Introduction
Science and Synthetic Biology has always had a mixed reception from the public, with some viewing it as a brilliant strategy to combat real-world problems and improve human life while others are mistrustful of the threats and dangers it can pose. In order to design a good solution to any problem, one must have a good idea of what those affected by the problem and, therefore, the solution needed. It is important to have a people-centered approach and to actively seek their input at every stage of your project. It is vital to understand their perspective and how your solution should cater to their needs.
Our integrated Human Practices is a story of our journey through understanding and identifying the problem , coming up with a suitable solution , and continuously modifying our solution based on the inputs we have received, ensuring that our project can move beyond being just a laboratory concept into a real-world therapeutic.
Highlights
A summary of our main findings and how they influenced our project:
- We researched extensively about Dengue in the news, from papers, on the World Health Organisation site, and from our friends, families, academicians, and virologists. We obtained a thorough understanding of the problem in terms of the disease pathology and how it can be stopped effectively. We spoke with the local municipal bodies in India - PMC and BBMP, to obtain a case-wise distribution and breakup in terms of age, gender, areas prone. We also spoke to a Dengue virologist who routinely interacts and is actively involved in spreading awareness about dengue, Dr Maulori Curio Cabral, from Brazil to get a deeper understanding of the situation in a different country and social context than ours.
- We learned that Dengue has no true cure, and interactions with several doctors in the field made us aware that the current treatment for Dengue is aimed at symptom control which is sufficient for a primary infection. However, most primary infections are undiagnosed which could lead to a worse secondary infection masquerading as a primary infection. Therefore, our therapeutic needs to be equally effective against both primary as well as secondary infections.
- Our initial project idea involved the production of IgY-IgG hybrid antibodies to target the NS1 antigen. However, based on inputs received from several experts, as outlined below, we modified our project to now be the production of scFvs with an engineered FcRn binding peptide to increase half-life to target the E dimer Epitope.
- We sought to quantify the public awareness of Dengue through an informative survey. The point of the survey was to gauge the general knowledge about Dengue and simultaneously help spread awareness.
- Since our project involved working with the Dengue virus, which is a risk group 2 organism and our epitopes contribute toward increasing the virulence of the organism, we looked into alternatives for conducting our assay and decided on using VLPs based on the suggestion of Dr Rahul Roy.
- We also conducted a webinar in collaboration with MIT_MAHE on Biosafety and Ethics and interacted with the speaker Dr Vinod Jyothikumar, regarding the possible safety concerns our project could have and alternative production methods.
- We spoke to several people from varying socio-economic backgrounds and sought to learn how dengue has affected them and to spread awareness about vector control measures.
Please click on the different buttons to get a detailed overview of our human practices!
Follow our Journey
as we interact with and learn from our various stakeholders
Don't forget to click on each of our stakeholders to get details on how they helped us take our project forward
Academician
-
Prof Srinivas Hotha
March
CategoryPrimary PI
TAKEAWAYHelped us get started with ideation and provided constant support
-
Dr MS Madhusudhan
March
CategoryComputational and Structural Biologist
TAKEAWAYHelped us throughout our project and helped us get started on the in-silico aspects of our project.
-
Dr Juho Choi
March
CategoryIgY expert
TAKEAWAYHelped and guided us with obtaining and putting together the sequence of IgY-IgG hybrid
-
Prof Satyajit Rath
March
CategoryImmunologist
TAKEAWAYProvided thoughtful inputs on our project and guided us with shifting our project from an IgY-IgG therapeutic to a NeoFv therapeutic
-
Prof. Vineeta Bal
March
CategoryImmunologist
TAKEAWAYProvided thoughtful inputs on our project and guided us with shifting our project from an IgY-IgG therapeutic to a NeoFv therapeutic
-
Dr Nishad Matange
April
CategoryDengue, SHuffle expert
TAKEAWAYProvided suggestions on our project and helped us decide our target epitope
-
Dr Alexander I Taylor
April
CategoryIgY expert
TAKEAWAYHelped us understand the functionality and efficacy of IgY antibodies and the right mode of drug delivery
-
Prof Gavin Screaton
May
CategoryImmunologist
TAKEAWAYHelped us understand the IgY-Host interactions better and helped us reprioritise our goals
-
Dr Shashank Tripathi
June
CategoryHost-Pathogen interaction - Dengue immunology
TAKEAWAYOffered suggestions on various aspects of our project
-
Dr Thomas Howard
June
CategoryBiotechnologist and Molecular Biologist
TAKEAWAYHelped us get started on our Statistical Design of Experiments
-
Dr Mayurika Lahiri
June
CategoryAntibody Production strategies
TAKEAWAYHelped us gain a better understanding of animal model systems to produce proteins
-
Dr Varadharajan Sundaramurthy
June
CategoryHost-Pathogen interaction - Dengue immunology
TAKEAWAYSuggested that we look into conducting phagocytosis and FcRn binding assays to assess functionality of our protein
-
Dr Vidya Mangala Prasad
June
CategoryDengue Structural Expert
TAKEAWAYGave crucial information regarding DENV structural changes in the body and suggested the right epitope to target
-
Gyanaranjan (IISER Berhampur)
July
CategoryPrevious iGEM Team worked on Dengue
TAKEAWAYProvided inputs on our project and suggested the different stakeholders we could contact
-
Dr Mugdha Gadgil
July
CategoryCHO cell expert, DOE Expert
TAKEAWAYGave us a rudimentary approach to DOE
-
Prof Milind Gore
July
CategoryVirologist, Immunologist
TAKEAWAYProvided multiple advices on how we could take our project forward and provided important information regarding DENV protein assembly
-
Dr Shannon Sirk
July
CategoryscFv expert
TAKEAWAYHelped us gain a deeper understanding of scFvs + FcRn BP
-
Mr Vince Kelly
July
CategoryscFv expert
TAKEAWAYHelped us gain a deeper understanding of scFvs + FcRn BP
-
Prof Sanjeev Galande
July
CategoryWetlab organisation
TAKEAWAYProvided thoughtful criticisms and suggestions and helped us reorganise our wet lab experiments
-
Dr Sunish Kumar Radhakrishnan
July
CategoryAcademician
TAKEAWAYProvided suggestions on assays we could conduct to test protein and chassis functionality
-
Dr Gayathri Pananghat
July
CategoryAcademician
TAKEAWAYProvided suggestions on mutations we could make to improve neutralising binding
-
Dr Rahul Roy
July
CategoryDengue virologist
TAKEAWAYGave crucial insights on our project, helped us conduct our proof of concept assays and provided data on DENV serotypic distribution across India
-
Prof Raghavan Varadarajan
July
CategoryBiophysicist
TAKEAWAYProvided thoughtful criticisms and suggestions and helped us reorganise our wet lab experiments
-
Dr Sandhya Ganesan
July
CategoryHost-Pathogen interaction
TAKEAWAYHelped us realise the setbacks of our project
-
Prof Vandana Patravale
August
CategoryDrug- interaction expert
TAKEAWAYHelped us understand the different modes of drug delivery better and helped us determine the safest mode of drug delivery for our therapeutic
-
Prof Maulori Curio Cabral
August
CategoryDengue virologist
TAKEAWAYProvided insights on the vector life cycle and the different measures taken in Brazil to prevent the spread of Dengue
-
Dr Siddhesh Kamat
August
CategoryAssays for quantification
TAKAWAYSuggested and helped us perform a SYPRO orange Thermal shift assay to determine protein folding
-
Dr Ratnesh Jain
August
CategoryDrug delivery and recombinant antibody production strategies
TAKEAWAYHelped us gain insight into drug delivery and alternative models for the production of antibodies
-
Prof Nishikant Subhedar
September
CategoryDrug and pharmacology expert
TAKEAWAYHelped us understand the different modes of drug delivery better and helped us determine the safest mode of drug delivery for our therapeutic
-
Prof Arnab Mukherjee
September
CategoryComputational Biologist
TAKEAWAYHelped us gain insights into running metadynamics simulations and approach towards binding energy calculations
Society
-
Dr Madhu Bashini
March
CategoryDoctor
TAKEAWAYHelped us understand the ground reality of the problem and guided us with ordering our priorities
-
Vasti visit
July
CategoryGeneral Public
TAKEAWAYTo discuss the various problems due to the recent rains and come up with solutions
-
PMC and BBMP
August
CategoryLocal municipal bodies
TAKEAWAYTo get a case-wise distribution of dengue in recent years and the measures undertaken
-
MIT_MAHE
August
CategorySociety
TAKEAWAYHelped us conduct our human practices in multiple areas
-
Mr Santosh Kadam
August
CategorySociety
TAKEAWAYGave his input on our project and provided insight on how our project could be viewed by the public
-
Prof Maulori Curio Cabral
August
CategoryDengue virologist
TAKEAWAYProvided insights on the vector life cycle and the different measures taken in Brazil to prevent the spread of Dengue
-
Construction Workers
September
CategoryGeneral Public
TAKEAWAYTo educate and spread awareness about dengue and find out how it has affected their lives personally
-
Traffic Police
September
CategoryGeneral Public
TAKEAWAYTo educate and spread awareness about dengue and find out how it has affected their lives personally
-
Local vendors
September
CategoryGeneral Public
TAKEAWAYTo educate and spread awareness about dengue and find out how it has affected their lives personally
-
Dr Smita Jog and Dr Shobha Rao
June
CategoryDirector, Research & Training at Society for Initiatives in Nutrition & Development and President at Rotary Club, Shivaji Nagar, Pune
TAKEAWAYHelped us understand the ground reality of the problem and guided us with ordering our priorities
-
Informative Survey
August
CategorySociety
TAKEAWAYTo gauge the public awareness of Dengue
-
Dr Pooja Sancheti
July
CategoryHumanities and Social Sciences
TAKEAWAYProvided advice on how to conduct effective human practices and ethical surveying methods
-
Dr Harsha Patel
August
CategoryDoctor
TAKEAWAYHelped us better understand the real-world applications of our project better
-
Dr Prema Raghunathan
August
CategoryDoctor
TAKEAWAYHelped us better understand the real-world applications of our project better
Industrialist
-
Dr Mehmet Berkmen
March
CategoryBacterial Geniticist
TAKEAWAYHelped us gain a deeper understanding of SHuffle and helped us get started with wet lab
-
Dr Rajeev Dhere
April
CategoryVaccine expert
TAKEAWAYGained a deeper understanding of effective drug trials
-
Supriya Kashikar
May
CategoryGenext genomics founder (industrialist)
TAKEAWAYProvided a better understanding of ideal drug delivery modes
-
Dr Vikram Paradkar
June
CategoryIndustrialist on bacterial Production
TAKEAWAYHelped us prioritise the requirements of an ideal therapeutic
-
Dr Narendra Chirmule
September
CategoryImmunology and Industrial drug development
TAKEAWAYProvided insights on corporate decision-making and on how best to scale our project
-
Dr Vinod Jyothikumar
September
CategoryBiosafety and Ethics
TAKEAWAYProvided multiple suggestions on safety and ethical considerations one needs to keep in mind while designing a project
-
Dr Pradeep Nagalkar
October
CategoryVaccine Producers
TAKEAWAYLearnt more about the various strategies to produce efficient vaccines
Identifying and Understanding the Problem
When one pulls up a map of the global spread of dengue in 2020 like the one released by the CDC, it is easy to see that South Asia, along with other tropical countries, is one of the major regions to be affected by dengue. It is the most widely spread mosquito-borne disease, with an estimated 100 to 400 million cases and tens of thousands of deaths occurring every year, and the numbers are only expected to increase with climate change.
According to the World Health Organization, dengue fever is one of the top ten global health threats – it's also the most rapidly spreading. There has been a 30-fold increase in global incidence over the past 50 years.
It has been estimated that there are roughly 390 million dengue infections per year, of which 96 million have clinical or subclinical manifestations. Which means that only roughly a quarter of the total infections are symptomatic and are reported. This means that 75% of infections remain unreported or undiagnosed.
Dengue wreaks havoc in our country, India, every year. In one of our first team bonding sessions, we found out that almost half of our team has had dengue at least once, and all of us have family members who have been affected by dengue - the issue is personal to us. We had also been reading multiple reports on Dengue as the hidden epidemic during the COVID-19 pandemic, especially in Pune.
When we started looking into dengue, we found out that the disease has no cure - it is only treated symptomatically. Most times, the disease is asymptomatic, which could inadvertently lead to a worse second infection.
We sought the help of our PI Dr Srinivas Hotha, Dr Siddhesh Kamat, Dr Nishad Matange, Dr Vineeta Bal, Dr Gayathri Pananghat, who
are all acclaimed experts in various fields currently working at IISER, Pune, during this early phase of ideation through multiple
meetings trying to pinpoint the problem and coming up with a viable solution.
Our conversations led to the conclusion that the problem to be tackled here is the severe Dengue Hemorrhagic fever (DHF) that usually
results from a second infection.
DHF could result in low platelet count, internal bleeding, shock, and even death. The worst part is that DHF does not even have a
specific treatment aimed at decreasing the viral load. We were determined to come up with a solution for this.
We identified the main cause behind the heightened secondary infection to be non-neutralizing antibodies due to a heterologous primary
infection or antibodies present in sub-neutralizing concentrations acting as trojan horses with the heterologous secondary infection
(infection with a different serotype) leading to an increased viral load. Keeping with the Trojan horse analogy, the gates of Troy here
would be the Fc gamma receptors present on cell surfaces. This phenomenon is known as Antibody-Dependent Enhancement.
In order to understand the problem and the gaps in science we needed to fill, we needed to understand the ground reality first. Early on in our cycle, we spoke to Dr Madhu Bashini M, a General Physician and Diabetologist with experience in treating Dengue Fever and Viral Fever at Chettinad Hospital in Chennai, to understand the problem better from the perspective of an experienced healthcare worker. She told us most Dengue cases go undiagnosed, which could lead to a worse secondary infection disguised as a primary infection later. She told us that the current treatments in place, aimed toward treating the symptoms and not the virus, are sufficient for a primary infection and so our solution had to be equally effective for a secondary infection as well as a primary infection.
Further along in our cycle, we spoke to Dr Prema Raghunathan, who is a professor of Pediatrics at Rajrajeshwari Medical College, Bangalore and Dr Harsha Patel, who is a postgraduate student at the Bowring Hospital, Bangalore. We presented our project to them and sought inputs. Dr Raghunathan told us that from her experience, most Indians tend not to visit doctors until the last minute. Dengue almost always goes undiagnosed, and confirmed that during the first wave of the pandemic, several cases of dengue were misdiagnosed as COVID-19. Additionally, she cautioned us against using antibody therapy for a progressed Dengue infection.
Dr Patel informed us of the stark reality of Dengue patients and cases in India. He said that during an outbreak one can expect upto 80-90 cases daily and that they, and most tertiary areas, face a shortage of beds and man-power. He also taught us about the 3 main phases of Dengue and advised on which phase to administer our therapeutic. He elaborated upon why the problem of Dengue is particularly unique and dangerous in India and said that it is very rarely true that clinicians can identify the different phases of dengue, and this is crucial since the type of fluid treatment depends on the phase of the disease.
In June, we spoke to Dr Shobha Rao, who is a Director of Research & Training at Society for Initiatives in Nutrition & Development, and Dr Smita Jog, who is a President at Rotary Club, Shivaji Nagar, Pune during the blood donation camp that we co-conducted. They pointed out a crucial point that we had missed about Dengue being passed on from mothers to unborn fetuses in pregnant individuals and that such cases are rarely documented because of lack of awareness and diagnostic centres.
To further get a detailed breakdown of cases in different Indian cities to understand the scope of the problem better, we spoke with
local municipal bodies - Pune Municipal Corporation (PMC) and the Bruhut Bengaluru Mahanagara Palike (BBMP). At the PMC, we met
Shri. Sanjiv Vavare from the Health Department. He spoke of the general trend seen in Pune over the years and said that due to the
intermittent rains that cause an increase in stagnant water-filled years which in turn see a rise in the incidences of Dengue during the
months of July-October. He was of the opinion that during COVID-19, the number of cases went down since people weren’t in closed spaces
as much and added that it could also be due to Aedes primarily being a day-biter. He also made it a point to mention that the prevention
of the spread of Dengue is entirely dependent on public participation and that their main control measures were holding rallies, society
meetings for vector control, demonstrations and distributing pamphlets. At the BBMP, we met
Dr Madhusudan from the Health Department. He
gave us extensive data on the ward-wise cases of dengue in the last few years and commented on the decrease in cases seen over the last
couple of years and agreed that it might be due to the pandemic. He asked us to reach out to Hospitals to gain more insight into
case-statistics. We were unable to do so on our own, and sought the help of a team we have been working very closely with.
Our friends from the iGEM MIT_MAHE team reached out to doctors, on our behalf, from the Infectious Disease Department in
a government
medical college located in Kerala, India and spoke with Dr. Veeresh Kumar, MBBS MD, Arun Clinic, Guntakal, Anantapur, located in
Andhra
Pradesh, India managed to obtain data regarding the daily cases, hospital measures taken to treat patients, and their opinion on the
government initiatives taken. The detailed information can be found
Fig: Yearly report of the confirmed cases of Dengue in Pune city.
Fig: Percentage yearly increase in the confirmed cases of Dengue in Pune city.
Fig: Yearly report of the confirmed cases of Dengue in Bangalore city.
Fig: Percentage yearly increase in the confirmed cases of Dengue in Bangalore city.
Here is the detailed data of the age-wise and sex-wise cases, the total number of confirmed cases in Pune, and the total number of cases in Bangalore we were given by PMC and BBMP.
The ones most affected by our solution is the general public. They are the ones who are at risk of contracting Dengue and the
ones whom our therapeutic would be administered to. It is important to understand the extent of the problem from their perspective and
to fit our project in accordance with their needs.
We visited a ‘vasti’ near our campus. A vasti is a small, slum-like settlement with very poor living conditions. This particular
vasti, at the time of visit, was water-logged, had multiple swamps and extremely unhygienic toilets and contaminated water supply. We
were appalled by their circumstances, and even more so when found out that it gets much worse as the monsoon progresses. Their
surroundings were filled with mosquitoes and other insects. Our conversations with them led us to try and reach out to our institute to
come up with a solution. We also realised that the primary consumer of our therapeutic would be people from rural and
slum areas, and
therefore it was crucial for us to minimise the cost of production and make it accessible and affordable to all.
We also spoke to several workers at our institute. One among them was Santosh Kadam, who is 34 years old and has been educated only
till the 8th grade but has picked up the skills of operating the autoclave and protocols of decontamination and discard of waste
biological materials. He raised several important points during our discussion. He talked at length about the low levels of medical care
in the village, and the dependence on homemade remedies.
When we asked him about how a therapeutic for Dengue fever could be received in his community, he brought up the point of
awareness. He drew parallels with the low COVID vaccination rates in his village, and erroneous beliefs like how COVID would
vanish because of the high heat in the summer. We realised that such low levels of awareness need to be tackled from the ground-up.
As a starting point, we came up with an informative survey designed to dispense tips on dealing with Dengue, vector control
measures, knowledge on the disease pathology etc.
Further along our cycle, we spoke to local construction workers, Traffic police and local vendors. One major point that stood out in all these meetings was the lack of awareness among the local people and mistrust of the Indian medical system. They told us that most Indians, especially in rural areas, tend to never visit health clinics (if there are clinics in their villages) and instead prefer self-treatments with indigenous medicines. We hope that our efforts to spread awareness would go a long way in removing erroneous beliefs.
Determined to ensure that our stakeholders’ needs are met, we proceeded with coming up with a solution and evaluating it[1][2][3][4][5][6][7].
Coming up with a Solution
What makes a good therapeutic? - is a question that we asked ourselves and our stakeholders over the course of our project. After talking to our stakeholders, we identified the hallmarks of a good therapeutic.
An ideal therapeutic for Dengue should:
Incorporating these properties into our solution would enable it to be a viable option for the treatment of Dengue.
Over the course of our project, we’ve done our best to meet the above requirements and have constantly edited our project to fit
into our vision of an ideal therapeutic.
However, we have been constrained by the nature of our solution in certain areas like having a low cost of production. Using a bacterial
system for the production of our antibodies is probably more expensive than the traditional method of immunizing animals and extracting
antibodies from them. However, we prioritised using a safe, ethical and modular method over having a low cost of production. Even
so, our
current method of using a bacterial chassis is relatively cheaper and easier than using eukaryotic cells, as outlined in detail below.
Additionally, we have also prioritised having a therapeutic that causes minimal immunogenic response over a minimally invasive mode of
drug delivery as outlined in detail below.
When we first sat down to think of a solution, an obvious direction for us was to find a molecule that would render the virus inactive
but not bind with the Fc receptors. After a literature study, we hit upon the avian class of antibodies - IgY, which checked all
of our requirements. Being a non-mammalian antibody, it is incompatible with the mammalian Fc receptor and they could be engineered to
bind and neutralize dengue virus or any virus with multiple virulent serotypes, for that matter, as long as we had the sequence.
We faced our first roadblock with acquiring the sequence and realized that the 3D structure of IgY had not yet been publicly resolved.
With the help of Dr David Bradley and Juho Choi, IgY researchers, who sent us the sequence of the constant region, we put together
the construct of an IgY-IgG hybrid with the constant region of IgY and the variable region of IgG and even resolved a 3D image of it. As a
placeholder, our hybrid antibody was targeting the Maltose Binding Protein. We were extremely lucky to have had in-depth discussions with
Dr Alexander I Taylor, who had worked extensively with IgYs before and our secondary PI Dr Mehmet Berkmen, a bacterial geneticist from
NEB, regarding the properties of IgY. Dr Taylor advised against using an IV mode of drug delivery and warned us about the possible
immunogenic response that could result from exposing our body to avian antibodies. We also had multiple discussions with Dr
Satyajit Rath and Dr Vineeta Bal, who are both immunologists at our institution, regarding the possible immune response of our body
against
IgY and what we could do to circumvent it. While the prospect of deimmunisation by removing the T-cell epitopes on our construct
was
considered, the risk of inadvertently destabilizing the structure and thereby compromising the efficacy of our antibody was too much. Dr
Rath also told us that our IgY-IgG construct was simply a very high-tech solution to a very low-tech industry. We also learnt from
Dr Supriya Kashikar, the founder of Genext Genomics, who told us that the half-life of IgYs in the body would be low since it
cannot bind to the FcRn receptor in our body and therefore cannot be recycled. Further, Dr Gavin Screaton, an Immunologist at the
University of Oxford, advised us not to continue with IgY and instead opt for an alternative.
We wanted our drug to offer a solution to ADE, to effectively neutralise the disease, for the virus-antibody complex to be cycled out of
our body with a minimal immune reaction from our body, and for the dosage levels to be non-toxic. Since our solution did not check all of
these boxes, we decided to shift away from it. This came as a setback for us, but we were determined to have a realistic, simple, and
effective solution for ADE and a good drug. Following advice given by Dr Screaton and Dr Rath, we looked into the functionality of Fc
mutated IgGs and aglycosylated IgGs - it had all the advantages of using IgY with the added benefit of not causing an immunogenic
response. However, circling back to Dr Kashikar’s warning and our subsequent literature review[8], Fc mutated antibodies would still have
meant that its half-life in our body would be low and the cost of use high.
In a bid to improve affordability and to simplify our solution further, we landed on single chain fragment variable (scFv).
ScFvs are small and have no constant regions (and thereby no effector functions). Their size makes them cost effective and
efficient. However their half-life in the human body is quite low. To solve this problem, we decided to insert a peptide extension to
the scFv that would increase its half-life by binding to the FcRn receptor. We decided to call this structure NeoFvs. We were very
fortunate in successfully reaching out to Dr Shannon Sirk and Mr Vince Kelly, who have both worked extensively with scFvs before,
to gain their inputs on working with scFvs with the FcRn binding peptide for dengue. Mr Kelly informed us that they were unable to
generate all the variants with the binding peptide in different regions of the scFv due to time constraints and resources and asked us to
look into it. We tried to surpass this by using HADDOCK simulations. He even suggested a possible future implementation to
engineer bacteria and release them into the gut such that they produce these NeoFvs when needed. He commended us for taking forward their
initial project of using these scFvs for breast cancer into viruses, calling it a true test of modularity.
Producing the Solution
A chassis is the platform that acts as a framework and support for biological parts and components.
When we looked into the existing production methods for IgY, we found that the popular method was to extract it from purified egg yolk
by infecting chickens with the virus. We felt that this method was unethical. Moreover, it had issues with
batch standardisation and sustained production. It also generated polyclonal antibodies, which increase chances of cross-reactivity,
leading to false positives and non-specific interactions with the antigen, which could be non-neutralising.
We began looking for an alternative which ticked off our expectations for a good chassis and locked onto SHuffle. The SHuffle B strain
derived from the E. coli B strain was a fit for most of our requirements. We reached out to Dr Mehmet Berkmen, who works at New England
Biolabs (NEB) and was instrumental in the creation and development of the SHuffle strain of bacteria and was the first to produce
full-length IgG antibodies with it. What started out as a zoom meeting ended up being a lengthy and fruitful relationship with him agreeing
to be our secondary PI. He was delighted at the prospect of mentoring us and was incredibly helpful in ironing out the myriad questions we
had regarding the culturing of SHuffle, production conditions and optimization.
Dr Raghavan Varadarajan, a biophysicist from IISc, Bangalore, urged us to look into alternative production methods like standardized
CHO cell lines and yeast systems when presented with our project. Following his advice, we did a thorough literature search and found that
while CHO cells produce accurate complex proteins with high yields, they are expensive to culture and are slow growing (both points
independently reiterated by Dr Mugdha Gadgil, a CHO cell expert at NCL, Pune, they can also have unwanted post-translational
modifications like glycosylation.
Furthermore, Dr Vinod Jyothikumar, a consultant for operational risk management at DSS+, during a question and answer
session after a webinar, pointed out that CHO cell lines do not retain stable protein expression over long-term culture and have a high
cost of production. Additionally, Dr Mayurika Lahiri, from our own institute, told us that most animal house facilities don’t keep
chickens
since they are only used for producing IgY. This traditional method of using chickens is removed from research and therefore our method
of
using a modular bacterial system could help promote further research into antibodies and antibody therapeutics.
A similar search regarding yeast systems and a conversation with Dr Umesh Shaligram, director of R&D at the Serum Institute, India
(intoduced to us by the GATES Foundation, India), showed us that while it is widely used in recombinant protein production, they can
mannosylate the antibody, which could make it immunogenic. Bacteria lack the machinery for N-linked glycosylation, and cannot do the
above. Dr Ratnesh Jain, involved in recombinant protein production from ICT, also advised against using eukaryotic cell lines since
Dengue is primarily a tropical disease and requires the therapeutic to be affordable to all.
Selecting our Epitope
Dengue virus belongs to the Flaviviridae family of viruses. It has 4 serotypes that can infect humans. India and Brazil have shown incidences of all four serotypes. Choosing an appropriate epitope that is equally conserved across all four serotypes, essential to the virulence of the virus and easily accessible was crucial to overcome ADE and neutralize the virus. After discussions with Dr Nishad Matange, a bacterial geneticist at IISER Pune, we looked into NS1 as a possible candidate based on his suggestions. NS1 protein is the only non-structural protein to be released extracellularly, which makes it an easy target for antibodies. Additionally, it is hypothesized to be crucial for the replication of the virus inside the host cells.
We then considered targeting the Fusion Loop epitope, which is essential for the virus to establish contact with the host cell and enter it. It is also highly conserved across serotypes. However, the FLE is partially hidden below EDI and ED-II and is exposed for a very short time, leading ot potential issues with accessibility. Meetings with Dr Varadarajan Sundaramurthy and Dr Shashank Tripathi, both host-pathogen interaction experts from NCBS, Bangalore and IISc, Bangalore respectively, yielded the same conclusion. They advised us to look into alternative epitopes.
Our conclusion was reached in a meeting with Dr Vidya Mangala Prasad, a Dengue structural expert from IISc, Bangalore. We
presented the candidates we had in mind - NS1 protein, Fusion Loop epitope, EDI and ED-II to her and sought her inputs. She suggested
that we target the E dimer Epitope, an epitope that is rarely targeted by the natural antibodies produced by our body, lessening
competition with the therapeutic. It is also highly conserved across all four serotypes. Additionally, as EDE is present largely during
the pre-mature stage, it will prevent binding and entry of the virus into the cell. She told us that the NS1 antibodies are only produced
in greater concentrations after the viral load crosses a certain threshold and asked us to look into the C-10 class of antibodies, which
had been isolated from human dengue patients. Following her suggestions, we did a thorough review of the literature on the E dimer
Epitope and the stages of the viral cycle it existed in[9][10]. We did a sequence comparison that showed that EDE was conserved across
serotypes. We finally derived our scFv sequence from the C-10 antibody.
We looked into acquiring the E dimer epitope and considered obtaining the Envelope protein and dimerising it in the solution. However,
Dr Milind Gore, a highly-acclaimed immunologist and the former director of the National Institute of Virology (NIV), made us aware
of the fact that the Envelope protein only dimerises and folds accurately in the presence of the pRM protein. This is the reason why
vaccines that use just the E protein tend to fail to elicit neutralizing antibodies against EDE.
Due to safety concerns, we could not use the entire virus and instead chose to work with a Dengue VLP whose cassette had been deposited
by Dr Stephen Harrisson, Harvard, in Addgene. We then had several discussions with Dr Rahul Roy who is a Dengue Virologist at IISc,
Bangalore, who was strongly supportive of going with the EDE and advised us against using a cocktail of antibodies, since that could
lessen chances of neutralization. He also offered to let us borrow his Dengue VLP construct and offered his help and lab space to
work
on neutralization assays for our proof of concept. Debayani Chakraborty, from his lab, very graciously gave us her time and helped
us perform our assay[9][11].
Designing our Experiments
Once we settled on our project after integrating and evaluating our project based on all the advice we received, we proceeded with designing our model and testing it out with our experiments. Our Dry Lab and Wet Lab components are truly entwined throughout our cycle, and we received constant support, advice and guidance from several professors and PhD mentors at IISER who were always ready to troubleshoot and offer alternative solutions. We also spoke to several experts from across the world to ensure that our project design was viable.
Dry Lab
Modeling was an important part of our project. Our Dry Lab journey began with trying to find sequences for a full-length IgY. We managed
to put together the constant region of IgY with the variable region of IgG, with the help extended by Dr David Bradley, and
Juho Choi was kind enough to give us the sequence of the constant region.
During this process, we realized that a 3D structure of IgY had never been publicly resolved and so sought to determine the 3D structure
for our IgY-IgG construct. Dr M.S. Madhusudhan, an Associate Professor at IISER, Pune, working in the field of Bioinformatics and
Structure, was a great help to us. He guided us through the usage of AlphaFold for structure prediction and was key in helping us
interpret the results. With his help, we managed to obtain a predicted structure for IgY-IgG.
The majority of our dry lab falls under two domains:
MOLECULAR MODELING: This is an umbrella domain for -
- AlphaFold structure prediction
- Molecular Docking
- Molecular Dynamics
Dr Madhusudhan helped us extensively in getting started with AlphaFold and in interpreting the results. He helped us with an overview of molecular docking and suggested us to set up differential protonation of histidine residues in molecular dynamics simulations in testing out the functionality of our NeoFvs in different pH conditions.
Dr Arnab Mukherjee, who is a professor working in the fields of Chemistry, Data Science, Theoretical and computational chemistry and biophysics at IISER, Pune, helped us with the different techniques in the molecular dynamics in our screening workflow.
Statistical Design of Experiments (DOE):
We had several meetings with the inventor of SHuffle, Dr Mehmet (Memo) Berkmen, who was incredibly patient and gracious enough to go over
the nitty-gritties of working with SHuffle and helped us design our plasmid construct for producing IgY-IgG and NeoFvs.
SHuffle bacterial strain was novel to us and largely to iGEM as well, so wanted to optimize the working conditions of SHuffle to
produce complex proteins. Memo suggested that we try statistical design of experiments (DOE) to find the optimal working conditions for
SHuffle. He put us in touch with Dr Thomas Howard, an international expert in DOE and synthetic biology. Dr Howard was very
helpful in getting us started with the technique, introducing us to the philosophy of DOE and the various softwares used. He also advised
us to have a BSA calibrated SDS-PAGE as a quantitative estimate of yield of protein as a tool to measure the success of DOE.
Dr Mugdha Gadgil, an expert in CHO cells and DOE, currently working at the National Chemical Laboratory (NCL), Pune, India, met
with us multiple times and helped us in adapting our project and factors to the DOE workflow. Rushik Bhatti, a PhD student at IISER,
Pune, helped us finalise our protocols, list of experiments and factors for DOE. He advised us against using RPM as a factor and told
us to normalize the OD measurements for all our cultures.
For further details on our DryLab front, do check out our Modeling Page!
Wet Lab
Our wet lab work began in early April. Most of us were largely inexperienced with molecular biology, and our PhD mentors played an irreplaceable role, guiding us and showing us how to perform each experiment. They were constantly present and ready to help us troubleshoot. Dr Mehmet Berkmen was instrumental in getting us started and helped us chart out our early experiments. He helped us design our plasmid constructs and even went on to send us both strains of SHuffle E.coli - SHuffle B and SHuffle K-12, plasmids for cytoplasmic protein chaperones, proteins and antibodies for ELISA and the cyclonal plasmid from his own work.
Dr Rahul Roy, as previously mentioned, had offered us VLPs for a VLP fusion assay and we needed properly folded, purified proteins to complete the assay. To test the proper functionality of SHuffle with regard to protein folding, we approached several experts.
Dr Sunish Radhakrishnan, who is an Associate Professor at IISER, Pune, cautioned us against trusting an ELISA for proper protein folding since an ELISA only requires the binding sequence in the correct conformation. He suggested that we perform a maleimide-PEG assay in conjunction with ELISA to determine if the correct disulphide bonds have been formed. We were also looking for an assay to measure dissolved oxygen in our culture without using a bioreactor and he suggested that we go for the Clark electrode method.
Dr Siddhesh Kamat, an Associate Professor at IISER, Pune, suggested that we perform a Thermal shift assay with SYPRO Orange to test for proper protein folding. He suggested that we perform a Thermal shift assay with SYPRO Orange to test for proper protein folding.
After folding, we needed to determine the overall strength of binding of our antibody or its avidity and the subsequent neutralization
capacity. Dr Gayathri Pananghat, Associate Professor at IISER Pune, offered to help us out by making mutations in our antibody
that would increase its binding affinity. Dr Varadarajan Sundaramurthy, a host-pathogen interaction expert from NCBS, Bangalore,
suggested that we try phagocytosis as a method for determining the neutralization extent of our antibodies. Since one of our antibodies
had a peptide linker to increase its half-life, we were recommended an FcRn binding assay by Dr Sundaramurthy to check if our antibody
could be recycled.
Dr Sanjeev Galande, a renowned epigeneticist at SNU, Delhi, helped us out with our wet lab organization and reagents.
For further details about our wetlab plans and list of experiments we conducted, check out our Experiments Page!
Devising the Drug Delivery System
Our literature review[12] suggested three common modes of transport for antibody treatments - subcutaneous, intramuscular and intravenous. While subcutaneous, followed by intramuscular, would be best for ease of administration and compliance, the primary concerns in making this choice are that of safety and efficacy, which must be judged in preclinical and clinical trials. During our search for a viable mode of drug delivery we received inputs from several experts - Dr Supriya Kashikar told us about IgY being made into an oral prophylactic treatment for Covid-19 and advised us to do something similar, as it can easily be absorbed into the digestive tract.
Dr Harsha Patel instead advised us to go for an IV mode of treatment
since it would be easier to administer in a government hospital set-up
and would have greater accountability since the patient would have to
come to the hospital to get treated and wouldn’t be responsible for
their own treatment. This is especially important in a country like
India where the majority of those infected by Dengue would be from poor
economic backgrounds, and likely to be mistrustful and ignorant of
medicines.
Dr Vandana Patravale, a drug-delivery expert from ICT, Mumbai and Prof Nishikant Subhedar, a pharmacology expert from IISER, Pune,
on the other hand,
advised us to go for an encapsulated mode of delivery and asked us to
look into sustained release to prolong drug titre in circulation.
We intend to look into all the possible modes of drug delivery to come
up with the best possible product.
Spreading Awareness
Our conversations with the people around us who made up a major component of our stakeholders, showed that the majority of the people
were unaware about Dengue or worse had superstitions and flawed perceptions about the disease, doctors and medicine in general. In a bid
to tackle this problem, we decided to come up with an informative survey that would serve the dual purpose of understanding the
distribution of awareness about Dengue and dispense information regarding the disease, its pathology, prevention methods and current
treatment. In order to make our survey more effective, we took the help of Dr Pooja Sancheti, an Assistant Professor in the field of
Humanities and Social Sciences at IISER, Pune. She asked us to put ourselves in the shoes of our survey takers and analyse the kind
of questions they would or would not prefer to answer. She suggested that we should ask if our survey taker was from a tropical or
non-tropical country since that might affect their level of knowledge, which we incorporated into our survey.
Here is the link to our
Fig: Pie chart showing the percentage of survey takers residing in tropical and non-tropical countries.
Fig: The distribution of responses to some of our questions.
Additionally, since India consists of a rich multitude of languages, in order to make our survey more accessible, we translated it into the main regional languages of
Conclusion
Our project, as it stands now, has consolidated and evaluated all the advice, inputs and suggestions we have received from various stakeholders, our own analysis of the stakeholders’ needs and through prioritising our achievable goals, can be presented as a viable solution. We have managed to fulfill most of our requirements of a good therapeutic, of having a good chassis and a target epitope.
Our therapeutic is a possible cure for a disease with no known cure. It is aimed at being affordable and accessible to everyone, especially people from poor economic backgrounds. Additionally, through our project, we are promoting research into Neglected tropical Diseases. We have also provided a mechanism for combating Dengue and Dengue like diseases that are caused by viruses having multiple virulent serotypes. Through our modular platform, we are also promoting research into production of engineered antibodies and antibody therapies.
We have several suggestions from leading experts that we plan on incorporating into our project in the future. For more details, please check out our Future Implementations page!.
References
- Neglected tropical diseases
- Dengue and severe dengue
- Dengue facts
- Antibody dependant enhancement
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- Khatri, G., Hasan, M.M., Shaikh, S. et al. The simultaneous crises of dengue and COVID-19 in Pakistan: a double hazard for the country’s debilitated healthcare system. Trop Med Health 50, 18 (2022). DOI
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