Pheromone Evolution, Reproductive Genes, and Comparative Transcriptomics in Mediterranean Earthworms (Annelida, Oligochaeta, Hormogastridae)

Abstract Genomic characterization is often used for the identification of therapeutic targets in tumors. Recently, comparative transcriptomics has begun to be utilized for this purpose. In this pilot, we compare the transcriptome of a patient with recurrent high grade glioma (HGG) to our cohort to identify potential therapies. We reviewed transcriptomic profiles from patients who had resection of HGG at our institution over the past year as well as the UCSC cancer compendium. Briefly, tumor RNA was extracted from embedded tumor tissue sections with tumor cellularity higher than 20%. RNA libraries were sequenced to obtain approximately 65 million reads on an Illumina HiSeq 4000 System utilizing patterned flow cell technology. The RNA profile of a 24 male with Li-Fraumeni syndrome and recurrent HGG with leptomeningeal spread underwent comparative transcriptomics to identify targets. A Bayesian statistical framework for gene expression outlier detection was used. These comparisons allowed for the identification of genes and pathways that are significantly overexpressed. Our internal HGG cohort consisted of 44 adult patients and was evenly distributed among the 4 HGG Verhaak subtypes. Our patient of interest had druggable outlier expression in HDAC1, STAT1 and STAT2 in comparison to our internal cohort indicating vorinostat and ruxolitinib as potential therapies, respectively. We then compared our patient of interest to 12,747 patients in the cancer compendium and STAT2 expression was high but not an outlier. In comparison to 738 glioma samples, STAT1 and STAT2 were outliers but not HDAC1 again indicating ruxolitinib as a potential targeted therapy. The patient did not have outlier expression in notch transcriptional targets or immune checkpoint biomarkers when compared to all cohorts. In conclusion, comparative Transcriptomics can identify therapeutic targets in a patient with recurrent HGG even in small cohorts. In our pilot, we identified ruxolitinib as a potential candidate to treat leptomeningeal recurrence.

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Comparative transcriptomics of albino and warningly‐coloured caterpillars

Ecology and Evolution ◽

10.1002/ece3.7581 ◽

2021 ◽

Author(s):

Juan A. Galarza

Keyword(s):

Comparative Transcriptomics

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Analysis of the molecular basis of Saccharomyces cerevisiae mutant with high nucleic acid content by comparative transcriptomics

Food Research International ◽

10.1016/j.foodres.2021.110188 ◽

2021 ◽

Vol 142 ◽

pp. 110188

Author(s):

Xuewu Guo ◽

Bin Zhao ◽

Xinran Zhou ◽

Dongxia Lu ◽

Yaping Wang ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Nucleic Acid ◽

Acid Content ◽

Molecular Basis ◽

Comparative Transcriptomics ◽

Nucleic Acid Content

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Elevated Evolutionary Rates among Functionally Diverged Reproductive Genes across Deep Vertebrate Lineages

International Journal of Evolutionary Biology ◽

10.4061/2011/274975 ◽

2011 ◽

Vol 2011 ◽

pp. 1-9 ◽

Cited By ~ 10

Author(s):

Christopher J. Grassa ◽

Rob J. Kulathinal

Keyword(s):

Gene Ontology ◽

Comparative Genomics ◽

Danio Rerio ◽

Mus Musculus ◽

Functional Divergence ◽

Anolis Carolinensis ◽

Egg Laying ◽

Reproductive Systems ◽

Evolutionary Patterns ◽

Reproductive Genes

Among closely related taxa, proteins involved in reproduction generally evolve more rapidly than other proteins. Here, we apply a functional and comparative genomics approach to compare functional divergence across a deep phylogenetic array of egg-laying and live-bearing vertebrate taxa. We aligned and annotated a set of 4,986 1 : 1 : 1 : 1 : 1 orthologs in Anolis carolinensis (green lizard), Danio rerio (zebrafish), Xenopus tropicalis (frog), Gallus gallus (chicken), and Mus musculus (mouse) according to function using ESTs from available reproductive (including testis and ovary) and non-reproductive tissues as well as Gene Ontology. For each species lineage, genes were further classified as tissue-specific (found in a single tissue) or tissue-expressed (found in multiple tissues). Within independent vertebrate lineages, we generally find that gonadal-specific genes evolve at a faster rate than gonadal-expressed genes and significantly faster than non-reproductive genes. Among the gonadal set, testis genes are generally more diverged than ovary genes. Surprisingly, an opposite but nonsignificant pattern is found among the subset of orthologs that remained functionally conserved across all five lineages. These contrasting evolutionary patterns found between functionally diverged and functionally conserved reproductive orthologs provide evidence for pervasive and potentially cryptic lineage-specific selective processes on ancestral reproductive systems in vertebrates.

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