CLUSTERING OF DELETIONS ON CHROMOSOME 13 IN BENIGN AND LOW-MALIGNANT LIPOMATOUS TUMORS Anna DAHL´ EN 1 * , Maria DEBIEC-RYCHTER 2 , Florence PEDEUTOUR 3 , Henryk A. DOMANSKI 4 , Mattias H¨ OGLUND 1 , Henrik C. F. BAUER 5 , Anders RYDHOLM 6 , Raf SCIOT 7 , Nils MANDAHL 1 and Fredrik MERTENS 1 1 Department of Clinical Genetics, University Hospital, Lund, Sweden 2 Center for Human Genetics, University of Leuven, Leuven, Belgium 3 Laboratoire de Ge ´ne ´tique, Ho ˆpital de l'Archet, Nice, France 4 Department of Pathology and Cytology, University Hospital, Lund, Sweden 5 Department of Orthopedics, Karolinska Hospital, Stockholm, Sweden 6 Department of Orthopedics, University Hospital, Lund, Sweden 7 Department of Pathology, University of Leuven, Leuven, Belgium Deletions and structural rearrangements of the long arm of chromosome 13 are frequently observed in benign and low-malignant lipomatous tumors, but nothing is known about their molecular genetic consequences. We assessed the karyotypes of 40 new and 22 previously published cases (35 ordinary lipomas, 15 spindle cell/pleomorphic lipomas, 2 myxolipomas, 1 angiomyxolipoma and 9 atypical lipomatous tumors) with chromosome 13-abnormalities, and found bands 13q12–22 to be frequently affected. Twenty-seven cases with structural abnormalities within this region were selected for breakpoint and deletion mapping by metaphase fluorescence in situ hybridization (FISH), using a set of 20 probes. Deletions were found in 23 of 27 cases. The remain- ing 4 cases had seemingly balanced rearrangements. The breakpoints were scattered but clustered to band 13q14, and in all cases with unbalanced abnormalities, a limited region within band 13q14 was partially or completely deleted. A deletion within band 13q14 was found together with a break- point on the other homologue in 5 cases, 4 of which could be tested further with regard to the status of the retinoblas- toma (RB1)-gene. In all 4 cases, only 1 copy of the gene was deleted. In addition to the breaks and deletions in the vicinity of the RB1-locus, several other regions of 13q were recur- rently affected, e.g., in the vicinity of the hereditary breast cancer (BRCA2; 13q12)- and lipoma HMGIC fusion partner (LHFP; 13q13)- genes. Our findings strongly indicate that deletion of a limited region (2.5 Mbp) within 13q14, distal to the RB1-locus, is of importance in the development of a subset of lipomatous tumors. © 2002 Wiley-Liss, Inc. Key words: lipoma; chromosome 13; deletion; fluorescence in situ hybridization; cytogenetics Adipocytic tumors constitute the largest subgroup of soft tissue tumors. Several histopathologic subtypes, associated with different clinical features, have been recognized. 1 Cytogenetic analysis of adipose tissue tumors has shown that the various histopathologic subtypes are characterized by distinctive clonal chromosomal ab- normalities. 1,2 Ordinary lipomas typically harbor abnormalities involving 12q13–15, 6p or 13q, 3,4 hibernomas exhibit 11q13 ab- normalities, 5 lipoblastomas are characterized by 8q11–13 abnor- malities 6 and spindle cell and pleomorphic lipomas typically dis- play complete or partial loss of 13q and chromosome 16. 7 Among the malignant adipose tissue tumors, the presence of giant chro- mosome markers and ring chromosomes, most often containing amplified chromosome 12-material, signifies atypical lipomatous tumors, 8 and the translocation t(12;16)(q13;p11) is pathognomonic for myxoid/round cell liposarcoma. 9 For most of these abnormal- ities, the molecular genetic consequences have been disclosed, revealing that the cytogenetic aberrations result in fusion or am- plification of specific genes. One of the more frequent abnormalities among benign and low-malignant adipose tissue tumors, i.e., rearrangement of 13q, has not yet been investigated at the molecular level. A survey of all published karyotypes from lipomatous tumors 2 revealed that rear- rangement of, or monosomy for, chromosome 13 had been de- tected in 72 of 463 cases (16%). Among the different histotypes, the frequency of chromosome 13-abnormalities varies greatly, ranging from 0% in lipoblastoma and hibernoma to 67% in spindle cell and pleomorphic lipomas (Table I). An assessment of the breakpoints involved in structural rearrangements shows 3 bands to be more frequently affected, i.e., 13q12, 13q14 and 13q22, and the region spanning 13q12–22 to be most frequently deleted (Fig. 1). The aim of the present study was to delineate, by fluorescence in situ hybridization (FISH), the localization of breakpoints and the extent of deletions on chromosome 13 among benign and low- grade malignant lipomatous tumors. MATERIAL AND METHODS Patients The material consisted of 62 benign and low-malignant lipoma- tous tumors that had been cytogenetically analyzed at the Depart- ment of Clinical Genetics in Lund, Sweden, at the Center for Human Genetics in Leuven, Belgium or at the Laboratoire de Ge ´ne ´tique in Nice, France. All cases included in the study were selected on the basis of their showing clonal loss and/or structural rearrangement of chromosome 13. Of the 62 tumors, 53 were diagnosed as benign lipomas (35 ordinary lipomas, 15 spindle cell/pleomorphic lipomas, 2 myxolipomas and 1 angiomyxoli- poma) and 9 as atypical lipomatous tumors. Four of the samples were from local recurrences, whereas the remaining 58 were from primary tumors. Cell culture and cytogenetic analysis Short-term culturing, harvesting and cytogenetic analysis were performed according to standard methods 10 and the karyotypes were written according to ISCN. 11 Twenty-two of the karyotypes have been published before. 4,7,12–17 Grant sponsor: Swedish Cancer Society, l’Association pour la Recherche contre le Cancer; Grant number: ARC 5955; Grant sponsor: Belgian Programme on Interuniversity Poles of Attraction, Belgian State, Prime Minister’s Office, Science Policy Programming; Grant sponsor: European Co-operation in the Field of Science and Technical Research (COST); Grant number: Action B19. *Correspondence to: Department of Clinical Genetics, University Hos- pital, SE-221 85 Lund, Sweden. Fax: +46-46-131061. E-mail:anna.dahlen@klingen.lu.se Received 23 July 2002; Revised 27 August 2002; Accepted 25 Septem- ber 2002 DOI 10.1002/ijc.10864 Int. J. Cancer: 103, 616 – 623 (2003) © 2002 Wiley-Liss, Inc. Publication of the International Union Against Cancer