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Aims/background: Johanson-Blizzard syndrome (JBS) is a rare autosomal recessive disease caused by pathogenic variants in the UBR1 gene. JBS is usually suspected based on characteristic anomalies, but only genetic testing provides a definitive diagnosis. Since most variants are inherited from the parents, we aimed to identify the causal variants in a Czech proband with clinically suspected JBS and perform segregation analysis., Methods: A proband with clinically suspected JBS underwent clinical exome sequencing (CES). Sanger sequencing was used for the validation, characterization, and segregation of variants in the family. The variants were also characterized using quantitative real-time PCR (qPCR) and in silico analysis., Results: Using CES in the proband, we identified two novel causal variants in the UBR1 gene, c.3482A>C and c.3509+6T>C. Although the variants were found in trans, neither was detected in the parents. Sanger sequencing of the cDNA revealed that the novel variant c.3509+6T>C caused activation of the non-canonical GC donor splice site. The inclusion of 70 bp of the intronic sequence generated a frameshift and a premature termination codon leading to nonsense-mediated decay, as detected by qPCR. In silico protein structural analysis showed that the novel missense variant c.3482A>C in the zinc-stabilized domain RING-H2 altered a highly conserved zinc-coordinating histidine by proline., Conclusion: To the best of our knowledge, we report the first molecular confirmation of JBS in the Czech Republic and the first identification of two de novo causal variants in two alleles. Our findings also expand the spectrum of pathogenic variants in the UBR1 gene., Competing Interests: The authors report no conflicts of interest in this work.

The accurate identification of the primary tumor origin in metastatic cancer cases is crucial for guiding treatment decisions and improving patient outcomes. Copy number alterations (CNAs) and copy number variation (CNV) have emerged as valuable genomic markers for predicting the origin of metastases. However, current models that predict cancer type based on CNV or CNA suffer from low AUC values. To address this challenge, we employed a cutting-edge neural network approach utilizing a dataset comprising CNA profiles from twenty different cancer types. We developed two workflows: the first evaluated the performance of two deep neural networks-one ReLU-based and the other a 2D convolutional network. In the second workflow, we stratified cancer types based on anatomical and physiological classifications, constructing shallow neural networks to differentiate between cancer types within the same cluster. Both approaches demonstrated high AUC values, with deep neural networks achieving a precision of 60%, suggesting a mathematical relationship between CNV type, location, and cancer type. Our findings highlight the potential of using CNA/CNV to aid pathologists in accurately identifying cancer origins with accessible clinical tests.

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., (Copyright © 2023, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

BAP1-inactivated melanocytic tumor (BIMT) is a group of melanocytic neoplasms with epithelioid cell morphology molecularly characterized by the loss of function of BAP1, a tumor suppressor gene located on chromosome 3p21, and a mutually exclusive mitogenic driver mutation, more commonly BRAF. BIMTs can occur as a sporadic lesion or, less commonly, in the setting of an autosomal dominant cancer susceptibility syndrome caused by a BAP1 germline inactivating mutation. Owing to the frequent identification of remnants of a conventional nevus, BIMTs are currently classified within the group of combined melanocytic nevi. "Pure" lesions can also be observed. We studied 50 BIMTs from 36 patients. Most lesions were composed of epithelioid melanocytes of varying size and shapes, resulting extreme cytomorphological heterogeneity. Several distinctive morphological variants of multinucleated/giant cells were identified. Some hitherto underrecognized microscopic features, especially regarding nuclear characteristics included nuclear blebbing, nuclear budding, micronuclei, shadow nuclei, peculiar cytoplasmic projections (ant-bear cells) often containing micronuclei and cell-in-cell structures (entosis). In addition, there were mixed nests of conventional and BAP1-inactivated melanocytes and squeezed remnants of the original nevus. Of the 26 lesions studied, 24 yielded a BRAF mutation, while in the remaining two cases there was a RAF1 fusion. BAP1 biallelic and singe allele mutations were found in 4/22 and 16/24 neoplasms, respectively. In five patients, there was a BAP1 germline mutation. Six novel, previously unreported BAP1 mutations have been identified. BAP1 heterozygous loss was detected in 11/22 lesions. Fluorescence in situ hybridization for copy number changes revealed a related amplification of both RREB1 and MYC genes in one tumor, whereas the remaining 20 lesions studied were negative; no TERT-p mutation was found in 14 studied neoplasms. Tetraploidy was identified in 5/21 BIMTs. Of the 21 patients with available follow-up, only one child had a locoregional lymph node metastasis. Our results support a progression of BIMTs from a conventional BRAF mutated in which the original nevus is gradually replaced by epithelioid BAP1-inactivated melanocytes. Some features suggest more complex underlying pathophysiological events that need to be elucidated., (© 2021. The Author(s), under exclusive licence to United States & Canadian Academy of Pathology.)

A number of recently described renal tumor entities share an eosinophilic/oncocytic morphology, somewhat solid architectural growth pattern, and tendency to present as low-stage tumors. The vast majority of such tumors follow a non-aggressive clinical behavior. In this review, we discuss the morphological, immunohistochemical, and molecular genetic profiles of the three most recent novel/emerging renal entities associated with TSC/mTOR pathway mutations. These are eosinophilic solid and cystic renal cell carcinoma, eosinophilic vacuolated tumors, and low-grade oncocytic tumors, which belong to a heterogeneous group of renal tumors, demonstrating mostly solid architecture, eosinophilic/oncocytic cytoplasm, and overlapping morphological and immunohistochemical features between renal oncocytoma and chromophobe renal cell carcinoma. All three tumors also share a molecular genetic background with mutations in the mTORC1 pathway ( TSC1/TSC2/mTOR/RHEB ). Despite the common genetic background, it appears that the tumors with TSC/mTOR mutations represent a diverse group of distinct renal neoplasms.

We present a 72 years old male with a left nasal cavity (mammary analogue) secretory carcinoma (SC) which exhibited classical morphological features on light microscopical examination, diffuse strong S100 and mammoglobin positivity on immunohistochemistry, and ETV6-NTRK3 gene fusion on next generation sequencing (NGS) analysis. Unusual features of this tumor are expression of p63 and DOG1 on immunohistochemistry and the atypical junction between Exon 4 of the ETV6 gene and Exon 14 of the NTRK3 gene.

The onset of routine use of the next generation sequencing (NGS) leads to discovery of new mutations in non-small cell lung cancer (NSCLC). In addition, comprehension of therapeutic potential of these genetic alterations in clinical practice is needed and required. Both, rare mutations and the therapeutic considerations they prompt, are dealt with in our case report describing a new fusion mutation of the fibroblast growth factor receptor (FGFR). Our case report describes a 45-year Caucasian female, non-smoker, with the tyrosine-protein kinase Met (cMET) skip 14 mutation and a newly described fibroblast growth factor receptor-cholinergic receptor, nicotinic, alpha 6 (FGFR-CHNRA6) fusion. The tumor in this patient showed aggressive growth and was resistant to all treatment modalities administered (including combination chemotherapy with bevacizumab, pemetrexed and nintedanib), with the exception of very short efficacy of crizotinib. The patient died 5 months after diagnosis. According to the published literature, a theoretical future solution could be to administer multidimensional targeted therapy simultaneously., Competing Interests: Conflicts of Interest: MS reports grants from Ministry of Health of the Czech Republic, during the conduct of the study; personal fees from Pharmaceutical industry - AZ, Roche, BI, BMS, MSD, outside the submitted work., (2020 Translational Cancer Research. All rights reserved.)

Background: Multiple familial trichoepithelioma type 1 (MFT1; MIM 601606), a rare monogenic skin disease with autosomal dominant inheritance, is characterized by the development of multiple skin-colored papules on the central area of the face, frequently occurring in the nasolabial area. The disease is associated with various mutations in the cylindromatosis (CYLD; MIM 605018) gene that are also responsible for familial cylindromatosis (FC) and Brooke-Spiegler syndrome (BSS)., Methods: Recently we have identified a Spanish MFT1 pedigree with two affected family members (father and daughter). Direct sequencing of the CYLD gene revealed a worldwide recurrent heterozygous nonsense mutation (c.2272C/T, p.R758X) in the patients., Results: This mutation has already been detected in patients with all three clinical variants - BSS, FC and MFT1 - of the CYLD-mutation spectrum. Haplotype analysis was performed for the Spanish patients with MFT1, Dutch patients with FC and an Austrian patient with BSS, all of whom carry the same heterozygous nonsense p.R758X CYLD mutation., Conclusions: Our results indicate that this position is a mutational hotspot on the gene and that patients carrying the mutation exhibit high phenotypic diversity.

It is generally accepted that the most ancient European mitochondrial haplogroup, U5, has evolved essentially in Europe. To resolve the phylogeny of this haplogroup, we completely sequenced 113 mitochondrial genomes (79 U5a and 34 U5b) of central and eastern Europeans (Czechs, Slovaks, Poles, Russians and Belorussians), and reconstructed a detailed phylogenetic tree, that incorporates previously published data. Molecular dating suggests that the coalescence time estimate for the U5 is approximately 25-30 thousand years (ky), and approximately 16-20 and approximately 20-24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe. In addition, during the Last Glacial Maximum central Europe (probably, the Carpathian Basin) apparently represented the area of intermingling between human flows from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees. Age estimations amounting for many U5 subclusters in eastern Europeans to approximately 15 ky ago and less are consistent with the view that during the Ice Age eastern Europe was an inhospitable place for modern humans.

The sequencing of the entire mitochondrial DNA belonging to haplogroup U2d reveals that this clade is defined by four coding-region mutations at positions 1700, 4025, 11893, and 14926. Phylogenetic analysis suggests that western Eurasian haplogroup U2d appears to be a sister clade with the Indo-Pakistani haplogroup U2c. Results of a phylogeographic analysis of published population data on the distribution of haplogroup U2d indicate that the presence of such mtDNA lineages in Europe may be mostly a consequence of medieval migrations of nomadic tribes from the Caucasus and eastern Europe to central Europe.

To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European-specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.

To elucidate the human colonization process of northern Asia and human dispersals to the Americas, a diverse subset of 71 mitochondrial DNA (mtDNA) lineages was chosen for complete genome sequencing from the collection of 1,432 control-region sequences sampled from 18 autochthonous populations of northern, central, eastern, and southwestern Asia. On the basis of complete mtDNA sequencing, we have revised the classification of haplogroups A, D2, G1, M7, and I; identified six new subhaplogroups (I4, N1e, G1c, M7d, M7e, and J1b2a); and fully characterized haplogroups N1a and G1b, which were previously described only by the first hypervariable segment (HVS1) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings indicate that the southern Siberian mtDNA pool harbors several lineages associated with the Late Upper Paleolithic and/or early Neolithic dispersals from both eastern Asia and southwestern Asia/southern Caucasus. Moreover, the phylogeography of the D2 lineages suggests that southern Siberia is likely to be a geographical source for the last postglacial maximum spread of this subhaplogroup to northern Siberia and that the expansion of the D2b branch occurred in Beringia ~7,000 years ago. In general, a detailed analysis of mtDNA gene pools of northern Asians provides the additional evidence to rule out the existence of a northern Asian route for the initial human colonization of Asia.

Mitochondrial DNA (mtDNA) variability was studied in a sample of 179 individuals representing the Czech population of Western Bohemia. Sequencing of two hypervariable segments, HVS I and HVS II, in combination with screening of coding-region haplogroup-specific RFLP markers revealed that most Czech mtDNAs belong to the common West Eurasian mitochondrial haplogroups (H, pre-V HV*, J, T, U, N1, W, and X). However, about 3% of Czech mtDNAs encompass East Eurasian lineages (A, N9a, D4, M*). A comparative analysis with published data showed that different Slavonic populations in Central and Eastern Europe contain small but marked amounts of East Eurasian mtDNAs. We suggest that the presence of East Eurasian mtDNA haplotypes is not an original feature of the gene pool of the proto-Slavs but rather may be mostly a consequence of admixture with Central Asian nomadic tribes, who migrated into Central and Eastern Europe in the early Middle Ages.

Gastrointestinal stromal tumor (GIST) is a rare neoplasm exhibiting, in most cases, mutations of c-kit. Recently it has been demonstrated that a majority of GIST patients with c-kit mutations respond to therapy with imatinib, a c-kit tyrosine kinase inhibitor. Although the response rate in patients treated with imatinib in prospective clinical studies is above 50%, complete response is rare, and the data on the use of imatinib as neoaduvant therapy facilitating radical surgery is still scanty. Here, we report on a patient with metastatic gastric GIST who underwent surgery after 6 months of imatinib therapy. No tumor cells were detected on pathological examination of resection specimen. This case report indicates that a pathological complete response could be achieved with imatinib therapy in patients with GIST, but a wider experience and longer follow-up is necessary to appreciate the prognostic significance of pathological complete response in GIST.