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Massive genome havoc in breast cancer is revealed

human chromosomes
Normal human chromosomes like these often undergo massive changes in cancerous cells. An improved method of sequencing DNA reveals how large chunks of chromosomes fall away or are fused with other chromosomes in breast cancer, causing genomic havoc and giving rise to harmful "fusion" proteins.

Cold Spring Harbor, NY — In cancer cells, genetic errors wreak havoc. Misspelled genes, as well as structural variations—larger-scale rearrangements of DNA that can encompass large chunks of chromosomes—disturb carefully balanced mechanisms that have evolved to regulate cell growth. Genes that are normally silent are massively activated and mutant proteins are formed. These and other disruptions cause a plethora of problems that cause cells to grow without restraint, cancer’s most infamous hallmark.

chromosomes 17 and 8
Long-read sequencing enabled the team to reconstruct in great detail “the history of how the HER2 gene gets massively amplified” in HER2-positive breast cancer cells, says Dr. Schatz. “The process, which really surprised us, is anything but simple.” The top rectangle shows a 2 million base-pair segment of chromosome 17 occupied by the HER2 gene (also called ERBB2). A small segment of the gene, already massively amplified, breaks off and fuses with chromosome 8 (lower rectangle). On that chromosome, parts of the gene are copied as many as 1000 times, with various segments jumping around within the chromosome (green arcs). “This shows why we want to identify HER2-positive patients as early as possible, to prevent the kind of chaos that we register here cumulatively,” says Schatz.

This week, scientists at Cold Spring Harbor Laboratory (CSHL) have published in Genome Research one of the most detailed maps ever made of structural variations in a cancer cell’s genome. The map reveals about 20,000 structural variations, few of which have ever been noted due to technological limitations in a long-popular method of genome sequencing.

The team, led by sequencing experts Michael C. Schatz and W. Richard McCombie, read genomes of the cancer cells with so-called long-read sequencing technology. This technology reads much lengthier segments of DNA than older short-read technology. When the results are interpreted with two sophisticated software packages recently published by the team, two advantages are evident: long-read sequencing is richer in terms of both information and context. It can, for instance, make better sense of repetitive stretches of DNA letters—which pervade the genome—in part by seeing them within a physically larger context.

The team demonstrated the power of long-read technology by using it to read the genomes of cells derived from a cell line called SK-BR-3, an important model for breast cancer cells with variations in a gene called HER2 (sometimes also called ERBB2). About 20% of breast cancers are “HER2-positive,” meaning they overproduce the HER2 protein. These cancers tend to be among the most aggressive.

“Most of the 20,000 variants we identified in this cell line were missed by short-read sequencing,” says Maria Nattestad, Ph.D., who performed the work with colleagues while still a member of the Schatz lab at CSHL and Johns Hopkins University. “Of particular interest, we found a highly complex set of DNA variations surrounding the HER2 gene.”

In their analysis, the team combined the results of long-read sequencing with results of another kind of experiment that reads the messages, or transcripts, that are being generated by activated genes. This fuller picture yielded an extraordinarily detailed account of how structural variations disrupt the genome in cancer cells and sheds light on how cancer cells rapidly evolve.

Schatz, Adjunct Associate Professor at CSHL and Bloomberg Distinguished Associate Professor at Johns Hopkins University, and McCombie, a CSHL Professor, say it is “essential to continue building a catalog of variant cancer cell types using the best available technologies. Long-read sequencing is an invaluable tool to capture the complexity of structural variations, so we expect its widespread adoption for use in research and clinical practice, especially as sequencing costs further decline.”

Written By: Peter Tarr, Senior Science Writer | tarr@cshl.edu | 516-367-5055


Funding

National Science Foundation; National Institutes of Health; CSHL Cancer Center; Watson School of Biological Sciences; Pacific Biosciences. Two employees of Pacific Biosciences were involved in the research and co-authored the paper. The SKBR3 genome was assembled with the support of DNAnexus.

Citation

Nattestad M et al, “Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line” is available online ahead of print and will appear in the August 2018 issue of Genome Research.

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. The Meetings & Courses Program annually hosts more than 12,000 scientists. The Laboratory’s education arm also includes an academic publishing house, a graduate school and the DNA Learning Center with programs for middle and high school students and teachers. For more information, visit www.cshl.edu

Principal Investigator

Michael Schatz

Michael Schatz

Adjunct Associate Professor

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