Acidovorax benzenivorans sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from a xylene-degrading enrichment culture.

A Gram-stain-negative strain, designated as D2M1T was isolated from xylene-degrading enrichment culture and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene sequence analysis revealed that strain D2M1T belongs to the genus Acidovorax, with the highest 16S rRNA gene similarity to Acidovorax delafieldii DSM 64T (99.93 %), followed by Acidovorax radicis DSM 23535T (98.77 %) and Acidovorax kalamii MTCC 12652T (98.76 %). The draft genome sequence of strain D2M1T is 5.49 Mb long, and the G+C content of the genome is 64.2 mol%. Orthologous average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain D2M1T and its closest relatives were below the threshold values for species demarcation confirming that strain D2M1T is distinctly separated from its closest relatives. The whole genome analysis of the strain revealed a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including an I.2.C-type catechol 2,3-dioxygenase (C23O) gene. The strain was able to degrade benzene and ethylbenzene as sole sources of carbon and energy under aerobic and microaerobic conditions. Cells were facultatively aerobic rods and motile with a single polar flagellum. The predominant fatty acids (>10 % of the total) of strain D2M1T were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). The major ubiquinone of strain D2M1T was Q8, while the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on polyphasic data, it is concluded that strain D2M1T represents a novel species of the genus Acidovorax, for which the name of Acidovorax benzenivorans sp. nov. is proposed. The type strain of the species is strain D2M1T (=DSM 115238T=NCAIM B.02679T).

Application of comprehensive molecular genetic profiling in precision cancer medicine, Hungarian experiences.

Recent developments in molecular genetic testing methods (e.g. next-generation sequencing [NGS]-panels) largely accelerated the process of finding the most appropriate targeted therapeutic intervention for cancer patients based on molecularly targetable genetic alterations. In Hungary, a centralized approval system following the recommendation of the National Molecular Tumor Board was launched for the coordination of all aspects of comprehensive genetic profiling (CGP) including patient selection and therapy reimbursement. AIM: The study aims to evaluate the clinical benefit of CGP in our Comprehensive Cancer Center Methods and patients: CGP was introduced into our routine clinical practice in 2021. An NGS-based large (> 500 genes) gene panel was used for cases where molecular genetic testing was approved by the National Molecular Tumor Board. From 2021 until August 2023 163 cases were tested. The majority of them were ECOG 0-1 patients with advanced-stage diseases, histologically rare cancer, or cancers with unknown primary tumours. RESULTS: Seventy-four cases (74 of 163, 45%) had clinically relevant genetic alterations. In 34 patients, the identified variants represented an indication for an approved therapy (approved by the Hungarian authorities, on-label indication), while in 40 cases the recommended therapy did not have an approved indication in Hungary for certain tumour types, but off-label indication could be recommended. Based on our CGP results, 24 patients (24/163; 14.7%) received targeted therapy. Treatment duration was between 1 and 60 months. In total 14 (14/163; 8.5% of the tested cases) patients had a positive clinical response (objective response or stable disease) and were treated for more than 16 weeks. INTERPRETATION: NGS-based CGP was successfully introduced in our institution and a significant number of patients benefited from comprehensive genetic tests. Our preliminary results can serve as the starting point of Drug Rediscovery Protocol (DRUP) studies.

EZH2 Expression in Head-and-Neck Squamous Cell Cancer in Young Patients.

EZH2 (Enhancer of zeste homolog 2) promotes tumor growth and survival through numerous mechanisms and is a promising target for novel therapeutic approaches. We aimed to characterize the expression of EZH2 in the tumors of young head-and-neck squamous cell cancer (HNSCC) patients in comparison with the general HNSCC patient population. We used formalin-fixed, paraffin-embedded tissue blocks from 68 random young HNSCC patients (≤39 years, median age: 36 years; diagnosed between 2000 and 2018), which were compared with the samples of 58 age- and gender-matched general HNSCC subjects (median age: 62 years; all diagnosed in the year 2014). EZH2 and p53 expression of the tumors was detected using immunohistochemical staining. Lower EZH2 expression was found to be characteristic of the tumors of young HNSCC patients as opposed to the general population (median EZH2 staining intensity: 1 vs. 1.5 respectively, p < 0.001; median fraction of EZH2 positive tumor cells: 40% vs. 60%, respectively, p = 0.003, Mann-Whitney). Cox analysis identified a more advanced T status (T3-4 vs. T1-2), a positive nodal status, and alcohol consumption, but neither intratumoral EZH2 nor p53 were identified as predictors of mortality in the young patient group. The lower EZH2 expression of young HNSCC patients' tumors discourages speculations of a more malignant phenotype of early-onset tumors and suggests the dominant role of patient characteristics. Furthermore, our results might indicate the possibility of an altered efficacy of the novel anti-EZH2 therapies in this patient subgroup.

Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater.

In this study, a Gram-stain-positive, non-motile, oxidase- and catalase-negative, rod-shaped, bacterial strain (SG_E_30_P1T) that formed light yellow colonies was isolated from a groundwater sample of Sztaravoda spring, Hungary. Based on 16S rRNA phylogenetic and phylogenomic analyses, the strain was found to form a distinct linage within the family Microbacteriaceae. Its closest relatives in terms of near full-length 16S rRNA gene sequences are Salinibacterium hongtaonis MH299814 (97.72 % sequence similarity) and Leifsonia psychrotolerans GQ406810 (97.57 %). The novel strain grows optimally at 20-28 °C, at neutral pH and in the presence of NaCl (1-2 w/v%). Strain SG_E_30_P1T contains MK-7 and B-type peptidoglycan with diaminobutyrate as the diagnostic amino acid. The major cellular fatty acids are anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0, and the polar lipid profile is composed of diphosphatidylglycerol and phosphatidylglycerol, as well as an unidentified aminoglycolipid, aminophospholipid and some unidentified phospholipids. The assembled draft genome is a contig with a total length of 2 897 968 bp and a DNA G+C content of 65.5 mol%. Amino acid identity values with it closest relatives with sequenced genomes of <62.54 %, as well as other genome distance results, indicate that this bacterium represents a novel genus within the family Microbacteriaceae. We suggest that SG_E_30_P1T (=DSM 111415T=NCAIM B.02656T) represents the type strain of a novel genus and species for which the name Antiquaquibacter oligotrophicus gen. nov., sp. nov. is proposed.

Comparison of Follicular Helper T-Cell Markers with the Expression of the Follicular Homing Marker CXCR5 in Peripheral T-Cell Lymphomas-A Reappraisal of Follicular Helper T-Cell Lymphomas.

Peripheral T-cell lymphomas (PTCLs) expressing multiple follicular T helper (TFH) cell-related antigens are now classified as TFH lymphomas (TFHL), including angioimmunoblastic, follicular, and not otherwise specified (NOS) types. CXCR5 is the TFH cell-defining chemokine receptor that, together with its ligand CXCL13, plays a critical role in the development of follicles and the positioning of TFH and B cells within follicles. A comprehensive immunomorphologic study was performed to investigate the expression pattern of CXCR5 in a large cohort of nodal PTCLs, particularly those with a TFH cell phenotype, and to compare its expression with six other TFH cell-related antigens. We found that CXCR5 is widely expressed in neoplastic TFH cells, except in TFHL-NOS, and represents a specific marker of this lymphoma entity. Our results suggest that CXCR5 directs the distribution of neoplastic T cells in the affected lymph nodes and may influence the formation of the pathognomic pathological FDC network.

Ewing Sarcoma of the Larynx with Thyroid Cartilage Destruction: A Case Report.

Ewing sarcoma of the larynx is extremely rare, only a few number of cases have been reported. In this report, we describe a case of extraskeletal Ewing sarcoma of the larynx with thyroid cartilage destruction. Laryngoscope, 2024.

POLE-Mutant Colon Adenocarcinoma-Case Presentation and Histopathological Evaluation.

INTRODUCTION: POLE mutant phenotype in colon adenocarcinomas represents a rare molecular subtype. These tumours are generally responsive to immune-checkpoint inhibition therapy and, therefore, are currently considered as a subtype with good prognosis. We hereby present the first detailed case presentation of a POLE mutant colon adenocarcinoma with useful microscopic features. CASE REPORT: A 53-year-old male patient's colon adenocarcinoma histologically showed wide variety of growth patterns and massive intra- and peritumoural lymphocytic infiltrate. The majority of the tumour consisted of a high-grade component resembling medullary carcinoma of the colon, while approximately one-third of the tumour was composed of conventional areas exhibiting a tubular pattern. A minority of the tumour was constituted by poorly cohesive rhabdoid cells. Immunohistochemistry was performed, and colorectal origin was proven with CDX-2 and SATB2. Furthermore, proficiency in mismatch repair proteins and SMARCB1 deficiency was observed. The unusually high-grade colon adenocarcinoma, with areas mimicking medullary carcinoma, and generally aggressive morphology raised suspicion of microsatellite instability. The diverse morphology and the SMARCB1 deficiency also raised suspicion of ultramutation caused by POLE alteration. Next-generation sequencing panel confirmed a pathogenetic mutation in POLE exon 9: p.Pro286Arg, c.857C > G. DISCUSSION: The diverse, high-grade morphology and increased intratumoural lymphoid infiltration should raise suspicion for POLE-mutated adenocarcinoma during everyday histopathological practice. Mismatch repair proficiency results on immunohistochemistry should not determine the final diagnosis, as only a minor percentage of these tumours are MSI. In every case suspicious for POLE-mutated adenocarcinoma, a 500-cancer gene panel should be carried out.

NTRK-rearranged spindle cell sarcoma of the uterine cervix with a novel NUMA1::NTRK1 fusion.

NTRK-rearranged uterine sarcoma is a recently described entity that represents a subset of uterine sarcomas with distinct clinicopathological features. From a molecular point of view, this tumour is defined by NTRK gene rearrangement, resulting in overexpression or constitutive activation of Trk receptors. The presence of NTRK fusion is indicative of treatment response with a selective small-molecule inhibitor of the Trk kinases. Here, we report a case of an NTRK-rearranged sarcoma of the uterine cervix in a 43-year-old patient, measuring 80 mm in its largest dimension, with a novel NUMA1-NTRK1 fusion, not previously reported in NTRK-rearranged uterine sarcomas or other NTRK-rearranged tumours. The fusion, involving NUMA1 exon 14 (NM_006185.4) and NTRK1 exon 11 (NM_002529.4), was identified by next-generation sequencing (NGS) studies (FusionPlex Pan Solid Tumor v2 panel). Although the presence of NTRK fusion has been reported in a variety of neoplasms, a fusion involving NUMA1 (nuclear mitotic apparatus protein 1) and a tyrosine kinase partner has previously been reported in human neoplasms only in a handful of cases. The resulting fusion protein comprises the oligomerization domain of NUMA1, which is predicted to cause constant activation of the tyrosine kinase domain of NTRK1. The recognition and accurate diagnosis of these tumours are important due to the availability of potential targeted therapeutic options.

[Mutation frequency of homologous recombination repair genes in prostate adenocarcinomas]. / A homológ rekombinációs hibajavító rendszer szomatikus génmutációinak vizsgálata prosztata-adenokarcinómában, újgenerációs szekvenálással.

The best predictive marker for the expected efficacy of PARP inhibitor therapy is mutations in BRCA1/2 or other homologous recombination repair genes. These tests are part of routine molecular pathology diagnostics. Among 281 patients with prostate adenocarcinoma, somatic pathogenic mutations in one of these genes were identified in 21.4% of patients. In 28.5% of the patients, the test was unsuccessful; the main limitation of successful testing was the age of the paraffin blocks and low DNA concentration. In the case of BRCA1/2 testing, the success rate was significantly reduced for samples older than 5 years, while in tests involving a broader set of homologous recombination repair genes, the success rate was significantly reduced for samples older than 2 years. Therefore, it is very important to test high-risk prostate cancers at the time of primary diagnosis, and probably also liquid biopsy testing of circulating tumor DNA will play an important role in safe diagnosis in the near future.

[Incidentally discovered ectopic tissue in the central neck region (level VI) of the neck - A case series, retrospective analysis and literature review]. / Incidentálisan felfedezett ektópiás szövetmaradványok elofordulása a nyaki VI. (centrális) régióban ­ Esetsorozat ismertetése, retrospektív feldolgozás és irodalmi áttekintés.

The thymus derives from the third branchial pouch, which migrates to the mediastinum through the central region of the neck. During the migration, particles split off and develop separately. The prevalence of ectopic thymus is 20-40%. The purpose of this retrospective case series study was to investigate the prevalence of embryological tissue remnants in the central region, in patients treated for thyroid lesions. Between January 1 2018 and September 1 2020, 84 patients who underwent central neck dissection were selected. Clinicopathological data as age, gender, histopathological result and TNM stage were analyzed. Ectopic tissue in the central neck region was discovered in 28 cases. The prevalence of ectopic lesions showed increase in Stage I thyroid carcinomas. There was no significant correlation with patients' age, gender, or with the stage. We emphasize the clinicopathological role of ectopic tissues, which can occur in the central region of the neck.

Temporal changes in the morphological and microbial diversity of biofilms on the surface of a submerged stone in the Danube River.

Epilithic biofilms are ubiquitous in large river environments and are crucial for biogeochemical processes, but their community structures and functions remain poorly understood. In this paper, the seasonal succession in the morphological structure and the taxonomic composition of an epilithic bacterial biofilm community at a polluted site of the Danube River were followed using electron microscopy, high-throughput 16S rRNA gene amplicon sequencing and multiplex/taxon-specific PCRs. The biofilm samples were collected from the same submerged stone and carried out bimonthly in the littoral zone of the Danube River, downstream of a large urban area. Scanning electron microscopy showed that the biofilm was composed of diatoms and a variety of bacteria with different morphologies. Based on amplicon sequencing, the bacterial communities were dominated by the phyla Pseudomonadota and Bacteroidota, while the most abundant archaea belonged to the phyla Nitrososphaerota and Nanoarchaeota. The changing environmental factors had an effect on the composition of the epilithic microbial community. Critical levels of faecal pollution in the water were associated with increased relative abundance of Sphaerotilus, a typical indicator of "sewage fungus", but the composition and diversity of the epilithic biofilms were also influenced by several other environmental factors such as temperature, water discharge and total suspended solids (TSS). The specific PCRs showed opportunistic pathogenic bacteria (e.g. Pseudomonas spp., Legionella spp., P. aeruginosa, L. pneumophila, Stenotrophomonas maltophilia) in some biofilm samples, but extended spectrum ß-lactamase (ESBL) genes and macrolide resistance genes could not be detected.

Multiple bronchial carcinoids associated with Cowden syndrome.

Cowden syndrome (CS) is a rare genetic condition due to the various germline mutations in the phosphatase and tensin homologue on chromosome ten (PTEN) tumour suppressor gene. As a result, CS is characterised by an increased risk of developing various benign and malignant tumours, such as thyroid, breast, endometrial and urogenital neoplasms, as well as gastrointestinal tract tumours. However, the neuroendocrine tumour association with CS is not elucidated yet. We present a case of a 46-year-old male patient diagnosed with testicular seminoma and follicular thyroid cancer in his medical history. Our patient met the clinical diagnostic criteria of Cowden syndrome. Genetic analysis established the clinical diagnosis; a known heterozygous PTEN mutation was detected [PTEN (LRG_311t1)c.388 C > T (p.Arg130Ter)]. Incidentally, he was also seen with multiple pulmonary lesions during his oncological follow-up. A video-assisted thoracoscopic left lingula wedge resection and later resections from the right lung were performed. Histological findings revealed typical pulmonary carcinoid tumours and smaller tumorlets. Somatostatin receptor SPECT-CT, 18F-FDG-PET-CT and 18F-FDOPA-PET-CT scans and endoscopy procedures could not identify any primary tumours in other locations. Our patient is the first published case of Cowden syndrome, associated with multifocal pulmonary carcinoids. Besides multiple endocrine neoplasia type 1, we propose Cowden syndrome as another hereditary condition predisposing to multiple pulmonary tumorlets and carcinoid tumours.

Sarco/endoplasmic reticulum calcium ATPase 3 (SERCA3) expression in gastrointestinal stromal tumours.

Accurate characterisation of gastrointestinal stromal tumours (GIST) is important for prognosis and the choice of targeted therapies. Histologically the diagnosis relies on positive immunostaining of tumours for KIT (CD117) and DOG1. Here we report that GISTs also abundantly express the type 3 Sarco/Endoplasmic Reticulum Calcium ATPase (SERCA3). SERCA enzymes transport calcium ions from the cytosol into the endoplasmic reticulum and play an important role in regulating the intensity and the periodicity of calcium-induced cell activation. GISTs from various localisations, histological and molecular subtypes or risk categories were intensely immunopositive for SERCA3 with the exception of PDGFRA-mutated cases where expression was high or moderate. Strong SERCA3 expression was observed also in normal and hyperplastic interstitial cells of Cajal. Decreased SERCA3 expression in GIST was exceptionally observed in a zonal pattern, where CD117 staining was similarly decreased, reflecting clonal heterogeneity. In contrast to GIST, SERCA3 immunostaining of spindle cell tumours and other gastrointestinal tumours resembling GIST was negative or weak. In conclusion, SERCA3 immunohistochemistry may be useful for the diagnosis of GIST with high confidence, when used as a third marker in parallel with KIT and DOG1. Moreover, SERCA3 immunopositivity may be particularly helpful in cases with negative or weak KIT or DOG1 staining, a situation that may be encountered de novo, or during the spontaneous or therapy-induced clonal evolution of GIST.

Linking antibiotic resistance gene patterns with advanced faecal pollution assessment and environmental key parameters along 2300 km of the Danube River.

The global spread of antimicrobial resistance (AMR) in the environment is a growing health threat. Large rivers are of particular concern as they are highly impacted by wastewater discharge while being vital lifelines serving various human needs. A comprehensive understanding of occurrence, spread and key drivers of AMR along whole river courses is largely lacking. We provide a holistic approach by studying spatiotemporal patterns and hotspots of antibiotic resistance genes (ARGs) along 2311 km of the navigable Danube River, combining a longitudinal and temporal monitoring campaign. The integration of advanced faecal pollution diagnostics and environmental and chemical key parameters allowed linking ARG concentrations to the major pollution sources and explaining the observed patterns. Nine AMR markers, including genes conferring resistance to five different antibiotic classes of clinical and environmental relevance, and one integrase gene were determined by probe-based qPCR. All AMR targets could be quantified in Danube River water, with intI1 and sul1 being ubiquitously abundant, qnrS, tetM, blaTEM with intermediate abundance and blaOXA-48like, blaCTX-M-1 group, blaCTX-M-9 group and blaKPC genes with rare occurrence. Human faecal pollution from municipal wastewater discharges was the dominant factor shaping ARG patterns along the Danube River. Other significant correlations of specific ARGs were observed with discharge, certain metals and pesticides. In contrast, intI1 was not associated with wastewater but was already established in the water microbiome. Animal contamination was detected only sporadically and was correlated with ARGs only in the temporal sampling set. During temporal monitoring, an extraordinary hotspot was identified emphasizing the variability within natural waters. This study provides the first comprehensive baseline concentrations of ARGs in the Danube River and lays the foundation for monitoring future trends and evaluating potential reduction measures. The applided holistic approach proved to be a valuable methodological contribution towards a better understanding of the environmental occurrence of AMR.

Neck Node Squamous Cell Metastasis from Unknown Primary and Mutagen Sensitivity: A Case Series.

Most of the neck node metastases from cancer of unknown primary (CUP) are squamous cell carcinomas (SCCs). The majority of which are human papillomavirus (HPV)-related, frequently show cystic morphology referring to Waldeyer's ring origin. Here, we report four cases of neck node SCCs metastases from CUP. In our institute, 432 patients with head and neck (HN) SCC underwent pretreatment mutagen sensitivity (MS) assay between 1996 and 2006. Among them, 4 patients ≤50 years of age had metastatic cervical nodes from CUP. The primary treatment was cervical node dissection ± radiotherapy. All patients had elevated (>1.0 chromatid break/cell) MS. One male patient died of progressive neck metastasis within 3 years and the 3 female patients are still alive more than 15 years after initial treatment of HPV+ (two) or cystic (one) SCC. Two female patients developed second and third distant site metachronous primary cancers. HPV+ or cystic HNSCC from CUP with elevated MS indicates good outcome. Distant site metachronous cancers of different histologic origins cannot be explained by field cancerization. The clinical significance of elevated MS in neck node SCC metastasis from CUP requires further investigation.

The master role of polarized NIS expression in regulating iodine metabolism in the human body

ABSTRACT Objective: The aim of this study was to investigate how polarized sodium iodide symporter (NIS) expression may regulate iodide metabolism in vivo. Materials and methods: Polarized NIS expression was analyzed in tissues that accumulate iodide by the use of immunohistochemistry and polyclonal antibody against the C-terminal end of human NIS (hNIS). Results: Iodide absorption in the human intestine occurs via NIS expressed in the apical membrane. Iodide is secreted into the lumen of the stomach and salivary glands via NIS expressed in the basolateral membrane and then circulates back from the small intestine to the bloodstream via NIS expressed in the apical membrane. Conclusion: Polarized NIS expression in the human body regulates intestinal-bloodstream recirculation of iodide, perhaps prolonging the availability of iodide in the bloodstream. This leads to more efficient iodide trapping by the thyroid gland. Understanding the regulation and manipulating gastrointestinal iodide recirculation could increase radioiodine availability during theranostic NIS applications.

Conocimiento sobre saberes populares del personal sanitario del Servicio Desconcentrado Hospital Universitario Pediátrico Dr. Agustin Zubillaga / Knoledge on popular beliefs of medical staff of the service desconcentrado Hospital Universitario Pediátrico Dr. Agustín Zubillaga

Este estudio se sustentó en el paradigma cuantitativo orientado bajo una investigación de tipo descriptivo cuyo propósito fue describir el conocimiento sobre saberes populares del personal sanitario que labora en el Servicio de Atención Médica Inmediata del Servicio Desconcentrado Hospital Universitario Pediátrico Dr. Agustín Zubillaga. La muestra estuvo conformada por 10 médicos y 8 enfermeras a quienes se les aplicó una encuesta a través de un cuestionario con escala tipo Likert el cual fue validado por la técnica de juicio de expertos. Los resultados indican que los encuestados manifiestan una tendencia positiva en cuanto a que a la consulta llegan pacientes cuyas madres usan las creencias y costumbres de sus ancestros para tratar las enfermedades que padecen, respetando y reconociendo el saber popular que poseen las madres de los pacientes. Existe una tendencia negativa en la utilización de los saberes populares en la práctica médica, así como en la combinación del saber popular y el saber científico para tratar la enfermedad y en la posibilidad de integrar de manera pedagógica los saberes populares en la educación para la salud. Por otra parte expresan una marcada tendencia positiva en cuanto a que las madres utilizan los saberes populares por sus condiciones socioeconómicas y en el hecho de que la educación o valores recibidos por ellas influyen en el uso de dichas creencias; de igual forma, la mayoría expresa una tendencia positiva en que las creencias y costumbres maternales puedan generar intoxicaciones en los pacientes y una tendencia negativa en su habilidad para curar la enfermedad(AU)

This study was based on a quantitative paradigm oriented under descriptive field research. The purpose of this study was to describe knowledge on popular beliefs of patient's parents of the medical staff who work in the Servicio de Atención Médica Inmediata of the Servicio Desconcentrado Hospital Universitario Pediátrico Dr. Agustín Zubillaga. The sample consisted of 10 doctors and 8 nurses who were given a Likert-scale questionnaire which was validated by the expert judgment technique. The results demonstrate that respondents show a positive view in regards to the fact that patients mothers with beliefs and customs of their ancestors attend the consult, respecting and recognizing their popular belief system; there is a negative view in the use of popular beliefs in medical practice, combination of popular and scientific knowledge and the possibility of integration of popular beliefs into health education. On the other hand, they express a marked positive view in regards to the use of popular belief based on socioeconomic conditions and that the education or values received by them influence the use of these beliefs; similarly, most respondents express a positive view in relation to beliefs and customs leading to poisoning in patients and a negative view in the possibility that these beliefs cure disease(AU)