INTRODUCTION:Early molecular profiling in non-squamous non-small cell lung carcinoma (NSCLC), particularly lung adenocarcinoma (LUAD), is critical for guiding individualized treatment strategies. Limited data exist on the genomic landscape of Stage 0-IA LUAD. This study assessed the feasibility and clinical relevance of reflex targeted next-generation sequencing (NGS) performed on-site at diagnosis in resected early-stage LUAD. METHODS:We retrospectively analyzed 239 consecutive Stage 0-IA LUAD cases diagnosed between 2022 and 2024 at a single institution. Ultra-fast reflex DNA- and RNA-based NGS was performed on resected specimens using a 50-gene targeted panel. Alterations were classified according to the ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT). Associations between genomic alterations, histologic subtypes, and tumor grades were evaluated. RESULTS:Stage IA1 was the most frequent diagnosis (46%). High-quality sequencing data were obtained in all cases, with a median turnaround time of 102 h. At least one genomic alteration was detected in 80% of tumors. KRAS mutations were most frequent (35.8%), including KRAS G12C in 16%. EGFR mutations were present in 27.2%, primarily classical sensitizing alterations. Other actionable findings included ALK fusions (3.3%), RET rearrangements (1.2%), MET exon 14 skipping (2.4%), HER2 mutations (3.7%), and BRAF V600E (0.8%). ESCAT Level I alterations were found in 34% of tumors; 20% of these co-occurred with TP53 mutations. Significant associations were observed between genomic alterations, histologic subtypes, and tumor grades. CONCLUSIONS:Reflex NGS at diagnosis in resected Stage 0-IA LUAD is feasible, rapid, and reveals a high rate of actionable alterations, which may support its integration in the future into early-stage diagnostic workflows.

Patients with lung squamous cell carcinoma (LSCC) rarely benefit from targeted therapies in daily practice. Current and future clinical trials targeting genomic alterations may open up promising therapeutic strategies for this population. We evaluated the usefulness and the clinical added value in the real world of the analysis of LSCC at diagnosis using reflex-targeted next-generation sequencing (NGS) on-site in a single hospital center. Targeted DNA and RNA NGS and diagnostic immunohistochemistry for PD-L1 and c-MET were performed on a consecutive series of 108 LSCC patients. The main genomic alterations included mutations in TP53 [56/102; (51.9

BACKGROUND:Liquid biopsies (LB) are used increasingly to detect actionable mutations in patients newly diagnosed with advanced non-small cell lung cancer (aNSCLC), though tissue biopsies (TB) still remain the gold standard. The value of systematically combining LB and TB next-generation sequencing (NGS) for genomic profiling in these patients remains controversial. METHODS:This single-centre retrospective study included 102 matched TB and LB samples collected from aNSCLC patients at diagnosis. Four circulating free DNA (cfDNA)-based NGS assays (1-4) were compared on site for performance and concordance with TB to detect ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) I/II. Additionally, cfDNA droplet digital PCR methylation (ddPCR-met) testing estimated the tumour fraction to refine the interpretation of wild-type (WT) results. RESULTS:Out of 102 patients, 13% had stage IIIB disease, and 11% presented with brain-only metastases. Adenocarcinoma was the predominant subtype (84%). Ninety LB samples yielded interpretable results across the four assays. Positive percent agreement with TB ranged from 56% (assay 2) to 79% (assay 4), with high concordance, particularly for single-nucleotide variants (SNVs). Hybrid capture-based assays (3 and 4) detected eight and seven gene fusions, respectively, while amplicon-based assays (1 and 2) detected only two each. Assay 3 only identified 12 MET amplifications, five of which were confirmed by fluorescence in situ hybridisation (FISH) but were missed by TB-based NGS. Five out of six negative cfDNA samples with ddPCR-met testing were WT across all assays. The plasma-first approach added incremental value, up to 21% (assay 3). Amplicon-based assays were faster and required less input of DNA for analysis. Patients with stage IIIB or brain-only metastases were significantly more likely to have negative/low levels of cfDNA ddPCR-met. CONCLUSIONS:LB-based NGS demonstrated high concordance with TB in newly diagnosed aNSCLC, particularly for detection of SNV. Hybrid capture assays showed superior performance in identifying gene fusions and MET amplifications. The incremental value of a plasma-first strategy was limited in this real-life study. Thus, LB-based NGS on site should be seen as a complementary tool to TB-based NGS or an alternative when tissue samples are unavailable. Additionally, cfDNA methylation analysis enhances diagnostic accuracy in specific cases.

BACKGROUND/OBJECTIVES:Immune checkpoint inhibitors (ICIs) benefit some lung cancer patients, but their efficacy is limited in advanced lung adenocarcinoma (LUAD) with EGFR mutations (EGFRm), largely due to a non-immunogenic tumour microenvironment (TME). Furthermore, EGFRm LUAD patients often experience increased toxicity with ICIs. CD73, an ectonucleotidase involved in adenosine production, promotes tumour immune evasion and could represent a novel therapeutic target. This study investigates CD73 expression in LUAD with EGFR alterations and its clinico-pathological correlations. METHODS:CD73 expression in tumour (CD73TC) and stromal (CD73SC) cells was assessed in 76 treatment-naive LUAD patients using immunohistochemistry (IHC) (D7F9A clone) alongside IHC PD-L1 (22C3 clone). EGFR alterations were identified by molecular sequencing and FISH. Event-free survival (EFS) was analysed based on CD73TC expression. RESULTS:CD73TC expression was observed in 66% of cases, with high expression (Tumour Proportion Score > 50%) correlating with improved EFS (p = 0.045). CD73TC and PD-L1 expression were not significantly correlated (p = 0.44), although a weak inverse trend was observed. CD73SC expression was detected in 18% of cases, predominantly in early-stage (p = 0.037), PD-L1-negative (p = 0.030), and non-EGFR-amplified (p = 0.0018) tumours. No significant associations were found with disease stage, histological subtype, EGFR mutation type, and amplification. CONCLUSIONS:CD73 expression in EGFRm LUAD is heterogeneous and associated with diverse TME profiles. These findings support the potential of CD73 as a predictive biomarker and therapeutic target, highlighting its clinical relevance in EGFRm LUAD.

Metastatic uveal melanomas are highly resistant to all existing treatments. To identify actionable vulnerabilities, we conducted a CRISPR-Cas9 knockout screen using a library composed of chromatin regulators. We revealed that the lysine methyltransferase, SETDB1, plays a critical role in metastatic uveal melanoma cell proliferation and survival. Functionally, SETDB1 deficiency induces a DNA damage response, senescence-like state and growth arrest. Knockdown of SETDB1 is associated with a decreased expression of genes related to replication and cell cycle. Moreover, deficiency in CDC6, an essential regulator of DNA replication, phenocopies SETDB1 inhibition. Using a pre-clinical model, we further demonstrated that anti-SETDB1 therapy impairs tumor growth in vivo. Therefore, we not only provide evidence that SETDB1 plays a critical role in metastatic uveal melanoma cell growth, but we also identify SETDB1 as a novel relevant therapeutic target for the treatment of metastatic uveal melanoma.

Purpose. - Treatment delays due to the COVID-19 pandemic in uveal melanoma (UM) patients have led to an increased rate of enucleations in Europe. The impact of multiple COVID-19 lockdowns on UM management has not been assessed in France. The goal of this study was to assess whether delayed diagnosis could have led to more advanced stages and thus a higher rate of enucleations.Methods. - Two datasets were analyzed: patients from two ocular oncology centers (dataset- 1), with recording of sizes, prognostic stages (TNM) and treatments, and a national database (dataset-2), obtained by ICD-10 codes and medical procedures for clip placement. After year- by-year comparison, the pre-COVID-19 (2018-2019) and post-COVID-19 (2021-2022) periods were compared for each dataset. Five hundred and thirty-seven patients were diagnosed with UM (dataset-1), including 213 patients in the pre-COVID-19 period and 212 patients in the post-COVID-19 period. Similarly, 2187 patients were diagnosed with UM (dataset-2), of whom 914 patients and 864 patients were diagnosed in the pre-COVID-19 and post-COVID-19 periods, respectively. Results. - A higher number of patients had locally advanced tumors during the post-COVID- 19 period compared to the pre-COVID-19 period (cT1 = 66, cT2 = 64, cT3 = 66 and cT4 = 21 vs. cT1 = 59, cT2 = 82, cT3 = 65 and cT4 = 7, P = 0.03), but without difference in ciliary body involve- ment, extraocular extension or AJCC stage (dataset-1). Treatments were similar between the pre-COVID-19 and post-COVID-19 periods in dataset-1 (P = 0.36) and dataset-2 (P = 0.47), with a higher ratio of proton beam therapy to primary enucleation in 2020 than in the pre-COVID-19 and post-COVID-19 periods (21.4 vs. 8.6 and 6.3, P = 0.02). Conclusion. - The COVID-19 pandemic did not impact the ophthalmological management of UM patients in France, but more locally advanced stages were observed upon initial presentation during the post-COVID-19 period. (c) 2024 The Author(s). Published by Elsevier Masson SAS. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Emerging therapies for non–small cell lung cancer targeting c-Met overexpression have recently demonstrated promising results. However, the evaluation of c-Met expression can be challenging. We aimed to study the inter and intraobserver reproducibility of c-Met expression evaluation. One hundred ten cases with non–small cell lung cancer (40 biopsies and 70 surgical specimens) were retrospectively selected in a single laboratory (LPCE) and evaluated for c-Met expression. Six pathologists (4 seniors and 2 juniors) evaluated the H-score and made a 3-tier classification of c-Met expression for all cases, using conventional light microscopy (CLM) and whole slide imaging (WSI). The interobserver reproducibility with CLM gave global Cohen Kappa coefficients (ƙ) ranging from 0.581 (95% CI: 0.364-0.771) to 0.763 (95% CI: 0.58-0.92) using the c-Met 3-tier classification and H-score, respectively. ƙ was higher for senior pathologists and biopsy samples. The interobserver reproducibility with WSI gave a global ƙ ranging from 0.543 (95% CI: 0.33-0.724) to 0.905 (95% CI: 0.618-1) using the c-Met H-score and 2-tier classification (≥25% 3+), respectively. ƙ for intraobserver reproducibility between CLM and WSI ranged from 0.713 to 0.898 for the c-Met H-score and from 0.600 to 0.779 for the c-Met 3-tier classification. We demonstrated a moderate to excellent interobserver agreement for c-Met expression with a substantial to excellent intraobserver agreement between CLM and WSI, thereby supporting the development of digital pathology. However, some factors (scoring method, type of tissue samples, and expertise level) affect reproducibility. Our findings highlight the importance of establishing a consensus definition and providing further training, particularly for inexperienced pathologists, for c-Met immunohistochemistry assessment in clinical practice.

ObjectiveTo evaluate and compare characteristics, diagnosis, treatment, visual prognosis, and course between ocular sarcoidosis with or without uveitis in a population in Southern France.MethodsWe retrospectively analyzed data from patients with ocular sarcoidosis in a tertiary eye care center in Nice from January 2003 to December 2021. The inclusion criterion was biopsy-proven ocular sarcoidosis according to IWOS criteria as the first clinical manifestation of sarcoidosis.ResultsA total of 25 patients were included. Twenty patients had uveitis (70% panuveitis, 20% intermediate uveitis, and 10% anterior uveitis) and five patients had non-uveitic ocular sarcoidosis (one patient with dacryoadenitis, one patient with orbital granuloma, two patients with palpebral granuloma, and one patient with episcleritis). Only the cases with uveitis had bilateral involvement (85% of cases). There was no significant difference in ethnicity, biopsy diagnosis, systemic manifestations, or treatment between the two groups. Final visual outcomes remained good for both groups, with 96% of patients with BCVA>20/50, with no significant difference. Patients with non-uveitic sarcoidosis experienced less recurrence on treatment (P=0.042) and more remission (P=0.038) than patients with uveitis. Eighty percent of patients with uveitis had at least three suggestive clinical intraocular signs meeting IWOS criteria.ConclusionIn this population in Southern France, uveitis was the most common presentation of ocular sarcoidosis. The type of ocular sarcoidosis does not appear to be correlated with the type of systemic manifestations, use of systemic therapy, or visual prognosis, but patients with non-uveitic ocular sarcoidosis appear to have a better course with fewer recurrences on treatment and more remission than patients with uveitic ocular sarcoidosis.

EGFR status assessment is mandatory for adjuvant decision-making of resected stage IB-IIIA non-squamous non-small cell lung cancer (NS-NSCLC). It is questionable whether single-gene RT-PCR versus next-generation sequencing (NGS) should be used for this evaluation. Moreover, co-occurring mutations have an impact on tumor behavior and may influence future therapeutic decision-making. We aimed to describe the clinico-pathological and molecular features, as well as the prognostic factors of resected EGFR-mutant NS-NSCLC evaluated with reflex NGS and RT-PCR, so as to compare the results of the two methods. We retrospectively included and collected data from patients with resected EGFR-mutant NS-NSCLC diagnosed in our institution between 2005 and 2024. Additional cases from another center were included. Tumors were analyzed using targeted NGS and RT-PCR. A total of 153 patients were selected. The median follow-up after surgery was 22 months. The positive percent agreement of RT-PCR compared to NGS for the detection of an EGFR mutation was 88

Several nomenclature and grading systems have been proposed for conjunctival melanocytic intraepithelial lesions (C-MIL). The fourth "WHO Classification of Eye Tumors" (WHO-EYE04) proposed a C-MIL classification, capturing the progression of noninvasive neoplastic melanocytes from low- to high-grade lesions, onto melanoma in situ (MIS), and then to invasive melanoma. This proposal was revised to the WHO-EYE05 C-MIL system, which simplified the high-grade C-MIL, whereby MIS was subsumed into high-grade C-MIL. Our aim was to validate the WHO-EYE05 C-MIL system using digitized images of C-MIL, stained with hematoxylin and eosin and immunohistochemistry. However, C-MIL cases were retrieved from 3 supraregional ocular pathology centers. Adequate conjunctival biopsies were stained with hematoxylin and eosin, Melan-A, SOX10, and PReferentially expressed Antigen in Melanoma. Digitized slides were uploaded on the SmartZoom platform and independently scored by 4 ocular pathologists to obtain a consensus score, before circulating to 14 expert eye pathologists for independent scoring. In total, 105 cases from 97 patients were evaluated. The initial consensus diagnoses using the WHO-EYE04 C-MIL system were as follows: 28 benign conjunctival melanoses, 13 low-grade C-MIL, 37 high-grade C-MIL, and 27 conjunctival MIS. Using this system resulted in 93% of the pathologists showing only fair-to-moderate agreement (kappa statistic) with the consensus score. The WHO-EYE05 C-MIL system (with high-grade C-MIL and MIS combined) improved consistency between pathologists, with the greatest level of agreement being seen with benign melanosis (74.5%) and high-grade C-MIL (85.4%). Lowest agreements remained between pathologists for low-grade C-MIL (38.7%). Regarding WHO-EYE05 C-MIL scoring and clinical outcomes, local recurrences of noninvasive lesions developed in 8% and 34% of the low- and high-grade cases. Invasive melanoma only occurred in 47% of the cases that were assessed as high-grade C-MIL. This extensive international collaborative study is the first to undertake a comprehensive review of the WHO-EYE05 C-MIL scoring system, which showed good interobserver agreement and reproducibility.

The identification of ALK fusions in advanced non-small-cell lung carcinoma (aNSCLC) is mandatory for targeted therapy. The current diagnostic approach employs an algorithm using ALK immunohistochemistry (IHC) screening, followed by confirmation through ALK FISH and/or next-generation sequencing (NGS). Challenges arise due to the infrequency of ALK fusions (3–7% of aNSCLC), the suboptimal specificity of ALK IHC and ALK FISH, and the growing molecular demands placed on small tissue samples, leading to interpretative, tissue availability, and time-related issues. This study investigates the effectiveness of RNA NGS as a reflex test for identifying ALK fusions in NSCLC, with the goal of replacing ALK IHC in the systematic screening process. The evaluation included 1246 NSCLC cases using paired techniques: ALK IHC, ALK FISH, and ALK NGS. ALK IHC identified 51 positive cases (4%), while RNA NGS detected ALK alterations in 59 cases (4.8%). Of the 59 ALK-positive cases identified via NGS, 53 (89.8%) were confirmed to be positive. This included 51 cases detected via both FISH and IHC, and 2 cases detected only via FISH, as they were completely negative according to IHC. The combined reporting time for ALK IHC and ALK FISH averaged 13 days, whereas ALK IHC and RNA NGS reports were obtained in an average of 4 days. These results emphasize the advantage of replacing systematic ALK IHC screening with RNA NGS reflex testing for a more comprehensive and accurate assessment of ALK status.

This retrospective cohort study was to assess the prognostic value of preoperative geriatric nutritional risk index (GNRI) on survival outcomes for patients with locally advanced oral squamous cell carcinoma (LAOSCC).Patients with LAOSCC receiving upfront radical surgery at a single institute from January 2007 to February 2017 were enrolled. The primary outcomes in the study were 5-year overall survival (OS) and cancer-specific survival (CSS) rates, and a nomogram based on GNRI and other clinical-pathological factors was established for individualized OS prediction.There were 343 patients enrolled in this study. The optimal cut-off value of GNRI was observed to be 97.8. Patients in the high-GNRI group (GNRI ≥97.8) had statistically significantly better outcomes in 5-year OS (74.7% vs. 57.2%, p = 0.001) and CSS (82.2% vs. 68.9%, p = 0.005) when compared with the low-GNRI group (GNRI <97.8). In Cox models, low GNRI remained an independent negative prognosticator of OS (HR: 1.6; 95% CI: 1.124–2.277; p = 0.009) and CSS (HR: 1.907; 95% CI: 1.219–2.984; p = 0.005). The c-index of the proposed nomogram, incorporating assorted clinicopathological factors and GNRI, had a statistically significant increase compared with the predictive nomogram constructed by the TNM staging system alone (0.692 vs. 0.637, p < 0.001).”Preoperative GNRI is an independent prognostic factor of OS and CSS in patients with LAOSCC. A multivariate nomogram that includes GNRI may better help us to accurately estimate individual survival outcomes.

The identification of gene fusions in cancer cells has been one of the most important breakthroughs in oncology in recent decades, with new actionable targets becoming available, as shown with the use of tropomyosin receptor kinase inhibitors (TRKi) in neurotrophic tropomyosin receptor kinase (NTRK) fusion-positive cancers.1 We report a pediatric case of spindle cell orbital tumour with an oncogenic NTRK1 fusion successfully treated with a TRKi despite a local recurrence.

PURPOSE:To investigate whether 18F-FDG PET/CT might be useful to predict the histology of various orbital tumors based on the maximum standard uptake value (SUVmax) and the OMSUV (orbital max SUV)/MLSUV (mean liver SUV) ratio. PATIENTS AND METHODS:A retrospective single-center study was conducted between May 2019 and December 2020. Patients with an orbital mass who underwent preoperative 18F-FDG PET/CT followed by an orbital biopsy were included. Tumor histology was classified as follows: orbital inflammation, solid tumor, low-grade lymphoid tumor, and high-grade lymphoid tumor. Orbital tumors were also classified as indolent or aggressive. Data recorded included the orbital SUVmax, OMSUV/MLSUV ratio and additional extra-orbital SUV sites. RESULTS:Forty-five patients (24 men) were included. There were 15 (33.3%), 14 (31.1%), 9 (20%), and 7 (15.5%) cases of orbital inflammation, solid tumor, low-grade lymphoid tumor, and high-grade lymphoid tumor, respectively. No correlation was found between the OMSUV/MLSUV ratio and orbital SUVmax and tumor histology (Z = -0.77, Z = -0.6, Z = -1.6, and Z = 0.94, all P > 0.05, respectively). No correlation was found between the OMSUV/MLSUV ratio (Z = -1.42, P > 0.05) and orbital SUVmax (Z = -0.82, P > 0.05) and tumor aggressiveness (indolent versus aggressive). Subgroup analyses showed that SUVmax was predictive of lymphoma aggressiveness (P = 0.05) and was able to distinguish orbital cancers (all lymphomas+solid tumors) from benign tumors (P = 0.02). CONCLUSION:18F-FDG PET/CT could not be used to predict the underlying orbital tumor histology. However, more aggressive tumors, especially high-grade lymphomas and cancers, tended to have a higher orbital SUVmax compared to indolent lesions.

•MET expression and correlation with PD-L1 TPS in NSCLC biopsy and resected specimens.•Significant correlation of MET H-score in surgical and matched biopsies.•Significant correlation of PD-L1 TPS in surgical and matched biopsies.•MET H-score higher in adenocarcinoma than in squamous cell carcinoma.•No correlation for MET and PD-L1 expression in paired biopsies and surgical samples.

As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 175 positive samples from individuals. An automated workflow used the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Sequencer. All samples were collected in the metropolitan area of the city of Nice (France) over a period of 32 weeks (from 19 July 2021 to 11 February 2022). In total, 76% of cases were identified with a low viral load (Ct ≥ 32, and ≤200 copies/µL). The NGS analysis was successful in 91% of cases, among which 57% of cases harbored the Delta variant, and 34% the Omicron BA.1.1 variant. Only 9% of cases had unreadable sequences. There was no significant difference in the viral load in patients infected with the Omicron variant compared to the Delta variant (Ct values, p = 0.0507; copy number, p = 0.252). We show that the NGS analysis of the SARS-CoV-2 genome provides reliable detection of the Delta and Omicron SARS-CoV-2 variants in low viral load samples.

The detection of ROS1 rearrangements in metastatic non-squamous non-small cell lung carcinoma (NS-NSCLC) permits administration of efficient targeted therapy. Detection is based on a testing algorithm associated with ROS1 immunohistochemistry (IHC) screening followed by ROS1 FISH and/or next generation sequencing (NGS) to confirm positivity. However, (i) ROS1 rearrangements are rare (1-2% of NS-NSCLC), (ii) the specificity of ROS1 IHC is not optimal, and (iii) ROS1 FISH is not widely available, making this algorithm challenging to interpret time-consuming. We evaluated RNA NGS, which was used as reflex testing for ROS1 rearrangements in NS-NSCLC with the aim of replacing ROS1 IHC as a screening method. ROS1 IHC and RNA NGS were prospectively performed in 810 NS-NSCLC. Positive results were analyzed by ROS1 FISH. ROS1 IHC was positive in 36/810 (4.4%) cases that showed variable staining intensity while NGS detected ROS1 rearrangements in 16/810 (1.9%) cases. ROS1 FISH was positive in 15/810 (1.8%) of ROS1 IHC positive cases and in all positive ROS1 NGS cases. Obtaining both ROS1 IHC and ROS1 FISH reports took an average of 6 days, while obtaining ROS1 IHC and RNA NGS reports took an average of 3 days. These results showed that systematic screening for the ROS1 status using IHC must be replaced by NGS reflex testing.