1
|
Camargo-Herrera V, Castellanos G, Rangel N, Jiménez-Tobón GA, Martínez-Agüero M, Rondón-Lagos M. Patterns of Chromosomal Instability and Clonal Heterogeneity in Luminal B Breast Cancer: A Pilot Study. Int J Mol Sci 2024; 25:4478. [PMID: 38674062 PMCID: PMC11049937 DOI: 10.3390/ijms25084478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 04/28/2024] Open
Abstract
Chromosomal instability (CIN), defined by variations in the number or structure of chromosomes from cell to cell, is recognized as a distinctive characteristic of cancer associated with the ability of tumors to adapt to challenging environments. CIN has been recognized as a source of genetic variation that leads to clonal heterogeneity (CH). Recent findings suggest a potential association between CIN and CH with the prognosis of BC patients, particularly in tumors expressing the epidermal growth factor receptor 2 (HER2+). In fact, information on the role of CIN in other BC subtypes, including luminal B BC, is limited. Additionally, it remains unknown whether CIN in luminal B BC tumors, above a specific threshold, could have a detrimental effect on the growth of human tumors or whether low or intermediate CIN levels could be linked to a more favorable BC patient prognosis when contrasted with elevated levels. Clarifying these relationships could have a substantial impact on risk stratification and the development of future therapeutic strategies aimed at targeting CIN in BC. This study aimed to assess CIN and CH in tumor tissue samples from ten patients with luminal B BC and compare them with established clinicopathological parameters. The results of this study reveal that luminal B BC patients exhibit intermediate CIN and stable aneuploidy, both of which correlate with lymphovascular invasion. Our results also provide valuable preliminary data that could contribute to the understanding of the implications of CIN and CH in risk stratification and the development of future therapeutic strategies in BC.
Collapse
Affiliation(s)
- Valentina Camargo-Herrera
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (V.C.-H.).; (G.C.)
| | - Giovanny Castellanos
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (V.C.-H.).; (G.C.)
| | - Nelson Rangel
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
| | - Guillermo Antonio Jiménez-Tobón
- Laboratorio de Patología, Hospital Universitario Mayor-Méderi, Bogotá 110311, Colombia;
- Grupo BIOmedUR, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá 110231, Colombia
| | - María Martínez-Agüero
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 110231, Colombia
| | - Milena Rondón-Lagos
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (V.C.-H.).; (G.C.)
| |
Collapse
|
2
|
Khalsa JK, Cha J, Utro F, Naeem A, Murali I, Kuang Y, Vasquez K, Li L, Tyekucheva S, Fernandes SM, Veronese L, Guieze R, Sasi BK, Wang Z, Machado JH, Bai H, Alasfour M, Rhrissorrakrai K, Levovitz C, Danysh BP, Slowik K, Jacobs RA, Davids MS, Paweletz CP, Leshchiner I, Parida L, Getz G, Brown JR. Genetic events associated with venetoclax resistance in CLL identified by whole-exome sequencing of patient samples. Blood 2023; 142:421-433. [PMID: 37146250 PMCID: PMC10447490 DOI: 10.1182/blood.2022016600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 05/07/2023] Open
Abstract
Although BCL2 mutations are reported as later occurring events leading to venetoclax resistance, many other mechanisms of progression have been reported though remain poorly understood. Here, we analyze longitudinal tumor samples from 11 patients with disease progression while receiving venetoclax to characterize the clonal evolution of resistance. All patients tested showed increased in vitro resistance to venetoclax at the posttreatment time point. We found the previously described acquired BCL2-G101V mutation in only 4 of 11 patients, with 2 patients showing a very low variant allele fraction (0.03%-4.68%). Whole-exome sequencing revealed acquired loss(8p) in 4 of 11 patients, of which 2 patients also had gain (1q21.2-21.3) in the same cells affecting the MCL1 gene. In vitro experiments showed that CLL cells from the 4 patients with loss(8p) were more resistant to venetoclax than cells from those without it, with the cells from 2 patients also carrying gain (1q21.2-21.3) showing increased sensitivity to MCL1 inhibition. Progression samples with gain (1q21.2-21.3) were more susceptible to the combination of MCL1 inhibitor and venetoclax. Differential gene expression analysis comparing bulk RNA sequencing data from pretreatment and progression time points of all patients showed upregulation of proliferation, B-cell receptor (BCR), and NF-κB gene sets including MAPK genes. Cells from progression time points demonstrated upregulation of surface immunoglobulin M and higher pERK levels compared with those from the preprogression time point, suggesting an upregulation of BCR signaling that activates the MAPK pathway. Overall, our data suggest several mechanisms of acquired resistance to venetoclax in CLL that could pave the way for rationally designed combination treatments for patients with venetoclax-resistant CLL.
Collapse
MESH Headings
- Humans
- Antineoplastic Agents/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Drug Resistance, Neoplasm/genetics
- Exome Sequencing
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Proto-Oncogene Proteins c-bcl-2
Collapse
Affiliation(s)
- Jasneet Kaur Khalsa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Justin Cha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Aishath Naeem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ishwarya Murali
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Yanan Kuang
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Kevin Vasquez
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Liang Li
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Svitlana Tyekucheva
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health, Boston, MA
| | - Stacey M. Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Lauren Veronese
- Service de Cytogénétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
- EA7453 CHELTER, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Romain Guieze
- EA7453 CHELTER, Université Clermont Auvergne, Clermont-Ferrand, France
- Service d’Hématologie clinique et thérapie cellulaire, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Binu Kandathilparambil Sasi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Zixu Wang
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health, Boston, MA
| | - John-Hanson Machado
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Harrison Bai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Maryam Alasfour
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - Brian P. Danysh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kara Slowik
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Raquel A. Jacobs
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Cloud P. Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Gad Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Cancer Center, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
3
|
Shi S, Zhong J, Peng W, Yin H, Zhong D, Cui H, Sun X. System analysis based on the migration- and invasion-related gene sets identifies the infiltration-related genes of glioma. Front Oncol 2023; 13:1075716. [PMID: 37091145 PMCID: PMC10117932 DOI: 10.3389/fonc.2023.1075716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The current database has no information on the infiltration of glioma samples. Here, we assessed the glioma samples' infiltration in The Cancer Gene Atlas (TCGA) through the single-sample Gene Set Enrichment Analysis (ssGSEA) with migration and invasion gene sets. The Weighted Gene Co-expression Network Analysis (WGCNA) and the differentially expressed genes (DEGs) were used to identify the genes most associated with infiltration. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the major biological processes and pathways. Protein-protein interaction (PPI) network analysis and the least absolute shrinkage and selection operator (LASSO) were used to screen the key genes. Furthermore, the nomograms and receiver operating characteristic (ROC) curve were used to evaluate the prognostic and predictive accuracy of this clinical model in patients in TCGA and the Chinese Glioma Genome Atlas (CGGA). The results showed that turquoise was selected as the hub module, and with the intersection of DEGs, we screened 104 common genes. Through LASSO regression, TIMP1, EMP3, IGFBP2, and the other nine genes were screened mostly in correlation with infiltration and prognosis. EMP3 was selected to be verified in vitro. These findings could help researchers better understand the infiltration of gliomas and provide novel therapeutic targets for the treatment of gliomas.
Collapse
Affiliation(s)
- Shuang Shi
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiacheng Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wen Peng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Haoyang Yin
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
4
|
Wang J, Thomas HR, Chen Y, Percival SM, Waldrep SC, Ramaker RC, Thompson RG, Cooper SJ, Chong Z, Parant JM. Reduced sister chromatid cohesion acts as a tumor penetrance modifier. PLoS Genet 2022; 18:e1010341. [PMID: 35994499 PMCID: PMC9436123 DOI: 10.1371/journal.pgen.1010341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/01/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Sister chromatid cohesion (SCC) is an important process in chromosome segregation. ESCO2 is essential for establishment of SCC and is often deleted/altered in human cancers. We demonstrate that esco2 haploinsufficiency results in reduced SCC and accelerates the timing of tumor onset in both zebrafish and mouse p53 heterozygous null models, but not in p53 homozygous mutant or wild-type animals. These data indicate that esco2 haploinsufficiency accelerates tumor onset in a loss of heterozygosity (LOH) sensitive background. Analysis of The Cancer Genome Atlas (TCGA) confirmed ESCO2 deficient tumors have elevated number of LOH events throughout the genome. Further, we demonstrated heterozygous loss of sgo1, important in maintaining SCC, also results in reduced SCC and accelerated tumor formation in a p53 heterozygous background. Surprisingly, while we did observe elevated levels of chromosome missegregation and micronuclei formation in esco2 heterozygous mutant animals, this chromosomal instability did not contribute to the accelerated tumor onset in a p53 heterozygous background. Interestingly, SCC also plays a role in homologous recombination, and we did observe elevated levels of mitotic recombination derived p53 LOH in tumors from esco2 haploinsufficient animals; as well as elevated levels of mitotic recombination throughout the genome of human ESCO2 deficient tumors. Together these data suggest that reduced SCC contributes to accelerated tumor penetrance through elevated mitotic recombination. Tumorigenesis often involves the inactivation of tumor suppressor genes. This often encompasses an inactivation mutation in one allele and loss of the other wild-type allele, referred to as loss of heterozygosity (LOH). The rate at which the cells lose the wild-type allele can influence the timing of tumor onset, and therefore an indicator of a patient’s risk of cancer. Factors that influence this process could be used as a predictive indicator of cancer risk, however these factors are still unclear. We demonstrate that partial impairment of sister chromatid cohesion (SCC), a fundamental component of the chromosome segregation in mitosis and homologous recombination repair, enhanced tumorigenesis. Our data suggest this is through elevated levels of mitotic recombination derived p53 LOH. This study emphasizes the importance of understanding how impaired SCC, mitotic recombination rates, and LOH rates influence cancer risk.
Collapse
Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Yu Chen
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - Stefanie M. Percival
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Ryne C. Ramaker
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Sara J. Cooper
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Zechen Chong
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
5
|
Suelmann BBM, Rademaker A, van Dooijeweert C, van der Wall E, van Diest PJ, Moelans CB. Genomic copy number alterations as biomarkers for triple negative pregnancy-associated breast cancer. Cell Oncol (Dordr) 2022; 45:591-600. [PMID: 35792986 PMCID: PMC9424154 DOI: 10.1007/s13402-022-00685-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 11/28/2022] Open
Abstract
Abstract
Background
PABC, commonly defined as breast cancer diagnosed during or ≤ 1 year after pregnancy, accounts for 7% of all breast cancers in women ≤ 45 years. Compared to age-matched non-PABC patients, PABC is characterized by a particularly aggressive histopathologic profile with poorly differentiated and estrogen- and progesterone receptor negative tumors and associated high mortality rates. This study assessed the genomic background of triple-negative PABC tumors by detection of copy number alterations (CNAs).
Methods
MLPA was used to compare CNAs in breast cancer-associated chromosomal loci between triple-negative PABC- and subtype-matched non-PABC patients. Both CNA patterns were evaluated by cluster analysis; associations between individual gene CNAs, pathological characteristics and survival were explored.
Results
Triple-negative PABC tumors exhibited unique CNAs compared to non-PABC tumors, including enrichment for TOP2A copy number loss, an independent predictor of worse overall survival (HR 8.96, p = 0.020). Cluster analysis based on CNA profiles identified a triple-negative PABC-subgroup with a particularly poor prognosis, characterized by chromosome 8p copy number loss. Individual gene CNAs analysis revealed that FGFR1 copy number loss on chromosome 8p11.23 was an independent predictor of poor outcome in multivariate analysis (HR 3.59, p = 0.053) and predicted the development of distant metastases (p = 0.048).
Conclusion
This study provides novel insights into the biology of triple-negative PABC tumors suggesting that CNAs, particularly 8p loss and TOP2A loss, are involved in the development of breast cancer during pregnancy. FGFR1 loss and TOP2A loss seem to be promising new biomarkers that independently identify subgroups of PABC patients with poor prognosis. These genomic biomarkers may provide clues for personalized therapy.
Collapse
Affiliation(s)
- B B M Suelmann
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A Rademaker
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands
| | - C van Dooijeweert
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands
| | - E van der Wall
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - P J van Diest
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands
| | - C B Moelans
- Department of Pathology, University Medical Center Utrecht, PO Box 85500, Utrecht, 3508 GA, The Netherlands.
| |
Collapse
|
6
|
Shishido SN, Masson R, Xu L, Welter L, Prabakar RK, D' Souza A, Spicer D, Kang I, Jayachandran P, Hicks J, Lu J, Kuhn P. Disease characterization in liquid biopsy from HER2-mutated, non-amplified metastatic breast cancer patients treated with neratinib. NPJ Breast Cancer 2022; 8:22. [PMID: 35181666 PMCID: PMC8857263 DOI: 10.1038/s41523-022-00390-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
Metastatic breast cancer (mBC) patients have a high risk of progression and face poor prognosis overall, with about one third (34%) surviving five years or more. In rare instances (2-4% of cases) patients with mBC have ERBB2 (HER2) activating mutations but are ERBB2 non-amplified. Neratinib is a potent, irreversible inhibitor that binds HER2 and inhibits downstream signaling. We used the previously validated high-definition single cell assay (HDSCA) workflow to investigate the clinical significance of the liquid biopsy in ERBB2 mutant, non-amplified, post-menopausal mBC patients starting neratinib and fulvestrant combination therapy. Characterization with a comprehensive liquid biopsy methodology (HDSCA) included genomic analysis of both the cell-free DNA (cfDNA) and single circulating tumor cells (CTCs) to monitor tumor evolution and identify potential mutational variants unique to the patient's clinical response. A limited series of five sequentially enrolled patients presented here were from the MutHER ( https://www.clinicaltrials.gov , NCT01670877) or SUMMIT ( https://www.clinicaltrials.gov , NCT01953926) trials. Patients had an average of 5.4 lines of therapy before enrollment, variable hormone receptor status, and ERBB2 mutations at diagnosis and during treatment. CTC enumeration alone was not sufficient to predict clinical response. Treatment pressure was shown to lead to an observable change in CTC morphology and genomic instability (GI), suggesting these parameters may inform prognosis. Single cell copy number alteration (CNA) analysis indicated that the persistence or development of a clonal population of CTCs during treatment was associated with a worse response. Hierarchical clustering analysis of the single cells across all patients and timepoints identified distinct aberrant regions shared among patients, comprised of 26 genes that are similarly affected and may be related to drug resistance. Additionally, the genomic analysis of the cfDNA, identified new mutations in ERBB2, PIK3CA, and TP53 that arose likely due to treatment pressure in a patient with poor response, further providing insights on the dynamics of the cancer genome over the course of therapy. The data presented in this small cohort study demonstrates the feasibility of real-time molecular profiling of the cellular and acellular fractions of the liquid biopsy using the HDSCA methodology. Additional studies are necessary to determine the potential use of morphometric and genomic analysis as a prognostic tool to advance personalized oncology.
Collapse
Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Rahul Masson
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Liya Xu
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Lisa Welter
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Rishvanth Kaliappan Prabakar
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Anishka D' Souza
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Darcy Spicer
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Irene Kang
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Priya Jayachandran
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - James Hicks
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA
| | - Janice Lu
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, NTT-3440, Los Angeles, CA, 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer (CSI-Cancer), Michelson Center for Convergent Bioscience, University of Southern California,1002 Childs Way, MCB 220, Los Angeles, CA, 90089, USA.
| |
Collapse
|
7
|
Matsumoto T, Okayama H, Nakajima S, Saito K, Ito M, Kaneta A, Kanke Y, Onozawa H, Hayase S, Fujita S, Sakamoto W, Saito M, Seze Z, Momma T, Mimura K, Kono K. SH2D4A downregulation due to loss of chromosome 8p is associated with poor prognosis and low T cell infiltration in colorectal cancer. Br J Cancer 2021; 126:917-926. [PMID: 34893760 DOI: 10.1038/s41416-021-01660-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/21/2021] [Accepted: 11/30/2021] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) develops through chromosomal instability (CIN) or microsatellite instability (MSI) due to deficient mismatch-repair (dMMR). We aimed to characterise novel cancer-associated genes that are downregulated upon malignant transformation in microsatellite stable (MSS) CRCs, which typically exhibit CIN with proficient mismatch-repair (pMMR). METHODS Comprehensive screening was conducted on adenomas, MSI/MSS CRCs and cell lines, followed by copy number analysis, and their genetic and prognostic relevance was confirmed in microarray and RNA-seq cohorts (n = 3262, in total). Immunohistochemistry for SH2D4A was performed in 524 specimens of adenoma, carcinoma in situ and dMMR/pMMR CRC. The functional role of SH2D4A was investigated using CRC cell lines. RESULTS A set of 11 genes, including SH2D4A, was downregulated during the adenoma-carcinoma sequence in MSS/CIN CRCs, mainly due to chromosome 8p deletions, and their negative prognostic impact was validated in independent cohorts. All adenomas were SH2D4A positive, but a subset of CRCs (5.3%) lacked SH2D4A immunohistochemical staining, correlating with poor prognosis and scarce T cell infiltration. SH2D4A depletion did not affect cell proliferation or IL-6-induced STAT3 phosphorylation. CONCLUSIONS Our findings suggest that downregulation of multiple genes on chromosome 8p, including SH2D4A, cooperatively contribute to tumorigenesis, resulting in the immune cold tumour microenvironment and poor prognosis.
Collapse
Affiliation(s)
- Takuro Matsumoto
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hirokazu Okayama
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan.
| | - Shotaro Nakajima
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Katsuharu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Misato Ito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Akinao Kaneta
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yasuyuki Kanke
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hisashi Onozawa
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Suguru Hayase
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Shotaro Fujita
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Wataru Sakamoto
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Zenichiro Seze
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tomoyuki Momma
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kosaku Mimura
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan.,Department of Blood Transfusion and Transplantation Immunology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| |
Collapse
|
8
|
Lebok P, Bönte H, Kluth M, Möller-Koop C, Witzel I, Wölber L, Paluchowski P, Wilke C, Heilenkötter U, Müller V, Schmalfeldt B, Simon R, Sauter G, Terracciano L, Krech RH, von der Assen A, Burandt E. 6q deletion is frequent but unrelated to patient prognosis in breast cancer. Breast Cancer 2021. [PMID: 34625909 DOI: 10.1007/s12282-021-01301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 09/28/2021] [Indexed: 11/02/2022]
Abstract
BACKGROUND Deletions involving the long arm of chromosome 6 have been reported to occur in breast cancer, but little is known about the clinical relevance of this alteration. METHODS We made use of a pre-existing tissue microarray with 2197 breast cancers and employed a 6q15/centromere 6 dual-labeling probe for fluorescence in situ (FISH) analysis RESULTS: Heterozygous 6q15 deletions were found in 202 (18%) of 1099 interpretable cancers, including 19% of 804 cancers of no special type (NST), 3% of 29 lobular cancers, 7% of 41 cribriform cancers, and 28% of 18 cancers with papillary features. Homozygous deletions were not detected. In the largest subset of NST tumors, 6q15 deletions were significantly linked to advanced tumor stage and high grade (p < 0.0001 each). 6q deletions were also associated with estrogen receptor negativity (p = 0.0182), high Ki67 proliferation index (p < 0.0001), amplifications of HER2 (p = 0.0159), CCND1 (p = 0.0069), and cMYC (p = 0.0411), as well as deletions of PTEN (p = 0.0003), 8p21 (p < 0.0001), and 9p21 (p = 0.0179). However, 6q15 deletion was unrelated to patient survival in all cancers, in NST cancers, or in subsets of cancers defined by the presence or absence of lymph-node metastases. CONCLUSION Our data demonstrate that 6q deletion is a frequent event in breast cancer that is statistically linked to unfavorable tumor phenotype and features of genomic instability. The absence of any prognostic impact argues against a clinical applicability of 6q15 deletion testing in breast cancer patients.
Collapse
|
9
|
Lebok P, Schütt K, Kluth M, Witzel I, Wölber L, Paluchowski P, Terracciano L, Wilke C, Heilenkötter U, Müller V, Schmalfeldt B, Simon R, Sauter G, Von Leffern I, Krech T, Krech RH, Jacobsen F, Burandt E. High mitochondrial content is associated with breast cancer aggressiveness. Mol Clin Oncol 2021; 15:203. [PMID: 34462659 PMCID: PMC8375016 DOI: 10.3892/mco.2021.2365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/23/2021] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are relevant for cancer initiation and progression. Antibodies against mitochondrially encoded cytochrome c oxidase II (MTCO2), targeting a mitochondria specific epitope, can be used to quantitate the mitochondria content of tumor cells. The present study evaluated the impact of the cellular mitochondrial content on the prognosis of patients with breast cancer using immunohistochemical analysis on 2,197 arrayed breast cancer specimens. Results were compared with histological tumor parameters, patient overall survival, tumor cell proliferation using Ki67 labeling index (Ki67LI) and various other molecular features. Tumor cells exhibited stronger MTCO2 expression than normal breast epithelial cells. MTCO2 immunostaining was largely absent in normal breast epithelium, but was observed in 71.9% of 1,797 analyzable cancer specimens, including 34.6% tumors with weak expression, 22.3% with moderate expression and 15.0% with strong expression. High MTCO2 expression was significantly associated with advanced tumor stage, high Bloom-Richardson-Elston/Nottingham (BRE) grade, nodal metastasis and shorter overall survival (P<0.0001 each). In multivariate analysis, MTCO2 expression did not provide prognostic information independent of BRE grade, pathological tumor and pathological lymph node status. Additionally, significant associations were observed for high MTCO2 expression and various molecular features, including high Ki67LI, amplifications of HER2, MYC, CCND1 and MDM2, deletions of PTEN, 8p21 and 9p, low estrogen receptor expression (P<0.0001 each) and progesterone receptor expression (P<0.0001). The present study demonstrated that high MTCO2 expression was strongly associated with a poor prognosis and unfavorable phenotypical and molecular tumor features in patients with breast cancer. This suggests that the mitochondrial content may have a pivotal role in breast cancer progression.
Collapse
Affiliation(s)
- Patrick Lebok
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Katharina Schütt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Isabell Witzel
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Linn Wölber
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Peter Paluchowski
- Department of Gynecology, Regio Clinic Pinneberg, D-25421 Pinneberg, Germany
| | - Luigi Terracciano
- Department of Pathology, Basel University Clinics, 4031 Basel, Switzerland
| | - Christian Wilke
- Department of Gynecology, Regio Clinic Elmshorn, D-25337 Elmshorn, Germany
| | - Uwe Heilenkötter
- Department of Gynecology, Clinical Centre Itzehoe, D-25524 Itzehoe, Germany
| | - Volkmar Müller
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Barbara Schmalfeldt
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Ingo Von Leffern
- Department of Gynecology, Albertinen Clinic Schnelsen, D-22457 Hamburg, Germany
| | - Till Krech
- Institute of Pathology, Clinical Centre Osnabrück, D-49076 Osnabrück, Germany
| | - Rainer Horst Krech
- Institute of Pathology, Clinical Centre Osnabrück, D-49076 Osnabrück, Germany
| | - Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| |
Collapse
|
10
|
Pariyar M, Johns A, Thorne RF, Scott RJ, Avery-Kiejda KA. Copy number variation in triple negative breast cancer samples associated with lymph node metastasis. Neoplasia 2021; 23:743-753. [PMID: 34225099 PMCID: PMC8259224 DOI: 10.1016/j.neo.2021.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a highly metastatic and aggressive subtype of breast cancer and cases presenting with lymph node involvement have worse outcomes. This study aimed to determine the regions of copy number variation (CNV) associated with lymph node metastasis in TNBC patients. CNV analyses were performed in a study cohort of 23 invasive ductal carcinomas (IDCs), 12 lymph node metastases (LNmets), and 7 normal adjacent tissues (NATs); as well as in an independent cohort containing 70 TNBC IDCs and the same 7 NATs. CNV-associated genes were analyzed using GO-enrichment and Pathway analysis. The prognostic role for genes showing CNV-based changes in messenger RNA expression was determined using the Kaplan-Meier plotter database. For the IDCs, there were a number of variations that were common in both the study and independent cohorts in the amplified regions of 1q, 8q, 19 (p and q), 2p, 5p and the deleted regions in 8p followed by 5q, and 19p. The most frequently amplified regions in the LNmets of the study cohort were 4q28.3, 2p, 3q24, 1q21.2, 10p, 12p11.1, 8q, 20p11.22-20p11.21, 21q22.13, 6p22.1 and the most frequently deleted regions were in 1p36.23, 4q21.1 and 5q. A total of 686 (441 amplified and 245 deleted) genes were associated with LNmets. The LNmet-associated genes were highly enriched for “regulation of complement activation,” “regulation of protein activation cascade,” “regulation of humoral immune response,” “oxytocin signalling pathway,” and “TRAIL binding” pathways. Moreover, 6/686 LNmet-associated genes showed CNV-based changes in their mRNA expression of which, high expression of ASPM and KIF14 was significantly associated with worse relapse-free survival. This study has identified several CNV regions in TNBC that could play a major role in metastasis to the lymph node.
Collapse
Affiliation(s)
- Mamta Pariyar
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Andrea Johns
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Rick F Thorne
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia; NSW Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
| |
Collapse
|
11
|
Tomasich E, Topakian T, Heller G, Udovica S, Krainer M, Marhold M. Loss of HCRP1 leads to upregulation of PD-L1 via STAT3 activation and is of prognostic significance in EGFR-dependent cancer. Transl Res 2021; 230:21-33. [PMID: 33197651 DOI: 10.1016/j.trsl.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/05/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022]
Abstract
Loss of hepatocellular carcinoma-related protein 1 (HCRP1) (alias VPS37A) plays a role in endocytosis of receptor tyrosine kinases as a member of the ESCRT complex and has been linked to poor patient outcome in various types of epithelial cancer. To this date, the molecular and biological mechanisms explaining how its absence would contribute to tumor progression remain unknown. Using genomic editing with CRISPR-Cas9, we generated ovarian and breast cancer cell lines with loss-of-function mutations of HCRP1. We hypothesized that pathways downstream of receptor tyrosine kinases such as epidermal growth factor receptor are affected by HCRP1 loss and looked for deregulated signaling using immunoblotting and classical cancer biology assays. In our study, we show that endogenous deletion of HCRP1 leads to elevated phosphorylation of the transcription factor Signal transducer and activator of transcription 3 (STAT3) and induces upregulation of PD-L1, an important regulator of immune checkpoint inhibition. HCRP1 loss further leads to a mesenchymal phenotype switch in cancer cells, leading to increased proliferation and migration. Concludingly, our data emphasize the role of the tumor microenvironment in tumors with low or absent HCRP1 expression and suggest HCRP1 loss as a potential marker for metastatic potential and immunogenicity of epidermal growth factor receptor-driven cancer.
Collapse
Affiliation(s)
- Erwin Tomasich
- Division of Oncology, Department for Medicine I, Medical University of Vienna, Vienna, Austria
| | - Thais Topakian
- Division of Oncology, Department for Medicine I, Medical University of Vienna, Vienna, Austria
| | - Gerwin Heller
- Division of Oncology, Department for Medicine I, Medical University of Vienna, Vienna, Austria
| | - Simon Udovica
- Wilhelminen Cancer Research Institute, Wilhelminenspital, Vienna, Austria
| | - Michael Krainer
- Division of Oncology, Department for Medicine I, Medical University of Vienna, Vienna, Austria
| | - Maximilian Marhold
- Division of Oncology, Department for Medicine I, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
12
|
Burgess SJ, Gibbs H, Toomes C, Coletta PL, Bell SM. The Role of Csmd1 during Mammary Gland Development. Genes (Basel) 2021; 12:162. [PMID: 33530646 DOI: 10.3390/genes12020162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/13/2021] [Accepted: 01/21/2021] [Indexed: 12/23/2022] Open
Abstract
The Cub Sushi Multiple Domains-1 (CSMD1) protein is a tumour suppressor which has been shown to play a role in regulating human mammary duct development in vitro. CSMD1 knockdown in vitro demonstrated increased cell proliferation, invasion and motility. However, the role of Csmd1 in vivo is poorly characterised when it comes to ductal development and is therefore an area which warrants further exploration. In this study a Csmd1 knockout (KO) mouse model was used to identify the role of Csmd1 in regulating mammary gland development during puberty. Changes in duct development and protein expression patterns were analysed by immunohistochemistry. This study identified increased ductal development during the early stages of puberty in the KO mice, characterised by increased ductal area and terminal end bud number at 6 weeks. Furthermore, increased expression of various proteins (Stat1, Fak, Akt, Slug/Snail and Progesterone receptor) was shown at 4 weeks in the KO mice, followed by lower expression levels from 6 weeks in the KO mice compared to the wild type mice. This study identifies a novel role for Csmd1 in mammary gland development, with Csmd1 KO causing significantly more rapid mammary gland development, suggesting an earlier adult mammary gland formation.
Collapse
|
13
|
Ploeger C, Huth T, Sugiyanto RN, Pusch S, Goeppert B, Singer S, Tabti R, Hausser I, Schirmacher P, Désaubry L, Roessler S. Prohibitin, STAT3 and SH2D4A physically and functionally interact in tumor cell mitochondria. Cell Death Dis 2020; 11:1023. [PMID: 33257655 DOI: 10.1038/s41419-020-03220-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022]
Abstract
Chromosome 8p is frequently deleted in various cancer entities and has been shown to correlate with poor patient survival. SH2D4A is located on chromosome 8p and prevents the nuclear translocation of the pro-tumorigenic transcription factor STAT3. Here, we investigated the interaction of SH2D4A and STAT3 to shed light on the non-canonical functions of STAT3 in cooperation with the tumor suppressor SH2D4A. Using an immunoprecipitation-mass spectrometry (IP-MS) approach, we identified the mitochondrial scaffold proteins prohibitin 1 (PHB1) and prohibitin 2 (PHB2) among other proteins to potentially bind to SH2D4A. Co-immunoprecipitation and proximity ligation assays confirmed direct interactions of STAT3, PHB1, and SH2D4A in situ and in vitro. In addition, cell fractionation and immunofluorescence staining revealed co-localization of these proteins with mitochondria. These interactions were selectively interrupted by the small molecule and PHB ligand FL3. Furthermore, FL3 led to a reduction of STAT3 protein levels, STAT3 transcriptional activity, and HIF1α protein stabilization upon dimethyloxalylglycine (DMOG) treatment. Besides, mitochondrial fusion and fission markers, L-OPA1, Mfn1, and FIS1, were dysregulated upon FL3 treatment. This dysregulated morphology was accompanied by significant reduction of mitochondrial respiration, thus, FL3 significantly diminished mitochondrial respirational capacity. In contrast, SH2D4A knockout increased mitochondrial respiration, whereas FL3 reversed the effect of SH2D4A knockout. The here described results indicate that the interaction of SH2D4A and PHB1 is involved in the mitochondrial function and integrity. The demonstrated interaction with STAT3, accompanied by its reduction of transcriptional activity, further suggests that SH2D4A is linking STAT3 to its mitochondrial functions, and inhibition of PHB-interaction may have therapeutic effects in tumor cells with STAT3 activation.
Collapse
|
14
|
Cabarcas-Petroski S, Meneses PI, Schramm L. A meta-analysis of BRF2 as a prognostic biomarker in invasive breast carcinoma. BMC Cancer 2020; 20:1093. [PMID: 33176745 PMCID: PMC7659115 DOI: 10.1186/s12885-020-07569-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/26/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Deregulation of the RNA polymerase III specific TFIIIB subunit BRF2 occurs in subtypes of human cancers. However, correlations between BRF2 alterations and clinical outcomes in breast cancer are limited. We conducted this review to analyze BRF2 alterations in genomic data sets housed in Oncomine and cBioPortal to identify potential correlations between BRF2 alterations and clinical outcomes. METHODS The authors queried both Oncomine and cBioPortal for alterations in BRF2 in human cancers and performed meta-analyses identifying significant correlations between BRF2 and clinical outcomes in invasive breast cancer (IBC). RESULTS A meta cancer outlier profile analysis (COPA) of 715 data sets (86,733 samples) in Oncomine identified BRF2 as overexpressed in 60% of breast cancer data sets. COPA scores in IBC data sets (3594 patients) are comparable for HER2 (24.211, median gene rank 60) and BRF2 (29.656, median gene rank 36.5). Overall survival in IBC patients with BRF2 alterations (21%) is significantly decreased (p = 9.332e-3). IBC patients with BRF2 alterations aged 46 to 50 have a significantly poor survival outcome (p = 7.093e-3). Strikingly, in metastatic breast cancer, BRF2 is altered in 33% of women aged 45-50. BRF2 deletions are predominant in this age group. CONCLUSION This study suggests BRF2 may be an prognostic biomarker in invasive breast carcinoma.
Collapse
Affiliation(s)
| | | | - Laura Schramm
- Department of Biological Sciences, St. John's University, Queens, NY, USA.
| |
Collapse
|
15
|
Kumar M, Bowers RR, Delaney JR. Single-cell analysis of copy-number alterations in serous ovarian cancer reveals substantial heterogeneity in both low- and high-grade tumors. Cell Cycle 2020; 19:3154-3166. [PMID: 33121339 DOI: 10.1080/15384101.2020.1836439] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Unusually high aneuploidy is a hallmark of epithelial serous ovarian cancer (SOC). Previous analyses have focused on aneuploidy on average across all tumor cells. With the expansion of single-cell sequencing technologies, however, an analysis of copy number heterogeneity cell-to-cell is now technically feasible. Here, we describe an analysis of single-cell RNA sequencing (scRNA-seq) data to infer arm-level aneuploidy in individual serous ovarian cancer cells. By first clustering high-quality sequenced epithelial versus non-epithelial cells, high-confidence tumor cell populations were identified. InferCNV was used to predict segmented copy-number alterations (CNAs), which were then used to determine arm-level aneuploidy at the single-cell level. Control comparisons of normal cells to normal cells showed zero arm-level aneuploidy, whereas a median of four aneuploid events were detectable in cancer cells. A heterogeneity analysis of high-grade tumor cells compared to low-grade tumor cells showed similar levels of cell-to-cell variation between cancer grades. Metastatic tumors potentially showed selection pressure with reduced cell-to-cell variation compared to cells from primary tumors. Minor cell populations with CNAs similar to metastatic cells were identified within the matched primary tumors. Taken together, these results provide a minimum estimate for single-cell aneuploidy in serous ovarian cancer and demonstrate the utility of single-cell sequencing for CNA analysis.
Collapse
Affiliation(s)
- Manonmani Kumar
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina , Charleston, SC, USA
| | - Robert R Bowers
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina , Charleston, SC, USA
| | - Joe R Delaney
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina , Charleston, SC, USA
| |
Collapse
|
16
|
Granados-Soler JL, Bornemann-Kolatzki K, Beck J, Brenig B, Schütz E, Betz D, Junginger J, Hewicker-Trautwein M, Murua Escobar H, Nolte I. Analysis of Copy-Number Variations and Feline Mammary Carcinoma Survival. Sci Rep 2020; 10:1003. [PMID: 31969654 PMCID: PMC6976565 DOI: 10.1038/s41598-020-57942-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 01/03/2020] [Indexed: 02/07/2023] Open
Abstract
Feline mammary carcinomas (FMCs) are highly malignant. As the disease-free survival (DFS) and overall survival (OS) are short, prognostication is crucial. Copy-number variations (CNVs) analysis by next-generation sequencing serves to identify critical cancer-related genomic regions. Thirty-three female cats with FMCs were followed during two years after surgery. Tumours represented tubulopapillary and solid carcinomas encompassing six molecular subtypes. Regardless of the histopathological diagnosis, molecular subtypes showed important differences in survival. Luminal A tumours exhibited the highest DFS (p = 0.002) and cancer-specific OS (p = 0.001), and the lowest amount of CNVs (p = 0.0001). In contrast, basal-like triple-negative FMCs had the worst outcome (DFS, p < 0.0001; and OS, p < 0.00001) and were the most aberrant (p = 0.05). In the multivariate analysis, copy-number losses (CNLs) in chromosome B1 (1-23 Mb) harbouring several tumour-repressors (e.g. CSMD1, MTUS1, MSR1, DBC2, and TUSC3) negatively influenced DFS. Whereas, copy-number gains (CNGs) in B4 (1-29 Mb) and F2 (64-82.3 Mb) comprising epithelial to mesenchymal transition genes and metastasis-promoting transcription factors (e.g. GATA3, VIM, ZEB1, and MYC) negatively influenced DFS and cancer-specific OS. These data evidence an association between specific CNVs in chromosomes B1, B4 and F2, and poor prognosis in FMCs.
Collapse
Affiliation(s)
- José Luis Granados-Soler
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- Haematology, Oncology and Palliative Medicine, Clinic III, University of Rostock, Rostock, Germany
| | | | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | | | - Daniela Betz
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Johannes Junginger
- Department of Pathology, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | | | - Hugo Murua Escobar
- Haematology, Oncology and Palliative Medicine, Clinic III, University of Rostock, Rostock, Germany
| | - Ingo Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany.
| |
Collapse
|
17
|
Singh D, Bharti A, Biswas D, Tewari M, Ansari MA, Singh S, Narayan G. Altered expression of NKX3.1 has significant prognostic value in gallbladder cancer. Gene Reports 2019. [DOI: 10.1016/j.genrep.2019.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
18
|
Eichenauer T, Bannenberg DC, Kluth M, Wittmer C, Büscheck F, Möller K, Dum D, Fraune C, Hube-Magg C, Möller-Koop C, Dahlem R, Fisch M, Rink M, Riechardt S, Tsourlakis MC, Bernreuther C, Minner S, Simon R, Sauter G, Wilczak W, Clauditz TS. 8p deletions in renal cell carcinoma are associated with unfavorable tumor features and poor overall survival. Urol Oncol 2020; 38:43.e13-20. [PMID: 31757738 DOI: 10.1016/j.urolonc.2019.09.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/02/2019] [Accepted: 09/25/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND METHODS 8p deletions are common in renal cell carcinoma. To study their prognostic impact and association with kidney cancer phenotype, a tissue microarray with 1,809 cancers was analyzed by fluorescence in situ hybridization for 8p21 copy numbers. RESULTS One thousand four hundred and seventy four interpretable tumors showed substantial differences between renal cancer subtypes. That 8p deletion was only seen in 1 (0.5%) of 216 papillary carcinomas underscores the biologic uniqueness of papillary kidney cancer, which is also defined by a highly distinct morphology. 8p deletions were found in 13.2% of 976 clear cell carcinomas, 7.8% of 77 chromophobe carcinomas, 0.8% of 119 oncocytomas, but also in several rare tumor entities including 1 of 4 collecting duct cancers, 1 of 3 multilocular cystic clear cell renal cell neoplasm of low malignancy, 2 of 10 Xp11.2 translocation cancers, 3 of 18 not otherwise specified carcinomas, and 1 analyzed medullary carcinoma. In clear cell carcinomas, 8p deletions were significantly associated with higher International Society of Urologic Pathologists (ISUP) grading (P = 0.0014), Fuhrman (P = 0.0003) and Thoenes grade (P = 0.0033), advanced tumor stage (P = 0.0002), large tumor diameter (P = 0.0019), distant metastases (P = 0.0183), overall survival (P = 0.0394), and recurrence free survival (P < 0.0001). In multivariate analysis, the prognostic role of 8p deletions was not independent of established clinic-pathological parameters. In conclusion, 8p deletions are strongly linked to tumor aggressiveness in clear cell kidney cancer. CONCLUSIONS Because 8p deletions are easy to measure by fluorescence in situ hybridization, 8p deletion assessment, most likely in combination with other parameters, may have a role in future prognosis assessment in clear cell kidney cancer.
Collapse
|
19
|
Lebok P, von Hassel A, Meiners J, Hube-Magg C, Simon R, Höflmayer D, Hinsch A, Dum D, Fraune C, Göbel C, Möller K, Sauter G, Jacobsen F, Büscheck F, Prien K, Krech T, Krech RH, von der Assen A, Wölber L, Witzel I, Schmalfeldt B, Geist S, Paluchoswski P, Wilke C, Heilenkötter U, Terracciano L, Müller V, Wilczak W, Burandt EC. Up-regulation of lysophosphatidylcholine acyltransferase 1 (LPCAT1) is linked to poor prognosis in breast cancer. Aging (Albany NY) 2019; 11:7796-7804. [PMID: 31533087 PMCID: PMC6781992 DOI: 10.18632/aging.102287] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/09/2019] [Indexed: 12/16/2022]
Abstract
Dysregulation of lipid metabolism is common in cancer. Lysophosphatidylcholine acyltransferase 1 (LPCAT1) has been implicated with various cancer types. Here we analyzed by immunohistochemistry its expression in 2,197 breast cancers. LPCAT1 staining was found in 97.8% of 1,774 interpretable tumors, including 48.1% with weak, 28.7% with moderate, and 14.4% with strong expression. The frequency of LPCAT1 positivity depended on the histological tumor type. Moderate or strong LPCAT1 positivity was more common in cancers of no special type (NST) (46.2%) than in lobular carcinomas (25.9%; p<0.0001). Strong LPCAT1 was associated with BRE grade, tumor cell proliferation and overall survival in all cancers and in the subgroup of NST cancers (p<0.0001, each). In the subset of NST cancers the prognostic effect of LPCAT1 expression was independent of pT, and BRE grade (p<0.0001 each). A comparison with molecular features showed that LPCAT1 was strongly associated with estrogen receptor negativity (p<0.0001), progesterone receptor negativity (p<0,0001), amplification of HER2 (p<0.0001) and MYC (p=0.0066), as well as deletions of PTEN (p<0.0001) and CDKNA2 (p=0.0151). It is concluded that LPCAT1 overexpression is linked to adverse tumor features and poor prognosis in breast cancer. These data also highlight the important role of lipid metabolism in breast cancer biology.
Collapse
Affiliation(s)
- Patrick Lebok
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Aurelia von Hassel
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Jan Meiners
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Claudia Hube-Magg
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Ronald Simon
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Doris Höflmayer
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Andrea Hinsch
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - David Dum
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Christoph Fraune
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Cosima Göbel
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Katharina Möller
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Guido Sauter
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Frank Jacobsen
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Franziska Büscheck
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Kristina Prien
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Till Krech
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany.,Department of Pathology, Clinical Center Osnabrück, Osnabrück D-49076, Germany
| | - Rainer Horst Krech
- Department of Pathology, Clinical Center Osnabrück, Osnabrück D-49076, Germany
| | - Albert von der Assen
- Breast cancer center, Niels-Stensen Clinic, Franziskus-Hospital Harderberg, Georgsmarienhütte D-49124, Germany
| | - Linn Wölber
- Department of Gynecology and Clinic, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Isabell Witzel
- Department of Gynecology and Clinic, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Barbara Schmalfeldt
- Department of Gynecology and Clinic, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Stefan Geist
- Department of Gynecology, Regio Clinic Pinneberg, Pinneberg D-25421, Germany
| | - Peter Paluchoswski
- Department of Gynecology, Regio Clinic Pinneberg, Pinneberg D-25421, Germany
| | - Christian Wilke
- Department of Gynecology, Regio Clinic Elmshorn, Elmshorn D-25337, Germany
| | - Uwe Heilenkötter
- Department of Gynecology, Regio Clinic and Senior Citizen Center Itzehoe, Itzehoe D-25524, Germany
| | - Luigi Terracciano
- Cantonal Hospital Basel, University of Basel, Basel CH-4031, Switzerland
| | - Volkmar Müller
- Department of Gynecology and Clinic, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Waldemar Wilczak
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| | - Eike Christian Burandt
- Department of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20246, Germany
| |
Collapse
|
20
|
Baity M, Wang L, Correa AM, Zhang X, Zhang R, Pataer A, Wu S, Meng QH, Antonoff MB, Hofstetter WL, Mehran RJ, Rice DC, Roth JA, Sepesi B, Swisher SG, Vaporciyan AA, Walsh GL, Zhao M, Gu J, Fang B. Glutathione reductase ( GSR) gene deletion and chromosome 8 aneuploidy in primary lung cancers detected by fluorescence in situ hybridization. Am J Cancer Res 2019; 9:1201-1211. [PMID: 31285952 PMCID: PMC6610060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/04/2019] [Indexed: 06/09/2023] Open
Abstract
Our recent study demonstrated that cancer cells with compromised glutathione homeostasis, including reduced expression of the glutathione reductase (GSR) gene, were selectively killed by inhibition of thioredoxin reductase. The human GSR gene is located on chromosome 8p, a region often lost in lung and other cancers. However, whether GSR is altered in primary lung cancer remains unknown. To analyze alterations of GSR in lung cancer, we performed fluorescence in situ hybridization with probes for GSR and the chromosome 8 centromere (CEP8) in 45 surgical specimens of primary lung cancer, including 24 lung adenocarcinomas, 10 squamous cell carcinomas, 8 neuroendocrine cancers, and 3 small cell lung cancers. Twenty-five surgically resected normal lung tissue specimens from these lung cancer patients were used as a controls. The signal ratio of GSR to CEP8 per cell was used to identify gain or loss of GSR. GSR loss was detected in 6 of 24 (25%) adenocarcinoma specimens and 5 of 10 (50%) squamous cell carcinoma specimens, but not in neuroendocrine cancer or small cell lung cancer specimens. We also found that 19 of 45 (42%) specimens had chromosome 8 aneuploidy (more or less than 2 signals for CEP8), including 8 with both aneuploidy and GSR deletion. Chromosome 8 aneuploidy was detected in all types of lung cancer analyzed. Univariate and multivariable logistic regression analyses indicated that male patients had an increased risk of GSR deletion (hazard ratio [HR] = 4.77, 95% confidence interval [CI] = 1.00-22.86, P = 0.051), and patients who had undergone preoperative radiation therapy or had a self-reported history of cigarette smoking had an increased risk of chromosome 8 aneuploidy (preoperative radiation: HR = 18.63, 95% CI = 0.90-384.17, P = 0.058; smoking: HR = 7.59, 95% CI = 0.86-66.75, P = 0.068), although the p values did not reach significance. Because GSR deficiency and chromosome 8 aneuploidy have implications in targeted therapy and/or immunotherapy for cancer, they might serve as predictive biomarkers for precision therapy of lung cancers.
Collapse
Affiliation(s)
- Mohamed Baity
- School of Health Professions, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Li Wang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Arlene M Correa
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Xiaoshan Zhang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Ran Zhang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Apar Pataer
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Shuhong Wu
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Qing H Meng
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Reza J Mehran
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - David C Rice
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Garrett L Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Ming Zhao
- School of Health Professions, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Jun Gu
- School of Health Professions, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| | - Bingliang Fang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer CenterHouston, TX 77030, USA
| |
Collapse
|
21
|
Rodrigues-Peres RM, de S Carvalho B, Anurag M, Lei JT, Conz L, Gonçalves R, Cardoso Filho C, Ramalho S, de Paiva GR, Derchain SFM, Lopes-Cendes I, Ellis MJ, Sarian LO. Copy number alterations associated with clinical features in an underrepresented population with breast cancer. Mol Genet Genomic Med 2019; 7:e00750. [PMID: 31099189 PMCID: PMC6625096 DOI: 10.1002/mgg3.750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022] Open
Abstract
Background As the most incident tumor among women worldwide, breast cancer is a heterogeneous disease. Tremendous efforts have been made to understand how tumor characteristics as histological type, molecular subtype, and tumor microenvironment collectively influence disease diagnosis to treatment, which impact outcomes. Differences between populations and environmental and cultural factors have impacts on the origin and evolution of the disease, as well as the therapeutic challenges that arise due to these factors. We, then, compared copy number variations (CNVs) in mucinous and nonmucinous luminal breast tumors from a Brazilian cohort to investigate major CNV imbalances in mucinous tumors versus non‐mucinous luminal tumors, taking into account their clinical and pathological features. Methods 48 breast tumor samples and 48 matched control blood samples from Brazilian women were assessed for CNVs by chromosome microarray. Logistic regression and random forest models were used in order to assess CNVs in chromosomal regions from tumors. Results CNVs that were identified in chromosomes 1, 5, 8, 17, 19, and 21 classify tumors according to their histological type, ethnicity, disease stage, and familial history. Conclusion Copy number alterations described in this study provide a better understanding of the landscape of genomic aberrations in mucinous breast cancers that are associated with clinical features.
Collapse
Affiliation(s)
- Raquel M Rodrigues-Peres
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Benilton de S Carvalho
- Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas-UNICAMP, Campinas, Brazil.,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Meenakshi Anurag
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX
| | - Jonathan T Lei
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX
| | - Livia Conz
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Rodrigo Gonçalves
- Department of Mastology, Hospital das Clínicas, Discipline of Gynecology, Department of Obstetrics and Gynecology, Faculty of Medicine, University of São Paulo, Brazil
| | - Cássio Cardoso Filho
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Susana Ramalho
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Geisilene R de Paiva
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Sophie F M Derchain
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Iscia Lopes-Cendes
- The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil.,Department of Medical Genetics, State University of Campinas-UNICAMP, Campinas, Brazil
| | - Matthew J Ellis
- Department of Medicine, Baylor College of Medicine, Houston, TX.,Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX.,Interdepartmental Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Luis O Sarian
- Faculty of Medical Sciences, Department of Obstetrics and Gynecology, State University of Campinas-UNICAMP, Campinas, Brazil
| |
Collapse
|
22
|
Moelans CB, van Maldegem CMG, van der Wall E, van Diest PJ. Copy number changes at 8p11-12 predict adverse clinical outcome and chemo- and radiotherapy response in breast cancer. Oncotarget 2018; 9:17078-17092. [PMID: 29682206 PMCID: PMC5908307 DOI: 10.18632/oncotarget.24904] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/12/2018] [Indexed: 01/15/2023] Open
Abstract
Purpose The short arm of chromosome 8 (8p) is a frequent target of loss of heterozygosity (LOH) in cancer, and 8p LOH is commonly associated with a more aggressive tumor phenotype. The 8p11-12 region is a recurrent breakpoint area characterized by a sharp decrease in gains/amplifications and increase in allelic loss towards 8pter. However, the clustering of genomic aberrations in this region, even in the absence of proximal amplifications or distal LOH, suggests that the 8p11-12 region could play a pivotal role in oncogenesis. Results Loss in the FGFR1 and ZNF703-containing 8p11 region was seen in 25% of patients, correlated with lower mRNA expression levels and independently predicted poor survival, particularly in systemic treatment-naïve patients and even without adjacent 8p12 loss. Amplification of FGFR1 at 8p11 and loss of DUSP26 and UNC5D, located in the 8p12 breakpoint region, independently predicted worse event free survival. Gains in the 8p12 region encompassing WRN, NRG1, DUSP26 and UNC5D, seen in 20-30% of patients, were associated with higher mRNA expression and independently predicted chemotherapy sensitivity. Losses at 8p12 independently predicted radiotherapy resistance. Material and methods Multiplex ligation-dependent probe amplification was used to investigate copy number aberrations at 8p11-12 in 234 female breast cancers. Alterations were correlated with clinicopathologic characteristics, survival and response to therapy. Results were validated using public METABRIC data. Conclusion Allelic loss and amplification in the 8p11-12 breakpoint region predict poor survival and chemo- and radiotherapy response. Assessment of 8p11-12 gene copy number status seems to augment existing prognostic and predictive tools.
Collapse
Affiliation(s)
- Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
23
|
Zagradišnik B, Krgović D, Herodež ŠS, Zagorac A, Ćižmarević B, Vokač NK. Identification of genomic copy number variations associated with specific clinical features of head and neck cancer. Mol Cytogenet 2018; 11:5. [PMID: 29371888 PMCID: PMC5769503 DOI: 10.1186/s13039-018-0354-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/03/2018] [Indexed: 12/15/2022] Open
Abstract
Background Copy number variations (CNSs) of large genomic regions are an important mechanism implicated in the development of head and neck cancer, however, for most changes their exact role is not well understood. The aim of this study was to find possible associations between gains/losses of genomic regions and clinically distinct subgroups of head and neck cancer patients. Results Array comparative genomic hybridization (aCGH) analysis was performed on DNA samples in 64 patients with cancer in oral cavity, oropharynx or hypopharynx. Overlapping genomic regions created from gains and losses were used for statistical analysis. Following regions were overrepresented: in tumors with stage I or II a gain of 2.98 Mb on 6p21.2-p11 and a gain of 7.4 Mb on 8q11.1-q11.23; in tumors with grade I histology a gain of 1.1 Mb on 8q24.13, a loss of a large part of p arm of chromosome 3, a loss of a 1.24 Mb on 6q14.3, and a loss of terminal 32 Mb region of 8p23.3; in cases with affected lymph nodes a gain of 0.75 Mb on 3q24, and a gain of 0.9 Mb on 3q26.32-q26.33; in cases with unaffected lymph nodes a gain of 1.1 Mb on 8q23.3, in patients not treated with surgery a gain of 12.2 Mb on 7q21.3-q22.3 and a gain of 0.33 Mb on 20q11.22. Conclusions Our study identified several genomic regions of interest which appear to be associated with various clinically distinct subgroups of head and neck cancer. They represent a potentially important source of biomarkers useful for the clinical management of head and neck cancer. In particular, the PIK3CA and AGTR1 genes could be singled out to predict the lymph node involvement.
Collapse
Affiliation(s)
- Boris Zagradišnik
- 1Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000 Maribor, Slovenia
| | - Danijela Krgović
- 1Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000 Maribor, Slovenia
| | - Špela Stangler Herodež
- 1Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000 Maribor, Slovenia
| | - Andreja Zagorac
- 1Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000 Maribor, Slovenia
| | - Bogdan Ćižmarević
- 2Department of Otorhinolaryngology, University Medical Centre Maribor, Ljubljanska 5, 2000 Maribor, Slovenia
| | - Nadja Kokalj Vokač
- 1Laboratory of Medical Genetics, University Medical Centre Maribor, Ljubljanska 5, 2000 Maribor, Slovenia
| |
Collapse
|
24
|
Shah V, Nowinski S, Levi D, Shinomiya I, Kebaier Ep Chaabouni N, Gillett C, Grigoriadis A, Graham TA, Roylance R, Simpson MA, Pinder SE, Sawyer EJ. PIK3CA mutations are common in lobular carcinoma in situ, but are not a biomarker of progression. Breast Cancer Res 2017; 19:7. [PMID: 28095868 PMCID: PMC5240238 DOI: 10.1186/s13058-016-0789-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/01/2016] [Indexed: 11/17/2022] Open
Abstract
Background Lobular carcinoma in situ (LCIS) is a non-invasive breast lesion that is typically found incidentally on biopsy and is often associated with invasive lobular carcinoma (ILC). LCIS is considered by some to be a risk factor for future breast cancer rather than a true precursor lesion. The aim of this study was to identify genetic changes that could be used as biomarkers of progression of LCIS to invasive disease using cases of pure LCIS and comparing their genetic profiles to LCIS which presented contemporaneously with associated ILC, on the hypothesis that the latter represents LCIS that has already progressed. Methods Somatic copy number aberrations (SCNAs) were assessed by SNP array in three subgroups: pure LCIS, LCIS associated with ILC and the paired ILC. In addition exome sequencing was performed on seven fresh frozen samples of LCIS associated with ILC, to identify recurrent somatic mutations. Results The copy number profiles of pure LCIS and LCIS associated with ILC were almost identical. However, four SCNAs were more frequent in ILC than LCIS associated with ILC, including gain/amplification of CCND1. CCND1 protein over-expression assessed by immunohistochemical analysis in a second set of samples from 32 patients with pure LCIS and long-term follow up, was associated with invasive recurrence (P = 0.02, Fisher’s exact test). Exome sequencing revealed that PIK3CA mutations were as frequent as CDH1 mutations in LCIS, but were not a useful biomarker of LCIS progression as they were as frequent in pure LCIS as in LCIS associated with ILC. We also observed heterogeneity of PIK3CA mutations and evidence of sub-clonal populations in LCIS irrespective of whether they were associated with ILC. Conclusions Our data shows that pure LCIS and LCIS co-existing with ILC have very similar SCNA profiles, supporting the hypothesis that LCIS is a true precursor lesion. We have provided evidence that over-expression of CCND1 may identify a subgroup of patients with pure LCIS who are more likely to develop invasive disease, in contrast to PIK3CA mutations, which occur too early in lobular tumorigenesis to be informative. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0789-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vandna Shah
- Division of Cancer Studies, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Salpie Nowinski
- Division of Cancer Studies, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Dina Levi
- Division of Cancer Studies, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Irek Shinomiya
- Division of Cancer Studies, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | | | - Cheryl Gillett
- Division of Cancer Studies, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Anita Grigoriadis
- Breast Cancer Now Unit, Research Oncology & Cancer Epidemiology, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Trevor A Graham
- Evolution and Cancer laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Rebecca Roylance
- Department of Oncology, UCLH Foundation Trust, London, NW1 2PG, UK
| | - Michael A Simpson
- Medical and Molecular Genetics, Guy's Hospital, King's College London, London, UK
| | - Sarah E Pinder
- Division of Cancer Studies, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Elinor J Sawyer
- Division of Cancer Studies, Guy's Hospital, King's College London, London, SE1 9RT, UK.
| |
Collapse
|
25
|
Kudryavtseva AV, Lipatova AV, Zaretsky AR, Moskalev AA, Fedorova MS, Rasskazova AS, Shibukhova GA, Snezhkina AV, Kaprin AD, Alekseev BY, Dmitriev AA, Krasnov GS. Important molecular genetic markers of colorectal cancer. Oncotarget 2016; 7:53959-53983. [PMID: 27276710 PMCID: PMC5288236 DOI: 10.18632/oncotarget.9796] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 05/21/2016] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) ranks third in the incidences of cancer morbidity and mortality worldwide. CRC is rather heterogeneous with regard to molecular genetic characteristics and pathogenic pathways. A wide spectrum of biomarkers is used for molecular subtype determination, prognosis, and estimation of sensitivity to different drugs in practice. These biomarkers can include germline and somatic mutations, chromosomal aberrations, genomic abnormalities, gene expression alterations at mRNA or protein level and changes in DNA methylation status. In the present review we discuss the most important and well-studied CRC biomarkers, and their potential clinical significance and current approaches to molecular classification of colorectal tumors.
Collapse
Affiliation(s)
- Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Anastasia V. Lipatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrew R. Zaretsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Galina A. Shibukhova
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | | | - Andrey D. Kaprin
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Boris Y. Alekseev
- National Medical Research Radiological Centre, Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia
| |
Collapse
|
26
|
Mikulasova A, Smetana J, Wayhelova M, Janyskova H, Sandecka V, Kufova Z, Almasi M, Jarkovsky J, Gregora E, Kessler P, Wrobel M, Walker BA, Wardell CP, Morgan GJ, Hajek R, Kuglik P. Genomewide profiling of copy-number alteration in monoclonal gammopathy of undetermined significance. Eur J Haematol 2016; 97:568-575. [PMID: 27157252 DOI: 10.1111/ejh.12774] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2016] [Indexed: 12/23/2022]
Abstract
Monoclonal gammopathy of undetermined significance (MGUS) is a benign condition with an approximate 1% annual risk of symptomatic plasma cell disorder development, mostly to multiple myeloma (MM). We performed genomewide screening of copy-number alterations (CNAs) in 90 MGUS and 33 MM patients using high-density DNA microarrays. We identified CNAs in a smaller proportion of MGUS (65.6%) than in MM (100.0%, P = 1.31 × 10-5 ) and showed median number of CNAs is lower in MGUS (3, range 0-22) than in MM (13, range 4-38, P = 1.82 × 10-10 ). In the MGUS cohort, the most frequent losses were located at 1p (5.6%), 6q (6.7%), 13q (30.0%), 14q (14.4%), 16q (8.9%), 21q (5.6%), and gains at 1q (23.3%), 2p (6.7%), 6p (13.3%), and Xq (7.8%). Hyperdiploidy was detected in 38.9% of MGUS cases, and the most frequent whole chromosome gains were 3 (25.6%), 5 (23.3%), 9 (37.8%), 15 (23.3%), and 19 (32.2%). We also identified CNAs such as 1p, 6q, 8p, 12p, 13q, 16q losses, 1q gain and hypodiploidy, which are potentially associated with an adverse prognosis in MGUS. In summary, we showed that MGUS is similar to MM in that it is a genetically heterogeneous disorder, but overall cytogenetic instability is lower than in MM, which confirms that genetic abnormalities play important role in monoclonal gammopathies.
Collapse
Affiliation(s)
- Aneta Mikulasova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic.,Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Jan Smetana
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic
| | - Marketa Wayhelova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic
| | - Helena Janyskova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Viera Sandecka
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Zuzana Kufova
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic.,Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - Martina Almasi
- Department of Clinical Hematology, University Hospital Brno, Brno, Czech Republic
| | - Jiri Jarkovsky
- Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Evzen Gregora
- Department of Internal Medicine and Hematology, University Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Petr Kessler
- Department of Hematology and Transfusion, General Hospital, Pelhrimov, Czech Republic
| | - Marek Wrobel
- Department of Oncology, Hospital Novy Jicin, Novy Jicin, Czech Republic
| | - Brian A Walker
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christopher P Wardell
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Gareth J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Roman Hajek
- Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic.,Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - Petr Kuglik
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic.,Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| |
Collapse
|