The role of the oral microbiome in obesity and metabolic disease: potential systemic implications and effects on taste perception

Obesity and its metabolic sequelae still comprise a challenge when it comes to understanding mechanisms, which drive these pandemic diseases. The human microbiome as a potential key player has attracted the attention of broader research for the past decade. Most of it focused on the gut microbiome while the oral microbiome has received less attention. As the second largest niche, the oral microbiome is associated with a multitude of mechanisms, which are potentially involved in the complex etiology of obesity and associated metabolic diseases. These mechanisms include local effects of oral bacteria on taste perception and subsequent food preference as well as systemic effects on adipose tissue function, the gut microbiome and systemic inflammation. This review summarizes a growing body of research, pointing towards a more prominent role of the oral microbiome in obesity and associated metabolic diseases than expected. Ultimately, our knowledge on the oral microbiome may support the development of new patient oriented therapeutic approaches inevitable to relieve the health burden of metabolic diseases and to reach long-term benefits in patients´ lives.

Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells

The cyclin-dependent kinase 1 (Cdk1) drives cell division. To uncover additional functions of Cdk1, we generated knockin mice expressing an analog-sensitive version of Cdk1 in place of wild-type Cdk1. In our study, we focused on embryonic stem cells (ESCs), because this cell type displays particularly high Cdk1 activity. We found that in ESCs, a large fraction of Cdk1 substrates is localized on chromatin. Cdk1 phosphorylates many proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. Consistent with these findings, inhibition of Cdk1 altered histone-modification status of ESCs. High levels of Cdk1 in ESCs phosphorylate and partially inactivate Dot1l, the H3K79 methyltransferase responsible for placing activating marks on gene bodies. Decrease of Cdk1 activity during ESC differentiation de-represses Dot1l, thereby allowing coordinated expression of differentiation genes. These analyses indicate that Cdk1 functions to maintain the epigenetic identity of ESCs.

JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia

A substantial subset of patients with T cell acute lymphoblastic leukemia (T-ALL) develops resistance to steroids and succumbs to their disease. JDP2 encodes a bZIP protein that has been implicated as a T-ALL oncogene from insertional mutagenesis studies in mice, but its role in human T-ALL pathogenesis has remained obscure. Here we show that JDP2 is aberrantly expressed in a subset of T-ALL patients and is associated with poor survival. JDP2 is required for T-ALL cell survival, as its depletion by short hairpin RNA knockdown leads to apoptosis. Mechanistically, JDP2 regulates prosurvival signaling through direct transcriptional regulation of MCL1. Furthermore, JDP2 is one of few oncogenes capable of initiating T-ALL in transgenic zebrafish. Notably, thymocytes from rag2:jdp2 transgenic zebrafish express high levels of mcl1 and demonstrate resistance to steroids in vivo. These studies establish JDP2 as a novel oncogene in high-risk T-ALL and implicate overexpression of MCL1 as a mechanism of steroid resistance in JDP2-overexpressing cells.

Cell-Cycle-Targeting MicroRNAs as Therapeutic Tools against Refractory Cancers

Cyclins and cyclin-dependent kinases (CDKs) are hyperactivated in numerous human tumors. To identify means of interfering with cyclins/CDKs, we performed nine genome-wide screens for human microRNAs (miRNAs) directly regulating cell-cycle proteins. We uncovered a distinct class of miRNAs that target nearly all cyclins/CDKs, which are very effective in inhibiting cancer cell proliferation. By profiling the response of over 120 human cancer cell lines, we derived an expression-based algorithm that can predict the response of tumors to cell-cycle-targeting miRNAs. Using systemic administration of nanoparticle-formulated miRNAs, we inhibited tumor progression in seven mouse xenograft models, including three treatment-refractory patient-derived tumors, without affecting normal tissues. Our results highlight the utility of using cell-cycle-targeting miRNAs for treatment of refractory cancer types.

Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy. BET bromodomain inhibitors, which have shown efficacy in several models of cancer, have not been evaluated in TNBC. These inhibitors displace BET bromodomain proteins such as BRD4 from chromatin by competing with their acetyl-lysine recognition modules, leading to inhibition of oncogenic transcriptional programs. Here we report the preferential sensitivity of TNBCs to BET bromodomain inhibition in vitro and in vivo, establishing a rationale for clinical investigation and further motivation to understand mechanisms of resistance. In paired cell lines selected for acquired resistance to BET inhibition from previously sensitive TNBCs, we failed to identify gatekeeper mutations, new driver events or drug pump activation. BET-resistant TNBC cells remain dependent on wild-type BRD4, which supports transcription and cell proliferation in a bromodomain-independent manner. Proteomic studies of resistant TNBC identify strong association with MED1 and hyper-phosphorylation of BRD4 attributable to decreased activity of PP2A, identified here as a principal BRD4 serine phosphatase. Together, these studies provide a rationale for BET inhibition in TNBC and present mechanism-based combination strategies to anticipate clinical drug resistance.

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

Neuroblastoma is a paediatric malignancy that typically arises in early childhood, and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumours with excellent outcomes to widely metastatic disease in which long-term survival is approximately 40% despite intensive therapy. A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumour cells. Here we investigate the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation and transcription factor binding sites. We show that SNP rs2168101 G>T is the most highly associated variant (combined P = 7.47 × 10(-29), odds ratio 0.65, 95% confidence interval 0.60-0.70), and resides in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumour formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P = 0.028) in neuroblastoma primary tumours, and ablates GATA3 binding (P < 0.0001). We demonstrate allelic imbalance favouring the G-containing strand in tumours heterozygous for this SNP, as demonstrated both by RNA sequencing (P < 0.0001) and reporter assays (P = 0.002). These findings indicate that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumour cells.

Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

In certain human cancers, the expression of critical oncogenes is driven from large regulatory elements, called super-enhancers, that recruit much of the cell's transcriptional apparatus and are defined by extensive acetylation of histone H3 lysine 27 (H3K27ac). In a subset of T-cell acute lymphoblastic leukemia (T-ALL) cases, we found that heterozygous somatic mutations are acquired that introduce binding motifs for the MYB transcription factor in a precise noncoding site, which creates a super-enhancer upstream of the TAL1 oncogene. MYB binds to this new site and recruits its H3K27 acetylase-binding partner CBP, as well as core components of a major leukemogenic transcriptional complex that contains RUNX1, GATA-3, and TAL1 itself. Additionally, most endogenous super-enhancers found in T-ALL cells are occupied by MYB and CBP, which suggests a general role for MYB in super-enhancer initiation. Thus, this study identifies a genetic mechanism responsible for the generation of oncogenic super-enhancers in malignant cells.

Cyclin D1 represses gluconeogenesis via inhibition of the transcriptional coactivator PGC1α

Hepatic gluconeogenesis is crucial to maintain normal blood glucose during periods of nutrient deprivation. Gluconeogenesis is controlled at multiple levels by a variety of signal transduction and transcriptional pathways. However, dysregulation of these pathways leads to hyperglycemia and type 2 diabetes. While the effects of various signaling pathways on gluconeogenesis are well established, the downstream signaling events repressing gluconeogenic gene expression are not as well understood. The cell-cycle regulator cyclin D1 is expressed in the liver, despite the liver being a quiescent tissue. The most well-studied function of cyclin D1 is activation of cyclin-dependent kinase 4 (CDK4), promoting progression of the cell cycle. We show here a novel role for cyclin D1 as a regulator of gluconeogenic and oxidative phosphorylation (OxPhos) gene expression. In mice, fasting decreases liver cyclin D1 expression, while refeeding induces cyclin D1 expression. Inhibition of CDK4 enhances the gluconeogenic gene expression, whereas cyclin D1-mediated activation of CDK4 represses the gluconeogenic gene-expression program in vitro and in vivo. Importantly, we show that cyclin D1 represses gluconeogenesis and OxPhos in part via inhibition of peroxisome proliferator-activated receptor γ coactivator-1α (PGC1α) activity in a CDK4-dependent manner. Indeed, we demonstrate that PGC1α is novel cyclin D1/CDK4 substrate. These studies reveal a novel role for cyclin D1 on metabolism via PGC1α and reveal a potential link between cell-cycle regulation and metabolic control of glucose homeostasis.

Abstract 3230: Genome-wide localization of anti-cancer drugs

A vast number of small-molecule ligands, including therapeutic drugs under development and in clinical use, elicit their effects by binding specific proteins associated with the genome. An ability to map the direct interactions of a chemical entity with chromatin genome-wide could provide new and important insights into the mechanisms by which such small molecules interfere with tumor cell functions. We have developed a method that couples affinity capture of chemical entities and massively parallel DNA sequencing (Chem-seq) to identify the sites bound by small molecules throughout the human genome. Using Chem-seq, we have uncovered the full repertoire of the genomic sites bound by a BET bromodomain inhibitor, a cyclin-dependent kinase (CDK) inhibitor and a DNA intercalating drug. Moreover, by combining Chem-seq with ChIP-seq, we have characterized the interactions of drugs with their targets throughout the genome of tumor cells. These methods provide a powerful approach to enhance understanding of therapeutic action and characterize the specificity of drugs that interact with DNA or genome-associated proteins.

Citation Format: Lars Anders, Matthew G. Guenther, Jun Qi, Zi Peng Fan, Jason J. Marineau, Peter B. Rahl, Jakob Lovén, Alla A. Sigova, William B. Smith, Tong Ihn Lee, James E. Bradner, Richard A. Young. Genome-wide localization of anti-cancer drugs. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3230. doi:10.1158/1538-7445.AM2014-3230

D-cyclins repress apoptosis in hematopoietic cells by controlling death receptor Fas and its ligand FasL

D-type cyclins (D1, D2, and D3) are components of the mammalian core cell-cycle machinery and function to drive cell proliferation. Here, we report that D-cyclins perform a rate-limiting antiapoptotic function in vivo. We found that acute shutdown of all three D-cyclins in bone marrow of adult mice resulted in massive apoptosis of all hematopoietic cell types. We demonstrate that adult hematopoietic stem cells are particularly dependent on D-cyclins for survival and that they are especially sensitive to cyclin D loss. Surprisingly, we found that the antiapoptotic function of D-cyclins also operates in quiescent hematopoietic stem and progenitor cells. Our analyses revealed that D-cyclins repress the expression of the death receptor Fas and its ligand, FasL. Acute ablation of D-cyclins upregulated these proapoptotic genes and led to Fas- and caspase 8-dependent apoptosis. These results reveal an unexpected function of cell-cycle proteins in controlling apoptosis in normal cell homeostasis.

Genome-wide localization of small molecules

A vast number of small-molecule ligands, including therapeutic drugs under development and in clinical use, elicit their effects by binding specific proteins associated with the genome. An ability to map the direct interactions of a chemical entity with chromatin genome-wide could provide important insights into chemical perturbation of cellular function. Here we describe a method that couples ligand-affinity capture and massively parallel DNA sequencing (Chem-seq) to identify the sites bound by small chemical molecules throughout the human genome. We show how Chem-seq can be combined with ChIP-seq to gain unique insights into the interaction of drugs with their target proteins throughout the genome of tumor cells. These methods will be broadly useful to enhance understanding of therapeutic action and to characterize the specificity of chemical entities that interact with DNA or genome-associated proteins.

A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells

Cyclin D-dependent kinases (CDK4 and CDK6) are positive regulators of cell cycle entry and they are overactive in the majority of human cancers. However, it is currently not completely understood by which cellular mechanisms CDK4/6 promote tumorigenesis, largely due to the limited number of identified substrates. Here we performed a systematic screen for substrates of cyclin D1-CDK4 and cyclin D3-CDK6. We identified the Forkhead Box M1 (FOXM1) transcription factor as a common critical phosphorylation target. CDK4/6 stabilize and activate FOXM1, thereby maintain expression of G1/S phase genes, suppress the levels of reactive oxygen species (ROS), and protect cancer cells from senescence. Melanoma cells, unlike melanocytes, are highly reliant on CDK4/6-mediated senescence suppression, which makes them particularly susceptible to CDK4/6 inhibition.

Furin-, ADAM 10-, and gamma-secretase-mediated cleavage of a receptor tyrosine phosphatase and regulation of beta-catenin's transcriptional activity

Several receptor protein tyrosine phosphatases (RPTPs) are cell adhesion molecules involved in homophilic interactions, suggesting that RPTP outside-in signaling is coupled to cell contact formation. However, little is known about the mechanisms by which cell density regulates RPTP function. We show that the MAM family prototype RPTPkappa is cleaved by three proteases: furin, ADAM 10, and gamma-secretase. Cell density promotes ADAM 10-mediated cleavage and shedding of RPTPkappa. This is followed by gamma-secretase-dependent intramembrane proteolysis of the remaining transmembrane part to release the phosphatase intracellular portion (PIC) from the membrane, thereby allowing its translocation to the nucleus. When cells were treated with leptomycin B, a nuclear export inhibitor, PIC accumulated in nuclear bodies. PIC is an active protein tyrosine phosphatase that binds to and dephosphorylates beta-catenin, an RPTPkappa substrate. The expression of RPTPkappa suppresses beta-catenin's transcriptional activity, whereas the expression of PIC increases it. Notably, this increase required the phosphatase activity of PIC. Thus, both isoforms have acquired opposing roles in the regulation of beta-catenin signaling. We also found that RPTPmu, another MAM family member, undergoes gamma-secretase-dependent processing. Our results identify intramembrane proteolysis as a regulatory switch in RPTPkappa signaling and implicate PIC in the activation of beta-catenin-mediated transcription.

Quantitative analysis of MRI signal intensity as a tool for evaluating tooth pulp vitality

OBJECTIVES

To assess whether it is possible to measure tooth vitality using magnetic resonance imaging (MRI).

METHODS

Signal intensity measurements were conducted using T(1) and T(2) sequences at the region of interest in 211 teeth (35 patients).

RESULTS

Clinical findings showed that 17.3% of the teeth were avital, whereas 82.7% were found to be vital. Neither the T(2) sequence nor the non-contrast-enhanced T(1) sequence showed significant differences between vital and avital teeth. However, the contrast-enhanced sequence and, in particular, a comparison of signal intensities between the non-contrast-enhanced T(1) sequence and the contrast-enhanced sequence showed a significant difference between vital and avital teeth.

CONCLUSION

Contrast-enhanced MRI enables us to draw conclusions on pulpal perfusion in vivo.

High-resolution dental magnetic resonance imaging of inferior alveolar nerve responses to the extraction of third molars

The objective of this study was to assess whether signal changes can be detected in the neurovascular bundle of the mandibular canal after the extraction of a third molar. We retrospectively analyzed MRI scans of 30 test subjects with healthy mandibles and 41 patients who had had a wisdom tooth extracted. Signal intensities were measured at particular sites in the neurovascular bundle, which were defined as regions of interest (ROI) in the sagittal T1-weighted images before and after intravenous administration of a paramagnetic contrast agent. On the basis of the signal intensity increases that were measured after contrast agent administration, we compared the signal increases obtained for the patients who had received surgical treatment with the results obtained for the population of test subjects with unremarkable mandibles ( t-test, P<0.05). Compared with the healthy test subjects, patients who had received surgical treatment showed significantly higher signal intensity increases at two measurement sites, i.e., the second molar and the second premolar ( P<0.05). We found no significant differences when the measurements were performed at the first molar ( P=0.06), the third molar ( P=0.47) and in the area of the ascending mandibular ramus ( P=0.79). Compared with a population of healthy test subjects, patients who had their third molars surgically removed show higher signal intensity increases in the neurovascular bundle after intravenous contrast agent administration. The underlying cause may be the higher blood flow in the arteries and veins and the perineural plexus, which may give evidence of the pathophysiological mechanism of nerve damage in the narrow canal as a result of osteotomy.

[Quantitative analysis of contrast enhanced MRI of the inferior alveolar nerve in inflammatory changes of the mandible]

PURPOSE

To evaluate the role of contrast enhanced MRI in quantifying signal changes of the inferior alveolar nerve following inflammatory changes of the mandible.

MATERIAL AND METHODS

30 patients with inflammatory changes of the mandible underwent MRI of the face. Both sides of the mandible, the affected as well as the unaffected healthy side were evaluated retrospectively. Regions of interest were placed at 5 defined places on both sides to assess signal intensity before and after intravenous application of paramagnetic contrast agent. The results of the measurements were compared between the healthy and the affected side (t-test, p < 0.05) and correlated with clinical findings (t-test, p < 0.05).

RESULTS

All patients with hypesthesia of the inferior alveolar nerve in areas of the lips or chin (n = 4) showed a marked increase in signal intensity from 35 % to 83 % distal to the inflammatory process. Patients without sensitivity disorders showed less increase in signal intensity with a maximum of 51 % distal to the inflammatory process. In nearly all patients no contrast enhancement was observed distal to the first molar on the unaffected side.

CONCLUSIONS

Quantitative analysis of contrast enhanced MRI of the neurovascular bundle is able to show pathologic mandibular lesions. In case of inflammatory changes of the mandible the neurovascular bundle is able to show pathologic mandibular lesions. In case of inflammatory changes of the mandible, the neurovascular bundle shows a significant increase in signal intensity distal to the lesion compared to the unaffected healthy side of the mandible.

High-resolution MR technique allowing visualization of the course of the inferior alveolar nerve along cystic processes

Magnetic resonance imaging is not established in the preoperative diagnosis of mandibular cystic lesions; therefore, no attempts have been made thus far to evaluate the course of the mandibular neurovascular bundle along the process. However, the radiologist can detect the neurovascular bundle along the cystic lesion by high-resolution MR imaging and convey this information to the maxillofacial surgeon. This reduces the risk of intraoperative damage of the nerve. The examination of the neurovascular bundle can easily be integrated in a tumor MRI protocol of the jaw if the slice orientation is adapted to the course of the mandibular canal.

[Topography of the inferior alveolar nerve in relation to cystic processes of the mandible in dental MRI]

PURPOSE

Cystic processes are changing the course of the inferior alveolar nerve in the mandible. This study evaluates the possibility of demonstrating the relationship between space-occupying processes and the course of the neurovascular bundle.

MATERIALS AND METHODS

Thirteen patients with cystic processes in the mandible (9 keratocystic lesions, 1 eosinophilic granuloma, 1 plasmocytoma, 2 adamantinomas) were examined by MRI (1.5-T magnet, 8-cm surface coil, PD-gradient-echo-sequences in sagittal and coronal orientation, without enhancement) and the results retrospectively evaluated.

RESULTS

The entire course of the nerve could be delineated in all patients. In six patients with minor cystic processes, the nerve was identified in both sagittal and coronal orientation. In seven patients with major cystic lesions, only parts of the nerve were detected in either image orientation, but the nerve could be visualized in its entire length by evaluating coronal and sagittal images side by side.

CONCLUSION

It is possible to delineate the inferior alveolar nerve in its entirety along pathologic mandibular lesions. For large cystic lesions, this requires the evaluation of both coronal and sagittal sections of multidirectional MRI.

Experimental and comparative study of the blood supply to the mandibular cortex in Göttingen minipigs and in man

INTRODUCTION

Since the blood supply to the mandibular cortex is an important factor for bone growth and bone repair, experimental studies on the blood supply in animal models (such as Göttingen minipigs) applicable to man are necessary. Their value depends on the requirement that the patterns of blood supply in the two species are similar.

MATERIAL AND METHODS

Twelve Göttingen minipig mandibles (24 halves) and four human mandibles (eight halves) were investigated for the blood supply to the mandibular cortex.

RESULTS

Only minor differences were found in blood supply to the mandibular cortex between the two species. Common to both was: in the cranial part of the mandible (including the condyle), the endosteal blood supply prevailed, whereas the periosteal blood supply predominated in the caudal part of the mandible (the body). Both patterns of blood supply were in balance in the centre section, i.e. angle and ascending ramus of the mandible.

CONCLUSION

The present study confirms that results obtained from Göttingen minipigs, used as an experimental animal model, are applicable to man: three different types of blood supply are evident in the mandibular cortex in both species.

Blood supply of the mandibular cortex: an experimental study in Göttingen minipigs with special reference to the condyle

INTRODUCTION

Blood supply of the mandible is an important factor that influences bone growth and bone repair.

MATERIAL AND METHODS

An experimental study was carried out in 24 mandibles of 12 Göttingen minipigs to study the blood supply of the mandibular cortex.

RESULTS

Endosteal blood supply prevails in the cranial part of the mandible including the condyle, whilst periosteal blood supply predominates in the caudal part of the mandible, the body. The two forms of blood supply are in balance in the ascending ramus and the angle of the mandible.

CONCLUSION

The mandibular cortex can be divided into three parts, each having different sources of blood supply. The results of this study may be of significance for man and could help to understand some pathological disorders of the mandible.