Gene, genetics and genetic medicines in gastroenterology: Current status and its future

Table 1 Different types of epigenetic changes and their impact on gene[6-9]

Mechanism	How it works	Effect on genes with example
DNA methylation[6]	Addition of methyl groups (-CH3) to DNA (usually at CpG islands)	MLH1 silenced: Leads to microsatellite instability increased mutation rate
Histone modification[7]	Acetylation, methylation, phosphorylation of histone proteins	CDH1 (E-cadherin) silenced by H3 acetylation in promoter regions of cytokine genes (e.g., TNF-α) leads to increased transcription
Chromatin remodeling[8]	Changing the physical structure of chromatin	Loss of ARID1A failure of chromatin remodeling improper gene silencing or activation. Progression of HCC, CRC
Non-coding RNAs (e.g., miRNA, lncRNA)[9]	Bind to mRNA or DNA to regulate expression	CRC (miR-21, miR-135b, lncRNA HOTAIR); gastric cancer (miR-148a, miR-21, lncRNA MALAT1, circPVT1); inflammatory bowel disease (miR-155, miR-21, lncRNA IFNG-AS1); HCC (miR-122, miR-221/222, lncRNA HULC); celiac disease (miR-449a)

miRNA: MicroRNA; lncRNA: Long non-coding RNA; CH₃: Methyl group; mRNA: Messenger RNA; TNF-α: Tumor necrosis factor alpha; CRC: Colorectal cancer; HCC: Hepatocellular carcinoma; circPVT1: Circular RNA plasmacytoma variant translocation 1.

Table 2 Different genetic pathway disorders, its mechanism of action in gastrointestinal tract

Genetic pathway disorder	Mechanism	Examples
Monogenic disorders	Mutations in a single gene that often follow Mendelian inheritance patterns	Hereditary hemochromatosis (HFE gene), Wilson disease (ATP7B gene), alpha-1 antitrypsin deficiency
Polygenic and multifactorial disorders	Involve multiple genes and environmental interactions	Inflammatory bowel disease (over 200 loci have been identified), celiac disease (HLA-DQ2 and HLA-DQ8)
Cancer predisposition syndromes	Inherited mutations in tumor suppressor genes or DNA repair genes increase GI cancer risk	Lynch syndrome (HNPCC) (MLH1, MSH2), familial adenomatous polyposis (APC) gene
Mosaicism	Two or more genetically distinct cell populations within the same individual, derived from a single zygote	Mosaic APC gene mutations may cause attenuated forms of FAP. Very early changes in IBD

GI: Gastrointestinal; FAP: Familial adenomatous polyposis; HNPCC: Hereditary non-polyposis colorectal cancer; IBD: Inflammatory bowel disease.

Table 3 Classification of genes based on their function and their association with gastrointestinal disorders[10-16]

Genes	Function	Associated disorders
Genes involved in DNA repair and genomic stability[10]
MLH1, MSH2, MSH6, PMS2, EPCAM	Mismatch repair (MMR) system	Lynch syndrome colorectal, gastric, pancreatic cancer
MUTYH	Base excision repair	MUTYH-associated polyposis
BRCA1/BRCA2, ATM, PALB2	Double-strand break repair	Familial pancreatic and gastric cancers
TP53	Tumor suppressor, DNA damage response	CRC, gastric, pancreatic, hepatocellular carcinoma
Genes involved in cell adhesion and structural integrity[11]
CDH1	E-cadherin (cell-cell adhesion)	Hereditary diffuse gastric cancer
CTNNA1	Catenin alpha-1 (adherens junctions)	HDGC
SMAD4, BMPR1A	TGF-β pathway mediators	Juvenile polyposis syndrome, pancreatic cancer
Genes regulating inflammation and immune response[12]
NOD2	Innate immunity, bacterial sensing	Crohn’s disease
IL23R, IL10, IL12B	Cytokine signaling	IBD susceptibility
IRGM, ATG16 L1	Autophagy genes	Crohn’s disease
HLA-DQA1/HLA-DQB1	Antigen presentation	Celiac disease
TLR4, TLR9	Pattern recognition receptors	Functional dyspepsia, IBD
Genes involved in bile acid transport and cholestasis[13]
ABCB11	Bile salt export pump	PFIC2, BRIC
ABCC2 (MRP2)	Bile excretion	Dubin-Johnson syndrome
ATP8B1	Phospholipid transporter	PFIC1
TJP2	Tight junction protein	PFIC4
Genes in neuronal/gut motility and enteric nervous system[14]
RET, EDNRB, GDNF	ENS development	Hirschsprung’s disease
SCN5A	Sodium channel in ICCs/ENS	IBS with constipation
NEUROG3	Enteroendocrine differentiation	Congenital malabsorptive diarrhoea
Genes affecting nutrient absorption and metabolism[15]
LCT	Lactase enzyme	Lactose intolerance
SAR1B	Chylomicron transport	Chylomicron retention disease
SLC26A3	Cl-/HCO3- exchange	Congenital chloride diarrhea
SLC5A1 (SGLT1)	Glucose transport	Glucose-galactose malabsorption
Genes in oncogenic signaling and growth factors[15]
KRAS, NRAS	MAPK signaling	CRC, pancreatic cancer
BRAF	Downstream of KRAS	CRC (BRAF V600E in MSI tumors)
PIK3CA	PI3K/AKT pathway	CRC, gastric cancer
EGFR, HER2 (ERBB2)	Receptor tyrosine kinases	Gastric, colorectal cancers
FGFR2, IDH1/IDH2	Growth factor pathways	Cholangiocarcinoma
Genes related to epigenetic and transcriptional regulation[16]
ARID1A	Chromatin remodeling	Biliary cancer, CRC, gastric
MLH3, MSH3	Mismatch repair (minor MMR genes)	Polyposis syndromes
TET2, DNMT3A	DNA methylation regulation	CRC and inflammatory epigenetic signatures

MMR: Mismatch repair; CRC: Colorectal cancer; HDGC: Hereditary diffuse gastric cancer; TGF-β: Transforming growth factor-beta; IBD: Inflammatory bowel disease; PFIC: Progressive familial intrahepatic cholestasis; BRIC: Benign recurrent intrahepatic cholestasis; ENS: Enteric nervous system; ICCs: Interstitial cells of Cajal; IBS: Irritable bowel syndrome; Cl^-: Chloride ion; HCO₃^-: Bicarbonate ion; MAPK: Mitogen activated protein kinase; MSI: Microsatellite instability; PI3K: Phosphoinositide 3-kinase; AKT: Protein kinase B.

Table 4 Genetic pathways, genes, and gastrointestinal disorders[17-32]

Pathway	Key genes	Associated disorders	Mechanism/role	Ref.
Wnt/β-catenin	APC, CTNNB1, AXIN2	Colorectal cancer, hepatocellular carcinoma (HCC), familial adenomatous polyposis	Controls cell proliferation and differentiation; mutation leads to uncontrolled growth	Li et al[17]
NF-κB	NFKB1, TNFAIP3, IKK complex	IBD (Crohn’s, UC), gastric cancer, colorectal cancer	Regulates inflammation, cell survival, immunity; chronic activation promotes inflammation and tumorigenesis	Peng et al[18]
TGF-β/SMAD	TGFBR2, SMAD4	Juvenile polyposis, CRC, pancreatic cancer	Controls growth inhibition and apoptosis; mutations cause evasion of tumor suppression	Hata and Chen[19]
JAK/STAT	JAK2, STAT3, STAT1	IBD, colitis-associated cancer	Regulates immune cell signaling and cytokine responses	Hu et al[20]
MAPK/ERK	KRAS, BRAF, EGFR	CRC, pancreatic cancer, gastric cancer	Regulates cell proliferation and survival; mutations oncogenic signaling	Guo et al[21]
PI3K/AKT/mTOR	PIK3CA, PTEN, AKT1, MTOR	CRC, gastric cancer, IBD	Promotes cell growth, metabolism, and angiogenesis; dysregulation contributes to tumor growth and inflammation	Glaviano et al[22]
Mismatch repair	MLH1, MSH2, MSH6, PMS2	Lynch syndrome, CRC, gastric cancer	Repairs DNA replication errors; loss leads to microsatellite instability (MSI)	Li[23]
P53 pathway	TP53	CRC, esophageal, gastric, HCC	Controls cell cycle arrest, apoptosis, DNA repair; mutations common in late cancer stages	Harris and Levine[24]
Hedgehog signaling	PTCH1, GLI1	Gastric cancer, GI developmental disorders	Controls tissue patterning and stem cell maintenance	Briscoe and Thérond[25]
Notch signaling	NOTCH1, DLL1, HES1	Colitis, CRC, esophageal cancer	Regulates differentiation, especially goblet cells; dysregulation affects intestinal homeostasis	Kopan[26]
Autophagy pathway	ATG16 L1, IRGM	Crohn’s disease, IBD-associated cancer	Maintains intracellular bacterial clearance and mucosal homeostasis	Yu et al[27]
Immune checkpoint pathway	PD-L1, CTLA4	MSI-high CRC, gastric cancer, IBD	Immune evasion in cancer; dysregulated tolerance in autoimmune GI diseases	He and Xu[28]
ER stress/UPR	XBP1, IRE1, PERK	IBD, Paneth cell dysfunction, CRC	Regulates response to unfolded proteins; chronic ER stress leads to inflammation and epithelial damage	Chen et al[29]
IL-23/Th17 pathway	IL23R, STAT3, RORC	Crohn’s disease, UC, CRC	Inflammatory cytokine signaling driving chronic inflammation	Bunte and Beikler[30]
Apoptosis/FAS-FASL	FAS, BAX, CASP8	Colitis-associated cancer, gastric cancer	Regulates programmed cell death; evasion supports tumor survival	Waring and Müllbacher[31]
DNA repair pathways (base/nucleotide excision)	OGG1, XPA, POLB	CRC, gastric cancer	Repair oxidative and chemical DNA damage; defects genomic instability	Kumar et al[32]

NF-κB: Nuclear factor kappa-B; TGF-β: Transforming growth factor-beta; JAK: Janus tyrosine kinase; STAT: Signal transducer and activator of transcription; MAPK: Mitogen-activated protein kinase; ERK: Extracellular regulated protein kinases; PI3K: Phosphatidylinositol 3-kinase; AKT: Protein kinase B; mTOR: Mammalian target of rapamycin; UPR: Unfolded protein response; ER: Endoplasmic reticulum; IL: Interleukin; Th: T helper; HCC: Hepatocellular carcinoma; IBD: Inflammatory bowel disease; UC: Ulcerative colitis; CRC: Colorectal cancer; GI: Gastrointestinal; MSI: Microsatellite instability.

Table 5 Various types of clinical genetic testing

Classification	Type	Purpose
Mutation origin	Germline testing	Detects inherited mutations; used for familial risk, carrier status, and predisposition
	Somatic testing	Identifies acquired mutations in specific tissues (e.g., tumors); guides cancer therapy
	Mosaicism testing	Identify mosaicism in FAP, IBD
Clinical purpose	Diagnostic testing	Confirms or rules out a specific genetic disorder in symptomatic individuals
	Prognostic testing	Predicts disease course, severity, or likelihood of complications
	Predictive/screening	Identifies asymptomatic individuals at risk of developing a genetic disorder
	Carrier testing	Identifies individuals who carry one copy of a gene mutation (relevant for recessive conditions)
	Pharmacogenetic testing	Assesses genetic variants affecting drug metabolism and response
	Somatic/tumor profiling	Detects actionable mutations in cancer cells to guide targeted therapy and prognosis
	Newborn screening	Early identification of treatable genetic disorders in neonates

FAP: Familial adenomatous polyposis; IBD: Inflammatory bowel disease.

Table 6 Germline testing available for screening

No.	GI disorder/syndrome	Guideline source	Genes recommended for testing	Testing criteria
1	Lynch syndrome (hereditary nonpolyposis colorectal cancer)	ACG, NCCN, ESMO	MLH1, MSH2, MSH6, PMS2, EPCAM	Personal/family history of colorectal, endometrial, or other LS-associated cancers; tumor MSI or IHC abnormality
2	Familial adenomatous polyposis (FAP)	ACG, NCCN	APC	> 100 colorectal adenomas or family history of FAP
3	Attenuated FAP	ACG	APC	Patients with 10-99 adenomas
4	MUTYH-associated polyposis	ACG	MUTYH (biallelic)	Multiple adenomas and autosomal recessive inheritance
5	Peutz-Jeghers syndrome	NCCN, ESMO	STK11	Mucocutaneous pigmentation and hamartomatous polyps; family history
6	Juvenile polyposis syndrome	ACG, NCCN	SMAD4, BMPR1A	≥ 5 juvenile polyps or family history
7	Cowden syndrome/PTEN hamartoma tumor syndrome	NCCN	PTEN	GI polyps with mucocutaneous lesions or macrocephaly
8	Hereditary pancreatic cancer	NCCN	BRCA1/BRCA2, PALB2, ATM, CDKN2A, STK11	Family history of pancreatic cancer or known mutation
9	Hereditary diffuse gastric cancer	NCCN	CDH1	Family history of diffuse gastric cancer or lobular breast cancer
10	Serrated polyposis syndrome	WHO, ACG	No known high-penetrance genes; RNF43 under investigation	Multiple serrated polyps meeting WHO criteria

FAP: Familial adenomatous polyposis; ACG: American College of Gastroenterology; NCCN: National Comprehensive Cancer Network; ESMO: European Society for Medical Oncology; WHO: World Health Organization; LS: Lynch syndrome; MSI: Microsatellite instability; GI: Gastrointestinal; IHC: Immunohistochemistry.

Table 7 Methods for genetic testing and its clinical implication[35-55]

Test	Detects	Clinical use	Benefit	Limitation	Ref.
Cytogenetic testing
Karyotyping (conventional cytogenetics)	Detects large chromosomal abnormalities: Trisomies, translocations, deletions, G-banding of metaphase chromosomes	Down syndrome, Turner syndrome	Whole-genome overview, identifies balanced/unbalanced rearrangements	Low resolution, cannot detect small deletions/duplications, requires dividing cells	Genetic Alliance[35]
Fluorescence in situ hybridization (FISH)	Fluorescent probes bind specific DNA sequences on chromosomes	Detects gene amplifications, deletions, rearrangements (e.g., HER2 in gastric cancer, ALK in GI stromal tumors)	Rapid, targeted, works on interphase cells	Limited to known targets, one probe/test, cannot assess whole genome	Yilmaz and Demiray[36]
Comparative genomic hybridization (aCGH)	DNA from patient and control hybridized to a microarray	Detects copy number variations (e.g., deletions in polyposis syndromes, microdeletion syndromes	High-resolution, genome-wide, detects sub microscopic CNV	Cannot detect balanced rearrangements (e.g., translocations), limited to CNVs only	Weiss et al[37]
Chromosomal microarray analysis	aCGH + SNP array	Used in syndromic GI diseases, unexplained developmental delay, congenital anomalies	Genome-wide, detects CNVs, uniparental disomy, mosaicism	Cannot detect balanced rearrangements, may report VUS	Myllykangas et al[38]
Spectral karyotyping	Whole chromosome painting with multicolor FISH	Identifies complex chromosomal rearrangements, often in cancers	Detects complex karyotypes, color-coded analysis	Expensive, not used for routine diagnostics, lower resolution than aCGH	Guo et al[39]
Molecular genetic testing
Sanger sequencing	SNV, small insertions/deletions	Confirmatory testing (e.g., known APC, MLH1 mutations	High accuracy for point mutation or small deletion/duplication/SNV, cost effective for single genetic testing	Only identify small subset of gene or single gene, not precisely quantifiable	Herpich et al[40]
NGS	Panel, exome, or genome-wide variants	Multigene panels for IBD, polyposis, CRC, gastric cancer, GIST	Multiple, individually produced readings of the target area mosaism, quantitative, whole exome or genome sequencing	Limited in their ability to detect copy number variations, incidental findings need to be verified by sanger sequencing	Satam et al[41]
Targeted gene panels	Focused sequencing of disease-specific genes	Panel specific to GIST, IBD, hereditary colorectal cancer panel, gist panel	Accurate diagnosis focus on specific genes cost-effective and efficient: Can be customized according to disorder	Limited coverage not detect structural rearrangements or copy number variants cannot identify novel or new gene related to disease	Málaga et al[42]
Whole exome sequencing	All coding regions	Early-onset or monogenic IBD, congenital diarrheal disorders (e.g., DGAT1, EPCAM mutations). Hereditary pancreatitis (e.g., PRSS1, SPINK1) colorectal cancer	Cost-effective WES allows deeper sequencies WES captures approximately 85% of known disease-causing mutations	Misses non-coding variants incomplete exome coverage	Rabbani et al[43]; Uhlig et a[[44]
WGS	Coding and non-coding genome variant	Identification of colorectal cancer genes. Undiagnosed complex disease	Cover both coding and non-coding reason detection of structural variant both germline and somatic mutation	High cost difficult to pathogenic variant from benign variant	de Voer et al[45]
MLPA	Large deletions/duplications	Detects large deletions, especially EPCAM deletions causing MSH2 inactivation	Efficient CNV detection cost-effective and high throughput applicable on degraded DNA	Cannot detect point mutations or small indels limited to pre-designed probes	Kuiper et al[46]; Schouten et al[47]
qPCR	Copy number variations or known mutations	Rapid screening for common mutations, detects bacterial, viral, and parasitic DNA/RNA rapidly and accurately, bacterial load determination in gastro intestinal disorder	High sensitivity and specificity, rapid turnaround, quantitative	Requires prior sequence knowledge	Shah et al[48]; Bamias et al[49]
Array comparative genomic hybridization (aCGH)	Sub microscopic deletions/duplications, germline CNVs in genes like APC, SMAD4, and BMPR1A	Genome-wide coverage, germline CNVs in genes like APC, SMAD4 and BMPR1A	High resolution can detect CNVs as small as 50-100 kb	Inability to detect balanced chromosomal rearrangements difficulties in interpreting CNVs of uncertain significance	McKay et al[50]; Assämäki et al[51]
HLA typing (PCR-SSP, NGS-based)	HLA allele identification	Celiac disease, IBD pharmacogenetics IBD, primary sclerosing cholangitis drug-induced GI injury, idiosyncratic reactions to drugs causing hepatic/GI damage. Transplant compatibility	Cost-effective, simple requires minimal computational support	Limited resolution may not differentiate similar alleles. May yield ambiguous results	Megiorni and Pizzuti[52]
FISH	Large chromosomal rearrangements, gene fusions	In Barretts esophagus identifies chromosomal instability (e.g., 20q gain, 18q loss), and BRAF rearrangements; detection of HER2 gene amplification (ERBB2 at 17q12) predicts response to trastuzumab therapy (gastric cancer)	High specificity and sensitivity for targeted chromosomal regions	Targeted approach only. Limited genomic coverage	Brankley et al[53]
PCR	Specific known mutations	Quick detection (e.g., PRSS1 in hereditary pancreatitis), KRAS in CRC	High sensitivity and specificity can detect minute amounts of target DNA/RNA. Rapid turnaround time. Typically, within a few hours. Quantitative provides absolute or relative quantification	Requires prior sequence knowledge. Primers must be designed for specific known targets. Cannot differentiate live from dead organisms, detects DNA from both	Tol et al[54]
RNA-seq	Gene expression, fusion transcripts	Detects tumor-specific expression changes, fusion transcripts (e.g., NTRK fusions), and provides prognostic biomarkers in CRC reveals deregulated pathways (e.g., WNT, PI3K), tumor microenvironment features, and therapeutic target molecular marker of pancreatic cancer	Unbiased and comprehensive: Captures all RNA species (mRNA, lncRNA, miRNA, circular RNA), high resolution. Detects single-nucleotide changes, splicing variants, and gene fusions	Expensive and resource-intensive, requires advanced sequencing and computational infrastructure, data analysis is complex, needs bioinformatics expertise and robust pipelines	Bailey et al[55]

GI: Gastrointestinal; FISH: Fluorescence in situ hybridization; CNV: Copy number variation; aCGH: Array comparative genomic hybridization; SNP: Single nucleotide polymorphism; VUS: Variant of uncertain significance; SNV: Single nucleotide variant; NGS: Next-generation sequencing; GIST: Gastrointestinal stromal tumor; IBD: Inflammatory bowel disease; CRC: Colorectal cancer; WES: Whole exome sequencing; WGS: Whole genome sequencing; MLPA: Multiplex ligation-dependent probe amplification; qPCR: Quantitative polymerase chain reaction; HLA: Human leukocyte antigen; PCR-SSP: Polymerase chain reaction sequence-specific primer; NTRK: Neurotrophic tyrosine receptor kinase; PCR: Polymerase chain reaction; PI3K: Phosphoinositide 3-kinase; RNA-seq: RNA sequencing; lncRNA: Long non-coding RNA; miRNA: MicroRNA; mRNA: Messenger RNA.

Table 8 Genes that help in prediction and poor prognostications[56-89]

Disease	Prediction and prognostication	Genes	Ref.
FAP	Profuse polyposis	APC codon 1250-1464, 1250-1311, 1309-1324	Nagase et al[56]; Enomoto et al[57]; Ficari et al[58]; Walon et al[59]; Gebert et al[60]
	Desmoid tumors	APC codon 1924, 1962, 1444-1560, 1403-1987	Caspari et al[61]
	Upper gastrointestinal polyps	1445-1578	Davies et al[62]
	Gastric adenomas	1403-1987	Caspari et al[61]
	Multiple extracolonic manifestations	3’14451995, 3’1403	Caspari et al[61]
	CHRPE	311-1444, 413-1387, 542-1309	Caspari et al[61]
Crohn’s disease	Stenotic/structuring behavior	NOD2, TLR4, IL-12B, CX3CR1, IL-10, IL-6	Tsianos et al[63]
	Penetrating/fistulizing behavior	NOD2, IRGM, TNF, HLADRB1, CDKAL1	Tsianos et al[63]
	Inflammatory behavior	HLA	Tsianos et al[63]
	Granulomatous disease	TLR4/CARD15	Tsianos et al[63]
	Upper gastrointestinal	NOD2, MIF	Tsianos et al[63]
	Ileal	IL-10, CRP, NOD2, ZNF365, STAT3	Tsianos et al[63]
	Ileocolonic	ATG16 L1, TCF-4 (TCF7 L2)	Tsianos et al[63]
	Colonic	HLA, TLR4, TLR1, TLR2, TLR6
	Crohn’s disease activity	HSP70-2, NOD2, PAI-1, CNR1	Tsianos et al[63]
	Surgery	NOD2, HLA-G	Tsianos et al[63]
	Dysplasia and cancer	FHIT
	Extraintestinal manifestations	CARD15, FcRL3, HLADRB103	Tsianos et al[63]
Ulcerative colitis
	Extensive colitis and increased colectomy risk	HLA-DRB1 alleles, CASP9 gene on 1p36, ATG16 L1 T300A	Nam et al[64]
	May influence severity and steroid dependence	IL23R, STAT3, HSP70-2, MDR1	Nam et al[64]
	Early response to infliximab	IL23R higher gene expression IL-17A and IFN-γ	Jürgens et al[65]; Rismo et al[66]
	Good response to therapy	TNF ALPHA expression	Olsen et al[67]
	Non response to infliximab	PR3-ANCA	Yoshida et al[68]
	Favorable response to treatment	FCGR3A, TNFRSF1A, IL-6, and IL-1B
	Failure of steroid therapy	MDR1 (ABCB1), TNFα (-308/-857 SNPs), HLA-DQA1 05/DRB1, NOD2, ATG16 L1, IL13RA2, IL6, IL11, TNFAIP6
	Unfavorable response to therapy (IBD)	TLR2 and TLR9 show a negative correlation	Sazonovs et al[69]
	Development of ADA against infliximab and adalimumab	HLA-DQA1 05	Sazonovs et al[69]
	Development of ADA against infliximab	HLA-DRB1
Celiac disease
	Increase severity of disease	DQA1 05 and DQB1 02, homozygous for DQ2.5 haplotype, second copy of the DQB1 0201	Murray et al[70]; Stanković et al[71]
Hereditary pancreatitis	Increased risk of disease	PRSS1 pathogenic variants include p.Asn29Ile and p.Arg122His, p.Asn29Ile and p.Arg122His	Avanthi et al[72]; Whitcomb[73]
	Increased severity and early onset of disease	SPINK1, c.101A>G p.Asn34Ser and SPINK1, c.56-37T>C	Abass et al[74]
GIST
	Increase severity and relapse	Exon 11, 13, 17, c-KIT mutation; SDH deficient, BRAF mutation	Zhang and Liu[75]
Colorectal cancer	Increased severity and predict recurrence	P53, KRAS codon 12, loss of 18q	Andreyev et al[76]; Walther et al[77]
HCC	Increased severity	EZH2, STAT3, YB-1, ANLN, NLRC5
	Poor prognosis	Overexpression of CDCA5	Wang and Lai[78]; Hashemi et al[79]; Svinka et al[80]; Chao et al[81]; Jia et al[82]; Peng et al[83]
		Overexpression of CDCA5	Tian et al[84]
Gall bladder cancer	Increased severity of disease	SERPINB5 (maspin) KRAS, E-cadherin/beta-catenin, PML, P53, CDKN21 loss	Kim et al[85]; Hirata et al[86]; Chang et al[87]
Intra hepatic cholangiocarcinoma	Increased severity and large tumor size	BRAF	Xin et al[88]
Pancreatic cancer	Poor prognosis	KRAS (G12D/G12V/G12R), CDKN2A (p16), SMAD4 (DPC4)	Zhou et al[89]

FAP: Familial adenomatous polyposis; HCC: Hepatocellular carcinoma; GIST: Gastrointestinal stromal tumor; CHRPE: Congenital hypertrophy of the retinal pigment epithelium; ADA: Anti-drug antibodies; IBD: Inflammatory bowel disease; TNF-α: Tumor necrosis factor alpha.

Table 9 Pharmacogenetics in gastrointestinal disorders[90-100]

Disorder	Gene	Drug(s)	Clinical impact	Ref.
CRC, gastric, pancreatic cancers	DPYD	5-fluorouracil, capecitabine	Deficiency life-threatening toxicity (mucositis, myelosuppression)	De Moraes et al[90]; Ruzzo et al[91]
CRC, pancreatic cancer	UGT1A1	Irinotecan	UGT1A1 28/28 reduced glucuronidation increased toxicity (neutropenia, diarrhea)	Maitland et al[92]
IBD, autoimmune hepatitis	TPMT/NUDT15	Azathioprine, 6-MP	TPMT or NUDT15 deficiency risk of myelosuppression	Moriyama et al[93]
IBD	HLA-DQA102:01, HLA-DQB102:02	Thiopurines	Increase risk of thiopurine-induced pancreatitis	Ås et al[94]
IBD	HLA-DQ2	Infliximab	Increased formation of antibody formation against infliximab	Brun et al[95]
GERD, H. pylori, ulcers	CYP2C19	PPIs (omeprazole, lansoprazole)	Poor metabolizers increase drug levels; rapid metabolizers treatment failure in H. pylori	El Rouby et al[96]
NAFLD, metabolic syndrome	SLCO1B1	Statins (e.g., simvastatin)	Variants statin-induced myopathy risk	SEARCH Collaborative Group[97]
IBD	ABCB1	Various (e.g., corticosteroids)	Associated with glucocorticoid resistance in some patients	Li et al[98]
Autoimmune hepatitis, liver transplant	CYP3A5	Tacrolimus	Expressors need higher doses; non-expressors risk overexposure	Kim et al[99]
IBD	G6PD deficiency	Sulfasalazine, dapsone	Increase risk of hemolysis	Dore et al[100]

CRC: Colorectal cancer; IBD: Inflammatory bowel disease; GERD: Gastroesophageal reflux disease; H. pylori: Helicobacter pylori; NAFLD: Non-alcoholic fatty liver disease; PPI: Prot on pump inhibitor.

Table 10 Genes which regulates response to targeted therapy[101-125]

Disorder	Gene/mutation	Role	Treatment/clinical implication	Ref.
Colorectal cancer	KRAS (codon 12/13)	Predicts resistance to anti-EGFR therapy	Avoid cetuximab/panitumumab in mutant cases	Zhu et al[101]
Colorectal cancer	NRAS mutations	Similar to KRAS	Also predicts non-response to EGFR inhibitors	Hu et al[102]
CRC, cholangiocarcinoma	BRAF V600E	Poor prognosis, targetable	Consider BRAF + MEK inhibitors	Rizzo et al[103]
Gastric, colorectal cancer	HER2 (ERBB2) amplification	Targetable mutation	Responds to trastuzumab, pertuzumab	Bang et al[104]
CRC, gastric, biliary	MSI-H/dMMR	Biomarker for immunotherapy. Poor response to chemotherapy in stage 2 tumor	Eligible for checkpoint inhibitors (e.g., pembrolizumab)	Le et al[105]
HCC	CTNNB1 (β-catenin)	Resistance to immunotherapy	Poor response to immunotherapy	Shah et al[106]
	EZH2	Resistance to immunotherapy	Negatively express PD-L1	Xiao et al[107]
Crohn’s disease (IBD)	SNP rs396991GG of gene FCGR3A, rs976881-AA + GA (TNFRSF1B), SNPs in loci DENND1B (rs2488397) and aryl hydrocarbon receptor (rs1077773) s1813443-CC and rs1568885-TT (CNTN5) from the immunoglobulin superfamily	Resistance to biologics	Poor response to immunotherapy	Curci et al[108]; Yoon et al[109]; Ye and McGovern[110]
	Polymorphisms in ATG16 L1 (C11orf30; rs7927894CC, CCNY; rs12777960CC) (rs10210302)		Clinical response to adalimumab	Koder et al[111]
Crohn’s disease (IBD)	Polymorphisms in NOD2		Loss of response to anti-TNF	Juanola et al[112]
UC	Polymorphisms in IL-23R		Early response to infliximab	Jürgens et al[65]; Golan et al[113]
Crohn’s disease	ATG16 L1, IRGM	Autophagy pathway genes	Predict disease course and microbiome interaction	Rioux et al[114]
	Polymorphisms in FcγRIIIa, HLA-DRB1, HLA-DQA1 05		Development of ADA against infliximab and adalimumab	Salvador-Martín et al[115]; Billiet et al[116]
	Polymorphisms in FAS, FASL, and CASP9 (apoptotic pharmacogenetic index)		Clinical response to infliximab and adalimumab	Hlavaty et al[117]
	Gene protein tyrosine phosphatase non-receptor type 2 (rs7234029AG + GG, CASP9)		Non-response to anti-TNF and ustekinumab	Hlavaty et al[117]
HCC	EZH2		Negatively regulate PD-L1 expression. Less response to PD-L1 agonist	Meng et al[118]
	TOP2A, PRC1		Resistance to chemotherapy	Meng et al[118]; Wang et al[119]
IBS	TJP1, TPH1, SERT (SLC6A4)	Serotonin signaling, barrier dysfunction	May guide use of 5-HT3 antagonists or SSRIs	Camilleri et al[120]; Kerckhoffs et al[121]
Hereditary pancreatitis	SPINK1, PRSS1, CTRC	Trypsin regulation defects	May influence early interventions and surveillance	Panchoo et al[122]
Autoimmune hepatitis	HLA-DRB103, 04	Susceptibility and severity	May predict treatment response to steroids/immunosuppressants
Gastric, pancreatic, cholangiocarcinoma	ARID1A mutations	Epigenetic dysregulation	May predict response to EZH2 inhibitors or immunotherapy
Pancreatic cancer	KRAS		Anti EGFR treatment in effective	Fotopoulos et al[123]
	hENT1		Good response to gemcitabine therapy
	DCK		Increase active form of gemcitabine and increase survival
	DPD		Low DPD level associated with increase survival
	hMLLH1/2		Pancreatic cancer with MSI associated with less response to 5-FU
	TS		Lower level of TS associated with better response to capecitabine and 5-FU
	WOXX		Decreased expression interferes with gemcitabine sensitivity
	SMAD4 (DPC4)		Poor response to chemotherapy
GBC	ARID1A		Potential sensitivity to EZH2 inhibitors or immunotherapy	Wardell et al[124]
	CDKN2A loss/mutation		Resistant to chemotherapy	Nakamura et al[125]

CRC: Colorectal cancer; HCC: Hepatocellular carcinoma; IBD: Inflammatory bowel disease; UC: Ulcerative colitis; IBS: Irritable bowel syndrome; GBC: Gallbladder cancer; MSI-H: Microsatellite instability-high; dMMR: Deficient mismatch repair; SNP: Single nucleotide polymorphism; EGFR: Epidermal growth factor receptor; MEK: Mitogen-activated protein kinase; PD-L1: Programmed death-ligand 1; ADA: Anti-drug antibody; TNF: Tumor necrosis factor; SSRIs: Selective serotonin reuptake inhibitors; 5-HT3: 5-hydroxytryptamine type 3 (serotonin receptor); DPD: Dihydro pyrimidine dehydrogenase; 5-FU: 5-fluorouracil.

Table 11 Gastrointestinal and hepatopancreatic biliary disorders targeted therapy based on genetic testing[128-148]

Gene/pathway	Targeted drug(s)	Clinical status and trial setting	Ref.
KRAS G12C	Sotorasib, adagrasib (+ cetuximab)	Colorectal cancer, FDA approved	Ros et al[128]
EGFR (mAB)	Cetuximab, panitumumab, necitumumab	Colorectal cancer, gastric, FDA approved	Xie et al[129]
EGFR TKI	Erlotinib, gefitinib, afatinib, osimertinib, amivantamab	Colorectal cancer, gastric cancer, FDA approved	Corvaja et al[130]
VEGF	Bevacizumab, aflibercept	Colorectal cancer, gastric cancer	Mahaki et al[131]
BRAF V600E	Encorafenib, dabrafenib	Colorectal cancer, gastric cancer	Elez et al[132]
CLDN18.2	Zolbetuximab	Gastric/GEJ adenocarcinoma	Shitara et al[133]
NTRK fusion (NTRK1/NTRK2/NTRK3)	Larotrectinib, entrectinib	CRC, pancreatic, cholangiocarcinoma, gastric, others	Manea et al[134]
PD-1 (CD274 gene, checkpoint pathway)	Dostarlimab, camrelizumab1, nivolumab and pembrolizumab (keytruda)	Hepatocellular carcinoma, gastric and esophagogastric cancer	Abou-Alfa et al[135]
RET fusion	Selpercatinib, pralsetinib, avelumab	Rare GI/HPB tumors (cholangiocarcinoma, pancreatic)	Li et al[136]
FGFR2 fusion/rearrangement	Pemigatinib, futibatinib, infigratinib1	Intrahepatic cholangiocarcinoma	Hyung et al[137]
IDH1 mutation	Ivosidenib	Cholangiocarcinoma	Carosi et al[138]
BRCA1/BRCA2, PALB2 (HRD pathway)	Olaparib (PARP inhibitor)	Pancreatic adenocarcinoma (germline BRCA)	Alhusaini et al[139]
VEGFR, FGFR, PDGFR, RAF (angiogenesis/multikinase)	Sorafenib, lenvatinib, regorafenib, cabozantinib, pazopanib	Hepatocellular carcinoma	Kim[140]
APC mutation/COX2 pathway	Celecoxib (COX2 inhibitor)	FAP	Steinbach et al[141]
NR1H4 (FXR nuclear receptor)	Obeticholic acid	Primary biliary cholangitis	Floreani et al[142]
AGXT mutation (glyoxylate metabolism)	Lumasiran (RNAi against glycolate oxidase)	Primary hyperoxaluria type 1	Garrelfs et al[143]
SERPINA1 mutation (A1AT deficiency, liver disease)	Fazirsiran, ARO-AAT (RNAi)	Alpha-1 antitrypsin liver disease	Strnad et al[144]
ATP7B mutation	Chelators (penicillamine, trientine); zinc	Wilson disease
Anti-TNF agents	Infliximab, adalimumab	IBD	Feng et al[145]
IL-12/23 pathway	Ustekinumab (anti-IL-12/23)	IBD	Feng et al[145]
α4β7 integrin/cell trafficking	Vedolizumab (gut-specific anti-integrin)	IBD	Feng et al[145]
JAK-STAT pathway	Tofacitinib (pan-JAK), upadacitinib (JAK1)	IBD	Liu et al[146]
PD-L1 antibody	Durvalumab (imfinzi), atezolizumab, tislelizumab	GBC, HCC	Li et al[147]
MET amplification/overexpression	Foretinib1, cabozantinib (multi-target TKIs), glumetinib1	GBC, HCC, gastric, cholangiocarcinoma	Zhang et al[148]

¹Not Food and Drug Administration approved.

TKI: Tyrosine kinase inhibitors; PD-L1: Programmed death-ligand 1; PD-1: Programmed death-1; HRD: Homologous recombination deficiency; TNF: Tumor necrosis factor; COX2: Cyclooxygenase-2; IL: Interleukin; JAK-STAT: Janus kinase-signal transducer and activator of transcription; PARP: Poly (adenosine diphosphate-ribose) polymerase; RNAi: RNA interference; GEJ: Gastroesophageal junction; FDA: Food and Drug Administration; CRC: Colorectal cancer; GI: Gastrointestinal; HPB: Hepatopancreatic biliary; FAP: Familial adenomatous polyposis; IBD: Inflammatory bowel disease; GBC: Gallbladder cancer; HCC: Hepatocellular carcinoma.

Table 12 Different gene therapy under research/evaluation[150-164]

Therapy/product	Target	Ref.
Alicaforsen (antisense targeting ICAM-1) (phase III)	Pouchitis, left-sided UC	Greuter et al[150]
Glybera (AAV1-LPL) (withdrawn)	Lipoprotein lipase deficiency (severe pancreatitis)	Ferreira et al[151]
Oncolytic AAV-DC-CTL (phase 1)	Stage IV gastric cancer	Yan et al[152]
CRISPRedited TIL therapy (phase 1 completed)	Metastatic GI cancers (colorectal, pancreas, gallbladder, esophagus, stomach)	Lou et al[153]
CTX131 (allogeneic, CRISPR-engineered CD70-CAR-T) (phase 1/2 trial)	Pancreatic/oesophageal cancers	Pal et al[154]
CAN2409 (HSV thymidine kinase gene + pro-drug) (phase 2a)	Pancreatic cancer	Garrett Nichols et al[155]
Mutogene cevumeran (personalized mRNA vaccine) (phase 1b)	Pancreatic ductal adenocarcinoma	Lopez et al[156]
GENEGUT (preclinical settings)	Crohn’s disease	Hoffmann et al[157]
AAVrh.10mAnti-Eos, a serotype rh.10 AAV vector coding for an anti-Siglec-F monoclonal antibody (preclinical)	Eosinophill esophagitis	Camilleri et al[158]
Local delivery of an adenoviral vector expressing the HSV-tk gene (aglatimagene besadenovec, AdV-tk) followed by anti-herpetic prodrug	Pancreatic cancer	Aguilar et al[159]
Thymidine kinase-based gene therapy	HCC	Sangro et al[160]
Adenovirus-mediated double-suicide gene therapy	PDAC	Lee et al[161]
Oncolytic virus pelareorep (reolysin) (phase 1/2 trial)	PDAC	Noonan et al[162]
GVAX pancreas prime and Listeria Monocytogenes expressing mesothelin (CRS-207) boost vaccines (preclinical)	PDAC	Le et al[163]
TNF-erade biologic (phase 1)	Esophageal cancer	Chang et al[164]
GNT-0003 (phase III trial)	Crigler-Najjar syndrome
Pexa-Vec (JX-594) (phase 3 trial)	HCC
DTX401 (AAV8-G6Pase gene therapy) (phase 3 trial)	Glycogen storage disorder 1a
DTX301 (avalotcagene ontaparvovec) (phase 3 trial)	Ornithine transcarbamylase deficiency
UX701 (rivunatpagene miziparvovec) (AAV9) (phase 1/2 trial)	Wilson disease
VTX-802 (preclinical study)	PFIC type 2 (BSEP)

ICAM-1: Intercellular adhesion molecule 1; AAV: Adeno-associated virus; LPL: Lipoprotein lipase; DC: Dendritic cell; CTL: Cytotoxic T lymphocyte; CRISPR: Clustered regularly interspaced short palindromic repeats; TIL: Tumor-infiltrating lymphocyte; CAR T: Chimeric antigen receptor T-cell; CD: Cluster of differentiation; HSV: Herpes simplex virus; mRNA: Messenger RNA; AAVrh.10: Adeno-associated virus serotype rh.10; Siglec-F: Sialic acid-binding immunoglobulin-like lectin F; HSV-tk: Herpes simplex virus thymidine kinase; AdV-tk: Adenoviral vector carrying herpes simplex virus thymidine kinase gene; GVAX: Granulocyte-macrophage colony-stimulating factor secreting tumor cell vaccine; TNF-erade: Tumor necrosis factor-alpha encoding adenoviral vector; UC: Ulcerative colitis; GI: Gastrointestinal; PDAC: Pancreatic ductal adenocarcinoma; HCC: Hepatocellular carcinoma; PFIC: Progressive familial intrahepatic cholestasis; BSEP: Bile salt export pump.

Table 13 Gene editing techniques and their application

Gene editing techniques	In vivo gene editing	Ex vivo gene editing
Technique	CRISPR-Cas system is delivered by various vectors to disease-associated cells or organs of the body to correct the mutations or treat the cause of diseases	Targeted cells of a patient are extracted, isolated, edited, expanded, and delivered back to the same patient
Application	Treatment of monogenic genetic disorders	Cancer immunotherapy. Treatment of hereditary diseases. Viral infection inhibition

CRISPR-Cas: Clustered regularly interspaced short palindromic repeats-associated protein 9.

Table 14 Representative studies using clustered regularly interspaced short palindromic repeats in gastrointestinal disorders and malignancies[153,175-177]

Serial No.	Model/sample size	Disease	CRISPR target	Key findings	Ref.
1	Phase 1 trial; 12 patients with metastatic colorectal cancer	Metastatic CRC (human trial)	CISH knockout in autologous T cells	CRISPR-edited T cells were safe, feasible, and showed preliminary anti-tumor activity	Lou et al[153]
2	Phase 1 trial; 3 patients with advanced cancers (incl 1 GI malignancy)	Advanced solid tumors	Knockout of TRAC, TRBC, PD-1; insertion of NY-ESO-1 TCR	Demonstrated safety and persistence of CRISPR-edited T cells in humans; proof of feasibility	Stadtmauer et al[175]
3	Ongoing; sample size approximately 20 planned	Solid tumors (GI cancers included)	Endogenous TCR knockout + NY-ESO-1 TCR insertion	Designed to enhance adoptive T-cell therapy; early feasibility data available	Clinical trial (No. NCT03399448)
4	Human colon organoids	Colorectal cancer modeling	DNA repair genes (MLH1, MSH2, APC, TP53)	Sequential CRISPR editing in organoids recapitulated colorectal tumorigenesis	Drost et al[176]
5	Human intestinal organoids	Tumor suppressor modeling	PTEN, APC	High-efficiency CRISPR editing showed functional loss-of-gene effects; robust platform for GI cancer studies	Skoufou-Papoutsaki et al[177]

GI: Gastrointestinal; CRISPR: Clustered regularly interspaced short palindromic repeats; CRC: Colorectal cancer; CISH: Chromogenic in situ hybridization; NY-ESO-1: New York esophageal squamous cell carcinoma-1; TCR: T-cell receptor.

Table 15 Newer techniques of gene editing tools and their applications in gastrointestinal tract disorders

Technique	Mechanism	GIT applications
CRISPR-Cas9/12/13	DNA or RNA targeting via guide RNA and nuclease	Cancer mutations (APC, KRAS), viral hepatitis, IBD models
Base/prime editing	Precise base or sequence correction without DSBs	CFTR mutations, APC mutations
ZFNs	DNA-binding proteins fused to nucleases	HBV suppression (preclinical)
TALENs	TALE DNA-binding fused to nucleases	Cancer cell targeting, liver disease models
Epigenome editing	dCas9 fused to activators/repressors	Regulation of PD-L1, IBD immune genes
RNAi (siRNA, ASO)	Degrade/block specific mRNAs	Lumasiran (PH1), fazirsiran (A1AT deficiency)

GIT: Gastrointestinal tract; CRISPR: Clustered regularly interspaced short palindromic repeats; ZFNs: Zinc finger nucleases; TALENs: Transcription activator-like effector nucleases; RNAi: RNA interference; ASO: Antisense oligonucleotides; siRNA: Small interfering RNA; mRNA: Messenger RNA; DSBs: Double-strand breaks; TALE: Transcription activator-like effector; dCas9: Dead clustered regularly interspaced short palindromic repeats-associated protein 9; IBD: Inflammatory bowel disease; HBV: Hepatitis B virus; PD-L1: Programmed death-ligand 1.

Table 16 Newer concepts in genetic medicine[185-189]

Area	Key advancements	Ref.
Multi-omics integration	Combined use of genomics, transcriptomics, proteomics, and metabolomics to understand complex GI diseases	Zhao et al[185]
Polygenic risk scores	Using multiple low-risk variants to predict risk of diseases like IBD, colorectal cancer	Cross et al[186]
Single-cell sequencing	Helps identify cell-specific pathways in diseases like IBD, gastric cancer	Misra et al[187]
Organoid models	Patient-derived GI organoids used for drug testing, personalized therapy, and gene editing studies	Yang et al[188]
Epigenomics	Studying methylation, histone modifications, especially in GI cancers (e.g., MLH1 methylation in CRC)	Struhl[189]
Artificial intelligence	AI-driven prediction models, imaging-genomics integration for early diagnosis and prognosis

GI: Gastrointestinal; IBD: Inflammatory bowel disease; AI: Artificial intelligence; CRC: Colorectal cancer.

Table 17 RNA therapies[150,190-193]

Type	Mechanism of action	Example use	Ref.
Antisense oligonucleotides	Single-stranded RNA/DNA binds mRNA blocks translation or triggers degradation (via RNase H)	Alicaforsen in IBD (targets ICAM-1 mRNA) (phase 2/3 study)	Greuter et al[150]
Small interfering RNA	Double-stranded RNA binds to target mRNA guides RISC complex degrades mRNA	STNM01 in Crohn’s disease (fibrosis gene CHST15) (phase 1)	Suzuki et al[190]
mRNA replacement therapy	Synthetic mRNA encoding a therapeutic protein is delivered translated into protein	mRNA vaccines, IL-10 mRNA for colitis. Arcturus “lunar” mRNA, IL-10 mRNA LNPs (phase 1/2 study)	Qin et a[191]
CRISPR-Cas9 mRNA	mRNA encodes Cas9 protein + guide RNA edits DNA directly via targeted cleavage	Casgevy (CRISPR for β-thalassemia) (FDA approved)	Parums[192]
RNA aptamers	Structured RNA molecules bind and inhibit specific proteins or receptors	Macugen for eye disease; potential GI targets in research (preclinical)	Nagpal et al[193]

CRISPR-Cas: Clustered regularly interspaced short palindromic repeats-associated protein 9; mRNA: Messenger RNA; RISC: RNA-induced silencing complex; IBD: Inflammatory bowel disease; ICAM-1: Intercellular adhesion molecule 1; IL-10: Interleukin 10; LNPs: Lipid nanoparticles; GI: Gastrointestinal; FDA: Food and Drug Administration.

Table 18 Messenger RNA therapy in disorders of gastrointestinal tract

Agent/platform	Target/indication (GIT)	Study type/phase
RNA-4157/V940 (Moderna)	Individualized neoantigen vaccine colorectal cancer	Phase 2b/3 trial undergoing
BioNTech iNeST/BNT-pipeline	Personalized or fixed mRNA cancer vaccines for CRC, pancreatic, HCC	Phase 1/2 trials
Gritstone GRANITE	Personalized neoantigen immunotherapy MSS colorectal cancer	Phase 2 trial
MSK/investigator-initiated mRNA vaccine	Personalized mRNA neoantigen vaccine pancreatic adenocarcinoma	Early phase trial
OX40 L mRNA (LNP delivery)	Immune costimulatory agonist mRNA for HCC	Preclinical

GIT: Gastrointestinal tract; LNP: Lipid nanoparticle; mRNA: Messenger RNA; CRC: Colorectal cancer; HCC: Hepatocellular carcinoma; MSS: Microsatellite stable.