Tag Archives: medicine

The Skinny on Cancer Immunotherapy: focus on CAR T Cells

Screen Shot 2015-10-22 at 9.47.44 AMOne of the more interesting modern therapies being used to fight cancer aims to coax, or engineer a patient’s own T Cells to fight disease.
In very basic terms, the principle is not dissimilar to vaccine strategies used against infectious disease. That is, they direct and boost the patient’s immune system against target cells. One reason vaccinations have been so successful in fighting disease is that they leave much of the hard work to nature – the same nature that has been keeping you and your ancestors healthy enough to successfully reproduce for millions of years. Give the immune system a push in the right direction with a well designed, safe vaccine and the body does the rest leading to (at least theoretically) life-long protection. At this point, the most limiting factor to how long protection lasts is because we live so much longer than humans have ever lived before.

William-Coley_206x236Immunotherapy against cancer has been an area of interest since the 1890s, when William Coley observed that cancer patients who had infections at the site of surgical resection fared better than those without infections. Rather than dismissing this observation as uninformative, he speculated that the immune system plays an active role in preventing or regressing tumors.

In fact, the immune system is constantly performing ‘immune surveillance’ to prevent newly-generated cancer cells from developing into tumors. Direct evidence for this involves ‘knocking out’ elements of the immune system and watching for cancer. As predicted by the theory, immunodeficient animals develop spontaneous tumors at a higher rate, and earlier than do immune-competent animals.

The pudding: (from :

Evidence for Immuno Surveillance

Evidence for Immuno Surveillance

But vaccinations used against infectious diseases are given before the patient is infected (known as prophylactic vaccination).

How can we immunize people against all the cancers that may crop up in all their various forms?

The answer is – we don’t. In the case of cancer, we perform vaccinations ‘therapeutically’, or after disease has started. Otherwise there really would simply be too many possible targets.
So, we wait, and help the body to fight the challenges that actually do arise.
A number of methods have been developed and tested to accomplish this, here, I want to specifically address a personalized therapy that takes cells from the patient, ‘aggravates’ and expands them, and then re-infuses them into the same patient.
Currently, there are several ways this is being done with various outcomes.

One method involves immunizing the patient against killed cancer cells isolated from the themselves (via surgery), then harvesting the reacting cells and expanding them to numbers much higher than those reached in vivo, and then re-administering to the patient as a jump-start to immunity. The advantages are that these immune cells are ‘self’ and therefore do not have to be ‘matched’ to the recipient a la transplantation surgery. It is also possible to remove any regulatory cells (T regs), that often impair immune responses, prior to re-administration.
A more engineered response has been investigated by investigators such as Carl June, of the Abramson Cancer Center at the University of Pennsylvania. These cells, known as CAR T Cells express ‘Chimeric Antigen Receptors’ directly target tumor cells using transgenic antibodies that incorporate the intracellular signaling domains of up to three immune-activating receptors. See the illustration below for details of this receptor’s design (taken from ‘Breakthroughs in Cancer Immunotherapy webinar by Dr. June )
Screen Shot 2015-10-21 at 7.20.04 PM
In the case of CAR T Cells, most have been made to fight B Cell Chronic Lymphocytic Leukemia (B Cell CLL). These cells are a good test case for the technique for a number of reasons, including the fact that they uniformly* express a marker called CD19 on their surface and also because they are a ‘liquid tumor’ – meaning that the cancer cells are individual cells moving through the body (at least many are). Treatment of solid tumors can bring added complications such as the need to infiltrate the tumor in order to find target cells.
As I said, CD19 is a common protein expressed on these cells. Therefore, at least the CAR receptor part is standardized between patients – this is the piece that is added to cells transgenically so that they will bear a receptor known to engage the target cells with high affinity. Because it must be added to the patient’s own cells, this is accomplished using a viral vector that infects the T Cells in culture and provides the DNA required to make the receptor. (In case you’re worried about the virus, these are engineered to only infect the first cell they encounter, they cannot reproduce themselves and continue an infection)
So, let’s walk through it:

Screen Shot 2015-10-21 at 7.20.04 PM
1. Blood cells are isolated from a patient
2. T Cells are purified (i.e. isolated)
3. T Cells are infected with virus in culture.
4. T Cells grow up with the chimeric antigen receptor expressed on their surface
5. These cells are then re-injected into the patient via I.V. drip over about 30 minutes time.
6. Let the cells do the work

Screen Shot 2015-10-22 at 10.33.53 AM
This therapy has an impressive track record so far with studies with success rates from ~60%- 90% of patients responding and remaining disease free for years (Maude et al).
Following the initial infusion of cells, CAR T Cells proliferate in vivo to very high numbers and can even form immunological memory cells to come to the rescue in the event of a relapse.
So, what next?
A number of startup companies have emerged to tackle the logistics of bringing this type of therapy – an extreme example of personalized medical care – into being. Unlike traditional drug therapies where a single compound is mass produced and distributed world-wide, each patient must have their own cells processed and returned to them for infusion. This therapy is much more of a service, and as such, will require physical locations across the country that can manage the handling of cells.
The up side, however, is potentially transforming fatal diseases into manageable ones with a high quality of life after therapy.
Just ask Emma:

*Well, most do, anyway.


Posted by on October 22, 2015 in Uncategorized


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To all my former students (as well as everyone else who reads this blog): please check out “Vaccines” a PBS documentary about the challenges faced by society revolving around maintaining society’s immunity against a number of vaccine-preventable diseases. Vaccines airs on PBS stations on August 26th at 9pm. You can also watch the film online here.

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Posted by on August 26, 2015 in Uncategorized


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CRISPR: Accelerating the pace of molecular biology

CRISPR stands for Clusters of Regularly Interspaced Short Palindromic Repeats. Dr. Jennifer Doudna was one of the first researchers to see these short palindromic repeats in bacteria and archaea where she speculated that they were being used as a form of molecular immune system to protect these organisms from viruses.

Even bacteria get sick, so having a protection against invading viruses is a matter of life and death to a cell. Recall that viruses are essentially genetic material that will reproduce itself again and again after it hijacks a cell. Viruses may have protein coats or membranes to protect them outside of the cell, but inside, they are little more than DNA. If this DNA can be damaged or destroyed, then the virus is rendered harmless.

Screen Shot 2015-07-27 at 9.54.10 PMTo the right is a clip from Dr. Doudna’s video illustrating the repeated elements (in black) flanking a variety of ‘other DNA’. This ‘other DNA’ is what the cell will use to identify  foreign DNA – presumably from retaining the genomic material from an earlier exposure either in the lifetime of the single cell or its parents.

So, how does it actually work?
Two videos do an excellent job of explaining how CRISPR works. A short, simple video from MIT gives a non-technical explanation (a good place to start).

MIT’s McGovern Institute

Jennifer Doudna explains the system in greater detail…

Basically, the natural system uses two RNA molecules to target specific DNA sequences in the genome and recruit a protein that acts as an endonuclease to cleave this target:

crRNA – a ‘targeting’ molecule
tracrRNA – an adaptor RNA that recruits CAS9 to the bound crRNA
CAS9 – an endonuclease enzyme that will bind and cleave DNA once recruited by the RNAs

Doudna’s lab improved the system by combining the two RNA molecules into a single RNA that still effectively recruits CAS9 but is easier for researchers to manipulate in the lab. This last element is essential because manipulating this RNA sequence gives researchers the power to target any DNA sequence in the cell.

As stated above, the system was originally identified in prokaryotic organisms where it appears to allow targeting of the viruses that attack them. CRISPR uses ‘stored’ DNA as the targeting RNA and then brings in CAS9. CAS9 binds to the targeted DNA and cleaves it resulting in one of two possibly outcomes. 1) the virus is destroyed and is no longer a problem, 2) the virus is cut, but then repairs itself – hopefully in a way that introduced fatal mutations.

How might this translate into clinical medicine?
The possibilities are endless, however a few low-hanging fruit present themselves immediately. Among these are therapies for sickle cell anemia (and a host of other blood disorders). Because sickle cell anemia is caused by a single base pair mutation, it is conceivable that hematopoietic (i.e. blood) stem cells can be isolated, the faulty gene repaired, and then re-introduce the corrected stem cell back into the body (possibly after the faulty stem cells have been ablated).

The newly altered and re-introduced stem cells now do the rest of the work for you by finding their place in the body where they reside while continually producing cells with the desired genetic changes.

The key is that these RNA molecules are quite simple to make exactly and in pure form (i.e. they can be manufactured chemically rather than needing cells to do the job for us and then we have to clean up all the extraneous contaminants). Most labs will design the molecules in-house and then order the constructed molecules from a ‘core lab’ that specializes in doing just that.

Jacob Corn, of UC Berkeley has compiled a simple protocol that anyone with a modicum of molecular biology training could follow. Find that protocol here.

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Posted by on July 27, 2015 in Uncategorized


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Invitation to Submit Questions for Microbiology (Mini) Exam II

infectious_diseaseMy microbiology class is having a special mini-exam on the Tuesday after we come back from Spring Break. This exam will cover chapters 11 and 12 of the Cowen Microbiology text, which is basically ‘how do we kill microbes outside of the body’ and ‘how do we kill microbes inside the body?’ This exam will also have elements taken directly from Exam I presented as an opportunity to retain that material and be sure that we keep these core ideas in mind.

That said, I will be happy to entertain any questions proposed by students (or non-students) on these topics.

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Posted by on March 12, 2015 in Uncategorized


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The value of life

coffee and tea doodles

value is what we make it

Episode 3 / Season 13 of WNYC’s Radiolab asks, “What is the value of human life?” in a story titled, Worth.

This article questions how much life is actually worth to us. On the street, they put the question to passers-by in the form of, “What would one year of healthy, productive life be worth to you?”

Answers ranged from the ridiculously small ($5 – surely life is worth more than a Venti Frappacuinno at Starbucks) to the absurdly high ($10,000,000 – perhaps it would we worth that to someone with a net worth in the billions, but probably not for the average person.

Is a year worth the salary you make in a year? Apparently non-working spouses (or young children) are worth zero.

Is it the same value for every person? Is a year of my life worth as much as that of a fortune 500 CEO’s. The President? A Nobel Prize winner? A crack dealer?

Read the rest of this entry »

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Posted by on December 29, 2014 in Uncategorized


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One snake or two?

My wife and I had a conversation this afternoon that prompted this post.

This is a caduceus:








This is the staff of Asclepius (as part of the American Medical Association symbol):







The caduceus is the staff carried by Hermes, the messenger of the gods.  As such, it is also a symbol associated with messengers and printers (considering that printing is a form of communication, and therefore within the realm of the messenger. It is also used today as a symbol of commerce.

 The rod of Asclepius is the symbol of the god of the same name, who is associated with healing and medicine. Today, this symbol retains its association with medicine and is often found incorporated in the signs of medical facilities.

Unfortunately, these two similar symbols are sometimes confused.


 For example, this student is clearly asking for donations so that he can afford the education to know the difference between a caduceus and a rod of Asclepius.

Maybe once he’s got that in order he can start studying medicine.













Posted by on January 5, 2014 in Uncategorized


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reviewing TEAS test questions

In preparing for a new semester, I’ve been downloading a few free question compilations for the TEAS test. TEAS is the ‘Test of Essential Academic Skills’ that students wishing to enter into nursing programs must take. Since many of my students in both my Biology and Microbiology classes wish to enter nursing programs and are taking required classes for that purpose, I find these questions to be very useful in directing my syllabus creation.

However, today, I found this question amongst the free samples offered at the website:

Category – Science

Q – What is a term used to describe the subtle energy running through the body?
A. The Tao
B. The Force
C. Chi
Your answer: –
Answer: C – Chi is a term used for the subtle energy that runs through the body.
Chi is specific to Traditional Chinese Medicine. Other terms used are ki, prana and life force.

What am I to think?

I’m not sure that I am comfortable with ‘Chi’ being a legitimate concept being taught in science classes.

Am I wrong to think that the science and medicine taught to students of these disciplines should be objectively verifiable? Is ‘Chi’ a documented phenomenon? Or is this just a word / description that describes some metaphysical concept?

Wikipedia uses the following to define Chi:

Qi is the central underlying principle in traditional Chinese medicine and martial arts…Elements of the qi concept can also be found in Western popular culture, for example “The Force” in Star Wars.”

Given this loose definition for an equally loose concept, I think “The Force” is an equally reasonable answer to the question as it is posed. And no answer to this question should be acceptable or expected in a serious exam. I certainly hope that this question is an example made up by, and not one that my students are ever likely to see on a real examination.

See this link for a review of chi, also known as qi or qidong, in medicine.

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Posted by on December 26, 2013 in Uncategorized


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Cell Division, Contact Inhibition and Cancer

imagesIn my general biology class we are now reading chapter 5 of Mader et al, on Cell Division. This chapter is a bridge between those chapters on descriptive cell biology and those describing the activities of the cell and how we explain the inheritance of traits from one generation to another.

We focused our attention on Mitosis and Meiosis of diploid Eukaryotic cells and followed how these two types of nuclear division manage the sorting of genetic material into daughter cells ensuring that each cell gets an appropriate set of instructions for life.

The body is comprised of somatic cells that include everything from skin to muscle and nerve cells. These are called somatic because soma comes from the greek word for body.

The other type of cell is the gametic cell, referring to germ-line, or sex, cells.

Each of these type of cells goes through its own type of division in order to end up with the correct amount of genetic material ( or ‘ploidy’) in the resulting cell or organism. Ploidy refers to the number of complete sets of genetic material a cell has. We, humans, are diploid organisms having two sets of genetic material in each cell.


Mitosis in Diploid Cells

Somatic cells undergo mitosis in a way that maintains the diploid state of cells creating two exact replicas of the parent cell.

This mechanism makes sense, because one skin cell might replace a neighboring skin cell following its demise in order to maintain a confluent layer. We would expect every skin cell to be genetically identical to every other and mitosis delivers just that.

However, if we imagine sex cells that were made from mitosis, these would also be diploid (2n). Then a diploid sperm would fuse with a diploid egg and make a tetraploid offspring. Then that organism would have octaploid offspring and so on. This, of course, does not happen.

ImageSex cells are instead produced by a different kind of division called meiosis. Meiosis is merely a specialized form of mitosis in which the genetic material (ploidy) is ‘halved’. The resulting cells are then haploid (1n or n). As part of the specialization, meiosis occurs in two steps so instead of producing two cells, it produces four (at least theoretically). Also, instead of being identical, each of the resulting sex cells is unique.

But this discussion is supposed to be about cancer, so let’s ignore meiosis for now. I’ve discussed cancer before here, but I just found a couple of good animations that I wanted to include.

The first is an excellent animation on cell cycle and contact inhibition. See how cancer is defined here as the lack of respect for cell-cell signaling, that would otherwise result in a healthy monolayer of cells.

The second, discusses how cancer cells would need to alter their environment in order to get the nutrients they need to survive. It can be tempting to think that cancer cells don’t need these things, but they certainly do.

Once cells mutate in a way that initiates cancer, the constant struggle with the immune system amounts to a selective pressure allowing only the strongest cells to survive. 😦 A brief article describing this battle can be found on the HHMI website. A more thorough treatment of the subject can be found in a freely available review by my friend Dr. Ezekiel Fuentes-Panana.

Here’s one last animation showing a tumor mass producing metastatic cells that leave the mass and migrate to new locations within the body. I’m not that fond of this video, but it does communicate the message I wanted to get across.

Alltogether, cancer cells are those that no longer obey the rules of polite cellular society and continue to reproduce through unchecked mitosis when such division is not in the best interest of the organism as a whole. One way these cells do this is to cease responding to contact inhibition signals. This results in the production of a tumor mass that will need to obtain energy and will often do so by sending out pro-angiogenic signals resulting in new blood vessel formation. As the tumor continues to grow, it may invade neighboring tissue and ultimately even metastasize into the blood or lymph leading to a number of secondary tumors throughout the body.

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Posted by on October 14, 2013 in Uncategorized


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Nobel Prize in Medicine Awarded

Three scientists were awarded the 2013 Nobel Prize in Medicine to:

James E. Rothman, Randy W. Schekman 
and Thomas C. Südhof

for their discoveries of machinery regulating vesicle traffic, 
a major transport system in our cells

– from the press release from

ImageThe full release can be found here. The  website  includes a link to a summary page illustrating the contributions of each scientist and how they come together to form a unified picture of vesicular traffic.

The New York Times article describing the award including an astute remark by NIH Director Francis Collins about the state of research in the United States. 

Dr. Francis Collins, the N.I.H. director, said in an interview on Monday. “Today we celebrate the three N.I.H.-supported Nobel Prize winners, but we’re being slammed by sequestration and a government shutdown.”

Even before the shutdown, scientists were facing severe budgetary difficulties that restrict the kind of research that led to this year’s Nobel Prize, Dr. Collins noted. “How many potential future Nobel Prize winners are struggling to find research support today, or have been sent home on furlough?” he said. “How many of them are wondering whether they should do something else — or move to another country? It is a bitter irony for the future of our nation’s health that N.I.H. is being hamstrung this way, just when the science is moving forward at an unprecedented pace.”

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Posted by on October 7, 2013 in Uncategorized


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This Week in MicroBiology Class



Instead of starting our chapter on Eukaryotic micro-organisms / parasites, we spent much of Thursday’s class discussing the second Chapter of ‘Vaccinated’. This chapter digs in and discusses how a number of vaccines were tested in the children of the Willowbrook institution in New York. We talked about how researchers must balance the (sometimes) competing interests of doing the best experiments to answer a question and looking out for the interests of those who can not look after themselves (the children of Willowbrook, in this case).

This chapter looked at the work of several investigators; Most evaluating vaccines, but one (Krugman) was also doing experiments to investigate how Hepatitis was spread. His work included the infection of a number of children with live virus, but no attempt at protecting them from infection.

This is presented as the most condemnable work of the lot as it presented no potential benefit to the children. In saying this we define the principle by which other work was done, ‘does the study do no intentional harm and does it provide at least some potential benefit to the subjects?’

This principle provides a challenge to doing the (scientifically) ideal experiment outlined below.

A basic, direct vaccine test would divide patients into two groups (vaccinated and unvaccinated) and then challenge half of each group with live virus (or whatever the vaccine is to protect against).

Ideal results:

vaccinated –> unchallenged –> 100% healthy

vaccinated –> challenged –> 100% healthy

unvaccinated –> unchallenged –> 100% healthy

unvaccinated –>challenged –> 100% sick

However, this means that the researcher would be knowingly (assume s/he is not blinded) injecting unprotected patients with live virus – an obvious ethical issue.

In looking through some old work done to investigate how hepatitis is spread, there was a mention of work conducted in just such a manner:


Bellin and Bailet J. Ped 1952

It’s unclear from this reference to a personal communication what, exactly the word ‘volunteer’ means.

I’ll bring up this paper in class the next time we discuss Vaccinated. I have an interesting person connection to it.

Instead of a experimentally controlled challenge, modern vaccine tests (as the other work described in this chapter) use much larger populations chosen because of their ‘at risk’ nature and then we wait and see if there are statistical differences between the infection rates of each group.

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Posted by on September 6, 2013 in Uncategorized


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