Radiation-induced changes in energy metabolism result in mitochondrial dysfunction in salivary glands

Salivary glands are indirectly damaged during radiotherapy for head and neck cancer, resulting in acute and chronic hyposalivation. Current treatments for radiation-induced hyposalivation do not permanently restore function to the gland; therefore, more mechanistic understanding of the damage response is needed to identify therapeutic targets for lasting restoration. Energy metabolism reprogramming has been observed in cancer and wound healing models to provide necessary fuel for cell proliferation; however, there is limited understanding of alterations in energy metabolism reprogramming in tissues that fail to heal. We measured extracellular acidification and oxygen consumption rates, assessed mitochondrial DNA copy number, and tested fuel dependency of irradiated primary salivary acinar cells. Radiation treatment leads to increases in glycolytic flux, oxidative phosphorylation, and ATP production rate at acute and intermediate time points. In contrast, at chronic radiation time points there is a significant decrease in glycolytic flux, oxidative phosphorylation, and ATP production rate. Irradiated salivary glands exhibit significant decreases in spare respiratory capacity and increases in mitochondrial DNA copy number at days 5 and 30 post-treatment, suggesting a mitochondrial dysfunction phenotype. These results elucidate kinetic changes in energy metabolism reprogramming of irradiated salivary glands that may underscore the chronic loss of function phenotype.

Radiation-Induced Changes in Energy Metabolism Result in Mitochondrial Dysfunction in Salivary Glands

Salivary glands are indirectly damaged during radiotherapy for head and neck cancer, resulting in acute and chronic hyposalivation. Current treatments for radiation-induced hyposalivation do not permanently restore function to the gland; therefore, more mechanistic understanding of the damage response is needed to identify therapeutic targets for lasting restoration. Energy metabolism reprogramming has been observed in cancer and wound healing models to provide necessary fuel for cell proliferation; however, there is limited understanding of alterations in energy metabolism reprogramming in tissues that fail to heal. We measured extracellular acidification and oxygen consumption rates, assessed mitochondrial DNA copy number, and tested fuel dependency of irradiated primary salivary acinar cells. Radiation treatment leads to increases in glycolytic flux, oxidative phosphorylation, and ATP production rate at acute and intermediate time points. In contrast, at chronic radiation time points there is a significant decrease in glycolytic flux, oxidative phosphorylation, and ATP production rate. Irradiated salivary glands exhibit significant decreases in spare respiratory capacity and increases in mitochondrial DNA copy number at days 5 and 30 post-treatment, suggesting a mitochondrial dysfunction phenotype. These results elucidate kinetic changes in energy metabolism reprogramming of irradiated salivary glands that may underscore the chronic loss of function phenotype.

Evaluating the transcriptional landscape and cell-cell communication networks in chronically irradiated parotid glands

Understanding the transcriptional landscape that results in chronic salivary hypofunction after irradiation will help identify injury mechanisms and develop regenerative therapies. We present scRNA-seq analysis from control and irradiated murine parotid glands collected 10 months after irradiation. We identify a population of secretory cells defined by specific expression of Etv1, which may be an acinar cell precursor. Acinar and Etv1+ secretory express Ntrk2 and Erbb3, respectively while the ligands for these receptors are expressed in myoepithelial and stromal cells. Furthermore, our data suggests that secretory cells and CD4⁺CD8⁺T-cells are the most transcriptionally affected during chronic injury with radiation, suggesting active immune involvement. Lastly, evaluation of cell-cell communication networks predicts that neurotrophin, neuregulin, ECM, and immune signaling are dysregulated after irradiation, and thus may play a role in the lack of repair. This resource will be helpful to understand cell-specific pathways that may be targeted to repair chronic damage in irradiated glands.

Clear cell renal cell carcinoma molecular variations in non-Hispanic White and Hispanic patients

BACKGROUND

The United States is becoming increasingly diverse, but few molecular studies have assessed the progression of clear cell renal cell carcinoma (ccRCC) in diverse patient populations. This study examined ccRCC molecular variations in non-Hispanic White (NHW) and Hispanic patients and their effect on the association of gene expression with high-grade (Grade 3 or 4) ccRCC and overall mortality.

METHODS

A total of 156 patients were included in VHL sequencing and/or TempO-Seq analysis. DESeq2 was used to identify the genes associated with high-grade ccRCC. Logistic regression analysis was performed to assess whether race and ethnicity was associated with high/moderate impact VHL somatic mutations and the ccA/ccB subtype. Cox regression analysis was performed to assess association of molecular subtype and gene expression with overall mortality.

RESULTS

NHWs had moderate or high impact mutations in the VHL gene at a higher frequency than Hispanics (40.2% vs. 27.4%), while Hispanics had a higher frequency of the ccA subtype than NHWs (61.9% vs. 45.8%). ccA was more common in patients with BMI≥35 (65.2%) than in those with BMI < 25 (45.0%). There were 11 differentially expressed genes between high- and low-grade tumors. The Haptoglobin (HP) gene was most significantly overexpressed in high- compared to low-grade ccRCC in all samples (p-adj = 1.7 × 10^-12 ). When stratified by subtype, the 11 genes were significantly differentially expressed in the ccB subtype, but none of them were significant after adjusting for multiple testing in ccA. Finally, patients with the ccB subtype had a significantly increased risk of overall mortality (HR 4.87; p = 0.01) compared to patients with ccA, and patients with high HP expression and ccB, had a significantly increased risk of mortality compared to those with low HP expression and ccA (HR 6.45, p = 0.04).

CONCLUSION

This study reports ccRCC molecular variations in Hispanic patients who were previously underrepresented.

Abstract A79: Post-transcriptional regulatory networks of pancreatic tumor invasion

Guidance molecules from the Slit gene family were originally described as cues for the directional guidance of axons in the developing nervous system. More recently, members of these families have been found to play critical roles in epithelial development, angiogenesis and tumorigenesis. SLIT2 has properties of a potential tumor suppressor, is mutated at a low frequency in pancreatic tumors and is epigenetically silenced in many cancers. mir-218-1 is an intronic microRNA found within intron 15 of the SLIT2 gene. We propose that cell intrinsic mir-218-1 expression and function is independent of SLIT2 signaling in pancreatic ductal adenocarcinoma. This dynamic expression of mir-218-1 can inhibit tumor dissemination following the conversion of precursor lesions to invasive carcinoma.

In normal pancreatic tissue, SLIT2 is highly expressed in the ductal compartment and expressed at a reduced level in the majority of primary pancreatic ductal adenocarcinomas (PDACs). We determined that KRAS-dependent pancreatic cancer cell lines express SLIT2 while KRAS-independent cell lines show silenced SLIT2 expression. Sequenom and chromatin immunoprecipitation (ChIP) confirmed that loss of SLIT2 in KRAS-independent lines was due to DNA hypermethylation and enrichment of silencing histone marks at the SLIT2 promoter and transcriptional start site with an inverse correlation between SLIT2 and EZH2 expression. Activating histone marks are found at both the SLIT2 promoter and transcriptional start site in KRAS-dependent lines suggesting that SLIT2 is lost during pancreatic cancer progression due to epigenetic silencing.

Many intronic microRNAs are transcribed from the host gene promoter; however, mir-218-1 expression is variable in pancreatic cancer cell lines and does not correlate with SLIT2 gene expression. Therefore, we examined whether mir-218-1 had an alternative promoter independent of the SLIT2 promoter. Using ChIP for H3K4me3, a marker for promoter regions, we discovered an alternative promoter of mir-218-1. ChIP for H4ac and Sequenom showed that the chromatin structure within this putative alternative promoter is acetylated, unmethylated, and, thus, permissive for transcription. The putative alternative mir-218-1 promoter was also found to have basal transcription via enhanced luciferase reporter activity and enrichment of RNA polymerase II at the H3K4me3/H4ac peak. In silico analysis of the mir-218-1 alternative promoter region indicated that DNA binding sites for transcriptional repressors MYC/MAX and ZEB1 are present. In silico analysis also showed the presence of DNA binding sites for transcriptional activators CDX1, LEF1/TCF1 and NF-κB. The transcription factor NF-κB and oncogene KRAS frequently function cooperatively to promote tumor progression; however, maintenance of ductal architecture is also important in pancreatic cancer invasion and metastasis. Site-directed mutagenesis of the NF-κB binding site decreased luciferase reporter activity suggesting that NF-κB is an activator of mir-218-1 expression at this alternative promoter. This suggests that mir-218-1 expression is uncoupled from SLIT2 expression and may contain its own tumor suppressor properties independent of SLIT2 signaling.

Matrix metalloproteinases (MMPs) are associated with tumor initiation and progression by targeting extracellular matrix (ECM) components. Invadopodia are structures that have been found to facilitate the invasive phenotype of many cancer types and are dynamic actin-rich cellular projections that localize proteases such as MMP2, MMP9, and MMP14 to degrade the ECM. In addition to ROBO1, we identified additional novel mir-218-1 target genes that control PDAC cell invasion. Our results further demonstrate that mir-218-1 functions in the suppression of invadopodia maturation and metalloproteinase matrix degradation. Overall, our data establishes that mir-218-1 is a key independent mediator of pancreatic cancer invasion through the extracellular matrix.

Citation Format: Brenna A. Rheinheimer, Lukas Vrba, Bernard W. Futscher, Ronald L. Heimark. Post-transcriptional regulatory networks of pancreatic tumor invasion. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr A79.

Abstract 127: Alternative transcription of the SLIT2/mir-218-1 signaling axis mediates pancreatic cancer invasion through the regulation of invadopodia

Guidance molecules from the Netrin, Slit, Ephrin, and Semaphorin gene families were originally described as cues for the directional guidance of axons in the developing nervous system. More recently, members of these families have been found to have critical roles in tumor invasion. The SLIT2/mir-218-1 signaling axis has properties of a tumor suppressor pathway via the inhibition of directional migration and is epigenetically silenced in many cancers.

We propose that mir-218-1 expression and function is independent of SLIT2 signaling in pancreatic ductal adenocarcinoma and inhibits tumor dissemination following the conversion of precursor lesions to invasive carcinoma. We determined that KRAS-dependent pancreatic cancer cell lines express SLIT2 mRNA while KRAS-independent lines show silenced SLIT2 expression. Using chromatin immunoprecipitation (ChIP) and Sequenom, we confirmed that loss of SLIT2 in KRAS-independent lines was due to enrichment of silencing histone mark H3K27me3 and DNA hypermethylation at the SLIT2 promoter, respectively. Activating marks H3K4me2 and H4ac are found at the SLIT2 promoter in KRAS-dependent lines suggesting that SLIT2 is lost during pancreatic cancer progression due to epigenetic silencing. mir-218-1 is an intronic microRNA found within intron 15 of the SLIT2 gene. Many intronic microRNAs are transcribed from the host gene promoter; however, mir-218-1 expression in pancreatic cancer cell lines does not correlate with SLIT2 gene expression. Therefore, we examined whether mir-218-1 had an alternative promoter independent of the SLIT2 promoter. Using ChIP for H3K4me3, a marker for promoter regions, and H4ac, a marker of permissive chromatin, we discovered a putative alternative promoter of mir-218-1 in all pancreatic cancer cell lines regardless of KRAS dependence. The putative alternative mir-218-1 promoter was also found to have basal transcription via enhanced luciferase reporter activity. This suggests that mir-218-1 expression is important and may contain its own tumor suppressor properties independent of SLIT2 signaling.

Since pancreatic cancer is an invasive disease we examined the role of miR-218 target genes in specialized cellular structures, termed invadopodia. These structures have been found to facilitate the invasive phenotype of many cancer types and are dynamic actin-rich cellular projections that localize proteases to degrade extracellular matrix. Transfection of a miR-218 antagomir enhanced invasion in a modified Boyden chamber while addition of mir-218 reduced cell invasion. Our results further demonstrate that mir-218 functions in the suppression of invadopodia maturation and metalloproteinase matrix degradation. Overall, our data establishes that the SLIT2/mir-218-1 signaling axis is an important mediator of pancreatic cancer invasion through the extracellular matrix.

Citation Format: Brenna A. Rheinheimer, Lukas Vrba, Bernard W. Futscher, Ronald L. Heimark. Alternative transcription of the SLIT2/mir-218-1 signaling axis mediates pancreatic cancer invasion through the regulation of invadopodia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 127. doi:10.1158/1538-7445.AM2014-127