TEAD transcription factors play a central role in the Hippo signaling pathway. In this study, we focused on transcriptional enhancer factor TEF-3 (TEAD4), exploring its regulation by the deubiquitinase OTU domain-containing protein 6A (OTUD6A). We identified OTUD6A as a TEAD4-interacting deubiquitinase, positively influencing TEAD-driven transcription without altering TEAD4 stability. Structural analyses revealed specific interaction domains: the N-terminal domain of OTUD6A and the YAP-binding domain of TEAD4. Functional assays demonstrated the positive impact of OTUD6A on the transcription of YAP-TEAD target genes. Despite no impact on TEAD4 nuclear localization, OTUD6A selectively modulated nuclear interactions, enhancing YAP-TEAD4 complex formation while suppressing VGLL4 (transcription cofactor vestigial-like protein 4)-TEAD4 interaction. Critically, OTUD6A facilitated YAP-TEAD4 complex binding to target gene promoters. Our study unveils the regulatory landscape of OTUD6A on TEAD4, providing insights into diseases regulated by YAP-TEAD complexes.

ETS2 is a member of the ETS family of transcription factors and has been implicated in the regulation of cell proliferation, differentiation, apoptosis, and tumorigenesis. The aberrant activation of ETS2 is associated with various human cancers, highlighting its importance as a therapeutic target. Understanding the regulatory mechanisms and interacting partners of ETS2 is crucial for elucidating its precise role in cellular processes and developing novel strategies to modulate its activity. In this study, we conducted binding assays using a human deubiquitinase (DUB) library and identified USP39 as a novel ETS2-binding DUB. USP39 interacts with ETS2 through their respective amino-terminal regions, and the zinc finger and PNT domains are not required for this binding. USP39 deubiquitinates ETS2 without affecting its protein stability. Interestingly, however, USP39 significantly suppresses the transcriptional activity of ETS2. Furthermore, we demonstrated that USP39 leads to a reduction in the nuclear localization of ETS2. Our findings provide valuable insights into the intricate regulatory mechanisms governing ETS2 function. Understanding the interplay between USP39 and ETS2 may have implications for therapeutic interventions targeting ETS2-related diseases, including cancer, where the dysregulation of ETS2 is frequently observed.

The Wnt signaling pathway plays a critical role in regulating normal cellular processes, including proliferation, differentiation, and apoptosis. Dysregulation of Wnt signaling has been implicated in various human diseases, including cancer. β-catenin and LEF1 are key mediators of Wnt signaling, and their dysregulation is a hallmark of many cancer types. In this study, we aimed to identify the deubiquitinases (DUBs) that regulate the Wnt signaling pathway through the essential component LEF1. Screening candidate DUBs from the human DUB library, we discovered that OTUD7B interacts with LEF1 and activates Wnt signaling. OTUD7B and LEF1 interact with each other through the UBA and HMG domains, respectively. Furthermore, OTUD7B promotes the nuclear localization of LEF1, leading to an increased interaction with β-catenin in the nucleus while not noticeably affecting ubiquitination on LEF1. Using qPCR array analysis, we found that OTUD7B overexpression leads to an upregulation of 75% of the tested Wnt target genes compared to the control. These findings suggest that OTUD7B may serve as a potential therapeutic target in human diseases, including cancers where Wnt signaling is frequently dysregulated.

Supplementary Materials and Methods

Additional details related to the Materials and Methods section that appears in the main text.

Figure S1. Detection of miR-10b, miR-10a, Hoxd4, and Hoxd3. Figure S2. Body and organ weight. Figure S3. Overall survival and fertility. Figure S4. Complete blood cell count. Figure S5. Organ histology. Figure S6. Mammary tumor cell proliferation. Figure S7. PyMT antibody characterization. Figure S8. miR-10b target screen. Figure S9. TBX5 target identification. Figure S10. TBX5 inhibits breast cancer cell proliferation, migration, and invasion. Figure S11. Clinical correlation.

Legends for Supplementary Figures S1-S11

Herein, a highly enantioselective Pictet-Spengler reaction for the synthesis of axially chiral tetrahydroisoquinolines via dynamic kinetic resolution is described. Chiral phosphoric acids catalyze cyclization to yield single regioisomeric isoquinolines with excellent enantioselectivities around the C-C bond up to 99% ee. The current protocol is effective for a wide range of substrates, and the observed enantiodivergence depends on the substituents on the catalysts.

Midkine (MDK), a secreted growth factor, regulates signal transduction and cancer progression by interacting with receptors, and it can be internalized into the cytoplasm by endocytosis. However, its intracellular function and signaling regulation remain unclear. Here, we show that intracellular MDK interacts with LKB1 and STRAD to disrupt the LKB1-STRAD-Mo25 complex. Consequently, MDK decreases the activity of LKB1 to dampen both the basal and stress-induced activation of AMPK by glucose starvation or treatment of 2-DG. We also found that MDK accelerates cancer cell proliferation by inhibiting the activation of the LKB1-AMPK axis. In human cancers, compared to other well-known growth factors, MDK expression is most significantly upregulated in cancers, especially in liver, kidney and breast cancers, correlating with clinical outcomes and inversely correlating with phosphorylated AMPK levels. Our study elucidates an inhibitory mechanism for AMPK activation, which is mediated by the intracellular MDK through disrupting the LKB1-STRAD-Mo25 complex.

Aurora kinases are serine/threonine kinases required for cell proliferation and are overexpressed in many human cancers. Targeting Aurora kinases has been a therapeutic strategy in cancer treatment. Here, we attempted to identify a deubiquitinase (DUB) that regulates Aurora kinase A (Aurora-A) protein stability and/or kinase activity as a potential cancer therapeutic target. Through pull-down assays with the human DUB library, we identified OTUD6A as an Aurora-A-specific DUB. OTUD6A interacts with Aurora-A through OTU and kinase domains, respectively, and deubiquitinates Aurora-A. Notably, OTUD6A promotes the protein half-life of Aurora-A and activates Aurora-A by increasing phosphorylation at threonine 288 of Aurora-A. From qPCR screening, we identified and validated that the cancer gene CKS2 encoding Cyclin-dependent kinases regulatory subunit 2 is the most upregulated cell cycle regulator when OTUD6A is overexpressed. The results suggest that OTUD6A may serve as a therapeutic target in human cancers.

Long noncoding RNAs (lncRNAs) exert their functions through binding to other RNA, genomic DNA, or proteins. The identification of proteins that associate with the lncRNA of interest sheds light on the molecular basis of its biological functions. This can be achieved by tagging the lncRNA with chemically modified ribonucleotides, or by using in vitro transcribed lncRNA to retrieve proteins from cell lysates. Alternatively, endogenous lncRNAs can be pulled down from cells or tissues with biotinylated antisense DNA oligonucleotides, which may overcome the potential pitfalls of using tagged lncRNAs, such as artifacts caused by tagging or non-physiological interactions. Here we describe the detailed protocol for chromatin isolation by RNA purification (ChIRP) from mammalian cell lines and mouse tissues, which captures endogenous lncRNAs and enables subsequent identification of their physiologically relevant binding partners.

Failures to treat triple-negative breast cancer (TNBC) are mainly due to chemoresistance or radioresistance. We and others previously discovered that zinc finger E-box-binding homeobox 1 (ZEB1) is a massive driver causing these resistance. However, how to dynamically modulate the intrinsic expression of ZEB1 during cell cycle progression is elusive. Here integrated affinity purification combined with mass spectrometry and TCGA analysis identify a cell cycle-related E3 ubiquitin ligase, checkpoint with forkhead and ring finger domains (CHFR), as a key negative regulator of ZEB1 in TNBC. Functional studies reveal that CHFR associates with and decreases ZEB1 expression in a ubiquitinating-dependent manner and that CHFR represses fatty acid synthase (FASN) expression through ZEB1, leading to significant cell death of TNBC under chemotherapy. Intriguingly, a small-molecule inhibitor of HDAC under clinical trial, Trichostatin A (TSA), increases the expression of CHFR independent of histone acetylation, thereby destabilizes ZEB1 and sensitizes the resistant TNBC cells to conventional chemotherapy. In patients with basal-like breast cancers, CHFR levels significantly correlates with survival. These findings suggest the therapeutic potential for targeting CHFR-ZEB1 signaling in resistant malignant breast cancers.

BACKGROUND:Identification of specific biological functions, pathways, and appropriate prognostic biomarkers is essential to accurately predict the clinical outcomes of and apply efficient treatment for breast cancer patients.METHODS:To search for metastatic breast cancer-specific biological functions, pathways, and novel biomarkers in breast cancer, gene expression datasets of metastatic breast cancer were obtained from Oncomine, an online data mining platform. Over- and under-expressed genesets were collected and the differentially expressed genes were screened from four datasets with large sample sizes (N > 200). They were analyzed for gene ontology (GO), KEGG pathway, protein-protein interaction, and hub gene analyses using online bioinformatic tools (Enrichr, STRING, and Cytoscape) to find enriched functions and pathways in metastatic breast cancer. To identify novel prognostic biomarkers in breast cancer, differentially expressed genes were screened from the entire twelve datasets with any sample sizes and tested for expression correlation and survival analyses using online tools such as KM plotter and bc-GenExMiner.RESULTS:Compared to non-metastatic breast cancer, 193 and 144 genes were differentially over- and under-expressed in metastatic breast cancer, respectively, and they were significantly enriched in regulating cell death, epidermal growth factor receptor signaling, and membrane and cytoskeletal structures according to the GO analyses. In addition, genes involved in progesterone- and estrogen-related signalings were enriched according to KEGG pathway analyses. Hub genes were identified via protein-protein interaction network analysis. Moreover, four differentially over-expressed (CCNA2, CENPN, DEPDC1, and TTK) and three differentially under-expressed genes (ABAT, LRIG1, and PGR) were further identified as novel biomarker candidate genes from the entire twelve datasets. Over- and under-expressed biomarker candidate genes were positively and negatively correlated with the aggressive and metastatic nature of breast cancer and were associated with poor and good prognosis of breast cancer patients, respectively.CONCLUSIONS:Transcriptome datasets of metastatic breast cancer obtained from Oncomine allow the identification of metastatic breast cancer-specific biological functions, pathways, and novel biomarkers to predict clinical outcomes of breast cancer patients. Further functional studies are needed to warrant validation of their roles as functional tumor-promoting or tumor-suppressing genes.

Infiltration of diverse cell types into tumor microenvironment plays a critical role in cancer progression including metastasis. We previously reported that SFMBT2 (Scm-like with four mbt domains 2) regulates the expression of matrix metalloproteinases (MMPs) and migration and invasion of cancer cells in prostate cancer. Here we investigated whether the down-regulation of SFMBT2 regulates the infiltration of preadipocytes and tumor-associated macrophages (TAMs) in prostate cancer. We found that the down-regulation of SFMBT2 promotes the infiltration of preadipocytes and TAMs through up-regulation of CXCL8, CCL2, CXCL10, and CCL20 expression in prostate cancer. Expression of CXCL8, CCL2, CXCL10, and CCL20 was also elevated in prostate cancer patients having a higher Gleason score (≥8), which had substantially lower SFMBT2 expression. We also found that the up-regulation of CXCL8, CCL2, CXCL10, and CCL20 expression is dependent on NF-κB activation in prostate cancer cells expressing a low level of SFMBT2. Moreover, increased IL-6 from infiltrated preadipocytes and TAMs promoted migration and invasion of prostate cancer cells expressing a low level of SFMBT2. Our study may suggest that SFMBT2 a critical regulator for the infiltration of preadipocytes and TAMs into the prostate tumor microenvironment. Thus, the regulation of SFMBT2 may provide a new therapeutic strategy to inhibit prostate cancer metastasis, and SFMBT2 could be used as a potential biomarker in prostate cancer metastasis.

Abstract Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely ‘hijacked’ by cytoplasmic Malat1 to the cytoplasm, resulting in the depletion of nuclear TDP-43 and redistribution of TDP-43 binding to repetitive element transcripts and mRNAs encoding mitotic and nuclear-cytoplasmic regulators. The SINE promotes Malat1 nuclear retention by facilitating Malat1 binding to HNRNPK, a protein that drives RNA nuclear retention, potentially through direct interactions of the SINE with KHDRBS1 and TRA2A, which bind to HNRNPK. Losing these RNA–protein interactions due to the SINE deletion likely creates more available TDP-43 binding sites on Malat1 and subsequent TDP-43 aggregation. These results highlight the significance of lncRNA TEs in TDP-43 proteostasis with potential implications in both cancer and neurodegenerative diseases.

Energy stress depletes ATP and induces cell death. Here we identify an unexpected inhibitory role of energy stress on ferroptosis, a form of regulated cell death induced by iron-dependent lipid peroxidation. We found that ferroptotic cell death and lipid peroxidation can be inhibited by treatments that induce or mimic energy stress. Inactivation of AMP-activated protein kinase (AMPK), a sensor of cellular energy status, largely abolishes the protective effects of energy stress on ferroptosis in vitro and on ferroptosis-associated renal ischaemia–reperfusion injury in vivo. Cancer cells with high basal AMPK activation are resistant to ferroptosis and AMPK inactivation sensitizes these cells to ferroptosis. Functional and lipidomic analyses further link AMPK regulation of ferroptosis to AMPK-mediated phosphorylation of acetyl-CoA carboxylase and polyunsaturated fatty acid biosynthesis. Our study demonstrates that energy stress inhibits ferroptosis partly through AMPK and reveals an unexpected coupling between ferroptosis and AMPK-mediated energy-stress signalling. Lee et al. show that energy stress inhibits ferroptosis through AMPK activation and demonstrate a role for AMPK in ferroptosis-associated renal ischaemia–reperfusion injury in vivo.

BACKGROUND:Basal-like breast cancer (BLBC) or triple-negative breast cancer (TNBC) is an aggressive and highly metastatic subtype of human breast cancer. The present study aimed to elucidate the potential tumor-suppressive function of MATR3, an abundant nuclear protein, in BLBC/TNBC, whose cancer-relevance has not been characterized.METHODS:We analyzed in vitro tumorigenecity by cell proliferation and soft agar colony formation assays, apoptotic cell death by flow cytometry and Poly (ADP-ribose) polymerase (PARP) cleavage, epithelial-mesenchymal transition (EMT) by checking specific EMT markers with real-time quantitative PCR and in vitro migration and invasion by Boyden Chamber assays. To elucidate the underlying mechanism by which MATR3 functions as a tumor suppressor, we performed Tandem affinity purification followed by mass spectrometry (TAP-MS) and pathway analysis. We also scrutinized MATR3 expression levels in the different subtypes of human breast cancer and the correlation between MATR3 expression and patient survival by bioinformatic analyses of publicly available transcriptome datasets.RESULTS:MATR3 suppressed in vitro tumorigenecity, promoted apoptotic cell death and inhibited EMT, migration, and invasion in BLBC/TNBC cells. Various proteins regulating apoptosis were identified as MATR3-binding proteins, and YAP/TAZ pathway was suppressed by MATR3. MATR3 expression was inversely correlated with the aggressive and metastatic nature of breast cancer. Moreover, high expression levels of MATR3 were associated with a good prognosis of breast cancer patients.CONCLUSIONS:Our data demonstrate that MATR3 functions as a putative tumor suppressor in BLBC/TNBC cells. Also, MATR3 potentially plays a role as a biomarker in predicting chemotherapy-sensitivity and patient survival in breast cancer patients.

SNAI1, an epithelial-mesenchymal transition (EMT)-inducing transcription factor, promotes tumor metastasis and resistance to apoptosis and chemotherapy. SNAI1 protein levels are tightly regulated by proteolytic ubiquitination. Here, we identified USP37 as a SNAI1 deubiquitinase that removes the polyubiquitination chain from SNAI1 and prevents its proteasomal degradation. USP37 directly binds, deubiquitinates, and stabilizes SNAI1. Overexpression of wild-type USP37, but not its catalytically inactive mutant C350S, promotes cancer cell migration. Importantly, depletion of USP37 downregulates endogenous SNAI1 protein and suppresses cell migration, which can be reversed by re-expression of SNAI1. Taken together, our findings suggest that USP37 is a SNAI1 deubiquitinase and a potential therapeutic target to inhibit tumor metastasis.

© Biotarget. All rights reserved. Biotarget 2019;3:5 biotarget.amegroups.com Since Malat1 was identified as a prognostic marker for poor clinical outcomes in non-small cell lung cancer (NSCLC) patients, number of Malat1 studies have revealed its roles in human cancers (1,2). Recently, we demonstrated unexpected Malat1 function in suppressing breast cancer metastasis using genetic mouse and cell line models of breast cancer (3). Here, I review the controversies in Malat1 studies conducted by ourselves and others by comparing research designs and interpreting the results. Previously, Malat1 was shown to co-localize with nuclear speckles enriched in pre-mRNA splicing factors. In vitro siRNA study revealed that Malat1 interacts with splicing factors in the nucleus and regulates pre-mRNA splicing (4). Malat1 genetic knockout mice were generated from independent research groups and exhibited no apparent phenotypic abnormalities (5,6). Surprisingly, unlike in vitro results, there were no significant changes in alternative splicing or global gene expression due to genetic loss of Malat1 (3,6). Arun et al. (7) generated Malat1 knockout mice by deleting 3 kb genomic locus spanning both upstream and downstream of transcription start site and crossed them to Polyomavirus middle T antigen (PyMT)-induced mouse mammary tumor model. Although Malat1 loss did not substantially alter primary tumorigenesis, mammary tumors of Malat1 PyMT mice exhibited cystic phenotype compared to Malat1 PyMT animals. Furthermore, lung metastasis was significantly suppressed by Malat1 loss. In addition to genetic ablation of Malat1, PyMT mice were treated with antisense oligonucleotides (ASOs). Compared to complete genetic Malat1 knockout, ASOs led to ~60% reduction in Malat1 levels but caused stronger suppression in mammary tumor growth and comparable inhibition in lung metastasis. Targeting Malat1 with less-effective ASOs demonstrated more evident tumor-suppressive outcome, which obviously raises a question of off-target effects of ASOs. We utilized Malat1 mouse knockout model generated by targeted insertional inactivation (5) and crossed them to PyMT mice (3). Unexpectedly, however, we observed dramatic induction of lung metastasis in Malat1 PyMT mice while there was no noticeable difference in mammary tumors compared to Malat1 PyMT mice; cystic and highgrade tumor areas were similarly found in both groups. Instead, we could see consistent increase in circulating tumor cells from the peripheral blood of Malat1 PyMT mice, which implies that Malat1 loss affects certain stage of metastatic process. This surprising result against the current dominant paradigm of Malat1’s pro-metastatic function prompted us to restore Malat1 in Malat1 PyMT mice using transgenic animals to determine if metastasispromoting function is attributed to Malat1 loss. When Malat1 was re-expressed, metastatic phenotype was dramatically reversed. Furthermore, considering higher Malat1 levels in Malat1-restored PyMT mice compared to Malat1 PyMT mice, Malat1-re-expression resulted in less metastasis than Malat1, which implies dose-dependent effect of Malat1 in lung metastasis suppression. Using more aggressive PyMT mice on FVB/N background, we overexpressed Malat1 by crossing them to Malat1 transgenic mice on FVB/N and observed that lung metastasis was significantly suppressed by transgenic overexpression of Malat1. In addition, we inactivated MALAT1 in MDA-MB-231 Letter to the Editor