Population genomics of the fission yeast Schizosaccharomyces pombe.

The fission yeast Schizosaccharomyces pombe has been widely used as a model eukaryote to study a diverse range of biological processes. However, population genetic studies of this species have been limited to date, and we know very little about the evolutionary processes and selective pressures that are shaping its genome. Here, we sequenced the genomes of 32 worldwide S. pombe strains and examined the pattern of polymorphisms across their genomes. In addition to introns and untranslated regions (UTRs), intergenic regions also exhibited lower levels of nucleotide diversity than synonymous sites, suggesting that a considerable amount of noncoding DNA is under selective constraint and thus likely to be functional. A number of genomic regions showed a reduction of nucleotide diversity probably caused by selective sweeps. We also identified a region close to the end of chromosome 3 where an extremely high level of divergence was observed between 5 of the 32 strains and the remain 27, possibly due to introgression, strong positive selection, or that region being responsible for reproductive isolation. Our study should serve as an important starting point in using a population genomics approach to further elucidate the biology of this important model organism

Novel quantitative immunohistochemical analysis for evaluating PD-L1 expression with phosphor-integrated dots for predicting the efficacy of patients with cancer treated with immune checkpoint inhibitors

IntroductionProgrammed cell death ligand 1 (PD-L1) expression in tumor tissues is measured as a predictor of the therapeutic efficacy of immune checkpoint inhibitors (ICIs) in many cancer types. PD-L1 expression is evaluated by immunohistochemical staining using 3,3´-diaminobenzidine (DAB) chronogenesis (IHC-DAB); however, quantitative and reproducibility issues remain. We focused on a highly sensitive quantitative immunohistochemical method using phosphor-integrated dots (PIDs), which are fluorescent nanoparticles, and evaluated PD-L1 expression between the PID method and conventional DAB method.MethodsIn total, 155 patients with metastatic or recurrent cancer treated with ICIs were enrolled from four university hospitals. Tumor tissue specimens collected before treatment were subjected to immunohistochemical staining with both the PID and conventional DAB methods to evaluate PD-L1 protein expression.ResultsPD-L1 expression assessed using the PID and DAB methods was positively correlated. We quantified PD-L1 expression using the PID method and calculated PD-L1 PID scores. The PID score was significantly higher in the responder group than in the non-responder group. Survival analysis demonstrated that PD-L1 expression evaluated using the IHC-DAB method was not associated with progression-free survival (PFS) or overall survival (OS). Yet, PFS and OS were strikingly prolonged in the high PD-L1 PID score group.ConclusionQuantification of PD-L1 expression as a PID score was more effective in predicting the treatment efficacy and prognosis of patients with cancer treated with ICIs. The quantitative evaluation of PD-L1 expression using the PID method is a novel strategy for protein detection. It is highly significant that the PID method was able to identify a group of patients with a favorable prognosis who could not be identified by the conventional DAB method

Population Genomics of the Fission Yeast <i>Schizosaccharomyces pombe</i>

<div><p>The fission yeast <i>Schizosaccharomyces pombe</i> has been widely used as a model eukaryote to study a diverse range of biological processes. However, population genetic studies of this species have been limited to date, and we know very little about the evolutionary processes and selective pressures that are shaping its genome. Here, we sequenced the genomes of 32 worldwide <i>S. pombe</i> strains and examined the pattern of polymorphisms across their genomes. In addition to introns and untranslated regions (UTRs), intergenic regions also exhibited lower levels of nucleotide diversity than synonymous sites, suggesting that a considerable amount of noncoding DNA is under selective constraint and thus likely to be functional. A number of genomic regions showed a reduction of nucleotide diversity probably caused by selective sweeps. We also identified a region close to the end of chromosome 3 where an extremely high level of divergence was observed between 5 of the 32 strains and the remain 27, possibly due to introgression, strong positive selection, or that region being responsible for reproductive isolation. Our study should serve as an important starting point in using a population genomics approach to further elucidate the biology of this important model organism.</p></div

Population structure of <i>S. pombe</i>.

<p>Neighbor-joining tree (a) and the results of principal component analysis (PCA) (b) and the program STRUCTURE (c). The numbers of the strains correspond to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104241#pone-0104241-t001" target="_blank">Table 1</a>. The 5 samples that strongly cluster together are colored in blue. The results of STRUCTURE with <i>K = 4</i> changes when different subsets of randomly chosen SNPs are used, and the result of <i>K = 4</i> shown here represents one example. The grouping of strains 15, 16, 17, 18, and 30, and the grouping of strains 2, 9, 32, and 1 are both always observed. The results of <i>K = 2</i> and <i>K = 3</i> are consistent.</p

The decay of linkage disequilibrium with distance between SNPs.

<p> is plotted as a function of distance in kilobase up to 500 kb. The average values over each non-overlapping 1 kb bin are shown.</p

Genome-wide distribution of nucleotide diversity and Tajima's <i>D</i>.

<p>The values were calculated for each sliding window of 20 kb with an increment of 4 kb. The putative selective sweep region on chromosome 1 with low nucleotide diversity and low Tajima's <i>D</i> is indicated by a blue downward triangle. The mating locus region on chromosome 2 and another region on chromosome 3 showing high nucleotide diversity are indicated by red downward triangles. The gray shaded regions correspond to centromeric regions.</p

Top 20 genes with highest Tajima's <i>D</i>.

<p>Only genes where more than 200 synonymous sites could be analyzed are shown.</p

Summary of nucleotide diversity.

<p>The sum of all these categories does not equal the numbers given in “All” as sequences that are too short or contain too many undetermined sites (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104241#s4" target="_blank">Methods</a>) are not included.</p