bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Regulation of USP37 Expression by REST-Associated G9a-Dependent Histone Methylation
Authors: Dobson Tara H.W. , Hatcher Rashieda J. , Swaminathan Jyothishmathi , Das Chandra M. , Shaik Shavali , Tao Rong-Hua , Milite Ciro , Castellano Sabrina , Taylor Pete H. , Sbardella Gianluca , Gopalakrishnan Vidya
Published: April 2023

Abstract
The deubiquitylase (DUB) USP37 is a component of the ubiquitin system and controls cell proliferation by regulating the stability of the cyclin-dependent kinase inhibitor 1B, (CDKN1B/p27Kip1). The expression of USP37 is downregulated in human medulloblastoma tumor specimens. In the current study, we show that USP37 prevents medulloblastoma growth in mouse orthotopic models, suggesting that it has tumor-suppressive properties in this neural cancer. Here, we also report on the mechanism underlying USP37 loss in medulloblastoma. Previously, we observed that the expression of USP37 is transcriptionally repressed by the RE1 silencing transcription factor (REST), which requires chromatin remodeling factors for its activity. Genetic and pharmacologic approaches were employed to identify a specific role for G9a, a histone methyltransferase (HMT), in promoting methylation of histone H3 lysine-9 (H3K9) mono- and dimethylation, and surprisingly trimethylation, at the USP37 promoter to repress its gene expression. G9a inhibition also blocked the tumorigenic potential of medulloblastoma cells in vivo. Using isogenic low- and high-REST medulloblastoma cells, we further showed a REST-dependent elevation in G9a activity, which further increased mono- and trimethylation of histone H3K9, accompanied by downregulation of USP37 expression. Together, these findings reveal a role for REST-associated G9a and histone H3K9 methylation in the repression of USP37 expression in medulloblastoma.

Implications: Reactivation of USP37 by G9a inhibition has the potential for therapeutic applications in REST-expressing medulloblastomas. Mol Cancer Res; 15(8); 1073–84. ©2017 AACR.
Data from Reversal of Triple-Negative Breast Cancer EMT by miR-200c Decreases Tryptophan Catabolism and a Program of Immunosuppression
Authors: Rogers Thomas J. , Christenson Jessica L. , Greene Lisa I. , O'Neill Kathleen I. , Williams Michelle M. , Gordon Michael A. , Nemkov Travis , D'Alessandro Angelo , Degala Greg D. , Shin Jimin , Tan Aik-Choon , Cittelly Diana M. , Lambert James R. , Richer Jennifer K.
Published: April 2023

Abstract
Tryptophan-2,3-dioxygenase (TDO2), a rate-limiting enzyme in the tryptophan catabolism pathway, is induced in triple-negative breast cancer (TNBC) by inflammatory signals and anchorage-independent conditions. TNBCs express extremely low levels of the miR-200 family compared with estrogen receptor–positive (ER+) breast cancer. In normal epithelial cells and ER+ breast cancers and cell lines, high levels of the family member miR-200c serve to target and repress genes involved in epithelial-to-mesenchymal transition (EMT). To identify mechanism(s) that permit TNBC to express TDO2 and other proteins not expressed in the more well-differentiated ER+ breast cancers, miRNA-200c was restored in TNBC cell lines. The data demonstrate that miR-200c targeted TDO2 directly resulting in reduced production of the immunosuppressive metabolite kynurenine. Furthermore, in addition to reversing a classic EMT signature, miR-200c repressed many genes encoding immunosuppressive factors including CD274/CD273, HMOX-1, and GDF15. Restoration of miR-200c revealed a mechanism, whereby TNBC hijacks a gene expression program reminiscent of that used by trophoblasts to suppress the maternal immune system to ensure fetal tolerance during pregnancy.
Implications:
Knowledge of the regulation of tumor-derived immunosuppressive factors will facilitate development of novel therapeutic strategies that complement current immunotherapy to reduce mortality for patients with TNBC.
Data from Real-Time Transferrin-Based PET Detects MYC-Positive Prostate Cancer
Authors: Aggarwal Rahul , Behr Spencer C. , Paris Pamela L. , Truillet Charles , Parker Matthew F.L. , Huynh Loc T. , Wei Junnian , Hann Byron , Youngren Jack , Huang Jiaoti , Premasekharan Gayatri , Ranatunga Nimna , Chang Emily , Gao Kenneth T. , Ryan Charles J. , Small Eric J. , Evans Michael J.
Published: April 2023

Abstract
Noninvasive biomarkers that detect the activity of important oncogenic drivers could significantly improve cancer diagnosis and management of treatment. The goal of this study was to determine whether 68Ga-citrate (which avidly binds to circulating transferrin) can detect MYC-positive prostate cancer tumors, as the transferrin receptor is a direct MYC target gene. PET imaging paired with 68Ga-citrate and molecular analysis of preclinical models, human cell-free DNA (cfDNA), and clinical biopsies were conducted to determine whether 68Ga-citrate can detect MYC-positive prostate cancer. Importantly, 68Ga-citrate detected human prostate cancer models in a MYC-dependent fashion. In patients with castration-resistant prostate cancer, analysis of cfDNA revealed that all patients with 68Ga-citrate avid tumors had a gain of at least one MYC copy number. Moreover, biopsy of two PET avid metastases showed molecular or histologic features characteristic of MYC hyperactivity. These data demonstrate that 68Ga-citrate targets prostate cancer tumors with MYC hyperactivity. A larger prospective study is ongoing to demonstrate the specificity of 68Ga-citrate for tumors with hyperactive MYC.

Implications: Noninvasive measurement of MYC activity with quantitative imaging modalities could substantially increase our understanding of the role of MYC signaling in clinical settings for which invasive techniques are challenging to implement or do not characterize the biology of all tumors in a patient. Moreover, measuring MYC activity noninvasively opens the opportunity to study changes in MYC signaling in patients under targeted therapeutic conditions thought to indirectly inhibit MYC. Mol Cancer Res; 15(9); 1221–9. ©2017 AACR.
Data from p21CIP1 Promotes Mammary Cancer–Initiating Cells via Activation of Wnt/TCF1/CyclinD1 Signaling
Authors: Benard Outhiriaradjou , Qian Xia , Liang Huizhi , Ren Zuen , Suyama Kimita , Norton Larry , Hazan Rachel B.
Published: April 2023

Abstract
Cancer stem cells (CSC) generate and sustain tumors due to tumor-initiating potential, resulting in recurrence or metastasis. We showed that knockout of the cell-cycle inhibitor, p21CIP1, in the PyMT mammary tumor model inhibits metastasis; however the mechanism remained unknown. Here, we show a pivotal role for p21 in potentiating a cancer stem–like phenotype. p21 knockout in PyMT mammary tumor cells caused dramatic suppression of CSC properties involving tumorsphere formation, ALDH1 activity, and tumor-initiating potential, which were in turn rescued by p21 overexpression into PyMT/p21 knockout cells. Interestingly, p21 knockout dramatically suppresses Wnt/β-catenin signaling activity, leading to striking inhibition of LEF1 and TCF1 expression. TCF1 knockdown in PyMT cells suppressed tumorsphere formation due to Cyclin D1 attenuation. These data demonstrate that p21 promotes a CSC-like phenotype via activation of Wnt/TCF1/Cyclin D1 signaling.
Implications:
p21 is a strong promoter of mammary CSCs.
Data from The Role of Alcohol-Induced Golgi Fragmentation for Androgen Receptor Signaling in Prostate Cancer
Authors: Manca Sonia , Frisbie Cole P. , LaGrange Chad A. , Casey Carol A. , Riethoven Jean-Jack M. , Petrosyan Armen
Published: April 2023

Abstract
Multiple epidemiologic observations and meta-analysis clearly indicate the link between alcohol abuse and the incidence and progression of prostate cancer; however, the mechanism remains enigmatic. Recently, it was found that ethanol (EtOH) induces disorganization of the Golgi complex caused by impaired function of the largest Golgi matrix protein, giantin (GOLGB1), which, in turn, alters the Golgi docking of resident Golgi proteins. Here, it is determined that in normal prostate cells, histone deacetylase 6 (HDAC6), the known regulator of androgen receptor (AR) signaling, localizes in the cytoplasm and nucleus, while its kinase, glycogen synthase kinase β (GSK3β), primarily resides in the Golgi. Progression of prostate cancer is accompanied by Golgi scattering, translocation of GSK3β from the Golgi to the cytoplasm, and the cytoplasmic shift in HDAC6 localization. Alcohol dehydrogenase–generated metabolites induces Golgi disorganization in androgen-responsive LNCaP and 22Rv1 cells, facilitates tumor growth in a mouse xenograft model and activates anchorage-independent proliferation, migration, and cell adhesion. EtOH-treated cells demonstrate reduced giantin and subsequent cytoplasmic GSK3β; this phenomenon was validated in giantin-depleted cells. Redistribution of GSK3β to the cytoplasm results in phosphorylation of HDAC6 and its retention in the cytoplasm, which, in turn, stimulates deacetylation of HSP90, AR import into the nucleus, and secretion of prostate-specific antigen (PSA). Finally, the relationship between Golgi morphology, HDAC6 cytoplasmic content, and clinicopathologic features was assessed in human prostate cancer patient specimens with and without a history of alcohol dependence.
Implications:
This study demonstrates the importance of alcohol-induced Golgi fragmentation in the activation of AR-mediated proliferation.
Data from Epigenetic Regulation of ZBTB18 Promotes Glioblastoma Progression
Authors: Fedele Vita , Dai Fangping , Masilamani Anie P. , Heiland Dieter H. , Kling Eva , Gätjens-Sanchez Ana M. , Ferrarese Roberto , Platania Leonardo , Doostkam Soroush , Kim Hyunsoo , Nelander Sven , Weyerbrock Astrid , Prinz Marco , Califano Andrea , Iavarone Antonio , Bredel Markus , Carro Maria S.
Published: April 2023

Abstract
Glioblastoma (GBM) comprises distinct subtypes characterized by their molecular profile. Mesenchymal identity in GBM has been associated with a comparatively unfavorable prognosis, primarily due to inherent resistance of these tumors to current therapies. The identification of molecular determinants of mesenchymal transformation could potentially allow for the discovery of new therapeutic targets. Zinc Finger and BTB Domain Containing 18 (ZBTB18/ZNF238/RP58) is a zinc finger transcriptional repressor with a crucial role in brain development and neuronal differentiation. Here, ZBTB18 is primarily silenced in the mesenchymal subtype of GBM through aberrant promoter methylation. Loss of ZBTB18 contributes to the aggressive phenotype of glioblastoma through regulation of poor prognosis–associated signatures. Restitution of ZBTB18 expression reverses the phenotype and impairs tumor-forming ability. These results indicate that ZBTB18 functions as a tumor suppressor in GBM through the regulation of genes associated with phenotypically aggressive properties.

Implications: This study characterizes the role of the putative tumor suppressor ZBTB18 and its regulation by promoter hypermethylation, which appears to be a common mechanism to silence ZBTB18 in the mesenchymal subtype of GBM and provides a new mechanistic opportunity to specifically target this tumor subclass. Mol Cancer Res; 15(8); 998–1011. ©2017 AACR.
Data from Mitotic DNA Synthesis Is Differentially Regulated between Cancer and Noncancerous Cells
Authors: Graber-Feesl Cari L. , Pederson Kayla D. , Aney Katherine J. , Shima Naoko
Published: April 2023

Abstract
Mitotic DNA synthesis is a recently discovered mechanism that resolves late replication intermediates, thereby supporting cell proliferation under replication stress. This unusual form of DNA synthesis occurs in the absence of RAD51 or BRCA2, which led to the identification of RAD52 as a key player in this process. Notably, mitotic DNA synthesis is predominantly observed at chromosome loci that colocalize with FANCD2 foci. However, the role of this protein in mitotic DNA synthesis remains largely unknown. In this study, we investigated the role of FANCD2 and its interplay with RAD52 in mitotic DNA synthesis using aphidicolin as a universal inducer of this process. After examining eight human cell lines, we provide evidence for FANCD2 rather than RAD52 as a fundamental supporter of mitotic DNA synthesis. In cancer cell lines, FANCD2 exerts this role independently of RAD52. Surprisingly, RAD52 is dispensable for mitotic DNA synthesis in noncancerous cell lines, but these cells strongly depend on FANCD2 for this process. Therefore, RAD52 functions selectively in cancer cells as a secondary regulator in addition to FANCD2 to facilitate mitotic DNA synthesis. As an alternative to aphidicolin, we found partial inhibition of origin licensing as an effective way to induce mitotic DNA synthesis preferentially in cancer cells. Importantly, cancer cells still perform mitotic DNA synthesis by dual regulation of FANCD2 and RAD52 under such conditions.
Implications:
These key differences in mitotic DNA synthesis between cancer and noncancerous cells advance our understanding of this mechanism and can be exploited for cancer therapies.
Data from A First-in-Class TWIST1 Inhibitor with Activity in Oncogene-Driven Lung Cancer
Authors: Yochum Zachary A. , Cades Jessica , Mazzacurati Lucia , Neumann Neil M. , Khetarpal Susheel K. , Chatterjee Suman , Wang Hailun , Attar Myriam A. , Huang Eric H.-B. , Chatley Sarah N. , Nugent Katriana , Somasundaram Ashwin , Engh Johnathan A. , Ewald Andrew J. , Cho Yoon-Jae , Rudin Charles M. , Tran Phuoc T. , Burns Timothy F.
Published: April 2023

Abstract
TWIST1, an epithelial–mesenchymal transition (EMT) transcription factor, is critical for oncogene-driven non–small cell lung cancer (NSCLC) tumorigenesis. Given the potential of TWIST1 as a therapeutic target, a chemical–bioinformatic approach using connectivity mapping (CMAP) analysis was used to identify TWIST1 inhibitors. Characterization of the top ranked candidates from the unbiased screen revealed that harmine, a harmala alkaloid, inhibited multiple TWIST1 functions, including single-cell dissemination, suppression of normal branching in 3D epithelial culture, and proliferation of oncogene driver-defined NSCLC cells. Harmine treatment phenocopied genetic loss of TWIST1 by inducing oncogene-induced senescence or apoptosis. Mechanistic investigation revealed that harmine targeted the TWIST1 pathway through its promotion of TWIST1 protein degradation. As dimerization is critical for TWIST1 function and stability, the effect of harmine on specific TWIST1 dimers was examined. TWIST1 and its dimer partners, the E2A proteins, which were found to be required for TWIST1-mediated functions, regulated the stability of the other heterodimeric partner posttranslationally. Harmine preferentially promoted degradation of the TWIST1-E2A heterodimer compared with the TWIST-TWIST1 homodimer, and targeting the TWIST1-E2A heterodimer was required for harmine cytotoxicity. Finally, harmine had activity in both transgenic and patient-derived xenograft mouse models of KRAS-mutant NSCLC. These studies identified harmine as a first-in-class TWIST1 inhibitor with marked anti-tumor activity in oncogene-driven NSCLC including EGFR mutant, KRAS mutant and MET altered NSCLC.

Implications: TWIST1 is required for oncogene-driven NSCLC tumorigenesis and EMT; thus, harmine and its analogues/derivatives represent a novel therapeutic strategy to treat oncogene-driven NSCLC as well as other solid tumor malignancies. Mol Cancer Res; 15(12); 1764–76. ©2017 AACR.
Data from Reprogramming of Isocitrate Dehydrogenases Expression and Activity by the Androgen Receptor in Prostate Cancer
Authors: Gonthier Kevin , Poluri Raghavendra Tejo Karthik , Weidmann Cindy , Tadros Maude , Audet-Walsh Étienne
Published: April 2023

Abstract
Mutations of the isocitrate dehydrogenase genes IDH1 and IDH2, key enzymes involved in citrate metabolism, are important oncogenic events in several cancer types, including in 1%–3% of all prostate cancer cases. However, if IDH1 and other IDH isoforms are associated with prostate cancer progression, as well as the regulatory factors controlling their expression and activity, remain mostly unknown. Using publicly available datasets, we showed that prostate cancer harbors the highest IDH1 expression across the human cancer spectrum and that IDH1 expression is altered during prostate cancer progression. We showed that the androgen receptor (AR), a key oncogene in prostate cancer, controls multiple IDH isoforms in both in vitro and in vivo models, predominantly positively regulating IDH1. Chromatin immunoprecipitation experiments confirmed the recruitment of AR at several regulatory regions of IDH1 and enzymatic assays demonstrated that AR significantly induces IDH activity. Genetic blockade of IDH1 significantly impaired prostate cancer cell proliferation, consistent with IDH1 having a key function in these cancer cells. Importantly, knockdown of IDH1 blocked the AR-mediated induction in IDH activity, indicating that AR promotes a mitochondrial to cytoplasmic reprogramming of IDH activity. Overall, our study demonstrates that IDH1 expression is associated with prostate cancer progression, that AR signaling integrates one of the first transcriptional mechanisms shown to regulate IDH1, and that AR reprograms prostate cancer cell metabolism by selectively inducing extra-mitochondrial IDH activity.
Implications:
The discovery that AR reprograms IDH activity highlights a novel metabolic reprogramming necessary for prostate cancer growth and suggests targeting IDH activity as a new therapeutic approach for prostate cancer treatment.
Data from Atorvastatin Decreases HBx-Induced Phospho-Akt in Hepatocytes via P2X Receptors
Authors: Ghalali Aram , Martin-Renedo Javier , Högberg Johan , Stenius Ulla
Published: April 2023

Abstract
Hepatocellular carcinoma (HCC) is rated as the fifth most common malignancy and third in cancer-related deaths worldwide. Statins, HMG-CoA reductase inhibitors, are potent cholesterol-lowering drugs, and recent epidemiologic evidence suggests that statins prevent aggressive HCC development. Previous experiments revealed that statins downregulate phosphorylated Akt (pAkt). Here, it is demonstrated that atorvastatin decreases nuclear pAkt levels in pancreatic and lung cancer cell lines within minutes, and this rapid effect is mediated by the purinergic P2X receptors. Akt is upregulated by hepatitis viruses and has oncogenic activity in HCC; therefore, we tested the possibility that the P2X–Akt pathway is important for the anticipated anticancer effects of statins in hepatocytes. Atorvastatin decreased hepatitis B virus X protein- and insulin-induced pAkt and pGsk3β (Ser9) levels. Furthermore, Akt-induced lipogenesis was counteracted by atorvastatin, and these statin-induced effects were dependent on P2X receptors. Statin also decreased proliferation and invasiveness of hepatocytes. These data provide mechanistic evidence for a P2X receptor–dependent signaling pathway by which statins decrease pAkt, its downstream phosphorylation target pGsk3β, and lipogenesis in hepatocytes.

Implications: The Akt pathway is deregulated and may act as a driver in HCC development; the P2X–Akt signaling pathway may have a role in anticancer effects of statins. Mol Cancer Res; 15(6); 714–22. ©2017 AACR.
Data from A Transcriptional Program for Detecting TGFβ-Induced EMT in Cancer
Authors: Foroutan Momeneh , Cursons Joseph , Hediyeh-Zadeh Soroor , Thompson Erik W. , Davis Melissa J.
Published: April 2023

Abstract
Most cancer deaths are due to metastasis, and epithelial-to-mesenchymal transition (EMT) plays a central role in driving cancer cell metastasis. EMT is induced by different stimuli, leading to different signaling patterns and therapeutic responses. TGFβ is one of the best-studied drivers of EMT, and many drugs are available to target this signaling pathway. A comprehensive bioinformatics approach was employed to derive a signature for TGFβ-induced EMT which can be used to score TGFβ-driven EMT in cells and clinical specimens. Considering this signature in pan-cancer cell and tumor datasets, a number of cell lines (including basal B breast cancer and cancers of the central nervous system) show evidence for TGFβ-driven EMT and carry a low mutational burden across the TGFβ signaling pathway. Furthermore, significant variation is observed in the response of high scoring cell lines to some common cancer drugs. Finally, this signature was applied to pan-cancer data from The Cancer Genome Atlas to identify tumor types with evidence of TGFβ-induced EMT. Tumor types with high scores showed significantly lower survival rates than those with low scores and also carry a lower mutational burden in the TGFβ pathway. The current transcriptomic signature demonstrates reproducible results across independent cell line and cancer datasets and identifies samples with strong mesenchymal phenotypes likely to be driven by TGFβ.

Implications: The TGFβ-induced EMT signature may be useful to identify patients with mesenchymal-like tumors who could benefit from targeted therapeutics to inhibit promesenchymal TGFβ signaling and disrupt the metastatic cascade. Mol Cancer Res; 15(5); 619–31. ©2017 AACR.
Data from Hypoxia-Associated Factor (HAF) Mediates Neurofibromin Ubiquitination and Degradation Leading to Ras–ERK Pathway Activation in Hypoxia
Authors: Green Yangsook Song , Sargis Timothy , Reichert Ethan Conrad , Rudasi Eleanor , Fuja Daniel , Jonasch Eric , Koh Mei Yee
Published: April 2023

Abstract
Low oxygen or hypoxia is a feature of all solid tumors and has been associated with aggressive disease. Here, we describe a novel mechanism for the hypoxia-dependent degradation of the Ras-GTPase–activating protein neurofibromin, by hypoxia-associated factor (HAF). We have previously characterized HAF as an oxygen-independent ubiquitin ligase for HIF-1α. Here, we show that HAF promotes neurofibromin ubiquitination and degradation independently of oxygen and pVHL, resulting in Ras–ERK pathway activation. Hypoxia enhanced HAF:neurofibromin binding independently of HAF-SUMOylation, whereas HAF knockdown increased neurofibromin levels primarily in hypoxia, supporting the role of HAF as a hypoxia-specific neurofibromin regulator. HAF overexpression increased p-ERK levels and promoted resistance of clear cell kidney cancer (ccRCC) cells to sorafenib and sunitinib in both normoxia and hypoxia. However, a greater-fold increase in sorafenib/sunitinib resistance was observed during hypoxia, particularly in pVHL-deficient cells. Intriguingly, HAF-mediated resistance was HIF-2α–dependent in normoxia, but HIF-2α–independent in hypoxia indicating two potential mechanisms of HAF-mediated resistance: a HIF-2α–dependent pathway dominant in normoxia, and the direct activation of the Ras–ERK pathway through neurofibromin degradation dominant in hypoxia. Patients with ccRCC with high HAF transcript or protein levels showed significantly decreased overall survival compared with those with low HAF. Thus, we establish a novel, nonmutational pathway of neurofibromin inactivation through hypoxia-induced HAF-mediated degradation, leading to Ras–ERK activation and poor prognosis in ccRCC.
Implications:
We describe a novel mechanism of neurofibromin degradation induced by hypoxia that leads to activation of the prooncogenic Ras–ERK pathway and resistance to therapy.
Data from Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models
Authors: Khandelwal Garima , Girotti María Romina , Smowton Christopher , Taylor Sam , Wirth Christopher , Dynowski Marek , Frese Kristopher K. , Brady Ged , Dive Caroline , Marais Richard , Miller Crispin
Published: April 2023

Abstract
Patient-derived xenograft (PDX) and circulating tumor cell–derived explant (CDX) models are powerful methods for the study of human disease. In cancer research, these methods have been applied to multiple questions, including the study of metastatic progression, genetic evolution, and therapeutic drug responses. As PDX and CDX models can recapitulate the highly heterogeneous characteristics of a patient tumor, as well as their response to chemotherapy, there is considerable interest in combining them with next-generation sequencing to monitor the genomic, transcriptional, and epigenetic changes that accompany oncogenesis. When used for this purpose, their reliability is highly dependent on being able to accurately distinguish between sequencing reads that originate from the host, and those that arise from the xenograft itself. Here, we demonstrate that failure to correctly identify contaminating host reads when analyzing DNA- and RNA-sequencing (DNA-Seq and RNA-Seq) data from PDX and CDX models is a major confounding factor that can lead to incorrect mutation calls and a failure to identify canonical mutation signatures associated with tumorigenicity. In addition, a highly sensitive algorithm and open source software tool for identifying and removing contaminating host sequences is described. Importantly, when applied to PDX and CDX models of melanoma, these data demonstrate its utility as a sensitive and selective tool for the correction of PDX- and CDX-derived whole-exome and RNA-Seq data.

Implications: This study describes a sensitive method to identify contaminating host reads in xenograft and explant DNA- and RNA-Seq data and is applicable to other forms of deep sequencing. Mol Cancer Res; 15(8); 1012–6. ©2017 AACR.
Data from Landscape of Tumor Mutation Load, Mismatch Repair Deficiency, and PD-L1 Expression in a Large Patient Cohort of Gastrointestinal Cancers
Authors: Salem Mohamed E. , Puccini Alberto , Grothey Axel , Raghavan Derek , Goldberg Richard M. , Xiu Joanne , Korn W. Michael , Weinberg Benjamin A. , Hwang Jimmy J. , Shields Anthony F. , Marshall John L. , Philip Philip A. , Lenz Heinz-Josef
Published: April 2023

Abstract
The efficacy of immunotherapy varies widely among different gastrointestinal cancers. Response to immune checkpoint inhibitors is shown to correlate with tumor mutation load (TML), mismatch repair deficiency (dMMR) status, and programmed cell death-ligand 1 (PD-L1) expression. Herein, we quantify TML, dMMR, and PD-L1 expression and determine their interrelationship in gastrointestinal cancers. Here, a total of 4,125 tumors from 14 different gastrointestinal cancer sites were studied using validated assays. Next-generation sequencing was performed on genomic DNA isolated from formalin-fixed paraffin-embedded tumor specimens using the NextSeq platform. TML was calculated using only somatic nonsynonymous missense mutations sequenced with a 592-gene panel. Microsatellite instability (MSI) was assessed using direct analysis of altered known MSI loci in the target regions of the sequenced genes. PD-L1 expression was analyzed by IHC. Interestingly, right-sided colon and small-bowel adenocarcinomas had the highest prevalence of TML-high tumors (14.6% and 10.2%, respectively). Pancreatic neuroendocrine tumors and gastrointestinal stromal tumors had the lowest rates of TML-high (1.3% and 0%, respectively). TML-high was strongly associated with MSI-H (P < 0.0001). However, all TML-high anal cancers (8.3%) were microsatellite stable (MSS). Higher PD-L1 expression was more likely to be seen in MSI compared with MSS tumors (20.6% vs. 7.8%, P < 0.0001).

Implications: TML-high rate varied widely among gastrointestinal cancers. Although MSI is conceivably the main driver for TML-high, other factors may be involved. Future clinical trials are needed to evaluate whether the integration of TML, MSI, and PD-L1 could better identify potential responders to immunotherapy. Mol Cancer Res; 16(5); 805–12. ©2018 AACR.
Data from Distinct Afatinib Resistance Mechanisms Identified in Lung Adenocarcinoma Harboring an EGFR Mutation
Authors: Yamaoka Toshimitsu , Ohmori Tohru , Ohba Motoi , Arata Satoru , Murata Yasunori , Kusumoto Sojiro , Ando Koichi , Ishida Hiroo , Ohnishi Tsukasa , Sasaki Yasutsuna
Published: April 2023

Abstract
EGFR tyrosine kinase inhibitors (TKI) are associated with significant responses in non–small cell lung cancer (NSCLC) patients harboring EGFR-activating mutations. However, acquired resistance to reversible EGFR-TKIs remains a major obstacle. In particular, although the second-generation irreversible EGFR-TKI afatinib is currently used for treating NSCLC patients, the mechanisms underlying acquired afatinib resistance remain poorly understood. Here, heterogeneous mechanisms of acquired resistance were identified following long-term exposure to increasing doses of afatinib in EGFR-mutant lung adenocarcinoma PC-9 cells. Notably, three resistant cell lines, PC-9AFR1, PC-9AFR2, and PC-9AFR3 (AFR1, AFR2, and AFR3, respectively) employed distinct mechanisms for avoiding EGFR inhibition, with increased EGFR expression being detected in all resistant cell lines. Moreover, an activating EGFR mutation was partially lost in AFR1 and AFR2 cells. AFR1 cells exhibited afatinib resistance as a result of wild-type KRAS amplification and overexpression; however, these cells showed a progressive decrease and eventual loss of the acquired KRAS dependence, as well as resensitization to afatinib, following a drug holiday. Meanwhile, AFR2 cells exhibited increased expression of insulin-like growth factor-binding protein 3 (IGFBP3), which promoted insulin-like growth factor 1 receptor (IGF1R) activity and subsequent AKT phosphorylation, thereby indicating a potential bypass signaling pathway associated with IGFR1. Finally, AFR3 cells harbored the secondary EGFR mutation T790M. Our findings constitute the first report showing acquired wild-type KRAS overexpression and attenuation of afatinib resistance following a drug holiday.

Implications: The heterogeneous mechanisms of afatinib resistance should facilitate the development of more effective therapeutic strategies for NSCLC patients. Mol Cancer Res; 15(7); 915–28. ©2017 AACR.
Data from Significance of Divergent Expression of Prostaglandin EP4 and EP3 Receptors in Human Prostate Cancer
Authors: Huang Hosea F. S. , Shu Ping , Murphy Thomas F. , Aisner Seena , Fitzhugh Valerie A. , Jordan Mark L.
Published: April 2023

Abstract
PGE2 has been implicated in prostate cancer tumorigenesis. We hypothesized that abnormal prostaglandin receptor (EPR) expression may contribute to prostate cancer growth. Twenty-six archived radical prostatectomy specimens were evaluated by immunohistochemistry (IHC) and Western blotting for the expression of EP1, EP2, EP3, and EP4. As a corollary, EPR expression in one normal (PZ-HPV7) and four prostate cancer cell lines (CA-HPV10, LNCaP, PC3, and Du145) were assessed by Western blotting. Prostate cancer and normal cell growth were compared in vitro after EPR blockade, siRNA EPR knockdown, or overexpression. EP1, EP2, EP3, and EP4 receptors were detected by IHC in all areas of benign tissue within the clinical prostate cancer specimens. In areas of prostate cancer, EP4 and EP2 were overexpressed in 85% (22 of 26) and 75% (18 of 24) and EP3 expression was reduced in all (26 of 26, 100%) specimens (P < 0.05 vs. benign tissue). EP1 showed no specific differential expression pattern. Increased EP4 and reduced EP3 was confirmed by Western blotting in fresh clinical specimens and in prostate cancer cell lines (CA-HPV10, LNCaP, PC3, and Du145) compared with the normal prostate cell line (PZ-HPV7). EP2 and EP4 siRNA knockdown resulted in reduced in vitro growth and metastasis-related gene expression (MMP9 and Runx2) of prostate cancer lines, and in vitro migration was inhibited by EP4 antagonists. As a corollary, EP3-overexpressing PC3 cells displayed impaired growth in vitro. Human prostate cancer is associated with EP4 and EP2 overexpression and reduced EP3 expression. These data suggest that targeting specific EPR may represent a novel therapeutic approach for prostate cancer. Mol Cancer Res; 11(4); 427–39. ©2013 AACR.
Data from TLE1 Is an Anoikis Regulator and Is Downregulated by Bit1 in Breast Cancer Cells
Authors: Brunquell Chris , Biliran Hector , Jennings Scott , Ireland Shubha Kale , Chen Renwei , Ruoslahti Erkki
Published: April 2023

Abstract
TLE1 is a Groucho-related transcriptional repressor protein that exerts survival and antiapoptotic function in several cellular systems and has been implicated in the pathogenesis of cancer. In the present study, we found that TLE1 is a regulator of anoikis in normal mammary epithelial and breast carcinoma cells. The induction of apoptosis following loss of cell attachment to the extracellular matrix (anoikis) in untransformed mammary epithelial MCF10A cells was associated with significant downregulation of TLE1 expression. Forced expression of exogenous TLE1 in these cells promoted resistance to anoikis. In breast cancer cells, TLE1 expression was significantly upregulated following detachment from the extracellular matrix. Genetic manipulation of TLE1 expression via overexpression and downregulation approaches indicated that TLE1 promotes the anoikis resistance and anchorage-independent growth of breast carcinoma cells. Mechanistically, we show that TLE1 inhibits the Bit1 anoikis pathway by reducing the formation of the proapoptotic Bit1-AES complex in part through sequestration of AES in the nucleus. The mitochondrial release of Bit1 during anoikis as well as exogenous expression of the cytoplasmic localized Bit1 or its cell death domain induced cytoplasmic translocation and degradation of nuclear TLE1 protein. These findings indicate a novel role for TLE1 in the maintenance of anoikis resistance in breast cancer cells. This conclusion is supported by an immunohistochemical analysis of a breast cancer tissue array illustrating that TLE1 is selectively upregulated in invasive breast tumors relative to noninvasive ductal carcinoma in situ and normal mammary epithelial tissues. Mol Cancer Res; 10(11); 1482–95. ©2012 AACR.
Data from A Vascular Model of Tsc1 Deficiency Accelerates Renal Tumor Formation with Accompanying Hemangiosarcomas
Authors: Leech Jarrett D. , Lammers Stephen H.T. , Goldman Sam , Auricchio Neil , Bronson Roderick T. , Kwiatkowski David J. , Sahin Mustafa
Published: April 2023

Abstract
Tuberous sclerosis complex (TSC) is an autosomal disease caused by inactivating mutations in either of the tumor suppressor genes TSC1 or TSC2. TSC-associated tumor growth is present in multiple tissues and organs including brain, kidney, liver, heart, lungs, and skin. In the kidney, TSC angiomyolipomas have aberrant vascular structures with abnormal endothelial cells, suggesting a role for endothelial mTORC1 function. In the current report, a genetically engineered mouse model (GEMM) with a conditional knockout allele of Tsc1 with a Darpp32-Cre allele displayed accelerated formation of both kidney cystadenomas and paw hemangiosarcomas. All mutant mice developed hemangiosarcomas on multiple paws by 6 weeks of age. By 16 weeks of age, the average mutant hind paw was 4.0 mm in diameter, nearly double the size of control mice. Furthermore, the hemangiosarcomas and kidney cystadenomas were responsive to intraperitoneal rapamycin treatment. Immunoblotting and immunostaining for phospho-S6 (pS6) and phospho-CAD showed that the effect of rapamycin on tumor size was through inhibition of the mTOR signaling pathway. Finally, elevated VEGF mRNA levels were also observed in hemangiosarcoma specimens. Because paw hemangiosarcomas are easily detectable and scorable for size and growth, this novel mouse model enables accelerated in vivo drug testing for therapies of TSC-related tumors.

Implications: These findings provide a strong rationale for simultaneous use of this conditional knockout mouse as an in vivo genetic model while seeking new cancer therapies for TSC-related tumors. Mol Cancer Res; 13(3); 548–55. ©2014 AACR.
Data from Ligand Binding Promotes CDK-Dependent Phosphorylation of ER-Alpha on Hinge Serine 294 but Inhibits Ligand-Independent Phosphorylation of Serine 305
Authors: Held Jason M. , Britton David J. , Scott Gary K. , Lee Elbert L. , Schilling Birgit , Baldwin Michael A. , Gibson Bradford W. , Benz Christopher C.
Published: April 2023

Abstract
Phosphorylation of estrogen receptor-α (ERα) is critical for its transcription factor activity and may determine its predictive and therapeutic value as a biomarker for ERα-positive breast cancers. Recent attention has turned to the poorly understood ERα hinge domain, as phosphorylation at serine 305 (Ser305) associates with poor clinical outcome and endocrine resistance. We show that phosphorylation of a neighboring hinge domain site, Ser294, analyzed by multiple reaction monitoring mass spectrometry of ERα immunoprecipitates from human breast cancer cells is robustly phosphorylated exclusively by ligand (estradiol and tamoxifen) activation of ERα and not by growth factor stimulation (EGF, insulin, heregulin-β). In a reciprocal fashion, Ser305 phosphorylation is induced by growth factors but not ligand activation of ERα. Phosphorylation at Ser294 and Ser305 is suppressed upon co-stimulation by EGF and ligand, respectively, unlike the N-terminal (AF-1) domain Ser118 and Ser167 sites of ERα where phosphorylation is enhanced by ligand and growth factor co-stimulation. Inhibition of cyclin-dependent kinases (CDK) by roscovitine or SNS-032 suppresses ligand-activated Ser294 phosphorylation without affecting Ser118 or Ser104/Ser106 phosphorylation. Likewise, cell-free studies using recombinant ERα and specific cyclin–CDK complexes suggest that Ser294 phosphorylation is primarily induced by the transcription-regulating and cell-cycle–independent kinase CDK7. Thus, CDK-dependent phosphorylation at Ser294 differentiates ligand-dependent from ligand-independent activation of Ser305 phosphorylation, showing that hinge domain phosphorylation patterns uniquely inform on the various ERα activation mechanisms thought to underlie the biologic and clinical diversity of hormone-dependent breast cancers. Mol Cancer Res; 10(8); 1120–32. ©2012 AACR.
Supplementary Figure-7 from Novel Evidence for Curcumin and Boswellic Acid–Induced Chemoprevention through Regulation of miR-34a and miR-27a in Colorectal Cancer
Authors: Toden Shusuke , Okugawa Yoshinaga , Buhrmann Constanze , Nattamai Durgha , Anguiano Esperanza , Baldwin Nicole , Shakibaei Mehdi , Boland C. Richard , Goel Ajay
Published: April 2023

Supplementary Figure-7. The effects of miR-27a knockdown on cell function in colorectal cancer cells.
Supplementary Figure-6 from Novel Evidence for Curcumin and Boswellic Acid–Induced Chemoprevention through Regulation of miR-34a and miR-27a in Colorectal Cancer
Authors: Toden Shusuke , Okugawa Yoshinaga , Buhrmann Constanze , Nattamai Durgha , Anguiano Esperanza , Baldwin Nicole , Shakibaei Mehdi , Boland C. Richard , Goel Ajay
Published: April 2023

Supplementary Figure-6. The effects of miR-34a over-expression on cell function colorectal cancer cells.
Supplemental Figures S1-9 from Nrf2 Activation Protects against Solar-Simulated Ultraviolet Radiation in Mice and Humans
Authors: Knatko Elena V. , Ibbotson Sally H. , Zhang Ying , Higgins Maureen , Fahey Jed W. , Talalay Paul , Dawe Robert S. , Ferguson James , Huang Jeffrey T.-J. , Clarke Rosemary , Zheng Suqing , Saito Akira , Kalra Sukirti , Benedict Andrea L. , Honda Tadashi , Proby Charlotte M. , Dinkova-Kostova Albena T.
Published: April 2023

Supplemental Figure S1. Spectral characteristics of UVA 340 lamps. Figure S2. Nrf2 disruption leads to an increase in the mRNA of Nrf3, but not Nrf1, in skin of SKH-1 hairless mice. Figure S3. TBE-31 treatment induces NQO1 in dermis and epidermis of WT SKH-1 hairless mice, but has no effect in Nrf2-KO animals. Figure S5. The architecture of the skin is similar among WT, Nrf2-KO and Keap1-KD SKH-1 hairless mice. Figure S6. Dose optimization for the use of TBE-31 as a pharmacological agent for protection against cutaneous carcinogenesis mediated by solar-simulated UV radiation. Figure S7. Optimization of azathioprine treatment in SKH-1 hairless mice. Figure S8. HPLC analysis of the sulforaphane (SF, active)- and glucoraphanin (GR, placebo) extracts used in the human study. Figure S9. NQO1 inducer activity of the sulforaphane (SF, active)- and glucoraphanin (GR, placebo) extracts used in the human study.
Supplementary data from Divergent Roles of PAX2 in the Etiology and Progression of Ovarian Cancer
Authors: Al-Hujaily Ensaf M. , Tang Yong , Yao De-Sheng , Carmona Euridice , Garson Kenneth , Vanderhyden Barbara C.
Published: April 2023

Supplementary Table 1: Primer pairs (forward [F] and reverse [R]) that were used to amplify murine genes. Supplementary Table 2: The primary antibodies that were used for western blot analysis in the current studies. Supplementary Table 3: The top 10 genes upregulated and downregulated by PAX2 in MO505 cells, as shown by microarray analysis, and their known relationships to ovarian tumorigenesis. Supplementary Table 4: Functional analysis of genes that were changed in M0505+PAX2 cells compared to M0505+WPI and M0505+PAX2+Cre and are involved in tumor growth and progression.
Supplementary Table 1 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition
Authors: Katz Tiffany A. , Liao Serena G. , Palmieri Vincent J. , Dearth Robert K. , Pathiraja Thushangi N. , Huo Zhiguang , Shaw Patricia , Small Sarah , Davidson Nancy E. , Peters David G. , Tseng George C. , Oesterreich Steffi , Lee Adrian V.
Published: April 2023

Primers used for quantitative PCR and bisulfite sequencing.
Supplementary Figure Legends from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition
Authors: Katz Tiffany A. , Liao Serena G. , Palmieri Vincent J. , Dearth Robert K. , Pathiraja Thushangi N. , Huo Zhiguang , Shaw Patricia , Small Sarah , Davidson Nancy E. , Peters David G. , Tseng George C. , Oesterreich Steffi , Lee Adrian V.
Published: April 2023

All Supplementary Figure legends are included in this document.
Supplementary Figure 4 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition
Authors: Katz Tiffany A. , Liao Serena G. , Palmieri Vincent J. , Dearth Robert K. , Pathiraja Thushangi N. , Huo Zhiguang , Shaw Patricia , Small Sarah , Davidson Nancy E. , Peters David G. , Tseng George C. , Oesterreich Steffi , Lee Adrian V.
Published: April 2023

Supplemental Figure S4. Full representation of CpG methylation analysis in the confirmation of Methyl-Seq DNA methylation by bisulfite sequencing. (A) The percent methylation for each CpG site after bisulfite sequencing on mammary gland genomic DNA is represented. Each of the top differentially methylated genes chosen for validation are depicted. (B) Bisulfite sequencing data of all clones from each animal are shown. Each circle represents a CpG site and each horizontal line represents DNA from a separate clone. Open circles = unmethylated, and closed circles = methylated.
Supplementary Figure 3 from Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition
Authors: Katz Tiffany A. , Liao Serena G. , Palmieri Vincent J. , Dearth Robert K. , Pathiraja Thushangi N. , Huo Zhiguang , Shaw Patricia , Small Sarah , Davidson Nancy E. , Peters David G. , Tseng George C. , Oesterreich Steffi , Lee Adrian V.
Published: April 2023

Supplemental Figure S3. Mapping efficiency was above 50 for all samples in both time points. One sample was an outlier in the early time point (P12) and one at the late time point (NP4) and were removed from further analysis. Both Pearson Correlation plots and Principal Component Analysis are displayed.
Supplementary Tables 1, 3-5, Methods from Noninvasive Detection of Candidate Molecular Biomarkers in Subjects with a History of Insulin Resistance and Colorectal Adenomas
Authors: Zhao Chen , Ivanov Ivan , Dougherty Edward R. , Hartman Terryl J. , Lanza Elaine , Bobe Gerd , Colburn Nancy H. , Lupton Joanne R. , Davidson Laurie A. , Chapkin Robert S.
Published: April 2023

Supplementary Tables 1, 3-5, Methods from Noninvasive Detection of Candidate Molecular Biomarkers in Subjects with a History of Insulin Resistance and Colorectal Adenomas
Supplement Table 2 from Chemopreventive Effects of Korean Angelica versus Its Major Pyranocoumarins on Two Lineages of Transgenic Adenocarcinoma of Mouse Prostate Carcinogenesis
Authors: Tang Su-Ni , Zhang Jinhui , Wu Wei , Jiang Peixin , Puppala Manohar , Zhang Yong , Xing Chengguo , Kim Sung-Hoon , Jiang Cheng , Lü Junxuan
Published: April 2023

Effect of daily gavage of AGN or D/DA on weights of prostate lobes in TRAMP mice vs. wild type.
Supplementary Table S1 from Assessment of Esophageal Adenocarcinoma Risk Using Somatic Chromosome Alterations in Longitudinal Samples in Barrett's Esophagus
Authors: Li Xiaohong , Paulson Thomas G. , Galipeau Patricia C. , Sanchez Carissa A. , Liu Karen , Kuhner Mary K. , Maley Carlo C. , Self Steven G. , Vaughan Thomas L. , Reid Brian J. , Blount Patricia L.
Published: April 2023

Population characteristics of study subjects.
Supplementary Figure S2 from Assessment of Esophageal Adenocarcinoma Risk Using Somatic Chromosome Alterations in Longitudinal Samples in Barrett's Esophagus
Authors: Li Xiaohong , Paulson Thomas G. , Galipeau Patricia C. , Sanchez Carissa A. , Liu Karen , Kuhner Mary K. , Maley Carlo C. , Self Steven G. , Vaughan Thomas L. , Reid Brian J. , Blount Patricia L.
Published: April 2023

Schematic describing SCA datasets and statistical methods used in model training, comparisons, cross-validations, and figures.
Supplemental Tables 1-4 from Notch1 Mutations Are Drivers of Oral Tumorigenesis
Authors: Izumchenko Evgeny , Sun Kai , Jones Sian , Brait Mariana , Agrawal Nishant , Koch Wayne , McCord Christine L. , Riley David R. , Angiuoli Samuel V. , Velculescu Victor E. , Jiang Wei-Wen , Sidransky David
Published: April 2023

Supplemental Tables 1-4. Supp. Table 1. A. List of all OSCC samples used in this study and clinical/pathological data. B. List of 22 matched tumor-normal pairs. Supp. Table 2. List of all normal samples used in this study and clinical/pathological data. Supp. Table 3. List of all oral leukoplakia samples used in this study and clinical/pathological data. Supp. Table 4. Summary of clinical characteristics for OSCC, leukoplakia and normal samples used in this study.
Supplemental table 1 from Effect of Combined Treatment with Ursolic Acid and Resveratrol on Skin Tumor Promotion by 12-O-Tetradecanoylphorbol-13-Acetate
Authors: Cho Jiyoon , Rho Okkyung , Junco Jacob , Carbajal Steve , Siegel Dionicio , Slaga Thomas J. , DiGiovanni John
Published: April 2023

Antibody information for Western blot analysis.
Supplemental figure 4 from Effect of Combined Treatment with Ursolic Acid and Resveratrol on Skin Tumor Promotion by 12-O-Tetradecanoylphorbol-13-Acetate
Authors: Cho Jiyoon , Rho Okkyung , Junco Jacob , Carbajal Steve , Siegel Dionicio , Slaga Thomas J. , DiGiovanni John
Published: April 2023

Effect of UA + Res on DNA binding activity and nuclear translocation of NF-κB, Egr-1, and AP-1 induced by TPA.
Supplementary Table S2 from St. John's Wort Attenuates Colorectal Carcinogenesis in Mice through Suppression of Inflammatory Signaling
Authors: Manna Soumen K. , Golla Srujana , Golla Jaya Prakash , Tanaka Naoki , Cai Yan , Takahashi Shogo , Krausz Kristopher W. , Matsubara Tsutomu , Korboukh Ilia , Gonzalez Frank J.
Published: April 2023

Supplementary Table S2. Diet composition (per 1000 gm).
Supplementary Figure S2B from St. John's Wort Attenuates Colorectal Carcinogenesis in Mice through Suppression of Inflammatory Signaling
Authors: Manna Soumen K. , Golla Srujana , Golla Jaya Prakash , Tanaka Naoki , Cai Yan , Takahashi Shogo , Krausz Kristopher W. , Matsubara Tsutomu , Korboukh Ilia , Gonzalez Frank J.
Published: April 2023

Supplementary Figure S2B: Confirmation of identities of (A) hyperforin and (B) hypericin peaksby comparison of fragmentation pattern with respective authentic standards.
Supplementary Figure S2A from St. John's Wort Attenuates Colorectal Carcinogenesis in Mice through Suppression of Inflammatory Signaling
Authors: Manna Soumen K. , Golla Srujana , Golla Jaya Prakash , Tanaka Naoki , Cai Yan , Takahashi Shogo , Krausz Kristopher W. , Matsubara Tsutomu , Korboukh Ilia , Gonzalez Frank J.
Published: April 2023

Supplementary Figure S2A: Confirmation of identities of (A) hyperforin and (B) hypericin peaksby comparison of fragmentation pattern with respective authentic standards.