DNA Methylation Studies and Molecular Therapy of Helicobacter pylori Strain for the Treatment of Gastric Cancer
Dowluru SVGK Kaladhar*
Department of Microbiology and Bioinformatics, UTD, Atal Bihari Vajpayee University, Bilaspur, Chhattisgarh, India
*Corresponding author: Dowluru SVGK Kaladhar, Department of Microbiology and Bioinformatics, UTD, Atal Bihari Vajpayee University, Bilaspur, Chhattisgarh, India
Received Date: 23 July, 2021 Accepted Date: 03 August, 2021 Published Date: 10 August, 2021
Citation: Kaladhar DSVGK. (2021) DNA Methylation Studies and Molecular Therapy of Helicobacter pylori Strain for the Treatment of Gastric Cancer. J Oncol Res Ther 6: 10106. DOI: https://doi.org/10.29011/2574-710X.010106
Abstract
DNA methylation is a cellular process in which DNA methyltransferase regulates in addition of a methyl group to DNA, which is an epigenetic and heritable alteration that leads to cancer. About 62 genes are reported as methylated as per SCDb database and based on analysis, CDH1 (Cadherin 1) gene is showing a good characteristic relationship with gastric cancer that is caused by Helicobacter pylori. The Methylation frequency above 50 is shown in genes like APC, BRCA1, DAPK1, and RARB. Tissue-specific circular RNA induction in the human fetal development is increased from 10 week to 20 week gradually due to the genes like CDH1, PTEN, HLA-B and TIMP3. Due to CDH1 gene mutation, Beta–catenin suppresses the T-cell responses and promotes the development of tumors due to H. pylori infection. The selected molecules like Pravastatin, Clopidogrel, Magnesium Sulfate and Nicotine have shown control of mutated APC and CDH1 proteins. The Pravastatin has shown best activity mutated APC and CDH1 proteins. Magnesium Sulfate has shown least activity in control of CDH1 and APC proteins. Hence the present work confirms that Pravastatin is the best option for the molecular therapy in control of gastric cancer followed by drugs like Clopidogrel, Nicotine and Magnesium Sulfate.
Keywords
Gastric cancer; DNA methylation; H. pylori; Molecular therapy
Introduction
Gastric cancer (also known as stomach cancer) is a disease that can affect the stomach due to growth of cancerous cells in the inner lining of the stomach [1,2]. An abnormal and uncontrolled cell growth in the stomach will be observed due to gastric cancer. The symptoms may include heartburn, blood in stool, indigestion, jaundice, or trouble in swallowing nausea, vomiting, weight loss, difficulty in swallowing, loss of appetite, whites of the eyes, yellowing of the skin, upper abdominal pain and blood in the stool [3,4].
The stomach is an organ that is present between the esophagus and the small intestine. Gastric cancer is mostly affects in older people having over the age of 45 years [5]. The risk of gastric cancer is due to having Helicobacter pylori infection in the stomach. Most of the genetic changes (mutations) are identified in some subset of humans affected by stomach cancer due to changes in environment and lifestyle [6]. Most of the gastric cancer cases are observed due to induced by Helicobacter pylori infection and the other causes include eating pickled vegetables, salted and smoked foods, drinking alcohol, cigarettes smoking, and genetic syndromes [7]. The treatment options include chemotherapy, surgery, radiation or a combination, and/or targeted therapy (such as monoclonal antibody therapy) [8]. The drugs Clopidogrel and Pravastatin are mostly using in the treatment of gastric cancer [9,10].
Helicobacter pylori (H. pylori :plural; H. pylorus: singular; Synonym: Campylobacter pylori) is a microaerophilic, gram-negative, spiral shaped bacterium with about 3 μm long and 0.5 μm diameter [11]. H. pylori will be found in the stomach that causes ulcers or gastritis (stomach inflammation). In the natural stomach ecology, H. pylorus plays a major role in influencing the other types of gastrointestinal probiotic bacteria like lactobacillus, Befidobacterium etc, which increase the levels of COX2 [12]. The probiotic bacteria trigger’s Helicobacter cysteine-rich proteins (Hcp), particularly HcpA (hp0211), increased genes like vacuolating toxin A (VacA) and the cytotoxin-associated gene A (CagA), tyrosine residues of host cell membrane-associated tyrosine kinase (TK), activation of protein tyrosine phosphatase/ protooncogene Shp2 and epidermal growth factor receptor (EGFR), high levels of TNF-α and/or interleukin 6 (IL-6), reduced protein expression of some of the DNA repair proteins like MLH1, MGMT and MRE11 that may be involved in gastric cancer [13].
A tumor suppressor gene produces proteins within the system that helps in regulation of cell division. Due to mutation in tumor suppressor gene like APC and CDH1, uncontrolled cell growth or apoptosis occurs and may lead to tumors [14].
Materials and Methods
Pubmeth
Pubmeth is a cancer methylation databased that is annotated and reviewed based on automated textmining of literature. The database includes reporting of genes that are methylated in several cancer types like Gastric cancer. The website for search for PUBMETH is http://pubmeth.biobix.be/search.html. The diseases that are related to Gastric cancer have been analyzed using pubmeth database.
SCDb
A comprehensive resource for the human Stomach Cancer database is SCDb. SCDb serves as search engines for Browse, Query, Summary and tools to know information of genes that are related to stomach cancer. The available website of SCDb is http:// www.stomachcancerdb.org/dblist/query. The Gene expression levels can be quantified using RPKM (Reads Per kilobase per Million mapped reads) method from SCDb.
KEGG / Kyoto Encyclopedia of Genes & Genomes Pathway Maps
The KEGG (Kyoto Encyclopedia of Genes & Genomes) Pathway database is a collection of graphical diagrams (KEGG pathway maps) and associated text information (KEGG pathway entries) for metabolism, various other cellular processes, and human diseases.
String v11.0
STRING v11.0 is a database that is know to predicted protein-protein interactions based on physical and functional associations from databases. The search site for multiple protein interactions is https://string-db.org/cgi/ input?sessionId=byDwXWOC0ymQ&input_page_active_ form=multiple_identifiers.
Retrieval/ Design of ligands and proteins
Molecules are visualized from Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/ searchId.do?chebiId=63618) (Table 1). The molecules are designed using ChemSketch from ACDLabs v10.2 and was saved as .mol file format.
iGEMDOCKv2.1
iGEMDOCK v2.1 is a graphical environment that is used for recognizing pharmacological interactions and for conducting virtual screening for ligands with selected proteins. The tool is available at http://gemdock.life.nctu.edu.tw/dock/download.php.
Results and Discussion
There are 9990 genes that are involved in Human Gastric Cancer out of which 62 genes are reported as methylated genes. The 62 genes that are reported as methylated as per SCDb database are ALDH1A3, ANXA5, APC, AREG, BCL2L10, BNIP3, BRCA1, CCND2, CDH1, CDH2, CDKN2A, CDX2, CLDN3, DAB2IP, DAPK1, DKK1, DNAJC15, ESR1, F2R, FADS1, FHIT, FYN, GSTP1, HLA-B, HLTF, ID4, IGFBP3, IGFBP7, INSIG1, LOX, LZTS1, MLF1, MLH1, MTSS1, MX1, NID1, NID2, NT5E, PAX6, PGR, PPIC, PTEN, PTGS2, PYCARD, RAB32, RARB, RASSF2, RB1, RBP1, RBP4, RGS2, RPRM, SCRN1, SNAI1, SYK, TFAP2C, THBD, THBS1, TIMP3, TNFSF9, WIF1 and FGFR2. The information has been retrieved from Genecards (https://www.genecards.org/) (Table 2).
Table 2 has shown that CDH1 (Cadherin 1) is showing characteristic relationship with gastric cancer.
Table 3 has shown that Methylation frequency above 50 is shown for APC, BRCA1, CDH1, DAPK1 and RARB.
Table 4 and Figure 1 have shown that CDH1 is related to several diseases related to gastric cancer.
Table 5 has shown that Tissue-specific circular RNA induction during human fetal development has been increased from 10week to 20 week gradually due to CDH1, HLA-B, PTEN and TIMP3.
Figure 2 has shown that CDH1 is related to several other cancer causing genes like PTEN, BRCA1, MLH1, APC etc.
Figure 3 has shown that CDH1 acts on Beta-catenin that is important in transcription of Wnt-specific genes. Due to CDH1 gene mutation, Beta –catenin suppresses T-cell responses and promotes the progression of tumors.
The selected molecules like Clopidogrel, Pravastatin, Magnesium Sulfate and Nicotine have shown control of mutated CDH1 and APC proteins. The Pravastatin has shown best activity and Magnesium Sulfate has shown least activity in control of CDH1 and APC proteins. Hence Pravastatin is the best option molecular therapy in control of gastric cancer followed by Clopidogrel, Nicotine and Magnesium Sulfate (Table 6). Figure 4 and 5 has shown the docking poses and active site of drugs against CDH1 and APC proteins respectively.
DNA methylation is an epigenetic mechanism that is most favorable eukaryotes, an important regulator of the gene transcription and play key role in carcinogenesis [15-18]. Alterations in the process of DNA methylation are common in the development of a wide variety of tumors. Helicobacter pylori (H. pylori) infection can induce epigenetic changes and involve most important risk factor for the development of gastric cancer [19]. Chemoprevention with pravastatin may be important in molecular therapy of gastric cancer.
Conclusion
Due to CDH1 gene mutation, Beta–catenin suppresses the T-cell responses and promotes the progression of tumors due to H.pylori infection. The Pravastatin has shown best activity and Magnesium Sulfate has shown least activity in control of CDH1 and APC proteins. Hence Pravastatin is the best option molecular therapy in control of gastric cancer followed by Clopidogrel, Nicotine and Magnesium Sulfate.
Acknowledgements
The author likes to thank administration of Atal Bihari Vajpayee University for providing assistance and support.
Disclosure statement
The authors declare no conflicts of interest.
S.No |
Name |
ChEBI |
PubChem Id |
1 |
Clopidogrel |
CHEBI:37941 |
60606 |
2 |
Pravastatin |
CHEBI:63618 |
54687 |
3 |
Magnesium Sulfate |
CHEBI:32599 |
24083 |
4 |
(S)-Nicotine |
CHEBI:17688 |
89594 |
Methylated Gene |
Name as on Gene Cards |
Entrez Gene Summary |
ALDH1A3 |
Aldehyde
dehydrogenase enzyme |
Associated with microphthalmia; detected
in tumor cells |
ANXA5 |
Annexin
5 gene |
Implicated in many obstetric
complications |
APC |
Adenomatosis
Polyposis Coli |
Colorectal
cancers |
AREG |
Amphiregulin |
Various types of cancers and
inflammatory conditions |
BCL2L10 |
BCL2
Like 10 |
Involved in many cellular activities
like anti- or pro-apoptotic regulators |
BNIP3 |
BCL2 Interacting Protein 3 |
Silenced
in tumors by DNA methylation |
BRCA1 |
Breast And Ovarian Cancer Susceptibility
Protein 1 |
Modulating
the subcellular localization; disease-associated mutations; transcription;
recombination; DNA repair of double-stranded breaks |
CCND2 |
Cyclin D2 |
Cell
cycle G1/S transition; germ cell proliferation; ovarian and testicular
tumors; megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome
3 |
CDH1 |
Cadherin 1 |
Gastric,
colorectal, breast, thyroid and ovarian cancer. |
CDH2 |
Cadherin 2 |
Development
of the nervous system; establishment of left-right asymmetry; formation of
cartilage and bone. |
CDKN2A |
Cyclin Dependent Kinase Inhibitor 2A |
Cell
cycle G1 control; mutated or deleted in a wide variety of tumors; tumor
suppressor gene |
CDX2 |
Caudal Type Homeobox 2 |
Major
regulator of intestine-specific genes; plays a major role in the early
embryonic development of the intestinal tract.; associated with intestinal
inflammation and tumorigenesis |
CLDN3 |
Claudin 3 |
An
integral membrane protein; component of tight junction strands; putative
apoptosis-related protein |
DAB2IP |
Disabled Homolog 2-Interacting Protein |
Tumor
suppressor; inactivated by methylation in prostate and breast cancers |
DAPK1 |
Death Associated Protein Kinase 1 |
Programmed
cell death; a tumor suppressor candidate; splicing results in multiple
transcript variants |
DKK1 |
Dickkopf WNT Signaling Pathway Inhibitor 1 |
Role in
embryonic development; important in bone formation in adults; Elevated
expression causes numerous human cancers; promote proliferation, invasion and
growth in cancer cell lines |
DNAJC15 |
DnaJ Heat Shock Protein Family (Hsp40) Member
C15 |
Protein
Coding gene; Cause of 3-methylglutaconic aciduria type 5; dilated
cardiomyopathy with ataxia; multiple transcript variants |
ESR1 |
Estrogen Receptor 1 |
Central
DNA binding domain; role in growth, metabolism, sexual development, gestation,
and other reproductive functions; breast cancer, endometrial cancer, and
osteoporosis; have dozens of transcript variants |
F2R |
Coagulation Factor II Thrombin Receptor |
Regulation
of thrombotic response; multiple transcript variants |
FADS1 |
Fatty Acid Desaturase 1 |
Conserved
histidine motifs; regulate unsaturation of fatty acids |
FHIT |
Fragile Histidine Triad Diadenosine
Triphosphatase |
Involved
in purine metabolism; carcinogen-induced damage; found in all
esophageal, stomach, and colon carcinomas; tumor suppressor; loss of activity
results in replication stress and DNA damage. |
FYN |
FYN Proto-Oncogene, Src Family Tyrosine
Kinase |
Protein-tyrosine
kinase oncogene family; implicated in the control of cell growth;
existence of distinct isoforms |
GSTP1 |
Glutathione S-Transferase Pi 1 |
Function
in xenobiotic metabolism; play a role
in susceptibility to cancer and other diseases |
HLA-B |
Major Histocompatibility Complex, Class I, B |
Central
role in the immune system by presenting peptides derived from the endoplasmic
reticulum lumen; |
HLTF |
Helicase Like Transcription Factor |
Helicase
and ATPase activities; regulate transcription |
ID4 |
Inhibitor Of DNA Binding 4, HLH Protein |
Regulation
of diverse cellular processes; development and tumorigenesis. |
IGFBP3 |
Insulin Like Growth Factor Binding Protein 3 |
Transcriptional
splice variants ; altering
interaction with cell surface receptors |
IGFBP7 |
Insulin Like Growth Factor Binding Protein 7 |
Stimulates
prostacyclin production and cell adhesion; associated with retinal arterial
macroaneurysm |
INSIG1 |
Insulin Induced Gene 1 |
Regulates
cholesterol metabolism, lipogenesis, and glucose homeostasis;
ubiquitin-mediated degradation; multiple transcript variants |
LOX |
Lysyl Oxidase |
Multiple
transcript variants; crosslinking of collagens and elastin; role in tumor
suppression; predisposition to thoracic aortic aneurysms and dissections |
LZTS1 |
Leucine Zipper Tumor Suppressor 1 |
Tumor
suppressor protein; protein is silenced in rapidly metastasizing and
metastatic tumor cells; role in cell-cycle control; Loss of heterozygosity
(LOH) in the 8p arm is a common characteristic of many types of cancer. |
MLF1 |
Myeloid Leukemia Factor 1 |
Phenotypic
determination of hemopoetic cells; associated with myelodysplastic syndrome
and acute myeloid leukemia; Multiple transcript variants |
MLH1 |
MutL Homolog 1 |
DNA
mismatch repair system; involved in meiosis; hereditary nonpolyposis colon
cancer |
MTSS1 |
MTSS I-BAR Domain Containing 1 |
Associated
with Lung Giant Cell Carcinoma and Oropharyngeal
Anthrax; identical protein binding and actin
binding |
MX1 |
MX Dynamin Like GTPase 1 |
Participates
in the cellular antiviral response; multiple transcript variants |
NID1 |
Nidogen 1 |
Basement
membrane glycoproteins; role in cell interactions with the extracellular
matrix |
NID2 |
Nidogen 2 |
Basement
membrane proteins; maintaining the structure of the basement membrane |
NT5E |
5'-Nucleotidase Ecto |
Determinant
of lymphocyte differentiation; Defects can lead to the calcification of
joints and arteries |
PAX6 |
Paired Box 6 |
Bind DNA
and function as regulators of gene transcription; multiple transcript
variants |
PGR |
Progesterone Receptor |
Central
role in reproductive events associated with the organization and maintenance
of pregnancy; mediates the physiological effects of progesterone |
PPIC |
Peptidylprolyl
Isomerase C |
Accelerate the folding of proteins; can
bind immunosuppressant cyclosporin A |
PTEN |
Phosphatase
And Tensin Homolog |
Tumor suppressor that is mutated in many
types of cancers at high frequency; multiple transcript variants |
PTGS2 |
Prostaglandin-Endoperoxide
Synthase 2 |
Enzyme in prostaglandin biosynthesis;
involved in inflammation and mitogenesis |
PYCARD |
PYRIN-PAAD-DAPIN
domain (PYD) and a C-terminal caspase-recruitment domain (CARD). |
Large signaling complexes in the inflammatory; undergoing apoptosis |
RAB32 |
RAB32,
Member RAS Oncogene Family |
Involved in autophagy; melanosome
secretion; linked to leprosy |
RARB |
Retinoic
Acid Receptor Beta |
Mediates cellular signalling in
embryonic morphogenesis; cell
growth; differentiation;
hepatocellular carcinoma; flanks a hepatitis B virus integration site;
multiple transcript variants |
RASSF2 |
Ras
Association Domain Family Member 2 |
Located near the prion gene; Ras
association |
RB1 |
Retinoblastoma-Associated
Protein |
First tumor suppressor gene found; cause
of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic
sarcoma |
RBP1 |
Retinol
Binding Protein 1 |
Necessary for growth, reproduction,
differentiation of epithelial tissues and vision; Multiple transcript
variants |
RBP4 |
Retinol
Binding Protein 4 |
Carrier for retinol (vitamin A alcohol)
in the blood; prevents its loss by filtration through the kidney glomeruli;
deficiency of vitamin A blocks secretion of the binding protein
posttranslationally; deficiency results in defective delivery and supply to
the epidermal cells |
RGS2 |
Regulator
Of G Protein Signaling 2 |
Mediator of myeloid
differentiation; play a role in
leukemogenesis |
RPRM |
Reprimo,
TP53 Dependent G2 Arrest Mediator Homolog |
Related pathways are DNA Damage Response |
SCRN1 |
Secernin
1 |
Regulation of exocytosis in mast cells;
spliced transcript variants |
SNAI1 |
Snail
Family Transcriptional Repressor 1 |
Zinc finger transcriptional repressor ;
critical for mesoderm formation in the developing embryo; downregulates the
expression of ectodermal genes within the mesoderm; |
SYK |
Spleen
Associated Tyrosine Kinase |
Widely expressed in hematopoietic cells;
mediate diverse cellular responses, including proliferation, differentiation,
and phagocytosis; potential tumor suppressor in human breast carcinomas;
spliced transcript variants |
TFAP2C |
Transcription
Factor AP-2 Gamma |
Activation of several developmental
genes; induced during retinoic acid-mediated differentiation; plays a role in
the development of the eyes, face, body wall, limbs, and neural tube |
THBD |
Thrombomodulin |
Activation of protein C, which degrades
clotting factors Va and VIIIa and reduces the amount of thrombin generated.;
mutation cause of thromboembolic disease, also known as inherited
thrombophilia. |
THBS1 |
Thrombospondin
1 |
An adhesive glycoprotein that mediates
cell-to-cell and cell-to-matrix interactions; play roles in platelet
aggregation, angiogenesis, and tumorigenesis. |
TIMP3 |
TIMP
Metallopeptidase Inhibitor 3 |
Inhibitors of the matrix
metalloproteinases; mutations cause autosomal dominant disorder Sorsby's
fundus dystrophy; induced in response to mitogenic stimulation |
TNFSF9 |
TNF
Superfamily Member 9 |
Bidirectional signal transducer;
generation of cytotoxic T cells; expressed in carcinoma cell lines, |
WIF1 |
WNT
Inhibitory Factor 1 |
Play a role in embryonic development;
involved in mesoderm segmentation; epigenetically silenced in various cancers |
FGFR2
|
Fibroblast
Growth Factor Receptor 2 |
Interacts with fibroblast growth
factors; influence mitogenesis and differentiation; associated with Crouzon
syndrome, Craniosynostosis, Pfeiffer syndrome, Saethre-Chotzen syndrome, Apert syndrome, Jackson-Weiss syndrome,
Beare-Stevenson cutis gyrata syndrome, and syndromic craniosynostosis;
Multiple alternatively spliced transcript variants |
Gene |
Number of references |
Number of references in gastric cancer |
Number of samples |
Methylation frequency |
Details for methylation In Gastric |
ALDH1A3 |
1 |
1 |
10 |
20 |
no
subtype specified (1) |
ANXA5 |
-- |
-- |
-- |
-- |
- |
APC |
65 |
7 |
343 |
59 |
adenoma (2);
adenocarcinoma (2); no subtype specified (2); Soft tissue sarcoma (1) |
AREG |
1 |
1 |
10 |
10 |
no
subtype specified (1) |
BCL2L10 |
-- |
-- |
-- |
-- |
-- |
BNIP3 |
3 |
-- |
-- |
-- |
-- |
BRCA1 |
16 |
1 |
83 |
55 |
no
subtype specified (1) |
CCND2 |
9 |
-- |
-- |
-- |
-- |
CDH1 |
81 |
13 |
597 |
52 |
carcinoma (8);
no subtype specified (2); adenocarcinoma (1); adenoma (1); soft tissue
sarcoma (1) |
CDH2 |
1 |
-- |
-- |
-- |
-- |
CDKN2A |
205 |
21 |
1433 |
30 |
no
subtype specified (8); carcinoma (6); adenocarcinoma (3); adenoma (3); soft
tissue sarcoma (1) |
CDX2 |
2 |
1 |
73 |
29 |
no
subtype specified (1) |
CLDN3 |
-- |
-- |
-- |
-- |
-- |
DAB2IP |
-- |
-- |
-- |
-- |
-- |
DAPK1
|
68 |
7 |
660 |
51 |
adenoma
(3), no subtype specified (3), carcinoma (1) |
DKK1 |
1 |
1 |
0 |
0 |
no
subtype specified (1) |
DNAJC15 |
1 |
1 |
10 |
30 |
neuroectodermal
tumour (1) |
ESR1 |
24 |
1 |
0 |
0 |
no
subtype specified (1) |
F2R |
1 |
1 |
10 |
20 |
no
subtype specified (1) |
FADS1 |
- |
-- |
-- |
-- |
-- |
FHIT |
24 |
-- |
-- |
-- |
-- |
FYN |
-- |
-- |
-- |
-- |
-- |
GSTP1 |
56 |
3 |
200 |
7 |
adenoma
(1); carcinoma (1); no subtype specified (1) |
HLA-B |
1 |
1 |
60 |
40 |
no
subtype specified (1) |
HLTF |
4 |
1 |
46 |
20 |
no
subtype specified (1)
|
ID4 |
4 |
1 |
76 |
30 |
adenocarcinoma
(1) |
IGFBP3 |
8 |
-- |
-- |
-- |
-- |
IGFBP7 |
2 |
-- |
-- |
-- |
-- |
INSIG1 |
1 |
1 |
22 |
50 |
no
subtype specified (1) |
LOX |
-- |
-- |
-- |
-- |
-- |
LZTS1 |
-- |
-- |
-- |
-- |
-- |
MLF1 |
-- |
-- |
-- |
-- |
-- |
MLH1 |
69 |
21 |
1154 |
22 |
carcinoma
(10); no subtype specified (5); adenocarcinoma (3); adenoma (2); intestinal
(1) |
MTSS1 |
-- |
-- |
-- |
-- |
-- |
MX1 |
-- |
-- |
-- |
-- |
-- |
NID1 |
-- |
-- |
-- |
-- |
-- |
NID2 |
-- |
-- |
-- |
-- |
-- |
NT5E |
-- |
-- |
-- |
-- |
-- |
PAX6 |
1 |
-- |
-- |
-- |
-- |
PGR |
6 |
-- |
-- |
-- |
-- |
PPIC |
-- |
-- |
-- |
-- |
-- |
PTEN |
15 |
1 |
66 |
39 |
carcinoma
(1) |
PTGS2 |
20 |
7 |
653 |
19 |
carcinoma
(3); no subtype specified (3); adenoma (1) |
PYCARD |
9 |
1 |
10 |
0 |
no
subtype specified (1) |
RAB32 |
1 |
1 |
48 |
27 |
adenocarcinoma
(1) |
RARB |
48 |
4 |
246 |
51 |
carcinoma
(2); no subtype specified (2) |
RASSF2 |
1 |
-- |
-- |
-- |
-- |
RB1 |
15 |
-- |
-- |
-- |
-- |
RBP1 |
2 |
-- |
-- |
-- |
-- |
RBP4 |
-- |
-- |
-- |
-- |
-- |
RGS2 |
1 |
1 |
10 |
0 |
no
subtype specified (1) |
RPRM |
8 |
1 |
0 |
0 |
no
subtype specified (1) |
SCRN1 |
-- |
-- |
-- |
-- |
-- |
SNAI1 |
1 |
1 |
10 |
0 |
no
subtype specified (1)
|
SYK |
8 |
2 |
61 |
34 |
carcinoma
(1); no subtype specified (1) |
TFAP2C |
-- |
-- |
-- |
-- |
-- |
THBD |
-- |
-- |
-- |
-- |
-- |
THBS1 |
19 |
6 |
625 |
38 |
no
subtype specified (3); carcinoma (2); adenoma (1) |
TIMP3 |
34 |
4 |
254 |
25 |
adenoma
(3); no subtype specified (1) |
TNFSF9 |
-- |
-- |
-- |
-- |
-- |
WIF1 |
8 |
-- |
-- |
-- |
-- |
FGFR2
|
-- |
-- |
-- |
-- |
-- |
S.No |
Related Disease |
Top Affiliating Genes (text searches by Pubmeth) |
1 |
Sarcoma |
APC, CDH1, CDKN2A, DAPK1 |
2 |
Adenoma |
APC, CDH1, CDKN2A, DAPK1 , GSTP1, MLH1, PTGS2,
THBS1, TIMP3 |
3 |
Neuroectodermal tumour |
DNAJC15 |
4 |
Adenocarcinoma |
APC, CDH1, CDKN2A, ID4, MLH1, RAB32, ID4 |
5 |
Carcinoma |
CDH1, CDKN2A, GSTP1, MLH1, PTEN, PTGS2,
RARB, SYK, THBS1 |
6 |
Intestinal |
MLH1 |
7 |
No subtype specified |
ALDH1A3, APC, AREG, BRCA1, CDH1, CDKN2A,
CDX2, DAPK1 , DKK1, ESR1, F2R, GSTP1, HLA-B, HLTF, NSIG1, MLH1, PTGS2,
PYCARD, RARB, RGS2, RPRM, SNAI1, SYK, THBS1, TIMP3 |
Gene |
Methylation frequency |
Reads Per Kilobase of transcript,
per Million mapped reads (RPKM) |
|||||
HPA RNA-seq normal tissues |
RNA sequencing of total RNA from 20 human tissues |
Tissue-specific circular RNA induction during human
fetal development
|
|||||
10Wk |
16WK |
18 wk |
20Wk |
||||
ALDH1A3 |
20 |
6.493± 2.886 |
1.571 |
1.339±0.081 |
2.585 |
1.949 |
3.325 ± 0.504 |
APC |
59 |
2.171 ± 0.773 |
1.521 |
4.506±0.49 |
6.645 |
6.024 |
5.741±0.485 |
AREG |
10 |
8.789±4.535 |
0.942 |
0.017±0.017 |
0.041 |
0.026 |
0.03±0.025 |
BRCA1 |
55 |
0.869±0.342 |
0.445 |
1.771±0.082 |
1.591 |
1.755 |
1.783±0.173 |
CDH1 |
52 |
49.374±13.587 |
13.78 |
9.971±0.239 |
18.684 |
18.918 |
18.719±0.886 |
CDKN2A |
30 |
0.344±0.347 |
0.042 |
0.01±0.001 |
0.012 |
0 |
0.015±0.021 |
CDX2 |
29 |
0 |
0.091 |
0.215±0.215 |
0 |
0.085 |
0 |
DAPK1 |
51 |
7.785±2.725 |
2.608 |
6.396±0.123 |
6.713 |
6.067 |
6.288±0.184 |
DNAJC15 |
30 |
5.177±1.071 |
2.408 |
2.767±0.01 |
4.014 |
5.941 |
5.12±0.65 |
F2R |
20 |
5.02±0.927 |
1.867 |
5.496±0.098 |
5.181 |
6.161 |
5.509±0.637 |
GSTP1 |
7 |
173.829±89.126 |
37.927 |
21.165±8.309 |
33.007 |
61.985 |
48.063±6.079 |
HLA-B |
40 |
269.516±86.645 |
36.153 |
3.013±1.096 |
6.595 |
8.141 |
14.092±9.148 |
HLTF |
20 |
4.47±1.498 |
1.457 |
4.334±0.426 |
5.186 |
5.527 |
5.13±0.415 |
ID4 |
30 |
8.625±5.243 |
1.802 |
5.459±0.884 |
7.885 |
10.285 |
9.941±0.693 |
INSIG1 |
50 |
17.359±1.653 |
4.373 |
2.492±0.185 |
6.034 |
8.679 |
5.683±0.157 |
MLH1 |
22 |
5.409±0.706 |
2.826 |
4.326±0.235 |
5.227 |
5.89 |
5.68±0.526 |
PTEN |
39 |
8.303±1.828 |
3.666 |
6.643±0.678 |
11.059 |
11.206 |
11.494±0.971 |
PTGS2 |
19 |
1.905±1.847 |
1.158 |
0.599±0.084 |
1.136 |
3.143 |
1.986±0.983 |
RAB32 |
27 |
6.901±1.864 |
1.066 |
1.934±0.385 |
2.3 |
3.832 |
3.441±0.61 |
RARB |
51 |
1.228±0.535 |
0.828 |
3.651±0.649 |
5.523 |
6.791 |
4.949±1.07 |
SYK |
34 |
9.23±1.112 |
3.317 |
2.41±0.271 |
2.485 |
4.019 |
3.064±0.169 |
THBS1 |
38 |
22.886±16.861 |
11.345 |
13.62±1.188 |
23.401 |
28.878 |
21.43±0.933 |
TIMP3 |
25 |
19.121±2.647 |
16.301 |
14.244±2.006 |
30.908 |
32.44 |
35.32±5.48 |
S.No |
Name of Drug |
APC |
CDH1 |
||
|
Total energy in Kcal/mol |
Active site |
Total energy in Kcal/mol |
Active site |
|
1 |
Clopidogrel |
-72.66 |
V-M-LEU-37-V-M-GLU-40-V-S-GLU-40-V-M-ALA-41-V-S-MET-44-V-M-ALA-41-V-S-MET-44
|
-63.8 |
H-S-GLN-23-V-M-PRO-5
-V-S-PRO-6-V-S-LYS-73-V-M-GLN-23-V-S-GLN-23 |
|
|
|
|
|
|
2 |
Pravastatin |
-92.21 |
H-S-ASN-22-H-S-GLU-26-H-M-LEU-27-V-S-GLU-19-V-S-LEU-23-V-S-GLU-26-V-S-ASN-30-V-M-LEU-27-V-S-LEU-27-V-M-GLU-28-V-S-GLU-28 |
-94.32 |
H-M-VAL-3-H-S-THR-97-H-M-GLN-23-H-M-LYS-25-V-S-VAL-3-V-M-ILE-4-V-M-PRO-5-V-S-PRO-6-V-S-LYS-73-V-S-VAL-95-V-S-THR-97-V-S-GLN-23-V-S-LYS-25 |
3 |
Magnesium Sulfate |
-39.85 |
H-S-ASN-20-H-S-ARG-24-V-S-LYS-17 |
-36.23 |
H-M-VAL-3-H-M-GLU-93 |
|
|
|
|
|
|
4 |
Nicotine |
-57.33 |
H-M-LEU-37-H-S-GLU-40-V-M-GLU-40-V-S-GLU-40-V-M-ALA-41-V-M-ALA-41-V-S-MET-44 |
-51.95 |
H-M-VAL-3-H-M-ILE-4-H-M-GLN-23-V-S-VAL-3-V-M-ILE-4-V-S-PRO-6-V-S-VAL-95-V-S-GLN-23 |
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