Targeted next generation sequencing of MLH1-deficient, MLH1 promoter hypermethylated, and BRAF/RAS-wild-type colorectal adenocarcinomas is effective in detecting tumors with actionable oncogenic gene fusions.

Oncogenic gene fusions represent attractive targets for therapy of cancer. However, the frequency of actionable genomic rearrangements in colorectal cancer (CRC) is very low, and universal screening for these alterations seems to be impractical and costly. To address this problem, several large scale studies retrospectivelly showed that CRC with gene fusions are highly enriched in groups of tumors defined by MLH1 DNA mismatch repair protein deficiency (MLH1d), and hypermethylation of MLH1 promoter (MLH1ph), and/or the presence of microsatellite instability, and BRAF/KRAS wild-type status (BRAFwt/KRASwt). In this study, we used targeted next generation sequencing (NGS) to explore the occurence of potentially therapeutically targetable gene fusions in an unselected series of BRAFwt/KRASwt CRC cases that displayed MLH1d/MLH1ph. From the initially identified group of 173 MLH1d CRC cases, 141 cases (81.5%) displayed MLH1ph. BRAFwt/RASwt genotype was confirmed in 23 of 141 (~16%) of MLH1d/MLH1ph cases. Targeted NGS of these 23 cases identified oncogenic gene fusions in nine patients (39.1%; CI95: 20.5%-61.2%). Detected fusions involved NTRK (four cases), ALK (two cases), and BRAF genes (three cases). As a secondary outcome of NGS testing, we identified PIK3K-AKT-mTOR pathway alterations in two CRC cases, which displayed PIK3CA mutation. Altogether, 11 of 23 (~48%) MLH1d/MLH1ph/BRAFwt/RASwt tumors showed genetic alterations that could induce resistance to anti-EGFR therapy. Our study confirms that targeted NGS of MLH1d/MLH1ph and BRAFwt/RASwt CRCs could be a cost-effective strategy in detecting patients with potentially druggable oncogenic kinase fusions.

Morphological features useful in the differential diagnosis between undifferentiated carcinoma and gastrointestinal stromal tumor.

Undifferentiated (sarcomatoid) carcinomas may closely mimic gastrointestinal stromal tumors (GISTs) due to possible histological and immunohistochemical overlap between these two entities. To avoid unnecessary employment of a wide spectrum of immunohistochemical stainings and molecular genetics and thus decrease costs, finding simple morphological features to target further investigation of such neoplasms of the gastrointestinal tract would be helpful. Five cases classified as undifferentiated (sarcomatoid) carcinomas with a definite proof of the diagnosis, i. e. the presence of a differentiated carcinomatous component, were retrieved from archives of several institutions. For comparison, 84 cases of GIST mutated in KIT or PDGFRA genes served as the control group. Hematoxylin and eosin stained slides were evaluated for the presence of patterns which might discriminate between sarcomatoid carcinoma and GIST. Lymphatic invasion and entrapment of fat tissue strongly favor the diagnosis of undifferentiated carcinoma, as it was found in all or almost all cases of undifferentiated carcinoma, but in no GIST. Alternation of low- and high- grade areas, formation of angiosarcomatous-like spaces, and the presence of yolk sac-like areas were also detected in all cases of undifferentiated carcinoma, but only in 1.2%, 2.4% and 7.2% of the GISTs, respectively. Furthermore, DOG1 was negative in all cases of undifferentiated carcinoma. According to this study, the presence of the histological findings listed above should prompt extensive tumor sampling in order to find a differentiated carcinomatous component. However, due to the small number of cases of undifferentiated carcinoma available for the study, a larger multi-institutional study is warranted.

Immunohistochemistry and molecular genetics in the differential diagnostics of mesenchymal lesions of gastrointestinal tract.

Although, in routine practice, the differential diagnostics of mesenchymal tumors of the gastrointestinal tract is still focused mainly on the correct diagnosis of gastrointestinal stromal tumor and its further therapeutic management based on predictive diagnostics, recent progress in the development of endoscopic techniques has led to increased detection of other mesenchymal lesions, which were previously commonly neglected due to their small size or absence of symptoms requiring surgical exploration. Diagnosis of some of these lesions may be reached based on their histologic pattern alone, while others may be recognized with the use of tissue specific antibodies related to the probable lineage of differentiation of the neoplastic cells. Finally, a subset of tumors, commonly with uncertain lineage of differentiation, is defined by pathognomonic genetic alterations of neoplastic cells. Recognition of such alterations, based either on methods of molecular genetics or immunohistochemical detection of an altered protein product, enables a precise diagnosis in a growing number of these cases. However, regarding the fact that most of these alterations are not unique to a single tumor type, but are often shared by more neoplastic entities, the diagnosis must still be based on a complex diagnostic attitude, reflecting histological, immunohistochemical and molecular genetic features of the investigated tumor.

Next Generation Sequencing Analysis and its Benefit for Targeted Therapy of Lung Adenocarcinoma.

BACKGROUND/AIM: Targeted therapy has become increasingly important in treating lung adenocarcinoma, the most common subtype of lung cancer. Next-generation sequencing (NGS) enables precise identification of specific genetic alterations in individual tumor tissues, thereby guiding targeted therapy selection. This study aimed to analyze mutations present in adenocarcinoma tissues using NGS, assess the benefit of targeted therapy and evaluate the progress in availability of targeted therapies over last five years. PATIENTS AND METHODS: The study included 237 lung adenocarcinoma patients treated between 2018-2020. The Archer FusionPlex CTL panel was used for NGS analysis. RESULTS: Gene variants covered by the panel were detected in 57% patients and fusion genes in 5.9% patients. At the time of the study, 34 patients (14.3% of patients) were identified with a targetable variant. Twenty-five patients with EGFR variants, 8 patients with EML4-ALK fusion and one patient with CD74-ROS1 fusion received targeted therapy. Prognosis of patients at advanced stages with EGFR variants treated by tyrosine kinase inhibitors and patients with EML4-ALK fusion treated by alectinib was significantly favorable compared to patients without any targetable variant treated by chemotherapy (p=0.0172, p=0.0096, respectively). Based on treatment guidelines applicable in May 2023, the number of patients who could profit from targeted therapy would be 64 (27.0% of patients), this is an increase by 88% in comparison to recommendations valid in 2018-2020. CONCLUSION: As lung adenocarcinoma patients significantly benefit from targeted therapy, the assessment of mutational profiles using NGS could become a crucial approach in the routine management of oncological patients.

Laboratory Parameters Associated With Inflammation Do Not Affect PD-L1 Expression in Non-small Cell Lung Cancer.

BACKGROUND/AIM: Due to some interconnectedness at the molecular level, this study assessed the possible influence of laboratory parameters associated with systemic inflammatory environment on programmed death-ligand 1 (PD-L1) expression in non-small cell lung carcinoma (NSCLC). PATIENTS AND METHODS: We assessed effects of c-reactive protein (CRP), albumin, haemoglobin, neutrophil, and lymphocyte levels on PD-L1 expression in NSCLC. Patient data were obtained retrospectively from LUCAS, the Czech registry of patients with lung carcinomas. Correlations of two continuous parameters (PD-L1 expression and laboratory parameters) were analysed by correlation coefficient. Differences in continuous parameters between two or more groups were tested by Mann-Whitney or Kruskal-Wallis tests. Independence of two categorical parameters was tested by chi-square test. RESULTS: We demonstrated no influence of the investigated laboratory parameters on PD-L1 expression in NSCLC, either in continuous or categorical division of variables. CONCLUSION: Inflammatory laboratory parameters at time of NSCLC diagnosis are unlikely to affect the determination of PD-L1 expression.

Comedication with corticosteroids and nonsteroidal antiphlogistics does not affect PD-L1 expression in non-small cell lung cancer.

Background: Programmed death-ligand 1 (PD-L1) expression is a standard predictor in the selection of immunotherapy for locally advanced/advanced non-small cell lung cancer (NSCLC). However, comedication with corticosteroids or non-steroidal anti-inflammatory drugs (NSAIDs) may influence the effectiveness of this treatment as documented in several previous studies. Due to certain molecular linkages between PD-L1 and corticosteroids or NSAIDs, we therefore addressed the question of whether there is a relationship between PD-L1 expression in NSCLC and the use of this comedication. Methods: This is a retrospective study using the Czech tumor registry LUng CAncer focuS (LUCAS), from which patient data were drawn. Independence of two categorical parameters was tested by Pearson's chi-square test. Results: In our group of 1,148 patients, we observed no significant relationship between PD-L1 expression and the use of corticosteroids or NSAIDs. Conclusions: According to our data, treatment with corticosteroids or NSAIDs during biopsy does not affect the expression of PD-L1 and it is therefore not necessary to take this treatment into account in this regard.

The Role of Serum Tumor Markers in Follow-up After Surgical Treatment of Malignant Lung Tumors.

AIM: The aim of this study was to evaluate the utility of selected tumor markers for the detection of lung cancer recurrence during follow-up. PATIENTS AND METHODS: The study group consisted of 109 patients and 109 healthy controls. The following biomarkers were selected: Carcinoembryonic antigen; cytokeratin fragment 19; neuron-specific enolase; tissue polypeptide-specific antigen; cytokeratin fragments 8, 18 and 19; insulin-like growth factor 1; pro-gastrin-releasing peptide; and 25-hydroxyvitamin D. The biomarkers were assessed individually or using a multivariate analysis. RESULTS: Carcinoembryonic antigen [area under the receiver operating characteristics curve (AUC)=0.6857, p<0.0001] and cytokeratin fragment 19 (AUC=0.6882, p<0.0001) proved best in detecting relapse. The multivariate model indicated insulin-like growth factor 1 (p=0.0006, AUC=0.6225) as the third most useful biomarker. The multivariate model using these three markers achieved the best AUC value of 0.7730 (p=0.0050). CONCLUSION: We demonstrated that carcinoembryonic antigen and cytokeratin fragment 19 play a key role in the detection of lung cancer recurrence. A multivariate approach can increase the effectiveness of detection.

Prognostic Significance of Lymph Node Examination by the OSNA Method in Lung Cancer Patients-Comparison with the Standard Histopathological Procedure.

The aim of the study was to compare the prognostic significance of lymph node status of patients with lung cancer analyzed by three different methods: hematoxylin and eosin (H&E), immunohistochemistry of cytokeratin 19 (IHC CK19), and One-Step Nucleic Acid Amplification (OSNA). The clinical relevance of the results was evaluated based on relation to prognosis; the disease-free interval (DFI) and overall survival (OS) were analyzed. During radical surgical treatment, a total of 1426 lymph nodes were obtained from 100 patients, creating 472 groups of nodes (4-5 groups per patient) and examined by H&E, IHC CK19 and OSNA. The median follow-up was 44 months. Concordant results on the lymph node status of the H&E, IHC CK19 and OSNA examinations were reported in 78% of patients. We recorded shorter OS in patients with positive results provided by both OSNA and H&E. The study demonstrated a higher percentage of detected micrometastases in lymph nodes by the OSNA method. However, the higher sensitivity of the OSNA, with the cut-off value 250 copies of mRNA of CK19/µL, resulted in a lower association of OSNA positivity with progress of the disease compared to H&E. Increasing the cut-off to 615 copies resulted in an increase in concordance between the OSNA and H&E, which means that the higher cut-off is more relevant in the case of lung tumors.

Outcomes and Prognostic Factors Following Surgical Treatment of Pulmonary Metastases from Colorectal Carcinoma.

BACKGROUND/AIM: The lungs are the second most common site of cancer dissemination. The aim of this study was to analyze a cohort of patients operated for pulmonary metastases from colorectal carcinoma over a period of 18 years. PATIENTS AND METHODS: In a group of 104 patients, relations were sought between overall survival or disease-free survival and preoperative levels of selected biomarkers, number of metastases and the condition of the intrathoracic lymphatic nodes. Median observation period was 63 months. RESULTS: The 5-year survival rate was 54.3%. Risk of disease progression and risk of death increases in case of occurrence of 2 or more metastases, affection of intrathoracic lymph nodes and levels of CA 19-9, TPS or CEA above cut-off value. CONCLUSION: Prognostic factors that determine overall survival as well as disease-free survival are the number of metastases, the condition of intrathoracic lymphatic nodes and the preoperative levels of biomarkers.