SUMMARY Determining the molecular identities of adult stem cells requires novel technologies for sensitive transcript detection in tissues. In mouse intestinal crypts, lineage-tracing studies suggested that different genes uniquely mark spatially distinct stem-cell populations, residing either at crypt bases or at position +4, but a detailed analysis of their spatial co-expression has not been feasible. Here we apply three-color single molecule fluorescence in-situ hybridization to study a comprehensive panel of intestinal stem-cell markers during homeostasis, aging and regeneration. We find that the expression of all markers overlap at crypt-base-cells. This co-expression includes Lgr5, Bmi1 and mTert, genes previously suggested to mark distinct stem cells. Strikingly, Dcamkl-1 tuft cells, distributed throughout the crypt axis, co-express Lgr5 and other stem cell markers that are otherwise confined to crypt bases. We also detect significant changes in the expression of some of the markers following irradiation, suggesting their potential role in the regeneration process. Our approach can enable the sensitive detection of putative stem cells in other tissues and in tumours, guiding complementary functional studies to evaluate their stem-cell properties.

Functional inactivation of the von Hippel-Lindau (VHL) tumor suppressor protein is the cause of familial VHL disease and sporadic kidney cancer. The VHL gene product (pVHL) is a component of an E3 ubiquitin ligase complex that targets the hypoxia-inducible factor (HIF) 1 and 2 ␣ subunits for polyubiquitylation. This process is dependent on the hydroxylation of conserved proline residues on the ␣ subunits of HIF-1/2 in the presence of oxygen. In our effort to identify orphan HIF-like proteins in the data base that are potential targets of the pVHL complex, we report multiple splice variants of the human HIF-3␣ locus as follows: hHIF-3␣1, hHIF-3␣2 (also referred to as hIPAS; human inhibitory PAS domain protein), hHIF-3␣3, hHIF-3␣4, hHIF-3␣5, and hHIF-3␣6. We demonstrate that the common oxygen-dependent degradation domain of hHIF-3␣1-3 splice variants is targeted for ubiquitylation by the pVHL complex in vitro and in vivo. This activity is enhanced in the presence of prolyl hydroxylase and is dependent on a proline residue at position 490. Furthermore, the ubiquitin conjugation occurs on lysine residues at position 465 and 568 within the oxygen-dependent degradation domain. These results demonstrate additional targets of the pVHL complex and suggest a growing complexity in the regulation of hypoxia-inducible genes by the HIF family of transcription factors.

Individuals who inherit one faulty von Hippel-Lindau gene (VHL) allele are predisposed to VHL disease, which is characterized by the development of cerebellar, spinal, and retinal hemangioblastoma, pheochromocytoma, and clear-cell renal cell carcinoma (CC-RCC) (29). The tumor develops upon the somatic loss of the remaining wild-type VHL allele in a susceptible cell. Importantly, biallelic loss of VHL is associated with the vast majority of sporadic CC-RCCs, establishing VHL as a critical suppressor of renal oncogenesis (29). CC-RCC is resistant to conventional radiation and chemotherapies, and approximately one-quarter of renal cancer patients present with advanced disease, including locally invasive or metastatic CC-RCC (12). Unfortunately, one-third of patients who undergo surgical removal of localized tumors have recurrence of the disease, and the median survival for patients harboring metastatic CC-RCC is 13 months (12). Moreover, the principal cause of morbidity and death of VHL patients is CC-RCC (29). Despite the need to better understand the aggressive nature of CC-RCC, the molecular pathways governing its malignant phenotype remain unresolved.The most well-characterized function of VHL is as a substrate-recognition component of the SCF (Skp1/Cdc53/F-box protein)-like E3 ubiquitin ligase complex called ECV (elongins/Cul2/VHL) that selectively ubiquitylates oxygen-dependent prolyl-hydroxylated ␣ subunits of hypoxia-inducible factor

A universal response to changes in cellular oxygen tension is governed by a family of heterodimeric transcription factors called hypoxia-inducible factor (HIF). Tumor hypoxia, as well as various cancer-causing mutations, has been shown to elevate the level of HIF-1alpha, signifying a critical role of the HIF pathway in cancer development. The recently identified third member of the human HIF-alpha family, HIF-3alpha, produces multiple splice variants that contain extra DNA binding elements and protein-protein interaction motifs not found in HIF-1alpha or HIF-2alpha. Here we report the molecular cloning of the alternatively spliced human HIF-3alpha variant HIF-3alpha4 and show that it attenuates the ability of HIF-1 to bind hypoxia-responsive elements located within the enhancer/promoter of HIF target genes. The overexpression of HIF-3alpha4 suppresses the transcriptional activity of HIF-1 and siRNA-mediated knockdown of the endogenous HIF-3alpha4 increases transcription by hypoxia-inducible genes. HIF-3alpha4 itself is oxygen-regulated, suggesting a novel feedback mechanism of controlling HIF-1 activity. Furthermore, the expression of HIF-3alpha4 is dramatically down-regulated in the majority of primary renal carcinomas. These results demonstrate an important dominant-negative regulation of HIF-1-mediated gene transcription by HIF-3alpha4 in vivo and underscore its potential significance in renal epithelial oncogenesis.

Hypoxia-inducible factor (HIF) is a heterodimeric transcription factor that mediates the adaptive responses to hypoxia by effecting the transcription of numerous hypoxia-inducible genes. HIF is frequently overexpressed in solid tumors, and the transactivation of HIF targets in transformed cells provides a distinct survival advantage. Accordingly, the upregulation of HIF correlates with increased progression or aggressiveness of the cancer and poor prognosis. In addition to the induction of HIF by hypoxia, its expression is induced by the loss of tumor suppressors VHL, PTEN, TSC1/2, PML, and SDH, as well as by the increased activity of PI3K and/or MAPK signaling pathways, underscoring the significance of HIF in oncogenesis.

The development of hereditary von Hippel-Lindau (VHL) disease and the majority of sporadic kidney cancers are due to the functional inactivation of the VHL gene. The product of the VHL gene, pVHL, in association with elongins B and C, cullin 2, and Rbx1 form an E3 ubiquitin-ligase complex VEC that targets the alpha subunits of hypoxia-inducible factor (HIF) for ubiquitination. Ubiquitin-tagged HIF-α proteins are subsequently degraded by the common 26S proteasome. pVHL functions as the substrate-docking interface that specifically recognizes prolyl-hydroxylated HIF-α. This hydroxylation occurs only in the presence of oxygen or normoxia. Thus, under hypoxia, HIF-α subunits are no longer subjected to degradation and are thereby able to dimerize with the common and constitutively stable β subunits. The heterodimeric HIFs upregulate a myriad of hypoxia-inducible genes, triggering our physiologic response to hypoxia. Inappropriate accumulations of HIF-α in VHL disease are believed to contribute to the pathogenesis via the upregulation of several of these HIF target genes. Our current molecular understanding of the roles of HIF and pVHL in the development of VHL-associated clear-cell renal cell carcinoma (CC-RCC) is the focus of this review.

The retinoblastoma protein gene RB-1 is mutated in one-third of human tumors. Its protein product, pRB (retinoblastoma protein), functions as a transcriptional coregulator in many fundamental cellular processes. Here, we report a nonnuclear role for pRB in apoptosis induction via pRB's direct participation in mitochondrial apoptosis. We uncovered this activity by finding that pRB potentiated TNFa-induced apoptosis even when translation was blocked. This proapoptotic function was highly BAX-dependent, suggesting a role in mitochondrial apoptosis, and accordingly, a fraction of endogenous pRB constitutively associated with mitochondria. Remarkably, we found that recombinant pRB was sufficient to trigger the BAX-dependent permeabilization of mitochondria or liposomes in vitro. Moreover, pRB interacted with BAX in vivo and could directly bind and conformationally activate BAX in vitro. Finally, by targeting pRB specifically to mitochondria, we generated a mutant that lacked pRB's classic nuclear roles. This mito-tagged pRB retained the ability to promote apoptosis in response to TNFa and also additional apoptotic stimuli. Most importantly, induced expression of mito-tagged pRB in Rb -/-;p53 -/-tumors was sufficient to block further tumor development. Together, these data establish a nontranscriptional role for pRB in direct activation of BAX and mitochondrial apoptosis in response to diverse stimuli, which is profoundly tumor-suppressive.

The most prevalent mutations associated with the development of clear-cell renal cell carcinoma (CC-RCC) are the loss-of-function mutations of von Hippel-Lindau (VHL) tumor suppressor gene. These mutations invariably result in an inappropriate accumulation of HIF-alpha due to a failure of VHL as a substrate-recognition component of an E3 ubiquitin ligase complex to target HIFalpha for oxygen-dependent ubiquitin-mediated destruction. Stabilization of HIF-2alpha, but not HIF-1alpha, is the critical oncogenic event upon the functional loss of VHL in the development of CC-RCC. Here, we show that HIF-3alpha4, an alternatively spliced variant of human HIF-3alpha with similar domain structure as the murine inhibitory PAS protein (IPAS), forms an abortive transcriptional complex with HIF-2alpha and prevents the engagement of HIF-2 to the hypoxia-responsive elements (HREs) located in the promoter/ enhancer regions of hypoxia-inducible genes. In addition, the re-expression of HIF-3alpha4 in VHL-null 786-O CC-RCC cells via adenovirus decreases the endogenous expression of HIF-2-driven gene expression and suppresses the growth of 786-O tumor xenografts in SCID mice. These results suggest that HIF-3alpha4 is a naturally occurring dominant-negative HIF-3alpha splice isoform with tumor suppressive activity and support the targeted delivery of HIF-3alpha4 as a potential therapeutic option to curtail HIF-dependent tumor progression.