Kevin K. Lin

Circadian clock genes contribute to the regulation of hair follicle cycling.

Hair follicles undergo recurrent cycling of controlled growth (anagen), regression (catagen), and relative quiescence (telogen) with a defined periodicity. Taking a genomics approach to study gene expression during synchronized mouse hair follicle cycling, we discovered that, in addition to circadian fluctuation, CLOCK–regulated genes are also modulated in phase with the hair growth cycle. During telogen and early anagen, circadian clock genes are prominently expressed in the secondary hair germ, which contains precursor cells for the growing follicle. Analysis of Clock and Bmal1 mutant mice reveals a delay in anagen progression, and the secondary hair germ cells show decreased levels of phosphorylated Rb and lack mitotic cells, suggesting that circadian clock genes regulate anagen progression via their effect on the cell cycle. Consistent with a block at the G1 phase of the cell cycle, we show a significant upregulation of p21 in Bmal1 mutant skin. While circadian clock mechanisms have been implicated in a variety of diurnal biological processes, our findings indicate that circadian clock genes may be utilized to modulate the progression of non-diurnal cyclic processes.

The epidermal differentiation‐associated Grainyhead gene Get1/Grhl3 also regulates urothelial differentiation

Skin and bladder epithelia form effective permeability barriers through the activation of distinct differentiation gene programs. Using a genome‐wide gene‐expression study, we identified transcriptional regulators whose expression correlates highly with that of differentiation markers in both the bladder and skin, including the Grainyhead factor Get1/Grhl3, which is already known to be important for epidermal barrier formation. In the bladder, Get1 is most highly expressed in the differentiated umbrella cells and its mutation in mice leads to a defective bladder epithelial barrier formation due to the failure of apical membrane specialization. Genes encoding components of the specialized urothelial membrane, the uroplakins, were downregulated in Get1−/− mice. At least one of these genes, uroplakin II, is a direct target of Get1. The urothelial‐specific activation of the uroplakin II gene is due to selective binding of Get1 to the uroplakin II promoter in urothelial cells, which is most likely regulated by histone modifications. These results show a crucial role for Get1 in urothelial differentiation and barrier formation.

The LIM-only factor LMO4 regulates expression of the BMP7 gene through an HDAC2-dependent mechanism, and controls cell proliferation and apoptosis of mammary epithelial cells

The nuclear LIM-only protein 4 (LMO4) is upregulated in breast cancer, especially estrogen receptor-negative tumors, and its overexpression in mice leads to hyperplasia and tumor formation. Here, we show that deletion of LMO4 in the mammary glands of mice leads to impaired lobuloalveolar development due to decreased epithelial cell proliferation. With the goal of discovering potential LMO4-target genes, we also developed a conditional expression system in MCF-7 cells for both LMO4 and a dominant negative (DN) form of its co-regulator, cofactor of LIM domains (Clim/Ldb/Nli). We then used DNA microarrays to identify genes responsive to LMO4 and DN-Clim upregulation. One of the genes common to both data sets was bone morphogenic protein 7 (BMP7), whose expression is also significantly correlated with LMO4 transcript levels in a large dataset of human breast cancers, suggesting that BMP7 is a bona fide target gene of LMO4 in breast cancer. Inhibition of BMP7 partially blocks the effects of LMO4 on apoptosis, indicating that BMP7 mediates at least some functions of LMO4. Gene transfer studies show that LMO4 regulates the BMP7 promoter, and chromatin immunoprecipitation studies show that LMO4 and its cofactor Clim2 are recruited to the BMP7 promoter. Furthermore, we demonstrate that HDAC2 recruitment to the BMP7 promoter is inhibited by upregulation of LMO4 and that HDAC2 knockdown upregulates the promoter. These studies suggest a novel mechanism of action for LMO4: LMO4, Clim2 and HDAC2 are part of a transcriptional complex, and increased LMO4 levels can disrupt the complex, leading to decreased HDAC2 recruitment and increased promoter activity.

Insulin stimulates Akt translocation to mitochondria: Implications on dysregulation of mitochondrial oxidative phosphorylation in diabetic myocardium

Mitochondrial oxidative phosphorylation is the major source of energy in cardiac muscle. In the streptozotocin-induced diabetic (STZ-DM) mice, myocardial oxidative phosphorylation was perturbated and oxidative phosphorylation complex V (ATP synthase) activity was significantly reduced. To determine the independent effects of hyperglycemia and insulin deficiency on the changes of myocardial complex V, we used phlorizin (Ph) to normalize blood glucose in the diabetic mice. Ph treatment did not improve myocardial complex V activity in the STZ-DM mice, whereas insulin treatment normalized myocardial complex V activity in the diabetic mice. Therefore, the reduction of complex V activity was caused by insulin deficiency and not by hyperglycemia in STZ-DM myocardium. Acute insulin stimulation induced phosphorylation of Akt and translocation of Akt to mitochondria in myocardium. Translocation of phospho-Akt to mitochondria was enhanced in the STZ-DM mice and was blunted in the diet-induced diabetic mice. In parallel, insulin activation of complex V was enhanced in the STZ-DM myocardium and suppressed in the diet-induced diabetic myocardium. In vivo inhibition of Akt blocked insulin stimulation of phospho-Akt translocation and blunted activation of complex V. Insulin-activated Akt translocation to mitochondria in cardiac muscle is a novel paradigm that may have important implications on myocardial bioenergetics.

Including probe-level uncertainty in model-based gene expression clustering

BackgroundClustering is an important analysis performed on microarray gene expression data since it groups genes which have similar expression patterns and enables the exploration of unknown gene functions. Microarray experiments are associated with many sources of experimental and biological variation and the resulting gene expression data are therefore very noisy. Many heuristic and model-based clustering approaches have been developed to cluster this noisy data. However, few of them include consideration of probe-level measurement error which provides rich information about technical variability.ResultsWe augment a standard model-based clustering method to incorporate probe-level measurement error. Using probe-level measurements from a recently developed Affymetrix probe-level model, multi-mgMOS, we include the probe-level measurement error directly into the standard Gaussian mixture model. Our augmented model is shown to provide improved clustering performance on simulated datasets and a real mouse time-course dataset.ConclusionThe performance of model-based clustering of gene expression data is improved by including probe-level measurement error and more biologically meaningful clustering results are obtained.

Bayesian detection of non-sinusoidal periodic patterns in circadian expression data

MOTIVATION Cyclical biological processes such as cell division and circadian regulation produce coordinated periodic expression of thousands of genes. Identification of such genes and their expression patterns is a crucial step in discovering underlying regulatory mechanisms. Existing computational methods are biased toward discovering genes that follow sine-wave patterns. RESULTS We present an analysis of variance (ANOVA) periodicity detector and its Bayesian extension that can be used to discover periodic transcripts of arbitrary shapes from replicated gene expression profiles. The models are applicable when the profiles are collected at comparable time points for at least two cycles. We provide an empirical Bayes procedure for estimating parameters of the prior distributions and derive closed-form expressions for the posterior probability of periodicity, enabling efficient computation. The model is applied to two datasets profiling circadian regulation in murine liver and skeletal muscle, revealing a substantial number of previously undetected non-sinusoidal periodic transcripts in each. We also apply quantitative real-time PCR to several highly ranked non-sinusoidal transcripts in liver tissue found by the model, providing independent evidence of circadian regulation of these genes. AVAILABILITY Matlab software for estimating prior distributions and performing inference is available for download from http://www.datalab.uci.edu/resources/periodicity/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Have hair follicle stem cells shed their tranquil image

In a recent issue of Nature Genetics, Jaks et al. (2008) demonstrate that hair follicle cells expressing the intestinal stem cell marker Lgr5 are hair follicle epithelial stem cells. In contrast to the established bulge stem cell population, Lrg5(+) cells are actively cycling and reside in part outside the bulge.