Matthias Nees
PhD, Dr. rer. nat.
Translational Oncology, Cell Culture Model Systems, Personalised Medicine, Organoids, Tumor Models
01/2015 – now: Adjunct Professor, University of Turku, Dept. Biomedicine and Anatomy; Coordinator of the High Content Screening Laboratory (HCSLab)
Physiologically relevant models for translational oncology and personalized medicine, advanced 3D cell & tissue-culture models for early stage drug discovery, functional drug target validation (siRNA, shRNA). Phenotypic & high content screening, automated image analyses, elucidation of MOA and functional validation of diagnostic biomarkers
09/2016 – 10/2018 Docent at SRH Fernhochschule „The Mobile University“: Bachelor Degree Program Pharmaceutical Management & Technologies
Preparation of teaching materials for eLearning platforms, text books, podcasts and ePubs, lectures, workshops, coaching of students – online and on-site
03/2005 – 12/2014 Group Leader and Principal Investigator, VTT Technical Research Centre of Finland OY, Turku (Teams “Systems Biology” and “Cell Culture Model Systems”)
Cell- and tissue-based model systems (3D organoid and tissue cultures) for phenotypic high content screening, automated image analysis & machine learning. Team Leader, management of interdisciplinary research groups (incl. Programmers, Biologists, Medical Students, Technicians, PostDocs, Masters’ and PhD students). Public/private partnerships PPP with industry partners, mainly funded by European Community (IMI, FP7, EuroTransBio, Marie Curie Training Networks, etc.), or Business Finland (formerly Tekes).
04/2002 – 02/2005: Staff Scientist - Molecular Medicine Partnership Unit – European Molecular Biology Laboratory EMBL & University Hospital Heidelberg
Laboratory operations and management: gene expression analyses (microarrays), personalized medicine (childhood leukaemia and sarcomas), biobanking, genetic analyses (DNA sequencing); Diagnostics
06/2000 – 03/2002 – Staff Scientist – Clinical Cooperation Unit German Cancer Research Center (DKFZ) and University Hospital Heidelberg, Germany
Translational oncology and personalized medicine: characterization of patient virus load and virus typing (HPV); primary cell- and tissue cultures, in vitro models for organotypic assays; microarray studies. Diagnostics: functional and diagnostic evaluation of biomarkers, DNA cloning and sequencing
06/1997 –05/2000: Postdoctoral Fellow – National Cancer Institute NCI, National Institutes of Health NIH – Bethesda, Maryland, USA
Personalized medicine: in vitro model systems for disease progression, based on primary patient tissues and cell cultures, immortalization of primary cells by viral vectors & oncogenes
11/1993-04/1997: PhD thesis at German Cancer Research Center (DKFZ) Heidelberg, Germany – Dept. Applied Tumour Virology/Prof. Harald zur Hausen
Translational oncology: primary cell culture models for cancer initiation and progression
08/1992 - 10/1993: Master’s Thesis at the University Hospital Heidelberg, Germany – Molecular Biology Laboratory of the Ear, Neck & Throat Clinics HNO
Translational oncology: analysis of mutations in primary patient materials, DNA sequencing
08/1990 – 07/1992 Scientific Research Assistant University Hospital Heidelberg/Germany
Drug Discovery: Coordination of contract research projects with the pharmaceutical industry, custom
research organizations (CROs), small- and medium-size enterprises SMEs, and
non-profit research institutes/universities. Early stage, preclinical drug discovery and lead development studies.
Model Systems for Cancer: Evaluation of in vitro & in vivo models (e.g. Xenografts, patient-derived PDX, genetically engineered mouse models GEMMs; tissue slices and explant cultures)
Cell- and tissue-based model systems: Complex
organotypic or 3D model systems (organoids) to recapitulate the architecture of
solid cancer tissues. Methods for microscopic imaging, automated image analysis
(“machine vision”), phenotypic- or imaging-based high content screening (HCS).
Cancer Biomarker Research: Protein/biomarker
expression in cancers using tissue
microarrays TMA, RNA- and antibody-based protein immune-fluorescence and
immune histochemistry methods on fresh & FFPE-tissues (IHC, ISH).
Clinical cooperation units with Department of Pathology and Dept. of Urology at Turku University
Hospital TYKS): Biobanking of primary,
patient-derived materials (“Turku
Prostate Cancer Consortium, TPCC”). Novel methods to isolate and
successfully propagate primary cell cultures for personalized medicine and drug
sensitivity-testing.
Bioinformatics & systems biology: Genome-wide mRNA studies (DNA Microarrays, Next Generation Sequencing,NGS, quantitative and realtime PCR,
qRT-PCR). Investigating alternative splicing, DNA
copy-number alterations and mutations (CGH & SNP arrays; Sanger & NG
Sequencing) in cancer and cancer progression.
Professor, SRH Fernhochschule – “The Mobile University” 09/(2016 – 09 /
2018: Bachelor degree program in Pharma-Management
& Technology
- Pre-clinical and clinical drug
development - Drug formulation and pharmaceutical
drug development - Quality control/quality management
and instrumental analytics, GMP - Industrial biotechnology,
biologicals/biosimilars, and fermentation technologies (Upstream- and Downstream Processing) - Organic chemistry and biochemistry; Biochemistry of Nutrition
- Molecular and cell biology
- Drug market registration (EMA and FDA)
- Drug safety and pharmacovigilance
Adjunct Professor and Docent, University of Turku/Finland; Master’s degree programme in Biomedical imaging (BIMA), Turku Bioimaging:
- “Fluorescence in Bioanalytical
Research” (ANAT5105, lecturer) 2015 - “Bioimaging and microscopy”,
ÅA_0432, lecturer) 2013, 2014, 2015
Masters’ Degree Program, University of Turku:
- “Bioinformatics in Drug Discovery”
(DRUG0007, lecturer) 2015 - “Genetics and drug discovery in
cancer research”, (FYGE3209, organizer and lecturer, 2013 -2014) - “Drug development in the
pharmaceutical industry” (FYGE3208, organizer & lecturer, 2012 -2013); - “Cancer Functional Genetics: From
Mechanisms to Drug Discovery” (organizer & lecturer, 2008-11) - “Cancer Genetics & Genomics”
(organizer & lecturer, 2005 - 2007 - FinPharma Doctoral Program Drug Discovery (FPDP-DD):
- “Epigenetic Processes as Drug
Targets in Prostate Cancer”, FinPharma Graduate School
Turku Centre for Biotechnology CBT - Turku Centre for Computer Science
(TUCS):
- Systems Biology at University of
Turku (2012 – 2015) - Computational Biology C, for
students of Bioinformatics; March 2012 - 2015 - “TERBIO Functional Genomics,
Proteomics & Bioinformatics Course”, 2006-2015
- Nanotoxicology MiniSymposium,
Institute for Toxicology, August 16, 2012 - Advanced Cell Culture Training
Course, Institute for Toxicology, Sept. 10- 12, 2010
- Loss of Sirtuin 7 impairs cell motility and proliferation and enhances S-phase cell arrest after 5-fluorouracil treatment in head and neck cancer (2025)
- Scientific ReportsCancer Cell International
(A1 Refereed original research article in a scientific journal) - Cover Image (2024)
- Cancer Medicine
(Other publication) - RUNX transcription factors are essential in maintaining epididymal epithelial differentiation (2024)
- Cellular and Molecular Life Sciences
(A1 Refereed original research article in a scientific journal) - Surface Modification of Mesoporous Silica Nanoparticles as a Means to Introduce Inherent Cancer-Targeting Ability in a 3D Tumor Microenvironment (2024)
- Small ScienceScientific Reports
(A1 Refereed original research article in a scientific journal) - Targeting the cancer cells and cancer-associated fibroblasts with next-generation FGFR inhibitors in prostate cancer co-culture modelsContext Matters: NOTCH Signatures and Pathway in Cancer Progression and Metastasis (2024)
- Cancer MedicineCells
(A1 Refereed original research article in a scientific journal) - The effect of matrices on the gene expression profile of patient-derived head and neck carcinoma cells for in vitro therapy testing (2023)
(A1 Refereed original research article in a scientific journal) - Increased Expression and Altered Cellular Localization of Fibroblast Growth Factor Receptor-Like 1 (FGFRL1) Are Associated with Prostate Cancer Progression (2022)
- CancersACS Chemical Biology
(A1 Refereed original research article in a scientific journal) - CD73 facilitates EMT progression and promotes lung metastases in triple-negative breast cancer (2021)
(A1 Refereed original research article in a scientific journal) - (2021)
(A2 Refereed review article in a scientific journal ) - Potent Inhibitor of Human Trypsins from the Aeruginosin Family of Natural Products (2021)
(A1 Refereed original research article in a scientific journal) - Shooting at Moving and Hidden Targets-Tumour Cell Plasticity and the Notch Signalling Pathway in Head and Neck Squamous Cell CarcinomasInhibition of histone methyltransferase DOT1L silences ER alpha gene and blocks proliferation of antiestrogen-resistant breast cancer cells (2021)
- CancersScience Advances
(A1 Refereed original research article in a scientific journal) - Density functional theory and molecular dynamics simulation support Ganoderma lucidum triterpenoids as broad range antagonist of matrix metalloproteinasesPreparing biomedical students for the unknown Some unusual challenges for students to help them understand the fundamentals of empirical research (2020)
- Journal of Molecular Liquids
(A1 Refereed original research article in a scientific journal) - Effects of FGFR inhibitors TKI258, BGJ398 and AZD4547 on breast cancer cells in 2D, 3D and tissue explant culturesFactors affecting intracellular delivery and release of hydrophilic versus hydrophobic cargo from mesoporous silica nanoparticles on 2D and 3D cell cultures (2020)
- Cellular Oncology
(A1 Refereed original research article in a scientific journal) - (2019)
(A1 Refereed original research article in a scientific journal) - (2019)
- EMBO Reports
(B1 Non-refereed article in a scientific journal) - (2018)
- PharmaceuticsScientific Reports
- Frizzled-8 integrates Wnt-11 and transforming growth factor-beta signaling in prostate cancer (2018)
- Nature Communications
(A1 Refereed original research article in a scientific journal) - Increased HSF1 expression predicts shorter disease-specific survival of prostate cancer patients following radical prostatectomy (2018)
- Oncotarget
(A1 Refereed original research article in a scientific journal) - A high-content image analysis approach for quantitative measurements of chemosensitivity in patient-derived tumor microtissues2017
(A1 Refereed original research article in a scientific journal) - Quantitative Phenotypic Image Analysis of Three-Dimensional Organotypic Cultures (2017) 3D Cell Culture Malin Åkerfelt, Mervi Toriseva, Matthias Nees
(A3 Refereed book chapter or chapter in a compilation book)