My Research

Click here to watch my Webinar on Organoids in Cancer therapy 

(sponsored by Thermo Fisher Scientific/Gibco) 

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Click here to watch my Webinar on modeling Infectious diseases in Organoids 

(sponsored by STEMCELL Technologies) 

 

stemcell technologies


My research interests include ~

> Translational studies using 3D adult stem cell derived organoid cultures

> Host-microbe interaction studies in 3D organoids

> Single cell RNASeq of  liver stage Malaria infection for drug discovery

> Understanding intra- tumor heterogeneity using clonal organoids

What are Organoids?

A few years ago, the Clevers lab introduced to the world a brilliant new tool “Organoids”. Organoids are 3D stem cell derived structures which mimic the in vivo architecture of tissues – structurally, functionally and genetically. Organoids can be grown from various tissues and maintained in culture for extended periods of time.

Watch how the Organoids grow :

The uniqueness of organoids stems from the fact that because they are derived from normal tissues, they are more representative of human organs. Furthermore, use of human tissue derived organoids limits the use of mouse models unless necessary.  Organoids find multiple applications in Bio-banking, drug testing, host-microbe interaction studies, toxicity studies, transplantation, personalized medicine etc.

Watch another cool video from Clevers lab on Organoids below :


1. Host-microbe interactions in Organoids

As Stem-cell-derived organoids recapitulate in vivo physiology of their original tissues, they represent valuable systems to model medical disorders such as infectious diseases and cancer. There are multiple ways in which organoids can be used for host-microbe studies. Below is a picture elaborating on the same:

1-s2.0-S0952791517300870-gr2Image 1: courtesy- Dutta and Clevers, Current Opinion in Immunology

Using small intestinal and lung organoids, in a recent study published in Nature Microbiology we showed  that apicomplexan parasite Cryptosporidium parvum can infect epithelial organoids derived from human small intestine and lung. The parasite propagates within the organoids and completes its full complex life cycle (asexual and sexual) within the organoid lumen within 120 -168 hrs.

Read the behind the scenes of the paper here !

Below is a picture showing the micro-injection procedure :

Picture2

Image 2: courtesy- Dutta,Heo and Clevers, Trends in Molecular Medicine

A picture speaks a thousand words…A video even more!

We made a video of our recent Organoid work…The parasites (in green) look so “cute”…I just couldn’t resist sharing it here too :)!


2. Single cell transcriptomics of liver stage Malaria

While the blood stage of Malaria infection has been widely studied, the liver stages remain widely unexplored primarily due to lack of good model systems. Mice models of malaria have widely been used, however the species which infect the rodents and humans are different. P. berghei infects the rodents, whereas P. falciparum and P. vivax  cause widespread human infection. Primary hepatocytes are now used for routine drug testing and modeling, however they can be maintained in culture for only about a week to 10 days. There is therefore a need for a more robust and long-term system to study Malaria infection.

The life cycle of the Malaria parasite~

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Image 3: courtesy-Malaria Vaccine InitiativeMedicines for Malaria Venture

> Malaria continues to be a global health crisis

> Causing more than 250 million new clinical cases and over 800,000 deaths annually

> Clinical pathologies are caused by the ensuing asexual erythrocytic stage of infection

> The erythrocytic stages are routinely studied in vitro in continuous culture systems that allows asexual parasite replication in human rbc (hurbc).

Using hepatocyte rich liver organoids, we are trying to understand the Transcriptomic landscape of the disease for drug discovery. Our pilot studies have confirmed that organoids are able to form the exo-erythrocytic forms (EEFs) which carry the merozoites. Merozoites released into blood then cause the disease to spread, causing various symptoms like chills and fever.

Seen below are HSP70 positive exo-erythrocytic forms (EEFs) formed in the liver organoids. Inside each EEF are thousands of merozoites which are released into blood causing full fledged Malaria infection.

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Image 4: courtesy- Sauerwein/Clever Lab, Nijmegen/Utrecht 

Using single cell transcriptomics, we aim to a) Decipher the cell type of infection in the liver b) Record the transcriptomic response of the the epithelial cells upon infection with malaria parasite c) Find novel invasion markers for the liver stage malaria parasite, which could then be used as targets for drug discovery.

Picture2Image 5:  Clustering of single cell data from infected Hepatocyte Organoids

3. Studying tumor heterogeneity using a “Triple co-culture” system 

Our understanding of cancer has progressed leaps and bounds in the recent years. From a standard chemotherapy regimen for all patients, we are moving towards a more personalized therapy approach. Recent studies have highlighted the heterogeneity in cancer tissue, not just inter -patient but also intra-patient. Using clonal organoid cultures, it was shown that the drug response of tumor clones derived from the same patient varied in their response to various drugs. It is therefore a need of the hour to understand tumor heterogeneity in further depths. While the current organoid cultures are of epithelial origin, it is important to introduce 2 other components – a) The immune cells b) The microbiome to make a “Triple culture system”. A plethora of data shows a role of the microbiota in a body’s response to immunotherapy drugs. This triple culture system using patient specific epithelial organoids, immune cells and microbiota would enable discovery of patient specific immunotherapy drugs  to target cancer.

Model for establishment of the “triple co-culture system”

Triple culture

Image 6:  The “Triple co-culture” design

My previous works:

4. Regionalization in the fruitfly midgut

During my PhD, I studied the transcriptome profiles of fruit-fly (Drosophila) intestinal cells. I standardized methods to use FACS and RNASeq to show presence of regionalization (5 distinct regions a.k.a R1-R5) in the midgut of the fly and found new stem cell markers like Snail, Smvt etc. I also found that Ptx1 transcription factor causes the acidity of R3 region in the gut. The data from my work has been developed into a database called the FlygutSeq. 

gut scheme          Image 7: courtesy- Flygutseq

 

FINAL GA             Image 8: courtesy- Dutta et al, Cell Reports

 

#science #stemcells #cells #liver #intestine #lung #nextgen #organoid #drosophila #rnaseq #devanjali #dutta #phd #clevers #HUB #Veni #research #patasite #hostmicrobe #microinjection #cancer #postdoc #traveller #artist

 

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