Research & Initiatives

Gene editing to treat hemoglobinopathies

FnCas9 based gene editing is being developed for potential treatment of Sickle cell anemia and thalassemia.

CRISPR based diagnostics

The high specificity and sensitivity of CRISPR-Cas systems make them a valuable tool for diagnostics, particularly for identifying pathogenic or disease signatures. 

FnCas9 (Cas9 isolated from Francisella novicida) has been adapted in the lab for FnCas9 Editor Linked Uniform Detection Assay (FELUDA). FELUDA output can be read through multiple signal detection platforms, and thus can be used for rapid diagnosis of both genetic as well as pathogenic signatures. The advantage of using FnCas9 is its extremely high base mismatch sensitivity under both in vitro and in vivo conditions.

FELUDA has been successfully applied for Sickle Cell Anemia diagnosis and its application for a several other monogenic diseases have been demonstrated. A web-based tool, JATAYU (Junction for Analysis and Target Design for Your FELUDA assay), has been created for design of sgRNA and primers using FELUDA.


For instrument-free visual detection, FELUDA has been adapted to be performed on lateral flow strips. FAM labelled sgRNA bound to FnCas9 (FAM labelled RNP complex) and biotinylated amplification products have been used for this assay. RNP complex (biotinylated amplicon DNA - FAM labelled sgRNA bound FnCas9) could be visualized as it gets captured by streptavidin present on the strip test line. This method  has been applied for developing a rapid, cost effective and instrument-free paper strip test for COVID-19. Currently, this technology has finished licensing, approvals and is available commercially.

 

Read more about FELUDA here:

https://www.tata.com/newsroom/covid19/covid-19-feluda-testing-digital-solutions-tata-sons

https://www.bbc.com/news/world-asia-india-54338864

https://www.cnn.com/2020/10/05/india/india-covid-19-hour-tests-approved-intl/index.html

 

Gene editing to treat hemoglobinopathies

The high prevalence of sickle cell anemia, a monogenic disease with a well characterized single point mutation in HBB gene makes India one of the worst affected countries in the world. Another factor that adds onto the gravity of this situation is the much higher prevalence of the disease in low socio-economic status communities. The current treatment approaches are restricted to use of Hydroxyurea, blood transfusions and eventually stem cell transplant. A crucial way to tackle this growing number of patients is identification of carriers and counseling of patients besides finding an effective, robust, and cheap gene editing method. In this direction, our lab is working on developing base editors and CRISPR-Cas based treatment options for SCD and other hemoglobonopathies like thalassemia. Additionally rapid diagnosis of SCA patients and carriers using FELUDA is being attempted.

3D organoids for disease modeling and dissecting developmental pathways

CRISPR-Cas has the potential to treat monogenic diseases. Multiple neurodevelopmental disorders are because of mutations that are well known but becuase the developmental trajectory gets affected it is difficult to understand the disease symptoms and their cause without ambiguity. 3D organoids, or mini brains that can be grown from patient derived iPSCs in a dish can help in modeling the disease. We use this model in the lab to study two different diseases, a polyQ disease like Spiocerebellar Ataxia Type 17 (in collaboration with Dr. Beena Pillai) and Megalencephalic Leukoencephalopathy  (MLC).  

We also use the organoid models  to understand how neurons migrate inside the brain. Neuronal migration occurs at the time of development which after attaining their position form circuits by interconnecting with each other that are the basic building blocks of any brain activity that executes behavior. If this circuitry is not formed properly then there could be malformed behaviors that can arise that are seen in diseases like Autism, Schizophrenia and Epilepsy.  Using assembloids (fused ventral and dorsal forebrain organoids), we are studying neuronal migration.