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Sajjad H, Imtiaz S, Noor T, Siddiqui YH, Sajjad A, Zia M. Cancer models in preclinical research: A chronicle review of advancement in effective cancer research. Animal Model Exp Med 2021; 4:87-103. [PMID: 34179717 PMCID: PMC8212826 DOI: 10.1002/ame2.12165] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer is a major stress for public well-being and is the most dreadful disease. The models used in the discovery of cancer treatment are continuously changing and extending toward advanced preclinical studies. Cancer models are either naturally existing or artificially prepared experimental systems that show similar features with human tumors though the heterogeneous nature of the tumor is very familiar. The choice of the most fitting model to best reflect the given tumor system is one of the real difficulties for cancer examination. Therefore, vast studies have been conducted on the cancer models for developing a better understanding of cancer invasion, progression, and early detection. These models give an insight into cancer etiology, molecular basis, host tumor interaction, the role of microenvironment, and tumor heterogeneity in tumor metastasis. These models are also used to predict novel cancer markers, targeted therapies, and are extremely helpful in drug development. In this review, the potential of cancer models to be used as a platform for drug screening and therapeutic discoveries are highlighted. Although none of the cancer models is regarded as ideal because each is associated with essential caveats that restraint its application yet by bridging the gap between preliminary cancer research and translational medicine. However, they promise a brighter future for cancer treatment.
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Affiliation(s)
- Humna Sajjad
- Department of BiotechnologyQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Saiqa Imtiaz
- Department of BiotechnologyQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Tayyaba Noor
- Department of BiotechnologyQuaid‐i‐Azam UniversityIslamabadPakistan
| | | | - Anila Sajjad
- Department of BiotechnologyQuaid‐i‐Azam UniversityIslamabadPakistan
| | - Muhammad Zia
- Department of BiotechnologyQuaid‐i‐Azam UniversityIslamabadPakistan
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Kamiyama H, Kakoki K, Yoshii H, Iwao M, Igawa T, Sakai H, Hayashi H, Matsuyama T, Yamamoto N, Kubo Y. Infection of XC cells by MLVs and Ebola virus is endosome-dependent but acidification-independent. PLoS One 2011; 6:e26180. [PMID: 22022555 PMCID: PMC3192169 DOI: 10.1371/journal.pone.0026180] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/21/2011] [Indexed: 11/18/2022] Open
Abstract
Inhibitors of endosome acidification or cathepsin proteases attenuated infections mediated by envelope proteins of xenotropic murine leukemia virus-related virus (XMRV) and Ebola virus, as well as ecotropic, amphotropic, polytropic, and xenotropic murine leukemia viruses (MLVs), indicating that infections by these viruses occur through acidic endosomes and require cathepsin proteases in the susceptible cells such as TE671 cells. However, as previously shown, the endosome acidification inhibitors did not inhibit these viral infections in XC cells. It is generally accepted that the ecotropic MLV infection in XC cells occurs at the plasma membrane. Because cathepsin proteases are activated by low pH in acidic endosomes, the acidification inhibitors may inhibit the viral infections by suppressing cathepsin protease activation. The acidification inhibitors attenuated the activities of cathepsin proteases B and L in TE671 cells, but not in XC cells. Processing of cathepsin protease L was suppressed by the acidification inhibitor in NIH3T3 cells, but again not in XC cells. These results indicate that cathepsin proteases are activated without endosome acidification in XC cells. Treatment with an endocytosis inhibitor or knockdown of dynamin 2 expression by siRNAs suppressed MLV infections in all examined cells including XC cells. Furthermore, endosomal cathepsin proteases were required for these viral infections in XC cells as other susceptible cells. These results suggest that infections of XC cells by the MLVs and Ebola virus occur through endosomes and pH-independent cathepsin activation induces pH-independent infection in XC cells.
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Affiliation(s)
- Haruka Kamiyama
- Department of AIDS Research, Institute of Tropical Medicine, Global COE Program, Nagasaki University, Nagasaki, Japan
- Graduate School of Science and Technology, Nagasaki University, Nagasaki, Japan
| | - Katsura Kakoki
- Department of AIDS Research, Institute of Tropical Medicine, Global COE Program, Nagasaki University, Nagasaki, Japan
- Department of Urology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroaki Yoshii
- Department of AIDS Research, Institute of Tropical Medicine, Global COE Program, Nagasaki University, Nagasaki, Japan
| | - Masatomo Iwao
- Graduate School of Science and Technology, Nagasaki University, Nagasaki, Japan
| | - Tsukasa Igawa
- Department of Urology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hideki Sakai
- Department of Urology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hideki Hayashi
- Division of Cytokine Signaling, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Toshifumi Matsuyama
- Division of Cytokine Signaling, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Naoki Yamamoto
- Department of AIDS Research, Institute of Tropical Medicine, Global COE Program, Nagasaki University, Nagasaki, Japan
- Department of Microbiology, National University of Singapore, Singapore, Singapore
| | - Yoshinao Kubo
- Department of AIDS Research, Institute of Tropical Medicine, Global COE Program, Nagasaki University, Nagasaki, Japan
- Division of Cytokine Signaling, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- * E-mail:
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3
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Chao M, Wang TC, Lee SE. Detection of hepatitis delta virus recombinants in cultured cells co-transfected with cloned genotypes I and IIb DNA sequences. J Virol Methods 2006; 137:252-8. [PMID: 16860882 DOI: 10.1016/j.jviromet.2006.06.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2005] [Revised: 06/13/2006] [Accepted: 06/15/2006] [Indexed: 01/03/2023]
Abstract
It was reported previously that hepatitis delta virus (HDV), the only animal virus in which replication is performed by cellular RNA polymerase(s), undergoes RNA recombination. However, the previous RNA transfection system was somewhat limited in terms of practical application. Cultured cells were transfected with plasmids expressing replication-competent genotypes I and IIb HDV genomic RNAs to develop a better system for studying the fundamental aspects of HDV RNA recombination and HDV-related RNA species were examined using restriction fragment length polymorphisms and sequence analysis of cloned RT-PCR products. This novel experimental system generated efficiently recombinants between the two parental HDV sequences, but not between replication-defective HDV constructs. The genome organization of the HDV recombinants produced in this system resembled that observed previously in cultured cells co-transfected with genome I and IIb RNAs. These data indicate that replication-dependent HDV RNA recombination can be catalyzed by host RNA polymerases in cultured cells co-transfected with two cloned HDV sequences. This new DNA-based system is simpler than the previous RNA-based method of study, and generates a higher recombination frequency, facilitating study of HDV RNA recombination.
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Affiliation(s)
- Mei Chao
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yang 333, Taiwan.
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Wickstead B, Ersfeld K, Gull K. The frequency of gene targeting in Trypanosoma brucei is independent of target site copy number. Nucleic Acids Res 2003; 31:3993-4000. [PMID: 12853615 PMCID: PMC165960 DOI: 10.1093/nar/gkg445] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have investigated the effect of target copy number on the efficiency of stable transformation of the protozoan parasite Trypanosoma brucei. Using a single strain of the organism, we targeted integrative vectors to several different genomic sequences, occurring at copy numbers ranging from 1 to approximately 30,000 per diploid genome, and undertook a systematic assessment of both transformation and integration efficiencies. Even over this vast copy number range, frequency of gene targeting was the same for all sites. An independence of targeting frequency and target copy number is characteristic of mammalian homologous recombination and is unlike the situation in budding yeast. It is also not seen in the related parasite Leishmania, a distinction that may be the consequence of the different usage of recombination within the mechanisms of pathogenicity in the two species.
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Affiliation(s)
- Bill Wickstead
- School of Biological Sciences, University of Manchester, 2.205 Stopford Building, Oxford Road, Manchester M13 9PT, UK
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5
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Arad U, Ben-Nun-Shaul O, El-Latif MA, Nissim O, Oppenheim A. A new packaging cell line for SV40 vectors that eliminates the generation of T-antigen-positive, replication-competent recombinants. Virology 2002; 304:155-9. [PMID: 12504557 DOI: 10.1006/viro.2002.1791] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Simian virus 40 (SV40) vectors are efficient vehicles for gene delivery to hematopoietic and hepatic cells. To ensure their replication incompetence and because of safety considerations, it is critical that the vectors do not contain T-antigen sequences. Available packaging cell lines for T-antigen replacement vectors, COS and CMT4, contain considerable sequence identity with the vectors, leading to homologous recombination and reacquisition of the T-antigen gene. We constructed a packaging cell line, COT18, with minimal sequence identity to the vector. Vector stocks produced by passaging on COT18 had high transducing activity and undetectable levels of T-antigen-positive, replication-competent contaminants. This cell line provides a means for the preparation of safe SV40 vector stocks.
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Affiliation(s)
- Uri Arad
- Department of Hematology, Hebrew University-Hadassah Medical School, Hadassah University Hospital, Jerusalem, Israel
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6
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Yáñez RJ, Porter ACG. A chromosomal position effect on gene targeting in human cells. Nucleic Acids Res 2002; 30:4892-901. [PMID: 12433992 PMCID: PMC137162 DOI: 10.1093/nar/gkf614] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2002] [Revised: 09/17/2002] [Accepted: 09/17/2002] [Indexed: 11/13/2022] Open
Abstract
We describe gene targeting experiments involving a human cell line (RAN10) containing, in addition to its endogenous alleles, two ectopic alleles of the interferon-inducible gene 6-16. The frequency of gene targeting at one of the ectopic 6-16 alleles (H3.7) was 34-fold greater than the combined frequency of gene targeting involving endogenous 6-16 alleles in RAN10. Preference for H3.7 was maintained when the target loci in RAN10 were transcriptionally activated by interferon. Despite the 34-fold preference for H3.7, the absolute gene targeting efficiency in RAN10 was only 3-fold higher than in the parental HT1080 cell line. These data suggest that different alleles can compete with each other, and perhaps with non-homologous loci, in a step which is necessary, but not normally rate-limiting, for gene targeting. The efficiency of this step can therefore be more sensitive to chromosomal position effects than the rate-determining steps for gene targeting. The nature of the position effects involved remains unknown but does not correlate with transcription status, which in our system has a very modest influence on the frequency of gene targeting. In summary, our work unequivocally identifies a position effect on gene targeting in human cells.
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Affiliation(s)
- Rafael J Yáñez
- Gene Targeting Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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7
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Lukacsovich T, Waldman BC, Waldman AS. Efficient recruitment of transfected DNA to a homologous chromosomal target in mammalian cells. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1521:89-96. [PMID: 11690640 DOI: 10.1016/s0167-4781(01)00296-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A Chinese hamster ovary cell line hemizygous for a defective adenine phosphoribosyltransferase (aprt) gene was transfected with a plasmid, pAG100, capable of correcting the endogenous aprt mutation by targeted homologous recombination. In some experiments, pAG100 was transfected in combination with one of two 'competitor' plasmids. Competitor pCOMP-A was identical to pAG100 except that the aprt sequence on pCOMP-A had the same mutation as the endogenous aprt gene. Competitor pCOMP-B was identical to pAG100 except for a 763 bp deletion in the aprt sequence encompassing the site of mutation in the endogenous gene. Neither pCOMP-A nor pCOMP-B was capable of correcting the defect in the endogenous aprt gene via gene targeting. We asked whether cotransfection of a 4-fold excess of either competitor DNA molecule with pAG100 would reduce the efficiency of targeted correction of the endogenous aprt gene. We report that while plasmid pCOMP-B did not influence the efficiency of gene targeting by pAG100, plasmid pCOMP-A reduced the number of gene targeting events about 5-fold. These observations indicate that the initial homologous interaction between transfected DNA and a genomic target sequence occurs rapidly and that targeting efficiency is limited by a step subsequent to homologous pairing.
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Affiliation(s)
- T Lukacsovich
- Department of Biological Sciences, University of South Carolina, 700 Sumter Street, Columbia, SC 29208, USA
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8
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Vasquez KM, Marburger K, Intody Z, Wilson JH. Manipulating the mammalian genome by homologous recombination. Proc Natl Acad Sci U S A 2001; 98:8403-10. [PMID: 11459982 PMCID: PMC37450 DOI: 10.1073/pnas.111009698] [Citation(s) in RCA: 231] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Gene targeting in mammalian cells has proven invaluable in biotechnology, in studies of gene structure and function, and in understanding chromosome dynamics. It also offers a potential tool for gene-therapeutic applications. Two limitations constrain the current technology: the low rate of homologous recombination in mammalian cells and the high rate of random (nontargeted) integration of the vector DNA. Here we consider possible ways to overcome these limitations within the framework of our present understanding of recombination mechanisms and machinery. Several studies suggest that transient alteration of the levels of recombination proteins, by overexpression or interference with expression, may be able to increase homologous recombination or decrease random integration, and we present a list of candidate genes. We consider potentially beneficial modifications to the vector DNA and discuss the effects of methods of DNA delivery on targeting efficiency. Finally, we present work showing that gene-specific DNA damage can stimulate local homologous recombination, and we discuss recent results with two general methodologies--chimeric nucleases and triplex-forming oligonucleotides--for stimulating recombination in cells.
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Affiliation(s)
- K M Vasquez
- Science Park Research Division, M. D. Anderson Cancer Center, Smithville, TX 78957, USA
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9
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Hofman CR, Dileo JP, Li Z, Li S, Huang L. Efficient in vivo gene transfer by PCR amplified fragment with reduced inflammatory activity. Gene Ther 2001; 8:71-4. [PMID: 11402304 DOI: 10.1038/sj.gt.3301373] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2000] [Accepted: 10/25/2000] [Indexed: 12/18/2022]
Abstract
There are many problems associated with plasmid DNA that may limit its use in systemic gene transfer. These problems could be solved by the use of synthetic genes. As a model to test the feasibility of using synthetic genes for gene therapy, we PCR-amplified a fragment containing the CMV promoter, the luciferase gene and a polyadenylation signal. The in vivo expression efficiency of the PCR fragment was determined by using two different methods, a hydrodynamics-based gene transfer of naked DNA to the liver and LPD (a lipid-based vector) mediated gene transfer to the lung. Our results show that linear fragments are at least as active as plasmid DNA following systemic delivery by LPD. However, PCR fragments are much less inflammatory than plasmid DNA as shown by a three-fold reduction in serum levels of both TNF-alpha and IL-12. Our results also showed that PCR fragments are highly efficient in liver gene transfer following systemic administration in a large volume. Thus, these results support the idea of using synthetic genes for gene therapy. Since gene sequence can be easily obtained as a PCR fragment, our results also imply that it may provide a useful and convenient method for determining the physiologic function of a putative gene in intact animals.
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Affiliation(s)
- C R Hofman
- Center for Pharmacogenetics, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, USA
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10
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Cheng RZ, Shammas MA, Li J, Shmookler Reis RJ. Expression of SV40 large T antigen stimulates reversion of a chromosomal gene duplication in human cells. Exp Cell Res 1997; 234:300-12. [PMID: 9260898 DOI: 10.1006/excr.1997.3649] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Transformation of human cells is characterized by altered cell morphology, frequent karyotypic abnormalities, reduced dependence on growth factors and substrate, and rare "immortalization"-clonal acquisition of unlimited proliferative potential. We previously reported a marked increase in DNA rearrangements, arising between two duplicated segments in a transfected plasmid substrate, for five immortal human cell lines relative to three normal fibroblast strains [Finn et al. (1989) Mol. Cell. Biol. 9, 4009-4017]. We have now assessed reversion of a 14-kilobase-pair duplication within the hypoxanthine phosphoribosyl transferase (HPRT) gene locus, in a fibroblast strain during its normal replicative lifespan and after stable transformation with SV40 large-T antigen. Revertants, selected under HPRT-dependent growth conditions immediately after purging preexisting HPRT+ cells, were confirmed as HPRT+ by hypoxanthine incorporation and 6-thioguanine sensitivity. Southern blot analyses indicate loss from most revertant clones of a restriction fragment representing the duplicated HPRT region, as predicted for homologous recombination between the 14-kilobase-pair repeats. Amplification of a subregion of HPRT mRNA implicated deletion of duplicated exons in 93% of revertant colonies. Reversion to HPRT+ was unaltered during the normal in vitro lifespan of these cells, but increased in 9 clones stably transformed with large-T antigen (mean = 3.8-fold; each P < 10(-5)). Stimulation of HPRT-reversion is abrogated in a variety of T-antigen mutants, and depends on continued induction of T antigen by glucocorticoid in two clones tested 10-30 doublings before replicative senescence. Since no immortal subclones arose from these clones, elevated reversion must precede immortalization. Increased DNA rearrangements, in cells expressing T-antigen, could facilitate the rare concurrence of multiple mutations necessary for immortalization.
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Affiliation(s)
- R Z Cheng
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock 72205, USA
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11
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Waldman BC, O'Quinn JR, Waldman AS. Enrichment for gene targeting in mammalian cells by inhibition of poly(ADP-ribosylation). BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1308:241-50. [PMID: 8809116 DOI: 10.1016/0167-4781(96)00111-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Inhibition of poly(ADP-ribosylation) reduces random genomic integration of transfected DNA and mildly stimulates intrachromosomal homologous recombination in mammalian cells. We investigated the effect of inhibition of poly(ADP-ribosylation) on the efficiency of gene targeting in Chinese hamster ovary (CHO) cell line ATS-49tg. This cell line is hemizygous for a defective adenine phosphoribosyltransferase (aprt) gene and is hypoxanthine phosphoribosyltransferase (hprt) deficient. Plasmid pAG100 contains a portion of the CHO aprt gene sufficient to correct the defect in ATS-49tg cells via gene targeting; pAG100 also contains an Escherichia coli guanine phosphoribosyltransferase (gpt) gene. Following transfection of ATS-49tg cells with pAG100, selection for gpt-positive transfectants allowed recovery of cells that had randomly integrated pAG100 while selection for aprt-positive cells allowed recovery of cells that had undergone gene targeting at the endogenous aprt locus. Treatment of cells with 3 mM 3-methoxybenzamide (3-MB), an inhibitor of poly(ADP-ribose) polymerase, decreased random integration and gene targeting of electroporated pAG100 about 5-fold. In contrast, treatment with 3 mM 3-MB during calcium phosphate transfection could reduce random integration more than 150-fold while reducing gene targeting less than two-fold. Therefore, as much as a 100-fold enrichment for gene targeting was achieved with calcium phosphate transfection.
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Affiliation(s)
- B C Waldman
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA.
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Affiliation(s)
- L Lashford
- Paterson Institute for Cancer Research, Christie Hospital NHS Trust, Manchester
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13
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Abstract
Gene-targeting techniques are now frequently applied to embryonic stem (ES) cells to introduce mutations of endogenous genes in mice. Modifications introduced into tumor-suppressor genes by this technology have produced mice and cell lines with unique tumorigenic and growth characteristics, respectively. A number of strategies have been developed to enhance the efficiency of homologous recombination between targeting vectors and endogenous genes. This review describes recent advances in the techniques used to construct mice with a variety of genetic alterations. In addition, an application of gene-targeting is illustrated in the study of a class of genes with tumor-suppressor function. Recent findings from experiments using gene targeted mice to study the p53 tumor-suppressor gene are discussed and the potential of gene-targeting for the discovery and study of novel tumor-suppressor genes are explored.
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Affiliation(s)
- A Sands
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
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Abstract
The simian virus 40 (SV40) enhancer contains three 8-bp purine-pyrimidine (R:Y) alternating sequences (Z-motifs) which are known to adopt the left-handed Z-DNA conformation in vitro. Mutations at these three Z-motifs seriously impair enhancer function. Reversion of one of these mutants (dpm12) is studied in this paper. The results indicate that, depending on growth conditions, recovery of the enhancer function is achieved through different mechanisms. Mutant viruses growing in solid-agar medium do not revert. On the other hand, revertants obtained in liquid medium contain a duplication of the enhancer sequences, showing no recovery of the original Z-motifs.
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Affiliation(s)
- M A Martínez-Balbás
- Department of Molecular and Cellular Biology, Centro de Investigación y Desarrollo-CSIC, Barcelona, Spain
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Waldman AS. The search for homology does not limit the rate of extrachromosomal homologous recombination in mammalian cells. Genetics 1994; 136:597-605. [PMID: 8150286 PMCID: PMC1205811 DOI: 10.1093/genetics/136.2.597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Mouse LTK- cells were transfected with a pair of defective Herpes simplex virus thymidine kinase (tk) genes. One tk gene had an 8-bp insertion mutation while the second gene had a 100-bp inversion. Extrachromosomal homologous recombination leading to the reconstruction of a functional tk gene was monitored by selecting for tk positive cells using medium supplemented with hypoxanthine/aminopterin/thymidine. To assess whether the search for homology may be a rate-limiting step of recombination, we asked whether the presence of an excess number of copies of a tk gene possessing both the insertion and inversion mutations could inhibit recombination between the singly mutated tk genes. Effective competitive inhibition would require that homology searching (homologous pairing) occur rapidly and efficiently. We cotransfected plasmid constructs containing the singly mutated genes in the presence or absence of competitor sequences in various combinations of linear or circular forms. We observed effective inhibition by the competitor DNA in six of the seven combinations studied. A lack of inhibition was observed only when the insertion mutant gene was cleaved within the insertion mutation and cotransfected with the two other molecules in circular form. Additional experiments suggested that homologous interactions between two DNA sequences may compete in trans with recombination between two other sequences. We conclude that homology searching is not a rate-limiting step of extrachromosomal recombination in mammalian cells. Additionally, we speculate that a limiting factor is involved in a recombination step following homologous pairing and has a high affinity for DNA termini.
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Affiliation(s)
- A S Waldman
- Department of Biological Sciences, University of South Carolina, Columbia 29208
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16
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Wilson JH, Leung WY, Bosco G, Dieu D, Haber JE. The frequency of gene targeting in yeast depends on the number of target copies. Proc Natl Acad Sci U S A 1994; 91:177-81. [PMID: 8278360 PMCID: PMC42909 DOI: 10.1073/pnas.91.1.177] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We have compared the efficiency of transformation by linear DNA fragments in yeast strains carrying different numbers of homologous targets for recombination. In strains carrying dispersed copies of a target and in strains carrying tandem arrays, the frequency of transformation is proportional to the number of targets. This result is in contrast to previous studies of transformation in mammalian cells, where targeted integration was insensitive to the number of targets. We conclude that, in yeast, the search for a homologous partner is a rate-limiting step in the successful recombination of linearized DNA fragments. Furthermore, the fact that we obtain the same results with both dispersed and clustered targets argues against models of homology searching in which DNA becomes nonspecifically associated with a chromosome and then slides along the DNA until homology is encountered.
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Affiliation(s)
- J H Wilson
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030
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17
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Nairn RS, Adair GM, Porter T, Pennington SL, Smith DG, Wilson JH, Seidman MM. Targeting vector configuration and method of gene transfer influence targeted correction of the APRT gene in Chinese hamster ovary cells. SOMATIC CELL AND MOLECULAR GENETICS 1993; 19:363-75. [PMID: 8105543 DOI: 10.1007/bf01232748] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A 21-bp deletion in the third exon of the APRT gene in Chinese hamster ovary (CHO) cells was corrected by transfection with a plasmid containing hamster APRT sequences. Targeted correction frequencies in the range of 0.3-3.0 x 10(-6) were obtained with a vector containing 3.2 kb of APRT sequence homology. To examine the influence of vector configuration on targeted gene correction, a double-strand break was introduced at one of two positions in the vector prior to transfection by calcium phosphate-DNA coprecipitation or electroporation. A double-strand break in the region of APRT homology contained in the vector produced an insertion-type vector, while placement of the break just outside the region of homology produced a replacement-type vector. Gene targeting with both linear vector configurations yielded equivalent ratios of targeted recombinants to nontargeted vector integrants; however, targeting with the two different vector configurations resulted in different distributions of targeted recombination products. Analysis of 66 independent APRT+ recombinant clones by Southern hybridization showed that targeting with the vector in a replacement-type configuration yielded fewer targeted integrants and more target gene convertants than did the integration vector configuration. Targeted recombination was about fivefold more efficient with electroporation than with calcium phosphate-DNA coprecipitation; however, both gene transfer methods produced similar distributions of targeted recombinants, which depended only on targeting vector configuration. Our results demonstrate that insertion-type and replacement-type gene targeting vectors produce similar overall targeting frequencies in gene correction experiments, but that vector configuration can significantly influence the yield of particular recombinant types.
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Affiliation(s)
- R S Nairn
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center, Smithville 78957
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Abstract
This article presents a review of recent progress in the field of targeted homologous recombination in mammalian cells. Beginning with an introduction of basic terminology and why 'gene targeting' is potentially such a powerful genetic tool, the article explores some of the obstacles that must be overcome in order for targeting to be generally useful. In particular, the different ways in which investigators have been able to work around the great inefficiency of gene targeting is covered in some detail. When possible, insights into the mechanisms(s) of gene targeting are extracted from the published literature. The use of targeted gene 'knockout' in mouse embryonic stems cells to create animal disease models is discussed. The need for systematic studies into the mechanisms(s) of targeting to make gene targeting useful for human gene therapy is recognized, and some suggestions are made.
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Affiliation(s)
- A S Waldman
- Walther Oncology Center, Indiana University School of Medicine, Indianapolis 46202
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20
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Pennington SL, Wilson JH. Gene targeting in Chinese hamster ovary cells is conservative. Proc Natl Acad Sci U S A 1991; 88:9498-502. [PMID: 1946364 PMCID: PMC52745 DOI: 10.1073/pnas.88.21.9498] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Two fundamentally different pathways for homologous recombination have been identified in mammalian cells. For most chromosomal recombination events, two copies of a homologous sequence recombine to yield two copies in the products; such events are said to be conservative because the number of copies is preserved. By contrast, virtually all extrachromosomal recombination events are nonconservative; two copies recombine to give a product containing a single intact copy (the other copy is destroyed in the mechanism). Since gene targeting involves an introduced (extrachromosomal) plasmid and a chromosomal target, it was not clear which pathway would apply. We used a marked vector to determine whether targeted integrants were products of recombination events that involved two copies (the conservative pathway) or three copies (the nonconservative pathway) of the homologous sequence. Among 51 gene targeting events, we identified 17 homologous integrants and analyzed their structures. All match the predictions for a conservative pathway. We conclude that the principal pathway for gene targeting in mammalian cells is conservative.
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Affiliation(s)
- S L Pennington
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030
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21
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Abstract
The ideal approach to gene therapy of hereditary diseases or gene correction therapy is considered. The advantages, disadvantages and limits of gene targeting by homologous recombination are discussed with regard to its possible application in gene correction therapy and in comparison with retroviral-mediated gene complementation therapy.
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Affiliation(s)
- M A Vega
- Institut für Virologie and Immunbiologie der Universität, Würzburg, Federal Republic of Germany
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22
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Hsieh P, Camerini-Otero CS, Camerini-Otero RD. Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA. Genes Dev 1990; 4:1951-63. [PMID: 2276627 DOI: 10.1101/gad.4.11.1951] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We show that recombinases form joint molecules over very short regions of homology. When these molecules are deproteinized the three strands are in a structure that is surprisingly resistant to dissociation by branch migration, even at elevated temperatures. The joint molecules dissociate at temperatures comparable to those required to melt DNA duplexes of the same length and sequence. We also show that nonenzymatically formed structures of the same length and sequence, which have a free third strand ready to branch migrate, dissociate at much lower temperatures. These results provide compelling evidence that the three DNA strands in the region of pairing are hydrogen bonded to each other. Our observations suggest that such a novel three-stranded DNA molecule, or a structure very similar to it, may be the intermediate in general recombination that is used in the recognition of sequence homology. We discuss some of the structural features implicit in this molecule containing any base sequence and compare them with those manifest in true DNA triple helices containing special sequence motifs.
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Affiliation(s)
- P Hsieh
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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23
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Waldman BC, Waldman AS. Illegitimate and homologous recombination in mammalian cells: differential sensitivity to an inhibitor of poly(ADP-ribosylation). Nucleic Acids Res 1990; 18:5981-8. [PMID: 2172923 PMCID: PMC332394 DOI: 10.1093/nar/18.20.5981] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We determined the effect of 3-methoxybenzamide (3-MB), a competitive inhibitor of poly(ADP-ribose)polymerase (E.C. 2.4.2.30), on illegitimate and extrachromosomal homologous recombination in mouse Ltk- cells. Cells were transfected with a wild type Herpes thymidine kinase (tk) gene or with two defective tk gene sequences followed by selection for tk-positive colonies. Using a wild type tk gene, colony formation required uptake, integration, and expression of the tk gene. Using defective tk genes, colony formation had the additional requirement for homologous recombination to reconstruct a functional tk gene. The presence of non-cytotoxic levels of 3-MB during and after transfection reduced the number of colonies recovered with a wild type tk gene in a dose-dependent manner, with 2 mM 3-MB causing a 10 to 20-fold reduction. 3-MB reduced the number of colonies recovered with defective tk genes only to the same extent as in transfections with a wild type gene. Treatment with 3-methoxybenzoic acid, a non-inhibitory analog of 3-MB, did not reduce the recovery of colonies in any experiment. Similar results were obtained using linear or supercoiled molecules and when defective tk genes were transfected into cells on one or two different DNA molecules. By assaying for transient expression of the tk gene, we found that 3-MB did not inhibit uptake or expression of the tk gene. We conclude that poly(ADP-ribosylation) plays a role in random integration (illegitimate recombination) of DNA but does not play an important role in extrachromosomal homologous recombination, demonstrating that these two recombination pathways in cultured mouse fibroblasts are biochemically distinct.
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Affiliation(s)
- B C Waldman
- Walther Oncology Center, Indiana University School of Medicine, Indianapolis 46202-5121
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24
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Abstract
Targeted recombination in mammalian cells is rare compared with non-homologous integration. In Saccharomyces cerevisiae the reverse is true. Differences in targeting efficiency could arise because a target of unique DNA is 200 times more dilute in mammalian genomes than it is in yeast. We tested this possibility by measuring gene targeting in normal CHO cells with two copies of the dihydrofolate reductase (DHFR) gene and in amplified CHOC 400 cells, which carry 800 copies. If the concentration of the target gene is critical, amplified cells should show an enhanced frequency of targeted recombination relative to non-homologous integration. Using a positive/negative selection protocol, we demonstrated that the efficiency of targeting into DHFR genes is indistinguishable in normal and amplified CHO cells. As targeting does not depend on the number of targets, the search for homology is not a rate-limiting step in the mammalian pathway of gene targeting. Thus, the difference in genome size is not the basis for the different outcomes of targeting experiments in S. cerevisiae and mammals.
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Affiliation(s)
- H Zheng
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030
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25
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Adair GM, Nairn RS, Wilson JH, Seidman MM, Brotherman KA, MacKinnon C, Scheerer JB. Targeted homologous recombination at the endogenous adenine phosphoribosyltransferase locus in Chinese hamster cells. Proc Natl Acad Sci U S A 1989; 86:4574-8. [PMID: 2734308 PMCID: PMC287313 DOI: 10.1073/pnas.86.12.4574] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have developed a system that permits analysis of targeted homologous recombination at an endogenous, chromosomal gene locus in cultured mammalian cells. Using a hemizygous, adenine phosphoribosyltransferase (APRT)-deficient, Chinese hamster ovary (CHO) cell mutant as a transfection recipient, we have demonstrated correction of a nonrevertible deletion mutation by targeted homologous recombination. Transfection with a plasmid carrying a fragment of the APRT gene yielded APRT+ recombinants at a frequency of approximately 4.1 x 10(-7). The ratio of targeted recombination to nontargeted integrations of plasmid sequences was approximately 1:4000. Analysis of 31 independent APRT+ recombinants revealed conversions of the endogenous APRT gene, targeted integration at the APRT locus, and a third class of events in which the plasmid donor APRT fragment was converted to a full-length, functional gene.
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Affiliation(s)
- G M Adair
- University of Texas M. D. Anderson Cancer Center, Science Park-Research Division, Smithville 78957
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26
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Kuo MY, Chao M, Taylor J. Initiation of replication of the human hepatitis delta virus genome from cloned DNA: role of delta antigen. J Virol 1989; 63:1945-50. [PMID: 2649689 PMCID: PMC250607 DOI: 10.1128/jvi.63.5.1945-1950.1989] [Citation(s) in RCA: 365] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Beginning with three partial cDNA clones of the RNA genome of human hepatitis delta virus (HDV), we assembled the complete 1,679-base sequence on a single molecule and then inserted a trimer of this into plasmid pSLV, a simian virus 40-based eucaryotic expression vector. This construct was used to transfect both monkey kidney (COS7) and human hepatocellular carcinoma (HuH7) cell lines. In this way we obtained replication of the HDV RNA genome and the appearance, in the nucleoli, of the delta antigen, the only known virus-coded protein. This proved both that the HDV genome could replicate in nonliver as well as liver cells and that there was no requirement for the presence of hepatitis B virus sequences or proteins. When the pSVL construct was made with a dimer of an HDV sequence with a 2-base-pair deletion in the open reading frame, genome replication was reduced at least 40-fold. However, when we cotransfected with a plasmid that expressed the correct delta antigen, the mutated dimer achieved a level of genome replication comparable to that of the nonmutated sequence. We thus conclude that the delta antigen can act in trans and is essential for replication of the HDV genome.
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Affiliation(s)
- M Y Kuo
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
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