Cancer Genetics[JOURNAL]
Sun
200 papers
Anticancer effect of palmitoyl piperidinopiperidine against human pancreatic ductal adenocarcinoma cells.
Yoshioka H, Hamanaka J, Horiuchi A … +3 more , Horita H, Horiguchi H, Suzui M
Cancer Genet · 2026 Apr · PMID 41719917 · Publisher ↗
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancer types owing to its early metastasis and resistance to treatment. Therefore, novel treatments for PDAC should be urgently developed....
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancer types owing to its early metastasis and resistance to treatment. Therefore, novel treatments for PDAC should be urgently developed. We previously demonstrated that1‑palmitoyl‑4‑piperidinopiperidine (PPI), a derivative of palmitic acid, showed anticancer effects against human colon cell lines by inhibiting signal transducer and activator of transcription 3 (STAT3) phosphorylation. However, no studies have focused on the potency of PPI against human PDAC BxPC-3 cells. METHODS: We examined cell viability after treatment with PPI for 72-h. We evaluated apoptosis- and cell cycle-related molecules using immunocytochemistry and western blotting. RESULT: PPI dose-dependently inhibited cell proliferation, with an IC of 4.93 μM. Moreover, PPI treatment induces apoptosis. We also observed G1 cell cycle arrest, as indicated by cyclin D1, Cdk4, Cdk6, cyclin E, and Cdk2 downregulation. Furthermore, the expression of phosphorylated STAT3 and its downstream proteins, including MMP2, MMP9, and VEGF, decreased following PPI treatment. CONCLUSION: These results suggest that PPI exerts antitumor effects against BxPC-3 cells by inhibiting STAT3 phosphorylation.
Context-specific roles of DDX60 in colorectal cancer via autophagy regulation and DDX58 signaling.
Wang K, Zhang C, Ma C … +3 more , Fu X, Geng L, Jiang H
Cancer Genet · 2026 Apr · PMID 41687471 · Publisher ↗
BACKGROUND: DEAD-box RNA helicases have emerged as critical regulators in cancer biology, yet the functional role of DDX60 in colorectal cancer (CRC) remains poorly characterized and tissue-context dependent. Existing re...
BACKGROUND: DEAD-box RNA helicases have emerged as critical regulators in cancer biology, yet the functional role of DDX60 in colorectal cancer (CRC) remains poorly characterized and tissue-context dependent. Existing reports suggest opposing roles of DDX60 across tumor types, potentially mediated by autophagy and innate immune signaling. Understanding the dual roles of DDX60 in CRC is crucial for delineating its therapeutic relevance. OBJECTIVE: DExD/H-box helicase 60 (DDX60) is a newly identified member of the DEAD-box (DDX) RNA helicase family. Existing evidence suggests that the expression patterns and functions of DDX60 vary across tumor types in a tissue-specific manner. However, its precise biological role and underlying molecular mechanisms in colorectal cancer (CRC) remain unclear. METHODS: The expression of DDX60 in CRC cell lines was examined by transcriptome sequencing (RNA-seq) and Western blot (WB) analysis. Lentiviral transduction was employed to achieve DDX60 overexpression (OE-DDX60) and knockdown (KD-DDX60) in both cellular assays and xenograft models. Cell proliferation, migration, and invasion were assessed using the Cell Counting Kit-8 (CCK-8), EdU incorporation, wound healing, and Transwell assays. Immunofluorescence staining was performed to detect microtubule-associated protein 1A/1B-light chain 3B (LC3B) and sequestosome 1 (p62/SQSTM1) levels. Co-immunoprecipitation (Co-IP) assays were conducted to evaluate the interaction between DDX60 and DExD/H-box helicase 58 (DDX58) Lipid peroxidation products and inflammatory cytokines were quantified using commercial assay kits, while mitochondrial membrane potential was assessed via JC-1 staining. SW620 cells were subcutaneously injected into the groin region of nude mice to establish xenograft tumors, and tumor weight and volume were monitored. Histological changes and apoptosis in tumor tissues were analyzed using hematoxylin and eosin (H&E) staining and flow cytometry. RESULTS: DDX60 is highly expressed in CRC cell lines. In vitro experiments revealed that OE-DDX60 significantly promoted the proliferation, migration, and invasion of SW620 cells while inhibiting apoptosis, confirming its pro-tumorigenic role. These effects were accompanied by reduced levels of lipid peroxidation products and pro-inflammatory cytokines. In contrast, in vivo experiments showed that OE-DDX60 suppressed tumor growth and enhanced apoptosis in tumor tissues, indicating an anti-tumor effect. This was associated with increased levels of inflammatory cytokines and enhanced DDX58 signaling, which contradicted the in vitro findings. Additionally, DDX60 markedly activated autophagy in both in vitro and in vivo settings. Notably, administration of the autophagy inhibitor CA-5f exerted anti-tumor effects on CRC. CONCLUSION: In summary, this study elucidates the biological functions of DDX60 in CRC and provides novel experimental evidence supporting its potential as a therapeutic biomarker.
Transcription factor FOXP2 attenuates the stemness of breast cancer cells by abolishing the transcription of Twist1.
Chen T, Liu Y, Yu L … +3 more , Chen Y, Huang M, Tan Y
Cancer Genet · 2026 Apr · PMID 41643273 · Publisher ↗
Transcription factor FOXP2 participates in language acquisition and increasing evidence suggests that dysregulation of FOXP2 is associated with human tumorigenesis and progression. Reducing FOXP2 levels has increased bre...
Transcription factor FOXP2 participates in language acquisition and increasing evidence suggests that dysregulation of FOXP2 is associated with human tumorigenesis and progression. Reducing FOXP2 levels has increased breast cancer stem cell viability, but its inhibitory mechanisms to cancer stem cells are still not fully understood. In this study, we found that the expression levels of FOXP2 were downregulated in clinical breast cancers and negatively correlated with the cancer stem cell marker ALDH1. We demonstrated that the expression of FOXP2 was significantly decreased in the mammosphere formed by breast cancer cells. The overexpression of FOXP2 reduced the expression of cancer stem cell markers and consequently the mammosphere formation ability in breast cancer cells. We found that FOXP2 directly inhibited the transcription of Twist1, a proto-oncogene promoting the metastasis and stemness of cancer cells. The compensatory expression of Twist1 in FOXP2-overexpressing breast cancer cells counteracted FOXP2's inhibitory effects on the stemness of breast cancer cells. Together, the results showed that FOXP2 attenuated the stemness of breast cancer cells by abolishing the transcription of Twist1.
Genetic polymorphisms of tumor necrosis factor receptor-associated factor 3 and their association with acute lymphoblastic leukemia.
Alkhulaifi FM, Hakami H, Alshammari J … +4 more , Alqarzae SA, Almuhaini A, Aloyouni SY, Alomar S
Cancer Genet · 2026 Apr · PMID 41619431 · Publisher ↗
BACKGROUND: Acute lymphoblastic leukemia (ALL) is an aggressive hematological malignancy driven by genetic and immunological dysregulation. Tumor necrosis factor receptor-associated factor 3 (TRAF3) plays an essential ro...
BACKGROUND: Acute lymphoblastic leukemia (ALL) is an aggressive hematological malignancy driven by genetic and immunological dysregulation. Tumor necrosis factor receptor-associated factor 3 (TRAF3) plays an essential role in regulating immune signaling, lymphocyte homeostasis, and NF-κB pathways. Although TRAF3 alterations have been implicated in various immune disorders and hematologic cancers, the contribution of TRAF3 genetic polymorphisms to ALL susceptibility remains insufficiently understood. PURPOSE: To investigate the association between three TRAF3 single nucleotide polymorphisms (SNPs); rs33980500, rs13210247, and rs1131877, and ALL susceptibility in Saudi patients, and to evaluate TRAF3 mRNA expression levels in ALL compared to healthy individuals. METHODS: A case-control study was conducted involving 150 newly diagnosed ALL patients and 115 age- and sex-matched healthy controls. Genotyping of the selected TRAF3 SNPs was performed using TaqMan allelic discrimination assays. TRAF3 mRNA expression in peripheral blood white cells was quantified through RT-qPCR. Statistical analyses included genotype/allele frequency comparisons, odds ratios, Hardy-Weinberg equilibrium testing, linkage disequilibrium assessment, and haplotype construction. RESULTS: None of the analyzed SNPs showed a statistically significant association with ALL across genotype, allele, or haplotype models. Linkage disequilibrium between the SNPs was absent. However, TRAF3 mRNA expression was significantly upregulated in ALL patients, exhibiting a 3.88-fold increase compared with controls (p < 0.05). CONCLUSION: Although the examined TRAF3 SNPs were not associated with ALL susceptibility in this cohort, the marked elevation of TRAF3 mRNA expression suggests a potential role for TRAF3-related signaling in ALL pathogenesis. TRAF3 expression may represent a promising biomarker warranting further investigation.
Germline APC I1307K and MITF E318K variants in a patient with high-grade serous ovarian carcinoma: A case report.
Covey SC, Ortiz MMJ, Jernigan A … +3 more , Balakrishnan R, Kim SY, Miele L
Cancer Genet · 2026 Apr · PMID 41616432 · Publisher ↗
We report the case of a 76‑year‑old woman with high‑grade serous ovarian carcinoma (HGSOC) who was found to carry germline variants in APC I1307K and MITF E318K. Although neither variant is an established contributor to...
We report the case of a 76‑year‑old woman with high‑grade serous ovarian carcinoma (HGSOC) who was found to carry germline variants in APC I1307K and MITF E318K. Although neither variant is an established contributor to ovarian cancer risk, their co‑occurrence raises the possibility of polygenic or modifier effects on tumor susceptibility. The APC I1307K allele is a founder variant linked to increased colorectal cancer risk through the creation of a hypermutable region that predisposes to somatic mutations rather than classical tumor‑suppressor inactivation. In contrast, MITF E318K is a gain‑of‑function variant associated with melanoma and renal cell carcinoma, acting through altered transcriptional regulation that promotes cell proliferation and survival. While these genes do not interact directly, both converge on signaling pathways-WNT/β‑catenin, MAPK/ERK, and PI3K/AKT-that are widely implicated in ovarian carcinogenesis. There is a possibility that HGSOC in this patient is sporadic and unrelated to these two variants. Nevertheless, the case underscores the importance of comprehensive germline testing and highlights potential, yet underexplored, genetic interactions that may influence ovarian cancer risk. To our knowledge, this represents the first reported case of HGSOC in a patient harboring both variants, offering a hypothesis‑generating observation for future investigation.
The role and prospects of the Fudan classification in precision medicine for triple-negative breast cancer.
Yang Q, Li B, Chen Y … +1 more , Yang H
Cancer Genet · 2026 Apr · PMID 41604874 · Publisher ↗
Triple-Negative Breast Cancer (TNBC) remains a major challenge in oncology because of its significant heterogeneity and the lack of established therapeutic targets. Conventional diagnostic and treatment methods often fal...
Triple-Negative Breast Cancer (TNBC) remains a major challenge in oncology because of its significant heterogeneity and the lack of established therapeutic targets. Conventional diagnostic and treatment methods often fall short in addressing this complexity, which creates a need for molecular subtyping frameworks to guide precision therapy. Here, we systematically review the evolution of TNBC molecular subtyping, with a focus on the "Fudan Classification" as a powerful and integrative system. This classification offers a systematic perspective for deciphering the biological essence of TNBC and for designing treatment strategies. Its four principal subtypes-immunomodulatory (IM), luminal androgen receptor (LAR), basal-like immunosuppressed (BLIS), and mesenchymal (MES)-uncover distinct disease entities driven by unique oncogenic pathways, thereby providing a rationale for aligning specific treatments like targeted agents and immunotherapies with the most likely-to-benefit patient subgroups. In parallel, we examine emerging treatments that go beyond traditional subtyping, including TROP-2-targeting Antibody-Drug Conjugates (ADCs). These ADCs, together with subtyping-guided approaches, are expanding the scope of precision medicine. This article aims to demonstrate that a more robust and comprehensive precision therapy system for TNBC can be built on a dual logic of "subtype-driven" and "target-driven" strategies, offering insights for future work on overcoming drug resistance and optimizing combination therapies.
Elucidation of MMP-9 expression and association of MMP-9 rs3918242-1562 C/T promoter polymorphism in the progression of cervical cancer.
Poleboyina PK, Pawar SC
Cancer Genet · 2026 Apr · PMID 41579783 · Publisher ↗
This study explores the expression of the MMP-9 gene through transcriptomic analysis and quantitative real-time PCR (qRT-PCR), along with the investigation of the promoter polymorphism rs3918242 (C-1562T) using RFLP, con...
This study explores the expression of the MMP-9 gene through transcriptomic analysis and quantitative real-time PCR (qRT-PCR), along with the investigation of the promoter polymorphism rs3918242 (C-1562T) using RFLP, confirmed by Sanger sequencing. A total of 200 samples were analyzed, including 100 cervical squamous cell carcinoma tissues and 100 normal control samples. Results revealed a significant upregulation of MMP-9 mRNA expression in cancerous tissues compared to normal counterparts. Furthermore, analysis of the rs3918242 polymorphism showed a higher prevalence of the C allele among controls, while the T allele was more frequently observed in patients. Notably, individuals with the T/T genotype, under a recessive genetic model, exhibited a significantly increased risk of cervical cancer (p < 0.02; OR = 2.98; 95 % CI: 1.12-7.98). Although no strong association was found between the polymorphism and overall cervical cancer risk, elevated MMP-9 expression was closely linked to disease progression. Transcription factor binding analysis using TRANSFAC revealed that the C-to-T substitution disrupts an SP1 binding site, potentially contributing to increased gene expression. Additionally, assessments of mRNA and pre-mRNA secondary structures indicated that the rs3918242 polymorphism alters RNA conformation, with the C allele displaying higher structural stability than the T allele. These findings suggest that while the polymorphism may not directly confer susceptibility, it could influence gene regulation mechanisms relevant to the development of cervical cancer.
Persistent monosomy 7 in Philadelphia chromosome-negative cells without disease progression over nearly two decades of follow-up in chronic myeloid leukemia.
Chen M, Tang G, Hu S
Cancer Genet · 2026 Apr · PMID 41579782 · Publisher ↗
Monosomy 7 (-7) is frequently associated with myelodysplastic neoplasm/syndrome (MDS) and acute myeloid leukemia (AML). In chronic myeloid leukemia (CML), the acquisition of -7 in Philadelphia chromosome-positive (Ph-pos...
Monosomy 7 (-7) is frequently associated with myelodysplastic neoplasm/syndrome (MDS) and acute myeloid leukemia (AML). In chronic myeloid leukemia (CML), the acquisition of -7 in Philadelphia chromosome-positive (Ph-positive) cells is considered a high-risk feature for progression to blast crisis. However, the clinical significance of -7 in Ph-negative cells remains less unclear. We report a patient with CML who developed a - 7 clone in Ph-negative cells during tyrosine kinase inhibitor (TKI) therapy. The -7 clone emerged after 14 months of TKI treatment, persisted for nearly six years, and subsequently disappeared. The patient continued treatment with sequential TKIs under long-term surveillance. Over nearly 20 years of follow-up, there was no evidence of significant dysplasia or progression to AML. This case suggests that the occurrence of -7 in Ph-negative cells does not reflect TKI-induced genotoxicity and does not necessarily confer an increased risk of MDS or AML.
Genome-wide cfDNA Methylation Profiling of Pleural Effusion Reveals an Immuno-epigenetic Signature for Differentiating Malignant from Benign Cases.
Sun Z, Xu F, Chen J … +9 more , Zhang N, Luo F, Huang X, Liu Z, Xing X, Li K, Chen X, Zhang L, Che N
Cancer Genet · 2026 Apr · PMID 41576511 · Publisher ↗
BACKGROUND: Distinguishing malignant pleural effusion (MPE) from benign pleural effusion (BPE) remains clinically challenging because conventional cytology has limited sensitivity. We investigated whether cfDNA methylati...
BACKGROUND: Distinguishing malignant pleural effusion (MPE) from benign pleural effusion (BPE) remains clinically challenging because conventional cytology has limited sensitivity. We investigated whether cfDNA methylation profiling of pleural effusion supernatant could provide a non‑invasive diagnostic alternative. METHODS: Patients with pleural effusion were consecutively and prospectively recruited from Beijing Chest Hospital between November 2022 and March 2024. We conducted genome-wide cfDNA methylation profiling on qualified pleural effusion samples. A mechanistically relevant diagnostic signature was developed using a knowledge-driven approach, integrating probes involving immune pathways and immune cell deconvolution data from the training set. The final signature's performance was subsequently tested in an internal validation cohort and benchmarked against conventional cytology. RESULTS: A total of 101 participants were enrolled, including 45 MPE and 56 BPE according to the composite reference standard. We observed a distinct methylation landscape between MPE and BPE, identifying 3,119 hypermethylated and 232 hypomethylated DMPs in MPE that were enriched in immune‑related pathways (such as T cell activation). Deconvolution indicated significant differences in immune cell-derived cfDNA (including CD8+ T cells, B cells, eosinophils) between groups. A 7‑CpG-model based on LASSO classifier achieved an AUC of 0.980 (95% CI: 0.954-1.000) in the training set and 0.963 (95% CI: 0.896-1.000) in the internal validation set. The classifier substantially improved MPE detection in cytology‑negative or indeterminate cases and identified MPEs missed by conventional methods. CONCLUSIONS: A 7‑CpG-model from pleural effusion cfDNA reliably discriminates MPE from BPE and shows promise as a reflex test for resolving cytologic uncertainty.
Functional impact assessment of tissue-specific missense variants in the PTPRH gene using a multi-tool computational framework.
Naseem AA, Khan R, Hameed U
Cancer Genet · 2026 Apr · PMID 41570449 · Publisher ↗
Cancer is driven by genetic alterations that disrupt cellular processes, and one key gene involved in this progression is Protein Tyrosine Phosphatase Receptor Type H (PTPRH). Acting as both a tumor suppressor and oncoge...
Cancer is driven by genetic alterations that disrupt cellular processes, and one key gene involved in this progression is Protein Tyrosine Phosphatase Receptor Type H (PTPRH). Acting as both a tumor suppressor and oncogene, the role of PTPRH varies across cancer types. Mutations in PTPRH can either promote cancer or act as tumor suppressors, depending on the type of tissue in which they occur. This project investigates missense variants of PTPRH using in silico analysis. From the COSMIC database, 478 unique missense variants were identified, with 14 variants consistently predicted as damaging across eight computational tools (fathmm, PROVEAN, PolyPhen-2, SIFT, PANTHER, Align-GVGD, SNPs&GO, and PhD-SNP). These variants were analyzed for their impact on protein stability using several prediction tools (MUpro, I-Mutant, MCSM, Missense3D, SDM, DUET, DynaMut, and ENCoM), with 10 variants showing potential disruption of PTPRH protein stability. Evolutionary conservation analysis revealed high conservation scores for all 14 variants, indicating the structural importance of these variants. The domain profiling also revealed their location in key regions of the protein. The 3D protein structures were constructed by homology modeling using the Swiss-Model server. Further analysis using GeneMANIA and STRING highlighted the broader impacts of these mutations on PTPRH interactions and cellular pathways. Investigating the association of PTPRH mutations with various cancer types using CanSAR.ai, cBioPortal, Kaplan-Meier Plotter, and GEPIA revealed their significance in cancer progression. These findings emphasize the utility of in silico analysis in prioritizing cancer-associated variants and provide a rational foundation for future experimental validation and targeted therapeutic investigation.
Investigation of hnRNPK's role in gastric cancer proliferation and migration and its interaction with TL1A.
Bo S, Jiang T, You Y … +5 more , Tian S, Bai B, Cheng Y, Gao Y, Wang Y
Cancer Genet · 2026 Apr · PMID 41544317 · Publisher ↗
The present investigation elucidated the pivotal involvement of heterogeneous nuclear ribonucleoprotein K (hnRNPK) in the oncogenic advancement of gastric carcinoma through an integrative, multi-tiered analytical framewo...
The present investigation elucidated the pivotal involvement of heterogeneous nuclear ribonucleoprotein K (hnRNPK) in the oncogenic advancement of gastric carcinoma through an integrative, multi-tiered analytical framework. Quantitative tissue microarray assessments indicated that elevated hnRNPK abundance exhibited a marked association with tumor differentiation grade, lymphatic dissemination, TNM classification, and unfavorable clinical outcome. Mechanistic exploration further substantiated that hnRNPK, predominantly confined to the nuclear compartment, facilitates gastric tumor aggressiveness by modulating the PI3K/Akt transduction cascade. Both in vivo and in vitro assays consistently verified that hnRNPK markedly augments the proliferative and motile potentials of gastric carcinoma cells. Importantly, this research constitutes the initial report delineating a molecular linkage between hnRNPK activity and gastric cancer pathogenesis. Rescue experiments demonstrated that TL1A knockdown in hnRNPK-overexpressing cells significantly reversed pro-tumor phenotypes, suggesting that hnRNPK exerts its oncogenic effects at least partially through a TL1A-dependent mechanism. These findings not only provide insights into the molecular mechanism of hnRNPK in GC but also offer experimental evidence for developing novel therapeutic strategies targeting the hnRNPK-TL1A axis in GC.
M6A methylation in thyroid cancer: Functions, mechanisms, and clinical significance.
Huang D, Xie Z, Zhang S … +3 more , Su Y, Liu C, Chen W
Cancer Genet · 2026 Apr · PMID 41539228 · Publisher ↗
Thyroid cancer (TC), the most prevalent endocrine malignancy, exhibits marked biological heterogeneity and a persistent therapeutic gap in aggressive, treatment-refractory subsets. N6-methyladenosine (m6A), pervasive acr...
Thyroid cancer (TC), the most prevalent endocrine malignancy, exhibits marked biological heterogeneity and a persistent therapeutic gap in aggressive, treatment-refractory subsets. N6-methyladenosine (m6A), pervasive across eukaryotic RNA processing-splicing, maturation, stability, translation, and localization-constitutes a central layer of epigenetic regulation. By reshaping post-transcriptional programs, m6A modifications govern tumor initiation and progression, sustaining stemness, accelerating proliferation and invasion, and mediating therapy resistance. A growing body of evidence implicates dysregulated m6A regulators in TC pathogenesis; yet the multiplicity of effectors and their context-dependent actions complicate mechanistic resolution. This review synthesizes current advances, delineating m6A's involvement in four cardinal arenas of thyroid tumorigenesis: altered cellular behaviors (proliferation, migration), metabolic reprogramming, programmed cell death (apoptosis and ferroptosis), and resistance to targeted, radioactive iodine, and immunotherapeutic strategies. We further examine the emerging interface between m6A and non-coding RNAs, highlighting how this axis rewires oncogenic networks. Finally, we appraise the translational potential of m6A as a diagnostic and prognostic biomarker and as a therapeutic target, offering perspective on opportunities and challenges for epitranscriptome-guided precision oncology in TC.
In silico identification of deleterious NT5C2 and PRPS1 mutations driving thiopurine resistance in relapsed acute lymphoblastic leukemia.
Sharma R, Kudithipudi J, Singh H … +2 more , Prabhu D, Vuree S
Cancer Genet · 2026 Apr · PMID 41518974 · Publisher ↗
Relapse in Acute Lymphoblastic Leukemia (ALL) are often driven by multiple factors, including thiopurine drug-resistant mutations in NT5C2 and PRPS1. To determine the functional significance of these mutations, we employ...
Relapse in Acute Lymphoblastic Leukemia (ALL) are often driven by multiple factors, including thiopurine drug-resistant mutations in NT5C2 and PRPS1. To determine the functional significance of these mutations, we employed comprehensive computational methods to assess their impact on protein stability, evolutionary conservation, and possible drug sensitivity, as well as molecular docking and simulations with 6-MP and 6-TG to show the impact of these mutations on drug binding. The top-ranked pathogenic variants investigated, NT5C2 rs775844720 (D431V) and PRPS1 rs2147684832 (D224G), exhibited the most pronounced destabilizing effects on proteins. Protein-protein interaction networks indicate that these variations are involved in nucleotide metabolism and pharmacological responses, confirming their role in thiopurine resistance. In summary, NT5C2 and PRPS1 gene variations may act as potential biomarkers for resistance and hence require more experimental validation of VUS to determine their significance.
Identifying transcriptional signatures of leukocytes in tissue and blood for multicancer diagnosis by using machine learning methods.
Ma Q, Ren J, Chen L … +6 more , Guo W, Feng K, Zhang Y, Shen W, Huang T, Cai YD
Cancer Genet · 2026 Apr · PMID 41518973 · Publisher ↗
Investigating the transcriptional signatures of immune cells in various cancer types is crucial for understanding their roles in the tumor microenvironment and developing effective immunotherapeutic strategies. In this s...
Investigating the transcriptional signatures of immune cells in various cancer types is crucial for understanding their roles in the tumor microenvironment and developing effective immunotherapeutic strategies. In this study, we employed machine learning methods to analyze RNA-seq data from patients with four different types of cancers and two immune cell types, including T cell and CD45+CD3- leukocyte cell types. We processed seven datasets, each divided into three groups on the basis of cell source: tumor, normal adjacent tissue, and peripheral blood. The datasets were downscaled by using the Boruta method, and the remaining genes were ranked for criticality in a list through the max-relevance and min-redundancy method. The obtained list of genes was fed into incremental feature selection (IFS), which employed decision tree or random forest to distinguish cells, for the identification of key genes associated with immune cell function in different cancer types and construction of efficient classifiers and classification rules (special patterns for different groups). Our results revealed distinct expression patterns of key genes, such as the downregulation of CST7 in T cells from tumor tissues and differential expression of CD2 in non-tumor sites. Furthermore, we identified LCP1, CD27, and MAL as immunologically relevant genes in T cells across different tissue origins, whereas IFI30, CXCR4, and FOSB played various roles in CD45+CD3- leukocytes. The identified key genes were supported by evidence in the literature, highlighting their involvement in antitumor processes in T cells and other immune cells. Our findings provide valuable insights into the transcriptional signatures of immune cells in different cancer types and lay the foundation for the development of novel diagnostic, prognostic, and therapeutic strategies in cancer immunology.
Plasma cell-free DNA biomarkers as novel diagnostic and prognostic tools in breast cancer.
El-Fatah RMA, Badawy HK, Pasha HF … +3 more , Mesbah NM, Abo-Elmatty DM, Abdel-Hamed AR
Cancer Genet · 2026 Apr · PMID 41512486 · Publisher ↗
Breast cancer remains the leading cause of cancer-related deaths among women, underscoring the need for more sensitive and specific biomarkers. Traditional markers such as CA15-3 lack sufficient diagnostic and prognostic...
Breast cancer remains the leading cause of cancer-related deaths among women, underscoring the need for more sensitive and specific biomarkers. Traditional markers such as CA15-3 lack sufficient diagnostic and prognostic accuracy. Quantification of plasma cell-free DNA (cfDNA) offers a minimally invasive liquid-biopsy approach for tumor detection and monitoring. This case-control study assessed a cfDNA panel comprising KLK10, SOX17, WNT5A, and MSH2 in 100 breast cancer patients and 100 matched controls. Plasma cfDNA levels, quantified by qPCR, and CA15-3 levels, measured by ELISA, were evaluated for diagnostic and prognostic value using ROC analyses and a 35-month follow-up for survival endpoints. All cfDNA genes were significantly elevated in patients (p<0.001) and exhibited superior diagnostic accuracy versus CA15-3, with MSH2 showing the highest AUC (95.3%), sensitivity (92%), and specificity (89%). Elevated cfDNA correlated strongly with metastasis and adverse pathological features, outperforming CA15-3 in predicting metastasis (AUC = 0.962-0.987). High cfDNA concentrations associated with poorer disease-free and overall survival (p<0.001). Detection of a cfDNA panel, rather than a single gene, demonstrates superior utility as a minimally invasive biomarker promising for early detection, risk assessment, and disease monitoring in breast cancer.
Single-Step CRISPR/Cas13a Assay for detection of small RNAs in Saliva : a proof-of-concept study.
Salodkar D, Dongarwar S, Nair A … +4 more , Ashtaputre P, Reddy S, Somkuwar S, Begde D
Cancer Genet · 2026 Jan · PMID 41421070 · Publisher ↗
OBJECTIVE: We describe a proof-of-concept study of a rapid, single-step CRISPR/Cas13a assay using Leptotrichia wadei (LwCas13a) for the detection of small RNA (miRNA) biomarkers in saliva, and compare its performance to...
OBJECTIVE: We describe a proof-of-concept study of a rapid, single-step CRISPR/Cas13a assay using Leptotrichia wadei (LwCas13a) for the detection of small RNA (miRNA) biomarkers in saliva, and compare its performance to real-time PCR (RT-PCR). METHODS: The single-step Cas13a assay was evaluated against RT-PCR for its detection efficiency, sensitivity, specificity, and its ability to function in a complex biological matrix. A proof-of-concept test was conducted on patient saliva samples to detect a known oral cancer biomarker, hsa-miR-21-3p RESULTS: The Cas13a assay successfully detected candidate miRNA at picomolar concentrations in both in vitro and saliva samples, demonstrating sensitivity and specificity comparable to RT-PCR. Notably, the assay provided discernible detection of the cancer biomarker directly in patient saliva without the need for RNA extraction or reverse transcription steps. CONCLUSION: The proposed single-step CRISPR/Cas13a assay may be developed into a promising platform for developing quick and affordable point-of-care diagnostics for cancer and other diseases, circumventing the need for expensive and time-consuming sample preparation steps.
Multiple endocrine neoplasia type 1 syndrome due to novel Alu insertion.
Cragg A, Boon H, Cranston T … +2 more , Richardson T, Schirwani S
Cancer Genet · 2026 Jan · PMID 41421069 · Publisher ↗
Multiple Endocrine Neoplasia type 1 syndrome is caused by pathogenic variants in the MEN1 gene, and is characterised by tumours in multiple endocrine glands. This case study looks at a family with four affected members o...
Multiple Endocrine Neoplasia type 1 syndrome is caused by pathogenic variants in the MEN1 gene, and is characterised by tumours in multiple endocrine glands. This case study looks at a family with four affected members over two generations who have been diagnosed with the syndrome after next generation sequencing identified a novel Alu insertion. Previous genetic testing in the index patient had not identified an underlying cause.
Exploration of a prognostic model for childhood acute lymphoblastic leukemia.
Bai Y, Feng WW, Tang L … +1 more , Sun YQ
Cancer Genet · 2026 Jan · PMID 41418644 · Publisher ↗
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Genetic modulation of ABCB1: Sunvozertinib reverses ABCB1-mediated multidrug resistance in cancer cells.
Cao LQ, Xie Y, Chen X … +5 more , Patel H, Yuan L, Wurpel J, Gong K, Chen ZS
Cancer Genet · 2026 Jan · PMID 41380312 · Publisher ↗
Sunvozertinib is an oral, irreversible epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) designed to treat non-small cell lung cancer (NSCLC) patients with EGFR exon 20 insertion mutations under a p...
Sunvozertinib is an oral, irreversible epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) designed to treat non-small cell lung cancer (NSCLC) patients with EGFR exon 20 insertion mutations under a phase II clinical trial. In this study, we investigated whether sunvozertinib could antagonize ABCB1, also known as multidrug resistance 1 (MDR1/P-gp). ABCB1 is a gene that encodes an important drug transport protein that pumps various substances, including drugs and toxins, out of cells. Sunvozertinib received a high score in docking analysis, indicating a strong interaction between sunvozertinib and ABCB1. ATPase assay indicated that sunvozertinib stimulated ABCB1 ATPase activity in a concentration-dependent manner. MTT assay shows that sunvozertinib significantly reversed ABCB1-mediated MDR but not ABCC1- and ABCG2-mediated MDR. Mechanistic studies show that sunvozertinib significantly reversed ABCB1-mediated MDR by attenuating the efflux activity of the ABCB1 transporter. Furthermore, treatment with sunvozertinib did not change protein expression or subcellular localization of ABCB1. Altogether, these data demonstrate that sunvozertinib, when combined with other conventional chemotherapeutic agents, can overcome MDR and improve therapeutic effect.
Quantitative and qualitative methods for measuring chromosomal instability in tumor cells.
Batistão HKA, Oliveira-Silva JM, Oliveira VB … +2 more , de Araújo Batistão II, Castro-Gamero AM
Cancer Genet · 2026 Jan · PMID 41349145 · Publisher ↗
To preserve cellular and tissue homeostasis, cells must maintain a coordinated network of molecular mechanisms that ensure accurate chromosome segregation during mitosis. Errors in this process, such as chromosome mis-se...
To preserve cellular and tissue homeostasis, cells must maintain a coordinated network of molecular mechanisms that ensure accurate chromosome segregation during mitosis. Errors in this process, such as chromosome mis-segregation, lagging chromosomes in anaphase, centrosome amplification, or chromosome breaks generating non-homologous fusions and dicentric chromosomes, can lead to chromosomal instability (CIN). Persistent CIN promotes chromosomal abnormalities, driving tumor cell proliferation, intratumoral genomic diversity, and ultimately tumor initiation and progression. Tumors exhibiting CIN, characterized by aneuploidy or large-scale structural rearrangements, are strongly associated with metastasis, angiogenesis, and chemoresistance. Despite its biological and clinical relevance, methods to detect, quantify, and evaluate CIN remain poorly standardized. In this work, we critically reviewed the scientific literature to compile and discuss the principal quantitative and qualitative strategies currently available for measuring CIN in vitro.
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