Correlation of tumor mutational burden and treatment outcomes in patients with colorectal cancer

Tumor Mutational Burden From Circulating Tumor DNA Predicts Recurrence of Hepatocellular Carcinoma After Resection: An Emerging Biomarker for Surveillance

OBJECTIVE

Describe the utility of circulating tumor DNA in the postoperative surveillance of hepatocellular carcinoma (HCC).

BACKGROUND

Current biomarkers for HCC like alpha-fetoprotein (AFP) are lacking. Circulating tumor DNA (ctDNA) has shown promise in colorectal and lung cancers, but its utility in HCC remains relatively unknown.

METHODS

Patients with HCC undergoing curative-intent resection from November 1, 2020, to July 1, 2023, received ctDNA testing using the Guardant360 platform. Tumor mutational burden (TMB) is calculated as the number of somatic mutations-per-megabase of genomic material identified.

RESULTS

Forty-seven patients had postoperative ctDNA testing. The mean follow-up was 27 months, and the maximum was 43.2 months. Twelve patients (26%) experienced recurrence. Most (n=41/47, 87.2%) had identifiable ctDNA postoperatively; 55.3% (n=26) were TMB-not detected versus 45.7% (n=21) TMB-detectable. Postoperative identifiable ctDNA was not associated with RFS ( P =0.518). Detectable TMB was associated with reduced RFS (6.9 vs 14.7 mo, P =0.049). There was a higher rate of recurrence in patients with TMB (n=9/21, 42.9%, vs n=3/26, 11.5%, P =0.02). Area under the curve for TMB-prediction of recurrence was 0.752 versus 0.550 for AFP. ROC analysis established a TMB cutoff of 4.8mut/mB for predicting post-operative recurrence ( P =0.002) and RFS ( P =0.025). AFP was not correlated with RFS using the lab-normal cutoff (<11 ng/mL, P =0.682) or the cutoff established by ROC analysis (≥4.6 ng/mL, P =0.494). TMB-high was associated with poorer RFS on cox-regression analysis (hazard ratio=5.386, 95% CI: 1.109-26.160, P =0.037), while microvascular invasion ( P =0.853) and AFP ( P =0.439) were not.

CONCLUSIONS

Identifiable TMB on postoperative ctDNA predicts HCC recurrence and outperformed AFP in this cohort. Perioperative ctDNA may be a useful surveillance tool following curative-intent hepatectomy. Larger-scale studies are needed to confirm this utility and investigate additional applications in HCC patients, including the potential for prophylactic treatment in patients with residual TMB after resection.

A Novel Neutrophil Extracellular Trap Signature Predicts Patient Chemotherapy Resistance and Prognosis in Lung Adenocarcinoma

Chemoresistance is a key obstacle in the long-term survival of patients with locally and advanced lung adenocarcinoma (LUAD). This study used bioinformatic analysis to reveal the chemoresistance of gene-neutrophil extracellular traps (NETs) associated with LUAD. RNA sequencing data and LUAD expression patterns were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, respectively. The GeneCards database was used to identify NETosis-related genes (NRGs). To identify hub genes with significant and consistent expression, differential analysis was performed using the TCGA-LUAD and GEO datasets. LUAD subtypes were determined based on these hub genes, followed by prognostic analysis. Immunological scoring and infiltration analysis were conducted using NETosis scores (N-scores) derived from the TCGA-LUAD dataset. A clinical prognostic model was established and analyzed, and its clinical applications explored. Twenty-two hub genes were identified, and consensus clustering was used to identify two subgroups based on their expression levels. The Kaplan-Meier (KM) curves demonstrated statistically significant differences in prognosis between the two LUAD subtypes. Based on the median score, patients were further divided into high and low N-score groups, and KM curves showed that the N-scores were more precise at predicting the prognosis of patients with LUAD for overall survival (OS). Immunological infiltration analysis revealed significant differences in the abundances of 10 immune cell infiltrates between the high and low N-score groups. Risk scores indicated significant differences in prognosis between the two extreme score groups. The risk scores for the prognostic model also indicated significant differences between the two groups. The results provide new insights into NETosis-related differentially expressed genes (NRDEGs) associated with chemotherapy resistance in patients with LUAD. The established prognostic model is promising and could help with clinical applications to evaluate patient survival and therapeutic efficiency.

Comprehensive analysis reveals TSPEAR as a prognostic biomarker in colorectal cancer

Background: Colorectal cancer (CRC) is one of the most common malignant tumors and has high morbidity and mortality rates. Previous studies have shown that TSPEAR mutations are involved in the development and progression of gastric cancer and liver cancer. However, the role of TSPEAR in CRC is still unclear. Methods: In The Cancer Genome Atlas (TCGA) database, 590 CRC patients with complete survival information were analyzed. We assessed TSPEAR expression in a pan-cancer dataset from the TCGA database. Cox regression analysis was performed to evaluate factors associated with prognosis. Enrichment analysis via the R package "clusterProfiler" was used to explore the potential function of TSPEAR. The single-sample GSEA (ssGSEA) method from the R package "GSVA" and the TIMER database were used to investigate the association between the immune infiltration level and TSPEAR expression in CRC. The R package "maftools" was used to explore the association between tumour mutation burden (TMB) and TSPEAR expression in CRC. CCK-8 assays and cell invasion assays were used to detect the effect of TSPEAR and TGIF2 on the biological behavior of CRC cells. Results: Pan-cancer analysis revealed that TSPEAR was upregulated in CRC tissues compared to normal tissues and that high TSPEAR expression was associated with poorer overall survival (OS) (p=0.0053). The expression of TSPEAR increased with increasing TNM stage, T stage, N stage, and M stage. The nomogram constructed with TSPEAR, age, and TNM stage showed better predictive value than TSPEAR, age, or TNM stage alone. Immune cell infiltration analysis revealed that high expression of TSPEAR was associated with lower immune cell infiltration. Tumor mutation burden (TMB) analysis indicated that high expression of TSPEAR was associated with lower TMB (p=0.005), and high TMB was associated with shorter OS (p=0.02). CCK-8 assays and cell invasion assays indicated that in vitro knockdown of TSPEAR inhibited the proliferation, migration, and invasion of CRC cells. In addition, TSPEAR expression may be regulated by the upstream transcription factor TGIF2. Conclusion: TSPEAR expression was higher in CRC tissues than in normal tissues. Its upregulation was significantly associated with a poor prognosis. Additionally, TSPEAR plays a significant role in tumor immunity and the biological behavior of CRC cells. Thus, TSPEAR may become a promising prognostic biomarker and therapeutic target for CRC patients.

Circulating Tumor DNA in Colorectal Cancer Liver Metastasis: Analysis of Patients Receiving Liver Resection and Transplant

PURPOSE

Liver metastases occur in about 50% of colorectal cancer cases and drive patient outcomes. Circulating tumor DNA (ctDNA) is emerging as a diagnostic, surveillance, and tumor mutational information tool.

METHODS

Patients with colorectal cancer liver metastasis (CCLM) seen in a multidisciplinary liver tumor clinic from January to August 2022 received ctDNA testing on each visit. ctDNA was obtained using the Guardant360 platform. Tumor mutational burden (TMB) is defined as the number of identified mutations per megabase of genome analyzed.

RESULTS

Fifty-two patients had available ctDNA, with 34 (65%) tested preoperatively and 18 (35%) postoperatively; nine patients had sequential pre- and postoperative testing. The median time to test result was 12 days (IQR, 10-13.5). There were a greater number of somatic mutations identified preoperatively (n = 29 v n = 11) and a greater genomic heterogeneity (P = .0069). The mean TMB score was 12.77 in those without pathologic response to cytotoxic therapy and 6.0 in those with pathologic response (P = .10). All nine patients with sequential testing were positive preoperatively, compared with just three (33.3%) postoperatively (P = .0090). Positive postoperative ctDNA was associated with the increased likelihood of disease recurrence after resection (57%) versus negative ctDNA (0%, P = .0419).

CONCLUSION

Routine ctDNA screening in patients with CCLM is logistically feasible. Liver resection and/or transplant may be associated with clearance of detectable ctDNA and a reduction in TMB or genomic heterogeneity. Persistence of ctDNA alterations postresection appears predictive of disease recurrence. Further studies are necessary to confirm these findings, and longitudinal ctDNA testing is needed to monitor changing tumor biology.

Identification of a chemoresistance-related prognostic gene signature by comprehensive analysis and experimental validation in pancreatic cancer

Background

Chemoresistance is a major hurdle to improving the prognosis of pancreatic cancer (PC). This study aimed to identify key genes regulating chemoresistance and develop a chemoresistance-related gene signature for prognosis prediction.

Methods

A total of 30 PC cell lines were subtyped according to gemcitabine sensitivity data from the Cancer Therapeutics Response Portal (CTRP v2). Differentially expressed genes (DEGs) between gemcitabine-resistant and gemcitabine-sensitive cells were subsequently identified. These upregulated DEGs associated with prognostic values were incorporated to build a LASSO Cox risk model for The Cancer Genome Atlas (TCGA) cohort. Four datasets (GSE28735, GSE62452, GSE85916, and GSE102238) from the Gene Expression Omnibus (GEO) were used as an external validation cohort. Then, a nomogram was developed based on independent prognostic factors. The responses to multiple anti-PC chemotherapeutics were estimated by the "oncoPredict" method. Tumor mutation burden (TMB) was calculated using the "TCGAbiolinks" package. Analysis of the tumor microenvironment (TME) was performed using the "IOBR" package, while the TIDE and "easier" algorithms were employed to estimate immunotherapy efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducted to validate the expression and functions of ALDH3B1 and NCEH1.

Results

A five-gene signature and a predictive nomogram were developed from six prognostic DEGs, including EGFR, MSLN, ERAP2, ALDH3B1, and NCEH1. Bulk and single-cell RNA sequencing analyses indicated that all five genes were highly expressed in tumor samples. This gene signature was not only an independent prognostic factor but also a biomarker forecasting chemoresistance, TMB, and immune cells. In vitro experiments suggested that ALDH3B1 and NCEH1 were involved in PC progression and gemcitabine chemoresistance.

Conclusion

This chemoresistance-related gene signature links prognosis with chemoresistance, TMB, and immune features. ALDH3B1 and NCEH1 are two promising targets for treating PC.

Elevated LILRB1 expression predicts poor prognosis and is associated with tumor immune infiltration in patients with glioma

BACKGROUND

Leukocyte immunoglobulin-like receptor subfamily B1 (LILRB1) is regarded as an inhibitory molecule. However, the importance of LILRB1 expression in glioma has not yet been determined. This investigation examined the immunological signature, clinicopathological importance and prognostic value of LILRB1 expression in glioma.

METHODS

We used data from the UCSC XENA database, the Cancer Genome Atlas (TCGA) database, the Chinese Glioma Genome Atlas (CGGA) database, the STRING database, the MEXPRESS database and our clinical glioma samples to perform bioinformatic analysis and used vitro experiments to examine the predictive value and potential biological roles of LILRB1 in glioma.

RESULTS

Higher LILRB1 expression was considerably present in the higher WHO grade glioma group and was linked to a poorer prognosis in patients with glioma. Gene set enrichment analysis (GSEA) revealed that LILRB1 was positively correlated with the JAK/STAT signaling pathway. LILRB1 combined with tumor mutational burden (TMB) and microsatellite instability (MSI) may be a promising indicator for the effectiveness of immunotherapy in patients with glioma. Increased LILRB1 expression was positively linked with the hypomethylation, M2 macrophage infiltration, immune checkpoints (ICPs) and M2 macrophage makers. Univariate and multivariate Cox regression analyses determined that increased LILRB1 expression was a standalone causal factor for glioma. Vitro experiments determined that LILRB1 positively enhanced the proliferation, migration and invasion in glioma cells. MRI images demonstrated that higher LILRB1 expression was related with larger tumor volume in patients with glioma.

CONCLUSION

Dysregulation of LILRB1 in glioma is correlated with immune infiltration and is a standalone causal factor for glioma.

Tumor Mutational Burden for Predicting Prognosis and Therapy Outcome of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), the primary hepatic malignancy, represents the second-highest cause of cancer-related death worldwide. Many efforts have been devoted to finding novel biomarkers for predicting both patients' survival and the outcome of pharmacological treatments, with a particular focus on immunotherapy. In this regard, recent studies have focused on unravelling the role of tumor mutational burden (TMB), i.e., the total number of mutations per coding area of a tumor genome, to ascertain whether it can be considered a reliable biomarker to be used either for the stratification of HCC patients in subgroups with different responsiveness to immunotherapy, or for the prediction of disease progression, particularly in relation to the different HCC etiologies. In this review, we summarize the recent advances on the study of TMB and TMB-related biomarkers in the HCC landscape, focusing on their feasibility as guides for therapy decisions and/or predictors of clinical outcome.

CAFs secrete CXCL12 to accelerate the progression and cisplatin resistance of colorectal cancer through promoting M2 polarization of macrophages

The purpose of this study was to investigate the effect of the interaction between tumor-associated fibroblasts (CAFs) and macrophage polarization on colorectal cancer (CRC) progression. Clinical tissue samples of CRC and health volunteers were collected to isolate normal fibroblasts (NFs) and CAFs. LoVo, HCT116, or THP-1 cells were co-cultured with NFs or CAFs. Immunofluorescence and western blot detected the expression of related markers. MTT assay measured cell viability and IC50. Cell proliferation and metastasis were detected through colony formation and transwell assays. CRC mice models were constructed by injection of HCT116 cells, with IHC assessing C-X-C Motif Chemokine Ligand 12 (CXCL12) expression. The proliferation, migration, invasion, and cisplatin (DDP) resistance of CRC cells were apparently increased after co-culture with CAFs. Compared to NFs, CAFs have a markedly higher ability to recruit macrophages and promote macrophages M2 polarization by secreting CXCL12. Further experiments affirmed that CXCL12 secreted by CAFs boosted proliferation, migration, invasion, and DDP resistance of CRC cells via induction of the M2 polarization of macrophages. In vivo experiments confirmed that CAFs promoted the progression of CRC and DDP resistance by affecting M2 polarization through CXCL12. CAFs recruit macrophages and secrete CXCL12 to induce M2 polarization of macrophages, thus mediating cell function and DDP resistance of CRC.

Tumor mutational burden and efficacy of chemotherapy in lung cancer

PURPOSE

TMB is one of the potent biomarkers of response to immune checkpoint blockade. The association between TMB and efficacy of chemotherapy in advanced lung cancer has not been comprehensively explored.

METHODS

Ninety lung cancer patients receiving first-line chemotherapy with large panel next-generation sequencing data of pre-treatment tumor tissue were identified. The effect of TMB on PFS of chemotherapy were evaluated in univariate and multivariate analyses.

RESULTS

The median TMB level of lung cancer patients enrolled in this study was 9.4 mutations/Mb, with TMB levels in smokers significantly higher than those in non-smokers. All patients were divided into high TMB and low TMB groups with the cutoff of the median TMB. The patients with low TMB had longer PFS of first-line chemotherapy (median PFS 9.77 vs 6.33 months, HR = 0.523, 95% CI 0.32-0.852, log-rank P = 0.009). Subgroup analysis showed that PFS of chemotherapy favored low TMB than high TMB among subgroups of male, age < 60, NSCLC, adenocarcinoma, stage IV, ECOG PS 0, driver mutation positive, TP53 wild type and patients not receiving bevacizumab. In multivariate analysis, PFS of chemotherapy remained significantly longer in low TMB group (HR = 0.554, p = 0.036). In those patients received immunotherapy upon unsatisfactory chemotherapy, PFS of immunotherapy was much longer in high TMB group (median PFS 32.88 vs 6.62 months, HR = 0.2426, 95% CI 0.06-0.977, log-rank P = 0.04).

CONCLUSIONS

TMB level of tumor tissue is a potent biomarker for efficacy of chemotherapy and immunotherapy in lung cancer. It may provide some clues for the decision of treatment strategy.

In Silico Identification and Validation of Cuproptosis-Related LncRNA Signature as a Novel Prognostic Model and Immune Function Analysis in Colon Adenocarcinoma

Background: Colon adenocarcinoma (COAD) is the most common subtype of colon cancer, and cuproptosis is a recently newly defined form of cell death that plays an important role in the development of several malignant cancers. However, studies of cuproptosis-related lncRNAs (CRLs) involved in regulating colon adenocarcinoma are limited. The purpose of this study is to develop a new prognostic CRLs signature of colon adenocarcinoma and explore its underlying biological mechanism. Methods: In this study, we downloaded RNA-seq profiles, clinical data and tumor mutational burden (TMB) data from the TCGA database, identified cuproptosis-associated lncRNAs using univariate Cox, lasso regression analysis and multivariate Cox analysis, and constructed a prognostic model with risk score based on these lncRNAs. COAD patients were divided into high- and low-risk subgroups based on the risk score. Cox regression was also used to test whether they were independent prognostic factors. The accuracy of this prognostic model was further validated by receiver operating characteristic curve (ROC), C-index and Nomogram. In addition, the lncRNA/miRNA/mRNA competing endogenous RNA (ceRNA) network and protein−protein interaction (PPI) network were constructed based on the weighted gene co-expression network analysis (WGCNA). Results: We constructed a prognostic model based on 15 cuproptosis-associated lncRNAs. The validation results showed that the risk score of the model (HR = 1.003, 95% CI = 1.001−1.004; p < 0.001) could serve as an independent prognostic factor with accurate and credible predictive power. The risk score had the highest AUC (0.793) among various factors such as risk score, stage, gender and age, also indicating that the model we constructed to predict patient survival was better than other clinical characteristics. Meanwhile, the possible biological mechanisms of colon adenocarcinoma were explored based on the lncRNA/miRNA/mRNA ceRNA network and PPI network constructed by WGCNA. Conclusion: The prognostic model based on 15 cuproptosis-related lncRNAs has accurate and reliable predictive power to effectively predict clinical outcomes in colon adenocarcinoma patients.

Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance

Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.

Skeletal muscle metastasis with bone metaplasia from colon cancer: A case report and review of the literature

BACKGROUND

Colon cancer is a common malignant disease of the gastrointestinal tract and usually occurs at the junction of the rectum and sigmoid colon. Lymphatic and hematogenous metastases occur frequently in colon cancer and the most common metastatic sites include the liver, lung, peritoneum, bone, and lymph nodes. As a manifestation of advanced tumor spread and metastasis, soft tissue metastasis, especially skeletal muscle metastasis with bone metaplasia caused by colon cancer, is rare, accounting for less than 1% of metastases.

CASE SUMMARY

A 43-year-old male patient developed skeletal muscle metastasis with bone metaplasia of the right proximal thigh 5 mo after colon cancer was diagnosed. The patient was admitted to the hospital because of pain caused by a local mass on his right thigh. Positron emission tomography-computed tomography showed many enlarged lymph nodes around the abdominal aorta but no signs of lung or liver metastases. Color ultrasound revealed a mass located in the skeletal muscle and the results of histological biopsy revealed a poorly differentiated adenocarcinoma suspected to be distant metastases from colon cancer. Immunohistochemistry showed small woven bone components that were considered to be ossified.

CONCLUSION

This case reminds us that for patients with advanced colorectal tumors, we should be alert to the possibility of unconventional metastasis.

Establishment of a novel ferroptosis-related lncRNA pair prognostic model in colon adenocarcinoma

Long non-coding RNAs (lncRNAs) have been reported to be prognostic factors for cancer. Ferroptosis is an iron-dependent process of programmed cell death. Here, we established a ferroptosis-related lncRNA (frlncRNA) pair signature and revealed its prognostic value in colon adenocarcinoma (COAD) by analyzing the data from The Cancer Genome Atlas (TCGA). FrlncRNAs were identified based on co-expression analysis using the Pearson correlation. Differentially expressed frlncRNAs (DEfrlncRNAs) were recognized and paired, followed by prognostic assessment using univariate Cox regression analysis. The least absolute shrinkage and selection operator (LASSO) penalized Cox analysis was used to determine and construct a risk score prognostic model, by which the receiver operating characteristic (ROC) curves for predicting the overall survival (OS) were conducted. Following the evaluation of whether it was an independent prognostic factor, correlations between the risk score model and clinicopathological characteristics, hypoxia- and immune-related factors, and somatic variants were investigated. In total, 148 DEfrlncRNA pairs were identified, 25 of which were involved in a risk score prognostic signature. The area under ROC curves (AUCs) representing the predictive effect for 1-, 3-, and 5-year survival rates were 0.860, 0.885, and 0.934, respectively. The risk score model was confirmed as an independent prognostic factor and was significantly superior to the clinicopathological characteristics. Correlation analyses showed disparities in clinicopathological characteristics, hypoxia- and immune-related factors, and somatic variants, as well as specific signaling pathways between high- and low-risk groups. The novel risk score prognostic model constructed by pairing DEfrlncRNAs showed promising clinical prediction value in COAD.

Integrative Analysis of Biomarkers Through Machine Learning Identifies Stemness Features in Colorectal Cancer

Background: Cancer stem cells (CSCs), which are characterized by self-renewal and plasticity, are highly correlated with tumor metastasis and drug resistance. To fully understand the role of CSCs in colorectal cancer (CRC), we evaluated the stemness traits and prognostic value of stemness-related genes in CRC.

Methods: In this study, the data from 616 CRC patients from The Cancer Genome Atlas (TCGA) were assessed and subtyped based on the mRNA expression-based stemness index (mRNAsi). The correlations of cancer stemness with the immune microenvironment, tumor mutational burden (TMB), and N6-methyladenosine (m6A) RNA methylation regulators were analyzed. Weighted gene co-expression network analysis (WGCNA) was performed to identify the crucial stemness-related genes and modules. Furthermore, a prognostic expression signature was constructed using the Lasso-penalized Cox regression analysis. The signature was validated via multiplex immunofluorescence staining of tissue samples in an independent cohort of 48 CRC patients.

Results: This study suggests that high-mRNAsi scores are associated with poor overall survival in stage IV CRC patients. Moreover, the levels of TMB and m6A RNA methylation regulators were positively correlated with mRNAsi scores, and low-mRNAsi scores were characterized by increased immune activity in CRC. The analysis identified 34 key genes as candidate prognosis biomarkers. Finally, a three-gene prognostic signature (PARPBP, KNSTRN, and KIF2C) was explored together with specific clinical features to construct a nomogram, which was successfully validated in an external cohort.

Conclusion: There is a unique correlation between CSCs and the prognosis of CRC patients, and the novel biomarkers related to cell stemness could accurately predict the clinical outcomes of these patients.

Identifying GNG4 might play an important role in colorectal cancer TMB

BACKGROUND

Colorectal carcinoma (CRC) is one of the most leading cause of cancer death all over the world. The tumor immune microenvironment is illustrated to be necessary for the progress of CRC. And the accumulating evidence indicated that tumor mutation burden (TMB) is effective in differentiating responding population of immune checkpoint inhibitor (ICI) therapies in various cancers. In this study, we aimed to evaluated the potential relationship between TMB and the recurrence risk of CRC.

METHODS

The transcriptomic and clinical data of CRC patients were collected from The Cancer Genome Atlas (TCGA) database (n= 382). Then the genomic analysis of tumor mutation burden and tumor purity were conducted by a computational method based on transcriptomic data.

RESULTS

Firstly, we accessed the distribution of TMB and preferences at the gene and mutation level using somatic mutation data from TCGA data about CRC. We identified that high TMB predicted better prognosis of CRC patients. Secondly, the differentially expressed genes (DEGs) between the low TMB and high TMB group was clarified. Then the protein-protein interaction (PPI) analysis was performed, and the results confirmed ten hub genes among the DEGs. Utilizing the GEPIA web-tool, we discovered that GNG4 was up-regulated in tumor tissues, and GNG4 was related to the overall survival (OS) and tumor free survival (TFS) of CRC patients. Therefore, we considered GNG4 was essential for the tumor immune microenvironment of CRC. Furthermore, we also accessed the protein level of GNG4 in CRC and liver metastases from CRC.

CONCLUSIONS

In this study, GNG4 was demonstrated to be the key element of the CRC TMB, which will be essential for the ICI therapy of CRC. Besides, GNG4 was up-regulated in CRC and liver metastases from CRC tissues. Thus, we thought that GNG4 might play an important role in colorectal cancer TMB and induce its metastasis in liver.

A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee

Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which we define as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.

Identification and validation of a miRNA-related expression signature for tumor mutational burden in colorectal cancer

Background

Tumor mutational burden (TMB) is a promising predictor, which could stratify colorectal cancer (CRC) patients based on the response to immune checkpoint inhibitors (ICIs). MicroRNAs (miRNAs) act as the key regulators of anti-cancer immune response. However, the relationship between TMB and miRNA expression profiles is not elucidated in CRC.

Methods

Differentially expressed miRNAs (DE miRNAs) between the TMB^high group and the TMB^low group were identified for the CRC cohort of the TCGA database. In the training cohort, a miRNA-related expression signature for predicting TMB level was developed by the least absolute shrinkage and selection operator (LASSO) method and tested with reference to its discrimination, calibration, and decision curve analysis (DCA) in the validation cohort. Functional enrichment analysis of these TMB-related miRNAs was performed. The correlation between this miRNA-related expression signature and three immune checkpoints was analyzed.

Results

Twenty-one out of 43 DE miRNAs were identified as TMB-related miRNAs, which were used to develop a miRNA-related expression signature. This TMB-related miRNA signature demonstrated great discrimination (AUC_{test set} = 0.970), satisfactory calibration (P > 0.05), and clinical utility in the validation cohort. Functional enrichment results revealed that these TMB-related miRNAs were mainly involved in biological processes associated with immune response and signaling pathways related with cancer. This miRNA-related expression signature showed a median positive correlation with PD-L1 (R = 0.47, P < 0.05) and CTLA4 (R = 0.39, P < 0.05) and a low positive correlation with PD-1 (R = 0.16, P < 0.05).

Conclusion

This study presents a miRNA-related expression signature which could stratify CRC patients with different TMB levels.

Characterization of genomic alterations in Chinese colorectal cancer patients

OBJECTIVE

Colorectal cancer is one of the most prevalent types of cancer worldwide. Right-sided and left-sided colorectal cancer (RCC and LCC) patients respond differently to treatment. We aimed to identify the different mutational profile between RCC and LCC and provided evidence for future precision therapy.

METHODS

A total of 630 Chinese colorectal cancer patients, including 467 (74.1%) LCC and 163 (25.9%) RCC, were enrolled in this cohort. Both formalin-fixed paraffin-embedded tumor tissues and matching blood samples were collected and deep sequenced targeting 450 cancer genes for genomic alteration analysis. Tumor mutational burden was measured by an algorithm developed in-house. Correlation analysis was performed by Fisher's exact test.

RESULTS

The most common mutated genes were TP53 (77.0%), APC (71.7%), KRAS (50.0%), SMAD4 (19.8%), PIK3CA (18.3%), FBXW7 (17.5%), TCF7L2 (12.5%), SOX9 (11.3%), LRP1B (10.8%), ARID1A (10.3%) and FAT4 (10.3%). The mutation frequencies of TP53 and APC in LCC were significantly higher than that of RCC, while the mutation frequency of PIK3CA was lower than that of RCC. Six gene fusions were specifically detected in RCC patients. Colorectal cancer sites were associated with gender (P = 4.15 × 10-5) and tumor differentiation (P = 0.059). In LCC, the gender-associated genes were FAT4, EP300, FAT1, LRP1, ARID1B, AR, FYN and TAF1, while in RCC, they were ARID1A, SMARCA4, LRP1 and GRIN2A. The mutations of 18 genes were associated with tumor differentiation (8 for LCC and 10 for RCC). High tumor mutational burden was more common in RCC. Our results implied more potential targeted drug therapy opportunities for RCC.

CONCLUSION

We describe the different molecular characteristics of LCC and RCC. Our result supported a better prognosis of RCC than LCC in Chinese colorectal cancer patients.

Comprehensive analysis of tumour mutation burden and the immune microenvironment in hepatocellular carcinoma

Tumour mutation burden (TMB) and the immune microenvironment (IME) are reportedly associated with immunotherapy responses, but this relationship remains unclear in hepatocellular carcinoma (HCC). We classified HCC patients in the liver hepatocellular carcinoma cohort from The Cancer Genome Atlas into low- and high-TMB groups and evaluated differences in immune infiltrates. Additionally, differentially expressed genes in the low- and high-TMB groups were identified, and functional analyses were conducted. A risk score model was constructed based on three differentially expressed immune genes (DEIGs). The Tumor Immune Estimation Resource database was utilized to analyse how the IME was affected by the three hub DEIGs. Finally, a prognostic nomogram combining risk scores and stages was established and externally validated with the International Cancer Genome Consortium and GSE14520 cohorts. High-TMB (top 20%) patients exhibited a worse prognosis (P = 0.017). Follicular helper cells (P = 0.001) and activated natural killer cells (P = 0.003) were enriched in high-TMB patients, while resting dendritic cells (P = 0.002) were enriched in low-TMB samples. A risk score model was generated with three hub DEIGs (CCR7, STC2 and S100A9) to predict overall survival in HCC cohorts. Moreover, copy number variations mainly reduced infiltration levels. The nomogram performed better than the risk score model in the training and validation datasets. Higher TMB was associated with IME diversification and worse prognosis in HCC. Mutations in three hub TMB-associated DEIGs correlated with lower immune cell infiltration.

Choosing tumor mutational burden wisely for immunotherapy: A hard road to explore

Immunotherapy has revolutionized the treatment of cancer due to its remarkable efficacy and extensive survival benefit in multiple tumor types. However, predictive biomarkers are required to identify patients who are likely to respond to immunotherapy. Recently, tumor mutational burden (TMB) has been shown to be associated with clinical outcomes in diverse cancers, such as melanoma, non-small-cell lung cancer and colorectal cancer. Several studies have demonstrated that high TMB can effectively predict the objective response rate and progression-free survival, but the ability of TMB to predict overall survival is limited. Thus, the clinical utility of TMB as a predictive and prognostic biomarker in immunotherapy is currently controversial. Importantly, multiple factors can affect the accurate assessment of TMB and further interfere with its prediction of clinical outcomes. These factors include preanalytical factors such as sample status, analytical factors such as differences in platforms and methods for determining TMB and variability of cutoff values, and postanalytical factors such as inconsistent interpretation and reporting of results. In addition, the optimal definition and quantification of TMB are unclear and require harmonization and standardization for reliable clinical application. This review elaborates on the factors affecting TMB status in primary tumors, summarizes the clinical utility of TMB as a biomarker in immunotherapy, and evaluates the impact of each analysis stage on the accurate estimation of TMB, especially its quantification, aiming to facilitate TMB assessment in routine clinical settings.

Single-nucleotide variants, tumour mutational burden and microsatellite instability in patients with metastatic colorectal cancer: Next-generation sequencing results of the FIRE-3 trial

BACKGROUND

Molecular biomarkers and primary tumour sidedness guide treatment decisions in metastatic colorectal cancer. Comprehensive molecular profiling aims to identify targetable alterations and measure tumour mutational burden (TMB) to enable precision oncology.

MATERIAL AND METHODS

FoundationOne® next-generation sequencing identified single-nucleotide variants (SNVs), copy number alterations, high TMB (TMB-H) and high-grade microsatellite instability (MSI-H) in patients treated in the FIRE-3 trial. Data were correlated with objective response rate (ORR), progression-free survival (PFS) and overall survival (OS).

RESULTS

Three hundred seventy-three (49.6%) of 752 patients provided material for this analysis. Frequent SNVs included TP53, APC, KRAS, PIK3CA, BRAF, SMAD4 and FBXW7. KRAS, BRAF V600E and SMAD4 mutations were confirmed as prognostic biomarkers by logistic penalised regression for ORR. OS was significantly longer in patients with SMAD4 wild-type (WT) tumours than in those with SMAD4-mutated tumours (hazard ratio = 0.59 [95% confidence interval {CI} = 0.34-1.01], p = 0.05), with a higher probability of ORR [odds ratio, SMAD4 SNV versus WT = 0.32 [95% CI = 0.10-0.98], p = 0.05] when treated with cetuximab. MSI-H (30.0%, p = 0.03) and TMB-H (17.3%, p = 0.003) tumours were enriched by FBXW7 mutations. Numerically lower ORR, OS and PFS were observed in MSI-H tumours.

CONCLUSIONS

RAS, BRAF V600E and SMAD4 mutations were identified as poor prognostic biomarkers in patients of the FIRE-3 trial, whereas improved outcome was observed for BRAF non-V600E mutation. SMAD4 mutation might provide predictive relevance for cetuximab efficacy. MSI-H tumours showed numerically lower ORR, OS and PFS.

Recommendations to improve the clinical adoption of NGS-based cancer diagnostics in Singapore

Next-generation sequencing (NGS)-based diagnostics have demonstrated clinical utility in predicting improved survival benefits with targeted treatment in certain cancer types, and positive cost-benefit in several healthcare systems. However, clinical adoption in Singapore remains low despite commercial availability of these diagnostics. This expert opinion review examines the key challenges to the clinical adoption of NGS-based diagnostics in Singapore, provides recommendations on impactful initiatives to improve adoption, and also offers practical guidance on specific cancer types in which NGS-based diagnostics are appropriate for use in Singapore. Limited patient affordability is one major challenge to clinical adoption of NGS-based diagnostics, which could be improved by enabling patient access to more funds for specific cancer types with clear benefits. Expert opinion based on current evidence and clinical experience supports the upfront use of hotspot panels in advanced non-small cell lung cancer (NSCLC), metastatic colorectal cancer, advanced and recurrent ovarian cancer, and acute myeloid leukemia. Comprehensive genomic profiling could be considered for upfront use in select patients with NSCLC and ovarian cancer, or in refractory patients with the four cancer types. Wider adoption of NGS-based diagnostics will improve the delivery of cancer care in Singapore and Asia-Pacific, and thus lead to better patient outcomes.

Microsatellite Stable Colorectal Cancer With an Immunogenic Phenotype: Challenges in Diagnosis and Treatment

BACKGROUND

Patients with deficient microsatellite mismatch repair (dMMR) colorectal cancer (CRC) may respond to immune checkpoint inhibition (ICI), whereas patients with microsatellite-stable (MSS) CRC have not demonstrated response. However, a proportion of MSS tumors display histomorphologic features characteristic of dMMR tumors consistent with an increased antigenicity. Therefore, a subset of patients with CRC not currently receiving ICI treatment may derive benefit from ICI therapy. We review tumors in which the histologic features suggestive of dMMR were in disagreement with the DNA mismatch repair proteins obtained by immunohistochemistry (IHC). Possible causes of such disagreement are discussed.

MATERIALS AND METHODS

Three patients with CRC suggestive of histomorphologic immunogenicity underwent evaluation by IHC staining for mismatch repair (MMR) status, next-generation sequencing assays, and/or polymerase chain reaction.

RESULTS

Findings compatible with an immunogenic response were similarly observed in all patients. Case 1 highlighted the limiting factors inherent to IHC staining for MMR status: a biopsy initially interpreted as MSS was subsequently interpreted as being dMMR. Case 2 examined the challenges in reconciling histologic characteristics traditionally associated with dMMR CRCs but ultimately determined to be MSS. Case 3 examined the microsatellite instability of CRC resulting from MLH1-methylation and/or MSH6 mutation.

CONCLUSIONS

We demonstrated the challenges in establishing MMR status when confronted with conflicting results from histology, IHC, polymerase chain reaction, and next-generation sequencing. Given that dMMR status has been shown to be a biomarker for ICI responsiveness, the importance of accurate identification is critical.

The prognostic value of tumor mutation burden in EGFR-mutant advanced lung adenocarcinoma, an analysis based on cBioPortal data base

Background

Tumor mutation burden (TMB) is novel biomarker of promising predict value in prediction of immune checkpoint inhibitors (ICPis) in non-small cell lung cancer (NSCLC). However, the distribution of TMB in epidermal growth factor receptor (EGFR)-mutant advanced lung adenocarcinoma (LUAD) patients and the impact on overall survival (OS) time are not well demonstrated.

Methods

Information regarding gene mutations and patients' survival time in advanced LUAD was downloaded from The Cancer Genome Atlas (TCGA) database. The diversity of TMB in different EGFR-mutant types was observed and the predicted value of TMB for OS as well as other co-mutations were analyzed. The diversity of TMB was also observed in another Chinese cohort of advanced LUAD patients.

Results

The median TMB values of EGFR wild-type, other types of EGFR mutations, exon 19 deletions and L858R were 6.12, 5.66, 3.77 and 4.72, differences between wild-type and EGFR sensitive mutations (exon 19 deletion or L858R) were significant (P<0.001 and P<0.01). OS time of high TMB group was inferior to that of the low TMB group (24.03 months vs. not reached, P=0.0020). TMB and TP53 together will make more accurate prediction of OS in EGFR-mutant advanced LUAD patients. Distribution of TMB in another Chinese cohort had the same trend.

Conclusions

In advanced LUAD patients, TMB was lower in patients with EGFR-mutant group than EGFR wild group. TMB was a negative prognostic biomarker of OS in EGFR-mutant LUAD patients, especially when TP53 was mutated together.

Exploration of the relationships between tumor mutation burden with immune infiltrates in clear cell renal cell carcinoma

Background

Whether tumor mutation burden (TMB) correlated with improved survival outcomes or promotion of immunotherapies remained controversy in various malignancies. We aimed to investigate the prognosis of TMB and the potential association with immune infiltrates in clear cell renal cell carcinoma (ccRCC).

Methods

We downloaded the somatic mutation data of 336 ccRCC patients from the Cancer Genome Atlas (TCGA) database, and analyzed the mutation profiles with "maftools" package. TMB was calculated and we classified the samples into high-TMB and low-TMB group. Differential analysis was conducted to compare the expression profiles between two groups using "limma" package, and we identified the 9 hub TMB-related signature from batch survival analysis. Gene ontology (GO) analysis and Gene Set Enrichment Analysis (GSEA) were performed to screen significantly enriched pathways between two groups. Based on the TIMER database, we further assessed the relationships of the mutants of 9 TMB-related signature with immune infiltration levels in ccRCC. Besides, we utilized the "CIBERSORT" package to estimate the abundance of 22 immune fractions between low- and high-TMB groups, and the significant difference were determined by Wilcoxon rank-sum test. Furthermore, Cox regression model combined with survival analysis were used to evaluate the prognostic value of immune cells. Last, we constructed a Tumor Mutation Burden Prognostic Index (TMBPI) from multivariate Cox results and Receiver Operating Characteristic (ROC) curve was drawn to assess the predictive accuracy.

Results

Single nucleotide polymorphism (SNP) occurred more frequently than insertion or deletion, and C>T was the most common of SNV in ccRCC. Higher TMB levels conferred poor survival outcomes, associated with higher tumor grades and advanced pathological stages. A total of 1,265 differentially expressed genes were obtained and top 19 immune-related genes were identified in Venn diagram. GSEA revealed that patients in higher TMB groups correlated with MAPK signaling pathway, Wnt signaling pathway and pathway in cancers. Moreover, we identified 9 hub TMB-related immune genes related with survival and mutants of 9 signature were associated with lower immune infiltrates. In addition, infiltration levels of CD8+ T cell, CD4+ memory resting T cell, M1 and M2 macrophages, as well as dendritic resting cells in high-TMB group were lower than that in low-TMB group, especially the level of CD8+ T cell and macrophage correlated negatively with prognosis of ccRCC. Last, the TMBPI was constructed and the AUC of ROC curve was 0.666.

Conclusions

Higher TMB correlated with poor survival outcomes and might inhibit the immune infiltrates in ccRCC. The mutants of 9 hub TMB-related immune signature conferred lower immune cells infiltration which deserved further validation.

Volumetric imaging parameters are significant for predicting the pathological complete response of preoperative concurrent chemoradiotherapy in local advanced rectal cancer

Preoperative concurrent chemoradiotherapy (CCRT) as the standard treatment for locally advanced rectal cancer (LARC) has been widely used in clinic. Its efficiency influences the prognosis and the selection of subsequent treatment. The current criteria for evaluating the prognosis of patients with extremely sensitive preoperative CCRT include the clinical complete remission response (cCR) and pathological complete response (pCR), but those with cCR may not necessarily achieve pCR, and the pCR can be confirmed only after surgery. Some scholars believe that patients with pCR after CCRT can be categorized as 'watch and wait'. Therefore, it is extremely important to find a way to predict the pCR status of patients before therapy. In this study, we examined the expression of stem cell markers and obtained direct and derivative volumetric imaging parameters before treatment. Subsequently, these factors and the general clinical data were adopted into a regression model, and the correlation between them and the pCR was analyzed. We found that the pCR of LARC was positively correlated with tumor compactness (TC), whereas it was negatively correlated with approximate tumor volume (ATV), real tumor volume (RTV), total surface area of the tumor (TSA) and tumor maximum longitudinal length (TML). In these meaningful predictors, the positive predictive values and the negative predictive values of TC were 74.73% and 94.61%, respectively. Compared with other possible predictors, TC is the most encouraging predictor of pCR. Our findings provide a way for clinicians to predict the sensitivity of preoperative CCRT and will help to select individualized treatment options for LARC patients.

Tracking longitudinal genetic changes of circulating tumor DNA (ctDNA) in advanced Lung adenocarcinoma treated with chemotherapy

Introduction

Pemetrexed combined with platinum complexes can be used as first-line treatment for advanced non-squamous non-small cell lung cancer (NSCLC), however, the efficacy and safety is varying from individuals. There is a need to better understand the genetic variations associated with platinum response.

Materials and Methods

We performed next-generation sequencing (NGS) based on BGI Oseq-ctDNA panel to analyze 98 longitudinal plasma samples from 32 lung adenocarcinoma patients during platinum-based chemotherapy, and a bioinformatic pipeline was developed to detect point mutations.

Results

We found that mutation burden was decreased after chemotherapy, which reflected chemotherapy sensitivity, especially the frequency of C>G and C>A substitutions. Moreover, neoplastic cells carrying a specific set of somatic mutations, such as EGFR(L858R), KRAS (p.G12C) were obviously correlated with platinum treatment. In addition, the MAPK pathway was found to have a pivotal role in NSCLC and platinum based response. Finally, we found that smokers benefit less from platinum-based chemotherapy.

Conclusions

Collectively, this work described the dynamic changes of ctDNA mutation status during platinum-based treatment, which may contribute to advanced lung adenocarcinoma patients stratification and precision treatment.

Multi-omics analysis of tumor mutation burden combined with immune infiltrates in bladder urothelial carcinoma

To explore the prognosis of tumor mutation burden (TMB) and underlying relationships with tumor-infiltrating immune cells in bladder cancer (BLCA). Transcriptome profiles and somatic mutation data from The Cancer Genome Atlas database by the GDC tool. A total of 437 samples were included, consisted of 412 BLCA patients and matched 25 normal samples. Specific mutation information was summarized and illustrated in waterfall plot. Higher TMB levels revealed improved overall survival (OS) and lower tumor recurrence. We found 68 differentially expressed genes in two TMB groups and identified eight independent hub TMB-related signature. Pathway analysis suggested that differential TMB-related signature correlated with multiple cancer-related crosstalk, including cell cycle, DNA replication, cellular senescence, and p53 signaling pathway. Besides, the tumor mutation burden related signature (TMBRS) model based on eight signature possessed well predictive value with area under curve (AUC) = 0.753, and patients with higher TMBRS scores showed worse OS outcomes (p < .001). Moreover, we exhibited the inferred immune cell fractions in box plot and differential abundance of immune cells were shown in the heatmap. The Wilcoxon rank-sum test suggested that CD8+ T cell (p = .001) and memory activated CD4+ T cell (p = .004) showed higher infiltrating levels in high-TMB group, while the density of resting mast cells showed lower infiltrating level in high-TMB group (p = .016). Finally, it is significant to note that CD8+ T cell and memory activated CD4+ T cell subsets not only revealed higher infiltrating abundance in high-TMB group but correlated with prolonged OS and lower risk of tumor recurrence, respectively.

The Evolving Biomarker Landscape for Treatment Selection in Metastatic Colorectal Cancer

The approval of targeted therapies for metastatic colorectal cancer (mCRC) has led to important improvements in patient outcomes. However, it is still necessary to increase individualisation of treatments based on tumour genetic profiles to optimise efficacy, while minimising toxicity. As such, there is currently great focus on the discovery and validation of further biomarkers in mCRC, with many new potential prognostic and predictive markers being identified alongside developments in patient molecular profiling technologies. Here, we review data for validated and emerging biomarkers impacting treatment strategies in mCRC. We completed a structured literature search of the PubMed database to identify relevant publications, limiting for English-language publications published between 1 January 2014 and 11 July 2018. In addition, we performed a manual search of the key general oncology and CRC-focused congresses to identify abstracts reporting emerging mCRC biomarker data, and of ClinicalTrials.gov to identify ongoing clinical trials investigating emerging biomarkers in mCRC and/or molecular-guided clinical trials. There is solid evidence supporting the use of BRAF status as a prognostic biomarker and DYPD, UGT1A1, RAS, and microsatellite instability as predictive biomarkers in mCRC. There are a number of emerging biomarkers that may prove to be clinically relevant in the future to have prognostic (HPP1 methylation), predictive (HER3, microRNAs, anti-angiogenic markers, and CRC intrinsic subtypes), or both prognostic and predictive values (HER2, CpG island methylator phenotype, tumour mutational load, gene fusions, and consensus molecular subtypes). As such, new biomarker-led treatment strategies in addition to anti-epidermal growth factor receptor and anti-angiogenetic treatments are being explored. Biomarkers that are not recommended to be tested in clinical practice or are unlikely to be imminently clinically relevant for mCRC include thymidylate transferase, ERCC1, PIK3CA, and PTEN. We highlight the clinical utility of existing and emerging biomarkers in mCRC and provide recommended treatment strategies according to the biomarker status. An update on ongoing molecular-guided clinical trials is also provided.

High tumor mutation burden predicts better efficacy of immunotherapy: a pooled analysis of 103078 cancer patients

The relation between tumor mutation burden (TMB) and outcome of cancer patients receiving immunotherapy has been reported. This study aimed to evaluate the prognostic role of TMB in cancer patients receiving immunotherapy. Databases including Embase, PubMed, and the Cochrane library were systematically searched to identify potentially eligible studies until Sep 2018 without language limitation. Studies assessing high versus low TMB in predicting survival of various cancer patients were selected. The pooled analyses were conducted using hazard ratio (HR) of high versus low TMB for overall survival (OS) and progression-free survival (PFS), and the odds ratio (OR) for overall response rate (ORR). The primary endpoint was OS. Secondary outcomes were PFS and ORR. A total of 45 studies consisting of 103078 cancer patients were included. The combined results showed that high TMB was associated with better OS (HR = 0.40; 95% confidence interval (CI):0.30-0.53; p< .00001), PFS (HR = 0.37; 95% CI: 0.26-0.53; p< .00001) and ORR (OR = 4.62; 95%CI: 2.90-7.34; p< .0001) when treated with immunotherapy. In studying patients with high TMB, these patients had improved OS (HR = 0.69; 95%CI: 0.47-1.03; p= .07) when comparing immunotherapy to chemotherapy. Subgroup analyses suggested that the prognostic role of TMB was independent of cancer types and TMB detection methods (all p< .05). Our findings suggest that high TMB is associated with better survival in cancer patients receiving immunotherapy. For cancer patients with high TMB, immunotherapy could be considered.

Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases

Adrenocortical carcinoma is a rare malignancy with a poor prognosis and few treatment options. Molecular characterization of this cancer remains limited. We present a case of an adrenocortical carcinoma (ACC) in a 37-yr-old female, with dual lung metastases identified 1 yr following commencement of adjuvant mitotane therapy. As standard therapeutic regimens are often unsuccessful in ACC, we undertook a comprehensive genomic study into this case to identify treatment options and monitor disease progress. We performed targeted and whole-genome sequencing of germline, primary tumor, and both metastatic tumors from this patient and monitored recurrence over 2 years using liquid biopsy for ctDNA and steroid hormone measurements. Sequencing revealed the primary and metastatic tumors were hyperhaploid, with extensive loss of heterozygosity but few structural rearrangements. Loss-of-function mutations were identified in MSH2, TP53, RB1, and PTEN, resulting in tumors with mismatch repair signatures and microsatellite instability. At the cellular level, tumors were populated by mitochondria-rich oncocytes. Longitudinal ctDNA mutation and hormone profiles were unable to detect micrometastatic disease, consistent with clinical indicators of disease remission. The molecular signatures in our ACC case suggested immunotherapy in the event of disease progression; however, the patient remains free of cancer. The extensive molecular analysis presented here could be applied to other rare and/or poorly stratified cancers to identify novel or repurpose existing therapeutic options, thereby broadly improving diagnoses, treatments, and prognoses.

Analysis of circulating tumor DNA by targeted ultra-deep sequencing across various non-Hodgkin lymphoma subtypes

Although targeted deep sequencing of cell-free DNA (cfDNA) was recently used to investigate tumor somatic mutations in particular subtypes of non-Hodgkin lymphomas (NHLs), the immense genetic heterogeneity across subtypes poses a hurdle to design a universal gene panel applicable for diverse subtypes of NHLs. We designed a panel targeting 66 genes associated with NHLs and performed targeted deep sequencing to analyze plasma cfDNA from patients with various subtypes of NHLs. Genetic profiling in plasma cfDNA using the method resulted in 88.0% sensitivity and >99% specificity in detecting mutations present at a frequency greater than 20% in the tumor biopsies. Furthermore, the level of ctDNA significantly decreased and increased depending on designated clinical responses to therapy and disease progression. These results demonstrated that ctDNA sensitively indicated the presence of cancer and reliably correlated with tumor burden, suggesting potential utility of the method for patients with various subtypes of NHLs.

Genomic landscape of synchronous tubulovillous adenoma and multiple non-familial colon cancers from a single patient

Colorectal cancer (CRC) is one of the leading causes of cancer-related death. We analyzed genomic of non-familial tubulovillous adenoma (TVA) and two synchronous malignant colorectal adenocarcinomas from a single patient. The number of somatic mutations was higher in the tumor sample (especially, AV 50 cm adenocarcinoma sample) than TVA sample, and also the allele frequency of mutation was higher on colon adenocarcinoma samples than TVA. Although they were very low frequency of sharing same genomic alterations between the three lesions, APC gene mutation was present in all three lesions, which confirm that APC gene mutation was an early event in this patient. The genetic alterations of APC, KRAS and TP53, which play an important role in the development of carcinoma from TVA, were shown through whole exome sequencing data of each sample. Of note, of the two synchronous adenocarcinoma samples, one lesion was KRAS mutant while the other one was KRAS wild-type. Our findings implicate that KRAS mutation may need to be taken from every primary cancer in a patient with multiple primary sites since KRAS status may differ amongst synchronous cancer lesions.

Early-onset colorectal cancer in young individuals

Treatment of young adults with colorectal cancer (CRC) represents an unmet clinical need, especially as diagnosis in this population might lead to the greatest loss of years of life. Since 1994, CRC incidence in individuals younger than 50 years has been increasing by 2% per year. The surge in CRC incidence in young adults is particularly alarming as the overall CRC frequency has been decreasing. Early-onset CRC are characterized by a more advanced stage at diagnosis, poorer cell differentiation, higher prevalence of signet ring cell histology, and left colon-sided location of the primary tumor. Among EO-CRC, approximately 30% of patients are affected by tumors harboring mutations causing hereditary cancer predisposing syndromes, and 20% have familial CRC. Most notably, the remaining 50% of EO-CRC patients have neither hereditary syndromes nor familial CRC, thus representing a formidable challenge for research. In this review article we summarize epidemiology, clinical and molecular features, heredity and outcome of treatments of EO-CRC, and provide considerations for future perspectives.

The mutational landscape of recurrent versus nonrecurrent human papillomavirus-related oropharyngeal cancer

BACKGROUND

Human papillomavirus-related (HPV-related) oropharyngeal squamous cell carcinomas (OPSCCs) have an excellent response rate to platinum-based chemoradiotherapy. Genomic differences between primary HPV-related OPSCCs that do or do not recur are unknown. Furthermore, it is unclear if HPV-related OPSCCs that recur share a genomic landscape with HPV-negative head and neck cancers (HNCs).

METHODS

We utilized whole exome sequencing to analyze somatic nucleotide (SNVs) and copy number variants (CNVs) among a unique set of 51 primary HPV-related OPSCCs, including 35 that did not recur and 16 that recurred. We evaluated 12 metachronous recurrent OPSCCs (7 with paired primary OPSCCs) and 33 primary HPV-unrelated oral cavity and OPSCCs.

RESULTS

KMT2D was the most frequently mutated gene among primary HPV-related OPSCCs (n = 51; 14%) and among metachronous recurrent OPSCCs (n = 12; 42%). Primary HPV-related OPSCCs that recurred shared a genomic landscape with primary HPV-related OPSCCs that did not recur. However, TSC2, BRIP1, NBN, and NFE2L2 mutations occurred in primary OPSCCs that recurred but not in those that did not recur. Moreover, primary HPV-related OPSCCs that recur harbor features of HPV-unrelated HNCs, notably including MAPK, JAK/STAT, and differentiation signaling pathway aberrations. Metachronous recurrent OPSCCs shared a genomic landscape with HPV-unrelated HNCs, including a high frequency of TP53, CASP8, FAT1, HLA-A, AJUBA, and NSD1 genomic alterations.

CONCLUSION

Overall, primary HPV-related OPSCCs that recur share a genomic landscape with nonrecurrent OPSCCs. Metachronous recurrent OPSCCs share genomic features with HPV-negative HNCs. These data aim to guide future deescalation endeavors and functional experiments.

FUNDING

This study is supported by the American Cancer Society (RSG TBG-123653), funding support for RAH (T32DC00018, Research Training in Otolaryngology, University of Washington), funds to EM from Seattle Translational Tumor Research (Fred Hutchinson Cancer Research Center), and center funds from the Fred Hutchinson Cancer Research Center to EM. UD is supported by the Department of Veterans Affairs, Biomedical Laboratory Research and Development (BLR&D), grant IO1-oo23456, and funds from the Pittsburgh Foundation and PNC Foundation.

Hsa_circ_0071589 promotes carcinogenesis via the miR-600/EZH2 axis in colorectal cancer

Previous studies have revealed that miRNAs and lncRNAs participate in the pathogenesis of colorectal cancer (CRC); however, whether circular RNAs (circRNAs) are also involved remains unclear. In the present study, qRT-PCR was used to examine the expression of hsa_circ_0071589, miR-600, and enhancer of zeste homolog 2 (EZH2) in CRC. MTT assay, colony formation assay, transwell assay, and wound-healing assay were performed to assess the effects of hsa_circ_0071589, miR-600, and EZH2 on CRC cell viability, proliferation, invasion, and migration. Bioinformatics analysis, luciferase reporter assay, and RIP assay were used to explore the correlations among hsa_circ_0071589, miR-600, and EZH2 expression in CRC cells. The results showed that hsa_circ_0071589 expression was significantly higher in CRC tissues than in normal tissues. Blockage of hsa_circ_0071589 in CRC cells inhibited tumor growth, invasion and migration. Hsa_circ_0071589 was able to promote the expression of EZH2 by acting as a sponge of miR-600. In addition, miR-600 expression was negatively correlated to hsa_circ_0071589 expression in CRC tissues. These results demonstrated that the hsa_circ_0071589/miR-600/EZH2 axis may play critical regulatory roles in the pathogenesis of CRC and may serve as a novel therapy target in CRC.