ALK fusion variant 3a/b, concomitant mutations, and high PD-L1 expression were associated with unfavorable clinical response to second-generation ALK TKIs in patients with advanced ALK-rearranged non-small cell lung cancer (GASTO 1061)

The impact of the immunological context on outcomes of solid cancer patients treated with genotype-matched targeted therapies: a comprehensive review

BACKGROUND

Outcomes with genotype-matched targeted therapy in solid cancer patients are heterogeneous: some have exceptional responses, whereas others have primary progression. This review explores the immunobiological features which may underlie this differential response.

METHODS

We conducted a literature review of studies assessing the impact of immune context following searches on Web of Science, Medline and Embase. Relevant outcomes include response, progression-free survival and overall survival. Data were extracted from multivariate analysis, univariate analysis or directly from Kaplan-Meier curves. Meta-analyses were carried out where three or more studies analysed the same immune factor for the same cancer type. The remaining studies were analysed descriptively.

RESULTS

In the adjuvant setting, assessment of the immune context does not highlight a group failing to derive benefit for the use of dabrafenib/trametinib after resection of BRAFV600E melanoma. Differential gene expression in exceptional responders show enrichment of genes associated with immune activation. BRAFV600E colorectal cancer patients with high cytolytic scores benefit from the addition of MEK inhibition whereas those with low scores fare better without. High programmed death-ligand 1 (PD-L1) expression is predictive of inferior outcomes to epidermal growth factor receptor (EGFR), ALK and G12C tyrosine kinase inhibitors. EGFR-mutant patients with high CD8+ T cells and PD-L1 positivity have very poor outcomes. Stromal tumour-infiltrating lymphocytes predict for efficacy of stromal-poor tumours in human epidermal growth factor receptor 2 (HER2)-positive breast cancer treated with short-course adjuvant trastuzumab. High immune metagene and single immune gene expression are predictive of benefit for chemotherapy plus trastuzumab, but not chemotherapy alone. The addition of pertuzumab or lapatanib appears to be beneficial in those with immune non-enriched microenvironments. High major histocompatibility complex (MHC)-I is negatively predictive and high MHC-II is positively predictive of outcomes with trastuzumab-based therapy.

CONCLUSIONS

To our knowledge, this is the first review assessing immunological context as a biomarker for targeted therapy. The results of this review represent an important resource to aid future translational studies in advancing stratified precision medicine oncology.

[ALK rearrangement in non-small cell lung cancer]

The discovery of ALK gene rearrangement in 3 to 5% of non-small cell lung carcinomas has revolutionized our understanding and therapeutic approach of these cancers. This oncogenic driver is associated with specific clinical and biological features is associated with specific clinical and biological features, mainly affecting young and never-smoker patients, with a particular tropism for brain metastases. The development of ALK tyrosine kinase inhibitors has transformed patient outcomes, with remarkable efficacy of latest-generation molecules, particularly in controlling brain metastases. However, the emergence of complex resistance mechanisms, whether ALK-dependent or ALK-independent, remains a major challenge. The comprehensive understanding of these resistance mechanisms now guides the development of next-generation inhibitors and innovative therapeutic strategies, paving the way for increasingly personalized precision medicine.

A Poor Prognostic ALK Phenotype: A Review of Molecular Markers of Poor Prognosis in ALK Rearranged Nonsmall Cell Lung Cancer

BACKGROUND

Patients with nonsmall cell lung cancer with anaplastic lymphoma kinase (ALK) rearrangements derive a significant and durable clinical benefit from tyrosine kinase inhibitors (TKIs). However, early progression/death on treatment occurs in a subset of patients, which we term the poor prognostic ALK phenotype. This review aims to summarize the known molecular mechanisms that underlie this phenotype with a focus on variant 3 and TP53 mutations.

METHODS

A scoping review was performed using scientific databases such as Ovid Medline, Ovid Embase, and Cochrane Central Register of Controlled Trials. Studies included molecular markers of poor prognosis, with a focus on TP53 mutations, variant 3 re-arrangements, and poor clinical response to TKIs.

RESULTS

Of 4371 studies screened, 108 were included. Numerous studies implicated a negative prognostic role of variant 3, likely mediated through the acquisition of on-target resistance mutations and TP53 mutations which are associated with greater chromosomal instability and mutational burden. Co-occurring variant 3 and TP53 mutations were associated with even worse survival. Other mediators of early resistance development include aberrations in cell cycle regulators and mutations in cell signaling pathways. Comprehensive genomic analysis from first-line TKI clinical trial data was unable to identify a singular genomic signature that underlies the poor prognostic phenotype but implicated a combination of pathways.

CONCLUSIONS

This scoping review highlights that the poor prognostic ALK phenotype is likely composed of a heterogeneous variety of genomic factors. There remains an unmet need for a genomic assay to integrate these various molecular markers to predict this ALK phenotype.

Comparing Genomic Profiles of ALK Fusion-Positive and ALK Fusion-Negative Nonsmall Cell Lung Cancer Patients

Background  Anaplastic lymphoma kinase ( ALK ) fusion events account for 3 to 7% of genetic alterations in patients with nonsmall cell lung cancer (NSCLC). This study aimed to explore the landscape of ALK fusion-positive and ALK fusion-negative in a large cohort of NSCLC patients. Methods  The formalin-fixed paraffin-embedded specimens of NSCLC patients who underwent next-generation sequencing from 2020 to 2023 in Yinfeng Gene Technology Co., Ltd. Clinical laboratory were included in this study. Results  In the current study, a total of 180 (3.20%) patients tested positive for ALK fusions in 5,622 NSCLC samples. Within the ALK -positive cohort, a total of 228 ALK fusions were identified. Furthermore, five novel ALK fusion partners, including DAB1-ALK , KCMF1-ALK , KIF13A-ALK , LOC643770-ALK , and XDH-ALK were identified. In cases with ALK fusion-positive, TP53 alterations were the most prevalent (26.3%), followed by CDKN2A (8.4%), epidermal growth factor receptor ( EGFR , 5.6%), and ALK (5.6%). By contrast, EGFR alterations were most prevalent (51%) in patients with ALK fusion-negative NSCLC, followed by TP53 (42.7%), KRAS (11.6%), and CDKN2A (11.3%). A total of 10 cases where ALK fusion co-occurred with EGFR mutations were also identified. Notably, the ALK fusion positivity rate was higher in younger patients ( p  < 0.0001) and in female patients ( p  = 0.0429). Additionally, positive ALK test results were more prevalent in patients with high programmed death-ligand 1 expression, especially when applying a 50% cutoff. Conclusions  Collectively, these findings offer valuable genomic insights that could inform the personalized clinical care of patients with NSCLC harboring ALK fusions within the context of precision medicine.

First-line immunotherapy for lung cancer with MET exon 14 skipping and the relevance of TP53 mutations

BACKGROUND

The efficacy of checkpoint inhibitors for non-small cell lung cancer (NSCLC) with MET exon 14 skipping (METΔ14ex) remains controversial.

MATERIALS AND METHODS

110 consecutive METΔ14ex NSCLC patients receiving first-line chemotherapy (CHT) and/or immunotherapy (IO) in 10 German centers between 2016-2022 were analyzed.

RESULTS

Combined CHT-IO was given to 35/110 (32%) patients, IO alone to 43/110 (39%), and CHT to 32/110 (29%) upfront. Compared to CHT, CHT-IO showed longer progression-free survival (median PFS 6 vs. 2.5 months, p = 0.004), more objective responses (ORR 49% vs. 28%, p = 0.086) and numerically longer overall survival (OS 16 vs. 10 months, p = 0.240). For IO monotherapy, OS (14 vs. 16 months) and duration of response (26 vs. 22 months) were comparable to those of CHT-IO. Primary progressive disease (PD) was more frequent with IO compared to CHT-IO (13/43 vs. 3/35, p = 0.018), particularly for never-smokers (p = 0.041). Higher PD-L1 TPS were not associated with better IO outcomes, but TP53 mutated tumors showed numerically improved ORR (56% vs. 32%, p = 0.088) and PFS (6 vs. 3 months, p = 0.160), as well as longer OS in multivariable analysis (HR=0.54, p = 0.034) compared to their wild-type counterparts. Any second-line treatment was administered to 35/75 (47%) patients, with longer survival for capmatinib or tepotinib compared to crizotinib (PFS 10 vs. 3 months, p = 0.013; OS 16 vs. 13 months, p = 0.270).

CONCLUSION

CHT-IO is superior to CHT, and IO alone also effective for METΔ14ex NSCLC, especially in the presence of TP53 mutations and independent of PD-L1 expression, but never-smokers are at higher risk of primary PD.

Impact of Concurrent Genomic Alterations on Clinical Outcomes in Patients With ALK-Rearranged NSCLC

INTRODUCTION

ALK tyrosine kinase inhibitors have exhibited promising activity against advanced ALK-rearranged NSCLC. However, co-occurring genetic alterations, such as CDKN2A/B or TP53, may negatively affect the efficacy of targeted therapies.

METHODS

From December 2017 to December 2022, this study cohort analyzed next-generation sequencing data of 116 patients with metastatic ALK-rearranged NSCLC from five Latin American cancer centers. Clinicopathologic and molecular features were associated with clinical outcomes and risk of brain metastasis (BrM) in patients with and without concurrent somatic alterations.

RESULTS

All patients (N = 116) received a second-generation ALK tyrosine kinase inhibitor, and alectinib was selected in 87.2% of cases. Coalterations occurred in 62% of the cases; the most frequent were TP53 mutations (27%) and CDKN2A/B loss (18%). The loss of CDKN2A/B was associated with an increased risk of BrM, with a cumulative incidence of 33.3% versus 7.4% in the non-coaltered subgroup. Compared with patients without coalterations, patients with concurrent CDKN2A/B loss (n = 21) had a shorter median progression-free survival (10.2 versus 34.2 mo, p < 0.001) and overall survival (26.2 versus 80.7 mo, p < 0.001). In the multivariate analysis, co-occurring CDKN2A/B loss was associated with poorer progression-free survival and OS despite the presence of other somatic coalterations, TP53 mutations, BrM, and Eastern Cooperative Oncology Group Performance Status.

CONCLUSIONS

This study confirmed the worse prognostic value, which depicted co-occurring alterations in patients with ALK rearrangement. CDKN2A/B loss was substantially associated with worse outcomes and a higher risk of brain metastases. The evidence presented in our study may help select patients with ALK-positive tumors suitable for treatment escalation and closer brain follow-up.

High PD-L1 Expression Correlates with an Immunosuppressive Tumour Immune Microenvironment and Worse Prognosis in ALK-Rearranged Non-Small Cell Lung Cancer

High tumour programmed cell death-ligand 1 (PD-L1) expression is associated with poor progression-free survival (PFS) after tyrosine kinase inhibitor (TKI) therapy in ALK-rearranged non-small cell lung cancer (NSCLC). However, the characteristics of the tumour microenvironment (TME) and their prognostic values in ALK-rearranged NSCLC are unknown. Here, we collected tumour tissues from pretreated ALK-rearranged NSCLC patients, immunohistochemical staining was used to assess PD-L1 expression, and tumour-infiltrating immune cells were determined via multiplex immunofluorescence staining (mIF). Our data showed that the median values of PFS for the high PD-L1 group and low PD-L1 group who received ALK-TKI treatment were 4.4 and 16.4 months, respectively (p = 0.008). The median overall survival (OS) of the two groups was 24.0 months and not reached, respectively (p = 0.021). Via univariate and multivariate analyses, a high PD-L1 expression and a worse ECOG PS were determined to be independent prognostic factors of OS (HR = 3.35, 95% CI: 1.23-9.11, p = 0.018; HR = 6.42, 95% CI: 1.45-28.44, p = 0.014, respectively). In addition, the high PD-L1 group had increased Tregs and exhausted CD8+ T cells in both the tumour and stroma (all p < 0.05). High PD-L1 expression was an adverse predictive and prognostic biomarker for ALK-rearranged NSCLC. The characteristics of the TME in patients with high PD-L1 expression were shown to have an immunosuppressive status.

Case report: anaplastic lymphoma kinase (ALK) rearranged adenocarcinoma with high level of microsatellite instability response to pembrolizumab

The presence of anaplastic lymphoma kinase (ALK) rearrangement is reported to be related to the lack of efficacy of immune checkpoint inhibitors (ICIs). High levels of microsatellite instability (MSI-high) are important biomarkers of ICIs, particularly in colorectal cancer. The therapeutic effect of ICIs for MSI-high NSCLC is uncertain because of the rarity of these tumors. Here we report a case of ALK rearranged NSCLC with MSI-high. A 48-year-old male was diagnosed with lung adenocarcinoma, cT4N3M1a, stage IVA with ALK rearrangement, high PD-L1 expression with a tumor proportion score (TPS) of 100%, and MSI-high. The patient was treated with alectinib as the first-line therapy but progressed at five months with left atrial invasion re-expansion. The patient discontinued alectinib and was switched to pembrolizumab monotherapy. After two months, left atrial invasion significantly decreased. The patient continued pembrolizumab for a year without noticeable adverse events, and tumor shrinkage persisted. This case supports the efficacy of ICIs for MSI-high NSCLC, even in the presence of ALK rearrangement.

Silibinin Overcomes EMT-Driven Lung Cancer Resistance to New-Generation ALK Inhibitors

Epithelial-to-mesenchymal transition (EMT) may drive the escape of ALK-rearranged non-small-cell lung cancer (NSCLC) tumors from ALK-tyrosine kinase inhibitors (TKIs). We investigated whether first-generation ALK-TKI therapy-induced EMT promotes cross-resistance to new-generation ALK-TKIs and whether this could be circumvented by the flavonolignan silibinin, an EMT inhibitor. ALK-rearranged NSCLC cells acquiring a bona fide EMT phenotype upon chronic exposure to the first-generation ALK-TKI crizotinib exhibited increased resistance to second-generation brigatinib and were fully refractory to third-generation lorlatinib. Such cross-resistance to new-generation ALK-TKIs, which was partially recapitulated upon chronic TGFβ stimulation, was less pronounced in ALK-rearranged NSCLC cells solely acquiring a partial/hybrid E/M transition state. Silibinin overcame EMT-induced resistance to brigatinib and lorlatinib and restored their efficacy involving the transforming growth factor-beta (TGFβ)/SMAD signaling pathway. Silibinin deactivated TGFβ-regulated SMAD2/3 phosphorylation and suppressed the transcriptional activation of genes under the control of SMAD binding elements. Computational modeling studies and kinase binding assays predicted a targeted inhibitory binding of silibinin to the ATP-binding pocket of TGFβ type-1 receptor 1 (TGFBR1) and TGFBR2 but solely at the two-digit micromolar range. A secretome profiling confirmed the ability of silibinin to normalize the augmented release of TGFβ into the extracellular fluid of ALK-TKIs-resistant NSCLC cells and reduce constitutive and inducible SMAD2/3 phosphorylation occurring in the presence of ALK-TKIs. In summary, the ab initio plasticity along the EMT spectrum may explain the propensity of ALK-rearranged NSCLC cells to acquire resistance to new-generation ALK-TKIs, a phenomenon that could be abrogated by the silibinin-driven attenuation of the TGFβ/SMAD signaling axis in mesenchymal ALK-rearranged NSCLC cells.

Response to treatment with an ALK-TKI in a patient with advanced lung adenocarcinoma with concurrent ALK fusion and high PD-L1 expression: A case report

RATIONALE

Previous studies have shown that PD-L1 TPS ≥50% in lung cancer rarely overlaps with driver oncogenes such as epidermal growth factor receptor and anaplastic lymphoma kinase (ALK). The initial gene detection of the patient in this study showed ALK fusion combined with high expression of PD-L1. We explored the treatment options for this patient.

PATIENT CONCERNS

A 34-year-old woman presented for the first time with "repeated fever and cough for 20 days." The patient denied any underlying medical history.

DIAGNOSIS

After a series of imaging examinations and needle biopsy, the patient was diagnosed as stage IV lung adenocarcinoma with multiple liver and bone metastases (EML4-ALK fusion, PD-L1 TPS 80%).

INTERVENTIONS

The patient was initially given alectinib targeted therapy. After progression, a second round of genetic testing was performed and the patient was detected to have both ALK fusion and BRAF mutation. The patient was then successively changed to treatment with ensatinib combined with dabrafenib, and lorlatinib combined with dabrafenib.

OUTCOMES

The initial efficacy evaluation of alectinib was PR, but its PFS was only 4 months. The patient only achieved an overall survival of 10 months.

LESSONS

Non-small cell lung cancer with an ALK fusion and high PD-L1 expression responds poorly to most current treatment options, with survival time after ALK-tyrosine kinase inhibitor treatment notably shorter than that of patients with an ALK fusion alone.