Noncoding RNA essential to DNA damage response

An NIEHS TaRGET I grantee and colleagues discovered that a long noncoding RNA (lnc-RNA) called damage induced noncoding (DINO) plays a key role in helping a cell decide whether to respond to DNA damage by repairing the damage or starting the pathway toward cell death. Cellular response to DNA damage is critical for normal cell growth and cancer suppression.

Scientists are only beginning to understand the biomolecular regulatory roles of lnc-RNAs, which are found throughout the genome, and unlike other RNAs, do not produce proteins. Defined as having more than 200 nucleotides, lnc-RNAs are often precisely regulated.

The tumor suppressor protein p53 recognizes and responds to DNA damage by increasing the expression of genes involved in DNA repair and cell division. Using cell and mouse studies, the researchers found that p53 increased expression of DINO, which binds to p53 and stabilizes it in a positive feedback loop that amplifies the p53 signal throughout the nucleus. When the researchers inhibited DINO expression, cells showed a reduced response to p53 signals. The investigators also found that when DINO expression was artificially increased, cells responded as if their DNA had been damaged, although there were no genome changes. Overall, these new findings showed that lnc-RNA helps the cell to appropriately respond to DNA damage.

Citation: Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY. 2016. An inducible long noncoding RNA amplifies DNA damage signaling. Nat Genet 48(11):1370−1376. (Story)

Formaldehyde damages DNA and proteins

An NIEHS-funded researcher and colleagues reported that formaldehyde not only damages DNA but can also cause extensive damage to proteins. New federal regulations limiting formaldehyde emissions from composite wood products were put in place earlier this year after the chemical was found to damage DNA, interfere with cell replication, and cause cancer.

To find out whether formaldehyde can directly damage proteins, the researchers examined the responses of three different types of human lung cells to formaldehyde. Because cells use a compound called ubiquitin to mark damaged proteins for removal, the team looked for polyubiquitinated proteins in the lung cells. In all three cell types, the researchers observed large amounts of polyubiquitinated proteins in the cell nucleus and cytoplasm, indicating high levels of protein damage.

Shortly after polyubiquitination began, the researchers observed a cell response similar to what happens when cells are exposed to excessive heat. This response indicated that the cell’s protective mechanisms were trying to clean up the damaged proteins before they accumulated enough to kill the cells. Ultimately, many of the cells died, despite activation of cellular defense responses. When the researchers disabled one of the key heat-shock response proteins, cells were even more likely to die.

The researchers say that their results indicate that formaldehyde strongly damages proteins, which helps explain the diverse effects observed with formaldehyde exposure.

Citation: Ortega-Atienza S, Rubis B, McCarthy C, Zhitkovich A. 2016. Formaldehyde is a potent proteotoxic stressor causing rapid heat shock factor protein 1 activation and lys48-linked polyubiquitination of proteins. Am J Pathol 186(11):2857−2868.

Mitochondrial DNA shows resistance to mutagen exposure

Research, funded in part by NIEHS, showed that the high rates of DNA mutations seen in mitochondria are not due to a sensitivity to damage or reduced repair capacity, as previously thought. The new work suggests that mitochondria can prevent induced DNA damage that leads to mutations in their genetic code.

The researchers examined effects of benzo[a]pyrene (B[a]P), a combustion byproduct in tobacco smoke and coal tar, and N ethyl N nitrosourea (ENU), which is known to induce mutations in the nuclear DNA of mice. After exposing mice to three different doses of B[a]P or one dose of ENU, every day for 28 days, the researchers applied a technique they developed previously to measure mutations in mitochondrial DNA.

The team found that after 4 weeks, none of the exposures led to an increased rate of mutations in mitochondrial DNA from the liver or bone marrow. However, the frequency of mutations in nuclear DNA increased significantly, from four to more than 150 times the usual rate, depending on the mutagen, dose, and tissue examined.

The researchers verified that B[a]P did cause DNA damage in the mitochondria, even though they detected no changes in the sequence of mitochondrial DNA. These results demonstrate that induced mitochondrial DNA damage does not readily convert into mutations. Further research is needed to better understand how mitochondria repress mutations after exposure to DNA-damaging agents.

Citation: Valente WJ, Ericson NG, Long AS, White PA, Marchetti F, Bielas JH. 2016. Mitochondrial DNA exhibits resistance to induced point and deletion mutations. Nucleic Acids Res 44(18):8513−8524.

Researchers discover how carbon nanotubes can harm cells from the inside

An NIEHS grantee and colleagues identified a nanochemical mechanism through which long and stiff carbon nanotubes damage lysosomes, which are membrane-enclosed organelles that break down damaged or unneeded biomolecules and debris inside the cell. These new findings could help scientists design safer nanomaterials.

Recent experimental studies have shown links between carbon nanotube toxicity and tube length and stiffness. However, scientists do not fully understand the reason for this or what happens to carbon nanotubes once they are inside cells. In the new study, the researchers combined analytical modeling, molecular dynamics simulations, and intracellular imaging of liver and lung cells, to form a picture of how one-dimensional carbon nanotubes behave inside lysosomes.

The researchers found that lysosomal membranes compressed long, stiff nanotubes, causing the nanotube tip to persistently contact the inner membrane. This contact led to the removal of lipids from the membrane, increased permeability of the lysosome, release of lysosomal protease into the cytoplasm, and eventually cell death. The researchers also created a classification diagram that showed the minimum and maximum nanotube dimensions required for this harmful process to occur in a wide variety of materials, including metals, oxides, and polymers.

Citation: Zhu W, von dem Bussche A, Yi X, Qiu Y, Wang Z, Weston P, Hurt RH, Kane AB, Gao H. 2016. Nanomechanical mechanism for lipid bilayer damage induced by carbon nanotubes confined in intracellular vesicles. Proc Natl Acad Sci U S A 113(44):12374−12379.