Anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase, plays a critical role in the pathogenesis of various cancers through gene alterations, such as point mutations, deletions, and chromosomal rearrangements. These alterations lead to the constitutive activation of ALK signaling pathways, driving oncogenesis. ALK-positive anaplastic large cell lymphoma (ALK+ ALCL) accounts for about 3% of adult non-Hodgkin lymphomas and 10-15% of childhood lymphomas. The most common genetic alteration in this disease, the t(2;5)(p23;q35) translocation, results in the NPM::ALK fusion protein. Additionally, non-small cell lung cancer (NSCLC), which represents 85% of all lung cancer cases, also harbors ALK alterations, primarily involving the EML4::ALK fusion protein due to an inversion in chromosome 2p. Despite significant progress with ALK inhibitors, many patients develop resistance, leading to disease relapse. In ALK+ ALCL, the median progression-free survival (PFS) stabilizes at around 65%, while in NSCLC, it averages 8-10 months, with a dramatic drop to 10% PFS at four years. Resistance arises due to secondary ALK mutations or activation of alternative pathways that bypass ALK inhibition. My PhD project aims to identify and characterize additional genetic alterations that coexist with ALK fusions in ALK+ ALCL and NSCLC patients. Using Next-Generation Sequencing (NGS) on matched tumor/normal pairs at both disease onset and/or relapse, this study combines genomic analysis, biological validation, and pharmacological translation to uncover novel genetic factors driving resistance. My PhD research addresses these challenges with the goal of better understanding the development of resistance and providing innovative therapeutic solutions. In the context of ALK+ ALCL, our initial study, carried out during my MSc internship, proposed a combined therapeutic strategy aimed at preventing the onset of resistance. This research demonstrated that the combination of crizotinib with other drugs, such as CHOP chemotherapy, showed superior efficacy compared to monotherapy, suggesting that combination approaches could represent a practical solution to reduce the risk of relapse. My PhD project, complementing the first study, investigated the genetic mechanisms underlying resistance in ALK+ ALCL patients. Using whole-exome sequencing, we identified recurrent mutations in the FAT4 and RUNX1T1 genes. These alterations affect key pathways such as β-catenin, YAP1, and STAT3, contributing to the tumor’s aggressiveness and resistance. These findings not only enhance our knowledge of the molecular biology of ALK+ ALCL but also open new possibilities for targeted therapeutic interventions against these altered signaling pathways. In the context of ALK+ NSCLC, our research contributed to a further understanding of resistance mechanisms. Through a clinical case and a study based on liquid biopsies, we demonstrated the importance of tumor genotyping in monitoring the evolution of mutations and guiding therapeutic management. Specifically, the newly discovered mutations, such as L1198R, C1237Y, and L1196P, revealed widespread resistance to ALK inhibitors, emphasizing the need to develop new drugs capable of overcoming these variants. In summary, the work conducted has contributed to a deeper understanding of ALK-induced resistance in both ALCL and NSCLC, providing new therapeutic perspectives for patients with limited traditional treatment options.
La chinasi del linfoma anaplastico (ALK), un recettore tirosin-chinasico, svolge un ruolo critico nella patogenesi di vari tipi di cancro attraverso alterazioni genetiche, come mutazioni puntiformi, delezioni e riarrangiamenti cromosomici. Queste alterazioni portano all'attivazione costitutiva delle vie di segnalazione ALK, alimentando l'oncogenesi. Il linfoma anaplastico a grandi cellule ALK-positivo (ALK+ ALCL) rappresenta circa il 3% dei linfomi non-Hodgkin negli adulti e il 10-15% dei linfomi infantili. L'alterazione genetica più comune in questa malattia, la traslocazione t(2;5)(p23;q35), porta alla formazione della proteina di fusione NPM::ALK. Inoltre, il carcinoma polmonare non a piccole cellule (NSCLC), che rappresenta l'85% di tutti i casi di cancro ai polmoni, presenta anch'esso alterazioni di ALK, principalmente legate alla proteina di fusione EML4::ALK, dovuta a un'inversione del cromosoma 2p. Nonostante i progressi significativi ottenuti con gli inibitori di ALK, molti pazienti sviluppano resistenza, portando a una ricaduta della malattia. Nell'ALK+ ALCL, la sopravvivenza libera da progressione (PFS) mediana si stabilizza intorno al 65%, mentre nel NSCLC si attesta in media a 8-10 mesi, con un calo drastico della PFS al 10% dopo quattro anni. La resistenza sorge a causa di mutazioni secondarie di ALK o dell'attivazione di vie alternative che bypassano l'inibizione di ALK. Il mio progetto di dottorato mira a identificare e caratterizzare ulteriori alterazioni genetiche che coesistono con le fusioni di ALK nei pazienti con ALK+ ALCL e NSCLC. Utilizzando il sequenziamento di nuova generazione (NGS) su coppie di campioni tumorali e normali, prelevati all'insorgenza della malattia e/o alla ricaduta, questo studio combina analisi genomiche, validazione biologica e traduzione farmacologica per scoprire nuovi fattori genetici che guidano la resistenza. La mia ricerca di dottorato affronta queste sfide con l'obiettivo di comprendere meglio lo sviluppo della resistenza e fornire soluzioni terapeutiche innovative. Nel contesto dell'ALK+ ALCL, il nostro studio iniziale, condotto durante il mio tirocinio di laurea magistrale, ha proposto una strategia terapeutica combinata volta a prevenire l'insorgenza della resistenza. Questa ricerca ha dimostrato che la combinazione di crizotinib con altri farmaci, come la chemioterapia CHOP, ha mostrato un'efficacia superiore rispetto alla monoterapia, suggerendo che approcci combinati potrebbero rappresentare una soluzione pratica per ridurre il rischio di recidiva. Il mio progetto di dottorato, complementare al primo studio, ha indagato i meccanismi genetici alla base della resistenza nei pazienti con ALK+ ALCL. Utilizzando il sequenziamento dell'esoma, abbiamo identificato mutazioni ricorrenti nei geni FAT4 e RUNX1T1. Queste alterazioni influenzano vie chiave come β-catenina, YAP1 e STAT3, contribuendo all'aggressività del tumore e alla resistenza. Questi risultati non solo ampliano la nostra conoscenza della biologia molecolare dell'ALK+ ALCL, ma aprono anche nuove possibilità per interventi terapeutici mirati contro queste vie di segnalazione alterate. Nel contesto dell'ALK+ NSCLC, la nostra ricerca ha contribuito a una maggiore comprensione dei meccanismi di resistenza. Attraverso un caso clinico e uno studio basato su biopsie liquide, abbiamo dimostrato l'importanza della genotipizzazione del tumore per monitorare l'evoluzione delle mutazioni e guidare la gestione terapeutica. In particolare, le nuove mutazioni scoperte, come L1198R, C1237Y e L1196P, hanno rivelato una resistenza diffusa agli inibitori di ALK, sottolineando la necessità di sviluppare nuovi farmaci capaci di superare queste varianti. In sintesi, il lavoro condotto ha contribuito a una comprensione più profonda della resistenza indotta da ALK sia nell'ALCL che nel NSCLC, offrendo nuove prospettive terapeutiche per i pazienti con opzioni di trattamento tradizionali limitate.
Investigation of drug resistance and co-mutational landscape of ALK-positive tumors
VILLA, MATTEO
2025
Abstract
Anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase, plays a critical role in the pathogenesis of various cancers through gene alterations, such as point mutations, deletions, and chromosomal rearrangements. These alterations lead to the constitutive activation of ALK signaling pathways, driving oncogenesis. ALK-positive anaplastic large cell lymphoma (ALK+ ALCL) accounts for about 3% of adult non-Hodgkin lymphomas and 10-15% of childhood lymphomas. The most common genetic alteration in this disease, the t(2;5)(p23;q35) translocation, results in the NPM::ALK fusion protein. Additionally, non-small cell lung cancer (NSCLC), which represents 85% of all lung cancer cases, also harbors ALK alterations, primarily involving the EML4::ALK fusion protein due to an inversion in chromosome 2p. Despite significant progress with ALK inhibitors, many patients develop resistance, leading to disease relapse. In ALK+ ALCL, the median progression-free survival (PFS) stabilizes at around 65%, while in NSCLC, it averages 8-10 months, with a dramatic drop to 10% PFS at four years. Resistance arises due to secondary ALK mutations or activation of alternative pathways that bypass ALK inhibition. My PhD project aims to identify and characterize additional genetic alterations that coexist with ALK fusions in ALK+ ALCL and NSCLC patients. Using Next-Generation Sequencing (NGS) on matched tumor/normal pairs at both disease onset and/or relapse, this study combines genomic analysis, biological validation, and pharmacological translation to uncover novel genetic factors driving resistance. My PhD research addresses these challenges with the goal of better understanding the development of resistance and providing innovative therapeutic solutions. In the context of ALK+ ALCL, our initial study, carried out during my MSc internship, proposed a combined therapeutic strategy aimed at preventing the onset of resistance. This research demonstrated that the combination of crizotinib with other drugs, such as CHOP chemotherapy, showed superior efficacy compared to monotherapy, suggesting that combination approaches could represent a practical solution to reduce the risk of relapse. My PhD project, complementing the first study, investigated the genetic mechanisms underlying resistance in ALK+ ALCL patients. Using whole-exome sequencing, we identified recurrent mutations in the FAT4 and RUNX1T1 genes. These alterations affect key pathways such as β-catenin, YAP1, and STAT3, contributing to the tumor’s aggressiveness and resistance. These findings not only enhance our knowledge of the molecular biology of ALK+ ALCL but also open new possibilities for targeted therapeutic interventions against these altered signaling pathways. In the context of ALK+ NSCLC, our research contributed to a further understanding of resistance mechanisms. Through a clinical case and a study based on liquid biopsies, we demonstrated the importance of tumor genotyping in monitoring the evolution of mutations and guiding therapeutic management. Specifically, the newly discovered mutations, such as L1198R, C1237Y, and L1196P, revealed widespread resistance to ALK inhibitors, emphasizing the need to develop new drugs capable of overcoming these variants. In summary, the work conducted has contributed to a deeper understanding of ALK-induced resistance in both ALCL and NSCLC, providing new therapeutic perspectives for patients with limited traditional treatment options.File | Dimensione | Formato | |
---|---|---|---|
phd_unimib_765881.pdf
accesso aperto
Dimensione
14.33 MB
Formato
Adobe PDF
|
14.33 MB | Adobe PDF | Visualizza/Apri |
I documenti in UNITESI sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
https://hdl.handle.net/20.500.14242/193896
URN:NBN:IT:UNIMIB-193896