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37 pages, 901 KB  
Review
m1A and m6A RNA Methylations as Druggable Targets in Cancer
by Yasemin Gazaloğlu, Buket Sağlam-Şen and Bünyamin Akgül
Pharmaceuticals 2026, 19(7), 990; https://doi.org/10.3390/ph19070990 (registering DOI) - 25 Jun 2026
Abstract
Epitranscriptomic modifications, particularly RNA methylations, have emerged as regulators of gene expression, with their dysregulation acting as a key factor in tumorigenesis and metastatic progression. This review evaluates the therapeutic landscapes of N6-methyladenosine (m6A) and N1-methyladenosine (m [...] Read more.
Epitranscriptomic modifications, particularly RNA methylations, have emerged as regulators of gene expression, with their dysregulation acting as a key factor in tumorigenesis and metastatic progression. This review evaluates the therapeutic landscapes of N6-methyladenosine (m6A) and N1-methyladenosine (m1A) modifications in cancer. While the m6A machinery predominantly dictates mRNA turnover and stability, the m1A network is uniquely positioned to drive translational reprogramming, allowing malignant cells to endure severe microenvironmental stress and evade cell death. Despite positional and chemical differences, these modifications exhibit profound epitranscriptomic crosstalk through shared regulatory proteins. Here, we comprehensively analyze current pharmacological strategies targeting the m6A axis, highlighting the transition from classical small-molecule inhibitors of regulatory proteins of these methylations, such as methyltransferase-like 3 (METTL3), fat mass and obesity-associated protein (FTO), and AlkB homolog 5 (ALKBH5), to the novel event-driven approach of proteolysis-targeting chimeras (PROTACs). Furthermore, we assess the emerging therapeutic potential of the m1A regulatory machinery, positioning tRNA methyltransferase 6/61A (TRMT6/61A) writers and AlkB homolog 1 to 3 (ALKBH1-3) erasers as promising therapeutic targets. Finally, we discuss clinical successes and current translational obstacles, including off-target toxicity, pharmacokinetic limitations, and epitranscriptomic escape, emphasizing that site-specific modulation and smart precision therapies will dictate the future of oncology. Full article
(This article belongs to the Section Pharmacology)
10 pages, 249 KB  
Hypothesis
Perspective for CAR T-Cell Therapy in Underrepresented Populations: A Hypothesis-Generating CD19 Genomic Analysis
by Maysa Al-Hussaini, Anas Al Okaily and Osama Alsmadi
J. Pers. Med. 2026, 16(7), 343; https://doi.org/10.3390/jpm16070343 (registering DOI) - 25 Jun 2026
Abstract
CD19-directed chimeric antigen receptor (CAR) T-cell therapy has fundamentally transformed the treatment landscape for relapsed and refractory B-cell malignancies, yet antigen escape remains a persistent therapeutic challenge that limits long-term remission durability. While antigen loss is typically considered a somatic event acquired during [...] Read more.
CD19-directed chimeric antigen receptor (CAR) T-cell therapy has fundamentally transformed the treatment landscape for relapsed and refractory B-cell malignancies, yet antigen escape remains a persistent therapeutic challenge that limits long-term remission durability. While antigen loss is typically considered a somatic event acquired during tumor evolution under therapeutic selective pressure, germline CD19 polymorphisms could theoretically influence CAR-binding kinetics, alter epitope presentation, and modulate therapeutic outcomes in ways that remain largely not characterized. Unfortunately, Middle Eastern populations are underrepresented in pharmacogenomic databases and CAR-T clinical trials, creating a knowledge gap that may perpetuate global health disparities in access to precision immunotherapy. We analyzed publicly available whole-exome sequencing data from 1196 individuals of Arab origin to comprehensively characterize CD19 variants with potential relevance to CAR T-cell immunotherapy. The L174V (rs2904880) variant stood out, and showed the Valine/Valine (V/V) genotype frequency was 65.3%, corresponding to a V174 allelic frequency of 76.6%, while the minor allele, L174, has a frequency of 23.4%. The missense mutation (c.520C > G) responsible for this variant results in a leucine-to-valine (L174V) substitution at position 174 of the CD19 protein, relative to the reference genome. The cohort genotypes (CC, CG, and GG) exhibited a significant deviation from Hardy–Weinberg equilibrium (p < 0.00001). While this deviation is consistent with the high consanguinity rates (25–60%) amongst Arab populations, it remains not fully explained, and may be attributed to population structure, relatedness, or technical factors. We further emphasize that our computational analysis cannot establish any direct clinical or functional impact due to this variant, and therefore we refrain from suggesting any specific actions at the current time. In light of these findings, we hypothesize that the distinctive genetic architecture of consanguineous populations should not be viewed as a confounding variable. Instead, it presents a unique opportunity to investigate the clinical relevance of germline variation in the context of precision oncology, particularly at therapy-relevant loci, pending functional validation. Full article
18 pages, 5929 KB  
Review
The Relationship Between Neutrophil Extracellular Traps and CD8+ T Lymphocytes in Cancer: A Comprehensive Review of Current Data
by Kellyn E. McKee, Hongji Zhang, Allan Tsung and Samantha M. Ruff
Cancers 2026, 18(13), 2059; https://doi.org/10.3390/cancers18132059 (registering DOI) - 25 Jun 2026
Abstract
Neutrophil extracellular traps (NETs) are web-like structures composed of decondensed DNA, histones, and proteins released by activated neutrophils. Originally identified as an innate defense mechanism against pathogens, NETs have since been implicated in cancer progression and immune evasion. Within the tumor microenvironment (TME), [...] Read more.
Neutrophil extracellular traps (NETs) are web-like structures composed of decondensed DNA, histones, and proteins released by activated neutrophils. Originally identified as an innate defense mechanism against pathogens, NETs have since been implicated in cancer progression and immune evasion. Within the tumor microenvironment (TME), NETs suppress anti-tumor immunity through multiple mechanisms, including the physical exclusion of CD8+ cytotoxic T lymphocytes from the tumor interior and upregulation of exhaustion markers via checkpoint ligands. This review synthesizes current preclinical and clinical evidence on the interplay between NETs and CD8+ T cells across multiple malignancies, including non-small cell lung cancer, pancreatic ductal adenocarcinoma, cholangiocarcinoma, colorectal cancer, bladder cancer, hepatocellular carcinoma, skin cancer, and penile cancer. Cancer-specific mechanisms of NET-mediated immune suppression are discussed, including IL-8, IL-17, CXCL6, and TGF-β-driven NETosis pathways. Clinical data consistently demonstrate that elevated NET levels correlate with reduced CD8+ T cell infiltration, T cell dysfunction, and worse patient outcomes. Emerging therapeutic strategies targeting this axis are reviewed, including DNase I-mediated NET degradation, Peptidyl arginine deiminase 4 (PAD4) inhibition, CXCR2 blockade, and combination approaches with immune checkpoint inhibitors. These interventions have shown promise in restoring CD8+ T cell cytotoxicity and overcoming immunotherapy resistance in preclinical models. Collectively, the evidence supports the NET-CD8+ T cell axis as a promising prognostic and therapeutic target warranting further clinical investigation. Full article
(This article belongs to the Section Cancer Immunology and Immunotherapy)
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33 pages, 1353 KB  
Review
Chimeric Antigen Receptor–Immune Cell-Based Therapies for Clear Cell Renal Cell Carcinoma: Latest Advancements and Directions
by Xuyuan Zhu, Yu Zhang, Yuxiang Chen, Shanda Li, Kun Wang, Tao Li, Xiaojie Ma, Zhuona Ni and Hongtao Jiang
Cancers 2026, 18(13), 2051; https://doi.org/10.3390/cancers18132051 (registering DOI) - 24 Jun 2026
Abstract
Clear cell renal cell carcinoma (ccRCC) accounts for approximately 75% of renal cell carcinomas and is defined by near-universal VHL inactivation, leading to constitutive HIF stabilisation, metabolic reprogramming, and an immunologically distinct tumour microenvironment (TME). Although ccRCC is characterised by abundant immune infiltration, [...] Read more.
Clear cell renal cell carcinoma (ccRCC) accounts for approximately 75% of renal cell carcinomas and is defined by near-universal VHL inactivation, leading to constitutive HIF stabilisation, metabolic reprogramming, and an immunologically distinct tumour microenvironment (TME). Although ccRCC is characterised by abundant immune infiltration, this paradoxically correlates with poor prognosis, reflecting a TME that imposes interconnected physical, immunological, and metabolic barriers to effective immunotherapy. Chimeric antigen receptor (CAR)-based therapies have revolutionised the treatment of haematological malignancies, but their translation to ccRCC has encountered substantial hurdles. The first-in-human trial targeting carbonic anhydrase IX (CAIX) was limited by on-target off-tumour toxicity and CAR immunogenicity—lessons that fundamentally reshaped the field. CD70 has since emerged as the dominant clinical target, expressed in over 80% of ccRCCs with a highly restricted normal tissue distribution. The phase I COBALT-RCC trial of CTX130, an allogeneic CRISPR-Cas9-edited CD70-directed CAR-T cell product, provided formal proof of concept, achieving disease control in 81.3% of heavily pretreated patients and a durable complete response now exceeding three years—the first such sustained remission reported for any CAR-T cell product in a solid malignancy. Nevertheless, the low frequency of durable responses and universal loss of CAR-T cell persistence by day 28 underscore that major barriers remain. Beyond CD70, the field has diversified across multiple platforms, including CAR–natural killer (NK) cells, CAR–natural killer T (NKT) cells, and CAR–macrophages, each offering distinct biological advantages. This review synthesises current knowledge of the ccRCC TME, the preclinical landscape of CAR-based therapies, and emerging clinical evidence from more than 30 registered trials. We discuss target antigens; engineering strategies to overcome TME barriers, including cytokine armouring, chemokine receptor co-expression, switch receptors, and metabolic reprogramming; and rational combination approaches. We argue that the convergence of optimised target selection, cellular engineering, combination strategies, and biomarker-driven trial design may ultimately improve outcomes for patients with ccRCC. However, achieving a cure remains an aspirational goal, and significant barriers must first be overcome. Full article
(This article belongs to the Special Issue Advances in Cell and Gene Therapy in Tumors: From Bench to Bedside)
22 pages, 1994 KB  
Article
Naphthoquinone-Amino Acids Regulate Cellular Cancer Associated Processes, p53 and miR-34a-5p Expression in Immortal and Tumorigenic Cervical Cell Lines
by Jessica Lizbeth Sifuentes-Padilla, Angelica Judith Granados-López, Antonia Monserrat Campos-Lujan, Abel Suárez-Castro, Mayra Denise Herrera, Yamilé López-Hernández, Hiram Hernández-López, José Antonio Varela-Silva, Rosalinda Gutiérrez-Hernández, Claudia Araceli Reyes-Estrada, Sergio Hugo Sánchez-Rodríguez, Ernesto Rivera-Ávalos, Denisse de Loera and Jesús Adrián López
Int. J. Mol. Sci. 2026, 27(13), 5703; https://doi.org/10.3390/ijms27135703 (registering DOI) - 24 Jun 2026
Abstract
Cervical cancer is a malignant disease that affects women worldwide and is associated with both high incidence and a high mortality rate. miR-34 is a direct transcriptional-target of p53 and is downregulated in several types of cancers. 1,4-Naphthoquinones (NQs) have anticancer properties and [...] Read more.
Cervical cancer is a malignant disease that affects women worldwide and is associated with both high incidence and a high mortality rate. miR-34 is a direct transcriptional-target of p53 and is downregulated in several types of cancers. 1,4-Naphthoquinones (NQs) have anticancer properties and have been used to modulate miR-34 expression. We tested (3-chloro-NQ-2-yl)-alanine (ANQCl), -methionine (MNQCl), -glycine (GNQCl), -phenylalanine (FNQCl), -asparagine (NNQCl), and (1,4-napthoquinon-2-yl)-asparagine (NNQ) in immortal and tumorigenic cells, both HPV-positive and -negative, simulating precancerous and cancerous status to observe the response of the p53-miR-34 system, migration and invasion. A dose–response was achieved to determine the IC50 of the compounds in SiHa, CaLo, C33-A and HaCaT cells. HaCaT cell migration inhibition was more potent than in SiHa, CaLo, and C33-A cells, while invasion hindrance was more evident in the tumorigenic SiHa, CaLo and C33-A. NNQCl, GNQCl, ANQCl and FNQCl compounds induced p53 overexpression in SiHa and CaLo cells. Compound ANQCl in SiHa and FNQCl in CaLo induced miR-34a overexpression, probably via p53. Migration and invasion of most compounds decreased independently of p53-miR-34. NQ-amino acids exert effect on cell proliferation, migration and invasion in cervical cancer cells, suggesting their potential use in the field of cancer treatment. Full article
(This article belongs to the Special Issue Recent Advances in Non-Coding RNAs in Human Research)
28 pages, 53779 KB  
Article
TDGF1 Mediates the Oncogenic Effects of the OLMALINC/miR-3614-5p ceRNA Axis in Colon Cancer Through Nodal/Smad2 and Glypican-1/MAPK-AKT Signaling
by Feng Gao, Xiaoli Li, Jiawei Li, Shuo Yang, Boyu Zhang, Ying Sun, Lihua Zheng, Guannan Wang, Lei Liu, Yongli Bao and Xiaoguang Yang
Cells 2026, 15(13), 1141; https://doi.org/10.3390/cells15131141 (registering DOI) - 23 Jun 2026
Viewed by 146
Abstract
The multifaceted oncogenic role of teratocarcinoma-derived growth factor 1 (TDGF1) in colon cancer remains incompletely understood. Through integrative bioinformatic and functional analyses, we identified a novel competing endogenous RNA (ceRNA) axis wherein the long non-coding RNA OLMALINC directly sponges hsa-miR-3614-5p, leading to the [...] Read more.
The multifaceted oncogenic role of teratocarcinoma-derived growth factor 1 (TDGF1) in colon cancer remains incompletely understood. Through integrative bioinformatic and functional analyses, we identified a novel competing endogenous RNA (ceRNA) axis wherein the long non-coding RNA OLMALINC directly sponges hsa-miR-3614-5p, leading to the derepression of TDGF1. This OLMALINC/miR-3614-5p/TDGF1 axis promoted colon cancer cell proliferation, migration, invasion, and anti-apoptosis in vitro, whereas TDGF1 knockdown significantly suppressed tumor growth in vivo. Mechanistically, TDGF1 co-activated oncogenic signaling via the Thr88-dependent Nodal/Smad2 cascade and the Glypican-1-mediated MAPK/AKT pathway. Beyond cell-autonomous effects, transcriptomic and single-cell analyses revealed that elevated TDGF1 correlates with an immunosuppressive microenvironment, characterized by reduced immune infiltration and altered LGALS9-CD44 malignant-T cell communication. Clinically, high TDGF1 expression in a tissue microarray cohort was significantly associated with advanced T stage, reduced expression of specific mismatch repair proteins (MLH1/PMS2), and poor overall survival. Collectively, this study delineates the OLMALINC/miR-3614-5p/TDGF1 regulatory circuit and establishes TDGF1 as a multifaceted driver of tumor progression, highlighting its potential as a prognostic biomarker and therapeutic target in colon cancer. Full article
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15 pages, 589 KB  
Review
Kidney Injury Molecule-1 (KIM-1) in Renal Cell Carcinoma: Biological Foundations and Emerging Clinical Applications
by Jason King Talao, Rohann Correa, Lakshman Gunaratnam and Ricardo Fernandes
Curr. Oncol. 2026, 33(7), 378; https://doi.org/10.3390/curroncol33070378 (registering DOI) - 23 Jun 2026
Viewed by 231
Abstract
Renal cell carcinoma (RCC) is a biologically heterogeneous malignancy characterized by variable clinical behavior and diverse molecular phenotypes. Although immune checkpoint inhibitors and targeted therapies have transformed the treatment landscape of advanced RCC, clinically validated biomarkers capable of improving risk stratification, therapeutic-decision making [...] Read more.
Renal cell carcinoma (RCC) is a biologically heterogeneous malignancy characterized by variable clinical behavior and diverse molecular phenotypes. Although immune checkpoint inhibitors and targeted therapies have transformed the treatment landscape of advanced RCC, clinically validated biomarkers capable of improving risk stratification, therapeutic-decision making and disease monitoring remain lacking. Kidney injury molecule-1 (KIM-1), also known as hepatitis A virus cellular receptor-1 (HAVCR1) or T-cell immunoglobulin and mucin domain-containing protein-1 (TIM-1), has emerged as a biologically compelling investigational biomarker e because of its close relationship to proximal tubular epithelial injury and renal carcinogenesis. KIM-1 is a transmembrane glycoprotein minimally expressed in normal kidney tissue but markedly upregulated in dedifferentiated proximal tubular epithelial cells following injury, and in clear cell RCC, where its extracellular domain can be shed into plasma and urine. Beyond its role as a marker of tubular injury, KIM-1 participates in immune regulation, phagocytosis, inflammatory signaling and tissue remodeling, supporting its potential relevance to tumor biology. Clinical studies have demonstrated associations between elevated circulating KIM-1 levels and RCC diagnosis, recurrence risk, and survival outcomes, particularly in localized and postoperative disease settings. KIM-1 has additionally been investigated as a therapeutic target through antibody–drug conjugate approaches. Despite promising translational data, important limitations yet remain. Current evidence is predominantly prognostic rather than predictive, and substantial analytical and biological challenges continue to limit implementation. Assay standardization, clinically meaningful cutoffs, specimen selection, timing of sampling, and confounding by chronic kidney disease or nonmalignant renal injury remain incompletely resolved. Furthermore, evidence supporting incremental value beyond established clinicopathologic models remains limited. This review critically evaluates the biological rationale, analytical considerations and clinical evidence supporting KIM-1 in RCC. Particular emphasis is placed on distinguishing prognostic, predictive, pharmacodynamic, and therapeutic applications, as well as defining the evidentiary gaps that must be addressed before clinical implementation. Current evidence is derived predominantly from retrospective and exploratory analyses, and important limitations remain regarding assay standardization, biological specificity, chronic kidney disease-related confounding, and prospective validation. The review concludes with a summary of the evolving landscape of KIM-1-directed biomarker strategies in RCC, which may ultimately contribute to improved biologic risk stratification and biomarker-driven clinical investigation in RCC. Full article
40 pages, 15205 KB  
Article
CXCL13 as a Prognostic Biomarker and Immune Microenvironment-Associated Gene in Endometrial Carcinoma: A Multi-Omics Investigation
by Yiwen Sun, Xiaoyv Wang, Fangzheng Wu, Yanglin Ji and Jun Xie
Biology 2026, 15(13), 987; https://doi.org/10.3390/biology15130987 (registering DOI) - 23 Jun 2026
Viewed by 169
Abstract
Immune remodeling within the tumor microenvironment (TME) influences the progression and clinical outcome of uterine corpus endometrial carcinoma (UCEC), but the contribution of chemokine-related regulatory genes remains incompletely characterized. This study aimed to evaluate the prognostic relevance of CXCL13 and its association with [...] Read more.
Immune remodeling within the tumor microenvironment (TME) influences the progression and clinical outcome of uterine corpus endometrial carcinoma (UCEC), but the contribution of chemokine-related regulatory genes remains incompletely characterized. This study aimed to evaluate the prognostic relevance of CXCL13 and its association with immune microenvironmental features in UCEC using publicly available transcriptomic and single-cell datasets. RNA-sequencing profiles and clinical annotations from 589 UCEC cases in The Cancer Genome Atlas (TCGA) were analyzed to assess TME composition using ESTIMATE (Estimation of Stromal and Immune cells in MAlignant Tumours using Expression data) and CIBERSORT (Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts), followed by survival analysis, differential gene expression analysis, protein–protein interaction network construction, Cox regression, and gene set enrichment analysis. A public single-cell RNA-sequencing dataset from the Gene Expression Omnibus (GEO; GSE173682) was further used to infer the cellular sources of CXCL13. Elevated CXCL13 expression was associated with favorable overall survival and enrichment of immune-activation pathways. CIBERSORT-based analysis indicated that high CXCL13 expression correlated with increased estimated fractions of CD8+ T cells and plasma cells, together with transcriptional features related to tertiary lymphoid structure-associated immune activation, whereas several immunosuppressive cell populations showed lower estimated abundance. Single-cell analysis suggested that CXCL13 was mainly expressed by follicular helper T cells and exhausted CD8+ T cells. These findings indicate that CXCL13 may serve as a prognostic biomarker associated with an immune-active TME in UCEC. Further histological, spatial, and functional validation is warranted to confirm its mechanistic role and translational potential. Full article
(This article belongs to the Section Immunology)
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19 pages, 11970 KB  
Data Descriptor
SCAPeSCLC: An Integrated Spatial Transcriptomic and Bayesian Pathway Enrichment Dataset for Survival Modeling in Extensive-Stage Small Cell Lung Cancer
by Milad Shirvaliloo
Data 2026, 11(7), 152; https://doi.org/10.3390/data11070152 (registering DOI) - 23 Jun 2026
Viewed by 147
Abstract
Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy with limited publicly available spatial transcriptomic resources, particularly for extensive-stage disease (ES-SCLC), which remains absent from major initiatives such as The Cancer Genome Atlas (TCGA). To improve accessibility, interoperability, and downstream analytical utility [...] Read more.
Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy with limited publicly available spatial transcriptomic resources, particularly for extensive-stage disease (ES-SCLC), which remains absent from major initiatives such as The Cancer Genome Atlas (TCGA). To improve accessibility, interoperability, and downstream analytical utility of existing spatial transcriptomic data, SCAPeSCLC was developed as a harmonized dataset derived from two publicly available Gene Expression Omnibus (GEO) series, GSE261345 and GSE261348, generated using the NanoString GeoMx Digital Spatial Profiler platform. The resource integrates normalized expression measurements from 296 tumor regions of interest (ROI) across 58 ES-SCLC patients treated with first-line chemoimmunotherapy. Normalized expression matrices were reformatted into survival-ready column-based datasets at both ROI and patient levels following log2-transformation and standardization. Clinical metadata were curated and harmonized, and progression-free survival (PFS), disease-specific survival (DSS), overall survival (OS), time-on-treatment (ToT), follow-up intervals, and censoring indicators were reconstructed from the original clinical records. Biological pathway (BP) activity scores were generated using Cancer Transcriptome Atlas (CTA) annotations encompassing 106 BPs. To account for variable ROI sampling across patients, Bayesian hierarchical modeling was applied to estimate patient-level pathway activity, yielding posterior estimates and corresponding credible intervals. The resulting resource includes harmonized expression matrices, pathway enrichment profiles, Bayesian posterior estimates, survival-ready clinical annotations, and standardized Cox proportional hazards modeling outputs, along with a dedicated GitHub repository. SCAPeSCLC is intended to facilitate confirmatory analyses, integrative statistical modeling, methodological benchmarking, and reproducible exploration of spatial transcriptomic determinants of survival in ES-SCLC. Full article
(This article belongs to the Special Issue Benchmarking Datasets in Bioinformatics, 3rd Edition)
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27 pages, 9848 KB  
Article
Comprehensive Bioinformatic Characterization of CD70, CD80, and TIGIT as Diagnostic, Prognostic, and Immune Biomarkers in Pan-Cancer
by Christos Panagiotis Rigopoulos, Ilias Georgakopoulos-Soares and Apostolos Zaravinos
Curr. Issues Mol. Biol. 2026, 48(6), 641; https://doi.org/10.3390/cimb48060641 (registering DOI) - 21 Jun 2026
Viewed by 120
Abstract
Immunotherapy has transformed cancer treatment; however, clinical benefit remains limited to a subset of patients, underscoring the need for robust biomarkers that capture tumor-immune interactions across cancer types. In this study, we performed a comprehensive pan-cancer, multi-omics characterization of the immune checkpoint–related molecules [...] Read more.
Immunotherapy has transformed cancer treatment; however, clinical benefit remains limited to a subset of patients, underscoring the need for robust biomarkers that capture tumor-immune interactions across cancer types. In this study, we performed a comprehensive pan-cancer, multi-omics characterization of the immune checkpoint–related molecules CD70, CD80, and TIGIT to evaluate their diagnostic, prognostic, and immunological relevance. Using integrative analyses of transcriptomic, epigenomic, genomic, pharmacogenomic, and single-cell RNA-sequencing data from The Cancer Genome Atlas and complementary resources, we assessed expression patterns, DNA methylation, somatic mutations, copy number alterations, immune infiltration, tumor stemness, and drug sensitivity. CD70, CD80, and TIGIT were broadly dysregulated across multiple malignancies, with coordinated overexpression particularly evident in kidney renal clear-cell carcinoma. Elevated expression of these immune checkpoints was associated with advanced tumor stage, aggressive molecular subtypes, and unfavorable survival outcomes in selected cancers, including uveal melanoma and renal malignancies. Functional analyses revealed significant associations between checkpoint expression and key oncogenic pathways, including epithelial–mesenchymal transition, apoptosis, and hormone receptor signaling, suggesting links with tumor progression and immune activation states. Immune deconvolution analyses indicated that TIGIT expression is associated with a T-cell–inflamed microenvironment and reduced neutrophil infiltration, while CD80 exhibited methylation-dependent associations with immune cell composition. Genomic and epigenetic alterations were found to correlate with checkpoint expression patterns and immune phenotypes across tumor types. Pharmacogenomic profiling identified associations between checkpoint expression and sensitivity to multiple anticancer agents; however, these findings are based on cell line datasets and should be considered predictive. Single-cell transcriptomic analyses further resolved cell-type–specific expression patterns, distinguishing tumor-intrinsic from immune-restricted expression profiles. Collectively, our findings establish CD70, CD80, and TIGIT as integrative biomarkers of tumor progression, immune contexture, and therapeutic response, providing a rationale for their clinical exploitation in precision immuno-oncology. Full article
(This article belongs to the Collection Bioinformatics Approaches to Biomedicine)
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13 pages, 664 KB  
Article
Has the Expected Shift in HIV-Related Cancers Occurred? Findings from a Long-Term HIV Cohort in Turkey
by İnci Yılmaz Nakir, Melike Nur Özçelik, Rumeysa Gülistan Karaduman and Esra Zerdali
J. Clin. Med. 2026, 15(12), 4818; https://doi.org/10.3390/jcm15124818 (registering DOI) - 21 Jun 2026
Viewed by 138
Abstract
Background/Objectives: Despite widespread antiretroviral therapy (ART) use, whether the expected transition from AIDS-defining to non-AIDS-defining cancers has occurred in settings with persistent late HIV presentation remains unclear. We examined long-term cancer patterns, determinants, and survival outcomes in a large HIV cohort. Methods [...] Read more.
Background/Objectives: Despite widespread antiretroviral therapy (ART) use, whether the expected transition from AIDS-defining to non-AIDS-defining cancers has occurred in settings with persistent late HIV presentation remains unclear. We examined long-term cancer patterns, determinants, and survival outcomes in a large HIV cohort. Methods: This retrospective, single-center cohort included 1419 people living with HIV followed between 2006 and 2024. Patients who developed malignancy were classified as AIDS-defining cancers (ADC) or non-AIDS-defining cancers (NADC). Immuno-virological parameters were assessed at HIV and cancer diagnosis. Survival was analyzed using Kaplan–Meier methods, and predictors of mortality were evaluated using Cox proportional hazards regression. Determinants of ADC development were assessed using multivariable logistic regression. Temporal changes were evaluated by trend analysis. Results: Sixty-six patients (4.6%) developed malignancy (31 ADC, 35 NADC). Late HIV presentation was common, with 72.7% having CD4+ T-lymphocyte counts < 350 cells/mm3 at cancer diagnosis, particularly among ADC cases. Most ADCs (93.5%) occurred within 24 months of HIV diagnosis. Overall survival did not differ between ADC and NADC groups (log-rank p = 0.14). Although mortality declined after 2015, temporal changes in ADC and NADC proportions did not reach statistical significance (p = 0.14). In Cox regression analysis, viral suppression before death or last follow-up was independently associated with lower mortality risk (HR 0.12; 95% CI 0.05–0.31). Lower CD4+ T-lymphocyte counts were associated with ADC development, and a CD4+ T-lymphocyte threshold of 295 cells/mm3 showed good discriminative performance (AUC = 0.83), although this cutoff should be interpreted cautiously due to the lack of external validation. Conclusions: In this long-term cohort from Türkiye, a clear epidemiological transition from ADC to NADC could not be demonstrated. The cancer spectrum remained strongly influenced by late HIV presentation and advanced immunodeficiency. Sustained viral suppression was independently associated with lower mortality risk, supporting the importance of early HIV diagnosis, timely ART initiation, and sustained virological control. Full article
(This article belongs to the Section Infectious Diseases)
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27 pages, 2393 KB  
Review
CAR-M Therapy: From Concept to Clinical Translation in Solid Tumors
by Chenxi Miao, Zhitao Chen, Juan Chen, Jiazeng Sun, Yanan Sun, Wenbiao Shi, Wentao Xu, Yixuan Li and Xingwang Zhao
Cells 2026, 15(12), 1113; https://doi.org/10.3390/cells15121113 - 19 Jun 2026
Viewed by 290
Abstract
While chimeric antigen receptor (CAR)-T-cell therapies have shown significant effectiveness in hematological malignancies, their efficacy in solid tumors remains limited by the hostile tumor microenvironment (TME) and antigen heterogeneity. Recently, CAR-Macrophage (CAR-M) therapy has emerged as a paradigm-shifting approach, leveraging the innate capability [...] Read more.
While chimeric antigen receptor (CAR)-T-cell therapies have shown significant effectiveness in hematological malignancies, their efficacy in solid tumors remains limited by the hostile tumor microenvironment (TME) and antigen heterogeneity. Recently, CAR-Macrophage (CAR-M) therapy has emerged as a paradigm-shifting approach, leveraging the innate capability of macrophages to deeply infiltrate tumors and their plasticity to reverse immunosuppression. Unlike T cells, CAR-Ms not only mediate direct phagocytosis but also initiate epitope spreading, effectively bridging innate and adaptive immunity. This review critically examines the trajectory of CAR-M therapy from biological rationale to clinical reality. We dissect the engineering evolution of CAR constructs, arguing for macrophage-specific signaling domains (e.g., FcRγ, Megf10) over traditional T-cell designs. Crucially, we address the major bottlenecks in clinical translation, including the manufacturing challenges of non-expanding primary macrophages and the emerging shift toward induced pluripotent stem cell (iPSC)-derived platforms. Furthermore, we evaluate current clinical trial landscapes and discuss next-generation strategies such as in vivo programming via lipid nanoparticles (LNPs) and synthetic logic-gating to enhance safety. Ultimately, overcoming manufacturing constraints and optimizing delivery systems will be pivotal for CAR-M to evolve from a niche therapy into a standard-of-care modality for solid tumors. Full article
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32 pages, 2706 KB  
Review
In Vivo CAR-Based Immune Cell Engineering: Future Applications and Challenges in Malignant Glioma
by Junya Yamaguchi, Alejandra Bergquist, Jianwen Lu, Senthilnath Lakshmanachetty, Safwaan H. Khan and Hideho Okada
Cancers 2026, 18(12), 1986; https://doi.org/10.3390/cancers18121986 - 18 Jun 2026
Viewed by 371
Abstract
Chimeric antigen receptor (CAR)-T cell therapy has achieved remarkable success in hematologic malignancies, and its development is being actively pursued across a broad range of cancer types. However, current CAR-T cell therapies rely on ex vivo engineering, which presents significant logistical, temporal, and [...] Read more.
Chimeric antigen receptor (CAR)-T cell therapy has achieved remarkable success in hematologic malignancies, and its development is being actively pursued across a broad range of cancer types. However, current CAR-T cell therapies rely on ex vivo engineering, which presents significant logistical, temporal, and biological limitations. In vivo CAR-T cell engineering is emerging as a new paradigm that may overcome these challenges by enabling the direct reprogramming of immune cells within the patient through the administration of CAR-encoding vectors. This approach represents an off-the-shelf form of autologous immune therapy. Advances in viral engineering and nanotechnology have enabled the development of diverse CAR delivery platforms that not only deliver CAR constructs but also facilitate the delivery of gene-editing components, such as Cas9, allowing for more sophisticated in vivo genetic modifications. Some of these approaches have already entered clinical evaluation and have shown promising early results in hematologic malignancies, with clinical trials in solid tumors now underway. However, the application of in vivo-engineered CAR-T cell therapies to malignant glioma remains largely unexplored, reflecting challenges distinct from those encountered in hematologic malignancies. In this review, we discuss these challenges and potential strategies to address them, while highlighting recent progress in in vivo CAR-T cell engineering. Full article
(This article belongs to the Special Issue Immune Microenvironment and Immunotherapy in Malignant Brain Tumors)
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42 pages, 3543 KB  
Review
Emerging Perspectives on How Metallic Nanoparticles and Their Oxide Forms Interact with the Tumor Microenvironment
by Carlos Caro
Processes 2026, 14(12), 1977; https://doi.org/10.3390/pr14121977 (registering DOI) - 18 Jun 2026
Viewed by 311
Abstract
Cancer remains one of the most formidable health challenges worldwide. Extensive research has shown that tumor progression is not driven solely by malignant cells but is profoundly shaped by the tumor microenvironment (TME), which influences cancer initiation, immune evasion, and metastatic spread. Consequently, [...] Read more.
Cancer remains one of the most formidable health challenges worldwide. Extensive research has shown that tumor progression is not driven solely by malignant cells but is profoundly shaped by the tumor microenvironment (TME), which influences cancer initiation, immune evasion, and metastatic spread. Consequently, the TME has become an increasingly compelling therapeutic target. Nanotechnology has transformed cancer diagnostics and therapy, with metallic nanoparticles (mNPs) gaining particular attention due to their distinctive physicochemical properties and broad therapeutic potential. However, their interactions within the TME remain insufficiently understood, particularly with the non-cancerous cellular components, such as Cancer-Associated Fibroblasts (CAFs), Tumor-Associated Macrophages (TAMs), Dendritic Cells (DCs), Natural Killer (NK) cells, and T cells. Most existing reviews emphasize nanoparticle interactions with non-cellular TME components, such as the extracellular matrix, while far less attention has been given to their effects on cellular constituents (a gap this work specifically addresses). Although several molecular pathways through which mNPs modulate TME-resident cells have been identified, these likely represent only a small portion of the underlying mechanisms explored in this review. Progress in the field is further hindered by the limited availability of physiologically relevant experimental models; current in vitro and in vivo systems often fail to capture the complexity and dynamic heterogeneity of the TME. These limitations highlight the urgent need for more comprehensive and mechanistically grounded studies to validate the TME as a viable therapeutic target for nanoparticle-based cancer interventions. In particular, deeper insights into how mNPs influence immune regulation, stromal remodeling, and metabolic reprogramming within the TME will be essential for unlocking their full therapeutic potential in oncology. Full article
(This article belongs to the Special Issue Multiscale Modeling and Control of Biomedical Systems)
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Article
Long-Term Cognitive Impairment After CAR-T Therapy Versus Autologous Stem Cell Transplantation: A Propensity Score-Matched Cohort Study
by Anna Blyzniuk, Po-Huang Chen, Wei-Cheng Chang, Hsin-Yu Chen, Li-Ting Kao, Tina Yi-Jin Hsieh, Ming-Shen Dai, Hong-Jie Jhou and Cho-Hao Lee
Diagnostics 2026, 16(12), 1862; https://doi.org/10.3390/diagnostics16121862 - 16 Jun 2026
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Abstract
Background/Objectives: Chimeric antigen receptor T-cell (CAR-T) therapy has transformed outcomes in relapsed or refractory hematologic malignancies, but long-term cognitive outcomes remain poorly understood. We compared the incidence and time course of cognitive impairment and associated neurological complications after CAR-T therapy compared with [...] Read more.
Background/Objectives: Chimeric antigen receptor T-cell (CAR-T) therapy has transformed outcomes in relapsed or refractory hematologic malignancies, but long-term cognitive outcomes remain poorly understood. We compared the incidence and time course of cognitive impairment and associated neurological complications after CAR-T therapy compared with autologous stem cell transplantation (ASCT). Methods: This retrospective, propensity-matched cohort study utilized the TriNetX US Collaborative Network (January 2014–April 2025). To ensure concurrent comparisons, ASCT recipients were restricted to an index date beginning in August 2017 or later. CAR-T recipients were matched 1:1 to ASCT recipients for demographics, disease, comorbidities, prior and concomitant treatments, and laboratory parameters. The primary endpoint was time to cognitive impairment, as defined by ICD-10 codes. Results: After comparing 3067 CAR-T patients (median follow-up 634 days) with 3067 ASCT patients (median follow-up 713 days), CAR-T recipients had a higher risk of cognitive impairment (HR 1.58; 95% CI 1.39–1.80; p < 0.001). Because the risks were not proportional (Schaenfeld p < 0.001), the difference was also expressed as restricted median survival time (RMST): CAR-T recipients spent approximately 25 and 53 days fewer days without cognitive impairment at 1 and 2 years, respectively (both p < 0.001). The risk was greatest at 30 days (HR 4.22; 95% CI 3.23–5.53), but remained elevated in control analyses at 30 and 90 days that excluded the acute ICANS window (HR 1.30 and 1.25, respectively; both p < 0.05). Neurological dysfunction, particularly encephalopathy (HR 2.04; 95% CI 1.73–2.40), was more common after CAR-T. Conversely, CAR-T was associated with a reduced risk of secondary acute myeloid leukemia (HR 0.46; 95% CI 0.38–0.55; p < 0.001). Conclusions: CAR-T therapy is associated with a higher risk of cognitive impairment that persists beyond the acute phase. As these are observational, code-based data, they should be interpreted as associations rather than evidence of a specific mechanism, and they highlight the need for informed consent discussions, long-term neurocognitive monitoring, and the development of neuroprotective strategies. Full article
(This article belongs to the Special Issue Recent Advances in Hematology and Oncology, 2nd Edition)
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