Matthias
Nees
Docent, Department of Biology
Senior Research Fellow, Institute of Biomedicine
PhD, Dr. rer. nat.

Contact

+358 45 606 6406
Itäinen Pitkäkatu 4
20520
Turku

Areas of expertise

Translational Oncology
Cell Culture Model Systems
Personalised Medicine
Organoids
Tumor Models

Biography

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


Teaching

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
Karolinska Institutet, Stockholm/Sweden
  • Nanotoxicology MiniSymposium, Institute for Toxicology, August 16, 2012
  • Advanced Cell Culture Training Course, Institute for Toxicology, Sept. 10- 12, 2010

Research

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.

Publications

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Increased Expression and Altered Cellular Localization of Fibroblast Growth Factor Receptor-Like 1 (FGFRL1) Are Associated with Prostate Cancer Progression (2022)

Cancers
Yu Lan, Toriseva Mervi, Afshan Syeda, Cangiano Mario, Fey Vidal, Erickson Andrew, Seikkula Heikki, Alanen Kalle, Taimen Pekka, Ettala Otto, Nurmi Martti, Boström Peter J, Kallajoki Markku, Tuomela Johanna, Mirtti Tuomas, Beumer Inès J, Nees Matthias, Härkönen Pirkko
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))

Potent Inhibitor of Human Trypsins from the Aeruginosin Family of Natural Products (2021)

ACS Chemical Biology
Ahmed Muhammad N., Wahlsten Matti, Jokela Jouni, Nees Matthias, Stenman Ulf-Håkan, Alvarenga Danillo O., Strandin Tomas, Sivonen Kaarina, Poso Antti, Permi Perttu, Metsä-Ketelä Mikko, Koistinen Hannu, Fewer David P.
(Vertaisarvioitu alkuperäisartikkeli tai data-artikkeli tieteellisessä aikakauslehdessä (A1))