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Cytogenetics Core

The Cytogenetics Core serves as both a scientific and technical resource to DF/HCC investigators. Cytogenetic studies can provide insight into regions of the genome that are pathogenic in various neoplasms leading to an understanding of the molecular pathways participating in the biology of cancer. Cytogenetic studies may also be important in establishing a diagnosis for correlation with clinical outcome. In overview, cytogenetics is a fundamental adjunct to a variety of investigations underway, including basic and translational research. For example, a rather simple cytogenetic analysis of mouse ES cells to determine ploidy prior to injections into blastulas leads to a greater success rate in establishing founders for knock-out and knock-in experiments. The finding of a consistent chromosomal aberration in a tumor (e.g. translocation, aneuploidy, amplification) may lead to development of a diagnostic FISH test. Furthermore, the availability of molecular probes for FISH analyses facilitates fine mapping studies in the mouse. Both copy number and SNP arrays illuminate genetic alterations at a molecular level that provide insights previously not available on a genome-wide scale. Indeed, unlike many molecular biology-based techniques, cytogenetic methodologies can provide analyses at a single cell level, and these methodologies provide a visualization of the presence, absence, and proximity of specific nucleic acid sequences with each other and to other cellular landmarks.

In addition to the technical component, the Core provides highly skilled professional cytogeneticists with extensive research and clinical experience for valuable consultation in experimental design and interpretation. The availability of routine mouse karyotyping and molecular cytogenetics provides DF/HCC scientists access to essential genotypic profiles that are not easily obtainable elsewhere.

Listed below are a few examples illustrating how the core has contributed to various projects:

1) PI: P. JanneDFCI (Lung Cancer and Cancer Genetics Programs). Copy number analysis of EGFR and MET (Case: CYT-09-0066) and chromosomal rearrangement of EML4-ALK in non-small cell lung carcinomas (Case: CYT-09-PJ-0051). This project was performed as part of a clinical trial, in part to determine whether EGFR was amplified in specific patients with non-small cell lung carcinoma. Amplification of EGFR and translocation of EML4-ALK were detected by FISH in five micron sections from paraffin-embedded lung tumor tissues.  Multiple EGFR and MET signals were observed in each nucleus and EML4-ALK translocations were detected by fused signals. FISH testing on non-small cell lung carcinoma has now been transitioned as a new diagnostic assay to the clinical cytogenetics laboratory at BWH for ~250 cases per year. Publications arising from this work include:
Turke AB, Zejnullahu K, Wu YL, Song Y, Dias-Santagata D, Lifshits E, Toschi L, Rogers A, Mok T, Sequist L, Lindeman NI, Murphy C, Akhavanfard S, Yeap BY, Xiao Y, Capelletti M, Iafrate AJ, Lee C, Christensen JG, Engelman JA, Jšnne PA. Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC. Cancer Cell. 2010 Jan 19;17(1):77-88

Chen Z, Sasaki T, Tan X, Carretero J, Shimamura T, Li D, Xu C, Wang Y, Adelmant GO, Capelletti M, Lee HJ, Rodig SJ, Borgman C, Park SI, Kim HR, Padera R, Marto JA, Gray NS, Kung AL, Shapiro GI, Jšnne PA, Wong KK. Inhibition of ALK, PI3K/MEK, and HSP90 in murine lung adenocarcinoma induced by EML4-ALK fusion oncogene. Cancer Res 2010 Dec 1;70(23):9827-36.

2) PI: D. ScaddenMGH (Leukemia and Lymphoma and Myeloma Programs). Genetic lesions in myeloid neoplasms arising from alterations in the tissue microenvironment (Case: CYT-10-MR-0001). In a mouse model, specific genetic alterations in the bone marrow microenvironment-induced myelodysplasia and acute myeloid leukemia, support a concept of niche-induced oncogenesis. In one of the tumors, array CGH identified a 19.5 kb one-copy loss on chromosome two and a 43.8 kb one-copy loss on chromosome 18. This information led to the identification of putative novel genes involved in leukemogenesis, a hypothesis that is currently being tested. A publication that resulted from this work was:

Raaijmakers MH, Mukherjee S, Guo S, Zhang S, Kobayashi T, Schoonmaker JA, Ebert BL, Al-Shahrour F, Hasserjian RP, Scadden EO, Aung Z, Matza M, Merkenschlager M, Lin C, Rommens JM, Scadden DT. Bone progenitor dysfunction induces myelodysplasia and secondary leukaemia. Nature. 2010 Apr 8;464(7290):852-7. Epub 2010 Mar 21. PubMed PMID: 20305640.