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Bai YR, Yang WG, Jia R, Sun JS, Shen DD, Liu HM, Yuan S. The recent advance and prospect of poly(ADP-ribose) polymerase inhibitors for the treatment of cancer. Med Res Rev 2024. [PMID: 39180380 DOI: 10.1002/med.22069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/29/2024] [Accepted: 07/30/2024] [Indexed: 08/26/2024]
Abstract
Chemotherapies are commonly used in cancer therapy, their applications are limited to low specificity, severe adverse reactions, and long-term medication-induced drug resistance. Poly(ADP-ribose) polymerase (PARP) inhibitors are a novel class of antitumor drugs developed to solve these intractable problems based on the mechanism of DNA damage repair, which have been widely applied in the treatment of ovarian cancer, breast cancer, and other cancers through inducing synthetic lethal effect and trapping PARP-DNA complex in BRCA gene mutated cancer cells. In recent years, PARP inhibitors have been widely used in combination with various first-line chemotherapy drugs, targeted drugs and immune checkpoint inhibitors to expand the scope of clinical application. However, the intricate mechanisms underlying the drug resistance to PARP inhibitors, including the restoration of homologous recombination, stabilization of DNA replication forks, overexpression of drug efflux protein, and epigenetic modifications pose great challenges and desirability in the development of novel PARP inhibitors. In this review, we will focus on the mechanism, structure-activity relationship, and multidrug resistance associated with the representative PARP inhibitors. Furthermore, we aim to provide insights into the development prospects and emerging trends to offer guidance for the clinical application and inspiration for the development of novel PARP inhibitors and degraders.
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Affiliation(s)
- Yi-Ru Bai
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
- Key Laboratory of Advanced Drug Preparation Technologies, School of Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Wei-Guang Yang
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Rui Jia
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Ju-Shan Sun
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Dan-Dan Shen
- Department of Obstetrics and Gynecology, Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment, Zhengzhou, China
- Gynecology Department, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong-Min Liu
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
- Key Laboratory of Advanced Drug Preparation Technologies, School of Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Shuo Yuan
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
- Key Laboratory of Advanced Drug Preparation Technologies, School of Pharmacy, Zhengzhou University, Zhengzhou, China
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2
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Li S, Xin Q, Li Y, Ma H, Yan H, Ao S, Li H, Wang Q, Wang Z, Liu P, Wang H, Zhang XD. Three-Dimensional Visualization of Breast Cancer Pathology Evolution in Clinical Patient Tissues with NIR-II Imaging. NANO LETTERS 2024; 24:10337-10347. [PMID: 39120122 DOI: 10.1021/acs.nanolett.4c02945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Breast cancer (BC) is the most common tumor worldwide and requires crucial molecular typing for treatment and prognosis assessment. Currently, approaches like pathological staining, immunohistochemistry (IHC), and immunofluorescence (IF) face limitations due to the low signal-to-background ratio (SBR) and high tumor heterogeneity, resulting in a high misdiagnosis rate. Fluorescent assay in the second near-infrared region (NIR-II, 1000-1700 nm) exhibits ultrahigh SBR owing to diminished scattering and tissue autofluorescence. Here, we present a NIR-II strategy for accurate BC molecular typing and three-dimensional (3D) visualization based on the atomically precise fluorescent Au24Pr1 clusters. Single-atom Pr doping results in 3.9-fold fluorescence enhancement and long-term photostability. The Au24Pr1 clusters possess high fluorescence centered at ∼1100 nm and the SBR on pathological section diagnosis was 4 times higher than that of NIR-I imaging. This enables high spatial resolution 3D visualization of biopsy specimens, which can surmount tissue heterogeneity for clinical diagnosis of BC.
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Affiliation(s)
- Shasha Li
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Qi Xin
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Yuan Li
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin 300350, China
| | - Huizhen Ma
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin 300350, China
| | - Haoyue Yan
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Siyu Ao
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Hongwei Li
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhidong Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Pengfei Liu
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Hao Wang
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Xiao-Dong Zhang
- Tianjin Key Laboratory of Brain Science and Neural Engineering, Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
- Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Sciences, Tianjin University, Tianjin 300350, China
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Dowling GP, Keelan S, Cosgrove NS, Daly GR, Giblin K, Toomey S, Hennessy BT, Hill ADK. Receptor Discordance in Metastatic Breast Cancer; a review of clinical and genetic subtype alterations from primary to metastatic disease. Breast Cancer Res Treat 2024:10.1007/s10549-024-07431-6. [PMID: 39090418 DOI: 10.1007/s10549-024-07431-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024]
Abstract
PURPOSE Receptor and subtype discordance between primary breast tumours and metastases is a frequently reported phenomenon. The aim of this article is to review the current evidence on receptor discordance in metastatic breast cancer and to explore the benefit of performing a repeat biopsy in this context. METHODS Searches were undertaken on PubMed and Clinicaltrials.gov for relevant publications and trials. CONCLUSION The current guidelines recommend offering to perform a biopsy of a metastatic lesion to evaluate receptor status. The choice of systemic therapy in metastatic disease is often based on the receptor status of the primary lesion. As therapeutic decision making is guided by subtype, biopsy of the metastatic lesion to determine receptor status may alter treatment. This article discusses discordance rates, the mechanisms of receptor discordance, the effect of discordance on treatment and survival outcomes, as well as highlighting some ongoing clinical trials in patients with metastatic breast cancer.
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Affiliation(s)
- Gavin P Dowling
- Medical Oncology Lab, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.
- The Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland.
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland.
| | - Stephen Keelan
- The Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Nicola S Cosgrove
- The Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gordon R Daly
- The Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Katie Giblin
- The Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Sinead Toomey
- Medical Oncology Lab, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Bryan T Hennessy
- Medical Oncology Lab, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Arnold D K Hill
- The Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland
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Zhang Y, Tan Y, Yuan J, Tang H, Zhang H, Tang Y, Xie Y, Wu L, Xie J, Xiao X, Li Y, Kong Y. circLIFR-007 reduces liver metastasis via promoting hnRNPA1 nuclear export and YAP phosphorylation in breast cancer. Cancer Lett 2024; 592:216907. [PMID: 38685451 DOI: 10.1016/j.canlet.2024.216907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 05/02/2024]
Abstract
Cancer metastasis is the major cause of death in patients with breast cancer (BC). The liver is a common site of breast cancer metastasis, and the 5-year survival rate of patients with breast cancer liver metastases (BCLMs) is only about 8.5 %. CircRNAs are involved in a variety of cancer-related pathological behaviors, and their unique structure and resistance to RNA degradation enable them to serve as ideal diagnostic biomarkers and therapeutic targets. Therefore, it is important to investigate the role and molecular mechanism of circRNAs in cancer metastasis. CircLIFR-007 was identified as a critical circular RNA in BC metastasis by circRNAs microarray and qRT-PCR experiment. Cell function assays were performed to explore the effect of circLIFR-007 in breast cancer cells. Experiments in vivo validated the function of circLIFR-007. Several molecular assays were performed to investigate the underlying mechanisms. We found that circLIFR-007 acted as a negative controller in breast cancer liver metastasis. CircLIFR-007 upregulates the phosphorylation level of YAP by exporting hnRNPA1 to promote the combination between hnRNPA1 and YAP in the cytoplasm. Overexpression of circLIFR-007 suppressed the expression of liver metastasis-related proteins, SREBF1 and SNAI1, which were regulated by transcription factor YAP. Functionally, circLIFR-007 inhibits the proliferation and metastasis of breast cancer cells both in vivo and in vitro.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yeru Tan
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Hanqi Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yuhui Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yi Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Linyu Wu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Jindong Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Xiangsheng Xiao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Yuehua Li
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Yanan Kong
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
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5
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Zhang Y, Chen F, Balic M, Creighton CJ. An essential gene signature of breast cancer metastasis reveals targetable pathways. Breast Cancer Res 2024; 26:98. [PMID: 38867323 PMCID: PMC11167932 DOI: 10.1186/s13058-024-01855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The differential gene expression profile of metastatic versus primary breast tumors represents an avenue for discovering new or underappreciated pathways underscoring processes of metastasis. However, as tumor biopsy samples are a mixture of cancer and non-cancer cells, most differentially expressed genes in metastases would represent confounders involving sample biopsy site rather than cancer cell biology. METHODS By paired analysis, we defined a top set of differentially expressed genes in breast cancer metastasis versus primary tumors using an RNA-sequencing dataset of 152 patients from The Breast International Group Aiming to Understand the Molecular Aberrations dataset (BIG-AURORA). To filter the genes higher in metastasis for genes essential for breast cancer proliferation, we incorporated CRISPR-based data from breast cancer cell lines. RESULTS A significant fraction of genes with higher expression in metastasis versus paired primary were essential by CRISPR. These 264 genes represented an essential signature of breast cancer metastasis. In contrast, nonessential metastasis genes largely involved tumor biopsy site. The essential signature predicted breast cancer patient outcome based on primary tumor expression patterns. Pathways underlying the essential signature included proteasome degradation, the electron transport chain, oxidative phosphorylation, and cancer metabolic reprogramming. Transcription factors MYC, MAX, HDAC3, and HCFC1 each bound significant fractions of essential genes. CONCLUSIONS Associations involving the essential gene signature of breast cancer metastasis indicate true biological changes intrinsic to cancer cells, with important implications for applying existing therapies or developing alternate therapeutic approaches.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX, 77030, USA
| | - Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX, 77030, USA
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Unit for Translational Breast Cancer Research, Medical University of Graz, Graz, Austria
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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6
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Jagust P, Powell AM, Ola M, Watson L, de Pablos-Aragoneses A, García-Gómez P, Fallon R, Bane F, Heiland M, Morris G, Cavanagh B, McGrath J, Ottaviani D, Hegarty A, Cocchiglia S, Sweeney KJ, MacNally S, Brett FM, Cryan J, Beausang A, Morris P, Valiente M, Hill ADK, Varešlija D, Young LS. RET overexpression leads to increased brain metastatic competency in luminal breast cancer. J Natl Cancer Inst 2024:djae091. [PMID: 38852945 DOI: 10.1093/jnci/djae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/22/2023] [Accepted: 04/14/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Breast cancer brain metastasis is a rising occurrence, necessitating a better understanding of the mechanisms involved for effective management. Breast cancer brain metastases diverge notably from the primary tumor, with gains in kinase and concomitant losses of steroid signaling observed. In this study, we explored the role of the kinase receptor RET in promoting breast cancer brain metastases and provide a rationale for targeting this receptor. METHODS RET expression was characterized in a cohort of patients with primary and brain metastatic tumors. RET functionality was assessed using pharmacological inhibition and gene silencing in patient-derived brain metastatic tumor explants and in vivo models, organoid models, and brain organotypic cultures. RNA sequencing was used to uncover novel brain metastatic relevant RET mechanisms of action. RESULTS A statistically significant enrichment of RET in brain metastases was observed in estrogen receptor-positive breast cancer, where it played a role in promoting cancer cell adhesion, survival, and outgrowth in the brain. In vivo, RET overexpression enhanced brain metastatic competency in patient-derived models. At a mechanistic level, RET overexpression was found to enhance the activation of gene programs involved in cell adhesion, requiring EGFR cooperation to deliver a pro-brain metastatic phenotype. CONCLUSION Our results illustrate, for the first time, the role of RET in regulating colonization and outgrowth of breast cancer brain metastasis and provide data to support the use of RET inhibitors in the management strategy for patients with breast cancer brain metastases.
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Affiliation(s)
- Petra Jagust
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Aoibhin M Powell
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Mihaela Ola
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Louise Watson
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | | | | | - Ramón Fallon
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Fiona Bane
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Mona Heiland
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Gareth Morris
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Brenton Cavanagh
- Cellular and Molecular Imaging Core, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Jason McGrath
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Daniela Ottaviani
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Aisling Hegarty
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Sinéad Cocchiglia
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Kieron J Sweeney
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Stephen MacNally
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | | | - Jane Cryan
- Department of Neuropathology, National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - Patrick Morris
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
| | | | - Arnold D K Hill
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Damir Varešlija
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
| | - Leonie S Young
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
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7
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Huang Y, Ren S, Ding L, Jiang Y, Luo J, Huang J, Yin X, Zhao J, Fu S, Liao J. TP53-specific mutations serve as a potential biomarker for homologous recombination deficiency in breast cancer: a clinical next-generation sequencing study. PRECISION CLINICAL MEDICINE 2024; 7:pbae009. [PMID: 38745917 PMCID: PMC11092399 DOI: 10.1093/pcmedi/pbae009] [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: 01/08/2024] [Accepted: 04/07/2024] [Indexed: 05/16/2024] Open
Abstract
Background TP53 mutations and homologous recombination deficiency (HRD) occur frequently in breast cancer. However, the characteristics of TP53 pathogenic mutations in breast cancer patients with/without HRD are not clear. Methods Clinical next-generation sequencing (NGS) of both tumor and paired blood DNA from 119 breast cancer patients (BRCA-119 cohort) was performed with a 520-gene panel. Mutations, tumor mutation burden (TMB), and genomic HRD scores were assessed from NGS data. NGS data from 47 breast cancer patients in the HRD test cohort were analyzed for further verification. Results All TP53 pathogenic mutations in patients had somatic origin, which was associated with the protein expression of estrogen receptor and progestogen receptor. Compared to patients without TP53 pathologic mutations, patients with TP53 pathologic mutations had higher levels of HRD scores and different genomic alterations. The frequency of TP53 pathologic mutation was higher in the HRD-high group (HRD score ≥ 42) relative to that in the HRD-low group (HRD score < 42). TP53 has different mutational characteristics between the HRD-low and HRD-high groups. TP53-specific mutation subgroups had diverse genomic features and TMB. Notably, TP53 pathogenic mutations predicted the HRD status of breast cancer patients with an area under the curve (AUC) of 0.61. TP53-specific mutations, namely HRD-low mutation, HRD-high mutation, and HRD common mutation, predicted the HRD status of breast cancer patients with AUC values of 0.32, 0.72, and 0.58, respectively. Interestingly, TP53 HRD-high mutation and HRD common mutation combinations showed the highest AUC values (0.80) in predicting HRD status. Conclusions TP53-specific mutation combinations predict the HRD status of patients, indicating that TP53 pathogenic mutations could serve as a potential biomarker for poly-ADP-ribose polymerase (PARP) inhibitors in breast cancer patients .
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Affiliation(s)
- Yongsheng Huang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Shuwei Ren
- Department of Clinical Laboratory, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Linxiaoxiao Ding
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuanling Jiang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jiahuan Luo
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jinghua Huang
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xinke Yin
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jianli Zhao
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Guangzhou Regenerative Medicine and Health, Guangdong Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Sha Fu
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jianwei Liao
- Cellular & Molecular Diagnostics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
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8
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Xue H, Lu H, Wang Y, Li N, Wang G. MCE: Medical Cognition Embedded in 3D MRI feature extraction for advancing glioma staging. PLoS One 2024; 19:e0304419. [PMID: 38820482 PMCID: PMC11142489 DOI: 10.1371/journal.pone.0304419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/12/2024] [Indexed: 06/02/2024] Open
Abstract
In recent years, various data-driven algorithms have been applied to the classification and staging of brain glioma MRI detection. However, the restricted availability of brain glioma MRI data in purely data-driven deep learning algorithms has presented challenges in extracting high-quality features and capturing their complex patterns. Moreover, the analysis methods designed for 2D data necessitate the selection of ideal tumor image slices, which does not align with practical clinical scenarios. Our research proposes an novel brain glioma staging model, Medical Cognition Embedded (MCE) model for 3D data. This model embeds knowledge characteristics into data-driven approaches to enhance the quality of feature extraction. Approach includes the following key components: (1) Deep feature extraction, drawing upon the imaging technical characteristics of different MRI sequences, has led to the design of two methods at both the algorithmic and strategic levels to mimic the learning process of real image interpretation by medical professionals during film reading; (2) We conduct an extensive Radiomics feature extraction, capturing relevant features such as texture, morphology, and grayscale distribution; (3) By referencing key points in radiological diagnosis, Radiomics feature experimental results, and the imaging characteristics of various MRI sequences, we manually create diagnostic features (Diag-Features). The efficacy of proposed methodology is rigorously evaluated on the publicly available BraTS2018 and BraTS2020 datasets. Comparing it to most well-known purely data-driven models, our method achieved higher accuracy, recall, and precision, reaching 96.14%, 93.4%, 97.06%, and 97.57%, 92.80%, 95.96%, respectively.
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Affiliation(s)
- Han Xue
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, Jilin, China
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China
- Jilin Provincial Smart Health Joint Innovation Laboratory for the New Generation of AI, Changchun, Jilin, China
| | - Huimin Lu
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, Jilin, China
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China
- Jilin Provincial Smart Health Joint Innovation Laboratory for the New Generation of AI, Changchun, Jilin, China
| | - Yilong Wang
- Jilin Provincial Smart Health Joint Innovation Laboratory for the New Generation of AI, Changchun, Jilin, China
- The First Hospital of Jilin University, Changchun, Jilin, China
- School of Mathematics and Statistics, Changchun University of Technology, Changchun, Jilin, China
| | - Niya Li
- Jilin Provincial Smart Health Joint Innovation Laboratory for the New Generation of AI, Changchun, Jilin, China
| | - Guizeng Wang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, Jilin, China
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, China
- Jilin Provincial Smart Health Joint Innovation Laboratory for the New Generation of AI, Changchun, Jilin, China
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9
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Di Lisa D, Cortese K, Chiappalone M, Arnaldi P, Martinoia S, Castagnola P, Pastorino L. Electrophysiological and morphological modulation of neuronal-glial network by breast cancer and nontumorigenic mammary cell conditioned medium. Front Bioeng Biotechnol 2024; 12:1368851. [PMID: 38638322 PMCID: PMC11024227 DOI: 10.3389/fbioe.2024.1368851] [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: 01/11/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Breast cancer is a significant global health concern, with the overexpression of human epidermal growth factor receptor 2 (HER2/ERBB2) being a driver oncogene in 20%-30% of cases. Indeed, HER2/ERBB2 plays a crucial role in regulating cell growth, differentiation, and survival via a complex signaling network. Overexpression of HER2/ERBB2 is associated with more aggressive behavior and increased risk of brain metastases, which remains a significant clinical challenge for treatment. Recent research has highlighted the role of breast cancer secretomes in promoting tumor progression, including excessive proliferation, immune invasion, and resistance to anti-cancer therapy, and their potential as cancer biomarkers. In this study, we investigated the impact of ERBB2+ breast cancer SKBR-3 cell line compared with MCF10-A mammary non-tumorigenic cell conditioned medium on the electrophysiological activity and morphology of neural networks derived from neurons differentiated from human induced pluripotent stem cells. Our findings provide evidence of active modulation of neuronal-glial networks by SKBR-3 and MCF10-A conditioned medium. These results provide insights into the complex interactions between breast cancer cells and the surrounding microenvironment. Further research is necessary to identify the specific factors within breast cancer conditioned medium that mediate these effects and to develop targeted therapies that disrupt this interaction.
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Affiliation(s)
- Donatella Di Lisa
- Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
| | - Katia Cortese
- Department of Experimental Medicine, Cellular Electron Microscopy Lab, University of Genoa, Genova, Italy
| | - Michela Chiappalone
- Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
- RAISE Ecosystem, Genova, Italy
| | - Pietro Arnaldi
- Department of Experimental Medicine, Cellular Electron Microscopy Lab, University of Genoa, Genova, Italy
| | - Sergio Martinoia
- Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
- RAISE Ecosystem, Genova, Italy
| | | | - Laura Pastorino
- Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
- RAISE Ecosystem, Genova, Italy
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10
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Cao Y, Meng F, Cai T, Gao L, Lee J, Solomevich SO, Aharodnikau UE, Guo T, Lan M, Liu F, Li Q, Viktor T, Li D, Cai Y. Nanoparticle drug delivery systems responsive to tumor microenvironment: Promising alternatives in the treatment of triple-negative breast cancer. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1950. [PMID: 38528388 DOI: 10.1002/wnan.1950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/04/2024] [Accepted: 02/11/2024] [Indexed: 03/27/2024]
Abstract
The conventional therapeutic treatment of triple-negative breast cancer (TNBC) is negatively influenced by the development of tumor cell drug resistant, and systemic toxicity of therapeutic agents due to off-target activity. In accordance with research findings, nanoparticles (NPs) responsive to the tumor microenvironment (TME) have been discovered for providing opportunities to selectively target tumor cells via active targeting or Enhanced Permeability and Retention (EPR) effect. The combination of the TME control and therapeutic NPs offers promising solutions for improving the prognosis of the TNBC because the TME actively participates in tumor growth, metastasis, and drug resistance. The NP-based systems leverage stimulus-responsive mechanisms, such as low pH value, hypoxic, excessive secretion enzyme, concentration of glutathione (GSH)/reactive oxygen species (ROS), and high concentration of Adenosine triphosphate (ATP) to combat TNBC progression. Concurrently, NP-based stimulus-responsive introduces a novel approach for drug dosage design, administration, and modification of the pharmacokinetics of conventional chemotherapy and immunotherapy drugs. This review provides a comprehensive examination of the strengths, limitations, applications, perspectives, and future expectations of both novel and traditional stimulus-responsive NP-based drug delivery systems for improving outcomes in the medical practice of TNBC. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Ye Cao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/Guangdong Key Lab of Traditional Chinese Medicine Informatization/International Science and Technology Cooperation Base of Guangdong Province/School of Pharmacy, Jinan University, Guangzhou, China
| | - Fansu Meng
- Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
| | - Tiange Cai
- College of Life Sciences, Liaoning University, Shenyang, China
| | - Lanwen Gao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/Guangdong Key Lab of Traditional Chinese Medicine Informatization/International Science and Technology Cooperation Base of Guangdong Province/School of Pharmacy, Jinan University, Guangzhou, China
| | - Jaiwoo Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sergey O Solomevich
- Research Institute for Physical Chemical Problems of the Belarusian State University, Minsk, Belarus
| | - Uladzislau E Aharodnikau
- Research Institute for Physical Chemical Problems of the Belarusian State University, Minsk, Belarus
| | - Tingting Guo
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/Guangdong Key Lab of Traditional Chinese Medicine Informatization/International Science and Technology Cooperation Base of Guangdong Province/School of Pharmacy, Jinan University, Guangzhou, China
| | - Meng Lan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/Guangdong Key Lab of Traditional Chinese Medicine Informatization/International Science and Technology Cooperation Base of Guangdong Province/School of Pharmacy, Jinan University, Guangzhou, China
| | - Fengjie Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/Guangdong Key Lab of Traditional Chinese Medicine Informatization/International Science and Technology Cooperation Base of Guangdong Province/School of Pharmacy, Jinan University, Guangzhou, China
| | - Qianwen Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/Guangdong Key Lab of Traditional Chinese Medicine Informatization/International Science and Technology Cooperation Base of Guangdong Province/School of Pharmacy, Jinan University, Guangzhou, China
| | - Timoshenko Viktor
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Detang Li
- The First Clinical Medical School of Guangzhou University of Chinese Medicine/Department of Pharmacy, The First Affiliated Hospital of Guangzhou University of Chinese Medicine/Guangdong Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Yu Cai
- State Key Laboratory of Bioactive Molecules and Druggability Assessment/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China/Guangdong Key Lab of Traditional Chinese Medicine Informatization/International Science and Technology Cooperation Base of Guangdong Province/School of Pharmacy, Jinan University, Guangzhou, China
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11
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Eder I, Yu V, Chen F, Gau D, Joy M, Lucas P, Boone D, Lee AV, Roy P. MRTF promotes breast cancer cell motility through SRF-dependent upregulation of DIAPH3 expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572883. [PMID: 38187641 PMCID: PMC10769385 DOI: 10.1101/2023.12.21.572883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Dysregulated actin cytoskeleton gives rise to aberrant cell motility and metastatic spread of tumor cells. The MRTF-SRF transcriptional complex plays a key role in regulating the expressions of actin cytoskeleton-modulatory genes. In this study, we demonstrate that MRTF's interaction with SRF is critical for migration and invasion of breast cancer cells. Disruption of the MRTF-SRF interaction suppresses membrane dynamics affecting the frequency and the effectiveness of membrane protrusion during cell motility. Consistent with these phenotypic changes, we further show that MRTF promotes actin polymerization at the leading edge, a key aspect of membrane protrusion, and migration of breast cancer cells through upregulating the expression of formin-family actin nucleating/elongating protein encoding gene DIAPH3 in an SRF-dependent manner. In support of these findings, multiplexed quantitative immunohistochemistry and transcriptome analyses of clinical specimens of breast cancer further demonstrate a positive correlation between nuclear localization of MRTF with malignant traits of cancer cells as well as enrichment of MRTF/SRF gene signature in distant metastases relative to primary tumors. In conclusion, this study for the first time links the MRTF/SRF signaling axis to cell migration through the regulation of a specific actin-binding protein, and provides evidence for an association between MRTF/SRF activity and malignancy in human breast cancer.
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12
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Prekovic S, Chalkiadakis T, Roest M, Roden D, Lutz C, Schuurman K, Opdam M, Hoekman L, Abbott N, Tesselaar T, Wajahat M, Dwyer AR, Mayayo‐Peralta I, Gomez G, Altelaar M, Beijersbergen R, Győrffy B, Young L, Linn S, Jonkers J, Tilley W, Hickey T, Vareslija D, Swarbrick A, Zwart W. Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity. EMBO Mol Med 2023; 15:e17737. [PMID: 37902007 PMCID: PMC10701603 DOI: 10.15252/emmm.202317737] [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: 03/21/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER-positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer-driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER-positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER-positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.
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Affiliation(s)
- Stefan Prekovic
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Center for Molecular MedicineUMC UtrechtUtrechtThe Netherlands
| | | | - Merel Roest
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Daniel Roden
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Karianne Schuurman
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Nina Abbott
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tanja Tesselaar
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Maliha Wajahat
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Isabel Mayayo‐Peralta
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Gabriela Gomez
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
| | - Maarten Altelaar
- Mass Spectrometry/Proteomics FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Roderick Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening CentreNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Balázs Győrffy
- TTK Cancer Biomarker Research GroupInstitute of EnzymologyBudapestHungary
- Department of Bioinformatics and 2nd Department of PediatricsSemmelweis UniversityBudapestHungary
| | - Leonie Young
- Endocrine Oncology Research Group, Department of SurgeryThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Sabine Linn
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Wayne Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
- Freemasons Centre for Male Health and WellbeingUniversity of AdelaideAdelaideSAAustralia
| | - Theresa Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical SchoolUniversity of AdelaideAdelaideSAAustralia
| | - Damir Vareslija
- School of Pharmacy and Biomolecular SciencesThe Royal College of Surgeons University of Medicine and Health SciencesDublinIreland
- Beaumont RCSI Cancer CentreBeaumont HospitalDublinIreland
| | - Alexander Swarbrick
- Cancer Ecosystems ProgramGarvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Clinical Medicine, Faculty of Medicine and HealthUNSW SydneySydneyNSWAustralia
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical EngineeringEindhoven University of TechnologyEindhovenThe Netherlands
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13
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Lu Y, Chen QM, An L. Semi-reference based cell type deconvolution with application to human metastatic cancers. NAR Genom Bioinform 2023; 5:lqad109. [PMID: 38143958 PMCID: PMC10748484 DOI: 10.1093/nargab/lqad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/01/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023] Open
Abstract
Bulk RNA-seq experiments, commonly used to discern gene expression changes across conditions, often neglect critical cell type-specific information due to their focus on average transcript abundance. Recognizing cell type contribution is crucial to understanding phenotype and disease variations. The advent of single-cell RNA sequencing has allowed detailed examination of cellular heterogeneity; however, the cost and analytic caveat prohibits such sequencing for a large number of samples. We introduce a novel deconvolution approach, SECRET, that employs cell type-specific gene expression profiles from single-cell RNA-seq to accurately estimate cell type proportions from bulk RNA-seq data. Notably, SECRET can adapt to scenarios where the cell type present in the bulk data is unrepresented in the reference, thereby offering increased flexibility in reference selection. SECRET has demonstrated superior accuracy compared to existing methods using synthetic data and has identified unknown tissue-specific cell types in real human metastatic cancers. Its versatility makes it broadly applicable across various human cancer studies.
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Affiliation(s)
- Yingying Lu
- Interdisciplinary Program in Statistics and Data Science, University of Arizona, Tucson, AZ, USA
| | - Qin M Chen
- College of Pharmacy, University of Arizona, Tucson, AZ, USA
- Cancer Biology Program, University of Arizona, Tucson, AZ, USA
| | - Lingling An
- Interdisciplinary Program in Statistics and Data Science, University of Arizona, Tucson, AZ, USA
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, USA
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, USA
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14
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Brozos-Vázquez EM, Rodríguez-López C, Cortegoso-Mosquera A, López-Landrove S, Muinelo-Romay L, García-González J, López-López R, León-Mateos L. Immunotherapy in patients with brain metastasis: advances and challenges for the treatment and the application of circulating biomarkers. Front Immunol 2023; 14:1221113. [PMID: 38022574 PMCID: PMC10654987 DOI: 10.3389/fimmu.2023.1221113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The central nervous system (CNS) is one of the most frequent metastatic sites of various cancers, including lung cancer, breast cancer and melanoma. The development of brain metastases requires a specific therapeutic approach and is associated with high mortality and morbidity in cancer patients. Advances in precision medicine and the introduction in recent years of new drugs, such as immunotherapy, have made it possible to improve the prognosis of these patients by improving survival and quality of life. New diagnostic techniques such as liquid biopsy allow real-time monitoring of tumor evolution, providing molecular information on prognostic and predictive biomarkers of response to treatment in blood or other fluids. In this review, we perform an exhaustive update of the clinical trials that demonstrate the utility of immunotherapy in patients with brain metastases and the potential of circulating biomarkers to improving the results of efficacy and toxicity in this subgroup of patients.
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Affiliation(s)
- E M Brozos-Vázquez
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Medical Oncology Department, Complexo Hospitalario Universitario de A Coruña, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - C Rodríguez-López
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - A Cortegoso-Mosquera
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - S López-Landrove
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - L Muinelo-Romay
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - J García-González
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - R López-López
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
| | - L León-Mateos
- Medical Oncology Department, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- ONCOMET, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- CIBERONC, Madrid, Spain
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15
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Uceda-Castro R, Margarido AS, Song JY, de Gooijer MC, Messal HA, Chambers CR, Nobis M, Çitirikkaya CH, Hahn K, Seinstra D, Herrmann D, Timpson P, Wesseling P, van Tellingen O, Vennin C, van Rheenen J. BCRP drives intrinsic chemoresistance in chemotherapy-naïve breast cancer brain metastasis. SCIENCE ADVANCES 2023; 9:eabp9530. [PMID: 37851804 PMCID: PMC10584345 DOI: 10.1126/sciadv.abp9530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/14/2023] [Indexed: 10/20/2023]
Abstract
Although initially successful, treatments with chemotherapy often fail because of the recurrence of chemoresistant metastases. Since these tumors develop after treatment, resistance is generally thought to occur in response to chemotherapy. However, alternative mechanisms of intrinsic chemoresistance in the chemotherapy-naïve setting may exist but remain poorly understood. Here, we study drug-naïve murine breast cancer brain metastases (BCBMs) to identify how cancer cells growing in a secondary site can acquire intrinsic chemoresistance without cytotoxic agent exposure. We demonstrate that drug-naïve murine breast cancer cells that form cancer lesions in the brain undergo vascular mimicry and concomitantly express the adenosine 5'-triphosphate-binding cassette transporter breast cancer resistance protein (BCRP), a common marker of brain endothelial cells. We reveal that expression of BCRP by the BCBM tumor cells protects them against doxorubicin and topotecan. We conclude that BCRP overexpression can cause intrinsic chemoresistance in cancer cells growing in metastatic sites without prior chemotherapy exposure.
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Affiliation(s)
- Rebeca Uceda-Castro
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Andreia S. Margarido
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ji-Ying Song
- Division of Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mark C. de Gooijer
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Hendrik A. Messal
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Cecilia R. Chambers
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Max Nobis
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ceren H. Çitirikkaya
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kerstin Hahn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Danielle Seinstra
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, Amsterdam, Netherlands
| | - David Herrmann
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Paul Timpson
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, Amsterdam, Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Olaf van Tellingen
- Division of Pharmacology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Mouse Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Claire Vennin
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
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16
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Zhu Z, Xuan X, Wang X, Wang M, Meng C, Li Z. Identification of testicular cancer immune infiltrates and novel immune cell subtypes. FEBS Open Bio 2023; 13:1967-1985. [PMID: 37543714 PMCID: PMC10549230 DOI: 10.1002/2211-5463.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Testicular germ cell tumors (TGCT) are the most common type of testicular cancer, comprising 90-95% of cases and representing the most prevalent solid malignancy in young adult men. Immune infiltrates play important regulatory roles in tumors, but their role in TGCT remains unclear. Molecular subtyping is a promising way to provide precisely personalized treatment and avoid unnecessary toxicities. This study investigated immune infiltrates, key biomarkers, and immune subtyping of TGCT. In GSE3218, 24 differentially expressed immune genes (immDEGs) were identified. A new risk signature consisting of six immDEGs was developed using these genes. Individuals in the high-risk group had poor overall survival (OS; hazard ratio of 4.61 and P-value < 0.001). We validated the six-immDEGs risk signature in pure seminoma and mixed TGCT types. Two distinct immune patterns (Cluster 1 and Cluster 2) were identified using the consensusclusterplus, and Cluster 1 possessed an unfavorable OS compared with Cluster 2 (hazard ratio, 2.56; P < 0.001). Cluster 1 patients had significantly lower naive B cells, memory B cells, plasma cells, naive CD4 T cells, gamma delta T cells, and activated dendritic cells than Cluster 2 patients. Genes relating to the WNT signaling pathway, TGF-β signaling pathway, antigen processing and presentation, and NK cell-mediated cytotoxicity were associated with TGCT. STC1 was elevated in TGCT tissues, and its high expression showed advanced clinicopathological characteristics and poor prognosis of TGCT. Our findings may contribute to an increased understanding of the onset and progression of TGCT.
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Affiliation(s)
- Zhiguo Zhu
- Department of Urology, Affiliated Hospital of Jining Medical UniversityJining Medical UniversityChina
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese MedicineJiningChina
| | - Xujun Xuan
- Department of Andrology, The Seventh Affiliated HospitalSun Yet‐sen UniversityShenzhenChina
| | - Xinkun Wang
- Department of Andrology, The Seventh Affiliated HospitalSun Yet‐sen UniversityShenzhenChina
| | - Miaomiao Wang
- Department of Medical, Affiliated Hospital of Jining Medical UniversityJining Medical UniversityChina
| | - Chunyang Meng
- Medical Research Center, Affiliated Hospital of Jining Medical UniversityJining Medical UniversityChina
| | - Zhonghai Li
- Department of Urology, Affiliated Hospital of Jining Medical UniversityJining Medical UniversityChina
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17
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Cosgrove N, Eustace AJ, O'Donovan P, Madden SF, Moran B, Crown J, Moulton B, Morris PG, Grogan L, Breathnach O, Power C, Allen M, Walshe JM, Hill AD, Blümel A, O'Connor D, Das S, Milewska M, Fay J, Kay E, Toomey S, Hennessy BT, Furney SJ. Predictive modelling of response to neoadjuvant therapy in HER2+ breast cancer. NPJ Breast Cancer 2023; 9:72. [PMID: 37758711 PMCID: PMC10533568 DOI: 10.1038/s41523-023-00572-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/26/2023] [Indexed: 09/29/2023] Open
Abstract
HER2-positive (HER2+) breast cancer accounts for 20-25% of all breast cancers. Predictive biomarkers of neoadjuvant therapy response are needed to better identify patients with early stage disease who may benefit from tailored treatments in the adjuvant setting. As part of the TCHL phase-II clinical trial (ICORG10-05/NCT01485926) whole exome DNA sequencing was carried out on normal-tumour pairs collected from 22 patients. Here we report predictive modelling of neoadjuvant therapy response using clinicopathological and genomic features of pre-treatment tumour biopsies identified age, estrogen receptor (ER) status and level of immune cell infiltration may together be important for predicting response. Clonal evolution analysis of longitudinally collected tumour samples show subclonal diversity and dynamics are evident with potential therapy resistant subclones detected. The sources of greater pre-treatment immunogenicity associated with a pathological complete response is largely unexplored in HER2+ tumours. However, here we point to the possibility of APOBEC associated mutagenesis, specifically in the ER-neg/HER2+ subtype as a potential mediator of this immunogenic phenotype.
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Affiliation(s)
- Nicola Cosgrove
- Genomic Oncology Research Group, Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Alex J Eustace
- School of Biotechnology, National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Peter O'Donovan
- Genomic Oncology Research Group, Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Stephen F Madden
- Data Science Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Bruce Moran
- Conway Institute, University College Dublin, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
| | - Brian Moulton
- Clinical Oncology Development Europe, Dublin, Ireland
| | - Patrick G Morris
- Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland
| | - Liam Grogan
- Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland
| | - Oscar Breathnach
- Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland
| | - Colm Power
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Michael Allen
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Janice M Walshe
- Department of Medical Oncology, St Vincent's University Hospital, Dublin, Ireland
| | - Arnold D Hill
- Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Anna Blümel
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Darren O'Connor
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Sudipto Das
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Małgorzata Milewska
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin, 9, Ireland
| | - Joanna Fay
- RCSI Biobank Service, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Dublin, 9, Ireland
| | - Elaine Kay
- Department of Pathology, RCSI University of Medicine and Health Sciences, Beaumont Hospital, Dublin, 9, Ireland
| | - Sinead Toomey
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin, 9, Ireland
| | - Bryan T Hennessy
- Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland.
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin, 9, Ireland.
| | - Simon J Furney
- Genomic Oncology Research Group, Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
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Yang L, Wei J, Ma X, Cheng R, Zhang H, Jin T. Pan-Cancer Analysis of the Prognostic and Immunological Role of SMG5: A Biomarker for Cancers. Oncology 2023; 102:168-182. [PMID: 37699361 DOI: 10.1159/000533421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/29/2023] [Indexed: 09/14/2023]
Abstract
INTRODUCTION SMG5 is involved in tumor cell development and viewed as a potential target for immunotherapy. The purpose of this study was to systematically analyze the expression level, function, and prognostic value of SMG5 in pan-cancers. METHODS Differential expression of SMG5 in normal and tumor tissues was analyzed using The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Database (GTEx) data. Survival analysis was performed by Kaplan-Meier method and Cox risk regression. The relationship between SMG5 expression and lymphocyte abundance, tumor cell immune infiltration level, molecular and immune subtypes as well as immune checkpoints was analyzed by tumor-immune system interactions database (TISIDB), Tumor Immune Estimation Resource (TIMER), and Sangerbox databases. The correlation between SMG5 and immune scores was studied using the Estimation of Stromal and Immune Cells in Malignant Tumours using Expression (ESTIMATE) data algorithm. Further, drug sensitivity analysis of SMG5 with low-grade glioma (LGG) was conducted using the CellMiner database. RESULTS SMG5 was highly expressed in 23 tumors and only had a significant impact on the prognosis of patients with LGG only. In addition, in tumor microenvironment and tumor immune analysis, we found that the level of immune infiltration, tumor mutational load, microsatellite instability, and immune checkpoints of LGG were significantly correlated with SMG5 expression. Furthermore, SMG5 was significantly associated with immune scores, stromal scores, and sensitivity of some drugs in LGG. CONCLUSION SMG5 is differentially expressed in several cancers and is significantly associated with prognosis, immune microenvironment, and immune checkpoints in LGG patients. Therefore, SMG5 could be a potential pan-cancer biomarker and an immunotherapeutic target for LGG.
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Affiliation(s)
- Leteng Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Jie Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Xiaoya Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Rui Cheng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Huan Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
- College of Life Science, Northwest University, Xi'an, China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
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19
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Fu C, Kou R, Meng J, Jiang D, Zhong R, Dong M. m6A genotypes and prognostic signature for assessing the prognosis of patients with acute myeloid leukemia. BMC Med Genomics 2023; 16:191. [PMID: 37596597 PMCID: PMC10436408 DOI: 10.1186/s12920-023-01629-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) has been confirmed to function critically in acute myeloid leukemia (AML) progression. Hitherto, the subtyping and prognostic predictive significance of m6A-correlated genes in AML is unclear. METHOD From The Cancer Genome Atlas (TCGA-LAML), Therapeutically Applicable Research to Generate Effective Treatments (TARGET-AML) and Gene Expression Omnibus (GEO, GSE71014) databases, we collected the sequencing data of AML patients. The batch effect was removed via limma package for TCGA-LAML and TARGET-AML, and the aggregated samples were AML cohorts. Samples in the AML cohort identified m6A models in AML by consensus clustering based on 23-m6A-related modulators. M6A-related differentially expressed genes (m6ARDEGs) influencing the overall survival (OS) of AML were determined by performing differential expression analysis and univariate COX analysis, and consensus-based clustering was utilized to access AML molecular subtypes. LASSO and multivariate COX analyses were performed to obtain the optimized m6ARDEGs to construct the m6A Prognostic Risk Score (m6APR_Score). Whether the model was robust was evaluated according to Kaplan-Meier (K-M) and receiver operator characteristic (ROC) curves. Further, the abundance of immune cell infiltration was explored in different m6A modification patterns and molecular subtypes and m6APR_Score groupings. Finally, nomogram was constructed to predict OS in AML. Quantitative real-time polymerase chain reaction (RT-qPCR) and cell counting kit-8 (CCK-8) assay were used to validate the genes in m6APR_Score in AML cells. RESULTS The m6A models (m6AM1, m6AM2, m6AM3) and molecular subtypes (C1, C2, C3) were identified in the AML cohort, exhibiting different prognosis and immunoreactivity. We recognized novel prognostic biomarkers of AML such as CD83, NRIP1, ACSL1, METTL7B, OGT, and C4orf48. AML patients were grouped into high-m6APR_Score and low-m6APR_Score groups, with the later group showing a better prognosis than former one. Both the AML cohort and the validation cohort GSE71014 demonstrated excellent prediction. Finally, the nomogram accurately predicted the survival of patients suffering from AML. Further, the decision curves showed that both nomogram and m6APR_Score showed excellent prediction. It was confirmed in vitro experiments that mRNA expressions of NRIP1, ACSL1, METTL7B and OGT were elevated, while CD83 and C4orf48 mRNA expressions downregulated in AML cells. A significant increase in the viability of U937 and THP-1 cell lines after inhibition of CD83, while siMETTL7B had contrast results. CONCLUSION Our study demonstrated that m6APR_Score and CD83, NRIP1, ACSL1, METTL7B, OGT, and C4orf48 potentially provided novel and promising prognostic support for AML patients.
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Affiliation(s)
- Caizhu Fu
- Hematology, the Second Affiliated Hospital of Hainan Medical University, Haikou, 570000, China
| | - Ruirui Kou
- Hematology, the Second Affiliated Hospital of Hainan Medical University, Haikou, 570000, China
| | - Jie Meng
- Hematology, the Second Affiliated Hospital of Hainan Medical University, Haikou, 570000, China
| | - Duanfeng Jiang
- Hematology, the Second Affiliated Hospital of Hainan Medical University, Haikou, 570000, China
| | - Ruilan Zhong
- Hematology, the Second Affiliated Hospital of Hainan Medical University, Haikou, 570000, China
| | - Min Dong
- Hematology, the Second Affiliated Hospital of Hainan Medical University, Haikou, 570000, China.
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Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, Liu JC, Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, Perou CM, Dupuy A, Bader GD, Egan SE, Taylor MD, Zacksenhaus E. Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer. Nat Commun 2023; 14:4313. [PMID: 37463901 PMCID: PMC10354065 DOI: 10.1038/s41467-023-39935-y] [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: 06/22/2022] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Metastatic breast-cancer is a major cause of death in women worldwide, yet the relationship between oncogenic drivers that promote metastatic versus primary cancer is still contentious. To elucidate this relationship in treatment-naive animals, we hereby describe mammary-specific transposon-mutagenesis screens in female mice together with loss-of-function Rb, which is frequently inactivated in breast-cancer. We report gene-centric common insertion-sites (gCIS) that are enriched in primary-tumors, in metastases or shared by both compartments. Shared-gCIS comprise a major MET-RAS network, whereas metastasis-gCIS form three additional hubs: Rho-signaling, Ubiquitination and RNA-processing. Pathway analysis of four clinical cohorts with paired primary-tumors and metastases reveals similar organization in human breast-cancer with subtype-specific shared-drivers (e.g. RB1-loss, TP53-loss, high MET, RAS, ER), primary-enriched (EGFR, TGFβ and STAT3) and metastasis-enriched (RHO, PI3K) oncogenic signaling. Inhibitors of RB1-deficiency or MET plus RHO-signaling cooperate to block cell migration and drive tumor cell-death. Thus, targeting shared- and metastasis- but not primary-enriched derivers offers a rational avenue to prevent metastatic breast-cancer.
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Affiliation(s)
- Zhe Jiang
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - YoungJun Ju
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Amjad Ali
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Philip E D Chung
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Patryk Skowron
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Dong-Yu Wang
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Mariusz Shrestha
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Huiqin Li
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | - Jeff C Liu
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Ioulia Vorobieva
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ronak Ghanbari-Azarnier
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ethel Mwewa
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada
| | | | - Yaacov Ben-David
- The Key laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou, 550014, China
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China
| | - James R Woodgett
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON, Canada
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, Departments of Genetics and Pathology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Adam Dupuy
- Department of Pathology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, 52242, USA
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sean E Egan
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D Taylor
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Program in Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eldad Zacksenhaus
- Toronto General Research Institute - University Health Network, 101 College Street, Max Bell Research Centre, suite 5R406, Toronto, ON, M5G 1L7, Canada.
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Department of Medicine, University of Toronto, Toronto, ON, Canada.
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Benjamin M, Malakar P, Sinha RA, Nasser MW, Batra SK, Siddiqui JA, Chakravarti B. Molecular signaling network and therapeutic developments in breast cancer brain metastasis. ADVANCES IN CANCER BIOLOGY - METASTASIS 2023; 7:100079. [PMID: 36536947 PMCID: PMC7613958 DOI: 10.1016/j.adcanc.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Breast cancer (BC) is one of the most frequently diagnosed cancers in women worldwide. It has surpassed lung cancer as the leading cause of cancer-related death. Breast cancer brain metastasis (BCBM) is becoming a major clinical concern that is commonly associated with ER-ve and HER2+ve subtypes of BC patients. Metastatic lesions in the brain originate when the cancer cells detach from a primary breast tumor and establish metastatic lesions and infiltrate near and distant organs via systemic blood circulation by traversing the BBB. The colonization of BC cells in the brain involves a complex interplay in the tumor microenvironment (TME), metastatic cells, and brain cells like endothelial cells, microglia, and astrocytes. BCBM is a significant cause of morbidity and mortality and presents a challenge to developing successful cancer therapy. In this review, we discuss the molecular mechanism of BCBM and novel therapeutic strategies for patients with brain metastatic BC.
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Affiliation(s)
- Mercilena Benjamin
- Lab Oncology, Dr. B.R.A.I.R.C.H. All India Institute of Medical Sciences, New Delhi, India
| | - Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, West Bengal, 700103, India
| | - Rohit Anthony Sinha
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Bandana Chakravarti
- Department of Endocrinology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, India
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22
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Zhu Z, Li X, Liu D, Li Z. A novel signature of aging-related genes associated with lymphatic metastasis for survival prediction in patients with bladder cancer. Front Oncol 2023; 13:1140891. [PMID: 37441420 PMCID: PMC10335803 DOI: 10.3389/fonc.2023.1140891] [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: 01/09/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Background The predominant and most prevalent form of metastatic bladder cancer (BCa) is lymphatic metastasis, which is associated with a highly dismal prognosis for patients. Aging-related genes (ARGs) are believed to contribute significantly to tumor development. However, the effect of ARGs on lymphatic metastasis of BCa is unclear. This research sought to establish a prognosis model based on ARGs associated with lymphatic metastasis in BCa. Methods We downloaded BCa data from the TCGA and GEO databases and ARGs from the Aging Atlas database. The least absolute shrinkage and selection operator (LASSO) approach was applied to obtain the characteristic ARGs of risk signature in the TCGA cohort. Verification was done using the GSE13507 dataset. The R package 'ConsensusClusterPlus' was employed to identify the molecular subtypes based on the characteristic ARGs. Protein-Protein interaction network, MCODE analysis, enrichment analysis (KEGG, GO, GSEA), and immune infiltration analysis were performed to investigate underlying mechanisms. EdU, migration and invasion assays, wound healing assays, immunofluorescence staining, and quantitative polymerase chain reaction were conducted to evaluate the impact of ELN on the proliferative, migratory, and invasive capacities of BCa cells. Results We identified 20 differently expressed ARGs. A four ARGs risk signature (EFEMP1, UCHL1, TP63, ELN) was constructed in the TCGA cohort. The high-risk group (category) recorded a reduced overall survival (OS) rate relative to the low-risk category (hazard ratio, 2.15; P <0.001). The risk score could predict lymphatic metastasis in TCGA cohort (AUC=0.67). The GSE13507 dataset was employed to verify the validity of this risk score. Based on the four ARGs, two distinct aging profiles (Cluster 1 and Cluster 2) were discovered utilizing the ConsensusClusterPlus, and Cluster 2 possessed a favorable OS in contrast with Cluster 1 (hazard ratio, 0.69; P =0.02). Classical tumor signaling pathways, ECM-associated signaling pathways, and immune-related signaling pathways participate in BCa progression. ELN recombinant protein affected the expression of collagen and increased migration and invasiveness in BCa cells. Conclusion We constructed a four-ARG risk signature and identified two aging molecular subtypes. This signature could serve as an effective survival predictor for patients with BCa.
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Affiliation(s)
- Zhiguo Zhu
- Department of Urology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
- Medical Research Center, Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jining, China
- The Seventh Affiliated Hospital (Shenzhen), Sun Yet-sen University, Shenzhen, China
| | - Xiaoli Li
- The Seventh Affiliated Hospital (Shenzhen), Sun Yet-sen University, Shenzhen, China
| | - Deqian Liu
- Department of Urology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Zhonghai Li
- Department of Urology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
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Chen H, Liu Y, Yin Z, Chen H, Wang Y, Qian Y. Homologous repair deficiency-associated genes in invasive breast cancer revealed by WGCNA co-expression network analysis and genetic perturbation similarity analysis. Cell Cycle 2023; 22:1077-1100. [PMID: 36757135 PMCID: PMC10081085 DOI: 10.1080/15384101.2023.2174339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Homologous repair deficiency (HRD) causes double-strand break repair to be impeded, which is a common driver of carcinogenesis. However, the therapeutic and prognostic potential of HRD in invasive breast cancer (BRCA) has not been fully explored using comprehensive bioinformatics analysis. MATERIALS AND METHODS HRD score was defined as the unweighted sum of LOH, TAI, and LST scores and obtained from the previous study according to Theo A et al. To characterize BRCA tumor microenvironment (TME) subtypes, "ConsensusClusterPlus" R package was used to conduct unsupervised clustering. The xCell algorithm was utilized for tumor composition analysis to estimate the TME in TCGA-BRCA. A WGCNA analysis was conducted to uncover the gene coexpression modules and hub genes in the HRD-related gene module of BRCA. The functional enrichment study was carried out using Metascape. A novel analysis pipeline, Genetic Perturbation Similarity Analysis (GPSA), was used to explore the single-gene perturbation closely related to HRD based on 3048 stable knockdown/knockout cell lines. The prognostic variables were evaluated using univariate COX analysis. Kaplan-Meier (KM) survival analysis was performed to assess the prognostic potential of HRD score. Receiver operator characteristic (ROC) curve was utilized to judge the diagnostic utility. Drug sensitivity was estimated through the R package "oncoPredict" and Genomics of Drug Sensitivity in Cancer (GDSC) database. XSum algorithm was performed to screen the candidate small molecule drugs based on the connectivity map (CMAP) database. RESULTS Low HRD score suggested a better prognosis in BRCA patients. The tumor with low HRD score had considerably greater degree of infiltration of stromal cells and infiltration of immunocytes was significantly enhanced in the high HRD score group. Using WGCNA, ten co-expression modules were obtained. The turquoise module and 25 hub genes were identified as the most correlated with HRD in BRCA. Functional enrichment analysis revealed that the turquoise gene module was mainly concentrated in the "cell cycle" pathways. Candidate HRD-related gene signatures (MELK) were screened out through WGCNA and GPSA analysis pipeline and then validated on independent validation sets. A small molecule drug (Clofibrate) that has the potential to reverse the increase of high HRD score was screened out to improve oncological outcomes in BRCA. Molecular docking suggested MELK to be one of possible molecular targets in the Clofibrate treatment of BRCA. CONCLUSION Based on bioinformatic analysis, we fully explored the therapeutic and prognostic potential of HRD in BRCA. A novel HRD-related gene signature (MELK) were identified through the combination of WGCNA and GPSA analysis. In addition, we detailed the TME landscape in BRCA and identified four unique TME subtypes in group with high or low HRD score group. Moreover, Clofibrate were screened out to improve oncological outcomes in BRCA by reversing the increase of high HRD score. Thus, our study contributes to the development of personalized clinical management and treatment regimens of BRCA.
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Affiliation(s)
- Haohao Chen
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yanyan Liu
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhenglang Yin
- Department of General surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hao Chen
- Department of Emergency Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yao Wang
- Department of Digestive Endoscopy, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Yeben Qian
- Department of General surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Cao C, Lu X, Guo X, Zhao H, Gao Y. Patient-derived models: Promising tools for accelerating the clinical translation of breast cancer research findings. Exp Cell Res 2023; 425:113538. [PMID: 36871856 DOI: 10.1016/j.yexcr.2023.113538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
Breast cancer has become the highest incidence of cancer in women. It was extensively and deeply studied by biologists and medical workers worldwide. However, the meaningful results in lab researches cannot be realized in clinical, and a part of new drugs in clinical experiments do not obtain as good results as the preclinical researches. It is urgently that promote a kind of breast cancer research models that can get study results closer to the physiological condition of the human body. Patient-derived models (PDMs) originating from clinical tumor, contain primary elements of tumor and maintain key clinical features of tumor. So they are promising research models to facilitate laboratory researches translate to clinical application, and predict the treatment outcome of patients. In this review, we summarize the establishment of PDMs of breast cancer, reviewed the application of PDMs in clinical translational researches and personalized precision medicine with breast cancer as an example, to improve the understanding of PDMs among researchers and clinician, facilitate them to use PDMs on a large scale of breast cancer researches and promote the clinical translation of laboratory research and new drug development.
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Affiliation(s)
- Changqing Cao
- Department of General Surgery, The Second Affiliated Hospital of Air Force Medical University, China; State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, China
| | - Xiyan Lu
- Department of Outpatient, The Second Affiliated Hospital of Air Force Medical University, China
| | - Xinyan Guo
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, China
| | - Huadong Zhao
- Department of General Surgery, The Second Affiliated Hospital of Air Force Medical University, China.
| | - Yuan Gao
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, The Fourth Military Medical University, China.
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25
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MMR Deficiency Defines Distinct Molecular Subtype of Breast Cancer with Histone Proteomic Networks. Int J Mol Sci 2023; 24:ijms24065327. [PMID: 36982402 PMCID: PMC10049366 DOI: 10.3390/ijms24065327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Mismatch repair (MMR) alterations are important prognostic and predictive biomarkers in a variety of cancer subtypes, including colorectal and endometrial. However, in breast cancer (BC), the distinction and clinical significance of MMR are largely unknown. This may be due in part to the fact that genetic alterations in MMR genes are rare and only seen to occur in around 3% of BCs. In the present study, we analyzed TCGA data using a multi-sample protein–protein interaction (PPI) analysis tool, Proteinarium, and showed a distinct separation between specific MMR-deficient and -intact networks in a cohort of 994 BC patients. In the PPI networks specific to MMR deficiency, highly connected clusters of histone genes were identified. We also found the distribution of MMR-deficient BC to be more prevalent in HER2-enriched and triple-negative (TN) BC subtypes compared to luminal BCs. We recommend defining MMR-deficient BC by next-generation sequencing (NGS) when any somatic mutation is detected in one of the seven MMR genes.
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Improving brain tumor classification performance with an effective approach based on new deep learning model named 3ACL from 3D MRI data. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2022.104424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Zhang Y, Chen F, Creighton CJ. Pan-cancer molecular subtypes of metastasis reveal distinct and evolving transcriptional programs. Cell Rep Med 2023; 4:100932. [PMID: 36731467 PMCID: PMC9975284 DOI: 10.1016/j.xcrm.2023.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/22/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023]
Abstract
Molecular mechanisms underlying cancer metastasis span diverse tissues of origin. Here, we synthesize and collate the transcriptomes of patient-derived xenografts and patient tumor metastases, and these data collectively represent 38 studies and over 3,000 patients and 4,000 tumors. We identify four expression-based subtypes of metastasis transcending tumor lineage. The first subtype has extensive copy alterations, higher expression of MYC transcriptional targets and DNA repair genes, and bromodomain inhibitor response association. The second subtype has higher expression of genes involving metabolism and prostaglandin synthesis and regulation. The third subtype has evidence of neuronal differentiation, higher expression of DNA and histone methylation genes and EZH2 transcriptional targets, and BCL2 inhibitor response association. The fourth subtype has higher expression of immune checkpoint and Notch pathway genes. The metastasis subtypes reflect expression differences from paired primaries, with subtype switching being common. These subtypes facilitate understanding of the molecular underpinnings of metastases beyond tissue-oriented domains, with therapeutic implications.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS305, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
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28
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Trapani D, Aizer AA, Lin NU. Multidisciplinary Management of Brain Metastasis from Breast Cancer. Hematol Oncol Clin North Am 2023; 37:183-202. [PMID: 36435610 DOI: 10.1016/j.hoc.2022.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The management of patients with breast cancer and brain metastases (BMs) is exquisitely multidisciplinary. Patients presenting with a symptomatic BM may be offered neurosurgical resection, followed by radiation. Stereotactic radiosurgery (SRS) is preferred over whole-brain radiotherapy (WBRT) in most patients presenting with a limited number of BMs, whereas WBRT with hippocampal-sparing and concomitant memantine is preferred for patients with multiple BMs. There is a growing role for systemic therapy, in some cases in lieu of local therapy, particularly in patients with HER2+ breast cancer.
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Affiliation(s)
- Dario Trapani
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Ayal A Aizer
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Nancy U Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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29
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Keelan S, Ola M, Charmsaz S, Cocchiglia S, Ottaviani D, Hickey S, Purcell S, Bane F, Hegarty A, Doherty B, Sheehan K, Hudson L, Cosgrove N, Roux B, Laine M, Greene G, Varešlija D, Hill AK, Young L. Dynamic epi-transcriptomic landscape mapping with disease progression in estrogen receptor-positive breast cancer. Cancer Commun (Lond) 2023; 43:615-619. [PMID: 36670046 PMCID: PMC10174082 DOI: 10.1002/cac2.12407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/21/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Affiliation(s)
- Stephen Keelan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Mihaela Ola
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Sara Charmsaz
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Sinéad Cocchiglia
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Daniela Ottaviani
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Seán Hickey
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Siobhan Purcell
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Fiona Bane
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Aisling Hegarty
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Ben Doherty
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Katherine Sheehan
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Lance Hudson
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Nicola Cosgrove
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Benjamin Roux
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | - Muriel Laine
- Ben May Department for Cancer Research, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Geoffrey Greene
- Ben May Department for Cancer Research, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,The School of Pharmacy and Biomolecular Sciences, The Royal College of Surgeons University of Medicine and Health Sciences, Dublin, Ireland
| | - Arnold Konrad Hill
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Leonie Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland.,Department of Surgery, Beaumont Hospital, Dublin, Ireland.,Beaumont Royal College of Surgeons in Ireland Cancer Centre, Beaumont Hospital, Dublin, Ireland
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Álvarez-Prado ÁF, Maas RR, Soukup K, Klemm F, Kornete M, Krebs FS, Zoete V, Berezowska S, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA. Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors. Cell Rep Med 2023; 4:100900. [PMID: 36652909 PMCID: PMC9873981 DOI: 10.1016/j.xcrm.2022.100900] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/20/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023]
Abstract
Brain metastases (BrMs) are the most common form of brain tumors in adults and frequently originate from lung and breast primary cancers. BrMs are associated with high mortality, emphasizing the need for more effective therapies. Genetic profiling of primary tumors is increasingly used as part of the effort to guide targeted therapies against BrMs, and immune-based strategies for the treatment of metastatic cancer are gaining momentum. However, the tumor immune microenvironment (TIME) of BrM is extremely heterogeneous, and whether specific genetic profiles are associated with distinct immune states remains unknown. Here, we perform an extensive characterization of the immunogenomic landscape of human BrMs by combining whole-exome/whole-genome sequencing, RNA sequencing of immune cell populations, flow cytometry, immunofluorescence staining, and tissue imaging analyses. This revealed unique TIME phenotypes in genetically distinct lung- and breast-BrMs, thereby enabling the development of personalized immunotherapies tailored by the genetic makeup of the tumors.
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Affiliation(s)
- Ángel F. Álvarez-Prado
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland,Agora Cancer Research Center, 1011 Lausanne, Switzerland,L. Lundin and Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Roeltje R. Maas
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland,Agora Cancer Research Center, 1011 Lausanne, Switzerland,L. Lundin and Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland,Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland,Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland,Agora Cancer Research Center, 1011 Lausanne, Switzerland
| | - Florian Klemm
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland,Agora Cancer Research Center, 1011 Lausanne, Switzerland
| | - Mara Kornete
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland,Agora Cancer Research Center, 1011 Lausanne, Switzerland
| | - Fanny S. Krebs
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vincent Zoete
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sabina Berezowska
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andreas F. Hottinger
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,L. Lundin and Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland,Brain and Spine Tumor Center, Departments of Clinical Neurosciences and Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Roy T. Daniel
- L. Lundin and Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland,Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Monika E. Hegi
- L. Lundin and Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland,Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland,Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Johanna A. Joyce
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland,Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland,Agora Cancer Research Center, 1011 Lausanne, Switzerland,L. Lundin and Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland,Corresponding author
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31
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Garcia-Recio S, Hinoue T, Wheeler GL, Kelly BJ, Garrido-Castro AC, Pascual T, De Cubas AA, Xia Y, Felsheim BM, McClure MB, Rajkovic A, Karaesmen E, Smith MA, Fan C, Ericsson PIG, Sanders ME, Creighton CJ, Bowen J, Leraas K, Burns RT, Coppens S, Wheless A, Rezk S, Garrett AL, Parker JS, Foy KK, Shen H, Park BH, Krop I, Anders C, Gastier-Foster J, Rimawi MF, Nanda R, Lin NU, Isaacs C, Marcom PK, Storniolo AM, Couch FJ, Chandran U, Davis M, Silverstein J, Ropelewski A, Liu MC, Hilsenbeck SG, Norton L, Richardson AL, Symmans WF, Wolff AC, Davidson NE, Carey LA, Lee AV, Balko JM, Hoadley KA, Laird PW, Mardis ER, King TA, Perou CM. Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis. NATURE CANCER 2023; 4:128-147. [PMID: 36585450 PMCID: PMC9886551 DOI: 10.1038/s43018-022-00491-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/11/2022] [Indexed: 12/31/2022]
Abstract
The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/germline DNA exome and low-pass whole-genome sequencing and global DNA methylation microarrays. Expression subtype changes were observed in ~30% of samples and were coincident with DNA clonality shifts, especially involving HER2. Downregulation of estrogen receptor (ER)-mediated cell-cell adhesion genes through DNA methylation mechanisms was observed in metastases. Microenvironment differences varied according to tumor subtype; the ER+/luminal subtype had lower fibroblast and endothelial content, while triple-negative breast cancer/basal metastases showed a decrease in B and T cells. In 17% of metastases, DNA hypermethylation and/or focal deletions were identified near HLA-A and were associated with reduced expression and lower immune cell infiltrates, especially in brain and liver metastases. These findings could have implications for treating individuals with metastatic breast cancer with immune- and HER2-targeting therapies.
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Affiliation(s)
| | | | | | | | | | - Tomas Pascual
- University of North Carolina, Chapel Hill, NC, USA
- SOLTI Cancer Research Group, Barcelona, Spain
| | - Aguirre A De Cubas
- Vanderbilt University Medical Center, Nashville, TN, USA
- Medical University of South Carolina, Charleston, SC, USA
| | - Youli Xia
- University of North Carolina, Chapel Hill, NC, USA
- Boehringer Ingelheim, Ridgefield, CT, USA
| | | | - Marni B McClure
- University of North Carolina, Chapel Hill, NC, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | - Cheng Fan
- University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Robyn T Burns
- Translational Breast Cancer Research Consortium, Baltimore, USA
| | - Sara Coppens
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Wheless
- University of North Carolina, Chapel Hill, NC, USA
| | - Salma Rezk
- University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | - Hui Shen
- Van Andel Institute, Grand Rapids, MI, USA
| | - Ben H Park
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ian Krop
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Nancy U Lin
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Uma Chandran
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Davis
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Alexander Ropelewski
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | | | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Nancy E Davidson
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
| | - Lisa A Carey
- University of North Carolina, Chapel Hill, NC, USA
| | - Adrian V Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Justin M Balko
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Tari A King
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Division of Breast Surgery, Brigham and Women's Hospital, Boston, MA, USA
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32
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Creighton CJ. Gene Expression Profiles in Cancers and Their Therapeutic Implications. Cancer J 2023; 29:9-14. [PMID: 36693152 PMCID: PMC9881750 DOI: 10.1097/ppo.0000000000000638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
ABSTRACT The vast amount of gene expression profiling data of bulk tumors and cell lines available in the public domain represents a tremendous resource. For any major cancer type, expression data can identify molecular subtypes, predict patient outcome, identify markers of therapeutic response, determine the functional consequences of somatic mutation, and elucidate the biology of metastatic and advanced cancers. This review provides a broad overview of gene expression profiling in cancer (which may include transcriptome and proteome levels) and the types of findings made using these data. This review also provides specific examples of accessing public cancer gene expression data sets and generating unique views of the data and the resulting genes of interest. These examples involve pan-cancer molecular subtyping, metabolism-associated expression correlates of patient survival involving multiple cancer types, and gene expression correlates of chemotherapy response in breast tumors.
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Affiliation(s)
- Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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Hintelmann K, Petersen C, Borgmann K. Radiotherapeutic Strategies to Overcome Resistance of Breast Cancer Brain Metastases by Considering Immunogenic Aspects of Cancer Stem Cells. Cancers (Basel) 2022; 15:211. [PMID: 36612206 PMCID: PMC9818478 DOI: 10.3390/cancers15010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Breast cancer is the most diagnosed cancer in women, and symptomatic brain metastases (BCBMs) occur in 15-20% of metastatic breast cancer cases. Despite technological advances in radiation therapy (RT), the prognosis of patients is limited. This has been attributed to radioresistant breast cancer stem cells (BCSCs), among other factors. The aim of this review article is to summarize the evidence of cancer-stem-cell-mediated radioresistance in brain metastases of breast cancer from radiobiologic and radiation oncologic perspectives to allow for the better interpretability of preclinical and clinical evidence and to facilitate its translation into new therapeutic strategies. To this end, the etiology of brain metastasis in breast cancer, its radiotherapeutic treatment options, resistance mechanisms in BCSCs, and effects of molecularly targeted therapies in combination with radiotherapy involving immune checkpoint inhibitors are described and classified. This is considered in the context of the central nervous system (CNS) as a particular metastatic niche involving the blood-brain barrier and the CNS immune system. The compilation of this existing knowledge serves to identify possible synergistic effects between systemic molecularly targeted therapies and ionizing radiation (IR) by considering both BCSCs' relevant resistance mechanisms and effects on normal tissue of the CNS.
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Affiliation(s)
- Katharina Hintelmann
- Department of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Cordula Petersen
- Department of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kerstin Borgmann
- Laboratory of Radiobiology and Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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Liu Y, Fang Y, Bao L, Wu F, Wang S, Hao S. Intercellular Communication Reveals Therapeutic Potential of Epithelial-Mesenchymal Transition in Triple-Negative Breast Cancer. Biomolecules 2022; 12:biom12101478. [PMID: 36291687 PMCID: PMC9599658 DOI: 10.3390/biom12101478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 12/07/2022] Open
Abstract
(1) Background: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with high intra-tumoral heterogeneity. The epithelial-mesenchymal transition (EMT) is one of the inducers of cancer metastasis and migration. However, the description of the EMT process in TNBC using single-cell RNA sequencing (scRNA-seq) remains unclear. (2) Methods: In this study, we analyzed 8938 cellular gene expression profiles from five TNBC patients. We first scored each malignant cell based on functional pathways to determine its EMT characteristics. Then, a pseudo-time trajectory analysis was employed to characterize the cell trajectories. Furthermore, CellChat was used to identify the cellular communications. (3) Results: We identified 888 epithelium-like and 846 mesenchyme-like malignant cells, respectively. A further pseudo-time trajectory analysis indicated the transition trends from epithelium-like to mesenchyme-like in malignant cells. To characterize the potential regulators of the EMT process, we identified 10 dysregulated transcription factors (TFs) between epithelium-like and mesenchyme-like malignant cells, in which overexpressed forkhead box protein A1 (FOXA1) was recognized as a poor prognosis marker of TNBC. Furthermore, we dissected the cell-cell communications via ligand-receptor (L-R) interactions. We observed that tumor-associated macrophages (TAMs) may support the invasion of malignant epithelial cells, based on CXCL-CXCR2 signaling. The tumor necrosis factor (TNF) signaling pathway secreted by TAMs was identified as an outgoing communication pattern, mediating the communications between monocytes/TAMs and malignant epithelial cells. Alternatively, the TNF-related ligand-receptor (L-R) pairs showed promising clinical implications. Some immunotherapy and anti-neoplastic drugs could interact with the L-R pairs as a potential strategy for the treatment of TNBC. In summary, this study enhances the understanding of the EMT process in the TNBC microenvironment, and dissections of EMT-related cell communications also provided us with potential treatment targets.
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Affiliation(s)
- Yang Liu
- Pharmacy Intravenous Admixture Services, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Yu Fang
- Department of Phase I Clinical Trial Ward, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Lili Bao
- Pharmacy Intravenous Admixture Services, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Feng Wu
- Department of Gastroenterology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Shilong Wang
- Pharmacy Intravenous Admixture Services, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
- Correspondence: (S.W.); (S.H.)
| | - Siyu Hao
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
- Correspondence: (S.W.); (S.H.)
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35
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Intralesional TLR4 agonist treatment strengthens the organ defense against colonizing cancer cells in the brain. Oncogene 2022; 41:5008-5019. [PMID: 36224342 DOI: 10.1038/s41388-022-02496-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 11/08/2022]
Abstract
Brain metastasis in breast cancer remains difficult to treat and its incidence is increasing. Therefore, the development of new therapies is of utmost clinical relevance. Recently, toll-like receptor (TLR) 4 was correlated with IL6 expression and poor prognosis in 1 215 breast cancer primaries. In contrast, we demonstrated that TLR4 stimulation reduces microglia-assisted breast cancer cell invasion. However, the expression, prognostic value, or therapeutic potential of TLR signaling in breast cancer brain metastasis have not been investigated. We thus tested the prognostic value of various TLRs in two brain-metastasis gene sets. Furthermore, we investigated different TLR agonists, as well as MyD88 and TRIF-deficient microenvironments in organotypic brain-slice ex vivo co-cultures and in vivo colonization experiments. These experiments underline the ambiguous roles of TLR4, its adapter MyD88, and the target nitric oxide (NO) during brain colonization. Moreover, analysis of the gene expression datasets of breast cancer brain metastasis patients revealed associations of TLR1 and IL6 with poor overall survival. Finally, our finding that a single LPS application at the onset of colonization shapes the later microglia/macrophage reaction at the macro-metastasis brain-parenchyma interface (MMPI) and reduces metastatic infiltration into the brain parenchyma may prove useful in immunotherapeutic considerations.
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36
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Dhakal A, Van Swearingen AED, O'Regan R, Anders CK. Systemic Therapy Approaches for Breast Cancer Brain and Leptomeningeal Metastases. Curr Treat Options Oncol 2022; 23:1457-1476. [PMID: 36136177 DOI: 10.1007/s11864-022-01011-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2022] [Indexed: 11/25/2022]
Abstract
OPINION STATEMENT Brain metastasis arising from breast cancer is associated with a poor prognosis. Various systemic chemotherapy and targeted therapies which are effective against breast cancer often fail to provide benefits against brain metastasis. This is mainly due to limited penetration of the therapies across the blood-brain barrier, and divergent evolution of brain metastasis compared to the primary tumor. Thus, brain metastasis is typically treated upfront with local therapies, such as surgery and radiation, followed by systemic therapies. Systemic therapies with CNS permeability are favored in patients with brain metastasis. This paper reviews various systemic therapy options for breast cancer brain metastasis.
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Affiliation(s)
| | | | | | - Carey K Anders
- Duke Center for Brain and Spine Metastasis, Duke Cancer Institute, Duke University, Durham, NC, USA.
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Hacking SM, Yakirevich E, Wang Y. From Immunohistochemistry to New Digital Ecosystems: A State-of-the-Art Biomarker Review for Precision Breast Cancer Medicine. Cancers (Basel) 2022; 14:cancers14143469. [PMID: 35884530 PMCID: PMC9315712 DOI: 10.3390/cancers14143469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary In this state-of-the-art breast biomarker review, we have tried to imagine and illustrate future, emerging digital breast cancer ecosystems which allow for greater incorporation of traditional immunohistochemical and molecular biomarkers, WSI, and radiomic features. Abstract Breast cancers represent complex ecosystem-like networks of malignant cells and their associated microenvironment. Estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) are biomarkers ubiquitous to clinical practice in evaluating prognosis and predicting response to therapy. Recent feats in breast cancer have led to a new digital era, and advanced clinical trials have resulted in a growing number of personalized therapies with corresponding biomarkers. In this state-of-the-art review, we included the latest 10-year updated recommendations for ER, PR, and HER2, along with the most salient information on tumor-infiltrating lymphocytes (TILs), Ki-67, PD-L1, and several prognostic/predictive biomarkers at genomic, transcriptomic, and proteomic levels recently developed for selection and optimization of breast cancer treatment. Looking forward, the multi-omic landscape of the tumor ecosystem could be integrated with computational findings from whole slide images and radiomics in predictive machine learning (ML) models. These are new digital ecosystems on the road to precision breast cancer medicine.
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Affiliation(s)
| | | | - Yihong Wang
- Correspondence: ; Tel.: +1-401-444-9897; Fax: +1-401-444-4377
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Feng P, Li Z, Li Y, Zhang Y, Miao X. Characterization of Different Subtypes of Immune Cell Infiltration in Glioblastoma to Aid Immunotherapy. Front Immunol 2022; 13:799509. [PMID: 35799789 PMCID: PMC9254719 DOI: 10.3389/fimmu.2022.799509] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Glioblastoma multiforme (GBM) has been identified as a frequently occurring adult primary brain cancer that is highly aggressive. Currently, the prognostic outcome for GBM patients is dismal, even with intensive treatment, and the median overall survival (OS) is 14.6 months. Immunotherapy, which is specific at the cellular level and can generate persistent immunosurveillance, is now becoming a promising tool to treat diverse cancers. However, the complicated nature of the tumor microenvironment (TME) makes it challenging to develop anti-GBM immunotherapy because several cell types, cytokines, and signaling pathways are involved in generating the immunosuppressive environment. Novel immunotherapies can illustrate novel tumor-induced immunosuppressive mechanisms. Here, we used unsupervised clustering analysis to identify different subtypes of immune cell infiltration that actuated different prognoses, biological actions, and immunotherapy responses. Gene cluster A, with a hot immune cell infiltration phenotype, had high levels of immune-related genes (IRGs), which were associated with immune pathways including the interferon-gamma response and interferon-alpha response, and had low IDH1 and ATRX mutation frequencies. Gene cluster B, a cold immune cell infiltration subtype, exhibited a high expression of the KCNIP2, SCRT1, CPLX2, JPH3, UNC13A, GABRB3, ARPP21, DLGAP1, NRXN1, DLL3, CA10, MAP2, SEZ6L, GRIA2, and GRIA4 genes and a low expression of immune-related genes, i.e., low levels of immune reactivity. Our study highlighted the complex interplay between immune cell infiltration and genetic mutation in the establishment of the tumor immune phenotype. Gene cluster A was identified as an important subtype with a better prognosis and improved immunotherapy response.
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Affiliation(s)
- Peng Feng
- Neurosurgery Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Zhenqing Li
- Medical College of Nantong University, Nantong, China
| | - Yuchen Li
- Hengyang Medical School, University of South China, Hengyang, China
| | - Yuelin Zhang
- Graduate Office Xi’an Medical University, Xi’an, China
| | - Xingyu Miao
- Neurosurgery Shaanxi Provincial People’s Hospital, Xi’an, China
- *Correspondence: Xingyu Miao,
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Menendez JA, Lupu R. Fatty acid synthase: A druggable driver of breast cancer brain metastasis. Expert Opin Ther Targets 2022; 26:427-444. [PMID: 35545806 DOI: 10.1080/14728222.2022.2077189] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Brain metastasis (BrM) is a key contributor to morbidity and mortality in breast cancer patients, especially among high-risk epidermal growth factor receptor 2-positive (HER2+) and triple-negative/basal-like molecular subtypes. Optimal management of BrM is focused on characterizing a "BrM dependency map" to prioritize targetable therapeutic vulnerabilities. AREAS COVERED We review recent studies addressing the targeting of BrM in the lipid-deprived brain environment, which selects for brain-tropic breast cancer cells capable of cell-autonomously generating fatty acids by upregulating de novo lipogenesis via fatty acid synthase (FASN). Disruption of FASN activity impairs breast cancer growth in the brain, but not extracranially, and mapping of the molecular causes of organ-specific patterns of metastasis has uncovered an enrichment of lipid metabolism signatures in brain metastasizing cells. Targeting SREBP1-the master regulator of lipogenic gene transcription-curtails the ability of breast cancer cells to survive in the brain microenvironment. EXPERT OPINION Targeting FASN represents a new therapeutic opportunity for patients with breast cancer and BrM. Delivery of brain-permeable FASN inhibitors and identifying strategies to target metabolic plasticity that might compensate for impaired brain FASN activity are two potential roadblocks that may hinder FASN-centered strategies against BrM.
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Affiliation(s)
- Javier A Menendez
- Metabolism and Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, 17007 Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), 17190 Girona, Spain
| | - Ruth Lupu
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Biochemistry and Molecular Biology Laboratory, Mayo Clinic Minnesota, Rochester, MN 55905, USA.,Mayo Clinic Cancer Center, Rochester, MN 55905, USA
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Stratification of radiosensitive brain metastases based on an actionable S100A9/RAGE resistance mechanism. Nat Med 2022; 28:752-765. [PMID: 35411077 PMCID: PMC9018424 DOI: 10.1038/s41591-022-01749-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 02/16/2022] [Indexed: 12/25/2022]
Abstract
AbstractWhole-brain radiotherapy (WBRT) is the treatment backbone for many patients with brain metastasis; however, its efficacy in preventing disease progression and the associated toxicity have questioned the clinical impact of this approach and emphasized the need for alternative treatments. Given the limited therapeutic options available for these patients and the poor understanding of the molecular mechanisms underlying the resistance of metastatic lesions to WBRT, we sought to uncover actionable targets and biomarkers that could help to refine patient selection. Through an unbiased analysis of experimental in vivo models of brain metastasis resistant to WBRT, we identified activation of the S100A9–RAGE–NF-κB–JunB pathway in brain metastases as a potential mediator of resistance in this organ. Targeting this pathway genetically or pharmacologically was sufficient to revert the WBRT resistance and increase therapeutic benefits in vivo at lower doses of radiation. In patients with primary melanoma, lung or breast adenocarcinoma developing brain metastasis, endogenous S100A9 levels in brain lesions correlated with clinical response to WBRT and underscored the potential of S100A9 levels in the blood as a noninvasive biomarker. Collectively, we provide a molecular framework to personalize WBRT and improve its efficacy through combination with a radiosensitizer that balances therapeutic benefit and toxicity.
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Knier NN, Pellizzari S, Zhou J, Foster PJ, Parsyan A. Preclinical Models of Brain Metastases in Breast Cancer. Biomedicines 2022; 10:biomedicines10030667. [PMID: 35327469 PMCID: PMC8945440 DOI: 10.3390/biomedicines10030667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 02/05/2023] Open
Abstract
Breast cancer remains a leading cause of mortality among women worldwide. Brain metastases confer extremely poor prognosis due to a lack of understanding of their specific biology, unique physiologic and anatomic features of the brain, and limited treatment strategies. A major roadblock in advancing the treatment of breast cancer brain metastases (BCBM) is the scarcity of representative experimental preclinical models. Current models are predominantly based on the use of animal xenograft models with immortalized breast cancer cell lines that poorly capture the disease’s heterogeneity. Recent years have witnessed the development of patient-derived in vitro and in vivo breast cancer culturing systems that more closely recapitulate the biology from individual patients. These advances led to the development of modern patient-tissue-based experimental models for BCBM. The success of preclinical models is also based on the imaging technologies used to detect metastases. Advances in animal brain imaging, including cellular MRI and multimodality imaging, allow sensitive and specific detection of brain metastases and monitoring treatment responses. These imaging technologies, together with novel translational breast cancer models based on patient-derived cancer tissues, represent a unique opportunity to advance our understanding of brain metastases biology and develop novel treatment approaches. This review discusses the state-of-the-art knowledge in preclinical models of this disease.
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Affiliation(s)
- Natasha N. Knier
- Department of Medical Biophysics, Western University, London, ON N6A 5C1, Canada; (N.N.K.); (P.J.F.)
- Imaging Laboratories, Robarts Research Institute, London, ON N6A 5B7, Canada
| | - Sierra Pellizzari
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 3K7, Canada;
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA;
| | - Paula J. Foster
- Department of Medical Biophysics, Western University, London, ON N6A 5C1, Canada; (N.N.K.); (P.J.F.)
- Imaging Laboratories, Robarts Research Institute, London, ON N6A 5B7, Canada
| | - Armen Parsyan
- Department of Anatomy and Cell Biology, Western University, London, ON N6A 3K7, Canada;
- London Regional Cancer Program, London Health Science Centre, London, ON N6A 5W9, Canada
- Department of Oncology, Western University, London, ON N6A 4L6, Canada
- Department of Surgery, Western University, London, ON N6A 3K7, Canada
- Correspondence: ; Tel.: +1-519-646-4831; Fax: +1-519-646-6327
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