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torsdag 2 juli 2020

Ubikviliini 2 UBQLN2. Mutaatio tässä geenissä linkkiytyy ALS- tautiin.

https://pubmed.ncbi.nlm.nih.gov/30442662/

  2018 Dec 4;115(49):E11485-E11494.
doi: 10.1073/pnas.1811997115. Epub 2018 Nov 15.
Ubiquilin 2 Modulates ALS/FTD-linked FUS-RNA Complex Dynamics and Stress Granule Formation
PMID: 30442662
PMCID: PMC6298105
DOI: 10.1073/pnas.1811997115
Free PMC article
Abstract
The ubiquitin-like protein ubiquilin 2 (UBQLN2) has been genetically and pathologically linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but its normal cellular functions are not well understood. In a search for UBQLN2-interacting proteins, we found an enrichment of stress granule (SG) components, including ALS/FTD-linked heterogeneous ribonucleoprotein fused in sarcoma (FUS). Through the use of an optimized SG detection method, we observed UBQLN2 and its interactors at SGs. A low complexity, Sti1-like repeat region in UBQLN2 was sufficient for its localization to SGs. Functionally, UBQLN2 negatively regulated SG formation. UBQLN2 increased the dynamics of FUS-RNA interaction and promoted the fluidity of FUS-RNA complexes at a single-molecule level. This solubilizing effect corresponded to a dispersal of FUS liquid droplets in vitro and a suppression of FUS SG formation in cells. ALS-linked mutations in UBQLN2 reduced its association with FUS and impaired its function in regulating FUS-RNA complex dynamics and SG formation. These results reveal a previously unrecognized role for UBQLN2 in regulating the early stages of liquid-liquid phase separation by directly modulating the fluidity of protein-RNA complexes and the dynamics of SG formation.
Keywords: ALS; FTD; FUS; stress granule; ubiquilin 2.

Conflict of interest statement

The authors declare no conflict of interest.

fredag 12 juni 2020

Substantia nigra kerryttää rautaa ja Se-Ferritiini voi olla matala neuroinflammaatiossa

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668412/

. 2017; 7: 14973.
Published online 2017 Nov 2. doi: 10.1038/s41598-017-14721-1
PMCID: PMC5668412
PMID: 29097764
Iron deposition in substantia nigra: abnormal iron metabolism, neuroinflammatory mechanism and clinical relevance
Zhuo Liu,#1 Hui-cong Shen et al.

torsdag 28 maj 2020

Tähän blogiin liitän geenin ZGRF1 , noin 15- 16 GRF sekvenssimotiivia ainakin

What's a GeneRIF?
sä isoformissa on yksi qpqp jakso ja ppp ja qpq , joitain pp ja qq ja qp.
  1. NM_001350397.1NP_001337326.1  protein ZGRF1 isoform 2
    Status: REVIEWED
    Source sequence(s)
    AC023886, AC106864
    Conserved Domains (4) summary
    pfam06839
    Location:12891333
    zf-GRF; GRF zinc finger
    pfam10382
    Location:473
    DUF2439; Protein of unknown function (DUF2439)
    pfam13087
    Location:17971981
    AAA_12; AAA domain
    cl26261
    Location:15912003
    AAA_11; AAA domain

ORIGIN      
        1 mesqefivly thqkmkkskv wqdgilkith lgnkailydd kgacleslfl kclevkpgdd
       61 lesdrylitv eevkvagaig ivkqnvnkea pelnsrtfis sgrslgcqps glkrkftgfq
      121 gprqvpkkmv imesgesaas heakktgpti fspfcsmppl fptvgkkdvn niladpeniv
      181 tyknrernam dfssvfspsf qinpevlcee nyfcspvnsg nklsdslltn epvkrdslas
      241 hysgvsqnir skaqilallk sessssceel nsemtehfpq kqpqgslkia tkpkyliqqe
      301 ecaemksten lyyqhqsent mrnksrwamy lssqsspihs stvdgndter kpkaqeddvn
      361 snlkdlslqk iiqfvetyae erkkynvdqs vgnndpswnq evkleipsfn essslqvtcs
      421 saendgilse sdiqednkip fnqndkgcik gsvlikenaq evntcgtlek eyeqsesslp
      481 elkhlqiess nnsrisddit dmiseskmdn eslnsihesl snvtqpflev tfnlnnfets
      541 dteeesqesn kisqdseswv kdilvndgns cfqkrsentn ceeiegehlp fltsvsdkpt
      601 vtfpvketlp sqfcdktyvg fdmgickten tgkeieeysd tlsnfesfkw tdavygdnke
      661 dankpiqevr inydfalppn kskginmnlh iphiqnqiae nsnlfsedaq pqpfilgsdl
      721 dkndehvlps tsssdnsvql lntnqnhyec ialdksnthi snslfyplgk khliskdtea
      781 hisepedlgk irspppdhve vetaregkqy wnprnssels glvntisilk slcehstald
      841 sleilkkknt vfqqgtqqty epdsppevrk pfitvvspks phlhkdsqqi lkedevelse
      901 plqsvqfsss gskeetafqa vipkqierkt cdpkvtspee nistlspvst fslnsrdedf
      961 mvefsetslk artlpddlhf lnlegmkksr slenenlqrl sllsrtqvpl itlprtdgpp
     1021 dldshsymin sntyessgsp mlnlceksav lsfsiepedq netffseesr evnpgdvsln
     1081 nistqskwlk yqntsqcnva tpnrvdkrit dgffaeavsg mhfrdtserq sdavnessld
     1141 svhlqmikgm lyqqrqdfss qdsvsrkkvl slnlkqtskt eeiknvlggs tcynysvkdl
     1201 qeisgselcf psgqkiksay lpqrqihipa vfqspahykq tftscliehl nillfglaqn
     1261 lqkalskvdi sfytslkgek lknaennvps chhsqpaklv mvkkegpnkg rlfytcdgpk
     1321 adrckffkwl edvtpgystq egarpgmvls diksiglylr sqkiplyeec qllvrkgfdf
     1381 qrkqygklkk fttvnpefyn epktklylkl srkerssays kndlwvvskt ldfeldtfia
     1441 csaffgpssi neieilplkg yfpsnwptnm vvhallvcna stelttlkni qdyfnpatlp
     1501 ltqyllttss ptivsnkrvs krkfippaft nvstkfells lgatlklase liqvhklnkd
     1561 qataliqiaq mmashesiee vkelqthtfp itiihgvfga gksyllavvi lffvqlfeks
     1621 eaptignarp wkllissstn vavdrvllgl lslgfenfir vgsvrkiakp ilpyslhags
     1681 eneseqlkel halmkedltp tervyvrksi eqhklgtnrt llkqvrvvgv tcaacpfpcm
     1741 ndlkfpvvvl decsqitepa sllpiarfec eklilvgdpk qlpptiqgsd aahengleqt
     1801 lfdrlclmgh kpillrtqyr chpaisaian dlfykgalmn gvteierspl lewlptlcfy
     1861 nvkgleqier dnsfhnvaea tftlkliqsl iasgiagsmi gvitlyksqm yklchllsav
     1921 dfhhpdiktv qvstvdafqg aekeiiilsc vrtrqvgfid sekrmnvalt rgkrhllivg
     1981 nlaclrknql wgrviqhceg redglqhanq yepqlnhllk dyfekqveek qkkksekeks
     2041 kdkshs
//
 
 Katson isomeerin 1  q ja p esiintymät. 
Paljon on leusiinia, lysiiniä ja seriiniäkin. On G-R-F sekvenssit 
isolla kirjaimella 
 ORIGIN      
        1 mesqefivly thqkmkkskv wqdGilkith lgnkailydd kgacleslfl kclevkpgdd
       61 lesdRylitv eevkvagaig ivkqnvnkea pelnsrtFis sGRslgcqps glkrkfFtGfq
      121 gpRqvpkkmv imesgesaas heakktgpti Fspfcsmppl fptvGkkdvn niladpeniv
      181 tyknRernam dFssvfspsf qinpevlcee nyfcspvnsG nklsdslltn epvkRdslas
      241 hysgvsqnir skaqilallk sessssceel nsemtehFpq kqpqGslkia tkpkyliqqe
      301 ecaemksten lyyqhqsent mRnksrwamy lssqsspihs stvdgndter kpkaqeddvn
      361 snlkdlslqk iiqFvetyae erkkynvdqs vGnndpswnq evkleipsfn essslqvtcs
      421 saendgilse sdiqednkip fnqndkgcik gsvlikenaq evntcgtlek eyeqsesslp
      481 elkhlqiess nnsRisddit dmiseskmdn eslnsihesl snvtqpFlev tfnlnnfets
      541 dteeesqesn kisqdseswv kdilvndGns cfqkRsentn ceeiegehlp Fltsvsdkpt
      601 vtfpvketlp sqfcdktyvG fdmgickten tgkeieeysd tlsnfesfkw tdavygdnke
      661 dankpiqevR inydFalppn kskGinmnlh iphiqnqiae nsnlfsedaq pqpfilgsdl
      721 dkndehvlps tsssdnsvql lntnqnhyec ialdksnthi snslfyplgk khliskdtea
      781 hisepedlgk irspppdhve vetaRegkqy wnprnssels glvntisilk slcehstald
      841 sleilkkknt vFqqGtqqty epdsppevRk pFitvvspks phlhkdsqqi lkedevelse
      901 plqsvqfsss Gskeetafqa vipkqieRkt cdpkpveFqG hqvkgsatsg vmvRghssql
      961 gcsqFpdste yenfmtetpe lpstcmqidf lqvtspeeni stlspvstfs lnsrdedfmv
     1021 efsetslkar tlpddlhfln leGmkksRsl enenlqrlsl lsrtqvplit lprtdgppdl
     1081 dshsyminsn tyessgspml nlceksavls Fsiepedqne tffseesrev npGdvslnni
     1141 stqskwlkyq ntsqcnvatp nRvdkritdg FfaeavsGmh fRdtserqsd avnessldsv
     1201 hlqmikgmly qqrqdFssqd svsrkkvlsl nlkqtsktee iknvlGgstc ynysvkdlqe
     1261 isgselcfps gqkiksaylp qRqihipavf qspahykqtF tscliehlni llfGlaqnlq
     1321 kalskvdisf ytslkgeklk naennvpsch hsqpaklvmv kkegpnkgRl FytcdGpkad
     1381 RckFfkwled vtpGystqeg aRpgmvlsdi ksiglylrsq kiplyeecql lvrkgFdfqr
     1441 kqyGklkkft tvnpefynep ktklylklsR kerssayskn dlwvvsktld Feldtfiacs
     1501 affGpssine ieilplkgyf psnwptnmvv hallvcnast elttlkniqd yfnpatlplt
     1561 qyllttsspt ivsnkRvskr kFippaftnv stkfellslG atlklaseli qvhklnkdqa
     1621 taliqiaqmm ashesieevk elqthtfpit iihgvfgagk syllavvilf fvqlfeksea
     1681 ptignaRpwk llissstnva vdrvllglls lgFenfirvG svRkiakpil pyslhagsen
     1741 eseqlkelha lmkedltpte rvyvrksieq hklgtnrtll kqvrvvgvtc aacpFpcmnd
     1801 lkfpvvvlde csqitepasl lpiarfecek lilvGdpkql pptiqgsdaa hengleqtlf
     1861 dRlclmghkp illrtqyrch paisaiandl FykgalmnGv teieRsplle wlptlcFynv
     1921 kGleqieRdn sFhnvaeatf tlkliqslia sGiagsmigv itlyksqmyk lchllsavdf
     1981 hhpdiktvqv stvdafqgae keiiilscvR trqvgFidse krmnvaltrG kRhllivgnl
     2041 aclrknqlwg rviqhcegre dglqhanqye pqlnhllkdy fekqveekqk kksekekskd
     2101 kshs
//
 

måndag 27 april 2020

GRASP12q13.13), Tamaliini , GRP1- assosioitunut proteiini tamaliini (12

https://www.ncbi.nlm.nih.gov/pubmed/12586822/. telineproteiineja ()scaffoldprotein)  assosioitunut PI- fosfolipideihin.

2003 Apr 25;278(17):14762-8. Epub 2003 Feb 13.
Tamalin is a scaffold protein that interacts with multiple neuronal proteins in distinct modes of protein-protein association.
Official Symbol
TAMALIN
Official Full Name
trafficking regulator and scaffold protein tamalin
Also known as
GRASP
Summary
This gene encodes a protein that functions as a molecular scaffold, linking receptors, including group 1 metabotropic glutamate receptors, to neuronal proteins. The encoded protein contains conserved domains, including a leucine zipper sequence, PDZ domain and a C-terminal PDZ-binding motif. Alternately spliced transcript variants have been observed for this gene.[provided by RefSeq, Dec 2012]
Expression
Broad expression in bone marrow (RPKM 8.3), fat (RPKM 7.8) and 23 other tissues See more
Orthologs
What's a GeneRIF?

torsdag 26 mars 2020

AIM2 inflammasomi ja PSCI, Gasdermiini D aukot

https://www.sciencedirect.com/science/article/pii/S0889159119315156?via%3Dihub
AIM2 inflammasome contributes to brain injury and chronic post-stroke cognitive impairment in mice
https://doi.org/10.1016/j.bbi.2020.03.011

https://www.nature.com/articles/s41419-020-2248-z 

Inhibition of AIM2 inflammasome activation alleviates GSDMD-induced pyroptosis in early brain injury after subarachnoid haemorrhage
Cell Death & Disease volume 11, Article number: 76 (2020)

Abstract
Only a few types of inflammasomes have been described in central nervous system cells. Among these, the absent in melanoma 2 (AIM2) inflammasome is primarily found in neurons, is highly specific and can be activated only by double-stranded DNA. Although it has been demonstrated that the AIM2 inflammasome is activated by poly(deoxyadenylic-deoxythymidylic) acid sodium salt and leads to pyroptotic neuronal cell death, the role of AIM2 inflammasome-mediated pyroptosis in early brain injury (EBI) after subarachnoid haemorrhage (SAH) has rarely been studied. Thus, we designed this study to explore the mechanism of gasdermin D(GSDMD)-induced pyroptosis mediated by the AIM2 inflammasome in EBI after SAH. The level of AIM2 from the cerebrospinal fluid (CSF) of patients with SAH was detected. The pathway of AIM2 inflammasome-mediated pyroptosis, the AIM2/Caspase-1/GSDMD pathway, was explored after experimental SAH in vivo and in primary cortical neurons stimulated by oxyhaemoglobin (oxyHb) in vitro. Then, we evaluated GSDMD-induced pyroptosis mediated by the AIM2 inflammasome in AIM2 and caspase-1- deficient mice and primary cortical neurons generated through lentivirus (LV) knockdown. Compared with that of the control samples, the AIM2 level in the CSF of the patients with SAH was significantly increased. Pyroptosis-associated proteins mediated by the AIM2 inflammasome were significantly increased in vivo and in vitro following experimentally induced SAH. After AIM2 and caspase-1 were knocked down by an LV, GSDMD-induced pyroptosis mediated by the AIM2 inflammasome was alleviated in EBI after SAH. Intriguingly, when caspase-1 was knocked down, apoptosis was significantly suppressed via impeding the activation of caspase-3. GSDMD-induced pyroptosis mediated by the AIM2 inflammasome may be involved in EBI following SAH. The inhibition of AIM2 inflammasome activation caused by knocking down AIM2 and caspase-1 alleviates GSDMD-induced pyroptosis in EBI after SAH...

In recent years, an increased number of studies have indicated that inflammasomes are involved in EBI following SAH. Although many inflammasomes have been identified, only a few have been described and characterised in the central nervous system (CNS)4. Absent in melanoma 2 (AIM2), a member of the haemopoietic interferon-inducible nuclear 200 family of proteins, induces the formation of a highly specific type of inflammasome in the neurons that can recognise aberrant double-stranded DNA (dsDNA). AIM2 triggers the formation of inflammasomes that also contain the apoptosis-associated speck-like protein containing a CARD (ASC) and caspase-1 and that induce the cleavage of caspase-1, the maturation of interleukin-1β (IL-1β) and interleukin-18 (IL-18) and pyroptosis. The AIM2 inflammasome mediates pyroptotic neuronal cell death, as has been shown in vivo by incubating cortical neurons with poly(deoxyadenylic-deoxythymidylic) acid sodium salt, a synthetic dsDNA5. However, the role of gasdermin D (GSDMD)-induced pyroptosis mediated by the AIM2 inflammasome in the pathogenesis of EBI after SAH has not been clearly elucidated.
GSDMD, a member of the gasdermin protein family, is highly conserved in mammals, but its function has not yet been clarified. Recently, an increasing body of work has suggested that GSDMD is the inducer of pyroptosis6. Activated inflammatory caspases efficiently cleave GSDMD at an aspartate site within the linking loop, which enables the release of the GSDMD N-terminus (GSDMD-N), which suspends its auto-inhibition, triggers pyroptosis and binds to phosphatidylinositol phosphates and phosphatidylserine of the cell membrane inner leaflet to induce membrane pore formation and IL-1β secretion7. As demonstrated by the crucial role of pyroptosis in immunity and disease, excessive uncontrolled pyroptosis may be detrimental to the host. However, despite these important functions, the potential effects of GSDMD-induced pyroptosis in EBI are still unknown.
Hence, to better understand the mechanism of GSDMD-induced pyroptosis mediated by the AIM2 inflammasome in EBI following SAH, we used an in vivo mouse model of SAH and in vitro cellular model of SAH with oxyhaemoglobin (oxyHb). We also re-assessed GSDMD-induced pyroptosis in EBI following SAH after respectively interfering with the expression of AIM2 and caspase-1 with lentivirus (LV).


Discussion

In the present study, we studied the possible role of GSDMD-induced pyroptosis mediated by the AIM2 inflammasome in the pathogenesis of EBI after SAH. The main findings can be summarised as follows: (1) Pyroptosis-related proteins mediated by the AIM2 inflammasome were upregulated in the brain temporal cortex after SAH and in primary cortical neurons exposed to oxyHb. The expression levels of AIM2, GSDMD, GSDMD-N, caspase-1, caspase-1 p20 and ASC increased continuously in a time-dependent manner. (2) The results from the immunohistochemistry and immunofluorescence staining showed that AIM2 inflammasome-mediated pyroptosis mainly occurred in brain neurons. (3) The inhibition of AIM2 inflammasome activation by knocking down AIM2 and caspase-1 could suppress GSDMD-induced neuronal pyroptosis by decreasing the expression and activation of the pyroptosis-related proteins that are mediated by the AIM2 inflammasome. (4) Knocking down caspase-1 suppressed not only GSDMD activation-induced neuronal pyroptosis but also caspase-3 activation-induced neuronal apoptosis. These findings suggested, for the first time, that pyroptosis could be involved in EBI after SAH through the AIM2/Caspase-1/GSDMD pathway. Moreover, inhibiting the expression and activation of caspase-1 could alleviate both pyroptosis and apoptosis (Supplementary Figure).
The pathophysiology of SAH is complicated and involves multiple pathogenic mechanisms (e.g., inflammation, oxidative stress, and apoptosis). A growing body of evidence indicates that the inflammatory response plays a vital role in injury expansion and brain damage after SAH, including EBI, vasospasm, and delayed neurological deterioration2. In recent years, inflammasomes have been demonstrated to be important participants in EBI after SAH10. The inflammasome is a cytosolic multimeric signalling complex that responds to invading pathogens and host-derived danger signals such that its activation leads to caspase-1 activation. Inflammasome activation proceeds via the formation of a multimolecular complex containing a receptor, an adaptor such as ASC and the cysteine protease caspase-113. Then, activated caspase-1 triggers the maturation of the pro-inflammatory cytokines IL-1β and IL-18 and induces pyroptotic cell death. Several nucleotide-binding oligomerisation domain (NOD)-like receptors (NLRs), as well as AIM2-like receptors (ALRs), have been shown to form inflammasomes. Most of the inflammasomes described to date contain an NLR protein, namely, NOD-like receptor containing pyrin domain 1(NLRP1), NLRP2, NLRP3, NLRP6, NLRP7, NLRP12, and NLR- and caspase-activating recruitment domain-containing 4 (NLRC4). However, only a few inflammasomes have been studied in the CNS, namely, NLRP1, NLRP2, NLRP3 and AIM2. Among these inflammasomes, the NLRP3 inflammasome has been the most studied. NLRP3 inflammasome-mediated neuroinflammation is involved in many acute and chronic CNS diseases, including SAH10,14,15. In SAH, activation of the NLRP3 inflammasome is also essential for the modulation of pro-inflammatory cytokines, and inhibition of the NLRP3 inflammasome by pharmacological treatment can alleviate brain injury after SAH10,16.
In addition to NLRP3, AIM2 is also an important inflammasome involved in CNS infection and injury17. In the present study, we collected and analysed CSF samples from patients with or without SAH. The results from the analysis of patient-derived CSF samples revealed that the level of the AIM2 protein in the CSF of the SAH patients was significantly greater than that in the CSF from non-SAH patients. The higher the Hunt-Hess grade was, the higher the level of AIM2 that was found in the CSF. In the experimental SAH model, we also found that the AIM2 inflammasome was activated in vivo at 24 h post-SAH and that in vitro, the AIM2 inflammasome was significantly unregulated in cultured cortical neurons 6 h after incubation with oxyHb and the levels continued to increase for 12 and 72 h. To verify the role of GSDMD-induced pyroptosis mediated by the AIM2 inflammasome in EBI after SAH, LV was used to knock down the expression of AIM2. The results showed that AIM2 inflammasome-mediated pyroptosis was significantly alleviated in EBI following SAH.
As reported, the AIM2 inflammasome could be activated by aberrant dsDNA, including bacterial DNA and viral DNA, from pathogens and hosts and by endogenous self-DNA within the cytosol, damaged DNA within the nucleus, and self-DNA secreted by exosomes18. Wang et al. detected CSF DNA levels in patients with SAH and found that both nuclear and mitochondrial DNA levels in the CSF were significantly increased in the patients with SAH compared with volunteers, and the CSF nuclear and mitochondrial DNA levels were significantly higher on days 1 and 419. Moreover, higher CSF DNA levels were associated with worse outcomes for patients with SAH19. This result was consistent with the increased AIM2 in the SAH patients in our study. Combined with the results of this study showing that the level of AIM2 in CSF increased significantly within 3 days after SAH, we found that the elevated level of DNA in the CSF after SAH was synchronous and consistent with that of AIM2. Thus, we speculate that pyroptosis mediated by the AIM2 inflammasome is involved in EBI after SAH. This kind of EBI should be considered, to be exact, a secondary brain injury.
Recently, some scholars believe that pyroptosis should be redefined as GSDMD-mediated, rather than caspase-1-mediated, programmed necrosis20. GSDMD was discovered to form a pore and act as an effector for pyroptosis. In GSDMD-deficient cells, pyroptosis cannot be triggered by known canonical inflammasome ligands21. GSDMD contains ~480 amino acids in two domains, and the N-terminal gasdermin domain (GSDMD-N) and the C-terminal gasdermin domain (GSDMD-C) are linked by a long loop. Mounting evidence has demonstrated that GSDMD plays a key role in CNS injury22,23. In our study, we also observed that GSDMD was upregulated after SAH. Although GSDMD is considered the initiator of pyroptosis, GSDMD-N is the direct and sole effector of pyroptosis. Activated caspase-1 or caspase-11 efficiently cleaves GSDMD at a conserved glutamic acid residue (D276 in mouse and D275 in humans)21,24. The cleaved GSDMD unleashes the pro-pyroptotic N-terminal fragment from the auto-inhibited state maintained by the C-terminus, thus separating the role of GSDMD into that of GSDMD-N and that of GSDMD-C. The released GSDMD-N is oligomerized, and only the oligomerised form of GSDMD-N is able to translocate to the plasma membrane, where it induces cell rupture and the release of inflammatory cytokines, such as IL-1β25. We also observed that the GSDMD-N generated by caspase-1 cleavage forms an oligomer and migrates to the plasma membrane to kill cells.
Furthermore, GSDMD-N alone localises to the plasma membrane, as evidenced by GSDMD-N binding to liposomes in studies in vitro. Binding studies with liposomes and lipid strips revealed that GSDMD-N has a high affinity for liposomes containing lipids such as cardiolipin, phosphatidylinositol 4-phosphate [PI(4)P] and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P] compared with other lipid types26. It is through its lipid-binding specificity that GSDMD-N disrupts plasma membranes, which it perpetrates only when exposed to the cytosolic PI-containing inner leaflet but not when exposed to the extracellular outer leaflet, which lacks PI26. While GSDMD-N kills from within the cell, its released form does not harm neighbouring cells. Mounting evidence has shown that the inner ring diameter of the pore formed by GSDMD-N is estimated to be between 10 and 20 nm6,27,28. Different methods have revealed a pore consisting of 16 or 24 GSDMD-N units27,28. This finding is consistent with the observation we made in the present study revealing that a large number of pore-like structures appear on the surface of neurons stimulated by oxyHb. The results of the membrane protein analysis suggest that the pore-like structure may be caused by the oligomerization of GSDMD-N at the cell membrane.
In the present study, we also interfered with the expression of caspase-1 by an LV. After caspase-1 was knocked down, GSDMD-induced pyroptosis was markedly reduced in EBI following SAH. Knocking down caspase-1 inhibited not only the expression and activation of GSDMD but also the expression of pyroptosis-related proteins mediated by the AIM2 inflammasome. We propose two explanations for this result: First, caspase-1-mediated inflammatory injury could be greatly alleviated after caspase-1 is knocked down. Caspase-1 is unequivocally required for the proteolytic processing of IL-1β and IL-18; these two cytokines engage their transmembrane receptors IL-1R and IL-18R to promote inflammation via the activation of nuclear factor-kappaB transcriptional programmes that are induced by the activation of myeloid differential protein-88, a key signalling adaptor29. When caspase-1 was knocked down, caspase-1-mediated inflammatory injury may have been alleviated, and the amount of dsDNA released from damaged cells could be reduced. Second, the non-functional AIM2/ASC complex was quickly depleted. Juruj et al. found that a negative feedback loop controlled by ASC/caspase-1 regulates AIM2 complex formation/stability13. In the absence of a functional AIM2 inflammasome, the AIM2/ASC complex formed very rapidly. However, this complex was then removed through activated autophagy following AIM2 speck formation13. Thus, when caspase-1 levels were deficient, the AIM2 inflammasome was not readily formed and pyroptosis was thus mediated after SAH.
Intriguingly, knocking down caspase-1 alleviated not only GSDMD activation-induced neuronal pyroptosis but also caspase-3 activation-induced neuronal apoptosis. A few other studies have reported that GSDMD-deficient cells may die because of the caspase-1 cleavage of caspase-3/721,30. Inhibiting caspase-1 activity may have attenuated caspase-3-dependent apoptosis, but the mechanism remains unclear31,32,33. We found that caspase-1 was essential for the activation of caspase-3. The cleavage of caspase-3 was significantly hindered when caspase-1 was knocked down in EBI following SAH. However, the expression of caspase-3 was not affected by caspase-1 knockdown. Therefore, we speculated that apoptosis was also alleviated in EBI after SAH, because knocking down caspase-1 hindered the cleavage of caspase-3. It was recently reported that GSDMD was also cleaved during apoptosis. GSDMD was cleaved by caspase-3/7 at D87 during apoptosis, while GSDMD was cleaved by caspase-1 at D275/D276 during pyroptosis34. The p30 N-terminal fragment of GSDMD (GSDMD p30) released by the cleavage at D275/D276 forms pores in the plasma membrane, thereby mediating pyroptotic cell death. Nevertheless, this cleaved GSDMD also generated the p43 fragment of GSDMD (GSDMD p43) at D87 during apoptosis, which inactivated or failed to trigger pyroptosis (Supplementary Figure). We preliminarily found that caspase-1 may be an important protein at the intersection of the pyroptosis and the apoptosis pathways. Inhibition of caspase-1 activity alleviated not only GSDMD activation-induced neuronal pyroptosis but also caspase-3 activation-induced neuronal apoptosis.
In this study, we demonstrated, for the first time, that the GSDMD-induced pyroptosis mediated by the AIM2 inflammasome may be involved in EBI after SAH. When inhibiting the activation of the AIM2 inflammasome by knocking down AIM2 and caspase-1 with LV, the pyroptosis mediated by the AIM2 inflammasome was significantly alleviated. The activation of caspase-3 was also decreased after caspase-1 was knocked down. However, a clearer regulatory mechanism between pyroptosis and apoptosis remains to be further explored.

References

onsdag 1 januari 2020

Amyloidibeeta interaktomi analyysi ( 2011). useita Znf proteiineja joukossa.

https://pubs.acs.org/doi/abs/10.1021/pr1009096
 Protein Array Based Interactome Analysis of Amyloid-β Indicates an Inhibition of Protein Translation
Dezso P. Virok*
Dóra Simon
View Author Information
Cite this: J. Proteome Res. 2011, 10, 4, 1538-1547
Publication Date:January 19, 2011
https://doi.org/10.1021/pr1009096

Oligomeric amyloid-β is currently of interest in amyloid-β mediated toxicity and the pathogenesis of Alzheimer’s disease. Mapping the amyloid-β interaction partners could help to discover novel pathways in disease pathogenesis. To discover the amyloid-β interaction partners, we applied a protein array with more than 8100 unique recombinantly expressed human proteins. We identified 324 proteins as potential interactors of oligomeric amyloid-β. The Gene Ontology functional analysis of these proteins showed that oligomeric amyloid-β bound to multiple proteins with diverse functions both from extra and intracellular localizations. This undiscriminating binding phenotype indicates that multiple protein interactions mediate the toxicity of the oligomeric amyloid-β. The most highly impacted cellular system was the protein translation machinery. Oligomeric amyloid-β could bind to altogether 24 proteins involved in translation initiation and elongation. The binding of amyloid-β to purified rat hippocampal ribosomes validated the protein array results. More importantly, in vitro translation assays showed that the oligomeric amyloid-β had a concentration dependent inhibitory activity on translation. Our results indicate that the inhibited protein synthesis is one of the pathways that can be involved in the amyloid-beta induced neurotoxicity.
      normalized signal intensity 
Protein Header Gene Symbol Database ID Ultimate ORF ID Swissprot ID  Array A Array B
  P2293    7110,22 7245,60
  PV4690    6835,22 8718,84
WD repeat domain 5 (WDR5), transcript variant 1 WDR5 NM_017588.1 IOH4895 P61964  6279,74 8539,23
signal recognition particle 19kDa (SRP19) SRP19 BC010947.1 IOH14455 P09132  6076,43 3232,90
hypothetical protein MGC42630 (MGC42630) FAM27E3 NM_175923.2 IOH22051 Q08E93  4909,23 4141,35
SUMO1/sentrin/SMT3 specific peptidase 2 (SENP2) SENP2 NM_021627.2 IOH26311 Q9HC62  3572,22 4621,71
DEAD (Asp-Glu-Ala-Asp) box polypeptide 18 (DDX18) DDX18 BC003360.1 IOH2892 Q9NVP1  3569,76 5607,45
RNA binding motif protein 11 (RBM11) RBM11 NM_144770.1 IOH22581 P57052  3386,34 2756,28
chromosome 12 open reading frame 52 (C12orf52) C12orf52 NM_032848.1 IOH13466 Q96K30  3103,24 5477,67
variable charge, Y-linked 1B (VCY) VCY BC056508.1 IOH29456 O14598  2827,13 3931,10
SECIS binding protein 2 (SECISBP2) SECISBP2 BC036109.1 IOH27253 Q96T21  2813,28 9535,04
hexokinase 1 (HK1) HK1 BC008730.2 IOH5942 P19367  2756,41 2624,89
Pumilio domain-containing protein KIAA0020 KIAA0020 NM_014878.2 IOH10030 Q15397  2648,09 3024,14
LTV1 homolog (S. cerevisiae) (LTV1) LTV1 NM_032860.2 IOH22948 Q96GA3  2627,18 1946,10
PP2C-like domain-containing protein C3orf48 C3orf48 NM_144714.1 IOH11221 A8MPX8  2626,93 4930,28
zinc finger protein 22 (KOX 15) (ZNF22) ZNF22 BC010642.1 IOH9701 P17026  2618,53 4538,58
olfactory receptor, family 6, subfamily B, member 3 (OR6B3), mRNA OR6B3 AB065662.1 IOH28287 Q8NGW1  2549,07 999,95
chromosome 3 open reading frame 37 (C3orf37) C3orf37 BC009993.2 IOH27830 Q96FZ2  2491,57 2484,15
guanine nucleotide binding protein-like 2 (nucleolar) (GNL2) GNL2 BC009250.1 IOH27775 Q13823  2316,56 4556,13
tubulin, gamma 1 (TUBG1) TUBG1 NM_001070.1 IOH4241 P23258  2312,38 3332,08
PDZ domain-containing protein 4 PDZD4 BC002606.1 IOH4132 Q76G19  2228,66 2043,16
arginine vasopressin-induced 1 (AVPI1) AVPI1 BC000877.1 IOH3268 Q5T686  2211,16 1588,71
general transcription factor IIE, polypeptide 2, beta 34kDa (GTF2E2) GTF2E2 NM_002095.1 IOH22963 P29084  2205,65 2998,21
occludin/ELL domain containing 1 (OCEL1) OCEL1 NM_024578.1 IOH23128 Q9H607  2186,50 2493,36
fibroblast growth factor 12 (FGF12), transcript variant 1 FGF12 NM_021032.2 IOH35339 P61328  2184,15 1519,12
ets variant gene 3 (ETV3) ETV3 NM_005240.1 IOH13301 P41162  2123,09 4535,51
PIN2-interacting protein 1 (PINX1) PINX1 BC015479.1 IOH11268 Q96BK5  2117,48 1544,14
nucleolar and coiled-body phosphoprotein 1 (NOLC1) NOLC1 BC006769.1 IOH3146 Q14978  2107,19 6902,87
small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen) (SNRP70) SNRP70 NM_003089.4 IOH40192 P08621  2104,52 6018,96
TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa (TAF1B) TAF1B BC018137.1 IOH10369 Q53T94  2100,47 2874,62
ribosomal protein L31 (RPL31), transcript variant 1 RPL31 NM_000993.2 IOH14051 P62899  2099,69 2492,06
ribosomal protein S16 (RPS16) RPS16 NM_001020.2 IOH13828 P62249  2054,42 3402,04
Phytanoyl-CoA dioxygenase domain-containing protein 1 PHYHD1 NM_174933.2 IOH12686 Q5SRE7  2007,02 1534,02
fibroblast growth factor 12 (FGF12), transcript variant 2 FGF12 NM_004113.3 IOH34727 P61328  1998,76 2687,61
activator of basal transcription 1 (ABT1) ABT1 NM_013375.2 IOH1920 Q9ULW3  1961,12 1638,59
eukaryotic translation initiation factor 2C, 1 (EIF2C1) EIF2C1 BC063275.1 IOH40423 Q9UL18  1951,40 2309,47
mitochondrial ribosomal protein S18A (MRPS18A), nuclear gene encoding mitochondrial protein MRPS18A NM_018135.2 IOH12060 Q9NVS2  1921,66 2847,10
DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 (DDX10) DDX10 NM_004398.2 IOH38427 Q13206  1900,80 2427,42
zinc finger protein 684 (ZNF684) ZNF684 NM_152373.2 IOH14361 Q5T5D7  1893,68 3233,24
intestinal cell (MAK-like) kinase (ICK), transcript variant 1 ICK NM_014920.2 IOH38087 Q9UPZ9  1888,31 1321,44
glyceraldehyde-3-phosphate dehydrogenase (GAPDH) GAPDH NM_002046.2 IOH3380 P04406  1857,17 1394,76
bobby sox homolog (Drosophila) (BBX) BBX NM_020235.2 IOH44025 Q8WY36  1843,23 5121,71
chromosome 18 open reading frame 56 (C18orf56) C18orf56 BC028301.1 IOH11759 Q8TAI1  1837,02 1453,78
zinc finger protein 747 (ZNF747) ZNF747 NM_023931.1 IOH3950 Q9BV97  1832,78 3096,57
fibroblast growth factor 13 (FGF13), transcript variant 1A FGF13 NM_004114.2 IOH13832 Q92913  1818,27 1295,24
MYB binding protein (P160) 1a (MYBBP1A) MYBBP1A BC050546.1 IOH26928 Q9BQG0  1796,01 2583,47
UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) (UTP14A) UTP14A BC001149.1 IOH4457 Q9BVJ6  1768,08 3006,02
calcium/calmodulin-dependent protein kinase kinase 2, beta (CAMKK2) CAMKK2 BC026060.2 IOH12294 Q96RR4  1751,72 2227,90
v-myc myelocytomatosis viral oncogene homolog (avian) (MYC) MYC BC000141.1 IOH2954 P01106  1706,09 740,84
dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2 (DYRK2), transcript variant 1 DYRK2 NM_003583.2 IOH2412 Q92630  1683,98 1931,17
RNA binding motif protein 34 (RBM34) RBM34 NM_015014.1 IOH23193 P42696  1682,76 1236,80
zinc finger CCCH-type containing 3 (ZC3H3) ZC3H3 BC034435.1 IOH21500 Q8IXZ2  1660,73 3548,28
inhibitor of growth family, member 2 (ING2) ING2 NM_001564.1 IOH22913 Q9H160  1635,98 2687,19
ubiquitin specific peptidase 2 (USP2) USP2 BC002955.1 IOH4931 O75604  1625,07 1150,06
zinc finger protein 622 (ZNF622) ZNF622 NM_033414.1 IOH10240 Q969S3  1581,93 1041,84
TGF-beta receptor type-2 TGFBR2 BC040499.1 IOH27240 P37173  1577,35 1738,98
Fanconi anemia, complementation group M (FANCM) FANCM BC036056.1 IOH27184 Q8IYD8  1577,11 2227,13
THAP domain containing 4 (THAP4) THAP4 NM_015963.4 IOH40797 Q8WY91  1563,75 1797,27
PHD finger protein 8 (PHF8) PHF8 BC053861.1 IOH28930 Q9UPP1  1515,09 2104,93
chromosome 9 open reading frame 43 (C9orf43) C9orf43 NM_152786.1 IOH11171 Q8TAL5  1456,72 1888,16
cytoplasmic polyadenylation element binding protein 1 (CPEB1) CPEB1 BC035348.1 IOH28673 Q9BZB8  1455,67 2662,34
histone cluster 2, H2ac (HIST2H2AC) HIST2H2AC NM_003517.2 IOH29296 Q16777  1448,87 1904,62
Uncharacterized protein C7orf50 C7orf50 NM_032350.3 IOH6347 Q9BRJ6  1447,63 1941,87
ADAM metallopeptidase domain 22 (ADAM22) ADAM22 BC036029.1 IOH27232 Q9P0K1  1439,91 1768,58
excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence) (ERCC1) ERCC1 BC052813.1 IOH29045 P07992  1436,51 778,43
pescadillo homolog 1, containing BRCT domain (zebrafish) (PES1) PES1 NM_014303.2 IOH21738 O00541  1427,79 1551,73
suppressor of cytokine signaling 5 (SOCS5) SOCS5 BC032862.1 IOH27139 O75159  1407,51 2254,47
dpy-19-like 2 pseudogene 4 (C. elegans) (DPY19L2P4) LOC554208 BC047471.1 IOH26529 Q86X12  1406,77 1943,02
Protein ZNF365 ZNF365 BC070073.1 IOH40070 Q70YC5  1403,99 2140,75
Wolf-Hirschhorn syndrome candidate 1 (WHSC1), transcript variant 5 WHSC1 NM_133332.1 IOH38113 O96028  1401,24 2409,90
protein tyrosine phosphatase, non-receptor type 12 (PTPN12) PTPN12 NM_002835.2 IOH28818 Q05209  1373,53 1801,50
ankyrin repeat and zinc finger domain containing 1 (ANKZF1) ANKZF1 BC000238.1 IOH4394 Q9H8Y5  1370,61 2532,16
ribosomal protein L3-like (RPL3L) RPL3L NM_005061.2 IOH26731 Q92901  1362,03 1458,56
IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast) (IMP4) IMP4 NM_033416.1 IOH12991 Q96G21  1358,14 1653,58
chromosome 8 open reading frame 33 (C8orf33) C8orf33 NM_023080.1 IOH13369 Q9H7E9  1355,97 1557,62
activation-induced cytidine deaminase (AICDA) AICDA NM_020661.1 IOH6382 Q546Y9  1355,44 1363,86
ligand of numb-protein X 1 (LNX1) LNX1 BC022983.1 IOH10747 Q8TBB1  1346,43 2079,80
death effector domain containing (DEDD), transcript variant 2 DEDD NM_004216.2 IOH14789 O75618  1335,77 1492,74
Ataxin-7-like protein 3 DKFZp761G2113 XM_375456.2 IOH43380 Q14CW9  1333,88 1061,27
Uncharacterized protein C6orf201 C6orf201 NM_206834.1 IOH40081 Q7Z4U5  1320,72 1843,81
ankyrin repeat and sterile alpha motif domain containing 6 (ANKS6) ANKS6 BC064367.1 IOH39904 Q68DC2  1313,67 704,43
PREDICTED: Homo sapiens hypothetical gene supported by NM_153241 (LOC442774) MGC42157 XM_499573.1 IOH22041 NA  1303,04 1354,58
AE binding protein 2 (AEBP2) AEBP2 NM_153207.2 IOH14301 Q96BG3  1299,74 1361,00
TRAF3-interacting protein 1 TRAF3IP1 BC059174.1 IOH28851 Q8TDR0  1298,92 1990,92
leucine rich repeat containing 8 family, member D (LRRC8D) LRRC8D BC009486.1 IOH22946 Q7L1W4  1284,92 2688,00
TBP-like 1 (TBPL1) TBPL1 BC000381.2 IOH3454 P62380  1276,34 2315,63
Kruppel-like factor 12 (KLF12) KLF12 NM_007249.3 IOH10654 Q9Y4X4  1272,22 1104,63
  BC006423.1    1269,40 2013,80
kinesin family member 3A (KIF3A) KIF3A NM_007054.1 IOH26900 Q9Y496  1249,02 1975,97
histone cluster 1, H2bm (HIST1H2BM) HIST1H2BM NM_003521.2 IOH40169 Q99879  1238,03 3276,52
Disks large-associated protein 5 DLG7 BC016276.1 IOH13621 Q15398  1226,51 2127,15
pituitary tumor-transforming 2 (PTTG2) PTTG2 NM_006607.1 IOH40244 Q9UNJ6  1226,06 2417,04
eukaryotic translation initiation factor 2C, 4 (EIF2C4) EIF2C4 NM_017629.2 IOH38411 Q9HCK5  1217,51 2117,44
casein kinase 1, epsilon (CSNK1E), transcript variant 2 CSNK1E NM_001894.2 IOH21160 P49674  1215,88 1263,57
chromosome 10 open reading frame 80 (C10orf80) C10orf80 NM_001008723.1 IOH43999 Q5T655  1213,37 1154,93
apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H (APOBEC3H) APOBEC3H BC069023.1 IOH40776 A8MV17  1204,18 2796,81
mitochondrial ribosomal protein L34 (MRPL34), nuclear gene encoding mitochondrial protein MRPL34 NM_023937.1 IOH4594 Q9BQ48  1193,89 2393,34
DEAD (Asp-Glu-Ala-Asp) box polypeptide 49 (DDX49) DDX49 NM_019070.1 IOH5264 Q9Y6V7  1193,01 656,92
olfactory receptor, family 4, subfamily D, member 6 (OR4D6) OR4D6 NM_001004708.1 IOH28245 Q8NGJ1  1190,23 1760,91
heterochromatin protein 1, binding protein 3 (HP1BP3) HP1BP3 NM_016287.2 IOH43530 Q5SSJ5  1188,24 2291,86
UPF3 regulator of nonsense transcripts homolog A (yeast) (UPF3A) UPF3A BC023569.1 IOH27860 A2A366  1185,97 863,55
DEAD (Asp-Glu-Ala-Asp) box polypeptide 55 (DDX55) DDX55 BC030020.2 IOH22410 Q8NHQ9  1183,21 1595,26
RNA-binding protein 42 MGC10433 BC031682.1 IOH22859 Q9BTD8  1176,92 1113,02
ribos