Mutational Landscape of Pirin and Elucidation of the Impact of Most Detrimental Missense Variants That Accelerate the Breast Cancer Pathways: A Computational Modelling Study

Pirin (PIR) protein is highly conserved in both prokaryotic and eukaryotic organisms. Recently, it has been identified that PIR positively regulates breast cancer cell proliferation, xenograft tumor formation, and metastasis, through an enforced transition of G1/S phase of the cell cycle by upregulation of E2F1 expression at the transcriptional level. Keeping in view the importance of PIR in many crucial cellular processes in humans, we used a variety of computational tools to identify non-synonymous single-nucleotide polymorphisms (SNPs) in the PIR gene that are highly deleterious for the structure and function of PIR protein. Out of 173 SNPs identified in the protein, 119 are non-synonymous, and by consensus, 24 mutations were confirmed to be deleterious in nature. Mutations such as V257A, I28T, and I264S were unveiled as highly destabilizing due to a significant stability fold change on the protein structure. This observation was further established through molecular dynamics (MD) simulation that demonstrated the role of the mutation in protein structure destability and affecting its internal dynamics. The findings of this study are believed to open doors to investigate the biological relevance of the mutations and drugability potential of the protein.

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Codon harmonization reduces amino acid misincorporation in bacterially expressed P. falciparum proteins and improves their immunogenicity

AMB Express ◽

10.1186/s13568-019-0890-6 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Neeraja Punde ◽

Jennifer Kooken ◽

Dagmar Leary ◽

Patricia M. Legler ◽

Evelina Angov

Keyword(s):

Protein Structure ◽

Amino Acid ◽

Codon Usage ◽

Dna Sequences ◽

Structural Integrity ◽

Host Cells ◽

Loss Of Function ◽

Species Specific ◽

And Function ◽

The Impact

Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.

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A stochastic roadmap method to model protein structural transitions

Robotica ◽

10.1017/s0263574715001058 ◽

2015 ◽

Vol 34 (8) ◽

pp. 1705-1733 ◽

Cited By ~ 8

Author(s):

Kevin Molloy ◽

Rudy Clausen ◽

Amarda Shehu

Keyword(s):

Protein Structure ◽

Molecular Basis ◽

Structure And Function ◽

Structural Transitions ◽

Simulation Framework ◽

Human Disorders ◽

Model Protein ◽

And Function ◽

The Impact

SUMMARYEvidence is emerging that the role of protein structure in disease needs to be rethought. Sequence mutations in proteins are often found to affect the rate at which a protein switches between structures. Modeling structural transitions in wildtype and variant proteins is central to understanding the molecular basis of disease. This paper investigates an efficient algorithmic realization of the stochastic roadmap simulation framework to model structural transitions in wildtype and variants of proteins implicated in human disorders. Our results indicate that the algorithm is able to extract useful information on the impact of mutations on protein structure and function.

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Single Nucleotide Polymorphism in hsa-mir-196a-2 and Breast Cancer Risk: A Case Control Study

Twin Research and Human Genetics ◽

10.1375/twin.14.5.417 ◽

2011 ◽

Vol 14 (5) ◽

pp. 417-421 ◽

Cited By ~ 31

Author(s):

Dominik J. Jedlinski ◽

Plamena N. Gabrovska ◽

Stephen R. Weinstein ◽

Robert A. Smith ◽

Lyn R. Griffiths

Keyword(s):

Breast Cancer ◽

Breast Cancer Risk ◽

Cancer Risk ◽

Cancer Susceptibility ◽

Breast Cancer Susceptibility ◽

Case Control ◽

Cancer Tissue ◽

Transcriptional Level ◽

Nucleotide Polymorphisms ◽

Single Nucleotide

microRNAs are small, non-coding RNAs that influence gene expression on a post-transcriptional level. They participate in diverse biological pathways and may act as either tumor suppressor genes or oncogenes. As they may have an effect on thousands of target mRNAs, single-nucleotide polymorphisms in microRNA genes might have major functional consequences, because the microRNA's properties and/or maturation may change. miR-196a has been reported to be aberrantly expressed in breast cancer tissue. Additionally, the SNP rs11614913 in hsa-mir-196a-2 has been found to be associated with breast cancer risk in some studies although not in others. This study evaluated the association between rs11614913 and breast cancer risk in a Caucasian case-control cohort in Queensland, Australia. Results do not support an association of the tested hsa-mir-196a-2 polymorphism with breast cancer susceptibility in this cohort. As there is a discrepancy between our results and previous findings, it is important to assess the role of rs11614913 in breast cancer by further larger studies investigating different ethnic groups.

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Insilico analysis of structural and functional impact of SNPs in Pleckstrin

10.1101/782623 ◽

2019 ◽

Author(s):

Arpit Kumar Pradhan ◽

Ashwin Jainarayanan ◽

M. A. Nithishwer ◽

Shyamasree Ghosh

Keyword(s):

Molecular Evolution ◽

Inflammatory Diseases ◽

Aortic Aneurysms ◽

Nucleotide Polymorphisms ◽

Over Expression ◽

Abdominal Aortic ◽

Obstructive Sleep ◽

Potential Structure ◽

And Function ◽

The Impact

AbstractPleckstrin (PLEK) gene has been associated with a variety of disorders including autoimmune, inflammatory diseases and cancer. Mutation in this gene has been reported to be associated with autoimmune celiac disease (CD), increased atrophy in multiple sclerosis (MS), obstructive sleep apnea (OSA), abdominal aortic aneurysms, over expression in inflammatory disorders including periodontis, risk for ependymoma relapse, bladder cancer, melanoma, lung, and colorectal cancer revealing the importance of study of the PLEK. PLEK gene has been reported from other animals and therefore we have studied the molecular evolution of the PLEK gene by insilico approaches. Single nucleotide polymorphisms (SNPs), in humans have been reported to cause potential structure-function alteration in proteins. In this study we have tried to understand by insilico approaches the (i) molecular evolution of PLEK and (ii) the impact of potentially deleterious single non-synonymous SNPs (nsSNPs) on the structure and function of Pleckstrin protein. We report for the first time using molecular dynamic simulation (MDS), the impact of SNPrs17035364 and rs3816281 on the structural alterations of Pleckstrin with implications in altering its biological function which may find importance as diagnostic markers.

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Analysis of the TP53 Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach

International Journal of Molecular Sciences ◽

10.3390/ijms20122962 ◽

2019 ◽

Vol 20 (12) ◽

pp. 2962 ◽

Cited By ~ 2

Author(s):

Kumaraswamy Naidu Chitrala ◽

Mitzi Nagarkatti ◽

Prakash Nagarkatti ◽

Suneetha Yeguvapalli

Keyword(s):

Breast Cancer ◽

Machine Learning ◽

Risk Factors ◽

Estrogen Receptor ◽

Estrogen Receptor Alpha ◽

Large Deviation ◽

The Other ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

The Impact

Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk factors, estrogen levels play a crucial role. Among the estrogen receptors, estrogen receptor alpha (ERα) is known to interact with tumor suppressor protein p53 directly thereby repressing its function. Previously, we have studied the impact of deleterious breast cancer-associated non-synonymous single nucleotide polymorphisms (nsnps) rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 gene on the p53 DNA-binding core domain. In the present study, we aimed to analyze the impact of these mutations on p53–ERα interaction. To this end, we, have modelled the full-length structure of human p53 and validated its quality using PROCHECK and subjected it to energy minimization using NOMAD-Ref web server. Three-dimensional structure of ERα activation function-2 (AF-2) domain was downloaded from the protein data bank. Interactions between the modelled native and mutant (R110P, P278A, P151T) p53 with ERα was studied using ZDOCK. Machine learning predictions on the interactions were performed using Weka software. Results from the protein–protein docking showed that the atoms, residues and solvent accessibility surface area (SASA) at the interface was increased in both p53 and ERα for R110P mutation compared to the native complexes indicating that the mutation R110P has more impact on the p53–ERα interaction compared to the other two mutants. Mutations P151T and P278A, on the other hand, showed a large deviation from the native p53-ERα complex in atoms and residues at the surface. Further, results from artificial neural network analysis showed that these structural features are important for predicting the impact of these three mutations on p53–ERα interaction. Overall, these three mutations showed a large deviation in total SASA in both p53 and ERα. In conclusion, results from our study will be crucial in making the decisions for hormone-based therapies against breast cancer.

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TFEB is a master regulator of tumor-associated macrophages in breast cancer

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-000543 ◽

2020 ◽

Vol 8 (1) ◽

pp. e000543 ◽

Cited By ~ 3

Author(s):

Yong Li ◽

Johnie Hodge ◽

Qing Liu ◽

Junfeng Wang ◽

Yuzhen Wang ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Tumor Growth ◽

Gene Expression Profile ◽

Expression Profile ◽

Breast Tumor ◽

Tumor Development ◽

Tumor Associated Macrophages ◽

And Function ◽

The Impact

BackgroundTumor-associated macrophages (TAMs) play key roles in the development of many malignant solid tumors including breast cancer. They are educated in the tumor microenvironment (TME) to promote tumor growth, metastasis, and therapy resistance. However, the phenotype of TAMs is elusive and how to regulate them for therapeutic purpose remains unclear; therefore, TAM-targeting therapies have not yet achieved clinical success. The purposes of this study were to examine the role of transcription factor EB (TFEB) in regulating TAM gene expression and function and to determine if TFEB activation can halt breast tumor development.MethodsMicroarrays were used to analyze the gene expression profile of macrophages (MΦs) in the context of breast cancer and to examine the impact of TFEB overexpression. Cell culture studies were performed to define the mechanisms by which TFEB affects MΦ gene expression and function. Mouse studies were carried out to investigate the impact of MΦ TFEB deficiency or activation on breast tumor growth. Human cancer genome data were analyzed to reveal the prognostic value of TFEB and its regulated genes.ResultsTAM-mimic MΦs display a unique gene expression profile, including significant reduction in TFEB expression. TFEB overexpression favorably modulates TAM gene expression through multiple signaling pathways. Specifically, TFEB upregulates suppressor of cytokine signaling 3 (SOCS3) and peroxisome proliferator-activated receptor γ (PPARγ) expression and autophagy/lysosome activities, inhibits NLRP3 (NLR Family Pyrin Domain Containing 3) inflammasome and hypoxia-inducible factor (HIF)-1α mediated hypoxia response, and thereby suppresses an array of effector molecules in TAMs including arginase 1, interleukin (IL)-10, IL-1β, IL-6 and prostaglandin E2. MΦ-specific TFEB deficiency promotes, while activation of TFEB using the natural disaccharide trehalose halts, breast tumor development by modulating TAMs. Analysis of human patient genome database reveals that expression levels of TFEB, SOCS3 and PPARγ are positive prognostic markers, while HIF-1α is a negative prognostic marker of breast cancer.ConclusionsOur study identifies TFEB as a master regulator of TAMs in breast cancer. TFEB controls TAM gene expression and function through multiple autophagy/lysosome-dependent and independent pathways. Therefore, pharmacological activation of TFEB would be a promising therapeutic approach to improve the efficacy of existing treatment including immune therapies for breast cancer by favorably modulating TAM function and the TME.

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Epigenetic Changes Induced by Bacteroides fragilis Toxin

Infection and Immunity ◽

10.1128/iai.00447-18 ◽

2019 ◽

Vol 87 (6) ◽

Cited By ~ 12

Author(s):

Jawara Allen ◽

Stephanie Hao ◽

Cynthia L. Sears ◽

Winston Timp

Keyword(s):

Bacteroides Fragilis ◽

Distal Colon ◽

Chromatin Accessibility ◽

Tumor Formation ◽

Content Type ◽

Intestinal Neoplasia ◽

And Function ◽

Gut Microbial Community ◽

The Impact

ABSTRACT Enterotoxigenic Bacteroides fragilis (ETBF) is a Gram-negative, obligate anaerobe member of the gut microbial community in up to 40% of healthy individuals. This bacterium is found more frequently in people with colorectal cancer (CRC) and causes tumor formation in the distal colon of multiple intestinal neoplasia (Apcmin/+) mice; tumor formation is dependent on ETBF-secreted Bacteroides fragilis toxin (BFT). Because of the extensive data connecting alterations in the epigenome with tumor formation, initial experiments attempting to connect BFT-induced tumor formation with methylation in colon epithelial cells (CECs) have been performed, but the effect of BFT on other epigenetic processes, such as chromatin structure, remains unexplored. Here, the changes in gene expression (transcriptome sequencing [RNA-seq]) and chromatin accessibility (assay for transposase-accessible chromatin using sequencing) induced by treatment of HT29/C1 cells with BFT for 24 and 48 h were examined. Our data show that several genes are differentially expressed after BFT treatment and that these changes relate to the interaction between bacteria and CECs. Further, sites of increased chromatin accessibility are associated with the location of enhancers in CECs and the binding sites of transcription factors in the AP-1/ATF family; they are also enriched for common differentially methylated regions (DMRs) in CRC. These data provide insight into the mechanisms by which BFT induces tumor formation and lay the groundwork for future in vivo studies to explore the impact of BFT on nuclear structure and function.

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Computational analysis of Cyclin D1 gene SNPs and association with breast cancer

Bioscience Reports ◽

10.1042/bsr20202269 ◽

2021 ◽

Vol 41 (1) ◽

Author(s):

Ayesha Aftab ◽

Ranjha Khan ◽

Wasim Shah ◽

Muhammad Azhar ◽

Ahsanullah Unar ◽

...

Keyword(s):

Breast Cancer ◽

Cyclin D1 ◽

Tertiary Structure ◽

D1 Protein ◽

Nucleotide Polymorphisms ◽

Breast Cancer Patients ◽

Kaplan Meier ◽

Cyclin D1 Protein ◽

The Impact ◽

Kaplan Meier Plotter

Abstract CCND1 encodes for Cyclin D1 protein and single-nucleotide polymorphisms (SNPs) can modulate its activity. In the present study, the impact of CCND1 SNPs on structure and/or function of Cyclin D1 protein using in silico tools was investigated. Our analysis revealed only one splice site SNP (c.1988+5G<A) can effect CCND1 function. Subsequently, 78 out of 169 missense variants were predicted as pathogenic by Polyphen2, SIFT, PROVEAN, SNPs&GO, and PANTHER, and 4/78 missense SNPs were further evaluated because these four SNPs were found to be reside in highly conserved region of Cyclin D1. However, they did not show any major impact on tertiary structure and domain of Cyclin D1 but overall R15S and A190S has displayed a significant diseased phenotype and an altered molecular mechanism predicted by MutPred, FATHMM, SNPeffect, SNAP2, and PredictSNP. Consistently, A190S, R179L, and R15S may also cause a decrease in stability of Cyclin D1 anticipated by I-Mutant, HOPE and SNP effect. Furthermore, the Kaplan–Meier plotter has explained that high expression of CCND1 is associated with less survival rate of breast cancer patients. Altogether our study suggests that c.1988+5G<A, R15S, R179L, and A190S SNPs could directly or indirectly destabilize Cyclin D1.

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Burden analysis of missense variants in 1,330 disease-associated genes on 3D provides insights into the mutation effects

10.1101/693259 ◽

2019 ◽

Cited By ~ 1

Author(s):

Sumaiya Iqbal ◽

Jakob B. Jespersen ◽

Eduardo Perez-Palma ◽

Patrick May ◽

David Hoksza ◽

...

Keyword(s):

Protein Structure ◽

Molecular Mechanisms ◽

Clinical Genetics ◽

Missense Variants ◽

New Associations ◽

Pathogenic Variants ◽

Mutational Hotspots ◽

Disease Associated Genes ◽

And Function ◽

The Impact

AbstractInterpretation of the colossal number of genetic variants identified from sequencing applications is one of the major bottlenecks in clinical genetics, with the inference of the effect of amino acid-substituting missense variants on protein structure and function being especially challenging. Here we evaluated the burden of amino acids affected in pathogenic variants (n=32,923) compared to the variants (n=164,915) from the general population in 1,330 disease-associated genes on forty protein features using over 14,000 experimentally-solved 3D structures. By analyzing the whole gene/variant set jointly, we identified 18 features associated with 3D mutational hotspots that are generally important for protein fitness and stability. Individual analyses performed for twenty-four protein functional classes further revealed 240 characteristics of mutational hotspots in total, including new associations recapitulating the sheer diversity across proteins essential structural regions. We demonstrated that the function-specific features of variants correspond to the readouts of mutagenesis experiments and positively correlate with clinically-interpreted pathogenic and benign missense variants. Finally, we made our results available through a web server to foster accessibility and downstream research. Our findings represent a crucial step towards translational genetics, from highlighting the impact of mutations on protein structure to rationalizing the pathogenicity of variants in terms of the perturbed molecular mechanisms.

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The haplotype of three polymorphisms in the SATB1 promoter-region and impact on survival in breast cancer patients.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.584 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 584-584

Author(s):

Martin Leonhard Heubner ◽

Rainer Kimmig ◽

Winfried Siffert ◽

Frey Ulrich

Keyword(s):

Breast Cancer ◽

Cancer Patients ◽

Promoter Region ◽

Promoter Activity ◽

Hek293 Cells ◽

Nucleotide Polymorphisms ◽

Breast Cancer Patients ◽

Regulatory Effects ◽

The Impact

584 Background: Special AT-rich sequence binding protein 1 (SATB1) has regulatory effects on gene expression and appears to play an important role in tumor progression. We screened the promoter region of the SATB1 gene for polymorphisms, evaluated the corresponding haplotypes regarding alterations in promoter activity in vitro and analyzed the impact of these haplotypes on the clinical course of breast cancer patients. Methods: 241 caucasian breast cancer patients who had been treated were enrolled in this retrospective analysis. The median follow up time was 93 months (4-155 months). PCR products from DNA of 10 healthy unrelated volunteers were analyzed to identify new polymorphisms within the promoter region. Genotyping was conducted using restriction length polymorphism and pyrosequencing. PCR constructs with the respective alleles from the four most frequent haplotypes were cloned into the vector pGEM-Teasy (Promega Corporation, Madison, WI, USA) and then transferred into the luc2-containing reporter vector pGl 4.10 Vector (Promega) for transfection of HEK293 cells. The pGl 4.73 Vector (Promega), containing hRluc, was used for norming the transfection rates. Results: Sequencing the region -3807bp to -2828 upstream from ATG of ten healthy blood donors, we found three single nucleotide polymorphisms SNPs consisting of base exchanges, -3600T>C, -3363A>G and -2984C>T.The SATB1 -3600T/-3363A/-2984C haplotype had a lower promoter activity than all other constructs in vitro and showed a significant association with the nodal status (p=0.049). Kaplan-Meier survival analysis revealed a significantly better survival for homozygous SATB1 -3600T/-3363A/-2984C haplotype carriers compared with heterozygous or the other haplotypes (p=0.033). Conclusions: The SATB1 -3600T/-3363A/-2984C haplotype is associated with lower promoter activity and appears to impact upon survival in breast cancer patients.

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