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ORIGINAL ARTICLE
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TP53 lacks tetramerization and N-terminal domains due to novel inactivating mutations detected in leukemia patients


 Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan

Date of Submission29-Jul-2019
Date of Decision17-Dec-2019
Date of Acceptance21-Jan-2020
Date of Web Publication06-Oct-2020

Correspondence Address:
Samina Ejaz,
Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur
Pakistan
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jcrt.JCRT_536_19

 > Abstract 


Background: TP53 is a highly conserved tumor suppressor gene present on chromosome 17 and comprised 11 exons and 12 introns. The TP53 protein maintained the genomic integrity of the cell by regulating different pathways. The association of TP53 with leukemia and the increasing prevalence of leukemia in Pakistan instigated us to initiate the current study.
Materials and Methods: The TP53 gene of acute myeloid leukemia patients (n = 23) and normal individuals (n = 30) was amplified through polymerase chain reaction (PCR). The PCR amplified products of 3 samples 1 normal (NC-30) and 2 cancerous (LK-6 and LK-19) were subjected to deoxyribonucleic acid (DNA) sequence analysis. Bioinformatics analysis of the obtained DNA sequences helped to identify nature, type, and functional impact of mutations, if any.
Results: Results revealed 2 novel mutations in Case No. 1 (c. G >A10987 and c. InsA13298_13299) and Case No. 2 (c. InsC13284_13285, c. T >A13365) which generate a premature codon (ocher) at position 239 and lead to truncated TP53 protein. In Case No. 3, 16 novel mutations were identified and c. delC11093 mutation created a premature codon (opal) at 59th position. Hence, the resultant protein will lack its tetramerization and N-terminal domain required for its normal functioning. Moreover, some intronic mutations were noticed and found to have a negative impact on splicing related regulatory sequences.
Conclusion: Results suggest the role of TP53 inactivating mutations in pathogenesis of leukemia.

Keywords: Bioinformatics analysis, exonic mutations, intronic mutations, leukemia, nonsense mutations, TP53



How to cite this URL:
Hameed Y, Ejaz S. TP53 lacks tetramerization and N-terminal domains due to novel inactivating mutations detected in leukemia patients. J Can Res Ther [Epub ahead of print] [cited 2020 Oct 20]. Available from: https://www.cancerjournal.net/preprintarticle.asp?id=297393




 > Introduction Top


Blood consists of three types of the cells red blood cells, white blood cells, and platelets. The increased number and abnormal behavior of any of the three blood cells are known as leukemia. Depending on the type of infected cells, leukemia is divided into four different types. Acute myeloid and lymphoid leukemia are the type of leukemia, in which immature large size myeloid and lymphoid blast cells are formed which do not let the normal cells to grow properly.[1] In chronic myeloid and lymphoid leukemia, mature myeloid and lymphoid lack the ability to work normally.[2]

After every 3 min, one new case of leukemia is reported in the USA. According to the Internal Agency for Research on Cancer report in 2018, a total of 10,590 cases and 1180 deaths are expected due to leukemia in the USA. Similarly, in Australia, leukemia is the eighth leading cause of cancer deaths. In Canada, the number of leukemia affected persons is reported to be 100,000/year.[3] According to Pakistan Observer mortality rate due to leukemia in Pakistan is 85,000 individuals per year and childhood myeloid leukemia is the most common type of leukemia.[4]

TP53 is a nuclear transcription factor and belongs to a highly conserved tumor suppressor gene family present on chromosome 17 and comprised of 11 exons and 12 introns. TP53 encodes a protein with a sequence length of 393 amino acids and molecular weight of 53 kilo Dalton, which maintains genomic integrity by controlling cell cycle progression, inducing apoptosis and repairing the damaged deoxyribonucleic acid (DNA) through activation of different other genes or proteins involved in these processes.[5],[6] In normal cells, mouse double minute 2 homolog protein regulates the level of TP53 protein by promoting its proteasomal ubiquitination and degradation. Whenever DNA is damaged the ataxia-telangiectasia mutated gene recognizes that damage and phosphorylates TP53 protein at serine 15 and serine 20 to stabilize and activate TP53 protein. The activated TP53 acts as a transcriptional factor of various downstream negative regulator genes of cell cycle such as P21 and The Growth Arrest and DNA Damage 45, which encode to inhibit cyclin-dependent kinases to perform cell cycle arrest. If the damage is not repairable, TP53 activates Bcl-2-associated X protein family proteins to induce cell apoptosis.[7] The loss of function mutations in TP53 are well-known oncogenic mutations. Genetic variations mostly target the transcription regulating role of the TP53 and make it unable to act as a transcriptional factor. It is known that inherited mutations in TP53 lead to the Li-Fraumeni syndrome, a disease which is thought to enhance predisposition to the early onset of cancers including leukemia.[8]

Moreover, many TP53 inactivating deletion, insertion, and substitution mutations have been noticed in a wide range of cancers including leukemia. Usually, both alleles of TP53 are mutated in leukemia.[9]

Many studies have been carried out worldwide to investigate the tumor suppressor activity of TP53 and identify general and population-specific leukemia-associated TP53 mutations and their consequences in leukemia.[10] In a majority of the studies region consisting of exons, 3–9 and introns (4 and 7) were screened. Amplification was done using polymerase chain reaction (PCR) and sequencing of amplified PCR products revealed various types of mutations in amplified regions [Supplementary Data Figure 1].



No data are available regarding TP53 mutations in Pakistani leukemia patients. However, few studies have been conducted to describe the role of TP53 in breast cancer patients of Pakistan. Results revealed few substitution mutations in Pakistani breast cancer patients, but the exact nature of these substitution mutations was not clearly explained.[14]

The Pakistani population is genetically unique than other worldwide population and experience exposure to different environmental and epidemiologic factors. Moreover, keeping in view the significant association of TP53 mutations with leukemia, known worldwide, and lack of information regarding the mutational status of TP53 in Pakistani leukemia patients, it was hypothesized that leukemia patients of southern Punjab, Pakistan, may harbor some novel TP53 mutations. Hence, it will be worth to investigate the status of TP53 mutations in leukemia patients of southern Punjab, Pakistan.


 > Materials and Methods Top


The experimental work followed guidelines of the Helsinki Declaration of 1965 (as revised in Brazil 2013). The experimental methodology used in the present study included two phases; wet-lab experiments and dry-lab experiments.

Phase I: Wet lab experiments

Sample collection

Blood samples were collected from a group of 53 individuals, including normal (n = 30) and acute myeloid leukemia patients (n = 23). All the participants of the study provided written consent and the anonymity of the participants were maintained. Collected samples were stored at −70°C for further process. The clinicopathological features of the leukemia patients are given in [Table 1].
Table 1: Clinicopathological features of the leukemia patients

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Inclusion criteria

Patients satisfying the following criteria were included in the study.

  1. The patient diagnosed with leukemia and received no chemotherapeutic treatment
  2. Patients who signed the consent form
  3. The patients of all age groups were included.


Exclusion criteria

The patients who refused to sign the consent form, going through the chemotherapy treatment and found positive for hepatitis C virus/hepatitis B virus infection were excluded from the study.

Genomic deoxyribonucleic acid extraction and amplification of TP53 gene

Genomic DNA was extracted from whole blood using an earlier reported organic extraction method[11] with some modifications. After lysis of blood cells, proteins and RNA were degraded using proteinase K and RNAse enzyme, respectively. DNA was precipitated by adding 20 μl of glycogen (10 mg/ml) solution to 500 μl of the aqueous phase. Extracted DNA was quantified using the Nanodrop method (Biotek/Take3) and subjected to agarose gel electrophoresis to evaluate the quality of extracted DNA. Already reported TP53 primers F1R1, F2R2, F3R3, and F4R4 [Supplementary Data Table 1] were selected for the present study. The selected primers helped to amplify the DNA binding domain of the TP53 (a major hotspot of TP53 mutations). The total volume of the PCR reaction mixture was 50 μl and contained 50 ng of template DNA, 20 pmol of each forward and reverse primer, 1.25 U of Taq DNA polymerase (Thermo Fisher Scientific, Boston, MA, USA), 200 μM of dNTPs, 2 mM of MgSO4, and 1× PCR buffer.



PCR amplification was performed in Mygene TmL series Peltier thermal cycler (UNIEQUIP, Germany using an initial denaturation period of 2 min at 94°C, followed by 40 cycles at 94°C for 45 s, with specific annealing temperature (62°C) for 1 min and a final extension period of 10 min at 72°C. After amplification, PCR products were resolved on 2% agarose gel.

Deoxyribonucleic acid sequencing

Depending on the availability of funds out of total 53 (30 normal and 23 leukemia patients), only 3 samples, 1 normal (NC-30), and 2 cancerous (LK-6 and LK-19), were subjected for DNA sequence analysis. The primers pairs [F1R1, F2R2, F3R3, F4R4; [Supplementary Data Table 1] used for PCR amplification were employed for DNA sequencing. For convenience 3 analyzed samples were referred to as three different cases (Case No. 1 = leukemia LK-6 sample, Case No. 2 = leukemia LK-19 sample, and Case No. 3 = normal NC-30 sample). While encoded proteins were categorized as mutant 1, mutant 2, and mutant 3 proteins, respectively. PCR amplicons were purified using Thermofisher, purification kit (Cat#T1030S) and sent to macrogen, Korea, for bidirectional DNA sequence analysis.

Phase II: Dry-lab experiments

Comparative and mutational dry-lab experiments of the retrieved DNA sequences were performed to find out the mutations and predict their effect on the encoded proteins. During mutational dry-lab experiments, the DNA sequences obtained from sequencing analysis were analyzed to find out the mutations, if any. For this purpose, the flanking regions of the DNA sequences were removed to get the refined sequences. Mutations were analyzed through pairwise sequence alignment, in which reference sequence (wild-type TP53 gene and consensus coding sequence [CCDS] sequences) were obtained from ENSEMBL and GenBank databases, respectively, whereas refined sequences (both forward and reverse) were subjected as query sequences. All the mutations were confirmed by both (forward and reverse) strand complementarity. After mutations confirmation, the studied sequences were joint with the unstudied sequences to get the CCDS sequence for functional analysis [Supplementary Data Table 2].




 > Results Top


Five coding exons of TP53 (E3–E7) along with small part of intron 3 (nt10895–nt10928), intron 4 (nt11170–nt11257), intron 5 (nt11558–nt11609), intron 6 (nt11499–nt11579), intron 7 (nt11202–nt13260), and intron 8 (nt13371–nt13438) were targeted.

Sequence analysis revealed various types of mutations (insertion, deletion, and substitution) at different positions in the TP53 gene. Mutations complemented/confirmed through bidirectional sequencing were considered for bioinformatics analysis. Bioinformatics tools were used to detect and explore the types and functional impact of the TP53 mutations [Supplementary Data Table 2]. Results of the present study are presented as follows:

Polymerase chain reaction amplification of TP53

PCR amplification of 53 samples, including leukemia patients (n = 23) and normal individuals (n = 30) using four different sets of primers revealed that the majority (33%) of cancerous samples were found positive for exon 3 (F1R1). However in contrast to this only a small fraction (7%) of the normal samples exhibited PCR amplification using F1R1 primers targeting exon 3. While the positivity ratio of exon 4 (F2R2) was slightly higher in cancerous samples (29%) as compared to normal ones (27%). Contrary to this, the positivity ratio of PCR amplification using F3R3 primer was slightly higher in normal (36%) than cancerous samples (33%). For primer F4R4, the positivity ratio was 10% in normal and slightly higher (13%) in cancerous samples [Supplementary Data Table 3] and [Supplementary Data Figure 2].



TP53 exonic mutations

In Case No. 1, two mutations including G >A substitution at nt10987 and frameshift mutation AIns13298 were identified. These sequence alterations modified the amino acid sequence of the translated protein (E11K, M237I, C238V) and generated a premature truncated codon (ocher) at position 239 [Figure 1].
Figure 1: Case No. 1 mutant TP53 gene and the encoded TP53 protein. All of the 11 exons are shown in TP53 gene. Coding exons are marked starting from exon 3 at the position of (nt10929) to exon 11 at the position of (nt17939). Mutations in the coding exons have been mentioned along with positions. TP53 gene was translated into TP53 protein to reflect the effect of genetic mutations on the sequence of the encoded protein TP53 protein

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In Case No. 2, two mutations, including one frameshift mutation CIns13284 and a substitution mutation T < A at nt13365 were identified. Bioinformatics analysis indicated that these mutations altered the amino acid sequence of the translated protein (H233P, Y234 L, N235Q, Y236 L, M237H, and C238V) and generated premature termination codon (ocher) at position 239 [Figure 2].
Figure 2: Case No. 2 mutant TP53 gene and the encoded TP53 protein. All of the 11 exons are shown in TP53 gene. Coding exons are marked starting from exon 3 (nt10929) to exon 11 (nt17939). Mutations in the coding exons have been mentioned along with positions. TP53 gene was translated into TP53 protein to reflect the effect of genetic mutation on the sequence of the encoded TP53 protein

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In normal controlled sample (Case No. 3), 10 frameshift mutations (Cdel11093, Cdel11094, Cdel11315, Cdel11353, Cdel11354, Cdel11355, Cdel13370, Cdel13381, Adel11095, Adel11352) and 5 substitution mutations (T > A at nt11392, C > A at nt11396, C > T at nt11510, G < A at nt11512, and C > A at nt13338) were observed. While the Cdel11093 mutation introduced a premature termination codon (opal) at position the 59 of encoded protein [Figure 3].
Figure 3: Case No. 3 mutant TP53 gene and the encoded TP53 protein. All of the 11 exons are shown in TP53 gene. Coding exons are marked starting from exon 3 (nt10929) to exon 11 (nt17939). Mutations in the coding exons have been mentioned along with positions. TP53 gene was translated into TP53 protein to reflect the effect of genetic mutations on sequence and function of the encoded protein

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Functional impact of TP53 exonic mutations

In case No. 1, a G > A substitution at nt10987 and a frameshift mutation (AIns13298) were identified. In addition to other changes in the translated protein sequence (E11K, M237I, C238V) a premature termination codon resulted at position 239 [Figure 1]. Resultant protein was predicted lacking different essential amino acids such as Cys242, Arg248, Arg273, and Cys276 and N terminal domain which is important for binding of TP53 protein with its target DNA.

Moreover, mutant 1 protein lacks tetramerization domain along with the nuclear localization signals (NLSs). As a result, it will not be localized to the nucleus and will be unable to undergo tetramerize for its normal function [Figure 4]. The lower isoelectric point (pI), small size and alter three-dimensional (3D) structure as compared with normal suggest the negative impact of observed TP53 mutations on mutant 1 protein [Table 2] and [Figure 5].
Figure 4: Functional impact of the observed mutations on the encoded TP53 proteins. Structurally, mutant TP53 proteins were compared with normal TP53 protein. This comparison revealed that various important domains are missed in mutant TP53 proteins due to the formation of premature termination codon (opal) and (ocher) at position 59 and 239. Premature termination codons unable mutant TP53 proteins to activate their target genes (p21, BCL-2, Bcl-2-associated X protein)

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Table 2: Characteristics of normal TP53 and mutant proteins

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Figure 5: Three-dimensional structure comparison of mutant 1, mutant 2 and mutant 3 proteins with normal TP53 protein. 3D models of mutant (1, 2, 3) and normal TP53 protein were constructed by using the phyre2 software

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A similar situation was observed in Case No. 2, in which total 2 mutations including a frameshift mutation (CIns13284) and a substitution mutation (T < A at nt13365) were identified. These genetic alterations change the translated protein sequence H233P, Y234 L, N235Q, Y236 L, M237H, C238V, N stop codon (ocher) at position 239 [Figure 2]. The formation of premature termination codon at position 239 results in a truncated protein lacking tetramerization domain, NLS and DNA binding essential amino acids (Cys242, Arg248, Arg273, and Cys276), present in the DNA binding core domain of TP53 protein. Hence, mutant 2 protein will be unable to bind with DNA, tetramerize and transport to the nucleus [Figure 4]. Moreover, mutant 2 protein has a lower molecular weight as compared with the normal TP53 protein [Table 2].

An interesting situation was seen in mutant 3 protein, which is a normal control and found to be highly mutated among all three analyzed proteins.

Case No. 3 sample contained 16 mutations, including frameshift mutations (Cdel11093, Cdel11094, Cdel11315, Cdel11353, Cdel11354, Cdel11355, Cdel13370, Cdel13381, Adel11095, Adel11352) substitution mutations (T > A at nt11392, C > A at nt11396, C > T at nt11510, G < A at nt11512 and substitution of C > A at nt13338). The observed mutation created a premature termination codon (opal) at position 59 [Figure 3]. Due to the premature termination codon at position 59 all of the functional domains of TP53 protein, including DNA-binding core domain, tetramerization domain, NLSs, and N-terminal domain, are missing. When mutant 3 protein was compared with normal TP53 protein, it was found to have lower pI, molecular weight, and altered 3D structure [Table 2], [Figure 4] and [Figure 5].

TP53 intronic mutations

Intronic mutations were observed in Case No. 1 and Case No. 3. Total 5 mutations, including delC11196, delT11197, delG11198, delG11199, and delA11200, were observed in intron 4 [Supplementary Data Figure 3]. Mutational analysis of mutant and reference or wild-type sequence was performed to understand the effect of observed intronic mutations on potential splice site, potential branch point sequences, enhancer, and silencer motifs. Results indicated the creation of 2 new enhancer and silencer motifs and weakening of an acceptor splice site [Supplementary Data Table 4] and [Supplementary Data Table 5].



Total 3 mutations, including InsA13268, InsC13275, and InsC13287, were examined in intron 7 of Case No. 3 sample [Supplementary Data Figure 3].

Functional impact of TP53 intronic mutations

Sequence analysis revealed various intronic mutations. Total 5 mutations (delC11196, delT11197, delG11198, delG11199, and delA11200) in intron 4 of case No. 1 sample and 3 mutations (InsA13268, InsC13275, and InsC13287) in intron 7 of case No. 3 sample were observed. Mutational analysis of mutated intronic sequences showed the creation and breakdown of various potential splice sites, potential branch point sequences, enhancer, and silencer motifs as the outcome of the observed mutations [Supplementary Data Table 4] and [Supplementary Data Table 5].


 > Discussion Top


The role of TP53 gene in the development of human cancer has been extensively studied.[7] Mutated TP53 gene increases the risk of different cancers, including leukemia. Therefore, this study was initiated to study the mutational spectrum of the TP53 gene in leukemia patients of southern Punjab, Pakistan. Although many noticed mutations in the leukemia patients from southern Punjab have the same location as noticed worldwide, the amino acid alteration is unique [Table 3]. However, many of the mutations documented during the present study are unique [Figure 6].
Table 3: Comparison of observed TP53 mutations with already reported mutations

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Figure 6: Nature and location of uniquely observed TP53 mutations. Nature and location of the unique observed TP53 mutations which have not been reported in the present literature are shown in this figure. Q = Glutamine, A = Alanine, H = Histidine, P = Proline, Y = Tyrosine, C = Cysteine, and N = Asparagine (a). Various types of deletion mutations were noticed at different positions in intron 4 (Case No. 1). Three insertion mutations were documented at different positions in intron 7 of TP53 g ene (Case N o. 3) (b)

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The positivity ratio of exon 4 was slightly higher in cancerous samples (29%) as compared to normal ones (27%). However, PCR detection of exons 5, 6, and 7 was slightly higher in normal controls as compared to leukemia samples. Negative results of PCR amplification with a specific primer indicate either the absence of the target region or the presence of mutated target region [Supplementary Data Table 3] and [Supplementary Data Figure 3].

As previously reported[16] major hotspot of noticed mutation in the present study was the region encoding DNA binding core domain of the TP53 protein. All the mutant TP53 proteins observed during the present study were truncated and lacked different essential domains, including NLSs. Due to the absence of NLSs, all the mutant proteins were restricted to cytoplasm instead of being transported into the nucleus that is a major destination of normal TP53 protein. Our results are in accordance with the findings of earlier studies reporting TP53 nonsense mutations and synthesis of truncated TP53 proteins [Supplementary Data Figure 1]. Different kinds of TP53 mutations including frameshift mutations, nonsense mutation, deletion, and insertion mutations have been already reported in different populations worldwide. The results of two major population-specific studies are summarized [Supplementary Data Figure 1]. Studies revealed that leukemia patients of Taiwan (Q144X) and Germany (Y126X, Q136X, Q165X, R196X, R342X) harbor a different kind of nonsense mutations. Frameshift mutations (A74fs, A51fs, R209fs, C229fs) leading to premature termination codon and different deletion and substitution mutations have been observed in the German population. Similar to our study, deletion, insertion, and frameshift mutations led to the creation of premature termination codon and ultimately truncated TP53 protein [Supplementary Data Figure 1].

During this study, we have noticed mutations in normal control as well. The presence of the highly mutated TP53 gene suggests normal control as a patient of Li-Fraumeni syndrome having a high risk of developing different types of cancers including leukemia. The Li-Fraumeni syndrome is a hereditary genetic condition that raises the susceptibility of the individual to develop cancer. The enhanced cancer risk can pass from generations to generations. This condition is mainly caused by alterations in the TP53 gene. It is well known that the highly mutated allele of TP53 increases the risk of cancer by inducing Li-Fraumeni syndrome.[18]

Moreover, leukemia may not be the outcome of mutated TP53. Like the majority of other diseases, leukemia may be a multifactorial disease and the normal individual found positive for TP53 may not be still exposed to the other contributing factors of leukemia. Leukemia is promoted by many factors such as microbial inaction, weak immune system, and certain other environmental factors which are capable to mutate normal TP53 allele.[19]

Many studies have previously suggested the role of intronic mutations in the progression of leukemia [Supplementary Data Figure 1]. Our results indicated the creation of potential splice site, branch point sequence, enhancer, and silencer motifs. It is therefore, speculated that the documented intronic variations can alter the normal process of splicing and results in abnormal TP53 protein.





The findings of the present study strengthened the initial hypothesis suggesting the occurrence of unique mutations in Pakistan leukemia patients. There is a need to experimentally confirm the functional impact of the noticed TP53 mutations and extend study on large scale. It is essential to isolate and characterize mutant TP53 isoforms/variants. Moreover, expression profiling is required to be done.

Acknowledgments

We are thankful to Dr. Abdul Rehman (senior child specialist, Victoria Hospital Bahawalpur, Pakistan) for his kind support in blood sample collection. The cooperation of leukemia patients is also highly appreciated.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.



 
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    Figures

  [Figure 1], [Figure 2], [Figure 3], [Figure 4], [Figure 5], [Figure 6]
 
 
    Tables

  [Table 1], [Table 2], [Table 3]



 

 
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