Annals of Oncology

BackgroundTriple-negative breast cancer (TNBC) is associated with poor survival rate and high genomic instability, generating complex tumour genomes. However, the processes that generate this complexity are poorly studied in longitudinal samples. Here, we study the temporal dynamics of TNBC somatic mutations, revealing major transitions in tumour genome evolution, from diagnostic biopsies, through treatment, to cancer remission or recurrence. MethodsDeep whole exome sequencing and CUTseq, a reduced representation whole genome sequencing approach, were performed in parallel, to comprehensively identify short nucleotide variants (SNVs), copy number alterations (CNAs) and aneuploidies. Tumour samples (N=74) from 22 patients were profiled before and after neoadjuvant chemotherapy (NACT), and encompassed spatially diverse samples from multiple primary breast tumours, to allow tracking of the gain and loss of candidate driver variants over time. ResultsGenome-wide SNV mutational burden remained stable across disease progression and RCB classes. However, recurrent SNVs were identified in several known TNBC driver genes in response to treatment, with TP53, MICA, CYP2D6, BRCA1, and BRCA2 being frequently altered. The candidate driver variants in these genes frequently exhibited dynamic changes throughout the course of a patients treatment, with the original SNVs in pre-treatment samples often lost, while novel variants in the same genes emerged at subsequent time points. In contrast to the stable genome-wide SNV burdens, dramatic changes in chromosome structure were seen in all tumours, with abundant CNAs and chromosome arm aneuploidies seen in pre-treatment samples, followed by frequent loss of these alterations post-treatment, and their re-emergence at recurrence. Whole genome duplication (WGD) events appear to drive these dynamics, with a higher frequency of pre-treatment WGD seen in patients with the best response to NACT. ConclusionsComprehensive longitudinal profiling of the TNBC genome demonstrates the complex interplay of SNVs and structural alterations during tumour progression, leading to diverse evolutionary trajectories impacting patient outcomes. Complex mutational patterns encompassing entire chromosomes emerge during progression, with WGD events making major contributions to intra-tumour heterogeneity, and emerging as a potential candidate biomarker of response at both tumour establishment and recurrence.

BackgroundThe HOXB13/IL17BR gene expression biomarker has been shown to predict response to adjuvant and extended endocrine therapy in patients with early-stage ER+ HER2- breast tumors. HOXB13 gene expression is the primary determinant driving the prognostic and endocrine treatment-predictive performance of the biomarker. Currently, there is limited data on HOXB13 expression in HER2+ and ER- breast cancers. Herein, we studied the expression of HOXB13 in large cohorts of HER2+ and ER- breast cancers. MethodsWe investigated gene expression, genomic copy number, mutational signatures, and clinical outcome data in the TGGA and METABRIC breast cancer cohorts. Genomic-based gene amplification data was validated with tri-colored fluorescence in situ hybridization. ResultsIn the TCGA breast cancer cohort, HOXB13 gene expression was significantly higher in HER2+ versus HER2- breast cancers, and its expression was also significantly higher in the ER- versus ER+ breast cancers. HOXB13 is frequently co-gained or co-amplified with ERBB2. Joint copy gains of HOXB13 and ERBB2 occurred with low-level co-gains or high-level co-amplifications (co-amp), the latter of which is associated with an interstitial deletion that includes the tumor suppressor BRCA1. ERBB2/HOXB13 co-amp tumors with interstitial BRCA1 loss exhibit a mutational signature associated with APOBEC deaminase activity, and copy number signatures associated with chromothripsis and genomic instability. Among ERBB2-amplified tumors of different tissue origins, ERBB2/HOXB13 co-amp with a BRCA1 loss appeared to be unique to breast cancer. Lastly, patients with ERBB2/HOXB13 co-amplified and BRCA1 lost tumors displayed a significantly shorter progression-free survival (PFS) than those with ERBB2-only amplifications. The difference in PFS was restricted to the ER- subset patients and this difference in PFS was not solely driven by HOXB13 gene expression. ConclusionsHOXB13 is frequently co-gained with ERBB2 at both low-copy number level or as complex high-level amplification with relative BRCA1 loss. ERBB2/HOXB13 amplified, BRCA1-lost tumors are strongly enriched in breast cancer, and patients with such breast tumors experience a shortened PFS.

Optimal selection of high-risk patients with stage II colon cancer is crucial to ensure clinical benefit of adjuvant chemotherapy after surgery. Here, we investigate the prognostic and predictive value of genomic intratumor heterogeneity and aneuploidy for disease recurrence. We combined SNP arrays, targeted next-generation sequencing, fluorescence in situ hybridization and inmunohistochemistry on a retrospective cohort of 84 untreated stage II colon cancer patients. We assessed the subclonality of copy-number alterations (CNAs) and mutations, CD8+ lymphocyte infiltration and their association with time to recurrence (TTR). Prognostic factors were included in machine learning analysis to evaluate their ability to predict individual relapse risk. Tumors from recurrent patients (N = 38) exhibited greater proportion of CNAs compared with non-recurrent (N = 46) (mean 31.3% vs. 23%, respectively; P = 0.014), which was confirmed in an independent cohort. Candidate chromosome-specific aberrations included the gain of the chromosome arm 13q (P = 0.02; HR, 2.67) and loss of heterozygosity at 17q22-q24.3 (P = 0.05; HR, 2.69), both associated with shorter TTR. CNA load positively correlated with intratumor heterogeneity (R = 0.52; P < 0.0001), indicating ongoing chromosomal instability. Consistently, subclonal copy-number heterogeneity was associated with elevated risk of relapse (P = 0.028; HR, 2.20), which we did not observe for subclonal mutations. The clinico-genomic model rated an area under the curve of 0.83, achieving a 10% incremental gain compared to clinicopathological markers. In conclusion, tumor aneuploidy and copy-number heterogeneity were predictive of a poor outcome in early-stage colon cancer, and improved discriminative performance in comparison to clinicopathological data.

Neoadjuvant therapy followed by surgery is the standard of care for locally advanced esophageal adenocarcinoma (EAC). Unfortunately, response to neoadjuvant chemotherapy (NAC) is poor (<20%), as is the overall survival benefit at 5 years (5%). The EAC genome is complex and heterogeneous between patients, and it is not yet understood whether specific mutational patterns may result in chemotherapy sensitivity or resistance. To identify associations between genomic events and response to NAC in EAC, a comparative genomic analysis was performed in 65 patients with extensive clinical and pathological annotation using whole-genome sequencing (WGS). We defined response using Mandard Tumor Regression Grade (TRG), with responders classified as TRG1-2 (n=27) and non-responders classified as TRG4-5 (n=38). We report a higher non-synonymous mutation burden in responders (median 2.08/Mb vs 1.70/Mb, P=0.036) and elevated copy number variation in non-responders (282 vs 136/patient, P<0.001). We identified copy number variants unique to each group in our cohort, with cell cycle (CDKN2A, CCND1), c-Myc (MYC), RTK/PIK3 (KRAS, EGFR) and gastrointestinal differentiation (GATA6) pathway genes being specifically altered in non-responders. Of note, NAV3 mutations were exclusively present in the non-responder group with a frequency of 22%. Thus, lower mutation burden, higher chromosomal instability and specific copy number alterations are associated with resistance to NAC.

BackgroundPrecision oncology is predominantly focused on nuclear genomic alterations, while mitochondrial DNA (mtDNA) variation remains largely excluded from routine pharmacogenomic testing. However, mitochondria regulate oxidative phosphorylation (OXPHOS), reactive oxygen species (ROS) production, apoptosis, and metabolic reprogramming pathways central to chemotherapy response. Methods468 Complete mitochondrial genomes from Kenyan individuals representing diverse ethnolinguistic groups were analyzed. Seven variants associated with effect on cancer treatment were identified. These include; m.310T>C(D-loop), m.10398A>G (MT-ND3), m.13708G>A (MT-ND5), m.16189T>C, m.13928G>C, m9055G>A and m.16519T>C (D-loop). Allele frequencies and distribution were assessed. ResultsThe coding-region variants (m.10398A>G and m.13708G>A) occur in Complex I subunits and are associated with altered oxidative phosphorylation efficiency and ROS production. The control-region variants (m.16189T>C and m.16519T>C) influence mtDNA replication and copy number. These variants have been implicated in differential response to chemotherapeutic agents including platinum-based therapies and anthracyclines. m.13928G>C sits in the MT-CYB gene and could possibly affect mitochondrial respiratory function; this variant could influence how tumors respond to therapies that rely on apoptosis or ROS generation.m.9055G>A is a MT-ATP6 variant classified as benign in mitochondrial disease but may represent a marker of haplogroup background rather than a direct cancer driver. While m.310T>C itself does not encode a protein, its location in the regulatory D-loop influences mitochondrial function, which can affect how tumor cells respond to chemotherapies that rely on mitochondrial-mediated apoptosis or oxidative stress. ConclusionPharmacogenomics relevant mitochondrial variants are present in the Kenyan population. With the rise of cancer burden in Kenya there is a need carry out more studies to understand the impact of these variations on cancer treatment. This can inform the integration of mtDNA analysis into precision oncology strategies in African populations.

BackgroundA common germline deletion polymorphism in the APOBEC3B gene increases the rate of somatic hypermutation in breast cancer, which in turn is associated with greater neoantigen burden and immune activation. This phase II study evaluated the impact of the APOBEC3B deletion polymorphism on the response to pembrolizumab monotherapy in metastatic HER2-negative breast cancer patients. Patients and methodsEligible patients had a confirmed diagnosis of metastatic HER2-negative breast cancer, 1-3 prior lines of therapy, and documented homozygous or heterozygous germline deletion of APOBEC3B. Patients received 200 mg of pembrolizumab intravenously every 3 weeks for up to 2 years. The primary endpoint was objective response rate. Secondary endpoints were disease control rate, progression-free survival, and overall survival. ResultsAll enrolled patients (N = 44) were women, 36% had PD-L1-positive tumours, and 62% had received [&ge;]2 previous lines of therapy for metastatic disease. ORR (95% CI) was 20.5% (9.8 - 35.5) in the total and 30.0% (6.7 - 65.3) in the PD-L1-positive populations. Disease control rate (95% CI) was 52.3% (36.7 - 67.5) and 40% (12.2 - 73.8), respectively. Median PFS was 3.1 months (95% CI, 2.1 - 4.3), and 6-month PFS rate was 29.5% (95% CI, 18.7 - 46.6). Median OS was 15.2 months (95% CI, 11.7 - 26.5), and 12-month OS rate was 60.2% (95% CI, 46.5 - 77.7). Treatment-related adverse events occurred in 30 (68.2%) patients, including 1 (2.3%) with grade 3 AE. There were no deaths due to AEs. ConclusionsPembrolizumab monotherapy demonstrated durable antitumour activity in a subset of previously treated metastatic HER2-breast cancer patients with germline APOBEC3B deletion. Clinical trial registrationClinicalTrials.gov, NCT03989089.

BackgroundThe immune response against tumors relies on distinguishing between self and non-self, the basis of cancer immunotherapy. Neoantigens from somatic mutations are central to many immunotherapeutic strategies and understanding their landscape in breast cancer is crucial for targeted interventions. We aimed to profile neoantigens in Kenyan breast cancer patients using genomic DNA and total RNA from paired tumor and adjacent non-cancerous tissue samples of 23 patients. MethodsWe sequenced the genome-wide exome (WES) and RNA, from which somatic mutations were identified and their expression quantified, respectively. Neoantigen prediction focused on human leukocyte antigens (HLA) crucial to cancer, HLA type I. HLA alleles were predicted from WES data covering the adjacent non-cancerous tissue samples, identifying four alleles that were present in at least 50% of the patients. Neoantigens were deemed potentially immunogenic if their predicted median IC50 binding scores were [&le;]500nM and were expressed [transcripts per million (TPM) >1] in tumor samples. ResultsAn average of 1465 neoantigens covering 10260 genes had [&le;]500nM median IC50 binding score and >1 TPM in the 23 patients and their presence significantly correlated with the somatic mutations (R2 =0.570, P=0.001). Assessing 58 genes reported in the catalog of somatic mutations in cancer (COSMIC, v99) to be commonly mutated in breast cancer, 44 (76%) produced >2 neoantigens among the 23 patients, with a mean of 10.5 ranging from 2 to 93. For the 44 genes, a total of 477 putative neoantigens were identified, predominantly derived from missense mutations (88%), indels (6%), and frameshift mutations (6%). Notably, 78% of the putative breast cancer neoantigens were patient-specific. HLA-C*06:01 allele was associated with the majority of neoantigens (194), followed by HLA-A*30:01 (131), HLA-A*02:01 (103), and HLA-B*58:01 (49). Among the genes of interest that produced putative neoantigens were MUC17, TTN, MUC16, AKAP9, NEB, RP1L1, CDH23, PCDHB10, BRCA2, TP53, TG, and RB1. ConclusionsThe unique neoantigen profiles in our patient group highlight the potential of immunotherapy in personalized breast cancer treatment as well as potential biomarkers for prognosis. The unique mutations producing these neoantigens, compared to other populations, provide an opportunity for validation in a much larger sample cohort.

Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and high molecular heterogeneity. In this study, we performed a genome-wide analysis of copy number variations (CNVs) using high-density microarrays in tumor tissue (TUM), tumor adjacent tissue (ADJ), and leukocytes (LEU) from five Mexican TNBC patients. We identified both unique and shared CNVs across tissues, including alterations in key chromosomal regions such as 1q23.3, 1q32.1, and 8q24.3, which harbor oncogenes like MYC, MCL1, and BCL9. Losses in 6q25.2 affecting ESR1 were also detected. CNVs were enriched in genes related to the Hallmarks of Cancer, with TUM samples showing profiles associated with proliferation, metastasis, and immune evasion; ADJ samples with growth suppression; and LEU samples with genomic instability. Pathway enrichment analyses revealed disrupted functions in DNA repair, extracellular matrix organization, and TP53 signaling in TUM. Notably, EGFR, ERCC4, and HSP90AB1 emerged as central nodes in interaction networks and may serve as markers or therapeutic targets. This is the first CNV profiling study of its kind in TNBC from Mexican patients, highlighting the importance of including underrepresented populations in genomic research to uncover distinct molecular signatures and potential diagnostic or therapeutic avenues. ImplicationsMolecular signatures of breast cancer (BC), predicted bioinformatically, involve common and distinct CNV-Hallmarks of Cancer genes, which are suitable candidates for screening as potential BC markers.

Structured AbstractO_ST_ABSPurpose/ObjectivesC_ST_ABSThe role of postmastectomy radiotherapy (PMRT) in patients with pathologic N1 (pN1) breast cancer, including triple-negative breast cancer (TNBC), remains controversial in the era of modern systemic therapy. We evaluated the association between PMRT and recurrence-free survival (RFS) and overall survival (OS) and identified prognostic factors in a contemporary single-institution pN1 cohort. Materials/MethodsWe retrospectively reviewed female patients with pT1-2N1M0 breast cancer treated with mastectomy between 2016 and 2022. RFS and OS were estimated using Kaplan-Meier methods and compared by PMRT status with log-rank testing. Univariable Cox proportional hazards models assessed associations between clinical factors--including tumor laterality, receptor subtype (TNBC vs non-TNBC), nodal burden, and adjuvant therapies--and survival outcomes, with subgroup analyses by PMRT status and receptor subtype. ResultsFifty-seven patients were included; 22 (38.6%) received PMRT. With a median follow-up of 85 months, PMRT was not associated with improved RFS (median 133 vs 120 months; p=0.256) or OS (not reached vs 195 months; p=0.154). Hormone therapy was significantly associated with improved RFS (HR 0.43; p=0.026) and OS (HR 0.13; p=0.003), while having 2-3 positive lymph nodes predicted worse RFS (HR 2.86; p=0.007). No significant differential benefit from PMRT was observed in patients with TNBC or non-TNBC disease. ConclusionsPMRT was not associated with a survival benefit in this pN1 cohort, including patients with TNBC. Interpretation is limited by modest sample size and statistical power. Outcomes appeared driven by tumor biology, nodal burden, and systemic therapy, supporting individualized PMRT decision-making.

BackgroundBoth neoadjuvant chemotherapy and endocrine therapy only result in trivial pathological complete response rates and moderate objective response rates (ORR) in hormone receptor (HR)-positive, human epidermal growth factor receptor-2 (HER2)-negative breast cancer, more promising alternatives are urgently needed. With proven synergistic effect of cyclin dependent kinase 4/6 (CDK4/6) inhibitor and radiotherapy in preclinical studies, this pilot study aimed to explore the efficacy and safety of neoadjuvant stereotactic body radiation therapy (SBRT) followed by dalpiciclib and exemestane in HR-positive, HER2-negative breast cancer. MethodsThis was a single-arm, non-controlled prospective pilot study. Treatment-naive patients with unilateral HR-positive, HER2-negative breast cancer received neoadjuvant radiotherapy (24Gy/3F) followed by dalpiciclib and exemestane for 6 cycles. The primary endpoint was the proportion of patients with residual cancer burden (RCB) score of 0-I. Key secondary endpoints included ORR, breast-conservation rate, biomarker analysis, and safety. ResultsAll 12 enrolled patients completed the study treatment and surgery. Two (16.7%) of them achieved the RCB 0-I with the ORR of 91.7% (11/12). Analyses of tumor specimens showed significant increase of infiltrating T cells rather than alteration of PD-L1 positive immune cells. The most common grade 3 adverse events (AEs) were neutropenia (66.7%) and leukopenia (25.0%), but no grade 4-5 AE or death occurred. ConclusionsOur results suggested neoadjuvant SBRT followed by dalpiciclib and exemestane are effective and tolerable, and provides novel insights for the neoadjuvant treatment of HR+/HER2-breast cancer, which may be considered as a feasible option for patients with HR-positive, HER2-negative breast cancer.

BackgroundGastric cancer (GC) constitute a significant cause of cancer-related mortality worldwide, with metastatic patterns including hematogenous, peritoneal, and ovarian routes. Although GC gene expression patterns have been extensively researched, the metastasis-specific gene expression landscape remains largely unexplored. MethodsWe undertook a whole transcriptome sequencing analysis of 66 paired primary and metastatic (hematogenous, peritoneal, or ovarian) GC tumors from 14 patients. Public databases including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) was used for validation. Single-cell RNA sequencing (scRNA-seq) of four ascites from serosa positive GC patients and five primary tumors by layer (superficial and deep) were analyzed. ResultsThrough differential expression analysis between paired primary and metastatic tumors by routes identified 122 unique metastasis-specific epithelial-mesenchymal transition (msEMT) genes. These genes demonstrated varying expression patterns depending on the metastatic route, suggesting route-specific molecular mechanisms in GC metastasis. High expression of msEMT genes in primary tumors was associated with more frequent CDH1 mutations, the genomically stable subtype, and poor prognosis in TCGA GC cohort. This association was further corroborated by poor prognosis and high predictive performance for peritoneal/ovarian recurrence in two independent cohorts (GSE66229; n=300, GSE84437; n=433). scRNA-seq analysis of five primary tumors (GSE167297) and four independent ascites samples from GC patients revealed that msEMT genes were predominantly expressed in diverse fibroblast sub-populations, rather than cancer cells. ConclusionsThis study illuminates the route-specific mechanisms and underlines the significance of msEMT genes and cancer-associated fibroblasts in peritoneal metastasis of GC.

IntroductionDespite rapidly improving therapeutics, challenges remain in treatment of advanced breast cancer. Vinorelbine, a semisynthetic vinca alkaloid, is effective and well-tolerated in breast cancer treatment. The combination of vinorelbine and platinum-combination is a well-tolerated but underreported chemotherapy regimen. Bevacizumab, a VEGF-neutralizing antibody, has shown efficacy in HER2-negative metastatic breast cancer (mBC) when combined with chemotherapy. In this study we aim to investigate the clinical and molecular effects of vinorelbine-platinum in heavily pretreated HER2-negative mBC, as well as the role of addition of bevacizumab. Material and methodsWe conducted a retrospective study at Taipei Veterans General Hospital to evaluate the effectiveness of the vinorelbine-platinum regimen in heavily pretreated HER2-negative mBC patients from 2016 to 2020, with a portion of patients receiving additional bevacizumab. To model the molecular perturbations at a cellular level, transcriptional profiling of a triple negative breast cancer cell line treated with cisplatin-vinorelbine was done by RNA-sequencing. ResultsThe cohort included 54 patients. 50% of the patients received [&ge;] 5 lines of systemic treatment in the metastatic setting. All the patients had received anthracyclines and taxane. In patients treated with vinorelbine-platinum combination, the median progression-free survival (PFS) and overall survival (OS) were 2.3 and 7.3 months, respectively. With bevacizumab, median PFS improved to 4.1 months. Objective response rate (ORR) and disease control rate (DCR) without bevacizumab were 11.1% and 27.7%, respectively, improving to 25% and 83.3% with bevacizumab. Adverse events occurred in 37.0% of patients, with no grade IV events reported. Transcriptional profiling revealed significant downregulation of MAPK pathway, angiogenesis, and growth factor signaling related genes. ConclusionThe vinorelbine-platinum regimen, particularly with bevacizumab, shows efficacy even in heavily pretreated HER2-negative metastatic breast cancer patients. Molecular analyses of treated cells highlight potential targets and mechanisms of action, providing a basis for future therapeutic strategies.

PurposeNational guidelines recommend next generation sequencing (NGS) of tumors in patients diagnosed with metastatic prostate cancer (mPCa) to identify potential actionable alterations. We sought to describe the spectrum and frequency of alterations in PCa-related genes and pathways, as well as associations with self-identified race/ethnicity, and overall survival in US Veterans. Patients and MethodsThis retrospective cohort study included Non-Hispanic Black (NHB) and Non-Hispanic white (NHW) Veterans with mPCa who obtained NGS through the Veterans Affairs National Precision Oncology Program. 45 genes in seven canonical or targetable mPCa pathways were evaluated in addition to TMB and MSI status. Multivariable logistic regression evaluated associations between race/ethnicity and genomic alteration frequencies. Cox proportional hazards models were used to determine associations between race/ethnicity, specific gene/pathway alteration, and overall survival. Results5,015 Veterans with mPCa who had NGS conducted were included (1,784 NHB, 3,231 NHW). NHB Veterans were younger, had higher PSA at diagnosis, were less likely to report Agent Orange exposure, and resided in more deprived neighborhoods compared to NHW Veterans. Nine of the top ten most commonly altered genes were the same in NHB v NHW Veterans; however, the frequencies of alterations varied by race/ethnicity. NHB race/ethnicity was associated with higher odds of genomic alterations in SPOP (OR 1.7 [1.2-2.6]) as well as immunotherapy targets (OR 1.7 [1.1-2.7]) including MSI high status (OR 3.1 [1.1-9.4]). Furthermore, NHB race/ethnicity was significantly associated with lower odds of genomic alterations in the AKT/PI3K pathway (OR 0.6 [0.4-0.7]), AR axis (OR 0.7 [0.5-0.9]), and tumor suppressor genes (OR 0.7 [0.5-0.8]). Cox proportional hazards modelling stratified by race/ethnicity demonstrated alterations in tumor suppressor genes including TP53 were associated with shorter OS in both NHB (HR 1.54 [1.13-2.11] and NHW individuals (HR 1.52 [1.25-1.85]). ConclusionIn the equal access VA healthcare setting, Veterans undergoing NGS for mPCa exhibited differences in alteration frequencies in both actionable and non-actionable pathways that may be associated with survival. This analysis affirms the utility of genomic testing for identifying candidates irrespective of race/ethnicity for precision oncology treatments, which could contribute to equitable outcomes in patients with mPCa.

BackgroundDespite chemo-immunotherapy has been applied to the neoadjuvant treatment of non-small cell lung cancer (NSCLC), the impacts of dosage and the order of medication on treatment efficacy and safety remain largely unexplored. We originally designed an exploratory study to investigate the efficacy and safety of reduced-dose chemotherapy combined with delayed immunotherapy as well as the dynamic changes of circulating tumor DNA (ctDNA) and T cell receptor (TCR) during the therapy. MethodsPatients with clinical stage IIA to IIIA resectable NSCLC were treated with 2 cycles of reduced-dose platinum-based chemotherapy on day 1 combined with immunotherapy on day 5. The same postoperative modified adjuvant therapy regimen was administered for 2 cycles. Plasma samples at different time-points were collected and performed with T cell receptor (TCR) and circulating tumor DNA (ctDNA) sequencing. Results38 patients received modified chemo-immunotherapy. The proportion of patients exhibiting complete response and partial response was 5.3% and 68.4%, respectively. The confirmed objective response rate was 73.7%. Radiological downstaging was achieved in 39.5%. Major pathologic response and complete pathologic response were observed in 47.4% and 31.6% of patients, respectively. Only one patient experienced grade 3 adverse event. Further analyses revealed that this modified chemo-immunotherapy led to the expansion of predominant TCR clones and reduction of tumor burden after the first cycle of chemotherapy. ConclusionThe promising clinical efficacy and low side effects of modified neoadjuvant chemo-immunotherapy position it as a prospective and innovative strategy for NSCLC. Trial registration: Registration Number: ChiCTR2000033092

Cancer survivors are at an increased risk of cardiovascular disease (CVD) compared to the general population. Here, we evaluated the impact of somatic mosaic chromosomal alterations (mCAs) on death of CVD causes, coronary artery disease (CAD) causes, from cancer, and of any cause in patients with a cancer diagnosis within the UK Biobank (n=48 919). mCAs were derived from DNA genotyping array intensity data and long-range chromosomal phase inference from participants. Overall, 10 070 individuals (20.6%) carried [&ge;]1 mCA clone. In adjusted analyses, mCA was associated with an increased risk of death of CAD causes (hazard ratio [HR]: 1.37, 95% confidence interval [CI]: 1.09-1.71, P=0.006), from cancer (HR: 1.06, 95% CI: 1.00-1.11, P=0.041), and death of any cause (HR: 1.07, 95% CI: 1.02-1.12, P=0.005). Among cancer survivors, carriers of any mCA are at an increased risk of death of CAD causes and of any cause as compared to non-carriers.

BackgroundBoth FLOT and SOX neoadjuvant regimens are widely used for locally advanced gastric cancer; however, direct head-to-head survival data to guide optimal treatment selection are lacking. MethodsWe conducted an open-label, randomized, phase 2 trial (NCT03636893) at a single center in China. Patients with locally advanced gastric cancer (cT3-4b, cN1-3, cM0) were randomized to receive neoadjuvant FLOT (four cycles) or SOX (three cycles) before D2 gastrectomy. We report the long-term survival outcomes with 5-year follow-up in 74 randomized patients through May 2025. ResultsThe first prospective comparison demonstrated remarkable outcomes for both regimens. With median follow-up of 65.7 months, median overall survival exceeded 5 years in both groups: 61.5 months (95% CI: not reached) for FLOT versus 67.8 months (95% CI: 25.7-109.9) for SOX, with no significant difference (HR 1.101, 95% CI: 0.595-2.036, p=0.759). Disease-free survival was equivalent (23.0 vs 25.5 months, HR 1.060, p=0.842). Clinicopathological factors proved to be more prognostic than regimen choice: complete/subtotal tumor regression achieved 80.5-month survival versus 47.6 months for partial response (p=0.017), whereas gastrectomy type emerged as the strongest independent predictor (HR 3.619 for total vs. partial gastrectomy, p=0.010). Both regimens demonstrated favorable safety profiles with manageable toxicity. ConclusionsThis study establishes equivalent long-term survival between the FLOT and SOX regimens. With both achieving 5-year survival, treatment selection should prioritize patient factors, institutional experience, and practical considerations, rather than expected survival differences. Optimizing the pathological response and surgical approach appears more critical than specific regimen choice. FundingThis research received no specific grant funding.

BackgroundPyrotinib, a pan-HER tyrosine kinase inhibitor, demonstrates efficacy in the treatment of HER2-positive breast cancer. However, the frequent occurrence of treatment-emergent diarrhea necessitating discontinuation, impacts patient outcomes. MethodsIn this multicenter, open-label, phase II PHAEDRA study enrolling early stage HER2-positive patients for postoperative treatment with nab-paclitaxel and pyrotinib, 120 patients were included in a sub-study and randomly divided into two groups to receive 21 days and 42 days of loperamide for primary prophylaxis of diarrhea, followed by as-needed usage. The primary outcome was the incidence of grade [&ge;]3 diarrhea. ResultsFifty-eight patients in the 21-day group and 59 patients in the 42-day group received at least one dose of pyrotinib. With a median follow-up of 12.1 months, all patients experienced diarrhea of any grade, with grade [&ge;]3 events in 39.7% of the 21-day group and 42.4% of the 42-day group (relative risk: 0.94; 95% confidence interval: 0.61-1.45). The most common treatment-emergent adverse events, other than diarrhea, were hypoesthesia, vomiting, nausea, and rash, mostly grade 1-2, except for one patient with a grade [&ge;]3 decreased neutrophil count in each group. ConclusionNo significant differences were observed between 21-day and 42-day loperamide durations in preventing grade [&ge;]3 diarrhea. Considering the economic cost and patient compliance, 21-day loperamide prophylaxis might represent a more pragmatic and appropriate approach for clinical application. Trial registration: ClinicalTrials.gov, NCT04659499

IntroductionBreast cancer (BC) is one of the most common cancers globally. Genetic testing can facilitate screening and risk-reducing recommendations, and inform use of targeted treatments. However, genes included in testing panels are from studies of European-ancestry participants. We sequenced Hispanic/Latina (H/L) women to identify BC susceptibility genes. MethodsWe conducted a pooled BC case-control analysis in H/L women from the San Francisco Bay area, Los Angeles County, and Mexico (4,178 cases and 4,344 controls). Whole exome sequencing was conducted on 1,043 cases and 1,188 controls and a targeted 857-gene panel on the remaining samples. Using ancestry-adjusted SKAT-O analyses, we tested the association of loss of function (LoF) variants with overall, estrogen receptor (ER)-positive, and ER-negative BC risk. We calculated odds ratios (OR) for BC using ancestry-adjusted logistic regression models. We also tested the association of single variants with BC risk. ResultsWe saw a strong association of LoF variants in FANCM with ER-negative BC (p=4.1x10-7, OR [CI]: 6.7 [2.9-15.6]) and a nominal association with overall BC risk. Among known susceptibility genes, BRCA1 (p=2.3x10-10, OR [CI]: 24.9 [6.1-102.5]), BRCA2 (p=8.4x10-10, OR [CI]: 7.0 [3.5-14.0]), and PALB2 (p=1.8x10-8, OR [CI]: 6.5 [3.2-13.1]) were strongly associated with BC. There were nominally significant associations with CHEK2, RAD51D, and TP53. ConclusionIn H/L women, LoF variants in FANCM were strongly associated with ER-negative breast cancer risk. It previously was proposed as a possible susceptibility gene for ER-negative BC, but is not routinely tested in clinical practice. Our results demonstrate that FANCM should be added to BC gene panels.

PurposeCirculating-tumor DNA (ctDNA) is an emerging, minimally invasive diagnostic and prognostic biomarker for patients receiving a variety of cancer therapies. Comprehensive and robust longitudinal monitoring of ctDNA can provide an understanding of tumor burden, heterogeneity, and response or resistance to treatment. Experimental DesignctDNA of 28 metastatic cancer patients receiving an individualized neoantigen-directed immunotherapy was monitored longitudinally, up to two years, using a unique hybrid next generation sequencing assay targeting tumor-informed and tumor-naive variants. Patient-specific panels were designed targeting an average of 144 variants per patient. A tumor-naive universal panel was also designed for inclusion with patient-specific panels to monitor recurrently mutated tumor hotspots (e.g., KRAS and TP53) and genes implicated in immunotherapy resistance (B2M, TAP1/2). ResultsAnalytical characterization of the assay established linearity with a mean variant allele frequency (VAF) [&ge;]0.049%, and a variant-level limit of detection (LOD95) of 0.12%. Tumor-informed variants were detected in 26/28 patients, and de novo variants were observed in 25/28 patients. HLA LOH was also observed. Longitudinal ctDNA data provided key insights into patients responses to vaccine treatment. ConclusionsThe hybrid design of the ctDNA monitoring assay provides the sensitivity and specificity required for evaluating patient samples undergoing individualized therapy. It provides an improved capability to understand patient response to experimental therapies and further supports the utility of ctDNA as a cancer biomarker.

Histologically normal mammary tissue from breast cancer patients can harbor significant genetic alterations. We analyzed the spectrum of DNA variants in 408 matched histologically normal tissue and tumors from 77 poor-prognosis patients, 49 patients recruited without prognosis bias, and mammary gland samples from 15 non-cancerous individuals. Whole exome sequencing revealed a higher prevalence of pathogenic post-zygotic variants in cancer-associated genes: AKT1, PIK3CA, PTEN, TBX3, and TP53, affecting poor-prognosis patients (29%), compared to 12.5% in those without prognosis criteria (p=0.0008578). PIK3CA variants were recurrent across patients, while TP53 variants were restricted to those with adverse prognoses. Duplex sequencing detected low-frequency pathogenic PIK3CA and TP53 variants in distant normal tissues of poor-prognosis patients. Disease recurrence significantly reduced survival rates, with poor prognosis patients experiencing higher mortality within 24 months (p=0.0088), further worsened by the presence of pathogenic post-zygotic variants. These findings highlight the importance of genetic monitoring even in microscopically normal mammary tissue.