LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq

LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method-5' scL1seq-that makes use of a widely available library preparation method (10x Genomics 5' single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors-present in cancer cells, absent from immune cells-and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.

Systemic toxicities of trastuzumab-emtansine predict tumor response in HER2+ metastatic breast cancer

The mechanism by which trastuzumab-emtansine (T-DM1) causes systemic toxicities apart from trastuzumab alone is currently unknown. We hypothesized that the systemic toxicities from T-DM1 may have been caused by the free and active maytansine released from the lysed HER2+ tumor cells, and if so, they may correlate with the response to treatment and eventually disease-free survival or patient outcome. In a retrospective, observational study, we evaluated 73 patients from three centers in the United States and Canada with advanced HER2+ breast cancer that received at least one dose of T-DM1. Toxicity grades were summed to create a corresponding toxicity sum score (TSS), and its association with clinical outcomes was analyzed. A higher TSS was significantly associated with longer progression-free survival with an HR = 0.66 [95% confidence interval [CI]: 0.47-0.92], P = .014, for each 1-point increase in the TSS score. Adjusted for baseline platelet count, aspartate transaminase and alanine transaminase, higher TSS remains significantly associated with longer progression-free survival with adjusted HR = 0.67 [95% CI: 0.47-0.93], P = .020. The analysis suggests that the systemic toxicities of T-DM1 were significantly correlated with its clinical efficacy. This is the first report to correlate the systemic toxicities of T-DM1 with clinical outcome. Further, this suggests that systemic toxicities of antibody-drug conjugates (ADCs) may serve as a predictive biomarker, particularly if noncleavable linkers are used. If confirmed in larger prospective studies, the present finding is significant because most ADCs do not have a biomarker predictive of clinical outcome other than the presence or absence of the antibody target.

Cold tolerance in the genus Arabidopsis

PREMISE

Cold tolerance is an important factor limiting the geographic distribution and growing season for many plant species, yet few studies have examined variation in cold tolerance extensively within and among closely related species and compared that to their geographic distribution.

METHODS

This study examines cold tolerance within and among species in the genus Arabidopsis. We assessed cold tolerance by measuring electrolyte leakage from detached leaves in multiple populations of five Arabidopsis taxa. The temperature at which 50% of cells were lysed was considered the lethal temperature (LT₅₀ ).

RESULTS

We found variability within and among taxa in cold tolerance. There was no significant within-species relationship between latitude and cold tolerance. However, the northern taxa, A. kamchatica, A. lyrata subsp. petraea, and A. lyrata subsp. lyrata, were more cold tolerant than A. thaliana and A. halleri subsp. gemmifera both before and after cold acclimation. Cold tolerance increased after cold acclimation (exposure to low, but nonfreezing temperatures) for all taxa, although the difference was not significant for A. halleri subsp. gemmifera. For all taxa except A. lyrata subsp. lyrata, the LT₅₀ values for cold-acclimated plants were higher than the January mean daily minimum temperature (T_min ), indicating that if plants were not insulated by snow cover, they would not likely survive winter at the northern edge of their range.

CONCLUSIONS

Arabidopsis lyrata and A. kamchatica were far more cold tolerant than A. thaliana. These extremely cold-tolerant taxa are excellent candidates for studying both the molecular and ecological aspects of cold tolerance.

Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR-based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics

PREMISE OF THE STUDY

Polyploidy has been long recognized as an important force in plant evolution. Previous studies had suggested widespread occurrence of polyploidy and the allopolyploid origin of several species in the diverse neotropical genus Lachemilla (Rosaceae). Nonetheless, this evidence has relied mostly on patterns of cytonuclear discordance, and direct evidence from nuclear allelic markers is still needed.

METHODS

Here we used PCR target enrichment in combination with high throughput sequencing to obtain multiple copies of the nuclear ribosomal (nr) DNA cistron and 45 regions of the plastid genome (cpDNA) from 219 accessions representing 48 species of Lachemilla and to explore the allopolyploid origin of species in this group.

KEY RESULTS

We were able to identify multiple nrDNA ribotypes and establish clear evidence of allopolyploidy in 33 species of Lachemilla, showing that this condition is common and widespread in the genus. Additionally, we found evidence for three autopolyploid species. We also established multiple, independent origins of several allopolyploid species. Finally, based solely on the cpDNA phylogeny, we identified that the monotypic genus Farinopsis is the sister group of Lachemilla and allied genera within subtribe Fragariinae.

CONCLUSIONS

Our study demonstrates the utility of the nuclear ribosomal DNA cistron to detect allopolyploidy when concerted evolution of this region is not complete. Additionally, with a robust chloroplast phylogeny in place, the direction of hybridization events can be established, and multiple, independent origins of allopolyploid species can be identified.