bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from First-in-Human Trial of the Oral Ataxia Telangiectasia and RAD3-Related (ATR) Inhibitor BAY 1895344 in Patients with Advanced Solid Tumors
Authors: Yap Timothy A. , Tan David S.P. , Terbuch Angelika , Caldwell Reece , Guo Christina , Goh Boon Cher , Heong Valerie , Haris Noor R. Md. , Bashir Saira , Drew Yvette , Hong David S. , Meric-Bernstam Funda , Wilkinson Gary , Hreiki Joseph , Wengner Antje M. , Bladt Friedhelm , Schlicker Andreas , Ludwig Matthias , Zhou Yinghui , Liu Li , Bordia Sonal , Plummer Ruth , Lagkadinou Eleni , de Bono Johann S.
Published: March 2024

Abstract
Targeting the ataxia telangiectasia and RAD3-related (ATR) enzyme represents a promising anticancer strategy for tumors with DNA damage response (DDR) defects and replication stress, including inactivation of ataxia telangiectasia mutated (ATM) signaling. We report the dose-escalation portion of the phase I first-in-human trial of oral ATR inhibitor BAY 1895344 intermittently dosed 5 to 80 mg twice daily in 21 patients with advanced solid tumors. The MTD was 40 mg twice daily 3 days on/4 days off. Most common adverse events were manageable and reversible hematologic toxicities. Partial responses were achieved in 4 patients and stable disease in 8 patients. Median duration of response was 315.5 days. Responders had ATM protein loss and/or deleterious ATM mutations and received doses ≥40 mg twice daily. Overall, BAY 1895344 is well tolerated, with antitumor activity against cancers with certain DDR defects, including ATM loss. An expansion phase continues in patients with DDR deficiency.
Significance:
Oral BAY 1895344 was tolerable, with antitumor activity in heavily pretreated patients with various advanced solid tumors, particularly those with ATM deleterious mutations and/or loss of ATM protein; pharmacodynamic results supported a mechanism of action of increased DNA damage. Further study is warranted in this patient population.

See related commentary by Italiano, p. 14.

This article is highlighted in the In This Issue feature, p. 1
Data from TAS-120 Overcomes Resistance to ATP-Competitive FGFR Inhibitors in Patients with FGFR2 Fusion–Positive Intrahepatic Cholangiocarcinoma
Authors: Goyal Lipika , Shi Lei , Liu Leah Y. , Fece de la Cruz Ferran , Lennerz Jochen K. , Raghavan Srivatsan , Leschiner Ignaty , Elagina Liudmila , Siravegna Giulia , Ng Raymond W.S. , Vu Phuong , Patra Krushna C. , Saha Supriya K. , Uppot Raul N. , Arellano Ron , Reyes Stephanie , Sagara Takeshi , Otsuki Sachie , Nadres Brandon , Shahzade Heather A. , Dey-Guha Ipsita , Fetter Isobel J. , Baiev Islam , Van Seventer Emily E. , Murphy Janet E. , Ferrone Cristina R. , Tanabe Kenneth K. , Deshpande Vikram , Harding James J. , Yaeger Rona , Kelley Robin K. , Bardelli Alberto , Iafrate A. John , Hahn William C. , Benes Cyril H. , Ting David T. , Hirai Hiroshi , Getz Gad , Juric Dejan , Zhu Andrew X. , Corcoran Ryan B. , Bardeesy Nabeel
Published: March 2024

Abstract
ATP-competitive fibroblast growth factor receptor (FGFR) kinase inhibitors, including BGJ398 and Debio 1347, show antitumor activity in patients with intrahepatic cholangiocarcinoma (ICC) harboring activating FGFR2 gene fusions. Unfortunately, acquired resistance develops and is often associated with the emergence of secondary FGFR2 kinase domain mutations. Here, we report that the irreversible pan-FGFR inhibitor TAS-120 demonstrated efficacy in 4 patients with FGFR2 fusion–positive ICC who developed resistance to BGJ398 or Debio 1347. Examination of serial biopsies, circulating tumor DNA (ctDNA), and patient-derived ICC cells revealed that TAS-120 was active against multiple FGFR2 mutations conferring resistance to BGJ398 or Debio 1347. Functional assessment and modeling the clonal outgrowth of individual resistance mutations from polyclonal cell pools mirrored the resistance profiles observed clinically for each inhibitor. Our findings suggest that strategic sequencing of FGFR inhibitors, guided by serial biopsy and ctDNA analysis, may prolong the duration of benefit from FGFR inhibition in patients with FGFR2 fusion–positive ICC.
Significance:
ATP-competitive FGFR inhibitors (BGJ398, Debio 1347) show efficacy in FGFR2-altered ICC; however, acquired FGFR2 kinase domain mutations cause drug resistance and tumor progression. We demonstrate that the irreversible FGFR inhibitor TAS-120 provides clinical benefit in patients with resistance to BGJ398 or Debio 1347 and overcomes several FGFR2 mutations in ICC models.

This article is highlighted in the In This Issue feature, p. 983
Data from Glioma Stem Cell–Specific Superenhancer Promotes Polyunsaturated Fatty-Acid Synthesis to Support EGFR Signaling
Authors: Gimple Ryan C. , Kidwell Reilly L. , Kim Leo J.Y. , Sun Tengqian , Gromovsky Anthony D. , Wu Qiulian , Wolf Megan , Lv Deguan , Bhargava Shruti , Jiang Li , Prager Briana C. , Wang Xiuxing , Ye Qing , Zhu Zhe , Zhang Guoxin , Dong Zhen , Zhao Linjie , Lee Derrick , Bi Junfeng , Sloan Andrew E. , Mischel Paul S. , Brown J. Mark , Cang Hu , Huan Tao , Mack Stephen C. , Xie Qi , Rich Jeremy N.
Published: March 2024

Abstract
Glioblastoma ranks among the most aggressive and lethal of all human cancers. Functionally defined glioma stem cells (GSC) contribute to this poor prognosis by driving therapeutic resistance and maintaining cellular heterogeneity. To understand the molecular processes essential for GSC maintenance and tumorigenicity, we interrogated the superenhancer landscapes of primary glioblastoma specimens and in vitro GSCs. GSCs epigenetically upregulated ELOVL2, a key polyunsaturated fatty-acid synthesis enzyme. Targeting ELOVL2 inhibited glioblastoma cell growth and tumor initiation. ELOVL2 depletion altered cellular membrane phospholipid composition, disrupted membrane structural properties, and diminished EGFR signaling through control of fatty-acid elongation. In support of the translational potential of these findings, dual targeting of polyunsaturated fatty-acid synthesis and EGFR signaling had a combinatorial cytotoxic effect on GSCs.
Significance:
Glioblastoma remains a devastating disease despite extensive characterization. We profiled epigenomic landscapes of glioblastoma to pinpoint cell state–specific dependencies and therapeutic vulnerabilities. GSCs utilize polyunsaturated fatty-acid synthesis to support membrane architecture, inhibition of which impairs EGFR signaling and GSC proliferation. Combinatorial targeting of these networks represents a promising therapeutic strategy.

See related commentary by Affronti and Wellen, p. 1161.

This article is highlighted in the In This Issue feature, p. 1143
Data from Innate αβ T Cells Mediate Antitumor Immunity by Orchestrating Immunogenic Macrophage Programming
Authors: Hundeyin Mautin , Kurz Emma , Mishra Ankita , Rossi Juan Andres Kochen , Liudahl Shannon M. , Leis Kenna R. , Mehrotra Harshita , Kim Mirhee , Torres Luisana E. , Ogunsakin Adesola , Link Jason , Sears Rosalie C. , Sivagnanam Shamilene , Goecks Jeremy , Islam K.M. Sadeq , Dolgalev Igor , Savadkar Shivraj , Wang Wei , Aykut Berk , Leinwand Joshua , Diskin Brian , Adam Salma , Israr Muhammad , Gelas Maeliss , Lish Justin , Chin Kathryn , Farooq Mohammad Saad , Wadowski Benjamin , Wu Jingjing , Shah Suhagi , Adeegbe Dennis O. , Pushalkar Smruti , Vasudevaraja Varshini , Saxena Deepak , Wong Kwok-Kin , Coussens Lisa M. , Miller George
Published: March 2024

Abstract
Unconventional T-lymphocyte populations are emerging as important regulators of tumor immunity. Despite this, the role of TCRαβ+CD4−CD8−NK1.1− innate αβ T cells (iαβT) in pancreatic ductal adenocarcinoma (PDA) has not been explored. We found that iαβTs represent ∼10% of T lymphocytes infiltrating PDA in mice and humans. Intratumoral iαβTs express a distinct T-cell receptor repertoire and profoundly immunogenic phenotype compared with their peripheral counterparts and conventional lymphocytes. iαβTs comprised ∼75% of the total intratumoral IL17+ cells. Moreover, iαβT-cell adoptive transfer is protective in both murine models of PDA and human organotypic systems. We show that iαβT cells induce a CCR5-dependent immunogenic macrophage reprogramming, thereby enabling marked CD4+ and CD8+ T-cell expansion/activation and tumor protection. Collectively, iαβTs govern fundamental intratumoral cross-talk between innate and adaptive immune populations and are attractive therapeutic targets.
Significance:
We found that iαβTs are a profoundly activated T-cell subset in PDA that slow tumor growth in murine and human models of disease. iαβTs induce a CCR5-dependent immunogenic tumor-associated macrophage program, T-cell activation and expansion, and should be considered as novel targets for immunotherapy.

See related commentary by Banerjee et al., p. 1164.

This article is highlighted in the In This Issue feature, p. 1143
Data from Targeting CD39 in Cancer Reveals an Extracellular ATP- and Inflammasome-Driven Tumor Immunity
Authors: Li Xian-Yang , Moesta Achim K. , Xiao Christos , Nakamura Kyohei , Casey Mika , Zhang Haiyan , Madore Jason , Lepletier Ailin , Aguilera Amelia Roman , Sundarrajan Ashmitha , Jacoberger-Foissac Celia , Wong Clifford , dela Cruz Tracy , Welch Megan , Lerner Alana G. , Spatola Bradley N. , Soros Vanessa B. , Corbin John , Anderson Ana C. , Effern Maike , Hölzel Michael , Robson Simon C. , Johnston Rebecca L. , Waddell Nicola , Smith Corey , Bald Tobias , Geetha Nishamol , Beers Courtney , Teng Michele W. L. , Smyth Mark J.
Published: March 2024

Abstract
We explored the mechanism of action of CD39 antibodies that inhibit ectoenzyme CD39 conversion of extracellular ATP (eATP) to AMP and thus potentially augment eATP–P2-mediated proinflammatory responses. Using syngeneic and humanized tumor models, we contrast the potency and mechanism of anti-CD39 mAbs with other agents targeting the adenosinergic pathway. We demonstrate the critical importance of an eATP–P2X7–ASC–NALP3-inflammasome–IL18 pathway in the antitumor activity mediated by CD39 enzyme blockade, rather than simply reducing adenosine as mechanism of action. Efficacy of anti-CD39 activity was underpinned by CD39 and P2X7 coexpression on intratumor myeloid subsets, an early signature of macrophage depletion, and active IL18 release that facilitated the significant expansion of intratumor effector T cells. More importantly, anti-CD39 facilitated infiltration into T cell–poor tumors and rescued anti–PD-1 resistance. Anti-human CD39 enhanced human T-cell proliferation and Th1 cytokine production and suppressed human B-cell lymphoma in the context of autologous Epstein–Barr virus–specific T-cell transfer.
Significance:
Overall, these data describe a potent and novel mechanism of action of antibodies that block mouse or human CD39, triggering an eATP–P2X7–inflammasome–IL18 axis that reduces intratumor macrophage number, enhances intratumor T-cell effector function, overcomes anti–PD-1 resistance, and potentially enhances the efficacy of adoptive T-cell transfer.

This article is highlighted in the In This Issue feature, p. 1631
Data from Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy
Authors: Chen Gregory M. , Chen Changya , Das Rajat K. , Gao Peng , Chen Chia-Hui , Bandyopadhyay Shovik , Ding Yang-Yang , Uzun Yasin , Yu Wenbao , Zhu Qin , Myers Regina M. , Grupp Stephan A. , Barrett David M. , Tan Kai
Published: March 2024

Abstract
The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. These findings provide key insights into the underlying molecular determinants of clinical CAR T-cell function.
Significance:
To improve clinical outcomes for CAR T-cell therapy, there is a need to understand the molecular determinants of CAR T-cell persistence. These data represent the largest clinically annotated molecular atlas in CAR T-cell therapy to date, and significantly advance our understanding of the mechanisms underlying therapeutic efficacy.

This article is highlighted in the In This Issue feature, p. 2113
Data from Oncogenic KRAS Recruits an Expansive Transcriptional Network through Mutant p53 to Drive Pancreatic Cancer Metastasis
Authors: Kim Michael P. , Li Xinqun , Deng Jenying , Zhang Yun , Dai Bingbing , Allton Kendra L. , Hughes Tara G. , Siangco Christian , Augustine Jithesh J. , Kang Ya'an , McDaniel Joy M. , Xiong Shunbin , Koay Eugene J. , McAllister Florencia , Bristow Christopher A. , Heffernan Timothy P. , Maitra Anirban , Liu Bin , Barton Michelle C. , Wasylishen Amanda R. , Fleming Jason B. , Lozano Guillermina
Published: March 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is almost uniformly fatal and characterized by early metastasis. Oncogenic KRAS mutations prevail in 95% of PDAC tumors and co-occur with genetic alterations in the TP53 tumor suppressor in nearly 70% of patients. Most TP53 alterations are missense mutations that exhibit gain-of-function phenotypes that include increased invasiveness and metastasis, yet the extent of direct cooperation between KRAS effectors and mutant p53 remains largely undefined. We show that oncogenic KRAS effectors activate CREB1 to allow physical interactions with mutant p53 that hyperactivate multiple prometastatic transcriptional networks. Specifically, mutant p53 and CREB1 upregulate the prometastatic, pioneer transcription factor FOXA1, activating its transcriptional network while promoting WNT/β-catenin signaling, together driving PDAC metastasis. Pharmacologic CREB1 inhibition dramatically reduced FOXA1 and β-catenin expression and dampened PDAC metastasis, identifying a new therapeutic strategy to disrupt cooperation between oncogenic KRAS and mutant p53 to mitigate metastasis.
Significance:
Oncogenic KRAS and mutant p53 are the most commonly mutated oncogene and tumor suppressor gene in human cancers, yet direct interactions between these genetic drivers remain undefined. We identified a cooperative node between oncogenic KRAS effectors and mutant p53 that can be therapeutically targeted to undermine cooperation and mitigate metastasis.

This article is highlighted in the In This Issue feature, p. 1861
Data from FGFR2 Extracellular Domain In-Frame Deletions Are Therapeutically Targetable Genomic Alterations That Function as Oncogenic Drivers in Cholangiocarcinoma
Authors: Cleary James M. , Raghavan Srivatsan , Wu Qibiao , Li Yvonne Y. , Spurr Liam F. , Gupta Hersh V. , Rubinson Douglas A. , Fetter Isobel J. , Hornick Jason L. , Nowak Jonathan A. , Siravegna Giulia , Goyal Lipika , Shi Lei , Brais Lauren K. , Loftus Maureen , Shinagare Atul B. , Abrams Thomas A. , Clancy Thomas E. , Wang Jiping , Patel Anuj K. , Brichory Franck , Vaslin Chessex Anne , Sullivan Ryan J. , Keller Rachel B. , Denning Sarah , Hill Emma R. , Shapiro Geoffrey I. , Pokorska-Bocci Anna , Zanna Claudio , Ng Kimmie , Schrag Deborah , Jänne Pasi A. , Hahn William C. , Cherniack Andrew D. , Corcoran Ryan B. , Meyerson Matthew , Daina Antoine , Zoete Vincent , Bardeesy Nabeel , Wolpin Brian M.
Published: March 2024

Abstract
We conducted next-generation DNA sequencing on 335 biliary tract cancers and characterized the genomic landscape by anatomic site within the biliary tree. In addition to frequent FGFR2 fusions among patients with intrahepatic cholangiocarcinoma (IHCC), we identified FGFR2 extracellular domain in-frame deletions (EID) in 5 of 178 (2.8%) patients with IHCC, including two patients with FGFR2 p.H167_N173del. Expression of this FGFR2 EID in NIH3T3 cells resulted in constitutive FGFR2 activation, oncogenic transformation, and sensitivity to FGFR inhibitors. Three patients with FGFR2 EIDs were treated with Debio 1347, an oral FGFR1/2/3 inhibitor, and all showed partial responses. One patient developed an acquired L618F FGFR2 kinase domain mutation at disease progression and experienced a further partial response for 17 months to an irreversible FGFR2 inhibitor, futibatinib. Together, these findings reveal FGFR2 EIDs as an alternative mechanism of FGFR2 activation in IHCC that predicts sensitivity to FGFR inhibitors in the clinic.
Significance:
FGFR2 EIDs are transforming genomic alterations that occur predominantly in patients with IHCC. These FGFR2 EIDs are sensitive to FGFR inhibition in vitro, and patients with these alterations benefited from treatment with FGFR inhibitors in the clinic.

This article is highlighted in the In This Issue feature, p. 2355
Data from Gut Microbiome Directs Hepatocytes to Recruit MDSCs and Promote Cholangiocarcinoma
Authors: Zhang Qianfei , Ma Chi , Duan Yi , Heinrich Bernd , Rosato Umberto , Diggs Laurence P. , Ma Lichun , Roy Soumen , Fu Qiong , Brown Zachary J. , Wabitsch Simon , Thovarai Vishal , Fu Jianyang , Feng Dechun , Ruf Benjamin , Cui Linda L. , Subramanyam Varun , Frank Karen M. , Wang Sophie , Kleiner David E. , Ritz Thomas , Rupp Christian , Gao Bin , Longerich Thomas , Kroemer Alexander , Wang Xin Wei , Ruchirawat Mathuros , Korangy Firouzeh , Schnabl Bernd , Trinchieri Giorgio , Greten Tim F.
Published: March 2024

Abstract
Gut dysbiosis is commonly observed in patients with cirrhosis and chronic gastrointestinal disorders; however, its effect on antitumor immunity in the liver is largely unknown. Here we studied how the gut microbiome affects antitumor immunity in cholangiocarcinoma. Primary sclerosing cholangitis (PSC) or colitis, two known risk factors for cholangiocarcinoma which promote tumor development in mice, caused an accumulation of CXCR2+ polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC). A decrease in gut barrier function observed in mice with PSC and colitis allowed gut-derived bacteria and lipopolysaccharide to appear in the liver and induced CXCL1 expression in hepatocytes through a TLR4-dependent mechanism and an accumulation of CXCR2+ PMN-MDSCs. In contrast, neomycin treatment blocked CXCL1 expression and PMN-MDSC accumulation and inhibited tumor growth even in the absence of liver disease or colitis. Our study demonstrates that the gut microbiome controls hepatocytes to form an immunosuppressive environment by increasing PMN-MDSCs to promote liver cancer.
Significance:
MDSCs have been shown to be induced by tumors and suppress antitumor immunity. Here we show that the gut microbiome can control accumulation of MDSCs in the liver in the context of a benign liver disease or colitis.

See related commentary by Chagani and Kwong, p. 1014.

This article is highlighted in the In This Issue feature, p. 995
Data from Proteomic Screens for Suppressors of Anoikis Identify IL1RAP as a Promising Surface Target in Ewing Sarcoma
Authors: Zhang Hai-Feng , Hughes Christopher S. , Li Wei , He Jian-Zhong , Surdez Didier , El-Naggar Amal M. , Cheng Hongwei , Prudova Anna , Delaidelli Alberto , Negri Gian Luca , Li Xiaojun , Ørum-Madsen Maj Sofie , Lizardo Michael M. , Oo Htoo Zarni , Colborne Shane , Shyp Taras , Scopim-Ribeiro Renata , Hammond Colin A. , Dhez Anne-Chloe , Langman Sofya , Lim Jonathan K.M. , Kung Sonia H.Y. , Li Amy , Steino Anne , Daugaard Mads , Parker Seth J. , Geltink Ramon I. Klein , Orentas Rimas J. , Xu Li-Yan , Morin Gregg B. , Delattre Olivier , Dimitrov Dimiter S. , Sorensen Poul H.
Published: March 2024

Abstract
Cancer cells must overcome anoikis (detachment-induced death) to successfully metastasize. Using proteomic screens, we found that distinct oncoproteins upregulate IL1 receptor accessory protein (IL1RAP) to suppress anoikis. IL1RAP is directly induced by oncogenic fusions of Ewing sarcoma, a highly metastatic childhood sarcoma. IL1RAP inactivation triggers anoikis and impedes metastatic dissemination of Ewing sarcoma cells. Mechanistically, IL1RAP binds the cell-surface system Xc− transporter to enhance exogenous cystine uptake, thereby replenishing cysteine and the glutathione antioxidant. Under cystine depletion, IL1RAP induces cystathionine gamma lyase (CTH) to activate the transsulfuration pathway for de novo cysteine synthesis. Therefore, IL1RAP maintains cyst(e)ine and glutathione pools, which are vital for redox homeostasis and anoikis resistance. IL1RAP is minimally expressed in pediatric and adult normal tissues, and human anti-IL1RAP antibodies induce potent antibody-dependent cellular cytotoxicity of Ewing sarcoma cells. Therefore, we define IL1RAP as a new cell-surface target in Ewing sarcoma, which is potentially exploitable for immunotherapy.
Significance:
Here, we identify cell-surface protein IL1RAP as a key driver of metastasis in Ewing sarcoma, a highly aggressive childhood sarcoma. Minimal expression in pediatric and adult normal tissues nominates IL1RAP as a promising target for immunotherapy.

See related commentary by Yoon and DeNicola, p. 2679.

This article is highlighted in the In This Issue feature, p. 2659
Data from GITR Pathway Activation Abrogates Tumor Immune Suppression through Loss of Regulatory T-cell Lineage Stability
Authors: Schaer David A. , Budhu Sadna , Liu Cailian , Bryson Campbell , Malandro Nicole , Cohen Adam , Zhong Hong , Yang Xia , Houghton Alan N. , Merghoub Taha , Wolchok Jedd D.
Published: March 2024

Abstract
Ligation of GITR (glucocorticoid-induced TNF receptor-related gene, or TNFRSF18) by agonist antibody has recently entered into early-phase clinical trials for the treatment of advanced malignancies. Although the ability of GITR modulation to induce tumor regression is well documented in preclinical studies, the underlying mechanisms of action, particularly its effects on CD4+Foxp3+ regulatory T cells (Treg), have not been fully elucidated. We have previously shown that GITR ligation in vivo by agonist antibody DTA-1 causes more than 50% reduction of intratumor Tregs with down modulation of Foxp3 expression. Here, we show that the loss of Foxp3 is tumor dependent. Adoptively transferred Foxp3+ Tregs from tumor-bearing animals lose Foxp3 expression in the host when treated with DTA-1, whereas Tregs from naïve mice maintain Foxp3 expression. GITR ligation also alters the expression of various transcription factors and cytokines important for Treg function. Complete Foxp3 loss in intratumor Tregs correlates with a dramatic decrease in Helios expression and is associated with the upregulation of transcription factors, T-Bet and Eomes. Changes in Helios correspond with a reduction in interleukin (IL)-10 and an increase in IFN-γ expression in DTA-1–treated Tregs. Together, these data show that GITR agonist antibody alters Treg lineage stability inducing an inflammatory effector T-cell phenotype. The resultant loss of lineage stability causes Tregs to lose their intratumor immune-suppressive function, making the tumor susceptible to killing by tumor-specific effector CD8+ T cells. Cancer Immunol Res; 1(5); 320–31. ©2013 AACR.
Data from NY-ESO-1 Expression in Meningioma Suggests a Rationale for New Immunotherapeutic Approaches
Authors: Baia Gilson S. , Caballero Otavia L. , Ho Janelle S.Y. , Zhao Qi , Cohen Tzeela , Binder Zev A. , Salmasi Vafi , Gallia Gary L. , Quinones-Hinojosa Alfredo , Olivi Alessandro , Brem Henry , Burger Peter , Strausberg Robert L. , Simpson Andrew J.G. , Eberhart Charles G. , Riggins Gregory J.
Published: March 2024

Abstract
Meningiomas are the most common primary intracranial tumors. Surgical resection remains the treatment of choice for these tumors. However, a significant number of tumors are not surgically accessible, recur, or become malignant, necessitating the repetition of surgery and sometimes radiation. Chemotherapy is rarely used and is generally not recognized as an effective treatment. Cancer/testis (CT) genes represent a unique class of genes, which are expressed by germ cells, normally silenced in somatic cells, but activated in various cancers. CT proteins can elicit spontaneous immune responses in patients with cancer and this feature makes them attractive targets for immunotherapy-based approaches. We analyzed mRNA expression of 37 testis-restricted CT genes in a discovery set of 18 meningiomas by reverse transcription PCR. The overall frequency of expression of CT genes ranged from 5.6% to 27.8%. The most frequently expressed was NY-ESO-1, in 5 patients (27.8%). We subsequently analyzed NY-ESO-1 protein expression in a larger set of meningiomas by immunohistochemistry and found expression in 108 of 110 cases. In some cases, NY-ESO-1 expression was diffused and homogenous, but in most instances it was heterogeneous. Importantly, NY-ESO-1 expression was positively correlated with higher grade and patients presenting with higher levels of NY-ESO-1 staining had significantly worse disease-free and overall survival. We have also shown that NY-ESO-1 expression may lead to humoral immune response in patients with meningioma. Considering the limited treatment options for patients with meningioma, the potential of NY-ESO-1–based immunotherapy should be explored. Cancer Immunol Res; 1(5); 296–302. ©2013 AACR.
Data from Nature of Tumor Control by Permanently and Transiently Modified GD2 Chimeric Antigen Receptor T Cells in Xenograft Models of Neuroblastoma
Authors: Singh Nathan , Liu Xiaojun , Hulitt Jessica , Jiang Shuguang , June Carl H. , Grupp Stephan A. , Barrett David M. , Zhao Yangbing
Published: March 2024

Abstract
Chimeric antigen receptor (CAR) therapy has begun to demonstrate success as a novel treatment modality for hematologic malignancies. The success observed thus far has been with T cells permanently engineered to express chimeric receptors. T cells engineered using RNA electroporation represent an alternative with the potential for similar efficacy and greater safety when initially targeting novel antigens. Neuroblastoma is a common pediatric solid tumor with the potential to be targeted using immunotherapy. We performed xenograft studies in NSG mice in which we assessed the efficacy of both permanently modified and transiently modified CAR T cells directed against the neuroblastoma antigen GD2 in both local and disseminated disease models. Disease response was monitored by tumor volume measurement and histologic examination, as well as in vivo bioluminescence. RNA-modified GD2 CAR T cells mediated rapid tumor destruction when delivered locally. A single infusion of lentivirally modified GD2 CAR T cells resulted in long-term control of disseminated disease. Multiple infusions of RNA GD2 CAR T cells slowed the progression of disseminated disease and improved survival, but did not result in long-term disease control. Histologic examination revealed that the transiently modified cells were unable to significantly penetrate the tumor environment when delivered systemically, despite multiple infusions of CAR T cells. Thus, we demonstrate that RNA-modified GD2 CAR T cells can mediate effective antitumor responses in vivo, and permanently modified cells are able to control disseminated neuroblastoma in xenograft mice. Lack of long-term disease control by RNA-engineered cells resulted from an inability to penetrate the tumor microenvironment. Cancer Immunol Res; 2(11); 1059–70. ©2014 AACR.
Data from c-Abl Modulates Tumor Cell Sensitivity to Antibody-Dependent Cellular Cytotoxicity
Authors: Murray Joseph C. , Aldeghaither Dalal , Wang Shangzi , Nasto Rochelle E. , Jablonski Sandra A. , Tang Yong , Weiner Louis M.
Published: March 2024

Abstract
Monoclonal antibodies (mAb) can modulate cancer cell signal transduction and recruit antitumor immune effector mechanisms—including antibody-dependent cellular cytotoxicity (ADCC). Although several clinically effective antibodies can promote ADCC, therapeutic resistance is common. We hypothesized that oncogenic signaling networks within tumor cells affect their sensitivity to ADCC. We developed a screening platform and targeted 60 genes derived from an EGFR gene network using RNAi in an in vitro ADCC model system. Knockdown of GRB7, PRKCE, and ABL1 enhanced ADCC by primary and secondary screens. ABL1 knockdown also reduced cell proliferation, independent of its ADCC enhancement effects. c-Abl overexpression decreased ADCC sensitivity and rescued the effects of ABL1 knockdown. Imatinib inhibition of c-Abl kinase activity also enhanced ADCC—phenocopying ABL1 knockdown—against several EGFR-expressing head-and-neck squamous cell carcinoma cell lines by ex vivo primary natural killer cells. Our findings suggest that combining c-Abl inhibition with ADCC-promoting antibodies, such as cetuximab, could translate into increased therapeutic efficacy of mAbs. Cancer Immunol Res; 2(12); 1186–98. ©2014 AACR.
Data from Novel Mechanism of Tumor Suppression by Polarity Gene Discs Large 1 (DLG1) Revealed in a Murine Model of Pediatric B-ALL
Authors: Sandoval Gabriel J. , Graham Daniel B. , Gmyrek Grzegorz B. , Akilesh Holly M. , Fujikawa Keiko , Sammut Benedicte , Bhattacharya Deepta , Srivatsan Shuba , Kim Alfred , Shaw Andrey S. , Yang-Iott Katherine , Bassing Craig H. , Duncavage Eric , Xavier Ramnik J. , Swat Wojciech
Published: March 2024

Abstract
Drosophila melanogaster discs large (dlg) is an essential tumor suppressor gene (TSG) controlling epithelial cell growth and polarity of the fly imaginal discs in pupal development. A mammalian ortholog, Dlg1, is involved in embryonic urogenital morphogenesis, postsynaptic densities in neurons, and immune synapses in lymphocytes. However, a potential role for Dlg1 as a mammalian TSG is unknown. Here, we present evidence that loss of Dlg1 confers strong predisposition to the development of malignancies in a murine model of pediatric B-cell acute lymphoblastic leukemia (B-ALL). Using mice with conditionally deleted Dlg1 alleles, we identify a novel “pre-leukemic” stage of developmentally arrested early B-lineage cells marked by preeminent c-Myc expression. Mechanistically, we show that in B-lineage progenitors Dlg1 interacts with and stabilizes the PTEN protein, regulating its half-life and steady-state abundance. The loss of Dlg1 does not affect the level of PTEN mRNAs but results in a dramatic decrease in PTEN protein, leading to excessive phosphoinositide 3-kinase signaling and proliferation. Our data suggest a novel model of tumor suppression by a PDZ domain-containing polarity gene in hematopoietic cancers. Cancer Immunol Res; 1(6); 426–37. ©2013 AACR.
Data from Targeting Fibroblast Activation Protein in Tumor Stroma with Chimeric Antigen Receptor T Cells Can Inhibit Tumor Growth and Augment Host Immunity without Severe Toxicity
Authors: Wang Liang-Chuan S. , Lo Albert , Scholler John , Sun Jing , Majumdar Rajrupa S. , Kapoor Veena , Antzis Michael , Cotner Cody E. , Johnson Laura A. , Durham Amy C. , Solomides Charalambos C. , June Carl H. , Puré Ellen , Albelda Steven M.
Published: March 2024

Abstract
The majority of chimeric antigen receptor (CAR) T-cell research has focused on attacking cancer cells. Here, we show that targeting the tumor-promoting, nontransformed stromal cells using CAR T cells may offer several advantages. We developed a retroviral CAR construct specific for the mouse fibroblast activation protein (FAP), comprising a single-chain Fv FAP [monoclonal antibody (mAb) 73.3] with the CD8α hinge and transmembrane regions, and the human CD3ζ and 4-1BB activation domains. The transduced muFAP-CAR mouse T cells secreted IFN-γ and killed FAP-expressing 3T3 target cells specifically. Adoptively transferred 73.3-FAP-CAR mouse T cells selectively reduced FAPhi stromal cells and inhibited the growth of multiple types of subcutaneously transplanted tumors in wild-type, but not FAP-null immune-competent syngeneic mice. The antitumor effects could be augmented by multiple injections of the CAR T cells, by using CAR T cells with a deficiency in diacylglycerol kinase, or by combination with a vaccine. A major mechanism of action of the muFAP-CAR T cells was the augmentation of the endogenous CD8+ T-cell antitumor responses. Off-tumor toxicity in our models was minimal following muFAP-CAR T-cell therapy. In summary, inhibiting tumor growth by targeting tumor stroma with adoptively transferred CAR T cells directed to FAP can be safe and effective, suggesting that further clinical development of anti-human FAP-CAR is warranted. Cancer Immunol Res; 2(2); 154–66. ©2013 AACR.
Data from Rescue of Notch-1 Signaling in Antigen-Specific CD8+ T Cells Overcomes Tumor-Induced T-cell Suppression and Enhances Immunotherapy in Cancer
Authors: Sierra Rosa A. , Thevenot Paul , Raber Patrick L. , Cui Yan , Parsons Chris , Ochoa Augusto C. , Trillo-Tinoco Jimena , Valle Luis Del , Rodriguez Paulo C.
Published: March 2024

Abstract
An impaired antitumor immunity is found in patients with cancer and represents a major obstacle in the successful development of different forms of immunotherapy. Signaling through Notch receptors regulates the differentiation and function of many cell types, including immune cells. However, the effect of Notch in CD8+ T-cell responses in tumors remains unclear. Thus, we aimed to determine the role of Notch signaling in CD8+ T cells in the induction of tumor-induced suppression. Our results using conditional knockout mice show that Notch-1 and Notch-2 were critical for the proliferation and IFNγ production of activated CD8+ T cells and were significantly decreased in tumor-infiltrating T cells. Conditional transgenic expression of Notch-1 intracellular domain (N1IC) in antigen-specific CD8+ T cells did not affect activation or proliferation of CD8+ T cells, but induced a central memory phenotype and increased cytotoxicity effects and granzyme B levels. Consequently, a higher antitumor response and resistance to tumor-induced tolerance were found after adoptive transfer of N1IC-transgenic CD8+ T cells into tumor-bearing mice. Additional results showed that myeloid-derived suppressor cells (MDSC) blocked the expression of Notch-1 and Notch-2 in T cells through nitric oxide–dependent mechanisms. Interestingly, N1IC overexpression rendered CD8+ T cells resistant to the tolerogenic effect induced by MDSC in vivo. Together, the results suggest the key role of Notch in the suppression of CD8+ T-cell responses in tumors and the therapeutic potential of N1IC in antigen-specific CD8+ T cells to reverse T-cell suppression and increase the efficacy of T cell–based immunotherapies in cancer. Cancer Immunol Res; 2(8); 800–11. ©2014 AACR.
Data from Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade
Authors: Johnson Douglas B. , Frampton Garrett M. , Rioth Matthew J. , Yusko Erik , Xu Yaomin , Guo Xingyi , Ennis Riley C. , Fabrizio David , Chalmers Zachary R. , Greenbowe Joel , Ali Siraj M. , Balasubramanian Sohail , Sun James X. , He Yuting , Frederick Dennie T. , Puzanov Igor , Balko Justin M. , Cates Justin M. , Ross Jeffrey S. , Sanders Catherine , Robins Harlan , Shyr Yu , Miller Vincent A. , Stephens Philip J. , Sullivan Ryan J. , Sosman Jeffrey A. , Lovly Christine M.
Published: March 2024

Abstract
Therapeutic antibodies blocking programmed death-1 and its ligand (PD-1/PD-L1) induce durable responses in a substantial fraction of melanoma patients. We sought to determine whether the number and/or type of mutations identified using a next-generation sequencing (NGS) panel available in the clinic was correlated with response to anti–PD-1 in melanoma. Using archival melanoma samples from anti–PD-1/PD-L1-treated patients, we performed hybrid capture–based NGS on 236–315 genes and T-cell receptor (TCR) sequencing on initial and validation cohorts from two centers. Patients who responded to anti–PD-1/PD-L1 had higher mutational loads in an initial cohort (median, 45.6 vs. 3.9 mutations/MB; P = 0.003) and a validation cohort (37.1 vs. 12.8 mutations/MB; P = 0.002) compared with nonresponders. Response rate, progression-free survival, and overall survival were superior in the high, compared with intermediate and low, mutation load groups. Melanomas with NF1 mutations harbored high mutational loads (median, 62.7 mutations/MB) and high response rates (74%), whereas BRAF/NRAS/NF1 wild-type melanomas had a lower mutational load. In these archival samples, TCR clonality did not predict response. Mutation numbers in the 315 genes in the NGS platform strongly correlated with those detected by whole-exome sequencing in The Cancer Genome Atlas samples, but was not associated with survival. In conclusion, mutational load, as determined by an NGS platform available in the clinic, effectively stratified patients by likelihood of response. This approach may provide a clinically feasible predictor of response to anti–PD-1/PD-L1. Cancer Immunol Res; 4(11); 959–67. ©2016 AACR.
Data from A Paracrine Role for IL6 in Prostate Cancer Patients: Lack of Production by Primary or Metastatic Tumor Cells
Authors: Yu Shu-Han , Zheng Qizhi , Esopi David , Macgregor-Das Anne , Luo Jun , Antonarakis Emmanuel S. , Drake Charles G. , Vessella Robert , Morrissey Colm , De Marzo Angelo M. , Sfanos Karen S.
Published: March 2024

Abstract
Correlative human studies suggest that the pleiotropic cytokine IL6 contributes to the development and/or progression of prostate cancer. However, the source of IL6 production in the prostate microenvironment in patients has yet to be determined. The cellular origin of IL6 in primary and metastatic prostate cancer was examined in formalin-fixed, paraffin-embedded tissues using a highly sensitive and specific chromogenic in situ hybridization (CISH) assay that underwent extensive analytical validation. Quantitative RT-PCR showed that benign prostate tissues often had higher expression of IL6 mRNA than matched tumor specimens. CISH analysis further indicated that both primary and metastatic prostate adenocarcinoma cells do not express IL6 mRNA. IL6 expression was highly heterogeneous across specimens and was nearly exclusively restricted to the prostate stromal compartment—including endothelial cells and macrophages, among other cell types. The number of IL6-expressing cells correlated positively with the presence of acute inflammation. In metastatic disease, tumor cells were negative in all lesions examined, and IL6 expression was restricted to endothelial cells within the vasculature of bone metastases. Finally, IL6 was not detected in any cells in soft tissue metastases. These data suggest that, in prostate cancer patients, paracrine rather than autocrine IL6 production is likely associated with any role for the cytokine in disease progression. Cancer Immunol Res; 3(10); 1175–84. ©2015 AACR.
Data from Extracellular Vesicles Present in Human Ovarian Tumor Microenvironments Induce a Phosphatidylserine-Dependent Arrest in the T-cell Signaling Cascade
Authors: Kelleher Raymond J. , Balu-Iyer Sathy , Loyall Jenni , Sacca Anthony J. , Shenoy Gautam N. , Peng Peng , Iyer Vandana , Fathallah Anas M. , Berenson Charles S. , Wallace Paul K. , Tario Joseph , Odunsi Kunle , Bankert Richard B.
Published: March 2024

Abstract
The identification of immunosuppressive factors within human tumor microenvironments, and the ability to block these factors, would be expected to enhance patients' antitumor immune responses. We previously established that an unidentified factor, or factors, present in ovarian tumor ascites fluids reversibly inhibited the activation of T cells by arresting the T-cell signaling cascade. Ultracentrifugation of the tumor ascites fluid has now revealed a pellet that contains small extracellular vesicles (EV) with an average diameter of 80 nm. The T-cell arrest was determined to be causally linked to phosphatidylserine (PS) that is present on the outer leaflet of the vesicle bilayer, as a depletion of PS-expressing EV or a blockade of PS with anti-PS antibody significantly inhibits the vesicle-induced signaling arrest. The inhibitory EV were also isolated from solid tumor tissues. The presence of immunosuppressive vesicles in the microenvironments of ovarian tumors and our ability to block their inhibition of T-cell function represent a potential therapeutic target for patients with ovarian cancer. Cancer Immunol Res; 3(11); 1269–78. ©2015 AACR.
Data from Using Quantitative Seroproteomics to Identify Antibody Biomarkers in Pancreatic Cancer
Authors: Jhaveri Darshil T. , Kim Min-Sik , Thompson Elizabeth D. , Huang Lanqing , Sharma Rajni , Klein Alison P. , Zheng Lei , Le Dung T. , Laheru Daniel A. , Pandey Akhilesh , Jaffee Elizabeth M. , Anders Robert A.
Published: March 2024

Abstract
Pancreatic cancer is the fourth leading cause of cancer-related deaths in the United States. Less than 6% of patients survive beyond the fifth year due to inadequate early diagnostics and ineffective treatment options. Our laboratory has developed an allogeneic, granulocyte-macrophage colony-stimulating factor (GM-CSF)–secreting pancreatic cancer vaccine (GVAX) that has been tested in phase II clinical trials. Here, we employed a serum antibodies–based SILAC immunoprecipitation (SASI) approach to identify proteins that elicit an antibody response after vaccination. The SASI approach uses immunoprecipitation with patient-derived antibodies that is coupled to quantitative stable isotope–labeled amino acids in cell culture (SILAC). Using mass spectrometric analysis, we identified more than 150 different proteins that induce an antibody response after vaccination. The regulatory subunit 12A of protein phosphatase 1 (MYPT1 or PPP1R12A), regulatory subunit 8 of the 26S proteasome (PSMC5), and the transferrin receptor (TFRC) were shown to be pancreatic cancer–associated antigens recognized by postvaccination antibodies in the sera of patients with favorable disease-free survival after GVAX therapy. We further interrogated these proteins in over 80 GVAX-treated patients' pancreases and uniformly found a significant increase in the expression of MYPT1, PSMC5, and TFRC in neoplastic compared with non-neoplastic pancreatic ductal epithelium. We show that the novel SASI approach can identify antibody targets specifically expressed in patients with improved disease-free survival after cancer vaccine therapy. These targets need further validation to be considered as possible pancreatic cancer biomarkers. Cancer Immunol Res; 4(3); 225–33. ©2016 AACR.
Data from Combination of 4-1BB Agonist and PD-1 Antagonist Promotes Antitumor Effector/Memory CD8 T Cells in a Poorly Immunogenic Tumor Model
Authors: Chen Shihao , Lee Li-Fen , Fisher Timothy S. , Jessen Bart , Elliott Mark , Evering Winston , Logronio Kathryn , Tu Guang Huan , Tsaparikos Konstantinos , Li Xiaoai , Wang Hui , Ying Chi , Xiong Mengli , VanArsdale Todd , Lin John C.
Published: March 2024

Abstract
Immunotherapies targeting the programmed death 1 (PD-1) coinhibitory receptor have shown great promise for a subset of patients with cancer. However, robust and safe combination therapies are still needed to bring the benefit of cancer immunotherapy to broader patient populations. To search for an optimal strategy of combinatorial immunotherapy, we have compared the antitumor activity of the anti–4-1BB/anti–PD-1 combination with that of the anti–PD-1/anti–LAG-3 combination in the poorly immunogenic B16F10 melanoma model. Pronounced tumor inhibition occurred only in animals receiving anti–PD-1 and anti–4-1BB concomitantly, while combining anti–PD-1 with anti–LAG-3 led to a modest degree of tumor suppression. The activity of the anti–4-1BB/anti–PD-1 combination was dependent on IFNγ and CD8+ T cells. Both 4-1BB and PD-1 proteins were elevated on the surface of CD8+ T cells by anti–4-1BB/anti–PD-1 cotreatment. In the tumor microenvironment, an effective antitumor immune response was induced as indicated by the increased CD8+/Treg ratio and the enrichment of genes such as Cd3e, Cd8a, Ifng, and Eomes. In the spleen, the combination treatment shaped the immune system to an effector/memory phenotype and increased the overall activity of tumor-specific CD8+ CTLs, reflecting a long-lasting systemic antitumor response. Furthermore, combination treatment in C57BL/6 mice showed no additional safety signals, and only minimally increased severity of the known toxicity relative to 4-1BB agonist alone. Therefore, in the absence of any cancer vaccine, anti–4-1BB/anti–PD-1 combination therapy is sufficient to elicit a robust antitumor effector/memory T-cell response in an aggressive tumor model and is therefore a candidate for combination trials in patients. Cancer Immunol Res; 3(2); 149–60. ©2014 AACR.
Data from Decitabine Enhances Lymphocyte Migration and Function and Synergizes with CTLA-4 Blockade in a Murine Ovarian Cancer Model
Authors: Wang Lei , Amoozgar Zohreh , Huang Jing , Saleh Mohammad H. , Xing Deyin , Orsulic Sandra , Goldberg Michael S.
Published: March 2024

Abstract
The lack of second-line treatment for relapsed ovarian cancer necessitates the development of improved combination therapies. Targeted therapy and immunotherapy each confer clinical benefit, albeit limited as monotherapies. Ovarian cancer is not particularly responsive to immune checkpoint blockade, so combination with a complementary therapy may be beneficial. Recent studies have revealed that a DNA methyl transferase inhibitor, azacytidine, alters expression of immunoregulatory genes in ovarian cancer. In this study, the antitumor effects of a related DNA methyl transferase inhibitor, decitabine (DAC), were demonstrated in a syngeneic murine ovarian cancer model. Low-dose DAC treatment increases the expression of chemokines that recruit NK cells and CD8+ T cells, promotes their production of IFNγ and TNFα, and extends the survival of mice bearing subcutaneous or orthotopic tumors. While neither DAC nor immune checkpoint blockade confers durable responses as a monotherapy in this model, the efficacy of anti–CTLA-4 was potentiated by combination with DAC. This combination promotes differentiation of naïve T cells into effector T cells and prolongs cytotoxic lymphocyte responses as well as mouse survival. These results suggest that this combination therapy may be worthy of further consideration for improved treatment of drug-resistant ovarian cancer. Cancer Immunol Res; 3(9); 1030–41. ©2015 AACR.