MCMB Medicinski center za molekularno biologijo Radovan Komel

MCMB: Medicinski center za molekularno biologijo Radovan Komel Univerza v Ljubljani Inštitut za biokemijo MF

Dr. Janez Zidar Prof. dr. Dušan Sket R. K. MCMB signatory members: • • • • 1992: Medical Centre for Molecular Biology – MCMB: • Coordination of research and education in molecular biology. • Training junior researchers. • Translation of knowledge and methodology to clinical institutions. • Assistance in establishing molecular diagnostic laboratories. MF Institute of Biochemistry: prof. Katja Breskvar MF Institutute of Pathophysiology: prof. Janez Sketelj MF Institute of Pathology: prof. Dušan Ferluga MF Institute of Cell Biology: prof. Nada Pipan MF Institute of Biophysics: prof. Saša Svetina MF Institute of Microbiology and Immunology: prof. Srečko Koren MF Institute of Forensic Medicine: prof. Anton Dolenc Institute of Oncology: prof. Zvonimir Rudolf UKC Clinic of Endocrinology: prof. Andreja Kocijančič UKC Institute of Neurophysiology: dr. Janez Zidar UKC Gineacological Clinic: prof. Srečko Rainer UKC Paediatric Clinic: prof. Ciril Kržišnik UKC Psychiatric Clinic: prof. Martina Tomori The philosophy of the Centre at the very beginning was (and still is) openness for all members with the purpose of training young researchers, either by integrating them into the ongoing projects of the Centre, or by establishing joint research projects that are in the interest of partner institutions. After training in most cases, researchers return to their home institution and start their own molecular biology laboratory, but they maintain research links with the MCMB.

MCMB: pioneering work and translation to medical practice, 1990/92 – 2011 Cystic fibrosis (CF) was the first genetic disease studied by genetic analysis in our laboratory and in Slovenia (1988 – 1994 – 2000). M. Ravnik Glavač Gasparini P. et al. (1990): Mutation analysis in cystic fibrosis : to the editor. New Engl J. Med. 323(1): 62 -63. B. Peterlin K. Vouk Clinical partners: Gyneacological Clinic UKC (Prof. Srečko Rainer, M. D. ; Prof. Nina Canki Klain, M. D. ) Paediatric Clinic UKC (Prof. Milan Štrukelj, M. D. ) The second monogenic disease studied systematically for entire Slovenian population was Haemophilia A. Genetic analysis was performed from 1995 to 2000. Strmecki L. et al. (1995): Determination of informativity for the intragenic polymorphic marker Bcl I and prenatal diagnosis of hemophilia A in Slovenian population. Zdravn. Vest. 64(10): 573 -576. Clinical partners: Paediatric Clinic UKC (Dr. Majda Benedik Dolničar, M. D. ) Slovenian Haemophilia Society (Dr. Jože Faganel) Keratin disorders: palmoplantar keratoderma Unna-Thost, epidermolysis bullosa simplex (EBS): Genetic analysis was performed from 1991 to 1994. . 2000. M. Liović Tomić S. et al. (1992): Keratin 5 associated restriction fragment length polymorphism in patients with palmoplantar keratoderma of unna-thost type. Acta Dermatovenerol. A. P. A. 1(4): 114 -118. Clinical partner: Clinic for Dermatovenerology in Ljubljana (Prof. Aleksej Kansky, M. D. ; Dr. Božena Podrumac, M. D. ; Dr. Vlasta Dragoš, M. D. ).

MCMB: pioneering work and translation to medical practice, 1990/92 – 2011 Ach. E gene expression in skeletal muscle: 1993 – 1995. . 2005 Grubič Z. , Komel R. (1993): Synthesis of the DNA probe for the determination of rat ACh. E m. RNA. Chemico -biological Interactions 87(1 -3): 245 -248. Faculty partner: Institute of Patophysiology, Faculty of Medicine, University of Ljubljana (Prof. Zoran Grubič, M. D. ). B cell lymphoma / synovial sarcoma: 1996 – 1998. Start of molecular genetic analysis in Slovenian oncology. Koković I. et al. (1996): Detection of immunoglobulin gene rearrangement of B cell lymphoma in formalinfixed, paraffin-embedded tissues by polymerase chain reaction. Molecular Oncology Today, 1996, pp. 155157. Clinical partner: Institute of Oncology, Department of Pathology (Prof. Rastko Golouh, M. D. ; Dr. Janez Jančar, M. D. ). Polycystic ovary syndrome – female hyperandrogenism: Genetic analysis was performed from 1996 to 1998. . . 2001. M. Liović M. et al. : (1997): CYP 17 gene analysis in hyperandrogenised women with and without exaggerated 17 -hydroxyprogesterone response to ovarian stimulation. J. Endocrinol. Invest. 20(4): 189 -193. I. Eminović G. Majdič Clinical partner: Clinic for Endocrinology and Metabolic Diseases UKC (Prof. Andreja Kocijančič, M. D. ; Prof. Janez Preželj, M. D. )

MCMB: pioneering work and translation to medical practice, 1990/92 – 2011 Genotyping forensic medicine – DNA profiling: 1995 – 2004. In 2003 -2005 DNA profiling was introduced at the Insitute of Forensic Medicine, and was in 2005 also officially accepted as a legal procedure for personal and relatedness identification and as procedure providing legal DNA evidences for criminal trials. I. Zupanič-Pajnič I. et al. (1998): Analysis of nine short tandem repeat (STR) loci in the Slovenian population. Int. J. Legal Medicine 111(5): 248 -250. Faculty/clinical partner: Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana (Prof. Jože Balažic, M. D. ). Osteoporosis: 1998 - 2005. Start of molecular genetic analysis in Slovenian oncology. J. Marc B. Arko Marc J. et al. (1999): VDR genotype and response to etidronate therapy in late postmenopausal women. Osteoporosis International 10(4 - suppl. ): 303 -306. Clinical partner: Clinic for Endocrinology and Metabolic Diseases in Ljubljana (Prof. Andreja Kocijančič, M. D. ; Prof. Janez Preželj, M. D. ). Polycystic kidney disease (ADPKD): Genetic analysis was performed from 1996 to 2006. K. Vouk K. et al. (1999): Linkage of Slovenian ADPKD families to PKD 1 locus. Eur. J. Hum. Genet. 7, Suppl. 1: 139. Clinical partners: Clinic for Paediatric Nephrology and Radiology Unit in Ljubljana (Dr. Matjaž Bidovec, M. D. ). Mayo Clinic, Division of Nephrology and Hypertension, Rochester, United States (Prof. Peter C. Harris, M. D. ) ROSSETTI S. , STRMECKI L. , GAMBLE V. , BURTON S. , SNEDDON V. , PERAL B. , ROY S. , BAKKALOGLU A. , KOMEL R. , WINEARLS C. G. , HARRIS P. C. Mutation analysis of the entire PKD 1 gene : genetic and diagnostic implications. Am J. Hum. Genet. , 2001, 68(1), 46 -63.

MCMB: pioneering work and translation to medical practice, 1990/92 – 2011 Eating disorders – anorexia and bulimia: 1999 – 2002. . . 2006. Gabrovšek M. et al. (2004): Combined family trio and case-control analysis of the COMT Val 158 Met polymorphism in European patients with anorexia nervosa. Am. J. Med. Genet. - Part B, Neuropsych. Genet. 124 B(1): 68 -72. M. Gabrovšek Partners: Psychiatric Clinic, Ljubljana (Prof. Martina Tomori, M. D. ) European Consortium » Factors in Healthy Eating « (coordinators David E. Collier and Jeanette Treasure, U. K. ) M. Brecelj King's College, London (Dr. David E. Collier, M. D. ) Cancer – genomic & transcriptomic analysis of GC / HNPCC: 2001 - 2007. . 2011. . . Rajčević U. et al. (2001): Assessment of differential expression of oncogenes in gastric adenocarcinoma by fluorescent multiplex RT-PCR assay. Pflugers Archiv: Eur. J. Physiol. 442(6, suppl. 1): R 190 -192. Clinical partners: University Clinical Centre Ljubljana (UKC), Gastroenterology Surgery Clinic (Prof. Stanislav Repše, M. D. , Robert Juvan, M. D. ) Institute of Oncology Ljubljana (OI), Pathology Dept. (Dr. Snježana Frković Grazio, M. D. ; Matej Bračko, M. D. ) U. Rajčević G. Mijovski M. Vogelsang P. Hudler

Molecular-genetic analysis of tissue regeneration: mexican axolotl as a model organism: 2004 – 2008. GORŠIČ Maša, MAJDIČ Gregor, KOMEL Radovan: Identification of differentially expresed during axolotl limb regeneration by supression subtractive hybridisation. Cellular and Molecular Basis of Regeneration, (Euresco, 2004), p. 32. M. Goršič Academic partner: University of Ljubljana, Veterinary Faculty (Prof. G. Majdič, Ph. D). LIMB REGENERATION Day 1 -2: After resection wound healing starts. Proliferation of epidermis. Day 3 -12: Dediferentiation. Loss of specialised histologic characteristics. Enervation dependent. Day 13 -21: Forming of balastema. Proliferation and migration of non-differentiated cellc. . Day 22 -40: Re-differentiation of cells. Limb pattern starts to form Goršič M. et al. (2008): Identification of differentially expressed genes in 4 -day axolotl limb blastema by suppression subtractive hybridization. J. Physiol. Biochem. 64(1): 37 -50.

ERSD Co. E Biotechnology wit Pharmacy (2004 – 2008/09) – 18 partners from: • University • National research institutes • Clinical institutions • S&M Entreprises Borut Štrukelj R. K. • Pharmaceutical industry • • • overcoming inter-institutional barriers deepening cooperation between the academic world and the economy a plan for joint projects and operations mutual respect and cooperation • • • Publications / patents Purchase and instalation of first postgenomic equipment First DNA expression bio-chips First transgenic animal (mouse model) Establishment of the national Centre for Functional Genomics and Bio-Chips Pier Franco Pignatti Wolfgang M. Heckl

Arturo Falaschi Tito Baralle Mauro Giacca 1987. . New Delhi Trieste Cape Town Richard Roberts Ananda Chakrabarty Radovan Komel, CSA Member and Chair Person (2004 -2013)) Khosrow Adeli Alberto Kornblihtt Muntaser El Tayeb Ibrahim Timothy Hunt Carlo Bruschi Lawrence Banks Vladimir Glišin

Recent research Molecular genetic background of Psychiatric Disorders – Suicidal Behavior Tomaž Zupanc Alja Videtič PUNGERČIČ Galina, VIDETIČ Alja, PESTOTNIK Anita, ZUPANIČ-PAJNIČ Irena, ZUPANC Tomaž, BALAŽIC Jože, TOMORI Martina, KOMEL Radovan: Serotonin transporter gene promoter (5 -HTTLPR) and intron 2 (VNTR) polymorphisms : a study on Slovenian population of suicide victims. Psychiatric Genetics, 2006, vol. 16, no. 5, pp. 187 -191. Sandra Ropret, Tomaž Zupanc, Radovan Komel, Alja Videtič Paska: Investigating the associations between polymorphisms in the NTRK 2 and NGFR genes and completed suicide in the Slovenian sample. Psych. Genet. , 2015, vol. 6, pp. 241 -248. Katarina Uršič, Tomaž Zupanc, Alja Videtič Paska: Analysis of promoter polymorphism in monoamine oxidase A (MAOA) gene in completed suicide on Slovenian population. Neuroscience Letters, 2018, vol. 673 , pp. 111 -115. Carcinogenesis - Molecular genetic background of Gastric Cancer Petra Hudler Marija Rogar I. Eminović, A. Mešić, R. Komel Cancer genomics: Genetic variants of chromosome segregation genes associated with initiation/progression of cancer Pia Pužar Dominkuš HUDLER Petra, REPŠE Stanislav, JUVAN Robert, KOMEL Radovan: A genomic approach to investigate expression profiles in Slovenian patients with gastric cancer. Oncology Letters, 2011, vol. 2, issue 5, pp. 1003 -1014. Martin Sill, Christoph Schröder, Ying Shen, Aseel Marzoq, Radovan Komel, Jörg D. Hoheisel, Henrik Nienhüser, Thomas Schmidt, Damjana Kastelic : Protein profiling gastric cancer and neighboring control tissues using high-content antibody microarrays. Microarrays, 2016, vol. 5, iss. 3, pp. 1 -12 (pii: E 19). Aner Mešić, Ela Markočič, Marija Rogar, Robert Juvan, Petra Hudler , Radovan Komel: Single nucleotide polymorphisms rs 911160 in AURKA and rs 2289590 in AURKB mitotic checkpoint genes contribute to gastric cancer susceptibility. Environmental and Molecular Mutagenesis, ISSN 0893 -6692, 2017, vol. 58 , iss. 9 , pp. 701 -711.

Molecular genetic background of erythrocytosis Pleiotropic effects of erythropoietin. Familial erythorcytosis. Arthur J. Sytkowsky Nina Trošt Nataša Debeljak ŠPANINGER Klemen, BORŠTNAR Simona, MATOS Erika, MOŽINA Barbara, SYTKOWSKI Arthur J. , KOMEL Radovan, DEBELJAK Nataša: Report on isoelectric focusing trial of erythropoietin profiling in two cancer patients during chemotherapy and darbepoetin treatment. Acta Chimica Slovenica, 2011, vol. 58, no. 1, pp. 139 -143. Lenka Ilkovičová, Nina Trošt, Erika Szentpéteriová, Peter Solár, Radovan Komel and Nataša Debeljak : Overexpression of the erythropoietin receptor in RAMA 37 breast cancer cells alters cell growth and sensitivity to tamoxifen. International Journal of Oncology, 2017, vol. 51, pp. 737 -746. Molecular and regenerative medicine of the cytoskeleton related diseases Wound healing mechanisms using induced pluripotent stem cells and complete 3 D skin models. Mirjana Liović Tina Zupančič, Mateja Ožir, Hans Torma, Radovan Komel, Mirjana Liović: Keratinocyte-based cell assays: their potential pitfalls. Archives of Dermatological Research, 2012, vol. 304, iss. 9, pp. 765 -8. Marija Rogar Tina Zupančič, Gregor Serša, Hans Törmä, Ellen Birgitte Lane, Herald Herrmann, Radovan Komel, Mirjana Liović: Keratin gene mutations influence the keratinocyte response to DNA damage and cytokine induced apoptosis. Archives of Dermatological Research, 2017, vol. 309, iss. 7, pp. 587 -593. ERA Co. Sys. Med Project 4 D-HEALING: Data-driven Drug Discovery for Wound Healing: 2018 – 2021. (8 partners; Lead Partner: M. J. Arauzo-Bravo, Spain; MCMB – project partner: M. Liovič & R. Komel)

Conventional & Nano-body reverse proteomics for identification of cancer biomarkers Mike Taussig Denis Pompon Damjana Kastelic KASTELIC Damjana, FRKOVIĆ-GRAZIO Snježana, BATY Daniel, TRUAN Gilles, KOMEL Radovan, POMPON Denis: A single-step procedure of recombinant library construction for the selection of efficiently produced llama VH binders directed against cancer markers. Journal of Immunological Methods, 2009, vol. 350, no. 1 -2, pp. 54 -62. KASTELIC Damjana, SOLER Nicolas, KOMEL Radovan, POMPON Denis: The Global Sequence Signature algorithm unveils a structural network surrounding heavy chain CDR 3 Loop in Camelidae variable domains. Biochimica et Biophysica Acta (G). General Subjects, 2013, vol. 1830, issue 6, pp. 3373 -3381. Serge Muyldermans

Brain tumor carcinogenesis Glioblastoma stem cell markers Ivana Jovčevska, Neja Zupanec, Nina Kočevar, Daniela Cesselli, Neža Podergajs, Clara Limbäck Stokin, Michael P. Myers, Serge Muyldermans, Gholamreza Hassanzadeh Ghassabeh, Helena Motaln, Maria Elisabetta Ruaro, Evgenia Bourkoula, Tamara Lah Turnšek, Radovan Komel: TRIM 28 and β-actin identified via nanobody-based reverse proteomics approach as possible human glioblastoma biomarkers. Plo. S One, 2014, vol. 9, iss. 11, pp. 1 -22. Apolonija Bedina Zavec, Ajda Ota, Tina Zupančič, Radovan Komel, Nataša Poklar Ulrih, Mirjana Liović: Archeosomes can efficiently deliver any type of cargo into skin cells. Journal of Biotechnology, 2014, vol. 192, pp. 130 -135. Ivana Jovchevska, Neja Zupanec, Žiga Urlep, Andrej Vranič, Boštjan Matos, Clara Limbaeck Stokin, Serge Muyldermans, Michael P. Myers, Anton A. Buzdin, Ivan Petrov, Radovan Komel: Differentially expressed proteins in glioblastoma multiforme identified with a Nanobody-based anti-proteome approach and confirmed by Onco. Finder as possible tumor class predictive biomarker candidates. Oncotarget, 2017, vol. 8 , no. 27 , pp. 44141 -44158. Neja Šamec, Ivana Jovčevska, Alja Zottel, Jure Stojan, Mirjana Liović, Michael P. Myers, Neža Podergajs, Serge Muyldermans, and Radovan Komel: Glioblastoma-specific anti-Tuf. M nanobody for in vitro immunoimaging and cancer stem cell targeting. Oncotarget, ISSN 1949 -2553, 3 April 2018, vol. 9, no. 25, pp. 17282 -17299. Marko Vidak, Mirjana Liović, Ivana Jovcevska, Neja Šamec, Damjana Rozman, Sašo Džeroski, Peter Juvan and Radovan Komel: Meta-analysis of transcriptome data from public databases and subsequent experimental validation exposed SPRY 1 and FREM 2 as new glioblastoma stem cell marker candidates. International Journal of Molecular Sciences, 2018, vol. 19, iss. 5, no. 1369, pp. 1 -24 online.

Tamara Lah T. Daniela Cesselli TRANS-GLIOMA – proteomic biomarkers and design of new therapeutic approaches GLIOBANK - 4 patients groups. - - NGS, transcriptomics. - Signal transduction/ communication pathways. - Drug repositioning. - Drugs specific for particular patient group(s), . - Toxicology analysis. - Personalisation. E-BANK & BIOLOGICAL SAMPLES Paola Storici Federica Rosin COMMUNICATION WITH EXPERT COMMUNITY • • NEW DIAGNOSTIC TOOLS • NEW THERAPEUTIC APPROACHES Jure Vindišar COMMUNICATION WITH BROADER PUBLIC • • BIOOMARKERS NEW THERAPEUTICS DELIVERY SYSTEMS COMMERCIALISATION OF KNOWLEDGE AND PRODUCTS • BIOMED / PHARM INDUSTRY • SPIN-OFF

The intendent Nb delivery systems for specific targeting of GSC/GBM cells Anti-SPRY 1 Nb Anti-Tuf. M Nb Plasmid with Anti-Tuf. M/Anti-TRIM 28 Nb c. DNA Anti-FREM 2 Nb Engineered archeosome Charged/Conducted exosomes Raposo G. , Stoorvogel W. , JCB 2013.

Future Perspective: Cancer Immonutherapy

Raziskovalni program P 1 -0401 /0390 Funkcijska genomika in biotehnologija za zdravje MCMB Medicinski center za molekularno biologijo Molekularna biologija/genetika Analiza SNP Metagenomika Proteomika Imunocitokemija CFGBC Center za funkcijsko genomiko in bio-čipe Transkriptomika: mikromreže NGS Bioinformatika Robot pipetor Eppendorf Fotodokumentacijski sistem LAS HPLC AKTA Pure IEF – 2 D elektroforezni sistem

Dubravka Germ Dr. Ivana Jovčevska R. K. Dr. Neja Šamec MR Alja Zottel Dr. Marija Rogar doc. dr. Petra Hudler Dr. Mirjana Liović Doc. Alja Videtič Paska Doc. dr. Nataša Debeljak MR Katarina Uršič Helena Klavžar