Oc Mutation Research Articles

Significance of tumor mutation burden combined with immune infiltrates in the progression and prognosis of ovarian cancer

BackgroundOvarian cancer (OC) is the most malignant tumor in the female reproductive system. About 75% of OC in complete remission of clinical symptoms still develop a recurrence. Therefore, searching for new treatment methods plays an important role in improving the prognosis of OC.MethodsWe downloaded the MAF files, RNA-seq data and clinical information from the TCGA database. The “maftools” package in R software was used to visualize the OC mutation data. We calculated the tumor mutation burden (TMB) of OC and analyzed its correlation with clinicopathological parameters and prognostic value. Tumor mutation burden related signature model was constructed to predict the overall survival (OS) of OC.ResultsThe results revealed that there was a statistical correlation between TMB and FIGO stage, grade and tumor residual size of ovarian cancer patients. The Kaplan–Meier curve indicated that a high TMB is associated with better clinical outcomes of OC. The difference analysis indicated 24 upregulated genes and 619 downregulated genes in the high-TMB group compared with the low-TMB group. Besides, the TMBRS model based on five hub genes (RBMS3, PLA2G5, CDH2, AMHR2 and ADAMTS8) was constructed to predict the OS of OC. The ROC curve and validation data sets all revealed that the TMBRS model was reliable in predicting recurrence risk. Immune microenvironment analysis indicated the correlations between TMB and infiltrating immune cells.ConclusionsOur results suggest that TMB plays an important role in the prognosis and guiding immunotherapy of OC. By detecting the TMB of OC, clinicians can more accurately treat patients with immunotherapy, thereby improving their survival rate.

Simultaneous germline and somatic sequencing in ovarian carcinoma: mutation rate and impact on clinical decision-making

ObjectiveGermline and somatic BRCA1 and BRCA2 (BRCA) mutations predict treatment response in patients with epithelial ovarian, peritoneal or fallopian tube cancer (OC), yet only germline testing is routinely pursued or reimbursed at diagnosis. We report our experience with clinical testing of paired tumor and germline DNA for OC mutations. MethodsSimultaneous sequencing using the BROCA assay of DNA from paired blood and neoplastic tissue became clinically available at our institution in 2017. We retrospectively reviewed the medical records of OC cases tested from 7/2017 to 7/2018. We calculated the rates of known pathogenic germline mutations and actionable somatic mutations, defined as those for which targeted therapies exist. ResultsWe identified 43 women (36 new diagnoses, seven recurrences) who underwent testing. Average age at diagnosis was 60. OC samples came from surgical specimens in 31 cases (72.1%), from biopsy in 11 cases (25.6%), and from cytology in one case (2.3%). We identified pathogenic germline mutations in six cases (14%), actionable somatic mutations in 15 cases (35%), and both a somatic and germline mutation in one case (2%). BRCA mutations accounted for 59% of all mutations. Of 40 cases with sufficient follow-up, providers documented reviewing results of genetic testing in 34 (85%), which influenced clinical decisions in 12 (30%). ConclusionsSimultaneous germline and tumor sequencing is an efficient way to provide enhanced information to guide the care of OC patients. This approach can identify somatic BRCA mutations at diagnosis, allowing physicians to provide PARP inhibitor maintenance and improve outcomes for those patients.

The gene encoding the mouse homologue of the human osteoclast-specific 116-kDa V-ATPase subunit bears a deletion in osteosclerotic ( oc/oc) mutants

Osteosclerosis ( oc) is an autosomal recessive lethal mutation that impairs bone resorption by osteoclasts, and induces a general increase of bone density in affected mice. Genetic mapping of the oc mutation was used as a backbone in a positional cloning approach in the pericentromeric region of mouse chromosome 19. Perfect cosegregation of the osteopetrotic phenotype with polymorphic markers enabled the construction of a sequence-ready bacterial artificial chromosome (BAC) contig of this region. Genomic sequencing of a 200-kb area revealed the presence of the mouse homologue to the human gene encoding the osteoclast-specific 116-kDa subunit of the vacuolar proton pump. This gene was located recently on human 11q13, a genomic region conserved with proximal mouse chromosome 19. Sequencing of the 5′ end of the gene in oc/oc mice showed a 1.6-kb deletion, including the translation start site, which impairs genuine transcription of this subunit. The inactivation of this osteoclast-specific vacuolar proton ATPase subunit could be responsible for the lack of this enzyme in the apical membranes of osteoclast cells in oc/oc mice, thereby preventing the resorption function of these cells, which leads to the osteopetrotic phenotype.

Regulation of purine biosynthetic genes expression inSalmonella typhimurium IV Oc mutation site ofpurG and its function analysis

Salmonella typhimurium 5 phosphoribosylformylglycinamide (FGAR) amidotransferase encoded bypurG gene catalyzes the conversion of FGAR to formylglycinamide ribonucleotide (FGAM) in the presence of glu- tamine and ATP for thede novo purine nucleotide biosynthesis.purG gene is negatively regulated by a repressor-operator system. The O(+) purG and O(c) purG were cloned respectivelyin vivo. Restriction enzymes analysis of preliminary clones pLBG-1 (O(+)) and pLBG-2 (O(c)) were carried out. The hybrid plasmids pLB1933 (O(+)) and pLB1927 (O(c)) containing 5' control region ofpurG were constructed and the DNA sequences were determined respectively, DNA sequences data showed that O(c) mutation ofpurG occurred at the 3rd position of 16 bp PUR box in the 5' control region (G-->A). Gel retardation experiment indicated that the repressor bound well with O(+) PUR box, but not with O(c) PUR box. The result strongly supported the idea that PUR box is the binding region of repressor protein and the 3rd position base G of PUR box is essential for the binding function with repressor protein.

Observations on the formation of deletions on monomeric and dimeric plasmids in Escherichia coli.

We have studied the formation of spontaneous mutations on plasmids present in the monomeric and dimeric states in a recF strain of Escherichia coli. Two test systems were employed: (i) the precise excision of Tn5 from the tetA gene of the plasmid pBR322 and (ii) operator constitutive (Oc) mutations on the pBR322-derived plasmid pPY97. The rate of Oc mutations was increased by a factor of three when this plasmid was present in the dimeric state compared to the monomeric state and the Oc phenotype was caused by small deletions in the operator sequence. No apparent mutational hot-spot was found. The rate of Tn5 excision was increased on dimeric compared to monomeric plasmids. Excision from a dimeric plasmid usually resulted in two types of mutant plasmids; a dimeric plasmid, where the Tn5 had excised from one of the plasmid units, and a monomeric parental pBR322. A mechanisms to account for this is suggested. Complementation tests revealed that the increased mutation rate on dimeric plasmids is the result of dimers being mutaphilic per se, rather than the result of a general, trans-acting increase in mutation rates of the host, induced by the presence of the dimeric plasmid. Furthermore, it was found that the rate of Tn5 excision from plasmids in the monomeric state was increased when the region carrying the inserted Tn5 was duplicated.

Osteosclerosis, a recessive skeletal mutation on chromosome 19 in the mouse.

Osteosclerosis (oc) is an osteopetrotic mutation in the mouse inherited as an autosomal recessive on chromosome 19. Affected animals (oc/oc) exhibit the characteristic radiologic and histologic hallmarks of osteopetrosis including a generalized increase in skeletal density and absence of marrow cavities. Most die within three weeks after birth. Osteoclasts are cytologically abnormal by light microscopy in that they do not have cytoplasmic vacuoles. Presumptive evidence of rickets in this mutation includes thick cartilagenous growth plates and excessive osteoid. Extensive extramedullary hemopoiesis occurs in the liver and spleen of mutants. This unique constellation of features suggests that the oc mutation is a valuable model in which to investigate the pathogenesis of osteopetrosis.

Kinetics of c2-repressor synthesis in a regulatory defective P22 mutant.

Phage P22 defective in gene 24 and harbouring the Oc mutation k5 in OR exhibits a strongly increased c2-repressor synthesis after infection of non-lysogenic S. typhimurium. The repressor synthesis depends strictly on an intact c1 gene. The kinetics of its synthesis, as monitored by polyacrylamide gel electrophoresis, is the same as with P22 c+, namely a turn off 8-10 min after infection. - After infection of P22-lysogenic bacteria with either P22 24- k5 or P22 24- k5 c1, much lower amounts of repressor are synthesized but again with the same kinetics. These results suggest a cro-like function acting at PRE and PRM of P22. The possible reason for the c2 overproduction is discussed.

Mutational analysis of the operators of bacteriophage lambda

Oc mutations in the operators of bacteriophage lambda have been used to analyze the functional organization of the operators. In each operator, repressor binding sites 1 and 2, as identified biochemically, were found to be primarily responsible for the repressor affinity of the operators in vitro and for the repression of lytic functions in vivo. In addition, both sites were shown to be involved in the action of cro product at the operators. The data obtained have been used to estimate the repressor affinities of the individual binding sites. These affinities suggest that repressor bound at OR1 and OR2 interacts cooperatively. The results obtained support a model for repression of the early lambda operons where repressor bound at binding sites 1 and 2 interferes with RNA polymerase binding to the promotor sites.

Isolation of pseudorevertants of lac oc mutants: selection system for superoperator mutations.

A selection procedure and rapid screening test are described that allow the isolation of rarely occurring pseudorevertants of lac oc mutants. These techniques were developed with the aim of isolating superoperator (os) mutants in which a secondary mutation in the operator would increase the affinity of the repressor of superoperator, thereby overcoming the effect of the oc mutation. The occurrence of superoperator mutants is predicted on the basis of a probable twofold symmetry in the lac repressor-operator recognition. Over 2,300 oc pseudorevertants were isolated and screened. In vitro measurements of the affinity of lac repressor for the operator region indicate that, among these, one oc pseudorevertant probably results from an oc mutation. The selection procedure also yielded other types of regulatory mutants that behave as promoter mutants and as i gene mutants in which the repressor is capable of overcoming an oc mutation.

Lac Repressor-operator interaction

Representative members of the six classes of operator constitutive (Oc) point mutations, which have been mapped and well characterized in vivo, were crossed into λφ80 lac phages. The phage DNAs containing the Oc mutations were used to measure the affinity of the lac repressor (R) for each Oc operator by determining the half-lives of the different ROc complexes in vitro. The results provide evidence that: (a) the higher the constitutive level of β-galactosidase in vivo, as the result of an Oc mutation, the lower the affinity of the lac repressor for that Oc operator, with a maximum difference of two orders of magnitude in affinity of the repressor for the highest Oc tested as compared to the wild type O+ operator; (b) the six classes of Oc operators appear to be twofold degenerate, in that two members of each class, which were previously distinguished by mapping, have the same affinity for the lac repressor; (c) an inducer and an anti-inducer have the same effect on the ROc complexes as on the RO+ complexes; (d) the relationship between induction ratios in vivo and the binding constant of the repressor for each Oc mutation in vitro does not follow the mass action equation but rather a more complex dependency, which is discussed. These results suggest a functional symmetry in the lac operator.

Specialized transducing phages carrying fusions of the trp and lac regions of the E. coli chromosome.

A method is described for preparing derivatives of bacteriophage λh80 carrying both the trp and lac regions of the E. coli chromosome. Deletions fusing the trp and lac regions have been crossed onto derivatives of these phage carrying the λCI857S7markers. Strains lysogenic for these phage were compared with the original chromosomal fusion strains with respect to their trp0 dependent regulation of lac z by trpR. Escape synthesis of beta-galactosidase was shown to occur after heat induction of the fusion phages. The endpoints of the fusion deletions in the lac operator were mapped against several different oc mutations.

The relation of catabolite repression to the induction system for β-galactosidase in Escherichia coli

The effect of glucose on the constitutive synthesis of β-galactosidase following conjugation of an Escherichia coli Hfr strain carrying lac i+z+ genes with different F− strains was investigated. It was found that the addition of glucose to a glycerol-containing medium reduces the rate of synthesis of the enzyme to approximately one-half, not only in the merozygotes formed from two i−z− strains, but also in the merozygotes formed from a strain in which the i and z genes are deleted. In merozygotes formed from a third i−z− strain, glucose reduces β-galactosidase synthesis by 90%. This exceptionally strong effect of glucose is a trait of the recipient strain and is not specific for β-galactosidase. Identical results were found in analogous F-duction crosses. It was concluded that the i+z+/lacdel merozygotes are susceptible to catabolite repression immediately after the entry of i+z+ genes. Therefore, it appears that the i product has no role in catabolite repression. An oc mutation was also studied and found not to limit catabolite repression. It is suggested that the system by which the level of a catabolite controls the synthesis of messenger RNA specific for β-galactosidase in E. coli is distinct from the induction system for the lac operon.