Identification of nuclear export signal in KLLN suggests potential role in proteasomal degradation in cancer cells

Germline and somatic promoter hypermethylation of KLLN has been found in diverse heritable and sporadic cancers, respectively. KLLN has many identified tumor suppressor functions, and when first reported, was thought to be exclusively nuclear. Here, we report on KLLN localization in both the nucleus and cytoplasm and the identification of a putative nuclear export signal (NES) sequence. KLLN overexpression in colon and breast cancer cells showed both nuclear and cytoplasmic presence. Inhibition of the CRM1 export pathway increased nuclear sequestration of KLLN, confirming the prediction of an NES sequence. Point mutations introduced in the predicted NES sequence decreased the strength of the NES and increased the nuclear sequestration of KLLN. Contrary to expectations, the transcription regulation and cellular proliferation functions of KLLN were unaffected by increased KLLN nuclear sequestration. Instead, increased nuclear KLLN correlated with increased nuclear sequestration of TRIM25 and decreased inhibitory phosphorylation of MDM2. Computational analysis of The Cancer Genome Atlas (TCGA) dataset showed positive correlation among KLLN, TRIM25 and MDM2 expression; pathway analysis of the common genes downstream of these three genes revealed protein degradation as one of the top canonical pathways. Together, our observations suggest that CRM1 pathway-based nuclear export of KLLN may impact proteasomal degradation.

The Microbiome of Temporal Arteries

Objective

A role for microorganisms in giant cell arteritis (GCA) has long been suspected. We describe the microbiomes of temporal arteries from patients with GCA and controls.

Methods

Temporal artery biopsies from patients suspected to have GCA were collected under aseptic conditions and snap-frozen. Fluorescence in situ hybridization (FISH) and long-read 16S rRNA-gene sequencing was used to examine microbiomes of temporal arteries. Taxonomic classification of bacterial sequences was performed to the genus level and relative abundances were calculated. Microbiome differential abundances were analyzed by principal coordinate analysis (PCoA) with comparative Unifrac distances and predicted functional profiling using PICRUSt.

Results

Forty-seven patients, including 9 with biopsy-positive GCA, 15 with biopsy-negative GCA and 23 controls without GCA, were enrolled. FISH for bacterial DNA revealed signal in the arterial media. Beta, but not alpha, diversity differed between GCA and control temporal arteries (P = 0.042). Importantly, there were no significant differences between biopsy-positive and biopsy-negative GCA (P > 0.99). The largest differential abundances seen between GCA and non-GCA temporal arteries included Proteobacteria (P), Bifidobacterium (g), Parasutterella (g), and Granulicatella (g) [Log 2-fold change ≥ 4].

Conclusion

Temporal arteries are not sterile, but rather are inhabited by a community of bacteria. We have demonstrated that there are microbiomic differences between GCA and non-GCA temporal arteries, but not between biopsy-positive and biopsy-negative GCA.

KLLN-mediated DNA damage-induced apoptosis is associated with regulation of p53 phosphorylation and acetylation in breast cancer cells

KLLN is a target of p53 involved in S-phase cell cycle regulation deemed necessary and sufficient for p53-mediated apoptosis. Germline promoter hypermethylation of KLLN is associated with a cancer-predisposition syndrome, Cowden syndrome. KLLN’s DNA-binding ability is associated with transcription regulation and maintenance of genomic stability. Here, we report on KLLN’s role in DNA damage response (DDR) mediated through apoptosis in breast cells with and without a cancer phenotype. KLLN expression was upregulated after doxorubicin-induced DNA damage and this upregulation can be abrogated using RNAi-mediated gene silencing. Silencing KLLN after doxorubicin treatment effected DDR shown by decreased γ-H2AX foci and expression, and apoptosis assessed by decreased frequency of apoptotic nuclei and decreased expression of definitive markers of apoptosis. Contrary to expectations, there was no change in cell cycle regulation after KLLN silencing. These results were observed in breast cells with wildtype and mutant p53. At early timepoints after doxorubicin treatment, knocking down KLLN resulted in decreased Ser15-phosphorylation of p53 but not Thr68-phosphorylation of CHK2 or the phosphorylation of upstream regulators such as ATM and ATR. Interestingly, a second pathway for p53 activation was also affected by knockdown of KLLN. After doxorubicin treatment, Thr454-phosphorylation of DBC1, required to inhibit deacetylation of p53 by SIRT1, was decreased and therefore acetylation of p53 was also decreased with KLLN knockdown. Therefore, our observations suggest that KLLN’s role in DNA damage-induced apoptosis is likely independent of p53 and is associated with a two-pronged regulation of p53 activation.

Abstract 317: Role of KLLN in DNA damage-induced apoptosis is associated with the regulation of p53 phosphorylation and acetylation in breast cancer cells

KLLN was initially discovered as a target of p53 involved in S-phase checkpoint regulation. Germline hypermethylation in the promoter of KLLN is known to increase the predisposition for breast and clear cell renal cell carcinomas in PTEN-wildtype Cowden syndrome (CS) patients. KLLN is a known tumor suppressor protein and required for p53-mediated apoptosis. In this study, we explore the underlying mechanism by which KLLN regulates DNA damage response (DDR), specifically apoptosis. Our DDR studies were conducted on one breast normal and four breast cancer cell lines using doxorubicin as the DNA damaging agent. We initially showed that doxorubicin-induced DNA damage increases KLLN expression at 16h and 24h post-damage which could be abrogated by RNAi-mediated knockdown of KLLN expression. Response to DNA damage as determined by the presence of γH2AX foci formation and expression of γH2AX protein were both decreased after KLLN knockdown. Using TUNEL assay and cell viability studies, we demonstrated that a lack of KLLN expression decreases apoptosis and increases cell viability at 16h and 24h post-damage. Definitive markers of apoptosis such as cleavage of caspase 3 and PARP were also decreased. Since KLLN is a known transcription factor and regulates the expression of DDR genes such as TP53 and CHK1, we assessed the regulation of these genes in response to DNA damage and found that lack of KLLN expression did not affect the expression of either TP53 or CHK1. Cell cycle analysis results using flow cytometry also suggested that KLLN does not play a role in S-phase cell cycle regulation in response to DNA damage as was previously thought, since KLLN knockdown did not change accumulation of cells in S-phase after doxorubicin-induced DNA damage. DDR in cells is immediate and therefore we assessed the abrogation of DDR after KLLN knockdown at early timepoints (1h and 2h) post-damage. We found that lack of KLLN expression decreased Ser15 phosphorylation of p53 and Thr68 phosphorylation of CHK2 at 1h and 2h post-damage. KLLN regulation of p53-mediated apoptosis could also be associated with its interaction with deleted in breast cancer (DBC1). DBC1 is a known inhibitor of SIRT1, a deacetylase that is known for its inhibitory deacetylation of p53. Phosphorylated DBC1 binds to SIRT1 and inhibits its deacetylation of p53. We found that lack of KLLN expression decreased the phosphorylation of DBC1 on Thr454 in response to DNA damage. Therefore, KLLN displays a 2-pronged regulation of the activation of p53 and the downstream cascade of proteins involved in apoptosis. SIGNIFICANCE: Our study demonstrates a clear role for KLLN in DNA damage-induced apoptosis and elucidates the underlying mechanism through the regulation of p53 phosphorylation and deacetylation in response to DNA damage. Our observations add to the basis of KLLN as a tumor suppressor and as a susceptibility gene for inherited cancers.

Citation Format: Madhav Sankunny, Charis Eng. Role of KLLN in DNA damage-induced apoptosis is associated with the regulation of p53 phosphorylation and acetylation in breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 317.

Abstract 3596: KLLN protects genomic stability by maintaining H3K9 trimethylation (H3K9me3) at the pericentric heterochromatin

Dysregulation in the maintenance of chromatin organization resulting in genomic instability is a major driving force for inappropriate development and carcinogenesis. Tumor suppressor genes play a critical role in this regulation through the maintenance of epigenetic marks. Our study focuses on the role of KLLN in the maintenance of pericentric H3K9 trimethylation (H3K9me3) and genomic stability. Germline hypermethylation of KLLN resulting in decreased KLLN expression has been linked to Cowden cancer-predisposition syndrome (CS) in PTEN mutation negative patients. KLLN is a tumor suppressor gene necessary for p53-mediated apoptosis. The protein mediates S-phase arrest and is known to have DNA binding ability. Here, we first used chromatin immunoprecipitation-based sequencing (ChIP-seq) to investigate regions of KLLN binding on the genome and compared it to regions of H3K9me3 enrichment. We used H3K9 specific histone methyltransferase (HMT) activity assay and immunoblotting to measure levels of H3K9me3. Immunostaining was used to study the localization of KLLN, and micronuclei frequency and aberrations in chromosome number was used to assess chromosomal instability. Analysis of ChIP-seq shows enrichment of KLLN binding in regions of H3K9me3. Overexpression of KLLN using plasmid-based transfection correlates with increased H3K9 methyltransferase activity and increased global H3K9me3, while loss of KLLN expression through siRNA-mediated knockdown had an opposite effect. We also established that KLLN localizes to pericentric regions, and loss of KLLN results in dysregulation of pericentric heterochromatin, with consequent chromosomal instability manifested by increased micronuclei frequency and numerical chromosomal aberrations. KLLN regulation of H3K9me3 could be correlated with its interaction with deleted in breast cancer (DBC1). DBC1 is a known inhibitor of SUV39H1, a H3K9 specific histone methyltransferase responsible for maintenance of pericentric heterochromatin. We hypothesize that KLLN sequesters DBC1 through their interaction, thereby abrogating DBC1 inhibition of SUV39H1, resulting in maintenance of pericentric heterochromatin and genomic stability. Our study therefore suggests a critical role for KLLN in the deterrence of tumor initiation and progression.

SIGNIFICANCE: Our study demonstrates a clear role for KLLN in maintenance of chromatin organization thereby maintaining genomic stability, which begins to uncover the basis of KLLN as a tumor suppressor and as a susceptibility gene for inherited cancers.

Citation Format: Madhav Sankunny, Emily Nizialek, Farshad Niazi, Charis Eng. KLLN protects genomic stability by maintaining H3K9 trimethylation (H3K9me3) at the pericentric heterochromatin. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3596.

Cancer-predisposition gene KLLN maintains pericentric H3K9 trimethylation protecting genomic stability

Maintenance of proper chromatin states and genomic stability is vital for normal development and health across a range of organisms. Here, we report on the role of KLLN in maintenance of pericentric H3K9 trimethylation (H3K9me3) and genomic stability. Germline hypermethylation of KLLN, a gene uncovered well after the human genome project, has been linked to Cowden cancer-predisposition syndrome (CS) in PTEN wild-type cases. KLLN first identified as a p53-dependent tumor suppressor gene, was believed to bind randomly to DNA and cause S-phase arrest. Using chromatin immunoprecipitation-based sequencing (ChIP-seq), we demonstrated that KLLN binds to DNA regions enriched with H3K9me3. KLLN overexpression correlated with increased H3K9 methyltransferase activity and increased global H3K9me3, while knockdown of KLLN had an opposite effect. We also found KLLN to localize to pericentric regions, with loss of KLLN resulting in dysregulation of pericentric heterochromatin, with consequent chromosomal instability manifested by increased micronuclei formation and numerical chromosomal aberrations. Interestingly, we show that KLLN interacts with DBC1, with consequent abrogation of DBC1 inhibition of SUV39H1, a H3K9 methyltransferase, suggesting the mode of KLLN regulating H3K9me3. These results suggest a critical role for KLLN as a potential regulator of pericentric heterochromatin formation, genomic stability and gene expression.

Germline Heterozygous Variants in SEC23B Are Associated with Cowden Syndrome and Enriched in Apparently Sporadic Thyroid Cancer

Cancer-predisposing genes associated with inherited cancer syndromes help explain mechanisms of sporadic carcinogenesis and often inform normal development. Cowden syndrome (CS) is an autosomal-dominant disorder characterized by high lifetime risks of epithelial cancers, such that ∼50% of affected individuals are wild-type for known cancer-predisposing genes. Using whole-exome and Sanger sequencing of a multi-generation CS family affected by thyroid and other cancers, we identified a pathogenic missense heterozygous SEC23B variant (c.1781T>G [p.Val594Gly]) that segregates with the phenotype. We also found germline heterozygous SEC23B variants in 3/96 (3%) unrelated mutation-negative CS probands with thyroid cancer and in The Cancer Genome Atlas (TCGA), representing apparently sporadic cancers. We note that the TCGA thyroid cancer dataset is enriched with unique germline deleterious SEC23B variants associated with a significantly younger age of onset. SEC23B encodes Sec23 homolog B (S. cerevisiae), a component of coat protein complex II (COPII), which transports proteins from the endoplasmic reticulum (ER) to the Golgi apparatus. Interestingly, germline homozygous or compound-heterozygous SEC23B mutations cause an unrelated disorder, congenital dyserythropoietic anemia type II, and SEC23B-deficient mice suffer from secretory organ degeneration due to ER-stress-associated apoptosis. By characterizing the p.Val594Gly variant in a normal thyroid cell line, we show that it is a functional alteration that results in ER-stress-mediated cell-colony formation and survival, growth, and invasion, which reflect aspects of a cancer phenotype. Our findings suggest a different role for SEC23B, whereby germline heterozygous variants associate with cancer predisposition potentially mediated by ER stress "addiction."

Targeted inhibition of ATR or CHEK1 reverses radioresistance in oral squamous cell carcinoma cells with distal chromosome arm 11q loss

Oral squamous cell carcinoma (OSCC), a subset of head and neck squamous cell carcinoma (HNSCC), is the eighth most common cancer in the U.S.. Amplification of chromosomal band 11q13 and its association with poor prognosis has been well established in OSCC. The first step in the breakage-fusion-bridge (BFB) cycle leading to 11q13 amplification involves breakage and loss of distal 11q. Distal 11q loss marked by copy number loss of the ATM gene is observed in 25% of all Cancer Genome Atlas (TCGA) tumors, including 48% of HNSCC. We showed previously that copy number loss of distal 11q is associated with decreased sensitivity (increased resistance) to ionizing radiation (IR) in OSCC cell lines. We hypothesized that this radioresistance phenotype associated with ATM copy number loss results from upregulation of the compensatory ATR-CHEK1 pathway, and that knocking down the ATR-CHEK1 pathway increases the sensitivity to IR of OSCC cells with distal 11q loss. Clonogenic survival assays confirmed the association between reduced sensitivity to IR in OSCC cell lines and distal 11q loss. Gene and protein expression studies revealed upregulation of the ATR-CHEK1 pathway and flow cytometry showed G2 M checkpoint arrest after IR treatment of cell lines with distal 11q loss. Targeted knockdown of the ATR-CHEK1 pathway using CHEK1 or ATR siRNA or a CHEK1 small molecule inhibitor (SMI, PF-00477736) resulted in increased sensitivity of the tumor cells to IR. Our results suggest that distal 11q loss is a useful biomarker in OSCC for radioresistance that can be reversed by ATR-CHEK1 pathway inhibition.

Upregulation of the ATR-CHEK1 pathway in oral squamous cell carcinomas

The ATR-CHEK1 pathway is upregulated and overactivated in Ataxia Telangiectasia (AT) cells, which lack functional ATM protein. Loss of ATM in AT confers radiosensitivity, although ATR-CHEK1 pathway overactivation compensates, leads to prolonged G(2) arrest after treatment with ionizing radiation (IR), and partially reverses the radiosensitivity. We observed similar upregulation of the ATR-CHEK1 pathway in a subset of oral squamous cell carcinoma (OSCC) cell lines with ATM loss. In the present study, we report copy number gain, amplification, or translocation of the ATR gene in 8 of 20 OSCC cell lines by FISH; whereas the CHEK1 gene showed copy number loss in 12 of 20 cell lines by FISH. Quantitative PCR showed overexpression of both ATR and CHEK1 in 7 of 11 representative OSCC cell lines. Inhibition of ATR or CHEK1 with their respective siRNAs resulted in increased sensitivity of OSCC cell lines to IR by the colony survival assay. siRNA-mediated ATR or CHEK1 knockdown led to loss of G(2) cell cycle accumulation and an increased sub-G(0) apoptotic cell population by flow cytometric analysis. In conclusion, the ATR-CHEK1 pathway is upregulated in a subset of OSCC with distal 11q loss and loss of the G(1) phase cell cycle checkpoint. The upregulated ATR-CHEK1 pathway appears to protect OSCC cells from mitotic catastrophe by enhancing the G(2) checkpoint. Knockdown of ATR and/or CHEK1 increases the sensitivity of OSCC cells to IR. These findings suggest that inhibition of the upregulated ATR-CHEK1 pathway may enhance the efficacy of ionizing radiation treatment of OSCC.

Abstract 2378: Upregulation of the ATR/CHK1 pathway and decreased therapeutic sensitivity in upper aerodigestive cancer cell lines with distal 11q loss

Gemcitabine, a pyrimidine analog/antimetabolite, is commonly used to treat breast, lung, head and neck, pancreatic, ovarian, biliary, urinary bladder, and cervical carcinomas. Gemcitabine inhibits DNA synthesis by direct inhibition of ribonucleotide reductase by its metabolite, gemcitabine diphosphate, and the incorporation of its active form, gemcitabine triphosphate into the elongating DNA strand, resulting in chain termination. Gemcitabine-induced DNA damage leads to activation of the ATR/CHK1 pathway and S-phase cell cycle arrest. Our previous studies showed that carcinoma cells with our biomarker (distal 11q loss) overexpress ATR and CHK1, resulting in decreased sensitivity to ionizing radiation in biomarker-positive head and neck squamous cell carcinoma (HNSCC) and non-small cell lung carcinoma (NSCLC) cell lines. Several studies in the literature have shown that inhibition of CHK1 increases the sensitivity of tumor cell lines to replication inhibitors, including gemcitabine. In pancreatic cancer cell lines, small molecule inhibitor (SMI)-mediated disruption of CHK1 signaling has been reported to potentiate the cytotoxic effect of gemcitabine. Based on the literature and our previous findings, we now report that biomarker-positive HNSCC and NSCLC cell lines also show ATR/CHK1 upregulation and decreased sensitivity to gemcitabine, Further, we observed that siRNA knockdown of the ATR/CHK1 pathway and SMI inhibition of CHK1 signaling in HNSCC and NSCLC cell lines increase their sensitivity to treatment with gemcitabine. Our previous results showed increased efficacy of ionizing radiation combined with CHK1 inhibition in biomarker-positive cell lines; our new results show increased efficacy of gemcitabine combined with CHK1 inhibition in biomarker-positive HNSCC and NSCLC cell lines. These results provide further support for combining CHK1-targeted therapy with standard therapy in conjunction with an appropriate companion diagnostic biomarker, like distal 11q loss. As is the case with other targeted therapies, biomarker-based selection of the right drug for the right patient appears to increase therapeutic efficacy.

Citation Format: Madhav Sankunny, Rahul A. Parikh, Susanne M. Gollin. Upregulation of the ATR/CHK1 pathway and decreased therapeutic sensitivity in upper aerodigestive cancer cell lines with distal 11q loss. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2378. doi:10.1158/1538-7445.AM2013-2378

Abstract 1309: Inhibition of the ATR/CHEK1 pathway overcomes reduced sensitivity to ionizing radiation associated with distal 11q loss

Genetic changes play a significant role in carcinogenesis. A commonly observed genetic alteration is amplification of chromosomal band 11q13. This has been reported at relatively high frequency in breast, ovarian, head and neck (HNSCC), and lung carcinomas. Previous studies in our lab have shown that the breakage-fusion-bridge (BFB) cycle mechanism responsible for this amplification results in distal 11q loss with concomitant loss of critical DNA damage response (DDR) genes, like ATM, MRE11A, and H2AFX. We showed in HNSCC that distal 11q loss leads to a defective DDR and decreased sensitivity to DNA damaging agents like ionizing radiation (IR). Further, HNSCC, Non-Small Cell Lung Carcinoma (NSCLC), and ovarian carcinoma cell lines with partial copy number loss of distal 11q show reduced sensitivity to IR and overexpression of the ATR/CHEK1 pathway. siRNA knockdown of CHEK1 in carcinoma cell lines with distal 11q loss resulted in 60-70% decreased cell survival in response to a single dose of IR. Cell lines without distal 11q loss did not show differential sensitivity to IR. These findings have led us to investigate whether these cell lines show decreased sensitivity to other DNA damaging agents such as various chemotherapeutic drugs.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1309.