Wednesday, September 28, 2016

Ten Great Science Articles and Blog Posts From Across the Internet

Some websites do a weekly best of the web and, frankly, I wish I were that well read or that ambitious. In lieu of such lofty ambitions, I will share a listicle of some of my favorite science articles and blog posts. Enjoy! 

The Man with the Golden Blood: This Mosaic Science piece explores the market for rare blood; easily one of the best long reads I have found. This makes a good compliment to the Radiolab episode on Blood.

Brazil's Cancer Curse: Title aside, this is a great story by Sue Armstrong, whose book about p53 I recently reviewed. She digs deep into a Brazilian cancer cluster and how the doctors made the link to p53 mutations. The best part is the speculations about where this mutation arose and how it fixed in the population.

He Thinks He's Untouchable: Yes, this is BuzzFeed and yes, it is worthy of this list. This is one of many well researched and frankly exasperating stories about sexual harassment in academia. I have read too many of these stories, this one is definitely the most extreme of them all.

The Unique Merger That Made Ewe, You and You: A list of great science reporting would not be complete without something from Ed Yong. Frankly, it's difficult to choose just one. This one is a favorite simply because it addresses a subject dear to my heart: endosymbiotic evolution. 

Lessons of Immortality and Mortality From My Father, Carl Sagan: A bit far adrift for science articles, but this story from Carl Sagan's daughter was published at the perfect time in my parenting lifeafter the death of a close friend of the family. It helped me find a way to frame life and death in a way consistent with my perspective as a scientist and a way that was understandable to a young child.

Medical Research: Cell Division: A title that doesn't really capture the awesomeness at the heart of this story. In the vein of Rebecca Skloot's HeLa cell book, this story captures the ethical issues surrounding the Leonard Hayflick's creation of the WI-38 cell line from an aborted fetus. The author, Meredith Wadman, has a book related to this topic coming out in early 2017.

He may have invented one of neuroscience’s biggest advances. But you’ve never heard of him: Another title I hate hiding a story I love from STAT news. This one surrounds the invention of optogenetics in neuroscience. For me, it highlights the need for researchers to be sure readers and editors understand the implications of their work.
How Elizabeth Holmes's House of Cards Came Tumbling Down: Again, this story is not in my usual wheelhouse, but I have been following the story of the Theranos company with great fascination. This Vanity Fair piece gets into how Holmes was able to convince everyone around her that this idea was the next Unicorn and that it was scientifically sound, even though she neglected to get the scientists and clinicians on board from the beginning.

Who was Phineas Gage?:This piece from Sam Kean gives you a great sense of what his book The Dueling Neurosurgeons is about. This may be one of the weirdest stories in science, so it makes sense that it was likely the start of Kean's book about the brain.

How Your Cat is Making you Crazy:  I should be embarrassed to admit how many times I have shared this story from 2012, but I find it oddly compelling read about the strange effects of Toxoplasmosis (that stuff in cat poo) on the brains of humans and mice. It has all the things necessary for a good science article: cats, weird scientists, and unexpected results.

Monday, September 19, 2016

p53: The gene that cracked the cancer code - a review

I wouldn't think that an entire popular science book could be written about one protein, unless that protein is p53. As of this writing, a PubMed search reveals 82,179 scholarly articles about p53. Thus, p53 The Gene That Cracked the Cancer Code by Sue Armstrong has an abundance of source material. Even with the all that information to cover, the author does an excellent job explaining the relevant research in a clear and concise way, using a chronological structure with the main source being interviews with the scientists that did the original research. Unlike many popular science books, Armstrong relies more on the direct quotes from the primary source, ensuring that she gets everything right.

Briefly, p53 (named because the protein is about 53 kilodaltons on a protein gela naming convention that swept through some circles of scientific research, but has since been eclipsed by more colorful naming styles) was discovered in 1979. While David Lane is typically credited first, Arnold Levine, Lloyd Old, and Pierre May also deserve acknowledgement for the discovery. Considered to be a tumor suppressor, p53 has cellular roles in genome stability, DNA repair, apoptosis/cell death, and cell metabolism. This book primarily focuses on p53's role as the "guardian of the genome", a term penned to describe that ability of p53 to keep the cell's DNA free of mutations. This role is the primary connection of p53 to cancer: normally, p53 induces cellular suicide (apoptosis/cell death) in cells with DNA damage. p53 is the most commonly mutated gene in cancer and when p53 is mutated, it loses its ability to protect from DNA damage, which can lead to excessive cell growth, a hallmark of tumorigenesis.

Like so many of the books on cancer that I have covered before, this book hit many of the key topics in the area of cancer research. What is unique about this book is that it leads the reader through the sometimes winding roads of scientific research. This includes an in-depth discussion of the p53 mutation database, which collects all the mutations in p53 that have been linked to a variety of cancers. This database has been a rich source of information for researchers over the years. For example, in 1996 researchers showed that lung cancer cases showed p53 mutations in a particular hotspot on the p53 gene. Interestingly, these same mutations were shown by the Pfeifer lab to be induced by the carcinogenic substance in cigarette smoke, benzopyrene diol epoxide (BPDE). This publication was a major win for the 1998 class action lawsuit against Big Tobacco.

Map of p53 mutations and their frequency.
The p53 database has also helped reveal the link between liver cancer, Hepatitis B, and aflatoxin, a poison produced by a fungus that grows on peanuts and other grains when they are stored without adequate ventilation. Typically, HepB causes liver cancer only after many years. However, in places like Asia and Africa, the risk is compounded by the exposure to aflatoxin, a carcinogen known to cause DNA damage. Aflatoxin can induce a mutation in p53 (at codon 2449), which can essentially turn p53 from a tumor suppressor into an oncogene.

The book delves into several of the most damaging p53 mutations. For example, Li-Frameni syndrome (LFS) is a genetic disordered characterized by the early and frequent acquisition of cancer at "every conceivable site in the body". The disease was first described in the early 1980s, but the connection to p53 was not established until the 1990s. A variety of mutations in p53 have been associated with LFS, but the most common hotspot connected to LFS is involved in p53's ability to bind to DNA.

Perhaps the most interesting story in the book describes the cancer clusters in Brazil. Sue Armstrong contributed the story of "Brazil's Cancer Curse" to Mosaic Science; it is a fascinating story and gives a great sense of her writing style. As discussed in the book Toms River, cancer clusters are typically assumed to be caused by a pollutant. Likewise, the Brazilian doctors wondered if that might be the case. However, the research about LFS was starting to garner attention, leading Brazilian clinicians to suspect p53 was also be responsible in the Brazilian cancer cluster. Indeed, sequencing of the p53 gene in affected individuals reveals a mutation at codon 337 to be the most common. Where the story gets really interesting is when scientists attempt to understand how an uncommon mutation fixed in the population at such high frequency. While the source is still debatable, the p53 mutation is now thought to be the result of a founder effect and bottleneck (as described for BRCA mutations in The Wandering Gene).

p53 structure (Wikipedia)
I think I learned the most in the section about the clinical approaches to treating p53 mutations. Here, Armstrong has done a deep dive into the literature about the latest drugs and trials connected to p53 function and dysfunction. Thus, the book is up to date on the available p53-related drugs (as of its publication in November 2014). Armstrong describes several different approaches to treating p53-related cancers, including drugs like Advexin, which uses a viral vector to induce cells to express wild type p53. For reasons that are unclear, Advexin has had mixed success in the US and is still awaiting FDA approval. Perhaps more interesting, is the research on PRIMA-1 (an acronym for p53 re-activation and induction of mass apoptosis), a drug designed to work on mutants of p53 that no longer bind DNA. Essentially, PRIMA-1 induces mutant p53 into its wild type shape, allowing it to re-activate and bind DNA. Thus, PRIMA-1 should target a wide range of p53 conformation mutants and leave wild type p53 alone. Both of these have been major roadblocks in the deisng of previous p53 therapies, especially since p53 is at the center of so many regulatory pathways. The drug is currently in Phase 2 trials. (Here, Armstrong takes a tangent into the history of chemotherapy, specifically its connection to the German use of mustard gas in WWII. This was a fascinating story that I recommend reading more about, for example here or here.) 

Sue Armstrong's p53 book distills a large amount of scientific literature into an interesting and readable book. I don't think I would recommend this as the first book to read if you are just starting to learn about cancer research. To me, the best starting place would be The Philadelphia Chromosome (some might recommend Mukherjee's The Emperor of All Maladies). However, this is an excellent book for those familiar with cancer and looking for the next level of science writing on the topic.