Telomerase Reverse Transcriptase Promoter Mutations in Melanoma, Non-Melanoma Skin Cancer and Glioma

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Hector Roberts
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1 Aus dem Deutschen Krebsforschungszentrum Heidelberg (Geschaftsfuhrender Direktor: Prof. Dr. Dr. h.c. Otmar D. Wiestler) Forschungsschwerpunkt Krebsriskofaktoren und Prevention Abteilung fur Molekulargenetische Epidemiologie (Abteilungsleiter: Prof. Dr. Kari Hemminki) Telomerase Reverse Transcriptase Promoter Mutations in Melanoma, Non-Melanoma Skin Cancer and Glioma Inauguraldissertation zur Erlangung des Doctor scientiarum humanarum (Dr.sc.hum.) an der Medizinischen Fakultat Heidelberg der Ruprecht-Karls-Universitat Tag Prufung: 1 h. DEZ vorgelegt von Barbara Heidenreich aus Pfaffenhofen an der Mm

2 TABLE OF CONTENTS 1. INTRODUCTION TELOMERES AND TELOMERASE Biological Background Historical Background: u Telomeric End-Protection: Shelterins ('End-Protection') The Function of Telomerase ('End-Replication') The Catalytic Subunit: Telomerase Reverse Transcriptase Structure and Regulation of the TERT Promoter TERT Promoter Mutations in Human Cancers The Discovery of TERT Promoter Mutations The Role of Telomeres and Telomerase in Cancer Alternative Lengthening of Telomeres Telomere Independent Activities of TERT in Human Cancers (Non-Canonical Functions) OBJECTIVE OF THE STUDY SKIN CANCER The Skin and its Role in Protection from UV-Light Melanoma Skin Cancer Melanoma Development and Progression Treatment of Melanoma Non-Melanoma Skin Cancer MALIGNANT GLIOMAS IN ADULTS Classification of Gliomas and Class-Specific Genetic Alterations Treatment of Gliomas Telomeres and Telomerase-associated Genes in Glioma MATERIAL AND METHODS PATIENTS AND TUMOURS Melanocytic Lesions Primary Lesions and Metastases from Melanoma Patients Clinical Details and Patient Data for Primary Melanomas Melanocytic Nevi Lesions Non-Melanocytic Skin Lesions Tumours and Recurrences from Glioma Patients EXTRACTION OF DNA AND RNA Extraction of DNA from Blood Extraction of DNA from FFPE Tissue DNA and RNA Extraction from Fresh-Frozen Tissues 37 III

3 2.3. METHODS Investigation of Genetic Alterations at Loci of Interest Mutational Analysis by PCR and Sanger Sequencing Multiplex Ligation-dependent Probe Amplification (MLPA) and Methylation-Sensitive MLPA (MS-MLPA) Quantitative Real-Time PCR (qrt-pcr) Methods cdna Reverse Transcription from RNA Measurement of mrna Expression by qrt-pcr Measurement of Relative Telomere Length by MM qrt-pcr STATISTICAL METHODS RESULTS MELANOCYTE LESIONS OF THE SKIN TERT Promoter Mutations and Alterations in BRAF, NRAS and CDKN2A in Melanocyte Lesions of the Skin TERT Promoter Mutations and Alterations in BRAF, NRAS and CDKN2A in Primary Melanomas TERT Promoter Mutations in Melanoma Metastases Association of Genetic Alterations and Patient and Clinical Data Patient and Clinical Data from Patients with Primary Melanoma TERT Promoter Mutations and Survival of Melanoma Patients Progression-free Survival in Melanoma Patients and Mutations Overall Survival of Melanoma Patients Effects of the TERT Promoter Mutations on Transcription and Telomere Length in Primary Melanomas TERT mrna Expression Levels Relative Telomere Length and Correlation with TERT Promoter Mutations Mutations in Melanocyte Nevi Alterations in the TERT Promoter, BRAF, NRAS and at 9p21 in Melanocyte Nevi Distribution of BRAF Mutations NON-MELANOCYTIC SKIN CANCER AND PRECURSOR LESIONS Basal Cell Carcinomas TERT Promoter Mutations in Basal Cell Carcinomas TERT Promoter Mutations and Clinical Data Relative Telomere Length and Correlation with TERT Promoter Mutations Non-Melanocytic Skin Lesions Originating from Keratinocytes: Seborrheic Keratoses, Actinic Keratoses and Squamous Cell Carcinomas TERT Promoter Mutations in Squamous Cell Carcinomas TERT Promoter Mutations in Seborrheic Keratosis and Actinic Keratoses FGFR3 mutations in SCC and Seborrheic Keratoses 82 IV

4 3.3. GENETIC ALTERATIONS IN ADULT GLIOMAS OF THE BRAIN Patient Characteristics TERT Promoter Mutations and Alterations in Other Genes in Glioma Tumours TERT Promoter Mutations TERT Promoter Mutations and Alterations in IDH1/2 and at 9p21,1p and 19q Estimating Effects of the TERT Promoter Mutations in Glioma TERT mrna Expression Levels Relative Telomere Length and Correlation with TERT Promoter Mutations Correlation between Relative Telomere Length and TERT mrna Expression Effect of TERT Promoter Mutations and Alterations in other Genes on Survival Estimation of Effects on Overall and Progression-free Survival Survival and Treatment Comparison between Alterations in Glioma Tumours and Matched Recurrences DISCUSSION TERT PROMOTER MUTATIONS IN MELANOMA Frequencies of TERT Promoter Mutations and Effect on TERT Expression and Telomere Length Association with other Alterations Association of TERT Promoter Mutations and UV-Radiation Association of TERT Promoter Mutations with Clinico-Histophathological Features and Effect on Survival TERT PROMOTER MUTATIONS IN NON-MELANOMA SKIN CANCER TERT PROMOTER MUTATIONS IN ADULT GLIOMAS OF THE BRAIN Frequencies of TERT Promoter Mutations and Association with other Alterations TERT Promoter Mutations in Glioma Recurrences Association with Survival of Patients Effect of TERT Promoter Mutations on TERT Expression TERT Promoter Mutations and Telomere Length IMPLICATION OF TERT PROMOTER MUTATIONS IN HUMAN CANCERS Major Findings of the Study Frequency and Distribution of TERT Promoter Mutations Association of TERT Promoter Mutations and UV-Radiation Association of TERT Promoter Mutations with Clinico-Histophathological Features and Effect on Survival Effect of TERT Promoter Mutations on TERT Expression TERT Promoter Mutations and Telomere Length Implications of Canonical and Non-Canonical Features of TERT in Human Cancers Conceptual Advancement and Therapeutic Possibilities SUMMARY 128 V

5 6. REFERENCES OWN PUBLICATIONS APPENDIX SUPPLEMENTARY FIGURES CURRICULUM VITAE ACKNOWLEDGEMENTS 147 VI

BAP1 germline mutations A new Cutaneous Nevus Melanoma Syndrome. Thomas Wiesner

BAP1 germline mutations A new Cutaneous Nevus Melanoma Syndrome Thomas Wiesner Disclosure Listed as co-inventor US patent application US 61/463,389 BAP1 mutational analysis in determining susceptibility