Z.F. Yang

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.

Significance A tumor comprising many cells can be compared to a natural population with many individuals. The amount of genetic diversity reflects how it has evolved and can influence its future evolution. We evaluated a single tumor by sequencing or genotyping nearly 300 regions from the tumor. When the data were analyzed by modern population genetic theory, we estimated more than 100 million coding region mutations in this unexceptional tumor. The extreme genetic diversity implies evolution under the non-Darwinian mode. In contrast, under the prevailing view of Darwinian selection, the genetic diversity would be orders of magnitude lower. Because genetic diversity accrues rapidly, a high probability of drug resistance should be heeded, even in the treatment of microscopic tumors. The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 “polymorphic” SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.

Retrospective case example using a comprehensive suitability index (CSI) for siting the Shisan-Ling power station, China

Abstract The purpose of this paper is to present a retrospective case example of using the rock engineering systems (RES) methodology to site a pumped storage power station in China. With such a siting problem, there are many interacting factors governing both the site and the specific underground position of the powerhouse. The RES approach, based on an interaction matrix for semi-quantitative characterization of the factors and their interactions, is used to develop a comprehensive suitability index (CSI). In this way, the factors governing the geological and rock mechanics related factors are structured and evaluated. Additionally, the complexity of the decision making process is condensed to the CSI values for different potential sites and underground locations, a higher CSI value indicating a more suitable site. The retrospective analysis uses information from the investigations made during the actual site investigation and design work for the Shisan-Ling Power Station, China — which has been constructed. For the first stage, site selection for the overall engineering arrangement, 11 parameters concerned with geology, geomorphology, engineering layout, environment, cost and construction are taken into account. After comparison of site options in conglomerate, andesite and limestone formations, the conglomerate formation proved to be most favorable — because it has the highest CSI value. For the second stage, specifically locating the underground powerhouse, another seven parameters associated with faults, joints, groundwater, etc. are evaluated. As a result, position II proved to be the most favorable location for the powerhouse. Since these were the same conclusions reached during the actual investigations, this retrospective application of the CSI demonstrates the value of the RES methodology and associated indices for assisting in rock engineering design.

Engineering geomechanical analysis and monitoring-control in design and construction of the Wuqiangxi ship lock slope, China

Abstract The Wuqiangxi Hydroelectric Power Station is located on the Yuan River in Hunan Province, Central China. Phyllitic slates (Pt 1 ) and sandstones (Pt 2 ) occurring on the left bank of the river belong to the Wuqiangxi Formation, the Shangbanxi Group of Pre-Sinian. The slope is intersected by a number of major faults, and rocks are intensely weathered. These factors make the engineering geological situation there unfavorable to the ship lock slope stability. The ship lock slope is threatened under landslides during deep excavation involved in the construction. In order to prevent the excavation of the slope and pouring concrete from failing, a technique of the Monitoring-Control in Design for Geotechnical Engineering (MCGE) was proposed and developed. Consequently, the slope passed smoothly through the excavation and afterward construction stages. This proves that the technique suggested is reasonable and applicable.

Genomic sequencing identifies a few mutations driving the independent origin of primary liver tumors in a chronic hepatitis murine model

With the development of high-throughput genomic analysis, sequencing a mouse primary cancer model provides a new opportunity to understand fundamental mechanisms of tumorigenesis and progression. Here, we characterized the genomic variations in a hepatitis-related primary hepatocellular carcinoma (HCC) mouse model. A total of 12 tumor sections and four adjacent non-tumor tissues from four mice were used for whole exome and/or whole genome sequencing and validation of genotyping. The functions of the mutated genes in tumorigenesis were studied by analyzing their mutation frequency and expression in clinical HCC samples. A total of 46 single nucleotide variations (SNVs) were detected within coding regions. All SNVs were only validated in the sequencing samples, except the Hras mutation, which was shared by three tumors in the M1 mouse. However, the mutated allele frequency varied from high (0.4) to low (0.1), and low frequency (0.1–0.2) mutations existed in almost every tumor. Together with a diploid karyotype and an equal distribution pattern of these SNVs within the tumor, these results suggest the existence of subclones within tumors. A total of 26 mutated genes were mapped to 17 terms describing different molecular and cellular functions. All 41 human homologs of the mutated genes were mutated in the clinical samples, and some mutations were associated with clinical outcomes, suggesting a high probability of cancer driver genes in the spontaneous tumors of the mouse model. Genomic sequencing shows that a few mutations can drive the independent origin of primary liver tumors and reveals high heterogeneity among tumors in the early stage of hepatitis-related primary hepatocellular carcinoma.

A Direct Test of Selection in Cell Populations Using the Diversity in Gene Expression within Tumors.

Although intratumor diversity driven by selection has been the prevailing view in cancer biology, recent population genetic analyses have been unable to reject the neutral interpretation. As the power to reject neutrality in tumors is often low, it will be desirable to have an alternative means to test selection directly. Here, we utilize gene expression data as a surrogate for functional significance in intra- and intertumor comparisons. The expression divergence between samples known to be driven by selection (e.g., between tumor and normal tissues) is always higher than the divergence between normal samples, which should be close to the neutral level of divergence. In contrast, the expression differentiation between regions of the same tumor, being lower than the neutral divergence, is incompatible with the hypothesis of selectively driven divergence. To further test the hypothesis of neutral evolution, we select a hepatocellular carcinoma tumor that has large intratumor SNV and CNV (single nucleotide variation and copy number variation, respectively) diversity. This tumor enables us to calibrate the level of expression divergence against that of genetic divergence. We observe that intratumor divergence in gene expression profile lags far behind genetic divergence, indicating insufficient phenotypic differences for selection to operate. All these expression analyses corroborate that natural selection does not operate effectively within tumors, supporting recent interpretations of within-tumor diversity. As the expected level of genetic diversity, hence the potential for drug resistance, would be much higher under neutrality than under selection, the issue is of both theoretical and clinical significance.