Genecast (China)

BackgroundMultiple primary lung cancers (MPLCs) present unique clinical difficulties because of their genetically diverse independent tumors, requiring genetic testing to distinguish synchronous primaries from intrapulmonary metastases. While circulating tumor DNA (ctDNA) analysis shows potential for detecting molecular residual disease (MRD), tumor heterogeneity hinders its application. Thus, there is an urgent need to develop specific biomarkers and standardize liquid biopsy protocols to improve monitoring and treatment. The aim of this study was to analyze the clinicopathological characteristics of postoperative MRD-positive stage I non-small cell lung cancer (NSCLC) patients, with a focus on the potential utility of ctDNA in detecting MRD and guiding therapeutic decisions.MethodsTwelve patients with pulmonary nodules were analyzed. Paired tissue and plasma samples underwent genomic profiling via next-generation sequencing (NGS) using validated extraction/library preparation kits, following ethical standards. Rigorous quality controls were implemented to ensure sensitive variant detection.ResultsBoth solitary (n=5) and multiple nodules (n=7) carried EGFR and TP53 mutations. Multiple nodules had significantly higher tumor mutational burden and clonal heterogeneity. Patients with positive MRD showed markedly elevated ctDNA levels, with clonal dynamics indicating increased shedding in multifocal disease.ConclusionsMultifocal lung disease exhibits greater genomic complexity and enhanced ctDNA shedding, supporting its use as a disease-tracking tool. The findings identify actionable signatures for MRD surveillance and guide personalized therapeutic interventions based on observed clonal architectures.

BackgroundNeoadjuvant chemoimmunotherapy does not benefit all non-small cell lung cancer (NSCLC) patients, and reliable biomarkers are urgently needed. We conducted this prospective phase II trial of neoadjuvant chemoimmunotherapy to explore the role of cell-free DNA (cfDNA) features in pathological response assessment.MethodsTotally, 100 patients with stage IIB-IIIB NSCLC were enrolled and treated with neoadjuvant toripalimab plus chemotherapy for at least 2 cycles. Targeted methylation panel sequencing and whole methylome sequencing were conducted on 195 cfDNA samples collected from 60 patients before each treatment cycle (C0, C1) and before surgery (BS), with subsequent calculations of methylation fragment ratio (MFR) and chromosome aneuploid of featured fragment (CAFF) scores, respectively. The correlations between MFR or CAFF and pathological response were evaluated.ResultsFinally, 83 patients underwent surgery, and 54 (65.1%) patients achieved major pathological response (MPR), including 38 (45.8%) with complete pathological response (pCR). The median MFR and CAFF scores in both the MPR and non-MPR groups significantly decreased after the first cycle, and the MPR group maintained low levels before surgery (P < 0.001). According to pre-defined cut-off values, the MFR and CAFF scores were recategorized as low or high status. Patients with low MFR status at BS (74.5% vs. 11.1%, P < 0.001) or low CAFF status at C1 (73.9% vs. 36.4%, P = 0.031) and BS (76.2% vs. 38.9%, P = 0.008) were more likely to achieve MPR than those with high status. Three dynamic patterns were identified: C0 low, C0 high/C1 low, and C0 high/C1 high. These patterns were further divided by BS low or high status, which indicated distinctive MPR rate (C0 low: BS low vs. high 78.9% vs 0%; C0 high/C1 low: BS low vs. high 73.9% vs. 25%; C0 high/C1 high: BS low vs. high 83.3% vs. 0%). An integrative model was constructed by incorporating immune parameters (PD-L1 and CD8 + CD28- T lymphocytes) and cfDNA features (MFR and CAFF) at C1 and BS, achieving an AUC of 0.86 (95% CI 0.80–0.92).ConclusionsDynamic monitoring of cfDNA methylation has potential to predict pathological response of neoadjuvant chemoimmunotherapy in NSCLC.Trial registrationRENAISSANCE study, NCT04606303, initiated on October 27, 2020.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12916-025-04419-x.

e18090 Background: Effective disease control in oral cancer heavily relies on the accurate identification and management of minimal residual disease (MRD). This study investigated the association of ctDNA-based MRD with progression-free survival (PFS), and its potential to predict treatment benefits. Patients and Methods: A prospective cohort study was conducted at Shanghai Ninth People’s Hospital, a tertiary care center involving patients with biopsy-proven squamous cell carcinoma of oral cavity reported between January 2021 and December 2023. Tumor tissues and plasma samples were collected, processed, and sequenced for ctDNA analysis using a 769-gene panel. A tumor-informed strategy, MinerVa (Genecast Biotechnology), was utilized for variants tracking and MRD assessment. ctDNA status was recorded at various time points, including pre-operative, post-operative, and follow-up visits. The primary endpoint of the study was progression-free survival (PFS). Results: As of November 2024, 46 patients were included in the analysis, with a median follow-up period of 297 days. All patients were HPV negative. Eleven (24%) patients experienced disease recurrence, of whom, 3 patients died. Out of 44 patients with post-operative MRD analyzed, 10 (23%) patients were MRD positive. MRD positivity significantly predicted poorer PFS, with a hazard ratio (HR) of 6.07 (95%CI=1.60-22.8, p=0.002) and a negative predictive value (NPV) of 85%. Both MRD and pathological N-stage (pN-stage) were significant predictors of PFS (p=0.002, and p=0.011, respectively). In multivariate analysis, MRD positivity remained an independent predictor of PFS (HR=8.50, p=0.024) even when adjusted for tumor size, pN-stage, and adjuvant treatment regimen. Notably, among post-operative MRD-positive patients, those receiving adjuvant therapy demonstrated significantly better PFS compared to those who did not (HR=5.68, p=0.035). Conversely, adjuvant therapy showed no significant effect in MRD-negative patients (p=0.656). Furthermore, longitudinal analysis of ctDNA in plasma samples collected after surgery but before relapse revealed a positivity rate of 28% (13/46), with the NPV increasing up to 91%. Conclusions : Post-operative ctDNA-based MRD shows promise for identifying disease recurrences and stratifying patients likely to benefit from adjuvant treatment. Continuous MRD assessment during and after adjuvant therapy plays a critical role in disease monitoring and potentially improving clinical outcomes for oral cancers patients. Clinical trial information: NCT05156970 .

Abstract Oligometastatic disease is recognized as an intermediate state between localised and systemically metastasised disease. The diagnosis, treatment and prognosis of oligometastatic disease is currently based mainly on imaging examination. Previous clinical studies indicated that standard systemic therapy followed by radical local therapy was beneficial for survival in tumor patients with oligometastatic disease. However, different clinical outcomes (such as oligopersistant and oligoprogression) were found in synchronous and/or metachronous oligometastatic disease after the same systemic therapy. This report explored potential factors of different outcomes in tumor patients with oligometastatic disease after neoadjuvant immuno-chemotherapy. A lymphoepithelioma-like carcinoma (LELC) case with stage IIIa was synchronous oligometastatic disease, which was treated with neoadjuvant immuno-chemotherapy (four courses of Albumin-Bound Paclitaxel (300 mg), Carboplatin (400 mg) and Durvalumab (500 mg)) and subsequent surgery. Lymph nodes 1R and 4R were considered as oligoprogression and oligopersistant, respectively. Whole exome sequencing results showed that single nucleotide variation (SNV), copy number variation (CNV), tumor mutational burden (TMB), microsatellite instability (MSI), human resource development (HRD) and mutant-allele tumor heterogeneity (MATH) were similar between 1R and 4R samples. Tumor-infiltrating immune cells using a multiplex immunoflourescence histochemistry (mIHC) test revealed that immune checkpoints PD1, PD-L1 and CD39 were high expression and there was a low level of CD8+ T cell in the 4R sample. But levels of CD39+CD8+ and PD-L1+CD8+ T cells were higher in the 1R sample than the 4R sample, suggesting a suppressive tumor immune microenvironment in the 1R oligoprogression lymph node. To demonstrate the result, oligometastatic samples from eight non-small-cell lung cancer (NSCLC) cases with neoadjuvant immuno-chemotherapy and surgery were examined using the mIHC. The results indicated that CD39+CD3+/PD-L1+CD3+/TIM3+CD3+ T cells and/or CD39+CD68+ macrophages in the oligometastatic samples with oligoprogression were high levels. Thus, suppression of tumor-infiltrating immune cells might result in one major factor of different outcomes in oligometastatic disease after neoadjuvant immuno-chemotherapy. Funding Sources: This work was supported by the Wu Jieping Medical Foundation (320.6750.2024-16-16). Citation Format: Peikun Ding, Xiaoxiang Huang, Quanzhou Peng, Kangqi Ren, Longlong Gong, Bin Wang, Lin Yang. Immune suppression of the lymph node microenvironment causes oligoprogression of metastatic cancer after neoadjuvant immuno-chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1597.

Skin cutaneous melanoma (SKCM) is one of the most lethal cancers translating into 75% of skin cancer-related deaths. Despite the advances in SKCM management and treatment strategies, the overall survival of patients remains unsatisfactory due to the metastatic properties of SKCM as well as the absence of effective prognostic biomarkers. Recent studies have shown that overload copper renders accumulation of mitochondrial proteins and fuels a form of cell death at odds with known death mechanisms and is hinged on mitochondrial respiration, the so-called cuproptosis. However, the exact role of cuproptosis in SKCM development and progression is unknown, and painting a clear picture of its functions in SKCM is fraught with challenges. A more systematic investigation is justified. In this study, we were posed to dissect the clout and latent regulatory mechanisms of cuproptosis-related genes (CRGs) in reining in SKCM progression. Also, we identified three CRGs that stood out were used to construct a prognostic model, which could be employed to predict the prognosis of patients with SKCM. Finally, through pan-cancer analysis, we found that the four cuproptosis key genes play a role in multiple tumors, suggesting that cuproptosis may impact tumor progression at the pan-cancer level. Taken together, these findings may not only contribute to the development of treatment strategies but also provide clues for treatment decision-making.

BackgroundDifferent colorectal cancer (CRC) studies rarely report overlapping prognostic genes. This study aimed to investigate the effects of sample size on prognostic genes analysis in CRC.MethodsWe included 418 CRC cases detected by whole-exome sequencing (WES) in the TCGA PanCancer cohort and 931 CRC cases detected by targeted sequencing in the MSK cohort. Prognostic genes analysis was repeated 200 times at each sample size level using a random resampling method.ResultsFor WES data, the number of prognostic genes increased in a power-law with increasing sample size in CRC cases with stage III and IV. This pattern also applied to CRC patients with stage II after the removal of patients with MSI-H or POLE mutations. However, for targeted sequencing data, the number of prognostic genes increased linearly with increasing sample size in CRC cases with stage III and IV. About 550 cases were required for stage IV CRC to reach the plateau of prognostic genes. In both cohorts, the proportion of true prognostic genes relative to sample size was consistent with a binomial distribution, indicating a significant effect of sample size on the reliability of prognostic genes. At the same sample size level, the number of prognostic genes from the WES data was higher than that from the targeted sequencing data, while the reliability of prognostic genes from the WES data was lower.ConclusionThis study shows the relationship between the number of prognostic genes and sample size in CRC and how mutation data affects this relationship. This will contribute to the trial design for prognostic genetic analysis in CRC.

ABSTRACT Small cell carcinoma of the esophagus (SCCE) is a rare and highly malignant type of esophageal cancer with no standard treatment, facing challenges of resistance to conventional therapies. This study presents the cases of one extensive-stage and two limited-stage SCCE patients treated with chemoimmunotherapy. The two limited-stage patients underwent surgery post-treatment and experienced notable and enduring positive responses. This represents the first documented application of neoadjuvant chemoimmunotherapy in limited-stage SCCE patients. Additionally, comprehensive immunohistochemical analysis and whole exome sequencing were performed on the case patients. The findings revealed that infiltration of CD8+ T cells and PD-L1 expression in the SCCE tumor were key factors for favorable responses in SCCE patients receiving chemoimmunotherapy.

Epidermal growth factor receptor (EGFR) is reportedly overexpressed in most esophageal squamous cell carcinoma (ESCC) patients, but anti-EGFR treatments offer limited survival benefits. Our preclinical data showed the promising antitumor activity of afatinib in EGFR-overexpressing ESCC. This proof-of-concept, phase II trial assessed the efficacy and safety of afatinib in pretreated metastatic ESCC patients (n = 41) with EGFR overexpression (NCT03940976). The study met its primary endpoint, with a confirmed objective response rate (ORR) of 39% in 38 efficacy-evaluable patients and a median overall survival of 7.8 months, with a manageable toxicity profile. Transcriptome analysis of pretreatment tumors revealed that neurotrophic receptor tyrosine kinase 2 (NTRK2) was negatively associated with afatinib sensitivity and might serve as a predictive biomarker, irrespective of EGFR expression. Notably, knocking down or inhibiting NTRK2 sensitized ESCC cells to afatinib treatment. Our study provides novel findings on the molecular factors underlying afatinib resistance and indicates that afatinib has the potential to become an important treatment for metastatic ESCC patients.

BackgroundAlthough adjuvant chemotherapy (ACT) is widely used to treat patients with Stage II/III colorectal cancer (CRC), administering ACT to specific patients remains a challenge. The decision to ACT requires an accurate assessment of recurrence risk and absolute treatment benefit. However, the traditional TNM staging system does not accurately assess a patient's individual risk of recurrence.MethodsTo identify recurrence risk‐related genetic factors for Stage II/III CRC patients after radical surgery, we conducted an analysis of whole‐exome sequencing of 47 patients with Stage II/III CRC who underwent radical surgery at five institutions. Patients were grouped into non‐recurrence group (NR, n = 24, recurrence‐free survival [RFS] > 5 years) and recurrence group (R, n = 23, RFS <2 years). The TCGA‐COAD/READ cohort was employed as the validation dataset.ResultsA recurrence‐predictive model (G8plus score) based on eight gene (CUL9, PCDHA12, HECTD3, DCX, SMARCA2, FAM193A, AATK, and SORCS2) mutations and tumor mutation burden/microsatellite instability (TMB/MSI) status was constructed, with 97.87% accuracy in our data and 100% negative predictive value in the TCGA‐COAD/READ cohort. For the TCGA‐COAD/READ cohort, the G8plus‐high group had better RFS (HR = 0.22, p = 0.024); the G8plus‐high tumors had significantly more infiltrated immune cell types, higher tertiary lymphoid structure signature scores, and higher immunological signature scores. The G8plus score was also a predict biomarker for immunotherapeutic in advanced CRC in the PUCH cohort.ConclusionsIn conclusion, the G8plus score is a powerful biomarker for predicting the risk of recurrence in patients with stage II/III CRC. It can be used to stratify patients who benefit from ACT and immunotherapy.