Systems Biology Guided by Chinese Medicine Reveals New Markers for Sub-Typing Rheumatoid Arthritis Patients

Association Between Human Metabolomics and Rheumatoid Arthritis: A Systematic Review and Meta-analysis

OBJECTIVE

The underdiagnosis and inadequate treatment of rheumatoid arthritis (RA) can be attributed to the various clinical manifestations presented by patients. To address this concern, we conducted an extensive review and meta-analysis, focusing on RA-related metabolites.

METHODS

A comprehensive literature search was conducted in PubMed, the Cochrane Library, Web of Science, and Embase to identify relevant studies published up to October 5, 2022. The quality of the included articles was evaluated and, subsequently, a meta-analysis was conducted using Review Manager software to analyze the association between metabolites and RA.

RESULTS

Forty nine studies met the inclusion criteria for the systematic review, and six of these studies were meta-analyzed to evaluate the association between 28 reproducible metabolites and RA. The results indicated that, compared to controls, the levels of histidine (RoM = 0.83, 95% CI = 0.79-0.88, I2 = 0%), asparagine (RoM = 0.83, 95% CI = 0.75-0.91, I2 = 0%), methionine (RoM = 0.82, 95% CI = 0.69-0.98, I2 = 85%), and glycine (RoM = 0.81, 95% CI = 0.67-0.97, I2 = 68%) were significantly lower in RA patients, while hypoxanthine levels (RoM = 1.14, 95% CI = 1.09-1.19, I2 = 0%) were significantly higher.

CONCLUSION

This study identified histidine, methionine, asparagine, hypoxanthine, and glycine as significantly correlated with RA, thus offering the potential for the advancement of biomarker discovery and the elucidation of disease mechanisms in RA.

The Holistic Philosophy of Traditional Chinese Medicine and Conflicts With Modern Medicine

Traditional Chinese medicine (TCM) has sparked the public's attention for its potential in new drug development and its holistic view toward health, which is totally different from the reductionistic science of modern medicine. Although many scholars try to connect TCM with precision medicine or apply new methods and technology to integrate TCM with modern medicine, the misunderstandings and gap between TCM and modern medicine limit the development of evidence-based TCM. Traditional Chinese medicine is actually a medical science encompassing not only medicine but also philosophy and art in direct contrast to molecular-based modern medicine. As more and more multidisciplinary studies are being published, finding ways to integrate TCM with modern or precision medicine through artificial intelligence, new study design and technology may become a critical issue. This article aims to briefly review the unique philosophy of TCM and its conflicts with modern medicine, with a focus on the potential integration of TCM and modern medicine. We also provide insight for the key attributes of TCM and the associated investigation with Western research approaches.

Rheumatoid arthritis characteristics and classification of heat and cold patterns-an observational study

Introduction

Traditional Chinese medicine (TCM) has been proven to be an effective complementary therapy in treating rheumatoid arthritis (RA). The cold pattern and the heat pattern were the two main TCM patterns for RA, which is crucial for TCM treatment. The cold pattern is characterized by fear of cold and wind, joint pain with a thin white tongue coating which can be relieved by hot herbs. In contrast, heat pattern patients suffer from severe joint pain with a yellow coating, with red swelling of the skin and high skin temperature which can be relieved by cooling herbs.

Objective

We aimed to classify the heat and cold patterns in RA patients with cluster analysis and factor analysis. Moreover, we aimed to explore the association of RA characteristics between these two patterns.

Methods

and Design: A cross-sectional observational research method was used, and data was collected on 300 RA patients in Hangzhou in China. Signs and symptoms associated with RA were clustered using SPSS 22.0 software. In addition, factor analysis was also used for the classification. After classification of heat and cold patterns, characteristics and treatment of the RA participants between the two patterns were explored.

Results

RA patients in the study were divided into two categories using cluster analysis. Twenty-two symptoms in the first category were included in the heat pattern of RA patients. After factor analysis, nine principal components were extracted to heat pattern. The component with the highest eigenvalue (2.530) were mainly contributed by shortness of breath, palpitation, heavy limbs, chest tightness and yellow greasy tongue with high factor loading values (0.765, 0.703, 0.504, 0.429 and 0.402, respectively). Ten symptoms in the second category were included in the cold pattern of RA patients. Four principal components were extracted to cold pattern. The component with the highest eigenvalue (2.089) were mainly contributed by joint distension and pain, joint stiffness, fatigue and upset with high factor loading values (0.597, 0.590, 0.491 and 0.481, respectively). Although there were no statistical differences between the levels of rheumatoid factor and anti-cyclic peptide containing citrulline (anti-CCP), the levels of C-reactive protein, platelet count and the disease activity score using 28 joint counts were significantly higher in the heat pattern RA patients compared to the ones in cold pattern. Moreover, heat pattern RA patients were more likely to be prescribed two more disease-modifying anti-rheumatic drugs (DMARDS) combined with Methotrexate (MTX) (70.59% versus 49.72%; P = 0.000).

Conclusions

In conclusion, heat and cold patterns in RA patients could be classified well using cluster analysis and factor analysis. Most of RA patients with heat pattern were active and likely to be prescribed two more DMARDs combined with MTX.

The Regulatory Effect of Phytochemicals on Chronic Diseases by Targeting Nrf2-ARE Signaling Pathway

Redox balance is essential to maintain the body's normal metabolism. Once disrupted, it may lead to various chronic diseases, such as diabetes, neurodegenerative diseases, cardiovascular diseases, inflammatory diseases, cancer, aging, etc. Oxidative stress can cause or aggravate a series of pathological processes. Inhibition of oxidative stress and related pathological processes can help to ameliorate these chronic diseases, which have been found to be associated with Nrf2 activation. Nrf2 activation can not only regulate the expression of a series of antioxidant genes that reduce oxidative stress and its damage, but also directly regulate genes related to the above-mentioned pathological processes to counter the corresponding changes. Therefore, targeting Nrf2 has great potential for the prevention or treatment of chronic diseases, and many natural phytochemicals have been reported as Nrf2 activators although the defined mechanisms remain to be elucidated. This review article focuses on the possible mechanism of Nrf2 activation by natural phytochemicals in the prevention or treatment of chronic diseases and the regulation of oxidative stress. Moreover, the current clinical trials of phytochemical-originated drug discovery by targeting the Nrf2-ARE pathway were also summarized; the outcomes or the relationship between phytochemicals and chronic diseases prevention are finally analyzed to propose the future research strategies and prospective.

Appraisal of treatment outcomes in integrative medicine using metabonomics: Taking non-alcoholic fatty liver disease with spleen deficiency syndrome as an example

OBJECTIVE

Appraisal of treatment outcomes in integrative medicine is a challenge due to a gap between the concepts of Western medicine (WM) disease and traditional Chinese medicine (TCM) syndrome. This study presents an approach for the appraisal of integrative medicine that is based on targeted metabolomics. We use non-alcoholic fatty liver disease with spleen deficiency syndrome as a test case.

METHODS

A patient-reported outcome (PRO) scale was developed based on literature review, Delphi consensus survey, and reliability and validity test, to quantitatively evaluate spleen deficiency syndrome. Then, a metabonomic foundation for the treatment of non-alcoholic fatty liver disease with spleen deficiency syndrome was identified via a longitudinal interventional trial and targeted metabolomics. Finally, an integrated appraisal model was established by identifying metabolites that responded in the treatment of WM disease and TCM syndrome as positive outcomes and using other aspects of the metabonomic foundation as independent variables.

RESULTS

Ten symptoms and signs were included in the spleen deficiency PRO scale. The internal reliability, content validity, discriminative validity and structural validity of the scale were all qualified. Based on treatment responses to treatments for WM disease (homeostasis model assessment of insulin resistance) or TCM syndrome (spleen deficiency PRO scale score) from a previous randomized controlled trial, two cohorts comprised of 30 participants each were established for targeted metabolomics detection. Twenty-five metabolites were found to be involved in successful treatment outcomes to both WM and TCM, following quantitative comparison and multivariate analysis. Finally, the model of the integrated appraisal system was exploratively established using binary logistic regression; it included 9 core metabolites and had the prediction probability of 83.3%.

CONCLUSION

This study presented a new and comprehensive research route for integrative appraisal of treatment outcomes for WM disease and TCM syndrome. Critical research techniques used in this research included the development of a TCM syndrome assessment tool, a longitudinal interventional trial with verified TCM treatment, identification of homogeneous metabolites, and statistical modeling.

Serum metabolomics analysis of deficiency pattern and excess pattern in patients with rheumatoid arthritis

Background

Rheumatoid arthritis (RA) is a chronic and refractory autoimmune disease. Deficiency pattern (DP) and excess pattern (EP), as crucial types of Chinese medicine pattern diagnoses published by International Classification of Diseases 11th Revision (ICD-11), could provide new strategies for RA diagnosis. However, the biological basis of DP and EP of RA is not explicit.

Methods

19 female RA DP patients, 41 female RA EP patients and 30 female healthy participants were included in the study. The serums of participants were collected and analyzed by metabolomics based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry to profile metabolic characteristics of RA DP and EP. Furthermore, bioinformatics analysis results were obtained by using Ingenuity Pathway Analysis (IPA) and statistical analysis was performed by SAS version 9.4 for further identification of potential biomarkers.

Results

Serum metabolic profiling revealed 25 and 24 differential metabolites in RA DP and EP respectively, and 19 metabolites were common to RA DP and EP. Compared with DP group, L-Homocysteic acid, LysoPE(P-16:0/0:0), N(omega)-Hydroxyarginine and LysoPC(16:0/0:0) decreased (P < 0.05), and Pyruvic acid, D-Ribose, Gamma-Glutamylserine, PE(22:0/24:1(15Z)), Inosinic acid increased (P < 0.05) in EP group. Menawhile, S-Nitrosoglutathione, 5-Thymidylic acid, SN38 glucuronide, PE(22:0/24:0), PC(24:0/24:1(15Z)) and Bisdiphosphoinositol tetrakisphosphate increased significantly in DP group compared to EP group (P < 0.05). For the unique metabolites, bioinformatics analysis results showed that 5-Methoxytryptamine involved in Melatonin Degradation II and Superpathway of Melatonin Degradation is the key metabolite to RA DP. Meanwhile, GABA is the key metabolite in EP group, which involved in Glutamate Dependent Acid Resistance, GABA Receptor Signaling, Glutamate Degradation III (via 4-aminobutyrate) and 4-aminobutyrate Degradation I. Bioinformatics analysis between unique metabolites of RA DP and EP groups with human target genes for RA showed that 5-methoxytryptamine and LysoPC(18:1(9Z)/0:0), the unique metabolites of RA DP, might participate in colorectal cancer metastasis signaling, tumor microenvironment pathway, apoptosis signaling, MYC mediated apoptosis signaling, erythropoietin signaling pathway and LXR/RXR activation. Simultaneously, GABA, LysoPA(18:1(9Z)/0:0) and L-Targinine, the unique metabolites of RA EP, might participate in neuroinflammation signaling pathway, osteoarthritis pathway, glucocorticoid receptor signaling, ILK signaling, IL-17 signaling and HIF1α signaling.

Conclusions

The study indicates that serum metabolomics preliminarily revealed the biological basis of RA DP and EP. 5-methoxytryptamine, LysoPC(18:1(9Z)/0:0) and GABA, LysoPA(18:1(9Z)/0:0), L-Targinine might be the predictors to distinguish the DP and EP of RA respectively. These interesting results provide thoughts for further study of traditional medicine patterns of ICD-11. It also contributes to provide strategy for personalized precision treatment of RA and further validation is needed.

Developing a Personalized Integrative Obesity-Coaching Program: A Systems Health Perspective

Current obesity management strategies are failing to achieve sustainable and favorable long-term results. We propose a more personalized, dynamic, and systemic perspective on the interactions of key determinants and coaching advice on obesity. The aim of this study was to use a systems view on overweight, complexity science, and a transdisciplinary process to develop a five-year personalized integrative obesity-coaching and research program. Managers, medical specialists, clinical psychologists, dieticians, physical- and psychomotor therapists, and lifestyle coaches aligned their perspectives and objectives with experts in systems thinking and systems biology. A systems health model of obesity was used to identify the causal relations of variables with the most influence on obesity. The model helped to align and design a personalized integrative obesity-coaching program and to identify the key variables to monitor the progress and to adjust the personalized program, depending on the goals and needs of the participant. It was decided to use subtyping of participants by a systems biologist, based on traditional Chinese medicine symptoms, as a novel method to personalize the intervention. The collaborative transdisciplinary approach based upon a systems view on obesity was successful in developing a personalized and adaptive five-year obesity-coaching and research program.

Si Miao San Attenuates Inflammation and Oxidative Stress in Rats with CIA via the Modulation of the Nrf2/ARE/PTEN Pathway

Objective

Si Miao San (SMS) is a traditional Chinese formula used in China to treat rheumatic diseases. To date, its mechanism in rheumatoid arthritis (RA) treatment is uncertain. Our study aims to assess the antiarthritic effects of SMS in experimental arthritic rats.

Materials and Methods

SMS (8.63, 4.31, and 2.16 g/kg/day) was orally administered after the first immunization from day 14 to day 53. The effects of SMS on rats with collagen-induced arthritis (CIA) were evaluated by arthritis score and histological assessment. The levels of cytokines and anti-CII antibodies in rat serum were measured by ELISAs. The expression of oxidative stress parameters was detected by biochemical assay kits. The levels of Nrf2, HO-1, NQO1, and PTEN were determined by western blotting.

Results

Medium- and high-dose SMS treatment significantly decreased arthritis scores and alleviated ankle joint histopathology in the rats with CIA. It inhibited the production of IL-6, TNF-α, COX-2, and PGE2 in rat serum. SMS also suppressed the expression of anti-CII antibodies IgG1 and IgG2a. Moreover, SMS significantly suppressed the levels of MDA and MPO in the synovial tissues while increasing the levels of SOD and CAT in the rats with CIA. The levels of Nrf2, HO-1, NQO1, and PTEN were upregulated by SMS in rat synovial tissues.

Conclusions

This study demonstrated that SMS effectively alleviated the disease progression of CIA by decreasing the levels of proinflammatory cytokines and reducing oxidative stress damage, as indicated by IL-6, TNF-α, COX-2, and PGE2 levels; inhibiting the overproduction of MDA and MPO; and enhancing antioxidant enzymes by upregulating the Nrf2/ARE/PTEN signalling pathway.

NMR-based plasma metabolomics of adult B-cell acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is one of the common malignant tumors. Compared with childhood ALL, the treatment effect of adult B-cell ALL is less effective and remains a big challenge. In order to explore the pathogenesis of adult B-cell ALL and find new diagnostic biomarkers to develop sensitive diagnostic tools, we investigated the plasma metabolites of adult B-cell ALL by using ¹H NMR (nuclear magnetic resonance) metabolomics. Relative to healthy controls, adult B-cell ALL patients showed abnormal metabolism, including glycolysis, gluconeogenesis, amino acid metabolism, fatty acid metabolism and choline phospholipid metabolism. What's more important, we also found that the optimal combination of choline, tyrosine and unsaturated lipids has the potential to diagnose and prognose adult B-cell ALL in the clinic.

Gyejigachulbutang (Gui-Zhi-Jia-Shu-Fu-Tang, Keishikajutsubuto, TJ-18) in Degenerative Knee Osteoarthritis Patients: Lessons and Responders from a Multicenter Randomized Placebo-Controlled Double-Blind Clinical Trial

Background

Gyejigachulbutang (GUI-ZHI-JIA-SHU-FU-TANG, GCB) is an herbal formula widely prescribed in traditional East Asian medicine practice for arthritis and muscle pain. We evaluated the efficacy and safety of GCB for degenerative knee osteoarthritis (KOA).

Methods

Eighty patients with KOA were randomly assigned to the GCB group or the placebo group in a 1 : 1 ratio in two Korean medicine hospitals. Patients took GCB or placebo three times a day for 4 weeks. Primary outcome was the change in the visual analogue scale (VAS) score for knee pain from baseline to 4^th week. Secondary outcomes were the change in the VAS score from baseline to 2^nd week and 8^th week, Korean Western Ontario and McMaster Universities Osteoarthritis Index (K-WOMAC), European Quality of Life Five Dimensions questionnaire (EQ-5D), and safety.

Results

There was no significant difference between the compared indicators of the GCB and placebo groups. However, in subgroup analysis, GCB was effective for subjects with a BMI lower than 25 kg/m². The dose of pain medication was significantly lower in the GCB group than in the placebo group after four weeks (p=0.016). There were no serious adverse events in the GCB group.

Conclusions

GCB was not effective in primary outcome analysis. In exploratory subgroup analysis, GCB might be effective for individuals with BMI lower than 25 kg/m² for the treatment of degenerative KOA. GCB may also help reduce the consumption of pain medication. Furthermore, research is required for our hypothesis. This trial is registered with KCT0003024.

Therapeutic targeting of the NRF2 and KEAP1 partnership in chronic diseases

The transcription factor NF-E2 p45-related factor 2 (NRF2; encoded by NFE2L2) and its principal negative regulator, the E3 ligase adaptor Kelch-like ECH-associated protein 1 (KEAP1), are critical in the maintenance of redox, metabolic and protein homeostasis, as well as the regulation of inflammation. Thus, NRF2 activation provides cytoprotection against numerous pathologies including chronic diseases of the lung and liver; autoimmune, neurodegenerative and metabolic disorders; and cancer initiation. One NRF2 activator has received clinical approval and several electrophilic modifiers of the cysteine-based sensor KEAP1 and inhibitors of its interaction with NRF2 are now in clinical development. However, challenges regarding target specificity, pharmacodynamic properties, efficacy and safety remain.

FBP2 and Talin-1 are potential protein markers for Mongolian medicine symptom evaluation in viral infectious diseases

BACKGROUND

Influenza, measles, and mumps are common viral infectious diseases in Mongolia. The traditional Mongolian medicine (TMM) classified them as warm disease, and still plays a major role in the diagnoses and treatments.

METHODS

To interpret the connotation of the complex theoretical system in TMM with scientific technique, in this study, a high throughput mass spectrometry was used to identify potential protein markers of TMM symptom types. Fifty venous blood samples were drawn from influenza, measles and mumps patients. Differential proteins between samples of patients diagnosed as immature and mature heat in TMM were detected by mass spectrometry.

RESULTS

After proteomics analysis, 1500 proteins and 7619 polypeptides were identified and 1323 in total showed differential expression between those 2 symptom types; then enrichment analysis of the differentially expressed proteins revealed the significant biological functions related to the differentially expressed proteins, including cardiomyopathy, several bacterial and parasitic infections, bacterial invasion of epithelial cells, insulin signaling pathway, and regulation of actin cytoskeleton. The network analysis showed that FBP2 and Talin-1 were critical points and might determine the evolution directions of TMM warm disease symptom.

CONCLUSIONS

This study suggests that the identified core differential proteins may be regarded as potential biomarkers, and benefit to evaluate the evolutionary tendency of TMM warm disease symptoms.

Nrf2 as a therapeutic target for rheumatic diseases

Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is a master regulator of cellular protective processes. Rheumatic diseases are chronic conditions characterized by inflammation, pain, tissue damage and limitations in function. Main examples are rheumatoid arthritis, systemic lupus erythematosus, osteoarthritis and osteoporosis. Their high prevalence constitutes a major health problem with an important social and economic impact. A wide range of evidence indicates that Nrf2 may control different mechanisms involved in the physiopathology of rheumatic conditions. Therefore, the appropriate expression and balance of Nrf2 is necessary for regulation of oxidative stress, inflammation, immune responses, and cartilage and bone metabolism. Numerous studies have demonstrated that Nrf2 deficiency aggravates the disease in experimental models while Nrf2 activation results in immunoregulatory and anti-inflammatory effects. These reports reinforce the increasing interest in the pharmacologic regulation of Nrf2 and its potential applications. Nevertheless, a majority of Nrf2 inducers are electrophilic molecules which may present off-target effects. In recent years, novel strategies have been sought to modulate the Nrf2 pathway which has emerged as a therapeutic target in rheumatic conditions.

Heritability of Cold and Heat Patterns: A Twin Study

In traditional East Asian medicine, cold-heat patterns have been widely used in the diagnosis and treatment of patients suffering from various diseases. The present study aimed to estimate the heritability of cold-heat patterns. Trained interviewers administered a cold-heat pattern questionnaire to 1,753 twins (mean age = 19.1 ± 3.1 years) recruited throughout South Korea. Correlations for the cold pattern (CP) were 0.42 (95% CI [0.28, 0.54]) for monozygotic (MZ) males, 0.16 (95% CI [-0.08, 0.39]) for dizygotic (DZ) males, 0.40 (95% CI [0.30, 0.49]) for MZ females, 0.30 (95% CI [0.12, 0.45]) for DZ females, and 0.07 (95% CI [-0.11, 0.25]) for opposite-sex DZ twins. The corresponding twin correlations for the heat pattern (HP) were 0.38 (95% CI [0.24, 0.51]), -0.22 (95% CI [-0.43, 0.02]), 0.34 (95% CI [0.24, 0.43]), 0.21 (95% CI [0.03, 0.37]), and 0.08 (95% CI [-0.10, 0.26]), respectively. These patterns of twin correlations suggested significant genetic effects on the HP and the CP. Model-fitting analysis revealed that heritability estimates in both sexes were 40% (95% CI [38, 42]) for the CP and 33% (95% CI [25, 42]) for the HP, with the remaining variances attributable to unique environmental variances. These estimates did not vary significantly with age during adolescence and young adulthood.

Systems Health: A Transition from Disease Management Toward Health Promotion

To date, most of the chronic diseases such as cancer, cardiovascular disease, and diabetes, are the leading cause of death. Current strategies toward disease treatment, e.g., risk prediction and target therapy, still have limitations for precision medicine due to the dynamic and complex nature of health. Interactions among genetics, lifestyle, and surrounding environments have nonnegligible effects on disease evolution. Thus a transition in health-care area is urgently needed to address the hysteresis of diagnosis and stabilize the increasing health-care costs. In this chapter, we explored new insights in the field of health promotion and introduced the integration of systems theories with health science and clinical practice. On the basis of systems biology and systems medicine, a novel concept called "systems health" was comprehensively advocated. Two types of bioinformatics models, i.e., causal loop diagram and quantitative model, were selected as examples for further illumination. Translational applications of these models in systems health were sequentially discussed. Moreover, we highlighted the bridging of ancient and modern views toward health and put forward a proposition for citizen science and citizen empowerment in health promotion.

Prediction of cold and heat patterns using anthropometric measures based on machine learning

OBJECTIVE

To examine the association of body shape with cold and heat patterns, to determine which anthropometric measure is the best indicator for discriminating between the two patterns, and to investigate whether using a combination of measures can improve the predictive power to diagnose these patterns.

METHODS

Based on a total of 4,859 subjects (3,000 women and 1,859 men), statistical analyses using binary logistic regression were performed to assess the significance of the difference and the predictive power of each anthropometric measure, and binary logistic regression and Naive Bayes with the variable selection technique were used to assess the improvement in the predictive power of the patterns using the combined measures.

RESULTS

In women, the strongest indicators for determining the cold and heat patterns among anthropometric measures were body mass index (BMI) and rib circumference; in men, the best indicator was BMI. In experiments using a combination of measures, the values of the area under the receiver operating characteristic curve in women were 0.776 by Naive Bayes and 0.772 by logistic regression, and the values in men were 0.788 by Naive Bayes and 0.779 by logistic regression.

CONCLUSIONS

Individuals with a higher BMI have a tendency toward a heat pattern in both women and men. The use of a combination of anthropometric measures can slightly improve the diagnostic accuracy. Our findings can provide fundamental information for the diagnosis of cold and heat patterns based on body shape for personalized medicine.

Targeted Metabolic Profiling of the Tg197 Mouse Model Reveals Itaconic Acid as a Marker of Rheumatoid Arthritis

Rheumatoid arthritis is a progressive, highly debilitating disease where early diagnosis, enabling rapid clinical intervention, would provide obvious benefits to patients, healthcare systems, and society. Novel biomarkers that enable noninvasive early diagnosis of the onset and progression of the disease provide one route to achieving this goal. Here a metabolic profiling method has been applied to investigate disease development in the Tg197 arthritis mouse model. Hind limb extract profiling demonstrated clear differences in metabolic phenotypes between control (wild type) and Tg197 transgenic mice and highlighted raised concentrations of itaconic acid as a potential marker of the disease. These changes in itaconic acid concentrations were moderated or indeed reversed when the Tg197 mice were treated with the anti-hTNF biologic infliximab (10 mg/kg twice weekly for 6 weeks). Further in vitro studies on synovial fibroblasts obtained from healthy wild-type, arthritic Tg197, and infliximab-treated Tg197 transgenic mice confirmed the association of itaconic acid with rheumatoid arthritis and disease-moderating drug effects. Preliminary indications of the potential value of itaconic acid as a translational biomarker were obtained when studies on K4IM human fibroblasts treated with hTNF showed an increase in the concentrations of this metabolite.

Differential Amino Acid, Carbohydrate and Lipid Metabolism Perpetuations Involved in a Subtype of Rheumatoid Arthritis with Chinese Medicine Cold Pattern

Pattern classification is a key approach in Traditional Chinese Medicine (TCM), and it is used to classify the patients for intervention selection accordingly. TCM cold and heat patterns, two main patterns of rheumatoid arthritis (RA) had been explored with systems biology approaches. Different regulations of apoptosis were found to be involved in cold and heat classification in our previous works. For this study, the metabolic profiling of plasma was explored in RA patients with typical TCM cold or heat patterns by integrating liquid chromatography/mass spectrometry (LC/MS) and gas chromatography/mass spectrometry (GC/MS) platforms in conjunction with the Ingenuity Pathway Analysis (IPA) software. Three main processes of metabolism, including amino acid, carbohydrate and lipid were focused on for function analysis. The results showed that 29 and 19 differential metabolites were found in cold and heat patterns respectively, compared with healthy controls. The perturbation of amino acid metabolism (increased essential amino acids), carbohydrate metabolism (galactose metabolism) and lipid metabolism, were found to be involved in both cold and heat pattern RA. In particular, more metabolic perturbations in protein and collagen breakdown, decreased glycolytic activity and aerobic oxidation, and increased energy utilization associated with RA cold pattern patients. These findings may be useful for obtaining a better understanding of RA pathogenesis and for achieving a better efficacy in RA clinical practice.

Proteomics of hot-wet and cold-dry temperaments proposed in Iranian traditional medicine: a Network-based Study

Lack of molecular biology evidence has led clinical success of alternative and complementary medicine (CAM) to be marginalized. In turn, a large portion of life Science researchers could not communicate and help to develop therapeutic potential laid in these therapeutic approaches. In this study, we began to quantify descriptive classification theory in one of the CAM branches i.e. Iranian traditional medicine (ITM). Using proteomic tools and network analysis, the expressed proteins and their relationships were studied in mitochondrial lysate isolated from PBMCs from two different temperaments i.e. Hot-wet (HW) and Cold-dry (CD). The 82% of the identified proteins are over- or under-represented in distinct temperaments. Also, our result showed the different protein-protein interaction networks (PPIN) represented in these two temperaments using centrality and module finding analysis. Following the gene ontology and pathway enrichment analysis, we have found enriched biological terms in each group which are in conformity with the physiologically known evidence in ITM. In conclusion, we argued that the network biology which naturally consider life at the system level along with the different omics data will pave the way toward explicit delineation of the CAM activities.

Indo-Tibetan Philosophical and Medical Systems: Perspectives on the Biofield

The word biofield is a term that Western scientists have used to describe various aspects of energy and information fields that guide health processes. Similar concepts and descriptions of energy and information patterns exist in various cultures and have guided whole systems of medicine such as Ayurveda and Tibetan medicine. This article describes Vedic, Jain, and Tibetan philosophical and medical systems' concepts of consciousness and subtle energy and their relationships to health processes in order to foster deeper crosscultural dialogue on the nature of the biofield. Similarities and differences within the 3 traditions are noted, and suggestions for considering these concepts to extend current biofield research are discussed.

Review of the regulations for clinical research in herbal medicines in USA

In 2012, USA Food and Drug Administration (FDA) approved 39 new drugs, however, there are only two botanical drugs (one topical and one oral) approved by FDA since the publication of the FDA's industry guidelines for the botanical drug product in June 2004. The approval shows the Western guideline can be used for herbal medicines, authors investigate current regulation on herbal medicine clinical research, identify challenges conducting clinical trials, and seek to produce some guidance for potential investigators and sponsors considering a clinical trial in this area. Key words were formulated for searching on Medline and FDA website to locate relevant regulations for clinical research in herbal medicines to understand current environment for herbal medicine usage and examine the barriers affecting herbal medicine in clinical trials. Authors critically explore case study of the 1st FDA approved botanical drugs, Veregen (sinecatechins), green tea leaves extract, a topical cream for perianal and genital condyloma. In consideration of current regulation environment in USA, based on the findings and analysis through the literature review and Veregen case study, authors produce and propose a Checklist for New Drug Application of Herbal Medicines for potential investigators and sponsors considering in a herbal medicine clinical trial.

Progress and perspectives of biomarker discovery in Chinese medicine research

Biomarker discovery in Chinese medicine (CM) has recently attracted a great deal of attention, owing to the promise of high-throughput technologies development and the potential of Chinese herbal medicine. Furthermore, it seems that pattern classification in CM might be serving as inspirational analogy and a practical guide, which might contribute to biomarkers discovery rather than just being used as diagnostic method. Although much work is still needed to identify markers, efforts are now being directed towards discovering biomarkers or biomarkers based network that could target herbal formulae. In this article, we review progress in biomarker discovery development, discuss current biomarker discovery in CM highlighting challenges and opportunities of pattern classification and presenting a perspective of the future integrative modeling approaches as an emerging trend in biomarker discovery.

Why is Research on Herbal Medicinal Products Important and How Can We Improve Its Quality?

Research on herbal medicinal products is increasingly published in “Western” scientific journals dedicated primarily to conventional medicines. Publications are concerned mainly not only on the issues of safety and interactions, but also on efficacy. In reviews, a recurring complaint has been a lack of quality studies. In this opinion article, we present the case of Chinese herbal medicines as an example, as they have been extensively used in the global market and increasingly studied worldwide. We analyze the potential reasons for problems and propose some ways forward. As in the case of any drug, clinical trials for safety, efficacy, and/or effectiveness are the ultimate demonstration of therapeutic usefulness of herbal products. These will only make scientific sense when the tested herbal products are authentic, standardized, and quality controlled, if good practice guidelines of evidence-based medicine are followed, and if relevant controls and outcome measures are scientifically defined. Herbal products are complex mixtures, and for such complexity, an obvious approach for mechanistic studies is network pharmacology based on omic tools and approaches, which has already begun to revolutionize the study of conventional drugs, emphasizing networks, interactions, and polypharmacological features behind the action of many drugs.

Convergent Lines of Descent: Symptoms, Patterns, Constellations, and the Emergent Interface of Systems Biology and Chinese Medicine

During the first decade of the twenty-first century, a network composed of politicians, regulators, bioscientists, clinical researchers, and Chinese medicine specialists has emerged that seeks to bridge an imagined gulf between the modern West and ancient China in order to create a new type of personalized medicine. The central building block of this bridge is the Chinese medical concept of zheng /, variously translated into English as syndrome, pattern, or type. My paper places side by side two different genealogies of how zheng assumed this central role. The first genealogy examines the process by means of which zheng came to be considered as something shared by both ancient China and cutting-edge biological science and, by extension, how it manages to hold together the entire institutional, political, and economic framework into which this bridge is embedded and which it co-creates. The second genealogy shows zheng to be central to a much older series of redefinitions of Chinese medicine and Chinese medical practice that extend from the eleventh century to the present. Read together, these two genealogies-neither of which should be seen as exhaustive-raise three important issues that are further discussed in the conclusion of the paper. First, I explore how the concept of zheng has come to tie a medical tradition derided by its adversaries for being a pseudoscience to one of the most cutting-edge fields of bioscience research. I ask what is at stake in this synthesis, for whom, and why, and how it transforms Chinese medicine and/or systems biology along the way. Second, I am interested in finding out how and why the very same concept can be at the heart of two apparently agonistic visions of Chinese medicine's future as it is popularly imagined in China today. Finally, I insist that the medical humanities need to become actively involved in the construction of emergent articulations such as the ones I am exploring. Merely writing a history of the present will not be productive unless its critique can somehow be articulated into the very processes of emergence that historians or anthropologists seek to examine.

Looking back into the future: 30 years of metabolomics at TNO

Metabolites have played an essential role in our understanding of life, health, and disease for thousands of years. This domain became much more important after the concept of metabolism was discovered. In the 1950s, mass spectrometry was coupled to chromatography and made the technique more application-oriented and allowed the development of new profiling technologies. Since 1980, TNO has performed system-based metabolic profiling of body fluids, and combined with pattern recognition has led to many discoveries and contributed to the field known as metabolomics and systems biology. This review describes the development of related concepts and applications at TNO in the biomedical, pharmaceutical, nutritional, and microbiological fields, and provides an outlook for the future.

Molecular network and chemical fragment-based characteristics of medicinal herbs with cold and hot properties from Chinese medicine

ETHNOPHARMACOLOGICAL RELEVANCE

Chinese herbal medicines (HMs) is one of the great herbal systems of the world, which play an important role in current health care system in many countries. In the view of tradition Chinese medicine (TCM) theory, Yin-yang and five-elements theory is the central theory, which is used to explain how the world and body work. Under the guidance of such philosophy, TCM considers that HMs have different properties, which are the important factors for prescribing herbal formulae; such prescriptions are based on TCM pattern classification in clinical practice. The cold and hot property are commonly defined for HM property identification; however, the biological activities that are related to the HM property remain a mystery because of a lack of appropriate methods. A bioinformatics approach was applied to identify the distinguishing biological activities of HMs that have these cold and hot properties.

MATERIAL AND METHODS

Twenty HMs with typical cold and hot properties (10 cold and 10 hot) were selected based on TCM clinical application records and Chinese pharmacopeia. The active target proteins of each HM were searched in the PubChem database and were analyzed in Ingenuity Pathway Analysis (IPA) platform to find out the HM property-related biological activities. In addition, the main compounds of the HMs were fragmented using a fragment-based approach and were analyzed for the purpose of deciphering the properties.

RESULTS

The main biological networks of HMs with cold and hot properties include cell cycle, cellular growth, proliferation and development, cancer, cytokine signaling, and intracellular and second messenger signaling; 11 specific pathways are presented to be perturbed only by HMs with the hot property, and the 27 specific target protein molecules include PRKACA, PRKCA, PRKCB, PRKCD, PRKCE, PRKCG, PRKD1, TLR4, TLR7, TLR8, TLR9, HTR4, HTR6, HTR7, HTR2A, HTR1B, HTR2B, GNAO1, GNAI1, TNF, IL8, ROCK2, AKT1, MAPK1, RPS6KA1, RPS6KA3 and JAK2, which are involved in the biological network. One specific pathway is detected to be involved in the biological network of HMs with the cold property, the specific molecules are RAN and KPNB1. Cold propertied HMs show intensive toxicity in the heart, liver and kidney compared with hot HMs, which is likely to be correlated with the specific chemical fragments constructions in the HMs with the cold property, such as long chain alkenes, Benzo heterocycle and azotic heterocycle according to the chemical fragment analysis for the HMs.

CONCLUSIONS

Inflammation and immunity regulation are more related to HMs with the hot property, and cold propertied HMs possess the tendency to impact cell growth, proliferation and development. Integrative bioinformatics analysis and chemical structure analysis are a promising methods for identifying the biological activity of HM properties.

Serum metabolic signatures of four types of human arthritis

Similar symptoms of the different types of arthritis have continued to confound the clinical diagnosis and represent a clinical dilemma making treatment choices with a more personalized or generalized approach. Here we report a mass spectrometry-based metabolic phenotyping study to identify the global metabolic defects associated with arthritis as well as metabolic signatures of four major types of arthritis--rheumatoid arthritis (n = 27), osteoarthritis (n = 27), ankylosing spondylitis (n = 27), and gout (n = 33)--compared with healthy control subjects (n = 60). A total of 196 metabolites were identified from serum samples using a combined gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF MS) and ultraperformance liquid chromatography quadrupole-time-of-flight mass spectrometry (UPLC-QTOF MS). A global metabolic profile is identified from all arthritic patients, suggesting that there are common metabolic defects resulting from joint inflammation and lesion. Meanwhile, differentially expressed serum metabolites are identified constituting an unique metabolic signature of each type of arthritis that can be used as biomarkers for diagnosis and patient stratification. The results highlight the applicability of metabonomic phenotyping as a novel diagnostic tool for arthritis complementary to existing clinical modalities.

Clinical Applications of Omics Technologies on ZHENG Differentiation Research in Traditional Chinese Medicine

Traditional Chinese medicine (TCM) ZHENG is the basic concept of TCM theory. The effectiveness of TCM treatment depends on the accuracy of ZHENG differentiation. ZHENG differentiation, using the "four diagnostic methods," has the drawbacks of subjectivity and variability. Following development of omics technologies, which study the functional activities of human body from a system-wide perspective, it has been more and more applied in study of objectivity differentiating TCM ZHENG and understanding its biological mechanisms. This paper reviewed the literatures of clinical TCM ZHENG differentiation researches, underlying omics technologies, and indicated the increased trends of related articles with four kinds of omics technologies, including genomics, transcriptomics, proteomics and metabolomics, and the correlations between ZHENG differentiation and findings in omics studies. Moreover, the paper summarized the typical omics application in common studied diseases and TCM ZHENGs and discussed the main problems and countermeasure of ZHENG differentiation researches. The work here may provide a reference for further research of TCM ZHENG differentiation using omics technologies.

Differences of excess and deficiency zheng in patients with chronic hepatitis B by urinary metabonomics

Traditional Chinese medicine (TCM) physicians stratify patients with the same disease into different subtypes in order to guide the appropriate treatment, which is called Zheng (TCM syndrome) classification. Excess and deficiency ZHENG is a couple of basic ZHENGs of maladjusted body nature, reflecting the struggling state of human body and pathogenic factor and is important and prevalently exists in the ZHENG classification of many diseases. The present work using chronic hepatitis B (CHB) as an entry point explored the substance connotation of excess and deficiency ZHENG with the metabonomic technology based on gas chromatography-mass spectrometry (GC-MS). The different substantial basis of two ZHENGs suggested that CHB patients could be categorized into two groups with diverse pathogenesis. The differential metabolites and disturbed pathways compared to not-obvious ZHENG characters patients (without ZHENG group/WZ) were selected in both of the two ZHENGs. The ROC analysis demonstrated that five metabolites had a greater potential to be the clinic biomarkers of EZ or DZ. And excess ZHENG revealed a higher level of immune function than deficiency ZHENG. We are eager to transform the concept of traditional excess and deficiency ZHENGs to modern therapeutic approaches, with the prospect to help to promote personalized medicine.

ZHENG-Omics Application in ZHENG Classification and Treatment: Chinese Personalized Medicine

With the hope to provide an effective approach for personalized diagnosis and treatment clinically, traditional chinese medicine (TCM) is being paid increasing attention as a complementary and alternative medicine. It performs treatment based on ZHENG (TCM syndrome) classification, which could be identified clinical special phenotypes by symptoms and signs of patients even if they have a different disease. However, it caused controversy because ZHENG classification only depends on observation, knowledge, and clinical experience of TCM practitioners, which lacks objectivity and repeatability. Although researchers and scientists of TCM have done some work with a lot of beneficial methods, the results could not reach satisfactory with the shortcomings of generalizing the entire state of the body or ignoring the patients' feelings. By total summary, mining, and integration of existing researches, the present paper attempts to introduce a novel macro-microconcept of ZHENG-omics, with the prospect of bright future in providing an objective and repeatable approach for Chinese personalized medicine in an effective way. In this paper, we give the brief introduction and preliminary validation, and discuss strategies and system-oriented technologies for achieving this goal.

Ultra performance liquid chromatography-based metabonomic study of therapeutic effect of the surface layer of Poria cocos on adenine-induced chronic kidney disease provides new insight into anti-fibrosis mechanism

The surface layer of Poria cocos (Fu-Ling-Pi, FLP) is commonly used in traditional Chinese medicine and its diuretic effect was confirmed in rat. Ultra performance liquid chromatography/quadrupole time-of-flight high-sensitivity mass spectrometry and a novel mass spectrometry^{Elevated Energy} data collection technique was employed to investigate metabonomic characteristics of chronic kidney disease (CKD) induced from adenine excess and the protective effects of FLP. Multiple metabolites are detected in the CKD and are correlated with progressive renal injury. Among these biomarkers, lysoPC(18∶0), tetracosahexaenoic acid, lysoPC(18∶2), creatinine, lysoPC (16∶0) and lysoPE(22∶0/0∶0) in the FLP-treated group were completely reversed to levels in the control group which lacked CKD. Combined with biochemistry and histopathology results, the changes in serum metabolites indicate that the perturbations of phospholipids metabolism, energy metabolism and amino acid metabolism are related to adenine-induced CKD and to the interventions of FLP on all the three metabolic pathways. FLP may regulate the metabolism of these biomarkers, especially their efficient utilization within the context of CKD. Furthermore, these biomarkers might serve as characteristics to explain the mechanisms of FLP.

Metabolomics as a tool for personalizing medicine: 2012 update

Numerous factors in conjunction with an individual’s genetic make up will determine predisposition to disease, adverse or beneficial effects of drug treatment or therapy, and disease progression. A major limitation of current clinical measures is that the disease phenotype, which is comprised of the genotype and other environmental factors, is underestimated. Rather, each disease is treated similarly even though the disease process is highly complex. Methods that evaluate the interaction of genotype and environmental factors would likely be a better indicator of patients’ response to medical treatments. The omics technologies, specifically metabolomics, will play a major role in the movement towards personalized medicine. Metabolomics is phenotype driven and should provide better clinical biomarkers. Furthermore, recent studies have shown that associations between genetic variants and downstream metabolite changes can provide a unique description of an individual’s genotype and phenotype, which will further enhance the movement towards personalized medicine.

A Metabolomics Profiling Study in Hand-Foot-and-Mouth Disease and Modulated Pathways of Clinical Intervention Using Liquid Chromatography/Quadrupole Time-of-Flight Mass Spectrometry

Hand-foot-and-mouth disease (HFMD), with poorly understood pathogenesis, has become a major public health threat across Asia Pacific. In order to characterize the metabolic changes of HFMD and to unravel the regulatory role of clinical intervention, we have performed a metabolomics approach in a clinical trial. In this study, metabolites profiling was performed by liquid chromatography/quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) platform from the HFMD clinical patient samples. The outcome of this study suggested that 31 endogenous metabolites were mainly involved and showed marked perturbation in HFMD patients. In addition, combination therapy intervention showed normalized tendency in HFMD patients in differential pathway. Taken together, these results indicate that metabolomics approach can be used as a complementary tool for the detection and the study of the etiology of HFMD.

Traditional chinese medicine-based network pharmacology could lead to new multicompound drug discovery

Current strategies for drug discovery have reached a bottleneck where the paradigm is generally “one gene, one drug, one disease.” However, using holistic and systemic views, network pharmacology may be the next paradigm in drug discovery. Based on network pharmacology, a combinational drug with two or more compounds could offer beneficial synergistic effects for complex diseases. Interestingly, traditional chinese medicine (TCM) has been practicing holistic views for over 3,000 years, and its distinguished feature is using herbal formulas to treat diseases based on the unique pattern classification. Though TCM herbal formulas are acknowledged as a great source for drug discovery, no drug discovery strategies compatible with the multidimensional complexities of TCM herbal formulas have been developed. In this paper, we highlighted some novel paradigms in TCM-based network pharmacology and new drug discovery. A multiple compound drug can be discovered by merging herbal formula-based pharmacological networks with TCM pattern-based disease molecular networks. Herbal formulas would be a source for multiple compound drug candidates, and the TCM pattern in the disease would be an indication for a new drug.

Bridging the traditional Chinese medicine pattern classification and biomedical disease diagnosis with systems biology

Being the unique core of traditional Chinese medicine (TCM), pattern classification exerts a direct effect on the efficacy and safety of herbal interventions. In this article, the authors integrated the pattern classification and disease diagnosis with many approaches from systems biology. Integration of pattern classification with biomedical diagnosis by systems biology is not only a new direction of personalized medicine development, but also provides a new drug development model. In the further study, the pattern classifications of major diseases will be the focus of research.

Characterization of rheumatoid arthritis subtypes using symptom profiles, clinical chemistry and metabolomics measurements

OBJECTIVE

The aim is to characterize subgroups or phenotypes of rheumatoid arthritis (RA) patients using a systems biology approach. The discovery of subtypes of rheumatoid arthritis patients is an essential research area for the improvement of response to therapy and the development of personalized medicine strategies.

METHODS

In this study, 39 RA patients are phenotyped using clinical chemistry measurements, urine and plasma metabolomics analysis and symptom profiles. In addition, a Chinese medicine expert classified each RA patient as a Cold or Heat type according to Chinese medicine theory. Multivariate data analysis techniques are employed to detect and validate biochemical and symptom relationships with the classification.

RESULTS

The questionnaire items 'Red joints', 'Swollen joints', 'Warm joints' suggest differences in the level of inflammation between the groups although c-reactive protein (CRP) and rheumatoid factor (RHF) levels were equal. Multivariate analysis of the urine metabolomics data revealed that the levels of 11 acylcarnitines were lower in the Cold RA than in the Heat RA patients, suggesting differences in muscle breakdown. Additionally, higher dehydroepiandrosterone sulfate (DHEAS) levels in Heat patients compared to Cold patients were found suggesting that the Cold RA group has a more suppressed hypothalamic-pituitary-adrenal (HPA) axis function.

CONCLUSION

Significant and relevant biochemical differences are found between Cold and Heat RA patients. Differences in immune function, HPA axis involvement and muscle breakdown point towards opportunities to tailor disease management strategies to each of the subgroups RA patient.

Future perspectives of Chinese medical formulae: chinmedomics as an effector

Traditional Chinese medicine (TCM) has been used for thousands of years to treat or prevent disease. The health care paradigm has shifted from a focus on disease to TCM therapy with a holistic approach. However, the actual value of TCM has not been fully recognized worldwide due to a lack of scientific approaches to its study. Today omics has become practically available, and resembles TCM in many aspects, and can serve as a key driving force for the translation of the traditional Chinese medical formulae (chinmediformulae) into practice, and will develop and advance the concept of the metabolomics of chinmediformulae (chinmedomics). Chinmedomics seeks to elucidate the therapeutic and synergistic properties and metabolism of chinmediformulae and the involved metabolic pathways using modern analytical techniques. It is an integral part of top-down systems biology, which aims to improve understanding of chinmediformulae. This approach of combining chinmedomics with chinmediformulae with modern health care systems may lead to a revolution in TCM therapy. Although the scientific study of chinmedomics is at an early stage and requires further scrutiny and validation, the approach has major implications to improve the efficacy of chinmediformulae. This article introduces and reviews the concept of chinmedomics, and highlights recent examples of the approach, which are presented for description and discussion.