Dayue Darrel Duan

Stable angina pectoris (SAP) is a common risk factor for myocardial infarction and death. The genomic, transcriptomic, and phenomic heterogeneities of SAP require combination therapies. Multi-target drugs with fixed doses are emerging as scalable and promising prevention and therapeutic strategies for SAP. However, the identification of targets and underlying mechanisms of multi-target drugs for optimal clinical efficacy remains insurmountable. Here, we report a modular phenome-wide association study (MoPheWAS) of Danhong Injection (DHI), a clinically proven effective anti-SAP drug. The interrelated multitargets of DHI were divided into 32 On-modules . Eleven clinical SAP phenotypes defined by the Seattle Angina Questionnaire and serum lipids were interactively associated with 14 DHI efficacy-related Phe-modules. The intrinsic polymorphic associations between SAP phenotypes and Phe-modules manifested systematic positive/negative regulation of specific one-to-one as well as complex many-to-many relationships. These Phe-modules were conserved, transformed, or newly emerged modules involving G-protein-coupled receptor signaling and kinase binding. In vitro RNAi analysis confirmed the hub genes GALR1/BCMO1 in Mod-29 as multiple targets for the anti-ischemic effect of DHI. The landscape of modular regulators and polymorphic phenomic associations revealed the multi-target mechanisms underlying the therapeutic heterogeneity of SAP. Therefore, MoPheWAS may provides a novel systematic paradigm for identifying multiple phenomic targets of complex polygenic diseases.

Colorectal cancer (CRC) is characterized by an immunosuppressive and inflammatory microenvironment, thus responds poorly to therapy. Previous studies show that norcantharidin (NCTD), a demethylated cantharidin (CTD) derived from Mylabris, exerts high efficacy in treating various cancers. In this study we investigated the antitumor effects of NCTD against CRC and the underlying mechanisms. Subcutaneous CRC models were established in balb/c mice using mouse colorectal cancer cell line CT26 and in balb/c nude mice using human colorectal cancer cell line HCT116. The mice were administered NCTD (2 or 4 mg·kg⁻¹·d⁻¹, i.p.) for 14 days. We showed that NCTD dose-dependently reduced the tumor growth in both the CRC models. Furthermore, NCTD markedly increased M1 macrophage infiltration in tumor tissue in both the CRC models. NCTD-induced macrophage M1 polarization was confirmed by flow cytometry and qPCR assays in both THP-1 cell-derived and RAW264.7 macrophage models in vitro. We demonstrated that NCTD (20, 40 μM) dose-dependently increased CSF2 secretion from CRC cells and macrophages, and suppressed the JAK2/STAT3 signaling pathway in CRC cells. Concurrently, NCTD (10–40 μM) dose-dependently inhibited CRC cell proliferation, invasion and migration in vitro. In conclusion, this study provides new evidence for the effects of NCTD against CRC and elucidates its antitumor mechanisms through remodeling the inflammatory microenvironment via CSF2-mediated macrophage M1 polarization and inhibiting JAK2/STAT3 phosphorylation in CRC cells.

To characterize serum microRNA (miR) and the miR interactome of active RA patients in RA aetiology and pathogenesis. The differentially expressed miRs (DEmiRs) in serum of naïve active RA patients (NARAPs, n = 9, into three pools) vs healthy controls (HCs, n = 15, into five pools) were identified with Agilent human miR microarray analysis. Candidate driver genes in epigenetic and pathogenic signalling pathway modules for RA were analysed using miRTarBase and a molecular complex detection algorithm. The interactome of these DEmiRs in RA pathogenesis were further characterized with gene ontology and Kyoto Encyclopaedia of Genes and Genomes. Three upregulated DEmiRs (hsa-miR-187-5p, -4532, -4516) and eight downregulated DEmiRs (hsa-miR-125a-3p, -575, -191-3p, -6865-3p, -197-3p, -6886-3p, -1237-3p, -4436b-5p) were identified in NARAPs. Interactomic analysis from heterogeneous experimentally validated sources yielded 1719 miR–target interactions containing 5.67% strong and 94.33% less strong experimental evidence. Gene ontology and Kyoto Encyclopaedia of Genes and Genomes analyses allocated the upregulated DEmiRs in the infection modules and the downregulated DEmiRs in the immune signalling pathways. Specifically, these DEmiRs revealed the significant contributions of the intestinal microbiome dysbiosis in the infection–inflammation–immune network for activation of T cells, immune pathways of IL-17, Toll-like receptor, TNF, Janus kinase-signal transducer and activator of transcription, osteoclast cell differentiation pathway and IgA production to the active RA pathogenesis. Our experiment-based interactomic study of DEmiRs in serum of NARAPs revealed novel clinically relevant miRs interactomes in the infection–inflammation–immune network of RA. These results provide valuable resources for understanding the integrated function of the miR network in RA pathogenesis and the application of circulating miRs as biomarkers for early aetiologic RA diagnosis.

Tumor cells produce and secrete more nucleic acids, proteins and lipids than normal cells. These molecules are transported in the blood or around the cells in membrane-encapsulated exosomes. Tumor-derived or tumor-associated exosomes (usually 30–100 nm in diameter) contain abundant biological contents resembling those of the parent cells along with signaling messengers for intercellular communication involved in the pathogenesis, development, progression, and metastasis of cancer. As these exosomes can be detected and isolated from various body fluids, they have become attractive new biomarkers for the diagnosis and prognosis of cancer. Furthermore, tumor exosomes have also attracted increasing attention due to their potential as novel therapeutic strategies for the treatment of cancers. On the one hand, the lipid bilayer membrane-encapsulated vesicles are promising carriers of drugs and other therapeutic materials targeting specific cancer cells. On the other hand, tumor exosomes are important mediators for modulation of the microenvironment that orchestrates events critical to the growth and metastasis of cancer cells as well as chemoresistance. Here, we summarize the advances in our understanding of tumor-associated or tumor-derived exosomes in recent years, and discuss their roles in cancer development, progression, invasion, and metastasis of cancers and, more importantly, their potential in strategies for precision therapy of various cancers as well as important caveats.

Abstract: Vascular diseases are usually caused by multifactorial pathogeneses involving genetic and environmental factors. Our current understanding of vascular disease is, however, based on the focused genotype/phenotype studies driven by the “one-gene/one-phenotype” hypothesis. Drugs with “pure target” at individual molecules involved in the pathophysiological pathways are the mainstream of current clinical treatments and the basis of combination therapy of vascular diseases. Recently, the combination of genomics, proteomics, and metabolomics has unraveled the etiology and pathophysiology of vascular disease in a big-data fashion and also revealed unmatched relationships between the omic variability and the much narrower definition of various clinical phenotypes of vascular disease in individual patients. Here, we introduce the phenomics strategy that will change the conventional focused phenotype/genotype/genome study to a new systematic phenome/genome/proteome approach to the understanding of pathophysiology and combination therapy of vascular disease. A phenome is the sum total of an organism’s phenotypic traits that signify the expression of genome and specific environmental influence. Phenomics is the study of phenome to quantitatively correlate complex traits to variability not only in genome, but also in transcriptome, proteome, metabolome, interactome, and environmental factors by exploring the systems biology that links the genomic and phenomic spaces. The application of phenomics and the phenome-wide associated study (PheWAS) will not only identify a systemically-integrated set of biomarkers for diagnosis and prognosis of vascular disease but also provide novel treatment targets for combination therapy and thus make a revolutionary paradigm shift in the clinical treatment of these devastating diseases.