Lynch syndrome‐related colorectal carcinomas are <scp>NTRK‐</scp>negative
Bibliographic record
Abstract
Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers found in ~1% of all solid tumour cancers with divergent incidence according to different tumour histotypes. NTRK-positive (NTRK+) metastatic patients can be treated by an “agnostic” molecular target therapy approach, but the low prevalence of these alterations can represent a potential barrier to their identification in clinical practice.1 For this reason, the identification of peculiar tumour histotypes characterized by high NTRK alterations represents an important goal in the current oncological setting. In colorectal cancers (CRC), NTRK fusions are rare, occurring in less than 1% of cases, and ranging in the literature from 0.2%2 to 2.4%.3 This difference in prevalence among the different studies is probably related to the absence of selection of the tested lesions. In fact, when restricted to DNA mismatch repair deficient (MMRd)/microsatellite instable (MSI) tumours, 0.9% of cases are positive for NTRK compared to 0.17% of MMR proficient/microsatellite stable lesions.4 Of interest, NTRK are found in up to 5.3%–6.3% of cases when cancers with a somatic loss of the MLH1/PMS2 heterodimer and a wildtype BRAF exon 15 are considered.2 Major oncogenic gene fusions, such as NTRK, have been found specifically in the sporadic MLH1-promoter methylated, MSI-high, BRAF wildtype subset.5 Of note, a relatively high prevalence of NTRK fusions were also observed in their premalignant counterpart, such as sessile serrated lesions with or without dysplasia, which showed a positivity in NTRK in 17% and 4% of the cases, respectively.3 In this context, we performed an exploratory evaluation of the incidence of NTRK alterations in Lynch-related CRC, which are universally recognized as MMRd, BRAF wildtype, and MLH1-promoter unmethylated lesions, mostly characterized by germline pathogenic variants in the MMR genes. Immunohistochemistry for pan-NTRK was performed on whole sections using the Leica-Bond III automated staining platform (Leica Micro Systems, Mount Waverley, Victoria, Australia). Two different rabbit monoclonal anti-NTRK antibodies were employed on all cases and sections—clone EPR17341 (Abcam, Cambridge, MA, USA) and clone A7H6R (Cell Signalling Technology, Danvers, MA, USA). A CRC case harbouring an NGS detected NTRK fusion was used as the positive control. All CRC samples tested consisted of surgically resected large bowel specimens. In our multicenter series, we recruited 88 Lynch syndrome CRC regardless of stage disease and the type of germline pathogenic variants: 46 (52%) patients with germline pathogenetic variants in MLH1, 31 (35%) in MSH2, seven (8%) in PMS2, and four in MSH6 (5%). The CRC were located in 49 (56%) cases in the right colon, 27 (30%) in the left colon (including sigma-rectum), and 12 (14%) in the transverse. Four (5%) patients had simultaneously more than one intestinal neoplasia. All cases were negative for panNTRK immunoexpression. To our knowledge, this is the first evaluation of NTRK in a large series of CRC in patients with Lynch syndrome. In CRC, the pan-NTRK IHC is highly specific (near 100%) for NTRK rearrangements without the high risk of false-positive staining reported for other malignancies (e.g. salivary gland neoplasms, sarcomas, etc.). Notably, pan-TRK has been reported to be higly sensitive for NTRK1 and NTRK2.2 The pan-NTRK sensivity for NTRK3 has been reported much lower, but this rearrangement is relatively rare in CRC.2 Notably, Zhang et al. recently reported almost perfect correlation between the weakly granular cytoplasmatic IHC positivity and in all CRC harbouring an NTRK3 fusion.6 According to these results, evaluation of NTRK is most likely to be negative, and therefore not suggested for these patients. As it is very rare or even absent in Lynch syndrome-related CRCs, NTRK positivity indicates most likely a sporadic nature of a given MMRd CRC, like BRAF mutation and MLH1 promoter hypermethylation. Given the low prevalence rate of NTRK rearrangements in CRC, a larger multicentre study is required to confirm these data. All authors took part in writing the article and approved the final submitted version. Andrea Remo: conceptualization, acquisition of data, analysis and interpretation of data, drafting the article, final approval of the version to be published. Federica Grillo: analysis and interpretation of data, drafting the article, final approval of the version to be published, final approval of the version to be published. Alessandro Vanoli: acquisition of data, drafting the article, final approval of the version to be published. Paola Parente: acquisition of data, final approval of the version to be published. Luca Mastracci: acquisition of data, analysis and interpretation of data, drafting the article, final approval of the version to be published. Valentina Angerilli: analysis and interpretation of data, final approval of the version to be published. Emanuele Damiano Urso: acquisition of data, final approval of the version to be published. Francesca Bergamo: drafting the article, final approval of the version to be published. Matteo Fassan: conceptualization, acquisition of data, analysis and interpretation of data, drafting the article, final approval of the version to be published. The authors have no competing interests to disclose. For this study, approval and/or informed consent were not required. The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.004 | 0.005 |
| Insufficient payload (model declined to judge) | 0.001 | 0.003 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; both teacher heads agree on what is shown here.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".