Monday, November 30, 2015

Culturing Life reveals the history of tissue culture, with some interesting details about HeLa cells

Culturing Life: How Cells Became Technology by Hannah Landecker is an extensive history of the culturing of cells in the lab. As such, it gave many details about the fits and starts involved in the early attempts to get cells to grow reliably. As is usually the case in scientific research, as much is owed to timing and serendipity as to careful repetition and fastidious lab work.

The idea that cells could be taken from an organism and cultured separately was initially met with skepticism. The general thinking was that cells could not become autonomous from the organism. By 1885, Wilhelm Roux showed that he could keep nerve cells from chicken embryos alive for several days in the lab. Once the principal was established, scientists began to search for the right media, the right glassware, and the right cells or tissue to make cell culture reliable.

The growth in virology was a major driver for the improvement of cell culture. Virologists needed a way to make large-scale cultures of infected samples for vaccine development. Early vaccines were grown using embryonated chicken eggs, a method that had a high yield for virus, but was quite costly. (Flu vaccines are still made using chicken eggs; the specifics of the process are described here.) By the 1930s, the yellow fever vaccine was the first to be produced with cultured cells, but it was not clear that these approaches would work for other viruses.

Alexis Carrel used specially designed flasks for growing cells
In the late 1940s, John Enders started using cell culture to grow viruses. His lab was the first to show that polio virus could be cultured in human tissues and that infection with the virus caused rapid changes in the appearance of the cells; these results meant that there was a quick and reliable assay for infection. Enders published his results in the journal Science in 1949 and soon after received the Nobel prize for his work.

It is important to consider Enders' work in the context of time and place. As Landecker writes, "It is not that Enders was particularly good at growing human cells." Instead, like so many scientific breakthroughs, Enders' success was due to being in the right place at the right time with the right reagents. The location of his lab in Boston Children's Hospital afforded Enders a ready supply of living tissues (from abortions, miscarriages, hysterectomies, and circumcisions, which were all used without concerns about patient consent or privacy). The timing was also critical as cell culture was becoming more feasible due to improved techniques and the increased availability of antibiotics. Enders' methods became the basis for the production of virus cultures for vaccine development, most significantly the creation of polio vaccine by Jonas Salk in 1954.

Importantly, Enders and Salk also had a major role in organizing the tissue culture community. One major push was for standardization of reagents and media; in the early days of cell culture, each lab made its own glassware and media, so it was nearly impossible to share cell lines between labs. Another proponent of standardization was cell biologist and electron microscopist Keith Porter. Porter wanted to image whole cells by EM, but was frustrated by the need to learn the exacting and often finicky methods of cell culture to get his experiments done. Porter and others started a group that would later become the Tissue Culture Association, which aimed to standardize media preparation and other elements of tissue culture.

The next major event in the history of cell culture happened in 1951, when an African-American patient named Henrietta Lacks was treated for cervical cancer at Johns Hopkins. Lacks' biopsy came into the hands of George Gey, who was able to generate the first human cell line (called HeLa cells) that in culture continuously. HeLa cells are unique in many respects: they grow rapidly and are robust enough to withstand shipping and freeze/thaw cycles. These unique features (which have been explained to some degree by the genome sequence) were what allowed researchers to culture the cells so easily, making HeLa cells a standard cell line in most laboratories.

The story of the origins of the cell line that was generated from Ms. Lacks' biopsy has been told in beautiful detail by Rebecca Skloot in The Immortal Life of Henrietta Lacks. Skloot's book (which is on my list of top science reads) focuses on the Lacks family as it comes to terms with the Henrietta's legacy. In Culturing Life, Landecker tells the HeLa story in broader strokes with a different historical context, focusing on how the tenor of the HeLa cell line origin story has changed over time. In 1968, with tissue culture techniques established and many cell lines available, Stanley Gartler published a Nature paper profiling eighteen cell lines; using the presence of a gene variant only present in African Americans, he showed that all were contaminated by HeLa cells. Predictably, these results created a major stir in the research community. Landecker details the language used to describe HeLa cells, particularly in regards to the contamination issue: aggressive, surreptitious, and malicious. Some scientists suggested that "one drop was enough" to contaminate and ruin a culture, which is evocative of the one-drop rule of racial classification in the US. Thus, unlike for most cells, the race and gender of the donor was central to the discussion of the cells.

While the language used to talk about HeLa cells has changed considerably, some elements have remained consistent. Scientists and science writers still connect the cells with Henrietta Lacks and talk about how the cells have allowed her to achieve immortality. Most articles will also detail how many HeLa cells have been grown since Gey started to culture the cells. Indeed, these are fascinating details. According to Skloot's book, "One scientist estimates that if you could pile all HeLa cells ever grown onto a scale, they’d weigh more than 50 million metric tons—an inconceivable number, given that an individual cell weighs almost nothing. Another scientist calculated that if you could lay all HeLa cells ever grown end-to-end, they’d wrap around the Earth at least three times, spanning more than 350 million feet." Thus, while the legacy of HeLa cells may be complicated, their utility in the research lab is not.

Wednesday, October 7, 2015

Frankenstein's Cat by Emily Anthes looks at how genetic engineering is changing the animals around us

Frankenstein's Cat: Cuddling up to Biotech's Brave New Beasts by Emily Anthes explores how biotechnology and genetic engineering are changing the animals around us. The book delves into the science behind these new creatures as well as the ethical issues and public perceptions. The result is an easy and interesting read that makes you imagine the genetically engineered animals that could be on the horizon.

GloFish were the first commercially available pets created using biotechnology. By inserting the gene that makes jellyfish glow (green fluorescent protein, or GFP) into a common pet store find (zebrafish), the inventor was able to create a fish that glowed green in certain lights. Despite seeming relatively benign, the company was required to perform extensive research on the possible environmental impacts in case of escape before GloFish were approved for sale in 2003. Interestingly, consumers had few concerns about these new creatures and were willing to pay almost 20 dollars for each fish. The company now has a variety of other colors and species available and sells special tanks to help you enjoy their fluorescent fish.

Pharming is a branch of biotechnology where researchers use farm animals to produce a range of pharmacological products. For example, goats can be engineered to produce the protein lysozyme in their milk. Lysozyme has been shown to inhibit bacterial growth; some preliminary results suggest that the lysozyme-enriched milk can improve the immune system. The scientists behind this project hope that this goat milk could help protect children from bacterial infections. Similar approaches have been used to engineer goats that have silk protein in their milk and silkworms that make collagen instead of silk. These additives are not harmful to the animals and have a range of potential applications.

The chapter on animal cloning starts with Dolly the sheep (the first cloned animal) and makes some interesting stops along the way. The story of Carbon Copy (CC), the first cloned cat (sometimes called Copy Cat), is scientifically notable because CC doesn't look much like her calico mother Rainbow. This is due to a process called X chromosome inactivation (you can learn more about this process in my recent post on Junk DNA). The gene for orange fur is on the X chromosome. CC's genome has an inactive copy of the X chromosome from her clone mother. Thus, while CC is genetically identical, she is phenotypically different. This result was interesting to scientists, but it likely gave future customers of cat cloning some pausewhat's the point of paying to have your favorite cat cloned if you can't be sure you will get a cat that looks the same?

Anthes tours a wildlife preserve and research center in Louisiana where researchers aim to develop and perfect methods for cloning animals with the long-term goal of preservation of endangered species. This is certainly worthwhile goal, but the barriers, both technical and ecological, are numerous. To me, the biggest problem with saving a species through cloning is the lack of genetic diversity. Until these problems are solved, many are banking on frozen zoos, large stocks of samples from a variety of animals that are endanger of extinction. The hope is that once cloning technology improves, it may become viable to add to the existing populations.

Roboroach from Backyard Brains
The chapter on cyborg animals was truly fascinating. For example, Anthes talks about the CIA's experiments with remote-controlled cats. Project Acoustic Kitty was predictably a failure due to the fiercely independent nature of cats. There are some notable success stories with insect cyborgs. In fact, for 99 dollars, you can build your own Roboroach. The newest approaches include the use of optogenetics, where specific neurons are made to be light sensitive, allowing researchers to control animals by shining a light. These experiments have some important applications, such as the removal of land mines and the detection of survivors in earthquake rubble, but people find animal mind control to be unsettling (even if it is a roach). It is important to consider that.

The book concludes with predictions of what may be possible in the future, like creating farm animals that are resistant to disease to decrease the use of antibiotics. Frankenstein's Cat was published in 2013 and the field has made amazing progress since that time. With the advent of the new genome editing technique CRISPR, the possibilities are truly endless, which has led to concerns about the ethical and safety considerations of this technology. Earlier this week a Chinese Institute caused a stir with its announcement of the commercial availability of gene-edited micro-pigs as pets. It will be interesting to see where we draw the line on genetically modified animals.  

Wednesday, September 23, 2015

Junk DNA: Nessa Carey's new book about the actually important stuff in the genome.

In 2001, when the first draft of the human genome was completed, researchers were surprised to learn that only 2% of the human genome codes for proteins. At the time, scientists were very focused on proteins and thought that there would be a much larger number of protein-coding genes in the human genome due to our complexity. The term "junk DNA" has been used to describe the other 98% of the genome. With only 20,000 protein-coding genes, the human genome contains almost the same number of genes as the simple roundworm and model organism C. elegans. However, C. elegans has very little excess DNA, suggesting that this junk DNA could be part of the explanation for the increased complexity of humans. This is the starting point for Nessa Carey's second book Junk DNA: A Journey Through The Dark Matter of the Genome, which explains the importance of the non-coding portion of the genome.

Some scientists have argued that the term junk DNA should be scrapped for a more neutral term like non-coding DNA. They suggest that the term is dated and inaccurate. In addition, calling it junk is rather pejorative and is based on the protein-focused view of the genome. Carey's book nicely demonstrates that the other 98% isn't always junk.

What is the other 98% of the genome good for then? Some non-coding DNA has well-established functions. For example, the centromeres are the stretches of DNA that allow the chromosomes to attach to the cell's chromosome segregation apparatus (the mitotic spindle) when the cell copies and divides its DNA. Another example is the telomeres, the lengthy repeat regions of DNA at the ends of the chromosomes. Because telomeres shorten with every cell division, they are linked with aging.

Junk DNA also encodes several special types of RNAs, including long non-coding RNA (lncRNA), microRNA (miRNA), and small interfering RNA (siRNA), that control gene expression. One of the earliest described examples of these special RNAs is found in the biology of sex determination. In XX females, one X chromosome is inactivated to ensure that genes on the X chromosome are not overexpressed. This process, called X chromosome inactivation, is controlled by a gene called Xist (X-inactive specific transcript). Xist encodes a long non-coding RNA, which covers one X chromosome and inactivates it (Xi). Interestingly, on the opposite strand from Xist is a gene called Tsix, which is expressed on the active X chromosome (Xa). The expression of these genes is mutually exclusive, ensuring that only one X chromosome is activated. The Xist/Tsix story highlights the power of special RNAs in controlling gene expression. These RNAs are the subject of intense research in both basic and clinical settings. Carey describes several approved drugs and promising clinical trials based on anti-sense approaches.

In short, Junk DNA was quite readable and should be informative for readers at any level of knowledge about molecular biology. My only complaint about the book was Carey's decision not to include protein or gene names in her writing. In the first chapter, she explains that this was due to the fact that half of her readers find it disruptive. Instead, where applicable, she includes footnotes with the gene or protein names. Unfortunately for me, I am in the half that finds it disruptive to read footnotes to learn the name of the gene in question. Otherwise, the book was very up to date and comprehensive. I also liked her use of simple graphics to explain complex concepts in molecular biology. I recommend Junk DNA for those who want to learn more about why the non-coding regions of our DNA are not junk.

Sunday, September 13, 2015

The Emperor of All Maladies - comments on the second part of the PBS special

In all my reading about cancer biology, I have not yet tackled The Emperor of All Maladies, which is said to be the best book on the subject.  Luckily, PBS and Ken Burns have delivered an excellent three-part series based on Siddhartha Mukherjee's 2011 book. This post covers the contents of part two, "The Blind Men and The Elephant."

This part of the series focuses on discovering the cause of cancer. The title, an allusion to the parable, refers to the fact that for many years scientists could not find the connection between the three major causes of cancer: viral, chemical, and genetic. The ideas were separated ideologically and scientifically. At conferences, the scientists that supported each of these ideas did not interact. It was only relatively recently that the connections between these causes were illuminated.

The earliest carcinogen was discovered in 1911 by Peyton Rous, who described the viral origin of avian sarcoma (for more information check out this great story by Jessica Wapner). In 1964, Burkitt lymphoma was linked to the Epstein-Barr virus. These results led to an rapid increase in the focus on viral carcinogenesis with the idea that a vaccine could prevent cancer. This focus came at the cost of other ideas about the causes of cancer. Unfortunately, Human papillomavirus (HPV) and Hepatitis (HepB and C) have been the only other viral carcinogens identified.

The second idea was that chemicals cause cancer. Lung cancers became increasingly common in the late 1940s. Epidemiological studies showed links between cigarette smoking and lung cancer, but tobacco companies obfuscated the results. In 1964, scientific links between cigarettes and lung cancer were firmly established thanks in part to the Kennedy administration's blue ribbon panel tasked with investigating the matter. Once the epidemiological methods were established for tobacco, other chemicals were added to the carcinogen list.

The final idea was that genes caused cancer. The major breakthrough came from Michael Bishop and Harold Varmos, who were studying the Rous sarcoma virus. Their timing was perfect the tools of molecular biology were becoming readily available. Work from their labs led to the discovery of a gene called Src, the first described oncogene. The oncogene idea was that normal genes in our bodies that control cell growth can be turned on at high levels and cause cancer. Robert Weinberg later identified the first human oncogene, Ras. Dozens of other oncogenes were found in subsequent years, leading to optimism that the cure for cancer was surely close at hand. However, we have since learned that cancer is a complex disease (some argue a collection of diseases) with a diverse range of etiologies, which makes it impossible to treat with a one-size-fits-all approach.

Interspersed with the description of cancer research was a narrative of one woman's treatment for breast cancer. This story begins with a history of breast cancer treatment, including a discussion of William Halsted's radical mastectomy. As I covered in more detail in my recent post on Pandora's DNA, Halsted's method was the standard treatment for breast cancer for nearly a century. The success rate was not impressive, but the treatment approach was unchallenged until Bernard Fisher criticized its use. Fisher performed a clinical trial to compare the use of the lumpectomy with the radical mastectomy. In 1985, his results showed that either approach was just as effective, but that the lumpectomy was less invasive and led to improved quality of life. Radical mastectomy was no longer the standard therapy: "cutting more did not mean curing more".

The intention of this segment was to illustrate the personal side of cancer, but for me the link between the two segments was how the treatment of cancer has evolved in parallel with developments in cancer research. This highlights how basic scientific research is a critical starting point for successful clinical outcomes.

Tuesday, August 18, 2015

The genetic wonders of red hair

I recently finished reading Armand Leroi's Mutantswhere I learned about some of the polymorphisms (small changes in DNA sequence) linked to variations in human skin and hair color, particularly red hair. With two different types of redheads in the house, I have always been curious about the genetic basis of this relatively rare trait.

red-haired mouse (from Flickr)
Hair and skin color are determined by the relative proportions of the two types of melanin pigment: eumelanin (dark brown) and pheomelanin (red/yellow). Large amounts eumelanin result in darker hair and very little produces blond hair. People with more pheomelanin have red hair. Red hair phenotypes can range from pale red to bright red or reddish brown, which is due to a balance of the two melanin types. Polymorphisms in the melanocortin 1 receptor gene (MC1R) are associated with variations in hair and skin color in mammals. The MC1R protein is a membrane receptor found only in melanin-producing cells (melanocytes). In response to melanocyte-stimulating hormones (MSHs), MC1R initiates a cascade of cellular events that turns on the production of pigment synthesizing genes, including pheomelanin or eumelanin. Essentially, MC1R determines pigmentation by regulating the relative proportion of eumelanin and pheomelanin.

The ancestral form of the MC1R allele produces eumelanin; variant alleles are less functional, decreasing eumelanin production or increasing the amount of yellow/red melanin. Variations in MC1R contribute to a spectrum of phenotypes, including freckling, red hair color, and sun sensitivity. MC1R alleles that disrupt function are present in ~80% of individuals with red hair and ~20% with brown-black hair. More than 80 MC1R allele variations have been identified in European populations. Association studies have shown that certain MC1R variants (p.D84E, p.R151C, p.R160W, p.D294H, p.R142H, and p.I155T) are linked with the red hair color phenotype.

One unanswered question is why these polymorphisms are more prevalent in Eurasians than in Africans. The current hypothesis is that paler skin permits better synthesis of Vitamin D in environments with less sunlight. A recent study using data from the 1000 Genomes Project revealed that the polymorphisms are also more common in Northern Europe than Southern Europe, which supports the Vitamin D hypothesis. Interestingly, a MC1R variant has been observed in Neanderthals, indicating that red hair and pale skin were also present in this population. A recent paper has shown that the Neanderthal MC1R variant is rare in Europeans, but can be found in East Asian populations. This result suggests that mutation of MC1R was a common mechanism to adapt to changes in sunlight intensity.

from David Fisher's lab

Some MC1R variants are associated with an increased risk of melanoma. Due to increased sun sensitivity and freckling of people with pale skin, this relationship seems obvious. However, darkly pigmented Caucasians with certain MC1R variants also show an increased incidence of melanoma. This result suggests that the MC1R pathway may have another role in the development of melanoma beyond differences in the ability to filter UV rays in light and dark skin. In fact, scientists think that MC1R may play a pigment-dependent and a pigment-independent role in skin carcinogenesis. There are a few hypotheses to explain the link between MC1R and melanoma. First, after UV exposure, cells with more pheomelanin show increases in DNA damage, which is correlated with increases in abnormal cell growth and proliferation, a hallmark of cancer. Second, a recent paper in Molecular Cell suggested that UV light triggers the interaction of a tumor suppressor called PTEN with MC1R. The tumor suppressor can interact with wild type MC1R, but not the red hair alleles of MC1R. The PTEN-MC1R interaction protects PTEN from degradation, which suppresses an oncogenic signaling pathway (PI3K/Akt). In contrast, MC1R variants do not interact with PTEN, allowing increased levels of oncogenic signaling pathways after UV irradiation. Unfortunately for redheads, sun exposure alone is not the sole mechanism for skin cancer. A Nature paper from David Fisher’s lab used a red-head mouse model with inactive MC1R to investigate a possible UV-independent pathway. They found that in the presence of the most common melanoma oncoprotein (BRAF 600E), ginger mice developed melanoma without UV exposure, while MC1R wild-type mice did not. Thus, shielding easily freckled skin from the sun may not be enough to protect from skin cancer for people with certain MC1R variants.

The association between red hair and melanoma suggested that there may be a scientific basis for the headline from 2014 that climate change was putting the red hair gene in danger of extinction. The story was exposed as alarmist and scientifically inaccurate. One of the many problems with the article is that they label the red hair gene as recessive. Because hair color is a complex phenotype, it is not surprising that the genetics of red hair are also complex. Red hair is usually inherited in a recessive manner, but it can also be dominant. A 2000 study showed that the inheritance pattern depends on the MC1R allele that is present: most alleles are recessive, but some alleles can be dominant. Individuals that are heterozygous for a mutant MC1R allele show variations in red hair color, beard color, or freckling. Thus, there is a dosage effect of MC1R variants on hair and skin color, which explains why some men have red beards and brown hair. These results also explain how two red-haired parents can (on rare occasions) have children that don't have red hair. Thankfully, the many variations in MC1R and the complex inheritance patterns mean that red hair isn't likely to die out any time soon.


For more information, I recommend the following links:

Red heads feel pain differently A blog post from 23andme about the population genetics of red hair.

Friday, July 31, 2015

Pandora's DNA: One woman's experience with a BRCA mutation

In Pandora's DNA: Tracing the Breast Cancer Gene through History, Science, and One Family Tree, Lizzie Stark describes her experience with a BRCA mutation, which has left its mark on generation after generation of women in her family. Like The Cancer Chronicles, Stark explores the science to understand the causes and consequences of the BRCA mutation. As a child, Stark watched her young mother as well as many of the women in her family endure breast and ovarian cancer and the subsequent treatments. In the nineties, when the BRCA gene test was first available, Stark accompanied her mother to appointments with a genetic counselor, who informed them that her family has a mutation in the BRCA1 gene called 3600del11 (a truncation mutation where 10 DNA bases are deleted from exon 11), a mutation that seems to be more prevalent in French families (for more on the population genetics of BRCA mutations, check out The Wandering Gene and the Indian Princess).

Upon learning of her mother's BRCA status, Stark realizes that she has a 50% chance of having the same mutation. Thus, she decides to learn more about the history of breast and ovarian cancer diagnosis and treatment to inform her decisions about her own treatment options. The radical mastectomy was introduced by the unusual and innovative surgeon William Halsted. Halsted (the basis for the drug-addicted surgeon on The Knick) started his career in 1880; he developed the first blood transfusion, pioneered the use of rubber gloves (through a partnership with the Goodyear rubber company) for surgery, and performed the first mastectomy in the US. Because patients regularly relapsed after this treatment, Halsted decided that a more extensive mastectomy was the solution to the problem; the radical mastectomy was designed to carve out the root of the cancer. However, the procedure, which takes both the breasts and the pectoral muscles, still has a recurrence rate of 60%. Despite these grim statistics and the fact that the procedure negatively affected women's posture and arm mobility, the radical mastectomy was the standard for care for breast cancer for nearly a hundred years.

A med student named Emil Grubbe experimented with the use of radiation to treat cancer recurrence following mastectomy; Grubbe reasoned that radiation might kill rapidly dividing cells like those in cancer. His treatment worked well for many patients, but cost the doctor his own life to radiation-induced cancer. Dr. Geoffrey Keynes (brother to the economist John Maynard Keynes) became a strong proponent the lumpectomy, a more conservative surgery that removes only the tumor and a bit of surrounding tissue, in combination with radiation therapy. In 1935, Keynes started comparing survival rates for patients receiving the combined treatment with those who had a radical mastectomy. Surprisingly, survival rates were nearly identical. Despite the fact that this less aggressive treatment was just as effective, the medical community ignored the results. It wasn't until a study published in 1981 confirmed these results that the Halsted method was finally called into question. In fact, until the 1970's, if a woman had a suspicious lump in her breast, she would be taken in for exploratory surgery, where the surgeons would biopsy the tumor and, if necessary, remove the breast without waking her up. Thus, women would go into surgery and not know whether they would wake up "with a band-aid or without breasts". This practice added psychological difficulty to the radical mastectomy. However, the women's health movement of the 1970's helped give women more power in this process and improve the life of women after treatment.

Location of the BRCA1 gene (Wikipedia)
One hero of the story is Mary-Claire King, who identified the BRCA1 gene's connection to inherited breast and ovarian cancers. (King has led an extraordinary life. In addition to her role in the BRCA story, her lab helped UN war crimes tribunals identify victims when DNA testing was still in its infancy. She tells a great story at The Moth about the connection between BRCA and Joe DiMaggio.**) After King announced her findings, a competing group formed Myriad Genetics, a company that would later patent the BRCA1 and BRCA2 genes, which allowed the company to set the price for the mutation screening. A 2013 Supreme Court decision eliminated this patent, which lowered the price for the test. Myriad Genetics has become the big bad in the BRCA story. Stark's interview with a patent attorney points out that by monetizing the BRCA test, the company was able to make it more widely available. This interview also includes an interesting discussion of the pros and cons of patenting a gene. Despite the patent ruling, Myriad Genetics has refused to share all of the data obtained from their BRCA testing, which could impede research on identifying additional BRCA mutations linked to cancer.

Stark is in the first cohort of women (along with Angelina Jolie) who are able to choose to test for the BRCA mutation. When Stark learns of her BRCA status, she then considers her treatment options: constant cancer screenings or preventative mastectomy and oopherectomy. Here, the author discusses her thought process as well as the published research as she comes to terms with her BRCA status and the health decisions she must make. Stark does an excellent job describing the research, especially considering she is not trained in science. Overall, I found the book both readable and informative; thus, it will be a useful read for a person whose family is affected by a BRCA mutation.

** For more on the story of Mary-Claire King and her research in hereditary breast and ovarian cancer, check out the film Decoding Annie Parker

Thursday, July 16, 2015

The Emperor of All Maladies - part three of Ken Burns' PBS documentary

In all my reading about cancer biology, I have yet to tackle The Emperor of All Maladies, which is said to be the best book on the subject. Luckily, PBS and Ken Burns have delivered a three-part series based on Siddhartha Mukherjee's 2011 book. Here, I will do a short synopsis of Part Three, "Finding the Achilles Heel", which focuses on the development of cancer therapies.

The documentary begins with the story of Gleevec (covered beautifully in Jessica Wapner's The Philadelphia Chromosome), which was designed specifically to treat a type of chronic myelogenous leukemia (CML) that is caused by a swapping of two chromosomes to create the Philadelphia chromosome. The success of Gleevec led to great hope  could this be the first of many targeted therapeutics? Indeed, there have been some successes in targeted therapies; ALK inhibitors have shown some promise for the treatment of cancers that are characterized by the presence of an ALK gene rearrangement. However, on average, only four targeted therapy drugs are approved per year. These drugs are typically very expensive and are not very successful in terms of extending patients' lives.

The complexity of cancer has been a major obstacle in the development of successful therapeutics. When the human genome was completed in 2001, a new hypothesis arose: if we sequence common cancers and compare with normal cells, we could begin to understand exactly how they differ. In 2005, The Cancer Genome Atlas (TCGA) project began; this large-scale sequencing project aims to identify mutations in 25 different types of commonly occurring cancers. The first results, released in September 2008, confirmed cancer's complexity. Many cancers had multiple mutations in as many as 100 genes. However, there were some cancers that had only a few mutations or showed recurrent mutations, which were found in many different patients. These less complex cancers are the focus of future directions. As more and more cancer genomes are completed, researchers can start to identify patterns in the mutations that appear in cancers; such analyses may lead to the identification of driver mutations (i.e., mutations that are causally linked to oncogenesis) versus passenger mutations (i.e., mutations that are picked up along the way). Mukherjee points out how much drug companies have benefited from the information from basic research. He suggests that the current funding environment, where increased funding of clinical and translational studies comes at the expense of basic research, is not likely to promote these types of success stories in the future.

ACS, anti-smoking ad 1968
The shift in focus from cancer treatment to cancer prevention has generally been a useful approach. For example, smoking was once a major contributor to cancer, but anti-smoking campaigns starting in the late 1960's have successfully reduced the number of new lung cancer cases. Obesity is another major contributor, but solving this health problem has been less straightforward. Viruses like human papilloma virus (HPV) and hepatitis are also common causes for cancers; these viruses are now decreasing in incidence with vaccines for both viruses available. Approximately 40% of cancers are due to unknown causes. Epidemiology focuses on determining a causal link between cancers and environmental factors (e.g., pollution, occupation, cell phones), but the connections are often difficult to prove (as was discussed in Toms River.) Overall, the combination of prevention, early detection, and targeted therapies has decreased the cancer mortality rate 20% in the US over the last two decades.

For me, the most interesting part of the this episode was about cancer immunotherapy. Cellular immunotherapy takes immune cells from a patient's blood, activates these cells, and then gives them back to the patient; this approach boosts the immune system by enriching for T cells. Some researchers have suggested that the immune system is held back from attacking cancer because it is the patient's own cells. In 1992, the FDA approved a therapy using interleukin-2 (IL-2), a protein produced by white blood cells during the immune response. Increasing IL-2 leads to increased T cell response, making T cells more likely to recognize and attack cancer cells. After that initial success, there were few breakthroughs, but some recent developments have increased interest in the field. For example, in 2011 the FDA approved Yervoy (ipilimumab), which binds and blocks CTLA-4, a checkpoint protein that prevents T-cell activation to keep cells from attacking healthy tissue. Thus, when CTLA-4 is blocked, T cells can attack tumors. Both Yervoy and IL-2 treatment show long-lasting responses, but only in a small percentage of patients; serious side effects are also common. The newest weapon in the immunotherapy arsenal is an inhibitor of PD-1, called Opdivo (nivolumab). PD-1 is another checkpoint protein, which some cancers use to disable the T cells in the area surrounding the tumor. PD-1's specificity to cancer cells suggests that Opdivo could be more powerful and less toxic than existing therapies. Based on these exciting developments, this is likely an area to watch in the coming years. 

** You can read more about cancer immunotherapy in this feature in Nature, this Nature review by Ira Mellman, or the April 2015 special issue of Cancer Cell focused on immunotherapy in cancer.

Saturday, June 27, 2015

Armand Leroi's Mutants: where the Mutter Museum meets Geek Love

Mutants: On Genetic Variety and the Human Body by Armand Marie Leroi explores the genetic and developmental reasons for variations in the human form. I thought this book would be a good follow up from Inheritance, which focuses on rare genetic disorders that often have a relatively minor physical abnormality, such as eyes that are widely space (hypertelorism). Based on the cover and title, I expected the book to be a bit of a carnivalesque spectacle part Mutter Museum, part Geek Love. In fact, the text treated these "mutants" respectfully and with due scientific diligence. The focus was generally on the developmental pathways that were altered in the mutations observed, but there was some exploration of the toll these mutations took on their bearer.

The book begins with the historical observations of mutants and the explanations for why these mutations arose. In the beginning, "monsters" were thought to be caused by the wrath of God. Eventually, scientists began to understand the developmental causes for these variations. In a chapter called "A Perfect Join", Leroi writes about conjoined twins, specifically how they form. Interestingly, conjoined twins are more likely to have a condition called situs inversus, where the internal organs are inverted on the left-right axis. In fact, the rare singleton birth with this condition has been useful in teaching us why our organs are oriented the way they are. Situs inversus is one symptom of Kartagener's syndrome, which is caused by a mutation in one of the proteins (dynein's outer arm) that control the movement of cilia (tiny projections on the surface of many different cell types). The other symptoms are chronic bronchitis (cilia are important for clearing the lung and nasal passages) and sterility in males (the same proteins are required for the movement of sperm). I always find it amazing how a small mutation in one protein can have such profound consequences. My favorite lines from the book describe how scientists study gene function: "It is actually quite hard to prove that a gene...does what one supposes. One to eliminate the gene and watch what happens. This is rather like removing a car see why it's there. Sometimes only a rear-view mirror falls off, but sometimes the car dies."

A funny story arises in the explanation of the Hox genes, which essentially control the pattern of embryonic development such that Hox1 makes a head, Hox2 makes a torso, etc. Mutations in Hox genes can lead to abnormal body plans, even changes in the number of vertebrae and ribs. About one in every ten adults has an extra pair of ribs, an abnormality that was first observed in a woman, leading the doctors on the case to conclude that it was evidence of the truth of Adam and Eve. In reality, the physiological variation occurs at equal rates in men and women.

The chapter on skin color explores the mutations that lead to albinism, piebaldism, and even red hair. Dozens of different mutations in MC1R (melanocortin 1 receptor), a protein that helps control pigmentation, have been described in red heads. (Because my house has three different types of red heads, I really fell into an Internet rabbit hole on this subject. I think I will write something more about this later.) The genetics of skin color are also complex and have been difficult to study due to the complicated social issues surrounding the subject. Leroi tells the story of a white woman living in Apartheid-era South Africa. Following a diagnosis with Cushing's disease, her adrenal glands were removed, which led to hyperpigmentation due to an abundance of the hormone melanotrophin. As her skin darkened, her social status and living conditions quickly changed. To me, the story highlights the problem with thinking that we can biologically define race. (A Troublesome Inheritance was released recently and covers this very topic, so watch this space for my review.)

Leroi also discusses the genetic basis for aging; in the simplest terms, aging is due to the "inability of natural selection to act against the mutations that cause disease in the very old." This hypothesis explains why dominant mutations like Huntington's can fix in the population. An experiment in fruit flies explored what would happen if only aged flies were reproducing; the effect should be an increase in genetic changes that promote longevity and fertility at an advanced age. After ten generations, the longevity of these flies increased by 30%; after fifty generations, life expectancy doubled. The flies were generally hardier, but the increased life expectancy came at a cost: the fruit flies were less active in their youth as they needed to preserve themselves to ensure survival and mating. This experiment supports the idea that aging comes at the expense of vitality in youth.

Overall, Mutants was quite readable; it had a nice balance of the science behind the mutations and the descriptions of the lives of the people who were affected with these mutations. I should note that the book was released in 2003, so some of the science is a bit out of date. For me, a good read is one that teaches me new science and spurs me to read and write more. Mutants definitely fits the bill in that regard. 

Tuesday, May 5, 2015

Resources for finding a career away from the bench

If you are a graduate student or postdoc in the sciences, you are likely aware of the "PhD problem"*, the academic bottleneck caused by an increasing number of PhDs with a concomitant decrease in the number of tenure track positions. Unfortunately, the statistics suggest that the problem is not likely to get better any time soon. In fact, the issue has gotten so bad that even the mainstream media has picked up the story. The default pathway is no longer PhD to postdoc to tenure track; this great infographic from ASCB  (see below) suggests that the tenure track is the real alternative career. While the statistics may seem grim, I think there is some good news: the academy is starting to wake up to the harsh reality**. In the past, postdocs and grad students complained that PIs were only capable of training them to become a PI. Increasingly, PIs and universities are aware of the prospects for their trainees and they are starting to find ways to help guide them for a number of careers. infographic

As a Scientific Editor, I often get questions from graduate students, post docs, and PIs about my transition away from the bench. After a recent chat with a grad student at a meeting, I decided it was time to put together a post of useful resources for finding a career away from the bench. Because I am in publishing, my links tend to focus on that path, but all of the websites I list below have articles about other career paths as well. 

The first two places you should be looking for a job in science are Nature Jobs and Science Careers. Both websites have listings for a variety of careers paths as well as an array of great content for helping you navigate your job search. Whether you are just starting to think about your future directions or preparing for an interview and negotiating your salary, there are relevant articles for you.

Nature Jobs has a very well-organized site. I recommend spending some time there to explore their content, especially their blog and their career toolkit. This article from their blog gives a great general overview of the types of jobs available to people with a PhD in the sciences. Be sure to check out The Postdoc Series for articles aimed at post docs at different stages of their careers. Nature Jobs also hosts a career expo, which I have read good things about.

On the Science Careers website, check out the tips and tools and explore the articles in the Career Magazine; they have more than 10 years of content available. By far the most valuable resources I found when I was searching for my current job were this collection of articles about science writing and editing and this 2002 article "Careers in Science Editing". These give a very general idea of what different types of scientific editing jobs entail. This informative article from Cell Press' Debbie Sweet describes the specifics of working for a reviews journal or a primary journal. Once you find something of interest, the related article feature (which seems to be available for newer articles only) will help you find more to read.

Societies relevant to your field will likely also have career resources available. For cell biology, ASCB's Career Development section has a number of articles available. My favorite among these is the Career Publications, which are free to download as PDFs. The ASBMB also has some useful articles, like these Career Case Studies.

The Chronicle of Higher Education is generally best for searching for a faculty job, but they also have some excellent articles on non-academic jobs, such as "The PhD's Guide to a Non-faculty Job Search".

If you are feeling isolated in your decision to leave the bench, you can find some comfort by reading some "quit lit". It seems many scientists find it cathartic to share their story;  indeed, I have written my own quit lit posts on this blog (here and here). Over the years, I have read many posts in this genre; I particularly enjoy finding updates, which tend to have a happier mood than the original post. Eva Amsen's (Outreach Director for Faculty of 1000) "Five Years Later" was very positive and shared some useful links and tips. Likewise, SciCurious (a science writer in neuroscience) tells her story in "The system failed me. It should have failed me sooner." 

To learn more about a career in science writing, read Ed Yong's collection called "On the Origin of Science Writers" where a variety of working science writers share their journey as well as tips on how to make a living writing about science. The National Association of Science Writers also has some great content in their resources section.

In short, these links should give you some ideas of the paths that are available to you. Hopefully you also have some valuable resources at your institution (e.g, postdoc association or a career development office). If you find other useful links, please share them in the comments. 


* There are numerous suitable links that describe the problem; I have chosen the one that I first discovered. Nature had a 2011 special issue called The Future of the PhD, which included the great story The PhD factory.  

** The Future of Research symposium has been putting together meetings to find solutions to these problems.

Friday, April 24, 2015

Gulp - Mary Roach documents her travels on the alimentary canal

Gulp: Adventures on the Alimentary Canal is Mary Roach's 2013 release about food and its journey from start to finish. Here, Roach brings her trademark style combining interviews and site visits with interesting vignettes. She is never afraid of the taboo (Ed Yong has said he has the "wow" beat in science writing; I think Mary Roach has the "ick" beat) and the subject of the physical process of eating and digestion is rife with such topics. Roach states that books about cuisine and food have eclipsed books about the process of eating, which serves her well because most of the interesting stories about digestion are untold.

One of these strange tidbits is that different animals perceive tastes differently. Catfish have taste receptors all over their skin, effectively making them "swimming tongues"; this also makes catfish a popular model organism for taste researchers. Flies taste with their feet. Humans have taste receptors in the gut and the esophagus as well as the tongue; luckily, only the receptors on the tongue are transmitted to the brain. Animals also have different preferences for tastes: rodents love sweetness, but cats cannot perceive sweet tastes. Dogs' tastes are driven by their sense of smell and they show a strong preference for things that smell like cadaverine or putrescine, odors emitted by decaying meat. Dog food manufacturers often use these scents in concentrations perceptible to your dog but not to you to increase a dog's interest in the food. Roach visits a pet food manufacturer and watches dogs taste testing dog food, which gives a fascinating behind-the-scene glimpse of the industry.  

Beaumont studying the digestion of his patient, St. Martin
Roach digs into the tale of scientific obsession at the heart of the relationship of William Beaumont and his patient and experimental subject, Alexis St. Martin. Over the course of thirty years, Beaumont performed hundreds of experiments into digestion via a fistula in St. Martin's stomach. These experiments did yield the first information about the function and contents of the stomach. However, the mental cost to the patient was likely very high. St. Martin eventually escaped Beaumont for his native Canada, but the doctor was constantly pursuing him. (For more on this strange tale, check out the Radiolab episode Guts.) 

I also learned some surprising facts about saliva. For one, the main digestive enzyme in saliva is amylase, which breaks down starches into simple sugars. This activity makes amylase an excellent way to treat food stains on clothing. Laundry detergents often contain at least three digestive enzymes: amylase to break down starchy stains, lipase for greasy stains, and protease to break down protein. It's good to know that there is a scientific basis to my instinct to spit on food stains.

The other interesting elements in the book are learning the techniques that scientists are using to study eating, digestion, and defecation. Roach visits labs that study topics like the function and components of saliva, the process of chewing, and the chemical composition of flatulence. Unfortunately, I felt that these serious topics were often glossed over for the sake of a punchline. I do find Roach's work easy to read, but her sense of humor does not always mesh with mine. I knew that talking about the journey that food takes from beginning to end would bring out her obsession with the scatological and yet I plowed through. I suppose I'm glad I did, as the penultimate chapter discussed Elvis Presley's digestive troubles; Elvis suffered from mega-colon, which was likely a confounding factor in his death. It's funny that my favorite Mary Roach book is Stiff: The Curious Lives of Human Cadavers (I admit to reading it after seeing it on Six Feet Under), which somehow seems less gross than this one. In the end, I would only recommend reading Gulp if you like Mary Roach's approach to science writing.

Thursday, April 9, 2015

Inheritance by Sharon Moalem: an excellent new perspective on human genetics and epigenetics

Inheritance: How Our Genes Change Our Lives
and Our Lives Change Our Genes, by Sharon Moalem, offers a unique perspective on the subject of human genetics. Moalem is a physician-scientist who specializes in rare diseases; his specialty has given him a keen eye for discerning subtle physical differences (phenotype) that are frequently linked to genetic differences (genotype). In some cases, the differences are insignificant. For example, if you have an extra row of eyelashes, you share something with Elizabeth Taylor, specifically a mutation in a gene called FOXC2. Other differences can serve as a diagnostic for rare genetic conditions. In one chapter, Moalem describes being at a dinner party when he noticed several physical traits that suggested that his hostess may have Noonan syndrome, which can be associated with heart disease and blood clotting. Another example is orbital hypertelorism, where the space between the eyes is large enough to accommodate another eye. This trait can be associated with Fanconi anemia, a blood disorder linked with an increased incidence of cancer. Wide-set eyes are commonly found in actresses and models (famous examples include Jackie Onassis and Michelle Pfeiffer). Our preference for certain physical traits may be explained by our interest in ensuring a good developmental and genetic history in our mates; Moalem suggests that facial features are an obvious indicator that brain and body development occurred properly.

Inheritance also highlights how minor differences in the sequence of our DNA can cause major differences in phenotypes. For example, congenital polycythemia (PFCP) is a genetic condition caused by a mutation in the EPOR gene that results in a greater number of red blood cells. This mutation gave Finnish athlete Eero Mäntyranta a distinct advantage in aerobic competition because his blood can carry more oxygen (essentially it's like he always has doped blood). However, PFCP can also lead to an increased risk of stroke. Thus, evolution took a different approach to solving the low oxygen problem for Sherpas: a mutation in the EPAS1 gene causes lower production of red blood cells, but increases the efficiency of oxygen delivery.  Interestingly, this mutation fixed in the population relatively quickly: Sherpas moved into their current low altitude environment around 1500. (This is a really fascinating story; if you want to read more, I recommend this Ed Yong piece.) These examples also underscore that while humans are ~99% similar, there is still a lot of variability in DNA sequence. In fact, in the 14 years since the first human genome was sequenced, we have learned that there really is no average genome. As I highlighted in my previous post on genomics, large-scale genomics projects (e.g., The 1000 Genomes Project) aim to get samples from a highly diverse set of people to remove the background noise so that significant differences can be identified.

Moalem also has an informative discussion of epigenetics (i.e., changes to DNA that do not occur at the sequence level). A great example in the book is the queen bee. Every bee in a colony is completely identical in their DNA sequence. How then does a queen bee become so different in size and function? Larval queens are fed royal jelly, which changes their DNA to allow them to express queen-specific genes. The protein DNA methyltransferase (Dnmt3) can methylate DNA and change its expression. In fact, if you shut down Dnmt3 in bee larvae, all of them become queen bees. The field of epigenetics is relatively young. However, there are already many fascinating ways in which our daily activities can alter the expression of our genes. The epigenome is dynamic and can be impacted by the things we eat and drink, the exercise we do, and, most surprisingly, the experiences we have. Accumulating evidence suggests that stress can alter your genome; in some cases, these changes can be inherited. The Radiolab episode Inheritance highlights a Swedish study that suggests that the eating habits of your grandfather could have an effect on your longevity. Geneticists are just beginning to find ways to track these changes and, more importantly, how to reprogram the methylated genes. As you can imagine, methylation is a very useful way for a cell to alter its gene expression. However, methylation can also mean the difference between a benign growth and a malignancy, making it an attractive target for therapeutic development.

Moalem makes an excellent argument for the support of the study of rare diseases. Most funding bodies think that funding diseases where many people are affected (e.g., cardiovascular disease, Alzheimer's) is the most cost-effective approach. However, studying the mutations and physiology of people with rare diseases can often shed light on the basic underpinnings of how normal cells work. For example, the study of familial hypercholesterolemia (FH) gave us insights into the function of LDL and HDL ("bad" and "good" cholesterol); these results facilitated the development of Lipitor, which has helped many people with elevated levels of LDL who do not have FH.

In short, Inheritance is immensely readable. The author uses clever and pertinent analogies. For example, he compares our cells to the production style of Toyota and Apple in that they stock only the supplies they need to avoid waste (an approach called production leveling). Another great example is when he is explaining a genetic condition that turns muscle into bone; he writes, "Osteoclasts are the Wreck-it Ralphs of the skeletal system. Osteoblasts are the Fix-It Felixes." Overall, the book is very topical and up to date; it would be an informative read for those who are well versed in genetics as well as those who are just becoming interested in the subject. Inheritance is definitely one of the best books I have read on the subject (a close second to Sam Kean's The Violinist's Thumb) and will be added to my list of great science reads.