Pub Date : 2026-03-02DOI: 10.1158/1078-0432.CCR-25-3282
Kristin M Wessel, Katherine A Janeway, Lara E Davis, Nicole Drezner, Martha Donoghue, Lee J Helman
Osteosarcoma is the most common primary malignant bone tumor in children and adolescents, with a peak incidence coinciding with the pubertal growth spurt. Metastatic disease occurs in approximately 10% to 20% of newly diagnosed patients, most commonly in the lung. Although 5-year overall survival (OS) for patients with localized disease at diagnosis is approximately 70% after standard upfront treatment of multi-agent chemotherapy and surgical resection, patients with metastatic or recurrent disease have a 5-year OS of approximately 30% in the pediatric age group. Currently, there is no standard treatment or FDA-approved therapy for relapsed and refractory osteosarcoma. Progress in identifying promising new treatments has been limited by its complex disease biology and rarity, as well as unique challenges of clinical trial design, including unreliability of objective response rate as a predictor of drug activity. Given these challenges and the unmet need for new therapies, the FDA Oncology Center of Excellence hosted an educational symposium, "Current Challenges in Clinical Trial Design for Relapsed and Refractory Osteosarcoma," in May 2023. During this mini symposium, patient advocates, regulators from the FDA, and academic thought leaders in the field of pediatric sarcoma discussed challenges in clinical trial design and implementation. Achieving progress in relapsed and refractory osteosarcoma will require intentional collaboration among all stakeholders to identify trial designs that are acceptable to patients and will provide sufficient evidence of efficacy and safety to support a marketing application. Herein, we summarize the key points and future directions discussed at this meeting.
{"title":"Considerations for Clinical Trial Design in Relapsed and Refractory Osteosarcoma: An FDA Symposium.","authors":"Kristin M Wessel, Katherine A Janeway, Lara E Davis, Nicole Drezner, Martha Donoghue, Lee J Helman","doi":"10.1158/1078-0432.CCR-25-3282","DOIUrl":"10.1158/1078-0432.CCR-25-3282","url":null,"abstract":"<p><p>Osteosarcoma is the most common primary malignant bone tumor in children and adolescents, with a peak incidence coinciding with the pubertal growth spurt. Metastatic disease occurs in approximately 10% to 20% of newly diagnosed patients, most commonly in the lung. Although 5-year overall survival (OS) for patients with localized disease at diagnosis is approximately 70% after standard upfront treatment of multi-agent chemotherapy and surgical resection, patients with metastatic or recurrent disease have a 5-year OS of approximately 30% in the pediatric age group. Currently, there is no standard treatment or FDA-approved therapy for relapsed and refractory osteosarcoma. Progress in identifying promising new treatments has been limited by its complex disease biology and rarity, as well as unique challenges of clinical trial design, including unreliability of objective response rate as a predictor of drug activity. Given these challenges and the unmet need for new therapies, the FDA Oncology Center of Excellence hosted an educational symposium, \"Current Challenges in Clinical Trial Design for Relapsed and Refractory Osteosarcoma,\" in May 2023. During this mini symposium, patient advocates, regulators from the FDA, and academic thought leaders in the field of pediatric sarcoma discussed challenges in clinical trial design and implementation. Achieving progress in relapsed and refractory osteosarcoma will require intentional collaboration among all stakeholders to identify trial designs that are acceptable to patients and will provide sufficient evidence of efficacy and safety to support a marketing application. Herein, we summarize the key points and future directions discussed at this meeting.</p>","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":" ","pages":"831-834"},"PeriodicalIF":10.2,"publicationDate":"2026-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12958155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145888565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-02-27DOI: 10.1158/1078-0432.ccr-25-4721
Nam Nguyen-Hoang, Kelly Nugent, Sophia Jaso, Faisal Shakeel, Jung Won Kwon, Kyoin Koo, Amy L. Pasternak, Daniel L. Hertz
Purpose: Fluoropyrimidine (FP) chemotherapy can cause life-threatening toxicity. Four DPYD polymorphisms (DPYD*2A, *13, p.Asp949Val, HapB3) are well-established to increase FP toxicity risk. This study aimed to identify additional DPYD polymorphisms that increase FP toxicity. Experimental Design: Adult patients treated with standard doses of systemic FP (5-fluorouracil/capecitabine) for any cancer with available DPYD genetic data were included. The primary endpoint was a composite of CTCAE grade ≥3 toxicity or treatment modification due to toxicity in the first two FP cycles. A literature-curated list of suspected deleterious unvalidated DPYD variants was classified as uncommon (minor allele frequency <0.01) or common. The genetic association with toxicity was analyzed via multivariable logistic regression. Results: Among 849 eligible patients, the composite toxicity endpoint occurred in 25%. Genetic data were available for five uncommon and six common suspected deleterious DPYD variants. In the primary analysis of 799 patients who did not carry a validated variant, carriers of uncommon deleterious variants (1.1% of patients) had significantly higher toxicity risk than non-carriers (67% vs. 24%; adjusted OR 7.36; 95% CI 1.75–38.20; p = 0.009). None of the common deleterious variants were associated with toxicity. Toxicity prediction in the entire cohort (n = 849) was slightly improved by testing the uncommon and validated variants vs. testing only the validated variants (positive predictive value: 44.1% vs. 40.0%). Conclusions: Five uncommon DPYD variants, in combination, increase FP toxicity risk and improve risk prediction. Testing these variants could identify more high-risk patients who should receive adjusted FP doses to prevent severe toxicity.
{"title":"Identification of additional DPYD polymorphisms that increase the risk of severe fluoropyrimidine toxicity and improved predictive accuracy when combined with previously validated variants","authors":"Nam Nguyen-Hoang, Kelly Nugent, Sophia Jaso, Faisal Shakeel, Jung Won Kwon, Kyoin Koo, Amy L. Pasternak, Daniel L. Hertz","doi":"10.1158/1078-0432.ccr-25-4721","DOIUrl":"https://doi.org/10.1158/1078-0432.ccr-25-4721","url":null,"abstract":"Purpose: Fluoropyrimidine (FP) chemotherapy can cause life-threatening toxicity. Four DPYD polymorphisms (DPYD*2A, *13, p.Asp949Val, HapB3) are well-established to increase FP toxicity risk. This study aimed to identify additional DPYD polymorphisms that increase FP toxicity. Experimental Design: Adult patients treated with standard doses of systemic FP (5-fluorouracil/capecitabine) for any cancer with available DPYD genetic data were included. The primary endpoint was a composite of CTCAE grade ≥3 toxicity or treatment modification due to toxicity in the first two FP cycles. A literature-curated list of suspected deleterious unvalidated DPYD variants was classified as uncommon (minor allele frequency &lt;0.01) or common. The genetic association with toxicity was analyzed via multivariable logistic regression. Results: Among 849 eligible patients, the composite toxicity endpoint occurred in 25%. Genetic data were available for five uncommon and six common suspected deleterious DPYD variants. In the primary analysis of 799 patients who did not carry a validated variant, carriers of uncommon deleterious variants (1.1% of patients) had significantly higher toxicity risk than non-carriers (67% vs. 24%; adjusted OR 7.36; 95% CI 1.75–38.20; p = 0.009). None of the common deleterious variants were associated with toxicity. Toxicity prediction in the entire cohort (n = 849) was slightly improved by testing the uncommon and validated variants vs. testing only the validated variants (positive predictive value: 44.1% vs. 40.0%). Conclusions: Five uncommon DPYD variants, in combination, increase FP toxicity risk and improve risk prediction. Testing these variants could identify more high-risk patients who should receive adjusted FP doses to prevent severe toxicity.","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"56 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147314851","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}
Pub Date : 2026-02-27DOI: 10.1158/1078-0432.ccr-25-4420
Shanye Yin, Lin Cheng, Erqiang Hu, Junpeng Li, Gujie Wu, Jianhong An, Leti Nunez, Nicole Kawachi, Jing Zhu, Gregory Rosenblatt, Jeffrey E. Segall, Harry Ostrer, Stelby Augustine, Evan Z. Song, Thomas J. Ow, Richard V. Smith, Michael B. Prystowsky, Amit Verma, Wenjun Deng
Purpose: To evaluate whether intratumoral bacterial load and diversity are associated with survival outcomes in HNSCC and to examine their relationship with HPV status. Experimental Design: This retrospective cohort study included 312 adults with surgically treated, primary HNSCC at Montefiore Einstein Cancer Center (2000–2023). Intratumoral bacterial load was quantified by qPCR, and microbial diversity was assessed by 16S rRNA sequencing in 312 tumor and 34 paired normal tissues. HPV status was determined by p16 immunohistochemistry and qPCR. Overall survival was the primary outcome. Results: HNSCC tumors showed higher bacterial load and lower bacterial diversity compared to adjacent normal tissues. High bacterial load (HR, 1.85; 95% CI, 1.31-2.61; P<0.001) and low bacterial diversity (HR, 1.65; 95% CI, 1.19-2.28; P=0.003) were independently associated with reduced OS, with the greatest risk in patients carrying both features (HR, 3.00; 95% CI, 1.76-5.09; P<0.001). The high-risk bacterial features were less frequent in HPV-positive than in HPV-negative tumors (high load: OR, 0.46; 95% CI, 0.29-0.73; P=0.001; low diversity: OR, 0.51; 95% CI, 0.32-0.81; P=0.004), and their prognostic significance was more pronounced in HPV-negative cases. Taxonomic profiling revealed marked depletion of predominant bacterial taxa in HNSCC, especially in HPV-negative tumors. Notably, loss of the class TM7-3 and the orders Actinomycetales and Burkholderiales was specifically associated with poor HNSCC survival, including early mortality. Conclusions: High intratumoral bacterial load and low diversity are prognostic factors associated with survival in HNSCC, particularly in HPV-negative patients. Incorporating microbiome assessment into risk stratification may enhance prognostic precision and inform microbiota-directed therapeutic approaches.
{"title":"Association of Intratumoral Microbiota with Prognosis in Head and Neck Squamous Cell Carcinoma","authors":"Shanye Yin, Lin Cheng, Erqiang Hu, Junpeng Li, Gujie Wu, Jianhong An, Leti Nunez, Nicole Kawachi, Jing Zhu, Gregory Rosenblatt, Jeffrey E. Segall, Harry Ostrer, Stelby Augustine, Evan Z. Song, Thomas J. Ow, Richard V. Smith, Michael B. Prystowsky, Amit Verma, Wenjun Deng","doi":"10.1158/1078-0432.ccr-25-4420","DOIUrl":"https://doi.org/10.1158/1078-0432.ccr-25-4420","url":null,"abstract":"Purpose: To evaluate whether intratumoral bacterial load and diversity are associated with survival outcomes in HNSCC and to examine their relationship with HPV status. Experimental Design: This retrospective cohort study included 312 adults with surgically treated, primary HNSCC at Montefiore Einstein Cancer Center (2000–2023). Intratumoral bacterial load was quantified by qPCR, and microbial diversity was assessed by 16S rRNA sequencing in 312 tumor and 34 paired normal tissues. HPV status was determined by p16 immunohistochemistry and qPCR. Overall survival was the primary outcome. Results: HNSCC tumors showed higher bacterial load and lower bacterial diversity compared to adjacent normal tissues. High bacterial load (HR, 1.85; 95% CI, 1.31-2.61; P&lt;0.001) and low bacterial diversity (HR, 1.65; 95% CI, 1.19-2.28; P=0.003) were independently associated with reduced OS, with the greatest risk in patients carrying both features (HR, 3.00; 95% CI, 1.76-5.09; P&lt;0.001). The high-risk bacterial features were less frequent in HPV-positive than in HPV-negative tumors (high load: OR, 0.46; 95% CI, 0.29-0.73; P=0.001; low diversity: OR, 0.51; 95% CI, 0.32-0.81; P=0.004), and their prognostic significance was more pronounced in HPV-negative cases. Taxonomic profiling revealed marked depletion of predominant bacterial taxa in HNSCC, especially in HPV-negative tumors. Notably, loss of the class TM7-3 and the orders Actinomycetales and Burkholderiales was specifically associated with poor HNSCC survival, including early mortality. Conclusions: High intratumoral bacterial load and low diversity are prognostic factors associated with survival in HNSCC, particularly in HPV-negative patients. Incorporating microbiome assessment into risk stratification may enhance prognostic precision and inform microbiota-directed therapeutic approaches.","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"98 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147314850","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}
Pub Date : 2026-02-26DOI: 10.1158/1078-0432.ccr-25-3071
Chinmay T. Jani, Eli Tran, Nicole Zhang, Jill Tsai, Jianjie Dong, Leslie Bucheit, Elizabeth Pan, Justine Panian, Yu-Wei Chen, Rana R. McKay
Purpose: Circulating tumor DNA (ctDNA) NGS complements tissue-based testing and offers insights into prognosis, treatment selection, and tumor evolution. Despite advances in mCRPC therapies, resistance remains a challenge. This real-world study evaluates longitudinal ctDNA changes following systemic treatments. Experimental Design: We analyzed data from GuardantINFORM, a clinical-genomic database linking ctDNA profiles with claims data. Patients with prostate cancer who received ARPi, PARPi, or taxanes and had ctDNA testing within 3 months before and after treatment discontinuation were included. We evaluated pre- and post-treatment mutational differences and survival outcomes [Overall Survival (OS), Time to treatment discontinuation (TTD), Time to new treatment (TTNT)], stratifying by treatment type and AR alterations. Results: From 36,774 prostate-cancer patients, we identified 678 with paired pre/post-ARPi, 188 with paired pre/post-PARPi, and 844 with paired pre/post-taxane ctDNA samples. Post-ARPi, the most frequent AR alterations included AR amplification (pre%/post%) (10.8%/25.6%), AR L702H (1.3%/7.9%), and AR T878A (2.9%/7.1%). Following PARPi, the most common HRR gene alterations were ATM (25%/23.4%), BRCA2 (22.9%/17%), BRCA1 (4%/2.1%), and CDK12 (5.9%/5.9%). Post-taxane, frequent alterations included TP53 (47.2%→54%), AR (33.2%/49.9%), PIK3CA (9.4%/15.9%), and EGFR (9.6%/14.6%). All treatment cohorts showed a significant increase in mutation burden post-therapy (mean increase 2.0–4.2 alterations; p<0.001). Across all three treatment groups, the presence of AR alterations was consistently associated with inferior clinical outcomes. Conclusions: Our study revealed dynamic shifts in genetic mutations in patients with mCRPC following ARPI, PARPi and taxanes. Furthermore, our findings highlight associations between AR alterations and clinical outcomes, emphasizing the potential for personalized treatment strategies.
{"title":"Characterizing Longitudinal Molecular Changes in ctDNA in Patients with Metastatic Castration-resistant Prostate Cancer","authors":"Chinmay T. Jani, Eli Tran, Nicole Zhang, Jill Tsai, Jianjie Dong, Leslie Bucheit, Elizabeth Pan, Justine Panian, Yu-Wei Chen, Rana R. McKay","doi":"10.1158/1078-0432.ccr-25-3071","DOIUrl":"https://doi.org/10.1158/1078-0432.ccr-25-3071","url":null,"abstract":"Purpose: Circulating tumor DNA (ctDNA) NGS complements tissue-based testing and offers insights into prognosis, treatment selection, and tumor evolution. Despite advances in mCRPC therapies, resistance remains a challenge. This real-world study evaluates longitudinal ctDNA changes following systemic treatments. Experimental Design: We analyzed data from GuardantINFORM, a clinical-genomic database linking ctDNA profiles with claims data. Patients with prostate cancer who received ARPi, PARPi, or taxanes and had ctDNA testing within 3 months before and after treatment discontinuation were included. We evaluated pre- and post-treatment mutational differences and survival outcomes [Overall Survival (OS), Time to treatment discontinuation (TTD), Time to new treatment (TTNT)], stratifying by treatment type and AR alterations. Results: From 36,774 prostate-cancer patients, we identified 678 with paired pre/post-ARPi, 188 with paired pre/post-PARPi, and 844 with paired pre/post-taxane ctDNA samples. Post-ARPi, the most frequent AR alterations included AR amplification (pre%/post%) (10.8%/25.6%), AR L702H (1.3%/7.9%), and AR T878A (2.9%/7.1%). Following PARPi, the most common HRR gene alterations were ATM (25%/23.4%), BRCA2 (22.9%/17%), BRCA1 (4%/2.1%), and CDK12 (5.9%/5.9%). Post-taxane, frequent alterations included TP53 (47.2%→54%), AR (33.2%/49.9%), PIK3CA (9.4%/15.9%), and EGFR (9.6%/14.6%). All treatment cohorts showed a significant increase in mutation burden post-therapy (mean increase 2.0–4.2 alterations; p&lt;0.001). Across all three treatment groups, the presence of AR alterations was consistently associated with inferior clinical outcomes. Conclusions: Our study revealed dynamic shifts in genetic mutations in patients with mCRPC following ARPI, PARPi and taxanes. Furthermore, our findings highlight associations between AR alterations and clinical outcomes, emphasizing the potential for personalized treatment strategies.","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"119 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147287125","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}
Purpose: Immune checkpoint blockade (ICB) has revolutionized clear cell renal cell carcinoma (ccRCC) therapy, yet resistance remains common. Tumor-associated macrophages (TAMs) shape the tumor-immune interface and contribute to ICB resistance. While IL8 (CXCL8) was known as a chemokine involved in tumor progression, the role of IL8+ TAMs in ccRCC remains poorly defined. Here, we aimed to define the clinical and functional relevance of IL8+ TAMs in ccRCC. Experimental Design: Two in-house and four external RCC cohorts, encompassing over 1400 patients were analyzed to determine the clinical relevance of IL8+TAMs. Immunofluorescence and immunohistochemistry were applied to quantify IL8+TAMs infiltration. Mass/flow cytometry and multi-omics were used to define their phenotype, metabolic profile and immune interactions. Ex vivo tumor cultures were performed to test IL8 blockade and combination with anti-PD-1 therapy. Results: High IL8+ TAMs infiltration was consistently associated with ICB resistance. Transcriptomic analyses revealed that IL8+ TAMs adopt a glycolysis-associated metabolic program and are responsive to lactate, which directly promotes IL8 expression. Phenotypically, IL8+ TAMs exhibited an immunosuppressive and chemotactic profile that correlated with CD8+ T-cell dysfunction and regulatory T-cell accumulation. Importantly, ex vivo IL8 blockade alleviated CD8+ T-cell exhaustion and synergized with PD-1 inhibition to enhance antitumor immune responses. Conclusions: IL8+ TAMs represent a metabolically reprogrammed and immunosuppressive subset driving ICB resistance in ccRCC. Targeting IL8 may overcome resistance and enhance immunotherapy efficacy.
{"title":"Lactate-driven IL8+ Tumor-Associated Macrophages Mediate Immunosuppression and Resistance to Immunotherapy in Clear Cell Renal Cell Carcinoma","authors":"Yu Dong, Wenbin Jiang, Youqi Qiu, Ziyang Xu, Jiangting Cheng, Peiqing Ke, Siyuan Dai, Yang Qu, Yu Xia, Jianming Guo, Li Liu, Jiejie Xu","doi":"10.1158/1078-0432.ccr-25-4384","DOIUrl":"https://doi.org/10.1158/1078-0432.ccr-25-4384","url":null,"abstract":"Purpose: Immune checkpoint blockade (ICB) has revolutionized clear cell renal cell carcinoma (ccRCC) therapy, yet resistance remains common. Tumor-associated macrophages (TAMs) shape the tumor-immune interface and contribute to ICB resistance. While IL8 (CXCL8) was known as a chemokine involved in tumor progression, the role of IL8+ TAMs in ccRCC remains poorly defined. Here, we aimed to define the clinical and functional relevance of IL8+ TAMs in ccRCC. Experimental Design: Two in-house and four external RCC cohorts, encompassing over 1400 patients were analyzed to determine the clinical relevance of IL8+TAMs. Immunofluorescence and immunohistochemistry were applied to quantify IL8+TAMs infiltration. Mass/flow cytometry and multi-omics were used to define their phenotype, metabolic profile and immune interactions. Ex vivo tumor cultures were performed to test IL8 blockade and combination with anti-PD-1 therapy. Results: High IL8+ TAMs infiltration was consistently associated with ICB resistance. Transcriptomic analyses revealed that IL8+ TAMs adopt a glycolysis-associated metabolic program and are responsive to lactate, which directly promotes IL8 expression. Phenotypically, IL8+ TAMs exhibited an immunosuppressive and chemotactic profile that correlated with CD8+ T-cell dysfunction and regulatory T-cell accumulation. Importantly, ex vivo IL8 blockade alleviated CD8+ T-cell exhaustion and synergized with PD-1 inhibition to enhance antitumor immune responses. Conclusions: IL8+ TAMs represent a metabolically reprogrammed and immunosuppressive subset driving ICB resistance in ccRCC. Targeting IL8 may overcome resistance and enhance immunotherapy efficacy.","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"246 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147278628","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}
Pub Date : 2026-02-23DOI: 10.1158/1078-0432.ccr-25-1444
Monica Román-Trufero, Gavin Whitlock, Claire Seydoux, Kevin Blighe, Bianca Perfler, Armin Zebisch, Richard Butt, Matthew J. Fuchter, Holger W. Auner, Nadine Clemo
Purpose: GCN2, one of the four kinases that activate the Integrated Stress Response to maintain proteostasis, has been shown to support cancer cell growth and survival in multiple preclinical cancer models. Acute myeloid leukemia (AML) is an aggressive hematological malignancy with dismal prognosis and high relapse rates that is marked by a dependency on finely tuned proteostasis. Here, we investigate the anti-leukemic potential of a new small-molecule GCN2 inhibitor, APL-4098. Experimental design: selectivity and potency of APL-4098 were assessed using biochemical and cell-based assays. Anti-leukemic effects were evaluated ex vivo in primary patient-derived AML and in vivo using cell line-derived (CDX) and patient-derived (PDX) xenograft models. Synergy of APL-4098 and venetoclax was examined in the PDX. RNA sequencing and metabolic assays were used to explore APL-4098 mechanism of action. Results: APL-4098 exhibited nanomolar-range potency against and high selectivity for GCN2. APL-4098 showed strong anti-proliferative activity ex vivo across two independent cohorts of primary AML patient cells, including cytotoxic effects on the leukemia stem cells (LSCs) and in vivo, achieving 98% tumor growth inhibition in an AML CDX. In a PDX, APL-4098 preferentially depleted the LSC-enriched compartment and, in combination with venetoclax, reduced leukemia burden by over 98%. Transcriptomic and metabolic analyses revealed APL-4098 compromises mitochondrial function and elicits the mitochondrial unfolded protein response. Conclusions: APL-4098 is a novel, potent and selective GCN2 inhibitor with strong preclinical efficacy against AML cells, including LSCs. Our findings support APL-4098 as a promising candidate for AML treatment.
{"title":"A novel potent and selective GCN2 inhibitor, APL-4098, has anti-leukemic activity through dysregulation of mitochondrial function","authors":"Monica Román-Trufero, Gavin Whitlock, Claire Seydoux, Kevin Blighe, Bianca Perfler, Armin Zebisch, Richard Butt, Matthew J. Fuchter, Holger W. Auner, Nadine Clemo","doi":"10.1158/1078-0432.ccr-25-1444","DOIUrl":"https://doi.org/10.1158/1078-0432.ccr-25-1444","url":null,"abstract":"Purpose: GCN2, one of the four kinases that activate the Integrated Stress Response to maintain proteostasis, has been shown to support cancer cell growth and survival in multiple preclinical cancer models. Acute myeloid leukemia (AML) is an aggressive hematological malignancy with dismal prognosis and high relapse rates that is marked by a dependency on finely tuned proteostasis. Here, we investigate the anti-leukemic potential of a new small-molecule GCN2 inhibitor, APL-4098. Experimental design: selectivity and potency of APL-4098 were assessed using biochemical and cell-based assays. Anti-leukemic effects were evaluated ex vivo in primary patient-derived AML and in vivo using cell line-derived (CDX) and patient-derived (PDX) xenograft models. Synergy of APL-4098 and venetoclax was examined in the PDX. RNA sequencing and metabolic assays were used to explore APL-4098 mechanism of action. Results: APL-4098 exhibited nanomolar-range potency against and high selectivity for GCN2. APL-4098 showed strong anti-proliferative activity ex vivo across two independent cohorts of primary AML patient cells, including cytotoxic effects on the leukemia stem cells (LSCs) and in vivo, achieving 98% tumor growth inhibition in an AML CDX. In a PDX, APL-4098 preferentially depleted the LSC-enriched compartment and, in combination with venetoclax, reduced leukemia burden by over 98%. Transcriptomic and metabolic analyses revealed APL-4098 compromises mitochondrial function and elicits the mitochondrial unfolded protein response. Conclusions: APL-4098 is a novel, potent and selective GCN2 inhibitor with strong preclinical efficacy against AML cells, including LSCs. Our findings support APL-4098 as a promising candidate for AML treatment.","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"31 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147274338","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}
Pub Date : 2026-02-20DOI: 10.1158/1557-3265.sabcs25-ps2-07-26
W. McHayleh, C. Scalise, E. Kalashnikova, B. Sridhar, J. Feeney, W. Tan, A. Hsieh, A. Butskova, J. Ortega, S. Velichko, C. Palsuledesai, H. Sethi, G. Heilek, J. McKenzie, A. Rodriguez, M. Liu, M. George
Background: Circulating tumor DNA (ctDNA) is a clinically validated biomarker in breast cancer for predicting the risk of recurrence, monitoring response to neoadjuvant treatment, and detecting molecular relapse after adjuvant therapy. Signatera™ is a tumor-informed, multiplex PCR-NGS ctDNA assay that may be developed from a backbone of whole-exome sequencing (WES) or whole-genome sequencing (WGS). Early clinical validation of Signatera Genome in a pan-cancer cohort demonstrated improved performance in certain clinical scenarios. In this study, we specifically assessed the performance of the Signatera Genome assay in the surveillance setting for breast cancer. Methods: A retrospective analysis was performed using clinically annotated residual patient samples from commercial testing with WES-based Signatera. Treatment decisions and cadence of ctDNA testing were at the provider’s discretion. Signatera Genome assays were designed, consisting of 64 high-quality tumor-specific variants, from matched tumor and normal whole genome sequencing data. These assays were then used to detect ctDNA in the corresponding patients’ plasma. ctDNA levels were quantified as mean tumor molecules per mL of plasma (MTM/mL). Longitudinal blood samples represented time points after surgery/definitive treatment until recurrence or the end of follow-up. The correlation between ctDNA status and distant recurrence-free survival (DRFS) was assessed using Cox regression analysis. Results: Clinical performance of the Signatera Genome assay was assessed in a real-world cohort of 228 patients with breast cancer [triple-negative breast cancer (TNBC), n=130; HR+/HER2-, n=85; and HER2+, n=13]. In a landmark analysis, patients with ctDNA-positivity within 3 months of surgery were significantly at a higher risk of distant disease and/or molecular recurrence (HR: 8.1, 95% CI: 3.5-8.6, P <0.001). With longitudinal testing, ctDNA-positivity at any time post-definitive treatment was associated with significantly worse DRFS (HR: 22.2, 95% CI: 11.0-44.7, P <0.0001). ctDNA detection in the surveillance setting preceded clinical recurrence as confirmed by imaging with a sensitivity and specificity of 100%. Upon analyzing ctDNA dynamics, patients with unfavorable ctDNA dynamics (persistently/converted to positive) were observed to have significantly shorter DRFS than those with favorable ctDNA dynamics (serially/converted to negative) (HR with Firth’s penalized likelihood hazard model: 97.8, 95% CI: 11.5-12768.9, P <0.001). Conclusions: These data indicate the robust clinical performance of the Signatera Genome in breast cancer for detecting recurrence after surgery or definitive treatment. Prospective clinical trials are warranted to establish the clinical utility of the assay for guiding treatment decisions for patients with molecular non-radiographic recurrence. Citation Format: W. McHayleh, C. Scalise, E. Kalashnikova, B. Sridhar, J. Feeney, W. Tan, A. Hsieh, A. Butskov
背景：循环肿瘤DNA （ctDNA）是临床验证的乳腺癌生物标志物，用于预测复发风险，监测对新辅助治疗的反应，以及检测辅助治疗后的分子复发。Signatera™是一种肿瘤信息，多重PCR-NGS ctDNA检测，可以从全外显子组测序（WES）或全基因组测序（WGS）的主干发展而来。Signatera基因组在泛癌症队列中的早期临床验证在某些临床情况下显示出改善的性能。在这项研究中，我们专门评估了Signatera基因组测定在乳腺癌监测环境中的性能。方法：使用基于wes的Signatera进行商业测试的临床注释剩余患者样本进行回顾性分析。治疗决定和ctDNA检测的节奏由提供者自行决定。Signatera基因组测定由64个高质量的肿瘤特异性变异组成，来自匹配的肿瘤和正常的全基因组测序数据。这些检测随后被用于检测相应患者血浆中的ctDNA。ctDNA水平被量化为每mL血浆中平均肿瘤分子数（MTM/mL）。纵向血液样本代表手术/最终治疗后的时间点，直到复发或随访结束。采用Cox回归分析评估ctDNA状态与远期无复发生存期（DRFS）的相关性。结果：Signatera基因组测定在228例乳腺癌患者(三阴性乳腺癌（TNBC）， n=130；人力资源+ / HER2 - n = 85;HER2+, n=13]。在一项具有里程碑意义的分析中，手术后3个月内ctdna阳性的患者发生远处疾病和/或分子复发的风险明显更高（HR: 8.1, 95% CI: 3.5-8.6, P <0.001）。纵向测试显示，确诊治疗后任何时间的ctdna阳性与DRFS显著恶化相关（HR: 22.2, 95% CI: 11.0-44.7, P <0.0001）。ctDNA检测在临床复发之前进行监测，经影像学证实其敏感性和特异性为100%。通过分析ctDNA动力学，观察到不良ctDNA动力学（持续/转化为阳性）的患者的DRFS明显短于良好ctDNA动力学（连续/转化为阴性）的患者（Firth的惩罚可能性风险模型的HR: 97.8, 95% CI: 11.5-12768.9, P <0.001）。结论：这些数据表明Signatera基因组在乳腺癌手术或最终治疗后检测复发方面具有强大的临床性能。有必要进行前瞻性临床试验，以确定该检测方法的临床实用性，以指导分子非放射学复发患者的治疗决策。引用格式：W. McHayleh， C. Scalise， E. Kalashnikova， B. Sridhar， J. Feeney， W. Tan， A. Hsieh， A. Butskova， J. Ortega， S. Velichko， C. Palsuledesai， H. Sethi， G. Heilek， J. McKenzie， A. Rodriguez， M. Liu， M. George。Signatera基因组测定预测乳腺癌复发的临床应用[摘要]。摘自：《2025年圣安东尼奥乳腺癌研讨会论文集》；2025年12月9-12日；费城（PA）： AACR；临床癌症杂志2026；32（4增刊）：nr PS2-07-26。
{"title":"Abstract PS2-07-26: Clinical performance of Signatera Genome assay for predicting recurrence in patients with breast cancer","authors":"W. McHayleh, C. Scalise, E. Kalashnikova, B. Sridhar, J. Feeney, W. Tan, A. Hsieh, A. Butskova, J. Ortega, S. Velichko, C. Palsuledesai, H. Sethi, G. Heilek, J. McKenzie, A. Rodriguez, M. Liu, M. George","doi":"10.1158/1557-3265.sabcs25-ps2-07-26","DOIUrl":"https://doi.org/10.1158/1557-3265.sabcs25-ps2-07-26","url":null,"abstract":"Background: Circulating tumor DNA (ctDNA) is a clinically validated biomarker in breast cancer for predicting the risk of recurrence, monitoring response to neoadjuvant treatment, and detecting molecular relapse after adjuvant therapy. Signatera™ is a tumor-informed, multiplex PCR-NGS ctDNA assay that may be developed from a backbone of whole-exome sequencing (WES) or whole-genome sequencing (WGS). Early clinical validation of Signatera Genome in a pan-cancer cohort demonstrated improved performance in certain clinical scenarios. In this study, we specifically assessed the performance of the Signatera Genome assay in the surveillance setting for breast cancer. Methods: A retrospective analysis was performed using clinically annotated residual patient samples from commercial testing with WES-based Signatera. Treatment decisions and cadence of ctDNA testing were at the provider’s discretion. Signatera Genome assays were designed, consisting of 64 high-quality tumor-specific variants, from matched tumor and normal whole genome sequencing data. These assays were then used to detect ctDNA in the corresponding patients’ plasma. ctDNA levels were quantified as mean tumor molecules per mL of plasma (MTM/mL). Longitudinal blood samples represented time points after surgery/definitive treatment until recurrence or the end of follow-up. The correlation between ctDNA status and distant recurrence-free survival (DRFS) was assessed using Cox regression analysis. Results: Clinical performance of the Signatera Genome assay was assessed in a real-world cohort of 228 patients with breast cancer [triple-negative breast cancer (TNBC), n=130; HR+/HER2-, n=85; and HER2+, n=13]. In a landmark analysis, patients with ctDNA-positivity within 3 months of surgery were significantly at a higher risk of distant disease and/or molecular recurrence (HR: 8.1, 95% CI: 3.5-8.6, P &lt;0.001). With longitudinal testing, ctDNA-positivity at any time post-definitive treatment was associated with significantly worse DRFS (HR: 22.2, 95% CI: 11.0-44.7, P &lt;0.0001). ctDNA detection in the surveillance setting preceded clinical recurrence as confirmed by imaging with a sensitivity and specificity of 100%. Upon analyzing ctDNA dynamics, patients with unfavorable ctDNA dynamics (persistently/converted to positive) were observed to have significantly shorter DRFS than those with favorable ctDNA dynamics (serially/converted to negative) (HR with Firth’s penalized likelihood hazard model: 97.8, 95% CI: 11.5-12768.9, P &lt;0.001). Conclusions: These data indicate the robust clinical performance of the Signatera Genome in breast cancer for detecting recurrence after surgery or definitive treatment. Prospective clinical trials are warranted to establish the clinical utility of the assay for guiding treatment decisions for patients with molecular non-radiographic recurrence. Citation Format: W. McHayleh, C. Scalise, E. Kalashnikova, B. Sridhar, J. Feeney, W. Tan, A. Hsieh, A. Butskov","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"56 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146230763","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}
Pub Date : 2026-02-20DOI: 10.1158/1557-3265.sabcs25-ps2-09-24
T. Sharma, A. Nasrazadani, W. Ma, J. Chen, M. Kai, B. Lim, M. Lewis, L. Dobrolecki, N. Kotlov, O. Baranov, A. Evdokimova, F. Paradiso, M. Hensley, The MDACC Inflammatory Breast Cancer Team, R. Layman, W. Woodward
Background: ER+ inflammatory breast cancer (IBC) is under-appreciated and under-investigated as an aggressive subset of ER+ breast cancer, despite having rates of metastasis comparable to triple negative (TN) IBC. Recent genome-wide profiling of tumors from patients with metastatic breast cancer has shown that IBC samples have a higher frequency of AURKA amplification than non-IBC samples. Our pilot studies in IBC validate these findings and suggest AURKA is amplified in TNIBC. We hypothesize that Aurora Kinase A (AURKA) is a viable therapeutic target in metastatic IBC and in particular ER+ IBC due synthetic lethality with ARID1A and SMARCA4 in IBC. Methods: We reviewed RNA and DNA data from clinically ordered Boston Gene tumor assays for IBC versus non-IBC breast cancer cases at MDACC. Using ER- IBC cell lines we examined the protein expression of AURKA and tested Alisertib efficacy was tested using the crystal violet staining in IBC cell lines. Senescence was examined using B-gal and ELISA assay. ER+ patient derived organoids were established from ER+PDX as an ER+ IBC model. Results: We previously demonstrated using a large multi-institutional IBC data set including 137 IBC patient tissues analyzed using Affymetrix gene expression arrays, no clear clustering among ER response genes by ER+ subtypes and high AURKA expression in both ER+ and ER- cases. Comparing 21 ER+ IBC to 432 ER+ NON-IBC patient samples, we find AURKA amplified in 14 cases, co-occurrence of AURKA amplification and proposed synthetic lethal targets in 14 cases, and a statistically significant inverse relationship between AURKA and SMARCA4 in IBC. In ER- IBC compared to non-IBC there is no enrichment in AURKA amplification in IBC, but it is highly prevalent occurring in 16 cases out of 28 and with co-occurrence of proposed synthetic lethal gene alterations in 15 cases. Expression of AURKA by immunoblotting in IBC cell lines demonstrates AURKA expression in four IBC cell lines, including two HER2+ (IBC3 and KPL4) and two triple negative (A3250 and SUM149). Higher doses promote reversible senescence assayed by SA-βgal assay and high IL6 by ELISA validated senescence associated secretory phenotype. In collaboration with the PDX program at Baylor College of Medicine led by Dr. Michael Lewis our team has developed a patient derived xenograft (PDX) from an ER+ IBC patient and passaged patient derived organoids for alisertib assessment in a novel ER_ IBC model. Conclusions: AURKA is commonly amplified in IBC and often associated with gene alterations that may predict synthetic lethality to AURKA targeting. In ER+ IBC AURKA amplification is inversely correlated with SMARCA4. We have characterized IBC models with high AURKA expression and demonstrated sensitivity to AURKA inhibition but senescence at higher doses which may provide a direction for targeting resistance or escape. Further studies in ER+ organoids are ongoing. Citation Format: T. Sharma, A. Nasrazadani, W. Ma, J. Chen, M. Ka
背景：ER+炎性乳腺癌（IBC）作为ER+乳腺癌的侵袭性亚群，尽管其转移率与三阴性（TN） IBC相当，但未得到充分的重视和研究。最近对转移性乳腺癌患者肿瘤的全基因组分析表明，IBC样本的AURKA扩增频率高于非IBC样本。我们在IBC中的试点研究证实了这些发现，并表明AURKA在tnbc中被放大。我们假设极光激酶A （AURKA）是转移性IBC，特别是ER+ IBC的可行治疗靶点，因为ARID1A和SMARCA4在IBC中具有合成致死率。方法：我们回顾了MDACC中IBC与非IBC乳腺癌患者的临床订购波士顿基因肿瘤检测的RNA和DNA数据。用ER- IBC细胞株检测AURKA蛋白表达，并用结晶紫染色法检测Alisertib在IBC细胞株中的药效。采用B-gal和ELISA法检测衰老情况。ER+PDX建立ER+患者源性类器官作为ER+ IBC模型。结果：我们之前使用Affymetrix基因表达阵列分析了包括137名IBC患者组织在内的大型多机构IBC数据集，发现ER+亚型之间没有明显的ER反应基因聚类，ER+和ER-病例中AURKA的表达都很高。比较21例ER+ IBC和432例ER+ NON-IBC患者样本，我们发现AURKA扩增在14例中，AURKA扩增与提出的合成致死靶点同时出现在14例中，AURKA与SMARCA4在IBC中呈显著负相关。在ER- IBC中，与非IBC相比，IBC中的AURKA扩增没有富集，但在28例中有16例高度普遍存在，并且在15例中合并了拟议的合成致死基因改变。通过免疫印迹法在IBC细胞系中表达AURKA，发现AURKA在4种IBC细胞系中表达，包括2种HER2+细胞系（IBC3和KPL4）和2种三阴性细胞系（A3250和SUM149）。高剂量的SA-βgal实验和ELISA检测的高il - 6证实了衰老相关的分泌表型。我们的团队与贝勒医学院（Baylor College of Medicine）由Michael Lewis博士领导的PDX项目合作，开发了一种来自ER+ IBC患者和传代患者来源的类器官的患者来源的异种移植物（PDX），用于在一种新的ER_ IBC模型中进行alisertib评估。结论：AURKA通常在IBC中扩增，并且通常与基因改变相关，这可能预测AURKA靶向的合成致死率。在ER+ IBC中，AURKA扩增与SMARCA4呈负相关。我们已经对AURKA高表达的IBC模型进行了表征，并显示出对AURKA抑制的敏感性，但在高剂量下会衰老，这可能为靶向抗性或逃逸提供了方向。ER+类器官的进一步研究正在进行中。引用格式：T. Sharma， A. Nasrazadani， W. Ma， J. Chen， M. Kai， B. Lim， M. Lewis， L. Dobrolecki， N. Kotlov， O. Baranov， A. Evdokimova， F. Paradiso， M. Hensley， MDACC炎性乳腺癌小组，R. Layman， W. Woodward。极光激酶A (Aurora Kinase A， AURKA): ER+炎性乳腺癌的新药物靶点[摘要]。摘自：《2025年圣安东尼奥乳腺癌研讨会论文集》；2025年12月9-12日；费城（PA）： AACR；临床癌症杂志2026；32（4增刊）：nr PS2-09-24。
{"title":"Abstract PS2-09-24: Aurora Kinase A (AURKA) a new druggable target in ER+ Inflammatory Breast Cancer","authors":"T. Sharma, A. Nasrazadani, W. Ma, J. Chen, M. Kai, B. Lim, M. Lewis, L. Dobrolecki, N. Kotlov, O. Baranov, A. Evdokimova, F. Paradiso, M. Hensley, The MDACC Inflammatory Breast Cancer Team, R. Layman, W. Woodward","doi":"10.1158/1557-3265.sabcs25-ps2-09-24","DOIUrl":"https://doi.org/10.1158/1557-3265.sabcs25-ps2-09-24","url":null,"abstract":"Background: ER+ inflammatory breast cancer (IBC) is under-appreciated and under-investigated as an aggressive subset of ER+ breast cancer, despite having rates of metastasis comparable to triple negative (TN) IBC. Recent genome-wide profiling of tumors from patients with metastatic breast cancer has shown that IBC samples have a higher frequency of AURKA amplification than non-IBC samples. Our pilot studies in IBC validate these findings and suggest AURKA is amplified in TNIBC. We hypothesize that Aurora Kinase A (AURKA) is a viable therapeutic target in metastatic IBC and in particular ER+ IBC due synthetic lethality with ARID1A and SMARCA4 in IBC. Methods: We reviewed RNA and DNA data from clinically ordered Boston Gene tumor assays for IBC versus non-IBC breast cancer cases at MDACC. Using ER- IBC cell lines we examined the protein expression of AURKA and tested Alisertib efficacy was tested using the crystal violet staining in IBC cell lines. Senescence was examined using B-gal and ELISA assay. ER+ patient derived organoids were established from ER+PDX as an ER+ IBC model. Results: We previously demonstrated using a large multi-institutional IBC data set including 137 IBC patient tissues analyzed using Affymetrix gene expression arrays, no clear clustering among ER response genes by ER+ subtypes and high AURKA expression in both ER+ and ER- cases. Comparing 21 ER+ IBC to 432 ER+ NON-IBC patient samples, we find AURKA amplified in 14 cases, co-occurrence of AURKA amplification and proposed synthetic lethal targets in 14 cases, and a statistically significant inverse relationship between AURKA and SMARCA4 in IBC. In ER- IBC compared to non-IBC there is no enrichment in AURKA amplification in IBC, but it is highly prevalent occurring in 16 cases out of 28 and with co-occurrence of proposed synthetic lethal gene alterations in 15 cases. Expression of AURKA by immunoblotting in IBC cell lines demonstrates AURKA expression in four IBC cell lines, including two HER2+ (IBC3 and KPL4) and two triple negative (A3250 and SUM149). Higher doses promote reversible senescence assayed by SA-βgal assay and high IL6 by ELISA validated senescence associated secretory phenotype. In collaboration with the PDX program at Baylor College of Medicine led by Dr. Michael Lewis our team has developed a patient derived xenograft (PDX) from an ER+ IBC patient and passaged patient derived organoids for alisertib assessment in a novel ER_ IBC model. Conclusions: AURKA is commonly amplified in IBC and often associated with gene alterations that may predict synthetic lethality to AURKA targeting. In ER+ IBC AURKA amplification is inversely correlated with SMARCA4. We have characterized IBC models with high AURKA expression and demonstrated sensitivity to AURKA inhibition but senescence at higher doses which may provide a direction for targeting resistance or escape. Further studies in ER+ organoids are ongoing. Citation Format: T. Sharma, A. Nasrazadani, W. Ma, J. Chen, M. Ka","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"5 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146230793","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}
Pub Date : 2026-02-20DOI: 10.1158/1557-3265.sabcs25-ps3-04-25
E. Kim, I. Do, S. Chae
Background Tumor-infiltrating lymphocytes (TILs) have been recognized as prognostic and predictive biomarkers in breast cancer. However, challenges such as interobserver variability and lack of standardized cut-off values have limited their clinical implementation. Recent advancements in artificial intelligence (AI)-based pathology have shown potential to enhance reproducibility and objectivity in TIL quantification. Concurrently, circulating tumor DNA (ctDNA) has emerged as a minimally invasive biomarker capable of detecting treatment response after neoadjuvant chemotherapy (NAC). Objectives This study aims to: (1) evaluate the predictive value of AI-quantified stromal TILs from H&E-stained slides; and (2) validate the clinical utility of ctDNA-based biomarkers for detection of responses in breast cancer patients after NAC. Methods TILs were assessed from pre-treatment tumor H&E slides using Lunit SCOPE IO, a validated AI-powered WSI analysis tool. Immune phenotypes were classified as inflamed, immune-excluded, or desert. PD-L1 expression was evaluated using PD-L1 IHC 22C3 pharmDx. TIL cut-off was set at 30%, Formalin-fixed paraffin-embedded samples (FFPEs) were obtained from biopsy tissue, and plasma samples were collected at baseline, pre-surgery (after NAC). Forty-seven breast cancer-related genes were analyzed using next-generation sequencing. The diagnostic performance of ctDNA was evaluated, and logistic regression analyses were conducted to assess the impact of clinical and molecular factors on ctDNA status. Parallel plasma samples were collected at predefined intervals for ctDNA extraction and sequencing using a customized Breast NGS panel targeting 157 hotspot mutations across 12 genes. Mutation validation was performed using ddPCR. Preliminary Results A total of 101 patients with early breast cancer were enrolled. The most frequently identified gene was TP53 (FFPE, 66.7%; ctDNA, 46.4%), followed by PIK3CA (FFPE, 36.2%;ctDNA, 17.4%). The triple-negative breast cancer (TNBC) subtype exhibited the strongest association with ctDNA detection (odds ratio [OR] 209.50, p = 0.005) in multivariate analysis. Patients with inflamed TIL phenotype at diagnosis and ctDNA clearance after NAC had higher pathological complete response (pCR) rate (38.5% vs. 11.1%, p = 0.238). Conclusion Our integrated approach using AI-based TIL quantification and ctDNA analysis using NGS and ddPCR provides a feasible and sensitive approach for NAC response in breast cancer patients. These findings support the clinical utility of combining digital pathology and liquid biopsy for treatment monitoring and risk stratification in conjunction with precision oncology. Citation Format: E. Kim, I. Do, S. Chae. Artificial intelligence (AI) based image analysis of PD-L1, TIL, immune signature and ctDNA for prediction of response to neoadjuvant chemotherapy in breast cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Anton
肿瘤浸润淋巴细胞（til）已被认为是乳腺癌的预后和预测性生物标志物。然而，诸如观察者之间的差异和缺乏标准化的临界值等挑战限制了它们的临床应用。基于人工智能（AI）的病理学的最新进展显示出增强TIL量化的可重复性和客观性的潜力。同时，循环肿瘤DNA （ctDNA）已成为一种微创生物标志物，能够检测新辅助化疗（NAC）后的治疗反应。本研究旨在：(1)评估ai量化H&； e染色载玻片间质TILs的预测价值；(2)验证基于ctdna的生物标志物在乳腺癌患者NAC后反应检测中的临床应用。方法使用Lunit SCOPE IO（一种经过验证的人工智能驱动的WSI分析工具）对治疗前肿瘤H&；E切片进行TILs评估。免疫表型分为炎症型、免疫排斥型和沙漠型。采用PD-L1 IHC 22C3 pharmDx检测PD-L1表达。TIL截止值设为30%，从活检组织中获得福尔马林固定石蜡包埋样本（FFPEs），并在基线、术前（NAC后）收集血浆样本。使用下一代测序技术分析了47个乳腺癌相关基因。评估ctDNA的诊断效能，并进行logistic回归分析，评估临床和分子因素对ctDNA状态的影响。在预先设定的时间间隔内收集平行血浆样本，使用定制的Breast NGS面板针对12个基因的157个热点突变进行ctDNA提取和测序。使用ddPCR进行突变验证。初步结果共纳入101例早期乳腺癌患者。最常发现的基因是TP53 (FFPE, 66.7%; ctDNA, 46.4%)，其次是PIK3CA （FFPE, 36.2%;ctDNA, 17.4%）。在多因素分析中，三阴性乳腺癌（TNBC）亚型与ctDNA检测的相关性最强（优势比[OR] 209.50, p = 0.005）。诊断时TIL表型为炎症的患者和NAC后ctDNA清除的患者病理完全缓解（pCR）率更高（38.5%比11.1%,p = 0.238）。结论基于人工智能的TIL定量与基于NGS和ddPCR的ctDNA分析相结合的方法为乳腺癌患者NAC反应提供了一种可行且敏感的方法。这些发现支持将数字病理学和液体活检结合精确肿瘤学进行治疗监测和风险分层的临床应用。引文格式：E. Kim， I. Do， S. Chae。基于人工智能（AI）的PD-L1、TIL、免疫特征和ctDNA图像分析预测乳腺癌对新辅助化疗的反应[摘要]。摘自：《2025年圣安东尼奥乳腺癌研讨会论文集》；2025年12月9-12日；费城（PA）： AACR；临床癌症杂志2026；32（4增刊）：nr PS3-04-25。
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Pub Date : 2026-02-20DOI: 10.1158/1557-3265.sabcs25-ps2-08-02
R. L. Mahtani, S. C. Smith, S. M. Swain, S. Wu, J. R. Klemp, M. Benrashid, S. Puri, T. Nicolaides, J. Xiu, M. Oberley, M. Chaki, G. Sledge
Introduction: PTEN, a key negative regulator of the PI3K/AKT signaling pathway, can get inactivated in hormone receptor positive (HR+), HER2-negative (HER2−) metastatic breast cancer (mBC). While genomic alterations can inactivate PTEN, a subset of tumors lose PTEN protein expression without any PTEN genomic alterations, resulting in a discordance between genomic and protein-based test results. The CAPItello-291 trial (NCT04305496) led to the approval of capivasertib (AKT inhibitor) in combination with fulvestrant in patients with HR+/HER2- mBC with alterations in PIK3CA, AKT1, and/or PTEN. Here, we report a prespecified exploratory analysis evaluating the concordance between PTEN loss of expression by IHC and its genomic alteration by NGS, as well as the respective co-occurrences with PIK3CA and AKT1 mutations. Methods: 2,716 breast tumors underwent comprehensive tumor profiling at Caris Life Sciences (Phoenix, AZ) between August 2024 to June 25, 2025. All tumors were identified as HR positive and HER2 negative by a combination of IHC and CISH based on ASCO/CAP guidelines. Gene mutations were determined by Whole Exome Sequencing. PTEN IHC was performed using 6H2.1 antibody and scored by board-certified pathologists; PTEN loss was defined as complete absence of staining (0+, 0%). Results: Among the 2,716 tumors, 196 (7.21%) demonstrated PTEN loss by IHC. The overall concordance between PTEN IHC loss and PTEN NGS genomic alterations was 92.9%. In the absence of a definitive reference standard, the positive percent agreement was 52%; negative percent agreement was 96%. Among the discordant cases, two distinct patterns were observed. In tumors with PTEN loss by IHC but wild-type (wt) by NGS (N=112), PIK3CA and AKT1 mutation rates were 36.6% (41/112) and 0.89% (1/112), respectively. Conversely, in tumors with intact PTEN by IHC but PTEN alterations (alt) by NGS (N=77), PIK3CA and AKT1 mutation rates were 49.4% (38/77) and 1.3% (1/77), respectively. Notably, 5.41% (70/1293) of tumors that were wild-type for PTEN, PIK3CA and AKT1 by NGS demonstrated PTEN loss by IHC suggesting PI3K pathway activation that would have been missed without IHC testing. Conclusion: To our knowledge, this is the largest study highlighting a substantial discordance between PTEN expression by IHC and genomic alterations by NGS in HR+/HER2− mBC. Our results underscore the necessity for a multimodal approach to patient selection for markers of treatment resistance and suggest that PTEN IHC may identify additional patients with PI3K/AKT pathway activation. Citation Format: R. L. Mahtani, S. C. Smith, S. M. Swain, S. Wu, J. R. Klemp, M. Benrashid, S. Puri, T. Nicolaides, J. Xiu, M. Oberley, M. Chaki, G. Sledge. Comprehensive Characterization of PTEN loss by IHC and PTEN alteration by NGS in Metastatic HR-Positive, HER2-Negative Breast Cancer-- An Exploratory Analysis of Biomarker Concordance and Co-Occurrence [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2
PTEN是PI3K/AKT信号通路的关键负调控因子，在激素受体阳性（HR+）、HER2阴性（HER2−）转移性乳腺癌（mBC）中可失活。虽然基因组改变可以使PTEN失活，但一部分肿瘤在没有任何PTEN基因组改变的情况下失去PTEN蛋白表达，从而导致基因组和基于蛋白质的测试结果之间的不一致。CAPItello-291试验（NCT04305496）批准了capivasertib （AKT抑制剂）与氟维司汀联合用于PIK3CA、AKT1和/或PTEN改变的HR+/HER2- mBC患者。在这里，我们报告了一项预先指定的探索性分析，评估了IHC导致的PTEN表达缺失与NGS导致的PTEN基因组改变之间的一致性，以及PTEN与PIK3CA和AKT1突变的共同发生。方法：从2024年8月到2025年6月25日，在Caris生命科学公司（Phoenix， AZ）对2716例乳腺肿瘤进行了全面的肿瘤分析。所有肿瘤均根据ASCO/CAP指南通过IHC和CISH联合鉴定为HR阳性和HER2阴性。基因突变通过全外显子组测序测定。采用6H2.1抗体进行PTEN IHC检测，由专业病理医师评分；PTEN损失定义为完全没有染色（0+,0%）。结果：2716例肿瘤中，196例（7.21%）经免疫组化证实PTEN丢失。PTEN IHC缺失与PTEN NGS基因组改变的总体一致性为92.9%。在没有明确参考标准的情况下，阳性满意率为52%；96%的人表示不同意。在不一致的病例中，观察到两种不同的模式。在IHC缺失PTEN而NGS缺失野生型（wt）的肿瘤（N=112）中，PIK3CA和AKT1的突变率分别为36.6%（41/112）和0.89%（1/112）。相反，在IHC中PTEN完整但NGS改变PTEN （alt）的肿瘤中（N=77）， PIK3CA和AKT1的突变率分别为49.4%（38/77）和1.3%（1/77）。值得注意的是，5.41%（70/1293）的NGS检测为PTEN、PIK3CA和AKT1野生型的肿瘤显示IHC导致PTEN缺失，这表明如果不进行IHC检测，PI3K通路的激活可能会被遗漏。结论：据我们所知，这是最大规模的研究，强调了在HR+/HER2 - mBC中IHC的PTEN表达和NGS的基因组改变之间的实质性不一致。我们的研究结果强调了采用多模式方法选择治疗耐药标志物的必要性，并表明PTEN免疫组化可能会识别出PI3K/AKT通路激活的其他患者。引用格式：R. L. Mahtani， S. C. Smith， S. M. Swain， S. Wu， J. R. Klemp， M. Benrashid， S. Puri， T. Nicolaides， J. Xiu， M. Oberley， M. Chaki， G. Sledge转移性hr阳性、her2阴性乳腺癌中IHC导致的PTEN缺失和NGS导致的PTEN改变的综合表征——生物标志物一致性和共现性的探索性分析[摘要]。摘自：《2025年圣安东尼奥乳腺癌研讨会论文集》；2025年12月9-12日；费城（PA）： AACR；临床癌症杂志2026；32（4增刊）：nr PS2-08-02。
{"title":"Abstract PS2-08-02: Comprehensive Characterization of PTEN loss by IHC and PTEN alteration by NGS in Metastatic HR-Positive, HER2-Negative Breast Cancer-- An Exploratory Analysis of Biomarker Concordance and Co-Occurrence","authors":"R. L. Mahtani, S. C. Smith, S. M. Swain, S. Wu, J. R. Klemp, M. Benrashid, S. Puri, T. Nicolaides, J. Xiu, M. Oberley, M. Chaki, G. Sledge","doi":"10.1158/1557-3265.sabcs25-ps2-08-02","DOIUrl":"https://doi.org/10.1158/1557-3265.sabcs25-ps2-08-02","url":null,"abstract":"Introduction: PTEN, a key negative regulator of the PI3K/AKT signaling pathway, can get inactivated in hormone receptor positive (HR+), HER2-negative (HER2−) metastatic breast cancer (mBC). While genomic alterations can inactivate PTEN, a subset of tumors lose PTEN protein expression without any PTEN genomic alterations, resulting in a discordance between genomic and protein-based test results. The CAPItello-291 trial (NCT04305496) led to the approval of capivasertib (AKT inhibitor) in combination with fulvestrant in patients with HR+/HER2- mBC with alterations in PIK3CA, AKT1, and/or PTEN. Here, we report a prespecified exploratory analysis evaluating the concordance between PTEN loss of expression by IHC and its genomic alteration by NGS, as well as the respective co-occurrences with PIK3CA and AKT1 mutations. Methods: 2,716 breast tumors underwent comprehensive tumor profiling at Caris Life Sciences (Phoenix, AZ) between August 2024 to June 25, 2025. All tumors were identified as HR positive and HER2 negative by a combination of IHC and CISH based on ASCO/CAP guidelines. Gene mutations were determined by Whole Exome Sequencing. PTEN IHC was performed using 6H2.1 antibody and scored by board-certified pathologists; PTEN loss was defined as complete absence of staining (0+, 0%). Results: Among the 2,716 tumors, 196 (7.21%) demonstrated PTEN loss by IHC. The overall concordance between PTEN IHC loss and PTEN NGS genomic alterations was 92.9%. In the absence of a definitive reference standard, the positive percent agreement was 52%; negative percent agreement was 96%. Among the discordant cases, two distinct patterns were observed. In tumors with PTEN loss by IHC but wild-type (wt) by NGS (N=112), PIK3CA and AKT1 mutation rates were 36.6% (41/112) and 0.89% (1/112), respectively. Conversely, in tumors with intact PTEN by IHC but PTEN alterations (alt) by NGS (N=77), PIK3CA and AKT1 mutation rates were 49.4% (38/77) and 1.3% (1/77), respectively. Notably, 5.41% (70/1293) of tumors that were wild-type for PTEN, PIK3CA and AKT1 by NGS demonstrated PTEN loss by IHC suggesting PI3K pathway activation that would have been missed without IHC testing. Conclusion: To our knowledge, this is the largest study highlighting a substantial discordance between PTEN expression by IHC and genomic alterations by NGS in HR+/HER2− mBC. Our results underscore the necessity for a multimodal approach to patient selection for markers of treatment resistance and suggest that PTEN IHC may identify additional patients with PI3K/AKT pathway activation. Citation Format: R. L. Mahtani, S. C. Smith, S. M. Swain, S. Wu, J. R. Klemp, M. Benrashid, S. Puri, T. Nicolaides, J. Xiu, M. Oberley, M. Chaki, G. Sledge. Comprehensive Characterization of PTEN loss by IHC and PTEN alteration by NGS in Metastatic HR-Positive, HER2-Negative Breast Cancer-- An Exploratory Analysis of Biomarker Concordance and Co-Occurrence [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2","PeriodicalId":10279,"journal":{"name":"Clinical Cancer Research","volume":"46 1 1","pages":""},"PeriodicalIF":11.5,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146230834","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}
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