Identification of potential pathogenic genes of intestinal metaplasia based on transcriptomic sequencing and bioinformatics analysis

doi:10.12122/j.issn.1673-4254.2024.05.16

Abstract

Abstract:

Objective To explore the potential pathogenic genes of intestinal metaplasia. Methods Twenty-one patients with intestinal metaplasia admitted to the Department of Gastroenterology at the Second Affiliated Hospital of Anhui University of Chinese Medicine from January, 2022 to June, 2022, and 21 healthy subjects undergoing gastroscopic examination during the same period were enrolled in this study. All the participants underwent gastroscopy and pathological examination, and gastric tissue samples were collected for transcriptome sequencing to screen for differentially expressed genes (DEGs). The biological functions of the DEGs were analyzed using bioinformatics analysis, and qRT-PCR was used to validate the results. Results Transcriptomic sequencing identified a total of 1373 DEGs, including 827 upregulated and 546 downregulated ones. The top 6 upregulated genes (AGMAT, CCL25, FABP1, CDX1, SPINK4, and MUC2), ranked based on their significance and average expression level, were selected for validation, and qRT-PCR showed significant upregulation of their mRNAs in the gastric tissues of patients with intestinal metaplasia (P<0.05). Conclusion AGMAT, CCL25, FABP1, CDX1, SPINK4, and MUC2 participate in the occurrence and development of intestinal metaplasia, and may serve as potential biomarkers for diagnosing intestinal metaplasia.

Key words: intestinal metaplasia, pathogenic genes, transcriptomics sequencing, bioinformatics

Bei PEI, Yi ZHANG, Siyuan WEI, Yu MEI, Biao SONG, Gang DONG, Ziang WEN, Xuejun LI. Identification of potential pathogenic genes of intestinal metaplasia based on transcriptomic sequencing and bioinformatics analysis[J]. Journal of Southern Medical University, 2024, 44(5): 941-949.

Figures/Tables 9

References 44

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Name	Forward primer	Reverse primer
AGMAT	5′-CTCACTCCTAGTCAGGCTC-3′	5′-TGAAACTTCGACAAGATCACAG-3′
CCL25	5′-CACCCAAGGTGTCTTTGAG-3′	5′-CTGGATCCGGTAAGTCCAG-3′
FABP1	5′-CATGAAGGCAATCGGTCTG-3′	5′-CCATTCTGCACGATTTCCG-3′
SPINK4	5′-TCAAGAATGCCCATCTGTG-3′	5′-ATATGTGAGCCCATCAGTG-3′
CDX1	5′-TCGGACCAAGGACAAGTACC-3′	5′-AGATCTTCACCTGCCGTTCA-3′
MUC2	5′-GCTGTCCCTTCTACTGGTGT-3′	5′-GTTGAGCAGGGTGTTGTTGT-3′

Name	Forward primer	Reverse primer
AGMAT	5′-CTCACTCCTAGTCAGGCTC-3′	5′-TGAAACTTCGACAAGATCACAG-3′
CCL25	5′-CACCCAAGGTGTCTTTGAG-3′	5′-CTGGATCCGGTAAGTCCAG-3′
FABP1	5′-CATGAAGGCAATCGGTCTG-3′	5′-CCATTCTGCACGATTTCCG-3′
SPINK4	5′-TCAAGAATGCCCATCTGTG-3′	5′-ATATGTGAGCCCATCAGTG-3′
CDX1	5′-TCGGACCAAGGACAAGTACC-3′	5′-AGATCTTCACCTGCCGTTCA-3′
MUC2	5′-GCTGTCCCTTCTACTGGTGT-3′	5′-GTTGAGCAGGGTGTTGTTGT-3′

Indexes	Control group	IM group	P
Age (year)	56.76±10.64	60.62±9.02	0.2124
Gender			0.7579
Male	10	12
Female	11	9
Smoking history			0.6965
Yes	3	5
No	18	16
Drinking history			0.4841
Yes	4	7
No	17	14
Diet			0.6060
Irregular	1	3
Regular	20	18
Diabetes			0.9999
Yes	0	1
No	21	20
Hypertension			0.6965
Yes	3	5
No	18	16
Hyperlipidemia			0.7186
Yes	4	6
No	17	15
Family history of tumors			0.6060
Yes	1	3
No	20	18
H. pylori infection			0.9999
Yes	0	0
No	21	21

Indexes	Control group	IM group	P
Age (year)	56.76±10.64	60.62±9.02	0.2124
Gender			0.7579
Male	10	12
Female	11	9
Smoking history			0.6965
Yes	3	5
No	18	16
Drinking history			0.4841
Yes	4	7
No	17	14
Diet			0.6060
Irregular	1	3
Regular	20	18
Diabetes			0.9999
Yes	0	1
No	21	20
Hypertension			0.6965
Yes	3	5
No	18	16
Hyperlipidemia			0.7186
Yes	4	6
No	17	15
Family history of tumors			0.6060
Yes	1	3
No	20	18
H. pylori infection			0.9999
Yes	0	0
No	21	21

Name	Description	P
AGMAT	Agmatinase	3.51×10^-13
CCL25	C-C motif chemokine ligand 25	8.86×10^-13
FABP1	Fatty acid binding protein 1	6.22×10^-11
MUC2	Mucin 2	1.95×10^-10
SPINK4	Serine peptidase inhibitor Kazal type 4	1.04×10^-9
ANXA13	Annexin A13	1.24×10^-9
GIP	Gastric inhibitory polypeptide	2.01×10^-9
KCP	Kielin cysteine rich BMP regulator	2.48×10^-9
DEFA5	Defensin alpha 5	2.55×10^-9
ZG16	Zymogen granule protein 16	4.38×10^-9
CDX1	Caudal type homeobox 1	9.33×10^-9
RAB3B	RAB3B, member RAS oncogene family	1.35×10^-8
PTAFR	Platelet activating factor receptor	2.37×10^-8
RBP2	Retinol binding protein 2	4.19×10^-8
OLFM4	Olfactomedin 4	4.19×10^-8
ALPI	Alkaline phosphatase, intestinal	6.04×10^-8
MOCOS	Molybdenum cofactor sulfurase	8.81×10^-8
SLC6A20	Solute carrier family 6 member 20	1.18×10^-7
HOXB9	Homeobox B9	2.88×10^-7
CPS1	Carbamoyl-phosphate synthase 1	3.00×10^-7