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Motivation and Research Objectives

Ageing has a profound impact on human society and modern medicine, yet it remains a major puzzle of biology. Our group aims to help understand the genetic, cellular, and molecular mechanisms of ageing. Although our research integrates different strategies, its focal point is developing and applying experimental and computational methods that help bridge the gap between genotype and phenotype, a major challenge of the post-genome era, and help decipher the human genome and how it regulates ageing and longevity.

In the long term, we would like our work to contribute to the development of interventions that preserve health and combat disease by manipulating the ageing process. By studying the mechanisms of ageing our work could also have an impact on diseases, like cancer and neurodegenerative diseases, for which age is a major risk factor. No other biomedical field has so much potential to improve human health as research on the basic mechanisms of ageing.

Seminar describing our research

Current Research Projects

The complexity and multi-dimensional nature of the ageing process require that this biological problem be tackled using a combination of disciplines and approaches. Below is a list of strategies and methods we employ in our work. Ultimately, however, we believe it is the integration of these different approaches that will mostly enhance our knowledge of longevity and ageing, which is why we aim to develop our research in a highly collaborative and interdisciplinary environment.

Systems Biology of Ageing

"Biologists can be divided into two classes: experimentalists who observe things that cannot be explained, and theoreticians who explain things that cannot be observed." — Aharon Katzir-Katchalsky

Protein-protein interaction network

Many genes have been shown to regulate ageing in model systems. It is now necessary, however, to study how these genes interact and how they exert their influence as an aggregate to modulate the ageing process. For that purpose, we have been developing a number of bioinformatics resources to try to understand how the parts, the genes, influence the ageing process as a whole. Specifically, we developed the GenAge database, the benchmark database of ageing-related genes in model organisms and in humans, and are now integrating GenAge with other types of data, such as gene expression profiles, protein-protein interactions (a protein-protein interaction network derived from GenAge is shown on the right), co-expression data and phenotypic data. Our goal is to enhance our understanding of gene networks and transcriptional regulation during ageing and build better models of ageing that help guide experiments, for example by identifying key network regulators of ageing. We also continue to develop algorithms that predict gene behaviour and provide testable hypotheses. Such methods could be applied to ageing but also to many other processes and diseases.

There is a lack of mathematical models of human ageing even at higher levels of abstraction. We would like to construct better mathematical representations of changes during the lifespan at the level of molecules, organelles, cells, and tissues and model how these affect each other to determine ageing and age-related diseases in whole organisms. In this context, we are developing a web portal of age-related changes at various biological levels. This portal, entitled Digital Ageing Atlas, aims to serve as a platform for modeling ageing, in particular for developing quantitative and integrative models and for developing system-level models of ageing. Moreover, we are taking advantage of single-cell sequencing to study ageing.

Dietary and Pharmacological Manipulations of Ageing

Findings from model organisms show that ageing is surprisingly plastic and can be manipulated not only by genes (as indicated above) but also by diet. The best-studied dietary manipulation of ageing is caloric restriction (CR), which consists of restricting the food intake of organisms without triggering malnutrition and has been shown to retard ageing across multiple model organisms. We are taking advantage of genomic technologies, including next-generation sequencing, to characterize the molecular changes during CR and gain mechanistic insights about ageing and its modulation by diet. Moreover, we are employing integrative and system-level approaches to study the signaling pathways and identify key genes mediating the life-extending effects of CR. Our lab established the first database of genes related to CR and then used a variety of approaches to analyse, for the first time in a systematic fashion, the gene network of CR. Understanding the underlying molecular and genetic mechanisms of CR and identifying key regulators may lead to drug discovery and development with unprecedented impact on human health. Indeed, we are also employing network pharmacology approaches to identify new caloric restriction mimetic drugs. In the long-term, we hope this line of research will open translational opportunities to develop therapies targeting age-related conditions.

Genomics of Complex Diseases

Because ageing impacts on so many diseases and genome analysis and interpretation have broad biomedical implications, we also have a great interest in the genomics of complex human diseases. By taking advantage of our expertise in genomics, bioinformatics, statistics and cell biology, we aim to help unravel the genetic and molecular mechanisms of complex human diseases. Given our group's interest in ageing, age-related diseases like cancer and neurological disorders are of particular interest. Our data-mining analyses have already revealed new candidate cancer-related genes (e.g., C1ORF112) which we are studying experimentally in vitro and in collaboration with clinicians. Moreover, we have been using machine learning methods for over 10 years, and we are very keen to apply machine learning/artificial intelligence approaches to large datasets in order to gain insights into human phenotypes and diseases.

Cellular Models of Ageing, Cancer and Cryobiology

Human embryonic stem cells

Cells are the fundamental building blocks of animals. It is clear that human ageing has a cellular component and that, for instance, some aspects of cell cycle regulation are related to the ageing process and crucial in many age-related diseases like cancer. Therefore, our work focuses considerably on cell biology and cell cycle regulation. For example, studies of cells from long-lived animals (see below) have a great potential to provide clues regarding mechanisms, such as DNA repair, cell cycle, and stress response mechanisms, that have been associated with longevity and cancer resistance. Besides, cell studies complement many of our genomic and bioinformatics approaches. In particular, our computational analyses have already revealed new candidate cancer-related genes. The unstudied C1ORF112 gene, in particular, appears to be overexpressed in various human tumours and is important for growth of cancer cell lines. Therefore, our lab is further studying this gene and its protein product in vitro and in vivo. Considering their therapeutic potential to ameliorate diseases of ageing, we are also interested in stem cells (see picture of human embryonic stem cells on the right). More recently we have been studying rejuvenation by cellular reprogramming.

Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of ageing and has been linked to ageing-related diseases. We previously developed CellAge, a new database of cell senescence human genes, and are now performing a systems biology analysis of cellular senescence. Our goal is to combine in silico and in vitro methods to identify communication and signalling pathways involved in mediating the actions of senescent cells as well as predict potential new drugs targeting senescence pathways.

Cryobiology is a crucial area of research for modern biotechnology due to the importance of biobanking, from developing reliable stem cell storage systems, organ banking for transplants as well as storage for engineered tissues. At present, cryopreservation technology is only successful for cell lines and very small tissues. More research is required before whole organs can successfully be cryopreserved while retaining their biological integrity. We are using many techniques combined with genomic methods to study cryopreservation as well as the mechanisms of cryoprotectant toxicity in human cells. Given the importance of organ transplants and the growing field of tissue engineering, perfecting cryopreservation methods would have a profound impact on medicine.

Evolutionary and Comparative Genomics

Human evolution

One of the most striking observations (and mysteries) in the field of ageing research is the variety of ageing rates among similar species such as mammals or even primates. Clearly, the genome determines the features of each species' ageing process to a large extent. Understanding why and how evolution gives rise to genomes that result in similar organisms with vastly different paces of ageing has an enormous potential to provide biologically-significant clues about the genetics of ageing. Therefore, one of the aims of our work is to develop and implement computational high-throughput approaches, such as comparative genomics, to study the evolution of complex processes such as ageing. As more organisms are sequenced, it is becoming possible to obtain detailed models of genome evolution to, for example, identify candidate human longevity genes by searching for genes with unique signatures of selection.

Because longevity evolved in the human lineage, we are particularly interested in employing modern computational methods in primates to study the evolution, structure, and function of genes associated with ageing, which may shed light on the genetic changes that contributed to the evolution of human longevity. Ultimately, our goal is to understand why we are different from each other and from other species and what is the role of each DNA base in the genome in determining these differences, in particular in the context of ageing and age-related diseases.

Biology of Long-Lived Animals

Heterocephalus glaber

Stemming from the above rationale for studying the biological underpinnings of species differences in longevity and ageing, we are interested in studying the unique genetics, physiology, and cell biology of long-lived animals. One of such animals is the naked mole-rat (Heterocephalus glaber, shown on the left), the longest-lived rodent not known to develop cancer. Furthermore, our lab has recently led the sequencing and analysis of the genome of the longest-lived mammal, the bowhead whale (Balaena mysticetus). We are also using next-generation sequencing platforms to unravel the longevity secrets of the naked mole-rat. Lastly, we are studying cells from the naked mole-rat. Because DNA damage accumulation is thought to be one of the causes of ageing and cancer, our hypothesis is that the naked mole-rat's unique mechanisms for coping with DNA damage are crucial for its longevity and healthy ageing.

Naked mole-rat photo courtesy of Pittsburgh Zoo & PPG Aquarium.

Theoretical Biology of Ageing

"Discovery consists of seeing what everybody has seen and thinking what nobody has thought." — Albert Szent-Gyørgyi

Lastly, we are interested in putting our findings and ideas together to address the big questions in gerontology and develop a coherent theoretical framework that explains ageing. One hypothesis we are particularly interested in is the idea that some developmental mechanisms shaped by evolution to optimize reproduction have an impact on ageing and age-related diseases. The free radical theory of ageing, for instance, can be interpreted in light of the roles of reactive oxygen species in development and cellular growth.

Our work on ageing is also of relevance to life history theory, which is encompasses the evolutionary theory of ageing. We are interested in refining the analytical framework that explains the relationship between growth, development, reproduction, and lifespan as well as investigating the causal basis of trade-offs between these traits. To this end and to serve as a tool for the comparative biology of ageing we developed AnAge, a database of ageing and life history in animals featuring over 4,000 species.