Ci a ion: Bonilla, D.A.; Mo eno, Y.;
Pe o, J.L.; Fo e o, D.A.; Va gas-Molina,
S.; Od iozola-Ma ínez, A.; O ozco,
C.A.; S ou , J.R.; Rawson, E.S.; K eide ,
R.B. A Bioin o ma ics-Assis ed Re iew
on I on Me abolism and Immune
Sys em o Iden i y Po en ial Bioma ke s
o Exe cise S ess-Induced
Immunosupp ession. Biomedicines
2022,10, 724. h ps://doi.o g/
10.3390/biomedicines10030724
Academic Edi o : Thomas Moh
Recei ed: 24 Decembe 2021
Accep ed: 9 Ma ch 2022
Published: 21 Ma ch 2022
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Licensee MDPI, Basel, Swi ze land.
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biomedicines
Re iew
A Bioin o ma ics-Assis ed Re iew on I on Me abolism and
Immune Sys em o Iden i y Po en ial Bioma ke s o Exe cise
S ess-Induced Immunosupp ession
Diego A. Bonilla 1,2,3,4,* , Yu any Mo eno 1,2, Jo ge L. Pe o 1,3 , Diego A. Fo e o 5, Sal ado Va gas-Molina 6,
Ad ián Od iozola-Ma ínez 4,7, Ca los A. O ozco 5, Je ey R. S ou 8, E ic S. Rawson 9and Richa d B. K eide 10
1
Resea ch Di ision, Dynamical Business & Science Socie y—DBSS In e na ional SAS, Bogo a 110311, Colombia;
[email p o ec ed]g (Y.M.); jlpe [email p o ec ed] (J.L.P.)
2Resea ch G oup in Biochemis y and Molecula Biology, Facul y o Science and Educa ion, Uni e sidad
Dis i al F ancisco Joséde Caldas, Bogo a 110311, Colombia
3Resea ch G oup in Physical Ac i i y, Spo s and Heal h Sciences (GICAFS), Uni e sidad de Có doba,
Mon e ía 230002, Colombia
4Spo Genomics Resea ch G oup, Depa men o Gene ics, Physical An h opology and Animal Physiology,
Facul y o Science and Technology, Uni e si y o he Basque Coun y (UPV/EHU), 48940 Leioa, Spain;
[email p o ec ed]
5
Heal h and Spo Sciences Resea ch G oup, School o Heal h and Spo Sciences, Fundación Uni e si a ia del Á ea
Andina, Bogo á111221, Colombia; d o e o41@a eandina.edu.co (D.A.F.); co ozco35@a eandina.edu.co (C.A.O.)
6Facul y o Spo Sciences, EADE-Uni e si y o Wales T ini y Sain Da id, 29018 Málaga, Spain;
[email p o ec ed]
7kDNA Genomics®, Joxe Ma i Ko a Resea ch Cen e , Uni e si y o he Basque Coun y UPV/EHU,
20018 Donos ia, Spain
8Physiology o Wo k and Exe cise Response (POWER) Labo a o y, Ins i u e o Exe cise Physiology and
Rehabili a ion Science, Uni e si y o Cen al Flo ida, O lando, FL 32816, USA; je ey[email p o ec ed]
9Depa men o Heal h, Nu i ion and Exe cise Science, Messiah Uni e si y, Mechanicsbu g, PA 17055, USA;
[email p o ec ed]
10 Exe cise & Spo Nu i ion Labo a o y, Human Clinical Resea ch Facili y, Depa men o Heal h &
Kinesiology, Texas A&M Uni e si y, College S a ion, TX 77843, USA; [email p o ec ed]
*Co espondence: [email p o ec ed]o; Tel.: +57-320-335-2050
Abs ac : The immune unc ion is closely ela ed o i on (Fe) homeos asis and allos asis. The aim o
his bioin o ma ics-assis ed e iew was wo old; (i) o upda e he cu en knowledge o Fe me abolism
and i s ela ionship o he immune sys em, and (ii) o pe o m a p edic ion analysis o egula o y
ne wo k hubs ha migh se e as po en ial bioma ke s du ing s ess-induced immunosupp ession.
Se e al li e a u e and bioin o ma ics da abases/ eposi o ies we e u ilized o e iew Fe me abolism
and complemen he molecula desc ip ion o p io i ized p o eins. The Sea ch Tool o he Re ie al o
In e ac ing Genes (STRING) was used o build a p o ein-p o ein in e ac ions ne wo k o subsequen
ne wo k opology analysis. Impo an ly, Fe is a sensi i e double-edged swo d whe e wo ex emes o
i s nu i ional s a us may ha e ha m ul e ec s on inna e and adap i e immuni y. We iden i ied clea ly
connec ed impo an hubs ha belong o wo clus e s: (i) p esen a ion o pep ide an igens o he
immune sys em wi h he in ol emen o edox eac ions o Fe, heme, and Fe a icking/ anspo ;
and (ii) ubiqui ina ion, endocy osis, and deg ada ion p ocesses o p o eins ela ed o Fe me abolism
in immune cells (e.g., mac ophages). The iden i ied po en ial bioma ke s we e in ag eemen wi h
he cu en expe imen al e idence, a e included in se e al immunological/bioma ke s da abases,
and/o a e eme ging gene ic ma ke s o di e en s ess ul condi ions. Al hough u he alida ion
is wa an ed, his hyb id me hod (human-machine collabo a ion) o ex ac meaning ul biological
applica ions using a ailable da a in li e a u e and bioin o ma ics ools should be highligh ed.
Keywo ds:
e i ins; hemep o eins; ans e in ecep o ; me abolic ne wo ks and pa hways; immune
sys em; physiological s ess esponse; exe cise; allos asis
Biomedicines 2022,10, 724. h ps://doi.o g/10.3390/biomedicines10030724 h ps://www.mdpi.com/jou nal/biomedicines
Biomedicines 2022,10, 724 2 o 31
1. In oduc ion
I on (Fe) is one o he mos abundan me als on ea h and is an essen ial ace elemen
o mos o he di e en li ing o ms. In human physiology, Fe is he mos abundan
mic oelemen in he o ganism [
1
]. Wi h a ela i e a omic mass o 55.847 and a omic numbe
26, na u al Fe is a s able mix u e o nuclides wi h co esponding ela i e masses o 54 (5.8%),
56 (91.7%), 57 (2.2%), and 58 (0.3%) [
2
]. This me al acili a es elec on ans e eac ions in
he espi a o y chain and is impo an in mi ochond ial ene gy me abolism. Fu he mo e,
Fe is an impo an componen o hemoglobin (needed o ca y oxygen and o he chemical
species) and myoglobin (s o es oxygen in he muscle and eleases i when needed du ing
con ac ion), besides se e al o he enzymes [
3
]. Fe is indispensable o he o ma ion and
unc ion o e y h ocy es due o hei high hemoglobin con en [4].
The a e age amoun o Fe in ou body is abou 4.5 g, ep esen ing 0.01% o body
mass. Rese es o his mine al a e ound in he li e , spleen, and bone ma ow, mainly in
he o m o e i in—a complex o med by e i in hea y chain (FTH1) and e i in ligh
chain (FTL)—and as hemoside in o a lesse ex en [
5
]. I is wo h no ing ha he e a e
wo ypes o Fe om he die : heme and non-heme Fe. While heme-Fe comes exclusi ely
om animal ood, gi en ha i pa icipa es in he s uc u e o he heme g oup ( o ming
a coo dina ion complex a ached o po phy in), non-heme Fe is p esen in bo h plan s
and animal ood. I should be no ed ha heme-Fe is abso bed mo e e icien ly han he
non-heme [
6
]. The ecommended die a y allowance (RDA) o Fe in all age g oups o men
and pos menopausal women is 8 mg pe day; howe e , his alue inc eases o 18 mg pe
day in p emenopausal women due o mens ual losses [
7
]. Fu he mo e, he RDA o Fe
ises o 27 mg pe day du ing p egnancy and dec eases in he lac a ion pe iod (10 mg
in emales aged 14–18 yea s and 9 mg in women aged 19–50 yea s) [
8
]. I is no ewo -
hy o men ion ha he RDA o ege a ians and/o egans is abou 1.8 imes highe
han he omni o ous popula ion [
7
]. The median die a y in ake o Fe is app oxima ely
16–18 mg·day−1
o men and 12 mg
·
day
−1
o women, while he ole able uppe in ake
le el o adul s is 45 mg
·
day
−1
, conside ing gas oin es inal dis ess as an ad e se e ec [
9
].
The bioa ailabili y o Fe is 14–18% in popula ions ha consume a mixed die and
5–12%
in
people wi h ege a ian die s [
10
]. Fe bioa ailabili y in a heal hy adul is be ween
10–15%
om he die , highligh ing he abso p ion a he in es inal mucosa le el as he main poin
o egula ion [
11
,
12
]. In iguingly, he human body has no con olled mechanisms o
he exc e ion o Fe, and he le els a e balanced by egula ing Fe abso p ion [
13
] a he
cellula and he sys emic le el [
14
]; hence, a daily quan i y o 1–2 mg o in es inal Fe
abso p ion is equi ed o main aining no mal Fe concen a ions [
12
]. No wi hs anding his,
based on iso opic and chemical analysis, p oposed mechanisms o Fe exc e ion encompass
sloughed mucosal cells, in es inal epi helium u no e , skin ex olia ion, and o he blood
losses (e.g., mens ua ion) [
15
–
17
]. In addi ion, i is p oposed ha Fe exc e ion occu s a a
basal a e ega dless o Fe de iciency o excess [2,17].
Humans, among o he mammals, need o ul ill hei ene gy and mic onu ien s
equi emen s o adequa e unc ioning in cases o physiological s ess [
18
]. Based on
Selye [
19
], s ess can be de ined as he esponse o any ex e nal and/o in e nal challenge
(i.e., s esso s) which p oduces ex eme dis u bances (media ed by ecep o s and seconda y
messenge s) beyond he no mal physiological unc ion (a ousal) in a gi en biological
sys em. This o e -ac i a ion igge s signaling pa hways ha aim o con ol he s ess
and each homeos asis h ough nega i e eedback and eed o wa d mo i s a he cellula
and sys emic le els [
20
–
22
]. Ex eme and cons an o e -ac i a ion modi ies se e al, i
no all, pa ame e s o he biological sys em o cope app op ia ely wi h ch onic demands
and main ain s abili y—e en ou side o he no mal homeos a ic ange [
23
]. Thus, he
biological sys em ese s he p ima y media o s o he physiological esponse a a new se
poin ha is di e en om he no mal (homeos a ic) ope a ing le el in a p ocess ha is
called allos asis o “s abili y h ough change” [
24
]. The cos he biological sys ems ha e o
pay o being o ced o adap o his new se poin has been de ined as allos a ic load [
25
].
In he con ex o physiological egula ion and adap a ion, he allos asis model ep esen s
Biomedicines 2022,10, 724 3 o 31
he cu en heal h pa adigm o an icipa e s ess-media ed needs (e.g., imely p o ision
o ood, adequa e en i onmen al condi ions) and unde s and he p ocess o diseases as
cons an ly changing biological si ua ions [
26
,
27
]. Mul iple mechanisms a e in ol ed in he
app op ia e esponse o s ess and he de elopmen o allos a ic s a us, wi h he immune
sys em—inna e and adap i e immuni y—as an impo an egula o (immunocompe ence).
Immune ac i i y should be enhanced in esponse o sho - e m ansien s ess (las ing
minu es o hou s) o ensu e su i al and op imal unc ion o he biological sys em; howe e ,
immuni y ends o be diminished i long- e m s ess con inues o e days o mon hs [
28
].
This down- egula ion o he immune sys em (immunosupp ession) canno be apid since
he biological sys em is a di use ne wo k o cells and issues ha equi e he ese o
egula o y pa ame e s o edi ec esou ces owa ds ac i i ies ha a e mo e immedia ely
aluable o su i al (allos a ic load) [
29
]. The allos a ic load can inc ease d ama ically
i he sys em has supe imposed on i addi ional loads ha exceed he capaci y o cope
(e.g., inhe i ed immunode iciency diso de s, HIV in ec ion, cance , malnu i ion, d ug-
induced side e ec s [including s e oids, ciclospo in, and apamycin] [
30
]), in so-called
allos a ic o e load (immunode iciency) [
31
]. Figu e 1shows he esponse pa e n o he
immune unc ion o di e en du a ion/in ensi y s esso s, al hough indi idual a ia ion
(i.e., p io knowledge) should be conside ed.
Physical exe ion is a common s esso ha has been e alua ed in many models [
32
].
As expec ed, i migh bene i o h ea en a biological sys em based on he in ensi y o he
s imulus (exe cise dosage) [
33
,
34
]. In e es ingly, adequa e doses o physical exe cise and
inc eased physical ac i i y le els ha e been associa ed wi h lowe allos a ic load [
27
,
35
].
Mechanisms ha p o ide an adequa e esponse o physical s ess ac o s, such as s enuous
o igo ous exe cise, in ol e molecula egula o s, such as hea shock p o eins [
36
] and
immune unc ion ac i a ion. The a ailabili y o Fe plays a key ole and is egula ed by
se e al pa hways and p o eins [
37
]. Da a accumula ed om se e al s udies ha e shown
ha exe cise i sel would no lead o a ue Fe de iciency [
38
–
40
], o so-called “spo s
anemia,” in a heal hy a hle e wi h adequa e daily Fe in ake. Hence, he g ea es p edis-
posi ion o Fe-de iciency anemia in young emale a hle es may no be exe cise i sel , bu
p obably low ene gy a ailabili y, inadequa e die a y choices, educed Fe in ake, and men-
s ua ion [
41
,
42
]. These ac o s may also induce Fe de iciency o anemia in he gene al
popula ion [
43
]. Howe e , ecogni ion o such scena ios has also been seen in male a hle es,
con ibu ing o he mo e inclusi e concep o ela i e ene gy de iciency in spo (RED-S)
synd ome [
44
] as an expanded concep o he emale a hle e iad. In his sense, i is im-
po an o moni o he esponses o he immune sys em o physical exe cise gi en ha i is
highly linked o Fe me abolism [
45
]. Al hough he exac mechanism is s ill unknown, he e
a e ce ain molecula bioma ke s associa ed wi h adap i e egula ion p ocesses and Fe
egula ion (e.g., inc ease in hepcidin [HAMP] le els) [
46
,
47
]. Iden i ying no el bioma ke s
du ing hese s ess- ela ed immune esponses migh help wi h he apeu ic guidance and
in moni o ing he allos a ic load [
48
,
49
], o example, du ing he a hle es’ p epa a ion o
physical compe i ion. Guidi e al. [
27
] ha e ecen ly sugges ed ha an in eg a ed app oach
ha includes biological ma ke s and clinical moni o ing o assess allos a ic load is highly
impo an o ack esponses o s ess. The e o e, he aim o his bioin o ma ics-assis ed
e iew is wo old; (i) o upda e he cu en knowledge o Fe me abolism and i s ela ionship
o he immune sys em wi h a special emphasis on he po en ial mechanisms o ac ion and
signaling pa hways, and (ii) o pe o m a p edic ion analysis o egula o y ne wo k hubs
ha migh se e as po en ial bioma ke s du ing s ess-induced immunosupp ession wi h
exe cise as a s ess model.
Biomedicines 2022,10, 724 4 o 31
Biomedicines 2022, 10, x FOR PEER REVIEW 4 o 35
analysis o egula o y ne wo k hubs ha migh se e as po en ial bioma ke s du ing
s ess-induced immunosupp ession wi h exe cise as a s ess model.
Figu e 1.
Rep esen a ion o he changes in he immune unc ion in esponse o s ess. The igu e
shows he esponse pa e n o immune ac i i y o dis inguish be ween allos a ic load in he no mal
li e cycle and allos a ic o e load ha exceeds he capaci y o he biological sys em o cope. See he
p e ious pa ag aphs o he manusc ip o u he a ionale. Sou ce: designed by he au ho s (D.A.B.)
based on published ma e ials [29,50–52].
Biomedicines 2022,10, 724 5 o 31
2. Me hods
2.1. Sea ch S a egy and In o ma ion Sou ces
The sea ching p ocess o he scien i ic li e a u e was ca ied ou using he ee e ms
“i on,” “me abolism,” and “immune sys em” h ough he da abases PubMed/MEDLINE
and Science Di ec . Fu he pape s we e sough by hand-sea ching in Google Schola .
2.2. Manual Cu a ion and Bioin o ma ics-Assis ed Re iew
The li e a u e e iew ollowed he basic amewo k o in eg a i e e iews desc ibed
by Whi emo e and Kna l [
53
], which allows o he inclusion o quan i a i e and quali a i e
s udies. In addi ion, we used he op imized me hodology es ablished by Hopia e al. [
54
]
o he e alua ion and analysis o scien i ic publica ions, including p oblem o mula ion,
li e a u e sea ch, e alua ion, analysis, and p esen a ion o indings.
Bioin o ma ics-assis ed e iew is a new app oach ha has been ecen ly de eloped
by Bonilla e al. [
55
] o add ess he lack o sys ema iza ion in na a i e e iews ha aim
o upda e and/o analyze po en ial mechanisms o ac ion. I also allows ex ac ing ex-
pe imen ally alida ed and biologically impo an in o ma ion o a gi en biological phe-
nomenon unde a sys ems biology app oach which would o he wise be cumbe some
o ex ac manually. Conside ing he impo ance o he a ious da a sou ces, a high-
le el o manual cu a ion and ep oducibili y (open sou ce) we e equi ed. Se e al bioin-
o ma ics da abases/ eposi o ies we e used o c oss- e e encing, unc ional anno a ion,
and o en ich biological signi icance, including UniP o KB (h ps://www.unip o .o g/,
accessed on 17 June 2021), PDB (h ps://www. csb.o g/, accessed on 17 June 2021),
Ensembl (h ps://www.ensembl.o g/index.h ml, accessed on 17 June 2021), The Gene
On ology (GO) Resou ce (h p://geneon ology.o g/, accessed on 17 June 2021) and he
BioGPS—Gene Po al Sys em (h p://biogps.o g/, accessed on 17 June 2021). The da a
sea ch/en ichmen was pe o med be ween Ap il and June 2021, al hough an upda ed
sea ch was conduc ed p io o manusc ip submission. Gene/p o ein p io i iza ion was
based on pa hways and egula ion o Fe me abolism (syn hesis and anspo ). Manual
cu a ion o li e a u e and bioin o ma ics da a was pe o med by one au ho (D.A.B.), wi h
expe ience in he ex ac ion o kinase-subs a e in e ac ions om he li e a u e [
55
,
56
], who
also pa icipa ed in he da a ex ac ion o he de elopmen o he Kinase En ichmen
Analysis e sion 2 by he Ma’ayan Labo a o y (caps one p ojec ) [
57
]. A second au ho ,
wi h ex ensi e expe ience in bioin o ma ics and sys ems biology (D.A.F.), e ised and
supe ised he analy ics wo k low.
2.3. Iden i ica ion o Po en ial Bioma ke s
The p io i ized gene/p o eins iden i ied in he manual cu a ion we e submi ed o
he Sea ch Tool o he Re ie al o In e ac ing Genes (STRING, h ps://s ing-db.o g/,
accessed on 17 June 2021) [
58
] o build a p o ein/p o ein in e ac ions ne wo k (PPIN). All
STRING sco es ank om 0 o 1, wi h 1 being he highes possible con idence. A sco e o
0.5 would indica e ha oughly e e y second in e ac ion migh be e oneous (i.e., a alse
posi i e). The ollowing op ions we e ac i a ed in he STRING ool o ob ain he PPIN:
(i) sea ch—by mul iple p o eins; (ii) ne wo k ype— ull STRING ne wo k; (iii) meaning
o ne wo k edges—e idence; (i ) minimum equi ed in e ac ion sco e—high con idence
(0.700); and ( ) max numbe o in e ac o s o show—1s shell = no mo e han i e in e -
ac o s, and 2nd shell = no mo e han i e in e ac o s. To clus e he mos simila nodes
o he ne wo k in o an easily dis inguishable unc ion-based classi ica ion (e.g., immune
sys em egula ion), we used he Ma ko clus e algo i hm o g aphs, which is based on
simula ion o s ochas ic low in he ob ained g aph. The in la ion ac o was se a 1.5 o
balance sensi i i y and selec i i y. STRING and GO ha e been complemen a ily used in
p e ious s udies as he main sou ces o da a o cons uc ing ne wo k models and p o iding
biological ou pu s o he PPIN, espec i ely [
59
,
60
]. The iden i ica ion o hub nodes was
based on ne wo k opology and STRING a e age sco e. Ne wo k opology analysis was
pe o med using he Ne wo k Analysis P o ile 2.0 (h p://bib. leming.g :3838/NAP/,
Biomedicines 2022,10, 724 6 o 31
accessed on 2 July 2021) [
61
]. Da a ep esen a ion in ne wo k models was u ilized as
he p io i iza ion app oach [
62
], al hough we also implemen ed manual cu a ion o he
STRING da a (in e ac ions in abula o m) u ilizing li e a u e e i ica ion o imp o e
eliabili y [
63
]. The esul s we e e i ied by con as ing he ne wo k hubs o he indi idual
expe imen al epo s a ailable in he li e a u e using exe cise-induced immunosupp ession
as a model example. We also sea ched in online da abases o (i) expe imen ally- e i ied
biological en i ies in ol ed in he immune esponse o humans, such as Inna eDB (a ail-
able a h p://inna edb.sahm i.com/index.jsp, accessed on 7 No embe 2021) [
64
], and
he Immunome Knowledge Base (a ailable a h p://s uc u e.bmc.lu.se/idbase/ikb/,
accessed on 7 No embe 2021) [
65
]; and (ii) bioma ke s a Bioma ke Base (a ailable a
h ps://www.bioma ke base.com/, accessed on 7 No embe 2021) and Ma ke DB (a ail-
able a h ps://ma ke db.ca/, accessed on 7 No embe 2021) [
66
]. These ools we e
accessed be ween Sep embe and Oc obe 2021. Figu e 2shows he gene al wo k low o
his s udy.
Biomedicines 2022, 10, x FOR PEER REVIEW 6 o 35
simula ion o s ochas ic low in he ob ained g aph. The in la ion ac o was se a 1.5 o
balance sensi i i y and selec i i y. STRING and GO ha e been complemen a ily used in
p e ious s udies as he main sou ces o da a o cons uc ing ne wo k models and
p o iding biological ou pu s o he PPIN, espec i ely [59,60]. The iden i ica ion o hub
nodes was based on ne wo k opology and STRING a e age sco e. Ne wo k opology
analysis was pe o med using he Ne wo k Analysis P o ile 2.0
(h p://bib. leming.g :3838/NAP/, accessed on 2 July 2021) [61]. Da a ep esen a ion in
ne wo k models was u ilized as he p io i iza ion app oach [62], al hough we also
implemen ed manual cu a ion o he STRING da a (in e ac ions in abula o m) u ilizing
li e a u e e i ica ion o imp o e eliabili y [63]. The esul s we e e i ied by con as ing
he ne wo k hubs o he indi idual expe imen al epo s a ailable in he li e a u e using
exe cise-induced immunosupp ession as a model example. We also sea ched in online
da abases o (i) expe imen ally- e i ied biological en i ies in ol ed in he immune
esponse o humans, such as Inna eDB (a ailable a h p://inna edb.sahm i.com/index.jsp,
accessed on 7 No embe 2021) [64], and he Immunome Knowledge Base (a ailable a
h p://s uc u e.bmc.lu.se/idbase/ikb/, accessed on 7 No embe 2021) [65]; and (ii)
bioma ke s a Bioma ke Base (a ailable a h ps://www.bioma ke base.com/, accessed on
7 No embe 2021) and Ma ke DB (a ailable a h ps://ma ke db.ca/, accessed on 7
No embe 2021) [66]. These ools we e accessed be ween Sep embe and Oc obe 2021.
Figu e 2 shows he gene al wo k low o his s udy.
Figu e 2. O e iew o he bioin o ma ics-assis ed e iew wo k low o iden i y po en ial bioma ke s.
3. I on Up ake and Me abolism
Fe in he body can be ound as non-heme Fe and heme-Fe. Non-heme Fe comes om
bo h plan and animal-de i ed oods and is abso bed in a small p opo ion (3–8%). The
p esence o i amin C inc eases i s abso p ion and o he o ganic acids ha ans o m non-
heme Fe om i s e ic (Fe
3+
) o e ous (Fe
2+
) s a e. The las is di ec ly abso bed a he le el
o he in es inal mucosa o o he cells [67]. Since non-heme Fe eaches he in es ine
p ima ily in he Fe
3+
s a e, i needs o be educed o Fe
2+
by he ac ion o e i educ ases. In
he duodenum, his educ ion is ca ied ou mainly by cy och ome b educ ase 1
Figu e 2.
O e iew o he bioin o ma ics-assis ed e iew wo k low o iden i y po en ial bioma ke s.
3. I on Up ake and Me abolism
Fe in he body can be ound as non-heme Fe and heme-Fe. Non-heme Fe comes om
bo h plan and animal-de i ed oods and is abso bed in a small p opo ion (3–8%). The p es-
ence o i amin C inc eases i s abso p ion and o he o ganic acids ha ans o m non-heme
Fe om i s e ic (Fe
3+
) o e ous (Fe
2+
) s a e. The las is di ec ly abso bed a he le el o he
in es inal mucosa o o he cells [
67
]. Since non-heme Fe eaches he in es ine p ima ily in
he Fe
3+
s a e, i needs o be educed o Fe
2+
by he ac ion o e i educ ases. In he duode-
num, his educ ion is ca ied ou mainly by cy och ome b educ ase 1 (CYBRD1) [
68
]. I is
hypo hesized ha he e a e o he e i educ ases in in es inal en e ocy es, since i has been
shown ha mice lacking CYBRD1 do no su e om impai ed Fe abso p ion [
69
]. Fe
2+
i-
nally en e s duodenal epi helial cells h ough he na u al esis ance-associa ed mac ophage
p o ein 2 (NRAMP, also known as di alen me al ion anspo e 1 o DMT1).
On he o he hand, heme-Fe pa icipa es in he s uc u e o he heme g oup, whe e
Fe is pa o a coo dina ion complex a ached o po phy in and comes exclusi ely om
animal ood as an easily abso bed sou ce [
70
]. This is pa o hemoglobin, myoglobin,
Biomedicines 2022,10, 724 7 o 31
and o he enzymes, such as cy och omes, ca alases, and pe oxidases, ha pa icipa e in
oxida i e p ocesses [
71
]. Whe eas he in e ac ion wi h hap oglobin and CD163 media es
he lysoendosomal a icking o hemoglobin om plasma o cells [
72
], heme-Fe can be
anspo ed in o duodenal cells by solu e ca ie amily 46 membe 1 (SLC46A1, also known
as he p o on-coupled ola e anspo e ) [
73
]. Once i eaches he en e ocy e endosomal
memb ane, he heme g oup is deg aded by he ac ion o heme oxygenases (HMOX1 and
HMOX2), and Fe
2+
is eleased o he cy osol. Al e na i ely, he sca enge ecep o class A
membe 5 (SCARA5) media es cellula up ake o e i in-bound Fe by s imula ing e i in
endocy osis om he cell su ace wi h consequen Fe deli e y wi hin he cell [
74
]. The
unc ional molecule o e i in o ms a oughly sphe ical shell o
24-me
FTL/FTH1 wi h a
diame e o 12 nm and con ains a cen al ca i y in o which he insoluble mine al Fe co e is
deposi ed (
≈
4000–4500 Fe a oms) [
75
]. Damaged e i in is called hemoside in, which is
unc ionally de ined as insoluble cellula Fe [
76
]. Depending on human body equi emen s,
cy osolic Fe
2+
: (i) can be s o ed in he en e ocy e by binding o FTL/FTH1, he in acellula
Fe s o age p o ein complex [
75
]; (ii) dis ibu ed a ound he cell, media ed by poly( C)-
binding p o eins (PCBPs, also known as in acellula Fe chape ones [
77
,
78
]); o , (iii) eleased
in o he bloods eam ia solu e ca ie amily 40 membe 1 (SLC40A1, also known as
e opo in) [
79
]. Thus, once wi hin he cell, Fe
2+
can be s o ed as e i in, bind o chape ones
(e.g., PCBPs) o a elling o o he o ganelles (e.g., mi ochond ia [
80
]), o e en be egula ed
a he ansc ip ional (less-known) and pos - ansc ip ional le el (i.e., he IREB/IRE sys em)
o con ol i s up ake, s o age and expo . The i on- esponsi e elemen -binding p o eins
(IREBs, also known as Fe-sensing p o eins o i on- egula o y p o eins, IRPs) and i on-
esponsi e elemen s (IREs, which a e 30-nucleo ide long RNA mo i s ha o m special s em-
loop s uc u es) c ea e he so-called IREB/IRE sys em, which enables he cell o minimize
o maximize i s Fe anspo o s o age acco ding o need [
81
]. The binding o he IREBs o
he IREs can be a ei he he 3
0
-un ansla ed egion (UTR) o 5
0
-UTR o a espec i e mRNA
o con ol i s ansla ion [
82
]. In e es ingly, binding o he 5
0
-UTR blocks ansla ion while
binding o he 3
0
UTR s abilizes he mRNA agains endonuclease clea age [
83
]. This key hub
o in acellula Fe me abolism pos - ansc ip ionally egula es many genes (e.g., FTL/FHL1,
SLC40A1,SLC11A2) [
84
] by speci ically binding o he conse ed IREs loca ed in he UTRs
o mRNAs [
85
]. Desc ip ion o he genes/ ansc ip s ha may be a ec ed by he IREB/IRE
sys em and how his binding impac s he ansla ion o hese ansc ip s can be ound in
he publica ions by Zhang e al. [84] and Khan e al. [81], espec i ely.
In e es ingly, Fe is anspo ed in he bloods eam bound o ans e in in i s Fe
3+
s a e. Fo his, he Fe
2+
ion is oxidized by a e oxidase Cu
2+
-dependen p o ein known as
hephaes in (HEPH) a he basola e al su ace o he duodenum [
86
,
87
], al hough, in mos
body cells, his p ocess is achie ed by he homolog ce uloplasmin (CP) [
77
,
88
]. The p o on
g adien ha uels se e al p ocesses (e.g., Fe
2+
up ake by NRAMP2 in o en e ocy es, o Fe
2+
anspo o he basola e al su ace by SLC40A1) is main ained by he combined ac ions
o apical sodium/hyd ogen exchange 1 (SLC9A1) and basola e al sodium/po assium-
anspo ing ATPase (ATP1A3) an ipo e s. A ep esen a ion o he p ocesses men ioned
abo e is shown in Figu e 3. Thus, Fe anspo and me abolism a e egula ed a di e en
le els ha in ol e mul iple mechanisms. A he memb ane, he egula ion is media ed by
plasma and o ganelle memb anes, such as p o ein/solu e ca ie s and he lysoendosomal
a icking memb ane; cy osolic egula ion in ol es he ac ion o FTL/FHL1 and PCBPs; a
he nucleus ansc ip ional (e.g., hypoxia-inducible ac o s, HIFs) and pos - ansc ip ional
( he IREB/IRE sys em) mechanisms a e emphasized; howe e , his las seems o be he
bes -unde s ood sys em [
12
,
13
,
69
]. The mos ele an genes/p o eins o Fe up ake and
me abolism ha we e p io i ized a e manual cu a ion a e desc ibed in de ail in Table 1.
Biomedicines 2022,10, 724 8 o 31
Biomedicines 2022, 10, x FOR PEER REVIEW 8 o 35
FTL/FHL1 and PCBPs; a he nucleus ansc ip ional (e.g., hypoxia-inducible ac o s, HIFs)
and pos - ansc ip ional ( he IREB/IRE sys em) mechanisms a e emphasized; howe e , his
las seems o be he bes -unde s ood sys em [12,13,69]. The mos ele an genes/p o eins o
Fe up ake and me abolism ha we e p io i ized a e manual cu a ion a e desc ibed in de ail
in Table 1.
Figu e 3. I on abso p ion in he duodenum. The p o ein s uc u es we e aken om UniP o KB and
PDB eposi o ies. S uc u e p edic ion by homology modeling was ca ied ou using SWISS-
MODEL ia he ExPASy web se e i he p o ein s uc u e was no a ailable a UniP o KB o PKB.
ATP1A3, basola e al sodium/po assium- anspo ing ATPase; CD163, sca enge ecep o cys eine-
Figu e 3.
I on abso p ion in he duodenum. The p o ein s uc u es we e aken om UniP o KB and
PDB eposi o ies. S uc u e p edic ion by homology modeling was ca ied ou using SWISS-MODEL
ia he ExPASy web se e i he p o ein s uc u e was no a ailable a UniP o KB o PKB. ATP1A3,
basola e al sodium/po assium- anspo ing ATPase; CD163, sca enge ecep o cys eine- ich ype
1 p o ein M130; CYBRD1, cy och ome b educ ase 1; CP, ce uloplasmin; Hb, hemoglobin; HEPH,
hephaes in; HMOX1/2, heme oxygenases 1/2; IREBs, i on- esponsi e elemen -binding p o eins;
IREs, i on- esponsi e elemen s; mRNA, messenge RNA; NRAM2, na u al esis ance-associa ed
mac ophage p o ein 2; PCBP, poly( C)-binding p o ein; SCARA5, sca enge ecep o class A membe
5; SLC9A1, apical sodium/hyd ogen exchange 1; SLC40A1, solu e ca ie amily 40 membe 1;
SLC46A1, p o on-coupled ola e anspo e ; TF, ans e in. Sou ce: designed by he au ho s (D.A.B.).
Biomedicines 2022,10, 724 9 o 31
Table 1. Cha ac e is ics o p io i ized p o eins o i on me abolism.
Recommended Name
(Al e na i e Names)
Gene Name
(Loca ion) Ensembl ID P o ein Fea u es
(UniP o KB/PDB En y) Cellula Loca ion Molecula Func ion P o ein Exp ession *
(BioGPS ID)
Cy och ome b
educ ase 1
(Duodenal cy och ome
b; Fe ic-chela e
educ ase 3)
CYBRD1
(2q31.1)
ENSG00000071967
Leng h: 286
Mass: 31,641 Da
(Q53TN4/5ZLE)
In eg al componen o
memb ane. P esen a he b ush
bo de o duodenal en e ocy es
whe e i p obably educes
die a y Fe3+ he eby acili a ing
i s anspo in o he
mucosal cells.
Fe ic-chela e educ ase ha educes
Fe3+ o Fe2+. Uses asco ba e as
elec on dono . May be in ol ed in
ex acellula asco ba e ecycling in
e y h ocy e memb anes. May also ac
as a e i educ ase in ai way
epi helial cells.
Thy oid gland, small
in es ine, colon, es is,
gallbladde , o a y,
b eas endome ium
(79901)
Na u al esis ance-
associa ed mac ophage
p o ein 2—NRAM2
(Solu e ca ie amily
11 membe 2; Di alen
me al ion anspo e 1
[DMT1])
SLC11A2
(12q13.12)
ENSG00000110911
Leng h: 568
Mass: 62,266 Da
(P49281/5F0L)
In eg al componen o plasma
memb ane. P esen a he apical
plasma memb ane whe e i is
in ol ed in Fe up ake in o
duodenal en e ocy es. May
se e o impo Fe in o
he mi ochond ia.
Impo an in me al anspo , in
pa icula Fe. Can also anspo
manganese, cobal , cadmium, nickel,
anadium and lead. May play an
impo an ole in hepa ic Fe
accumula ion and issue
Fe dis ibu ion.
Sali a y gland, ce eb al
co ex, ad enal gland,
b onchus, lung, s omach,
colon, ec um, li e ,
gallbladde , panc eas,
kidney (4891)
P o on-coupled ola e
anspo e
(Heme ca ie
p o ein 1)
SLC46A1
(17q11.2)
ENSG00000076351
Leng h: 459
Mass: 49,771 Da
(Q96NT5/-)
Apical plasma memb ane.
Localizes o he apical
memb ane o in es inal cells in
Fe-de icien cells, while i
esides in he cy oplasm in
Fe- eple e cells.
I has been shown o ac bo h as an
in es inal p o on-coupled
high-a ini y ola e anspo e and as
an in es inal heme anspo e , which
media es heme up ake om he gu
lumen in o duodenal epi helial cells.
Tes is, small in es ine,
duodenum, colon
(113235)
Sca enge ecep o
cys eine- ich ype 1
p o ein †
(Hemoglobin
sca enge ecep o )
CD163
(12p13.31)
ENSG00000177575
Leng h: 1156
Mass: 125,45 Da
(Q86VB7/-SWISS-
MODEL Reposi o y
Q86VB7)
Ex acellula egion o sec e ed
and plasma memb ane. Acu e
phase- egula ed ecep o
in ol ed in clea ance
and endocy osis o
hemoglobin/hap oglobin
complexes.
May play a ole in he up ake and
ecycling o Fe, ia endocy osis o
hemoglobin/hap oglobin and
subsequen b eakdown o heme.
Binds hemoglobin/hap oglobin
complexes in a calcium-dependen
and pH-dependen manne .
Lung, spleen, bone
ma ow, lymph node,
appendix, onsil (9332)
Biomedicines 2022,10, 724 16 o 31
in he di e en phases o i s allos a ic esponse a e needed. Hence, bioin o ma ics migh
p o ide impo an in o ma ion on sys em-le el cellula p ocesses and u u e di ec ions o
expe imen al esea ch in exe cise immunology [146].
Based on his, we buil a PPIN o he p io i ized p o eins o Fe me abolism by mapping
hem in o he STRING ool o e alua e he po en ial in e ac o s di ec ly ela ed o he
immune sys em (Figu e 5). The p elimina y opological analysis o he ne wo k showed an
a e age local clus e ing coe icien o 0.535 wi h an a e age node deg ee equal o 5.15. The
main connec ed componen was cons uc ed wi h 24 nodes and 67 edges (MB and SLC46A1
did no connec o o he p o eins unde he se ings o his ne wo k, bu bo h in e ac
wi h membe s o he human leukocy e an igen sys em). The e y low p o ein-p o ein
in e ac ions en ichmen p- alue (<1.0
−16
) indica ed ha he nodes we e no andom and
ha he obse ed numbe o edges was signi ican , and his was expec ed conside ing all
inpu p o eins belong o Fe me abolism.
Biomedicines 2022, 10, x FOR PEER REVIEW 18 o 35
Figu e 5. P o ein-p o ein in e ac ions ne wo k o i on me abolism and he immune sys em. The
colo ed nodes ep esen he esul s o he Ma ko clus e algo i hm o g oup p o eins in wo main
biological unc ions: p esen a ion o pep ide an igens o he immune sys em ( ed) and
ubiqui ina ion, endocy osis, and deg ada ion p ocesses o p o eins ela ed o Fe me abolism in
immune cells (e.g., mac ophages) (g een). The colo s o in e ac ions co espond o: known om
cu a ed da abases (cyan), expe imen ally de e mined (pu ple); p edic ed in e ac ions based on gene
neighbo hood (g een), gene usions ( ed), and gene co-occu ence (da k blue); and o he s, such as
ex -mining (yellow), co-exp ession (black), and p o ein homology (ligh blue). The inpu p o eins
we e: CD163, sca enge ecep o cys eine- ich ype 1 p o ein M130; CP, ce uloplasmin; CYBRD1,
cy och ome b educ ase 1; FTH1, e i in hea y chain; FTL, e i in ligh chain; HAMP, hepcidin;
HEPH, hephaes in; HMOX1, heme oxygenase 1; IREB2, i on- esponsi e elemen -binding p o ein 2;
MB, myoglobin; SCARA5, sca enge ecep o class A membe 5; SLC11A2, na u al esis ance-
associa ed mac ophage p o ein 2; SLC40A1, solu e ca ie amily 40 membe 1; SLC46A1, p o on-
coupled ola e anspo e ; TF, ans e in; TFRC, ans e in ecep o p o ein 1. The ne wo k is
a ailable a h ps:// e sion-11-0b.s ing-db.o g/cgi/ne wo k?ne wo kId=b1HF4 eAW2N (accessed
in 17 June 2021).
Based on he GO anno a ion, he Kyo o Encyclopedia o Genes and Genomes (KEGG)
pa hway analysis, and he P o ein Families (PFAM) P o ein Domains analysis, an
en ichmen analysis o he ne wo k was pe o med (Table 2). Besides Fe anspo and
oxido educ ase ac i i y, he GO molecula unc ion showed ha pep ide an igen binding
and an igen pep ide anspo e 1 (TAP binding) a e among he op unc ions o he
ne wo k. The GO cellula componen e ealed ha mos p o eins a e loca ed in he
ecycling endosome, MHC class I p o ein complex, ea ly endosome, cell su ace, and he
HFE- ans e in ecep o complex. As expec ed, he KEGG pa hway en ichmen analysis
showed ha hese p o eins we e mainly associa ed wi h mine al abso p ion and
e op osis; howe e , he PPIN o p io i ized p o eins o Fe me abolism a e highly
in ol ed in pa hways modula ing he an igen p ocessing and p esen a ion, allog a
ejec ion (a consequence o he ecipien ’s alloimmune esponse o non-sel -an igens
exp essed by dono issues), and g a - e sus-hos disease. In e es ingly, he PFAM
analysis showed conse a ion o he immunoglobulin C1-se domain, he MHC_I C-
e minus, and he MHC class I alpha chain, alpha1 alpha2 domains. Fu he mo e,
clus e ing he ne wo k wi h a Ma ko algo i hm allowed iden i ying ha se e al p o eins
Figu e 5.
P o ein-p o ein in e ac ions ne wo k o i on me abolism and he immune sys em. The
colo ed nodes ep esen he esul s o he Ma ko clus e algo i hm o g oup p o eins in wo main
biological unc ions: p esen a ion o pep ide an igens o he immune sys em ( ed) and ubiqui ina-
ion, endocy osis, and deg ada ion p ocesses o p o eins ela ed o Fe me abolism in immune cells
(e.g., mac ophages) (g een). The colo s o in e ac ions co espond o: known om cu a ed da abases
(cyan), expe imen ally de e mined (pu ple); p edic ed in e ac ions based on gene neighbo hood
(g een), gene usions ( ed), and gene co-occu ence (da k blue); and o he s, such as ex -mining
(yellow), co-exp ession (black), and p o ein homology (ligh blue). The inpu p o eins we e: CD163,
sca enge ecep o cys eine- ich ype 1 p o ein M130; CP, ce uloplasmin; CYBRD1, cy och ome b
educ ase 1; FTH1, e i in hea y chain; FTL, e i in ligh chain; HAMP, hepcidin; HEPH, hep-
haes in; HMOX1, heme oxygenase 1; IREB2, i on- esponsi e elemen -binding p o ein 2; MB, myo-
globin; SCARA5, sca enge ecep o class A membe 5; SLC11A2, na u al esis ance-associa ed
mac ophage p o ein 2; SLC40A1, solu e ca ie amily 40 membe 1; SLC46A1, p o on-coupled
ola e anspo e ; TF, ans e in; TFRC, ans e in ecep o p o ein 1. The ne wo k is a ailable a
h ps:// e sion-11-0b.s ing-db.o g/cgi/ne wo k?ne wo kId=b1HF4 eAW2N (accessed on 17 June 2021).
Based on he GO anno a ion, he Kyo o Encyclopedia o Genes and Genomes (KEGG)
pa hway analysis, and he P o ein Families (PFAM) P o ein Domains analysis, an en ich-
men analysis o he ne wo k was pe o med (Table 2). Besides Fe anspo and oxido e-
duc ase ac i i y, he GO molecula unc ion showed ha pep ide an igen binding and
an igen pep ide anspo e 1 (TAP binding) a e among he op unc ions o he ne wo k.
Biomedicines 2022,10, 724 17 o 31
The GO cellula componen e ealed ha mos p o eins a e loca ed in he ecycling endo-
some, MHC class I p o ein complex, ea ly endosome, cell su ace, and he HFE- ans e in
ecep o complex. As expec ed, he KEGG pa hway en ichmen analysis showed ha hese
p o eins we e mainly associa ed wi h mine al abso p ion and e op osis; howe e , he
PPIN o p io i ized p o eins o Fe me abolism a e highly in ol ed in pa hways modula ing
he an igen p ocessing and p esen a ion, allog a ejec ion (a consequence o he ecipien ’s
alloimmune esponse o non-sel -an igens exp essed by dono issues), and g a - e sus-
hos disease. In e es ingly, he PFAM analysis showed conse a ion o he immunoglobulin
C1-se domain, he MHC_I C- e minus, and he MHC class I alpha chain, alpha1 alpha2
domains. Fu he mo e, clus e ing he ne wo k wi h a Ma ko algo i hm allowed iden i y-
ing ha se e al p o eins we e g ouped in wo main biological unc ions: (i) p esen a ion
o pep ide an igens o he immune sys em wi h he in ol emen o edox eac ions o Fe,
heme, and Fe a icking/ anspo ; and (ii) ubiqui ina ion, endocy osis and deg ada ion
p ocesses o p o eins ela ed o Fe me abolism in immune cells (e.g., mac ophages).
Table 2. Resul s o he unc ional en ichmen analysis o he PPIN.
Biological P ocess (GO)
GO- e m Desc ip ion FDR p- alue
GO:0055072
i on ion homeos asis 9.58 ×10−31
GO:0006879
cellula i on ion homeos asis 5.91 ×10−30
GO:0006826
i on ion anspo 3.30 ×10−20
GO:0000041
ansi ion me al ion anspo 7.82 ×10−20
GO:0019725
cellula homeos asis 6.48 ×10−16
Molecula Func ion (GO)
GO- e m Desc ip ion FDR p- alue
GO:0005381
i on ion ansmemb ane anspo e ac i i y 5.37 ×10−7
GO:0016722
oxido educ ase ac i i y, oxidizing me al ions 7.59 ×10−7
GO:0042605
pep ide an igen binding 1.94 ×10−6
GO:0004322
e oxidase ac i i y 7.06 ×10−6
GO:0046977
TAP binding 7.06 ×10−6
Cellula Componen (GO)
GO- e m Desc ip ion FDR p- alue
GO:0055037
ecycling endosome 1.41 ×10−10
GO:0042612
MHC class I p o ein complex 3.39 ×10−10
GO:0005769
ea ly endosome 1.94 ×10−8
GO:0009986
cell su ace 2.09 ×10−8
GO:1990712
HFE- ans e in ecep o complex 3.87 ×10−8
KEGG Pa hways
Pa hway ID
Desc ip ion FDR p- alue
hsa04978 mine al abso p ion 1.25 ×10−15
hsa04216 e op osis 1.75 ×10−14
hsa04612 an igen p ocessing and p esen a ion 3.69 ×10−7
hsa05330 allog a ejec ion 1.60 ×10−6
hsa05332 g a - e sus-hos disease 1.60 ×10−6
PFAM P o ein Domains
Domain Desc ip ion FDR p- alue
PF07654 immunoglobulin C1-se domain 1.98 ×10−9
PF06623 MHC_I C- e minus 2.78 ×10−9
PF00129 Class I his ocompa ibili y an igen, domains alpha 1 and 2 2.78 ×10−9
PF00210 e i in-like domain 0.00025
PF07731 mul icoppe oxidase 0.00025
Shown a e p- alues co ec ed o mul iple es ing wi hin each ca ego y using he Benjamini–Hochbe g p ocedu e
( his measu e desc ibes how signi ican he en ichmen is). FDR, alse disco e y a e; GO, gene on ology; HFE,
homeos a ic i on egula o ; KEGG, Kyo o Encyclopedia o Genes and Genome; MHC, majo his ocompa ibili y
complex; PFAM, P o ein Families da abase; TAP, an igen pep ide anspo e 1.
Biomedicines 2022,10, 724 18 o 31
We explo ed he opological ea u es o he ne wo k and anked he nodes based
on cen ali y measu es. Table 3shows he op- anked p o eins wi h HFE, TFRC, be a-2
mic oglobulin (B2M), and SLC11A2 as he nodes wi h highe sco es. A ma ix-like plo
showing pai wise compa isons shows he high co ela ion be ween any combina ion o
selec ed in a-ne wo k opological ea u es (Figu e 6) [61].
Table 3. Iden i ica ion o hub-p o eins based on ne wo k opology.
P o ein
Name
Deg ee
Cen ali y
Be weenness
Cen ali y
Eigen ec o
Cen ali y
Subg aph
Cen ali y
A e age
Sco e †
HFE 22 44.85 1.00 215,209.80 0.831272727
TFRC 20 30.41 0.99 195,055.82 0.9057
B2M 18 38.04 0.78 97,724.47 0.955555556
SLC11A2 18 16.37 0.88 178,173.90 0.852666667
FTH1 16 34.26 0.64 87,931.41 0.872375
HEPH 16 35.32 0.78 140,287.68 0.857
SLC40A1 16 7.12 0.85 159,359.04 0.882625
CP 12 15.58 0.52 54,947.33 0.906166667
HAMP 12 0.33 0.73 111,523.40 0.889166667
CYBRD1 10 0.00 0.55 78,214.76 0.8214
†
All sco es ank om 0 o 1, wi h 1 being he highes possible con idence. A sco e o 0.5 would indica e ha
oughly e e y second in e ac ion migh be e oneous (i.e., a alse posi i e). B2M, be a-2 mic oglobulin; HFE,
homeos a ic i on egula o ; TFRC, ans e in ecep o p o ein 1; HEPH, hephaes in; CP, ce uloplasmin; HAMP,
hepcidin.
Biomedicines 2022, 10, x FOR PEER REVIEW 20 o 35
Table 3. Iden i ica ion o hub-p o eins based on ne wo k opology.
P o ein Name Deg ee Cen ali y Be weenness
Cen ali y
Eigen ec o
Cen ali y
Subg aph
Cen ali y A e age Sco e †
HFE 22 44.85 1.00 215,209.80 0.831272727
TFRC 20 30.41 0.99 195,055.82 0.9057
B2M 18 38.04 0.78 97,724.47 0.955555556
SLC11A2 18 16.37 0.88 178
,
173.90 0.852666667
FTH1 16 34.26 0.64 87,931.41 0.872375
HEPH 16 35.32 0.78 140,287.68 0.857
SLC40A1 16 7.12 0.85 159,359.04 0.882625
CP 12 15.58 0.52 54,947.33 0.906166667
HAMP 12 0.33 0.73 111
,
523.40 0.889166667
CYBRD1 10 0.00 0.55 78,214.76 0.8214
† All sco es ank om 0 o 1, wi h 1 being he highes possible con idence. A sco e o 0.5 would
indica e ha oughly e e y second in e ac ion migh be e oneous (i.e., a alse posi i e). B2M,
be a-2 mic oglobulin; HFE, homeos a ic i on egula o ; TFRC, ans e in ecep o p o ein 1;
HEPH, hephaes in; CP, ce uloplasmin; HAMP, hepcidin.
Figu e 6. Ma ix-like plo showing pai wise co ela ions o he cen ali y sco es. The uppe - igh
pa shows he nume ical co ela ion be ween he gi en opological ea u es, whe eas he lowe -
igh pa o he ma ix is he sca e plo o one ea u e agains ano he . These high co ela ions
be ween cen ali y me ics p o ide use ul insigh s in o he po en ial o di e en nodes wi hin a
ne wo k [147]; pa icula ly, he p esence o highly connec ed nodes is likely o be a ed as cen al
by o he me ics, ep esen ing a pu a i e co e ha o he aims o his s udy migh esul in po en ial
bioma ke s. Figu es we e ob ained om he Ne wo k Analysis P o ile 2.0 [61]. *** S a is ically
signi ican co ela ion (p < 0.001).
Figu e 6.
Ma ix-like plo showing pai wise co ela ions o he cen ali y sco es. The uppe - igh
pa shows he nume ical co ela ion be ween he gi en opological ea u es, whe eas he lowe - igh
pa o he ma ix is he sca e plo o one ea u e agains ano he . These high co ela ions be ween
cen ali y me ics p o ide use ul insigh s in o he po en ial o di e en nodes wi hin a ne wo k [
147
];
pa icula ly, he p esence o highly connec ed nodes is likely o be a ed as cen al by o he me ics,
ep esen ing a pu a i e co e ha o he aims o his s udy migh esul in po en ial bioma ke s.
Figu es we e ob ained om he Ne wo k Analysis P o ile 2.0 [
61
]. *** S a is ically signi ican
co ela ion (p< 0.001).
Biomedicines 2022,10, 724 19 o 31
5.1. E idence-Based Ve i ica ion o he Iden i ied Po en ial Bioma ke s
We highligh ha ou esul s a e meaning ul since almos all he iden i ied po en ial
bioma ke s ag ee wi h a ailable expe imen al e idence and a e cu en ly pa o se e al
immunological/bioma ke s da abases. In con as , he o he s a e eme ging gene ic ma ke s
o di e en s ess condi ions, including exe cise (Table 4). I is accep ed ha ma ke s o Fe
s a us no only de e mine he ca dio espi a o y i ness bu also should be in e p e ed in
he con ex o he indi iduals’ s imuli- esponse p ocess (e.g., compe i ion season, ecen
aining in ensi y, equency, du a ion, in lamma ion s a e, and nu i ional changes) [
148
].
We mus poin o he scien i ic communi y’s cu en consensus ha es ablishes he need
o assess Fe le els, HAMP, o al Fe-binding capaci y, TF sa u a ion, soluble TFRC and
FTH1/FTL ( e i in) o moni o he Fe me abolism- ela ed exe cise-induced physiological
pe u ba ions in ec ea ional and eli e a hle es [41,49,149].
Table 4. Con as ing iden i ied bioma ke s o expe imen ally and manually cu a ed e idence.
P o ein ImmunomeBase IKB Inna eDB
In e ac ions
Bioma ke Base™ Ma ke DB No mal Abno mal Exe cise
CTs Condi ions
HFE Yes 16 19 988 Yes * G/G
C/C
C282Y (A/G, A/A)
H63D (C/G, G/G) FFFFF
TFRC Yes 73
146
849 Yes F †: 1.9–4.4 mg·L−1
M †: 2.2–5 mg·L−1F: >4.4 mg·L−1
M: >5 mg·L−1FFFFF
B2M Yes 188
176
946 Yes 1.21–2.7 µg·mL−1>4 µg·mL−1FF
SLC11A2
No 8 3 338 No 258/258 bp and 258 bp alleles
o e ep esen ed in a hle es FFF
FTH1 Yes 54
886
1176 Yes F: 11–307 µg·L−1
M: 24–336 µg·L−1F: <11 µg·L−1
M: <24 µg·L−1FFFFF
HEPH No - 0 115 No NA NA ?
SLC40A1
No - 9 513 Yes * C/C R178Q (C/T) FFF
CP No 7 53 1020 Yes 200–350 mg·L−1<200 mg·L−1?
HAMP Yes 5
173
669 Yes *
C/C
F: 1–4.1 nM
F ‡: 3.2–8.5 nM
M: 1–7.8 nM
C72Te (C/A, C/T)
>8.5 nM FFFFF
CYBRD1
No 3 0 59 No NA NA ?
ImmunomeBase con ains in o ma ion abou immune- ela ed p o eins and is pa o he Immunome Knowledge
Base (IKB). The IKB does no include p o eins speci ic o he adap i e immune esponse (e.g., immunoglobulins,
T-cell ecep o s, and majo his ocompa ibili y complex). Inna eDB is a da abase ha cap u es an imp o ed
co e age o he inna e immuni y in e ac ome by in eg a ing known in e ac ions and pa hways om majo public
da abases oge he wi h manually cu a ed da a in o a cen alized esou ce. Bioma ke Base
™
is a comme cial
esou ce ha exclusi ely lis s e e y molecula bioma ke in ac i e clinical use, and acks bioma ke usage in
clinical ials (CTs) ac oss di e en condi ions. Ma ke DB is a eely a ailable elec onic da abase ha a emp s o
consolida e in o ma ion on all known clinical, and a selec ed se o p e-clinical, bioma ke s in o a single esou ce.
Li e a u e-based e i ica ion was used o epo he bioma ke use in exe cise. F: emale; M: male; NA: no
a ailable. * Gene ic ma ke ;
†
People o A ican descen and hose esiding a 1600 m abo e sea le el we e ound
o ha e a 6% highe no mal alue ( hese di e ences we e addi i e);
‡
pos -menopausal women (55 yea s o age
and olde ); FF weak e idence; FFF medium e idence; FFFFF s ong e idence; ?no s udied.
HFE was iden i ied as he op biological egula o a e ou ne wo k opology analysis.
The HFE gene encodes his MHC-class I ype memb ane p o ein [
150
]. HFE binds o B2M
and he ex acellula domain o he TFRC o egula e HAMP exp ession and, hus, he
closed link o he immune unc ion and Fe me abolism [
151
]. A high p e alence o wo HFE
mu a ions is p esen in p o essional endu ance a hle es (49.2%) compa ed wi h seden a y
con ols (33.5%): C282Y ( s1800562) and H63D ( s1799945) [
149
]. I has been epo ed ha
subjec s bea ing he H63D polymo phism ha e lowe ca dio ascula i ness and achie e
lowe maximal powe ou pu han a con ol g oup e en in he absence o Fe accumula ion
(no di e ences we e seen in blood FTH1/FTL concen a ions) [
152
]. In iguingly, physical
exe cise wi h inc easing in ensi y o e ime seems o ake a dis inc HAMP pa hway
Biomedicines 2022,10, 724 20 o 31
depending on he modula ing e ec o he HFE geno ype, gi en ha young male H63D
ca ie s no mally p esen highe basal HAMP concen a ions han wild- ype males [153].
I should be no ed ha only 63.6% o ama eu endu ance unne s ha bo ing he H63D
polymo phism ha e shown an inc ease in HAMP le els a e a ma a hon (mean ace ime:
3 h 44 min 35 s) [
154
]. Con e sely, Ko as e al. (2020) demons a ed ha a educ ion in body
Fe s o es migh cons i u e an impo an aspec o he heal h-p omo ing e ec o exe cise,
ega dless o he HFE gene ic backg ound in non-physically ac i e olde women [
155
]. In
a ecen me a-analysis, Semeno a e al. (2020) concluded ha he HFE H63D polymo -
phism is s ongly associa ed wi h eli e endu ance a hle e s a us (associa ion be ween he
HFE G allele and high VO
2max
in male a hle es was epo ed) ega dless o e hnici y and
ca dio espi a o y capaci y [
156
]. Conside ing ha hese wo HFE polymo phisms (C282Y
and H63D) can be used o p edic he isk o he edi a y hemoch oma osis, Thakka e al.
(2021) classi ied a hle es based on low isk o medium/high isk using an algo i hm ha
in eg a ed he HFE geno ype. They epo ed ha indi iduals wi h he medium- o high- isk
geno ype we e ~8% as e and showed a ~17% highe VO
2peak
han hose wi h he low- isk
geno ype [157].
In e es ingly, independen o age, ca ie s o ei he C282Y and/o H63D polymo -
phisms ha e shown a highe load o Fe in he pu amen (a componen o he do sal s ia um
in he b ain), highe TF sa u a ion, and lowe TF and TFRC in blood han non-ca ie s;
u he mo e, he pu aminal Fe le el posi i ely co ela ed wi h cogni i e and mo o unc-
ion [
158
]. Acco ding o he au ho s, HFE s a us is cha ac e ized by highe egional b ain Fe
load ac oss adul hood and is linked o cogni i e and mo o unc ion in heal hy adul s. In
summa y, (i) hese wo single nucleo ide polymo phisms o HFE (C282Y and H63D) can be
combined o ca ego ize indi iduals as ha ing a high, medium, o low isk o Fe o e load;
(ii) while he gene ic isk o i on o e load may ha e a a o able impac on pe o mance, i
is necessa y o a hle es wi h a medium o high isk o a oid Fe supplemen a ion as his
could lead o ad e se heal h ou comes and diminished pe o mance [159].
TFRC and FTH1 (pa o he FTH1/FTL complex o e i in) we e o he impo an
iden i ied p o eins. Al hough TFRC is a memb ane p o ein, a unca ed soluble o m,
known as soluble TFRC, co ela es wi h he cellula exp ession a he memb ane and ises
wi h Fe needs [
14
]. Soluble TFRC is ele a ed in acu e s a es and cons i u es a ma ke o
Fe de iciency in issues a he han a measu e o anemia [
160
]. I is wo h men ioning ha
highly ained (a hle es) [
161
] and un ained [
162
] heal hy indi iduals exhibi inc eased
soluble TRFC le els solely in esponse o high-in ense o maximal exe cise wi h a subse-
quen e u n o baseline du ing he eco e y pe iod. On he o he hand, FTH1/FTL migh
be sligh ly al e ed a e ene gy- o mechanical s ess, including exe cise and nu i ion in e -
en ions [
163
]. Indeed, a ecen me a-analysis has shown ha blood FTH1/FTL inc eases
signi ican ly a e in ensi ied non- esis ance-based aining [
164
]. Since FTH1/FTL ( e i in)
and TF ( ans e in) a e no su icien ly accu a e, as hey a e bo h ele a ed in any anemia
o in lamma ion p ocess [
160
], he e i in index ( a io o soluble TFRC o log e i in) has
been sugges ed as a mo e s able, eliable and sensi i e ma ke [165].
In e es ingly, his index has a lowe mean day- o-day a iabili y and emains s able,
despi e daily changes in FTH1/FTL o soluble TFRC le els; and has also been used o
e alua e he e ec o di e en exe cise aining phases on whole body Fe in endu ance
a hle es [
166
]. Sie a e al. (2019) ha e epo ed ha bo h TF concen a ion and sa u a ion
inc ease immedia ely a e p olonged exe cise-induced s ess (São Paulo In e na ional
Ma a hon) and educe up o 15 days a e ha ; in addi ion, he au ho s ound ha he
ACTN3 R577X polymo phism migh pa ially explain he di e en hema ological esponses
in endu ance a hle es gi en ha indi iduals bea ing he RR geno ype seem o be mo e
suscep ible o hemoly ic anemia and hema u ia [
167
]. This highligh s he ele ance o
moni o ing Fe supplemen a ion and enal unc ion e alua ion on a geno ype-dependen
basis, as men ioned p e iously.
We also ound HAMP wi hin he lis o iden i ied po en ial bioma ke s, which ag ees
wi h cu en p ac ice o moni o a hle es [
168
]. Besides inc easing FTH1/FTL, augmen-
Biomedicines 2022,10, 724 21 o 31
a ion in HAMP le els has been epo ed a e se en days o high- aining load in eli e
male owe s [
166
]. As men ioned p e iously, HAMP inc eases in esponse o in lamma-
ion [
169
,
170
] and is an impo an egula o o Fe s a us in se e al physiological condi ions
(e.g., hemolysis, hema u ia, and in es inal bleeding) [
170
,
171
]. HAMP concen a ions a e
no mally exp essed in nanomoles pe li e (1 nM se um HAMP equals 2.79
µ
g
·
L
−1
) [
172
].
I should be no ed ha an inc ease in IL-6 le els has been linked o he enhanced exp ession
o HAMP in he li e [
129
]. Expe imen al e idence in animal models has demons a ed
inc eases in plasma IL-6 concen a ion, which co ela ed wi h li e exp ession o he IL-6
alpha ecep o (IL6R) and supp esso o cy okine signaling 3 (SOCS3) a e in ense exe -
cise [
173
]. Simila ly, Liu e al. [
174
] epo ed exe cise-induced anemia in a s and ound
IL-6 concen a ions induced hepa ic HAMP exp ession. These signi ican inc eases in IL-6
and HAMP ha e been demons a ed in young emales a e acu e exe cise bou s (60 and
120 min a 65% o VO
2max
) [
175
], al hough Fe le els seem no o be a ec ed a e a pe iod
(un il ou weeks) o high load in young a hle es [
166
]. I mus be highligh ed ha H63D
HFE gene polymo phism has a modula ing impac on HAMP sec e ion [153].
Two o he iden i ied po en ial bioma ke s ha e eme ged. SLC11A2 (DMT1) and
SLC40A1 ( e opo in) ha e been s udied as po en ial molecula egula o s o neu oin lam-
ma ion [
176
] and exe cise-induced changes in Fe s a us [
177
]. Fo example, in lamma ion in
aging and neu odegene a i e pheno ypes is associa ed wi h Fe accumula ion in he cen al
ne ous sys em h ough he al e ed exp essions o SLC11A2, SLC40A1, and HAMP [
178
].
Neu oin lamma ion has led o o e exp ession o SLC11A2 in neu ons, as ocy es, and
mic oglia and a pa allel educ ion in SLC40A1 exp ession [
176
]. Choi e al. (2021) showed
ha eadmill exe cise educed in acellula Fe accumula ion, p obably by dec easing TF,
TFRC, and SLC11A2 (lowe Fe anspo in o cells) while inc easing SLC40A1 exp ession
(Fe- eleasing p o ein) in he mo o co ex o aging Alzheime ’s disease mice [179].
Fu he mo e, while no changes we e seen in he seden a y and he s enuously exe -
cised g oups, i seems ha mode a e-in ensi y exe cise in heal hy animal models inc eases
he exp ession o SLC11A2 wi h IRE and SLC40A1, bu down- egula es HAMP, which
migh ha e imp o ed Fe duodenal eabso p ion (highe Fe s a us) [
180
]. Con a iwise,
s enuously exe cised a s ha e shown unde -exp ession o duodenal SLC11A2, heme-
ca ie p o ein 1, and SLC40A1, which may pa ially explain he educed Fe abso p ion
s ess-associa ed s ess anemia a e in ensi e exe cise [
174
]. In e es ingly, ecen esea ch
pe o med by Wuyun e al. (2021) ound ha a SLC11A2 258/258 bp homozygous geno ype
and 258 bp alleles a e o e ep esen ed in eli e Chinese long-dis ance unne s and concluded
ha his migh be conside ed a gene ic ma ke due o a signi ican associa ion wi h ca -
dio espi a o y i ness [
181
]. A p e ious gene ics case s udy has also associa ed a mu a ion
in SLC11A2 wi h a sligh inc ease in se um Fe le el in se e e anemia and he hepa ic Fe o e -
load pheno ype [
182
]. In addi ion, he SLC40A1 R178Q mu a ion ( s1449300685), among
o he a ian s [
183
], has ecen ly been shown o a ec he HAMP-SLC40A1 in e ac ion,
which migh con ibu e o he spec um o Fe o e load [
184
,
185
]. The e o e, he di e en
magni ude and di ec ion in he exp ession o SLC11A2 and SLC40A1 migh depend on he
allos a ic load o he biological sys em and he basal immune unc ion (e.g., gene ics—see
Figu e 1), bu u he esea ch is wa an ed o es ablish accu a e mechanisms.
Fu u e s udies migh e alua e he alidi y and sensi i i y o o he iden i ied p o eins
ha a e less moni o ed bioma ke s in he exe cise and spo s ields, such as B2M, HEPH,
and CP. Se um le els o B2M a e no mally ele a ed in human immunode iciency i us
in ec ion and acqui ed immunode iciency synd ome, heuma oid a h i is, and hema o-
logic malignancies—which possibly e a d he gene a ion o monocy e-de i ed dend i ic
cells and migh be in ol ed in he down- egula ion o majo his ocompa ibili y complex
class I molecules, inac i a ion o Ra /MEK/ERK cascade and NF-
κ
B, and ac i a ion o
STAT3 [
186
]. Exe cise in young hype ensi e pa ien s p oduced a dec ease in B2M, al-
hough no changes we e seen in heal hy con ol indi iduals [
187
], which migh con ibu e
o he heal h bene i s ha ha e been seen a e a mode a e-in ensi y exe cise p og am in
hype ensi e pos menopausal women [
188
]. B2M has been desc ibed as a conse a i e mul-
Biomedicines 2022,10, 724 22 o 31
i unc ional egula o o immune su eillance and modula ion o immune unc ion [
189
].
B2M has no only been epo ed as a classic ma ke o assess kidney unc ion [
190
] bu also
as an eme ging sc eening ool in se e al non- enal diseases, such as pe iphe al a e ial dis-
ease [191], cance [192], and aging- ela ed oxida i e s ess [193]. Bo h plasma and u ina y
B2M le els may be eliably and cos -e ec i ely measu ed [
194
]. Al hough i has also been
used as a housekeeping o e e ence gene in exe cise and nu i ion in e en ions [
195
,
196
],
esea che s should conside ha B2M migh be unsui able o some condi ions [
197
,
198
]. I
has been demons a ed ha educ ion in he in es inal HEPH and CP- e oxidase ac i i y
may impai Fe abso p ion and Fe elease om in acellula s o es, espec i ely, which
dec eases Fe le els and esul s in dis u bances o Fe deli e y in he bone ma ow o suppo
e y h opoiesis [
199
]. In he absence o HEPH, he e is anemia, possibly due o Fe malab-
so p ion o he sys emic ci cula ion [
69
]. In addi ion, down egula ion o HEPH exp ession
has been ound du ing he ex ahepa ic [
200
] and in ahepa ic [
201
] acu e-phase esponse
in immunosupp essan -induced animal models. Impo an ly, simila o ou esul s, a ecen
bioin o ma ics analysis based on mRNA exp ession da a indica ed HEPH as a po en ial
no el p ognos ic bioma ke o lung cance pa hologies [
202
]. Mo e esea ch is necessa y
o e alua e hese ma ke s.
5.2. Limi a ions, S eng hs, and Fu u e Di ec ions
The esul s o his s udy should be discussed in ligh o he ollowing limi a ions and
s eng hs. Fi s ly, da abases o e iewing li e a u e we e es ic ed o PubMed, ScienceDi-
ec , and Google Schola . Secondly, he bioin o ma ics-assis ed e iew is based on he FAIR
guiding p inciples [
203
] and, he eby, akes ad an age o (i) he scien i ic soundness o
manual cu a ion, and (ii) he use o simple, eely accessible, and cu a ed bioin o ma ics
ools o enhance c oss- e e encing, en ich he biological in e p e a ion and anno a ion o
molecula en i ies. A bioin o ma ics-assis ed app oach o e iewing li e a u e exceeds
human-based o machine-based indi idual me hods in e ms o e ec i eness due o a e-
ined e ie al and cu a ion p ocess. Thi dly, i should be conside ed ha he bioin o ma ics
en ichmen analysis and he conclusions om non-clinical esea ch should be in e p e ed
wi h cau ion, gi en ha hey migh no ully e lec adap i e esponses in humans du -
ing changes in immune unc ion a e a gi en s ess esponse. Fou hly, we ha e used a
mechanis ic-based app oach o e alua e cellula and sys emic changes in Fe me abolism.
Howe e , expe imen al esea ch is s ill needed o be e comp ehend he molecula and
cellula mechanisms ha migh link he bidi ec ional al e a ions in Fe me abolism and
immune sys em. Fi hly, we limi ed ou discussions o exe cise as a model example o
s ess-induced changes in immune unc ion and, he eby, in i e eade s and esea che s
o explo e o he pheno ypes, such as cance [
204
], neu oin lamma o y diseases [
205
], and
in ec ions [
138
,
206
], among o he s. Finally, we mus highligh he high pe o mance o ou
bioin o ma ics-assis ed app oach o iden i y po en ial molecula and gene ic bioma ke s
based on molecula p io i iza ion, en ichmen , and ne wo k opology analysis. This has
been success ully implemen ed o iden i y p o eins/genes ha migh ha e impo an bio-
logical unc ions [
207
] and bioma ke s [
208
,
209
]. Ou e idence-based e i ica ion closely
ma ched ou iden i ied biological ma ke s; none heless, we a e awa e ha mo e esea ch
is needed o alida e he p oposed bioma ke s in di e en s ages du ing he acu e and
ch onic in lamma o y esponse and how his may a ec human adap a ion p ocesses.
We expec ha his s udy’s esul s migh con ibu e o hypo hesis gene a ion o
subsequen esea ch o deciphe he mechanisms ha link se e al Fe me abolism- ela ed
genes/p o eins and he immune esponse in se e al pheno ypes. Resea che s should
ake ad an age o he di e en we - and d y-based immunosupp ession models o s udy:
(i) he no el indings ega ding he in ahepa ic acu e-phase esponse-like eac ion and Fe
o e load [
201
]; (ii) he la ge in e -indi idual a iabili y in bioma ke esponses ha migh
esul om gene ic-de i ed indi idual esponses, such as he a ian s in HFE,SLC11A2,
SLC40A1 and HAMP; (iii) sex-based di e ences, gi en ha p e-clinical esea ch has shown,
o example, highe le els o e opo in p o ein o educ ion o hepa ic HAMP mRNA in
Biomedicines 2022,10, 724 23 o 31
he li e , spleen, and kidney in males han in emales [
210
]— o a ecen and comp ehensi e
e iew o he cu en knowledge in ega ds o Fe s a us and Fe supplemen a ion o he
emale a hle e, please e e o [
211
,
212
]); (i ) al i ude-based di e ences, i s e ec s on Fe
egula ion and he impac on he immune unc ion [
213
]; ( ) he po en ial o compu a ional
p edic ion by PPI mapping o help de e mine a ge p o eins/genes conside ing ha he
unc ional s udy o bioma ke s is a ime- and cos -consuming p ocess [
214
], especially
unde he immunoin o ma ics pa adigm which opens a new doo in o he s udy o he
immune esponse in di e en biological con ex s [215].
6. Conclusions
Fe is an impo an mic onu ien ha may cons i u e a double-edged swo d since he
wo ex emes o nu i ional s a us (i.e., Fe de iciency o o e load) ha e ha m ul e ec s
on inna e and acqui ed immuni y. Thus, Fe is highly egula ed a di e en cell le els,
including memb ane (e.g., p o ein/solu e ca ie s and lysoendosomal a icking), cy oso-
lic (e.g., FTL/FTH1 complex, Fe-chape ones), ansc ip ional, and pos - ansc ip ional
(i.e., IREB/IRE sys em) le els. Fu he mo e, la ge di e ences in in acellula and ex acel-
lula Fe le els may a ec he immune esponse; in ac , eme ging e idence also e e s o
c i ical pheno ypes based on in ahepa ic o ex ahepa ic concen a ions o Fe me abolism-
ela ed p o eins. In his sense, ou bioin o ma ics- and ne wo k opology-based analysis
iden i ied po en ial molecula bioma ke s ela ed o he close link be ween Fe me abolism
and immune unc ion. In de ail, he g aph-based Ma ko algo i hm g ouped se e al p i-
o i ized p o eins in wo main clus e s: (i) p esen a ion o pep ide an igens o he immune
sys em wi h he in ol emen o edox eac ions o Fe, heme, and Fe a icking/ anspo ;
and (ii) ubiqui ina ion, endocy osis, and deg ada ion p ocesses o p o eins ela ed o Fe
me abolism in immune cells (e.g., mac ophages).
Impo an ly, he no el y o he app oach and ou esul s we e meaning ul since he
iden i ied po en ial bioma ke s we e in ag eemen wi h he cu en expe imen al e idence,
belong o se e al immunological/bioma ke s da abases, and/o a e eme ging gene ic
ma ke s o di e en s ess ul condi ions. This highligh s he high e iciency o human-
machine collabo a ion, using human-gene a ed eedback o imp o e compu e esul s.
Besides he esponse o exe cise, he e alua ion o molecula mechanisms and he clinical
implica ions o Fe le el (de iciency o o e load) a e impo an esea ch a eas o he design
and implemen a ion o nu i ion- o exe cise-based immunomodula o y in e en ions in
di e en con ex s (e.g., obesi y, cance , neu oin lamma o y diseases, in ec ions). The e is no
doub ha he iden i ied bioma ke s dese e u he esea ch o con i m e ec s and de i e
clinical ecommenda ions; hus, we encou age esea che s o use he in o ma ion con ained
in his s udy and adop a mo e in ui i e, in eg a i e, and allos a ic iew based on complex
sys ems, ne wo k analysis, and he e e -changing and adap i e esponses o biological
o ganisms (a ‘Bio-Logic’ app oach).
Au ho Con ibu ions:
Concep ualiza ion, D.A.B.; o mal analysis, D.A.B.; w i ing—o iginal d a
p epa a ion and igu es, D.A.B.; w i ing— edi ing, Y.M. and J.L.P.; w i ing— c i ical e iew, D.A.F.,
S.V.-M., A.O.-M., C.A.O., J.R.S., E.S.R. and R.B.K. All au ho s ha e ead and ag eed o he published
e sion o he manusc ip .
Funding:
The ‘Bioin o ma ics-assis ed Re iew’ is a p ojec de eloped and suppo ed by he Resea ch
Di ision a he Dynamical Business and Science Socie y—DBSS In e na ional SAS. The APC was
unded by he Exe cise & Spo Nu i ion Labo a o y (ESNL) a Texas A&M Uni e si y, he POWER
LAB a Uni e si y o Cen al Flo ida and he Spo Genomics Resea ch G oup a Uni e si y o he
Basque Coun y UPV/EHU.
Ins i u ional Re iew Boa d S a emen : No applicable.
In o med Consen S a emen : No applicable.
Da a A ailabili y S a emen :
The da a suppo ing his e iew a e om p e iously epo ed s udies
and da ase s, which ha e been ci ed.
Biomedicines 2022,10, 724 24 o 31
Con lic s o In e es :
D.A.B. se es as a Science P oduc Manage o a company p oducing die a y
supplemen s in Eu ope (MTX Co po a ion
®
) ha sells i on-based p oduc s and has ac ed as scien i ic
consul an o MET-Rx and Heal hy Spo s in Colombia. D.A.F. has been p e iously suppo ed by
g an s om MinCiencias bu no ela ed o i on. J.R.S. has conduc ed indus y-sponso ed esea ch on
nu aceu icals o e he pas 25 yea s. J.R.S has also ecei ed inancial suppo o p esen ing on he
science o a ious nu aceu icals a indus y-sponso ed scien i ic con e ences. E.S.R. has conduc ed
indus y-sponso ed esea ch and ecei ed inancial suppo o p esen ing on nu ien s a indus y-
sponso ed scien i ic con e ences. R.B.K. has conduc ed a numbe o indus y-sponso ed s udies on
spo s-nu i ion- ela ed nu ien s, has se ed as a paid consul an and has ecei ed hono a iums
o speak a con e ences by indus y. Addi ionally, R.B.K. se es as chai o he “C ea ine in Heal h”
scien i ic ad iso y boa d o Alzchem G oup AG, while D.A.B., J.R.S. and E.S.R. se e as membe s
o his boa d. The ins i u ions conce ning he nu ien s e iewed had no ole in he collec ion,
in e p e a ion o da a, w i ing o he manusc ip , o in he decision o publish he esul s. The o he
au ho s epo ed no po en ial con lic o in e es ele an o his a icle.
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