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Guo L, Cheng H, Liu J, Shao W, Luo L, Zheng W, Sun S, Kong D, Chen C. Based on whole-exome sequencing to explore the rule of Herceptin and TKI resistance in breast cancer patients. BMC Med Genomics 2024; 17:25. [PMID: 38243282 PMCID: PMC10799408 DOI: 10.1186/s12920-023-01762-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/05/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Breast cancer is the second leading cause of cancer-related death in women, and drug resistance during treatment is a major challenge. However, the mechanisms underlying drug resistance are not fully understood. Here we applied whole-exome sequencing (WES) to clarify resistant rules to Herceptin and tyrosine kinase inhibitors (TKIs). METHODS There are 12 HER2+ breast cancer patients who were done WES. Samples from tumor and surrounding tissues underwent DNA sequencing and analysis. Various experimental and bioinformatics techniques were employed, including genomic capture, mutation analysis (Genome Analysis Toolkit (GATK), etc.), bioinformatics assessments, and drug-gene interaction investigations. Ultimately, the study explored the association of APOB gene expression with breast cancer recurrence rates, immune cell infiltration, and drug response. RESULTS The C > T mutation frequency was highest in the Herceptin-insensitive (HI) and verification groups, codenamed YI, contrasting with the Herceptin-sensitive (HE) group. No microsatellite instability (MSI)-H patients were in the HE group, but both HI and YI groups had 1 each. Significant differences in transition-transversion (TiTv) were observed in the HI and YI groups rather than the HE group. In the TKI- insensitive (TI) group, C > T mutations were highest, differing from the TKI-sensitive (TE) group. TE group included 2 MSI-H patients. Significant differences in TiTv were found in the TI group rather than the TE group. Mutated APOB may resist Herceptin and TKI, increasing immune infiltration. We identified potential drugs targeting it. CONCLUSIONS Our study suggested that a higher percentage of C > T mutations, significant differences in TiTv, and MSI-H status may indicate Herceptin resistance, while a higher percentage of C > T mutations, significant differences in TiTv, and the absence of MSI-H may indicate TKI resistance in breast cancer patients. For patients resistant to both Herceptin and TKI, mutated APOB may play a crucial role in resistance.
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Affiliation(s)
- Liantao Guo
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Hong Cheng
- Department of Breast Surgery, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, 430060, People's Republic of China
| | - Jianhua Liu
- Department of breast surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Provincial Clinical Research Center for Breast Cancer, Wuhan Clinical Research Center for Breast Cancer, No.116 Zhuo Daoquan South Road, Wuhan, Hubei, 430079, People's Republic of China
| | - Weikang Shao
- Genecast Biotechnology Co., Ltd., Wuxi, Jiangsu, 214000, People's Republic of China
| | - Lan Luo
- Department of Breast Surgery, The Affiliated Hospital of Guizhou Medical University, No. 28 Guiyi Road, Yunyan District, Guiyang, Guizhou, 550001, People's Republic of China
| | - Weijie Zheng
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China
| | - Deguang Kong
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China.
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuhan, Hubei, 430060, People's Republic of China.
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Zhang S, Cai Z, Li H. AHNAKs roles in physiology and malignant tumors. Front Oncol 2023; 13:1258951. [PMID: 38033502 PMCID: PMC10682155 DOI: 10.3389/fonc.2023.1258951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The AHNAK family currently consists of two members, namely AHNAK and AHNAK2, both of which have a molecular weight exceeding 600 kDa. Homologous sequences account for approximately 90% of their composition, indicating a certain degree of similarity in terms of molecular structure and biological functions. AHNAK family members are involved in the regulation of various biological functions, such as calcium channel modulation and membrane repair. Furthermore, with advancements in biological and bioinformatics technologies, research on the relationship between the AHNAK family and tumors has rapidly increased in recent years, and its regulatory role in tumor progression has gradually been discovered. This article briefly describes the physiological functions of the AHNAK family, and reviews and analyzes the expression and molecular regulatory mechanisms of the AHNAK family in malignant tumors using Pubmed and TCGA databases. In summary, AHNAK participates in various physiological and pathological processes in the human body. In multiple types of cancers, abnormal expression of AHNAK and AHNAK2 is associated with prognosis, and they play a key regulatory role in tumor progression by activating signaling pathways such as ERK, MAPK, Wnt, and MEK, as well as promoting epithelial-mesenchymal transition.
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Affiliation(s)
- Shusen Zhang
- Hebei Province Xingtai People’s Hospital Postdoctoral Workstation, Xingtai, China
- Postdoctoral Mobile Station, Hebei Medical University, Shijiazhuang, China
- Department of Pulmonary and Critical Care Medicine, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, China
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhigang Cai
- Postdoctoral Mobile Station, Hebei Medical University, Shijiazhuang, China
- The First Department of Pulmonary and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hui Li
- Department of surgery, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, China
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Souza VGP, Forder A, Telkar N, Stewart GL, Carvalho RF, Mur LAJ, Lam WL, Reis PP. Identifying New Contributors to Brain Metastasis in Lung Adenocarcinoma: A Transcriptomic Meta-Analysis. Cancers (Basel) 2023; 15:4526. [PMID: 37760494 PMCID: PMC10526208 DOI: 10.3390/cancers15184526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Lung tumors frequently metastasize to the brain. Brain metastasis (BM) is common in advanced cases, and a major cause of patient morbidity and mortality. The precise molecular mechanisms governing BM are still unclear, in part attributed to the rarity of BM specimens. In this work, we compile a unique transcriptomic dataset encompassing RNA-seq, microarray, and single-cell analyses from BM samples obtained from patients with lung adenocarcinoma (LUAD). By integrating this comprehensive dataset, we aimed to enhance understanding of the molecular landscape of BM, thereby facilitating the identification of novel and efficient treatment strategies. We identified 102 genes with significantly deregulated expression levels in BM tissues, and discovered transcriptional alterations affecting the key driver 'hub' genes CD69 (a type II C-lectin receptor) and GZMA (Granzyme A), indicating an important role of the immune system in the development of BM from primary LUAD. Our study demonstrated a BM-specific gene expression pattern and revealed the presence of dendritic cells and neutrophils in BM, suggesting an immunosuppressive tumor microenvironment. These findings highlight key drivers of LUAD-BM that may yield therapeutic targets to improve patient outcomes.
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Affiliation(s)
- Vanessa G. P. Souza
- Molecular Oncology Laboratory, Experimental Research Unit (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (A.F.); (N.T.); (G.L.S.); (W.L.L.)
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (A.F.); (N.T.); (G.L.S.); (W.L.L.)
| | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (A.F.); (N.T.); (G.L.S.); (W.L.L.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Greg L. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (A.F.); (N.T.); (G.L.S.); (W.L.L.)
| | - Robson F. Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil;
| | - Luis A. J. Mur
- Department of Life Science, Aberystwyth University, Aberystwyth, Wales SY23 3FL, UK;
| | - Wan L. Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (A.F.); (N.T.); (G.L.S.); (W.L.L.)
| | - Patricia P. Reis
- Molecular Oncology Laboratory, Experimental Research Unit (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
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Desette A, Guichet PO, Emambux S, Masliantsev K, Cortes U, Ndiaye B, Milin S, George S, Faigner M, Tisserand J, Gaillard A, Brot S, Wager M, Tougeron D, Karayan-Tapon L. Deciphering Brain Metastasis Stem Cell Properties From Colorectal Cancer Highlights Specific Stemness Signature and Shared Molecular Features. Cell Mol Gastroenterol Hepatol 2023; 16:757-782. [PMID: 37482243 PMCID: PMC10520365 DOI: 10.1016/j.jcmgh.2023.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND & AIMS Brain metastases (BMs) from colorectal cancer (CRC) are associated with significant morbidity and mortality, with chemoresistance and short overall survival. Migrating cancer stem cells with the ability to initiate BM have been described in breast and lung cancers. In this study, we describe the identification and characterization of cancer stem cells in BM from CRC. METHODS Four brain metastasis stem cell lines from patients with colorectal cancer (BM-SC-CRC1 to BM-SC-CRC4) were obtained by mechanical dissociation of patient's tumors and selection of cancer stem cells by appropriate culture conditions. BM-SC-CRCs were characterized in vitro by clonogenic and limiting-dilution assays, as well as immunofluorescence and Western blot analyses. In ovo, a chicken chorioallantoic membrane (CAM) model and in vivo, xenograft experiments using BALB/c-nude mice were realized. Finally, a whole exome and RNA sequencing analyses were performed. RESULTS BM-SC-CRC formed metaspheres and contained tumor-initiating cells with self-renewal properties. They expressed stem cell surface markers (CD44v6, CD44, and EpCAM) in serum-free medium and CRC markers (CK19, CK20 and CDX-2) in fetal bovine serum-enriched medium. The CAM model demonstrated their invasive and migratory capabilities. Moreover, mice intracranial xenotransplantation of BM-SC-CRCs adequately recapitulated the original patient BM phenotype. Finally, transcriptomic and genomic approaches showed a significant enrichment of invasiveness and specific stemness signatures and highlighted KMT2C as a potential candidate gene to potentially identify high-risk CRC patients. CONCLUSIONS This original study represents the first step in CRC BM initiation and progression comprehension, and further investigation could open the way to new therapeutics avenues to improve patient prognosis.
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Affiliation(s)
- Amandine Desette
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France.
| | - Pierre-Olivier Guichet
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
| | - Sheik Emambux
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Service d'oncologie médicale, CHU de Poitiers, Poitiers, France
| | - Konstantin Masliantsev
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
| | - Ulrich Cortes
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
| | - Birama Ndiaye
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
| | - Serge Milin
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Service d'Anatomie et de Cytologie Pathologiques, CHU de Poitiers, Poitiers, France
| | - Simon George
- MGX-Montpellier GenomiX, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Mathieu Faigner
- Service d'oncologie médicale, CHU de Poitiers, Poitiers, France
| | | | - Afsaneh Gaillard
- Université de Poitiers, CHU de Poitiers, INSERM, LNEC, Poitiers, France
| | - Sébastien Brot
- Université de Poitiers, CHU de Poitiers, INSERM, LNEC, Poitiers, France
| | - Michel Wager
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Service de Neurochirurgie, CHU de Poitiers, Poitiers, France
| | - David Tougeron
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Service d'hépato-gastro-entérologie, CHU de Poitiers, Poitiers, France
| | - Lucie Karayan-Tapon
- Université de Poitiers, CHU Poitiers, ProDiCeT, UR 24144, Poitiers, France; Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
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Advances in the Molecular Landscape of Lung Cancer Brain Metastasis. Cancers (Basel) 2023; 15:cancers15030722. [PMID: 36765679 PMCID: PMC9913505 DOI: 10.3390/cancers15030722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is one of the most frequent tumors that metastasize to the brain. Brain metastasis (BM) is common in advanced cases, being the major cause of patient morbidity and mortality. BMs are thought to arise via the seeding of circulating tumor cells into the brain microvasculature. In brain tissue, the interaction with immune cells promotes a microenvironment favorable to the growth of cancer cells. Despite multimodal treatments and advances in systemic therapies, lung cancer patients still have poor prognoses. Therefore, there is an urgent need to identify the molecular drivers of BM and clinically applicable biomarkers in order to improve disease outcomes and patient survival. The goal of this review is to summarize the current state of knowledge on the mechanisms of the metastatic spread of lung cancer to the brain and how the metastatic spread is influenced by the brain microenvironment, and to elucidate the molecular determinants of brain metastasis regarding the role of genomic and transcriptomic changes, including coding and non-coding RNAs. We also present an overview of the current therapeutics and novel treatment strategies for patients diagnosed with BM from NSCLC.
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Andrews LJ, Thornton ZA, Saleh R, Dawson S, Short SC, Daly R, Higgins JPT, Davies P, Kurian KM. Genomic landscape and actionable mutations of brain metastases derived from non-small cell lung cancer: A systematic review. Neurooncol Adv 2023; 5:vdad145. [PMID: 38130901 PMCID: PMC10734675 DOI: 10.1093/noajnl/vdad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Background Brain metastases derived from non-small cell lung cancer (NSCLC) represent a significant clinical problem. We aim to characterize the genomic landscape of brain metastases derived from NSCLC and assess clinical actionability. Methods We searched Embase, MEDLINE, Web of Science, and BIOSIS from inception to 18/19 May 2022. We extracted information on patient demographics, smoking status, genomic data, matched primary NSCLC, and programmed cell death ligand 1 expression. Results We found 72 included papers and data on 2346 patients. The most frequently mutated genes from our data were EGFR (n = 559), TP53 (n = 331), KRAS (n = 328), CDKN2A (n = 97), and STK11 (n = 72). Common missense mutations included EGFR L858R (n = 80) and KRAS G12C (n = 17). Brain metastases of ever versus never smokers had differing missense mutations in TP53 and EGFR, except for L858R and T790M in EGFR, which were seen in both subgroups. Of the top 10 frequently mutated genes that had primary NSCLC data, we found 37% of the specific mutations assessed to be discordant between the primary NSCLC and brain metastases. Conclusions To our knowledge, this is the first systematic review to describe the genomic landscape of brain metastases derived from NSCLC. These results provide a comprehensive outline of frequently mutated genes and missense mutations that could be clinically actionable. These data also provide evidence of differing genomic landscapes between ever versus never smokers and primary NSCLC compared to the BM. This information could have important consequences for the selection and development of targeted drugs for these patients.
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Affiliation(s)
- Lily J Andrews
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Zak A Thornton
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Ruqiya Saleh
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan C Short
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Richard Daly
- Cellular Pathology Department, North Bristol NHS Trust, Bristol, UK
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Philippa Davies
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
- Brain Tumour Research Centre, Bristol Medical School, University of Bristol, Bristol, UK
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Genomic Profiling Identifies Putative Pathogenic Alterations in NSCLC Brain Metastases. JTO Clin Res Rep 2022; 3:100435. [PMID: 36561283 PMCID: PMC9763853 DOI: 10.1016/j.jtocrr.2022.100435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Brain metastases (BM) severely affect the prognosis and quality of life of patients with NSCLC. Recently, molecularly targeted agents were found to have promising activity against BM in patients with NSCLC whose primary tumors carry "druggable" mutations. Nevertheless, it remains critical to identify specific pathogenic alterations that drive NSCLC-BM and that can provide novel and more effective therapeutic targets. Methods To identify potentially targetable pathogenic alterations in NSCLC-BM, we profiled somatic copy number alterations (SCNAs) in 51 matched pairs of primary NSCLC and BM samples from 33 patients with lung adenocarcinoma and 18 patients with lung squamous cell carcinoma. In addition, we performed multiregion copy number profiling on 15 BM samples and whole-exome sequencing on 40 of 51 NSCLC-BM pairs. Results BM consistently had a higher burden of SCNAs compared with the matched primary tumors, and SCNAs were typically homogeneously distributed within BM, suggesting BM do not undergo extensive evolution once formed. By comparing focal SCNAs in matched NSCLC-BM pairs, we identified putative BM-driving alterations affecting multiple cancer genes, including several potentially targetable alterations in genes such as CDK12, DDR2, ERBB2, and NTRK1, which we validated in an independent cohort of 84 BM samples. Finally, we identified putative pathogenic alterations in multiple cancer genes, including genes involved in epigenome editing and 3D genome organization, such as EP300, CTCF, and STAG2, which we validated by targeted sequencing of an independent cohort of 115 BM samples. Conclusions Our study represents the most comprehensive genomic characterization of NSCLC-BM available to date, paving the way to functional studies aimed at assessing the potential of the identified pathogenic alterations as clinical biomarkers and targets.
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