Research progress on the role of urothelial somatic mutations in the occurrence and recurrence of bladder cancer / 现代泌尿外科杂志

Bladder cancer is characterized by high incidence and high recurrence; however, the mechanism of pathogenesis, especially of recurrence is still unclear. This paper reviews the molecular characteristics of bladder cancer, urothelial somatic mutation, driver genes and mutation characteristics, and prospects the future research directions.

Comparative genomic analysis of esophageal squamous cell carcinoma and adenocarcinoma: New opportunities towards molecularly targeted therapy

Esophageal cancer is one of the most lethal cancers worldwide because of its rapid progression and poor prognosis. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are two major subtypes of esophageal cancer. ESCC predominantly affects African and Asian populations, which is closely related to chronic smoking and alcohol consumption. EAC typically arises in Barrett's esophagus with a predilection for Western countries. While surgical operation and chemoradiotherapy have been applied to combat this deadly cancer, molecularly targeted therapy is still at the early stages. With the development of large-scale next-generation sequencing, various genomic alterations in ESCC and EAC have been revealed and their potential roles in the initiation and progression of esophageal cancer have been studied. Potential therapeutic targets have been identified and novel approaches have been developed to combat esophageal cancer. In this review, we comprehensively analyze the genomic alterations in EAC and ESCC and summarize the potential role of the genetic alterations in the development of esophageal cancer. Progresses in the therapeutics based on the different tissue types and molecular signatures have also been reviewed and discussed.

Hematopoyesis Clonal de Potencial Indeterminado (HCPI): más allá de un modelo de campo de cancerización / Clonal hematopoiesis of indeterminate potential (CHIP): Beyond a model of field cancerization

Resumen La Hematopoyesis Clonal de Potencial Indeterminado (HCPI), más conocida como CHIP por sus siglas en inglés, se define como la expansión clonal de Células Madre Hematopoyéticas (CMHs) que albergan una o más mutaciones somáticas (en la mayoría de los casos una sola mutación) sin un cáncer hematológico subyacente ni evidencia morfológica definitiva de displasia, con una frecuencia alélica mayor al 2%. Los individuos con HCPI progresan a malignidad a una tasa de cerca del 0.5% a 1% por año, convirtiéndose así en un modelo de campo de cancerización. Sin embargo, sus implicaciones van más allá debido a que se ha encontrado asociación con enfermedades inflamatorias crónicas, como enfermedad cardiovascular ateroesclerótica, diabetes y enfermedades autoinmunes. Además, es considerado un factor predictivo en pacientes con cáncer hematolológico y no hematológico que reciben quimioterapia y radioterapia.

Abstract Clonal hematopoiesis of indeterminate potential (CHIP) is the expansion of hematopoietic stem cells harboring one or more somatic mutations. These patients do not have underlying hematologic neoplasia, myelodysplasia, or dysplasia, but can progress to a malignant state at a rate of 0.5 to 1% per year. CHIP could be used as a model of field cancerization, since it has been associated with chronic inflammatory diseases, arteriosclerosis, diabetes, and autoimmune conditions. CHIP is also considered a predictive factor in hematological and non-hematological cancer patients receiving chemotherapy and radiotherapy.

Germline and Somatic mutations in postmenopausal breast cancer patients

OBJECTIVES: In breast cancer (BC) patients, the frequency of germline BRCA mutations (gBRCA) may vary according to the ethnic background, age, and family history of cancer. Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is the second most common somatic mutated gene in BC; however, the association of mutations in both genes with cancer has not been thoroughly investigated. Thus, our aims were to investigate gBRCA mutation frequency in a cohort of postmenopausal Brazilian BC patients and the association of gBRCA1/BRCA2 and PIK3CA somatic mutations. METHODS: Forty-nine postmenopausal (>55 years) and forty-one young (≤35 years) BC patients were included in this study. The postmenopausal group included patients who reported a positive family history of cancer. For these patients, gBRCA1/BRCA2 were sequenced using next-generation sequencing (NGS) or Sanger sequencing. Data for gBRCA in young patients were already available from a previous study. DNA from formalin-fixed, paraffin-embedded (FFPE) tumors was obtained from 27 postmenopausal and 41 young patients for analyzing exons 9 and 20 of PIK3CA. The association between gBRCA1/BRCA2 and somatic mutations in PIK3CA was investigated. RESULTS: The overall frequency of gBRCA1/BRCA2 among the 49 postmenopausal patients was 10.2%. The frequencies of somatic mutations in PIK3CA in the postmenopausal and young patients were 37% and 17%, respectively (ns). The most common PIK3CA mutation was found to be E454A. Nonsense and frameshift mutations, which may counteract the oncogenic potential of PIK3CA were also detected. Regardless of age, 25% of BRCA1/BRCA2 mutation carriers and non-carriers , each, had PIK3CA somatic mutations. CONCLUSIONS: Data obtained indicate that BRCA1/BRCA2 gene testing may be considered for postmenopausal patients with BC who have a family history of cancer. Although some of them are not considered pathogenic, somatic variants of PIK3CA are frequently observed in BC patients, especially in postmenopausal patients.

Identification of an acute myeloid leukaemia associated noncoding somatic mutation at 3′ end of HOXA cluster

Noncoding somatic mutations have been demonstrated to play important role in tumourigenesis. Here we show that there exists an acute myeloid leukaemia associated noncoding somatic mutation at 3′ terminal of conserved HOXA cluster. The mutation was identified in the bone marrow blasts but not peripheral blood mononuclear cells or buccal cells of two M3 (acute promyelocytic leukaemia, APL) type patients from 45 acute myeloid leukaemia patients. The mutation also existed in a pair of twins one of them developed acute myeloid leukaemia M4 (acute myelomonocytic leukaemia) type. The mutation resides in about 2-kb downstream of HOXA1 gene where a functional retinoic acid response element is located and also bound by histone demethylase KDM3B. Reporter assay showed that the mutation results in the upregulation of transcriptional activity and unresponsiveness to retinoic acid receptor. To sum up, we identified a new acute myeloid leukaemia associated noncoding somatic mutation.

Somatic Mutations in Circulating Cell-Free D-Loop Region of Mitochondrial DNA: A Study from North-East India

Head and neck Squamous cell carcinoma (HNSCC) is highly prevalent in Northeast India. The widespread use of tobacco exposure is a known risk factor, makingmitochondrial DNA (mtDNA) more susceptible to damage by oxidative stress incomparison to nuclear DNA. Mitochondrial dysfunction being a hallmark of cancer, thestudy aims to evaluate liquid biopsy involving circulating cell-free mitochondrial DNA(cfmtDNA) as an early diagnostic marker by reducing the dependability over tumor tissuebiopsy specimen. A total of 50 HNSCC cases reported at Cancer Hospital, Guwahati MedicalCollege from January 2018 to August 2018 were included in this study. Cell-free DNA wasisolated using QIAamp Circulating Nucleic Acid Kit. PCR based amplification ofmitochondrial D-loop, followed by direct sequencing. Our result indicated the presence ofsomatic mutations (73(A/G), 93(G/A), 146(T/C) and 207 (G/A)). Polymorphism was alsoobserved in the sequences (263A>G, 275G>A, 318T>C, 16034T>C, 16257C>A and16519T>C) upon comparison with reference sequence. Analysis of c-tract region showedthe presence of an additional cytosine nucleotide at position 309.Identifying somaticmutations in cfmtDNA using liquid biopsy approach will certainly minimize thedependency of clinicians and molecular biologist over the availability of tumor tissuespecimens. The identified somatic variations from our study will help in theimplementation of preventive measure. Therefore, our study provides an early mtDNAdiagnostic marker using liquid biopsy approach.

Analysis of somatic mutations in metastatic ovarian carcinoma and related functional pathways / 第二军医大学学报

Objective: To screen the different mutated somatic genes between primary ovarian cancer and metastatic ovarian carcinoma using the whole exon sequencing data of catalogue of somatic mutations in cancer (COSMIC) database, and to analyze their function and signal pathway. Methods: The whole exon sequencing data of all tumors were downloaded from the COSMIC database, and the whole exon sequencing data of all ovarian cancer were extracted. In the R 3.5.3 environment, mutation rate of each mutated gene in the primary and metastatic ovarian carcinoma samples were performed. The χ2 test or Fisher's exact probability method was used to identify the mutated gene groups which had statistically significant difference in mutation rate. The mutated gene groups were further analyzed for gene ontology (GO) function and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment. Results: We found a total of 520 somatic mutations with statistically significant differences in mutation rate between primary ovarian cancer and metastatic ovarian carcinoma tissues, such as transmembrane protease serine 13 (TMPRSS13), Golgi brefeldin A resistance factor 1 (GBF1), Fos-like antigen 2 (FOSL2), mastermind-like 3 (MAML3), etc. Enriched GO function included presynapse organization, dendrite development, cell-cell adhesion via plasma membrane adhesion molecules, and actin binding, and so on. KEGG pathway included regulation of actin cytoskeleton, tricarboxylic acid carrier, and the like. Conclusion: It can provide clues for revealing the metastasis regulation mechanism of ovarian cancer by exploring different mutated gene group between primary ovarian cancer and metastatic ovarian carcinoma and its related functional pathways. The significant mutated gene group may be used as biomarkers for the diagnosis and treatment of ovarian metastatic cancer.

C: Consensus Cancer Driver Gene Caller / 基因组蛋白质组与生物信息学报·英文版

Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations. To address this issue, we present the first web-based application, consensus cancer driver gene caller (C), to identify the consensus driver genes using six different complementary strategies, i.e., frequency-based, machine learning-based, functional bias-based, clustering-based, statistics model-based, and network-based strategies. This application allows users to specify customized operations when calling driver genes, and provides solid statistical evaluations and interpretable visualizations on the integration results. C is implemented in Python and is freely available for public use at http://drivergene.rwebox.com/c3.

Screening and predication on tumor neoantigen for primary plasma cell leukemia / 中国肿瘤生物治疗杂志

@#Objective:To investigate the tumor-specific neoantigen for primary plasma cell leukemia (PCL) using gene sequencing technology combined with bioinformatic analysis. Methods: Peripheral blood samples of one patient with primary PCL during relapse and remission periods were collected. HLA molecular typing was performed using polymerase chain reaction with sequencing-based typing; whole-exome and transcriptome were sequenced by next-generation sequencing method; and bioinformatics software NetMHCpan was used to predict neoantigens. Results: Six tumor-specific missense mutations were found in the patient's peripheral blood during relapse period, located in genes FRG1, MLL3, SVIL, MYOM1, ZDHHC11 and RFPL4A.Considering patient's HLA sub-types, 43 neoantigens were predicted via bioinformatics. Considering that FRG1 and MLL3 had relatively high gene expression levels, 20 neoantigens derived from mutations of the two genes were preferentially selected, among which four neoantigens had high affinity with the patient's HLA molecules and thus had potential clinical application value. Conclusion: The study has completed a tumor neoantigen screen and prediction for primary PCL. This practice demonstrates that predicting neoantigen based on tumor-specific somatic mutation is feasible for primary PCL.

A clinical study of Proteus syndrome caused by a mosaic somatic mutation in AKT1 gene / 中华内科杂志

Objective Proteus syndrome is a rare disease. The aim of the present study was to analyze the clinical characteristics and gene mutations of Proteus syndrome with a case report and relevant literature review. Methods Clinical data of the patient with Proteus syndrome were collected in detail and biochemical measurements and radiological examinations were conducted. Tissues from phalanges with lesions were obtained to extract DNA, and Sanger sequencing of AKT1 gene was carried on. The pathogenic mutation was further tested in peripheral blood samples of the patient, his parents and 250 healthy volunteers. Orthopaedic surgery was performed on the affected limbs of the patient. Results The patient was presented with progressive overgrowth of the right extremity, scoliosis, cerebral connective tissue nevus and lower extremity venous. A heterozygous mutation of AKT1 gene (c. 49G>A) was identified in DNA extracted from the affected bone tissue of the patient, but not be found in genomic DNA of peripheral blood samples from the patient, his parents and 250 healthy volunteers. Movement function of the affected limb improved significantly after the operations. Conclusions The prominent features of Proteus syndrome are overgrowth of one extremity and cerebral connective tissue nevus. A mosaic somatic mutation of AKT1 gene is one of the pathogenic mutations for Proteus syndrome, and orthopedic surgery may be a good way to improve symptoms of the disease.

Identification of genomic aberrations associated with lymph node metastasis in esoph-ageal squamous cell carcinoma / 中国肿瘤临床

Objective: To investigate molecular markers associated with lymph node metastasis in esophageal squamous cell carcino-ma. Methods: Patients who meet the inclusion criteria were assigned into two groups, with and without lymph node metastasis. The statistically significant risk factors were evaluated using univariate analysis and multivariate Logistic regression analysis. The diagnostic threshold, sensitivity, and specificity were analyzed by Youden's index. The area under the ROC curve (AUC) was used to evaluate the power of test. Result: Univariate analysis and multivariate Logistic regression analysis showed that GC% of wild type base in the first somatic mutational position of the codons was a risk factor for lymph node metastasis [OR (95% CI): 0.931 (0.874-0.991), P<0.05]. AUC was 0.639 (P<0.05, 95% CI: 0.522-0.756). The Youden's index was 0.277, and the sensitivity and specificity were 56.6% and 71.1%, re-spectively. Conclusions: GC% of wild type base in the first somatic mutational position of the codons is significantly associated with lymph node metastasis in esophageal squamous cell carcinoma. The marker was found to be a protective factor for lymph node metas-tasis and has potential significance in clinical applications.

TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis / 基因组蛋白质组与生物信息学报·英文版

Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients, which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.

HER2 somatic mutations S310F and V777L are associated with poor survival in breast cancer patients / 中华普通外科杂志

Objective To assess the prognostic value of HER2 (human epidermal growth factor receptor-2) somatic mutations S310F and V777L in breast cancer patients.Methods HER2 somatic mutations S310F and V777L was screened in 338 consecutive patients with operable primary breast cancer using direct Sanger sequencing analysis.Results A total of 12 carriers of HER2 gene S310F and V777L mutations were found,10 were HER2-negative and 2 were HER2-positive.The median follow-up was 43 months (range from 1 to 61 months).4 were found with local or distant metastasis,and all were HER2-negative patients.Survival analysis found significantly lower survival rates in patients with S3 10F and V777L mutations than in non-carriers (RFS,unadjusted hazard ratio [HR]:5.89,95％ confidence interval [CI]:1.96-17.71,P ＜ 0.001;DRFS,unadjusted HR:5.53,95％ CI:1.56-19.55,P =0.003) and this difference was more manifest in the HER2-negative patients (RFS,unadjusted HR:8.93,95％ CI:2.79-28.62,P ＜ 0.001;DRFS,unadjusted HR:9.89,95％ CI:2.54-38.49,P ＜ 0.001).HER2 somatic mutations S310F and V777L are independent predictors of poor prognosis in breast cancer.Conclusion The prognosis of breast cancer patients carrying HER2 somatic mutations S310F and V777L is significantly worse than that of non-carriers,especially in HER2-negative patients.

Síndrome de Proteus: reporte de un caso y revisión de la literatura / Proteus syndrome: a case report and literature review

El síndrome de Proteus corresponde a una entidad poco frecuente caracterizada por un sobrecrecimiento progresivo de piel, tejido óseo y adiposo, debido a una mutación somática activante del gen AKT1. Existen distintas manifestaciones cutáneas entre las que se incluyen nevo cerebriforme de tejido conectivo plantar, nevo epidérmico, malformaciones vasculares y trastornos del tejido adiposo que pueden alertar al dermatólogo para poder diagnosticar esta condición, permitiendo un manejo precoz que impida el desarrollo de complicaciones y la muerte temprana. Presentamos el caso de una paciente de 9 años cuya historia clínica y examen físico reflejan los hallazgos clásicos del síndrome de Proteus, recalcando la importancia de un manejo multidisciplinario oportuno.

Proteus syndrome is a rare condition characterized by a progressive overgrowth of skin, bone tissue and adipose tissue, due to an activating somatic mutation of the AKT1 gene. Different cutaneous manifestations that include cerebriform connective tissue nevi, epidermal nevus, vascular malformations and adipose tissue disorders can alert the dermatologist to diagnose this condition, allowing an early management that prevents the complications and early death. We present the case of a 9-year-old patient whose clinical history and physical examination reflect the classic findings of Proteus syndrome, highlighting the importance of a multidisciplinary management.

Utilization of the oncoscan microarray assay in cancer diagnostics

Current strategies for cancer patient management include the use of genomic and proteomic test results to help guide therapeutic selection. The need for multi-target variant analysis is highlighted by the growing number of novel therapies to treat tumors with specific profiles and the increasing recognition that cancer is an extremely heterogeneous syndrome. Microarray analysis is a powerful genomic tool that provides genome-wide genetic information that is critical for guiding cancer treatments. Unlike constitutional applications of microarray analysis which are performed on whole blood samples, microarray analysis of solid tumors is challenging because tumor tissues are typically formalin fixed and paraffin embedded (FFPE). Genomic DNA extracted from FFPE tissues can also be fragmented into small pieces and yield much lower concentrations of DNA. We validated and implemented the Affymetrix OncoScan® FFPE assay to enable genome-wide analysis from these types of samples. The Affymetrix OncoScan® assay utilizes molecular inversion probes that generate multiplexed array hybridization targets from as short as 40 base-pairs of sequence and as low as approximately 80 ng of genomic DNA. OncoScan microarray analysis provides genomic information that includes structural variations, copy number variations and SNPs in a timely and a cost-effective manner from FFPE tumor tissues (AU)

Identification of genes associated with gastric cancer prognosis from TCGA datasets / 基础医学与临床

Objective To identify genes associated with prognosis or differentiated type in gastric cancer from fre quently mutated genes or highly-expressed genes,using large-scale genomic data from The Cancer Genome Atlas.Methods The somatic mutation data,RNAseqV2 data and clinical information were downloaded from the TCGA website.The frequency of deleterious somatic mutations for each gene was counted to select the frequently mutated genes.DESeq2 was used to analyze the gene expression data.Then survival analysis was performed on genes highlyexpressed in the tumor tissue.Kaplan-Meier curves were generated by R-survival package,and significance was evaluated by log-rank test.Results The frequency for pathogenic mutations in PIK3CA and APC was significantly discordant between different grades of gastric cancer.2 040 genes were up-regulated in tumor tissue,while 2 357 genes were down-regulated.Among the up-regulated genes,7 genes were associated with poor prognosis of gastric cancer and one was associated with better prognosis.Conclusions Genes associated with differentiation types or prognosis in gastric cancer are identified.The result may clue us future research on potential prognostic markers in clinical treatment.

Recent progress of myelodysplastic syndromes / 白血病·淋巴瘤

The myelodysplastic syndromes (MDS), which are characterized by the presence of ineffective hematopoiesis and an increased risk of transformation into acute myeloid leukemia (AML), are a group of clonal disorders deriving from damage of the hematopoietic stem/progenitor cells. Researches in the past few years have still highly recommended the pathogenesis,clinical new agents and combination therapy, immunotherapy and hematopoietic stem cell transplantation of the MDS. This article will introduce several highlights of MDS combined with the relevant reports in the 57th American Society of Hematology annual meeting.

Recognizing Paradigm Instability in Theories of Carcinogenesis.

The dominant view that cancer arises from successive mutations in somatic cells is so unquestioned that accumulating challenges from experimental and observational results are rarely addressed in the scientific literature. Based on these challenges, we argue that the scientific understanding of carcinogenesis has entered a period of paradigm instability. New research directions are therefore needed.

Hypothesis: Somatic Mosaicism and Parkinson Disease

Mutations causing genetic disorders can occur during mitotic cell division after fertilization, which is called somatic mutations. This leads to somatic mosaicism, where two or more genetically distinct cells are present in one individual. Somatic mutations are the most well studied in cancer where it plays an important role and also have been associated with some neurodegenerative disorders. The study of somatic mosaicism in Parkinson disease (PD) is only in its infancy, and a case with somatic mutation has not yet been described. However, we can speculate that a somatic mutation affecting cells in the central nervous system including substantia nigra dopaminergic neurons could lead to the development of PD through the same pathomechanisms of genetic PD even in the absence of a germ-line mutation. Theoretically, a number of genes could be candidates for genetic analysis for the presence of somatic mosaicism. Among them, SNCA and PARK2 could be the best candidates to analyze. Because analyzing brain tissues in living patients is impossible, alternative tissues could be used to indicate the genetic status of the brain. Performance of the technology is another factor to consider when analyzing the tissues.

New Lung Cancer Panel for High-Throughput Targeted Resequencing

We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture assay was designed to cover 99% of it. This method exhibited about 97% mean coverage at 30x sequencing depth and 42% average specificity when sequencing of more than 3.25 Gb was carried out for the normal sample. We discovered 513 variations from targeted exome sequencing of lung cancer cells, which is 3.9-fold higher than in the normal sample. The variations in cancer cells included previously reported somatic mutations in the COSMIC database, such as variations in TP53, KRAS, and STK11 of sample H-23 and in EGFR of sample H-1650, especially with more than 1,000x coverage. Among the somatic mutations, up to 91% of single nucleotide polymorphisms from the two cancer samples were validated by DNA microarray-based genotyping. Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples, and the profiling method can be used as a robust and effective protocol for somatic variant screening.