Transcriptomic Profiling of Fibropapillomatosis in Green Sea Turtles (Chelonia mydas) From South Texas

Abstract

Sea turtle fibropapillomatosis (FP) is a tumor promoting disease that is one of several threats globally to endangered sea turtle populations. The prevalence of FP is highest in green sea turtle (Chelonia mydas) populations, and historically has shown considerable temporal growth. FP tumors can significantly affect the ability of turtles to forage for food and avoid predation and can grow to debilitating sizes. In the current study, based in South Texas, we have applied transcriptome sequencing to FP tumors and healthy control tissue to study the gene expression profiles of FP. By identifying differentially expressed turtle genes in FP, and matching these genes to their closest human ortholog we draw on the wealth of human based knowledge, specifically human cancer, to identify new insights into the biology of sea turtle FP. We show that several genes aberrantly expressed in FP tumors have known tumor promoting biology in humans, including CTHRC1 and NLRC5, and provide support that disruption of the Wnt signaling pathway is a feature of FP. Further, we profiled the expression of current targets of immune checkpoint inhibitors from human oncology in FP tumors and identified potential candidates for future studies.

Insights on Immune Function in Free-Ranging Green Sea Turtles (Chelonia mydas) with and without Fibropapillomatosis

“…Only a handful of studies to date have examined natural killer cell activities in turtles, which suggest differences by sex and season, and that activity can decrease upon exposure to certain contaminants [74,112,113]; however, no studies have examined natural killer cell activity in response to disease in sea turtles. Interestingly, several natural killer cell-related cytotoxicity genes were found to be upregulated in FP tumors from juvenile green turtles undergoing rehabilitative care [114]. Additionally, several putative proteins observed in FP tumors that are considered atypical of alphaherpesviruses (e.g., F-lec1 and F-lec2) are associated with activation or inhibition of natural killer cells [115].…”

Evolutionary Genomic Comparisons of Chelonid Herpesvirus 5 (chhv5) From Fibropapillomatosis-Afflicted Green (Chelonia Mydas), Olive Ridley (Lepidochelys Olivacea), And Kemp’s Ridley (Lepidochelys Kempii) Sea Turtles.

“…We also identified between 88 and 2,284 SNPs in ChHV5 genomes from Kemp's ridley and olive ridley turtles compared with those of the Hawaiian (green turtle derived) ChHV5 reference genome. Viral enrichment prior to sequencing resulted in a substantially lower level of SNP detection, however, potentially because limited extra-cellular lytic virus is present in FP tumours [20,[23][24][25]. Together, these results suggest that significant ChHV5 genetic variation can occur, and that current variant calling based on short stretches of ChHV5 nucleotides, likely underrepresents the true extent of ChHV5 variants globally.…”

“…Multiple researchers have linked the occurrence of FP with various forms of anthropogenic habitat degradation [44][45][46][47] leading to the current hypothesis that the disease is caused by viral infection in conjunction with environmental cofactors. Such previous data indicate a latent state of this virus which may recrudesce in times of immunological stress, enabling ChHV5 loads to pass an oncogenic threshold [5,7,20,24,25], however, specific co-factors and their role in tumourigenesis have yet to be identified. FP has occurred in isolated regions globally within a relatively short timeframe, with differing geographic variants making it unlikely that recent virulence mutations in the virus independently evolved to drive these outbreaks [14].…”

“…Fibropapillomatosis is one of the most significant transmissible diseases known in marine turtles and remains a persistent health concern despite conservation successes and significant growth of some affected populations [17]. The FP epizootic has been identified as one of the five major threats to marine turtles, which has been reflected in the renewed scientific interest in this disease in the last decade [5,7,11,13,[18][19][20][21][22][23][24][25][26]. Prevalence statistics reveal the rapid establishment of FP among many sea turtle populations; with reported increases from 13.3 to 42% in Florida, USA (2005-2016), 13.2 to 35.3% in northeastern Brazil (2012)(2013)(2014)(2015), 0% to 33% in Guinea-Bissau and 0 to 35.2% in Texas, USA [7,17,[27][28][29][30][31].…”

“…Morrision et al (2018) [39] also used a smaller subset of genes (Amplicons IV, V, UL30 and gB) of 6,280bp in length for phylogenetic analysis. Increasingly, Next Generation Sequencing (NGS) approaches are being utilised more widely to study ChHV5 [6,7,20,24,25,39], as this powerful analysis tool can provide comprehensive genomic data of study organisms.…”