Pingtao Ding is an Assistant Professor of Molecular Plant Biology at Leiden University. His research investigates how plants perceive pathogens, activate immune signalling and coordinate defence responses across cells and tissues. His group integrates molecular genetics, single-cell genomics, systems biology and computational approaches to uncover fundamental principles of plant immunity.

More information about Pingtao Ding

Brief biography

Pingtao Ding is an Assistant Professor of Molecular Plant Biology at Leiden University, where he established the Ding Lab in 2021 with support from a European Research Council (ERC) Starting Grant. Previously, he conducted research at The Sainsbury Laboratory, UK, supported by Marie Skłodowska-Curie and BBSRC Future Leader Fellowships.

His interdisciplinary research explores how biological systems perceive, integrate, communicate and remember information to coordinate adaptive responses, using plant immunity as a model. His group investigates immune signalling, cell-autonomous and non-cell-autonomous immunity, gene regulatory networks, chromatin biology, immune memory, and the evolution of defence mechanisms. By integrating molecular genetics, single-cell and spatial genomics, systems biology, machine learning and artificial intelligence, his research seeks to uncover fundamental principles of cellular decision-making and multicellular coordination.

His long-term vision is to translate these discoveries into predictive strategies for bioengineering disease-resistant crops, harnessing biodiversity and advancing sustainable agriculture. He welcomes interdisciplinary collaborations spanning fundamental biology, computational sciences, evolutionary biology and biotechnology.

Research

Decoding the Molecular, Cellular and Spatial Principles of Plant Immunity

Plants have evolved sophisticated immune systems to detect pathogens and activate defence responses. However, how immune recognition is translated into specific molecular signals, transcriptional programmes, cellular decisions and coordinated tissue-wide immunity remains poorly understood.

The Ding Lab aims to uncover the fundamental principles governing the activation, regulation and evolution of plant immunity. We integrate molecular genetics, functional genomics, single-cell and spatial technologies, structural biology, systems biology and computational approaches to investigate immune responses across molecular, cellular and tissue scales.

Our research is organised around five interconnected themes.

I. Immune receptor signalling and functional diversification

Plant intracellular immune receptors, particularly nucleotide-binding leucine-rich repeat proteins (NLRs), activate complex signalling networks that control pathogen resistance, transcriptional reprogramming and cell death. We investigate how distinct NLR signalling modules generate specific immune outputs. A particular focus is the functional diversification of helper NLR pathways, including ADR1- and NRG1-mediated signalling, and their interactions with EDS1-family proteins. By combining genetic perturbations, inducible immune activation, time-resolved transcriptomics and molecular characterisation, we aim to understand how different signalling modules encode distinct transcriptional programmes and determine immune outcomes. A central question is how closely related immune signalling components generate fundamentally different cellular responses.

II. Molecular regulation of cell death and disease resistance

Hypersensitive cell death is a prominent feature of plant effector-triggered immunity, yet its relationship with effective pathogen resistance remains incompletely understood. Our research investigates how plants coordinate defence activation, cell survival and programmed cell death, and whether these immune outputs can be independently regulated. Using genetic, transcriptomic and molecular approaches, we have identified regulatory mechanisms that genetically uncouple hypersensitive cell death from disease resistance. We are investigating how transcriptional regulators, including CBP60g and SARD1, coordinate defence-promoting and cell-death-limiting programmes. We also explore how immune-associated cell death can be mechanistically dissected and synthetically manipulated. Ultimately, we aim to understand how plants achieve robust pathogen resistance while minimising unnecessary cellular damage and growth penalties.

III. Transcriptional regulation, chromatin dynamics and gene regulatory networks

Rapid and precisely controlled transcriptional reprogramming is essential for effective plant immunity. However, how immune signals are translated into specific transcriptional responses remains a fundamental biological question. We investigate how transcription factors integrate immune-associated signals, including calcium signalling, protein phosphorylation and interactions with transcriptional co-regulators, to control gene expression. Our research particularly focuses on the regulatory functions of CBP60g, SARD1, CAMTA proteins and their associated molecular networks. We combine time-resolved transcriptomics, chromatin profiling, molecular genetics, structural and biochemical approaches, and computational modelling to identify direct regulatory targets, reconstruct gene regulatory networks and investigate their dynamic organisation. We are also developing machine-learning and AI-assisted approaches to predict regulatory interactions and uncover previously uncharacterised transcriptional regulators. Our long-term goal is to understand how immune signalling establishes transcriptional specificity and how chromatin regulatory mechanisms determine the competence of plant cells to activate defence programmes.

IV. Single-cell and spatial organisation of plant immunity

Plant immune responses are spatially heterogeneous and involve coordinated activities across diverse cell types. Yet much of our current understanding is derived from bulk tissue analyses that obscure cell-specific immune responses. We employ single-cell transcriptomics, epigenomics, proteomics, metabolomics, spatially resolved approaches, functional genetics and computational analysis to investigate the cellular organisation of plant immunity. Our research explores how different plant cell types perceive immune signals, activate distinct defence programmes and contribute to pathogen resistance. Building on our single-cell studies of effector-triggered immunity, we are particularly interested in understanding communication between pathogen-recognising cells and neighbouring bystander cells. We also investigate how immune responses propagate across tissues, how local defence responses contribute to systemic immunity, and how pathogens interfere with these processes. Our ultimate objective is to establish a mechanistic understanding of how immune responses are coordinated across space and time.

V. Evolution, systems biology and engineering of plant immunity

Plant immune systems have diversified throughout evolution, yet many of their molecular and regulatory principles are conserved across species. We investigate the evolutionary origins and functional diversification of immune signalling pathways, including metabolic and signalling components associated with systemic acquired resistance. By integrating comparative genomics, evolutionary analysis, protein structure–function studies, molecular genetics and computational modelling, we aim to uncover how immune mechanisms emerge, diversify and acquire new functions. We also explore opportunities to translate fundamental discoveries into crop protection, including the engineering of immune receptors, signalling components and defence regulatory networks. Our long-term vision is to develop a predictive and mechanistic framework for plant immunity that enables the rational design of disease-resistant crops.

Experimental approaches: Molecular genetics, functional genomics, time-resolved transcriptomics, single-cell and spatial genomics, chromatin profiling, structural biology, comparative genomics, computational modelling and machine learning.

Model systems: Arabidopsis thaliana, Nicotiana benthamiana, tomato (Solanum lycopersicum), barley (Hordeum vulgare) and other experimentally tractable plant systems.

Grants

• 2016 - 2018: Marie Skłodowska-Curie Actions (MSCA) Individual Fellowship (IF), Horizon 2020
• 2018 - 2021: Biotechnology and Biological Sciences Research Council (BBSRC) Future Leader Fellowship (FLF)
• 2022 – 2027: ERC Starting Grant
• 2023 – 2025: Horizon EU Marie Skłodowska-Curie Actions Individual Postdoctoral Fellowship
• 2025 – 2027: Horizon EU Marie Skłodowska-Curie Actions Individual Postdoctoral Fellowship
• 2027 – 2029: ERC Proof-of-concept Grant
• 2027: NWO XS Grant
• 2027 – 2029: Horizon EU Marie Skłodowska-Curie Actions Individual Postdoctoral Fellowship

Key publications

• Himanshu Chhillar, Leonardo Jo, Volkan Cevik, Amey Redkar, Kaisa Kajala, Jonathan D.G. Jones, Pingtao Ding (丁平涛). Cell-type-specific activation of broadly perceived effector-triggered immunity restricts pathogen invasion in plants. Cell Host & Microbe 34, 1843-1853.e4 (2026). https://doi.org/10.1016/j.chom.2026.07.009
• Richalynn Leong, Xin He, Bob Sebastiaan Beijen, Toshiyuki Sakai, Jorge Goncalves, Pingtao Ding. Unlocking gene regulatory networks for crop resilience and sustainable agriculture. Nature Biotechnology 43, 1254–1265 (2025). https://doi.org/10.1038/s41587-025-02727-4
• Himanshu Chhillar, Hoang Hung Nguyen, Pei-Min Yeh, Jonathan DG Jones, Pingtao Ding. Modular mechanisms of immune priming and growth inhibition mediated by plant effector-triggered immunity. Cell Reports 44 (3) (2025). https://doi.org/10.1016/j.celrep.2025.11539

Publications