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Tang DY, Mao YJ, Zhao J, Yang J, Li SY, Ren FX, Zheng J. SEEI: spherical evolution with feedback mechanism for identifying epistatic interactions. BMC Genomics 2024; 25:462. [PMID: 38735952 DOI: 10.1186/s12864-024-10373-4] [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: 12/29/2023] [Accepted: 05/03/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Detecting epistatic interactions (EIs) involves the exploration of associations among single nucleotide polymorphisms (SNPs) and complex diseases, which is an important task in genome-wide association studies. The EI detection problem is dependent on epistasis models and corresponding optimization methods. Although various models and methods have been proposed to detect EIs, identifying EIs efficiently and accurately is still a challenge. RESULTS Here, we propose a linear mixed statistical epistasis model (LMSE) and a spherical evolution approach with a feedback mechanism (named SEEI). The LMSE model expands the existing single epistasis models such as LR-Score, K2-Score, Mutual information, and Gini index. The SEEI includes an adaptive spherical search strategy and population updating strategy, which ensures that the algorithm is not easily trapped in local optima. We analyzed the performances of 8 random disease models, 12 disease models with marginal effects, 30 disease models without marginal effects, and 10 high-order disease models. The 60 simulated disease models and a real breast cancer dataset were used to evaluate eight algorithms (SEEI, EACO, EpiACO, FDHEIW, MP-HS-DHSI, NHSA-DHSC, SNPHarvester, CSE). Three evaluation criteria (pow1, pow2, pow3), a T-test, and a Friedman test were used to compare the performances of these algorithms. The results show that the SEEI algorithm (order 1, averages ranks = 13.125) outperformed the other algorithms in detecting EIs. CONCLUSIONS Here, we propose an LMSE model and an evolutionary computing method (SEEI) to solve the optimization problem of the LMSE model. The proposed method performed better than the other seven algorithms tested in its ability to identify EIs in genome-wide association datasets. We identified new SNP-SNP combinations in the real breast cancer dataset and verified the results. Our findings provide new insights for the diagnosis and treatment of breast cancer. AVAILABILITY AND IMPLEMENTATION https://github.com/scutdy/SSO/blob/master/SEEI.zip .
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Affiliation(s)
- De-Yu Tang
- Department of Computer Science, School of Mathematics and Informatics, School of Software Engineering, South China Agricultural University, Guangzhou, 510642, PR China.
- School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Yi-Jun Mao
- Department of Computer Science, School of Mathematics and Informatics, School of Software Engineering, South China Agricultural University, Guangzhou, 510642, PR China.
| | - Jie Zhao
- School of Management, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Jin Yang
- School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Shi-Yin Li
- School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Fu-Xiang Ren
- School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China
| | - Junxi Zheng
- School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
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Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [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: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
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Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
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Zhang L, Xu M, Zhang W, Zhu C, Cui Z, Fu H, Ma Y, Huang S, Cui J, Liang S, Huang L, Wang H. Three-dimensional genome landscape comprehensively reveals patterns of spatial gene regulation in papillary and anaplastic thyroid cancers: a study using representative cell lines for each cancer type. Cell Mol Biol Lett 2023; 28:1. [PMID: 36609218 PMCID: PMC9825046 DOI: 10.1186/s11658-022-00409-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/21/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Spatial chromatin structure is intricately linked with somatic aberrations, and somatic mutations of various cancer-related genes, termed co-mutations (CoMuts), occur in certain patterns during cancer initiation and progression. The functional mechanisms underlying these genetic events remain largely unclear in thyroid cancer (TC). With discrepant differentiation, papillary thyroid cancer (PTC) and anaplastic thyroid cancer (ATC) differ greatly in characteristics and prognosis. We aimed to reveal the spatial gene alterations and regulations between the two TC subtypes. METHODS We systematically investigated and compared the spatial co-mutations between ATC (8305C), PTC (BCPAP and TPC-1), and normal thyroid cells (Nthy-ori-3-1). We constructed a framework integrating whole-genome sequencing (WGS), high-throughput chromosome conformation capture (Hi-C), and transcriptome sequencing, to systematically detect the associations between the somatic co-mutations of cancer-related genes, structural variations (SVs), copy number variations (CNVs), and high-order chromatin conformation. RESULTS Spatial co-mutation hotspots were enriched around topologically associating domains (TADs) in TC. A common set of 227 boundaries were identified in both ATC and PTC, with significant overlaps between them. The spatial proximities of the co-mutated gene pairs in the two TC types were significantly greater than in the gene-level and overall backgrounds, and ATC cells had higher TAD contact frequency with CoMuts > 10 compared with PTC cells. Compared with normal thyroid cells, in ATC the number of the created novel three-dimensional chromatin structural domains increased by 10%, and the number of shifted TADs decreased by 7%. We found five TAD blocks with CoMut genes/events specific to ATC with certain mutations in genes including MAST-NSUN4, AM129B/TRUB2, COL5A1/PPP1R26, PPP1R26/GPSM1/CCDC183, and PRAC2/DLX4. For the majority of ATC and PTC cells, the HOXA10 and HIF2α signals close to the transcription start sites of CoMut genes within TADs were significantly stronger than those at the background. CNV breakpoints significantly overlapped with TAD boundaries in both TC subtypes. ATCs had more CNV losses overlapping with TAD boundaries, and noncoding SVs involved in intrachromosomal SVs, amplified inversions, and tandem duplication differed between ATC and PTC. TADs with short range were more abundant in ATC than PTC. More switches of A/B compartment types existed in ATC cells compared with PTC. Gene expression was significantly synchronized, and orchestrated by complex epigenetics and regulatory elements. CONCLUSION Chromatin interactions and gene alterations and regulations are largely heterogeneous in TC. CNVs and complex SVs may function in the TC genome by interplaying with TADs, and are largely different between ATC and PTC. Complexity of TC genomes, which are highly organized by 3D genome-wide interactions mediating mutational and structural variations and gene activation, may have been largely underappreciated. Our comprehensive analysis may provide key evidence and targets for more customized diagnosis and treatment of TC.
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Affiliation(s)
- Linlin Zhang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Miaomiao Xu
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Wanchun Zhang
- grid.470966.aDepartment of Nuclear Medicine, Shanxi Bethune Hospital (Shanxi Academy of Medical Sciences), Taiyuan, 03003 China
| | - Chuanying Zhu
- grid.16821.3c0000 0004 0368 8293Department of Oncology, Xin Hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200092 China
| | - Zhilei Cui
- grid.412987.10000 0004 0630 1330Department of Respiratory Medicine, XinHua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Hongliang Fu
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Yufei Ma
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Shuo Huang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Jian Cui
- BioGenius Bioinformatics Institute, Shanghai, 200050 People’s Republic of China
| | - Sheng Liang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Lei Huang
- grid.16821.3c0000 0004 0368 8293Department of Oncology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China ,grid.16821.3c0000 0004 0368 8293Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Hui Wang
- grid.412987.10000 0004 0630 1330Department of Nuclear Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
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Kim P, Park J, Lee DJ, Mizuno S, Shinohara M, Hong CP, Jeong Y, Yun R, Park H, Park S, Yang KM, Lee MJ, Jang SP, Kim HY, Lee SJ, Song SU, Park KS, Tanaka M, Ohshima H, Cho JW, Sugiyama F, Takahashi S, Jung HS, Kim SJ. Mast4 determines the cell fate of MSCs for bone and cartilage development. Nat Commun 2022; 13:3960. [PMID: 35803931 PMCID: PMC9270402 DOI: 10.1038/s41467-022-31697-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/28/2022] [Indexed: 11/26/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) differentiation into different lineages is precisely controlled by signaling pathways. Given that protein kinases play a crucial role in signal transduction, here we show that Microtubule Associated Serine/Threonine Kinase Family Member 4 (Mast4) serves as an important mediator of TGF-β and Wnt signal transduction in regulating chondro-osteogenic differentiation of MSCs. Suppression of Mast4 by TGF-β1 led to increased Sox9 stability by blocking Mast4-induced Sox9 serine 494 phosphorylation and subsequent proteasomal degradation, ultimately enhancing chondrogenesis of MSCs. On the other hand, Mast4 protein, which stability was enhanced by Wnt-mediated inhibition of GSK-3β and subsequent Smurf1 recruitment, promoted β-catenin nuclear localization and Runx2 activity, increasing osteogenesis of MSCs. Consistently, Mast4-/- mice demonstrated excessive cartilage synthesis, while exhibiting osteoporotic phenotype. Interestingly, Mast4 depletion in MSCs facilitated cartilage formation and regeneration in vivo. Altogether, our findings uncover essential roles of Mast4 in determining the fate of MSC development into cartilage or bone.
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Affiliation(s)
- Pyunggang Kim
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam City, 463-400, Kyunggi-do, Korea
| | - Jinah Park
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
- Amoris Bio Inc, Seoul, 06668, Korea
| | - Dong-Joon Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Masahiro Shinohara
- Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Saitama, 359-8555, Japan
| | | | - Yealeen Jeong
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | - Rebecca Yun
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | - Hyeyeon Park
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | - Sujin Park
- GILO Institute, GILO Foundation, Seoul, 06668, Korea
| | | | - Min-Jung Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | | | - Hyun-Yi Kim
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
- NGeneS Inc., Ansan-si, 15495, Korea
| | - Seung-Jun Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | - Sun U Song
- Research Institute, SCM Lifescience Inc., Incheon, Korea
- Department of Biomedical Sciences, Inha University College of Medicine, Incheon, Korea
| | - Kyung-Soon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam City, 463-400, Kyunggi-do, Korea
| | - Mikako Tanaka
- Division of Anatomy and Cell Biology of the Hard Tissue, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8514, Japan
- Division of Dental Laboratory Technology, Meirin College, Niigata, 950-2086, Japan
| | - Hayato Ohshima
- Division of Anatomy and Cell Biology of the Hard Tissue, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8514, Japan
| | - Jin Won Cho
- Department of Systems Biology and Glycosylation Network Research Center, Yonsei University, Seoul, Korea
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Han-Sung Jung
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Taste Research Center, Oral Science Research Center, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | - Seong-Jin Kim
- GILO Institute, GILO Foundation, Seoul, 06668, Korea.
- Medpacto Inc., Seoul, 06668, Korea.
- TheragenEtex Co., Gyeonggi-do, Korea.
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A rare coding mutation in the MAST2 gene causes venous thrombosis in a French family with unexplained thrombophilia: The Breizh MAST2 Arg89Gln variant. PLoS Genet 2021; 17:e1009284. [PMID: 33465109 PMCID: PMC7846112 DOI: 10.1371/journal.pgen.1009284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/29/2021] [Accepted: 11/18/2020] [Indexed: 11/19/2022] Open
Abstract
Rare variants outside the classical coagulation cascade might cause inherited thrombosis. We aimed to identify the variant(s) causing venous thromboembolism (VTE) in a family with multiple relatives affected with unprovoked VTE and no thrombophilia defects. We identified by whole exome sequencing an extremely rare Arg to Gln variant (Arg89Gln) in the Microtubule Associated Serine/Threonine Kinase 2 (MAST2) gene that segregates with VTE in the family. Free-tissue factor pathway inhibitor (f-TFPI) plasma levels were significantly decreased in affected family members compared to healthy relatives. Conversely, plasminogen activator inhibitor-1 (PAI-1) levels were significantly higher in affected members than in healthy relatives. RNA sequencing analysis of RNA interference experimental data conducted in endothelial cells revealed that, of the 13,387 detected expressed genes, 2,354 have their level of expression modified by MAST2 knockdown, including SERPINE1 coding for PAI-1 and TFPI. In HEK293 cells overexpressing the MAST2 Gln89 variant, TFPI and SERPINE1 promoter activities were respectively lower and higher than in cells overexpressing the MAST2 wild type. This study identifies a novel thrombophilia-causing Arg89Gln variant in the MAST2 gene that is here proposed as a new molecular player in the etiology of VTE by interfering with hemostatic balance of endothelial cells.
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Notch and Wnt Dysregulation and Its Relevance for Breast Cancer and Tumor Initiation. Biomedicines 2018; 6:biomedicines6040101. [PMID: 30388742 PMCID: PMC6315509 DOI: 10.3390/biomedicines6040101] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the second leading cause of cancer deaths among women in the world. Treatment has been improved and, in combination with early detection, this has resulted in reduced mortality rates. Further improvement in therapy development is however warranted. This will be particularly important for certain sub-classes of breast cancer, such as triple-negative breast cancer, where currently no specific therapies are available. An important therapy development focus emerges from the notion that dysregulation of two major signaling pathways, Notch and Wnt signaling, are major drivers for breast cancer development. In this review, we discuss recent insights into the Notch and Wnt signaling pathways and into how they act synergistically both in normal development and cancer. We also discuss how dysregulation of the two pathways contributes to breast cancer and strategies to develop novel breast cancer therapies starting from a Notch and Wnt dysregulation perspective.
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Goriki A, Seiler R, Wyatt AW, Contreras-Sanz A, Bhat A, Matsubara A, Hayashi T, Black PC. Unravelling disparate roles of NOTCH in bladder cancer. Nat Rev Urol 2018; 15:345-357. [DOI: 10.1038/s41585-018-0005-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Veeraraghavan J, Ma J, Hu Y, Wang XS. Recurrent and pathological gene fusions in breast cancer: current advances in genomic discovery and clinical implications. Breast Cancer Res Treat 2016; 158:219-32. [PMID: 27372070 DOI: 10.1007/s10549-016-3876-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/18/2016] [Indexed: 12/22/2022]
Abstract
Gene fusions have long been considered principally as the oncogenic events of hematologic malignancies, but have recently gained wide attention in solid tumors due to several milestone discoveries and the advancement of deep sequencing technologies. With the progress in deep sequencing studies of breast cancer transcriptomes and genomes, the discovery of recurrent and pathological gene fusions in breast cancer is on the focus. Recently, driven by new deep sequencing studies, several recurrent or pathological gene fusions have been identified in breast cancer, including ESR1-CCDC170, SEC16A-NOTCH1, SEC22B-NOTCH2, and ESR1-YAP1 etc. More important, most of these gene fusions are preferentially identified in the more aggressive breast cancers, such as luminal B, basal-like, or endocrine-resistant breast cancer, suggesting recurrent gene fusions as additional key driver events in these tumors other than the known drivers such as the estrogen receptor. In this paper, we have comprehensively summarized the newly identified recurrent or pathological gene fusion events in breast cancer, reviewed the contributions of new genomic and deep sequencing technologies to new fusion discovery and the integrative bioinformatics tools to analyze these data, highlighted the biological relevance and clinical implications of these fusion discoveries, and discussed future directions of gene fusion research in breast cancer.
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Affiliation(s)
- Jamunarani Veeraraghavan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiacheng Ma
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiheng Hu
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiao-Song Wang
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15232, USA. .,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15232, USA. .,Hillman Cancer Center, Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Room G.5a, Pittsburgh, PA, 15213, USA.
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Liu L, Yang ZL, Wang C, Miao X, Liu Z, Li D, Zou Q, Li J, Liang L, Zeng G, Chen S. The Expression of Notch 1 and Notch 3 in Gallbladder Cancer and Their Clinicopathological Significance. Pathol Oncol Res 2015; 22:483-92. [PMID: 26634853 DOI: 10.1007/s12253-015-0019-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 11/16/2015] [Indexed: 12/16/2022]
Abstract
Gallbladder cancers (GBCs) are highly malignant gastrointestinal cancers. The biological makers for the prognosis and targeting therapy of GBCs have not been established. The protein expression of Notch 1 and Notch 3 in 46 squamous cell/adenosquamous carcinomas (SC/ASCs) and 80 adenocarcinomas (AC) was measured using immunohistochemistry. Positive Notch 1 and Notch 3 expression in both SC/ASC and AC was significantly associated with large tumor size, invasion, metastasis, and low surgical curability (P < 0.05 or P < 0.01). Univariate Kaplan-Meier analysis showed that positive Notch 1 and Notch 3 expression was significantly associated with mean survival of SC/ASC and AC patients (P < 0.01 or P < 0.001). Multivariate Cox regression analysis showed that positive Notch 1 and Notch 3 expression, as well as low differentiation, large tumor size, high TNM stage, invasion, lymph node metastasis, and surgical curability are independent poor-prognostic factors in both SC/ASC and AC patients. Positive Notch 1 and Notch 3 expression is closely correlated with severe clinicopathological characteristics and poor prognosis in both SC/ASC and AC patients.
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Affiliation(s)
- Luyao Liu
- Research Laboratory of Hepatobiliary Diseases, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Zhu-Lin Yang
- Research Laboratory of Hepatobiliary Diseases, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China.
| | - Chunwei Wang
- Research Laboratory of Hepatobiliary Diseases, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Xiongying Miao
- Research Laboratory of Hepatobiliary Diseases, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Zhiyu Liu
- Research Laboratory of Hepatobiliary Diseases, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Daiqiang Li
- Department of Pathology, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Qiong Zou
- Department of Pathology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Jinghe Li
- Department of Pathology, Basic School of Medicine, Central South University, Changsha, Hunan, 410078, People's Republic of China
| | - Lufeng Liang
- Department of Hepatobiliary and Pancreatic Surgery, Hunan Provincial People's Hospital, Changsha, Hunan, 410007, People's Republic of China
| | - Guixiang Zeng
- Department of Pathology, Loudi Central Hospital, Loudi, Hunan, 417011, People's Republic of China
| | - Senlin Chen
- Department of Pathology, Hunan Provincial Tumor Hospital, Changsha, Hunan, 410013, People's Republic of China
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Afghahi A, Forgó E, Mitani AA, Desai M, Varma S, Seto T, Rigdon J, Jensen KC, Troxell ML, Gomez SL, Das AK, Beck AH, Kurian AW, West RB. Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer. Breast Cancer Res 2015; 17:108. [PMID: 26265211 PMCID: PMC4534146 DOI: 10.1186/s13058-015-0623-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/24/2015] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Screening mammography has contributed to a significant increase in the diagnosis of ductal carcinoma in situ (DCIS), raising concerns about overdiagnosis and overtreatment. Building on prior observations from lineage evolution analysis, we examined whether measuring genomic features of DCIS would predict association with invasive breast carcinoma (IBC). The long-term goal is to enhance standard clinicopathologic measures of low- versus high-risk DCIS and to enable risk-appropriate treatment. METHODS We studied three common chromosomal copy number alterations (CNA) in IBC and designed fluorescence in situ hybridization-based assay to measure copy number at these loci in DCIS samples. Clinicopathologic data were extracted from the electronic medical records of Stanford Cancer Institute and linked to demographic data from the population-based California Cancer Registry; results were integrated with data from tissue microarrays of specimens containing DCIS that did not develop IBC versus DCIS with concurrent IBC. Multivariable logistic regression analysis was performed to describe associations of CNAs with these two groups of DCIS. RESULTS We examined 271 patients with DCIS (120 that did not develop IBC and 151 with concurrent IBC) for the presence of 1q, 8q24 and 11q13 copy number gains. Compared to DCIS-only patients, patients with concurrent IBC had higher frequencies of CNAs in their DCIS samples. On multivariable analysis with conventional clinicopathologic features, the copy number gains were significantly associated with concurrent IBC. The state of two of the three copy number gains in DCIS was associated with a risk of IBC that was 9.07 times that of no copy number gains, and the presence of gains at all three genomic loci in DCIS was associated with a more than 17-fold risk (P = 0.0013). CONCLUSIONS CNAs have the potential to improve the identification of high-risk DCIS, defined by presence of concurrent IBC. Expanding and validating this approach in both additional cross-sectional and longitudinal cohorts may enable improved risk stratification and risk-appropriate treatment in DCIS.
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Affiliation(s)
- Anosheh Afghahi
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
| | - Aya A Mitani
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Manisha Desai
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
| | - Tina Seto
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Joseph Rigdon
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Kristin C Jensen
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
- Pathology and Laboratory Medicine, Palo Alto Veterans Affairs Health Care System, 795 Willow Road, Palo Alto, CA, 94025, USA.
| | - Megan L Troxell
- Department of Pathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
| | - Scarlett Lin Gomez
- Department of Health Research and Policy, Stanford University School of Medicine, 900 Blake Wilbur Drive, Stanford, CA, 94305, USA.
- Cancer Prevention Institute of California (CPIC), 2201 Walnut Avenue, Fremont, CA, 94538, USA.
| | - Amar K Das
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
- Department of Psychiatry and The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine, 1 Rope Ferry Road, Lebanon, NH, 03755, USA.
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA.
| | - Allison W Kurian
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
- Department of Health Research and Policy, Stanford University School of Medicine, 900 Blake Wilbur Drive, Stanford, CA, 94305, USA.
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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11
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Pang JMB, Gorringe KL, Wong SQ, Dobrovic A, Campbell IG, Fox SB. Appraisal of the technologies and review of the genomic landscape of ductal carcinoma in situ of the breast. Breast Cancer Res 2015; 17:80. [PMID: 26078038 PMCID: PMC4469314 DOI: 10.1186/s13058-015-0586-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ductal carcinoma in situ is a biologically diverse entity. Whereas some lesions are cured by local surgical excision, others recur as in situ disease or progress to invasive carcinoma with subsequent potential for metastatic spread. Reliable prognostic biomarkers are therefore desirable for appropriate clinical management but remain elusive. In common with invasive breast cancer, ductal carcinoma in situ exhibits many genomic changes, predominantly copy number alterations. Although studies have revealed the genomic heterogeneity within individual ductal carcinoma in situ lesions and the association of certain copy number alterations with nuclear grade, none of the genomic changes defined so far is consistently associated with invasive transformation or recurrence risk in pure ductal carcinoma in situ. This article will review the current landscape of genomic alterations in ductal carcinoma in situ and their potential as prognostic biomarkers together with the technologies used to define these.
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Affiliation(s)
- Jia-Min B Pang
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia.
| | - Kylie L Gorringe
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Stephen Q Wong
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Translational Research Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Alexander Dobrovic
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Translational Genomics & Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ian G Campbell
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia.
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12
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Greife A, Jankowiak S, Steinbring J, Nikpour P, Niegisch G, Hoffmann MJ, Schulz WA. Canonical Notch signalling is inactive in urothelial carcinoma. BMC Cancer 2014; 14:628. [PMID: 25167871 PMCID: PMC4242495 DOI: 10.1186/1471-2407-14-628] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/15/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Notch signalling regulates cell fate in most tissues, promoting precursor cell proliferation in some, but differentiation in others. Accordingly, downregulation or overactivity variously contributes to cancer development. So far, little is known about Notch pathway activity and function in the normal urothelium and in urothelial carcinoma (UC). We have therefore investigated expression of Notch pathway components in UC tissues and cell lines and studied the function of one receptor, NOTCH1, in detail. METHODS Expression of canonical Notch pathway components were studied in UC and normal bladder tissues by immunohistochemistry and quantitative RT-PCR and in UC cell lines and normal cultured urothelial cells by qRT-PCR, immunocytochemistry and Western blotting. Pathway activity was measured by reporter gene assays. Its influence on cell proliferation was investigated by γ-secretase inhibition. Effects of NOTCH1 restoration were followed by measuring cell cycle distribution, proliferation, clonogenicity and nuclear morphology. RESULTS NOTCH1 and its ligand, DLL1, were expressed at plasma membranes and in the cytoplasm of cells in the upper normal urothelium layer, but became downregulated in UC tissues, especially in high-stage tumours. In addition, the proteins were often delocalized intracellularly. According differences were observed in UC cell lines compared to normal urothelial cells. Canonical Notch pathway activity in reporter assays was repressed in UC cell lines compared to normal cells and a mammary carcinoma cell line, but was induced by transfected NOTCH1. Inhibitors of Notch signalling acting at the γ-secretase step did not affect UC cell proliferation at concentrations efficacious against a cell line with known Notch activity. Surprisingly, overexpression of NOTCH1 into UC cell lines did not significantly affect short-term cell proliferation, but induced nuclear abnormalities and diminished clonogenicity. CONCLUSION Our data indicate that canonical Notch signalling is suppressed in urothelial carcinoma mainly through downregulation of NOTCH1. These findings can be explained by proposing that canonical Notch signalling may promote differentiation in the urothelium, like in many squamous epithelia, and its suppression may therefore be advantageous for tumour progression. As an important corollary, inhibition of canonical Notch signalling is unlikely to be efficacious and might be counter-productive in the treatment of urothelial carcinoma.
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Affiliation(s)
| | | | | | | | | | | | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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