Cancer genome sequencing: a routine examination in the near future?

        Bill Gates is not necessarily right in every investment. However, as a shrewd businessman, he will not invest without a solid reason.  Recently, Foundation Medicine, a new biotechnology company launched in 2010, said they received an investment of 13.5 millions from Bill Gates. Its first product, FoundationOne, is an integrated service of cancer genomic test which will suggest the best therapy for a cancer patient based on his genome information. What made Gates send money to this company? The answer is simple: this company is promising. It was rated as one of the 15 fierce biotechnology companies in 2012. It has won investments not only from Gates but also from big capitals such as the Third Rock and Google Ventures.

        In fact, I would rather say that Bill Gates and other venture capitals invested in the future of cancer genome sequencing than the company. Cancer genome sequencing and relevant analysis hold the promise for cancer control in the future.

        Currently four types of cancer treatment are available in clinic: surgery, radiation therapy, chemotherapy, and targeted therapy. These four treatments have all been adopted as routine therapy in clinic practice. Targeted therapy, in which the drug is designed against specific cancer mutations, becomes increasingly popular for its specificity and low toxicity. It is likely to surpass radiation and chemical therapy to become the primary option for cancer patients in the future. Since cancerous mutations are tremendously diverse among individuals, cell types, and clinical stages, the success of targeted therapy is highly dependent on how accurately the mutations can be measured. FoundationOne, as the company has described, can probe the whole genome information of a patient using a piece of solid tumor tissue. Moreover, FoundationOne service can be updated regularly as more mutations are indentified and more targeted therapies become available. FoundationOne represents one of available clinical practices translated from the so-called personalized medicine, a concept favored by today’s oncologists.  

        How good is FoundationOne?

        It is not as good as it sounds to be. There are some reasons for the imperfection of personalized cancer treatment. First of all, targeted therapy itself is not perfect. The biggest problem of targeted therapy is drug resistance. All known anti-tumor drugs targeting mutations result in drug resistance in 6 to 18 months after usage. Secondly, targeted therapy is more expensive than the traditional therapies. For example, Erlotinib, a drug targeting mutations in lung cancer, extends life by an average of 3.3 month at a cost of $95000. Thirdly, not all cancerous mutations are suitable for drug targets. For example, there is currently no drug against Ras mutation, a frequently mutated gene in cancer. Fouthly, tumor genome, which is different from normal genome, changes rapidly, thus requires periodical examination.       

        Although FoundationOne is not perfect  at this point, it is  being improved, as stated on the company’s website. As the cost goes down, cancer genome sequencing will hopefully become a routine medical examination in the future, just like blood test and urine test. As new drugs are being designed and drug resistance mechanisms being unraveled, the power of cancer genome sequencing may truly come to play.    

DNA disk

        Animals use urine to mark territory. By using urine, they broadcast the news: I am the boss of this place! Other animals read the information that the place has been owned by someone else from urine. Then the newcomers may choose to leave or stay to fight for the territory. In this case, urine was used to store information. Urine is so cheap that it is practical for animals to claim territory. However, urine cannot hold too much information. For example, it is hard for newcomers to tell how strong the settlers are so that they can decide if they might stay to fight. Urine cannot last too long either so animals have to pee frequently to make a territory claim. To sum up, urine is practical to store simple information for a short while, that can be read by other animals. From this example, we can learn a lesson about how humans store information. When we store information, we usually consider four factors: practicality (how easy the information can be produced), capacity (how much information can be accommodated), maintenance (how long information can be kept), and readability (how easy information can be read).

        Books written in papers are first milestone of information storage. Books are practical because papers are cheap and easy to handle. Books can last many years. People with normal intellect can learn how to read and write without too much difficulty. With the emergency of silicon chips, humans achieved tremendous progression in information storage. Simple symbols, namely 0s and 1s, were used to represent everything. Silicon chips beat books in every aspects: higher capacity, easier to maintain, and easier to read. Smaller hard drives with higher capacity are created continuously.

         However, we still face unmet need for information storage. More and more information was produced especially in biology field. For example, genome sequencing has produced and is producing a vast volume of information. How to store these massive amounts of information poses a huge challenge to humans.

        What should be the next-generation carrier of information deluge after books and silicon chips? DNA may be the qualified candidate since it has been used to store information by nature for millions of years. Scientists figured out how to use DNA to store information.

        Nick Goldman designed a method to store information in DNA. They tried to store in DNA Shakespeare’s sonnets (ASCII text), Waston and Crick’s paper about the identification of DNA double helix (PDF), a colorful photo of European Bioinformatics Institutes (JPEG 2000), Martin Luther King’s “I have a dream” speech (MP3), and Huffman code. These documents were encoded into binary text, namely 0s and 1s. Subsequently, these binary texts were translated into base 3 encoded files (0s, 1s and 2s) that correspond to long DNA sequences. Long DNA sequence is supposed to store information but it is hard to read by sequencing. Thus, short DNA sequences with overlapping segments were designed to represent long DNA.  Moreover, indexing information were added to short DNA sequences so that it is possible to find which DNA corresponds to which document. Overall, the five files listed above were represented by a total of 153,335 strings of DNA, each comprising 117 nucleotides (nt). The DNA was synthesized and lyophilized for shipment in ambient temperature from USA to Germany via UK. In Germany, DNA was resuspended, amplified, purified and sequenced. Then full-length DNA sequence corresponding original files was reconstructed based on sequencing results. For these five files, it turned out to be a 100% accuracy of reconstruction.  Martin Luther King's speech is still clear and heart-stirring. 

        Needless to say that DNA can hold much more information and can be maintained more easily than magnetic tapes. But Is DNA storage practical? Currently the cost of DNA storage is about $12400/MB for information storage and $220/MB for information decoding. This cost is much higher than magnetic tapes. However, information stored in magnetic tapes needs to be copied frequently in case they will not be extracted because magnetic tapes cannot last very long. By contrast, synthesized DNA can last thousands of years under normal maintenance. DNA encoding will also be cheaper if the current trend of DNA manipulating continues. In less than 50 years, DNA storage will be practical. The information writing and reading into DNA is not competitive with current technology but can be accelerated. In summary, DNA storage holds a big promise for massive amounts of information storage.

        It is possible to connect a DNA synthesizing machine and a DNA sequencing machine to a computer. Then we will be able to manipulate information in a DNA based format.  

[1] Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature (2013) doi:10.1038/nature11875 Received 15 May 2012 Accepted 12 December 2012 Published online 23 January 2013

Body size vs. cancer: the bigger the better, or the smaller the better?

        The hypothesis that cancer arises from accumulated mutations can account for many findings. For example, the longer an organism lives, the more likely it is to have cancer, because theoretically it builds up more mutations over time. This has been supported by epidemiological studies that showed a vast increase in the number of cancer patients in many countries owing to an aging population.

        Aside from longevity, another interesting issue is body size. One may assume that the bigger  organisms are more likely to get cancer than smaller ones, because bigger bodies have more cells and thus more mutations. Although this idea sounds logical, it has been proven to be only partly true. Larger individuals do appear to have increased risk of cancer than smaller ones of the same species,. However, cross-species studies failed to support this hypothesis. No correlation was found between body size and the incidence of cancer between different species. For example, the incidence of cancer in humans is much higher than that in whales, which are about 100 times the size and about 1000 times the cell number of humans. In another example, humans and rodents have similar incidences of cancer despite the fact that they are enormously different in size.

        One explanation scientists have for this paradox is that bigger-sized species are usually more resistant to carcinogenesis.  They do so by developing many mechanisms, one of which is low metabolic rate. At lower metabolic rate the body produces fewer free radicals, which are an essential culprit that leads to cancer.

[1] Peto’s Paradox: evolution’s prescription for cancer prevention. Trends in Ecology and Evolution, April 2011, Vol. 26, No. 4.

The memory of mental trauma

     What we experienced mentally as a child may have unspoken impact on our characters as an adult. It is well-known that Hitler experienced a miserable adolescence when he was severely abused. This troubled upbringing was believed to have a dominant negative effect on Hitler’s moral psychological development. On the contrary, Beethoven grew into a great musician with the tough training from his abusive father. Both environmental stresses and our genetic factors shape us. But how does this happen? 

        Imagine an injury when we got cut by a knife. Suppose that a child got hurt on his finger when he was carelessly playing with a sharp knife. He was left with a scar that may be conspicuous even years later. Four things are important during this process: the finger, the knife, the injury represented by blood, and a hidden genetic profiling of the kid. This fourth hidden genetic factor can be easily overlooked, but it is very important. For example, when a kid with haemophilia is cut in the finger, he will experience excessive bleeding.

What resembles the finger, the knife, the injury and the genetics when we get mentally stressed? They are dopaminergic neurons, specific stress, glucocorticoids, and similar genetic factors. Dopaminergic neurons are located in the midbrain. Although fewer in numbers, they are involved in a lot of behavioral processes, including mood, reward, addiction, and in particular, stress. One specific example of mental stress is social isolation. Glucocorticoids are important hormones responsible for regulating a lot of physiological events. It is glucocorticoids that affect dopaminergic neurons. The hidden genetic factors can be complicated, and a great number of genes are related to mental stress response. One gene called DISC1 was found to predispose individuals to schizophrenia and clinical depression. When an adolescent boy gets socially isolated, the “knife” of stress leaves “cuts” in the dopaminergic neurons. He will experience changes in his dopaminergic neurons and in the secretion of glucocorticoids. These changes will reshape, to a degree, his personality.If the kid unfortunately has an altered DISC1, the changes will probably have more severe consequences. 

        Then how are the changes in dopaminergic neurons retained in the mind to allow a profound influence to present itself years later? It is unlikely that the genes in dopaminergic neurons have changed, because DNA sequences, except those in tumors, often remain the same during one's lifetime. However, DNA can undergo some modification, such as methylation. The modifications may last for a long time. In dopaminergic neurons, a gene named tyrosine hydroxylase can undergo DNA methylation, and such methylation can be burnt into memory that will affect behavior years later. Therefore, although the DNA sequence remains the same, the function has changed. The DNA modifications such as methylation, acetylation, and histone modification, constitute the so-called epigenetics, which is a hot research field in genetics.

        What a surprise to know that our genetics is susceptible to mental trauma, and that DNA modifications can stay with us for so long! Please rest assured because the other side of the coin is that these discoveries bring forward new solutions. First, with the aid of personal genome sequencing, which is becoming affordable nowadays, a clinician can tell if a person is predisposed to sustain certain mental diseases. This can lead to early prevention and better diagnosis of mental illness. Secondly, scientists can develop new medicine to re-modify the DNA modifications and to help patients recover from mental trauma. 

[1] Dopaminergic neurons. Int J Biochem Cell Biol. 2005 May;37(5):942-6.

[2] Adolescent Stress−Induced Epigenetic Control of Dopaminergic Neurons via Glucocorticoids. Science 339, 335 (2013)

Sequencing dominates latest biological research

        Having worked in biology field for 10 years, I witnessed the tremendous change in the focus researchers devote themselves to in order to solve the challenging puzzles in life sciences. Essentially, protein has given way to RNA and then RNA was surpassed by DNA. Protein dominated the stage decades ago. Western blotting, a way to detect protein, was once favored by researchers. Then RNA took the leading role. This owed to two key techniques: PCR (first developed in 1983 and awarded with Nobel prize) and microarray (nominated for Nobel prize a couple of times). Both methods use short oligos (primers in PCR and probes in microarray) to detect the amount of RNA. In this day and age, it becomes more about DNA.

        DNA has many advantages to be used to account for phenotypes. First, it is DNA that stores genetic information. Secondly, DNA encodes RNA and protein. Thirdly, DNA is more stable than RNA and protein. Protein and RNA were once heavily used to explain interesting phenotypes at a time when DNA sequencing was impractical. Nowadays, owing to the rapid progress in faster, more accurate, and more affordable DNA sequencing technology, DNA is becoming the primary choice of researchers.

       An adequate mass of tissue is favorable for DNA sequencing. However, not all cells in an organism have identical genomes. For example, tumor cells may harbor DNA mutations (the so-called tumor heterogeneity) which account for many clinical problems, such as drug resistance. Under this circumstance, single-cell sequencing would be ideal. In other occasions, single-cell sequencing is desirable because the available material is very limited. For example, in prenatal tests, only a few cells are collected from the fetus; in circulating tumor cell screening, only a few cells are shed into the bloodstream from the primary tumor; and in a forensic test, only a few cells are preserved.

        Since DNA content from a single cell is trace amount, an amplification of DNA is necessary to obtain enough DNA for sequencing. This is usually achieved by PCR amplification. However, PCR introduces extra bias, and it may not cover the whole genome. Primers (short DNA oligos used for PCR) and polymerase (the enzyme for DNA amplification in PCR) have been optimized to boost the PCR yield and the genome coverage, but the results are yet to be satisfying.  

        Recently Zong and colleagues (Science 2012: 338:6114, 1622-1626) developed a new method, MALBAC, to improve the coverage in DNA sequencing from a single cell. This method adopted multiple random primers, a DNA polymerase with strand-displacement activity, and semi-amplification process at various temperatures. By using this method, they successfully identified single-nucleotide polymorphism (SNPs) and copy-number variations (CNVs) from single human cells. This technology may prove to be a great contribution to life sciences at DNA age.

Rumor vs tumor: not only from R to T

           

        When 12-21-2012 was approaching, a girl in Shanghai, China, left Shanghai for a shelter in a small village far away, hoping to escape the catastrophe of the doomsday. We know that the world did not end on the so-called doomsday, and, with good wishes, we thought all those rumors would be soon gone. They did not. They still linger around us. One day, my friend asked me: do you know why it is so warm this winter? After getting an indifferent "I don’t know", he told me mystically about his theory: the volcanoes in Yellowstone will erupt this year! 
 

        People have so many weird ideas, and with the help of internet and especially social media like facebook, twitter, etc., these ideas can go viral. Then faulty ideas may become rumors. Interestingly, tumors are just like rumors. Both spread rapidly, both can boom out of control and both are dangerous. Now let’s make an in-depth comparison between rumors and tumors.

        Social phycologists have been studying rumors since long ago. Four concepts have been brought forward to help people understand rumors: motivation, situation, narrative context, and trust. We can find a counterpart for each of these four concepts in tumors.
        

        People are often motivated to find out if a rumor is true.  Sometimes it is hard to prove or disprove a rumor. So they rely on watching how other people respond to it. When they cannot disprove it, they pass it on. This is so-called motivation. Tumors, on the other hand, are initiated when they become wrong. Tumors harbor a variety of DNA mutations that frequently undergo scrutinizing by safeguard mechanisms of our body. When the body fails to fix mutated DNA, owing to genetic or environment factors, tumors may begin to develop. 


        Situation to a rumor is like drought weather to a wildfire. Situations that pose ambiguity or threats to assets (life, health, wealth, group honor, and cherished values) can foster rumors. Government policies which fails to avoid ambiguity to assets, For example, can stir up a lot of rumors in the stock market. Likewise, tumors can not exist without appropriate situations. The environment that surrounds tumors, the so-called niche or tumor microenvironment, plays a far more important role in tumor initiation and development than we originally recognized. Different from rumor situation that usually aids in rumor spreading, tumor niche contains both good and bad components. Several subsets of cells reside in tumor niche, including cancer stem cells, cancer associated fibroblast cells, immune inflammatory cells, endothelial cells, pericytes, and others. These cells can be good or bad, depending on various factors such as their numbers and ratios. 


       Narrative context is important, too. Chinese people may not get a joke told by an American. Rumors may sound more plausible in one group than another. Likewise, tumors don’t metastasize just anywhere. Certain tumors are predisposed to seed in particular organs. For example, prostate cancer tends to metastasize to the bones, colon cancer to the liver, and stomach cancer to the ovaries. This was first proposed as the “seed-soil” theory by Stephen Paget in 1889.      
    

         Trust may be the most important factor to the spread of rumors. Similarly, tumors can not exist without the trust of the immune system. Immune system, except its role in controlling pathogens, may also monitor proliferative cells that may develop into tumors and will kill them when they are threatening the health of the body. Immunosurveillance and succedent immunoediting were proposed to explain how tumors are monitored and even sculpted by immune system. Tumors have developed many ways to win the trust of the immune system and escape being killed. For example, tumors may enter dormancy and stop dividing so that the immune system will mark them as good cells.  

        Neither rumors nor tumors are like humor. They are not good, and they are not rare. The longer a rumor or tumor has existed, the more it will do harm to the world and our body. It is impossible to live in a world without rumors or tumors, but it is possible to tell a rumor from truth, tumor from normal cell earlier. In that way, we will be able to have more humor when facing both rumor and tumor.

[1] Rumour research can douse digital wildfires. Nature. 2013 493, 135-135, doi:10.1038/493135a

[2] Cancer immunoediting: from immunosurveillance to tumor escape.Nat Immunol. 2002 Nov;3(11):991-8.

Tumor sleeps

        All higher animals need sleep. Mammalian sleeps regularly. Some animals like bear even take prolonged winter sleep. Reptiles that are unable to keep constant body temperature go into various periods of dormancy depending on the latitude and the local environment. Adders in north Europe have a dormancy of 275 days, whereas adders in south Europe have a dormancy of 105 days. The dormancy period for adders In UK is only two weeks, owing to the warm climate provided by the Gulf Stream. Dormancy is a state of being relative less active and more resistant. It helps organisms to adapt to unfavorable environments.

        Tumors also enter dormancy to avoid certain extreme environments, such as the microenvironment in their early progression, during micrometastases, or after a successful anti-tumor treatment. During early progression, the immune system of the host attempts to nip tumors in the bud. In the process of micrometastases, tumors endure angiogenesis suppression. Right after anti-tumor treatment such as surgery, chemotherapy, or radiation, tumors face even tougher situations caused by invasive procedures or drugs. Some tumors get around these extreme environments by going dormant.

        The phenomenon of tumor dormancy poses many interesting questions: How do we detect sleeping tumors? Can they be killed more easily or will they go rampant if awakened? How is tumor dormancy initiated? If we can take advantage of tumor dormancy, we may be able to switch tumors to dormancy indefinitely so that patients will die with tumors but not of tumor.

        

      

       

How severe is PM2.5>900 in Beijing?

       

I am not surprised to see a picture which shows vividly how notorious Beijing’s air is. Last year I took a flight from Seattle to Beijing. Right before landing, I noticed that the sky was yellow and smoggy. When I went to the restroom, the worker there complained to me how he had to mop the floor and wipe the counter all day long to prevent the dust from smothering everything. 

        This time I am not surprised. What I saw in this picture is similar to that of last year. But this time, instead of giving it a casual glance, I stopped to think: how severely will this air pollution affect our health? 

       Some indexes by size have been used to classify particulates in the air. Unlike other parameters such as component and shape, size is a simple yet concrete standard, and is easy to measure. PM2.5 and PM10 (particulate matter with diameters of up to 2.5 micrometer and 10 micrometer, respectively) are two common categories. PM10 can enter the lung; PM2.5 can penetrate the air exchange membranes of the lung.

Some studies showed that PM2.5, once in the body, can induce oxidative stress and damage DNA. It has been associated with high risks of heart disease, cancer, and asthma. Even short-term exposure to high concentrations of PM2.5 can pose significant health risks. PM2.5 at 10 (10 microgram per cubic meter) or less is considered safe. PM2.5 at 75 or less is acceptable. Based on the news, some cities (not only Beijing) have detected PM2.5 at a concentration of over 900. That is more than 10 times of the acceptable level! 

        Needless to say, something must be done to curb this severe air pollution.

Drug resistance: maybe it is only because we have worked too much!

       

        People are no strangers to drug resistance of microbes: Bacteria and viruses cannot be killed by a certain amount of antibiotics which used to work miraculously. Unfortunately, drug resistance is not only limited to microbes but also occurs frequently in cancer cells exposed to drugs each of which targets a few dysfunctional genes in tumors. Such effective targeted anti-cancer drugs often lose its momentum after 6 or 12 month of usage. It seems that the tiny pathogen or tumor cells outsmart the human brain at almost every turn.

        Cancer cells with specific mutations that are targeted by drugs develop drug resistance by producing new mutations that cannot be targeted by drugs any more. Thus, designing new drugs that can target new mutations of cancer cells sounds to be the only way to overcome drug resistance. However, these new drugs will also encounter drug resistance due to the emergence of even more mutations. The scenario is the harder researchers work, the harder and smarter cancer cells work because they want to survive. Can we be smarter to figure out how to conquer drug resistance?  

       Here is the good news: a very simple method, discontinuous drug administration, may be a powerful weapon to help us defeat drug resistance. The so-called discontinuous drug application contains three steps: drug administration, pause of drug administration, and another round of drug administration. Depending on the specific situation of patients, this cycle of drug usage can be repeated or not. Although this strategy seems to be too simple to work, it is in fact working wonderfully.

        A latest paper published in Nature showed the effectiveness of discontinuous drug administration. Frequent mutations in a gene BRAF have been linked to melanoma, a notorious malignant skin tumor. A drug named Vemurafenib can target BRAF to inhibit melanoma. However, long term use of Vemurafenib can lead to drug resistance. Researchers showed that discontinuous dosing of Vemurafenib resulted in effective regression (healing) from drug-resistant tumors. The explanation is as follows: while the survived tumors develop drug resistance, they also become dependent on the drug exposure environment. By discontinuing the drug temporarily, tumors that have established drug resistance will regain the sensitivity to the drug.

        It is of great interest to see whether the discontinuous strategy works on other targeted therapies as well.  If this is proven true, patients will spend less money and suffer less pain in cancer therapy. Scientists will find their lives easier, too.

[1] Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance. Nature(2013) doi:10.1038/nature11814