Research interests and expertise
My main research interest is to understand the role of gene regulatory elements such as enhancers in human enhanceropathies. Special focus is to delineate the lineage-specificity of human cancers to understand the role of lineage-specific transcription factors controlling cellular fate, state of differentiation and their collaboration with cancer-specific oncogenic drivers in human tumorigenesis.
I am an expert in transcription factor biology and cancer epigenomics as well as state-of-the-art functional genomics methods including bulk and single-cell RNA-sequencing for gene expression programs and their trajectories, ChIP-seq and CUT&RUN for transcription factor function and epigenomics, bisulfite- and nanopore sequencing for DNA methylome, ATAC-seq/DHS-seq, HiChIP, in situ Hi-C, and ChIA-PET for chromatin structure and higher-order interactions, massively parallel reporter assays (MPRA) for measuring promoter and enhancer activity from billions of unique sequences, perturbation of cellular pathways using RNAi, lentiviral expression and CRISPR-Cas9 systems as well as cell transcription factor-mediated fate conversion/transdifferentiation approaches.
Nuclear receptors and pioneer factors in hormonal cancers especially their role in epigenome reprogramming and lineage-plasticity.
Non-coding regulatory genome and the role of transposable elements in human cancers.
Research experience
2022 - NCMBM Group Leader, Precision Cancer Epigenomics
2018 - Academy Research Fellow, Principal investigator, Research Programs Unit, Faculty of Medicine, University of Helsinki, Finland and Docent (Adjunct Professor in Molecular Genetics, University of Helsinki)
2018 – 2020: Visiting Scientist, Department of Biochemistry, University of Cambridge, United Kingdom
2013 – 2018: Post-doctoral fellow, Genome-scale Biology Program, University of Helsinki, Finland. Centre of Excellence in Cancer Genetics and Centre of Excellence in Tumor Genetics (Professor Jussi Taipale’s laboratory)
2015: Post-doctoral mobility to Professor Richard Young’s laboratory, Whitehead Institute of Biomedical Research, Cambridge, USA
2007 – 2012: Doctoral student, Faculty of Medicine, University of Helsinki, Finland
Education
2012: PhD, Biomedicine and cancer research, Faculty of Medicine, University of Helsinki, Finland
2003: MSc, Molecular Biology and Human Genetics, Banaras Hindu University, Varanasi, India
Awards and Titles
2020: Docent in Molecular Genetics, Faculty of Medicine, University of Helsinki
2018 – 2023: Research Fellowship, Academy of Finland
2018: Early-career Investigator Award, Faculty of Medicine, University of Helsinki
2014 – 2017: Postdoctoral Fellowship, Academy of Finland
Recent talks
2022: Invited speaker at the Single-cell Symposium, University of Helsinki, Finland
2022: Invited speaker at 4th Oslo Epigenetics Symposium, University of Oslo, Norway
2022: Oral presentation in Keystone Symposium for Gene Regulation: From Emerging Technologies to New Models, Santa Fe, NM, USA
2022: Oral presentation in Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor Laboratory, USA
2017: Oral presentation in Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor Laboratory, USA
Outreach
Active collaborations in delineating the role of transcription factors, enhancer malfunction and epigenome reprogramming in human physiology and several human diseases not limited to cancer.
Novel methods from my research:
– Human cell transdifferentiation–transformation approach to understand the molecular determinants of human tumorigenesis by combining cell fate conversion and oncogene expression (Sahu et al, Oncogene 2021).
– Created several novel designs for massively parallel reporter assays for measuring human gene regulatory activity at 100x sequence space of human genome and for de novo construction of human promoters and enhancers using completely random synthetic sequences (Sahu et al, Nature Genetics, 2022).