Genetic Alterations in Lung Cancer

Introduction

Methods

GENETIC LANDSCAPE OF NSCLC
KRAS Gene: The first mutation identified in adenocarcinomas, the first type of lung cancer to be evaluated genetically, was KRAS. Additionally, KRAS is the most commonly mutated gene in NSCLC, occurring in approximately 30% of cases.[] The KRAS gene, belonging to the RAS family, codes for a protein that exhibits GTPase activity and is involved in critical intracellular processes such as cell survival, proliferation, and regulation of the cytoskeleton. KRAS, which is stimulated by GTPase-activating proteins (GAPs) through its binding to GTP, initiates the downstream MAPK/ERK, PI3K/AKT/mTOR C1 signaling pathways and induces cell proliferation. Genetic mutations in the KRAS gene prevent the process of GTP hydrolysis, resulting in persistent activation of the protein.[]

The majority (95%) of KRAS mutations consist of single nucleotide alterations in codons 12 and 13, resulting in variants such as G12D, G12V, and G12C. These genetic alterations cause the loss of GTPase activity. Non-smoking patients typically exhibit G12D and G12V mutations, whereas smokers commonly have the G12C mutation.[] While the exact prognostic significance of KRAS mutations in NSCLC remains uncertain, they have been linked to a reduced response to chemotherapy and increased resistance to EGFR inhibitors, particularly. The FDA (The U.S. Food and Drug Administration) approved Sotorasib in May 2021 as the initial treatment for patients with locally advanced or metastatic NSCLC whose tumors have KRAS G12C mutations.[] Ongoing clinical studies are assessing the efficacy of Adagrasib (MRTX849), an alternative tyrosine kinase inhibitor (TKI), in patients harboring the KRAS G12C mutation.[] On the other side, there are ongoing treatment trials that target different molecules in the gene's downstream signaling pathway.

The creation of mRNA vaccines is another therapeutic approach that targets cells that have KRAS mutations. The objective of the Phase I clinical trial is to assess the safety and tolerability of the combination treatment of mRNA-5671/V941 and Pembrolizumab in patients with NSCLC, colorectal cancer, and pancreatic cancer who have the KRAS mutation. The latest update on the study findings indicated that the immune response was stimulated in animal models.[]

EGFR Gene: Epidermal growth factor receptor (EGFR) belongs to a family of tyrosine kinase receptors consisting of four members. EGFR modulates crucial cellular processes including proliferation, cell migration, cell death, and adhesion. The receptor involves dimerization and activation of tyrosine kinase activity by autophosphorylation in response to the binding of particular ligands. This stimulation leads to subsequent activation of the EGFR-associated PI3K-AKT-mTOR pathway, JNK pathway, and MAPK/ERK pathways.[]

EGFR gene mutations in NSCLC are restricted to exons 18?21, which are specifically associated with the tyrosine kinase activity of the protein. The majority (90%) of the mutations consist of microdeletions occurring in exon 19 (Del19) and exon 21 (Del21). These two mutations, which are classified as the prevalent mutation of EGFR, result in comparable alterations in the ATP binding domain of the protein. The mutations G719X in exon 18, S768I in exon 20, and L861Q in exon 21 are infrequent variants of the EGFR gene. EGFR mutations in precancerous neoplasms inhibit apoptosis, triggering angiogenesis and metastatic progression.[]

EGFR mutation prevalence rates differ among various ethnic populations. The prevalence of EGFR mutation in NSCLC patients is 78?90% in the East Asian population, but drops to 16% in Europe and 12% in Atlantic and Mediterranean populations. The cause of this phenomenon remains unknown.[]

EGFR mutation is associated with poor prognosis. Nevertheless, individuals with EGFR mutation exhibit a favorable response to TKI therapy, with a success rate ranging from 55% to 78%. TKI is primarily administered as the initial treatment for patients with metastatic lung cancer. Gefitinib or Erlotinib, which have been approved by the FDA for patients with EGFR mutations initially, exhibit a progression-free survival (PFS) rate that is about twice as high as that of conventional chemotherapy (11.0 months versus 5.6 months). Fatinib, Dacomitinib, and Osimertinib are the other three TKIs approved for lung cancer patients with EGFR mutations.[] It has been demonstrated that Osimertinib is especially effective in preventing secondary mutations from developing during treatment.[]

BRAF Gene: The BRAF gene is responsible for producing the BRAF protein, which is a member of the RAF kinase family and functions as a serine-threonine kinase. When activated, this protein forms homo- and heterodimers and plays a role in the regulation of the MAPK/ERK signaling pathway. Oncogenic mutations in the BRAF gene cause phosphorylation of MEK in the MAPK/ERK pathway, thus causing downstream activation of this pathway. This stimulus triggers cellular proliferation and ensures its viability.[]

BRAF mutations are prevalent in various forms of cancer, including colorectal, thyroid, and melanomas. The presence of BRAF mutation is observed in 5-8% of NSCLC adenocarcinomas. The V600E mutant variation accounts for 90% of all BRAF mutations. The prevalence of this mutation variant in cases of lung cancer is approximately 20-30%.[] This mutation leads to activation of the MAPK/ERK pathway independent of RAS proteins. The existence of the BRAF V600E mutation has been associated with the advancement of aggressive tumors and poor clinical outcomes. Furthermore, whereas the occurrence of axillary lymph node involvement is detected in only 0.6% of individuals with lung cancer, this percentage has been demonstrated to rise significantly to around 15% in patients who have the BRAF mutation.[]

Vemurafenib and Dabrafenib are BRAF inhibitors specifically designed for the therapeutic management of several cancer types, including lung cancer. Research has demonstrated that a combination of MEK inhibitors with them results in a 33% to 42% enhancement in the response rate for lung cancer.[]

Encorafenib and Binimetinib in combination therapy was approved by the FDA on October 11, 2023, for adult patients with metastatic NSCLC with BRAF V600E mutation.[]

ALK Gene: The ALK (anaplastic lymphoma kinase) gene encodes a transmembrane protein that belongs to the insulin receptor family of tyrosine kinase receptors. This gene is prone to form fusion genes with different genes such as GCC2, STRN, PTPN3, TPR, HIP1, PHACTR1, DCTN1. However, the fusion gene variation generated by the EML4 (Echinoderm microtubule-associated protein-like 4) gene is the first and most commonly detected fusion gene in NSCLC. This gene abnormality accounts for 80% of all gene fusions in NSCLC patients and is present in about 7% of cases of the disease. Based on differences in the breakpoint, 15 different variants of the ALK-EML4 gene fusions have been found in NSCLC. [] The most common of these are the fusion variants between exon 20 of the ALK gene and exon 13 (v1), exon 20, and exon 6 (v3) of EML4 gene. Compared to v1, tumors containing a v3 translocation exhibit a more aggressive course and a lower response rate to TKIs.[]

The ALK-EML4 gene fusion produces a chimeric protein with higher tyrosine kinase activity. This protein, which has developed an oncogenic function, promotes the development of cancer by increasing metabolism, stimulating cell division, and preventing apoptosis.[]

Crizotinib, an ALK inhibitor, is used therapeutically to treat lung cancer with ALK fusions. Crizotinib-treated patients have an increased PFS rate and 57-74% inhibitor sensitivity. Nevertheless, specific genetic alterations, such as L1196M, F1174L, and C1156Y, occurring in the kinase domain of EML4-ALK, result in patients acquiring resistance to Crizotinib. Novel ALK inhibitors of the second generation, namely Alectinib and Ceritinib, are now under development with the aim of specifically targeting secondary mutations in patients with ALK-positive NSCLC. Lorlatinib, a third-generation TKI, has demonstrated a PFS efficacy of 72% in patients with ALK mutations.[]

Other Gene Mutations Observed in NSCLC: Different types of mutations, such as point mutations, insertion/ deletions, and amplifications, have been identified in the ERBB2 gene in NSCLC as well as in many other cancers. The most common mutations in this gene are often found in the exon 20 region, involving insertions or duplications. Additionally, point mutations leading to single or double nucleotide changes in ERBB2 are frequently observed. However, unlike insertion/duplication mutations, comprehensive genomic studies have shown that these mutations do not exhibit activating oncogenic effects. ERBB2 mutations have been associated with a positive response to anti-HER2 targeted therapy.[]

Another targetable molecule in lung cancer is the NTRK1/2/3 (neurotrophic tyrosine receptor kinase) gene fusions. These gene fusions result in increased tyrosine kinase activity. Among the NRTK genes, with numerous fusion partners identified, the most common ones are MPRIP-NTRK1 and CD74-NTRK1 fusions, which have demonstrated oncogenic effects. Point mutations in NTRK1/2/3 are also common, although their activating effects have not been demonstrated. Targeted therapies associated with these mutations have not been extensively studied.[]

Gene rearrangements of RET, a tyrosine kinase receptor (rearrangement during transfection), are observed in 1-2% of NSCLC cases. Fusions of this gene result in dysregulated and increased signaling in the RET-i kinase domain. Although numerous fusion partners have been reported, the most common ones are KIF5B, CCDC6, and NCOA4. Fusion of this gene is typically associated with a positive response to tyrosine kinase inhibitors (TKIs). Selpercatinib, Pralsetinib, and Cabozantinib are FDA-approved TKIs for RET rearrangements.[]

Information on the first-line and subsequent treatment following the gene mutations detected in NSCLC according to the NCCN Guidelines v2.2024 is given in Table 1.

GENETIC LANDSCAPE OF SCLC
Compared to NSCLC, comprehensive whole genome studies of oncogenic driver mutations for SCLC are progressing slowly due to the limited number of patient samples available for research. Therefore, our understanding of the pathways influencing oncogenesis is incomplete. Oncogenesis has been suggested to be initiated by the simultaneous inactivation of RB1 and TP53 genes in pulmonary neuroendocrine cells, which leads to tumor growth. Subsequent clinical studies have revealed that epithelial cells (basal and type II alveolar cells) as well as neuroendocrine cells may be the source of SCLC. The following section provides information about the tumor suppressor TP53, RB1 gene mutation, and MYC amplification, which are the most common gene alterations found in SCLC patients.

Comprehensive whole genome investigations of oncogenic driver mutations for SCLC are not as advanced as those for NSCLC since there are fewer patient samples available for study. Consequently, our understanding of the pathways influencing oncogenesis is incomplete. Oncogenesis is believed to be initiated by the simultaneous inactivation of RB1 and TP53 genes in pulmonary neuroendocrine cells, which leads to tumor growth. Subsequent clinical studies have shown that SCLC may arise from epithelial cells, such as basal and type II alveolar cells, as well as neuroendocrine cells.[]

The following section provides more detailed information on the most common gene changes in SCLC patients, such as biallelic loss of tumor suppressors such as TP53, RB1, and MYC amplification.[]

TP53 Gene: Under conditions of intracellular stress, such as hypoxia, aging of cells, or damage to DNA, the tumor suppressor gene TP53 is activated, arresting the cell cycle, controlling genomic stability, and inducing apoptosis. When this gene is inactive, the cell loses its ability to regulate its responses, which leads to a loss of genomic stability and malignant transformation. Most mutations in the TP53 gene occur in the area responsible for binding to DNA. TP53 mutation is correlated with poor survival and poor clinical outcome. The five most common and clinically significant mutation variants of TP53, which have extremely different and numerous mutations in SCLC, have been identified. These mutations cause the formation of R249M, Y220C, M237I, R273L, and R248W substitutions in the p53 protein.[]

Smoking is commonly associated with TP53 mutations. Approximately three times as many smokers as nonsmokers have this mutation. The TP53 mutation profile of these groups also varies. G>C or G>A transversions are prevalent in individuals who have never smoked, whereas the G>T mutation is typically found among smokers.[]

Genome sequencing conducted on samples from 110 patients with SCLC revealed somatic mutations in TP73, another member of the p53 family. This finding reaffirms the involvement of TP53 family genes in the progression of SCLC.[]

RB1 Gene: The RB1 gene, together with RBL1 and RBL2, forms the pocket protein family and is a tumor suppressor first identified in retinoblastoma but commonly encountered in many malignancies, including prostate and breast cancer. RB1 is responsible for cell cycle regulation and cell proliferation.[] Transcriptome analyses have shown that other mutation variants, such as insertion/deletion seen in the RB1 gene, cause incorrect protein formation since they are generally seen at splicing points. The RB1 gene also regulates the activation of transcription factors such as Sox2 and Oct4. It is known that when this gene is silenced, cells gain pluripotent properties and exhibit aggressive tumor formation as a result of excessive activation of these transcription factors.[] It has also been shown that loss of RB1 causes overexpression of the EZH2 gene, which is associated with tumor development in lung cancer. These results support the role of mutations in the RB1 gene in SCLC formation and tumor development.[]

In comprehensive genomic studies, biallelic loss of RB1 and TP53 genes has been found at a rate of 93% and 100% respectively in patients, and this has come to be recognized as the hallmark of SCLC carcinogenesis. Since both genes are crucial for controlling the cell cycle, losing one of them means losing control over the cell cycle. In addition, inhibition of other kinases such as CHK1 and ATR, which are involved in the cell cycle, is also triggered. The resulting genomic instability continues with DNA damage, activation of the PI3K-AKTmTOR pathway, resistance to apoptosis, and results in the cell gaining malignant transformation.[]

Both TP53 and RB1 are not therapeutically targetable.[]

MYC Gene: The MYCL, MYCN, and MYC genes, which have different functions but strong structural homology, make up the MYC gene family. In 20% of cases of SCLC, the MYC gene is overexpressed. This gene's amplification has been linked to chemotherapy resistance and poor clinical outcomes.[] However, the mechanisms of action of these gene family members have not been fully determined. While experiments with mice have shown that loss of the MYCN and MYCL genes stops tumor development, the same is not true for the MYC gene.[] These genes also differ in sensitivity to aurora kinase inhibitors. In fact, the MYC gene showed hypersensitivity, while MYCL and MYCN showed a very mild response.[]

Other Gene Mutations Observed in SCLC: The PTEN gene, situated on chromosome 10, functions as a tumor suppressor gene and governs the AKT/PKB pathway. The prevalence of these genetic abnormalities in patients with SCLC is 9%. However, its role in the development of lung cancer is not completely understood. Suppressing the expression of this gene in mice models has been reported to expedite the advancement of SCLC. In another study, it was reported that biallelic inactivation of this gene triggered the transformation of adenocarcinomas into neuroendocrine carcinoma.[]

Located on chromosome 8 and consisting of 24 exons, the fibroblast growth factor receptor (FGFR) gene is a member of the fibroblast growth factor (FGF) family. Mutation of this gene is observed in 8% of SCLC patients. Gene amplification typically leads to overexpression, which is primarily observed during the early stages of carcinogenesis. Although there have been suggestions on the potential of TKIs to inhibit FGFR1 activity, there have not been enough studies done due to the small patient population.[]

Conclusion

Conflict of Interest: All authors declared no conflict of interest.

Use of AI for Writing Assistance: All authors declare that they did not use AI while preparing the review article.

Financial Support: None declared.

Peer-review: Externally peer-reviewed.

References