bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from RNA Helicase A Is a Downstream Mediator of KIF1Bβ Tumor-Suppressor Function in Neuroblastoma
Authors: Chen Zhi Xiong , Wallis Karin , Fell Stuart M. , Sobrado Veronica R. , Hemmer Marie C. , Ramsköld Daniel , Hellman Ulf , Sandberg Rickard , Kenchappa Rajappa S. , Martinson Tommy , Johnsen John I. , Kogner Per , Schlisio Susanne
Published: March 2024

Abstract
Inherited KIF1B loss-of-function mutations in neuroblastomas and pheochromocytomas implicate the kinesin KIF1B as a 1p36.2 tumor suppressor. However, the mechanism of tumor suppression is unknown. We found that KIF1B isoform β (KIF1Bβ) interacts with RNA helicase A (DHX9), causing nuclear accumulation of DHX9, followed by subsequent induction of the proapoptotic XIAP-associated factor 1 (XAF1) and, consequently, apoptosis. Pheochromocytoma and neuroblastoma arise from neural crest progenitors that compete for growth factors such as nerve growth factor (NGF) during development. KIF1Bβ is required for developmental apoptosis induced by competition for NGF. We show that DHX9 is induced by and required for apoptosis stimulated by NGF deprivation. Moreover, neuroblastomas with chromosomal deletion of 1p36 exhibit loss of KIF1Bβ expression and impaired DHX9 nuclear localization, implicating the loss of DHX9 nuclear activity in neuroblastoma pathogenesis.

Significance: KIF1Bβ has neuroblastoma tumor-suppressor properties and promotes and requires nuclear-localized DHX9 for its apoptotic function by activating XAF1 expression. Loss of KIF1Bβ alters subcellular localization of DHX9 and diminishes NGF dependence of sympathetic neurons, leading to reduced culling of neural progenitors, and, therefore, might predispose to tumor formation. Cancer Discov; 4(4); 434–51. ©2014 AACR.

See related commentary by Bernards, p. 392

This article is highlighted in the In This Issue feature, p. 377
Data from Defective Stromal Remodeling and Neutrophil Extracellular Traps in Lymphoid Tissues Favor the Transition from Autoimmunity to Lymphoma
Authors: Sangaletti Sabina , Tripodo Claudio , Vitali Caterina , Portararo Paola , Guarnotta Carla , Casalini Patrizia , Cappetti Barbara , Miotti Silvia , Pinciroli Patrizia , Fuligni Fabio , Fais Franco , Piccaluga Pier Paolo , Colombo Mario P.
Published: March 2024

Abstract
Altered expression of matricellular proteins can become pathogenic in the presence of persistent perturbations in tissue homeostasis. Here, we show that autoimmunity associated with Fas mutation was exacerbated and transitioned to lymphomagenesis in the absence of SPARC (secreted protein acidic rich in cysteine). The absence of SPARC resulted in defective collagen assembly, with uneven compartmentalization of lymphoid and myeloid populations within secondary lymphoid organs (SLO), and faulty delivery of inhibitory signals from the extracellular matrix. These conditions promoted aberrant interactions between neutrophil extracellular traps and CD5+ B cells, which underwent malignant transformation due to defective apoptosis under the pressure of neutrophil-derived trophic factors and NF-κB activation. Furthermore, this model of defective stromal remodeling during lymphomagenesis correlates with human lymphomas arising in a SPARC-defective environment, which is prototypical of CD5+ B–cell chronic lymphocytic leukemia (CLL).

Significance: These results reveal the importance of stromal remodeling in SLO to accommodate autoimmune lymphoproliferation while preventing lymphomagenesis. Our findings reveal a link between SPARC, collagen deposition, and the engagement of the immune-inhibitory receptor LAIR-1 on neutrophils, neutrophil cell death via NETosis, and the stimulation of CD5+ B–cell proliferation. Moreover, we show that SPARC deficiency promotes CD5+ B–cell lymphomagenesis and is correlated with CLL in humans. Cancer Discov; 4(1); 110–29. ©2013 AACR.

See related commentary by Brekken, p. 25

This article is highlighted in the In This Issue feature, p. 1
Data from A Gnotobiotic Mouse Model Demonstrates That Dietary Fiber Protects against Colorectal Tumorigenesis in a Microbiota- and Butyrate-Dependent Manner
Authors: Donohoe Dallas R. , Holley Darcy , Collins Leonard B. , Montgomery Stephanie A. , Whitmore Alan C. , Hillhouse Andrew , Curry Kaitlin P. , Renner Sarah W. , Greenwalt Alicia , Ryan Elizabeth P. , Godfrey Virginia , Heise Mark T. , Threadgill Deborah S. , Han Anna , Swenberg James A. , Threadgill David W. , Bultman Scott J.
Published: March 2024

Abstract
Whether dietary fiber protects against colorectal cancer is controversial because of conflicting results from human epidemiologic studies. However, these studies and mouse models of colorectal cancer have not controlled the composition of gut microbiota, which ferment fiber into short-chain fatty acids such as butyrate. Butyrate is noteworthy because it has energetic and epigenetic functions in colonocytes and tumor-suppressive properties in colorectal cancer cell lines. We used gnotobiotic mouse models colonized with wild-type or mutant strains of a butyrate-producing bacterium to demonstrate that fiber does have a potent tumor-suppressive effect but in a microbiota- and butyrate-dependent manner. Furthermore, due to the Warburg effect, butyrate was metabolized less in tumors where it accumulated and functioned as a histone deacetylase (HDAC) inhibitor to stimulate histone acetylation and affect apoptosis and cell proliferation. To support the relevance of this mechanism in human cancer, we demonstrate that butyrate and histone-acetylation levels are elevated in colorectal adenocarcinomas compared with normal colonic tissues.

Significance: These results, which link diet and microbiota to a tumor-suppressive metabolite, provide insight into conflicting epidemiologic findings and suggest that probiotic/prebiotic strategies can modulate an endogenous HDAC inhibitor for anticancer chemoprevention without the adverse effects associated with synthetic HDAC inhibitors used in chemotherapy. Cancer Discov; 4(12); 1387–97. ©2014 AACR.

See related commentary by Sebastián and Mostoslavsky, p. 1368

This article is highlighted in the In This Issue feature, p. 1355
Data from Aberrant Glycosylation Promotes Lung Cancer Metastasis through Adhesion to Galectins in the Metastatic Niche
Authors: Reticker-Flynn Nathan E. , Bhatia Sangeeta N.
Published: March 2024

Abstract
Metastasis is the leading cause of cancer-associated deaths. Although dissemination of tumor cells likely occurs early in tumorigenesis, the constituents of the microenvironment play essential rate-limiting roles in determining whether these cells will form clinically relevant tumors. Recent studies have uncovered many molecular factors that contribute to the establishment of a protumorigenic metastatic niche. Here, we demonstrate that galectin-3, whose expression has clinical associations with advanced malignancy and poor outcome, contributes to metastatic niche formation by binding to carbohydrates on metastatic cells. We show that galectin-3 is expressed early during tumorigenesis by both CD11b+Gr-1+ and CD11b+Ly-6Chi leukocytes. Tumors mobilize these myeloid populations through secretion of soluble factors, including IL6. We find that metastatic cancer cells exhibit elevated presentation of the oncofetal galectin-3 carbohydrate ligand, the Thomsen–Friedenreich antigen, on their surfaces as a result of altered C2GnT2 and St6GalNAc4 glycosyltransferase activity that inhibits further glycosylation of this carbohydrate motif and promotes metastasis.

Significance: Although clinical observations of elevated serum galectin-3 levels and altered glycosylation have been associated with malignancy, we identify novel roles for glycosyltransferases in promoting adhesion to galectins in the metastatic niche. This identification of a cytokine–leukocyte–glycosylation axis in metastasis provides mechanistic explanations for clinical associations between malignancy and aberrant glycosylation. Cancer Discov; 5(2); 168–81. ©2014 AACR.

See related commentary by Arnal-Estapé and Nguyen, p. 109

This article is highlighted in the In This Issue feature, p. 97
Data from NSD3–NUT Fusion Oncoprotein in NUT Midline Carcinoma: Implications for a Novel Oncogenic Mechanism
Authors: French Christopher A. , Rahman Shaila , Walsh Erica M. , Kühnle Simone , Grayson Adlai R. , Lemieux Madeleine E. , Grunfeld Noam , Rubin Brian P. , Antonescu Cristina R. , Zhang Songlin , Venkatramani Rajkumar , Dal Cin Paola , Howley Peter M.
Published: March 2024

Abstract
NUT midline carcinoma (NMC) is an aggressive subtype of squamous cell carcinoma that typically harbors BRD4/3–NUT fusion oncoproteins that block differentiation and maintain tumor growth. In 20% of cases, NUT is fused to uncharacterized non-BRD gene(s). We established a new patient-derived NMC cell line (1221) and demonstrated that it harbors a novel NSD3–NUT fusion oncogene. We find that NSD3–NUT is both necessary and sufficient for the blockade of differentiation and maintenance of proliferation in NMC cells. NSD3–NUT binds to BRD4, and BRD bromodomain inhibitors induce differentiation and arrest proliferation of 1221 cells. We find further that NSD3 is required for the blockade of differentiation in BRD4–NUT-expressing NMCs. These findings identify NSD3 as a novel critical oncogenic component and potential therapeutic target in NMC.

Significance: The existence of a family of fusion oncogenes in squamous cell carcinoma is unprecedented, and should lead to key insights into aberrant differentiation in NMC and possibly other squamous cell carcinomas. The involvement of the NSD3 methyltransferase as a component of the NUT fusion protein oncogenic complex identifies a new potential therapeutic target. Cancer Discov; 4(8); 928–41. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 855
Data from Addressing Genetic Tumor Heterogeneity through Computationally Predictive Combination Therapy
Authors: Zhao Boyang , Pritchard Justin R. , Lauffenburger Douglas A. , Hemann Michael T.
Published: March 2024

Abstract
Recent tumor sequencing data suggest an urgent need to develop a methodology to directly address intratumoral heterogeneity in the design of anticancer treatment regimens. We use RNA interference to model heterogeneous tumors, and demonstrate successful validation of computational predictions for how optimized drug combinations can yield superior effects on these tumors both in vitro and in vivo. Importantly, we discover here that for many such tumors knowledge of the predominant subpopulation is insufficient for determining the best drug combination. Surprisingly, in some cases, the optimal drug combination does not include drugs that would treat any particular subpopulation most effectively, challenging straightforward intuition. We confirm examples of such a case with survival studies in a murine preclinical lymphoma model. Altogether, our approach provides new insights about design principles for combination therapy in the context of intratumoral diversity, data that should inform the development of drug regimens superior for complex tumors.

Significance: This study provides the first example of how combination drug regimens, using existing chemotherapies, can be rationally designed to maximize tumor cell death, while minimizing the outgrowth of clonal subpopulations. Cancer Discov; 4(2); 166–74. ©2013 AACR.

See related commentary by Fedele et al., p. 146

This article is highlighted in the In This Issue feature, p. 131
Data from Identifying the Ubiquitin Ligase Complex That Regulates the NF1 Tumor Suppressor and Ras
Authors: Hollstein Pablo E. , Cichowski Karen
Published: March 2024

Abstract
The NF1 tumor suppressor protein neurofibromin is a negative regulator of Ras. Neurofibromin is dynamically regulated by the proteasome, and its degradation and reexpression are essential for maintaining appropriate levels of Ras-GTP. Like p53, NF1/neurofibromin can be inactivated in cancer by both mutations and excessive proteasomal destruction; however, little is known about the mechanisms that underlie this latter process. Here, we show that a Cullin 3 (Cul3)/kelch repeat and BTB domain-containing 7 complex controls both the regulated proteasomal degradation of neurofibromin and the pathogenic destabilization of neurofibromin in glioblastomas. Importantly, RNAi-mediated Cul3 ablation and a dominant-negative Cul3 directly stabilize neurofibromin, suppress Ras and extracellular signal-regulated kinase, and inhibit proliferation in an NF1-dependent manner. Moreover, in glioblastomas where neurofibromin is chronically destabilized, Cul3 inhibition restabilizes the protein and suppresses tumor development. Collectively, these studies show a previously unrecognized role for Cul3 in regulating Ras and provide a molecular framework that can be exploited to develop potential cancer therapies.

Significance: This study identifies the ubiquitin ligase complex that controls the regulated and pathogenic destruction of the NF1 tumor suppressor protein. These observations provide a molecular framework for developing potential therapies for glioblastoma, where neurofibromin is chronically destabilized, and reveal a new strategy to attenuate Ras that has broader therapeutic implications. Cancer Discov; 3(8); 880–93. ©2013 AACR.

This article is highlighted in the In This Issue feature, p. 826
Data from EGFR Variant Heterogeneity in Glioblastoma Resolved through Single-Nucleus Sequencing
Authors: Francis Joshua M. , Zhang Cheng-Zhong , Maire Cecile L. , Jung Joonil , Manzo Veronica E. , Adalsteinsson Viktor A. , Homer Heather , Haidar Sam , Blumenstiel Brendan , Pedamallu Chandra Sekhar , Ligon Azra H. , Love J. Christopher , Meyerson Matthew , Ligon Keith L.
Published: March 2024

Abstract
Glioblastomas (GBM) with EGFR amplification represent approximately 50% of newly diagnosed cases, and recent studies have revealed frequent coexistence of multiple EGFR aberrations within the same tumor, which has implications for mutation cooperation and treatment resistance. However, bulk tumor sequencing studies cannot resolve the patterns of how the multiple EGFR aberrations coexist with other mutations within single tumor cells. Here, we applied a population-based single-cell whole-genome sequencing methodology to characterize genomic heterogeneity in EGFR-amplified glioblastomas. Our analysis effectively identified clonal events, including a novel translocation of a super enhancer to the TERT promoter, as well as subclonal LOH and multiple EGFR mutational variants within tumors. Correlating the EGFR mutations onto the cellular hierarchy revealed that EGFR truncation variants (EGFRvII and EGFR carboxyl-terminal deletions) identified in the bulk tumor segregate into nonoverlapping subclonal populations. In vitro and in vivo functional studies show that EGFRvII is oncogenic and sensitive to EGFR inhibitors currently in clinical trials. Thus, the association between diverse activating mutations in EGFR and other subclonal mutations within a single tumor supports an intrinsic mechanism for proliferative and clonal diversification with broad implications in resistance to treatment.

Significance: We developed a novel single-cell sequencing methodology capable of identifying unique, nonoverlapping subclonal alterations from archived frozen clinical specimens. Using GBM as an example, we validated our method to successfully define tumor cell subpopulations containing distinct genetic and treatment resistance profiles and potentially mutually cooperative combinations of alterations in EGFR and other genes. Cancer Discov; 4(8); 956–71. ©2014 AACR.

See related commentary by Gini and Mischel, p. 876

This article is highlighted in the In This Issue feature, p. 855
Data from Safety and Activity of the First-in-Class Sym004 Anti-EGFR Antibody Mixture in Patients with Refractory Colorectal Cancer
Authors: Dienstmann Rodrigo , Patnaik Amita , Garcia-Carbonero Rocio , Cervantes Andrés , Benavent Marta , Roselló Susana , Tops Bastiaan B.J. , van der Post Rachel S. , Argilés Guillem , Skartved Niels J.Ø. , Hansen Ulla H. , Hald Rikke , Pedersen Mikkel W. , Kragh Michael , Horak Ivan D. , Braun Stephan , Van Cutsem Eric , Tolcher Anthony W. , Tabernero Josep
Published: March 2024

Abstract
Tumor growth in the context of EGFR inhibitor resistance may remain EGFR-dependent and is mediated by mechanisms including compensatory ligand upregulation and de novo gene alterations. Sym004 is a two-antibody mixture targeting nonoverlapping EGFR epitopes. In preclinical models, Sym004 causes significant EGFR internalization and degradation, which translates into superior growth inhibition in the presence of ligands. In this phase I trial, we observed grade 3 skin toxicity and hypomagnesemia as mechanism-based dose-limiting events during dose escalation. In dose-expansion cohorts of 9 and 12 mg/kg of Sym004 weekly, patients with metastatic colorectal cancer and acquired EGFR inhibitor resistance were enrolled; 17 of 39 patients (44%) had tumor shrinkage, with 5 patients (13%) achieving partial response. Pharmacodynamic studies confirmed marked Sym004-induced EGFR downmodulation. MET gene amplification emerged in 1 patient during Sym004 treatment, and a partial response was seen in a patient with EGFRS492R mutation that is predictive of cetuximab resistance.

Significance: Potent EGFR downmodulation with Sym004 in patients with metastatic colorectal cancer and acquired resistance to cetuximab/panitumumab translates into significant antitumor activity and validates the preclinical hypothesis that a proportion of tumors remains dependent on EGFR signaling. Further clinical development and expanded correlative analyses of response patterns with secondary RAS/EGFR mutations are warranted. Cancer Discov; 5(6);598–609. ©2015 AACR.

See related commentary by Stintzing and Heinemann, p. 578

This article is highlighted in the In This Issue feature, p. 565
Data from Immune Cell–Poor Melanomas Benefit from PD-1 Blockade after Targeted Type I IFN Activation
Authors: Bald Tobias , Landsberg Jennifer , Lopez-Ramos Dorys , Renn Marcel , Glodde Nicole , Jansen Philipp , Gaffal Evelyn , Steitz Julia , Tolba Rene , Kalinke Ulrich , Limmer Andreas , Jönsson Göran , Hölzel Michael , Tüting Thomas
Published: March 2024

Abstract
Infiltration of human melanomas with cytotoxic immune cells correlates with spontaneous type I IFN activation and a favorable prognosis. Therapeutic blockade of immune-inhibitory receptors in patients with preexisting lymphocytic infiltrates prolongs survival, but new complementary strategies are needed to activate cellular antitumor immunity in immune cell–poor melanomas. Here, we show that primary melanomas in Hgf-Cdk4R24C mice, which imitate human immune cell–poor melanomas with a poor outcome, escape IFN-induced immune surveillance and editing. Peritumoral injections of immunostimulatory RNA initiated a cytotoxic inflammatory response in the tumor microenvironment and significantly impaired tumor growth. This critically required the coordinated induction of type I IFN responses by dendritic, myeloid, natural killer, and T cells. Importantly, antibody-mediated blockade of the IFN-induced immune-inhibitory interaction between PD-L1 and PD-1 receptors further prolonged the survival. These results highlight important interconnections between type I IFNs and immune-inhibitory receptors in melanoma pathogenesis, which serve as targets for combination immunotherapies.

Significance: Using a genetically engineered mouse melanoma model, we demonstrate that targeted activation of the type I IFN system with immunostimulatory RNA in combination with blockade of immune-inhibitory receptors is a rational strategy to expose immune cell–poor tumors to cellular immune surveillance. Cancer Discov; 4(6); 674–87. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 621
Data from Suppression of Early Hematogenous Dissemination of Human Breast Cancer Cells to Bone Marrow by Retinoic Acid–Induced 2
Authors: Werner Stefan , Brors Benedikt , Eick Julia , Marques Elsa , Pogenberg Vivian , Parret Annabel , Kemming Dirk , Wood Antony W. , Edgren Henrik , Neubauer Hans , Streichert Thomas , Riethdorf Sabine , Bedi Upasana , Baccelli Irène , Jücker Manfred , Eils Roland , Fehm Tanja , Trumpp Andreas , Johnsen Steven A. , Klefström Juha , Wilmanns Matthias , Müller Volkmar , Pantel Klaus , Wikman Harriet
Published: March 2024

Abstract
Regulatory pathways that drive early hematogenous dissemination of tumor cells are insufficiently defined. Here, we used the presence of disseminated tumor cells (DTC) in the bone marrow to define patients with early disseminated breast cancer and identified low retinoic acid–induced 2 (RAI2) expression to be significantly associated with DTC status. Low RAI2 expression was also shown to be an independent poor prognostic factor in 10 different cancer datasets. Depletion of RAI2 protein in luminal breast cancer cell lines resulted in dedifferentiation marked by downregulation of ERα, FOXA1, and GATA3, together with increased invasiveness and activation of AKT signaling. Functional analysis of the previously uncharacterized RAI2 protein revealed molecular interaction with CtBP transcriptional regulators and an overlapping function in controlling the expression of a number of key target genes involved in breast cancer. These results suggest that RAI2 is a new metastasis-associated protein that sustains differentiation of luminal breast epithelial cells.

Significance: We identified downregulation of RAI2 as a novel metastasis-associated genetic alteration especially associated with early occurring bone metastasis in ERα-positive breast tumors. We specified the role of the RAI2 protein to function as a transcriptional regulator that controls the expression of several key regulators of breast epithelial integrity and cancer. Cancer Discov; 5(5); 506–19. ©2015 AACR.

See related commentary by Esposito and Kang, p. 466

This article is highlighted in the In This Issue feature, p. 453
Data from First Selective Small Molecule Inhibitor of FGFR4 for the Treatment of Hepatocellular Carcinomas with an Activated FGFR4 Signaling Pathway
Authors: Hagel Margit , Miduturu Chandra , Sheets Michael , Rubin Nooreen , Weng Weifan , Stransky Nicolas , Bifulco Neil , Kim Joseph L. , Hodous Brian , Brooijmans Natasja , Shutes Adam , Winter Christopher , Lengauer Christoph , Kohl Nancy E. , Guzi Timothy
Published: March 2024

Abstract
Aberrant signaling through the fibroblast growth factor 19 (FGF19)/fibroblast growth factor receptor 4 (FGFR 4) signaling complex has been shown to cause hepatocellular carcinoma (HCC) in mice and has been implicated to play a similar role in humans. We have developed BLU9931, a potent and irreversible small-molecule inhibitor of FGFR4, as a targeted therapy to treat patients with HCC whose tumors have an activated FGFR4 signaling pathway. BLU9931 is exquisitely selective for FGFR4 versus other FGFR family members and all other kinases. BLU9931 shows remarkable antitumor activity in mice bearing an HCC tumor xenograft that overexpresses FGF19 due to amplification as well as a liver tumor xenograft that overexpresses FGF19 mRNA but lacks FGF19 amplification. Approximately one third of patients with HCC whose tumors express FGF19 together with FGFR4 and its coreceptor klotho β (KLB) could potentially respond to treatment with an FGFR4 inhibitor. These findings are the first demonstration of a therapeutic strategy that targets a subset of patients with HCC.

Significance: This article documents the discovery of BLU9931, a novel irreversible kinase inhibitor that specifically targets FGFR4 while sparing all other FGFR paralogs and demonstrates exquisite kinome selectivity. BLU9931 is efficacious in tumors with an intact FGFR4 signaling pathway that includes FGF19, FGFR4, and KLB. BLU9931 is the first FGFR4-selective molecule for the treatment of patients with HCC with aberrant FGFR4 signaling. Cancer Discov; 5(4); 424–37. ©2015 AACR.

See related commentary by Packer and Pollock, p. 355

This article is highlighted in the In This Issue feature, p. 333
Data from PARP1-Driven Poly-ADP-Ribosylation Regulates BRCA1 Function in Homologous Recombination–Mediated DNA Repair
Authors: Hu Yiduo , Petit Sarah A. , Ficarro Scott B. , Toomire Kimberly J. , Xie Anyong , Lim Elgene , Cao Shiliang A. , Park Eunyoung , Eck Michael J. , Scully Ralph , Brown Myles , Marto Jarrod A. , Livingston David M.
Published: March 2024

Abstract
BRCA1 promotes homologous recombination–mediated DNA repair (HRR). However, HRR must be tightly regulated to prevent illegitimate recombination. We previously found that BRCA1 HRR function is regulated by the RAP80 complex, but the mechanism was unclear. We have now observed that PARP1 interacts with and poly-ADP-ribosylates (aka PARsylates) BRCA1. PARsylation is directed at the BRCA1 DNA binding domain and downmodulates its function. Moreover, RAP80 contains a poly-ADP-ribose–interacting domain that binds PARsylated BRCA1 and helps to maintain the stability of PARP1–BRCA1–RAP80 complexes. BRCA1 PARsylation is a key step in BRCA1 HRR control. When BRCA1 PARsylation is defective, it gives rise to excessive HRR and manifestations of genome instability. BRCA1 PARsylation and/or RAP80 expression is defective in a subset of sporadic breast cancer cell lines and patient-derived tumor xenograft models. These observations are consistent with the possibility that such defects, when chronic, contribute to tumor development in BRCA1+/+ individuals.

Significance: We propose a model that describes how BRCA1 functions to both support and restrict HRR. BRCA1 PARsylation is a key event in this process, failure of which triggers hyper-recombination and chromosome instability. Thus, hyperfunctioning BRCA1 can elicit genomic abnormalities similar to those observed in the absence of certain BRCA1 functions. Cancer Discov; 4(12); 1430–47. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 1355
Data from DNA-Damage Response during Mitosis Induces Whole-Chromosome Missegregation
Authors: Bakhoum Samuel F. , Kabeche Lilian , Murnane John P. , Zaki Bassem I. , Compton Duane A.
Published: March 2024

Abstract
Many cancers display both structural (s-CIN) and numerical (w-CIN) chromosomal instabilities. Defective chromosome segregation during mitosis has been shown to cause DNA damage that induces structural rearrangements of chromosomes (s-CIN). In contrast, whether DNA damage can disrupt mitotic processes to generate whole chromosomal instability (w-CIN) is unknown. Here, we show that activation of the DNA-damage response (DDR) during mitosis selectively stabilizes kinetochore–microtubule (k-MT) attachments to chromosomes through Aurora-A and PLK1 kinases, thereby increasing the frequency of lagging chromosomes during anaphase. Inhibition of DDR proteins, ATM or CHK2, abolishes the effect of DNA damage on k-MTs and chromosome segregation, whereas activation of the DDR in the absence of DNA damage is sufficient to induce chromosome segregation errors. Finally, inhibiting the DDR during mitosis in cancer cells with persistent DNA damage suppresses inherent chromosome segregation defects. Thus, the DDR during mitosis inappropriately stabilizes k-MTs, creating a link between s-CIN and w-CIN.

Significance: The genome-protective role of the DDR depends on its ability to delay cell division until damaged DNA can be fully repaired. Here, we show that when DNA damage is induced during mitosis, the DDR unexpectedly induces errors in the segregation of entire chromosomes, thus linking structural and numerical chromosomal instabilities. Cancer Discov; 4(11); 1281–9. ©2014 AACR.

See related commentary by Jelluma and Kops, p. 1256

This article is highlighted in the In This Issue feature, p. 1243
Data from Heterogeneity Underlies the Emergence of EGFRT790 Wild-Type Clones Following Treatment of T790M-Positive Cancers with a Third-Generation EGFR Inhibitor
Authors: Piotrowska Zofia , Niederst Matthew J. , Karlovich Chris A. , Wakelee Heather A. , Neal Joel W. , Mino-Kenudson Mari , Fulton Linnea , Hata Aaron N. , Lockerman Elizabeth L. , Kalsy Anuj , Digumarthy Subba , Muzikansky Alona , Raponi Mitch , Garcia Angel R. , Mulvey Hillary E. , Parks Melissa K. , DiCecca Richard H. , Dias-Santagata Dora , Iafrate A. John , Shaw Alice T. , Allen Andrew R. , Engelman Jeffrey A. , Sequist Lecia V.
Published: March 2024

Abstract
Rociletinib is a third-generation EGFR inhibitor active in lung cancers with T790M, the gatekeeper mutation underlying most first-generation EGFR drug resistance. We biopsied patients at rociletinib progression to explore resistance mechanisms. Among 12 patients with T790M-positive cancers at rociletinib initiation, six had T790–wild-type rociletinib-resistant biopsies. Two T790–wild-type cancers underwent small cell lung cancer transformation; three T790M-positive cancers acquired EGFR amplification. We documented T790–wild-type and T790M-positive clones coexisting within a single pre-rociletinib biopsy. The pretreatment fraction of T790M-positive cells affected response to rociletinib. Longitudinal circulating tumor DNA (ctDNA) analysis revealed an increase in plasma EGFR-activating mutation, and T790M heralded rociletinib resistance in some patients, whereas in others the activating mutation increased but T790M remained suppressed. Together, these findings demonstrate the role of tumor heterogeneity when therapies targeting a singular resistance mechanism are used. To further improve outcomes, combination regimens that also target T790–wild-type clones are required.

Significance: This report documents that half of T790M-positive EGFR-mutant lung cancers treated with rociletinib are T790–wild-type upon progression, suggesting that T790–wild-type clones can emerge as the dominant source of resistance. We show that tumor heterogeneity has important clinical implications and that plasma ctDNA analyses can sometimes predict emerging resistance mechanisms. Cancer Discov; 5(7); 713–22. ©2015 AACR.

See related commentary by Ichihara and Lovly, p. 694.

This article is highlighted in the In This Issue feature, p. 681
Data from First-in-Humans Trial of an RNA Interference Therapeutic Targeting VEGF and KSP in Cancer Patients with Liver Involvement
Authors: Tabernero Josep , Shapiro Geoffrey I. , LoRusso Patricia M. , Cervantes Andres , Schwartz Gary K. , Weiss Glen J. , Paz-Ares Luis , Cho Daniel C. , Infante Jeffrey R. , Alsina Maria , Gounder Mrinal M. , Falzone Rick , Harrop Jamie , White Amy C. Seila , Toudjarska Iva , Bumcrot David , Meyers Rachel E. , Hinkle Gregory , Svrzikapa Nenad , Hutabarat Renta M. , Clausen Valerie A. , Cehelsky Jeffrey , Nochur Saraswathy V. , Gamba-Vitalo Christina , Vaishnaw Akshay K. , Sah Dinah W.Y. , Gollob Jared A. , Burris Howard A.
Published: March 2024

Abstract
RNA interference (RNAi) is a potent and specific mechanism for regulating gene expression. Harnessing RNAi to silence genes involved in disease holds promise for the development of a new class of therapeutics. Delivery is key to realizing the potential of RNAi, and lipid nanoparticles (LNP) have proved effective in delivery of siRNAs to the liver and to tumors in animals. To examine the activity and safety of LNP-formulated siRNAs in humans, we initiated a trial of ALN-VSP, an LNP formulation of siRNAs targeting VEGF and kinesin spindle protein (KSP), in patients with cancer. Here, we show detection of drug in tumor biopsies, siRNA-mediated mRNA cleavage in the liver, pharmacodynamics suggestive of target downregulation, and antitumor activity, including complete regression of liver metastases in endometrial cancer. In addition, we show that biweekly intravenous administration of ALN-VSP was safe and well tolerated. These data provide proof-of-concept for RNAi therapeutics in humans and form the basis for further development in cancer.

Significance: The findings in this report show safety, pharmacokinetics, RNAi mechanism of action, and clinical activity with a novel first-in-class LNP-formulated RNAi therapeutic in patients with cancer. The ability to harness RNAi to facilitate specific multitargeting, as well as increase the number of druggable targets, has important implications for future drug development in oncology. Cancer Discov; 3(4); 406–17. ©2012 AACR.

This article is highlighted in the In This Issue feature, p. 363
Data from Brain Tumor Cells in Circulation Are Enriched for Mesenchymal Gene Expression
Authors: Sullivan James P. , Nahed Brian V. , Madden Marissa W. , Oliveira Samantha M. , Springer Simeon , Bhere Deepak , Chi Andrew S. , Wakimoto Hiroaki , Rothenberg S. Michael , Sequist Lecia V. , Kapur Ravi , Shah Khalid , Iafrate A. John , Curry William T. , Loeffler Jay S. , Batchelor Tracy T. , Louis David N. , Toner Mehmet , Maheswaran Shyamala , Haber Daniel A.
Published: March 2024

Abstract
Glioblastoma (GBM) is a highly aggressive brain cancer characterized by local invasion and angiogenic recruitment, yet metastatic dissemination is extremely rare. Here, we adapted a microfluidic device to deplete hematopoietic cells from blood specimens of patients with GBM, uncovering evidence of circulating brain tumor cells (CTC). Staining and scoring criteria for GBM CTCs were first established using orthotopic patient-derived xenografts (PDX), and then applied clinically: CTCs were identified in at least one blood specimen from 13 of 33 patients (39%; 26 of 87 samples). Single GBM CTCs isolated from both patients and mouse PDX models demonstrated enrichment for mesenchymal over neural differentiation markers compared with primary GBMs. Within primary GBMs, RNA in situ hybridization identified a subpopulation of highly migratory mesenchymal tumor cells, and in a rare patient with disseminated GBM, systemic lesions were exclusively mesenchymal. Thus, a mesenchymal subset of GBM cells invades the vasculature and may proliferate outside the brain.

Significance: GBMs are locally invasive within the brain but rarely metastasize to distant organs, exemplifying the debate over “seed” versus “soil.” We demonstrate that GBMs shed CTCs with invasive mesenchymal characteristics into the circulation. Rare metastatic GBM lesions are primarily mesenchymal and show additional mutations absent in the primary tumor. Cancer Discov; 4(11); 1299–1309. ©2014 AACR.

See related commentary by Seoane and De Mattos-Arruda, p. 1259

This article is highlighted in the In This Issue feature, p. 1243
Data from Efficacy of Intermittent Combined RAF and MEK Inhibition in a Patient with Concurrent BRAF- and NRAS-Mutant Malignancies
Authors: Abdel-Wahab Omar , Klimek Virginia M. , Gaskell Alisa A. , Viale Agnes , Cheng Donavan , Kim Eunhee , Rampal Raajit , Bluth Mark , Harding James J. , Callahan Margaret K. , Merghoub Taha , Berger Michael F. , Solit David B. , Rosen Neal , Levine Ross L. , Chapman Paul B.
Published: March 2024

Abstract
Vemurafenib, a RAF inhibitor, extends survival in patients with BRAFV600-mutant melanoma but activates extracellular signal–regulated kinase (ERK) signaling in RAS-mutant cells. In a patient with a BRAFV600K-mutant melanoma responding to vemurafenib, we observed accelerated progression of a previously unrecognized NRAS-mutant leukemia. We hypothesized that combining vemurafenib with a MAP–ERK kinase (MEK) inhibitor would inhibit ERK activation in the melanoma and prevent ERK activation by vemurafenib in the leukemia, and thus suppress both malignancies. We demonstrate that intermittent administration of vemurafenib led to a near-complete remission of the melanoma, and the addition of the MEK inhibitor cobimetinib (GDC-0973) caused suppression of vemurafenib-induced leukemic proliferation and ERK activation. Antimelanoma and antileukemia responses have been maintained for nearly 20 months, as documented by serial measurements of tumor-derived DNA in plasma in addition to conventional radiographic and clinical assessments of response. These data support testing of intermittent ERK pathway inhibition in the therapy for both RAS-mutant leukemia and BRAF-mutant melanoma.

Significance: We show that in a patient with simultaneous RAS-mutant leukemia and BRAF-mutant melanoma, intermittent RAF inhibitor therapy induced a near-complete melanoma response, and addition of a MEK inhibitor prevented RAF inhibitor-induced activation of the RAS-mutant leukemia. Intermittent therapy may permit greater pathway inhibition with less toxicity, avoid chronic relief of pathway feedback, and have enhanced effectiveness compared with chronic administration. Cancer Discov; 4(5); 538–45. ©2014 AACR.

See related commentary by Davies, p. 510

This article is highlighted in the In This Issue feature, p. 495
Data from JAK–STAT Pathway Activation in Malignant and Nonmalignant Cells Contributes to MPN Pathogenesis and Therapeutic Response
Authors: Kleppe Maria , Kwak Minsuk , Koppikar Priya , Riester Markus , Keller Matthew , Bastian Lennart , Hricik Todd , Bhagwat Neha , McKenney Anna Sophia , Papalexi Efthymia , Abdel-Wahab Omar , Rampal Raajit , Marubayashi Sachie , Chen Jonathan J. , Romanet Vincent , Fridman Jordan S. , Bromberg Jacqueline , Teruya-Feldstein Julie , Murakami Masato , Radimerski Thomas , Michor Franziska , Fan Rong , Levine Ross L.
Published: March 2024

Abstract
The identification of JAK2/MPL mutations in patients with myeloproliferative neoplasms (MPN) has led to the clinical development of JAK kinase inhibitors, including ruxolitinib. Ruxolitinib reduces splenomegaly and systemic symptoms in myelofibrosis and improves overall survival; however, the mechanism by which JAK inhibitors achieve efficacy has not been delineated. Patients with MPN present with increased levels of circulating proinflammatory cytokines, which are mitigated by JAK inhibitor therapy. We sought to elucidate mechanisms by which JAK inhibitors attenuate cytokine-mediated pathophysiology. Single-cell profiling demonstrated that hematopoietic cells from myelofibrosis models and patient samples aberrantly secrete inflammatory cytokines. Pan-hematopoietic Stat3 deletion reduced disease severity and attenuated cytokine secretion, with similar efficacy as observed with ruxolitinib therapy. In contrast, Stat3 deletion restricted to MPN cells did not reduce disease severity or cytokine production. Consistent with these observations, we found that malignant and nonmalignant cells aberrantly secrete cytokines and JAK inhibition reduces cytokine production from both populations.

Significance: Our results demonstrate that JAK–STAT3-mediated cytokine production from malignant and nonmalignant cells contributes to MPN pathogenesis and that JAK inhibition in both populations is required for therapeutic efficacy. These findings provide novel insight into the mechanisms by which JAK kinase inhibition achieves therapeutic efficacy in MPNs. Cancer Discov; 5(3); 316–31. ©2015 AACR.

See related commentary by Belver and Ferrando, p. 234

This article is highlighted in the In This Issue feature, p. 213
Data from Autophagy-Dependent Production of Secreted Factors Facilitates Oncogenic RAS-Driven Invasion
Authors: Lock Rebecca , Kenific Candia M. , Leidal Andrew M. , Salas Eduardo , Debnath Jayanta
Published: March 2024

Abstract
The tumor-promoting functions of autophagy are primarily attributed to its ability to promote cancer cell survival. However, emerging evidence suggests that autophagy plays other roles during tumorigenesis. Here, we uncover that autophagy promotes oncogenic RAS-driven invasion. In epithelial cells transformed with oncogenic RAS, depletion of autophagy-related genes suppresses invasion in three-dimensional culture, decreases cell motility, and reduces pulmonary metastases in vivo. Treatment with conditioned media from autophagy-competent cells rescues the invasive capacity of autophagy-deficient cells, indicating that these cells fail to secrete factors required for RAS-driven invasion. Reduced autophagy diminishes the secretion of the promigratory cytokine interleukin-6 (IL-6), which is necessary to restore invasion of autophagy-deficient cells. Moreover, autophagy-deficient cells exhibit reduced levels of matrix metalloproteinase 2 and WNT5A. These results support a previously unrecognized function for autophagy in promoting cancer cell invasion via the coordinate production of multiple secreted factors.

Significance: Our results delineate a previously unrecognized function for autophagy in facilitating oncogenic RAS-driven invasion. We demonstrate that an intact autophagy pathway is required for the elaboration of multiple secreted factors favoring invasion, including IL-6. Cancer Discov; 4(4); 466–79. ©2014 AACR.

This article is highlighted in the In This Issue feature, p. 377
Data from Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis
Authors: Van Rechem Capucine , Black Joshua C. , Boukhali Myriam , Aryee Martin J. , Gräslund Susanne , Haas Wilhelm , Benes Cyril H. , Whetstine Johnathan R.
Published: March 2024

Abstract
Chromatin-modifying enzymes are predominantly nuclear; however, these factors are also localized to the cytoplasm, and very little is known about their role in this compartment. In this report, we reveal a non–chromatin-linked role for the lysine-specific demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation complex and affects the distribution of translation initiation factors within polysome fractions. Furthermore, KDM4A depletion reduced protein synthesis and enhanced the protein synthesis suppression observed with mTOR inhibitors, which paralleled an increased sensitivity to these drugs. Finally, we demonstrate that JIB-04, a JmjC demethylase inhibitor, suppresses translation initiation and enhances mTOR inhibitor sensitivity. These data highlight an unexpected cytoplasmic role for KDM4A in regulating protein synthesis and suggest novel potential therapeutic applications for this class of enzyme.

Significance: This report documents an unexpected cytoplasmic role for the lysine demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation machinery, regulates protein synthesis and, upon coinhibition with mTOR inhibitors, enhances the translation suppression and cell sensitivity to these therapeutics. Cancer Discov; 5(3); 255–63. ©2015 AACR.

See related commentary by Rothbart et al., p. 228

See related article by Van Rechem et al., p. 245

This article is highlighted in the In This Issue feature, p. 213
Data from The p53 Target Gene SIVA Enables Non–Small Cell Lung Cancer Development
Authors: Van Nostrand Jeanine L. , Brisac Alice , Mello Stephano S. , Jacobs Suzanne B.R. , Luong Richard , Attardi Laura D.
Published: March 2024

Abstract
Although p53 transcriptional activation potential is critical for its ability to suppress cancer, the specific target genes involved in tumor suppression remain unclear. SIVA is a p53 target gene essential for p53-dependent apoptosis, although it can also promote proliferation through inhibition of p53 in some settings. Thus, the role of SIVA in tumorigenesis remains unclear. Here, we seek to define the contribution of SIVA to tumorigenesis by generating Siva conditional knockout mice. Surprisingly, we find that SIVA loss inhibits non–small cell lung cancer (NSCLC) development, suggesting that SIVA facilitates tumorigenesis. Similarly, SIVA knockdown in mouse and human NSCLC cell lines decreases proliferation and transformation. Consistent with this protumorigenic role for SIVA, high-level SIVA expression correlates with reduced NSCLC patient survival. SIVA acts independently of p53 and, instead, stimulates mTOR signaling and metabolism in NSCLC cells. Thus, SIVA enables tumorigenesis in a p53-independent manner, revealing a potential new cancer therapy target.

Significance: These findings collectively reveal a novel role for the p53 target gene SIVA both in regulating metabolism and in enabling tumorigenesis, independently of p53. Importantly, these studies further identify SIVA as a new prognostic marker and as a potential target for NSCLC cancer therapy. Cancer Discov; 5(6); 622–35. ©2015 AACR.

See related commentary by Resnick-Silverman and Manfredi, p. 581

This article is highlighted in the In This Issue feature, p. 565
Data from Selective BCL-2 Inhibition by ABT-199 Causes On-Target Cell Death in Acute Myeloid Leukemia
Authors: Pan Rongqing , Hogdal Leah J. , Benito Juliana M. , Bucci Donna , Han Lina , Borthakur Gautam , Cortes Jorge , DeAngelo Daniel J. , Debose LaKeisha , Mu Hong , Döhner Hartmut , Gaidzik Verena I. , Galinsky Ilene , Golfman Leonard S. , Haferlach Torsten , Harutyunyan Karine G. , Hu Jianhua , Leverson Joel D. , Marcucci Guido , Müschen Markus , Newman Rachel , Park Eugene , Ruvolo Peter P. , Ruvolo Vivian , Ryan Jeremy , Schindela Sonja , Zweidler-McKay Patrick , Stone Richard M. , Kantarjian Hagop , Andreeff Michael , Konopleva Marina , Letai Anthony G.
Published: March 2024

Abstract
B-cell leukemia/lymphoma 2 (BCL-2) prevents commitment to programmed cell death at the mitochondrion. It remains a challenge to identify those tumors that are best treated by inhibition of BCL-2. Here, we demonstrate that acute myeloid leukemia (AML) cell lines, primary patient samples, and murine primary xenografts are very sensitive to treatment with the selective BCL-2 antagonist ABT-199. In primary patient cells, the median IC50 was approximately 10 nmol/L, and cell death occurred within 2 hours. Our ex vivo sensitivity results compare favorably with those observed for chronic lymphocytic leukemia, a disease for which ABT-199 has demonstrated consistent activity in clinical trials. Moreover, mitochondrial studies using BH3 profiling demonstrate activity at the mitochondrion that correlates well with cytotoxicity, supporting an on-target mitochondrial mechanism of action. Our protein and BH3 profiling studies provide promising tools that can be tested as predictive biomarkers in any clinical trial of ABT-199 in AML.

Significance: Although targeting BCL-2 has largely been investigated in lymphoid cancers, we present preclinical results of targeting BCL-2 in AML. These results support clinical testing of the small-molecule BCL-2 antagonist ABT-199 in AML, accompanied by testing of predictive biomarkers used in this study. Cancer Discov; 4(3); 362–75. ©2013 AACR.

See related commentary by Hockenbery, p. 278

This article is highlighted in the In This Issue feature, p. 259
Data from IL35-Producing B Cells Promote the Development of Pancreatic Neoplasia
Authors: Pylayeva-Gupta Yuliya , Das Shipra , Handler Jesse S. , Hajdu Cristina H. , Coffre Maryaline , Koralov Sergei B. , Bar-Sagi Dafna
Published: March 2024

Abstract
A salient feature of pancreatic ductal adenocarcinoma (PDAC) is an abundant fibroinflammatory response characterized by the recruitment of immune and mesenchymal cells and the consequent establishment of a protumorigenic microenvironment. Here, we report the prominent presence of B cells in human pancreatic intraepithelial neoplasia and PDAC lesions as well as in oncogenic Kras-driven pancreatic neoplasms in the mouse. The growth of orthotopic pancreatic neoplasms harboring oncogenic Kras was significantly compromised in B-cell–deficient mice (μMT), and this growth deficiency could be rescued by the reconstitution of a CD1dhiCD5+ B-cell subset. The protumorigenic effect of B cells was mediated by their expression of IL35 through a mechanism involving IL35-mediated stimulation of tumor cell proliferation. Our results identify a previously unrecognized role for IL35-producing CD1dhiCD5+ B cells in the pathogenesis of pancreatic cancer and underscore the potential significance of a B-cell/IL35 axis as a therapeutic target.

Significance: This study identifies a B-cell subpopulation that accumulates in the pancreatic parenchyma during early neoplasia and is required to support tumor cell growth. Our findings provide a rationale for exploring B-cell–based targeting approaches for the treatment of pancreatic cancer. Cancer Discov; 6(3); 247–55. ©2015 AACR.

See related commentary by Roghanian et al., p. 230.

See related article by Lee et al., p. 256.

See related article by Gunderson et al., p. 270.

This article is highlighted in the In This Issue feature, p. 217