Anteroposterior axis formation in Xenopus limb bud recombinants: a model of pattern formation during limb regeneration

A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration

Amphibians and molting arthropods have the remarkable capacity to regenerate amputated limbs, as described by an extensive literature of experimental cuts, amputations, grafts, and molecular techniques. Despite a rich history of experimental efforts, no comprehensive mechanistic model exists that can account for the pattern regulation observed in these experiments. While bioinformatics algorithms have revolutionized the study of signaling pathways, no such tools have heretofore been available to assist scientists in formulating testable models of large-scale morphogenesis that match published data in the limb regeneration field. Major barriers preventing an algorithmic approach are the lack of formal descriptions for experimental regenerative information and a repository to centralize storage and mining of functional data on limb regeneration. Establishing a new bioinformatics of shape would significantly accelerate the discovery of key insights into the mechanisms that implement complex regeneration. Here, we describe a novel mathematical ontology for limb regeneration to unambiguously encode phenotype, manipulation, and experiment data. Based on this formalism, we present the first centralized formal database of published limb regeneration experiments together with a user-friendly expert system tool to facilitate its access and mining. These resources are freely available for the community and will assist both human biologists and artificial intelligence systems to discover testable, mechanistic models of limb regeneration.

Analysis of hoxa11 and hoxa13 expression during patternless limb regeneration in Xenopus

During limb regeneration, anuran tadpoles and urodele amphibians generate pattern-organizing, multipotent, mesenchymal blastema cells, which give rise to a replica of the lost limb including patterning in three dimensions. To facilitate the regeneration of nonregenerative limbs in other vertebrates, it is important to elucidate the molecular differences between blastema cells that can regenerate the pattern of limbs and those that cannot. In Xenopus froglet (soon after metamorphosis), an amputated limb generates blastema cells that do not produce proper patterning, resulting in a patternless regenerate, a spike, regardless of the amputation level. We found that re-expression of hoxa11 and hoxa13 in the froglet blastema is initiated although the subsequent proximal-distal patterning, including separation of the hoxa11 and hoxa13 expression domains, is disrupted. We also observed an absence of EphA4 gene expression in the froglet blastema and a failure of position-dependent cell sorting, which correlated with the altered hoxa11 and hoxa13 expression. Quantitative analysis of hoxa11 and hoxa13 expression revealed that hoxa13 transcript levels were reduced in the froglet blastema compared with the tadpole blastema. Moreover, the expression of sox9, an important regulator of chondrogenic differentiation, was detected earlier in patternless blastemas than in tadpole blastemas. These results suggest that appropriate spatial, temporal, and quantitative gene expression is necessary for pattern regeneration by blastema cells.

Effects of activation of hedgehog signaling on patterning, growth, and differentiation in Xenopus froglet limb regeneration

Regenerating limbs of urodele amphibians and Xenopus tadpole are reconstructed along proximal-distal, anterior-posterior (AP), and dorsal-ventral axes. In contrast, a regenerated limb of the Xenopus froglet does not have digits, and only a simple cartilaginous structure referred to as a "spike" is formed. This suggests that repatterning along the AP axis is absent in the froglet blastema. Previous studies have shown that Shh and its target genes are not expressed in the froglet blastema. In this study, we activated Hedgehog signaling in the froglet blastema and found that target genes of Shh were inducible in the mesenchyme of limb blastema. Furthermore, we found that activation of the signaling had effects on blastema cell proliferation and chondrogenesis and resulted in the formation of multiple cartilaginous structures. These findings indicate that activation of signaling that is absent in the froglet blastema is effective for improvement of limb regeneration ability in the Xenopus froglet.