Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

The generality and spectrum of chromatin-remodeling requirements for nuclear receptor function are unknown. We have characterized glucocorticoid receptor (GR) binding events and chromatin structural transitions across GR-induced or -repressed genes. This analysis reveals that GR binding invariably occurs at nuclease-accessible sites (DHS). A remarkable diversity of mechanisms, however, render these sites available for GR binding. Accessibility of the GR binding sites is either constitutive or hormone inducible. Within each category, some DHS sites require the Brg1-containing Swi/Snf complex, but others are Brg1 independent, implicating a different remodeling complex. The H2A.Z histone variant is highly enriched at both inducible and constitutive DHS sites and is subject to exchange during hormone activation. The DHS profile is highly cell specific, implicating cell-selective organization of the chromatin landscape as a critical determinant of tissue-selective receptor function. Furthermore, the widespread requirement for chromatin remodeling supports the recent hypothesis that the rapid exchange of receptor proteins occurs during nucleosome reorganization.

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

MLL-AF4 Acute Lymphocytic Leukemia has a poor prognosis, and the mechanisms by which these leukemias develop are not understood despite intensive research based on well-known concepts and methods MicroRNAs (miRNAs) are a new class of small noncoding RNAs that post-transcriptionally regulate expression of target mRNA transcripts We recently reported that ectopic expression of miR-128b together with miR-221, two of the miRNAs downregulated in MLL-AF4 ALL, restores glucocorticoid resistance through downregulation of the MLL-AF4 chimeric fusion proteins MLL-AF4 and AF4-MLL that are generated by chromosomal translocation t(4;11) Here we report the identification of new mutations in miR-128b in RS4;11 cells, derived from MLL-AF4 ALL patient One novel mutation significantly reduces the processing of miR-128b Finally, this base change occurs in a primary MLL-AF4 ALL sample as an acquired mutation These results demonstrate that the novel mutation in miR-128b in MLL-AF4 ALL alters the processing of miR-128b and that the resultant downregulation of mature miR-128b contributes to gluco-corticoid resistance through the failure to downregulate the fusion oncogenes

A novel mutation in the miR-128b gene reduces miRNA processing and leads to glucocorticoid resistance of MLL-AF4 Acute Lymphocytic Leukemia cells

CRLF2 Rearrangement Status in Ph-like ALL Predicts Intrinsic Glucocorticoid Resistance In Vitro that is Reversible with Targeted MAPK and PI3K Pathway Inhibition

Glucocorticoids Paradoxically Induce Intrinsic Steroid Resistance through a STAT5-Mediated Survival Mechanism in T-Cell Acute Lymphoblastic Leukemia

Author(s): Meyer, Lauren Kimberly | Advisor(s): Hermiston, Michelle; Shannon, Kevin | Abstract: Glucocorticoids (GCs) are potently immunosuppressive due to their pro-apoptotic effects on lymphoid cells, leading to their utility in a wide range of clinical contexts including autoimmune diseases, hyperinflammatory conditions, and lymphoid malignancies. In addition, GCs are endogenously produced hormones that mediate a wide range of physiologic functions that are essential for life. As a result, cells of the immune system face constant exposure to GCs and therefore require intrinsic mechanisms by which to resist their pro-apoptotic effects under certain developmental and environmental conditions. The retention of these resistance mechanisms in lymphoid-driven diseases thereby poses a challenge to the clinical use of GCs in these contexts. Common -chain cytokines, through activation of the JAK/STAT signal transduction pathway, play essential roles in the differentiation, survival, and function of lymphoid cells. Here, we assess the interplay between GC activity and cytokine-mediated pro-survival signaling in two lymphoid-driven diseases, acute lymphoblastic leukemia and hemophagocytic lymphohistiocytosis, and demonstrate that cytokines are potent mediators of GC resistance. Mechanistically, we show that activation of STAT5 downstream of cytokine receptor signaling is necessary for cytokine-induced GC resistance. STAT5 functions as a transcription factor to upregulate expression of anti-apoptotic mediators, thereby reducing the apoptotic potential and promoting the survival of lymphoid cells. Through both genetic and pharmacologic approaches, we demonstrate that targeted inhibition of cytokine receptor signaling effectively restores GC sensitivity, and we establish the feasibility of this therapeutic approach in two in vivo models of disease.

Lauren Kimberly Meyer

Papers

Interrogating the Mechanistic Basis for Cytokine-Mediated Glucocorticoid Resistance in Lymphoid-Driven Diseases