Forward and reverse mutations in stages of cancer development

Abstract

BackgroundMassive occurrences of interstitial loss of heterozygosity (LOH) likely resulting from gene conversions were found by us in different cancers as a type of single-nucleotide variations (SNVs), comparable in abundance to the commonly investigated gain of heterozygosity (GOH) type of SNVs, raising the question of the relationships between these two opposing types of cancer mutations.MethodsIn the present study, SNVs in 12 tetra sample and 17 trio sample sets from four cancer types along with copy number variations (CNVs) were analyzed by AluScan sequencing, comparing tumor with white blood cells as well as tissues vicinal to the tumor. Four published “nontumor”-tumor metastasis trios and 246 pan-cancer pairs analyzed by whole-genome sequencing (WGS) and 67 trios by whole-exome sequencing (WES) were also examined.ResultsWidespread GOHs enriched with CG-to-TG changes and associated with nearby CNVs and LOHs enriched with TG-to-CG changes were observed. Occurrences of GOH were 1.9-fold higher than LOH in “nontumor” tissues more than 2 cm away from the tumors, and a majority of these GOHs and LOHs were reversed in “paratumor” tissues within 2 cm of the tumors, forming forward-reverse mutation cycles where the revertant LOHs displayed strong lineage effects that pointed to a sequential instead of parallel development from “nontumor” to “paratumor” and onto tumor cells, which was also supported by the relative frequencies of 26 distinct classes of CNVs between these three types of cell populations.ConclusionsThese findings suggest that developing cancer cells undergo sequential changes that enable the “nontumor” cells to acquire a wide range of forward mutations including ones that are essential for oncogenicity, followed by revertant mutations in the “paratumor” cells to avoid growth retardation by excessive mutation load. Such utilization of forward-reverse mutation cycles as an adaptive mechanism was also observed in cultured HeLa cells upon successive replatings. An understanding of forward-reverse mutation cycles in cancer development could provide a genomic basis for improved early diagnosis, staging, and treatment of cancers.Electronic supplementary materialThe online version of this article (10.1186/s40246-018-0170-6) contains supplementary material, which is available to authorized users.

Biomarkers for Bladder Cancer Diagnosis and Surveillance: A Comprehensive Review

“…Other authors [102] are trying new approaches in the development of mutation driven cancer biomarkers based on the dynamic process of cancer cells. The authors also describe that mutations, leading to loss-of-heterozygosity can be a consequence of defective DNA damage response mechanisms.…”

Genomic subtyping of liver cancers with prognostic application

“…In conclusion, because different types of cancers are caused by dissimilar oncogenic factors and mutational pathways, it was surprising that the generalized genomic variables of SNV load, LOH% and Signature α%, and srCNV could be significant correlates of the probability of survival against clinical cancers. A possible explanation might be that, while a cancer may be initiated by a small number of somatic mutations, its progression to outright malignancy often requires the continual accumulation of a large number of SNV, LOH and CNV mutations [18,19], which is in accord with the large number of cancerrelated genes discovered. Moreover, extensive doublestrand DNA break repair by gene conversion may result in global genomic changes [18], and impact the genomic parameters as measured in this study.…”

“…White blood cell genomic DNA samples from the same patients were used as the controls in sequencing analyses for somatic variations in forms of SNVs and CNVs. This choice of blood over normal tissue as control was based on previous reports by us [19] and others [21,22] that phenotypically normal tissue cells often contain many mutations, while blood cells even under cancerous situation, such as leukemia, bear minimal mutations [19]. Therefore, blood-tumor pairing could be a better design than normal-tumor pairing in somatic mutation analysis of genomic DNA, where tissue specific expression is not a major concern as in the case of RNA analyses.…”

“…White blood cell DNA was prepared by phenolchloroform extraction, and HCC tumor DNA was prepared using DNAzol Reagent (Life Technologies, USA). Experimental AluScan analysis was carried out as previously described [17][18][19]. In brief, multiplex inter-Alu PCR amplification was performed for each sample of 0.1 μg genomic DNA, using the four Alu consensus sequence-based primers AluY278T18 (5′-GAGCGA GACTCGTCTCA-3′), R12A/267 (5′-AGCGAGACTC CG-3′), AluY66H21 5′-TGGTCTCGATCTCC TGACCTC-3′) and L12A/8 (5′-TGAGCCACCGCG-3′), followed by sequencing library construction before subjected to next generation sequencing on the Illumina platform [17].…”

“…Although SNV analyses of cancer genomes have long focused solely on GOH mutations, AluScan sequencing enabled the simultaneous amplification of myriads of inter-Alu sequences in the human genome through polymerase chain reaction (PCR) using Alu retrotransposonconsensus sequences as PCR primers, and revealed that a variety of tumors including HCCs and leukemia were massively burdened with interstitial copy-number neutral LOHs arising from a defective DNA-damage response [17,18]. Examination of LOHs along with GOHs and CNVs also furnished support for a sequential model of cancer development [19]. In view of the importance of LOHs in cancer development, in the present study genomic parameters based on SNV, LOH, GOH and CNV contents, as well as SNV mutational signatures, of liver cancers have been analyzed regarding their utility for the prognosis of patient survival.…”