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Damaged DNA

MD Anderson researcher uses TACC's Stampede2 supercomputer to explore mutations in cancer cells

By Faith Singer-Villalobos, Texas Advanced Computing Center (TACC)

G4 DNA structures are readily detected in cell nuclei. Confocal microscopy of 293T, HAP1, and Hela cells stained with DAPI (blue) for nuclear DNA; a G4 DNA-structure specific antibody (red); and with Phalloidin for cytoplasmic cytoskeleton (green) display nuclear colocalization of G4 DNA structural foci with chromosomal DNA. Credit: Albino Bacolla, MD Anderson.

 

All life depends upon DNA repair and replication.

In every human cell the essential ability to replicate and repair genomes depends upon the coordinated actions of the genome sequence. Flaws or mistakes in repair and cell cycle regulation can lead to defects in the structure of the DNA and can prevent the replication from functioning properly.

Albino Bacolla has dedicated his life to exploring the biological laws that govern how cells function within the body. His scientific work is impressive, ranging from detecting thyroid deficiencies in children, to the identification of one of the earliest non-canonical DNA structures, to the genetic engineering of an inhibitor of HIV, which is used to treat HIV/AIDS patients.

Members of the John A. Tainer Lab, Department of Molecular and Cellular Oncology, MD Anderson Cancer Center. John Tainer (middle with beard) and Albino Bacolla (second from left with glasses). The authors of the paper are Albino Bacolla, Zu Ye, Zamal Ahmed, and John A. Tainer.

Today, Bacolla studies cancer as a research investigator at The University of Texas MD Anderson Cancer Center. His recent research, published in Progress in Biophysics and Molecular Biology in October 2019, focuses on genome instability and uses a computational approach to uncover mechanisms underlying cancer.

Defects in DNA replication and repair processes contribute to the onset, progression, and prognosis of cancer. Bacolla and other researchers are using data and advanced computing to examine relevant responses in cells.

"There is an enormous amount of data available in the public domain concerning cancer patients," Bacolla said. "What is lacking is the ability to analyze and mine the data. Advanced computing resources allow me to query a large number of data to probe its meaning."

Bacolla uses supercomputing resources allocated through the Extreme Science and Engineering Discovery Environment (XSEDE). XSEDE is a single virtual system funded by the National Science Foundation used by scientists to interactively share computing resources, data, and expertise. Specifically, Bacolla uses the XSEDE-allocated Stampede2 supercomputer at the Texas Advanced Computing Center (TACC).

"Stampede2 allows me to parallelize and run the code on many processors," he said. "In some cases, that's more than half a million data points — it was very convenient to use the capability of Stampede2 to run as many as 600 processors at one time to get the job done in a few days instead of months."

Mechanisms that Give Rise to Mutations in Cancer

Exposure to radiation and chemotherapy is one way to damage DNA. It can also be damaged by oxidants normally produced by the body. In every cell, the genome experiences about 70,000 lesions every day. If left unrepaired, this damage can result in mutations within the cell, which results in unusual and dangerous rearrangements of chromosomes. 

"These breaks in the double strand helix are extremely damaging and can cause the cell to die," Bacolla said. "And tumors use these breaks to rearrange the genome to their advantage. For example, a gene that is not usually expressed may be put under the control of a DNA sequence that expresses that gene very strongly. Tumors take advantage of the rearrangement of the genome to grow."

The underlying questions for Bacolla were: Where do these breaks occur in the DNA? And are they randomly distributed or not?

His research started at sites where the DNA breaks into sequences that form a quadruplex DNA structure. He found that many of these sequences are inside pieces of DNA called transposons that jump from one place to another in the genome, inserting themselves inside the gene and causing disruption.

"We found that one family of transposons was much more frequent near where the chromosomes break in the cancer genomes," Bacolla said. Transposons are known to cause rearrangements in cancer; however, it was not known that some do so using their quadruplex DNA structure. This discovery means that scientists can potentially stabilize these structures and induce cancer cell death by overwhelming it with DNA damage, as it is done with other anti-cancer treatments such as cisplatin.

Panel A. In cancer it is more likely to find a DNA sequence that can form quadruplex (G4) structure just next to breaks in chromosomes (maroon bar) than further away from such breaks (green bars) or elsewhere in the genome (gray bars), implying that in cancer G4 DNA facilitates breaks in the genome. Panel B. Cancer patients with mutations in the gene known as TP53 are more likely to incur breaks in the genome next to G4 DNA than patients without mutations in TP53. TP53 is the most commonly mutated gene in cancer. Panel C. These genes are more active in patients with many mutations than in patients with just few mutations, implying that by stimulating tumor growth they indirectly induce mutations. Three stars mean that the difference between tumor and normal tissue is statistically significant. Panel D. Patients with mesothelioma (MESO) who express high levels (blue line) of the MYBL2 gene (from Panel C) are at risk of dying earlier than patients who express low levels (red line) of the MYBL2 gene.

Scientists know that tumors have mutations, and mutated genes allow the tumor cells to grow. What's not understood, however, is how tumors grow with the help of additional genes that promote mutations.  

Bacolla set out to learn about these supplemental, mutation-promoting genes. He used public data sets to make correlations from 11,000 patients, such as the number of mutations the patient had and the degree to which each gene in the human body was expressed in that patient.

"I expected that the type of genes that would show this correlation were genes that had to do with repairing the damage that occurs in the DNA," he said. "In fact, I discovered the opposite. The genes that most strongly correlated with the number of mutations are [mutation-promoting] genes that the tumor uses to replicate and invade other tissues. That was surprising."

It became evident to Bacolla that tumors use these supplemental genes to grow very fast. "We found that it's the tumor cell that's pushed to replicate that causes many mutations — it's called replication stress."

Most of the cancer literature today focuses on what kind of mutations are in tumors and how they arise.

Instead, Bacolla's question centered on the iteration of mutated tumor cells, or the extent to which a tumor cell expresses one gene compared to its adjacent normal tissue. For genes used by the tumor to grow, such as one called CENPA, these genes are expressed up to 10 times more than in normal tissues.

"I suspect that these genes are protected by the tumor — they are the tumor's friends," Bacolla said. "These friends are upregulated genes in the tumor cell and cause mutations that support disease. There are about 190 of these genes and the tumor relies on them – it needs the machinery that takes the chromosomes apart and distributes them to the dividing cells. Best friends for the tumor, but the worst enemies for us."

The paper is called "Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction'. It appeared in Progress in Biophysics and Molecular Biology, October 2019. Authors: Albino Bacolla, Zu Ye, Zamal Ahmed and John A. Tainer, Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center. The researchers are grateful for funding by the National Institutes of Health and the Cancer Prevention and Research Institute of Texas for their efforts to understand DNA damage.

At a Glance:

  • Defects in DNA replication and repair processes contribute to the onset, progression, and prognosis of cancer.
  • Albino Bacolla studies cancer as a research investigator at the MD Anderson Cancer Center. His research focuses on genome instability and uses a computational approach to uncover mechanisms underlying cancer.
  • Specifically, Bacolla uses the XSEDE-allocated Stampede2 supercomputer at TACC to parallelize and run code on many processors to get the research done in a few days instead of months.
  • The paper is called "Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction'. It appeared in Progress in Biophysics and Molecular Biology, October 2019.