The Histone Demethylase KDM3A, Increased in Human Pancreatic Tumors, Regulates Expression of DCLK1 and Promotes Tumorigenesis in Mice

Abstract

BACKGROUND & AIMS: The histone lysine demethylase 3A (KDM3A) demethylates H3K9me1 and H3K9Me2 to increase gene transcription and is upregulated in tumors, including pancreatic tumors. We investigated its activities in pancreatic cancer cell lines and its regulation of the gene encoding doublecortin calmodulin-like kinase 1 (DCLK1), a marker of cancer stem cells. METHODS: We knocked down KDM3A in MiaPaCa-2 and S2-007 pancreatic cancer cell lines and overexpressed KDM3A in HPNE cells (human noncancerous pancreatic ductal cell line); we evaluated cell migration, invasion, and spheroid formation under hypoxic and normoxic conditions. Nude mice were given orthotopic injections of S2-007 cells, with or without (control) knockdown of KDM3A, and HPNE cells, with or without (control) overexpression of KDM3A; tumor growth was assessed. We analyzed pancreatic tumor tissues from mice and pancreatic cancer cell lines by immunohistochemistry and immunoblotting. We performed RNA-sequencing analysis of MiaPaCa-2 and S2-007 cells with knockdown of KDM3A and evaluated localization of DCLK1 and KDM3A by immunofluorescence. We analyzed the cancer genome atlas for levels of KDM3A and DCLK1 messenger RNA in human pancreatic ductal adenocarcinoma (PDAC) tissues and association with patient survival time. RESULTS: Levels of KDM3A were increased in human pancreatic tumor tissues and cell lines, compared with adjacent nontumor pancreatic tissues, such as islet and acinar cells. Knockdown of KDM3A in S2-007 cells significantly reduced colony formation, invasion, migration, and spheroid formation, compared with control cells, and slowed growth of orthotopic tumors in mice. We identified KDM3A-binding sites in the DCLK1 promoter; S2-007 cells with knockdown of KDM3A had reduced levels of DCLK1. HPNE cells that overexpressed KDM3A formed foci and spheres in culture and formed tumors and metastases in mice, whereas control HPNE cells did not. Hypoxia induced sphere formation and increased levels of KDM3A in S2-007 cells and in HPNE cells that overexpressed DCLK1, but not control HPNE cells. Levels of KDM3A and DCLK1 messenger RNA were higher in human PDAC than nontumor pancreatic tissues and correlated with shorter survival times of patients. CONCLUSIONS: We found human PDAC samples and pancreatic cancer cell lines to overexpress KDM3A. KDM3A increases expression of DCLK1, and levels of both proteins are increased in human PDAC samples. Knockdown of KDM3A in pancreatic cancer cell lines reduced their invasive and sphereforming activities in culture and formation of orthotopic tumors in mice. Hypoxia increased expression of KDM3A in pancreatic cancer cells. Strategies to disrupt this pathway might be developed for treatment of pancreatic cancer.

Deletion of Histone Methyltransferase G9a Suppresses Mutant Kras-driven Pancreatic Carcinogenesis

“…H3K9 dimethylation status can be demethylated by a histone demethylase KDM3A/JHDM2A/JMJD1A (46). A recent study showed that KDM3A knockdown suppresses DCLK1 expression in human pancreatic cancer cell (47). While our data contradicted these previous findings, there was a clear difference in the model used in the two studies.…”

<p>Histone Demethylase <em>KDM3A</em> Promotes Cervical Cancer Malignancy Through the <em>ETS1</em>/KIF14/Hedgehog Axis</p>

“…[17][18][19] Methylation of histone lysine is crucial for epigenetic correlated gene expression profiles in cancer. 20 In this study, we validated an interaction network involving KDM3A/ETS1/KIF14, in which KDM3A governs ETS1-mediated KIF14 transcription to promote CC growth in either cell and animal models with the further involvement of the Hedgehog signaling pathway.…”

“…[21][22][23] Here, the initial finding of the current study was that KDM3A was highly expressed in the collected tumor tissues from CC patients, and it led to a dismal 5-year survival rate, increased lymphatic metastasis, and decreased tumor differentiation rate in patients. Similarly, abundant expression of KDM3A has been noted as an independent unfavorable factor in patients with pancreatic tumor 20 and colorectal cancer 24 and epithelial ovarian cancer. 25 A high-expression profile of KDM3A was also found in CC cell lines.…”

Incorporating multiple sets of eQTL weights into gene‐by‐environment interaction analysis identifies novel susceptibility loci for pancreatic cancer

“…KDM3A , which belongs to the Lysine demethylases family, has been shown to play a role in carcinogenesis in multiple cancers and to be an optimal pharmacological target for pancreatic cancer (Lomberk, Iovanna, & Urrutia, 2016). A recent mice study showed knockdown of KDM3A in pancreatic cancer cell line reduced the invasive and sphere‐forming activities in culture and formation of orthotopic tumors (Dandawate et al, 2019). TRIP10 , whose overexpression may enhance pancreatic cancer cell migration, could be involved in the carcinogenesis of pancreatic cancer (Roignot et al, 2010).…”