A Brief Study on Analysis of Genes Important for Endometrial Cancer

A Brief Study on Analysis of Genes Important for Endometrial Cancer

Atreyee Majumder and Malavika Bhattacharya#

Department of Biotechnology Techno India University, West Bengal

Kolkata, India

Abstract Endometrial cancer begins in the layer of cells that form the lining (endometrium) of the uterus. The genetic causes, mainly hereditary causes, contribute to 210% of endometrial cancer. Since endometrial cancer is becoming one of the main cancers effecting women in eastern India, the genes important in its context need to be identified and studied thoroughly. This study was performed with the aim of understanding conservation of the genes and the proteins encoded by them which are important with reference to endometrial cancer. For this purpose, the genes that were analyzed included PTEN, Tp53, WNT4, BRAF, PIK3CA, MGMT and SMAD family. The GENE

similarity between Human (Homo sapiens), Mice (Mus musculus) and Zebra fish (Danio rerio) were analyzed. The FASTA Nucleotide Sequences were taken from NCBI-GENE and the FASTA Protein sequences were taken from UNIPROT. The Phylogenetic tree view of Nucleotide and Protein and Cobalt Multiple Sequence Alignment of protein showed GENE similarity between the three organisms. Around 70%-85% identity was observed between genes of human, mice and zebra fish.

KeywordsEndometrial Cancer; Hereditary factors; Gene conservation; Sequence analysis

1. INTRODUCTION :

   Endometrial cancers are responsible for about 5% and 2% of worldwide cancer incidence and mortality among women, respectively. In women, endometrial cell carcinomas (ECCs) are the most common malignancy of the female genital tract in the world and the fourth most common one after breast, lung, and colorectal cancer. Studies have indicated that although approximately 90% of cases of endometrial cancer are sporadic, the remaining 10% of cases are hereditary (Mikuta, 1993; Lentz, 1994; Rose, 1996; Murali et al., 2014).

   Based on reports of genes affected under endometrial cancer incidences, seven genes were selected for analysis. They included PTEN, Tp53, WNT4, BRAF, PIK3CA, MGMT and

   SMAD family (Doll et al., 2008; Prat and Franceschi, 2014).

2. MATERIALS AND METHODS

   The genes that were analyzed included PTEN, Tp53, WNT4, BRAF, PIK3CA, MGMT and SMAD family. The GENE

   similarity between Human (Homo sapiens), Mice (Mus

   musculus) and Zebra fish (Danio rerio) were analyzed. The FASTA Nucleotide Sequences were taken from NCBI- Nucleotide and the FASTA Protein sequences were taken from UNIPROT. Basic Local Alignment Search Tool Analysis (BLAST) comparison between nucleotide or protein sequences was done and regions of local similarity between sequences were identified.

   BIOINFORMATICS TOOLS IN GENETIC ANALYSIS

   (Zhang et al., 2000; Morgulis et al., 2008):

   BLAST: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

   FASTA: FASTA format is a text-based DNA and protein sequence alignment software package format for representing either nucleotide sequences or amino acid sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences.

   UNIPROT: UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

3. RESULTS:

   The Phylogenetic tree view of Nucleotide and Protein and Cobalt Multiple Sequence Alignment of protein showed GENE similarity between the three organisms.

   FIGURES

   1. Nucleotide Blast (NucleotideNucleotide):

      Optimized for Highly similar sequences (megablast)

      Nucleotide Sequence: The nucleotide collection consists of GenBank+EMBL+DDBJ+PDB+RefSeq sequences, but excludes EST, STS, GSS, WGS, TSA, patent sequences as well as phase 0, 1, and 2 HTGS sequences and sequences longer than 100Mb. The database is non-redundant. Identical sequences have been merged into one entry, while preserving the accession, GI, title and taxonomy information for each entry.

      1) PTEN:

      >NC_000010.11:87863625-87971930 Homo sapiens

      chromosome 10, GRCp8.p13 Primary Assembly

      >NC_000085.6:32757577-32826160 Mus musculus strain C57BL/6J chromosome 19, GRCm38.p6 C57BL/6J

      >NC_007123.7:c17424162-17400669 Danio rerio strain Tuebingen chromosome 12, GRCz11 Primary Assembly]

      NB:– In this sequence chromosome 9 complex DNA sequence of PTEN

      Figure 1: Nucleotide Blast results for PTEN

      2) P53:

      >NC_000017.11:c7687550-7668402 Homo sapiens

      chromosome 17, GRCp8.p13 Primary Assembly

      >NC_000077.6:69580348-69591873 Mus musculus strain C57BL/6J chromosome 11, GRCm38.p6 C57BL/6J

      >NC_007116.7:24086227-24097807 Danio rerio strain Tuebingen chromosome 5, GRCz11 Primary Assembly]

      NB: Antisense of TP53 transcript variant, mRNA WD repeats.

      Figure 2: Nucleotide Blast results for P53

      1. WNT4:

         >NC_000001.11:c22143981-22117308 Homo sapiens

         chromosome 1, GRCp8.p13 Primary Assembly

         >NC_000070.6:137277635-137299501 Mus musculus strain C57BL/6J chromosome 4, GRCm38.p6 C57BL/6J

         >NC_007122.7:c39202915-39167846 Danio rerio strain Tuebingen chromosome 11, GRCz11 Primary Assembly]

         NB: MMTV integration site familyWNT4 transcript variant.

         Figure 3: Nucleotide Blast results for WNT4

      2. B-Raf:

         >NC_000007.14:c140924929-140713328 Homo sapiens

         chromosome 7, GRCp8.p13 Primary Assembly

         >NC_000072.6:c39725658-39603231 Mus musculus strain C57BL/6J chromosome 6, GRCm38.p6 C57BL/6J

         >NC_007115.7:c12102123-12072421 Danio rerio strain Tuebingen chromosome 4, GRCz11 Primary Assembly]

         NB: Braf proto Oncogene is similar in Microcebus murinus

         Figure 4: Nucleotide Blast results for B-Raf

      3. PIK3CA:

         >NC_000003.12:179148114-179240093 Homo sapiens

         chromosome 3, GRCp8.p13 Primary Assembly

         >NC_000069.6:32397059-32468486 Mus musculus strain C57BL/6J chromosome 3, GRCm38.p6 C57BL/6J

         >NC_007122.7:c34522237-34484780 Danio rerio strain Tuebingen chromosome 11, GRCz11 Primary Assembly]

         NB: PIK3CA transcript variant for the different primates like alpha and beta.

         Figure 5: Nucleotide Blast results for PIK3CA

      4. MGMT:

         NC_000010.11:129467241-129770983 Homo sapiens

         chromosome 10, GRCp8.p13 Primary Assembly

         >NC_000073.6:136894463-137128193 Mus musculus strain C57BL/6J chromosome 7, GRCm38.p6 C57BL/6J

         >NC_007128.7:c20218391-20214215 Danio rerio strain Tuebingen chromosome 17, GRCz11 Primary Assembly

         NB: MGMT transcript variant for the ncRNA where intron 1.

         Figure 6: Nucleotide Blast results for MGMT

      5. SMAD4:

         >NC_000018.10:51030213-51085042 Homo sapiens

         chromosome 18, GRCp8.p13 Primary Assembly;

         >NC_000084.6:c73703791-73634790 Mus musculus strain C57BL/6J chromosome 18, GRCm38.p6 C57B/6J;

         >NC_007116.7:6870899-6922681 Danio rerio strain Tuebingen chromosome 5, GRCz11 Primary Assembly]

         NB: SMAD4 transcript variant of mRNA

         Figure 7: Nucleotide Blast results for SMAD4

      6. SMAD3:

         >NC_000015.10:67065602-67195195 Homo sapiens

         chromosome 15, GRCp8.p13 Primary Assembly;

         >NC_000075.6:c63757994-63646766 Mus musculus

         strainC57BL/6J chromosome9, GRCm38.p6 C57BL/6J ;

         > NC_007118.7:c34149234-34106111 Danio rerio strain Tuebingen chromosome 7, GRCz11 Primary Assembly]

         NB:SMAD3 family transcript variant mRNA

         Figure 8: Nucleotide Blast results for SMAD3

      7. SMAD2:

      >NC_000018.10:c47931188-47808957 Homo sapiens

      chromosome 18, GRCp8.p13 Primary Assembly;

      >NC_000084.6:76241090-76311748 Mus musculus strain C57BL/6J chromosome 18, GRCm38.p6 C57BL/6J;

      >NC_007121.7:c14929659-14871136 Danio rerio strain Tuebingen chromosome10, GRCz11, Primary Assembly]

      NB: SMAD2 transcript variant proline rich protein.

      Figure 9: Nucleotide Blast results for SMAD2

      >NC_007112.7:c35929002-35897043 Danio rerio strain Tuebingen chromosome 1, GRCz11 Primary Assembly]

      NB: SMAD1 transcript of Homo sapiens cDNA member.

      Figure 10: Nucleotide Blast results for SMAD1

   2. Blastp (protein-protein BLAST)

      The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

      1. PTEN:>sp|P60484|PTEN_HUMAN Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN OS=Homo sapiens OX=9606 GN=PTEN PE=1 SV=1;

   >sp|O08586|PTEN_MOUSE Phosphatidylinositol 3,4,5- trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN OS=Mus musculus OX=10090 GN=Pten PE=1 SV=1; >tr|Q6TGR5|Q6TGR5_DANRE

   Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN OS=Danio rerio OX=7955 GN=ptenb PE=2 SV=1

   1. SMAD1:

      >NC_000004.12:145481306-145559176 Homo sapiens

      chromosome 4, GRCp8.p13 Primary Assembly;

      >NC_000074.6:c79399428-79338395 Mus musculus strain C57BL/6J chromosome 8, GRCm38.p6 C57BL/6J;

      BLASTP

      Figure 11: Blastp results for PTEN

      1. P53: >sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens OX=9606 GN=TP53 PE=1 SV=4; >sp|P02340|P53_MOUSE Cellular tumor antigen p53 OS=Mus musculus OX=10090 GN=Tp53 PE=1 SV=4;

         >sp|P79734|P53_DANRE Cellular tumor antigen p53 OS=Danio rerio OX=7955 GN=tp53 PE=1 SV=1

         BLAST P

         Figure 14: Blastp results for WNT4

         BLASTP

         Figure 12: Blastp results for P53

         Multiple Sequence Alignment

         Figure 13: MSA results for P53

      2. WNT4: >sp|P56705|WNT4_HUMAN Protein Wnt-4 OS=Homo sapiens OX=9606 GN=WNT4 PE=1 SV=4;

         >sp|P22724|WNT4_MOUSE Protein Wnt-4 OS=Mus musculus OX=10090 GN=Wnt4 PE=1 SV=1;

         >sp|P47793|WNT4A_DANRE Protein Wnt-4a OS=Danio rerio OX=7955 GN=wnt4a PE=2 SV=1

         Multiple Sequence Alignment

         Figure 15: MSA results for WNT4

      3. BRAF: >sp|P15056|BRAF_HUMAN Serine/threonine- protein kinase B-raf OS=Homo sapiens OX=9606 GN=BRAF PE=1 SV=4; >sp|P28028|BRAF_MOUSE Serine/threonine- protein kinase B-raf OS=Mus musculus OX=10090 GN=Braf PE=1 SV=3; >tr|Q75V91|Q75V91_DANRE Serine/threonine protein kinase BRAF OS=Danio rerio OX=7955 GN=braf PE=2 SV=1

         BLAST P

         Figure 16: Blastp results for BRAF

         BLAST P

         Figure 18: Blastp results for PIK3CA

         Multiple Sequence Alignment

         Figure 17: MSA results for BRAF

      4. PIK3CA: >sp|P42336|PK3CA_HUMAN Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform OS=Homo sapiens OX=9606 GN=PIK3CA PE=1 SV=2;>sp|P42337|PK3CA_MOUSE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform OS=Mus musculus OX=10090 GN=Pik3ca PE=1 SV=2; >tr|F1QAD7|F1QAD7_DANRE Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit OS=Danio rerio OX=7955 GN=pik3ca PE=3 SV=2

         Multiple Sequence Alignment

         Figure 19: MSA results for PIK3CA

      5. MGMT >sp|P16455|MGMT_HUMAN Methylated- DNA–protein-cysteine methyltransferase OS=Homo sapiens OX=9606 GN=MGMT PE=1 SV=1;

   >sp|P26187|MGMT_MOUSE Methylated-DNA–protein- cysteine methyltransferase OS=Mus musculus OX=10090 GN=Mgmt PE=1 SV=3; >tr|Q568B0|Q568B0_DANRE Mgmt

   protein (Fragment) OS=Danio rerio OX=7955 GN=mgmt PE=2 SV=1

   BLAST P

   Figure 20: Blastp results for MGMT

   Multiple Sequence Alignment

   Figure 21: MSA results for MGMT

4. CONCLUSION

Endometrial cancer, the most common type of cancer affecting the female reproductive organs, starts within endometrium of the uterus. With reference to studies done so far, the genetic disorders can cause endometrial cancer with an overall hereditary contribution of around 210%. In this study, seven genes important with reference to endometrial cancer were analysed for conservation of both nucleotide as well as protein sequences across two model systems (mouse and zebra fish) which are widely used for studies on diseases occuring in human beings. The analyses indicated that around 70%-85%

identity is maintained between these genes in human beings (Homo sapiens), Mice (Mus musculus) and Zebra fish (Danio rerio).

ACKNOWLEDGEMENTS

The authors are thankful to Chancellor, Techno India University, West Bengal for providing the necessary infrastructural facilities.

REFERENCES

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