Ubaid Ullah

Kalim

I am an experienced systems immunologist at the University of Turku. I studied at the University of Allahabad and Jawaharlal Nehru University and did a PhD on T cell activation and differentiation from the International Center for Genetic Engineering and Biotechnology, New Delhi in the year 2012. For my postdoctoral training, I moved to the laboratory of Professor Riitta Lahesmaa at the University of Turku, Turku, Finland.

During my postdoc, I developed unique scientific approaches using novel cutting-edge technologies to understand the role of dark matter of our genome, non-coding DNA, in regulating the immune system. The postdoc phase included the utilization and supervision of a full range of laboratory methods for cellular and molecular biology. I have gained in-depth expertise in experimental design and the interpretation of modern sequencing and epigenetics data, such as RNA-seq, scRNA-seq, ATAC-seq and CUT&Tag-seq, and have successfully applied these in T cell immunology and immunology of type 1 diabetes (T1D).

In T cell immunology, I was the first to identify HIC1 as a novel transcriptional regulator of regulatory T (Treg) cell function (Ullah et al., Cell Reports 2018). I developed completely novel and unique strategies to identify, validate and functionally characterize long noncoding RNAs in T cell differentiation. Through these methods, I identified a new gene on chromosome 6 that regulates FOXP3 expression and Treg cell differentiation (invention disclosure filed). I was a key contributor to a human-mouse comparative study of Th2 cell differentiation in collaboration with the laboratory of Professor Sarah Teichmann, Sanger Institute, UK  (Henriksson et al., Cell 2019). Recently, we determined CIP2A as a negative regulator of human Th17 differentiation (Khan et al., iScience 2020).

In immunology of T1D, I led a project to demonstrate that alteration in the transcriptional signature can be used for early prediction of T1D already before the appearance of T1D specific autoantibodies, which are current markers for T1D progression (Kallionpää et al., Diabetes 2019). We also studied the potential differences in cord blood DNA methylation of children progressing to T1D to identify if that can be used as an early biomarker for T1D progression (Laajala et al., medRxiv 2021). Besides my practical work, I have supervised six undergraduate and summer students and contributed to the training of altogether nine graduate students and postdoctoral fellows.