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Ergun P, Kipcak S, Gunel NS, Bor S, Sozmen EY. Roles of Cytokines in Pathological and Physiological Gastroesophageal Reflux Exposure. J Neurogastroenterol Motil 2024; 30:290-302. [PMID: 37957115 PMCID: PMC11238103 DOI: 10.5056/jnm22186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/29/2023] [Accepted: 04/10/2023] [Indexed: 11/15/2023] Open
Abstract
Background/Aims Gastroesophageal reflux disease is frequently observed and has no definitive treatment. There are 2 main views on the pathogenesis of gastroesophageal reflux disease. The first is that epithelial damage starts from the mucosa by acidic-peptic damage and the inflammatory response of granulocytes. The other view is that T-lymphocytes attract chemoattractants from the basal layer to the mucosa, and granulocytes do not migrate until damage occurs. We aim to investigate the inflammatory processes occurring in the esophageal epithelium of the phenotypes at the molecular level. We also examined the effects of these changes on tissue integrity. Methods Patients with mild and severe erosive reflux, nonerosive reflux, reflux hypersensitivity, and functional heartburn were included. Inflammatory gene expressions (JAK/STAT Signaling and NFKappaB Primer Libraries), chemokine protein levels, and tissue integrity were examined in the esophageal biopsies. Results There was chronic inflammation in the severe erosion group, the acute response was also triggered. In the mild erosion group, these 2 processes worked together, but homeostatic cytokines were also secreted. In nonerosive groups, T-lymphocytes were more dominant. In addition, the inflammatory response was highly triggered in the reflux hypersensitivity and functional heartburn groups, and it was associated with physiological reflux exposure and sensitivity. Conclusions "Microinflammation" in physiological acid exposure groups indicates that even a mild trigger is sufficient for the initiation and progression of inflammatory activity. Additionally, the anti-inflammatory cytokines were highly increased. The results may have a potential role in the treatment of heartburn symptoms and healing of the mucosa.
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Affiliation(s)
- Pelin Ergun
- Departments of Medical Biochemistry, Faculty of Medicine, Ege University, Izmir, Turkey
- Division of Gastroenterology, Faculty of Medicine, Ege University, Ege Reflux Study Group, Izmir, Turkey
| | - Sezgi Kipcak
- Departments of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
- Division of Gastroenterology, Faculty of Medicine, Ege University, Ege Reflux Study Group, Izmir, Turkey
| | - Nur S Gunel
- Departments of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Serhat Bor
- Division of Gastroenterology, Faculty of Medicine, Ege University, Ege Reflux Study Group, Izmir, Turkey
| | - Eser Y Sozmen
- Departments of Medical Biochemistry, Faculty of Medicine, Ege University, Izmir, Turkey
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2
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Goleij P, Pourali G, Raisi A, Ravaei F, Golestan S, Abed A, Razavi ZS, Zarepour F, Taghavi SP, Ahmadi Asouri S, Rafiei M, Mousavi SM, Hamblin MR, Talei S, Sheida A, Mirzaei H. Role of Non-coding RNAs in the Response of Glioblastoma to Temozolomide. Mol Neurobiol 2024:10.1007/s12035-024-04316-z. [PMID: 39023794 DOI: 10.1007/s12035-024-04316-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 06/16/2024] [Indexed: 07/20/2024]
Abstract
Chemotherapy and radiotherapy are widely used in clinical practice across the globe as cancer treatments. Intrinsic or acquired chemoresistance poses a significant problem for medical practitioners and researchers, causing tumor recurrence and metastasis. The most dangerous kind of malignant brain tumor is called glioblastoma multiforme (GBM) that often recurs following surgery. The most often used medication for treating GBM is temozolomide chemotherapy; however, most patients eventually become resistant. Researchers are studying preclinical models that accurately reflect human disease and can be used to speed up drug development to overcome chemoresistance in GBM. Non-coding RNAs (ncRNAs) have been shown to be substantial in regulating tumor development and facilitating treatment resistance in several cancers, such as GBM. In this work, we mentioned the mechanisms of how different ncRNAs (microRNAs, long non-coding RNAs, circular RNAs) can regulate temozolomide chemosensitivity in GBM. We also address the role of these ncRNAs encapsulated inside secreted exosomes.
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Affiliation(s)
- Pouya Goleij
- Department of Genetics, Faculty of Biology, Sana Institute of Higher Education, Sari, Iran
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ghazaleh Pourali
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arash Raisi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Ravaei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Shahin Golestan
- Department of Ophthalmology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atena Abed
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Zahra Sadat Razavi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Zarepour
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Pouya Taghavi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Moein Rafiei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Mojtaba Mousavi
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
| | - Sahand Talei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Amirhossein Sheida
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran.
| | - Hamed Mirzaei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Vasei H, Foroughmand-Araabi MH, Daneshgar A. Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference. Bioinformatics 2024; 40:btae120. [PMID: 38984735 DOI: 10.1093/bioinformatics/btae120] [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: 09/21/2023] [Revised: 02/19/2024] [Accepted: 07/09/2024] [Indexed: 07/11/2024] Open
Abstract
MOTIVATION Tumor trees, which depict the evolutionary process of cancer, provide a backbone for discovering recurring evolutionary processes in cancer. While they are not the primary information extracted from genomic data, they are valuable for this purpose. One such extraction method involves summarizing multiple trees into a single representative tree, such as consensus trees or supertrees. RESULTS We define the "weighted centroid tree problem" to find the centroid tree of a set of single-labeled rooted trees through the following steps: (i) mapping the given trees into the Euclidean space, (ii) computing the weighted centroid matrix of the mapped trees, and (iii) finding the nearest mapped tree (NMTP) to the centroid matrix. We show that this setup encompasses previously studied parent-child and ancestor-descendent metrics as well as the GraPhyC and TuELiP consensus tree algorithms. Moreover, we show that, while the NMTP problem is polynomial-time solvable for the adjacency embedding, it is NP-hard for ancestry and distance mappings. We introduce integer linear programs for NMTP in different setups where we also provide a new algorithm for the case of ancestry embedding called 2-AncL2, that uses a novel weighting scheme for ancestry signals. Our experimental results show that 2-AncL2 has a superior performance compared to available consensus tree algorithms. We also illustrate our setup's application on providing representative trees for a large real breast cancer dataset, deducing that the cluster centroid trees summarize reliable evolutionary information about the original dataset. AVAILABILITY AND IMPLEMENTATION https://github.com/vasei/WAncILP.
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Affiliation(s)
- Hamed Vasei
- Department of Mathematical Sciences, Sharif University of Technology, Tehran 111559415, Iran
| | | | - Amir Daneshgar
- Department of Mathematical Sciences, Sharif University of Technology, Tehran 111559415, Iran
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Faridi R, Yousaf R, Inagaki S, Olszewski R, Gu S, Morell RJ, Wilson E, Xia Y, Qaiser TA, Rashid M, Fenollar-Ferrer C, Hoa M, Riazuddin S, Friedman TB. Deafness DFNB128 Associated with a Recessive Variant of Human MAP3K1 Recapitulates Hearing Loss of Map3k1-Deficient Mice. Genes (Basel) 2024; 15:845. [PMID: 39062623 PMCID: PMC11276321 DOI: 10.3390/genes15070845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
Deafness in vertebrates is associated with variants of hundreds of genes. Yet, many mutant genes causing rare forms of deafness remain to be discovered. A consanguineous Pakistani family segregating nonsyndromic deafness in two sibships were studied using microarrays and exome sequencing. A 1.2 Mb locus (DFNB128) on chromosome 5q11.2 encompassing six genes was identified. In one of the two sibships of this family, a novel homozygous recessive variant NM_005921.2:c.4460G>A p.(Arg1487His) in the kinase domain of MAP3K1 co-segregated with nonsyndromic deafness. There are two previously reported Map3k1-kinase-deficient mouse models that are associated with recessively inherited syndromic deafness. MAP3K1 phosphorylates serine and threonine and functions in a signaling pathway where pathogenic variants of HGF, MET, and GAB1 were previously reported to be associated with human deafness DFNB39, DFNB97, and DFNB26, respectively. Our single-cell transcriptome data of mouse cochlea mRNA show expression of Map3k1 and its signaling partners in several inner ear cell types suggesting a requirement of wild-type MAP3K1 for normal hearing. In contrast to dominant variants of MAP3K1 associated with Disorders of Sex Development 46,XY sex-reversal, our computational modeling of the recessive substitution p.(Arg1487His) predicts a subtle structural alteration in MAP3K1, consistent with the limited phenotype of nonsyndromic deafness.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Sayaka Inagaki
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Shoujun Gu
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Robert J. Morell
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - Elizabeth Wilson
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Ying Xia
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Tanveer Ahmed Qaiser
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Sector G-8/3, Ravi Road, Islamabad 44000, Pakistan;
| | - Muhammad Rashid
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Center, Jinnah Burn and Reconstructive Surgery Center, University of Health Sciences, Lahore 54550, Pakistan;
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
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Takeshita T, Iwamoto T, Niikura N, Watanabe K, Kikawa Y, Kobayashi K, Iwakuma N, Okamura T, Tada H, Ozaki S, Okuno T, Toh U, Yamamoto Y, Tsuneizumi M, Ishiguro H, Masuda N, Saji S. Identifying prognostic biomarkers for palbociclib add-on therapy in fulvestrant-resistant breast cancer using cell-free DNA sequencing. ESMO Open 2024; 9:102385. [PMID: 38387111 PMCID: PMC11076976 DOI: 10.1016/j.esmoop.2024.102385] [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: 11/22/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The FUTURE trial (UMIN000029294) demonstrated the safety and efficacy of adding palbociclib after fulvestrant resistance in patients with hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) advanced and metastatic breast cancer (ABC/MBC). In this planned sub-study, cancer panel sequencing of cell-free DNA (cfDNA) was utilized to explore prognostic and predictive biomarkers for further palbociclib treatment following fulvestrant resistance. MATERIALS AND METHODS Herein, 149 cfDNA samples from 65 patients with fulvestrant-resistant disease were analysed at the time of palbociclib addition after fulvestrant resistance (baseline), on day 15 of cycle 1, and at the end of treatment using the assay for identifying diverse mutations in 34 cancer-related genes. RESULTS During the course of treatment, mutations in ESR1, PIK3CA, FOXA1, RUNX1, TBX3, and TP53 were the most common genomic alterations observed. Analysis of genomic mutations revealed that before fulvestrant introduction, baseline PIK3CA mutations were marginally lower in metastatic aromatase inhibitor (AI)-treated patients compared to adjuvant AI-treated patients (P = 0.063). Baseline PIK3CA mutations were associated with poorer progression-free survival [hazard ratio: 1.62, P = 0.04]. Comparative analysis between baseline and early-changing gene mutations identified poor prognostic factors including early-changing MAP3K1 mutations (hazard ratio: 4.66, P = 0.04), baseline AR mutations (hazard ratio: 3.53, P = 0.04), and baseline PIK3CA mutations (hazard ratio: 3.41, P = 0.02). Notably, the relationship between ESR1 mutations and mutations in PIK3CA, MAP3K1, and TP53 weakened as treatment progressed. Instead, PIK3CA mutations became correlated with TP53 and FOXA1 mutations. CONCLUSIONS Cancer panel testing for cfDNA identified prognostic and predictive biomarkers for palbociclib add-on therapy after acquiring fulvestrant resistance in patients with HR+/HER2- ABC/MBC.
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Affiliation(s)
- T Takeshita
- Department of Breast and Endocrine Surgery, Kumamoto City Hospital, Kumamoto.
| | - T Iwamoto
- Department of Breast and Thyroid Surgery, Kawasaki Medical School Hospital, Kurashiki
| | - N Niikura
- Department of Breast Oncology, Tokai University School of Medicine, Isehara, Kanagawa
| | - K Watanabe
- Department of Breast Surgery, Hokkaido Cancer Center, Sapporo, Hokkaido
| | - Y Kikawa
- Department of Breast Surgery, Kansai Medical University Hospital, Hirakata, Osaka
| | - K Kobayashi
- Department of Medical Oncology, Saitama Red Cross Hospital, Chuo-ku, Saitama
| | - N Iwakuma
- Breast Center, Department of Breast Surgery, NHO Kyushu Medical Center, Fukuoka
| | - T Okamura
- Department of Breast Oncology, Tokai University School of Medicine, Isehara, Kanagawa
| | - H Tada
- Division of Breast and Endocrine Surgery, Tohoku University Graduate School of Medicine, Sendai, Miyagi
| | - S Ozaki
- Department of Gastrointestinal and Breast Surgery, Hiroshima Prefectural Hospital, Hiroshima
| | - T Okuno
- Department of Breast Surgery, Kobe City Nishi-Kobe Medical Center, Kobe, Hyogo
| | - U Toh
- Department of Breast Surgery, Kurume University Hospital, Kurume, Fukuoka
| | - Y Yamamoto
- Department of Breast and Endocrine Surgery, Kumamoto University Hospital, Kumamoto
| | - M Tsuneizumi
- Department of Breast Surgery, Shizuoka General Hospital, Shizuoka
| | - H Ishiguro
- Breast Oncology Service, Saitama Medical University International Medical Center, Hidaka, Saitama
| | - N Masuda
- Department of Breast and Endocrine Surgery, Nagoya University Graduate School of Medicine, Nagoya
| | - S Saji
- Department of Medical Oncology, Fukushima Medical University, School of Medicine, Fukushima, Japan
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Yamaoka S. RelA and mitogen-activated protein kinase kinase kinases potently enhance lentiviral vector production. Biochem Biophys Rep 2024; 37:101637. [PMID: 38328371 PMCID: PMC10847020 DOI: 10.1016/j.bbrep.2024.101637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
The growing demands for gene therapy have encouraged development of safe and efficient lentiviral vector (LV) preparation. While much progress has been made in this field, it remains to be explored how to boost its production from producer cells. This paper reports that transient co-expression of RelA or several mitogen-activated protein kinase kinase kinases (MAP3Ks) with packaging constructs can potently enhance LV production in HEK293T producer cells. Adding in transfection a small amount of effector plasmid is sufficient to achieve 3- to 4-fold enhancement, which can further be augmented by co-expression of IκB kinase 2 or HIV Tat. It is also shown that expression of RelA or MAP3K1 can increase LV production in HEK293T/17SF cells grown in suspension. These results indicate that stimulation of intracellular signaling pathways in producer cells represents a powerful means for enhancing LV production.
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Affiliation(s)
- Shoji Yamaoka
- Department of Parasitology and Tropical Medicine, Graduate School of Medicine and Dentistry, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan.
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7
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Caputo C, Falco M, Grimaldi A, Lombardi A, Miceli CC, Cocule M, Montella M, Pompella L, Tirino G, Campione S, Tammaro C, Cossu A, Fenu Pintori G, Maioli M, Coradduzza D, Savarese G, Fico A, Ottaiano A, Conzo G, Tathode MS, Ciardiello F, Caraglia M, De Vita F, Misso G. Identification of Tissue miRNA Signatures for Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2024; 16:824. [PMID: 38398215 PMCID: PMC10887387 DOI: 10.3390/cancers16040824] [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: 12/30/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), a neoplasm of the gastrointestinal tract, is the most common pancreatic malignancy (90%) and the fourth highest cause of cancer mortality worldwide. Surgery intervention is currently the only strategy able to offer an advantage in terms of overall survival, but prognosis remains poor even for operated patients. Therefore, the development of robust biomarkers for early diagnosis and prognostic stratification in clinical practice is urgently needed. In this work, we investigated deregulated microRNAs (miRNAs) in tissues from PDAC patients with high (G3) or low (G2) histological grade and with (N+) or without (N-) lymph node metastases. miRNA expression profiling was performed by a comprehensive PCR array and subsequent validation by RT-qPCR. The results showed a significant increase in miR-1-3p, miR-31-5p, and miR-205-5p expression in G3 compared to G2 patients (** p < 0.01; *** p < 0.001; *** p < 0.001). miR-518d-3p upregulation and miR-215-5p downregulation were observed in N+ compared to N- patients. A statistical analysis performed using OncomiR program showed the significant involvement (p < 0.05) of two miRNAs (miR-31 and miR-205) in the histological grade of PDAC patients. Also, an expression analysis in PDAC patients showed that miR-31 and miR-205 had the highest expression at grade 3 compared with normal and other tumor grades. Overall, survival plots confirmed that the overexpression of miR-31 and miR-205 was significantly correlated with decreased survival in TCGA PDAC clinical samples. A KEGG pathway analysis showed that all three miRNAs are involved in the regulation of multiple pathways, including the Hippo signaling, adherens junction and microRNAs in cancer, along with several target genes. Based on in silico analysis and experimental validation, our study suggests the potential role of miR-1-3p, miR-31-5p, and miR-205-5p as useful clinical biomarkers and putative therapeutic targets in PDAC, which should be further investigated to determine the specific molecular processes affected by their aberrant expression.
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Affiliation(s)
- Carlo Caputo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.); (M.F.); (C.T.); (M.S.T.); (F.C.); (M.C.)
| | - Michela Falco
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.); (M.F.); (C.T.); (M.S.T.); (F.C.); (M.C.)
- Laboratory of Precision and Molecular Oncology, Institute of Genetic Research, Biogem Scarl, Contrada Camporeale, 83031 Ariano Irpino, Italy
| | - Anna Grimaldi
- U.P. Cytometric and Mutational Diagnostics, AOU Policlinico, University of Campania “Luigi Vanvitelli”, Via Luciano Armanni 5, 83031 Naples, Italy;
| | - Angela Lombardi
- U.P. Cytometric and Mutational Diagnostics, AOU Policlinico, University of Campania “Luigi Vanvitelli”, Via Luciano Armanni 5, 83031 Naples, Italy;
| | - Chiara Carmen Miceli
- Department of Precision Medicine, Division of Medical Oncology, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.M.); (M.C.); (L.P.); (G.T.); (F.D.V.)
| | - Mariateresa Cocule
- Department of Precision Medicine, Division of Medical Oncology, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.M.); (M.C.); (L.P.); (G.T.); (F.D.V.)
| | - Marco Montella
- Department of Mental and Physical Health and Preventive Medicine, UOC Pathological Anatomy, University of Campania “Luigi Vanvitelli”, Via Luciano Armanni 5, 83031 Naples, Italy;
| | - Luca Pompella
- Department of Precision Medicine, Division of Medical Oncology, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.M.); (M.C.); (L.P.); (G.T.); (F.D.V.)
| | - Giuseppe Tirino
- Department of Precision Medicine, Division of Medical Oncology, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.M.); (M.C.); (L.P.); (G.T.); (F.D.V.)
| | - Severo Campione
- Division of Anatomic Pathology, A.O.R.N. Antonio Cardarelli, 80131 Naples, Italy;
| | - Chiara Tammaro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.); (M.F.); (C.T.); (M.S.T.); (F.C.); (M.C.)
| | - Antonio Cossu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Grazia Fenu Pintori
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (G.F.P.); (M.M.); (D.C.)
| | - Margherita Maioli
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (G.F.P.); (M.M.); (D.C.)
- Center for Developmental Biology and Reprogramming (CEDEBIOR), Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
| | - Donatella Coradduzza
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (G.F.P.); (M.M.); (D.C.)
| | - Giovanni Savarese
- AMES Center, Centro Polidiagnostico Strumentale SRL, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (G.S.); (A.F.)
| | - Antonio Fico
- AMES Center, Centro Polidiagnostico Strumentale SRL, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (G.S.); (A.F.)
| | - Alessandro Ottaiano
- Department of Abdominal Oncology, SSD-Innovative Therapies for Abdominal Metastases, Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, National Cancer Institute, 80131 Naples, Italy;
| | - Giovanni Conzo
- Division of General, Oncological, Mini-Invasive and Obesity Surgery, University of Study of Campania “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Madhura S. Tathode
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.); (M.F.); (C.T.); (M.S.T.); (F.C.); (M.C.)
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.); (M.F.); (C.T.); (M.S.T.); (F.C.); (M.C.)
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.); (M.F.); (C.T.); (M.S.T.); (F.C.); (M.C.)
- Laboratory of Precision and Molecular Oncology, Institute of Genetic Research, Biogem Scarl, Contrada Camporeale, 83031 Ariano Irpino, Italy
| | - Ferdinando De Vita
- Department of Precision Medicine, Division of Medical Oncology, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.M.); (M.C.); (L.P.); (G.T.); (F.D.V.)
| | - Gabriella Misso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (C.C.); (M.F.); (C.T.); (M.S.T.); (F.C.); (M.C.)
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Morales-Pison S, Tapia JC, Morales-González S, Maldonado E, Acuña M, Calaf GM, Jara L. Association of Germline Variation in Driver Genes with Breast Cancer Risk in Chilean Population. Int J Mol Sci 2023; 24:16076. [PMID: 38003265 PMCID: PMC10671568 DOI: 10.3390/ijms242216076] [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: 09/27/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Cancer is a genomic disease, with driver mutations contributing to tumorigenesis. These potentially heritable variants influence risk and underlie familial breast cancer (BC). This study evaluated associations between BC risk and 13 SNPs in driver genes MAP3K1, SF3B1, SMAD4, ARID2, ATR, KMT2C, MAP3K13, NCOR1, and TBX3, in BRCA1/2-negative Chilean families. SNPs were genotyped using TaqMan Assay in 492 cases and 1285 controls. There were no associations between rs75704921:C>T (ARID2); rs2229032:A>C (ATR); rs3735156:C>G (KMT2C); rs2276738:G>C, rs2293906:C>T, rs4075943T:>A, rs13091808:C>T (MAP3K13); rs178831:G>A (NCOR1); or rs3759173:C>A (TBX3) and risk. The MAP3K1 rs832583 A allele (C/A+A/A) showed a protective effect in families with moderate BC history (OR = 0.7 [95% CI 0.5-0.9] p = 0.01). SF3B1 rs16865677-T (G/T+T/T) increased risk in sporadic early-onset BC (OR = 1.4 [95% CI 1.0-2.0] p = 0.01). SMAD4 rs3819122-C (A/C+C/C) increased risk in cases with moderate family history (OR = 2.0 [95% CI 1.3-2.9] p ≤ 0.0001) and sporadic cases diagnosed ≤50 years (OR = 1.6 [95% CI 1.1-2.2] p = 0.006). SMAD4 rs12456284:A>G increased BC risk in G-allele carriers (A/G + G/G) in cases with ≥2 BC/OC cases and early-onset cases (OR = 1.2 [95% CI 1.0-1.6] p = 0.04 and OR = 1.4 [95% CI 1.0-1.9] p = 0.03, respectively). Our study suggests that specific germline variants in driver genes MAP3K1, SF3B1, and SMAD4 contribute to BC risk in Chilean population.
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Affiliation(s)
- Sebastián Morales-Pison
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Las Condes, Santiago 7560908, Chile;
| | - Julio C. Tapia
- Laboratorio de Transformación Celular, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Sarai Morales-González
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Edio Maldonado
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile;
| | - Mónica Acuña
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
| | - Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1010069, Chile;
| | - Lilian Jara
- Laboratorio de Genética Humana, Programa de Genética Humana, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia, Santiago 783090, Chile; (S.M.-G.); (M.A.)
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Black MA, Neumann NM, Krings G, Najjar S, Troxell ML, Wang A, Devine WP, Vohra P, Gasper C, Chen YY, Cohen JN, Bean GR. Genetic and Immunohistochemical Profiling of Mammary Hidradenoma and Comparison to Mucoepidermoid Carcinoma. Mod Pathol 2023; 36:100270. [PMID: 37422157 DOI: 10.1016/j.modpat.2023.100270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/18/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
Mucoepidermoid carcinoma (MEC) is exceedingly rare in the breast, with <45 cases reported in the literature. Although estrogen receptor/progesterone receptor/human epidermal growth factor 2 triple-negative, MEC is characterized as a special subtype of breast carcinoma with significantly better prognosis than conventional basal-type tumors. Cutaneous hidradenoma (HA) is considered a benign adnexal neoplasm showing histomorphologic overlap with MEC. Rare cases of HA have also been reported in the breast, but these are relatively uncharacterized. In this study, we examined the clinicopathologic, immunohistochemical (IHC), and genetic features of 8 breast HAs, in comparison to 3 mammary MECs. All cases were positive for MAML2 break-apart fluorescence in situ hybridization. Eight cases demonstrated a CRTC1::MAML2 fusion, and one MEC harbored a CRTC3::MAML2 fusion; the latter is a novel finding in the breast. Mutational burden was very low, with only one HA exhibiting a MAP3K1 pathogenic alteration. By IHC, both MEC and HA demonstrated cell type-dependent expression of high- and low-molecular-weight keratins and p63, as well as negative to low-positive estrogen receptor and androgen receptor. Smooth muscle myosin and calponin highlighted an in situ component in the 3 cases of MEC; expression of these myoepithelial markers was negative in HAs. Additional distinguishing characteristics included the growth pattern and tumor architecture, the presence of glandular/luminal cells in HA, and overall higher IHC expression of SOX10, S100 protein, MUC4, and mammaglobin in MEC. Morphologic findings were also compared to a series of 27 cutaneous nonmammary HAs. Mucinous and glandular/luminal cells were identified in significantly more mammary HAs than nonmammary lesions. The findings provide insight into the pathogenesis of MAML2-rearranged neoplasms of the breast, underscore the overlapping genetic features of MEC and HA, and highlight similarities to their extramammary counterparts.
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Affiliation(s)
- Margaret A Black
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Neil M Neumann
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Gregor Krings
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Saleh Najjar
- Department of Pathology, King Faisal Specialist Hospital & Research Centre, Saudi Arabia
| | - Megan L Troxell
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Aihui Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - W Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Poonam Vohra
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Cynthia Gasper
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Yunn-Yi Chen
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Jarish N Cohen
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Gregory R Bean
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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Kuo SH, Wei MF, Lee YH, Lin JC, Yang WC, Yang SY, Huang CS. MAP3K1 expression is associated with progression and poor prognosis of hormone receptor-positive, HER2-negative early-stage breast cancer. Cell Oncol (Dordr) 2023; 46:1213-1234. [PMID: 37166744 DOI: 10.1007/s13402-023-00805-w] [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] [Accepted: 03/26/2023] [Indexed: 05/12/2023] Open
Abstract
PURPOSE In this study, we assessed whether the overexpression of MAP3K1 promotes the proliferation, migration, and invasion of breast cancer cells, which affect the prognosis of hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative early stage breast cancer. METHODS Two HR-positive, HER2-negative breast cancer cell lines (MCF7 and T-47D) overexpressing MAP3K1 were transfected with two MAP3K1 short hairpin RNA plasmids (shMAP3K1 [#3] and shMAP3K1 [#5]). The proliferation, migration, and invasion of these cells were then examined. We assessed whether shMAP3K1 affects the cell cycle, levels of downstream signaling molecules (ERK, JNK, p38 MAPK, and NF-κB), and sensitivity to chemotherapeutic and hormonal agents. To assess the anti-tumor effect of MAP3K1 knockdown in the breast cancer orthotopic model, MCF7 and T-47D cells treated with or without shMAP3K1 (#3) and shMAP3K1 (#5) were inoculated into the mammary fat pads of mice. In total, 182 patients with HR-positive, HER2-negative T1 and T2 breast cancer and 0-3 nodal metastases were included. Additionally, 73 patients with T1 and T2 breast cancer and negative nodes who received adjuvant endocrine therapy alone were selected as an independent validation cohort. RESULTS In both cell lines, shMAP3K1 (#3) and shMAP3K1 (#5) significantly reduced cell growth, migration, and invasion by downregulating MMP-9 and by blocking the G2/M phase of the cell cycle and its regulatory molecule cyclin B1. Moreover, both shMAP3K1 (#3) and shMAP3K1 (#5) downregulated ERK-, JNK-, p38 MAPK-, and NF-κB-dependent gene transcription and enhanced the sensitivity of both cell lines to doxorubicin, docetaxel, and tamoxifen. We observed that both shMAP3K1 (#3) and shMAP3K1 (#5) inhibited tumor growth compared with that in the scrambled group of MCF7 and T-47D cell orthotopic tumors. Patients with MAP3K1 overexpression exhibited significantly poorer 10-year disease-free survival (DFS) (70.4% vs. 88.6%, p = 0.003) and overall survival (OS) (81.9% vs. 96.3%, p = 0.001) than those without MAP3K1 overexpression. Furthermore, phospho-ERK (p < 0.001) and phospho-JNK (p < 0.001) expressions were significantly associated with MAP3K1 expression, and both phospho-ERK and phospho-JNK expressions were significantly correlated with poor 10-year DFS and OS. These biological findings, including a significant association between DFS and OS, and the expressions of MAP3K1, phospho-ERK, and phospho-JNK were further validated in an independent cohort. Multivariate analysis identified MAP3K1 expression as an independent poor prognostic factor for DFS and OS. CONCLUSION Our results indicate that the overexpression of MAP3K1 plays a major role in the poor prognosis of HR-positive, HER2-negative early stage breast cancer.
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Affiliation(s)
- Sung-Hsin Kuo
- Departments of Oncology, National Taiwan University Hospital , Taipei, Taiwan
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Cancer Research Center, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Feng Wei
- Departments of Oncology, National Taiwan University Hospital , Taipei, Taiwan
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Cancer Research Center, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Hsuan Lee
- Departments of Pathology, National Taiwan University Hospital, and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jui-Chueh Lin
- Departments of Oncology, National Taiwan University Hospital , Taipei, Taiwan
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Cancer Research Center, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chi Yang
- Departments of Oncology, National Taiwan University Hospital , Taipei, Taiwan
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Cancer Research Center, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shi-Yi Yang
- Department of Surgery, National Taiwan University Hospital, and College of Medicine, National Taiwan University, No. 7, Chung-Shan South Rd, Taipei, Taiwan
- Graduate Institute of Epidemiology, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, and College of Medicine, National Taiwan University, No. 7, Chung-Shan South Rd, Taipei, Taiwan.
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11
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Fatemi N, Tu SJ, Chung CC, Moghadam PK, Mojarad EN, Sadeghi A, Totonchi M, Aghdaei HA, Chang JG. Whole exome sequencing identifies MAP3K1, MSH2, and MLH1 as potential cancer-predisposing genes in familial early-onset colorectal cancer. Kaohsiung J Med Sci 2023; 39:896-903. [PMID: 37314251 DOI: 10.1002/kjm2.12715] [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: 01/20/2023] [Revised: 05/01/2023] [Accepted: 05/21/2023] [Indexed: 06/15/2023] Open
Abstract
The incidence of early-onset colorectal cancer (CRC), which affects people under 50, is increasing for unknown reasons. Additionally, no underlying genetic cause is found in 20%-30% of patients suspected of having familial CRC syndrome. Whole exome sequencing (WES) has generated evidence for new genes associated with CRC susceptibility, but many patients remain undiagnosed. This study applied WES in five early-onset CRC patients from three unrelated families to identify novel genetic variants that could be linked to rapid disease development. Furthermore, the candidate variants were validated using Sanger sequencing. Two heterozygote variations, c.1077-2A>G and c.199G>A, were found in the MSH2 and the MLH1 genes, respectively. Sanger sequencing analysis confirmed that these (likely) pathogenic mutations segregated in all the affected families' members. In addition, we identified a rare heterozygote variant (c.175C>T) with suspected pathogenic potential in the MAP3K1 gene; formally the variant is of uncertain significance (VUS). Our findings support the hypothesis that CRC onset may be oligogenic and molecularly heterogeneous. Larger and more robust studies are needed to understand the genetic basis of early-onset CRC development, combined with novel functional analyses and omics approaches.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Siang-Jyun Tu
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chin-Chun Chung
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Pardis Ketabi Moghadam
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Totonchi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jan-Gowth Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
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12
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Jorns JM, Farooq A, Puzyrenko A, Jarzembowski J, Thike AA, Nasir NDM, Ng CCY, Liu W, Lee JY, Lim AH, Guan P, Teh BT, Tan PH. Giant juvenile fibroadenomas with and without prominent pseudoangiomatous stromal hyperplasia (PASH)-like change: clinicopathological and molecular characteristics. Histopathology 2023; 83:357-365. [PMID: 37140543 DOI: 10.1111/his.14935] [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: 02/15/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
AIMS Juvenile fibroadenomas (JFA) are biphasic fibroepithelial lesions (FEL) usually occurring in adolescent female patients. Giant (G) JFA, like other FEL, may exhibit prominent pseudoangiomatous stromal hyperplasia (PASH)-like change. We sought to determine clinicopathological and molecular characteristics of GJFA with and without PASH. METHODS AND RESULTS Archives were searched for cases of GJFA (1985-2020). All were stained for androgen receptor (AR), beta-catenin, CD34 and progesterone receptor (PR). Cases were sequenced using a custom 16-gene panel - MED12 (exons 1 and 2), TERT promoter (-124C>T and -146Ctable>T), SETD2, KMT2D, RARA (exons 5-9), FLNA, NF1, PIK3CA (exons 10, 11 and 21), EGFR, RB1, BCOR, TP53, PTEN, ERBB4, IGF1R and MAP3K1. Twenty-seven GJFA from 21 female patients aged 10.1-25.2 years were identified. Size ranged from 5.2 to 21 cm. Two patients had multiple, bilateral and later recurrent GJFA. Thirteen (48%) cases showed prominent PASH-like stroma. All were positive for stromal CD34, negative for AR and beta-catenin and one case showed focal PR expression. Sequencing showed MAP3K1 and SETD2 mutations in 17 samples, with KMT2D, TP53 and BCOR aberrations in 10 (45%), 10 (45%) and seven (32%) cases, respectively. Tumours with a PASH-like pattern had higher prevalence of SETD2 (P = 0.004) and TP53 (P = 0.029) mutations, while those without PASH had more RB1 mutations (P = 0.043). MED12 mutation was identified in one case. TERT promoter mutation was observed in four (18%), including two recurrences. CONCLUSIONS Gene mutations along more advanced phases of the proposed FEL pathogenetic pathway in GJFA are unusual, and suggest a mechanism for more aggressive growth in these tumours.
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Affiliation(s)
- Julie M Jorns
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ayesha Farooq
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Andrii Puzyrenko
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jason Jarzembowski
- Department of Pathology, Children's Hospital of Wisconsin, Madison, WI, USA
| | - Aye Aye Thike
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | | | | | - Wei Liu
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
| | - Jing Yi Lee
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
| | - Abner Herbert Lim
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
| | - Peiyong Guan
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
- Quantitative Biology and Medicine Programme, Duke-NUS Medical School, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
| | - Puay Hoon Tan
- Luma Medical Centre, Singapore
- KK Women's and Children's Hospital, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Pathology, University of Western Sydney, Sydney, NSW, Australia
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13
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Kaur J, Chandrashekar DS, Varga Z, Sobottka B, Janssen E, Gandhi K, Kowalski J, Kiraz U, Varambally S, Aneja R. Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers. Genes (Basel) 2023; 14:1690. [PMID: 37761830 PMCID: PMC10531222 DOI: 10.3390/genes14091690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is a molecularly complex and heterogeneous breast cancer subtype with distinct biological features and clinical behavior. Although TNBC is associated with an increased risk of metastasis and recurrence, the molecular mechanisms underlying TNBC metastasis remain unclear. We performed whole-exome sequencing (WES) analysis of primary TNBC and paired recurrent tumors to investigate the genetic profile of TNBC. METHODS Genomic DNA extracted from 35 formalin-fixed paraffin-embedded tissue samples from 26 TNBC patients was subjected to WES. Of these, 15 were primary tumors that did not have recurrence, and 11 were primary tumors that had recurrence (nine paired primary and recurrent tumors). Tumors were analyzed for single-nucleotide variants and insertions/deletions. RESULTS The tumor mutational burden (TMB) was 7.6 variants/megabase in primary tumors that recurred (n = 9); 8.2 variants/megabase in corresponding recurrent tumors (n = 9); and 7.3 variants/megabase in primary tumors that did not recur (n = 15). MUC3A was the most frequently mutated gene in all groups. Mutations in MAP3K1 and MUC16 were more common in our dataset. No alterations in PI3KCA were detected in our dataset. CONCLUSIONS We found similar mutational profiles between primary and paired recurrent tumors, suggesting that genomic features may be retained during local recurrence.
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Affiliation(s)
- Jaspreet Kaur
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
| | - Darshan S. Chandrashekar
- Department of Pathology—Molecular and Cellular, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (D.S.C.); (S.V.)
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (Z.V.); (B.S.)
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (Z.V.); (B.S.)
| | - Emiel Janssen
- Department of Pathology, Stavanger University Hospital, Health Stavanger HF, 4068 Stavanger, Norway; (E.J.); (U.K.)
| | - Khanjan Gandhi
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA;
| | - Jeanne Kowalski
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Umay Kiraz
- Department of Pathology, Stavanger University Hospital, Health Stavanger HF, 4068 Stavanger, Norway; (E.J.); (U.K.)
| | - Sooryanarayana Varambally
- Department of Pathology—Molecular and Cellular, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (D.S.C.); (S.V.)
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
- Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Joo JI, Park H, Cho K. Normalizing Input-Output Relationships of Cancer Networks for Reversion Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207322. [PMID: 37269056 PMCID: PMC10460890 DOI: 10.1002/advs.202207322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/17/2023] [Indexed: 06/04/2023]
Abstract
Accumulated genetic alterations in cancer cells distort cellular stimulus-response (or input-output) relationships, resulting in uncontrolled proliferation. However, the complex molecular interaction network within a cell implicates a possibility of restoring such distorted input-output relationships by rewiring the signal flow through controlling hidden molecular switches. Here, a system framework of analyzing cellular input-output relationships in consideration of various genetic alterations and identifying possible molecular switches that can normalize the distorted relationships based on Boolean network modeling and dynamics analysis is presented. Such reversion is demonstrated by the analysis of a number of cancer molecular networks together with a focused case study on bladder cancer with in vitro experiments and patient survival data analysis. The origin of reversibility from an evolutionary point of view based on the redundancy and robustness intrinsically embedded in complex molecular regulatory networks is further discussed.
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Affiliation(s)
- Jae Il Joo
- Department of Bio and Brain EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Present address:
biorevert IncDaejeon34051Republic of Korea
| | - Hwa‐Jeong Park
- Department of Bio and Brain EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Present address:
Promega Corporationan affiliate of PromegaSouth Korea
| | - Kwang‐Hyun Cho
- Department of Bio and Brain EngineeringKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
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15
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Goodarzi V, Nouri S, Nassaj ZS, Bighash M, Abbasian S, Hagh RA. Long non coding RNAs reveal important pathways in childhood asthma: a future perspective. J Mol Histol 2023; 54:257-269. [PMID: 37537509 DOI: 10.1007/s10735-023-10131-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/04/2023] [Indexed: 08/05/2023]
Abstract
Asthma is a long-term inflammatory disease of the airways of the lungs refers changes that occur in conjunction with, or as a result of, chronic airway inflammation. Airway remodeling the subsequent of inflammation constitutes cellular and extracellular matrix changes in the wall airways, epithelial-to-mesenchymal-transition and airway smooth muscle cell proliferation. Diseases often begin in childhood and despite extensive research, causative pathogenic mechanisms still remain unclear. Transcriptome analysis of childhood asthma reveals distinct gene expression profiles of Long noncoding RNAs which have been reported to play a central regulatory role in various aspects of pathogenesis, clinical course and treatment of asthma. We briefly review current understanding of lnc-RNA dysregulation in children with asthma, focusing on their complex role in the inflammation, cell proliferation and remodeling of airway to guide future researches. We found that the lnc-RNAs increases activity of several oncogenes such c-Myc, Akt, and ERK and various signaling pathways such as MAPK (PI3K, Ras, JNK and p38), NF-κB and Wnt and crosstalk between these pathways by TGFβ, β-catenin, ERK and SKP2. Moreover, two different signal transduction pathways, Wnt and Notch1, can be activated by two lnc-RNAs through sponging the same miRNA for exacerbation cell proliferation.
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Affiliation(s)
- Vahid Goodarzi
- Department of Anesthesiology, Rasoul-Akram Medical Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Shadi Nouri
- Arak University of Medical Sciences, Arak, Iran
| | - Zohre Saleh Nassaj
- Center for Health Related Social and Behavioral Sciences Research, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mansoureh Bighash
- Bachelor of Nursing, School of Paramedical Sciences, Qazvin University of Medical Sciences, Qazvn, Iran
| | - Sadegh Abbasian
- Department of Laboratory Science, School of Paramedical Sciences, Ilam University of Medical Sciences, Ilam, Iran
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16
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Gao P, Duan W, Shi H, Wang Q. Silencing circPalm2 inhibits sepsis-induced acute lung injury by sponging miR-376b-3p and targeting MAP3K1. Toxicol Res 2023; 39:275-294. [PMID: 37008689 PMCID: PMC10050541 DOI: 10.1007/s43188-022-00169-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
The apoptosis and inflammation of pulmonary epithelial cells are important pathogenic factors of sepsis-induced acute lung injury (ALI). Upregulation of circPalm2 (circ_0001212) expression levels has been previously detected in the lung tissue of ALI rats. Herein, the biological significance and detailed mechanism of circPalm2 in ALI pathogenesis were investigated. In vivo models of sepsis-induced ALI were established by treating C57BL/6 mice with cecal ligation and puncture (CLP) surgery. Murine pulmonary epithelial cells (MLE-12 cells) were stimulated with lipopolysaccharide (LPS) to establish in vitro septic ALI models. MLE-12 cell viability and apoptosis were evaluated by CCK-8 assay and flow cytometry analysis, respectively. The pathological alterations of the lung tissue were analysed based on hematoxylin-eosin (H&E) staining. Cell apoptosis in the lung tissue samples was examined by TUNEL staining assay. LPS administration suppressed the viability and accelerated the inflammation and apoptotic behaviours of MLE-12 cells. CircPalm2 displayed high expression in LPS-stimulated MLE-12 cells and possessed circular characteristics. The silencing of circPalm2 impeded apoptosis and inflammation in LPS-stimulated MLE-12 cells. Mechanistically, circPalm2 bound with miR-376b-3p, which targeted MAP3K1. In rescue assays, MAP3K1 enhancement reversed the repressive effects of circPalm2 depletion on LPS-triggered inflammatory injury and MLE-12 cell apoptosis. Furthermore, the lung tissue collected from CLP model mice displayed low miR-376b-3p expression and high levels of circPalm2 and MAP3K1. CircPalm2 positively regulated MAP3K1 expression by downregulating miR-376b-3p in murine lung tissues. Importantly, circPalm2 knockdown attenuated CLP-induced inflammation, apoptosis, and pathological alterations in lung tissues collected from mice. Silenced circPalm2 inhibits LPS-induced pulmonary epithelial cell dysfunction and mitigates abnormalities in lung tissues collected from CLP-stimulated mice via the miR-376b-3p/MAP3K1 axis in septic ALI. Supplementary Information The online version contains supplementary material available at 10.1007/s43188-022-00169-7.
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Affiliation(s)
- Pengfei Gao
- Shanghai East Clinical Medical College, Nanjing Medical University, No. 150, Jimo Road, Pudong New Area, Shanghai, 200120 China
- Department of Anesthesiology, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Huaian, Jiangsu 223300 China
| | - Wenying Duan
- Shanghai East Clinical Medical College, Nanjing Medical University, No. 150, Jimo Road, Pudong New Area, Shanghai, 200120 China
| | - Huiyan Shi
- Jinzhou Medical University, Jinzhou, Liaoning 121001 China
| | - Qingxiu Wang
- Shanghai East Clinical Medical College, Nanjing Medical University, No. 150, Jimo Road, Pudong New Area, Shanghai, 200120 China
- Shanghai East Hopital, Tongji University School of Medicine, Shanghai, 200120 China
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17
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Lack of Association of Polymorphism Located Upstream of ABCA1 (rs2472493), in FNDC3B (rs7636836), and Near ANKRD55–MAP3K1 Genes (rs61275591) in Primary Open-Angle Glaucoma Patients of Saudi Origin. Genes (Basel) 2023; 14:genes14030704. [PMID: 36980976 PMCID: PMC10048255 DOI: 10.3390/genes14030704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Polymorphisms rs2472493 near ABCA1, rs7636836 in FNDC3B, and rs61275591 near the ANKRD55–MAP3K1 genes were previously reported to exhibit genome-wide significance in primary open-angle glaucoma (POAG). Since these polymorphisms have not been investigated in the Arab population of Saudi Arabia, we examined their association with POAG in a Saudi cohort. Genotyping was performed in 152 POAG cases and 246 controls using Taqman real-time assays and their associations with POAG and clinical markers, such as intraocular pressure, cup/disc ratio, and the number of antiglaucoma medications, were tested by statistical methods. There was no association observed between POAG and the minor allele frequencies of rs2472493[G], rs7636836[T], or rs61275591[A]. None of the genetic models such as co-dominant, dominant, recessive, over-dominant, and log-additive demonstrated any genotype link. The Rs2472493 genotype showed a modest association (p = 0.044) with the number of antiglaucoma medications in the POAG group, but no significant genotype effect on post hoc analysis. In addition, a G-T allelic haplotype of rs2472493 (ABCA1) and rs7636836 (FNDC3B) did show an over two-fold increased risk of POAG (odds ratio = 2.18), albeit non-significantly (p = 0.092). Similarly, no other allelic haplotype of the three variants showed any significant association with POAG. Our study did not replicate the genetic association of rs2472493 (ABCA1), rs763683 (FNDC3B), and rs61275591 (ANKRD55–MAP3K1) in POAG and related clinical phenotypes, suggesting that these polymorphisms are not associated with POAG in a Saudi cohort of Arab ethnicity. However, large population-based multicenter studies are needed to validate these results.
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18
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Guo H, Cao W, Zhu Y, Li T, Hu B. A genome-wide cross-cancer meta-analysis highlights the shared genetic links of five solid cancers. Front Microbiol 2023; 14:1116592. [PMID: 36819030 PMCID: PMC9935838 DOI: 10.3389/fmicb.2023.1116592] [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: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Breast, ovarian, prostate, lung, and head/neck cancers are five solid cancers with complex interrelationships. However, the shared genetic factors of the five cancers were often revealed either by the combination of individual genome-wide association study (GWAS) approach or by the fixed-effect model-based meta-analysis approach with practically impossible assumptions. Here, we presented a random-effect model-based cross-cancer meta-analysis framework for identifying the genetic variants jointly influencing the five solid cancers. A comprehensive genetic correlation analysis (genome-wide, partitioned, and local) approach was performed by using GWAS summary statistics of the five cancers, and we observed three cancer pairs with significant genetic correlation: breast-ovarian cancer (r g = 0.221, p = 0.0003), breast-lung cancer (r g = 0.234, p = 7.6 × 10-6), and lung-head/neck cancer (r g = 0.652, p = 0.010). Furthermore, a random-effect model-based cross-trait meta-analysis was conducted for each significant cancer pair, and we found 27 shared genetic loci between breast and ovarian cancers, 18 loci between breast and lung cancers, and three loci between lung and head/neck cancers. Functional analysis indicates that the shared genes are enriched in human T-cell leukemia virus 1 infection (HTLV-1) and antigen processing and presentation (APP) pathways. Our study investigates the shared genetic links across five solid cancers and will help to reveal their potential molecular mechanisms.
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Affiliation(s)
- Hongping Guo
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China,*Correspondence: Hongping Guo ✉
| | - Wenhao Cao
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, United States
| | - Yiran Zhu
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China
| | - Tong Li
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China
| | - Boheng Hu
- School of Mathematics and Statistics, Hubei Normal University, Huangshi, China
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Sex-dependent associations between MAP3K1 gene polymorphisms and soy products with the gastric cancer risk in Korea: a case-control study. BMC Gastroenterol 2022; 22:513. [PMID: 36510163 PMCID: PMC9743679 DOI: 10.1186/s12876-022-02569-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/10/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND/OBJECTIVES The hormone-dependent effect of MAP3K1 gene polymorphisms may explain sex-specific differences in gastric cancer (GC) risk. Phytoestrogens have been shown to interact with this genetic factor. Here, we investigated the association between MAP3K1 gene polymorphisms and GC risk by sex and whether these associations differ depending on soy products intake. METHODS Participants aged 20-79 years were recruited from two hospitals between December 2002 and September 2006. In all, 440 cases and 485 controls were recruited, among, 246 pairs of cases and controls, matched by sex, age (± 5 years), study admission period (± 1 years), and hospital, were included for the analysis. RESULTS In dominant model, men with the A allele of rs252902 showed significantly increased GC risk (odd ratio; OR=2.19, 95% confidence interval; CI=1.31-3.64) compared to GG homozygotes. When stratified by intake of soy products, men with the A allele of rs252902 and low intake of soy products showed significantly higher GC risk (OR=3.29, 95% CI=1.55-6.78) than that in GG homozygotes. CONCLUSIONS Men with the risk allele of MAP3K1 had a significantly increased GC risk compared to GG homozygotes; this trend was more pronounced in those with low intake of soy products.
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Llaurado Fernandez M, Hijmans EM, Gennissen AM, Wong NK, Li S, Wisman GBA, Hamilton A, Hoenisch J, Dawson A, Lee CH, Bittner M, Kim H, DiMattia GE, Lok CA, Lieftink C, Beijersbergen RL, de Jong S, Carey MS, Bernards R, Berns K. NOTCH Signaling Limits the Response of Low-Grade Serous Ovarian Cancers to MEK Inhibition. Mol Cancer Ther 2022; 21:1862-1874. [PMID: 36198031 PMCID: PMC9716250 DOI: 10.1158/1535-7163.mct-22-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/30/2022] [Accepted: 10/03/2022] [Indexed: 01/12/2023]
Abstract
Low-grade serous ovarian cancer (LGSOC) is a rare subtype of epithelial ovarian cancer with high fatality rates in advanced stages due to its chemoresistant properties. LGSOC is characterized by activation of MAPK signaling, and recent clinical trials indicate that the MEK inhibitor (MEKi) trametinib may be a good treatment option for a subset of patients. Understanding MEKi-resistance mechanisms and subsequent identification of rational drug combinations to suppress resistance may greatly improve LGSOC treatment strategies. Both gain-of-function and loss-of-function CRISPR-Cas9 genome-wide libraries were used to screen LGSOC cell lines to identify genes that modulate the response to MEKi. Overexpression of MAML2 and loss of MAP3K1 were identified, both leading to overexpression of the NOTCH target HES1, which has a causal role in this process as its knockdown reversed MEKi resistance. Interestingly, increased HES1 expression was also observed in selected spontaneous trametinib-resistant clones, next to activating MAP2K1 (MEK1) mutations. Subsequent trametinib synthetic lethality screens identified SHOC2 downregulation as being synthetic lethal with MEKis. Targeting SHOC2 with pan-RAF inhibitors (pan-RAFis) in combination with MEKi was effective in parental LGSOC cell lines, in MEKi-resistant derivatives, in primary ascites cultures from patients with LGSOC, and in LGSOC (cell line-derived and patient-derived) xenograft mouse models. We found that the combination of pan-RAFi with MEKi downregulated HES1 levels in trametinib-resistant cells, providing an explanation for the synergy that was observed. Combining MEKis with pan-RAFis may provide a promising treatment strategy for patients with LGSOC, which warrants further clinical validation.
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Affiliation(s)
- Marta Llaurado Fernandez
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - E. Marielle Hijmans
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Annemiek M.C. Gennissen
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Nelson K.Y. Wong
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada.,Department of Experimental Therapeutics, BC Cancer, Vancouver, British Columbia, Canada
| | - Shang Li
- Department of Medical Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - G. Bea A. Wisman
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Aleksandra Hamilton
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Joshua Hoenisch
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Amy Dawson
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Cheng-Han Lee
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Madison Bittner
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Hannah Kim
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada
| | - Gabriel E. DiMattia
- Mary and John Knight Translational Ovarian Cancer Research Unit, London Health Sciences Center
| | - Christianne A.R. Lok
- Center for Gynecologic Oncology Amsterdam, Antoni van Leeuwenhoek/The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roderick L. Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Steven de Jong
- Department of Medical Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mark S. Carey
- Department of Obstetrics and Gynaecology, University of British Columbia Vancouver, British Columbia, Canada.,Corresponding Authors: Katrien Berns, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121955. E-mail: ; and Mark S. Carey, Vancouver, British Columbia V6Z 2K8, Canada. Phone: 160-4875-4268; E-mail: ; René Bernards, Plesmanlaan 121,1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121952; E-mail:
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Corresponding Authors: Katrien Berns, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121955. E-mail: ; and Mark S. Carey, Vancouver, British Columbia V6Z 2K8, Canada. Phone: 160-4875-4268; E-mail: ; René Bernards, Plesmanlaan 121,1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121952; E-mail:
| | - Katrien Berns
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Center Netherlands, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Corresponding Authors: Katrien Berns, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121955. E-mail: ; and Mark S. Carey, Vancouver, British Columbia V6Z 2K8, Canada. Phone: 160-4875-4268; E-mail: ; René Bernards, Plesmanlaan 121,1066 CX Amsterdam, the Netherlands. Phone: 31-20-5121952; E-mail:
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21
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Zhang J, Pei J, Durham J, Bos T, Cong Q. Computed cancer interactome explains the effects of somatic mutations in cancers. Protein Sci 2022; 31:e4479. [PMID: 36261849 PMCID: PMC9667826 DOI: 10.1002/pro.4479] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPIs) are involved in almost all essential cellular processes. Perturbation of PPI networks plays critical roles in tumorigenesis, cancer progression, and metastasis. While numerous high-throughput experiments have produced a vast amount of data for PPIs, these data sets suffer from high false positive rates and exhibit a high degree of discrepancy. Coevolution of amino acid positions between protein pairs has proven to be useful in identifying interacting proteins and providing structural details of the interaction interfaces with the help of deep learning methods like AlphaFold (AF). In this study, we applied AF to investigate the cancer protein-protein interactome. We predicted 1,798 PPIs for cancer driver proteins involved in diverse cellular processes such as transcription regulation, signal transduction, DNA repair, and cell cycle. We modeled the spatial structures for the predicted binary protein complexes, 1,087 of which lacked previous 3D structure information. Our predictions offer novel structural insight into many cancer-related processes such as the MAP kinase cascade and Fanconi anemia pathway. We further investigated the cancer mutation landscape by mapping somatic missense mutations (SMMs) in cancer to the predicted PPI interfaces and performing enrichment and depletion analyses. Interfaces enriched or depleted with SMMs exhibit different preferences for functional categories. Interfaces enriched in mutations tend to function in pathways that are deregulated in cancers and they may help explain the molecular mechanisms of cancers in patients; interfaces lacking mutations appear to be essential for the survival of cancer cells and thus may be future targets for PPI modulating drugs.
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Affiliation(s)
- Jing Zhang
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Jimin Pei
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Jesse Durham
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Tasia Bos
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
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22
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Kostecka A, Nowikiewicz T, Olszewski P, Koczkowska M, Horbacz M, Heinzl M, Andreou M, Salazar R, Mair T, Madanecki P, Gucwa M, Davies H, Skokowski J, Buckley PG, Pęksa R, Śrutek E, Szylberg Ł, Hartman J, Jankowski M, Zegarski W, Tiemann-Boege I, Dumanski JP, Piotrowski A. High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing. NPJ Breast Cancer 2022; 8:76. [PMID: 35768433 PMCID: PMC9243094 DOI: 10.1038/s41523-022-00443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10-2- 5.2 × 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.
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Affiliation(s)
- Anna Kostecka
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
| | - Tomasz Nowikiewicz
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland.
- Department of Breast Cancer and Reconstructive Surgery, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland.
| | - Paweł Olszewski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Koczkowska
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Horbacz
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Heinzl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Maria Andreou
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gucwa
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | | | - Rafał Pęksa
- Department of Patomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Śrutek
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Perinatology, Gynaecology and Gynaecologic, Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
- MedTech Labs, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Michał Jankowski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | | | - Jan P Dumanski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arkadiusz Piotrowski
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
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23
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Luo Y, Yao Q. Circ_0085315 promotes cell proliferation, invasion, and migration in colon cancer through miR-1200/MAP3K1 signaling pathway. Cell Cycle 2022; 21:1194-1211. [PMID: 35230926 PMCID: PMC9103513 DOI: 10.1080/15384101.2022.2044137] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/02/2022] [Accepted: 02/06/2022] [Indexed: 12/30/2022] Open
Abstract
Colon cancer (CC) is a common malignant tumor of the digestive tract. Circular RNAs (circRNAs) play important roles in the progression of CC. This study aimed to explore the role and mechanism of circRNA_0085315 in CC. In this study, we used qRT-PCR and Western blot assays to analyze the expressions of circRNA, miRNA, and mRNA as well as the expression of the related proteins. Luciferase reporter, RNA pull-down, and qRT-PCR assays were used to prove the relationship among circRNA, miRNA, and mRNA. CCK-8, colony formation, and transwell assays were used to perform the analysis of cell proliferation, migration, and invasion. Our results showed that the higher circRNA_0085315 expression led to the poorer prognosis of CC patients. The function of circRNA_0085315 as a ceRNA in competing with MAP3K1 mRNA to sponge miR-1200. CircRNA_0085315 sponged miR-1200 to promote cell proliferation, migration, and invasion and affected the expression of Ki67, MMP2, E-cadherin, and N-cadherin, but not circRNA_0085315-mut without the binding site of miR-1200. MAP3K1-overexpression or miR-1200 mimics prevented the suppression on the enhanced cell proliferation, migration, and invasion caused by circRNA_0085315-overexpression. circRNA_0085315 increased the phosphorylation levels of JNK, p38, and ERK1/2 by stimulating MAP3K1 up-regulation caused by miR-1200 inhibition. In conclusion, circRNA_0085315 serves as a ceRNA and promotes CC progression through the activation of the MAPK signaling pathway mediated via the miR-1200/MAP3K1 axis, suggesting that circRNA_0085315 may be a promising diagnostic and therapeutic target for CC.
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Affiliation(s)
- Yuan Luo
- Department of Geriatrics, Ningbo First Hospital, Ningbo, Zhejiang Province, China
| | - Qi Yao
- Department of Geriatrics, Ningbo First Hospital, Ningbo, Zhejiang Province, China
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24
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Xie HL, Zhang YH, Tan XD, Zheng Y, Ni HY, Dong LP, Zheng JL, Diao JZ, Yin YJ, Zhang JB, Sun XQ, Yang YW. miR-375 Induced the Formation and Transgenerational Inheritance of Fatty Liver in Poultry by Targeting MAP3K1. DNA Cell Biol 2022; 41:590-599. [PMID: 35533015 DOI: 10.1089/dna.2022.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The liver of poultry is the primary site of lipid synthesis. The excessive production of lipids accumulates in liver tissues causing lipid metabolism disorders, which result in fatty liver disease and have a transgenerational effect of acquired phenotypes. However, its specific mechanisms have not yet been fully understood. In this study, the differentially expressed miR-375 as well as its target gene MAP3K1 (mitogen-activated protein kinase kinase kinase 1) were screened out by interaction network analysis of microRNA sequencing results and transcriptome profiling in the fatty liver group of the F0-F3 generation (p < 0.05 or p < 0.01). Furthermore, the results showed that the number of lipid droplets and triglyceride content were significantly decreased after upregulation of miR-375 in primary hepatocyte culture in vitro (p < 0.05 or p < 0.01). The MAP3K1 knockdown group exhibited the opposite trends (p < 0.05 or p < 0.01). P53, Bcl-x, PMP22, and CDKN2C related to cell proliferation were significantly upregulated or downregulated after knocking down MAP3K1 (p < 0.05). This research uniquely revealed that silencing miR-375 inhibits lipid biosynthesis and promotes cell proliferation, which may be due to the partial regulation of the expression level of MAP3K1, thereby further participating in the transgenerational inheritance process of regulating liver lipid metabolism. These results reveal the pathogenesis of fatty liver in noncoding RNA and provide good candidate genes for breeding progress of disease resistance in chickens.
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Affiliation(s)
- Heng-Li Xie
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Yong-Hong Zhang
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Xiao-Dong Tan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yi Zheng
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Hong-Yu Ni
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Li-Ping Dong
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Jin-Lei Zheng
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Ji-Zhe Diao
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Yi-Jing Yin
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Jia-Bao Zhang
- College of Animal Science, Jilin University, Changchun, P.R. China
| | - Xue-Qi Sun
- College of Animal Science, Jilin University, Changchun, P.R. China.,Jilin Academy of Agricultural Sciences, Changchun, P.R. China
| | - Yu-Wei Yang
- College of Animal Science, Jilin University, Changchun, P.R. China
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25
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Abstract
Immunity could be viewed as the common factor in neurodevelopmental disorders and cancer. The immune and nervous systems coevolve as the embryo develops. Immunity can release cytokines that activate MAPK signaling in neural cells. In specific embryonic brain cell types, dysregulated signaling that results from germline or embryonic mutations can promote changes in chromatin organization and gene accessibility, and thus expression levels of essential genes in neurodevelopment. In cancer, dysregulated signaling can emerge from sporadic somatic mutations during human life. Neurodevelopmental disorders and cancer share similarities. In neurodevelopmental disorders, immunity, and cancer, there appears an almost invariable involvement of small GTPases (e.g., Ras, RhoA, and Rac) and their pathways. TLRs, IL-1, GIT1, and FGFR signaling pathways, all can be dysregulated in neurodevelopmental disorders and cancer. Although there are signaling similarities, decisive differentiating factors are timing windows, and cell type specific perturbation levels, pointing to chromatin reorganization. Finally, we discuss drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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26
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Zhou S, Niu R, Sun H, Kim SH, Jin X, Yin J. The MAP3K1/c-JUN signaling axis regulates glioblastoma stem cell invasion and tumor progression. Biochem Biophys Res Commun 2022; 612:188-195. [PMID: 35567901 DOI: 10.1016/j.bbrc.2022.04.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Glioblastoma (GBM) stem cells (GSCs) are responsible for GBM initiation, progression, infiltration, standard therapy resistance, and recurrence. However, the mechanisms underlying GSC invasion remain incompletely understood. Using public single-cell RNA-Seq data, we identified MAP3K1 as a master regulator of infiltrative GSCs through c-JUN signaling regulation. MAP3K1 knockdown significantly decreased GSC invasion capacity, proliferation, and stemness in vitro. Moreover, in an orthotopic xenograft model, knockdown of MAP3K1 prominently suppressed GSC infiltration along the corpus callosum and tumor progression and prolonged mouse survival. Mechanistically, MAP3K1 regulates GSC invasion through phosphorylation of downstream c-JUN at serine 63 and 73, as confirmed using the CPTAC phosphoproteome dataset. Furthermore, the c-JUN inhibitor JNK-IN-8 significantly decreased GSC invasion, proliferation, and stemness. Taken together, our study demonstrates that MAP3K1 regulates GSC invasion and tumor progression via activation of c-JUN signaling and indicates that the MAP3K1/c-JUN signaling axis is a therapeutic target for infiltrative GBM.
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Affiliation(s)
- Shuchang Zhou
- Henan Key Laboratory of Brain Targeted Bio-Nanomedicine, School of Life Sciences & School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China; Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Rui Niu
- Henan Key Laboratory of Brain Targeted Bio-Nanomedicine, School of Life Sciences & School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China; Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Han Sun
- Henan Key Laboratory of Brain Targeted Bio-Nanomedicine, School of Life Sciences & School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China; Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Sung-Hak Kim
- Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Xiong Jin
- Henan Key Laboratory of Brain Targeted Bio-Nanomedicine, School of Life Sciences & School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China; Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China.
| | - Jinlong Yin
- Henan Key Laboratory of Brain Targeted Bio-Nanomedicine, School of Life Sciences & School of Pharmacy, Henan University, Kaifeng, Henan, 475004, China; Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China.
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27
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Li C, Zhang G, Wang Y, Chen B, Li K, Cao L, Ren C, Wen L, Jia M, Mok H, Lai J, Xiao W, Li X, Liao N. Spectrum of MAP3K1 mutations in breast cancer is luminal subtype-predominant and related to prognosis. Oncol Lett 2022; 23:68. [PMID: 35069877 PMCID: PMC8756433 DOI: 10.3892/ol.2022.13187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 01/28/2021] [Indexed: 12/03/2022] Open
Abstract
MAP3K1 is a MAPK family serine-threonine kinase that is frequently mutated in human cancer. The association between mutations in the MAP3K1 gene and the clinicopathological characteristics and prognosis of patients with breast cancer remain unclear in the Chinese population. Thus, the aim of the present retrospective study was to investigate the possible role and function of MAP3K1 in breast cancer. Data obtained from 412 consecutive patients with breast cancer were selected from Guangdong Provincial People's Hospital (GDPH) for analysis in the present study. Mutations were assessed using next-generation sequencing. The association between MAP3K1 mutations and clinicopathological features were analyzed and further compared with the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort and data from The Cancer Genome Atlas (TCGA). In the GDPH cohort, a total of 45 mutations MAP3K1 were identified in 8.5% (n=35) of the 412 patients, compared with 9.7% (n=244) in METABRIC and 7.9% (n=88) in TCGA. The majority of the mutations identified in the in three cohorts were truncating mutations, followed by mis-sense mutations. Mutations in MAP3K1 were predominant in patients with the luminal A and B breast cancer subtypes in METABRIC datasets (P<0.001), although no significant differences were observed in the GDPH cohort (P=0.227). In the METABRIC cohort, patients with MAP3K1 mutations experienced a improved overall survival (OS) rate than patients without MAP3K1 mutations (P=0.006). In patient with hormone receptor (HR)+ breast cancer, a more significantly higher OS rate was observed in patients with MAP3K1 mutations (P<0.001). MAP3K1 expression was associated with OS in the HR+ subgroup. Moreover, the MAP3K1 methylation levels were reduced in primary breast cancer tissue, compared with normal tissue. Thus, the present findings identified MAP3K1 mutations in Chinese patients with breast cancer, and compared MAP3K1 mutations between the cohorts from Western and Eastern countries.
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Affiliation(s)
- Cheukfai Li
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Guochun Zhang
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Yulei Wang
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Bo Chen
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Kai Li
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Li Cao
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Chongyang Ren
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Lingzhu Wen
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Minghan Jia
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Hsiaopei Mok
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Jianguo Lai
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Weikai Xiao
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Xuerui Li
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Ning Liao
- Department of Breast Cancer, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
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28
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Das S, Ge X, Han H, Desert R, Song Z, Athavale D, Chen W, Gaskell H, Lantvit D, Guzman G, Nieto N. The Integrated "Multiomics" Landscape at Peak Injury and Resolution From Alcohol-Associated Liver Disease. Hepatol Commun 2022; 6:133-160. [PMID: 34558855 PMCID: PMC8710802 DOI: 10.1002/hep4.1793] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/09/2023] Open
Abstract
Alcohol-associated liver disease (ALD) is a significant clinical problem for which the most effective therapy is alcohol abstinence. The two aims of this study were, first, to identify the liver transcriptome, fecal microbiome, and portal serum metabolome at peak injury and during early and late resolution from ALD; and second, to integrate their interactions and understand better the pathogenesis of ALD. To provoke alcohol-induced liver injury, female and male wild-type mice were fed the control or ethanol Lieber-DeCarli diets for 6 weeks. To study early and late resolution, alcohol was withdrawn from the diet and mice were sacrificed after 3 and 14 days, respectively. At peak injury, there was increased signal transducer and activator of transcription (Stat3), Rho-GTPases, Tec kinase and glycoprotein VI (Gp6), and decreased peroxisome proliferator-activated receptor signaling. During resolution from ALD, there was up-regulation of vitamin D receptor/retinoid X receptor, toll-like receptor, p38 and Stat3, and down-regulation of liver X receptor signaling. Females showed significant changes in catabolic pathways, whereas males increased cellular stress, injury, and immune-response pathways that decreased during resolution. The bacterial genus Alistipes and the metabolite dipeptide glycyl-L-leucine increased at peak but decreased during resolution from ALD in both genders. Hepatic induction of mitogen-activated protein kinase (Map3k1) correlated with changes in the microbiome and metabolome at peak but was restored during ALD resolution. Inhibition of MAP3K1 protected from ALD in mice. Conclusion: Alcohol abstinence restores the liver transcriptome, fecal microbiome, and portal serum metabolome in a gender-specific manner. Integration of multiomics data identified Map3k1 as a key gene driving pathogenesis and resolution from ALD.
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Affiliation(s)
- Sukanta Das
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Xiaodong Ge
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Hui Han
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Romain Desert
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Zhuolun Song
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Dipti Athavale
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Wei Chen
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Harriet Gaskell
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Daniel Lantvit
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Grace Guzman
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
| | - Natalia Nieto
- Department of PathologyUniversity of Illinois at ChicagoChicagoILUSA
- Department of MedicineDivision of Gastroenterology and HepatologyUniversity of Illinois at ChicagoChicagoILUSA
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29
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Wang J, Kimura E, Mongan M, Xia Y. Genetic Control of MAP3K1 in Eye Development and Sex Differentiation. Cells 2021; 11:cells11010034. [PMID: 35011600 PMCID: PMC8750206 DOI: 10.3390/cells11010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/03/2021] [Accepted: 12/21/2021] [Indexed: 01/11/2023] Open
Abstract
The MAP3K1 is responsible for transmitting signals to activate specific MAP2K-MAPK cascades. Following the initial biochemical characterization, genetic mouse models have taken center stage to elucidate how MAP3K1 regulates biological functions. To that end, mice were generated with the ablation of the entire Map3k1 gene, the kinase domain coding sequences, or ubiquitin ligase domain mutations. Analyses of the mutants identify diverse roles that MAP3K1 plays in embryonic survival, maturation of T/B cells, and development of sensory organs, including eye and ear. Specifically in eye development, Map3k1 loss-of-function was found to be autosomal recessive for congenital eye abnormalities, but became autosomal dominant in combination with Jnk and RhoA mutations. Additionally, Map3k1 mutation increased eye defects with an exposure to environmental agents such as dioxin. Data from eye developmental models reveal the nexus role of MAP3K1 in integrating genetic and environmental signals to control developmental activities. Here, we focus the discussions on recent advances in understanding the signaling mechanisms of MAP3K1 in eye development in mice and in sex differentiation from human genomics findings. The research works featured here lead to a deeper understanding of the in vivo signaling network, the mechanisms of gene-environment interactions, and the relevance of this multifaceted protein kinase in disease etiology and pathogenesis.
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Affiliation(s)
| | | | | | - Ying Xia
- Correspondence: ; Tel.: +1-513-558-0371
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30
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Mathien S, Tesnière C, Meloche S. Regulation of Mitogen-Activated Protein Kinase Signaling Pathways by the Ubiquitin-Proteasome System and Its Pharmacological Potential. Pharmacol Rev 2021; 73:263-296. [PMID: 34732541 DOI: 10.1124/pharmrev.120.000170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are evolutionarily conserved signaling pathways that play essential roles in transducing extracellular environmental signals into diverse cellular responses to maintain homeostasis. These pathways are classically organized into an architecture of three sequentially acting protein kinases: a MAPK kinase kinase that phosphorylates and activates a MAPK kinase, which in turn phosphorylates and activates the effector MAPK. The activity of MAPKs is tightly regulated by phosphorylation of their activation loop, which can be modulated by positive and negative feedback mechanisms to control the amplitude and duration of the signal. The signaling outcomes of MAPK pathways are further regulated by interactions of MAPKs with scaffolding and regulatory proteins. Accumulating evidence indicates that, in addition to these mechanisms, MAPK signaling is commonly regulated by ubiquitin-proteasome system (UPS)-mediated control of the stability and abundance of MAPK pathway components. Notably, the biologic activity of some MAPKs appears to be regulated mainly at the level of protein turnover. Recent studies have started to explore the potential of targeted protein degradation as a powerful strategy to investigate the biologic functions of individual MAPK pathway components and as a new therapeutic approach to overcome resistance to current small-molecule kinase inhibitors. Here, we comprehensively review the mechanisms, physiologic importance, and pharmacological potential of UPS-mediated protein degradation in the control of MAPK signaling. SIGNIFICANCE STATEMENT: Accumulating evidence highlights the importance of targeted protein degradation by the ubiquitin-proteasome system in regulating and fine-tuning the signaling output of mitogen-activated protein kinase (MAPK) pathways. Manipulating protein levels of MAPK cascade components may provide a novel approach for the development of selective pharmacological tools and therapeutics.
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Affiliation(s)
- Simon Mathien
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada (S.Ma., C.T., S.Me.); and Molecular Biology Program, Faculty of Medicine (C.T., S.Me.) and Department of Pharmacology and Physiology (S.Me.), Université de Montréal, Montreal, Quebec, Canada
| | - Chloé Tesnière
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada (S.Ma., C.T., S.Me.); and Molecular Biology Program, Faculty of Medicine (C.T., S.Me.) and Department of Pharmacology and Physiology (S.Me.), Université de Montréal, Montreal, Quebec, Canada
| | - Sylvain Meloche
- Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada (S.Ma., C.T., S.Me.); and Molecular Biology Program, Faculty of Medicine (C.T., S.Me.) and Department of Pharmacology and Physiology (S.Me.), Université de Montréal, Montreal, Quebec, Canada
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31
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Van Herck Y, Feyaerts A, Alibhai S, Papamichael D, Decoster L, Lambrechts Y, Pinchuk M, Bechter O, Herrera-Caceres J, Bibeau F, Desmedt C, Hatse S, Wildiers H. Is cancer biology different in older patients? THE LANCET HEALTHY LONGEVITY 2021; 2:e663-e677. [DOI: 10.1016/s2666-7568(21)00179-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022]
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32
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Martins JRB, Moraes LN, Cury SS, Capannacci J, Carvalho RF, Nogueira CR, Hokama NK, Hokama POM. MiR-125a-3p and MiR-320b Differentially Expressed in Patients with Chronic Myeloid Leukemia Treated with Allogeneic Hematopoietic Stem Cell Transplantation and Imatinib Mesylate. Int J Mol Sci 2021; 22:ijms221910216. [PMID: 34638557 PMCID: PMC8508688 DOI: 10.3390/ijms221910216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
Chronic myeloid leukemia (CML), a hematopoietic neoplasm arising from the fusion of BCR (breakpoint cluster region) gene on chromosome 22 to the ABL (Abelson leukemia virus) gene on chromosome 9 (BCR-ABL1 oncogene), originates from a small population of leukemic stem cells with extensive capacity for self-renewal and an inflammatory microenvironment. Currently, CML treatment is based on tyrosine kinase inhibitors (TKIs). However, allogeneic hematopoietic stem cell transplantation (HSCT-allo) is currently the only effective treatment of CML. The difficulty of finding a compatible donor and high rates of morbidity and mortality limit transplantation treatment. Despite the safety and efficacy of TKIs, patients can develop resistance. Thus, microRNAs (miRNAs) play a prominent role as biomarkers and post-transcriptional regulators of gene expression. The aim of this study was to analyze the miRNA profile in CML patients who achieved cytogenetic remission after treatment with both HSCT-allo and TKI. Expression analyses of the 758 miRNAs were performed using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Bioinformatics tools were used for data analysis. We detected miRNA profiles using their possible target genes and target pathways. MiR-125a-3p stood out among the downregulated miRNAs, showing an interaction network with 52 target genes. MiR-320b was the only upregulated miRNA, with an interaction network of 26 genes. The results are expected to aid future studies of miRNAs, residual leukemic cells, and prognosis in CML.
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Affiliation(s)
- Juliana R. B. Martins
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (FMB-UNESP), Botucatu 18618-687, Brazil; (J.R.B.M.); (J.C.); (C.R.N.); (N.K.H.)
| | - Leonardo N. Moraes
- Department of Bioprocesses and Biotechnology, School of Agriculture, São Paulo State University (FCA-UNESP), Botucatu 18610-034, Brazil;
| | - Sarah S. Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (IBB-UNESP), Botucatu 18618-970, Brazil; (S.S.C.); (R.F.C.)
| | - Juliana Capannacci
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (FMB-UNESP), Botucatu 18618-687, Brazil; (J.R.B.M.); (J.C.); (C.R.N.); (N.K.H.)
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (IBB-UNESP), Botucatu 18618-970, Brazil; (S.S.C.); (R.F.C.)
| | - Célia Regina Nogueira
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (FMB-UNESP), Botucatu 18618-687, Brazil; (J.R.B.M.); (J.C.); (C.R.N.); (N.K.H.)
| | - Newton Key Hokama
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (FMB-UNESP), Botucatu 18618-687, Brazil; (J.R.B.M.); (J.C.); (C.R.N.); (N.K.H.)
| | - Paula O. M. Hokama
- Department of Internal Medicine, Botucatu Medical School, São Paulo State University (FMB-UNESP), Botucatu 18618-687, Brazil; (J.R.B.M.); (J.C.); (C.R.N.); (N.K.H.)
- Correspondence:
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33
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Tang D, Luo Y, Jiang Y, Hu P, Peng H, Wu S, Zhang G, Wang Y. LncRNA KCNQ1OT1 activated by c-Myc promotes cell proliferation via interacting with FUS to stabilize MAP3K1 in acute promyelocytic leukemia. Cell Death Dis 2021; 12:795. [PMID: 34404765 PMCID: PMC8371007 DOI: 10.1038/s41419-021-04080-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022]
Abstract
Uncontrolled proliferation is the hallmark of cancer cells. Previous studies mainly focused on the role of protein-coding genes in cancer cell proliferation. Emerging evidence showed that long non-coding RNAs (lncRNAs) also play critical roles in cancer cell proliferation and growth. LncRNA KCNQ1OT1 is found to contribute to carcinogenesis, but its role in acute promyelocytic leukemia (APL) is unclear. In this study, by analyzing data from Gene Expression Omnibus, The Cancer Genome Atlas database and our clinical samples, we found that KCNQ1OT1 was selectively highly expressed in APL. Functional assays demonstrated that knockdown of KCNQ1OT1 reduced APL cell proliferation and increased apoptosis. Further evidence showed that KCNQ1OT1 was mainly located in the cytoplasm of APL patient-derived NB4 cells and APL patient bone marrow samples. Mechanistically, KCNQ1OT1 bound to RNA binding protein FUS, and silencing either KCNQ1OT1 or FUS reduced the expression level and stability of MAP3K1 mRNA. Whereas KCNQ1OT1 and FUS did not affect each other. Importantly, knockdown of MAP3K1 impaired APL cell proliferation. Finally, c-Myc transactivated KCNQ1OT1 in APL cells through binding to its promoter while knockdown of c-Myc decreased KCNQ1OT1 expression. Our results not only revealed that c-Myc transactivated KCNQ1OT1 and upregulated KCNQ1OT1 promoted APL cell proliferation, but also demonstrated that KCNQ1OT1 bound to FUS to synergistically stabilize MAP3K1 mRNA, thus facilitating APL cell proliferation. This study established a previously unidentified role of KCNQ1OT1 in the development of APL, and KCNQ1OT1 may serve as a potential therapeutic target for APL.
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Affiliation(s)
- Doudou Tang
- Department of Respiratory and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Centre for Evidence-based Medicine, Central South University, Changsha, Hunan, China
| | - Yujiao Luo
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yafeng Jiang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Piao Hu
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Shangjie Wu
- Department of Respiratory and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Centre for Evidence-based Medicine, Central South University, Changsha, Hunan, China
| | - Guangsen Zhang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yewei Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Institute of Molecular Hematology, Central South University, Changsha, Hunan, China.
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MEKK1-dependent activation of the CRL4 complex is important for DNA damage-induced degradation of p21 and DDB2 and cell survival. Mol Cell Biol 2021; 41:e0008121. [PMID: 34251884 PMCID: PMC8462458 DOI: 10.1128/mcb.00081-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cullin-4 ubiquitin ligase (CRL4) complexes are differentially composed and highly dynamic protein assemblies that control many biological processes including the global genome nucleotide excision repair (GG-NER) pathway. Here we identified the kinase mitogen-activated protein kinase kinase kinase 1 (MEKK1) as a novel constitutive interactor of a cytosolic CRL4 complex that disassembles after DNA damage due to the Caspase-mediated cleavage of MEKK1. The kinase activity of MEKK1 was important to trigger auto-ubiquitination of the CRL4 complex by K48- and K63-linked ubiquitin chains. MEKK1 knockdown prohibited DNA damage-induced degradation of the CRL4 component DNA-damage binding protein 2 (DDB2) and the CRL4 substrate p21 and also cell recovery and survival. A ubiquitin replacement strategy revealed a contribution of K63-branched ubiquitin chains for DNA damage-induced DDB2/p21 decay, cell cycle regulation and cell survival. These data might have also implications for cancer, as frequently occurring mutations of MEKK1 might have an impact on genome stability and the therapeutic efficacy of CRL4-dependent immunomodulatory drugs such as thalidomide-derivatives.
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35
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Del Corvo M, Lazzari B, Capra E, Zavarez L, Milanesi M, Utsunomiya YT, Utsunomiya ATH, Stella A, de Paula Nogueira G, Garcia JF, Ajmone-Marsan P. Methylome Patterns of Cattle Adaptation to Heat Stress. Front Genet 2021; 12:633132. [PMID: 34122501 PMCID: PMC8194315 DOI: 10.3389/fgene.2021.633132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism and immune response, but little is known on the epigenetic mechanisms mediating the effect of temperature at the cellular and organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls of the heat stress resilient Nellore breed and 5 bulls of the Angus that are more heat stress susceptible, exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region. The methylomes were analyzed during and after the exposure by Reduced Representation Bisulfite Sequencing, which provided genome-wide single-base resolution methylation profiles. Significant methylation changes between stressful and recovery periods were observed in 819 genes. Among these, 351 were only seen in Angus, 366 were specific to Nellore, and 102 showed significant changes in methylation patterns in both breeds. KEGG and Gene Ontology (GO) enrichment analyses showed that responses were breed-specific. Interestingly, in Nellore significant genes and pathways were mainly involved in stress responses and cellular defense and were under methylated during heat stress, whereas in Angus the response was less focused. These preliminary results suggest that heat challenge induces changes in methylation patterns in specific loci, which should be further scrutinized to assess their role in heat tolerance.
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Affiliation(s)
- Marcello Del Corvo
- Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Barbara Lazzari
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Ludmilla Zavarez
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Marco Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Yuri Tani Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Adam Taiti Harth Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Milan, Italy
| | - Guilherme de Paula Nogueira
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil
| | - Josè Fernando Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Paolo Ajmone-Marsan
- Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
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36
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Yang YF, Yu B, Zhang XX, Zhu YH. Identification of TNIK as a novel potential drug target in thyroid cancer based on protein druggability prediction. Medicine (Baltimore) 2021; 100:e25541. [PMID: 33879700 PMCID: PMC8078263 DOI: 10.1097/md.0000000000025541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/25/2021] [Indexed: 01/04/2023] Open
Abstract
Thyroid cancer is a common endocrine malignancy; however, surgery remains its primary treatment option. A novel targeted drug for the development and application of targeted therapy in thyroid cancer treatment remain underexplored.We obtained RNA sequence data of thyroid cancer from The Cancer Genome Atlas database and identified differentially expressed genes (DEGs). Then, we constructed co-expression network with DEGs and combined it with differentially methylation analysis to screen the key genes in thyroid cancer. PockDrug-Server, an online tool, was applied to predict the druggability of the key genes. Finally, we constructed protein-protein interaction (PPI) network to observe potential targeted drugs for thyroid cancer.We identified 3 genes correlated with altered DNA methylation level and oncogenesis of thyroid cancer. According to the druggable analysis and PPI network, we predicted TRAF2 and NCK-interacting protein kinase (TNIK) sever as the drug targeted for thyroid cancer. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that genes in protein-protein interaction network of TNIK enriched in mitogen-activated protein kinase signaling pathway. For drug repositioning, we identified a targeted drug of genes in PPI network.Our study provides a bioinformatics method for screening drug targets and provides a theoretical basis for thyroid cancer targeted therapy.
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37
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Deepak Singh D, Han I, Choi EH, Yadav DK. CRISPR/Cas9 based genome editing for targeted transcriptional control in triple-negative breast cancer. Comput Struct Biotechnol J 2021; 19:2384-2397. [PMID: 34025931 PMCID: PMC8120801 DOI: 10.1016/j.csbj.2021.04.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) is the most common type of cancer in women at the global level and the highest mortality rate has been observed with triple-negative breast cancer (TNBC). Accumulation of genetic lesions an aberrant gene expression and protein degradation are considered to underlie the onset of tumorigenesis and metastasis. Therefore, the challenge to identify the genes and molecules that could be potentially used as potent biomarkers for personalized medicine against TNBC with minimal or no associated side effects. Discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) arrangement and an increasing repertoire of its new variants has provided a much-needed fillip towards editing TNBC genomes. In this review, we discuss the CRISPR/Cas9 genome editing, CRISPR Technology for diagnosis of (Triple-negative breast cancer) TNBC, Drug Resistance, and potential applications of CRISPR/Cas9 and its variants in deciphering or engineering intricate molecular and epigenetic mechanisms associated with TNBC. Furthermore, we have also explored the TNBC and CRISPR/Cas9 genome editing potential for repairing, genetic modifications in TNBC.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul, Republic of Korea
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro 191, Yeonsu-gu, Incheon City, Republic of Korea
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38
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Fu CN, Song JW, Song ZP, Wang QW, Bai WW, Guo T, Li P, Liu C, Wang SX, Dong B. Excessive expression of miR-1a by statin causes skeletal injury through targeting mitogen-activated protein kinase kinase kinase 1. Aging (Albany NY) 2021; 13:11470-11490. [PMID: 33864447 PMCID: PMC8109097 DOI: 10.18632/aging.202839] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022]
Abstract
Backgrounds: A major side effect of statin, a widely used drug to treat hyperlipidemia, is skeletal myopathy through cell apoptosis. The aim of this study is to investigate the roles of microRNA in statin-induced injury. Methods: Apolipoprotein E knockout (ApoE-/-) mice were administered with simvastatin (20 mg/kg/day) for 8 weeks. Exercise capacity was evaluated by hanging grid test, forelimb grip strength, and running tolerance test. Results: In cultured skeletal muscle cells, statin increased the levels of miR-1a but decreased the levels of mitogen-activated protein kinase kinase kinase 1 (MAP3K1) in a time or dose dependent manner. Both computational target-scan analysis and luciferase gene reporter assay indicated that MAP3K1 is the target gene of miR-1a. Statin induced cell apoptosis of skeletal muscle cells, but abolished by downregulating of miR-1a or upregulation of MAP3K1. Further, the effects of miR-1a inhibition on statin-induced cell apoptosis were ablated by MAP3K1 siRNA. In ApoE-/- mice, statin induced cell apoptosis of skeletal muscle cells and decreased exercise capacity in mice infected with vector, but not in mice with lentivirus-mediated miR-1a gene silence. Conclusion: Statin causes skeletal injury through induction of miR-1a excessive expression to decrease MAP3K1 gene expression.
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Affiliation(s)
- Chang-Ning Fu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Cardiology, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Jia-Wen Song
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhi-Peng Song
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qian-Wen Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wen-Wu Bai
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tao Guo
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Peng Li
- Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
| | - Shuang-Xi Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Henan International Joint Laboratory of Cardiovascular Remodeling and Drug Intervention, School of Pharmacy, Xinxiang Medical University, Xinxiang, China.,Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
| | - Bo Dong
- Department of Cardiology, Shandong Provincial Hospital, Shandong University, Jinan, China
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Molecular features of tumor-derived genetic alterations in circulating cell-free DNA in virtue of autopsy analysis. Sci Rep 2021; 11:8398. [PMID: 33863951 PMCID: PMC8052353 DOI: 10.1038/s41598-021-87094-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/23/2021] [Indexed: 12/28/2022] Open
Abstract
In cancer patients, circulating cell-free DNA (cfDNA) includes tumor-derived DNA (tDNA). cfDNA has been used clinically for non-invasive gene mutation testing. The aim of this study was to characterize the features of the genetic alterations detected in cfDNA. This study included 6 patients with primary lung cancer who died due to cancer progression. Tumors were biopsied at autopsy. Genetic alteration profiles were obtained using next generation sequencing. The features of the tDNA genetic alterations detected in cfDNA included a higher frequency of being present in multiple tumors (67% truncal mutations, 36% shared mutations, and 4% individual mutations) and a higher variant allele frequency (VAF; 47.6% versus 4.1% for tDNA alterations detected in cfDNA versus not detected in cfDNA, respectively). The data revealed that the tumor-derived genetic alterations most easily detected in cfDNA were truncal mutations with a high VAF. These results showed that essential genetic alterations enriched in cfDNA could help to characterize cancer cells and that genetic testing using cfDNA has advantages in the detection of fundamental regulatory aberrations occurring during tumorigenesis.
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40
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Novel compound variants of the AR and MAP3K1 genes are related to the clinical heterogeneity of androgen insensitivity syndrome. Biosci Rep 2021; 40:222776. [PMID: 32338288 PMCID: PMC7953519 DOI: 10.1042/bsr20200616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Androgen insensitivity syndrome (AIS; OMIM 300068) is the most frequent cause of 46, XY disorders of sex development (DSD). However, the correlation between genotype and phenotype has not been determined. We conducted a systematic analysis of the clinical characteristics, hormone levels, ultrasonography data and histopathology of a 46, XY Chinese patient with AIS. The family was followed up for nearly 8 years. We applied whole-exome sequencing (WES) for genetic analysis of the pedigree and performed bioinformatic analysis of the identified variants. Human embryonic kidney 293T/17 (HEK293T/17) cells were transiently transfected with wild-type or mutant AR and MAP3K1 plasmid. Cell lysates were used to analyze androgen receptor (AR) production. A novel hemizygous AR variant (c.2070C>A, p. His690Glu) and a rare heterozygous MAP3K1 variant (c.778C>T, p. Arg260Cys) were identified by WES in the proband and her mother. Bioinformatic analysis predicted these two variants to be pathogenic. Multiple amino acid sequence alignments showed that p. His690 and p. Arg260 are conserved among various species. His690Glu is a mutation that decreased the AR production, whereas the Arg260Cys mutation increased the AR production. The novel compound variants of the AR and MAP3K1 genes also increased the production of AR protein. Thus, the phenotype of the patient may be caused by defects in both the AR and MAP3K1 signaling pathways. Compound variants of the AR and MAP3K1 genes resulted in a specific phenotype in this patient with AIS. WES might reveal genetic variants that explain the heterogeneity of AIS.
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41
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JNK signaling as a target for anticancer therapy. Pharmacol Rep 2021; 73:405-434. [PMID: 33710509 DOI: 10.1007/s43440-021-00238-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/30/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022]
Abstract
The JNKs are members of mitogen-activated protein kinases (MAPK) which regulate many physiological processes including inflammatory responses, macrophages, cell proliferation, differentiation, survival, and death. It is increasingly clear that the continuous activation of JNKs has a role in cancer development and progression. Therefore, JNKs represent attractive oncogenic targets for cancer therapy using small molecule kinase inhibitors. Studies showed that the two major JNK proteins JNK1 and JNK2 have opposite functions in different types of cancers, which need more specification in the design of JNK inhibitors. Some of ATP- competitive and ATP non-competitive inhibitors have been developed and widely used in vitro, but this type of inhibitors lack selectivity and inhibits phosphorylation of all JNK substrates and may lead to cellular toxicity. In this review, we summarized and discussed the strategies of JNK binding inhibitors and the role of JNK signaling in the pathogenesis of different solid and hematological malignancies.
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42
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Qin Y, Li T, Zhao H, Mao Z, Ding C, Kang Y. Integrated Transcriptomic and Epigenetic Study of PCOS: Impact of Map3k1 and Map1lc3a Promoter Methylation on Autophagy. Front Genet 2021; 12:620241. [PMID: 33763111 PMCID: PMC7982605 DOI: 10.3389/fgene.2021.620241] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a prevalent heterogeneous endocrine and metabolic disorder in women of reproductive age. Epigenetic mechanisms contribute to the development of PCOS. Nevertheless, the role of DNA methylation in the development of PCOS remains unclear. To investigate the molecular mechanisms underlying the hyperandrogenic phenotype of PCOS, dihydrotestosterone (DHT)-induced prenatally androgenized (PNA) mice were used to mimic this phenotype. Ovarian samples from PNA and control mice were subjected to methyl-CpG-binding domain (MBD)-seq and RNA-seq, and validation was conducted using methylation-specific polymerase chain reaction (MSP) and quantitative real-time PCR (RT-qPCR). Immunohistochemical analysis (using anti-LC3II antibody) and transmission electron microscopy were conducted using ovarian tissue sections (which included granulosa cells) from PNA and control mice. There were 857 genes with differentially methylated promoter regions and 3,317 differentially expressed genes (DEGs) in the PNA mice compared to the control mice. Downregulation of Dnmt1 (which encodes DNA methyltransferase 1), accompanied by global hypomethylation, was observed in the PNA mice compared to the control mice. The promoter regions of Map3k1 (which encodes MEKK1) and Map1lc3a (which encodes LC3II) were hypomethylated, accompanied by upregulation of Map3k1 and Map1lc3a mRNA expression. The autophagy profiling results showed that LC3II protein expression and autophagosomes were significantly increased in the granulosa cells of PNA mice. Additionally, the mRNA expression of genes related to the mitogen-activated protein kinase (MAPK)/p53 pathway (Mapk14, Mapkapk3, and Trp53) and the autophagy-related gene Becn1 were significantly increased. DHT could change the DNA methylation and transcription level of Map3k1 and lead to an activation of autophagy in granulosa cells. These observations indicated that the change in autophagy may be driven by MAPK/p53 pathway activation, which may have been caused by DHT-induced transcriptional, and the methylation level changed of the key upstream gene Map3k1. Our study provides a novel genetic basis and new insights regarding the pathogenesis of PCOS.
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Affiliation(s)
- Yulan Qin
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Li
- Department of Obstetrics and Gynecology, Yuncheng Central Hospital, Yuncheng, China
| | - Hui Zhao
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Zhanrui Mao
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Chunxia Ding
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yani Kang
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
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Liu CC, Veeraraghavan J, Tan Y, Kim JA, Wang X, Loo SK, Lee S, Hu Y, Wang XS. A Novel Neoplastic Fusion Transcript, RAD51AP1-DYRK4, Confers Sensitivity to the MEK Inhibitor Trametinib in Aggressive Breast Cancers. Clin Cancer Res 2021; 27:785-798. [PMID: 33172895 PMCID: PMC7934498 DOI: 10.1158/1078-0432.ccr-20-2769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/18/2020] [Accepted: 11/04/2020] [Indexed: 01/19/2023]
Abstract
PURPOSE Luminal B breast tumors are more aggressive estrogen receptor-positive (ER+) breast cancers characterized by aggressive clinical behavior and a high risk of metastatic dissemination. The underlying pathologic molecular events remain poorly understood with a paucity of actionable genetic drivers, which hinders the development of new treatment strategies. EXPERIMENTAL DESIGN We performed large-scale RNA sequencing analysis to identify chimerical transcripts preferentially expressed in luminal B breast cancer. The lead candidate was validated by reverse transcription PCR in breast cancer tissues. The effects of inducible ectopic expression or genetic silencing were assessed by phenotypic assays such as MTS, transwell, and transendothelial migration assays, and by clonogenic assays to assess MEK inhibitor sensitivity. Subcellular fractionation, Western blots, and immunoprecipitation were performed to characterize the protein products and elucidate the engaged mechanisms. RESULTS Here we report a novel tumor-specific chimeric transcript RAD51AP1-DYRK4 preferentially expressed in luminal B tumors. Analysis of 200 ER+ breast tumors detected RAD51AP1-DYRK4 overexpression in 19 tumors (9.5%), which is markedly enriched in the luminal B tumors (17.5%). Ectopic expression of RAD51AP1-DYRK4, but not wild-type RAD51AP1, leads to marked activation of MEK/ERK signaling, and endows increased cell motility and transendothelial migration. More importantly, RAD51AP1-DYRK4 appears to endow increased sensitivity to the MEK inhibitor trametinib through attenuating compensatory activation of HER2/PI3K/AKT under MEK inhibition. CONCLUSIONS This discovery sheds light on a new area of molecular pathobiology of luminal B tumors and implies potential new therapeutic opportunities for more aggressive breast tumors overexpressing this fusion.
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Affiliation(s)
- Chia-Chia Liu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jamunarani Veeraraghavan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ying Tan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jin-Ah Kim
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xian Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
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44
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Efficient gene expression signature for a breast cancer immuno-subtype. PLoS One 2021; 16:e0245215. [PMID: 33434192 PMCID: PMC7802952 DOI: 10.1371/journal.pone.0245215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022] Open
Abstract
MOTIVATION AND BACKGROUND The patient's immune system plays an important role in cancer pathogenesis, prognosis and susceptibility to treatment. Recent work introduced an immune related breast cancer. This subtyping is based on the expression profiles of the tumor samples. Specifically, one study showed that analyzing 658 genes can lead to a signature for subtyping tumors. Furthermore, this classification is independent of other known molecular and clinical breast cancer subtyping. Finally, that study shows that the suggested subtyping has significant prognostic implications. RESULTS In this work we develop an efficient signature associated with survival in breast cancer. We begin by developing a more efficient signature for the above-mentioned breast cancer immune-based subtyping. This signature represents better performance with a set of 579 genes that obtains an improved Area Under Curve (AUC). We then determine a set of 193 genes and an associated classification rule that yield subtypes with a much stronger statistically significant (log rank p-value < 2 × 10-4 in a test cohort) difference in survival. To obtain these improved results we develop a feature selection process that matches the high-dimensionality character of the data and the dual performance objectives, driven by survival and anchored by the literature subtyping.
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Ma H, Song B, Guo S, Li G, Jin G. Identification of germline and somatic mutations in pancreatic adenosquamous carcinoma using whole exome sequencing. Cancer Biomark 2020; 27:389-397. [PMID: 31958074 DOI: 10.3233/cbm-190236] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Pancreatic cancer is one of the most lethal malignancies worldwide. Pancreatic adenosquamous carcinoma (PASC) is a rare histological type of pancreatic carcinoma with a poor prognosis. The median survival time after diagnosis is less than one year. It is believed that the pathogenesis of PASC is different from pancreatic adenocarcinoma. In this study, we tried to reveal the intrinsic gene mutations associated with PASC through whole exome sequencing. METHODS Both cancerous and paracancerous tissues were collected from 12 pathologically diagnosed PASC patients. Their clinical characteristics were collected, and patient survival information was obtained through follow-up. The correlations between the mutations and clinical characteristics were analysed. RESULTS Germline mutations were identified in MAP3K1 (9 cases), PDE4DIP (7), BCR (7), ALK (6), USP6 (5), AR (4), HLA-A (4), SPEN (4), KMT2D (3), NUTM2B (3), ZFHX3 (3), and MN1 (3), while somatic mutations were found in TP53 (5), KRAS (3), HRNR (3), and OBSCN (3). Peripheral tissue invasion was associated with somatic mutations in KRAS (P= 0.0339). Additionally, there were significant correlations between lymphatic metastasis and germline mutations in USP6 (P= 0.0228) and somatic mutations in OBSCN and HRNR (P= 0.0339). CONCLUSION In conclusion, susceptibility genes including MAP3K1, PDE4DIP, and BCR are frequently found to be mutated in the germlines of PASC patients. Somatic mutations in KRAS, OBSCN, and HRNR and germline mutations in USP6 are related to tumour invasion and metastasis, reinforcing the necessity of translating these potential biomarkers into clinical practice.
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Affiliation(s)
- Hongyun Ma
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bin Song
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Shiwei Guo
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gang Li
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Gang Jin
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute for Advanced Communication and Data Science, Shanghai University, Shanghai, China
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Sweett H, Fonseca PAS, Suárez-Vega A, Livernois A, Miglior F, Cánovas A. Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle. Sci Rep 2020; 10:20102. [PMID: 33208801 PMCID: PMC7676258 DOI: 10.1038/s41598-020-75758-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
Fertility plays a key role in the success of calf production, but there is evidence that reproductive efficiency in beef cattle has decreased during the past half-century worldwide. Therefore, identifying animals with superior fertility could significantly impact cow-calf production efficiency. The objective of this research was to identify candidate regions affecting bull fertility in beef cattle and positional candidate genes annotated within these regions. A GWAS using a weighted single-step genomic BLUP approach was performed on 265 crossbred beef bulls to identify markers associated with scrotal circumference (SC) and sperm motility (SM). Eight windows containing 32 positional candidate genes and five windows containing 28 positional candidate genes explained more than 1% of the genetic variance for SC and SM, respectively. These windows were selected to perform gene annotation, QTL enrichment, and functional analyses. Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. A different set of 14 prioritized genes were identified for SM and five were previously identified as regulators of male fertility (SOD2, TCP1, PACRG, SPEF2, PRLR). Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. Gene ontology enrichment analysis including biological processes, molecular functions, and cellular components revealed significant GO terms associated with male fertility. The identification of these regions contributes to a better understanding of fertility associated traits and facilitates the discovery of positional candidate genes for future investigation of causal mutations and their implications.
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Affiliation(s)
- H Sweett
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - P A S Fonseca
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Suárez-Vega
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Livernois
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Patient-derived xenograft (PDX) models of colorectal carcinoma (CRC) as a platform for chemosensitivity and biomarker analysis in personalized medicine. Neoplasia 2020; 23:21-35. [PMID: 33212364 PMCID: PMC7680704 DOI: 10.1016/j.neo.2020.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 12/16/2022] Open
Abstract
Patient-derived xenograft (PDX) tumor models represent a valuable platform for identifying new biomarkers and novel targets, to evaluate therapy response and resistance mechanisms. This study aimed at establishment, characterization and therapy testing of colorectal carcinoma-derived PDX. We generated 49 PDX and validated identity between patient tumor and corresponding PDX. Sensitivity of PDX toward conventional and targeted drugs revealed that 92% of PDX responded toward irinotecan, 45% toward 5-FU, 65% toward bevacizumab, and 61% toward cetuximab. Expression of epidermal growth factor receptor (EGFR) ligands correlated to the sensitivity toward cetuximab. Proto-oncogene B-RAF, EGFR, Kirsten rat sarcoma virus oncogene homolog gene copy number correlated positively with cetuximab and erlotinib sensitivity. The mutational analyses revealed an individual mutational profile of PDX and mainly identical profiles of PDX from primary tumor vs corresponding metastasis. Mutation in PIK3CA was a determinant of accelerated tumor doubling time. PDX with wildtype Kirsten rat sarcoma virus oncogene homolog, proto-oncogene B-RAF, and phosphatidylinositol-4,5-bisphosphate 3-kinaseM catalytic subunit alfa showed higher sensitivity toward cetuximab and erlotinib. To study the molecular mechanism of cetuximab resistance, cetuximab resistant PDX models were generated, and changes in HER2, HER3, betacellulin, transforming growth factor alfa were observed. Global proteome and phosphoproteome profiling showed a reduction in canonical EGFR-mediated signaling via PTPN11 (SHP2) and AKT1S1 (PRAS40) and an increase in anti-apoptotic signaling as a consequence of acquired cetuximab resistance. This demonstrates that PDX models provide a multitude of possibilities to identify and validate biomarkers, signaling pathways and resistance mechanisms for clinically relevant improvement in cancer therapy.
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AL-Eitan LN, ababa’h DM, Aman HA. The Associations of Common Genetic Susceptibility Variants with Breast Cancer in Jordanian Arabs: A Case-Control Study. Asian Pac J Cancer Prev 2020; 21:3045-3054. [PMID: 33112566 PMCID: PMC7798142 DOI: 10.31557/apjcp.2020.21.10.3045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE In Jordan, breast cancer (BC) affects a substantial proportion of Jordanian women, highlighting the need for studies to be carried out regarding the genetic component of the disease. The aim of the present study was to investigate the interaction between BC risk and prognosis and polymorphisms in genes (ATM, CASP8, FGFR2, FN1, IGF1, LSP1, MAP3K, MMP7, and RHOC) that were chosen for this study previously reported as having a role in the disease. MATERIALS AND METHODS Blood samples were collected from 242 BC patients and 231 disease-free volunteers recruited from the Jordanian population. DNA was extracted from blood and each sample was sent to the Australian Genome Research Facility for genotyping. RESULTS The rs1219648 SNP of the FGFR2 gene was the only investigated variant to show any direct association with BC in Jordanian women (p-value = 0.04). However, the CASP8rs6760993 SNP was found to be significantly associated with BC (p-value = 0.04) when using the dominant model. Other gene polymorphisms showed varying levels of association between some investigated SNPs and different BC risk and prognostic factors. CONCLUSION Despite reports to the contrary in other populations, most of the investigated genes and their respective SNPs did not show any significant association with BC in Jordanian women. Our results underline the need for independent BC research to be carried out in the Jordanian population to decipher the genetic basis of the disease. .
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Affiliation(s)
- Laith N AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Doaa M ababa’h
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Hatem A Aman
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
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Yang Y, Zhou Q, Pan H, Wang L, Qian C. Association Study of MAP3K1 SNPs and Risk Factors with Susceptibility to Esophageal Squamous Cell Carcinoma in a Chinese Population: A Case-Control Study. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2020; 13:189-197. [PMID: 32753933 PMCID: PMC7342385 DOI: 10.2147/pgpm.s256230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/04/2020] [Indexed: 11/23/2022]
Abstract
Purpose The aim of this study was to screen the predisposed population and explore possible interactions between genetic polymorphisms and risk factors involved in the tumorigenesis and progression of ESCC (esophageal squamous cell carcinoma), in hope of identifying possible therapeutic targets along the way. Patients and Methods Cases (1043) and controls (1315) were enrolled to evaluate the possible association between MAP3K1 SNPs and ESCC risk. Subgroup analyses include MAP3K1 variants, gender, age, smoking and drinking status. Results Among all three single locus polymorphisms of MAP3K1, only the heterozygote genotype of rs702689 AG is shown to be associated with increased risk for developing ESCC (OR=1.272, 95% confidence interval=1.061–1.525, p=0.009). Moreover, stratified analysis results observed altered susceptibility among patients with exposure to risk factors combined with certain genetic variant to ESCC. Conclusion This study reveals that MAP3K1 rs702689 AG genotype might facilitate the tumorigenesis in ESCC, particularly among women, patients who were over 63y and those who never drink nor smoke.
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Affiliation(s)
- Yiling Yang
- Department of Oncology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
| | - Qiang Zhou
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
| | - Huiwen Pan
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China
| | - Liming Wang
- Department of Oncology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu 212002, People's Republic of China.,Department of Respiratory, Xuhui Hospital-Affiliated Hospital of Zhongshan Hospital of Fudan University, Shanghai 200032, People's Republic of China
| | - Cheng Qian
- Department of Thoracic Surgery, Zhongshan Hospital of Fudan University, Shanghai 200032, People's Republic of China
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A lncRNA landscape in breast cancer reveals a potential role for AC009283.1 in proliferation and apoptosis in HER2-enriched subtype. Sci Rep 2020; 10:13146. [PMID: 32753692 PMCID: PMC7403317 DOI: 10.1038/s41598-020-69905-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 07/19/2020] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is the most commonly diagnosed neoplasm in women worldwide with a well-recognized heterogeneous pathology, classified into four molecular subtypes: Luminal A, Luminal B, HER2-enriched and Basal-like, each one with different biological and clinical characteristics. Long non-coding RNAs (lncRNAs) represent 33% of the human transcriptome and play critical roles in breast carcinogenesis, but most of their functions are still unknown. Therefore, cancer research could benefit from continued exploration into the biology of lncRNAs in this neoplasm. We characterized lncRNA expression portraits in 74 breast tumors belonging to the four molecular subtypes using transcriptome microarrays. To infer the biological role of the deregulated lncRNAs in the molecular subtypes, we performed co-expression analysis of lncRNA-mRNA and gene ontology analysis. We identified 307 deregulated lncRNAs in tumor compared to normal tissue and 354 deregulated lncRNAs among the different molecular subtypes. Through co-expression analysis between lncRNAs and protein-coding genes, along with gene enrichment analysis, we inferred the potential function of the most deregulated lncRNAs in each molecular subtype, and independently validated our results taking advantage of TCGA data. Overexpression of the AC009283.1 was observed in the HER2-enriched subtype and it is localized in an amplification zone at chromosome 17q12, suggesting it to be a potential tumorigenic lncRNA. The functional role of lncRNA AC009283.1 was examined through loss of function assays in vitro and determining its impact on global gene expression. These studies revealed that AC009283.1 regulates genes involved in proliferation, cell cycle and apoptosis in a HER2 cellular model. We further confirmed these findings through ssGSEA and CEMITool analysis in an independent HER2-amplified breast cancer cohort. Our findings suggest a wide range of biological functions for lncRNAs in each breast cancer molecular subtype and provide a basis for their biological and functional study, as was conducted for AC009283.1, showing it to be a potential regulator of proliferation and apoptosis in the HER2-enriched subtype.
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