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Patiabadi Z, Razmkabir M, EsmailizadehKoshkoiyeh A, Moradi MH, Rashidi A, Mahmoudi P. Whole-genome scan for selection signature associated with temperature adaptation in Iranian sheep breeds. PLoS One 2024; 19:e0309023. [PMID: 39150936 PMCID: PMC11329119 DOI: 10.1371/journal.pone.0309023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/31/2024] [Indexed: 08/18/2024] Open
Abstract
The present study aimed to identify the selection signature associated with temperature adaptation in Iranian sheep breeds raised in cold and hot environments. The Illumina HD ovine SNP600K BeadChip genomic arrays were utilized to analyze 114 animals from eight Iranian sheep breeds, namely Ghezel, Afshari, Shall, Sanjabi, Lori-Bakhtiari, Karakul, Kermani, and Balochi. All animals were classified into two groups: cold-weather breeds and hot-weather breeds, based on the environments to which they are adapted and the regions where they have been raised for many years. The unbiased FST (Theta) and hapFLK tests were used to identify the selection signatures. The results revealed five genomic regions on chromosomes 2, 10, 11, 13, and 14 using the FST test, and three genomic regions on chromosomes 10, 14, and 15 using the hapFLK test to be under selection in cold and hot groups. Further exploration of these genomic regions revealed that most of these regions overlapped with genes previously identified to affect cold and heat stress, nervous system function, cell division and gene expression, skin growth and development, embryo and skeletal development, adaptation to hypoxia conditions, and the immune system. These regions overlapped with QTLs that had previously been identified as being associated with various important economic traits, such as body weight, skin color, and horn characteristics. The gene ontology and gene network analyses revealed significant pathways and networks that distinguished Iranian cold and hot climates sheep breeds from each other. We identified positively selected genomic regions in Iranian sheep associated with pathways related to cell division, biological processes, cellular responses to calcium ions, metal ions and inorganic substances. This study represents the initial effort to identify selective sweeps linked to temperature adaptation in Iranian indigenous sheep breeds. It may provide valuable insights into the genomic regions involved in climate adaptation in sheep.
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Affiliation(s)
- Zahra Patiabadi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Mohammad Razmkabir
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | | | | | - Amir Rashidi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Peyman Mahmoudi
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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2
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Wang Y, Cheng S, Fleishman JS, Chen J, Tang H, Chen ZS, Chen W, Ding M. Targeting anoikis resistance as a strategy for cancer therapy. Drug Resist Updat 2024; 75:101099. [PMID: 38850692 DOI: 10.1016/j.drup.2024.101099] [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: 04/07/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Anoikis, known as matrix detachment-induced apoptosis or detachment-induced cell death, is crucial for tissue development and homeostasis. Cancer cells develop means to evade anoikis, e.g. anoikis resistance, thereby allowing for cells to survive under anchorage-independent conditions. Uncovering the mechanisms of anoikis resistance will provide details about cancer metastasis, and potential strategies against cancer cell dissemination and metastasis. Here, we summarize the principal elements and core molecular mechanisms of anoikis and anoikis resistance. We discuss the latest progress of how anoikis and anoikis resistance are regulated in cancers. Furthermore, we summarize emerging data on selective compounds and nanomedicines, explaining how inhibiting anoikis resistance can serve as a meaningful treatment modality against cancers. Finally, we discuss the key limitations of this therapeutic paradigm and possible strategies to overcome them. In this review, we suggest that pharmacological modulation of anoikis and anoikis resistance by bioactive compounds could surmount anoikis resistance, highlighting a promising therapeutic regimen that could be used to overcome anoikis resistance in cancers.
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Affiliation(s)
- Yumin Wang
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing 100049, China
| | - Sihang Cheng
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Joshua S Fleishman
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Jichao Chen
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing 100049, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
| | - Wenkuan Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| | - Mingchao Ding
- Department of Peripheral Vascular Intervention, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing 100049, China.
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3
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Parolek J, Burd CG. Bridge-like lipid transfer protein family member 2 suppresses ciliogenesis. Mol Biol Cell 2024; 35:br11. [PMID: 38536441 PMCID: PMC11151097 DOI: 10.1091/mbc.e24-02-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Bridge-like lipid transfer protein family member 2 (BLTP2) is an evolutionary conserved protein with unknown function(s). The absence of BLTP2 in Drosophila melanogaster results in impaired cellular secretion and larval death, while in mice (Mus musculus), it causes preweaning lethality. Structural predictions propose that BLTP2 belongs to the repeating β-groove domain-containing (also called the VPS13) protein family, forming a long tube with a hydrophobic core, suggesting that it operates as a lipid transfer protein (LTP). We establish BLTP2 as a negative regulator of ciliogenesis in RPE-1 cells based on a strong genetic interaction with WDR44, a gene that also suppresses ciliogenesis. Like WDR44, BLTP2 localizes to membrane contact sites involving the endoplasmic reticulum and the tubular endosome network in HeLa cells and that BLTP2 depletion enhanced ciliogenesis in RPE-1 cells grown in serum-containing medium, a condition where ciliogenesis is normally suppressed. This study establishes human BLTP2 as a putative LTP acting between tubular endosomes and ER that regulates primary cilium biogenesis.
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Affiliation(s)
- Jan Parolek
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
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4
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Gao L, Wei Z, Ying F, Huang L, Zhang J, Sun S, Wang Z, Cai J, Zhang Y. Glutamine metabolism prognostic index predicts tumour microenvironment characteristics and therapeutic efficacy in ovarian cancer. J Cell Mol Med 2024; 28:e18198. [PMID: 38506093 PMCID: PMC10951877 DOI: 10.1111/jcmm.18198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/17/2024] [Accepted: 02/09/2024] [Indexed: 03/21/2024] Open
Abstract
Mounting evidence has highlighted the multifunctional characteristics of glutamine metabolism (GM) in cancer initiation, progression and therapeutic regimens. However, the overall role of GM in the tumour microenvironment (TME), clinical stratification and therapeutic efficacy in patients with ovarian cancer (OC) has not been fully elucidated. Here, three distinct GM clusters were identified and exhibited different prognostic values, biological functions and immune infiltration in TME. Subsequently, glutamine metabolism prognostic index (GMPI) was constructed as a new scoring model to quantify the GM subtypes and was verified as an independent predictor of OC. Patients with low-GMPI exhibited favourable survival outcomes, lower enrichment of several oncogenic pathways, less immunosuppressive cell infiltration and better immunotherapy responses. Single-cell sequencing analysis revealed a unique evolutionary trajectory of OC cells from high-GMPI to low-GMPI, and OC cells with different GMPI might communicate with distinct cell populations through ligand-receptor interactions. Critically, the therapeutic efficacy of several drug candidates was validated based on patient-derived organoids (PDOs). The proposed GMPI could serve as a reliable signature for predicting patient prognosis and contribute to optimising therapeutic strategies for OC.
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Affiliation(s)
- Lingling Gao
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Zheng Wei
- Department of Obstetrics and GynecologyThird Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi HospitalTaiyuanChina
| | - Feiquan Ying
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Lin Huang
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Jingni Zhang
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Si Sun
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Zehua Wang
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Jing Cai
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Yuan Zhang
- Department of Obstetrics and Gynecology, Union HospitalTongji Medical College, Huazhong University of Science and TechnologyWuhanChina
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Banerjee S, Daetwyler S, Bai X, Michaud M, Jouhet J, Madhugiri S, Johnson E, Wang CW, Fiolka R, Toulmay A, Prinz WA. The Vps13-like protein BLTP2 is pro-survival and regulates phosphatidylethanolamine levels in the plasma membrane to maintain its fluidity and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578804. [PMID: 38370643 PMCID: PMC10871178 DOI: 10.1101/2024.02.04.578804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Lipid transport proteins (LTPs) facilitate nonvesicular lipid exchange between cellular compartments and have critical roles in lipid homeostasis1. A new family of bridge-like LTPs (BLTPs) is thought to form lipid-transporting conduits between organelles2. One, BLTP2, is conserved across species but its function is not known. Here, we show that BLTP2 and its homolog directly regulate plasma membrane (PM) fluidity by increasing the phosphatidylethanolamine (PE) level in the PM. BLTP2 localizes to endoplasmic reticulum (ER)-PM contact sites34, 5, suggesting it transports PE from the ER to the PM. We find BLTP2 works in parallel with another pathway that regulates intracellular PE distribution and PM fluidity6, 7. BLTP2 expression correlates with breast cancer aggressiveness8-10. We found BLTP2 facilitates growth of a human cancer cell line and sustains its aggressiveness in an in vivo model of metastasis, suggesting maintenance of PM fluidity by BLTP2 may be critical for tumorigenesis in humans.
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Affiliation(s)
- Subhrajit Banerjee
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofei Bai
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Morgane Michaud
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Juliette Jouhet
- Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG, LPCV, Grenoble, France
| | - Shruthi Madhugiri
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emma Johnson
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao-Wen Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alexandre Toulmay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William A Prinz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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6
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Ng JK, Chen Y, Akinwe TM, Heins HB, Mehinovic E, Chang Y, Payne ZL, Manuel JG, Karchin R, Turner TN. Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.02.24302238. [PMID: 38352539 PMCID: PMC10863034 DOI: 10.1101/2024.02.02.24302238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Missense de novo variants (DNVs) and missense somatic variants contribute to neurodevelopmental disorders (NDDs) and cancer, respectively. Proteins with statistical enrichment based on analyses of these variants exhibit convergence in the differing NDD and cancer phenotypes. Herein, the question of why some of the same proteins are identified in both phenotypes is examined through investigation of clustering of missense variation at the protein level. Our hypothesis is that missense variation is present in different protein locations in the two phenotypes leading to the distinct phenotypic outcomes. We tested this hypothesis in 1D protein space using our software CLUMP. Furthermore, we newly developed 3D-CLUMP that uses 3D protein structures to spatially test clustering of missense variation for proteome-wide significance. We examined missense DNVs in 39,883 parent-child sequenced trios with NDDs and missense somatic variants from 10,543 sequenced tumors covering five TCGA cancer types and two COSMIC pan-cancer aggregates of tissue types. There were 57 proteins with proteome-wide significant missense variation clustering in NDDs when compared to cancers and 79 proteins with proteome-wide significant missense clustering in cancers compared to NDDs. While our main objective was to identify differences in patterns of missense variation, we also identified a novel NDD protein BLTP2. Overall, our study is innovative, provides new insights into differential missense variation in NDDs and cancer at the protein-level, and contributes necessary information toward building a framework for thinking about prognostic and therapeutic aspects of these proteins.
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Affiliation(s)
- Jeffrey K. Ng
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yilin Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Titilope M. Akinwe
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hillary B. Heins
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elvisa Mehinovic
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoonhoo Chang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Human & Statistical Genetics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary L. Payne
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Molecular Genetics & Genomics Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juana G. Manuel
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- The Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tychele N. Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
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7
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Dai Y, Zhang X, Ou Y, Zou L, Zhang D, Yang Q, Qin Y, Du X, Li W, Yuan Z, Xiao Z, Wen Q. Anoikis resistance--protagonists of breast cancer cells survive and metastasize after ECM detachment. Cell Commun Signal 2023; 21:190. [PMID: 37537585 PMCID: PMC10399053 DOI: 10.1186/s12964-023-01183-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/04/2023] [Indexed: 08/05/2023] Open
Abstract
Breast cancer exhibits the highest global incidence among all tumor types. Regardless of the type of breast cancer, metastasis is a crucial cause of poor prognosis. Anoikis, a form of apoptosis initiated by cell detachment from the native environment, is an outside-in process commencing with the disruption of cytosolic connectors such as integrin-ECM and cadherin-cell. This disruption subsequently leads to intracellular cytoskeletal and signaling pathway alterations, ultimately activating caspases and initiating programmed cell death. Development of an anoikis-resistant phenotype is a critical initial step in tumor metastasis. Breast cancer employs a series of stromal alterations to suppress anoikis in cancer cells. Comprehensive investigation of anoikis resistance mechanisms can inform strategies for preventing and regressing metastatic breast cancer. The present review first outlines the physiological mechanisms of anoikis, elucidating the alterations in signaling pathways, cytoskeleton, and protein targets that transpire from the outside in upon adhesion loss in normal breast cells. The specific anoikis resistance mechanisms induced by pathological changes in various spatial structures during breast cancer development are also discussed. Additionally, the genetic loci of targets altered in the development of anoikis resistance in breast cancer, are summarized. Finally, the micro-RNAs and targeted drugs reported in the literature concerning anoikis are compiled, with keratocin being the most functionally comprehensive. Video Abstract.
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Affiliation(s)
- Yalan Dai
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Department of Oncology, Garze Tibetan Autonomous Prefecture People's Hospital, Kangding, China
| | - Xinyi Zhang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Yingjun Ou
- Clinical Medicine School, Southwest Medicial Univercity, Luzhou, China
- Orthopaedics, Garze Tibetan Autonomous Prefecture People's Hospital, Kangding, China
| | - Linglin Zou
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Duoli Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Qingfan Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yi Qin
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiuju Du
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Wei Li
- Southwest Medical University, Luzhou, China
| | | | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
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8
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Ding YC, Song H, Adamson AW, Schmolze D, Hu D, Huntsman S, Steele L, Patrick CS, Tao S, Hernandez N, Adams CD, Fejerman L, Gardner K, Nápoles AM, Pérez-Stable EJ, Weitzel JN, Bengtsson H, Huang FW, Neuhausen SL, Ziv E. Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics. Cancer Res 2023; 83:2600-2613. [PMID: 37145128 PMCID: PMC10390863 DOI: 10.1158/0008-5472.can-22-2510] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/16/2023] [Accepted: 05/02/2023] [Indexed: 05/06/2023]
Abstract
Somatic mutational profiling is increasingly being used to identify potential targets for breast cancer. However, limited tumor-sequencing data from Hispanic/Latinas (H/L) are available to guide treatment. To address this gap, we performed whole-exome sequencing (WES) and RNA sequencing on 146 tumors and WES of matched germline DNA from 140 H/L women in California. Tumor intrinsic subtype, somatic mutations, copy-number alterations, and expression profiles of the tumors were characterized and compared with data from tumors of non-Hispanic White (White) women in The Cancer Genome Atlas (TCGA). Eight genes were significantly mutated in the H/L tumors including PIK3CA, TP53, GATA3, MAP3K1, CDH1, CBFB, PTEN, and RUNX1; the prevalence of mutations in these genes was similar to that observed in White women in TCGA. Four previously reported Catalogue of Somatic Mutations in Cancer (COSMIC) mutation signatures (1, 2, 3, 13) were found in the H/L dataset, along with signature 16 that has not been previously reported in other breast cancer datasets. Recurrent amplifications were observed in breast cancer drivers including MYC, FGFR1, CCND1, and ERBB2, as well as a recurrent amplification in 17q11.2 associated with high KIAA0100 gene expression that has been implicated in breast cancer aggressiveness. In conclusion, this study identified a higher prevalence of COSMIC signature 16 and a recurrent copy-number amplification affecting expression of KIAA0100 in breast tumors from H/L compared with White women. These results highlight the necessity of studying underrepresented populations. SIGNIFICANCE Comprehensive characterization of genomic and transcriptomic alterations in breast tumors from Hispanic/Latina patients reveals distinct genetic alterations and signatures, demonstrating the importance of inclusive studies to ensure equitable care for patients. See related commentary by Schmit et al., p. 2443.
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Affiliation(s)
- Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Hanbing Song
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Aaron W. Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Daniel Schmolze
- Department of Pathology, City of Hope Medical Center, Duarte, California
| | - Donglei Hu
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Scott Huntsman
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Carmina S. Patrick
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Shu Tao
- Integrative Genomics Shared Resource, Beckman Research Institute of City of Hope, Duarte, California
| | - Natalie Hernandez
- Western University of Health Sciences College of Graduate Nursing, Pomona, California
| | | | - Laura Fejerman
- Department of Public Health Sciences and Comprehensive Cancer Center, University of California Davis, Davis, California
| | - Kevin Gardner
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, New York
| | - Anna María Nápoles
- Division of Intramural Research, National Institute on Minority and Health Disparities, National Institutes of Health, Bethesda, Maryland
| | | | | | - Henrik Bengtsson
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Franklin W. Huang
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
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9
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Peerapen P, Sueksakit K, Boonmark W, Yoodee S, Thongboonkerd V. ARID1A knockdown enhances carcinogenesis features and aggressiveness of Caco-2 colon cancer cells: An in vitro cellular mechanism study. J Cancer 2022; 13:373-384. [PMID: 35069887 PMCID: PMC8771531 DOI: 10.7150/jca.65511] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/30/2021] [Indexed: 01/05/2023] Open
Abstract
Loss of ARID1A, a tumor suppressor gene, is associated with the higher grade of colorectal cancer (CRC). However, molecular and cellular mechanisms underlying the progression and aggressiveness of CRC induced by the loss of ARID1A remain poorly understood. Herein, we evaluated cellular mechanisms underlying the effects of ARID1A knockdown on the carcinogenesis features and aggressiveness of CRC cells. A human CRC cell line (Caco-2) was transfected with small interfering RNA (siRNA) specific to ARID1A (siARID1A) or scrambled (non-specific) siRNA (siControl). Cell death, proliferation, senescence, chemoresistance and invasion were then evaluated. In addition, formation of polyploid giant cancer cells (PGCCs), self-aggregation (multicellular spheroid) and secretion of an angiogenic factor, vascular endothelial growth factor (VEGF), were examined. The results showed that ARID1A knockdown led to significant decreases in cell death and senescence. On the other hand, ARID1A knockdown enhanced cell proliferation, chemoresistance and invasion. The siARID1A-transfected cells also had greater number of PGCCs and larger spheroid size and secreted greater level of VEGF compared with the siControl-transfected cells. These data, at least in part, explain the cellular mechanisms of ARID1A deficiency in carcinogenesis and aggressiveness features of CRC.
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Affiliation(s)
- Paleerath Peerapen
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Kanyarat Sueksakit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanida Boonmark
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sunisa Yoodee
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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10
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Aurrière J, Goudenège D, Baris OR, Boguenet M, May-Panloup P, Lenaers G, Khiati S. Cancer/Testis Antigens into mitochondria: a hub between spermatogenesis, tumorigenesis and mitochondrial physiology adaptation. Mitochondrion 2020; 56:73-81. [PMID: 33220498 DOI: 10.1016/j.mito.2020.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/18/2020] [Accepted: 11/02/2020] [Indexed: 01/05/2023]
Abstract
Cancer/Testis Antigens (CTAs) genes are expressed only during spermatogenesis and tumorigenesis. Both processes share common specific metabolic adaptation related to energy supply, with a glucose to lactate gradient, leading to changes in mitochondrial physiology paralleling CTAs expression. In this review, we address the role of CTAs in mitochondria (mitoCTAs), by reviewing all published data, and assessing the putative localization of CTAs by screening for the presence of a mitochondrial targeting sequence (MTS). We evidenced that among the 276 CTAs, five were already shown to interfere with mitochondrial activities and 67 display a potential MTS.
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Affiliation(s)
- Jade Aurrière
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - David Goudenège
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France; Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Olivier R Baris
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - Magalie Boguenet
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - Pascale May-Panloup
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France; Reproductive Biology Unit, Angers University Hospital, 49000 Angers, France
| | - Guy Lenaers
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - Salim Khiati
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France.
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11
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Wang W, Wang S, Pan L. Identification of key differentially expressed mRNAs and microRNAs in non-small cell lung cancer using bioinformatics analysis. Exp Ther Med 2020; 20:3720-3732. [PMID: 32855723 PMCID: PMC7444408 DOI: 10.3892/etm.2020.9105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a leading cause of mortality worldwide. However, the pathogenesis of NSCLC remains to be fully elucidated. Therefore, the present study aimed to explore the differential expression of mRNAs and microRNAs (miRNAs/miRs) in NSCLC and to determine how these RNA molecules interact with one another to affect disease progression. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were identified from the GSE18842, GSE32863 and GSE29250 datasets downloaded from the Gene Expression Omnibus (GEO database). Functional and pathway enrichment analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. STRING, Cytoscape and MCODE were applied to construct a protein-protein interaction (PPI) network and to screen hub genes. The interactions between miRNAs and mRNAs were predicted using miRWalk 3.0 and a miRNA-mRNA regulatory network was constructed. The prognostic value of the identified hub genes was then evaluated via Kaplan-Meier survival analyses using datasets from The Cancer Genome Atlas. A total of 782 DEGs and 46 DEMs were identified from the 3 GEO datasets. The enriched pathways and functions of the DEGs and target genes of the DEMs included osteoclast differentiation, cell adhesion, response to a drug, plasma membrane, extracellular exosome and protein binding. A subnetwork composed of 11 genes was extracted from the PPI network and the genes in this subnetwork were mainly involved in the cell cycle, cell division and DNA replication. A miRNA-gene regulatory network was constructed with 247 miRNA-gene pairs based on 6 DEMs and 210 DEGs. Kaplan-Meier survival analysis indicated that the expression of ubiquitin E2 ligase C, cell division cycle protein 20, DNA topoisomerase IIα, aurora kinase A and B, cyclin B2, maternal embryonic leucine zipper kinase, slit guidance ligand 3, phosphoglucomutase 5, endomucin, cysteine dioxygenase type 1, dihydropyrimidinase-like 2, miR-130b, miR-1181 and miR-127 was significantly associated with overall survival of patients with lung adenocarcinoma. In the present study, a miRNA-mRNA regulatory network in NSCLC was established, which may provide future avenues for scientific exploration and therapeutic targeting of NSCLC.
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Affiliation(s)
- Weiwei Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Shanshan Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
| | - Lei Pan
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, P.R. China
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12
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Zhang S, Wang B, Xiao H, Dong J, Li Y, Zhu C, Jin Y, Li H, Cui M, Fan S. LncRNA HOTAIR enhances breast cancer radioresistance through facilitating HSPA1A expression via sequestering miR-449b-5p. Thorac Cancer 2020; 11:1801-1816. [PMID: 32374522 PMCID: PMC7327697 DOI: 10.1111/1759-7714.13450] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Breast cancer (BRCA) is the leading cause of cancer-related death in women worldwide. Pre- and postoperative radiotherapy play a pivotal role in BRCA treatment but its efficacy remains limited and plagued by the emergence of radiation resistance, which aggravates patient prognosis. The long noncoding RNA (lncRNA)-implicated mechanisms underlying radiation resistance are rarely reported. The aim of this study was to determine whether lncRNA HOX transcript antisense RNA (HOTAIR) modulated the radiosensitivity of breast cancer through HSPA1A. METHODS A Gammacell 40 Exactor was used for irradiation treatment. Bioinformatic tools and luciferase reporter assay were adopted to explore gene expression profile and demonstrate the interactions between lncRNA, miRNA and target mRNA 3'-untranslated region (3'-UTR). The expression levels of certain genes were determined by real-time PCR and western-blot analyses. in vitro and in vivo functional assays were conducted by cell viability and tumorigenicity assays. RESULTS The levels of oncogenic lncRNA HOTAIR were positively correlated with the malignancy of BRCA but reversely correlated with the radiosensitivity of breast cancer cells. Moreover, the expression levels of HOTAIR were positively associated with those of heat shock protein family A (Hsp70) member 1A (HSPA1A) in clinical BRCA tissues and HOTAIR upregulated HSPA1A at the mRNA and protein levels in irradiated BRCA cells. Mechanistically, miR-449b-5p restrained HSPA1A expression through targeting the 3'-UTR of HSPA1A mRNA, whereas HOTAIR acted as a competing sponge to sequester miR-449b-5p and thereby relieved the miR-449b-5p-mediated HSPA1A repression. Functionally, HOTAIR conferred decreased radiosensitivity on BRCA cells, while miR-449b-5p overexpression or HSPA1A knockdown abrogated the HOTAIR-enhanced BRCA growth under the irradiation exposure both in vitro and in vivo. CONCLUSIONS LncRNA HOTAIR facilitates the expression of HSPA1A by sequestering miR-449b-5p post-transcriptionally and thereby endows BRCA with radiation resistance. KEY POINTS Therapeutically, HOTAIR and HSPA1A may be employed as potential targets for BRCA radiotherapy. Our findings shed new light into the mechanism by which lncRNAs modulate the radiosensitivity of tumors.
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Affiliation(s)
- Shuqin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Bin Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Huiwen Xiao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Yuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Changchun Zhu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Yuxiao Jin
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Hang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Ming Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear MedicineInstitute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical CollegeTianjinChina
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13
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Caffeine and Cisplatin Effectively Targets the Metabolism of a Triple-Negative Breast Cancer Cell Line Assessed via Phasor-FLIM. Int J Mol Sci 2020; 21:ijms21072443. [PMID: 32244616 PMCID: PMC7177700 DOI: 10.3390/ijms21072443] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Triple-negative tumor cells, a malignant subtype of breast cancer, lack a biologically targeted therapy. Given its DNA repair inhibiting properties, caffeine has been shown to enhance the effectiveness of specific tumor chemotherapies. In this work, we have investigated the effects of caffeine, cisplatin, and a combination of the two as potential treatments in energy metabolism for three cell lines, triple-negative breast cancer (MDA-MB-231), estrogen-receptor lacking breast cancer (MCF7) and breast epithelial cells (MCF10A) using a sensitive label-free approach, phasor-fluorescence lifetime imaging microscopy (phasor-FLIM). We found that solely using caffeine to treat MDA-MB-231 shifts their metabolism towards respiratory-chain phosphorylation with a lower ratio of free to bound NADH, and a similar trend is seen in MCF7. However, MDA-MB-231 cells shifted to a higher ratio of free to bound NADH when cisplatin was added. The combination of cisplatin and caffeine together reduced the survival rate for MDA-MD231 and shifted their energy metabolism to a higher fraction of bound NADH indicative of oxidative phosphorylation. The FLIM and viability results of MCF10A cells demonstrate that the treatments targeted cancer cells over the normal breast tissue. The identification of energy metabolism alteration could open up strategies of improving chemotherapy for malignant breast cancer.
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