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Decrypting Oncogenic Circuitry Through Translocation-Induced Enhancer Hijacking by TransFinder [SMRT-seq]

ABSTRACT: While IGH enhancer translocations are well-established drivers of multiple myeloma (MM), routine diagnostics detect these events in only 32~38% of patients. Here we introduce TransFinder, a multi-omics pipeline integrating SMRT-seq, Hi-C, RNA-seq, and CUT&Tag to systematically resolve cryptic translocations and their hijacked oncogenes by deconvoluting enhancer-promoter neo-loops at rearrangement breakpoints. Applied to MM, TransFinder identified that t(16;22)(q23;q11), a canonical translocation known to activate MAF, also hijacks enhancers to activate RAB36. It further uncovered previously unrecognized translocations, t(5;8)(q35;q24) and t(1;22)(q25;q13), that activate MYC and CBX7 transcription, respectively, through chromatin topology rewiring. CRISPR-Cas9-engineered t(1;22)(q25;q13) recapitulated CBX7 induction, and pharmacological inhibition of CBX7 suppressed myeloma cell proliferation. Beyond MM, TransFinder identified enhancer-hijacking events in other malignancies, including chronic myeloid leukemia (CML), where t(9;22)(q34;q11) repositioned an enhancer to activate BCR-ABL1 transcription, and pancreatic ductal adenocarcinoma (PDAC), where t(2;12)(p24;q24) hijacked an enhancer to ectopically activate SDC1. By bridging 3D genome architecture with oncogene activation, TransFinder decodes oncogenic structural variants and their trans-activities, establishing clinically actionable dependencies of non-coding drivers in malignancies with complex karyotypic alterations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE294550 | GEO | 2026/09/03

REPOSITORIES: GEO

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Decrypting Oncogenic Circuitry Through Translocation-Induced Enhancer Hijacking by TransFinder [Hi-C]

Project description:While IGH enhancer translocations are well-established drivers of multiple myeloma (MM), routine diagnostics detect these events in only 32~38% of patients. Here we introduce TransFinder, a multi-omics pipeline integrating SMRT-seq, Hi-C, RNA-seq, and CUT&Tag to systematically resolve cryptic translocations and their hijacked oncogenes by deconvoluting enhancer-promoter neo-loops at rearrangement breakpoints. Applied to MM, TransFinder identified that t(16;22)(q23;q11), a canonical translocation known to activate MAF, also hijacks enhancers to activate RAB36. It further uncovered previously unrecognized translocations, t(5;8)(q35;q24) and t(1;22)(q25;q13), that activate MYC and CBX7 transcription, respectively, through chromatin topology rewiring. CRISPR-Cas9-engineered t(1;22)(q25;q13) recapitulated CBX7 induction, and pharmacological inhibition of CBX7 suppressed myeloma cell proliferation. Beyond MM, TransFinder identified enhancer-hijacking events in other malignancies, including chronic myeloid leukemia (CML), where t(9;22)(q34;q11) repositioned an enhancer to activate BCR-ABL1 transcription, and pancreatic ductal adenocarcinoma (PDAC), where t(2;12)(p24;q24) hijacked an enhancer to ectopically activate SDC1. By bridging 3D genome architecture with oncogene activation, TransFinder decodes oncogenic structural variants and their trans-activities, establishing clinically actionable dependencies of non-coding drivers in malignancies with complex karyotypic alterations.

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Decrypting Oncogenic Circuitry Through Translocation-Induced Enhancer Hijacking by TransFinder [Micro-C]

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Decrypting Oncogenic Circuitry Through Translocation-Induced Enhancer Hijacking by TransFinder [CUT&Tag]

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Genetic characterization and therapeutic targeting of MYC rearranged T-cell acute lymphoblastic leukemia

Project description:T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological tumor that arises from T-cell precursor cells, is often characterized by T cell receptor (TCR) translocations that drive aberrant activation of specific proto-oncogenes. Here, we performed a detailed molecular genetic characterization of a rare but aggressive genetic subtype of human T-ALL, ie. patients that present with a t(8;14)(q24;q11) translocation, in which high MYC levels are driven by enhancer elements of the TCR a/d locus (TCRAD-MYC). Notably, analysis of an extensive series of primary leukemia samples confirmed that TCRAD-MYC translocation positive T-ALLs represent a NOTCH1 independent subtype of T-cell leukemia characterized by aberrant activation of the TAL1 and/or LMO2 transcription factor oncogenes and frequent activation of the PI3K/AKT signaling pathway. From a therapeutic perspective, in vivo drug treatment experiments using primary patient derived xenografts revealed that TCRAD-MYC positive T-ALLs are sensitive to BET bromodomain inhibition, providing a rationale to develop BRD4 inhibitors as an adjuvant therapy for this rare, but genetically well-defined, high-risk subtype of human leukemia.

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Gene expression profiling of chronic myeloid leukemia with variant t(9;22) reveals a different signature from cases with classic translocation.

Project description:The t(9;22)(q34;q11) generating the Philadelphia chromosome and the BCR/ABL1 fusion gene represents the cytogenetic hallmark of chronic myeloid leukemia (CML). About 5M-bM-^@M-^S10% of CML cases show variant translocations with the involvement of other chromosomes in addition to chromosomes 9 and 22. The molecular bases of differences between CML patients with classic and variant t(9;22) have never been elucidated. In this study, we performed gene expression microarrays analysis to compare CML patients bearing variant rearrangements and those with classic t(9;22)(q34;q11). We identified a list of 59 differentially expressed genes significantly associated with the two analyzed groups. These genes are mostly involved in the intracellular protein kinase cascade and their upregulation enhances cellular processes already known to sustain the CML pathogenesis. According to conventional and molecular cytogenetics (FISH) data, 12 CML cases with classic t(9;22) and of 8 cases with variant translocations were selected and analyzed by GEP.

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Project description:Acute megakaryoblastic leukemia (AMKL) is a heterogeneous disease generally associated with poor prognosis. Gene expression profiles indicate the existence of distinct molecular subgroups, and several genetic alterations have been characterized in the past years, including the t(1;22)(p13;q13) and the trisomy 21 associated with GATA1 mutations. However, the majority of patients do not present known mutations, and the limited access to primary patient leukemic cells impedes the efficient development of novel therapeutic strategies. In this study, using a xenotransplantation approach, we have modeled human pediatric AMKL in immunodeficient mice. Analysis of high-throughput RNA sequencing identified recurrent fusion genes defining new molecular subgroups.

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Gene expression profiling of chronic myeloid leukemia with variant t(9;22) reveals a different signature from cases with classic translocation.

Project description:The t(9;22)(q34;q11) generating the Philadelphia chromosome and the BCR/ABL1 fusion gene represents the cytogenetic hallmark of chronic myeloid leukemia (CML). About 5–10% of CML cases show variant translocations with the involvement of other chromosomes in addition to chromosomes 9 and 22. The molecular bases of differences between CML patients with classic and variant t(9;22) have never been elucidated. In this study, we performed gene expression microarrays analysis to compare CML patients bearing variant rearrangements and those with classic t(9;22)(q34;q11). We identified a list of 59 differentially expressed genes significantly associated with the two analyzed groups. These genes are mostly involved in the intracellular protein kinase cascade and their upregulation enhances cellular processes already known to sustain the CML pathogenesis.

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