Application of proteomics in research on traditional Chinese medicine

An herbal formula Shenlian decoction upregulates M1/M2 macrophage proportion in hepatocellular carcinoma by suppressing complement cascade

The immunosuppressive microenvironment is a vital factor for the hepatocellular carcinoma (HCC) progression. However, effective treatment is lacking at current. Shenlian decoction (SLD) is a registered herbal therapy for the HCC treatment, but the underlying mechanism of SLD remains largely elusive. Here, we aimed to explore the anti-tumor effect of SLD in the treatment of HCC. SLD was intragastrically given after the tumor initiation in β-catenin/C-Met or DEN and CCl4 induced HCC mouse model. The tumor growth levels were evaluated by liver weight and histological staining. The tumor-infiltrating immune cells were detected by immunological staining and flow cytometry. The mechanism of the SLD was detected by non-targeted proteomics and verified by a cell co-culture system. The result showed that SLD significantly attenuated HCC progression. SLD promoted macrophage infiltration and increased the M1/M2 macrophage ratio within the tumor tissues. Non-targeted proteomics showed the inhibition of complement C5/C5a signaling is the key mechanism of SLD. Immunological staining showed SLD inhibited C5/C5a expression and C5aR1+ macrophage infiltration. The suggested mechanism was demonstrated by application of C5aR1 inhibitor, PMX-53 in mouse HCC model. Hepatoma cell-macrophage co-culture showed SLD targeted hepatoma cells and inhibited the supernatant-induced macrophage M2 polarization. SLD inhibited AMPK/p38 signaling which is an upstream mechanism of C5 transcription. In conclusion, we found SLD relieved immune-suppressive environment by inhibiting C5 expression. SLD could suppress the C5 secretion in hepatoma cells via inhibition of AMPK/p38 signaling. We suggested that SLD is a potential herbal therapy for the treatment of HCC by alleviating immune-suppressive status.

Tandem mass tag-based quantitative proteomics analyses of the spermatogenesis-ameliorating effect of Youjing granule on rats

RATIONALE

Male infertility is a common reproductive system disease manifested as aberrant spermatogenesis and identified as "kidney deficiency and dampness" in Chinese traditional medicine. Youjing granule (YG) is a Chinese material medica based on tonifying kidneys and removing dampness. It has proven to be able to regulate semen quality in clinical application, but the underlying mechanism has not been clarified.

METHODS

Using serum containing YG to treat primarily cultured spermatogonial stem cells (SSCs), the apoptotic rate and mitosis phase ratio of SSCs were measured. The liquid chromatography-tandem mass spectrometry with tandem mass tags method was applied for analyzing the serum of rats treated with YG/distilled water, and proteomic analyses were performed to clarify the mechanisms of YG.

RESULTS

Totally, 111 proteins in YG-treated serum samples were differentially expressed compared with control groups, and 43 of them were identified as potential target proteins, which were further annotated based on their enrichment in Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. Proteomic analyses showed that the mechanisms of YG may involve regulation of glycolysis, gluconeogenesis and nucleotide-binding and oligomerization domain-like receptor signaling pathway. In addition, RhoA and Lamp2 were found to be possible responders of YG through reviewing the literature.

CONCLUSIONS

The results demonstrate that our serum proteomics platform is clinically useful in understanding the mechanisms of YG.

From Xiaoke to diabetes mellitus: a review of the research progress in traditional Chinese medicine for diabetes mellitus treatment

Diabetes mellitus (DM) is a chronic metabolic disorder characterized by hyperglycemia resulting from insulin secretion defects or insulin resistance. The global incidence of DM has been gradually increasing due to improvements in living standards and changes in dietary habits, making it a major non-communicable disease that poses a significant threat to human health and life. The pathogenesis of DM remains incompletely understood till now, and current pharmacotherapeutic interventions are largely inadequate, resulting in relapses and severe adverse reactions. Although DM is not explicitly mentioned in traditional Chinese medicine (TCM) theory and clinical practice, it is often classified as "Xiaoke" due to similarities in etiology, pathogenesis, and symptoms. With its overall regulation, multiple targets, and personalized medication approach, TCM treatment can effectively alleviate the clinical manifestations of DM and prevent or treat its complications. Furthermore, TCM exhibits desirable therapeutic effects with minimal side effects and a favorable safety profile. This paper provides a comprehensive comparison and contrast of Xiaoke and DM by examining the involvement of TCM in their etiology, pathogenesis, treatment guidelines, and other relevant aspects based on classical literature and research reports. The current TCM experimental research on the treatment of DM by lowering blood glucose levels also be generalized. This innovative focus not only illuminates the role of TCM in DM treatment, but also underscores the potential of TCM in DM management.

Mechanisms of the Ping-wei-san plus herbal decoction against Parkinson's disease: Multiomics analyses

Introduction

Parkinson's disease is a neurodegenerative disorder involving loss of dopaminergic neurons. Multiple studies implicate the microbiota-gut-brain axis in Parkinson's disease pathophysiology. Ping-wei-san plus Herbal Decoction, a traditional Chinese medicine composition with beneficial effects in Parkinson's disease, may have a complex array of actions. Here we sought to determine whether gut microbiota and metabolic pathways are involved in Ping-wei-san plus herbal therapy for Parkinson's disease and to identify functional pathways to guide research.

Methods and results

The model of Parkinson's disease were induced with the rotenone. The Ping-wei-san plus group received the PWP herbal decoction for 90 days, after which all groups were analyzed experimentally. PWP herbal treatment improved motor behavior and emotional performance, balanced gut microbiota, and benefited dietary metabolism. Tandem Mass Tags mass spectrometry identified many differentially expressed proteins (DEPs) in the substantia nigra and duodenum in the PWP group, and these DEPs were enriched in pathways such as those involving cAMP signaling, glutamatergic synapses, dopaminergic synapses, and ribosome-rich functions in the gut. The PWP group showed increases in recombinant tissue inhibitors of metalloproteinase 3, and nucleotide-binding oligomerization domain, leucine rich repeat, and pyrin domain containing proteins 6 in the substantia nigra and decreased parkin, gasdermin D, recombinant tissue inhibitors of metalloproteinase 3, and nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing proteins 6 in the duodenum.

Discussion

In conclusion, this study combined gut microbiota, metabolomics, and proteomics to evaluate the mechanism of action of Ping-wei-san plus on Parkinson's disease and revealed that PWP herbal treatment modulated gut microbiota, altered metabolite biological pathways, and affected functional pathway protein expression in Parkinson's disease mice, resulting in therapeutic effects.

Exploring the comorbidity mechanisms between asthma and idiopathic pulmonary fibrosis and the pharmacological mechanisms of Bu-Shen-Yi-Qi decoction therapy via network pharmacology

Backgrounds

Asthma and idiopathic pulmonary fibrosis (IPF) are common chronic diseases of the respiratory system in clinical practice. However, the relationship and molecular links remain unclear, and the current treatment’s efficacy is disappointing. Bu-Shen-Yi-Qi (BSYQ) decoction has proven effective in treating various chronic airway inflammatory diseases, including asthma and IPF. But the underlying pharmacological mechanisms are still to be elucidated.

Methods

This study searched the proteins related to asthma and IPF via TTD, CTD, and DisGeNET databases and then submitted to the STRING to establish the protein–protein interaction (PPI) network. The co-bioinformatics analysis was conducted by Metascape. The active ingredients of BSYQ decoction were screened from TCMSP, ETCM, BATMAN-TCM databases, and HPLC/MS experiment. The corresponding targets were predicted based on TCMSP, ETCM, and BATMAN-TCM databases. The shared targets for asthma and IPF treatment were recognized, and further GO and KEGG analyses were conducted with the DAVID platform. Finally, molecule docking via Autodock Vina was employed to predict the potential binding mode between core potential compounds and targets.

Results

Finally, 1333 asthma-related targets and 404 IPF-related proteins were retrieved, 120 were overlapped between them, and many of the asthma-related proteins fall into the same statistically significant GO terms with IPF. Moreover, 116 active ingredients of BSYQ decoction were acquired, and 1535 corresponding targets were retrieved. Eighty-three potential compounds and 56 potential targets were recognized for both asthma and IPF treatment. GO and KEGG analysis indicated that the inflammation response, cytokine production, leukocyte differentiation, oxygen level response, etc., were the common pathological processes in asthma and IPF, which were regulated by BSYQ decoction. Molecule docking further predicted the potential binding modes between the core potential compounds and targets.

Conclusion

The current study successfully clarified the complex molecule links between asthma and IPF and found the potential common targets. Then we demonstrated the efficacy of BSYQ decoction for asthma and IPF treatment from the angle of network pharmacology, which may provide valuable references for further studies and clinical use.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03637-7.

Ancient Herbal Formula Mahuang Lianqiao Chixiaodou Decoction Protects Acute and Acute-on-Chronic Liver Failure via Inhibiting von Willebrand Factor Signaling

BACKGROUND

Acute liver failure (ALF) and acute-on-chronic liver failure (ACLF) are characterized by systemic inflammation and high mortality, but there is no effective clinical treatment. As a classic traditional Chinese medicine (TCM) formula, MaHuang-LianQiao-ChiXiaoDou decoction (MHLQD) has been used clinically for centuries to treat liver diseases.

METHODS

The LPS/D-GalN-induced ALF mice model and the CCl4+LPS/D-GalN-induced ACLF mice model were used to observe the therapeutic effects of MHLQD on mice mortality, hepatocytes death, liver injury, and immune responses.

RESULTS

MHLQD treatment significantly improved mice mortality. Liver injury and systemic and hepatic immune responses were also ameliorated after MHLQD treatment. Mechanistically, proteomic changes in MHLQD-treated liver tissues were analyzed and the result showed that the thrombogenic von Willebrand factor (VWF) was significantly inhibited in MHLQD-treated ALF and ACLF models. Histological staining and western blotting confirmed that VWF/RAP1B/ITGB3 signaling was suppressed in MHLQD-treated ALF and ACLF models. Furthermore, mice treated with the VWF inhibitor ADAMTS13 showed a reduced therapeutic effect from MHLQD treatment.

CONCLUSIONS

Our study indicated that MHLQD is an effective herbal formula for the treatment of ALF and ACLF, which might be attributed to the protection of hepatocytes from death via VWF/RAP1B/ITGB3 signaling.

Application of network pharmacology in the study of mechanism of Chinese medicine in the treatment of ulcerative colitis: A review

Network pharmacology is a research method based on a multidisciplinary holistic analysis of biological systems, which coincides with the idea of the holistic view of traditional Chinese medicine. In this review, we summarized the use of network pharmacology technology through studying Chinese medicine single medicine or Chinese medicine compound research ideas and methods for the treatment of ulcerative colitis, based on the application of the current network pharmacology in Chinese medicine research, including the important role in the mechanism of the prediction and verification, to search for new ideas for disease diagnosis and treatment, this study summarizes the application of network pharmacology in the treatment of ulcerative colitis in traditional Chinese medicine, including monotherapy and compound therapy, and considers that relevant research studies have fully demonstrated the function characteristics of the multi-component, multi-target, and multi-pathway of traditional Chinese medicine, and can also explain the connotation of “selecting appropriate treatment methods according to the differences and similarities of pathogenesis” of traditional Chinese medicine. Finally, we raised important questions about the prospects and limitations of network pharmacology, such as differences caused by different data collection methods, a considerable lag, and so on.

Traditional Chinese medicine promotes bone regeneration in bone tissue engineering

Bone tissue engineering (BTE) is a promising method for the repair of difficult-to-heal bone tissue damage by providing three-dimensional structures for cell attachment, proliferation, and differentiation. Traditional Chinese medicine (TCM) has been introduced as an effective global medical program by the World Health Organization, comprising intricate components, and promoting bone regeneration by regulating multiple mechanisms and targets. This study outlines the potential therapeutic capabilities of TCM combined with BTE in bone regeneration. The effective active components promoting bone regeneration can be generally divided into flavonoids, alkaloids, glycosides, terpenoids, and polyphenols, among others. The chemical structures of the monomers, their sources, efficacy, and mechanisms are described. We summarize the use of compounds and medicinal parts of TCM to stimulate bone regeneration. Finally, the limitations and prospects of applying TCM in BTE are introduced, providing a direction for further development of novel and potential TCM.

A novel strategy for optimal component formula of anti-PRRSV from natural compounds using tandem mass tag labeled proteomic analyses

BACKGROUND

Porcine Reproductive and Respiratory Syndrome (PRRS) is one of the most important porcine viral diseases which have been threatening the pig industry in China. At present, most commercial vaccines fail to provide complete protection because of highly genetic diversity of PRRSV strains. This study aimed to optimize a component formula from traditional Chinese medicine(TCM)compounds with defined chemical characteristics and clear mechanism of action against PRRSV.

METHODS

A total of 13 natural compounds were screened for the anti-PRRSV activity using porcine alveolar macrophages (PAMs). Three compounds with strong anti-PRRSV activity were selected to identify their potential protein targets by proteomic analysis. The optimal compound formula was determined by orthogonal design based on the results of proteomics. MTT assay was used to determine the maximum non-cytotoxic concentration (MNTC) of each compound using PAMs. QPCR and western blot were used to investigate the PRRSV N gene and protein expression, respectively. The Tandem Mass Tag (TMT) technique of relative quantitative proteomics was used to detect the differential protein expression of PAMs treated with PRRSV, matrine (MT), glycyrrhizic acid (GA) and tea saponin (TS), respectively. The three concentrations of these compounds with anti-PRRSV activity were used for orthogonal design. Four formulas with high safety were screened by MTT assay and their anti-PRRSV effects were evaluated.

RESULTS

MT, GA and TS inhibited PRRSV replication in a dose-dependent manner. CCL8, IFIT3, IFIH1 and ISG15 were the top four proteins in expression level change in cells treated with MT, GA or TS. The relative expression of IFIT3, IFIH1, ISG15 and IFN-β mRNAs were consistent with the results of proteomics. The component formula (0.4 mg/mL MT + 0.25 mg/mL GA + 1.95 μg/mL TS) showed synergistic anti-PRRSV effect.

CONCLUSIONS

The component formula possessed anti-PRRSV activity in vitro, in which the optimal dosage on PAMs was 0.4 mg/mL MT + 0.25 mg/mL GA + 1.95 μg/mL TS. Compatibility of the formula was superposition of the same target with GA and TS, while different targets of MT. IFN-β may be one of the targets of the component formula possessed anti-PRRSV activity.

Comparative Proteomic Analysis Reveals Antibacterial Mechanism of Patrinia scabiosaefolia Against Methicillin Resistant Staphylococcus epidermidis

Purpose

As a kind of opportunist pathogen, Staphylococcus epidermidis (MRSE) can cause nosocomial infections and easily evolve into resistant bacteria. Among these, methicillin-resistant Staphylococcus epidermidis (MRSE) exhibit significantly higher rates. Our previous study showed that Patrinia scabiosaefolia (PS) possessed strong antibacterial activity against MRSE. However, the mechanism of PS against MRSE is not clear.

Methods

Here, a tandem mass tag-based (TMT) proteomic analysis was performed to elucidate the potential mechanism of PS against MRSE. We compared the differential expression proteins of MRSE under PS stress.

Results

Based on a fold change of >1.2 or < 1/1.2 (with p value set at <0.05), a total of 248 proteins (128 up-regulated proteins, 120 down-regulated proteins) were identified. Bioinformatic analysis showed that proteins including arginine deiminase (arcA), ornithine carbamoyltransferase (arcB) and carbamate kinase (arcC), serine–tRNA ligase (serS), phenylalanine–tRNA ligase beta and subunit (pheT), DltD (dlt), d-alanyl carrier protein (dlt), accumulation-associated protein (SasG), serine-aspartate repeat-containing protein C (SdrC) and hemin transport system permease protein HrtB (VraG) played important roles in mechanism of PS against MRSE.

Conclusion

In summary, these results indicated that arginine deiminase pathway (ADI) pathway, protein synthesis, cell wall synthesis, biofilm formation and uptake of iron were related to mechanisms of PS against MRSE. Our findings provide an insight into the the mechanism of PS against MRSE, and may be valuable in offering new targets to develop more anti-MRSE drugs.

Identification and Comparison of Potential Biomarkers by Proteomic Analysis in Traditional Chinese Medicine-Based Heart Failure Syndromes

Heart failure (HF) is an epidemic disease affecting a large population worldwide. Traditional Chinese medicine (TCM) is playing an increasingly important role in the clinical treatment of HF. According to the TCM theory, HF could be classified into Yang deficiency and Qi-yin deficiency; however, there are few objective and biological lines of evidence for differentiation of TCM HF syndromes to date. In this study, data-independent acquisition (DIA) mass spectrometry was applied to comparatively analyze the protein expression in serum samples obtained from 12 Yang deficiency patients, 12 Qi-yin deficiency patients, and 12 healthy volunteers. Compared to the healthy controls, a total of 121 differentially expressed proteins (DEPs) (77 upregulated and 44 downregulated proteins) were identified in Yang deficiency samples, while 59 DEPs (49 upregulated and 10 downregulated proteins) were detected in Qi-yin deficiency samples. Enrichment analyses of these DEPs based on the GO and KEGG databases revealed functional clusters associated with the immune system, signal transduction, and infectious disease. Several previously reported HF biomarker proteins were found to be the hub proteins in a protein-protein interaction network analysis. Three novel hub DEPs were identified as potential biomarkers for differentiation between different TCM syndromes of HF. The results provide biological insight into the differences of different TCM HF syndromes and an opportunity for specific biomarker identification for different TCM HF syndromes.

Proteomics analysis reveals suppression of IL-17 signaling pathways contributed to the therapeutic effects of Jia-Wei Bu-Shen-Yi-Qi formula in a murine asthma model

BACKGROUND

Jia-Wei Bu-Shen-Yi-Qi formula (JWBSYQF), a Chinese herbal formula, is a commonly used prescription for treating asthma patients. However, the targeted proteins associated with JWBSYQF treatment remain unknown.

PURPOSE

Present study aims to evaluate the therapeutic efficacy of JWBSYQF and identify the targeted proteins in addition to functional pathways.

STUDY DESIGN

The ovalbumin (OVA)-induced murine asthma model was established to explore the therapeutic effect of JWBSYQF treatment. Proteomic profiling and quantifications were performed using data-independent acquisition (DIA) methods. Differentially expressed proteins (DEPs) were validated via western blot (WB) and immunohistochemistry (IHC).

METHODS

A murine asthma model was made by OVA sensitization and challenge, and JWBSYQF (2.25, 4.50, 9,00 g/kg body weight) or dexamethasone (1 mg/ kg body weight) were administered orally. Airway hyperresponsiveness (AHR) to methacholine (Mch), inflammatory cell counts and classification in bronchoalveolar lavage fluid (BALF), lung histopathology, and cytokine levels were measured. Furthermore, DIA proteomic analyses were performed to explore the DEPs targeted by JWBSYQF and were further validated by WB and IHC.

RESULTS

Our results exhibited that JWBSYQF attenuated AHR which was mirrored by decreased airway resistance and increased lung compliance. In addition, JWBSYQF-treated mice showed reduced inflammatory score, mucus hypersecretion, as well as reduced the number of BALF leukocytes along with decreased content of BALF Th2 inflammatory cytokines (IL-4, IL-5, IL-13) and serum IgE. Proteomics analysis identified 704 DEPs between the asthmatic mice and control group (MOD vs CON), and 120 DEPs between the JWBSYQF-treatment and the asthmatic mice (JWB-M vs MOD). A total of 33 overlapped DEPs were identified among the three groups. Pathway enrichment analysis showed that DEPs were significantly enriched in IL-17 signaling pathway, in which DEPs, Lcn2, TGF-β1, Gngt2, and Ppp2r5e were common DEPs between three experimental groups. WB and IHC results further validated expressional levels and tendency of these proteins. Our results also showed that JWBSYQF affects mitogen activated protein kinase (MAPK) and nuclear factor-κB (NF-κB) signaling pathways, that are activated by IL-17 signaling.

CONCLUSION

The present study suggested that JWBSYQF could attenuate AHR and airway inflammation in OVA-induced asthmatic mice. In addition, proteomics analysis revealed that suppression of IL-17 signaling pathways contributes to the therapeutic effects of JWBSYQF.

Proteomic Analysis Reveals the Protective Effects of Yiqi Fumai Lyophilized Injection on Chronic Heart Failure by Improving Myocardial Energy Metabolism

Yiqi Fumai lyophilized injection (YQFM) is the recombination of Sheng mai san (SMS).YQFM has been applied clinically to efficaciously and safely treat chronic heart failure (CHF). However, the mechanism of YQFM is still not fully elucidated. The purpose of our study was to investigate the protective mechanism of YQFM against abdominal aortic coarctation (AAC) in rats by proteomic methods. After YQFM treatment, the cardiac function were obviously meliorated. One hundred and fifty-seven important differentially expressed proteins (DEPs) were identified, including 109 in model rat compared with that in control rat (M:C) and 48 in YQFM-treated rat compared with that in model rat (T:M) by iTRAQ technology to analyze the proteomic characteristics of heart tissue. Bioinformatics analysis showed that DEPs was mainly involved in the body’s energy metabolism and was closely related to oxidative phosphorylation. YQFM had also displayed efficient mitochondrial dysfunction alleviation properties in hydrogen peroxide (H₂O₂)-induced cardiomyocyte damage by Transmission Electron Microscope (TEM), Metabolic assay, and Mitotracker staining. What’s more, the levels of total cardiomyocyte apoptosis were markedly reduced following YQFM treatment. Furthermore, Western blot analysis showed that the expressions of peroxisome proliferator activated receptor co-activator-1α(PGC-1α) (p < 0.01 or p < 0.001), perixisome proliferation-activated receptor alpha (PPAR-α) (p < 0.001)and retinoid X receptor alpha (RXR-α) were upregulated (p < 0.001), PGC-1α as well as its downstream effectors were also found to be upregulated in cardiomyocytes after YQFM treatment(p < 0.001).These results provided evidence that YQFM could enhance mitochondrial function of cardiomyocytes to play a role in the treatment of CHF by regulating mitochondrial biogenesis-related proteins.

Elucidating direct kinase targets of compound Danshen dropping pills employing archived data and prediction models

Research on direct targets of traditional Chinese medicine (TCM) is the key to study the mechanism and material basis of it, but there is still no effective methods at present. We took Compound Danshen dropping pills (CDDP) as a study case to establish a strategy to identify significant direct targets of TCM. As a result, thirty potential active kinase targets of CDDP were identified. Nine of them had potential dose-dependent effects. In addition, the direct inhibitory effect of CDDP on three kinases, AURKB, MET and PIM1 were observed both on biochemical level and cellular level, which could not only shed light on the mechanisms of action involved in CDDP, but also suggesting the potency of drug repositioning of CDDP. Our results indicated that the research strategy including both in silico models and experimental validation that we built, were relatively efficient and reliable for direct targets identification for TCM prescription, which will help elucidating the mechanisms of TCM and promoting the modernization of TCM.

Marker peptide screening and species-specific authentication of Pheretima using proteomics

Pheretima is a common and valuable animal-derived medication used in traditional Chinese medicine. There are four species of Pheretima specified in the Chinese Pharmacopoeia (2015 edition), i.e. Pheretima aspergillum, P. vulgaris, P. guillelmi, and P. pectinifera. A recent report revealed ~ 55% of Pheretima in the commercial marketplace may be adulterated by other species, contrary to the Pharmacopoeia standard. The safety, efficacy, and authenticity of Pheretima is an important issue. Currently, the availability of specific quality-markers for the various species and effective identification methods are still limited. In this study, label-free quantification proteomics of species from Pheretima and Amynthas was carried out using nanoscale liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS), and marker peptides were identified based on their ion intensities using multivariate data analysis (principal component analysis and supervised partial least-squares discriminant analysis). A total of 48,476 peptides with high confidence corresponding to 13,397 proteins were identified from all samples. The marker peptides were validated by comparison with synthetic peptide reference standards using LC-MS/MS operating in a multiple-reaction monitoring mode. A multiple-peptide identification strategy was proposed for the authentication of Pheretima and subsequently applied to samples obtained from retail outlets in various regions of China. The results showed that eight out of the 15 samples tested were deemed authentic Pheretima.

The Advantages of Connectivity Map Applied in Traditional Chinese Medicine

Amid the establishment and optimization of Connectivity Map (CMAP), the functional relationships among drugs, genes, and diseases are further explored. This biological database has been widely used to identify drugs with common mechanisms, repurpose existing drugs, discover the molecular mechanisms of unknown drugs, and find potential drugs for some diseases. Research on traditional Chinese medicine (TCM) has entered a new era in the wake of the development of bioinformatics and other subjects including network pharmacology, proteomics, metabolomics, herbgenomics, and so on. TCM gradually conforms to modern science, but there is still a torrent of limitations. In recent years, CMAP has shown its distinct advantages in the study of the components of TCM and the synergetic mechanism of TCM formulas; hence, the combination of them is inevitable.

De novo transcriptomic and proteomic analysis and potential toxin screening of Mesobuthus martensii samples from four different provinces

ETHNOPHARMACOLOGICAL RELEVANCE

As well-known medicinal materials in traditional Chinese medicine, scorpions, commonly called as Quanxie () in Chinese, have been widely used to treat several diseases such as rheumatoid arthritis, apoplexy, epilepsy and chronic pain for more than a thousand years. Not only in the ancient times, the scorpions have also been recorded nowadays in the Pharmacopoeia of the People's Republic of China since 1963.

AIM OF STUDY

This study aims to explore the differences in composition of the venom of scorpions from different regions by using the method of transcriptomics and proteomics.

MATERIALS AND METHODS

Whole de novo transcriptomes, proteomics and their bioinformatic analyses were performed on samples of the scorpion Mesobuthus martensii and their venoms from four different provinces with clear geographical boundaries, including Hebei, Henan, Shandong and Shanxi.

RESULTS

The four captured samples had the same morphology, and the conserved CO-1 sequence matched that of M. martensii. A total of 141,003 of 174,653 transcripts were identified as unigenes, of which we successfully annotated 51,627 (36.61%), 21,970 (15.58%), 7,168 (5.08%), and 45,263 (32.10%) unigenes with the NR, GO, KEGG and SWISSPROT databases, respectively, while a total of 427 proteins were collected from the protein extracted from venoms. Both GO and KEGG annotations exhibited only slight differences among the four samples while the expression level of gene and protein was quite different. A total of 249 toxin-related unigenes were successfully screened, including 41 serine proteases and serine protease inhibitors, 39 potassium channel toxins, 38 phospholipases, 16 host defense peptides, 9 metalloproteases, and 50 other toxins. Although the toxin species were similar among the four samples, the gene expression of each toxin varied considerably, for example, the scorpion from HB province has the most abundant expression quality in sequences c48391_g1, c55239_g1 and c47749_g1 while the lowest expressions of c51178_g1, c62033_g3 and c63754_g2.

CONCLUSION

The regional differences in the transcriptomes and proteomes of M. martensii are mainly from expression levels e.g. toxins rather than expression species, of which the method can be further extended to evaluate the qualities of traditional Chinese medicines obtained from different regions.

UNaProd: A Universal Natural Product Database for Materia Medica of Iranian Traditional Medicine

BACKGROUND

Iranian traditional medicine (ITM) is a holistic medical system that uses a wide range of medicinal substances to treat disease. Reorganization and standardization of the data on ITM concepts is a necessity for optimal use of this rich source. In an initial step towards this goal, we created a database of ITM materia medica. Main Body. Primarily based on Makhzan al-Advieh, which is the most recent encyclopedia of materia medica in ITM with the largest number of monographs, a database of natural medicinal substances was created using both text mining methods and manual editing. UNaProd, a Universal Natural Product database for materia medica of ITM, is currently host to 2696 monographs, from herbal to animal to mineral compounds in 16 diverse attributes such as origin and scientific name. Currently, systems biology, and more precisely systems medicine and pharmacology, can be an aid in providing rationalizations for many traditional medicines and elucidating a great deal of knowledge they can offer to guide future research in medicine.

CONCLUSIONS

A database of materia medica is a stepping stone in creating a systems pharmacology platform of ITM that encompasses the relationships between the drugs, their targets, and diseases. UNaProd is hyperlinked to IrGO and CMAUP databases for Mizaj and molecular features, respectively, and it is freely available at http://jafarilab.com/unaprod/.

Applications of Network Pharmacology in Traditional Chinese Medicine Research

Human diseases, especially infectious ones, have been evolving constantly. However, their treatment strategies are not developing quickly. Some diseases are caused by a variety of factors with very complex pathologies, and the use of a single drug cannot solve these problems. Traditional Chinese Medicine (TCM) medication is a unique treatment method in China. TCM formulae contain multiple herbs with multitarget, multichannel, and multilink characteristics. In recent years, with the flourishing development of network pharmacology, a new method for searching therapeutic drugs has emerged. The multitarget action in network pharmacology is consistent with the complex mechanisms of disease and drug action. Using network pharmacology to understand TCM is an emerging trend.

Serum proteomics analysis based on label-free revealed the protective effect of Chinese herbal formula Gu-Ben-Fang-Xiao

Gubenfangxiao decoction (GBFXD) is a traditional Chinese medicine formula derived from Yupingfengsan, an ancient formula widely used to treat respiratory diseases. In recent years, GBFXD has been applied to efficaciously and safely treat asthma. However, the mechanism of GBFXD is still not fully elucidated. The aim of this study was to employ the label-free proteomic method to explore the protective mechanism of GBFXD in respiratory syncytial virus (RSV)-ovalbumin (OVA) induced chronic persistent asthmatic mice. After RSV-OVA challenge, mice were orally administered GBFXD at a dose of 36 g/kg accompanied with OVA nasal spray once every 3 days for 28 days. The label-free proteomics-based liquid chromatography-tandem mass spectrometry method was used to explore the differentially abundant proteins (DAPs) in the serum from model mice compared with that in control mice (M:C), and in GBFXD-treated mice compared with that in model mice (G:M). The mass spectrometry proteomics data have been deposited to the ProteomeXchange with identifier PXD013244. A total of 69 significant DAPs were identified including 39 in M:C, 46 in G:M, and 16 common differential proteins. Bioinformatics analysis revealed that the DAPs of M:C were mainly involved in inflammatory response and were related to lipid metabolism. However, the DAPs of G:M mostly participated in stress response, inflammatory response, and epithelial cell proliferation. Serum levels of Apoa-1, Apoc-1, Cfd, and Lrg1, EGFR and Lrg1 in the lungs were consistent with the results of proteomic analysis. Apoa-1 and Apoc-1 were closely related to cholesterol transport, lipid metabolism balance, and airway epithelial integrity; Cfd participated in immune response, affecting the occurrence and development of inflammation; EGFR and Lrg1 were involved in epithelial cell proliferation, influencing the process of airway remodeling. In summary, these results indicated that GBFXD may affect inflammatory and immune response of asthma by regulating cholesterol transport and complement factor activation. Furthermore, it could repair damaged airway epithelium and avoid airway remodeling to prevent and treat asthma.

iTRAQ-Based Proteomics to Reveal the Mechanism of Hypothalamus in Kidney-Yin Deficiency Rats Induced by Levothyroxine

Kidney-yin deficiency syndrome (KYDS) is a typical syndrome encountered in traditional Chinese medicine (TCM) and is characterized by impaired lipid and glucose homeostasis. The hypothalamus acts as an important regulatory organ by controlling lipid and glucose metabolism in the body. Therefore, proteins in the hypothalamus could play important roles in KYDS development; however, the mechanisms responsible for KYDS remain unclear. Herein, iTRAQ-based proteomics was performed to analyze the protein expression in the hypothalamus of KYDS rats induced by levothyroxine (L-T₄). Results revealed a total of 44 downregulated and 18 upregulated proteins in KYDS group relative to the control group. Gene Ontology (GO) analysis revealed that the differently expressed proteins (DEPs) were related to single-organism metabolism process under the biological process (BP), extracellular region part and organelle under the cellular component (CC), and oxidoreductase activity under the molecular function (MF). Kyoto Encyclopedia of Gene and Genomes (KEGG) analysis showed that fatty acid degradation and pyruvate metabolism participated in the metabolism regulation in KYDS rats. RT-PCR validation of five distinctly expressed proteins related to the two pathways was consistent with the results of proteomics analysis. Taken together, the inhibition of fatty acid degradation and pyruvate metabolism in hypothalamus could potentially cause the dysfunction of the lipid and glucose metabolism in KYDS rats. This current study identified some novel potential biomarkers of KYDS and provided the basis for further research of KYDS.

The Recent Applications and Developments of Bioinformatics and Omics Technologies in Traditional Chinese Medicine

Background:

Traditional Chinese Medicine (TCM) is widely utilized as complementary health care in China whose acceptance is still hindered by conventional scientific research methodology, although it has been exercised and implemented for nearly 2000 years. Identifying the molecular mechanisms, targets and bioactive components in TCM is a critical step in the modernization of TCM because of the complexity and uniqueness of the TCM system. With recent advances in computational approaches and high throughput technologies, it has become possible to understand the potential TCM mechanisms at the molecular and systematic level, to evaluate the effectiveness and toxicity of TCM treatments. Bioinformatics is gaining considerable attention to unearth the in-depth molecular mechanisms of TCM, which emerges as an interdisciplinary approach owing to the explosive omics data and development of computer science. Systems biology, based on the omics techniques, opens up a new perspective which enables us to investigate the holistic modulation effect on the body.

Objective:

This review aims to sum up the recent efforts of bioinformatics and omics techniques in the research of TCM including Systems biology, Metabolomics, Proteomics, Genomics and Transcriptomics.

Conclusion:

Overall, bioinformatics tools combined with omics techniques have been extensively used to scientifically support the ancient practice of TCM to be scientific and international through the acquisition, storage and analysis of biomedical data.

High Throughput mRNA Sequencing Reveals Potential Therapeutic Targets of Tao-Hong-Si-Wu Decoction in Experimental Middle Cerebral Artery Occlusion

Background: Experimental and clinical studies have shown that Tao-Hong-Si-Wu decoction (THSWD) improved neurological deficits resulting from Middle Cerebral Artery Occlusion (MCAO). However, the mechanisms of action of THSWD in MCAO have not been characterized. In this study, the mRNA transcriptome was used to study various therapeutic targets of THSWD.

Methods: RNA-seq was used to identify differentially expressed genes (DEGs). MCAO-induced up-regulated genes (MCAO vs. control) and THSWD-induced down-regulated genes (compared to MCAO) were identified. Intersection genes were defined as up-regulated differentially expression genes (up-DEGs) identified as MCAO-induced gene expression that were reversed by THSWD. Genes down-regulated by MCAO and up-regulated by THSWD were grouped as another series of intersections. Biological functions and signaling pathways were determined by gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses. In addition, several identified genes were validated by RT-qPCR.

Results: A total of 339 DEGs were filtered based on the 2 series (MCAO vs. control and MCAO vs. THSWD), and were represented by genes involved in cell cycle (rno04110), ECM–receptor interaction (rno04512), complement and coagulation cascades (rno04610), focal adhesion (rno04510), hematopoietic cell lineage (rno04640), neuroactive ligand–receptor interaction (rno04080), cocaine addiction (rno05030), amphetamine addiction (rno05031), nicotine addiction (rno05033), fat digestion and absorption (rno04975), glycerophospholipid metabolism (rno00564), and others. The protein–protein interaction (PPI) network consisted of 202 nodes and 1,700 connections, and identified two main modules by MOCDE.

Conclusion: Cell cycle (rno04110), ECM–receptor interaction (rno04512), complement and coagulation cascades (rno04610), focal adhesion (rno04510), hematopoietic cell lineage (rno04640), and neuroactive ligand–receptor interactions (rno04080) are potential therapeutic targets of THSWD in MCAO. This study provided a theoretical basis for THSWD prevention of neurological deficits resulting from intracerebral hemorrhage.

A Real-World Evidence Study for Distribution of Traditional Chinese Medicine Syndrome and Its Elements on Respiratory Disease

Background

This study aimed to investigate the distribution and characteristics of traditional Chinese medicine (TCM) syndrome and its elements on respiratory diseases (RDs) based on real-world data (RWD).

Methods

A real-world study was performed to explore the relationships among TCM syndrome and RDs based on electronic medical information. A total of 26,074 medical records with complete data were available for data analysis. Factor analyses were used to reduce dimensions of TCM syndrome elements and detect common factors. Additionally, cluster analyses were employed to assess combinations of TCM syndrome elements. Finally, association rule analyses were performed to investigate the structures of TCM syndrome elements to estimate the patterns of TCM syndrome.

Results

A total of 27 TCM syndromes were extracted from RWD in this work. There were four TCM syndromes with >5.0% frequency based on the distribution frequency. The top five pathogenesis TCM syndrome elements were Tan, Huo, Feng, Qi_Xu, and Han. Factor analysis, cluster analysis, and association rule analysis demonstrated that Tan, Huo, Feng, Qi_Xu, Shen, and Fei were the core TCM syndrome elements.

Conclusion

Four common Shi TCM syndromes on RDs were identified: Tan_Re_Yong_Fei, Tan_Zhuo_Zu_Fei, Feng_Re_Fan_Fei, and Feng_Han_Xi_Fei; two core common Xu TCM syndromes (Fei_Shen_Qi_Xu and Fei_Yin_Xu) and two core common Mix TCM syndromes (Fei_Pi_Qi_Xu-Tan_Shi_Yun_Fei and Fei_Shen_Qi_Xu-Tan_Yu_Zu_Fei) were also determined. The core TCM syndrome elements of Tan, Huo, Feng, Qi_Xu, Shen, and Fei were identified in this work.

Application of metabolomics in toxicity evaluation of traditional Chinese medicines

Traditional Chinese medicines (TCM) have a long history of use because of its potential complementary therapy and fewer adverse effects. However, the toxicity and safety issues of TCM have drawn considerable attention in the past two decades. Metabolomics is an “omics” approach that aims to comprehensively analyze all metabolites in biological samples. In agreement with the holistic concept of TCM, metabolomics has shown great potential in efficacy and toxicity evaluation of TCM. Recently, a large amount of metabolomic researches have been devoted to exploring the mechanism of toxicity induced by TCM, such as hepatotoxicity, nephrotoxicity, and cardiotoxicity. In this paper, the application of metabolomics in toxicity evaluation of bioactive compounds, TCM extracts and TCM prescriptions are reviewed, and the potential problems and further perspectives for application of metabolomics in toxicological studies are also discussed.

Anti-Angiogenic Alternative and Complementary Medicines for the Treatment of Endometriosis: A Review of Potential Molecular Mechanisms

Endometriosis is caused by the growth or infiltration of endometrial tissues outside of the endometrium and myometrium. Symptoms include pain and infertility. Surgery and hormonal therapy are widely used in Western medicine for the treatment of endometriosis; however, the side effects associated with this practice include disease recurrence and menopause, which can severely influence quality of life. Angiogenesis is the main biological mechanism underlying the development of endometriosis. Numerous natural products and Chinese medicines with potent anti-angiogenic effects have been investigated, and the molecular basis underlying their therapeutic effects in endometriosis has been explored. This review aims to describe natural products and compounds that suppress angiogenesis associated with endometriosis and to assess their diverse molecular mechanisms of action. Furthermore, this review provides a source of information relating to alternative and complementary therapeutic products that mediate anti-angiogenesis. An extensive review of the literature and electronic databases, such as the China National Knowledge Infrastructure, PubMed, and Embase, was conducted using the keywords 'endometriosis,' 'traditional Chinese medicine,' 'Chinese herbal medicine,' 'natural compounds,' and 'anti-angiogenic' therapy. Anti-angiogenic therapy is an emerging strategy for the treatment of endometriosis. Natural anti-angiogenic products and Chinese medicines provide several beneficial clinical effects, including pain relief. In this review, we summarize clinical trials and experimental studies of endometriosis using natural products and Chinese medicines. In particular, we focus on anti-angiogenic products and alternative and complementary medicines for the treatment of endometriosis and additionally examine their therapeutic efficacy and mechanisms of action. Anti-angiogenic natural products and/or compounds provide a new approach for the treatment of endometriosis. Future work will require randomized trials with larger numbers of subjects, as well as long-term follow-up to confirm the findings described here.

Chinese Medicine: A Hope for Neurodegenerative Diseases?

With the increase in the proportion of aged population due to the rapid increase of life expectancy, the worldwide prevalence rate of multiple neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and Huntington's disease has been increased dramatically. The demographic trend toward an older population has drawn the attention to new drug discovery and treatment on age-related diseases. Although a panel of drugs and/or therapies are currently available for treating the neurodegenerative diseases, side effects or insufficient drug efficacy have been reported. With the long history in prescription of Chinese medicine or natural compounds for modulating aged-related diseases, emerging evidence was reported to support the pharmacological role of Chinese medicine in ameliorating the symptoms, or interfering with the pathogenesis of several neurodegenerative diseases. This review brings evidence about today's trends and development of a list of potential neuroprotective herbal compounds from both the traditional and modern pharmacological point of view. With future projections, the potential hope and implication of using Chinese medicine as an alternative source for novel drug discovery for neurodegenerative diseases is proposed.

Synovial tissue quantitative proteomics analysis reveals paeoniflorin decreases LIFR and ASPN proteins in experimental rheumatoid arthritis

Background

Rheumatoid arthritis (RA) is a common worldwide public health problem, which causes a chronic, systemic inflammatory disorder of synovial joints. Paeoniflorin (PA) has achieved positive results to some extent for the treatment of RA.

Purpose

This study aimed to reveal the potential druggable targets of PA in an experimental RA model using quantitative proteomics analysis.

Study design and methods

Thirty Sprague-Dawley rats were randomly divided into a normal group, model group and PA group. PA (1 mg/kg) was used to treat collagen-induced arthritis (CIA) rats for 42 days. We used isobaric tags for relative and absolute quantitation-based quantitative proteomics to analyze the synovial tissue of rats. Ingenuity pathway analysis (IPA) software was applied to process the data. The proteins that were targeted via IPA software were verified by Western blots.

Results

We found that PA caused 86 differentially expressed proteins (≥1.2-fold or ≤0.84-fold) compared with the CIA group. Of these varied proteins, 20 significantly changed (p<0.05) proteins referred to 41 CIA-relative top pathways after IPA pathway analysis. Thirteen of the PA-regulated pathways were anchored, which intervened in 24 biological functions. Next, network analysis revealed that leukemia inhibitory factor receptor (LIFR) and asporin (ASPN), which participate in two significant networks, contributed the most to the efficacy of PA treatment. Additionally, Western blots confirmed the aforementioned druggable targets of PA for the treatment of RA.

Conclusion

The results reveal that PA may treat RA by decreasing two key proteins, LIFR and ASPN. Our research helps to identify potential agents for RA treatment.

Determination of the effect of Pinellia ternata (Thunb.) Breit. on nervous system development by proteomics

ETHNOPHARMACOLOGICAL RELEVANCE

Banxia (BX) is the dried tuber of Pinellia ternata (Thunb.) Breit., a commonly prescribed Chinese medicinal herb for the treatment of cough, phlegm, and vomiting in pregnant women. However, raw BX has been demonstrated to exert toxic effects on reproduction and the precise and comprehensive mechanisms remain elusive.

AIM OF THE STUDY

We applied an iTRAQ (isobaric tags for relative and absolute quantitation, iTRAQ)-based proteomic method to explore the mechanisms of raw BX-induced fetal toxicity in mice.

MATERIALS AND METHODS

The mice were separated into two groups, control mice and BX-treated mice. From gestation days 6-8, the control group was treated with normal saline and the BX group was exposed to BX suspension (2.275g/kg/day). Gastrulae were obtained and analyzed using the quantitative proteomic approach of iTRAQ coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS). A multi-omics data analysis tool, OmicsBean (http://www.omicsbean.cn), was employed to conduct bioinformatic analysis of differentially abundant proteins (DAPs). Quantitative real-time PCR (qRT-PCR) and western blotting methods were applied to detect the protein expression levels and validate the quality of the proteomics.

RESULTS

A total of 1245 proteins were identified with < 1% false discovery rate (FDR) and 583 protein abundance changes were confidently assessed. Moreover, 153 proteins identified in BX-treated samples showed significant differences in abundance. Bioinformatics analysis showed that the functions of 37 DAPs were predominantly related to nervous system development. The expression levels of the selected proteins for quantification by qRT-PCR or western blotting were consistent with the results in iTRAQ-labeled proteomics data.

CONCLUSION

The results suggested that oral administration of BX in mice may cause fetal abnormality of the nervous system. The findings may be helpful to elucidate the underlying mechanisms of BX-induced embryotoxicity.