Investigating the genomic alteration improved the clinical outcome of aged patients with lung carcinoma

Background Lung carcinoma is a common geriatric disease. The development of genotype-targeted therapies greatly improved the management of lung carcinoma. However, the treatment for old patients can be more complex than that for young individuals. Results To investigate the benefits of genetic detection for older patients with lung carcinoma, we explored the genomic profiling of 258 patients with more than 55 years using a targeted next generation sequencing, and some of these patients were treated with targeted therapies based on the results of genomic detection. KRAS codon 61 mutations were found in 15.2% KRAS-mutated patients, which tend to be co-existing with other classical activating mutations other than codons 12/13. Acquired EGFR C797S mutations were identified in 2 cases and ERBB2 amplification was identified in 1 case. All these 3 cases developed resistance to EGFR tyrosine kinase inhibitors and showed expected results of their followed therapies. The median progression-free survival and median overall survival of patients treated with molecular targeted therapies were better than those of patients treated with chemoradiotherapy alone. Conclusions Our findings revealed the specific genomic profiles of patients older than 55 years with lung carcinoma and suggested that these old patients have been benefit from the genetic detection, which helped identify druggable mutations and distinguish resistance mechanisms.

Gliosarcoma with Osteosarcomatous Component: A Case Report and Short Review Illustration

Background: Gliosarcoma (GS) represents a rare variant of glioblastoma in the central nervous system, characterized by biphasic histopathological features of gliomatous and sarcomatous components. Here, we present an unusual case of GS, which also demonstrated osteosarcomatous component. Case presentations: The patient underwent gross total resection (GTR) of right temporal lobe lesion. Subsequently received external beam radiation therapy with 60 Gy and chemotherapy, postoperatively. The sarcomatous portion of the typical fibrosarcoma pattern mingled with areas of osteoid structure in this 65-year-old feminine case. The molecular pathological analysis demonstrated IDH1/2 wild-type and MGMT promoter island methylated phenotype. Target Enrichment Sequencing (TES) was performed on the gliomatous and sarcomatous components of the tumor tissues. TERT promoter, RB1, NF1, TP53 mutations and copy number variations (CNVs) on chromosome 7, 10q, 11q, 12, 13, 17 and 22 were observed in gliomatous and fibro-sarcomatous mixed tumor tissue; While we found TERT promoter, RB1, TP53 mutations and CNVs on chromosome 2q, 3q, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19 and 22 in osteosarcomatous tumor tissue. Noteworthy, EGFR amplification was not observed in both gliomatous and sarcomatous tumor tissues. Conclusions: In conclusion, integrated with histopathology, molecular pathology, and genomic alteration analysis, we report a case of GS with an extremely rare histopathologic phenotype of osteosarcomatous differentiation, also suffered lung multi-metastases. Additionally, by reviewing the literature, our study of this unusual differentiation of GS into osteosarcoma provides novel insight into the natural history of GS.

Identification of cross-talk between m6A/m5C regulators and ferroptosis associated with immune infiltration and prognosis in pan-cancer

Although it has been recognized that m6A/5mC methylation and ferroptosis play critical roles in different types of cancers, little is known about the relationship between them. In addition, there is also a growing appreciation that m6A/5mC methylation and ferroptosis may affect immune cell infiltration and activation. This study aimed to reveal the extensive cross-talk between epigenetic modification and ferroptosis. A total of 31 cancer type-specific datasets in TCGA were individually collected by the publicly available web servers for multiple bioinformatic analyses of m6A/5mC regulators and ferroptosis-related genes. Intriguingly, m6A/5mC regulators and ferroptosis-related genes were identified to have considerable global coverage and prognostic significance across multiple cancer types. Moreover, m6A/5mC regulators showed interactive potential with ferroptosis-related genes, and genomic alteration of ferroptosis-related genes coupled with m6A/5mC regulators, at least in pancreatic cancer. Furthermore, m6A/5mC regulators and ferroptosis-related genes were found to be significantly associated with TILs. Finally, m6A/5mC regulators and ferroptosis-related genes exhibited functionally related to each other or co-regulated by TF or non-coding RNA. Together, m6A/5mC methylation and ferroptosis show a wide-ranging connection, and a combination strategy of epigenetic and ferroptosis therapies with ICP inhibitors may benefit more cancer patients in the future.

675 Genomic drivers of large B-cell lymphoma resistance to CD19 CAR-T therapy

BackgroundCD19-directed chimeric antigen receptor-reprogrammed autologous T cells are breakthrough immunotherapies for heavily pretreated patients with diffuse large B-cell lymphoma (DLBCL), but across CAR-19 products, ~60% of patients fail to respond or relapse. Inflammatory markers and clinical factors associate with impaired responses, but tumor-intrinsic resistance drivers are largely undefined.MethodsTo characterize the genomic mechanisms involved resistance to CAR-19, we interrogated whole genome sequencing (WGS) from 28 relapsed/refractory (r/r) aggressive lymphoma patients uniformly treated with axicabtagene ciloleucel (axi-cel).ResultsBecause prognostic factors defined in the frontline treatment setting are largely inapplicable to CAR-19, we leveraged the WGS data, including comparative analyses with untreated DLBCL cases in the Pan-Cancer Analysis of Whole Genomes (PCAWG) (figure 1). In analyses of individual mutated genes, TP53 was significantly enriched (p=0.002) in CAR-19 patients, but did not predict outcome. However, mutations in either NFKBIA or MYC associated with worse PFS after CAR-19 (p=0.04, p=0.025 respectively). We next identified 12 single base substitution (SBS) mutational signatures in our cohort and found presence of APOBEC (SBS2 and SBS13) signatures associated with worse PFS, with 4/5 patients progressing (p=0.03). Copy number analysis by GISTIC2.0 revealed focal deletions of RHOA and RB1 to be significantly enriched in our cohort and independently predicted poor outcome (p=0.0007, p=0.05 respectively). WGS identifies structural variants and complex events. We found chromothripsis, a catastrophic shattering and reassembly of chromosomes, in 39.3% of r/r DLBCL, which was strongly associated with poor CAR-19 outcome, with 9/11 affected cases progressing (p=0.041). Finally, reduced expression (n=3) or genomic alteration (n=3) of CD19 did not associate with poor outcome. One case with durable response contained a sub-clonal CD19 mutation (L174V) previously reported as associated with CAR-19 resistance. These findings demonstrate predominance of CD19-independent resistance and indicate antigen-mediated tumor killing is not the only mechanism of tumor eradication. Genomic complexity appears to promote an immunosuppressive tumor microenvironment (TME), limiting CAR-19 efficacy.ConclusionsLeveraging the resolution of WGS, we observed that markers of genomic complexity (chromothripsis and APOBEC) and specific genomic alterations (RHOA and RB1 deletions) associate with resistance to CAR-19 immunotherapy for aggressive B-cell lymphomas (figure 1). 93.8% of CAR-19 relapsed patients contained at least one or these genomic alterations. Recent patient data demonstrate that an immunosuppressed TME leads to CAR-19 failure. Combining these findings with our genomics findings, successful CAR-19 therapy must overcome the immune-exhausted TME to mobilize the host immune system and eliminate the tumor.Abstract 675 Figure 1Genomic alterations associated with disease progression. (a) The heatmap shows the significant genomic alteration present in at least 4 patients associated with progression after CD19 CAR-T cell therapy. (b) Kaplan-Meier curve of progression free survival with the combination of statistically significant genomic anomalies

Plasma-Based Genotyping in Advanced Solid Tumors: A Comprehensive Review

Molecular genotyping for advanced solid malignancies has transformed the clinical management of patients with metastatic disease. Treatment decisions in a growing number of tumors require knowledge of molecularly driven alterations in order to select optimal targeted therapy. Although genomic testing of tumor tissue is the gold standard for identifying targetable genomic alterations, biopsy samples are often limited or difficult to access. This has paved the way for the development of plasma-based approaches for genomic profiling. Recent advances in the detection of plasma-circulating tumor DNA (ctDNA) have enabled the integration of plasma-based molecular profiling into clinical practice as an alternative or complementary tool for genomic testing in the setting of advanced cancer, to facilitate the identification of driver mutations to guide initial treatment and diagnose resistance. Several guidelines now recommend the use of plasma where tumor tissue is limited to identify a targetable genomic alteration. Current plasma-based assays can evaluate multiple genes in comprehensive panels, and their application in advanced disease will be increasingly incorporated into standard practice. This review focuses on current and future applications of plasma ctDNA-based assays in advanced solid malignancies, while highlighting some limitations in implementing this technology into clinical practice.

Identification of an Immune-Related Prognostic Gene CLEC5A Based on Immune Microenvironment and Risk Modeling of Ovarian Cancer

Objective: To understand the immune characteristics of the ovarian cancer (OC) microenvironment and explore the differences of immune-related molecules and cells to establish an effective risk model and identify the molecules that significantly affected the immune response of OC, to help guide the diagnosis.Methods: First, we calculate the TMEscore which reflects the immune microenvironment, and then analyze the molecular differences between patients with different immune characteristics, and determine the prognostic genes. Then, the risk model was established by least absolute shrinkage and selection operator (LASSO) analysis and combined with clinical data into a nomogram for diagnosis and prediction. Subsequently, the potential gene CLEC5A influencing the immune response of OC was identified from the prognostic genes by integrative immune-stromal analysis. The genomic alteration was explored based on copy number variant (CNV) and somatic mutation data.Results: TMEscore was a prognostic indicator of OC. The prognosis of patients with high TMEscore was better. The risk model based on immune characteristics was a reliable index to predict the prognosis of patients, and the nomogram could comprehensively evaluate the prognosis of patients. Besides, CLEC5A was closely related to the abundance of immune cells, immune response, and the expression of immune checkpoints in the OC microenvironment. OC cells with high expression of CLEC5A increased the polarization of M2 macrophages. CLEC5A expression was significantly associated with TTN and CDK12 mutations and affected the copy number of tumor progression and immune-related genes.Conclusion: The study of immune characteristics in the OC microenvironment and the risk model can reveal the factors affecting the prognosis and guide the clinical hierarchical treatment. CLEC5A can be used as a potential key gene affecting the immune microenvironment remodeling of OC, which provides a new perspective for improving the effect of OC immunotherapy.

Novel genomic alteration in superficial esophageal squamous cell neoplasms in non-smoker non-drinker females

Alcohol consumption and smoking pose a significant risk for esophageal squamous cell neoplasia (ESCN) development in males; however, ESCN is often diagnosed in non-drinking and non-smoking females. The mechanisms underlying these differences remain elusive, and understanding them can potentially identify novel pathways involved in ESCN development. We performed short-read sequencing to identify somatic variants on a cancer panel targeting 409 genes using DNA extracted from the superficial squamous cell carcinoma (ESCC) tissues and adjacent non-neoplastic epithelium (NE), and immunohistochemical staining of the protein encoded by the target gene. All male patients (n = 117) were drinkers or smokers, whereas 45% of the female patients (n = 33) were not. Somatic variants were compared among three age-matched groups: 13 female ESCC patients with smoking and drinking habits (known-risk group, F-KR), 13 female ESCC patients without these habits (unknown-risk group, F-UR), and 27 males with ESCC and smoking and drinking habits (M-KR). In the NE, the frequencies of CDKN2A variants were significantly higher in F-UR than in F-KR and M-KR. In both ESCC and NE, p14ARF was significantly overexpressed in F-UR than in the other groups. In conclusion, CDKN2A might be important in ESCC development, independent of known risk factors.

Case Report: A Pancreatic Ductal Adenocarcinoma Patient With Concurrent Targetable Somatic Novel KANK1-ALK, UPP2-NTRK3 Fusion, and Pathogenetic Germline BRCA Mutation

Pancreatic ductal adenocarcinoma (PDAC) is presently one of the cancers with the worst survival rates. The current treatment options for PDAC are relatively scarce due to insufficient understanding of molecular characteristics and subtypes of PDAC. Based on next-generation sequencing (NGS), we firstly presented a case about a KRAS wild-type pancreatic ductal adenocarcinoma patient harboring a concurrent targetable rare somatic novel KANK1-ALK, UPP2-NTRK3 fusion, and pathogenetic germline BRCA mutation. These two novel fusion statuses were assayed by immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH). Our findings demonstrated that comprehensive and systematic screening of PDAC for actionable genomic alteration may substantially improve the therapeutic prospects for a sizeable fraction of patients with PDAC. To improve the management of PDAC in an era of precision medicine, it is important to identify ALK or NTRK fusion-positive and pathogenic germline mutation subsets of patients who can benefit from targeted therapies.