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Laboratory validation of formal concept analysis of the methylation status of microarray-detected genes in primary breast cancer.

Abstract Breast cancer is the leading cause of cancer-related mortality. DNA methylations play important roles in cancer development and progression. Formal concept analysis was previously utilized for data mining hypermethylated and hypomethylated genes in breast cancer molecular subtypes in illumina methylation-based microarray database, to laboratory validate their outputs; HS3ST2 (heparan sulfate d-glucosaminyl 3-O-sulfonyl transferase-2) and MUC1 (mucin-1) were retrieved. Both play important roles in progression and invasion of breast cancer. The methylation status of both genes was laboratory validated using methylation-based polymerase chain reaction in breast cancer subtypes luminal A (early stages) and luminal B (late stages) in comparison with benign conditions and normal breast to conclude their roles in tumor invasion and to validate the newly developed algorithm (formal concept analysis). Significant cancer-specific hypermethylation of HS3ST2 was detected in luminal B (chi square = 30.6, p = 0.000), while significant cancer-specific hypomethylation of MUC1 was detected in luminal B (chi square = 30.5, p = 0.001) breast cancer. The median levels of the percentage of methylated allele of both genes were significantly discriminative between luminal A and luminal B subtypes and benign and healthy control groups. Detection of MUC1 and HS3ST2 promoter methylation status appears to be useful molecular markers for assessing the progressive state of the disease and could be helpful in discriminating breast cancer molecular subtypes. These results validate the methylation-based microarray analysis, thus trust their output in the future.
PMID
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Authors

Mayor MeshTerms
Keywords

DNA methylation

breast cancer

heparan sulfate 3-O-sulfotransferase

mucin-1

Journal Title tumour biology : the journal of the international society for oncodevelopmental biology and medicine
Publication Year Start




PMID- 28618938
OWN - NLM
STAT- MEDLINE
DA  - 20170616
DCOM- 20170705
LR  - 20170705
IS  - 1423-0380 (Electronic)
IS  - 1010-4283 (Linking)
VI  - 39
IP  - 6
DP  - 2017 Jun
TI  - Laboratory validation of formal concept analysis of the methylation status of
      microarray-detected genes in primary breast cancer.
PG  - 1010428317698390
LID - 10.1177/1010428317698390 [doi]
AB  - Breast cancer is the leading cause of cancer-related mortality. DNA methylations 
      play important roles in cancer development and progression. Formal concept
      analysis was previously utilized for data mining hypermethylated and
      hypomethylated genes in breast cancer molecular subtypes in illumina
      methylation-based microarray database, to laboratory validate their outputs;
      HS3ST2 (heparan sulfate d-glucosaminyl 3-O-sulfonyl transferase-2) and MUC1
      (mucin-1) were retrieved. Both play important roles in progression and invasion
      of breast cancer. The methylation status of both genes was laboratory validated
      using methylation-based polymerase chain reaction in breast cancer subtypes
      luminal A (early stages) and luminal B (late stages) in comparison with benign
      conditions and normal breast to conclude their roles in tumor invasion and to
      validate the newly developed algorithm (formal concept analysis). Significant
      cancer-specific hypermethylation of HS3ST2 was detected in luminal B (chi square 
      = 30.6, p = 0.000), while significant cancer-specific hypomethylation of MUC1 was
      detected in luminal B (chi square = 30.5, p = 0.001) breast cancer. The median
      levels of the percentage of methylated allele of both genes were significantly
      discriminative between luminal A and luminal B subtypes and benign and healthy
      control groups. Detection of MUC1 and HS3ST2 promoter methylation status appears 
      to be useful molecular markers for assessing the progressive state of the disease
      and could be helpful in discriminating breast cancer molecular subtypes. These
      results validate the methylation-based microarray analysis, thus trust their
      output in the future.
FAU - Kassim, Samar K
AU  - Kassim SK
AD  - 1 Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain
      Shams University, Cairo, Egypt.
FAU - Shehata, Hanan H
AU  - Shehata HH
AD  - 1 Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain
      Shams University, Cairo, Egypt.
FAU - Abou-Alhussein, Marwa M
AU  - Abou-Alhussein MM
AD  - 1 Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain
      Shams University, Cairo, Egypt.
FAU - Sallam, Maha M
AU  - Sallam MM
AD  - 1 Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain
      Shams University, Cairo, Egypt.
FAU - Amin, Islam Ibrahim
AU  - Amin II
AD  - 2 Institute of Statistical Studies and Researches, Cairo University, Giza, Egypt.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Tumour Biol
JT  - Tumour biology : the journal of the International Society for Oncodevelopmental
      Biology and Medicine
JID - 8409922
RN  - 0 (MUC1 protein, human)
RN  - 0 (Mucin-1)
RN  - EC 2.8.2.- (Sulfotransferases)
RN  - EC 2.8.2.30 (HS3ST3A1 protein, human)
SB  - IM
MH  - Breast Neoplasms/*genetics/pathology
MH  - CpG Islands
MH  - DNA Methylation/*genetics
MH  - Female
MH  - Humans
MH  - Mucin-1/*genetics
MH  - Neoplasm Staging
MH  - Promoter Regions, Genetic
MH  - Sulfotransferases/*genetics
OTO - NOTNLM
OT  - DNA methylation
OT  - breast cancer
OT  - heparan sulfate 3-O-sulfotransferase
OT  - mucin-1
EDAT- 2017/06/18 06:00
MHDA- 2017/07/06 06:00
CRDT- 2017/06/17 06:00
AID - 10.1177/1010428317698390 [doi]
PST - ppublish
SO  - Tumour Biol. 2017 Jun;39(6):1010428317698390. doi: 10.1177/1010428317698390.