A role for Timeless in epithelial morphogenesis during kidney development

An integrative evaluation of circadian gene TIMELESS as a pan-cancer immunological and predictive biomarker

BACKGROUND

The gene TIMELESS, which is involved in the circadian clock and the cell cycle, has recently been linked to various human cancers. Nevertheless, the association between TIMELESS expression and the prognosis of individuals afflicted with pan-cancer remains largely unknown.

OBJECTIVES

The present study aims to exhaustively scrutinize the expression patterns, functional attributes, prognostic implications, and immunological contributions of TIMELESS across diverse types of human cancer.

METHODS

The expression of TIMELESS in normal and malignant tissues was examined, as well as their clinicopathologic and survival data. The characteristics of genetic alteration and molecular subtypes of cancers were also investigated. In addition, the relationship of TIMELESS with immune infiltration, tumor mutation burden (TMB), microsatellite instability (MSI), and drug sensitivity was illustrated. Immunohistochemistry (IHC) was used to validate the expression of TIMELESS in clinical patients with several types of cancer.

RESULTS

In contrast to the matching normal controls, most tumor types were found to often overexpress TIMELESS. Abnormal expression of TIMELESS was significantly related to more advanced tumor stage and poorer prognosis of breast cancer, as well as infiltrating immune cells such as cancer-associated fibroblast infiltration in various tumors. Multiple cancer types exhibited abnormal expression of TIMELESS, which was also highly correlated with MSI and TMB. More crucially, TIMELESS showed promise in predicting the effectiveness of immunotherapy and medication sensitivity in cancer therapy. Moreover, cell cycle, DNA replication, circadian rhythm, and mismatch repair were involved in the functional mechanisms of TIMELESS on carcinogenesis. Furthermore, immunohistochemical results manifested that the TIMELESS expression was abnormal in some cancers.

CONCLUSIONS

This study provides new insights into the link between the circadian gene TIMELESS and the development of various malignant tumors. The findings suggest that TIMELESS could be a prospective prognostic and immunological biomarker for pan-cancer.

ERK-mediated TIMELESS expression suppresses G2/M arrest in colon cancer cells

The cell cycle is under circadian regulation. Oncogenes can dysregulate circadian-regulated genes to disrupt the cell cycle, promoting tumor cell proliferation. As a regulator of G2/M arrest in response to DNA damage, the circadian gene Timeless Circadian Clock (TIMELESS) coordinates this connection and is a potential locus for oncogenic manipulation. TIMELESS expression was evaluated using RNASeq data from TCGA and by RT-qPCR and western blot analysis in a panel of colon cancer cell lines. TIMELESS expression following ERK inhibition was examined via western blot. Cell metabolic capacity, propidium iodide, and CFSE staining were used to evaluate the effect of TIMELESS depletion on colon cancer cell survival and proliferation. Cell metabolic capacity following TIMELESS depletion in combination with Wee1 or CHK1 inhibition was assessed. TIMELESS is overexpressed in cancer and required for increased cancer cell proliferation. ERK activation promotes TIMELESS expression. TIMELESS depletion increases γH2AX, a marker of DNA damage, and triggers G2/M arrest via increased CHK1 and CDK1 phosphorylation. TIMELESS depletion in combination with Wee1 or CHK1 inhibition causes an additive decrease in cancer cell metabolic capacity with limited effects in non-transformed human colon epithelial cells. The data show that ERK activation contributes to the overexpression of TIMELESS in cancer. Depletion of TIMELESS increases γH2AX and causes G2/M arrest, limiting cell proliferation. These results demonstrate a role for TIMELESS in cancer and encourage further examination of the link between circadian rhythm dysregulation and cancer cell proliferation.

Circadian Rhythms and Hormonal Homeostasis: Pathophysiological Implications

Over recent years, a deeper comprehension of the molecular mechanisms that control biological clocks and circadian rhythms has been achieved. In fact, many studies have contributed to unravelling the importance of the molecular clock for the regulation of our physiology, including hormonal and metabolic homeostasis. Here we will review the structure, organisation and molecular machinery that make our circadian clock work, and its relevance for the proper functioning of physiological processes. We will also describe the interconnections between circadian rhythms and endocrine homeostasis, as well as the underlying consequences that circadian dysregulations might have in the development of several pathologic affections. Finally, we will discuss how a better knowledge of such relationships might prove helpful in designing new therapeutic approaches for endocrine and metabolic diseases.

Lipids around the Clock: Focus on Circadian Rhythms and Lipid Metabolism

Disorders of lipid and lipoprotein metabolism and transport are responsible for the development of a large spectrum of pathologies, ranging from cardiovascular diseases, to metabolic syndrome, even to tumour development. Recently, a deeper knowledge of the molecular mechanisms that control our biological clock and circadian rhythms has been achieved. From these studies it has clearly emerged how the molecular clock tightly regulates every aspect of our lives, including our metabolism. This review analyses the organisation and functioning of the circadian clock and its relevance in the regulation of physiological processes. We also describe metabolism and transport of lipids and lipoproteins as an essential aspect for our health, and we will focus on how the circadian clock and lipid metabolism are greatly interconnected. Finally, we discuss how a deeper knowledge of this relationship might be useful to improve the recent spread of metabolic diseases.

Individual Src-family tyrosine kinases direct the degradation or protection of the clock protein Timeless via differential ubiquitylation

Timeless was originally identified in Drosophila as an essential component of circadian cycle regulation, where its function is tightly controlled at the protein level by tyrosine phosphorylation and subsequent degradation. In mammals, Timeless has also been implicated in circadian rhythms as well as cell cycle control and embryonic development. Here we report that mammalian Timeless is an SH3 domain-binding protein and substrate for several members of the Src protein-tyrosine kinase family, including Fyn, Hck, c-Src and c-Yes. Co-expression of Tim with Fyn or Hck was followed by ubiquitylation and subsequent degradation in human 293T cells. While c-Src and c-Yes also promoted Tim ubiquitylation, in this case ubiquitylation correlated with Tim protein accumulation rather than degradation. Both c-Src and c-Yes selectively promoted modification of Tim through Lys63-linked polyubiquitin, which may explain the differential effects on Tim protein turnover. These data show distinct and opposing roles for individual Src-family members in the regulation of Tim protein levels, suggesting a unique mechanism for the regulation of Tim function in mammals.

The human Tim-Tipin complex interacts directly with DNA polymerase epsilon and stimulates its synthetic activity

The Tim-Tipin complex plays an important role in the S phase checkpoint and replication fork stability in metazoans, but the molecular mechanism underlying its biological function is poorly understood. Here, we present evidence that the recombinant human Tim-Tipin complex (and Tim alone) markedly enhances the synthetic activity of DNA polymerase ε. In contrast, no significant effect on the synthetic ability of human DNA polymerase α and δ by Tim-Tipin was observed. Surface plasmon resonance measurements and co-immunoprecipitation experiments revealed that recombinant DNA polymerase ε directly interacts with either Tim or Tipin. In addition, the results of DNA band shift assays suggest that the Tim-Tipin complex (or Tim alone) is able to associate with DNA polymerase ε bound to a 40-/80-mer DNA ligand. Our results are discussed in view of the molecular dynamics at the human DNA replication fork.

The daily rhythm of mice

The house mouse Mus musculus represents a valuable tool for the analysis and the understanding of the mammalian circadian oscillator. Forward and reverse genetics allowed the identification of clock components and the verification of their function within the circadian clockwork. In many cases unforeseen links were discovered between a particular circadian regulatory protein and various diseases or syndromes. Thus, this model system is not only perfectly suited to pinpoint the components of the mammalian circadian clock, but also to unravel metabolic, physiological, and pathological processes linked to the circadian timing system.

An unexpected role for the clock protein timeless in developmental apoptosis

Background

Programmed cell death is critical not only in adult tissue homeostasis but for embryogenesis as well. One of the earliest steps in development, formation of the proamniotic cavity, involves coordinated apoptosis of embryonic cells. Recent work from our group demonstrated that c-Src protein-tyrosine kinase activity triggers differentiation of mouse embryonic stem (mES) cells to primitive ectoderm-like cells. In this report, we identified Timeless (Tim), the mammalian ortholog of a Drosophila circadian rhythm protein, as a binding partner and substrate for c-Src and probed its role in the differentiation of mES cells.

Methodology/Principal Findings

To determine whether Tim is involved in ES cell differentiation, Tim protein levels were stably suppressed using shRNA. Tim-defective ES cell lines were then tested for embryoid body (EB) formation, which models early mammalian development. Remarkably, confocal microscopy revealed that EBs formed from the Tim-knockdown ES cells failed to cavitate. Cells retained within the centers of the failed cavities strongly expressed the pluripotency marker Oct4, suggesting that further development is arrested without Tim. Immunoblots revealed reduced basal Caspase activity in the Tim-defective EBs compared to wild-type controls. Furthermore, EBs formed from Tim-knockdown cells demonstrated resistance to staurosporine-induced apoptosis, consistent with a link between Tim and programmed cell death during cavitation.

Conclusions/Significance

Our data demonstrate a novel function for the clock protein Tim during a key stage of early development. Specifically, EBs formed from ES cells lacking Tim showed reduced caspase activity and failed to cavitate. As a consequence, further development was halted, and the cells present in the failed cavity remained pluripotent. These findings reveal a new function for Tim in the coordination of ES cell differentiation, and raise the intriguing possibility that circadian rhythms and early development may be intimately linked.

Stimulatory and inhibitory signaling molecules that regulate renal branching morphogenesis

Branching morphogenesis, defined as the growth and branching of epithelial tubules, is a fundamental developmental process involved in the formation of a variety of mammalian tissues, including the kidney. Defective renal branching may result in a number of clinically relevant abnormalities, including renal agenesis, renal dysplasia, multiplex kidneys, and hypertension. In this review we describe the morphological events that generate the characteristic tree-like structure of the mammalian collecting system. We also highlight new knowledge related to both established and novel signaling systems that are important for stimulating and inhibiting branching morphogenesis.

Tumor suppression and circadian function

Circadian clock and cell division cycle are two fundamental biological processes. The circadian clock is the body's molecular time-keeping system, while the cell division cycle regulates development and cellular renewal. The expression of cell cycle genes such as Wee1, Cyclins, and c-Myc are under circadian control and could be directly under the regulation of the circadian transcriptional complex. This complex is composed of heterodimer transactivators CLOCK/NPAS2 with BMAL1, which regulate the transcription of PER1, PER2, CRY1, and CRY2. In turn, the repressors CRY1 and CRY2 turn off the gene expressions of Per1/Per2, Cry1/Cry2 in a periodic manner by acting on the transcriptional complex. Two of these circadian rhythm regulators, PER1 and PER2, have now been linked to DNA damage response pathways in a series of papers that examined gene dosage. Overexpression of either Per1 or Per2 in cancer cells inhibits their neoplastic growth and increases their apoptotic rate. In vivo studies showed that mice deficient in mPer2 showed significant higher incidences of tumor development after genotoxic stress. Loss and dysregulation of Per1 and Per2 gene expression have been found in many types of human cancers. Recent studies demonstrate that both PER1 and PER2 are involved in ATM-Chk1/Chk2 DNA damage response pathways and implicate normal circadian function as a factor in tumor suppression.

Clock controls timing of mouse pancreatic differentiation through regulation of Wnt- and Notch-based and cell division components

The oscillations of circadian genes control the daily circadian clock, regulating a diverse array of physiologies with the 24-hour light/dark cue across a wide variety of organisms. Here we first show that before embryonic circadian rhythms occur, the oscillation (nucleocytoplasmic shuttling) of core circadian gene Clock is tissue-specific and correlated with the state of differentiation during both early development and later pancreas organogenesis. Disruption of Clock as well as Timeless in the embryonic pancreas does not block pancreatic differentiation but alters the balance and maturity of endocrine and exocrine cells. Molecular analysis indicates that inhibition of Clock or Timeless expression disturbs not only cell cycle regulators, but also Wnt- and Notch-signaling components, whose oscillations establish the timing mechanism in somitogenesis. Thus, our results provide new insights about circadian genes' function in control of the timing of differentiation during embryonic development.

Pygo1 and Pygo2 roles in Wnt signaling in mammalian kidney development

BACKGROUND

The pygopus gene of Drosophila encodes an essential component of the Armadillo (beta-catenin) transcription factor complex of canonical Wnt signaling. To better understand the functions of Pygopus-mediated canonical Wnt signaling in kidney development, targeted mutations were made in the two mammalian orthologs, Pygo1 and Pygo2.

RESULTS

Each mutation deleted >80% of the coding sequence, including the critical PHD domain, and almost certainly resulted in null function. Pygo2 homozygous mutants, with rare exception, died shortly after birth, with a phenotype including lens agenesis, growth retardation, altered kidney development, and in some cases exencephaly and cleft palate. Pygo1 homozygous mutants, however, were viable and fertile, with no detectable developmental defects. Double Pygo1/Pygo2 homozygous mutants showed no apparent synergy in phenotype severity. The BAT-gal transgene reporter of canonical Wnt signaling showed reduced levels of expression in Pygo1-/-/Pygo2-/- mutants, with tissue-specific variation in degree of diminution. The Pygo1 and Pygo2 genes both showed widespread expression in the developing kidney, with raised levels in the stromal cell compartment. Confocal analysis of the double mutant kidneys showed disturbance of both the ureteric bud and metanephric mesenchyme-derived compartments. Branching morphogenesis of the ureteric bud was altered, with expanded tips and reduced tip density, probably contributing to the smaller size of the mutant kidney. In addition, there was an expansion of the zone of condensed mesenchyme capping the ureteric bud. Nephron formation, however, proceeded normally. Microarray analysis showed changed expression of several genes, including Cxcl13, Slc5a2, Klk5, Ren2 and Timeless, which represent candidate Wnt targets in kidney development.

CONCLUSION

The mammalian Pygopus genes are required for normal branching morphogenesis of the ureteric bud during kidney development. Nevertheless, the relatively mild phenotype observed in the kidney, as well as other organ systems, indicates a striking evolutionary divergence of Pygopus function between mammals and Drosophila. In mammals, the Pygo1/Pygo2 genes are not absolutely required for canonical Wnt signaling in most developing systems, but rather function as quantitative transducers, or modulators, of Wnt signal intensity.

Mammalian TIMELESS and Tipin are evolutionarily conserved replication fork-associated factors

The function of the mammalian TIMELESS protein (TIM) has been enigmatic. TIM is essential for early embryonic development, but little is known regarding its biochemical and cellular function. Although identified based on similarity to a Drosophila circadian clock factor, it also shares similarity with a second family of proteins that is more widely conserved throughout eukaryotes. Members of this second protein family in yeast (S.c. Tof1p, S.p. Swi1p) have been implicated in DNA synthesis, S-phase-dependent checkpoint activation and chromosome cohesion, three processes coordinated at the level of the replication fork complex. The present work demonstrates that mammalian TIM and its constitutive binding partner, Tipin (ortholog of S.c. Csm3p, S.p. Swi3p), are replisome-associated proteins. Both proteins associate with components of the endogenous replication fork complex, and are present at BrdU-positive DNA replication sites. Knock-down of TIM also compromises DNA replication efficiency. Further, the direct binding of the TIM-Tipin complex to the 34 kDa subunit of replication protein A provides a biochemical explanation for the potential coupling role of these proteins. Like TIM, Tipin is also involved in the molecular mechanism of UV-dependent checkpoint activation and cell growth arrest. Tipin additionally associates with peroxiredoxin2 and appears to be involved in checkpoint responses to H(2)O(2), a role recently described for yeast versions of TIM and Tipin. Together, this work establishes TIM and Tipin as functional orthologs of their replisome-associated yeast counterparts capable of coordinating replication with genotoxic stress responses, and distinguishes mammalian TIM from the circadian-specific paralogs from which it was originally identified.

Circadian clock, cancer and lipid metabolism

Genetic analysis has revealed that mammalian circadian oscillator is driven by a cell autonomous transcription/translation-based negative feedback loop, wherein positive elements (CLOCK and BMAL1) induce the expression of negative regulators (Periods, CRY1 and CRY2) that inhibit the transactivation of positive regulators. Recent research reveals that this clock feedback loop affects many aspects of our physiology, such as cell cycle and lipid metabolism. In this review, I summarize the molecular links between the circadian clock mechanism and the cell cycle, and between the clock and lipid metabolism. Recent studies of clock mutants also suggest that clock molecules play a role as stress sensors. Lastly, we propose the importance of sterol for entraining peripheral clocks.

LC-MS/MS analysis of apical and basolateral plasma membranes of rat renal collecting duct cells

We used biotinylation and streptavidin affinity chromatography to label and enrich proteins from apical and basolateral membranes of rat kidney inner medullary collecting ducts (IMCDs) prior to LC-MS/MS protein identification. To enrich apical membrane proteins and bound peripheral membrane proteins, IMCDs were perfusion-labeled with primary amine-reactive biotinylation reagents at 2 degrees C using a double barreled pipette. The perfusion-biotinylated proteins and proteins bound to them were isolated with CaptAvidin-agarose beads, separated with SDS-PAGE, and sliced into continuous gel pieces for LC-MS/MS protein identification (LTQ, Thermo Electron Corp.). 17 integral and glycosylphosphatidylinositol (GPI)-linked membrane proteins and 44 non-integral membrane proteins were identified. Immunofluorescence confocal microscopy confirmed ACVRL1, H(+)/K(+)-ATPase alpha1, NHE2, and TauT expression in the IMCDs. Basement membrane and basolateral membrane proteins were biotinylated via incubation of IMCD suspensions with biotinylation reagents on ice. 23 integral and GPI-linked membrane proteins and 134 non-integral membrane proteins were identified. Analyses of non-integral membrane proteins preferentially identified in the perfusion-biotinylated and not in the incubation-biotinylated IMCDs revealed protein kinases, scaffold proteins, SNARE proteins, motor proteins, small GTP-binding proteins, and related proteins that may be involved in vasopressin-stimulated AQP2, UT-A1, and ENaC regulation. A World Wide Web-accessible database was constructed of 222 membrane proteins (integral and GPI-linked) from this study and prior studies.

Getting a buzz out of the bee genome

The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence.

A Timeless debate: resolving TIM's noncircadian roles with possible clock function

Mammalian TIMELESS (TIM) was identified due to its sequence similarity to Drosophila TIM, an essential circadian clock protein in flies. Published literature is inconsistent regarding the rhythmic expression of mammalian Tim, the interaction of the TIM protein with other clock proteins and its role in regulating clock gene transcription. Comprehensive sequence analysis not only demonstrates that mammalian TIM is more similar to a second, TIM-like sequence in Drosophila (TIMEOUT), but is also a member of an evolutionarily conserved family of TIM orthologs that is distinct from the circadian-specific TIM proteins found in insects. The vital cellular function of these widely conserved TIM orthologs makes it difficult to determine the specific role of mammalian TIM in the circadian clock mechanism.

Coupling of human circadian and cell cycles by the timeless protein

The Timeless protein is essential for circadian rhythm in Drosophila. The Timeless orthologue in mice is essential for viability and appears to be required for the maintenance of a robust circadian rhythm as well. We have found that the human Timeless protein interacts with both the circadian clock protein cryptochrome 2 and with the cell cycle checkpoint proteins Chk1 and the ATR-ATRIP complex and plays an important role in the DNA damage checkpoint response. Down-regulation of Timeless in human cells seriously compromises replication and intra-S checkpoints, indicating an intimate connection between the circadian cycle and the DNA damage checkpoints that is in part mediated by the Timeless protein.

Oligodeoxynucleotide methods for analyzing the circadian clock in the suprachiasmatic nucleus

The recent identification of specific genes responsible for the generation of endogenous circadian rhythmicity in the suprachiasmatic nucleus presents a new level of investigation into endogenous rhythmicity and mechanisms of synchronization of this circadian clock with the environmental light?dark cycle. This article describes techniques that employ antisense and decoy oligodeoxynucleotides (ODN) to determine the roles of specific molecular substrates both in endogenous rhythmicity and in regulating the effects of light on the mammalian circadian clock. Application of antisense ODN technology has revealed a role for timeless (Tim) in the core clock mechanism and established that induction of period1 (Per1) is required for light responsiveness. Likewise, a decoy ODN designed to sequester activated CREB protein definitively demonstrated a requirement for CRE-mediated transcription in light signaling. Experiments designed with these molecular tools offer new insights on the interaction of cellular processes and signaling with the molecular clockworks.

Gene duplication and complex circadian clocks in mammals

The circadian clock arose early in the evolution of life to enable organisms to adapt to the cycle of day and night. Recently, the extent and importance of circadian regulation of behaviour and physiology has come to be more fully realized. Core molecular cogs of circadian oscillators appear to have been largely conserved between such diverse organisms as Drosophila melanogaster and mammals. However, gene duplication events have produced multiple copies of many clock genes in mammals. Recent studies suggest that genome duplication has lead to increased circadian complexity and local tissue regulation. This has important implications for temporal regulation of behaviour via multiple clocks in the central nervous system, and also extends to the local physiology of major body organs and tissues.

Mammalian circadian biology: elucidating genome-wide levels of temporal organization

During the past decade, the molecular mechanisms underlying the mammalian circadian clock have been defined. A core set of circadian clock genes common to most cells throughout the body code for proteins that feed back to regulate not only their own expression, but also that of clock output genes and pathways throughout the genome. The circadian system represents a complex multioscillatory temporal network in which an ensemble of coupled neurons comprising the principal circadian pacemaker in the suprachiasmatic nucleus of the hypothalamus is entrained to the daily light/dark cycle and subsequently transmits synchronizing signals to local circadian oscillators in peripheral tissues. Only recently has the importance of this system to the regulation of such fundamental biological processes as the cell cycle and metabolism become apparent. A convergence of data from microarray studies, quantitative trait locus analysis, and mutagenesis screens demonstrates the pervasiveness of circadian regulation in biological systems. The importance of maintaining the internal temporal homeostasis conferred by the circadian system is revealed by animal models in which mutations in genes coding for core components of the clock result in disease, including cancer and disturbances to the sleep/wake cycle.

Cloning and characterization of a novel gene promoting ureteric bud branching in the metanephros

BACKGROUND

The ureteric buds and metanephric mesenchymal cells reciprocally induce each other's maturation during kidney development, and implicated transcription factors, secreted growth factors, and cell surface signaling peptides are critical regulators of renal branching morphogenesis. Protein kinase C (PKC) is a key enzyme in the signal transduction mechanisms in various biologic processes, including development, because it regulates growth and differentiation. Inhibition of PKC by the sphingolipid product ceramide interferes with nephron formation in the developing kidney, but the molecule that controls ureteric bud branching downstream of PKC is still unknown.

METHODS

Differential display polymerase chain reaction (PCR) of metanephroi cultured with a PKC activator and inhibitor was performed. We also examined the role of a novel gene in kidney development with organ culture system.

RESULTS

A novel gene encoding a 759 bp mRNA was identified, and we named it metanephros-derived tubulogenic factor (MTF)/L47. Inhibition of MTF with antisense oligonucleotide impaired ureteric bud branching by cultured metanephroi, and addition of recombinant MTF protein promoted ureteric bud branching in cultured metanephroi and increased cell proliferation.

CONCLUSION

We identified a novel molecule in developing kidney that is capable of modulating ureteric bud branching and kidney differentiation.

Changes in gene expression patterns in the ureteric bud and metanephric mesenchyme in models of kidney development

BACKGROUND

In a recent study, the pattern of gene expression during development of the rat kidney was analyzed using high-density DNA array technology (Stuart RO, Bush KT, Nigam SK, Proc Natl Acad Sci USA 98:5649-5654, 2001). This approach, while shedding light on global patterns of gene expression in the developing kidney, does not provide insight into the contributions of genes that might be part of the morphogenetic program of the ureteric bud (UB) and metanephric mesenchyme (MM), the two tissues that interact closely during nephron formation.

METHODS

We have now used high-density DNA arrays together with a double in vitro transcription (dIVT) approach to examine gene expression patterns in in vitro models for morphogenesis of the rat UB (isolated UB culture) and MM (coculture with embryonic spinal cord) and compared this data with patterns of gene expression in the whole embryonic kidney at different stages of development.

RESULTS

The results indicate that different sets of genes are expressed in the UB and MM as morphogenesis occurs. The dIVT data from the in vitro UB and MM culture models was clustered hierarchically with single IVT data from the whole embryonic kidney obtained at different stages of development, and the global patterns of gene expression were remarkably compatible, supporting the validity of the approach. The potential roles of genes whose expression was associated with the individual tissues were examined, and several pathways were identified that could have roles in kidney development. For example, hepatocyte nuclear factor-6 (HNF-6), a transcription factor potentially upstream in a pathway leading to the expression of KSP-cadherin was highly expressed in the UB. Embigin, a cell adhesion molecule important in cell/extracellular matrix (ECM) interactions, was also found in the UB and may serve as a Dolichos biflorus binding protein in the kidney. ADAM10, a disintegrin-metalloprotease involved in Delta-Notch signaling and perhaps Slit-Robo signaling, was also highly expressed in late UB. Celsr-3, a protein, which along with members of the Wnt-frizzled transduction cascade, might be involved in the polarization of the forming nephron, was found to be highly expressed in differentiating MM. DDR2, a member of the discoidin domain receptor family, which is thought to function in the activation of matrix metalloproteinase-2 (MMP-2), was also found to be highly expressed in differentiating MM. It is also interesting to note that almost 10% of the highly expressed genes in both tissues were associated with neuronal growth and/or differentiation.

CONCLUSION

The data presented in this study point to the power of combining in vitro models of kidney development with high-density DNA arrays to identify the genes involved in the morphogenetic process. Clear differences were found between patterns of genes expressed by the UB and MM at different stages of morphogenesis, and many of these were associated with neuronal growth and/or differentiation. Together, the high-density microarray data not only begin to suggest how separate genetic programs in the UB and MM orchestrate the formation of the whole kidney, but also suggest the involvement of heretofore largely unexplored developmental pathways (involving HNF-6, ADAM-10, Celsr-3, DDR2, and other genes) in nephrogenesis.

Requirement of mammalian Timeless for circadian rhythmicity

Despite a central circadian role in Drosophila for the transcriptional regulator Timeless (dTim), the relevance of mammalian Timeless (mTim) remains equivocal. Conditional knockdown of mTim protein expression in the rat suprachiasmatic nucleus (SCN) disrupted SCN neuronal activity rhythms, and altered levels of known core clock elements. Full-length mTim protein (mTIM-fl) exhibited a 24-hour oscillation, where as a truncated isoform (mTIM-s) was constitutively expressed. mTIM-fl associated with the mammalian clock Period proteins (mPERs) in oscillating SCN cells. These data suggest that mTim is required for rhythmicity and is a functional homolog of dTim on the negative-feedback arm of the mammalian molecular clockwork.

Timeless in lung morphogenesis

The Clock gene, timeless, regulates circadian rhythm in Drosophila, but its vertebrate homolog is critical to embryonic development. Timeless was shown to be involved in murine urethral bud branching morphogenesis. We generated a polyclonal antibody to mouse TIMELESS (mTIM) and studied its distribution and its potential role during lung development, which also requires branching morphogenesis. In the early mouse embryo, TIM was localized to all organs, especially the neural epithelium. In embryonic day (E) 9.5 embryos, TIM was present in both epithelial and mesenchymal cells at the onset of lung morphogenesis. In E15 embryos, TIM decreased in the mesenchyme but remained pronounced in the epithelium of both large and small airways. Later, TIM was localized to a specific subset of epithelial cells with alveolar type 2 phenotype. This finding was verified by immunostaining of isolated alveolar type 2 cells. In the proximal airways, TIM was colocalized with CCSP to nonciliated columnar epithelial cells. Antisense oligonucleotides to mTim specifically inhibited branching morphogenesis of embryonic lungs in explant culture without affecting SpC expression an alveolar type 2 cell marker. In cultured lung cells, expression of TIM is independent of cell cycle and proliferation. These studies indicate that the function of Timeless is highly conserved in organs whose formation requires branching morphogenesis.

Tipin, a novel timeless-interacting protein, is developmentally co-expressed with timeless and disrupts its self-association

The mouse Timeless gene (mTim) was identified originally on the basis of its similarity to a Drosophila circadian gene, but has no substantiated role in the circadian clock mechanism. The importance of mTim in cellular processes involved in development, however, is undeniable, since targeted mutagenesis of this gene arrests embryonic development. To connect mTim to known pathways controlling cellular processes important for early development, a yeast two-hybrid approach was used to identify embryonic mTIM-interacting proteins. One positive interactor, a previously uncharacterized protein that is here termed TIPIN (TIMELESS interacting protein), was shown to interact with mTIM in vitro and in cultured cells. mTim and Tipin transcripts are co-expressed in similar tissues during embryonic development and in the adult brain. In transiently transfected cultures, mTIM promotes the nuclear localization of TIPIN. Immunoprecipitation experiments suggest that TIPIN is capable of regulating mTIM activity by disrupting the ability of mTIM to form homo-multimeric complexes. Together, these results indicate that mTIM forms a functional complex with TIPIN, and provide a starting point from which to link mTim to biochemical pathways controlling vital cellular functions.

Debt91, a putative zinc finger protein differentially expressed during epithelial morphogenesis

In a differential screen for genes that might be important in the regulation of epithelial morphogenesis, we identified a novel gene, Debt91 (differentially expressed in branching tubulogenesis), which is up-regulated in an in vitro model of renal tubulogenesis and branching. Debt91 appears to encode a 381 amino acid molecule with high Ser and Thr composition and is highly conserved at its N-terminus across species. Sequence analysis suggests that it is a coiled-coil nuclear phosphoprotein with zinc finger motifs at the N-terminal conserved region, which is rich in cysteine and histidine. Debt91 is located on mouse chromosome 6 at a region that has conserved synteny with human chromosome 2p11.2, and appears to express two transcripts in several mouse cell lines and adult tissues. On whole murine embryo blots Debt91 expresses primarily its small transcript and is differentially regulated during development. Analysis of expression in in vitro cell culture models suggests that Debt91 is an immediate early gene up-regulated during growth factor-induced branching tubulogenesis.

Elevated thrombopoietin levels in patients with myelofibrosis may not be due to enhanced production of thrombopoietin by bone marrow

Thrombopoietin (TPO) is recognized as the primary regulator of megakaryocyte and platelet production. Two alternative hypotheses for the mechanism of regulation have been proposed: (1) platelet and/or megakaryocyte mass regulate circulating TPO levels by binding to TPO through TPO receptors (c-MPL), with subsequent internalization and degradation of the protein; (2) TPO mRNA produced by bone marrow (BM) stromal cells or BM cells modulates blood TPO levels or platelet counts. In myeloproliferative disorders (MPD), including primary myelofibrosis (MF) and essential thrombocythemia (ET), elevated blood TPO levels occur despite increased platelet and megakaryocyte mass. Therefore, in these diseases, elevated blood TPO levels cannot be explained by the first mechanism. The present study, was designed to measure TPO mRNA production by BM mononuclear cells and BM stromal cells using a relative RT-PCR technique, to verify the second mechanism. We found no increase of TPO mRNA production in either BM cells or in BM stromal cells in patients with MF and ET. Furthermore, in those patients with MF who had elevated plasma TPO levels, TPO mRNA levels in bone marrow fibroblasts (BMFs) or BM cells were not elevated as compared with controls. Therefore, we concluded that in patients with MF, the elevated plasma TPO levels are not due to enhanced production of TPO mRNA either by BMF, or BM cells. The TPO receptor (c-MPL) abnormalities including reduced MPL protein levels or defective TPO induced signal transduction pathways are the likely mechanisms.

Pediatric liver tumors and hepatic ontogenesis: common and distinctive pathways

Several types of pediatric liver tumors exhibit structural features apparently reflecting processes which normally occur during hepatic ontogenesis: some hepatoblastomas mimic distinct phases of hepatogenesis, including the formation of mesenchymal structures closely associated with immature epithelia, and there are tumors almost exclusively consisting of complex mesenchymal patterns. Current classifications of hepatoblastomas refer to the identification of more or less mature (differentiated) single or mixed components seen in histologic preparations. These do not, however, attempt to integrate ontogenic pathways, in contrast for example, to nephroblastoma and associated lesions, where such a view has proved to be highly fruitful. Based on the fact that an enormous amount of knowledge has recently been accumulated regarding hepatic ontogenesis, time may have come to look at these tumors with a new eye. In what follows, we aim at trying to analyze distinct features of pediatric hepatic tumors (except vascular tumors) within the background of ontogenesis. Some key steps of hepatogenesis and the regulatory factors involved may, in the future, deliver an armamentarium to search for novel molecular mechanisms involved in tumorigenic pathways.

Genes and proteins in renal development

Metanephric kidney development begins with the formation of the metanephrogenic mesenchyme; this event depends on the prior action in the intermediate mesoderm of transcription factors such as Lim-1, Pax-2, Eya-1, and Foxc-1. Once it has formed, the mesenchyme secretes GDNF; this induces the nearby wolffian duct to produce a ureteric bud which invades the metanephrogenic mesenchyme and begins to arborize. Ureteric bud development and branching depends on the transcription factor Emx-2, the GDNF-cRet and probably the HGF/cMet, signalling systems, and the intracellular regulatory molecules formin IV and timeless. Proteins of the BMP family modulate ureteric bud branching and keep bud development in step with that of other tissue types. Proteins and glycosaminoglycans of the matrix, and their receptors, and also required. The metanephrogenic mesenchyme has a default fate of apoptosis and is dissuaded from suicide by factors secreted from the bud such as TGF-alpha, TIMP-2, EGF, and FGF-2. Other factors such as LIF and TGFbeta2 cooperate with these to induce clumps of mesenchyme cells to differentiate into nephrons, while BMP-7 appears to lead them instead to form stroma. As nephrons form, they express critical transcription factors such as WT-1, Pax-2, and Hoxa11 and d11, condense, and secrete Wnt-4. Wnt-4 acts in an autocrine loop to stimulate its own synthesis and is required for cells to differentiate into epithelia; its action is antagonized by sFRP-1, secreted by stroma, but this antagonism is itself inhibited by sFRP-2 made by the developing nephron. This system probably acts both to limit the spread of Wnt-4's influence and also to commit responding cells to their epithelial fate. As nephrons mature, regions of them differentiate to perform specific physiological functions, a process that requires the proteins WT-1, Lmx-1b, Notch-2, Jagged-1, and Hnf-1.

Invited review: regulation of mammalian circadian clock genes

The circadian clock is a self-sustaining oscillator that has a period of approximately 24 h and controls many physiological and behavioral systems. This clock can synchronize itself to changing environmental conditions to optimize an organisms performance. The underlying circadian rhythms are generated by periodic activation of transcription by a set of clock genes. Besides their own regulation, clock genes can influence biochemical processes by modulating specific genes of biochemical pathways. Developments in the last few years using genetics and molecular biological tools have led to a new understanding of the molecular basis of the circadian clock in mammals. In this mini-review, I will summarize these advances that have led us to begin understanding the mammalian circadian clock at the molecular level.

Toward an etiological classification of developmental disorders of the kidney and upper urinary tract

Toward an etiological classification of developmental disorders of the kidney and upper urinary tract. There are a large number of developmental disorders and syndromes that affect the kidney and upper urinary tract. These have generally been classified according to morphological criteria established decades ago. Although these classifications have been useful, they are incomplete, including some developmental disorders while excluding others. Here, basic cellular and molecular biology studies of kidney and upper urinary tract development in both rodents and humans are utilized to suggest the basis of a new etiologic, if still tentative, classification scheme. This classification may help to identify candidate genes for human diseases by correlating morphology with pathogenetic mechanisms.

EEG1, a putative transporter expressed during epithelial organogenesis: comparison with embryonic transporter expression during nephrogenesis

A screen for genes differentially regulated in a model of kidney development identified the novel gene embryonic epithelia gene 1 (EEG1). EEG1 exists as two transcripts of 2.4 and 3.5 kb that are most highly expressed at embryonic day 7 and later in the fetal liver, lung, placenta, and kidney. The EEG1 gene is composed of 14 exons spanning a 20-kb region at human chromosome 11p12 and the syntenic region of mouse chromosome 2. Six EEG1 exons have previously been assigned to a longer isoform of eosinophil major basic protein termed proteoglycan 2. Another gene distantly related to EEG1, POV1/PB39, is located 88 kb upstream from the EEG1 gene on chromosome 11. Temporal expression of 65 members of the solute carrier (SLC)-class of transport proteins was followed during kidney development using DNA arrays. POV-1 and EEG1, like glucose transporters, displayed very early maximal gene expression. In contrast, other SLC genes, such as organic anion and cation transporters, amino acid permeases, and nucleoside transporters, had maximal expression later in development. Thus, although the bulk of transporters are expressed late in kidney development, a fraction are expressed near the onset of nephrogenesis. The data raise the possibility that EEG1 and POV1 may define a new family of transport proteins involved in the transport of nutrients or metabolites in rapidly growing and/or developing tissues.