Search Results (202)

Gene amplification resulting from double strand breaks (DSBs) is a typical genetic alteration in tumorigenesis and drug-resistant progression. Amplified oncogenes and drug-resistant genes are present on extrachromosomal DNAs (ecDNAs), or chromosomal homogeneously staining regions (HSRs). Considering the role of mismatch repair (MMR) as a sensor of DSBs, we hypothesized that MMR may be involved in gene amplification. We used two MTX-resistant HT-29 colorectal cancer cell lines, which served as models with amplified genes mainly in HSRs or ecDNAs. Expression of MSH2, a key protein in MMR, was increased following the acquisition of MTX-resistant. MMR inhibition was achieved by depleting MSH2. Suppression of MMR led to decreased copy numbers of amplified genes as well as the quantity of ecDNAs and HSR. This was caused by the decreased efficiency of DSBs repair, which resulted from the reduced ability of MMR to recruit DSBs repair proteins. Additionally, it accelerated the formation of micronuclei (MN)/nuclear buds (NBUDs), which functioned to eliminate the amplified genes. Furthermore, the suppression of MMR was capable of inhibiting cell proliferation and enhancing MTX-sensitivity in ecDNA-containing cells. Conversely, suppression of MMR had no effect on gene amplification in HSR-containing cells. Our findings demonstrate that MMR plays a pivotal role in gene amplification through mediating DSBs repair pathways and facilitating the formation of MN/NBUDs in ecDNA-containing cells. MMR is likely to emerge as a prime therapeutic target worthy of in-depth exploration in future clinical investigations. Full article

Endometrial cancer (EC) is the sixth most common cancer in women. Its overall incidence has increased by 132% over the past 30 years, reflecting an increase in the prevalence of risk factors. The mortality rate decreased by 15% in the last 30 years, despite the high number of endometrial cancer-related deaths occurring world-wide. An inverse relationship has been observed between the incidence of EC, mortality and socio-economic status: more patients living in low-income countries die from EC because they do not have access to timely and effective treatment. About 80% of EC cases are diagnosed in an early stage and have a good prognosis. However, about 20% of cases present in advanced stages and are characterized by a poor prognosis. The molecular classification proposed by The Cancer Genome Atlas (TGCA) and its surrogate for clinical use allowed the adoption of personalized treatments. The assessment of the status of the MMR has revolutionized the treatment of advanced ECs, leading to significant results both in terms of PFS and OS. In this review we will focus on MMR deficiency (dMMR)/microsatellite instability-hypermutated (MSI-H) tumors, which globally account for 20–30% of ECs. The dMMR group encompasses multiple etiologies, including sporadic defects in MMR genes, germline mutations, and hypermethylation of the MLH1 promoter. Currently, the combination of immunotherapy (I-O) with standard chemotherapy has become the new standard first-line treatment for dMMR advanced or recurrent ECs. Although the main clinical trials involving patients with MMRd/MSI-H ECs treated with I-O and chemotherapy have demonstrated efficacy and long-term control of the disease, a significant number of patients do not respond to treatment (intrinsic or primary resistance) and others develop progression during treatment (acquired or secondary resistance). In this narrative approach the biological and molecular bases of these tumors have been integrated with recent advances involving diagnostic techniques, therapeutic opportunities and the genomic and phenotypical alterations underpinning the mechanisms of resistance. Special attention was given to the need for robust, clinically affordable biomarkers to promptly identify responders and non-responders to the current treatment regimens. Full article

Next-generation sequencing (NGS) has impacted the treatment landscape for mCRC, leading to improved outcomes through the use of molecularly targeted and immune checkpoint inhibitor therapies. The National Comprehensive Cancer Network (NCCN) and the American Society of Clinical Oncology (ASCO) recommend, at a minimum, initial testing to assess RAS, BRAF, HER2, and microsatellite instability (MSI)/mismatch repair (MMR) status, as these results determine therapeutic eligibility. Broader testing to identify the eligibility for tumor-agnostic therapy for a tumor mutation burden (TMB), NTRK gene fusions, and RET fusions is encouraged for all patients with advanced solid tumors. Patients with metastatic disease may develop progressive disease, often as a result of adaptive resistance mechanisms and selective therapeutic pressure on disease heterogeneity. Repeat biomarker testing at progression has the potential to define these resistance mechanisms and to guide the next therapy or clinical trial enrollment. While these practices have become more commonplace, unified guidelines have yet to be established. In this review of the literature, we evaluate the advantages and pitfalls of sequential biomarker testing during disease progression in patients with mCRC. Full article

Colorectal cancer (CRC) is a major public health concern in the United States. It is currently the fourth most diagnosed cancer and, despite advancements in screening and treatment, the second leading cause of cancer-related deaths. Approximately 153,000 new cases are diagnosed annually, with over 53,000 deaths reported. Understanding the molecular and genetic underpinnings of CRC biomarkers plays a crucial role in diagnosis, prognosis, and treatment planning. Specific gene mutations, including MMR deficiency leading to high microsatellite instability (MSI), as well as several other common mutations in CRC, including APC, TP53, KRAS, NRAS, SMAD4, PIK3CA and BRAF, provide valuable insights into tumor biology, therapeutic resistance, and response to targeted therapies. This review explores the mutations and co-mutations most relevant to CRC, their prevalence, prognostic significance, and implications for precision oncology. By focusing on these genetic and epigenetic alterations, we aim to contextualize how biomarker-driven strategies are reshaping the management of CRC in both early and advanced disease settings. Full article

Background/Objectives: In metastatic colorectal cancer (mCRC) the evaluation of mismatch repair (MMR) and microsatellite instability (MSI) status is essential to identify patients eligible for treatment with immune-checkpoint inhibitors (ICI). This study aims to evaluate the potential utility of Comprehensive Genomic Profiling (CGP) in assessing MSI status, in addition to other immunotherapy-predictive biomarkers such as high tumor molecular burden (TMB) and the POLE and POLD1 mutations. Methods: A total of 138 mCRC tumor samples underwent a first-level molecular test (MMR status by immunohistochemistry, MSI by a melting-based PCR approach and RAS/BRAF mutational status by a small next-generation sequencing (NGS) panel) and second-level CGP analysis by the FoundationOne CDx assay. The prevalence of dMMR and MSI tumors was reported. Moreover, the concordance between the MMR and MSI status was determined, and discordant cases were discussed. Results: Twelve cases (8.7%) were MMR-deficient (dMMR); 10 showed high MSI and TMB (>10 mut/Mb). MSI status assessed by CGP and PCR was concordant in all cases except one MSH6-deficient tumor. Two dMMR cases were stable with low TMB. Moreover, in two MLH1/PMS2-deficient cases CGP revealed pathogenic alterations in the MSH2 and MSH6 genes; in both cases, the MLH1 promoter was hypermethylated. A high TMB was the only positive biomarker in 11 cases with a proficient MMR system and no MSI. Conclusions: MSI assessment by CGP analysis showed high concordance (98%) with MMR and was helpful in evaluating ICI eligibility in three out of twelve dMMR cases. Overall, compared to standard methods, analyzing a broader range of microsatellite loci and the simultaneous assessment of multiple predictive biomarkers by CGP may increase diagnostic accuracy and improve therapeutic assessment. Full article

Background/Objectives: Colorectal cancer (CRC) shows significant molecular diversity influenced by tumor location. Right- and left-sided CRCs differ in terms of microsatellite instability (MSI), mutational burden, and actionable biomarkers. This study aimed to characterize the clinicopathological and molecular features of CRC stratified upon tumor location. Methods: A consecutive series of CRC cases was retrospectively analyzed. Tissue samples were obtained from primary tumors (71%) or metastatic lesions (29%). All cases were evaluated by histopathology, immunohistochemistry (IHC), and targeted next-generation sequencing (NGS). Tumor location was assigned based on the primary tumor (43 right-sided and 35 left-sided cases). Results: Right-sided CRCs were more frequent in older patients and females and showed higher rates of deficient MMR (42% vs. 17%, p = 0.02), MSI-H (39% vs. 14%, p = 0.02), and high tumor mutational burden (TMB-high, ≥10 Mutations/Mb, 56% vs. 28%, p = 0.02). The most frequent pathogenic class 5 mutations were TP53 (65%), APC (49%), and KRAS (44%). APC was the most frequently mutated gene in both pathogenic (class 5) and likely pathogenic (class 4) categories, with class 5 variants more common in left-sided tumors and class 4 variants predominating in right-sided tumors. BRAF mutations showed a statistically significant trend toward higher frequency in right-sided tumors (p = 0.05). HER2/neu overexpression (3+) was seen in 15% of patients, exclusively in MSS left-sided tumors. PD-L1 expression (CPS ≥ 1) was detected in 20% of patients, irrespective of location, and pan-TRK IHC was negative in all cases. The 29% of samples derived from metastatic lesions were predominantly MSS/pMMR (87%). Conclusions: Tumor location in CRC correlates with distinct molecular patterns. Right-sided tumors are associated with dMMR, MSI-H, and higher TMB, while left-sided CRCs display more ERBB2 alterations and class 5 APC mutations. The results highlight the importance of integrating tumor location into personalized molecular diagnostics and therapeutic planning for CRC patients. Full article

Background/Objectives: Lynch syndrome (LS), is traditionally managed uniformly despite being caused by pathogenic variants in four distinct mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2). This approach fails to leverage gene-specific characteristics for precision healthcare delivery. This review redefines LS as four distinct genetic syndromes and establishes a genotype-guided precision management framework to optimize risk stratification, surveillance, and therapeutic interventions. Methods: We synthesized molecular, clinical, and outcomes data from the Prospective Lynch Syndrome Database (8500+ carriers; 70,000 person-years), genomic studies characterizing gene-specific mutational patterns, and immunotherapy trials while referencing international guidelines [National Comprehensive Cancer Network (NCCN), European Hereditary Tumour Group (EHTG)/European Society of Coloproctology (ESCP), and European Society for Medical Oncology (ESMO)] to formulate genotype-stratified recommendations. Results: Fundamental molecular differences necessitate differentiated management strategies. MLH1 deficiency exhibits unique “two-in-one hit” mechanisms driving aggressive tumorigenesis with high interval cancer rates. MSH2 deficiency presents the highest tumor mutational burden (≈47 mutations per megabase; Mut/Mb) and broadest cancer spectrum. MSH6 deficiency displays distinctive high-single-nucleotide variant (SNV)/low-insertion–deletion (Indel) patterns often presenting as microsatellite instability-low (MSI-low) or microsatellite stable (MSS), complicating conventional detection. PMS2 deficiency demonstrates substantial attenuation due to redundancy. These translate into precision interventions: MLH1/MSH2 carriers require colonoscopy from age 25 at 1–2-year intervals with extended colectomy preferred, while MSH6/PMS2 carriers can defer surveillance to age 35–40 with longer intervals and undergo segmental resection. Immune checkpoint inhibitors (ICIs) are effective in deficient MMR (dMMR)/microsatellite instability-high (MSI-H) tumors across all four MMR genotypes. Conclusions: Genotype-specific precision management optimizes the benefit–burden balance, enhances early cancer detection, reduces overtreatment, and enables personalized genetic counseling, advancing precision healthcare for LS families and addressing critical gaps in hereditary cancer care. Full article

This study systematically investigated the genomic alterations in Saccharomyces cerevisiae driven by Replication Factor A (RFA) dosage insufficiency using a promoter-replacement strategy combined with mutation accumulation and whole-genome sequencing. Our findings reveal that transcriptional suppression of RFA2 or RFA3 leads to severe growth inhibition. RFA deficiency induces a distinct mutational spectrum characterized by a high frequency of monosomy and terminal deletions, indicative of severe replication stress. Furthermore, loss of heterozygosity is significantly enriched at centromeres and high-GC regions, underscoring the role of RFA in stabilizing intrinsic genomic barriers. Utilizing an APOBEC3B-induced mutagenesis assay, we demonstrate that RFA insufficiency leads to the extensive accumulation of exposed ssDNA with a distinct bias towards the lagging strand template. Notably, we observed that cells spontaneously inactivate Mismatch Repair (MMR) genes, such as MSH2 and PMS1, to survive RFA-induced stress. This hypermutant phenotype grants a certain degree of growth recovery on Low Galactose (LG) medium. Overall, these findings demonstrate that RFA dosage is a key determinant of genomic integrity and elucidate how repair pathway modulation drives adaptive evolution under replication stress. Full article

Endometrial cancer is the most common gynaecologic malignancy in high-income countries, with a rising incidence largely driven by reproductive factors, obesity, and prolonged exposure to unopposed oestrogens. Although most cases are sporadic, approximately 2–5% are associated with hereditary cancer syndromes, of which Lynch syndrome represents the most important contributor. Lynch syndrome results from germline mutations in DNA mismatch repair (MMR) genes and is associated with a substantially increased lifetime risk of endometrial cancer, reaching up to 71% in carriers of MutS homologue 6 (MSH6) mutations. Hereditary cancer predisposition typically follows an autosomal dominant inheritance pattern and may be suspected based on clinical warning signs such as early disease onset, multiple primary malignancies, a strong family history, or the presence of microsatellite instability in tumour tissue. In addition to Lynch syndrome, rarer genetic conditions—including Cowden syndrome (PTEN), Li–Fraumeni syndrome (TP53), polymerase proofreading–associated polyposis (POLE/POLD1), and hereditary breast and ovarian cancer syndromes (BRCA1/2)—also contribute to hereditary endometrial cancer risk. Recognition of these genetic backgrounds is essential for accurate diagnosis, personalised surveillance, and the implementation of targeted preventive and therapeutic strategies. Despite major advances in molecular diagnostics, hereditary endometrial cancer remains frequently underdiagnosed, leading to missed opportunities for cancer prevention among affected individuals and their families. This comprehensive review summarises current evidence on hereditary predispositions to endometrial cancer, with a particular emphasis on Lynch syndrome, and discusses underlying genetic mechanisms, inheritance patterns, diagnostic strategies, and clinical implications for screening, genetic counselling, and treatment optimisation. Full article

Background/Objectives: Immune checkpoint inhibitors (ICIs) show durable efficacy in tumors with deficient mismatch repair (dMMR) or high microsatellite instability (MSI-H), yet clinical responses remain heterogeneous. This study aimed to define immune subgroups within dMMR/MSI-H tumors and develop a reproducible transcriptomic signature predictive of ICI response. Methods: Four MSI-H-enriched cancer types (UCEC, COAD, READ, STAD) from The Cancer Genome Atlas were analyzed. Tumors were stratified by immune cell infiltration (MCP-counter immune composite score) and T-cell-inflamed gene expression profiles (GEP score). Integrating these two axes defined four immune subgroups. Differential expression, random forest feature selection, and pathway enrichment were performed to identify immune programs. A 20-gene immune signature representing the most immune-active subgroup was developed and validated across TCGA, GEO (GSE39582), and IMvigor210 cohorts. Results: Among the four subgroups, the most immune-active group showed strong activation of interferon signaling, antigen presentation, and T-cell-mediated pathways. The 20-gene signature—including CD74, STAT1, TAP1, and HLA-class genes—achieved high reproducibility (mean AUC = 0.95 ± 0.02; accuracy ≈ 89%). In the IMvigor210 cohort, this signature identified tumors with higher PD-L1 blockade response (55.6% vs. 32.8%, p = 0.034) and improved survival trends in the TMB-high subset. Conclusions: The proposed 20-gene signature quantitatively captures immune heterogeneity in dMMR/MSI-H tumors and serves as a practical, interpretable biomarker to identify true ICI responders and guide precision immunotherapy. Full article

Background: Metastatic colorectal cancer (mCRC) with TP53 gene mutations, which are commonly found in tumors that are microsatellite stable (MSS) and not prone to genetic errors seen in some cancers, is associated with aggressive cancer behavior and poor outcomes. While MSI-high (MSI-H, referring to high levels of gene instability) disease benefits markedly from PD-1-based immunotherapy (drugs that inhibit the PD-1 protein on immune cells), TP53-mutated MSS tumors rarely receive immune checkpoint inhibitors (ICIs, drugs that help immune cells attack cancer) outside of trials and often only in later lines of therapy. Objective: We aimed to synthesize translational and clinical evidence regarding the effects of early rationale-driven immunotherapy combinations on survival outcomes, in TP53-mutated metastatic colorectal cancer, with a focus on practical clinical implications. Methods: This narrative review was conducted in accordance with SANRA criteria. Literature searches were performed in PubMed/MEDLINE, Scopus, and Web of Science (2010–2025). Relevant ESMO and NCCN guidelines and key references were also reviewed. Results: In KEYNOTE-177 study (MSI-H/dMMR), pembrolizumab improved PFS (HR 0.60) and showed durable OS with >5-year follow-up. CheckMate-142 reported sustained activity with nivolumab ± ipilimumab. Preclinical/early clinical data in MSS/TP53 suggest that ICIs may become effective when combined with priming (chemo/DDR) and vascular normalization (anti-VEGF), particularly in subsets with elevated TMB. The randomized ROME trial supports the clinical utility of genomically matched, NGS-guided strategies. Conclusions: A precision approach integrating TP53 status, TMB, and TME modulation could extend the immunotherapy benefit beyond MSI-H to TP53-mutated MSS mCRC; prospective first-line trials are warranted. Full article

Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is a hereditary cancer syndrome significantly increasing the risk of colorectal cancer (CRC) and various extracolonic cancers, including endometrial, ovarian, and gastric cancers. LS results from germline pathogenic variants (GPVs) in DNA mismatch repair (MMR) genes, such as MLH1, MSH2, MSH6, and PMS2, leading to microsatellite instability (MSI). This review explores the multifaceted aspects of LS, covering clinical presentation, genetic underpinnings, and emerging therapeutic strategies. The discussion explores the importance of identifying at-risk individuals, facilitating personalized cancer surveillance and prevention strategies. Molecular insights into distinguishing between sporadic and LS-associated cancers are also examined, with a focus on somatic testing methods, including MSI and immunohistochemistry (IHC). The gynecological cancer risks, particularly those related to endometrial and ovarian malignancies, are addressed, underscoring the need for early detection and risk-reducing interventions. Recent advancements in the management of colorectal and other LS-related cancers are highlighted, with particular attention to the growing role of immunotherapy, including immune checkpoint inhibitors, and immunoprevention strategies. With ongoing advances in our understanding of LS, opportunities for earlier detection, more effective prevention, and innovative treatments continue to expand. This narrative review adopts a multidisciplinary approach to provide a comprehensive understanding of LS, from its genetic basis to current clinical and therapeutic practices, with the ultimate goal of improving patient outcomes and enhancing the quality of care. Full article

Hereditary predisposition substantially shapes prevention and management across urologic oncology. This narrative review synthesizes contemporary, practice-oriented guidance on whom to test, what to test, how to act on results, and how to implement care equitably for hereditary forms of prostate cancer, renal cell carcinoma (RCC), urothelial carcinoma, pheochromocytoma/paraganglioma (PPGL), and adrenocortical carcinoma (ACC). We delineate between forms of indication-driven germline testing (e.g., universal testing in metastatic prostate cancer; early-onset, bilateral/multifocal, or syndromic RCC; reflex tumor mismatch repair (MMR)/microsatellite instability (MSI) screening in upper-tract urothelial carcinoma (UTUC); universal testing in PPGL; universal TP53 testing in ACC) and pair these strategies with minimum actionable gene sets and syndrome-specific surveillance frameworks. Key points include targeted prostate-specific antigen screening in BRCA2 carriers and the impact of BRCA/ATM variants on reclassification during active surveillance; major hereditary RCC syndromes with genotype-tailored surveillance and pathway-directed therapy (e.g., HIF-2α inhibition for von Hippel–Lindau disease); UTUC/bladder cancer in Lynch syndrome with tumor MMR/MSI screening, annual urinalysis (selective cytology), and immunotherapy opportunities in deficient MMR disease/MSI-H; PPGL management emphasizing universal germline testing, intensified surveillance for SDHB, cortical-sparing adrenalectomy, and emerging HIF-2α inhibition; and ACC care modified by Li–Fraumeni syndrome (minimization of radiation/genotoxic therapy with whole-body imaging surveillance). Testicular germ cell tumor remains largely polygenic, with no routine germline testing in typical presentations. Finally, we provide pre-/post-test genetic-counseling checklists and mainstreamed workflows with equity metrics to operationalize precision care and close real-world access gaps. Full article

Background/Objectives: Colorectal cancer (CRC) is the second leading cause of cancer-related death in the US. The presence of deficient DNA mismatch repair and microsatellite instability (dMMR/MSI) in CRC is linked to responses to immune checkpoint inhibitors (ICIs). This study investigates the impact of metformin on the tumor microenvironment (TME) and clinical outcomes of patients with dMMR/MSI CRC treated with ICIs, aiming to better understand its potential role in enhancing ICI efficacy. Methods: Of 25,011 CRC patients in Caris database, 47 received both metformin and ICI therapy (Met-ICI group), and 475 patients received ICI therapy alone (ICI group). Samples underwent genomic or transcriptome sequencing at Caris Life Sciences. Immune cell fractions were estimated using quanTIseq. Univariate and multivariate survival analyses were conducted using the Cox proportional model. Results: The TME analysis of CRC patient samples revealed that TMB-High (≥10 mut/Mb) was more prevalent in the “ICI” group compared to the “Met-ICI” group (99.1% vs. 95.6%, p = 0.036). Mutation rates for most genes between the two groups were similar, but CIC gene mutations were more common in the “ICI” group than in the “Met-ICI” group (23.2% vs. 4.8%, p = 0.006). No significant differences were observed in the PD-L1 positivity rate or immune checkpoint gene expression (including IDO1, IFNG, TIM3, and CTLA4). M1 macrophages and neutrophils showed the highest infiltration among immune cells. However, the fractions of infiltrated immune cells were similar between the two cohorts. Univariate and multivariate analyses showed that there was no significant difference in patient survival between “ICI” and “Met-ICI” cohorts. Conclusions: In this retrospective analysis of real-world clinical outcomes, the concurrent use of metformin with ICIs in patients with dMMR/MSI CRC did not reveal an impact on clinical outcomes. Full article

Background: Lynch syndrome (LS) is a cancer-susceptibility syndrome associated with autosomal dominant predisposition to a spectrum of cancers, primarily of the colorectum and endometrium, which exhibit impaired DNA mismatch repair (MMR) activity. LS is caused by a hereditary (germline) pathogenic (PV) or likely pathogenic variant (LPV) in one of the mismatch repair (MMR) genes—MLH1, MSH2, MSH6, PMS2, or EPCAM. Although point mutations are the most common genetic changes in MMR genes, >20% are large genomic rearrangements. We hypothesized that a two-tier diagnostic strategy for Lynch syndrome (LS) using next generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) can increase diagnostic yield of patients with Lynch syndrome. Methods: This study included 60 patients suspected of LS. After genetic counseling, they were referred to genetic testing. Genomic DNA was extracted from peripheral blood and sequenced using NGS multigene panel testing covering 113 cancer susceptibility genes, including MMR genes. Regarding limitations of NGS analysis, which cannot reliably detect genomic alterations larger than 50 base pairs in length, the MLPA method was used for NGS negative DNA samples in order to identify larger deletions and duplications, commonly referred to as copy number variations (CNVs). Results: Different PVs were detected by NGS in 10 patients and CNVs were detected by MLPA in 7 more patients: 3xMLH1 del ex9-15, 2xMSH2 del ex1 and upstream, 1xMSH2 del ex9, and 1xMSH2 del ex1. We did not detect LPVs or variants of uncertain significance (VUS). In our cohort, the addition of MLPA provided an incremental yield of seven pathogenic CNVs, representing an 11.6% absolute increase in diagnostic sensitivity (from 16.7% to 28.3%) over the NGS-alone workflow, with CNVs accounting for 41% of all pathogenic findings. Conclusions: Our results show that MLPA is a very useful method in molecular diagnostics of LS and its implementation in routine genetic testing in combination with NGS using multigene panel testing would benefit both patients and health care providers. Full article