Brief Reports Open Access
Copyright ©2005 Baishideng Publishing Group Co., Limited. All rights reserved.
World J Gastroenterol. Jan 14, 2005; 11(2): 264-267
Published online Jan 14, 2005. doi: 10.3748/wjg.v11.i2.264
Mitochondrial DNA sequence analysis of two mouse hepatocarcinoma cell lines
Ji-Gang Dai, Xia Lei, Jia-Xin Min, Guo-Qiang Zhang, Hong Wei
Ji-Gang Dai, Xia Lei, Jia-Xin Min, Guo-Qiang Zhang, Hong Wei, Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
Author contributions: All authors contributed equally to the work.
Supported by the National Natural Science Foundation of China, No. 39900173
Correspondence to: Jia-Xin Min, Department of Thoracic Surgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
Telephone: +86-23-68755616 Fax: +86-23-68755616
Received: December 28, 2003
Revised: December 29, 2003
Accepted: January 15, 2004
Published online: January 14, 2005


AIM: To study genetic difference of mitochondrial DNA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells and their oncogenic phenotype.

METHODS: Mitochondrial DNA D-loop, tRNAMet+Glu+Ile and ND3 gene fragments from the hepatocarcinoma cell lines with 1100, 1126 and 534 bp in length respectively were analysed by PCR amplification and restriction fragment length polymorphism techniques. The D-loop 3’ end sequence of the hepatocarcinoma cell lines was determined by sequencing.

RESULTS: No amplification fragment length polymorphism and restriction fragment length polymorphism were observed in tRNAMet+Glu+Ile, ND3 and D-loop of mitochondrial DNA of the hepatocarcinoma cells. Sequence differences between Hca-F and Hca-P were found in mtDNA D-loop.

CONCLUSION: Deletion mutations of mitochondrial DNA restriction fragment may not play a significant role in carcinogenesis. Genetic difference of mtDNA D-loop between Hca-F and Hca-P, which may reflect the environmental and genetic influences during tumor progression, could be linked to their tumorigenic phenotypes.

Key Words: Hepatocarcinoma, Mitochondrial DNA, Base Sequence


Mammalian mitochondrial DNA (mtDNA) is a 15-16 kb circular double-stranded DNA. The genome contains genes coding for 13 polypeptides involved in respiration and oxidative phosphorylation, 2 rRNAs and a set of 22 tRNAs that are essential for protein synthesis of mitochondria. In contrast to the nuclear DNA, mtDNA is a naked DNA molecule without introns and is replicated at a much higher rate without an effective DNA repair mechanism. Therefore, mtDNA is more vulnerable to reactive oxygen species and free radicals that are generated in electron leak pathway of the respiratory chain[1-3].

The possibility that the mitochondrial genome may be involved in carcinogenesis can be extrapolated back to Warburg, who demonstrated that increased anaerobic glycolysis was a common feature of tumor cells[4]. One scenario is that the somatic mtDNA mutations in tumor cells play an active role in shifting metabolism away from mitochondrial oxidative phosphorylation and towards enhanced glycolysis[5,6]. mtDNA mutation is a prominent feature of cancer cells and has been identified in various tumors and tumor cell lines[7]. However, the direct link between mtDNA mutations of cancer cells and their oncogenic phenotype has not been demonstrated.

Hca-F and Hca-P are two types of cell lines originating from an identical parent cell line, hepatocarcinoma H22, with high and low metastatic abilities, respectively. To inquire into the role of mtDNA mutations in tumorigenic phenotype, the genetic variations of mtDNA from Hca-F and Hca-P cell lines were analyzed by PCR and restriction fragment length polymorphism (RFLP) and DNA sequencing.


The restriction endonucleases including Hae III, BamH I, Apa I, Nde II, Xho I, Xba I, Alu I, Rsa I, Stu I, Dra I, Ava I, and Hae II were purchased from German Boehringer Mannheing and American Promega companies; PCR test kits were also obtained from German Boehringer Mannhening Company. Hca-F and Hca-P hepatocarcinoma cell lines were supplied by Professor Mao-Yin Lin of Dalian Medical University, China.

Amplification of PCR

The primers were synthesized by Shanghai Cell Biological Institute of China (Table 1). Mitochondrial DNA of the tumor cell lines was prepared by the method of nuclei/cytoplasm partition[8]. PCR amplification was carried out in a final volume of 100 μL containing 0.5 μg mtDNA, 0.5 mmol/L of each primer, 2.5 mmol/L MgCl2, 200 mmol/L of each dNTP, and 2.5 U Taq DNA polymerase (TaKaRa Ex TaqTM). PCR (an initial incubation at 94 °C for 4 min, followed by 30 cycles at 94 °C for 30 s, at 55 °C for 1 min, and at 72 °C for 1 min; the final step at 72 °C was extended to 10 min) was performed in a Biometra Personal PCR system.

Table 1 Primer sequence and length of amplified fragments.
Amplified fragmentLength (bp)LocationPrimer sequence
D-loop1100L strand (15 294-15 320)5’-TAAACATTACTCTGGTCTTGTAAACC-3’
tRNAMet+Glu+Ile1126L strand (3 401-3 419)5’-CGGCCCATTCGCGTTATTC-3’
H strand (4 527-4 508)5’-AGGTTGAGTAGAGTGAGGGA-3’
ND3 fragment534L strand (9 364-9 385)5’-ACGTCTCCATTTATTGATGAGG-3’
H strand (9 897-9 876)5’-GAGGTTGAAGAAGGTAGATGGC-3’
D-loop 3’ end fragment437L strand (15 950-15 968)5’-AGGCATGAAAGGACAGCAC-3’
H strand (91-73)5’-ATAAGGCCAGGACCAAACC-3’
PCR-RFLP analysis of D-loop, tRNAMet+Glu+Ile l and ND3 gene fragments

Two U restriction endonucleases and 1.2 μL 10×Buffer were added to 5 μL of every PCR product separately and each dilution was mixed with sterilized water until the total volume was 12 μL; then incubated at 37 °C overnight. After digested by the restriction endonucleases, each sample was analyzed by 1% agarose gel electrophoresis (the buffer fluid was TBE buffer). Performed at 3 V/cm for 1-2 h, the electrophoresis was observed under ultraviolet and photographs were taken. The standard marker of Huamei Company was adopted as the molecular weight standard to determine the length of the fragments.

DNA sequencing of PCR products

PCR products for the D-loop 3 end fragment of 437 bp in length were sent to United Gene Technology Company, Ltd, Shanghai, China for direct sequencing.


Mitochondrial DNA D-loop, tRNAMet+Glu+Ile and ND3 gene fragments from the hepatocarcinoma cell lines with 1 100, 1 126 and 534 bp in length respectively were analysed by PCR amplification. No amplification fragment length polymorphism and negative amplification were observed. Mitochondrial DNA D-loop, tRNAMet+Glu+Ile and ND3 fragments were cleaved respectively by 12 kinds of restriction endonucleases including Hae III, BamH I, Apa I, Nde II, Xho I, Xba I, Alu I, Rsa I, Stu I, Dra I, Ava I and Hae II. But no difference was observed in all restriction maps of D-loop, tRNAMet+Glu+Ile and ND3 fragments of mtDNA from hepatocarcinoma cell lines and no variation was found in 41 restriction endonuclease sites (Figure 1, Table 2).

Figure 1
Figure 1 Restriction patterns of amplified fragments. F: Hca-F cells; P: Hca-P cells; M: PCR standard marker. A: Restriction patterns of tRNA Met+Glu+Ile digested by Apa I, Alu I, BamH I, Rsa I and Stu I, respectively; B: Restriction patterns of D-loop digested by Xba I, Apa I, Rsa I, Stu I and Alu I, respectively; C: Restriction patterns of ND3 digested by Hae III, Dra I, Stu I, Rsa I and Alu I, respectively.
Table 2 Mitochondrial tRNAMet+Glu+Ile, ND3 and D-loop restriction patterns.
EnzymeD-loop (1 100 bp)
tRNAMet+Glu+Ile (1 126 bp)
ND3 (534 bp)
Hae III4456445122, ...4470290136...1392142
Apa I165544516584690534
Alu I4545269102, ...3665318135...1310224
BamH I0110027102521640534
Dra I011001634493145183
Stu I0110026052972251391143
Nde II284 511 83701 1260534
Rsa I6720178125...4392259228...235310378
Xba I1680420011260524

The D-loop 3’ end fragment sequence of two hepatocarcinoma cell lines was determined by sequencing. Compared with published mouse mtDNA sequence, we had found 3 mutations: G:C→A:T transition was detected at nucleotide 16007 in Hca-F and Hca-P cell lines and a T:A→C:G occurred at nucleotide 16268 only in Hca-F cell line (Figure 2).

Figure 2
Figure 2 Variations identified in the D-loop (bases 15 950-91) of mitochondrial DNA from two types of hepatocarcinoma cell lines. Sequence and base number were from the complete mouse mtDNA sequence reported by Bibb et al. (Cell 1981; 26: 167-180 ). The G at nucleotide 16007 was mutated to A in two hepatocarcinoma cell lines and T at nucleotide 16268 was mutated to C in Hca-F cell line.

Carcinogenesis is a multi-step process involving the accumulation of genetic changes that ends in malignant cell transformation. Much attention has been paid to the genetic events in the nDNA, such as activation of oncogene, inactivation of tumor suppressor gene, and defects of mismatch DNA repair gene. However, several aspects in the process of carcinogenesis are still unclear. Contribution of mtDNA mutations to carcinogenesis was postulated when wide spectra of the mtDNA alterations were reported in different types of cancer: colon, ovarian, lung, pancreatic, liver, thyroid, bladder, prostate, esophageal and gastric cancer[7,9-12]. Reported sequence changes include point mutations (mostly transitions), multiple deletions and microsatellite instability in coding and noncoding regions. However, of all these mutations and polymorphisms only a few can be linked to a known phenotypic effect. Alonso[13] suggested different mechanisms, such as clonal expansion, increased oxidative damage and mutator mutations, to explain this high frequency of homoplasmic mtDNA variation in cancer samples. Because most tumors are a clonal expansion of a single cell, it is possible that mtDNA homoplasmic mutations are just the results of clonal expansion of spontaneous somatic mutations, which occur at a very low frequency during previous replication of this precursor cell and later become predominant or homoplasmic by clonal expansion of its cell[14]. However, the selective advantage of mtDNA changes in the development of tumors cannot be excluded. In principle, these mutations could contribute to neoplastic transformation by changing cellular energy capacities, increasing mitochondrial oxidative stress, and/or modulating apoptosis.

In this study, large-scale deletion mutations of D-loop, tRNAMet+Glu+Ile and ND3 gene fragments in hot-spot regions of mtDNA were analysed by PCR amplification and RFLP techniques. There were no amplification fragment length polymorphism and negative amplification, and all restriction patterns of D-loop, tRNAMet+Glu+Ile and ND3 fragments from Hca-F and Hca-P hepatocarcinoma cell lines were also identical. In contrast to previous studies, we failed to find mtDNA large-scale deletions in tumor cell lines, which differ from the observation that multiple mtDNA deletions were detected in tumors and normal human tissue cells[15,16]. We propose possible mechanisms to explain the phenomenon. Firstly, the increased proliferation of tumor cell lines promotes the cytoplasmic segregation of deleted mtDNAs, and thus the mtDNA molecules with deletions are passively eliminated in tumor cells. Secondly, the mtDNA deletions accumulated in tumor cells may result in impaired mitochondrial respiration and decrease ATP synthesis. After cytoplasmic segregation of deleted mtDNAs, the cells harboring higher proportion of mtDNA deletions could not survive and lead to dropout from the population. So, we suggest that mtDNA fragment deletion mutations in tumors unlikely play a significant role in carcinogenesis, probably just as age-related increases in DNA damage due to cellular oxidative stress and environmental factors.

Mitochondrial DNA control region (non-coding region, D-loop), containing the origin of replication for H-strand synthesis, mitochondrial transcription promoters, mtTF1 binding site and conserved sequence block, etc., serves as the main site for mitochondrial genomic replication and transcription. Point mutations and genetic instabilities at the D-loop region are potentially involved in the maintenance of structure and function or even the expression of other mitochondrial genes, and probably also involved in the progressive stage of the disease[17,18]. In the present study, we have found sequence difference in mtDNA D-loop region between two types of hepatocarcinoma cell lines with diverse metastatic abilities. G:C→A:T transition was detected at nucleotide 16007 in Hca-F and Hca-P cell lines and T:A→C:G occurred at nucleotide 16268 only in Hca-F cell line. Little is known about the presence of genetic alterations, especially of point mutations, localized at crucial sites or adjacent place in the mtDNA control region, and their contribution to carcinogenesis. Although it is unlikely that mutations in the mtDNA control region are immediately deleterious or tumorigenic, the frequency of mtDNA mutations may reflect underlying genetic and environmental influences during tumor progression[19]. It is also possible that sequence variants in the mtDNA control region could influence disease-associated mutations in the coding regions[20,21]. There is considerable evidence that the mutation rate of both mitochondrial coding region and non-coding region loci is increased as a result of tumorigenicity[22-25]. It is likely, therefore, that the difference of mtDNA D-loop region observed in different hepatocarcinoma cell lines is a reflection of this increased mutation rate and can be linked to their tumorigenic phenotype. More extensive biochemical and molecular studies will be necessary for determining the pathological effect of these mtDNA genetic alterations.


Edited by Chen WW Proofread by Zhu LH

1.  Lee HC, Lim ML, Lu CY, Liu VW, Fahn HJ, Zhang C, Nagley P, Wei YH. Concurrent increase of oxidative DNA damage and lipid peroxidation together with mitochondrial DNA mutation in human lung tissues during aging--smoking enhances oxidative stress on the aged tissues. Arch Biochem Biophys. 1999;362:309-316.  [PubMed]  [DOI]
2.  Taanman JWThe mitochondrial genome: structure, transcription, translation and replication. Biochim Biophys Acta. 1999;1410:103-123.  [PubMed]  [DOI]
3.  Li JM, Cai Q, Zhou H, Xiao GX. Effects of hydrogen peroxide on mitochondrial gene expression of intestinal epithelial cells. World J Gastroenterol. 2002;8:1117-1122.  [PubMed]  [DOI]
4.  Dang CV, Semenza GL. Oncogenic alterations of metabolism. Trends Biochem Sci. 1999;24:68-72.  [PubMed]  [DOI]
5.  Polyak K, Li Y, Zhu H, Lengauer C, Willson JK, Markowitz SD, Trush MA, Kinzler KW, Vogelstein B. Somatic mutations of the mitochondrial genome in human colorectal tumours. Nat Genet. 1998;20:291-293.  [PubMed]  [DOI]
6.  Yeh JJ, Lunetta KL, van Orsouw NJ, Moore FD, Mutter GL, Vijg J, Dahia PL, Eng C. Somatic mitochondrial DNA (mtDNA) mutations in papillary thyroid carcinomas and differential mtDNA sequence variants in cases with thyroid tumours. Oncogene. 2000;19:2060-2066.  [PubMed]  [DOI]
7.  Carew JS, Huang P. Mitochondrial defects in cancer. Mol Cancer. 2002;1:9.  [PubMed]  [DOI]
8.  Dai JG, Wu YG, Wei H, Xiao YB. A simple and rapid method for the preparation the mtDNA. Disan Junyi Daxue Xuebao. 2000;15:391-392.  [PubMed]  [DOI]
9.  Fliss MS, Usadel H, Caballero OL, Wu L, Buta MR, Eleff SM, Jen J, Sidransky D. Facile detection of mitochondrial DNA mutations in tumors and bodily fluids. Science. 2000;287:2017-2019.  [PubMed]  [DOI]
10.  Luciaková K, Kuzela S. Increased steady-state levels of several mitochondrial and nuclear gene transcripts in rat hepatoma with a low content of mitochondria. Eur J Biochem. 1992;205:1187-1193.  [PubMed]  [DOI]
11.  Tamura G, Nishizuka S, Maesawa C, Suzuki Y, Iwaya T, Sakata K, Endoh Y, Motoyama T. Mutations in mitochondrial control region DNA in gastric tumours of Japanese patients. Eur J Cancer. 1999;35:316-319.  [PubMed]  [DOI]
12.  Clayton DA, Vinograd J. Circular dimer and catenate forms of mitochondrial DNA in human leukaemic leucocytes. J Pers. 1967;35:652-657.  [PubMed]  [DOI]
13.  Alonso A, Martin P, Albarran C, Aquilera B, Garcia O, Guzman A, Oliva H, Sancho M. Detection of somatic mutations in the mitochondrial DNA control region of colorectal and gastric tumors by heteroduplex and single-strand conformation analysis. Electrophoresis. 1997;18:682-685.  [PubMed]  [DOI]
14.  Perucho MMicrosatellite instability: the mutator that mutates the other mutator. Nat Med. 1996;2:630-631.  [PubMed]  [DOI]
15.  Lee HC, Yin PH, Yu TN, Chang YD, Hsu WC, Kao SY, Chi CW, Liu TY, Wei YH. Accumulation of mitochondrial DNA deletions in human oral tissues -- effects of betel quid chewing and oral cancer. Mutat Res. 2001;493:67-74.  [PubMed]  [DOI]
16.  Kotake K, Nonami T, Kurokawa T, Nakao A, Murakami T, Shimomura Y. Human livers with cirrhosis and hepatocellular carcinoma have less mitochondrial DNA deletion than normal human livers. Life Sci. 1999;64:1785-1791.  [PubMed]  [DOI]
17.  Bianchi NO, Bianchi MS, Richard SM. Mitochondrial genome instability in human cancers. Mutat Res. 2001;488:9-23.  [PubMed]  [DOI]
18.  Máximo V, Soares P, Seruca R, Rocha AS, Castro P, Sobrinho-Simões M. Microsatellite instability, mitochondrial DNA large deletions, and mitochondrial DNA mutations in gastric carcinoma. Genes Chromosomes Cancer. 2001;32:136-143.  [PubMed]  [DOI]
19.  Burgart LJ, Zheng J, Shu Q, Strickler JG, Shibata D. Somatic mitochondrial mutation in gastric cancer. Am J Pathol. 1995;147:1105-1111.  [PubMed]  [DOI]
20.  Marchington DR, Poulton J, Sellar A, Holt IJ. Do sequence variants in the major non-coding region of the mitochondrial genome influence mitochondrial mutations associated with disease? Hum Mol Genet. 1996;5:473-479.  [PubMed]  [DOI]
21.  Poulton J, Macaulay V, Marchington DR. Mitochondrial genetics '98 is the bottleneck cracked? Am J Hum Genet. 1998;62:752-757.  [PubMed]  [DOI]
22.  Loeb LA. A mutator phenotype in cancer. Cancer Res. 2001;61:3230-3239.  [PubMed]  [DOI]
23.  Penta JS, Johnson FM, Wachsman JT, Copeland WC. Mitochondrial DNA in human malignancy. Mutat Res. 2001;488:119-133.  [PubMed]  [DOI]
24.  Sanchez-Cespedes M, Parrella P, Nomoto S, Cohen D, Xiao Y, Esteller M, Jeronimo C, Jordan RC, Nicol T, Koch WM. Identification of a mononucleotide repeat as a major target for mitochondrial DNA alterations in human tumors. Cancer Res. 2001;61:7015-7019.  [PubMed]  [DOI]
25.  Richard SM, Bailliet G, Páez GL, Bianchi MS, Peltomäki P, Bianchi NO. Nuclear and mitochondrial genome instability in human breast cancer. Cancer Res. 2000;60:4231-4237.  [PubMed]  [DOI]