Explore the vast range of titles available.

Introduction Ewing sarcoma (ES) is a highly aggressive malignancy of bone and soft tissues characterized by the presence of a genetic fusion involving the EWSR1 gene. More than one-third of patients develop distant metastases, which are associated with unfavorable prognosis. Knowledge about the disease’s genetic landscape may help foster progress in using targeted therapies in the treatment of ES. Aim of the study The objective is to assess the mutational landscape of ES in pretreatment samples, tumor samples after neoadjuvant chemotherapy, and in metastatic/recurrent tumors in children and adults. Material and methods DNA from 39 for­malin-fixed paraffin-embedded tumor samples of 22 patients (17 adults, 5 children) were analyzed by targeted next generation sequencing (NGS) using the Oncomine Comprehensive Assay v3gene panel. Additional functional analyses were performed between patient subgroups. Results All samples were characterized by low tumor mutation burden (< 10 mut/Mb). The most commonly mutated genes were PIK3R1 (59%) and POLE (50%). The most widely detected variants in biopsy samples were PIK3R1 T369I (50%), FGFR1 E159K, and TP53 at codon 72 (both in 27.3%). Additionally, the ATR, BRCA1, RAD50, ATM, CHEK1, and NBN genes showed a significantly higher number of mutations in ES. Mutations in PIK3R1 were significantly more frequent in adults, while mutations in the pathways responsible for cell cycle control, DNA repair, and transcriptional regulation were more frequent in children. Conclusions Besides EWSR1 fusion, ES is characterized by numerous point mutations that are potential targets for precision medicine. There is high genomic heterogeneity that may explain differences in outcomes between patient subgroups.

The gut microbiome, crucial to human health, changes with age and disease, and influences metabolic profiles. Gut bacteria produce short-chain fatty acids (SCFAs), essential for maintaining homeostasis and modulating inflammation. Dysbiosis, commonly due to poor diet or lifestyle, disrupts the integrity of the intestinal barrier and may contribute to conditions such as obesity, diabetes, and non-alcoholic fatty liver disease (NAFLD). Analytical methods such as gas chromatography–mass spectrometry (GC/MS) are vital for SCFA analysis, with various preparation and storage techniques improving the accuracy. Advances in these methods have improved the reliability and sensitivity of SCFA quantification, which is crucial for the identification of disease biomarkers. Evidence from GC/MS-based studies has revealed that accurate SCFA quantification requires meticulous sample preparation and handling. The process begins with the extraction of SCFAs from biological samples using methods such as direct solvent extraction or solid-phase microextraction (SPME), both of which require optimization for maximum recovery. Derivatization, which chemically modifies SCFAs to enhance volatility and detectability, is a crucial step, typically involving esterification or silylation. Following this, the cleanup process removes impurities that might interfere with the analysis. Although recent advances in GC/MS technology have significantly improved SCFA-detection sensitivity and specificity, proper sample storage, with acid preservatives and the avoidance of repeated thawing, is essential for maintaining SCFA integrity.

The gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria , Actinobacteriota , and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota , Proteobacteria , Fusobacteriota , and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota . Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs ( Neisseriaceae , Neisseria , Absconditabacteriales , and Microbacteriaceae ) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori- negative CD patients and controls.

Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m2), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m2), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m2) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m2 had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m2. Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m2 obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index.

Somatic copy number alterations play a critical role in oncogenesis. Loss of chromosomal regions containing tumor suppressors can lead to collateral deletion of passenger genes. This can be exploited therapeutically if synthetic lethal partners of such passenger genes are known and represent druggable targets. Here, we report that VPS4B gene, encoding an ATPase involved in ESCRT‐dependent membrane remodeling, is such a passenger gene frequently deleted in many cancer types, notably in colorectal cancer (CRC). We observed downregulation of VPS4B mRNA and protein levels from CRC patient samples. We identified VPS4A paralog as a synthetic lethal interactor for VPS4B in vitro and in mouse xenografts. Depleting both proteins profoundly altered the cellular transcriptome and induced cell death accompanied by the release of immunomodulatory molecules that mediate inflammatory and anti‐tumor responses. Our results identify a pair of novel druggable targets for personalized oncology and provide a rationale to develop VPS4 inhibitors for precision therapy of VPS4B‐deficient cancers. Synopsis VPS4B and VPS4A paralogs are involved in the remodeling of biological membranes, a critical step for many intracellular processes. This study highlights the possibility of using synthetic lethality between these paralogs for treatment of VPS4B‐deficient cancers. VPS4B protein abundance was decreased in colorectal cancer (CRC) patient samples. A synthetic lethal phenotype was generated by simultaneous depletion of VPS4A and B in various CRC cell lines grown in vitro and in vivo . Synthetic lethality between VPS4A and B was independent of other oncogenic mutations, and conserved between human and mouse, thus of high penetrance. Simultaneous depletion of VPS4A and B caused pleiotropic effects e.g. inhibited endocytosis and cell cycle progression, and induced a stress‐associated sterile inflammatory response. DAMPs and other immunomodulatory molecules released by VPS4A+B‐depleted dying cells may favor the induction of anti‐tumor innate and adaptive immune responses. Graphical Abstract VPS4B and VPS4A paralogs are involved in the remodeling of biological membranes, a critical step for many intracellular processes. This study highlights the possibility of using synthetic lethality between these paralogs for treatment of VPS4B‐deficient cancers.

Colorectal cancer (CRC) treatment remains challenging due to genetic heterogeneity and resistance mechanisms. To address this, we developed a drug discovery pipeline using patient-derived primary CRC cultures with diverse genomic profiles. These cultures closely resemble certain molecular characteristics of primary and metastatic CRC, highlighting their promise as a translational platform for therapeutic evaluation. Importantly, our engineered model and patient-derived cells reflect the complexity and heterogeneity of primary tumors, not observed with standard immortalized cell lines, offering a more clinically relevant system, although further validation is needed. High-throughput screening (HTS) of 4255 compounds identified 33 with selective efficacy against CRC cells, sparing normal, healthy epithelial cells. Among the tested combinations, everolimus (mTOR inhibitor) and uprosertib (AKT inhibitor) demonstrated promising synergy at clinically relevant concentrations, with favorable therapeutic windows confirmed across tested patient-derived cultures. Notably, this synergy, revealed through advanced models, might have been overlooked in traditional immortalized cell lines, highlighting the translational advantage of patient-derived systems. Furthermore, the integration of machine learning into the HTS pipeline significantly improved scalability, cost-efficiency, and predictive accuracy. Our findings underscore the potential of patient-derived materials combined with machine learning-enhanced drug discovery to advance personalized therapies. Specifically, mTOR-AKT inhibition emerges as a promising strategy for CRC treatment, paving the way for more effective and targeted therapeutic approaches.

Low diversity gut dysbiosis can take different forms depending on the disease context. In this study, we used shotgun metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) to compared the metagenomic and metabolomic profiles of diarrheal cancer and inflammatory bowel disease (IBD) patients and defined the additive effect of infection (CDI) on intestinal dysbiosis. The study cohort consisted of 138 case-mix cancer patients, 43 IBD patients, and 45 healthy control individuals. Thirty-three patients were also infected with . In the control group, three well-known enterotypes were identified, while the other groups presented with an additional -driven enterotype. Bacterial diversity was significantly lower in all groups than in healthy controls, while the highest level of bacterial species richness was observed in cancer patients. Fifty-six bacterial species had abundance levels that differentiated diarrheal patient groups from the control group. Of these species, 52 and 4 ( , , , and ) were under-represented and over-represented, respectively, in all diarrheal patient groups. The relative abundances of propionate and butyrate were significantly lower in fecal samples from IBD and CDI patients than in control samples. Isobutyrate, propanate, and butyrate concentrations were lower in cancer, IBD, and CDI samples, respectively. Glycine and valine amino acids were over- represented in diarrheal patients. Our data indicate that different external and internal factors drive comparable profiles of low diversity dysbiosis. While diarrheal-related low diversity dysbiosis may be a consequence of systemic cancer therapy, a similar phenotype is observed in cases of moderate to severe IBD, and in both cases, dysbiosis is exacerbated by incidence of CDI.

Background Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contribute to its high virulence. Herein we examined whether the genome conservation, measured as non-synonymous to synonymous mutations ratio (dN/dS) in core genes, presence of single genes, plasmids and prophages increased the risk of reinfection in a subset of 134 C. difficile isolates from our previous study in a singly hemato-oncology ward. Methods C. difficile isolates were subjected to whole-genome sequencing (WGS) on Ion Torrent PGM sequencer. Genomes were assembled with MIRA5 and annotated with prokka and VRprofile. Logistic regression was used to asses the relationship between single gene presence and the odds of infection recurrence. DN/dS ratios were computed with codeml. Functional annotation was conducted with eggNOG-Mapper. Results We have found that the presence of certain genes, associated with carbon metabolism and oxidative phosphorylation, increased the odds of infection recurrence. More core genes were under positive selective pressure in recurrent disease isolates – they were mostly associated with the metabolism of aminoacids. Finally, prophage elements were more prevalent in single infection isolates and plasmids did not influence the odds of recurrence. Conclusions Our findings suggest higher genetic plasticity in isolates causing recurrent infection, associated mainly with metabolism. On the other hand, the presence of prophages seems to reduce the isolates’ virulence.

The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.

Spleen tyrosine kinase (SYK) is an important oncogene and signaling mediator activated by cell surface receptors crucial for acute myeloid leukemia (AML) maintenance and progression. Genetic or pharmacologic inhibition of SYK in AML cells leads to increased differentiation, reduced proliferation, and cellular apoptosis. Herein, we addressed the consequences of SYK inhibition to leukemia stem-cell (LSC) function and assessed SYK-associated pathways in AML cell biology. Using gain-of-function MEK kinase mutant and constitutively active STAT5A, we demonstrate that R406, the active metabolite of a small-molecule SYK inhibitor fostamatinib, induces differentiation and blocks clonogenic potential of AML cells through the MEK/ERK1/2 pathway and STAT5A transcription factor, respectively. Pharmacological inhibition of SYK with R406 reduced LSC compartment defined as CD34 + CD38 − CD123 + and CD34 + CD38 − CD25 + in vitro, and decreased viability of LSCs identified by a low abundance of reactive oxygen species. Primary leukemic blasts treated ex vivo with R406 exhibited lower engraftment potential when xenotransplanted to immunodeficient NSG/J mice. Mechanistically, these effects are mediated by disturbed mitochondrial biogenesis and suppression of oxidative metabolism (OXPHOS) in LSCs. These mechanisms appear to be partially dependent on inhibition of STAT5 and its target gene MYC, a well-defined inducer of mitochondrial biogenesis. In addition, inhibition of SYK increases the sensitivity of LSCs to cytarabine (AraC), a standard of AML induction therapy. Taken together, our findings indicate that SYK fosters OXPHOS and participates in metabolic reprogramming of AML LSCs in a mechanism that at least partially involves STAT5, and that SYK inhibition targets LSCs in AML. Since active SYK is expressed in a majority of AML patients and confers inferior prognosis, the combination of SYK inhibitors with standard chemotherapeutics such as AraC constitutes a new therapeutic modality that should be evaluated in future clinical trials.