Molecular diagnosis has revolutionized cancer precision medicine. However, therapeutic resistance, recurrence, and metastasis remain critical challenges, since conventional diagnostic patterns mainly focus on molecular alterations of tumor cells while overlooking other important factors, thus leading to limited guidance for clinical decision-making. The critical role of tumor microenvironment (TME) has been well recognized in recent years. Therefore, establishing diagnostic systems based on TME molecular signatures represents a promising strategy. This review outlines the evidence in support of TME-derived molecules as potential biomarkers, and details their biological functions and clinical significance. Emerging molecular analytical technologies, scoring models, and subtyping frameworks for TME assessment are also summarized. Finally, current challenges and future directions in the field of TME-based molecular diagnostics are discussed to provide valuable insights for this new trend.

Oxidative phosphorylation (OXPHOS) plays a complex and dynamic role in cancer biology, with its involvement varying depending on tumor type, cancer progression stage, and microenvironmental conditions. While many cancer cells primarily rely on aerobic glycolysis for energy production, recent studies have demonstrated that OXPHOS is critical for the survival, proliferation, and metastasis of certain cancer cells. With the advent of OXPHOS-targeted anticancer drugs, their therapeutic potential has become increasingly evident. However, achieving precision therapy necessitates the development of accurate diagnostic techniques for identifying OXPHOS dysfunction. This review focuses on the fundamental role of OXPHOS in tumors and the tumor microenvironment, as well as recent advancements in the laboratory methods for assessing OXPHOS function.

Tumors pose an enormous burden to human health due to their high incidence and mortality rates, constituting a major global public health concern. Tumor immunotherapy is a revolutionary treatment for patients with complicated conditions or for those who have not responded well to conventional treatment. Vaccine technology effectively prevents infectious diseases, and tumor vaccines have been recently demonstrated to have significant potential as a tumor therapy. Antigens for tumor vaccines can be derived from several different types of tumor cell materials, including entire cells, cell lysates, cell vesicles, and cell membranes. The selection and optimization of antigens are critical for vaccine effectiveness, as they should trigger a precise immune system defensive response against a specific pathogen (or cells) without producing overwhelming negative side effects. They should precisely trigger the immune system's defensive responses against specific pathogens or cells without producing overwhelming negative side effects. Supported by a robust theoretical basis and substantial preclinical evidence, tumor cell-derived vaccines hold considerable potential for future research and clinical translation. This review introduces the current state of tumor cell-derived vaccines, discusses their limitations, and explores future pathways to their advancement. Tumor cell-derived vaccines may emerge as a novel strategy for the treatment of cancer, allowing patients to have more effective treatment options.

Archival formalin-fixed paraffin-embedded (FFPE) specimens are greatly useful for mitochondrial DNA (mtDNA) biomarker studies. However, formalin-induced artifacts mimic somatic mutations, confounding clinical interpretations. Current artifact-removal tools, which are optimized for nuclear DNA, lack mtDNA-specific adaptation to address its high copy number, GC-content disparity between strands, and characteristics of heteroplasmy, necessitating tailored computational solutions. We developed mtFFPECleaner, a machine learning framework integrating multidimensional features of mtDNA mutations, including variant allele frequency (VAF) distribution, strand orientation bias score, sequence context, and local base composition. The framework employed a random forest classifier trained on 837 ground-truth genuine mutations and 1169 artifacts from 23 paired FFPE-fresh frozen (FF) samples. Model training was performed using tenfold cross-validation, followed by independent validation on an additional 15 paired FFPE-FF samples. Our analyses revealed that formalin-induced artifacts in mtDNA next-generation sequencing (NGS) data predominantly occur as C > T/G > A transitions, particularly in low VAF ranges, with significant strand bias and sequence context dependence. The mtFFPECleaner classifier, optimized through balanced sampling (1:2 ratio of artifacts to genuine mutations), achieved outstanding discrimination accuracy in an independent validation set (98.7% specificity and 98.2% sensitivity), outperforming conventional nuclear DNA artifact-removal tools, including SOBDetector and DEEPOMOICS FFPE. Furthermore, following artifact removal by mtFFPECleaner, the mutational spectra of 314 FFPE samples showed remarkable concordance with those observed in FF samples. Importantly, we observed that the artifact burden correlated with the duration of FFPE sample storage, underscoring mtFFPECleaner's capability to effectively mitigate formalin-induced damage accumulated over decades in archival biospecimens. mtFFPECleaner represents the first dedicated solution for enhancing mutational fidelity in mtDNA NGS data from FFPE specimens. The open-source R package (https://github.com/AlienLemon117/mtFFPECleaner) ensures scalability for large-scale archival studies, unlocking the translational potential of FFPE biobanks.

Human mesenchymal stem cell-derived small extracellular vesicles (MSC-sEVs) have demonstrated significant immunomodulatory and pro-regenerative potentials. However, the lack of specific markers to define MSC-sEVs presents a major challenge for their clinical application. Here, the proteomic datasets of MSC-sEVs from three cell sources were synchronously analyzed, and several surface antigens commonly found on MSCs were selected as candidate markers due to their high abundances in MSC-sEVs. Next, MSC-sEVs from three cell sources (adipose tissue, umbilical cord, and induced pluripotent stem cells) were stained with fluorescein-conjugated antibodies and analyzed by NanoFCM at single-vesicle resolution. The positive rates of CD13, CD29, and CD90 all exceeded 60% across sEVs derived from three MSCs sources, whereas other candidates generally exhibited lower positive rates. The high positive rates of them were further verified in MSC-sEVs purified via other methods. Moreover, high-resolution microscopy, as an orthogonal method, visually validated their high presence in MSC-sEVs. Meanwhile, none of the non-MSC-sEVs showed concurrent positive rates for CD13, CD29, and CD90 exceeding 40%, suggesting that this marker panel (with a positive rate threshold of 50% for all three markers) could specifically distinguish MSC-sEVs from non-MSC-sEVs. Finally, the positive rates of this panel of markers were assessed in sEVs derived from MSCs at successive passages. The results revealed a progressive diminution of the positive rates of CD29 and CD90 in the sEVs secreted by MSCs with successive passages, accompanied by a reduction in the pro-proliferative activity of these sEVs. Taken together, we have identified a specific and quantifiable marker panel for MSC-sEVs characterization, which facilitates the development of standardized assays for defining MSC-sEVs and ultimately accelerates the clinical translation of MSC-sEVs.

Screening of tumor-specific markers and targeted therapy has achieved significant clinical efficacy in recent years. PIWI-interacting RNAs (piRNAs), which are crucial in the progression of tumors, are anticipated to be significant targets for the research and development of tumor molecular drugs aimed at tumors. This study corroborated the role of piR-hsa-164586 in enhancing the invasion and metastasis of non-small cell lung cancer (NSCLC) cells, as previously observed with its unusually high expression in NSCLC tissue and serum extracellular vesicles, through both in vitro and in vivo experiments. Single-cell RNA sequencing (scRNA-seq) combined with other molecular techniques revealed that the overexpression of piR-hsa-164586 regulates the tumor niche of NSCLC by upregulating mesenchymal subtypes of tumor epithelial cells. Furthermore, piR-hsa-164586 is involved in regulating PI3K-AKT pathway and epithelial–mesenchymal transition, thereby accelerating the invasion and metastasis of NSCLC cells. MYH9 (a non-PIWI protein) could bind to piR-hsa-164586 and the knockdown of piR-hsa-164586 or MYH9 links to better NSCLC prognoses. In conclusion, this work not only revealed the specific regulatory mechanism of piR-hsa-164586 as a tumor marker of NSCLC, but also provided support for developing molecular targeted therapies for NSCLC.

Vascular aging, which is marked by brain endothelial cell (EC) senescence and functional impairment, plays a significant role in diverse age-related cerebrovascular and neurodegenerative disorders. EC-derived microvesicles (EMVs) and exosomes (EEXs) preserve the molecular signatures of their source cells and deliver bioactive cargo to regulate the activity of target cells, but their potentials in vascular aging remain unclear. Here, as indicated by SA-β-gal staining, cerebral blood flow, blood brain barrier function, aging related markers and cognitive ability test, we found that young ECs released EMVs could more effectively alleviate mice cerebrovascular and brain aging than EEXs. Aged ECs released EMVs were more effective than their released EEXs on aggravating mice cerebrovascular and brain aging. We further identified that these EMVs regulated cerebrovascular and brain aging by transferring miR-17-5p and could modulate ECs senescence and functions via miR-17-5p/PI3K/Akt pathway. Plasma EMV concentrations and EMV-miR-17-5p expression were altered in older adults, showing strong associations with reactive oxygen species and vascular aging. Receiver operating characteristic analysis demonstrated the potential of EMVs and EMV-miR-17-5p as diagnostic biomarkers for vascular aging. Our results revealed the novel roles for EMVs that could more effectively modulate vascular and brain aging than EEXs by regulating ECs functions through miR-17-5p/PI3K/Akt pathway, and also suggested that EMVs and EMV-miR-17-5p represent promising biomarkers and therapeutic targets for vascular aging.

Chemoresistance and immune evasion constitute formidable obstacles in triple-negative breast cancer (TNBC) therapy, exacerbated by the suboptimal pharmacokinetics and acquired resistance of antibody–drug conjugates (ADCs). Herein, we describe the engineering of antibody-guided nanoparticles (NPs) co-delivering the trophoblast cell-surface antigen 2 (TROP2)-targeting ADC sacituzumab govitecan (SG) with the mitochondria-directed near-infrared (NIR) photosensitizer AIE780. These AIE780–SG nanoconstructs exploit hRS7 antibody–mediated targeting to preferentially accumulate in TROP2-overexpressing, SG-resistant TNBC cells and patient-derived organoid. Upon NIR irradiation, AIE780 induces a mitochondrial redox imbalance via localized reactive oxygen species generation, precipitating tumor-selective immunogenic cell death (ICD) through membrane destabilization and oxidative necrosis. Concurrently, SG undergoes acid-responsive cleavage to release SN-38—a potent topoisomerase I inhibitor—and the hRS7 antibody fragment, which orchestrates natural killer (NK) cell recruitment and activation. In murine TNBC xenograft models, AIE780–SG NPs achieved synergistic chemophotodynamic tumor eradication, surmounting SG resistance and revitalizing antitumor immunity. This TROP2-targeted, light-sensitive theranostic platform offers a multimodal paradigm to potentiate ADC efficacy and reprogram the immunosuppressive TNBC microenvironment, heralding a novel strategy against SG-resistant TNBC. A dual-therapeutic nanoplatform combining targeted ADC delivery with photodynamic induction of ICD overcomes SG resistance in TNBC and amplifies NK cell-mediated antitumor responses.

Mitochondrial quality control (MQC), a key cellular mechanism for maintaining mitochondrial integrity and function, contributes to cellular homeostasis. Mitochondrial fission protein 1 (FIS1) is located on the outer mitochondrial membrane and is closely related to MQC. FIS1 represents a critical regulatory factor in mitochondrial biogenesis, fission, fusion, and mitophagy, participates in cellular energy metabolism, and is closely associated with tumor progression in maintaining intracellular homeostasis and signal transduction. Expression levels of FIS1 differ significantly between various tumor types; its overexpression is closely related to enhanced proliferation and invasiveness of tumor cells, and its downregulation may lead to tumor cell apoptosis. While the potential role of FIS1 in cancer has been reported, gaps in knowledge regarding functional changes in different tumor microenvironments and its regulatory mechanisms remain. This review focuses on current perspectives regarding the mechanisms by which FIS1 participates in MQC, its impact on tumors, and its role in clinical diagnosis and treatment. Further research on specific mechanisms of FIS1 in tumor progression and its interactions with other signaling pathways is required to provide new targets and strategies for cancer diagnosis and treatment.

This review explores the application of cold atmospheric plasma (CAP) and nanoparticles (NPs) in cancer therapy, highlighting their potential to enhance treatment efficacy and minimize side effects. CAP generates reactive oxygen and nitrogen species that selectively induce apoptosis in cancer cells, while NPs improve drug delivery, enhance targeting precision, and reduce adverse effects on healthy tissues. By summarizing various types of NPs, including gold, silver, magnetic, and other NPs, we evaluate their individual and combined effects with CAP across different cancer models. Our findings suggest that combined CAP-NPs significantly enhance therapeutic outcomes by increasing cancer cell sensitivity and minimizing damage to surrounding tissues. This synergistic approach not only aligns with previous research on CAP's selective toxicity but also reveals new possibilities for optimizing cancer treatment through targeted NP delivery. Further clinical research is needed to establish the safety and efficacy of this combination, paving the way for novel, patient-specific treatment strategies with improved outcomes.

Hereditary disorders are a group of diseases caused by genetic mutations or chromosomal variations. Although the incidence of each genetic disorder is relatively low, patients affected by the disease generally experience a range of severe symptoms, including blindness, disability, and even premature death. In addition, the available treatments for hereditary disorders are limited. Fortunately, the emergence of advanced gene-editing tools such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and base editors (BEs) has provided promising prospects for gene editing therapies in treating hereditary disorders. In this review, we mainly summarize the recent progress on BEs and their applications in hereditary disorders. Additionally, we discuss the prospects and challenges associated with the use of BEs, aiming to provide new insights into the area of gene therapy.