Table 1 Selected examples of genes altered by structural variation in cancers
From: Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis
| Malignancy | Structural variation type | Affected gene | Alteration in TADs | Effect | References |
|---|---|---|---|---|---|
| T-ALL | Deletion | TAL1, LMO2, etc. | Deletion of a loop boundary CTCF site | Key oncogenic drivers TAL1 and LMO2 expression from the silent state | [130] |
| Lung squamous carcinoma | Deletion | IRS4 | Deletion of TAD boundary or insulator | IRS4 overexpression caused by new enhancer–promoter interactions | [129] |
| Prostate cancer | Deletion (17p13.1) | TP53 | Bifurcation of a single TAD into two distinct smaller TADs | Dysregulation of several genes | [124] |
| Colorectal cancer | Tandem duplications | IGF2 | Formation of neo-TAD | De novo formation of a 3D contact domain comprising IGF2 and a lineage-specific super-enhancer | [129] |
| Lung adenocarcinoma | Inv (2)(p21;p23) | EML4-ALK | – | – | [107] |
| AML | Inv(3)(q21;q26.2) | RPN1-EVI1 | Fusion of two TADs | EVI oncogene expression caused by new enhancer–promoter interactions | [132] |
| Rhabdomyosarcoma | t(2;13)(q35;q14) | PAX3-FOXO1 | Formation of neo-TAD | [133] | |
| AML | t(8;21) | RUNX1-ETO | – | – | [78] |