Prognostic methylation markers for overall survival in cytogenetically normal patients with acute myeloid leukemia treated on SWOG trials.

BACKGROUND: Aberrant DNA methylation is known to occur in patients with acute myeloid leukemia (AML), whereas methylation signatures and prognostic markers have been proposed. The objective of the current study was to evaluate all CpG sites of the genome and identify prognostic methylation markers for overall survival in patients with AML with normal karyotype (AML-NK). METHODS: AML-NK samples from 7 SWOG trials were analyzed using a novel genome-wide approach called "CHARMcox" (comprehensive high-throughput array-based relative methylation analysis combined with the Cox proportional hazards model) controlling for known clinical covariates. CHARMcox was applied to a phase 1 discovery cohort (72 patients) to identify survival-associated methylation regions (SAMRs). Subsequently, using bisulfite pyrosequencing, SAMRs were studied in phase 2 model-building (65 patients) and phase 3 validation (65 patients) cohorts. An independent external cohort from The Cancer Genome Atlas (TCGA) AML study (LAML) was used for further validation (93 patients). RESULTS: Two SAMRs, located at the CpG island shores of leucine zipper tumor suppressor 2 (LZTS2) and nuclear receptor subfamily 6 group a member 1 (NR6A1), respectively, were identified. Multivariable analyses demonstrated that hypomethylation of either LZTS2 or NR6A1 was associated with worse overall survival in the SWOG cohort (P<.001). The prognosis was validated in patients with AML-NK from the TCGA-LAML cohort. Methylation values below the median at both markers predicted worse overall survival (SWOG: hazard ratio, 1.89 [P<.001]; and TCGA-LAML: hazard ratio, 2.08 [P=.006]). The C-statistic was 0.71 for both cohorts, and the impact was independent of the Fms-related tyrosine kinase 3 internal tandem duplication (FLT3-ITD) status. CONCLUSIONS: The 2 methylation markers, measurable by clinically applicable assays such as bisulfite pyrosequencing, are promising for risk stratification among patients with AML-NK. Cancer 2017;123:2472-81. © 2017 American Cancer Society.

Sipa1l3/SPAR3 is targeted to postsynaptic specializations and interacts with the Fezzin ProSAPiP1/Lzts3.

Rap GTPase-activating proteins (RapGAPs) are essential for synaptic function as they tightly regulate synaptic Rap signaling. Among the most abundant synaptic RapGAPs in brain are the Spine-associated RapGAPs (SPARs) Sipa1l1/SPAR and Sipa1l2/SPAR2, whereas nothing has been reported on Sipa1l3/SPAR3. In this study, we show that Sipa1l3/SPAR3 is conserved across species, has a distinct expression pattern in the developing rat brain and is localized at excitatory postsynapses. We further demonstrate that the Sipa1l3/SPAR3 C-terminus is required for postsynaptic targeting and represents an interaction module for Fezzins such as ProSAPiP1/Lzts3, a binding partner of the postsynaptic scaffold protein Shank3. Taken together, our data imply that Sipa1l3/SPAR3 is a hitherto unknown synaptic RapGAP, which is targeted to postsynaptic specializations and interacts with Fezzins. Spine-associated RapGAPs (SPARs) are essential modulators of synaptic signaling. Our study is the first to characterize the SPAR family member Sipa1l3/SPAR3 in neuronal tissue. We show that Sipa1l3/SPAR3 is conserved across species, has a distinct expression pattern in brain and is localized to excitatory postsynapses via its C-terminus, which represents an interaction module for other postsynaptic proteins including the Fezzin ProSAPiP1/Lzts3.

Mechanistic insights into super-enhancer-related genes as prognostic signatures in colon cancer.

BACKGROUND: Colon cancer (CC) is the most frequently occurring digestive system malignancy and is associated with a dismal prognosis. While super-enhancer (SE) genes have been identified as prognostic markers in several cancers, their potential as practical prognostic markers for CC patients remains unexplored. METHODS: We obtained super-enhancer-related genes (SERGs) from the Human Super-Enhancer Database (SEdb). Transcriptome and relevant clinical data for colon cancer (CC) were sourced from the Gene Expression Omnibus (GEO) database. Subsequently, we identified up-regulated SERGs by the Weighted Gene Co-expression Network Analysis (WGCNA). Prognostic signatures were constructed via univariate and multivariate Cox regression analysis. We then delved into the mechanisms of these predictive genes by examining immune infiltration. We also assessed differential sensitivities to chemotherapeutic drugs between high- and low-SERGs risk patients. The critical gene was further validated using external datasets and finally confirmed by qRT PCR. RESULTS: We established a ten-gene risk score prognostic model (S100A11, LZTS2, CYP2S1, ZNF552, PSMG1, GJC1, NXN, and DCBLD2), which can effectively predict patient survival rates. This model demonstrated effective prediction capabilities in survival rates at 1, 3, and 5 years and was successfully validated using external datasets. Furthermore, we detected significant differences in immune cell infiltration between high- and low-SERGs risk groups. Notably, high-risk patients exhibited heightened sensitivity to four chemotherapeutic agents, suggesting potential benefits for precision therapy in CC patients. Finally, qRT-PCR validation revealed a significant upregulation of LZTS2 mRNA expression in CC cells. CONCLUSION: These findings reveal that the SERGs model could effectively predict the prognosis of CC.

Phosphorylation of LZTS2 by PLK1 activates the Wnt pathway.

Lung adenocarcinoma (LUAD), responsible for nearly half of lung cancer cases, is one of the most prevalent and lethal malignant tumors globally. There is increasing evidence suggesting that the oncoprotein PLK1 plays a role in the onset and advancement of different types of cancer, including LUAD. Nonetheless, the precise mechanism by which PLK1 promotes tumorigenesis remains unclear. In this study, we demonstrate the upregulation of PLK1 in LUAD samples, which leads to a poor prognosis for LUAD patients. Intriguingly, PLK1 enables to bind to LZTS2 and promote its phosphorylation without affecting LZTS2 degradation. Furthermore, we identify that Ser451 is a key phosphorylation site in LZTS2 protein. LZTS2 exerts an anti-tumor effect by restricting the translocation of the transcription factor ß-Catenin into the nucleus, thereby suppressing the Wnt pathway. PLK1 disrupts the interaction between LZTS2 and ß-Catenin, resulting in the nuclear accumulation of ß-Catenin and the activation of the Wnt pathway. Additionally, we reveal that LZTS2 inhibits the proliferation and migration of LUAD cells, which is rescued by PLK1. Finally, PLK1 inhibitors exhibit a dose-dependent suppression of LUAD cell proliferation and migration. Collectively, this study uncovers the pro-tumorigenic mechanism of PLK1, positioning it as a promising therapeutic target for Wnt-related LUAD.

Long non-coding RNA linc00921 suppresses tumorigenesis and epithelial-to-mesenchymal transition of triple-negative breast cancer via targeting miR-9-5p/LZTS2 axis.

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Dysregulation of long non-coding RNAs (lncRNAs) plays crucial roles in the initiation and progression of TNBC. In this study, we analyzed public GEO profiles to verify the key lncRNAs in TNBC. Linc00921 was selected for further study. Low expression of linc00921 was observed in 49 of 95 TNBC tissues. Low expression of linc00921 was correlated with poor postoperative disease-free survival (DFS) and overall survival (OS) of TNBC patients. Overexpression of linc00921 with lentivirus suppressed the proliferation, migration and invasion of TNBC cells. A luciferase reporter assay showed that linc00921 could sponge miR-9-5p in TNBC. Moreover, linc00921 and miR-9-5p occupied the same Argonaute-2 (Ago2) protein in TNBC cells. Leucine zipper tumor suppressor 2 (LZTS2) was recognized as a target gene of miR-9-5p, and thereby a linc00921/miR-9-5p/LZTS2 axis was identified in TNBC cells. Overexpression of linc00921 promoted nuclear export of ß-catenin, neutralized its function, and subsequently promoted epithelial-to-mesenchymal transition (EMT) in TNBC. A xenograft tumor mouse model showed that the miR-9-5p inhibitor upregulates LZTS2 expression and induce nuclear export of ß-catenin in TNBC. Thus, linc00921 upregulates LZTS2 by sponging miR-9-5p to suppress tumorigenesis and EMT of TNBC. Linc00921/miR-9-5p/LZTS2 axis may be a novel biomarker and therapeutic target for TNBC patients.

LZTS2: A novel and independent prognostic biomarker for clear cell renal cell carcinoma.

PURPOSE: Leucine zipper tumor suppressor 2 (LZTS2), a putative tumor suppressor gene, has been demonstrated to be a negative regulator of microtubule severing during cytokinesis and a negative regulator of the Wnt signaling pathway. In a genetically modified mouse model, deletion of Lzts2 altered normal ureteric bud branching morphogenesis and caused cystogenesis in mice. Cyst-lining cells demonstrated atypical features, closely resembling those observed in mouse models of human clear cell renal cell carcinoma (ccRCC), which could represent a preneoplastic lesion. These findings suggest that LZTS2 may play a role in ccRCC tumorigenesis. The aim of this study was to establish an association between LZTS2 differential expression and clinicopathological features of ccRCC and to investigate its prognostic value as well as the underlying mechanisms in ccRCC progression. MATERIALS AND METHODS: Gene expression data by RNA-sequencing for cohorts of 510 ccRCC cases with clinical outcome data were extracted from The Cancer Genome Atlas (TCGA) using cBioPortal. Chi-square test of independence, Kaplan-Meier curves, and Cox regression models were used to investigate the possible relationship between LZTS2 mRNA expression levels and clinicopathological parameters as well as patient survival to establish its prognostic values. To examine its cellular localization, we performed LZTS2 antibody staining and scored the expression levels in a pilot study on a tissue microarray (TMA) containing 31 clear cell RCCs, 32 chromophobe RCCs, 12 papillary RCCs, and 20 adjacent benign renal tissue, as well as placental tissue diagnosed between 2001 and 2007 at the University of California San Francisco Medical Center. Staining was subsequently repeated in 15 ccRCCs on whole section slides to confirm the results. RESULTS: Our analysis of TCGA data demonstrated that LZTS2 expression levels were associated with tumor grade (p = 0.005), T stage (p < 0.001), metastasis status (p < 0.001), and overall clinical stage (p < 0.001). High level of expression was correlated with worse overall survival (p < 0.001), disease-specific survival (p < 0.001), progression-free survival (p < 0.001), and disease-free survival (p < 0.001) compared to low level of expression. Multivariate Cox regression analysis revealed that high LZTS2 expression was an independent poor prognostic factor for overall survival (HR = 2.083, p < 0.001), disease-specific survival (HR = 2.298, p < 0.001), and progression-free survival (HR = 1.896, p < 0.001) in patients with ccRCC. A few known driver mutations in ccRCC pathogenesis, including BAP1, NF2, and RELN, were enriched in LZTS2 high expression tumors. In particular, LZTS2 expression level could be a biomarker for risk stratification of the prognosis of BAP1-mutated ccRCCs. Immunohistochemical staining with anti-LZTS2 antibody was performed to examine its cellular localization in ccRCC and demonstrated centrosomal and acentrosomal distribution in tumors of various Fuhrman nuclear grades. Furthermore, high LZTS2 cytoplasmic expression was associated with centrosomal amplification (p = 0.030) in this small-scale study. CONCLUSIONS: The current study established an independent prognostic value of LZTS2 expression in ccRCC and explored the molecular mechanisms of LZTS2 in predicting the prognosis of ccRCC. Further studies are needed to validate our analysis and to provide a precise understanding of the function of LZTS2 in ccRCC.

LZTS2 inhibits PI3K/AKT activation and radioresistance in nasopharyngeal carcinoma by interacting with p85.

Phosphoinositide 3-kinase (PI3K) activity is aberrantly activated in nasopharyngeal carcinoma. However, the underlying mechanisms remain unclear. Here, we found that Leucine zipper tumor suppressor 2 (LZTS2) was downregulated and predicted poor prognosis in nasopharyngeal carcinoma patients. Furthermore, we identified the PI3K subunit p85 as a novel LZTS2-interacting protein using an unbiased proteomics approach. Moreover, we demonstrated that LZTS2 competes with p110 for p85 binding and inhibits activation of the PI3K/AKT signaling pathway. Functionally, we showed that LZTS2 suppresses tumorigenesis and radioresistance in nasopharyngeal carcinoma in a p85-dependent manner. Taken together, our results not only provide understanding of the molecular mechanisms by which PI3K/AKT signaling is activated but also suggest that targeting the LZTS2/PI3K/AKT signaling axis is a promising therapeutic strategy for radiosensitization of nasopharyngeal carcinoma.

The Shank3 Interaction Partner ProSAPiP1 Regulates Postsynaptic SPAR Levels and the Maturation of Dendritic Spines in Hippocampal Neurons.

The postsynaptic density or PSD is a submembranous compartment containing a wide array of proteins that contribute to both morphology and function of excitatory glutamatergic synapses. In this study, we have analyzed functional aspects of the Fezzin ProSAP-interacting protein 1 (ProSAPiP1), an interaction partner of the well-known PSD proteins Shank3 and SPAR. Using lentiviral-mediated overexpression and knockdown of ProSAPiP1, we found that this protein is dispensable for the formation of both pre- and postsynaptic specializations per se. We further show that ProSAPiP1 regulates SPAR levels at the PSD and the maturation of dendritic spines. In line with previous findings on the ProSAPiP1 homolog PSD-Zip70, we conclude that Fezzins essentially contribute to the maturation of excitatory spine synapses.

Leucine zipper tumor suppressor 2 inhibits cell proliferation and regulates Lef/Tcf-dependent transcription through Akt/GSK3ß signaling pathway in lung cancer.

Leucine zipper tumor suppressor 2 (LZTS2) is implicated in several cancers; however, its biological mechanisms in non-small cell lung cancer (NSCLC) are not yet understood. We found that low levels of LZTS2 in NSCLC were correlated with tumor and nodal status. LZTS2 could inhibit cell proliferation and cell cycle transition at the G1/S phase and was implicated in the regulation of proteins associated with the canonical Wnt pathway, including GSK3ß and ß-catenin through inactivating the Akt pathway. These results provide novel mechanistic insight into the biological roles of LZTS2 in lung cancer cells.

Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains.

The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1-3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information.