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Depression 基因資料庫

https://www.dropbox.com/s/x847vhc17mhg9vn/MaND_v1.0.xlsx?dl=0

https://sites.google.com/site/depressiondatabase/
MaND這個資料庫內包含了許多的Depression影像的資料，不過我希望要用的是Depression的基因資料庫, 幫我找好biomarker的，因為只要確定目前Depression的機轉還是很不清楚，那用系統生物學的方法應該就是對的。
接下來就是共病性的問題，但是有多少的可能性是共病性的因子，或者是系統生物學網路的可能潛在相同的關係與交互的關係。
憂鬱症有多少的因素是天生，有多少的因素是因為吃了例如糖尿病的藥物，結果導致憂鬱症，或者是憂鬱症與糖尿病潛在有共病性的現象，那這樣的部份潛在的是如何解釋。



http://www.polygenicpathways.co.uk/depression.htm

Genes

Multiple genes of small effect, whose risk promoting ability is conditioned by other genes and risk factors: For this reason any positive studies are reported.
See also:- The fox and the rabbits, environmental variables and population genetics.1: Replication problems in association studies and the untapped power of GWAS. ISRN Neurology, 2011
GWAS ADCYAP1R1 AK294384 AMPD2 ATP6V1B2 ATXN7L2 BC043421 C2orf71 C3orf70 CCND2 CDH13 CDH18 CNIH4 CPM CYB561 D1SP4 DDX21 EHHADH EIF3 FAM155A FAM179A FHIT FITGB1 GDNF GNAI3 GNAT2 GRM7 GRM8 HOMER1 LAPTM4A LOC647167 LOC728275 LY86 LZTS1 NLGN1 NVL PARD3 PCLO PTPRG RORA SHC4 SLC6A15 SLC18A1 SLFN12L SP4 SYPL2 VCAN WDR26
Genes needing KEGG mapping:NOS3 SYNE1 CDH7 DHH. ACSM1 NDUFV2
KEGG pathway analysis of depression genes

Maternal, paternal and prenatal effects
Adult Infections
  • Depression is frequently observed in Hepatitis C infected patients Weinstein et al, 2011
  • and in Hepatitis B infection Altindag et al, 2009
  • or HIV-1 infection Bragança and Palha, 2011
  • and associated with herpes simplex encephalitis Fazekas et al, 2006
  • Depression has been associated with human T-cell lymphotropic virus( HTLV-1) infection Stumpf et al, 2008
  • Bornavirus infection or reactivation have been linked to depression and other affective disorders Ferszt et al, 1999
    • Bornavirus related symptomatology has been reported to be improved after CSF filtration Bechter et al, 2000
  • Seropositivity for influenza A, Influenza B and coronaviruses has been associated with a history of mood disorders but not with the specific diagnosis of unipolar or bipolar depression. Seropositivity for influenza B was associated with a history of suicide attempts and a history of psychotic symptoms Okusaga et al, 2011 .
  • Depression has been observed in poliomyelitis survivors Kang and Lin 2011
  • Chagas disease, caused by Trypanosoma Cruzi is associated with depression Ozaki et al, 2011
  • Varicella Zoster cell specific immunity was lower in depressed patients and inversely correlated with the severity of depressive symptoms .
    • Depression may increase the severity of herpes zoster (shingles) Irwin et al, 2011
  • Neurobrucellosis has been linked to depression Eren et al, 2006
  • Nipah virus encephalitis has been associated with depression Ng et al, 2004
  • Lyme disease (Borrelia infection) has ben aaaociated with depression Kaplan et al, 1999
  • Suicide attempts in recurrent mood disorders have been linked to T.Gondii seropositivity Arling et al, 2009
  • Sexually transmitted infections have been linked to depression Lee et al, 2009
  • High salivary Lactobacillus counts have been associated with depressive symptoms Anttila et al, 1999
  • Depression has been associated with tooth loss in older men Anttila et al, 2001
  • Antibodies to lipopolysaccharide of commensal bacteria (gram-negative enterobacteria, Hafnia Alvei, Pseudomonas Aeruginosa, Morganella Morganii, Pseudomonas Putida, Citrobacter Koseri, and Klebsielle Pneumoniae) have been associated with depression (bacterial translocation and "leaky gut") Maes et al, 2012 See also "So depression is an inflammatory disease, but where does the inflammation come from?" Berk et al, 2013
  • Skin infections commonly associated with psychiatric disorders including depression Gupta et al, 2013
  • Meta-analysis showed statistically significant associations between depression and infection with Borna disease virus, herpes simplex virus-1, varicella zoster virus, Epstein-Barr virus, and Chlamydophila trachomatis Wang et al, 2014.
The microbiome in depression
  • The order Bacteroidales showed an overrepresentation , while the family Lachnospiraceae showed an underrepresentation of Operational Taxonomic Units associated with depression (faecal microbiome) Naseribafrouei et al, 2014
  • Increased levels of Enterobacteriaceae and Alistipes but reduced levels of Faecalibacterium in the faecal microbiome in major depression Jiang et al, 2015.
  • Lower Bifidobacterium and/or Lactobacillus counts more common in patients with major depression disorders (faecal microbiome) Aizawa et al, 2016
Social factors
Association with other diseases
Dietary and environmental factors and drugs
  • Ecstasy use ( Methylenedioxymethamphetamine ) has been associated with depression Matthews and Bruno, 2010
  • Vitamin B12 or Holotranscobalamin deficiency has been linked with depression Robinson et al, 2011 coupled with high levels of homocysteine Almedia et al, 2008
    • High total intakes of vitamins B-6 and B-12 may protect against depresion in the elderly Skarupski et al, 2010
    • Long-term treatment of poststroke survivors with folic acid, vitamin B6, and B12 was associated with a reduction in major depression risk Almeida et al, 2010
  • Diethylstilbestrol use has been associated with depression in women Kebir and Krebs, 2011
  • Interferon alpha (used for hepatitis C treatment) is often associated with depression .Galvão-de Almeida et al, 2011
  • Childhood depression may be associated with future smoking Niemelä et al, 2009
  • Low fish consumption has been associated with severely depressed mood in men Li et al, 2011
  • Air pollution has been linked to depression Szyszkowicz and Tremblay, 2011
  • Serum cotinine levels ( an index of second hand smoke) has been associated with major depressive disorder, generalized anxiety disorder, attention-deficit/hyperactivity disorder, and conduct disorder Bandiera et al, 2011
  • Pesticide use, particularly paraquat, has ben associated with depression in farmers Kim et al, 2013
  • Herbicide use has been associated with depression in agricultural workers Weisskopf et al, 2013
  • Population suicide rates have been linked to the distribution of coal-fired electricity plants Spangler, 2013
  • higher urinary levels of manganese, tin, and phthalates including mono-2-ethyl-5-carboxypentyl, mono-n-butyl, mono-isobutyl, and mono-benzyl were associated with adult depression. Urinary polyaromatic hydrocarbons including 2-hydroxyfluorene, 3-hydroxyfluorene, 9-hydroxyfluorene, 1-hydroxyphenanthrene, 2-hydroxyphenanthrene, 3-hydroxyphenanthrene, 1-hydroxypyrene, 1-hydroxynaphthalene (1-naphthol), 2-hydroxynaphthalene (2-naphthol) and 4-hydroxyphenanthrene were associated with depression Shiue 2015.
  • Long-term particulate matter (PM2.5) exposure increases the risk of major depressive disorder Kim et al, 2016
  • Comparative toxicogenomics database: Bioinformatic predictions of environmental toxins, drugs , endogenous compounds and others related to depression
Biochemistry and pathology
  • Loss of white matter intergrity in the limbic system and frontal cortex related to demyelination Korgaonkar et al, 2011
  • Grey matter loss in the limbic system and frontal cortex characterised by synaptic poverty Bennett, 2011
  • Lower hippocampal volume Baaré et al, 2010
  • Plasma levels of beta-amyloid (1-42) may predict late life depression Blasko et al, 2010
  • Depression associated with low high-density lipoprotein cholesterol in women, but low low-density lipoprotein cholesterol in men Ancelin et al, 2010
  • High plasma levels of lipoprotein a ( LPA ) have been reported in depression Hamidifard et al, 2009
  • Increased superoxide dismutase (SOD1) and catalase activity and malondialdehyde levels in erythrocytes during depressive episodes (oxidative stress) Galecki et al, 2009
  • Low whole blood glutathione peroxidase acivity Maes et al, 2011
  • Reduced levels of glutathione in the prefrontal cortex Gawryluk et al, 2011
  • Multiple aberrations in inflammatory, oxidative and nitic oxide related stress pathways Maes et al, 2010
  • Lower levels of omega-3 polyunsaturated fatty acids in depressed patients Baghai et al, 2010
    • lower levels of eicosapentaenoic acid , docosahexaenoic acid , and total n-3 polyunsaturated fatty acids in patients with depression Lin et al, 2010
  • Reduced expression of fatty acid synthesis genes in the frontal cortex in depression McNamara and Liu, 2011
  • Low levels of plasma tryptophan and induction of indoleamine 2,3-dioxygenase indicative of infection/immune activation Maes, 2011
  • Plasma levels of kynurenine elevated in severe depression Sublette et al, 2011Modified ratios of kynureine to kynerenic acid have been reported in depression and other psychiatric disorders Myint , 2012
  • Lower blood levels of BDNF in depressed patients Yoshimura et al, 2010
  • High plasma nesfatin-1 levels have been reported in depression Ari et al, 2010
  • Suicidal patients display a distinct peripheral blood cytokine profile compared to non-suicidal depressed patients (increased levels of IL-6 and TNF-alpha and decreased IL-2) Janelidze et al, 2011
    • Plasma aldosterone levels have also been reported to be lower in suicidal depression Hallberg et al, 2011
  • Increased plasma oxytocin levels Parker et al, 2010
  • Low levels of CSF S-adenosylmethionine have been reported in depressionBottiglieri et al, 1990
    • S-adenosylmethionine has been reported to possess antidepressant effects Papakostas , 2009
Depression and the immune system
  • Pro-inflammatory cytokines and lipopolysacharide ( a bacterial cell wall component ) may induce depressive symptoms Maes et al, 2008.
  • Depression is associated with a suppression of mitogen-induced lymphocyte proliferation and with a reduction of natural killer kell activity activity Irwin, 1999
  • Depression has been frequently associated with Vitamin D deficiency Stalpers-Konijnenburg et al, 2011 :
  • Low 25(OH)-vitamin D status associated with a higher level of postnatal depression symptoms Robinson et al, 2014
    • and with lack of sunshine (needed for vitamin D synthesis)
    • See Seasonal affective disorder Gagné et al, 2010
  • Atopy (Immunoglobulin E related allergies) can be associated with a greater risk for developing depression in women Timonen et al, 2002
  • Depression and fatigue during chronic Interferon alpha treatment were associated with alterations in the expression (OAS2) and transcriptional control (CREB/ATF) of genes linked to behavioral disorders including chronic fatigue syndrome and major depression, supporting an immune contribution to these diseases Felger et al, 2011.
  • An inflammatory signature (CAPRIN1, CLEC4A, KRT23, MLC1, PLSCR1, PROK2, ZBTB16) in lipopolysaccharide stimulated blood Spijker et al, 2010
  • Autoantibodies to serotonin Maes et al, 2011
  • Depression is characterized by IgM-related autoimmune responses directed against a) neoepitopes that are normally not detected by the immune system but that due to damage by oxidative and nitrosative stress have become immunogenic; and b) anchorage epitopes, i.e. palmitic and myristic acids, and S-farnesyl-L-cysteine
    • IgM levels directed against conjugated palmitic and myristic acids, acetylcholine, S-farnesyl-L-cysteine; and the conjugated NO adducts, NO-tyrosine, NO-phenylalanine, NO-aspartate, NO-histidine, and NO-creatine increased in depression Maes et al, 2011
  • Suicide risk has been linked to pollen counts (Danish register) Qin et al, 2013

Treatment

  • Mainly serotonin (SSRI's) or varying combinations of serotonin/noradrenaline /dopamine uptake blockers, and monoamine oxidase inhibitors (see Wikipedia)
  • N-acetyl cysteine (glutathione precursor) has been used as a supplement in bipolar depression Berk et al, 2008
  • Supplementation with n-3 polyunsaturated fatty acids is effictive in depression treatment in elderly female patients Rondanelli et al, 2010
  • Excercise may have beneficial effects in depression Trivedi et al, 2011
  • Ketamine has been shown to be effective

Geography/season and other

  • Major depression has been associated with height above sea-level (possibly related to hypoxic stress) DelMastro et al, 2011
  • Suicide peaks in the spring months were observed in a large Danish study Postolache et al, 2010
  • Seasonal affective disorder related to latitude (greater in the north in Greenland ) Kegel et al, 2009
  • Old age is a risk factor for depression and after dementia, is the most common disease in the over 65 Orzechowska et al. 2008
  • Television and total media exposure in adolescence are associated with increased odds of depressive symptoms in young adulthood, especially in young men Primak et al, 2009.
  • Depressed patients show accelerated cellular aging as measured by shorter telomere length Verhoeven et al, 2013

Unipolar depressive disorders world map from Wikimedia commons Lokal_Profil

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