Note | It is known that the aberrant expression of lncRNAs, as pseudogenes as well as the others ncRNAs, could have an important role in cancer development and progression (Chan and Tay, 2018; An et al., 2017). EEF1DP3 was found highly expressed in some healthy tissue types and also in many cancer types and this suggests that it could act as a positive regulator of gene expression, with high probability for its parental gene EEF1D and maybe also for other genes. In fact, it is known that the pseudogenes may act as positive regulators or negative regulators of gene expression (Hu et al., 2008). However, its role is still to be determined. Name | 5' end | 3' end | Loc1 | Loc2 | Description | Type | Disease | Organ | Code | Ref.< | APC/EEF1DP3 | APC | EEF1DP3 | 5q22.2 | 13q13.1 | t(5;13)(q22;q13) | Translocation | (?) | - | - | - | EEF1DP3/BLVRB | EEF1DP3 | BLVRB | 13q13.1 | 19q13.2 | t(13;19)(q13;q13) | Translocation | Sarcoma | Soft tissue | SARC | - | EEF1DP3/CLDN10 | EEF1DP3 | CLDN10 | 13q13.1 | 13q32.1 | t(13;13)(q13;q32) | Fusion gene | Adenocarcinoma | Breast | BRCA | Alaei-Mahabadi et al., 2016 | EEF1DP3/FRY | EEF1DP3 | FRY | 13q13.1 | 13q13.1 | Readthrough transcription | Fusion gene | Adenocarcinoma | Breast | BRCA | Kim et al., 2015 | Burkitt lymphoma | Blood | BL | - | Adenocarcinoma | Lung | LUAD | - | Malignant melanoma | Skin | SKCM | - | Nonneoplastic epithelial disorder/lesion | Adrenal gland | - | Babiceanu et al., 2016 | Nonneoplastic epithelial disorder/lesion | Bladder | - | - | Bone marrow | - | - | Embryonic stem cells (cell line) | ESC | Nonneoplastic mesenchymal disorder/lesion | Heart | - | Nonneoplastic epithelial disorder/lesion | Skin | - | Nonneoplastic epithelial disorder/lesion | Stomach | - | Nonneoplastic epithelial disorder/lesion | Testis | - | Nonneoplastic epithelial disorder/lesion | Thyroid | - | EEF1DP3/N4BP2L1 | EEF1DP3 | N4BP2L1 | 13q13.1 | 13q13.1 | t(13;13)(q13;q13) | Fusion gene | Adenocarcinoma | Breast | BRCA | - | EEF1DP3/TEX26 | EEF1DP3 | TEX26 | 13q13.1 | 13q12.3 | t(13;13)(q13;q12) | Fusion gene | Adenocarcinoma | Breast | BRCA | - | EEF1DP3/TLK1 | EEF1DP3 | TLK1 | 13q13.1 | 2q31.1 | t(2;13)(q31;q13) | Translocation | Burkitt lymphoma | Blood | BL | - | NCL/EEF1DP3 | NCL | EEF1DP3 | 13q13.1 | 13q13.1 | t(13;13)(q13;q13) | Fusion gene | (?) | - | - | - |
Table.1 EEF1DP3 rearrangements: translocations and fusion genes (reworked from https://cgap.nci.nih.gov/Chromosomes; http://atlasgeneticsoncology.org//Bands/13q13.html#REFERENCES; https://fusionhub.persistent.co.in/home.html; https://ccsm.uth.edu/FusionGDB/index.html)[ (?) ] unknown; [ - ] no reference |
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Entity | EEF1DP3/FRY read-through fusion |
Note | EEF1DP3/FRY is a recurrent read-through fusion transcript that is found in some types of nonneoplastic disorders and in some types of tumors such as malignant melanoma, Burkitt lymphoma, lung cancer and breast cancer (Babiceanu et al., 2016; Kim et al., 2015; Kim et al., 2011; https://fusionhub.persistent.co.in/home.html; https://ccsm.uth.edu/FusionGDB/index.html). The off-frame fusion of these two adjacent genes brings to the formation of a novel transcript formed by the 1 and 2 exons of EEF1DP3 joined with the exons from 2 to 61 of FRY. This results in an insertion of a stop codon in the nucleotidic sequence with an early truncation with loss-of-function of the FRY gene (Kim et al., 2015). |
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Entity | Adrenal carcinoma |
Note | EEF1DP3 is reported to be highly expressed inadrenocortical carcinoma (ACC) and pheochromocytoma and other paraganglioma (PCPG) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Ankylosing Spondylitis |
Note | EEF1DP3 seems to be involved in some variants associated with ankylosing spondylitis (AS), a chronic and complex autoimmune disorder. In particular, it was found a loss in EEF1DP3 due to its deletion and this has been associated with an increased risk and predisposition for AS (Shahba et al., 2018; Yim et al., 2015; Jung et al., 2014). |
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Entity | Brain and central nervous system (CNS) cancers |
Note | EEF1DP3 is reported to be highly expressed in brain lower grade glioma (LGG) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Breast Cancer |
Note | Some fusion genes caused by intrachromosomal translocations were reported for EEFDP3 in breast cancer (Alaei-Mahabadi et al., 2016; Babiceanu et al., 2016; Kim et al., 2015; https://fusionhub.persistent.co.in/home.html). |
Hybrid/Mutated Gene | All fusion genes reported until now between EEF1DP3 and other partner genes are due to intrachromosomal translocations except the more known fusion gene EEF1DP3/FRY that is the result of a fusion between EEF1DP3 at 5'-end and "FRY microtubule binding protein" ( FRY) gene at 3'-end (Kim et al., 2015) and it is due to a readthrough transcription. This fusion gene was found also in nonneoplastic epithelial disorders or in healthy tissues, so its presence in the cell seems to be not only linked with neoplastic transformation. Its biological significance needs to be clarified as well as its role in the cells and in cancer cells. Other fusion genes are reported such as EEF1DP3/CLDN10 that is originated by fusion of EEF1DP3 at 5'-end with "claudin 10" ( CLDN10) gene at 3'-end (Alaei-Mahabadi et al., 2016), EEF1DP3/N4BP2L1 that is originated by fusion of EEF1DP3 at 5'-end with "NEDD4 binding protein 2 like 1" ( N4BP2L1) gene at 3'-end and finally EEF1DP3/TEX26 that is originated by fusion of EEF1DP3 at 5'-end with "testis expressed 26" ( TEX26) gene at 3'-end. The significance of these genomic alterations is still poorly understood. |
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Entity | Colorectal cancer |
Note | EEF1DP3 is reported to be highly expressed in rectum adenocarcinoma (READ) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Gynaecological cancers |
Note | EEF1DP3 is reported to be highly expressed in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) samples and also in uterine carcinosarcoma (UCS) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Head and neck squamous cell carcinoma (HNSC) |
Note | EEF1DP3 is reported to be highly expressed in head and neck squamous cell carcinoma (HNSC) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Liver cancer |
Note | EEF1DP3 is reported to be highly expressed in liver hepatocellular carcinoma samples (LIHC) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Lung cancer |
Note | EEF1DP3 is reported to be highly expressed in lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and mesothelioma (MESO) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Lymphoma, leukaemia and other blood cancers |
Note | EEF1DP3 is reported to be highly expressed in acute myeloid leukemia (AML) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3) and are reported the fusion gene EEF1DP3 /FRY and the translocation t(2;13)(q31;q13) EEF1DP3/TLK1 in Burkitt lymphoma (https://fusionhub.persistent.co.in/home.html). |
Hybrid/Mutated Gene | The t(2;13)(q31;q13) EEF1DP3/TLK1 and EEF1DP3/FRY fusion gene were found in Burkitt lymphoma. The first rearrangement is originated by the fusion of EEF1D gene at 5'-end with "tousled like kinase 1" (TLK1) gene at 3' end while the EEF1DP3/FRY fusion gene is originated by the fusion of EEF1D gene at 5'-end with "FRY microtubule binding protein" (FRY) gene at 3' end and it is probably due to readthrough transcription. In fact, EEF1D and FRY are two neighboring genes on the same chromosome. There are no data about the chimeric transcripts or proteins and the role of these genomic alterations are still unknown. |
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Entity | Melanoma |
Note | EEF1DP3 is reported to be highly expressed in skin cutaneous melanoma (SKCM) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Neurodegenerative disorders |
Note | EEF1DP3 seems to be related to various neurodegenerative disorders as synucleinopathy and Parkinson's disease (https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Pancreatic cancer |
Note | EEF1DP3 is reported to be highly expressed in pancreatic adenocarcinoma (PAAD) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Prostate Cancer |
Note | Erho and colleagues found that EEF1DP3 is differentially expressed between normal prostate tissues and primary and metastatic prostate cancer samples (Erho et al., 2012) and other authors confirm this overexpression in prostate adenocarcinoma (PRAD) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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Entity | Sarcoma |
Note | EEF1DP3 is revealed to be highly expressed in sarcoma (SARC) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3) and was reported the translocation t(13;19)(q13;q13) EEF1DP3/BLVRB (https://fusionhub.persistent.co.in/home.html). |
Hybrid/Mutated Gene | The t(13;19)(q13;q13) EEF1DP3/BLVRB was found in sarcoma. This rearrangement is originated by the fusion of EEF1D gene at 5'-end with 'biliverdin reductase B' (BLVRB) gene at 3' end. There are no data about the respective chimeric transcript or protein and the role of this genomic alteration is unknown. |
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Entity | Urinary tract cancers |
Note | EEF1DP3 is reported to be highly expressed in bladder urothelial carcinoma (BLCA) samples and also in chromophobe renal cell carcinoma (KICH), clear cell renal cell carcinoma (KIRC) and papillary renal cell carcinoma (KIRP) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). |
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