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Sharma D, Dhobi M, Lather V, Pandita D. An insight into the therapeutic effects of isoliquiritigenin in breast cancer. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03282-6. [PMID: 39007925 DOI: 10.1007/s00210-024-03282-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
Breast cancer ranks as the most widespread malignant condition in women, emerging as a primary contributor to mortality. The primary challenges in cancer treatments involve undesirable side effects. Therefore, exploring natural compounds as additional therapy could provide valuable insights. Isoliquiritigenin (ILN), an isoflavonoid featuring a chalcone moiety primarily sourced from Glycyrrhiza species, has garnered increasing interest in breast cancer research. This review aims to provide a comprehensive understanding of ILN's mechanisms of action in breast cancer, drawing from a range of in vitro and in vivo studies. ILN primarily acts by inhibiting angiogenesis, aromatase, inflammation, and cell proliferation, and preventing invasion and metastasis. Mechanistically, it downregulates miR-374a, phosphoinositide-3-kinase-protein kinase B/Akt, maternal embryonic leucine zipper kinase, vascular endothelial growth factor, and estrogen receptor protein levels, and causes enhancement of Wnt inhibitory factor-1, and Unc-51-like kinase 1 expression to treat breast cancer. ILN emerges as a promising natural option, offering therapeutic advantages with minimal side effects. However, it is important to note that current research on ILN is primarily limited to preclinical models, underscoring the need for further investigation to validate its potential efficacy.
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Affiliation(s)
- Divya Sharma
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Sector-III, Pushp Vihar, Government of NCT of Delhi, New Delhi, 110017, India
| | - Mahaveer Dhobi
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Sector-III, Pushp Vihar, Government of NCT of Delhi, New Delhi, 110017, India.
| | - Viney Lather
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Sector 125, Noida, 201313, India.
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Institute of Pharmaceutical Sciences & Research (DIPSAR) Delhi Pharmaceutical Sciences and Research University, Sector-III, Pushp Vihar, Government of NCT of Delhi, New Delhi, 110017, India.
- Centre for Advanced Formulation Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, Sector-III, Pushp Vihar, Government of NCT of Delhi, New Delhi, 110017, India.
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2
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Sim N, Carter JM, Deka K, Tan BKT, Sim Y, Tan SM, Li Y. TWEAK/Fn14 signalling driven super-enhancer reprogramming promotes pro-metastatic metabolic rewiring in triple-negative breast cancer. Nat Commun 2024; 15:5638. [PMID: 38965263 PMCID: PMC11224303 DOI: 10.1038/s41467-024-50071-z] [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: 07/28/2023] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Triple Negative Breast Cancer (TNBC) is the most aggressive breast cancer subtype suffering from limited targeted treatment options. Following recent reports correlating Fibroblast growth factor-inducible 14 (Fn14) receptor overexpression in Estrogen Receptor (ER)-negative breast cancers with metastatic events, we show that Fn14 is specifically overexpressed in TNBC patients and associated with poor survival. We demonstrate that constitutive Fn14 signalling rewires the transcriptomic and epigenomic landscape of TNBC, leading to enhanced tumour growth and metastasis. We further illustrate that such mechanisms activate TNBC-specific super enhancers (SE) to drive the transcriptional activation of cancer dependency genes via chromatin looping. In particular, we uncover the SE-driven upregulation of Nicotinamide phosphoribosyltransferase (NAMPT), which promotes NAD+ and ATP metabolic reprogramming critical for filopodia formation and metastasis. Collectively, our study details the complex mechanistic link between TWEAK/Fn14 signalling and TNBC metastasis, which reveals several vulnerabilities which could be pursued for the targeted treatment of TNBC patients.
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Affiliation(s)
- Nicholas Sim
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jean-Michel Carter
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Kamalakshi Deka
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Benita Kiat Tee Tan
- Division of Surgery and Surgical Oncology, Department of Breast Surgery, National Cancer Centre Singapore, 30 Hospital Blvd, Singapore, 168583, Singapore
- Division of Surgery and Surgical Oncology, Department of Breast Surgery, Singapore General Hospital, 31 Third Hospital Ave, Singapore, 168753, Singapore
- SingHealth Duke-NUS Breast Centre, Singapore, Singapore
| | - Yirong Sim
- Division of Surgery and Surgical Oncology, Department of Breast Surgery, National Cancer Centre Singapore, 30 Hospital Blvd, Singapore, 168583, Singapore
- Division of Surgery and Surgical Oncology, Department of Breast Surgery, Singapore General Hospital, 31 Third Hospital Ave, Singapore, 168753, Singapore
- SingHealth Duke-NUS Breast Centre, Singapore, Singapore
| | - Suet-Mien Tan
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore.
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3
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Li JR, Li LY, Zhang HX, Zhong MQ, Zou ZM. Atramacronoid A induces the PANoptosis-like cell death of human breast cancer cells through the CASP-3/PARP-GSDMD-MLKL pathways. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024:1-14. [PMID: 38958645 DOI: 10.1080/10286020.2024.2368841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024]
Abstract
Breast cancer is the most common malignant tumor and a major cause of mortality among women worldwide. Atramacronoid A (AM-A) is a unique natural sesquiterpene lactone isolated from the rhizome of Atractylodes macrocephala Koidz (known as Baizhu in Chinese). Our study demonstrated that AM-A triggers a specific form of cell death resembling PANoptosis-like cell death. Further analysis indicated that AM-A-induced PANoptosis-like cell death is associated with the CASP-3/PARP-GSDMD-MLKL pathways, which are mediated by mitochondrial dysfunction. These results suggest the potential of AM-A as a lead compound and offer insights for the development of therapeutic agents for breast cancer from natural products.
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Affiliation(s)
- Jing-Rong Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Ling-Yu Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Hai-Xin Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Ming-Qin Zhong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Zhong-Mei Zou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China
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4
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Chaubal R, Gardi N, Joshi S, Pantvaidya G, Kadam R, Vanmali V, Hawaldar R, Talker E, Chitra J, Gera P, Bhatia D, Kalkar P, Gurav M, Shetty O, Desai S, Krishnan NM, Nair N, Parmar V, Dutt A, Panda B, Gupta S, Badwe R. Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment. Mol Cancer Res 2024; 22:572-584. [PMID: 38394149 PMCID: PMC11148542 DOI: 10.1158/1541-7786.mcr-23-0265] [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: 04/13/2023] [Revised: 08/24/2023] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Surgery exposes tumor tissue to severe hypoxia and mechanical stress leading to rapid gene expression changes in the tumor and its microenvironment, which remain poorly characterized. We biopsied tumor and adjacent normal tissues from patients with breast (n = 81) and head/neck squamous cancers (HNSC; n = 10) at the beginning (A), during (B), and end of surgery (C). Tumor/normal RNA from 46/81 patients with breast cancer was subjected to mRNA-Seq using Illumina short-read technology, and from nine patients with HNSC to whole-transcriptome microarray with Illumina BeadArray. Pathways and genes involved in 7 of 10 known cancer hallmarks, namely, tumor-promoting inflammation (TNF-A, NFK-B, IL18 pathways), activation of invasion and migration (various extracellular matrix-related pathways, cell migration), sustained proliferative signaling (K-Ras Signaling), evasion of growth suppressors (P53 signaling, regulation of cell death), deregulating cellular energetics (response to lipid, secreted factors, and adipogenesis), inducing angiogenesis (hypoxia signaling, myogenesis), and avoiding immune destruction (CTLA4 and PDL1) were significantly deregulated during surgical resection (time points A vs. B vs. C). These findings were validated using NanoString assays in independent pre/intra/post-operative breast cancer samples from 48 patients. In a comparison of gene expression data from biopsy (analogous to time point A) with surgical resection samples (analogous to time point C) from The Cancer Genome Atlas study, the top deregulated genes were the same as identified in our analysis, in five of the seven studied cancer types. This study suggests that surgical extirpation deregulates the hallmarks of cancer in primary tumors and adjacent normal tissue across different cancers. IMPLICATIONS Surgery deregulates hallmarks of cancer in human tissue.
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Affiliation(s)
- Rohan Chaubal
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Nilesh Gardi
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Shalaka Joshi
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Gouri Pantvaidya
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Rasika Kadam
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Vaibhav Vanmali
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Clinical Research Secretariat, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Rohini Hawaldar
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Clinical Research Secretariat, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Elizabeth Talker
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Jaya Chitra
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Poonam Gera
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Dimple Bhatia
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Prajakta Kalkar
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Mamta Gurav
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Omshree Shetty
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Sangeeta Desai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Department of Pathology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | | | - Nita Nair
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
| | - Vani Parmar
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- 3D Printing Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Amit Dutt
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
| | - Binay Panda
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Sudeep Gupta
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
- Department of Medical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
| | - Rajendra Badwe
- Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai, India
- Hypoxia and Clinical Genomics Lab (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, India
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5
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Rathore Y, Lakhanpal T, Chakraborty S, Chakravarty R, Mittal BR, Irrinki RNS, Laroiya I, Kaur K, Shukla J. Targeting Breast Cancer Using 177 Lu-Labeled Trastuzumab and Trastuzumab Fragment : First-in-Human Clinical Experience. Clin Nucl Med 2024; 49:e258-e265. [PMID: 38579266 DOI: 10.1097/rlu.0000000000005208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
PURPOSE A monoclonal antibody, trastuzumab, is used for immunotherapy for HER2-expressing breast cancers. Large-sized antibodies demonstrate hepatobiliary clearance and slower pharmacokinetics. A trastuzumab fragment (Fab; 45 kDa) has been generated for theranostic use. PATIENTS AND METHODS Fab was generated by papain digestion. Trastuzumab and Fab have been radiolabelled with 177 Lu after being conjugated with a bifunctional chelating. The affinity and target specificity were studied in vitro. The first-in-human study was performed. RESULTS The bifunctional chelating agent conjugation of 1-2 molecules with trastuzumab and Fab was detected at the molar ratio 1:10 in bicarbonate buffer (0.5 M, pH 8) at 37°-40°C. However, 2-3 molecules of bifunctional chelating agent were conjugated when DMSO in PBS (0.1 M, pH 7) was used as a conjugation buffer at a molar ratio of 1:10. The radiolabelling yield of DOTA-conjugated Fab and trastuzumab at pH 5, 45°C to 50°C, with incubation time 2.5-3 hours was 80% and 41.67%, respectively. However, with DOTAGA-conjugated trastuzumab and Fab, the maximum radiolabelling yield at pH 5.5, 37°C, and at 2.5-3 hours was 80.83% and 83%, respectively. The calculated K d of DOTAGA Fab and trastuzumab with HER2-positive SKBR3 cells was 6.85 ± 0.24 × 10 -8 M and 1.71 ± 0.10 × 10 -8 M, respectively. DOTAGA-Fab and trastuzumab showed better radiolabelling yield at mild reaction conditions.177 Lu-DOTAGA-Fab demonstrated higher lesion uptake and lower liver retention as compared with 177 Lu-DOTAGA-trastuzumab. However, 177 Lu-DOTAGA-Fab as compared with 177 Lu-DOTAGA-trastuzumab showed a relatively early washout (5 days) from the lesion. CONCLUSIONS 177 Lu-DOTAGA-Fab and trastuzumab are suitable for targeting the HER2 receptors.
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Affiliation(s)
- Yogesh Rathore
- From the Department of Nuclear Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh
| | - Tamanna Lakhanpal
- From the Department of Nuclear Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh
| | | | | | - B R Mittal
- From the Department of Nuclear Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh
| | - R N Santhosh Irrinki
- Department of General Surgery, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ishita Laroiya
- Department of General Surgery, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Komalpreet Kaur
- From the Department of Nuclear Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh
| | - Jaya Shukla
- From the Department of Nuclear Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh
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6
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Torland LA, Lai X, Kumar S, Riis MH, Geisler J, Lüders T, Tekpli X, Kristensen V, Sahlberg K, Tahiri A. Benign breast tumors may arise on different immunological backgrounds. Mol Oncol 2024. [PMID: 38757377 DOI: 10.1002/1878-0261.13655] [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: 09/07/2023] [Revised: 12/21/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024] Open
Abstract
Benign breast tumors are a nonthreatening condition defined as abnormal cell growth within the breast without the ability to invade nearby tissue. However, benign lesions hold valuable biological information that can lead us toward better understanding of tumor biology. In this study, we have used two pathway analysis algorithms, Pathifier and gene set variation analysis (GSVA), to identify biological differences between normal breast tissue, benign tumors and malignant tumors in our clinical dataset. Our results revealed that one-third of all pathways that were significantly different between benign and malignant tumors were immune-related pathways, and 227 of them were validated by both methods and in the METABRIC dataset. Furthermore, five of these pathways (all including genes involved in cytokine and interferon signaling) were related to overall survival in cancer patients in both datasets. The cellular moieties that contribute to immune differences in malignant and benign tumors were analyzed using the deconvolution tool, CIBERSORT. The results showed that levels of some immune cells were specifically higher in benign than in malignant tumors, and this was especially the case for resting dendritic cells and follicular T-helper cells. Understanding the distinct immune profiles of benign and malignant breast tumors may aid in developing noninvasive diagnostic methods to differentiate between them in the future.
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Affiliation(s)
- Lilly Anne Torland
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
- Department of Research and Innovation, Vestre Viken HF, Drammen Hospital, Norway
| | - Xiaoran Lai
- Oslo Centre for Biostatistics and Epidemiology, Faculty of Medicine, University of Oslo, Norway
| | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, Canada
| | - Margit H Riis
- Department of Breast and Endocrine Surgery, Clinic of Cancer, Oslo University Hospital, Norway
| | - Jürgen Geisler
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Torben Lüders
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Vessela Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kristine Sahlberg
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
- Department of Research and Innovation, Vestre Viken HF, Drammen Hospital, Norway
| | - Andliena Tahiri
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
- Department of Research and Innovation, Vestre Viken HF, Drammen Hospital, Norway
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7
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Qiu Y, Chen A, Yu R, Llevenes P, Seen M, Ko NY, Monti S, Denis GV. Insulin Resistance Increases TNBC Aggressiveness and Brain Metastasis via Adipocyte-derived Exosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592097. [PMID: 38746141 PMCID: PMC11092600 DOI: 10.1101/2024.05.01.592097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Patients with triple negative breast cancer (TNBC) and comorbid Type 2 Diabetes (T2D), characterized by insulin resistance of adipose tissue, have higher risk of metastasis and shorter survival. Adipocytes are the main non-malignant cells of the breast tumor microenvironment (TME). However, adipocyte metabolism is usually ignored in oncology and mechanisms that couple T2D to TNBC outcomes are poorly understood. Here we hypothesized that exosomes, small vesicles secreted by TME breast adipocytes, drive epithelial-to-mesenchymal transition (EMT) and metastasis in TNBC via miRNAs. Exosomes were purified from conditioned media of 3T3-L1 mature adipocytes, either insulin-sensitive (IS) or insulin-resistant (IR). Murine 4T1 cells, a TNBC model, were treated with exosomes in vitro (72h). EMT, proliferation and angiogenesis were elevated in IR vs. control and IS. Brain metastases showed more mesenchymal morphology and EMT enrichment in the IR group. MiR-145a-3p is highly differentially expressed between IS and IR, and potentially regulates metastasis. Significance IR adipocyte exosomes modify TME, increase EMT and promote metastasis to distant organs, likely through miRNA pathways. We suggest metabolic diseases such as T2D reshape the TME, promoting metastasis and decreasing survival. Therefore, TNBC patients with T2D should be closely monitored for metastasis, with metabolic medications considered.
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8
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Zhou XX, Zhang L, Cui QX, Li H, Sang XQ, Zhang HX, Zhu YM, Kuai ZX. A Channel-Dimensional Feature-Reconstructed Deep Learning Model for Predicting Breast Cancer Molecular Subtypes on Overall b-Value Diffusion-Weighted MRI. J Magn Reson Imaging 2024; 59:1425-1435. [PMID: 37403945 DOI: 10.1002/jmri.28895] [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: 06/02/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Dynamic contrast-enhanced (DCE) MRI commonly outperforms diffusion-weighted (DW) MRI in breast cancer discrimination. However, the side effects of contrast agents limit the use of DCE-MRI, particularly in patients with chronic kidney disease. PURPOSE To develop a novel deep learning model to fully exploit the potential of overall b-value DW-MRI without the need for a contrast agent in predicting breast cancer molecular subtypes and to evaluate its performance in comparison with DCE-MRI. STUDY TYPE Prospective. SUBJECTS 486 female breast cancer patients (training/validation/test: 64%/16%/20%). FIELD STRENGTH/SEQUENCE 3.0 T/DW-MRI (13 b-values) and DCE-MRI (one precontrast and five postcontrast phases). ASSESSMENT The breast cancers were divided into four subtypes: luminal A, luminal B, HER2+, and triple negative. A channel-dimensional feature-reconstructed (CDFR) deep neural network (DNN) was proposed to predict these subtypes using pathological diagnosis as the reference standard. Additionally, a non-CDFR DNN (NCDFR-DNN) was built for comparative purposes. A mixture ensemble DNN (ME-DNN) integrating two CDFR-DNNs was constructed to identify subtypes on multiparametric MRI (MP-MRI) combing DW-MRI and DCE-MRI. STATISTICAL TESTS Model performance was evaluated using accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). Model comparisons were performed using the one-way analysis of variance with least significant difference post hoc test and the DeLong test. P < 0.05 was considered significant. RESULTS The CDFR-DNN (accuracies, 0.79 ~ 0.80; AUCs, 0.93 ~ 0.94) demonstrated significantly improved predictive performance than the NCDFR-DNN (accuracies, 0.76 ~ 0.78; AUCs, 0.92 ~ 0.93) on DW-MRI. Utilizing the CDFR-DNN, DW-MRI attained the predictive performance equal (P = 0.065 ~ 1.000) to DCE-MRI (accuracies, 0.79 ~ 0.80; AUCs, 0.93 ~ 0.95). The predictive performance of the ME-DNN on MP-MRI (accuracies, 0.85 ~ 0.87; AUCs, 0.96 ~ 0.97) was superior to those of both the CDFR-DNN and NCDFR-DNN on either DW-MRI or DCE-MRI. DATA CONCLUSION The CDFR-DNN enabled overall b-value DW-MRI to achieve the predictive performance comparable to DCE-MRI. MP-MRI outperformed DW-MRI and DCE-MRI in subtype prediction. LEVEL OF EVIDENCE 2 TECHNICAL EFFICACY STAGE: 1.
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Affiliation(s)
- Xin-Xiang Zhou
- Imaging Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Lan Zhang
- Imaging Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Quan-Xiang Cui
- Imaging Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hui Li
- Imaging Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xi-Qiao Sang
- Division of Respiratory Disease, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hong-Xia Zhang
- Imaging Center, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yue-Min Zhu
- CREATIS, CNRS UMR 5220-INSERM U1294-University Lyon 1-INSA Lyon-University Jean Monnet Saint-Etienne, Villeurbanne, France
| | - Zi-Xiang Kuai
- Imaging Center, Harbin Medical University Cancer Hospital, Harbin, China
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9
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Yashar WM, Estabrook J, Holly HD, Somers J, Nikolova O, Babur Ö, Braun TP, Demir E. Predicting transcription factor activity using prior biological information. iScience 2024; 27:109124. [PMID: 38455978 PMCID: PMC10918219 DOI: 10.1016/j.isci.2024.109124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/20/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.
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Affiliation(s)
- William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hannah D. Holly
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Olga Nikolova
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts, Boston, MA 02125, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Oncologic Sciences, Department of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
- Pacific Northwest National Laboratories, Richland, WA 99354, USA
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Chen BF, Tsai YF, Lien PJ, Lin YS, Feng CJ, Chen YJ, Cheng HF, Liu CY, Chao TC, Lai JI, Tseng LM, Huang CC. Prevalent landscape of tumor genomic alterations of luminal B1 breast cancers using a comprehensive genomic profiling assay in Taiwan. Breast Cancer 2024; 31:217-227. [PMID: 38070067 DOI: 10.1007/s12282-023-01524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/06/2023] [Indexed: 03/01/2024]
Abstract
BACKGROUND The human epidermal growth factor receptor 2 (HER2) negative luminal B1 subtype of breast cancer has been reported with a poorer outcome than luminal A in recent studies. This study aimed to investigate the molecular alterations and identify potential therapeutic targets by analyzing the genetic profiling from a cohort of luminal B1 breast cancer in Taiwan. METHODS We enrolled patients with luminal B1 breast cancer in our study. They were classified as patients who received curative surgery and adjuvant or neoadjuvant chemotherapy as the low-risk group, and who had advanced or metastatic disease or early relapse during the follow-up time as the high-risk group. Using targeted sequencing, we evaluated genomic alterations, interpreting variants with the ESMO Scale of clinical actionability of molecular targets (ESCAT). RESULTS A total of 305 luminal B1 breast cancer patients underwent targeted sequencing analyses. The high-risk patients reported more actionable genes and called variants than the low-risk group (P < 0.05). PIK3CA (42%), FGFR1 (25%), and BRCA1/2 (10.5%) were the most prevalent ESCAT actionable alterations in luminal B1 breast cancer. There was no difference in the prevalence of actionable mutations between these two groups, except for ERBB2 oncogenic mutations, which were more prevalent among the high-risk than the low-risk group (P < 0.05). Alterations in PTEN, ERBB2, and BRCA1/2 were associated with disease relapse events in luminal B1 breast cancer. CONCLUSIONS PIK3CA, FGFR1, and BRCA1/2 were the most prevalent actionable alterations among Taiwanese luminal B1 breast cancer. Moreover, PTEN and BRCA1/2 was significantly associated with disease relapse.
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Affiliation(s)
- Bo-Fang Chen
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Fang Tsai
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Shu Lin
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Jen Chen
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Han-Fang Cheng
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ta-Chung Chao
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
- Division of Cancer Prevention, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jiun-I Lai
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- Center of Immuno-Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Ling-Ming Tseng
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan.
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.
- School of Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan.
- Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan.
| | - Chi-Cheng Huang
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, 201, Section 2, Shih-Pai Road, Taipei, 112, Taiwan.
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.
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11
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Koh M, Lim H, Jin H, Kim M, Hong Y, Hwang YK, Woo Y, Kim ES, Kim SY, Kim KM, Lim HK, Jung J, Kang S, Park B, Lee HB, Han W, Lee MS, Moon A. ANXA2 (annexin A2) is crucial to ATG7-mediated autophagy, leading to tumor aggressiveness in triple-negative breast cancer cells. Autophagy 2024; 20:659-674. [PMID: 38290972 PMCID: PMC10936647 DOI: 10.1080/15548627.2024.2305063] [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: 04/14/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is associated with a poor prognosis and metastatic growth. TNBC cells frequently undergo macroautophagy/autophagy, contributing to tumor progression and chemotherapeutic resistance. ANXA2 (annexin A2), a potential therapeutic target for TNBC, has been reported to stimulate autophagy. In this study, we investigated the role of ANXA2 in autophagic processes in TNBC cells. TNBC patients exhibited high levels of ANXA2, which correlated with poor outcomes. ANXA2 increased LC3B-II levels following bafilomycin A1 treatment and enhanced autophagic flux in TNBC cells. Notably, ANXA2 upregulated the phosphorylation of HSF1 (heat shock transcription factor 1), resulting in the transcriptional activation of ATG7 (autophagy related 7). The mechanistic target of rapamycin kinase complex 2 (MTORC2) played an important role in ANXA2-mediated ATG7 transcription by HSF1. MTORC2 did not affect the mRNA level of ANXA2, but it was involved in the protein stability of ANXA2. HSPA (heat shock protein family A (Hsp70)) was a potential interacting protein with ANXA2, which may protect ANXA2 from lysosomal proteolysis. ANXA2 knockdown significantly increased sensitivity to doxorubicin, the first-line chemotherapeutic regimen for TNBC treatment, suggesting that the inhibition of autophagy by ANXA2 knockdown may overcome doxorubicin resistance. In a TNBC xenograft mouse model, we demonstrated that ANXA2 knockdown combined with doxorubicin administration significantly inhibited tumor growth compared to doxorubicin treatment alone, offering a promising avenue to enhance the effectiveness of chemotherapy. In summary, our study elucidated the molecular mechanism by which ANXA2 modulates autophagy, suggesting a potential therapeutic approach for TNBC treatment.Abbreviation: ATG: autophagy related; ChIP: chromatin-immunoprecipitation; HBSS: Hanks' balanced salt solution; HSF1: heat shock transcription factor 1; MTOR: mechanistic target of rapamycin kinase; TNBC: triple-negative breast cancer; TFEB: transcription factor EB; TFE3: transcription factor binding to IGHM enhancer 3.
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Affiliation(s)
- Minsoo Koh
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Hyesol Lim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Hao Jin
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Minjoo Kim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Yeji Hong
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Young Keun Hwang
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Yunjung Woo
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Eun-Sook Kim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Sun Young Kim
- Department of Chemistry, College of Science and Technology, Duksung Women’s University, Seoul, Korea
| | - Kyung Mee Kim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Hyun Kyung Lim
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Joohee Jung
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
| | - Sujin Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Boyoun Park
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea
| | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Myung-Shik Lee
- Avison Biomedical Research Center, Yonsei University College of Medicine, Seoul, Korea
| | - Aree Moon
- Duksung Innovative Drug Center, College of Pharmacy, Duksung Women’s University, Seoul, Korea
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Kariotis S, Tan PF, Lu H, Rhodes CJ, Wilkins MR, Lawrie A, Wang D. Omada: robust clustering of transcriptomes through multiple testing. Gigascience 2024; 13:giae039. [PMID: 38991852 PMCID: PMC11238428 DOI: 10.1093/gigascience/giae039] [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: 07/28/2023] [Revised: 02/09/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Cohort studies increasingly collect biosamples for molecular profiling and are observing molecular heterogeneity. High-throughput RNA sequencing is providing large datasets capable of reflecting disease mechanisms. Clustering approaches have produced a number of tools to help dissect complex heterogeneous datasets, but selecting the appropriate method and parameters to perform exploratory clustering analysis of transcriptomic data requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent. To address this, we have developed Omada, a suite of tools aiming to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning-based functions. FINDINGS The efficiency of each tool was tested with 7 datasets characterized by different expression signal strengths to capture a wide spectrum of RNA expression datasets. Our toolkit's decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Within datasets with less clear biological distinctions, our tools either formed stable subgroups with different expression profiles and robust clinical associations or revealed signs of problematic data such as biased measurements. CONCLUSIONS In conclusion, Omada successfully automates the robust unsupervised clustering of transcriptomic data, making advanced analysis accessible and reliable even for those without extensive machine learning expertise. Implementation of Omada is available at http://bioconductor.org/packages/omada/.
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Affiliation(s)
- Sokratis Kariotis
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Pei Fang Tan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
| | - Haiping Lu
- Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, S1 4DP, Sheffield, United Kingdom
| | - Christopher J Rhodes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Martin R Wilkins
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Allan Lawrie
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
| | - Dennis Wang
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 30 Medical Dr, 117609, Singapore, Republic of Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis St, Matrix, 138671, Singapore, Republic of Singapore
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse St, SW3 6LY, London, United Kingdom
- Department of Computer Science, University of Sheffield, Regent Court, 211 Portobello, S1 4DP, Sheffield, United Kingdom
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13
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Desterke C, Xiang Y, Elhage R, Duruel C, Chang Y, Hamaï A. Ferroptosis Inducers Upregulate PD-L1 in Recurrent Triple-Negative Breast Cancer. Cancers (Basel) 2023; 16:155. [PMID: 38201582 PMCID: PMC10778345 DOI: 10.3390/cancers16010155] [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: 11/26/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
(1) Background: Triple-negative breast cancer (TNBC) is a distinct subgroup of breast cancer presenting a high level of recurrence, and neo-adjuvant chemotherapy is beneficial in its therapy management. Anti-PD-L1 immunotherapy improves the effect of neo-adjuvant therapy in TNBC. (2) Methods: Immune-modulation and ferroptosis-related R-packages were developed for integrative omics analyses under ferroptosis-inducer treatments: TNBC cells stimulated with ferroptosis inducers (GSE173905, GSE154425), single cell data (GSE191246) and mass spectrometry on breast cancer stem cells. Clinical association analyses were carried out with breast tumors (TCGA and METABRIC cohorts). Protein-level validation was investigated through protein atlas proteome experiments. (3) Results: Erastin/RSL3 ferroptosis inducers upregulate CD274 in TNBC cells (MDA-MB-231 and HCC38). In breast cancer, CD274 expression is associated with overall survival. Breast tumors presenting high expression of CD274 upregulated some ferroptosis drivers associated with prognosis: IDO1, IFNG and TNFAIP3. At the protein level, the induction of Cd274 and Tnfaip3 was confirmed in breast cancer stem cells under salinomycin treatment. In a 4T1 tumor treated with cyclophosphamide, the single cell expression of Cd274 was found to increase both in myeloid- and lymphoid-infiltrated cells, independently of its receptor Pdcd1. The CD274 ferroptosis-driver score computed on a breast tumor transcriptome stratified patients on their prognosis: low score was observed in the basal subgroup, with a higher level of recurrent risk scores (oncotypeDx, ggi and gene70 scores). In the METABRIC cohort, CD274, IDO1, IFNG and TNFAIP3 were found to be overexpressed in the TNBC subgroup. The CD274 ferroptosis-driver score was found to be associated with overall survival, independently of TNM classification and age diagnosis. The tumor expression of CD274, TNFAIP3, IFNG and IDO1, in a biopsy of breast ductal carcinoma, was confirmed at the protein level (4) Conclusions: Ferroptosis inducers upregulate PD-L1 in TNBC cells, known to be an effective target of immunotherapy in high-risk early TNBC patients who received neo-adjuvant therapy. Basal and TNBC tumors highly expressed CD274 and ferroptosis drivers: IFNG, TNFAIP3 and IDO1. The CD274 ferroptosis-driver score is associated with prognosis and to the risk of recurrence in breast cancer. A potential synergy of ferroptosis inducers with anti-PD-L1 immunotherapy is suggested for recurrent TNBC.
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Affiliation(s)
- Christophe Desterke
- UFR Médecine-INSERM UMRS1310, Université Paris-Saclay, F-94800 Villejuif, France
| | - Yao Xiang
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Université Paris Cité, F-75015 Paris, France; (Y.X.); (R.E.); (C.D.); (Y.C.)
| | - Rima Elhage
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Université Paris Cité, F-75015 Paris, France; (Y.X.); (R.E.); (C.D.); (Y.C.)
- Team 5/Ferostem Group, F-75015 Paris, France
| | - Clémence Duruel
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Université Paris Cité, F-75015 Paris, France; (Y.X.); (R.E.); (C.D.); (Y.C.)
- Team 5/Ferostem Group, F-75015 Paris, France
| | - Yunhua Chang
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Université Paris Cité, F-75015 Paris, France; (Y.X.); (R.E.); (C.D.); (Y.C.)
| | - Ahmed Hamaï
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Université Paris Cité, F-75015 Paris, France; (Y.X.); (R.E.); (C.D.); (Y.C.)
- Team 5/Ferostem Group, F-75015 Paris, France
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Hu Z, Yang S, Xu Z, Zhang X, Wang H, Fan G, Liao X. Prevalence and risk factors of bone metastasis and the development of bone metastatic prognostic classification system: a pan-cancer population study. Aging (Albany NY) 2023; 15:13134-13149. [PMID: 37983179 DOI: 10.18632/aging.205224] [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: 07/05/2023] [Accepted: 10/12/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND The prevalence of bone metastasis (BM) varies among primary cancer patients, and it has a significant impact on prognosis. However, there is a lack of research in this area. This study aims to explore the clinical characteristics, prevalence, and risk factors, and to establish a prognostic classification system for pan-cancer patients with BM. METHODS The data obtained from the Surveillance, Epidemiology and End Results database were investigated. The prevalence and prognosis of patients with BM were analyzed. Hierarchical clustering was used to develop a prognostic classification system. RESULTS From 2010 to 2019, the prevalence of BM has increased by 41.43%. BM most commonly occurs in cancers that originate in the adrenal gland, lung and bronchus and overlapping lesion of digestive systems. Negative prognostic factors included older age, male sex, poorer grade, unmarried status, low income, non-metropolitan living, advanced tumor stages, previous chemotherapy, and synchronous liver, lung, and brain metastasis. Three categories with significantly different survival time were identified in the classification system. CONCLUSIONS The clinical features, prevalence, risk factors, and prognostic factors in pan-cancer patients with BM were investigated. A prognostic classification system was developed to provide survival information and aid physicians in selecting personalized treatment plans for patients with BM.
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Affiliation(s)
- Zhouyang Hu
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Sheng Yang
- Department of Orthopedics, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Spinal Pain Research Institute, Tongji University School of Medicine, Shanghai, China
| | - Zhipeng Xu
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xiaoling Zhang
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Hong Wang
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Guoxin Fan
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xiang Liao
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
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Liu M, Zhang S, Du Y, Zhang X, Wang D, Ren W, Sun J, Yang S, Zhang G. Identification of Luminal A breast cancer by using deep learning analysis based on multi-modal images. Front Oncol 2023; 13:1243126. [PMID: 38044991 PMCID: PMC10691590 DOI: 10.3389/fonc.2023.1243126] [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: 06/20/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
Purpose To evaluate the diagnostic performance of a deep learning model based on multi-modal images in identifying molecular subtype of breast cancer. Materials and methods A total of 158 breast cancer patients (170 lesions, median age, 50.8 ± 11.0 years), including 78 Luminal A subtype and 92 non-Luminal A subtype lesions, were retrospectively analyzed and divided into a training set (n = 100), test set (n = 45), and validation set (n = 25). Mammography (MG) and magnetic resonance imaging (MRI) images were used. Five single-mode models, i.e., MG, T2-weighted imaging (T2WI), diffusion weighting imaging (DWI), axial apparent dispersion coefficient (ADC), and dynamic contrast-enhanced MRI (DCE-MRI), were selected. The deep learning network ResNet50 was used as the basic feature extraction and classification network to construct the molecular subtype identification model. The receiver operating characteristic curve were used to evaluate the prediction efficiency of each model. Results The accuracy, sensitivity and specificity of a multi-modal tool for identifying Luminal A subtype were 0.711, 0.889, and 0.593, respectively, and the area under the curve (AUC) was 0.802 (95% CI, 0.657- 0.906); the accuracy, sensitivity, and AUC were higher than those of any single-modal model, but the specificity was slightly lower than that of DCE-MRI model. The AUC value of MG, T2WI, DWI, ADC, and DCE-MRI model was 0.593 (95%CI, 0.436-0.737), 0.700 (95%CI, 0.545-0.827), 0.564 (95%CI, 0.408-0.711), 0.679 (95%CI, 0.523-0.810), and 0.553 (95%CI, 0.398-0.702), respectively. Conclusion The combination of deep learning and multi-modal imaging is of great significance for diagnosing breast cancer subtypes and selecting personalized treatment plans for doctors.
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Affiliation(s)
- Menghan Liu
- Department of Health Management, The First Affiliated Hospital of Shandong First Medical University & Shandong Engineering Laboratory for Health Management, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Shuai Zhang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Postgraduate Department, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, China
| | - Yanan Du
- Department of Health Management, The First Affiliated Hospital of Shandong First Medical University & Shandong Engineering Laboratory for Health Management, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Xiaodong Zhang
- Postgraduate Department, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, China
| | - Dawei Wang
- Department of Radiology, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Wanqing Ren
- Postgraduate Department, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, China
| | - Jingxiang Sun
- Postgraduate Department, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, China
| | - Shiwei Yang
- Department of Anorectal Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Guang Zhang
- Department of Health Management, The First Affiliated Hospital of Shandong First Medical University & Shandong Engineering Laboratory for Health Management, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Shandong Provincial Qianfoshan Hospital, Jinan, China
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16
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Rodríguez M, González DM, El-Sharkawy F, Castaño M, Madrid J. Complete pathological response in patients with HER2 positive breast cancer treated with neoadjuvant therapy in Colombia. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:396-405. [PMID: 37871573 PMCID: PMC10637353 DOI: 10.7705/biomedica.6665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/16/2023] [Indexed: 10/25/2023]
Abstract
Introduction Breast cancer is the most common type of cancer and the leading cause of death by cancer in women in Colombia. Approximately 15 to 20% of breast cancers overexpress HER2. Objective To analyze the relationship between multiple clinical and histological variables and pathological complete response in patients with HER2-positive breast cancer undergoing neoadjuvant therapy in a specialized cancer center in Colombia. Materials and methods We performed a retrospective analysis of non-metastatic HER2-positive breast cancer patients who received neoadjuvant therapy between 2007 and 2020 at the Instituto de Cancerología Las Americas Auna (Medellín, Colombia). Assessed parameters were tumor grade, proliferation index, estrogen receptor, progesterone receptor, HER2 status, type of neoadjuvant therapy, pathologic complete response rates, and overall survival. Results Variables associated with low pathologic complete response rates were tumor grades 1-2 (OR = 0.55; 95% CI = 0.37-0.81; p = 0.03), estrogen receptor positivity (OR =0.65; 95%; CI = 0.43-0.97; p=0.04), and progesterone receptor positivity (OR = 0.44; 95% CI = 0.29-0.65; p = 0.0001). HER2 strong positivity (score 3+) was associated with high pathological complete response rates (OR = 3.3; 95% CI = 1.3-8.35; p=0.013). Five-year overall survival was 91.5% (95% CI = 82.6-95.9) in patients with pathological complete response and 73.6% (95% CI = 66.4-79.6) in patients who did not achieve pathological complete response (p = 0.001). Additionally, the pathological complete response rate was three times higher in patients receiving combined neoadjuvant chemotherapy with anti-HER2 therapy than in those with chemotherapy alone (48% versus 16%). Conclusions In patients with HER2-positive breast cancer, tumor grade 3, estrogen receptor negativity, progesterone receptor negativity, strong HER2 positivity (score 3+), and the use of the neoadjuvant trastuzumab are associated with higher pathological complete response rates.
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Affiliation(s)
- Mauricio Rodríguez
- Departamento de Cirugía Oncológica, Universidad de Antioquia, Medellín, Colombia.
| | - Diego M González
- Departamento de Cirugía Oncológica, Universidad de Antioquia, Medellín, Colombia; Instituto de Cancerología Las Américas Auna, Medellín, Colombia.
| | - Farah El-Sharkawy
- Department of Pathology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America.
| | - Mileny Castaño
- Instituto de Cancerología Las Américas Auna, Medellín, Colombia.
| | - Jorge Madrid
- Departamento de Cirugía Oncológica, Universidad de Antioquia, Medellín, Colombia.
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17
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Desterke C, Cosialls E, Xiang Y, Elhage R, Duruel C, Chang Y, Hamaï A. Adverse Crosstalk between Extracellular Matrix Remodeling and Ferroptosis in Basal Breast Cancer. Cells 2023; 12:2176. [PMID: 37681908 PMCID: PMC10486747 DOI: 10.3390/cells12172176] [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: 06/07/2023] [Revised: 08/04/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
(1) Background: Breast cancer is a frequent heterogeneous disorder diagnosed in women and causes a high number of mortality among this population due to rapid metastasis and disease recurrence. Ferroptosis can inhibit breast cancer cell growth, improve the sensitivity of chemotherapy and radiotherapy, and inhibit distant metastases, potentially impacting the tumor microenvironment. (2) Methods: Through data mining, the ferroptosis/extracellular matrix remodeling literature text-mining results were integrated into the breast cancer transcriptome cohort, taking into account patients with distant relapse-free survival (DRFS) under adjuvant therapy (anthracyclin + taxanes) with validation in an independent METABRIC cohort, along with the MDA-MB-231 and HCC338 transcriptome functional experiments with ferroptosis activations (GSE173905). (3) Results: Ferroptosis/extracellular matrix remodeling text-mining identified 910 associated genes. Univariate Cox analyses focused on breast cancer (GSE25066) selected 252 individual significant genes, of which 170 were found to have an adverse expression. Functional enrichment of these 170 adverse genes predicted basal breast cancer signatures. Through text-mining, some ferroptosis-significant adverse-selected genes shared citations in the domain of ECM remodeling, such as TNF, IL6, SET, CDKN2A, EGFR, HMGB1, KRAS, MET, LCN2, HIF1A, and TLR4. A molecular score based on the expression of the eleven genes was found predictive of the worst prognosis breast cancer at the univariate level: basal subtype, short DRFS, high-grade values 3 and 4, and estrogen and progesterone receptor negative and nodal stages 2 and 3. This eleven-gene signature was validated as regulated by ferroptosis inductors (erastin and RSL3) in the triple-negative breast cancer cellular model MDA-MB-231. (4) Conclusions: The crosstalk between ECM remodeling-ferroptosis functionalities allowed for defining a molecular score, which has been characterized as an independent adverse parameter in the prognosis of breast cancer patients. The gene signature of this molecular score has been validated to be regulated by erastin/RSL3 ferroptosis activators. This molecular score could be promising to evaluate the ECM-related impact of ferroptosis target therapies in breast cancer.
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Affiliation(s)
- Christophe Desterke
- UFR Médecine-INSERM UMRS1310, Université Paris-Saclay, F-94800 Villejuif, France
| | - Emma Cosialls
- Institut Necker Enfants Malades, INSERM UMR-S1151-CNRS UMR-S8253, Université Paris Cité, F-75015 Paris, France; (E.C.); (Y.X.); (R.E.); (C.D.); (Y.C.)
- Team 5/Ferostem Group, F-75015 Paris, France
| | - Yao Xiang
- Institut Necker Enfants Malades, INSERM UMR-S1151-CNRS UMR-S8253, Université Paris Cité, F-75015 Paris, France; (E.C.); (Y.X.); (R.E.); (C.D.); (Y.C.)
| | - Rima Elhage
- Institut Necker Enfants Malades, INSERM UMR-S1151-CNRS UMR-S8253, Université Paris Cité, F-75015 Paris, France; (E.C.); (Y.X.); (R.E.); (C.D.); (Y.C.)
- Team 5/Ferostem Group, F-75015 Paris, France
| | - Clémence Duruel
- Institut Necker Enfants Malades, INSERM UMR-S1151-CNRS UMR-S8253, Université Paris Cité, F-75015 Paris, France; (E.C.); (Y.X.); (R.E.); (C.D.); (Y.C.)
- Team 5/Ferostem Group, F-75015 Paris, France
| | - Yunhua Chang
- Institut Necker Enfants Malades, INSERM UMR-S1151-CNRS UMR-S8253, Université Paris Cité, F-75015 Paris, France; (E.C.); (Y.X.); (R.E.); (C.D.); (Y.C.)
| | - Ahmed Hamaï
- Institut Necker Enfants Malades, INSERM UMR-S1151-CNRS UMR-S8253, Université Paris Cité, F-75015 Paris, France; (E.C.); (Y.X.); (R.E.); (C.D.); (Y.C.)
- Team 5/Ferostem Group, F-75015 Paris, France
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18
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Tobiasz J, Polanska J. Proteomic Profile Distinguishes New Subpopulations of Breast Cancer Patients with Different Survival Outcomes. Cancers (Basel) 2023; 15:4230. [PMID: 37686507 PMCID: PMC10486506 DOI: 10.3390/cancers15174230] [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: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
As a highly heterogeneous disease, breast cancer (BRCA) demonstrates a diverse molecular portrait. The well-established molecular classification (PAM50) relies on gene expression profiling. It insufficiently explains the observed clinical and histopathological diversity of BRCAs. This study aims to demographically and clinically characterize the six BRCA subpopulations (basal, HER2-enriched, and four luminal ones) revealed by their proteomic portraits. GMM-based high variate protein selection combined with PCA/UMAP was used for dimensionality reduction, while the k-means algorithm allowed patient clustering. The statistical analysis (log-rank and Gehan-Wilcoxon tests, hazard ratio HR as the effect size ES) showed significant differences across identified subpopulations in Disease-Specific Survival (p = 0.0160) and Progression-Free Interval (p = 0.0264). Luminal subpopulations vary in prognosis (Disease-Free Interval, p = 0.0277). The A2 subpopulation is of the poorest, comparable to the HER2-enriched subpopulation, prognoses (HR = 1.748, referenced to Luminal B, small ES), while A3 is of the best (HR = 0.250, large ES). Similar to PAM50 subtypes, no substantial dependency on demographic and clinical factors was detected across Luminal subpopulations, as measured by χ2 test and Cramér's V for ES, and ANOVA with appropriate post hocs combined with η2 or Cohen's d-type ES, respectively. Progesterone receptors can serve as the potential A2 biomarker within Luminal patients. Further investigation of molecular differences is required to examine the potential prognostic or clinical applications.
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Affiliation(s)
- Joanna Tobiasz
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
- Department of Computer Graphics, Vision and Digital Systems, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland;
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19
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de Winter RFP, Meijer CM, Enterman JH, Kool-Goudzwaard N, Gemen M, van den Bos AT, Steentjes D, van Son GE, Hazewinkel MC, de Beurs DP, de Groot MH. A Clinical Model for the Differentiation of Suicidality: Protocol for a Usability Study of the Proposed Model. JMIR Res Protoc 2023; 12:e45438. [PMID: 37566444 PMCID: PMC10457700 DOI: 10.2196/45438] [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: 12/31/2022] [Revised: 04/24/2023] [Accepted: 05/29/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Even though various types of suicidality are observed in clinical practice, suicidality is still considered a uniform concept. To distinguish different types of suicidality and consequently improve detection and management of suicidality, we developed a clinical differentiation model for suicidality. We believe that the model allows for a more targeted assessment of suicidal conditions and improves the use of evidence-based treatment strategies. The differentiation model is based on the experience with suicidality that we have encountered in clinical practice. This model distinguishes 4 subtypes of entrapment leading to suicidality. The earliest description of this model and a proposal for usability research has been previously presented in a book chapter. OBJECTIVE In this study, we present the most recent version of the 4-type differentiation model of suicidality and a protocol for a study into the usability of the proposed model. METHODS The 4-type differentiation model of suicidality distinguishes the following subtypes: (1) perceptual disintegration, (2) primary depressive cognition, (3) psychosocial turmoil, and (4) inadequate coping or communication. We plan to test the usability of the 4 subtypes in a pilot study of 25 cases, and subsequently, we will include 75 cases in a follow-up study. We looked at the case notes of 100 anonymized patients with suicidality who presented to mental health care emergency service in The Hague International Center. The summary and conclusions of the letters sent to the patients' general practitioners after suicide risk assessment will be independently rated by 3 psychiatrists and 3 nurse-scientists for absolute and dimensional scores. The Suicidality Differentiation version 2 (SUICIDI-II) instrument, developed for this study, is used for rating all the cases. Intraclass correlation coefficients for absolute and dimensional scores will be calculated to examine type agreement between raters to examine the usability of the model and the feasibility of the SUICIDI-II instrument. RESULTS We consider the model tentatively valid if the intraclass correlation coefficients are ≥0.70. Subsequently, if the model turns out to be valid, we plan to rate 75 other cases in a follow-up study, according to a similar or adjusted procedure. Study results are expected to be published by the end of 2023. CONCLUSIONS The theoretical roots of the differentiation model stem from classic and contemporary theoretical models of suicidality and from our clinical practice experiences with suicidal behaviors. We believe that this model can be used to adjust the diagnosis, management, treatment, and research of suicidality, in addition to distinguishing different dynamics between practitioners and patients with suicidality and their families. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/45438.
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Affiliation(s)
- Remco F P de Winter
- Mental Health Institute Rivierduinen, Leiden, Netherlands
- VU University, Section of Clinical Psychology, Amsterdam Public Health Research Institute, Amsterdam, Netherlands
- Maastricht University, MHeNs School for Mental Health and Neuroscience, Maastricht, Netherlands
| | - Connie M Meijer
- Sussex Partnership National Health Service Foundation Trust, Eastbourne, United Kingdom
| | | | | | - Manuela Gemen
- Mental Health Institute Rivierduinen, Leiden, Netherlands
| | | | | | | | | | - Derek P de Beurs
- VU University, Section of Clinical Psychology, Amsterdam Public Health Research Institute, Amsterdam, Netherlands
- Trimbos Institute, Utrecht, Netherlands
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20
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Girithar HN, Staats Pires A, Ahn SB, Guillemin GJ, Gluch L, Heng B. Involvement of the kynurenine pathway in breast cancer: updates on clinical research and trials. Br J Cancer 2023; 129:185-203. [PMID: 37041200 PMCID: PMC10338682 DOI: 10.1038/s41416-023-02245-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/04/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Breast cancer (BrCa) is the leading cause of cancer incidence and mortality in women worldwide. While BrCa treatment has been shown to be highly successful if detected at an early stage, there are few effective strategies to treat metastatic tumours. Hence, metastasis remains the main cause in most of BrCa deaths, highlighting the need for new approaches in this group of patients. Immunotherapy has been gaining attention as a new treatment for BrCa metastasis and the kynurenine pathway (KP) has been suggested as one of the potential targets. The KP is the major biochemical pathway in tryptophan (TRP) metabolism, catabolising TRP to nicotinamide adenine dinucleotide (NAD+). The KP has been reported to be elevated under inflammatory conditions such as cancers and that its activity suppresses immune surveillance. Dysregulation of the KP has previously been reported implicated in BrCa. This review aims to discuss and provide an update on the current mechanisms involved in KP-mediated immune suppression and cancer growth. Furthermore, we also provide a summary on 58 studies about the involvement of the KP and BrCa and five clinical trials targeting KP enzymes and their outcome.
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Affiliation(s)
- Hemaasri-Neya Girithar
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ananda Staats Pires
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Gilles J Guillemin
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | - Laurence Gluch
- The Strathfield Breast Centre, Strathfield, NSW, Australia
| | - Benjamin Heng
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
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21
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Awasthi S, Gupta P, Mittal A. Association of Proliferative Indices With Various Grades of Breast Carcinoma. Cureus 2023; 15:e41865. [PMID: 37583729 PMCID: PMC10423845 DOI: 10.7759/cureus.41865] [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: 06/06/2023] [Accepted: 07/12/2023] [Indexed: 08/17/2023] Open
Abstract
AIMS AND OBJECTIVES Various grades of breast carcinoma and proliferative indices used as nuclear protein Ki-67 and argyrophilic nucleolar organizer regions (AgNOR) are being compared to each other. MATERIALS AND METHOD In this observational cross-sectional investigation, 42 breast biopsies from questionable breast areas were collected and preserved in formalin and paraffin before the tissue blocks were made. A thorough medical history regarding the breast tumor and thorough physical examination results were recorded. Two sections were produced, one stained with an immunohistochemical marker called Ki-67 and the other with a unique stain called AgNOR. RESULTS Grade I in Nottingham was found to be highest in subjects with Ki-67 1%, grade II in subjects with Ki-67 1-10%, and grade III in subjects with Ki-67>10%. Therefore, a higher Ki-67 score and a higher Nottingham grade were more closely associated. The mean AgNOR score was determined to be highest in Nottingham grade III and lowest in Nottingham grade I. In contrast to grade I and grade II of carcinoma (CA) breast, where there was no statistically significant association between Ki-67 and AgNOR, grade III of CA breast showed a statistically significant link between Ki-67 and AgNOR. CONCLUSION Proliferation has been identified as a distinctive feature of cancer and as a key factor in the prognosis of the disease.
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Affiliation(s)
- Seema Awasthi
- Department of Pathology, Teerthanker Mahaveer Medical College, Moradabad, IND
| | - Pooja Gupta
- Department of Pathology, Teerthanker Mahaveer Medical College, Moradabad, IND
| | - Ankita Mittal
- Department of Pathology, Teerthanker Mahaveer Medical College, Moradabad, IND
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22
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Graham R, Gazinska P, Zhang B, Khiabany A, Sinha S, Alaguthurai T, Flores-Borja F, Vicencio J, Beuron F, Roxanis I, Matkowski R, Liam-Or R, Tutt A, Ng T, Al-Jamal KT, Zhou Y, Irshad S. Serum-derived extracellular vesicles from breast cancer patients contribute to differential regulation of T-cell-mediated immune-escape mechanisms in breast cancer subtypes. Front Immunol 2023; 14:1204224. [PMID: 37441083 PMCID: PMC10335744 DOI: 10.3389/fimmu.2023.1204224] [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: 04/11/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Background Intracellular communication within the tumour is complex and extracellular vesicles (EVs) have been identified as major contributing factors for the cell-to-cell communication in the local and distant tumour environments. Here, we examine the differential effects of breast cancer (BC) subtype-specific patient serum and cell-line derived EVs in the regulation of T cell mediated immune responses. Methods Ultracentrifugation was used to isolate EVs from sera of 63 BC patients, 15 healthy volunteers and 4 human breast cancer cell lines. Longitudinal blood draws for EV isolation for patients on neoadjuvant chemotherapy was also performed. Characterization of EVs was performed by Nanoparticle Tracking Analysis (NTA), transmission electron microscopy (TEM) and immunoblotting. CD63 staining was performed on a tissue microarray of 218 BC patients. In-house bioinformatics algorithms were utilized for the computation of EV associated expression scores within The Cancer Genome Atlas (TCGA) and correlated with tumour infiltrating lymphocyte (TIL) scores. In vitro stimulation of PBMCs with EVs from serum and cell-line derived EVs was performed and changes in the immune phenotypes characterized by flow cytometry. Cytokine profiles were assessed using a 105-plex immunoassay or IL10 ELISA. Results Patients with triple negative breast cancers (TNBCs) exhibited the lowest number of EVs in the sera; whilst the highest was detected in ER+HER2+ cancers; reflected also in the higher level of CD63+ vesicles found within the ER+HER2+ local tumour microenvironment. Transcriptomic analysis of the TCGA data identified that samples assigned with lower EV scores had significantly higher abundance of CD4+ memory activated T cells, T follicular cells and CD8 T cells, plasma, and memory B cells; whilst samples with high EV scores were more enriched for anti-inflammatory M2 macrophages and mast cells. A negative correlation between EV expression scores and stromal TIL counts was also observed. In vitro experiments confirmed that circulating EVs within breast cancer subtypes have functionally differing immunomodulatory capabilities, with EVs from patients with the most aggressive breast cancer subtype (TNBCs) demonstrating the most immune-suppressive phenotype (decreased CD3+HLA-DR+ but increased CD3+PD-L1 T cells, increased CD4+CD127-CD25hi T regulatory cells with associated increase in IL10 cytokine production). In depth assessment of the cytokine modulation triggered by the serum/cell line derived exosomes confirmed differential inflammatory cytokine profiles across differing breast cancer subtypes. Studies using the MDA-231 TNBC breast cancer cell-line derived EVs provided further support that TNBC EVs induced the most immunosuppressive response within PBMCs. Discussion Our study supports further investigations into how tumour derived EVs are a mechanism that cancers can exploit to promote immune suppression; and breast cancer subtypes produce EVs with differing immunomodulatory capabilities. Understanding the intracellular/extracellular pathways implicated in alteration from active to suppressed immune state may provide a promising way forward for restoring immune competence in specific breast cancer patient populations.
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Affiliation(s)
- Rosalind Graham
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Patrycja Gazinska
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
- Biobank Research Group, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Birong Zhang
- Systems Immunity University Research Institute and Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Atousa Khiabany
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Shubhankar Sinha
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Thanussuyah Alaguthurai
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
| | - Fabian Flores-Borja
- Richard Dimbleby Laboratory of Cancer Research School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - Jose Vicencio
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Fabienne Beuron
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Ioannis Roxanis
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Rafal Matkowski
- Breast Unit, Lower Silesian Oncology, Pulmunology and Hematology Center, Wroclaw, Poland
- Department of Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Revadee Liam-Or
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Tony Ng
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Richard Dimbleby Laboratory of Cancer Research School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Khuloud T. Al-Jamal
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - You Zhou
- Systems Immunity University Research Institute and Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sheeba Irshad
- Breast Immunology Group, School of Cancer & Pharmaceutical Sciences, King’s College London, London, United Kingdom
- Breast Cancer Now Research Unit, King's College London, Guy's Hospital, London, United Kingdom
- Medical Oncology, Guy's & St Thomas' NHS Trust, London, United Kingdom
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23
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Coria-Rodríguez H, Ochoa S, de Anda-Jáuregui G, Hernández-Lemus E. Drug repurposing for Basal breast cancer subpopulations using modular network signatures. Comput Biol Chem 2023; 105:107902. [PMID: 37348299 DOI: 10.1016/j.compbiolchem.2023.107902] [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: 07/20/2022] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
Breast cancer is characterized as being a heterogeneous pathology with a broad phenotype variability. Breast cancer subtypes have been developed in order to capture some of this heterogeneity. Each of these breast cancer subtypes, in turns retains varied characteristic features impacting diagnostic, prognostic and therapeutics. Basal breast tumors, in particular have been challenging in these regards. Basal breast cancer is often more aggressive, of rapid evolution and no tailor-made targeted therapies are available yet to treat it. Arguably, epigenetic variability is behind some of these intricacies. It is possible to further classify basal breast tumor in groups based on their non-coding transcriptome and methylome profiles. It is expected that these groups will have differences in survival as well as in sensitivity to certain classes of drugs. With this in mind, we implemented a computational learning approach to infer different subpopulations of basal breast cancer (from TCGA multi-omic data) based on their epigenetic signatures. Such epigenomic signatures were associated with different survival profiles; we then identified their associated gene co-expression network structure, extracted a signature based on modules within these networks, and use these signatures to find and prioritize drugs (in the LINCS dataset) that may be used to target these types of cancer. In this way we are introducing the analytical workflow for an epigenomic signature-based drug repurposing structure.
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Affiliation(s)
- Hiram Coria-Rodríguez
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico; Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Circuito Exterior, Mexico City, 04510, Mexico; Catedras Conacyt, National Council on Science and Technology, Insurgentes Sur, Mexico City, 03940, Mexico.
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Periferico Sur 4809, Mexico City, 14610, Mexico; Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Circuito Exterior, Mexico City, 04510, Mexico.
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Goel RK, Kim N, Lukong KE. Seeking a better understanding of the non-receptor tyrosine kinase, SRMS. Heliyon 2023; 9:e16421. [PMID: 37251450 PMCID: PMC10220380 DOI: 10.1016/j.heliyon.2023.e16421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
SRMS (Src-Related kinase lacking C-terminal regulatory tyrosine and N-terminal Myristoylation Sites) is a non-receptor tyrosine kinase first reported in a 1994 screen for genes regulating murine neural precursor cells. SRMS, pronounced "Shrims", lacks the C-terminal regulatory tyrosine critical for the regulation of the enzymatic activity of Src-family kinases (SFKs). Another remarkable characteristic of SRMS is its localization into distinct SRMS cytoplasmic punctae (SCPs) or GREL (Goel Raghuveera-Erique Lukong) bodies, a pattern not observed in the SFKs. This unique subcellular localization of SRMS could dictate its cellular targets, proteome, and potentially, substrates. However, the function of SRMS is still relatively unknown. Further, how is its activity regulated and by what cellular targets? Studies have emerged highlighting the potential role of SRMS in autophagy and in regulating the activation of BRK/PTK6. Potential novel cellular substrates have also been identified, including DOK1, vimentin, Sam68, FBKP51, and OTUB1. Recent studies have also demonstrated the potential role of the kinase in various cancers, including gastric and colorectal cancers and platinum resistance in ovarian cancer. This review discusses the advancements made in SRMS-related biology to date and the path to understanding the cellular and physiological significance of the kinase.
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Affiliation(s)
- Raghuveera Kumar Goel
- Center for Network Systems Biology, Boston University, Boston, MA, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Nayoung Kim
- Department of Biochemistry, Microbiology, and Immunology, 107 Wiggins Road, Health Sciences Building, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada
| | - Kiven Erique Lukong
- Department of Biochemistry, Microbiology, and Immunology, 107 Wiggins Road, Health Sciences Building, University of Saskatchewan, Saskatoon S7N 5E5, Saskatchewan, Canada
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25
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Ji Y, Whitney HM, Li H, Liu P, Giger ML, Zhang X. Differences in Molecular Subtype Reference Standards Impact AI-based Breast Cancer Classification with Dynamic Contrast-enhanced MRI. Radiology 2023; 307:e220984. [PMID: 36594836 PMCID: PMC10068887 DOI: 10.1148/radiol.220984] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/20/2022] [Accepted: 11/01/2022] [Indexed: 01/04/2023]
Abstract
Background Breast cancer tumors can be identified as different luminal molecular subtypes depending on either immunohistochemical (IHC) staining or St Gallen criteria that includes Ki-67. Purpose To characterize molecular subtypes and understand the impact of disagreement among IHC and St Gallen molecular subtype reference standards on artificial intelligence classification of luminal A and luminal B tumors with use of radiomic features extracted from dynamic contrast-enhanced (DCE) MRI scans. Materials and Methods In this retrospective study, 28 radiomic features previously extracted from DCE-MRI scans of breast tumors imaged between February 2015 and October 2017 were examined in the following groups: (a) tumors classified as luminal A by both reference standards ("agreement"), (b) tumors classified as luminal A by IHC and luminal B by St Gallen ("disagreement"), and (c) tumors classified as luminal B by both ("agreement"). Luminal A or luminal B tumor classification with use of radiomic features was conducted with use of three sets: (a) IHC molecular subtyping, (b) St Gallen molecular subtyping, and (c) agreement tumors. The Kruskal-Wallis test was followed by the Mann-Whitney U test to determine pair-wise differences of radiomic features among agreement and disagreement tumors. Fivefold cross-validation with use of stepwise feature selection and linear discriminant analysis classified tumors in each set, with performance measured with use of area under the receiver operating characteristic curve (AUC). Results A total of 877 breast cancer tumors from 872 women (mean age, 48 years [range, 19-75 years]) were analyzed. Six features (sphericity, irregularity, surface area to volume ratio, variance of radial gradient histogram, sum average, volume of most enhancing voxels) were different (P ≤ .001) among agreement and disagreement tumors. AUC (median, 0.74 [95% CI: 0.68, 0.80]) was higher than when using tumors subtyped by either reference standard (IHC, 0.66 [0.60, 0.71], P = .003; St Gallen, 0.62 [0.58, 0.67], P = .001). Conclusion Differences in reference standards can hinder artificial intelligence classification performance of luminal molecular subtypes with dynamic contrast-enhanced MRI. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Bae in this issue.
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Affiliation(s)
- Yu Ji
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Heather M. Whitney
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Hui Li
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Peifang Liu
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Maryellen L. Giger
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
| | - Xuening Zhang
- From the Department of Radiology, The Second Hospital of Tianjin
Medical University, No. 23 Pingjiang Rd, Hexi District, Tianjin, China 300211
(Y.J., X.Z.); National Clinical Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin, China (Y.J., P.L.);
Department of Radiology, The University of Chicago, Chicago, Ill (H.M.W., H.L.,
M.L.G.); and Department of Physics, Wheaton College, Wheaton, Ill
(H.M.W.)
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Alromema N, Syed AH, Khan T. A Hybrid Machine Learning Approach to Screen Optimal Predictors for the Classification of Primary Breast Tumors from Gene Expression Microarray Data. Diagnostics (Basel) 2023; 13:diagnostics13040708. [PMID: 36832196 PMCID: PMC9955903 DOI: 10.3390/diagnostics13040708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
The high dimensionality and sparsity of the microarray gene expression data make it challenging to analyze and screen the optimal subset of genes as predictors of breast cancer (BC). The authors in the present study propose a novel hybrid Feature Selection (FS) sequential framework involving minimum Redundancy-Maximum Relevance (mRMR), a two-tailed unpaired t-test, and meta-heuristics to screen the most optimal set of gene biomarkers as predictors for BC. The proposed framework identified a set of three most optimal gene biomarkers, namely, MAPK 1, APOBEC3B, and ENAH. In addition, the state-of-the-art supervised Machine Learning (ML) algorithms, namely Support Vector Machine (SVM), K-Nearest Neighbors (KNN), Neural Net (NN), Naïve Bayes (NB), Decision Tree (DT), eXtreme Gradient Boosting (XGBoost), and Logistic Regression (LR) were used to test the predictive capability of the selected gene biomarkers and select the most effective breast cancer diagnostic model with higher values of performance matrices. Our study found that the XGBoost-based model was the superior performer with an accuracy of 0.976 ± 0.027, an F1-Score of 0.974 ± 0.030, and an AUC value of 0.961 ± 0.035 when tested on an independent test dataset. The screened gene biomarkers-based classification system efficiently detects primary breast tumors from normal breast samples.
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Affiliation(s)
- Nashwan Alromema
- Department of Computer Science, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah 22254, Saudi Arabia
- Correspondence:
| | - Asif Hassan Syed
- Department of Computer Science, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Tabrej Khan
- Department of Information Systems, Faculty of Computing and Information Technology Rabigh (FCITR), King Abdulaziz University, Jeddah 22254, Saudi Arabia
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27
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Molecular targets that sensitize cancer to radiation killing: From the bench to the bedside. Biomed Pharmacother 2023; 158:114126. [PMID: 36521246 DOI: 10.1016/j.biopha.2022.114126] [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: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a standard cytotoxic therapy against solid cancers. It uses ionizing radiation to kill tumor cells through damage to DNA, either directly or indirectly. Radioresistance is often associated with dysregulated DNA damage repair processes. Most radiosensitizers enhance radiation-mediated DNA damage and reduce the rate of DNA repair ultimately leading to accumulation of DNA damages, cell-cycle arrest, and cell death. Recently, agents targeting key signals in DNA damage response such as DNA repair pathways and cell-cycle have been developed. This new class of molecularly targeted radiosensitizing agents is being evaluated in preclinical and clinical studies to monitor their activity in potentiating radiation cytotoxicity of tumors and reducing normal tissue toxicity. The molecular pathways of DNA damage response are reviewed with a focus on the repair mechanisms, therapeutic targets under current clinical evaluation including ATM, ATR, CDK1, CDK4/6, CHK1, DNA-PKcs, PARP-1, Wee1, & MPS1/TTK and potential new targets (BUB1, and DNA LIG4) for radiation sensitization.
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28
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Comparing the Biology of Young versus Old Age Estrogen-Receptor-Positive Breast Cancer through Gene and Protein Expression Analyses. Biomedicines 2023; 11:biomedicines11010200. [PMID: 36672708 PMCID: PMC9855392 DOI: 10.3390/biomedicines11010200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/26/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Background: Breast cancer developed at a young age (≤45 years) is hypothesized to have unique biology; however, findings in this field are controversial. Methods: We compared the whole transcriptomic profile of young vs. old-age breast cancer using DNA microarray. RNA was extracted from 13 fresh estrogen receptor (ER)-positive primary breast cancer tissues of untreated patients (7 = young age ≤45 years and 6 = old age ≥55 years). In silico validation for the differentially expressed genes (DEGs) by young-age patients was conducted using The Cancer Genome Atlas (TCGA) database. Next, we analyzed the protein expression encoded by two of the significantly down-regulated genes by young-age patients, Glycine N-acyltransferase-like 1 (GLYATL-1) and Ran-binding protein 3 like (RANBP3L), using immunohistochemical analysis in an independent cohort of 56 and 74 ER-positive pre-therapeutic primary breast cancer tissues, respectively. Results: 12 genes were significantly differentially expressed by young-age breast cancers (fold change >2 or <2- with FDR p-value < 0.05). TCGA data confirmed the differential expression of six genes. Protein expression analysis of GLYATL-1 and RANBP3L did not show heterogeneous expression between young and old-age breast cancer tissues. Loss of expression of GLYATL-1 was significantly (p-value 0.005) associated with positive lymph node status. Higher expression of RANBP3L was significantly associated with breast cancers with lower histopathological grades (p-value 0.038). Conclusions: At the transcriptomic level, breast cancer developed in young and old age patients seems homogenous. The variation in the transcriptomic profiles can be attributed to the other clinicopathological characteristics rather than the age of the patient.
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Chalise P, Kwon D, Fridley BL, Mo Q. Statistical Methods for Integrative Clustering of Multi-omics Data. Methods Mol Biol 2023; 2629:73-93. [PMID: 36929074 PMCID: PMC10950392 DOI: 10.1007/978-1-0716-2986-4_5] [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] [Indexed: 03/18/2023]
Abstract
Cancers are heterogeneous diseases caused by accumulated mutations or abnormal alterations at multi-levels of biological processes including genomics, epigenomics, transcriptomics, and proteomics. There is a great clinical interest in identifying cancer molecular subtypes for disease prognosis and personalized medicine. Integrative clustering is a powerful unsupervised learning method that has been increasingly used to identify cancer molecular subtypes using multi-omics data including somatic mutations, DNA copy numbers, DNA methylation, and gene expression. Integrative clustering methods are generally classified into model-based or nonparametric approaches. In this chapter, we will give an overview of the frequently used model-based methods, including iCluster, iClusterPlus, and iClusterBayes, and the nonparametric method, integrative nonnegative matrix factorization (intNMF). We will use the integrative analyses of uveal melanoma and lower-grade glioma to illustrate these representative methods. Finally, we will discuss the strengths and limitations of these representative methods and give suggestions for performing integrative analyses of cancer multi-omics data in practice.
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Affiliation(s)
- Prabhakar Chalise
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Deukwoo Kwon
- Department of Population Health Science & Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brooke L Fridley
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Qianxing Mo
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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Bernet L, Hardisson D, Rodrigo M, Córdoba A, Sancho M, Peg V, Ruiz I, Godey F, Sánchez-Méndez JI, Prat A. OSNA Total Tumor Load for the Prediction of Axillary Involvement in Breast Cancer Patients: Should We use Different Thresholds According to the Intrinsic Molecular Subtype? MOTTO Study. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2023; 16:2632010X231183693. [PMID: 37534372 PMCID: PMC10392164 DOI: 10.1177/2632010x231183693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/05/2023] [Indexed: 08/04/2023]
Abstract
Aims To assess the impact of the molecular subtype (MS) on the total number of CK19 mRNA copies in all positive SLN (TTL) threshold, to predict non-SLN affectation, and to compare 5 years progression-free survival (PFS) according to the risk of recurrence (ROR) group by PAM50. Methods Cohort with infiltrating breast cancer with intra-operative metastatic SLN detected by one-step nucleic acid amplification (OSNA) assay who underwent subsequent ALND. Logistic regression was used to assess a possible interaction between TTL and MS(Triple Negative, Her-2-Enriched, Luminal A, or Luminal B), or hormone receptors (HR: positive or negative) by immunohistochemistry (IMH). Cox regression was used to compare PFS and OS in the 3 ROR groups (high, medium, or low). Results TTL was predictive of non-SLN affectation in both univariate (OR [95% CI]: 1.72 [1.43, 2.05], P < .001) and multivariate (1.55 [95% CI: 1.04, 2.32], P = .030) models, but MS-IMH or HR-IMH, and their interactions with TTL were not (best multivariate model: HR + main effect OR 1.16 [95% CI: 0.18, 7.64], P = .874; interaction OR: 1.04 [0.7, 1.55], P = .835; univariate model: HR + main effect OR: 1.44 [95% CI: 0.85, 2.44], P = .180). PFS was lower in the high-risk ROR group (81.1%) than in the low-risk group (93.9%) (HR: 3.68 [95 CI: 1.70, 7.94], P < .001). Conclusions our results do not provide evidence to support the utilization of subtype-specific thresholds for TTL values to make therapeutic decisions on the axilla. The ROR group was predictive of 5 years-PFS.
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Affiliation(s)
- L Bernet
- Department of Pathology, Hospital Universitario del Vinalopó, Elche, Spain
| | - D Hardisson
- Department of Pathology, Hospital Universitario La Paz, Madrid
- Hospital La Paz Institute for health Research (IdiPAZ), Universidad Autónoma de Madrid
| | - M Rodrigo
- Department of Pathology, Hospital Universitario de Burgos, Burgos, Spain
| | - A Córdoba
- Department of Pathology, Hospital Universitario de Navarra, Navarra, Spain
| | - M Sancho
- Department of Pathology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - V Peg
- Department of Pathology, Vall d’Hebron University Hospital, Barcelona, Spain
- Universidad Autónoma de Barcelona, Barcelona, Spain
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - I Ruiz
- Department of Pathology, Hospital Universitario de Donostia, Donostia, Spain
| | - F Godey
- Department of Pathology, Centre Eugène Marquis, Rennes, France
| | - JI Sánchez-Méndez
- Department of Ginecology and Obstetrics, Hospital Universitario La Paz, Madrid
- Hospital La Paz Institute for Health Research (IdiPAZ), Universidad Autónoma de Madrid
| | - A Prat
- Medical Oncology department, Hospital Clínic de Barcelona, Barcelona, Spain
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Urso L, Evangelista L, Alongi P, Quartuccio N, Cittanti C, Rambaldi I, Ortolan N, Borgia F, Nieri A, Uccelli L, Schirone A, Panareo S, Arnone G, Bartolomei M. The Value of Semiquantitative Parameters Derived from 18F-FDG PET/CT for Predicting Response to Neoadjuvant Chemotherapy in a Cohort of Patients with Different Molecular Subtypes of Breast Cancer. Cancers (Basel) 2022; 14:cancers14235869. [PMID: 36497351 PMCID: PMC9738922 DOI: 10.3390/cancers14235869] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/03/2022] Open
Abstract
Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) is a strong prognostic factor in breast cancer (BC). The aim of this study was to investigate whether semiquantitative parameters derived from baseline [18F]Fluorodeoxyglucose ([18F]FDG) positron emission computed tomography/computed tomography (PET/CT) could predict pCR after NAC and survival outcomes in patients affected by different molecular subtypes of BC. We retrospectively retrieved patients from the databases of two Italian hospitals (Centre A: University Hospital of Ferrara; Centre B: University of Padua) meeting the following inclusion criteria: (1) diagnosis of BC; (2) history of NAC; (3) baseline [18F]FDG PET/CT performed before the first cycle of NAC; (4) available follow-up data (response after NAC and survival information). For each [18F]FDG PET/CT scan, semiquantitative parameters (SUVmax, SUVmean, MTV and TLG) related to the primary tumor (B), to the reference lesion for both axillary (N) and distant lymph node (DN), and to the whole-body burden of disease (WB) were evaluated. Patients enrolled were 133: 34 from centre A and 99 from centre B. Patients' molecular subtypes were: 9 luminal A, 49 luminal B, 33 luminal B + HER-2, 10 HER-2 enriched, and 32 triple negative (TNBC). Luminal A and HER-2 enriched BC patients were excluded from the analysis due to the small sample size. pCR after NAC was achieved in 47 patients (41.2%). [18F]FDG PET/CT detected the primary tumor in 98.3% of patients and lymph node metastases were more frequently detected in Luminal B subgroup. Among Luminal B patients, median SUVmean_B values were significantly higher (p = 0.027) in responders (7.06 ± 5.9) vs. non-responders (4.4 ± 2.1) to NAC. Luminal B + HER-2 non-responders showed a statistically significantly higher median MTV_B (7.3 ± 4.2 cm3 vs. 3.5 ± 2.5 cm3; p = 0.003) and TLG_B (36.5 ± 24.9 vs. 18.9 ± 17.7; p = 0.025) than responders at baseline [18F]FDG PET/CT. None of the semiquantitative parameters predicted pCR after NAC in TNBC patients. However, among TNBC patients who achieved pCR after NAC, 4 volumetric parameters (MTV_B, TLG_B, MTV_WB and TLG_WB) were significantly higher in patients dead at follow-up. If confirmed in further studies, these results could open up a widespread use of [18F]FDG PET/CT as a baseline predictor of response to NAC in luminal B and luminal B + HER-2 patients and as a prognostic tool in TNBC.
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Affiliation(s)
- Luca Urso
- Department of Translational Medicine, University of Ferrara, Via Aldo Moro 8, 44124 Ferrara, Italy
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
| | - Laura Evangelista
- Department of Medicine DIMED, University of Padua, 35128 Padua, Italy
| | - Pierpaolo Alongi
- Nuclear Medicine Unit, ARNAS Ospedali Civico, Di Cristina e Benfratelli, 90127 Palermo, Italy
| | - Natale Quartuccio
- Nuclear Medicine Unit, Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy
| | - Corrado Cittanti
- Department of Translational Medicine, University of Ferrara, Via Aldo Moro 8, 44124 Ferrara, Italy
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
- Correspondence: ; Tel.: +39-0532326387
| | - Ilaria Rambaldi
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
| | - Naima Ortolan
- Department of Translational Medicine, University of Ferrara, Via Aldo Moro 8, 44124 Ferrara, Italy
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
| | - Francesca Borgia
- Department of Translational Medicine, University of Ferrara, Via Aldo Moro 8, 44124 Ferrara, Italy
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
| | - Alberto Nieri
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
| | - Licia Uccelli
- Department of Translational Medicine, University of Ferrara, Via Aldo Moro 8, 44124 Ferrara, Italy
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
| | - Alessio Schirone
- Oncology Unit, Oncological Medical and Specialists Department, University Hospital of Ferrara, 44124 Ferrara, Italy
| | - Stefano Panareo
- Nuclear Medicine Unit, Oncology and Haematology Department, University Hospital of Modena, 41125 Modena, Italy
| | - Gaspare Arnone
- Nuclear Medicine Unit, ARNAS Ospedali Civico, Di Cristina e Benfratelli, 90127 Palermo, Italy
| | - Mirco Bartolomei
- Nuclear Medicine Unit, Oncological Medical and Specialist Department, University Hospital of Ferrara, 44124 Cona, Italy
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Le NQK, Ho DKN, Ta HDK, Nguyen HT. Using ensemble learning and genetic algorithm on magnetic resonance imaging radiomics to classify molecular subtypes of breast cancer. PRECISION MEDICAL SCIENCES 2022. [DOI: 10.1002/prm2.12089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine Taipei Medical University Taipei Taiwan
- Research Center for Artificial Intelligence in Medicine Taipei Medical University Taipei Taiwan
- Translational Imaging Research Center Taipei Medical University Hospital Taipei Taiwan
| | - Dang Khanh Ngan Ho
- School of Nutrition and Health Sciences, College of Nutrition Taipei Medical University Taipei Taiwan
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology Taipei Medical University and Academia Sinica Taipei Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology Taipei Medical University Taipei Taiwan
| | - Hieu Trung Nguyen
- Department of Orthopedic and Trauma, Faculty of Medicine University of Medicine and Pharmacy at Ho Chi Minh City Ho Chi Minh City Vietnam
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Mukherjee B, Tiwari A, Palo A, Pattnaik N, Samantara S, Dixit M. Reduced expression of FRG1 facilitates breast cancer progression via GM-CSF/MEK-ERK axis by abating FRG1 mediated transcriptional repression of GM-CSF. Cell Death Dis 2022; 8:442. [PMID: 36329016 PMCID: PMC9633810 DOI: 10.1038/s41420-022-01240-w] [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: 07/20/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Multiple molecular subtypes and distinct clinical outcomes in breast cancer, necessitate specific therapy. Moreover, despite the improvements in breast cancer therapy, it remains the fifth cause of cancer-related deaths, indicating the involvement of unknown genes. To identify novel contributors and molecular subtype independent therapeutic options, we report reduced expression of FRG1 in breast cancer patients, which regulates GM-CSF expression via direct binding to its promoter. Reduction in FRG1 expression enhanced EMT and increased cell proliferation, migration, and invasion, in breast cancer cell lines. Loss of FRG1 increased GM-CSF levels which activated MEK/ERK axis and prevented apoptosis by inhibiting p53 in an ERK-dependent manner. FRG1 depletion in the mouse model increased tumor volume, phospho-ERK, and EMT marker levels. The therapeutic potential of anti-GM-CSF therapy was evident by reduced tumor size, when tumors with decreased FRG1 were treated with anti-GM-CSF mAb. We found an inverse expression pattern of FRG1 and phospho-ERK levels in breast cancer patient tissues, corroborating the in vitro and mouse model-based findings. Our findings first time elucidate the role of FRG1 as a metastatic suppressor of breast cancer by regulating the GM-CSF/MEK-ERK axis.
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Affiliation(s)
- Bratati Mukherjee
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Ankit Tiwari
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Ananya Palo
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | | | - Subrat Samantara
- Acharya Harihar Regional Cancer Centre (AHRCC), Cuttack, 753007, Odisha, India
| | - Manjusha Dixit
- National Institute of Science Education and Research, School of Biological Sciences, Bhubaneswar, Odisha, 752050, India. .,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India.
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Impact of preoperative magnetic resonance imaging on surgery and eligibility for intraoperative radiotherapy in early breast cancer. PLoS One 2022; 17:e0274385. [PMID: 36256643 PMCID: PMC9578617 DOI: 10.1371/journal.pone.0274385] [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: 10/11/2021] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
We looked at the usefulness of magnetic resonance imaging (MRI) in decision-making and surgical management of patients selected for intraoperative radiotherapy (IORT). We also compared lesion size measurements in different modalities (ultrasound (US), mammogram (MMG), MRI) against pathological size as the gold standard. 63 patients eligible for IORT based on clinical and imaging criteria over a 34-month period were enrolled. All had MMG and US, while 42 had additional preoperative MRI for locoregional preoperative staging. Imaging findings and pathological size concordances were analysed across the three modalities. MRI changed the surgical management of 5 patients (11.9%) whereby breast-conserving surgery (BCS) and IORT was cancelled due to detection of satellite lesion, tumor size exceeding 30mm and detection of axillary nodal metastases. Ten of 42 patients (23.8%) who underwent preoperative MRI were subjected to additional external beam radiotherapy (EBRT); 7 due to lymphovascular invasion (LVI), 2 due to involved margins, and 1 due to axillary lymph node metastatic carcinoma detected in the surgical specimen. Five of 21 (23.8%) patients without prior MRI were subjected to additional EBRT post-surgery; 3 had LVI and 2 had involved margins. The rest underwent BCS and IORT as planned. MRI and MMG show better imaging-pathological size correlation. Significant increase in the mean 'waiting time' were seen in the MRI group (34.1 days) compared to the conventional imaging group (24.4 days). MRI is a useful adjunct to conventional imaging and impacts decision making in IORT. It is also the best imaging modality to determine the actual tumour size.
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Bahl S, Carroll JS, Lupien M. Chromatin Variants Reveal the Genetic Determinants of Oncogenesis in Breast Cancer. Cold Spring Harb Perspect Med 2022; 12:a041322. [PMID: 36041880 PMCID: PMC9524388 DOI: 10.1101/cshperspect.a041322] [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: 11/24/2022]
Abstract
Breast cancer presents as multiple distinct disease entities. Each tumor harbors diverse cell populations defining a phenotypic heterogeneity that impinges on our ability to treat patients. To date, efforts mainly focused on genetic variants to find drivers of inter- and intratumor phenotypic heterogeneity. However, these efforts have failed to fully capture the genetic basis of breast cancer. Through recent technological and analytical approaches, the genetic basis of phenotypes can now be decoded by characterizing chromatin variants. These variants correspond to polymorphisms in chromatin states at DNA sequences that serve a distinct role across cell populations. Here, we review the function and causes of chromatin variants as they relate to breast cancer inter- and intratumor heterogeneity and how they can guide the development of treatment alternatives to fulfill the goal of precision cancer medicine.
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Affiliation(s)
- Shalini Bahl
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
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Abdelraouf EM, Hussein RRS, Shaaban AH, El-Sherief HAM, Embaby AS, Abd El-Aleem SA. Annexin A2 (AnxA2) association with the clinicopathological data in different breast cancer subtypes: A possible role for AnxA2 in tumor heterogeneity and cancer progression. Life Sci 2022; 308:120967. [PMID: 36116530 DOI: 10.1016/j.lfs.2022.120967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Breast cancer is a highly heterogeneous type of neoplasia with molecular and biochemical alterations in the ductal epithelium. AnxA2 has a diverse functions and through intracellular interaction with other molecules promotes carcinogenesis. AIMS To study the possible involvement of AnxA2 in breast cancer heterogeneity and cancer progression. PATIENTS AND METHODS Tumor tissue and serum were obtained from different breast cancer subtypes. Tumor tissues were processed for histopathological studies. AnxA2 levels were assessed in the tissues by H scoring and in the serum by ELISA. AnxA2 levels were correlated with HER2 and Ki67 and with clinicopathological data. Normal breast tissues and serum from healthy subjects were used as controls. RESULTS AnxA2 showed a peculiar distribution in tumor tissues and nearby interstitial tissues. Pattern of expressions varied in different subtypes with the highest expression in triple negative subtype. Tissue and serum AnxA2 showed significant co-upregulations in breast cancer. Moreover, they showed positive correlations with HER2 and Ki67 and associations with clinicopathological data including cancer staging and lymph node metastasis. CONCLUSION For the best of our knowledge this is the first study showing correlation between AnxA2, the proposed prognostic marker and the well-established tumor markers; HER2 and Ki67. AnxA2 might contribute to breast cancer heterogeneity and is associated with poor prognosis. AnxA2 might be a prognostic marker and an additional marker for breast cancer grading and clinical staging. Interestingly, tissue and serum AnxA2 showed a strong correlation. Thus, assessing serum AnxA2 can be a noninvasive prognostic tool.
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Affiliation(s)
| | - Raghda R S Hussein
- Clinical Pharmacy, Faculty of Pharmacy, Beni-Suef University, Egypt; Department of Clinical Pharmacy, Faculty of Pharmacy, October 6 University, 6 October City, Giza, Egypt
| | - Ahmed Hassan Shaaban
- Department of clinical Oncology, Faculty of Medicine, Beni-Suef University, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Egypt
| | - Azza S Embaby
- Department of Histology, Faculty of Medicine, Beni-Suef University, Egypt
| | - Seham A Abd El-Aleem
- Department of Cell Biology and Histology, Faculty of Medicine, Minia University, Egypt.
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Aurora Kinase A and Bcl-xL Inhibition Suppresses Metastasis in Triple-Negative Breast Cancer. Int J Mol Sci 2022; 23:ijms231710053. [PMID: 36077449 PMCID: PMC9456092 DOI: 10.3390/ijms231710053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous disease that accounts for 10–15% of all breast cancer cases. Within TNBC, the treatment of basal B is the most challenging due to its highly invasive potential, and thus treatments to suppress metastasis formation in this subgroup are urgently needed. However, the mechanisms underlying the metastatic ability of TNBC remain unclear. In the present study, we investigated the role of Aurora A and Bcl-xL in regulating basal B cell invasion. We found gene amplification and elevated protein expression in the basal B cells, which also showed increased invasiveness in vitro, compared to basal A cells. Chemical inhibition of Aurora A with alisertib and siRNA-mediated knockdown of BCL2L1 decreased the number of invading cells compared to non-treated cells in basal B cell lines. The analysis of the correlation between AURKA and BCL2L1 expression in TNBC and patient survival revealed significantly decreased relapse-free survival (n = 534, p = 0.012) and distant metastasis-free survival (n = 424, p = 0.017) in patients with primary tumors exhibiting a high combined expression of AURKA and BCL2L1. Together, our findings suggest that high levels of Aurora A and Bcl-xL promote metastasis, and inhibition of these proteins may suppress metastasis and improve patient survival in basal B TNBC.
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Verret B, Bottosso M, Hervais S, Pistilli B. The Molecular Predictive and Prognostic Biomarkers in Metastatic Breast Cancer: The Contribution of Molecular Profiling. Cancers (Basel) 2022; 14:4203. [PMID: 36077738 PMCID: PMC9454488 DOI: 10.3390/cancers14174203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/22/2022] Open
Abstract
The past decade was marked by several important studies deciphering the molecular landscape of metastatic breast cancer. Although the initial goal of these studies was to find driver oncogenic events to explain cancer progression and metastatic spreading, they have also permitted the identification of several molecular alterations associated with treatment response or resistance. Herein, we review validated (PI3KCA, ESR1, MSI, NTRK translocation) and emergent molecular biomarkers (ERBB2, AKT, PTEN, HRR gene, CD274 amplification RB1, NF1, mutational process) in metastatic breast cancer, on the bases of the largest molecular profiling studies. These biomarkers will be classed according the level of evidence and, if possible, the ESCAT (ESMO) classification. Finally, we will provide some perspective on development in clinical practice for the main biomarkers.
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Affiliation(s)
- Benjamin Verret
- Medical Oncology Department, Gustave Roussy Cancer Campus, 94800 Villejuif, France
- INSERM Unit U981, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Michele Bottosso
- INSERM Unit U981, Gustave Roussy Cancer Campus, 94805 Villejuif, France
- Department of Surgery, Oncology and Gastroenterology, University of Padova, 35122 Padova, Italy
| | - Sofia Hervais
- INSERM Unit U981, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Barbara Pistilli
- Medical Oncology Department, Gustave Roussy Cancer Campus, 94800 Villejuif, France
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Pereira A, Siegrist J, Lizarraga S, Pérez-Medina T. Clustering Molecular Subtypes in Breast Cancer, Immunohistochemical Parameters and Risk of Axillary Nodal Involvement. J Pers Med 2022; 12:jpm12091404. [PMID: 36143189 PMCID: PMC9505126 DOI: 10.3390/jpm12091404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/22/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: To establish similarities in the risk of axillary lymph node metastasis between different groups of women with breast cancer according to immunohistochemical (IHC) parameters. (2) Methods: Data was collected retrospectively, from 2000 to 2013, of 1058 node-positive breast tumours. All patients were divided according to the St Gallen 2013 criteria and IHC features. The proportion of axillary involvement (pN > pN0; pN > pN1mi; pN > pN1) was calculated for each group. Similarities in axillary nodal dissemination were explored by cluster analysis and association between IHC and risk of axillary disease was studied with multivariate analysis. (3) Results: Among clinico-pathological surrogates of intrinsic subtypes, axillary involvement was more frequent in Luminal-B like HER2 negative (45.8%) and less frequent in Luminal-B HER2 positive (33.8%; p = 0.044). Axillary macroscopic involvement was more frequent in Luminal-B like HER2 negative (37.9%) and HER2 positive (37.8%) and less frequent in Luminal-B HER2 positive (25.5%) and Luminal-A like (25.6%; p = 0.002). Axillary involvement ≥pN2 was significantly less frequent in Luminal-A like (7.4%; p < 0.001). Luminal-A with Luminal-B HER2 positive, and triple-negative with Erb-B2 overexpressing tumours were clustered together regarding any axillary involvement, macroscopic disease or ≥pN2. Among the defined subgroups, axillary metastases were more frequent when Ki67 was higher. In a multivariate analysis, Ki67>14% were associated with a risk of axillary metastases (HR: 1.31; 95% CI, 1.51−6.80; p < 0.037). (4) Conclusions: there are two lymphatic drainage pathways of the breast according to the expression of hormone receptor-related genes. Positive-ER tumors are associated with lower axillary involvement and negative-ER tumors and Ki67 > 14% with higher nodal involvement.
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Affiliation(s)
- Augusto Pereira
- Department of Gynecologic Surgery, Puerta de Hierro University Hospital, 28222 Madrid, Spain
- Correspondence:
| | - Jaime Siegrist
- Division of Gynecologic Oncology, La Paz University Hospital, 28046 Madrid, Spain
| | - Santiago Lizarraga
- Department of Obstetrics and Gynecology, Gregorio Marañon University General Hospital, 28009 Madrid, Spain
| | - Tirso Pérez-Medina
- Department of Gynecologic Surgery, Puerta de Hierro University Hospital, 28222 Madrid, Spain
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Athira K, Gopakumar G. Breast cancer stage prediction: a computational approach guided by transcriptome analysis. Mol Genet Genomics 2022; 297:1467-1479. [PMID: 35922530 DOI: 10.1007/s00438-022-01932-z] [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: 12/08/2020] [Accepted: 07/17/2022] [Indexed: 11/25/2022]
Abstract
Breast cancer is the second leading cancer among women in terms of mortality rate. In recent years, its incidence frequency has been continuously rising across the globe. In this context, the new therapeutic strategies to manage the deadly disease attracts tremendous research focus. However, finding new prognostic predictors to refine the selection of therapy for the various stages of breast cancer is an unattempted issue. Aberrant expression of genes at various stages of cancer progression can be studied to identify specific genes that play a critical role in cancer staging. Moreover, while many schemes for subtype prediction in breast cancer have been explored in the literature, stage-wise classification remains a challenge. These observations motivated the proposed two-phased method: stage-specific gene signature selection and stage classification. In the first phase, meta-analysis of gene expression data is conducted to identify stage-wise biomarkers that were then used in the second phase of cancer classification. From the analysis, 118, 12 and 4 genes respectively in stage I, stage II and stage III are determined as potential biomarkers. Pathway enrichment, gene network and literature analysis validate the significance of the identified genes in breast cancer. In this study, machine learning methods were combined with principal component and posterior probability analysis. Such a scheme offers a unique opportunity to build a meaningful model for predicting breast cancer staging. Among the machine learning models compared, Support Vector Machine (SVM) is found to perform the best for the selected datasets with an accuracy of 92.21% during test data evaluation. Perhaps, biomarker identification performed here for stage-specific cancer treatment would be a meaningful step towards predictive medicine. Significantly, the determination of correct cancer stage using the proposed 134 gene signature set can possibly act as potential target for breast cancer therapeutics.
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Affiliation(s)
- K Athira
- Department of Computer Science and Engineering, NIT Campus PO, National Institute of Technology Calicut, Calicut, Kerala, India.
| | - G Gopakumar
- Department of Computer Science and Engineering, NIT Campus PO, National Institute of Technology Calicut, Calicut, Kerala, India
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A perspective on the development and lack of interchangeability of the breast cancer intrinsic subtypes. NPJ Breast Cancer 2022; 8:85. [PMID: 35853907 PMCID: PMC9296605 DOI: 10.1038/s41523-022-00451-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/29/2022] [Indexed: 12/14/2022] Open
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Hossain FM, Danos DM, Fu Q, Wang X, Scribner RA, Chu ST, Horswell RL, Price-Haywood EG, Collins-Burow BM, Wu XC, Ochoa AC, Miele L. Association of Obesity and Diabetes With the Incidence of Breast Cancer in Louisiana. Am J Prev Med 2022; 63:S83-S92. [PMID: 35725146 PMCID: PMC9973383 DOI: 10.1016/j.amepre.2022.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Breast cancer is a heterogeneous disease, consisting of multiple molecular subtypes. Obesity has been associated with an increased risk for postmenopausal breast cancer, but few studies have examined breast cancer subtypes separately. Obesity is often complicated by type 2 diabetes, but the possible association of diabetes with specific breast cancer subtypes remains poorly understood. METHODS In this retrospective case-control study, Louisiana Tumor Registry records of primary invasive breast cancer diagnosed in 2010-2015 were linked to electronic health records in the Louisiana Public Health Institute's Research Action for Health Network. Controls were selected from Research Action for Health Network and matched to cases by age and race. Conditional logistic regression was used to identify metabolic risk factors. Data analysis was conducted in 2020‒2021. RESULTS There was a significant association between diabetes and breast cancer for Luminal A, Triple-Negative Breast Cancer, and human epidermal growth factor 2‒positive subtypes. In multiple logistic regression, including both obesity status and diabetes as independent risk factors, Luminal A breast cancer was also associated with overweight status. Diabetes was associated with increased risk for Luminal A and Triple-Negative Breast Cancer in subgroup analyses, including women aged ≥50 years, Black women, and White women. CONCLUSIONS Although research has identified obesity and diabetes as risk factors for breast cancer, these results underscore that comorbid risk is complex and may differ by molecular subtype. There was a significant association between diabetes and the incidence of Luminal A, Triple-Negative Breast Cancer, and human epidermal growth factor 2‒positive breast cancer in Louisiana.
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Affiliation(s)
- Fokhrul M Hossain
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana; Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Denise M Danos
- Department of Behavioral & Community Health Sciences (BCHS), School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Qiufan Fu
- Department of Biostatistics, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Xinnan Wang
- Department of Biostatistics, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Richard A Scribner
- Department of Epidemiology, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - San T Chu
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, Louisiana
| | - Ronald L Horswell
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, Louisiana
| | | | - Bridgette M Collins-Burow
- Hematology/Oncology, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Xiao-Cheng Wu
- Department of Epidemiology, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana; Louisiana Tumor Registry, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Augusto C Ochoa
- Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana; Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Lucio Miele
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana; Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana.
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Sukocheva OA, Lukina E, Friedemann M, Menschikowski M, Hagelgans A, Aliev G. The crucial role of epigenetic regulation in breast cancer anti-estrogen resistance: Current findings and future perspectives. Semin Cancer Biol 2022; 82:35-59. [PMID: 33301860 DOI: 10.1016/j.semcancer.2020.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/22/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer (BC) cell de-sensitization to Tamoxifen (TAM) or other selective estrogen receptor (ER) modulators (SERM) is a complex process associated with BC heterogeneity and the transformation of ER signalling. The most influential resistance-related mechanisms include modifications in ER expression and gene regulation patterns. During TAM/SERM treatment, epigenetic mechanisms can effectively silence ER expression and facilitate the development of endocrine resistance. ER status is efficiently regulated by specific epigenetic tools including hypermethylation of CpG islands within ER promoters, increased histone deacetylase activity in the ER promoter, and/or translational repression by miRNAs. Over-methylation of the ER α gene (ESR1) promoter by DNA methyltransferases was associated with poor prognosis and indicated the development of resistance. Moreover, BC progression and spreading were marked by transformed chromatin remodelling, post-translational histone modifications, and expression of specific miRNAs and/or long non-coding RNAs. Therefore, targeted inhibition of histone acetyltransferases (e.g. MYST3), deacetylases (e.g. HDAC1), and/or demethylases (e.g. lysine-specific demethylase LSD1) was shown to recover and increase BC sensitivity to anti-estrogens. Indicated as a powerful molecular instrument, the administration of epigenetic drugs can regain ER expression along with the activation of tumour suppressor genes, which can in turn prevent selection of resistant cells and cancer stem cell survival. This review examines recent advances in the epigenetic regulation of endocrine drug resistance and evaluates novel anti-resistance strategies. Underlying molecular mechanisms of epigenetic regulation will be discussed, emphasising the utilization of epigenetic enzymes and their inhibitors to re-program irresponsive BCs.
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Affiliation(s)
- Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia.
| | - Elena Lukina
- Discipline of Biology, College of Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Markus Friedemann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Albert Hagelgans
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Gjumrakch Aliev
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia; Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, 142432, Russia; Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation; GALLY International Research Institute, San Antonio, TX, 78229, USA.
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Combinatorial immunotherapies overcome MYC-driven immune evasion in triple negative breast cancer. Nat Commun 2022; 13:3671. [PMID: 35760778 PMCID: PMC9237085 DOI: 10.1038/s41467-022-31238-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/09/2022] [Indexed: 12/14/2022] Open
Abstract
Few patients with triple negative breast cancer (TNBC) benefit from immune checkpoint inhibitors with complete and durable remissions being quite rare. Oncogenes can regulate tumor immune infiltration, however whether oncogenes dictate diminished response to immunotherapy and whether these effects are reversible remains poorly understood. Here, we report that TNBCs with elevated MYC expression are resistant to immune checkpoint inhibitor therapy. Using mouse models and patient data, we show that MYC signaling is associated with low tumor cell PD-L1, low overall immune cell infiltration, and low tumor cell MHC-I expression. Restoring interferon signaling in the tumor increases MHC-I expression. By combining a TLR9 agonist and an agonistic antibody against OX40 with anti-PD-L1, mice experience tumor regression and are protected from new TNBC tumor outgrowth. Our findings demonstrate that MYC-dependent immune evasion is reversible and druggable, and when strategically targeted, may improve outcomes for patients treated with immune checkpoint inhibitors.
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Nath A, Cohen AL, Bild AH. ENDORSE: a prognostic model for endocrine therapy in estrogen-receptor-positive breast cancers. Mol Syst Biol 2022; 18:e10558. [PMID: 35671075 PMCID: PMC9172932 DOI: 10.15252/msb.202110558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/14/2022] Open
Abstract
Advanced and metastatic estrogen receptor-positive (ER+ ) breast cancers are often endocrine resistant. However, endocrine therapy remains the primary treatment for all advanced ER+ breast cancers. Treatment options that may benefit resistant cancers, such as add-on drugs that target resistance pathways or switching to chemotherapy, are only available after progression on endocrine therapy. Here we developed an endocrine therapy prognostic model for early and advanced ER+ breast cancers. The endocrine resistance (ENDORSE) model is composed of two components, each based on the empirical cumulative distribution function of ranked expression of gene signatures. These signatures include a feature set associated with long-term survival outcomes on endocrine therapy selected using lasso-regularized Cox regression and a pathway-based curated set of genes expressed in response to estrogen. We extensively validated ENDORSE in multiple ER+ clinical trial datasets and demonstrated superior and consistent performance of the model over clinical covariates, proliferation markers, and multiple published signatures. Finally, genomic and pathway analyses in patient data revealed possible mechanisms that may help develop rational stratification strategies for endocrine-resistant ER+ breast cancer patients.
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Affiliation(s)
- Aritro Nath
- Department of Medical Oncology and TherapeuticsCity of Hope Comprehensive Cancer CenterMonroviaCAUSA
| | - Adam L Cohen
- Neuro Oncology ProgramInova Schar Cancer InstituteFairfaxVAUSA
| | - Andrea H Bild
- Department of Medical Oncology and TherapeuticsCity of Hope Comprehensive Cancer CenterMonroviaCAUSA
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Moody L, Xu GB, Pan YX, Chen H. Genome-wide cross-cancer analysis illustrates the critical role of bimodal miRNA in patient survival and drug responses to PI3K inhibitors. PLoS Comput Biol 2022; 18:e1010109. [PMID: 35639779 PMCID: PMC9187341 DOI: 10.1371/journal.pcbi.1010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/10/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Heterogeneity of cancer means many tumorigenic genes are only aberrantly expressed in a subset of patients and thus follow a bimodal distribution, having two modes of expression within a single population. Traditional statistical techniques that compare sample means between cancer patients and healthy controls fail to detect bimodally expressed genes. We utilize a mixture modeling approach to identify bimodal microRNA (miRNA) across cancers, find consistent sources of heterogeneity, and identify potential oncogenic miRNA that may be used to guide personalized therapies. Pathway analysis was conducted using target genes of the bimodal miRNA to identify potential functional implications in cancer. In vivo overexpression experiments were conducted to elucidate the clinical importance of bimodal miRNA in chemotherapy treatments. In nine types of cancer, tumors consistently displayed greater bimodality than normal tissue. Specifically, in liver and lung cancers, high expression of miR-105 and miR-767 was indicative of poor prognosis. Functional pathway analysis identified target genes of miR-105 and miR-767 enriched in the phosphoinositide-3-kinase (PI3K) pathway, and analysis of over 200 cancer drugs in vitro showed that drugs targeting the same pathway had greater efficacy in cell lines with high miR-105 and miR-767 levels. Overexpression of the two miRNA facilitated response to PI3K inhibitor treatment. We demonstrate that while cancer is marked by considerable genetic heterogeneity, there is between-cancer concordance regarding the particular miRNA that are more variable. Bimodal miRNA are ideal biomarkers that can be used to stratify patients for prognosis and drug response in certain types of cancer. Bimodal genes can be defined as those having two modes of expression within the same population. A variety of statistical methodologies have been employed to assess bimodal gene expression, but current methods and their applications have been limited. Given the advances in next-generation sequencing as well as the extensive regulatory role of miRNA, assessing bimodality in miRNA-seq data can greatly broaden our understanding of factors underlying tumor progression. The goal of the current study was to utilize a novel mixture modeling approach to identify bimodal miRNA and then demonstrate their importance in cancer by evaluating their ability to predict overall survival and drug response. Our results showed that high levels of bimodal miRNA expression was characteristic of cancer. Additionally, several bimodal miRNA were common to multiple cancer types, suggesting that certain miRNA consistently account for tumor heterogeneity and may be involved in general oncogenic processes. Our study points to the potential of bimodal miRNA to facilitate precise prognostic evaluation and effective treatment strategies.
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Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Guanying Bianca Xu
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Hong Chen
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Lau TY, Kwan HY. Fucoxanthin Is a Potential Therapeutic Agent for the Treatment of Breast Cancer. Mar Drugs 2022; 20:md20060370. [PMID: 35736173 PMCID: PMC9229252 DOI: 10.3390/md20060370] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 12/04/2022] Open
Abstract
Breast cancer (BC) is one of the most common cancers diagnosed and the leading cause of cancer-related death in women. Although there are first-line treatments for BC, drug resistances and adverse events have been reported. Given the incidence of BC keeps increasing, seeking novel therapeutics is urgently needed. Fucoxanthin (Fx) is a dietary carotenoid commonly found in seaweeds and diatoms. Both in vitro and in vivo studies show that Fx and its deacetylated metabolite fucoxanthinol (Fxol) inhibit and prevent BC growth. The NF-κB signaling pathway is considered the major pathway contributing to the anti-proliferation, anti-angiogenesis and pro-apoptotic effects of Fx and Fxol. Other signaling molecules such as MAPK, MMP2/9, CYP and ROS are also involved in the anti-cancer effects by regulating the tumor microenvironment, cancer metastasis, carcinogen metabolism and oxidation. Besides, Fx also possesses anti-obesity effects by regulating UCP1 levels and lipid metabolism, which may help to reduce BC risk. More importantly, mounting evidence demonstrates that Fx overcomes drug resistance. This review aims to give an updated summary of the anti-cancer effects of Fx and summarize the underlying mechanisms of action, which will provide novel strategies for the development of Fx as an anti-cancer therapeutic agent.
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Pal AK, Sharma P, Zia A, Siwan D, Nandave D, Nandave M, Gautam RK. Metabolomics and EMT Markers of Breast Cancer: A Crosstalk and Future Perspective. PATHOPHYSIOLOGY 2022; 29:200-222. [PMID: 35736645 PMCID: PMC9230911 DOI: 10.3390/pathophysiology29020017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/17/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Cancer cells undergo transient EMT and MET phenomena or vice versa, along with the parallel interplay of various markers, often correlated as the determining factor in decoding metabolic profiling of breast cancers. Moreover, various cancer signaling pathways and metabolic changes occurring in breast cancer cells modulate the expression of such markers to varying extents. The existing research completed so far considers the expression of such markers as determinants regulating the invasiveness and survival of breast cancer cells. Therefore, this manuscript is crosstalk among the expression levels of such markers and their correlation in regulating the aggressiveness and invasiveness of breast cancer. We also attempted to cover the possible EMT-based metabolic targets to retard migration and invasion of breast cancer.
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Affiliation(s)
- Ajay Kumar Pal
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India; (A.K.P.); (P.S.); (A.Z.); (D.S.)
| | - Prateek Sharma
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India; (A.K.P.); (P.S.); (A.Z.); (D.S.)
| | - Alishan Zia
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India; (A.K.P.); (P.S.); (A.Z.); (D.S.)
| | - Deepali Siwan
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India; (A.K.P.); (P.S.); (A.Z.); (D.S.)
| | - Dipali Nandave
- Department of Dravyaguna, Karmavir V. T. Randhir Ayurved College, Boradi 425428, India;
| | - Mukesh Nandave
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India; (A.K.P.); (P.S.); (A.Z.); (D.S.)
- Correspondence: (M.N.); (R.K.G.)
| | - Rupesh K. Gautam
- Department of Pharmacology, MM School of Pharmacy, Maharishi Markandeshwar University, Ambala 134007, India
- Correspondence: (M.N.); (R.K.G.)
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Abreu de Oliveira WA, El Laithy Y, Bruna A, Annibali D, Lluis F. Wnt Signaling in the Breast: From Development to Disease. Front Cell Dev Biol 2022; 10:884467. [PMID: 35663403 PMCID: PMC9157790 DOI: 10.3389/fcell.2022.884467] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/22/2022] [Indexed: 12/11/2022] Open
Abstract
The Wnt cascade is a primordial developmental signaling pathway that plays a myriad of essential functions throughout development and adult homeostasis in virtually all animal species. Aberrant Wnt activity is implicated in embryonic and tissue morphogenesis defects, and several diseases, most notably cancer. The role of Wnt signaling in mammary gland development and breast cancer initiation, maintenance, and progression is far from being completely understood and is rather shrouded in controversy. In this review, we dissect the fundamental role of Wnt signaling in mammary gland development and adult homeostasis and explore how defects in its tightly regulated and intricated molecular network are interlinked with cancer, with a focus on the breast.
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Affiliation(s)
- Willy Antoni Abreu de Oliveira
- Department of Development and Regeneration, Stem Cell Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- *Correspondence: Willy Antoni Abreu de Oliveira, ; Frederic Lluis,
| | - Youssef El Laithy
- Department of Development and Regeneration, Stem Cell Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Alejandra Bruna
- Centre for Paediatric Oncology Experimental Medicine, Centre for Cancer Evolution, Molecular Pathology Division, London, United Kingdom
| | - Daniela Annibali
- Department of Oncology, Gynecological Oncology Laboratory, Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Frederic Lluis
- Department of Development and Regeneration, Stem Cell Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
- *Correspondence: Willy Antoni Abreu de Oliveira, ; Frederic Lluis,
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50
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Luo Z, Yao X, Sun Y, Fan X. Regression-based heterogeneity analysis to identify overlapping subgroup structure in high-dimensional data. Biom J 2022; 64:1109-1141. [PMID: 35524586 DOI: 10.1002/bimj.202100119] [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: 04/14/2021] [Revised: 01/08/2022] [Accepted: 01/12/2022] [Indexed: 11/09/2022]
Abstract
Heterogeneity is a hallmark of complex diseases. Regression-based heterogeneity analysis, which is directly concerned with outcome-feature relationships, has led to a deeper understanding of disease biology. Such an analysis identifies the underlying subgroup structure and estimates the subgroup-specific regression coefficients. However, most of the existing regression-based heterogeneity analyses can only address disjoint subgroups; that is, each sample is assigned to only one subgroup. In reality, some samples have multiple labels, for example, many genes have several biological functions, and some cells of pure cell types transition into other types over time, which suggest that their outcome-feature relationships (regression coefficients) can be a mixture of relationships in more than one subgroups, and as a result, the disjoint subgrouping results can be unsatisfactory. To this end, we develop a novel approach to regression-based heterogeneity analysis, which takes into account possible overlaps between subgroups and high data dimensions. A subgroup membership vector is introduced for each sample, which is combined with a loss function. Considering the lack of information arising from small sample sizes, an l 2 $l_2$ norm penalty is developed for each membership vector to encourage similarity in its elements. A sparse penalization is also applied for regularized estimation and feature selection. Extensive simulations demonstrate its superiority over direct competitors. The analysis of Cancer Cell Line Encyclopedia data and lung cancer data from The Cancer Genome Atlas show that the proposed approach can identify an overlapping subgroup structure with favorable performance in prediction and stability.
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Affiliation(s)
- Ziye Luo
- School of Statistics, Renmin University of China, Beijing, P. R. China
| | - Xinyue Yao
- School of Foreign Languages, Renmin University of China, Beijing, P. R. China
| | - Yifan Sun
- School of Statistics, Renmin University of China, Beijing, P. R. China.,Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, P. R. China
| | - Xinyan Fan
- School of Statistics, Renmin University of China, Beijing, P. R. China.,Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, P. R. China
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