Saturday, 23 July 2016

SurveySpeak: is wound healing a problem on DMTs?

I am sick and tired of my current DMT; it seems to be affecting wound healing. What about you? #SurveySpeak #MSBlog 

"Prof B (aka the MouseDoctor) was speaking to a person with MS who mentioned to him that since starting drug X they had noticed that minor cuts and abrasions were taking much longer to heal. The process of wound healing is complex and uses many of the same biological processes that the immune system uses to function. Therefore it is quite possible that some DMTs that are used in MS may impact on wound healing. To assess whether or not this is an anecdote, or a real phenomenon, ProfB has asked me to do a quick poll. We would therefore appreciate it if you could complete the following survey. Thank you."

Eming et al. Wound repair and regeneration: mechanisms, signaling, and translation. Sci Transl Med. 2014 Dec 3;6(265):265sr6.

The cellular and molecular mechanisms underpinning tissue repair and its failure to heal are still poorly understood, and current therapies are limited. Poor wound healing after trauma, surgery, acute illness, or chronic disease conditions affects millions of people worldwide each year and is the consequence of poorly regulated elements of the healthy tissue repair response, including inflammation, angiogenesis, matrix deposition, and cell recruitment. Failure of one or several of these cellular processes is generally linked to an underlying clinical condition, such as vascular disease, diabetes, or aging, which are all frequently associated with healing pathologies. The search for clinical strategies that might improve the body's natural repair mechanisms will need to be based on a thorough understanding of the basic biology of repair and regeneration. In this review, we highlight emerging concepts in tissue regeneration and repair, and provide some perspectives on how to translate current knowledge into viable clinical approaches for treating patients with wound-healing pathologies.

Assessing Animal Data is it Pants or Not?

This week ProfB presented to a group of students on EAE and left his slides on the blog. The students also had a session on experimental design. Central to this is how to analyse data. Someone commented on this.

I must admit we are all pretty bad a statistics, but it seems that some EAEologists are worse than others

Someone I know had a grant sent back because the referees were saying that they had to analyse their EAE data in a certain way, that was........statistically wrong.

It is amazing how many people do their EAE analysis in the wrong way. 

They often use a test called a Student's t test to measure the severity of a neurological score. 

Here signs are given a arbitaory score say 0-5 see in the example below. This test assumes a few things such that the measurement item is continuous (such as height where you could be 1m tall or 2m tall but also everything in between as an example of parametric data), but a few other things too. If those assumuptions are not evident you need to use non-parametric analysis such as the Wilcoxon/Mann Whitney U tests.

It is amazing that 65% of the EAE paper published in Nature/Science/Cell journals assume neurological scores are parametric and of those a whopping 67% of studies use a t test to analyse their data. This is in my humble opinion not correct.

In the picture you can see the crux of the problem. In EAE you get T cells infiltrating the spinal cord and in the picture above the cells are red. In the picture above look at the extra amount of red between 0 = normal and 1 = limp tail. Now look at the difference between 3 = paresis= partial paralysis and 4 = hindlimb paralysis. So the amount of red detween 0 and 1 and 3 and 4 is not the same  yet they get an arbitary score of diffeence of 1. But you can see there is more red in 3 than 1 and more red in 4 than 3. So the neurological score is non-linear and non-parametric meaning that non-parametric statistics should be used. This is based on ranking from the smallest to the largest. Does this mak a difference?

It can do. This is an real example that we use to teach, It was a nature paper and the animal experiment was the culmination of the work. In the study they used a t test and showed the drug gave a signficant inhibition (p=0.029)...Yipppie they said. But if only the referees had asked them to do it properly.  Look at the graph and the drug drops the neurological score by about a half

Or does it?
They seem to show the actual scores of individual animals and yes if you do a t test it is P=0.029. But looking at the data 5 animals have no disease but the drug does essentialy nothing in the six animals that got disease. 

However if you do non-parametric statistics the result is P=0.082 and so the drug does nothing and the value of the Nature paper is flushed down the loo. 

So the paper may not get a mention because of the idea but as a teching example of data analysis

Was it a fluke where it just happened that 5 animals failed to get disease. We never know because the work was not repeated. So looks like there is no quality control which is a problem with some EAE studies.

So when you read EAE papers look out for the way the data is analysed. Does it pass the "snack you in the eye test" or are the results pants?

Pharma is having to deposit trial data  with the regulators so that it can be re-analysed by others requesting the info. It is a probably only a matter of time before they make people deposit raw data when they publish (people are asking about this), so the data can be re-analysed. This will be fun and games. How many other studies will fail?

Should we not do these posts and pretend it is all great?
It clearly isn't

Mapping the Brain

Glasser MF, Coalson TS, Robinson EC, Hacker CD, Harwell J, Yacoub E, Ugurbil K, Andersson J, Beckmann CF, Jenkinson M, Smith SM, Van Essen DC. A multi-modal parcellation of human cerebral cortex. Nature. 2016 Jul 20. doi: 10.1038/nature18933. [Epub ahead of print]

Understanding the amazingly complex human cerebral cortex requires a map (or parcellation) of its major subdivisions, known as cortical areas. Making an accurate areal map has been a century-old objective in neuroscience. Using multi-modal magnetic resonance images from the Human Connectome Project (HCP) and an objective semi-automated neuroanatomical approach, we delineated 180 areas per hemisphere bounded by sharp changes in cortical architecture, function, connectivity, and/or topography in a precisely aligned group average of 210 healthy young adults. We characterized 97 new areas and 83 areas previously reported using post-mortem microscopy or other specialized study-specific approaches. To enable automated delineation and identification of these areas in new HCP subjects and in future studies, we trained a machine-learning classifier to recognize the multi-modal 'fingerprint' of each cortical area. This classifier detected the presence of 96.6% of the cortical areas in new subjects, replicated the group parcellation, and could correctly locate areas in individuals with atypical parcellations. The freely available parcellation and classifier will enable substantially improved neuroanatomical precision for studies of the structural and functional organization of human cerebral cortex and its variation across individuals and in development, aging, and disease.

Think of a political map (These are designed to show governmental boundaries of countries, states, and counties, the location of major cities, and they usually include significant bodies of water. Differing colours are often used to help the user differentiate between nations). it shows us where we are but it gives us borders between counties and the countries which may give an impression how we may be different from or similar to our neighbours. This study made use of the Human Connectome project which is plotting out how the nerves are interconnected.

                       210p = parcellation group and 210v= 210 in a validation group

In this study they have down the same thing with the brain. Over 440 young adults were scanned and they have divided the cortex (outside of the brain) into 180 different counties (which have been called parcels like plots of land) in each half of the brain. Most previous parcellations were based on only one neurobiological property (such as architecture, function, connectivity or topography). In this study the finger print of each parcel was made (e.g. majority didn’t vote brexit; kilt not national costume; famous for spa water; in gods own country, so with just 4 categories = Harrogate) and in this study information included measurements of size; brain function; connectivity between regions; spacial organization of cells in brain tissue; and levels of myelin and used these to create borders. In the study this approach confirmed the existence of 83 previously reported brain areas but also found 97 new areas. This map was then tested in 210 different people and the map was found to be accurate (ordinance survey standardJ) but the size of the parcel may vary between different people. This was validated in another 210 people. However this is just the beginning as the map doesn’t yet include the biochemical underpinnings of the brain. 

Just as ProfGs tube map started with a few stations there will be more to come. By parcelling these areas it will help us to make structure to function relationships in even finer detail just as we map the hippocampus to memory and the cerebellum to movement. This may help us to delineate problems associated with MS where lesions in one area or pathway of the brain may link to different signs and symptoms.

Friday, 22 July 2016

ClinicSpeak: pregnancy the new DMT battle ground

What type of patient would choose daclizumab as a treatment for MS? #ClinicSpeak #MSBlog #MSResearch

"I am often asked if there a place for daclizumab in the treatment of MS and what profile of patients would I recommend daclizumab for. Yes, there is a place for daclizumab in the treatment of MS and the profile of patients I would recommend daclizumab for is very wide, i.e. within the EU label."

"Given daclizumab's efficacy and safety profile there is definitely a place for daclizumab in the treatment of MS in 2016. As you are aware daclizumab has a very liberal first-line label in the EU for use in 'adults with relapsing forms of MS'. This means it can be used first-, second- and even third-line. The good news is that alongside alemtuzumab, daclizumab is the second monoclonal that can be offered as a first-line treatment. Some of you will be saying '.... but so can natalizumab be offered first-line'. I agree that natalizumab can be used first-line, but only in patients with rapidly-evolving severe MS (two disabling attacks in a 12 month period with objective evidence on MRI of disease activity, i.e. new T2-lesions or Gd-enhancing lesions); this group of patients represents a relatively small group of patients." 

"I envisage well-educated patients, who want a high-efficacy monoclonal therapy first-line, choosing between daclizumab and alemtuzumab. Patients who want a treatment that has a reversible mode of action, is not associated with infusion reactions, who can't take time-off work for infusions, and don't want transient immunosuppression will possibly choose daclizumab over alemtuzumab. When it comes to second-line therapies daclizumab's attributes will differentiate it from fingolimod, natalizumab and alemtuzumab. Although patients on daclizumab require monthly blood monitoring the fact that the drug is administered subcutaneously monthly, by self-injection, will appeal to some MSers. Finally third-line, I suspect it will become the agent of choice post-natalizumab in patients who are JCV+ve. Reasons for this are that daclizumab has a rapid onset of action, which should prevent rebound disease activity, daclizumab is not immunosuppressive so if there is carry-over PML you should be able to mount a robust immune response to the virus and finally daclizumab expands the population of natural-killer cells (NK-cells) that have anti-viral properties."

"Many commentators state that the immune-mediated adverse events due to daclizumab (skin reactions and liver function abnormalities) are too risky to justify prescribing daclizumab. Too risky for whom? The neurologist prescribing the drug or the patient receiving the drug? The important thing to stress is that the immune-mediated adverse events of daclizumab, similar to those that occur post-alemtuzumab, can be detected early and managed. I don't think we should assume that because daclizumab will come bungled with a monitoring programme that patients will necessarily be put off being treated with daclizumab. As I have said many times before patient-engagement is the name of the game and I think we need to  be open and honest with our patients; if they are eligible for treatment with daclizumab we should be obliged to provide them with information about daclizumab so that they can make an informed decision. Some patients may not want to make a choice and will ask you to do it for them, but that is still engaging them in the decision-making process."

"What is becoming increasingly clear that decisions about DMTs and how to use them is not simply based on the risks and benefits of the drug, but other attributes. A very important attribute is pregnancy. The majority of people with MS are women who may be wanting to start, or extend, their families. The safety of these treatments in pregnancy and how they are used in, and around, pregnancy is becoming a new marketing battle ground. The paper below describes the latest pregnancy data on daclizumab; although the data is reassuring there is too little data to be confident of daclizumab's safety in pregnancy. The good news is  that there is no obvious teratogenic (causing foetal abnormalities) signal. If over time daclizumab is shown to be safe in pregnancy then I see it being used more widely."

INTRODUCTION: Multiple sclerosis (MS) is more common in women and can occur during childbearing years; thus, information on outcomes following exposure to MS therapy during pregnancy is important. No formal studies of daclizumab have been conducted in pregnant women. Here, we report available nonclinical and clinical data on pregnancy outcomes from the daclizumab clinical study program.

METHODS: Reproductive and developmental toxicity studies were conducted in cynomolgus monkeys. Reports of pregnancies that occurred during the daclizumab clinical study program through March 9, 2015 were collated and summarized. In the event of pregnancy, daclizumab was discontinued and safety monitoring continued.

RESULTS: Studies in cynomolgus monkeys showed no daclizumab-related effects on maternal well-being, embryo-fetal development, indirect fertility end points, and pre- and postnatal development and growth. Across the clinical study program, 38 pregnancies were reported in 36 daclizumab-exposed women (on treatment ≤6 months from last dose); 20 resulted in live births and four (11%) in spontaneous abortions or miscarriages. One congenital heart defect (complex transposition of great vessels) occurred in one live birth (considered unrelated to daclizumab); daclizumab had been discontinued and intramuscular interferon beta-1a and lisinopril were used at conception. Eight women had an elective termination, two had an ectopic pregnancy, and two were lost to follow-up; two pregnancy outcomes are pending. Six additional pregnancies occurred in five women >6 months after their last daclizumab dose; in one additional pregnancy, exposure was unknown.

CONCLUSION: Spontaneous abortion rate in daclizumab-exposed women was consistent with early pregnancy loss in the general population (12%-26%). Data on pregnancies exposed to daclizumab do not suggest an increased risk of adverse fetal or maternal outcomes, although the numbers are too small for definitive conclusions.

CoI: multiple

Thursday, 21 July 2016

Animals in MS Research

This is my talk presented at the NC3Rs meeting. 

The unpublished data have been blanked out