Melanoma and microbiota: Current understanding and future directions

Over the last decade, the composition of the gut microbiota has been found to correlate with the outcomes of cancer patients treated with immunotherapy. Accumulating evidence points to the various mechanisms by which intestinal bacteria act on distal tumors and how to harness this complex ecosystem to circumvent primary resistance to immune checkpoint inhibitors. Here, we review the state of the microbiota field in the context of melanoma, the recent breakthroughs in defining microbial modes of action, and how to modulate the microbiota to enhance response to cancer immunotherapy. The host-microbe interaction may be deciphered by the use of "omics" technologies, and will guide patient stratification and the development of microbiota-centered interventions. Efforts needed to advance the field and current gaps of knowledge are also discussed.

Expanding PROTACtable genome universe of E3 ligases

Proteolysis-targeting chimera (PROTAC) and other targeted protein degradation (TPD) molecules that induce degradation by the ubiquitin-proteasome system (UPS) offer new opportunities to engage targets that remain challenging to be inhibited by conventional small molecules. One fundamental element in the degradation process is the E3 ligase. However, less than 2% amongst hundreds of E3 ligases in the human genome have been engaged in current studies in the TPD field, calling for the recruiting of additional ones to further enhance the therapeutic potential of TPD. To accelerate the development of PROTACs utilizing under-explored E3 ligases, we systematically characterize E3 ligases from seven different aspects, including chemical ligandability, expression patterns, protein-protein interactions (PPI), structure availability, functional essentiality, cellular location, and PPI interface by analyzing 30 large-scale data sets. Our analysis uncovers several E3 ligases as promising extant PROTACs. In total, combining confidence score, ligandability, expression pattern, and PPI, we identified 76 E3 ligases as PROTAC-interacting candidates. We develop a user-friendly and flexible web portal ( https://hanlaboratory.com/E3Atlas/ ) aimed at assisting researchers to rapidly identify E3 ligases with promising TPD activities against specifically desired targets, facilitating the development of these therapies in cancer and beyond.

Abstract 957: Prediction of patient response to targeted and immunotherapies from the tumor transcriptome in a wide set of indications and clinical trials

Background: Precision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers.

Methods: We present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patient’s response to a variety of therapies in multiple cancer types, importantly, without training on previous treatment response data. Consequently, in addition to its ability to predict patients' response to approved and well-studied therapies, ENLIGHT can predict the response to new treatments in early development, even before clinical data has accumulated. Accordingly, we study ENLIGHT in two translationally relevant scenarios: Personalized Oncology (PO), aimed at prioritizing approved treatments to a given patient, and Clinical Trial Design (CTD), selecting the subset of most likely responders in a patient cohort.

Results: Evaluating ENLIGHT’s performance on 21 blinded clinical trial datasets spanning 11 indications and 15 different drugs in the PO setting, we show that it can effectively predict a patient’s treatment response across multiple therapies and cancer types, with an overall odds ratio of 2.59 (p=3.41e-8), and a 36% increase in response rate over the baseline (p=3.30e-13). Its prediction accuracy is better than other state-of-the-art transcriptomics-based signatures. Unlike most signatures that are prognostic or provide insights for only very few, specific treatments, ENLIGHT provides matching scores to a broad range of treatments. Quite strikingly, its performance is comparable to that of supervised predictors developed for specific indications and drugs. In combination with the IFN-γ signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, our results show that by excluding non-responders ENLIGHT can enhance clinical trial success for immunotherapies and other monoclonal antibodies, achieving > 90% of the response rate attainable under an optimal exclusion strategy.

Conclusion: ENLIGHT is a powerful transcriptomics-based precision oncology pipeline developed by Pangea Biomed that broadly predicts response to both extant and novel targeted and immune therapies, going beyond context-specific biomarkers.

Citation Format: Gal Dinstag, Eldad D. Shulman, Efrat Elis, Doreen S. Ben-Zvi, Omer Tirosh, Eden Maimon, Isaac Meilijson, Emmanuel Elalouf, Boris Temkin, Philipp Vitkovsky, Eyal Schiff, Danh-Tai Hoang, Sanju Sinha, Nishanth Ulhas Nair, Joo Sang-Lee, Alejandro A. Schäffer, Ze'ev Ronai, Dejan Juric, Andrea B. Apolo, William L. Dahut, Stanley Lipkowitz, Raanan Berger, Razelle Kurzrock, Antonios Papanicolau-Sengos, Fatima Karzai, Mark R. Gilbert, Kenneth Aldape, Padma S. Rajagopal, Tuvik Beker, Eytan Ruppin, Ranit Aharonov. Prediction of patient response to targeted and immunotherapies from the tumor transcriptome in a wide set of indications and clinical trials [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 957.

Casper: A phase I, open-label, dose finding study of calaspargase pegol-mnkl (cala) in combination with cobimetinib (cobi) in locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC)

TPS772

Background: Metabolic adaptation provides rapidly dividing cancer cells the flexibility to maintain homeostasis as nutrient supplies are continuously exhausted in the tumor microenvironment. Asparagine synthetase (ASNS) catalyzes ATP-dependent biosynthesis of the non-essential amino acid asparagine from aspartate and glutamine. Cells lacking ASNS, however, are auxotrophic for asparagine. Use of L-asparaginase (ASNase) to promote asparagine starvation in PDAC and other solid tumors with low ASNS levels is a rationale treatment strategy; however, aberrant RAS/MAPK signaling can circumvent effects of ASNase. Preclinical data shows that targeted inhibition of MAPK signaling along with ASNase is active against PDAC; however, this has not been tested in patients to date. Methods: CASPER is an open-label, phase IB, single-arm, dose-escalation study to evaluate the safety and tolerability of combining cala and cobi in patients with locally-advanced or metastatic PDAC. Participants receive cala and cobi at assigned dose level. The study uses a Bayesian Optimal Interval (BOIN) design to determine the maximum tolerated dose (MTD) for the combination of study agents. Up to 15 participants will be enrolled and treated, with a cohort of 3 participants assessed before a decision is made to escalate, de-escalate, or maintain the current dose level before initiating the next cohort. MTD is defined as the dose level where dose-limiting toxicity (DLT) probability is closest to the target toxicity rate of 30% after applying isotonic regression to the observed dose-level-specific DLT rate. Per BOIN, the dose level is escalated, maintained, or de-escalated based on comparisons of the observed DLT rate and pre-specified boundaries (0.236, 0.359). Starting in Cycle (C) 1, patients receive cobi (at assigned dose level) for Days (D) 1-14, and their assigned dose of cala on D1 of each 21-day cycle. If the combination of cala and cobi is tolerated and does not incur DLTs, participants will continue receiving their assigned dose of cala and cobi until evidence of disease progression, unacceptable toxicity, or study withdrawal. The DLT period starts on C1D1 and ends C2D21. Secondary endpoints include preliminary assessment of overall response rate (ORR), disease control rate (DCR), and mean levels of plasma ASNase. Paired tumor biopsies and serial blood will be used for exploratory objectives combining deep multi-omic analytics with clinical data. The trial is currently open with 1 patient enrolled at time of submission. Clinical trial information: NCT05034627 . [Table: see text]

Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome

BACKGROUND

Precision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers.

METHODS

We present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patient's response to a variety of therapies in multiple cancer types without training on previous treatment response data. We study ENLIGHT in two translationally oriented scenarios: personalized oncology (PO), aimed at prioritizing treatments for a single patient, and clinical trial design (CTD), selecting the most likely responders in a patient cohort.

FINDINGS

Evaluating ENLIGHT's performance on 21 blinded clinical trial datasets in the PO setting, we show that it can effectively predict a patient's treatment response across multiple therapies and cancer types. Its prediction accuracy is better than previously published transcriptomics-based signatures and is comparable with that of supervised predictors developed for specific indications and drugs. In combination with the interferon-γ signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, ENLIGHT can potentially enhance clinical trial success for immunotherapies and other monoclonal antibodies by excluding non-responders while overall achieving more than 90% of the response rate attainable under an optimal exclusion strategy.

CONCLUSIONS

ENLIGHT demonstrably enhances the ability to predict therapeutic response across multiple cancer types from the bulk tumor transcriptome.

FUNDING

This research was supported in part by the Intramural Research Program, NIH and by the Israeli Innovation Authority.

Lineage-Restricted Regulation of SCD and Fatty Acid Saturation by MITF Controls Melanoma Phenotypic Plasticity

Phenotypic and metabolic heterogeneity within tumors is a major barrier to effective cancer therapy. How metabolism is implicated in specific phenotypes and whether lineage-restricted mechanisms control key metabolic vulnerabilities remain poorly understood. In melanoma, downregulation of the lineage addiction oncogene microphthalmia-associated transcription factor (MITF) is a hallmark of the proliferative-to-invasive phenotype switch, although how MITF promotes proliferation and suppresses invasion is poorly defined. Here, we show that MITF is a lineage-restricted activator of the key lipogenic enzyme stearoyl-CoA desaturase (SCD) and that SCD is required for MITF^High melanoma cell proliferation. By contrast MITF^Low cells are insensitive to SCD inhibition. Significantly, the MITF-SCD axis suppresses metastasis, inflammatory signaling, and an ATF4-mediated feedback loop that maintains de-differentiation. Our results reveal that MITF is a lineage-specific regulator of metabolic reprogramming, whereby fatty acid composition is a driver of melanoma phenotype switching, and highlight that cell phenotype dictates the response to drugs targeting lipid metabolism.

Lessons from the canine Oxtr gene: populations, variants and functional aspects

Oxytocin receptor (OXTR) acts as a key behavioral modulator of the central nervous system, affecting social behavior, stress, affiliation and cognitive functions. Variants of the Oxtr gene are known to influence behavior both in animals and humans; however, canine Oxtr polymorphisms are less characterized in terms of possible relevance to function, selection criteria in breeding and domestication. In this report, we provide a detailed characterization of common variants of the canine Oxtr gene. In particular (1) novel polymorphisms were identified by direct sequencing of wolf and dog samples, (2) allelic distributions and pairwise linkage disequilibrium patterns of several canine populations were compared, (3) neighbor joining (NJ) tree based on common single nucleotide polymorphisms (SNPs) was constructed, (4) mRNA expression features were assessed, (5) a novel splice variant was detected and (6) in vitro functional assays were performed. Results indicate marked differences regarding Oxtr variations between purebred dogs of different breeds, free-ranging dog populations, wolf subspecies and golden jackals. This, together with existence of explicitly dog-specific alleles and data obtained from the NJ tree implies that Oxtr could indeed have been a target gene during domestication and selection for human preferred aspects of temperament and social behavior. This assumption is further supported by the present observations on gene expression patterns within the brain and luciferase reporter experiments, providing a molecular level link between certain canine Oxtr polymorphisms and differences in nervous system function and behavior.

Siah: New Players in the Cellular Response to Hypoxia

Prolyl-hydroxylation of HIF-1alpha is a prerequisite for pVHL binding to HIF-1alpha, which results in degradation of HIF-1alpha by the ubiquitin-proteasome pathway. Hydroxylation of HIF-1alpha is mediated by the family of prolyl-hydroxylase proteins (PHD). In hypoxia, HIF-1alpha is stabilized as a result of inhibition of HIF-1alpha hydroxylation, which in part is achieved by decreased activity of PHD enzymes at very low oxygen concentrations. We recently demonstrated that in hypoxia the stability of 2 of 3 PHDs (1 and 3) is regulated by the E3 ligases Siah1/2. Consequently, in hypoxia Siah determines the availability of PHD1/3, which otherwise modify HIF-1alpha to enable its association-dependent degradation by pVHL. These findings define a newly discovered layer in the regulation of HIF-1alpha in hypoxia. The roles of Siah activities in hypoxia responses are discussed.

Autophosphorylation Properties of Inactive and Active JNK2

The c-Jun N-terminal kinases (JNKs) are ubiquitous proteins that phosphorylate their substrates, such as transcription factors, in response to physical stress, cytokines or UV radiation. This leads to changes in gene expression, ensuing either cell cycle progression or apoptosis. Active phospho JNK1 is the main in vivo kinase component of the JNK cascade, whereas JNK2 is presumed not to participate as a kinase during JNK signalling. However, there is evidence that JNK isoforms interact functionally in vivo. Also, a recent chemical genetics investigation has confirmed that JNK transient activation leads to cellular proliferation, whereas a sustained one is pro-apoptotic. Here we investigate the phosphorylation pattern of JNK2, with protein biochemistry tools and tandem mass spectrometry. We choose to focus on JNK2 because of its reported constitutive activity in glioma cells. Our results indicate that purified JNK2 from transfected nonstressed 293T cells is a mixture of the mono-sites pThr183 and pTyr185 of its activation loop and of pThr386 along its unique C-terminal region. Upon UV stimulation, its phosphorylation stoichiometry is upregulated on the activation loop, generating a mixture of mono-pTyr185 and the expected dual-pThr183/pTyr185 species, with the pThr386 specie present but unaltered respect to the basal conditions.

Abstract 1795: Small molecule SBI-601 inhibits Siah1/2 ubiquitin ligases, attenuates HIF1α expression and growth of melanoma and prostate cancer cells

The ubiquitin ligases Siah1/2 have been implicated in the control of key cellular pathways, including hypoxia (through the control of prolyl hydroxylase 1/3 stability), mitochondrial fission (through the control of AKAP121 stability) and Ras/Raf signaling (through its control of Sprouty 2 stability). Expression or activity of Siah1/2 is upregulated in number of cancer types and correspondingly, inhibition of Siah1/2 effectively attenuates growth of prostate, melanoma, lung and pancreatic tumors. To identify possibly Siah1/2 inhibitors, we have performed a HTS screen using affinity selection-mass spectrometry (AS-MS). Using a select set of 32,000 drug-like molecules in mass-encoded mixtures of 400 compounds per assay well, we identified 36 distinct clusters of structurally related scaffolds that demonstrate high-binding affinity to full-length bacterially produced purified and active Siah2. Of those, 9 out of 21 closely related analogs were evaluated in functional assays. One compound, SBI-0640601, showed potent and reproducible inhibition of Siah2, as measured by the reduction in HIF1α levels and activity, measured by HRE-Luciferase assays in both melanoma and prostate cancer cultures. SBI-0640601 is a natural product known as betulonic acid (BA) and is one of a family of triterpenoid natural medicinal products derived from birch trees (genera Betula). Independent binding studies (differential scanning calorimetry) confirmed that SBI-0640601 binds to full-length bacterially produced Siah2 and to a RING domain-deleted version of Siah1. In vitro, SBI-0640601 attenuated the binding of PHD3 to Siah2, in keeping with the observation that ubiquitination of most substrates requires binding to the Siah2 substrate-binding domain. SBI-0640601 inhibited growth of melanoma and prostate cancer cells in 2D and 3D cultures. Further, SBI-0640601 effectively attenuated neuroendocrine differentiation phenotype in adenocarcinoma cells, consistent with the effect seen upon inhibition of Siah1/2 expression. RPPA analysis identified that SBI-0640601 effectively attenuates AMPK and mTOR signaling pathways, in addition to affecting MAPK signaling. Overall, SBI-0640601 appears to inhibit key processes previously shown to be regulated by Siah1/2, holding promise for further assessment in preclinical setting.

Note: This abstract was not presented at the meeting.

Citation Format: Yongmei Feng, Tal Varsano, Hampton Sessions, Michael Davies, Greg Roth, Ze'ev Ronai. Small molecule SBI-601 inhibits Siah1/2 ubiquitin ligases, attenuates HIF1α expression and growth of melanoma and prostate cancer cells. [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 1795. doi:10.1158/1538-7445.AM2014-1795

Abstract 59: PDK1 in melanoma development and metastasis

Phosphoinositide-dependent kinase-1 (PDK-1) is a serine/threonine protein kinase that phosphorylates members of the conserved AGC kinase superfamily, including AKT and PKC, and is implicated in important cellular processes including survival, metabolism and tumorigenesis. In large cohorts of nevi and melanoma samples, PDK1 expression was significantly higher in primary melanoma, compared with nevi, and was further increased in metastatic melanoma. Selective inactivation of Pdk1 in the melanocytes of BrafV600E::Pten-/- or BrafV600E::Cdkn2a-/-::Pten-/- mice delayed the development of pigmented lesions and melanoma induced by systemic or local administration of 4-HT. Melanoma invasion and metastasis were significantly reduced or completely prevented by Pdk1 deletion. Administration of the PDK1 inhibitor GSK2334470 (PDKi) effectively delayed melanomagenesis and metastasis in BrafV600E::Pten-/- mice. Pdk1-/- melanomas exhibit a marked decrease in the activity of AKT, p70S6K and PKC. Notably, genetic inactivation or pharmacological inhibition of PDK1 were even more effective in attenuating melanoma development and metastasis of human tumors with Pten WT as in genetic model of BrafV600E::Cdkn2a-/-::Pten+/+ mice, representing an additional fraction of human tumors harboring such mutation. Gene expression analyses identified Pdk1-dependent changes in FOXO3a-regulated genes and inhibition of FOXO3a restored proliferation and colony formation of Pdk1-/- melanoma cells. PDK1 effect on FOXO3a and melanoma development and progression appears to be AKT independent. Our studies provide direct genetic evidence for the importance of PDK1, in part through FOXO3a-dependent pathway, in melanoma development and progression.

Citation Format: Marzia Scortegagna, Chelsea Ruller, Yongmei Feng, Rossitza Lazova, Harriet Kluger, Jian-Liang Li, Surya K. De, Robert Rickert, Maurizio Pellecchia, Marcus Bosenberg, Ze'ev Ronai. PDK1 in melanoma development and metastasis. [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 59. doi:10.1158/1538-7445.AM2014-59

Abstract 4520: Inhibition of melanoma growth by small molecules that attenuate PI3K/PDK1 signaling and promote ATF2 mitochondrial localization

Phosphoinositide-dependent kinase-1 (PDK-1) phosphorylates members of the AGC kinase superfamily, including AKT and PKC. We recently demonstrated the importance of PDK1 in melanoma development and progression (Oncogene 2013). Genetic ablation of PDK1 in melanocytes effectively delayed melanoma development and inhibited metastasis in a Braf/Cdkn2a model with WT or mutant Pten. In an effort to identify small molecule inhibitors that could affect the PDK1 signaling we characterized SBI-0089410, a small molecule identified in a screen for nuclear exclusion of the transcription factor ATF2, which attenuates its oncogenic activity while enabling its function at the mitochondrial membrane to promote apoptosis. SBI-0089410 reduced melanoma cell viability, inhibited colony formation and spheroid growth, decreased mitochondrial membrane permeability, decreased ATF2 phosphorylation by PKCϵ and altered ATF2 transcriptional activity. Notably, the effect of SBI-0089401 was attenuated by the overexpression of constitutively active PKCϵ or ATF2T52E, which carries a phosphomimetic mutation at the PKCϵ phosphorylation site. Reverse phase protein array (RPPA), validated by western blot analysis, revealed that SBI-408910 attenuates PI3K/AKT/PDK1 signaling pathways. In vivo, SBI-089410 attenuated the growth of Braf/Cdkn2a/Pten tumors in a syngeneic B6 mouse model, as well as prevented their resistance to BRAFi. Our studies substantiate the importance of targeting PI3K/PDK1 signaling in melanoma as a means for effective therapy and prevention of chemoresistance.

Citation Format: Tal Varsano, Yongmei Feng, Giuseppina Claps, Marzia Scortegagna, Eric Lau, Marilyn Leonard, Anthony Pinkerton, Maurizio Pellecchia, Michael Davies, Marcus Bosenberg, Ze'ev Ronai. Inhibition of melanoma growth by small molecules that attenuate PI3K/PDK1 signaling and promote ATF2 mitochondrial localization. [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 4520. doi:10.1158/1538-7445.AM2014-4520

Abstract 2440: RNF5 mediates ER stress-induced degradation of SLC1A5 in breast cancer

Tumor cells have an altered metabolism that distinguishes it from their normal counterpart. Intriguingly, tumor cells show increased use of glutamine to fuel catabolic processes. Therefore, altered metabolic tumors have been considered as a good target for anticancer therapy. Ring finger protein 5 (RNF5) is an ER membrane-associated ubiquitin E3 ligase. RNF5 expression has been associated with breast cancer progression. We identified solute carrier family 1 member 5 (SLC1A5) as a possible RNF5 regulated protein using a MS analysis of breast cancer cells. SLC1A5 is a high affinity L-glutamine transporter, which is highly expressed in tumors such as breast, liver and lung. RNF5 promotes ubiquitination-mediated degradation of SLC1A5 in response to chemotherapeutic drugs known to induce ER stress. RNF5-mediated SLC1A5 instability attenuated mTOR signaling, leading to inhibition of tumor cell proliferation and promotion of apoptosis/autophagy. The loss of RNF5 in PyMT-MMTV crossed with RNF5 mutant animals developed less differentiated mammary tumors, which exhibit increased levels of SLC1A5. TMA analysis of human breast cancer tumors identified a fraction that exhibited an inverse correlation between RNF5 and SLC1A5 expression. Notably, reduced expression of SLC1A5 exhibited a strong association with improved prognosis of breast cancer. Taken together, our observations identify mechanisms underlying the control of SLC1A5 stability, and the implications of such regulation for mTOR signaling and breast cancer survival in response to therapy.

Citation Format: Young Joo Jeon, Sihem Khelifa, Yongmei Feng, Eric Lau, Robert Cardiff, Hyungsoo Kim, David L. Rimm, Yuval Kluger, Ze'ev Ronai. RNF5 mediates ER stress-induced degradation of SLC1A5 in breast cancer. [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 2440. doi:10.1158/1538-7445.AM2014-2440

Roquin-2 promotes ubiquitin-mediated degradation of ASK1 to regulate stress responses

Apoptosis signal-regulating kinase 1 (ASK1, also known as MAP3K5) mediates reactive oxygen species (ROS)-induced cell death. When activated by ROS, ASK1 ultimately becomes ubiquitinated and degraded by the proteasome, a process that is antagonized by the ubiquitin-specific protease USP9X. Using a functional siRNA (small interfering RNA) screen in HeLa cells, we identified Roquin-2 (also called RC3H2) as an E3 ubiquitin ligase required for ROS-induced ubiquitination and degradation of ASK1. In cells treated with H2O2, knockdown of Roquin-2 promoted sustained activation of ASK1 and the downstream stress-responsive kinases JNK (c-Jun amino-terminal kinase) and p38 MAPK (mitogen-activated protein kinase), and led to cell death. The nematode Caenorhabditis elegans produces ROS as a defense mechanism in response to bacterial infection. In C. elegans, mutation of the gene encoding the Roquin-2 ortholog RLE-1 promoted accumulation of the activated form of the ASK1 ortholog NSY-1 and conferred resistance to infection by the bacteria Pseudomonas aeruginosa. Thus, these data suggest that degradation of ASK1 mediated by Roquin-2 is an evolutionarily conserved mechanism required for the appropriate regulation of stress responses, including pathogen resistance and cell death.

Synthesis and SAR studies of dual AKT/NF-κB inhibitors against melanoma

The protein Kinase B alpha (AKT) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways are central regulators of cellular signaling events at the basis of tumor development and progression. Both pathways are often up-regulated in different tumor types including melanoma. We recently reported the identification of compound 1 (BI-69A11) as inhibitor of the AKT and the NF-κB pathways. Here, we describe SAR studies that led to novel fluorinated derivatives with increased cellular potency, reflected in efficient inhibition of AKT and IKKs. Selected compounds demonstrated effective toxicity on melanoma, breast, and prostate cell lines. Finally, a representative derivative showed promising efficacy in an in vivo melanoma xenograft model.

Detection of ki-ras mutation in nonneoplastic mucosa of Japanese patients with colorectal cancers

About 50% of colorectal adenocarcinoma in humans have been reported to contain mutated Ki-ras gene. To provide a better understanding for the possible role of this mutation and to examine whether its presence can reliably predict a risk of colorectal cancer, we have analyzed the normal appearing mucosa of patients with colorectal adenocarcinoma. With an Enriched PCR procedure, we can detect mutated Ki-ras allele in the presence of 10(3) to 10(4) normal alleles. Only by this procedure was Ki-ras mutation detected in the non-neoplastic colonic mucosa of 9 out of 50 (18%) Japanese patients with colorectal cancer. This analysis indicated that epithelial cells which carry mutated Ki-ras gene were 100- to 1000-fold less frequent in the non-neoplastic mucosa than at the tumor site. The presence of ras gene mutation in normal appearing mucosa points to a previous exposure which had initiated the multistage process of colorectal carcinogenesis.

Effects of linoleic-Acid on mammary-tumor cell-proliferation are associated with changes in p53 protein expression

A rat mammary tumor cell line maintained in low serum (1%) medium exhibited a slower growth rate, altered cell cycle distribution, decreased DNA synthesis, and increased immunoprecipitable p53, when compared with culture in 10% serum. Addition of linoleic acid (LA; 18:2, n-6) to low serum medium partially restored normal cell cycle distribution, increased synthesis of DNA, and decreased immunoprecipitable p53 to levels normally seen in cells cultured in 10% serum. In contrast, exposure of the cells to docosahexaenoic acid (DHA, 22:6, n-6) induced further suppression of cell proliferation in medium containing 1% serum, and up-regulated expression of p53. The inverse correlation between p53 levels and cell proliferation is consistent with a role for p53 in negative regulation of growth of these tumor cells. The data suggest that growth stimulation of rat mammary tumor cells by LA is mediated in part through modulation of p53 expression.

Functional specialization in proline biosynthesis of melanoma

Proline metabolism is linked to hyperprolinemia, schizophrenia, cutis laxa, and cancer. In the latter case, tumor cells tend to rely on proline biosynthesis rather than salvage. Proline is synthesized from either glutamate or ornithine; both are converted to pyrroline-5-carboxylate (P5C), and then to proline via pyrroline-5-carboxylate reductases (PYCRs). Here, the role of three isozymic versions of PYCR was addressed in human melanoma cells by tracking the fate of (13)C-labeled precursors. Based on these studies we conclude that PYCR1 and PYCR2, which are localized in the mitochondria, are primarily involved in conversion of glutamate to proline. PYCRL, localized in the cytosol, is exclusively linked to the conversion of ornithine to proline. This analysis provides the first clarification of the role of PYCRs to proline biosynthesis.

Vascular normalization by loss of Siah2 results in increased chemotherapeutic efficacy

Tumor hypoxia is associated with resistance to antiangiogenic therapy and poor prognosis. The Siah E3 ubiquitin ligases regulate the hypoxic response pathway by modulating the turnover of the master proangiogenic transcription factor hypoxia-inducible factor-1α (Hif-1α). In this study, we show that genetic deficiency in the Siah family member Siah2 results in vascular normalization and delayed tumor growth in an established transgenic model of aggressive breast cancer. Tumors arising in a Siah2(-/-) genetic background showed increased perfusion and pericyte-associated vasculature, similar to that occurring with antiangiogenic therapy. In support of the role of Siah2 in regulating levels of Hif-1α, expression of angiogenic factors was decreased in Siah2(-/-) tumors. Blood vessel normalization in Siah2(-/-) tumors resulted in an increased response to chemotherapy and prolonged survival. Together, our findings offer a preclinical proof of concept that targeting Siah2 is sufficient to attenuate Hif-1α-mediated angiogenesis and hypoxia signaling, thereby improving responses to chemotherapy.

Siah1/SIP regulates p27(kip1) stability and cell migration under metabolic stress

p27(kip1) has been implicated in cell cycle regulation, functioning as an inhibitor of cyclin-dependent kinase activity. In addition, p27 was also shown to affect cell migration, with accumulation of cytoplasmic p27 associated with tumor invasiveness. However, the mechanism underlying p27 regulation as a cytoplasmic protein is poorly understood. Here we show that glucose starvation induces proteasome-dependent degradation of cytoplasmic p27, accompanied by a decrease in cell motility. We also show that the glucose limitation-induced p27 degradation is regulated through an ubiquitin E3 ligase complex involving Siah1 and SIP/CacyBP. SIP (-/-) embryonic fibroblasts have increased levels of cytosolic p27 and exhibit increased cell motility compared to wild-type cells. These observations suggest that the Siah1/SIP E3 ligase complex regulates cell motility through degradation of p27.

Emerging roles of ATF2 and the dynamic AP1 network in cancer

Cooperation among transcription factors is central for their ability to execute specific transcriptional programmes. The AP1 complex exemplifies a network of transcription factors that function in unison under normal circumstances and during the course of tumour development and progression. This Perspective summarizes our current understanding of the changes in members of the AP1 complex and the role of ATF2 as part of this complex in tumorigenesis.

c-Jun regulates phosphoinositide-dependent kinase 1 transcription: implication for Akt and protein kinase C activities and melanoma tumorigenesis

Mutations in N-RAS and B-RAF, which commonly occur in melanomas, result in constitutive activation of the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated protein kinase (ERK) signaling. Active ERK increases expression and activity of the c-Jun transcription factor, linking ERK and Jun N-terminal kinase (JNK) cascades. Here, we show that c-Jun regulates transcription of phosphoinositide-dependent kinase 1 (PDK1) with a concomitant impact on Akt and protein kinase C (PKC) activity and related substrates. Inhibition of c-Jun reduces PDK1 expression and attenuates Akt and PKC activity, which can be restored by exogenous PDK1. c-Jun regulation of PDK1 in melanoma contributes to growth rate and the ability to form tumors in mice. Correspondingly, increased levels of c-Jun in melanoma cell lines coincide with up-regulation of PDK1 and phosphorylation of PKC and Akt. The identification of c-Jun as a transcriptional regulator of PDK1 expression highlights key mechanisms underlying c-Jun oncogenic activity, and provides new insight into the nature of up-regulated Akt and PKC in melanoma.

Tricking melanoma to self-digest: a deal of a meal!

Melanoma cells acquire multiple genetic and epigenetic alterations that promote their metastasis and resistance to available therapies. In this issue of Cancer Cell, Soengas and colleagues reveal that the induction of endosome-mediated autophagy results in efficient melanoma cell death, thereby offering new potential means for treatment of this devastating cancer.

The ubiquitin ligase Siah2 and the hypoxia response

Growing evidence indicates that ubiquitin ligases play a critical role in the hypoxia response. Among them, Siah2, a RING finger ligase, is an important regulator of pathways activated under hypoxia. Siah2 regulates prolyl hydroxylases PHD3 and 1 under oxygen concentration of 2% to 5%, thereby allowing accumulation of hypoxia-inducible factor (HIF)-1alpha, a master regulator of the hypoxia response within the range of physiological normoxic to mild hypoxic conditions. Growing evidence also indicates an important function for Siah2 in tumor development and progression based on pancreatic cancer, mammary tumor, and melanoma mouse models. This review summarizes our current understanding of Siah2 regulation and function with emphasis on hypoxia and tumorigenesis.

Parkin, PINK1, and DJ-1 form a ubiquitin E3 ligase complex promoting unfolded protein degradation

Mutations in PARKIN, pten-induced putative kinase 1 (PINK1), and DJ-1 are individually linked to autosomal recessive early-onset familial forms of Parkinson disease (PD). Although mutations in these genes lead to the same disease state, the functional relationships between them and how their respective disease-associated mutations cause PD are largely unknown. Here, we show that Parkin, PINK1, and DJ-1 formed a complex (termed PPD complex) to promote ubiquitination and degradation of Parkin substrates, including Parkin itself and Synphilin-1 in neuroblastoma cells and human brain lysates. Genetic ablation of either Pink1 or Dj-1 resulted in reduced ubiquitination of endogenous Parkin as well as decreased degradation and increased accumulation of aberrantly expressed Parkin substrates. Expression of PINK1 enhanced Parkin-mediated degradation of heat shock-induced misfolded protein. In contrast, PD-pathogenic Parkin and PINK1 mutations showed reduced ability to promote degradation of Parkin substrates. This study identified a functional ubiquitin E3 ligase complex consisting of PD-associated Parkin, PINK1, and DJ-1 to promote degradation of un-/misfolded proteins and suggests that their PD-pathogenic mutations impair E3 ligase activity of the complex, which may constitute a mechanism underlying PD pathogenesis.

BI-69A11-mediated inhibition of AKT leads to effective regression of xenograft melanoma

The AKT/PKB pathway plays a central role in tumor development and progression and is often up-regulated in different tumor types, including melanomas. We have recently reported on the in silico approach to identify putative inhibitors for AKT/PKB. Of the reported hits, we selected BI-69A11, a compound which was shown to inhibit AKT activity in in vitro kinase assays. Analysis of BI-69A11 was performed in melanoma cells, a tumor type that commonly exhibits up-regulation of AKT. Treatment of the UACC903 human melanoma cells, harboring the PTEN mutation, with BI-69A11 caused efficient inhibition of AKT S473 phosphorylation with concomitant inhibition of AKT phosphorylation of PRAS40. Treatment of melanoma cells with BI-69A11 also reduced AKT protein expression, which coincided with inhibition of AKT association with HSP-90. BI-69A11 treatment not only caused cell death of melanoma, but also prostate tumor cell lines. Notably, the effect of BI-69A11 on cell death was more pronounced in cells that express an active form of AKT. Significantly, intra-peritoneal injection of BI-69A11 caused effective regression of melanoma tumor xenografts, which coincided with elevated levels of cell death. These findings identify BI-69A11 as a potent inhibitor of AKT that is capable of eliciting effective regression of xenograft melanoma tumors.

The ubiquitin ligase Siah2 regulates tumorigenesis and metastasis by HIF-dependent and -independent pathways

The ubiquitin ligase Siah2 has been shown to regulate prolyl hydroxylase 3 (PHD3) stability with concomitant effect on HIF-1alpha availability. Because HIF-1alpha is implicated in tumorigenesis and metastasis, we used SW1 mouse melanoma cells, which develop primary tumors with a propensity to metastasize, in a syngeneic mouse model to assess a possible role for Siah2 in these processes. Inhibiting Siah2 activity by expressing a peptide designed to outcompete association of Siah2-interacting proteins reduced metastasis through HIF-1alpha without affecting tumorigenesis. Conversely, inhibiting Siah2 activity by means of a dominant-negative Siah2 RING mutant primarily reduced tumorigenesis through the action of Sprouty 2, a negative regulator of Ras signaling. Consistent with our findings, reduced expression of PHD3 and Sprouty2 was observed in more advanced stages of melanoma tumors. Using complementary approaches, our data establish the role of Siah2 in tumorigenesis and metastasis by HIF-dependent and -independent mechanisms.

JAMP optimizes ERAD to protect cells from unfolded proteins

Clearance of misfolded proteins from the ER is central for maintenance of cellular homeostasis. This process requires coordinated recognition, ER-cytosol translocation, and finally ubiquitination-dependent proteasomal degradation. Here, we identify an ER resident seven-transmembrane protein (JAMP) that links ER chaperones, channel proteins, ubiquitin ligases, and 26S proteasome subunits, thereby optimizing degradation of misfolded proteins. Elevated JAMP expression promotes localization of proteasomes at the ER, with a concomitant effect on degradation of specific ER-resident misfolded proteins, whereas inhibiting JAMP promotes the opposite response. Correspondingly, a jamp-1 deleted Caenorhabditis elegans strain exhibits hypersensitivity to ER stress and increased UPR. Using biochemical and genetic approaches, we identify JAMP as important component for coordinated clearance of misfolded proteins from the ER.

ATF2: a transcription factor that elicits oncogenic or tumor suppressor activities

The Activating Transcription Factor (ATF2) gene encodes a transcription factor important for normal cellular development and survival. In addition to its role as a transcription factor, ATF2 functions in the DNA damage response and in control of HAT complex activity. So far genetic changes in ATF2 have not been identified in human tumors. Yet altered expression and subcellular localization of ATF2 are associated with tumor stage and prognosis. Our studies in melanoma tumor models identified oncogenic ATF2 activity correlating with development of this tumor type. Inhibiting ATF2 suffices to impede melanoma development. Yet work in other tumor models, including breast and skin tumors reveals that ATF2, in cooperation with mutated oncogenes or tumor suppressor genes, can also elicit tumor suppressor function. These findings suggest tissue- and tumor-specific function of ATF2. This review summarizes the current understanding of ATF2 regulation and function.

Muscle-epidermis interactions affect exoskeleton patterning in Caenorhabditis elegans

The C. elegans hypodermis is a single epithelial cell layer separated from the musculature by a thin basement membrane on its basal surface. The hypodermis secretes the extracellular material of the cuticle from its apical surface. The regulation of cuticle synthesis and apical secretion is not well understood. UNC-95 is a component of the muscle dense bodies and M-lines, which are integrin-based adhesion complexes required for force transduction to the cuticle. Using gene expression profiling and in vivo assays, we show that, in unc-95 mutant worms, there is an increase in expression levels of a group of hypodermal and pharyngeal genes related to cuticle structure and molting. Moreover, the cuticle structure of unc-95 mutant adult is impaired. Our findings suggest that aberrant force transduction from the structurally impaired muscle attachments across the basement membrane to the underlying hypodermis elicits intercellular signaling that plays a role in regulating cuticle synthesis and patterning.

The ER-bound RING finger protein 5 (RNF5/RMA1) causes degenerative myopathy in transgenic mice and is deregulated in inclusion body myositis

Growing evidence supports the importance of ubiquitin ligases in the pathogenesis of muscular disorders, although underlying mechanisms remain largely elusive. Here we show that the expression of RNF5 (aka RMA1), an ER-anchored RING finger E3 ligase implicated in muscle organization and in recognition and processing of malfolded proteins, is elevated and mislocalized to cytoplasmic aggregates in biopsies from patients suffering from sporadic-Inclusion Body Myositis (sIBM). Consistent with these findings, an animal model for hereditary IBM (hIBM), but not their control littermates, revealed deregulated expression of RNF5. Further studies for the role of RNF5 in the pathogenesis of s-IBM and more generally in muscle physiology were performed using RNF5 transgenic and KO animals. Transgenic mice carrying inducible expression of RNF5, under control of beta-actin or muscle specific promoter, exhibit an early onset of muscle wasting, muscle degeneration and extensive fiber regeneration. Prolonged expression of RNF5 in the muscle also results in the formation of fibers containing congophilic material, blue-rimmed vacuoles and inclusion bodies. These phenotypes were associated with altered expression and activity of ER chaperones, characteristic of myodegenerative diseases such as s-IBM. Conversely, muscle regeneration and induction of ER stress markers were delayed in RNF5 KO mice subjected to cardiotoxin treatment. While supporting a role for RNF5 Tg mice as model for s-IBM, our study also establishes the importance of RNF5 in muscle physiology and its deregulation in ER stress associated muscular disorders.

Roadmap for new opportunities in melanoma research

Investigators representing all major melanoma research areas present an overview of the most important challenges for the field. Four major research areas are covered plus the training of new investigators. For each area we first describe the present status, its strengths and weaknesses, and then outline specific recommendations. In basic research of melanoma, we outline the pertinent issues for melanoma classification, understanding melanocyte development and transformation, melanoma resistance, tumor microenvironment, metastasis, animal models, immune response, and blood and tissue diagnostics. In clinical research we provide an overview of the current challenges and the strategies for characterization, monitoring, and therapy. It will be important to develop strong research and clinical infrastructures by establishing tumor banks, identifying and validating biomarkers, developing new imaging techniques, and increasing multidisciplinary collaboration and communication. To strengthen the field we need to recruit both young and established investigators and foster career development plans that cover all disciplines. Recent research advances provide significant opportunities to have a major impact on this devastating disease. This group provides recommendations for both short- and long-term strategies that build on research strengths and opportunities established by the many members of the research community.

Suppressor role of activating transcription factor 2 (ATF2) in skin cancer

Activating transcription factor 2 (ATF2) regulates transcription in response to stress and growth factor stimuli. Here, we use a mouse model in which ATF2 was selectively deleted in keratinocytes. Crossing the conditionally expressed ATF2 mutant with K14-Cre mice (K14.ATF2(f/f)) resulted in selective expression of mutant ATF2 within the basal layer of the epidermis. When subjected to a two-stage skin carcinogenesis protocol [7,12-dimethylbenz[a]anthracene/phorbol 12-tetradecanoate 13-acetate (DMBA/TPA)], K14.ATF2(f/f) mice showed significant increases in both the incidence and prevalence of papilloma development compared with the WT ATF2 mice. Consistent with these findings, keratinocytes of K14.ATF2(f/f) mice exhibit greater anchorage-independent growth compared with ATF2 WT keratinocytes. Papillomas of K14.ATF2(f/f) mice exhibit reduced expression of presenilin1, which is associated with enhanced beta-catenin and cyclin D1, and reduced Notch1 expression. Significantly, a reduction of nuclear ATF2 and increased beta-catenin expression were seen in samples of squamous and basal cell carcinoma, as opposed to normal skin. Our data reveal that loss of ATF2 transcriptional activity serves to promote skin tumor formation, thereby indicating a suppressor activity of ATF2 in skin tumor formation.

ATF2 on the double - activating transcription factor and DNA damage response protein

Signal transduction pathways play a key role in the regulation of key cellular processes, including survival and death. Growing evidence points to changes in signaling pathway that occur during skin tumor development and progression. Such changes impact the activity of downstream substrates, including transcription factors. The activating transcription factor 2 (ATF2) has been implicated in malignant and non-malignant skin tumor developments. ATF2 mediates both transcription and DNA damage control, through its phosphorylation by JNK/p38 or ATM/ATR respectively. Here, we summarize our present understanding of ATF2 regulation, function and contribution to malignant and non-malignant skin tumor development.