Frida Rosengren

Multiregion whole-exome sequencing uncovers the genetic evolution and mutational heterogeneity of early-stage metastatic melanoma

Cancer genome sequencing has shed light on the underlying genetic aberrations that drive tumorigenesis. However, current sequencing-based strategies, which focus on a single tumor biopsy, fail to take into account intratumoral heterogeneity. To address this challenge and elucidate the evolutionary history of melanoma, we performed whole-exome and transcriptome sequencing of 41 multiple melanoma biopsies from eight individual tumors. This approach revealed heterogeneous somatic mutations in the range of 3%-38% in individual tumors. Known mutations in melanoma drivers BRAF and NRAS were always ubiquitous events. Using RNA sequencing, we found that the majority of mutations were not expressed or were expressed at very low levels, and preferential expression of a particular mutated allele did not occur frequently. In addition, we found that the proportion of ultraviolet B (UVB) radiation-induced C>T transitions differed significantly (P < 0.001) between early and late mutation acquisition, suggesting that different mutational processes operate during the evolution of metastatic melanoma. Finally, clinical history reports revealed that patients harboring a high degree of mutational heterogeneity were associated with more aggressive disease progression. In conclusion, our multiregion tumor-sequencing approach highlights the genetic evolution and non-UVB mutational signatures associated with melanoma development and progression, and may provide a more comprehensive perspective of patient outcome. Cancer Res; 76(16); 4765-74. ©2016 AACR.

Genome-wide DNA methylation analysis in melanoma reveals the importance of CpG methylation in MITF regulation

The microphthalmia-associated transcription factor (MITF) is a key regulator of melanocyte development and a lineage-specific oncogene in melanoma; a highly lethal cancer known for its unpredictable clinical course. MITF is regulated by multiple intracellular signaling pathways, although the exact mechanisms that determine MITF expression and activity remain incompletely understood. In this study, we obtained genome-wide DNA methylation profiles from 50 stage IV melanomas, normal melanocytes, keratinocytes, and dermal fibroblasts and utilized The Cancer Genome Atlas data for experimental validation. By integrating DNA methylation and gene expression data, we found that hypermethylation of MITF and its co-regulated differentiation pathway genes corresponded to decreased gene expression levels. In cell lines with a hypermethylated MITF-pathway, overexpression of MITF did not alter the expression level or methylation status of the MITF pathway genes. In contrast, however, demethylation treatment of these cell lines induced MITF-pathway activity, confirming that gene regulation was controlled via methylation. The discovery that the activity of the master regulator of pigmentation, MITF, and its downstream targets may be regulated by hypermethylation has significant implications for understanding the development and evolvement of melanoma.

Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

Adoptive T-cell therapy (ACT) is a highly intensive immunotherapy regime that has yielded remarkable response rates and many durable responses in clinical trials in melanoma; however, 50–60% of the patients have no clinical benefit. Here, we searched for predictive biomarkers to ACT in melanoma. Whole exome- and transcriptome sequencing and neoantigen prediction were applied to pre-treatment samples from 27 patients recruited to a clinical phase I/II trial of ACT in stage IV melanoma. All patients had previously progressed on other immunotherapies. We report that clinical benefit is associated with significantly higher predicted neoantigen load. High mutation and predicted neoantigen load are significantly associated with improved progression-free and overall survival. Further, clinical benefit is associated with the expression of immune activation signatures including a high MHC-I antigen processing and presentation score. These results improve our understanding of mechanisms behind clinical benefit of ACT in melanoma.Adoptive T cell therapy (ACT) has yielded high response rates in melanoma, however 50–60% of patients experience no clinical benefit. Here, the authors identify predictive biomarkers, high non-synonymous mutation and high expressed neoantigen load, that associate with clinical benefit in ACT melanoma patients.

Sexual reproduction in the phyllodioicous bryophyte Homalothecium lutescens (Hedw.) H.Rob. in relation to habitat age, growth conditions and genetic variation

Abstract Sporophyte production and female fertility were investigated in seventeen calcareous grassland demes of the moss Homalothecium lutescens (Hedw.) H.Rob. on the Baltic island of Öland, with the aim of understanding the relationships between sexual reproduction, habitat age, genetic variation and factors related to growth conditions. The overall proportion of fertile female shoots (with perichaetia) was 35%. Fertility status at the level of individual shoots was positively associated with shoot length and density, while within deme fertility was positively associated with bush cover. There was no association between female fertility and habitat age, genetic diversity (HS) or allelic richness. Out of 1344 investigated shoots, only two were normal-sized fertile males. Dwarf males were also extremely rare, and found almost exclusively on shoots with sporophytes. Few sporophytes were observed (in the two demes with highest fertility and bush cover). No relationship between genetic variation and the frequency of sporophytes and males was found. The lack of a relationship between sexual reproduction and genetic variation suggests that sexual reproduction may not occur in the same grassland fragments as the recruitment of new clones (from spores or vegetative fragments). The majority of the dry, open grassland habitats, where H. lutescens is typically found in the study area, appear to be suboptimal for both dwarf males and fertilization. Sexual reproduction is more likely to occur in shaded (although grazed) grassland patches, where moisture levels are likely to be higher and the moss colonies are generally more vigorous.

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (˜90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK, three RET, two ROS1) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.

Selective spore germination on shoots of Homalothecium lutescens, a moss with dwarf males.

Spores from three bryophyte species with dwarf males (Homalothecium lutescens, Homalothecium sericeum and Isothecium alopecuroides) were sown on shoots of H. lutescens in vitro. After 10 months, presence and fertility of dwarf plants were scored. Spores of the more distantly related I. alopecuroides were unable to develop into dwarf plants on H. lutescens. Spores of both H. lutescens and H. sericeum developed into dwarf plants. In fact, dwarf plants of H. sericeum were both more abundant and more often fertile than those of H. lutescens. The ability of H. sericeum spores to develop into dwarf males on shoots of H. lutescens suggests a possible pathway for hybridization between the two species. On the other hand, the inability of I. alopecuroides to develop into dwarf males on shoots of H. lutescens suggests that regulation of spore germination and dwarf male development on host shoots is associated with the degree of relatedness between species.

Balance between inbreeding and outcrossing in a nannandrous species, the moss Homalothecium lutescens.

Epiphytic dwarf males on the females present a possible solution to the problem of short fertilization distances in mosses. However, leptokurtic spore dispersal makes dwarf males likely to be closely related to their host shoot, with an accompanying risk of inbreeding. The capacity of a female to harbour a high number of different dwarf males suggests that there may be mechanisms in place that counteract inbreeding, such as polyandry and post-fertilization selection. We have genotyped sporophytes, female host shoots and dwarf males in four populations of the moss Homalothecium lutescens. We found no evidence of selective sporophyte abortion based on level of heterozygosity. The occurrence of entirely homozygous sporophytes together with significantly positive inbreeding coefficients in three of the populations (mean FIS between 0.48 and 0.64) suggest frequent mother–son mating events. However, 23% of all sampled sporophytes had a higher level of heterozygosity compared with the mean expected heterozygosity at the population level. Polyandry was frequent, on average 59% of the sporophytes on a female shoot were sired by distinct fathers. In conclusion, sporadic fertilizations by dwarf males originating from nonhost female shoots appear to counteract strong inbreeding.

On the diversity and richness of understory bryophytes at Nectandra Cloud Forest Reserve, Costa Rica

Abstract Background A survey of the understory bryophytes in the Nectandra Cloud Forest Preserve yielded 1083 specimens distributed among 55 families, represented by 74 genera of mosses, 75 genera of liverworts and 3 of hornworts. We studied and analyzed the bryophytic distribution on six types of substrates: 1) corticolous, 2) epiphyllous, 3) saxicolous, 4) terricolous, 5) aquatic and 6) lignicolous. The richness and composition of bryophyte genera are compared to those of other previous bryophyte surveys from 4 other sites with different oceanic exposures, climatic and geographic conditions in Costa Rica. New information This is a report of the first extensive general survey of bryophytes at the Nectandra Reserve, a premontane cloud forest located on the Atlantic slope of Costa Rica, an area much less studied compared to the Monteverde cloud forest on the Pacific slope.