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[This corrects the article on p. e62317 in vol. 8.].

Systematic analysis of more than 5,900 human tumor exomes yields a new genomic classifier of microsatellite instability and insight into its prevalence and biological implications. Microsatellite instability (MSI), the spontaneous loss or gain of nucleotides from repetitive DNA tracts, is a diagnostic phenotype for gastrointestinal, endometrial, and colorectal tumors, yet the landscape of instability events across a wider variety of cancer types remains poorly understood. To explore MSI across malignancies, we examined 5,930 cancer exomes from 18 cancer types at more than 200,000 microsatellite loci and constructed a genomic classifier for MSI. We identified MSI-positive tumors in 14 of the 18 cancer types. We also identified loci that were more likely to be unstable in particular cancer types, resulting in specific instability signatures that involved cancer-associated genes, suggesting that instability patterns reflect selective pressures and can potentially identify novel cancer drivers. We also observed a correlation between survival outcomes and the overall burden of unstable microsatellites, suggesting that MSI may be a continuous, rather than discrete, phenotype that is informative across cancer types. These analyses offer insight into conserved and cancer-specific properties of MSI and reveal opportunities for improved methods of clinical MSI diagnosis and cancer gene discovery.

Due mainly to large genome size and prevalence of repetitive sequences in the nuclear genome of spruce (Picea Mill.), it is very difficult to develop single-copy genomic microsatellite markers. We have developed and characterized 25 polymorphic, single-copy genic microsatellites from white spruce (Picea glauca (Moench) Voss) EST sequences and determined their informativeness in white spruce and black spruce (Picea mariana (Mill.) B.S.P.) and inheritance in black spruce. White spruce EST sequences from NCBI dbEST were searched for the presence of microsatellite repeats. Forty-seven sequences containing dinucleotide, trinucleotide, tetranucleotide and compound repeats were selected to develop primers. Twenty-five of the designed primer pairs yielded scorable amplicons, with single-locus patterns, and were characterized in 20 individuals each of white spruce and black spruce. All 25 microsatellites were polymorphic in white spruce and 24 in black spruce. The number of alleles at a locus ranged from two to 18, with a mean of 8.8 in white spruce, and from one to 17, with a mean of 7.6 in black spruce. The expected heterozygosity/polymorphic information content ranged from 0.10 to 0.92, with a mean of 0.67 in white spruce, and from 0 to 0.93, with a mean of 0.59 in black spruce. Microsatellites with dinucleotide and compound repeats were more informative than those with trinucleotide and tetranucleotide repeats. Eighteen microsatellite markers polymorphic between the parents of a black spruce controlled cross inherited in a single-locus Mendelian fashion. The microsatellite markers developed can be applied for various genetics, genomics, breeding, and conservation studies and applications.

PD-1 blockade has demonstrated impressive clinical outcomes in colorectal cancers that have high microsatellite instability. However, the therapeutic efficacy for patients with tumors with low microsatellite instability or stable microsatellites needs further improvement. Here, we have demonstrated that low-dose decitabine could increase the expression of immune-related genes such as major histocompatibility complex genes and cytokine-related genes as well as the number of lymphocytes at the tumor site in CT26 colorectal cancer-bearing mice. A more significant inhibition of tumor growth and a prolongation of survival were observed in the CT26 mouse model after treatment with a combination of PD-1 blockade and decitabine than in mice treated with decitabine or PD-1 blockade alone. The anti-tumor effect of the PD-1 blockade was enhanced by low-dose decitabine. The results of RNA sequencing and whole-genome bisulfite sequencing of decitabine-treated CT26 cells and tumor samples with microsatellite stability from the patient tumor-derived xenograft model have shown that many immune-related genes, including antigen-processing and antigen-presenting genes, were upregulated, whereas the promoter demethylation was downregulated after decitabine exposure. Therefore, decitabine-based tumor microenvironment re-modulation could improve the effect of the PD-1 blockade. The application of decitabine in PD-1 blockade-based immunotherapy may elicit more potent immune responses, which can provide clinical benefits to the colorectal cancer patients with low microsatellite instability or stable microsatellites.

Background Rhododendron nymphaeoides is explicitly listed as an endangered species in the “ the International Union for Conservation of Nature’s Red List (IUCN)”, “ The Red List of Rhododendrons ”, “ Red List of China’s Higher Plants ” and “ Threatened Species List of China’s Higher Plants ”. It is also listed as a provincial-level key protected wild plant in Sichuan, with few individuals in the wild and significant conservation value. The genetic diversity and population structure have never been described, making it difficult to plan conservation strategies for this plant. Results This study utilized 15 pairs of microsatellite markers to examine the genetic diversity of 79 samples of R. nymphaeoides sourced from five different geographic populations. A total of 214 alleles were detected, with the average effective number of alleles ( N e ) of 7.0324. The averages for the polymorphism information index ( PIC ) and expected heterozygosity ( H e ) were 0.7832 and 0.8102, respectively, indicating that the R. nymphaeoides populations harbor a rich genetic information content, the genetic differentiation coefficients ( F ST ) average was 1.2607. There was high genetic diversity among populations, with average observed heterozygosity ( H o ) and expected heterozygosity ( H e ) values of 0.6375 and 0.6663, respectively, suggesting a degree of inbreeding within populations. Mantel test results showed a significant positive correlation between geographic distance and genetic distance amongst populations ( r  = 0.8456, P  = 0.0021), which conforms to the isolation-by-distance (IBD) model. Due to geographical barriers, there is also a high level of genetic differentiation among populations, with an average genetic differentiation coefficient ( F ST ) of 0.2685. Analysis of molecular variance (AMOVA) indicated that the main source of molecular variance exists within populations (73%), rather than between populations (27%). There was higher historical gene flow (average = 1.0850) and lower contemporary gene flow (average = 1.2849), with seed and pollen dispersal being impeded. Under the Two-Phase Model (TPM) assumption, findings are consistent with the mutation-migration model, suggesting that there has been no genetic bottleneck. STRUCTURE analysis, principal coordinate analysis (PCoA), and UPGMA analysis all support the division of the five natural populations into three genetic clusters. Conclusions This is the first comprehensive analysis of the genetic diversity and population structure of the endangered plant R. nymphaeoides using microsatellite markers. The study results indicate that this endangered plant’s natural populations maintain a high level of genetic diversity. Due to geographical barriers, there is also a high level of genetic differentiation, with the primary source of genetic variation originating within populations. There is higher historical gene flow and lower contemporary gene flow, with seed and pollen dispersal being obstructed. The five populations can be divided into three evolutionary units, for which corresponding conservation management units should be established. These findings will benefit the conservation and development of the species and provide a theoretical basis for further studies on its evolution and biogeography.

The Qianfan constellation has been proposed by joint task teams in Shanghai, China, which has been under development. Its goal is to form a constellation of more than 10, 000 microsatellites, which is dedicated to providing space-based internet services. Based on an open data set of orbit information online, authors have made simulations of the Qianfan constellation, consisting temporarily of 90 microsatellites. Semi-major axis, inclination, and eccentricity data analyses are made, which have shown the status quo of 90 satellites in orbit. 10 deg *10 deg grids are assumed on the surface of the Earth; 90-satellite coverage has been simulated with respect to the assumed ground grids. These simulations and analyses will help technicians learn the current state of the Qianfan constellation, and further promote the effective development of the follow-up Qianfan satellites.

Background Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. Despite the huge resource of genomic information currently available, SSRs have been studied in a limited context and compared across relatively few species. Results We have identified ~ 685 million eukaryotic microsatellites and analyzed their genomic trends across 15 taxonomic subgroups from protists to mammals. The distribution of SSRs reveals taxon-specific variations in their exonic, intronic and intergenic densities. Our analysis reveals the differences among non-related species and novel patterns uniquely demarcating closely related species. We document several repeats common across subgroups as well as rare SSRs that are excluded almost throughout evolution. We further identify species-specific signatures in pathogens like Leishmania as well as in cereal crops, Drosophila , birds and primates. We also find that distinct SSRs preferentially exist as long repeating units in different subgroups; most unicellular organisms show no length preference for any SSR class, while many SSR motifs accumulate as long repeats in complex organisms, especially in mammals. Conclusions We present a comprehensive analysis of SSRs across taxa at an unprecedented scale. Our analysis indicates that the SSR composition of organisms with heterogeneous cell types is highly constrained, while simpler organisms such as protists, green algae and fungi show greater diversity in motif abundance, density and GC content. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and for studying their roles across the evolutionary landscape.

Background Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq). Results Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR- H e ) was not significantly correlated with genome-wide SNP diversity estimates (SNP- H e and θ Watterson ) in A. halleri . Instead, microsatellite allelic richness ( A r ) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations ( F ST ) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation. Conclusions We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri , a few thousand SNPs are sufficient to achieve this goal.

A high tumour mutational burden (hypermutation) is observed in some gliomas 1 – 5 ; however, the mechanisms by which hypermutation develops and whether it predicts the response to immunotherapy are poorly understood. Here we comprehensively analyse the molecular determinants of mutational burden and signatures in 10,294 gliomas. We delineate two main pathways to hypermutation: a de novo pathway associated with constitutional defects in DNA polymerase and mismatch repair (MMR) genes, and a more common post-treatment pathway, associated with acquired resistance driven by MMR defects in chemotherapy-sensitive gliomas that recur after treatment with the chemotherapy drug temozolomide. Experimentally, the mutational signature of post-treatment hypermutated gliomas was recapitulated by temozolomide-induced damage in cells with MMR deficiency. MMR-deficient gliomas were characterized by a lack of prominent T cell infiltrates, extensive intratumoral heterogeneity, poor patient survival and a low rate of response to PD-1 blockade. Moreover, although bulk analyses did not detect microsatellite instability in MMR-deficient gliomas, single-cell whole-genome sequencing analysis of post-treatment hypermutated glioma cells identified microsatellite mutations. These results show that chemotherapy can drive the acquisition of hypermutated populations without promoting a response to PD-1 blockade and supports the diagnostic use of mutational burden and signatures in cancer. Temozolomide therapy seems to lead to mismatch repair deficiency and hypermutation in gliomas, but not to an increase in response to immunotherapy.