A genomic mutation spectrum of collecting duct carcinoma in the Chinese population

Background Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In this study, we aimed to identify the genomic mutation spectrum of CDC in the Chinese population. Methods Whole-exome sequencing was performed using the Illumina Novaseq™ 6000 platform. MuTect2 detects single-nucleotide variants (SNVs) and small scale insertions/deletions (INDELs). The identified mutations were annotated with ANNOVAR and validated by Sanger sequencing. Control-FREEC was used to detect copy number variation (CNV), and GISTIC was applied to detect frequently mutated altered regions. These data were compared with associated The Cancer Genome Atlas cohorts. Results Ten normal-matched CDC patients were included. The mean tumour mutation burden was 1.37 Mut/Mb. Six new recurrent somatic mutated genes were identified, including RBM14, MTUS1, GAK, DST, RNF213 and XIRP2 (20% and 2 of 10, respectively), and validated by Sanger sequencing. In terms of common mutated genes, SETD2 was altered in both CDC and other RCC subtypes but not in bladder urothelial carcinoma (BLCA); CDKN2A was a driver gene in both CDC (SNV: 10%, 1 of 10) and BLCA but not in other RCC subtypes. Next, 29 amplifications and 6 deletions of recurrent focal somatic CNVs were identified by GISTIC2.0, which displayed differences from kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP) and BLCA cohorts. Of note, CDKN2A (CNV alteration: 30%, 3 of 10) and CDKN2A-AS1 were the only overlapping genes of these four cohorts. Importantly, the CDKN2A mutation in our cohort differed from previous studies in urinary carcinomas. Moreover, CDKN2A-altered cases had significantly worse overall survival than wild-type cases in both KIRC and KIRP cohorts. In addition, the most frequently altered genomic pathway of our CDC cohort was the CDKN2A-mediated p53/RB1 pathway. Conclusions Our study offers the first genomic spectrum of the Chinese population with CDC, which differs from that of the Western population. The altered CDKN2A-mediated p53/RB1 pathway might provide new insight into potential therapeutic targets for CDC patients.

Role of Resin Microsphere Y90 Dosimetry in Predicting Objective Tumor Response, Survival and Treatment Related Toxicity in Surgically Unresectable Colorectal Liver Metastasis: A Retrospective Single Institution Study

Purpose: To Evaluate the correlation between tumor dosimetric parameters with objective tumor response (OR) and overall survival (OS) in patients with surgically unresectable colorectal liver metastasis (CRLM) undergoing resin-based Ytrrium-90 selective internal radiation therapy (Y90 SIRT). Materials and Methods: 45 consecutive patients with CRLM underwent resin-based Y90 SIRT in one or both hepatic lobes (66 treated lobes total). Dose volume histograms were created with MIM Sureplan® v.6.9 using post-treatment SPECT/CT. Dosimetry analyses were based on the cumulative volume of the five largest tumors in each treatment session and non-tumoral liver (NTL) dose. Receiver operating characteristic (ROC) curve was used to evaluate tumor dosimetric factors in predicting OR by Response Evaluation Criteria for Solid Tumors at 3 months post-Y90. Additionally, ROC curve was used to evaluate non-tumoral liver dose as a predictor of grade ≥ 3 liver toxicity and radioembolization induced liver disease (REILD) 3 months post Y90. To minimize for potential confounding demographic and clinical factors, univariate and multivariate analysis of survival with mean tumor dose as one of the factors were also performed. Kaplan-Meier estimation was used for OS analysis from initial Y90 SIRT. Results: 26 out of 45 patients had OR with a median OS of 17.2 months versus 6.8 months for patients without OR (p < 0.001). Mean tumor dose (TD) of the five largest tumors was the strongest predictor of OR with an area under the curve of 0.73 (p < 0.001). Minimum TD, and TD to 30%, 50%, and 70% of tumor volume also predicted OR (p’s < 0.05). Mean TD ≥ 100 Gy predicted a significantly prolonged median OS of 19 vs. 11 months for those receiving TD < 100 Gy (p = 0.016). On univariate analysis, mean TD < 100 Gy, presence of any genomic mutation, presence of MAPK pathway mutation, bilobar hepatic metastases and diffuse metastatic disease (>10 lesions per liver lobe) were found to be predictors of shorter median OS. On multivariate analysis, mean TD < 100 Gy, presence of any genomic mutation, and diffuse hepatic metastatic disease were found to be independent predictors of shorter OS. Overall, six (13.3%) patients developed grade ≥ 3 liver toxicity post Y90 of whom two (4.4%) patients developed REILD. No dose threshold predicting grade ≥ 3 liver toxicity or REILD was identified. Conclusions: Mean TD ≥ 100 Gy in patients with unresectable CRLM undergoing resin-based Y90 SIRT predicts OR and prolonged OS.

Effect of Three Types of Ion Beam Irradiation on Gerbera (Gerbera hybrida) In Vitro Shoots with Mutagenesis Efficiency

Gerbera in vitro shoots were irradiated using three types of ion beams with different line energy transfers (LETs) to investigate the effective LET and absorbed doses for mutagenesis. Furthermore, genomic mutation analyses were conducted on the obtained mutants. Survival rate analysis showed a lower lethal dose 50% (LD50) with ion beams with higher LETs. Trait/morphological mutations exhibited changes in the color and shape of petals and male sterility. Irradiation conditions with the highest growth change and trait/morphological mutation rates in each ion were C irradiation at 10 Gy, Ar irradiation at 5 Gy, and Fe irradiation at 5 Gy, with a range of absorbed dose of around LD50 to about 10 Gy lower. The highest trait/morphological mutation rate was 14.1% with Ar irradiation at 5 Gy, which was one of the criteria for ion beam irradiation of gerbera in vitro shoots. Furthermore, the genomic mutation in the flower color, petal shape, and male sterile mutants were confirmed by genotype analysis using Genotyping by Random Amplicon Sequencing-Direct technology. This is the first study to report the efficient production of gerbera mutants that could be analyzed. Our findings may lead to more efficient gerbera mutant production and analysis technology.

A 5-Genomic Mutation Signature Can Predict the Survival for Patients With NSCLC Receiving Atezolizumab

BackgroundAt present, there is a lack of studies focusing on the survival prediction of patients with non-small cell lung cancer (NSCLC) receiving atezolizumab in light of gene mutation characteristic.MethodsPatients with NSCLC receiving atezolizumab from the OAK study were defined as the training group. LASSO Cox regressions were applied to establish the gene mutation signature model to predict the overall survival (OS) rate of the training group. NSCLC patients receiving atezolizumab from the POPLAR study were defined as the testing group to validate the gene mutation signature model. In addition, we compared the OS rate between patients receiving atezolizumab and docetaxel classified according to their risk score based on our gene mutation signature model.ResultsWe successfully established a 5-genomic mutation signature that included CREBBP, KEAP1, RAF1, STK11 and TP53 mutations. We found it was superior to the blood tumor mutation burden (bTMB) score and programmed death ligand 1 (PDL1) expression in the prediction of the OS rate for patients receiving atezolizumab. High-risk patients receiving atezolizumab had a worse OS rate compared with low-risk patients in the training (P = 0.0004) and testing (P = 0.0001) groups. In addition, low-risk patients using atezolizumab had a better OS rate compared with those in use of docetaxel for the training (P &lt;0.0001) and testing groups (P = 0.0095). High-risk patients of the training group (P = 0.0265) using atezolizumab had a better OS rate compared with those using docetaxel. However, the OS difference between atezolizumab and docetaxel was not found in high-risk patients from the testing group (P = 0.6403). Multivariate Cox regression analysis showed that the risk model in light of 5-genomic mutation signature was an independent prognostic factor on OS for patients receiving atezolizumab (P &lt;0.0001). In addition, significant OS benefit could only be found in low-risk patients receiving atezolizumab compared with docetaxel (P &lt;0.0001).ConclusionsThe 5-genomic mutation signature could predict OS benefit for patients with NSCLC receiving atezolizumab. Therefore, the establishment of the 5-genomic mutation panel will guide clinicians to identify optimal patients who could benefit from atezolizumab treatment.

Genomic profiling of Chinese esophageal squamous cell carcinoma patients and difference of genomic mutation between Chinese and American cohorts.

e16108 Background: Esophageal squamous cell carcinoma (ESCC) remains an aggressive malignancy and most patients are diagnosed at advantage stage with limited treatments. Large amount of evidence has demonstrated that immune biomarkers such as PD-l/PD-L1 and tumor mutational burden (TMB) are associated with clinical outcomes and disease prognosis. Methods: A total of 475 ECSS patients enrolled in this study. Deep sequencing of 450 cancer genes performed on formalin-fixed paraffin-embedded tumor tissues and matched blood. Results: Genomic mutation landscape indicated the top five mutated genes are TP53 (95.0%), CCND1 (42%), FGF3 (42%), FGF19 (41%), FGF4（41%. We found that CCHD2, FOXL2 and PIK3CA were tumor-driver genes in 475 ECSS patients. BCL6 ( p< 0.02), CCND1 ( p< 0.03), FGF12 ( p< 0.04), FGF19 ( p< 0.04), FGF3 ( p< 0.02) and FGF4 ( p< 0.05) mutations are significantly associated with high expression of PD-L1 Moreover, we found that BCL6 ( p< 0.04), BRD4 ( p< 0.03), EP300 ( p< 0.03), HGF ( p< 0.02), KMT2C ( p< 0.005), KMT2D ( p< 0.04), MET ( p< 0.006), NSD1 ( p< 0.04), PBRM1 ( p< 0.003), PTCH1 ( p< 0.01), SPEN ( p< 0.006), SPTA ( p< 0.02), ZHF750 ( p< 0.004), TP53 ( p< 0.01) mutation are significantly associated with high TMB as well. The cutoff for TMB is set for 6.9 mut/Mb. The target gene analysis indicated that over half of Chinese ECSS patient might benefit from gene target therapy. By comparison between Chinese and TCGA cohorts, EBFR ( p< 0.05), FGRF1 ( p< 0.05) and CDKN2A ( p< 0.001) have significantly mutated frequency, which indicated the gene mutated profiling is significantly different between Chinese and American ECSS patients. Conclusions: This study identified certain gene alteration associated with PD-L1 and TMB status. It is necessary to conduct large clinical study to identify biomarker for evaluation the efficacy of novel adjunct immunochemotherapy.

The complexity of genomic mutation dictates the prognosis of acute leukemia with ambiguous lineage

Acute leukemia with ambiguous lineage (ALAL) is a rare and highly aggressive malignancy with limited molecular characterization and therapeutic recommendations. In this study, we retrospectively analyzed 1635 acute leukemia cases in our center from January 2012 to June 2018.The diagnose of ALAL was based on either EGIL or 2016 WHO criteria, a total of 39 patients were included. Four patients diagnosed as acute undifferentiated leukemia (AUL) by both classification systems. The mutations detected in bi-phenotypic acute leukemia enriched in genes related to genomic stability and transcriptional regulation; while AUL cases frequently mutated in genes involved in signaling pathway. Survival analysis of all patients suggested that the prognosis of ALAL was independent of immunophenotype, chromosome karyotype, treatment, but significantly associated with the mutation complexity, also termed numbers of the mutations carried by each patient (Log rank p = 0.009 for progression-free survival [PFS] and Log rank p = 0.047 for overall survival [OS], respectively). Similar results were obtained when the WHO diagnostic system were applied (Log rank p < 0.001 for both PFS and OS). Among these patients, those excluded by WHO criteria had even worse clinical outcome than the patients included (Log rank p = 0.023 for PFS and Log rank p = 0.031 for OS). Collectively, the complexity of genomic mutation of ALAL patients is significantly associated with the clinical outcomes. The rationality and clinical applicability of the diagnostic criteria of WHO system need to be evaluated by more large-scale clinical studies.

Comprehensive analysis of genomic mutation signature and tumor mutation burden for prognosis of intrahepatic cholangiocarcinoma

Background Intrahepatic cholangiocarcinoma (iCCA) is a highly lethal malignancy of the biliary tract. Analysis of somatic mutational profiling can reveal new prognostic markers and actionable treatment targets. In this study, we explored the utility of genomic mutation signature and tumor mutation burden (TMB) in predicting prognosis in iCCA patients. Methods Whole-exome sequencing and corresponding clinical data were collected from the ICGC portal and cBioPortal database to detect the prognostic mutated genes and determine TMB values. To identify the hub prognostic mutant signature, we used Cox regression and Lasso feature selection. Mutation-related signature (MRS) was constructed using multivariate Cox regression. The predictive performances of MRS and TMB were assessed using Kaplan–Meier (KM) analysis and receiver operating characteristic (ROC). We performed a functional enrichment pathway analysis using gene set enrichment analysis (GSEA) for mutated genes. Based on the MRS, TMB, and the TNM stage, a nomogram was constructed to visualize prognosis in iCCA patients. Results The mutation landscape illustrated distributions of mutation frequencies and types in iCCA, and generated a list of most frequently mutated genes (such as Tp53, KRAS, ARID1A, and IDH1). Thirty-two mutated genes associated with overall survival (OS) were identified in iCCA patients. We obtained a six-gene signature using the Lasso and Cox method. AUCs for the MRS in the prediction of 1-, 3-, and 5-year OS were 0.759, 0.732, and 0.728, respectively. Kaplan–Meier analysis showed a significant difference in prognosis for patients with iCCA having a high and low MRS score (P < 0.001). GSEA was used to show that several signaling pathways, including MAPK, PI3K-AKT, and proteoglycan, were involved in cancer. Conversely, survival analysis indicated that TMB was significantly associated with prognosis. GSEA indicated that samples with high MRS or TMB also showed an upregulated expression of pathways involved in tumor signaling and the immune response. Finally, the predictive nomogram (that included MRS, TMB, and the TNM stage) demonstrated satisfactory performance in predicting survival in patients with iCCA. Conclusions Mutation-related signature and TMB were associated with prognosis in patients with iCCA. Our study provides a valuable prognostic predictor for determining outcomes in patients with iCCA.