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‘Humanised’ worms for the discovery of new anti-epileptic drugs

Written by Lucy Job: https://www.linkedin.com/in/lucyjob/

Caenorhabditis elegans is a type of tiny soil-dwelling worm, found to accept certain human genes into their own genome [1]. These ‘humanised’ worms are a very useful tool to study human disease, with researchers at the University of Liverpool now using them to study human epilepsy and discover new anti-epileptic drugs [1] [2].

“C. elegans, model organism in life sciences” by ZEISS Microscopy

What is epilepsy?

Epilepsy is one of the most common conditions affecting the brain, shaping the lives of an estimated 50 million people worldwide [3]. In the UK alone, there are an estimated 600,000 epilepsy patients, which is almost 1 in every 100 people, with 87 people diagnosed every day [4]. There are a lot of different causes of epilepsy, and it can affect people of all ages [5].

Known causes of epilepsy, adapted from the World Health Organisation Infographics of Epilepsy [5]

Those with epilepsy suffer from recurrent seizures, which is caused by sudden bursts of electrical activity within the brain. The most well-known seizure type affects movement, causing muscle jerking, twitching, and/or weakness. Lesser known seizures affect the person’s awareness to their surroundings and can cause changes in sensation or emotion [6].

Currently, there are over 20 anti-epileptic drugs available with many different drug targets [7]. These drugs try to stop the sudden uncontrolled bursts of electrical activity within the brain. However, these anti-epileptic drugs do not work for one third of patients, named ‘refractory epilepsy’, with the reason for this not fully understood [8]. Therefore, new drugs are desperately needed for those patients with refractory epilepsy.

Why worms for drug development?

Making new drugs is controversial as testing on mammals, like mice and primates, has many ethical and financial issues. As these worms are invertebrates, less complex animals, they do not require extensive ethical training for use [9]. Also, these worms have a short reproduction time (~3 days) and lifespan (~3 weeks) and do not need expensive equipment take care of them, making them a much cheaper alternative [10]. Therefore, it is beneficial to test new drugs on less complex animals first, and then move onto more complex animals later in the drug development process. However, it is hard to justify using tiny soil-dwelling worms to test drugs for humans when we are so different [9].

Humanising the worm

To tackle this, researchers led by Professor Alan Morgan at the University of Liverpool have created humanised worms to study severe forms of epilepsy, such as Ohtahara syndrome [1]. This was achieved, in part, using the highly specialised gene editing process CRIPSR-Cas9 and which is used to insert, delete, or substitute target genes, to fix or introduce gene mutations [11].

Brief summary of CRISPR-Cas9. The Cas9 enzyme cuts the target genetic code, causing a DNA break. Once broken, a DNA repair process, leads to the desired insertion, deletions, or substitution at the target site.

GABA is a neurotransmitter (a biological chemical) which can prevent sudden electrical activity in the human brain. Studies by multiple different research teams have found GABA mutations (more specifically GABAA receptors) in patients with a spectrum of epileptic encephalopathies, such as Lennox-Gastaut syndrome and West syndrome [12].

In this project we aim to introduce mutated human GABAA receptor genes found in epilepsy patients into worms. We will then induce seizures in the worms and test a range of new anti-seizure drugs to see which compounds are most effective. Therefore, we will be able to assess the effect the new anti-seizure drugs may have in humans with the same genetic mutations.

Humanised worms used to study anti-epileptic drugs at the University of Liverpool.

Using these humanised worms as a first step in drug development is beneficial as it gives researchers the opportunity to fast-track the selection process, whittling down large numbers of drug candidates to a select few in a short space of time [2].

References

1.              Zhu, B., et al., Functional analysis of epilepsy-associated variants in STXBP1/Munc18-1 using humanized Caenorhabditis elegans. Epilepsia, 2020. 61(4): p. 810-821.

2.              Wong, S.Q., et al., A Caenorhabditis elegans assay of seizure-like activity optimised for identifying antiepileptic drugs and their mechanisms of action. J Neurosci Methods, 2018. 309: p. 132-142.

3.              Organization, W.H., Epilepsy: a public health imperative. 2019: World Health Organization,.

4.              Action, E. What is epilepsy? 2019 2019 [cited 2020 29.06.2020]; Available from: https://www.epilepsy.org.uk/info/what-is-epilepsy.

5.              Organization, W.H. Infographics on epilepsy. 2016-2017  [cited 2020 29.06.2020]; Available from: https://www.who.int/mediacentre/infographic/mental-health/epilepsy/en/.

6.              NHS. Symptoms – Epilepsy. 2017  [cited 2020 29.06.2020]; Available from: https://www.nhs.uk/conditions/epilepsy/symptoms/.

7.              Loscher, W., et al., New avenues for anti-epileptic drug discovery and development. Nat Rev Drug Discov, 2013. 12(10): p. 757-76.

8.              Kwan, P. and M.J. Brodie, Early identification of refractory epilepsy. N Engl J Med, 2000. 342(5): p. 314-9.

9.              Cunliffe, V.T., et al., Epilepsy research methods update: Understanding the causes of epileptic seizures and identifying new treatments using non-mammalian model organisms. Seizure, 2015. 24: p. 44-51.

10.            Chen, X., et al., Using C. elegans to discover therapeutic compounds for ageing-associated neurodegenerative diseases. Chem Cent J, 2015. 9: p. 65.

11.            Zhang, F., Y. Wen, and X. Guo, CRISPR/Cas9 for genome editing: progress, implications and challenges. Hum Mol Genet, 2014. 23(R1): p. R40-6.

12.            O’Reilly, L.P., et al., C. elegans in high-throughput drug discovery. Adv Drug Deliv Rev, 2014. 69-70: p. 247-53.

13.            Hernandez, C.C. and R.L. Macdonald, A structural look at GABAA receptor mutations linked to epilepsy syndromes. Brain Res, 2019. 1714: p. 234-247.

Read more Guest blogs here:

  1. The COVID-19 Vaccine Landscape
  2. Back to school. What do the students think? 49% of students say no.
  3. Natural or Nasty? Traditional Chinese Medicine and COVID-19
Blog COVID-19 Guest Blog Research Summaries

Back to school. What do the students think? 49% of students say no.

Freya is a year 12 student A-level student who has recently conducted her first research project.

“This is the first research project I have conducted, and I did it because I want to advocate for young people. I think it is important that young people have a say in the decisions which impact them. They do not vote, and it seems unfair that their thoughts and valid contributions are not taken into account by the Government. I hope that through this research project I can provide some insight into what young people are saying and so that their concerns with returning to partial schooling can be addressed.”
Written by Freya Semple

Back to school

On May 10th, 2020 the UK Government announced that Secondary Schools, Sixth Forms and Further Education Colleges could provide some face-to-face support for year 10 and year 12 students after June 1st 2020. This was subsequently deferred to start on 15th June (1). Students in these year groups have national exams in Summer 2021. This means this time in year 10 and year 12 is critical as the bulk of the curriculum is delivered.   

To reduce the spread of COVID-19 in schools on the return of students, the government has advised the  regular cleaning of frequently touched surfaces, changing classroom layouts to reduce student contact and to stagger timetables (2). However, what are the students’ views on returning to school?

It was important to me to get this question answered, so I designed a study in aim to voice the views of students.

Why is this research important?

It is not apparent that the Government has engaged with the school students affected most by this decision. Students have not been given a platform to raise their concerns about returning to education. Their views have not been heard.

This motivated me to conduct a prospective study to collate the views of young people and publicise their concerns. It is important to involve young people in decisions that affect their situation so that they engage with the policy (3). Year 10 and year 12 students are also of an age where their opinions should be taken into account.

Aims of the research project:

This study was conducted to explore the opinions of year 10s and 12s concerning returning to partial school after the first wave of the covid-19 outbreak in June 2020. The aim was to provide a voice to young people on returning to partial schooling in June 2020.

Students were invited to express:

  • Their preferences on returning to school
  • Their views about safety with respect to government guidance on return to school
  • How they feel COVID-19 will impact on their future
  • How COVID-19 has impacted on their education

This study will inform members of the public and policy makers about the opinions of year 10 and 12 students returning to school in the UK at the end of the first wave of the SARS-CoV-2 outbreak.

How the research was conducted:

The aims of this study were addressed with qualitative research using a prospective survey conducted from the 20th to 27th May 2020. Participants were year 10 (age 14 to 15 years old) and year 12 (age 16 to 17 years old) school students in the United Kingdom.

A 12-question survey was compiled on Google Forms™ with 9 close-ended questions and 3 open-ended questions. The survey was distributed to the students via two online Facebook™ forums specific to their year groups: The A level Forum (6,500 members) and a GCSE forum (36,000 members). The survey was accessible on multiple platforms (computers and smartphones) and multiple web browsers.

The 3 open ended questions were subject to Braun and Clarke themed analysis. Thematic analysis is a method for identifying and interpreting patterns of meaning across qualitative data. This meant recurring themes in the written data could be addressed and the reasons behind students’ answers could be found without influence. Braun and Clarke analysis provides a qualitative six phased method of thematic analysis. Firstly, I familiarised myself with the qualitative data and noted general ideas. NVIVO (v12) software was used to group the qualitative data into codes (similar patterns in the data). Themes were then put together by grouping the codes. I then reviewed and defined each theme in relation to the research measures.

The results:

There was a rapid uptake from students with 1534 responses in 7 days.

An infographic breaking down the key findings in "Year 10 and 12 school students' opinions on returning to partial schooling during the COVID-19 pandemic: an action research prospective survey" DOI: 10.31235/osf.io/mdjsn

Conclusions:

Year 10 and 12 school students are evenly divided in opinion about whether they should return to school on 15th June. This uncertainty appears based on the majority of students having concerns about schools’ ability to comply with government guidance, particularly around social distancing and the risk of transmission. Some students recognised a need to return to education despite this perceived risk. This uncertainty could be addressed by better engagement from policy makers with school students. School students expressed desire that their students’ concerns are addressed by the Government and better explanation of the reasoning behind returning certain students to school at this time whilst other members of the community continue to isolate.

Policy makers should standardise remote learning. This will ensure all students receive some educational support during pandemics, ensuring the educational divide caused by a lockdown is minimized.

If you would like to read the full report click here! https://osf.io/preprints/socarxiv/mdjsn/

Reference list:

1. Actions for schools during the coronavirus outbreak [Internet]. GOV.UK. 2020 [cited 2020 Jun 9]. Available from: https://www.gov.uk/government/publications/covid-19-school-closures/guidance-for-schools-about-temporarily-closing

2. Coronavirus (COVID-19): implementing protective measures in education and childcare settings [Internet]. GOV.UK. 2020 [cited 2020 Jun 9]. Available from: https://www.gov.uk/government/publications/coronavirus-covid-19-implementing-protective-measures-in-education-and-childcare-settings/coronavirus-covid-19-implementing-protective-measures-in-education-and-childcare-settings

3. Mitchell C. “The Girl Should Just Clean Up the Mess”: On Studying Audiences in Understanding the Meaningful Engagement of Young People in Policy-Making. Int J Qual Methods [Internet]. 2017 Dec 1 [cited 2020 Jun 6];16(1):1609406917703501. Available from: https://doi.org/10.1177/1609406917703501

Read our other guest blogs here:

COVID-19 Research Summaries

Report Summary: Features of 20,133 UK patients in hospital with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study

Written by Rebekah Penrice-Randal and Lucia Livoti

Features of 20,133 UK patients in hospital with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study 1 was published in The British Medical Journal (BMJ) this week. This report defines clinical characteristics of patients in hospital in the UK, using the ISARIC WHO Clinical Characterisation Protocol. We have written a brief summary to define what this means, discuss the report itself and highlight the key findings to aid public understanding.


What is ISARIC?

ISARIC is the acronym for International Severe Acute Respiratory and emerging Infections Consortium. ISARIC are a global federation of clinical research networks, with a core goal of generating evidence to improve clinical care and public health responses. They provide a “proficient, coordinated and agile research response to outbreak-prone infectious diseases”.

You can follow the study on twitter for more updates: @CCPUKstudy


What is the ISARIC WHO Clinical Characterisation Protocol?

A research protocol is the set of documents that includes the instructions for conducting a study, the participant information sheets and consent forms. A clinical research protocol has to be approved by an independent Research Ethics Committee to ensure patient safety and dignity, and in the UK, by the Health Research Authority to ensure that health care resources are used appropriately.

 The ISARIC WHO Clinical Characterisation Protocol for Severe Emerging Infection (ISARIC WHO CCP-UK) was designed in 2012 to understand the clinical characteristics  of “any severe or potentially severe acute infection of public health interest”.

In other words, the study was set up in advance of an outbreak to ask the “who, what and why” of a new disease. Who is affected means, age, sex, ethnicity and underlying medical problems. What means, what does the disease cause any of: breathing problems, diarrhoea, vomiting, sepsis or bleeding.

The ISARIC WHO CCP allows for the collecting of clinical data and biological samples, and their analysis and processing to be done in a globally-harmonised manner. This protocol has been curated by multidisciplinary experts across the world 2, and employed in response to outbreaks such as:

  • Middle Eastern Respiratory Virus Syndrome coronavirus (MERS-CoV) in 2012,
  • Influenza in 2013,
  • Ebola virus in 2014,
  • Monkeypox and MERS-CoV in 2018,
  • Tick-borne encephalitis virus (TBEV) in 2019 and
  • SARS-CoV-2 in 2020.

The ISARIC WHO CCP has been central to the swift and cohesive research response to COVID-19. As a free, readily available resource it has been instrumental in the standardised collection of samples and data for the COVID-19 outbreak. This in turn has allowed clinical investigation to progress as quickly as possible. Global generic documents can be accessed here. Countries are also encouraged to develop “localised” instructions and seek local research permissions. The documents pertaining to UK protocols are available here.


Definitions:

Cohort: a cohort of patients are a group of individuals affected by a common factor, such as a disease, treatments or environmental factors.

Cohort study: cohort studies are central to the study of epidemiology and are often used in the fields of medicine, nursing, psychology and social sciences.

Comorbidity: presence of one or more medical conditions in addition to the condition being studied.

Epidemiology: the study and analysis of factors contributing to disease and health outcomes. In this case it may refer to the frequency and pattern of COVID-19 infection, risk factors, super-spreader events and study of specific populations. 

Median: the median is defined as the ‘middle’ value of a data set, such that other values are equally likely to be above or below.

Risk factor: a factor that increases an individual’s risk or susceptibility to a disease.


Aim of the study:

  • To rapidly understand the clinical characteristics of people severely affected by COVID-19. Severely affected, meaning those who need hospital care.


Why is this work important?

This work is essential to appreciate the clinical features of patients that present with COVID-19 and identify risk factors associated with poor outcome. It is only through the understanding of such aspects that public policy can be informed, particularly around shielding of vulnerable groups and planning of resources such as oxygen and ventilator provision.   


Who took part?

20,133 hospital in-patients with COVID-19 from 208 acute care hospitals across the UK were enrolled into the study. Clinical data was collected from patients admitted to hospital between 6th February and 19th April 2020. Patient outcomes are described as known on 3rd May 2020, as people admitted on the 19th April need at least 14 days to complete their admission or “declare the nature of their illness”.


The Results


Conclusions

The ISARIC WHO CCP-UK is a large ongoing study of patients hospitalised with COVID-19. This study found that the mortality rate was high in those admitted to hospital. Certain risk factors were associated with higher mortality rate such as; increasing age, male sex, and chronic comorbidity, including obesity. This report provides the first clinical insight of hospital patients with COVID-19 in the UK. The data gathered throughout this study will assist decision-making in the management of COVID-19, from patient to nation.

This report acknowledges the 2648 frontline NHS clinical and research staff, volunteer medical students and many researchers, who have worked tirelessly to make this study happen. Thank you to all involved and congratulations from The Science Social.


A note on ‘open access’

Open access journal articles are available to everyone and are not behind a pay wall. This article is freely available to all, if you would like to read the original article click here.

References

1          Docherty, A. B. et al. Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study. BMJ 369, m1985, doi:10.1136/bmj.m1985 (2020).

2          Dunning, J. W. et al. Open source clinical science for emerging infections. The Lancet Infectious Diseases 14, 8-9, doi:10.1016/S1473-3099(13)70327-X (2014).

Thank you to Professor Calum Semple (@tweediechap), an ISARIC investigator and co-author of the original article for permission to write this blog, and for the valuable comments.

All feedback and comments are welcome, get in touch:

Blog COVID-19 Research Summaries

Coronavirus: A natural phenomenon or a man-made weapon?

Often during virus outbreaks, conspiracy theories arise which purportedly explain the emergence of the virus. These range from deliberate government release as an agent of population control to Illuminati concocted plagues designed to disrupt our way of life in order to usher in the New World Order. The Covid-19 pandemic is no exception and there has been a wave of conspiracy theories relating to SARS-COV-19, the virus behind Covid-19. Writing in NatureKristian G. AndersenAndrew Rambaut , Ian Lipkin, Edward C. Holmes  and Robert F. Garry sought to investigate the origins of SARS-COV-2, not only in order to dispel some of these theories, but also because during a pandemic it’s important to know where the virus came from as this may inform future preventative strategies. 

Read the article yourself here: https://www.nature.com/articles/s41591-020-0820-9

The authors first start by analysing the receptor binding domain (RBD) of the SARS-COV-2 spike protein. This protein is present on the outside of the SARS-COV-2 virus particle and is responsible for the binding of the virus to the receptor ACE2, which is found on the surface of cells. It’s this protein which the virus exploits to enter our cells, and it’s been shown to be very important for coronavirus host range and pathogenicity. 

Spike proteins are present on the outside of the virus particle which bind with to ACE2 receptors on the outside of our cells.

While it’s clear the SARS-COV-2 RBD is able to successfully bind the ACE2 receptor found in human, ferret and other similar species, this interaction is not exactly perfect. In fact, SARS-COV-2 binds with less efficiency than SARS. If a super plague was generated in a lab, computational studies could have been carried out to formulate better binding of ACE2, therefore improving the infectivity of the pathogen. Pretty sloppy work, Illuminati. It’s much more likely that the RBD of SARS-COV-2 evolved to bind a human-like ACE2 and has been acted upon by natural selection. What do I mean by a human-like ACE2? Remember that we share about 98.5% of our DNA with chimps and around 85% with mice, so its highly likely that SARS-COV-2 evolved to infect a similar, but different species, which provided it with some limited ability to infect humans. Once this human transmission was set up natural selection can allow the virus to adjust to humans in order to infect us more efficiently – more on that later. 

There’s also good evidence that SARS-COV-2 wasn’t generated in a lab due to the fact it doesn’t appear to have been designed according to other viral “reverse genetics” systems. Reverse genetics systems are what scientists use to produce genetically manipulated viruses in the lab. These techniques employ the use of the virus genetic material which has been probed and packaged through a variety of molecular techniques which allows infectious virus to be generated. The authors make it quite clear that SARS-COV-2 shows no evidence of being generated by the use of these existing virus reverse genetics systems. So, if SARS-COV-2 is naturally occurring, how did it infect humans in the first place and start the whole pandemic off? 

The authors provide two hypotheses:

1) The virus arose in animals and, through natural selection, acquired the necessary genetic changes needed to infect humans, whereupon it jumped the species barrier and infected people. 
 
Or 

 2) The virus jumped from an animal species into humans, whereupon it spread through the human population and, through natural selection, acquired the genetic changes needed to successfully cause a pandemic. 

By comparing the genetic material of SARS-COV-2 and other coronaviruses which have been sampled from different species, it has been shown that SARS-COV-2 shares high sequence similarity with those coronaviruses found in bats. The Huanan market in Wuhan is considered to be ground zero for this pandemic and it is known that bats were stored and sold here, in addition to a myriad of other species. It is therefore highly probable that one of these species was host to the progenitor of SARS-COV-2, which then found its way into the human population. 

Interestingly, the RBD of SARS-COV-2 is unlike those found in bats but shares high homology with those found in pangolins. Pangolins are an endangered, and very cute, little species of mammal which are the most illegally trafficked animals in the world. Coronaviruses isolated from these creatures exhibit RBDs with high similarity to those found in SARS-COV-2. Pangolins are also thought to have been present at the Huanan market in Wuhan. 

A very cute, pangolin. https://ichef.bbci.co.uk/images/ic/640×360/p066n3f4.jpg

Coronaviruses are also known to undergo genetic recombination, in which they swap genetic material. This happens when two different coronaviruses find themselves infecting the same host. It’s therefore highly likely that SARS-COV-2 arose from a recombination event between two coronaviruses, possibly from bats and pangolins, which was then able to jump into humans. 

There’s one more feature of SARS-COV-2 that the authors draw attention to: the addition of a polybasic cleavage site which sits between the two subunits of the spike protein. This site is unique to SARS-COV-2 and may result in efficient cleavage by cellular proteases such as furin. This sounds quite complicated. Simply, the virus has evolved a site in the portion of the virus which is responsible for invading our cells which improves its ability to function, therefore making it more infectious. 

We see such adaptations in avian influenza all the time – they arise through natural selection when flu spreads through chicken populations. Such adaptations result in the generation of highly pathogenic bird flu strains and are a major public health concern. Mutations of this type which affect the spike protein subunit junction have also been found in nature many times before. These inserted residues also change the structure of the spike protein slightly in a way that the authors hypothesise may help the virus evade the host immune response. 

“OK, so where did this genetic change come from? Is it possible for this to happen in the lab? Can it happen in nature?” 

Simply, both are possible, but one is less likely. Looking at our two theories it’s entirely possible that this mutation, which likely allows for increased pathogenicity, arose during repeated human to human transmission, similar to what we see in birds with flu. This would mean that, after making the jump from bats/pangolins/unknown species to human, SARS-COV-2 spread through the human populace, acquiring this mutation, and then setting off the chain of events which led to the pandemic. We see this in SARS often, in which the virus jumps from camels to humans and then spreads from human to human for a short period. Crucially SARS has not yet been able to sustain its human-human transmission, whereas SARS-COV-2 has. It’s also possible that this mutation arose in the progenitor to SARS-COV-2 in an animal host. To have arisen this would require sustained transmission between hosts that are in high density and have human-like ACE2 receptors. 

Both theories are plausible…

What isn’t as likely is that the virus gained this adaptation in a laboratory setting. In labs around the world viruses are routinely grown in cell culture. Viruses are introduced to cells in culture, allowed to grow, and eventually harvested. This is known as “passage”. For this mutation to arise in cell culture the virus must have been serially passaged through cells which contain a human-like ACE2 receptor. While these passages take place, the virus is continually evolving, so much so that serial passage in cells eventually leads to viruses getting so good at infecting cells in culture they become worse at infecting whole animals. It’s theoretically possible that the virus could have been serially passaged through an animal, one which contains sufficiently human-like ACE2, however this has never been documented. 

It is very unlikely that SARS-COV-2 originated in a laboratory setting

…and it doesn’t exhibit the genetic fingerprints we’d expect a genetically modified super plague to exhibit. Unfortunately, at the moment all we can do is theorise about its origins until the exact host, or progenitor virus, is found. There are a staggering number of viruses present in nature which we simply haven’t discovered yet (think of a tip of the iceberg kind of thing) which are currently quietly circulating in animals, and possibly humans, throughout the world. The conditions which we saw at the Huanan market in Wuhan in which various different exotic animals are stacked, live and dead, in cages in close proximity to each other, and humans, makes the perfect melting pot for these pandemics to arise. Furthermore, as humans clear more habitat, and as global temperature rise allowing vector species such as mosquitos and midges to extend into higher latitudes, it’s a matter of time until this happens again. While this pandemic is ongoing, the next one in line is lurking out there and it’s vitally important that we learn what we can from SARS-COV-2 so that we are prepared when it finally emerges. 

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Coronavirus: A natural phenomenon or a man-made weapon? Read a lay summary of @NatureMedicine article: The proximal origin of SARS-CoV-2 by @K_G_Andersen, @arambaut and @edwardcholmes and co. Written by @jordandoesflu with @thescisocial #covid19 #sarscov2 #mythbusters https://thesciencesocial694680041.wordpress.com/?p=104

Written by Dr Jordan Clark

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