Document Detail

Haploinsufficiency of Tumor Suppressor Genes is Driven by the Cumulative Effect of microRNAs, microRNA Binding Site Polymorphisms and microRNA Polymorphisms: An In silico Approach.
Jump to Full Text
MedLine Citation:
PMID:  23032637     Owner:  NLM     Status:  PubMed-not-MEDLINE    
Haploinsufficiency of tumor suppressor genes, wherein the reduced production and activity of proteins results in the inability of the cell to maintain normal cellular function, is one among the various causes of cancer. However the precise molecular mechanisms underlying this condition remain unclear. Here we hypothesize that single nucleotide polymorphisms (SNPs) in the 3'untranslated region (UTR) of mRNAs and microRNA seed sequence (miR-SNPs) may cause haploinsufficiency at the level of proteins through altered binding specificity of microRNAs (miRNAs). Bioinformatics analysis of haploinsufficient genes for variations in their 3'UTR showed that the occurrence of SNPs result in the creation of new binding sites for miRNAs, thereby bringing the respective mRNA variant under the control of more miRNAs. In addition, 19 miR-SNPs were found to result in non-specific binding of microRNAs to tumor suppressors. Networking analysis suggests that the haploinsufficient tumor suppressor genes strongly interact with one another, and any subtle alterations in this network will contribute to tumorigenesis.
Mayakannan Manikandan; Ganesh Raksha; Arasambattu Kannan Munirajan
Related Documents :
24788517 - Coordination of trna transcription with export at nuclear pore complexes in budding yeast.
21070277 - Targets of selection in the thoroughbred genome contain exercise-relevant gene snps ass...
900887 - Genetic polymorphisms in afghanistan.
20937887 - Ecosystem-specific selection pressures revealed through comparative population genomics.
15791247 - Full-genome rnai profiling of early embryogenesis in caenorhabditis elegans.
7553627 - The retinoblastoma gene product in acute myeloid leukemia: a possible involvement in pr...
Publication Detail:
Type:  Journal Article     Date:  2012-08-29
Journal Detail:
Title:  Cancer informatics     Volume:  11     ISSN:  1176-9351     ISO Abbreviation:  Cancer Inform     Publication Date:  2012  
Date Detail:
Created Date:  2012-10-03     Completed Date:  2012-10-04     Revised Date:  2013-05-30    
Medline Journal Info:
Nlm Unique ID:  101258149     Medline TA:  Cancer Inform     Country:  New Zealand    
Other Details:
Languages:  eng     Pagination:  157-71     Citation Subset:  -    
Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai - 600113, Tamil Nadu, India.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

Full Text
Journal Information
Journal ID (nlm-ta): Cancer Inform
Journal ID (iso-abbrev): Cancer Inform
Journal ID (publisher-id): 101258149
ISSN: 1176-9351
Publisher: Libertas Academica
Article Information
Download PDF
© the author(s), publisher and licensee Libertas Academica Ltd.
collection publication date: Year: 2012
Electronic publication date: Day: 29 Month: 8 Year: 2012
Volume: 11First Page: 157 Last Page: 171
ID: 3433856
PubMed Id: 23032637
DOI: 10.4137/CIN.S10176
Publisher Id: cin-11-2012-157

Haploinsufficiency of Tumor Suppressor Genes is Driven by the Cumulative Effect of microRNAs, microRNA Binding Site Polymorphisms and microRNA Polymorphisms: An In silico Approach
Mayakannan Manikandan
Ganesh Raksha
Arasambattu Kannan Munirajan
Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai – 600113, Tamil Nadu, India.
Correspondence: Corresponding author email:


Cancer is a complex genetic disease involving structural and expression abnormalities of both coding and non-coding genes. The search for cancer causing genes has identified two major classes namely the oncogenes and tumor suppressor genes (TSGs). Activation or over expression of a proto-oncogene, such as cMyc,1 or inactivation of a tumor suppressor, such as TP53,2,3 causes tumorigenicity. Oncogene activation in tumors is straightforward, while the inactivation of TSGs is a complex process attained by different means including mutations, deletions, down regulation by microRNAs, epigenetic silencing etc. Although complete loss of TSG is common in tumors, recent studies indicate that a partial compromise in TSG function termed ‘haploinsufficiency’ contributes to the development and progression of many cancers.4 The condition where one functional allele of a gene is lost by mutation or deletion, and the remaining normal allele is insufficient to execute its original physiological function, is called haploinsufficiency. This phenomenon is extensively applicable to TSGs5 as they offer a benefit for cancer cells in regards to proliferation,6 survival,7 and metastasis.8

In principle, haploinsufficient TSGs are impaired by a 50% reduction in expression or activity. However, in vivo studies demonstrate that even a subtle 20% reduction of PTEN protein level—termed as ‘quasi-insufficiency’— could contribute to the development of cancer.9 Another example is that TP53, when targeted by short hairpin RNAs (shRNAs), is shown to elicit distinct phenotypes ranging from hyperplasia to malignancy in mouse models depending on the reduction in its protein level.10 This proves that some TSGs, like PTEN, are exquisitely sensitive to dose, while some, like TP53, are intermediately sensitive. Based on such observations, Berger et al has proposed a continuum model that accounts for subtle dosage effects of tumor suppressors including their regulation by microRNAs.11 The dosage and function of haploinsufficient genes are critical, and understanding the impact of haploinsufficiency is important for assessment of interindividual genetic variation, as well as the molecular basis of haploinsufficiency disorders.

Haploinsufficiency of multiple genes cooperate to promote tumorigenesis, a phenomenon called ‘compound haploinsufficiency’. The 5q deletion syndrome (5q-) is a paradigm of compound haploinsufficiency and demonstrates the importance of combinatorial interactions to elicit specific phenotypes.12 Experimental evidence has shown that co-suppression of linked 8p TSGs promotes tumor formation more potently than any individual gene.13 All the available evidence indicates that the functioning of a cell depends on the appropriate expression levels of proteins and, more importantly, that cell signalling pathways involve complex interactions between many proteins. Not only genes, but also microRNAs (miRNAs), a class of small noncoding RNAs, are shown to be haploinsufficient and to cause developmental abnormalities in humans.14 In addition, genes involved in miRNA biosynthesis pathway, such as DICER1, TARBP2 and XPO5, are identified as haploinsufficient tumor suppressors.1517

miRNAs act at the post-transcriptional level of gene regulation through RNA-induced silencing complex (RISC) mediated translational inhibition or mRNA cleavage. The miRNA target recognition is mediated through the sequence complementarity between the 2–8 nt at the 5′ end of miRNA (seed sequence) and the 3′-UTR of target mRNA.18 Based on the degree of complementarity, the mRNA is either guided for inhibition of translation or degradation resulting in the decrease of protein encoded by the target messenger.19 This has extended the dimensions of haploinsufficiency as miRNAs can lead to the production of insufficient amount of proteins. Bioinformatics prediction and experimental analysis suggested that miRNAs can regulate approximately half of the mammalian genes, with a significant number of important oncogenes and tumor suppressor genes involved.20,21 A recent genome-wide association study has suggested that a gene with more than two miRNA target sites will have higher variability of expression than a gene which is not regulated by a miRNA. The variability is further increased by SNPs in the miRNA target sites.22 Polymorphisms in the miRNA regulatory pathway are a novel class of functional polymorphisms present in the human genome. The initial demonstration that miRNA binding site variations can result in a phenotype was provided by Abelson et al who identified a mutation in the miR-189 binding site of SLITRK1 and its association with Tourette’s syndrome.23 A pioneering study conducted by Carlo Croce’s group showed that a germline mutation in pri-miR-16-1 resulted in low levels of miR-16-1 expression in familial chronic lymphocytic leukemia,24,25 providing evidence that sequence variation in miRNA genes may affect function and result in cancer susceptibility. Pre- and pri-miRNA SNPs in miR-124-1, miR-146a, miR-196-a2, miR-218, miR-219-1, miR-26a-1, miR-27a, miR-423, miR-492, and miR-499 have already been shown to increase/decrease cancer risk in various populations.26

Single nucleotide polymorphisms (SNPs) are single base pair changes in DNA that occur with a frequency of about 1 in 12,500 bp in the genome.27 Several studies have shown that SNPs in microRNA networks moderately increase the risk of cancer incidence.28 In general, sequence variations in pri-miRNAs, premiRNAs, mature miRNAs, and microRNA binding sites potentially affects the processing and/or target selection of miRNAs. As a consequence, aberrant expression of hundreds of genes and pathways greatly affecting miRNA function may occur.29 SNPs in mature miRNAs and miRNA binding sites function analogously to modulate the miRNA-mRNA interaction and create or destroy miRNA binding sites. Supporting this idea, SNPs within the miRNA binding sites of genes have been implicated in susceptibility to various types of cancer.3033 Additionally, functional support for individual miR-SNPs implicated in cancer do exist.

In this study we analyzed the role of SNPs that occur at miRNA binding sites and miR-SNPs and their contribution towards haploinsufficiency of tumor suppressor genes.

Materials and Methods

A total of 110 haploinsufficient genes known to have a role in tumor initiation and progression were considered for the study. Among the total list, 63 tumorigenic haploinsufficient genes were obtained from Dang et al, 200834 while the remaining 47 genes were compiled using keyword search in PubMed and Online Mendelian Inheritance in Man (OMIM) database. For a comprehensive list of the haploinsufficient tumorigenic genes included in this study with their corresponding reference, see Supplement 1.

Analysis of 3′UTR polymorphisms in mRNA targets and miR seed

The haploinsufficient genes were analyzed for polymorphisms in their 3′UTR by submitting the respective gene ID in ‘Polymorphism in microRNA Target Site’ (PolymiRTS) database,35, designed to identify SNPs that disrupt the regulation of gene expression by miRNAs in human and mouse (last accessed on June 7th, 2012). The database is organized to provide links between SNPs in miRNA target sites, cis-acting expression quantitative trait loci (eQTLs), and the results of genome-wide association studies (GWAS) of human diseases. We applied filters to identify only the SNPs in the 3′UTR that were known to create binding sites for miRNAs and SNPs occurring in the seed region of miRNA themselves.

Classification and validation of SNPs obtained from polymiRTS

The SNPs predicted by the polymiRTS database were classified based on their effect into the following categories: (i) SNPs that lead to the creation of miRNA binding sites in the mRNA, (ii) SNPs that disrupted the originally existing miRNA binding sites and also resulted in creation of new miRNA binding sites in the mRNA, and (iii) miR-SNPs that altered the binding specificity of miRNAs. After classification, the SNPs were verified by submitting their rs ID in the NCBI’s dbSNP Short genetic variation database the batch query option. The output was downloaded in BED format and analyzed. Among the total 158 SNPs submitted, 156 SNPs were validated by dbSNP while 2 miR-SNPs (rs116596918 and rs116838571) were found to be new entries and validated by microRNA-related Single Nucleotide Polymorphism database (

Functional network prediction using GeneMANIA Cytoscape plug-in

To identify the functional significance, GeneMANIA Cytoscape plug-in which employs the GeneMANIA algorithm37,38 was utilized with default settings to plot the interactions among the haploinsufficient TSGs. The complete list of tumorigenic haploinsufficient genes were uploaded to Cytoscape39 using GeneMANIA plug-in ( Further, only the genes that were found to have SNPs in their miRNA binding sites and those that are non-specifically targeted by miRNAs harboring miR-SNPs were uploaded individually to study the interactions among this subgroup. The GeneMANIA Cytoscape plug-in integrates association networks from multiple sources into a single composite network using a conjugate gradient optimization algorithm. This algorithm produces networks from the data either directly (as in the case of protein or genetic interactions) or by using an in-house analysis pipeline to convert profiles to functional association networks.

Results and Discussion
Polymorphisms in 3′UTR of mRNA

Our analysis of tumorigenic haploinsufficient genes for genetic variations in the 3′UTR showed that 26% (29 out of 110) of them had at least one 3′UTR SNP resulting in creation of new binding sites for miRNAs thereby bringing the respective mRNA variant under the control of more new miRNAs. In total, 129 SNPs were found to create binding sites for 234 miRNAs in 29 genes (Table 1). Altogether, these SNPs contribute to haploinsufficiency by bringing the polymorphic mRNA under the control of more new microRNAs thereby leading to translational repression or mRNA degradation. PPARA, a nuclear transcription factor and KIF1B, a kinesin implicated in neuronal and non-neuronal tumors was found to harbor 17 SNPs creating putative binding sites for many miRNAs. On the contrary, the SNP rs121912664 in TP53 creates putative miRNA binding site for miRNA-302 family, miR-520 family, miR-372, and miR-373-3p. The cell adhesion molecule CDH1, an important gene in tumor invasion with frequent allelic loss in metastatic tumors, was found to have 5 different SNPs that create putative binding sites for new miRNAs thereby altering the repertoire of miRNAs controlling this gene. Even RB1, the classical TSG, was predicted to have 3 SNPs that may down regulate its expression. If one allele is already lost in tumors, the remaining allele having at least one of these SNPs may be targeted by miRNAs and thereby lead to complete loss of cellular function, as postulated by Knudson’s “two-hit hypothesis.”

Another 10 SNPs were found to bring 8 different genes under the control of additional new miRNAs due to the presence of the respective SNP (Fig. 1). A single SNP can create miR binding site for several miRNAs as well as delete a miR binding site. For example, the SNP rs186304832 in the 3′UTR of KIF1B results in the loss of binding of 2 different microRNAs to the variant mRNA while 7 new microRNAs will be targeting this particular variant. This alters the miRNA mediated gene expression control resulting in aberrant regulation of expression. A gene that was previously under the control of one miRNA comes under the control of 3 different new miRNAs which leads to extensive translational repression resulting in protein haploinsufficiency as represented by the polymorphism rs1138533 in CDH1. This mechanism is totally new, since one allele is not lost due to mutation or deletion, as in the case of classical haploinsufficiency. Rather there is a decrease in the overall protein product. In homozygous state, this SNP may result in complete or partial reduction in the expression based on the ability of the repressing miRNA. However, in heterozygous state, the same SNP can lead to 50% or even subtler reduction in expression, which can explain ‘quasi-insufficiency’.

Ours is the first study to identify the SNP and miRNA mediated control of tumor suppressor dose as well as highlighting the importance of genetic variations in cancer. This mechanism is in agreement with the continuum model for tumor suppression that is related to the level of expression or activity of the TSG rather than to the discrete step-by-step changes in gene copy number.11

Polymorphisms in microRNA seed sequence

In addition, SNPs that occur in the seed sequence of miRNAs can alter the binding specificity of these miRNAs resulting in the binding to new non-target mRNAs. We analyzed 19 such miR-SNPs that cause miRNAs to bind new haploinsufficient tumor suppressor genes (Table 2). The SNP rs4636784 occurring in the seed of hsa-miR-4305 alters the binding specificity, thereby enabling it to target 6 new haploinsufficient genes (CDH1, KIF1B, SMAD4, DFFB, FOXP1, and PTEN). This can contribute to compound haploinsufficiency, wherein multiple genes cooperate to cause a particular phenotype.7,13 Alteration in one miRNA can alter the entire set of genes under its control thereby providing an advantage for cancer initiation and progression. In addition, the acquisition of miR-SNPs in tumors is simple enough to deregulate many genes than the need for individual mutations in all of them. This mechanism of miR-SNP mediated down regulation can also be extended to the unexplained allelic loss of KIF1B in neuroblastomas, where the tumor suppressor was shown to have no mutations or promoter methylation.40 Tumors not showing genetic alterations in the TSG, but with aberrant TSG levels due to miRNA misregulation, could behave like tumors with deletion or mutation of the gene. Importantly, mapping the interactions between miRNAs and TSGs could be useful for defining and predicting cancer susceptibility and therapeutic response.


Although reports on haploinsufficient genes associated with cancer is limited, analysis of the existing data shows that at least one third of total haploinsufficient genes to be tumorigenic. Tumor suppressors often act as components of complex networks, the overall function of which can be impaired by genetic and epigenetic alterations.41,42 For this reason we analyzed whether the haploinsufficient tumor suppressor genes share a common pathway or fall in a common interacting or functional network. The GeneMANIA algorithm was utilized for this purpose, and results indicate that almost 99% of haploinsufficient genes have a strong interaction, either directly or indirectly. SMAD5 was excluded from the list as it was not recognized by the algorithm. Co-expression, co-localization, physical and genetic interactions, pathway interactions, and other interactions that arise through shared structural domains were shown to exist between the queried genes (Fig. 2). SPRED1 was the only gene to fall out of this network however co-expression links it to the group. Apart from the queried list of genes, the algorithm identified several other genes to be a part of this network including DROSHA, DFFA, MRE11A, TRAPPC2L, TERF2, CDK6, BUB1, WRN, CCNA2, and RAD51. Interestingly, the haploinsufficient status of some of these genes has already been described in developmental abnormalities and other diseases,4345 while some others are shown to have a role in tumor formation and their haploinsufficient status is yet to be established.46

Next we tested whether the 39 genes with SNPs in miRNA binding sites or targeted by miRNAs with altered specificity due to miR-SNPs fall in to a particular network or pathway. Results of GeneMANIA networking analysis suggested strong interactions between these genes (Fig. 3). DNA repair genes and cell cycle checkpoint genes were enriched in this network and any aberrations in their expression offers selective advantage for the tumors to acquire additional genomic changes or mutations. DFFB was linked by co-expression, while DIRC2 was shown to be completely out of the group. The following genes were found to be a part of this network and to mediate interactions between the queried genes: MRE11A, DFFA, CCNB1, POLQ, AP1B1, RAD51, CCNG1, NPM1, DDB1, and WRN. The identification of the mRNA targets that mediate the actions of miRNAs in disease pathways can reveal previously unrecognized components that may serve as targets for more traditional drug development.


With the expanding understanding of the roles of miRNAs in various cellular processes and diseases, this is the first report to discuss the role of miRNAs and its contribution towards tumor suppressor gene haploinsufficiency at the protein level via 3′UTR SNPs and miR-SNPs. Further, this could be an alternate means for attaining compound heterozygosity observed in several tumors and the mechanism is in complete agreement with the continuum model of tumor suppression.11 Our data suggests that 26% of the tumorigenic haploinsufficient genes were brought under the control of new miRNAs due to 3′UTR SNPs. The identification of 10 SNPs that drive haploinsufficiency by bringing the polymorphic mRNA under the control of miRNAs, other than the miRNAs which are deleted, needs experimental validation in tumors. This alteration in the miRNA mediated gene regulation may cause predisposition to cancer initiation and progression.

Evidence for co-operative contribution of oncogenic mutations with tumor suppressor haploinsufficiency also exist.47 The realization that miR-SNPs play central roles in the aberrant regulation of tumor suppressor genes has provided a new perspective on our understanding of pathophysiologic mechanisms. In addition, networking analysis reveals strong interactions between the haploinsufficient tumor suppressor genes. Any subtle alteration in this network of genes due to SNPs at the 3′UTR and miR-SNPs may contribute to pathogenesis. We suggest that at least a few among these SNPs and their effect on miRNA binding will aid in the diagnosis and/or prognosis of such type of cancers, if experimentally validated. While challenges remain in this regard, the pace of development in this field suggests that new discoveries are forthcoming.

Our approach has currently focused only on analyzing 3′UTRs, although a small subset of miRNAs can target 5′UTRs, coding regions, and gene promoters. miR-SNPs leading to non-specific binding of miRNAs to tumor suppressors may also result in the loss of binding to their original targets. If the target is an oncogene, it will be over expressed and will result in tumorigenesis. This has not been focused on in this study. Since the rules for miRNA binding to its target changes constantly,48 the databases need constant updating. The 110 tumor suppressor genes chosen for our study were already proven to be haploinsufficient in several cancers through experimental evidence. This list may likely grow due to continuous identification of haploinsufficient tumor suppressors.

Supplementary Data
1. Amsterdam A,Sadler KC,et al. Many ribosomal protein genes are cancer genes in zebrafishPLoS BiolYear: 200425E13915138505
2. Bahubeshi A,Bal N,et al. Germline DICER1 mutations and familial cystic nephromaJ Med GenetYear: 20104712863621036787
3. Barlow JL,Drynan LF,et al. A p53-dependent mechanism underlies macrocytic anemia in a mouse model of human 5q- syndromeNat MedYear: 2010161596619966810
4. Berger AH,Niki M,et al. Identification of DOK genes as lung tumor suppressorsNat GenetYear: 20104232162320139980
5. Blough RI,Petrij F,et al. Variation in microdeletions of the cyclic AMP-responsive element-binding protein gene at chromosome band 16p13.3 in the Rubinstein-Taybi syndromeAm J Med GenetYear: 2000901293410602114
6. Bouffler SD,Hofland N,et al. Evidence for Msh2 haploinsufficiency in mice revealed by MNU-induced sister-chromatid exchange analysisBr J CancerYear: 200083101291411044352
7. Braggio E,Keats JJ,et al. Identification of copy number abnormalities and inactivating mutations in two negative regulators of nuclear factor-kappaB signaling pathways in Waldenstrom’s macroglobulinemiaCancer ResYear: 200969835798819351844
8. Bric A,Miething C,et al. Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma modelCancer CellYear: 20091643243519800577
9. Chayka O,Corvetta D,et al. Clusterin, a haploinsufficient tumor suppressor gene in neuroblastomasJ Natl Cancer InstYear: 200910196637719401549
10. Chen C,Bhalala HV,et al. A possible tumor suppressor role of the KLF5 transcription factor in human breast cancerOncogeneYear: 2002214365677212242654
11. Dang VT,Kassahn KS,et al. Identification of human haploinsufficient genes and their genomic proximity to segmental duplicationsEur J Hum GenetYear: 200816111350718523451
12. de Wind N,Dekker M,et al. Mouse models for hereditary nonpolyposis colorectal cancerCancer ResYear: 1998582248559443401
13. DeWeese TL,Shipman JM,et al. Mouse embryonic stem cells carrying one or two defective Msh2 alleles respond abnormally to oxidative stress inflicted by low-level radiationProc Natl Acad Sci U S AYear: 1998952011915209751765
14. Duan S,Cermak L,et al. FBXO11 targets BCL6 for degradation and is inactivated in diffuse large B-cell lymphomasNatureYear: 2012481737990322113614
15. Dumon-Jones V,Frappart PO,et al. Nbn heterozygosity renders mice susceptible to tumor formation and ionizing radiation-induced tumorigenesisCancer ResYear: 200363217263914612522
16. Ebert BL,Pretz J,et al. Identification of RPS14 as a 5q- syndrome gene by RNA interference screenNatureYear: 20084517176335918202658
17. Egle A,Harris AW,et al. Bim is a suppressor of Myc-induced mouse B cell leukemiaProc Natl Acad Sci U S AYear: 2004101166164915079075
18. Fang Y,Tsao CC,et al. ATR functions as a gene dosage-dependent tumor suppressor on a mismatch repair-deficient backgroundEMBO JYear: 2004231531647415282542
19. Gale NW,Dominguez MG,et al. Haploinsufficiency of delta-like 4 ligand results in embryonic lethality due to major defects in arterial and vascular developmentProc Natl Acad Sci U S AYear: 200410145159495415520367
20. Gorrini C,Squatrito M,et al. Tip60 is a haplo-insufficient tumour suppressor required for an oncogene-induced DNA damage responseNatureYear: 200744871571063717728759
21. Goss KH,Risinger MA,et al. Enhanced tumor formation in mice heterozygous for Blm mutationScienceYear: 200229755892051312242442
22. Grosshans H,Bussing I. MicroRNA biogenesis takes another single hit from microsatellite instabilityCancer CellYear: 2010184295720951937
23. Hellstrom M,Phng LK,et al. Dll4 signalling through Notch1 regulates formation of tip cells during angiogenesisNatureYear: 200744571297768017259973
24. Huang J,Powell WC,et al. Prostatic intraepithelial neoplasia in mice with conditional disruption of the retinoid X receptor alpha allele in the prostate epitheliumCancer ResYear: 200262164812912183441
25. Inoue K,Zindy F,et al. Dmp1 is haplo-insufficient for tumor suppression and modifies the frequencies of Arf and p53 mutations in Myc-induced lymphomasGenes DevYear: 200115222934911711428
26. Itoh T,Iwashita S,et al. Ddb2 is a haploinsufficient tumor suppressor and controls spontaneous germ cell apoptosisHum Mol GenetYear: 2007161315788617468495
27. Jacks T,Shih TS,et al. Tumour predisposition in mice heterozygous for a targeted mutation in Nf1Nat GenetYear: 199473353617920653
28. Jackson RJ,Engelman RW,et al. p21Cip1 nullizygosity increases tumor metastasis in irradiated miceCancer ResYear: 200363123021512810620
29. Jager R,Gisslinger H,et al. Deletions of the transcription factor Ikaros in myeloproliferative neoplasmsLeukemiaYear: 20102471290820508609
30. Kalitsis P,Fowler KJ,et al. Increased chromosome instability but not cancer predisposition in haploinsufficient Bub3 miceGenes Chromosomes CancerYear: 2005441293615898111
31. Kucherlapati M,Yang K,et al. Haploinsufficiency of Flap endonuclease (Fen1) leads to rapid tumor progressionProc Natl Acad Sci U S AYear: 200299159924912119409
32. Kumar MS,Pester RE,et al. Dicer1 functions as a haploinsufficient tumor suppressorGenes DevYear: 200923232700419903759
33. Lam MH,Liu Q,et al. Chk1 is haploinsufficient for multiple functions critical to tumor suppressionCancer CellYear: 200461455915261141
34. Mallakin A,Sugiyama T,et al. Mutually exclusive inactivation of DMP1 and ARF/p53 in lung cancerCancer CellYear: 20071243819417936562
35. McClatchey AI,Saotome I,et al. The Nf2 tumor suppressor gene product is essential for extraembryonic development immediately prior to gastrulationGenes DevYear: 199711101253659171370
36. McPherson JP,Lemmers B,et al. Involvement of mammalian Mus81 in genome integrity and tumor suppressionScienceYear: 200430456781822615205536
37. Melo SA,Ropero S,et al. A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 functionNat GenetYear: 20094133657019219043
38. Michel LS,Liberal V,et al. MAD2 haplo-insufficiency causes premature anaphase and chromosome instability in mammalian cellsNatureYear: 20014096818355911201745
39. Mullighan CG,Miller CB,et al. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of IkarosNatureYear: 20084537191110418408710
40. Munirajan AK,Ando K,et al. KIF1Bbeta functions as a haploinsufficient tumor suppressor gene mapped to chromosome 1p36.2 by inducing apoptotic cell deathJ Biol ChemYear: 200828336244263418614535
41. Rio Frio T,Bahubeshi A,et al. DICER1 mutations in familial multinodular goiter with and without ovarian Sertoli-Leydig cell tumorsJAMAYear: 20113051687721205968
42. Schofield CM,Hsu R,et al. Monoallelic deletion of the microRNA biogenesis gene Dgcr8 produces deficits in the development of excitatory synaptic transmission in the prefrontal cortexNeural DevYear: 201161121466685
43. Shao LJ,Shi HY,et al. Haploinsufficiency of the maspin tumor suppressor gene leads to hyperplastic lesions in prostateCancer ResYear: 2008681351435118593913
44. Smits R,Ruiz P,et al. E-cadherin and adenomatous polyposis coli mutations are synergistic in intestinal tumor initiation in miceGastroenterologyYear: 2000119410455311040191
45. Song WJ,Sullivan MG,et al. Haploinsufficiency of CBFA2 causes familial thrombocytopenia with propensity to develop acute myelogenous leukaemiaNat GenetYear: 19992321667510508512
46. Su X,Chakravarti D,et al. TAp63 suppresses metastasis through coordinate regulation of Dicer and miRNAsNatureYear: 201046773189869020962848
47. Taine L,Goizet C,et al. Submicroscopic deletion of chromosome 16p13.3 in patients with Rubinstein-Taybi syndromeAm J Med GenetYear: 1998783267709677064
48. Takagi Y,Takahashi M,et al. Roles of MGMT and MLH1 proteins in alkylation-induced apoptosis and mutagenesisDNA Repair (Amst)Year: 200321011354613679151
49. Tanaka Y,Naruse I,et al. Abnormal skeletal patterning in embryos lacking a single Cbp allele: a partial similarity with Rubinstein-Taybi syndromeProc Natl Acad Sci U S AYear: 1997941910215209294190
50. Terzian T,Wang Y,et al. Haploinsufficiency of Mdm2 and Mdm4 in tumorigenesis and developmentMol Cell BiolYear: 2007271554798517526734
51. Umesako S,Fujisawa K,et al. Atm heterozygous deficiency enhances development of mammary carcinomas in p53 heterozygous knockout miceBreast Cancer ResYear: 200571R1647015642165
52. Virely C,Moulin S,et al. Haploinsufficiency of the IKZF1 (IKAROS) tumor suppressor gene cooperates with BCR-ABL in a transgenic model of acute lymphoblastic leukemiaLeukemiaYear: 20102461200420393504
53. Vooijs M,Berns A. Developmental defects and tumor predisposition in Rb mutant miceOncogeneYear: 19991838529330310498881
54. Ward IM,Difilippantonio S,et al. 53BP1 cooperates with p53 and functions as a haploinsufficient tumor suppressor in miceMol Cell BiolYear: 20052522100798616260621
55. Wolfrum S,Teupser D,et al. The protective effect of A20 on atherosclerosis in apolipoprotein E-deficient mice is associated with reduced expression of NF-kappaB target genesProc Natl Acad Sci U S AYear: 20071044718601618006655
56. Xu X,Brodie SG,et al. Haploid loss of the tumor suppressor Smad4/Dpc4 initiates gastric polyposis and cancer in miceOncogeneYear: 2000191518687410773876
57. Zheng L,Flesken-Nikitin A,et al. Deficiency of Retinoblastoma gene in mouse embryonic stem cells leads to genetic instabilityCancer ResYear: 2002629249850211980640
58. Zhou XZ,Huang P,et al. The telomerase inhibitor PinX1 is a major haploin-sufficient tumor suppressor essential for chromosome stability in miceJ Clin InvestYear: 2011121412668221436583
59. Zhu Y,Ghosh P,et al. Neurofibromas in NF1: Schwann cell origin and role of tumor environmentScienceYear: 20022965569920211988578


fn1-cin-11-2012-157Author Contributions

AKM conceived and designed the study. MM and GR performed the experiments. AKM, MM, and GR analyzed the data. MM and AKM prepared the manuscript. All authors read and approved the final manuscript.

fn2-cin-11-2012-157Competing Interests

Author(s) disclose no potential conflicts of interest.

fn3-cin-11-2012-157Disclosures and Ethics

As a requirement of publication author(s) have provided to the publisher signed confirmation of compliance with legal and ethical obligations including but not limited to the following: authorship and contributorship, conflicts of interest, privacy and confidentiality and (where applicable) protection of human and animal research subjects. The authors have read and confirmed their agreement with the ICMJE authorship and conflict of interest criteria. The authors have also confirmed that this article is unique and not under consideration or published in any other publication, and that they have permission from rights holders to reproduce any copyrighted material. Any disclosures are made in this section. The external blind peer reviewers report no conflicts of interest.

fn4-cin-11-2012-157Funding Sources

This research was supported in part by a grant from the Department of Biotechnology (DBT), New Delhi (Grant Number BT/PR10023/AGR/36/27/2007) to AKM. MM is a recipient of research fellowship from Council of Scientific and Industrial Research (CSIR), New Delhi. We also thank DST-FIST and UGC-SAP for the infrastructure provided by grants to the department.

1. Nesbit CE,Tersak JM,Prochownik EV. MYC oncogenes and human neoplastic diseaseOncogeneYear: 1999181930041610378696
2. Caron de Fromentel C,Soussi T. TP53 tumor suppressor gene: a model for investigating human mutagenesisGenes Chromosomes CancerYear: 1992411151377002
3. Hainaut P,Hernandez T,Robinson A,et al. IARCDatabase of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation toolsNucleic Acids ResYear: 199826120513
4. Santarosa M,Ashworth A. Haploinsufficiency for tumor suppressor genes: when you don’t need to go all the wayBiochim Biophys ActaYear: 2004165421052215172699
5. Payne SR,Kemp CJ. Tumor suppressor geneticsCarcinogenesisYear: 2005261220314516150895
6. Solimini NL,Xu Q,Mermel CH,et al. Recurrent hemizygous feletions in cancers may optimize proliferative potentialScienceYear: 20123376090104922628553
7. Smilenov LB,Lieberman HB,Mitchell SA,Baker RA,Hopkins KM,Hall EJ. Combined haploinsufficiency for ATM and RAD9 as a factor in cell transformation, apoptosis, and DNA lesion repair dynamicsCancer ResYear: 2005653933815705893
8. Iwakuma T,Tochigi Y,Van Pelt CS,et al. Mtbp haploinsufficiency in mice increases tumor metastasisOncogeneYear: 2008271318132017906694
9. Alimonti A,Carracedo A,Clohessy JG,et al. Subtle variations in Pten dose determine cancer susceptibilityNat GenetYear: 2010425454820400965
10. Hemann MT,Fridman JS,Zilfou JT,et al. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivoNat GenetYear: 200333339640012567186
11. Berger AH,Knudson AG,Pandolfi PP. A continuum model for tumor suppressionNatureYear: 20114767359163921833082
12. Ebert BL. Deletion 5q in myelodysplastic syndrome: a paradigm for the study of hemizygous deletions in cancerLeukemiaYear: 20092371252619322210
13. Xue W,Kitzing T,Roessler S,et al. A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletionsProc Natl Acad Sci U S AYear: 2012109218212722566646
14. de Pontual L,Yao E,Callier P,et al. Germline deletion of the miR-17 ~92 cluster causes skeletal and growth defects in humansNat GenetYear: 2011431010263021892160
15. Kumar MS,Pester RE,Chen CY,et al. Dicer1 functions as a haploinsufficient tumor suppressorGenes DevYear: 200923232700419903759
16. Melo SA,Ropero S,Moutinho C,et al. A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 functionNat GenetYear: 20094133657019219043
17. Grosshans H,Bussing I. MicroRNA biogenesis takes another single hit from microsatellite instabilityCancer CellYear: 2010184295720951937
18. Lewis BP,Burge CB,Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targetsCellYear: 20051201152015652477
19. Bartel DP. MicroRNAs: target recognition and regulatory functionsCellYear: 200913622153319167326
20. Krol J,Loedige I,Filipowicz W. The widespread regulation of microRNA biogenesis, function and decayNat Rev GenetYear: 201011959761020661255
21. Fabbri M,Croce CM,Calin GA. MicroRNAsCancer JYear: 20081411618303474
22. Liu J,Rivas FV,Wohlschlegel J,Yates JR 3rd,Parker R,Hannon GJ. A role for the P-body component GW182 in microRNA functionNat Cell BiolYear: 20057121261616284623
23. Abelson JF,Kwan KY,O’Roak BJ,et al. Sequence variants in SLITRK1 are associated with Tourette’s syndromeScienceYear: 200531057463172016224024
24. Calin GA,Ferracin M,Cimmino A,et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemiaN Engl J MedYear: 200535317179380116251535
25. Wojcik SE,Rossi S,Shimizu M,et al. Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancerCarcinogenesisYear: 20103122081519926640
26. Slaby O,Bienertova-Vasku J,Svoboda M,Vyzula R. Genetic polymorphisms and microRNAs: new direction in molecular epidemiology of solid cancerJ Cell Mol MedYear: 201216182121692980
27. Kruglyak L,Nickerson DA. Variation is the spice of lifeNat GenetYear: 2001273234611242096
28. Ryan BM,Robles AI,Harris CC. Genetic variation in microRNA networks: the implications for cancer researchNat Rev CancerYear: 201010638940220495573
29. Georges M,Coppieters W,Charlier C. Polymorphic miRNA-mediated gene regulation: contribution to phenotypic variation and diseaseCurr Opin Genet DevYear: 20071731667617467975
30. Nicoloso MS,Sun H,Spizzo R,et al. Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibilityCancer ResYear: 201070727899820332227
31. Brendle A,Lei H,Brandt A,et al. Polymorphisms in predicted microRNA-binding sites in integrin genes and breast cancer: ITGB4 as prognostic markerCarcinogenesisYear: 20082971394918550570
32. Chin LJ,Ratner E,Leng S,et al. A SNP in a let-7 microRNA complementary site in the KRAS 3′untranslated region increases non-small cell lung cancer riskCancer ResYear: 2008682085354018922928
33. Saetrom P,Biesinger J,Li SM,et al. A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesisCancer ResMonth: 9 Day: 15 Year: 2009691874596519738052
34. Dang VT,Kassahn KS,Marcos AE,Ragan MA. Identification of human haploinsufficient genes and their genomic proximity to segmental duplicationsEur J Hum GenetYear: 200816111350718523451
35. Ziebarth JD,Bhattacharya A,Chen A,Cui Y. PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traitsNucleic Acids ResYear: 201240Database issueD2162122080514
36. Gong J,Tong Y,Zhang HM,et al. Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesisHum MutatYear: 20123312546322045659
37. Warde-Farley D,Donaldson SL,Comes O,et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene functionNucleic Acids ResYear: 201038Web Server issueW2142020576703
38. Montojo J,Zuberi K,Rodriguez H,et al. GeneMANIA Cytoscape plug-in: fast gene function predictions on the desktopBioinformaticsYear: 201026222927820926419
39. Smoot ME,Ono K,Ruscheinski J,Wang PL,Ideker T. Cytoscape 2.8: new features for data integration and network visualizationBioinformaticsYear: 2011273431221149340
40. Munirajan AK,Ando K,Mukai A,et al. KIF1Bbeta functions as a haploinsufficient tumor suppressor gene mapped to chromosome 1p36.2 by inducing apoptotic cell deathJ Biol ChemYear: 200828336244263418614535
41. Jones RG,Thompson CB. Tumor suppressors and cell metabolism: a recipe for cancer growthGenes DevYear: 20092355374819270154
42. Scuoppo C,Miething C,Lindqvist L,et al. A tumor suppressor network relying on the polyamine-hypusine axisNatureYear: 20124877406244822722845
43. Chong MM,Rasmussen JP,Rudensky AY,Littman DR. The RNAseIII enzyme Drosha is critical in T cells for preventing lethal inflammatory diseaseJ Exp MedYear: 2008205920051718725527
44. Moser MJ,Kamath-Loeb AS,Jacob JE,Bennett SE,Oshima J,Monnat RJ Jr. WRN helicase expression in Werner syndrome cell linesNucleic Acids ResYear: 20002826485410606667
45. Depienne C,Bouteiller D,Meneret A,et al. RAD51 haploinsufficiency causes congenital mirror movements in humansAm J Hum GenetYear: 2012902301722305526
46. Kim DH,Park SE,Kim M,et al. A functional single nucleotide polymorphism at the promoter region of cyclin A2 is associated with increased risk of colon, liver, and lung cancersCancerYear: 20111171740809121858804
47. Izeradjene K,Combs C,Best M,et al. Kras(G12D) and Smad4/Dpc4 haplo-insufficiency cooperate to induce mucinous cystic neoplasms and invasive adenocarcinoma of the pancreasCancer CellYear: 20071132294317349581
48. Stefani G,Slack FJ. A ‘pivotal’ new rule for microRNA-mRNA interactionsNat Struct Mol BiolYear: 2012193265622388780

[TableWrap ID: t3-cin-11-2012-157] Supplement I 

List of Haploinsufficient genes known to be involved in tumorigenesis.

Haploinsufficient genes References
ATR 18
BIM (BCL2 L11) 17
BLM 21
BUB3 30
CDH1 44
CDKN1 A 28
CHK1 (CHEK1) 33
CREBBP (CBP) 49, 47, 5
DDB2 26
DGCR8 42
DICER1 32, 2, 41
DLL4 19, 23
DMP1 25, 51, 34
DOK2 4
FBXO11 14
FEN1 31
IKZF1 (IKAROS) 39, 29, 52
KIF1Bβ 40
KLF5 10
MAD2 L1 38
MDM2 and MDM4 50
MLH1 48
MSH2 12, 13, 6
MUS81 36
NBN 15
NF1 27, 59
NF2 35
PINX1 58
RAD17 8
RB1 53, 57
Ribosomal proteins (RPL35, RPL37 A, RPS19 and RPS8) 1
RPS14 16, 3
RUNX1 45
SERPINB5 (Maspin) 43
TIP60 20
TNFAIP3 55, 7
TP53BP1 54
TP63 (TAp63) 46
XPO5 22

[TableWrap ID: t4-cin-11-2012-157] Supplement 2 

Supporting information for Table 1.

Gene Location SNP ID Allele change miR ID
ATM 108237837 rs227091 C to T hsa-miR-3664-3p, hsa-miR-4433-3p, hsa-miR-4768-3p, hsa-miR-512-5p
CDH1 68867609 rs35942505 C to T hsa-miR-548ae, hsa-miR-548ah-3p, hsa-miR-548aj-3p, hsa-miR-548am-3p, hsa-miR-548aq-3p, hsa-miR-548x-3p
DFFB 3800570 rs140704651 C to T hsa-miR-3664-3p, hsa-miR-4433-3p, hsa-miR-4768-3p, hsa-miR-512-5p
KIF1B 10367348 rs142468272 C to A hsa-miR-4435, hsa-miR-4701-5p, hsa-miR-548s, hsa-miR-588
10367422 rs2004034 G to A hsa-miR-25-3p, hsa-miR-32-5p, hsa-miR-363-3p, hsa-miR-367-3p, hsa-miR-92a-3p, hsa-miR-92b-3p
10437247 rs2155760 C to T hsa-miR-125a-5p, hsa-miR-125b-5p, hsa-miR-4319, hsa-miR-4446-5p, hsa-miR-4732-3p, hsa-miR-4755-5p, hsa-miR-5006-3p, hsa-miR-670
MDM2 69236548 rs1690917 G to T hsa-miR-548ac, hsa-miR-548d-3p, hsa-miR-548h-3p, hsa-miR-548z
69238940 rs184278637 G to A hsa-miR-3609, hsa-miR-4796-3p, hsa-miR-519a-3p, hsa-miR-519b-3p, hsa-miR-519c-3p, hsa-miR-548ah-5p
RAD50 131980270 rs75939007 A to G hsa-miR-199a-3p, hsa-miR-199b-3p, hsa-miR-3129-5p, hsa-miR-936
RXRA 137330802 rs10119893 G to A hsa-miR-1254, hsa-miR-1271-3p, hsa-miR-3116, hsa-miR-550a-3-5p, hsa-miR-550a-5p
SMAD4 48610254 rs146551171 T to C hsa-miR-142-5p, hsa-miR-548a-5p, hsa-miR-548ab, hsa-miR-548ak, hsa-miR-548am-5p, hsa-miR-548ap-5p, hsa-miR-548aq-5p, hsamiR-548ar-5p, hsa-miR-548as-5p, hsa-miR-548au-5p, hsa-miR-548av-5p, hsa-miR-548b-5p, hsa-miR-548c-5p, hsa-miR-548d-5p, hsa-miR-548h-5p, hsa-miR-548i, hsa-miR-548j, hsa-miR-548k, hsamiR-548o-5p, hsa-miR-548w, hsa-miR-548y, hsa-miR-559, hsa-miR- 5590-3p
TP53 7574015 rs121912664 G to A hsa-miR-302a-3p, hsa-miR-302b-3p, hsa-miR-302c-3p, hsa-miR-302d-3p, hsa-miR-302e, hsa-miR-372, hsa-miR-373-3p, hsa-miR-520a-3p, hsa-miR-520b, hsa-miR-520c-3p, hsa-miR- 520d-3p, hsa-miR-520e

Article Categories:
  • Perspective

Keywords: haploinsufficiency, microRNA, single nucleotide polymorphism, miR-SNPs, tumor suppressor genes, cancer.

Previous Document:  Renal perforation due to the migration of metal cerclage in hip arthroplasty.
Next Document:  CT to cone-beam CT deformable registration with simultaneous intensity correction.