Cross-species hybridization of microarrays for studying tumor transcriptome of brain metastasis

Abstract

Although the importance of the cellular microenvironment (soil) during invasion and metastasis of cancer cells (seed) has been well-recognized, technical challenges have limited the ability to assess the influence of the microenvironment on cancer cells at the molecular level. Here, we show that an experimental strategy, competitive cross-species hybridization of microarray experiments, can characterize the influence of different microenvironments on cancer cells by independently extracting gene expression data of cancer and host cells when human cancer cells were xenografted into different organ sites of immunocompromised mice. Surprisingly, the analysis of gene expression data showed that the brain microenvironment induces complete reprogramming of metastasized cancer cells, resulting in a gain of neuronal cell characteristics and mimicking neurogenesis during development. We also show that epigenetic changes coincide with transcriptional reprogramming in cancer cells. These observations provide proof of principle for competitive cross-species hybridization of microarray experiments to characterize the effect of the microenvironment on tumor cell behavior.genomics | tumor microenvironment | stromal cells | DNA methylation D uring tumorgenesis, the changes in the local microenvironment play major roles in each step in metastasis from dissemination to colonization of distant organ sites (1-4). Therefore, inhibition of the cross-talk between invasive cancer cells and stromal cells might delay or completely block tumor invasion and subsequent colonization of cancer cells. However, a lack of understanding of the bidirectional communication between cancer cells and stromal cells at the molecular level hampers the ability to develop and implement useful targeted therapies.Despite the potential to obtain stromal-and cancer-specific signatures using laser-captured microdissection (5), segregating cancer cells from stromal cells and vice versa remain a timeconsuming and labor-intensive procedure that is technically challenging. There is also a high risk of failure because of instability of RNA during cell isolation as well as the potential systemic bias of gene expression during amplification of partially degraded RNA (6, 7). Thus, there is an urgent need for the development of new experimental strategies that can delineate cancer cell-specific gene expression signatures from stromal cell signatures or vice versa.In vivo xenografting of human cancer cells to different mouse organs has the potential to elucidate the influence of the tumor microenvironment on gene expression in cancer cells by mimicking the conditions that human metastases undergo at different organ sites. Characterization of these in vivo models might provide clues for the specific role of each unique tumor microenvironment in determining the propensity of particular tumors to metastasize to different sites as well as the sensitivity and resistance to therapy at different sites. In the current study, we have devised and performed proof of concept studies...

Interdisciplinary management of central nervous system metastasis and neoplastic meningitis: recent developments and future perspectives

“…for protection from cytotoxic effects of chemotherapeutic agents). [21,22] A very interesting study on the impact of astrocyte-derived reshaping of the brain microenvironment was recently published by Zhang and colleagues: Mouse tumor cells lost PTEN expression only after dissemination to the brain, but not to other organs, and PTEN levels in PTEN-loss brain metastatic tumor cells were again rescued after leaving the brain microenvironment. This brain microenvironment-dependent plasticity of PTEN expression is epigenetically regulated by astrocyte-derived exosomes mediating an intercellular transfer of PTENtargeting microRNAs to metastatic tumor cells.…”

The Biology of Brain Metastasis

“…In addition, the protective effects were determined to be unique to astrocytes because fibroblasts (or other tumor cells) were unable to protect tumor cells. To further examine how the organ microenvironment influences cancer cells, Park and colleagues (74 ) applied competitive cross-species hybridization of microarray experiments to extract gene expression data of cancer and host cells when human cancer cells were engrafted into different organs of immunocompromised mice. Analyses of gene expression data sets showed that the brain microenvironment induces a change in gene expression by metastatic cells (74 ), similar to the data obtained by coculturing tumor cells with astrocytes (73 ).…”

“…To further examine how the organ microenvironment influences cancer cells, Park and colleagues (74 ) applied competitive cross-species hybridization of microarray experiments to extract gene expression data of cancer and host cells when human cancer cells were engrafted into different organs of immunocompromised mice. Analyses of gene expression data sets showed that the brain microenvironment induces a change in gene expression by metastatic cells (74 ), similar to the data obtained by coculturing tumor cells with astrocytes (73 ). Interestingly, the analyses performed on 4 different cell lines that were implanted orthotopically or subcutaneously were clustered on the basis of the identity of the cancer cell line and were independent of the location of the transplant, with few exceptions.…”

Closing the gap: astrocytes and brain metastasis

“…Furthermore, Chen et al confirm that Cx43 gap junction-dependent mechanisms are shared between breast and lung cancer brain metastases. In some ways, this comes as no surprise because the brain microenvironment is known to reprogram breast, lung and melanoma cells [10]. Focusing on the tumor-brain microenvironment and cancer cellextrinsic mechanisms of resistance may lead to novel strategies to treat brain metastasis as a single disease entity regardless of the type and subtype of disease.…”