Identification Of Homocysteine-Methionine Cycle Metabolic Genes Expression And The Role Of HMC In Physiological And Pathological Conditions By Bioinformatics Analysis

Homocysteine(Hcy)is metabolized by homocysteine-methionine cycle(HMC).Impaired metabolism due to genetic alteration in metabolic genes including cystathionine ?-synthase(CBS)or deficiency in cofactors including folate may lead to hyperhomocysteinemia(HHcy).HHcy is a risk factor for many diseases such as coronary artery disease(CAD),ischemia stroke.Numerous studies revealed that normal subcellular distribution of HMC metabolic genes plays an important role in maintaining methylation status and physiological functions.However,the questions regarding how HMC metabolic genes expressed in tissue and whether HMC metabolism in nuclear and cytoplasmic is the same or not are largely unknown.Furthermore,how tissue cells detect the increases of Hcy and its methylated metabolites and initiate specific SAM-dependent methylation signaling to maintain physiological functions are not clear.In addition,mechanisms underlying HHcyinduced diseases remain unclear.Objective:To establish tissue expression profiles of HMC metabolic genes in 21 human and 20 mouse tissues,identify the differences in HMC metabolism between nuclear and cytoplasmic,explore the role of HMC in detecting the concentrations of Hcy and its methylated metabolites and initiating specific SAM-dependent methylation pathways,investigate genes expression change,modulated pathways and induced site-specific histone in diseases and metabolic stimulations.Methods:One hundred fifteen HMC metabolic genes were selected for the assessment of tissue expression profiles.The mRNA expression levels(REU/ mREU)of selected genes across 21 human and 20 mouse tissues were examined and normalized by mining NIH UniGene database.Tissue expression levels of HMC metabolic genes were identification by percentage of gene significant expression,which defined as REU/ mREU more than 25%.According to the distribution of HMC metabolic enzymes in cytoplasm and nucleus,the differences of HMC metabolism in nuclear and cytoplasmic were identified and the possible mechanisms were proposed.To investigate the role of HMC in physiological and pathological conditions,we proposed a new concept that HMC can serve as a new sensor for detecting the increases of homocysteine(Hcy),methionine,S-adenosylmethione(SAM),and S-adenosylhomocysteine(SAH)and initiate methyl-donating signals,which can be “delivered” to specific methyltransferases.To examine our novel hypothesis that pathological conditions modulate the expressions of HMC metabolic genes for specific signaling,gene expression changes were analyzed with experimental data from the microarray datasets in diseases and metabolic stimulations.We also conducted Ingenuity pathway analysis(IPA)analysis on significantly upregulated genes,downregulated genes,up/downregulated genes,and no changed genes to summarize signaling pathways modulated in diseases and metabolic stimulations.Based on the differences of genes expression change in HMC four parts including AHCY,folate cycle,transsulfuration and remethylation,nine new patterns of gene expression changes in 20 diseases have been to discuss redox and methylation status.We also investigated the methylation change of lysine residues(Ks)and arginine residues(Rs)on the N-terminus of histone 3 and histone 4(H3 and H4)according to the expression change of histone methyltransferases in diseases and metabolic stimulations.Results:1).HMC genes are differentially expressed in human and mouse tissues.Twentyone human and 20 mouse tissues can be classified to 3 tiers,tier 1 tissue was termed as high frequency(H%?50%);tier 2 tissue was termed as middle frequency(20%?H%<50%);tier 3 tissue was termed as low frequency(H%<20%).2).Sadenosylhomocysteine hydrolase(AHCY),2 remethylation enzymes(BHMT,MAT1A),2 enzymes in folate cycle(MTR,SHMT1),2 transsulfuration enzymes(CBS,CTH),7 adenosine metabolic enzymes(SLC29A3,NT5C1 A,NT5C1B,NT5C2,NT5C3,NT5 C,ADK)and 21 methyltransferases(25%,21/84)are located in the cytosol.One enzyme in folate cycle(SHMT1),1 transsulfuration enzyme(CBS),2 adenosine metabolic enzymes(SLC29A2,NT5C1B)and 61 methyltransferases(73%,61/84)are located in the nucleus,however,AHCY,BHMT,MAT1 A are not located in the nucleus.3).In addition to enzymatic generation of SAH,Hcy,methionine,and SAM,HMC could serve as a new sensor for Hcy,SAM and SAH increase and SAM/SAH ratio changes via specific substrate-enzyme bindings and recognitions in HMC,and initiate specific SAM-dependent methyl donating signals.4).Diseases and metabolic stimulations unregulated 23 signaling pathways and downregulated 18 signaling pathways via modulated expression changes of HMC metabolic genes by IPA analysis.5).HHcy-induced diseases not only modulate genes in folate cycle and remethylation pathyways,but also modulate AHCY and genes in transsufulation parts,suggesting different change of Hcy metabolism.6).Twenty-five diseases conditions and 4 metabolic stimulations increase 84.5% of methylations on H3 residues but only increase 15.5% of methylations on H4 residues;pathological conditions decrease 79.5% of methylations on H3 residues but only decrease 20.5% of methylations on H4 residues.Interestingly,diseases share same histone methylation pattern.Conclusions:1).HMC genes are differentially expressed in human and mouse tissues.2).Methionine cycle is functional in cytosol rather than in nucleus,cytosol-nuclear SAM transporter and SAH transporter are required to keep HMC metabolic balance in cell since SAM and SAH cannot be generated or hydrolyzed in the nucleus,respectively.3).HMC serves as a novel metabolic sensor for detecting concentration changes of Hcy,methionine,SAM and SAH and initiate a broad spectrum of signaling pathways in modulating the pathogenesis of various diseases and physiological conditions.4).Classification of diseases according to changes in the expression of various parts of HMC contributes to the precise treatment of HHcy-related diseases,suggesting that the efficiency of folic acid and vitamin supplement may be compromised in some diseases.5).Histone methylation plays an important role in pathological conditions.One disease can induce methylation on different histone residues,different diseases can share same or similar methylation pattern.