Echinoderm Microtubule-associated Protein-like 4 Research Articles

Clinical difference on the variants and co-mutation in a Chinese cohort with ALK-positive advanced non-small cell lung cancer.

Despite the generally favourable prognoses observed in patients with ALK-positive non-small cell lung cancer (NSCLC), there remains significant variability in clinical outcomes. The objective of this study is to enhance patient stratification by examining both the specific sites of gene fusion and the presence of co-occurring mutations. We collected retrospective clinical and pathological data on ALK-positive patients with locally advanced or metastatic disease. ALK fusion variants and concomitant mutations were identified through next-generation sequencing technology. We then assessed treatment efficacy via tumor response and survival metrics. This study included a total of 59 patients, with 49 harboring echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusions and 10 presenting with rare fusions. The median follow-up period was 33 months. Clinical outcomes between non-EML4-ALK and EML4-ALK patients were comparable. Among the EML4-ALK cohort, patients with longer variants (v1, v2, v8) demonstrated superior progression-free survival (PFS) (median PFS: 34 months vs. 11 months; hazard ratio [HR]: 2.28; P = 0.05) compared to those with shorter variants (v3, v5). Furthermore, patients treated with second-generation ALK inhibitors (ALKi) displayed a progression-free survival advantage (median PFS: not reached [NR] vs. 9 months; HR: 5.37; P = 0.013). Baseline TP53 co-mutation were linked with a substantially shorter OS (median OS,37 months vs. NR; HR 2.74; P = 0.047). In ALK+ NSCLC, longer EML4-ALK variants correlate with improved prognosis and enhanced response to second-generation ALKi, while TP53 co-mutations indicate a negative prognosis.

Response to lorlatinib rechallenge in a case of ALK-rearranged metastatic NSCLC with a resistance mutation to second generation TKIs.

Several anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) have been developed for the treatment of echinoderm microtubule-associated protein-like 4 (EML4)-ALK-rearranged non-small cell lung cancer (NSCLC), with the newer generation agents brigatinib, alectinib and lorlatinib showing prolonged responses. With the increasing number of target therapies available, the optimal sequence is yet to be defined, as resistance profiles may evolve over time and in response to sequential ALK inhibitors. Therefore, ALK-targeted strategies may be personalized based upon the presence of specific ALK resistance mutations. Here, we report on the case of a patient who has been treated with a sequence of three ALK TKIs after receiving diagnosis of ALK-rearranged metastatic NSCLC in 2015 and gained further benefit upon lorlatinib rechallenge after the acquisition of the G1202R resistance mutation to second generation TKIs. In this case, the first ALK resistance mutation detected after progression on first line TKI, the I1171N, is a common resistance mutation after alectinib and confers sensitivity to brigatinib, that the patient received afterwards with a long-term disease stability. The second ALK resistance mutation detected after a chemotherapy interval, the G1202R, is the most common resistance mutation after second generation ALK TKIs and has been associated with sensitivity to third generation TKIs, such as lorlatinib. This case of a patient with EML4-ALK-rearranged NSCLC shows that sequential treatment with next-generation ALK TKIs, including rechallenge, can induce profound remissions, even in heavily pretreated patients, and that ALK-targeted strategies may be personalized by considering the presence of distinct ALK resistance mutations.

Abstract 1657: Microfluidics-based screening platform identifies a novel therapeutic approach to targeting EML4-ALK driven cancers

Abstract To achieve proliferative dysregulation, a hallmark of cancer, tumor cells utilize a variety of mechanisms to maintain constitutive oncogenic signaling in the absence of extracellular cues. One such mechanism occurs in cells expressing the EML4-ALK fusion protein. This fusion, found in about 4% of non-small cell lung cancer (NSCLC), is a result of an inversion within chromosome 2, placing the 3’ end of the ALK (anaplastic lymphoma kinase) gene downstream of the 5’ end of the EML4 (echinoderm microtubule associated protein-like 4) gene. The resulting fusion protein contains the oligomerization domain and additional disordered sequence elements of EML4 upstream of a functional ALK kinase domain. EML4-ALK is a critical driver for these tumors, promoting aberrant ALK-dependent oncogenic signaling. While tumors harboring the EML4-ALK fusion initially respond to ALK tyrosine kinase inhibitors (TKIs), resistance remains a significant clinical challenge requiring new therapeutic approaches. Recently, it has come to be understood that rather than responding through extracellular proliferative cues, the EML4-ALK fusion protein elicits constitutive ALK signaling through the formation of cytoplasmic biomolecular condensates. These condensates are the result of phase separation and have been shown to be causal for disease phenotypes in cell and animal models driven by EML4-ALK, establishing condensate modulation as a novel means by which to treat TKI-resistant tumors. Here, we have developed a novel proprietary microfluidics-based high throughput screening platform (termed PhaseScanTM) to identify small-molecule modulators of EML4-ALK condensates. Using this technology, we identified compounds that disrupt EML4-ALK condensates in vitro and in cells through a novel mechanism, distinct from that of known ALK TKIs, providing utility in both TKI-resistant as well as TKI-naïve tumors. Further profiling of the mechanism of action (MoA) revealed specific modification within the disordered region of EML4, disruption of EML4 oligomerization, and defective ALK signaling in cancer cells. Thus, our PhaseScanTM methodology enabled the identification of novel, functionally active chemical matter that would have otherwise been challenging to identify utilizing any conventional hit identification methodology. Citation Format: Richard C. Centore, Matthew Watson, Julia Doh, Jerome Cattin, Cinzia Sgambato, Amal Alex, Janhavi Sawant, Prathima Radhakrishnan, Jasmine Cornish, Alex Howarth, Nagakumar Bharatham, William E. Arter, Seema Qamar, Kadi L. Saar, Douglas Williamson, Andrew Seeber, Neils Groenewegen, Magdalena Czekalska, Tadas Kartanas, Niklas Ermann, Ahmed Taher, Tuomas Knowles, Shilpi Arora. Microfluidics-based screening platform identifies a novel therapeutic approach to targeting EML4-ALK driven cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1657.

Abstract 351: Quaratusugene ozeplasmid mediated TUSC2 upregulation in EML4-ALK bearing non-small cell lung carcinoma can induce cellular apoptosis

Abstract Anaplastic Lymphoma Kinase (ALK), a potent oncogenic driver in Non-Small Cell Lung Carcinoma (NSCLC), is found to be rearranged and fused to Echinoderm microtubule-associated protein-like 4 (EML4), contributing to approximately 5% of NSCLC as a distinct clinicopathological subset. Tumors bearing the EML4-ALK fusion are sensitive to ALK Tyrosine Kinase Inhibitors (TKIs), that form the first and second line of treatment for these patients. However, ALK+ lung cancers develop resistance to ALK inhibitors, creating the need for newer treatment strategies in ALK+ NSCLC. Tumor Suppressor Candidate 2 (TUSC2) is a tumor suppressor gene that is known to have low endogenous expression in NSCLC in general but data on TUSC2 in ALK+ lung cancers are not available. Quaratusugene ozeplasmid, developed by Genprex, is an immunogene therapy that upregulates TUSC2 expression in cancer cells by delivering the functional TUSC2 gene. It consists of the TUSC2 gene expressing plasmid encapsulated in non viral lipid nanoparticles. We evaluated TUSC2 expression in 3 ALK+ cell lines, both before and after exposure to quaratusugene ozeplasmid and to a TUSC2-containing plasmid. Controls were non-ALK+ cell lines and transfection with a plasmid containing no insert. Our studies in ALK+ lung cancer reveal that overexpressing TUSC2 using quaratusugene ozeplasmid treatment of ALK+ lung cancer cell lines is able to suppress colony formation by 50%, the effect being more significant than using a TUSC2-containing plasmid. Furthermore, we have observed a robust pro-apoptotic response to TUSC2 expression in ALK+ NSCLC, as both quaratusugene ozeplasmid and TUSC2-containing plasmid induced an increase in caspase 3/7 activity in the cancer cells, accompanied by an increase in cleaved PARP expression. Taken together, our data indicate that overexpression of TUSC2 in ALK+ NSCLC cell lines with quaratusugene ozeplasmid or with TUSC2-containing plasmid is effective in decreasing growth and proliferation through the activation of apoptotic pathways and warrants further investigation as an anti-ALK NSCLC strategy. Citation Format: Ananya Banerjee, Neeke Busette, Mark S. Berger, Matthew B. Soellner, Angel Qin, Sofia D. Merajver, Nathan M. Merrill. Quaratusugene ozeplasmid mediated TUSC2 upregulation in EML4-ALK bearing non-small cell lung carcinoma can induce cellular apoptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 351.

Expansion of targeted degradation by Gilteritinib-Warheaded PROTACs to ALK fusion proteins

Proteolysis targeting chimeras (PROTACs) induce the ubiquitination and subsequent proteasomal degradation of targeted proteins. Numerous PROTACs have emerged as promising drug candidates for various disease-related proteins. This study investigates PROTACs targeted to degrade anaplastic lymphoma kinase (ALK) fusion proteins, which are implicated in diseases such as anaplastic large cell lymphoma and non-small cell lung cancer. We recently reported the development of a gilteritinib-warheaded PROTAC to target and degrade the Fms-like tyrosine kinase 3 (FLT3) protein. Gilteritinib is a tyrosine kinase inhibitor that targets FLT3, and recent studies have revealed that it also functions as an ALK inhibitor. We conducted a structure–activity relationship (SAR) study and expanded the range of target proteins for gilteritinib-warheaded PROTACs to include echinoderm microtubule-associated protein-like 4 (EML4)-ALK and nucleophosmin (NPM)-ALK, in addition to FLT3. Our SAR study utilized three types of ligands for E3 ligase— inhibitor of apoptosis protein (IAP), cereblon (CRBN), and von Hippel-Lindau (VHL)— in the PROTAC designs and we observed varied efficacy in the degradation of target proteins. The CRBN-based PROTAC effectively reduced the protein expression of FLT3, EML4-ALK, and NPM-ALK. The IAP-based PROTAC reduced expression of both FLT3 and EML4-ALK proteins but not that of NPM-ALK, while the VHL-based PROTAC was ineffective against all target proteins. Several ALK-targeted PROTACs have already been developed using CRBN or VHL as E3 ligase, but this is the first report of an IAP-based ALK degrader. The length of the linker structure utilized in PROTAC also had a significant effect on their efficacy and activity. PROTACs formed with shorter linkers demonstrated an enhanced degradation activity to target proteins compared with those formed with longer linkers. These findings provide valuable insight for the development of effective PROTACs to target and degrade ALK fusion proteins.

ALK F1174S mutation impairs ALK kinase activity in EML4-ALK variant 1 and sensitizes EML4-ALK variant 3 to crizotinib.

To assess the influence of F1174S mutation on kinase activity and drug sensitivity of the echinoderm microtubule-associated protein-like 4 (EML4) and anaplastic lymphoma kinase (ALK) fusion (EML4-ALK) variants 1 and 3. We constructed mammalian expression plasmids of both wildtype and F1174 mutant EML4-ALK variants 1 and 3, and then characterized them with cell models by performing immunoblotting, neurite outgrowth assay, focus formation assay as well as protein stability assay. Drug sensitivity to ALK tyrosine kinase inhibitors was also compared between wildtype and F1174 mutant EML4-ALK fusions. In addition, we characterized the effect of different F1174 kinase domain mutations in the context of EML4-ALK fusions. In contrast to the oncogenic ALK-F1174S mutation that has been reported to be activating in the context of full-length ALK in neuroblastoma, EML4-ALK (F1174S) variant 1 exhibits impaired kinase activity leading to loss of oncogenicity. Furthermore, unlike the previously reported F1174C/L/V mutations, mutation of F1174 to S sensitizes EML4-ALK variants 3a and 3b to crizotinib. These findings highlight the complexity of drug selection when treating patients harboring resistance mutations and suggest that the F1174S mutation in EML4-ALK variant 1 is likely not a potent oncogenic driver. Additional oncogenic driver or other resistance mechanisms should be considered in the case of EML4-ALK variant 1 with F1174S mutation.

Efficacy of alectinib in lung adenocarcinoma patients with different anaplastic lymphoma kinase (ALK) rearrangements and co-existing alterations-a retrospective cohort study.

Alectinib significantly improves survival of non-small cell lung cancer (NSCLC) patients with anaplastic lymphoma kinase (ALK)-rearrangement. In this study, we analyzed the effects of different ALK rearrangements and co-mutations on the efficacy of alectinib. Using the electronic medical record system, we reviewed in terms of clinical and pathological features patients with advanced (IIIB/IV stage) ALK-rearranged NSCLC at Shanghai Chest Hospital between January 2018 and December 2021 who were treated with alectinib in first or second line and were assessed for objective response rate (ORR), disease control rate (DCR), and progression-free survival (PFS). A total of 66 patients were enrolled in the study, and 17 types of ALK rearrangements were detected, of which five types of ALK rearrangements responded well to alectinib. We classified ALK-rearrangements into four main types, namely echinoderm microtubule-associated protein-like 4 (EML4)-ALK (E6:A20), EML4-ALK (E13:A20), EML4-ALK (E20:A20), and others. There was no significant difference in ORR and DCR of these types (ORR: 31.3% vs. 13.0% vs. 18.2% vs. 17.6%, P=0.575; DCR: 93.8% vs. 95.6% vs. 100.0% vs. 88.2%, P=0.627). The 3-year PFS rates were 25.0% (4/16) vs. 13.0% (3/23) vs. 27.3% (3/11) vs. 18.8% (3/16) for EML4-ALK (E6:A20), EML4-ALK (E13:A20), EML4-ALK (E20:A20), and others, respectively (P=0.725). The results of co-mutation analysis showed that the median PFS (mPFS) for patients with tumors harboring TP53 mutations was 30.4 months, significantly shorter than that of patients with tumors without co-mutations and whose mPFS was not mature (P=0.026). TSC1 co-mutation was also identified as a detrimental factor in outcome, with a DCR of 60% vs. 100% (P=0.031), mPFS of 30.4 months vs. not applicable (P=0.160) in patients with vs. those without this co-mutation, respectively. The efficacy of alectinib in patients with brain metastases is comparable to that in patients without distant organ metastases. There were two cases with specific fusion types that also responded to alectinib; namely, double ALK-rearrangements: EML4-ALK (E13:A20) and MSH2-ALK (M7:A20), and with a rare fusion partner, SPECC1L-ALK (S8:A20). Their PFS were 8.7 and 38.0 months, respectively. In this study, the efficacy of alectinib in different types of ALK-rearrangements varied slightly. TP53 and TSC1 co-mutations were identified as detrimental factors affecting efficacy. This study provides references for the response to alectinib in patients with different types of ALK rearrangements and co-mutation.

First-line treatment option for patients with ALK-positive metastatic NSCLC

Non-small cell lung cancer (NSCLC) that occupies a leading place in the pattern of cancer incidence and mortality is a highly heterogeneous group of diseases. The presence of a wide spectrum of NSCLC driver mutations has led to a fundamentally different understanding of the treatment strategy for this cohort of patients and a significant improvement in long-term oncological outcomes, even in the metastatic process. Chromosomal rearrangements involving the anaplastic lymphoma kinase (ALK) gene loci on chromosome 2 are found in approximately 3–5% of patients with metastatic NSCLC (mNSCLC) and in most cases are associated not only with a number of specific clinical features, but also with high sensitivity to targeted therapy with tyrosine kinase inhibitors (TKI). Crizotinib was the first approved ALK inhibitor, but although most patients achieved response within the first two years after start of the treatment, disease progression occurred often due to intracranial injury. The development of second-(ceritinib, alectinib), brigatinib and third-generation (lorlatinib) drugs has led to a statistically significant improvement in progression-free survival (PFS) rates, as well as control over intracranial manifestations of the disease and a change in the initial treatment strategy for these patients. In addition, new-generations of TKIs were developed to solve the problem of acquired resistance, as well as to achieve the best outcomes in the presence of such unfavourable factors as the presence of a TP53 mutation and/or ALK inhibitor low-sensitive translocation variants of the intracellular kinase domain of EML4 (echinoderm microtubule‐associated protein‐like 4)‐ALK (anaplastic lymphoma kinase) protein. Thus, advances in the therapeutic options for ALK-positive mNSCLC has completely changed the course of the disease, resulting in a significant increase in overall survival (OS) rates not only with the sequential use of different generation TKIs, but also with the choice of the most effective first-line option. In this article, we present an analysis of data on the efficacy and toxicity of lorlatinib, a third-generation TKI, in the first-line treatment for ALK+ mNSCLC.

EML4-ALK fusion protein in Lung cancer cells enhances venous thrombogenicity through the pERK1/2-AP-1-tissue factor axis

BackgroundAccumulating evidence links the echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) rearrangement to venous thromboembolism (VTE) in non-small cell lung cancer (NSCLC) patients. However, the corresponding mechanisms remain unclear.MethodHigh-throughput sequencing analysis of H3122 human ALK-positive NSCLC cells treated with ALK inhibitor/ dimethyl sulfoxide (DMSO) was performed to identify coagulation-associated differential genes between EML4-ALK fusion protein inhibited cells and control cells. Sequentially, we confirmed its expression in NSCLC patients’ tissues and in the plasma of a subcutaneous xenograft mouse model. An inferior vena cava (IVC) ligation model was used to assess clot formation potential. Additionally, pathways involved in tissue factor (TF) regulation were explored in ALK-positive cell lines H3122 and H2228. Statistical significance was determined by Student t-test and one-way ANOVA using SPSS.ResultsSequencing analysis identified a significant downregulation of TF after inhibiting EML4-ALK fusion protein activity in H3122 cells. In clinical NSCLC cases, TF expression was increased especially in ALK-positive NSCLC tissues. Meanwhile, H3122 and H2228 with high TF expression exhibited shorter plasma clotting time and higher TF activity versus ALK-negative H1299 and A549 in cell culture supernatant. Mice bearing H2228 tumor showed a higher concentration of tumor-derived TF and TF activity in plasma and the highest adjusted IVC clot weights. Limiting EML4-ALK protein phosphorylation downregulated extracellular regulated protein kinases 1/2 (ERK1/2)-activating the protein-1(AP-1) signaling pathway and thus attenuated TF expression.ConclusionEML4-ALK fusion protein may enhance venous thrombogenicity by regulating coagulation factor TF expression. There was potential involvement of the pERK1/2-AP-1 pathway in this process.

Superior clinical outcomes in patients with non-small cell lung cancer harboring multiple ALK fusions treated with tyrosine kinase inhibitors.

Patients with non-small cell lung cancer (NSCLC) harboring anaplastic lymphoma kinase (ALK) fusions may benefit from ALK-tyrosine kinase inhibitors (ALK-TKIs). However, few studies have analyzed the clinical outcome in patients harboring multiple ALK fusions, including double or triple ALK fusions. Here, our study aimed to analyze the impact of harboring multiple ALK fusions on the efficacy of receiving ALK-TKIs in NSCLC patients. A total of 125 patients with ALK-rearranged NSCLC detected by targeted capture DNA-based next-generation sequencing (NGS) at West China Hospital were enrolled. The literature on patients harboring multiple ALK fusions was systematically reviewed. The clinical response to ALK-TKIs was evaluated according to ALK fusion patterns in 62 patients: 56 from our center and 6 from the literature. Among the 125 patients, a single canonical echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion was detected in 65.6% (82/125), a single non-EML4-ALK fusion was detected in 13.6% (17/125), and multiple ALK fusions were detected in 20.8% (26/125). Among the 62 patients with ALK fusion treated with ALK-TKIs, the median progression-free survival (PFS) was significantly longer in patients with multiple ALK fusions than in those with a single ALK fusion (26.9 vs. 11.2 months, P=0.009), irrespective of brain metastasis, type of TKI drug, and treatment lines. The multiple ALK fusion group also tended to have a longer overall survival (OS) (P=0.26). Multivariate Cox regression analysis revealed that harboring multiple ALK fusions had the potential to be an independent predictor of better PFS for ALK-positive NSCLC [hazard ratio (HR) =0.490; 95% confidence interval (CI): 0.229-1.049]. Harboring multiple ALK fusions could serve as an independent predictive marker of better clinical outcome for patients with NSCLC and ALK rearrangement who have received ALK-TKIs treatment.

EML4-ALK biology and drug resistance in non-small cell lung cancer: a new phase of discoveries.

Anaplastic lymphoma kinase (ALK) can be driven to oncogenic activity by different types of mutational events such as point-mutations, for example F1174L in neuroblastoma, and gene fusions, for example with echinoderm microtubule-associated protein-like 4 (EML4) in non-small cell lung cancer (NSCLC). EML4-ALK variants result from different breakpoints, generating fusions of different sizes and properties. The most common variants (Variant 1 and Variant 3) form cellular compartments with distinct physical properties. The presence of a partial, probably misfolded beta-propeller domain in variant 1 confers solid-like properties to the compartments it forms, greater dependence on Hsp90 for protein stability and higher cell sensitivity to ALK tyrosine kinase inhibitors (TKIs). These differences translate to the clinic because variant 3, on average, worsens patient prognosis and increases metastatic risk. Latest generation ALK-TKIs are beneficial for most patients with EML4-ALK fusions. However, resistance to ALK inhibitors can occur via point-mutations within the kinase domain of the EML4-ALK fusion, for example G1202R, reducing inhibitor effectiveness. Here, we discuss the biology of EML4-ALK variants, their impact on treatment response, ALK-TKI drug resistance mechanisms and potential combination therapies.

Coexistence of a novel SETD2-ALK, EML4-ALK double-fusion in an advanced lung adenocarcinoma patient after alectinib resistant and response to immunotherapy combined with chemotherapy: a case report

The single echinoderm microtubule-associated protein-like 4 (EML4) gene and anaplastic lymphoma kinase (ALK) gene fusion is the most common variant of ALK rearrangements in non-small cell lung cancer (NSCLC). Herein, we firstly report that coexistence of a novel histone methyltransferase (SETD2)-ALK, EML4-ALK double-fusion is sensitive to alectinib as first-line therapy, and response to immunotherapy combined with chemotherapy after resistant. The patient responded to alectinib as a first-line therapy and achieved progression-free survival (PFS) for 26 months. After resistance, liquid biopsy showed that the reason of drug resistance was the disappearance of SETD2-ALK and EML4-ALK fusion variants. In addition, chemotherapy combined with immunotherapy subsequently achieved a survival benefit of more than 25 months. Therefore, alectinib may be a viable therapeutic option for NSCLC patients with double ALK fusion and immunotherapy combined with chemotherapy may be a viable therapeutic option when double ALK fusion loss may be the mechanism of alectinib resistance.

Molecular Anatomy of the EML4-ALK Fusion Protein for the Development of Novel Anticancer Drugs.

The EML4 (echinoderm microtubule-associated protein-like 4)-ALK (anaplastic lymphoma kinase) fusion gene in non-small-cell lung cancer (NSCLC) was first identified in 2007. As the EML4-ALK fusion protein promotes carcinogenesis in lung cells, much attention has been paid to it, leading to the development of therapies for patients with NSCLC. These therapies include ALK tyrosine kinase inhibitors and heat shock protein 90 inhibitors. However, detailed information on the entire structure and function of the EML4-ALK protein remains deficient, and there are many obstacles to overcome in the development of novel anticancer agents. In this review, we describe the respective partial structures of EML4 and ALK that are known to date. In addition to their structures, noteworthy structural features and launched inhibitors of the EML4-ALK protein are summarized. Furthermore, based on the structural features and inhibitor-binding modes, we discuss strategies for the development of novel inhibitors targeting the EML4-ALK protein.

Testing modalities for ALK-driven lung cancer: A narrative review

ABSTRACT Anaplastic lymphoma kinase (ALK) rearranged non-small-cell lung cancer (NSCLC) comprises a distinct molecular entity with a reported global prevalence of 5–7%. The development and rapid approvals of small molecule ALK tyrosine kinase inhibitors (TKIs) have led to the development of diagnostic strategies with robust methodology and superior attributes. Owing to myriad alterations which can be present in the ALK gene in NSCLC, it is important to understand the principal attributes as well as limitations of each to aid in optimal therapeutic decision making. To prepare this review, we used the keywords, “ALK detection,” “ALK NGS,” “ALK TKI,” and “EML4 (echinoderm microtubule-associated protein-like 4)-ALK,” to search within scientific databases like Scopus, PubMed, and Embase. We chose 55 articles that we identified from this search. Detection of ALK is an essential frontline diagnostic test as per all international and national recommendations. The various modalities available include immunohistochemistry, fluorescence in situ hybridization, reverse transcriptase polymerase chain reaction, and DNA/RNA-based next-generation sequencing. Each has its own advantages and limitations with respect to test metrics like sensitivity and specificity, as well as ease of use, availability, and cost. This is a detailed review of these various techniques and their attributes.

Molecular determinants of clinical outcomes for anaplastic lymphoma kinase–positive non-small cell lung cancer in Chinese patients: A retrospective study

Gene complexity affects the clinical outcomes of anaplastic lymphoma kinase (ALK)-rearranged non-small cell lung cancer (NSCLC). Here, we reviewed the medical records of patients with NSCLC between September 2015 and December 2020 in a single institution. We examined the clinical and genomic predictors of these outcomes using multivariate Cox proportional hazards analysis. Overall, 105 patients with ALK-rearranged NSCLC were included. Echinoderm microtubule-associated protein-like 4 (EML4) was the predominant fusion partner (96.2%). Five patients (4.8%) had non-EML4 fusion partners; three had novel partners. EML4::ALK variant 3 (36.5%) was predominant. One patient had the following three subtypes: E13::A20, E6ins33::A20, and E20::A20. Median progression-free survival (PFS), but not overall survival (OS), was significantly different between patients with variants 3 and 1. TP53 was the most common concomitant mutation (21.4%). The presence of TP53 mutations was associated with shorter PFS among patients who received ALK-TKI. Patients with concomitant oncogene mutations presented significantly shorter OS and PFS than those with only ALK rearrangement. In a multivariate Cox regression model, concomitant oncogene mutations and variant 3 carrier status were prognostic factors for PFS, whereas baseline brain metastasis was a prognostic factor for OS.

Therapeutic Advances of Rare ALK Fusions in Non-Small Cell Lung Cancer.

Non-small cell lung cancer (NSCLC) accounts for approximately 85% of all lung cancer cases and is the leading cause of cancer-related death. Despite advances in chemotherapy and immunotherapy, the prognosis for advanced patients remains poor. The discovery of oncogenic driver mutations, such as anaplastic lymphoma kinase (ALK) mutations, means that a subset of patients has opportunities for targeted therapy. With the improvement of genetic testing coverage, more and more ALK fusion subtypes and ALK partners have been discovered, and more than 90 rare ALK fusion subtypes have been found in NSCLC. However, unlike the common fusion, echinoderm microtubule-associated protein-like 4 (EML4)-ALK, some rare ALK fusions such as striatin (STRN)-ALK and huntingtin interacting protein 1 (HIP1)-ALK, etc., the large-scale clinical data related to its efficacy are still immature. The clinical application of ALK-tyrosine kinase inhibitors (ALK-TKIs) mainly depends on the positivity of the ALK gene, regardless of the molecular characteristics of the fusion partner. Recent clinical studies in the ALK-positive NSCLC population have demonstrated differences in progression-free survival (PFS) among patients based on different ALK fusion subtypes. This article will introduce the biological characteristics of ALK fusion kinase and common detection methods of ALK fusion and focus on summarizing the differential responses of several rare ALK fusions to ALK-TKIs, and propose corresponding treatment strategies, so as to better guide the application of ALK-TKIs in rare ALK fusion population.

Fibroblast growth factor receptor 3 overexpression mediates ALK inhibitor resistance in ALK-rearranged non-small cell lung cancer.

The rearrangement of anaplastic lymphoma kinase (ALK) occurs in 3%-5% of patients with non-small cell lung cancer (NSCLC) and confers sensitivity to ALK-tyrosine kinase inhibitors (TKIs). For the treatment of patients with ALK-rearranged NSCLC, various additional ALK-TKIs have been developed. Ceritinib is a second-generation ALK-TKI and has shown great efficacy in the treatment of patients with both newly diagnosed and crizotinib (a first-generation ALK-TKI)-refractory ALK-rearranged NSCLC. However, tumors can also develop ceritinib resistance. This may result from secondary ALK mutations, but other mechanisms responsible for this have not been fully elucidated. In this study, we explored the mechanisms of ceritinib resistance by establishing ceritinib-resistant, echinoderm microtubule-associated protein-like 4 (EML4)-ALK-positive H3122 cells and ceritinib-resistant patient-derived cells. We identified a mechanism of ceritinib resistance induced by bypass signals that is mediated by the overexpression and activation of fibroblast growth factor receptor 3 (FGFR3). FGFR3 knockdown by small hairpin RNA or treatment with FGFR inhibitors was found to resensitize the resistant cells to ceritinib in vitro and in vivo. FGFR ligands from either human serum or fetal bovine serum were able to activate FGFR3 and induce ceritinib resistance. A detailed analysis of ceritinib-resistant patient-derived specimens confirmed that tyrosine-protein kinase Met (cMET) amplification induces ceritinib resistance. Amplified cMET counteractivated EGFR and/or Her3 and induced ceritinib resistance. These results reveal multiple ceritinib resistance mechanisms and suggest that ceritinib resistance might be overcome by identifying precise resistance mechanisms.

EP16.03-012 Novel Human-derived EML4-ALK Fusion cell lines identify ribonucleotide reductase RRM2 as a Target of Activated ALK in NSCLC

Echinoderm microtubule-associated protein-like 4 (EML4)-Anaplastic Lymphoma Kinase (ALK) rearrangements occur in 7% to 10% of lung adenocarcinomas and are targets for treatment with tyrosine kinase inhibitors. Here we have developed three novel EML4-ALK-positive patient-derived Non-Small-Cell-Lung-Cancer (NSCLC) cancer cell lines, CUTO8 (variant 1), 9 (variant 1), and 29 (variant 3), and included a fourth ALK-positive cell line YU1077 (EML4-ALK variant 3) to study ALK-positive signaling and responses.

Integrated analysis of the clinical consequence and associated gene expression of ALK in ALK-positive human cancers

Anaplastic lymphoma kinase (ALK) is a tyrosine kinase receptor that is genetically altered in several cancers, including NSCLC, melanoma, lymphoma, and other tumors. Although ALK is associated with various cancers, the relationship between ALK expression and patient prognosis in different cancers is poorly understood. Here, using multidimensional approaches, we revealed the correlation between ALK expression and the clinical outcomes of patients with LUAD, melanoma, OV, DLBC, AML, and BC. We analyzed ALK transcriptional expression, patient survival rate, genetic alteration, protein network, and gene and microRNA (miRNA) co-expression. Compared to that in normal tissues, higher ALK expression was found in LUAD, melanoma, and OV, which are associated with poor patient survival rates. In contrast, lower transcriptional expression was found to decrease the survival rate of patients with DLBC, AML, and BC. A total of 202 missense mutations, 17 truncating mutations, 7 fusions, and 3 in-frame mutations were identified. Further, 17 genes and 19 miRNAs were found to be exclusively co-expressed and echinoderm microtubule-associated protein-like 4 (EML4) was identified as the most positively correlated gene (log odds ratio >3). The gene ontology and signaling pathways of the genes co-expressed with ALK in these six cancers were also identified. Our findings offer a basis for ALK as a prognostic biomarker and therapeutic target in cancers, which will potentially contribute to precision oncology and assist clinicians in identifying suitable treatment options.

Abstract B032: Deciphering the mechanisms of environmentally mediated Alectinib resistance in ALK+NSCLC

Abstract Non-small cell lung cancer (NSCLC) is a devastating disease with a subset containing targetable oncogenic mutations that strongly benefit from targeted therapies. 3-7% of NSCLC patients bear an amplification of the Anaplastic lymphoma kinase (ALK) and Echinoderm microtubule-associated protein like 4 (EML4) fusion gene. These tumors typically show strong durable responses to first line therapy, Alectinib, an ALK tyrosine kinase inhibitors (ALK-TKIs). However, there is a high degree of patient-to-patient variability in the level of response to this drug; with some patients being innately resistant or less sensitive. Moreover, weak initial sensitivity to therapy has been linked to poor long-term responses with early acquisition of resistance. Thus, to improve clinical outcomes, we need to understand the mechanisms that lead to this reduced sensitivity to ALK inhibition. While, historically, reduced sensitivity to ALK TKI was thought to reflect cell intrinsic mechanisms, a growing body of evidence points to the importance of tumor microenvironmentally (TME) mediated mechanisms. We fortuitously encountered an observation of strong environment-mediated desensitization to Alectinib. We found that combining Alectinib with a small molecule inhibitor, Jumonji histone demethylase inhibitor, JIB04 in vitro overcomes tolerance, preventing ALK+NSCLC cells from developing resistance to Alectinib. Surprisingly, our validation experiments in mouse models revealed the opposite effect, where, JIB04 desensitized tumors to ALK inhibition. The disparity in the in vitro versus the in vivo response indicates the contribution of the TME in the reduced Alectinib sensitivity observed in vivo. The resistance phenotype in Alectinib+JIB04 treated mice was strongly associated with extensive inflammation in the tumor proximal tissues, along with higher circulating levels of inflammatory markers, IL6, LIF and monocytes, suggesting that inflammation may play a role in mediating this resistance. This is consistent with the recent findings where the markers of systemic inflammation such as Neutrophil to Lymphocyte ratio (NLR) have been associated with poor prognosis in ALK+NSCLC. While the mechanistic understanding is not well characterized, our model may help us explore the mechanisms of this correlation. Thus, our objective is to understand the underlying microenvironmental mechanism of this resistance to Alectinib. We hypothesize that Alectinib+JIB04 associated inflammation reduces ALK+NSCLC’s sensitivity to Alectinib. We envision two possibilities, either inflammation may directly affect resistance to Alectinib or indirectly where inflammation enhances tumor cell plasticity that then leads to resistance. We posit that the underlying molecular mechanisms of Alectinib+JIB04 mediated resistance are likely to be relevant to a subset of patients with poor initial responses with weak sensitivity or innate resistance to Alectinib observed in the clinics and will improve our knowledge about microenvironmental regulation of resistance. Citation Format: Pragya Kumar, Virginia Turati, Andriy Marusyk. Deciphering the mechanisms of environmentally mediated Alectinib resistance in ALK+NSCLC [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B032.