Emily Boxer, Nisan Feigin, Roi Tschernichovsky, Noam Galili Darnell, Alissa R. Greenwald, Rouven Hoefflin, Daniel Kovarsky, Dor Simkin, Shira Turgeman, Lingling Zhang, Itay Tirosh
{"title":"Emerging clinical applications of single-cell RNA sequencing in oncology","authors":"Emily Boxer, Nisan Feigin, Roi Tschernichovsky, Noam Galili Darnell, Alissa R. Greenwald, Rouven Hoefflin, Daniel Kovarsky, Dor Simkin, Shira Turgeman, Lingling Zhang, Itay Tirosh","doi":"10.1038/s41571-025-01003-3","DOIUrl":"https://doi.org/10.1038/s41571-025-01003-3","url":null,"abstract":"<p>Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of complex tissues both in health and in disease. Over the past decade, scRNA-seq has been applied to tumour samples obtained from patients with cancer in hundreds of studies, thereby advancing the view that each tumour is a complex ecosystem and uncovering the diverse states of both cancer cells and the tumour microenvironment. Such studies have primarily investigated and provided insights into the basic biology of cancer, although considerable research interest exists in leveraging these findings towards clinical applications. In this Review, we summarize the available data from scRNA-seq studies investigating samples from patients with cancer with a particular focus on findings that are of potential clinical relevance. We highlight four main research objectives of scRNA-seq studies and describe some of the most relevant findings towards such goals. We also describe the limitations of scRNA-seq, as well as future approaches in this field that are anticipated to further advance clinical applicability.</p>","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"54 1","pages":""},"PeriodicalIF":78.8,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143518494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Using oncolytic viruses to induce hyperacute rejection against cancer","authors":"Howard L. Kaufman, Ann W. Silk","doi":"10.1038/s41571-025-01006-0","DOIUrl":"https://doi.org/10.1038/s41571-025-01006-0","url":null,"abstract":"In a recently reported study, a novel engineered oncolytic Newcastle disease virus encoding porcine α1,3-galactosyltransferase was evaluated in monkeys with CRISPR-induced primary hepatocellular carcinoma and in a phase I clinical trial. The virus induced hyperacute tumour rejection and an objective response rate of 35% in 20 evaluable patients. This approach highlights the promises and challenges of oncolytic virus drug development.","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"68 1","pages":""},"PeriodicalIF":78.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The SONIA trial shows the power and challenges of academic research","authors":"Shani Paluch-Shimon, Fatima Cardoso","doi":"10.1038/s41571-025-01004-2","DOIUrl":"https://doi.org/10.1038/s41571-025-01004-2","url":null,"abstract":"The thought-provoking SONIA trial showed that patients with hormone receptor-positive, HER2-negative advanced-stage breast cancer receiving deferred (second-line) versus first-line cyclin dependent-kinase (CDK) 4/6 inhibitors have noninferior progression-free survival after second-line treatment; such an approach also results in substantial cost savings. Herein, we discuss some important limitations of this trial and argue that, owing to their effect on overall survival, CDK4/6 inhibitors should remain the standard-of-care first-line therapy.","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"22 1","pages":""},"PeriodicalIF":78.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Zenocutuzumab shows efficacy in NRG1 fusion-positive solid tumours","authors":"Diana Romero","doi":"10.1038/s41571-025-01005-1","DOIUrl":"https://doi.org/10.1038/s41571-025-01005-1","url":null,"abstract":"<p>Chimeric proteins resulting from fusions involving <i>NRG1</i>, which encodes a growth factor from the EGF family, promote HER2–HER3 heterodimerization and subsequent oncogenic activation of cell proliferation. These fusions occur in <1% of solid tumours including non-small-cell lung cancer (NSCLC) and pancreatic adenocarcinoma (PDAC). Now, data from the phase II eNRGy trial demonstrate that the HER2 × HER3 bispecific antibody zenocutuzumab is efficacious and safe in patients with advanced-stage <i>NRG1</i> fusion-positive solid tumours.</p><p>The primary efficacy population comprised 158 patients with one of ten solid tumour types, primarily NSCLC (<i>n</i> = 94) and PDAC (<i>n</i> = 36). Most patients had received previous systemic therapy for metastatic disease, including 77% and 92% of those with NSCLC and PDAC, respectively. The primary end point was objective response rate (ORR).</p>","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"2 1","pages":""},"PeriodicalIF":78.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tamara J. Bock, Chanukya K. Colonne, Salvatore Fiorenza, Cameron J. Turtle
{"title":"Outcome correlates of approved CD19-targeted CAR T cells for large B cell lymphoma","authors":"Tamara J. Bock, Chanukya K. Colonne, Salvatore Fiorenza, Cameron J. Turtle","doi":"10.1038/s41571-025-00992-5","DOIUrl":"10.1038/s41571-025-00992-5","url":null,"abstract":"CD19-targeted chimeric antigen receptor (CAR) T cells have provided a breakthrough in the treatment of patients with relapsed and/or refractory large B cell lymphoma (LBCL). Currently, three CD19-targeted CAR T cell products are approved by the FDA and various other regulators for the treatment of patients with LBCL: axicabtagene ciloleucel, tisagenlecleucel and lisocabtagene maraleucel. Response rates following infusion of these CD19-targeted CAR T cells have been promising; however, approximately half of treated patients show relapse within 2 years. Furthermore, receiving these agents can be associated with serious toxicities, including cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome. In this Review, we summarize the factors associated with the efficacy, including response and survival outcomes, and toxicity of CD19-targeted CAR T cells in pivotal clinical trials and large real-world datasets describing the outcomes of patients with LBCL who received treatment with these products. CD19-targeted CAR T cells have transformed the management of patients with relapsed and/or refractory large B cell lymphoma, and these therapies are increasingly being administered as earlier-line therapies. Nonetheless, the prognosis of these patients is often difficult to predict, with various prospective and real-world studies suggesting that a wide range of factors are associated with treatment outcomes. In this Review, the authors summarize these various associations as well as their implications for patient selection and management.","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"22 4","pages":"241-261"},"PeriodicalIF":81.1,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Artificial intelligence in digital pathology — time for a reality check","authors":"Arpit Aggarwal, Satvika Bharadwaj, Germán Corredor, Tilak Pathak, Sunil Badve, Anant Madabhushi","doi":"10.1038/s41571-025-00991-6","DOIUrl":"10.1038/s41571-025-00991-6","url":null,"abstract":"The past decade has seen the introduction of artificial intelligence (AI)-based approaches aimed at optimizing several workflows across many medical specialties. In clinical oncology, the most promising applications include those involving image analysis, such as digital pathology. In this Perspective, we provide a comprehensive examination of the developments in AI in digital pathology between 2019 and 2024. We evaluate the current landscape from the lens of technological innovations, regulatory trends, deployment and implementation, reimbursement and commercial implications. We assess the technological advances that have driven improvements in AI, enabling more robust and scalable solutions for digital pathology. We also examine regulatory developments, in particular those affecting in-house devices and laboratory-developed tests, which are shaping the landscape of AI-based tools in digital pathology. Finally, we discuss the role of reimbursement frameworks and commercial investment in the clinical adoption of AI-based technologies. In this Perspective, we highlight both the progress and challenges in AI-driven digital pathology over the past 5 years, outlining the path forward for its adoption into routine practice in clinical oncology. The authors of this Perspective evaluate the developments in the use of artificial intelligence (AI) in digital pathology for oncology applications between 2019 and 2024, addressing technological innovations, regulatory trends, implementation and financial implications. Importantly, they explore the current landscape of clinical deployment, highlighting future opportunities for the integration of AI into clinical oncology routine practice.","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"22 4","pages":"283-291"},"PeriodicalIF":81.1,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Intermediate-affinity CD19-directed CAR T cell product obecabtagene autoleucel demonstrates favourable safety and efficacy in R/R B-ALL","authors":"Rawan G. Faramand, Frederick L. Locke","doi":"10.1038/s41571-025-00993-4","DOIUrl":"10.1038/s41571-025-00993-4","url":null,"abstract":"Recent data from the FELIX trial evaluating obecabtagene autoleucel in patients with relapsed and/or refractory B acute lymphoblastic leukaemia (R/R B-ALL) suggest that this novel intermediate-affinity CD19-directed chimeric antigen receptor (CAR) T cell therapy is associated with a reduced incidence of severe immune-mediated toxicities compared with other commercially available CAR T cell products. The increasing number of therapies available for B-ALL makes treatment selection and sequencing of therapies increasingly challenging.","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"22 3","pages":"161-162"},"PeriodicalIF":81.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"AI accurately identifies targetable alterations in lung cancer histological images","authors":"Hortense Le, Aristotelis Tsirigos","doi":"10.1038/s41571-025-00999-y","DOIUrl":"10.1038/s41571-025-00999-y","url":null,"abstract":"DeepGEM, an artificial intelligence (AI)-based model, accurately predicts the presence of key genomic alterations in histological slides prepared from samples obtained from patients with lung cancer. This approach provides a cost-effective alternative to genomic testing, generates spatial mutation maps and might support personalized treatment strategies. Validated in diverse datasets, DeepGEM highlights the potential of AI to transform precision oncology and improve global healthcare equity.","PeriodicalId":19079,"journal":{"name":"Nature Reviews Clinical Oncology","volume":"22 4","pages":"239-240"},"PeriodicalIF":81.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}