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Keywords = homologous recombination-deficiency

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16 pages, 2433 KB  
Article
Broadening SARS-CoV-2 Immunity by Combining ORFV and Protein-Based Vaccines
by Alena Reguzova, Melanie Müller, Madeleine Fandrich, Alex Dulovic and Ralf Amann
Vaccines 2026, 14(1), 64; https://doi.org/10.3390/vaccines14010064 - 4 Jan 2026
Viewed by 128
Abstract
Background: Emerging immune-evasive viral variants threaten the efficacy of current vaccines, underscoring the need for strategies that elicit broad and durable protection. Heterologous prime–boost regimens combining distinct vaccine platforms can enhance humoral and cellular immunity through complementary mechanisms. Methods: Using an intramuscular immunization [...] Read more.
Background: Emerging immune-evasive viral variants threaten the efficacy of current vaccines, underscoring the need for strategies that elicit broad and durable protection. Heterologous prime–boost regimens combining distinct vaccine platforms can enhance humoral and cellular immunity through complementary mechanisms. Methods: Using an intramuscular immunization scheme aligned with clinical vaccination practice, CD-1 mice received homologous or heterologous prime–boost regimens combining a replication-deficient Orf virus (Parapoxvirus orf, ORFV)-based spike vaccine (ORFV-S) with the licensed adjuvanted recombinant protein vaccine VidPrevtyn Beta. Spike-specific humoral and cellular immune responses were assessed. Results: ORFV-S alone induced potent and broad spike-specific IgG responses and achieved the strongest ACE2-binding inhibition across variants of concern. ORFV-S priming followed by VidPrevtyn Beta boosting markedly enhanced the magnitude and cross-variant breadth of antibody responses compared with homologous protein vaccination. Both homologous ORFV-S and heterologous regimens incorporating ORFV-S elicited strong CD4+ and CD8+ T-cell responses, whereas VidPrevtyn Beta alone induced only modest T-cell activity, demonstrating that ORFV-S effectively complements protein-based vaccines. Conclusions: The ORFV-S vector represents a potent vaccine platform capable of inducing broad humoral and cellular immunity. Its use in heterologous prime–boost combinations enhances both antibody magnitude and breadth beyond homologous protein vaccination, supporting its application in vaccination strategies against evolving viral pathogens. Full article
(This article belongs to the Section Vaccine Design, Development, and Delivery)
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15 pages, 6814 KB  
Article
Apoptosis of Mesothelial Cells Is Associated with the Pattern of Peritoneal Metastases in Ovarian Cancer
by Konstantin Maksin, Magdalena Nadolna, Mateusz Wozniak, Tetiana Bocharova, Piotr Jasinski, Michal Nowicki, Ewa Nowak-Markwitz and Sebastian Szubert
Cancers 2026, 18(1), 102; https://doi.org/10.3390/cancers18010102 - 29 Dec 2025
Viewed by 192
Abstract
Background/Objectives: Peritoneal carcinomatosis is the leading cause of death in advanced ovarian cancer (AOC). Mesothelial cells lining the peritoneum modulate tumor implantation, yet the role of their apoptosis in metastasis development remains unclear. This study investigated the relationship between mesothelial cell apoptosis [...] Read more.
Background/Objectives: Peritoneal carcinomatosis is the leading cause of death in advanced ovarian cancer (AOC). Mesothelial cells lining the peritoneum modulate tumor implantation, yet the role of their apoptosis in metastasis development remains unclear. This study investigated the relationship between mesothelial cell apoptosis and metastatic spread in ovarian cancer (OC). Methods: The study included 26 patients with AOC, 11 with early-stage OC (EOC), and 13 healthy controls. Apoptotic activity in parietal peritoneal wall and omental mesothelial cells was assessed using the TUNEL technique. Metastases were classified as pushing or infiltrating. Associations with the peritoneal cancer index (PCI), BRCA mutation, and homologous recombination deficiency (HRD) status were analyzed. Results: Mesothelial cells adjacent to AOC metastases exhibited significantly higher apoptotic activity compared to controls (p < 0.05). Apoptosis was greater near infiltrating metastases than near pushing ones in both parietal (p < 0.01) and omental (p = 0.04) sites. The infiltration pattern was consistent between omental and parietal metastases (R = 0.588, p < 0.01). No significant differences in apoptosis were found between EOC and healthy controls, or in tumor and stromal cells between invasion types. Mesothelial apoptosis was independent of PCI, BRCA mutation, and HRD status. Conclusions: Our study suggests that mesothelial cell apoptosis may be associated with peritoneal spread in OC. Mesothelial cell apoptosis is more pronounced near infiltrative-type lesions, independent of BRCA/HRD status. These findings highlight mesothelial apoptosis as a relevant process in peritoneal dissemination. Further studies are needed to clarify its role in ovarian cancer progression. Full article
(This article belongs to the Section Cancer Metastasis)
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13 pages, 2039 KB  
Article
Metabolomics Plasma Biomarkers Associated with the HRD Phenotype in Ovarian Cancer
by Alessandro Tubita, Claudia De Angelis, Daniela Grasso, Flavia Sorbi, Francesca Castiglione, Lorenzo Anela, Maria Cristina Petrella, Massimiliano Fambrini, Federico Scolari, Andrea Bernini, Giulia Petroni, Serena Pillozzi and Lorenzo Antonuzzo
Metabolites 2026, 16(1), 2; https://doi.org/10.3390/metabo16010002 - 19 Dec 2025
Viewed by 268
Abstract
Background: Ovarian cancer (OC) remains one of the most lethal gynecologic malignancies due to its often-late diagnosis and complex molecular heterogeneity. Understanding the metabolic alterations in OC can provide insights into its pathophysiology and potential therapeutic targets. This study aimed to explore [...] Read more.
Background: Ovarian cancer (OC) remains one of the most lethal gynecologic malignancies due to its often-late diagnosis and complex molecular heterogeneity. Understanding the metabolic alterations in OC can provide insights into its pathophysiology and potential therapeutic targets. This study aimed to explore serum metabolomic profiles and their correlation with clinical and pathological features in OC patients. Materials and Methods: Thirty serum samples were collected from patients diagnosed with ovarian tumors (OTs) (n = 24 malignant, n = 6 benign) and undergoing treatment at Careggi University Hospital. Additionally, 47 samples were obtained from age-matched healthy female donors. Serum samples underwent processing and analysis using an H-NMR (Nuclear Magnetic Resonance) platform to identify a panel of metabolites. Correlation analysis between the metabolomic data and clinical parameters was performed using R software (v.4.4.0). Results: Differential metabolomic profiling showed a significant upregulation of metabolites associated with the purine salvage pathway (i.e., hypoxanthine and inosine) and the ketone bodies axis (i.e., acetone, 3-hydroxybutyrate, and acetate) in samples from ovarian tumor (OT) patients compared to healthy donors. Within malignant OC samples, metabolomic profiles significantly correlated with BRCA1/2 mutation status (BRCA1/2-mutated vs. wild-type) and homologous recombination deficiency (HRD) status. Conclusions: The analysis revealed significant variation in specific metabolites such as betaine, creatinine, carnitine, glycerol, and mannose; notably, a downregulation of these metabolites was observed in HRD-positive patients. The study identifies significant metabolomic alterations in OC, implicating pathways such as purine salvage and ketone bodies. Intriguingly, consistent variation in specific metabolites across BRCA/HRD phenotypes underscores their potential as OC biomarkers. Further research is needed to validate these findings and explore their prognostic and therapeutic implications. Full article
(This article belongs to the Section Cell Metabolism)
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18 pages, 8266 KB  
Article
Homologous Recombination Is Associated with Enhanced Anti-Tumor Innate Immunity and Favorable Prognosis in Head and Neck Cancer
by Negin Soghli, Aminollah Khormali and Aimin Peng
Cancers 2025, 17(24), 3999; https://doi.org/10.3390/cancers17243999 - 15 Dec 2025
Viewed by 442
Abstract
Background/Objectives: Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy, often diagnosed at advanced stages with poor survival outcomes. Homologous recombination (HR), a major DNA double-strand break (DSB) repair pathway, safeguards genomic stability via error-free repair. While HR deficiency has been [...] Read more.
Background/Objectives: Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy, often diagnosed at advanced stages with poor survival outcomes. Homologous recombination (HR), a major DNA double-strand break (DSB) repair pathway, safeguards genomic stability via error-free repair. While HR deficiency has been well established as a driver of genomic instability and tumorigenesis in several cancer types, the role of HR in HNSCC remains relatively understudied. Methods: Here, we analyzed the expression patterns of key HR proteins in HNSCC and investigated their association with clinical parameters, DNA methylation, immune cell infiltration, and patient survival outcome. Results: Surprisingly, our results demonstrate that HR factors are consistently upregulated in HNSCC, in both HPV-positive and HPV-negative groups. Survival analysis identified many HR factors, including ATM, BRCA1, BRCA2, PALB2, LIG1, RPA1, and RPA2, as potential prognostic biomarkers for better overall survival. Interestingly, we observed a significant correlation between HR protein overexpression and immune cell infiltration in HNSCC, suggesting a potential immunomodulatory role of HR proteins. To experimentally validate this association in both HPV-positive and -negative cell lines, we showed that MRE11 and RAD51 overexpression in HNSCC cells led to increased phosphorylation of IRF3 and STAT1, indicating activation of the cGAS/STING-mediated innate immune signaling. Conclusion: Together, our findings provide a comprehensive overview of the HR pathway in HNSCC, highlighting the dual role of HR proteins in both genomic maintenance and immune regulation. The consistent upregulation of HR proteins, their association with disease progression, and potential immunogenic effects underscore their promise as diagnostic/prognostic biomarkers and therapeutic targets in HNSCC. Full article
(This article belongs to the Special Issue New Biomarkers in Cancers 2nd Edition)
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10 pages, 494 KB  
Article
BRCA1 and 2 Mutations and Efficacy of Pembrolizumab-Based Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer: A Real-World Multicenter Analysis
by Palma Fedele, Alessandro Rizzo, Matteo Landriscina, Stefania Luigia Stucci, Maria Morritti, Francesco Giuliani, Lucia Moraca, Giuseppe Cairo, Raffaele Ardito, Marianna Giampaglia, Domenico Bilancia, Assunta Melaccio, Antonella Terenzio, Antonio Gnoni, Antonella Licchetta, Federica Fumai, Laura Lanotte and Gennaro Gadaleta-Caldarola
J. Clin. Med. 2025, 14(24), 8854; https://doi.org/10.3390/jcm14248854 - 14 Dec 2025
Viewed by 576
Abstract
Background: Pembrolizumab has reshaped the neoadjuvant treatment landscape for triple-negative breast cancer (TNBC). However, the influence of BRCA1/2 mutational status on the efficacy of chemo-immunotherapy remains unclear, particularly in real-world settings. Since BRCA-mutated tumors exhibit homologous recombination deficiency (HRD) and high genomic instability, [...] Read more.
Background: Pembrolizumab has reshaped the neoadjuvant treatment landscape for triple-negative breast cancer (TNBC). However, the influence of BRCA1/2 mutational status on the efficacy of chemo-immunotherapy remains unclear, particularly in real-world settings. Since BRCA-mutated tumors exhibit homologous recombination deficiency (HRD) and high genomic instability, they may be more immunogenic and responsive to immune checkpoint inhibitors. This multicenter study investigated the association between BRCA1/2 mutations and pathologic complete response (pCR) in TNBC patients treated with pembrolizumab-based neoadjuvant chemotherapy (NACT). Methods: We retrospectively analyzed 184 patients with stage II–III TNBC treated between 2021 and 2024 across eleven Italian oncology centers. All received pembrolizumab combined with platinum- and taxane-based NACT followed by anthracyclines, according to the KEYNOTE-522 regimen. Germline BRCA1/2 status was determined by next-generation sequencing. The primary endpoint was pCR, defined as ypT0/is ypN0. Fisher’s exact test and logistic regression models were used to assess associations between clinical–pathological variables and pCR. Results: Among 184 patients, 25 (13.6%) harbored BRCA1 mutations, 12 (6.5%) BRCA2 mutations, and 147 (79.9%) were wild-type. pCR was achieved in 80.0% of BRCA1-mutated, 75.0% of BRCA2-mutated, and 61.1% of wild-type tumors. When pooled, BRCA1/2-mutated cases showed a higher likelihood of achieving pCR (78.4% vs. 61.1%; odds ratio [OR] = 2.17; 95% CI 1.01–4.97; p = 0.056). High tumor-infiltrating lymphocytes (≥30%) were also associated with increased pCR rates. The frequency of BRCA mutations (20.1%) was consistent with that reported in major TNBC series. No comparative analysis of toxicity or survival outcomes was performed due to the retrospective design and limited follow-up. Conclusions: In this multicenter real-world cohort, TNBC patients carrying BRCA1/2 mutations exhibited a trend toward higher pCR rates with pembrolizumab-based NACT compared with wild-type tumors. These findings suggest enhanced chemosensitivity and immune responsiveness in BRCA-deficient disease, warranting further validation in larger prospective studies with survival endpoints. Full article
(This article belongs to the Section Oncology)
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14 pages, 977 KB  
Article
Integrative sWGS: A New Paradigm for HRD Detection in Ovarian Cancer
by Dan Corneliu Jinga, Georgiana Duta-Cornescu, Danut Cimponeriu, Eirini Papadopoulou, Angeliki Meintani, George Tsaousis, Amalia Chirnogea, Irina Bucatariu, Polixenia-Georgeta Iorga, Diana Chetroiu, Sorin-Cornel Hosu, Amalia Hogea-Zah, Mircea-Dragos Median, Bogdan Diana, Dana-Lucia Stănculeanu, Raluca Mihaila, Dana-Sonia Nagy, Pompilia-Elena Motatu, Turcanu Eugeniu, Elena-Octaviana Cristea, Ion-Cristian Iaciu, Paul Kubelac and Andreea Truicanadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2025, 26(24), 11968; https://doi.org/10.3390/ijms262411968 - 12 Dec 2025
Viewed by 325
Abstract
Homologous recombination deficiency (HRD) is a clinically relevant biomarker that predicts sensitivity to PARP inhibitors and enables personalized cancer therapy. Validated local HRD testing solutions are essential to ensure timely and equitable access, ultimately improving treatment outcomes. We evaluated a shallow whole-genome sequencing [...] Read more.
Homologous recombination deficiency (HRD) is a clinically relevant biomarker that predicts sensitivity to PARP inhibitors and enables personalized cancer therapy. Validated local HRD testing solutions are essential to ensure timely and equitable access, ultimately improving treatment outcomes. We evaluated a shallow whole-genome sequencing (sWGS) approach for genomic instability (GI) assessment combined with a 52-gene targeted panel in ovarian cancer. Validation used reference materials and 24 archival samples with prior HRD characterization, comparing performance with the Myriad myChoice® HRD test. A prospective cohort of 124 newly diagnosed ovarian cancer patients was then analyzed. sWGS-derived GI status showed strong concordance with the reference test (95.8% overall agreement; κ = 0.913; NPV 100%, PPV 93.3%). Pathogenic BRCA1/2 variants were detected in 30 patients (24.19%). An additional 22.76% were BRCA1/2-negative but GI-positive, giving an overall HRD prevalence of 47.15%. Platinum sensitivity occurred in 90.0% (18/20) of HRD-positive patients with follow-up. Among 12 patients assessed for PARP-inhibitor response, the overall response rate was 66.7% (95% CI 39.1–86.2) and disease control rate 83.3% (95% CI 55.2–95.3). TP53 alterations were most frequent (62.90%), followed by BRCA1 (19.35%) and BRCA2 (4.83%). Pathogenic variants in other HR-pathway genes (ATM, CHEK2, BRIP1, RAD51C, BARD1) appeared in 9.57% of BRCA-wild-type cases, with heterogeneous GI impact. Two cases showed concurrent BRCA2 variants and microsatellite instability, indicating possible eligibility for anti-PD-1/PD-L1 therapy in addition to PARPi. This first comprehensive analysis of Romanian ovarian cancer patients suggests that integrating sWGS-based genomic instability assessment with BRCA testing can improve HRD detection and reflects the heterogeneity of HR-pathway variants. Preliminary clinical observations were consistent with known HRD-associated treatment responses, although larger studies are needed to confirm these findings. Full article
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18 pages, 5812 KB  
Article
Phosphoproteomic Analysis Reveals Differences in Intercellular Spread Among Feline Herpesvirus Type 1 Mutants
by Weiwei Lin, Xianglin Zhang, Qian Jiang, Hongtao Kang, Yijing Li, Honglin Jia and Jiasen Liu
Vet. Sci. 2025, 12(12), 1185; https://doi.org/10.3390/vetsci12121185 - 11 Dec 2025
Viewed by 259
Abstract
Feline herpesvirus-1 (FHV-1) is taxonomically classified within the family Herpesviridae, subfamily Alphaherpesvirinae, genus Varicellovirus, and species Felid alphaherpesvirus 1. The genome of FHV-1 is 135,797 bp in length and encodes 74 proteins. Among these proteins, serine/threonine protein kinase (pK) and thymidine kinase (TK) [...] Read more.
Feline herpesvirus-1 (FHV-1) is taxonomically classified within the family Herpesviridae, subfamily Alphaherpesvirinae, genus Varicellovirus, and species Felid alphaherpesvirus 1. The genome of FHV-1 is 135,797 bp in length and encodes 74 proteins. Among these proteins, serine/threonine protein kinase (pK) and thymidine kinase (TK) have been identified as potential virulence factors in alphaherpesviruses, although these kinases are dispensable for viral replication. As kinases, regulating phosphorylation modification is one of their functions, while the mechanism by which phosphorylation modification affects cell physiological functions and thereby influences viral replication remains unclear. In this study, we generated pK- and TK-deficient FHV-1 mutants by CRISPR/Cas9-mediated homologous recombination. The pK-deficient virus produced significantly smaller plaques than the TK-deficient virus. The replication kinetics of the pK-deficient virus were attenuated in multistep growth compared to the TK-deficient virus. These results indicate that deletion of the pK gene markedly reduces the replicative capacity of FHV-1. We applied data-independent acquisition (DIA) quantitative proteomics to profile changes in global protein expression and phosphorylation in F81 cells upon infection with TK, pK−, and wild-type FHV-1 strain. The pK-deficient virus exhibited 3632 differentially phosphorylated proteins containing 11,936 modification sites; the TK-deficient virus showed 4529 differentially phosphorylated proteins with 19,225 phosphorylation sites. Functional characterization through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses identified significant involvement of phosphoproteins in spliceosome pathways in pK-deficient virus and ATP-dependent chromatin remodeling pathway in TK-deficient virus. Notably, several splicing regulators—including Ess-2 and CDK13, which modulate host spliceosomal function—displayed significantly reduced phosphorylation levels in pK-deficient viruses. A significant enrichment of ATP-dependent factors, such as SMARCA5 and RSF1, was observed in the TK-deficient virus. To our knowledge, this is the first investigation into the effects of FHV-1 infection on the host cell phosphoproteome. These data offer new insights into the phosphoregulatory circuits and signaling networks triggered by FHV-1 and may enhance our understanding of the FHV-1 replication mechanism. Full article
(This article belongs to the Special Issue Advanced Therapy in Companion Animals—2nd Edition)
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21 pages, 6705 KB  
Article
DNMT3B Knockdown Enhances PARP Inhibitor Sensitivity in Biliary Tract Cancer Cells via Opioid Growth Factor Receptor-Mediated Homologous Recombination Impairment
by Soichiro Oda, Kazumichi Kawakubo, Masaki Kuwatani, Shugo Tanaka, Katsuma Nakajima, Shoya Shiratori, Hiroki Yonemura, Shunichiro Nozawa, Koji Hirata, Ryo Sugiura and Naoya Sakamoto
Cancers 2025, 17(24), 3936; https://doi.org/10.3390/cancers17243936 - 9 Dec 2025
Viewed by 350
Abstract
Background: Biliary tract cancer (BTC) is an aggressive malignancy with poor prognosis and limited therapeutic options. Poly(ADP-ribose) polymerase (PARP) inhibitors have demonstrated efficacy in tumors with homologous recombination repair (HRR) deficiency. However, actionable BRCA1/2 mutations are rare in BTC. Epigenetic modulation via [...] Read more.
Background: Biliary tract cancer (BTC) is an aggressive malignancy with poor prognosis and limited therapeutic options. Poly(ADP-ribose) polymerase (PARP) inhibitors have demonstrated efficacy in tumors with homologous recombination repair (HRR) deficiency. However, actionable BRCA1/2 mutations are rare in BTC. Epigenetic modulation via DNA methyltransferase (DNMT) inhibition is a proposed strategy for inducing an HR-deficient (“BRCAness”) phenotype and thereby enhancing therapeutic response to PARP inhibitors. This study aimed to determine whether the DNMT inhibitor azacitidine (AZA) enhances the antitumor effects of the PARP inhibitor niraparib (NIR) and to identify molecular mechanisms underlying this interaction. Methods: Two BTC cell lines, TFK-1 and RBE, were treated with AZA and/or NIR or subjected to siRNA-mediated DNMT1, DNMT3A, or DNMT3B knockdown. Functional analyses included homologous recombination (HR) assays, flow cytometric evaluation of cell-cycle distribution and apoptosis, proliferation and survival assays, and IC50 determination. Whole-transcriptome RNA sequencing was performed to identify differentially expressed genes after AZA treatment or DNMT3B knockdown, followed by validation via qPCR and Western blotting. To explore epigenetic regulation, whole-genome bisulfite sequencing was performed on TFK-1 cells following DNMT3B knockdown. Results: AZA treatment decreased HR frequency in a dose-dependent manner and enhanced the sensitivity of BTC cells to NIR, as evidenced by increased apoptosis, suppressed proliferation, and reduced IC50 values. DNMT3B knockdown recapitulated these effects, establishing a causal relationship between DNMT3B suppression and disrupted HR repair. RNA sequencing identified opioid growth factor receptor (OGFR) as a commonly upregulated gene after DNMT3B knockdown. Functional validation showed that OGFR overexpression reduced HR activity, increased apoptosis, and enhanced NIR sensitivity. Contrarily, OGFR knockdown conferred relative resistance. Whole-genome bisulfite sequencing showed no significant CpG methylation changes at the OGFR promoter region, indicating that OGFR induction is mediated through DNMT3B-dependent transcriptional regulation rather than direct promoter demethylation. Conclusions: DNMT3B inhibition sensitizes BTC cells to PARP inhibitors by disrupting HR repair. OGFR was identified as a novel regulator of HR and PARP inhibitor sensitivity, controlled via noncanonical DNMT3B-dependent transcriptional mechanisms that operate independently of CpG methylation. These findings provide new mechanistic insights into the epigenetic control of DNA repair and support the rationale for combining DNMT and PARP inhibitors as a promising therapeutic strategy for BTC beyond genetically HR-deficient cases. Full article
(This article belongs to the Special Issue Molecular Markers and Targeted Therapy for Hepatobiliary Tumors)
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16 pages, 1691 KB  
Article
Complex Relationships Between Homologous Recombination Deficiency (HRD) Score and Mutational Status of Homologous Recombination Repair (HRR) Genes in Prostate Carcinomas
by Aglaya G. Iyevleva, Svetlana N. Aleksakhina, Anna P. Sokolenko, Ekaterina A. Otradnova, Alisa S. Nikitina, Kira A. Kashko, Maria V. Syomina, Anna D. Shestakova, Ekaterina S. Kuligina, Natalia S. Morozova, Sergey V. Popov, Pavel V. Vyazovcev, Tatyana Y. Luchkova, Aleksey S. Peremyshlenko, Timur M. Topuzov, Olga M. Gudkova, Rashida V. Orlova, Andrey V. Levushkin, Daniil O. Moiseev, Oksana N. Shkodenko, Demyan V. Gubarev, Aleksandr V. Dzyuba, Irina Y. Povorina, Anna V. Agaeva, Vladislav F. Kutyan, Mhitar M. Grigoryan, Alexey N. Orlov, Spartak I. Lefterov, Aleksey V. Belousov, Marina N. Nechaeva, Elena N. Vorobyeva, Irina K. Amirkhanova, Nadezhda V. Kryukova, Lyubov I. Zatulivetrova, Aryuna B. Gomboeva, Vladimir N. Krivtsov, Olga I. Shchiglik, Natalya V. Prokudina, Natalya A. Butunina, Aleksey M. Belyaev and Evgeny N. Imyanitovadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2025, 26(24), 11851; https://doi.org/10.3390/ijms262411851 - 8 Dec 2025
Viewed by 366
Abstract
Homologous recombination deficiency (HRD) resulting from inactivation of BRCA1/2 genes promotes chromosomal instability and renders tumor cells susceptible to platinum derivatives and PARP inhibitors (PARPi). The contribution of alterations in other homologous recombination repair (HRR) genes to HRD remains understudied. This investigation aimed [...] Read more.
Homologous recombination deficiency (HRD) resulting from inactivation of BRCA1/2 genes promotes chromosomal instability and renders tumor cells susceptible to platinum derivatives and PARP inhibitors (PARPi). The contribution of alterations in other homologous recombination repair (HRR) genes to HRD remains understudied. This investigation aimed to analyze the spectrum of mutations in 34 HRR genes in prostate carcinomas (PCs) and study the relationship between HRR status and HRD. HRR mutations and HRD scores were examined by NGS in 1131 and 680 PCs, respectively. Pathogenic or likely pathogenic variants in HRR genes were detected in 216/1131 cases (19.1%). HRD, defined by an HRD score cut-off of ≥42, was observed more frequently in HRR-mutated than in wild-type tumors (23/120 (19.2%) vs. 29/560 (5.2%), p < 0.0001). The highest HRD scores were detected in PCs with biallelic inactivation of the BRCA2 or PALB2 genes, as well as in tumors with BRIP1 mutations. HRD was also occasionally seen in PCs with ATM, NBN, FANCM, BRCA1 and CDK12 alterations, but never in cases with CHEK2 mutations. HRD was significantly more associated with aggressive PC features than HRR mutations. The majority of CDK12-mutated tumors exhibited a distinct type of copy number variations (CNV)–a tandem duplication phenotype. Our study suggests that the selection of PC patients for PARPi treatment requires a significant revision of existing attitudes towards tumor genetic profiling. Full article
(This article belongs to the Section Molecular Oncology)
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18 pages, 1385 KB  
Review
Identification of Actionable Mutations in Metastatic Castration-Resistant Prostate Cancer Through Circulating Tumor DNA: Are We There Yet?
by Wensi Tao, Amanda Sabel and R. Daniel Bonfil
Curr. Oncol. 2025, 32(12), 692; https://doi.org/10.3390/curroncol32120692 - 8 Dec 2025
Viewed by 578
Abstract
Circulating tumor DNA (ctDNA) analysis has emerged as a powerful and minimally invasive approach for genomic profiling of metastatic castration-resistant prostate cancer (mCRPC), enabling real-time detection of tumor-derived mutations that guide therapy. Approximately 20% of mCRPC patients harbor alterations in homologous recombination repair [...] Read more.
Circulating tumor DNA (ctDNA) analysis has emerged as a powerful and minimally invasive approach for genomic profiling of metastatic castration-resistant prostate cancer (mCRPC), enabling real-time detection of tumor-derived mutations that guide therapy. Approximately 20% of mCRPC patients harbor alterations in homologous recombination repair (HRR) genes, most commonly BRCA1/2 and ATM, which are actionable with different poly-(ADP-ribose) polymerase inhibitors (PARPIs) used as monotherapy or in combination with androgen receptor signaling inhibitors (ARSIs). A smaller subset of patients with mismatch repair deficiency (MMRd) or microsatellite instability-high (MSI-high) tumors may benefit from immune checkpoint blockade with pembrolizumab. Different FDA-approved liquid biopsy assays detect these actionable alterations when tissue biopsies are unavailable or insufficient. This review summarizes current evidence on ctDNA-based genotyping in mCRPC, highlighting clinically actionable mutations, corresponding targeted therapies, and technical and analytical considerations for clinical implementation. By capturing DNA shed from multiple metastatic sites, ctDNA profiling provides a comprehensive view of tumor heterogeneity and enables serial monitoring of molecular evolution. Overall, ctDNA analysis represents a transformative advance in precision oncology, supporting personalized treatment selection and ongoing assessment of therapeutic response in mCRPC. Full article
(This article belongs to the Section Genitourinary Oncology)
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18 pages, 1175 KB  
Review
The Role of Homologous Recombination Deficiency (HRD) in Renal Cell Carcinoma (RCC): Biology, Biomarkers, and Therapeutic Opportunities
by Alberto Bongiovanni, Pierfranco Conte, Vincenza Conteduca, Matteo Landriscina, Giuseppe Di Lorenzo and Francesco Cognetti
Curr. Oncol. 2025, 32(12), 690; https://doi.org/10.3390/curroncol32120690 - 7 Dec 2025
Viewed by 516
Abstract
Renal Cell Carcinoma (RCC) is a common malignancy, often diagnosed incidentally. In recent years, the prognosis of metastatic disease has been improved due to the development of immune checkpoint inhibitors (ICI) and tyrosine kinase inhibitors (TKI) as first-line treatments. However, when progression occurs, [...] Read more.
Renal Cell Carcinoma (RCC) is a common malignancy, often diagnosed incidentally. In recent years, the prognosis of metastatic disease has been improved due to the development of immune checkpoint inhibitors (ICI) and tyrosine kinase inhibitors (TKI) as first-line treatments. However, when progression occurs, the therapeutic options are limited. Understanding crucial biological pathways could lead to a greater understanding of the natural history of the disease, which could help to overcome the mechanism of resistance and to develop new treatments. The clinical significance of homologous recombination deficiency (HRD) in RCC remains to be investigated. To improve the knowledge about this topic, we conducted a narrative review to summarize the current evidence on HRD-related variations and signatures in RCC, together with their prognostic and predictive implications. Preliminary evidence indicates that canonical HRD variants (BRCA1/2) are infrequent in RCC, while broader DNA damage response (DDR) alterations like BAP1, PBRM1, ATM, and SETD2 are more prevalent. Elevated HRD genomic scores in clear-cell RCC correlate with a worse prognosis and an immunologically exhausted microenvironment. From a therapeutic point of view, PARP inhibitor monotherapy has exhibited initial efficacy in small cohorts with high levels of DDR mutation, yet remains investigational for RCC. Full article
(This article belongs to the Section Genitourinary Oncology)
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20 pages, 4494 KB  
Article
Global Proteomic Determination of the Poly-Pharmacological Effects of PARP Inhibitors Following Treatment of High-Grade Serous Ovarian Cancer Cells
by Jesenia M. Perez, Valerie Barrera-Estrada, Carly A. I. Twigg and Stefani N. Thomas
Int. J. Mol. Sci. 2025, 26(24), 11820; https://doi.org/10.3390/ijms262411820 - 7 Dec 2025
Viewed by 316
Abstract
High-grade serous ovarian cancer (HGSOC) is the most commonly diagnosed ovarian cancer subtype. Approximately half of all patients diagnosed with HGSOC are deficient in homologous recombination (HR), harbor BRCA1/2 mutations, and are treated with poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis). FDA-approved PARPis Olaparib, [...] Read more.
High-grade serous ovarian cancer (HGSOC) is the most commonly diagnosed ovarian cancer subtype. Approximately half of all patients diagnosed with HGSOC are deficient in homologous recombination (HR), harbor BRCA1/2 mutations, and are treated with poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis). FDA-approved PARPis Olaparib, Niraparib, and Rucaparib all contribute to adverse effects in patients due to their poly-pharmacological properties. This feature necessitates investigation of global protein responses to PARPi treatment beyond DNA repair in the context of BRCA mutational status and HR deficiency. We sought to determine the landscape of differential PARPi-induced proteomes in HGSOC cells exhibiting different BRCA1/2 mutational statuses. Here, we applied immunofluorescence microscopy to detect γH2AX, Rad51, and geminin foci as markers of DNA damage and repair upon treatment of HGSOC cells with IC50 doses of PARPis. Global proteome perturbations upon PARPi treatment were measured using quantitative mass spectrometry-based proteomics. The proteomic data highlighted cell line effects, masking high-dose PARPi treatment response. Interrogation of PARPi response within biological pathways identified through gene set enrichment analysis (GSEA) revealed significant changes to proteins involved in Epithelial–Mesenchymal Transition (EMT), E2F targets, and cholesterol homeostasis. Our study establishes proteomic evidence supporting the poly-pharmacological characteristics of Niraparib, Olaparib, and Rucaparib in HGSOC cells. Full article
(This article belongs to the Special Issue Molecular Genetics in Ovarian Cancer)
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17 pages, 3776 KB  
Article
SLX1 Inhibition Enhances Olaparib Sensitivity by Impairing Homologous Recombination Repair in Breast Cancer
by Jin-Young Kim, Jeeho Kim, In-Youb Chang, Sang-Gon Park, Ho Jin You, Young Jin Jeon and Jung-Hee Lee
Int. J. Mol. Sci. 2025, 26(23), 11621; https://doi.org/10.3390/ijms262311621 - 30 Nov 2025
Viewed by 439
Abstract
While PARP inhibitors like Olaparib are effective against BRCA1-deficient breast cancers, their efficacy in BRCA1-proficient tumors depends on the functional status of homologous recombination (HR) repair. Here, we identify the structure-specific endonuclease SLX1 as a key regulator of HR and a determinant of [...] Read more.
While PARP inhibitors like Olaparib are effective against BRCA1-deficient breast cancers, their efficacy in BRCA1-proficient tumors depends on the functional status of homologous recombination (HR) repair. Here, we identify the structure-specific endonuclease SLX1 as a key regulator of HR and a determinant of Olaparib sensitivity in BRCA1-intact breast cancer. SLX1 is frequently upregulated in breast cancer and associated with poor prognosis. Functional studies revealed that SLX1 promotes RAD51-mediated HR repair of DNA double-strand breaks. Consequently, SLX1 depletion reduces HR efficiency, increases chromosomal instability, and sensitizes breast-proficient breast cancer cells to DNA-damaging agents, including camptothecin, ionizing radiation, and Olaparib. In contrast, SLX1 overexpression enhances DNA repair capacity and promotes Olaparib resistance. In vivo, SLX1 knockdown synergizes with Olaparib to suppress tumor growth in xenograft models. These findings establish SLX1 as a critical regulator of HR function in BRCA1-proficient breast cancer and a promising target for restoring PARP inhibitor sensitivity through induced HR deficiency. Full article
(This article belongs to the Section Molecular Oncology)
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27 pages, 1300 KB  
Review
Neoadjuvant Immunotherapy in Hormone Receptor-Positive Breast Cancer: From Tumor Microenvironment Reprogramming to Combination Therapy Strategies
by Zimei Tang, Tao Huang and Tinglin Yang
Int. J. Mol. Sci. 2025, 26(23), 11596; https://doi.org/10.3390/ijms262311596 - 29 Nov 2025
Viewed by 870
Abstract
Breast cancer remains the most prevalent malignancy among women worldwide, with hormone receptor-positive (HR+) tumors comprising approximately 70% of cases. Traditionally, HR+ breast cancer has been classified as immunologically “cold” due to its low PD-L1 expression, reduced tumor-infiltrating lymphocytes, and low tumor mutational [...] Read more.
Breast cancer remains the most prevalent malignancy among women worldwide, with hormone receptor-positive (HR+) tumors comprising approximately 70% of cases. Traditionally, HR+ breast cancer has been classified as immunologically “cold” due to its low PD-L1 expression, reduced tumor-infiltrating lymphocytes, and low tumor mutational burden, collectively limiting immunotherapy responsiveness. However, emerging evidence indicates significant molecular heterogeneity within HR+ tumors, characterized by specific genetic signatures and features of the tumor microenvironment (TME) that can be therapeutically reprogramed through chemotherapy-induced immunogenic cell death combined with immune checkpoint inhibition. Recent clinical trials demonstrate that biomarker-selected immune-enriched HR+ subsets, identified by MammaPrint Ultra-High 2 classification, homologous recombination deficiency, or elevated tumor-infiltrating lymphocytes, achieve notable pathological complete response rates with immune checkpoint inhibitor combinations. This review summarizes the dynamic interactions between genetic determinants and TME plasticity in HR+ breast cancer and critically assesses combination strategies across 31 neoadjuvant trials. We demonstrate that optimal efficacy requires biomarker-guided patient selection integrating genetic and TME features, precise sequencing, and a mechanistic understanding of drug-specific immunomodulatory effects. The integration of platform trial designs (I-SPY2, CheckMate-7FL) with composite biomarker algorithms represents a paradigm shift toward precision neoadjuvant immunotherapy, offering a conceptual framework for transforming outcomes in molecularly defined HR+ breast cancer subsets. Full article
(This article belongs to the Special Issue Breast Cancer: From Pathophysiology to Novel Therapies)
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16 pages, 1905 KB  
Systematic Review
Comparative Analysis of Maintenance Treatments in Patients with Newly Diagnosed Advanced Ovarian Cancer After First-Line Platinum-Based Regimens
by Lorenzo Gasperoni, Luca Cancanelli, Andrea Ossato, Luna Del Bono, Stefano Vecchia, Caterina Fontanella, Vera Damuzzo and Andrea Messori
Cancers 2025, 17(22), 3714; https://doi.org/10.3390/cancers17223714 - 20 Nov 2025
Viewed by 1136
Abstract
Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) are the standard of care for first-line maintenance in advanced ovarian cancer, but their benefit varies by BRCA and homologous recombination deficiency (HRD) status, and no head-to-head comparisons are available. Methods: We conducted an indirect comparison of [...] Read more.
Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) are the standard of care for first-line maintenance in advanced ovarian cancer, but their benefit varies by BRCA and homologous recombination deficiency (HRD) status, and no head-to-head comparisons are available. Methods: We conducted an indirect comparison of PARPi regimens using reconstructed individual patient data (IPD) from Kaplan–Meier curves of phase III randomized trials (SOLO1, PRIMA, PAOLA1, ATHENA, FLAMES). Progression-free survival (PFS) was the primary endpoint; overall survival (OS) was exploratory. Subgroups were defined as BRCA−mutated (BRCA+), BRCA−/HRD+, and BRCA−/HRD−. Safety outcomes were assessed through a network meta-analysis of adverse drug reactions (ADRs). Results: In BRCA+ patients, olaparib + bevacizumab achieved the largest PFS improvement (HR = 0.27; 95%CI: 0.19–0.39), followed by olaparib monotherapy, while niraparib performed significantly worse. In BRCA−/HRD+, olaparib + bevacizumab was superior to niraparib and rucaparib, with restricted mean survival time (RMST) gains of 3–4 months. In BRCA−/HRD−, PARPi produced only a modest benefit, with no advantage over bevacizumab monotherapy. Exploratory OS analysis confirmed long-term survival with olaparib in BRCA+ but not in the other subgroups. Safety analysis indicated olaparib had the most favorable hematological profile, while niraparib was associated with the highest rates of severe anemia, thrombocytopenia, and neutropenia, despite showing lower gastrointestinal toxicity and fatigue incidence. Conclusions: PARPi efficacy depends strongly on BRCA and HRD status. Olaparib-based regimens provide the greatest clinical benefit with acceptable safety in BRCA+ and HRD+ disease, whereas PARPi appear to be of limited value in HRD-negative ovarian cancer. Full article
(This article belongs to the Section Systematic Review or Meta-Analysis in Cancer Research)
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