Mean Expression of the X Chromosome is Associated With Neuronal Density

7/25/2019 Mean Expression of the X Chromosome is Associated With Neuronal Density

1/21

Mean expression of the X chromosome is associated with neuronal

density

James T. Swingland1*, Pascal F. Durrenberger2, Richard Reynolds3, Daid T. De!"er#, $na

Pombo%, &anuel De're(), Federico Roncaroli#and Federico . Tur+heimer1

1Institute of Psychiatry, Kings College London, De Crespigny Park, London SE5 !"

#Centre for $euroscience, Di%ision of E&peri'ental (edicine, "aculty of (edicine, I'perial

College London, Cyclotron )uilding, Du Cane *d, +1# $$, -K.

/+olfson $euroscience La)oratories Di%ision of E&peri'ental (edicine, "aculty of (edicine,

I'perial College London, Du Cane *d, +1# $$, -K.

0Depart'ent of Cellular (olecular $euroscience, Di%ision of $euroscience (ental 2ealth,

I'perial College London Du Cane *d, +1# $$, -K.

5(*C Clinical Sciences Centre, I'perial College School of (edicine, 2a''ers'ith 2ospital

Ca'pus, London Du Cane *d, +1# $$, -K.

3La)oratory of $europathology, Depart'ent of Pathology, -ni%ersity 2ospital of Li4ge, elgiu'

6Corresponding author

$r"icle ord -oun" 2/21

0umber o igures 3

1


2/21

ABSTRACT

Background:0eurodegenera"ie diseases are charac"erised by neuronal loss. 0euronal loss causes

a arying densi"y o neurons across sam'les which conounds resul"s rom gene e!'ression s"udies.

-hromosome is +nown "o be s'eciically im'or"an" in brain. e hy'o"hesised "he e!is"ence o a

chromosomal signa"ure o gene e!'ression associa"ed wi"h "he chromosome or neurological

condi"ions no" normally associa"ed wi"h "ha" chromosome. The hy'o"hesis was ines"iga"ed using

microarray da"ase"s rom s"udies on Par+inson4s disease, $l(heimer4s disease and 5un"ing"on4s

disease. Da"a were analysed using Chro'o7a%e, an analy"ical "ool or de"ec"ing s'a"ially e!"ended

e!'ression changes across chromosomes. To e!amine associa"ions wi"h neuronal densi"y,

e!'ressions rom a se" o neuron s'eciic genes were e!"rac"ed. The associa"ion be"ween "hese genes

and "he e!'ression 'a""erns e!"rac"ed by Chro'o7a%ewas "hen analy(ed.

Results: e obsered an e!"ended 'a""ern o low e!'ression o -hr consis"en" in all "he

neurodegenera"ie disease brain da"ase"s. There was a s"rong correla"ion be"ween mean -hr

e!'ression and "he 'a""ern e!"rac"ed rom "he au"osomal neuronal s'eciic genes, bu" no correla"ion

wi"h mean au"osomal e!'ression. 0o chromosomal 'a""erns associa"ed wi"h "he neuron s'eciic

genes were ound on o"her chromosomes. The chromosomal e!'ression 'a""ern was no" 'resen" in

da"ase"s rom blood cells. The -hr$u"osome e!'ression ra"io was also higher in neuronal cells

"han in "issues wi"h a mi! o cell "y'es.

Conclusions: The resul"s sugges" "ha" a loss o neurons manies"s in gene e!'ression e!'erimen"s

'rimarily as a reduc"ion in mean e!'ression o genes along -hr. The mos" li+ely e!'lana"ion or

"his inding rela"es "o "he documen"ed general u'regula"ion o -hr in brain "issue which, "his

wor+ sugges"s, occurs 'rimarily in neurons. The 'ur'ose and mechanisms behind "his cell s'eciic

higher e!'ression warran" ur"her research, which may also hel' elucida"e connec"ions wi"h "he

deelo'men" o neurological disorders.

2


3/21

!"#$R%S

-hromowae, chromosome , dosage com'ensa"ion, waele"s, neuronal concen"ra"ion

&'TR$%(CT&$'

The chromosome 6-hr7 con"ains an abnormally large number o genes "ha" are essen"ial or

brain deelo'men" and unc"ion 68aumonnier e" al., 299/7. Seeral brain disorders are also

associa"ed wi"h mu"a"ions o genes on -hr 6:os"ra and illemsen, 2992; -hadwic+ and ade,

299/; rres'ec"ie o "he condi"ion, "he aec"ed brains wi"h degenera"ie show a

'rogressie and irreersible nere cell loss "ha" increases wi"h "he seeri"y o "he disease 6=ossers e"

al., 299B; Cme(>sla e" al., 1BB/; 5edreen and Fols"ein, 1BB%7. =rains wi"h neurodegenera"ie

diseases also show reac"ie as"rocy"osis and microglial ac"ia"ion. Such changes resul" in an al"ered

ra"io o neuronal and nonneuronal mR0$ and re'resen" an im'or"an" ariable in gene e!'ression

s"udies 6-lar+e e" al., 2919; :ldham e" al., 299E7. Cene e!'ression da"a is an im'or"an" resource or

3


4/21

ines"iga"ing diseases, howeer lis"s o dieren"ially e!'ressed genes o"en do li""le "o im'roe

unders"anding o disease mechanisms or o "he underlying biology. $''roaches which sim'liy "his

by loo+ing a" ne"wor+s 6&i"chell and &irnics, 29127 or o"her sys"ems leel analysis can 'roide a

more in"er're"able iew'oin" by in"er're"ing genes in 'a"hways 68angelder and 5ora"h, 299E;

&ar e" al., 29117. 5oweer such a''roaches ignore ano"her im'or"an" ac"or, "he role o s'a"ial

loca"ion 65urs" e" al., 299#; Tur+heimer e" al., 299)7. S'a"ial loca"ion can be im'or"an" in sys"ems

based on chroma"in modiica"ions 6$nderson e" al., 299E7. Chro'o7a%e6Tur+heimer e" al., 299);

$nderson e" al., 299E7, is an analy"ical "ool designed "o analy(e chromosomal 'a""erns o e!'ression

aria"ion rom adacen" genes "o include s'a"ial ac"ors in"o "he modelling 'rocess.

>n "he 'resen" s"udy, we used da"ase"s ob"ained rom "he brains o subec"s wi"h Par+insonGs

disease 6PD7 6&oran e" al., 299); Pa'a'e"ro'oulos e" al., 299); Durrenberger e" al., 29127,

$l(heimerGs disease 6$D7 6=laloc+ e" al., 299#7 and 5un"ing"onGs disease 65D7 65odges e" al.,

299)7 and age ma"ched con"rols "o "es" whe"her similar s'a"ial e!'ression 'a""erns occur in dieren"

neurological condi"ions. Fur"her i" was hy'o"hesised "ha" "he 'a""erns would mirror "he changes in

neurons and "ha" "he 'a""erns would arise s'eciically on -hr. &aor 'a""erns o e!'ression were

e!"rac"ed rom "he chromosome and au"osomes using Chro'o7a%e. These da"ase"s used a range

o dieren" microarray 'la"orms and 're'rocessing me"hods. Fur"her e!'ression da"ase"s rom

blood cells in PD and 5D were used as nega"ie con"rols. The case loadings rom "hese -hr

'a""erns were "hen com'ared wi"h "he 'rimary e!'ression 'a""ern rom a series o neuronal

reerence genes on "he au"osomes as a way "o iner "heir rela"ionshi' wi"h arying densi"ies o

neurons in "he sam'les. &ean ra"ios o -hr$u"osome e!'ression were ob"ained rom con"rol

subec"s and laser dissec"ed neurons 6Dunc+ley e" al., 299);


5/21

Microarray %ata

Da"a rom whole "issues were ob"ained rom online da"abases 6mos"ly C: e!ce'" or "he 5D

cauda"e sam'les rom $rray e!'ress7 rom dieren" diseases and 'la"orms. These da"ase"s are

summarised in "able 1, wi"h clinical de"ails aailable in "he original reerences. Da"a was also

ob"ained rom blood sam'les or PD and 5D. =lood sam'les were used "o de"ermine whe"her

indings were "issue s'eciic. These da"ase"s were ur"her su''lemen"ed by "wo 'ublicly aailable

da"ase"s o laser microsco'y dissec"ed neurons. :nly "he con"rol sam'les rom "hese da"ase"s were

used and only genes labeled 4'resen"4 were included. De"ails are aailable in "he original

'ublica"ions.

0euronal re'or"er genes were selec"ed by combining mar+ers used in immunohis"ochemis"ry

wi"h genes +nown "o be associa"ed wi"h neurons and addi"ional genes rom an an"ibody ca"alogue.

Cenes which were mos" s"able across da"ase"s were "hen selec"ed and used as re'or"er genes.

Ta,le -. %ata used

%isease region Reference Accession /latform Su,0ects

PD 8a"eral nigra &oran e" al., 299) CSE3B/ $yme"ri!

5CH133$ =

) con"rols,

13 PD

PD &edial nigra &oran e" al., 299) CSE3B/ $yme"ri!

5CH133$ =

% con"rols,

13 PD

PD Subs"an"ia

nigra

6Pa'a'e"ro'oulos e"

al., 299)7

CS/)21 $yme"ri!

5CH133 'lus 2

B con"rols,

1) PD

PD Subs"an"ia

nigra

Durrenberger e" al.,

2912

CS2)B2/ >llumina

humanReE 2.9

/ con"rols,

12 PD

5


6/21

$D 5i''ocam'us 6=laloc+ e" al., 299#7 CS12B/ $yme"ri!

5CH133$

E con"rols,

1E $D

5D -auda"e 5odges e" al. 299) $F&) $yme"ri!

5CH133$ =

11 con"rols,

1/ 5D

5D blood 5odges e" al. 299) CS1/%1 $yme"ri!5CH133$

12 con"rols,1# 5D

PD blood 6Scher(er e" al.,

299/7

CS))13 $yme"ri!

5CH133$

21 con"rols,

%9 PD

con"rols Subs"an"ia

nigra neurons

6nc., 0a"ic+, &$, HS$7. Chro'o7a%e irs" ma''ed "he

'robes rom "he da"ase"s "o "heir corres'onding chromosomal loca"ionand "hen a''lied "he waele"

"ransorm "o "heir s'a"ial dis"ribu"ion, coner"ing "he original e!'ression alues in"o waele"

coeicien"s. ach waele" coeicien" re'resen"s "he aerage alue o adacen" 'robes a" dieren"

6


7/21

leng"h scales 62#E1)K adacen" 'robes de'ending on "he scale7 in each s'eciic loca"ion on a

chromosome and can be mani'ula"ed using s"andard s"a"is"ical me"hodologies "o e!"rac" cohesie

s'a"ial 'a""erns in "he da"a 6Tur+heimer e" al., 299)7. The waele" "ransorm is widely used in many

ields, including gene analysis 68io, 29937 and here is 'rimarily used "o remoe noise rom "he

e!'ression da"a, leaing only "he s'a"ially coheren" com'onen" o "he e!'ression.

(nsuper2ised !xtraction of Chromosomal /rofiles

aele" coeicien"s can be analysed using s"andard s"a"is"ical "echniLues. >n "his s"udy,

Chro'o7a%ee!"rac"ed "he main 'a""ern o e!'ression o each indiidual chromosome across each

da"ase" irres'ec"ie o grou'ings 6unsu'erised analysis7 "o eriy a"erwards i"s si(e, e!"en" and

associa"ion wi"h ariables o in"eres". Hnsu'erised analysis in Chro'o7a%e is 'erormed using

singular alue decom'osi"ion 6SD7, a 'roen "echniLue or analysing noisy microarray da"a 6$l"er

e" al., 29997. SD allows "he iden"iica"ion and Luan"iica"ion 6in "erms o 'ercen"age o "o"al

ariabili"y7 o "he 'a""erns o aria"ion in "he da"a. SD also re"urns a 'arame"er called "he ?case

loading@ "ha" indica"es "he numerical e!'ression o "he 'a""ern or each subec". -ase loadings can

be used in a regression model "o eriy "he associa"ion o "he 'a""ern wi"h ariables o in"eres"

6neuronal loss, disease s"a"e, gender e"c7.

To denoise "he da"a, "he waele" coeicien"s ob"ained rom "he unsu'erised analysis are

au"oma"ically analysed and "hose inerred "o re'resen" noise 6by es"ima"ion o noise leels in "he

da"a7 are remoed 6Tur+heimer e" al., 299)7. The waele" s'ace re'resen"a"ion is "hen coner"ed

bac+ in"o real s'ace. This 'rocedure resul"s in smoo"h e!'ression 'roiles re'resen"ing "he s'a"ially

coheren" e!'ression changes along chromosomes associa"ed wi"h "he res'ec"ie case loadings.

Pa""erns "hus 'roduced are based on "he coheren" e!'ression o mul"i'le adacen" 'robes and are

undamen"ally dieren" rom "hose ob"ained using me"hods based on indiidual 'robes.

7


8/21

!xtraction of patterns of neuronal loss

Fi"your au"osomal genes were chosen "o re'resen" neurons 6su''lemen"ary "able 17. Cenes rom

"he -hr were a'riori e!cluded "o aoid biasing. The e!'ression o all "he 'robes re'resen"ing "hese

%# genes in each da"ase" were e!"rac"ed, logged and analysed using SD. This allowed or "he

e!"rac"ion o "he 'rimary e!'ression 'a""ern rom "hese genes, which is a more robus" me"hod "o

summarise "he da"a "han a sim'le aerage, "hough aerages were subseLuen"ly used "o eriy "he

direc"ion o associa"ion. The correla"ion coeicien"s be"ween "he 'rimary 'a""erns e!"rac"ed here

and "he case loadings ob"ained rom chromosomal e!'ression were "hen calcula"ed.

Statistical analysis

S"a"is"ical analysis was 'erormed in &$T8$= / 6The &a"hwor+s >nc., 0a"ic+, &$, HS$7, using

'arame"ric me"hods 6Pearson correla"ion coeicien"s, S"uden" ""es"s, bo"h 2"ailed7.

R!S()TS

)oss of X1expression is associated with neuronal loss

$ll da"ase"s rom whole "issue brain sam'les demons"ra"ed similar, near chromosome wide, 'a""erns

o -hr e!'ression 6see igure 17. Pa""erns were re'roducible des'i"e "he arie"y o 'la"orms,

'ro"ocols, and normalisa"ion me"hods used. $ll case loadings rom -hr correla"ed wi"h "he

'a""erns o e!'ression e!"rac"ed rom "he au"osomal genes re'resen"ing neuronal densi"y 6"able 27.

> emale subec"s were e!cluded, "he Par+inson4s disease brain "issue resul"s could be "a+en

as signiican"ly dieren" be"ween 'a"ien"s and con"rols 6p M 9.9#/, 9.9999#, 9.99/ and 9.992

8


9/21

res'ec"iely7. >n "he 5D cauda"e "he case loadings diered signiican"ly be"ween 'a"ien"s and

con"rols 6pM ) ! 19%7. 0ei"her male or emale case loadings diered signiican"ly in o"her da"ase"s.

Pa""erns and associa"ions were no" re'roduced in da"ase"s deried rom blood "issues 6see igure 27.

Table 2. -orrela"ion o whole "issue 'a""ern wi"h neuronal re'or"er genes

%isease Tissue region /latform Correlation

Par+inson4s 8a"eral nigra $yme"ri! 5CH133$ and = rM 9./,p M 9.91

Par+insons &edial nigra $yme"ri! 5CH133$ and = rM 9./2,pM 9.991

Par+insons Subs"an"ia nigra $yme"ri! 5CH133 'lus 2 rM 9.E,pM 3 ! 19)

Par+insons Subs"an"ia nigra >llumina 5umanReE 2 rM 9.E%,pM % ! 19)

$l(heimer4s 5i''ocam'us $yme"ri! 5CH133$ rM 9.)%,pM ) ! 19#

5un"ing"on4s -auda"e $yme"ri! 5CH133$ N = rM 9.B,pM 1 ! 1911

Par+inson4s =lood $yme"ri! 5CH133$ rM 9.92,pM 9.E

5un"ing"on4s =lood $yme"ri! 5CH133$ r M 9.2%, ' M 9.1

9


10/21

Figure 1.

10


11/21

Figure 2

!ffects of 'euronal loss in the autosomes

$''lying -hromowae "o "he au"osomes indica"ed associa"ion wi"h neuronal genes in "he

$l(heimer4s da"a, bu" was generally no" associa"ed wi"h "heir e!'ression 'a""ern 6see "able 37.

$''lying "he me"hod "o indiidual chromosomes did also rela"e some chromosomes which were

associa"ed wi"h "he e!'ression 'a""ern, bu" none were consis"en" in all brain "issue da"ase"s. Resul"s

such as "hese are li+ely "o re'resen" ei"her alse 'osi"ies or disease s'eciic indings, and as such

are ou"side "he sco'e o "his 'a'er. &ean alues or all non 'robes was no" associa"ed wi"h "he

neuronal re'or"er genes in any da"ase".

Table 3. -orrela"ion o au"osomal global 'a""ern wi"h neuronal re'or"er genes

%isease Tissue region /latform Correlation

Par+inson4s 8a"eral nigra $yme"ri! 5CH133$ and = r M 9.%,pM 9.9)

Par+insons &edial nigra $yme"ri! 5CH133$ and = rM 9.9%,pM 9.E

Par+insons Subs"an"ia nigra $yme"ri! 5CH133 'lus 2 rM 9.3,pM 9.1

11


12/21

Subs"an"ia nigra >llumina 5umanReE 2 r M 9.3,pM 9.2

$l(heimer4s 5i''ocam'us $yme"ri! 5CH133$ rM 9.#,pM 9.93

5un"ing"on4s -auda"e $yme"ri! 5CH133$ N = rM 9.93,pM 9.B

Statistical ro,ustness of association

To eriy "he Chro'o7a%eanalysis, "he resul"s o "he SD analysis on -hr were re'lica"ed by

calcula"ing "he aerages o "he normali(ed and log2 "ransormed in"ensi"y alues or "he 'robes on

"he chromosome and "hen 'lo""ed agains" "he neuronal e!'ression alues 'reiously calcula"ed.

This is illus"ra"ed in igure 3.

12


13/21

Figure 3

ChrX:Autosome ratio for laser micro1dissected neurons and whole tissue

To ines"iga"e whe"her neurons hae higher mean e!'ression o -hr "han o"her brain "issues,

'ublicly aailable neuronal da"a acLuired "hrough laser dissec"ion microsco'y was used. The

au"osome ra"io or each laser dissec"ed sam'le was com'ared wi"h "he ra"io or con"rol subec"s

or each whole "issue da"ase". The "wo se"s o dissec"ed neurons had higher mean au"osome ra"ios

"han "hose rom "he whole "issue sam'les. Thepalues or each com'arison is ound in "able #.

13


14/21

Table #. Dierence in $u"osome ra"io or laser dissec"ed neurons ersus whole "issues

'euron sample

location

Array type #hole tissue

location

Array type /12alue

Subs"an"ia nigra $yme"ri!

5CH133 'lus 2


5CH133 'lus 2

pM % ! 19%


5CH133 'lus 2

&edial subs"an"ia

nigra

$yme"ri!

5CH133$ and =

pM / ! 19%


5CH133 'lus 2

8a"eral subs"an"ia

nigra

$yme"ri!

5CH133$ and =

pM / ! 19%


5CH133 'lus 2

Subs"an"ia nigra >llumina

5umanReE 2

pM # ! 19%

Subs"an"ia nigra $yme"ri!5CH133 'lus 2

5i''ocam'us $yme"ri!5CH133$

pM 1 ! 19#


5CH133 'lus 2

-auda"e $yme"ri!

5CH133$ and =

pM ) ! 19%

n"orhinal cor"e! $yme"ri!

5CH133 'lus 2


5CH133 'lus 2

pM % ! 193


5CH133 'lus 2

&edial subs"an"ia

nigra

$yme"ri!

5CH133$ and =

pM # ! 193


5CH133 'lus 2

8a"eral subs"an"ia

nigra

$yme"ri!

5CH133$ and =

pM / ! 193


5CH133 'lus 2

Subs"an"ia nigra >llumina

5umanReE 2

pM 3 ! 19%


5CH133 'lus 2

5i''ocam'us $yme"ri!

5CH133$

pM ) ! 192


5CH133 'lus 2

-auda"e $yme"ri!

5CH133$ and =

pM % ! 19%

%&SC(SS&$'

:ur resul"s demons"ra"e "ha" a generali(ed reduc"ion o e!'ression o -hr, wi"h "he e!clusion o

"he ar "elomeric ' region associa"ed wi"h neurodegenera"ie disorders. Fur"her "he resul"s sugges"

14


15/21

"ha" "his re'resen"s "he maor eec" o neuronal loss in brains wi"h neurodegenera"ie disease. This

resul" has been re'roduced consis"en"ly in mul"i'le da"ase"s, diseases and across dieren" array

'la"orms, sam'ling 'ro"ocols and normalisa"ion me"hods. -hromosome s'eciici"y was s"ri+ing and

"he 'a""ern o e!'ression e!"ended "hrough "he whole o -hr wi"h "he e!ce'"ion o "he ar 'end.

The s'eciica"ion o "his loca"ion is necessarily ague bo"h due "o aria"ions be"ween da"ase"s and

because Chro'o7a%e resul"s are based on denoised s'a"ial e!'ression 'a""erns ra"her "han

indiidual genes.

>n"eres"ingly, "he 'a""ern ob"ained is similar "o "he 'a""ern re'or"ed in -hrinac"ia"ion.

inac"ia"ion is an e'igene"ic een" in mammalian emales "ha" resul"s in "he "ranscri'"ional silencing

o one chromosome. >n inac"ia"ion no" all lin+ed genes are re'ressed and, in humans, "he

'ro'or"ion o genes on "he chromosome "ha" esca'es inac"ia"ion is more "han 1%O, mos"ly

loca"ed on "he 'end 6=rown and Creally, 29937.

The mos" 'lausible e!'lana"ion or "he demons"ra"ed 'a""ern o low e!'ression is "ha"

neurons e!'ress "he genes on -hr a" a higher leel "han nonneuronal cells. >ndeed since i" is

+nown "ha" "he -hr is s'eciically more "ranscribed in "he brain "han o"her "issues 60guyen and

Dis"eche, 299)b7 "hese resul"s sugges"s i" occurs 'rimarily in neurons. 5igher $u"osomal ra"ios in

"he laser dissec"ed neurons su''or" "his e!'lana"ion. The diuse and near chromosome wide na"ure

o "he changes obsered sugges"s "ha" an e'igene"ic mechanism may underlie "his higher e!'ression.

Fur"her our indings seem "o su''or" "he sugges"ion "ha" u'regula"ion in brain 6or s'eciically in

neurons7 is lin+ed "o dosage con"rol mechanisms 6Aharchen+o e" al., 2911; Deng e" al., 2911;

0guyen and Dis"eche, 299)a, 299)b7 as "he dis"ribu"ion ma"ches "he dis"ribu"ion o genes esca'ing

inac"ia"ion 6=rown and Creally, 29937. Hnders"anding "he reasons or high e!'ression in

neurons reLuires ur"her research. 5oweer, chromosome dosage has been lin+ed "o "he immune

sys"em and "o au"oimmune disorders 68iber" e" al., 2919; Syryd e" al., 29127sugges" a 'o"en"ial

'ro"ec"ie role or "he higher e!'ression. Fur"her, "his may be rela"ed "o "he deelo'men" o

15


16/21

neurological condi"ions gien "he sugges" role o neuroinlamma"ion in neuronal loss 6Fang e" al.,

2912; &edeiros e" al., 2912; Saing e" al., 29127. >n any case, generally higher e!'ression im'lies

"ha" "ha" "he resul"s or indiidual genes on may be biased by "he eec"s o changing numbers o

neurons and so 'rac"ically, "his is li+ely "o aec" microarray resul"s on chr.

>n "he 5D brain da"ase" "he resul"s could be "a+en as a signiican" dierence be"ween

'a"ien"s and con"rols. Similarly in "he arious PD da"ase"s "he resul"s could be in"er're"ed as

signiican" dierences or male 6bu" no" emale7 subec"s and con"rols. Par"ly "his resul" is ham'ered

by "he smaller number o emale subec"s in "hese da"ase"s. 5oweer, "his also i"s wi"h "he inding

"ha" emale PD subec"s show a more benign 'heno"y'e wi"h milder s"ria"al degenera"ion 65aa!ma

e" al., 299/7 and "hereore less neuronal loss. These resul"s show "ha" i" is im'or"an" "o be careul

when in"er're"ing da"a rom whole "issue and "his reduc"ion is li+ely "o bias indiidual gene

e!'ression resul"s.

Sam'les used in "his ines"iga"ion came rom a range o diseases, "hough more were "a+en

rom PD "han o"her neurological condi"ions. Since resul"s were similar in all da"ase"s, PD and non

PD i" is unli+ely "ha" "his has added any meaningul bias "o "he analysis. $ddi"ionally al"hough "here

are clear similari"ies be"ween "he 'roiles ob"ained rom "hese dieren" condi"ions "he analysis does

no" rule ou" disease s'eciic changes occurring on -hr and in "he au"osomes. 5oweer any disease

s'eciic resul"s are ou"side "he sco'e o "his 'a'er and none were re'lica"ed in all PD da"ase"s.

>n order "o "es" whe"her "he use o Chro'o7a%eand waele"s in"roduced any dis"or"ions or

biases, "he resul"s were re'lica"ed using sim'le aerages on "he log"ransormed e!'ression alues

o "he lin+ed 'robes. >" is wor"h no"ing "ha" since Chro'o7a%eresul"s are made u' o many

hundreds o 'robes. >ndiidually "hese 'robes hae only wea+ 6mos"ly nonsigniican"7 associa"ions

wi"h "he neuronal densi"y and so s"andard single genes a''roaches are unli+ely "o re'lica"e "hese

indings. Ta+ing "he aerage o many 'robes does re'roduce "he associa"ion, howeer i" does no"

'roide "he 'a""ern -hromowae 'roided, and is no" da"a drien, reLuiring a hy'o"hesis abou"

16


17/21

chromosome wide e!'ression changes. This hel's "o demons"ra"e "he useulness o "he

Chro'o7a%ea''roach.

>n conclusion, we obsered "ha" aria"ion in "he densi"y o neurons in e!'ression s"udies is

associa"ed wi"h a reduc"ion in "he -hr e!'ression and "ha" "his a''ears inde'enden" o disease and

gender. This resul" li+ely relec"s high e!'ression in neurons, su''or"ed by "he higher

au"osome ra"io ound in microdissec"ed "issue. >ndiidual gene e!'ression on -hr will be biased

by "his eec" and Chro'o7a%ecan "hereore be a''lied "o e!'ression microarray s"udies "o iden"iy

"his lowleel, largescale eec" and hel' correc" "he resul"s rom indiidual 'robes. The 'a""ern o

high e!'ression in neurons more in"eres"ingly sugges"s a s"rong lin+ be"ween "he mechanism

behind dosage com'ensa"ion, -hr u'regula"ion in brain and "he deelo'men" and unc"ion o

neuronal cells. >" is also "o our +nowledge "he only "ime "ha" a s'eciic cell "y'e has been lin+ed "o

s'a"ially coheren" "ranscri'"ion.

)&ST $3 ABBR!4&AT&$'S

$D $l(heimer4s disease

-hr -hromosome

5D 5un"ing"on4s disease

PD Par+inson4s disease

SD Singular alue Decom'osi"ion

C$'3)&CT $3 &'T!R!STS

0one declared.

17


18/21

A(T+$RS C$'TR&B(T&$'S

JTS dra"ed manuscri'" and 'erormed "he analysis. PFD collec"ed da"a, hel'ed 'erorm analysis,

discussed indings and hel'ed dra" "he manuscri'". RR 5el'ed wi"h da"a collec"ion and dra"ing o

manuscri'". DTD hel'ed wi"h da"a collec"ion and dra"ing o "he manuscri'". $P hel'ed in"er're" "he

da"a and dra" "he manuscri'". &D discussed in"er're"a"ion and hel'ed dra" manuscri'". FR

collec"ed da"a, discussed indings and hel'ed dra" manuscri'". FT hel'ed wi"h da"a analysis,

designed s"udy, discussed indings and in"er're"a"ion and hel'ed dra" manuscri'".

R!3!R!'C!S

$l"er, :., =rown, P. :., and =o"s"ein, D. 629997. Singular alue decom'osi"ion or genomewide

e!'ression da"a 'rocessing and modeling.Proc $atl !cad Sci - S !B/, 19191).

$nderson, $. 0., Roncaroli, F., 5odges, $., De're(, &., and Tur+heimer, F. . 6299E7.

-hromosomal 'roiles o gene e!'ression in 5un"ing"onGs disease.rain131, 3E13EE.

=laloc+, . &., Ceddes, J. ., -hen, A. -., Por"er, 0. &., &ar+esbery, . R., and 8andield, P. .

6299#7. >nci'ien" $l(heimerGs disease microarray correla"ion analyses reeal maor

"ranscri'"ional and "umor su''ressor res'onses.Proc. $atl. !cad. Sci. -.S.!191, 21/321/E.

=ossers, A., &eerho, C., =alesar, R., an Dongen, J. ., Aruse, -. C., Swaab, D. F., and

erhaagen, J. 6299B7. $nalysis o gene e!'ression in Par+insonGs disease 'ossible

inolemen" o neuro"ro'hic su''or" and a!on guidance in do'aminergic cell dea"h.rain

Pathol1B, B119/.

=rown, -. J., and Creally, J. &. 629937. $ s"ain u'on "he silence genes esca'ing inac"ia"ion.

8rends 9enet1B, #32#3E.

-hadwic+, 8. 5., and ade, P. $. 6299/7. &e-P2 in Re"" syndrome "ranscri'"ional re'ressor orchroma"in archi"ec"ural 'ro"einQ Curr. :pin. 9enet. De%1/, 12112%.

-lar+e, J., Seo, P., and -lar+e, =. 629197. S"a"is"ical e!'ression deconolu"ion rom mi!ed "issue

sam'les.ioinfor'atics2), 19#319#B.

Deng, ., 5ia"", J. =., 0guyen, D. A., rcan, S., S"urgill, D., 5illier, 8. ., Schlesinger, F., Dais,

-. $., Rein+e, . J., Cingeras, T. R., e" al. 629117. idence or com'ensa"ory u'regula"ion

o e!'ressed lin+ed genes in mammals, -aenorhabdi"is elegans and Droso'hila

melanogas"er.$at 9enet#3, 11/B11E%.

Dunc+ley, T., =each, T. C., Ramsey, A. ., Croer, $., &as"roeni, D., al+er, D. C., 8aFleur, =. J.,

-oon, A. D., =rown, A. &., -aselli, R., e" al. 6299)7. Cene e!'ression correla"es o

18


19/21

neuroibrillary "angles in $l(heimerGs disease.$euro)iol. !ging2/, 13%B13/1.

Durrenberger, P. F., Crnbla"", ., Fernando, F. S., &onoranu, -. &., ans, J., Riederer, P.,

Reynolds, R., and De!"er, D. T. 629127. >nlamma"ory Pa"hways in Par+insonGs Disease; $

=0 &icroarray S"udy.Parkinsons Disease2912, 11).

Fang, F., irdeeld", A., Jac+s, $., Aamel, F., e, ., and -hen, 5. 629127. -0S inec"ions, se'sisand ris+ o Par+insonGs disease.International ;ournal of epide'iology. $ailable a"

h""'www.ncbi.nlm.nih.go'ubmed22%23291 U$ccessed &ay 2B, 2912V.

Cme(>sla, T., 5ollis"er, R., es", 5., &ui, S., Crowdon, J. 5., Pe"ersen, R. -., Parisi, J. ., and

5yman, =. T. 61BB/7. 0euronal loss correla"es wi"h bu" e!ceeds neuroibrillary "angles in

$l(heimerGs disease.!nn. $eurol#1, 1/2#.

5aa!ma, -. $., =loem, =. R., =orm, C. F., :yen, . J., 8eenders, A. 8., shuis, S., =ooi, J.,

Dlu(en, D. ., and 5ors"in+, &. . 6299/7. Cender dierences in Par+insonGs disease.

den"iies $l"ered

0e"wor+ -ons"rain"s in 0eurological Disease.PLoS 9enet/, e199229/.

&edeiros, R., -habrier, &. $., and 8aerla, F. &. 629127. lucida"ing "he Triggers, Progression, and

ec"s o $l(heimerGs Disease.


20/21

ic"ion.$euro)iology of Disease#%, 3/.

&oran, 8. =., Du+e, D. -., De're(, &., De!"er, D. T., Pearce, R. A. =., and Craeber, &. =. 6299)7.

hole genome e!'ression 'roiling o "he medial and la"eral subs"an"ia nigra in Par+insonGs

disease.$eurogenetics/, 111.

0guyen, D. A., and Dis"eche, -. &. 6299)a7. Dosage com'ensa"ion o "he ac"ie chromosome inmammals.$at. 9enet3E, #/%3.

0guyen, D. A., and Dis"eche, -. &. 6299)b7. 5igh e!'ression o "he mammalian chromosome in

brain.rain *es112), #)#B.

:ldham, &. -., Aono'+a, C., >wamo"o, A., 8angelder, P., Aa"o, T., 5ora"h, S., and Ceschwind,

D. 5. 6299E7. Func"ional organi(a"ion o "he "ranscri'"ome in human brain.$at. $eurosci

11, 12/112E2.

:os"ra, =. $., and illemsen, R. 629927. The chromosome and ragile men"al re"arda"ion.

Cytogenet. 9eno'e *esBB, 2%/2)#.

Pa'a'e"ro'oulos, S., French&ullen, J., &c-orLuodale, D., Xin, ., Pablo, J., and &ash, D. -.

6299)7. &ul"iregional gene e!'ression 'roiling iden"iies &RPS) as a 'ossible candida"e

gene or Par+insonGs disease. 9ene E&pr13, 29%21%.

Saing, T., Dic+, &., 0elson, P. T., Aim, R. -., -ribbs, D. 5., and 5ead, . 629127. Fron"al cor"e!

neuro'a"hology in demen"ia 'ugilis"ica.


21/21

8C0DS

3igure -: Primary e!'ression 'a""ern rom -hr e!'ression ia Chro'o7a%erom all brain sam'les. $ll

'a""erns shown are signiican"ly associa"ed wi"h "he concen"ra"ion o neurons e!"rac"ed. 0ega"ie

alues indica"e down regula"ion o -hromosome associa"ed wi"h reduced neuronal e!'ression,

'osi"ie alues indica"ed increased e!'ression. The 'a""erns demons"ra"e reduced e!'ression

oer "he maori"y o -hr wi"h "he e!ce'"ion o "he 'end.

3igure 5: Primary e!'ression 'a""ern rom $D blood 6le"7 and 5D blood 6righ"7 da"ase"s. Proiles were no"

associa"ed wi"h neuronal re'or"er and are isually dieren" rom each o"her and "hose ob"ained

rom brain "issue.

3igure 6: Sca""er diagrams o "he Chro'o7a%ecaseloadings 'lo""ed ersus "he e!'ression o neuronal

reerence genes or all "he brain da"ase"s used.

21

Mean Expression of the X Chromosome is Associated With Neuronal Density

Documents

Transcript of Mean Expression of the X Chromosome is Associated With Neuronal Density