Statistical measures of transcriptional diversity capture genomic heterogeneity of cancer.

BACKGROUND: Molecular heterogeneity of tumors suggests the presence of multiple different subclones that may limit response to targeted therapies and contribute to acquisition of drug resistance, but its quantification has remained challenging. RESULTS: We performed simulations to evaluate statistical measures that best capture the molecular diversity within a group of tumors for either continuous (gene expression) or discrete (mutations, copy number alterations) molecular data. Dispersion based metrics in the principal component space best captured the underlying heterogeneity. To demonstrate utility of these measures, we characterized the diversity in transcriptional and genomic profiles of different breast tumor subtypes, and showed that basal-like or triple-negative breast cancers (TNBC) are significantly more heterogeneous molecularly than other subtypes. Our analysis also suggests that transcriptional diversity is a global characteristic of the tumors observed across the majority of molecular pathways. Among basal-like tumors, those that were resistant to multi-agent chemotherapy showed greater transcriptional diversity compared to chemotherapy-sensitive tumors, suggesting that potentially multiple mechanisms may be contributing to chemotherapy resistance. CONCLUSIONS: We proposed and validated measures of transcriptional and genomic diversity that can quantify the molecular diversity of tumors. We applied the new measures to genomic data from breast tumors and demonstrated that basal-like breast cancers are significantly more diverse than other breast cancers. The observation that chemo-resistant tumors are significantly more diverse molecularly than chemosensitive tumors implies that multiple resistance mechanisms may be active, thus limiting the sensitivity and accuracy of predictive markers of chemotherapy response.

Global gene expression changes induced by prolonged cold ischemic stress and preservation method of breast cancer tissue.

BACKGROUND: Tissue handling can alter global gene expression potentially affecting the analytical performance of genomic signatures, but such effects have not been systematically evaluated. METHODS: Tissue samples from 11 previously untreated breast tumors were minced and aliquots were either snap frozen or placed in RNAlater immediately or after 20, 40, 60, 120 or 180 min at room temperature. RNA was profiled on Affymetrix HG-U133A arrays. We used probe-set-wise hierarchical models to evaluate the effect of preservation method on transcript expression and linear mixed effects models to assess the effect of cold ischemic delay on the expression of individual probe sets. Gene set enrichment analysis identified pathways overrepresented in the affected transcripts. We combined the levels of 41 most sensitive transcripts to develop an index of ischemic stress. RESULTS: Concordance in global gene expression between the baseline and 40 min delay was higher for samples preserved in RNAlater (average concordance correlation coefficient CCC = 0.92 compared to 0.88 for snap frozen). Overall, 481 transcripts (3%) were significantly affected by the preservation method, most of them involved in processes important in cancer. Prolonged cold ischemic delay of up to 3 h induced marginal global gene expression changes (average CCC = 0.90 between baseline and 3 h delay). However 41 transcripts were significantly affected by cold ischemic delay. Among the induced transcripts were stress response genes, apoptotic response genes; among the downregulated were genes involved in metabolism, protein processing and cell cycle regulation. An index combining the expression levels of these genes was proportional to the cold ischemic delay. CONCLUSIONS: Prolonged cold ischemia induces significant transcriptional changes in a small subset of transcripts in the tissue. Furthermore, the expression level of about 3% of the transcripts is affected by the preservation method. These sensitive transcripts should not be included in genomic signatures for more reliable analytical performance.

Studies on the antiproliferative effects of tropolone derivatives in Jurkat T-lymphocyte cells.

Thujaplicins are tropolone-derived natural products with antiproliferative properties. We recently reported that certain tropolones potently and selectively target histone deacetylases (HDAC) and inhibit the growth of hematological cell lines. Here, we investigated the mechanisms by which these compounds exert their antiproliferative activity in comparison with the pan-selective HDAC inhibitor, vorinostat, using Jurkat T-cell leukemia cells. The tropolones appear to work through a mechanism distinct from vorinostat. These studies suggest that tropolone derivatives may serve as selective epigenetic modulators of hematological cells with potential applications as anti-leukemic or anti-inflammatory agents.

Tropolones as lead-like natural products: the development of potent and selective histone deacetylase inhibitors.

Natural products have long been recognized as a rich source of potent therapeutics but further development is often limited by high structural complexity and high molecular weight. In contrast, at the core of the thujaplicins is a lead-like tropolone scaffold characterized by relatively low molecular weight, ample sites for diversification, and metal-binding functionality poised for targeting a range of metalloenzyme drug targets. Here, we describe the development of this underutilized scaffold for the discovery of tropolone derivatives that function as isozyme-selective inhibitors of the validated anticancer drug target, histone deacetylase (HDAC). Several monosubstituted tropolones display remarkable levels of selectivity for HDAC2 and potently inhibit the growth of T-cell lymphocyte cell lines. The tropolones represent a new chemotype of isozyme-selective HDAC inhibitors.

Viridin analogs derived from steroidal building blocks.

Naturally occurring furanosteroids such as viridin and wortmannin have long been known as potent inhibitors of the lipid kinase PI-3K. We have been interested in directly accessing analogs of these complex natural products from abundant steroid feedstock materials. In this communication, we describe the synthesis of viridin/wortmannin hybrid molecules from readily available building blocks that function as PI-3K inhibitors and maintain their electrophilic properties. The compounds also show anti-proliferative effects against a breast cancer line.

The furan route to tropolones: probing the antiproliferative effects of ß-thujaplicin analogs.

A direct route to analogs of the naturally occurring tropolone ß-thujaplicin has been developed in just four steps from furan. Using this method, a series of derivatives were synthesized and evaluated. Several of these compounds demonstrated very high levels of potency against bacterial and fungal pathogens with good selectivity over mammalian cells.

Toward isozyme-selective inhibitors of histone deacetylase as therapeutic agents for the treatment of cancer.

Since post-translational modifications of proteins are key mechanisms for controlling cellular function, targeting the machinery involved in these modifications offers new opportunities for the development of therapeutic agents.The histone deacetylases (HDACs) represent an important family of enzymes that are involved in controlling the acetylation state of key lysine residues in histones and other proteins. The development of HDAC inhibitors for the treatment of several diseases, most notably cancer, has proceeded rapidly. Recent attention has turned towards the development of isozyme-specific inhibitors that will provide selective targeting. It is believed that the ability to target-specific HDACs rather than all family members will lead to superior therapeutics with better efficacy and lower toxicity. A review of recent patents shows that researchers are targeting a wide range of isozymes and that key advances in the structural biology of HDACs are providing important design information.