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Updated: 14 hours 46 min ago
Study IDs key protein for cell death
When cells suffer too much DNA damage, they are usually forced to undergo programmed cell death, or apoptosis. However, cancer cells often ignore these signals, flourishing even after chemotherapy drugs have ravaged their DNA.
A new finding from MIT researchers may offer a way to overcome that resistance: The team has identified a key protein involved in an alternative death pathway known as programmed necrosis. Drugs that mimic the effects of this protein could push cancer cells that are resistant to apoptosis into necrosis instead.
While apoptosis is a tightly controlled procedure that breaks down and disposes of the dying cell in a very orderly way, necrosis is a messier process in which the cell’s membrane ruptures and its contents spill out.
“People really used to think of necrosis as cells just falling apart, that it wasn’t programmed and didn’t require gene products to make it happen,” says Leona Samson, a member of MIT’s Center for Environmental Health Sciences and Koch Institute for Integrative Cancer Research. “In the last few years it has become more clear that this is an active process that requires proteins to take place.”
In the May 10 online edition of the journal Genes and Development, Samson and colleagues report that a protein known as ALKBH7 plays a key role in controlling the programmed necrosis pathway. Dragony Fu, a former postdoc in Samson’s lab, is the paper’s lead author, and postdoc Jennifer Jordan is also an author.
Unexpected findings
ALKBH7 belongs to a family of proteins first discovered in E. coli about a dozen years ago as part of a DNA-repair mechanism. In humans, there are nine different ALKBH proteins, which Samson’s lab has been studying for several years.
Most of the mammalian ALKBH proteins appear to be involved in DNA repair, similar to the original E. coli version. In particular, they respond to DNA damage caused by alkylating agents. These agents can be found in pollutants such as fuel exhaust and tobacco smoke, and are also used to treat cancer.
In the new paper, Samson, a professor of biology and biological engineering, and her colleagues found that ALKBH7 has an unexpected effect. When the researchers lowered ALKBH7 levels in human cells grown in the lab, those cells were much more likely to survive DNA damage than cells with normal ALKBH7 levels. This suggests that ALKBH7 actually promotes cell death.
“That was a surprising finding, because previously all of these ALKBH proteins were shown to be helping the cell survive when exposed to damage,” says Fu, who is now a visiting research fellow at the University of Zurich.
Upon further investigation, the researchers found that when healthy cells suffer massive DNA damage from alkylating agents, they enter the programmed necrosis pathway. Necrosis, which can also be initiated by bacterial or viral infection, is believed to help the body’s immune system detect threats.
“When dying cells release their contents during necrosis, it serves as a warning signal for your body that there is a virus there and recruits macrophages and other immune cells to the area,” Fu says.
Potential drug targets
The findings suggest that when DNA is so badly harmed that cells can’t repair it, the programmed necrosis pathway kicks in to prevent cells with major genetic damage from potentially become cancerous.
Other researchers have shown that some types of cancer cells have much lower ALKBH7 levels than normal cells. This suggests that the cancer cells have gained the ability to evade programmed necrosis, helping them to survive, Fu says.
The necrosis pathway appears to be initiated by an enzyme called PARP, which becomes hyperactive following DNA damage and shuts down the cell’s production of two molecules that carry energy, ATP and NAD. The MIT team found that ALKBH7 prevents ATP and NAD levels from returning to normal by disrupting the function of mitochondria — the cell structures that generate energy for a cell.
Without an adequate supply of those critical energy-carrying molecules, the cell cannot survive and undergoes necrosis. In cells that lack ALKBH7, ATP and NAD levels rebound, and the cells survive, carrying a heavy burden of DNA damage.
The researchers are now investigating the molecular details of the programmed necrosis pathway in hopes of identifying ways to activate it in cancer cells.
“The observations reported in this paper open up the possibility that novel treatments could be developed to treat tumors that are relatively resistant to killing via the apoptotic pathway,” says Ashok Bhagwat, a professor of chemistry at Wayne State University who was not part of the research team.
The research was funded by the National Institutes of Health and the American Cancer Society.
A new finding from MIT researchers may offer a way to overcome that resistance: The team has identified a key protein involved in an alternative death pathway known as programmed necrosis. Drugs that mimic the effects of this protein could push cancer cells that are resistant to apoptosis into necrosis instead.
While apoptosis is a tightly controlled procedure that breaks down and disposes of the dying cell in a very orderly way, necrosis is a messier process in which the cell’s membrane ruptures and its contents spill out.
“People really used to think of necrosis as cells just falling apart, that it wasn’t programmed and didn’t require gene products to make it happen,” says Leona Samson, a member of MIT’s Center for Environmental Health Sciences and Koch Institute for Integrative Cancer Research. “In the last few years it has become more clear that this is an active process that requires proteins to take place.”
In the May 10 online edition of the journal Genes and Development, Samson and colleagues report that a protein known as ALKBH7 plays a key role in controlling the programmed necrosis pathway. Dragony Fu, a former postdoc in Samson’s lab, is the paper’s lead author, and postdoc Jennifer Jordan is also an author.
Unexpected findings
ALKBH7 belongs to a family of proteins first discovered in E. coli about a dozen years ago as part of a DNA-repair mechanism. In humans, there are nine different ALKBH proteins, which Samson’s lab has been studying for several years.
Most of the mammalian ALKBH proteins appear to be involved in DNA repair, similar to the original E. coli version. In particular, they respond to DNA damage caused by alkylating agents. These agents can be found in pollutants such as fuel exhaust and tobacco smoke, and are also used to treat cancer.
In the new paper, Samson, a professor of biology and biological engineering, and her colleagues found that ALKBH7 has an unexpected effect. When the researchers lowered ALKBH7 levels in human cells grown in the lab, those cells were much more likely to survive DNA damage than cells with normal ALKBH7 levels. This suggests that ALKBH7 actually promotes cell death.
“That was a surprising finding, because previously all of these ALKBH proteins were shown to be helping the cell survive when exposed to damage,” says Fu, who is now a visiting research fellow at the University of Zurich.
Upon further investigation, the researchers found that when healthy cells suffer massive DNA damage from alkylating agents, they enter the programmed necrosis pathway. Necrosis, which can also be initiated by bacterial or viral infection, is believed to help the body’s immune system detect threats.
“When dying cells release their contents during necrosis, it serves as a warning signal for your body that there is a virus there and recruits macrophages and other immune cells to the area,” Fu says.
Potential drug targets
The findings suggest that when DNA is so badly harmed that cells can’t repair it, the programmed necrosis pathway kicks in to prevent cells with major genetic damage from potentially become cancerous.
Other researchers have shown that some types of cancer cells have much lower ALKBH7 levels than normal cells. This suggests that the cancer cells have gained the ability to evade programmed necrosis, helping them to survive, Fu says.
The necrosis pathway appears to be initiated by an enzyme called PARP, which becomes hyperactive following DNA damage and shuts down the cell’s production of two molecules that carry energy, ATP and NAD. The MIT team found that ALKBH7 prevents ATP and NAD levels from returning to normal by disrupting the function of mitochondria — the cell structures that generate energy for a cell.
Without an adequate supply of those critical energy-carrying molecules, the cell cannot survive and undergoes necrosis. In cells that lack ALKBH7, ATP and NAD levels rebound, and the cells survive, carrying a heavy burden of DNA damage.
The researchers are now investigating the molecular details of the programmed necrosis pathway in hopes of identifying ways to activate it in cancer cells.
“The observations reported in this paper open up the possibility that novel treatments could be developed to treat tumors that are relatively resistant to killing via the apoptotic pathway,” says Ashok Bhagwat, a professor of chemistry at Wayne State University who was not part of the research team.
The research was funded by the National Institutes of Health and the American Cancer Society.
Categories: Cancer Research
A different view of cancer cells
Most cancer deaths are caused by metastatic tumors, which break free from the original cancer site and spread throughout the body. For that to happen, cancer cells must undergo many genetic and physical changes.
Many of those genetic changes have been studied extensively, but it has been more difficult to study the physical changes. Now, MIT researchers have developed a way to study three key physical properties of cancer cells — their mass, stiffness and friction — on a large scale.
Using this system, the researchers have analyzed how changes in those traits may allow cancer cells to migrate to new sites: Scientists have previously observed that cell lines with higher metastatic potential are generally more deformable, but the MIT team found that decreased friction also appears to help cancer cells traverse narrow channels, suggesting that friction may play a role in the ability of cancer cells to travel in blood vessels and reach new tumor sites.
“Our measurements provide an additional perspective on cell properties that may complement genomic and proteomic approaches,” says Sangwon Byun, an MIT postdoc and lead author of a paper describing the findings in the Proceedings of the National Academy of Sciences the week of April 22.
The system that Byun and colleagues used to study the cancer cells is based on a device previously developed by Scott Manalis, a member of MIT's Koch Institute for Integrative Cancer Research and an MIT professor of biological engineering. Manalis, the senior author of the PNAS paper, has previously demonstrated that this system, known as a suspended microchannel resonator (SMR), can very accurately measure the mass and density of individual cells.
Inside the SMR, cells flow through a channel carved into a tiny slab that vibrates at a resonant frequency that can be measured with a laser beam. As each cell flows through the channel, the slab’s resonant frequency changes, allowing the researchers to calculate the cell’s mass and density.
Putting the squeeze on cells
For the new study, the researchers modified the system so they can also track each cell’s velocity as it passes through a narrow constriction in the channel. This allows them to estimate both the cell’s deformability and how much friction it experiences as it travels through the constriction, which is slightly smaller than the diameter of the cells under study. Cells that squeeze through this opening faster are more deformable.
In one set of experiments, the researchers compared the deformability of two types of mouse lung-cancer cells. The two cell types differ in the expression of only one transcription factor, known as NKX2-1: Cancer cells not expressing this factor are more aggressive and likely to metastasize. The researchers found that cells that do not express NKX2-1 entered the narrow channel more rapidly, confirming previous studies showing that metastatic cells are more deformable.
The researchers then compared nonmetastatic and metastatic cells from the same mouse model, and found that these metastatic cells were not only more deformable, but they also traveled faster through the length of the constriction (about 50 microns). A similar observation was made when comparing nonmetastatic to metastatic human lung-cancer cell lines. “It seems that the cells experience less friction, making it easier for them to get through the channels,” Byun says.
This phenomenon has not been seen before, in part because scientists haven’t had a good way to simultaneously define the size, deformability and friction of individual flowing cells. Many factors could influence the friction between the cell and the channel wall, including changes in cell-surface expression. For example, metastatic cancer cells often have an increased amount of sialic acid molecules on their surfaces, which may alter friction, the researchers say.
The new MIT system is “probably the world’s most sensitive instrument for measuring a number of different biophysical properties of individual cells,” says Mehmet Toner, a professor of biomedical engineering at Massachusetts General Hospital and Harvard Medical School who was not part of the research team. “It’s very important to know whether metastatic cells have biophysical properties different than normal or nonmetastatic cancer cells, allowing them to go through narrow spaces.”
Circulating tumor cells
The researchers are now using their system to detect circulating tumor cells (CTCs) in cancer patients’ blood samples. The current approach to finding CTCs, which can range in number from a few to several thousand per milliliter of blood, is by looking for a marker (a molecule found on a cell’s surface) that is preferentially expressed by epithelial cells. However, that approach may miss CTCs that don’t express the chosen epithelial markers.
“When you use a specific marker to look for these cells, you find the cells that you’re looking for, but you may be missing a whole population of cells,” says Josephine Shaw, an MIT graduate student and a co-author of the paper. “It’s possible that by using a more holistic and physical approach, we may be able to find certain cells that we wouldn’t be able to find molecularly, because we wouldn’t be able to guess ahead of time what these cells would be expressing.”
Once those cells were captured, scientists could do many more types of tests on them, including analysis of genes expressed and proteins produced, to learn more about how they break free from tumors.
The researchers also plan to study physical changes that occur in cells as they go through the epithelial-mesenchymal transition — a process that allows cancer cells to lose their adhesion and become mobile, helping them metastasize.
Other authors of the paper are MIT postdoc Sungmin Son; Stanford University postdoc Dario Amodei; MIT grad students Nathan Cermak, Joon Ho Kang and Vivian Hecht; former MIT postdoc Monte Winslow; Tyler Jacks, the David H. Koch Professor of Biology at MIT and director of the Koch Institute; and Parag Mallick, an assistant professor of radiology at Stanford.
The research was funded by the National Cancer Institute, through MIT’s Physical Sciences Oncology Center and Stanford’s Center for Cancer Nanotechnology Excellence and Translation, and Stand Up to Cancer.
Many of those genetic changes have been studied extensively, but it has been more difficult to study the physical changes. Now, MIT researchers have developed a way to study three key physical properties of cancer cells — their mass, stiffness and friction — on a large scale.
Using this system, the researchers have analyzed how changes in those traits may allow cancer cells to migrate to new sites: Scientists have previously observed that cell lines with higher metastatic potential are generally more deformable, but the MIT team found that decreased friction also appears to help cancer cells traverse narrow channels, suggesting that friction may play a role in the ability of cancer cells to travel in blood vessels and reach new tumor sites.
“Our measurements provide an additional perspective on cell properties that may complement genomic and proteomic approaches,” says Sangwon Byun, an MIT postdoc and lead author of a paper describing the findings in the Proceedings of the National Academy of Sciences the week of April 22.
The system that Byun and colleagues used to study the cancer cells is based on a device previously developed by Scott Manalis, a member of MIT's Koch Institute for Integrative Cancer Research and an MIT professor of biological engineering. Manalis, the senior author of the PNAS paper, has previously demonstrated that this system, known as a suspended microchannel resonator (SMR), can very accurately measure the mass and density of individual cells.
Inside the SMR, cells flow through a channel carved into a tiny slab that vibrates at a resonant frequency that can be measured with a laser beam. As each cell flows through the channel, the slab’s resonant frequency changes, allowing the researchers to calculate the cell’s mass and density.
Putting the squeeze on cells
For the new study, the researchers modified the system so they can also track each cell’s velocity as it passes through a narrow constriction in the channel. This allows them to estimate both the cell’s deformability and how much friction it experiences as it travels through the constriction, which is slightly smaller than the diameter of the cells under study. Cells that squeeze through this opening faster are more deformable.
In one set of experiments, the researchers compared the deformability of two types of mouse lung-cancer cells. The two cell types differ in the expression of only one transcription factor, known as NKX2-1: Cancer cells not expressing this factor are more aggressive and likely to metastasize. The researchers found that cells that do not express NKX2-1 entered the narrow channel more rapidly, confirming previous studies showing that metastatic cells are more deformable.
The researchers then compared nonmetastatic and metastatic cells from the same mouse model, and found that these metastatic cells were not only more deformable, but they also traveled faster through the length of the constriction (about 50 microns). A similar observation was made when comparing nonmetastatic to metastatic human lung-cancer cell lines. “It seems that the cells experience less friction, making it easier for them to get through the channels,” Byun says.
This phenomenon has not been seen before, in part because scientists haven’t had a good way to simultaneously define the size, deformability and friction of individual flowing cells. Many factors could influence the friction between the cell and the channel wall, including changes in cell-surface expression. For example, metastatic cancer cells often have an increased amount of sialic acid molecules on their surfaces, which may alter friction, the researchers say.
The new MIT system is “probably the world’s most sensitive instrument for measuring a number of different biophysical properties of individual cells,” says Mehmet Toner, a professor of biomedical engineering at Massachusetts General Hospital and Harvard Medical School who was not part of the research team. “It’s very important to know whether metastatic cells have biophysical properties different than normal or nonmetastatic cancer cells, allowing them to go through narrow spaces.”
Circulating tumor cells
The researchers are now using their system to detect circulating tumor cells (CTCs) in cancer patients’ blood samples. The current approach to finding CTCs, which can range in number from a few to several thousand per milliliter of blood, is by looking for a marker (a molecule found on a cell’s surface) that is preferentially expressed by epithelial cells. However, that approach may miss CTCs that don’t express the chosen epithelial markers.
“When you use a specific marker to look for these cells, you find the cells that you’re looking for, but you may be missing a whole population of cells,” says Josephine Shaw, an MIT graduate student and a co-author of the paper. “It’s possible that by using a more holistic and physical approach, we may be able to find certain cells that we wouldn’t be able to find molecularly, because we wouldn’t be able to guess ahead of time what these cells would be expressing.”
Once those cells were captured, scientists could do many more types of tests on them, including analysis of genes expressed and proteins produced, to learn more about how they break free from tumors.
The researchers also plan to study physical changes that occur in cells as they go through the epithelial-mesenchymal transition — a process that allows cancer cells to lose their adhesion and become mobile, helping them metastasize.
Other authors of the paper are MIT postdoc Sungmin Son; Stanford University postdoc Dario Amodei; MIT grad students Nathan Cermak, Joon Ho Kang and Vivian Hecht; former MIT postdoc Monte Winslow; Tyler Jacks, the David H. Koch Professor of Biology at MIT and director of the Koch Institute; and Parag Mallick, an assistant professor of radiology at Stanford.
The research was funded by the National Cancer Institute, through MIT’s Physical Sciences Oncology Center and Stanford’s Center for Cancer Nanotechnology Excellence and Translation, and Stand Up to Cancer.
Categories: Cancer Research
Study reveals how melanoma evades chemotherapy
Nitric oxide (NO), a gas with many biological functions in healthy cells, can also help some cancer cells survive chemotherapy. A new study from MIT reveals one way in which this resistance may arise, and raises the possibility of weakening cancer cells by cutting off their supply of NO.
The findings, presented today at the annual meeting of the American Association for Cancer Research, focus on melanoma — a cancer that is difficult to treat, especially in its later stages. The prognosis is generally worse for patients whose tumors have high levels of NO, says Luiz Godoy, an MIT research associate and lead author of the study.
Luiz Godoy Photo: M. Scott Brauer
Godoy and his colleagues have unraveled the mechanism behind melanoma’s resistance to cisplatin, a commonly used chemotherapy drug, and, in ongoing studies, have found that cisplatin treatment also increases NO levels in breast and colon cancers.
“This could be a mechanism that is widely shared in different cancers, and if you use the drugs that are already used to treat cancer, along with other drugs that could scavenge or decrease the production of NO, you may have a synergistic effect,” says Godoy, who works in the lab of Gerald Wogan, an MIT professor emeritus of biological engineering and senior author of the study.
NO has many roles within living cells. At low concentrations, it helps regulate processes such as cell death and muscle contraction. NO, which is a free radical, is also important for immune-system function. Immune cells, such as macrophages, produce large amounts of NO during infection, helping to kill invading microbes by damaging their DNA or other cell components.
“It’s really a molecule that has a dual effect,” Godoy says. “At low concentrations it can act as a signaling molecule, while high concentrations will be toxic.”
Knocking out NO
In the new study, the researchers treated melanoma cells grown in the lab with drugs that capture NO before it can act. They then treated the cells with cisplatin and tracked cell-death rates. The NO-depleted cells became much more sensitive to the drug, confirming earlier findings.
The MIT team then went a step further, investigating how NO confers its survival benefits. It was already known that NO can alter protein function through a process known as S-nitrosation, which involves attaching NO to the target protein. S-nitrosation can affect many proteins, but in this study the researchers focused on two that are strongly linked with cell death and survival, known as caspase-3 and PHD2.
The role of caspase-3 is to stimulate cell suicide, under the appropriate conditions, but adding NO to the protein deactivates it. This prevents the cell from dying even when treated with cisplatin, a drug that produces massive DNA damage.
PHD2 is also involved in cell death; its role is to help break down another protein called HIF-1 alpha, which is a pro-survival protein. When NO inactivates PHD2, HIF-1 alpha stays intact and keeps the cell alive.
“Now we have a mechanistic link between nitric oxide and the increased aggressiveness of melanoma,” says Douglas Thomas, an assistant professor of medicinal chemistry and pharmacognosy at the University of Illinois at Chicago, who was not part of the research team. “It certainly would be worth exploring whether this mechanism is also present in different tumor types as well.”
The MIT researchers also found in some cancer cells, NO levels were five times higher than normal following cisplatin treatment. Godoy is now investigating how cisplatin stimulates that NO boost, and is also looking for other proteins that NO may be targeting.
Researchers in Wogan’s lab also plan to start testing cisplatin in combination with drugs that block NO production in animals.
The research was funded by the National Cancer Institute and the National Institute of Environmental Health Sciences. The research team also published its findings in a November 2012 article in the Proceedings of the National Academy of Sciences. Other authors of that paper were graduate student Chase Anderson, postdoc Rajdeep Chowdhury and technical associate Laura Trudel.
The findings, presented today at the annual meeting of the American Association for Cancer Research, focus on melanoma — a cancer that is difficult to treat, especially in its later stages. The prognosis is generally worse for patients whose tumors have high levels of NO, says Luiz Godoy, an MIT research associate and lead author of the study.
Luiz Godoy Photo: M. Scott Brauer
Godoy and his colleagues have unraveled the mechanism behind melanoma’s resistance to cisplatin, a commonly used chemotherapy drug, and, in ongoing studies, have found that cisplatin treatment also increases NO levels in breast and colon cancers.
“This could be a mechanism that is widely shared in different cancers, and if you use the drugs that are already used to treat cancer, along with other drugs that could scavenge or decrease the production of NO, you may have a synergistic effect,” says Godoy, who works in the lab of Gerald Wogan, an MIT professor emeritus of biological engineering and senior author of the study.
NO has many roles within living cells. At low concentrations, it helps regulate processes such as cell death and muscle contraction. NO, which is a free radical, is also important for immune-system function. Immune cells, such as macrophages, produce large amounts of NO during infection, helping to kill invading microbes by damaging their DNA or other cell components.
“It’s really a molecule that has a dual effect,” Godoy says. “At low concentrations it can act as a signaling molecule, while high concentrations will be toxic.”
Knocking out NO
In the new study, the researchers treated melanoma cells grown in the lab with drugs that capture NO before it can act. They then treated the cells with cisplatin and tracked cell-death rates. The NO-depleted cells became much more sensitive to the drug, confirming earlier findings.
The MIT team then went a step further, investigating how NO confers its survival benefits. It was already known that NO can alter protein function through a process known as S-nitrosation, which involves attaching NO to the target protein. S-nitrosation can affect many proteins, but in this study the researchers focused on two that are strongly linked with cell death and survival, known as caspase-3 and PHD2.
The role of caspase-3 is to stimulate cell suicide, under the appropriate conditions, but adding NO to the protein deactivates it. This prevents the cell from dying even when treated with cisplatin, a drug that produces massive DNA damage.
PHD2 is also involved in cell death; its role is to help break down another protein called HIF-1 alpha, which is a pro-survival protein. When NO inactivates PHD2, HIF-1 alpha stays intact and keeps the cell alive.
“Now we have a mechanistic link between nitric oxide and the increased aggressiveness of melanoma,” says Douglas Thomas, an assistant professor of medicinal chemistry and pharmacognosy at the University of Illinois at Chicago, who was not part of the research team. “It certainly would be worth exploring whether this mechanism is also present in different tumor types as well.”
The MIT researchers also found in some cancer cells, NO levels were five times higher than normal following cisplatin treatment. Godoy is now investigating how cisplatin stimulates that NO boost, and is also looking for other proteins that NO may be targeting.
Researchers in Wogan’s lab also plan to start testing cisplatin in combination with drugs that block NO production in animals.
The research was funded by the National Cancer Institute and the National Institute of Environmental Health Sciences. The research team also published its findings in a November 2012 article in the Proceedings of the National Academy of Sciences. Other authors of that paper were graduate student Chase Anderson, postdoc Rajdeep Chowdhury and technical associate Laura Trudel.
Categories: Cancer Research
How to minimize the side effects of cancer treatment
New research from MIT may allow scientists to develop a test that can predict the severity of side effects of some common chemotherapy agents in individual patients, allowing doctors to tailor treatments to minimize the damage.
The study focused on powerful cancer drugs known as alkylating agents, which damage DNA by attaching molecules containing carbon atoms to it. Found in tobacco smoke and in byproducts of fuel combustion, these compounds can actually cause cancer. However, because they can kill tumor cells, very reactive alkylating agents are also used to treat cancer.
The new paper, which appears in the April 4 issue of the journal PLoS Genetics, reveals that the amount of cellular damage that alkylating agents produce in healthy tissues can depend on how much of a certain DNA-repair enzyme is present in those cells. Levels of this enzyme, known as Aag, vary widely among different tissues within an individual, and among different individuals.
Leona Samson, a member of MIT’s Center for Environmental Health Sciences and the David H. Koch Institute for Integrative Cancer Research, is the senior author of the paper. She has previously shown that when alkylating agents damage DNA, the Aag enzyme is called into action as part of a DNA-repair process known as base excision repair. Aag cuts out the DNA base that is damaged, and other enzymes cleave the DNA sugar-phosphate backbone, trim the DNA ends and then fill in the empty spot with new DNA.
In this work, the researchers studied mice engineered to produce varying levels of Aag over a 10- to 15-fold range. This is similar to the natural range found in the human population.
The mice with increased levels of Aag resembled normal mice in their lifespan and likelihood of developing cancer, says Jennifer Calvo, a research scientist in Samson’s lab and lead author of the paper. However, “we found drastic differences when we started challenging them with these alkylating agents,” she says.
Mice with excessive or even normal levels of the Aag enzyme showed much greater levels of cell death in certain tissues after being treated with alkylating agents.
“It’s counterintuitive that extra DNA-repair capacity, or even the normal level, is bad for you,” says Samson, who is a professor of biological engineering and biology at MIT. “It seems that you can have too much of a good thing.”
A fine balance
It appears that too much Aag can upset the balance in the base excision repair pathway, the researchers say. This pathway involves several steps, some of which produce intermediates that can be extremely toxic to the cell if they do not promptly move to the next step. The researchers theorize that when Aag is too active, these toxic intermediates build up and destroy the cell.
Certain organs appear more vulnerable to this Aag-mediated tissue damage — in particular, the retina, pancreas, cerebellum and bone marrow — and the tissue damage is specific to certain types of cells within those tissues. Samson says all of the cells are likely experiencing similar DNA damage, but for some reason they don’t all respond the same way.
“It’s a very cell-specific phenomenon,” she says. “We haven’t completely gotten to the bottom of what it is that makes some cells behave in a certain way when they make zero or extra of a certain enzyme.”
That kind of specificity has not been seen before, notes Samuel Wilson, a principal investigator at the National Institute of Environmental Health Sciences. “It points to a different dynamic for base-lesion repair in different tissues,” says Wilson, who was not involved in the research. “That fundamental question of why there are tissue-specific differences would be very interesting to follow up on.”
The researchers found that an enzyme called Parp1 also plays an important role in Aag-related tissue damage. Parp1 helps to promote the repair of single-stranded breaks in DNA; such breaks are readily produced after Aag cuts out a damaged base. When Parp1 recognizes such a break, it starts to coat itself with chains of molecules called PolyADP-ribose, which then helps to recruit some of the additional proteins needed to continue the repair process.
When there is too much Aag, Parp1 becomes overactive and begins to deplete the cell’s stores of NAD and ATP, which are critical for energy transfer in cells. Without enough NAD and ATP, the cell goes into an energetic crisis and dies.
Measuring levels of Aag, Parp1 and other enzymes before chemotherapy could be useful for doctors, not only to minimize side effects but also to maximize drugs’ effects on cancer cells, Samson says.
“Aag is just one of many enzymes that you’d probably want to know the level of, and in the end make some kind of matrix to determine what the therapeutic window would be,” she says. “We’re trying to develop ways of measuring the activity of a whole battery of different DNA repair pathways in one mega-assay.”
The study focused on powerful cancer drugs known as alkylating agents, which damage DNA by attaching molecules containing carbon atoms to it. Found in tobacco smoke and in byproducts of fuel combustion, these compounds can actually cause cancer. However, because they can kill tumor cells, very reactive alkylating agents are also used to treat cancer.
The new paper, which appears in the April 4 issue of the journal PLoS Genetics, reveals that the amount of cellular damage that alkylating agents produce in healthy tissues can depend on how much of a certain DNA-repair enzyme is present in those cells. Levels of this enzyme, known as Aag, vary widely among different tissues within an individual, and among different individuals.
Leona Samson, a member of MIT’s Center for Environmental Health Sciences and the David H. Koch Institute for Integrative Cancer Research, is the senior author of the paper. She has previously shown that when alkylating agents damage DNA, the Aag enzyme is called into action as part of a DNA-repair process known as base excision repair. Aag cuts out the DNA base that is damaged, and other enzymes cleave the DNA sugar-phosphate backbone, trim the DNA ends and then fill in the empty spot with new DNA.
In this work, the researchers studied mice engineered to produce varying levels of Aag over a 10- to 15-fold range. This is similar to the natural range found in the human population.
The mice with increased levels of Aag resembled normal mice in their lifespan and likelihood of developing cancer, says Jennifer Calvo, a research scientist in Samson’s lab and lead author of the paper. However, “we found drastic differences when we started challenging them with these alkylating agents,” she says.
Mice with excessive or even normal levels of the Aag enzyme showed much greater levels of cell death in certain tissues after being treated with alkylating agents.
“It’s counterintuitive that extra DNA-repair capacity, or even the normal level, is bad for you,” says Samson, who is a professor of biological engineering and biology at MIT. “It seems that you can have too much of a good thing.”
A fine balance
It appears that too much Aag can upset the balance in the base excision repair pathway, the researchers say. This pathway involves several steps, some of which produce intermediates that can be extremely toxic to the cell if they do not promptly move to the next step. The researchers theorize that when Aag is too active, these toxic intermediates build up and destroy the cell.
Certain organs appear more vulnerable to this Aag-mediated tissue damage — in particular, the retina, pancreas, cerebellum and bone marrow — and the tissue damage is specific to certain types of cells within those tissues. Samson says all of the cells are likely experiencing similar DNA damage, but for some reason they don’t all respond the same way.
“It’s a very cell-specific phenomenon,” she says. “We haven’t completely gotten to the bottom of what it is that makes some cells behave in a certain way when they make zero or extra of a certain enzyme.”
That kind of specificity has not been seen before, notes Samuel Wilson, a principal investigator at the National Institute of Environmental Health Sciences. “It points to a different dynamic for base-lesion repair in different tissues,” says Wilson, who was not involved in the research. “That fundamental question of why there are tissue-specific differences would be very interesting to follow up on.”
The researchers found that an enzyme called Parp1 also plays an important role in Aag-related tissue damage. Parp1 helps to promote the repair of single-stranded breaks in DNA; such breaks are readily produced after Aag cuts out a damaged base. When Parp1 recognizes such a break, it starts to coat itself with chains of molecules called PolyADP-ribose, which then helps to recruit some of the additional proteins needed to continue the repair process.
When there is too much Aag, Parp1 becomes overactive and begins to deplete the cell’s stores of NAD and ATP, which are critical for energy transfer in cells. Without enough NAD and ATP, the cell goes into an energetic crisis and dies.
Measuring levels of Aag, Parp1 and other enzymes before chemotherapy could be useful for doctors, not only to minimize side effects but also to maximize drugs’ effects on cancer cells, Samson says.
“Aag is just one of many enzymes that you’d probably want to know the level of, and in the end make some kind of matrix to determine what the therapeutic window would be,” she says. “We’re trying to develop ways of measuring the activity of a whole battery of different DNA repair pathways in one mega-assay.”
Categories: Cancer Research
Practicing medicine at the nanoscale
With the recent launch of MIT’s Institute for Medical Engineering and Science, MIT News examines research with the potential to reshape medicine and health care through new scientific knowledge, novel treatments and products, better management of medical data, and improvements in health-care delivery.
Modern medicine is largely based on treating patients with “small-molecule” drugs, which include pain relievers like aspirin and antibiotics such as penicillin.
Those drugs have prolonged the human lifespan and made many life-threatening ailments easily treatable, but scientists believe the new approach of nanoscale drug delivery can offer even more progress. Delivering RNA or DNA to specific cells offers the promise of selectively turning genes on or off, while nanoscale devices that can be injected or implanted in the body could allow doctors to target drugs to specific tissues over a defined period of time.
“There’s a growing understanding of the biological basis of disease, and a growing understanding of the roles certain genes play in disease,” says Daniel Anderson, the Samuel A. Goldblith Associate Professor of Chemical Engineering and a member of MIT’s Institute for Medical Engineering and Science and David H. Koch Institute for Integrative Cancer Research. “The question is, ‘How can we take advantage of this?’”
Researchers in Anderson’s lab, as well as many others at MIT, are working on new ways to deliver RNA and DNA to treat a variety of diseases. Cancer is a primary target, but deliveries of genetic material could also help with many diseases caused by defective genes, including Huntington’s disease and hemophilia. “There are many genes that we think if we could just turn them off or turn them on, it could be therapeutic,” Anderson says.
One promising avenue is RNA interference (RNAi), a naturally occurring process that allows cells to fine-tune their gene expression. Short strands of RNA called siRNA intercept and destroy messenger RNA before it can carry protein-building instructions from DNA to the rest of the cell. Scientists hope that by creating their own siRNA to target specific genes, they will be able to turn off genes that cause disease.
However, this potential has not yet been realized because of challenges in safely delivering siRNA to the right tissues and avoiding other tissues. Using viruses is one possibility, but is an option that carries some safety risks, so many researchers are now investigating synthetic delivery vehicles for genetic material.
Anderson’s lab is developing materials called lipidoids, fatty molecules that can envelop and deliver strands of siRNA. Studies have shown that these materials can effectively deliver RNA and shrink tumors in animals; MIT researchers are now working on developing them for human tests. These particles can deliver many RNA sequences at once, allowing researchers to target multiple genes. “A lot of these diseases, in particular cancer, are complicated and may require turning off multiple genes, or turning some genes off and some genes on,” Anderson says.
Anderson is also using a technique called nucleic-acid origami to fold DNA and RNA into structures suitable for targeting cancer cells. Nucleic-acid origami, developed within the past few years, allows for extremely precise control over the location of every atom within a structure — something that is difficult to achieve with other types of nanoparticles, Anderson says.
In a 2012 study involving mice, Anderson showed that folded DNA nanoparticles tagged with folate accumulated in ovarian cancer cells, which express many more folate receptors on their surfaces than healthy cells.
Multipronged approach
Paula Hammond, the David H. Koch Professor of Engineering and a member of the Koch Institute, is also developing new materials for delivering both RNA and traditional drugs. Using her layer-by-layer assembly technique, she is creating nanoparticles that incorporate layers of multiple types of RNA, or combine RNA with a chemotherapy drug.
This multipronged attack could allow researchers to design treatments that cut off many of tumor cells’ possible escape routes. “We’re very interested in looking at combinations that would involve RNAi that knocks down the ability of cells to counteract chemotherapy attack,” Hammond says.
Hammond’s research in this area is now focused on cancer, but the approach could also lend itself to treating the inflammation produced by infectious diseases, she says. “With RNAi, the approach is fairly modular, and once you understand which genes you need to impact, you can work on targeting them,” Hammond says.
Hammond’s lab is also working on medical-device coatings that could secrete useful drugs, hormones or growth factors. One such project involves coating hip implants with layers that secrete bone growth factors. In studies with animals, she has shown that these coatings can promote the growth of natural bone, and stronger adhesion between hip implants and the body’s own bone. If the work translates to human clinical use, it could allow hip implants to last longer and reduce the need for additional surgeries to replace the implants.
Hammond is also working on materials that promote wound healing by preprogrammed release of growth factors from bandages and dressings, and on ultrathin, transparent coatings for cataract-replacement lenses that release anti-inflammatory drugs.
Delivery and diagnostics
Michael Cima, the David H. Koch Professor of Engineering, and Robert Langer, the David H. Koch Institute Professor, both members of the Koch Institute, are working on nano- and microscale devices that can be implanted in the body to release drugs or diagnose disease.
Several years ago, Cima and Langer began working on an implantable chip that can dispense medicine inside the body, but which is controlled wirelessly from outside the body. In clinical trials last year, the company developing the chip for commercial use showed that it could reliably deliver precise doses of an osteoporosis medication that is normally given by injection.
The company developing the chip, MicroCHIPS Inc., is now shrinking the device and increasing the number of drug reservoirs on the chip (the version used in last year’s trial had 20 such wells). That may enable the device to be used for much longer time periods — up to 30 years, Cima says. That would allow it to serve as an artificial gland, releasing hormones as necessary, he says, especially if a sensor could be incorporated to alert the chip when to release a dose.
Such a device could be useful for many endocrine diseases. “Diseases of growth, development and reproduction are all areas where there are significant unmet needs, or therapies that are very difficult to implement,” Cima says.
Cima is also working on diagnostic devices that could help monitor tumor response to treatment, or detect whether someone has had a heart attack. His strategy is to take tests originally developed for in-vitro use (where a sample is removed from the body and tested in a lab), and instead put the sensing device inside the body. These diagnostic devices would be implanted in conjunction with a medical procedure.
For example, when cancer is suspected, a biopsy is done on a patient. Cima is now developing devices that could be implanted at the tumor site during the biopsy and later used to monitor oxygen level or acidity, both of which reveal important information about how the disease should be treated and whether the treatment is working.
Another sensor he developed uses magnetic nanoparticles, housed in an 8-millimeter disk implanted in the skin, to detect three proteins that are released during a heart attack. Anyone showing up at a hospital with chest pain is tested for those proteins, but results can appear inconclusive because the proteins are secreted at different times. The sensor, which is read using magnetic resonance imaging (MRI), could be implanted in patients known to be at high risk for a heart attack, making it much easier for doctors to determine if they have had one.
All of his projects, Cima says, are motivated by the desire to improve medical care for patients. “We’re doing this because we can do some cool technology, but more importantly, we’re doing it is because there’s a clinically meaningful need,” he says.
Modern medicine is largely based on treating patients with “small-molecule” drugs, which include pain relievers like aspirin and antibiotics such as penicillin.
Those drugs have prolonged the human lifespan and made many life-threatening ailments easily treatable, but scientists believe the new approach of nanoscale drug delivery can offer even more progress. Delivering RNA or DNA to specific cells offers the promise of selectively turning genes on or off, while nanoscale devices that can be injected or implanted in the body could allow doctors to target drugs to specific tissues over a defined period of time.
“There’s a growing understanding of the biological basis of disease, and a growing understanding of the roles certain genes play in disease,” says Daniel Anderson, the Samuel A. Goldblith Associate Professor of Chemical Engineering and a member of MIT’s Institute for Medical Engineering and Science and David H. Koch Institute for Integrative Cancer Research. “The question is, ‘How can we take advantage of this?’”
Researchers in Anderson’s lab, as well as many others at MIT, are working on new ways to deliver RNA and DNA to treat a variety of diseases. Cancer is a primary target, but deliveries of genetic material could also help with many diseases caused by defective genes, including Huntington’s disease and hemophilia. “There are many genes that we think if we could just turn them off or turn them on, it could be therapeutic,” Anderson says.
One promising avenue is RNA interference (RNAi), a naturally occurring process that allows cells to fine-tune their gene expression. Short strands of RNA called siRNA intercept and destroy messenger RNA before it can carry protein-building instructions from DNA to the rest of the cell. Scientists hope that by creating their own siRNA to target specific genes, they will be able to turn off genes that cause disease.
However, this potential has not yet been realized because of challenges in safely delivering siRNA to the right tissues and avoiding other tissues. Using viruses is one possibility, but is an option that carries some safety risks, so many researchers are now investigating synthetic delivery vehicles for genetic material.
Anderson’s lab is developing materials called lipidoids, fatty molecules that can envelop and deliver strands of siRNA. Studies have shown that these materials can effectively deliver RNA and shrink tumors in animals; MIT researchers are now working on developing them for human tests. These particles can deliver many RNA sequences at once, allowing researchers to target multiple genes. “A lot of these diseases, in particular cancer, are complicated and may require turning off multiple genes, or turning some genes off and some genes on,” Anderson says.
Anderson is also using a technique called nucleic-acid origami to fold DNA and RNA into structures suitable for targeting cancer cells. Nucleic-acid origami, developed within the past few years, allows for extremely precise control over the location of every atom within a structure — something that is difficult to achieve with other types of nanoparticles, Anderson says.
In a 2012 study involving mice, Anderson showed that folded DNA nanoparticles tagged with folate accumulated in ovarian cancer cells, which express many more folate receptors on their surfaces than healthy cells.
Multipronged approach
Paula Hammond, the David H. Koch Professor of Engineering and a member of the Koch Institute, is also developing new materials for delivering both RNA and traditional drugs. Using her layer-by-layer assembly technique, she is creating nanoparticles that incorporate layers of multiple types of RNA, or combine RNA with a chemotherapy drug.
This multipronged attack could allow researchers to design treatments that cut off many of tumor cells’ possible escape routes. “We’re very interested in looking at combinations that would involve RNAi that knocks down the ability of cells to counteract chemotherapy attack,” Hammond says.
Hammond’s research in this area is now focused on cancer, but the approach could also lend itself to treating the inflammation produced by infectious diseases, she says. “With RNAi, the approach is fairly modular, and once you understand which genes you need to impact, you can work on targeting them,” Hammond says.
Hammond’s lab is also working on medical-device coatings that could secrete useful drugs, hormones or growth factors. One such project involves coating hip implants with layers that secrete bone growth factors. In studies with animals, she has shown that these coatings can promote the growth of natural bone, and stronger adhesion between hip implants and the body’s own bone. If the work translates to human clinical use, it could allow hip implants to last longer and reduce the need for additional surgeries to replace the implants.
Hammond is also working on materials that promote wound healing by preprogrammed release of growth factors from bandages and dressings, and on ultrathin, transparent coatings for cataract-replacement lenses that release anti-inflammatory drugs.
Delivery and diagnostics
Michael Cima, the David H. Koch Professor of Engineering, and Robert Langer, the David H. Koch Institute Professor, both members of the Koch Institute, are working on nano- and microscale devices that can be implanted in the body to release drugs or diagnose disease.
Several years ago, Cima and Langer began working on an implantable chip that can dispense medicine inside the body, but which is controlled wirelessly from outside the body. In clinical trials last year, the company developing the chip for commercial use showed that it could reliably deliver precise doses of an osteoporosis medication that is normally given by injection.
The company developing the chip, MicroCHIPS Inc., is now shrinking the device and increasing the number of drug reservoirs on the chip (the version used in last year’s trial had 20 such wells). That may enable the device to be used for much longer time periods — up to 30 years, Cima says. That would allow it to serve as an artificial gland, releasing hormones as necessary, he says, especially if a sensor could be incorporated to alert the chip when to release a dose.
Such a device could be useful for many endocrine diseases. “Diseases of growth, development and reproduction are all areas where there are significant unmet needs, or therapies that are very difficult to implement,” Cima says.
Cima is also working on diagnostic devices that could help monitor tumor response to treatment, or detect whether someone has had a heart attack. His strategy is to take tests originally developed for in-vitro use (where a sample is removed from the body and tested in a lab), and instead put the sensing device inside the body. These diagnostic devices would be implanted in conjunction with a medical procedure.
For example, when cancer is suspected, a biopsy is done on a patient. Cima is now developing devices that could be implanted at the tumor site during the biopsy and later used to monitor oxygen level or acidity, both of which reveal important information about how the disease should be treated and whether the treatment is working.
Another sensor he developed uses magnetic nanoparticles, housed in an 8-millimeter disk implanted in the skin, to detect three proteins that are released during a heart attack. Anyone showing up at a hospital with chest pain is tested for those proteins, but results can appear inconclusive because the proteins are secreted at different times. The sensor, which is read using magnetic resonance imaging (MRI), could be implanted in patients known to be at high risk for a heart attack, making it much easier for doctors to determine if they have had one.
All of his projects, Cima says, are motivated by the desire to improve medical care for patients. “We’re doing this because we can do some cool technology, but more importantly, we’re doing it is because there’s a clinically meaningful need,” he says.
Categories: Cancer Research
Research update: Chemists find help from nature in fighting cancer
Inspired by a chemical that fungi secrete to defend their territory, MIT chemists have synthesized and tested several dozen compounds that may hold promise as potential cancer drugs.
A few years ago, MIT researchers led by associate professor of chemistry Mohammad Movassaghi became the first to chemically synthesize 11,11’-dideoxyverticillin, a highly complex fungal compound that has shown anti-cancer activity in previous studies. This and related compounds naturally occur in such small amounts that it has been difficult to do a comprehensive study of the relationship between the compound’s structure and its activity — research that could aid drug development, Movassaghi says.
“There’s a lot of data out there, very exciting data, but one thing we were interested in doing is taking a large panel of these compounds, and for the first time, evaluating them in a uniform manner,” Movassaghi says.
In the new study, recently published online in the journal Chemical Science, Movassaghi and colleagues at MIT and the University of Illinois at Urbana-Champaign (UIUC) designed and tested 60 compounds for their ability to kill human cancer cells.
“What was particularly exciting to us was to see, across various cancer cell lines, that some of them are quite potent,” Movassaghi says.
Lead author of the paper is MIT postdoc Nicolas Boyer. Other authors are MIT graduate student Justin Kim, UIUC chemistry professor Paul Hergenrother and UIUC graduate student Karen Morrison.
Improving nature’s design
Many of the compounds tested in this study, known as epipolythiodiketopiperazine (ETP) alkaloids, are naturally produced by fungi. Scientists believe these compounds help fungi prevent other organisms from encroaching on their territory.
In the process of synthesizing ETP natural products in their lab, the MIT researchers produced many similar compounds that they suspected might also have anti-cancer activity. For the new study, they created even more compounds by systematically varying the natural structures — adding or removing certain chemical groups from different locations.
The researchers tested 60 compounds against two different human cancer cell lines — cervical cancer and lymphoma. Then they chose the best 25 to test against three additional lines, from lung, kidney and breast tumors. Overall, dimeric compounds — those with two ETP molecules joined together — appeared to be more effective at killing cancer cells than single molecules (known as monomers).
The structure of an ETP natural product typically has at least one set of fused rings containing one or more sulfur atoms that link to a six-member ring known as a cyclo-dipeptide. The researchers found that another key to tumor-killing ability is the arrangement and number of these sulfur atoms: Compounds with at least two sulfur atoms were the most effective, those with only one sulfur atom were less effective, and those without sulfur did not kill tumor cells efficiently.
Other rings typically have chemical groups of varying sizes attached in certain positions; a key position is that next to the ETP ring. The researchers found that the larger this group, the more powerful the compound was against cancer.
The compounds that kill cancer cells appear to be very selective, destroying them 1,000 times more effectively than they kill healthy blood cells.
The researchers also identified sections of the compounds that can be altered without discernably changing their activity. This is useful because it could allow chemists to use those points to attach the compounds to a delivery agent such as an antibody that would target them to cancer cells, without impairing their cancer-killing ability.
Complex synthesis
Larry Overman, a professor of chemistry at the University of California at Irvine, says the new study is an impressive advance. “Movassaghi and coworkers reveal for the first time a number of relationships between the chemical structure of molecules in the ETP series and their in-vitro anti-cancer activity,” says Overman, who was not part of the research team. “Knowledge of this type will be essential for the future development of ETP-type molecules into attractive clinical candidates and potential novel anti-cancer drugs.”
Now that they have some initial data, the researchers can use their findings to design additional compounds that might be even more effective. “We can go in with far greater precision and test the hypotheses we’re developing in terms of what portions of the molecules are most significant at retaining or enhancing biological activity,” Movassaghi says.
The research was funded by the National Institute of General Medical Sciences.
A few years ago, MIT researchers led by associate professor of chemistry Mohammad Movassaghi became the first to chemically synthesize 11,11’-dideoxyverticillin, a highly complex fungal compound that has shown anti-cancer activity in previous studies. This and related compounds naturally occur in such small amounts that it has been difficult to do a comprehensive study of the relationship between the compound’s structure and its activity — research that could aid drug development, Movassaghi says.
“There’s a lot of data out there, very exciting data, but one thing we were interested in doing is taking a large panel of these compounds, and for the first time, evaluating them in a uniform manner,” Movassaghi says.
In the new study, recently published online in the journal Chemical Science, Movassaghi and colleagues at MIT and the University of Illinois at Urbana-Champaign (UIUC) designed and tested 60 compounds for their ability to kill human cancer cells.
“What was particularly exciting to us was to see, across various cancer cell lines, that some of them are quite potent,” Movassaghi says.
Lead author of the paper is MIT postdoc Nicolas Boyer. Other authors are MIT graduate student Justin Kim, UIUC chemistry professor Paul Hergenrother and UIUC graduate student Karen Morrison.
Improving nature’s design
Many of the compounds tested in this study, known as epipolythiodiketopiperazine (ETP) alkaloids, are naturally produced by fungi. Scientists believe these compounds help fungi prevent other organisms from encroaching on their territory.
In the process of synthesizing ETP natural products in their lab, the MIT researchers produced many similar compounds that they suspected might also have anti-cancer activity. For the new study, they created even more compounds by systematically varying the natural structures — adding or removing certain chemical groups from different locations.
The researchers tested 60 compounds against two different human cancer cell lines — cervical cancer and lymphoma. Then they chose the best 25 to test against three additional lines, from lung, kidney and breast tumors. Overall, dimeric compounds — those with two ETP molecules joined together — appeared to be more effective at killing cancer cells than single molecules (known as monomers).
The structure of an ETP natural product typically has at least one set of fused rings containing one or more sulfur atoms that link to a six-member ring known as a cyclo-dipeptide. The researchers found that another key to tumor-killing ability is the arrangement and number of these sulfur atoms: Compounds with at least two sulfur atoms were the most effective, those with only one sulfur atom were less effective, and those without sulfur did not kill tumor cells efficiently.
Other rings typically have chemical groups of varying sizes attached in certain positions; a key position is that next to the ETP ring. The researchers found that the larger this group, the more powerful the compound was against cancer.
The compounds that kill cancer cells appear to be very selective, destroying them 1,000 times more effectively than they kill healthy blood cells.
The researchers also identified sections of the compounds that can be altered without discernably changing their activity. This is useful because it could allow chemists to use those points to attach the compounds to a delivery agent such as an antibody that would target them to cancer cells, without impairing their cancer-killing ability.
Complex synthesis
Larry Overman, a professor of chemistry at the University of California at Irvine, says the new study is an impressive advance. “Movassaghi and coworkers reveal for the first time a number of relationships between the chemical structure of molecules in the ETP series and their in-vitro anti-cancer activity,” says Overman, who was not part of the research team. “Knowledge of this type will be essential for the future development of ETP-type molecules into attractive clinical candidates and potential novel anti-cancer drugs.”
Now that they have some initial data, the researchers can use their findings to design additional compounds that might be even more effective. “We can go in with far greater precision and test the hypotheses we’re developing in terms of what portions of the molecules are most significant at retaining or enhancing biological activity,” Movassaghi says.
The research was funded by the National Institute of General Medical Sciences.
Categories: Cancer Research
Some cancer mutations slow tumor growth
A typical cancer cell has thousands of mutations scattered throughout its genome and hundreds of mutated genes. However, only a handful of those genes, known as drivers, are responsible for cancerous traits such as uncontrolled growth. Cancer biologists have largely ignored the other mutations, believing they had little or no impact on cancer progression.
But a new study from MIT, Harvard University, the Broad Institute and Brigham and Women’s Hospital reveals, for the first time, that these so-called passenger mutations are not just along for the ride. When enough of them accumulate, they can slow or even halt tumor growth.
The findings, reported in this week’s Proceedings of the National Academy of Sciences, suggest that cancer should be viewed as an evolutionary process whose course is determined by a delicate balance between driver-propelled growth and the gradual buildup of passenger mutations that are damaging to cancer, says Leonid Mirny, an associate professor of physics and health sciences and technology at MIT and senior author of the paper.
Furthermore, drugs that tip the balance in favor of the passenger mutations could offer a new way to treat cancer, the researchers say, beating it with its own weapon — mutations. Although the influence of a single passenger mutation is minuscule, “collectively they can have a profound effect,” Mirny says. “If a drug can make them a little bit more deleterious, it’s still a tiny effect for each passenger, but collectively this can build up.”
Lead author of the paper is Christopher McFarland, a graduate student at Harvard. Other authors are Kirill Korolev, a Pappalardo postdoctoral fellow at MIT, Gregory Kryukov, a senior computational biologist at the Broad Institute, and Shamil Sunyaev, an associate professor at Brigham and Women’s.
Power struggle
Cancer can take years or even decades to develop, as cells gradually accumulate the necessary driver mutations. Those mutations usually stimulate oncogenes such as Ras, which promotes cell growth, or turn off tumor-suppressing genes such as p53, which normally restrains growth.
Passenger mutations that arise randomly alongside drivers were believed to be fairly benign: In natural populations, selection weeds out deleterious mutations. However, Mirny and his colleagues suspected that the evolutionary process in cancer can proceed differently, allowing mutations with only a slightly harmful effect to accumulate.
To test this theory, the researchers created a computer model that simulates cancer growth as an evolutionary process during which a cell acquires random mutations. These simulations followed millions of cells: every cell division, mutation and cell death.
They found that during the long periods between acquisition of driver mutations, many passenger mutations arose. When one of the cancerous cells gains a new driver mutation, that cell and its progeny take over the entire population, bringing along all of the original cell’s baggage of passenger mutations. “Those mutations otherwise would never spread in the population,” Mirny says. “They essentially hitchhike on the driver.”
This process repeats five to 10 times during cancer development; each time, a new wave of damaging passengers is accumulated. If enough deleterious passengers are present, their cumulative effects can slow tumor growth, the simulations found. Tumors may become dormant, or even regress, but growth can start up again if new driver mutations are acquired. This matches the cancer growth patterns often seen in human patients.
“Cancer may not be a sequence of inevitable accumulation of driver events, but may be actually a delicate balance between drivers and passengers,” Mirny says. “Spontaneous remissions or remissions triggered by drugs may actually be mediated by the load of deleterious passenger mutations.”
When they analyzed passenger mutations found in genomic data taken from cancer patients, the researchers found the same pattern predicted by their model — accumulation of large quantities of slightly deleterious mutations.
The findings “really put front and center these mutations that we have often seen as not being clinically relevant,” says Denis Wirtz, a professor of chemical and biomolecular engineering at Johns Hopkins University, who was not part of the research team. “This suggests the opportunity for an alternative cancer therapy, which is always exciting.”
Tipping the balance
In computer simulations, the researchers tested the possibility of treating tumors by boosting the impact of deleterious mutations. In their original simulation, each deleterious passenger mutation reduced the cell’s fitness by about 0.1 percent. When that was increased to 0.3 percent, tumors shrank under the load of their own mutations.
The same effect could be achieved in real tumors with drugs that interfere with proteins known as chaperones, Mirny suggests. After proteins are synthesized, they need to be folded into the correct shape, and chaperones help with that process. In cancerous cells, chaperones help proteins fold into the correct shape even when they are mutated, helping to suppress the effects of deleterious mutations.
Several potential drugs that inhibit chaperone proteins are now in clinical trials to treat cancer, although researchers had believed that they acted by suppressing the effects of driver mutations, not by enhancing the effects of passengers.
In current studies, the researchers are comparing cancer cell lines that have identical driver mutations but a different load of passenger mutations, to see which grow faster. They are also injecting the cancer cell lines into mice to see which are likeliest to metastasize.
The research was funded by the National Institutes of Health/National Cancer Institute Physical Sciences Oncology Center at MIT.
But a new study from MIT, Harvard University, the Broad Institute and Brigham and Women’s Hospital reveals, for the first time, that these so-called passenger mutations are not just along for the ride. When enough of them accumulate, they can slow or even halt tumor growth.
The findings, reported in this week’s Proceedings of the National Academy of Sciences, suggest that cancer should be viewed as an evolutionary process whose course is determined by a delicate balance between driver-propelled growth and the gradual buildup of passenger mutations that are damaging to cancer, says Leonid Mirny, an associate professor of physics and health sciences and technology at MIT and senior author of the paper.
Furthermore, drugs that tip the balance in favor of the passenger mutations could offer a new way to treat cancer, the researchers say, beating it with its own weapon — mutations. Although the influence of a single passenger mutation is minuscule, “collectively they can have a profound effect,” Mirny says. “If a drug can make them a little bit more deleterious, it’s still a tiny effect for each passenger, but collectively this can build up.”
Lead author of the paper is Christopher McFarland, a graduate student at Harvard. Other authors are Kirill Korolev, a Pappalardo postdoctoral fellow at MIT, Gregory Kryukov, a senior computational biologist at the Broad Institute, and Shamil Sunyaev, an associate professor at Brigham and Women’s.
Power struggle
Cancer can take years or even decades to develop, as cells gradually accumulate the necessary driver mutations. Those mutations usually stimulate oncogenes such as Ras, which promotes cell growth, or turn off tumor-suppressing genes such as p53, which normally restrains growth.
Passenger mutations that arise randomly alongside drivers were believed to be fairly benign: In natural populations, selection weeds out deleterious mutations. However, Mirny and his colleagues suspected that the evolutionary process in cancer can proceed differently, allowing mutations with only a slightly harmful effect to accumulate.
To test this theory, the researchers created a computer model that simulates cancer growth as an evolutionary process during which a cell acquires random mutations. These simulations followed millions of cells: every cell division, mutation and cell death.
They found that during the long periods between acquisition of driver mutations, many passenger mutations arose. When one of the cancerous cells gains a new driver mutation, that cell and its progeny take over the entire population, bringing along all of the original cell’s baggage of passenger mutations. “Those mutations otherwise would never spread in the population,” Mirny says. “They essentially hitchhike on the driver.”
This process repeats five to 10 times during cancer development; each time, a new wave of damaging passengers is accumulated. If enough deleterious passengers are present, their cumulative effects can slow tumor growth, the simulations found. Tumors may become dormant, or even regress, but growth can start up again if new driver mutations are acquired. This matches the cancer growth patterns often seen in human patients.
“Cancer may not be a sequence of inevitable accumulation of driver events, but may be actually a delicate balance between drivers and passengers,” Mirny says. “Spontaneous remissions or remissions triggered by drugs may actually be mediated by the load of deleterious passenger mutations.”
When they analyzed passenger mutations found in genomic data taken from cancer patients, the researchers found the same pattern predicted by their model — accumulation of large quantities of slightly deleterious mutations.
The findings “really put front and center these mutations that we have often seen as not being clinically relevant,” says Denis Wirtz, a professor of chemical and biomolecular engineering at Johns Hopkins University, who was not part of the research team. “This suggests the opportunity for an alternative cancer therapy, which is always exciting.”
Tipping the balance
In computer simulations, the researchers tested the possibility of treating tumors by boosting the impact of deleterious mutations. In their original simulation, each deleterious passenger mutation reduced the cell’s fitness by about 0.1 percent. When that was increased to 0.3 percent, tumors shrank under the load of their own mutations.
The same effect could be achieved in real tumors with drugs that interfere with proteins known as chaperones, Mirny suggests. After proteins are synthesized, they need to be folded into the correct shape, and chaperones help with that process. In cancerous cells, chaperones help proteins fold into the correct shape even when they are mutated, helping to suppress the effects of deleterious mutations.
Several potential drugs that inhibit chaperone proteins are now in clinical trials to treat cancer, although researchers had believed that they acted by suppressing the effects of driver mutations, not by enhancing the effects of passengers.
In current studies, the researchers are comparing cancer cell lines that have identical driver mutations but a different load of passenger mutations, to see which grow faster. They are also injecting the cancer cell lines into mice to see which are likeliest to metastasize.
The research was funded by the National Institutes of Health/National Cancer Institute Physical Sciences Oncology Center at MIT.
Categories: Cancer Research
