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 Reports
(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 Science
(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 models (2024)
- Cancer Medicine
(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)
- Cancer Cell International
(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)
- Cancers
(A1 Refereed original research article in a scientific journal) - CD73 facilitates EMT progression and promotes lung metastases in triple-negative breast cancer (2021)
- Scientific Reports
(A1 Refereed original research article in a scientific journal) - Context Matters: NOTCH Signatures and Pathway in Cancer Progression and Metastasis (2021)
- Cells
(A2 Refereed review article in a scientific journal ) - Potent Inhibitor of Human Trypsins from the Aeruginosin Family of Natural Products (2021)
- ACS Chemical Biology
(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 Carcinomas (2021)
- Cancers
(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 metalloproteinases (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 cultures (2020)
- Cellular Oncology
(A1 Refereed original research article in a scientific journal) - Inhibition of histone methyltransferase DOT1L silences ER alpha gene and blocks proliferation of antiestrogen-resistant breast cancer cells (2019)
- Science Advances
(A1 Refereed original research article in a scientific journal) - Preparing biomedical students for the unknown Some unusual challenges for students to help them understand the fundamentals of empirical research (2019)
- EMBO Reports
(B1 Non-refereed article in a scientific journal) - Factors affecting intracellular delivery and release of hydrophilic versus hydrophobic cargo from mesoporous silica nanoparticles on 2D and 3D cell cultures (2018)
- Pharmaceutics
(A1 Refereed original research article in a scientific journal) - 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 microtissues (2017)
- Scientific Reports
(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)