WJG h ps://www.wjgne .com 1Janua y 21, 2025 Volume 31 Issue 3
Wo ld Jou nal o
Gas oen e ology
W J G
Submi a Manusc ip : h ps://www. 6publishing.com Wo ld J Gas oen e ol 2025 Janua y 21; 31(3): 95207
DOI: 10.3748/wjg. 31.i3.95207 ISSN 1007-9327 (p in ) ISSN 2219-2840 (online)
ORIGINAL ARTICLE
Basic S udy
In silico analysis o lncRNA-miRNA-mRNA signa u es ela ed o
So a enib e ec i eness in li e cance cells
Pa icia de la C uz-Ojeda, Es e Pa as-Ma ínez, Raquel Rey-Pé ez, Jo di Mun ané
Special y ype: Gas oen e ology
and hepa ology
P o enance and pee e iew:
Unsolici ed a icle; Ex e nally pee
e iewed.
Pee - e iew model: Single blind
Pee - e iew epo ’s classi ica ion
Scien i ic Quali y: G ade C
No el y: G ade B
C ea i i y o Inno a ion: G ade B
Scien i ic Signi icance: G ade B
P-Re iewe : Wang W
Recei ed: Ap il 4, 2024
Re ised: Augus 30, 2024
Accep ed: Sep embe 12, 2024
Published online: Janua y 21, 2025
P ocessing ime: 259 Days and 20.4
Hou s
Pa icia de la C uz-Ojeda, Func ional Genomics o Solid Tumo s Labo a o y, Cen e de Reche -
che des Co delie s, Pa is 75006, F ance
Pa icia de la C uz-Ojeda, Es e Pa as-Ma ínez, Raquel Rey-Pé ez, Jo di Mun ané, Depa men o
Oncology Su ge y, Cell The apy and O gan T ansplan a ion, Ins i u e o Biomedicine o
Se ille, Vi gen del Rocio Uni e si y Hospi al, Se ille 41013, Spain
Pa icia de la C uz-Ojeda, Jo di Mun ané, Biomedical Resea ch Cen e o Hepa ic and Diges i e
Diseases, CIBERehd, Mad id 28029, Spain
Jo di Mun ané, Depa men o Medical Physiology and Biophysics, Uni e si y o Se ille,
Se ille 41009, Spain
Co esponding au ho : Jo di Mun ané, PhD, Depa men o Oncology Su ge y, Cell The apy
and O gan T ansplan a ion, Ins i u e o Biomedicine o Se ille, Vi gen del Rocio Uni e si y
Hospi al, A n. Manuel Siu o S/N, Se ille 41013, Spain. [email p o ec ed]
Abs ac
BACKGROUND
Hepa ocellula ca cinoma (HCC) is he mos common sub ype o p ima y li e
cance wi h a ied incidence and epidemiology wo ldwide. So a enib is s ill a
ecommended ea men o a la ge p opo ion o pa ien s wi h ad anced HCC.
Di e en pa e ns o ea men esponsi eness ha e been iden i ied in di e en-
ia ed hepa oblas oma HepG2 cells and me as a ic HCC SNU449 cells.
AIM
To de ine he long non-codingRNA-mic oRNA-mRNA (lncRNA-miRNA-mRNA)
p edic ed signa u es ela ed o selec ed hallma ks o cance (apop osis, au o-
phagy, cell s ess, cell dedi e en ia ion and in asi eness) in RNAseq s udies
using So a enib- ea ed HepG2 and SNU449 cells. Va ious a ailable so wa e
analyses allowed us o es ablish he lncRNA-miRNA-mRNA egula o y axes
ollowing ea men in HepG2 and SNU449 cells.
METHODS
HepG2 and SNU449 cells we e ea ed wi h So a enib (10 μmol/L) o 24 hou s.
To al RNA, including small and long RNA, was ex ac ed wi h a comme cial
miRNeasy ki . RNAseq was ca ied ou o he iden i ica ion o changes in
lncRNA-miRNA-mRNA egula o y axes.
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 2Janua y 21, 2025 Volume 31 Issue 3
RESULTS
MALAT, THAP9-AS1 and SNGH17 appea ed o coo dina ely egula e miR-374b-3p and miR-769-5p ha led o
up egula ion o SMAD7, TIRARP, TFAP4 and FAXDC2 in HepG2 cells. SNHG12, EPB41 L4A-AS1, LINC01578,
SNHG12 and GAS5 in e ac ed wi h le -7b-3p, miR-195-5p and VEGFA in SNU449 cells. The axes MALAT1/hsa-
mi -374b-3p/SMAD7 and MALAT1/hsa-mi -769-5p/TFAP4 we e o high ele ance o So a enib esponse in
HepG2 cells, whe eas PVT1/hsa-miR-195-5p/VEGFA was esponsible o he di e en ial esponse o SNU449 cells
o So a enib ea men .
CONCLUSION
C i ical lncRNAs ac ing as sponges o miRNA we e iden i ied ha egula ed mRNA exp ession, whose p o eins
mainly inc eased he an i umo e ec i eness o he ea men (SMAD7, TIRARP, TFAP4, FAXDC2 and ADRB2).
Howe e , he b oad egula o y axis leading o inc eased VEGFA exp ession may be ela ed o he side e ec o
So a enib in SNU449 cells.
Key Wo ds: Cell cul u e; Hepa ocellula ca cinoma; Non-coding RNA; RNAseq; So a enib
©The Au ho (s) 2025. Published by Baishideng Publishing G oup Inc. All igh s ese ed.
Co e Tip: In he cu en s udy, we in es iga ed he di e en ial lncRNA-miRNA-mRNA egula o y axes in HepG2 and
SNU449 unde So a enib ea men . The s udy iden i ied lncRNA-miRNA egula o y axes leading o inc eased exp ession
mRNA wi h posi i e (SMAD7, TIRARP, TFAP4, FAXDC2 and ADRB2) and nega i e (VEGFA) he apeu ic e ec s in HepG2
and SNU449 unde So a enib ea men .
Ci a ion: de la C uz-Ojeda P, Pa as-Ma ínez E, Rey-Pé ez R, Mun ané J. In silico analysis o lncRNA-miRNA-mRNA signa u es
ela ed o So a enib e ec i eness in li e cance cells. Wo ld J Gas oen e ol 2025; 31(3): 95207
URL: h ps://www.wjgne .com/1007-9327/ ull/ 31/i3/95207.h m
DOI: h ps://dx.doi.o g/10.3748/wjg. 31.i3.95207
INTRODUCTION
Hepa ocellula ca cinoma (HCC) is he mos common ype o p ima y li e cance , accoun ing o 75%-86% o cases[1].
The impac o isk ac o s on HCC has a a iable geog aphic dis ibu ion, including hepa i is C i us and hepa i is B i us
in ec ion, alcohol, a la oxin B1, me abolic-associa ed a y li e disease (MAFLD), obacco and congeni al diseases.
Fu he mo e, only one hi d o HCC pa ien s a e diagnosed a he ini ial s ages suscep ible o ecei ing cu a i e
ea men , he emaining pa ien s a e a in e media e/ad anced s age wi h poo p ognosis and a 5-yea su i al a e
below 10%[2]. The Ba celona Clinic Li e Cance classi ica ion conside s he numbe and size o umo nodules, li e
unc ion, gene al condi ion o he pa ien and he p esence o ascula in asi eness and me as ases[3]. Acco ding o his
classi ica ion, HCC s age C includes pa ien s wi h p ese ed li e unc ion bu wi h ascula in asion and/o he
p esence o ex ahepa ic nodules. The landscape o ea men s o ad anced s age HCC has been changing due o he
app o al o A ezolizumab-Be acizumab and Du alumab-T emelimumab as i s -line he apies, ex ending he median
su i al up o 19.2 mon hs[3]. Howe e , pa ien s wi hou p ese ed li e unc ion, a high- isk o bleeding, ascula
diso de s, and a e ial hype ension, as well as se e e au oimmune diso de s and p io ansplan a ion a e no
ecommended o ecei e immune checkpoin and an iangiogenic ea men s[3]. Fu he mo e, subg oup analysis o
se e al phase III clinical ials sugges s ha So a enib ends o be mo e e ec i e han immune checkpoin inhibi o -based
he apy in pa ien s wi h non- i al e iologies (alcohol, MAFLD o unknown)[4].
So a enib is an o ally adminis e ed mul i y osine kinase inhibi o app o ed by he FDA o he ea men o HCC in
2008[5,6]. I a ge s se e al p oli e a ion ecep o s such as ascula endo helial g ow h ac o (VEGFR)-1, VEGFR-2,
VEGFR-3, pla ele -de i ed g ow h ac o ecep o (PDGFR)-β, c-KIT, FLT-3 and RET. Fu he mo e, i also inhibi s
downs eam kinases wi h se ine/ h eonine phospho yla ing ac i i y[7-11]. So a enib induces ea ly endoplasmic
e iculum s ess wi h ac i a ion o he JNK/AMPK/au ophagy-dependen pa hway ha leads o a swi ch owa ds
apop o ic cell dea h in HepG2 cells[7]. Gi en ha So a enib exe s a g ea e p oapop o ic ac i i y in HepG2 cells han in
SNU449 cells[12], a link be ween ea men esis ance p ocesses and induc ion o he epi helial-mesenchymal ansi ion
(EMT) p ocess has also been demons a ed. In his ega d, SNU449, HLF and HLE li e cance cell lines exp essing
mesenchymal ma ke s (CD44, Vimen in and Snail) a e e ac o y o So a enib ea men compa ed o HepG2, Hep3B and
PLC/PRF/5, which exp ess epi helial ma ke s (E-cadhe in and CK-18)[13]. So a enib esis ance migh also in ol e
o e exp ession o ATP-binding box (ABC) anspo e s ha expo d ugs and educe he e icacy o ea men [14].
The human genome is made up o 70% in e genic egions, while genes accoun o only 30%. Among non-coding
RNAs (ncRNAs), mic oRNAs (miRNAs), long non-coding RNAs (lncRNAs) and ci cula RNAs (ci cRNAs) ha e been
ela ed o he ini ia ion, p og ession and me as asis o HCC[15]. In b oad e ms, miRNAs a e a ype o ncRNAs, 22
nucleo ides in leng h, which bind o he complemen a y sequence o he mRNA and induce i s deg ada ion media ed by
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 3Janua y 21, 2025 Volume 31 Issue 3
he RNA-Induced Silencing Complex. Al hough se e al miRNA signa u es ha e been associa ed wi h he diagnosis o
HCC, ew models ha e assessed he isk associa ed wi h ea men e ec i eness[16,17]. We ha e ecen ly iden i ied miR-
200c-3p, miR-222-5p, and miR-512-3p as p ognos ic miRNA ma ke s in pa ien s unde So a enib ea men [18]. On he
o he hand, lncRNAs and ci cRNAs a e mo e han 200 nucleo ides long; howe e , lncRNAs a e linea , while ci cRNAs
a e ing-shaped. Bo h can be ansc ibed om exons, in ons, in e genic egions o 5′/3′ non- ansla ional egions and
olded in o complica ed second s uc u es, acili a ing hei in e ac ions wi h DNA, RNA, and p o eins. lncRNAs ha e
been implica ed in he egula ion o ansc ip ional ac i i y, and hey a e speci ically exp essed in cells in esponse o
nume ous s imuli and se e as molecula signals[19]. They can also ac as sca olds, cen al pla o ms on which he
ele an molecula componen s will be assembled[20].
Gi en ha So a enib exe s a g ea e p oapop o ic ac i i y in HepG2 cells han in SNU449 cells[12], he p esen s udy
aimed o de e mine a ea men -associa ed lncRNA p o ile di ec ly co ela ed o di e en ial signa u es o lncRNAs-
miRNA-mRNAs ela ed o apop osis, au ophagy, endoplasmic e iculum s ess, di e en ia ion, and me as asis in RNA-
seq da a ob ained om So a enib- ea ed HepG2 and SNU449 cells.
MATERIALS AND METHODS
Cell cul u e
The s udy in ol ed he di e en ia ed hepa oblas oma cell line HepG2 (HB-8065™, ATCC-LGC S anda ds, S.L.U.,
Ba celona, Spain) and he me as a ic HCC SNU449 cell line (CRL-2234 HB-8065™, ATCC-LGC S anda ds). Cells we e
cul u ed in MEM con aining Ea le's sal s wi h L-glu amine and 10% FBS (F7524, lo BCBX9154, Me ck-Sigma, S . Louis,
MO, Uni ed S a es), sodium py u a e (1 mmol/L) (Re . 11360070, The mo Fishe Scien i ic, Wal ham, MA, Uni ed S a es),
non-essen ial amino acids (Re . 11140035, The mo Fishe Scien i ic), penicillin-s ep omycin solu ion (100 U/mL-100 μg/
mL) (Re . 15640055, The mo Fishe Scien i ic) a 37 °C, 21% O2 and 5% CO2. Cells we e pla ed a 100000 cells/cm2, and
a e 24 hou s o s abiliza ion So a enib (10 μM) (FS10808, Ca bosyn h, Uni ed Kingdom) was added. Cells we e
ha es ed a 6 and 24 hou s a e So a enib ea men . So a enib dose, ea men imes and esponse we e pe o med as
op imized in he s udy by Rod íguez-He nández e al[7].
RNA-seq
To al RNA, including small and long RNA, was ex ac ed wi h he miRNeasy ki (Re . 217004, Qiagen, Hilden, Ge many).
Lysis was pe o med wi h Qiazol and he RNA ac ion was bound o he RNeasy mini spin column, washed, and elu ed
in RNase- ee wa e . The DNA was emo ed by DNase I diges ion. RNA was hen quan i ied using he NanoD op™
One/OneC mic o olume UV-Vis UV-Vis spec opho ome e (The mo Fishe Scien i ic). RNA was quan i ied using he
RNA Qubi ™ HS assay (Q32852, The mo Fishe Scien i ic), and he quali y was assessed wi h he Bioanalyze ® 2100
Euka yo e To al RNA Nano Chip (Agilen Technologies, San a Cla a, CA, Uni ed S a es). All samples had an RNA
In eg i y Numbe ≥ 8.8. To al RNA lib a ies we e p epa ed wi h he Illumina S anded To al RNA P ep Liga ion wi h
Ribo-Ze o™ Plus ki (Re . 20040529, Illumina Inc., San Diego, CA, Uni ed S a es). B ie ly, RNA was deple ed and he
o al ansc ip ome was agmen ed. cDNA was syn hesized, adap e s and dual indices we e joined and hen he lib a y
was ampli ied. The lib a ies we e hen quan i ied wi h he Qubi ™ DNA HS assay and he quali y was analyzed wi h he
highly sensi i e Bioanalyze ® 2100 DNA chip (Agilen Technologies). The size o he o al RNA lib a ies was 260-280 bp.
They we e pooled a 2.4 nM, dena u ed and dilu ed o 1.2 nM. PhiX was used as an in e nal quali y con ol. Pai ed-end
sequencing (75 cycles) was pe o med in S1 low cells on a No aSEq 6000 ins umen (Illumina. Inc.).
Analysis o RNA-seq da a
Long RNA-seq da a analysis: P ima y analysis o RNA sequencing da a, including quali y es ing, imming and
demul iplexing, was conduc ed using he Illumina DRAGEN FASTQ Gene a ion .3.8.4 app o BaseSpace. Nex ,
alignmen o he human genome e sion GRCh38 was pe o med wi h he RNA-Seq Alignmen ool .2.02, using he
STAR aligne . Di e en ial exp ession analysis (DEA) was ca ied ou wi h he DRAGEN Di e en ial Exp ession app
.3.9.0 by unning he DESeq2 algo i hm[21]. BioMa da a mining ool (Ensembl)[22] was used o de e mine gene ype.
Gene On ology (GO) e ms and Kyo o Encyclopedia o Genes and Genomes (KEGG) pa hways anno a ion and
en ichmen o p o ein coding genes was pe o med wi h Da abase o Anno a ion, Visualiza ion and In eg a ed
Disco e y (DAVID) 6.8. Gene Se En ichmen Analysis (GSEA) was ca ied ou wi h he Hallma k and GO Biological
P ocess gene se s[23,24].
Small RNA-seq da a analysis: P ima y analysis o small RNA sequencing da a, including quali y es ing, imming and
demul iplexing, was conduc ed using he Illumina DRAGEN FASTQ Gene a ion .3.8.4 app o BaseSpace. Nex , he
adap o sequence was elimina ed, and da a we e il e ed by size o 23 bp, aking in o accoun a minimum size inse o 15
bp. Also, eadings we e cu i s and las 4 nucleo ides, ollowing he manu ac u e ’s ins uc ions. Mapping and
alignmen o he human genome e sion GRCh38 using bow ie aligne was pe o med in Galaxy RNA[25] en i onmen
wi h he miRDeep Mappe ool[26]. Quan i a ion o eads mapping o known miRBase hai pin miRNA p ecu so and
ma u e miRNA sequences was done wi h he miRDeep Quan i ie ool[26]. Finally, DEA was pe o med wi h R S udio
using he DSeq2 package.
Hea maps we e cons uc ed using R S udio wi h ComplexHea map, i idis and dply packages. GO e ms and KEGG
pa hways en ichmen analysis was pe o med wi h he DAVID online ool[27] using all genes wi h coun s > 0 as
backg ound. Biological connec ions among selec ed a ge s we e es ima ed using Sea ch Tool o he Re ie al o
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 4Janua y 21, 2025 Volume 31 Issue 3
In e ac ing Genes/P o eins (STRING)[28]. STRING analysis was pe o med wi h medium con idence (in e ac ion sco e
0.4). Valida ion o p oposed in e ac ing ne wo ks based on umo and non- umo li e issue exp ession da a was
pe o med using GEPIA using he Co ela ion ool (Pea son me hod)[29].
In silico es ablishmen o lncRNA-miRNA-mRNA egula o y axis
lncRNA as a sponge o miRNAs: mRNAs o ele ance in So a enib esponse we e selec ed among GSEA GO Biological
P ocess e ms ela ed o apop osis, au ophagy, endoplasmic e iculum s ess, di e en ia ion, and me as asis (including
de elopmen and angiogenesis ela ed e ms). Mode a ely and highly exp essed mRNAs in ele an signi ican ly
en iched GO e ms in GSEA wi h log2FC > 1 o log2FC < -1 and P-adj < 0.05 we e used as candida es o miRNA
egula ion. miRNAs ha could a ge hese candida es we e p edic ed wi h he miRDB da abase, wi h a cu -o o Ta ge
Sco e ≥ 80. F om his miRNA lis , we selec ed hose ha we e down- o up- egula ed acco dingly in ou s udy. Then,
miRNA-lncRNA in e ac ions we e p edic ed wi h DIANA-LncBase 3 (DIANA ools)[30,31]. lncRNAs signi ican ly up-
egula ed in ou s udy we e used o u he analysis.
lncRNA-mRNA in e ac ions o egula e s abili y: mRNAs p e iously selec ed o be egula ed by miRNAs we e used o
es possible in e ac ions wi h egula o y lncRNAs in ou s udy as desc ibed abo e. LncRRI sea ch web se e was used
o es in e ac ions wi h an ene gy h eshold o -12Kcal/mol[32], using speci ic ansc ip s.
lncRNA-p o ein in e ac ions: Finally, o iden i y lncRNA in e ac ions wi h p o eins whose mRNA is egula ed in ou
s udy we used he RNAc ool[33], using bo h p edic ed and expe imen ally con i med a ge s.
RESULTS
So a enib exe s di e en ial an i- umo p ope ies in di e en cell lines. Whe eas HepG2 cells a e conside ed o be
sensi i e o So a enib, he poo ly-di e en ia ed SNU449 cell line showed a lowe pa e n o ea men esponse.
The e o e, we in es iga ed RNA p o iles o un a el po en ial candida es o So a enib esponse in i o. Fi s , o iden i y
pa hways ela ed o di e en ial ea men esponse in HepG2 and SNU449 cells, we selec ed di e en ially exp essed (DE)
genes wi h a base mean > 30, log2FC > 0.5 (up egula ed) o < -0.5 (down egula ed) and P-adjus ed (P-adj) < 0.05 o Venn
analysis. The s udy o long RNA species iden i ied 8345 DE genes, among which 243 RNAs we e common o all
condi ions s udied, indica ing a common mechanism o So a enib in bo h cell lines (Figu e 1A). Mos o hese genes we e
mRNAs coding o p o eins, ollowed by lncRNAs (Figu e 1B). Hie a chical clus e ing allowed o he g ouping o
exp ession p o iles in o 4 clus e s (Figu e 1C). Clus e 1 co esponded wi h genes ha we e up- egula ed in esponse o
So a enib, and his e ec was mo e p ominen in HepG2 cells compa ed o SNU449 cells. Clus e 2 was composed o
genes up- egula ed in SNU449 cells, whe eas clus e 3 was ep esen a i e o genes wi h highe exp ession in HepG2 cells.
Clus e 4 in ol ed down- egula ed genes a e So a enib ea men . As in he case o clus e 1, he e ec o So a enib was
mo e p ominen in HepG2 cells. These esul s con i med he di e en ial e ec i eness o So a enib in hese cells lines. GO
e m and KEGG pa hway analysis was pe o med wi h genes o each clus e (Figu e 1D-G). Clus e 1 was ocused on he
cell nucleus, con olling ansc ip ion and RNA p ocessing (Figu e 1D). Genes wi h inc eased exp ession in SNU449 cells
(clus e 2) we e in ol ed in he egula ion o ocal adhesions, ex acellula ma ix and pa hways in ol ing MAPK and
se ine- h eonine p o ein kinase ac i i y (Figu e 1E). On he o he hand, clus e 3 ha con ained genes wi h highe
exp ession in HepG2 cells we e ela ed o lipid, ca bon and amino acid me abolism, mi ochond ia, and EMT (Figu e 1F).
Clus e 4, which was down egula ed in esponse o So a enib, was in ol ed in DNA epai and epigene ic ch oma in
emodeling p ocesses (Figu e 1G).
Nex , we sequenced small RNA species o iden i y a miRNA pa e n ela ed o So a enib esponse in each cell line. DE
genes wi h a base mean > 15, log2FC > 0.5 (up egula ed) o < -0.5 (down egula ed) and P- alue < 0.05 we e selec ed. In
his case, we ound 110 DE miRNAs in HepG2 and SNU449 cells (Figu e 2A). miRNAs could also be clus e ed acco ding
o exp ession p o iles (Figu e 2B). Clus e 1 con ained miRNAs wi h highe exp ession in SNU449 cells. Clus e 2 was up-
egula ed in esponse o So a enib. Clus e 3 was mo e he e ogeneous and included miRNAs ha we e sligh ly up-
egula ed in HepG2 cells. Clus e 4 included miRNAs wi h highe exp ession in HepG2 cells.
Nex , we in es iga ed whe he he di e ences in So a enib esponse in HepG2 and SNU449 cells we e due o a di e -
en ial RNA in eg a ion ne wo k. The e o e, we de e mined egula o y loops among mRNAs, lncRNAs and miRNAs. In
his sense, we explo ed he ole o lncRNAs as sponges o miRNAs ha egula e mRNA exp ession, as well as hei ole
in con olling mRNAs and lncRNA-p o ein in e ac ions. We pe o med a a ge ed sea ch o mRNAs acco ding o
p e iously desc ibed So a enib an i- umo p ope ies. We selec ed mRNAs om signi ican ly en iched GSEA e ms
ela ed o apop osis, au ophagy, endoplasmic e iculum s ess, di e en ia ion, and me as asis, including di e en ia ion
and angiogenesis (Figu e 3A). In HepG2 cells, So a enib induced he de egula ion o e ms ela ed o cell dea h induc ion
(endoplasmic e iculum s ess, apop osis, au ophagy) mo e p ominen ly a 24 hou s o ea men (34/118, 28.8%),
compa ed o 6 hou s (13/79, 16.4%) (Figu e 3B, Supplemen a y Figu e 1A, Supplemen a y Table 1). Su p isingly,
So a enib had a g ea e impac on he p ocesses selec ed a 6 hou s han a longe ea men imes in SNU449 cells. In
pa icula , he e ec on cell dea h was en iched a 6 hou s (18/56, 32.1%), compa ed o 24 hou s (3/28, 10.7%), when
e ms ela ed o mig a ion and in asion we e dominan (Figu e 3C, Supplemen a y Figu e 1B, Supplemen a y Table 1). A
o al o 441 mRNAs ela ed o So a enib p ope ies we e de egula ed in his s udy, whose exp ession is shown in
Figu e 3D.
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 5Janua y 21, 2025 Volume 31 Issue 3
Figu e 1 Exp ession p o ile o long RNA species and en ichmen analysis. A: Venn diag am o di e en ially exp essed (DE) genes in HepG2 and
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 6Janua y 21, 2025 Volume 31 Issue 3
SNU449 cells ea ed wi h So a enib o 6 and 24 hou s; B: Pie cha showing iden i ica ion o RNA species; C: Hea map o he 8345 DE genes g ouped in o 4 ow
clus e s; D: Top 4 Gene On ology e ms and Kyo o Encyclopedia o Genes and Genome pa hways in clus e 1; E: Clus e 2; F: Clus e 3; G: Clus e 4 iden i ied in he
hea map.
Figu e 2 Exp ession p o ile o small RNAs. A: Venn diag am o di e en ially exp essed (DE) miRNAs in HepG2 and SNU449 cells ea ed wi h So a enib o
6 and 24 hou s; B: Hea map o he 110 DE miRNAs g ouped in o 4 ow clus e s.
An in silico p edic ion o miRNAs a ge ing selec ed mRNAs in Figu e 3D was ca ied ou o sea ch o sou ces o pos -
ansc ip ional mRNA egula ion (Figu e 4A and B; Supplemen a y Figu e 2). F om hese miRNAs, we selec ed o
u he analysis hose ha we e DE in ou s udy wi h a P- alue < 0.05 and log2FC < -1 o > 1 (Figu e 4C). A o al o 49
pu a i e miRNA-mRNA in e ac ions we e iden i ied, in which 23 unique miRNAs pa icipa ed. Di e en miRNA p o iles
we e obse ed in each condi ion, being hsa-miR-19b-3p and hsa-miR-29b-3p speci ic o HepG2 cells ea ed wi h
So a enib a 6 hou s, compa ed o 24 hou s, a imepoin ha in ol ed he speci ic egula ion o hsa-miR-27b-5p, hsa-miR-
193b-3p, hsa-miR-194-3p, hsa-miR-374a-3p, hsa-miR-374b-3p, hsa-miR-769-5p, hsa-miR-3187-3p, hsa-miR-4488, hsa-miR-
4521 and hsa-miR-7974. HRK, JMY, TNFAIP3, RORA and ZNF385B mRNAs we e speci ically egula ed a 6 hou s o
So a enib ea men , whe eas MBNL1, CREB3 L3, ARHGAP24, HOXA1, SH3GLB1, OXR1, GOLGA4, OPTN, SIAH1,
LAMC2, PLK2, ATOH8, SMAD7, TIRARP, TFAP4, FAXDC2, and MELTF we e speci ic o 24 hou s. ARRDC3 was he only
common mRNA in HepG2 cells a 6 and 24 hou s o ea men . Al hough bo h cell lines sha ed miR-374 amily (hsa-miR-
374c-5p in SNU499 cells), hsa-miR-4488 was he only common miRNA sha ed by ea men s a 24 hou s, cons i u ing hsa-
le -7b-3p, hsa-miR-29b-1-5p, hsa-miR-32-3p, hsa-miR-34a-5p, hsa-miR-195-5p, hsa-miR-12136, hsa-miR-4492 and hsa-miR-
5701 a speci ic signa u e o SNU449 cells (24 hou s). Cohe en ly, no mRNAs we e common in bo h cell lines a 24 hou s.
HEY1, CEBPB, VEGFA, ADM, YOD1, TNFAIP3, KLF4, ADRB2, HSPA1B, SYNGR3, RFLNB, ACVR2B, NR4A2, CSPG5,
AREG, NRARP, MAF, IGFBP5, and PDGFB we e speci ically ela ed o SNU449 cells (24 hou s). As in he case o HepG2
cells, So a enib a 6 hou s had a low e ec on miRNA-mRNA based in e ac ions (hsa-miR-15a-5p, hsa-miR-12135)
(CHAC1, FOXJ1) (Table 1).
The nex s ep in he s udy consis ed o p edic ing plausible in e ac ions o lncRNAs wi h selec ed miRNAs in Figu e 4C
using DIANA-LncBase 3 (DIANA ools) (Figu e 5A and B). F om o al p edic ions, only signi ican ly de egula ed
lncRNA wi h cohe en exp ession wi h a ge miRNAs we e selec ed o u he analysis (log2FC > 1, P-adj < 0.05). No
down egula ed lncRNAs by So a enib we e ound o be cohe en ly al e ed. Nine een up egula ed lncRNAs we e selec ed,
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
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Table 1 miRNA-mRNA in e ac ions obse ed in HepG2 and SNU449 cells ea ed wi h So a enib o 6 and 24 hou s
Condi ion hsa-miR log2 (Fold-change) P alue P-adj mRNA a ge T ansc ip ID log2 (Fold-change) P-adj
HepG2 6 hou s hsa-miR-29b-3p -1.374 3.23E-02 0.9961 HRK ENSG00000135116.9 1.967 8.926E-08
HepG2 6 hou s hsa-miR-29b-3p -1.374 3.23E-02 0.9961 JMY ENSG00000152409.9 1.105 2.253E-13
HepG2 6 hou s hsa-miR-29b-3p -1.374 3.23E-02 0.9961 TNFAIP3 ENSG00000118503.15 1.186 4.131E-07
HepG2 6 hou s hsa-miR-19b-3p -1.277 4.29E-02 0.9961 RORA ENSG00000069667.16 1.048 1.506E-03
HepG2 6 hou s hsa-miR-19b-3p -1.277 4.29E-02 0.9961 TNFAIP3 ENSG00000118503.15 1.186 4.131E-07
HepG2 6 hou s hsa-miR-19b-3p -1.277 4.29E-02 0.9961 ZNF385B ENSG00000144331.20 1.159 1.233E-02
HepG2 6 hou s hsa-miR-19b-3p -1.277 4.29E-02 0.9961 ARRDC3 ENSG00000113369.9 1.697 4.636E-30
HepG2 24 hou s hsa-miR-4521 -4.496 1.09E-04 0.1484 MBNL1 ENSG00000152601.17 1.242 2.599E-16
HepG2 24 hou s hsa-miR-7974 -3.432 1.97E-42 0.0000 CREB3 L3 ENSG00000060566.14 1.062 4.001E-06
HepG2 24 hou s hsa-miR-194-3p -1.463 2.73E-08 0.0000 ARHGAP24 ENSG00000138639.18 1.281 1.186E-08
HepG2 24 hou s hsa-miR-194-3p -1.463 4.47E-05 0.0020 HOXA1 ENSG00000105991.9 1.192 2.484E-06
HepG2 24 hou s hsa-miR-374a-3p -1.327 4.47E-05 0.0020 SH3GLB1 ENSG00000097033.14 1.296 1.800E-13
HepG2 24 hou s hsa-miR-374a-3p -1.327 8.95E-03 0.1859 OXR1 ENSG00000164830.18 1.050 2.089E-08
HepG2 24 hou s hsa-miR-374a-3p -1.327 8.95E-03 0.1859 GOLGA4 ENSG00000144674.16 1.230 8.419E-03
HepG2 24 hou s hsa-miR-374a-3p -1.327 8.95E-03 0.1859 ARRDC3 ENSG00000113369.9 2.849 2.203E-41
HepG2 24 hou s hsa-miR-27b-5p -1.236 8.95E-03 0.1859 OPTN ENSG00000123240.17 1.531 6.346E-20
HepG2 24 hou s hsa-miR-193b-3p -1.193 3.74E-04 0.0143 SIAH1 ENSG00000196470.12 1.581 1.144E-38
HepG2 24 hou s hsa-miR-193b-3p -1.193 2.29E-02 0.3864 LAMC2 ENSG00000058085.15 1.327 2.152E-03
HepG2 24 hou s hsa-miR-3187-3p -1.169 2.29E-02 0.3864 PLK2 ENSG00000145632.15 1.634 3.009E-08
HepG2 24 hou s hsa-miR-3187-3p -1.169 3.59E-02 0.4538 ATOH8 ENSG00000168874.13 1.691 6.502E-08
HepG2 24 hou s hsa-miR-374b-3p -1.064 3.59E-02 0.4538 SMAD7 ENSG00000101665.9 1.999 1.669E-42
HepG2 24 hou s hsa-miR-374b-3p -1.064 7.47E-03 0.1693 TIRARP ENSG00000163659.13 1.070 1.555E-18
HepG2 24 hou s hsa-miR-769-5p -1.058 7.47E-03 0.1693 TFAP4 ENSG00000090447.12 1.010 1.161E-11
HepG2 24 hou s hsa-miR-769-5p -1.058 8.79E-03 0.1859 FAXDC2 ENSG00000170271.11 1.565 1.249E-13
HepG2 24 hou s hsa-miR-4488 9.059 8.79E-03 0.1859 MELTF ENSG00000163975.12 -1.085 2.722E-05
SNU 6 hou s hsa-miR-15a-5p -1.526 9.20E-03 0.6536 CHAC1 ENSG00000128965.13 2.262 5.787E-28
SNU 6 hou s hsa-miR-12135 -1.298 2.11E-02 0.6536 FOXJ1 ENSG00000129654.8 1.240 2.099E-06
SNU 24 hou s hsa-miR-29b-1-5p -2.126 2.50E-05 0.0007 HEY1 ENSG00000164683.17 1.692 2.304E-07
SNU 24 hou s hsa-miR-374c-5p -1.884 5.25E-03 0.0787 CEBPB ENSG00000172216.6 1.002 5.306E-17
SNU 24 hou s hsa-miR-374c-5p -1.884 5.25E-03 0.0787 VEGFA ENSG00000112715.22 1.448 2.131E-45
SNU 24 hou s hsa-miR-374c-5p -1.884 5.25E-03 0.0787 ADM ENSG00000148926.10 2.340 1.782E-143
SNU 24 hou s hsa-miR-32-3p -1.821 9.41E-04 0.0175 YOD1 ENSG00000180667.10 1.658 1.063E-111
SNU 24 hou s hsa-miR-32-3p -1.821 9.41E-04 0.0175 TNFAIP3 ENSG00000118503.15 2.316 3.471E-10
SNU 24 hou s hsa-le -7b-3p -1.541 1.72E-02 0.1785 KLF4 ENSG00000136826.15 1.572 1.166E-31
SNU 24 hou s hsa-le -7b-3p -1.541 1.72E-02 0.1785 ADRB2 ENSG00000169252.5 1.743 9.094E-48
SNU 24 hou s hsa-miR-195-5p -1.456 1.51E-02 0.1770 VEGFA ENSG00000112715.22 1.448 2.131E-45
SNU 24 hou s hsa-miR-195-5p -1.456 1.51E-02 0.1770 ADRB2 ENSG00000169252.5 1.743 9.094E-48
SNU 24 hou s hsa-miR-34a-5p -1.316 2.62E-02 0.2364 KLF4 ENSG00000136826.15 1.572 1.166E-31
SNU 24 hou s hsa-miR-34a-5p -1.316 2.62E-02 0.2364 HSPA1B ENSG00000204388.7 1.676 2.822E-82
SNU 24 hou s hsa-miR-5701 1.535 3.44E-02 0.2740 SYNGR3 ENSG00000127561.15 -1.505 1.627E-08
SNU 24 hou s hsa-miR-5701 1.535 3.44E-02 0.2740 RFLNB ENSG00000183688.4 -1.340 1.864E-27
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SNU 24 hou s hsa-miR-12136 3.334 4.93E-16 0.0000 ACVR2B ENSG00000114739.14 -1.075 3.211E-13
SNU 24 hou s hsa-miR-12136 3.334 4.93E-16 0.0000 NR4A2 ENSG00000153234.14 -1.754 9.174E-06
SNU 24 hou s hsa-miR-12136 3.334 4.93E-16 0.0000 CSPG5 ENSG00000114646.10 -1.089 1.709E-08
SNU 24 hou s hsa-miR-12136 3.334 4.93E-16 0.0000 AREG ENSG00000109321.11 -1.016 2.623E-03
SNU 24 hou s hsa-miR-12136 3.334 4.93E-16 0.0000 NRARP ENSG00000198435.4 -1.763 3.743E-12
SNU 24 hou s hsa-miR-12136 3.334 4.93E-16 0.0000 MAF ENSG00000178573.7 -1.748 5.311E-04
SNU 24 hou s hsa-miR-4492 8.427 4.75E-12 0.0000 IGFBP5 ENSG00000115461.5 -1.073 2.379E-18
SNU 24 hou s hsa-miR-4488 13.091 1.08E-32 0.0000 PDGFB ENSG00000100311.17 -1.101 1.086E-51
Figu e 3 Iden i ica ion o mRNA candida es. A: Diag am ep esen ing he s udy design; B: Bubble plo s o en iched GSEA e ms in HepG2 cells; C: SNU449
cells ea ed wi h So a enib 24 hou s. Bubble size is ep esen a i e o gene coun and colo is ep esen a i e o he no malized en ichmen sco e; D: Hea map o
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 9Janua y 21, 2025 Volume 31 Issue 3
selec ed mRNAs in HepG2 and SNU449 cells.
Figu e 4 Iden i ica ion o miRNA candida es. A: Gene egula o y ne wo k showing miRNA-mRNA a ge p edic ions in HepG2 cells; B: SNU449 cells ea ed
wi h So a enib o 24 hou s; C: Hea map o selec ed miRNAs.
p e e en ially exp essed a 24 hou s o So a enib ea men (Figu e 5C). CYTOR, DANT2, MALAT1, MIR4435-2HG,
PCBP2-OT1, SNHG17, THAP9-AS1 and ZFAS1 we e speci ically egula ed in HepG2 cells, whe eas AZIN1-AS1,
CARMN, EPB41 L4A-AS1, GAS5, LINC01578, LMCD1-AS1, PVT1, SNHG12, SNHG20, SNHG5 and SNHG7 we e
speci ically ela ed o SNU499 cells (Table 2). The ole o lncRNA egula ing mRNA ins abili y was nex explo ed. To
comple e he lncRNA-miRNA-mRNA ne wo k, we pe o med ou in silico analysis using as a ge s hose mRNAs ha
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 16 Janua y 21, 2025 Volume 31 Issue 3
CONCLUSION
In conclusion, his s udy iden i ied di e en ial lncRNA-miRNA egula o y axes in HepG2 and SNU449 li e cance cells.
They lead o inc eased exp ession o mRNAs wi h posi i e (SMAD7, TIRARP, TFAP4, FAXDC2 and ADRB2) and nega i e
(VEGFA) he apeu ic e ec s in HepG2 and SNU449 unde So a enib ea men .
FOOTNOTES
Au ho con ibu ions: de la C uz-Ojeda P pe o med he esea ch, con ibu ed o he implemen a ion o analy ical ools and edi ed he
manusc ip ; Pa as-Ma ínez E and Rey-Pé ez R analyzed da a; Mun ané J designed he esea ch, w o e he pape , and ob ained unding.
All au ho s ha e ead and app o ed he inal manusc ip .
Suppo ed by Ins i u o de Salud Ca los III (ISCiii), No. PI19/01266 and No. PI22/00857; Conseje ía de Salud y Familias (Jun a de
Andalucía), No. PI-0216-2020 and No. PIP-0215-2020; Biomedical Resea ch Ne wo k Cen e o Li e and Diges i e Diseases (CIBERehd)
ounded by he ISCIII and co- inanced by Eu opean Regional De elopmen Fund “A way o achie e Eu ope” ERDF.
Ins i u ional e iew boa d s a emen : This s udy is based on he use o he HepG2 and SNU449 cell lines. The s udy did no equi e an
Ins i u ional e iew boa d.
Ins i u ional animal ca e and use commi ee s a emen : This s udy is based on he use o HepG2 and SNU449 cell lines. The s udy did no
equi e an Ins i u ional Animal Ca e and Use Commi ee app o al o m.
Con lic -o -in e es s a emen : All he au ho s epo no ele an con lic s o in e es o his a icle.
Da a sha ing s a emen : Da a will be eely a ailable acco ding o he equi emen o he WJG as an open-access a icle.
Open-Access: This a icle is an open-access a icle ha was selec ed by an in-house edi o and ully pee - e iewed by ex e nal e iewe s.
I is dis ibu ed in acco dance wi h he C ea i e Commons A ibu ion NonComme cial (CC BY-NC 4.0) license, which pe mi s o he s o
dis ibu e, emix, adap , build upon his wo k non-comme cially, and license hei de i a i e wo ks on di e en e ms, p o ided he
o iginal wo k is p ope ly ci ed and he use is non-comme cial. See: h ps://c ea i ecommons.o g/Licenses/by-nc/4.0/
Coun y o o igin: Spain
ORCID numbe : Jo di Mun ané 0000-0002-6744-1121.
S-Edi o : Qu XL
L-Edi o : Webs e JR
P-Edi o : Zhang L
REFERENCES
1Sung H, Fe lay J, Siegel RL, La e sanne M, Soe joma a am I, Jemal A, B ay F. Global Cance S a is ics 2020: GLOBOCAN Es ima es o
Incidence and Mo ali y Wo ldwide o 36 Cance s in 185 Coun ies. CA Cance J Clin 2021; 71: 209-249 [PMID: 33538338 DOI:
10.3322/caac.21660]
2Eu opean Associa ion o he S udy o he Li e . EASL Clinical P ac ice Guidelines o he managemen o pa ien s wi h decompensa ed
ci hosis. J Hepa ol 2018; 69: 406-460 [PMID: 29653741 DOI: 10.1016/j.jhep.2018.03.024]
3Reig M, Fo ne A, Rimola J, Fe e -Fàb ega J, Bu el M, Ga cia-C iado Á, Kelley RK, Galle PR, Mazza e o V, Salem R, Sang o B, Singal
AG, Vogel A, Fus e J, Ayuso C, B uix J. BCLC s a egy o p ognosis p edic ion and ea men ecommenda ion: The 2022 upda e. J Hepa ol
2022; 76: 681-693 [PMID: 34801630 DOI: 10.1016/j.jhep.2021.11.018]
4P is e D, Núñez NG, Pinyol R, Go ae e O, Pin e M, Szydlowska M, Gup a R, Qiu M, Deczkowska A, Weine A, Mülle F, Sinha A, F iebel
E, Englei ne T, Lenggenhage D, Moncsek A, Heide D, S i m K, Kosla J, Ko sili i E, Leone V, Dudek M, Yousu S, In e so D, Singh I,
Teijei o A, Cas e F, Mon i oni C, Habe PK, Tiniakos D, Bedossa P, Cockell S, Younes R, Vacca M, Ma a F, Scha enbe g JM, Allison M,
Bugianesi E, Ra ziu V, P essiani T, D'Alessio A, Pe soneni N, Rimassa L, Daly AK, Scheine B, Pomej K, Ki s ein MM, Vogel A, Peck-
Radosa lje ic M, Hucke F, Finkelmeie F, Waidmann O, T ojan J, Schulze K, Wege H, Koch S, Weinmann A, Bue e M, Rössle F,
Siebenhüne A, De Dosso S, Mallm JP, Umansky V, Jugold M, Luedde T, Schie inge A, Schi mache P, Emu B, Augus in HG, Bille e A,
Mülle -S ich B, Kikuchi H, Duda DG, Kü ing F, Waldschmid DT, Ebe MP, Rahba i N, Mei HE, Schulz AR, Ringelhan M, Malek N, Spahn
S, Bi ze M, Ruiz de Gala e a M, Lujambio A, Du ou JF, Ma on TU, Kaseb A, Kudo M, Huang YH, Djoude N, Wol e K, Zende L,
Ma che PN, Decaens T, Pina o DJ, Rad R, Me ens JC, Webe A, Unge K, Meissne F, Ro h S, Jilko a ZM, Claassen M, Ans ee QM, Ami I,
Knolle P, Beche B, Llo e JM, Heikenwalde M. NASH limi s an i- umou su eillance in immuno he apy- ea ed HCC. Na u e 2021; 592:
450-456 [PMID: 33762733 DOI: 10.1038/s41586-021-03362-0]
5Llo e JM, Ricci S, Mazza e o V, Hilga d P, Gane E, Blanc JF, de Oli ei a AC, San o o A, Raoul JL, Fo ne A, Schwa z M, Po a C,
Zeuzem S, Bolondi L, G e en TF, Galle PR, Sei z JF, Bo ba h I, Häussinge D, Gianna is T, Shan M, Mosco ici M, Volio is D, B uix J;
SHARP In es iga o s S udy G oup. So a enib in ad anced hepa ocellula ca cinoma. N Engl J Med 2008; 359: 378-390 [PMID: 18650514
DOI: 10.1056/NEJMoa0708857]
Cheng AL, Kang YK, Chen Z, Tsao CJ, Qin S, Kim JS, Luo R, Feng J, Ye S, Yang TS, Xu J, Sun Y, Liang H, Liu J, Wang J, Tak WY, Pan H,
6
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 17 Janua y 21, 2025 Volume 31 Issue 3
Bu ock K, Zou J, Volio is D, Guan Z. E icacy and sa e y o so a enib in pa ien s in he Asia-Paci ic egion wi h ad anced hepa ocellula
ca cinoma: a phase III andomised, double-blind, placebo-con olled ial. Lance Oncol 2009; 10: 25-34 [PMID: 19095497 DOI:
10.1016/S1470-2045(08)70285-7]
7Rod íguez-He nández MA, González R, de la Rosa ÁJ, Gallego P, O dóñez R, Na a o-Villa án E, Con e as L, Rod íguez-A ibas M, Gonz
ález-Gallego J, Álamo-Ma ínez JM, Ma ín-Gómez LM, Del Campo JA, Quiles JL, Fuen es JM, de la C uz J, Mau iz JL, Padillo FJ, Mun ané
J. Molecula cha ac e iza ion o au ophagic and apop o ic signaling induced by so a enib in li e cance cells. J Cell Physiol 2018; 234: 692-
708 [PMID: 30132846 DOI: 10.1002/jcp.26855]
8Fe nando J, Sancho P, Fe nández-Rod iguez CM, Lledó JL, Caja L, Campbell JS, Faus o N, Fab ega I. So a enib sensi izes hepa ocellula
ca cinoma cells o physiological apop o ic s imuli. J Cell Physiol 2012; 227: 1319-1325 [PMID: 21604268 DOI: 10.1002/jcp.22843]
9Wei JC, Meng FD, Qu K, Wang ZX, Wu QF, Zhang LQ, Pang Q, Liu C. So a enib inhibi s p oli e a ion and in asion o human hepa ocellula
ca cinoma cells ia up- egula ion o p53 and supp essing FoxM1. Ac a Pha macol Sin 2015; 36: 241-251 [PMID: 25557114 DOI:
10.1038/aps.2014.122]
10 Zhai B, Hu F, Jiang X, Xu J, Zhao D, Liu B, Pan S, Dong X, Tan G, Wei Z, Qiao H, Jiang H, Sun X. Inhibi ion o Ak e e ses he acqui ed
esis ance o so a enib by swi ching p o ec i e au ophagy o au ophagic cell dea h in hepa ocellula ca cinoma. Mol Cance The 2014; 13:
1589-1598 [PMID: 24705351 DOI: 10.1158/1535-7163.MCT-13-1043]
11 To a V, Co nella H, Moeini A, Vidal S, Hoshida Y, Sia D, Peix J, Cabellos L, Alsine C, To ecilla S, Ma inez-Que glas I, Lozano JJ,
Desbois-Mou hon C, Solé M, Domingo-Domenech J, Villanue a A, Llo e JM. Tumou ini ia ing cells and IGF/FGF signalling con ibu e o
so a enib esis ance in hepa ocellula ca cinoma. Gu 2017; 66: 530-540 [PMID: 26658144 DOI: 10.1136/gu jnl-2015-309501]
12 Rod íguez-He nández MA, Chap es o-Ga zón R, Cadenas M, Na a o-Villa án E, Neg e e M, Gómez-B a o MA, Vic o VM, Padillo FJ,
Mun ané J. Di e en ial e ec i eness o y osine kinase inhibi o s in 2D/3D cul u e acco ding o cell di e en ia ion, p53 s a us and
mi ochond ial espi a ion in li e cance cells. Cell Dea h Dis 2020; 11: 339 [PMID: 32382022 DOI: 10.1038/s41419-020-2558-1]
13 Chen X, Lingala S, Khoobya i S, Nol a J, Ze n MA, Wu J. Epi helial mesenchymal ansi ion and hedgehog signaling ac i a ion a e associa ed
wi h chemo esis ance and in asion o hepa oma subpopula ions. J Hepa ol 2011; 55: 838-845 [PMID: 21334406 DOI:
10.1016/j.jhep.2010.12.043]
14 Tang W, Chen Z, Zhang W, Cheng Y, Zhang B, Wu F, Wang Q, Wang S, Rong D, Rei e FP, De Toni EN, Wang X. The mechanisms o
so a enib esis ance in hepa ocellula ca cinoma: heo e ical basis and he apeu ic aspec s. Signal T ansduc Ta ge The 2020; 5: 87 [PMID:
32532960 DOI: 10.1038/s41392-020-0187-x]
15 Wong CM, Tsang FH, Ng IO. Non-coding RNAs in hepa ocellula ca cinoma: molecula unc ions and pa hological implica ions. Na Re
Gas oen e ol Hepa ol 2018; 15: 137-151 [PMID: 29317776 DOI: 10.1038/n gas o.2017.169]
16 Wang S, Yang Y, Sun L, Qiao G, Song Y, Liu B. Exosomal Mic oRNAs as Liquid Biopsy Bioma ke s in Hepa ocellula Ca cinoma. Onco
Ta ge s The 2020; 13: 2021-2030 [PMID: 32210570 DOI: 10.2147/OTT.S232453]
17 Manganelli M, G ossi I, Fe acin M, Gue ie o P, Neg ini M, Ghidini M, Sen i C, Ra i M, Pizzo C, Passalacqua R, Mol ino S, Baiocchi G,
Po olani N, Ma china E, De Pe o G, Sal i A. Longi udinal Ci cula ing Le els o miR-23b-3p, miR-126-3p and lncRNA GAS5 in HCC
Pa ien s T ea ed wi h So a enib. Biomedicines 2021; 9 [PMID: 34356875 DOI: 10.3390/biomedicines9070813]
18 de la C uz-Ojeda P, Schmid T, Boix L, Mo eno M, Sapena V, P aena-Fe nández JM, Cas ell FJ, Falcón-Pé ez JM, Reig M, B üne B, Gómez-
B a o MA, Gi áldez Á, B uix J, Fe e MT, Mun ané J. miR-200c-3p, miR-222-5p, and miR-512-3p Cons i u e a Bioma ke Signa u e o
So a enib E ec i eness in Ad anced Hepa ocellula Ca cinoma. Cells 2022; 11 [PMID: 36078082 DOI: 10.3390/cells11172673]
19 Wang KC, Chang HY. Molecula mechanisms o long noncoding RNAs. Mol Cell 2011; 43: 904-914 [PMID: 21925379 DOI:
10.1016/j.molcel.2011.08.018]
20 Chowdha y A, Sa agopam V, Schneide R. Long Non-coding RNAs: Mechanisms, Expe imen al, and Compu a ional App oaches in
Iden i ica ion, Cha ac e iza ion, and Thei Bioma ke Po en ial in Cance . F on Gene 2021; 12: 649619 [PMID: 34276764 DOI:
10.3389/ gene.2021.649619]
21 Lo e MI, Hube W, Ande s S. Mode a ed es ima ion o old change and dispe sion o RNA-seq da a wi h DESeq2. Genome Biol 2014; 15:
550 [PMID: 25516281 DOI: 10.1186/s13059-014-0550-8]
22 Du inck S, Spellman PT, Bi ney E, Hube W. Mapping iden i ie s o he in eg a ion o genomic da ase s wi h he R/Bioconduc o package
biomaR . Na P o oc 2009; 4: 1184-1191 [PMID: 19617889 DOI: 10.1038/np o .2009.97]
23 Sub amanian A, Tamayo P, Moo ha VK, Mukhe jee S, Ebe BL, Gille e MA, Paulo ich A, Pome oy SL, Golub TR, Lande ES, Mesi o JP.
Gene se en ichmen analysis: a knowledge-based app oach o in e p e ing genome-wide exp ession p o iles. P oc Na l Acad Sci U S A 2005;
102: 15545-15550 [PMID: 16199517 DOI: 10.1073/pnas.0506580102]
24 Moo ha VK, Lindg en CM, E iksson KF, Sub amanian A, Sihag S, Leha J, Puigse e P, Ca lsson E, Ridde s åle M, Lau ila E, Hous is N,
Daly MJ, Pa e son N, Mesi o JP, Golub TR, Tamayo P, Spiegelman B, Lande ES, Hi schho n JN, Al shule D, G oop LC. PGC-1alpha-
esponsi e genes in ol ed in oxida i e phospho yla ion a e coo dina ely down egula ed in human diabe es. Na Gene 2003; 34: 267-273
[PMID: 12808457 DOI: 10.1038/ng1180]
25 Fallmann J, Videm P, Bagnacani A, Ba u B, Doyle MA, Klings om T, Eggenho e F, S adle PF, Backo en R, G üning B. The RNA
wo kbench 2.0: nex gene a ion RNA da a analysis. Nucleic Acids Res 2019; 47: W511-W515 [PMID: 31073612 DOI: 10.1093/na /gkz353]
26 Mackowiak SD. Iden i ica ion o no el and known miRNAs in deep-sequencing da a wi h miRDeep2. Cu P o oc Bioin o ma ics 2011;
Chap e 12: 12.10.1-12.10.15 [PMID: 22161567 DOI: 10.1002/0471250953.bi1210s36]
27 Huang da W, She man BT, Lempicki RA. Sys ema ic and in eg a i e analysis o la ge gene lis s using DAVID bioin o ma ics esou ces. Na
P o oc 2009; 4: 44-57 [PMID: 19131956 DOI: 10.1038/np o .2008.211]
28 Szkla czyk D, Gable AL, Nas ou KC, Lyon D, Ki sch R, Pyysalo S, Donche a NT, Legeay M, Fang T, Bo k P, Jensen LJ, on Me ing C. The
STRING da abase in 2021: cus omizable p o ein-p o ein ne wo ks, and unc ional cha ac e iza ion o use -uploaded gene/measu emen se s.
Nucleic Acids Res 2021; 49: D605-D612 [PMID: 33237311 DOI: 10.1093/na /gkaa1074]
29 Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web se e o cance and no mal gene exp ession p o iling and in e ac i e analyses.
Nucleic Acids Res 2017; 45: W98-W102 [PMID: 28407145 DOI: 10.1093/na /gkx247]
30 Ka agkouni D, Pa aske opoulou MD, Tas soglou S, Skou os G, Ka a angeli A, Pie os V, Zacha opoulou E, Ha zigeo giou AG. DIANA-
LncBase 3: indexing expe imen ally suppo ed miRNA a ge s on non-coding ansc ip s. Nucleic Acids Res 2020; 48: D101-D110 [PMID:
31732741 DOI: 10.1093/na /gkz1036]
31 Pa aske opoulou MD, Ka agkouni D, Vlachos IS, Tas soglou S, Ha zigeo giou AG. mic oCLIP supe lea ning amewo k unco e s
unc ional ansc ip ome-wide miRNA in e ac ions. Na Commun 2018; 9: 3601 [PMID: 30190538 DOI: 10.1038/s41467-018-06046-y]
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 18 Janua y 21, 2025 Volume 31 Issue 3
32 Fukunaga T, Iwaki i J, Ono Y, Hamada M. LncRRIsea ch: A Web Se e o lncRNA-RNA In e ac ion P edic ion In eg a ed Wi h Tissue-
Speci ic Exp ession and Subcellula Localiza ion Da a. F on Gene 2019; 10: 462 [PMID: 31191601 DOI: 10.3389/ gene.2019.00462]
33 Lang B, A maos A, Ta aglia GG. RNAc : P o ein-RNA in e ac ion p edic ions o model o ganisms wi h suppo ing expe imen al da a.
Nucleic Acids Res 2019; 47: D601-D606 [PMID: 30445601 DOI: 10.1093/na /gky967]
34 Villanue a A. Hepa ocellula Ca cinoma. N Engl J Med 2019; 380: 1450-1462 [PMID: 30970190 DOI: 10.1056/NEJM a1713263]
35 He J, He J, Min L, He Y, Guan H, Wang J, Peng X. Ex acellula esicles ansmi ed miR-31-5p p omo es so a enib esis ance by a ge ing
MLH1 in enal cell ca cinoma. In J Cance 2020; 146: 1052-1063 [PMID: 31259424 DOI: 10.1002/ijc.32543]
36 Fo na i F, Pollu i D, Pa izi C, La Bella T, Ma inelli S, Casadei Ga dini A, Ma isi G, Ba on Toaldo M, Baglioni M, Sal a o e V, Callega i E,
Baldassa e M, Galassi M, Gio annini C, Cescon M, Ra aioli M, Neg ini M, Bolondi L, G aman ie i L. In Hepa ocellula Ca cinoma miR-221
Modula es So a enib Resis ance h ough Inhibi ion o Caspase-3-Media ed Apop osis. Clin Cance Res 2017; 23: 3953-3965 [PMID:
28096271 DOI: 10.1158/1078-0432.CCR-16-1464]
37 G aman ie i L, Pollu i D, Gaglia di M, Gio annini C, Qua a S, Fe acin M, Casadei-Ga dini A, Callega i E, De Ca olis S, Ma inelli S,
Bene en o F, Vasu i F, Ra aioli M, Cescon M, Piscaglia F, Neg ini M, Bolondi L, Fo na i F. MiR-30e-3p In luences Tumo Pheno ype
h ough MDM2/TP53 Axis and P edic s So a enib Resis ance in Hepa ocellula Ca cinoma. Cance Res 2020; 80: 1720-1734 [PMID:
32015093 DOI: 10.1158/0008-5472.CAN-19-0472]
38 Kohno T, Mo ishi a A, Iwama H, Fuji a K, Tani J, Takuma K, Nakaha a M, Ou a K, Tadoko o T, Nomu a T, Yoneyama H, Ka o K, Okano K,
Suzuki Y, Nishiyama A, Himo o T, Masaki T. Comp ehensi e analysis o ci cula ing mic oRNAs as p edic i e bioma ke s o so a enib
he apy ou come in hepa ocellula ca cinoma. Oncol Le 2020; 20: 1727-1733 [PMID: 32724415 DOI: 10.3892/ol.2020.11696]
39 Chen S, Xia X. Long noncoding RNA NEAT1 supp esses so a enib sensi i i y o hepa ocellula ca cinoma cells ia egula ing miR-335-c-
Me . J Cell Physiol 2019; 234: 14999-15009 [PMID: 30937906 DOI: 10.1002/jcp.27567]
40 Chen YT, Xiang D, Zhao XY, Chu XY. Up egula ion o lncRNA NIFK-AS1 in hepa ocellula ca cinoma by m(6)A me hyla ion p omo es
disease p og ession and so a enib esis ance. Hum Cell 2021; 34: 1800-1811 [PMID: 34374933 DOI: 10.1007/s13577-021-00587-z]
41 Zhang PF, Wang F, Wu J, Wu Y, Huang W, Liu D, Huang XY, Zhang XM, Ke AW. LncRNA SNHG3 induces EMT and so a enib esis ance
by modula ing he miR-128/CD151 pa hway in hepa ocellula ca cinoma. J Cell Physiol 2019; 234: 2788-2794 [PMID: 30132868 DOI:
10.1002/jcp.27095]
42 Li W, Dong X, He C, Tan G, Li Z, Zhai B, Feng J, Jiang X, Liu C, Jiang H, Sun X. LncRNA SNHG1 con ibu es o so a enib esis ance by
ac i a ing he Ak pa hway and is posi i ely egula ed by miR-21 in hepa ocellula ca cinoma cells. J Exp Clin Cance Res 2019; 38: 183
[PMID: 31053148 DOI: 10.1186/s13046-019-1177-0]
43 Guo Z, Zhang J, Fan L, Liu J, Yu H, Li X, Sun G. Long Noncoding RNA (lncRNA) Small Nucleola RNA Hos Gene 16 (SNHG16) P edic s
Poo P ognosis and So a enib Resis ance in Hepa ocellula Ca cinoma. Med Sci Moni 2019; 25: 2079-2086 [PMID: 30893293 DOI:
10.12659/MSM.915541]
44 Qin M, Meng Y, Luo C, He S, Qin F, Yin Y, Huang J, Zhao H, Hu J, Deng Z, Qiu Y, Hu G, Pan H, Qin Z, Huang Z, Yi T. lncRNA PRR34-
AS1 p omo es HCC de elopmen ia modula ing Wn /β-ca enin pa hway by abso bing miR-296-5p and up egula ing E2F2 and SOX12. Mol
The Nucleic Acids 2021; 25: 37-52 [PMID: 34168917 DOI: 10.1016/j.om n.2021.04.016]
45 Liu C, Tang L, Xu M, Lin Y, Shen J, Zhou L, Ho L, Lu J, Ai X. LncRNA RUSC1-AS1 con ibu es o he p og ession o hepa ocellula
ca cinoma cells by modula ing miR-340-5p/CREB1 axis. Am J T ansl Res 2021; 13: 1022-1036 [PMID: 33841637]
46 Chan LK, Tsui YM, Ho DW, Ng IO. Cellula he e ogenei y and plas ici y in li e cance . Semin Cance Biol 2022; 82: 134-149 [PMID:
33647386 DOI: 10.1016/j.semcance .2021.02.015]
47 Sa i F, Nguyen R, Ze ehpooshnes chi S, Geo ge J, Qiao L. He e ogenei y o hepa ocellula ca cinoma: om mechanisms o clinical
implica ions. Cance Gene The 2024; 31: 1105-1112 [PMID: 38499648 DOI: 10.1038/s41417-024-00764-w]
48 Lu J, Guo J, Liu J, Mao X, Xu K. Long Non-coding RNA MALAT1: A Key Playe in Li e Diseases. F on Med (Lausanne) 2021; 8: 734643
[PMID: 35145971 DOI: 10.3389/ med.2021.734643]
49 Fan L, Huang X, Chen J, Zhang K, Gu YH, Sun J, Cui SY. Long Noncoding RNA MALAT1 Con ibu es o So a enib Resis ance by Ta ge ing
miR-140-5p/Au o a-A Signaling in Hepa ocellula Ca cinoma. Mol Cance The 2020; 19: 1197-1209 [PMID: 32220970 DOI:
10.1158/1535-7163.MCT-19-0203]
50 Jones S. An o e iew o he basic helix-loop-helix p o eins. Genome Biol 2004; 5: 226 [PMID: 15186484 DOI: 10.1186/gb-2004-5-6-226]
51 Po s MA, Mizu ani S, Ga nham AL, Li Wai Suen CSN, Kueh AJ, Tai L, Pal M, S asse A, He old MJ. Dele ion o he ansc ip ional
egula o TFAP4 accele a es c-MYC-d i en lymphomagenesis. Cell Dea h Di e 2023; 30: 1447-1456 [PMID: 36894688 DOI:
10.1038/s41418-023-01145-w]
52 Yang Z, He J, Gao P, Niu Y, Zhang J, Wang L, Liu M, Wei X, Liu C, Zhang C, Wang W, Du J, Li H, Hu W, Sun G. miR-769-5p supp essed
cell p oli e a ion, mig a ion and in asion by a ge ing TGFBR1 in non-small cell lung ca cinoma. Onco a ge 2017; 8: 113558-113570 [PMID:
29371929 DOI: 10.18632/onco a ge .23060]
53 Ding L, Feng Y, Li L. Ci c_0001955 p omo es he p og ession o non-small cell lung cance ia miR-769-5p/EGFR axis. Cell Cycle 2022; 21:
2433-2443 [PMID: 35920610 DOI: 10.1080/15384101.2022.2100681]
54 Chen Q, Cao M, Ge H. Knockdown o MALAT1 Inhibi s he P og ession o Ch onic Pe iodon i is ia Ta ge ing miR-769-5p/HIF3A Axis.
Biomed Res In 2021; 2021: 8899863 [PMID: 33604388 DOI: 10.1155/2021/8899863]
55 Yan X, Liu Z, Chen Y. Regula ion o TGF-be a signaling by Smad7. Ac a Biochim Biophys Sin (Shanghai) 2009; 41: 263-272 [PMID:
19352540 DOI: 10.1093/abbs/gmp018]
56 Ou Y, Dai X, Chen X, Chen Y, Wu S, Zhou Q, Yang C, Jiang H. Ci c-AFAP1 p omo e clea cell enal cell ca cinoma g ow h and angiogenesis
by he Ci c-AFAP1/miR-374b-3p/VEGFA signaling axis. Cell Dea h Disco 2022; 8: 68 [PMID: 35173146 DOI:
10.1038/s41420-022-00865-1]
57 Hopp AK, Ho ige MO. Unco e ing he In isible: Mono-ADP- ibosyla ion Mo ed in o he Spo ligh . Cells 2021; 10 [PMID: 33808662 DOI:
10.3390/cells10030680]
58 Su Y, Xie R, Xu Q. LncRNA THAP9-AS1 highly exp essed in issues o hepa ocellula ca cinoma and accele a es umo cell p oli e a ion.
Clin Res Hepa ol Gas oen e ol 2022; 46: 102025 [PMID: 36170961 DOI: 10.1016/j.clin e.2022.102025]
59 Ji K, Zhang Q, Song W, Mao T, Guo J, Min C, Zhang C, Tian Z, Li X. LncRNA PVT1 P omo es Cell P oli e a ion, In asion, and Mig a ion
and Inhibi s Cell Apop osis by Phospho yla ing YAP. Can J Gas oen e ol Hepa ol 2022; 2022: 5332129 [PMID: 35664988 DOI:
10.1155/2022/5332129]
Zhou C, Yi C, Yi Y, Qin W, Yan Y, Dong X, Zhang X, Huang Y, Zhang R, Wei J, Ali DW, Michalak M, Chen XZ, Tang J. LncRNA PVT1
60
de la C uz-Ojeda P e al. lncRNA-miRNA-mRNA in So a enib- ea ed li e cance
WJG h ps://www.wjgne .com 19 Janua y 21, 2025 Volume 31 Issue 3
p omo es gemci abine esis ance o panc ea ic cance ia ac i a ing Wn /β-ca enin and au ophagy pa hway h ough modula ing he miR-619-
5p/Pygo2 and miR-619-5p/ATG14 axes. Mol Cance 2020; 19: 118 [PMID: 32727463 DOI: 10.1186/s12943-020-01237-y]
61 Xu H, Hu YW, Zhao JY, Hu XM, Li SF, Wang YC, Gao JJ, Sha YH, Kang CM, Lin L, Huang C, Zhao JJ, Zheng L, Wang Q. Mic oRNA-195-
5p ac s as an an i-oncogene by a ge ing PHF19 in hepa ocellula ca cinoma. Oncol Rep 2015; 34: 175-182 [PMID: 25955388 DOI:
10.3892/o .2015.3957]
62 Riba i D. Immunosupp essi e e ec s o ascula endo helial g ow h ac o . Oncol Le 2022; 24: 369 [PMID: 36238855 DOI:
10.3892/ol.2022.13489]
63 Ka z JP, Pe eaul N, Golds ein BG, Ac man L, McNally SR, Silbe g DG, Fu h EE, Kaes ne KH. Loss o Kl 4 in mice causes al e ed
p oli e a ion and di e en ia ion and p ecance ous changes in he adul s omach. Gas oen e ology 2005; 128: 935-945 [PMID: 15825076 DOI:
10.1053/j.gas o.2005.02.022]
64 Li Y, Yu S, Li L, Chen J, Quan M, Li Q, Gao Y. KLF4-media ed up egula ion o CD9 and CD81 supp esses hepa ocellula ca cinoma
de elopmen ia JNK signaling. Cell Dea h Dis 2020; 11: 299 [PMID: 32350244 DOI: 10.1038/s41419-020-2479-z]
65 Su JL, Chen PS, Johansson G, Kuo ML. Func ion and egula ion o le -7 amily mic oRNAs. Mic o na 2012; 1: 34-39 [PMID: 25048088 DOI:
10.2174/2211536611201010034]
66 Yu J, Cao Q, Meh a R, Laxman B, Yu J, Tomlins SA, C eigh on CJ, Dhanaseka an SM, Shen R, Chen G, Mo is DS, Ma quez VE, Shah RB,
Ghosh D, Va ambally S, Chinnaiyan AM. In eg a i e genomics analysis e eals silencing o be a-ad ene gic signaling by polycomb in p os a e
cance . Cance Cell 2007; 12: 419-431 [PMID: 17996646 DOI: 10.1016/j.cc .2007.10.016]
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