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Molecular and Metabolic Subtypes Correspondence for Pancreatic Ductal Adenocarcinoma Classification

Abstract

Pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, is an extremely lethal disease due to late diagnosis, aggressiveness and lack of effective therapies. Considering its intrinsic heterogeneity, patient stratification models based on transcriptomic and genomic signatures, with partially overlapping subgroups, have been established. Besides molecular alterations, PDAC tumours show a strong desmoplastic response, resulting in profound metabolic reprogramming involving increased glucose and amino acid consumption, as well as lipid scavenging and biosynthesis. Interestingly, recent works have also revealed the existence of metabolic subtypes with differential prognosis within PDAC, which correlated to defined molecular subclasses in patients: lipogenic subtype correlated with a classical/progenitor signature, while glycolytic tumours associated with the highly aggressive basal/squamous profile. Bioinformatic analyses have demonstrated that the representative genes of each metabolic subtype are up-regulated in PDAC samples and predict patient survival. This suggests a relationship between the genetic signature, metabolic profile, and aggressiveness of the tumour. Considering all this, defining metabolic subtypes represents a clear opportunity for patient stratification considering tumour functional behaviour independently of their mutational background. Espiau-Romera, P.; Courtois, S.; Parejo-Alonso, B.; Sancho, P.

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Molecular and Metabolic Subtypes Correspondence for Pancreatic Ductal Adenocarcinoma Classification

Author: Espiau-Romera, P.; Parejo-Alonso, B.; Courtois, S.; Sancho, P.
Year: 2020
DOI: 10.3390/jcm9124128
Source: https://zaguan.unizar.es/record/99228/files/texto_completo.pdf
Jou nal o
Clinical Medicine
Re iew
Molecula and Me abolic Sub ypes Co espondence
o Panc ea ic Duc al Adenoca cinoma Classi ica ion
Pila Espiau-Rome a , Sa ah Cou ois, Bea iz Pa ejo-Alonso and Pa icia Sancho *
T ansla ional Resea ch Uni , Hospi al Uni e si a io Miguel Se e , IIS A agon, 50009 Za agoza, Spain;
[email p o ec ed] (P.E.-R.); [email p o ec ed] (S.C.); [email p o ec ed] (B.P.-A.)
*Co espondence: [email p o ec ed]
Recei ed: 14 Oc obe 2020; Accep ed: 17 Decembe 2020; Published: 21 Decembe 2020


Abs ac :
Panc ea ic duc al adenoca cinoma (PDAC), he mos common o m o panc ea ic cance ,
is an ex emely le hal disease due o la e diagnosis, agg essi eness and lack o e ec i e he apies.
Conside ing i s in insic he e ogenei y, pa ien s a i ica ion models based on ansc ip omic and genomic
signa u es, wi h pa ially o e lapping subg oups, ha e been es ablished. Besides molecula al e a ions,
PDAC umou s show a s ong desmoplas ic esponse, esul ing in p o ound me abolic ep og amming
in ol ing inc eased glucose and amino acid consump ion, as well as lipid sca enging and biosyn hesis.
In e es ingly, ecen wo ks ha e also e ealed he exis ence o me abolic sub ypes wi h di e en ial
p ognosis wi hin PDAC, which co ela ed o de ined molecula subclasses in pa ien s: lipogenic sub ype
co ela ed wi h a classical/p ogeni o signa u e, while glycoly ic umou s associa ed wi h he highly
agg essi e basal/squamous p o ile. Bioin o ma ic analyses ha e demons a ed ha he ep esen a i e
genes o each me abolic sub ype a e up- egula ed in PDAC samples and p edic pa ien su i al.
This sugges s a ela ionship be ween he gene ic signa u e, me abolic p o ile, and agg essi eness o he
umou . Conside ing all his, de ining me abolic sub ypes ep esen s a clea oppo uni y o pa ien
s a i ica ion conside ing umou unc ional beha iou independen ly o hei mu a ional backg ound.
Keywo ds: PDAC; panc ea ic cance ; glycolysis; lipid me abolism; classi ica ion; s a i ica ion
1. In oduc ion
Panc ea ic duc al adenoca cinoma (PDAC) is conside ed one o he mos agg essi e solid
malignancies. I ep esen s he hi d cause o cance - ela ed dea hs in indus ialised coun ies oday [
1
]
and i is p edic ed o become he second by 2030 [
2
]. Despi e p og ess in he unde s anding o he
molecula and gene ic basis o his disease, i e-yea su i al a es ha e emained below 10% a e
diagnosis and one-yea su i al occu s in only 28% o cases [3].
The easons o he poo p ognosis o his disease include bad accessibili y o he o gan, absence o
dis inc symp omsandhigh a eo me as asis, occu inginabou 50%o pa ien s[
4
].
On he o he hand,
he e a e no eliable bioma ke s app o ed o ea ly diagnosis [5].
Cu en ly, he only a ailable cu a i e op ion o PDAC pa ien s is su gical esec ion ollowed by
adju an chemo he apy [
4
]. Howe e , his occu s in a mino i y o pa ien s, since 80–90% o hem a e
diagnosed wi h ad anced disease when he umou is no esec able [
6
,
7
]. In addi ion, he he e ogenei y
andplas ici yo PDAC umou slead ochemo esis ance[
8
]. In ac , se e alphaseIII ials o chemo he apy
agen s o a ge ed he apies e ec i e in o he malignancies ha e ailed o bene i unselec ed PDAC
popula ions. In addi ion, wi h he excep ion o he a e subse o misma ch epai -de icien umou s,
checkpoin inhibi o s ha e ailed o show e icacy in me as a ic pa ien s.
Unde such ci cums ances, he solu ion possibly lies in ea ly de ec ion and p ope classi ica ion
o pa ien s [
4
]. Pa ien s a i ica ion has become an in aluable ool o he clinical managemen o
cance pa ien s, p o iding diagnos ic and p ognos ic in o ma ion and, c ucially, guiding he apeu ic
J. Clin. Med. 2020,9, 4128; doi:10.3390/jcm9124128 www.mdpi.com/jou nal/jcm
J. Clin. Med. 2020,9, 4128 2 o 21
decisions, especially when a ge ed he apies o a speci ic mu a ion o subg oup a e a ailable.
In ac , s a i ica ion had a key ole imp o ing su i al a es in diseases such as b eas cance .
Howe e , pa ien s a i ica ion based on his omo phological o molecula ea u es in PDAC has p o ed
challenging, se e ely delaying he iden i ica ion o such a ge ed he apies. This, oge he wi h he
und uggable na u e o mu a ed K-RAS (al hough clinical ials a e unde way o inhibi he mu a ion
K-RAS
G12C
), limi s PDAC ea men o ine ec i e con en ional chemo he apy. Genomic s udies ha e
e ealed sub ypes o PDAC based on hei molecula ea u es, bu di e se s udies ha e epo ed
di e en classi ica ion sys ems incomple ely o e lapping. In e es ingly, inc easing e o s a e being
made in di e en di ec ions. In ac , ecen da a sugges ha PDAC umou s could also be classi ied
a ending o hei me abolic pheno ype.
In his e iew, we desc ibe and analyse he co espondence o mos o he published molecula
and me abolic signa u es o PDAC and p opose a modi ied me abolic signa u e ha could s a i y
pa ien s acco ding o me abolic needs independen ly o he mu a ional load.
2. PDAC Mu a ional P o ile
Many s udies ha e been conduc ed on PDAC samples o de e mine molecula abe a ions a DNA,
RNA, p o ein and epigene ic le els [
9
]. In gene al e ms, mu a ions in indi idual genes comp ise 10 main
pa hways: DNA damage epai (TP53 o BRCA2), cell cycle egula ion (Cyclin-Dependen Kinase
Inhibi o 2A,CDKN2A),T ans o mingg ow h ac o -be a(TGF-
β
)pa hway (SMAD4), NOTCHandWNT
signalling, ch oma in egula ion, Ex acellula Signalling Regula ed Kinases (ERK)-Mi ogen-Ac i a ed
P o ein Kinases (MAPK) signalling (K-RAS,B-RAF), axonal guidance and RNA p ocessing [10,11].
Al oge he , K-RAS gain o unc ion, accoun ing o up o 90% o PDAC cases, and inac i a ion
o he umou supp esso genes p16/CDKN2A,SMAD4 and TP53 con ibu e o PDAC o ma ion,
main enance, p og ession and, ul ima ely, me as asis onse . Occasionally, he mu a ions occu in o he
componen s o he pa hway in which hey a e in ol ed [
9
,
12
,
13
]. In addi ion, genome-wide and
exome-wide analyses ha e iden i ied a long lis o less equen al e a ions in genes ela ed o axon
o ien a ion o DNA damage epai , such as BRCA1 o BRCA2 [
12
,
14
,
15
]. Mo eo e , mos PDACs show
complex pa e ns o ch omosomal ea angemen [16,17].
Some indings ha e sugges ed a linea pa hway o e olu ion om no mal cells o PDAC cells,
in which no all mu a ions occu a he same ime. Telome e sho ening is conside ed he igge o
panc ea ic umo igenesis by inducing gene ic ins abili y, coupled wi h a mu a ion in he K-RAS gene.
Su i ing cells a e hen al e ed by loss o CDKN2A unc ion. In hi d place, he umou supp esso genes
TP53 and SMAD4 a e inac i a ed, leading o in e media e s ages called panc ea ic in aduc al neoplasias
(PanINs) and, ul ima ely, ull-blown PDAC [
10
,
18
]. Howe e , i seems ha in some cases, CDKN2A,
TP53 and SMAD4 mu a ions can occu in a single e en , which is called “punc ua ed equilib ium” [
11
].
2.1. K-RAS
K-RAS is one o he h ee mu a ionally ac i a ed o ms o he Ras p o ein, oge he wi h H-RAS
and N-RAS. I is he mos ep esen ed one among all cance s bea ing RAS mu a ions, and he one
exclusi ely mu a ed in PDAC. Mo eo e , i is known o be he main d i e mu a ion o his disease,
since K-RAS is mu a ed in >90% o he cases, hus making PDAC he mos RAS-addic ed o all cance
ypes [19]. Howe e , K-RAS ac i a ion alone is no su icien o PDAC de elopmen [20,21].
Ras p o eins a e small GTPases ha ac as signalling swi ches egula ing cell p oli e a ion, su i al,
di e en ia ion and in lamma ion, by ac i a ing he MAPK module. In a no mal scena io, Ras is ound
in i s inac i e o m coupled o guanosine diphospha e (GDP) and, upon ac i a ion by di e se
ex acellula s imuli, Ras becomes ac i e by coupling guanosine iphospha e (GTP), hus swi ching on
downs eam e ec o s such as ERKs, Jun Amino-Te minal Kinases (JNKs), S ess-Ac i a ed P o ein
Kinases (p38/SAPKs) and PI3K/PDK1/AKT, amongs o he s [
22
,
23
]. In PDAC and o he cance s bea ing
oncogenic K-RAS mu a ions, his p o ein is cons i u i ely ac i e in a GTP-bound s a e. PDAC-associa ed
K-RAS al e a ions mainly ha bou missense mu a ions ha depend on allele dosage o umo igenesis
J. Clin. Med. 2020,9, 4128 3 o 21
and me as asis onse , and con ibu e o PDAC e olu ion om PanINs o inal cance o ma ion wi h
he loss o o he key PDAC-d i ing playe s [24].
2.2. p16/CDKN2A
Along he e olu iona y cou se o PDAC onse , K-RAS mu a ion is ollowed by he occu ence o
gene ic al e a ions in he umou supp esso gene CDKN2A in 95% o PDAC pa ien s [
24
]. Tumou
supp esso genes a e impo an o es ain abe an cell p oli e a ion in he con ex o oncogenic
signalling and, o ha end, hese genes ely on di e en s a egies such as cell cycle a es , apop osis o
senescence induc ion. Speci ically, he gene CDKN2A, encoding o P16INK4a and P14RF p o eins,
shows a dual mechanism: P16INK4a inhibi s Cyclin Dependen Kinases (CDK) 2 and 4, hus p e en ing
cell cycle o p og ess in o S-phase, while P14RF igge s P53 by inhibi ing i s inhibi o , Mouse double
minu e 2 homolog (MDM2), he eby inducing g ow h a es and apop osis [25].
2.3. TP53
P53, he p o ein encoded by heTP53 gene, isknown obe he“genome gua dian”due oi sessen ial
ole upon ch oma in damage. Amongs i s main unc ions, we ind cell cycle blockade and ac i a ion
o DNA epai enzymes. Ul ima ely, P53 may lead he cell o a senescence s a e and/o apop osis
when DNA damage is no longe epa able. Gene ic inac i a ion o TP53 is p esen in up o 75% o
all PDAC cases and appea in ad anced PanINs a e loss o CDKN2A. Loss o unc ional P53 leads
o an uncon olled s a e o p oli e a ion [
25
]. Impo an ly, mu an P53 may con ibu e o me as a ic
p og ession o K-RAS-d i ing PDAC-bea ing mice, highligh ing a no el ole o his ansc ip ion ac o
in la e s ages o PDAC beyond he malignan ans o ma ion o PanINs in o PDAC [26,27].
2.4. SMAD4
SMAD4 se es as he cen al media o o TGF-
β
pa hway and i is known o be he ou h
and, oge he wi h TP53, ul ima e d i e o PDAC ini ia ion [
28
]. Howe e , he ole o SMAD4
in he pa hogenesis o PDAC is complex and i s inal esul s a e con ex -dependen . On he one
hand, he TGF-
β
pa hway is a well-accep ed epi helial- o-mesenchymal ansi ion (EMT) induce [
29
],
and also in PDAC [
25
], hus highligh ing i s p o- umo igenic po en ial. Con e sely, Smad4 signalling
in he KPC (LSL-K asG12D/+;LSL-T p53R172H/+;Pdx-1-C e) mouse PDAC model media es a umou
supp essi e p ocess known as “le hal EMT”. In his scena io, Smad4 igge s apop osis h ough
ep ession o he gas oin es inal lineage-mas e egula o Kl 5 and, consequen ly, inhibi s PDAC
p og ession induced by Kl 5/Sox4. Consequen ly, he loss o SMAD4 umou supp essi e unc ion
may con ibu e o panc ea ic oncogenesis h ough he TFG-βcanonical pa hway [30].
3. PDAC Molecula Signa u es
Besides pu ely mu a ional analyses, a conside able numbe o genomic and ansc ip omic s udies
in pa ien samples ha e iden i ied he exis ence o PDAC sub ypes wi h p ognos ic and biological
ele ance, as de ailed below.
Collisson e al. [
31
] epo ed he i s exhaus i e ansc ip omic analysis on clinical samples,
and based hei classi ica ion on gene exp ession and molecula p o iling. PDAC issues we e classi ied
in o “classical”, “quasi-mesenchymal” and “exoc ine-like” (Table 1), wi h di e en p ognoses and
esponses o selec ed he apies. The classical sub ype showed high exp ession o epi helial and
adhesion-associa ed genes, such as he ansc ip ion ac o GATA6, and a ou able p ognosis ega ding
su i al a e PDAC esec ion. On he o he hand, he quasi-mesenchymal sub ype exhibi ed high
exp ession o mesenchymal-associa ed genes, was ela i ely less dependen on K-RAS han he classical
one, and, impo an ly, was associa ed wi h poo p ognosis. Finally, he exoc ine-like sub ype e ealed
high exp ession o diges i e exoc ine enzyme genes. Howe e , he las sub ype was no ound in
cance cell lines, aising conce ns abou i s speci ici y [32].
J. Clin. Med. 2020,9, 4128 4 o 21
Table 1. Molecula Panc ea ic Duc al Adenoca cinoma (PDAC) signa u es.
Au ho Type o S udy Type and Numbe o
PDAC Samples
Dys egula ed Pa hways
and Mu a ions Ou come
Collison e al. [31] T ansc ip ional
1. Clinical samples
mic oa ay da ase s
Mic odissec ed (n=27)
GSE15471 (n=36)
GSE11838 (n=107)
GSE16515 (n=52)
E-MEXP-950 (n=50)
2. Valida ion:
Mouse cell lines (n=15)
Human cell lines (n=19)
Classical: (↑) Adhesion-
associa ed genes (GATA6).
Mo e K-RAS-dependen
Good
Quasi-mesenchymal: (↑)
Mesenchymal associa ed genes Bad
Exoc ine: (↑) Diges i e exoc ine
enzyme genes
Mo i e al. [33] T ansc ip ional
1. Mic oa ay da a
P ima y umou (n=145)
Me as a ic umou (n=61)
Cell lines (n=17)
Panc eas no mal samples (n=46)
Dis an si e adjacen samples (n=88)
2. Valida ion
P ima y umou s (n =15)
PDXs (n=37)
Cell lines (n=3)
CAF lines (n=6)
Classical: Classical Collison ((↑)
adhesion-associa ed genes (GATA6))
and SMAD4
Good
Basal: (
↑
) Genes also highly exp essed
in basal umou s in bladde and
b eas cance
Bad
No mal s oma: (
↑
) Panc ea ic s ella e
cells, smoo h muscle ac in, imen in
and desmin ma ke s
Good
Ac i a ed s oma: (↑) Mac ophages,
umou p omo ion and ib oblas
ac i a ion-associa ed genes
Bad
Bailey e al. [10]Mu a ional
T ansc ip ional
P ima y PDAC umou samples and
a e acina cell ca cinoma (n=382)
PDAC exomes (n=74)
Squamous: Hype me hyla ion and (
↓
)
panc ea ic endode mal cell a e genes.
TP53,KDM6A and TP63∆N
Bad
Panc ea ic p ogeni o : (↑) Panc ea ic
ea ly de elopmen genes (PDX1)Good
ADEX: (↑) K-RAS ac i a ion and
panc ea ic la e de elopmen and
di e en ia ion genes
Immunogenic: (↑) Immune
supp ession and s ong
immune in il a ion
Zhao e al. [34]T ansc ip ional
(me analysis)
1. Mic oa ay da ase s o PDAC
p ima y umou samples (n=1268)
TCGA (n=172)
GSE79670 (n=51)
TCGC PACA-AU (n=71)
MTAB-1791 (n=195)
ICGC a ay (n=178)
GSE71729 (n=145)
GSE62165 (n=118)
GSE62452 (n=69)
GSE57495 (n=63)
GSE60980 (n=49)
GSE77858 (n=46)
GSE55643 (n=45)
GSE15471 (n=39)
L1: (↑) Me abolic genes
L2: (↑) Me abolic, cell p oli e a ion
and epi helium genes (CDKN2A)Bad
L3: (↑) Collagen and ECM
associa ed genes
L4: (↑) Immune p o ile Good
L5: (↑) Neu oendoc ine and insulin
ela ed pa hways Good
L6: (↑) Me abolic and diges i e
enzyme genes
Lombe k e al. [35]Epigene ic
1. PDXs (n=24)
2. Clinical samples
mic oa ay da ase s
GSE71729 (n=145)
ICGC (n=178)
TCGA (n=172)
Classical: (↑) TFs in ol ed in
panc ea ic de elopmen , me abolic
egula o s and Ras signalling
Good
Basal: (↑) TF p oli e a i e and
ansc ip ion nodes Bad
Mau e e al. [36]
T ansc ip ional
Compu a ional
modelling
1. P ima y PDAC umou
samples (n=122)
2. Clinical samples
mic oa ay da ase s
GSE71729 (UNC) (n=125)
ICGC (n=93)
TCGA (n=127)
Classical: Classical Mo i Good
Basal: Basal Mo i Bad
Immune- ich: (↑) immune and
in e leukin le els Good
ECM- ich: (↑) ma ix
ex acellula pa hways Bad
Dijk e al. [37] T ansc ip ional
1. P ima y PDAC umou
samples (n=90)
2. Panc ea ic cance PDXs
coho (n=14)
3. PDAC Cell lines coho (n=51)
Epi helial: (↑)MYC, mi ochond ial
componen s and ibosome signa u e Good
Mesenchymal: (↑)K-RAS, pa hways
ela ed o EMT, s omal signalling
and TGF-β
Bad
Compound panc ea ic: Simila o he
mesenchymal sub ype and (↑)
endoc ine pa hways
Good
J. Clin. Med. 2020,9, 4128 5 o 21
Table 1. Con .
Au ho Type o S udy Type and Numbe o
PDAC Samples
Dys egula ed Pa hways
and Mu a ions Ou come
Chan-Seng-Yue
e al. [38]
Whole genome
sequencing
T ansc ip ional
Lase cap u e mic odissec ed samples
om la e-s age PDAC
1. WGS (n=314)
2. Bulk RNAseq (n=248)
3. Single-cell RNAseq (n=15)
Classical A/B: (↑)SMAD4 and
GATA6 al e a ions Good
Basal-like A/B: (↑) EMT and TGF-β
pa hways, loss o CDKN2A,TP53
mu a ions, K-RAS imbalance
Bad
Hyb id Mid
Nicolle e al. [39] T ansc ip ional PDXs (n=76) G aded ypes be ween classical and
basal based on umou di e en ia ion
G ade
dependan
Fo each classi ica ion, ype o s udy, ype and numbe o samples, dys egula ed pa hways and mu a ions and p ognosis
a e desc ibed in each column. Up- egula ed and down- egula ed pa hways a e shown as (
↑
) and (
↓
), espec i ely. CAF,
Cance -Associa ed Fib oblas ; EMT, Epi helial- o-Mesenchymal T ansi ion; PDAC, Panc ea ic Duc al Adenoca cinoma;
PDX, Pa ien -De i ed Xenog a ; TF, T ansc ip ion Fac o ; WGS, Whole Genome Sequencing.
Mo i e al. [
33
] pe o med ansc ip ional analysis o classi y PDAC umou s in o wo sub ypes
wi hin wo di e en issues (Table 1): umou and s oma. Based on umou cells, PDAC samples
we e classi ied in o “classical” and “basal” sub ypes. The classical g oup was en iched in SMAD4
and GATA6, while he basal sub ype was molecula ly simila o basal umou s in bladde and b eas
cance . Al hough classical umou s showed be e p ognosis, pa ien s wi h basal umou s esponded
be e o adju an he apy. On he o he hand, he s oma was di ided in o “no mal” and “ac i a ed”
sub ypes. The no mal s omal g oup showed high le els o ma ke s o panc ea ic s ella e cells,
smoo h muscle ac in, imen in and desmin. Howe e , he ac i a ed s omal sub ype was de ined by
a complex se o genes associa ed wi h mac ophages, umou p omo ion and ib oblas ac i a ion;
his desc ibed an ac i a ed p o- umo igenic in lamma o y s omal esponse wi h poo p ognosis.
Compa ing hei signa u e wi h Collisson’s [
31
], Mo i e al. ound an o e lap be ween bo h classical
sub ypes, while genes in he quasi-mesenchymal sub ype seemed a mixed selec ion o genes om
basal and s omal sub ypes (Table 2) [33].
Table 2. Molecula sub ypes co esponding o PDAC classi ica ion.
Au ho s Common Sub ypes O he s
Collisson e al. [31] Classical
Quasi-mesenchymal
Exoc ine-like
Mo i e al. [33] Classical Basal-like No mal and ac i a ed
s oma
Bailey e al. [39] P ogeni o Squamous ADEX Immunogenic
Zhao e al. [34] L1 L2 L6 L3, L4 and L5
Lombe k e al. [35] Classical Basal
Mau e e al. [36] Classical Basal Immune- ich and ECM- ich
Dijk e al. [37] Epi helial Mesenchymal Sec e o y Compound panc ea ic
Chan-Seng-Yue e al. [
38
]
Classical (A, B) Basal-like (A, B) Hyb id
Nicolle e al. [39] F om Classical o Basal
Co ela ed sub ypes a e g ouped in columns. Colou s de ine he subg oups wi h he bes (g een) o wo s ( ed)
p ognosis. ECM, Ex acellula Ma ix.
La e , Bailey e al. [
10
] de ined new molecula sub ypes o PDAC based on comp ehensi e
in eg a ed genomic analysis and RNA exp ession p o iles: “squamous”, “panc ea ic p ogeni o ”,
“abe an ly di e en ia ed endoc ine exoc ine” (ADEX) and “immunogenic” (Table 1). The squamous
sub ype was linked o hype me hyla ion and down- egula ion o genes de e mining endode mal
iden i y in panc eas, wi h poo p ognosis in pa ien s. I was also en iched in TP53 and KDM6A
mu a ions and up- egula ion o he ansc ip ional ne wo k TP63
∆
N. PDAC p ogeni o - ype umou s
exp essed genes in ol ed in ea ly de elopmen o he panc eas, such as PDX1. The ADEX class
o e exp essed ansc ip ional pa hways p esen in K-RAS ac i a ion and in la e s ages o panc ea ic
de elopmen and di e en ia ion. Las ly, he immunogenic sub ype had panc ea ic p ogeni o ea u es,
bu i was ela ed o acqui ed immune supp ession pa hways (CTLA4 and PD-1) and s ong immune
in il a ion (B and T cells). When hey compa ed hei classi ica ion wi h ea lie s udies, h ee o hei

J. Clin. Med. 2020,9, 4128 6 o 21
classes di ec ly o e lapped wi h Collisson’s g oups [
31
]: Collisson’s classical, quasi-mesenchymal
and exoc ine-like sub ypes ma ched Bailey’s panc ea ic p ogeni o , squamous and ADEX g oups,
espec i ely (Table 2). In addi ion, 50% o he squamous sub ype umou s we e included in Mo i ’s
basal subg oup [33].
In 2018, Zhao e al. [
34
] conduc ed a e ospec i e me a-analysis o comple e ansc ip ome da a
om pa ien s wi h PDAC (Table 1). They ob ained six di e en sub ypes g ouped in umou - (L1, L2
and L6) and s omal-speci ic (L3, L4 and L5) sub ypes. L1, L2 and L6 we e all en iched in me abolic
genes, as de ailed in Sec ion 5. Besides me abolism, he sub ypes we e di e en ially en iched in o he
ou es: L2 was ela ed o cell p oli e a ion and epi helium genes, such as CDKN2A; L3 had inc eased
egula ion o collagen and ex acellula ma ix (ECM)-associa ed genes; L4 had an immune p o ile;
L5 was in ol ed in neu oendoc ine and insulin- ela ed pa hways; L6 showed ac i i y o diges i e
enzymes. Each exp ession p o ile was ela ed o clinical da a: epi helium and p oli e a ion in L2
showed he poo es p ognosis, immune and neu oendoc ine p o iles a L4 and L5 showed he bes
ou comes. Conside ing he abo e s a i ica ions o PDAC, Zhao e al. ound ha L1 and L6 we e e y
simila o he classical Mo i ’s sub ype, while L2 app oached hei basal sub ype (Table 2). L1, L2 and
L6 we e close o he ac i a ed sub ype. In Bailey’s da ase , L1 and L4 app oxima ed he immunogenic
sub ype, L2 he squamous, L3 he panc ea ic p ogeni o and L6 esembled he ADEX sub ype. Finally,
L1 and L3 we e simila o Collison’s classical sub ype, L2 app oached he quasi-mesenchymal and L6
ela ed o he exoc ine-like one.
Lombe k e al. [
35
] iden i ied epigenomic landscapes o PDAC sub ypes by pe o ming
an in eg a i e analysis o genome-wide Ch oma in Immunop ecipi a ion-sequencing (ChIP-seq) on
mul iple his one modi ica ions, as well as RNA-sequencing (RNA-seq) and DNA me hyla ion s udies
(Table 1). They epo ed wo sub ypes: “classical” and “basal”, which co ela ed wi h clinical pa ame e s.
Supe enhance mapping coupled wi h T ansc ip ion Fac o (TF) binding mo i and up- egula ion
analysis showed ha classical umou s we e ela ed o TFs in ol ed in de elopmen o he panc eas,
me abolic egula o s and K-RAS signalling, while basal umou s co ela ed wi h p oli e a i e and EMT
TF nodes. The basal samples we e linked o a mo e agg essi e pheno ype han he classical ones.
Mau e e al. [
36
] used Lase Cap u e Mic odissec ion (LCM) o sepa a e s omal and epi helial
compa men s o PDAC bulk umou samples, and con i med using machine lea ning echniques ha
s omal con amina ion may in e e e wi h PDAC classi ica ion (Table 1). In addi ion, hey desc ibed
wo epi helial sub ypes o PDAC ha co ela ed wi h he classical and basal sub ypes om Mo i e al.,
wi h he basal sub ype ha ing a poo e p ognosis han he classical (Table 2). Mo eo e , hey iden i ied
wo s omal sub ypes, an “immune- ich” g oup cha ac e ised by high immune and in e leukin le els,
and an “ECM- ich” g oup, associa ed wi h ex acellula ma ix pa hways. The ECM- ich sub ype
appea ed o ha e dec eased su i al compa ed wi h he immune- ich one. Finally, hey ound an
associa ion o he epi helial and s omal sub ypes in which he basal epi helium sub ype and he
ECM- ich s oma we e linked.
In 2020, Dijk e al. [
37
] conduc ed an unsupe ised consensus clus e ing and iden i ied ou
molecula sub ypes: “sec e o y”, “epi helial”, “compound panc ea ic” and “mesenchymal” (Table 1).
The sec e o y sub ype showed en ichmen in endoc ine and exoc ine pa hways o he panc eas.
Tumou s o he epi helial sub ype we e cha ac e ised by up- egula ion o he MYC oncogene and high
exp ession o mi ochond ial componen s and ibosome signa u e. The mesenchymal sub ype had
high le els o K-RAS ansc ip ion and was en iched in pa hways ela ed o EMT, s omal signalling
and TGF-
β
. The compound panc ea ic sub ype p esen ed simila cha ac e is ics o he mesenchymal
sub ype bu , in addi ion, was en iched in endoc ine unc ions. The sec e o y and mesenchymal
sub ypes p esen ed wo se p ognosis han he epi helial and compound panc ea ic ones. Dijk e al.
ound an in e connec ion be ween hese sub ypes and hose desc ibed by Collison, Bailey and Mo i
(Table 2). Fo example, he sec e o y sub ype co ela ed signi ican ly wi h Collison’s exoc ine-like,
Bailey’s ADEX, and Mo i ’s basal sub ypes. The epi helial sub ype sha ed cha ac e is ics wi h he
Collison’s and Mo i ’s classical sub ypes, bu also wi h he Bailey
´
s panc ea ic p ogeni o and squamous
J. Clin. Med. 2020,9, 4128 7 o 21
sub ypes. The compound panc ea ic g oup was simila o Collison’s exoc ine, Bailey’s ADEX and
Mo i ’s classical. Las ly, he mesenchymal sub ype co ela ed wi h Collison’s quasi-mesenchymal,
Bailey’s squamous and Mo i ’s basal.
Chan-Seng-Yue e al. [
38
] pe o med whole genome sequencing and bo h bulk and single-cell
RNAseq analyses on lase cap u e mic odissec ed umou s om mo e han 200 la e-s age pa ien s.
They iden i ied h ee majo sub ypes: “classical”, “basal-like” and “hyb id” (Table 1). Al hough he
classical and basal-like sub ypes we e ai ly o e lapped wi h he p e ious classi ica ions by Mo i ,
Bailey and Collison (Table 2), hey ound ha hese sub ypes could be subdi ided in o A and B subclasses
wi h di e ences in hei esponse o chemo he apy, agg essi eness and disease s age. Fo example,
basal-like A umou s a e highly chemo esis an and ea u e a high squamous signa u e en iched in
me as a ic umou s, while basal-like B umou s co espond o a low squamous signa u e p esen in
esec able umou s. Impo an ly, hey ound ha classical and basal-like p og ams co-exis wi hin
a umou and demons a ed ha molecula sub ypes a e linked o a speci ic copy numbe abe a ions
in genes such as mu an K-RAS (basal-like sub ype) and GATA6 (classical sub ype).
Finally, Nicolle e al. [
39
] p oposed a molecula g adien classi ica ion o s ablish a PDAC
ansc ip omic signa u e ha could be e ep esen he exis ence o in e media e cellula pheno ypes
be ween classical and basal-like sub ypes (Table 1). In his s udy, hey g aded Pa ien -De i ed Xenog a s
(PDXs) acco ding o di e en molecula le els o di e en ia ion and con i med ha he highe exp ession
o genes linked o he classical PDAC sub ype (GATA6) was co ela ed wi h inc eased di e en ia ion o
PDX samples, while lowe exp ession o genes was linked o he basal-like sub ype. They also ound
ha he highe he di e en ia ion o he umou , he be e he p ognosis and esponse o chemo he apy.
In e es ingly, al hough pa ial o e lap amongs he di e en signa u es and molecula sub ypes
can be ound in hese s udies, ecen wo ks using single-cell ansc ip omics demons a ed ha se e al
sub ypes can co-exis wi hin a umou [
38
,
40
], u he unde lining he high le el o he e ogenei y
p esen in PDAC umou s. Undoub edly, mo e e o s in his di ec ion a e equi ed o u he dissec
he complexi y o hese umou s, as well as o deciphe he in e play o he di e en subpopula ions
du ing disease p og ession.
4. Me abolic Rep og amming in PDAC
A he his ological le el, one o he mos no able cha ac e is ics o PDAC is i s dense s oma,
being up o 90% o he umou olume. I s main ea u es a e ex ensi e ib osis, lack o ascula isa ion,
hypoxia and immune in il a ion. Hypoxia is associa ed wi h inc eased cance cell p oli e a ion,
su i al, EMT, in asi eness and me as asis [41].
The lack o ascula isa ion no only causes hypoxia in he umou , bu also causes me abolic s ess
due o nu ien dep i a ion. As a esul , umou cells unde go he so-called “me abolic ep og amming”,
an upda ed hallma k o cance [
32
,
42
]. Cance cells inc ease nu ien acquisi ion along wi h enhanced
low h oughanabolic pa hways. Thisleads oinc easedglycolysisandglucose anspo , highglu amine
consump ion, lipid and amino acid biosyn hesis and main enance o edox homeos asis. In addi ion,
ecycling o cellula componen s also occu s h ough au ophagy, which deg ades mac omolecula
complexes and o ganelles in o indi idual me aboli es [41,43–45].
4.1. Wa bu g Pheno ype
The majo example o me abolic ep og amming is highe glucose consump ion. The ole o
glucose me abolism in cance was well de ined by O o Wa bu g back in he la e 1920s, leading o be
conside ed one o he hallma ks o cance [
46
]. Glycoly ic low is p ecisely con olled o ul il apid
p oli e a i e and syn he ic needs. Unlike no mal cells, umou cells ha e high le els o glycolysis,
e en in he p esence o oxygen and educed mi ochond ial unc ion, leading o a s a e called “ae obic
glycolysis”, also called he “Wa bu g e ec ”. On he o he hand, he “ e e se Wa bu g e ec ”
desc ibes a wo-compa men model in which cance cells induce ae obic glycolysis in he s omal
cells, whose glycolysis end-p oduc s a e ans e ed o he cance cells o eed mi ochond ial oxida i e
J. Clin. Med. 2020,9, 4128 8 o 21
phospho yla ion (OXPHOS). This allows umou s o espond o a ia ions in nu ien a ailabili y and
o op imise cell p oli e a ion and g ow h [
47
]. In e es ingly, his wo-compa men model can also
be applied conside ing he unc ional he e ogenei y o cance cells in PDAC: glycoly ic di e en ia ed
umou cells could p o ide subs a es o oxida i e cance s em cells (CSCs) [48].
A hypo hesis o me abolic ewi ing owa ds enhanced glycolysis o e he educ ion o
mi ochond ial oxida ion as a sou ce o ATP in PDAC is he p esence o a dense desmoplas ic
s oma, which basically impedes neo ascula isa ion. This c ea es a hypoxic mic oen i onmen in
which oxygen and nu ien s a e limi ed [
49
]. This s a e c ea es a posi i e eedback loop by which, on he
one hand, panc ea ic cance cells eel a selec i e p essu e unde he hypoxic and nu ien sho age
whe e only he mos agg essi e popula ions will emain. On he o he hand, unde such s ess-d i en
si ua ions, panc ea ic cance cells a e o ced o modi y hei me abolism in o de o cope wi h hei
bioene ge ic demands o PDAC p og ession, expansion and dissemina ion h ough he blood essels
owa ds less sca ce en i onmen s [
50
]. Indeed, a ecen s udy demons a ed ha glycolysis and hypoxia
signa u es co ela e in PDAC and ha P olyl 4-Hyd oxylase subuni Alpha 1 (P4HA1), a c i ical enzyme
in ol ed in collagen syn hesis, con ols glycolysis h ough HIF1
α
s abilisa ion [
51
]. Mo eo e , gene
exp ession a ays o me as a ic PDAC e ealed a glycolysis-based signa u e cha ac e ised by inc eased
exp ession o many glycoly ic enzymes [52], highligh ing he impo ance o glycoly ic me abolism in
PDAC p og ession. In ac , Liu e al. ecen ly demons a ed ha he EMT- ela ed gene SNAIL was
able o induce a mig a o y pheno ype in PDAC cell lines by p omo ing mesenchymal- ela ed genes
exp ession along wi h enhanced glucose up ake and lac a e p oduc ion [53].
O e all, he glycoly ic s a e is cha ac e ised by an inc eased exp ession o glycoly ic enzymes
and glucose and lac a e anspo e s, such as Glucose T anspo e 1 (GLUT1), and Monoca boxyla e
T anspo e s 1 and 4 (MCT1, MCT4) [
54
,
55
]. Speci ically, he o e exp ession o hese memb ane
anspo e s leads o an enhanced glucose sca enging om he hypo ascula ised umou
mic oen i onmen , which esul s in inc eased glucose a ailabili y in he cance cell as well as a be e
balance o he glucose pa hway in o de o keep glycolysis a high a e. On he one hand, GLUT1 is
an ATP-independen glucose anspo e ha enables glucose ans e ence om a high-g adien
ex acellula compa men o low-g adien cy oplasmic compa men . I s exp ession dosage has been
epo ed o be associa ed wi h PDAC p og ession om low- o high-g ade panc ea ic p eneoplas ic
lesionswhencompa ed ono mal panc eas[
54
]. On heo he hand, MCT1 andMCT4a e p o on-coupled
sympo anspo e s wi h highe a ini y o lac a e e lux. These anspo e s implica ed in glucose
homeos asis a e equi ed o cance cells o neu alise in acellula acidi ica ion due o he inc eased
glycoly ic a e and ha e been epo ed o be o e exp essed in PDAC. Kong e al. showed ha inhibi ion
o knockdown o MCT esul ed in an inhibi ed lac a e lux. In e es ingly, hey also demons a ed ha
hese anspo e s a e implica ed in PDAC cell lines in asi eness, hus highligh ing once again he
implica ions o glucose homeos asis in panc ea ic cance [56].
Impo an ly, he up- egula ion o mos o hese genes is media ed by PDAC d i e mu a ions on
K-RAS and TP53. As e iewed by B yan e al. [
57
], oncogenic K-RAS enhances he exp ession o many
glycoly ic enzymes such as GLUT1, Hexokinase 1 and 2 (HK1, HK2) and Lac a e Dehyd ogenase A
(LDHA), hus inc easing glycoly ic lux. This me abolic ep og amming owa ds glycolysis con ibu es
o an enhanced su i al o glycoly ic PDAC cell lines in he p esence o low le els o glucose.
Mo eo e , ano he s udy based on ansc ip ome and me abolome analyses showed ha mu an
K-RAS in ad anced PDAC mouse models is necessa y o an enhanced glucose up ake [
57
]. This s udy
also e ealed ha abe an K-RAS is implica ed in glucose me abolism in e media es channelling
in o di e en anabolic pa hways, such as he hexosamine biosyn hesis pa hway (HBP) and pen ose
phospha e pa hway (PPP), hus p o ing ha glucose me abolism is necessa y o uel anabolic b anches
o PDAC me abolism o p o ide he cance cells wi h building blocks o i s inc eased p oli e a ion
demands [
58
]. Mo eo e , he enhanced exp ession o he glycoly ic enzymes was demons a ed o be
ela ed o bad PDAC p ognosis, in asi eness and me as ases onse [59].
J. Clin. Med. 2020,9, 4128 9 o 21
4.2. Lipid Me abolism in PDAC
PDAC umou s a e also highly dependen on lipid me abolism [
60
,
61
] and, in ac , a high a die
was shown o suppo umou g ow h in mu ine models [
60
]. On he one hand, a y acids (FA) can be
p o ided exogenously by he abso p ion o ex acellula lipids ( om die , li e syn hesis o adipose
issue). Fo example, cance -associa ed adipocy es can p o ide adipokines and lipids o cance cells [
62
],
inc easing panc ea ic cance cell agg essi eness [
63
]. The exogenous FA up ake equi es he p esence o
he anspo e CD36 and FA-binding p o eins (FABPs). CD36 can also in luence gemci abine esis ance
in PDAC, by egula ing an i-apop osis p o eins [
64
,
65
]. Unsu p isingly, PDAC pa ien s wi h high
CD36 exp ession ha e lowe o e all su i al and ecu ence- ee su i al a es han pa ien s wi h low
exp ession. In his con ex , CD36 could be conside ed as an un a ou able p ognosis ac o and he use
o an i-CD36 s a egies in associa ion wi h con en ional chemo he apies could ep esen a p omising
he apeu ic app oach [64,66].
On he o he hand, panc ea ic cance cells can syn hesise de no o lipids h ough he lipogenesis
p ocess, p oducing mo e han 90% o he iacylglyce ol-FA. This p ocess uses he mi ochond ial
ci a e p oduced om he ica boxylic acid (TCA) cycle uelled by glucose and/o glu amine as
ca bon sou ces [
67
]. Lipogenic enzymes a e o en o e exp essed in PDAC cells; o example Fa y
Acid Syn hase (FASN) is pa icula ly p ominen and associa ed wi h poo p ognosis [
61
,
68
–
70
].
The pha macological inhibi ion o his enzyme educes s emness ea u es and gemci abine esis ance
in panc ea ic cance cells [
71
]. The p oduced iacylglyce ol molecules a e s o ed in lipid d ople s and
a co ela ion was es ablished be ween he accumula ion o lipid d ople s and umou p og ession and
agg essi eness [72]. Likewise, an ele a ed lipid syn hesis co ela es wi h CSC p ope ies and su i al
in di e en ypes o cance [
72
]. Thus, cance cells acqui e FA h ough ei he lipid up ake o de no o
lipogenesis, and ac i a e in acellula lipolysis o mobilise he FA s ocks.
FA sus ain h ee equi emen s o PDAC de elopmen and cance cells in gene al: cell memb ane
o ma ion, biosyn hesis o signalling molecules and lipid-de i ed messenge s, and ene gy p oduc ion.
Fi s o all, lipid syn hesis is an impo an equi emen o highly p oli e a i e cance cells o sus ain
memb ane o ma ion [
72
]. F om de no o syn hesis, sa u a ed o monounsa u a ed FA modula e
memb ane luidi y and o m mo e dense memb ane laye s ha may educe he up ake o d ugs
and con ibu e o he apy- esis ance [
73
]. Mo eo e , lipids a e implica ed in signal ansduc ion in
wo di e en ways: by building lipid a s modula ing p o ein ec ui men s and in e ac ions, as well as
by o ma ion o lipidic signalling molecules. This is he case o phospha idylinosi ol-3,4,5- isphospha e
[PI(3,4,5)P3], able o ac i a e he p o ein kinase B/AKT and s imula e cell p oli e a ion and su i al [
73
].
Finally, FA ep esen an impo an sou ce o ene gy in non-glycoly ic umou s, using he mi ochond ial
β
-oxida ion ( a y acid oxida ion, FAO) o p oduce ATP [
72
,
73
]. In ha con ex , Luo e al. demons a ed
ha he use o e omoxi , an inhibi o o FAO by blocking he en ance o FA in he mi ochond ia ia
Ca ni ine Palmi oyl T ans e ase 1A (CPT1A), can es o e he sensi i i y o panc ea ic CSCs o gemci abine
by inducing an ene gy c isis in hose cells [
74
]. These da a sugges ha CPT1A is an impo an ac o o he
cance me abolism ep og amming and could ep esen an a ac i e he apeu ic a ge , and highligh
how his p ocess is impo an o he cance cell o supply ATP unde ene gy s ess.
Addi ionally, PDAC cells a e also highly dependen on choles e ol, as i con ibu es, o example,
o he o ma ion o lipid a s, hus modula ing he ec ui men o key oncogenes ecep o such as he
Epide mal G ow h Fac o (EGF)- ecep o and egula ing su i al pa hways. Cance cells can inc ease
hei con en h ough ei he syn hesis ( h ough me alona e pa hway) o endocy osis media ed by
low-densi y lipop o eins (LDL) and LDL Recep o (LDLR). In PDAC pa ien s, choles e ol biosyn hesis
is associa ed wi h a mo e di e en ia ed pheno ype (classical sub ype), while high LDLR exp ession
co ela es wi h a highe isk o umou ecu ence. In e es ingly, inhibi ion o choles e ol syn hesis
induced a mesenchymal pheno ype [
75
] while blocking choles e ol up ake ia he knock-down o
LDLR was able o sensi ise PDAC cells o chemo he apy [76,77].
Taken oge he , all hese epo s p o e he po en ial o lipid me abolism a ge ing in o de o
sensi ise PDAC cells o chemo he apy. Howe e , some an i umou igenic e ec s o speci ic FA like
J. Clin. Med. 2020,9, 4128 16 o 21
7. Conclusions
PDAC is a he e ogeneous disease ha can be classi ied, acco ding o i s me abolic needs, in o
glycoly ic and lipogenic sub ypes wi h di e en p ognosis. Indeed, he glycoly ic sub ype would be
mo e agg essi e and esis an o con en ional chemo he apy han he lipogenic one. This me abolic
s a i ica ion co ela es wi h p e ious molecula classi ica ion sys ems, as hey show sub ypes sha ing
simila cha ac e is ics and p ognosis. In his con ex , classi ica ion in o me abolic sub ypes may be
be e placed o clinical use, since i could p o ide in o ma ion on he unc ional pheno ype o he
umou , co ela ing o agg essi eness, chemo esis ance and me as a ic abili ies independen ly om i s
mu a ional s a e. The in o ma ion collec ed in his e iew s ongly sugges s ha pa ien s a i ica ion
based on me abolic ea u es may bea p ognos ic alue and guide he apeu ic decisions in he u u e,
iden i ying a subg oup o pa ien s wi h poo p ognosis ha may be eligible o pe sonalised ea men s
designed acco ding o me abolic ulne abili ies.
Au ho Con ibu ions:
Concep ualisa ion, P.E.-R. and P.S.; da a analysis and in es iga ion P.E.-R.; w i ing—o iginal
d a p epa a ion, P.E.-R., S.C. and B.P.-A.; w i ing— e iew and edi ing and supe ision and unding acquisi ion, P.S.
All au ho s ha e ead and ag eed o he published e sion o he manusc ip .
Funding:
This esea ch was unded by he Ins i u o de Salud Ca los III h ough he Miguel Se e P og am
(CP16/00121) and Fondo de In es igaciones Sani a ias (PI17/00082) (bo h co- inanced by Eu opean unds (FSE: “El
FSE in ie e en u u u o” and FEDER: “Una mane a de hace Eu opa,” espec i ely) and he Wo ldwide Cance
Resea ch Cha i y oge he wi h Fundaci
ó
n Cien
í
ica Asociaci
ó
n Española con a el C
á
nce (FCAECC) (19-0250).
Acknowledgmen s: We wan o hank Alba Royo and Lau a Sancho o p oo eading he manusc ip .
Con lic s o In e es : The au ho s decla e no con lic o in e es .
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