New sequencing approach discovers triple-negative breast cancers continue collecting hereditary changes throughout tumor development


DNA < img src =""alt=""> A representation of the double helical structure of DNA. Its 4 coding units (A, T, C, G) are color-coded in pink, orange, purple and yellow. Credit: NHGRI

Conquering previous technical challenges with single-cell DNA (scDNA) sequencing, a group led by scientists at The University of Texas MD Anderson Cancer Center has actually developed an unique approach for scDNA sequencing at single-molecule resolution. This strategy revealed for the very first time that triple-negative breast cancers undergo continued hereditary copy number modifications after an initial burst of chromosome instability.

The findings, released today in Nature, offer a precise and efficient new method for sequencing numerous private cancer cells while likewise providing novel insights into cancer advancement. These insights may describe why treatments are not always efficient and why scientists are not able to produce homogenous cell cultures in the laboratory.

“This represents substantial development from our first methods in single-cell DNA sequencing, with significantly increased throughput, precision and ease of usage,” stated senior author Nicholas Navin, Ph.D., associate teacher of Genetics and Bioinformatics & Computational Biology. “We are now able to fix really small differences in copy number within the population of tumor cells in a way that wasn’t possible formerly.”

The brand-new strategy, called Acoustic Cell Tagmentation (ACT), begins with fluorescent-activated cell sorting to isolate single nuclei from countless cells. A three-step chemistry procedure then cuts the DNA from each cell into accurate fragments, includes universal adaptors and incorporates barcodes for next-generation sequencing.

The chemistry is carried out with acoustic liquid transfer technology, which utilizes sound waves to transfer minute volumes of liquid quickly and efficiently. Whereas early scDNA sequencing approaches required three days from start to complete, the brand-new technique can be finished in just 3 hours, Navin explained.

With this improved technique for sequencing DNA from a limited number of cells, the researchers looked for to respond to a standing concern about cancer advancement. Navin’s team formerly developed that triple-negative breast cancers experience punctuated evolution, obtaining copy number changes in an initial burst of chromosomal instability, however it was unidentified if the cancer cells continued to collect changes after that occasion.

Led by graduate student Darlan Conterno Minussi, Navin’s team dealt with the lab of Franziska Michor, Ph.D., at Dana-Farber Cancer Institute, to perform copy number analysis on 16,178 single cells from eight triple-negative breast cancers and 4 cell lines utilizing the ACT technique.

“We found that punctuated advancement in these cells is followed by transient instability,” Navin said. “After the preliminary event, there is a time period with copy number changes building up at high rates that eventually slow to a basal rate.”

The understanding that triple-negative breast cancers continue to evolve over time may discuss why treatments are not constantly reliable– a little part of the cancer cells may have gotten an anomaly that communicates resistance to an offered therapy. Going forward, the researchers want to determine if the variety of genetic modifications a tumor undergoes is predictive of clinical outcomes.

The findings likewise have ramifications for preclinical research study, as the researchers verified that triple-negative breast cancer cell lines likewise continue to build up changes when cultured in the laboratory. Importantly, the scientists showed that commonly utilized lab cell culture treatments are unable to produce homogenous populations of tumor cells, because they rapidly re-diversify their genomes.

The research group continues to build upon this work by investigating extra cancer types, seeking to understand if this design of cancer evolution may be broadly relevant beyond triple-negative breast cancers.

New computational tool dependably differentiates between cancer and typical cells from single-cell RNA-sequencing data More info: Breast tumours maintain a reservoir of subclonal diversity during expansion, Nature (2021 ). Provided by University of Texas M. D. Anderson Cancer Center

Citation: New sequencing technique discovers triple-negative breast cancers continue accumulating genetic changes throughout tumor development (2021, March 24) recovered 25 March 2021 from

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