Front Immunol. 2025 May 29;16:1585505. doi: 10.3389/fimmu.2025.1585505. eCollection 2025.

ABSTRACT

BACKGROUND: Lung adenocarcinoma (LUAD) is a common and aggressive subtype of lung cancer associated with poor clinical outcomes. The role of mitochondrial dynamics (MD)-related genes in tumor progression and immune regulation remains poorly understood.

METHODS: Data from public databases were integrated, and subtypes were classified based on 23 MD-related genes. A five-gene prognostic model was constructed. Associations between the model and immune infiltration, tumor mutational burden (TMB), tumor stemness, and drug sensitivity were analyzed. The function of the key gene MTCH2 was validated through in vitro experiments.

RESULTS: Two distinct MD molecular subtypes were identified, exhibiting significant differences in prognosis and immune characteristics. A corresponding risk score model was established. Patients in the low-risk group showed better prognosis and enhanced immune activity, whereas the high-risk group displayed higher TMB and stemness scores. Drug sensitivity analysis revealed distinct responses to chemotherapeutic agents such as cisplatin and docetaxel between risk groups. Functional assays demonstrated that MTCH2 knockout significantly inhibited LUAD cell proliferation, migration, and invasion, and induced G0/G1 phase arrest, suggesting that MTCH2 may act as a potential adverse prognostic marker.

CONCLUSION: MD-related genes exhibit strong prognostic and immune subtyping value. The proposed risk model holds clinical potential, and MTCH2 may serve as a promising target for precision therapy in LUAD.

PMID:40510359 | PMC:PMC12159055 | DOI:10.3389/fimmu.2025.1585505

Genome Biol. 2025 Jun 13;26(1):165. doi: 10.1186/s13059-025-03557-y.

ABSTRACT

Existing approaches to identifying cancer genes rely overwhelmingly on DNA sequencing data. Here, we introduce RVdriver, a computational tool that leverages paired bulk genomic and transcriptomic data to classify RNA variant allele frequencies (VAFs) of non-synonymous mutations relative to a synonymous mutation background. We analyze 7882 paired exomes and transcriptomes from 31 cancer types and identify novel, as well as known, cancer genes, complementing other DNA-based approaches. Furthermore, RNA VAFs of individual mutations are able to distinguish "driver" from "passenger" mutations within established cancer genes. This approach highlights the value of multi-omic approaches for cancer gene discovery.

PMID:40514689 | PMC:PMC12164115 | DOI:10.1186/s13059-025-03557-y

J Adv Res. 2025 Jun 11:S2090-1232(25)00427-8. doi: 10.1016/j.jare.2025.06.017. Online ahead of print.

ABSTRACT

INTRODUCTION: Lung neuroendocrine carcinomas (Lu-NECs) are rare, highly aggressive lung tumors with poor prognosis and limited therapeutic options. Understanding the tumor immune microenvironment (TIME) is crucial towards personalized therapeutic strategies.

OBJECTIVES: This study aims to systematically characterize the heterogeneity and complexity of the TIME in Lu-NECs by integrating proteomic, transcriptomic, and genomic data.

METHODS: We performed comprehensive immune-proteomic profiling of 76 Lu-NECs across diverse histopathological subtypes to elucidate intra-tumoral TIME heterogeneity at the proteomic level. Validation was conducted in multiple independent cohorts, including 112 Lu-NECs using immunohistochemistry, 147 Lu-NECs, and 17 small cell lung carcinoma samples using transcriptomics. We integrated proteomic, transcriptomic, genomic, and clinical data to assess molecular, immunological, and clinical features, as well as therapeutic vulnerabilities across different immune subtypes.

RESULTS: We delineated the immuno-proteomic landscape of Lu-NECs and identified two major immuno-proteomic clusters with distinct immunological, molecular, and clinical characteristics. IPC1 was characterized by high immune cell infiltration, while IPC2 exhibited sparse immune cell presence. Genomic analysis revealed distinct mutational patterns, with IPC1 showing a higher incidence of APOBEC-associated mutation signatures and IPC2 being enriched for mutations associated with defective DNA mismatch repair and tobacco-related mutagens. Functional analyses indicated that IPC1 was related to immune and oncogenic signaling activity, whereas IPC2 was associated with cancer stemness and proliferation-related features. Furthermore, IPC1 and IPC2 demonstrated histological subtype-specific clinical benefits from postoperative chemotherapy. Finally, we developed a machine learning model (iPROM) to predict Lu-NECs immune classification and improve risk stratification, which was validated across multiple independent cohorts.

CONCLUSIONS: This study advances the understanding of the tumor immune microenvironment in Lu-NECs through multi-omics characterization and highlights potential personalized therapeutic vulnerabilities tailored to the specific immune landscapes of Lu-NECs.

PMID:40513660 | DOI:10.1016/j.jare.2025.06.017

Cell Stem Cell. 2025 Jun 6:S1934-5909(25)00191-2. doi: 10.1016/j.stem.2025.05.011. Online ahead of print.

ABSTRACT

Deciphering interactions between tumor micro- and systemic immune macroenvironments is essential for developing more effective cancer diagnosis and therapeutic strategies. Here, we established a gel-liquid interface (GLI) co-culture model of lung cancer organoids (LCOs) and paired peripheral-blood mononuclear cells (PBMCs), featuring enhanced interactions between immune cells and tumor organoids for optimized simulation of in vivo systemic anti-tumor immunity. By constructing a cohort of lung cancer patients, we demonstrated that the responses of GLI models under αPD1 treatment reflected the immunotherapy outcomes of the corresponding patients precisely. Furthermore, we dissected the various tumor immune processes mediated by PBMC-derived T cells within GLI models through functional multi-omics analyses, along with the characterization of circulating tumor-reactive T cells (GNLY⁺CD44⁺CD9⁺) with effector memory-like phenotypes as a potential indicator of immunotherapy efficacy. Our findings indicate that the GLI co-culture model can be used to develop diagnostic strategies for precision immunotherapies, as well as understanding the underlying mechanisms.

PMID:40513558 | DOI:10.1016/j.stem.2025.05.011

J Exp Clin Cancer Res. 2025 Jun 12;44(1):174. doi: 10.1186/s13046-025-03433-4.

ABSTRACT

BACKGROUND: Epithelial ovarian cancer (EOC) is a leading cause of cancer mortality in women, often diagnosed at advanced stages. While first-line treatments improve survival, relapses remain common, with 5-year survival rates below 40%. Circulating tumor DNA (ctDNA) is a promising biomarker for non-invasive EOC detection and monitoring. It may help assess treatment response, notably microscopic residual disease. Our objective was to compare two ctDNA characterization strategies in EOC for assessing tumor burden during first-line treatment: a tumor-informed approach based on somatic mutations and a tumor-type informed approach utilizing DNA methylation patterns.

METHODS: In the tumor-informed approach, whole exome sequencing (WES) was performed on EOC tumor DNA and matched PBMCs from 22 patients to identify tumor-specific mutations. Personalized panels were then designed to track these mutations in plasma cfDNA. In the tumor-type informed approach, differentially methylated loci (DMLs) were identified by comparing EOC samples, healthy ovarian tissues, and PBMCs. A unique custom methylation panel was designed, and a support vector machine classifier was trained to distinguish between methylation profiles in plasma cfDNA from healthy donors and from EOC patients. Plasma samples from 47 advanced-stage EOC patients receiving chemotherapy and 54 healthy subjects were analyzed.

RESULTS: For the tumor-informed approach, WES identified an average of 72 somatic mutations per patient. For the tumor-type informed approach, 52,173 DMLs were identified as tumor-specific markers. In 47 plasma samples tested by both approaches, ctDNA levels were significantly correlated (R = 0.56, p = 4.3 × 10^-5), with 70.2% concordance in detection. At baseline, ctDNA was detected in 21/22 patients with the tumor-informed approach, and in 11/12 non-training baseline samples with the tumor-type-informed classifier. At end-of-treatment, the latter detected ctDNA in 16/22 samples, outperforming the former. Detection using this more sensitive approach was significantly associated with relapse (log-rank p = 0.009; hazard ratio = 9.44; 95% CI 1.22-73.26) and poorer overall survival (log-rank p = 0.041).

CONCLUSION: The tumor-type informed classifier demonstrated sensitivity and specificity for ctDNA detection, outperforming the tumor-informed approach in monitoring EOC progression. Requiring fewer sequencing data, it offers a practical, efficient solution for clinical management of EOC.

PMID:40506726 | PMC:PMC12160408 | DOI:10.1186/s13046-025-03433-4

Crit Rev Oncol Hematol. 2025 May 28;213:104776. doi: 10.1016/j.critrevonc.2025.104776. Online ahead of print.

ABSTRACT

Over the past decade, liquid biopsy (LB) has emerged as a key tool in oncology. Its utility in non-invasive sampling and real-time monitoring has made it a cornerstone in precision medicine. Since 2020, publications on LB in solid tumors have doubled, underscoring its pivotal role in advancing cancer care. Notably, 2024 marked a peak in scientific papers on this topic. Blood remained the most studied biofluid, with circulating tumor DNA (ctDNA) as the most frequently analyzed analyte, followed by circulating tumor cells, extracellular vesicles, and microRNAs. Among tumor types, gastrointestinal, lung, breast, and genitourinary cancers were the most investigated, collectively accounting for more than half of the studies. Early cancer and minimal residual disease detection are critical areas of interest, emphasizing the expanding potential of fragmentomics and methylation profiling, as well as the prognostic significance of ctDNA across various cancer types. Moreover, serial ctDNA monitoring demonstrated the ability to predict relapse and guide treatment (de)-escalation strategies. In metastatic setting, ctDNA profiling plays a crucial role in capturing tumor heterogeneity, detecting resistance mechanisms, and informing treatment selection. Non-blood biofluids gained interest for their potential to enhance the detection of clinically relevant alterations in different cancer types such as central nervous system and head and neck cancers. Other than biomarkers selection, the technological advancements and artificial intelligence significantly improved the sensitivity and specificity of LB assays. This evidence in combination with the rapid advancement of machine learning and other computational approaches, are paving the way for a new chapter of LB research.

PMID:40447209 | DOI:10.1016/j.critrevonc.2025.104776

Front Oncol. 2025 May 15;15:1520733. doi: 10.3389/fonc.2025.1520733. eCollection 2025.

ABSTRACT

Circulating tumor DNA (ctDNA), a subset of cell-free DNA (cfDNA), originates from primary tumors and metastatic lesions in cancer patients, often carrying genomic variations identical to those of the primary tumor. ctDNA analysis via liquid biopsy has proven to be a valuable biomarker for early cancer detection, minimal residual disease (MRD) assessment, monitoring tumor recurrence, and evaluating treatment efficacy. However, despite advancements in ctDNA analysis technologies, standardized protocols for its extraction and detection have yet to be established. Each step of the process-from pre-analytical variables to detection techniques-significantly impacts the accuracy and reliability of ctDNA analysis. This review examines recent developments in ctDNA detection methods, focusing on pre-analytical factors such as specimen types, collection tubes, centrifugation protocols, and storage conditions, alongside high-throughput and ultra-sensitive detection technologies. It also briefly discusses the clinical potential of liquid biopsy in nasopharyngeal carcinoma (NPC).

PMID:40444084 | PMC:PMC12119280 | DOI:10.3389/fonc.2025.1520733