title: Tissue-specific transcriptomics and proteomics of a filarial nematode and its Wolbachia endosymbiont.
abstract: BACKGROUND
  Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although transcriptomic and proteomic studies around the nematode life cycle have greatly enhanced our knowledge, whole organism approaches have not provided spatial resolution of gene expression, which can be gained by examining individual tissues. Generally, due to their small size, tissue dissection of human-infecting filarial nematodes remains extremely challenging. However, canine heartworm disease is caused by a closely related and much larger filarial nematode, Dirofilaria immitis. As with many other filarial nematodes, D. immitis contains Wolbachia, an obligate bacterial endosymbiont present in the hypodermis and developing oocytes within the uterus. Here, we describe the first concurrent tissue-specific transcriptomic and proteomic profiling of a filarial nematode (D. immitis) and its Wolbachia (wDi) in order to better understand tissue functions and identify tissue-specific antigens that may be used for the development of new diagnostic and therapeutic tools.
  
  
  METHODS
  Adult D. immitis worms were dissected into female body wall (FBW), female uterus (FU), female intestine (FI), female head (FH), male body wall (MBW), male testis (MT), male intestine (MI), male head (MH) and 10.1186/s12864-015-2083-2 male spicule (MS) and used to prepare transcriptomic and proteomic libraries.
  
  
  RESULTS
  Transcriptomic and proteomic analysis of several D. immitis tissues identified many biological functions enriched within certain tissues. Hierarchical clustering of the D. immitis tissue transcriptomes, along with the recently published whole-worm adult male and female D. immitis transcriptomes, revealed that the whole-worm transcriptome is typically dominated by transcripts originating from reproductive tissue. The uterus appeared to have the most variable transcriptome, possibly due to age. Although many functions are shared between the reproductive tissues, the most significant differences in gene expression were observed between the uterus and testis. Interestingly, wDi gene expression in the male and female body wall is fairly similar, yet slightly different to that of Wolbachia gene expression in the uterus. Proteomic methods verified 32 % of the predicted D. immitis proteome, including over 700 hypothetical proteins of D. immitis. Of note, hypothetical proteins were among some of the most abundant Wolbachia proteins identified, which may fulfill some important yet still uncharacterized biological function.
  
  
  CONCLUSIONS
  The spatial resolution gained from this parallel transcriptomic and proteomic analysis adds to our understanding of filarial biology and serves as a resource with which to develop future therapeutic strategies against filarial nematodes and their Wolbachia endosymbionts.
authors.affiliation: Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
authors.forename: Ashley N
authors.initials: AN
authors.lastname: Luck
authors.affiliation: Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA.
authors.forename: Kathryn G
authors.initials: KG
authors.lastname: Anderson
authors.affiliation: Chemical Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
authors.forename: Colleen M
authors.initials: CM
authors.lastname: McClung
authors.affiliation: Chemical Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
authors.forename: Nathan C
authors.initials: NC
authors.lastname: VerBerkmoes
authors.affiliation: Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Foster
authors.affiliation: Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA.
authors.forename: Michelle L
authors.initials: ML
authors.lastname: Michalski
authors.affiliation: Genome Biology Division, New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA. slatko@neb.com.
authors.forename: Barton E
authors.initials: BE
authors.lastname: Slatko
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004183:Dirofilaria immitis / Q000235:genetics* / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D008297:Male; D009928:Organ Specificity / Q000235:genetics; D020543:Proteome; D040901:Proteomics; D013559:Symbiosis; D059467:Transcriptome; D020577:Wolbachia / Q000235:genetics* / Q000378:metabolism*
chemical_list: D020543:Proteome