bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Mesenchymal-Type Neuroblastoma Cells Escape ALK Inhibitors
Authors: Westerhout Ellen M. , Hamdi Mohamed , Stroeken Peter , Nowakowska Natalia E. , Lakeman Arjan , van Arkel Jennemiek , Hasselt Nancy E. , Bleijlevens Boris , Akogul Nurdan , Haneveld Franciska , Chan Alvin , van Sluis Peter , Zwijnenburg Danny , Volckmann Richard , van Noesel Carel J.M. , Adameyko Igor , van Groningen Tim , Koster Jan , Valentijn Linda J. , van Nes Johan , Versteeg Rogier
Published: March 2023

Abstract
Cancer therapy frequently fails due to the emergence of resistance. Many tumors include phenotypically immature tumor cells, which have been implicated in therapy resistance. Neuroblastoma cells can adopt a lineage-committed adrenergic (ADRN) or an immature mesenchymal (MES) state. They differ in epigenetic landscape and transcription factors, and MES cells are more resistant to chemotherapy. Here we analyzed the response of MES cells to targeted drugs. Activating anaplastic lymphoma kinase (ALK) mutations are frequently found in neuroblastoma and ALK inhibitors (ALKi) are in clinical trials. ALKi treatment of ADRN neuroblastoma cells with a tumor-driving ALK mutation induced cell death. Conversely, MES cells did not express either mutant or wild-type ALK and were resistant to ALKi, and MES cells formed tumors that progressed under ALKi therapy. In assessing the role of MES cells in relapse development, TRAIL was identified to specifically induce apoptosis in MES cells and to suppress MES tumor growth. Addition of TRAIL to ALKi treatment of neuroblastoma xenografts delayed relapses in a subset of the animals, suggesting a role for MES cells in relapse formation. While ADRN cells resembled normal embryonal neuroblasts, MES cells resembled immature precursor cells, which also lacked ALK expression. Resistance to targeted drugs can therefore be an intrinsic property of immature cancer cells based on their resemblance to developmental precursors.
Significance:
In neuroblastoma, mesenchymal tumor cells lack expression of the tumor-driving ALK oncogene and are resistant to ALKi, but dual treatment with ALKi and mesenchymal cell–targeting TRAIL delays tumor relapse.
Data from Concurrent Activation of Kras and Canonical Wnt Signaling Induces Premalignant Lesions That Progress to Extrahepatic Biliary Cancer in Mice
Authors: Nagao Munemasa , Fukuda Akihisa , Omatsu Mayuki , Namikawa Mio , Sono Makoto , Fukunaga Yuichi , Masuda Tomonori , Araki Osamu , Yoshikawa Takaaki , Ogawa Satoshi , Masuo Kenji , Goto Norihiro , Hiramatsu Yukiko , Muta Yu , Tsuda Motoyuki , Maruno Takahisa , Nakanishi Yuki , Taketo Makoto Mark , Ferrer Jorge , Tsuruyama Tatsuaki , Nakanuma Yasuni , Taura Kojiro , Uemoto Shinji , Seno Hiroshi
Published: March 2023

Abstract
Biliary cancer has long been known to carry a poor prognosis, yet the molecular pathogenesis of carcinoma of the extrahepatic biliary system and its precursor lesions remains elusive. Here we investigated the role of Kras and canonical Wnt pathways in the tumorigenesis of the extrahepatic bile duct (EHBD) and gall bladder (GB). In mice, concurrent activation of Kras and Wnt pathways induced biliary neoplasms that resembled human intracholecystic papillary-tubular neoplasm (ICPN) and biliary intraepithelial neoplasia (BilIN), putative precursors to invasive biliary cancer. At a low frequency, these lesions progressed to adenocarcinoma in a xenograft model, establishing them as precancerous lesions. Global gene expression analysis revealed increased expression of genes associated with c-Myc and TGFβ pathways in mutant biliary spheroids. Silencing or pharmacologic inhibition of c-Myc suppressed proliferation of mutant biliary spheroids, whereas silencing of Smad4/Tgfbr2 or pharmacologic inhibition of TGFβ signaling increased proliferation of mutant biliary spheroids and cancer formation in vivo. Human ICPNs displayed activated Kras and Wnt signals and c-Myc and TGFβ pathways. Thus, these data provide direct evidence that concurrent activation of the Kras and canonical Wnt pathways results in formation of ICPN and BilIN, which could develop into biliary cancer.
Significance:
This work shows how dysregulation of canonical cell growth pathways drives precursors to biliary cancers and identifies several molecular vulnerabilities as potential therapeutic targets in these precursors to prevent oncogenic progression.
Data from M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression
Authors: Yadav Pooja , Subbarayalu Panneerdoss , Medina Daisy , Nirzhor Saif , Timilsina Santosh , Rajamanickam Subapriya , Eedunuri Vijay K. , Gupta Yogesh , Zheng Siyuan , Abdelfattah Nourhan , Huang Yufei , Vadlamudi Ratna , Hromas Robert , Meltzer Paul , Houghton Peter , Chen Yidong , Rao Manjeet K.
Published: March 2023

Abstract
Osteosarcoma is the most common malignancy of the bone, yet the survival for patients with osteosarcoma is virtually unchanged over the past 30 years. This is principally because development of new therapies is hampered by a lack of recurrent mutations that can be targeted in osteosarcoma. Here, we report that epigenetic changes via mRNA methylation holds great promise to better understand the mechanisms of osteosarcoma growth and to develop targeted therapeutics. In patients with osteosarcoma, the RNA demethylase ALKBH5 was amplified and higher expression correlated with copy-number changes. ALKBH5 was critical for promoting osteosarcoma growth and metastasis, yet it was dispensable for normal cell survival. Methyl RNA immunoprecipitation sequencing analysis and functional studies showed that ALKBH5 mediates its protumorigenic function by regulating m6A levels of histone deubiquitinase USP22 and the ubiquitin ligase RNF40. ALKBH5-mediated m6A deficiency in osteosarcoma led to increased expression of USP22 and RNF40 that resulted in inhibition of histone H2A monoubiquitination and induction of key protumorigenic genes, consequently driving unchecked cell-cycle progression, incessant replication, and DNA repair. RNF40, which is historically known to ubiquitinate H2B, inhibited H2A ubiquitination in cancer by interacting with and affecting the stability of DDB1-CUL4–based ubiquitin E3 ligase complex. Taken together, this study directly links increased activity of ALKBH5 with dysregulation of USP22/RNF40 and histone ubiquitination in cancers. More broadly, these results suggest that m6A RNA methylation works in concert with other epigenetic mechanisms to control cancer growth.
Significance:
RNA demethylase ALKBH5 upregulates USP22 and RNF40 to inhibit histone H2A ubiquitination and induces expression of key replication and DNA repair–associated genes, driving osteosarcoma progression.
Data from Disruption of Prostaglandin E2 Signaling in Cancer-Associated Fibroblasts Limits Mammary Carcinoma Growth but Promotes Metastasis
Authors: Elwakeel Eiman , Brüggemann Mirko , Wagih Jessica , Lityagina Olga , Elewa Mohammed A.F. , Han Yingying , Frömel Timo , Popp Rüdiger , Nicolas Adele M. , Schreiber Yannick , Gradhand Elise , Thomas Dominique , Nüsing Rolf , Steinmetz-Späh Julia , Savai Rajkumar , Fokas Emmanouil , Fleming Ingrid , Greten Florian R. , Zarnack Kathi , Brüne Bernhard , Weigert Andreas
Published: March 2023

Abstract
The activation and differentiation of cancer-associated fibroblasts (CAF) are involved in tumor progression. Here, we show that the tumor-promoting lipid mediator prostaglandin E2 (PGE2) plays a paradoxical role in CAF activation and tumor progression. Restricting PGE2 signaling via knockout of microsomal prostaglandin E synthase-1 (mPGES-1) in PyMT mice or of the prostanoid E receptor 3 (EP3) in CAFs stunted mammary carcinoma growth associated with strong CAF proliferation. CAF proliferation upon EP3 inhibition required p38 MAPK signaling. Mechanistically, TGFβ–activated kinase-like protein (TAK1L), which was identified as a negative regulator of p38 MAPK activation, was decreased following ablation of mPGES-1 or EP3. In contrast with its effects on primary tumor growth, disruption of PGE2 signaling in CAFs induced epithelial-to-mesenchymal transition in cancer organoids and promoted metastasis in mice. Moreover, TAK1L expression in CAFs was associated with decreased CAF activation, reduced metastasis, and prolonged survival in human breast cancer. These data characterize a new pathway of regulating inflammatory CAF activation, which affects breast cancer progression.
Significance:
The inflammatory lipid prostaglandin E2 suppresses cancer-associated fibroblast expansion and activation to limit primary mammary tumor growth while promoting metastasis.
Data from Orthovoltage X-Rays Exhibit Increased Efficacy Compared with γ-Rays in Preclinical Irradiation
Authors: Bell Brett I. , Vercellino Justin , Brodin N. Patrik , Velten Christian , Nanduri Lalitha S.Y. , Nagesh Prashanth K.B. , Tanaka Kathryn E. , Fang Yanan , Wang Yanhua , Macedo Rodney , English Jeb , Schumacher Michelle M. , Duddempudi Phaneendra K. , Asp Patrik , Koba Wade , Shajahan Shahin , Liu Laibin , Tomé Wolfgang A. , Yang Weng-Lang , Kolesnick Richard , Guha Chandan
Published: March 2023

Abstract
Radionuclide irradiators (137Cs and 60Co) are commonly used in preclinical studies ranging from cancer therapy to stem cell biology. Amidst concerns of radiological terrorism, there are institutional initiatives to replace radionuclide sources with lower energy X-ray sources. As researchers transition, questions remain regarding whether the biological effects of γ-rays may be recapitulated with orthovoltage X-rays because different energies may induce divergent biological effects. We therefore sought to compare the effects of orthovoltage X-rays with 1-mm Cu or Thoraeus filtration and 137Cs γ-rays using mouse models of acute radiation syndrome. Following whole-body irradiation, 30-day overall survival was assessed, and the lethal dose to provoke 50% mortality within 30-days (LD50) was calculated by logistic regression. LD50 doses were 6.7 Gy, 7.4 Gy, and 8.1 Gy with 1-mm Cu-filtered X-rays, Thoraeus-filtered X-rays, and 137Cs γ-rays, respectively. Comparison of bone marrow, spleen, and intestinal tissue from mice irradiated with equivalent doses indicated that injury was most severe with 1-mm Cu-filtered X-rays, which resulted in the greatest reduction in bone marrow cellularity, hematopoietic stem and progenitor populations, intestinal crypts, and OLFM4+ intestinal stem cells. Thoraeus-filtered X-rays provoked an intermediate phenotype, with 137Cs showing the least damage. This study reveals a dichotomy between physical dose and biological effect as researchers transition to orthovoltage X-rays. With decreasing energy, there is increasing hematopoietic and intestinal injury, necessitating dose reduction to achieve comparable biological effects.
Significance:
Understanding the significance of physical dose delivered using energetically different methods of radiation treatment will aid the transition from radionuclide γ-irradiators to orthovoltage X-irradiators.
Data from Inhibition of Karyopherin β1-Mediated Nuclear Import Disrupts Oncogenic Lineage-Defining Transcription Factor Activity in Small Cell Lung Cancer
Authors: Kelenis Demetra P. , Rodarte Kathia E. , Kollipara Rahul K. , Pozo Karine , Choudhuri Shreoshi Pal , Spainhower Kyle B. , Wait Sarah J. , Stastny Victor , Oliver Trudy G. , Johnson Jane E.
Published: March 2023

Abstract
Genomic studies support the classification of small cell lung cancer (SCLC) into subtypes based on the expression of lineage-defining transcription factors ASCL1 and NEUROD1, which together are expressed in ∼86% of SCLC. ASCL1 and NEUROD1 activate SCLC oncogene expression, drive distinct transcriptional programs, and maintain the in vitro growth and oncogenic properties of ASCL1 or NEUROD1-expressing SCLC. ASCL1 is also required for tumor formation in SCLC mouse models. A strategy to inhibit the activity of these oncogenic drivers may therefore provide both a targeted therapy for the predominant SCLC subtypes and a tool to investigate the underlying lineage plasticity of established SCLC tumors. However, there are no known agents that inhibit ASCL1 or NEUROD1 function. In this study, we identify a novel strategy to pharmacologically target ASCL1 and NEUROD1 activity in SCLC by exploiting the nuclear localization required for the function of these transcription factors. Karyopherin β1 (KPNB1) was identified as a nuclear import receptor for both ASCL1 and NEUROD1 in SCLC, and inhibition of KPNB1 led to impaired ASCL1 and NEUROD1 nuclear accumulation and transcriptional activity. Pharmacologic targeting of KPNB1 preferentially disrupted the growth of ASCL1+ and NEUROD1+ SCLC cells in vitro and suppressed ASCL1+ tumor growth in vivo, an effect mediated by a combination of impaired ASCL1 downstream target expression, cell-cycle activity, and proteostasis. These findings broaden the support for targeting nuclear transport as an anticancer therapeutic strategy and have implications for targeting lineage-transcription factors in tumors beyond SCLC.
Significance:
The identification of KPNB1 as a nuclear import receptor for lineage-defining transcription factors in SCLC reveals a viable therapeutic strategy for cancer treatment.
Data from Efficient Correction of Oncogenic KRAS and TP53 Mutations through CRISPR Base Editing
Authors: Sayed Shady , Sidorova Olga A. , Hennig Alexander , Augsburg Martina , Cortés Vesga Catherine P. , Abohawya Moustafa , Schmitt Lukas T. , Sürün Duran , Stange Daniel E. , Mircetic Jovan , Buchholz Frank
Published: March 2023

Abstract
KRAS is the most frequently mutated oncogene in human cancer, and its activating mutations represent long-sought therapeutic targets. Programmable nucleases, particularly the CRISPR-Cas9 system, provide an attractive tool for genetically targeting KRAS mutations in cancer cells. Here, we show that cleavage of a panel of KRAS driver mutations suppresses growth in various human cancer cell lines, revealing their dependence on mutant KRAS. However, analysis of the remaining cell population after long-term Cas9 expression unmasked the occurence of oncogenic KRAS escape variants that were resistant to Cas9-cleavage. In contrast, the use of an adenine base editor to correct oncogenic KRAS mutations progressively depleted the targeted cells without the appearance of escape variants and allowed efficient and simultaneous correction of a cancer-associated TP53 mutation. Oncogenic KRAS and TP53 base editing was possible in patient-derived cancer organoids, suggesting that base editor approaches to correct oncogenic mutations could be developed for functional interrogation of vulnerabilities in a personalized manner for future precision oncology applications.
Significance:
Repairing KRAS mutations with base editors can be used for providing a better understanding of RAS biology and may lay the foundation for improved treatments for KRAS-mutant cancers.
Data from A Programmable In Vivo CRISPR Activation Model Elucidates the Oncogenic and Immunosuppressive Functions of MYC in Lung Adenocarcinoma
Authors: Thege Fredrik I. , Rupani Dhwani N. , Barathi Bhargavi Brahmendra , Manning Sara L. , Maitra Anirban , Rhim Andrew D. , Wörmann Sonja M.
Published: March 2023

Conventional genetically engineered mouse models (GEMM) are time-consuming, laborious, and offer limited spatiotemporal control. Here, we describe the development of a streamlined platform for in vivo gene activation using CRISPR activation (CRISPRa) technology. Unlike conventional GEMMs, this model system allows for flexible, sustained, and timed activation of one or more target genes using single or pooled lentiviral guides. Myc and Yap1 were used as model oncogenes to demonstrate gene activation in primary pancreatic organoid cultures in vitro and enhanced tumorigenic potential in Myc-activated organoids when transplanted orthotopically in vivo. Implementation of this model as an autochthonous lung cancer model showed that transduction-mediated activation of Myc led to accelerated tumor progression and significantly reduced overall survival relative to nontargeted tumor controls. Furthermore, Myc activation led to the acquisition of an immune suppressive, “cold” tumor microenvironment. Cross-species validation of these results using publicly available RNA/DNA-seq datasets linked MYC to a previously described immunosuppressive molecular subtype in patient tumors, thus identifying a patient cohort that may benefit from combined MYC- and immune-targeted therapies. Overall, this work demonstrates how CRISPRa can be used for rapid functional validation of putative oncogenes and may allow for the identification and evaluation of potential metastatic and oncogenic drivers through competitive screening.
Significance:
A streamlined platform for programmable CRISPR gene activation enables rapid evaluation and functional validation of putative oncogenes in vivo.
Data from Poziotinib Inhibits HER2-Mutant–Driven Therapeutic Resistance and Multiorgan Metastasis in Breast Cancer
Authors: Kalra Rashi , Chen Ching Hui , Wang Junkai , Salam Ahmad Bin , Dobrolecki Lacey E. , Lewis Alaina , Sallas Christina , Yates Clayton C. , Gutierrez Carolina , Karanam Balasubramanyam , Anurag Meenakshi , Lim Bora , Ellis Matthew J. , Kavuri Shyam M.
Published: March 2023

Abstract
The pan-HER tyrosine kinase inhibitor (TKI) neratinib is therapeutically active against metastatic breast cancers harboring activating HER2 mutations, but responses are variable and often not durable. Here we demonstrate that recurrent HER2 mutations have differential effects on endocrine therapy responsiveness, metastasis, and pan-HER TKI therapeutic sensitivity. The prevalence and prognostic significance may also depend on whether the HER2 mutant has arisen in the context of lobular versus ductal histology. The most highly recurrent HER2 mutant, L755S, was particularly resistant to neratinib but sensitive to the pan-HER TKI poziotinib, alone or in combination with fulvestrant. Poziotinib reduced tumor growth, diminished multiorgan metastasis, and inhibited mTOR activation more effectively than neratinib. Similar therapeutic effects of poziotinib were observed in both an engineered HER2L755S MCF7 model and a patient-derived xenograft harboring a HER2G778_P780dup mutation. Overall, these findings support the need for clinical evaluation of poziotinib for the treatment of HER2-mutant metastatic breast cancer.
Significance:
Evaluation of the functional impact of HER2 mutations on therapy-induced resistance and metastasis identifies robust antitumor activity of poziotinib and supports the clinical evaluation of poziotinib in ER+ HER2 mutant breast cancer.
Data from Single-Cell Transcriptome Profiling Reveals Intratumoral Heterogeneity and Molecular Features of Ductal Carcinoma In Situ
Authors: Tokura Momoko , Nakayama Jun , Prieto-Vila Marta , Shiino Sho , Yoshida Masayuki , Yamamoto Tomofumi , Watanabe Naoaki , Takayama Shin , Suzuki Yutaka , Okamoto Koji , Ochiya Takahiro , Kohno Takashi , Yatabe Yasushi , Suto Akihiko , Yamamoto Yusuke
Published: March 2023

Abstract
Ductal carcinoma in situ (DCIS) is a precursor to invasive breast cancer. The frequency of DCIS is increasing because of routine mammography; however, the biological features and intratumoral heterogeneity of DCIS remain obscure. To address this deficiency, we performed single-cell transcriptomic profiling of DCIS and invasive ductal carcinoma (IDC). DCIS was found to be composed of several transcriptionally distinct subpopulations of cancer cells with specific functions. Several transcripts, including long noncoding RNAs, were highly expressed in IDC compared with DCIS and might be related to the invasive phenotype. Closeness centrality analysis revealed extensive heterogeneity in DCIS, and the prediction model for cell-to-cell interactions implied that the interaction network among luminal cells and immune cells in DCIS was comparable with that in IDC. In addition, transcriptomic profiling of HER2+ luminal DCIS indicated HER2 genomic amplification at the DCIS stage. These data provide novel insight into the intratumoral heterogeneity and molecular features of DCIS, which exhibit properties similar to IDC.
Significance:
Investigation of the molecular features of ductal carcinoma in situ at single cell resolution provides new insights into breast cancer biology and identifies candidate therapeutic targets and diagnostic biomarkers.
Data from A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer
Authors: Nardone Agostina , Qiu Xintao , Spisak Sandor , Nagy Zsuzsanna , Feiglin Ariel , Feit Avery , Cohen Feit Gabriela , Xie Yingtian , Font-Tello Alba , Guarducci Cristina , Hermida-Prado Francisco , Syamala Sudeepa , Lim Klothilda , Munoz Gomez Miguel , Pun Matthew , Cornwell MacIntosh , Liu Weihan , Ors Aysegul , Mohammed Hisham , Cejas Paloma , Brock Jane B. , Freedman Matthew L. , Winer Eric P. , Fu Xiaoyong , Schiff Rachel , Long Henry W. , Metzger Filho Otto , Jeselsohn Rinath
Published: March 2023

Abstract
Most invasive lobular breast cancers (ILC) are of the luminal A subtype and are strongly hormone receptor–positive. Yet, ILC is relatively resistant to tamoxifen and associated with inferior long-term outcomes compared with invasive ductal cancers (IDC). In this study, we sought to gain mechanistic insights into these clinical findings that are not explained by the genetic landscape of ILC and to identify strategies to improve patient outcomes. A comprehensive analysis of the epigenome of ILC in preclinical models and clinical samples showed that, compared with IDC, ILC harbored a distinct chromatin state linked to gained recruitment of FOXA1, a lineage-defining pioneer transcription factor. This resulted in an ILC-unique FOXA1–estrogen receptor (ER) axis that promoted the transcription of genes associated with tumor progression and poor outcomes. The ILC-unique FOXA1–ER axis led to retained ER chromatin binding after tamoxifen treatment, which facilitated tamoxifen resistance while remaining strongly dependent on ER signaling. Mechanistically, gained FOXA1 binding was associated with the autoinduction of FOXA1 in ILC through an ILC-unique FOXA1 binding site. Targeted silencing of this regulatory site resulted in the disruption of the feed-forward loop and growth inhibition in ILC. In summary, ILC is characterized by a unique chromatin state and FOXA1–ER axis that is associated with tumor progression, offering a novel mechanism of tamoxifen resistance. These results underscore the importance of conducting clinical trials dedicated to patients with ILC in order to optimize treatments in this breast cancer subtype.
Significance:
A unique FOXA1–ER axis in invasive lobular breast cancer promotes disease progression and tamoxifen resistance, highlighting a potential therapeutic avenue for clinical investigations dedicated to this disease.

See related commentary by Blawski and Toska, p. 3668
Data from Dual Inhibition of CDK12/CDK13 Targets Both Tumor and Immune Cells in Ovarian Cancer
Authors: Cheng Lin , Zhou Shichao , Zhou Shaoqing , Shi Kaixuan , Cheng Yan , Cai Mei-Chun , Ye Kaiyan , Lin Lifeng , Zhang Zhenfeng , Jia Chenqiang , Xiang Huaijiang , Zang Jingyu , Zhang Meiying , Yin Xia , Li Ying , Di Wen , Zhuang Guanglei , Tan Li
Published: March 2023

Abstract
Therapeutic perturbation of cyclin-dependent kinase 12 (CDK12) is proposed to have pleiotropic effects in ovarian cancer, including direct cytotoxicity against tumor cells and indirect induction of immunogenicity that confer synthetic sensitivity to immune-based treatment. However, formal testing of this hypothesis has been hindered by an insufficient mechanistic understanding of CDK12 and its close homolog CDK13, as well as generally unfavorable pharmacokinetics of available CDK12/CDK13 covalent inhibitors. In this study, we used an innovative arsenous warhead modality to develop an orally bioavailable CDK12/CDK13 covalent compound. The dual CDK12/CDK13 inhibitors ZSQ836 exerted potent anticancer activity in cell culture and mouse models and induced transcriptional reprogramming, including downregulation of DNA damage response genes. CDK12 and CDK13 were both ubiquitously expressed in primary and metastatic ovarian cancer, and the two kinases performed independent and synergistic functions to promote tumorigenicity. Unexpectedly, although ZSQ836 triggered genomic instability in malignant cells, it counterintuitively impaired lymphocytic infiltration in neoplastic lesions by interfering with T-cell proliferation and activation. These findings highlight the Janus-faced effects of dual CDK12/CDK13 inhibitors by simultaneously suppressing tumor and immune cells, offering valuable insights into the future direction of drug discovery to pharmacologically target CDK12.
Significance:
This study dissects the specific roles of CDK12 and CDK13 in ovarian cancer and develops a CDK12/CDK13 inhibitor that impairs both tumor and immune cells, which could guide future CDK12 inhibitor development.
Data from CYP4F2-Catalyzed Metabolism of Arachidonic Acid Promotes Stromal Cell-Mediated Immunosuppression in Non–Small Cell Lung Cancer
Authors: Chen Xuehan , Liu Yanzhuo , Wang Yang , Wang Chenlong , Chen Xuewei , Xiong Yu , Liu Lilong , Yuan Xi , Tang Honglin , Shu Chong , Zhang Jing , Guo Austin M. , Chen Honglei , Yang Jing
Published: March 2023

Abstract
Fatty acid synthesis facilitates tumor cell immune escape and immunotherapy resistance. Cytochrome P450 (CYP) 4A and 4F, the major ω-hydroxylases that convert arachidonic acid (AA) into 20-hydroxyeicosatetraenoic acid (20-HETE), are implicated in inflammation and cancer. However, the role of CYP4 ω-hydroxylases in immune evasion remains unclear. Here, we determined that 20-HETE derived from the CYP4F2 isoenzyme governs immune evasion in non–small cell lung cancer (NSCLC) in a CD8+ T-cell-dependent manner. Mechanistically, CYP4F2 induced expression of immune checkpoint PD-L1 and production of proangiogenic factors IL6 and TGFβ in cancer-associated fibroblasts (CAF) via the 20-HETE-GPR75-STAT3-c-Jun axis. Tumors with high CYP4F2 expression were more resistant to anti-PD-1 treatment, whereas inhibition of CYP4F2 enhanced the efficacy of anti-PD-1 therapy in human NSCLC organoids and mouse models. Collectively, these data delineate that CYP4F2-dependent AA metabolism controls CAF-mediated immune evasion. CYP4F2 inhibition combined with PD-1 antibody represents a promising therapeutic approach for immunotherapy-resistant lung cancer.
Significance:
The identification of a role for CYP4F2-dependent metabolism in driving immune evasion in non–small cell lung cancer reveals a strategy to improve the efficacy of immunotherapy by inhibiting CYP4F2.

See related article by Van Ginderachter, p. 3882
Data from Single-Cell Dissection of the Multiomic Landscape of High-Grade Serous Ovarian Cancer
Authors: Wang Yicheng , Xie Haoling , Chang Xiaohong , Hu Wenqi , Li Mengyao , Li Yi , Liu Huiping , Cheng Hongyan , Wang Shang , Zhou Ling , Shen Danhua , Dou Sha , Ma Ruiqiong , Mao Yunuo , Zhu Honglan , Zhang Xiaobo , Zheng Yuxuan , Ye Xue , Wen Lu , Kee Kehkooi , Cui Heng , Tang Fuchou
Published: March 2023

Abstract
High-grade serous cancer (HGSC) is the most common subtype of ovarian cancer. HGSC is highly aggressive with poor patient outcomes, and a deeper understanding of HGSC tumorigenesis could help guide future treatment development. To systematically characterize the underlying pathologic mechanisms and intratumoral heterogeneity in human HGSC, we used an optimized single-cell multiomics sequencing technology to simultaneously analyze somatic copy-number alterations (SCNA), DNA methylation, chromatin accessibility, and transcriptome in individual cancer cells. Genes associated with interferon signaling, metallothioneins, and metabolism were commonly upregulated in ovarian cancer cells. Integrated multiomics analyses revealed that upregulation of interferon signaling and metallothioneins was influenced by both demethylation of their promoters and hypomethylation of satellites and LINE1, and potential key transcription factors regulating glycolysis using chromatin accessibility data were uncovered. In addition, gene expression and DNA methylation displayed similar patterns in matched primary and abdominal metastatic tumor cells of the same genetic lineage, suggesting that metastatic cells potentially preexist in the subclones of primary tumors. Finally, the lineages of cancer cells with higher residual DNA methylation levels and upregulated expression of CCN1 and HSP90AA1 presented greater metastatic potential. This study characterizes the critical genetic, epigenetic, and transcriptomic features and their mutual regulatory relationships in ovarian cancer, providing valuable resources for identifying new molecular mechanisms and potential therapeutic targets for HGSC.
Significance:
Integrated analysis of multiomic changes and epigenetic regulation in high-grade serous ovarian cancer provides insights into the molecular characteristics of this disease, which could help improve diagnosis and treatment.
Data from Integrative Single-Cell Analysis Reveals Transcriptional and Epigenetic Regulatory Features of Clear Cell Renal Cell Carcinoma
Authors: Yu Zhenyuan , Lv Yufang , Su Cheng , Lu Wenhao , Zhang RuiRui , Li Jiaping , Guo Bingqian , Yan Haibiao , Liu Deyun , Yang Zhanbin , Mi Hua , Mo Linjian , Guo Yi , Feng Wenyu , Xu Haotian , Peng Wenyi , Cheng Jiwen , Nan Aruo , Mo Zengnan
Published: March 2023

Abstract
Clear cell renal cell carcinoma (ccRCC) frequently features a high level of tumor heterogeneity. Elucidating the chromatin landscape of ccRCC at the single-cell level could provide a deeper understanding of the functional states and regulatory dynamics underlying the disease. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on 19 ccRCC samples, and whole-exome sequencing was used to understand the heterogeneity between individuals. Single-cell transcriptome and chromatin accessibility maps of ccRCC were constructed to reveal the regulatory characteristics of different tumor cell subtypes in ccRCC. Two long noncoding RNAs (RP11-661C8.2 and CTB-164N12.1) were identified that promoted the invasion and migration of ccRCC, which was validated with in vitro experiments. Taken together, this study comprehensively characterized the gene expression and DNA regulation landscape of ccRCC, which could provide new insights into the biology and treatment of ccRCC.
Significance:
A comprehensive analysis of gene expression and DNA regulation in ccRCC using scATAC-seq and scRNA-seq reveals the DNA regulatory programs of ccRCC at the single-cell level.
Data from Phagocytosis of Glioma Cells Enhances the Immunosuppressive Phenotype of Bone Marrow–Derived Macrophages
Authors: Wu Min , Wu Lingxiang , Wu Wei , Zhu Mengyan , Li Jianyu , Wang Ziyu , Li Jie , Ding Rong , Liang Yuan , Li Liangyu , Zhang Tingting , Huang Bin , Cai Yun , Li Kening , Li Lu , Zhang Rui , Hu Baoli , Lin Fan , Wang Xiuxing , Zheng Siyuan , Chen Jian , You Yongping , Jiang Tao , Zhang Junxia , Chen Hongshan , Wang Qianghu
Published: March 2023

Abstract
Tumor-associated macrophages (TAM) play a crucial role in immunosuppression. However, how TAMs are transformed into immunosuppressive phenotypes and influence the tumor microenvironment (TME) is not fully understood. Here, we utilized single-cell RNA sequencing and whole-exome sequencing data of glioblastoma (GBM) tissues and identified a subset of TAMs dually expressing macrophage and tumor signatures, which were termed double-positive TAMs. Double-positive TAMs tended to be bone marrow–derived macrophages (BMDM) and were characterized by immunosuppressive phenotypes. Phagocytosis of glioma cells by BMDMs in vitro generated double-positive TAMs with similar immunosuppressive phenotypes to double-positive TAMs in the GBM TME of patients. The double-positive TAMs were transformed into M2-like macrophages and drove immunosuppression by expressing immune-checkpoint proteins CD276, PD-L1, and PD-L2 and suppressing the proliferation of activated T cells. Together, glioma cell phagocytosis by BMDMs in the TME leads to the formation of double-positive TAMs with enhanced immunosuppressive phenotypes, shedding light on the processes driving TAM-mediated immunosuppression in GBM.
Significance:
Bone marrow–derived macrophages phagocytose glioblastoma cells to form double-positive cells, dually expressing macrophage and tumor signatures that are transformed into M2-like macrophages and drive immunosuppression.
Data from Mitochondrial Uncoupling Induces Epigenome Remodeling and Promotes Differentiation in Neuroblastoma
Authors: Jiang Haowen , Greathouse Rachel L. , Tiche Sarah Jane , Zhao Man , He Bo , Li Yang , Li Albert M. , Forgo Balint , Yip Michaela , Li Allison , Shih Moriah , Banuelos Selene , Zhou Meng-Ning , Gruber Joshua J. , Rankin Erinn B. , Hu Zhen , Shimada Hiroyuki , Chiu Bill , Ye Jiangbin
Published: March 2023

Abstract
The Warburg effect is the major metabolic hallmark of cancer. According to Warburg himself, the consequence of the Warburg effect is cell dedifferentiation. Therefore, reversing the Warburg effect might be an approach to restore cell differentiation in cancer. In this study, we used a mitochondrial uncoupler, niclosamide ethanolamine (NEN), to activate mitochondrial respiration, which induced neural differentiation in neuroblastoma cells. NEN treatment increased the NAD+/NADH and pyruvate/lactate ratios and also the α-ketoglutarate/2-hydroxyglutarate (2-HG) ratio. Consequently, NEN treatment induced promoter CpG island demethylation and epigenetic landscape remodeling, activating the neural differentiation program. In addition, NEN treatment upregulated p53 but downregulated N-Myc and β-catenin signaling in neuroblastoma cells. Importantly, even under hypoxia, NEN treatment remained effective in inhibiting 2-HG generation, promoting DNA demethylation, and suppressing hypoxia-inducible factor signaling. Dietary NEN intervention reduced tumor growth rate, 2-HG levels, and expression of N-Myc and β-catenin in tumors in an orthotopic neuroblastoma mouse model. Integrative analysis indicated that NEN treatment upregulated favorable prognosis genes and downregulated unfavorable prognosis genes, which were defined using multiple neuroblastoma patient datasets. Altogether, these results suggest that mitochondrial uncoupling is an effective metabolic and epigenetic therapy for reversing the Warburg effect and inducing differentiation in neuroblastoma.
Significance:
Targeting cancer metabolism using the mitochondrial uncoupler niclosamide ethanolamine leads to methylome reprogramming and differentiation in neuroblastoma, providing a therapeutic opportunity to reverse the Warburg effect and suppress tumor growth.

See related commentary by Byrne and Bell, p.167
Data from Spatial Transcriptomic Analysis of Ovarian Cancer Precursors Reveals Reactivation of IGFBP2 during Pathogenesis
Authors: Wang Yeh , Huang Peng , Wang Brant G. , Murdock Tricia , Cope Leslie , Hsu Fang-Chi , Wang Tian-Li , Shih Ie-Ming
Published: March 2023

Abstract
Elucidating the earliest pathogenic steps in cancer development is fundamental to improving its early detection and prevention. Ovarian high-grade serous carcinoma (HGSC), a highly aggressive cancer, mostly originates from the fallopian tube epithelium through a precursor stage, serous tubal intraepithelial carcinoma (STIC). In this study, we performed spatial transcriptomic analysis to compare STICs, carcinoma, and their matched normal fallopian tube epithelium. Several differentially expressed genes in STICs and carcinomas were involved in cancer metabolism and detected in a larger independent transcriptomic dataset of ovarian HGSCs. Among these, insulin-like growth factor binding protein-2 (IGFBP2) was found to undergo DNA hypomethylation and to be increased at the protein level in STICs. Pyrosequencing revealed an association of IGFBP2 expression with the methylation state of its proximal enhancer, and 5-azacytidine treatment increased IGFBP2 expression. In postmenopausal fallopian tubes, where most STICs are detected, IGFBP2 immunoreactivity was detected in all 38 proliferatively active STICs but was undetectable in morphologically normal tubal epithelia, including those with TP53 mutations. In premenopausal fallopian tubes, IGFBP2 expression was limited to the secretory epithelium at the proliferative phase, and estradiol treatment increased IGFBP2 expression levels. IGFBP2 knockdown suppressed the growth of IGFBP2-expressing tubal epithelial cells via inactivation of the AKT pathway. Taken together, demethylation of the proximal enhancer of IGFBP2 drives tumor development by maintaining the increased IGFBP2 required for proliferation in an otherwise estrogen-deprived, proliferation-quiescent, and postmenopausal tubal microenvironment.
Significance:
Molecular studies of the earliest precursor lesions of ovarian cancer reveal a role of IGFBP2 in propelling tumor initiation, providing new insights into ovarian cancer development.
Supplementary Figures 81 - 147 from Imaging Features of HER2 Overexpression in Breast Cancer: A Systematic Review and Meta-analysis
Authors: Elias Sjoerd G. , Adams Arthur , Wisner Dorota J. , Esserman Laura J. , van't Veer Laura J. , Mali Willem P.Th.M. , Gilhuijs Kenneth G.A. , Hylton Nola M.
Published: March 2023

PDF file - 3944KB, Supplementary Figure S68 - Studies focused on invasive cancer only. Supplementary Figure S69 - Studies without the exclusion of a molecular subtype in the analyses. Supplementary Figure S70 - Studies exclusively using analog mammography. Supplementary Figure S71 - Studies exclusively using digital mammography. Supplementary Figure S72 - Studies based on BI-RADS. Supplementary Figure S73 - Studies focused on invasive cancer only. Supplementary Figure S74 - Studies without the exclusion of a molecular subtype in the analyses. Supplementary Figure S75 - Studies based on BI-RADS. Supplementary Figure S76 - Studies focused on invasive cancer only. Supplementary Figure S77 - Studies exclusively using 1.5T field strength. Supplementary Figure S78 - Studies (also) using 3T field strength. Supplementary Figure S79 - Studies with high spatial resolution (i.e. sub-mm in plane resolution and smaller than 2mm slice thickness). Supplementary Figure S80 - Studies based on BI-RADS.
Supplementary Tables 1-5 from A Case-Control Study of Body Mass Index and Breast Cancer Risk in White and African-American Women
Authors: Berstad Paula , Coates Ralph J. , Bernstein Leslie , Folger Suzanne G. , Malone Kathleen E. , Marchbanks Polly A. , Weiss Linda K. , Liff Jonathan M. , McDonald Jill A. , Strom Brian L. , Simon Michael S. , Deapen Dennis , Press Michael F. , Burkman Ronald T. , Spirtas Robert , Ursin Giske
Published: March 2023

Supplementary Tables 1-5 from A Case-Control Study of Body Mass Index and Breast Cancer Risk in White and African-American Women
Supplementary Data from Determinants of VIA (Visual Inspection of the Cervix After Acetic Acid Application) Positivity in Cervical Cancer Screening of Women in a Peri-Urban Area in Andhra Pradesh, India
Authors: Vedantham Haripriya , Silver Michelle I. , Kalpana B. , Rekha C. , Karuna B.P. , Vidyadhari K. , Mrudula S. , Ronnett Brigitte M. , Vijayaraghavan K. , Ramakrishna Gayatri , Sowjanya Pavani , Laxmi Shantha , Shah Keerti V. , Gravitt Patti E.
Published: March 2023

Supplementary Data from Determinants of VIA (Visual Inspection of the Cervix After Acetic Acid Application) Positivity in Cervical Cancer Screening of Women in a Peri-Urban Area in Andhra Pradesh, India
Supplementary Figure 2 from Distribution and Hepatocellular Carcinoma–Related Viral Properties of Hepatitis B Virus Genotypes in Mainland China: A Community-Based Study
Authors: Yin Jianhua , Zhang Hongwei , He Yongchao , Xie Jiaxin , Liu Shijian , Chang Wenjun , Tan Xiaojie , Gu Chunying , Lu Wei , Wang Hongyang , Bi Shengli , Cui Fuqiang , Liang Xiaofeng , Schaefer Stephan , Cao Guangwen
Published: March 2023

Supplementary Figure 2 from Distribution and Hepatocellular Carcinoma–Related Viral Properties of Hepatitis B Virus Genotypes in Mainland China: A Community-Based Study
Supplementary Figure 1A from TP53 Arg72Pro Polymorphism and Colorectal Cancer Risk: A Systematic Review and Meta-Analysis
Authors: Dahabreh Issa J. , Linardou Helena , Bouzika Peggy , Varvarigou Vasileia , Murray Samuel
Published: March 2023

Supplementary Figure 1A from TP53 Arg72Pro Polymorphism and Colorectal Cancer Risk: A Systematic Review and Meta-Analysis
Supplementary Figure 1 from Polymorphic Variants in Hereditary Pancreatic Cancer Genes Are Not Associated with Pancreatic Cancer Risk
Authors: McWilliams Robert R. , Bamlet William R. , de Andrade Mariza , Rider David N. , Couch Fergus J. , Cunningham Julie M. , Matsumoto Martha E. , Rabe Kari G. , Hammer Traci J. , Petersen Gloria M.
Published: March 2023

Supplementary Figure 1 from Polymorphic Variants in Hereditary Pancreatic Cancer Genes Are Not Associated with Pancreatic Cancer Risk
Supplementary Table 2 from Serum Pepsinogens and Helicobacter pylori in Relation to the Risk of Esophageal Squamous Cell Carcinoma in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study
Authors: Cook Michael B. , Dawsey Sanford M. , Diaw Lena , Blaser Martin J. , Perez-Perez Guillermo I. , Abnet Christian C. , Taylor Philip R. , Albanes Demetrius , Virtamo Jarmo , Kamangar Farin
Published: March 2023

Supplementary Table 2 from Serum Pepsinogens and Helicobacter pylori in Relation to the Risk of Esophageal Squamous Cell Carcinoma in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study
Supplementary Figure 9 from Global Patterns of Cancer Incidence and Mortality Rates and Trends
Authors: Jemal Ahmedin , Center Melissa M. , DeSantis Carol , Ward Elizabeth M.
Published: March 2023

Supplementary Figure 9 from Global Patterns of Cancer Incidence and Mortality Rates and Trends
Data Supplement from Sun Exposure and Melanoma Survival: A GEM Study
Authors: Berwick Marianne , Reiner Anne S. , Paine Susan , Armstrong Bruce K. , Kricker Anne , Goumas Chris , Cust Anne E. , Thomas Nancy E. , Groben Pamela A. , From Lynn , Busam Klaus , Orlow Irene , Marrett Loraine D. , Gallagher Richard P. , Gruber Stephen B. , Anton-Culver Hoda , Rosso Stefano , Zanetti Roberto , Kanetsky Peter A. , Dwyer Terry , Venn Alison , Lee-Taylor Julia , Begg Colin B.
Published: March 2023

Supplementary Table S4. Recent sun exposure and its association with overall survival.
Data Supplement from Occupational Exposure to Extremely Low-Frequency Magnetic Fields and Brain Tumor Risks in the INTEROCC Study
Authors: Turner Michelle C. , Benke Geza , Bowman Joseph D. , Figuerola Jordi , Fleming Sarah , Hours Martine , Kincl Laurel , Krewski Daniel , McLean Dave , Parent Marie-Elise , Richardson Lesley , Sadetzki Siegal , Schlaefer Klaus , Schlehofer Brigitte , Schüz Joachim , Siemiatycki Jack , van Tongeren Martie , Cardis Elisabeth
Published: March 2023

Supplementary Table S1. Description of ELF levels in the most frequent jobs in low (<0.12 microT), medium (0.12 -< 0.15 microT), and high ({greater than or equal to} 0.15 microT) ELF categories based on the 33rd, and 66th percentile of jobs among study participants. Supplementary Table S2. Distribution of cumulative (uT-years) and average (uT) occupational ELF exposure levels, INTEROCC study, 2000-2004, Australia, Canada, France, Germany, Israel, New Zealand, and United Kingdom. Supplementary Table S3. Correlation between cumulative ELF in the three exposure time windows, 1-4, 5-9, and 10+ years prior to the date of diagnosis/reference date, INTEROCC study, 2000-2004, Australia, Canada, France, Germany, Israel, New Zealand, and United Kingdom. Supplementary Table S4. Adjusted ORs (95% CIs)a for high- and low-grade glioma in relation to categorical indicators of cumulative occupational ELF exposure, overall and in selected separate exposure time windows, 1-4, 5-9, and 10+ years prior to the date of diagnosis/reference date, INTEROCC study, 2000-2004, Australia, Canada, France, Germany, Israel, New Zealand, and United Kingdom. Supplementary Table S5. Adjusted ORs (95% CIs)a for glioma and meningioma in relation to categorical indicators of time-weighted average occupational ELF exposure in three separate exposure time windows, 1-4, 5-9, and 10+ years prior to the date of diagnosis/reference date, INTEROCC study, 2000-2004, Australia, Canada, France, Germany, Israel, New Zealand, and United Kingdom. Supplementary Table S6. Adjusted ORs (95% CIs)a for glioma and meningioma in relation to categorical indicators of maximum ELF exposed job in three separate exposure time windows, 1-4, 5-9, and 10+ years prior to the date of diagnosis/reference date, INTEROCC study, 2000-2004, Australia, Canada, France, Germany, Israel, New Zealand, and United Kingdom. Supplementary Table S7. Adjusted ORs (95% CIs)a for glioma in relation to categorical indicators of cumulative occupational ELF exposure in the 1-4 year time window prior to the date of diagnosis/reference date, adjusting for occupational BAP and PAH chemical exposure, INTEROCC study, 2000-2004, Australia, Canada, France, Germany, Israel, New Zealand, and United Kingdom.
Supplementary Table 1 from Variation in TP63 is Associated with Lung Adenocarcinoma in the UK Population
Authors: Wang Yufei , Broderick Peter , Matakidou Athena , Vijayakrishnan Jayaram , Eisen Timothy , Houlston Richard S.
Published: March 2023

Supplementary Table 1 from Variation in TP63 is Associated with Lung Adenocarcinoma in the UK Population
Supplementary Tables 1-4 from Changes in CpG Islands Promoter Methylation Patterns during Ductal Breast Carcinoma Progression
Authors: Hoque Mohammad Obaidul , Prencipe Maria , Poeta Maria Luana , Barbano Raffaela , Valori Vanna Maria , Copetti Massimiliano , Gallo Antonietta Pia , Brait Mariana , Maiello Evaristo , Apicella Adolfo , Rossiello Raffaele , Zito Francesco , Stefania Tommasi , Paradiso Angelo , Carella Massimo , Dallapiccola Bruno , Murgo Roberto , Carosi Illuminato , Bisceglia Michele , Fazio Vito Michele , Sidransky David , Parrella Paola
Published: March 2023

Supplementary Tables 1-4 from Changes in CpG Islands Promoter Methylation Patterns during Ductal Breast Carcinoma Progression
Supplementary Table 2 from A Genome-Wide Survey over the ChIP-On-Chip Identified Androgen Receptor-Binding Genomic Regions Identifies a Novel Prostate Cancer Susceptibility Locus at 12q13.13
Authors: Feng Junjie , Sun Jielin , Kim Seong-Tae , Lu Yizhen , Wang Zhong , Zhang Zheng , Gronberg Henrik , Isaacs William B. , Zheng S. Lilly , Xu Jianfeng
Published: March 2023

PDF file - 40.4KB
Supplementary Table 3 from Effect of Long-term Storage in TRIzol on Microarray-Based Gene Expression Profiling
Authors: Ma Wencai , Wang Michael , Wang Zhi-Qiang , Sun Luhong , Graber David , Matthews Jairo , Champlin Richard , Yi Qing , Orlowski Robert Z. , Kwak Larry W. , Weber Donna M. , Thomas Sheeba K. , Shah Jatin , Kornblau Steven , Davis Richard E.
Published: March 2023

Supplementary Table 3 from Effect of Long-term Storage in TRIzol on Microarray-Based Gene Expression Profiling
Supplementary Tables 1-2 from Interaction between Cigarette Smoking and Hepatitis B and C Virus Infection on the Risk of Liver Cancer: A Meta-analysis
Authors: Chuang Shu-Chun , Lee Yuan-Chin Amy , Hashibe Mia , Dai Min , Zheng Tongzhang , Boffetta Paolo
Published: March 2023

Supplementary Tables 1-2 from Interaction between Cigarette Smoking and Hepatitis B and C Virus Infection on the Risk of Liver Cancer: A Meta-analysis
Supplementary Figure Legends from ST14 Gene Variant and Decreased Matriptase Protein Expression Predict Poor Breast Cancer Survival
Authors: Kauppinen Jaana M. , Kosma Veli-Matti , Soini Ylermi , Sironen Reijo , Nissinen Minna , Nykopp Timo K. , Kärjä Vesa , Eskelinen Matti , Kataja Vesa , Mannermaa Arto
Published: March 2023

Supplementary Figure Legends from ST14 Gene Variant and Decreased Matriptase Protein Expression Predict Poor Breast Cancer Survival
Supplementary Figure 3 from ST14 Gene Variant and Decreased Matriptase Protein Expression Predict Poor Breast Cancer Survival
Authors: Kauppinen Jaana M. , Kosma Veli-Matti , Soini Ylermi , Sironen Reijo , Nissinen Minna , Nykopp Timo K. , Kärjä Vesa , Eskelinen Matti , Kataja Vesa , Mannermaa Arto
Published: March 2023

Supplementary Figure 3 from ST14 Gene Variant and Decreased Matriptase Protein Expression Predict Poor Breast Cancer Survival