Cardiovascular utility of single cell RNA-Seq.

PURPOSE OF REVIEW: Cardiovascular diseases remain the leading causes of morbidity and mortality globally. Single-cell RNA sequencing has the potential to improve diagnostics, risk stratification, and provide novel therapeutic targets that have the potential to improve patient outcomes. RECENT FINDINGS: Here, we provide an overview of the basic processes underlying single-cell RNA sequencing, including library preparation, data processing, and downstream analyses. We briefly discuss how the technique has been adapted to related medical disciplines, including hematology and oncology, with short term translational impact. We discuss potential applications of this technology within cardiology as well as recent innovative research within the field. We also discuss future directions to translate this technology to other high impact clinical areas. SUMMARY: The use of single-cell RNA sequencing technology has made significant advancements in the field of cardiology, with ongoing growth in terms of applications and uptake. Most of the current research has focused on structural or atherosclerotic heart disease. Future areas that stand to benefit from this technology include cardiac electrophysiology and cardio-oncology.

Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk.

Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements. Here, we applied single-nucleus assay for transposase-accessible chromatin with sequencing to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell-type-specific elements and transcription factors, and prioritized functional CAD risk variants. We identified elements in smooth muscle cell transition states (for example, fibromyocytes) and functional variants predicted to alter smooth muscle cell- and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single-nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.

Pan-Cancer Analysis Shows TP53 Mutations Modulate the Association of NOX4 with Genetic Programs of Cancer Progression and Clinical Outcome.

Previously, we have shown TGF-ß-induced NOX4 expression is involved in the epithelial-to-mesenchymal transition (EMT), a process critical for cancer metastasis, and that wild-type (WT) and mutant (Mut) p53 have divergent effects on TGF-ß induction of NOX4: WT-p53 suppresses whereas Mut-p53 augments NOX4 mRNA and protein production in several tumor cell models. We sought to validate and extend our model by analyzing whole-exome data of primary tumor samples in The Cancer Genome Atlas (TCGA). We constructed a Pan-Cancer dataset from 23 tumor types and explored NOX4 expression patterns in relation to EMT and patient survival. NOX4 mRNA levels increase as a function of cancer progression in several cancers and correlate with Mut-p53 mRNA and genes involved in programs of EMT, cellular adhesion, migration, and angiogenesis. Tumor macrophages appear to be a source of NOX2, whose association with genetic programs of cancer progression emulate that of NOX4. Notably, increased NOX4 expression is linked to poorer survival in patients with Mut-TP53, but better survival in patients with WT-TP53. NOX4 is negatively associated with markers of apoptosis and positively with markers of proliferation in patients with Mut-TP53, consistent with their poorer survival. These findings suggest that TP53 mutations could "switch" NOX4 from being protective and an indicator of good prognosis to deleterious by promoting programs favoring cancer progression.

Novel [1,2,4]triazolo[1,5-a]pyrimidine derivatives as potent antitubulin agents: Design, multicomponent synthesis and antiproliferative activities.

As restricted CA-4 analogues, a novel series of [1,2,4]triazolo[1,5-a]pyrimidines possessing 3,4,5-trimethoxylphenyl groups has been achieved successfully via an efficient one-pot three-component reaction of 3-(3,4,5-trimethoxyphenyl)-1H-1,2,4-triazol-5-amine, 1,3-dicarbonyl compounds and aldehydes. Initial biological evaluation demonstrated some of target compounds displayed potent antitumor activity in vitro against three cancer cell lines. Among them, the most highly active analogue 26 inhibited the growth of HeLa, and A549 cell lines with IC50 values at 0.75, and 1.02 µM, respectively, indicating excellent selectivity over non-tumoural cell line HEK-293 (IC50 = 29.94 µM) which suggested that the target compounds might possess a high safety index. Moreover, cell cycle analysis illustrated that the analogue 26 significantly induced HeLa cells arrest in G2/M phase, meanwhile the compound could dramatically affect cell morphology and microtubule networks. In addition, compound 28 exhibited potent anti-tubulin activity with IC50 values of 9.90 µM, and molecular docking studies revealed the analogue occupied the colchicine-binding site of tubulin. These observations suggest that [1,2,4]triazolo[1,5-a]pyrimidines represent a new class of tubulin polymerization inhibitors and well worth further investigation aiming to generate potential anticancer agents.

Histone modifications affect differential regulation of TGFß- induced NADPH oxidase 4 (NOX4) by wild-type and mutant p53.

Previously, we showed wild-type (WT) and mutant (mut) p53 differentially regulate reactive oxygen species (ROS) generation by NADPH oxidase-4 (NOX4): p53-WT suppresses TGFß-induced NOX4, ROS and cell migration, whereas tumor-associated mut-p53 proteins enhance NOX4 expression and cell migration. Here, we extended our findings on the effects of p53 on NOX4 in several tumors and examined the basis of NOX4 transcriptional regulation by p53 and SMAD3. Statistical analysis of expression data from primary tumors available from The Cancer Genome Atlas (TCGA) detected correlations between mut-p53 and increased NOX4 expression. Furthermore, by altering p53 levels in cell culture models we showed several common tumor-associated mutant forms support TGFß/SMAD3-dependent NOX4 expression. Deletion analysis revealed two critical SMAD3 binding elements (SBE) required for mut-p53-dependent NOX4 induction, whereas p53-WT caused dose-dependent suppression of NOX4 transcription. ChIP analysis revealed SMAD3 and p53-WT or mut-p53 associate with SBEs and p53 response elements in a TGFß-dependent manner. Interestingly, the repressive effects of p53-WT on NOX4 were relieved by mutation of its transactivation domain or histone deacetylase (HDAC) inhibitor treatment. Overexpression of p300, a transcriptional co-regulator and histone acetyltransferase (HAT), enhanced p53-mediated NOX4 induction, whereas HAT-inactive p300 reduced NOX4 expression. Mut-p53 augmented TGFß-stimulated histone acetylation within the NOX4 promoter. Finally, wound assays demonstrated NOX4 and p300 promote TGFß/mut-p53-mediated cell migration. Our studies provide new insight into TGFß/SMAD3 and mut-p53-mediated NOX4 induction involving epigenetic control of NOX4 in tumor cell migration, suggesting NOX4 is a potential therapeutic target to combat tumor progression and metastasis.

Bortezomib Relieves Immune Tolerance in Nasopharyngeal Carcinoma via STAT1 Suppression and Indoleamine 2,3-Dioxygenase Downregulation.

Radiotherapy is the primary treatment for nasopharyngeal carcinoma (NPC). Patients with intermediate and advanced stage NPC receiving only radiotherapy have limited survival, so newer immunotherapeutic approaches are sought. The major impediment to better clinical outcomes is tumor immune tolerance. Indoleamine 2,3-dioxygenase (IDO), an IFNγ-inducible enzyme, is a major inducer of immune tolerance during tumor development; therefore, inhibition of the IDO pathway is an important modality for cancer treatment. We show that bortezomib, a proteasomal inhibitor, inhibited the pathways leading to STAT1 and IRF-1 activation, both of which are necessary for IDO expression. Bortezomib downregulated IFNγ-induced IDO expression via inhibition of STAT1 phosphorylation and nuclear translocation, thereby suppressing STAT1-driven IDO transcription in NPC cells. Bortezomib also promoted IκB-α phosphorylation-ubiquitination, which released NF-κB from IκB-α. However, the released NF-κB could not enter the nucleus to conduct its biological effects and accumulated in the cytoplasm. Negative feedback inhibited the transcription of NF-κB, which is important for activating IRF-1 expression. IDO expression is regulated by two important transcription factor binding sites, ISREs, which bind STAT1 and IRF-1, and GASs, which binds STAT1. Bortezomib upregulated IRF-1 protein by inhibiting its proteasome-dependent degradation, but it also inhibited STAT1 phosphorylation, which directly inhibited the activation of GAS and indirectly inhibited the activation of ISRE, which needs both STAT1 and IRF-1. These discoveries provide a mechanism for the antitumor action of bortezomib and have implications for the development of clinical cancer immunotherapy for preventing and treating NPC. Cancer Immunol Res; 5(1); 42-51. ©2016 AACR.

Phenotypic Knockout of CXCR4 Expression by a Novel Intrakine Mutant hSDF-1α/54/KDEL Inhibits Breast Cancer Metastasis.

Many malignant tumors express high levels of the chemokine receptor CXCR4, and the interaction between CXCR4 and its ligand, SDF-1, promotes migration, invasion, and metastasis of breast cancer cells. Therefore, blocking the interaction between CXCR4 and SDF-1 could alter the tumor's metastatic phenotype and control the development and progression of cancers. We used a cellular phenotypic knockout strategy and developed a novel recombinant gene, AdSDF-1α/54/KDEL, which contains an adenovirus vector, a mutant form of SDF-1 that lacks a C-terminal α-helix, and a KDEL tetrapeptide sequence that promotes retention at the endoplasmic reticulum (ER). We hypothesized that SDF-1α/54/KDEL could efficiently block metastasis of breast cancer cells with less inflammatory side effects than SDF-1α/KDEL. Using the MCF-7 cell line, which expresses a stable, high level of CXCR4, we found that SDF-1α/54/KDEL efficiently becomes localized at the ER of tumor cells, where it specifically binds to newly synthesized CXCR4 and prevents it from reaching the cell surface. Chemotaxis and invasion assays revealed that the cells treated with SDF-1α/54/KDEL failed to migrate toward SDF-1. We also found that SDF-1α/54/KDEL impaired lung metastasis of metastatic breast cancer by decreasing CXCR4 on the cell surface. The novel recombinant gene, SDF-1α/54/KDEL, played an instrumental role in blocking SDF-1/CXCR4-mediated cell migration, and we found that this gene-based strategy for targeting the SDF-1/CXCR4 axis offers a very effective alternative method for preventing metastasis of breast cancer and other cancers expressing high levels of CXCR4.

One-pot synthesis and antiproliferative activity of novel 2,4-diaminopyrimidine derivatives bearing piperidine and piperazine moieties.

A series of novel 2,4-diaminopyrimidines containing piperidine and piperazine moieties were synthesized via an efficient one-pot methodology. The bioassay tests demonstrated that compounds 27 and 28 displayed much stronger antitumor activities against four human cancer cell lines (HepG2, A549, MDA-MB-231 and MCF-7) than positive control fluorouracil. Particularly, compound 28 showed a two-fold improvement compared to fluorouracil in inhibiting MDA-MB-231 and A549 cell proliferation with IC50 values of 7.46 and 12.78 µM, respectively. Further flow-activated cell sorting analysis revealed that the most promising compound 28 displayed a significant effect on G2/M cell-cycle arrest in a dose-dependent manner in MDA-MB-231 cells.

One-pot synthesis of novel isoindoline-1,3-dione derivatives bearing 1,2,4-triazole moiety and their preliminary biological evaluation.

A series of novel isoindoline-1,3-diones containing 1,2,4-triazole moiety were synthesized via a one-pot reaction. Bioassay indicated that compounds 33, 35, 37 and 39 exhibited much higher activities against Botryodiplodia theobromae than commercial fungicide triadimefon at the dosage of 150 mg/L. Most interestingly, compounds 36, 37 and 45 displayed much stronger antitumor activities against four human cell lines than positive control Fluorouracil. Particularly, compound 37 had four-fold improvement compared to Fluorouracil in inhibiting A549 and HepG2 cell proliferation with IC(50) values of 6.76 and 9.44 µM, respectively. Further flow-activated cell sorting analysis revealed that compound 37 displayed apoptosis-inducing effect on HepG2 cells in a dose-dependent manner. These encouraging results could be helpful for the development of new antitumor compounds.

Phenotypic knockout of CXCR4 by a novel recombinant protein TAT/54R/KDEL inhibits tumors metastasis.

The chemokine receptor, CXCR4, and its specific ligand, CXCL12, have been proven to regulate the directional trafficking and invasion of breast cancer cells to sites of metastases, and similar phenomena have also been identified in many malignant tumors that aberrantly overexpress CXCR4. Therefore, blocking the interaction between CXCR4 and CXCL12 is considered a possible approach to efficiently prevent cancer metastasis. Employing a cellular phenotypic knockout strategy based on intrakines, we developed a novel recombinant chimeric protein, TAT/54R/KDEL, which contains three distinct functional domains: CXCL12/54R, a mutant of CXCL12 with CXCR4 antagonism, as well as HIV-derived TAT (47-57) and an endoplasmic reticulum retention four-peptide sequence KDEL that links at its NH(2) and COOH termini, respectively. Using the MOLT-4 cell line, which expressed CXCR4 highly and stably in vitro, we determined that TAT/54R/KDEL was able to efficiently transfer into the endoplasmic reticulum of tumor cells, where it specifically binds to the newly synthesized CXCR4 and prevents the latter from reaching the surface. Chemotaxis assays showed that the cells treated with TAT/54R/KDEL failed to migrate toward CXCL12. Furthermore, we observed that the systemic treatment of TAT/54R/KDEL could impair lung metastasis in a highly metastatic mammary cancer cell line, 4T1 cells, with the decrease of CXCR4 on their membrane. Our results suggest that the phenotypic knockout strategy of CXCR4 using a novel recombinant protein TAT/54R/KDEL might be a possible approach for inhibiting relative tumor metastasis mediated by CXCR4/CXCL12 interaction.

A novel recombinant protein TAT-GFP-KDEL with dual-function of penetrating cell membrane and locating at endoplasm reticulum.

Although the potential value of phenotypic/functional knockout technology with intrabody/kine in prevention and cure of some serious diseases, such as AIDS and cancer, is being regarded, there are still several technical difficulties. One of the the most critical problems is how to directly deliver the intrabody/kine proteins into endoplasm reticulum (ER). In this study, a novel recombinant protein, TAT-GFP-KDEL, was designed and constructed. In this recombinant protein, HIV-derived TAT (47-57) and an ER retention four-peptide sequence KDEL were fused at the N-terminal and C-terminal of GFP respectively. The results showed that TAT-GFP-KDEL had been successfully expressed in bacteria BL21 and its purity reached to 95%. Moreover, we observed that this recombinant protein was able to efficiently transduce into MOLT-4 cells and accurately locate at ER. This study may provide an available strategy to promote the transmembrane delivery and ER localization of protein-based intrabody/kine.

[Preliminary study on molecular mechanism of curcumine anti-mouse melanoma].

OBJECTIVE: To investigate the effects of curcumine on mouse B16 melanoma growth and possible mechanism of Bcl-2, P53 and glutathione in tumor cells. METHODS: The inhibitory effect on growth of melanoma in vivo were examined by mice melanoma models transplanted B16 cells to C57BL/6J mice. MTT method was used to assay the contribution of curcumine to B16 cells in vitro. The apoptosis and expression of Bcl-2, P53 gene of B16 cells were analyzed by flow cytometry, and HPLC assay was used to detect the change of GSH in B16 melanom tissues of C57BL/6J mouse caused by curcumine. RESULTS: Curcumine had obvious inhibitory effect on the growth of mouse B16 melanoma in time and dose dependent manner and the gene expression of bcl-2 in B16 cells decreased after 24 hours supplied with curcumine, whereas P53 protein expression increased; Curcumine depressed the GSH quantity in melanoma tissues. CONCLUSION: The growth inhibitory effect of curcumine on mouse melanom is proved in vivo and in vitro respectively. Curcumine can induce some cells to apoptosis which may be relevant to downregulation of bcl-2 expression and upregulation of P53 expression as well as exhaustion of GSH in tumor organization.