Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

Hepatocellular carcinoma (HCC) is the sixth most common malignancy worldwide, representing the third leading cause of cancer-related deaths. HCC genetic characterization at the tumor level has been recently completed, highlighting how a number of genes are frequently mutated in this pathology. Actionable somatic mutations found in a HCC tumor may represent targets for innovative drugs as well as prognostic/predictive markers. Nonetheless, surgical or bioptic tissue is hardly accessible in HCC and a single tumor sample is poorly representative of the tumor genetic heterogeneity. In this context, analyzing the circulating cell-free DNA (ccfDNA) and its tumor-derived fraction (ctDNA) could represent a promising strategy of liquid biopsy. Recent data suggested that the fluctuation of the ccfDNA quantity in the plasma of HCC patients could anticipate the detection of tumor progression. The presence of somatic mutations in p53 signaling, Wnt/β-catenin, chromatin remodeling, response to oxidative stress and telomerase maintenance pathways can also be studied in ccfDNA bypassing the need to perform a tumor biopsy. The profiling of ccfDNA fragmentation and the methylation pattern could further improve the clinical management of HCC patients. Performing a dynamic monitoring in the course of systemic treatment with sorafenib or regorafenib is a possible way to provide insights into the resistance mechanism, and to identify predictive and prognostic genetic alterations, helping the clinicians in terms of treatment decision making. This review will discuss the most recent literature data about the use of ccfDNA to monitor and improve the treatment of HCC.

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Identification of a gene encoding adaptin-like protein in the Paracoccidioides brasiliensis genome by random amplified polymorphic DNA analysis

Journal of Medical Microbiology ◽

10.1099/jmm.0.47127-0 ◽

2007 ◽

Vol 56 (7) ◽

pp. 884-887 ◽

Cited By ~ 2

Author(s):

Patrícia Ferrari Andreotti ◽

Juliana Leal Monteiro da Silva ◽

Elaine Cristina Teixeira ◽

Maria Célia Bertolini ◽

Christiane Pienna Soares ◽

...

Keyword(s):

Dna Analysis ◽

Paracoccidioides Brasiliensis ◽

Random Amplified Polymorphic Dna ◽

Genotypic Differences ◽

Gene Encoding ◽

Two Samples ◽

Yeast Phase ◽

Dna Fragment ◽

Micro Organisms

Paracoccidioides brasiliensis isolates are not homogeneous in their patterns of pathogenicity in animals and adhesion to epithelial cells. During this investigation, genotypic differences were observed between two samples of P. brasiliensis strain 18 yeast phase (Pb18) previously cultured many times, one taken before (Pb18a) and the other after (Pb18b) animal inoculation. Random amplified polymorphic DNA analysis using the primer OPJ4 distinguished Pb18b from Pb18a by one 308 bp DNA fragment, which after cloning and sequencing was shown to encode a polypeptide sequence homologous to the protein β-adaptin. It is suggested, by comparison to other micro-organisms, that this protein might play an important role in the virulence of P. brasiliensis. This result demonstrates the influence of in vitro subculturing on the genotype of this organism.

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Assessment of genomic instability in blood and tissues from prostate cancer patients by random amplified polymorphic DNA analysis

Journal of Biotechnology Research Center ◽

10.24126/jobrc.2009.3.2.65 ◽

2009 ◽

Vol 3 (2) ◽

pp. 30-39

Author(s):

Zafir H. Ghali ◽

Intisar H. Ahmed ◽

Esmail K. Shubber ◽

Badry A. Al-Ani ◽

Bilal K. Sulaiman ◽

...

Keyword(s):

Prostate Cancer ◽

Cancer Patients ◽

Genomic Instability ◽

Dna Analysis ◽

Random Amplified Polymorphic Dna ◽

Genetic Alterations ◽

Arbitrary Primers ◽

Molecular Events ◽

Genomic Damage ◽

Cancer Tissues

All genetic alterations in the genome that predispose to the development of cancer are utmost importance in gaining a complete understanding of the exact molecular events involved in the development of tumorigenesis. In this study, the random amplified polymorphic DNA (RAPD) technique was used for assessing genomic instability in prostate cancer patients. DNAs were obtained from blood and tumor tissues of five prostate cancer patients, then amplified individually by RAPD with five different 10-mer arbitrary primers. The ability to detect genomic instability in five cancer tissues by each primer ranged from 20 to 100 percent. Change in the genome that revealed by RAPD technique included deletion or insertion and allelic losses or gains. The most important finding is that deletions were also observed in blood DNAs, while the corresponding fragments were present in the tumor DNA. Our results display an insertion of a 1093 bp fragment in 2 of 5 tumor samples using primer OPA-03. A deletion of the same 1093 bp fragment was observed in a blood sample using the primer OPA-03. These results confirm other reports that RAPD technique is useful for assessing genomic damage in cancer

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Expression and prognostic roles of PRDXs gene family in hepatocellular carcinoma

Journal of Translational Medicine ◽

10.1186/s12967-021-02792-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Mingxing Xu ◽

Jianliang Xu ◽

Dun Zhu ◽

Rishun Su ◽

Baoding Zhuang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Acid Metabolism ◽

Family Members ◽

Interaction Network ◽

Genetic Alterations ◽

Database Analysis ◽

Kaplan Meier ◽

Canonical Pathways ◽

Human Protein Atlas ◽

Kaplan Meier Plotter

Abstract Background As the fourth leading cause of cancer-related death in the world, the therapeutic effect and 5-year overall survival of hepatocellular carcinoma (HCC) are not optimistic. Previous researches indicated that the disorder of PRDXs was related to the occurrence and development of cancers. Methods In this study, PRDXs were found in various tumor cell lines by CCLE database analysis. The analysis results of UALCAN, HCCDB and Human Protein Atlas databases showed the expression of PRDXs mRNA and protein in HCC tissues was dysregulated. Besides, UALCAN was used to assess the correlations between PRDXs mRNA as well as methylation levels and clinical characterization. Results High expression of PRDX1 or low expression of PRDX2/3 suggested poor prognosis for HCC patients which was demonstrated by Kaplan–Meier Plotter. The genetic alterations and biological interaction network of PRDXs in HCC samples were obtained from c-Bioportal. In addition, LinkedOmics was employed to analyze PRDXs related differentially expressed genes, and on this basis, enrichment of KEGG pathway and miRNAs targets of PRDXs were conducted. The results indicated that these genes were involved in several canonical pathways and certain amino acid metabolism, some of which may effect on the progression of HCC. Conclusions In conclusion, the disordered expression of some PRDX family members was associated with the prognosis of HCC patients, suggesting that these PRDX family members may become new molecular targets for the treatment and prognosis prediction of HCC.

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Significance of TERT Genetic Alterations and Telomere Length in Hepatocellular Carcinoma

Cancers ◽

10.3390/cancers13092160 ◽

2021 ◽

Vol 13 (9) ◽

pp. 2160

Author(s):

Jeong-Won Jang ◽

Jin-Seoub Kim ◽

Hye-Seon Kim ◽

Kwon-Yong Tak ◽

Soon-Kyu Lee ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Telomere Length ◽

Differentially Expressed Gene ◽

Genetic Alterations ◽

Tissue Samples ◽

Protein Protein Interaction ◽

Tert Promoter ◽

Tert Promoter Mutations ◽

Promoter Mutations ◽

Tert Expression

Telomerase reverse transcriptase (TERT) mutations are reportedly the most frequent somatic genetic alterations in hepatocellular carcinoma (HCC). An integrative analysis of TERT-telomere signaling during hepatocarcinogenesis is lacking. This study aimed to investigate the clinicopathological association and prognostic value of TERT gene alterations and telomere length in HCC patients undergoing hepatectomy as well as transarterial chemotherapy (TACE). TERT promoter mutation, expression, and telomere length were analyzed by Sanger sequencing and real-time PCR in 305 tissue samples. Protein–protein interaction (PPI) analysis was performed to identify a set of genes that physically interact with TERT. The PPI analysis identified eight key TERT-interacting genes, namely CCT5, TUBA1B, mTOR, RPS6KB1, AKT1, WHAZ, YWHAQ, and TERT. Among these, TERT was the most strongly differentially expressed gene. TERT promoter mutations were more frequent, TERT expression was significantly higher, and telomere length was longer in tumors versus non-tumors. TERT promoter mutations were most frequent in HCV-related HCCs and less frequent in HBV-related HCCs. TERT promoter mutations were associated with higher TERT levels and longer telomere length and were an independent predictor of worse overall survival after hepatectomy. TERT expression was positively correlated with tumor differentiation and stage progression, and independently predicted shorter time to progression after TACE. The TERT-telomere network may have a crucial role in the development and progression of HCC. TERT-telomere abnormalities might serve as useful biomarkers for HCC, but the prognostic values may differ with tumor characteristics and treatment.

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DNA clonal heterogeneity of hepatocellular carcinoma demonstrated by Feulgen-DNA analysis

Liver International ◽

10.1111/j.1600-0676.1987.tb00367.x ◽

2008 ◽

Vol 7 (6) ◽

pp. 359-363 ◽

Cited By ~ 16

Author(s):

Sow-Hsong Kuo ◽

Jin-Chuan Sheu ◽

Ding-Shinn Chen ◽

Juei-Low Sung ◽

Chi-Chung Lin ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Dna Analysis ◽

Clonal Heterogeneity

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Analysis of the genetic polymorphism of Paracoccidioides brasiliensis and Paracoccidioides cerebriformis "Moore" by random amplified polymorphic DNA (RAPD) and 28S ribosomal DNA sequencing: Paracoccidioides cerebriformis revisited

Revista do Instituto de Medicina Tropical de São Paulo ◽

10.1590/s0036-46652005000300001 ◽

2005 ◽

Vol 47 (3) ◽

pp. 119-123 ◽

Cited By ~ 1

Author(s):

Sarah Desirée Barbosa Cavalcanti ◽

José Eduardo Levi ◽

Kátia Cristina Dantas ◽

José Eduardo Costa Martins

Keyword(s):

Genetic Polymorphism ◽

Dna Sequence ◽

Ribosomal Dna ◽

Dna Analysis ◽

Paracoccidioides Brasiliensis ◽

Random Amplified Polymorphic Dna ◽

Distinct Species ◽

De Medicina ◽

28S Ribosomal Dna ◽

Mycological Laboratory

Our purpose was to compare the genetic polymorphism of six samples of P. brasiliensis (113, 339, BAT, T1F1, T3B6, T5LN1), with four samples of P. cerebriformis (735, 741, 750, 361) from the Mycological Laboratory of the Instituto de Medicina Tropical de São Paulo, using Random Amplified Polymorphic DNA Analysis (RAPD). RAPD profiles clearly segregated P. brasiliensis and P. cerebriformis isolates. However, the variation on band patterns among P. cerebriformis isolates was high. Sequencing of the 28S rDNA gene showed nucleotide conservancy among P. cerebriformis isolates, providing basis for taxonomical grouping, and disclosing high divergence to P. brasiliensis supporting that they are in fact two distinct species. Moreover, DNA sequence suggests that P. cerebriformis belongs in fact to the Aspergillus genus.

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Genetic variation between susceptible and non-susceptible snails to Schistosoma infection using random amplified polymorphic DNA analysis (RAPDs)

Revista do Instituto de Medicina Tropical de São Paulo ◽

10.1590/s0036-46651999000500005 ◽

1999 ◽

Vol 41 (5) ◽

pp. 291-295 ◽

Cited By ~ 17

Author(s):

Abdel-Hamid Zaki ABDEL-HAMID ◽

Jeanne Blanco de MOLFETTA ◽

Vania FERNANDEZ ◽

Vanderlei RODRIGUES

Keyword(s):

Dna Analysis ◽

Random Amplified Polymorphic Dna ◽

Polyacrylamide Gel Electrophoresis ◽

Genome Comparison ◽

Gene Products ◽

Chain Reaction ◽

High Molecular Weight Dna ◽

Polymerase Chain ◽

Or Gene ◽

Host Parasite

Susceptibility of snails to infection by certain trematodes and their suitability as hosts for continued development has been a bewildering problem in host-parasite relationships. The present work emphasizes our interest in snail genetics to determine what genes or gene products are specifically responsible for susceptibility of snails to infection. High molecular weight DNA was extracted from both susceptible and non-susceptible snails within the same species Biomphalaria tenagophila. RAPD was undertaken to distinguish between the two types of snails. Random primers (10 mers) were used to amplify the extracted DNA by the polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis (PAGE) and silver staining. The results suggest that RAPD represents an efficient means of genome comparison, since many molecular markers were detected as genetic variations between susceptible and non-susceptible snails.

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Random Amplification of Polymorphic DNA Analysis for Genetic Characterization of Two Breeds of Dogs, German Shepherd and Japanese Spitz

Nepal Journal of Science and Technology ◽

10.3126/njst.v13i2.7717 ◽

2013 ◽

Vol 13 (2) ◽

pp. 73-78

Author(s):

Jarina Joshsi ◽

Lumanti Manandhar ◽

Patima Shrestha ◽

Rani Gupta ◽

Rojlina Manadhar ◽

...

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Dna Analysis ◽

Genetic Characterization ◽

Random Amplified Polymorphic Dna ◽

Neighbor Joining ◽

German Shepherd ◽

Polymorphic Loci ◽

Random Amplification

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity in dog samples belonging to populations of German Shepherd and Japanese Spitz. A total of twelve samples were typed using eight RAPD primers. Out of eight primers, three primers gave result in six individuals of dogs. The phylogenetic tree constructed by the neighbor joining method based on Nei. Original measures revealed highest genetic identity found in German Shepherd as 0.9444 and highest genetic distance as 1.2809. The analysis predicts the number of polymorphic loci as 15 and the percentage of polymorphic loci as 83.3. Nepal Journal of Science and Technology Vol. 13, No. 2 (2012) 73-78 DOI: http://dx.doi.org/10.3126/njst.v13i2.7717

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Bioinformatics Analysis Identifies Precision Treatment with Paclitaxel for Hepatocellular Carcinoma Patients Harboring Mutant TP53 or Wild-Type CTNNB1 Gene

Journal of Personalized Medicine ◽

10.3390/jpm11111199 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1199

Author(s):

Jiunn-Chang Lin ◽

Tsang-Pai Liu ◽

Vivin Andriani ◽

Muhammad Athoillah ◽

Chih-Yang Wang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Mitotic Cell ◽

Gene Signature ◽

Genetic Alterations ◽

Cancer Type ◽

Wild Type ◽

Tumor Protein P53 ◽

Novel Therapeutic Strategies ◽

Cycle Regulation ◽

Lower Expression

Hepatocellular carcinoma (HCC) is an aggressive and chemoresistant cancer type. The development of novel therapeutic strategies is still urgently needed. Personalized or precision medicine is a new trend in cancer therapy, which treats cancer patients with specific genetic alterations. In this study, a gene signature was identified from the transcriptome of HCC patients, which was correlated with the patients’ poorer prognoses. This gene signature is functionally related to mitotic cell cycle regulation, and its higher or lower expression is linked to the mutation in tumor protein p53 (TP53) or catenin beta 1 (CTNNB1), respectively. Gene–drug association analysis indicated that the taxanes, such as the clinically approved anticancer drug paclitaxel, are potential drugs targeting this mitotic gene signature. Accordingly, HCC cell lines harboring mutant TP53 or wild-type CTNNB1 genes are more sensitive to paclitaxel treatment. Therefore, our results imply that HCC patients with mutant TP53 or wild-type CTNNB1 genes may benefit from the paclitaxel therapy.

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