bHLH-PAS Family Of Transcription Factors Research Articles

Multi-level interaction between HIF and AHR transcriptional pathways in kidney carcinoma.

Hypoxia-inducible factor (HIF) and aryl hydrocarbon receptor (AHR) are members of the bHLH-PAS family of transcription factors that underpin cellular responses to oxygen and to endogenous and exogenous ligands, respectively, and have central roles in the pathogenesis of renal cancer. Composed of heterodimers, they share a common HIF-1β/ARNT subunit and similar DNA-binding motifs, raising the possibility of crosstalk between the two transcriptional pathways. Here, we identify both general and locus-specific mechanisms of interaction between HIF and AHR that act both antagonistically and cooperatively. Specifically, we observe competition for the common HIF-1β/ARNT subunit, in cis synergy for chromatin binding, and overlap in their transcriptional targets. Recently, both HIF and AHR inhibitors have been developed for the treatment of solid tumours. However, inhibition of one pathway may promote the oncogenic effects of the other. Therefore, our work raises important questions as to whether combination therapy targeting both of these pro-tumourigenic pathways might show greater efficacy than targeting each system independently.

Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family

Neuronal PER-ARNT-SIM (PAS) domain protein 4 (NPAS4) is a protective transcriptional regulator whose dysfunction has been linked to a variety of neuropsychiatric and metabolic diseases. As a member of the basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) transcription factor family, NPAS4 is distinguished by an ability to form functional heterodimers with aryl hydrocarbon receptor nuclear translocator (ARNT) and ARNT2, both of which are also bHLH-PAS family members. Here, we describe the quaternary architectures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers in complexes involving DNA response elements. Our crystallographic studies reveal a uniquely interconnected domain conformation for the NPAS4 protein itself, as well as its differentially configured heterodimeric arrangements with both ARNT and ARNT2. Notably, the PAS-A domains of ARNT and ARNT2 exhibit variable conformations within these two heterodimers. The ARNT PAS-A domain also forms a set of interfaces with the PAS-A and PAS-B domains of NPAS4, different from those previously noted in ARNT heterodimers formed with other class I bHLH-PAS family proteins. Our structural observations together with biochemical and cell-based interrogations of these NPAS4 heterodimers provide molecular glimpses of the NPAS4 protein architecture and extend the known repertoire of heterodimerization patterns within the bHLH-PAS family. The PAS-B domains of NPAS4, ARNT, and ARNT2 all contain ligand-accessible pockets with appropriate volumes required for small-molecule binding. Given NPAS4's linkage to human diseases, the direct visualization of these PAS domains and the further understanding of their relative positioning and interconnections within the NPAS4-ARNT and NPAS4-ARNT2 heterodimers may provide a road map for therapeutic discovery targeting these complexes.

Structural basis for the allosteric inhibition of hypoxia-inducible factor (HIF)-2 by belzutifan.

Hypoxia-inducible factor (HIF)-2α and its obligate heterodimerization partner aryl hydrocarbon receptor nuclear translocator (ARNT), are both members of the basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factor family. Previous studies have identified HIF-2α as a key oncogenic driver in clear cell renal cell carcinoma (ccRCC), rendering it a promising drug target for this type of kidney cancer. Belzutifan is the first HIF-2α inhibitor approved for treating ccRCC and other cancers associated with the von Hippel-Lindau (VHL) disease. However, the detailed inhibitory mechanism of belzutifan at molecular level is still unclear. Here we obtained the crystal structure of HIF-2α-ARNT heterodimer in complex with belzutifan at 2.75 Å resolution. The complex structure shows that belzutifan binds into the PAS-B pocket of HIF-2α, and it destabilizes the dimerization of HIF-2α and ARNT through allosteric effects mainly mediated by the key residue M252 of HIF-2α near the dimer interface. We further explored the inhibitory effects of belzutifan using biochemical and functional assays. The time-resolved fluorescence energy transfer (TR-FRET)-based binding assay showed that belzutifan disrupts the dimerization of HIF-2α and ARNT with a Ki value of 20 nM. The luciferase reporter assay indicated that belzutifan can efficiently inhibit the transcriptional activity of HIF-2α with an IC50 value of 17 nM. Besides, the real-time PCR assay illustrated that belzutifan can reduce the expression of HIF-2α downstream genes in 786-O kidney cancer cells in a dose-dependent manner. Our work reveals the molecular mechanism by which belzutifan allosterically inhibits HIF-2α and provides valuable information for the subsequent drug development targeting HIF-2α. Significance Statement The bHLH-PAS family of transcription factors are an emerging group of small-molecule drug targets. Belzutifan, originally developed by Peloton Therapeutics, is the first FDA-approved drug directly binding to a bHLH-PAS protein, the hypoxia-inducible factor (HIF)-2α. Based on the protein-drug complex structure, biochemical binding assays, and functional profiling of downstream gene expression, this study reveals the regulatory mechanism of how belzutifan allosterically destabilizes HIF-2α's heterodimerization with its obligate partner protein, thus reducing their transcriptional activity that links to tumor progression.

Molecular selection and functional divergence of HIF-α proteins in vertebrates

HIF-α transcription factors, as key master regulators of oxygen homeostasis, constitute a subgroup of the large bHLH-PAS transcription factor family and have been identified in many vertebrates. Although the amino acid sequences of bHLH-PAS domain are conserved, the physiological and pathological roles of this family are variable. They also have different patterns of expression. It is possible that the HIF-α copies have been retained as a consequence of adaptive amino acid replacements or relaxed selective constraint which have conferred subtle changes in function after duplications. Phylogenetic analysis indicated that at least two major duplications had occurred early in the vertebrate lineages. Analyses of the ratios of nonsynonymous/synonymous substitution rates revealed that relaxation of selective constraints might play important roles over evolutionary time and shape variation in some members of the family. The coefficients of functional divergence (θ) estimated between pairwise comparisons of gene groups from HIF-1α, HIF-2α, and HIF-3α indicated statistically significant site-specific shift of evolutionary rates between them, suggesting that altered functional constraints may have taken place at some amino acid residues after their duplications. Moreover, we also mapped sites identified to have been relaxed from purifying selection onto the three-dimensional structure of human HIF-2α. Overall, our study demonstrated that the functional diversity of HIF-αs members may be caused by relaxed negative selection on the N-terminal transactivation domains after HIF-αs duplications, which recruited new partners leading to functional specificity.

Fine distribution of CLOCK protein in hepatocytes of hibernating dormice.

CLOCK protein is a member of the bHLH-PAS family of transcription factors, it is expressed in several tissues including the liver and is essential for normal circadian rhythms. In this study we investigate the distribution of CLOCK protein in hepatocytes of euthermic and hibernating edible dormice Glis glis as well as in hepatocytes taken from the hibernating animals submitted in vitro to experimental conditions mimicking the arousal process. Our results demonstrate that CLOCK protein is expressed in all animals and is mostly located in the nucleus, in particular, on perichromatin fibrils and nucleoli. During deep hibernation CLOCK protein becomes more abundant but an intracellular redistribution occurs: the protein significantly decreases in all cellular compartments, but it accumulates in the amorphous bodies. These nuclear bodies, typical of the hibernating state, probably represent storage sites for CLOCK protein to be quickly used upon arousal. Accordingly, in hepatocytes submitted to in vitro conditions mimicking arousal CLOCK protein levels rapidly reach the euthermic values, while amorphous bodies disappear.

Mitochondria and Hypoxia‐induced Gene Expression Mediated by Hypoxia‐inducible Factors

The influence of mitochondrial activity on gene expression programs, particularly those involved in neuroprotection and repair, is likely to play an important role in the pathophysiology of neurodegenerative diseases. One such gene expression program is activated by the cellular pathway that senses a decrease in optimal oxygen levels and leads to activation of a family of transcriptional activators called hypoxia-inducible factors (HIFs). HIFs are members of the bHLH-PAS family of transcription factors and are heterodimers composed of HIF-alpha and HIF-beta (also known as aryl hydrocarbon receptor nuclear translocator) subunits that bind to canonical DNA sequences (hypoxia-regulated elements) in the promoters or enhancers of target genes. HIFs activate the expression of more than a hundred genes encoding proteins that regulate cell metabolism, survival, angiogenesis, vascular tone, hematopoiesis, and other functions. There is considerable evidence showing a bidirectional crosstalk between mitochondrial signals and HIF activity. For instance, mitochondrial reactive oxygen species and metabolic substrates from the tricarboxylic acid cycle are implicated in the regulation of the HIF pathway. Conversely, HIF activity leads to the expression of target genes that influence mitochondrial function. In this chapter we will review the complex interactions between mitochondria and the HIF pathway and we will discuss the relevance of this interaction for metabolic adaptation to hypoxia.

Ah Receptor Binding to its Cognate Response Element is Required for Dioxin-Mediated Toxicity

The aryl hydrocarbon receptor (AHR) is a ligand-activated member of the bHLH-PAS family of transcription factors. Members of this family include HIF1α, EPAS, and SIM, which are involved in hypoxia and nervous system development. Another member of this family, aryl hydrocarbon nuclear translocator (ARNT), is the dimerization partner for the AHR. The AHR is often classified as a sensor of a wide range of xenobiotics, leading to induction of xenobiotic metabolism through enhanced expression of phase I/II enzymes. The environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a prototypic ligand for the AHR and is often used to study the effects of prolonged AHR activation. Rodent exposure to TCDD results in a plethora of toxic effects, including wasting syndrome, tumor promotion, developmental defects, and liver toxicity (reviewed in Vanden Heuvel and Lucier, 1993). The key target genes that lead to these toxic end points are largely unknown. AHR activation can occur through a growing list of chemicals that appear to be structurally diverse and include many polycyclic aromatic hydrocarbons, tryptophan metabolites, and flavones (Denison and Nagy, 2003). Soluble receptors such as the AHR could possibility alter transcription of target genes through several distinct mechanisms. The work of Bunger and coworkers (Bunger et al., 2008) has examined whether TCDD-mediated liver toxicity can be mediated by the AHR in the absence of DNA binding.

Inhibition of breast cancer growth and invasion by single-minded 2s

Single-minded 2 (SIM2) is a member of the bHLH-PAS family of transcription factors. SIM2 was initially identified by positional cloning on chromosome 21 and is thought to contribute to the etiology of trisomy-21 [Down syndrome (DS)]. In addition to the physical and mental deficiencies associated with this genetic disease, it has become apparent that women with DS are 10-25 times less likely to die from breast cancer in comparison with age-matched normal populations. This is thought to be a result of gene dosage effect of tumor suppressor genes on chromosome 21. Here, we report that a splice variant of SIM2, SIM2 short (SIM2s), is differentially expressed in normal breast and breast cancer-derived cell lines and is downregulated in human breast cancer samples. Re-establishment of SIM2s in MDA-MB-435 breast cancer cells significantly reduced proliferation, anchorage-independent growth and invasive potential. Consistent with its role as a transcriptional repressor, SIM2s directly decreased expression of matrix metalloprotease-3, a known mediator of breast cancer metastasis. These results suggest that SIM2s has breast tumor suppressive activity.

CDNA cloning and characterization of a high affinity aryl hydrocarbon receptor in a cetacean, the beluga, Delphinapterus leucas.

Some cetaceans bioaccumulate substantial concentrations of planar halogenated aromatic hydrocarbons (PHAHs) in their tissues, but little is known about the effects of such burdens on cetacean health. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and related PHAHs cause toxicity via activation of the aryl hydrocarbon receptor (AHR), a member of the bHLH-PAS family of transcription factors. Differences in AHR structure and function are known to contribute to species-specific differences in susceptibility to PHAH toxicity. To ascertain the potential for PHAH effects in a cetacean, we characterized an AHR from the beluga whale, Delphinapterus leucas. The 3.2 kb cDNA encodes an 845-amino acid protein with a predicted size of 95.5 kDa. Overall, the beluga AHR shares 85% amino acid sequence identity with the human AHR and 75% identity with the mouse AHR Ah(b-1) allele. Beluga AHR protein synthesized in a rabbit reticulocyte lysate system demonstrated specific, high-affinity [(3)H]TCDD binding. Saturation binding analysis was used to compare the [(3)H]TCDD binding affinity of the in vitro-expressed beluga AHR with affinities of in vitro-expressed AHRs from a dioxin-sensitive mouse strain (Ah(b-1) allele) and humans. The beluga AHR bound [(3)H]TCDD with an affinity (K(d)= 0.43 +/- 0.16 nM) that was at least as high as that of the mouse AHR (K(d)= 0.68 +/- 0.23 nM), and significantly greater than that of the human AHR (K(d)= 1.63 +/- 0.64 nM). In electrophoretic mobility shift assays, the beluga AHR exhibited sequence-specific, Arnt-dependent binding to a dioxin responsive enhancer (DRE). Upon transient transfection into mammalian cells, the beluga AHR activated transcription of a luciferase reporter under control of a DRE-containing fragment of the mouse Cyp1a1 promoter. These results show that in an in vitro system, the beluga AHR possesses characteristics similar to those of AHRs from other mammals that are considered sensitive to toxic effects of PHAHs. Together, these results demonstrate that the use of in vitro-expressed proteins is a promising approach for addressing molecular and biochemical questions concerning PHAH toxicity in endangered or protected species.

The murine IL-2 promoter contains distal regulatory elements responsive to the Ah receptor, a member of the evolutionarily conserved bHLH-PAS transcription factor family.

Signaling through the TCR and costimulatory signals primarily control transcription of the IL-2 gene in naive T cells. The minimal promoter necessary for this expression lies proximal, between -300 and the transcription start site. We had previously shown that activation of the arylhydrocarbon receptor (AHR), a member of the bHLH-PAS family of transcription factors, leads to increased mRNA expression of IL-2 in murine fetal thymocytes. The AHR is abundant in the thymus and may play a role for the development of the immune system. Moreover, its overactivation by chemicals such as dioxins leads to immunosuppression and thymic involution. Binding motifs for the liganded AHR can be identified in the distal region -1300 to -800 of the mouse IL-2 promoter. We show here that these DNA motifs, the so-called dioxin response elements, after binding to the liganded AHR are sufficient to transactivate luciferase expression in a reporter gene system. The IL-2 gene can be induced by the AHR also in thymocytes in vivo after injection of 2,3,7, 8-tetrachlorodibenzo-p-dioxin, a potent ligand of the AHR. The AHR mediates the IL-2 induction as shown with AHR-deficient mice. However, in spleen cells in vitro costimulation via the TCR is necessary for optimal IL-2 gene induction. Thus, the IL-2 promoter region contains novel distal regulatory elements that can be addressed by the AHR to induce IL-2 and can cooperate with the proximal promoter in this.

The aryl hydrocarbon receptor in early vertebrates

The Ah receptor (AhR), which mediates effects of dioxins and related halogenated aromatic hydrocarbons, belongs to the emerging bHLH-PAS family of transcription factors. A reverse-transcription-polymerase chain reaction (RT-PCR) method using degenerate primers was used to search for the AhR in early vertebrates, including bony, cartilaginous, and jawless fish. AhR cDNA sequences were obtained for the killifish Fundulus heteroclitus, smooth dogfish Mustelus canis, the little skate Raja erinacea and the sea lamprey Petromyzon marinus. Further studies revealed evidence for a second AhR gene (AHR2) in Fundulus and Mustelus. The fish AhR1 and AhR2 genes are as different from each other as each is from mammalian AhRs, suggesting that they are the result of an ancient gene duplication, possibly occurring prior to the divergence of lineages leading to present-day mammals and fish. These studies demonstrate the conservation of AhR structure over more than 500 million years of vertebrate evolution. A search of the GenBank protein sequence database revealed a possible AhR homolog in the nematode Caenorhabditis elegans. Phylogenetic analysis of fish AhR sequences in comparison to mammalian AhRs and other members of the bHLH-PAS gene family provides an evolutionary perspective to the study of dioxin toxicity and Ah receptor function.