Departamento de Medicina Interna Non-Small-Cell-Lung-Carcinoma

Universitat Autònoma de Barcelona
Facultat de Medicina
PhD programme:
Departamento de Medicina Interna
Thesis entitled:
LKB1/ AMPK / TSC2 signaling pathway alterations in
Non-Small-Cell-Lung-Carcinoma
Present by:
Itziar de Aguirre Egaña
Thesis Advisors:
Director: Dr. Paula Vertino
Director: Dr. Rafael Rosell i Costa
Itziar de Aguirre Egaña Dr. PM Vertino Dr. Rafael Rosell Costa
Badalona, 2014

Paula M. Vertino , Professor at the Department of Radiation Oncology at Emory University School of
Medicine and leader of ¨Cancer Genetics and Epigenetics Program¨, Winship Cancer Institute of Emory
University (Atlanta, Georgia).
CERTIFICA
Que la Tesi Doctoral titulada: ¨ LKB1/ AMPK / TSC2 signaling pathway alterations in Non-Small-Cell-
Lung-Carcinoma ¨ , ha estat realitzada per la llicenciada Itziar de Aguirre Egaña sota la seva direcció, en
codirecció amb el Dr. Rafael Rosell i Costa, i considera que és apta per a la seva defensa pública davant
d’un Tribunal per optar al grau de Doctora per la Universitat Autònoma de Barcelona.
I per tal que quedi constància , signa aquest document .
Dra. Paula M. Vertino
Badalona, Juny 2014

En Rafael Rosell i Costa, Professor Associat del Departament de Medicina de la Universitat Autònoma
de Barcelona i director del ¨Cancer Biology & Precision Medicine Program¨ de l´Institut Català
d’Oncologia, Hospital Universitari Germans Trias i Pujol,
CERTIFICA
Que la Tesi Doctoral titulada: ¨ LKB1/ AMPK / TSC2 signaling pathway alterations in Non-Small-Cell-
Lung-Carcinoma ¨ , ha estat realitzada per la llicenciada Itziar de Aguirre Egaña sota la seva direcció, en
codirecció amb la Dra. Paula M.Vertino, i considera que és apta per a la seva defensa pública davant
d’un Tribunal per optar al grau de Doctora per la Universitat Autònoma de Barcelona.
I per tal que quedi constància , signa aquest document .
Dr. Rafael Rosell i Costa
Badalona, Juny 2014

Acknowledgements
These lines are to deserve my sincere acknowledgment to all the people who helped me to
develop this work:
First of all, words cannot express how grateful I feel toward my advisors, Paula M. Vertino and
Rafael Rosell i Costa, each of them is a great scientist and an expert in their field.
Thanks to Paula M. Vertino for her kindness providing unlimited support over the last years,
without her guidance and supervision have not been able to develop this research. Also I ´m
grateful to her to motivate me in difficult moments and for all she kindly taught me about
molecular biology.
A massive thank you to Rafael Rosell i Costa, for the opportunity he offered me to live my
¨american experience¨. It was a very rich, an extremely useful, and a fruitful experience.
Thanks to Wei Zhou, Diansheng Zhong and Michael, lovely people who always had the
willingness to help with a big smile. Thanks for their generosity.
I would like to thank ¨Vertino´s lab¨: Krithika Subramanian, Doris Powell, Melissa Pourpak,
Annalisa Stoney and Mary Lucas Smith, for their help in the laboratory and the excellent time I
enjoyed working and entertaining with them. You made me feel at home!!!
Many thanks to Professor Xavier León Vintró, a generous person who without knowing me, he
developed the statistical analysis of this thesis, at a time when it was not any exit.
I´m grateful to Pedro Lopez de Castro, for his contribution in the tedious and laborious step of
collecting the clinical data of patients analyzed.
I´m grateful to Jose Luis Mate, for his cooperation from the Department of Pathology.
I would also like to thank all members of the Oncology Service, Hospital Germans Trias i Pujol,
they always found time to answer my queries.
Last but certainly not least, I would like to express my enormous gratitude to all my family and
friends for their unlimited support, unconditional encouragement and patience.
It would take too long to acknowledge everyone by name, but you know who you are, to all of
you
ESKERRIK ASKO, MOLTES GRÀCIES, THANKS!!!

INDEX
INDEX
Page
Abbreviations …………………………………………………………………………...IV
I. Introduction ................................................................................................................ - 1 -
1. Lung Cancer .................................................................................................... - 2 -
1.1 Epidemiology of Lung Cancer ......................................................................... - 2 -
1.1.1 Incidence ..................................................................................................... - 2 -
1.1.2 Mortality ....................................................................................................... - 6 -
1.2 Lung cancer causes.......................................................................................... - 7 -
1.3 Types of Lung Cancer .................................................................................... - 11 -
1.3.1 SCLC .......................................................................................................... - 11 -
1.3.2 NSCLC ....................................................................................................... - 12 -
1.4 Stage of lung cancer ....................................................................................... - 12 -
1.4.1 Stages of Small Cell Lung Cancer ........................................................ - 12 -
1.4.2 Stages of Non-Small Cell Lung Cancer ................................................ - 13 -
2. Epigenetic alterations in DNA .................................................................. - 15 -
2.1 Epigenetic modifications ................................................................................ - 16 -
2.1.1 X chromosome inactivation .................................................................... - 16 -
2.1.2 Genomic imprinting .................................................................................. - 16 -
2.2 DNA methylation ............................................................................................. - 17 -
2.2.1 What is methylation? ............................................................................... - 17 -
2.2.2 Distribution of methylated cytosines and CpG islands ....................... - 17 -
2.2.3 DNA methyltransferases ......................................................................... - 20 -
2.2.4 DNA Methyation in Cancer ..................................................................... - 21 -
2.2.5 Techniques to study DNA methylation ................................................. - 24 -
2.2.6 Clinical implications of DNA methylation .............................................. - 25 -
2.2.7 Methylation &Tumor suppressor genes................................................ - 25 -
2.3 Chromatin and Methylation ............................................................................... - 26 -
2.3.1 Histone Acetylation/ Deacetylation........................................................ - 27 -
2.3.2 Histone deacetylase and Methyl-binding domain ............................... - 28 -