Targeting MET in 2025: From Exon 14 Skipping to MET-Amplified Acquired Resistance in Non-Small Cell Lung Cancer

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,
Thank you for providing the manuscript on MET-targeted therapy in NSCLC. I found the review highly relevant, well structured, and educational, particularly regarding the integration of recent clinical studies, resistance mechanisms, and translational aspects of MET-directed therapy. Major strengths of the manuscript include the comprehensive discussion of biologically distinct MET alterations, integration of recent clinically relevant trials (including SAVANNAH, SACHI, INSIGHT-2, and MARIPOSA-2), detailed overview of resistance mutations and inhibitor sensitivity patterns, as well as the inclusion of ADCs, bispecific antibodies, and re-biopsy/liquid biopsy strategies.
I have included my detailed comments and questions in the attached review file. Most suggestions are intended to further strengthen the biological precision, translational interpretation, and clarity of several important concepts, particularly regarding MET amplification biology, resistance mechanisms, and biomarker interpretation.
I hope that my comments will be helpful and constructive for the further improvement of the manuscript.

Best regards,

Comments for author File: Comments.pdf

Author Response

We are grateful for the reviewer’s positive overall assessment and for the detailed, scientifically precise critique. The annotated comments have now reached us, and we address each major and minor point below.

Major comments

1. Novelty and conceptual contribution. Many concepts have been addressed in prior MET reviews; the main novelty appears to be integration of recent data rather than a new conceptual framework. Could the authors define the specific conceptual or clinical novelty?

Response: We have added an explicit statement of contribution to the Introduction. We agree the value is partly the 2024–2025 update, but we frame the conceptual contribution as the organizing framework itself: a mutation-class → drug-class → resistance-mechanism scaffold that treats METex14, primary high-level amplification, acquired amplification, and c-Met overexpression as biologically distinct entities with distinct diagnostics, drug classes, and resistance patterns, integrated with an explicit, evidence-referenced treatment algorithm. We do not claim a new biological discovery; we claim a clinically actionable synthesis.

Change made: Introduction (contribution statement).

2. MET amplification biology and diagnostic complexity (focal vs polysomy; clonal vs subclonal; borderline gains; true dependency). A more critical discussion of which amplification states represent true MET dependency would improve translational relevance. Distinguish focal amplification from polysomy; do current thresholds identify MET-dependent tumors; how should borderline gains be interpreted?

Response: Section 2.3 has been expanded accordingly. We now state that focal high-level amplification with a high MET/CEP7 ratio is the state most likely to reflect true MET dependency, whereas a proportional rise in MET and centromere-7 signals indicates chromosome 7 polysomy and is a weaker predictor; that clonal (truncal) amplification is more likely to drive dependency than subclonal/heterogeneous gains; and—directly answering the reviewer’s second question—that current FISH/NGS thresholds identify truly MET-dependent tumors only imperfectly. For routine practice we recommend interpreting borderline/intermediate gains cautiously, reconciling FISH (with explicit MET/CEP7 ratio) and quantitative NGS, and weighing the clinical context rather than treating a single number as definitively actionable.

Change made: Section 2.3 (expanded amplification-biology paragraph).

3. De novo versus acquired MET amplification; meaning of “mutually exclusive.” Acquired high-level amplification can coexist with persistent EGFR mutation; cases evolving from low- to high-level focal amplification (>15 copies) while retaining EGFR have been described (Urbanska et al., IJMS 2023). MET amplification may also co-occur with METex14 (Awad 2015; Socinski 2021; co-occurrence 0–~40%). Does mutual exclusivity refer to primary disease? How is “mutually exclusive” defined given METex14–amplification co-occurrence?

Response: This was imprecise and is corrected. Section 2.3 now states that mutual exclusivity applies specifically to primary (de novo) high-level amplification in treatment-naïve disease, and that acquired high-level amplification arising under EGFR-TKI pressure characteristically coexists with the persistent original EGFR driver as a bona fide resistance mechanism. We also now state explicitly that MET amplification can co-occur with METex14 and c-Met overexpression, with co-occurrence ranging widely across series (negligible to ~40%) and stage IV METex14 tumors enriched for concurrent amplification. We have added Urbanska et al. (Int. J. Mol. Sci. 2023, 24, 13077) [74] and Awad et al. [75]—correcting the latter to its actual citation, J. Clin. Oncol. 2016;34:721–730, rather than Cancer Discovery 2015. We were unable to confirm the exact Socinski et al. (Cancer Treatment Reviews 2021) details and have not added it to avoid an inaccurate entry; we are glad to include it if the reviewer can confirm the citation.

Change made: Section 2.3; new references [74] Urbanska 2023 and [75] Awad 2016.

4. Cross-trial comparison and biomarker heterogeneity. Direct comparison of SAVANNAH, SACHI, INSIGHT-2 is difficult due to differing thresholds, assays, selection, and biomarker definitions; this warrants explicit discussion.

Response: Agreed; Section 5 now makes this explicit. We added a passage stating that cross-trial comparison is hazardous because each trial used a different amplification definition and assay (SAVANNAH, IHC3+/≥90% or FISH GCN ≥10; INSIGHT 2, FISH GCN ≥5; SACHI, centrally confirmed amplification), different selection stringency, and different comparators, so apparent differences in ORR and PFS partly reflect biomarker definition rather than true differences in drug activity. Tables 1 and 3 tabulate these selection criteria side by side.

Change made: Section 5 (cross-trial heterogeneity passage); Tables 1 and 3.

5. Immunotherapy discussion may oversimplify. Occasional durable responses occur (Mayenga 2020); benefit may vary by smoking history, TMB, co-mutation profile (TP53), treatment line, and chemoimmunotherapy vs ICI monotherapy (Blasi 2024). Could the authors provide a more nuanced discussion of subsets that may still benefit?

Response: We have added a nuanced passage to Section 3.3.1. It now notes documented durable ICI responses in a minority of METex14 patients (Mayenga et al., six cases with PFS >18 months) [76] and the real-world finding that benefit varies with smoking history, TMB, co-mutation profile (notably TP53, associated with better outcomes), and treatment line, with chemoimmunotherapy and even ICI monotherapy producing meaningful responses in selected (often older, comorbid ex-smoker) patients despite PD-L1 not reliably predicting benefit (Blasi et al.) [77]. We conclude that selected subsets may still benefit and that the population is underrepresented in prospective biomarker studies.

Change made: Section 3.3.1; new references [76] Mayenga 2020 and [77] Blasi 2024.

6. Real-world applicability. Algorithms are idealized; barriers (limited RNA-NGS access, reimbursement, regional approval differences, limited MET combination availability, repeat-biopsy challenges) are insufficiently discussed, especially in community settings.

Response: We have added a dedicated real-world implementation paragraph at the end of Section 6.2. It acknowledges uneven access to RNA-NGS, payer/region-dependent reimbursement, jurisdictional differences in approval (e.g., savolitinib + osimertinib approved only in China), limited local availability of MET combinations, and the practical constraints of repeat tissue biopsy; it notes that in community and non-academic settings these constraints are amplified and that pragmatic compromises (single-platform testing, plasma-only genotyping, empirical chemotherapy) are common, and frames the algorithm as an ideal to be adapted to local capacity.

Change made: Section 6.2 (new real-world implementation paragraph).

7. Liquid biopsy — limitations specific to MET amplification. Reliable plasma detection of MET amplification (especially low-level, and distinction from polysomy) is technically challenging; tissue–plasma concordance is imperfect and influenced by tumor fraction and shedding.

Response: Section 6.1 now addresses this specifically, distinct from METex14/resistance-mutation detection: we state that low-level amplification and its distinction from chromosome 7 polysomy are difficult to resolve in ctDNA, that tissue-FISH/plasma-NGS concordance for amplification is imperfect and influenced by tumor fraction and shedding, and that a negative plasma amplification result is weak evidence that should prompt tissue confirmation.

Change made: Section 6.1 (MET-amplification ctDNA caveat).

8. Figure 1 — mechanistic precision. Grouping STAT3 with GAB1/SHP2 is imprecise; the figure centers on METex14/HGF-dependent biology while amplification and EGFR-MET bypass are under-represented; combination strategies mix validated and investigational approaches.

Response: We have revised the Figure 1 legend to address all three points: it now states that the schematic emphasizes METex14/HGF-dependent activation and represents amplification-driven signaling and EGFR–MET bypass more schematically; that STAT3 is a transcriptional output mechanistically distinct from the GAB1/SHP2 adaptor/scaffold proteins (upstream mediators, not equivalent outputs); and that among the combinations shown, MET + EGFR is clinically validated whereas MET + KRAS G12C and MET + SHP2/DDR are investigational. The legend changes make these distinctions explicit; if the editor prefers, we can also revise the artwork itself to separate the STAT3 and GAB1/SHP2 nodes graphically.

Change made: Figure 1 legend (caption-level clarification; artwork revision offered).

9. Figure 2 — heterogeneity and the “mPFS ≈ 10–14 months” figure. The schematic may oversimplify by grouping METex14 and MET-amplified tumors; resistance patterns (D1228/Y1230) may differ by amplification context; “mPFS ≈ 10–14 months” may be overgeneralized.

Response: Addressed in two places. The Figure 2 legend now states that the schematic applies predominantly to METex14-driven and high-level MET-dependent tumors treated with selective MET TKIs, that the depicted on-target mutations are characteristic of that setting, and that resistance patterns may differ in MET-amplified NSCLC (especially low-level/polysomic amplification). In Section 4 we have qualified the “10–14 month” range as applying chiefly to METex14 populations on selective MET TKIs, noting that MET-amplified outcomes are more heterogeneous and depend on amplification level, focality, assay, and context—directly answering all three of the reviewer’s questions in the affirmative.

Change made: Figure 2 legend; Section 4 (mPFS qualifier).

10. Amivantamab contextualization. Amivantamab’s established role is primarily in EGFR-mutant NSCLC (exon 20 insertion, post-osimertinib MET-mediated resistance), not pure METex14 or primary MET-amplified disease.

Response: Agreed and clarified in Section 3.2.1. We now state that amivantamab’s established clinical role is within EGFR-mutant NSCLC—exon 20 insertion disease and the post-osimertinib setting, where MET-mediated resistance is one of several mechanisms it may address—rather than in pure METex14-driven or primary MET-amplified disease, where its activity is far less established and it is not a standard option, and that we discuss it for its MET-directed mechanism rather than as a METex14 treatment.

Change made: Section 3.2.1 (amivantamab contextualization).

Minor comments

1. MET nomenclature. “Mesenchymal–epithelial transition factor” is not the current official gene nomenclature (Religa et al., J Thorac Oncol 2025;20:1032–1034).

Response: Corrected. At first use we now give MET as the official HGNC symbol (MET proto-oncogene, receptor tyrosine kinase), note that the acronym derives from the MNNG-HOS transforming gene, and identify “mesenchymal–epithelial transition factor” as a recognized misnomer, citing Religa et al. [73].

Change made: Introduction; new reference [73] Religa 2025.

2. Gene names in italics. Gene names should be italicized throughout.

Response: We will italicize gene symbols (MET, EGFR, KRAS, ALK, TP53, etc.) throughout at the copy-editing stage; because this is a global typographic change affecting hundreds of instances, we have flagged it for production rather than introducing it as tracked formatting changes that would obscure the substantive edits.

Change made: Throughout (italicization at copy-edit).

3. Introduction sentence may suggest de novo amplification is not a focus. The sentence emphasizing METex14 and MET amplification “as a mechanism of resistance” may unintentionally exclude de novo amplification.

Response: Clarified. The sentence now states that the review emphasizes MET amplification both as a primary (de novo) oncogenic driver and as a mechanism of acquired resistance to EGFR-directed therapy.

Change made: Introduction (scope sentence).

4. METex14 detection — DNA/RNA-NGS complementarity. Discussion should address concordance/complementarity of DNA- and RNA-NGS and panel coverage limitations, not only RNA-NGS superiority (Urbanska et al., IJMS 2025).

Response: Section 2.2 now states that DNA- and RNA-based NGS are complementary rather than mutually exclusive—DNA panels capture many canonical splice-site alterations but vary in intronic coverage, while RNA confirms the functional skipping event—that concordance is high but imperfect, and that panel design/coverage limitations matter when a suspected case tests negative on one platform. We were unable to verify the exact details of the suggested Urbanska et al. 2025 reference (the volume/article number appeared inconsistent for a 2025 IJMS issue) and would be glad to cite it once the reviewer confirms the citation.

Change made: Section 2.2 (DNA/RNA complementarity).

5. Repetition. Some sections repeat (amplification frequencies, D1228/Y1230, re-biopsy, amplification cutoffs); condensation would improve flow.

Response: We have reviewed these recurrences. Some repetition is intentional cross-referencing (e.g., amplification thresholds in Sections 2.3 and 7 serve different purposes), but we have tightened redundant statements of amplification frequency and re-biopsy recommendations and will complete a final condensation pass at copy-editing to reduce repeated D1228/Y1230 and cutoff descriptions while preserving the cross-references.

Change made: Throughout (condensation at copy-edit).

Reviewer 2 Report

Comments and Suggestions for Authors

• The topic is important and current, especially the distinction between MET exon 14 skipping, MET amplification, and c-Met overexpression.

some points are overstated:

• The manuscript presents several 2025 treatment advances as settled practice, but some are still trial-derived or jurisdiction-specific, so the tone should distinguish approved, guideline-supported, and investigational uses more clearly.
• The statement that MET amplification thresholds “matter clinically” is correct, but the review should explain the uncertainty more explicitly rather than implying a universal cutoff.
• The discussion of c-Met overexpression and telisotuzumab vedotin would be stronger if it emphasized how assay choice and scoring method affect eligibility and response prediction.
• The suggestion that plasma ctDNA can guide progression management is reasonable, but the limitations in shedding-poor and brain-dominant disease should be foregrounded more strongly.

I suggest:

• Clarify which statements are based on approved indications versus emerging trial data.
  Tighten claims about response rates and biomarker thresholds so they are tied to the exact trial population and assay used.
• Make the distinction between METex14, MET amplification, and c-Met overexpression even sharper throughout the text.
• Add a brief paragraph on unresolved controversies, especially assay standardization and the lack of universally accepted amplification thresholds.

Author Response

 

We thank the reviewer for endorsing the central framing—METex14 vs MET amplification vs c-Met overexpression—and for the specific points on overstatement, which we have addressed directly.

1. Some 2025 advances are presented as settled practice but are trial-derived or jurisdiction-specific. The manuscript presents several 2025 treatment advances as settled practice … the tone should distinguish approved, guideline-supported, and investigational uses more clearly.

Response: Agreed and corrected throughout. We now state regulatory status precisely and by jurisdiction: capmatinib (accelerated 2020 → regular 2022) and tepotinib (accelerated 2021 → regular 2024) are FDA-approved for METex14; savolitinib has full NMPA (China) approval only; and the savolitinib + osimertinib combination is approved in China (NMPA, June 2025) but not FDA/EMA-approved, with global confirmation awaited from SAFFRON. The abstract now flags the review as a narrative synthesis, and Sections 3.1.2, 5, and 7, Table 1, and the Figure 3 caption consistently separate approved from investigational use.

Change made: Abstract; Sections 3.1.2, 5, 7; Table 1; Figure 3 caption.

2. “Thresholds matter clinically” is correct, but the uncertainty should be explicit rather than implying a universal cutoff. The review should explain the uncertainty more explicitly rather than implying a universal cutoff.

Response: We have added an explicit caveat in Section 2.3 that the commonly cited cutoffs (GCN ≥10, MET/CEP7 ≥2) are not universally standardized—definitions differ across trials and platforms, no single threshold is accepted across guidelines, and the same numerical value carries different predictive weight depending on assay and context. This is reinforced in the Discussion (Section 7). We retained the SAVANNAH high- vs low-cutoff contrast because it empirically demonstrates threshold dependence rather than asserting a universal value.

Change made: Section 2.3 (new caveat); Section 7.

3. The c-Met overexpression / telisotuzumab vedotin discussion should emphasize how assay choice and scoring affect eligibility and response prediction. … emphasized how assay choice and scoring method affect eligibility and response prediction.

Response: Section 3.2.2 already specifies the FDA companion diagnostic (VENTANA MET SP44, IHC 3+ in ≥50% of cells) and notes that H-score versus percentage-3+ scoring metrics differ across platforms and predict response with imperfect concordance; Section 6.1 reiterates the assay/scoring requirement, and Section 7 lists c-Met IHC scoring as an unresolved controversy. We have ensured these passages explicitly tie scoring method to both eligibility and response prediction. We are happy to expand this into a dedicated assay-comparison paragraph if the reviewer prefers.

Change made: Sections 3.2.2, 6.1, 7 (emphasis clarified).

4. The limitations of plasma ctDNA in shedding-poor and brain-dominant disease should be foregrounded more strongly. … the limitations in shedding-poor and brain-dominant disease should be foregrounded more strongly.

Response: Section 6.1 states that plasma genotyping is a complementary—not substitute—test and that false negatives occur with shedding-poor tumors and predominantly intracranial disease, with the recommendation that a negative plasma result not preclude tissue confirmation. We have foregrounded this caveat within the liquid-biopsy paragraph so it is not subordinate to the validation data. Section 6.3 separately notes CNS tropism, reinforcing the brain-dominant limitation.

Change made: Section 6.1 (caveat foregrounded).

5. Add a brief paragraph on unresolved controversies (assay standardization, lack of universally accepted amplification thresholds). Add a brief paragraph on unresolved controversies, especially assay standardization and the lack of universally accepted amplification thresholds.

Response: The Discussion (Section 7) already contains a dedicated “tensions” treatment of exactly these controversies—non-interchangeable FISH/NGS measurements, diluted benefit at lower cutoffs, and platform-dependent c-Met IHC scoring. We have strengthened it by adding the explicit “no universally accepted threshold” statement in Section 2.3 that cross-references Section 7, so the controversy is flagged at first mention and synthesized in the Discussion.

Change made: Sections 2.3 and 7.

Reviewer 3 Report

Comments and Suggestions for Authors

This manuscript presents a comprehensive narrative review of MET alterations in non-small cell lung cancer, with emphasis on molecular mechanisms, targeted therapies, and resistance patterns. The topic is clinically relevant and timely, given recent advances in MET-directed treatments. Overall, the paper is informative, but several issues related to focus, structure, and critical analysis need to be addressed to improve clarity and scientific rigor. To the best of my understanding, I summarize below points for the improvement of present version of the manuscript-

1. The paper provides a broad overview of MET-altered NSCLC, but its main contribution is not clearly stated early. It reads more like an extensive narrative review than a focused critical analysis. The authors should clearly explain what is new compared to existing reviews.
2. The manuscript does not describe how the literature was selected or filtered. There is no explanation of search strategy, databases, or inclusion criteria. Please include it in abstract.
3. Many clinical trials and therapies are described, but there is limited direct comparison between them. Differences in patient populations, biomarkers, and endpoints are not clearly discussed. A more critical comparison would strengthen the paper’s scientific depth.
4. The discussion on MET amplification, IHC, FISH, and NGS is informative but scattered. Clear subheadings and summary tables would help readers understand key differences and challenges. This section currently feels dense and difficult to follow.
5. The future directions section is strong but somewhat speculative. Some claims are not clearly linked to existing clinical evidence. The authors should better separate what is proven, what is emerging, and what is hypothetical.
6. The proposed 2025 treatment algorithm is useful, but it appears opinion-based. The paper should clarify whether this algorithm is evidence-driven or expert consensus. Adding references or justification for each step would improve credibility.
7. The manuscript uses many abbreviations, sometimes several in a single paragraph. This makes reading difficult, even with an abbreviation list. Consider reducing repeated or less critical abbreviations.
8. Some tables and figures could be better integrated into the text. Explicitly explaining what key message each figure supports would improve clarity. This will help readers connect visuals with the narrative.
9. The review comprehensively discusses molecular diagnostics and biomarker-guided therapeutic strategies in MET-altered NSCLC. The authors may also consider citing recent translational biomarker discovery studies utilizing advanced mass spectrometry and multi-omics approaches, which further support the growing role of precision diagnostics and therapeutic monitoring in oncology. For Eg- 1016/j.ebiom.2023.104627 External Link

Author Response

We thank the reviewer for a detailed and rigorous critique. We have made the requested clarifications and, where a comment would convert the article into a systematic review or require an off-topic citation, we explain our reasoning.

1. The main contribution is not stated early; explain what is new versus existing reviews. It reads more like an extensive narrative review than a focused critical analysis. The authors should clearly explain what is new compared to existing reviews.

Response: We have added a sentence to the Introduction stating the review’s distinct contribution: an explicit mutation-class → drug-class → resistance-mechanism framework that integrates the most recent 2025 developments (telisotuzumab vedotin’s approval, the SACHI phase III readout and China approval of savolitinib + osimertinib, and the maturation of type I/type II resistance biology) into a single clinically oriented synthesis with an explicit treatment algorithm.

Change made: Introduction (new contribution statement).

2. No description of literature selection; include a search strategy in the abstract. The manuscript does not describe how the literature was selected … Please include it in abstract.

Response: We have added a scope sentence to the abstract identifying this as a narrative review synthesizing peer-reviewed literature and pivotal trial and regulatory data through early 2026, drawn from PubMed and major oncology congress proceedings, prioritizing sources linking mutation class to drug class and resistance mechanism. We have phrased this to reflect a narrative (non-systematic) review honestly; we will refine the exact databases and date range to match our records before acceptance.

Change made: Abstract (scope/search statement).

3. Limited direct comparison between trials (populations, biomarkers, endpoints). A more critical comparison would strengthen the paper’s scientific depth.

Response: Tables 1 and 3 are structured precisely for cross-trial comparison (agent, phase/setting, selection biomarker, endpoint, and a comparative comment), and the text now flags the key differences: SAVANNAH’s high-cutoff selection (IHC3+/≥90% or FISH GCN ≥10) versus INSIGHT 2’s FISH GCN ≥5, SACHI’s randomized chemotherapy comparator, and MARIPOSA-2’s MET-unselected population. Section 5 explicitly states that assay, threshold, and biopsy timing drive the divergent amplification frequencies, making formal pooling inappropriate. We have reinforced these comparative points but, as a narrative review of heterogeneously designed trials, we do not present a quantitative meta-analysis, which would imply a comparability the data do not support.

Change made: Sections 5; Tables 1 and 3 (comparative emphasis).

4. The MET amplification / IHC / FISH / NGS discussion is scattered; add subheadings and a summary table. Clear subheadings and summary tables would help … This section currently feels dense.

Response: The diagnostic material is consolidated in Section 6.1 (Diagnostic Considerations), which now distinguishes the three lesions and their respective assays. We agree a compact diagnostic summary table (lesion → preferred assay → reporting requirement → caveats) would aid readability and are happy to add one as a new Table 4; we have not inserted it pre-emptively to avoid duplicating Tables 1–3, and would welcome the editor’s guidance on placement.

Change made: Section 6.1 (consolidated); diagnostic summary table offered.

5. The future directions section is speculative; separate proven, emerging, and hypothetical. The authors should better separate what is proven, what is emerging, and what is hypothetical.

Response: Section 8 already labels each priority by maturity (e.g., “hypothesis-generating,” “preliminary,” “prospective evidence remains limited”). We have reviewed the section to ensure each item carries an explicit evidence qualifier separating established class effects from emerging signals and from preclinical or conceptual proposals.

Change made: Section 8 (evidence-level qualifiers reviewed).

6. The 2025 treatment algorithm appears opinion-based; clarify whether it is evidence-driven or expert consensus, and justify each step. The paper should clarify whether this algorithm is evidence-driven or expert consensus.

Response: Clarified. The Figure 3 caption now states that the algorithm is the authors’ evidence-informed proposal—an expert synthesis of the cited trial and biomarker data—rather than a formal guideline or consensus statement, and that each entry point is supported by the approvals and trials referenced in Sections 3 and 5. The caption also notes that availability is jurisdiction-dependent and that frontline MET TKI use in primary high-level amplification remains off-label or investigational.

Change made: Figure 3 caption.

7. Too many abbreviations. This makes reading difficult … Consider reducing repeated or less critical abbreviations.

Response: We have reviewed the text and will spell out infrequently used abbreviations on the (rare) occasions they appear and remove those used only once, retaining only high-frequency, field-standard abbreviations (NSCLC, MET, METex14, TKI, ORR, PFS, IHC, FISH, NGS, ctDNA). The abbreviation list will be reconciled with the final text.

Change made: Throughout (abbreviation reduction at copy-edit).

8. Better integrate tables and figures into the text; explain each figure’s key message. Explicitly explaining what key message each figure supports would improve clarity.

Response: We have added in-text callouts so each display item is now cited where it is first relevant and its message is stated: Figure 1 (signaling and points of pharmacologic intervention, Section 2.1), Table 1 (comparative summary of agents, Section 3.1), Table 2 (on-target resistance mutations and cross-sensitivity, Section 4.1), Table 3 (pivotal MET-amplification combination trials, Section 5), and Figure 3 (treatment algorithm, Section 6.2); Figure 2 was already cited in Section 4.

Change made: Sections 2.1, 3.1, 4.1, 5, 6.2 (figure/table callouts).

9. Consider citing recent translational biomarker discovery studies using mass spectrometry / multi-omics (example DOI 10.1016/j.ebiom.2023.104627). … recent translational biomarker discovery studies utilizing advanced mass spectrometry and multi-omics approaches … (e.g., 10.1016/j.ebiom.2023.104627).

Response: We considered the suggested reference but respectfully do not include it. The cited article (Kell et al., eBioMedicine 2023;92:104627) reports a mass-spectrometry pentasaccharide biomarker for monitoring gene therapy in GM1 gangliosidosis, a pediatric lysosomal storage disorder; it does not concern MET, NSCLC, or oncologic precision diagnostics, and citing it would not be germane to the manuscript’s scope or arguments. If the reviewer intended a specific MET- or NSCLC-relevant proteomic/multi-omics study, we would be glad to incorporate an on-topic reference; we are otherwise reluctant to add a citation that does not bear on the work.

Change made: No change — rationale provided (off-topic reference).

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

Thank you for your careful and thorough revision of the manuscript. I appreciate the considerable effort you have put into addressing the reviewers’ comments. Your responses are scientifically sound and satisfactorily address all major and minor issues raised during the review process. The revised manuscript has been significantly enhanced and provides a balanced and up-to-date review of MET-targeted therapies for NSCLC.
Only two minor issues related to citations remain. The references that could not be identified in the response letter are:

Socinski MA, Pennell NA, Davies KD. MET exon 14 skipping mutations in non-small cell lung cancer: a review of biology, clinical outcomes, and research issues. JCO Precision Oncology. 2021;5:653–663. doi:10.1200/PO.20.00516.

Urbanska EM, Doktor TK, Melchior LC, Petersson ES, Santoni-Rugiu E, Andresen BS, Grauslund M, Sørensen JB. Improving the diagnosis of patients with NSCLC harboring MET exon 14 mutations using complementary DNA/RNA sequencing (NGS) and identification of two novel exon-skipping mutations. Int J Mol Sci. 2025;27(1):106.

These references may be considered for inclusion as they are directly related to relevant discussion points.

Kind regards

Author Response

We thank the Reviewer for the careful re-evaluation of our manuscript and for the encouraging assessment that the revision is scientifically sound, balanced, and up to date. We appreciate the constructive engagement throughout the review process. Below we address the two remaining minor points concerning citations. The Reviewer’s comment is reproduced in purple italics, followed by our response. All corresponding changes in the manuscript are marked using tracked changes.

Comment 1 — Remaining citation items

“Only two minor issues related to citations remain. The references that could not be identified in the response letter are: (i) Socinski MA, Pennell NA, Davies KD. MET exon 14 skipping mutations in non-small cell lung cancer… JCO Precision Oncology. 2021;5:653–663; and (ii) Urbanska EM, et al. … NSCLC harboring MET exon 14 mutations using complementary DNA/RNA sequencing (NGS) … Int J Mol Sci. 2025. These references may be considered for inclusion as they are directly related to relevant discussion points.”

Response

We thank the Reviewer for highlighting these two relevant references. Both have been incorporated into Section 2.2, within the discussion of METex14 detection and the complementary roles of DNA- and RNA-based NGS, where they directly support the diagnostic points raised. The specific edits are as follows.

(i) Socinski et al. This review has been added to support the rationale for RNA-based NGS detection and the broader diagnostic considerations for METex14 skipping. It is now cited together with references 5 and 67 in the sentence on detection methodology (revised to read “…deep intronic regions that affect splicing [5,67,78]”). The reference has been added to the reference list as entry 78:

Socinski, M.A.; Pennell, N.A.; Davies, K.D. MET exon 14 skipping mutations in non-small-cell lung cancer: an overview of biology, clinical outcomes, and testing considerations. JCO Precis. Oncol. 2021, 5, 653–663, doi:10.1200/PO.20.00516.

(ii) Urbanska et al. This study has been added to support the value of complementary DNA/RNA-NGS testing and the identification of novel exonic splicing variants. A new sentence has been added to Section 2.2: “Consistent with this, complementary DNA/RNA-NGS testing has been shown to increase the detection rate of METex14 and to uncover previously uncharacterized exonic splicing variants, reinforcing the value of an integrated DNA- and RNA-based diagnostic strategy [79].” The reference has been added to the reference list as entry 79:

Urbanska, E.M.; Doktor, T.K.; Melchior, L.C.; Petersson, E.S.; Sørensen, J.B.; Santoni-Rugiu, E.; Andresen, B.S.; Grauslund, M. Improvement of diagnostics in NSCLC patients with MET exon 14 mutations using complementary DNA/RNA-NGS and identification of two novel exonic splicing mutations. Int. J. Mol. Sci. 2026, 27, 106, doi:10.3390/ijms27010106.

Note on bibliographic details: the citations above have been verified against the publishers’ records and DOIs. For the Urbanska et al. article, the version of record was published online on 22 December 2025 and assigned to Volume 27 (2026); the year, volume, and article number above reflect the definitive citation provided by the publisher.

We believe these additions strengthen the diagnostic discussion and are grateful to the Reviewer for the suggestion. We hope the revised manuscript is now suitable for publication and remain available for any further clarification.