The Mehta Family Centre for Engineering in Medicine

Indian Institute of Technology Kanpur

Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background
Slide background

MFCEM@IITK

The next generation of healthcare innovation lies at the interface of multiple disciplines involving engineering and medicine. The Mehta Family Centre for Engineering in Medicine at IIT Kanpur strives to act as a catalyst for biomedical researchers and engineers to work together on challenging medical problems.

MFCEM Building
Foundation Day Celebration at IITK
Inauguration of the Mehta Family Centre for Engineering in Medicine
MFCEM Inaugural Research Symposium: Session1- Molecular Medicine
MFCEM Inaugural and Research Sympoisum: Quiz Bowl
MFCEM inauguration and research symposium: Session on Regenerative Medicine
MFCEM inaugural and research symposium
MFCEM Inaugural and Research Symposium: Felicitation and Concluding session
MFCEM inauguration and research symposium: session on Digital Medicine
In conversation with First Author, Namrata Baruah

On her recent publication

Stable Recombinant Invasion Plasmid Antigen C (IpaC)-Based Single Dose Nanovaccine for Shigellosis. Baruah N, Halder P, Koley H, Katti DS. Mol Pharm. 2022.

MFCEM: Congratulations on this publication. It follows your previous study on Ipa-based nasal vaccine for Shigellosis. What was the motivation to engineer this vaccine and further improvise it?

Namrata Baruah: Thank you! This is year 2022 and hundreds of people are still dying due to shigellosis- a diarrheal disease, for which a commercial vaccine is unfortunately, not available. The situation is grim because most strains of Shigella, the bacterial pathogen, have become multi-drug resistant. There may soon be an outbreak we do not have antibiotics for. Therefore, the requirement of a vaccine is paramount.

Although there have been considerable research, a vaccine passing all the phases of clinical trials is still not available mainly because of low immunogenicity of the antigen(s) or serotype specific narrow-range protection of the vaccine candidates. Instability of immunogenic, potential vaccine antigens, exacerbates the problem. Therefore, we first stabilized a potential immunogen –IpaC, a protein found in all Shigella strains. We then assessed its vaccine potential with the available resources, and surprisingly found it to be cross-protective (heterologous protection) without any adjuvant. To further reduce dosing and increase eventual patient compliance, we encapsulated the minimum protective amount of the stabilized protein into PLGA (polymer with several FDA approved applications) nanoparticles to obtain a minimalistic single dose nanovaccine for shigellosis which is expected to protect against all Shigella strains.

MFCEM: Can you explain for the larger scientific community the technology used to develop this vaccine. How do the improvisations implemented by you push the field of vaccine development forward?

Namrata Baruah: To develop the nanovaccine, we first stabilized an immunogenic recombinant Shigella protein-IpaC (origin- Shigella dysenteriae 1, the most harmful Shigella with the most unstable IpaC) which resulted in a self-adjuvanting single-antigen nasal vaccine. Nasal immunization can provide protection at a different site such as the intestine because of the common mucosal immune system (CMIS).

 Further, compared to oral, nasal vaccines provide higher protection with lesser dose and thus, most Shigella vaccine candidates currently being explored are intranasally administered. The stabilized IpaC vaccine could protect the immunized mice against a high dose challenge of a heterologous Shigella (S. flexneri 2a, the most common type around the globe) whereas, all the unimmunized control mice died after severe diarrhea. Therefore, we obtained a cross-protective vaccine. Cross-protection against Shigella dysenteriae is difficult to achieve and there are only few reports showing minimal protection. Therefore, we chose IpaC protein of S. dysenteriae origin (most vaccine candidates currently being explored are from S. flexneri origin), as it is bound to show homologous protection. Therefore, as expected, it protected immunized mice from bloody diarrhea. However, the vaccine needed to be administered in 3 doses which meant that eventually, patients would be required to visit a hospital or care facility for 3 times at regular intervals. As the disease mainly affects the infants and the elderly, decreasing hospital visits was a priority. Therefore, we explored a single-dose nasal vaccine. As biodegradable polymeric nanoparticles are known to show a depot effect leading to slow release of the encapsulants, we chose a nanoparticle system which was expected to result in greater circulation time of the stabilized IpaC in the body and hence, equivalent immunogenicity at 1/3rd the dose. We chose the biodegradable polymer PLGA with established safety (FDA approved for multiple applications) as it is expected to shorten the entire process of lab to the market.

Since, the current vaccine candidate is a single antigen, single dose, cross-protective, facile formulation, therefore, our work should accelerate the progress towards a protective commercial Shigella vaccine.

MFCEM: Could you comment on the possibility of translating this technique for developing vaccines for human use. Do you envisage it happening in the near future?

Namrata Baruah: The minimalistic, cross-protective, single dose nanovaccine is amenable to translation at a large scale because of the following reasons-

First, being recombinant, IpaC protein purification omits pathogenic Shigella culture requiring a BSL 2 facility. Second, the stabilized IpaC protein was found to be stable at a multitude of temperatures, which would ultimately reduce the cost of storage and/or transportation of the protein. Third, the nanovaccine is minimalistic requiring only a few elements to complete the whole process after which it can be lyophilized and stored for years at room temperature. Fourth, as it is an intranasal vaccine, trained personnels for vaccine administration would not be required. Finally, due to a single dose, it is expected to increase patient compliance and overall acceptance. All of these factors can reduce cost and effort and therefore, after rigorous testing, I expect the nanovaccine to at least be part of the solution especially in low and middle income countries where the disease causes greater harm.

In conversation with First Author, Shreya Ghosh

On her recent publication

Amyloid deposition in granuloma of tuberculosis patients: A single-center pilot study. Ghosh S, Kala C, Garg A, Thakur AK. Tuberculosis (Edinb). 2022 Sep;136:102249.

MFCEM: Shreya congratulations on your publication! India, unfortunately, still contributes to a major chunk of Tuberculosis cases worldwide. Does your study on the formation Amyloid deposits in frequently occurring granulomas in TB patients, encourage the medical community to think of alternate or additional therapeutic strategies for TB?

Shreya Ghosh: Thank you so much for your appreciation. Protein misfolding is accompanied by the formation of insoluble protein-derived fibrillar deposits termed as amyloid fibrils. The linkage between tuberculosis and SAA-driven amyloid formation is well documented. However, SAA-derived amyloid onset and deposition start sites are not well understood in tuberculosis. In this study, for the first time, we have identified granuloma as the amyloid deposition site in TB patients. The findings of our study might set a stage for clinicians to diagnose the progression of amyloid formation in the early stages of tuberculosis. In addition, this work would encourage the medical community to devise therapeutic strategies to prevent the amyloid formation in TB patients. However, this study reflects preliminary findings on a limited number of samples and needs to be validated in a large number of patients to implement those therapeutic strategies.

MFCEM: Would it be right to assume that amyloid formations could be used as a marker for the progression of the disease. If yes could you elaborate?

Shreya Ghosh: Our paper does not directly deal with this aspect. However, I think that it is a realistic possibility. Previous studies identified amyloid formation in TB patients several years after its onset. We captured such amyloid formation in early-staged TB patients. Future studies should foretell if there is any correlation between the progress of amyloid formation and tuberculosis.

MFCEM: I understand that this study was a collaborative effort by IIT Kanpur and the GSVM Medical College, Kanpur. How critical was this collaboration? Also do you envisage a possibility of a clinical translation of the study in the near future?

Shreya Ghosh: This paper made us believe in Alexandar Graham Bell: “Great discoveries and improvements invariably involve the cooperation of many minds”. This work would not have been possible without collaboration. Initially, Professor Ashwani and I spent a lot of time convincing the clinicians and patients to obtain the biopsy specimens for our research. Finally, we could collaborate with GSVM Medical College, Kanpur. Dr. Chayanika Kala’s active participation helped us a lot to conduct our study successfully.
Yes, of course. I genuinely believe that identifying amyloids in the early stages of TB patients has a high potential to be clinically translated. However, a huge effort involving multi-centers is needed to accomplish it.


Systems Medicine

Lectures by Prof Shankar Subramaniam, UCSD & International Advisor, MFCEM, IIT Kanpur

Multi-omics and multi-model measurements have revolutionized our understanding of human physiology. The looming challenge, however, is converting the burgeoning data into insightful predictions and mechanistic models. The multiscale models would facilitate the "engineering" concepts of human cells, tissues and organs. This series of lectures aims to 1. Present the basic concepts of biology/physiology, 2. Delve into phenotypes, 3. Explore the underlying molecular and cellular underpinnings of working of cells, tissues and organs, and 4. Illustrate the use of omics data and its analysis.
Link- https://genome.ucsd.edu/index.php/systems-medicine-lectures/


Introduction to Neurobiology

Lectures by Prof. Nitin Gupta, Lab of Neural Systems, Indian Institute of Technology Kanpur

The lectures cover a wide range of topics in Neurobiology, starting with a historical and evolutionary perspective to Neurobiology; to introduction to the diverse neuronal cell types, sensory systems and the simple circuits that constitute neural networks. Through these lectures one is introduced to the chemical and electrical natures of synapses, and to different concepts such as capacitance, membrane potential and active conductance of neurons. The lectures also delve into different neuronal systems, such as of olfaction and of holistic visual perception.
Link- https://www.youtube.com/playlist?list=PLs6UM3rH5tQwuhURavq5o4CGtAdGYnqZ4


Human Molecular Genetics

Lectures by Prof S. Ganesh, Human Molecular Genetics Laboratory, Indian Institute of Technology Kanpur

Through these series of lectures on human molecular genetics one would gain an understanding of the fundamental principles of genetics and its applications in uncovering the genetic basis of human diseases. These lectures cover a wide range of topics, such as, 1) The Central Dogma of Molecular Biology 2) Mendelian laws 3) Pedigree Analysis 4) Chromosome structure and function 5) Genetic Engineering Techniques 6) Animal models of human diseases and 7) Human Genome and HapMap project, among others.
Link- https://www.youtube.com/watch?v=_ZIYtps-jow&&list=PLoNoar1DlEikt8SLTQ2CZue3kvE5DgRR1

Cell and Molecular Biology

Lectures by Prof Amitabha Bandyopadhyay, Indian Institute of Technology Kanpur

This lecture series on Cell and Molecular Biology provides a comprehensive introduction to various aspects of cellular processes and the molecular players orchestrating these processes. A plethora of topics namely 1) Genes, mutants, genotypes and phenotypes 2) Genetic screens, temperature sensitive mutants 3) Recombinant technologies including Mouse Gene Knockout technology 4) Translation and post-translation regulation 5) Intra-cellular trafficking and secretion of proteins, Work of Gunter Blobel - identification of SRP, SRP receptor, and 6) Protein conducting channel and work of Randy Schekman in identification of Sec mutants etc will be discussed.
Link- https://www.youtube.com/channel/UC429KQKPhYCcVfooCQ9ObrA/videos

Functional Genomics

Lectures by Prof S. Ganesh, Human Molecular Genetics Laboratory, Indian Institute of Technology Kanpur

High throughput DNA sequencing technologies have led to availability of the complete genome sequences of many organisms. Identification of functional components of the genome—be the genes, their regulatory regions or the non-coding part of the genome however remains a great challenge. The emerging field of "Functional Genomics" aims to develop and promote high throughput and large scale approaches to functionally annotate the genomes and uncover the genetic networks that regulate their functions. These lectures provide a comprehensive overview of the concept of Functional Genomics and contemporary approaches used to understand the genome function.
Link- http://www.infocobuild.com/education/audio-video-courses/biology/FunctionalGenomics-IIT-Kanpur/lecture-01.html

In conversation with

Kushagra Pandey

on his recent study:

Pandey K, Zafar H. Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET. Nucleic Acids Research, 25 may, 2022

MFCEM: Congratulations to you Kushagra, and to your advisor Prof. Hamim Zafar on your recent publication. Let me start by acknowledging that single-cell-omic studies is happening in a huge way resulting in an overload of data, having said so, what “gap” did you identify that motivated you to come up with MARGARET.

Kushagra Pandey: The main computational problem that we try to tackle in this work is that of Trajectory Inference or TI where the goal is to study how certain biological processes evolve over time. For instance, consider a fundamental biological process like cell differentiation where immature cells gradually undergo cell division to form more mature cell types which are important for performing different functions in our body. Using TI to model the landscape of cell differentiation can help us in understanding why certain types of cells give rise to some other types of cells. This type of modelling becomes even more important when dealing with scenarios which hinder the normal workflow of these biological processes (like cancer). When we first started with the problem, we found that even though TI as a computational problem is well studied, existing computational methods make certain assumptions on the type of trajectory underlying these biological processes. Now, these assumptions can hold for some biological systems but not for others. This was the primary motivation behind MARGARET: To come up with a TI method that does not make any assumptions about the underlying trajectory and can generalize to different biological processes.

MMFCEM: What was the most challenging part of developing MARGARET?

Kushagra Pandey: In the development of any computational method there are usually two stages involved in development: method design and experimental justification. Interestingly, I feel the method design was not very challenging since we had some clarity on the abstract design framework from the very beginning. However, since MARGARET is a computational tool to be used by biologists, we wanted to see if we can indeed recover correct biological insights from different biological systems which the end-users might ultimately care about. Therefore, we undertook validation case studies in this work involving well-studied biological processes like hematopoiesis (the process of blood formation) and we found that the insights we obtained by applying our method to these biological processes well conformed with the experimental findings in the existing literature. I feel this part was the most challenging during the development phase since we had to perform an extensive literature survey in each of the case studies to justify our findings. However, I have to admit it was also the most fun part since you are effectively finding out novel biological insights directly from single-cell data.

MFCEM: Could you share with us one feature of the platform that you have developed that is a game changer? Will we see the diversifying further in the near future?

Kushagra Pandey: Without going into too much method details, MARGARET kind of provides a playground for interactively visualizing single-cell datasets at the cell-level and also at the cluster-level. So any user can get started with exploring the dataset by projecting gene or transcription factor expressions on the visualized graph to get important biological insights from the dataset which I think is important. We are also planning to work on extending MARGARET to gain insights from different multi-omic views (like scRNA-seq, CITE-seq etc.) of the same biological process collectively. We believe this would improve our method when dealing with complex biological processes like cell differentiation in cancer tissues etc.

The Bhupat & Jyoti Mehta Family Foundation

MFCEM at the Indian Institute of Technology Kanpur is generously supported by the Mehta Family Foundation.

Visit Website...