Evolutionary dynamics of tipifarnib in HRAS mutated head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is a highly prevalent malignancy worldwide, with a significant proportion of patients developing recurrent and/or metastatic (R/M) disease. Despite recent advances in therapy, the prognosis for patients with advanced HNSCC remains poor. Here, we present the case of a patient with recurrent metastatic HNSCC harboring an HRAS G12S mutation who achieved a durable response to treatment with tipifarnib, a selective inhibitor of farnesyltransferase. The patient was a 48-year-old woman who had previously received multiple lines of therapy with no significant clinical response. However, treatment with tipifarnib resulted in a durable partial response that lasted 8 months. Serial genomic and transcriptomic analyses demonstrated upregulation of YAP1 and AXL in metastatic lesions compared with the primary tumor, the evolution of the tumor microenvironment from an immune-enriched to a fibrotic subtype with increased angiogenesis, and activation of the PI3K/AKT/mTOR pathway in tipifarnib treatment. Lastly, in HRAS-mutated PDXs and in the syngeneic HRAS model, we demonstrated that tipifarnib efficacy is limited by activation of the AKT pathway, and dual treatment with tipifarnib and the PI3K inhibitor, BYL719, resulted in enhanced anti-tumor efficacy. Our case study highlights the potential of targeting HRAS mutations with tipifarnib in R/M HNSCC and identifies potential mechanisms of acquired resistance to tipifarnib, along with immuno-, chemo-, and radiation therapy. Preclinical results provide a firm foundation for further investigation of drug combinations of HRAS-and PI3K -targeting therapeutics in R/M HRAS-driven HNSCC.

A pre-Miocene Irano-Turanian cradle: Origin and diversification of the species-rich monocot genus Gagea (Liliaceae).

The Irano-Turanian (IT) floristic region is considered an important center of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighboring areas. The species-rich monocot genus Gagea Salisb. shows a center of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighboring areas (East Asia, Euro-Siberia, Himalaya, and Mediterranean). We aimed at (a) testing the origin of the genus and of its major lineages in the IT region, (b) reconstructing divergence times, and (c) reconstructing colonization events. To address these problems, sequences of the ribosomal DNA internal transcribed spacer (ITS) region of 418 individuals and chloroplast intergenic spacers sequences (psbA-trnH, trnL-trnF) of 497 individuals, representing 116 species from all sections of the genus and nearly its entire distribution area were analyzed. Divergence times were estimated under a random molecular clock based on nrITS phylogeny, which was the most complete data set regarding the representation of species and distribution areas. Ancestral distribution ranges were estimated for the nrITS data set as well as for a combined data set, revealing that Gagea most likely originated in southwestern Asia. This genus first diversified there starting in the Early Miocene. In the Middle Miocene, Gagea migrated to the Mediterranean and to East Asia, while migration into Euro-Siberia took place in the Late Miocene. During the Pleistocene, the Arctic was colonized and Gagea serotina, the most widespread species, reached North America. The Mediterranean basin was colonized multiple times from southwestern Asia or Euro-Siberia. Most of the currently existing species originated during the last 3 Ma.

Studies of life history of Gagea graeca (Liliaceae) based on morphological and molecular methods.

BACKGROUND: We studied the life history of Gagea graeca (L.) A. Terracc. (sect. Anthericoides) by field surveys on the Greek island of Crete, including quantitative analyses of 405 individuals, estimation of resource allocation by measuring the nitrogen content of different plant organs, assessing seed set and recording genetic diversity via amplified fragment length polymorphism (AFLP) analyses. In contrast to most species of the genus G. graeca seems to be a short-lived perennial, developing several characters that are rather typical for annual plants. RESULTS: Although seed set varies largely, flowering plants produce many (68 ± 79) small, flattened seeds (mean weight 73 ± 22 µg) in comparison to a single bulbil. If measured as nitrogen content of the respective plant parts, investment in seeds (25%) is much higher than that in bulbils (4%). In addition, the threshold for flower formation (expressed as bulb size where 50% of the plants form the respective structure) is with 2.17 ± 0.05 mm lower than that for bulbils with 2.80 ± 0.16 mm. This is in accordance with AFLP analyses revealing predominantly sexual reproduction (only 9.1% of 110 investigated plants belonged to clones). CONCLUSION: In the genus Gagea early, predominantly sexual reproduction seems to be characteristic for species from arid habitats, coupled with a low proportion of clonal plants.

Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions.

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

Systematics of Gagea and Lloydia (Liliaceae) and infrageneric classification of Gagea based on molecular and morphological data.

Our study represents the first phylogenetic analyses of the genus Gagea Salisb. (Liliaceae), including 58 species of Gagea and 6 species of the closely related genus Lloydia Salisb. ex Rchb. Our molecular results support the infrageneric classification of the genus Gagea in sections according to Levichev and demonstrate that Pascher's subdivision of this genus into two subgenera can no longer be upheld. Certain Gagea sections (e.g., Gagea, Minimae, and Plecostigma) are well supported by cpDNA and nrDNA data. Gagea sect. Fistulosae is closely related to G. sect. Didymobolbos. Gagea sect. Graminifoliae and G. sect. Incrustatae are closely related to G. sect Platyspermum. The analyses support the monophyly of Gagea and Lloydia collectively. The molecular analyses reveal the basal position of G. graeca in proportion to all other species of Gagea and Lloydia investigated. Minor morphological differences could be established between both genera which support their close relationship.

Non-concerted ITS evolution in Mammillaria (Cactaceae).

Molecular studies of 21 species of the large Cactaceae genus Mammillaria representing a variety of intrageneric taxonomic levels revealed a high degree of intra-individual polymorphism of the internal transcribed spacer region (ITS1, 5.8S rDNA, ITS2). Only a few of these ITS copies belong to apparently functional genes, whereas most are probably non-functional (pseudogenes). As a multiple gene family, the ITS region is subjected to concerted evolution. However, the high degree of intra-individual polymorphism of up to 36% in ITS1 and up to 35% in ITS2 suggests a non-concerted evolution of these loci in Mammillaria. Conserved angiosperm motifs of ITS1 and ITS2 were compared between genomic and cDNA ITS clones of Mammillaria. Some of these motifs (e.g., ITS1 motif 1, 'TGGT' within ITS2) in combination with the determination of GC-content, length comparisons of the spacers and ITS2 secondary structure (helices II and III) are helpful in the identification of pseudogene rDNA regions.