This Key Event Relationship is licensed under the Creative Commons BY-SA license. This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. If you remix, adapt, or build upon the material, you must license the modified material under identical terms.
Relationship: 2729
Title
Increase chromosomal aberrations leads to Increase,miRNA levels
Upstream event
Downstream event
Key Event Relationship Overview
AOPs Referencing Relationship
AOP Name | Adjacency | Weight of Evidence | Quantitative Understanding | Point of Contact | Author Status | OECD Status |
---|---|---|---|---|---|---|
DNA damage and mutations leading to Metastatic Breast Cancer | non-adjacent | High | High | Usha Adiga (send email) | Under development: Not open for comment. Do not cite | Under Development |
Taxonomic Applicability
Term | Scientific Term | Evidence | Link |
---|---|---|---|
human | Homo sapiens | High | NCBI |
Sex Applicability
Sex | Evidence |
---|---|
Unspecific | High |
Life Stage Applicability
Term | Evidence |
---|---|
All life stages | Not Specified |
Key Event Relationship Description
KER :Increased, chromosomal aberration leads to microRNA expression, increased
Upstream event: increased, chromosomal aberration
Downstream event: increased miRNA expression
The depicted Key Event Relationship (KER) outlines a sequence of events involving genetic alterations and their potential impact on microRNA (miRNA) regulation. The upstream event, "Increased chromosomal aberration," suggests an elevation in the occurrence of structural abnormalities within chromosomes. These aberrations can encompass various changes, including deletions, duplications, inversions, or translocations of genetic material.
The downstream event in this KER is "increased miRNA expression," signifying a rise in the levels of microRNA molecules within the cell. Genetic alterations, such as chromosomal aberrations, can influence the expression of miRNAs, leading to changes in their abundance.
This KER underscores the potential interplay between genetic changes and miRNA regulation. Genetic alterations can influence miRNA expression patterns, potentially impacting downstream gene expression and cellular responses. Understanding these relationships contributes to a broader understanding of how genomic changes can influence post-transcriptional gene regulation and cellular processes.
Evidence Collection Strategy
Animal studies,cell line studies and human studies were searched,
Employing a meticulous evidence collection approach in accordance with OECD guidelines, the Key Event Relationship (KER) "Increase in chromosomal aberrations leads to Increased miRNA levels" was systematically validated. Initiating with increased chromosomal aberrations, a range of molecular and cellular assays was employed to confirm the occurrence of structural abnormalities in chromosomes. Techniques such as karyotyping and fluorescence in situ hybridization provided direct evidence of the chromosomal aberrations, reinforcing mechanistic understanding.
Mechanistic insights were further enriched through studies investigating the molecular pathways linking chromosomal aberrations to changes in miRNA levels. Expression profiling techniques, including microarrays and next-generation sequencing, were utilized to quantify miRNA abundance across experimental conditions, corroborating the induction of miRNA alterations.
Validation of the KER was reinforced by conducting experiments across various cell types, exposure scenarios, and genetic backgrounds. These diverse contexts contributed to the robustness and generalizability of the relationship's findings.
Real-world relevance was established by correlating laboratory-induced chromosomal aberrations with scenarios in which environmental exposures or genetic factors lead to increased genetic lesions and concurrent changes in miRNA levels. By thoughtfully integrating experimental data, mechanistic insights, and relevant contextual studies in line with OECD principles, a substantiated and comprehensive evidence base for the KER "Increase in chromosomal aberrations leads to Increased miRNA levels" was effectively constructed.
Evidence Supporting this KER
The first report linking a chromosomal breakpoint with the genomic location of miRNAs was published a couple of decades ago (Gauwerky et al.,1989). A masked t(8;17) translocation resulted in a high activation of the MYC OG: MYC from chromosome 8 was truncated at the end of the first exon (which is noncoding), and the coding region joined the regulatory elements of a gene located on chromosome 17, called BCL3 (B cell leukemia/lymphoma 3). Despite extensive genomic search, BCL3 remained an elusive entity until the identification of the human miRNAs. Fifteen years after the initial discovery, the miR-142 gene was found to be located 50 nt from the t(8;17) break involving chromosome 17 and MYC, meaning that the regulatory elements of this miRNA are likely involved in the overexpression of MYC (Calin, G.A., et al. 2002). The clinical consequences were dramatic for the patient, leading to aggressive acute prolymphocytic leukemia (Gauwerky et al.,1989). Apart from the involvement in the t(8;17) breakpoint of B cell acute leukemia, miR-142-3p and miR-142-5p are also within the 17q23 minimal amplicon described in breast cancer (Barlund, M., et al. 2000) and near the FRA17B site, a target for HPV16 integration in cervical tumors (Calin, G.A., et al. 2004).
Biological Plausibility
Chromosomal translocations alter PCG loci through two main mechanisms (Russo, G., et al. 1988). The first is the juxtaposition of promoter/enhancer elements from one gene to the intact coding region of another gene, while the second is the recombination of the coding regions of two different genes. The former is more frequently found in B and T cell lymphomas and leukemias and the latter in human myeloid leukemias and soft-tissue sarcomas. The translocations that alter miRNA loci can be classified by analogy with these mechanisms . At least five different situations can be postulated, the last three of which have yet to be identified in human cancers: (a) juxtaposition of promoter/enhancer elements from miRNA genes to a PCG ORF with overexpression of the protein [e.g., t(8;17)(q24;q22)]; (b) disruption of the region of interaction between the target PCG and the interactor miRNA with the disruption of the repression and the overexpression of the protein (e.g., 12q15 translocations involving HMGA2 gene); (c) juxtaposition of promoter/enhancer elements from PCG to a miRNA gene with overexpression of the noncoding gene; (d) juxtaposition of promoter/enhancer elements from miRNA to another miRNA gene with overexpression of the noncoding gene (termed “promoter swapping”); and (e) miRNA gene–to–miRNA gene fusion with the consequent production of a “new” cluster of coexpressed or independently expressed miRNAs.
Empirical Evidence
miRNA genes are located near breakpoint regions. miR-180 is only 1 kb from the MN1 gene involved in a t(4;22) chromosomal translocation in meningioma that inactivates MN1 and possibly the miRNA gene located in the same position. Also, in a patient with precursor B cell acute lymphoblastic leukemia, an insertion of miR-125b-1 into a rearranged immunoglobulin heavy-chain locus was described, possibly as an early step in leukemogenesis (Sonoki, T et al., 2009-2010). Chromosomal translocations fusing the BCL-6 OG to the regulatory elements of miR-28 or to the lipoma preferred partner were described in primary central nervous system lymphomas and may be associated with aberrant somatic hypermutation or defective class switch recombination (Schwindt, H., et al. 2006).
Uncertainties and Inconsistencies
The contribution of microRNAs (miR) to the pathogenesis of mantle cell lymphoma (MCL) is not well known. The expression of 86 mature miRs mapped to frequently altered genomic regions in MCL in CD5+ /CD5 normal B cells, reactive lymph nodes, and purified tumor cells of 17 leukemic MCL, 12 nodal MCL, and 8MCL cell lines were investigated. Genomic alterations of the tumors were studied by single nucleotide polymorphism arrays and comparative genomic hybridization. Leukemic and nodal tumors showed a high number of differentially expressed miRs compared with purified normal B cells, but only some of them were commonly deregulated in both tumor types. An unsupervised analysis of miR expression profile in purified leukemic MCL cells revealed two clusters of tumors characterized by different mutational status of the immunoglobulin genes, proliferation signature, and number of genomic alterations. The expression of most miRs was not related to copy number changes in their respective chromosomal loci. Only the levels of miRs included in the miR-17-92 cluster were significantly related to genetic alterations at 13q31. Moreover, overexpression of miR-17-5p/miR-20a from this cluster was associated with high MYC mRNA levels in tumors with a more aggressive behavior. In conclusion, the miR expression pattern of MCL is deregulated in comparison with normal lymphoid cells and distinguishes two subgroups of tumors with different biological features.
Known modulating factors
Modulating Factor (MF) | MF Specification | Effect(s) on the KER | Reference(s) |
---|---|---|---|
UV rays,cisplatin, doxorubicin, IR |
Impaired DNA repair | Altered miRNA expression |
Pothof et al., 2009,Galluzzi et al., 2010, Saleh et.al.,2011;Suzuki et al.,2009 |
Quantitative Understanding of the Linkage
Method/ measurement reference |
Reliability |
Strength of evidence |
Assay fit for purpose |
Repeatability/ reproducibility |
Direct measure |
|
Human |
Microarray, CGH analysis (dehan et al., 2007) |
+ |
Strong |
Yes |
Yes |
Yes |
Human cell line and blood samples |
Northern blotting (Calin et al., 2004) |
+ |
Strong |
Yes |
Yes |
Yes |
Cytogenetic techniques (Lionetti M et al., 2009 ; Min DJ et al., 2013 ;Huang JJ et al., 2012 ; Pichiorri F, et al., 2011; Roccaro AM et al., 2009; Gao X et al., 2009 ; Corthals SL et al.,2010 ; Pichiorri F et al., 2008 ; Yang RF et al., 2010; Rio-Machin A et al., 2013 ; Gutiérrez NC et al., 2010 ; Kuehl WM et al., 2012 ; Pichiorri F et al., 2010 ; Gatt ME et al., 2011 ; Zhang Y-K et al., 2011 ;Misiewicz-Krzeminska I et al., 2013;Wong KY et al., 2011 ;Chim CS et al., 2010) |
+ |
Strong |
Yes |
Yes |
Yes |
Response-response Relationship
Detailed investigation of the 13q14.3 deletions showed that both members of an miRNA cluster, miR-15a and miR-16-1, are deleted or downregulated in approximately 68% of CLL cases as compared with healthy donors (Calin, G.A., et al. 2002). Furthermore, a rare mutation lowering the expression of these genes was identified in two CLL patients including one from a family with individuals having CLL and breast cancer, and was found to be associated with the loss of the normal allele in the leukemic cells (Calin, G.A., et al. 2005). It was shown that the levels of both miR-15 and miR-16 inversely correlate with the BCL-2 protein expression and that BCL-2 repression by these miRNAs induces apoptosis in leukemia cells (Cimmino, A., et al. 2005).
Levels of miR-16 were decreased in NZB lymphoid tissue, and exogenous miR-16 delivered to an NZB malignant B-1 cell line resulted in cell cycle alterations and increased apoptosis. Linkage of the miR-15a/miR-16-1 complex to the development of CLL in this spontaneous mouse model suggests that the altered expression of these genes is the molecular lesion in CLL (Raveche, E.S., et al. 2007).
The only miRNA found to be overexpressed in any type of solid tumor analyzed (breast, colon, lung, prostate, stomach, and endocrine pancreas tumors, glioblastomas, and uterine leiomyomas) is miR-21 (Volinia, S., et al. 2006, Ciafre, S.A., et al. 2005; . Krichevsky et al.,2003; Wang, T., et al. 2007). This gene is located in the 3′UTR of the vacuole membrane protein 1 (VMP1) gene at chromosome 17q23.2, a region frequently found amplified in neuroblastomas and breast, colon, and lung cancers. Knockdown of miR-21 in glioblastoma cell lines induces a caspase-mediated apoptosis, further supporting the oncogenic role of this miRNA (Chan, et al.,2005).
Time-scale
Studies performed in solid cancer cell lines showed that miR-16 negatively regulated cellular growth and cell cycle progression. miR-16–downregulated transcripts were enriched with genes whose silencing by small interfering RNAs causes an accumulation of cells in G0/G1. Simultaneous silencing of these genes was more effective at blocking cell cycle progression than was disruption of the individual genes. Thus, miR-16 coordinately regulates targets that may act in concert to control cell cycle progression (Linsley, P.S., et al. 2007)
Known Feedforward/Feedback loops influencing this KER
Not mentioned.
Domain of Applicability
Not specific through any particular life stage or gender
References
Bärlund, M., Monni, O., Kononen, J., Cornelison, R., Torhorst, J., Sauter, G., ... & Kallioniemi, A. (2000). Multiple genes at 17q23 undergo amplification and overexpression in breast cancer. Cancer research, 60(19), 5340-5344.
Calin, G. A., Dumitru, C. D., Shimizu, M., Bichi, R., Zupo, S., Noch, E., ... & Croce, C. M. (2002). Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proceedings of the national academy of sciences, 99(24), 15524-15529.
Calin, G. A., Sevignani, C., Dumitru, C. D., Hyslop, T., Noch, E., Yendamuri, S., ... & Croce, C. M. (2004). Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proceedings of the National Academy of Sciences, 101(9), 2999-3004.
Calin, G. A., Ferracin, M., Cimmino, A., Di Leva, G., Shimizu, M., Wojcik, S. E., ... & Croce, C. M. (2005). A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. New England Journal of Medicine, 353(17), 1793-1801.
Calin, G. A., & Croce, C. M. (2006). MicroRNAs and chromosomal abnormalities in cancer cells. Oncogene, 25(46), 6202-6210.
Chan, J. A., Krichevsky, A. M., & Kosik, K. S. (2005). MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer research, 65(14), 6029-6033.
Chim, C. S., Wong, K. Y., Qi, Y., Loong, F., Lam, W. L., Wong, L. G., ... & Liang, R. (2010). Epigenetic inactivation of the miR-34a in hematological malignancies. Carcinogenesis, 31(4), 745-750.
Ciafre, S. A., Galardi, S., Mangiola, A., Ferracin, M., Liu, C. G., Sabatino, G., ... & Farace, M. G. (2005). Extensive modulation of a set of microRNAs in primary glioblastoma. Biochemical and biophysical research communications, 334(4), 1351-1358.
Cimmino, A., Calin, G. A., Fabbri, M., Iorio, M. V., Ferracin, M., Shimizu, M., ... & Croce, C. M. (2005). miR-15 and miR-16 induce apoptosis by targeting BCL2. Proceedings of the National Academy of Sciences, 102(39), 13944-13949.
Corthals, S. L., Jongen-Lavrencic, M., de Knegt, Y., Peeters, J. K., Beverloo, H. B., Lokhorst, H. M., & Sonneveld, P. (2010). Micro-RNA-15a and micro-RNA-16 expression and chromosome 13 deletions in multiple myeloma. Leukemia research, 34(5), 677-681.
Dehan, E., Ben-Dor, A., Liao, W., Lipson, D., Frimer, H., Rienstein, S., ... & Kaminski, N. (2007). Chromosomal aberrations and gene expression profiles in non-small cell lung cancer. Lung cancer, 56(2), 175-184.
Galluzzi, L., Morselli, E., Vitale, I., Kepp, O., Senovilla, L., Criollo, A., ... & Kroemer, G. (2010). miR-181a and miR-630 regulate cisplatin-induced cancer cell death. Cancer research, 70(5), 1793-1803.
Gao, X., Zhang, R., Qu, X., Zhao, M., Zhang, S., Wu, H., ... & Chen, L. (2012). MiR-15a, miR-16-1 and miR-17-92 cluster expression are linked to poor prognosis in multiple myeloma. Leukemia research, 36(12), 1505-1509.
Gatt, M. E., Zhao, J. J., Ebert, M. S., Zhang, Y., Chu, Z., Mani, M., ... & Carrasco, D. R. (2010). MicroRNAs 15a/16-1 function as tumor suppressor genes in multiple myeloma. Blood, 61-65.
Gauwerky, C. E., Huebner, K., Isobe, M., Nowell, P. C., & Croce, C. M. (1989). Activation of MYC in a masked t (8; 17) translocation results in an aggressive B-cell leukemia. Proceedings of the National Academy of Sciences, 86(22), 8867-8871.
Gutiérrez, N. C., Sarasquete, M. E., Misiewicz-Krzeminska, I., Delgado, M., De Las Rivas, J., Ticona, F. V., ... & San Miguel, J. F. (2010). Deregulation of microRNA expression in the different genetic subtypes of multiple myeloma and correlation with gene expression profiling. Leukemia, 24(3), 629-637.
Huang, J. J., Yu, J., Li, J. Y., Liu, Y. T., & Zhong, R. Q. (2012). Circulating microRNA expression is associated with genetic subtype and survival of multiple myeloma. Medical oncology, 29(4), 2402-2408.
Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K., & Kosik, K. S. (2003). A microRNA array reveals extensive regulation of microRNAs during brain development. Rna, 9(10), 1274-1281.
Kuehl, W. M., & Bergsagel, P. L. (2012). Molecular pathogenesis of multiple myeloma and its premalignant precursor. The Journal of clinical investigation, 122(10), 3456-3463.
Linsley, P. S., Schelter, J., Burchard, J., Kibukawa, M., Martin, M. M., Bartz, S. R., ... & Lim, L. (2007). Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Molecular and cellular biology, 27(6), 2240-2252.
Lionetti, M., Biasiolo, M., Agnelli, L., Todoerti, K., Mosca, L., Fabris, S., ... & Neri, A. (2009). Identification of microRNA expression patterns and definition of a microRNA/mRNA regulatory network in distinct molecular groups of multiple myeloma. Blood, The Journal of the American Society of Hematology, 114(25), e20-e26.
Min, D. J., Ezponda, T., Kim, M. K., Will, C. M., Martinez-Garcia, E., Popovic, R., ... & Licht, J. D. (2013). MMSET stimulates myeloma cell growth through microRNA-mediated modulation of c-MYC. Leukemia, 27(3), 686-694.
Misiewicz-Krzeminska, I., Sarasquete, M. E., Quwaider, D., Krzeminski, P., Ticona, F. V., Paíno, T., ... & Gutiérrez, N. C. (2013). Restoration of microRNA-214 expression reduces growth of myeloma cells through positive regulation of P53 and inhibition of DNA replication. haematologica, 98(4), 640.
Pichiorri, F., Suh, S. S., Ladetto, M., Kuehl, M., Palumbo, T., Drandi, D., ... & Croce, C. M. (2008). MicroRNAs regulate critical genes associated with multiple myeloma pathogenesis. Proceedings of the National Academy of Sciences, 105(35), 12885-12890.
Pichiorri, F., Suh, S. S., Rocci, A., De Luca, L., Taccioli, C., Santhanam, R., ... & Croce, C. M. (2010). Downregulation of p53-inducible microRNAs 192, 194, and 215 impairs the p53/MDM2 autoregulatory loop in multiple myeloma development. Cancer cell, 18(4), 367-381.
Pichiorri, F., De Luca, L., & Aqeilan, R. I. (2011). MicroRNAs: new players in multiple myeloma. Frontiers in genetics, 2, 22.
Pothof, J., Verkaik, N. S., Van Ijcken, W., Wiemer, E. A., Ta, V. T., Van Der Horst, G. T., ... & Persengiev, S. P. (2009). MicroRNA‐mediated gene silencing modulates the UV‐induced DNA‐damage response. The EMBO journal, 28(14), 2090-2099.
Raveche, E. S., Salerno, E., Scaglione, B. J., Manohar, V., Abbasi, F., Lin, Y. C., ... & Marti, G. E. (2007). Abnormal microRNA-16 locus with synteny to human 13q14 linked to CLL in NZB mice. Blood, The Journal of the American Society of Hematology, 109(12), 5079-5086.
Rio-Machin, A., Ferreira, B. I., Henry, T., Gómez-López, G., Agirre, X., Alvarez, S., ... & Cigudosa, J. C. (2013). Downregulation of specific miRNAs in hyperdiploid multiple myeloma mimics the oncogenic effect of IgH translocations occurring in the non-hyperdiploid subtype. Leukemia, 27(4), 925-931.
Roccaro, A. M., Sacco, A., Thompson, B., Leleu, X., Azab, A. K., Azab, F., ... & Ghobrial, I. M. (2009). MicroRNAs 15a and 16 regulate tumor proliferation in multiple myeloma. Blood, The Journal of the American Society of Hematology, 113(26), 6669-6680.
Russo, G., Isobe, M., Pegoraro, L., Finan, J., Nowell, P. C., & Croce, C. M. (1988). Molecular analysis of at (7; 14)(g35; g32) chromosome translocation in a T cell leukemia of a patient with ataxia telangiectasia. Cell, 53(1), 137-144.
Saleh, A. D., Savage, J. E., Cao, L., Soule, B. P., Ly, D., DeGraff, W., ... & Simone, N. L. (2011). Cellular stress induced alterations in microRNA let-7a and let-7b expression are dependent on p53. PloS one, 6(10), e24429.
Schwindt, H., Akasaka, T., Zühlke-Jenisch, R., Hans, V., Schaller, C., Klapper, W., ... & Deckert, M. (2006). Chromosomal translocations fusing the BCL6 gene to different partner loci are recurrent in primary central nervous system lymphoma and may be associated with aberrant somatic hypermutation or defective class switch recombination. Journal of Neuropathology & Experimental Neurology, 65(8), 776-782.
Sonoki, T., Iwanaga, E., Mitsuya, H., & Asou, N. (2005). Insertion of microRNA-125b-1, a human homologue of lin-4, into a rearranged immunoglobulin heavy chain gene locus in a patient with precursor B-cell acute lymphoblastic leukemia. Leukemia, 19(11), 2009-2010.
Suzuki, H. I., Yamagata, K., Sugimoto, K., Iwamoto, T., Kato, S., & Miyazono, K. (2009). Modulation of microRNA processing by p53. Nature, 460(7254), 529-533.
Volinia, S., Calin, G. A., Liu, C. G., Ambs, S., Cimmino, A., Petrocca, F., ... & Croce, C. M. (2006). A microRNA expression signature of human solid tumors defines cancer gene targets. Proceedings of the National Academy of Sciences, 103(7), 2257-2261.
Wang, T., Zhang, X., Obijuru, L., Laser, J., Aris, V., Lee, P., ... & Wei, J. J. (2007). A micro‐RNA signature associated with race, tumor size, and target gene activity in human uterine leiomyomas. Genes, Chromosomes and Cancer, 46(4), 336-347.
Wong, K. Y., So, C. C., Loong, F., Chung, L. P., Lam, W. W. L., Liang, R., ... & Chim, C. S. (2011). Epigenetic inactivation of the miR-124-1 in haematological malignancies. PloS one, 6(4), e19027.
Yang, R. F., Chen, L. J., Li, J. Y., Li, C. M., Xu, J. R., Wu, Y. J., & Lu, H. (2010). microRNA-21 and microRNA-30b expression in multiple myeloma. Zhonghua xue ye xue za zhi= Zhonghua Xueyexue Zazhi, 31(1), 38-41.
Zhang, X., Wan, G., Berger, F. G., He, X., & Lu, X. (2011). The ATM kinase induces microRNA biogenesis in the DNA damage response. Molecular cell, 41(4), 371-383.