Terms Of Gene Mutations Research Articles

Exploration and validation of a combined Hypoxia and m6A/m5C/m1A regulated gene signature for prognosis prediction of liver cancer

BackgroundIt is widely acknowledged that hypoxia and m6A/m5C/m1A RNA modifications promote the occurrence and development of tumors by regulating the tumor microenvironment. This study aimed to establish a novel liver cancer risk signature based on hypoxia and m6A/m5C/m1A modifications.MethodsWe collected data from The Cancer Genome Atlas (TCGA-LIHC), the National Omics Data Encyclopedia (NODE-HCC), the International Cancer Genome Consortium (ICGC), and the Gene Expression Omnibus (GEO) databases for our study (GSE59729, GSE41666). Using Cox regression and least absolute shrinkage and selection operator (LASSO) method, we developed a risk signature for liver cancer based on differentially expressed genes related to hypoxia and genes regulated by m6A/m5C/m1A modifications. We stratified patients into high- and low-risk groups and assessed differences between these groups in terms of gene mutations, copy number variations, pathway enrichment, stemness scores, immune infiltration, and predictive capabilities of the model for immunotherapy and chemotherapy efficacy.ResultsOur analysis revealed a significantly correlated between hypoxia and methylation as well as m6A/m5C/m1A RNA methylation. The three-gene prognosis signature (CEP55, DPH2, SMS) combining hypoxia and m6A/m5C/m1A regulated genes exhibited strong predictive performance in TCGA-LIHC, NODE-HCC, and ICGC-LIHC-JP cohorts. The low-risk group demonstrated a significantly better overall survival compared to the high-risk group (p < 0.0001 in TCGA, p = 0.0043 in NODE, p = 0.0015 in ICGC). The area under the curve (AUC) values for survival at 1, 2, and 3 years are all greater than 0.65 in the three cohorts. Univariate and Multivariate Cox regression analyses of the three datasets indicated that the signature could serve as an independent prognostic predictor (p < 0.001 in the three cohorts). The high-risk group exhibited more genome changes and higher homologous recombination deficiency scores and stemness scores. Analysis of immune infiltration and immune activation confirmed that the signature was associated with various immune microenvironment characteristics. Finally, patients in the high-risk group experienced a more favorable response to immunotherapy, and various common chemotherapy drugs.ConclusionOur prognostic signature which integrates hypoxia and m6A/m5C/m1A-regulated genes, provides valuable insights for clinical prediction and treatment guidance for liver cancer patients.

BALB.NCT-Cpoxnct is a unique mouse model of hereditary coproporphyria

In humans, mutations in the coproporphyrinogen oxidase (CPOX) gene can result in hereditary coproporphyria (HCP), characterized by high levels of coproporphyrin excretion in the urine and feces, as well as acute neurovisceral and chronic cutaneous manifestations. Appropriate animal models for comprehending the precise pathogenesis mechanism of HCP have not been reported that show similarities in terms of gene mutation, reduced CPOX activity, excess coproporphyrin accumulation, and clinical symptoms. As previously discovered, the BALB.NCT-Cpoxnct mouse carries a hypomorphic mutation in the Cpox gene. Due to the mutation, BALB.NCT-Cpoxnct had a drastic increase in coproporphyrin in the blood and liver persistently from a young age. In this study, we found that BALB.NCT-Cpoxnct mice manifested HCP symptoms. Similar to HCP patients, BALB.NCT-Cpoxnct excreted an excessive amount of coproporphyrin and porphyrin precursors in the urine and displayed neuromuscular symptoms, such as a lack of grip strength and impaired motor coordination. Male BALB.NCT-Cpoxnct had nonalcoholic steatohepatitis (NASH)-like liver pathology and sclerodermatous skin pathology. A portion of male mice had liver tumors as well, whereas female BALB.NCT-Cpoxnct lacked these hepatic and cutaneous pathologies. In addition, we discovered that BALB.NCT-Cpoxnct exhibited microcytic anemia. These results indicate that BALB.NCT-Cpoxnct mice serve as the suitable animal model to help gain insight into the pathogenesis and therapy of HCP.

Sex differences in the clinicopathological and molecular biological features of gastric cancer.

421 Background: The prevalence of gastric cancer is higher in males than in females. Reports have revealed that female gastric cancer patients exhibit some distinctive features, such as a high proportion of undifferentiated cancer and poor survival outcomes. The therapeutic effects of anti-PD-1 antibody have also been reported to be different between males and females. However, precise differences in molecular profiling features between males and females are yet to be reported. To elucidate sex differences in the clinicopathological and molecular biological characteristics of gastric cancer, we performed whole-exon sequencing and comprehensive gene expression analysis. Methods: We compared the clinicopathological factors and disease-specific survival (DSS) in 499 patients who underwent gastrectomy for gastric cancer between January 2014 and April 2019, excluding those with special types of gastric cancer and R2 resection. We also performed whole-exome sequencing using peripheral blood and tumor tissue, gene panel testing, and transcriptome analysis of tumor and nontumor tissues. Results: Among the 499 patients, 358 were male and 141 were female. Women had significantly more undifferentiated and M-region cancers (P &lt; 0.05 for both). In terms of gene mutations, TP53 mutations were significantly more common in males (P = 0.002), whereas CDH1 (P = 0.005), PIK3CA (P = 0.046), and ERBB3 (P = 0.021) mutations were significantly more common in females. Expression profiles reflecting the tumor microenvironment were classified into two groups: T cell high group (290 patients) and T cell low group (209 patients), via cluster analysis. Men in the T-cell high group had significantly better DSS than those in the T-cell low group (P = 0.005), whereas no significant difference was observed among women in the T-cell high and low groups (P = 0.402). Among the 136 genes significantly upregulated in the T-cell high group, CCL18 (P = 0.048) gene was significantly upregulated in males and CD8A (P = 0.026) gene was upregulated in females. Conclusions: TP53 mutations were more common in male patients with gastric cancer, whereas CDH1, PIK3CA, and ERBB3 mutations were more common in female patients with gastric cancer. Additionally, women did not demonstrate good survival outcomes even in the T-cell high group considered to have enhanced tumor immunity.

Immune-Related RNA-Binding Protein-Based Signature With Predictive and Prognostic Implications in Patients With Lung Adenocarcinoma.

Background: Dysregulation of RNA-binding proteins (RBPs) in cancers is associated with immune and cancer development. Here, we aimed to profile immune-related RBPs in lung adenocarcinoma (LUAD) and construct an immune-related RBP signature (IRBPS) to predict the survival and response to immunotherapy. Methods: A correlation analysis was performed to establish a co-expression network of RBPs and immune-related genes (IRGs) to characterize immune-related RBPs in the TCGA–LUAD cohort (n = 497 cases). Then, a combination of the Random survival forest (RSF) and Cox regression analysis was performed to screen the RBPs and establish IRBPS. This was followed by independent validation of IRBPS in GSE72094 (n = 398 cases), GSE31210, (n = 226 cases), and GSE26939 (n = 114 cases). Differences between the low- and high-risk groups were compared in terms of gene mutations, tumor mutation burden, tumor-infiltrating lymphocytes, and biomarkers responsive to immunotherapy. Results: DDX56, CTSL, ZC3H12D, and PSMC5 were selected and used to construct IRBPS. The high-risk scores of patients had a significantly worse prognosis in both training and testing cohorts (p < 0.0001 and p < 0.05, respectively), and they tended to be older and have an advanced TNM stage. Furthermore, IRBPS was a prognostic factor independent of age, gender, smoking history, TNM stage, and EGFR mutation status (p = 0.002). In addition, high-risk scores of IRBPS were significantly correlated with tumor-infiltrating lymphocytes (p < 0.05). They also had a high level of PD-L1 protein expression (p < 0.01), number of neoantigens (p < 0.001), and TMB (p < 0.001), implying the possible prediction of IRBPS in the immunotherapy of LUAD. Conclusion: The currently established IRBPS encompassing immune-related RBPs might serve as a promising tool to predict survival, reflect the immune microenvironment, and predict the efficacy of immunotherapy among LUAD patients.

The genomic landscape of pediatric renal cell carcinomas

SummaryPediatric renal cell carcinomas (RCC) differ from their adult counterparts not only in histologic subtypes but also in clinical characteristics and outcome. However, the underlying biology is still largely unclear. For this reason, we performed whole-exome and transcriptome sequencing analyses on a cohort of 25 pediatric RCC patients with various histologic subtypes, including 10 MiT family translocation (MiT) and 10 papillary RCCs. In this cohort of pediatric RCC, we find only limited genomic overlap with adult RCC, even within the same histologic subtype. Recurrent somatic mutations in genes not previously reported in RCC were detected, such as in CCDC168, PLEKHA1, VWF, and MAP3K9. Our papillary pediatric RCCs, which represent the largest cohort to date with comprehensive molecular profiling in this age group, appeared as a distinct genomic subtype differing in terms of gene mutations and gene expression patterns not only from MiT-RCC but also from their adult counterparts.

The Role of Deleted in Colorectal Cancer (Dcc) and P53 Mrna Expression In Young Colorectal Cancer Patients

Background : The incidence of colorectal malignancies at a young age, and the absence of sufficient data to explain about it, including in terms of gene mutations that play a role. The research will be done here is to determine whether changes in mRNA expression of genes DCC ( deleted in colorectal cancer ) and p53 play a role in colorectal malignancy is less than 40 years of age. Researchers also will perform immunohistochemistry to look at protein expression of the gene and protein expression was evaluated whether these correlated with mRNA expression.&#x0D; Methods : This study is an observational analytic cross sectional design, carried out in the Laboratory of Biomedical Faculty of Medicine Sebelas Maret University from June 2013 to March 2014. Subjects were 30 patients with stage III colorectal adenocarcinoma, with details of the 15 subjects for each group. Subjects taken by consecutive sampling. Immunohistochemical examination of paraffin block preparation and reverse transcriptase - polymerase chain reaction (RT - PCR) of tumor tissue samples for evaluation of the presence of the protein and mRNA expression of DCC and p53 genes .Statistical analysis using the chi-square test and Phi correlation. &#x0D; Results : the 4 subjects in the age group ≤ 40 years was not accompanied by DCC protein expression while in the age group &gt; 40 years of protein expression obtained in all preparations. Expression of p53 protein more available in the age group &gt; 40 years ( 3 subjects ), in the age group ≤ 40 years is only found in 1 subject. Examination results of RT-PCR to assess the mRNA expression results are consistent with the results of immunohistochemistry. Eleven subjects from the age group ≤ 40 years obtained DCC mRNA expression, whereas p53 mRNA expression was found in 12 subjects. From statistical analysis using the chi-square test and Phi correlation, we found significant association between protein and mRNA expression of DCC with colorectal cancer aged ≤ 40 years. Correlation of test results, obtained significant correlation between mRNA expression of DCC with colorectal cancer aged ≤ 40 years and the results of protein expression were significantly correlated with mRNA expression of DCC and p53 genes. &#x0D; Conclusion : the expression of p53 protein and mRNA did not play a role in colorectal cancer ≤ 40 years of age. Protein expression was positively correlated with mRNA expression .

Abstract 164: Clonal evolution in noncancerous esophageal mucosa in normal and cancer-bearing individuals

Abstract Background Esophageal squamous cell carcinoma (ESCC) represents the most common form of esophageal cancer worldwide, especially in East Asia, where alcohol drinking and smoking have been implicated in the field carcinogenesis of ESCC. However, the oncogenic process therein has been poorly understood in terms of gene mutations. Patients &amp; Methods A total of 100 samples, including cancer, dysplastic, and non-dysplastic esophageal tissues, were obtained from 24 individual with (N = 14) or without (N = 10) ESCC (a median of 2.5 samples per case: 1−29) either by endoscopy or surgery and were subjected to whole exome sequencing (WES). An additional paired cancer/non-caner samples from 32 patients was analyzed by targeted sequencing (TS). All samples were analyzed for copy number alterations (CNAs) using SNP array- and/or digital sequencing-based karyotyping. Results In WES, clonal evolution in esophageal epithelia, as determined by the presence of somatic mutations, was detected in 21 of 21 cancer, 12 of 12 dysplastic, and 63 of 67 non-dysplastic samples, where the mean number of mutation per sample showed a significant trend to increase in cancer (65) and dysplastic samples (50) compared to non-dysplastic samples (13) (P = 2.1×10-11). CNAs, especially those involving CDKN2A, CCND1, YAP1, and EGFR, were frequently affected in cancer samples, but rarely so in non-dysplastic samples. Non-dysplastic samples tended to have smaller allelic burden and therefore, clone size, compared to dysplastic and cancer samples (P = 2.2×10-16). Mutations had a predominant age-related signature in non-dysplastic samples but increasing APOBEC3A/3B patterns was observed in cancer and dysplastic samples. Shared mutations were found only within cancer tissues but never among dysplastic or non-dysplastic samples, suggesting the latter lesions are clonally independent from each other. In accordance with previous reports, TP53 mutations were found in 21/21 cancer samples and also found in dysplastic (11/12) and non-dysplastic samples at a lower frequency (26/67). Strikingly, non-dysplastic samples harbored a very high frequency of NOTCH1 mutations (51/67), which were also found in cancer (3/21) and non-dysplastic (8/12) samples but at much lower frequencies (P = 6.6×10-7). TS of validation samples confirmed the trend of higher NOTCH1 (84% vs. 25%) and lower TP53 mutation rates (38% vs. 100%) in non-dysplastic samples compared to cancer samples. The number of mutations in non-dysplastic samples was higher in drinkers than non-drinkers. Multiple NOTCH1 mutations were more common in cancer patients and drinkers than non-drinkers. Conclusion Clonal proliferation in non-cancer esophageal epithelia is common even in non-ESCC cases and extensive in ESCC cases. NOTCH1 and TP53 mutations play major roles in clonal evolution in common but may have differential impacts on esophageal carcinogenesis, which is likely to be shaped by APOBEC-induced mutations and CNAs. Citation Format: Akira Yokoyama, Hiromichi Suzuki, Tetsuichi Yoshizato, Kosuke Aoki, Yusuke Shiozawa, Youichi Fujii, Yusuke Sato, Nobuyuki Kakiuchi, Sugi Kin, Keisuke Kataoka, Kenichi Yoshida, Hideki Makishima, Yusuke Amanuma, Shinya Oohashi, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Brown J.B., Masashi Sanada, Shigeru Tsunoda, Sachiko Minamiguchi, Yoshiharu Sakai, Hironori Haga, Tsutome Chiba, Satoru Miyano, Manabu Muto, Seishi Ogawa. Clonal evolution in noncancerous esophageal mucosa in normal and cancer-bearing individuals. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 164.

Evolution of ontogeny and nature of heterochronies

Every aspect of biological orderliness is a result of evolution, which expresses the systemic reorganization of organismal body plan, along with the way of its ontogenetic formation. Phyletic changes in the developmental rates (heterochronies) experienced by the organism or its structures exemplify just a kind of such consequences. The current belief that heterochronies are the causes of evolutionary events is based on the assumption that evolution of ontogeny proceeds in the same way as the ontogeny itself, i.e., from a germ cell to adult state. This premise (termed here “the central dogma”) is the cornerstone of traditional ideas of the evolutionary mechanism, regardless of whether it is perceived in terms of gene mutations or “embryonic modes.” In fact, the directions of two transformations compared are opposite each other. An evolutionary change in the body plan results from reorganization of the developmental system, which comes in response to disturbance of stability of the system’s terminal (adult) state. Realized by selection, this change starts immediately from the terminal state and then spreads in generations towards early ontogenetic stages. Heterochronies show just the same dynamics of events irrespective of whether they reflect the acceleration or delay of development. Empirically, such course of evolutionary changes was grounded most evidently by Severtsov in the early version of his concept of the phylembryogenesis. The theoretical basis of the same regularity is provided by the Schmalhausen–Waddington’s theory.

Everything is on the Head

Everything is on the Head

Mutation analysis of the Gadd45 gene at exon 4 in atypical fibroxanthoma

BackgroundAtypical fibroxanthoma (AFX) histologically mimics high-grade sarcoma in the skin, although it follows a benign clinical course. AFX occurs in the sun-exposed skin and for this reason, an association with ultraviolet light has long been suspected. Bax and Gadd45 are p53 effector proteins. Bax is a programmed cell death protein and belongs to the Bcl-2 family. Gadd45 is a multifunctional DNA damage-inducible gene associated with the process of DNA damage.MethodsImmunohistochemical expression of Bax was analyzed in 7 cases of AFX, and in 7 cases of benign fibrous histiocytoma (BFH) used as a comparison. The expression pattern of Bax was compared to previously reported p53 and Gadd45 expressions in a correspondent series. Mutation of the Gadd45 gene at exon 4 was also analyzed in AFX.ResultsAFX and BFH showed immunoreactivities respectively for Bax (3/7, 0/7), Gadd45 (4/7, 1/7) and p53 (2/7, 0/7). There was no exact correlation between p53 expression and Bax or Gadd45 expression. However, the pattern of expression between Bax and Gadd45 was also the same, with the exception of one case. No mutation of the Gadd45 gene at exon 4 was observed in a series of 6 AFX cases where DNA was available (0/6).ConclusionThese results suggest a possible association between Bax and Gadd45 in AFX, and may refute any possibility of dysfunction of Gadd45 in terms of gene mutation, at least at exon 4 of the Gadd45 gene.

Isolation and characterization of a temperature-sensitive mutant of Bombyx mori nucleopolyhedrovirus for a putative RNA polymerase gene.

Temperature-sensitive (ts) mutants of Bombyx mori nucleopolyhedrovirus (BmNPV), which exhibited no polyhedra formation at the non-permissive temperature of 33 degrees C, were produced using the base analogue 5-bromodeoxyuridine. A unique ts mutant, designated ts-S1, was characterized in terms of gene mutation and virulence in cultured cells and silkworm larvae. Mutant-infected BmN4 cells at 33 degrees C showed normal viral DNA synthesis but defective budded virus production and polyhedrin synthesis, suggesting the absence of late and very late gene expression. Silkworm larvae were injected with ts-S1 and reared at 33.5 degrees C. At 7 days post-injection, none of the larvae exhibited nucleopolyhedrosis but some possessed viral DNA, detected by PCR using virus-specific primers. Continued rearing of the larvae at a permissive temperature of 25 degrees C showed that, while most developed into normal adults, some developed nucleopolyhedrosis, indicating that the former larvae had aborted the virus infection during the course of rearing at 33.5 degrees C. No viral DNA was detected in the adults. Marker rescue tests to identify the lesion involved in the ts phenotype of ts-S1, and nucleotide sequencing of the identified genome region, showed a single nucleotide mutation of a putative RNA polymerase gene, late expression factor-8 (lef-8). These results indicate that lef-8 is essential for BmNPV replication in vitro and in vivo.

A search for DNA alterations in the aging mammalian genome: An experimental strategy

In order to experimentally test the hypothesis that at the basal level senescence is caused by instabilities in DNA, techniques are required that allow the sensitive detection, quantification and characterization of DNA damage and DNA sequence changes in various organs and tissues of naturally aging mammals. In this article a strategy is presented that should allow the analysis of DNA damage metabolism in aging mammals from the original changes in the chemical structure of DNA (DNA damages) via their processing (DNA repair) to the molecular endpoints in terms of gene mutations and DNA rearrangements. With respect to the detection of DNA damage, a short overview is provided of recently emerged biochemical and immunochemical methods that can be applied immediately to study the spectrum of DNA damages in various organs and tissues of aging animals or humans. By contrast, before one is able to study low frequency changes in DNA sequence organization in somatic tissues, formidable problems have yet to be overcome. This is mainly due to the fact that the scale of highly advanced recombinant DNA techniques recently developed is almost totally devoted to the analysis of heritable genetic factors. In order to be able to study low frequency changes in DNA sequence organization in somatic tissues, we have initiated experimental approaches based on recently emerged shuttle vector technology in combination with transagenic mice, and on new electrophoretic separation principles. These approaches and their potentialities for testing somatic mutation theories of aging are discussed.