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Credit: NIGMS
Cells have several major repair systems that can fix DNA damage, which may lead to cancer and other diseases if not mended.
Unfortunately, the effectiveness of these repair systems varies greatly from person to person.
Now, researchers have developed a test that can rapidly assess several of these repair systems, which could potentially help us determine an individual’s risk of developing cancer and predict how a patient might respond to chemotherapy.
The new test, described in Proceedings of the National Academy of Sciences, can analyze 4 types of DNA repair capacity simultaneously, in less than 24 hours. Previous tests have only been able to evaluate a single system at a time.
“All of the repair pathways work differently, and the existing technology to measure each of those pathways is very different for each one,” said study author Zachary Nagel, PhD, of the Massachusetts Institute of Technology in Cambridge.
“What we wanted to do was come up with one way of measuring all DNA repair pathways at the same time so you have a single readout that’s easy to measure.”
The researchers used this approach to measure DNA repair in lymphoblastoid cells taken from 24 healthy subjects. The team found a huge range of variability, especially in one repair system, where some subjects’ cells were more than 10 times more efficient than others.
“None of the cells came out looking the same,” said study author Leona Samson, PhD, also of MIT. “They each have their own spectrum of what they can repair well and what they don’t repair well. It’s like a fingerprint for each person.”
Measuring repair
With the new test, the team can measure how well cells repair the most common DNA lesions, including single-strand breaks, double-strand breaks, mismatches, and the introduction of alkyl groups caused by pollutants such as fuel exhaust and tobacco smoke.
To achieve this, the researchers created 5 different circular pieces of DNA, 4 of which carry DNA lesions. Each of these circular DNA strands, or plasmids, also carries a gene for a different colored fluorescent protein.
In some cases, the DNA lesions prevent those genes from being expressed, so when the DNA is successfully repaired, the cell begins to produce the fluorescent protein. In others, repairing the DNA lesion turns the fluorescent gene off.
By introducing these plasmids into cells and reading the fluorescent output, scientists can determine how efficiently each kind of lesion has been repaired. In theory, more than 5 plasmids could go into each cell, but the researchers limited each experiment to 5 reporter plasmids to avoid potential overlap among colors.
To overcome that limitation, the researchers are also developing an alternative tactic that involves sequencing the messenger RNA produced by cells when they copy the plasmid genes, instead of measuring fluorescence.
In this study, the team tested the sequencing approach with just one type of DNA repair, but it could allow for unlimited tests at one time. And the researchers could customize the target DNA sequence to reveal information about which type of lesion the plasmid carries, as well as information about which patient’s cells are being tested.
This would provide the ability for many different patient samples to be tested in the same batch, making the test more cost-effective.
Making predictions
Previous studies have shown that many different types of DNA repair capacity can vary greatly among apparently healthy individuals. Some of these differences have been linked with cancer vulnerability.
Scientists have also identified links between DNA repair and neurological, developmental, and immunological disorders. But useful predictive DNA-repair-based tests have not been developed, largely because it has been impossible to rapidly analyze several different types of DNA repair capacity at once.
Dr Samson’s lab is now working on adapting the new test so it can be used with blood samples taken from patients, allowing researchers to identify patients who are at higher risk of disease and potentially enabling prevention or earlier diagnosis of diseases linked to DNA repair.
Such a test could also be used to predict a patient’s response to chemotherapy or to determine how much radiation treatment a patient can tolerate.
The researchers also believe this test could be exploited to screen for new drugs that inhibit or enhance DNA repair. Inhibitors could be targeted to tumors to make them more susceptible to chemotherapy, while enhancers could help protect people who have been accidentally exposed to DNA-damaging agents, such as radiation. 
Credit: NIGMS
Cells have several major repair systems that can fix DNA damage, which may lead to cancer and other diseases if not mended.
Unfortunately, the effectiveness of these repair systems varies greatly from person to person.
Now, researchers have developed a test that can rapidly assess several of these repair systems, which could potentially help us determine an individual’s risk of developing cancer and predict how a patient might respond to chemotherapy.
The new test, described in Proceedings of the National Academy of Sciences, can analyze 4 types of DNA repair capacity simultaneously, in less than 24 hours. Previous tests have only been able to evaluate a single system at a time.
“All of the repair pathways work differently, and the existing technology to measure each of those pathways is very different for each one,” said study author Zachary Nagel, PhD, of the Massachusetts Institute of Technology in Cambridge.
“What we wanted to do was come up with one way of measuring all DNA repair pathways at the same time so you have a single readout that’s easy to measure.”
The researchers used this approach to measure DNA repair in lymphoblastoid cells taken from 24 healthy subjects. The team found a huge range of variability, especially in one repair system, where some subjects’ cells were more than 10 times more efficient than others.
“None of the cells came out looking the same,” said study author Leona Samson, PhD, also of MIT. “They each have their own spectrum of what they can repair well and what they don’t repair well. It’s like a fingerprint for each person.”
Measuring repair
With the new test, the team can measure how well cells repair the most common DNA lesions, including single-strand breaks, double-strand breaks, mismatches, and the introduction of alkyl groups caused by pollutants such as fuel exhaust and tobacco smoke.
To achieve this, the researchers created 5 different circular pieces of DNA, 4 of which carry DNA lesions. Each of these circular DNA strands, or plasmids, also carries a gene for a different colored fluorescent protein.
In some cases, the DNA lesions prevent those genes from being expressed, so when the DNA is successfully repaired, the cell begins to produce the fluorescent protein. In others, repairing the DNA lesion turns the fluorescent gene off.
By introducing these plasmids into cells and reading the fluorescent output, scientists can determine how efficiently each kind of lesion has been repaired. In theory, more than 5 plasmids could go into each cell, but the researchers limited each experiment to 5 reporter plasmids to avoid potential overlap among colors.
To overcome that limitation, the researchers are also developing an alternative tactic that involves sequencing the messenger RNA produced by cells when they copy the plasmid genes, instead of measuring fluorescence.
In this study, the team tested the sequencing approach with just one type of DNA repair, but it could allow for unlimited tests at one time. And the researchers could customize the target DNA sequence to reveal information about which type of lesion the plasmid carries, as well as information about which patient’s cells are being tested.
This would provide the ability for many different patient samples to be tested in the same batch, making the test more cost-effective.
Making predictions
Previous studies have shown that many different types of DNA repair capacity can vary greatly among apparently healthy individuals. Some of these differences have been linked with cancer vulnerability.
Scientists have also identified links between DNA repair and neurological, developmental, and immunological disorders. But useful predictive DNA-repair-based tests have not been developed, largely because it has been impossible to rapidly analyze several different types of DNA repair capacity at once.
Dr Samson’s lab is now working on adapting the new test so it can be used with blood samples taken from patients, allowing researchers to identify patients who are at higher risk of disease and potentially enabling prevention or earlier diagnosis of diseases linked to DNA repair.
Such a test could also be used to predict a patient’s response to chemotherapy or to determine how much radiation treatment a patient can tolerate.
The researchers also believe this test could be exploited to screen for new drugs that inhibit or enhance DNA repair. Inhibitors could be targeted to tumors to make them more susceptible to chemotherapy, while enhancers could help protect people who have been accidentally exposed to DNA-damaging agents, such as radiation.
Credit: NIGMS
Cells have several major repair systems that can fix DNA damage, which may lead to cancer and other diseases if not mended.
Unfortunately, the effectiveness of these repair systems varies greatly from person to person.
Now, researchers have developed a test that can rapidly assess several of these repair systems, which could potentially help us determine an individual’s risk of developing cancer and predict how a patient might respond to chemotherapy.
The new test, described in Proceedings of the National Academy of Sciences, can analyze 4 types of DNA repair capacity simultaneously, in less than 24 hours. Previous tests have only been able to evaluate a single system at a time.
“All of the repair pathways work differently, and the existing technology to measure each of those pathways is very different for each one,” said study author Zachary Nagel, PhD, of the Massachusetts Institute of Technology in Cambridge.
“What we wanted to do was come up with one way of measuring all DNA repair pathways at the same time so you have a single readout that’s easy to measure.”
The researchers used this approach to measure DNA repair in lymphoblastoid cells taken from 24 healthy subjects. The team found a huge range of variability, especially in one repair system, where some subjects’ cells were more than 10 times more efficient than others.
“None of the cells came out looking the same,” said study author Leona Samson, PhD, also of MIT. “They each have their own spectrum of what they can repair well and what they don’t repair well. It’s like a fingerprint for each person.”
Measuring repair
With the new test, the team can measure how well cells repair the most common DNA lesions, including single-strand breaks, double-strand breaks, mismatches, and the introduction of alkyl groups caused by pollutants such as fuel exhaust and tobacco smoke.
To achieve this, the researchers created 5 different circular pieces of DNA, 4 of which carry DNA lesions. Each of these circular DNA strands, or plasmids, also carries a gene for a different colored fluorescent protein.
In some cases, the DNA lesions prevent those genes from being expressed, so when the DNA is successfully repaired, the cell begins to produce the fluorescent protein. In others, repairing the DNA lesion turns the fluorescent gene off.
By introducing these plasmids into cells and reading the fluorescent output, scientists can determine how efficiently each kind of lesion has been repaired. In theory, more than 5 plasmids could go into each cell, but the researchers limited each experiment to 5 reporter plasmids to avoid potential overlap among colors.
To overcome that limitation, the researchers are also developing an alternative tactic that involves sequencing the messenger RNA produced by cells when they copy the plasmid genes, instead of measuring fluorescence.
In this study, the team tested the sequencing approach with just one type of DNA repair, but it could allow for unlimited tests at one time. And the researchers could customize the target DNA sequence to reveal information about which type of lesion the plasmid carries, as well as information about which patient’s cells are being tested.
This would provide the ability for many different patient samples to be tested in the same batch, making the test more cost-effective.
Making predictions
Previous studies have shown that many different types of DNA repair capacity can vary greatly among apparently healthy individuals. Some of these differences have been linked with cancer vulnerability.
Scientists have also identified links between DNA repair and neurological, developmental, and immunological disorders. But useful predictive DNA-repair-based tests have not been developed, largely because it has been impossible to rapidly analyze several different types of DNA repair capacity at once.
Dr Samson’s lab is now working on adapting the new test so it can be used with blood samples taken from patients, allowing researchers to identify patients who are at higher risk of disease and potentially enabling prevention or earlier diagnosis of diseases linked to DNA repair.
Such a test could also be used to predict a patient’s response to chemotherapy or to determine how much radiation treatment a patient can tolerate.
The researchers also believe this test could be exploited to screen for new drugs that inhibit or enhance DNA repair. Inhibitors could be targeted to tumors to make them more susceptible to chemotherapy, while enhancers could help protect people who have been accidentally exposed to DNA-damaging agents, such as radiation.