Genetic Study of Complex Diseases in the Post-GWAS Era

Genome-wide association studies （GWASs） have identified thousands of genes and genetic variants （mainly SNPs） that contribute to complex diseases in humans. Functional characterization and mechanistic elucidation of these SNPs and genes action are the next major challenge. It has been well established that SNPs altering the amino acids of protein-coding genes can drastically impact protein function, and play an important role in molecular pathogenesis. Functions of regulatory SNPs can be complex and elusive, and involve gene expression regulation through the effect on RNA splicing, transcription factor binding, DNA metbylation and miRNA recruitment. In the present review, we summarize the recent progress in our understanding of functional consequences of GWAS-associated non-coding regulatory SNPs, and discuss the application of systems genetics and network biology in the interpretation of GWAS findings.

Twin-Based DNA Methylation Analysis Takes the Center Stage of Studies of Human Complex Diseases

The etiology of complex diseases is characterized by the interaction between the genome and environmental conditions and the interface of epigenetics may be a central mechanism. Current technologies already allow us high-throughput profiling of epigenetic patterns at genome level. However, our understanding of the epigenetic processes remains limited. Twins are special samples in genetic studies due to their genetic similarity and rearing-environment sharing. In the past decades, twins have made a great contribution in dissecting the genetic and environmental contributions to human diseases and complex traits. In the era of functional genomics, the valuable samples of twins are helping to bridge the gap between gene activity and environmental conditions through epigenetic mech- anisms unlimited to DNA sequence variations. We review the recent progresses in using twins to study disease-related molecular epigenetic pbenotypes and link them with environmental exposures especially early life events. Various study designs and application issues will be highlighted and discussed with aim at making uses of twins in assessing the environmental impact on epigenetic changes during the development of complex diseases.

Pathway-based Analysis Tools for Complex Diseases: A Review

Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehen- sive understanding of the molecular mechanisms underlying complex diseases. Extensive studies uti- lizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available path- way-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are dis- cussed. This review will provide a useful guide to dissect complex diseases.

Role of renin-angiotensin system/angiotensin converting enzyme-2 mechanism and enhanced COVID-19 susceptibility in type 2 diabetes mellitus

Coronavirus disease 2019(COVID-19)is a disease that caused a global pandemic and is caused by infection of severe acute respiratory syndrome coronavirus 2 virus.It has affected over 768 million people worldwide,resulting in approx-imately 6900000 deaths.High-risk groups,identified by the Centers for Disease Control and Prevention,include individuals with conditions like type 2 diabetes mellitus(T2DM),obesity,chronic lung disease,serious heart conditions,and chronic kidney disease.Research indicates that those with T2DM face a hei-ghtened susceptibility to COVID-19 and increased mortality compared to non-diabetic individuals.Examining the renin-angiotensin system(RAS),a vital regulator of blood pressure and pulmonary stability,reveals the significance of the angiotensin-converting enzyme(ACE)and ACE2 enzymes.ACE converts angiotensin-I to the vasoconstrictor angiotensin-II,while ACE2 counters this by converting angiotensin-II to angiotensin 1-7,a vasodilator.Reduced ACE2 exp-ression,common in diabetes,intensifies RAS activity,contributing to conditions like inflammation and fibrosis.Although ACE inhibitors and angiotensin receptor blockers can be therapeutically beneficial by increasing ACE2 levels,concerns arise regarding the potential elevation of ACE2 receptors on cell membranes,potentially facilitating COVID-19 entry.This review explored the role of the RAS/ACE2 mechanism in amplifying severe acute respiratory syndrome cor-onavirus 2 infection and associated complications in T2DM.Potential treatment strategies,including recombinant human ACE2 therapy,broad-spectrum antiviral drugs,and epigenetic signature detection,are discussed as promising avenues in the battle against this pandemic.

Application of SYNTAX and its Derivative Scores in the Selection of Revascularization Strategies for Complex Coronary Heart Disease

Complex coronary heart disease(CHD)has become a hot spot in medicine due to its complex coronary anatomy,variable clinical factors,difficult hemodynamic reconstruction,and limited effect of conservative drug treatment.Identifying complex CHD and selecting optimal treatment methods have become more scientific as revascularization technology has improved,and coronary risk stratification scores have been introduced.SYNTAX and its derivative scores are decision-making tools that quantitatively describe the characteristics of coronary lesions in patients based on their complexity and severity.The SYNTAX and its derivative scores could assist clinicians in rationalizing the selection of hemodynamic reconstruction treatment strategies,and have demon-strated outstanding value in evaluating the prognosis of patients with complex CHD undergoing revascularization treatment.The authors in this article summary the practical application of SYNTAX and its derivative scores in complex CHD in order to deepen the understanding of the relationship between the choice of different revascularization strategies and SYNTAX and its derived scores in complex CHD and provide a further reference for clinical treatment of complex CHD.

Complement Protection Against Immune Complex and Acute Glomerulonephritis

in this study serum complement mediated immune complex solubilizing capacity (CMSC) and immune complement precipitation capacity (ICPIC) of 32 children with acute glomerulonephritis (AGN) were measured. The data showed that the level of serum CMSC and ICPIC was markedly decreased in acute phase and returned to normal in the 7th week after onset of disease.Correlation analysis revealed that there were positive correlation between the level of serum CMSC and ICPIC and the serum concentration of CH50, C3, C4, but no linear correlation between the level of serum CMSC and ICPIC and the amount of CIC. These results suggest that the declined serum CMSC and ICPIC in AGN may be associ ated with the pathogenesis of AGN.

Management of Wilt Complex of Eggplant (<i>Solanum melongena</i>L.) Caused by <i>Fusarium oxysporum, Ralstonia solanacearum</i>and <i>Meloidogyne</i>spp.

Wilt complex disease of eggplant is a severe problem in Bangladesh as well as in the world. The pathogenic variability and their survival nature make the disease complex. The pathogen includes a fungus (Fusarium oxysporum), a bacterium (Ralstonia solanacearum) and a nematode (Meloidogyne spp.) that attack the plant individually or combinedly. The present investigation aimed to evaluate the integrated effects of different chemicals, poultry manure and Trichoderma harzianum to manage the disease. Carbendazim (Autostin 50WP), Streptomycin sulphate 9% and Tetracycline hydrochloride 1% (Krosin 10SP) and Carbofuran (Furadan 3G) were used as a fungicide, bactericide and nematicide, respectively which were integrated with poultry manure and Trichoderma harzianum resulting in sixteen treatments. The treatment efficacy varied significantly in comparison to control in respect of wilt incidence, yield and yield contributing characters. No wilt incidence was observed where Trichoderma harzianum was applied individually or in combination with Furadan 3G, Krosin 10SP, Autostin 50WP and poultry manure. The highest yield increase (300%) over control was noted in the treatment where Krosin 10SP, Furadan 3G, Trichoderma harzianum and Poultry manure were applied combinedly. The same treatment showed the best performance over control by 32%, 29%, 60%, 53% in case of the number of branches, number of leaves, number of fruits and fruit length, respectively. This treatment (Krosin 10SP + Furadan 3G + Trichoderma sp. + Poultry manure) also provided the highest Benefit Cost Ration (5.68).

Assessment of Intracardiac and Extracardiac Deformities in Patients with Various Types of Pulmonary Atresia by Dual-Source Computed Tomography

Background:Pulmonary atresia(PA)is a group of heterogeneous complex congenital heart disease.Only one study modality might not get a correct diagnosis.This study aims to investigate the diagnostic power of dualsource computed tomography(DSCT)for all intracardiac and extracardiac deformities in patients with PA compared with transthoracic echocardiography(TTE).Materials and Methods:This retrospective study enrolled 79 patients and divided them into three groups according to their main diagnosis.All associated malformations and clinical information,including treatments,were recorded and compared among the three groups.The diagnostic power of DSCT and TTE on all associated malformations were compared.The surgical index(McGoon ratio,pulmonary arterials index(PAI),and total neopulmonary arterial index)and radiation dose were calculated on the basis of DSCT.Results:Of the patients,32,30,and 17 were divided into the groups of PA with ventricular septal defect(VSD),PA with VSD and major aortopulmonary collateral arteries,and PA with other major malformations,respectively.Consequently,182,162,and 13 intracardiac,extracardiac,and other major malformations were diagnosed,respectively.Moreover,DSCT showed a better diagnostic performance in extracardiac deformities(154 vs.117,p<0.001),whereas TTE could diagnose intracardiac deformities better(159 vs.139,p=0.001).The McGoon ratio,PAI,and treatment methods were significantly different among the three groups(p=0.014,p=0.008,and p=0.018,respectively).Conclusion:More than one imaging modality should be used to make a correct diagnosis when clinically suspecting PA.DSCT is superior to TTE in diagnosing extracardiac deformities and could be used to roughly calculate surgical indices to optimize treatment strategy.

Future impact of integrated high-throughput methylome analyses on human health and disease

A spate of high-powered genome-wide association studies （GWAS） have recently identified numerous single-nucleotide polymorphisms （SNPs） robustly linked with complex disease. Despite interrogating the majority of common human variation, these SNPs only account for a small proportion of the phenotypic variance, which suggests genetic factors are acting in concert with non-genetic factors. Although environmental measures are logical covariants for genotype-phenotype investigations, another non-genetic intermediary exists： epigenetics. Epigenetics is the analysis of somatically-acquired and, in some cases, transgenerationally inherited epigenetic modifications that regulate gene expression, and offers to bridge the gap between genetics and environment to understand phenotype. The most widely studied epigenetic mark is DNA methylation. Aberrant methylation at gene promoters is strongly implicated in disease etiology, most notably cancer. This review will highlight the importance of DNA methylation as an epigenetic regulator, outline techniques to characterize the DNA methylome and present the idea of reverse phenotyping, where multiple layers of analysis are integrated at the individual level to create personalized digital phenotypes and, at a phenotype level, to identify novel molecular signatures of disease.

Balloon Angioplasty as a Modality to Treat Children with Pulmonary Stenosis Secondary to Complex Congenital Heart Diseases

Background： Pulmonary stenosis is common in children with complex congenital heart diseases. Proper management of this problem, especially postoperatively, is still controversial. This study was designed to assess the rate and determinants of success or failure of balloon angioplasty for such lesions. Methods： Clinical and hemodynamic data from 40 pediatric patients （24 boys and 16 girls） with complex congenital heart diseases who underwent balloon angioplasty were reviewed retrospectively from January 2012 to December 2016. Patients were divided into four groups according to the site of stenosis, which included pulmonary valve stenosis （PVS）, valved conduit stenosis, pulmonary artery stenosis （PAS）, and supravalvular pulmonary stenosis （SVPS）. Success rates were calculated according to defined criteria for initial success and favorable clinical impacts, and comparison between the successful subgroup and the unsuccessful subgroups was analyzed. Results： Grouped by the site of stenosis, initial success rates varied from 40.0% to 52.4% with the greatest success being seen in the PVS group, followed by the PAS group and SVPS group. In the PVS group and the PAS group, there was no statistical difference among age at dilation, postoperative interval, balloon/stenosis ratio, or pressure gradient predilation between the successful and the unsuccessful subgroups. Favorable clinical impacts included success rates of balloon angioplasty in the SVPS group, which was best （100%）, followed by the PVS group （90.9%） and the PAS group （85.7%）. There were a total of two transient complications （5.0%）. Conclusions： Balloon angioplasty was proven to be a safe and useful modality in children with complex congenital heart diseases and postoperative pulmonary stenosis, which should be the initial therapeutic modality in selected patients.

Correlation between Hypertension and SYNTAX Score in Patients with Chest Pain Admitted to Cardiology Department for Coronary Angiography

Background: Hypertension is associated with an increased risk of cardiovascular events, cardiovascular and all-cause mortality. However, the diagnostic ability of hypertension for the presence and severity of CAD (coronary artery disease) has not been elucidated. This study investigates the relationship between hypertension and CAD complexity using the SYNTAX score to determine hypertension’s roles in coronary heart disease progression. Method: This is a prospective study that includes consecutive 410 adult patients at mean age (61 ± 11 years) who are admitted to Cardiology Department and undergo invasive coronary angiography (CAG) where a significant coronary lesion (SCL) is defined as stenosis ≥50% in vessel diameter ≥ 1.5 mm. The SYNTAX scores were calculated using the SYNTAX score algorithm. Results: The mean rank of SYNTAX score was significantly higher among hypertension than non-hypertension (mean rank: 279, 184, p = 0.006) groups. SYNTAX score was positively correlated with age (r: 0.263, p < 0.001) and LDL (correlation coefficient 0.102, p = 0.038) but inversely with HDL (r: 0.107, p = 0.031), in multivariate linear regression age (regression coefficient 0.3, p < 0.001), male (-4.4, p = 0.002), HDL (-6.4, p = 0.002) were significant independent risk factors for SYNTAX score, in ordinal regression model aging (odd ratio: 1.08, p < 0.001), being a male (2.84, p = 0.026), HDL (0.05, p < 0.001), BMI (0.86, p = 0.020) were significantly independent predictor of increase or decrease probability of falling in high syntax score group. Conclusion Hypertension affects the distribution of SYNTAX score among patients with and without hypertension, and the prevalence of significant coronary lesions was more frequent in hypertensive patients. Hypertension was not a predictor of significant or complex coronary artery lesion, but advanced age, being a male, HDL, LDL and BMI are considered as independent risk factors for high SYNTAX score, Subsequently and the complexity of CAD. Therefore, when patients with CAD have these factors, we expect that the Patient’s CAD complexity will be high.

Amyloid β and free heme：bloody new insights into the pathogenesis of Alzheimer＇s disease

The cerebral formation of Amyloid β（Aβ） is a critical pathological feature of Alzheimer＇s disease（AD）.An accumulation of this peptide as senile plaques（SP） was already reported by Alois Alzheimer,the discoverer of the disease.Yet the exact contribution of Aβ to AD development remains elusive.Moreover,while extensive cerebral Aβ formation leads to fibril formation in many species,AD-like symptoms apparently depend on the highly conserved N-terminal residues R5,Y10 and H13.The amino acids were also shown to lead to the formation of Aβ-heme complexes,which exhibit peroxidase activity in the presence of H_2O_2.Taking together these observations we propose that the formation and enzymatic activity of the named complexes may represent an essential aspect of AD pathology.Furthermore,Aβ is also known to lead to cerebral micro-vessel destruction（CAA） as well as to hemolytic events.Thus we suggest that the Aβ-derived cerebral accumulation of blood-derived free heme represents a likely precondition for the subsequent formation of Aβ-heme complexes.

Targeting Ageing to Decrease Complex Non-Communicable Human Diseases

During the last two centuries, there have been many spectacular advances in medical science, the main consequence of which has been the dramatically reduced burden of infectious diseases. While in the 1800s many people died before reaching adult- hood, nowadays most people survive. Hence average life ex- pectancy in 1800s was around 30-40, which was barely higher than it had been in Greek and Roman times （Finch, 2010）, but nowadays life expectancy in most modernised economies is around 75 - 80. This demographic shift, which has happened in only 200 years, has created a dramatic change in the causes of mortality. The major killers in the modern world are non- communicable diseases （NCDs）： principally cardiovascular disease, cancer and neurodegenerative disorders such as Alz- heimer＇s disease. A major factor that influences susceptibility to all these diseases is age. As we get older, our risk of developing these NCDs increases enormously. For example, the rate of breast cancer in females at age 15-19 is less than 10 per 100,000 population, but this increases to 100 at age 40-44, 275 at age 55--59 and 450 at age 85 ＋ （http：//www.cancerresearchuk.org/ cancer-info/cancerstats/types/breast/incidence/#age）. Ageing has consequently become a major medical, social and economic burden to many countries.

Low-Dose Unfractionated Heparin with Sequential Enoxaparin in Patients with Diabetes Mellitus and Complex Coronary Artery Disease during Elective Percutaneous Coronary Intervention

Background： Despite its limitations, unfractionated heparin （UFH） has been the standard anticoagulant used during percutaneous coronary intervention （PCl）. This study compared the safety of low-dose UFH with sequential enoxaparin with that of UFH in patients with diabetes mellitus （DM） and complex coronary artery disease receiving elective PCl. Methods： In this retrospective study, 514 consecutive patients with atherosclerotic cardiovascular diseases and type 2 DM were admitted to the hospital and received selective PCI, from January 2013 to December 2015. All patients with PCl received low-dose UFH with enoxaparin （intraductal 50 U/kg UFH and 0.75 mg/kg enoxaparin, n = 254; UFH-Enox group） or UFH only （intraductal 100 U/kg UFH, n = 260; UFH group）. The study endpoints were major adverse cardiac events （MACEs）, namely death, myocardial infarction （MI）, stroke, target-vessel immediate revascularization （TVR）, and thrombolysis in MI （TIMI） major bleeding, within 30 days and 1 year after PCI. Any catheter thrombosis during the procedure was recorded. Results： Only one patient had an intraductal thrombus in the UFH group. At the 30-day follow-up, no MACE occurred in any group; seven and five cases of recurrent angina and/or rehospitalization were reported in the UFH-Enox and UFH groups, respectively; there was no significant difference between the two groups （χ^2= 0.11, P = 0.77）. There was no TIMI major bleeding in the groups. With respect to the 1-year endpoint, two cases of recurrent MI and two of TVRs were reported in the UFH-Enox group, whereas in the UFH group, one case of recurrent MI and three of TVRs were reported; no significant difference existed between the two groups （χ^2 0, P= 0.99）. There were 30 and 25 recurrent angina and/or rehospitalizations in the UFH-Enox and UFH groups, respectively; there was no significant difl＇erence between the two groups （χ^2 = 0.37, P= 0.57）. Conclusion： In elective PCI, low-dose UFH with sequential enoxaparin has similar effects and safety to the UFH-only method.

Unfractionated Heparin with Sequential Enoxaparin in Patients with Complex Coronary Artery Lesions during Percutaneous Coronary Intervention

Background： Unfractionated heparin （UFH）, despite its limitations, has been used as the primary anticoagulant alternative during the percutaneous coronary intervention （PCI）. Some studies indicated that intravenous enoxaparin could be an effective and safe option. Our team used enoxaparin alone at one time according to the guidelines （Class IIA） and found a little catheter thrombosis during PCI. We recommend a new anticoagulation strategy using enoxaparin in combination with UFH. Enoxaparin has a more predictable anticoagulant response with no need of repeatedly monitoring anticoagulation during PCI. This retrospective study aimed to evaluate the efficacy and safety of using enoxaparin in combination with UFH in PCI patients with complex coronary artery disease. Methods： Between January 2015 and April 2017, 600 PCI patients who received intravenous UFH at an initial dose of 3000 U plus intravenous enoxaparin at a dose of 0.75 mg/kg （observation group） and 600 PCI patients who received UFH at a dose of 100 U/kg （control group） were consecutively included in this retrospective study. The endpoints were postoperative 48-h thrombolysis in myocardial infarction （TIMI） bleeding and transfusion and 30-day and l-year major adverse cardio-cerebrovascular events （MACCE）. Results： Baseline clinical, angiographic, and procedural characteristics were similar between groups, except there was less stent implantation per patient in the observation group （2.13 vs. 2.25 in the control group, P = 0.002）. TIMI bleeding （3.3% vs. 4.7%） showed no significant difference between the observation group and control group. During the 30-day follow-up, the rate of MACCE was 0.9% in the observation group and 1.5% in the control group. There was no significant difference in the rates of MACCE, death, myocardial infarction, target vessel revascularization, cerebrovascular event, and angina within 30 days and 1 year after PC1 between groups as well as in the subgroup analysis of transfemoral approach. Conclusions： UFH with sequential enoxaparin has similar anticoagulant effect and safety as UFH in PCI of complex coronary artery disease.

Genome-Wide Interaction-Based Association of Human Diseases—A Survey

Genome-Wide Association Studies（GWASs） aim to identify genetic variants that are associated with disease by assaying and analyzing hundreds of thousands of Single Nucleotide Polymorphisms（SNPs）. Although traditional single-locus statistical approaches have been standardized and led to many interesting findings, a substantial number of recent GWASs indicate that for most disorders, the individual SNPs explain only a small fraction of the genetic causes. Consequently, exploring multi-SNPs interactions in the hope of discovering more significant associations has attracted more attentions. Due to the huge search space for complicated multilocus interactions, many fast and effective methods have recently been proposed for detecting disease-associated epistatic interactions using GWAS data. In this paper, we provide a critical review and comparison of eight popular methods, i.e., BOOST, TEAM, epi Forest, EDCF, SNPHarvester, epi MODE, MECPM, and MIC, which are used for detecting gene-gene interactions among genetic loci. In views of the assumption model on the data and searching strategies, we divide the methods into seven categories. Moreover, the evaluation methodologies,including detecting powers, disease models for simulation, resources of real GWAS data, and the control of false discover rate, are elaborated as references for new approach developers. At the end of the paper, we summarize the methods and discuss the future directions in genome-wide association studies for detecting epistatic interactions.

Sorting and Processing of the Alzheimer's Disease Amyloid Precursor Protein Mediated by the AP-4 Complex

Proteolytic processing of the transmembrane amyloid precursor protein (APP) to aggregation-prone amyloid-β (Aβ) peptide underlies the development of Alzheimer’s disease.

The forty years of medical genetics in China

Medical genetics is the newest cutting-edge discipline that focuses on solving medical problems using genetics knowledge and methods. In China, medical genetics research activities initiated from a poor inner basis but a prosperous outer environment. During the 40 years of reform and opening-up policy,Chinese scientists contributed significantly in the field of medical genetics, garnering considerable attention worldwide. In this review, we highlight the significant findings and/or results discovered by Chinese scientists in monogenic diseases, complex diseases, cancer, genetic diagnosis, as well as gene manipulation and gene therapy. Due to these achievements, China is widely recognized to be at the forefront of medical genetics research and development. However, the significant progress and development that has been achieved could not have been accomplished without sufficient funding and a wellconstructed logistics network. The successful implementation of translational and precise medicine sourced from medical genetics will depend on an open ethics policy and intellectual property protection,along with strong support at the national industry level.

Protein interaction networks:centrality,modularity,dynamics,and applications

In the post-genomic era,proteomics has achieved significant theoretical and practical advances with the development of high-throughput technologies.Especially the rapid accumulation of protein-protein interactions(PPIs)provides a foundation for constructing protein interaction networks(PINs),which can furnish a new perspective for understanding cellular organizations,processes,and functions at network level.In this paper,we present a comprehensive survey on three main characteristics of PINs:centrality,modularity,and dynamics.1)Different centrality measures,which are used to calculate the importance of proteins,are summarized based on the structural characteristics of PINs or on the basis of its integrated biological information;2)Different modularity definitions and various clustering algorithms for predicting protein complexes or identifying functional modules are introduced;3)The dynamics of proteins,PPIs and sub-networks are discussed,respectively.Finally,the main applications of PINs in the complex diseases are reviewed,and the challenges and future research directions are also discussed.

Exploring Traditional Chinese Medicine by A Novel Therapeutic Concept of Network Target

Traditional Chinese medicine（TCM） holds a holistic theory, and specializes in balancing disordered human body using numerous natural products, particularly Chinese herbal formulae. TCM has certain treatment advantages for patients suffering from various complex diseases. However, due to the complex nature of TCM, it remains difficult to unveil such holistic medicine by the current reductionism research strategies, which treat both herbal ingredients and targets in isolation. Recently, an emerging network pharmacology approach has been introduced to tackle this bottleneck problem. A TCM-derived novel therapeutic concept, ＂network target＂, which is different from the Western medicine＇s ＂onetarget＂ concept, has been proposed from China. The network target strategy is able to illustrate the complex interactions among the biological systems, drugs, and complex diseases from a network perspective, and thus provides an innovative approach to access ancient remedies in a precision manner and at a systematic level, which also highlights TCM＇s potential in current medical systems.