Category Archives: Science

Immunotherapy: T cells vs Leukemia

Image credit: Singularity Hub
Image credit: Singularity Hub

Cancer immunotherapy, named Science’s “breakthrough of the year” 2013, is the manipulation of the patient’s own immune system to combat a disease. Since its initial beginnings in the late 1980s cancer immunotherapy has grown to be one of the most exciting prospects in biomedical science today. The first treatment of this type came in the form of an antibody against cytotoxic T-lymphocyte antigen 4 (CTLA4), a protein on T cells that is known to reduce the T cell response when active. Blocking this function with an antibody it was hypothesized, by immunologist James Allison, may enhance the immune response and let it properly attack cancerous cells, as the researchers then demonstrated in mice. This idea was developed by a small biotech,Medarex, which was then bought by Bristol-Myers Squibb. It wasn’t until 2010 that the company could report that their antibody had increased the life-span of patients with metastatic melanoma from 6 months to 10 months, the first treatment shown to extend life in this form of cancer trial.

Another aspect of immunotherapy, aside from antibodies and other biologics, is the manipulation of T cells directly harvested from the patient to be active cancer hunters when re-administered. This work, a form of cellular therapy, was pioneered by Steven Rosenberg and has been followed up on by a multitude of researchers, commonly looking at types of blood cancer due to its accessibility in comparison to cancer of other areas of the body. In 2010 Rosenberg described chimeric antigen receptor (CAR) therapy, in which a patients T cells are genetically engineered to express a receptor that allows them to target specific cells, in this case cancerous cells. This is also referred to as T cell “re-education”.

Now a team of researchers at the Memorial Sloan-Kettering Cancer Centre in New York has published new data from a study using their CAR, 19-28z. This specific CAR targets the marker CD19, also known as B-lymphocyte antigen, which is present on another type of immune cell, the B cell. These cells are normally involved in antibody production and in providing one type of the long-lasting immunological memory, but as with many cell types when things go wrong they can become malignant, cancerous. Adult B cell acute lymphoblastic leukemia (ALL) is a form of blood cancer caused by malignant B cells that have yet to fully mature. Importantly therapies targeting B cells expressing CD19 would not affect fully matured B cells, or plasma cells which do not express CD19. As mentioned previously these cells are responsible for the vital mechanisms of antibody production and immunological memory, hence these hugely important aspects of the immune system would survive treatment with CD19-targeting therapies, whereas (hopefully) the cancerous CD19 positive cells would not. Interestingly, other studies have shown that CD19 may in fact be directly involved in the development of some cancers making the choice of targeting this molecule even more attractive.

In their latest study the researchers showed that, in a group of 16 patients, 88% showed a complete response to the CAR therapy. This means that 14 of the 16 were able to reach complete remission and then begin hematopoietic stem cell transplant to maintain this state. These patients had previously relapsed from remission after standard treatments and so had been offered this treatment instead of salvage chemotherapy, which is only effective in 30% of relapsed ALL patients. These results build on the 2013 data by the same group that first showed that 19-28z CAR was well-tolerated and showed significant ability to treat relapsed ALL. Unfortunately there are some adverse risks with this treatment. Some patients have shown markedly increased levels of serum cytokines in what is known as severe cytokine release syndrome (sCRS). This is treatable with corticosteroids amid other therapies but it is essential that research is undertaken to identify those patients who are likely to develop this issue. CAR therapy is at its heart a personalised medicine and so understanding these adverse effects and their likelihood between different people is of great importance. Adverse effects aside, the researchers and the data, which speaks for itself (88% v 30% seems like an obvious choice to me), claim that this treatment is deserving of moving on to phase II trials. Steven Rosenberg said in a paper in 2013 that anti-CD19 CAR T cells could become the standard therapy for some B cell cancers and it seems that this latest data supports this. It has been a long road for cancer immunotherapy but with results like this from an ever more popular field of research, one can hope that soon there will be multiple therapies of this type advancing to the point where they become the standard-of-care and herald a new era of personalised cancer treatment.

Transplantation, rejection and the genome

Image credit: Mark Gray, Spectrum Health
Image credit: Mark Gray, Spectrum Health

Transplantation is always a risky business when you use tissues and organs that are genetically dissimilar to those of your recipient, but sometimes it is the only option. With conditions such as Idiopathic Pulmonary Fibrosis (IPF) lung transplantation remains the only viable treatment that truly offers a chance at increased survival. Those people with end-stage heart disease or those with a failing liver, due to conditions such as Primary sclerosing cholangitis for example, can all require a transplant. Unfortunately not all of these people will get them. Qualifying for a transplant is no easy feat, the rest of the body must be in good condition, you must show that you have a willingness and the ability to improve your lifestyle, and of course you must be able to take the multitude of medications required to prepare for such an extreme operation. All in all those tasked with the difficult duty of deciding who gets a transplant, must get the rare and valuable transplant tissues to those who will benefit the most, and to those with the greatest need.

But I digress, it is the rejection of tissues, not the process and huge benefits of transplantation that will be the focus here…

Rejection of transplanted tissues is a complex and unique response mounted by the immune system. While I don’t plan on going into too much detail concerning the mechanisms behind transplant rejection, I will attempt to give a brief overview of some of the important points. It is the major histocompatibility (MHC) complexes that are responsible for advertising a cells identity as “self” or “non-self”. They essentially form a barcode that identifies a person’s cells as the cells of that person. If they are scanned and found to be incorrect they are identified as “non-self”. There are multiple pathways in acute rejection of transplanted tissues all involving these MHC molecules. The recipient’s immune system responds to recognising foreign MHC molecules in a variety of ways with the adaptive system charging ahead with cytotoxic T cells and/or antibody-producing B cells. This means that both chronic and acute rejection are associated with the death of cells from the donated tissue leading to eventual damage to the organ and finally necrosis, death of the tissue or organ. The MHC molecules are encoded by polymorphic alleles and expressed co-dominantly, which means that a person’s genome encodes 12 different MHC molecules and that even siblings still have only a 1 in 4 chance of having identical MHC complexes. Essentially, the take home message is that MHC matching is essential for clinical transplantation and has a clear beneficial effect on the outcome. Saying that, it is not necessary for MHC molecules to be matched perfectly, some mismatches are less disadvantageous than others due to the possibility of shared sections of structure between different MHC types. Of course it would be too simple if this was the only problem presented by transplantations, there are other factors to consider, for example, in some cases the recipient’s immune system may already have been exposed to, and so be ready to mount a fast and effective response against, a similar foreign molecule leading to what is called hyper-acute rejection that takes place within minutes of the donor organ being transplanted.

Acute rejection usually occurs within the first two weeks of the operation but rejection of transplanted organs can in fact be a long process spread over several months or even years. This chronic rejection is very understudied and not completely understood for most types of transplant. Chronic rejection of lung transplants is actually more common than with other solid organ transplants, and the survival rate is still only 50% after 5 years. Monitoring the acceptance of an organ such as this requires biopsies be done routinely to monitor the organs acceptance, or keep track of the rejection. With heart transplants this involves an endomyocardial biopsy that is expensive, painful and not without risk of complication. Another method to monitor this process, or to initially diagnose it, was developed by Stephen Quake from the Howard Hughes Medical Institute back in 2011. A non-invasive procedure to detect solid organ transplant rejection was proposed by Dr Quake and his colleagues. Other attempts have been made to produce a non-invasive procedure, such as the FDA-approved AlloMap molecular expression test, that focuses on monitoring the immune system of the patient by measuring the expression of certain genes. In contrast to this, the method developed by Stephen Quake relies upon the fact that, as I mentioned in the very first sentence, the genomes of transplanted tissues differ from those tissues and cells of the recipient. It also works from the fact that that cells die and are routinely shed, breaking apart to leave cell-free DNA in the bloodstream. The same team has used this knowledge to produce a diagnostic test that allows the determination of whether an unborn child has Down syndrome by analysing the blood of the expecting mother.

This latest technique, aimed at diagnosing transplant rejection, utilises high-throughput sequencing to identify the “signature” of cells from the donated tissue which can then be monitored over time. If there is a detectable change in the level of donor DNA in the bloodstream then it is implied that there is an increase in the rate of death of the donor cells that in turn implies the transplant is being rejected. The results of the study show that during organ rejection the levels of donor DNA can increase up to 4 times the level seen normally. Previous attempts to identify cell-free DNA in organ transplantation have been met with limited success, only managing to detect the Y chromosome present when a female has received a transplant from a male. However, Quake has managed to demonstrate that this technique is sex-independent and can be applied to any donor and recipient. While so far only demonstrated in patients who have undergone heart transplant, the theory behind the technique could be applied to the majority of transplantations if it can be shown that donor DNA is present in the bloodstream. Unlike the AlloMap this procedure has been shown to detect rejection before a biopsy and so could be a good diagnostic tool for allowing treatment to start early (with corticosteroids) before confirmation with a biopsy. If this, or a similar non-invasive technique were adopted, the savings made through reducing the number of biopsies could be up to $12 million in the United States. This is without even mentioning the cost of the impact on quality of life caused by routine biopsies.

While a good example of one way in which advances in sequencing and in genetic testing could have a positive impact on patients this could just be the start. Over the coming years further advances will be made in personalised medicine, for example Quake writes that taking a snapshot of the antibodies present in a person’s blood could be used outside of the field of transplantation and have an impact on monitoring the success of vaccinations, whether someone has an allergy or an autoimmune disease. He points out quite rightly that the immune system is not static, it fluctuates in its activity throughout a person’s lifetime and so testing could one day become a routine tool used for a huge variety of conditions at many points throughout the lifetime of a patient.

In the UK there always seems to be quite a lot of talk about waiting times with the National Health Service, while from the US I seem to hear complaints about pricing and inadequate insurers. With advances in sequencing (as well as the price coming down) and the development of techniques such as this, I can only hope that one day genetic and immunological testing has advanced to such a stage that a simple test, that can be done in my local practice, could diagnose any condition known to mankind simply and effectively. Of course we are a long way from that point but it does not feel impossible that we could see some significant steps towards this in the coming years.


Author: David Busse

The Nature of Mars

The surface of Mars as seen by the Curiosity rover.
Image credit: NASA/JPL

Controversy has raged about the nature of Mars for hundreds, possibly even thousands of years. There are records documenting that ancient civilizations such as the Egyptians and the Babylonians observed and studied Mars as it appeared in the night sky. The planet was named after the roman god of war and was given its own day, Tuesday, or martis dies (Mars’s day) in Latin. But it was not until the last few centuries that modern telescopes and imaging technology, as well as spacecraft and rovers, enabled us to properly study Mars, albeit from afar, and consider whether there is, or could have been life on our local red planet.

Role models for Martian life

Mars is a dry, practically giant dust bowl of a planet, spotted with humongous volcanoes, mountains and some of the most extreme, yet beautiful, landscapes quite unlike anything you can find here on Earth. Yet it is on Earth we may find clues and hints as to what life may be, or have been like on Mars. Here we find life in all sorts of places, from blistering deserts to the frozen wastelands at our poles, and even at the very depths of our seas. These organisms are referred to as extremophiles due to their ability to survive in, and their penchant for, extreme conditions. Astrobiologists view these organisms as possible models, displaying potential features and characteristics of the kind of life we might find elsewhere in our universe. The life-forms found in these ecological niches on Earth are commonly microbial, although there are eukaryotic and multicellular examples, and some even class penguins and polar bears as extremophiles. Life has been found flourishing in extremes of temperature, radiation, pressure and acidity, such as the algae Ferroplasma acidarmanus that has been found to survive in acidic mine drainage with a pH of near 0 (the lower the pH the more acidic a solution is). This has reaped the organism the sub-classification as an acidophile, and considering our stomach acid has a pH of 2 (with each pH separated by a factor of 10) this is definitely an accurate description. Another common example is Thermocrinis ruber, a pink filamentous bacterium that seems to thrive in the hot springs (83-88°C) of Yellowstone national park. Since the discovery of this bacterial species by Thomas Brock in the 1960s, there have been dozens of groups of “heat-loving” thermophilic species discovered in and around hot springs, and other high temperature environments. To be classed as an extremophile an organism does not have to be able to survive extreme conditions all the time, but just during some stages of its life cycle or when exposed to certain conditions, say at different times of the year. With this, one could apply the term to the majority of plant life who have a seed-like stage in their life cycle, as seeds are commonly resistant to many environmental extremes. More obvious temporary extremophiles include the Tardigrades, also known as water bears, who are able to enter a hibernation phase in which they are resistant to extreme temperatures, pressures and exposure to chemicals such as fluorocarbons.

The tardigrade, “water bear” image credit: Nicole Ottawa & Oliver Meckes / Eye of Science

It is a combination of harsh conditions and almost constant exposure to them that life would have to survive if placed on Mars. The planet itself is exposed, with an atmosphere 100 times thinner than that of Earth, and therefore cold. The surface temperature of the planet can range from -125 to 20 degrees Celsius, at the extremes of the seasons. Even if you can survive the temperature and the thin atmosphere you must then battle with even more of the elements. The soil itself is full of oxidants, possibly hydrogen peroxide and perchlorate to name just a few. Combining this fact with the radiation the surface of the planet is exposed to, the atmospheric conditions, and the low water content of the soil, scientists predict the formation of reactive species that would be very damaging to organic matter both at the surface and beneath it.

The hunt for ancient signs of life

Our search for extra-terrestrial life is an inevitable one. It is hard to imagine when you look up at the night sky that there is not life somewhere out there, possibly looking back. On Mars though, this search is a search of the planets past. In 1976 the Viking landers attempted the first in situ experiments on Mars in an attempt to find signs of biological activity. The spacecraft subjected soil samples to four different tests, but any positive results have been negated by scientists who argue that the data can be explained by chemical processes happening in the soil, partly due to the presence of oxidants or exposure to radiation. Mars looks to us now as if it can no longer support life, (although there is always a chance, extremophiles have previously been found on Earth living inside rocks in harsh conditions) but could it have done so in the past? Scientists have had to break the search down into steps, the first of which is to assess the habitability of the planet billions of years ago when conditions may have been more supportive of life. In doing so they must answer the question of whether the essential building blocks of life were present, including carbon, hydrogen, nitrogen, oxygen, phosphorous and sulphur. Another sign that microbial life was once present would be the finding of redox gradients, and molecules in varying redox states below the surface of Mars, implying that certain microbial metabolisms had once taken place there. Another potential sign of life on Mars would be the detection of certain biomarkers. These are organic molecules that, in medicine, refer to specific signs and molecules present in disease. In this case finding biomarkers would mean the identification of molecules such as amino acids that are the basic building blocks of proteins in all known life. The ExoMars Rover mission, due to launch in 2018, will carry a Raman spectrometer with this aim in mind. Unfortunately this method may present some complications as some inorganic processes, unrelated to life, can produce structures very similar to the biomarkers which scientists hope to find. These biomarkers would be very simple structures that will have subjected to various conditions throughout the last few billion years therefore detection, and accurate identification, will be no easy feat. One positive is that unlike Earth, Mars has undergone no widespread tectonic activity which on Earth has led to the reformation of ancient terrains, making it very difficult to find geological samples, including fossils, older than 3 billion years in condition suitable for accurate analysis.

Water on Mars

Ever since the first detailed maps of Mars were produced it has been hypothesized that Mars was once a planet that was able to support an environment in which water was present in liquid form. In fact much of the terrain can be seen to have formed as a result of water activity. Confirming this was the task given to, and completed by the rovers Spirit and Opportunity, who launched back in 2003 and arrived on the planet on the 25th January 2004. While Spirit lost contact in 2010, Opportunity is still functioning and sending back valuable data, even though its initial mission was only 90 days long. Joining Opportunity on the planet (although separated by some distance) is Curiosity, who touched down at Gale crater in 2012. This rover, nearly the size of a car, is practically a mobile inter-planetary chemistry laboratory; with ten distinct machines all geared towards assessing whether the ancient aqueous environments confirmed by Spirit and Opportunity could have supported life. These ancient environments would have formed relatively early on in the planets life, perhaps within the first billion years after planetary formation. This prediction has arisen from comparing the conditions to those on Earth when microbial life first appeared, and the possible conditions present on ancient Mars. Habitable after all A recent number of publications in Science, coinciding with the 10th anniversary of the landing of Opportunity and Spirit, have described a system of ancient environments, at Gale crater, that the researchers say, could have been inhabitable by chemoautotrophic microorganisms during the Hesperian age, about 3.7 billion years ago. Chemoautotrophs are organisms that use inorganic compounds to produce energy, such as iron or hydrogen sulfide  and obtain carbon from carbon dioxide. Using readouts from Curiosity, scientists now believe that there was water flow around the crater rim that pooled at the bottom, with a neutral pH low levels of salt. With organisms being found on Earth that can survive the harshest acidic conditions as well as the most hypersaline (high salt) waters this is a promising find. Interestingly the data also indicates that there was a colder and/or drier environment at the time, which is quite impressive considering the environment today is cold and dry already in comparison to our planet. Thermal decomposition of rock powder collected by the rover revealed the presence of materials bearing carbon and nitrogen that may have been generated by organic materials.

Future prospects

Overall the work of the rovers over the last ten years and the many fly-bys by spacecraft before that, as well as our initial, and modern observations from Earth, all seem to indicate that ancient Mars was indeed habitable, if only for perhaps a period as short as tens of thousands of years. Of course there are no confirmations as to whether the planet actually was inhabited at this time and it may be many years and missions yet until this question is answered. To find fossils from this ancient time would be a great achievement and one that will require a lot of work. One of the major problems is that due to the radiation levels the planet’s surface is exposed to, the top few meters of the surface are penetrated by ionizing radiation that could have damaged any preserved fossils. Now the focus of the missions on Mars turns towards understanding how organisms would have decayed, been preserved as fossils, and then how they would have been affected by factors such as this radiation, in order to begin to understand where we might be able to find any fossils that may have escaped the ravages of time unharmed. Mars may be the second smallest planet in our solar system with a mass of 0.107 of Earths but it is not a small search area. The terrain is rough, varied and realistically rovers can only move so fast (Curiosity has an average speed of 30 feet per hour). There is also the chance that scientists could conclude fossils would not have survived close to the surface and so we may have to search deeper and so design spacecraft capable of this. It is the European Space Agency’s ExoMars mission, planned for 2018 that will next shoulder that task of searching for these ancient signs of life now that habitability has been confirmed by its predecessors. So far the search for life on Mars has been met with no ultimate success, although proving the planet was habitable in some areas is a major step forward. Yet it is quite simple to put a positive spin on this. In 1976 the Viking landers did not search the entire planet, and the 2018 mission will launch with much more advanced equipment with controllers and scientists behind its operation and design armed with much more knowledge and experience. It is a long process but proving there is life on Mars is ultimately easier than proving the planet is, and always has been lifeless. One sample, one exquisite find and the years of searching will be vindicated. Even if we search the entire surface of the planet and find nothing with todays, or even tomorrows technology, that will not be enough to dishearten the men and women involved in the search. It can only lead to new thoughts, new theories, and new missions looking in perhaps even more difficult to reach places.

Author: David Busse

Originally published at