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Hulahan TS, Spruill L, Wallace EN, Park Y, West RB, Marks JR, Hwang ES, Drake RR, Angel PM. Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics. Int J Mol Sci 2024; 25:6748. [PMID: 38928454 PMCID: PMC11203487 DOI: 10.3390/ijms25126748] [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: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detailed pathological annotations were investigated by multiplexed spatial proteomics. Across tissues, 1,005 ECM peptides were detected in pathologically annotated regions and their surrounding extracellular microenvironments. A comparison of DCIS to IBC pathologies demonstrated 43 significantly altered ECM peptides. Notably, eight fibrillar collagen peptides could distinguish with high specificity and sensitivity between DCIS and IBC. Lesion-targeted proteomic imaging revealed heterogeneity of the ECM proteome surrounding individual DCIS lesions. Multiplexed spatial proteomics reported an invasive cancer field effect, in which DCIS lesions in closer proximity to IBC shared a more similar ECM profile to IBC than distal counterparts. Defining the ECM proteomic microenvironment provides novel molecular insights relating to DCIS and IBC.
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Affiliation(s)
- Taylor S. Hulahan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Elizabeth N. Wallace
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA;
| | - Robert B. West
- Department of Pathology Clinical, Stanford University, Stanford, CA 94305, USA;
| | - Jeffrey R. Marks
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - E. Shelley Hwang
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
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Kim MY, Yoen H, Ji H, Park SJ, Kim SM, Han W, Cho N. Ultrafast MRI and T1 and T2 Radiomics for Predicting Invasive Components in Ductal Carcinoma in Situ Diagnosed With Percutaneous Needle Biopsy. Korean J Radiol 2023; 24:1190-1199. [PMID: 38016679 DOI: 10.3348/kjr.2023.0208] [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: 08/18/2022] [Revised: 07/26/2023] [Accepted: 09/05/2023] [Indexed: 11/30/2023] Open
Abstract
OBJECTIVE This study aimed to investigate the feasibility of ultrafast magnetic resonance imaging (MRI) and radiomic features derived from breast MRI for predicting the upstaging of ductal carcinoma in situ (DCIS) diagnosed using percutaneous needle biopsy. MATERIALS AND METHODS Between August 2018 and June 2020, 95 patients with 98 DCIS lesions who underwent preoperative breast MRI, including an ultrafast sequence, and subsequent surgery were included. Four ultrafast MRI parameters were analyzed: time-to-enhancement, maximum slope (MS), area under the curve for 60 s after enhancement, and time-to-peak enhancement. One hundred and seven radiomic features were extracted for the whole tumor on the first post-contrast T1WI and T2WI using PyRadiomics. Clinicopathological characteristics, ultrafast MRI findings, and radiomic features were compared between the pure DCIS and DCIS with invasion groups. Prediction models, incorporating clinicopathological, ultrafast MRI, and radiomic features, were developed. Receiver operating characteristic curve analysis and area under the curve (AUC) were used to evaluate model performance in distinguishing between the two groups using leave-one-out cross-validation. RESULTS Thirty-six of the 98 lesions (36.7%) were confirmed to have invasive components after surgery. Compared to the pure DCIS group, the DCIS with invasion group had a higher nuclear grade (P < 0.001), larger mean lesion size (P = 0.038), larger mean MS (P = 0.002), and different radiomic-related characteristics, including a more extensive tumor volume; higher maximum gray-level intensity; coarser, more complex, and heterogeneous texture; and a greater concentration of high gray-level intensity. No significant differences in AUCs were found between the model incorporating nuclear grade and lesion size (0.687) and the models integrating additional ultrafast MRI and radiomic features (0.680-0.732). CONCLUSION High nuclear grade, larger lesion size, larger MS, and multiple radiomic features were associated with DCIS upstaging. However, the addition of MS and radiomic features to the prediction model did not significantly improve the prediction performance.
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Affiliation(s)
- Min Young Kim
- Department of Radiology, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Radiology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Radiation Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Heera Yoen
- Department of Radiology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hye Ji
- Department of Radiology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sang Joon Park
- Department of Radiology, Seoul National University College of Medicine, Seoul, Republic of Korea
- MEDICALIP Co. Ltd., Seoul, Republic of Korea
| | - Sun Mi Kim
- Department of Radiology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
| | - Wonshik Han
- Department of Surgery and Cancer Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nariya Cho
- Department of Radiology, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Radiology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Radiation Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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Varisli L, Dancik GM, Tolan V, Vlahopoulos S. Critical Roles of SRC-3 in the Development and Progression of Breast Cancer, Rendering It a Prospective Clinical Target. Cancers (Basel) 2023; 15:5242. [PMID: 37958417 PMCID: PMC10648290 DOI: 10.3390/cancers15215242] [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: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Breast cancer (BCa) is the most frequently diagnosed malignant tumor in women and is also one of the leading causes of cancer-related death. Most breast tumors are hormone-dependent and estrogen signaling plays a critical role in promoting the survival and malignant behaviors of these cells. Estrogen signaling involves ligand-activated cytoplasmic estrogen receptors that translocate to the nucleus with various co-regulators, such as steroid receptor co-activator (SRC) family members, and bind to the promoters of target genes and regulate their expression. SRC-3 is a member of this family that interacts with, and enhances, the transcriptional activity of the ligand activated estrogen receptor. Although SRC-3 has important roles in normal homeostasis and developmental processes, it has been shown to be amplified and overexpressed in breast cancer and to promote malignancy. The malignancy-promoting potential of SRC-3 is diverse and involves both promoting malignant behavior of tumor cells and creating a tumor microenvironment that has an immunosuppressive phenotype. SRC-3 also inhibits the recruitment of tumor-infiltrating lymphocytes with effector function and promotes stemness. Furthermore, SRC-3 is also involved in the development of resistance to hormone therapy and immunotherapy during breast cancer treatment. The versatility of SRC-3 in promoting breast cancer malignancy in this way makes it a good target, and methodical targeting of SRC-3 probably will be important for the success of breast cancer treatment.
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Affiliation(s)
- Lokman Varisli
- Department of Molecular Biology and Genetics, Science Faculty, Dicle University, Diyarbakir 21280, Turkey;
| | - Garrett M. Dancik
- Department of Computer Science, Eastern Connecticut State University, Willimantic, CT 06226, USA;
| | - Veysel Tolan
- Department of Molecular Biology and Genetics, Science Faculty, Dicle University, Diyarbakir 21280, Turkey;
| | - Spiros Vlahopoulos
- First Department of Pediatrics, National and Kapodistrian University of Athens, Thivon & Levadeias 8, Goudi, 11527 Athens, Greece
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Schandiz H, Park D, Kaiser YL, Lyngra M, Talleraas IS, Geisler J, Sauer T. Subtypes of high-grade breast ductal carcinoma in situ (DCIS): incidence and potential clinical impact. Breast Cancer Res Treat 2023:10.1007/s10549-023-07016-9. [PMID: 37453021 PMCID: PMC10361903 DOI: 10.1007/s10549-023-07016-9] [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: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
OBJECTIVE The purpose of this study was to investigate and classify the molecular subtypes of high-grade ductal carcinoma in situ (DCIS) and identify possible high-risk subtypes. The heterogenicity of DCIS with variable clinical and histopathological presentations has been recognized. Nevertheless, only histopathological grading and diameter are currently implemented in clinical decision-making following the diagnosis of DCIS. The molecular subtypes of DCIS and their IHC surrogate markers have not been defined in conventional treatment guidelines and recommendations. We applied the definitions of molecular subtypes according to the IHC surrogate markers defined for IBC and subclassified high-grade DCIS, accordingly. METHODS Histopathological specimens were collected, revised, and regraded from 494 patients diagnosed with DCIS between 1996 and 2018. Other in situ and papillary lesions observed in breast biopsies were excluded from this study. 357 high-grade DCIS cases were submitted to IHC analysis. The markers investigated were ER, PR, HER2, and Ki67. RESULTS 45 cases were classified as grade 1, 19 as grade 2, and 430 as grade 3. Sixty patients with high-grade DCIS had an additional invasive component in the surgical specimen. Thirty-three patients were diagnosed with recurrent DCIS or invasive cancer (minimum one year after their primary DCIS diagnosis). The proportions of luminal A and luminal B HER2-negative subtypes varied depending on whether 2011 or 2013 St. Gallen Consensus Conference guidelines were adopted. Luminal A was the most prevalent subtype, according to both classifications. The luminal B HER2-positive subtype was found in 22.1% of cases, HER2-enriched subtype in 21.8%, and TPN subtype in 5.6%. There were strong indications that HER2-enriched subtype was significantly more frequent among DCIS with invasive component (p = 0.0169). CONCLUSIONS High-grade DCIS exhibits all the molecular subtypes previously identified in IBC, but with a somewhat different distribution in our cohort. HER2-enriched subtype is substantially related to the presence of an invasive component in DCIS; consequently, it is regarded as a high-risk entity.
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Affiliation(s)
- Hossein Schandiz
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway.
| | - Daehoon Park
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Yan Liu Kaiser
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital (AHUS), Lørenskog, Norway
| | - Marianne Lyngra
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
| | | | - Jürgen Geisler
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Campus AHUS, Oslo, Norway
| | - Torill Sauer
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Campus AHUS, Oslo, Norway
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5
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Sundararajan V, Burk UC, Bajdak-Rusinek K. Revisiting the miR-200 Family: A Clan of Five Siblings with Essential Roles in Development and Disease. Biomolecules 2022; 12:biom12060781. [PMID: 35740906 PMCID: PMC9221129 DOI: 10.3390/biom12060781] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 12/07/2022] Open
Abstract
Over two decades of studies on small noncoding RNA molecules illustrate the significance of microRNAs (miRNAs/miRs) in controlling multiple physiological and pathological functions through post-transcriptional and spatiotemporal gene expression. Among the plethora of miRs that are essential during animal embryonic development, in this review, we elaborate the indispensable role of the miR-200 family (comprising miR-200a, -200b, 200c, -141, and -429) in governing the cellular functions associated with epithelial homeostasis, such as epithelial differentiation and neurogenesis. Additionally, in pathological contexts, miR-200 family members are primarily involved in tumor-suppressive roles, including the reversal of the cancer-associated epithelial–mesenchymal transition dedifferentiation process, and are dysregulated during organ fibrosis. Moreover, recent eminent studies have elucidated the crucial roles of miR-200s in the pathophysiology of multiple neurodegenerative diseases and tissue fibrosis. Lastly, we summarize the key studies that have recognized the potential use of miR-200 members as biomarkers for the diagnosis and prognosis of cancers, elaborating the application of these small biomolecules in aiding early cancer detection and intervention.
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Affiliation(s)
- Vignesh Sundararajan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore 117599, Singapore;
| | - Ulrike C. Burk
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
| | - Karolina Bajdak-Rusinek
- Department of Medical Genetics, Faculty of Medical Sciences, Medical University of Silesia, 40-752 Katowice, Poland
- Correspondence: ; Tel.: +48-32-208-8382
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6
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Spatial charting of single-cell transcriptomes in tissues. Nat Biotechnol 2022; 40:1190-1199. [PMID: 35314812 PMCID: PMC9673606 DOI: 10.1038/s41587-022-01233-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing methods can profile the transcriptomes of single cells but cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile spatial regions in tissue sections, but do not have single-cell resolution. Here, we developed a computational method called CellTrek that combines these two datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches. We benchmarked CellTrek using simulation and in situ hybridization datasets, which demonstrated its accuracy and robustness. We then applied CellTrek to existing mouse brain and kidney datasets and showed that CellTrek can detect topological patterns of different cell types and cell states. We performed single-cell RNA sequencing and spatial transcriptomics experiments on two ductal carcinoma in situ tissues and applied CellTrek to identify tumor subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas. Our data show that CellTrek can accurately map single cells in diverse tissue types to resolve their spatial organization.
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7
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Nachmanson D, Officer A, Mori H, Gordon J, Evans MF, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky AD, Stein JL, Harismendy O. The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ. NPJ Breast Cancer 2022; 8:6. [PMID: 35027560 PMCID: PMC8758681 DOI: 10.1038/s41523-021-00365-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Microenvironmental and molecular factors mediating the progression of Breast Ductal Carcinoma In Situ (DCIS) are not well understood, impeding the development of prevention strategies and the safe testing of treatment de-escalation. We addressed methodological barriers and characterized the mutational, transcriptional, histological, and microenvironmental landscape across 85 multiple microdissected regions from 39 cases. Most somatic alterations, including whole-genome duplications, were clonal, but genetic divergence increased with physical distance. Phenotypic and subtype heterogeneity was frequently associated with underlying genetic heterogeneity and regions with low-risk features preceded those with high-risk features according to the inferred phylogeny. B- and T-lymphocytes spatial analysis identified three immune states, including an epithelial excluded state located preferentially at DCIS regions, and characterized by histological and molecular features of immune escape, independently from molecular subtypes. Such breast pre-cancer atlas with uniquely integrated observations will help scope future expansion studies and build finer models of outcomes and progression risk.
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Affiliation(s)
- Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Hidetoshi Mori
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA
| | - Jonathan Gordon
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Mark F Evans
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Joseph Steward
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA
| | - Huazhen Yao
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Thomas O'Keefe
- Department of Surgery, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Farnaz Hasteh
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA
- Department of Pathology, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Gary S Stein
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA
| | - Donald L Weaver
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Brian L Sprague
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Surgery, University of Vermont, Burlington, VT, 05405, USA
| | - Laura J Esserman
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, Center for Immunology and Infectious Diseases, School of Medicine, University of California Davis, 2315 Stockton Blvd, Sacramento, CA, 95817, USA
| | - Janet L Stein
- University of Vermont Cancer Center, 111 Colchester Avenue Main Campus, Main Pavillion, Level, 2, Burlington, VT, 05401, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Olivier Harismendy
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, San Diego, CA, 92093, USA.
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Sinha VC, Rinkenbaugh AL, Xu M, Zhou X, Zhang X, Jeter-Jones S, Shao J, Qi Y, Zebala JA, Maeda DY, McAllister F, Piwnica-Worms H. Single-cell evaluation reveals shifts in the tumor-immune niches that shape and maintain aggressive lesions in the breast. Nat Commun 2021; 12:5024. [PMID: 34408137 PMCID: PMC8373912 DOI: 10.1038/s41467-021-25240-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
There is an unmet clinical need for stratification of breast lesions as indolent or aggressive to tailor treatment. Here, single-cell transcriptomics and multiparametric imaging applied to a mouse model of breast cancer reveals that the aggressive tumor niche is characterized by an expanded basal-like population, specialization of tumor subpopulations, and mixed-lineage tumor cells potentially serving as a transition state between luminal and basal phenotypes. Despite vast tumor cell-intrinsic differences, aggressive and indolent tumor cells are functionally indistinguishable once isolated from their local niche, suggesting a role for non-tumor collaborators in determining aggressiveness. Aggressive lesions harbor fewer total but more suppressed-like T cells, and elevated tumor-promoting neutrophils and IL-17 signaling, disruption of which increase tumor latency and reduce the number of aggressive lesions. Our study provides insight into tumor-immune features distinguishing indolent from aggressive lesions, identifies heterogeneous populations comprising these lesions, and supports a role for IL-17 signaling in aggressive progression.
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Affiliation(s)
- Vidya C. Sinha
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Amanda L. Rinkenbaugh
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Mingchu Xu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Xinhui Zhou
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Xiaomei Zhang
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Sabrina Jeter-Jones
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jiansu Shao
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Yuan Qi
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | | | | | - Florencia McAllister
- grid.240145.60000 0001 2291 4776Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Helen Piwnica-Worms
- grid.240145.60000 0001 2291 4776Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
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9
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Onoyama I, Nakayama S, Shimizu H, Nakayama KI. Loss of Fbxw7 Impairs Development of and Induces Heterogeneous Tumor Formation in the Mouse Mammary Gland. Cancer Res 2020; 80:5515-5530. [PMID: 33234509 DOI: 10.1158/0008-5472.can-20-0271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 08/17/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022]
Abstract
Fbxw7 is an F-box protein that contributes to regulation of cell proliferation and cell fate determination as well as to tumor suppression in various tissues. In this study, we generated mice with mammary gland-specific ablation of Fbxw7 (Blg-Cre/Fbxw7 F/F mice) and found that most neonates born to mutant dams die soon after birth as a result of defective maternal lactation. The mammary gland of mutant dams was markedly atrophic and manifested both excessive cell proliferation and apoptosis in association with the accumulation of Notch1 and p63. Despite the hypoplastic nature of the mutant mammary gland, Blg-Cre/Fbxw7 F/F mice spontaneously developed mammary tumors that resembled basal-like carcinoma with marked intratumoral heterogeneity. Additional inactivation of Trp53 in Blg-Cre/Fbxw7 F/F mice further promoted onset and development of mammary tumors, suggesting that spontaneous mutation of Trp53 may facilitate transition of hypoplastic mammary lesions to aggressive cancer in mice lacking Fbxw7. RNA-sequencing analysis of epithelial- and mesenchymal-like cell lines from a Blg-Cre/Fbxw7 F/F mouse tumor revealed an increased mutation rate and structural alterations in the tumor and differential expression of upstream transcription factors including known targets of Fbxw7. Together, our results implicate Fbxw7 in the regulation of cell differentiation and in tumor suppression in the mammary gland. Loss of Fbxw7 increases mutation rate and chromosome instability, activates signaling pathways governed by transcription factors regulated by Fbxw7, and triggers the development of mammary tumors with prominent heterogeneity. SIGNIFICANCE: Mammary gland-specific ablation of Fbxw7 in mice results in defective gland development and spontaneous mammary tumor formation reminiscent of human basal-like carcinoma with intratumoral heterogeneity. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/24/5515/F1.large.jpg.
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Affiliation(s)
- Ichiro Onoyama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka Japan
| | - Shogo Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka Japan
| | - Hideyuki Shimizu
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Fukuoka Japan.
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10
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Nachmanson D, Steward J, Yao H, Officer A, Jeong E, O'Keefe TJ, Hasteh F, Jepsen K, Hirst GL, Esserman LJ, Borowsky AD, Harismendy O. Mutational profiling of micro-dissected pre-malignant lesions from archived specimens. BMC Med Genomics 2020; 13:173. [PMID: 33208147 PMCID: PMC7672910 DOI: 10.1186/s12920-020-00820-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Systematic cancer screening has led to the increased detection of pre-malignant lesions (PMLs). The absence of reliable prognostic markers has led mostly to over treatment resulting in potentially unnecessary stress, or insufficient treatment and avoidable progression. Importantly, most mutational profiling studies have relied on PML synchronous to invasive cancer, or performed in patients without outcome information, hence limiting their utility for biomarker discovery. The limitations in comprehensive mutational profiling of PMLs are in large part due to the significant technical and methodological challenges: most PML specimens are small, fixed in formalin and paraffin embedded (FFPE) and lack matching normal DNA. METHODS Using test DNA from a highly degraded FFPE specimen, multiple targeted sequencing approaches were evaluated, varying DNA input amount (3-200 ng), library preparation strategy (BE: Blunt-End, SS: Single-Strand, AT: A-Tailing) and target size (whole exome vs. cancer gene panel). Variants in high-input DNA from FFPE and mirrored frozen specimens were used for PML-specific variant calling training and testing, respectively. The resulting approach was applied to profile and compare multiple regions micro-dissected (mean area 5 mm2) from 3 breast ductal carcinoma in situ (DCIS). RESULTS Using low-input FFPE DNA, BE and SS libraries resulted in 4.9 and 3.7 increase over AT libraries in the fraction of whole exome covered at 20x (BE:87%, SS:63%, AT:17%). Compared to high-confidence somatic mutations from frozen specimens, PML-specific variant filtering increased recall (BE:85%, SS:80%, AT:75%) and precision (BE:93%, SS:91%, AT:84%) to levels expected from sampling variation. Copy number alterations were consistent across all tested approaches and only impacted by the design of the capture probe-set. Applied to DNA extracted from 9 micro-dissected regions (8 PML, 1 normal epithelium), the approach achieved comparable performance, illustrated the data adequacy to identify candidate driver events (GATA3 mutations, ERBB2 or FGFR1 gains, TP53 loss) and measure intra-lesion genetic heterogeneity. CONCLUSION Alternate experimental and analytical strategies increased the accuracy of DNA sequencing from archived micro-dissected PML regions, supporting the deeper molecular characterization of early cancer lesions and achieving a critical milestone in the development of biology-informed prognostic markers and precision chemo-prevention strategies.
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Affiliation(s)
- Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Joseph Steward
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Huazhen Yao
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Eliza Jeong
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Thomas J O'Keefe
- Division of Breast Surgery and The Comprehensive Breast Health Center - UC San Diego School of Medicine, 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Farnaz Hasteh
- Department of Pathology - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Laura J Esserman
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine - UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, 2279 45th Street, Sacramento, CA, 95817, USA
| | - Olivier Harismendy
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA. .,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
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11
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Van Bockstal MR, Berlière M, Duhoux FP, Galant C. Interobserver Variability in Ductal Carcinoma In Situ of the Breast. Am J Clin Pathol 2020; 154:596-609. [PMID: 32566938 DOI: 10.1093/ajcp/aqaa077] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Since most patients with ductal carcinoma in situ (DCIS) of the breast are treated upon diagnosis, evidence on its natural progression to invasive carcinoma is limited. It is estimated that around half of the screen-detected DCIS lesions would have remained indolent if they had never been detected. Many patients with DCIS are therefore probably overtreated. Four ongoing randomized noninferiority trials explore active surveillance as a treatment option. Eligibility for these trials is mainly based on histopathologic features. Hence, the call for reproducible histopathologic assessment has never sounded louder. METHODS Here, the available classification systems for DCIS are discussed in depth. RESULTS This comprehensive review illustrates that histopathologic evaluation of DCIS is characterized by significant interobserver variability. Future digitalization of pathology, combined with development of deep learning algorithms or so-called artificial intelligence, may be an innovative solution to tackle this problem. However, implementation of digital pathology is not within reach for each laboratory worldwide. An alternative classification system could reduce the disagreement among histopathologists who use "conventional" light microscopy: the introduction of dichotomous histopathologic assessment is likely to increase interobserver concordance. CONCLUSIONS Reproducible histopathologic assessment is a prerequisite for robust risk stratification and adequate clinical decision-making. Two-tier histopathologic assessment might enhance the quality of care.
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Affiliation(s)
- Mieke R Van Bockstal
- Department of Pathology, Brussels, Belgium
- Breast Clinic, Brussels, Belgium
- Department of Medical Oncology, King Albert II Cancer Institute, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - Martine Berlière
- Department of Medical Oncology, King Albert II Cancer Institute, Cliniques universitaires Saint-Luc, Brussels, Belgium
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Francois P Duhoux
- Department of Medical Oncology, King Albert II Cancer Institute, Cliniques universitaires Saint-Luc, Brussels, Belgium
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
- Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Christine Galant
- Department of Pathology, Brussels, Belgium
- Department of Medical Oncology, King Albert II Cancer Institute, Cliniques universitaires Saint-Luc, Brussels, Belgium
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12
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Badve SS, Gökmen-Polar Y. Ductal carcinoma in situ of breast: update 2019. Pathology 2019; 51:563-569. [PMID: 31472981 DOI: 10.1016/j.pathol.2019.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 01/12/2023]
Abstract
Ductal carcinoma in situ is a non-invasive form of breast cancer. Its incidence is increasing due to widespread use of mammographic screening. It presents several diagnostic and management challenges in part due to its relatively indolent behaviour. Most series analysing biomarkers in these lesions are small (<100 patients) and large clinical trials have not been frequent. Herein, we review the recent progress made in understanding the biology of this entity and the tools available for prognostication.
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Affiliation(s)
- Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, United States.
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, United States
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