Understanding the genetic basis of psoriatic disease severity using spatial transcriptomics
Work done in the lab of Prof. Shruti Naik at Dept of Pathology, NYU Grossman School of Medicine.
Ikjot Sidhu was born and raised in Chandigarh, India. He comes from a middle-class family and has been an inquisitive minded person since a young boy. He developed a keen interest in biological sciences starting from middle school age and decided to pursue a career in biological research. To this end, he pursued a BS in Bioinformatics at Panjab University. Bioinformatics is a fusion of biological sciences and computer science that is designed to help build a skill set in topics like algorithm development, machine learning and deep learning, while also gaining necessary biological knowledge including molecular biology and functional genomics.
He further pursued an MS in Bioinformatics at Boston University where he worked as a research intern and also trained as a bioinformatics analyst by working at BU Bioinformatics Hub.
After graduating in May 2019, he joined NYU Langone Health as a bioinformatics analyst, working under Dr. Shruti Naik and Dr. Aristotelis Tsirigos. He has since worked on many projects, many of which have been published in high-impact journals. His most recent work was published in Science Immunology, and is also his first ever co-first author publication.
Author Interview
How would you explain your research outcomes to the non-scientific community?
My research work involves studying human skin and skin disorders using cutting edge technologies such as spatial transcriptomics (ST) and single cell RNA sequencing. These modern technologies allow us to investigate tissues at a depth and with a resolution like never before and has allowed us to discover several underlying genetic changes that drive different diseases at a more cellular / genetic level. One of the more recent advances include ST, crowned as Method of the Year in 2020 by Nature Methods, which is what we heavily employed in our skin study. It provided us a major upgrade from single cell sequencing with an introduction of spatial context for gene expression data, and helped us further demystify immune cell neighborhoods that govern inflammation in psoriasis.
How do these findings contribute to your research area?
Psoriasis has been studied extensively over the past few years. It has been linked to many other inflammatory conditions including psoriatic arthritis, type-2 diabetes, cardiovascular disease and inflammatory bowel disease (IBD). The mechanisms of how psoriasis might increase the risk of developing other inflammatory disorders is not well understood but our study offers new clues to this as we detected an upregulation in gene activity in many molecular pathways tied to metabolism and control of lipid levels. Moreover, these changes were also detected in normal / unaffected skin samples from patients with moderate-to-severe psoriatic disease.
What was the exciting moment during your research?
I experienced many exciting moments during my research. A major part of my work involved building a computational workflow to process these ST samples, and I went through so many tweaks including optimizing quality control, statistical tests and data structure. My goal was to create a workflow that offers full reproducibility and also a resource for future projects utilizing ST technology. Reproducibility has been an important but overlooked topic in the scientific community and is now becoming increasingly critical for all papers based around computational workflows.
What do you hope to do next?
My current plan is to keep working for Dr. Naik at NYU Langone Health for the next few years. We have many exciting projects in the pipeline but no spoilers for now. My current work continues to revolve studying inflammatory disorders in the context of skin and utilizing next generation sequencing technologies.
Where do you seek scientific inspiration from?
My most inspirational person is most certainly my mentor Dr. Shruti Naik. I joined her lab in July 2019, a few months after finishing my MS degree at Boston University. Over these four years, I have learned a great deal from her. Her strong work ethics, passion for scientific research and perseverance during tough periods, has left a lasting impact on me and my own desire to become a better scientist.
How do you intend to help Indian science improve?
I am very much motivated to help spread scientific passion in India. Whenever I travel back, I always make time to visit my undergraduate college and meet up with my former professors and also interact with any current students at the college. I am very proud of the work being done by the scientific community in India.
Reference: Rochelle L. Castillo, I. Sidhu et al., Spatial transcriptomics stratifies psoriatic disease severity by emergent cellular ecosystems. Sci. Immunol. 8, eabq7991(2023). DOI:10.1126/sciimmunol.abq7991
Edited by: Anjali Mahilkar
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