bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from HER2-Mediated Internalization of Cytotoxic Agents in ERBB2 Amplified or Mutant Lung Cancers
Authors: Li Bob T. , Michelini Flavia , Misale Sandra , Cocco Emiliano , Baldino Laura , Cai Yanyan , Shifman Sophie , Tu Hai-Yan , Myers Mackenzie L. , Xu Chongrui , Mattar Marissa , Khodos Inna , Little Megan , Qeriqi Besnik , Weitsman Gregory , Wilhem Clare J. , Lalani Alshad S. , Diala Irmina , Freedman Rachel A. , Lin Nancy U. , Solit David B. , Berger Michael F. , Barber Paul R. , Ng Tony , Offin Michael , Isbell James M. , Jones David R. , Yu Helena A. , Thyparambil Sheeno , Liao Wei-Li , Bhalkikar Anuja , Cecchi Fabiola , Hyman David M. , Lewis Jason S. , Buonocore Darren J. , Ho Alan L. , Makker Vicky , Reis-Filho Jorge S. , Razavi Pedram , Arcila Maria E. , Kris Mark G. , Poirier John T. , Shen Ronglai , Tsurutani Junji , Ulaner Gary A. , de Stanchina Elisa , Rosen Neal , Rudin Charles M. , Scaltriti Maurizio
Published: April 2023

Abstract
Amplification of and oncogenic mutations in ERBB2, the gene encoding the HER2 receptor tyrosine kinase, promote receptor hyperactivation and tumor growth. Here we demonstrate that HER2 ubiquitination and internalization, rather than its overexpression, are key mechanisms underlying endocytosis and consequent efficacy of the anti-HER2 antibody–drug conjugates (ADC) ado-trastuzumab emtansine (T-DM1) and trastuzumab deruxtecan (T-DXd) in lung cancer cell lines and patient-derived xenograft models. These data translated into a 51% response rate in a clinical trial of T-DM1 in 49 patients with ERBB2-amplified or -mutant lung cancers. We show that cotreatment with irreversible pan-HER inhibitors enhances receptor ubiquitination and consequent ADC internalization and efficacy. We also demonstrate that ADC switching to T-DXd, which harbors a different cytotoxic payload, achieves durable responses in a patient with lung cancer and corresponding xenograft model developing resistance to T-DM1. Our findings may help guide future clinical trials and expand the field of ADC as cancer therapy.
Significance:
T-DM1 is clinically effective in lung cancers with amplification of or mutations in ERBB2. This activity is enhanced by cotreatment with irreversible pan-HER inhibitors, or ADC switching to T-DXd. These results may help address unmet needs of patients with HER2-activated tumors and no approved targeted therapy.

See related commentary by Rolfo and Russo, p. 643.

This article is highlighted in the In This Issue feature, p. 627
Data from Tumor Mutational Burden as a Predictive Biomarker in Solid Tumors
Authors: Sha Dan , Jin Zhaohui , Budczies Jan , Kluck Klaus , Stenzinger Albrecht , Sinicrope Frank A.
Published: April 2023

Abstract
Tumor mutational burden (TMB), defined as the number of somatic mutations per megabase of interrogated genomic sequence, varies across malignancies. Panel sequencing–based estimates of TMB have largely replaced whole-exome sequencing–derived TMB in the clinic. Retrospective evidence suggests that TMB can predict the efficacy of immune checkpoint inhibitors, and data from KEYNOTE-158 led to the recent FDA approval of pembrolizumab for the TMB-high tumor subgroup. Unmet needs include prospective validation of TMB cutoffs in relationship to tumor type and patient outcomes. Furthermore, standardization and harmonization of TMB measurement across test platforms are important to the successful implementation of TMB in clinical practice.
Significance:
Evaluation of TMB as a predictive biomarker creates the need to harmonize panel-based TMB estimation and standardize its reporting. TMB can improve the predictive accuracy for immunotherapy outcomes, and has the potential to expand the candidate pool of patients for treatment with immune checkpoint inhibitors.
Data from Genetic Ancestry Contributes to Somatic Mutations in Lung Cancers from Admixed Latin American Populations
Authors: Carrot-Zhang Jian , Soca-Chafre Giovanny , Patterson Nick , Thorner Aaron R. , Nag Anwesha , Watson Jacqueline , Genovese Giulio , Rodriguez July , Gelbard Maya K. , Corrales-Rodriguez Luis , Mitsuishi Yoichiro , Ha Gavin , Campbell Joshua D. , Oxnard Geoffrey R. , Arrieta Oscar , Cardona Andres F. , Gusev Alexander , Meyerson Matthew
Published: April 2023

Abstract
Inherited lung cancer risk, particularly in nonsmokers, is poorly understood. Genomic and ancestry analysis of 1,153 lung cancers from Latin America revealed striking associations between Native American ancestry and their somatic landscape, including tumor mutational burden, and specific driver mutations in EGFR, KRAS, and STK11. A local Native American ancestry risk score was more strongly correlated with EGFR mutation frequency compared with global ancestry correlation, suggesting that germline genetics (rather than environmental exposure) underlie these disparities.
Significance:
The frequency of somatic EGFR and KRAS mutations in lung cancer varies by ethnicity, but we do not understand why. Our study suggests that the variation in EGFR and KRAS mutation frequency is associated with genetic ancestry and suggests further studies to identify germline alleles that underpin this association.

See related commentary by Gomez et al., p. 534.

This article is highlighted in the In This Issue feature, p. 521
Data from A First-in-Human Study and Biomarker Analysis of NKTR-214, a Novel IL2Rβγ-Biased Cytokine, in Patients with Advanced or Metastatic Solid Tumors
Authors: Bentebibel Salah-Eddine , Hurwitz Michael E. , Bernatchez Chantale , Haymaker Cara , Hudgens Courtney W. , Kluger Harriet M. , Tetzlaff Michael T. , Tagliaferri Mary A. , Zalevsky Jonathan , Hoch Ute , Fanton Christie , Aung Sandra , Hwu Patrick , Curti Brendan D. , Tannir Nizar M. , Sznol Mario , Diab Adi
Published: April 2023

Abstract
NKTR-214 (bempegaldesleukin) is a novel IL2 pathway agonist, designed to provide sustained signaling through heterodimeric IL2 receptor βγ to drive increased proliferation and activation of CD8+ T and natural killer cells without unwanted expansion of T regulatory cells (Treg) in the tumor microenvironment. In this first-in-human multicenter phase I study, NKTR-214 administered as an outpatient regimen was well tolerated and showed clinical activity including tumor shrinkage and durable disease stabilization in heavily pretreated patients. Immune activation and increased numbers of immune cells were observed in the periphery across all doses and cycles with no loss of NKTR-214 activity with repeated administration. On-treatment tumor biopsies demonstrated that NKTR-214 promoted immune cell increase with limited increase of Tregs. Transcriptional analysis of tumor biopsies showed that NKTR-214 engaged the IL2 receptor pathway and significantly increased genes associated with an effector phenotype. Based on safety and pharmacodynamic markers, the recommended phase II dose was determined to be 0.006 mg/kg every three weeks.
Significance:
We believe that IL2- and IL2 pathway–targeted agents such as NKTR-214 are key components to an optimal immunotherapy treatment algorithm. Based on its biological activity and tolerability, NKTR-214 is being studied with approved immuno-oncology agents including checkpoint inhibitors.

See related commentary by Sullivan, p. 694.

This article is highlighted in the In This Issue feature, p. 681
Data from Inactivation of Fbxw7 Impairs dsRNA Sensing and Confers Resistance to PD-1 Blockade
Authors: Gstalder Cécile , Liu David , Miao Diana , Lutterbach Bart , DeVine Alexander L. , Lin Chenyu , Shettigar Megha , Pancholi Priya , Buchbinder Elizabeth I. , Carter Scott L. , Manos Michael P. , Rojas-Rudilla Vanesa , Brennick Ryan , Gjini Evisa , Chen Pei-Hsuan , Lako Ana , Rodig Scott , Yoon Charles H. , Freeman Gordon J. , Barbie David A. , Hodi F. Stephen , Miles Wayne , Van Allen Eliezer M. , Haq Rizwan
Published: April 2023

Abstract
The molecular mechanisms leading to resistance to PD-1 blockade are largely unknown. Here, we characterize tumor biopsies from a patient with melanoma who displayed heterogeneous responses to anti–PD-1 therapy. We observe that a resistant tumor exhibited a loss-of-function mutation in the tumor suppressor gene FBXW7, whereas a sensitive tumor from the same patient did not. Consistent with a functional role in immunotherapy response, inactivation of Fbxw7 in murine tumor cell lines caused resistance to anti–PD-1 in immunocompetent animals. Loss of Fbxw7 was associated with altered immune microenvironment, decreased tumor-intrinsic expression of the double-stranded RNA (dsRNA) sensors MDA5 and RIG-I, and diminished induction of type I IFN and MHC-I expression. In contrast, restoration of dsRNA sensing in Fbxw7-deficient cells was sufficient to sensitize them to anti–PD-1. Our results thus establish a new role for the commonly inactivated tumor suppressor FBXW7 in viral sensing and sensitivity to immunotherapy.
Significance:
Our findings establish a role of the commonly inactivated tumor suppressor FBXW7 as a genomic driver of response to anti–PD-1 therapy. Fbxw7 loss promotes resistance to anti–PD-1 through the downregulation of viral sensing pathways, suggesting that therapeutic reactivation of these pathways could improve clinical responses to checkpoint inhibitors in genomically defined cancer patient populations.

This article is highlighted in the In This Issue feature, p. 1241
Data from Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site
Authors: Fowler Joanna C. , King Charlotte , Bryant Christopher , Hall Michael W.J. , Sood Roshan , Ong Swee Hoe , Earp Eleanor , Fernandez-Antoran David , Koeppel Jonas , Dentro Stefan C. , Shorthouse David , Durrani Amer , Fife Kate , Rytina Edward , Milne Doreen , Roshan Amit , Mahububani Krishnaa , Saeb-Parsy Kourosh , Hall Benjamin A. , Gerstung Moritz , Jones Philip H.
Published: April 2023

Abstract
Skin cancer risk varies substantially across the body, yet how this relates to the mutations found in normal skin is unknown. Here we mapped mutant clones in skin from high- and low-risk sites. The density of mutations varied by location. The prevalence of NOTCH1 and FAT1 mutations in forearm, trunk, and leg skin was similar to that in keratinocyte cancers. Most mutations were caused by ultraviolet light, but mutational signature analysis suggested differences in DNA-repair processes between sites. Eleven mutant genes were under positive selection, with TP53 preferentially selected in the head and FAT1 in the leg. Fine-scale mapping revealed 10% of clones had copy-number alterations. Analysis of hair follicles showed mutations in the upper follicle resembled adjacent skin, but the lower follicle was sparsely mutated. Normal skin is a dense patchwork of mutant clones arising from competitive selection that varies by location.
Significance:
Mapping mutant clones across the body reveals normal skin is a dense patchwork of mutant cells. The variation in cancer risk between sites substantially exceeds that in mutant clone density. More generally, mutant genes cannot be assigned as cancer drivers until their prevalence in normal tissue is known.

See related commentary by De Dominici and DeGregori, p. 227.

This article is highlighted in the In This Issue feature, p. 211
Data from Clinical Portrait of the SARS-CoV-2 Epidemic in European Patients with Cancer
Authors: Pinato David J. , Zambelli Alberto , Aguilar-Company Juan , Bower Mark , Sng Christopher C.T. , Salazar Ramon , Bertuzzi Alexia , Brunet Joan , Mesia Ricard , Seguí Elia , Biello Federica , Generali Daniele , Grisanti Salvatore , Rizzo Gianpiero , Libertini Michela , Maconi Antonio , Harbeck Nadia , Vincenzi Bruno , Bertulli Rossella , Ottaviani Diego , Carbó Anna , Bruna Riccardo , Benafif Sarah , Marrari Andrea , Wuerstlein Rachel , Carmona-Garcia M. Carmen , Chopra Neha , Tondini Carlo , Mirallas Oriol , Tovazzi Valeria , Betti Marta , Provenzano Salvatore , Fotia Vittoria , Cruz Claudia Andrea , Dalla Pria Alessia , D'Avanzo Francesca , Evans Joanne S. , Saoudi-Gonzalez Nadia , Felip Eudald , Galazi Myria , Garcia-Fructuoso Isabel , Lee Alvin J.X. , Newsom-Davis Thomas , Patriarca Andrea , García-Illescas David , Reyes Roxana , Dileo Palma , Sharkey Rachel , Wong Yien Ning Sophia , Ferrante Daniela , Marco-Hernández Javier , Sureda Anna , Maluquer Clara , Ruiz-Camps Isabel , Gaidano Gianluca , Rimassa Lorenza , Chiudinelli Lorenzo , Izuzquiza Macarena , Cabirta Alba , Franchi Michela , Santoro Armando , Prat Aleix , Tabernero Josep , Gennari Alessandra , Avanzi Gian Carlo , Bellan Mattia , Castello Luigi Mario , Martinez Maria , Mollà Meritxell , Pirisi Mario , Scotti Lorenza , Swallow Judith
Published: April 2023

Abstract
The SARS-CoV-2 pandemic significantly affected oncology practice across the globe. There is uncertainty as to the contribution of patients' demographics and oncologic features to severity and mortality from COVID-19 and little guidance as to the role of anticancer and anti–COVID-19 therapy in this population. In a multicenter study of 890 patients with cancer with confirmed COVID-19, we demonstrated a worsening gradient of mortality from breast cancer to hematologic malignancies and showed that male gender, older age, and number of comorbidities identify a subset of patients with significantly worse mortality rates from COVID-19. Provision of chemotherapy, targeted therapy, or immunotherapy did not worsen mortality. Exposure to antimalarials was associated with improved mortality rates independent of baseline prognostic factors. This study highlights the clinical utility of demographic factors for individualized risk stratification of patients and supports further research into emerging anti–COVID-19 therapeutics in SARS-CoV-2–infected patients with cancer.
Significance:
In this observational study of 890 patients with cancer diagnosed with SARS-CoV-2, mortality was 33.6% and predicted by male gender, age ≥65, and comorbidity burden. Delivery of cancer therapy was not detrimental to severity or mortality from COVID-19. These patients should be the focus of shielding efforts during the SARS-CoV-2 pandemic.

This article is highlighted in the In This Issue feature, p. 1426
Data from Machine-Learning and Chemicogenomics Approach Defines and Predicts Cross-Talk of Hippo and MAPK Pathways
Authors: Pham Trang H. , Hagenbeek Thijs J. , Lee Ho-June , Li Jason , Rose Christopher M. , Lin Eva , Yu Mamie , Martin Scott E. , Piskol Robert , Lacap Jennifer A. , Sampath Deepak , Pham Victoria C. , Modrusan Zora , Lill Jennie R. , Klijn Christiaan , Malek Shiva , Chang Matthew T. , Dey Anwesha
Published: April 2023

Abstract
Hippo pathway dysregulation occurs in multiple cancers through genetic and nongenetic alterations, resulting in translocation of YAP to the nucleus and activation of the TEAD family of transcription factors. Unlike other oncogenic pathways such as RAS, defining tumors that are Hippo pathway–dependent is far more complex due to the lack of hotspot genetic alterations. Here, we developed a machine-learning framework to identify a robust, cancer type–agnostic gene expression signature to quantitate Hippo pathway activity and cross-talk as well as predict YAP/TEAD dependency across cancers. Further, through chemical genetic interaction screens and multiomics analyses, we discover a direct interaction between MAPK signaling and TEAD stability such that knockdown of YAP combined with MEK inhibition results in robust inhibition of tumor cell growth in Hippo dysregulated tumors. This multifaceted approach underscores how computational models combined with experimental studies can inform precision medicine approaches including predictive diagnostics and combination strategies.
Significance:
An integrated chemicogenomics strategy was developed to identify a lineage-independent signature for the Hippo pathway in cancers. Evaluating transcriptional profiles using a machine-learning method led to identification of a relationship between YAP/TAZ dependency and MAPK pathway activity. The results help to nominate potential combination therapies with Hippo pathway inhibition.

This article is highlighted in the In This Issue feature, p. 521
Data from Timed Ang2-Targeted Therapy Identifies the Angiopoietin–Tie Pathway as Key Regulator of Fatal Lymphogenous Metastasis
Authors: Gengenbacher Nicolas , Singhal Mahak , Mogler Carolin , Hai Ling , Milde Laura , Pari Ashik Ahmed Abdul , Besemfelder Eva , Fricke Claudine , Baumann Daniel , Gehrs Stephanie , Utikal Jochen , Felcht Moritz , Hu Junhao , Schlesner Matthias , Offringa Rienk , Chintharlapalli Sudhakar R. , Augustin Hellmut G.
Published: April 2023

Abstract
Recent clinical and preclinical advances have highlighted the existence of a previously hypothesized lymphogenous route of metastasis. However, due to a lack of suitable preclinical modeling tools, its contribution to long-term disease outcome and relevance for therapy remain controversial. Here, we established a genetically engineered mouse model (GEMM) fragment–based tumor model uniquely sustaining a functional network of intratumoral lymphatics that facilitates seeding of fatal peripheral metastases. Multiregimen survival studies and correlative patient data identified primary tumor–derived Angiopoietin-2 (Ang2) as a potent therapeutic target to restrict lymphogenous tumor cell dissemination. Mechanistically, tumor-associated lymphatic endothelial cells (EC), in contrast to blood vascular EC, were found to be critically addicted to the Angiopoietin–Tie pathway. Genetic manipulation experiments in combination with single-cell mapping revealed agonistically acting Ang2–Tie2 signaling as key regulator of lymphatic maintenance. Correspondingly, acute presurgical Ang2 neutralization was sufficient to prolong survival by regressing established intratumoral lymphatics, hence identifying a therapeutic regimen that warrants further clinical evaluation.
Significance:
Exploiting multiple mouse tumor models including a unique GEMM-derived allograft system in combination with preclinical therapy designs closely matching the human situation, this study provides fundamental insight into the biology of tumor-associated lymphatic EC and defines an innovative presurgical therapeutic window of migrastatic Ang2 neutralization to restrict lymphogenous metastasis.

This article is highlighted in the In This Issue feature, p. 211
Data from A Critical Role for Fas-Mediated Off-Target Tumor Killing in T-cell Immunotherapy
Authors: Upadhyay Ranjan , Boiarsky Jonathan A. , Pantsulaia Gvantsa , Svensson-Arvelund Judit , Lin Matthew J. , Wroblewska Aleksandra , Bhalla Sherry , Scholler Nathalie , Bot Adrian , Rossi John M. , Sadek Norah , Parekh Samir , Lagana Alessandro , Baccarini Alessia , Merad Miriam , Brown Brian D. , Brody Joshua D.
Published: April 2023

Abstract
T cell–based therapies have induced cancer remissions, though most tumors ultimately progress, reflecting inherent or acquired resistance including antigen escape. Better understanding of how T cells eliminate tumors will help decipher resistance mechanisms. We used a CRISPR/Cas9 screen and identified a necessary role for Fas–FasL in antigen-specific T-cell killing. We also found that Fas–FasL mediated off-target “bystander” killing of antigen-negative tumor cells. This localized bystander cytotoxicity enhanced clearance of antigen-heterogeneous tumors in vivo, a finding that has not been shown previously. Fas-mediated on-target and bystander killing was reproduced in chimeric antigen receptor (CAR-T) and bispecific antibody T-cell models and was augmented by inhibiting regulators of Fas signaling. Tumoral FAS expression alone predicted survival of CAR-T–treated patients in a large clinical trial (NCT02348216). These data suggest strategies to prevent immune escape by targeting both the antigen expression of most tumor cells and the geography of antigen-loss variants.
Significance:
This study demonstrates the first report of in vivo Fas-dependent bystander killing of antigen-negative tumors by T cells, a phenomenon that may be contributing to the high response rates of antigen-directed immunotherapies despite tumoral heterogeneity. Small molecules that target the Fas pathway may potentiate this mechanism to prevent cancer relapse.

This article is highlighted in the In This Issue feature, p. 521
Data from TRK xDFG Mutations Trigger a Sensitivity Switch from Type I to II Kinase Inhibitors
Authors: Cocco Emiliano , Lee Ji Eun , Kannan Srinivasaraghavan , Schram Alison M. , Won Helen H. , Shifman Sophie , Kulick Amanda , Baldino Laura , Toska Eneda , Arruabarrena-Aristorena Amaia , Kittane Srushti , Wu Fan , Cai Yanyan , Arena Sabrina , Mussolin Benedetta , Kannan Ram , Vasan Neil , Gorelick Alexander N. , Berger Michael F. , Novoplansky Ofra , Jagadeeshan Sankar , Liao Yi , Rix Uwe , Misale Sandra , Taylor Barry S. , Bardelli Alberto , Hechtman Jaclyn F. , Hyman David M. , Elkabets Moshe , de Stanchina Elisa , Verma Chandra S. , Ventura Andrea , Drilon Alexander , Scaltriti Maurizio
Published: April 2023

Abstract
On-target resistance to next-generation TRK inhibitors in TRK fusion–positive cancers is largely uncharacterized. In patients with these tumors, we found that TRK xDFG mutations confer resistance to type I next-generation TRK inhibitors designed to maintain potency against several kinase domain mutations. Computational modeling and biochemical assays showed that TRKAG667 and TRKCG696 xDFG substitutions reduce drug binding by generating steric hindrance. Concurrently, these mutations stabilize the inactive (DFG-out) conformations of the kinases, thus sensitizing these kinases to type II TRK inhibitors. Consistently, type II inhibitors impede the growth and TRK-mediated signaling of xDFG-mutant isogenic and patient-derived models. Collectively, these data demonstrate that adaptive conformational resistance can be abrogated by shifting kinase engagement modes. Given the prior identification of paralogous xDFG resistance mutations in other oncogene-addicted cancers, these findings provide insights into rational type II drug design by leveraging inhibitor class affinity switching to address recalcitrant resistant alterations.
Significance:
In TRK fusion–positive cancers, TRK xDFG substitutions represent a shared liability for type I TRK inhibitors. In contrast, they represent a potential biomarker of type II TRK inhibitor activity. As all currently available type II agents are multikinase inhibitors, rational drug design should focus on selective type II inhibitor creation.

This article is highlighted in the In This Issue feature, p. 1
Data from Clinicogenomic Analysis of FGFR2-Rearranged Cholangiocarcinoma Identifies Correlates of Response and Mechanisms of Resistance to Pemigatinib
Authors: Silverman Ian M. , Hollebecque Antoine , Friboulet Luc , Owens Sherry , Newton Robert C. , Zhen Huiling , Féliz Luis , Zecchetto Camilla , Melisi Davide , Burn Timothy C.
Published: April 2023

Abstract
Pemigatinib, a selective FGFR1–3 inhibitor, has demonstrated antitumor activity in FIGHT-202, a phase II study in patients with cholangiocarcinoma harboring FGFR2 fusions/rearrangements, and has gained regulatory approval in the United States. Eligibility for FIGHT-202 was assessed using genomic profiling; here, these data were utilized to characterize the genomic landscape of cholangiocarcinoma and to uncover unique molecular features of patients harboring FGFR2 rearrangements. The results highlight the high percentage of patients with cholangiocarcinoma harboring potentially actionable genomic alterations and the diversity in gene partners that rearrange with FGFR2. Clinicogenomic analysis of pemigatinib-treated patients identified mechanisms of primary and acquired resistance. Genomic subsets of patients with other potentially actionable FGF/FGFR alterations were also identified. Our study provides a framework for molecularly guided clinical trials and underscores the importance of genomic profiling to enable a deeper understanding of the molecular basis for response and nonresponse to targeted therapy.
Significance:
We utilized genomic profiling data from FIGHT-202 to gain insights into the genomic landscape of cholangiocarcinoma, to understand the molecular diversity of patients with FGFR2 fusions or rearrangements, and to interrogate the clinicogenomics of patients treated with pemigatinib. Our study highlights the utility of genomic profiling in clinical trials.

This article is highlighted in the In This Issue feature, p. 211
Data from Combination Olaparib and Temozolomide in Relapsed Small-Cell Lung Cancer
Authors: Farago Anna F. , Yeap Beow Y. , Stanzione Marcello , Hung Yin P. , Heist Rebecca S. , Marcoux J. Paul , Zhong Jun , Rangachari Deepa , Barbie David A. , Phat Sarah , Myers David T. , Morris Robert , Kem Marina , Dubash Taronish D. , Kennedy Elizabeth A. , Digumarthy Subba R. , Sequist Lecia V. , Hata Aaron N. , Maheswaran Shyamala , Haber Daniel A. , Lawrence Michael S. , Shaw Alice T. , Mino-Kenudson Mari , Dyson Nicholas J. , Drapkin Benjamin J.
Published: April 2023

Abstract
Small-cell lung cancer (SCLC) is an aggressive malignancy in which inhibitors of PARP have modest single-agent activity. We performed a phase I/II trial of combination olaparib tablets and temozolomide (OT) in patients with previously treated SCLC. We established a recommended phase II dose of olaparib 200 mg orally twice daily with temozolomide 75 mg/m2 daily, both on days 1 to 7 of a 21-day cycle, and expanded to a total of 50 patients. The confirmed overall response rate was 41.7% (20/48 evaluable); median progression-free survival was 4.2 months [95% confidence interval (CI), 2.8–5.7]; and median overall survival was 8.5 months (95% CI, 5.1–11.3). Patient-derived xenografts (PDX) from trial patients recapitulated clinical OT responses, enabling a 32-PDX coclinical trial. This revealed a correlation between low basal expression of inflammatory-response genes and cross-resistance to both OT and standard first-line chemotherapy (etoposide/platinum). These results demonstrate a promising new therapeutic strategy in SCLC and uncover a molecular signature of those tumors most likely to respond.
Significance:
We demonstrate substantial clinical activity of combination olaparib/temozolomide in relapsed SCLC, revealing a promising new therapeutic strategy for this highly recalcitrant malignancy. Through an integrated coclinical trial in PDXs, we then identify a molecular signature predictive of response to OT, and describe the common molecular features of cross-resistant SCLC.

See related commentary by Pacheco and Byers, p. 1340.

This article is highlighted in the In This Issue feature, p. 1325
Data from Resistance to Avapritinib in PDGFRA-Driven GIST Is Caused by Secondary Mutations in the PDGFRA Kinase Domain
Authors: Grunewald Susanne , Klug Lillian R. , Mühlenberg Thomas , Lategahn Jonas , Falkenhorst Johanna , Town Ajia , Ehrt Christiane , Wardelmann Eva , Hartmann Wolfgang , Schildhaus Hans-Ulrich , Treckmann Juergen , Fletcher Jonathan A. , Jung Sascha , Czodrowski Paul , Miller Stephen , Schmidt-Kittler Oleg , Rauh Daniel , Heinrich Michael C. , Bauer Sebastian
Published: April 2023

Abstract
Gastrointestinal stromal tumors (GIST) harboring activating mutations of PDGFRA respond to imatinib, with the notable exception of the most common mutation, D842V. Avapritinib is a novel, potent KIT/PDGFRA inhibitor with substantial clinical activity in patients with the D842V genotype. To date, only a minority of PDGFRA-mutant patients treated with avapritinib have developed secondary resistance. Tumor and plasma biopsies in 6 of 7 patients with PDGFRA primary mutations who progressed on avapritinib or imatinib had secondary resistance mutations within PDGFRA exons 13, 14, and 15 that interfere with avapritinib binding. Secondary PDGFRA mutations causing V658A, N659K, Y676C, and G680R substitutions were found in 2 or more patients each, representing recurrent mechanisms of PDGFRA GIST drug resistance. Notably, most PDGFRA-mutant GISTs refractory to avapritinib remain dependent on the PDGFRA oncogenic signal. Inhibitors that target PDGFRA protein stability or inhibition of PDGFRA-dependent signaling pathways may overcome avapritinib resistance.
Significance:
Here, we provide the first description of avapritinib resistance mechanisms in PDGFRA-mutant GIST.

This article is highlighted in the In This Issue feature, p. 1
Data from Phenotypic Mapping of Pathologic Cross-Talk between Glioblastoma and Innate Immune Cells by Synthetic Genetic Tracing
Authors: Schmitt Matthias Jürgen , Company Carlos , Dramaretska Yuliia , Barozzi Iros , Göhrig Andreas , Kertalli Sonia , Großmann Melanie , Naumann Heike , Sanchez-Bailon Maria Pilar , Hulsman Danielle , Glass Rainer , Squatrito Massimo , Serresi Michela , Gargiulo Gaetano
Published: April 2023

Abstract
Glioblastoma is a lethal brain tumor that exhibits heterogeneity and resistance to therapy. Our understanding of tumor homeostasis is limited by a lack of genetic tools to selectively identify tumor states and fate transitions. Here, we use glioblastoma subtype signatures to construct synthetic genetic tracing cassettes and investigate tumor heterogeneity at cellular and molecular levels, in vitro and in vivo. Through synthetic locus control regions, we demonstrate that proneural glioblastoma is a hardwired identity, whereas mesenchymal glioblastoma is an adaptive and metastable cell state driven by proinflammatory and differentiation cues and DNA damage, but not hypoxia. Importantly, we discovered that innate immune cells divert glioblastoma cells to a proneural-to-mesenchymal transition that confers therapeutic resistance. Our synthetic genetic tracing methodology is simple, scalable, and widely applicable to study homeostasis in development and diseases. In glioblastoma, the method causally links distinct (micro)environmental, genetic, and pharmacologic perturbations and mesenchymal commitment.
Significance:
Glioblastoma is heterogeneous and incurable. Here, we designed synthetic reporters to reflect the transcriptional output of tumor cell states and signaling pathways' activity. This method is generally applicable to study homeostasis in normal tissues and diseases. In glioblastoma, synthetic genetic tracing causally connects cellular and molecular heterogeneity to therapeutic responses.

This article is highlighted in the In This Issue feature, p. 521
Data from A Procarcinogenic Colon Microbe Promotes Breast Tumorigenesis and Metastatic Progression and Concomitantly Activates Notch and β-Catenin Axes
Authors: Parida Sheetal , Wu Shaoguang , Siddharth Sumit , Wang Guannan , Muniraj Nethaji , Nagalingam Arumugam , Hum Christina , Mistriotis Panagiotis , Hao Haiping , Talbot C. Conover , Konstantopoulos Konstantinos , Gabrielson Kathleen L. , Sears Cynthia L. , Sharma Dipali
Published: April 2023

Abstract
The existence of distinct breast microbiota has been recently established, but their biological impact in breast cancer remains elusive. Focusing on the shift in microbial community composition in diseased breast compared with normal breast, we identified the presence of Bacteroides fragilis in cancerous breast. Mammary gland as well as gut colonization with enterotoxigenic Bacteroides fragilis (ETBF), which secretes B. fragilis toxin (BFT), rapidly induces epithelial hyperplasia in the mammary gland. Breast cancer cells exposed to BFT exhibit “BFT memory” from the initial exposure. Intriguingly, gut or breast duct colonization with ETBF strongly induces growth and metastatic progression of tumor cells implanted in mammary ducts, in contrast to nontoxigenic Bacteroides fragilis. This work sheds light on the oncogenic impact of a procarcinogenic colon bacterium ETBF on breast cancer progression, implicates the β-catenin and Notch1 axis as its functional mediators, and proposes the concept of “BFT memory” that can have far-reaching biological implications after initial exposure to ETBF.
Significance:
B. fragilis is an inhabitant of breast tissue, and gut or mammary duct colonization with ETBF triggers epithelial hyperplasia and augments breast cancer growth and metastasis. Short-term exposure to BFT elicits a “BFT memory” with long-term implications, functionally mediated by the β-catenin and Notch1 pathways.

This article is highlighted in the In This Issue feature, p. 995
Data from Preexisting and Post–COVID-19 Immune Responses to SARS-CoV-2 in Patients with Cancer
Authors: Bilich Tatjana , Roerden Malte , Maringer Yacine , Nelde Annika , Heitmann Jonas S. , Dubbelaar Marissa L. , Peter Andreas , Hörber Sebastian , Bauer Jens , Rieth Jonas , Wacker Marcel , Berner Fiamma , Flatz Lukas , Held Stefanie , Brossart Peter , Märklin Melanie , Wagner Philipp , Erne Eva , Klein Reinhild , Rammensee Hans-Georg , Salih Helmut R. , Walz Juliane S.
Published: April 2023

Abstract
Patients with cancer, in particular patients with hematologic malignancies, are at increased risk for critical illness upon COVID-19. We here assessed antibody as well as CD4+ and CD8+ T-cell responses in unexposed and SARS-CoV-2–infected patients with cancer to characterize SARS-CoV-2 immunity and to identify immunologic parameters contributing to COVID-19 outcome. Unexposed patients with hematologic malignancies presented with reduced prevalence of preexisting SARS-CoV-2 cross-reactive CD4+ T-cell responses and signs of T-cell exhaustion compared with patients with solid tumors and healthy volunteers. Whereas SARS-CoV-2 antibody responses did not differ between patients with COVID-19 and cancer and healthy volunteers, intensity, expandability, and diversity of SARS-CoV-2 T-cell responses were profoundly reduced in patients with cancer, and the latter associated with a severe course of COVID-19. This identifies impaired SARS-CoV-2 T-cell immunity as a potential determinant for dismal outcome of COVID-19 in patients with cancer.
Significance:
This first comprehensive analysis of SARS-CoV-2 immune responses in patients with cancer reports on the potential implications of impaired SARS-CoV-2 T-cell responses for understanding pathophysiology and predicting severity of COVID-19, which in turn might allow for the development of therapeutic measures and vaccines for this vulnerable patient population.

See related commentary by Salomé and Horowitz, p. 1877.

This article is highlighted in the In This Issue feature, p. 1861
Data from Splicing Patterns in SF3B1-Mutated Uveal Melanoma Generate Shared Immunogenic Tumor-Specific Neoepitopes
Authors: Bigot Jeremy , Lalanne Ana I. , Lucibello Francesca , Gueguen Paul , Houy Alexandre , Dayot Stephane , Ganier Olivier , Gilet Jules , Tosello Jimena , Nemati Fariba , Pierron Gaelle , Waterfall Joshua J. , Barnhill Raymond , Gardrat Sophie , Piperno-Neumann Sophie , Popova Tatiana , Masson Vanessa , Loew Damarys , Mariani Pascale , Cassoux Nathalie , Amigorena Sebastian , Rodrigues Manuel , Alsafadi Samar , Stern Marc-Henri , Lantz Olivier
Published: April 2023

Abstract
Disruption of splicing patterns due to mutations of genes coding splicing factors in tumors represents a potential source of tumor neoantigens, which would be both public (shared between patients) and tumor-specific (not expressed in normal tissues). In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma generate such immunogenic neoantigens. Memory CD8+ T cells specific for these neoantigens are preferentially found in 20% of patients with uveal melanoma bearing SF3B1-mutated tumors. Single-cell analyses of neoepitope-specific T cells from the blood identified large clonal T-cell expansions, with distinct effector transcription patterns. Some of these expanded T-cell receptors are also present in the corresponding tumors. CD8+ T-cell clones specific for the neoepitopes specifically recognize and kill SF3B1-mutated tumor cells, supporting the use of this new family of neoantigens as therapeutic targets.
Significance:
Mutations of the splicing factor SF3B1 in uveal melanoma generate shared neoantigens that are uniquely expressed by tumor cells, leading to recognition and killing by specific CD8 T cells. Mutations in splicing factors can be sources of new therapeutic strategies applicable to diverse tumors.

This article is highlighted in the In This Issue feature, p. 1861
Data from Identification of Novel Therapeutic Targets for Fibrolamellar Carcinoma Using Patient-Derived Xenografts and Direct-from-Patient Screening
Authors: Lalazar Gadi , Requena David , Ramos-Espiritu Lavoisier , Ng Denise , Bhola Patrick D. , de Jong Ype P. , Wang Ruisi , Narayan Nicole J.C. , Shebl Bassem , Levin Solomon , Michailidis Eleftherios , Kabbani Mohammad , Vercauteren Koen O.A. , Hurley Arlene M. , Farber Benjamin A. , Hammond William J. , Saltsman James A. , Weinberg Ethan M. , Glickman J. Fraser , Lyons Barbara A. , Ellison Jessica , Schadde Erik , Hertl Martin , Leiting Jennifer L. , Truty Mark J. , Smoot Rory L. , Tierney Faith , Kato Tomoaki , Wendel Hans-Guido , LaQuaglia Michael P. , Rice Charles M. , Letai Anthony , Coffino Philip , Torbenson Michael S. , Ortiz Michael V. , Simon Sanford M.
Published: April 2023

Abstract
To repurpose therapeutics for fibrolamellar carcinoma (FLC), we developed and validated patient-derived xenografts (PDX) from surgical resections. Most agents used clinically and inhibitors of oncogenes overexpressed in FLC showed little efficacy on PDX. A high-throughput functional drug screen found primary and metastatic FLC were vulnerable to clinically available inhibitors of TOPO1 and HDAC and to napabucasin. Napabucasin's efficacy was mediated through reactive oxygen species and inhibition of translation initiation, and specific inhibition of eIF4A was effective. The sensitivity of each PDX line inversely correlated with expression of the antiapoptotic protein Bcl-xL, and inhibition of Bcl-xL synergized with other drugs. Screening directly on cells dissociated from patient resections validated these results. This demonstrates that a direct functional screen on patient tumors provides therapeutically informative data within a clinically useful time frame. Identifying these novel therapeutic targets and combination therapies is an urgent need, as effective therapeutics for FLC are currently unavailable.
Significance:
Therapeutics informed by genomics have not yielded effective therapies for FLC. A functional screen identified TOPO1, HDAC inhibitors, and napabucasin as efficacious and synergistic with inhibition of Bcl-xL. Validation on cells dissociated directly from patient tumors demonstrates the ability for functional precision medicine in a solid tumor.

This article is highlighted in the In This Issue feature, p. 2355
Data from Selective Modulation of a Pan-Essential Protein as a Therapeutic Strategy in Cancer
Authors: Malone Clare F. , Dharia Neekesh V. , Kugener Guillaume , Forman Alexandra B. , Rothberg Michael V. , Abdusamad Mai , Gonzalez Alfredo , Kuljanin Miljan , Robichaud Amanda L. , Conway Amy Saur , Dempster Joshua M. , Paolella Brenton R. , Dumont Nancy , Hovestadt Volker , Mancias Joseph D. , Younger Scott T. , Root David E. , Golub Todd R. , Vazquez Francisca , Stegmaier Kimberly
Published: April 2023

Abstract
Cancer dependency maps, which use CRISPR/Cas9 depletion screens to profile the landscape of genetic dependencies in hundreds of cancer cell lines, have identified context-specific dependencies that could be therapeutically exploited. An ideal therapy is both lethal and precise, but these depletion screens cannot readily distinguish between gene effects that are cytostatic or cytotoxic. Here, we use a diverse panel of functional genomic screening assays to identify NXT1 as a selective and rapidly lethal in vivo relevant genetic dependency in MYCN-amplified neuroblastoma. NXT1 heterodimerizes with NXF1, and together they form the principal mRNA nuclear export machinery. We describe a previously unrecognized mechanism of synthetic lethality between NXT1 and its paralog NXT2: their common essential binding partner NXF1 is lost only in the absence of both. We propose a potential therapeutic strategy for tumor-selective elimination of a protein that, if targeted directly, is expected to cause widespread toxicity.
Significance:
We provide a framework for identifying new therapeutic targets from functional genomic screens. We nominate NXT1 as a selective lethal target in neuroblastoma and propose a therapeutic approach where the essential protein NXF1 can be selectively eliminated in tumor cells by exploiting the NXT1–NXT2 paralog relationship.

See related commentary by Wang and Abdel-Wahab, p. 2129.

This article is highlighted in the In This Issue feature, p. 2113
Data from Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia
Authors: Yang Zhaolin , Wu Xiaoli S. , Wei Yiliang , Polyanskaya Sofya A. , Iyer Shruti V. , Jung Moonjung , Lach Francis P. , Adelman Emmalee R. , Klingbeil Olaf , Milazzo Joseph P. , Kramer Melissa , Demerdash Osama E. , Chang Kenneth , Goodwin Sara , Hodges Emily , McCombie W. Richard , Figueroa Maria E. , Smogorzewska Agata , Vakoc Christopher R.
Published: April 2023

Abstract
Hundreds of genes become aberrantly silenced in acute myeloid leukemia (AML), with most of these epigenetic changes being of unknown functional consequence. Here, we demonstrate how gene silencing can lead to an acquired dependency on the DNA repair machinery in AML. We make this observation by profiling the essentiality of the ubiquitination machinery in cancer cell lines using domain-focused CRISPR screening, which revealed Fanconi anemia (FA) proteins UBE2T and FANCL as unique dependencies in AML. We demonstrate that these dependencies are due to a synthetic lethal interaction between FA proteins and aldehyde dehydrogenase 2 (ALDH2), which function in parallel pathways to counteract the genotoxicity of endogenous aldehydes. We show DNA hypermethylation and silencing of ALDH2 occur in a recurrent manner in human AML, which is sufficient to confer FA pathway dependency. Our study suggests that targeting of the ubiquitination reaction catalyzed by FA proteins can eliminate ALDH2-deficient AML.
Significance:
Aberrant gene silencing is an epigenetic hallmark of human cancer, but the functional consequences of this process are largely unknown. In this study, we show how an epigenetic alteration leads to an actionable dependency on a DNA repair pathway through the disabling of genetic redundancy.

This article is highlighted in the In This Issue feature, p. 2113
Data from Pharmacologic Activation of p53 Triggers Viral Mimicry Response Thereby Abolishing Tumor Immune Evasion and Promoting Antitumor Immunity
Authors: Zhou Xiaolei , Singh Madhurendra , Sanz Santos Gema , Guerlavais Vincent , Carvajal Luis A. , Aivado Manuel , Zhan Yue , Oliveira Mariana M.S. , Westerberg Lisa S. , Annis D. Allen , Johnsen John Inge , Selivanova Galina
Published: April 2023

Abstract
The repression of repetitive elements is an important facet of p53's function as a guardian of the genome. Paradoxically, we found that p53 activated by MDM2 inhibitors induced the expression of endogenous retroviruses (ERV) via increased occupancy on ERV promoters and inhibition of two major ERV repressors, histone demethylase LSD1 and DNA methyltransferase DNMT1. Double-stranded RNA stress caused by ERVs triggered type I/III interferon expression and antigen processing and presentation. Pharmacologic activation of p53 in vivo unleashed the IFN program, promoted T-cell infiltration, and significantly enhanced the efficacy of checkpoint therapy in an allograft tumor model. Furthermore, the MDM2 inhibitor ALRN-6924 induced a viral mimicry pathway and tumor inflammation signature genes in patients with melanoma. Our results identify ERV expression as the central mechanism whereby p53 induction overcomes tumor immune evasion and transforms tumor microenvironment to a favorable phenotype, providing a rationale for the synergy of MDM2 inhibitors and immunotherapy.
Significance:
We found that p53 activated by MDM2 inhibitors induced the expression of ERVs, in part via epigenetic factors LSD1 and DNMT1. Induction of IFN response caused by ERV derepression upon p53-targeting therapies provides a possibility to overcome resistance to immune checkpoint blockade and potentially transform “cold” tumors into “hot.”

This article is highlighted in the In This Issue feature, p. 2945
Data from A Humanized Animal Model Predicts Clonal Evolution and Therapeutic Vulnerabilities in Myeloproliferative Neoplasms
Authors: Celik Hamza , Krug Ethan , Zhang Christine R. , Han Wentao , Issa Nancy , Koh Won Kyun , Bjeije Hassan , Kukhar Ostap , Allen Maggie , Li Tiandao , Fisher Daniel A.C. , Fowles Jared S. , Wong Terrence N. , Stubbs Matthew C. , Koblish Holly K. , Oh Stephen T. , Challen Grant A.
Published: April 2023

Abstract
Myeloproliferative neoplasms (MPN) are chronic blood diseases with significant morbidity and mortality. Although sequencing studies have elucidated the genetic mutations that drive these diseases, MPNs remain largely incurable with a significant proportion of patients progressing to rapidly fatal secondary acute myeloid leukemia (sAML). Therapeutic discovery has been hampered by the inability of genetically engineered mouse models to generate key human pathologies such as bone marrow fibrosis. To circumvent these limitations, here we present a humanized animal model of myelofibrosis (MF) patient-derived xenografts (PDX). These PDXs robustly engrafted patient cells that recapitulated the patient's genetic hierarchy and pathologies such as reticulin fibrosis and propagation of MPN-initiating stem cells. The model can select for engraftment of rare leukemic subclones to identify patients with MF at risk for sAML transformation and can be used as a platform for genetic target validation and therapeutic discovery. We present a novel but generalizable model to study human MPN biology.
Significance:
Although the genetic events driving MPNs are well defined, therapeutic discovery has been hampered by the inability of murine models to replicate key patient pathologies. Here, we present a PDX system to model human myelofibrosis that reproduces human pathologies and is amenable to genetic and pharmacologic manipulation.

This article is highlighted in the In This Issue feature, p. 2945
Data from Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History
Authors: Penter Livius , Gohil Satyen H. , Lareau Caleb , Ludwig Leif S. , Parry Erin M. , Huang Teddy , Li Shuqiang , Zhang Wandi , Livitz Dimitri , Leshchiner Ignaty , Parida Laxmi , Getz Gad , Rassenti Laura Z. , Kipps Thomas J. , Brown Jennifer R. , Davids Matthew S. , Neuberg Donna S. , Livak Kenneth J. , Sankaran Vijay G. , Wu Catherine J.
Published: April 2023

Abstract
While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones in vivo. We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure, indicating clonal persistence, but dramatic changes following tight bottlenecks, including disease transformation and relapse posttherapy, paralleled by acquisition of copy-number variants and changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into nongenetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics.
Significance:
Single-cell multi-omic profiling of CLL reveals the utility of somatic mtDNA mutations as in vivo barcodes, which mark subclones that can evolve over time along with changes in accessible chromatin and gene expression profiles to capture dynamics of disease evolution.

See related commentary by Hilton and Scott, p. 2965.

This article is highlighted in the In This Issue feature, p. 2945