Original articles
Vol. 116: Issue 5 - October 2024
RNA-Based Next-Generation Sequencing in Non-Small Cell Lung Cancer patients: data from Campania, Italy
Abstract
Objective. ALK, ROS1, NTRK, and RET gene fusions and MET exon 14 skipping alterations represent fundamental predictive biomarkers for advanced non-small cell lung cancer (NSCLC) patients to ensure the best treatment choice. In this scenario, RNA-based NGS approach has emerged as an extremely useful tool for detecting these alterations. In this study, we report our NGS molecular records on ALK, ROS1, NTRK, and RET gene fusions and MET exon 14 skipping alterations detected by using a narrow RNA-based NGS panel, namely SiRe fusion.
Methods. We retrospectively reviewed data on 201 advanced stage NSCLC patients who were referred to our laboratory for RNA-based molecular evaluation of ALK, ROS1, RET, NTRK gene rearrangements as well as MET exon 14 skipping.
Results. Overall, 23 (11.4%) positive cases were retrieved. Regarding molecular assessment, 11 (5.5%), 2 (1.0%), 9 (4.5%), and 1 (0.5%) out of 201 harbored an ALK, ROS1, RET gene rearrangement, or MET exon 14 skipping, respectively.
Conclusions. In this study, we provide real-world experience on RNA-based NGS analysis in patients with advanced stage NSCLC.
Introduction
Non-small cell lung cancer (NSCLC) represents the leading cause of cancer mortality worldwide 1. Unfortunately, the vast majority of patients (more than 80%) are diagnosed in an advanced stage of disease, with a significant impact on treatment decision making and overall outcome 2. However, several efforts have been spent to improve the quality of life, progression free survival and overall survival of these patients through personalized medicine 3. As a consequence, the number of approved predictive biomarkers that must be tested has rapidly increased 4-6. Among these are point mutations and indels in Epidermal Growth Factor Receptor (EGFR), Erb-B2 Receptor Tyrosine Kinase 2 (ERBB2), V-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF) exon 15 p.V600E, Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) exon 2 p.G12C, that can be investigated at a DNA-level 7. Another important biomarker is immunohistochemical/immunocytochemical evaluation of the expression levels of Programmed Death-Ligand 1 (PD-L1) for immune-checkpoint inhibitors (ICIs) administration 8-11. Beyond DNA-based biomarkers and PD-L1 expression evaluation, another group of biomarkers is represented by Anaplastic Lymphoma Kinase (ALK), ROS Proto-Oncogene 1 Receptor Tyrosine Kinase (ROS1), Neurotrophic Receptor Tyrosine Kinase (NTRK), REarranged during Transfection (RET) gene rearrangements, and MET Proto-Oncogene, Receptor Tyrosine Kinase (MET) exon 14 skipping, which can be analyzed on RNA 12. Despite the increasing number of biomarkers, in the vast majority of advanced NSCLC patients only small tissue samples are available for morph-molecular analysis 13. In this scenario, next generation sequencing (NGS), able to analyze all biomarkers at lower costs and turnaround time respect to single-gene testing approaches 14, represents a valid solution. In our referral Molecular Predictive Pathology Laboratory at the Department of Public Health of the University of Naples Federico II, we routinely perform IHC/ICC to evaluate PD-L1 expression 10,11, and we employ a complementary DNA-based and RNA-based NGS approaches to evaluate genomic alterations useful for target therapy administration in advanced stage NSCLC patients 15-18.
Here, we retrospectively evaluated data collected from our archives on advanced stage NSCLC patients tested by our NGS RNA-based approach who were referred to our laboratory for the evaluation of ALK, ROS1, NTRK, RET gene rearrangements and MET exon 14 skipping during two years of diagnostic routine practice. In addition, in a subset of patients, we were also able to retrieve information about patients’ medical treatments.
Materials and methods
STUDY DESIGN
We retrospectively retrieved from our electronic archives advanced stage NSCLC cases tested by our DNA- and RNA-based NGS approach as well as PD-L1 expression level evaluation referred to our laboratory from December 2020 to December 2022. Data regarding sex, median age, sample type and subtype, and diagnosis was also retrieved for ALK, ROS1, RET, NTRK rearranged and MET exon 14 skipping patients (Figs. 1-4, Tabs. I-II). In addition, for a subset of these patients, information related to the duration of the first or other line treatments, or until the loss of data for any causes, was also gathered.
Written informed consent was obtained from all patients, in accordance with the general authorization to process personal data for scientific research purposes from “The Italian Data Protection Authority” (http://www.garanteprivacy.it/web/guest/home/docweb/-/docwebdisplay/export/2485392). All information regarding human material was managed using anonymous numerical codes, and all samples were handled in compliance with the Declaration of Helsinki (https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/).
MOLECULAR TESTING
Molecular testing was carried out as previously described 15-18. Briefly, DNA and RNA were extracted from formalin-fixed paraffin embedded (FFPE) tissues and cytological smears by using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. Regarding RNA analysis, retro-transcription was performed. DNA and cDNA were analyzed on an Ion S5™ System (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were constructed and purified on the Ion Chef Instrument (Thermo Fisher Scientifics, Waltham, MA, USA) according to the manufacturer’s instructions. After preparation, they were loaded onto a 520 chip and sequenced on the S5 NGS platform (Thermo Fisher Scientifics). Overall, DNA-based NGS analysis was performed by using our narrow NGS panel, namely, SiRe®,which is able to cover multiple hotspot gene alterations in seven genes (EGFR, KRAS, BRAF, Neuroblastoma RAS Viral Oncogene Homolog [NRAS], KIT Proto-Oncogene, Receptor Tyrosine Kinase [KIT], Platelet Derived Growth Factor Receptor Alpha [PDGFRα], and Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha [PIK3CA]), as previously described 15,16. RNA-based NGS analysis was performed with another narrow NGS panel, namely, SiRe fusion, able to detect ALK, ROS1, RET, NTRK gene rearrangements, as well as MET exon 14 skipping alterations, as previously described 17,18. In addition, internal controls were built for the purpose of monitoring the overall quality of the sample and housekeeping genes were used to assess the RNA quality, as previously reported 17,18.
PD-L1 IHC/ICC evaluation was performed by adopting the companion diagnostic kit sp263 assay (Ventana Medical Systems, Oro Valley, AZ, USA), as previously described 10,11. Briefly, PD-L1 expression was evaluated by using tumor proportion score (TPS), as previously reported 10,11,19.
Results
PATIENT AND SAMPLE CHARACTERISTICS
We retrospectively retrieved data on a total of 201 samples from advanced stage NSCLC patients who were referred to our laboratory for DNA- and RNA-based NGS analysis as well as PD-L1 expression level evaluation. Overall, 200 (99.5%) were successfully analyzed by our NGS SiRe fusion panel. Of note, 23 (11.5%) SiRe fusion panel positive cases were retrieved. The vast majority of cases were female (17/23, 73.9%), with a median age of 59.0 years (ranging from 33 to 78 years); whereas the remaining cases were male (6/23, 26.1%), with a median age of 54.7 years (ranging from 24 to 79 years). Almost all cases diagnosed with NSCLC were adenocarcinoma (NSCLC favor ADC, 21/23, 91.4%), followed by NSCLC adeno-squamous (1/23, 4.3%) and NSCLC not otherwise specified (NSCLC NOS, 1/23, 4.3%). Considering sample type, the number of histological samples (16, 69.6%) was higher than cytological specimens (7, 30.4%). Histological samples comprised small biopsies (13, 81.3%), and surgical resections (3, 18.7%). As for the cytological samples, they were mostly made up of cell blocks (5, 71.4%), whereas the remaining cases were direct smears (2, 28.6%). Regarding molecular assessment, 11 (5.5%), 2 (1.0%), 9 (4.5%), and 1 (0.5%) out of 200 cases harbored an ALK, ROS1, RET gene rearrangement, or MET exon 14 skipping, respectively. Interestingly, only 2 (22.2%) RET rearranged cases harbored a concomitant genomic alteration detected at DNA-level (KRAS exon 2 p.G12D and PIK3CA exon 9 p.E545K). Regarding PD-L1 expression level, about half (11/23, 47.8%) of patients showed PD-L1 expression level between 1-49% (4 ALK, and 3 RET) or ≥ 50% (2 ALK, 1 ROS1, and 1 MET exon 14 skipping).
Results are summarized in Figures 1-4 and Tables I-II.
CLINICAL MANAGEMENT
Overall, data on the clinical management of 15 (65.2%) patients were retrieved. Among these, 8 (53.3%), 1 (6.7%), and 6 (40.0%) showed an ALK, ROS1, or RET rearrangement. A concomitant PD-L1 expression 1-49% was observed in 5 instances (33.3%, 4 ALK, and 1 RET), whereas an expression level ≥ 50% was reported i 2 cases (13.3%, 1 ALK, and 1 ROS1). In only 1 instance (6.7%) a RET rearrangement was associated with a KRAS exon 2 p.G12D. Overall, about half of analyzed cases (8, 53.3%) are still undergoing target treatments at the last oncological evaluation (April 18, 2024).
Results are summarized in Table III.
Discussion
In addition to DNA-based biomarkers, the evaluation of ALK, ROS1, RET, NTRK gene rearrangements as well as MET exon 14 skipping is crucial for advanced stage NSCLC patients clinical management. In this study, we retrospectively retrieved molecular data of a total of 201 advanced stage NSCLC patients who were referred to our referral laboratory for the molecular evaluation of RNA-based biomarkers. Focusing the attention on the 23 positive cases in our series, the vast majority (17/23, 73.9%) of analyzed samples were represented by small tissue specimens. Overall, we confirmed the feasibility of a complementary DNA- and RNA-based NGS approach with narrow, custom, gene panels, namely SiRe® and SiRe fusion, to optimize small tissue samples for molecular analysis respect to the adoption of single gene assays 20-23. In our study, 11 (5.5%), 2 (1.0%), 9 (4.5%), and 1 (0.5%) out of 200 successfully analyzed cases harbored an ALK, ROS1, RET gene rearrangement, or MET exon 14 skipping, respectively. Similar with those reported in the literature, almost all cases were diagnosed with NSCLC were ADC (21/23, 91.4%) 24. As expected, ALK rearranged cases were most frequent in young (< 65 years, 7/11, 63.6%), female (10/11, 90.9%) ADC patients (11/11, 100.0%).23 In almost all instances (9/11, 81.8%) the fusion partner was Echinoderm Microtubule-Associated Protein-Like 4 (EML4) gene 24. Similarly, the only 2 CD74 Molecule, Major Histocompatibility Complex, Class II Invariant Chain (CD74)::ROS1 rearranged patients were young patients (22 and 33 years, respectively) with an ADC morphology 24. Considering RET rearranged cases, no significant differences were reported regarding sex (5 female and 4 male) or age (5 < 65 years and 4 ≥ 65 years) 24. Overall, almost all cases (8/9, 88.9%) were diagnosed as NSCLC favor ADC 24. As reported in the literature, the most common fusion partner was Kinesin Family Member 5B (KIF5B) gene 24. Noteworthy, in 2 instances RET rearrangements were identified in association with a concomitant DNA-based alteration (1 KRAS exon 2 p.G12D and 1 PIK3CA exon 9 p.E545K). In addition, only 1 (0.5%) MET exon 14 skipping was detected. Interestingly, in this case a PD-L1 expression ≥ 50% was observed. As reported in the IMMUNOTARGET registry study, patients harboring a concomitant MET exon 14 skipping and PD-L1 expression ≥ 50% may be sensitive to ICIs; in fact, 23.4% of patients with MET alterations were long-term responders to ICIs, second only to KRAS mutated NSCLC 25. Regarding PD-L1 expression, in our study other 10 rearranged cases showed a concomitant PD-L1 ≥ 1% (6 ALK, 1 ROS1, and 3 RET). However, taking into account the results of IMMUNOTARGET registry study, ICIs monotherapy is not recommended in these patients 25.
As for the data on treatment regimens, 8 (53.3%) patients (#4, #8, #9, #12, #15, #16, #17, #19, Table III) are still in treatment at the last oncological evaluation (April 18, 2024) with a specific target treatment for the gene rearrangement identified by our SiRe fusion panel. Among these, clinical efficacy of specific target treatments was observed in 2 ALK rearranged patients in whom gene rearrangements were identified without the knowledge of the specific fusion partner (patients #4 and #8 Table III). In these cases, despite Ambrosini-Spaltro et al. highlighted that patients with gene fusions with unknown partners showed a poor response to targeted therapy 26, our data, albeit limited, may suggest to further investigate the role of gene fusions with unknown partners in clinical trials for target treatment administration. Considering single gene testing approaches, fluorescence in situ hybridization (FISH) is still considered the “gold standard” methodology for gene rearrangement detection and does not require a previous knowledge of the fusion partner. Nevertheless, acting at the DNA level, FISH suffers from “false positive” results (not all the detected DNA rearrangements determine an expressed fusion transcript). In addition, break apart probes can miss small intrachromosomal rearrangements. Of note, FISH is time consuming, influenced by interobserver variability and has a limited multiplexing power 27. IHC/ICC has the advantage to be more familiar to all anatomic pathologists, as well as less time consuming, automater, less costly, and different clinically validated antibodies are commercially available. However, it can be influenced by interobserver variability, has a limited multiplexing power, and, except for ALK protein evaluation, requires confirmation by orthogonal techniques 27. Finally, retro-transcriptase polymerase chain reaction (RT-PCR), despite the high sensitivity for fusion transcripts at RNA levels, is able to identify only known gene fusions, missing all the unknown variants 26. Thus, in this complex scenario, as RNA-based NGS approach, through its multiplexing power and the possibility to identify known and unknown variants, represents a valid solution to overcome all these limitations 27. However, all that glitters is not gold. RNA-based NGS analysis can be hampered by low RNA quality and purity. Moreover, since RNA is less stable than DNA, special care must be taken during the pre-analytical phase to minimize the risk of false-negative results. In addition, RNA-based NGS-based analyses also requires trained personnel and good communication must be established with clinicians to ensure the correct interpretation of NGS reports 27. Other limitations are specifically related to the use of a narrow panel instead of comprehensive genome profile or whole exome sequencing approaches, including the risk of overlooking potentially actionable translocations, such as those involving NTRK2 and -3, as well as neuregulin 1 (NRG1). This could possibly prevent some patients from receiving effective treatment, also considering that the list of actionable alterations is constantly expanding, with several novel agents currently being evaluated in clinical trials (e.g., seribantumab in tumors with NRG1 fusions) 28.
In conclusion, in this study we provide a real world experience on RNA-based NGS analysis in patients with advanced stage NSCLC. The most significant limitations of our study were the limited number of cases and the lack of clinical data in some instances. Further studies are required to better assess the role of the complex genomic landscape in advanced stage NSCLC patients, not only on tissue but also on liquid biopsy specimens 29.
CONFLICT OF INTEREST STATEMENT
Umberto Malapelle has received personal fees (as consultant and/or speaker bureau) from Boehringer Ingelheim, Roche, MSD, Amgen, Thermo Fisher Scientific, Eli Lilly, Diaceutics, GSK, Merck and AstraZeneca, Janssen, Diatech, Novartis and Hedera for work performed unrelated to the current work. Giancarlo Troncone reports personal fees (as speaker bureau or advisor) from Roche, MSD, Pfizer and Bayer, unrelated to the current work.
The other Authors have nothing to disclose.
FUNDING
This study has partly been supported by the following grants: 1. POR Campania FESR 2014-2020 Progetto “Sviluppo di Approcci Terapeutici Innovativi per patologie Neoplastiche resistenti ai trattamenti – SATIN” 2. The Italian Health Ministry’s research program (ID: NET-2016-02363853). National Center for Gene Therapy and Drugs based on RNA Technology MUR-CN3 CUP E63C22000940007 to DS. No funding or sponsorship was received for the publication of this article.
AUTHORS CONTRIBUTION
Conceptualization, Pasquale Pisapia, Umberto Malapelle; Methodology, all authors; Software, all authors; Validation, all authors; Formal Analysis, all authors; Investigation, all authors; Resources, all authors; Data Curation, all authors; Writing – Original Draft Preparation, Pasquale Pisapia; Writing – Review & Editing, all authors; Visualization, all authors; Supervision, Pasquale Pisapia, Giancarlo Troncone, Umberto Malapelle; Project Administration, Pasquale Pisapia, Giancarlo Troncone, Umberto Malapelle; Funding acquisition, Giancarlo Troncone.
ETHICAL CONSIDERATION
Institutional Review Board approval was waived since this study was retrospective and, thus, required no deviation from the standard of care. Written informed consent was obtained from all the patients in accordance with the general authorization for processing personal data for scientific research purposes from “The Italian Data Protection Authority” (http://www.garanteprivacy.it/web/guest/home/docweb/-/docwebdisplay/export/2485392). All information regarding human material was managed using anonymous numerical codes, and all samples were handled in compliance with the Declaration of Helsinki (https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/).
History
Received: April 19, 2024
Accepted: August 29, 2024
Figures and tables
Figure 1. ALK rearranged cases with clinical variables. This figure was created by using Protein Data Bank (PDB) (https://www.rcsb.org/). ADC: adenocarcinoma; ALK: Anaplastic Lymphoma Receptor Tyrosine Kinase; EML4: Echinoderm Microtubule-Associated Protein-Like 4; F: female; M: male; MET: MET Proto-Oncogene, Receptor Tyrosine Kinase; n: number; PD-L1: Programmed death-ligand 1.
Figure 2. ROS1 rearranged cases with clinical variables. This figure was created by using Protein Data Bank (PDB) (https://www.rcsb.org/). ADC: adenocarcinoma; CD74: CD74 Molecule, Major Histocompatibility Complex, Class II Invariant Chain; F: female; M: male; n: number; PD-L1: Programmed death-ligand 1; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.
Figure 3. RET rearranged cases with clinical variables. This figure was created by using Protein Data Bank (PDB) (https://www.rcsb.org/). ADC: adenocarcinoma; F: female; KIF5B: Kinesin Family Member 5B; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; M: male; n: number; PD-L1: Programmed death-ligand 1; PIK3CA: Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha; RET: Rearranged During Transfection; SqCC: squamous cell carcinoma.
Figure 4. MET exon 14 skipping case with clinical variables. This figure was created by using Protein Data Bank (PDB) (https://www.rcsb.org/). F: female; MET: MET Proto-Oncogene, Receptor Tyrosine Kinase; n: number; NOS: not otherwise specified; PD-L1: Programmed death-ligand 1.
| Global | |
|---|---|
| Total (%) | 201 (100.0) |
| Adequacy rate (n, %) | Adequate (200, 99.5) |
| Inadequate (1, 0.5) | |
| RNA-based molecular alteration (n, %) | Negative (177, 88.5) |
| Positive (23, 11.5) | |
| RNA-based molecular alteration type (n, %) | ALK (11, 5.5) |
| ROS1 (2, 1.0) | |
| RET (9, 4.5) | |
| MET exon 14 skipping (1, 0.5) | |
| Sex (%) | M: 6 (26.1) |
| F: 17 (73.9) | |
| Median Age (range) | 57.9 y (24.0 – 79.0 y) |
| Sample type (n; %)- subtype (n; %) | Histological (16, 69.6) |
| - Biopsy (13, 81.3) | |
| - Resection (3, 18.7) | |
| Cytological (7, 30.4) | |
| - Cell block (5, 71.4) | |
| - Smear (2, 28.6) | |
| Diagnosis (n, %) | NSCLC ADC (1, 4.3) |
| NSCLC favor ADC (20, 87.1) | |
| NSCLC NOS (1, 4.3) | |
| NSCLC ADC + SqCC (1, 4.3) | |
| ADC: adenocarcinoma; ALK: Anaplastic Lymphoma Receptor Tyrosine Kinase; F: female; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; M: male; MET: MET Proto-Oncogene, Receptor Tyrosine Kinase; n: number; NOS: not otherwise specified; PD-L1: Programmed death-ligand 1; PIK3CA: Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha; RET: Rearranged During Transfection; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase; SqCC: squamous cell carcinoma; y: years. | |
| N | Sex | Age | Sample type | Sample subtype | Site | Primitive/metastasis | Diagnosis | Note | RNA-based alteration | Other alterations/PD-L1 expression level |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | F | 46 | Cytological | Cell block | Lymph node | Metastasis | NSCLC favor ADC | — | EML4(13)::ALK(20) | — |
| 2 | F | 76 | Cytological | Cell block | Lung | Primitive | NSCLC favor ADC | — | EML4(13)::ALK(20) | PD-L1 ≥ 50% |
| 3 | F | 69 | Histological | Biopsy | Lung | Primitive | NSCLC favor ADC | — | EML4(6)::ALK(20) | PD-L1 ≥ 50% |
| 4 | F | 54 | Histological | Resection | Lung | Primitive | NSCLC ADC | Mucinous, signet ring cells, micropapillary | unknown::ALK(20) | PD-L1 1-49% |
| 5 | M | 79 | Histological | Biopsy | Lung | Primitive | NSCLC favor ADC | G2 | unknown::RET(12) | KRAS p.G12D |
| 6 | F | 78 | Cytological | Smear | Lung | Primitive | NSCLC favor ADC | — | KIF5B(15)::RET(12) | PIK3CA p.E545K |
| 7 | M | 52 | Histological | Biopsy | Pleura | Metastasis | NSCLC favor ADC | — | EML4(6)::ALK(20) | — |
| 8 | F | 65 | Histological | Biopsy | Lung | Primitive | NSCLC favor ADC | G2, solid | unknown::ALK(20) | — |
| 9 | F | 65 | Cytological | Cell Block | Lung | Primitive | NSCLC favor ADC | G3 | EML4(20)::ALK(20) | — |
| 10 | M | 57 | Histological | Biopsy | Brain | Metastasis | NSCLC favor ADC | G3 | unknown::RET(12) | PD-L1 1-49% |
| 11 | M | 56 | Cytological | Cell Block | Lung | Primitive | NSCLC favor ADC | — | unknown::RET(12) | — |
| 12 | F | 60 | Histological | Biopsy | Lung | Primitive | NSCLC favor ADC | Acinar, papillar | EML4(13)::ALK(20) | PD-L1 1-49% |
| 13 | M | 24 | Histological | Biopsy | Lymph node | Metastasis | NSCLC favor ADC | G3, solid | CD74(6)::ROS1(34) | PD-L1 ≥50% |
| 14 | F | 72 | Cytological | Cell Block | Lung | Primitive | NSCLC favor ADC | — | KIF5B(15)::RET(12) | PD-L1 1-49% |
| 15 | F | 35 | Histological | Biopsy | Breast | Metastasis | NSCLC favor ADC | G2 | EML4(13)::ALK(20) | PD-L1 1-49% |
| 16 | F | 71 | Histological | Resection | Lymph node | Metastasis | NSCLC favor ADC | G3 | CCDC6(1)::RET(12) | — |
| 17 | F | 63 | Histological | Resection | Brain | Metastasis | NSCLC favor ADC | G3 | KIF5B(15)::RET(12) | — |
| 18 | F | 47 | Cytological | Smear | Mediastinum | Metastasis | NSCLC ADC + SqCC | — | KIF5B(15)::RET(12) | — |
| 19 | F | 60 | Histological | Biopsy | Liver | Metastasis | NSCLC favor ADC | G3, trabecular, solid | EML4(6)::ALK(20) | PD-L1 1-49% |
| 20 | F | 37 | Histological | Biopsy | Lymph node | Metastasis | NSCLC favor ADC | Solid | EML4(20)::ALK(20) | — |
| 21 | F | 72 | Histological | Biopsy | Lung | Primitive | NSCLC NOS | G3 | MET exon 14 skipping | PD-L1 ≥ 50% |
| 22 | F | 33 | Histological | Biopsy | Lung | Primitive | NSCLC favor ADC | — | CD74(6)::ROS1(34) | — |
| 23 | M | 60 | Histological | Biopsy | Lung | Primitive | NSCLC favor ADC | Acinar, papillary, mucinous | KIF5B(15)::RET(12) | PD-L1 1-49% |
| ADC: adenocarcinoma; ALK: Anaplastic Lymphoma Receptor Tyrosine Kinase; CD74: CD74 Molecule, Major Histocompatibility Complex, Class II Invariant Chain; EML4: Echinoderm Microtubule-Associated Protein-Like 4; F: female; KIF5B: Kinesin Family Member 5B; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; M: male; MET: MET Proto-Oncogene, Receptor Tyrosine Kinase; n: number; NOS: not otherwise specified; PD-L1: Programmed death-ligand 1; PIK3CA: Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha; RET: Rearranged During Transfection; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase; SqCC: squamous cell carcinoma. | ||||||||||
| N | Sex | Age | Diagnosis | Note | Fusion/skipping | Other alterations/PD-L1 expression level | First Line treatment | First Line treatment Starting Date | First Line treatment End Date | Second Line treatment | Second Line treatment Starting Date | Second Line treatment End Date | Third Line treatment | Third Line treatment Starting Date | Third Line treatment End Date |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | F | 69 | NSCLC favor ADC | — | EML4(6)::ALK(20) | PD-L1 ≥ 50% | Brigatinib | December 2020 | July 2021 | NA | NA | NA | NA | NA | NA |
| 4 | F | 54 | NSCLC ADC | Mucinous, signet ring cells, micropapillar | Unknown::ALK(20) | PD-L1 1-49% | Alectinib | February 2021 | Ongoing | NA | NA | NA | NA | NA | NA |
| 5 | M | 79 | NSCLC favor ADC | G2 | Unknown::RET(12) | KRAS p.G12D | Brain RT | December 2021 | May 2022 | NA | NA | NA | NA | NA | NA |
| 8 | F | 65 | NSCLC favor ADC | G2, solid | Unknown::ALK(20) | — | Alectinib | September 2021 | Ongoing | NA | NA | NA | NA | NA | NA |
| 9 | F | 65 | NSCLC favor ADC | G3 | EML4(20)::ALK(20) | — | Alectinib | February 2021 | Ongoing | NA | NA | NA | NA | NA | NA |
| 10 | M | 57 | NSCLC favor ADC | G3 | Unknown::RET(12) | PD-L1 1-49% | Carboplatin + pemetrexed | November 2021 | January 2022 | NA | NA | NA | NA | NA | NA |
| 11 | M | 56 | NSCLC favor ADC | — | Unknown::RET(12) | — | Carboplatin + paclitaxel + RT | October 2021 | September 2022 | Selpercatinib | September 2022 | April 2023 | Atezolizumab | April 2023 | Ongoing |
| 12 | F | 60 | NSCLC favor ADC | Acinar, papillar | EML4(13)::ALK(20) | PD-L1 1-49% | Alectinib | November 2021 | Ongoing | NA | NA | NA | NA | NA | NA |
| 13 | M | 24 | NSCLC favor ADC | G3, solid | CD74(6)::ROS1(34) | PD-L1 ≥ 50% | Entrectinib | March 2022 | March 2023 | Best supportive care | March 2023 | Ongoing | NA | NA | NA |
| 15 | F | 35 | NSCLC favor ADC | G2 | EML4(13)::ALK(20) | PD-L1 1-49% | Alectinib | February 2022 | Ongoing | NA | NA | NA | NA | NA | NA |
| 16 | F | 71 | NSCLC favor ADC | G3 | CCDC6(1)::RET(12) | — | Carboplatin + pemetrexed, then pemetrexed | April 2019 | January 2022 | Selpercatinib | January 2022 | Ongoing | NA | NA | NA |
| 17 | F | 63 | NSCLC favor ADC | G3 | KIF5B(15)::RET(12) | — | Selpercatinib | October 2022 | Ongoing | NA | NA | NA | NA | NA | NA |
| 18 | F | 47 | NSCLC ADC + SqCC | — | KIF5B(15)::RET(12) | — | Carboplatin + paclitaxel + pembrolizumab, then pembrolizumab | May 2022 | Ongoing | NA | NA | NA | NA | NA | NA |
| 19 | F | 60 | NSCLC favor ADC | G3, trabecular, solid | EML4(6)::ALK(20) | PD-L1 1-49% | Alectinib | May 2022 | July 2022 | NA | NA | NA | NA | NA | NA |
| 20* | F | 37 | NSCLC favor ADC | Solid | EML4(20)::ALK(20) | — | Alectinib | May 2020 | July 2022 | Lorlatinib | July 2022 | November 2022 | Brigatinib | November 2022 | March 2023 |
| ADC: adenocarcinoma; ALK: Anaplastic Lymphoma Receptor Tyrosine Kinase; CD74: CD74 Molecule, Major Histocompatibility Complex, Class II Invariant Chain; EML4: Echinoderm Microtubule-Associated Protein-Like 4; F: female; KIF5B: Kinesin Family Member 5B; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; M: male; n: number; NA: not assessed; NOS: not otherwise specified; PD-L1: Programmed death-ligand 1; RET: Rearranged During Transfection; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase; RT: radiotherapy; SqCC: squamous cell carcinoma. | |||||||||||||||
| * Patient 20: Fourth Line treatment: Carboplatin + pemetrexed, then pemetrexed; Fourth Line treatment Starting Date: March 2023; Fourth Line treatment End Date: August 2023; Fifth Line treatment: Docetaxel; Fifth Line treatment Starting Date: August 2023; Fifth Line treatment End Date: January 2024; Sixth Line treatment: Nivolumab; Sixth Line treatment Starting Date: January 2024; Sixth Line treatment End Date: Ongoing. | |||||||||||||||
References
- Siegel R, Giaquinto A, Jemal A. Cancer statistics, 2024. CA Cancer J Clin. 2024;74:12-49. doi:https://doi.org/10.3322/caac.21820
- Nicholson A, Tsao M, Beasley M. The 2021 WHO Classification of Lung Tumors: Impact of Advances Since 2015. J Thorac Oncol. 2022;17:362-387. doi:https://doi.org/10.1016/j.jtho.2021.11.003
- Adeniji A, Dulal S, Martin M. Personalized Medicine in Oncology in the Developing World: Barriers and Concepts to Improve Status Quo. World J Oncol. 2021;12:50-60. doi:https://doi.org/10.14740/wjon1345
- Hofman P, Berezowska S, Kazdal D. Current challenges and practical aspects of molecular pathology for non-small cell lung cancers. Virchows Arch. 2024;484:233-246. doi:https://doi.org/10.1007/s00428-023-03651-1
- Hendriks L, Kerr K, Menis J. Oncogene-addicted metastatic non-small-cell lung cancer: ESMO Clinical Practice Guideline for diagnosis, treatment and follow-up. Ann Oncol. 2023;34:339-357. doi:https://doi.org/10.1016/j.annonc.2022.12.009
- Singh N, Temin S, Baker S. Therapy for Stage IV Non-Small-Cell Lung Cancer With Driver Alterations: ASCO Living Guideline. J Clin Oncol. 2022;40:3310-3322. doi:https://doi.org/10.1200/JCO.23.02744
- Kerr K, Bibeau F, Thunnissen E. The evolving landscape of biomarker testing for non-small cell lung cancer in Europe. Lung Cancer. 2021;154:161-175. doi:https://doi.org/10.1016/j.lungcan.2021.02.026
- Passiglia F, Reale M, Cetoretta V. Immune-Checkpoint Inhibitors Combinations in Metastatic NSCLC: New Options on the Horizon?. Immunotargets Ther. 2021;10:9-26. doi:https://doi.org/10.2147/ITT.S253581
- Addeo A, Passaro A, Malapelle U. Immunotherapy in non-small cell lung cancer harbouring driver mutations. Cancer Treat Rev. 2021;96. doi:https://doi.org/10.1016/j.ctrv.2021.102179
- Vigliar E, Iaccarino A, Campione S. PD-L1 expression in cell-blocks of non-small cell lung cancer: The impact of prolonged fixation. Diagn Cytopathol. 2020;48:595-603. doi:https://doi.org/10.1002/dc.24439
- Vigliar E, Malapelle U, Iaccarino A. PD-L1 expression on routine samples of non-small cell lung cancer: results and critical issues from a 1-year experience of a centralised laboratory. J Clin Pathol. 2019;72:412-417. doi:https://doi.org/10.1136/jclinpath-2019-205732
- Ettinger D, Wood D, Aisner D. NCCN Guidelines® Insights: Non-Small Cell Lung Cancer, Version 2.2023. J Natl Compr Canc Netw. 2023;21:340-350. doi:https://doi.org/10.6004/jnccn.2023.0020
- Lindeman N, Cagle P, Aisner D. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med. 2018;142:321-346. doi:https://doi.org/10.5858/arpa.2017-0388-CP
- Pisapia P, Pepe F, Baggi A. Next generation diagnostic algorithm in non-small cell lung cancer predictive molecular pathology: The KWAY Italian multicenter cost evaluation study. Crit Rev Oncol Hematol. 2022;169. doi:https://doi.org/10.1016/j.critrevonc.2021.103525
- Malapelle U, Mayo de-Las-Casas C, Rocco D. Development of a gene panel for next-generation sequencing of clinically relevant mutations in cell-free DNA from cancer patients. Br J Cancer. 2017;116:802-810. doi:https://doi.org/10.1038/bjc.2017.8
- Pepe F, De Luca C, Smeraglio R. Performance analysis of SiRe next-generation sequencing panel in diagnostic setting: focus on NSCLC routine samples. J Clin Pathol. 2019;72:38-45. doi:https://doi.org/10.1136/jclinpath-2018-205386
- De Luca C, Pepe F, Iaccarino A. RNA-Based Assay for Next-Generation Sequencing of Clinically Relevant Gene Fusions in Non-Small Cell Lung Cancer. Cancers (Basel). 2021;13. doi:https://doi.org/10.3390/cancers13010139
- Luca C, Pepe F, Pisapia P. RNA-based next-generation sequencing in non-small-cell lung cancer in a routine setting: an experience from an Italian referral center. Per Med. 2022;19:395-401. doi:https://doi.org/10.2217/pme-2022-0020
- Walker P, Jayananda S, Pasli M. Plasma cell-free RNA PD-L1 or tissue PD-L1 protein expression and outcomes with first-line immunotherapy in metastatic non-small cell lung cancer. The Journal of Liquid Biopsy. 2024;3. doi:https://doi.org/10.1016/j.jlb.2023.100130
- Penault-Llorca F, Kerr K, Garrido P. Expert opinion on NSCLC small specimen biomarker testing – Part 1: Tissue collection and management. Virchows Arch. 2022;481:335-350. doi:https://doi.org/10.1007/s00428-022-03343-2
- Penault-Llorca F, Kerr K, Garrido P. Expert opinion on NSCLC small specimen biomarker testing - Part 2: Analysis, reporting, and quality assessment. Virchows Arch. 2022;481:351-366. doi:https://doi.org/10.1007/s00428-022-03344-1
- Kerr K, Bubendorf L, Lopez-Rios F. Optimizing tissue stewardship in non-small cell lung cancer to support molecular characterization and treatment selection: statement from a working group of thoracic pathologists. Histopathology. 2024;84:429-439. doi:https://doi.org/10.1111/his.15078
- Pisapia P, Iaccarino A, De Luca C. Evaluation of the Molecular Landscape in PD-L1 Positive Metastatic NSCLC: Data from Campania, Italy. Int J Mol Sci. 2022;23. doi:https://doi.org/10.3390/ijms23158541
- Pan Y, Zhang Y, Li Y. ALK, ROS1 and RET fusions in 1139 lung adenocarcinomas: a comprehensive study of common and fusion pattern-specific clinicopathologic, histologic and cytologic features. Lung Cancer. 2014;84:121-6. doi:https://doi.org/10.1016/j.lungcan.2014.02.007
- Mazieres J, Drilon A, Lusque A. Immune checkpoint inhibitors for patients with advanced lung cancer and oncogenic driver alterations: results from the IMMUNOTARGET registry. Ann Oncol. 2019;30:1321-1328. doi:https://doi.org/10.1093/annonc/mdz167
- Ambrosini-Spaltro A, Farnedi A, Calistri D. The role of next-generation sequencing in detecting gene fusions with known and unknown partners: a single-center experience with methodologies’ integration. Hum Pathol. 2022;123:20-30. doi:https://doi.org/10.1016/j.humpath.2022.02.005
- Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel). 2020;10. doi:https://doi.org/10.3390/diagnostics10080521
- Carrizosa D, Burkard M, Elamin Y. CRESTONE: Initial efficacy and safety of seribantumab in solid tumors harboring NRG1 fusions. Journal of Clinical Oncology. 2022;40(16). doi:https://doi.org/10.1200/JCO.2022.40.16_suppl.3006
- Verzè M, Boscolo Bragadin A. NGS detection of gene rearrangements and METexon14 mutations in liquid biopsy of advanced NSCLC patients: A study of two Italian centers. The Journal of Liquid Biopsy. 2024;4. doi:https://doi.org/10.1016/j.jlb.2024.100143
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