Precision Medicine will need to get out of the pharma silo that is based on symptoms

Welcome to the digital era of biology (and to this modest blog I started in early 2005).

To cure many diseases, like cancer or cystic fibrosis, we will need to target genes (mutations, for ex.), not organs! I am convinced that the future of replacement medicine (organ transplant) is genomics (the science of the human genome). In 10 years we will be replacing (modifying) genes; not organs!

Anticipating the $100 genome era and the P4™ medicine revolution. P4 Medicine (Predictive, Personalized, Preventive, & Participatory): Catalyzing a Revolution from Reactive to Proactive Medicine.

After low-cost airlines (Ryanair, Easyjet ...) comes "low-cost" participatory medicine. Some of my readers have recently christened this long-lasting, clumsy attempt at e-writing of mine "THE LOW-COSTE INNOVATION BLOG". I am an
early adopter of scientific MOOCs. My name's Catherine Coste. I've earned myself four MIT digital diplomas: 7.00x, 7.28x1, 7.28.x2 and 7QBWx. Instructor of 7.00x: Eric Lander PhD.

Upcoming books: Airpocalypse, a medical thriller (action taking place in Beijing) 2017; Jesus CRISPR Superstar, a sci-fi -- French title: La Passion du CRISPR (2018).

I love Genomics. Would you rather donate your data, or... your vital organs?

Audio files on this blog are Windows files ; if you have a Mac, you might want to use VLC ( to read them.

Concernant les fichiers son ou audio (audio files) sur ce blog : ce sont des fichiers Windows ; pour les lire sur Mac, il faut les ouvrir avec VLC (

What do our genes have to do with quantitative biology, statistics & probability? Everything.

To cure many diseases in the future, we will have to target genes; NOT the organs. We have a LOT of cells and DNA (as opposed to the limited number of organs, of course).

MIT is currently offering a MOOC for you to learn quantitative or systems biology: 7QBWx. Week 6 is now live. On the menu: statistics in biology and genomics with R. Making disease predictions like you are in some casino (I'l go for Vegas), trying to evaluate what your chances are with, let's say, the roulette wheel spinning? Looks like fun!

Links to my previous posts about MIT-edX MOOC 7.QBWx here & here.
(On Twitter: #7QBWx)

Week 6:
"- Cool, huh?"
Thank you, Professor Paul Blainey!

Au MIT, on fait la médecine de demain - avec Apple, Google et IBM Watson

"C'est très embêtant ... Savez-vous combien il y aurait d'erreurs médicales en France ? Entre 600 et 700.000 par an ! Conduisant à quelque chose comme 30.000 décès ! ( ces chiffres m'ont été donnés par la précédente présidente du Ciss. Naturellement vous ne verrez pas ces chiffres sur la place publique). Les médecins comme tout être humain ne sont pas fiables ..." Jean-Michel Billaut

On pourrait imaginer que la médecine des organes fasse preuve d'une plus grande précision que celle attendue de la part de la médecine du "big data" avec le génome. Il n'en est rien. Cette nouvelle forme de médecine "quantitative" est dite : "de précision" ("genomic precision medicine"). Faut-il rappeler qu'en ciblant la cellule et son ADN, on se situe à un niveau de précision bien supérieur à celui de l'organe ? ... La programmation informatique avec R, Python, MATLAB, et des logiciels tels que PyMOL, ainsi que le Watson d'IBM sont les scalpels (ou plutôt, les microscopes; les scalpels, ce seront des protéines - CRISPr et la protéine associée Cas9) du futur à COURT terme (5 ans disent les experts). Ces scalpels seront nettement moins invasifs que celui de la chirurgie traditionnelle "à ciel ouvert". Encore une bonne nouvelle, non ? ...

Il nous reste encore beaucoup à découvrir sur l'ADN. Nous n'en sommes qu'aux débuts, mais cela va très vite grâce à la puissance numérique dont peut désormais bénéficier la biologie. La croisée des deux domaines est déjà vertigineuse, et ce n'est que le début de l'aventure ...

Confused, I took a peek at Eric Topol MD's account on Twitter, see what this "Moonshot" thing was all about... Ah, ok lah, got it now...

"Using high throughput sequencing or microarray technologies, we can identify RNA levels of every gene across a large number of cancer patients. While #python excels at mapping sequence-level changes to genes, R is useful for analysing and visualizing these changes across a patient cohort." #7QBWx

You know what? Between mammography and genomic "precision" medicine, guess which one I'm gonna choose... Thank you, #QBWx!


From Broad Institute to Broadway?...

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"MIT Hacking Medicine is much in demand as hospitals look for new ways to solve long-standing problems with a diverse group of brainstormers keen to share ideas. A few weeks ago it hosted a session at the BIO conference and even as I caught up with co-director Andrea Ippolito after her keynote at CONVERGE, she is gearing up for a business trip to India and has a long list of hackathons lined up this fall.
I’ll bet she wishes she could clone herself. Oddly enough, the organization is moving in that direction.
It is working on a website that would package its hacking medicine model to make it available to a wider audience. Although it typically works with hospitals, it has been approached by companies, institutions and organizations such as AARP, big pharma, medical device companies and surgical groups.
“I’ve gotten such a tremendous amount out of running medical hackathons, but we want this medical hackathon model to scale and to be sustainable,” said Ippolito.
This fall, the organization has an exciting schedule advancing its hacking medicine model. Its calendar includes a collaboration with the Clinton Foundation on a hackathon for women’s health. It will be limited to female participants who are engineers, entrepreneurs, clinicians and designers to promote STEM.
A critical care data hackathon at Beth Israel Deaconess will bring together data scientists and clinicians to analyze de-identified data on ICU patients pulled from electronic medical records by the hospital that could lead to new practice guidelines.
It has a second hackathon with Boston Children’s Hospital to develop innovative ideas in the pediatric space.  It’s also doing a Shark Tank challenge at Brigham Women’s Hospital that will look at ways to improve the in-patient experience as its theme.
Emergency department physicians are embracing the hackathon trend, too. MIT Hacking Medicine is doing a hackathon in Chicago with the American College of Emergency Physicians and Health 2.0.
Other projects it is eyeing include a medical hackathon for pain points in behavioral health and collaborations with surgeons."

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I'd love to be the "Security Princess" of my own genome!

Studying genomics & quantitative biology at MIT

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Professor Ernest Fraenkel, MIT: systems biology is the new tool that could help disrupt the cost escalation (exponential increase in the cost of drug development): welcome to the era of biology and big data.

7QBWx MIT and edX
Link to MOOC, June 2014
Why do we need systems biology?

"There's still a huge need to be able to measure other aspects of what's going on in the cell. And do very high throughput experiments, so we can cheaply and efficiently test not just one prediction from a model, but thousands of predictions, because one of the challenges of systems biology, is that if we're measuring thousands of things but we're only testing two, three, five, 10, then are we truly testing our models? And usually not, so we need better ways of doing the experimentation as well." Professor Ernest Fraenkel, MIT.

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In 10 years we will be replacing genes; NOT organs

"Genetic 'typo' corrector": from organ donation to CRISPR
"Another way doctors could use CRISPR is to assist in regenerating tissue within damaged organs. Epstein ultimately wants to place embryonic stem cells that have developed into cardiac muscle cells back into the heart. But the main danger with this lies in accidentally injecting any non-cardiac cells. "If you put a cell into the heart meant to make a tooth or a hair, it might cause a tumor," said Epstein.
So instead of blindly inserting a group of cells hoping they are all cardiac muscle, he is using CRISPR to insert marker genes - such as a gene that includes a glowing, green fluorescent indicator - to be able to clear out every other non-heart cell in mouse models.
Earlier methods of performing genomic surgery had barriers of high costs and low flexibility that kept many researchers from adopting them.
"Then CRISPR started coming out, and since then it has absolutely exploded," said biologist Montserrat Anguera of Penn's School of Veterinary Medicine. "CRISPR seems to be the easiest and fastest way for labs to edit the genome."
She studies how embryonic stem cells develop into specialized cells within organs such as the liver or heart. Using CRISPR, she can delete regions of the stem cell genome to help decipher their function in human development.
Bao first began his work with sickle-cell disease using older systems such as zinc finger nucleases, but has since switched to CRISPR - and he is a believer.
"I call them nanoscissors - a truly amazing tool," Bao said.
Anguera joined Penn's faculty a year and a half ago after a postdoctoral fellowship at Harvard Medical School, where CRISPR-guided research flourishes. Both she and Epstein hope to grow Penn's community of users, now just a handful.
The Broad Institute, a Harvard-MIT biomedical research collaborative, holds the patent for the tool's components and methods. Its main inventor? A 32-year-old neuroscientist, Feng Zhang. Early last year, Zhang and his team were the first to demonstrate the system's search-and-edit capabilities in the cells of mice and humans.
Researchers at the University of California, Berkeley, first used CRISPR to make targeted DNA cuts. After more work by Zhang, CRISPR has become the powerful tool seen today, with a proven record in many animals and plants.
"The analogy would be like the search-and-replace function in Microsoft Word," Zhang said. "In the genome, we don't have a biological search function, so we use a specific string of letters."
This string of 20 letters, or bases, is used as a template to search for a specific matching section of the genome, which is no small feat. In humans, double-stranded DNA is made up of three billion base pairs. But once you engineer the special 20-letter-long code, or guide RNA, the CRISPR system will target the desired gene by searching along the DNA until it makes a match. Once locked in, an enzyme then acts like DNA scissors and cuts the two strands.
Because many CRISPRs can act at once, you can delete whole regions or cut and paste from different areas of the genome. The tool can also exploit the cell's natural DNA repair mechanism and weave a new piece of genetic code into a gap.
Zhang has cofounded a Cambridge, Mass.-based start-up, Editas Medicine, to develop new treatments using CRISPR.
"In areas of research, CRISPR can help us understand and identify genetic mutations that can lead to disease," he said. "Clinically in the long run, we might be able to use it to repair mutations."
Zhang also notes that real-world applications abound beyond medicine too: making better crops or biofuels. But experts say it will be years before genomic surgery comes to a hospital near you.
"It may take 10 years, could be shorter," Bao said. "The most important challenge is off-target cutting - not only cutting where you want to cut, but also at other locations you don't want."
For instance, if 19 out of 20 letters match up, the guide RNA may still bind and cause the enzyme to cut the wrong gene. Zhang is working on ways to make the search more stringent, such as increasing the number of letters.
And even when the correct edits are made, an organ could have other issues. Researchers recently regenerated damaged heart muscle in monkeys using an older gene editing technique, and found that the animals had episodes of irregular heartbeats after the procedure.
Still, Epstein remains optimistic about CRISPR's future, and predicts it will be available to patients within a decade.
"It's not pie-in-the-sky anymore, it's real," he said. "Changes can occur in surprising, quantum leaps."

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