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Lai YJ, Wang LJ, Yasaka TM, Shin Y, Ning M, Tan Y, Shih CH, Guo Y, Chen PY, Galloway H, Liu Z, Das A, Tseng GC, Monga SP, Huang Y, Chiu YC. Inferring Drug-Gene Relationships in Cancer Using Literature-Augmented Large Language Models. CANCER RESEARCH COMMUNICATIONS 2025; 5:706-718. [PMID: 40293950 PMCID: PMC12036822 DOI: 10.1158/2767-9764.crc-25-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2025] [Revised: 03/17/2025] [Accepted: 04/15/2025] [Indexed: 04/30/2025]
Abstract
SIGNIFICANCE This study presents a novel approach that integrates LLMs with real-time biomedical literature to uncover drug-gene relationships, transforming how cancer researchers identify therapeutic targets, repurpose drugs, and interpret complex molecular interactions. GeneRxGPT, our user-friendly tool, enables researchers to leverage this approach without requiring computational expertise.
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Affiliation(s)
- Ying-Ju Lai
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Biostatistics and Health Data Science, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Li-Ju Wang
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Tyler M. Yasaka
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yuna Shin
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Michael Ning
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Computer Science, The University of Texas at Austin, Austin, Texas
| | - Yanhao Tan
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Chien-Hung Shih
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yibing Guo
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Po-Yuan Chen
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Hugh Galloway
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Zhentao Liu
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Arun Das
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - George C. Tseng
- Department of Biostatistics and Health Data Science, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Satdarshan P. Monga
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Organ Pathobiology and Therapeutics Institute, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yufei Huang
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yu-Chiao Chiu
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Kınıkoğlu O, Odabas H, Altıntaş YE, Yıldız A, Çakan B, Akdağ G, Yıldırım S, Bal H, Kaya T, Tünbekici S, Işık D, Başoğlu T, Yıldırım ME, Turan N. Combining Endocrine Therapy with Trastuzumab Emtansine Improves Progression-Free Survival and Overall Survival in HER2-Positive, Hormone Receptor-Positive Metastatic Breast Cancer. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:951. [PMID: 38929568 PMCID: PMC11205527 DOI: 10.3390/medicina60060951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Background and Objectives: Patients with human epidermal growth factor receptor 2 (HER2) -positive, hormone receptor-positive (HR-positive) metastatic breast cancer (MBC) usually undergo trastuzumab emtansine (T-DM1) therapy in subsequent lines. Combining endocrine therapy (ET) with T-DM1 can improve treatment outcomes in this subtype. Therefore, this study aimed to investigate the benefits of using T-DM1 with ET in HER2-positive and HR-positive MBC. This study was the first to investigate the benefits of combining ET with T-DM1. Material and Methods: This study analyzed the medical records of patients with HER2-positive and HR-positive MBC who were treated with T-DM1 from June 2010 to December 2021. The patients were divided into groups based on whether they received concomitant ET with T-DM1. The primary endpoint was to determine the progression-free survival (PFS), while the secondary endpoints were overall survival (OS), objective response rate, and safety of the treatment. Results: Our analysis examined 88 patients, of whom 32 (36.4%) were treated with T-DM1 in combination with ET. The combination therapy showed a significant improvement in median PFS (15.4 vs. 6.4 months; p = 0.00004) and median OS (35.0 vs. 23.1 months; p = 0.026) compared to T-DM1 alone. The ORR was also higher in the combination group (65.6% vs. 29.3%; p = 0.026). Patients treated with pertuzumab priorly had reduced median PFS on T-DM1 compared to those who were not treated with pertuzumab (11.7 vs. 5.4 months, respectively; p < 0.01). T-DM1 demonstrated better median PFS in HER2 3+ patients compared to HER2 2+ patients, with an amplification ratio of >2.0 (10.8 vs 5.8 months, respectively; p = 0.049). The safety profiles were consistent with previous T-DM1 studies. Conclusions: The combination of T-DM1 with ET can significantly improve PFS and OS in patients with HER2-positive and HR-positive MBC. Our study suggests that prior pertuzumab treatment plus trastuzumab treatment might decrease T-DM1 efficacy.
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Affiliation(s)
- Oğuzcan Kınıkoğlu
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Hatice Odabas
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Yunus Emre Altıntaş
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Anıl Yıldız
- Department of Medical Oncology, Istanbul University Oncology Institute, Istanbul 34093, Turkey;
| | - Burçin Çakan
- Department of Medical Oncology, Bağcılar Research and Training Hospital, Istanbul 34212, Turkey;
| | - Goncagül Akdağ
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Sedat Yıldırım
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Hamit Bal
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Tuğba Kaya
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Salih Tünbekici
- Department of Medical Oncology, Ege University Faculty of Medicine, Izmir 35100, Turkey;
| | - Deniz Işık
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Tuğba Başoğlu
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Mahmut Emre Yıldırım
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
| | - Nedim Turan
- Department of Medical Oncology, Health Science University, Kartal Dr. Lütfi Kirdar City Hospital, Istanbul 34865, Turkey; (H.O.); (Y.E.A.); (G.A.); (S.Y.); (H.B.); (T.K.); (D.I.); (T.B.); (M.E.Y.); (N.T.)
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Kuemmel S, Harper-Wynne C, Park YH, Franke F, de Laurentiis M, Schumacher-Wulf E, Eiger D, Heeson S, Cardona A, Özyilkan Ö, Morales-Vàsquez F, Metcalfe C, Hafner M, Restuccia E, O'Shaughnessy J. heredERA Breast Cancer: a phase III, randomized, open-label study evaluating the efficacy and safety of giredestrant plus the fixed-dose combination of pertuzumab and trastuzumab for subcutaneous injection in patients with previously untreated HER2-positive, estrogen receptor-positive locally advanced or metastatic breast cancer. BMC Cancer 2024; 24:641. [PMID: 38789924 PMCID: PMC11127459 DOI: 10.1186/s12885-024-12179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/25/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND HER2-positive, estrogen receptor-positive breast cancer (HER2+, ER+ BC) is a distinct disease subtype associated with inferior response to chemotherapy plus HER2-targeted therapy compared with HER2+, ER-negative BC. Bi-directional crosstalk leads to cooperation of the HER2 and ER pathways that may drive treatment resistance; thus, simultaneous co-targeting may optimize treatment impact and survival outcomes in patients with HER2+, ER+ BC. First-line (1L) treatment for patients with HER2+ metastatic BC (mBC) is pertuzumab, trastuzumab, and taxane chemotherapy. In clinical practice, dual HER2 blockade plus a fixed number of chemotherapy cycles are given as induction therapy to maximize tumor response, with subsequent HER2-targeted maintenance treatment given as a more tolerable regimen for long-term disease control. For patients whose tumors co-express ER, maintenance endocrine therapy (ET) can be added, but uptake varies due to lack of data from randomized clinical trials investigating the superiority of maintenance ET plus dual HER2 blockade versus dual HER2 blockade alone. Giredestrant, a novel oral selective ER antagonist and degrader, shows promising clinical activity and manageable safety across phase I-II trials of patients with ER+, HER2-negative BC, with therapeutic potential in those with HER2 co-expression. METHODS This phase III, randomized, open-label, two-arm study aims to recruit 812 patients with HER2+, ER+ locally advanced (LA)/mBC into the induction phase (fixed-dose combination of pertuzumab and trastuzumab for subcutaneous injection [PH FDC SC] plus a taxane) to enable 730 patients to be randomized 1:1 to the maintenance phase (giredestrant plus PH FDC SC or PH FDC SC [plus optional ET]), stratified by disease site (visceral versus non-visceral), type of LA/metastatic presentation (de novo versus recurrent), best overall response to induction therapy (partial/complete response versus stable disease), and intent to give ET (yes versus no). The primary endpoint is investigator-assessed progression-free survival. Secondary endpoints include overall survival, objective response rate, clinical benefit rate, duration of response, safety, and patient-reported outcomes. DISCUSSION heredERA BC will address whether giredestrant plus dual HER2 blockade is superior to dual HER2 blockade alone, to inform the use of this combination in clinical practice for maintenance 1L treatment of patients with HER2+, ER+ LA/mBC. TRIAL REGISTRATION ClinicalTrials.gov, NCT05296798; registered on March 25, 2022. Protocol version 3.0 (November 18, 2022). SPONSOR F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124 4070, Basel, Switzerland.
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Affiliation(s)
- Sherko Kuemmel
- Breast Unit, Kliniken Essen Mitte, Essen, Germany
- Department of Gynecology with Breast Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Yeon Hee Park
- Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
| | - Fábio Franke
- Oncosite, Centro de Pesquisa Clínica Em Oncologia, Ijuí, Brazil
| | | | | | | | | | | | | | | | | | - Marc Hafner
- Genentech, Inc., South San Francisco, CA, USA
| | | | - Joyce O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, US Oncology, 3410 Worth Street, Suite 400, Dallas, TX, 75246, USA.
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Sang B, Fan Y, Wang X, Dong L, Gong Y, Zou W, Zhao G, He J. The prognostic value of absolute lymphocyte count and neutrophil-to-lymphocyte ratio for patients with metastatic breast cancer: a systematic review and meta-analysis. Front Oncol 2024; 14:1360975. [PMID: 38515567 PMCID: PMC10955091 DOI: 10.3389/fonc.2024.1360975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
Background Neutrophil-to-lymphocyte ratio (NLR) is considered a potential prognostic marker in early breast cancer. However, the prognosis of absolute lymphocyte count (ALC) and NLR in metastatic breast cancer (MBC) has been reported in a few studies, and conclusions are still conflicting. This present manuscript aims to provide further solid evidence regarding the prognostic values of ALC and NLR in MBC patients. Method Eligible studies that reported the associations between ALC or NLR and MBC were included by searching relative electronic databases. Overall survival (OS) and progression-free survival (PFS) were used as outcome measures. The hazard ratio (HR) values and 95% confidence interval (CI) of the outcome measures were collected as effect sizes, and further analysis and discussion were conducted according to the pooled HR, subgroup analysis, publication bias, and interstudy heterogeneity. Results Twenty-nine studies comprising 3,973 patients with MBC were included. According to our findings, lower ALC was significantly associated with poorer prognosis of OS (HR = 0.57, 95% CI 0.48 to 0.68) and PFS (HR = 0.68, 95% CI 0.58 to 0.79), and greater NLR was associated with poorer OS (HR = 1.50, 95% CI 1.35 to 1.67) and PFS (HR = 1.82, 95% CI 1.42 to 2.35). Furthermore, the prognostic values of ALC and NLR in MBC were also observed in the subgroup analyses regarding cutoff values and ethnicities. Conclusion Low ALC and elevated NLR were observed to be significantly associated with adverse OS and PFS in MBC, indicating that ALC and NLR may act as potential prognostic biomarkers of MBC patients. Meanwhile, our results will also provide some novel evidence and research clues for the selection and development of clinical treatment strategies for MBC patients. Systematic review registration https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42021224114.
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Affiliation(s)
- Bulin Sang
- Clinical Pharmacology Research Center, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, China
| | - Yuxin Fan
- Clinical Pharmacology Research Center, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, China
| | - Xurao Wang
- College of Pharmacy, Dali University, Dali, China
| | - Lixian Dong
- Clinical Pharmacology Research Center, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, China
| | - Yuanyuan Gong
- Department of Clinical Pharmacy, 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Wenhong Zou
- Clinical Pharmacology Research Center, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, China
| | - Guanhua Zhao
- Clinical Pharmacology Research Center, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, China
| | - Jianchang He
- Clinical Pharmacology Research Center, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, China
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Yang R, Yu Y. Patient-derived organoids in translational oncology and drug screening. Cancer Lett 2023; 562:216180. [PMID: 37061121 DOI: 10.1016/j.canlet.2023.216180] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023]
Abstract
Patient-derived organoids (PDO) are a new biomedical research model that can reconstruct phenotypic and genetic characteristics of the original tissue and are useful for research on pathogenesis and drug screening. To introduce the progression in this field, we review the key factors of constructing organoids derived from epithelial tissues and cancers, covering culture medium and matrix, morphological characteristics, genetic profiles, high-throughput drug screening, and application potential. We also discuss the co-culture system of cancer organoids with tumor microenvironment (TME) associated cells. The co-culture system is widely used in evaluating crosstalk of cancer cells with TME components, such as fibroblasts, endothelial cells, immune cells, and microorganisms. The article provides a prospective for standardized cultivation mode, automatic morphological evaluation, and drug sensitivity screening using high-throughput methods.
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Affiliation(s)
- Ruixin Yang
- Department of General Surgery of Ruijin Hospital, Shanghai Institute of Digestive Surgery, and Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingyan Yu
- Department of General Surgery of Ruijin Hospital, Shanghai Institute of Digestive Surgery, and Shanghai Key Laboratory for Gastric Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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