms 9p and 16q but not 9q and 16p. Tumor 5807 did not display any LOH on either arm of chromosome 18, paradoxically this tumor showed most LOH on all other chromosomal arms.

No Smad4/DPC4 mutations could be revealed by the sequencing analysis of this TSG. Only exons 8-11 were examined since the majority of previously described mutations are found within this region (117).

The immunohistochemical staining with antibodies to the Smad4/DPC4 protein revealed ex-pression of Smad4/DPC4 in the seven analyzed tumors (data not shown). Tumor 5216 was not analyzed due to shortage of tumor material. Thus, no evidence of aberrant Smad4/DPC4 was found.

●=Loss of heterozygosity, ○=Retention of heterozygosity,†=Non-informative
Chromosomal arms

Tumor

number

2283

2762

4017

5184

5216

5692

5718

5807

1p

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○

○

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○

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1q

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2p

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2q

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3p

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3q

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4p

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●

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4q

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●

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5p

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†

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●

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5q

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6p

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†

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6q

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7p

†

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●

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7q

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●

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●

8p

†

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†

8q

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9p

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●

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●

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9q

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●

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10p

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10q

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†

†

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11p

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11q

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12p

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12q

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13q

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14q

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15q

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16p

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16q

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17p

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†

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17q

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†

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18p

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18q

●

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●

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●

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19p

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†

19q

†

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●

20p

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†

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●

20q

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†

●

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●

21q

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22q

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†

○

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○

○

Table 4. Genome-wide LOH screening of midgut carcinoid tumors