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Cysteine plays critical roles in cellular biosynthesis, enzyme catalysis, and redox metabolism. The intracellular cysteine pool can be sustained by cystine uptake or de novo synthesis from serine and homocysteine. Demand for cysteine is increased during tumorigenesis for generating glutathione to deal with oxidative stress. While cultured cells have been shown to be highly dependent on exogenous cystine for proliferation and survival, how diverse tissues obtain and use cysteine in vivo has not been characterized. We comprehensively interrogated cysteine metabolism in normal murine tissues and cancers that arise from them using stable isotope 13C1-serine and 13C6-cystine tracing. De novo cysteine synthesis was highest in normal liver and pancreas and absent in lung tissue, while cysteine synthesis was either inactive or downregulated during tumorigenesis. In contrast, cystine uptake and metabolism to downstream metabolites was a universal feature of normal tissues and tumors. However, differences in glutathione labeling from cysteine were evident across tumor types. Thus, cystine is a major contributor to the cysteine pool in tumors, and glutathione metabolism is differentially active across tumor types. Significance: Stable isotope 13C1-serine and 13C6-cystine tracing characterizes cysteine metabolism in normal murine tissues and its rewiring in tumors using genetically engineered mouse models of liver, pancreas, and lung cancers.

TP53 mutation is the most frequent genetic event in head and neck squamous cell carcinoma (HNSCC), found in more than 80% of patients with human papillomavirus–negative disease. As mutations in the TP53 gene are associated with worse outcomes in HNSCC, novel therapeutic approaches are needed for patients with TP53-mutated tumors. The National Cancer Institute sponsored a Clinical Trials Planning Meeting to address the issues of identifying and developing clinical trials for patients with TP53 mutations. Subcommittees, or breakout groups, were tasked with developing clinical studies in both the locally advanced and recurrent and/or metastatic (R/M) disease settings as well as considering signal-seeking trial designs. A fourth breakout group was focused on identifying and standardizing biomarker integration into trial design; this information was provided to the other breakout groups prior to the meeting to aid in study development. A total of 4 concepts were prioritized to move forward for further development and implementation. This article summarizes the proceedings of the Clinical Trials Planning Meeting with the goal of developing clinical trials for patients with TP53-mutant HNSCC that can be conducted within the National Clinical Trials Network.

Figure S4 contains the total metabolite levels in healthy mouse tissues related to Figure 3

Cysteine plays critical roles in cellular biosynthesis, enzyme catalysis, and redox metabolism. The intracellular cysteine pool can be sustained by cystine uptake or de novo synthesis from serine and homocysteine. Demand for cysteine is increased during tumorigenesis for generating glutathione to deal with oxidative stress. While cultured cells have been shown to be highly dependent on exogenous cystine for proliferation and survival, how diverse tissues obtain and use cysteine in vivo has not been characterized. We comprehensively interrogated cysteine metabolism in normal murine tissues and cancers that arise from them using stable isotope 13C1-serine and 13C6-cystine tracing. De novo cysteine synthesis was highest in normal liver and pancreas and absent in lung tissue, while cysteine synthesis was either inactive or downregulated during tumorigenesis. In contrast, cystine uptake and metabolism to downstream metabolites was a universal feature of normal tissues and tumors. However, differences in glutathione labeling from cysteine were evident across tumor types. Thus, cystine is a major contributor to the cysteine pool in tumors, and glutathione metabolism is differentially active across tumor types.Significance:Stable isotope 13C1-serine and 13C6-cystine tracing characterizes cysteine metabolism in normal murine tissues and its rewiring in tumors using genetically engineered mouse models of liver, pancreas, and lung cancers.

Distinct lung stem cells give rise to lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). ΔNp63, the p53 family member and p63 isoform, guides the maturation of these stem cells through the regulation of their self-renewal and terminal differentiation; however, the underlying mechanistic role regulated by ∆Np63 in lung cancer development has remained elusive. By utilizing a ΔNp63-specific conditional knockout mouse model and xenograft models of LUAD and LUSC, we found that ∆Np63 promotes non-small cell lung cancer by maintaining the lung stem cells necessary for lung cancer cell initiation and progression in quiescence. ChIP-seq analysis of lung basal cells, alveolar type 2 (AT2) cells, and LUAD reveals robust ∆Np63 regulation of a common landscape of enhancers of cell identity genes. Importantly, one of these genes, BCL9L, is among the enhancer associated genes regulated by ∆Np63 in Kras-driven LUAD and mediates the oncogenic effects of ∆Np63 in both LUAD and LUSC. Accordingly, high BCL9L levels correlate with poor prognosis in LUAD patients. Taken together, our findings provide a unifying oncogenic role for ∆Np63 in both LUAD and LUSC through the regulation of a common landscape of enhancer associated genes., The mechanistic role regulated by the oncogene ∆Np63 in lung cancer development is currently unclear. Here, the authors show that ΔNp63 is pro-tumorigenic in lung adenocarcinoma as well as squamous cell carcinoma, and maintains lung cancer progenitor cells via regulation of super-enhancer-associated genes, including BCL9L

Supplementary information includes Supplementary figure legends, Materials and Methods, and Reference

TAp63-/- versus wildtype keratinocytes signature analysis

Figure S3. Pathways regulated by ∆Np63-induced and -repressed genes.

Supplementary methods tables and figures of Pro-tumorigenic function of HP1γ for lung adenocarcinoma

TP63 is required to maintain stem cell pluripotency and suppresses the metastatic potential of cancer cells through multiple mechanisms. These functions are differentially regulated by individual isoforms, necessitating a deeper understanding of how the distinct transcriptional programs controlled by these isoforms affect cancer progression and outcomes. In this study, we conducted a pan-cancer analysis of The Cancer Genome Atlas to identify transcriptional networks regulated by TAp63 and ΔNp63 using transcriptomes derived from epidermal cells of TAp63−/− and ΔNp63−/− mice. Analysis of 17 cancer developmental and 27 cancer progression signatures revealed a consistent tumor suppressive pattern for TAp63. In contrast, we identified pleiotropic roles for ΔNp63 in tumor development and found that its regulation of Lef1 was crucial for its oncogenic role. ΔNp63 performed a distinctive role as suppressor of tumor progression by cooperating with TAp63 to modulate key biological pathways, principally cell-cycle regulation, extracellular matrix remodeling, epithelial-to-mesenchymal transition, and the enrichment of pluripotent stem cells. Importantly, these TAp63 and ΔNp63 signatures prognosticated progression and survival, even within specific stages, in bladder and renal carcinomas as well as low-grade gliomas. These data describe a novel approach for understanding transcriptional activities of TP63 isoforms across a large number of cancer types, potentially enabling identification of patient subsets most likely to benefit from therapies predicated on manipulating specific TP63 isoforms.Significance: Transcriptomic analyses of patient samples and murine knockout models highlight the prognostic role of several critical mechanisms of tumor suppression that are regulated by TP63. Cancer Res; 78(2); 451–62. ©2017 AACR.

This file contains the following: Supplementary Figure 1: Representative H&E staining and immunohistochemistry for keratin 5 of a metastasis in the lung of a tumor-bearing TAp63-/- mouse. Supplementary Figure 2: TAp63-deficient tumors exhibit deregulated mRNA and miRNA expression. Supplementary Figure 3: TAp63-regulated miR-30c-2* and miR-497-5p suppresses cuSCC through induction of cell death and cell cycle arrest. Supplementary Figure 4: Identification of miRNA targets through the use of TMT-LC-MS/MS. Supplementary Figure 5: Inhibition of miR-30c-2-3p and miR-497-5p targets affects cuSCC cell proliferation and survival. Supplementary Figure 6: AURKA is a viable therapeutic target in cuSCC. Supplementary Methods and Materials. Supplementary References.

Myeloid-derived suppressor cells (MDSC) represent a primary mechanism of immune evasion in tumors and have emerged as a major obstacle for cancer immunotherapy. The immunoinhibitory activity of MDSC is tightly regulated by the tumor microenvironment and occurs through mechanistic mediators that remain unclear. Here, we elucidated the intrinsic interaction between the expression of AMP-activated protein kinase alpha (AMPKα) and the immunoregulatory activity of MDSC in tumors. AMPKα signaling was increased in tumor-MDSC from tumor-bearing mice and patients with ovarian cancer. Transcription of the Ampkα1-coding gene, Prkaa1, in tumor-MDSC was induced by cancer cell–derived granulocyte–monocyte colony-stimulating factor (GM-CSF) and occurred in a Stat5–dependent manner. Conditional deletion of Prkaa1 in myeloid cells, or therapeutic inhibition of Ampkα in tumor-bearing mice, delayed tumor growth, inhibited the immunosuppressive potential of MDSC, triggered antitumor CD8+ T-cell immunity, and boosted the efficacy of T-cell immunotherapy. Complementarily, therapeutic stimulation of AMPKα signaling intrinsically promoted MDSC immunoregulatory activity. In addition, Prkaa1 deletion antagonized the differentiation of monocytic-MDSC (M-MDSC) to macrophages and re-routed M-MDSC, but not granulocytic-MDSC (PMN-MDSC), into cells that elicited direct antitumor cytotoxic effects through nitric oxide synthase 2-mediated actions. Thus, our results demonstrate the primary role of AMPKα1 in the immunosuppressive effects induced by tumor-MDSC and support the therapeutic use of AMPK inhibitors to overcome MDSC-induced T-cell dysfunction in cancer.Significance:AMPKα1 regulates the immunosuppressive activity and differentiation of tumor-MDSC, suggesting AMPK inhibition as a potential therapeutic strategy to restore protective myelopoiesis in cancer.

Table S4. PCA scores for each patient in the four COCA molecular subtypes from TCGA.

This file contains the Supplementary Figures 1-5. Supplementary Figure 1. Phospho-AMPKα1 levels increase in tumor-MDSC. Supplementary Figure 2. Tumor cell-derived GM-CSF triggers Ampkα expression in MDSC through Stat-5 activation. Supplementary Figure 3. MDSC in human myeloid progenitors treated with GM-CSF plus IL-6 for 7 days. Supplementary Figure 4. Extended survival of Prkaa1-null mice bearing ovarian tumors. Supplementary Figure 5. Effects of Prkaa1KO PMN-MDSC in tumor growth.

Supplementary Figure 1. Pathways enriched in PCSSTAp63 and PCSSÎ"Np63 signatures. a-b, -Log10(p-value) of pathways enriched in (a) PCSSTAp63 and (b) PCSSÎ"Np63 signatures. Supplementary Figure 2. Differential expression of Î"Np63 in MCF10-CA1D, HCC95 and Caki-1 cells. a-b, (a) Western blot analysis for Î"Np63 expression in MCF10-CA1D, HCC95 and Caki-1 cells. NHEK-WT and NHEK-shÎ"Np63 were used as positive and negative control for Î"Np63 expression. Actin was used as internal loading control. (b) Western blot analysis for either Î"Np63 knockdown efficiency in MCF10-CA1D and HCC95 treated with either siC or siÎ"Np63, or Î"Np63 overexpression in Caki-1 cells treated with either empty vector (EV) or Î"Np63α-overexpressing plasmid (Î"Np63α). Supplementary Figure 3: Lef1 is a downstream target of Î"Np63 in MCF10-CA1D and HCC95. a-e, (a) Western blot analysis for Î"Np63 and Lef1 expression in MCF10-CA1D and HCC95 cells treated with siÎ"Np63 and Lef1-overexpressing plasmid (Lef1). Actin was used as internal loading control. (b-e) Quantification and fluorescence representative images of EdU (green) incorporation of indicated cell lines. Data are mean {plus minus} SD, n = 3. Asterisks indicate statistical significance, p < 0.05 versus siC or siÎ"Np63, two-tailed t test. Supplementary Figure 4. Lef1 is a downstream target of Î"Np63 in Caki-1. a-j, (a) qRT-PCR for Lef1 in Caki-1 cells expressing either empty vector (EV) or Î"Np63α-overexpressing plasmid (Î"Np63α). Asterisks indicate statistical significance, p < 0.005 two-tailed t test. (b) Western blot analysis for Lef1 in Caki-1 cells expressing either empty vector (EV) or Î"Np63α-overexpressing plasmid (Î"Np63α). Actin was used as internal loading control. (c) Western blot analysis for Lef1 overexpression efficiency in Caki-1 cells expressing either with empty vector (EV) or Î"Np63α-overexpressing plasmid (Î"Np63α). Actin was used as internal loading control. (d-e) Quantification and bright field representative images of anchorage-independent colony formation of indicated cell lines in soft agar assay (per 10X field). Data are mean {plus minus} SD, n = 3. (f) Western blot analysis for Î"Np63 and Lef1 expression in Caki-1 cells treated with Î"Np63α-overexpressing plasmid (Î"Np63α) and siLef1. Actin was used as internal loading control. (g-h) Quantification and fluorescence representative images of EdU (green) incorporation of indicated cell lines. Data are mean {plus minus} SD, n = 3. (i-j) Quantification and bright field representative images of anchorage-independent colony formation of indicated cell lines in soft agar assay (per 10X field). Data are mean {plus minus} SD, n = 3. Asterisks indicate statistical significance, p < 0.0005 versus EV, two-tailed t test. Supplementary Figure 5. Circos plots of the overlap and expression of TAp63 and Î"Np63 signatures with progression signatures of BLCA, KIRC, KIRP and LGG. a-b. (a) Expression profile of genes common to TAp63-/- signature and each cancer progression signature. (b) Expression profile of genes common to Î"Np63-/- signature and each cancer progression signature. Supplementary Figure 6. Validation of TAp63 and Î"Np63 activities in independent KIRC cohorts. a-b, (a) TAp63KIRC and (b) Î"Np63KIRC activities in independent cohort of KIRC across high and low stages. Supplementary Figure 7. Common pathways enriched in corresponding TAp63 and Î"Np63 signatures of BLCA, KIRC, KIRP and LGG. a-f. (a) -Log10(p-value) of pathways enriched in TAp63KIRC, TAp63KIRP and TAp63LGG. (b) -Log10(p-value) of pathways enriched in Î"Np63BLCA, Î"Np63KIRC, Î"Np63KIRP and Î"Np63LGG. ClueGo plots of overlap in corresponding TAp63 and Î"Np63 in (c) BLCA, (d) KIRC, (e) KIRP and (f) LGG progression signatures. Supplementary Figure 8. Î"Np63CTHRC1/COL5A1 in tumor progression of BLCA, KIRC, KIRP and LGG. a-b, (a) Activity and (b) Kaplan-Meier survival of BLCA, KIRC, KIRP and LGG with respect to Î"Np63CTHRC1/COL5A1. Supplementary Figure 9. Survival of BLCA, KIRC, KIRP and LGG cancers with respect to bottom and top quartile gene expression of (a) CTHRC1 and (b) COL5A1.

Components of tumor progression TAp63 (4.1) and Î"Np63 (4.2) signatures used in this study. Pathways enriched in TAp63 (4.3) and Î"Np63 (4.4) tumor progression signatures.

Components of tumor development TAp63 (3.1) and Î"Np63 (3.2) signatures used in this study. Pathways enriched in TAp63 (3.3) and Î"Np63 (3.4) tumor development signatures.

ΔNp63 is a transcription factor of the p53 family and has crucial functions in normal development and disease. The expression pattern of ΔNp63 in human cancer suggests dynamic regulation of this isoform during cancer progression and metastasis. Many primary and metastatic tumors express high levels of ΔNp63, while ΔNp63 loss is crucial for tumor dissemination, indicating an oscillatory expression of ΔNp63 during cancer progression. Here, we use genetically engineered orthotopic mouse models of breast cancer to show that while depletion of ΔNp63 inhibits primary mammary adenocarcinoma development, oscillatory expression of ΔNp63 in established tumors is crucial for metastatic dissemination in breast cancer. A TGFβ-regulated miRNA network acted as upstream regulators of this oscillatory expression of ΔNp63 during cancer progression. This work sheds light on the pleiotropic roles of ΔNp63 in cancer and unveils critical functions of TGFβ in the metastatic process.Significance:This study unveils TGFβ signaling and a network of four miRNAs as upstream regulators of ΔNp63, providing key information for the development of therapeutic strategies to treat cancers that commonly overexpress ΔNp63.

Lung adenocarcinoma is a major form of lung cancer, which is the leading cause of cancer death. Histone methylation reader proteins mediate the effect of histone methylation, a hallmark of epigenetic and transcriptional regulation of gene expression. However, their roles in lung adenocarcinoma are poorly understood. Here, our bioinformatic screening and analysis in search of a lung adenocarcinoma–promoting histone methylation reader protein show that heterochromatin protein 1γ (HP1γ; also called CBX3) is among the most frequently overexpressed and amplified histone reader proteins in human lung adenocarcinoma, and that high HP1γ mRNA levels are associated with poor prognosis in patients with lung adenocarcinoma. In vivo depletion of HP1γ reduced K-RasG12D–driven lung adenocarcinoma and lengthened survival of mice bearing K-RasG12D–induced lung adenocarcinoma. HP1γ and its binding activity to methylated histone H3 lysine 9 were required for the proliferation, colony formation, and migration of lung adenocarcinoma cells. HP1γ directly repressed expression of the transcription-repressive regulators NCOR2 and ZBTB7A. Knockdown of NCOR2 or ZBTB7A significantly restored defects in proliferation, colony formation, and migration in HP1γ-depleted lung adenocarcinoma cells. Low NCOR2 or ZBTB7A mRNA levels were associated with poor prognosis in patients with lung adenocarcinoma and correlated with high HP1γ mRNA levels in lung adenocarcinoma samples. NCOR2 and ZBTB7A downregulated expression of tumor-promoting factors such as ELK1 and AXL, respectively. These findings highlight the importance of HP1γ and its reader activity in lung adenocarcinoma tumorigenesis and reveal a unique lung adenocarcinoma–promoting mechanism in which HP1γ downregulates NCOR2 and ZBTB7A to enhance expression of protumorigenic genes.Significance: Direct epigenetic repression of the transcription-repressive regulators NCOR2 and ZBTB7A by the histone reader protein HP1γ leads to activation of protumorigenic genes in lung adenocarcinoma. Cancer Res; 78(14); 3834–48. ©2018 AACR.

TAp63 is a p53 family member and potent tumor and metastasis suppressor. Here, we show that TAp63−/− mice exhibit an increased susceptibility to ultraviolet radiation–induced cutaneous squamous cell carcinoma (cuSCC). A human-to-mouse comparison of cuSCC tumors identified miR-30c-2* and miR-497 as underexpressed in TAp63-deficient cuSCC. Reintroduction of these miRNAs significantly inhibited the growth of cuSCC cell lines and tumors. Proteomic profiling of cells expressing either miRNA showed downregulation of cell-cycle progression and mitosis-associated proteins. A mouse to human and cross-platform comparison of RNA-sequencing and proteomics data identified a 7-gene signature, including AURKA, KIF18B, PKMYT1, and ORC1, which were overexpressed in cuSCC. Knockdown of these factors in cuSCC cell lines suppressed tumor cell proliferation and induced apoptosis. In addition, selective inhibition of AURKA suppressed cuSCC cell proliferation, induced apoptosis, and showed antitumor effects in vivo. Finally, treatment with miR-30c-2* or miR-497 miRNA mimics was highly effective in suppressing cuSCC growth in vivo. Our data establish TAp63 as an essential regulator of novel miRNAs that can be therapeutically targeted for potent suppression of cuSCC.Significance:This study provides preclinical evidence for the use of miR-30c-2*/miR-497 delivery and AURKA inhibition in the treatment of cuSCC, which currently has no FDA-approved targeted therapies.See related commentary by Parrales and Iwakuma, p. 2439

Supplementary Table 1: Differentially expressed genes in TAp63-/- cuSCC vs. TAp63-/- skin Supplementary Table 2: Differentially expressed miRNAs in TAp63-/- cuSCC vs. TAp63-/- skin Supplementary Table 3: microRNA-mRNA pair analysis of TAp63-/- cuSCC vs. TAp63-/- skin: Underexpressed miRNAs and overexpressed mRNAs. Supplementary Table 4: microRNA-mRNA pair analysis of TAp63-/- cuSCC vs. TAp63-/- skin: Overexpressed miRNAs and underexpressed mRNAs. Supplementary Table 5: Differentially expressed mRNAs from TAp63-/- cuSCC vs cuSCC and Human cuSCC vs. skin. Supplementary Table 6: Differentially expressed miRNAs from TAp63-/- cuSCC vs cuSCC and Human cuSCC vs. skin. Supplementary Table 7: GSEA of common differentially expressed mRNAs in TAp63-/- cuSCC and human cuSCC. Supplementary Table 8: Differentially expressed proteins in miR-30c-2* mimic transfected COLO16 cells measured by TMT-6-plex LC-MS/MS. Supplementary Table 9: Differentially expressed proteins in miR-497 mimic transfected COLO16 cells measured by TMT-6-plex LC-MS/MS. Supplementary Table 10: miRNA target prediction of corresponding mRNAs for the differentially expressed proteins in the miR-30c-2* transfected COLO16 cells. Supplementary Table 11: miRNA target prediction of corresponding mRNAs for the differentially expressed proteins in the miR-497 transfected COLO16 cells. Supplementary Table 12: Overexpressed mRNAs in both mouse TAp63-/- cuSCC and human cuSCC RNA-Seq signatures

Normalized enriched scores from GSEA results across developmental and progression cancer signatures in light of TAp63 and Î"Np63 transcriptome profiles.

Supplementary table S1 of Pro-tumorigenic function of HP1γ for lung adenocarcinoma

This file contains the Supplementary legends describing the Supplementary Figures 1-5.

The major clinical problem in human cancer is metastasis. Metastases are the cause of 90% of human cancer deaths. TAp63 is a critical suppressor of tumorigenesis and metastasis. ΔNp63 acts as a dominant-negative inhibitor to block the function of p53 and TAp63. Although several ubiquitin E3 ligases have been reported to regulate p63 stability, the mechanism of p63 regulation remains partially understood. Herein, we show that CHIP, an E3 ligase with a U-box domain, physically interacts with p63 and promotes p63 degradation. Notably, Hsp70 depletion by siRNA stabilizes TAp63 in H1299 cells and destabilizes ΔNp63 in SCC9 cells. Loss of Hsp70 results in a reduction in the TAp63-CHIP interaction in H1299 cells and an increase in the interaction between ΔNp63 and CHIP in SCC9 cells. Our results reveal that Hsp70 acts as a molecular switch to control CHIP-mediated ubiquitination and degradation of p63 isoforms. Furthermore, regulation of p63 by the Hsp70-CHIP axis contributes to the migration and invasion of tumor cells. Hence, our findings demonstrate that Hsp70 is a crucial regulator of CHIP-mediated ubiquitination and degradation of p63 isoforms and identify a new pathway for maintaining TAp63 or ΔNp63 stability in cancers.

In 1990, Baker and colleagues reported their seminal findings in Cancer Research focusing on the transition from adenoma to carcinoma of the colon. By sequencing the TP53 locus in 58 colorectal tumors (25 adenomas and 33 carcinomas) and measuring its allelic deletions, they discovered that this transition requires the loss of one TP53 allele and the mutation of the other one. Here, we discuss how this landmark discovery shed a new light on p53 mutations, prompting the generation of novel mouse models that definitively proved the mutant p53 gain-of-function hypothesis suggested by these results. Finally, we evaluate the implications that the Vogelstein model of cancer progression had on numerous aspects of cancer biology and cancer care, including the characterization of tumor evolution and the response to therapy, and how it ultimately contributed to the wider adoption of early detection screenings and personalized medicine. See related article by Baker and colleagues, Cancer Res 1990;50:7717–22

TAp63 is a p53 family member and potent tumor and metastasis suppressor. Here, we show that TAp63−/− mice exhibit an increased susceptibility to ultraviolet radiation–induced cutaneous squamous cell carcinoma (cuSCC). A human-to-mouse comparison of cuSCC tumors identified miR-30c-2* and miR-497 as underexpressed in TAp63-deficient cuSCC. Reintroduction of these miRNAs significantly inhibited the growth of cuSCC cell lines and tumors. Proteomic profiling of cells expressing either miRNA showed downregulation of cell-cycle progression and mitosis-associated proteins. A mouse to human and cross-platform comparison of RNA-sequencing and proteomics data identified a 7-gene signature, including AURKA, KIF18B, PKMYT1, and ORC1, which were overexpressed in cuSCC. Knockdown of these factors in cuSCC cell lines suppressed tumor cell proliferation and induced apoptosis. In addition, selective inhibition of AURKA suppressed cuSCC cell proliferation, induced apoptosis, and showed antitumor effects in vivo. Finally, treatment with miR-30c-2* or miR-497 miRNA mimics was highly effective in suppressing cuSCC growth in vivo. Our data establish TAp63 as an essential regulator of novel miRNAs that can be therapeutically targeted for potent suppression of cuSCC. Significance: This study provides preclinical evidence for the use of miR-30c-2*/miR-497 delivery and AURKA inhibition in the treatment of cuSCC, which currently has no FDA-approved targeted therapies. See related commentary by Parrales and Iwakuma, p. 2439

Summary The heterogeneous cell types of the tumor-immune microenvironment (TIME) play key roles in determining cancer progression, metastasis and response to treatment. We report the development of TIMEx, a novel TIME deconvolution method emphasizing on estimating infiltrating immune cells for bulk transcriptomics using pan-cancer single-cell RNA-seq signatures. We also implemented a comprehensive, user-friendly web-portal for users to evaluate TIMEx and other deconvolution methods with bulk transcriptomic profiles. Availability and implementation TIMEx web-portal is freely accessible at http://timex.moffitt.org. Supplementary information Supplementary data are available at Bioinformatics online.

The tumor immune microenvironment (TIME) encompasses many heterogeneous cell types that engage in extensive crosstalk among the cancer, immune, and stromal components. The spatial organization of these different cell types in TIME could be used as biomarkers for predicting drug responses, prognosis and metastasis. Recently, deep learning approaches have been widely used for digital histopathology images for cancer diagnoses and prognoses. Furthermore, some recent approaches have attempted to integrate spatial and molecular omics data to better characterize the TIME. In this review we focus on machine learning-based digital histopathology image analysis methods for characterizing tumor ecosystem. In this review, we will consider three different scales of histopathological analyses that machine learning can operate within: whole slide image (WSI)-level, region of interest (ROI)-level, and cell-level. We will systematically review the various machine learning methods in these three scales with a focus on cell-level analysis. We will provide a perspective of workflow on generating cell-level training data sets using immunohistochemistry markers to “weakly-label” the cell types. We will describe some common steps in the workflow of preparing the data, as well as some limitations of this approach. Finally, we will discuss future opportunities of integrating molecular omics data with digital histopathology images for characterizing tumor ecosystem.

Abstract As a key component of the RNA-induced silencing complex (RISC), Argonaute2 (Ago2) exhibits a dual function regulatory role in tumor progression. However, the mechanistic basis of differential regulation remains elusive. p63 is a homolog of the tumor suppressor p53. p63 isoforms play a critical role in tumorigenesis and metastasis. Herein, we show that p63 isoforms physically interact with and stabilize Ago2. Expression of p63 isoforms increases the levels of Ago2 protein, while depletion of p63 isoforms by shRNA decreases Ago2 protein levels. p63 strongly guides Ago2 dual functions in vitro and in vivo. Ectopic expression of the miR-144/451 cluster increases p63 protein levels; TAp63 transactivates the miR-144/451 cluster, forming a positive feedback loop. Notably, miR-144 activates p63 by directly targeting Itch, an E3 ligase of p63. Ectopic expression of miR-144 induces apoptosis in H1299 cells. miR-144 enhances TAp63 tumor suppressor function and inhibits cell invasion. Our findings uncover a novel function of p63 linking the miRNA-144 cluster and the Ago2 pathway. Facts and questions Identification of Ago2 as a p63 target. Ago2 exhibits a dual function regulatory role in tumor progression; however, the molecular mechanism of Ago2 regulation remains unknown. p63 strongly guides Ago2 dual functions in vitro and in vivo. Unraveling a novel function of p63 links the miRNA-144 cluster and the Ago2 pathway.

Tumours often grow entangled among neurons, which makes the cancer difficult to treat. The finding that cancer cells hijack neighbouring neurons to promote tumour growth suggests new therapeutic targets. Head and neck cancers drive the formation and reprogramming of neurons.

The tumour suppressor p53 and its paralogues, p63 and p73, are essential to maintain cellular homoeostasis and the integrity of the cell’s genetic material, thus meriting the title of ‘guardians of the genome’. The p53 family members are transcription factors and fulfill their activities by controlling the expression of protein-coding and non-coding genes. Here, we review how the latter group transcended from the ‘dark matter’ of the transcriptome, providing unexpected and intriguing anti-cancer therapeutic strategies.

Myeloid-derived suppressor cells (MDSC) represent a primary mechanism of immune evasion in tumors and have emerged as a major obstacle for cancer immunotherapy. The immunoinhibitory activity of MDSC is tightly regulated by the tumor microenvironment and occurs through mechanistic mediators that remain unclear. Here, we elucidated the intrinsic interaction between the expression of AMP-activated protein kinase alpha (AMPKα) and the immunoregulatory activity of MDSC in tumors. AMPKα signaling was increased in tumor-MDSC from tumor-bearing mice and patients with ovarian cancer. Transcription of the Ampkα1-coding gene, Prkaa1, in tumor-MDSC was induced by cancer cell–derived granulocyte–monocyte colony-stimulating factor (GM-CSF) and occurred in a Stat5–dependent manner. Conditional deletion of Prkaa1 in myeloid cells, or therapeutic inhibition of Ampkα in tumor-bearing mice, delayed tumor growth, inhibited the immunosuppressive potential of MDSC, triggered antitumor CD8+ T-cell immunity, and boosted the efficacy of T-cell immunotherapy. Complementarily, therapeutic stimulation of AMPKα signaling intrinsically promoted MDSC immunoregulatory activity. In addition, Prkaa1 deletion antagonized the differentiation of monocytic-MDSC (M-MDSC) to macrophages and re-routed M-MDSC, but not granulocytic-MDSC (PMN-MDSC), into cells that elicited direct antitumor cytotoxic effects through nitric oxide synthase 2-mediated actions. Thus, our results demonstrate the primary role of AMPKα1 in the immunosuppressive effects induced by tumor-MDSC and support the therapeutic use of AMPK inhibitors to overcome MDSC-induced T-cell dysfunction in cancer. Significance: AMPKα1 regulates the immunosuppressive activity and differentiation of tumor-MDSC, suggesting AMPK inhibition as a potential therapeutic strategy to restore protective myelopoiesis in cancer.

Background Over 96% of high‐grade ovarian carcinomas and 50% of all cancers are characterized by alterations in the p53 gene. Therapeutic strategies to restore and/or reactivate the p53 pathway have been challenging. By contrast, p63, which shares many of the downstream targets and functions of p53, is rarely mutated in cancer. Methods A novel strategy is presented for circumventing alterations in p53 by inducing the tumor‐suppressor isoform TAp63 (transactivation domain of tumor protein p63) through its direct downstream target, microRNA‐130b (miR‐130b), which is epigenetically silenced and/or downregulated in chemoresistant ovarian cancer. Results Treatment with miR‐130b resulted in: 1) decreased migration/invasion in HEYA8 cells (p53 wild‐type) and disruption of multicellular spheroids in OVCAR8 cells (p53‐mutant) in vitro, 2) sensitization of HEYA8 and OVCAR8 cells to cisplatin (CDDP) in vitro and in vivo, and 3) transcriptional activation of TAp63 and the B‐cell lymphoma (Bcl)‐inhibitor B‐cell lymphoma 2‐like protein 11 (BIM). Overexpression of TAp63 was sufficient to decrease cell viability, suggesting that it is a critical downstream effector of miR‐130b. In vivo, combined miR‐130b plus CDDP exhibited greater therapeutic efficacy than miR‐130b or CDDP alone. Mice that carried OVCAR8 xenograft tumors and were injected with miR‐130b in 1,2‐dioleoyl‐sn‐glycero‐3‐phosphatidylcholine (DOPC) liposomes had a significant decrease in tumor burden at rates similar to those observed in CDDP‐treated mice, and 20% of DOPC–miR‐130b plus CDDP‐treated mice were living tumor free. Systemic injections of scL–miR‐130b plus CDDP in a clinically tested, tumor‐targeted nanocomplex (scL) improved survival in 60% and complete remissions in 40% of mice that carried HEYA8 xenografts. Conclusions The miR‐130b/TAp63 axis is proposed as a new druggable pathway that has the potential to uncover broad‐spectrum therapeutic options for the majority of p53‐altered cancers., This study uncovered a new feed‐forward loop that involves tumor protein p53 family member TAp63 and its downstream target microRNA 130b (miR‐130b). Injection of miR‐130b using 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine liposomes (nontargeted) and a clinically tested, tumor‐targeted nanocomplex (scL) resulted in significantly decreased tumor burden and improved overall survival, suggesting that the miR‐130b/TAp63 tumor‐suppressor axis could open up novel therapeutic options for many cancers with alterations in the p53 gene and/or pathway.

Despite aggressive combination chemotherapy and surgery, outcomes for patients with osteosarcoma have remained stagnant for more than 25 years, and numerous clinical trials have identified no new therapies. p53 deletion or mutation is found in more than 80% of osteosarcoma tumors. In p53-deficient cancers with structurally altered p63 and p73, interfering with tumor cell metabolism using Pramlintide (an FDA-approved drug for type 2 diabetes) results in tumor regression. Pramlintide response is mediated through upregulation of islet amyloid polypeptide (IAPP). Here, we showed that osteosarcoma cells have altered p63, p73, and p53, and decreased IAPP expression but have the two main IAPP receptors, CalcR and RAMP3, which inhibit glycolysis and induce apoptosis. We showed that in osteosarcoma cells with high- or mid-range glycolytic activity, Pramlintide decreased cell glycolysis, resulting in decreased proliferation and increased apoptosis in vitro. In contrast, Pramlintide had no effect in osteosarcoma cells with low glycolytic activity. Using a subcutaneous osteosarcoma mouse model, we showed that intratumoral injection of Pramlintide-induced tumor regression. Tumor sections showed increased apoptosis and a decrease in Ki-67 and HIF-1α. These data suggest that in osteosarcoma cells with altered p53, p63, and p73 and a high glycolytic function, Pramlintide therapy can modulate metabolic programming and inhibit tumor growth.

A subset of hepatocellular carcinoma (HCC) overexpresses the chromosome 19 miRNA cluster (C19MC) and is associated with an undifferentiated phenotype marked by overexpression of cancer testis antigens (CTAs) including anti-apoptotic melanoma-A antigens (MAGEAs). However, the regulation of C19MC miRNA and MAGEA expression in HCCs are not understood. Here we show that, C19MC overexpression is tightly linked to a sub-set of HCCs with transcription-incompetent p53. Using next-generation and Sanger sequencing we found that, p53 in Hep3B cells is impaired by TP53-FXR2 fusion, and that overexpression of the C19MC miRNA-520G in Hep3B cells promotes the expression of MAGEA-3, 6 and 12 mRNAs. Furthermore, overexpression of p53-R175H and p53-R273H mutants promote miR-520G and MAGEA RNA expression and cellular transformation. Moreover, IFN-γ co-operates with miR-520G to promote MAGEA expression. On the other hand, metals such as nickel and zinc promote miR-526B but not miR-520G, to result in the suppression of MAGEA mRNA expression, and evoke cell death through mitochondrial membrane depolarization. Therefore our study demonstrates that a MAGEA-promoting network involving miR-520G, p53-defects and IFN-γ that govern cellular transformation and cell survival pathways, but MAGEA expression and survival are counteracted by nickel and zinc combination.

Background The survival benefit of elective neck dissection (END) for patients with cutaneous squamous cell carcinoma (cSCC) of the head and neck and no evidence of regional metastasis (cN0) has never been reported. The aim of this study was to determine the effect of END on patient survival. Methods The authors included patients with head and neck cSCC who had undergone primary surgery from 1995 to 2017. The primary end point was survival, and the secondary end points were the incidence of occult regional disease and regional disease control. To assess the impact of END on survival, the authors used multivariable Cox proportional hazards models with propensity score and matching techniques for internal validation. Results A total of 1111 patients presented with no evidence of nodal disease; 173 had END, and 938 were observed. Adjuvant radiotherapy to the neck was administered to 101 patients (9%). END resulted in a 5-year overall survival rate of 52%, whereas the rate was 63% in the observation group (P = .003 [log-rank]). The 5-year disease-free survival rate for patients undergoing END was similar to that for the observation group (73% vs 75%; P = .429). A multivariate regression model showed that the performance of END was not associated with improved rates of overall, disease-specific, or disease-free survival; similarly, among patients with advanced disease (T3-4), those who underwent END did not have improved survival rates. Conclusions Among patients with cSCC of the head and neck, observation of the neck nodes resulted in noninferior survival rates in comparison with END at the time of primary surgery. Further studies are required to elucidate the role of END in patients with advanced disease.

Background: The impact of chronic UV exposure on clonal dynamics and genomic diversity remains unclear. Our central hypothesis is that skin cancer is induced not by solely accumulation of somatic mutations, but rather a combination of mutations and disruption of the spatial and temporal constraints imposed by the skin’s 3-D architecture. Here we characterize clonal dynamics and transcriptional signatures during skin carcinogenesis using multicolor lineage tracing. Methods: We generated a K14Cre-ERT2 Confetti mice with inducible fluorophore (flr) expression. Mice were UV-irradiated for 3 months. Clones were 3-D digitized using confocal microscopy (z-stacks) and clone volumes estimated computationally. scRNAseq was used to compare UV-exposed (EXP) vs. non-exposed (NON) epidermis vs. skin tumors. Results: We generated 914 serial images of the EXP/NON skin over the course of 6 months following initiation of UV. We analyzed 16,135 clones from the EXP and 21,506 clones from the NON skin. We classified clone sizes into 3 classes represented by the small ( 500,000 μm3). The median size of clones does not differ between UV treatments and does not change with time. However, clones from EXP samples have significantly greater mean size than NON ones. Their mean sizes differed by some 1.5-fold, with an over 6-fold increase in variance, resulting in the sizes distribution to be highly skewed towards large clones with a long, narrow tail. Goliath clones are rarely present in the NON skin; however, they increase in number dramatically by months 3-4, plateauing between months 5-6. Using 3 ecological metrics (clone size, clone numbers, and coefficient of variation) we see phase shifts, which primarily distinguish months 1 & 2 from months 3 & 4. scRNAseq of EXP/NON epidermis and tumors revealed differential representation of 16 clusters, the majority of which could be mapped to previously defined keratinocyte populations. We observe dynamic changes to these clusters when progressing from normal skin to chronically exposed skin, and then to tumors. EXP clusters were associated with expression of cystatins (Scfa 3, BC100530), and alarmins/proliferative keratins (Krt16, Krt6a), which have been associated with skin injury. Clusters expressing cystatins and alarmins also increased in tumors. Flr-expressing keratinocytes harvested from large clones in EXP epidermis exhibited altered keratinocyte differentiation (downregulation of Krt77, Loricrin and Nfkbia, upregulation of cystatin), inflammation (downregulation of Nfkbia), and upregulation of metabolic regulators (carbonic anhydrase II and retinol transport (Rbp1)). Genes differentially expressed in exposed skin and retained in tumors may be required for carcinogenesis, while those expressed only in exposed skin likely required for adaptive responses to UV. Our findings have important implications for understanding cancer through an eco-evolutionary framework and designing novel approaches to cancer prevention. Citation Format: Stanislav Avdieiev, Leticia Tordesillas, Omar Chavez Chiang, Zhihua Chen, Luiza Silva Simoes, Y. Ann Chen, Noemi Andor, Robert Gatenby, Elsa R. Flores, Joel S. Brown, Kenneth Y. Tsai. In vivo tracking of clonal dynamics during UV-induced skin carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr PR004.

This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Proffered Abstracts section (PR004) of the Conference Proceedings. Citation Format: Stanislav Avdieiev, Leticia Tordesillas, Omar Chavez Chiang, Zhihua Chen, Luiza Silva Simoes, Y. Ann Chen, Noemi Andor, Robert Gatenby, Elsa R. Flores, Joel S. Brown, Kenneth Y. Tsai. In vivo tracking of clonal dynamics during UV-induced skin carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A017.

Cutaneous squamous cell carcinoma (cuSCC) is the second most common skin cancer and commonly arises in chronically UV-exposed skin or chronic wounds. Since UV exposure and chronic wounds are the two most prominent environmental factors that lead to cuSCC initiation, we undertook this study to test whether more acute molecular responses to UV and wounding overlapped with molecular signatures of cuSCC. We reasoned that transcriptional signatures in common between acutely UV-exposed skin, wounded skin, and cuSCC tumors, might enable us to identify important pathways contributing to cuSCC. We performed transcriptomic analysis on acutely UV-exposed human skin and integrated those findings with datasets from wounded skin and our transcriptomic data on cuSCC using functional pair analysis, GSEA, and pathway analysis. Integrated analyses revealed significant overlap between these three datasets, thus highlighting deep molecular similarities these biological processes, and we identified Oncostatin M (OSM) as a potential common upstream driver. Expression of OSM and its downstream targets correlated with poorer overall survival in head and neck SCC patients. In vitro, OSM promoted invasiveness of keratinocytes and cuSCC cells and suppressed apoptosis of irradiated keratinocytes. Together, these results support the concept of using an integrated, biologically-informed approach to identify potential promoters of tumorigenesis.