bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Frequent Alterations and Epigenetic Silencing of Differentiation Pathway Genes in Structurally Rearranged Liposarcomas
Authors: Taylor Barry S. , DeCarolis Penelope L. , Angeles Christina V. , Brenet Fabienne , Schultz Nikolaus , Antonescu Cristina R. , Scandura Joseph M. , Sander Chris , Viale Agnes J. , Socci Nicholas D. , Singer Samuel
Published: March 2024

Abstract
We explored diverse alterations contributing to liposarcomagenesis by sequencing the genome, exome, transcriptome, and cytosine methylome of a primary and recurrent dedifferentiated liposarcoma (DLPS) from distinct chemotherapy/radiotherapy-naïve patients. The liposarcoma genomes had complex structural rearrangements, but in different patterns, and with varied effects on the structure and expression of affected genes. While the point mutation rate was modest, integrative analyses and additional screening identified somatic mutations in HDAC1 in 8.3% of DLPS. Liposarcoma methylomes revealed alterations in differentiation pathway genes, including CEBPA methylation in 24% of DLPS. Treatment with demethylating agents, which restored CEBPA expression in DLPS cells, was antiproliferative and proapoptotic in vitro and reduced tumor growth in vivo. Both genetic and epigenetic abnormalities established a role for small RNAs in liposarcomagenesis, typified by methylation-induced silencing of microRNA-193b in DLPS but not its well-differentiated counterpart. These findings reveal an unanticipated role for epigenetic abnormalities in DLPS tumors and suggest demethylating agents as potential therapeutics.

Significance: Multimodality sequence analysis of DLPS revealed recurrent mutations and epigenetic abnormalities critical to liposarcomagenesis and to the suppression of adipocyte differentiation. Pharmacologic inhibition of DNA methylation promoted apoptosis and differentiated DLPS cells in vitro and inhibited tumor growth in vivo, providing a rationale for investigating methylation inhibitors in this disease. Cancer Discovery; 1(7); 587–97. ©2011 AACR.

Read the Commentary on this article by Meltzer and Helman, p. 555

This article is highlighted in the In This Issue feature, p. 539
Data from Therapeutic Synergy between microRNA and siRNA in Ovarian Cancer Treatment
Authors: Nishimura Masato , Jung Eun-Jung , Shah Maitri Y. , Lu Chunhua , Spizzo Riccardo , Shimizu Masayoshi , Han Hee Dong , Ivan Cristina , Rossi Simona , Zhang Xinna , Nicoloso Milena S. , Wu Sherry Y. , Almeida Maria Ines , Bottsford-Miller Justin , Pecot Chad V. , Zand Behrouz , Matsuo Koji , Shahzad Mian M. , Jennings Nicholas B. , Rodriguez-Aguayo Cristian , Lopez-Berestein Gabriel , Sood Anil K. , Calin George A.
Published: March 2024

Abstract
Development of improved RNA interference–based strategies is of utmost clinical importance. Although siRNA-mediated silencing of EphA2, an ovarian cancer oncogene, results in reduction of tumor growth, we present evidence that additional inhibition of EphA2 by a microRNA (miRNA) further “boosts” its antitumor effects. We identified miR-520d-3p as a tumor suppressor upstream of EphA2, whose expression correlated with favorable outcomes in two independent patient cohorts comprising 647 patients. Restoration of miR-520d-3p prominently decreased EphA2 protein levels, and suppressed tumor growth and migration/invasion both in vitro and in vivo. Dual inhibition of EphA2 in vivo using 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) nanoliposomes loaded with miR-520d-3p and EphA2 siRNA showed synergistic antitumor efficiency and greater therapeutic efficacy than either monotherapy alone. This synergy is at least in part due to miR-520d-3p targeting EphB2, another Eph receptor. Our data emphasize the feasibility of combined miRNA–siRNA therapy, and will have broad implications for innovative gene silencing therapies for cancer and other diseases.

Significance: This study addresses a new concept of RNA inhibition therapy by combining miRNA and siRNA in nanoliposomal particles to target oncogenic pathways altered in ovarian cancer. Combined targeting of the Eph pathway using EphA2-targeting siRNA and the tumor suppressor miR-520d-3p exhibits remarkable therapeutic synergy and enhanced tumor suppression in vitro and in vivo compared with either monotherapy alone. Cancer Discov; 3(11); 1302–15. ©2013 AACR.

See related commentary by Kasinski and Slack, p. 1220

This article is highlighted in the In This Issue feature, p. 1207
Data from A20 Ubiquitin Ligase–Mediated Polyubiquitination of RIP1 Inhibits Caspase-8 Cleavage and TRAIL-Induced Apoptosis in Glioblastoma
Authors: Bellail Anita C. , Olson Jeffrey J. , Yang Xiaolu , Chen Zhijian J. , Hao Chunhai
Published: March 2024

Abstract
The TNF-related apoptosis-inducing ligand (TRAIL) apoptotic pathway has emerged as a therapeutic target for the treatment of cancer. However, clinical trials have proven that the vast majority of human cancers are resistant to TRAIL apoptotic pathway-targeted therapies. We show that A20-mediated ubiquitination inhibits caspase-8 cleavage and TRAIL-induced apoptosis in glioblastoma through 2 signaling complexes. A20 is highly expressed in glioblastomas and, together with the death receptor 5 and receptor-interacting protein 1, forms a plasma membrane-bound preligand assembly complex under physiologic conditions. Treatment with TRAIL leads to the recruitment of caspase-8 to the plasma membrane-bound preligand assembly complex for the assembly of a death-inducing signaling complex. In the death-inducing signaling complex, the C-terminal zinc finger (Znf) domain of the A20 ubiquitin ligase mediates receptor-interacting protein 1 polyubiquitination through lysine-63-linked polyubiquitin chains, which bind to the caspase-8 protease domain and inhibit caspase-8 dimerization, cleavage, and the initiation of TRAIL-induced apoptosis in glioblastoma-derived cell lines and tumor-initiating cells.

Significance: These results identify A20 E3 ligase as a therapeutic target whose inhibition can overcome TNF-related apoptosis-inducing ligand resistance in glioblastoma and thus have an impact on ongoing clinical trials of TNF-related apoptosis-inducing ligand-targeted combination cancer therapies. Cancer Discovery; 2(2); 140–55. © 2012 AACR.

Read the Commentary on this article by Verbrugge and Johnstone, p. 112.

This article is highlighted in the In This Issue feature, p. 95.
Data from NOTCH Decoys That Selectively Block DLL/NOTCH or JAG/NOTCH Disrupt Angiogenesis by Unique Mechanisms to Inhibit Tumor Growth
Authors: Kangsamaksin Thaned , Murtomaki Aino , Kofler Natalie M. , Cuervo Henar , Chaudhri Reyhaan A. , Tattersall Ian W. , Rosenstiel Paul E. , Shawber Carrie J. , Kitajewski Jan
Published: March 2024

Abstract
A proangiogenic role for Jagged (JAG)-dependent activation of NOTCH signaling in the endothelium has yet to be described. Using proteins that encoded different NOTCH1 EGF-like repeats, we identified unique regions of Delta-like ligand (DLL)–class and JAG-class ligand–receptor interactions, and developed NOTCH decoys that function as ligand-specific NOTCH inhibitors. N110–24 decoy blocked JAG1/JAG2–mediated NOTCH1 signaling, angiogenic sprouting in vitro, and retinal angiogenesis, demonstrating that JAG-dependent NOTCH signal activation promotes angiogenesis. In tumors, N110–24 decoy reduced angiogenic sprouting, vessel perfusion, pericyte coverage, and tumor growth. JAG–NOTCH signaling uniquely inhibited expression of antiangiogenic soluble (s) VEGFR1/sFLT1. N11–13 decoy interfered with DLL1–DLL4-mediated NOTCH1 signaling and caused endothelial hypersprouting in vitro, in retinal angiogenesis, and in tumors. Thus, blockade of JAG- or DLL-mediated NOTCH signaling inhibits angiogenesis by distinct mechanisms. JAG–NOTCH signaling positively regulates angiogenesis by suppressing sVEGFR1–sFLT1 and promoting mural–endothelial cell interactions. Blockade of JAG-class ligands represents a novel, viable therapeutic approach to block tumor angiogenesis and growth.

Significance: This is the first report identifying unique regions of the NOTCH1 extracellular domain that interact with JAG-class and DLL-class ligands. Using this knowledge, we developed therapeutic agents that block JAG-dependent NOTCH signaling and demonstrate for the first time that JAG blockade inhibits experimental tumor growth by targeting tumor angiogenesis. Cancer Discov; 5(2); 182–97. ©2014 AACR.

See related commentary by Briot and Iruela-Arispe, p. 112

This article is highlighted in the In This Issue feature, p. 97
Data from Primary Melanoma of the CNS in Children Is Driven by Congenital Expression of Oncogenic NRAS in Melanocytes
Authors: Pedersen Malin , Küsters-Vandevelde Heidi V.N. , Viros Amaya , Groenen Patricia J.T.A. , Sanchez-Laorden Berta , Gilhuis Jacobus H. , van Engen-van Grunsven Ilse A. , Renier Willy , Schieving Jolanda , Niculescu-Duvaz Ion , Springer Caroline J. , Küsters Benno , Wesseling Pieter , Blokx Willeke A.M. , Marais Richard
Published: March 2024

Abstract
NRAS mutations are common in human melanoma. To produce a mouse model of NRAS-driven melanoma, we expressed oncogenic NRAS (NRASG12D) in mouse melanocytes. When NRASG12D was expressed in the melanocytes of developing embryos, it induced melanocyte proliferation and congenital melanocytic lesions reminiscent of human blue nevi but did not induce cutaneous melanoma. Unexpectedly, however, it did induce early-onset primary melanoma of the central nervous system (CNS). The tumors were rapidly proliferating and caused neurologic symptoms, rapid health deterioration, and death. NRAS is not a common driver oncogene of primary melanoma of the CNS in adults, but we report two cases of primary melanoma of the CNS in children, both of which carried oncogenic mutations in NRAS. We conclude that acquisition of somatic mutations in NRAS in CNS melanocytes is a predisposing risk factor for primary melanoma of the CNS in children, and we present a mouse model of this disease.

Significance: We show that the acquisition of NRAS mutations in melanocytes during embryogenesis is a risk factor for early-onset melanoma of the CNS. We have developed a powerful mouse model to study this rare but devastating childhood disease, and to develop therapeutic approaches for its treatment. Cancer Discov; 3(4); 458–69. ©2013 AACR.

See related commentary by Ciarlo and Zon, p. 382

This article is highlighted in the In This Issue feature, p. 363
Data from MEK-Dependent Negative Feedback Underlies BCR–ABL-Mediated Oncogene Addiction
Authors: Asmussen Jennifer , Lasater Elisabeth A. , Tajon Cheryl , Oses-Prieto Juan , Jun Young-wook , Taylor Barry S. , Burlingame Alma , Craik Charles S. , Shah Neil P.
Published: March 2024

Abstract
The clinical experience with BCR–ABL tyrosine kinase inhibitors (TKI) for the treatment of chronic myelogenous leukemia (CML) provides compelling evidence for oncogene addiction. Yet, the molecular basis of oncogene addiction remains elusive. Through unbiased quantitative phosphoproteomic analyses of CML cells transiently exposed to BCR–ABL TKI, we identified persistent downregulation of growth factor receptor (GF-R) signaling pathways. We then established and validated a tissue-relevant isogenic model of BCR–ABL-mediated addiction, and found evidence for myeloid GF-R signaling pathway rewiring that profoundly and persistently dampens physiologic pathway activation. We demonstrate that eventual restoration of ligand-mediated GF-R pathway activation is insufficient to fully rescue cells from a competing apoptotic fate. In contrast to previous work with BRAFV600E in melanoma cells, feedback inhibition following BCR–ABL TKI treatment is markedly prolonged, extending beyond the time required to initiate apoptosis. Mechanistically, BCR–ABL-mediated oncogene addiction is facilitated by persistent high levels of MAP–ERK kinase (MEK)-dependent negative feedback.

Significance: We found that BCR–ABL can confer addiction in vitro by rewiring myeloid GF-R signaling through establishment of MEK-dependent negative feedback. Our findings predict that deeper, more durable responses to targeted agents across a range of malignancies may be facilitated by maintaining negative feedback concurrently with oncoprotein inhibition. Cancer Discov; 4(2); 200–15. ©2013 AACR.

This article is highlighted in the In This Issue feature, p. 131
Data from Induction of Telomere Dysfunction Mediated by the Telomerase Substrate Precursor 6-Thio-2′-Deoxyguanosine
Authors: Mender Ilgen , Gryaznov Sergei , Dikmen Z. Gunnur , Wright Woodring E. , Shay Jerry W.
Published: March 2024

Abstract
The relationships between telomerase and telomeres represent attractive targets for new anticancer agents. Here, we report that the nucleoside analogue 6-thio-2′-deoxyguanosine (6-thio-dG) is recognized by telomerase and is incorporated into de novo–synthesized telomeres. This results in modified telomeres, leading to telomere dysfunction, but only in cells expressing telomerase. 6-Thio-dG, but not 6-thioguanine, induced telomere dysfunction in telomerase-positive human cancer cells and hTERT-expressing human fibroblasts, but not in telomerase-negative cells. Treatment with 6-thio-dG resulted in rapid cell death for the vast majority of the cancer cell lines tested, whereas normal human fibroblasts and human colonic epithelial cells were largely unaffected. In A549 lung cancer cell–based mouse xenograft studies, 6-thio-dG caused a decrease in the tumor growth rate superior to that observed with 6-thioguanine treatment. In addition, 6-thio-dG increased telomere dysfunction in tumor cells in vivo. These results indicate that 6-thio-dG may provide a new telomere-addressed telomerase-dependent anticancer approach.

Significance: Telomerase is an almost universal oncology target, yet there are few telomerase-directed therapies in human clinical trials. In the present study, we demonstrate a small-molecule telomerase substrate approach that induces telomerase-mediated targeted “telomere uncapping,” but only in telomerase-positive cancer cells, with minimal effects in normal telomerase-negative cells. Cancer Discov; 5(1); 82–95. ©2014 AACR.

See related commentary by Wellinger, p. 19.

This article is highlighted in the In This Issue feature, p. 1
Data from Biallelic Deleterious BRCA1 Mutations in a Woman with Early-Onset Ovarian Cancer
Authors: Domchek Susan M. , Tang Jiangbo , Stopfer Jill , Lilli Dana R. , Hamel Nancy , Tischkowitz Marc , Monteiro Alvaro N.A. , Messick Troy E. , Powers Jacquelyn , Yonker Alexandria , Couch Fergus J. , Goldgar David E. , Davidson H. Rosemarie , Nathanson Katherine L. , Foulkes William D. , Greenberg Roger A.
Published: March 2024

Abstract
BRCA1 and BRCA2 are the most important breast and ovarian cancer susceptibility genes. Biallelic mutations in BRCA2 can lead to Fanconi anemia and predisposition to cancers, whereas biallelic BRCA1 mutations have not been confirmed, presumably because one wild-type BRCA1 allele is required during embryogenesis. This study describes an individual who was diagnosed with ovarian carcinoma at age 28 and found to have one allele with a deleterious mutation in BRCA1, c.2457delC (p.Asp821Ilefs*25), and a second allele with a variant of unknown significance in BRCA1, c.5207T>C (p.Val1736Ala). Medical records revealed short stature, microcephaly, developmental delay, and significant toxicity from chemotherapy. BRCA1 p.Val1736Ala cosegregated with cancer in multiple families, associated tumors showed loss of wild-type BRCA1, and BRCA1 p.Val1736Ala showed reduced DNA damage localization. These findings represent the first validated example of biallelic deleterious human BRCA1 mutations and have implications for the interpretation of genetic test results.

Significance: Accurate assessment of genetic testing data for BRCA1 mutations is essential for clinical monitoring and treatment strategies. Here, we report the first validated example of an individual with biallelic BRCA1 mutations, early-onset ovarian cancer, and clinically significant hypersensitivity to chemotherapy. Cancer Discov; 3(4); 399–405. ©2012 AACR.

See related commentary by D'Andrea, p. 376

This article is highlighted in the In This Issue feature, p. 363
Data from Prospective Blinded Study of BRAFV600E Mutation Detection in Cell-Free DNA of Patients with Systemic Histiocytic Disorders
Authors: Hyman David M. , Diamond Eli L. , Vibat Cecile Rose T. , Hassaine Latifa , Poole Jason C. , Patel Minal , Holley Veronica R. , Cabrilo Goran , Lu Timothy T. , Arcila Maria E. , Chung Young Rock , Rampal Raajit , Lacouture Mario E. , Rosen Neal , Meric-Bernstam Funda , Baselga José , Kurzrock Razelle , Erlander Mark G. , Janku Filip , Abdel-Wahab Omar
Published: March 2024

Abstract
Patients with Langerhans cell histiocytosis (LCH) and Erdheim–Chester disease (ECD) have a high frequency of BRAFV600E mutations and respond to RAF inhibitors. However, detection of mutations in tissue biopsies is particularly challenging in histiocytoses due to low tumor content and stromal contamination. We applied a droplet-digital PCR assay for quantitative detection of the BRAFV600E mutation in plasma and urine cell-free (cf) DNA and performed a prospective, blinded study in 30 patients with ECD/LCH. There was 100% concordance between tissue and urinary cfDNA genotype in treatment-naïve samples. cfDNA analysis facilitated identification of previously undescribed KRASG12S-mutant ECD and dynamically tracked disease burden in patients treated with a variety of therapies. These results indicate that cfDNA BRAFV600E mutational analysis in plasma and urine provides a convenient and reliable method of detecting mutational status and can serve as a noninvasive biomarker to monitor response to therapy in LCH and ECD.

Significance: Patients with BRAFV600E-mutant histiocytic disorders have remarkable responses to RAF inhibition, but mutation detection in tissue in these disorders is challenging. Here, we identify that analysis of plasma and urinary cfDNA provides a reliable method to detect the BRAFV600E mutation and monitor response to therapy in these disorders. Cancer Discov; 5(1); 64–71. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 1
Data from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
Authors: Brastianos Priscilla K. , Carter Scott L. , Santagata Sandro , Cahill Daniel P. , Taylor-Weiner Amaro , Jones Robert T. , Van Allen Eliezer M. , Lawrence Michael S. , Horowitz Peleg M. , Cibulskis Kristian , Ligon Keith L. , Tabernero Josep , Seoane Joan , Martinez-Saez Elena , Curry William T. , Dunn Ian F. , Paek Sun Ha , Park Sung-Hye , McKenna Aaron , Chevalier Aaron , Rosenberg Mara , Barker Frederick G. , Gill Corey M. , Van Hummelen Paul , Thorner Aaron R. , Johnson Bruce E. , Hoang Mai P. , Choueiri Toni K. , Signoretti Sabina , Sougnez Carrie , Rabin Michael S. , Lin Nancy U. , Winer Eric P. , Stemmer-Rachamimov Anat , Meyerson Matthew , Garraway Levi , Gabriel Stacey , Lander Eric S. , Beroukhim Rameen , Batchelor Tracy T. , Baselga José , Louis David N. , Getz Gad , Hahn William C.
Published: March 2024

Abstract
Brain metastases are associated with a dismal prognosis. Whether brain metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. We performed whole-exome sequencing of 86 matched brain metastases, primary tumors, and normal tissue. In all clonally related cancer samples, we observed branched evolution, where all metastatic and primary sites shared a common ancestor yet continued to evolve independently. In 53% of cases, we found potentially clinically informative alterations in the brain metastases not detected in the matched primary-tumor sample. In contrast, spatially and temporally separated brain metastasis sites were genetically homogenous. Distal extracranial and regional lymph node metastases were highly divergent from brain metastases. We detected alterations associated with sensitivity to PI3K/AKT/mTOR, CDK, and HER2/EGFR inhibitors in the brain metastases. Genomic analysis of brain metastases provides an opportunity to identify potentially clinically informative alterations not detected in clinically sampled primary tumors, regional lymph nodes, or extracranial metastases.

Significance: Decisions for individualized therapies in patients with brain metastasis are often made from primary-tumor biopsies. We demonstrate that clinically actionable alterations present in brain metastases are frequently not detected in primary biopsies, suggesting that sequencing of primary biopsies alone may miss a substantial number of opportunities for targeted therapy. Cancer Discov; 5(11); 1164–77. ©2015 AACR.

See related commentary by Stricker and Arteaga, p. 1124.

This article is highlighted in the In This Issue feature, p. 1111
Data from GSK-3α Promotes Oncogenic KRAS Function in Pancreatic Cancer via TAK1–TAB Stabilization and Regulation of Noncanonical NF-κB
Authors: Bang Deepali , Wilson Willie , Ryan Meagan , Yeh Jen Jen , Baldwin Albert S.
Published: March 2024

Abstract
Mutations in KRAS drive the oncogenic phenotype in a variety of tumors of epithelial origin. The NF-κB transcription factor pathway is important for oncogenic RAS to transform cells and to drive tumorigenesis in animal models. Recently, TGF-β–activated kinase 1 (TAK1), an upstream regulator of IκB kinase (IKK), which controls canonical NF-κB signaling, was shown to be important for chemoresistance in pancreatic cancer and for regulating KRAS-mutant colorectal cancer cell growth and survival. Here, we show that mutant KRAS upregulates glycogen synthase kinase 3α (GSK-3α), leading to its interaction with TAK1 to stabilize the TAK1–TAB complex to promote IKK activity. In addition, GSK-3α is required for promoting critical noncanonical NF-κB signaling in pancreatic cancer cells. Pharmacologic inhibition of GSK-3 suppresses growth of human pancreatic tumor explants, consistent with the loss of expression of oncogenic genes such as c-myc and TERT. These data identify GSK-3α as a key downstream effector of oncogenic KRAS via its ability to coordinately regulate distinct NF-κB signaling pathways.

Significance: GSK-3α functions to promote IKK/NF-κB activity downstream of oncogenic KRAS via stabilization and activation of the TAK1/TAB complex and to promote noncanonical NF-κB activity via control of nuclear levels of NF-κB2. Inhibition of GSK-3 strongly suppresses growth of human pancreatic tumor explants with downregulation of certain oncogenic NF-κB target genes such as c-myc and TERT. Cancer Discov; 3(6); 690–703. ©2013 AACR.

This article is highlighted in the In This Issue feature, p. 591
Data from Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma
Authors: Ryan Russell J.H. , Drier Yotam , Whitton Holly , Cotton M. Joel , Kaur Jasleen , Issner Robbyn , Gillespie Shawn , Epstein Charles B. , Nardi Valentina , Sohani Aliyah R. , Hochberg Ephraim P. , Bernstein Bradley E.
Published: March 2024

Abstract
B-cell lymphomas frequently contain genomic rearrangements that lead to oncogene activation by heterologous distal regulatory elements. We used a novel approach called “pinpointing enhancer-associated rearrangements by chromatin immunoprecipitation,” or PEAR-ChIP, to simultaneously map enhancer activity and proximal rearrangements in lymphoma cell lines and patient biopsies. This method detects rearrangements involving known cancer genes, including CCND1, BCL2, MYC, PDCD1LG2, NOTCH1, CIITA, and SGK1, as well as novel enhancer duplication events of likely oncogenic significance. We identify lymphoma subtype–specific enhancers in the MYC locus that are silenced in lymphomas with MYC-activating rearrangements and are associated with germline polymorphisms that alter lymphoma risk. We show that BCL6-locus enhancers are acetylated by the BCL6-activating transcription factor MEF2B, and can undergo genomic duplication, or target the MYC promoter for activation in the context of a “pseudo-double-hit” t(3;8)(q27;q24) rearrangement linking the BCL6 and MYC loci. Our work provides novel insights regarding enhancer-driven oncogene activation in lymphoma.

Significance: We demonstrate a novel approach for simultaneous detection of genomic rearrangements and enhancer activity in tumor biopsies. We identify novel mechanisms of enhancer-driven regulation of the oncogenes MYC and BCL6, and show that the BCL6 locus can serve as an enhancer donor in an “enhancer hijacking” translocation. Cancer Discov; 5(10); 1058–71. ©2015 AACR.

See related commentary by Mack et al., p. 1018.

This article is highlighted in the In This Issue feature, p. 1005
Data from The Basic Principles of Chimeric Antigen Receptor Design
Authors: Sadelain Michel , Brentjens Renier , Rivière Isabelle
Published: March 2024

Abstract
Chimeric antigen receptors (CAR) are recombinant receptors that provide both antigen-binding and T-cell–activating functions. A multitude of CARs has been reported over the past decade, targeting an array of cell surface tumor antigens. Their biologic functions have dramatically changed following the introduction of tripartite receptors comprising a costimulatory domain, termed second-generation CARs. These have recently shown clinical benefit in patients treated with CD19-targeted autologous T cells. CARs may be combined with costimulatory ligands, chimeric costimulatory receptors, or cytokines to further enhance T-cell potency, specificity, and safety. CARs represent a new class of drugs with exciting potential for cancer immunotherapy.

Significance: CARs are a new class of drugs with great potential for cancer immunotherapy. Upon their expression in T lymphocytes, CARs direct potent, targeted immune responses that have recently shown encouraging clinical outcomes in a subset of patients with B-cell malignancies. This review focuses on the design of CARs, including the requirements for optimal antigen recognition and different modalities to provide costimulatory support to targeted T cells, which include the use of second- and third-generation CARs, costimulatory ligands, chimeric costimulatory receptors, and cytokines. Cancer Discov; 3(4); 388–98. ©2013 AACR.
Data from Evolution of DNA Methylation Is Linked to Genetic Aberrations in Chronic Lymphocytic Leukemia
Authors: Oakes Christopher C. , Claus Rainer , Gu Lei , Assenov Yassen , Hüllein Jennifer , Zucknick Manuela , Bieg Matthias , Brocks David , Bogatyrova Olga , Schmidt Christopher R. , Rassenti Laura , Kipps Thomas J. , Mertens Daniel , Lichter Peter , Döhner Hartmut , Stilgenbauer Stephan , Byrd John C. , Zenz Thorsten , Plass Christoph
Published: March 2024

Abstract
Although clonal selection by genetic driver aberrations in cancer is well documented, the ability of epigenetic alterations to promote tumor evolution is undefined. We used 450k arrays and next-generation sequencing to evaluate intratumor heterogeneity and evolution of DNA methylation and genetic aberrations in chronic lymphocytic leukemia (CLL). CLL cases exhibit vast interpatient differences in intratumor methylation heterogeneity, with genetically clonal cases maintaining low methylation heterogeneity and up to 10% of total CpGs in a monoallelically methylated state. Increasing methylation heterogeneity correlates with advanced genetic subclonal complexity. Selection of novel DNA methylation patterns is observed only in cases that undergo genetic evolution, and independent genetic evolution is uncommon and is restricted to low-risk alterations. These results reveal that although evolution of DNA methylation occurs in high-risk, clinically progressive cases, positive selection of novel methylation patterns entails coevolution of genetic alteration(s) in CLL.

Significance: Epigenetic alterations are pervasive in cancer and continually develop during disease progression; however, the mechanisms that promote changes in the tumor epigenome at large are currently undefined. The current work provides insight into the coevolution of genetic and epigenetic aberrations and highlights the influential role of genetic aberrations in the selection of novel methylation patterns. Cancer Discov; 4(3); 348–61. ©2013 AACR.

This article is highlighted in the In This Issue feature, p. 259
Data from The Androgen-Regulated Protease TMPRSS2 Activates a Proteolytic Cascade Involving Components of the Tumor Microenvironment and Promotes Prostate Cancer Metastasis
Authors: Lucas Jared M. , Heinlein Cynthia , Kim Tom , Hernandez Susana A. , Malik Muzdah S. , True Lawrence D. , Morrissey Colm , Corey Eva , Montgomery Bruce , Mostaghel Elahe , Clegg Nigel , Coleman Ilsa , Brown Christopher M. , Schneider Eric L. , Craik Charles , Simon Julian A. , Bedalov Antonio , Nelson Peter S.
Published: March 2024

Abstract
TMPRSS2 is an androgen-regulated cell-surface serine protease expressed predominantly in prostate epithelium. TMPRSS2 is expressed highly in localized high-grade prostate cancers and in the majority of human prostate cancer metastases. Through the generation of mouse models with a targeted deletion of Tmprss2, we demonstrate that the activity of this protease regulates cancer cell invasion and metastasis to distant organs. By screening combinatorial peptide libraries, we identified a spectrum of TMPRSS2 substrates that include pro-hepatocyte growth factor (HGF). HGF activated by TMPRSS2 promoted c-MET receptor tyrosine kinase signaling, and initiated a proinvasive epithelial-to-mesenchymal transition phenotype. Chemical library screens identified a potent bioavailable TMPRSS2 inhibitor that suppressed prostate cancer metastasis in vivo. Together, these findings provide a mechanistic link between androgen-regulated signaling programs and prostate cancer metastasis that operate via context-dependent interactions with extracellular constituents of the tumor microenvironment.

Significance: The vast majority of prostate cancer deaths are due to metastasis. Loss of TMPRSS2 activity dramatically attenuated the metastatic phenotype through mechanisms involving the HGF–c-MET axis. Therapeutic approaches directed toward inhibiting TMPRSS2 may reduce the incidence or progression of metastasis in patients with prostate cancer. Cancer Discov; 4(11); 1310–25. ©2014 AACR.

See related commentary by Rubin, p. 1262

This article is highlighted in the In This Issue feature, p. 1243
Data from A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors
Authors: Konieczkowski David J. , Johannessen Cory M. , Abudayyeh Omar , Kim Jong Wook , Cooper Zachary A. , Piris Adriano , Frederick Dennie T. , Barzily-Rokni Michal , Straussman Ravid , Haq Rizwan , Fisher David E. , Mesirov Jill P. , Hahn William C. , Flaherty Keith T. , Wargo Jennifer A. , Tamayo Pablo , Garraway Levi A.
Published: March 2024

Abstract
Most melanomas harbor oncogenic BRAFV600 mutations, which constitutively activate the MAPK pathway. Although MAPK pathway inhibitors show clinical benefit in BRAFV600-mutant melanoma, it remains incompletely understood why 10% to 20% of patients fail to respond. Here, we show that RAF inhibitor–sensitive and inhibitor-resistant BRAFV600-mutant melanomas display distinct transcriptional profiles. Whereas most drug-sensitive cell lines and patient biopsies showed high expression and activity of the melanocytic lineage transcription factor MITF, intrinsically resistant cell lines and biopsies displayed low MITF expression but higher levels of NF-κB signaling and the receptor tyrosine kinase AXL. In vitro, these MITF-low/NF-κB–high melanomas were resistant to inhibition of RAF and MEK, singly or in combination, and ERK. Moreover, in cell lines, NF-κB activation antagonized MITF expression and induced both resistance marker genes and drug resistance. Thus, distinct cell states characterized by MITF or NF-κB activity may influence intrinsic resistance to MAPK pathway inhibitors in BRAFV600-mutant melanoma.

Significance: Although most BRAFV600-mutant melanomas are sensitive to RAF and/or MEK inhibitors, a subset fails to respond to such treatment. This study characterizes a transcriptional cell state distinction linked to MITF and NF-κB that may modulate intrinsic sensitivity of melanomas to MAPK pathway inhibitors. Cancer Discov; 4(7); 816–27. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 745
Data from Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer
Authors: Junankar Simon , Shay Gemma , Jurczyluk Julie , Ali Naveid , Down Jenny , Pocock Nicholas , Parker Andrew , Nguyen Akira , Sun Shuting , Kashemirov Boris , McKenna Charles E. , Croucher Peter I. , Swarbrick Alexander , Weilbaecher Katherine , Phan Tri Giang , Rogers Michael J.
Published: March 2024

Abstract
Recent clinical trials have shown that bisphosphonate drugs improve breast cancer patient survival independent of their antiresorptive effects on the skeleton. However, because bisphosphonates bind rapidly to bone mineral, the exact mechanisms of their antitumor action, particularly on cells outside of bone, remain unknown. Here, we used real-time intravital two-photon microscopy to show extensive leakage of fluorescent bisphosphonate from the vasculature in 4T1 mouse mammary tumors, where it initially binds to areas of small, granular microcalcifications that are engulfed by tumor-associated macrophages (TAM), but not tumor cells. Importantly, we also observed uptake of radiolabeled bisphosphonate in the primary breast tumor of a patient and showed the resected tumor to be infiltrated with TAMs and to contain similar granular microcalcifications. These data represent the first compelling in vivo evidence that bisphosphonates can target cells in tumors outside the skeleton and that their antitumor activity is likely to be mediated via TAMs.

Significance: Bisphosphonates are assumed to act solely in bone. However, mouse models and clinical trials show that they have surprising antitumor effects outside bone. We provide unequivocal evidence that bisphosphonates target TAMs, but not tumor cells, to exert their extraskeletal effects, offering a rationale for use in patients with early disease. Cancer Discov; 5(1); 35–42. ©2014 AACR.

See related commentary by Sterling, p. 14

This article is highlighted in the In This Issue feature, p. 1
Data from PI3′-Kinase Inhibition Forestalls the Onset of MEK1/2 Inhibitor Resistance in BRAF-Mutated Melanoma
Authors: Deuker Marian M. , Marsh Durban Victoria , Phillips Wayne A. , McMahon Martin
Published: March 2024

Abstract
Phosphatidylinositide 3′ (PI3′)-lipid signaling cooperates with oncogenic BRAFV600E to promote melanomagenesis. Sustained PI3′-lipid production commonly occurs via silencing of the PI3′-lipid phosphatase PTEN or, less commonly, through mutational activation of PIK3CA, encoding the 110-kDa catalytic subunit of PI3′-kinase-α (PI3Kα). To define the PI3K catalytic isoform dependency of BRAF-mutated melanoma, we used pharmacologic, isoform-selective PI3K inhibitors in conjunction with melanoma-derived cell lines and genetically engineered mouse (GEM) models. Although BRAFV600E/PIK3CAH1047R melanomas were sensitive to the antiproliferative effects of selective PI3Kα blockade, inhibition of BRAFV600E/PTENNull melanoma proliferation required combined blockade of PI3Kα, PI3Kδ, and PI3Kγ, and was insensitive to PI3Kβ blockade. In GEM models, isoform-selective PI3K inhibition elicited cytostatic effects, but significantly potentiated melanoma regression in response to BRAFV600E pathway–targeted inhibition. Interestingly, PI3K inhibition forestalled the onset of MEK inhibitor resistance in two independent GEM models of BRAFV600E-driven melanoma. These results suggest that combination therapy with PI3K inhibitors may be a useful strategy to extend the duration of clinical response of patients with BRAF-mutated melanoma to BRAFV600E pathway–targeted therapies.

Significance: Although BRAFV600E pathway–targeted therapies elicit melanoma regression, the onset of drug resistance limits the durability of response. Here, we show that combined treatment with PI3K inhibitors significantly forestalled the onset of MEK1/2 inhibitor–resistant disease in BRAF-mutated GEM melanoma models. These results provide a conceptual framework for the combined deployment of BRAFV600E plus PI3K pathway–targeted inhibitors in the treatment of a subset of patients with BRAF-mutated melanoma. Cancer Discov; 5(2); 143–53. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 97
Data from An In Vivo Functional Screen Identifies ST6GalNAc2 Sialyltransferase as a Breast Cancer Metastasis Suppressor
Authors: Murugaesu Nirupa , Iravani Marjan , van Weverwijk Antoinette , Ivetic Aleksandar , Johnson Damian A. , Antonopoulos Aristotelis , Fearns Antony , Jamal-Hanjani Mariam , Sims David , Fenwick Kerry , Mitsopoulos Costas , Gao Qiong , Orr Nick , Zvelebil Marketa , Haslam Stuart M. , Dell Anne , Yarwood Helen , Lord Christopher J. , Ashworth Alan , Isacke Clare M.
Published: March 2024

Abstract
To interrogate the complex mechanisms involved in the later stages of cancer metastasis, we designed a functional in vivo RNA interference (RNAi) screen combined with next-generation sequencing. Using this approach, we identified the sialyltransferase ST6GalNAc2 as a novel breast cancer metastasis suppressor. Mechanistically, ST6GalNAc2 silencing alters the profile of O-glycans on the tumor cell surface, facilitating binding of the soluble lectin galectin-3. This then enhances tumor cell retention and emboli formation at metastatic sites leading to increased metastatic burden, events that can be completely blocked by galectin-3 inhibition. Critically, elevated ST6GALNAC2, but not galectin-3, expression in estrogen receptor–negative breast cancers significantly correlates with reduced frequency of metastatic events and improved survival. These data demonstrate that the prometastatic role of galectin-3 is regulated by its ability to bind to the tumor cell surface and highlight the potential of monitoring ST6GalNAc2 expression to stratify patients with breast cancer for treatment with galectin-3 inhibitors.

Significance: RNAi screens have the potential to uncover novel mechanisms in metastasis but do not necessarily identify clinically relevant therapeutic targets. Our demonstration that the sialyltransferase ST6GalNAc2 acts as a metastasis suppressor by impairing binding of galectin-3 to the tumor cell surface offers the opportunity to identify patients with breast cancer suitable for treatment with clinically well-tolerated galectin-3 inhibitors. Cancer Discov; 4(3); 304–17. ©2014 AACR.

See related commentary by Ferrer and Reginato, p. 275

This article is highlighted in the In This Issue feature, p. 259
Data from l-2-Hydroxyglutarate: An Epigenetic Modifier and Putative Oncometabolite in Renal Cancer
Authors: Shim Eun-Hee , Livi Carolina B. , Rakheja Dinesh , Tan Jubilee , Benson Daniel , Parekh Vishwas , Kho Eun-Young , Ghosh Arindam P. , Kirkman Richard , Velu Sadanan , Dutta Shilpa , Chenna Balachandra , Rea Shane L. , Mishur Robert J. , Li Qiuhua , Johnson-Pais Teresa L. , Guo Lining , Bae Sejong , Wei Shi , Block Karen , Sudarshan Sunil
Published: March 2024

Abstract
Through unbiased metabolomics, we identified elevations of the metabolite 2-hydroxyglutarate (2HG) in renal cell carcinoma (RCC). 2HG can inhibit 2-oxoglutaratre (2-OG)–dependent dioxygenases that mediate epigenetic events, including DNA and histone demethylation. 2HG accumulation, specifically the d enantiomer, can result from gain-of-function mutations of isocitrate dehydrogenase (IDH1, IDH2) found in several different tumors. In contrast, kidney tumors demonstrate elevations of the l enantiomer of 2HG (l-2HG). High-2HG tumors demonstrate reduced DNA levels of 5-hydroxymethylcytosine (5hmC), consistent with 2HG-mediated inhibition of ten-eleven translocation (TET) enzymes, which convert 5-methylcytosine (5mC) to 5hmC. l-2HG elevation is mediated in part by reduced expression of l-2HG dehydrogenase (L2HGDH). L2HGDH reconstitution in RCC cells lowers l-2HG and promotes 5hmC accumulation. In addition, L2HGDH expression in RCC cells reduces histone methylation and suppresses in vitro tumor phenotypes. Our report identifies l-2HG as an epigenetic modifier and putative oncometabolite in kidney cancer.

Significance: Here, we report elevations of the putative oncometabolite l-2HG in the most common subtype of kidney cancer and describe a novel mechanism for the regulation of DNA 5hmC levels. Our findings provide new insight into the metabolic basis for the epigenetic landscape of renal cancer. Cancer Discov; 4(11); 1290–8. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 1243
Data from MAX Inactivation in Small Cell Lung Cancer Disrupts MYC–SWI/SNF Programs and Is Synthetic Lethal with BRG1
Authors: Romero Octavio A. , Torres-Diz Manuel , Pros Eva , Savola Suvi , Gomez Antonio , Moran Sebastian , Saez Carmen , Iwakawa Reika , Villanueva Alberto , Montuenga Luis M. , Kohno Takashi , Yokota Jun , Sanchez-Cespedes Montse
Published: March 2024

Abstract
Our knowledge of small cell lung cancer (SCLC) genetics is still very limited, amplification of L-MYC, N-MYC, and C-MYC being some of the well-established gene alterations. Here, we report our discovery of tumor-specific inactivation of the MYC-associated factor X gene, MAX, in SCLC. MAX inactivation is mutually exclusive with alterations of MYC and BRG1, the latter coding for an ATPase of the switch/sucrose nonfermentable (SWI/SNF) complex. We demonstrate that BRG1 regulates the expression of MAX through direct recruitment to the MAX promoter, and that depletion of BRG1 strongly hinders cell growth, specifically in MAX-deficient cells, heralding a synthetic lethal interaction. Furthermore, MAX requires BRG1 to activate neuroendocrine transcriptional programs and to upregulate MYC targets, such as glycolysis-related genes. Finally, inactivation of the MAX dimerization protein, MGA, was also observed in both non–small cell lung cancer and SCLC. Our results provide evidence that an aberrant SWI/SNF–MYC network is essential for lung cancer development.

Significance: We discovered that the MYC-associated factor X gene, MAX, is inactivated in SCLCs. Furthermore, we revealed a preferential toxicity of the inactivation of the chromatin remodeler BRG1 in MAX-deficient lung cancer cells, which opens novel therapeutic possibilities for the treatment of patients with SCLC with MAX-deficient tumors. Cancer Discov; 4(3); 292–303. ©2013 AACR.

See related commentary by Rudin and Poirier, p. 273

This article is highlighted in the In This Issue feature, p. 259
Data from A Large-Scale Analysis of Genetic Variants within Putative miRNA Binding Sites in Prostate Cancer
Authors: Stegeman Shane , Amankwah Ernest , Klein Kerenaftali , O'Mara Tracy A. , Kim Donghwa , Lin Hui-Yi , Permuth-Wey Jennifer , Sellers Thomas A. , Srinivasan Srilakshmi , Eeles Rosalind , Easton Doug , Kote-Jarai Zsofia , Amin Al Olama Ali , Benlloch Sara , Muir Kenneth , Giles Graham G. , Wiklund Fredrik , Gronberg Henrik , Haiman Christopher A. , Schleutker Johanna , Nordestgaard Børge G. , Travis Ruth C. , Neal David , Pharoah Paul , Khaw Kay-Tee , Stanford Janet L. , Blot William J. , Thibodeau Stephen , Maier Christiane , Kibel Adam S. , Cybulski Cezary , Cannon-Albright Lisa , Brenner Hermann , Kaneva Radka , Teixeira Manuel R. , Spurdle Amanda B. , Clements Judith A. , Park Jong Y. , Batra Jyotsna
Published: March 2024

Abstract
Prostate cancer is the second most common malignancy among men worldwide. Genome-wide association studies have identified 100 risk variants for prostate cancer, which can explain approximately 33% of the familial risk of the disease. We hypothesized that a comprehensive analysis of genetic variations found within the 3′ untranslated region of genes predicted to affect miRNA binding (miRSNP) can identify additional prostate cancer risk variants. We investigated the association between 2,169 miRSNPs and prostate cancer risk in a large-scale analysis of 22,301 cases and 22,320 controls of European ancestry from 23 participating studies. Twenty-two miRSNPs were associated (P < 2.3 × 10−5) with risk of prostate cancer, 10 of which were within 7 genes previously not mapped by GWAS studies. Further, using miRNA mimics and reporter gene assays, we showed that miR-3162-5p has specific affinity for the KLK3 rs1058205 miRSNP T-allele, whereas miR-370 has greater affinity for the VAMP8 rs1010 miRSNP A-allele, validating their functional role.

Significance: Findings from this large association study suggest that a focus on miRSNPs, including functional evaluation, can identify candidate risk loci below currently accepted statistical levels of genome-wide significance. Studies of miRNAs and their interactions with SNPs could provide further insights into the mechanisms of prostate cancer risk. Cancer Discov; 5(4); 368–79. ©2015 AACR.

See related commentary by Yousef, p. 351

This article is highlighted in the In This Issue feature, p. 333
Data from Active CREB1 Promotes a Malignant TGFβ2 Autocrine Loop in Glioblastoma
Authors: Rodón Laura , Gonzàlez-Juncà Alba , del Mar Inda María , Sala-Hojman Ada , Martínez-Sáez Elena , Seoane Joan
Published: March 2024

Abstract
In advanced cancer, including glioblastoma, the TGFβ pathway acts as an oncogenic factor. Some tumors exhibit aberrantly high TGFβ activity, and the mechanisms underlying this phenomenon are not well understood. We have observed that TGFβ can induce TGFβ2, generating an autocrine loop leading to aberrantly high levels of TGFβ2. We identified cAMP-responsive element–binding protein 1 (CREB1) as the critical mediator of the induction of TGFβ2 by TGFβ. CREB1 binds to the TGFB2 gene promoter in cooperation with SMAD3 and is required for TGFβ to activate transcription. Moreover, the PI3K–AKT and RSK pathways regulate the TGFβ2 autocrine loop through CREB1. The levels of CREB1 and active phosphorylated CREB1 correlate with TGFβ2 in glioblastoma. In addition, using patient-derived in vivo models of glioblastoma, we found that CREB1 levels determine the expression of TGFβ2. Our results show that CREB1 can be considered a biomarker to stratify patients for anti-TGFβ treatments and a therapeutic target in glioblastoma.

Significance: TGFβ is considered a promising therapeutic target, and several clinical trials using TGFβ inhibitors are generating encouraging results. Here, we discerned the molecular mechanisms responsible for the aberrantly high levels of TGFβ2 found in certain tumors, and we propose biomarkers to predict the clinical response to anti-TGFβ therapies. Cancer Discov; 4(10); 1230–41. ©2014 AACR.

See related commentary by Wotton, p. 1123

This article is highlighted in the In This Issue feature, p. 1103