PRUNE2 Gene

Name	prune homolog 2 (Drosophila)
Description	The protein encoded by this gene belongs to the B-cell CLL/lymphoma 2 and adenovirus E1B 19 kDa interacting family, whose members play roles in many cellular processes including apotosis, cell transformation, and synaptic function. Several functions for this protein have been demonstrated including suppression of Ras homolog family member A activity, which results in reduced stress fiber formation and suppression of oncogenic cellular transformation. A high molecular weight isoform of this protein has also been shown to colocalize with Adaptor protein complex 2, beta-Adaptin and endodermal markers, suggesting an involvement in post-endocytic trafficking. In prostate cancer cells, this gene acts as a tumor suppressor and its expression is regulated by prostate cancer antigen 3, a non-protein coding gene on the opposite DNA strand in an intron of this gene. Prostate cancer antigen 3 regulates levels of this gene through formation of a double-stranded RNA that undergoes adenosine deaminase actin on RNA-dependent adenosine-to-inosine RNA editing. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nIn prostate cancer and related smooth‐muscle tumors, PRUNE2—the protein encoded by the gene overlapping with the lncRNA PCA3—has been shown to act as a potent tumor suppressor. In these settings, PCA3 regulates PRUNE2 levels by forming a double‐stranded RNA that is subsequently edited by ADAR enzymes, thereby downregulating PRUNE2 and promoting cell proliferation and tumor growth. Conversely, restoration or upregulation of PRUNE2 expression suppresses tumorigenicity, and its altered expression alongside PCA3 has diagnostic potential in distinguishing leiomyosarcomas from other mesenchymal tumors."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "4"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn neuroblastoma, high expression of BMCC1/PRUNE2 correlates with a favorable prognosis. Elevated PRUNE2 expression promotes apoptosis by attenuating survival signals such as those mediated by AKT, inducing proapoptotic factors, and interacting with key regulators like BCL2. Furthermore, transcriptional activation by factors such as E2F1 accentuates PRUNE2 expression, reinforcing its role as a tumor suppressor in the neuroblastoma context."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "5", "end_ref": "8"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its tumor‐suppressive functions, PRUNE2 plays important roles in neuronal physiology. The full‐length PRUNE2 protein binds both GTP and its oxidized derivative 8-oxo-GTP, with the highest expression observed in dorsal root ganglia and other mature nerve tissues—suggesting a role in maintaining synaptic integrity and neural function. In addition, in colorectal cancer Forkhead box F2 directly upregulates PRUNE2 transcription, contributing to reduced proliferation and invasiveness, while regions within the protein (notably the BCH motif) modulate RhoA-dependent signaling to restrain oncogenic transformation."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "9", "end_ref": "12"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Maciej Salagierski, Gerald W Verhaegh, Sander A Jannink, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Differential expression of PCA3 and its overlapping PRUNE2 transcript in prostate cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Prostate (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/pros.21040"}], "href": "https://doi.org/10.1002/pros.21040"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19760627"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19760627"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Ji-long Yang, David Cogdell, James Eddy, et al. "}, {"type": "b", "children": [{"type": "t", "text": "[Expression of PRUNE2 mRNA and its positive correlation with non-coding RNA PCA3 in leiomyosarcoma]."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Zhonghua Zhong Liu Za Zhi (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3760/cma.j.issn.0253-3766.2012.07.005"}], "href": "https://doi.org/10.3760/cma.j.issn.0253-3766.2012.07.005"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22967466"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22967466"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Janelle L Harris, Renée S Richards, Clement W K Chow, et al. "}, {"type": "b", "children": [{"type": "t", "text": "BMCC1 is an AP-2 associated endosomal protein in prostate cancer cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0073880"}], "href": "https://doi.org/10.1371/journal.pone.0073880"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24040105"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24040105"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Ahmad Salameh, Alessandro K Lee, Marina Cardó-Vila, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1507882112"}], "href": "https://doi.org/10.1073/pnas.1507882112"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26080435"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26080435"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "T Machida, T Fujita, M L Ooo, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Increased expression of proapoptotic BMCC1, a novel gene with the BNIP2 and Cdc42GAP homology (BCH) domain, is associated with favorable prognosis in human neuroblastomas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oncogene (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/sj.onc.1209225"}], "href": "https://doi.org/10.1038/sj.onc.1209225"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16288218"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16288218"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Y Tatsumi, R Takano, M S Islam, et al. "}, {"type": "b", "children": [{"type": "t", "text": "BMCC1, which is an interacting partner of BCL2, attenuates AKT activity, accompanied by apoptosis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Death Dis (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/cddis.2014.568"}], "href": "https://doi.org/10.1038/cddis.2014.568"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25611382"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25611382"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Mohammad Sazzadul Islam, Yasutoshi Tatsumi, Ryo Takano, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Transcriptional regulation of BMCC1 mediated by E2F1 in neuroblastoma cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2016.07.089"}], "href": "https://doi.org/10.1016/j.bbrc.2016.07.089"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27453342"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27453342"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Mohammad Sazzadul Islam, Ryo Takano, Tomoki Yokochi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Programmed expression of pro-apoptotic BMCC1 during apoptosis, triggered by DNA damage in neuroblastoma cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "BMC Cancer (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12885-019-5772-4"}], "href": "https://doi.org/10.1186/s12885-019-5772-4"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31170959"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31170959"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Unice J K Soh, Boon Chuan Low "}, {"type": "b", "children": [{"type": "t", "text": "BNIP2 extra long inhibits RhoA and cellular transformation by Lbc RhoGEF via its BCH domain."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.021774"}], "href": "https://doi.org/10.1242/jcs.021774"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18445682"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18445682"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Eiji Iwama, Daisuke Tsuchimoto, Teruaki Iyama, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Cancer-related PRUNE2 protein is associated with nucleotides and is highly expressed in mature nerve tissues."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Mol Neurosci (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s12031-010-9490-2"}], "href": "https://doi.org/10.1007/s12031-010-9490-2"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21234814"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21234814"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Shimo Li, Yoshika Hayakawa-Yano, Masanori Itoh, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Olfaxin as a novel Prune2 isoform predominantly expressed in olfactory system."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Brain Res (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.brainres.2012.10.001"}], "href": "https://doi.org/10.1016/j.brainres.2012.10.001"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23059019"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23059019"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Ting Li, Silin Huang, Wei Yan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "FOXF2 Regulates PRUNE2 Transcription in the Pathogenesis of Colorectal Cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Technol Cancer Res Treat (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1177/15330338221118717"}], "href": "https://doi.org/10.1177/15330338221118717"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35929169"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35929169"}]}]}]}
Synonyms	BA214N16.3, A214N16.3, BMCC1, BNIPXL, C9ORF65, KIAA0367
Proteins	PRUN2_HUMAN
NCBI Gene ID	158471
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

PRUNE2 has 8,905 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 119 datasets.

Click the + buttons to view associations for PRUNE2 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

PRUNE2 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PRUNE2 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of PRUNE2 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of PRUNE2 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of PRUNE2 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of PRUNE2 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PRUNE2 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of PRUNE2 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PRUNE2 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PRUNE2 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of PRUNE2 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of PRUNE2 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of PRUNE2 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with PRUNE2 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with PRUNE2 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PRUNE2 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of PRUNE2 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of PRUNE2 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of PRUNE2 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing PRUNE2 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing PRUNE2 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing PRUNE2 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing PRUNE2 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with PRUNE2 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with PRUNE2 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of PRUNE2 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with PRUNE2 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with PRUNE2 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with PRUNE2 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of PRUNE2 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by PRUNE2 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores	diseases associated with PRUNE2 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with PRUNE2 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with PRUNE2 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with PRUNE2 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with PRUNE2 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with PRUNE2 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at PRUNE2 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PRUNE2 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of PRUNE2 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing PRUNE2 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.