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Search Results (1,969)

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25 pages, 982 KB  
Article
Association of Resistance-Associated 23S rRNA and gyrA Mutations with Antimicrobial Resistance and Eradication Outcomes in Helicobacter pylori
by Sergiu Dorin Matei, Tiberia Ilias, Ramona Nicoleta Suciu, Corina Suteu, Cornel Dragos Cheregi, Laura Ioana Bondar, Anamaria Violeta Țuțuianu, Brigitte Osser and Ovidiu Frățilă
Antibiotics 2026, 15(7), 661; https://doi.org/10.3390/antibiotics15070661 (registering DOI) - 4 Jul 2026
Abstract
Background/Objectives: The increasing prevalence of antimicrobial resistance has become a major challenge in the management of Helicobacter pylori infection and is a leading cause of eradication failure. Resistance to clarithromycin and fluoroquinolones is primarily mediated by mutations in the 23S rRNA and gyrA [...] Read more.
Background/Objectives: The increasing prevalence of antimicrobial resistance has become a major challenge in the management of Helicobacter pylori infection and is a leading cause of eradication failure. Resistance to clarithromycin and fluoroquinolones is primarily mediated by mutations in the 23S rRNA and gyrA genes, respectively. This study aimed to evaluate the prevalence of resistance-associated mutations in the 23S rRNA and gyrA genes, investigate their relationship with phenotypic antimicrobial resistance, assess their impact on eradication outcomes, and develop a prediction model for treatment failure. Methods: This retrospective real-world cohort study included 294 adult patients with confirmed H. pylori infection evaluated at the Oradea County Emergency Clinical Hospital, Romania, between November 2022 and November 2025. Clinical, endoscopic, histopathological, microbiological, molecular, and treatment outcome data were collected from medical records. Resistance-associated mutations in the 23S rRNA (A2143G, A2142G, and A2142C) and gyrA (N87K, D91G, and D91N) genes were analyzed and correlated with phenotypic antimicrobial resistance and eradication outcomes. Independent predictors of eradication failure were identified using multivariable logistic regression, and a prediction model was subsequently developed. Results: Overall, 101 patients (34.4%) harbored 23S rRNA mutations and 64 (21.8%) carried gyrA mutations, while 27 patients (9.2%) exhibited mutations in both genes. A2143G was the most frequent mutation (25.2%). Resistance-associated mutations showed strong concordance with phenotypic antimicrobial resistance. Patients with wild-type strains achieved eradication rates exceeding 90%, whereas significantly lower success rates were observed among patients carrying A2143G, A2142G, or gyrA mutations. Multivariable analysis identified previous eradication attempts (aOR 3.12, 95% CI 1.71–5.68), A2143G mutation (aOR 4.86, 95% CI 2.43–9.72), gyrA mutation (aOR 2.91, 95% CI 1.45–5.84), increasing age (aOR 1.03, 95% CI 1.01–1.05), and treatment with clarithromycin-based triple therapy (aOR 2.18, 95% CI 1.02–4.63) as independent predictors of eradication failure. The prediction model demonstrated excellent discriminatory performance (AUC 0.88, 95% CI 0.84–0.92), with a sensitivity of 82.5%, specificity of 80.1%, and satisfactory calibration (Hosmer–Lemeshow p = 0.68). Conclusions: Resistance-associated mutations in the 23S rRNA and gyrA genes are strongly associated with phenotypic antimicrobial resistance and reduced H. pylori eradication success. Molecular resistance testing may facilitate individualized treatment selection and improve clinical outcomes. The proposed prediction model, integrating clinical characteristics, treatment regimen, and molecular resistance markers, demonstrated excellent performance and may represent a useful tool for identifying patients at increased risk of eradication failure. Full article
26 pages, 6027 KB  
Article
Evidence for a Constrained Mutational Pathway to High-Level Spectinomycin Resistance in Neisseria: RpsE Loop 2 Mutations and Associated Growth Costs
by Dmitry V. Kravtsov, Dmitry A. Gryadunov, Anastasia A. Anashkina and Boris L. Shaskolskiy
Int. J. Mol. Sci. 2026, 27(13), 5971; https://doi.org/10.3390/ijms27135971 - 3 Jul 2026
Viewed by 171
Abstract
Antimicrobial resistance in Neisseria gonorrhoeae is a global concern. Spectinomycin is unusual in that resistance can emerge rapidly during localized outbreaks yet often disappears from clinical populations after drug withdrawal, suggesting an associated growth cost. To investigate evolutionary routes to spectinomycin resistance, we [...] Read more.
Antimicrobial resistance in Neisseria gonorrhoeae is a global concern. Spectinomycin is unusual in that resistance can emerge rapidly during localized outbreaks yet often disappears from clinical populations after drug withdrawal, suggesting an associated growth cost. To investigate evolutionary routes to spectinomycin resistance, we performed in vitro selection on two N. gonorrhoeae strains and two commensal Neisseria species. Derived cell lines were characterized by minimum inhibitory concentration (MIC) determination, whole-genome sequencing, growth-kinetics analysis, and molecular modelling of the RpsE (ribosomal protein S5) interface with the ribosome. All high-level resistant isolates (MIC > 2048 mg/L) acquired substitutions or deletions in loop 2 of RpsE. Modelling showed that these mutations perturb the conserved network of stabilizing contacts between RpsE residues Lys25 (Lys23 in E. coli numbering) and Lys28 (Lys26), as well as helix 34 nucleotides G922, A923, and C1069 of 16S rRNA, potentially altering the architecture of the spectinomycin-binding site. These mutations were associated with high-level resistance but reduced growth rates, with the resulting growth costs depending on the specific pattern of contact rearrangements. Convergent evolution towards loop 2 mutations supports the existence of a constrained mutational pathway to high-level spectinomycin resistance in the strains and species examined here. This constraint may help explain the rapid decline of resistant variants in the absence of drug pressure and underscores the importance of genomic surveillance. Full article
(This article belongs to the Special Issue Advanced Strategies in Bacterial Antibiotic Resistance)
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18 pages, 2042 KB  
Article
Clinical and Genomic Characterization of High-Risk Multidrug-Resistant Klebsiella pneumoniae Lineages in Pakistan
by Aakash Ahmad Khattak, Sadiq Azam, Noor Rehman, Muhammad Asghar, Aiman Waheed, Sajjad Ahmad, Jody E. Phelan, Susana Campino, Taj Ali Khan and Taane G. Clark
Microorganisms 2026, 14(7), 1462; https://doi.org/10.3390/microorganisms14071462 - 2 Jul 2026
Viewed by 203
Abstract
Multidrug-resistant (MDR) Klebsiella pneumoniae represents a major clinical and public health challenge worldwide, particularly in regions with limited genomic surveillance. This study investigated the clinical, phenotypic, and genomic characteristics of clinical K. pneumoniae isolates recovered from a tertiary-care hospital in Peshawar, Pakistan. A [...] Read more.
Multidrug-resistant (MDR) Klebsiella pneumoniae represents a major clinical and public health challenge worldwide, particularly in regions with limited genomic surveillance. This study investigated the clinical, phenotypic, and genomic characteristics of clinical K. pneumoniae isolates recovered from a tertiary-care hospital in Peshawar, Pakistan. A total of 2400 non-duplicate clinical specimens were processed, and antimicrobial susceptibility testing was performed according to CLSI guidelines. Whole-genome sequencing (WGS) was conducted on a purposively selected subset of 18 isolates representing diverse resistance and phenotypic profiles. Genomic analyses included multilocus sequence typing, resistome and virulome profiling, identification of resistance-associated chromosomal mutations, plasmid replicon typing, and phylogenomic comparison with publicly available international genomes. K. pneumoniae was identified in 256/2400 (10.7%) specimens, predominantly from urine samples. MDR and extensively drug-resistant (XDR) phenotypes were detected in 83.2% and 13.3% of isolates, respectively. WGS revealed substantial genomic heterogeneity, with ST147 identified as the most frequent lineage among sequenced isolates. Extended-spectrum β-lactamase genes, particularly blaCTX-M-15, together with carbapenemase genes including blaOXA-48-like and blaNDM-5, were identified in multiple isolates alongside resistance-associated chromosomal alterations in gyrA, parC, ompK36, mgrB, pmrB, and ramR. Yersiniabactin-associated loci were detected in all sequenced isolates, whereas canonical hypervirulence-associated determinants (rmpA, iuc, iro) were absent. These findings highlight the complex genomic landscape of MDR K. pneumoniae in Pakistan and underscore the need for continued genomic surveillance and antimicrobial stewardship. Full article
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15 pages, 881 KB  
Article
Integrated Phenotypic, Molecular, and Genomic Analysis of Antimicrobial Resistance in Yersinia pestis Isolates from Natural Plague Foci of Kazakhstan
by Ziyat Abdel, Zauresh Zhumadilova, Raikhan Mussagalieva, Aigul Abdirassilova, Bolatbek Baitursyn, Beck Abdeliyev, Zhandos Dalibayev, Dinmukhammed Otebay, Nurbol Shaki and Svetlana Issaeva
Bacteria 2026, 5(3), 37; https://doi.org/10.3390/bacteria5030037 - 1 Jul 2026
Viewed by 75
Abstract
Plague remains a globally important zoonotic disease maintained in natural foci, with ongoing epizootic activity and periodic human cases reported in several regions of the world. Continuous monitoring of antimicrobial susceptibility in Yersinia pestis is essential because the emergence of resistant strains could [...] Read more.
Plague remains a globally important zoonotic disease maintained in natural foci, with ongoing epizootic activity and periodic human cases reported in several regions of the world. Continuous monitoring of antimicrobial susceptibility in Yersinia pestis is essential because the emergence of resistant strains could compromise the effectiveness of currently recommended therapeutic regimens. In this study, 75 Y. pestis isolates originating from natural plague foci of Kazakhstan were investigated using an integrated approach combining phenotypic susceptibility testing, targeted molecular screening, and whole-genome sequencing (WGS)-based resistome analysis. The collection included historical clinical isolates obtained during plague outbreaks as well as more recent epizootic strains recovered from animal hosts and flea vectors. Phenotypic testing demonstrated uniformly high susceptibility to clinically relevant antimicrobial agents used for plague treatment. Targeted molecular screening by real-time PCR did not detect the analyzed resistance determinants. Genome-wide analysis based on WGS data from NCBI BioProject PRJNA1249055 did not identify acquired antimicrobial resistance genes, major resistance-associated mutations in key chromosomal loci (rpsL, gyrA, and parC), or plasmid-borne resistance determinants. Regulatory loci associated with adaptive responses were highly conserved across the analyzed genomes. The complete concordance between phenotypic, molecular, and genomic findings indicates a stable antimicrobial susceptibility profile of Y. pestis circulating in natural plague foci of Kazakhstan. These results support the continued effectiveness of current therapeutic strategies for plague and highlight the value of integrating genomic surveillance into long-term monitoring programs for this pathogen. Full article
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16 pages, 1703 KB  
Article
Strain Matching of Seasonal Influenza Vaccines and Emergence of Neuraminidase Inhibitor Resistance in China from 2015 to 2025
by Peiqing He, Junhao Luo, Siyu Pu, Simin Cui, Haijun Zhu, Wenfei Zhu and Rongbao Gao
Vaccines 2026, 14(7), 586; https://doi.org/10.3390/vaccines14070586 - 30 Jun 2026
Viewed by 144
Abstract
Background: Influenza remains a major global public health threat, and vaccination is one of the most effective preventive measures. However, frequent antigenic drift and occasional antigenic shift, along with the lead time required for vaccine development and regional differences in the evolution [...] Read more.
Background: Influenza remains a major global public health threat, and vaccination is one of the most effective preventive measures. However, frequent antigenic drift and occasional antigenic shift, along with the lead time required for vaccine development and regional differences in the evolution of circulating strains, may lead to mismatches between WHO-recommended vaccine strains and circulating viruses. In addition, antiviral resistance further complicates precise influenza prevention and control. Objectives: This study aimed to evaluate the concordance of vaccine strains with circulating influenza viruses and the emergence of neuraminidase inhibitor (NAI) resistance in China. Methods: Data on antigenic characterization and antiviral susceptibility testing were extracted from weekly influenza surveillance reports published by the Chinese National Influenza Center from 2015 to 2025. Viral evolution, substitutions at key antigenic sites, and resistance-associated mutations were further examined based on sequences of circulating influenza viruses in China. Results: The overall vaccine match rates were 95.72% (95% CI: 94.02–97.43%) for A(H1N1)pdm09, 58.96% (95% CI: 54.93–62.96%) for A(H3N2), 64.45% (95% CI: 59.49–69.41%) for B/Victoria, and 95.19% (95% CI: 91.32–99.05%) for B/Yamagata in China during the 2015–2025 influenza seasons, with marked year-to-year fluctuations observed particularly for A(H3N2) and B/Victoria. The vaccine matching for cell-based A(H3N2) (70.41%, 95% CI: 65.04–75.77%) vaccine reference strains was significantly higher than that for egg-based A(H3N2) (48.09%, 95% CI: 42.63–53.55%) vaccine reference strains. Sequence analysis indicated that circulating A(H3N2) viruses showed the greatest genetic divergence from the matched egg-based vaccine strains (2.71%, 95% CI: 2.66–2.75%). Phenotypic NAI resistance was detected only in A(H1N1)pdm09 viruses, with resistance rates of 0.18% (95% CI: 0.07–0.45%) in 2023, 3.47% (95% CI: 2.63–4.57%) in 2024, and 3.01% (95% CI: 2.46–3.68%) in 2025. Neuraminidase (NA) sequence analysis showed that the key NAI resistance-associated substitution H274Y has been detected in A(H1N1)pdm09 viruses since 2015, at relatively high frequencies observed during 2015–2018. The mutation re-emerged in 2023 and presented increase trends thereafter, although no A(H1N1) pdm09 circulated during the COVID-19 pandemic. Conclusions: Antigenic concordance between vaccine strains and circulating A(H3N2) or B/Victoria viruses showed marked year-to-year fluctuations in China. Cell-based A(H3N2) vaccine reference strains showed higher antigenic concordance than egg-based strains, supporting further consideration of vaccine production platforms in A(H3N2)-predominant seasons. Phenotypic NAI resistance in circulating A(H1N1)pdm09 viruses was detected from 2023 onward in China, whereas resistance-associated NA substitutions had been detected earlier at the sequence level. Full article
(This article belongs to the Section Vaccines and Public Health)
17 pages, 2875 KB  
Article
Genome Re-Sequencing and Functional Analysis Reveal an α-1,3-Glucosyltransferase Conferring Metalaxyl Resistance in Phytophthora sojae
by Jian Gao, Xiong Zhang, Peilin Wang and Shaocheng Chen
J. Fungi 2026, 12(7), 479; https://doi.org/10.3390/jof12070479 - 30 Jun 2026
Viewed by 194
Abstract
Phytophthora and allied oomycete pathogens pose a perennial challenge to global food security through their devastating impact on crop systems. While metalaxyl has demonstrated remarkable efficacy in controlling Phytophthora diseases since its introduction decades ago, the persistent emergence of metalaxyl-resistant strains has severely [...] Read more.
Phytophthora and allied oomycete pathogens pose a perennial challenge to global food security through their devastating impact on crop systems. While metalaxyl has demonstrated remarkable efficacy in controlling Phytophthora diseases since its introduction decades ago, the persistent emergence of metalaxyl-resistant strains has severely compromised its field efficacy. Elucidating the genetic determinants underlying resistance mechanisms is critical to developing surveillance strategies and sustainable countermeasures against evolving oomycete resistance. Through experimental evolution, we generated six metalaxyl-resistant Phytophthora sojae mutants exhibiting extreme resistance levels (resistance factor > 2000). Comparative whole-genome re-sequencing of resistant mutants versus the wild-type parental strain identified 64 candidate genes containing conserved nonsynonymous mutations across all resistant lineages. Among these, PsALG8, encoding a putative alpha-1,3-glucosyltransferase, was identified as the primary determinant, carrying a recurrent homozygous missense mutation across all resistant lineages. CRISPR/Cas9-mediated knockout of PsALG8 in both wild-type and resistant backgrounds significantly reduced metalaxyl tolerance (p < 0.01), confirming its functional involvement in resistance modulation. These results suggest that PsALG8 is associated with metalaxyl sensitivity and mycelial growth in P. sojae under laboratory conditions. The conservation of ALG8 homologs suggests that PsALG8 may have a conserved cellular function related to protein glycosylation across eukaryotes. Although this glucosyltransferase is universally conserved among oomycete species, whether its association with metalaxyl sensitivity constitutes a shared resistance adaptation pathway still requires extensive functional validation in diverse Phytophthora pathogens, which may offer insights into future fungicide resistance management strategies in P. sojae. Full article
(This article belongs to the Special Issue Research Advances on Fungal Plant Pathogens)
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18 pages, 341 KB  
Article
In Silico Mutational Analysis of Two-Component System Genes Associated with Colistin Resistance in Clinical Pseudomonas aeruginosa Isolates from Peshawar
by Bashir Ahmad, Qaisar Ali, Sadiq Azam, Muhammad Asghar, Noor Rehman, Gul-e-Sehra Mujib, Syed Sohail Shah, Jamila Javed, Ibrar Khan, Taj Ali Khan and Taane G. Clark
Biomolecules 2026, 16(7), 962; https://doi.org/10.3390/biom16070962 - 29 Jun 2026
Viewed by 218
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen causing healthcare-associated infections. Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative bacteria. Resistance arises through mutations in two-component systems (TCS) regulating the arn operon. Data on colistin resistance in P. aeruginosa from Pakistan remain limited. A total [...] Read more.
Pseudomonas aeruginosa is an opportunistic pathogen causing healthcare-associated infections. Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative bacteria. Resistance arises through mutations in two-component systems (TCS) regulating the arn operon. Data on colistin resistance in P. aeruginosa from Pakistan remain limited. A total of 3189 clinical samples (urine, blood, sputum, pus, wound swabs) were cultured. P. aeruginosa was identified by Gram staining, biochemical tests (catalase, oxidase, API 20E), and oprL gene amplification. Antibiotic susceptibility was determined by disk diffusion and MIC strips. Resistance genes (PhoP, PhoQ, PmrA, PmrB, mcr-1, oprD) were detected by PCR and Sanger sequencing. Wild-type protein structures were retrieved from PDB; mutant structures were predicted using AlphaFold3. ANP (phosphoaminophosphonic acid-adenylate ester) was docked using MOE 2019.0102. Of 3189 samples, 384 (12.0%) yielded P. aeruginosa. Wound/pus (38.0%) and surgical wards (30.0%) were the predominant sources. Colistin and polymyxin B showed 99.0% susceptibility (MIC50/MIC90 = 1 µg/mL). High resistance was observed for Piperacillin–Tazobactam (96.4%), Aztreonam (70.6%), and Gentamicin (64.2%). oprD was the most prevalent gene (87.5%), followed by PmrB (54.0%), PhoQ (44.0%), PhoP (36.0%), PmrA (18.0%), and mcr-1 (8.0%). Docking revealed the strongest binding in wild-type PhoQ (1ID0; −12.0 kcal/mol, LYS392), wild-type PmrB (2JSO; −9.8 kcal/mol, ASP37), and wild-type PhoP (2PKX; −9.1 kcal/mol, LYS87/ARG111). Mutant proteins showed reduced binding affinities and dispersed interaction networks. Mutant PhoP formed 16 contacts (strongest −4.3 kcal/mol) versus wild-type PhoP with 13 contacts (−9.1 kcal/mol). Colistin remains highly effective against P. aeruginosa in this setting (99.0% susceptibility). The presence of mcr-1 (8.0%) and high oprD prevalence (87.5%) require continued surveillance. Mutations in TCS proteins reduce ANP binding affinity and alter interaction specificity, suggesting that ATP-competitive inhibitors targeting these kinases merit further investigation and experimental validation. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
28 pages, 2237 KB  
Review
Multidimensional Regulatory Networks of Immune Resistance in Intrahepatic Cholangiocarcinoma: Synergistic Mechanisms of Tumor Microenvironment, Immune Cells, and Microbiota, and Novel Therapeutic Strategies
by Lingyu Kong and Hongxin Piao
Gastrointest. Disord. 2026, 8(3), 32; https://doi.org/10.3390/gidisord8030032 - 29 Jun 2026
Viewed by 256
Abstract
Cholangiocarcinoma (CCA) is a highly malignant tumor originating from the epithelium of the bile ducts. It has an insidious onset, is difficult to diagnose in its early stages, has a low rate of curative resection, and carries an extremely poor prognosis. Among these, [...] Read more.
Cholangiocarcinoma (CCA) is a highly malignant tumor originating from the epithelium of the bile ducts. It has an insidious onset, is difficult to diagnose in its early stages, has a low rate of curative resection, and carries an extremely poor prognosis. Among these, intrahepatic cholangiocarcinoma (iCCA), as the most representative subtype, is a classic “immunologically cold tumor.” The response rate to single-agent immunotherapy is only 5–10%, and the mechanisms of immune resistance are complex and not yet fully elucidated. The tumor microenvironment, serving as the core site of immune resistance, forms a highly immunosuppressive network composed of cancer-associated fibroblasts, hypoxia, metabolic reprogramming, and epigenetic abnormalities; a population of immunosuppressive cells centered on tumor-associated macrophages further amplifies tolerance signals; and the gut–biliary microbiome exerts systemic immune regulation via the gut–liver axis. Based on mutant mouse models generated via tail vein injection and in-depth studies of mutations in key signaling pathways, our understanding of the mechanisms underlying iCCA’s immune resistance is deepening at both the molecular and systems levels. This article reviews the local and systemic regulatory mechanisms of immune resistance in primary iCCA, summarizes the research value of experimental and preclinical models, and reviews novel strategies such as tumor microenvironment remodeling, activation of immune cell networks, microbiome interventions, and multidimensional combination therapies. It analyzes current research bottlenecks and clinical challenges and outlines the future direction of precision immunotherapy, aiming to provide a theoretical basis and new insights for overcoming iCCA immunotherapy resistance and advancing clinical translation. Full article
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28 pages, 1115 KB  
Review
Genetics and Molecular Mechanisms in Oral Squamous Cell Carcinoma: A Narrative Review
by Cǎtǎlina Ionescu, Ecaterina Tomaziu-Todosia Anton, Viorica Rarinca, Malina Visternicu, Alin Ciobîcă, Bogdan Novac, Daniela Tomița and Mihai Hogas
Medicina 2026, 62(7), 1247; https://doi.org/10.3390/medicina62071247 - 28 Jun 2026
Viewed by 139
Abstract
Oral squamous-cell carcinoma (OSCC) is the most common form of oral cancer, accounting for over 90% of malignancies in the oral cavity. Its pathogenesis is driven by a complex interplay of genetic alterations, transcriptomic dysregulation, epigenetic modifications, environmental exposures, and tumor microenvironment dynamics. [...] Read more.
Oral squamous-cell carcinoma (OSCC) is the most common form of oral cancer, accounting for over 90% of malignancies in the oral cavity. Its pathogenesis is driven by a complex interplay of genetic alterations, transcriptomic dysregulation, epigenetic modifications, environmental exposures, and tumor microenvironment dynamics. Despite advances in therapy, OSCC remains associated with poor survival due to late diagnosis, therapeutic resistance, and tumor heterogeneity. This narrative review explores genetic determinants and molecular mechanisms underlying OSCC, focusing on recurrent mutations, deregulated pathways, epigenetic control, gene expression changes, insights from cell models, and potential biomarkers for diagnosis and therapy. We integrate findings from the recent literature to provide a comprehensive overview of the current state of research and emerging trends in OSCC genetics. Full article
(This article belongs to the Section Genetics and Molecular Medicine)
17 pages, 4107 KB  
Article
Identification and Validation of a Lipid Metabolism-Related Gene Signature for Predicting Prognosis and Immunotherapy Response in Oral Squamous Cell Carcinoma
by Yu Xie, Ziying Chen, Zhen Chen and Yiming Yang
Metabolites 2026, 16(7), 455; https://doi.org/10.3390/metabo16070455 - 28 Jun 2026
Viewed by 243
Abstract
Background/Objectives: Lipid metabolism plays a critical role in tumor progression and immunotherapy efficacy in oral squamous cell carcinoma (OSCC). However, clinically applicable lipid metabolism-based models for predicting prognosis and immunotherapy response remain limited. This study aimed to develop and validate such a model [...] Read more.
Background/Objectives: Lipid metabolism plays a critical role in tumor progression and immunotherapy efficacy in oral squamous cell carcinoma (OSCC). However, clinically applicable lipid metabolism-based models for predicting prognosis and immunotherapy response remain limited. This study aimed to develop and validate such a model in OSCC. Methods: Using transcriptomic data of OSCC from the TCGA database and a set of lipid metabolism-related genes (LMRGs), we constructed an LMRG-based risk score model via LASSO regression to predict patient survival. This model was subsequently validated using the independent GEO dataset GSE41613. Results: Patients in the high-risk group exhibited significantly poorer overall survival than those in the low-risk group (training cohort: p < 0.0001; validation cohort: p = 0.0086). We also developed a nomogram incorporating the risk score and clinical characteristics, and the risk score was identified as an independent prognostic factor for OSCC patients. Furthermore, the risk score was significantly associated with the tumor immune microenvironment; samples with a lower risk score showed elevated CD8+ T cell infiltration and a better response to immunotherapy. Additionally, the high-risk group exhibited an increased tumor mutation burden and resistance to most chemotherapeutic agents. Notably, several drugs (e.g., obatoclax mesylate) showed significant efficacy in the high-risk group, representing promising therapeutic candidates. Conclusions: This study reveals that the LMRG signature could serve as a valuable tool for prognosis assessment, risk stratification, and therapy guidance in OSCC. Full article
(This article belongs to the Special Issue Advances in Immune Metabolism: Lipid Regulation and Disease Outcomes)
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13 pages, 4970 KB  
Article
Non-Canonical Binding of Nelfinavir in HIV-1 Protease Variants Reveals Structural Mechanisms of Antiretroviral Resistance
by Christian Cadena-Cruz, Marcio De Avila-Arias, Fabio Guzmán, Mariana Pérez, María Angelica Zuluaga, Elkin Navarro Quiroz, Alejandro Angulo, Luz Elena Prieto Garcerant, Hector Rodríguez Rojas, Dinno Alberto Fernández Chica, Guillermo Cervantes and Jose Luis Villarreal-Camacho
Viruses 2026, 18(7), 701; https://doi.org/10.3390/v18070701 (registering DOI) - 25 Jun 2026
Viewed by 308
Abstract
Background: Antiretroviral resistance-associated mutations, within the broader context of HIV-1 genetic variability, represent a growing challenge for HIV-1 control, highlighting the need for continuous molecular surveillance and mechanistic understanding of drug resistance. This study aimed to characterize mutations in the pol gene associated [...] Read more.
Background: Antiretroviral resistance-associated mutations, within the broader context of HIV-1 genetic variability, represent a growing challenge for HIV-1 control, highlighting the need for continuous molecular surveillance and mechanistic understanding of drug resistance. This study aimed to characterize mutations in the pol gene associated with resistance to protease inhibitors and to explore their structural implications. Methods: Viral RNA was extracted from plasma samples of HIV-positive patients, and a 266 bp fragment of the HIV-1 pol gene was amplified by RT-PCR and sequenced using the Sanger method. Sequences showing ≥98% homology were aligned and analyzed using MEGA v11 and the Stanford HIV Drug Resistance Database to identify resistance-associated mutations, while viral subtypes were determined using COMET, jpHMM-HIV, and STAR tools. Amino acid sequences were used for structural modeling with AlphaFold, followed by molecular docking with Nelfinavir using the CB-Dock2 server. Results: Four samples exhibited resistance-associated profiles, including high-level, intermediate, and low-level resistance, with one isolate showing high-level resistance to multiple protease inhibitors. Structural analyses revealed that Nelfinavir preferentially binds to alternative hydrophobic cavities rather than the canonical catalytic site, lacking direct interactions with the Asp25/Asp25′ dyad. Conclusions: These findings suggest a structural mechanism of resistance based on non-canonical ligand binding that may impair effective protease inhibition. Full article
(This article belongs to the Section General Virology)
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22 pages, 1269 KB  
Review
Critical Prognostic and Predictive Factors in Colorectal Liver Metastasis: A Thorough Analysis of Existing Literature and Future Outlook
by Paul Pasca, Flaviu Ionut Faur, Cosmin Burta, Dan Brebu, Carmen Neamtu, Vlad Braicu, Ciprian Duta, Ioana Adelina Faur, Razvan Danau, Amadeus Dobrescu and Marius Murariu
J. Clin. Med. 2026, 15(13), 4907; https://doi.org/10.3390/jcm15134907 - 24 Jun 2026
Viewed by 163
Abstract
Background: Colorectal cancer (CRC) prognosis, particularly in liver metastasis (CRLM), is influenced by histopathological and molecular factors. Methods: A narrative analysis of the specialized literature was conducted using databases such as PubMed, MEDLINE, Scopus, and Embase. The review focused on original articles published [...] Read more.
Background: Colorectal cancer (CRC) prognosis, particularly in liver metastasis (CRLM), is influenced by histopathological and molecular factors. Methods: A narrative analysis of the specialized literature was conducted using databases such as PubMed, MEDLINE, Scopus, and Embase. The review focused on original articles published between 2005 and 2025. Results: Lymph node involvement is a critical prognostic factor, with lymph node-positive CRC correlating with increased risk of liver metastasis and significantly reduced survival rates. Poorly differentiated tumors (G3) exhibit a higher likelihood of metastasis, including liver involvement, and are associated with worse clinical outcomes. Vascular emboli and perineural invasion are indicative of hematogenous spread and higher metastatic potential, leading to poorer survival outcomes. Genetic mutations, such as KRAS, NRAS, and BRAF, are associated with therapy resistance, complicating treatment and highlighting the importance of personalized approaches. MSI-H and HER2 amplification further affect treatment response, with MSI-H tumors showing a favorable response to immunotherapy, while HER2-positive CRCs may benefit from targeted therapies. Tumor budding, high levels of which predict poor survival, is another key histopathological feature associated with aggressive metastatic behavior. Systemic inflammatory markers, such as the Neutrophil-to-Lymphocyte Ratio (NLR), Platelet-to-Lymphocyte Ratio (PLR), and C-Reactive Protein-to-Albumin Ratio (CAR), offer prognostic insights into CRLM patient survival. Conclusions: Histopathological features, molecular alterations, and immune microenvironment factors significantly impact the prognosis of CRC with liver metastasis. The integration of molecular profiling, immunotherapy, and targeted therapies offers promise for improving treatment outcomes. Personalized treatment strategies, incorporating these factors, are essential for overcoming therapy resistance and improving survival in CRLM patients. Full article
(This article belongs to the Section Gastroenterology & Hepatopancreatobiliary Medicine)
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32 pages, 1322 KB  
Review
Intra-Tumor Heterogeneity of Pancreatic Ductal Adenocarcinoma (PDAC)—Microenvironmental Interaction and Precision Immunotherapy Strategies: A Multi-Omics-Based Integrated Perspective
by Boyeon Kim and Jee-Hyung Lee
Int. J. Mol. Sci. 2026, 27(13), 5682; https://doi.org/10.3390/ijms27135682 - 24 Jun 2026
Viewed by 191
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains among the most therapeutically intractable malignancies, with a 5-year survival rate of approximately 10% and near-universal resistance to immune checkpoint inhibitor (ICI) therapy. This refractoriness arises from the convergence of pronounced intratumoral heterogeneity (ITH) and a profoundly immunosuppressive [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) remains among the most therapeutically intractable malignancies, with a 5-year survival rate of approximately 10% and near-universal resistance to immune checkpoint inhibitor (ICI) therapy. This refractoriness arises from the convergence of pronounced intratumoral heterogeneity (ITH) and a profoundly immunosuppressive tumor microenvironment (TME), which together configure PDAC as a prototypical immune-excluded tumor. Beyond low tumor mutational burden, PDAC exhibits layered genetic, epigenetic, transcriptional, and metabolic heterogeneity that enables rapid adaptation and immune evasion under selective pressure, while dense desmoplastic stroma, cancer-associated fibroblasts (CAFs), and immunosuppressive immune populations collectively impose formidable physical and immunologic barriers to antitumor immunity. In this review, we synthesize multi-omics, spatial transcriptomic, and immunologic evidence to elucidate how ITH and the TME dynamically interact to reinforce immune resistance. We examine reciprocal crosstalk mechanisms—including immune-driven clonal selection, interclonal cooperation, metabolic niche specialization, and metabolic–epigenetic coupling—and discuss emerging platforms such as single-cell spatial omics, patient-derived organoid immune co-culture systems, and longitudinal circulating tumor DNA monitoring that enable high-resolution mapping of ITH–TME dynamics. Finally, we evaluate ITH–TME-guided combination therapeutic strategies targeting oncogenic drivers, stromal architecture, myeloid suppression, and metabolic checkpoints, and propose a prioritized framework for near-term and speculative clinical translation in PDAC. Full article
(This article belongs to the Special Issue Deciphering Molecular Complexity of Pancreatic Cancer)
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15 pages, 1812 KB  
Systematic Review
Prevalence and Prognostic Impact of ASXL1 Somatic Mutation in Patients with Chronic Myeloid Leukemia: A Systematic Review and Meta-Analysis
by Rita Ahmad, Motaz Almahmood, Rasha Kaddoura, Muhammad Ali Tariq, Ayman Abdullah Dalol, Marrita Rabadi, Aadhila Abbas Manthiri, Abdulrahman F. Al-Mashdali, Hatem Ahmed, Mohammed Abdulgayoom, Ayah Al Qaryoute, Sara Westall, Fadi Haddad and Shehab F. Mohamed
Cancers 2026, 18(13), 2041; https://doi.org/10.3390/cancers18132041 - 24 Jun 2026
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Abstract
Background: Outcomes in chronic myeloid leukemia (CML) remain heterogeneous despite effective BCR::ABL1 tyrosine kinase inhibitors (TKIs). Somatic mutations in epigenetic regulators, particularly additional sex combs-like 1 (ASXL1), have been implicated in adverse prognosis, but their clinical impact in CML has not been systematically [...] Read more.
Background: Outcomes in chronic myeloid leukemia (CML) remain heterogeneous despite effective BCR::ABL1 tyrosine kinase inhibitors (TKIs). Somatic mutations in epigenetic regulators, particularly additional sex combs-like 1 (ASXL1), have been implicated in adverse prognosis, but their clinical impact in CML has not been systematically defined. Methods: A systematic review was conducted using CINAHL, EMBASE, MEDLINE Ultimate, and PubMed from inception through August 2025. A total of 1339 records were identified; the eligible studies included adult and pediatric patients with chronic and advanced-phase (accelerated or blast) CML. After duplicate removal and screening, 11 studies met the inclusion criteria; these included adult patients only and were included in a qualitative synthesis and meta-analysis. ASXL1 mutation status was assessed using validated molecular methods. The outcomes included the molecular response, cytogenetic response, survival, and treatment resistance. Random-effects models were used to calculate the pooled odds ratios (ORs) with 95% confidence intervals (CIs). Statistical heterogeneity was assessed using the I2 statistic. Results: Across the included studies, ASXL1 mutations were detected in approximately 15% of patients. At 12 months, patients with ASXL1 mutations had significantly lower odds of achieving a major molecular response (MMR) compared with ASXL1-wildtype patients (OR 0.29; 95% CI 0.16–0.51; p < 0.0001; I2 = 30%). No statistically significant difference was observed in the complete cytogenetic response (CCyR) (OR 0.30; 95% CI 0.02–5.31; p = 0.41; I2 = 68%). Compared with patients harboring other non-ASXL1 somatic mutations, an ASXL1 mutation was not associated with a significant difference in MMR (OR 0.49; 95% CI 0.23–1.05; p = 0.067; I2 = 0%). Conclusions: ASXL1 mutations may be associated with an inferior molecular response to TKI therapy in CML, supporting their role as an adverse prognostic biomarker. These findings highlight the potential value of incorporating myeloid mutation profiling into future CML risk-stratification strategies. Full article
(This article belongs to the Section Systematic Review or Meta-Analysis in Cancer Research)
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16 pages, 1328 KB  
Article
KRAS Subtype Modifies Outcomes with Immunomodulatory Therapy in Advanced Pancreatic Ductal Adenocarcinoma: Evidence from Early-Phase Trials
by Dilsa Mizrak Kaya, Yangruijue Ma, Tarik Demir, Nicole J. Altomare, Aparna Kalyan, Sheetal Kircher, Mary Mulcahy, Al B. Benson, Ruohui Chen and Devalingam Mahalingam
Cancers 2026, 18(13), 2037; https://doi.org/10.3390/cancers18132037 - 23 Jun 2026
Viewed by 201
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is characterized by a near-universal presence of KRAS mutations and limited responsiveness to immunotherapy. Biologic heterogeneity among KRAS subtypes may shape tumor immunobiology and treatment resistance. Methods: We evaluated 109 patients with advanced PDAC treated in early-phase trials [...] Read more.
Background: Pancreatic ductal adenocarcinoma (PDAC) is characterized by a near-universal presence of KRAS mutations and limited responsiveness to immunotherapy. Biologic heterogeneity among KRAS subtypes may shape tumor immunobiology and treatment resistance. Methods: We evaluated 109 patients with advanced PDAC treated in early-phase trials between August 2014 and August 2023. Overall survival (OS) and progression-free survival (PFS) were estimated using the Kaplan–Meier method, and Cox proportional hazard models were used to assess the clinical and molecular predictors of survival. Results: Among the 109 patients, 64% harbored KRAS mutations, 18% were KRAS wild type, and 17% had an unknown KRAS status. The median age was 65 years, and 83% had liver metastases. Among the KRAS-mutant tumors, subtype distribution was G12D (46%), G12V (31%), G12R (13%), and other variants (10%). Immunomodulatory agents were administered to 39% of the patients, most commonly in the first-line setting (49%). The median OS and PFS for the entire cohort were 5.65 and 2.73 months, respectively. The restricted mean OS (7.54 vs. 8.65, p = 0.53) and PFS (3.82 vs. 4.24, p = 0.70) did not differ between patients with KRAS mutants and wild-type KRAS. Among patients with KRAS mutations, receipt of immunomodulatory therapy was associated with shorter OS compared with those who did not receive immunomodulatory therapy, with the strongest association observed in the KRAS G12D subgroup. This pattern was not observed in KRAS wild-type tumors. On univariate analysis, immunomodulatory therapy exposure, number of prior treatment lines, and presence of liver metastases were each associated with inferior OS. On multivariable analysis, immunotherapy exposure demonstrated a non-significant trend toward inferior OS (hazard ratio [HR] 1.61, 95% Cl 0.98–2.66; p = 0.06), while the other variables remained independently associated with worse OS, suggesting confounding in the unadjusted association between immunomodulatory therapy and survival. Conclusions: Among patients with KRAS-mutant PDAC—particularly those with G12D—receipt of immunomodulatory therapy in early-phase trials was associated with shorter OS in this exploratory analysis. These findings should be considered hypothesis-generating and require validation in prospective, KRAS-subtype-informed studies. Full article
(This article belongs to the Special Issue Advancements in “Cancer Biomarkers” for 2025–2026)
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