Comprehensive clinicopathological, molecular, and methylation analysis of mesenchymal tumors with NTRK and other kinase gene aberrations.

Alterations in kinase genes such as NTRK1/2/3, RET, and BRAF underlie infantile fibrosarcoma (IFS), the emerging entity 'NTRK-rearranged spindle cell neoplasms' included in the latest WHO classification, and a growing set of tumors with overlapping clinical and pathological features. In this study, we conducted a comprehensive clinicopathological and molecular analysis of 22 cases of IFS and other kinase gene-altered spindle cell neoplasms affecting both pediatric and adult patients. Follow-up periods for 16 patients ranged in length from 10 to 130 months (mean 38 months). Six patients were treated with targeted therapy, achieving a partial or complete response in five cases. Overall, three cases recurred and one metastasized. Eight patients were free of disease, five were alive with disease, and two patients died. All cases showed previously reported morphological patterns. Based on the cellularity and level of atypia, cases were divided into three morphological grade groups. S100 protein and CD34 were at least focally positive in 12/22 and 14/22 cases, respectively. Novel PWWP2A::RET, NUMA1::RET, ITSN1::RAF1, and CAPZA2::MET fusions, which we report herein in mesenchymal tumors for the first time, were detected by RNA sequencing. Additionally, the first uterine case with BRAF and EGFR mutations and CD34 and S100 co-expression is described. DNA sequencing performed in 13 cases uncovered very rare additional genetic aberrations. The CNV profiles showed that high-grade tumors demonstrate a significantly higher percentage of copy number gains and losses across the genome compared with low- and intermediate-grade tumors. Unsupervised clustering of the tumors' methylation profiles revealed that in 8/9 cases, the methylation profiles clustered with the IFS methylation class, irrespective of their clinicopathological or molecular features. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Desmoplasia in non-small cell lung carcinomas is associated with low programmed death-ligand 1 expression and the absence of tumor-infiltrating lymphocytes.

Programmed death-ligand 1 (PD-L1) is the most widely utilized predictive marker used to identify non-small cell lung carcinoma (NSCLC) patients most suitable for immunotherapy approaches. The relationship between PD-L1 expression, the presence of CD8+ T cells, and other clinicopathological characteristics of NSCLC patients has not been elucidated yet. In this retrospective study, we immunohistochemically determined PD-L1 expression (using clone 22C3) and CD8+ T cell count (using clone c8/144B) in surgical resection specimens from 698 advanced NSCLC patients. Results of PD-L1 expression and CD8+ T cell count were correlated to various clinicopathological characteristics, including the presence of desmoplasia in NSCLC. Regarding the immunological attributes of the tumor microenvironment, we identified major differences between desmoplastic and non-desmoplastic areas in NSCLC. Tumor areas without desmoplasia were significantly more often PD-L1 positive than tumor cell clusters encased in a dense collagenous stroma (p=0.004). Furthermore, the desmoplastic stroma contained significantly less often an immune cell infiltrate rich in CD8+ T cells (p<0.001). Also, the positivity of PD-L1 significantly correlated with advanced N-stage (p<0.001) and poor differentiation in adenocarcinomas (p=0.032) but not with other clinicopathological characteristics. In conclusion, to our knowledge, this is the first study that points to major differences in terms of immunological attributes between desmoplastic and non-desmoplastic areas in NSCLC. The desmoplastic component, therefore, may represent an immunologically distinct tumor area in which PD-L1 immunohistochemistry and CD8+ T cell count should be evaluated separately.

Modelling Duchenne muscular dystrophy in vitro with newly generated, blood cell-derived induced pluripotent stem cell line ORIONi003-A.

Here, we present newly derived in vitro model for modeling Duchenne muscular dystrophy. Our new cell line was derived by reprogramming of peripheral blood mononuclear cells (isolated from blood from pediatric patient) with Sendai virus encoding Yamanaka factors. Derived iPS cells are capable to differentiate in vitro into three germ layers as verified by immunocytochemistry. When differentiated in special medium, our iPSc formed spontaneously beating cardiomyocytes. As cardiomyopathy is the main clinical complication in patients with Duchenne muscular dystrophy, the cell line bearing the dystrophin gene mutation might be of interest to the research community.

Small-scale variants and large deletions in BRCA1/2 genes in Slovak high-grade serous ovarian cancer.

The role of PARP inhibitors is to prevent the polymerase from repairing the single-strand break that occurred due to tumor growth and thus induce cell apoptosis when the homologous recombination deficiency (HRD) system is disabled. The eliminated system can be monitored especially in patients with serous ovarian epithelial tumors. Current studies still show the highest progression-free survival (PFS) in the examined groups with BRCA mutant status, even though they are also effective in the case of a disrupted HRD system, apart from BRCA genes. The study cohort consists of women diagnosed with high-grade serous ovarian cancer (HGSOC), after at least two lines of chemotherapy and after relapse of the disease, as determined by ESMO standards and guidelines. The commercially available tool SOPHIA DDM™ (SophiaGenetics, Switzerland) was used to classify the variants after sequencing. The most common variants (pathogenic or likely pathogenic) were in BRCA1 c.1067 A>G (rs1799950) and c.5266dupC (rs80357906) and in BRCA2 c.9976 A>T (rs11571833). Large deletions were detected in one and three cases in the BRCA1 and BRCA2 genes, respectively. A mutation in the BRCA1/2 genes was confirmed in 50% of the examined patients. In the study, we focused on the identification of mutated BRCA genes by a commercially available Sophia DDM™ system to identify a pathogenic or probable pathogenic variant in a cohort of patients with HGSOC in the Slovak population, which could result in better management and stratification of the individual.

Programmed death ligand-1 expression and its association with the degree of differentiation and the presence of necrosis in non-small cell lung carcinoma.

The mechanisms underlying the expression of programmed death ligand-1 (PD-L1) in non-small cell lung carcinoma (NSCLC) are not yet fully clarified. In this study, surgical resections of 730 lung cancer patients with diagnosed NSCLC were analyzed. Results of PD-L1 immunohistochemistry (using clone 22C3) were correlated with clinicopathological variables including the degree of tumor differentiation and the presence of confluent areas of coagulative necrosis. PD-L1 immunohistochemistry was analyzed in tumor cells, whereas PD-L1 positivity was defined as membranous staining in ≥ 1 of tumor cells. A significantly higher proportion of PD-L1 positive cases was noted in poorly differentiated (grade 3) adenocarcinomas compared to better differentiated (grade 1 and grade 2) subtypes (63.8 % vs. 28.7 %; p < 0.001). Contrary to this, better differentiated (keratinizing) and less differentiated (non-keratinizing) squamous cell carcinoma subtypes were found to have a similar proportion of PD-L1 positive cases (51.4 % vs. 55.8 %; p = 0.570). High levels of PD-L1 expression significantly correlated with the presence of necrosis in NSCLC: seventy-nine of 109 NSCLC cases with the presence of necrosis were PD-L1 positive compared to 256 out of 621 NSCLC without necrosis (72.5 % vs. 41.2 %; p < 0.001). High PD-L1 expression was not positively correlated with age, gender, and advanced T stage but a significant association between PD-L1 positivity and higher N stage was observed (p < 0.001) in NSCLC patients. In conclusion, the proportion of PD-L1 positive cases is higher only in poorly differentiated NSCLC of the adenocarcinoma type. A significantly higher overall rate of PD-L1 positive cases was noted in NSCLC with the presence of necrosis. Further investigation is suggested to elucidate the intricated interconnections between the plethora of hypoxic biomarkers and immunological factors in different types and subtypes of NSCLC.

An EGFR-mutant lung adenocarcinoma that transformed into small-cell lung cancer. A case report.

BACKGROUND: Transformation of EGFR (epidermal growth factor receptor) - mutant non-small cell lung cancer (NSCLC) into small-cell lung cancer (SCLC) is one mechanism of resistance to tyrosine kinase inhibitor (TKI) treatment, seen in approximately 3-10% cases. Such transformed SCLC often retains the original EGFR mutation (EGFRM), which is not otherwise observed in SCLC. CASE REPORT: We present a 67 y/o woman with pulmonary adenocarcinoma (AC) and EGFRM deletion on exon 19. After initial treatment with whole brain radiotherapy and 7 months of TKI afatinib, progression was observed. Liquid biopsy detected deletion on exon 19 and T790M mutation. Chemotherapy carboplatin plus pemetrexed was administered, with no response. Genetics from a rebiopsy of lung revealed deletion on exon 19. After 12 months treatment with TKI osimertinib, a progression in lung and pancreas lesions was detected, docetaxel was used, with followig progression. The lung biopsy revealed SCLC. Significant elevation of serum markers carcinoembryonic antigen (CEA) and neuron-specific enolase (NSE) was observed at the time of the SCLC diagnosis. Treatment with carboplatin and etoposide was not effective. The next biopsy found two populations of cells: SCLC and AC. The biopsy from the pancreatic lesion revealed metastasis of SCLC. PCR confirmed EGFRM deletion on exon 19 in the lung SCLC tissue sample. The following treatment lines of topotecan, erlotinib were not effective. The patient survived 36 months from diagnosis, 7 months from detection of SCLC. CONCLUSION: Screening for transformation of EGFR-mutant NSCLC to SCLC should be considered in resistance to TKI. In the presented case, this rare transformation was confirmed by histopathologic examination and by PCR. EGFRM in the lung SCLC, identical to that found in the original lung AC, was detected. Further, the observed elevation of serum tumor markers NSE and CEA can indicate this infrequent transformation and help to decide on rebiopsy.

In vitro modeling of amyotrophic lateral sclerosis with induced pluripotent stem cell technology-derived cell line ORIONi002-A.

We present here a new iPS cell line for modeling sporadic form of ALS. Cell line was generated by reprogramming skin fibroblasts isolated with explant culture technology from skin biopsy, donated by ALS patient. For reprogramming, polycistronic self-replicating RNA vector was used and derived iPS cells were characterized by immunocytochemistry and FACS (pluripotent factors expression), karyotyping, STR fingerprinting analysis and in vitro differentiation assay. New cell line showed normal (46, XY) karyotype and differentiated in vitro into cells from three germ layers. STR analysis proved the origin and originality of the cell line.

High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements: Biopsy analysis of 70 cases from the Slovak Lymphoma Registry.

We performed a twelve-year retrospective analysis of diffuse large B-cell lymphoma (DLBCL) patients' biopsies with rearrangements of genes MYC, BCL2, and/or BCL6, commonly referred to as double-hit and triple-hit high-grade B-cell lymphomas (DH/TH HGBL). Our aim was to present complex characteristics of the DH/TH HGBL group of patients diagnosed in the Slovak National Lymphoma Register together with the evaluation of the relationship between immunohistochemical (IHC) protein expressions of c-myc, bcl2, bcl6, and cyclin D1 in tissue specimens and the presence of rearrangements of their protein-coding genes by FISH analysis in order to find a clinically relevant diagnostic algorithm that would be the most time- and cost-efficient. For this study, a standard panel of histomorphological, IHC, and FISH methods was used to analyze the characteristics of 70 DH/TH HGBL patients' biopsies. Our study showed a predominance of the immunohistochemical GCB subtype over the non-GCB subtype (59:10 cases) in DH/TH lymphomas. The centroblastic morphology was the most commonly observed (30/70 cases; 43%). Furthermore, our study showed a high predominance of DH lymphoma cases with simultaneous MYC and BCL2 genes rearrangements (40/70; 57%), followed by an almost equal incidence of DH lymphomas with rearrangements of MYC and BCL6 genes (16/70; 23%) and of TH lymphomas (14/70; 20%). 15 of 16 FISH-examined DLBCL cases were negative for CCND1 rearrangement. A great majority of DH/TH cases showed also immunohistochemical overexpression of corresponding proteins (62/70; 89%), mostly in a form of triple expressor of c-myc/bcl2/bcl6 proteins (36/70; 51%), followed by c-myc/bcl2 and c-myc/bcl6 double expressor proteins positivity (20/70 and 6/70, respectively). Comparing preferential FISH testing of DE/TE and GCB DLBCL cases for genetic rearrangements we would be able to detect 89% and 84% of our HGBL-DH, TH group of patients, respectively. None of the examined methods for economically rational FISH testing showed enough concordance with IHC analysis results. We might, therefore, advocate the complex testing of all DLBCL patients' biopsies including FISH analyses.

Expression of programmed death-ligand 1 protein in pulmonary squamous cell carcinoma correlates with tumour necrosis but not with tumour differentiation.

AIMS: Pulmonary squamous cell carcinoma (SqCC) represents the second most common non-small cell lung carcinoma type. The mechanisms which regulate programmed death ligand 1 (PD-L1) expression in this form of lung cancer are not fully elucidated yet. METHODS: We immunohistochemically determined the level of PD-L1 expression using the Tumour Proportion Score system in surgical resections of 133 patients with pulmonary SqCC. The results from PD-L1 immunohistochemistry were analysed in relation to tumour differentiation and the presence of necrotic areas comprising at least 20% of the tumour mass. RESULTS: No significant differences in terms of PD-L1 expression were found between SqCC subtypes as defined by the current WHO classification: better differentiated, keratinising tumours (12/24, 50.0 %) compared with less differentiated, non-keratinising and basaloid forms (62/109, 56.9 %) were PD-L1 positive in a comparable proportion of cases (p=0.1903). Contrary to that, SqCCs with the presence of necrosis (51/61, 83.6 %) had significantly more PD-L1-positive cases (p<0.001) compared with SqCCs without necrotic areas (23/72, 32.0 %) CONCLUSIONS: We demonstrated that PD-L1 expression in pulmonary SqCCs does not correlate with the traditionally defined degree of differentiation of these tumours. On the other hand, we found a significant association between the positive result of PD-L1 immunohistochemistry and tumour necrosis. Further investigation regarding the role of hypoxic pathways as presumable inducers of PD-L1 expression in pulmonary SqCCs might contribute to the understanding of this phenomenon.

Establishment of PANDA - a new human pancreatic ductal adenocarcinoma cell line with 3D cell culture technology.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive type of malignancy with one of the worst prognoses amongst any type of cancer. Surgery is applicable only to the limited number of patients with locally resectable tumors and currently represents the only curative treatment option. Treatment with chemotherapy and radiotherapy can only extend patient survival. Despite advances in conventional therapies, the five-year survival of PDAC remained largely unchanged. New in vitro and in vivo models are therefore urgently needed to investigate this type of cancer. Here, we present the establishment and characterization of a novel pancreatic cancer cell line, isolated from a patient with PDAC. Cell line abbreviated as PANDA (PANncreatic Ductal Adenocarcinoma) was established with an optimized 3D culture protocol published previously by our group. The new cancer cell line "PANDA" represents a novel in vitro approach for PDAC cancer research and new therapy testing.

Screening for the Key Proteins Associated with Rete Testis Invasion in Clinical Stage I Seminoma via Label-Free Quantitative Mass Spectrometry.

Rete testis invasion (RTI) is an unfavourable prognostic factor for the risk of relapse in clinical stage I (CS I) seminoma patients. Notably, no evidence of difference in the proteome of RTI-positive vs. -negative CS I seminomas has been reported yet. Here, a quantitative proteomic approach was used to investigate RTI-associated proteins. 64 proteins were differentially expressed in RTI-positive compared to -negative CS I seminomas. Of them, 14-3-3γ, ezrin, filamin A, Parkinsonism-associated deglycase 7 (PARK7), vimentin and vinculin, were validated in CS I seminoma patient cohort. As shown by multivariate analysis controlling for clinical confounders, PARK7 and filamin A expression lowered the risk of RTI, while 14-3-3γ expression increased it. Therefore, we suggest that in real clinical biopsy specimens, the expression level of these proteins may reflect prognosis in CS I seminoma patients.

Detection of therapeutically relevant and concomitant rare somatic variants in colorectal cancer.

In colorectal cancer (CRC), clinically relevant biomarkers are known for genome-guided therapy that can be detected by both first and next generation methods. The aim of our work was to introduce a robust NGS assay that will be able to detect, in addition to standard predictive single nucleotide-based biomarkers, even rare and concomitant clinically relevant variants. Another aim was to identify truncating mutations in APC and pathogenic variants in TP53 to divide patients into potentially prognostic groups. A multigene panel with hotspots in 50 cancer-critical genes was used. Finally, 86 patients diagnosed with primary or metastatic colorectal cancer were enrolled. In total, there were identified 163 pathogenic variants, among them in the genes most recurrent mutated in CRC such as TP53 (49%), the RAS family genes KRAS and NRAS (47%), APC (43%), and PIK3CA (15%). In 30 samples, two driver mutations were present in one sample, 11 patients were without any mutations covered by this panel. In one patient, a novel variant in BRAF p.D594E was found, not previously seen in CRC, and was concomitant with KRAS p.G12A. In KRAS, a potentially sensitive mutation to anti-EGFR therapy p.A59T was found along with the PIK3CA missense variant p.E545K. It was possible to divide patients into groups based on the occurrence of truncating APC variant alone or concomitant with TP53 or KRAS. Our results demonstrate the potential of small multigene panels that can be used in diagnostics for the detection of rare therapeutically relevant variants. Moreover, the division of patients into groups based on the presence of APC and TP53 mutations enables this panel to be used in retrospective studies on the effectiveness of treatment with anti-EGFR inhibitors.

Placental pathology concerning sudden foetal demise in SARS-CoV-2 positive asymptomatic pregnant female.

AIMS: Coronavirus disease 2019 is responsible for a worldwide increase in morbidity and mortality. The relationship of this infection to mother-to-child vertical transmission has not been elucidated yet. However, recent reports indicate a foetal death rate of up to 3%. METHODS: We report a case of sudden pre-term foetal demise in a woman positive for SARS-CoV-2 but asymptomatic, with physiological course of pregnancy. RESULTS: One of the possible explanations of sudden foetal death may be acute placental insufficiency caused by a SARS-CoV-2 placental infection or the development of foetal inflammatory response syndrome (FIRS). CONCLUSION: Considering the potential risk of foetal demise, questions remain regarding foetal monitoring and the timing of labour and delivery in the second and third trimesters, particularly in asymptomatic or mild maternal SARS-CoV-2 infection. A relevant multidisciplinary team must also be aware of these risks associated with possibly fatal consequences.

High-grade serous ovarian carcinoma and detection of inactivated BRCA genes from biopsy material of Slovak patients.

Ovarian cancer is the leading cause of mortality among all gynecological cancers in developed countries and its most common and most lethal type is the high-grade serous ovarian carcinoma (HGSC). At the molecular level, nearly half of all HGSCs exhibit ineffective homologous DNA recombination and disruption of DNA damage/repair pathway inactivation caused often by BRCA1 and BRCA2 gene mutation. Recently, the detection of BRCA1/2 mutations became important for personalized treatment of HGSC patients with the PARP-inhibitors in the defined clinical setting of relapse after positive adjuvant platinum-based chemotherapeutic response. Based on the selection of patients by regional oncologists, we attempted to verify the possibilities of BRCA1/2 mutation testing on archival formalin-fixed paraffin-embedded (FFPE) biopsy material from regional hospitals. In the study we used: a/ FFPE tumor resections of 97 patients sent to our laboratory, originally stored in archives of regional departments for a period of 1-3 years and retrieved on the principle to contain a maximum of non-necrotic tumor tissue, b/ next-generation sequencing (NGS) assay covering all known mutations in the BRCA1/2 genes on MiSeq (Illumina® platform), and c/ Sophia DDM® bioinformatics platform. After processing of FFPE samples, 5 cases were excluded due to the insufficient genomic DNA quantity. Bioinformatics results of NGS analyses of 92 patients' samples indicated 17.39% pathogenic mutations and 32.61% potentially pathogenic mutations in genes BRCA1/2. Overall, 50% pathogenic and potentially pathogenic mutations were detected in the patient's cohort. The relatively high incidence of BRCA1/2 mutations in our series may be influenced by various indicators including the selection of patients based on adjuvant therapy response as well as regional or population heterogeneity in their frequency. Based on the interdisciplinary cooperation, the use of archival biopsy material processed primarily and stored for a longer period in different laboratories without uniformly defined pre-analytical conditions allows identifying the HGSC patients who might better respond to the PARP-inhibition therapy.

Pyoderma gangrenosum-like ulceration as a presenting feature of pediatric granulomatosis with polyangiitis.

BACKGROUND: Granulomatosis with polyangiitis (GPA) is an anti-neutrophilic cytoplasmic antibody-associated vasculitis affecting small to medium-sized vessels and involves most commonly the kidneys and the respiratory tract. Skin involvement can be seen in up to 50% of children with GPA and is the initial presenting symptom in 7.7%. Pyoderma gangrenosum (PG)-like ulcers are rarely described as a skin manifestation in GPA and very few cases have been reported previously in children. CASE PRESENTATION: We describe 3 new pediatric cases of GPA with PG-like ulcerations. The median age at first symptom was 15 years. Two patients had PG-like ulceration as their initial presentation; additional symptoms eventually led to the diagnosis of GPA 2-24 months later. In 1 case, proteinase 3 (PR3) was negative when first tested, but converted to positive when systemic symptoms emerged; in the other 2 cases PR3 was positive at presentation. All 3 patients had prominent facial lesions. None of the patients responded to treatment with antibiotics or medications commonly used to manage PG, including corticosteroids and cyclosporine. All patients had excellent responses to rituximab. An electronic database literature review was performed and 4 previously reported cases were identified. We assessed the clinical characteristics, serology, and response to treatment of the previously reported and our newly diagnosed cases. CONCLUSION: PG-like ulceration is a rare presentation of pediatric GPA which may precede classic systemic GPA symptoms. The predominance of facial ulcer, granulomatous and neutrophilic inflammation on skin biopsy and lack of response to PG treatments are characteristic of GPA-associated PG-like ulcers. Our review suggests that treatment with rituximab may be needed to improve the skin lesions. Recognizing that PG-like ulcerations can occur in pediatric GPA may result in timely diagnosis, appropriate treatment and improved prognosis.

Novel BRAF gene fusions and activating point mutations in spindle cell sarcomas with histologic overlap with infantile fibrosarcoma.

Infantile fibrosarcoma (IFS)/cellular congenital mesoblastic nephroma (cCMN) commonly harbors the classic ETV6-NTRK3 translocation. However, there are recent reports of mesenchymal tumors with IFS-like morphology harboring fusions of other receptor tyrosine kinases or downstream effectors, including NTRK1/2/3, MET, RET, and RAF1 fusions as well as one prior series with BRAF fusions. Discovery of these additional molecular drivers contributes to a more integrated diagnostic approach and presents important targets for therapy. Here we report the clinicopathologic and molecular features of 14 BRAF-altered tumors, of which 5 had BRAF point mutations and 10 harbored one or more BRAF fusions. Of the BRAF fusion-positive tumors, one harbored two BRAF fusions (FOXN3-BRAF, TRIP11-BRAF) and another harbored three unique alternative splice variants of EPB41L2-BRAF. Tumors occurred in ten males and four females, aged from birth to 32 years (median 6 months). Twelve were soft tissue based; two were visceral including one located in the kidney (cCMN). All neoplasms demonstrated ovoid to short spindle cells most frequently arranged haphazardly or in intersecting fascicles, often with collagenized stroma and a chronic inflammatory infiltrate. No specific immunophenotype was observed; expression of CD34, S100, and SMA was variable. To date, this is the largest cohort of BRAF-altered spindle cell neoplasms with IFS-like morphology, including not only seven novel BRAF fusion partners but also the first description of oncogenic BRAF point mutations in these tumors.

Prevalence and significance of M541L single nucleotide polymorphism in the central European cohort of gastrointestinal stromal tumor patients.

BACKGROUND: Single nucleotide polymorphisms can create a genetic microenvironment in some tumors that affects the course of treatment, resistance, etc. Whether single nucleotide polymorphisms have an impact on gastrointestinal stromal tumor (GIST) development and disease progression is not yet accurately verified. KIT SNPM541L in exon 10 correlates with a worse prognosis of many cancers. The impact of KIT SNPM541L in GISTs is relatively unknown and, therefore, its analyses could have potential in patient therapy and could provide more detailed information on tumor character, clinical presentation, or tumor behavior in treatment. AIM: The aim of the study was the analysis of the biological and clinical significance of the KIT SNPM541L polymorphism in exon 10. MATERIALS AND METHODS: Paraffin sample tissues were obtained from the National GIST Register in Martin. Retrospective samples from 177 GIST patients were divided into several groups. Detection of SNPM541L was performed by Sanger sequencing. Statisitical analyses were performed to determine the prevalence of KIT SNPM541L in the Slovak GIST cohort, to search for correlation between c-KIT status and clinicopathological, molecular and biological data. RESULTS: Overall, 29 samples out of 177 showed KIT SNPM541L polymorphism. CONCLUSION: Our results do not support the association between KIT SNPM541L and increased risk of relapse in localized primary GISTs. Additionally, we found a positive correlation between KIT SNPM541L occurrence and earlier onset of relapse in PDGFRa and WT subgroup of GISTs.

Non-small cell lung carcinomas with a minor sarcomatoid component and pleomorphic carcinomas are associated with high expression of programmed death ligand 1.

Pleomorphic carcinomas are known to be highly programmed death ligand 1 (PD-L1) positive non-small cell lung cancer (NSCLC) types. However, the level of PD-L1 expression in lung carcinomas with a minor sarcomatoid component, comprising less than 10 % of the tumor mass, has not been determined yet. We hypothesized that NSCLC with a minor sarcomatoid component is more closely related to pleomorphic carcinomas in terms of PD-L1 expression than to NSCLC types without sarcomatoid features. The surgical resections from 690 lung carcinoma patients were retrospectively analyzed for the presence of PD-L1 by means of immunohistochemistry using the 22C3 PharmDx assay. The tumor proportion score system was applied to quantify the level of PD-L1 expression. Membranous staining present in ≥ 1 % of tumor cells was chosen as the cut-off to define a positive result for PD-L1 expression. Tumors were allocated into one of four subgroups: "adenocarcinoma", "squamous cell carcinoma", "pleomorphic carcinoma", or "NSCLC with a minor sarcomatoid component". PD-L1 expression in pleomorphic carcinomas (26/32, 81.3 %) and in the subgroup of NSCLC with a minor sarcomatoid component (35/46, 76.1 %) was identified in a comparable proportion of cases. Pleomorphic carcinomas were significantly more often PD-L1 positive than adenocarcinomas (p < 0.001) or squamous cell carcinomas (p = 0.0015). Accordingly, the proportion of PD-L1 expressing NSCLC with a minor sarcomatoid component was significantly higher than that of the adenocarcinoma (p < 0.001) or squamous cell carcinoma (p = 0.002) subgroup. In summary, we identified a presumable new subgroup of highly PD-L1 positive neoplasms within the NSCLC spectrum that is related to pleomorphic carcinomas in terms of PD-L1 expression. Further investigation regarding genetic relation and mechanism of PD-L1 expression in these two NSCLC categories is recommended.

BRAF mutations in KIT/PDGFRA positive gastrointestinal stromal tumours (GISTs): Is their frequency underestimated?

BRAF V600E mutations in GISTs are considered to be one of the mutational events in KIT/PDGFRA negative or positive GISTs, respectively. BRAF mutated GISTs usually do not respond to imatinib treatment, even more GISTs with imatinib sensitive KIT mutation. However, they are almost phenotypically and morphologically identical with KIT/PDGFRA positive GISTs. In general, due to the small number of BRAF mutations in GIST and because of the rarity of concomitant BRAF/KIT or BRAF/PDGFRA mutations, their frequency may be depreciated. The aim of this study was BRAF mutation detection in KIT/PDGFRA positive GISTs and their verification by other molecular methods. We applied the sensitive droplet digital PCR on 35 randomly selected KIT/PDGFRA positive GISTs to detect V600E mutations. We have established two criteria for the evaluation of samples: false positive rate (FPR) based on the negative controls; Limit of Detection (LoD) based on the serial dilution of positive control from RKO cell line harboring heterozygous V600E mutation in constant wild-type DNA background. Results from ddPCR were verified by other molecular methods: allele-specific PCR, dideoxysequencing, competitive allele-specific TaqMan PCR (castPCR). FPR was determined as 5 (∼4.4) positive droplets, and LoD was assessed to 3.4293 copies/µL what is the method sensitivity of 0.0162 %. We identified eight KIT/PDGFRA positive patients with concomitant V600E mutation. The five of them were in coexistence with KIT mutation and three with PDGFRA mutation. We also included the liver metastasis, but data from primary tumour were not available. We achieved the very high sensitivity of the ddPCR method for detecting BRAF mutation in GISTs to have importance from the point of view of therapy.

Programmed death ligand 1 protein expression, histological tumour differentiation and intratumoural heterogeneity in pulmonary adenocarcinoma.

Intratumoural heterogeneity of pulmonary adenocarcinoma challenges the accurate interpretation of programmed death ligand 1 (PD-L1) immunohistochemistry, which is the only validated predictive marker for successful anti-PD-1/PD-L1 immunotherapy. The aim of this study was to determine whether PD-L1 expression is related to adenocarcinoma histological differentiation in a retrospective analysis of tumour biopsies with intratumoural histological heterogeneity. Adenocarcinomas with high intratumoural heterogeneity were categorised as 'mixed adenocarcinomas'. PD-L1 expression was determined immunohistochemically using tumour proportion scores (TPS). In 'mixed adenocarcinomas' PD-L1 scores were assessed across tumour areas with specific histological patterns. Comparisons were performed between histologically distinct differentiated tumours and/or histological areas. Poorly differentiated adenocarcinomas, represented by predominantly solid or micropapillary histological patterns, showed significantly higher expression of PD-L1 than other subtypes (p<0.001). Differentiation of intra-adenocarcinoma components was inversely correlated with PD-L1 expression: there were more PD-L1 positive cells in poorly differentiated areas than less differentiated (p<0.001), or than well differentiated areas (p<0.001), and in less differentiated more than well differentiated areas (p=0.001). In conclusion, PD-L1 expression is associated with poorly differentiated morphology in adenocarcinomas with intratumoural histological heterogeneity. Consequently, a TPS approach may not account for the contribution of more aggressive tumour components with higher levels of PD-L1 expression in within the tumour. Performing spectral analyses of PD-L1 expression across tumours is likely to be more accurate.