World J Oncol

World Journal of Oncology, ISSN 1920-4531 print, 1920-454X online, Open Access

Article copyright, the authors; Journal compilation copyright, World J Oncol and Elmer Press Inc

Journal website https://www.wjon.org

Original Article

Volume 13, Number 6, December 2022, pages 387-402

Glycine Decarboxylase Suppresses the Renal Cell Carcinoma Growth and Regulates Its Gene Expressions and Functions

Figure 1. Protein and messenger RNA (mRNA) levels of glycine decarboxylase (GLDC). (a) Relative mRNA expression of GLDC in renal cell carcinoma (RCC) cell lines. (b) Relative mRNA expression of GLDC in normal and RCC primary tumor tissues. (c) GLDC protein expression in tumor tissues (T) and RCC adjacent non-neoplastic tissues (ANT). (d) Quantification of protein expression in (c). *P < 0.05, **P < 0.01, ***P < 0.001.

Figure 2. Glycine decarboxylase (GLDC) inhibits renal cell carcinoma (RCC) cell growth. (a) Relative mRNA expression in GLDC-overexpressing RCC cell lines. (b) Protein expression in GLDC-overexpressing RCC cell lines. (c) Quantification of protein expression in (b). (d) Growth curves of A498 and 786-O cells. (e) Cell viability detected using the EdU assay. The blue fluorescence was Hoechst stains and the red fluorescence was EdU labeled proliferating cells. (f) Quantification of proliferating cell ratio. *P < 0.05, **P < 0.01, ***P < 0.001

Figure 3. Glycine decarboxylase (GLDC) inhibits the invasion and migration of renal cell carcinoma (RCC) cells. (a) Representative micrographs of the wound healing assay at 0 and 24 h. (b) Quantification of the results shown in (a). (c) Migration examined utilizing the transwell assay. (d) Quantification of the findings indicated in (c). (e) Invasion ability evaluated using the transwell assay. (f) Quantification of the findings presented in (e). *P < 0.05, **P < 0.01, ***P < 0.001.

Figure 4. Bioinformatic analysis of differentially expressed genes. (a) Volcano plot. (b) Cluster analysis results of differentially expressed proteins. (c) Pie chart of differential expression of protein subcellular localization. (d) Analysis of differentially expressed protein domains. (e) Analysis map of domain enrichment. (f) Gene Ontology (GO) function enrichment under biological process (BP) classification. (g) Function enrichment bubble diagram under molecular function (MF) classification. (h) Cellular component (CC) of GO function enrichment. (i) Enrichment bubble diagram of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.

Figure 5. Protein-protein interaction network. (a) Diagram of differential expression of the protein-protein interaction network. (b) Interaction network for functional classification. (c) Cluster 1. (d) Cluster 2. (e) Cluster 3. (f) Cluster 4. (g) Cluster 5.

**Table 1.** Upregulated/Downregulated Differential Proteins (Top 20)
Upregulated/downregulated	Protein name	Gene name	GLDC/NC	P value (t-test)
Upregulated	Glycine decarboxylase	GLDC	3.767	8.83 × 10^-5
Upregulated	Vomeronasal type-1 receptor 5	VN1R5	3.566	4.20 × 10^-2
Upregulated	Tetratricopeptide repeat protein 13	TTC13	2.512	9.28 × 10^-5
Upregulated	Membrane-spanning 4-domains subfamily A member 14	MS4A14	2.126	2.25 × 10^-4
Upregulated	Complement factor I	CFI	2.041	1.26 × 10^-2
Upregulated	Calcium-binding and coiled-coil domain-containing protein 2	CALCOCO2	2.034	2.84 × 10^-2
Upregulated	Regulator of G-protein signaling protein-like	RGSL1	2.029	5.85 × 10^-4
Upregulated	Cilia- and flagella-associated protein 54	CFAP54	1.857	7.17 × 10^-3
Upregulated	Thioredoxin domain-containing protein 9	TXNDC9	1.830	5.97 × 10^-3
Upregulated	Unconventional myosin-If	MYO1F	1.818	2.84 × 10^-3
Upregulated	Mitochondrial 10-formyltetrahydrofolate dehydrogenase	ALDH1L2	1.756	1.73 × 10^-3
Upregulated	Clusterin	CLU	1.744	4.82 × 10^-2
Upregulated	Claudin-6	CLDN6	1.744	1.50 × 10^-2
Upregulated	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-4	GNG4	1.736	3.38 × 10^-2
Upregulated	N6-adenosine-methyltransferase catalytic subunit	METTL3	1.735	4.50 × 10^-2
Upregulated	Uncharacterized protein C1orf167	C1orf167	1.709	4.86 × 10^-2
Upregulated	RWD domain-containing protein 1	RWDD1	1.701	2.13 × 10^-2
Upregulated	Phosphoserine aminotransferase	PSAT1	1.698	1.95 × 10^-4
Upregulated	Rabenosyn-5	RBSN	1.698	2.22 × 10^-2
Upregulated	Prosaposin	PSAP	1.689	1.23 × 10^-3
Downregulated	UPF0488 protein C8orf33	C8orf33	0.833	5.34 × 10^-3
Downregulated	Synaptobrevin homolog YKT6	YKT6	0.833	3.90 × 10^-4
Downregulated	SPATS2-like protein	SPATS2L	0.833	1.26 × 10^-2
Downregulated	E3 ubiquitin-protein ligase RNF114	RNF114	0.833	2.27 × 10^-2
Downregulated	Transcription initiation factor IIB	GTF2B	0.833	2.55 × 10^-3
Downregulated	Tyrosine-protein phosphatase non-receptor type 2	PTPN2	0.832	2.69 × 10^-2
Downregulated	MOB kinase activator 3A	MOB3A	0.832	3.84 × 10^-3
Downregulated	Copine-2	CPNE2	0.832	4.00 × 10^-2
Downregulated	FERM domain-containing protein 5	FRMD5	0.832	1.90 × 10^-2
Downregulated	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform	PPP2R2C	0.831	4.78 × 10^-2
Downregulated	FLYWCH family member 2	FLYWCH2	0.831	3.89 × 10^-2
Downregulated	F-box/LRR-repeat protein 6	FBXL6	0.830	1.57 × 10^-3
Downregulated	Exportin-6	XPO6	0.830	8.37 × 10^-3
Downregulated	Starch-binding domain-containing protein 1	STBD1	0.829	4.82 × 10^-2
Downregulated	Microfibrillar-associated protein 1	MFAP1	0.828	3.46 × 10^-2
Downregulated	Autism susceptibility gene 2 protein	AUTS2	0.828	4.84 × 10^-2
Downregulated	tRNA (guanine-N(7)-)-methyltransferase	METTL1	0.828	2.41 × 10^-2
Downregulated	E3 ubiquitin-protein ligase UHRF2	UHRF2	0.828	1.03 × 10^-2
Downregulated	DNA replication licensing factor MCM3	MCM3	0.827	1.61 × 10^-3
Downregulated	Ras GTPase-activating protein nGAP	RASAL2	0.827	4.42 × 10^-2

Table 1. Upregulated/Downregulated Differential Proteins (Top 20)

Upregulated/downregulated

Protein name

Gene name

GLDC/NC

P value (t-test)

Upregulated

Glycine decarboxylase

GLDC

3.767

8.83 × 10^-5

Upregulated

Vomeronasal type-1 receptor 5

VN1R5

3.566

4.20 × 10^-2

Upregulated

Tetratricopeptide repeat protein 13

TTC13

2.512

9.28 × 10^-5

Upregulated

Membrane-spanning 4-domains subfamily A member 14

MS4A14

2.126

2.25 × 10^-4

Upregulated

Complement factor I

CFI

2.041

1.26 × 10^-2

Upregulated

Calcium-binding and coiled-coil domain-containing protein 2

CALCOCO2

2.034

2.84 × 10^-2

Upregulated

Regulator of G-protein signaling protein-like

RGSL1

2.029

5.85 × 10^-4

Upregulated

Cilia- and flagella-associated protein 54

CFAP54

1.857

7.17 × 10^-3

Upregulated

Thioredoxin domain-containing protein 9

TXNDC9

1.830

5.97 × 10^-3

Upregulated

Unconventional myosin-If

MYO1F

1.818

2.84 × 10^-3

Upregulated

Mitochondrial 10-formyltetrahydrofolate dehydrogenase

ALDH1L2

1.756

1.73 × 10^-3

Upregulated

Clusterin

CLU

1.744

4.82 × 10^-2

Upregulated

Claudin-6

CLDN6

1.744

1.50 × 10^-2

Upregulated

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-4

GNG4

1.736

3.38 × 10^-2

Upregulated

N6-adenosine-methyltransferase catalytic subunit

METTL3

1.735

4.50 × 10^-2

Upregulated

Uncharacterized protein C1orf167

C1orf167

1.709

4.86 × 10^-2

Upregulated

RWD domain-containing protein 1

RWDD1

1.701

2.13 × 10^-2

Upregulated

Phosphoserine aminotransferase

PSAT1

1.698

1.95 × 10^-4

Upregulated

Rabenosyn-5

RBSN

1.698

2.22 × 10^-2

Upregulated

Prosaposin

PSAP

1.689

1.23 × 10^-3

Downregulated

UPF0488 protein C8orf33

C8orf33

0.833

5.34 × 10^-3

Downregulated

Synaptobrevin homolog YKT6

YKT6

0.833

3.90 × 10^-4

Downregulated

SPATS2-like protein

SPATS2L

0.833

1.26 × 10^-2

Downregulated

E3 ubiquitin-protein ligase RNF114

RNF114

0.833

2.27 × 10^-2

Downregulated

Transcription initiation factor IIB

GTF2B

0.833

2.55 × 10^-3

Downregulated

Tyrosine-protein phosphatase non-receptor type 2

PTPN2

0.832

2.69 × 10^-2

Downregulated

MOB kinase activator 3A

MOB3A

0.832

3.84 × 10^-3

Downregulated

Copine-2

CPNE2

0.832

4.00 × 10^-2

Downregulated

FERM domain-containing protein 5

FRMD5

0.832

1.90 × 10^-2

Downregulated

Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform

PPP2R2C

0.831

4.78 × 10^-2

Downregulated

FLYWCH family member 2

FLYWCH2

0.831

3.89 × 10^-2

Downregulated

F-box/LRR-repeat protein 6

FBXL6

0.830

1.57 × 10^-3

Downregulated

Exportin-6

XPO6

0.830

8.37 × 10^-3

Downregulated

Starch-binding domain-containing protein 1

STBD1

0.829

4.82 × 10^-2

Downregulated

Microfibrillar-associated protein 1

MFAP1

0.828

3.46 × 10^-2

Downregulated

Autism susceptibility gene 2 protein

AUTS2

0.828

4.84 × 10^-2

Downregulated

tRNA (guanine-N(7)-)-methyltransferase

METTL1

0.828

2.41 × 10^-2

Downregulated

E3 ubiquitin-protein ligase UHRF2

UHRF2

0.828

1.03 × 10^-2

Downregulated

DNA replication licensing factor MCM3

MCM3

0.827

1.61 × 10^-3

Downregulated

Ras GTPase-activating protein nGAP

RASAL2

0.827

4.42 × 10^-2

**Table 2.** The Interacting Proteins (Top 10) in PPI Network in Different Clusters
Cluster	Protein	Protein name	Gene name	Subcellular localization
Cluster1	Q9Y6C9	Mitochondrial carrier homolog 2	MTCH2	Plasma membrane
	Q9Y617	Phosphoserine aminotransferase	PSAT1	Cytoplasmic
	Q9Y5Y2	Cytosolic Fe-S cluster assembly factor NUBP2	NUBP2	Cytoplasmic
	Q9Y5T5	Ubiquitin carboxyl-terminal hydrolase 16	USP16	Nuclear
	Q9Y4W6	AFG3-like protein 2	AFG3L2	Mitochondrial
	Q9Y4F3	Meiosis regulator and mRNA stability factor 1	MARF1	Nuclear
	Q9Y2Z4	Tyrosine—tRNA ligase, mitochondrial	YARS2	Mitochondrial
	Q9UJS0	Calcium-binding mitochondrial carrier protein Aralar2	SLC25A13	Plasma membrane; cytoplasmic; mitochondrial
	Q9UJF2	Ras GTPase-activating protein nGAP	RASAL2	Nuclear
	Q9UHQ9	NADH-cytochrome b5 reductase 1	CYB5R1	Mitochondrial
Cluster2	Q9Y6R4	Mitogen-activated protein kinase kinase kinase 4	MAP3K4	Nuclear
	Q9Y618	Nuclear receptor corepressor 2	NCOR2	Nuclear
	Q9Y3Y2	Chromatin target of PRMT1 protein	CHTOP	Mitochondrial; nuclear
	Q9Y388	RNA-binding motif protein, X-linked 2	RBMX2	Nuclear
	Q9Y2W2	WW domain-binding protein 11	WBP11	Nuclear
	Q9UKX7	Nuclear pore complex protein Nup50	NUP50	Nuclear
	Q9UBU8	Mortality factor 4-like protein 1	MORF4L1	Mitochondrial; nuclear
	Q9P013	Spliceosome-associated protein CWC15 homolog	CWC15	Nuclear
	Q9NYV4	Cyclin-dependent kinase 12	CDK12	Nuclear
	Q9NYF8	Bcl-2-associated transcription factor 1	BCLAF1	Nuclear
Cluster3	Q9Y508	E3 ubiquitin-protein ligase RNF114	RNF114	Extracellular
	Q9Y448	Small kinetochore-associated protein	KNSTRN	Extracellular; nuclear
	Q9Y248	DNA replication complex GINS protein PSF2	GINS2	Cytoplasmic; nuclear
	Q9Y232	Chromodomain Y-like protein	CDYL	Nuclear
	Q9UQR0	Sex comb on midleg-like protein 2	SCML2	Nuclear
	Q9UPN4	Centrosomal protein of 131 kDa	CEP131	Nuclear
	Q9ULW0	Targeting protein for Xklp2	TPX2	Nuclear
	Q9P270	SLAIN motif-containing protein 2	SLAIN2	Nuclear
	Q9P1Y6	PHD and RING finger domain-containing protein 1	PHRF1	Nuclear
	Q9NYZ3	G2 and S phase-expressed protein 1	GTSE1	Nuclear
Cluster4	Q9Y6K8	Adenylate kinase isoenzyme 5	AK5	Cytoplasmic; nuclear
	Q9Y6I9	Testis-expressed protein 264	TEX264	Extracellular; plasma membrane
	Q9Y646	Carboxypeptidase Q	CPQ	Cytoplasmic
	Q9Y2Q5	Ragulator complex protein LAMTOR2	LAMTOR2	Extracellular
	Q9Y233	cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	PDE10A	Plasma membrane; cytoplasmic
	Q9P2L0	WD repeat-containing protein 35	WDR35	Cytoplasmic
	Q9H8M9	Protein eva-1 homolog A	EVA1A	Extracellular; nuclear
	Q9BY42	Replication termination factor 2	RTF2	Nuclear
	Q9BXB4	Oxysterol-binding protein-related protein 11	OSBPL11	Nuclear
	Q9BX10	GTP-binding protein 2	GTPBP2	Cytoplasmic; nuclear
Cluster5	Q9Y520	Protein PRRC2C	PRRC2C	Nuclear
	Q9Y3B9	RRP15-like protein	RRP15	Nuclear
	Q9Y3A6	Transmembrane emp24 domain-containing protein 5	TMED5	Cytoplasmic
	Q9Y2L5	Trafficking protein particle complex subunit 8	TRAPPC8	Nuclear
	Q9UNQ2	Probable dimethyladenosine transferase	DIMT1	Mitochondrial; nuclear
	Q9ULX3	RNA-binding protein NOB1	NOB1	Nuclear
	Q9ULW3	Activator of basal transcription 1	ABT1	Nuclear
	Q9UBQ5	Eukaryotic translation initiation factor 3 subunit K	EIF3K	Cytoplasmic
	Q9UBP6	tRNA (guanine-N(7)-)-methyltransferase	METTL1	Cytoplasmic; mitochondrial; nuclear
	Q9P015	39S ribosomal protein L15, mitochondrial	MRPL15	Cytoplasmic; mitochondrial; nuclear

Table 2. The Interacting Proteins (Top 10) in PPI Network in Different Clusters

Cluster

Protein

Protein name

Gene name

Subcellular localization

Cluster1

Q9Y6C9

Mitochondrial carrier homolog 2

MTCH2

Plasma membrane

Q9Y617

Phosphoserine aminotransferase

PSAT1

Cytoplasmic

Q9Y5Y2

Cytosolic Fe-S cluster assembly factor NUBP2

NUBP2

Cytoplasmic

Q9Y5T5

Ubiquitin carboxyl-terminal hydrolase 16

USP16

Nuclear

Q9Y4W6

AFG3-like protein 2

AFG3L2

Mitochondrial

Q9Y4F3

Meiosis regulator and mRNA stability factor 1

MARF1

Nuclear

Q9Y2Z4

Tyrosine—tRNA ligase, mitochondrial

YARS2

Mitochondrial

Q9UJS0

Calcium-binding mitochondrial carrier protein Aralar2

SLC25A13

Plasma membrane; cytoplasmic; mitochondrial

Q9UJF2

Ras GTPase-activating protein nGAP

RASAL2

Nuclear

Q9UHQ9

NADH-cytochrome b5 reductase 1

CYB5R1

Mitochondrial

Cluster2

Q9Y6R4

Mitogen-activated protein kinase kinase kinase 4

MAP3K4

Nuclear

Q9Y618

Nuclear receptor corepressor 2

NCOR2

Nuclear

Q9Y3Y2

Chromatin target of PRMT1 protein

CHTOP

Mitochondrial; nuclear

Q9Y388

RNA-binding motif protein, X-linked 2

RBMX2

Nuclear

Q9Y2W2

WW domain-binding protein 11

WBP11

Nuclear

Q9UKX7

Nuclear pore complex protein Nup50

NUP50

Nuclear

Q9UBU8

Mortality factor 4-like protein 1

MORF4L1

Mitochondrial; nuclear

Q9P013

Spliceosome-associated protein CWC15 homolog

CWC15

Nuclear

Q9NYV4

Cyclin-dependent kinase 12

CDK12

Nuclear

Q9NYF8

Bcl-2-associated transcription factor 1

BCLAF1

Nuclear

Cluster3

Q9Y508

E3 ubiquitin-protein ligase RNF114

RNF114

Extracellular

Q9Y448

Small kinetochore-associated protein

KNSTRN

Extracellular; nuclear

Q9Y248

DNA replication complex GINS protein PSF2

GINS2

Cytoplasmic; nuclear

Q9Y232

Chromodomain Y-like protein

CDYL

Nuclear

Q9UQR0

Sex comb on midleg-like protein 2

SCML2

Nuclear

Q9UPN4

Centrosomal protein of 131 kDa

CEP131

Nuclear

Q9ULW0

Targeting protein for Xklp2

TPX2

Nuclear

Q9P270

SLAIN motif-containing protein 2

SLAIN2

Nuclear

Q9P1Y6

PHD and RING finger domain-containing protein 1

PHRF1

Nuclear

Q9NYZ3

G2 and S phase-expressed protein 1

GTSE1

Nuclear

Cluster4

Q9Y6K8

Adenylate kinase isoenzyme 5

AK5

Cytoplasmic; nuclear

Q9Y6I9

Testis-expressed protein 264

TEX264

Extracellular; plasma membrane

Q9Y646

Carboxypeptidase Q

CPQ

Cytoplasmic

Q9Y2Q5

Ragulator complex protein LAMTOR2

LAMTOR2

Extracellular

Q9Y233

cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A

PDE10A

Plasma membrane; cytoplasmic

Q9P2L0

WD repeat-containing protein 35

WDR35

Cytoplasmic

Q9H8M9

Protein eva-1 homolog A

EVA1A

Extracellular; nuclear

Q9BY42

Replication termination factor 2

RTF2

Nuclear

Q9BXB4

Oxysterol-binding protein-related protein 11

OSBPL11

Nuclear

Q9BX10

GTP-binding protein 2

GTPBP2

Cytoplasmic; nuclear

Cluster5

Q9Y520

Protein PRRC2C

PRRC2C

Nuclear

Q9Y3B9

RRP15-like protein

RRP15

Nuclear

Q9Y3A6

Transmembrane emp24 domain-containing protein 5

TMED5

Cytoplasmic

Q9Y2L5

Trafficking protein particle complex subunit 8

TRAPPC8

Nuclear

Q9UNQ2

Probable dimethyladenosine transferase

DIMT1

Mitochondrial; nuclear

Q9ULX3

RNA-binding protein NOB1

NOB1

Nuclear

Q9ULW3

Activator of basal transcription 1

ABT1

Nuclear

Q9UBQ5

Eukaryotic translation initiation factor 3 subunit K

EIF3K

Cytoplasmic

Q9UBP6

tRNA (guanine-N(7)-)-methyltransferase

METTL1

Cytoplasmic; mitochondrial; nuclear

Q9P015

39S ribosomal protein L15, mitochondrial

MRPL15

Cytoplasmic; mitochondrial; nuclear