Genomic Analysis and Comparative Transcriptomics of Growth Pathways and Cancer Susceptibility Genes in the Soft-shell Clam Mya arenaria

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Growth and signaling pathways are critical determinants in carcinogenesis. Thus, a deeper understanding of gene expression in fast-growing cells is of clear relevance to human health. Our model system of choice is the soft-shell clam Mya arenaria, chosen because 1) the soft-shell clam is susceptible to tumors; 2) it is a readily accessible, commercially important species; 3) U. Maine Machias already has, in hand, a strain of fast-growing clams and 4) it provides useful information for comparative functional mollusk genomics. Because mollusks are understudied, close orthologues are lacking and the nucleotide sequence within the phylum is divergent enough that sequence information is needed. Using genomic DNA from the soft-shell clam sequenced through our institutional partners, we will perform partial annotation of the genome, focusing particularly on pathways of signaling and growth. Comparative functional genomics will allow us to evaluate gene structure, role in growth and development and evolutionary relationships, based on the gene sequence of M. arenaria and related species. Those genes of interest will then be analyzed by quantitative polymerase chain reaction (qPCR) and transcriptome sequencing (RNAseq), utilizing the fast-growing strain of clams versus wild-type. Our experience and infrastructure positions us well to conduct these studies with undergraduate researchers. These analyses will allow us to gain insight into growth, tumorigenicity, and evolutionary relationships among mollusks, an important but understudied group—thus providing information relevant to evolution and to public health. In addition, we will analyze the origin of the fast growth phenotype, which has economic implications, as well as connections to the etiology of cancers. Future plans are to conduct comparative studies utilizing tissue from induced clam tumors.

Recent Publications and Presentations

  • Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Bruce Kingham, Shallee T. Page, Marc F. Rendino, W. Kelley Thomas, Daniel W. Udwary, Cathy H. Wu and the North East Bioinformatics Collaborative Curation Team. 2012.  Community annotation and bioinformatics workforce development in concert ─ Little skate genome
    annotation workshops and jamborees. Accepted, Database.
  • Page, S., Grisar, A.. Melford, K. and A. Bensadoun. 2006. “”Interaction of lipoprotein lipase and receptor associated protein” Journal of Biological Chemistry. 281: 13931-13938.
  • Page, S. 2004. “Determining the Empirical Formula of a Copper Chloride Compound”. Chemical Education Resources, Thomson Learning.
  • Page, S. 2002. Neuronal migration: communication across the border of biological membranes. The Maine Scholar.
  • van Vlijmen,B.J.; Rohlmann,A.; Bensadoun,A.; Page,S.; Bos,I.S.T.; van Berkel,T.J.; Havekes,L.M., and J.Herz. 1999. “An extrahepatic LDL receptor- and LRP-independent RAP-sensitive site is involved in the metabolism of chylomicron remnants.” Journal of Biological Chemistry 274: 35219-35226.