Dr Mirjana Efremova

MSc, PhD
Group Leader
www.efremovalab.org/ Twitter
Research Focus

We are interested in understanding the cellular and molecular mechanisms that promote cancer cell plasticity and adaptation of tumour cells in metastatic niches and under therapeutic pressure. By using dynamic analyses of the tumour microenvironment and metastatic niche in human samples and preclinical models, in conjunction with single-cell omics, imaging and computational analyses, we aim to achieve a systems-level understanding of the molecular circuits and cellular crosstalk driving metastasis and therapy resistance.

Key Publications

MultiMAP: dimensionality reduction and integration of multimodal data. Genome Biology (2021) 22(1):346. PMID: 34930412

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth. Cell Reports (2020) 31(7):107628. PMID: 32433953

CellPhoneDB: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes. Nature Protocols (2020) 15(4):1484-1506. PMID: 32103204

Single-cell reconstruction of the early maternal-fetal interface in humans. Nature (2018) 563(7731):347-353. PMID: 30429548

Major Funding
  • 2022 - Leukaemia UK, John Goldman Fellowship, “Investigating the mechanisms underlying plasticity in therapy resistance in B cell lymphomas”, £150,000
  • 2021-2024 - Chan Zuckerberg Initiative, Single-Cell Multi-omic and Spatial Cell Atlas of Pediatric Skin
  • 2020-2023 - Barts Charity, Dissecting the molecular circuits driving metastasis in melanoma
Other Activities

We employ a multidisciplinary approach that integrates computational and experimental strategies. Through collaborations with clinicians and researchers, we have access to patient samples and preclinical models, focusing on melanoma, pancreatic and colorectal cancer. By integrating single-cell multi-omics data, imaging and computational methods, our lab aims to dissect the cancer cell intrinsic traits and cell-cell communication networks that promote metastasis and therapy resistance.

The main areas of focus are:

Cancer Cell Plasticity

Cancer cells maintain an intrinsic plasticity that allows them to reversibly change their phenotype in response to microenvironmental signals and switch between cellular states. Single-cell studies have revealed extensive transcriptional heterogeneity along with lineage mixing and plasticity in several cancer types. In metastases, cells co-opt developmental programs and are reset to an even more primitive differentiation state, mimicking organ formation to reinitiate growth in a new location.

Using patient samples and multi-omics single-cell and bulk data, we are investigating the genetic vs non-genetic tumour heterogeneity and the regulatory networks underlying plasticity and invasiveness during metastasis.

Cell-cell communication

There is a growing understanding that the metastatic microenvironment is crucial in enabling the growth of disseminated cancer cells. In addition to the tumour cell intrinsic plasticity, local niche factors from stromal and immune cells influence tumour cell phenotypes and likewise, distinct cancer phenotypes shape the tumour microenvironment.

Our aim is to understand how cancer cells adapt to the metastatic niche and how in turn, immune and stromal cells support tumour cell plasticity and metastasis formation.

Therapy Resistance

Accumulating evidence implicates phenotypic plasticity as a key mechanism towards development of resistance to both targeted and immunotherapy. We aim to understand the molecular and cellular mechanisms driving phenotypic transitions in therapy resistance. By characterising the repertoire of phenotypes present both prior to and after therapy exposure, we are investigating the phenotypic states that promote resistance and their therapeutic vulnerabilities.

Our overarching goal is to identify key targets that drive metastasis formation and therapy resistance and find potential therapeutic strategies that disrupt crucial tumour-microenvironment interactions.

Visit my laboratory website here.

Other Activities
Major Funding
  • 2022 - Leukaemia UK, John Goldman Fellowship, “Investigating the mechanisms underlying plasticity in therapy resistance in B cell lymphomas”, £150,000
  • 2021-2024 - Chan Zuckerberg Initiative, Single-Cell Multi-omic and Spatial Cell Atlas of Pediatric Skin
  • 2020-2023 - Barts Charity, Dissecting the molecular circuits driving metastasis in melanoma
Recent Publications

scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection Zhang Z, Sun H, Mariappan R et al. Nature Communications (2023) 14(7)

Longitudinal Single Cell Analyses Reveal the Co-Evolutionary Dynamics of the Tumor and Microenvironment Accompanying Follicular Lymphoma Transformation Perrett M, Pickard L, Kumar E et al. Blood (2022) 140(10) 748-749

A Roadmap for the Human Oral and Craniofacial Cell Atlas Caetano AJ, Sequeira I, Byrd KM et al. Journal of Dental Research (2022) 101(7) 1274-1288

Spatially resolved poised immunity in human skin Fletcher J, Vegh P, Reynolds G et al. BRITISH JOURNAL OF DERMATOLOGY (2022) 187(11) E7-E8

MultiMAP: dimensionality reduction and integration of multimodal data Jain MS, Polanski K, Conde CD et al. Genome Biology (2021) 22(7)

Blood and immune development in human fetal bone marrow and Down syndrome Jardine L, Webb S, Goh I et al. Nature (2021) 598(7) 327-331

Mapping Rora expression in resting and activated CD4+ T cells Haim-Vilmovsky L, Henriksson J, Walker JA et al. PLoS ONE (2021) 16(7)

Developmental cell programs are co-opted in inflammatory skin disease Reynolds G, Vegh P, Fletcher J et al. Science (2021) 371(7)

Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy Prokopi A, Tripp CH, Tummers B et al. Journal for ImmunoTherapy of Cancer (2021) 9(7)

Inference of Ligand–Receptor Pairs from Single-Cell Transcriptomics Data Efremova M, Vento-Tormo R Methods in Molecular Biology (2021) 2346(1) 1-10

For additional publications, please click here
Postdoctoral Researchers PhD Students
  • Nasrine Metic
During my PhD in Computational Biology in the lab of Prof Trajanoski at the Medical University of Innsbruck, Austria, I investigated the process of clonal evolution of cancer under immunosurveillance and how the immune system shapes tumour progression. For my postdoctoral research, I joined the Teichmann Lab (Wellcome Sanger Institute) where I co-led the development of the first human atlas of the maternal-fetal interface in early pregnancy using single cell transcriptomics. I also developed a cell-cell communication statistical framework CellPhoneDB (www.cellphonedb.org) for predicting enriched receptor-ligand pairs between the different cell types and inference of cellular communication networks. This framework allowed me to dissect the complex interplay between stromal and immune cells in the dynamic tumour microenvironment of a mouse melanoma model. In May 2020 I started my own lab at Barts Cancer Institute, Queen Mary University of London (UK) within the Centre for Cancer Genomics and Computational Biology. I am part of the Programme Team for the Cancer Genomics & Data Sciences MSc Programme at BCI, Queen Mary University of London. Find out more about the programme.