Nov 20, 2014

The Architecture and Evolution of Cancer Neochromosomes

Leonardo A. Meza-Zepeda and Ola Myklebost in collaboration with David M. Thomas’ group in Australia co-author an article recently published in Cancer Cell (journal impact factor 23.89), entitled “The Architecture and Evolution of Cancer Neochromosomes”. This article describes for the first time, at single base resolution, the architecture of cancer-associated neochromosomes in well- and dedifferentiated liposarcomas.

Neochromosomes are large marker chromosomes whose origin cannot be determined by conventional chromosome banding. These very large structures contain amplified material from multiple genomic loci, making them different from normal chromosomes. Little is known about the structure of these neochromosomes and the mechanism by which they develop. A number of malignancies have been shown to have this characteristic neochromosome structures, among them well-differentiated/dedifferentiated liposarcoma (WD/ DDLPS). In WD/ DDLPS, neochromosomes have been shown to consistently contain high-level amplifications of chromosome 12q13-q15, with frequent involvement of MDM2 and CDK4 oncogenes. This co-amplification provides a selective benefit for increased survival and proliferation by blocking p53 and RB1, respectively.

By combining chromosome flow sorting and high-throughput sequencing the structure of WD/ DDLPS neochromosomes has been revealed at single nucleotide resolution. Using mathematical modeling, a model for the genesis of neochromosomes has been proposed. This model starts by the formation of episomal structures, stitching together different donor loci in a non-amplifying process suggestive of chromothripsis. These initial structures include the chromosome 12 regions. These double minute structures continue to receive donor sequences through additional chromothripsis cycles. On a second stage, neochromosomes undergo multiple rounds of breakage-fusion-bridge cycles, resulting in amplification and deletion of material, which select for the content of the neochromosome. Under selective pressure, amplified oncogenes are overexpressed, while coamplified passenger genes may be silenced epigenetically. The final stabilizing of the neochromosomes occurs by linearization and telomere capture.

The work is part of a Liddy Shriver Sarcoma Initiative collaborative grant between the Meza-Zepeda’s and Myklebost’s groups in Norway and Thomas’ in Australia. This work has recently been awarded a new extension grant, which also includes Andrew J. Wagner’s group at the Dana-Farber Cancer Institute.



Sep 15, 2018

The Genomics Core Facility has recently installed a NanoString nCounter system. The nCounter utilizes a novel digital barcode technology for direct multiplexed measurement of analytes and offers high levels of precision and sensitivity. This technology allows the analysis of expression of up to 800 mRNAs, miRNAs, DNA regions, or proteins simultaneously, using predesigned assays, as well as custom solutions. 

May 5, 2018
The Genomics Core Facility has recently acquired new instrumentation, the ChromiumTM(10X Genomics) and RhapsodyTM(BD Genomics) enabling Single Cell Sequencing and sequencing of Artificial Long Reads.

Contact Information:

Unit Leader Core Facility
Susanne Lorenz, PhD

Head of Core Facility
Leonardo A. Meza-Zepeda, Dr. philos.

Visiting address:

Genomics Core Facility (Room 3-F8-04)
Department of Core facilities
Institute for Cancer Research
New OCCI-building 
Norwegian Radium Hospital 
Ullernchaussen 66, Lamell 3, 2B 
NO-0379 Oslo, NORWAY

+47 - 9183 2772 Laboratory
+47 - 9183 3425 Office