Establishing a human adrenocortical carcinoma (ACC)-specific gene mutation signature

Rahane, Chinmay Satish; Kutzner, Arne; Heese, Klaus

doi:10.1016/j.cancergen.2018.10.005

Cited by 21 publications

(29 citation statements)

References 78 publications

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“…Interestingly, these mutations were localized in a hotspot region and OncodriveCLUST results suggested it could be putatively considered a cancer driver gene in this malignancy [45]. These results were confirmed by a complete analysis of the mutational data of ACC, which was performed on the same public database and validated through further algorithms (Mutsig and 20/20 rule); this study identified a new ACC-specific gene mutation signature, also comprising ZFPM1 among the six genes [277]. In addition, in our analysis we found that ZFPM1 is mutated also in colorectal cancers at relatively high frequencies [45].…”

Section: Zfpm1/fog1supporting

confidence: 66%

Multifaceted Role of PRDM Proteins in Human Cancer

Casamassimi

Rienzo

Zazzo

et al. 2020

IJMS

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The PR/SET domain family (PRDM) comprise a family of genes whose protein products share a conserved N-terminal PR [PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1)] homologous domain structurally and functionally similar to the catalytic SET [Su(var)3-9, enhancer-of-zeste and trithorax] domain of histone methyltransferases (HMTs). These genes are involved in epigenetic regulation of gene expression through their intrinsic HMTase activity or via interactions with other chromatin modifying enzymes. In this way they control a broad spectrum of biological processes, including proliferation and differentiation control, cell cycle progression, and maintenance of immune cell homeostasis. In cancer, tumor-specific dysfunctions of PRDM genes alter their expression by genetic and/or epigenetic modifications. A common characteristic of most PRDM genes is to encode for two main molecular variants with or without the PR domain. They are generated by either alternative splicing or alternative use of different promoters and play opposite roles, particularly in cancer where their imbalance can be often observed. In this scenario, PRDM proteins are involved in cancer onset, invasion, and metastasis and their altered expression is related to poor prognosis and clinical outcome. These functions strongly suggest their potential use in cancer management as diagnostic or prognostic tools and as new targets of therapeutic intervention.

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Section: Zfpm1/fog1supporting

confidence: 66%

Multifaceted Role of PRDM Proteins in Human Cancer

Casamassimi

Rienzo

Zazzo

et al. 2020

IJMS

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“…Mutations in GARS1 also serve to increase proliferation via a cascade that is, however, independent of the phosphoinositide-3-kinase (PI3K)/mitogen-activated protein kinase 1 (MAPK1)/WNT1 signaling pathways. Muta-tions in our novel gene set thus appear to be more influential in ACC tumorigenesis than those described in earlier studies and could serve as a powerful therapeutic target [28,29]. Experimental evidence-based schematic illustration of FAM72 and MKI67 co-activation in adrenocortical carcinoma (ACC).…”

Section: Fam72 In Adrenocortical Carcinomamentioning

confidence: 77%

“…FAM72 does not appear to be a protooncogene and the reciprocal expression dependency of SRGAP2 and FAM72 seems to be limited to the nervous system. Outside the nervous system, FAM72 expression appears to be induced by a different cancer-causing oncogene [12,27,28].…”

Section: The |-Srgap2-fam72-| Master Gene In Other Cancerous Tissuesmentioning

confidence: 99%

“…Recently, we identified a complex novel ACC-specific gene signature: CRIPAK, DGKZ, GARS1, LRIG1, ZFPM1, and ZNF517, which was significantly, specifically, and most repeatedly mutated in ACC and correlated with high FAM72 expression ( Figure 3) [28]. This gene set is involved in tumor suppression and cellular proliferation and thus could be useful for the prognosis and development of therapeutic approaches for the treatment of ACC.…”

Section: Fam72 In Adrenocortical Carcinomamentioning

confidence: 99%

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FAM72, Glioblastoma Multiforme (GBM) and Beyond

Rahane

Pramanik

et al. 2021

Cancers

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Neural stem cells (NSCs) offer great potential for regenerative medicine due to their excellent ability to differentiate into various specialized cell types of the brain. In the central nervous system (CNS), NSC renewal and differentiation are under strict control by the regulation of the pivotal SLIT-ROBO Rho GTPase activating protein 2 (SRGAP2)—Family with sequence similarity to the 72 (FAM72) master gene (i.e., |-SRGAP2–FAM72-|) via a divergent gene transcription activation mechanism. If the gene transcription control unit (i.e., the intergenic region of the two sub-gene units, SRGAP2 and FAM72) gets out of control, NSCs may transform into cancer stem cells and generate brain tumor cells responsible for brain cancer such as glioblastoma multiforme (GBM). Here, we discuss the surveillance of this |-SRGAP2–FAM72-| master gene and its role in GBM, and also in light of FAM72 for diagnosing various types of cancers outside of the CNS.

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“…Mutsig 2.0 [17] software was used to recognize genes with significant mutations based on the MAF of TCGA mutation data at P<0.05.…”

Section: Analysis Of Gene Mutationmentioning

confidence: 99%

Peer Review #2 of "Searching for a signature involving 10 genes to predict the survival of patients with acute myelocytic leukemia through a combined multi-omics analysis (v0.1)"

2020

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Background Currently, acute myelocytic leukemia (AML) still has a poor prognosis. As a result, gene markers for predicting AML prognosis must be identified through systemic analysis of multi-omics data. Methods First of all, the copy number variation (CNV), mutation, RNA-Seq, and single nucleotide polymorphism (SNP) data, as well as those clinical follow-up data, were obtained based on TCGA database. Thereafter, all samples (n=229) were randomized as test set and training set, respectively. Of them, the training set was used to screen for genes related to prognosis, and genes with mutation, SNP or CNV. Then, shrinkage estimate was used for feature selection of all the as-screened genes, to select those stable biomarkers. Eventually, a prognosis model related to those genes was established, and validated within the GEO verification (n=124 and 72) and test set (n=127). Moreover, it was compared with the AML prognosis prediction model reported in literature. Results Altogether 832 genes related to prognosis, 23 related to copy amplification, 774 associated with copy deletion, and 189 with significant genomic variations were acquired in this study. Later, genes with genomic variations and those related to prognosis were integrated to obtain 38 candidate genes, eventually, shrinkage estimate was adopted to obtain 10 feature genes (including FAT2, CAMK2A, TCERG1, GDF9, PTGIS, DOC2B, DNTTIP1, PREX1, CRISPLD1 and C22orf42). Further, a signature was established using these 10 genes based on Cox regression analysis, and it served as an independent factor to predict AML prognosis. More importantly, it was able to stratify those external verification, test and training set samples with regard to the risk (P<0.01). Compared with the prognosis prediction model reported in literature, the model established in this study was advantageous in terms of the prediction performance. Conclusion The signature based on 10 genes had been established in this study, which is promising to be used to be a new marker for predicting AML prognosis.

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Establishing a human adrenocortical carcinoma (ACC)-specific gene mutation signature

Cited by 21 publications

References 78 publications

Multifaceted Role of PRDM Proteins in Human Cancer

Multifaceted Role of PRDM Proteins in Human Cancer

FAM72, Glioblastoma Multiforme (GBM) and Beyond

Peer Review #2 of "Searching for a signature involving 10 genes to predict the survival of patients with acute myelocytic leukemia through a combined multi-omics analysis (v0.1)"

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