Mutational landscape of TP53 and CDH1 in gastric cancer

In this editorial we comment on an article published in a recent issue of the World J Gastrointest Surg.A common gene mutation in gastric cancer(GC)is the TP53 mutation.As a tumor suppressor gene,TP53 is implicated in more than half of all tumor occurrences.TP53 gene mutations in GC tissue may be related with clinical pathological aspects.The TP53 mutation arose late in the progression of GC and aided in the final switch to malignancy.CDH1 encodes E-cadherin,which is involved in cell-to-cell adhesion,epithelial structure maintenance,cell polarity,differentiation,and intracellular signaling pathway modulation.CDH1 mutations and functional loss can result in diffuse GC,and CDH1 mutations can serve as independent prognostic indicators for poor prognosis.GC patients can benefit from genetic counseling and testing for CDH1 mutations.Demethylation therapy may assist to postpone the onset and progression of GC.The investigation of TP53 and CDH1 gene mutations in GC allows for the investigation of the relationship between these two gene mutations,as well as providing some basis for evaluating the prognosis of GC patients.

The complete plastome sequences of five Aponogeton species(Aponogetonaceae):Insights into the structural organization and mutational hotspots

Members of the aquatic plant genus Aponogeton are widely used commercially in aquariums because of their variable leaf shape and unique inflorescences.However,due to extensive similarity between species in this genus,morphological characters are generally inadequate for taxonomic classification.Currently,molecular makers available for taxonomic and phylogenetic studies of Aponogeton are limited.One approach to clarifying relationships between species in these complex groups is to use divergence hotspot regions within the genome.Here,we sequenced and analyzed the plastomes of five Aponogeton species collected from China,Zambia,and Kenya,and subsequently screened these plastomes for divergent DNA hotspots.The five plastomes are circular structures with sizes ranging from 154,167 bp to 154,860 bp.The Large and the Small Single Copies are separated by two Inverted Repeats.One hundred and thirteen unique genes were identified including 79 protein-coding,30 tRNA,and four rRNA genes.We found that the most abundant repeats in all but one species were mononucleotide repeats(A/T)and that there were 23 potential RNA ending sites.Interestingly,a^3 kb inversion,which includes the accD gene,was detected within the Asian species of Aponogeton.The inversion may be related to more frequent exchanges between this region and the nuclear genome.Furthermore,we detected mutational hotspot sites among the five Aponogeton species.Three of these hotspots are intergenic spacer regions(accD-psaI,rbcL-accD and trnH-GUG-psbA)that might be suitable for use as barcodes to resolve intra-generic relationships.We also identified four highly variable protein-coding genes(ccsA,rpl22,rps16 and ycf1)may be used as barcodes to resolve the higher-level phylogenies.Our study will provide valuable molecular resources for the taxonomic and phylogenomic study of the complex genus Aponogeton.

Epidemiology and Mutational Analysis of Global Strains of Crimean-Congo Haemorrhagic Fever Virus

Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high fatality.Cases are reported in several countries in Africa,Europe,the Middle East,and Asia.Phylogenetic analyses based on the virus S (nucleocapsid),M (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require elucidation.In this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 samples.We then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain volume.Finally,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific lineage.Based on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.

Mutational and Phylogenetic Analysis of <i>nfxB</i>Gene in Multidrug-Resistant Clinical Isolates of <i>Pseudomonas aeruginosa</i>Hyperexpressing MexCD-OprJ Efflux Pump

The present study focused on MexCD-OprJ efflux pump and its regulatory gene nfxB in multidrug resistant (MDR) clinical isolates of Pseudomonas aeruginosa collected from Kerala, South India. Semi-quantitative reverse transcription-PCR technique was employed to detect hyperexpression of the efflux pump gene, mexD. Amplicons from nfxB gene of isolates hyperexpressing the efflux pump were sequenced for mutational and phylogenetic analysis. Among 29 isolates of MDR P. aeruginosa, increased mexD transcription was detected in 10.3% of the isolates when compared with P. aeruginosa reference strain, PAO (MTCC-3541). Various synonymous and non-synonymous mutations in nfxB regulatory gene sequences were detected. Notably, mutations detected in the strains designate Pa6 and Pa7 have been found to be novel and are hitherto unreported in GenBank data base. The genetic divergence and homogeneity of the nfxB regulatory gene sequences of mexCD-oprJ operon were clearly apparent in the phylogram generated employing similar sequences retrieved from the public database.

Tumour mutational burden is overestimated by target cancer gene panels

Background:Tumour mutational burden(TMB)has emerged as a predictive marker for responsiveness to immune checkpoint inhibitors(ICI)in multiple tumour types.It can be calculated from somatic mutations detected from whole exome or targeted panel sequencing data.As mutations are unevenly distributed across the cancer genome,the clinical implications from TMB calculated using different genomic regions are not clear.Methods:Pan-cancer data of 10,179 samples were collected from The Cancer Genome Atlas cohort and 6,831 cancer patients with either ICI or non-ICI treatment outcomes were derived from published papers.TMB was calculated as the count of non-synonymous mutations and normalised by the size of genomic regions.Dirichlet method,linear regression and Poisson calibration models are used to unify TMB from different gene panels.Results:We found that panels based on cancer genes usually overestimate TMB compared to whole exome,potentially leading to misclassification of patients to receive ICI.The overestimation is caused by positive selection for mutations in cancer genes and cannot be completely addressed by the removal of mutational hotspots.We compared different approaches to address this discrepancy and developed a generalised statistical model capable of interconverting TMB derived from whole exome and different panel sequencing data,enabling TMB correction for patient stratification for ICI treatment.We show that in a cohort of lung cancer patients treated with ICI,when using a TMB cutoffof 10 mut/Mb,our corrected TMB outperforms the original panel-based TMB.Conclusion:Cancer gene-based panels usually overestimate TMB,and these findings will be valuable for unifying TMB calculations across cancer gene panels in clinical practice.

Germline MLH1 and MSH2 mutational spectrum including frequent large genomic aberrations in Hungarian hereditary non-polyposis colorectal cancer families:Implications for genetic testing

AIM: To analyze the prevalence of germline MLH1 and MSH2 gene mutations and evaluate the clinical characteristics of Hungarian hereditary non-polyposis colorectal cancer (HNPCC) families. METHODS: Thirty-six kindreds were tested for mutations using conformation sensitive gel electrophoreses, direct sequencing and also screening for genomic rearrangements applying multiplex ligation-dependent probe amplifi cation (MLPA). RESULTS: Eighteen germline mutations (50%) were identifi ed, 9 in MLH1 and 9 in MSH2. Sixteen of these sequence alterations were considered pathogenic, the remaining two were non-conservative missense alterations occurring at highly conserved functional motifs. The majority of the defi nite pathogenic mutations (81%, 13/16) were found in families fulfilling the stringent Amsterdam Ⅰ/Ⅱ criteria, including three rearrangements revealed by MLPA (two in MSH2 and one in MLH1). However, in three out of sixteen HNPCC-suspected families (19%), a disease-causing alteration could be revealed. Furthermore, nine mutations described here are novel, and none of the sequence changes were found in more than one family.CONCLUSION: Our study describes for the f irst time the prevalence and spectrum of germline mismatch repair gene mutations in Hungarian HNPCC and suspected-HNPCC families. The results presented here suggest that clinical selection criteria should be relaxed and detection of genomic rearrangements should be included in genetic screening in this population.

Mutational Analysis of Region-cytotoxicity Relationship in Human Transmembrane Tumor Necrosis Factor-alpha

Objective To determine the region of human transmembrane tumor necrosis factor-alpha (TM-TNFa) , essential for cytotoxic activity a-gainst human breast cancer cell line MCF-7.Methods Single amino-acid-substituted TM-TNFa mutant proteins (muteins) were produced by in vitro transcription linked translation techniques. The cDNA of TM-TNFa was site-directed mutagenized by recombinant PCR.Results 13 single ammo-acid substituted TM-TNFa muteins were generated and assayed for cytotoxic activity. The cytotoxic activities of TM-TNFa muteins, eg, TM-TNFa -71/Lys, -28/Phe and 117/Leu were significantly decreased (P < 0.01) compared to that of parent TM-TNFa, 143/Tyr decreased 4-folds, and -17/Thr, -39/Ser, 119/His, 35/Gly, 95/Cys and 147/Phe decreased 1.5-2.5-folds, respectively. However, the cytotoxic activities of TM-TNFa-8/Arg, 31/Gly and 87/Phe showed no significant change. Conclusion These results indicate that the regions associated with cytotoxic-activity of TM-TNFa are different with that of secretory TNF-alpha (S-TNFa) . The inner cell region and transmembrane region of TM-TNFa are related to the cytotoxic activity of TM-TNFa.

Mutational separation and clinical outcomes of TP53 and CDH1 in gastric cancer

BACKGROUND Gastric cancer(GC)is a deadly tumor with the fifth highest occurrence and highest global mortality rates.Owing to its heterogeneity,the underlying mechanism of GC remains unclear,and chemotherapy offers little benefit to individuals.AIM To investigate the clinical outcomes of TP53 and CDH1 mutations in GC.METHODS In this study,202 gastric adenocarcinoma tumor tissues and their corresponding normal tissues were collected.A total of 490 genes were identified using target capture.Through t-test and Wilcoxon rank-sum test,somatic mutations,microsatellite instability,and clinical statistics,including overall survival,were detected,compared,and calculated.RESULTS The mutation rates of 32 genes,including TP53,SPEN,FAT1,and CDH1 exceeded 10%.TP53 mutations had a slightly lower overall occurrence rate(33%).The TP53 mutation rate was significantly higher in advanced stages(stage Ⅲ/Ⅳ)than that in early stages(stage Ⅰ/Ⅱ)(P<0.05).In contrast,CDH1 mutations were significantly associated with diffuse GC.TP53 is related to poor prognosis of advanced-stage tumors;nevertheless,CDH1 corresponds to a diffuse type of cancer.TP53 is exclusively mutated in CDH1 and is primarily affected by two distinct GC mechanisms.CONCLUSION Different somatic mutation patterns in TP53 and CDH1 indicate two major mechanisms of GC.

New mutational trends in the HA protein of 2009 H1N1 pandemic influenza virus from May 2010 to February 2011

As we enter the year of 2011, the 2009 H1N1 pandemic influenza virus is in the news again. At least 20 people have died of this virus in China since the beginning of 2011 and it is now the predominant flu strain in the country. Although this novel virus was quite stable during its run in the flu season of 2009-2010, a genetic variant of this virus was found in Singapore in early 2010, and then in Australia and New Zealand during their 2010 winter influenza season. Several critical mutations in the HA protein of this variant were uncovered in the strains collected from January 2010 to April 2010. Moreover, a structural homology model of HA from the A/Brisbane/10/2010(H1N1) strain was made based on the structure of A/California/04/2009 (H1N1). The purpose of this study was to investigate mutations in the HA protein of 2009 H1N1 from sequence data collected worldwide from May 2010 to February 2011. A fundamental problem in bioinformatics and biology is to find the similar gene sequences for a given gene sequence of interest. Here we proposed the inverse problem, i.e., finding the exemplars from a group of related gene sequences. With a clustering algorithm affinity propagation, six exemplars of the HA sequences were identified to represent six clusters. One of the clusters contained strain A/Brisbane/12/2010(H1N1) that only differed from A/Brisbane/10/2010 in the HA sequence at position 449. Based on the sequence identity of the six exemplars, nine mutations in HA were located that could be used to distinguish these six clusters. Finally, we discovered the change of correlation patterns for the HA and NA of 2009 H1N1 as a result of the HA receptor binding specificity switch, revealing the balanced interplay between these two surface proteins of the virus.

Mutational analysis of Ras hotspots in patients with urothelial carcinoma of the bladder

BACKGROUND Mutational activation of Ras genes is established as a prognostic factor for the genesis of a constitutively active RAS-mitogen activated protein kinase pathway that leads to cancer.Heterogeneity among the distribution of the most frequent mutations in Ras isoforms is reported in different patient populations with urothelial carcinoma of the bladder(UCB).AIM To determine the presence/absence of mutations in Ras isoforms in patients with UCB in order to predict disease outcome.METHODS This study was performed to determine the mutational spectrum at the hotspot regions of H-Ras,K-Ras and N-Ras genes by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP)and DNA sequencing followed by their clinical impact(if any)by examining the relationship of mutational spectrum with clinical histopathological variables in 87 UCB patients.RESULTS None of the 87 UCB patients showed point mutations in codon 12 of H-Ras gene;codon 61 of N-Ras gene and codons 12,13 of K-Ras gene by PCR-RFLP.Direct DNA sequencing of tumor and normal control bladder mucosal specimens followed by Blastn alignment with the reference wild-type sequences failed to identify even one nucleotide difference in the coding exons 1 and 2 of H-Ras,NRas and K-Ras genes in the tumor and control bladder mucosal specimens.CONCLUSION Our findings on the lack of mutations in H-Ras,K-Ras and N-Ras genes could be explained on the basis of different etiological mechanisms involved in tumor development/progression,inherent genetic susceptibility,tissue specificity or alternative Ras dysfunction such as gene amplification and/or overexpression in a given cohort of patients.

Active motif finder-a bio-tool based on mutational structures in DNA sequences

Active Motif Finder （AMF） is a novel algorithmic tool, designed based on mutations in DNA sequences. Tools available at present for finding motifs are based on matching a given motif in the query sequence. AMF describes a new algorithm that identifies the occurrences of patterns which possess all kinds of mutations like insertion, deletion and mismatch. The algorithm is mainly based on the Alignment Score Matrix （ASM） computation by com paring input motif with full length sequence. Much of the effort in bioinformatics is directed to identify these motifs in the sequences of newly discovered genes. The proposed bio-tool serves as an open resource for analysis and useful for studying polymorphisms in DNA sequences. AMF can be searched via a user-friendly interface. This tool is intended to serve the scientific community working in the areas of chemical and structural biology, and is freely available to all users, at http：//www.sastra.edu/scbt/amf/.

Mutational analysis of KCNJll in Chinese elderly essential hypertensive patients

Objective To compare the distribution ofKCNJll polymorphisms between elderly Chinese population with and without hypertension. Methods We examined the mutation of KCNJll gene by directly sequencing. Data for the present study were obtained from 250 hypertensive subjects （60 to 83 years old） as well as 250 normotensive subjects （60 to 86 years old）. Results We found nine different mutations in KCNJ11, including six novel mutations （1131M, L1471, L147V, L147L, Q235H, G245C）. None of the novel mutations were found in the normotensive subjects, and all the residues were conserved in other species. These sequence variants in Chinese population indicate the diversity of the human library and the complexity of hypertension. Conclusions The consistent finding of our present study provided a basis for the development of new strategies to diagnosis and treat hypertension in the elderly.

Mutational screening of affected cardiac tissues and peripheral blood cells identified novel somatic mutations in GATA4 in patients with ventricular septal defect

The aim of this study was to examine how somatic mutations of the GATA4 gene contributed to the genesis of ventricular septal defect （VSD）. The coding and intron-exon boundary regions of GATA4 were sequenced of DNA samples from peripheral blood cells and cardiac tissues of twenty surgically treated probands with VSD. Seven novel heterozygous variants were detected in cardiac tissues from VSD patients, but they were not detected in the peripheral blood cells of VSD patients or in 500 healthy control samples. We replicated 14 single nucleotide polymorphisms （SNPs） reported in NCBI. Bioinformatics analysis was performed to analyze the possible mechanism by which mutations were linked to VSD. Among those variants, c. 1004C〉A （p.S335X） occurred in the highly conserved domain of GATA4 and generated a termination codon, which led to the production of truncated GATA4. The seven novel heterozygous GATA4 mutations were only identified in cardiac tissues with VSD, suggesting that they are of somatic origin. A higher mutation rate in cardiac tissues than in peripheral blood cells implies that the genetic contribution to VSD may have been underestimated.

New era of cystic fibrosis:Full mutational analysis and personalized therapy

Despite its apparently simple genetics,cystic fibrosis(CF) is a rather complex genetic disease.A lot of variability in the steps of the path from the cystic fibrosis transmembrane conductance regulator(CFTR) gene to the clinical manifestations originates an uncertain genotype- phenotype relationship.A major determinant of this uncertainty is the incomplete knowledge of the CFTR mutated genotypes,due to the high number of CFTR mutations and to the higher number of their combinations in trans and in cis.Also the very limited knowledge of functional effects of CFTR mutated alleles severely impairs our diagnostic and prognostic ability.The final phenotypic modulation exerted by CFTR modifier genes and interactome further complicates the framework.The next generation sequencing approach is a rapid,lowcost and high-throughput tool that allows a near complete structural characterization of CFTR mutated genotypes,as well as of genotypes of several other genes cooperating to the final CF clinical manifestations.This powerful method perfectly complements the new personalized therapeutic approach for CF.Drugs active on specific CFTR mutational classes are already available for CF patients or are in phase 3 trials.A complete genetic characterization has been becoming crucial for a correct personalized therapy.However,the need of a functional classification of each CFTR mutation potently arises.Future big efforts towards an ever more detailed knowledge of both structural and functional CFTR defects,coupled to parallel personalized therapeutic interventions decisive for CF cure can be foreseen.

The correlation of miRNA expression and tumor mutational burden in uterine corpus endometrial carcinoma

Background:The relationship between microRNA(miRNA)expression patterns and tumor mutation burden(TMB)in uterine corpus endometrial carcinoma(UCEC)was investigated in this study.Methods:The UCEC dataset from The Cancer Genome Atlas(TCGA)database was used to identify the miRNAs that differ in expression between high TMB and low TMB sample sets.The total sample sets were divided into a training set and a test set.TMB levels were predicted using miRNA-based signature classifiers developed by Lasso Cox regression.Test sets were used to validate the classifier.This study investigated the relationship between a miRNA-based signature classifier and three immune checkpoint molecules(programmed cell death protein 1[PD-1],programmed cell death ligand 1[PD-L1],cytotoxic T lymphocyte-associated antigen 4[CTLA-4]).For the miRNA-based signature classifier,functional enrichment analysis was performed on the miRNAs.An analysis of the relationship between PD-1,PD-L1,and CTLA-4 immune checkpoint genes was carried out using the miRNA-based signature classifier.Results:We identified 27 differentially expressed miRNAs in miRNA-base signature.For predicting the TMB level,27-miRNA-based signature classifiers had accuracies of 0.8689 in the training cohort,0.8276 in the test cohort,and 0.8524 in the total cohort.The correlation between the miRNA-based signature classifier and PD-1 was negative,while the correlation between PD-L1 and CTLA4 was positive.Based on the miRNA profiling described above,we validated the expression levels of 9 miRNAs in clinical samples by quantitative reverse transcription PCR(qRT-PCR).Four of them were highly expressed and many cancer-related and immune-associated biological processes were linked to these 27 miRNAs.Thus,the developed miRNA-based signature classifier was correlated with TMB levels that could also predict TMB levels in UCEC samples.Conclusion:In this study,we investigated the relationship between a miRNAbased signature classifier and TMB levels in Uterine Corpus Endometrial Carcinoma.Further,this is the first study to confirm their relationship in clinical samples,which may provide more evidence support for immunotherapy of endometrial cancer.

Mutational analysis of the PTEN gene in soft tissue sarcomas

Objective： This study was to investigate whether PTEN mutations play a role in the carcinogenesis of soft tissue sarcomas （STS）. Methods： Polymerase chain reaction-single strand conformation polymorphism （PCR-SSCP） was used to amplify 4 exons of PTEN and to analyze the conformation polymorphism, then DNA sequencing methods was used to detect point mutation of PTEN gene four exons of abnormal single strand conformation in soft tissue sarcomas. Results： Two of 86 cases showed 130th condon G→A missense mutation in the exon 8 of PTEN gene, and this mutation made Arg to change to Gin in PTEN protein structure 334th condon A→T missense mutation in the exon 8 of PTEN gene, and this mutation made Asn to change to Lys in PI-EN protein structure. Conclusion： These data indicated the existence of PTEN mutation in soft tissue sarcomas, but PTEN gene mutation rate is very low. PTEN mutation may prays an less important role in the development and malignant transformation of soft tissue sarcomas.

<i>PAH</i>mutational spectrum: still expanding

Phenylketonuria (PKU, MIM 261600) is the most common inborn error of amino acid metabolism. To date, a total of more than 500 mutations have been associated with the disease. In this report, the novel p.Glu182Lys mutation, found in a Portuguese family in combination with the previously reported p.Leu 348Val, is presented and its putative deleterious impact discussed.

Mutational search for high temperature (60^oC) tolerant variant of Rhizobium species CWP G34A—Mutation generates high temperature variant of Rhizobium species Cwp G34A

This study focused on the development of thermophilic strain/s of a cowpea (Vigna unguiculata) compatible nitrogen fixing bacterium. A preliminary plant screening was carried out using some strains of tropical rhizobia and cowpea. Rhizobium species CWP G34A that formed Fix+ nodules repeatedly was selected for further studies. First, it was tested for growth at high temperatures of 40 to 55oC at 5oC interval with 28oC as the control temperature. Mutagenesis was conducted on the bacterium with ethylmethane sulphonate (EMS). The wildtype and mutants generated were tested for high temperature tolerance by growing them individually in nutrient broth at 60oC for 24 hours. Optical density (670 nm) was read before and after incubation. The mutants were grouped into classes based on percentage difference in OD values obtained before and after exposure to 60oC. Rhizobium species CWP G34A produced functional pink nodules on the cowpea consistently in three different plant tests. There was no growth at all the temperatures tested except at 28oC and 40oC after 24 hours of incubation. It grew better at former (51 × 1010 Cfu/ml) than latter (11 Cfu/ml) temperature. Like the parental strain, all the mutants but one, did not grow after exposure to 60oC. Sixty degree centigrade caused various reductions in optical density (OD) values of the variants. Eleven classes of the mutants were formed with membership percentage ranging from 1 to 22%. Class 1 contains only one member while class 11 has the highest mutant population of 22% with OD difference of 0 to 10% and –90 to –100% respectively. The high percentage reduction in the OD of variants in class 11 is similar to that of the unmutated cells (–94.56%). The only mutant that survived the 60oC and grew was MU70. An increase of 1.67% in OD was obtained for MU70. Mutant MU70 therefore appeared a promising strain that can be further tested to inoculate cowpea in the dry and warm season for increased nitrogen fixation. This will provide encouraging information for farmers to grow the cowpea throughout the year particularly under high temperatures in summer in order to boost the yield of the legume.

The unique genomic landscape and prognostic mutational signature of Chinese clear cell renal cell carcinoma

Background:The genomic background affects the occurrence and metastasis of cancers,including clear cell renal cell carcinoma(ccRCC).However,reports focusing on the prognostic mutational signature of Chinese ccRCC are lacking.Methods:Overall,929 patients,including a training cohort with Chinese patients(n=201),a testing cohort with Caucasian patients(n=274),and a validation cohort(n=454)were analyzed for the genomic landscape of ccRCC.Then,machine-learning algorithms were used to identify and evaluate the genomic mutational signature(GMS)in ccRCC.Analyses for prognosis,immune microenvironment,association with independent clinicopathological features,and predictive responses for immune checkpoint therapies(ICTs)were performed.Results:The DNA variation data of 929 patients with ccRCC suggested markedly differential genomic mutational frequency of the most frequent genes,such as VHL,PBRM1,BAP1,SETD2,and KDM5C between the Chinese and Caucasian populations.PBRM1 showed significant co-occurrence with VHL and SETD2.We then successfully iden-tified a seven-gene mutational signature(GMS^(Mut))that included mutations in FBN1,SHPRH,CELSR1,COL6A6,DST,ABCA13,and BAP1.The GMS^(Mut)significantly predicted progressive progression(P<0.0001,HR=2.81)and poor prognosis(P<0.0001,HR=3.89)in the Chinese training cohort.Moreover,ccRCC patients with the GMS^(Mut)had poor survival rates in the testing cohort(P=0.020)and poor outcomes were predicted for those treated with ICTs in the validation cohort(P=0.036).Interestingly,a favorable clinical response to ICTs,ele-vated expression of immune checkpoints,and increased abundance of tumor-infiltrated lymphocytes,specifically CD8^(+)T cells,Tregs,and macrophages,were observed in the GMS^(Mut)cluster.Conclusions:This study described the pro-tumorigenic GMS^(Mut)cluster that improved the prognostic accuracy in Chinese patients with ccRCC.Our discovery of the novel independent prognostic signature highlights the relationship between tumor phenotype and genomic mutational characteristics of ccRCC.

Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39

Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic stability.However,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)lines.This rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T direction.The high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in nature.In line with this,S.pneumoniae D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among bacteria.Treatment with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and S.pneumoniae lacks a stress response pathway.Our findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.