Multivariate analysis of a 3D mass spectral image for examining tissue heterogeneity.

The tissue microenvironment critically influences the molecular characteristics of a tumor. However, as tumorous tissue is highly heterogeneous it may harbor various sub-populations with different microenvironments, greatly complicating the unambiguous analysis of tumor biology. Mass spectrometry imaging techniques allow for the direct analysis of tumors in the spatial context of their microenvironment. However, discovery of heterogeneous sub-populations often depends on the use of multivariate statistical methods. While this is routinely used for 2D images, multivariate statistical approaches are rarely seen in the context of 3D images. Here we present the automatic alignment of 2D images recorded by nanostructure-initiator mass spectrometry (NIMS) to reconstruct a 3D model of a mouse mammary tumor. Multivariate statistical analysis was applied to the whole 3D reconstruction at once, revealing distinct tumor regions, an observation that would not have been possible in such clarity through the analysis of isolated 2D sections. These sub-structures were confirmed by H&E and Oil Red O stains. This study shows that the combination of 3D imaging and multivariate statistics can be used to define tumor regions.

Correction of chromosomal mutation and random integration in embryonic stem cells with helper-dependent adenoviral vectors.

For gene therapy of inherited diseases, targeted integration/gene repair through homologous recombination (HR) between exogenous and chromosomal DNA would be an ideal strategy to avoid potentially serious problems of random integration such as cellular transformation and gene silencing. Efficient sequence-specific modification of chromosomes by HR would also advance both biological studies and therapeutic applications of a variety of stem cells. Toward these goals, we developed an improved strategy of adenoviral vector (AdV)-mediated HR and examined its ability to correct an insertional mutation in the hypoxanthine phosphoribosyl transferase (Hprt) locus in male mouse ES cells. The efficiency of HR was compared between four types of AdVs that contained various lengths of homologies at the Hprt locus and with various multiplicities of infections. The frequency of HR with helper-dependent AdVs (HD AdVs) with an 18.6-kb homology reached 0.2% per transduced cell at a multiplicity of infection of 10 genomes per cell. Detection of random integration at DNA levels by PCR revealed extremely high efficiency of 5% per cell. We also isolated and characterized chromosomal sites where HD AdVs integrated in a random manner. In contrast to retroviral, lentiviral, and adeno-associated viral vectors, which tend to integrate into genes, the integration sites of AdV was distributed randomly inside and outside genes. These findings suggest that HR mediated by HD AdVs is efficient and relatively safe and might be a new viable option for ex vivo gene therapy as well as a tool for chromosomal manipulation of a variety of stem cells.