Forward and reverse mutations in stages of cancer development

Background

Massive 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.

Methods

In 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.

Results

Widespread 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.

Conclusions

These 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.

     

Fourth International Workgroup on Genotoxicity testing: results of the in vivo Comet assay workgroup

As part of the Fourth International Workshop on Genotoxicity Testing (IWGT), held 9-10 September 2005 in San Francisco, California, an expert working group on the Comet assay was convened to review and discuss some of the procedures and methods recommended in previous documents. Particular attention was directed at the in vivo rodent, alkaline (pH >13) version of the assay. The aim was to review those protocol areas which were unclear or which required more detail in order to produce a standardized protocol with maximum acceptability by international regulatory agencies. The areas covered were: number of dose levels required, cell isolation techniques, measures of cytotoxicity, scoring of comets (i.e., manually or by image analysis), and the need for historical negative/positive control data. It was decided that a single limit dose was not sufficient although the required number of dose levels was not stipulated. The method of isolating cells was thought not to have a qualitative effect on the assay but more data were needed before a conclusion could be drawn. Concurrent measures of cytotoxicity were required with histopathological examination of tissues for necrosis or apoptosis as the "Gold Standard". As for analysing the comets, the consensus was that image analysis was preferred but not required. Finally, the minimal number of studies required to generate a historical positive or negative control database was not defined; rather the emphasis was placed on demonstrating the stability of the negative/positive control data. It was also agreed that a minimum reporting standard would be developed which would be consistent with OECD in vivo genotoxicity test method guidelines.     

SO2熏气对油桐叶片细胞膜脂组成和叶绿体超微结构的影响

经SO2熏气处理的油桐叶片电导率增加,叶片中脂质过氧化作用增强,总类脂、极性脂、非极性脂、糖脂含量下降,磷脂含量稍有增加;极性脂和非极性脂中不饱和脂肪酸C18:3含量、C18:3/IUFA、不饱和指标UFA和IUFA值下降,叶绿体结构受到破坏,片层结构模糊不清;随着熏气时间的延长叶绿体中的淀粉颗粒增大,脂滴变小.     

Location of the gene causing hyperimmunoglobulinemia D and periodic fever syndrome differs from that for familial mediterranean fever

The hyperimmunoglobulinemia D and periodic fever (hyper-IgD) syndrome is typified by recurrent febrile attacks with abdominal distress, joint involvement (arthralgias/arthritis), headache, skin lesions, and an elevated serum IgD level (>100U/ml). This familial disorder has been diagnosed in 56 subjects worldwide. As the hyper-IgD syndrome resembles familial Mediterranean fever, one could speculate that both result from mutations in the same gene. The gene causing familial Mediterranean fever (MEF) has been located on chromosome 16p. We have studied 10 families with 19 affected and 28 non-affected subjects. The clinical findings and IgD determinations from these families are compatible with autosomal recessive inheritance. Using highly polymorphic markers surrounding the MEF gene, only negative Lod scores were obtained, whereas haplotype analysis excluded this locus as the cause of the hyper-IgD syndrome. In addition, no indication for linkage was obtained with markers from other candidate gene regions on chromosomes 17q and 14q.Participants listed in the appendix     

肝素的抗肿瘤转移活性及其与选凝素的关系

肝素作为传统抗凝剂,常用来治疗癌症患者静脉血栓。临床和实验数据证实,肝素具有抗肿瘤活性。同时也有大量研究发现,肝素有抗肿瘤转移的作用。肝素可以通过各种机制抑制肿瘤转移,包括抑制细胞间的相互作用;抑制肝素酶的表达;调节各种生长因子以及调节机体凝血功能等。选凝素(seletin)是介导肿瘤转移初始阶段的重要因子,而肝素能够抑制选凝素介导的的肿瘤细胞与白细胞、血小板及内皮细胞的相互作用,从而达到抗转移的效果。本文综述了肝素抑制选凝素介导的肿瘤转移的作用机制,为肝素在抗肿瘤转移方面的临床应用提供参考。     

Quality control in databanks for molecular biology

Using a scientific measurement without an estimate of its error is like lending money to a stranger. Given the explosion in nucleic acid and protein sequence and structural data, what risks are the scientific and medical communities running in using these databases. Is there an ‘ombudsman’ who speaks for the users of the data? CODATA, the Committee on Data for Science and Technology of the International Council of Scientific Unions was established to improve the quality, reliability, processing, management, and accessibility of data for science and technology. The CODATA Task Group on Biological Macromolecules has surveyed quality control procedures of archival databanks in molecular biology. Our role is ‘to advise, to be consulted, and to warn.’ This report describes the kinds and extents of errors that may appear in nucleic acid and protein databases, and presents an agenda for future work to improve the quality of these databases. The results of the survey appear on the web http://www.codata.org/codata/tgreports/tg_reps.html . BioEssays 22:1024–1034, 2000. © 2000 John Wiley & Sons, Inc.     

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex

The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection.