Mapping the interaction between Trim28 and the <scp>KRAB</scp> domain at the center of Trim28 silencing of endogenous retroviruses

Taka, Jamie R. H.; Sun, Yunyuan; Goldstone, David C.

doi:10.1002/pro.4436

Cited by 6 publications

(8 citation statements)

References 40 publications

(133 reference statements)

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“…In particular, mutations of cysteine or histidine residues in critical zinc coordinating clusters of the RING, B2, and PHD domains appear to affect protein folding and stability. Other variants that lie in the same domains as our mutations were previously shown to impair protein function [26–28,30]. It would therefore seem likely that the nontruncating mutations we found alter protein stability as well as function.…”

Section: Discussionmentioning

confidence: 54%

“…Finally, the K304del mutation in WT7 disrupts heptad periodicity of a four‐helix bundle in the center of the coiled coil domain that interacts with the KRAB domain of DNA‐binding zinc finger transcription factors to mediate transcriptional silencing. A similar K304E mutation has been shown to decrease the affinity of TRIM28 for the ZNF932 KRAB domain by three orders of magnitude, which would abolish its gene‐silencing capacity [26].…”

Section: Resultsmentioning

confidence: 99%

“…We now identified 11 missense mutations and two in-frame deletions. We placed these variants onto the known 3D structure of TRIM28, which suggested a common mechanisms for disruption of TRIM28 function, as all mutations were located in critical regions of the protein [26][27][28].…”

Section: Missense Mutations Destabilize Trim28mentioning

confidence: 99%

“…Similarly, B-box 2 is a RING-like motif (CHC4H2-type) with dual cross-braced Zn 2+ coordination, extending from cysteine 209 to histidine 240 [28]. The C209Y, C224Y, and H240N mutations may thus likewise impair B-box 2 folding and destabilize the mutant protein [26,27]. The more distal deletion R629_C631delRVC in WT132 affects the PHD domain, where cysteine 631 is part of a zinc binding cluster that is essential for autosumoylation and target gene repression before [30].…”

Section: Missense Mutations Destabilize Trim28mentioning

confidence: 99%

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TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants

Wegert,

Fischer,

Palhazi

et al. 2023

The Journal of Pathology

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Wilms tumors (WTs) are histologically diverse childhood cancers with variable contributions of blastema, stroma, and epithelia. A variety of cancer genes operate in WTs, including the tripartite‐motif‐containing‐28 gene (TRIM28). Case reports and small case series suggest that TRIM28 mutations are associated with epithelial morphology and WT predisposition. Here, we systematically investigated the prevalence of TRIM28 inactivation and predisposing mutations in a cohort of 126 WTs with >2/3 epithelial cells, spanning 20 years of biobanking in the German SIOP93‐01/GPOH and SIOP2001/GPOH studies. Overall, 44.4% (56/126) cases exhibited loss of TRIM28 by immunohistochemical staining. Of these, 48 could be further analyzed molecularly, revealing TRIM28 sequence variants in each case – either homozygous (~2/3) or heterozygous with epigenetic silencing of the second allele (~1/3). The majority (80%) of the mutations resulted in premature stops and frameshifts. In addition, we detected missense mutations and small deletions predicted to destabilize the protein through interference with folding of key structural elements such as the zinc‐binding clusters of the RING, B‐box‐2, and PHD domains or the central coiled‐coil region. TRIM28‐mutant tumors otherwise lacked WT‐typical IGF2 alterations or driver events, except for rare TP53 progression events that occurred with expected frequency. Expression profiling identified TRIM28‐mutant tumors as a homogeneous subset of epithelial WTs that mostly present with stage I disease. There was a high prevalence of perilobar nephrogenic rests, putative precursor lesions, that carried the same biallelic TRIM28 alterations in 7/7 cases tested. Importantly, 46% of the TRIM28 mutations were present in blood cells or normal kidney tissue, suggesting germline events or somatic mosaicism, partly supported by family history. Given the high prevalence of predisposing variants in TRIM28‐driven WT, we suggest that immunohistochemical testing of TRIM28 be integrated into diagnostic practice as the management of WT in predisposed children differs from that with sporadic tumors. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

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Section: Discussionmentioning

confidence: 54%

Section: Resultsmentioning

confidence: 99%

Section: Missense Mutations Destabilize Trim28mentioning

confidence: 99%

Section: Missense Mutations Destabilize Trim28mentioning

confidence: 99%

See 2 more Smart Citations

TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants

Wegert,

Fischer,

Palhazi

et al. 2023

The Journal of Pathology

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“…Some novel investigations have unraveled the mechanism of ZNF-mediated repression of transcription in genome. The proteins coded by ZNF genes have a Canonical Kruppel-associated box (KRAB) domain that has affinity for KRAB-associated protein-1 (KAP-1) or Trim28 [67]. KRAB-ZFP identifies a specific region in the genome that is intended for suppression.…”

Section: Discussionmentioning

confidence: 99%

A retrospective case-control study for Clinical Validation of mutated ZNF208 as a novel biomarker of fatal blast crisis in Chronic Myeloid Leukemia

Alanazi,

Siyal,

Basit

et al. 2024

Preprint

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The hallmark of Chronic Myeloid Leukemia (CML) is Philadelphia chromosome t(9:22), which leads to formation of BCR-ABL1 fusion oncogene. BCR-ABL1 induces genetic instability, causing the progression of chronic myeloid leukemia (CML) from the manageable Chronic Phase (CP-CML) to the accelerated phase (AP-CML) and ultimately to the lethal blast crisis (BC-CML). The precise mechanism responsible for CML progression are not well comprehended, and there is a lack of specific molecular biomarkers for advanced phase CML. Mutations in transcription factors (TFs) have a significant role in cancer initiation, relapses, invasion, metastasis, and resistance to anti-cancer drugs. Recently, our group reported association of a novel transcription factor, ZNF208, with CML progression and there was a dire need for clinical validation of this novel biomarker. Therefore, the aim of this study was to clinically validate mutated ZNF208 as a novel biomarker for CML progression in a larger cohort of AP- and BC-CML patients using control-case studies. A total of 73 CML patients (N=73) from King Saud University Medical City Riyadh and King Abdulaziz National Guard Hospital, Al-Ahsa, Saudi Arabia were enrolled in the study (2020-2023) , with the experimental group (cases) consisting of patients AP-CML (n=20) and BC-CML (n=12). The controls consisted of age/sex matched CP-CML (n=41). The study was approved by Research Ethics Committees of participating institutes and all patients provided informed consent for the study. Clinical evaluations for patients were conducted according to the guidelines established by the European LeukemiaNet in 2020. Targeted resequencing of ZNF 208 was employed using Illumina NextSeq500 instrument (Illumina, San Diego, CA, USA) and mutations confirmed using Sanger sequencing. Both next generation sequencing as well as Sanger sequencing identified a novel missense mutation (c.64G>A) in novel ZNF208 . in 56 (93.3) and12 (100) CP-, AP- and BC-CML patients respectively, while in none (0%) of CP-CML patients or healthy controls from genomic databases (p=0.0001). Therefore, our studies show that ZNF208 mutation (c.64G>A) is novel and very specific biomarker for AP-and BC-CML patients. ZNF208 and other such proteins may cause carcinogenesis by interacting with KAP-1 repressor to silence many target genes and thus may prove to be novel drug targets as well. Therefore, we recommend carrying out prospective clinical trials for further clinical validation of this biomarker for its utilization in clinical decision, investigating its precise role in cancer pathogenesis and investigate its potential for novel drug target in advanced phase CML patients.

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Mapping the interaction between Trim28 and the KRAB domain at the center of Trim28 silencing of endogenous retroviruses

2022

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Transcription of endogenous retroviral elements are tightly regulated during development by members of the KRAB‐containing zinc finger proteins (KRAB‐ZFPs) and the co‐repressor Trim28 (also known as Kap‐1 or Tif1β). KRAB‐ZFPs form the largest family of transcription regulators in mammals and initiate transcriptional silencing by tethering Trim28 to a target locus. Subsequently, Trim28 recruits chromatin modifying effectors resulting in the formation of heterochromatin. In the present study, we identify surface exposed residues on the central six turns of the Trim28 coiled‐coil region forming the binding interface for the KRAB domain. Using AlphaFold2 (AF2) we provide high confidence models of the interface between Trim28 and the KRAB domain and identified leucine 301 on each chain of the Trim28 monomer to act as a pin extending into a hydrophobic pocket on the KRAB domain surface. Site directed mutations in the Trim28‐KRAB binding interface abolished binding to the KRAB domain. Our work provides a detailed understanding of the specific interactions between the KRAB domain and the Trim28 coiled‐coil and how this interaction may be regulated during silencing events.

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Mapping the interaction between Trim28 and the KRAB domain at the center of Trim28 silencing of endogenous retroviruses

Cited by 6 publications

References 40 publications

TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants

TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants

A retrospective case-control study for Clinical Validation of mutated ZNF208 as a novel biomarker of fatal blast crisis in Chronic Myeloid Leukemia

Mapping the interaction between Trim28 and the KRAB domain at the center of Trim28 silencing of endogenous retroviruses

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