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In the era of precision medicine, understanding disease at a systems level requires more than a snapshot of genetic information — it demands a dynamic and comprehensive view of how genes and environmental influences interact. Molecular phenotyping, an emerging approach that captures this interplay, is rapidly gaining traction in research and clinical diagnostics alike.
In this interview, Technology Networks spoke with Janne Lehtiö, PhD, professor of medical proteomics at the Karolinska Institutet and Platform Scientific Director of Proteomics at SciLifeLab, to explore how molecular phenotyping and omics-based technologies are reshaping our understanding of disease mechanisms.
Isabel Ely, PhD (IE):
Science Writer
Technology Networks
Isabel is a Science Writer and Editor at Technology Networks . She holds a BSc in exercise and sport science from the University of Exeter, a MRes in medicine and health and a PhD in medicine from the University of Nottingham. Her doctoral research explored the role of dietary protein and exercise in optimizing muscle health as we age.
How does molecular phenotyping contribute to a better understanding of disease mechanisms at the systems biology level?
Professor
Karolinska Institutet
Janne Lehtiö has MSc degree from Helsinki University, Finland and PhD in engineering at Royal Institute of Technology (KTH) in Stockholm, Sweden. Post the PhD, Lehtiö worked in USA based biotech industry; and obtained his postdoctoral experience in cancer research at Karolinska Institutet (KI), Stockholm, Sweden. In 2015, he was selected
to faculty Professor position at KI and since 2021 holds shared clinical professor position at Karolinska Univ. Hospital heading proteomics unit.
Lehtiö-labs major research focus in on proteome analysis, systems biology and cancer precision medicine. He’s lab is working from methods development to clinical applications mainly focusing on lung and breast cancer as well as in leukaemia research. Lehtiö has also vast experience on research infrastructures, from heading core facilities and
national infrastructure initiatives to expert assignments in the field of technology driven personalized medicine.
Between 2018-2023 Lehtiö serves, as Scientific Director for SciLifeLab, Sweden’s national bioscience infrastructure and is engaged in SciLifeLab-KAW Data Driven Life Science program as steering group member and precision medicine area-lead. He also serves in Karolinska Comprehensive Cancer Center board of directors and scientific advisory boards for national infrastructures in both Finland (Biocenter Finland) and Norway (NAPI) as well as Cancer Core Europe. Lehtiö is member of Nobel Assembly at Karolinska Institutet warding Nobel Prize in Medicine or Physiology.
Molecular phenotyping is an exciting diagnostic tool because it combines both genotype and environmental factors. This approach allows us to understand how a specific genotype behaves in various environmental contexts, such as in response to disease or treatment. Incorporating treatment-specific data provides crucial insights for selecting personalized treatment options in precision medicine diagnostics.
By combining these elements, molecular phenotyping provides a more holistic view of an individual's health status. This is particularly valuable in the realm of precision medicine, where treatments are tailored based on an individual's unique genetic makeup and environmental exposures. The data generated from molecular phenotyping can offer vital treatment-specific information, helping clinicians make more informed decisions when selecting the most appropriate and effective treatment options for each patient. As a result, it promises to enhance the accuracy of diagnostics and the personalization of treatment plans, ultimately improving patient outcomes.
Science Writer
Technology Networks
Isabel is a Science Writer and Editor at Technology Networks . She holds a BSc in exercise and sport science from the University of Exeter, a MRes in medicine and health and a PhD in medicine from the University of Nottingham. Her doctoral research explored the role of dietary protein and exercise in optimizing muscle health as we age.
What role do omics-based technologies play in linking molecular phenotypes to actionable clinical decisions?
Professor
Karolinska Institutet
Janne Lehtiö has MSc degree from Helsinki University, Finland and PhD in engineering at Royal Institute of Technology (KTH) in Stockholm, Sweden. Post the PhD, Lehtiö worked in USA based biotech industry; and obtained his postdoctoral experience in cancer research at Karolinska Institutet (KI), Stockholm, Sweden. In 2015, he was selected
to faculty Professor position at KI and since 2021 holds shared clinical professor position at Karolinska Univ. Hospital heading proteomics unit.
Lehtiö-labs major research focus in on proteome analysis, systems biology and cancer precision medicine. He’s lab is working from methods development to clinical applications mainly focusing on lung and breast cancer as well as in leukaemia research. Lehtiö has also vast experience on research infrastructures, from heading core facilities and
national infrastructure initiatives to expert assignments in the field of technology driven personalized medicine.
Between 2018-2023 Lehtiö serves, as Scientific Director for SciLifeLab, Sweden’s national bioscience infrastructure and is engaged in SciLifeLab-KAW Data Driven Life Science program as steering group member and precision medicine area-lead. He also serves in Karolinska Comprehensive Cancer Center board of directors and scientific advisory boards for national infrastructures in both Finland (Biocenter Finland) and Norway (NAPI) as well as Cancer Core Europe. Lehtiö is member of Nobel Assembly at Karolinska Institutet warding Nobel Prize in Medicine or Physiology.
I believe omics data offers a truly compelling and holistic perspective on biological systems. It's akin to observing a broad landscape and then zooming in on specific details, allowing for a much deeper understanding of the intricate interactions within the body. Traditionally, we’ve relied on selective measures, often choosing individual assays based on specific research or clinical needs. However, this approach can be limiting, as it isolates certain aspects of the system rather than considering the broader context.
Omics technologies, such as genomics, proteomics and metabolomics, allow us to capture the full complexity of biological systems comprehensively. By examining the entire 'omics landscape,' we can observe how different layers of molecular data interact and influence one another. This integrated approach offers invaluable insights that are often missed when we rely on piecemeal measurements.
The power of omics lies in its ability to guide clinical decisions with a more nuanced understanding of a patient’s condition. Instead of making decisions based on isolated data points, we can now zoom in on the most relevant factors from a wide array of information. This allows clinicians to tailor treatments more precisely, identify new biomarkers and predict disease progression with greater accuracy. In essence, omics transforms clinical decision-making, shifting it from an ad hoc approach to a more informed, data-driven strategy.
Science Writer
Technology Networks
Isabel is a Science Writer and Editor at Technology Networks . She holds a BSc in exercise and sport science from the University of Exeter, a MRes in medicine and health and a PhD in medicine from the University of Nottingham. Her doctoral research explored the role of dietary protein and exercise in optimizing muscle health as we age.
How do molecular phenotyping approaches improve the accuracy and speed of diagnosis compared to traditional methods?
Professor
Karolinska Institutet
Janne Lehtiö has MSc degree from Helsinki University, Finland and PhD in engineering at Royal Institute of Technology (KTH) in Stockholm, Sweden. Post the PhD, Lehtiö worked in USA based biotech industry; and obtained his postdoctoral experience in cancer research at Karolinska Institutet (KI), Stockholm, Sweden. In 2015, he was selected
to faculty Professor position at KI and since 2021 holds shared clinical professor position at Karolinska Univ. Hospital heading proteomics unit.
Lehtiö-labs major research focus in on proteome analysis, systems biology and cancer precision medicine. He’s lab is working from methods development to clinical applications mainly focusing on lung and breast cancer as well as in leukaemia research. Lehtiö has also vast experience on research infrastructures, from heading core facilities and
national infrastructure initiatives to expert assignments in the field of technology driven personalized medicine.
Between 2018-2023 Lehtiö serves, as Scientific Director for SciLifeLab, Sweden’s national bioscience infrastructure and is engaged in SciLifeLab-KAW Data Driven Life Science program as steering group member and precision medicine area-lead. He also serves in Karolinska Comprehensive Cancer Center board of directors and scientific advisory boards for national infrastructures in both Finland (Biocenter Finland) and Norway (NAPI) as well as Cancer Core Europe. Lehtiö is member of Nobel Assembly at Karolinska Institutet warding Nobel Prize in Medicine or Physiology.
Molecular phenotyping allows us to pinpoint the most relevant areas of interest much more efficiently. By using this approach, we can rapidly identify key biological features that may be driving disease progression or influencing treatment response. The real power comes from the ability to integrate data from multiple levels of biological information. By examining genetic, transcriptomic, proteomic and even metabolomic data, we can build a much more secure and comprehensive picture of the disease at hand.
For instance, molecular phenotyping allows us to uncover genomic aberrations, such as mutations or structural variations, that might be contributing to disease. From there, we can observe how these genetic changes impact the protein level, altering the function of key targets involved in the disease. These protein-level alterations can significantly modulate the disease process, affecting everything from cellular behavior to disease progression and treatment responses.
By combining these layers of data, we gain a more nuanced understanding of how different factors interact within the biological system. This approach not only helps us identify the underlying causes of disease with greater accuracy, but it also enables us to make more informed clinical decisions.
Science Writer
Technology Networks
Isabel is a Science Writer and Editor at Technology Networks . She holds a BSc in exercise and sport science from the University of Exeter, a MRes in medicine and health and a PhD in medicine from the University of Nottingham. Her doctoral research explored the role of dietary protein and exercise in optimizing muscle health as we age.
How do you see the future of precision medicine evolving with advancements in molecular phenotyping, and what innovations seem the most promising for bridging the gap between research and clinical application?
Professor
Karolinska Institutet
Janne Lehtiö has MSc degree from Helsinki University, Finland and PhD in engineering at Royal Institute of Technology (KTH) in Stockholm, Sweden. Post the PhD, Lehtiö worked in USA based biotech industry; and obtained his postdoctoral experience in cancer research at Karolinska Institutet (KI), Stockholm, Sweden. In 2015, he was selected
to faculty Professor position at KI and since 2021 holds shared clinical professor position at Karolinska Univ. Hospital heading proteomics unit.
Lehtiö-labs major research focus in on proteome analysis, systems biology and cancer precision medicine. He’s lab is working from methods development to clinical applications mainly focusing on lung and breast cancer as well as in leukaemia research. Lehtiö has also vast experience on research infrastructures, from heading core facilities and
national infrastructure initiatives to expert assignments in the field of technology driven personalized medicine.
Between 2018-2023 Lehtiö serves, as Scientific Director for SciLifeLab, Sweden’s national bioscience infrastructure and is engaged in SciLifeLab-KAW Data Driven Life Science program as steering group member and precision medicine area-lead. He also serves in Karolinska Comprehensive Cancer Center board of directors and scientific advisory boards for national infrastructures in both Finland (Biocenter Finland) and Norway (NAPI) as well as Cancer Core Europe. Lehtiö is member of Nobel Assembly at Karolinska Institutet warding Nobel Prize in Medicine or Physiology.
I believe we are on the cusp of making significant advancements in medicine, particularly using omics technologies and systems medicine. Currently, in cancer treatment, for example, we typically rely on a single type of omics data, primarily genomics, to guide treatment decisions. For example in cancer, this approach often leads to the addition of one targeted drug, which might improve outcomes for a short period, possibly just a few months. While this has brought some benefits, the potential for improvement is far greater.
By expanding beyond single-omics approaches and embracing multi-omics in diagnostics, we can dramatically shift the current paradigm. Multi-omics offers a much more holistic view of the disease. This approach allows us to understand not just one driver of disease at a time, but how certain disease-causing events combined in a person impact multiple proteins at the same time, enabling the design of effective individualized combination treatments. This understanding of how, for example, a mutation impacts the entire proteome system depending on that individual's genome makeup, is a key for tailoring truly curative and precise combination treatments.
With this deeper, more integrated understanding, we can select and combine multiple targeted drugs that are specifically designed to address different facets of the disease. This enables us to create personalized, multi-drug treatment combinations tailored to the unique characteristics of each patient's cancer. In doing so, we have the potential to transform a typically lethal disease like cancer into a more manageable chronic condition, much like how we treat other chronic diseases such as diabetes or hypertension. This approach might even be able to cure advanced cancers by adding tailored immunotherapy to keep the cancer at bay after first eliminating most of it by effective combination treatments.
