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Li J, Sun Y, Zhi X, Sun Y, Abudousalamu Z, Lin Q, Li B, Yao L, Chen M. Unraveling the molecular mechanisms of lymph node metastasis in ovarian cancer: focus on MEOX1. J Ovarian Res 2024; 17:61. [PMID: 38486335 PMCID: PMC10938838 DOI: 10.1186/s13048-024-01384-6] [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: 11/16/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Lymph node metastasis (LNM) is a major factor contributing to the high mortality rate of ovarian cancer, making the treatment of this disease challenging. However, the molecular mechanism underlying LNM in ovarian cancer is still not well understood, posing a significant obstacle to overcome. RESULTS Through data mining from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, we have identified MEOX1 as a specific gene associated with LNM in ovarian cancer. The expression of MEOX1 was found to be relatively high in serous ovarian adenocarcinoma, and its higher expression were associated with increased tumor grade and poorer clinical prognosis for ovarian cancer patients. Bioinformatics analysis revealed that MEOX1 exhibited the highest mRNA levels among all cancer types in ovarian cancer tissues and cell lines. Furthermore, gene set enrichment analysis (GSEA) and pathway analysis demonstrated that MEOX1 was involved in various LNM-related biological activities, such as lymphangiogenesis, lymphatic vessel formation during metastasis, epithelial-mesenchymal transition (EMT), G2/M checkpoint, degradation of extracellular matrix, and collagen formation. Additionally, the expression of MEOX1 was positively correlated with the expression of numerous prolymphangiogenic factors in ovarian cancer. To validate our findings, we conducted experiments using clinical tissue specimens and cell lines, which confirmed that MEOX1 was highly expressed in high-grade serous ovarian cancer (HGSOC) tissues and various ovarian cancer cell lines (A2780, SKOV3, HO8910, and OVCAR5) compared to normal ovarian tissues and normal ovarian epithelial cell line IOSE-80, respectively. Notably, we observed a higher protein level of MEOX1 in tumor tissues of LNM-positive HGSOC compared to LNM-negative HGSOC. Moreover, our fundamental experiments demonstrated that suppression of MEOX1 led to inhibitory effects on ovarian cancer cell proliferation and EMT, while overexpression of MEOX1 enhanced the proliferation and EMT capacities of ovarian cancer cells. CONCLUSIONS The results of our study indicate that MEOX1 plays a role in the lymph node metastasis of ovarian cancer by regulating multiple biological activities, including the proliferation and EMT of ovarian cancer, lymphangiogenesis, and ECM remodeling. Our findings suggest that MEOX1 could serve as a potential biomarker for the diagnosis and treatment of ovarian cancer with LNM.
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Affiliation(s)
- Jiajia Li
- Department of Gynecology Oncology, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Yihua Sun
- Department of Pathology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China
| | - Xiuling Zhi
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yating Sun
- Department of Gynecology Oncology, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Zulimire Abudousalamu
- Department of Gynecology Oncology, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Qianhan Lin
- Department of Gynecology Oncology, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Bin Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Liangqing Yao
- Department of Gynecology Oncology, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011, China.
| | - Mo Chen
- Department of Gynecology Oncology, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011, China.
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2
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Rachman T, Bartlett D, LaFramboise W, Wagner P, Schwartz R, Carja O. Modeling the Effect of Spatial Structure on Solid Tumor Evolution and Circulating Tumor DNA Composition. Cancers (Basel) 2024; 16:844. [PMID: 38473206 PMCID: PMC10930890 DOI: 10.3390/cancers16050844] [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: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones are over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.
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Affiliation(s)
- Thomas Rachman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA 15213, USA
| | - David Bartlett
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - William LaFramboise
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Patrick Wagner
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Cui R, Zou J, Zhao Y, Zhao T, Ren L, Li Y. The dual-crosslinked prospective values of RAI14 for the diagnosis and chemosurveillance in triple negative breast cancer. Ann Med 2023; 55:820-836. [PMID: 36880986 PMCID: PMC10795645 DOI: 10.1080/07853890.2023.2177722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/01/2023] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE The exploration of non-invasive biomarkers for assessing tumor response is critical to optimize treatment decisions. In this study, we aimed at determining the potential role of RAI14 in the early diagnosis and evaluation of chemotherapy efficacy in triple-negative breast cancer (TNBC). METHODS We recruited 116 patients newly diagnosed with breast cancer, 30 patients with benign breast disease and 30 healthy controls. In addition, 57 TNBC patients were collected in serum at different time points (C0, C2 and C4) for chemotherapy monitoring. The expression of serum RAI14 and CA15-3 were quantified by Elisa and electrochemiluminescence assay, respectively. Then we compared the performances of markers with the chemotherapy efficacy assessed by imaging. RESULTS RAI14 is significantly overexpressed in TNBC and is linked to adverse clinicopathological features such as tumor burden, CA15-3 levels and the ER, PR, and HER2 status of the patients. ROC curve analysis showed that RAI14 improves the diagnostic performance for CA15-3(AUCRAI14 = 0.934 vs. AUCCA15-3 = 0.836), especially embodied in early-stage breast cancer diagnosis and patients with CA15-3 negativity. Furthermore, RAI14 behaves well in reproducing treatment response which was consistent with clinical Imaging assessment. CONCLUSIONS Recent studies showed that RAI14 has a complementary effect to CA15-3 and a test combining the two parameters can improve the detection rate of early triple-negative breast cancer. At the same time, RAI14 plays a more important role in chemotherapy monitoring than CA15-3 as the change in its concentration is in line with the tumor volume variation. Taken together, RAI14 is a reliable novel marker in the early diagnosis and chemotherapy monitoring of triple-negative breast cancer.
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Affiliation(s)
- Ranliang Cui
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Jie Zou
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Yan Zhao
- Nankai University, Tianjin, China
| | - Ting Zhao
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Li Ren
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Yueguo Li
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
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4
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Rachman T, Bartlett D, Laframboise W, Wagner P, Schwartz R, Carja O. Modeling the effect of spatial structure on solid tumor evolution and ctDNA composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566658. [PMID: 37986965 PMCID: PMC10659436 DOI: 10.1101/2023.11.10.566658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform on cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones end up over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases, but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.
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Affiliation(s)
- Thomas Rachman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology
| | - David Bartlett
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh PA
| | | | - Patrick Wagner
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh PA
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
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5
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Chintapally N, Englander K, Gallagher J, Elleson K, Sun W, Whiting J, Laronga C, Lee MC. Tumor Characteristics Associated with Axillary Nodal Positivity in Triple Negative Breast Cancer. Diseases 2023; 11:118. [PMID: 37754314 PMCID: PMC10529347 DOI: 10.3390/diseases11030118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
Larger-size primary tumors are correlated with axillary metastases and worse outcomes. We evaluated the relationships among tumor size, location, and distance to nipple relative to axillary node metastases in triple-negative breast cancer (TNBC) patients, as well as the predictive capacity of imaging. We conducted a single-institution, retrospective chart review of stage I-III TNBC patients diagnosed from 1998 to 2019 who underwent upfront surgery. Seventy-three patients had a mean tumor size of 20 mm (range 1-53 mm). All patients were clinically node negative. Thirty-two patients were sentinel lymph node positive, of whom 25 underwent axillary lymph node dissection. Larger tumor size was associated with positive nodes (p < 0.001): the mean tumor size was 14.30 mm in node negative patients and 27.31 mm in node positive patients. Tumor to nipple distance was shorter in node positive patients (51.0 mm) vs. node negative patients (73.3 mm) (p = 0.005). The presence of LVI was associated with nodal positivity (p < 0.001). Tumor quadrant was not associated with nodal metastasis. Ultrasound yielded the largest number of suspicious findings (21/49), with sensitivity of 0.25 and specificity of 0.40. On univariate analysis, age younger than 60 at diagnosis was also associated with nodal positivity (p < 0.002). Comparative analyses with other subtypes may identify biologic determinants.
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Affiliation(s)
- Neha Chintapally
- University of South Florida Morsani College of Medicine, Tampa, FL 33602, USA; (N.C.); (K.E.); (J.G.)
| | - Katherine Englander
- University of South Florida Morsani College of Medicine, Tampa, FL 33602, USA; (N.C.); (K.E.); (J.G.)
| | - Julia Gallagher
- University of South Florida Morsani College of Medicine, Tampa, FL 33602, USA; (N.C.); (K.E.); (J.G.)
| | - Kelly Elleson
- Regional Breast Care, Genesis Care Network, 8931 Colonial Center Dr #301, Fort Myers, FL 33905, USA;
| | - Weihong Sun
- Comprehensive Breast Program, Moffitt Cancer Center, Tampa, FL 33612, USA; (W.S.); (C.L.)
| | - Junmin Whiting
- Department of Biostatistics & Bioinformatics, Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Christine Laronga
- Comprehensive Breast Program, Moffitt Cancer Center, Tampa, FL 33612, USA; (W.S.); (C.L.)
| | - Marie Catherine Lee
- Comprehensive Breast Program, Moffitt Cancer Center, Tampa, FL 33612, USA; (W.S.); (C.L.)
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6
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Sun M, Chen G, Ouyang S, Chen C, Zheng Z, Lin P, Song X, Chen H, Chen Y, You Y, Tao J, Lin B, Zhao P. Magnetic Resonance Diagnosis of Early Triple-Negative Breast Cancer Based on the Ionic Covalent Organic Framework with High Relaxivity and Long Retention Time. Anal Chem 2023; 95:8267-8276. [PMID: 37191204 DOI: 10.1021/acs.analchem.3c00307] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Patients with triple-negative breast cancer (TNBC) have dismal prognoses due to the lack of therapeutic targets and susceptibility to lymph node (LN) metastasis. Therefore, it is essential to develop more effective approaches to identify early TNBC tissues and LNs. In this work, a magnetic resonance imaging (MRI) contrast agent (Mn-iCOF) was constructed based on the Mn(II)-chelated ionic covalent organic framework (iCOF). Because of the porous structure and hydrophilicity, the Mn-iCOF has a high longitudinal relaxivity (r1) of 8.02 mM-1 s-1 at 3.0 T. For the tumor-bearing mice, a lower dose (0.02 mmol [Mn]/kg) of Mn-iCOF demonstrated a higher signal-to-noise ratio (SNR) value (1.8) and longer retention time (2 h) compared to a 10-fold dose of commercial Gd-DOTA (0.2 mmol [Gd]/kg). Moreover, the Mn-iCOF can provide continuous and significant MR contrast for the popliteal LNs within 24 h, allowing for accurate evaluation and dissection of LNs. These excellent MRI properties of the Mn-iCOF may open new avenues for designing more biocompatible MRI contrast agents with higher resolutions, particularly in the diagnosis of TNBC.
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Affiliation(s)
- Mingyan Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Guanjun Chen
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, 510515 Guangzhou, China
| | - Sixue Ouyang
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
| | - Chuyao Chen
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, 510515 Guangzhou, China
| | - Zhiyuan Zheng
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Peiru Lin
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Xiangfei Song
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Huiting Chen
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
| | - Yuying Chen
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
| | - Yuanyuan You
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
| | - Jia Tao
- School of Chemistry and Chemical Engineering, South China University of Technology, 510640 Guangzhou, China
| | - Bingquan Lin
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, 510515 Guangzhou, China
| | - Peng Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of Cardiac Function and Microcirculation, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, 510515 Guangzhou, China
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A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Commun Biol 2022; 5:617. [PMID: 35732905 PMCID: PMC9217972 DOI: 10.1038/s42003-022-03560-0] [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: 09/29/2021] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
Cancer cell genomes change continuously due to mutations, and mutational processes change over time in patients, leaving dynamic signatures in the accumulated genomic variation in tumors. Many computational methods detect the relative activities of known mutation signatures. However, these methods may produce erroneous signatures when applied to individual branches in cancer cell phylogenies. Here, we show that the inference of branch-specific mutational signatures can be improved through a joint analysis of the collections of mutations mapped on proximal branches of the cancer cell phylogeny. This approach reduces the false-positive discovery rate of branch-specific signatures and can sometimes detect faint signatures. An analysis of empirical data from 61 lung cancer patients supports trends based on computer-simulated datasets for which the correct signatures are known. In lung cancer somatic variation, we detect a decreasing trend of smoking-related mutational processes over time and an increasing influence of APOBEC mutational processes as the tumor evolution progresses. These analyses also reveal patterns of conservation and divergence of mutational processes in cell lineages within patients.
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8
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Specific diagnosis of lymph node micrometastasis in breast cancer by targeting activatable near-infrared fluorescence imaging. Biomaterials 2022; 282:121388. [DOI: 10.1016/j.biomaterials.2022.121388] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 12/14/2022]
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Martínez-Gregorio H, Rojas-Jiménez E, Mejía-Gómez JC, Díaz-Velásquez C, Quezada-Urban R, Vallejo-Lecuona F, de la Cruz-Montoya A, Porras-Reyes FI, Pérez-Sánchez VM, Maldonado-Martínez HA, Robles-Estrada M, Bargalló-Rocha E, Cabrera-Galeana P, Ramos-Ramírez M, Chirino YI, Alonso Herrera L, Terrazas LI, Frecha C, Oliver J, Perdomo S, Vaca-Paniagua F. The Evolution of Clinically Aggressive Triple-Negative Breast Cancer Shows a Large Mutational Diversity and Early Metastasis to Lymph Nodes. Cancers (Basel) 2021; 13:5091. [PMID: 34680239 PMCID: PMC8534164 DOI: 10.3390/cancers13205091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
In triple-negative breast cancer (TNBC), only 30% of patients treated with neoadjuvant chemotherapy achieve a pathological complete response after treatment and more than 90% die due to metastasis formation. The diverse clinical responses and metastatic developments are attributed to extensive intrapatient genetic heterogeneity and tumor evolution acting on this neoplasm. In this work, we aimed to evaluate genomic alterations and tumor evolution in TNBC patients with aggressive disease. We sequenced the whole exome of 16 lesions from four patients who did not respond to therapy, and took several follow-up samples, including samples from tumors before and after treatment, as well as from the lymph nodes and skin metastases. We found substantial intrapatient genetic heterogeneity, with a variable tumor mutational composition. Early truncal events were MCL1 amplifications. Metastatic lesions had deletions in RB1 and PTEN, along with TERT, AKT2, and CCNE1 amplifications. Mutational signatures 06 and 12 were mainly detected in skin metastases and lymph nodes. According to phylogenetic analysis, the lymph node metastases occurred at an early stage of TNBC development. Finally, each patient had three to eight candidate driving mutations for targeted treatments. This study delves into the genomic complexity and the phylogenetic and evolutionary development of aggressive TNBC, supporting early metastatic development, and identifies specific genetic alterations associated with a response to targeted therapies.
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Affiliation(s)
- Héctor Martínez-Gregorio
- Posgrado en Ciencias Biológicas de la Universidad Nacional Autonóma de Mexico, Facultad de Estudios Superiores Iztacala, UNAM, Mexico City 54090, Mexico;
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Ernesto Rojas-Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Javier César Mejía-Gómez
- Division of Breast Cancer, Department of Medical Oncology, Mt. Sinai Hospital, University of Toronto, Toronto, ON M5G 1X5, Canada;
| | - Clara Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
| | - Rosalía Quezada-Urban
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Fernando Vallejo-Lecuona
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Aldo de la Cruz-Montoya
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Fany Iris Porras-Reyes
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Víctor Manuel Pérez-Sánchez
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Héctor Aquiles Maldonado-Martínez
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | | | - Enrique Bargalló-Rocha
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Paula Cabrera-Galeana
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Maritza Ramos-Ramírez
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
| | - Yolanda Irasema Chirino
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Luis Alonso Herrera
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
- Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas—Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
| | - Cecilia Frecha
- Unidad de Producción Celular del Hospital Regional Universitario de Málaga—IBIMA—Málaga, 29010 Málaga, Spain;
| | - Javier Oliver
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, 29010 Málaga, Spain;
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), 150 Cours Albert Thomas, 69372 Lyon, France;
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (E.R.-J.); (C.D.-V.); (R.Q.-U.); (F.V.-L.); (L.I.T.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico; (A.d.l.C.-M.); (Y.I.C.)
- Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (F.I.P.-R.); (V.M.P.-S.); (H.A.M.-M.); (E.B.-R.); (P.C.-G.); (M.R.-R.); (L.A.H.)
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10
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Yao X, Xie R, Cao Y, Tang J, Men Y, Peng H, Yang W. Simvastatin induced ferroptosis for triple-negative breast cancer therapy. J Nanobiotechnology 2021; 19:311. [PMID: 34627266 PMCID: PMC8502296 DOI: 10.1186/s12951-021-01058-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/22/2021] [Indexed: 01/21/2023] Open
Abstract
Triple-negative breast cancer (TNBC), a management of aggressive breast cancer, remains an unmet medical challenge. Although a wave of efforts had spurred to design novel therapeutic method of TNBC, unpredictable prognosis with lacking effective therapeutic targets along with the resistance to apoptosis seriously limited survival benefits. Ferroptosis is a non-apoptotic form of cell death that is induced by excessive lipid peroxidation, which provide an innovative way to combat cancer. Emerging evidence suggests that ferroptosis plays an important role in the treatment of TNBC cells. Herein, a novel ferroptosis nanomedicine was prepared by loading simvastatin (SIM), a ferroptosis drug, into zwitterionic polymer coated magnetic nanoparticles (Fe3O4@PCBMA) to improve the therapeutic effect of TNBC. The as-obtained Fe3O4@PCBMA-SIM nanoparticles demonstrated more cytotoxicity against MDA-MB-231 than MCF-7 due to the higher expression of 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGCR), which demonstrated that statins could effectively kill TNBC. Further experiments showed that SIM could inhibit the expression of HMGCR to downregulate the mevalonate (MVA) pathway and glutathione peroxidase 4 (GPX4), thereby inducing cancer cell ferroptosis. What's more, PCBMA endows Fe3O4@PCBMA longer blood circulation performance to enhance their accumulation at tumor sites. Given that Fe3O4 have proven for clinical applications by the U.S. Food and Drug Administration (FDA) and SIM could induce cancer cell ferroptosis, the developed Fe3O4@PCBMA-SIM nanosystem would have great potential in clinics for overcoming the drug resistance brought about by apoptotic drugs to cancer cells.
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Affiliation(s)
- Xianxian Yao
- State Key Laboratory of Molecular Engineering of Polymers & Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Ruihong Xie
- State Key Laboratory of Molecular Engineering of Polymers & Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Yongbin Cao
- State Key Laboratory of Molecular Engineering of Polymers & Department of Macromolecular Science, Fudan University, Shanghai, 200433, China
| | - Jing Tang
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Yongzhi Men
- Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Haibao Peng
- Institute for Translational Brain Research, Fudan University, Shanghai, 200032, China.
| | - Wuli Yang
- State Key Laboratory of Molecular Engineering of Polymers & Department of Macromolecular Science, Fudan University, Shanghai, 200433, China.
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11
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Zhao X, Bai X, Li W, Gao X, Wang X, Li B. microRNA-506-3p suppresses the proliferation of triple negative breast cancer cells via targeting SNAI2. Mol Cell Toxicol 2021. [DOI: 10.1007/s13273-021-00160-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Abstract
Tumour evolution is a complex interplay between the acquisition of somatic (epi)genomic changes in tumour cells and the phenotypic consequences they cause, all in the context of a changing microenvironment. Single-cell sequencing offers a window into this dynamic process at the ultimate resolution of individual cells. In this review, we discuss the transformative insight offered by single-cell sequencing technologies for understanding tumour evolution.
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Affiliation(s)
- Maximilian Mossner
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Ann-Marie C Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
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13
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Bailey C, Black JRM, Reading JL, Litchfield K, Turajlic S, McGranahan N, Jamal-Hanjani M, Swanton C. Tracking Cancer Evolution through the Disease Course. Cancer Discov 2021; 11:916-932. [PMID: 33811124 PMCID: PMC7611362 DOI: 10.1158/2159-8290.cd-20-1559] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023]
Abstract
During cancer evolution, constituent tumor cells compete under dynamic selection pressures. Phenotypic variation can be observed as intratumor heterogeneity, which is propagated by genome instability leading to mutations, somatic copy-number alterations, and epigenomic changes. TRACERx was set up in 2014 to observe the relationship between intratumor heterogeneity and patient outcome. By integrating multiregion sequencing of primary tumors with longitudinal sampling of a prospectively recruited patient cohort, cancer evolution can be tracked from early- to late-stage disease and through therapy. Here we review some of the key features of the studies and look to the future of the field. SIGNIFICANCE: Cancers evolve and adapt to environmental challenges such as immune surveillance and treatment pressures. The TRACERx studies track cancer evolution in a clinical setting, through primary disease to recurrence. Through multiregion and longitudinal sampling, evolutionary processes have been detailed in the tumor and the immune microenvironment in non-small cell lung cancer and clear-cell renal cell carcinoma. TRACERx has revealed the potential therapeutic utility of targeting clonal neoantigens and ctDNA detection in the adjuvant setting as a minimal residual disease detection tool primed for translation into clinical trials.
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Affiliation(s)
- Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - James R M Black
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
| | - James L Reading
- Research Department of Haematology, University College London Cancer Institute, University College London, London, UK
| | - Kevin Litchfield
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, University College London Cancer Institute, University College London, London, UK
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Trust, London, UK
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14
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Wu SL, Zhang X, Chang M, Huang C, Qian J, Li Q, Yuan F, Sun L, Yu X, Cui X, Jiang J, Cui M, Liu Y, Wu HW, Liang ZY, Wang X, Niu Y, Tong WM, Jin F. Genome-wide 5-hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:64-79. [PMID: 33716151 PMCID: PMC8498923 DOI: 10.1016/j.gpb.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/07/2019] [Accepted: 05/31/2019] [Indexed: 11/28/2022]
Abstract
Although DNA 5-hydroxymethylcytosine (5hmC) is recognized as an important epigenetic mark in cancer, its precise role in lymph node metastasis remains elusive. In this study, we investigated how 5hmC associates with lymph node metastasis in breast cancer. Accompanying with high expression of TET1 and TET2 proteins, large numbers of genes in the metastasis-positive primary tumors exhibit higher 5hmC levels than those in the metastasis-negative primary tumors. In contrast, the TET protein expression and DNA 5hmC decrease significantly within the metastatic lesions in the lymph nodes compared to those in their matched primary tumors. Through genome-wide analysis of 8 sets of primary tumors, we identified 100 high-confidence metastasis-associated 5hmC signatures, and it is found that increased levels of DNA 5hmC and gene expression of MAP7D1 associate with high risk of lymph node metastasis. Furthermore, we demonstrate that MAP7D1, regulated by TET1, promotes tumor growth and metastasis. In conclusion, the dynamic 5hmC profiles during lymph node metastasis suggest a link between DNA 5hmC and lymph node metastasis. Meanwhile, the role of MAP7D1 in breast cancer progression suggests that the metastasis-associated 5hmC signatures are potential biomarkers to predict the risk for lymph node metastasis, which may serve as diagnostic and therapeutic targets for metastatic breast cancer.
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Affiliation(s)
- Shuang-Ling Wu
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China; Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xiaoyi Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Mengqi Chang
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Changcai Huang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jun Qian
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Qing Li
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
| | - Lihong Sun
- Center for Experimental Animal Research, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College. Beijing 100005, China
| | - Xinmiao Yu
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Xinmiao Cui
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Jiayi Jiang
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Mengyao Cui
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Ye Liu
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Huan-Wen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences. Beijing 100005, China
| | - Zhi-Yong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences. Beijing 100005, China
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China.
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China; Center for Experimental Animal Research, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College. Beijing 100005, China.
| | - Feng Jin
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China.
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15
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Stevenson J, Barrow-McGee R, Yu L, Paul A, Mansfield D, Owen J, Woodman N, Natrajan R, Haider S, Gillett C, Tutt A, Pinder SE, Choudary J, Naidoo K. Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment. NPJ Breast Cancer 2021; 7:24. [PMID: 33674617 PMCID: PMC7935848 DOI: 10.1038/s41523-021-00227-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/20/2021] [Indexed: 02/08/2023] Open
Abstract
In breast cancer (BC), detecting low volumes of axillary lymph node (ALN) metastasis pre-operatively is difficult and novel biomarkers are needed. We recently showed that patient-derived ALNs can be sustained ex-vivo using normothermic perfusion. We now compare reactive (tumour-free; n = 5) and macrometastatic (containing tumour deposits >2 mm; n = 4) ALNs by combining whole section multiplex immunofluorescence with TMT-labelled LC-MS/MS of the circulating perfusate. Macrometastases contained significantly fewer B cells and T cells (CD4+/CD8+/regulatory) than reactive nodes (p = 0.02). Similarly, pathway analysis of the perfusate proteome (119/1453 proteins significantly differentially expressed) showed that immune function was diminished in macrometastases in favour of ‘extracellular matrix degradation’; only ‘neutrophil degranulation’ was preserved. Qualitative comparison of the perfusate proteome to that of node-positive pancreatic and prostatic adenocarcinoma also highlighted ‘neutrophil degranulation’ as a contributing factor to nodal metastasis. Thus, metastasis-induced changes in the REPLICANT perfusate proteome are detectable, and could facilitate biomarker discovery.
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Affiliation(s)
- Julia Stevenson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachel Barrow-McGee
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Angela Paul
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - David Mansfield
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Julie Owen
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Natalie Woodman
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Cheryl Gillett
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Andrew Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Comprehensive Cancer Centre, London, UK
| | - Jyoti Choudary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Kalnisha Naidoo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK. .,Department of Cellular Pathology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, UK.
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16
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Caswell-Jin JL, Lorenz C, Curtis C. Molecular Heterogeneity and Evolution in Breast Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2021. [DOI: 10.1146/annurev-cancerbio-060220-014137] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Breast cancer comprises a heterogeneous group of tumor subtypes, whether defined by immunohistochemistry of key proteins, RNA expression profiles, or genetic alterations, and each of these subtypes may benefit from a distinct treatment approach. However, there can be striking heterogeneity within tumors, which may pose challenges to the development of personalized approaches to therapy. Intratumor heterogeneity can be divided into three main categories: genetic, phenotypic, and microenvironmental. Here, we review technologies to interrogate these three categories of heterogeneity in patient samples, as well as the current state of understanding of these categories in breast cancer, from cell to cell, across different regions of the same tumor mass, across treatment, and across metastasis. Efforts to characterize tumor heterogeneity longitudinally will be crucial to the development of personalized oncology for breast cancer.
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Affiliation(s)
- Jennifer L. Caswell-Jin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Carina Lorenz
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christina Curtis
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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17
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Cui X, Zhu H, Huang J. Nomogram for Predicting Lymph Node Involvement in Triple-Negative Breast Cancer. Front Oncol 2020; 10:608334. [PMID: 33344259 PMCID: PMC7747752 DOI: 10.3389/fonc.2020.608334] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
Background Lymph node metastasis of triple-negative breast cancer (TNBC) is essential in treatment strategy formulation. This study aimed to build a nomogram that predicts lymph node metastasis in patients with TNBC. Materials and Methods A total of 28,966 TNBC patients diagnosed from 2010 to 2017 in the Surveillance, Epidemiology and End Results (SEER) database were enrolled, and randomized 1:1 into the training and validation sets, respectively. Univariate and multivariate logistic regression analysis were applied to identify the predictive factors, which composed the nomogram. The receiver operating characteristic curves showed the efficacy of the nomogram. Result Multivariate logistic regression analyses revealed that age, race, tumor size, tumor primary site, and pathological grade were independent predictive factors of lymph node status. Integrating these independent predictive factors, a nomogram was successfully developed for predicting lymph node status, and further validated in the validation set. The areas under the receiver operating characteristic curves of the nomogram in the training and validation sets were 0.684 and 0.689 respectively, showing a satisfactory performance. Conclusion We constructed a nomogram to predict the lymph node status in TNBC patients. After further validation in additional large cohorts, the nomogram developed here would do better in predicting, providing more information for staging and treatment, and enabling tailored treatment in TNBC patients.
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Affiliation(s)
- Xiang Cui
- Department of Thyroid and Breast Surgery, The First People's Hospital of Shangqiu, Shangqiu, China
| | - Hao Zhu
- Department of Thyroid and Breast Surgery, The First People's Hospital of Shangqiu, Shangqiu, China
| | - Jisheng Huang
- Department of Thyroid and Breast Surgery, The First People's Hospital of Shangqiu, Shangqiu, China
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18
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Yalcin GD, Danisik N, Baygin RC, Acar A. Systems Biology and Experimental Model Systems of Cancer. J Pers Med 2020; 10:E180. [PMID: 33086677 PMCID: PMC7712848 DOI: 10.3390/jpm10040180] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/29/2022] Open
Abstract
Over the past decade, we have witnessed an increasing number of large-scale studies that have provided multi-omics data by high-throughput sequencing approaches. This has particularly helped with identifying key (epi)genetic alterations in cancers. Importantly, aberrations that lead to the activation of signaling networks through the disruption of normal cellular homeostasis is seen both in cancer cells and also in the neighboring tumor microenvironment. Cancer systems biology approaches have enabled the efficient integration of experimental data with computational algorithms and the implementation of actionable targeted therapies, as the exceptions, for the treatment of cancer. Comprehensive multi-omics data obtained through the sequencing of tumor samples and experimental model systems will be important in implementing novel cancer systems biology approaches and increasing their efficacy for tailoring novel personalized treatment modalities in cancer. In this review, we discuss emerging cancer systems biology approaches based on multi-omics data derived from bulk and single-cell genomics studies in addition to existing experimental model systems that play a critical role in understanding (epi)genetic heterogeneity and therapy resistance in cancer.
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Affiliation(s)
| | | | | | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, Ankara 06800, Turkey; (G.D.Y.); (N.D.); (R.C.B.)
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19
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Karihtala P, Jääskeläinen A, Roininen N, Jukkola A. Prognostic factors in metastatic breast cancer: a prospective single-centre cohort study in a Finnish University Hospital. BMJ Open 2020; 10:e038798. [PMID: 33046470 PMCID: PMC7552835 DOI: 10.1136/bmjopen-2020-038798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Although novel early breast cancer prognostic factors are being continuously discovered, only rare factors predicting survival in metastatic breast cancer have been validated. The prognostic role of early breast cancer prognostic factors in metastatic disease also remains mostly unclear. DESIGN AND SETTING Prospective cohort study in a Finnish University Hospital. PARTICIPANTS AND OUTCOMES 594 women with early breast cancer were originally followed. Sixty-one of these patients developed distant metastases during the follow-up, and their primary breast cancer properties, such as tumour size, nodal status, oestrogen receptor (ER) and progesterone receptor expression, grade, proliferation rate, histopathological subtype and breast cancer subtype were analysed as potential prognostic factors for metastatic disease. RESULTS In multivariate analysis, the presence of lymph node metastases at the time of early breast cancer surgery (HR, 2.17; 95% CI, 1.09-4.31; p=0.027) and ER status (negative vs positive, HR, 2.16; 95% CI, 1.14-4.10; p=0.018) were significant predictors of survival in metastatic disease. CONCLUSIONS These results confirm ER status as a primary prognostic factor in metastatic breast cancer. Furthermore, it also suggests that the presence of initial lymph node metastases could serve as a prognostic factor in recurrent breast cancer.
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Affiliation(s)
- Peeter Karihtala
- Department of Oncology and Radiotherapy, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Centre and University of Helsinki, Helsinki, Finland
| | - Anniina Jääskeläinen
- Department of Oncology and Radiotherapy, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Nelli Roininen
- Department of Oncology and Radiotherapy, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Arja Jukkola
- Department of Oncology, Tampere University Hospital, Cancer Center, Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
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20
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Wakae K, Kondo S, Pham HT, Wakisaka N, Que L, Li Y, Zheng X, Fukano K, Kitamura K, Watashi K, Aizaki H, Ueno T, Moriyama‐Kita M, Ishikawa K, Nakanishi Y, Endo K, Muramatsu M, Yoshizaki T. EBV-LMP1 induces APOBEC3s and mitochondrial DNA hypermutation in nasopharyngeal cancer. Cancer Med 2020; 9:7663-7671. [PMID: 32815637 PMCID: PMC7571841 DOI: 10.1002/cam4.3357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
An Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMP1) is a principal oncogene that plays a pivotal role in EBV-associated malignant tumors including nasopharyngeal cancer (NPC). Recent genomic landscape studies revealed that NPC also contained many genomic mutations, suggesting the role of LMP1 as a driver gene for the induction of these genomic mutations. Nonetheless, its exact mechanism has not been investigated. In this study, we report that LMP1 alters the expression profile of APOBEC3s(A3s), host deaminases that introduce consecutive C-to-U mutations (hypermutation). In vitro, LMP1 induces APOBEC3B (A3B) and 3F(A3F), in a nasopharyngeal cell line, AdAH. Overexpression of LMP1, A3B, or A3F induces mtDNA hypermutation, which is also detectable from NPC specimens. Expression of LMP1 and A3B in NPC was correlated with neck metastasis. These results provide evidence as to which LMP1 induces A3s and mtDNA hypermutation, and how LMP1 facilitates metastasis is also discussed.
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Affiliation(s)
- Kousho Wakae
- Department of Molecular GeneticsGraduate School of Medical ScienceKanazawa UniversityKanazawaJapan
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Satoru Kondo
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Hai Thanh Pham
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Naohiro Wakisaka
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Lusheng Que
- Department of Molecular GeneticsGraduate School of Medical ScienceKanazawa UniversityKanazawaJapan
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Yingfang Li
- Department of Molecular GeneticsGraduate School of Medical ScienceKanazawa UniversityKanazawaJapan
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Xin Zheng
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Kento Fukano
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Kouichi Kitamura
- Department of Molecular GeneticsGraduate School of Medical ScienceKanazawa UniversityKanazawaJapan
- Department of Virology IINational Institute of Infectious DiseasesMusashi‐MurayamaTokyoJapan
| | - Koichi Watashi
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Hideki Aizaki
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Takayoshi Ueno
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Makiko Moriyama‐Kita
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Kazuya Ishikawa
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Yosuke Nakanishi
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Kazuhira Endo
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
| | - Masamichi Muramatsu
- Department of Molecular GeneticsGraduate School of Medical ScienceKanazawa UniversityKanazawaJapan
- Department of Virology IINational Institute of Infectious DiseasesTokyoJapan
| | - Tomokazu Yoshizaki
- Division of Otorhinolaryngology and Head and Neck SurgeryKanazawa UniversityKanazawaJapan
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21
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Tan W, Xie X, Huang Z, Chen L, Tang W, Zhu R, Ye X, Zhang X, Pan L, Gao J, Tang H, Zheng W. Construction of an immune-related genes nomogram for the preoperative prediction of axillary lymph node metastasis in triple-negative breast cancer. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2020; 48:288-297. [PMID: 31858816 DOI: 10.1080/21691401.2019.1703731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immune system disorder is associated with metastasis of triple-negative breast cancers (TNBCs). A robust, individualized immune-related genes (IRGs)-based classifier was aimed to develop and validate in our study to precisely estimate the axillary lymph node (ALN) status preoperatively in patients with early-stage TNBC. We first analyzed RNA sequencing profiles in TNBC patients from The Cancer Genome Atlas database by using bioinformatics approaches, and screened 23 differentially expressed IRGs. A 9-gene panel was generated with an area under the curve (AUC) of 0.77 [95% confidence interval (95% CI), 0.68-0.87]. We detected the 9 ALN-status-related IRGs in the training set (n = 133) and developed a reduced and optimized five-IRGs signature, which effectively distinguished TNBC patients with ALN metastasis (AUC, 0.80; 95% CI, 0.65-0.86), and was superior to preoperative ultrasound-based ALN status (AUC, 0.73; 95% CI, 0.53-0.93). Predictive efficiency (AUC, 0.77; 95% CI 0.61-0.93) of this five-IRGs signature was validated in the validation set (n = 81). Furthermore, IRGs nomogram incorporated IRGs signature with US-based ALN status showed higher ALN status prediction efficacy than US-based ALN status and five-IRGs signature alone in both training and validation sets. IRGs nomogram may aid in identifying patients who can be exempted from axillary surgery.Novelty and impact: An immune-related genes (IRGs) nomogram was first developed and externally validated in our study, which incorporated the IRGs signature with ultrasound (US)-based axillary lymph nodes (ALN) status. IRGs nomogram is superior to IRGs signature alone for preoperative estimation of ALN metastasis in patients with triple-negative breast cancer (TNBC). It is a favourable biomarker for preoperatively predicting ALN metastasis risk and may aid in clinical decision-making in early-stage TNBCs.
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Affiliation(s)
- Weige Tan
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xinhua Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Zhongying Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Lun Chen
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Tang
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Renjie Zhu
- East Hospital Affiliated to Tongji University, Shanghai, China
| | - Xigang Ye
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaoshen Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lingxiao Pan
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jin Gao
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wenbo Zheng
- Department of Breast Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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22
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Rey-Vargas L, Mejía-Henao JC, Sanabria-Salas MC, Serrano-Gomez SJ. Effect of neoadjuvant therapy on breast cancer biomarker profile. BMC Cancer 2020; 20:675. [PMID: 32682413 PMCID: PMC7368678 DOI: 10.1186/s12885-020-07179-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Breast cancer clinical management requires the assessment of hormone receptors (estrogen (ER) and progesterone receptor (PR)), human epidermal growth factor receptor 2 (HER2) and cellular proliferation index Ki67, by immunohistochemistry (IHC), in order to choose and guide therapy according to tumor biology. Many studies have reported contradictory results regarding changes in the biomarker profile after neoadjuvant therapy (NAT). Given its clinical implications for the disease management, we aimed to analyze changes in ER, PR, HER2, and Ki67 expression in paired core-needle biopsies and surgical samples in breast cancer patients that had either been treated or not with NAT. METHODS We included 139 patients with confirmed diagnosis of invasive ductal breast carcinoma from the Colombian National Cancer Institute. Variation in biomarker profile were assessed according to NAT administration (NAT and no-NAT treated cases) and NAT scheme (hormonal, cytotoxic, cytotoxic + trastuzumab, combined). Chi-squared and Wilcoxon signed-rank test were used to identify changes in biomarker status and percentage expression, respectively, in the corresponding groups. RESULTS We did not find any significant variations in biomarker status or expression values in the no-NAT group. In cases previously treated with NAT, we did find a statistically significant decrease in Ki67 (p < 0.001) and PR (p = 0.02605) expression. When changes were evaluated according to NAT scheme, we found a significant decrease in both Ki67 status (p = 0.02977) and its expression values (p < 0.001) in cases that received the cytotoxic treatment. CONCLUSIONS Our results suggest that PR and Ki67 expression can be altered by NAT administration, whereas cases not previously treated with NAT do not present IHC biomarker profile variations. The re-evaluation of these two biomarkers after NAT could provide valuable information regarding treatment response and prognosis for breast cancer patients.
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Affiliation(s)
- Laura Rey-Vargas
- Grupo de investigación en biología del cáncer, Instituto Nacional de Cancerología, Calle 1a #9-85, Bogotá D. C, Colombia.,Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | | | - Silvia J Serrano-Gomez
- Grupo de investigación en biología del cáncer, Instituto Nacional de Cancerología, Calle 1a #9-85, Bogotá D. C, Colombia.
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23
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Pathology of triple negative breast cancer. Semin Cancer Biol 2020; 72:136-145. [PMID: 32544511 DOI: 10.1016/j.semcancer.2020.06.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 01/14/2023]
Abstract
Triple negative breast cancer (TNBC) is a subtype of breast tumor lacking hormone receptors expression and HER2 gene amplification and represents 24 % of newly diagnosed breast neoplasms. In this review, pathological aspects of triple-negative breast cancer are illustrated, with particular attention to the seminal studies that defined this subtype of breast cancer by a molecular point of view. This paper also focuses on practical issues raised in clinical routine by the introduction of genetic expression breast cancer profiling and the innovative prognostic and predictive impact on triple-negative breast cancer pathology. Moreover, histopathological aspects of triple-negative neoplasms are also mentioned, underlying the importance of histologic diagnosis of particular cancer subtypes with decisive impact on clinical outcome. Importantly, focus on new therapeutic frontier represented by immunotherapy is illustrated, with particular mention of immune checkpoint inhibitors introduction in TNBC therapy and their impact on future treatments.
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24
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Cresswell GD, Nichol D, Spiteri I, Tari H, Zapata L, Heide T, Maley CC, Magnani L, Schiavon G, Ashworth A, Barry P, Sottoriva A. Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking. Nat Commun 2020; 11:1446. [PMID: 32221288 PMCID: PMC7101390 DOI: 10.1038/s41467-020-15047-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
Circulating tumour DNA (ctDNA) allows tracking of the evolution of human cancers at high resolution, overcoming many limitations of tissue biopsies. However, exploiting ctDNA to determine how a patient's cancer is evolving in order to aid clinical decisions remains difficult. This is because ctDNA is a mix of fragmented alleles, and the contribution of different cancer deposits to ctDNA is largely unknown. Profiling ctDNA almost invariably requires prior knowledge of what genomic alterations to track. Here, we leverage on a rapid autopsy programme to demonstrate that unbiased genomic characterisation of several metastatic sites and concomitant ctDNA profiling at whole-genome resolution reveals the extent to which ctDNA is representative of widespread disease. We also present a methylation profiling method that allows tracking evolutionary changes in ctDNA at single-molecule resolution without prior knowledge. These results have critical implications for the use of liquid biopsies to monitor cancer evolution in humans and guide treatment.
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Affiliation(s)
- George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Haider Tari
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Glioma Lab, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaia Schiavon
- Breast Unit, Royal Marsden Hospital, London, UK
- AstraZeneca, Oncology R&D, Cambridge, UK
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Peter Barry
- Breast Unit, Royal Marsden Hospital, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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25
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Engel J, Weichert W, Jung A, Emeny R, Hölzel D. Lymph node infiltration, parallel metastasis and treatment success in breast cancer. Breast 2019; 48:1-6. [DOI: 10.1016/j.breast.2019.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/28/2019] [Accepted: 07/31/2019] [Indexed: 02/05/2023] Open
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26
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Kleftogiannis D, Punta M, Jayaram A, Sandhu S, Wong SQ, Gasi Tandefelt D, Conteduca V, Wetterskog D, Attard G, Lise S. Identification of single nucleotide variants using position-specific error estimation in deep sequencing data. BMC Med Genomics 2019; 12:115. [PMID: 31375105 PMCID: PMC6679440 DOI: 10.1186/s12920-019-0557-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/15/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. However, identification of SNVs using deep sequencing data is a challenging computational problem as different sequencing artifacts limit the analytical sensitivity of SNV detection, especially at low variant allele frequencies (VAFs). METHODS To address the problem of relatively high noise levels in amplicon-based deep sequencing data (e.g. with the Ion AmpliSeq technology) in the context of SNV calling, we have developed a new bioinformatics tool called AmpliSolve. AmpliSolve uses a set of normal samples to model position-specific, strand-specific and nucleotide-specific background artifacts (noise), and deploys a Poisson model-based statistical framework for SNV detection. RESULTS Our tests on both synthetic and real data indicate that AmpliSolve achieves a good trade-off between precision and sensitivity, even at VAF below 5% and as low as 1%. We further validate AmpliSolve by applying it to the detection of SNVs in 96 circulating tumor DNA samples at three clinically relevant genomic positions and compare the results to digital droplet PCR experiments. CONCLUSIONS AmpliSolve is a new tool for in-silico estimation of background noise and for detection of low frequency SNVs in targeted deep sequencing data. Although AmpliSolve has been specifically designed for and tested on amplicon-based libraries sequenced with the Ion Torrent platform it can, in principle, be applied to other sequencing platforms as well. AmpliSolve is freely available at https://github.com/dkleftogi/AmpliSolve .
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Affiliation(s)
- Dimitrios Kleftogiannis
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Present address: Genome Institute of Singapore (GIS), Agency of Science Research and Technology (A*STAR), Singapore, 138672, Singapore
| | - Marco Punta
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Shahneen Sandhu
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
| | - Delila Gasi Tandefelt
- Department of Urology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Vincenza Conteduca
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014, Meldola, Italy
| | | | - Gerhardt Attard
- UCL Cancer Institute, University College London, London, UK.
| | - Stefano Lise
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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27
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Williams MJ, Sottoriva A, Graham TA. Measuring Clonal Evolution in Cancer with Genomics. Annu Rev Genomics Hum Genet 2019; 20:309-329. [PMID: 31059289 DOI: 10.1146/annurev-genom-083117-021712] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancers originate from somatic cells in the human body that have accumulated genetic alterations. These mutations modify the phenotype of the cells, allowing them to escape the homeostatic regulation that maintains normal cell number. Viewed through the lens of evolutionary biology, the transformation of normal cells into malignant cells is evolution in action. Evolution continues throughout cancer growth, progression, treatment resistance, and disease relapse, driven by adaptation to changes in the cancer's environment, and intratumor heterogeneity is an inevitable consequence of this evolutionary process. Genomics provides a powerful means to characterize tumor evolution, enabling quantitative measurement of evolving clones across space and time. In this review, we discuss concepts and approaches to quantify and measure this evolutionary process in cancer using genomics.
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Affiliation(s)
- Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom; ,
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom; ,
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28
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Caswell-Jin JL, McNamara K, Reiter JG, Sun R, Hu Z, Ma Z, Ding J, Suarez CJ, Tilk S, Raghavendra A, Forte V, Chin SF, Bardwell H, Provenzano E, Caldas C, Lang J, West R, Tripathy D, Press MF, Curtis C. Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy. Nat Commun 2019; 10:657. [PMID: 30737380 PMCID: PMC6368565 DOI: 10.1038/s41467-019-08593-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/18/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic changes observed across treatment may result from either clonal evolution or geographically disparate sampling of heterogeneous tumors. Here we use computational modeling based on analysis of fifteen primary breast tumors and find that apparent clonal change between two tumor samples can frequently be explained by pre-treatment heterogeneity, such that at least two regions are necessary to detect treatment-induced clonal shifts. To assess for clonal replacement, we devise a summary statistic based on whole-exome sequencing of a pre-treatment biopsy and multi-region sampling of the post-treatment surgical specimen and apply this measure to five breast tumors treated with neoadjuvant HER2-targeted therapy. Two tumors underwent clonal replacement with treatment, and mathematical modeling indicates these two tumors had resistant subclones prior to treatment and rates of resistance-related genomic changes that were substantially larger than previous estimates. Our results provide a needed framework to incorporate primary tumor heterogeneity in investigating the evolution of resistance.
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Affiliation(s)
- Jennifer L Caswell-Jin
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
| | - Katherine McNamara
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Johannes G Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, 94305, CA, USA
| | - Ruping Sun
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Zheng Hu
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Zhicheng Ma
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Jie Ding
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Susanne Tilk
- Department of Biology, Stanford University, Stanford, 94305, CA, USA
| | - Akshara Raghavendra
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Victoria Forte
- Maimonides Medical Center, Brooklyn, 11219, NY, USA
- Norris Comprehensive Cancer Center, Los Angeles, 90033, CA, USA
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Helen Bardwell
- Cancer Research UK Cambridge Institute, Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Elena Provenzano
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Department of Oncology, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Julie Lang
- Norris Comprehensive Cancer Center, Los Angeles, 90033, CA, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, 90333, CA, USA
| | - Robert West
- Department of Pathology, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Michael F Press
- Norris Comprehensive Cancer Center, Los Angeles, 90033, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
| | - Christina Curtis
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, 94305, California, United States.
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, 94305, CA, USA.
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