More Related Content Similar to PhilipAllenThesis Similar to PhilipAllenThesis (20) 2. i!!
Acknowledgments!
!
I!would!like!to!give!special!thanks!to!my!supervisors!on!this!project,!Dr.!Joan!Ní!
Gabhann!and!Dr.!Jay!Chandanshive.!Throughout!the!project,!both!of!you!have!
been!wonderful!mentors!and!have!given!me!unlimited!support,!for!which!I!am!
immensely!grateful.!
!
I!would!also!like!to!extend!my!thanks!to!Professor!Caroline!Jefferies,!Professor!
Conor!Murphy,!Dr.!Qistina!Pilson,!Dr.!Siobhán!Smith,!Shane!O’Grady,!Leah!Arkins!
and!all!the!researchers!in!the!MCT!Molecular!Immunology!Department!for!all!
their!kind!help!and!support!everyone!have!aided!me!during!my!time!in!your!lab.!
Thank!you!for!making!me!feel!welcome!and!I!wish!each!and!every!one!in!MCT!
great!success!in!their!respective!future!endeavours.!Also,!Dr.!Claire!Wynne’s!
efforts!with!helping!me!get!around!RCSI!and!for!her!kind!donation!of!293Ts,!
thank!you!!
!
Lastly,!to!my!family!and!friends!who!have!been!there!since!the!beginning!and!all!
the!encouragements!and!neverXending!support!for!which!I!am!exceptionally!
thankful!!
!
!
!
!
!
3. ii!!
List!of!Abbreviations!
Abbreviations, Description,
AECG! AmericanXEuropean!Consensus!Group!
ALS! Amyotrophic!Lateral!Sclerosis!
AML! Acute!Myeloid!Leukaemia!
BCA! Bicinchoninic!Acid!
BS! Binding!Site!
CC! CoiledXCoil!
CD! Cyclodextrin!
CD80! Cluster!of!Differentiation!80!
cDNA! Complementary!DNA!
CFC! Californian!Fox!Criteria!
CFTR! Cystic!Fibrosis!Transmembrane!Conductance!Regulator!
CRC! Colorectal!Cancer!
CSF2! Colony!Stimulating!Factor!2!
CXCL3! Chemokine!(CXXXC!motif)!Ligand!3!
DB! Database!
DC! Drug!Compound!
DCM! Dilated!Cardiomyopathy!
DGCR8! DiGeorge!Syndrome!Critical!Region!Gene!8!
DMD! Duchenne!Muscular!Dystrophy!
DMEM! Dulbecco’s!Modified!Eagle!Medium!
DMSO! Dimethyl!Sulphoxide!
DNA! Deoxyribonucleic!Acid!
DSF! Differential!Scanning!Fluorimetry!
E.coli& Escherichia&coli&
E2F3! E2F!Transcription!Factor!3!
ECC! European!Community!Criteria!
EDTA! Ethylenediaminetetraacetic!Acid!
EV! Empty!Vector!
FBS! Foetal!Bovine!Serum!
GHD! Growth!Hormone!Deficiency!
HCC! Hepatocellular!Carcinoma!
HEK293XT! Human!Embryonic!Kidney!293XT!cells!
HGT! Hepatocyte!Growth!Factor!
HIV! Human!Immunodeficiency!Virus!
HLA! Human!Leukocyte!Antigen!
IFN! Interferon!
IGF1! InsulinXlike!Growth!Factor!1!
!
4. iii!!
IL! Interleukin!
IL10! Interleukin!10!
IL17D! Interleukin!17D!
IRF! Interferon!Regulatory!Factor!
ITP! Idiopathic!Thrombocytopenic!Purpura!
JAK3! Janus!Kinase!3!
LB! Lysogeny!Broth!
MACC1! Metastasis!Associated!in!Colon!Cancer!1!
MALT! MucosaXAssociated!Lymphoid!Tissue!
MHC! Major!Histocompatibility!Complex!
miRNA/miR! microRNA!
MS! Multiple!Sclerosis!
MyD88! Myeloid!Differentiation!Primary!Response!88!
NaOH! Sodium!Hydroxide!
NCBI! National!Centre!for!Biotechnology!Information!
NPSLE! Neuropsychiatric!Lupus!
NSAIDS! Nonsteroidal!AntiXInflammatory!Drugs!
OSCC! Oral!Squamous!Cell!Carcinoma!
PBMC! Peripheral!Blood!Mononuclear!Cells!
PBS! Phosphate!Buffered!Saline!
PCR! Polymerase!Chain!Reaction!
PEG! Polyethylene!Glycol!
PRR! Pathogen!Recognition!Receptor!
pSS! Primary!Sjögren’s!Syndrome!
qPCR! Qualitative!Polymerase!Chain!Reaction!
RA! Rheumatoid!Arthritis!
RISC! RNAXInduced!Silencing!Complex!
RNA! Ribonucleic!Acid!
RPMI!1640! Roswell!Park!Memorial!Institute!1640!
RT! Room!Temperature!
SCD! Sickle!Cell!Disease!
SEM! Standard!Error!of!the!Mean!
SLE! Systemic!Lupus!Erythematosus!
SOCS1! Suppressor!of!Cytokine!Signalling!1!
SS! Sjögren’s!Syndrome!
TAE! TrisXAcetateXEDTA!
TBS! TrisXBuffered!Saline!
TE! TrisXEDTA!
TFA! Trifluoroacetic!Acid!
TLR! TollXlike!Receptors!
7. vi!!
List!of!Figures!
!
FIGURE!1.1:!EFFECTS!OF!SJÖGREN’S!SYNDROME!IN!THE!BODY.!TAKEN!FROM!(KALLEN,!2014).!................................!6!
FIGURE!1.2:!COMMON!SYMPTOMS!OF!SYSTEMIC!LUPUS!ERYTHEMATOSUS,!WHICH!CAN!VARY!BETWEEN!
INDIVIDUALS.!TAKEN!FROM!(THE!LUPUS!EFFECT,!X).!..............................................................................................!8!
FIGURE!1.3:!OVERVIEW!OF!THE!PATHOGENESIS!OF!SLE.!ADAPTED!FROM!(TSOKOS,!2011).!.....................................!9!
FIGURE!1.4:!BIOGENESIS!OF!MIRNA.!TAKEN!FROM!(SIGMAXALDRICH,!X).!...................................................................!13!
FIGURE!1.5:!THE!STRUCTURAL!DOMAINS!OF!RO52.!TAKEN!FROM!(OKE!AND!WAHRENXHERLENIUS,!2012).!......!15!
FIGURE!2.1:!THE!BLUE!PUREYIELD™!
CLEARING!COLUMN!IN!A!WHITE!PUREYIELDTM!
MAXI!BINDING!COLUMN!ON!A!
VACXMAN®!LABORATORY!VACUUM!MANIFOLD!PORT.!..........................................................................................!21!
FIGURE!2.2:!STEPS!IN!MAXIPREP!SYSTEM!(SIGMAXALDRICH,!N.D.).!..............................................................................!21!
FIGURE!2.3:!ASSEMBLY!OF!MICROCENTRIFUGE!TUBE!ONTO!THE!BASE!OF!THE!ELUATOR™!VACUUM!ELUTION!
DEVICE.!..........................................................................................................................................................................!22!
FIGURE!2.4:!LAYOUT!OF!A!96XWELL!PLATE!TRANSFECTION!FOR!THE!ADDITION!OF!PLASMID!DNAS.!......................!25!
FIGURE!2.5:!DUAL!REPORTER!LUCIFERASE!ASSAY!SYSTEM.!.............................................................................................!26!
FIGURE!2.6:!SCHEMATIC!DIAGRAM!OF!THE!REACTION!FOR!THE!BICINCHONINIC!ACIDXCONTAINING!PROTEIN!ASSAY!
(WHITE,!2007).!..........................................................................................................................................................!27!
FIGURE!2.7:!SCHEMATIC!DIAGRAM!FOR!HIGH!THROUGHPUT!DYNAMIC!SCANNING!FLUORIMETRY!THERMAL!
STABILITY!ASSAY.!A,!ILLUSTRATES!THE!SAMPLE!PREPARATION!AND!B,!REPRESENTS!THE!NATIVE,!
DENATURED,!AND!AGGREGATED!STATES!OF!PROTEIN!ALONGSIDE!ITS!TYPICAL!EXOGENOUS!FLUORESCENCE!
RESPONSE!(VOLLRATH!ET!AL.,!2014).!.....................................................................................................................!29!
FIGURE!2.8:!SCHEMATIC!DIAGRAM!OF!THE!STEPS!INVOLVED!IN!GEL!ELECTROPHORESIS!(PREMEDHQ,!2001).!....!32!
FIGURE!2.9:!REALXTIME!PCR!MECHANISM!(SIGMAXALDRICH,!2002).!.........................................................................!35!
FIGURE!3.1:!TRIM21!NEGATIVELY!REGULATES!TRIF!DRIVEN!IFNXΒ!PROMOTER!ACTIVITY.!HEK293TXCELLS!
WERE!SEEDED!AT!1X105!CELLS/ML,!200ΜL/WELL,!IN!A!96XWELL!PLATE.!CELLS!WERE!TRANSFECTED!
WITH!PLASMIDS!CONTAINING!100NG!OF!TRIF!TO!DRIVE!THE!SYSTEM,!P125,!RENILLA,!TRIM21,!AND!AN!
EV!CONTROL.!18HR!POSTXTRANSFECTION!CELLS!WERE!HARVESTED!AND!COMPOUNDS!ADDED!AND!
LUCIFERASE!ASSAY!WAS!MEASURED!FOLLOWING!6HR!INCUBATION.!A,!CYCLODEXTRIN!(CD)!VEHICLE!
CONTROL;!B,!POLYETHYLENE!GLYCOL!(PEG)!VEHICLE!CONTROL;!AND!C,!SODIUM!HYDROXIDE!(NAOH)!
VEHICLE!CONTROL.!THE!ABOVE!DATA!IS!GRAPHED!FROM!THE!AVERAGE!OF!THREE!SEPARATE!EXPERIMENTS,!
±!STANDARD!ERROR!OF!THE!MEAN!SEM!(N=3).!....................................................................................................!38!
FIGURE!3.2:!TRIM21!NEGATIVELY!REGULATES!TRIF!DRIVEN!IFNXΒ!PROMOTER!ACTIVITY.!HEK293TXCELLS!
WERE!SEEDED!AT!1X105!CELLS/ML,!200ΜL/WELL,!IN!A!96XWELL!PLATE.!CELLS!WERE!TRANSFECTED!
WITH!PLASMIDS!CONTAINING!100NG!OF!TRIF!TO!DRIVE!THE!SYSTEM,!P125,!RENILLA,!TRIM21,!AND!AN!
EV!CONTROL.!18HR!POSTXTRANSFECTION!CELLS!WERE!HARVESTED!AND!COMPOUNDS!ADDED!AND!
LUCIFERASE!ASSAY!WAS!MEASURED!FOLLOWING!6HR!INCUBATION.!A,!3A&COMPOUND!IN!CYCLODEXTRIN!
(CD)!VEHICLE!CONTROL!WITH!DILUENTS!INCLUDING!VC!ITSELF,!PBS,!AND!STERILEXFILTERED!DMEM;!
AND!B,!3A&COMPOUND!IN!POLYETHYLENE!GLYCOL!(PEG)!VEHICLE!CONTROL!WITH!DILUENTS!INCLUDING!VC!
8. vii!!
ITSELF,!PBS,!AND!STERILEXFILTERED!DMEM.!BOTH!COMPOUNDS!ARE!AT!0.05ΜM!CONCENTRATION.!THE!
ABOVE!DATA!IS!GRAPHED!FROM!THE!AVERAGE!OF!THREE!SEPARATE!EXPERIMENTS,!±!SEM!(N=3).!............!39!
FIGURE!3.3:!TRIM21!NEGATIVELY!REGULATES!TRIF!DRIVEN!IFNXΒ!PROMOTER!ACTIVITY.!HEK293TXCELLS!
WERE!SEEDED!AT!1X105!CELLS/ML,!200ΜL/WELL,!IN!A!96XWELL!PLATE.!CELLS!WERE!TRANSFECTED!
WITH!PLASMIDS!CONTAINING!100NG!OF!TRIF!TO!DRIVE!THE!SYSTEM,!P125,!RENILLA,!TRIM21,!AND!AN!
EV!CONTROL.!18HR!POSTXTRANSFECTION!CELLS!WERE!HARVESTED!AND!COMPOUNDS!ADDED!AND!
LUCIFERASE!ASSAY!WAS!MEASURED!FOLLOWING!6HR!INCUBATION.!A,!4A&COMPOUND!IN!CYCLODEXTRIN!
(CD)!VEHICLE!CONTROL!WITH!DILUENTS!INCLUDING!VC!ITSELF,!PBS,!AND!STERILEXFILTERED!DMEM;!
AND!B,!4A&COMPOUND&IN!POLYETHYLENE!GLYCOL!(PEG)!VEHICLE!CONTROL!WITH!DILUENTS!INCLUDING!VC!
ITSELF,!PBS,!AND!STERILEXFILTERED!DMEM.!BOTH!COMPOUNDS!ARE!AT!0.05ΜM!CONCENTRATION.!THE!
ABOVE!DATA!IS!GRAPHED!FROM!THE!AVERAGE!OF!THREE!SEPARATE!EXPERIMENTS,!±!SEM!(N=3).!............!40!
FIGURE!3.4:!TRIM21!NEGATIVELY!REGULATES!TRIF!DRIVEN!IFNXΒ!PROMOTER!ACTIVITY.!HEK293TXCELLS!
WERE!SEEDED!AT!1X105!CELLS/ML,!200ΜL/WELL,!IN!A!96XWELL!PLATE.!CELLS!WERE!TRANSFECTED!
WITH!PLASMIDS!CONTAINING!100NG!OF!TRIF!TO!DRIVE!THE!SYSTEM,!P125,!RENILLA,!TRIM21,!AND!AN!
EV!CONTROL.!18HR!POSTXTRANSFECTION!CELLS!WERE!HARVESTED!AND!COMPOUNDS!ADDED!AND!
LUCIFERASE!ASSAY!WAS!MEASURED!FOLLOWING!6HR!INCUBATION.!A,!3A&COMPOUND!IN!CYCLODEXTRIN!
(CD)!VEHICLE!CONTROL;!B,!3A&COMPOUND&IN!POLYETHYLENE!GLYCOL!(PEG)!VEHICLE!CONTROL;!AND!C,!
3A&COMPOUND!IN!TRIFLUOROACETIC!ACID!(TFA)!VEHICLE!CONTROL.!THE!ABOVE!DATA!IS!GRAPHED!FROM!
THE!AVERAGE!OF!THREE!SEPARATE!EXPERIMENTS,!±!SEM!(N=3).!*P<0.05!WAS!CONSIDERED!SIGNIFICANT.
!........................................................................................................................................................................................!42!
FIGURE!3.5:!TRIM21!NEGATIVELY!REGULATES!TRIF!DRIVEN!IFNXΒ!PROMOTER!ACTIVITY.!HEK293TXCELLS!
WERE!SEEDED!AT!1X105!CELLS/ML,!200ΜL/WELL,!IN!A!96XWELL!PLATE.!CELLS!WERE!TRANSFECTED!
WITH!PLASMIDS!CONTAINING!100NG!OF!TRIF!TO!DRIVE!THE!SYSTEM,!P125,!RENILLA,!TRIM21,!AND!AN!
EV!CONTROL.!18HR!POSTXTRANSFECTION!CELLS!WERE!HARVESTED!AND!COMPOUNDS!ADDED!AND!
LUCIFERASE!ASSAY!WAS!MEASURED!FOLLOWING!6HR!INCUBATION.!A,!4A&COMPOUND!IN!CYCLODEXTRIN!
(CD)!VEHICLE!CONTROL;!B,!4A!COMPOUND!IN!POLYETHYLENE!GLYCOL!(PEG)!VEHICLE!CONTROL;!AND!C,!
4A&COMPOUND&IN!TRIFLUOROACETIC!ACID!(TFA)!VEHICLE!CONTROL.!THE!ABOVE!DATA!IS!GRAPHED!FROM!
THE!AVERAGE!OF!THREE!SEPARATE!EXPERIMENTS,!±!SEM!(N=3).!*P<0.05!WAS!CONSIDERED!SIGNIFICANT.
!........................................................................................................................................................................................!43!
FIGURE!3.6:!TRIM21!NEGATIVELY!REGULATES!TRIF!DRIVEN!IFNXΒ!PROMOTER!ACTIVITY.!HEK293TXCELLS!
WERE!SEEDED!AT!1X105!CELLS/ML,!200ΜL/WELL,!IN!A!96XWELL!PLATE.!CELLS!WERE!TRANSFECTED!
WITH!PLASMIDS!CONTAINING!100NG!OF!TRIF!TO!DRIVE!THE!SYSTEM,!P125,!RENILLA,!TRIM21,!AND!AN!
EV!CONTROL.!18HR!POSTXTRANSFECTION!CELLS!WERE!HARVESTED!AND!COMPOUNDS!ADDED!AND!
LUCIFERASE!ASSAY!WAS!MEASURED!FOLLOWING!6HR!INCUBATION.!A,!3A&COMPOUND!IN!CYCLODEXTRIN!
(CD)!VEHICLE!CONTROL;!B,!3A&COMPOUND&IN!POLYETHYLENE!GLYCOL!(PEG)!VEHICLE!CONTROL;!AND!C,!
3A&COMPOUND&IN!TRIFLUOROACETIC!ACID!(TFA)!VEHICLE!CONTROL.!THE!ABOVE!DATA!IS!GRAPHED!FROM!
THE!AVERAGE!OF!THREE!SEPARATE!EXPERIMENTS,!±!SEM!(N=3).!*P<0.05!WAS!CONSIDERED!SIGNIFICANT.
!........................................................................................................................................................................................!45!
FIGURE!3.7:!TRIM21!NEGATIVELY!REGULATES!TRIF!DRIVEN!IFNXΒ!PROMOTER!ACTIVITY.!HEK293TXCELLS!
WERE!SEEDED!AT!1X105!CELLS/ML,!200ΜL/WELL,!IN!A!96XWELL!PLATE.!CELLS!WERE!TRANSFECTED!
9. viii!!
WITH!PLASMIDS!CONTAINING!100NG!OF!TRIF!TO!DRIVE!THE!SYSTEM,!P125,!RENILLA,!TRIM21,!AND!AN!
EV!CONTROL.!18HR!POSTXTRANSFECTION!CELLS!WERE!HARVESTED!AND!COMPOUNDS!ADDED!AND!
LUCIFERASE!ASSAY!WAS!MEASURED!FOLLOWING!6HR!INCUBATION.!A,!4A&COMPOUND!IN!CYCLODEXTRIN!
(CD)!VEHICLE!CONTROL;!B,&4A&COMPOUND&IN!POLYETHYLENE!GLYCOL!(PEG)!VEHICLE!CONTROL;!AND!C,&
4A&COMPOUND&IN!TRIFLUOROACETIC!ACID!(TFA)!VEHICLE!CONTROL.!THE!ABOVE!DATA!IS!GRAPHED!FROM!
THE!AVERAGE!OF!THREE!SEPARATE!EXPERIMENTS,!±!SEM!(N=3).!*P<0.05!WAS!CONSIDERED!SIGNIFICANT.
!........................................................................................................................................................................................!46!
FIGURE!3.8:!STANDARD!CURVE!OF!THE!BCA!STANDARDS.!.............................................................................................!48!
FIGURE!3.9:!DETERMINING!PROTEIN!CONCENTRATIONS!OF!TRIM21!FOR!FURTHER!ANALYSIS!IN!THERMAL!SHIFT!
ASSAY.!............................................................................................................................................................................!51!
FIGURE!3.10:!DETERMINING!PROTEIN!CONCENTRATIONS!OF!IRF3!FOR!FURTHER!ANALYSIS!IN!THERMAL!SHIFT!
ASSAY.!............................................................................................................................................................................!51!
FIGURE!3.11:!DETERMINING!PERCENTAGE!OF!DMSO!USED!IN!TRIM21!PROTEIN!IN!THERMAL!SHIFT!ASSAY.!.......!52!
FIGURE!3.12:!DETERMINING!PERCENTAGE!OF!DMSO!USED!IN!IRF3!PROTEIN!IN!THERMAL!SHIFT!ASSAY.!............!52!
FIGURE!3.13:!ANALYSIS!OF!SERIES!A!COMPOUNDS!ON!TRIM21!PROTEIN!USING!THERMAL!DENATURATION!ASSAY.
!........................................................................................................................................................................................!53!
FIGURE!3.14:!ANALYSIS!OF!SERIES!A!COMPOUNDS!ON!IRF3!PROTEIN!USING!THERMAL!DENATURATION!ASSAY.!..!53!
FIGURE!3.15:!OPTIMISATION!OF!MIRX30E!AND!MIRX125A!AT!50˚,!55˚,!AND!62˚C!ANNELING!TEMPERATURES!
USING!STERILE!NUCLEASEXFREE!WATER!AND!CONTROL!CDNA!AND!1KB!DNA!LADDER!VISUALISED!BY!
SYPRORED!STAINING!ON!A!1%!AGAROSE!GEL.!........................................................................................................!58!
FIGURE!3.16:!OPTIMISATION!OF!MIRX194!AND!MIRX98!AT!50˚,!55˚,!AND!62˚C!ANNEALING!TEMPERATURES!
USING!STERILE!NUCLEASEXFREE!WATER!AND!CONTROL!CDNA!AND!1KB!DNA!LADDER!VISUALISED!BY!
SYPRORED!STAINING!ON!A!1%!AGAROSE!GEL.!........................................................................................................!59!
FIGURE!3.17:!OPTIMISATION!OF!THE!PREDICTED!GENE!TARGETS!OF!MIRS!OF!INTEREST!INCLUDING!CXCL3!AT!
62˚,!65˚,!AND!68˚C!ANNEALING!TEMPERATURE!AND!JAK3,!IL10,!AND!SOCS1!AT!62˚C!ANNEALING!
TEMPERATURE!USING!STERILE!NUCLEASEXFREE!WATER!AND!CONTROL!CDNA!AND!1KB!DNA!LADDER!
VISUALISED!BY!SYPRORED!STAINING!ON!A!1%!AGAROSE!GEL.!.............................................................................!59!
FIGURE!3.18:!EXPRESSION!LEVELS!OF!MIRX30E!IN!PBMCS!OF!PSS!PATIENT!VERSUS!HEALTHY!CONTROLS.!A,!MIRX
30E!RAW!SPECTRUM!EXPRESSION!WITH!A!PDVALUE!OF!0.5714.!B,!MIRX30E!EXPRESSION!MINUS!THE!
OUTLIERS!WITH!A!PDVALUE&OF!0.6571.!ENDOGENOUS!RNU6B!WAS!USED!AS!REFERENCE!CONTROL!FOR!MIR!
EXPRESSION.!..................................................................................................................................................................!62!
FIGURE!3.19:!EXPRESSION!LEVELS!OF!MIRX125A!IN!PBMCS!OF!PSS!PATIENT!VERSUS!HEALTHY!CONTROLS.!!A,!
MIRX125A!RAW!SPECTRUM!EXPRESSION!WITH!A!PDVALUE&OF!0.3754.!B,!MIRX125A!EXPRESSION!MINUS!
THE!OUTLIERS!WITH!A!PDVALUE!OF!0.6667.!ENDOGENOUS!RNU6B!WAS!USED!AS!REFERENCE!CONTROL!FOR!
MIR!EXPRESSION.!.........................................................................................................................................................!62!
FIGURE!3.20:!EXPRESSION!LEVELS!OF!MIRX194!IN!PBMCS!OF!PSS!PATIENT!VERSUS!HEALTHY!CONTROLS.!A,!MIRX
194!RAW!SPECTRUM!EXPRESSION!WITH!A!PDVALUE!OF!0.7023.!B,!MIRX125A!EXPRESSION!MINUS!THE!
OUTLIERS!WITH!A!PDVALUE!OF!>0.9999.!ENDOGENOUS!RNU6B!WAS!USED!AS!REFERENCE!CONTROL!FOR!
MIR!EXPRESSION.!.........................................................................................................................................................!63!
13. 1""
Abstract(
Autoimmune"diseases,"in"particular"Sjögren’s"Syndrome"and"Systemic"Lupus"
Erythematosus,"are"conditions"that"result"from"dysregulated"immune"responses"
culminating"in"loss"of"tolerance"to"self–"antigens"and"immune>mediated"injury."In"
addition"to"the"primary"pathologies"associated"with"these"diseases,"patients"can"
develop"additional"complications."These"complications"can"range"in"severity"
from"fatigue,"rash,"and"joint"pain"to"the"development"of"cardiovascular,"
neurological,"and"renal"complications"in"addition"to"pulmonary"fibrosis,"
interstitial"lung"disease"and"in"certain"cases"for"Sjögren"patients,"non>Hodgkin’s"
lymphoma."To"date,"overproduction"of"inflammatory"cytokines"(IL>6,"IL>12,"IL>23"
and"TNFα)"and"type"I"interferons"(IFN>α"and"IFN>β)"have"been"suggested"to"play"
a"key"role"in"the"development"and"pathogenesis"of"these"autoimmune"conditions."
Trim21"has"been"identified"as"key"negative"regulator"of"inflammation,"whose"
expression"and"function"are"altered"in"patients"with"SLE."Trim21"is"a"negative"
regulator"of"innate"immune"signalling"through"the"interaction,"ubiquitination,"
and"subsequent"proteosomal"degradation"of"the"transcription"factors"IRF3"and"
IRF7."By"ubiquitinating"and"targeting"IRF3"and"IRF7"for"degradation,"Trim21"
effectively"turns"off"the"production"of"type"I"IFNs,"thus"preventing"
overproduction"of"this"potentially"pathogenic"cytokine."Drug"compounds,"
specifically"3A"and"4A,"have"been"applied"to"demonstrate"its"ability"to"increase"
Trim21"activity"hence,"increased"inhibition"of"IFN>β"promoter"activity."
Preliminary"results"with"4A"compounds"looked"to"be"significant"(p<0.05)."
Recently,"non>coding"microRNAs"have"been"shown"to"regulate"immune"function"
in"a"variety"of"autoimmune"conditions,"which"suggests"that"micro>RNA"based"
strategies"hold"therapeutic"potential"in"treatment"of"autoimmune"disorders."This"
project"hypothesises"that"dysregulation"of"miRNAs"in"PBMCs"of"pSS"patients"
versus"healthy"controls"results"in"uncontrolled"expression"of"their"gene"targets"
leading"to"disease"pathogenesis."Through"bioinformatics"analysis,"the"miRNAs"of"
interest"showed"a"lot"promise"signifying"a"potential"future"role"of"microRNAs"as"
novel"therapeutics.
14. 2""
1.0!Introduction!
Autoimmune"disorders"such"as"Sjögren’s"Syndrome"(SS)"and"Systemic"Lupus"
Erythematosus"(SLE),"result"from"impairment"of"the"immune"response"leading"to"
recognition"and"the"attack"of"the"patient’s"own"tissues,"and"thus"a"loss"of"selfX
tolerance"(Snow"et"al.,"2003)."
"
1.1!Sjögren’s!Syndrome!
Henrik"Sjögren,"an"ophthalmologist"in"the"1930s,"observed"and"reported"detailed"
clinical"and"histological"findings"in"women"with"chronic"xerostomia"and"
keratoconjunctivitis"sicca"(Delaleu"et"al.,"2005)."It"was"previously"known"as"sicca"
syndrome,"and"associated"with"low"secretions"from"both"the"lacrimal"and"
salivary"gland."Sjögren’s"syndrome,"as"it"is"now"referred"to,"is"a"chronic"
autoimmune"disease"that"affects"the"exocrine"glands"and"together"with"excessive"
inflammation"(Bayetto"and"Logan,"2010)"are"the"main"pathophysiological"
associations"essentially"leading"to"dry"eyes"and"dry"mouth."SS"primarily"affects"
90%"of"women,"notably"menopausal"women,"with"a"9:1"ratio"to"men."SS"can"exist"
either"as"a"primary"disorder"(pSS)"or"in"patients"associated"with"other"rheumatic"
disorders,"such"as"SLE,"rheumatoid"arthritis"(RA)"or"scleroderma,"and"is"then"
termed"‘secondary’"SS,"typically"as"a"late"complication."
"
1.2!Systemic!Lupus!Erythematosus!
Although"the"term"“Lupus"Erythematosus”"was"introduced"by"19thXcentury"
physicians"to"define"skin"lesions,"it"took"almost"100"years"to"realise"that"the"
disease"is"systemic"and"spares"no"organ"and"that"it"is"caused"by"aberrant"
autoimmune"response"(Duarte"et"al.,"2011)."SLE"is"a"complex"autoimmune"
condition"with"heterogeneous"clinical"manifestations"of"unknown"origin"known"
to"affect"virtually"every"organ"in"the"body"(YildirimXToruner"and"Diamond,"
2011)."SLE"is"primarily"caused"by"autoantibodies"and"immune"complex"
deposition."Similar"to"SS,"most"patients"afflicted"are"women,"especially"of"
childbearing"age"with"a"9:1"ratio"commonly"reported."
15. 3""
"
1.3!Epidemiology!
Together"with"RA,"SS"is"one"of"the"most"frequent"autoimmune"diseases"and"it"
occurs"all"over"the"world."The"disease"can"appear"at"any"age,"with"a"significant"
peak"incidence"between"40"and"50"years."Depending"on"the"applied"classification"
criteria"the"prevalence"for"SS"reaches"from"0.5%"of"all"adult"females"when"
employing"the"Californian"Fox"Criteria"(CFC)"(Fox"et"al.,"1986),"up"to"1X3%"of"
total"population,"when"using"the"European"Community"Criteria"(ECC)"(Vitali"et"
al.,"1993)"or"the"AmericanXEuropean"Consensus"Group"(AECG)"criteria"(Vitali"et"
al.,"2002)."Recently,"the"revised"AECG"criteria"are"now"considered"the"gold"
standard"for"the"classification"of"SS"(refer"to"Table,1.1)"and"have"repudiated"
preceding"criteria"sets."However,"most"studies"start"from"the"assumption"of"a"
prevalence"of"0.6%"of"the"total"population"(Delaleu"et"al.,"2005)."
Table!1.1:!Sjögren's!Syndrome!–!Revised!AECG!Criteria.!Adapted!from!(Vitali!et!al.,!2002).!
"
Until"the"AECG"criteria"were"devised,"it"was"difficult"to"compare"different"
epidemiological"studies"that"used"different"definitions"for"SS."Kivity"et&al."has"
reported"prevalence"ranging"from"0.1%"to"4.8%"but"significantly"depended"on"
different"geographical"and"ethnical"regions"(Kivity"et"al.,"2014)."For"example,"
China"has"reported"a"prevalence"of"only"0.77%,"while"Greece"appears"to"have"an"
incidence"six"times"greater"of"approximately"4.8%"(Mavragani"and"
Moutsopoulos,"2010)."It"is"possible"that"the"variability"observed"might"reflect"
differences"in"the"diagnostic"criteria"between"different"regions"and"ethnicities,"as"
well"as"the"diverse"geographic"study"region,"which"implies"contribution"from"
16. 4""
both"genetic"and"environmental"pressures,"not"to"mention"sample"size"and"
gender"distribution."
"
The"incidence"and"prevalence"of"SLE"seems"to"be"increasing,"probably"due"to"the"
identification"of"milder"cases"and"improved"survival."According"to"D’Cruz"et&al."
there"is"an"obvious"difference"in"geographical"variability"in"disease"incidence"and"
prevalence"(D'Cruz"et"al.,"2007)."They"reported"that"in"the"US"population,"the"
entire"race"incidence"was"5.1"per"100,000"per"year"and"the"prevalence"was"52.2"
per"100,000,"with"comparative"figures"of"3.8"and"26.2"in"the"UK,"and"2.9"and"28.4"
in"Japan,"respectively."These"figures"are"substantially"higher"in"some"ethnic"
populations,"markedly"in"individuals"of"AfricanXAmerican"or"AfricanXCaribbean"
descent"(Johnson"et"al.,"1995)."However,"reliable"data"about"the"prevalence"of"
SLE"are"difficult"to"come"by"due"to"variable"methods"for"data"collection"as"well"as"
inconsistency"regarding"case"definition"are"known"to"be"contributing"factors"
(refer"to"Table,1.2)."
Table!1.2:!American!College!of!Rheumatology!Criteria!for!the!Diagnosis!of!Systemic!Lupus!
Erythematosus.!Adapted!from!(Tsokos,!2011).!
"
17. 5""
1.4!Symptoms!
Dry"eyes"and"dry"mouth"are"the"commonest"complaints"of"patients"suffering"
from"SS."The"onset"is"usually"insidious"with"the"general"discomfort"typically"
accompanied"by"systemic"pain"and"intense"fatigue"leading"to"an"impaired"quality"
of"life"(Cornec"et"al.,"2014)."
"
Patients"with"mild"dry"eyes"can"usually"get"away"with"selfXmedication"with"overX
theXcounter"lubricating"eye"drops."Although"many"patients"with"SS"are"still"able"
to"produce"tears"with"stimulation,"it"is"inhibition"of"basal"tear"production"that"
makes"the"eyes"feel"dry"(Bowman"and"Rao,"2014)."Occasionally,"dry"eyes"are"
treated"with"local"application"of"cyclosporine"(ThanouXStavraki"and"James,"2008)"
that"can"ameliorate"the"ocular"sicca"aspects"of"the"disease.""
"
Deficiencies"in"the"quantity"and"quality"of"saliva"have"a"negative"impact"on"dental"
and"oral"health."Dental"caries,"mucositis,"oral"candidiasis,"and"swelling"of"the"
salivary"glands"are"the"most"frequent"oral"signs"of"SS"(Delaleu"et"al.,"2005)."The"
most"common"cause"of"dry"mouth,"as"believed"by"Bowman"and"Rao,"are"
medications"such"as"antiXdepressants,"antihistamines,"diuretics"or"betaXblockers"
(Bowman"and"Rao,"2014)."Clinical"features"include"a"lack"of"obvious"saliva"in"the"
mouth"and"absence"of"a"normal"‘pool’"of"saliva"underneath"the"tongue."The"
simplest"solution"in"terms"of"treatment"is"to"keep"the"mouth"moistened"using"
water"followed"by"a"saline"mixture."
"
SS"comprises"a"broad"spectrum"of"symptoms"ranging"from"organ"specific"
autoimmune"exocrinopathy"to"systemic"disease"manifestations"(refer"to"Figure,
1.1)."Systemic"features"of"SS"occur"in"about"twoXthirds"of"all"patients"(GarciaX
Carrasco"et"al.,"2002)"and"include"joint"involvement,"Raynaud’s"phenomenon,"
vasculitis,"involvement"of"the"central"and"peripheral"nervous"systems,"and"renal"
and"pulmonary"involvement"(Hatron"et"al.,"2011)."In"addition,"patients"with"SS"
have"a"16X"to"44Xfold"increased"risk"of"lymphoma"compared"to"the"general"
population"(Theander"et"al.,"2006)"and"particularly"in"pSS"patients,"mucosaX
associated"lymphoid"tissue"(MALT)"type"B"cell"lymphoma"(Bowman"and"Rao,"
18. 6""
2014)."The"prevalence"of"malignant"lymphoma"in"pSS"was"shown"to"be"stronger"
than"in"SLE"or"RA"(Voulgarelis"and"Moutsopoulos,"2003)."
"
Hatron"et&al."reported"that"pulmonary"involvement"is"also"common"in"pSS"
patients,"but"only"about"10%"of"them"are"symptomatic"(Hatron"et"al.,"2011)."The"
main"pulmonary"manifestations"are"sicca"cough,"and"mild"to"moderate"airways"
obstruction."Pulmonary"manifestations"in"SS"typically"develop"late"in"the"course"
of"disease"(Cain"et"al.,"1998)"and"are"rarely"the"presenting"feature."Pulmonary"
involvement"is"associated"with"a"4Xfold"increased"mortality"risk"after"10"years"of"
disease"(Stojan"et"al.,"2013)."
"
Figure!1.1:!Effects!of!Sjögren’s!syndrome!in!the!body.!Taken!from!(Kallen,!2014).!
The"clinical"features"of"SLE"are"diverse"(refer"to"Figure,1.2)."As"with"SS,"the"
symptoms"of"SLE"vary"from"person"to"person."The"skin,"musculoskeletal,"and"
haematologic"organs"are"commonly"involved"with"some"patients"presenting"with"
19. 7""
predominantly"haematologic,"renal,"or"neuropsychiatric"manifestations"(Gill"et"
al.,"2003)."
"
Constitutional"symptoms"mainly"include"fatigue,"weight"loss,"and"fever"(in"the"
absence"of"infection)"are"commonly"not"lifeXthreatening"but"have"an"impact"on"
the"patient’s"quality"of"life."Renal"disease"affects"about"30%"of"patients"with"SLE"
(Manson"and"Rahman,"2006),"and"remains"the"most"dangerous,"lifeXthreatening"
complication."Regular"urinalysis"and"blood"pressure"monitoring"is"crucial"since"
renal"involvement"is"often"asymptomatic,"especially"in"the"initial"stages."
"
Neuropsychiatric"lupus"(NPSLE)"is"seen"in"about"20%"of"cases"but"is"often"
difficult"to"make"a"diagnosis."The"American"College"of"Rheumatology"
(Rheumatology,"1999)"described"19"different"clinical"manifestations"(refer"to"
Table,1.3)"but"no"single,"simple"diagnostic"test"can"be"made."
Table!1.3:!Neuropsychiatric!syndromes!observed!in!systemic!lupus!erythematosus.!Adapted!from!
(Manson!and!Rahman,!2006).!
"
Skin"involvement"in"SLE"is"very"common."In"addition"to"the"classic"malar"and"
discoid"rashes"seen,"more"generalised"photosensitivity"is"often"present,"and"
furthermore"exposure"to"sunlight"is"known"to"trigger"systemic"disease"flares."
Recurrent"crops"of"mouth"ulcers"have"also"been"found"to"be"a"feature"of"active"
disease"(Manson"and"Rahman,"2006)."There"are"also"other"oral"manifestations"
known"to"contribute"including"dryness"as"a"result"of"secondary"Sjögren’s"
syndrome,"with"patients"also"experiencing"dryness"of"the"eyes"and"vagina."
20. 8""
The"clinical"manifestations"of"SLE"are"fundamentally"the"same"in"children"and"
adults."Studies"conducted"by"(Singh"et"al.,"1997;"Marini"and"Costallat,"1999)"of"
children"with"SLE,"reported"that"the"most"frequent"manifestations"of"the"disease"
were"fever,"rash,"arthritis,"alopecia,"and"renal"involvement."In"comparison,"
children"have"a"higher"incidence"of"malar"rash,"anaemia,"leukocytopeania"(Rood"
et"al.,"1999),"and"severe"manifestations"such"as"neurologic"or"renal"involvement"
(Carreño"et"al.,"1999)."
"
"
Figure! 1.2:! Common! symptoms! of! systemic! lupus! erythematosus,! which! can! vary! between!
individuals.!Taken!from!(The!Lupus!Effect,!`).!
!
1.5!Pathogenesis!
The"pathogenesis"of"SS"has"not"been"delineated,"but"it"is"believed"that"both"
immunologically"mediated"and"nonXimmune"mechanisms"contribute"
significantly"(Cotrim"and"Alevizos,"2014)."Genetic"susceptibility"as"well"as"
epigenetic"contributions"are"within"the"basis"of"the"disease"along"with"
21. 9""
immensely"influencing"environmental"triggers."Kivity"et&al."suggested"that"genes"
involved"in"innate"and"adaptive"immunity"are"crucial"for"susceptibility"(Kivity"et"
al.,"2014)."
"
SLE"is"a"multisystem"disease"(refer"to"Figure,1.3)"with"evidence"of"genetic"
susceptibility,"environmental"effects,"and"disturbances"in"both"innate"and"
adaptive"immunity"manifest"by"disturbances"in"apoptotic"cell"clearance,"
cytokines,"BXcell"immunity,"and"TXcell"signalling"(Lisnevskaia"et"al.,"2014)."
Genetic,"environmental,"hormonal,"epigenetic,"and"immunoregulatory"factors"act"
either"sequentially"or"simultaneously"on"the"immune"system."The"action"of"
pathogenic"factors"results"in"the"generation"of"autoantibodies,"immune"
complexes,"autoreactive"or"inflammatory"T"cells,"and"inflammatory"cytokines"
that"may"initiate"and"amplify"inflammation"and"damage"to"various"organs."
!
Figure!1.3:!Overview!of!the!Pathogenesis!of!SLE.!Adapted!from!(Tsokos,!2011).!
22. 10""
1.6!Genetic!Predisposition!
Both"Sjögren’s"syndrome"and"systemic"lupus"erythematosus"are"considered"
complex"disorders."Susceptibility"to"both"diseases"can"be"attributed"to"interplay"
between"genetic"factors"and"the"environment."In"complex"diseases,"one"specific"
gene"is"neither"necessary"nor"sufficient"for"disease"expression."
"
Genetic"factors"associated"with"SS"are"particular"human"leukocyte"antigen"
(HLA)XDR"allele"subtypes"of"the"major"histocompatibility"complex"(MHC)"class"II"
genes"and"specific"gene"polymorphisms"such"as"STAT4,"ILX12A,"TNIP1,"IRF5,"
BLK,"and"CXCR5"(Lessard"et"al.,"2013)."Patients"of"different"ethnic"origins"exhibit"
different"HLA"gene"associations."There"have"been"reports"to"suggest"that"several"
families"involving"two"or"more"cases"of"Sjögren’s"syndrome"(Reveille"et"al.,"1984;"
Lichtenfeld"et"al.,"1976;"Sabio"et"al.,"2001)."However,"the"level"of"genetic"
contribution"is"not"known"(Bolstad"and"Jonsson,"2002),"since"there"has"not"been"
genetic"linkage"studies"of"SS"families."SS"in"twins"(Scofield"et"al.,"1997;"Bolstad"et"
al.,"2000)"have"also"been"described"but"the"concordance"rate"cannot"be"
estimated"due"to"a"lack"of"large"cohort"studies"on"twins"with"SS."They"reported"
that"twins"exhibited"a"very"similar"phenotype"with"almost"identical"clinical"
manifestation,"including"dry"eyes"and"dry"mouth."
"
HLA"is"associated"with"the"presence"of"certain"degrees"of"diversification"of"Ro"
(SSA)"and"La"(SSB)"autoantibodies"in"SS."However,"the"contribution"of"these"
autoantibodies"in"SS"has"not"been"fully"understood."The"tolerance"breakdown"as"
well"as"the"autoantibody"response"generation"is"still"unknown."Ultraviolet"
radiation,"viral"infections"and"apoptosis"have"been"suggested"to"lead"to"
undesirable"cell"surface"exposure"of"autoantigens"to"the"immune"system"
(Ohlsson"et"al.,"2002)."Ro/SSA"and"La/SSB"have"been"demonstrated"in"surface"
blebs"of"apoptotic"ultravioletXirradiated"keratinocytes,"which"implies"a"possible"
role"in"systemic"lupus"erythematosus"(CasciolaXRosen"et"al.,"1994)."
"
The"concordance"rate"of"SLE"in"identical"twins"is"approximately"25X50%"and"that"
in"dizygotic"twins"is"around"5%"(Pisetsky,"1997)."This"suggests"that"genetic"
factors"play"an"important"role"in"the"predisposition"of"the"disease."However,"
23. 11""
most"cases"of"SLE"are"sporadic"without"identifiable"genetic"predisposing"factors,"
implying"that"multiple"environmental"or"yet"unknown"factors"may"also"be"
responsible."
"
Many"different"genes"contribute"to"disease"susceptibility"and"(Byrne"et"al.,"2012)"
indicated"that"susceptibility"to"SLE"is"heritable."In"a"small"proportion"of"patients"
(<5%),"a"single"gene"may"be"responsible."For"instance,"(Walport"et"al.,"1998)"
reported"that"patients"with"homozygous"deficiencies"of"the"early"component"of"
complement"are"at"risk"of"developing"SLE"or"a"lupusXlike"disease."Those"encoding"
complement"components"C2"and"C4"confer"risk"for"SLE"in"certain"ethnic"groups,"
but"patients"with"homozygous"C4A"null"alleles,"irrespective"of"ethnic"origin,"are"
at"high"risk"of"developing"SLE."For"most"of"the"remaining"patients,"multiple"genes"
are"required."It"is"estimated"that"at"least"four"susceptibility"genes"are"needed"for"
the"development"of"the"disease"(Mok"and"Lau,"2003)."
"
HLA"class"II"genes"have"also"been"extensively"studied"for"their"contribution"to"
human"SLE."An"association"of"HLA"DR2"and"DR"with"SLE"is"a"common"finding"in"
patients"of"different"ethnicities,"with"a"relative"risk"for"the"development"of"
disease"of"approximately"two"to"five"(Pisetsky,"1997)."SLE"shows"a"strong"
familial"aggregation,"with"a"much"higher"frequency"among"firstXdegree"relatives"
of"patients."
"
1.7!Environmental!Factors!
Exogenous"agents"such"as"EpsteinXBarr"virus"have"been"suggested"to"cause"SS"in"
genetically"predisposed"individuals"(Pflugfelder"et"al.,"1993)"but"no"definite"
trigger"has"yet"been"identified"in"SS."Delaleu"et&al."concluded"that"there"has"not"
been"definite"exogenous"triggers"with"precise"association"with"SS"(Delaleu"et"al.,"
2004)."The"long"time"span"between"disease"initiation"and"diagnosis"makes"it"
particularly"difficult"to"solve"this"problem."
"
Although"genetic"factors"may"create"a"predisposition"towards"SLE,"the"initiation"
of"the"disease"probably"results"from"several"environmental"factors"and"
24. 12""
exogenous"factors"(refer"to"Table,1.4)."Certain"environmental"factors,"such"as"
chemicals"and"drugs,"ultraviolet"light"(especially"UVB),"dietary"factors,"viruses,"
and"circulating"oestrogen"are"probably"needed"to"precipitate"the"onset"of"SLE"
(Mok"and"Lau,"2003)."
Table!1.4:!Environmental!factors!that!may!be!relevant!in!the!pathogenesis!of!systemic!lupus!
erythematosus.!Adapted!from!(Mok!and!Lau,!2003).!
"
"
1.8!Distinctions!between!SS!and!SLE!
Since"Sjögren’s"and"Lupus"are"both"autoimmune"diseases,"there"is"a"coXexistent"
association"between"the"two"conditions."Both"SS"and"SLE"are"collagen"vascular"
diseases"that"can"be"accompanied"by"Ro"antibodies."Findings"report"that"a"
gender"bias"preference"is"seen"where"both"primarily"affect"women"more"than"
men."They"also"share"the"same"autoantibody"profile"with"similar"HLA"haplotypes"
of"class"II"markers,"which"often"results"in"the"generation"of"antiXRo/La"antibodies"
rather"than"from"the"diseases"themselves."Clinical"evidence"suggests"that"they"
are"wholly"distinct"diseases."The"antinuclear"antibody"laboratory"diagnosis"is"
more"often"positive"in"SLE"patients"vs."SS"patients."A"major"difference"between"
the"two"diseases"is"the"infrequent"encounter"of"photosensitivity"often"associated"
with"high"levels"of"Ro/SSA"antibodies"in"SS"patients"(Scheinfeld,"2006)."SS"does"
not"respond"to"hydroxychloroquine"in"a"reproducible"fashion"whereas"SLE"
usually"responds"to"hydroxychloroquine"in"a"consistent"manner"as"means"of"
treatment."
25. 13""
Since"the"discovery"of"microRNAs"(miRNAs),"several"papers"have"revealed"that"
miRNAs"can"play"a"role"in"autoimmune"diseases."It"is"well"known"that"miRNAs"
are"involved"in"the"development"of"mature"immune"cells"as"well"as"controlling"
their"functions"(Carissimi"et"al.,"2009),"which"suggests"that"these"molecules"may"
also"be"implicated"in"the"development"of"inflammatory"and"autoimmune"
diseases."
"
1.9!MicroRNAs!in!Autoimmune!Diseases!
miRs"are"small"nonXcoding"RNA"molecules"of"21X24"nucleotides"long"(Dai"et"al.,"
2007)."The"genes"that"encode"miRs"comprise"1X5%"of"all"genes,"making"miRs"the"
most"abundant"class"of"fineXtuning"regulators"of"diverse"biological"processes,"
including"the"ability"to"control"the"expression"of"approximately"30%"of"proteinX
coding"genes"(Kapsogeorgou"et"al.,"2011)"as"well"as"regulating"immune"
development"and"normal"function"and"autoimmunity"(Alevizos"and"Illei,"2010)."
"
"
Figure!1.4:!Biogenesis!of!miRNA.!Taken!from!(Sigma`Aldrich,!`).!
miRNA"originate"in"the"nucleus"of"the"cell"from"the"larger"RNA"transcripts"that"
are"transcribed"by"RNA"polymerase"II"(Lee"et"al.,"2004)."These"transcripts"(priX
miRNAs)"are"transcribed"by"a"complex"of"RNase"III"enzyme"along"with"Drosha,"
26. 14""
and"the"doubleXstranded"RNAXbinding"protein,"DGCR8"(DiGeorge"syndrome"
critical"region"gene"8)"to"form"small"stemXloop"(or"hairpin"shaped)"preXmiRNA"
precursors"of"about"60X70"nucleotides"in"length"(Gregory"et"al.,"2004)."The"preX
miRNAs"are"then"actively"exported"by"exportinX5"to"the"cytoplasm,"where"they"
lose"nucleotides"due"to"the"activity"of"the"cytoplasmic"RNase"III"enzyme"Dicer,"to"
achieve"a"final"mature"miRNA"form"(Yi"et"al.,"2003)."To"exert"their"actions,"
miRNA"must"selectively"attach"to"a"large"complex"of"proteins"called"RISC"(RNAX
induced"silencing"complex),"which"escort"miRNA"to"specific"mRNA"transcripts"
for"their"final"destination"(Amarilyo"and"La"Cava,"2012)."At"this"point,"miRNA"can"
diminish"the"production"of"proteins"through"two"major"mechanisms:"firstly,"the"
attachment"of"antiXsense"sequences"to"specific"complementary"mRNA"targets"
and"secondly"the"degradation"of"targeted"miRNAs."In"both"cases,"the"net"effect"of"
miRNA"activities"is"the"repression"of"the"expression"of"targeted"gene"products"
(Nilsen,"2007)."The"pathway"of"miRNA"is"shown"on"Figure,1.4."
"
Liston"et&al."reported"that"the"expression"of"miRs"are"firmly"controlled"during"
haematopoiesis"and"lymphoid"cell"differentiation"(Liston"et"al.,"2010)."By"
disabling"Dicer"or"RISC,"lineage"specific"disruption"of"the"entire"miR"network"
leads"to"dysregulated"lineage"differentiation"and/or"activation,"thus"may"lead"to"
autoimmunity."
"
Despite"the"vast"interest"in"miRNAs"expression"in"various"autoimmune"
conditions,"there"have"not"been"comprehensively"studies"in"SS."A"study"
conducted"by"Alevizos"et&al.,"investigated"miRNA"signatures"in"salivary"glands"
(SG)"and"found"94"miRNAs"to"be"differentially"expressed"between"SS"patients"
and"healthy"controls"(Alevizos"et"al.,"2011)."Kapsogeorgou"et&al."reported"that"
there"is"overlapping"of"distinct"biologic"pathways"and"processes"in"SS"patients"
with"miRNAs"associated"inflammation"or"SG"dysfunction"(Kapsogeorgou"et"al.,"
2011)"suggesting"that"saliva"is"an"obvious"source"for"a"nonXinvasive"biomarker"in"
Sjögren’s"syndrome"since"it"is"a"direct"product"of"the"affected"target"organ"
(Alevizos"and"Illei,"2010)."Some"of"the"differentially"expressed"miRNAs"identified"
by"researchers"(Iborra"et"al.,"2012;"Furer"et"al.,"2010)"may"have"diagnostic"and"
prognostic"value"for"disease"type"and"severity"suggesting"that"miRNAs"are"
27. 15""
implicated"in"the"pathogenesis"of"not"only"SS"but"also"autoimmune"diseases;"
however"further"studies"are"still"required."
"
The"first"report"of"a"difference"in"miRNA"expression"between"SLE"patients"and"
healthy"controls"dates"back"to"2007,"when"a"study"comparing"miRNA"expression"
profiles"in"peripheral"blood"mononuclear"cell"(PBMC)"of"patients"with"SLE"and"
idiopathic"thrombocytopaenic"purpura"(ITP)"patients,"identified"7"
downregulated"and"9"upregulated"miRNA"in"SLE"as"compared"controls"(Dai"et"al.,"
2007)."Preliminary"studies"have"shown"that"modulation"of"the"expression"of"
dysregulated"miRNA"in"lupus"patients’"cells"can"influence"some"parameters"of"
the"disease"(Amarilyo"and"La"Cava,"2012)."Yet"it"is"expected"that"factors"such"as"
variability"of"symptoms,"organ"involvement"and"clinical"characteristics"of"the"
SLE"patients"(due"to"genetic,"environmental"and"immunological"differences)"will"
pose"challenges"to"translational"approaches"that"could"target"miRNA"in"SLE"for"
therapeutic"benefits."
"
Due"to"the"complex"regulation"of"the"miRNA"networks"and"the"lack"of"inXvivo"
functional"studies,"the"understanding"of"the"role"of"miRNA"regulatory"pathways"
in"human"disease"remains"inadequate,"and"so"far"restricted"to"association"
studies."
"
1.10!Trim21!
Ro52"(or"Trim21)"is"a"common"target"of"circulating"autoantibodies"in"
autoimmune"disease"(Oke"and"WahrenXHerlenius,"2012)."Trim21"contains"a"
RING"and"a"BXbox"motif,"followed"by"a"coiledXcoil"(CC)"domain"and"a"B30.2"(or"
PRYSPRY)"region"in"the"CXterminal"end"as"seen"in"Figure,1.5."
"
Figure!1.5:!The!structural!domains!of!Ro52.!Taken!from!(Oke!and!Wahren`Herlenius,!2012).!
28. 16""
Autoantibodies"to"the"Ro52"protein"were"historically"denoted"by"the"common"
name"antiXRo/SSA"antibodies."AntiXRo52"is"the"most"common"specificity"in"
patients"with"pSS"(75.4%)"and"42.7%"in"SLE"patients"(SchulteXPelkum"et"al.,"
2009)."However,"it"is"not"known"if"these"autoantibodies"affect"the"function"of"
Ro52."
"
Bozic"et&al."have"reported"that"the"CC"domain"is"the"most"commonly"targeted"
region"of"the"Ro52"protein"in"patients"with"SLE"(Bozic"et"al.,"1993)."Interestingly,"
SS"patients"appear"to"have"specificities"against"several"different"Ro52"epitopes"
including"the"Ring,"BXbox,"and"CC"domains."
"
Members"of"the"tripartite"motifXcontaining"protein"(TRIM)"family"are"single"
protein"E3"ligases"(Higgs"et"al.,"2008)"that"have"ample"roles"in"cellular"biology."
Ro52"(Trim21)"is"targeted"as"an"autoantigen"in"SLE"and"SS."The"RING"domains"of"
TRIM"family"members"have"been"shown"to"have"E3"ubiquitin"ligase"activity"
(Yoshimi"et"al.,"2012),"mediating"ubiquitination"events"such"as"protein"
degradation,"trafficking,"and"activation."This"RING"domain,"according"to"Espinosa"
et&al.,"is"required"for"the"E3"activity"of"Trim21"and"that"SS"and"SLE"patient"antiX
Ro52"autoantibodies"directed"to"the"RING"domain"inhibit"Ro52"activity"
(Espinosa"et"al.,"2011)."They"concluded"that"antiXRo52"autoantibodies"might"
have"indicated"a"direct"pathogenic"role"in"disease"development."
"
31. 19""
2.1.2!List!of!Suppliers!
Argus"Fine"Chemicals"Ltd,"Sussex"Innovation"Centre,"Science"Park"Square,"
Falmer,"Brighton,"East"Sussex"BN1"9SB,"UK"
"
Bioline"Reagents"Ltd,"Unit"16"The"Edge"Business"Centre,"Humber"Road,"London,"
NW2"6EW,"UK"
"
Biontex"Laboratories"GmbH,"Landsberger"Str."234,"80687"München,"Germany"
"
Biosera,"1"Acorn"House,"The"Broyle,"Ringmer,"East"Sussex,"BN8"5NN,"UK"
"
GE"Healthcare,"Pollards"Wood,"Nightingales"Ln,"Chalfont"St."Giles,"HP8"4SP,"UK"
"
Lennox"Laboratory"Supplies"Ltd.,"John"F."Kennedy"Drive,"Naas"Road,"Dublin"12,"
Ireland"
"
Promega"Ltd.,"Delta"House,"Enterprise"Road,"Chilworth"Research"Centre,"
Southhampton,"SO1"7NS,"UK"
"
SigmaXAldrich"Company"Ltd.,"Fancy"Road,"Poole,"Dorset"BH12"4QH,"UK"
"
Thermo"Fisher"Scientific"Inc.,"PO"BOX"117,"Rockford,"IL"61105,"USA"
"
2.2!Plasmid!Purification!
"
2.2.1!Transformation!of!Competent!Cells!with!Plasmid!DNA!
The"transformation"of"competent"cells"with"a"plasmid"DNA"molecule"is"a"
technique"used"to"enable"the"plasmid"DNA"to"be"replicated"within"a"cell"
independently"of"the"replication"of"the"cell’s"own"chromosome."The"technique"
involves"the"addition"of"the"plasmid"DNA"to"the"competent"cells,"followed"by"the"
plating"of"these"cells"in"bacterial"broth"onto"agar"plates"containing"an"antibiotic"
that"the"plasmid"is"resistant"to."This"allows"for"the"growth"of"only"the"
transformed"cells,"those"that"the"plasmid"has"been"acquired,"on"the"agar"plates."
"
35. 23""
2.3!Cell!Culture!
"
2.3.1!Growth!and!Maintenance!of!HEK293`T!cells!
Human"Embryonic"Kidney"(HEK)"293XT"cells"were"cultured"in"Dulbecco’s"
Modified"Essential"Medium"(DMEM)"containing"stable"glutamine"with"sodium"
pyruvate,"supplemented"with"10%"(v/v)"foetal"bovine"serum"(FBS),"2%"
penicillinXstreptomycin,"and"50mg/ml"gentamicin."Cells"were"maintained"at"37˚C"
in"a"humidified"atmosphere"of"5%"CO2."For"use"in"transfection"assays,"HEK293XT"
cells"were"typically"seeded"at"1x105"cells/ml"24hr"prior"to"transfection."For"
continuing"cell"culture,"cells"were"seeded"at"5x105"cells/ml"and"subXcultured"two"
to"three"times"a"week."For"subXculture,"HEK293XT"cells"were"washed"in"5ml"of"
Dulbecco’s"Phosphate"Buffered"Saline"(PBS)"and"then"incubated"at"27˚C"bathed"
in"4ml"of"1x"Trypsin/"EDTA"(TE)"containing"0.05%"trypsin"and"0.02%"EDTA"for"
5mins."
"
2.3.2!Preparation!of!Instruments,!Culture!Medium,!and!Plates!
All"reagents"must"be"incubated"in"the"waterbath"at"37˚C"for"at"least"20mins."Turn"
on"and"clean"the"laminar"flow"hood"with"70%"ethanol"in"order"to"work"under"
sterile"conditions"at"all"times."Prepare"a"waste"beaker"filled"with"10X14%"sodium"
hypochlorite"solution."To"maintain"complete"sterility,"all"instruments"and"
solutions"going"into"hood"must"be"sprayed"with"ethanol."To"prepare"the"HEK293X
T"cell"culture"medium,"aliquot"50ml"of"the"neat"medium"into"a"sterile"50ml"falcon"
tube"and"label"as"serumXfree"DMEM."To"the"neat"bottle"of"medium,"add"50ml"of"
FBS,"10ml"of"penicillinXstreptomycin"mixture"and"500μl"of"gentamycin."
"
After"neutralising"the"HEK293XT"cell"culture"flask,"10ml"of"DMEM"was"added"and"
transferred"to"a"sterile"50ml"falcon"tube"and"centrifuged"at"1500"x"g"for"5mins"at"
room"temperature."The"supernatant"is"aspirated"and"the"pellet"is"washed"with"
2ml"of"DMEM,"depending"on"the"volume"of"the"pellet"(the"more"concentrated"the"
pellet,"the"more"DMEM"was"added)."
"
36. 24""
2.3.3!Cell!Counting!
Estimation"of"the"number"of"cells"present"in"the"cell"suspension"was"carried"out"
using"a"haemocytometer"to"ensure"a"specific"number"of"cells"were"used"in"each"
well"for"all"experiments."The"cell"pellet"was"resuspended"in"DMEM"and"a"10μl"
sample"was"added"to"a"10μl"of"dye"(trypan"blue)."The"dye"is"used"to"assess"the"
viability"of"the"cells,"as"it"is"expected"from"healthy"cells"but"is"takenXup"by"nonX
viable"cells."10μl"of"the"mix"was"then"added"to"the"chamber"of"the"
haemocytometer"with"the"number"of"cells"present"in"the"central"1mm2"grid"
representing"0.1μl"of"the"cell"suspension."The"number"of"cells/ml"was"calculated"
(cells/μl"x"dilution"factor"x"10,000)"and"from"this"the"required"volume"of"cell"
suspension"was"seeded"for"each"well"in"a"96Xwell"plate."Each"well"was"seeded"
with"200μl"of"cell"suspension."
"
2.3.4!Sub`culture!of!HEK293`T!cells!
From"the"cell"suspension,"1ml"of"the"cell"suspension"was"added"to"the"TX75"cell"
culture"flask"with"34ml"of"DMEM"and"then"incubated"at"37˚C."
"
2.3.5!Transient!Transfection!
When"cells"are"transiently"transfected"with"plasmids,"the"DNA"is"introduced"into"
the"nucleus"of"the"cell,"but"does"not"integrate"into"the"chromosome."This"means"
that"many"copies"of"the"gene"of"interest"are"present,"leading"to"high"levels"of"
expressed"protein.""
"
Metafectene®"is"a"liposomal"based"transfection"reagent"from"Biontex"and"was"
used"for"transfection"of"HEK293XT"cells."For"96Xwell"plate"transfections,"cells"
were"seeded"at"1x105"cells/ml"and"grown"overnight."Cells"were"transfected"in"
triplicates"per"transfection."The"volume,"per"plate,"was"brought"up"to"1050μl"
with"serumXfree"DMEM."86.1μl"Metafectene"was"mixed"with"963.9μl"serumXfree"
DMEM"per"transfection"of"plate"and"incubated"at"room"temperature"for"5mins."
30μl"of"this"mixture"was"added"to"triplicate"amounts"of"100ng"DNA"(1.75μl"of"
P125,"Renilla,"TRIF,"TRIM21,"and"EV"per"respective"well)"and"incubated"for"
15mins"at"room"temperature."DNA/"Metafectene/"serumXfree"DMEM"
39. 27
determined
using
20μl
of
cell
lysate
and
an
equivalent
amount
(20μl)
was
used
for
determination
of
Renilla
luciferase
activity.
Firefly
luciferase
activity
was
assayed
by
the
addition
of
40μl
of
luciferase
assay
mix
(20mM
tricine,
1.07mM
(MgCO3)4Mg(OH)2.5H2O,
2.6mM
MgSO4,
0.1mM
EDTA,
33.3mM
DTT,
270mM
coenzyme
A,
470mM
luciferin,
530mM
ATP)
to
the
sample
and
Renilla
luciferase
activity
was
assayed
by
the
addition
of
40μl
of
a
1:1000
dilution
of
Coelentrazine
in
PBS.
Luminescence
was
read
using
Wallac
luminometer.
Firefly
luminescence
readings
were
corrected
for
Renilla
activity
and
expressed
as
fold
stimulation
over
unstimulated
empty
vector
(EV)
control.
2.5
Bicinchoninic
Acid
(BCA)
Assay
The
BCA
assay
is
a
biochemical
assay
commonly
performed
to
determine
total
concentration
of
protein
in
a
solution.
It
relies
primarily
on
two
reactions,
as
shown
in
Figure
2.6.
Figure
2.6:
Schematic
diagram
of
the
reaction
for
the
bicinchoninic
acid-‐containing
protein
assay
(White,
2007).
The
concentration
of
the
protein
needed
for
the
thermal
melt
shift
assay
was
conducted
using
the
BCA
method.
