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Zhang YM, Jia Z, Xie SQ, Wen J, Wang S, Zhang YW. Editorial: Advances in statistical methods for the genetic dissection of complex traits in plants. Front Plant Sci 2024; 15:1357564. [PMID: 38287980 PMCID: PMC10822929 DOI: 10.3389/fpls.2024.1357564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024]
Affiliation(s)
- Yuan-Ming Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Shang-Qian Xie
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID, United States
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shibo Wang
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Ya-Wen Zhang
- International Genome Center, Jiangsu University, Zhenjiang, China
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2
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Poverennaya EV, Pyatnitskiy MA, Dolgalev GV, Arzumanian VA, Kiseleva OI, Kurbatov IY, Kurbatov LK, Vakhrushev IV, Romashin DD, Kim YS, Ponomarenko EA. Exploiting Multi-Omics Profiling and Systems Biology to Investigate Functions of TOMM34. Biology (Basel) 2023; 12:biology12020198. [PMID: 36829477 PMCID: PMC9952762 DOI: 10.3390/biology12020198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/17/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Although modern biology is now in the post-genomic era with vastly increased access to high-quality data, the set of human genes with a known function remains far from complete. This is especially true for hundreds of mitochondria-associated genes, which are under-characterized and lack clear functional annotation. However, with the advent of multi-omics profiling methods coupled with systems biology algorithms, the cellular role of many such genes can be elucidated. Here, we report genes and pathways associated with TOMM34, Translocase of Outer Mitochondrial Membrane, which plays role in the mitochondrial protein import as a part of cytosolic complex together with Hsp70/Hsp90 and is upregulated in various cancers. We identified genes, proteins, and metabolites altered in TOMM34-/- HepG2 cells. To our knowledge, this is the first attempt to study the functional capacity of TOMM34 using a multi-omics strategy. We demonstrate that TOMM34 affects various processes including oxidative phosphorylation, citric acid cycle, metabolism of purine, and several amino acids. Besides the analysis of already known pathways, we utilized de novo network enrichment algorithm to extract novel perturbed subnetworks, thus obtaining evidence that TOMM34 potentially plays role in several other cellular processes, including NOTCH-, MAPK-, and STAT3-signaling. Collectively, our findings provide new insights into TOMM34's cellular functions.
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Affiliation(s)
| | - Mikhail A. Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow 119121, Russia
- Faculty Of Computer Science, National Research University Higher School of Economics, Moscow 101000, Russia
- Correspondence:
| | | | | | | | | | | | | | | | - Yan S. Kim
- Institute of Biomedical Chemistry, Moscow 119121, Russia
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Zheng F, Zhang W, Yang B, Chen M. Multi-omics profiling identifies C1QA/B + macrophages with multiple immune checkpoints associated with esophageal squamous cell carcinoma (ESCC) liver metastasis. Ann Transl Med 2022; 10:1249. [PMID: 36544679 PMCID: PMC9761157 DOI: 10.21037/atm-22-5351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is a highly lethal malignant tumor lacking effective treatments; 20% of ESCC patients develop liver metastasis with an extremely short survival time of ≈5 months. The tumor microenvironment (TME) plays a crucial role in tumor homeostasis, but the relationship between the ESCC TME and liver metastasis is still unknown. Methods To identify potential cell populations contributing to ESCC liver metastasis, single-cell RNA (scRNA) sequencing data were analyzed to identify the major cell populations within the TME. Each of the major cell populations was re-clustered to define detailed cell subsets. Thereafter, the gene set variation analysis (GSVA) score was calculated for the bulk RNA-seq data based on the gene signatures of each cell subset. The relationship between the GSVA score of each cellular subset and clinical outcome was further analyzed to identify the cellular subset associated with ESCC liver metastasis, which was validated by multiplex immunohistochemistry. Results C1QA/B+ tumor-associated macrophages (TAMs) acted as the central regulator of the ESCC TME, closely associated with several key cell subsets. Several immune checkpoints, including CD40, CD47 and LGALS9, were all positively expressed in C1QA/B+ macrophages, which may exert central regulatory control of immune evasion by ESCC via these immune checkpoints expressions. Conclusions Our results comprehensively revealed the landscape of tumor-infiltrating immune cells associated with ESCC prognosis and metastasis, and suggest a novel strategy for developing immunotherapies for ESCC liver metastasis by targeting C1QA/B+ TAMs.
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Affiliation(s)
- Fei Zheng
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Wei Zhang
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Baihua Yang
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Mingqiu Chen
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
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Li Z, Wang S, Liu S, Xu Z, Yi X, Wang H, Dang J, Wei X, Feng B, Liu Z, Zhao M, Wu Q, Hu D. New insights into aging-associated characteristics of female subcutaneous adipose tissue through integrative analysis of multi-omics data. Bioengineered 2022; 13:2044-2057. [PMID: 35001792 PMCID: PMC8973830 DOI: 10.1080/21655979.2021.2020467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aging could be critical in limiting the application of subcutaneous adipose tissue (SAT) in tissue repair and reconstruction. However, no systematic study on the characteristics of SAT aging has been conducted. In this study, a scanning electronic microscope was used to detect the structural and compositional changes of SAT collected from nine females in three age groups. Multi-omics data of SAT from 37 females were obtained from Gene Expression Omnibus database, and 1860 genes, 56 miRNAs, and 332 methylated genes were identified as being differentially expressed during aging among non-obese females. Using Weighted Correlation Network Analysis (WGCNA), 1754 DEGs were defined as aging-associated genes for non-obese females, distributed among ten co-expression modules. Through Gene Ontology enrichment analysis and Gene Set enrichment analysis on those aging-associated DEGs, SAT aging was observed to be characterized by variations in immune and inflammatory states, mitochondria, lipid and carbohydrate metabolism, and regulation of vascular development. SUPV3L1, OGT, and ARPC1B were identified as conserved and core SAT-aging-related genes, as verified by RT-qPCR among 18 samples in different age groups. Multi-omics regulatory networks of core aging-associated biological processes of SAT were also constructed. Based on WGCNA, we performed differential co-expression analysis to unveil the differences in aging-related co-expression patterns between obese and non-obese females and determined that obesity could be an important accelerating factor in aging processes. Our work provides a landscape of SAT aging, which could be helpful for further research in fields such as repair and reconstruction as well as aging.
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Affiliation(s)
- Zichao Li
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Shun Wang
- BD Life Science (Guangzhou) Co., Guangzhou Laidi Innovation and Technology Park, Guangzhou, Guangdong, China
| | - Shaojie Liu
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ziwen Xu
- Department of Basic Medicine, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xiaowei Yi
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongtao Wang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Juanli Dang
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xinxin Wei
- School of Stomatology, Jiamusi University, Jiamusi, Heilongjiang, China
| | - Bingyue Feng
- Department of Basic Medicine, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Zinuo Liu
- Department of Basic Medicine, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ming Zhao
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Qiong Wu
- Provincial Key Laboratory of Biotechnology of Shaanxi, Key Laboratory of Resource Biology and Modern Biotechnology in Western China, Faculty of Life Science, Northwest University, Xi'an, Shaanxi Province, China
| | - Dahai Hu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
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5
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Rauscher B, Mueller WF, Clauder-Münster S, Jakob P, Islam MS, Sun H, Ghidelli-Disse S, Boesche M, Bantscheff M, Pflaumer H, Collier P, Haase B, Chen S, Hoffman R, Wang G, Benes V, Drewes G, Snyder M, Steinmetz LM. Patient-derived gene and protein expression signatures of NGLY1 deficiency. J Biochem 2021; 171:187-199. [PMID: 34878535 DOI: 10.1093/jb/mvab131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/13/2021] [Indexed: 11/14/2022] Open
Abstract
N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parents, residual and likely non-functional NGLY1 protein was detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosome biogenesis and mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cysteine ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.
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Affiliation(s)
- Benedikt Rauscher
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | | | - Sandra Clauder-Münster
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Petra Jakob
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - M Saiful Islam
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Han Sun
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Markus Boesche
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Marcus Bantscheff
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Hannah Pflaumer
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Paul Collier
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Bettina Haase
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Songjie Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rene Hoffman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Guangwen Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Gerard Drewes
- Cellzome GmbH, a GlaxoSmithKline Company, Meyerhofstrasse 1, Heidelberg, Germany, 69117
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany, Meyerhofstrasse 1, Heidelberg, Germany, 69117.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
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6
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Hu C, Jia W. Multi-omics profiling: the way towards precision medicine in metabolic diseases. J Mol Cell Biol 2021; 13:mjab051. [PMID: 34406397 PMCID: PMC8697344 DOI: 10.1093/jmcb/mjab051] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Metabolic diseases including type 2 diabetes mellitus (T2DM), non-alcoholic fatty liver disease (NAFLD), and metabolic syndrome (MetS) are alarming health burdens around the world, while therapies for these diseases are far from satisfying as their etiologies are not completely clear yet. T2DM, NAFLD, and MetS are all complex and multifactorial metabolic disorders based on the interactions between genetics and environment. Omics studies such as genetics, transcriptomics, epigenetics, proteomics, and metabolomics are all promising approaches in accurately characterizing these diseases. And the most effective treatments for individuals can be achieved via omics pathways, which is the theme of precision medicine. In this review, we summarized the multi-omics studies of T2DM, NAFLD, and MetS in recent years, provided a theoretical basis for their pathogenesis and the effective prevention and treatment, and highlighted the biomarkers and future strategies for precision medicine.
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Affiliation(s)
- Cheng Hu
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus,
Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth
People's Hospital, Shanghai 200233, China
- Institute for Metabolic Disease, Fengxian Central Hospital, The Third School of
Clinical Medicine, Southern Medical University, Shanghai 201499, China
| | - Weiping Jia
- Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus,
Shanghai Clinical Center for Diabetes, Shanghai Jiao Tong University Affiliated Sixth
People's Hospital, Shanghai 200233, China
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Sun B, Bugarin-Estrada E, Overend LE, Walker CE, Tucci FA, Bashford-Rogers RJM. Double-jeopardy: scRNA-seq doublet/multiplet detection using multi-omic profiling. Cell Rep Methods 2021; 1:None. [PMID: 34278374 PMCID: PMC8262260 DOI: 10.1016/j.crmeth.2021.100008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/09/2021] [Accepted: 03/26/2021] [Indexed: 11/25/2022]
Abstract
The computational detection and exclusion of cellular doublets and/or multiplets is a cornerstone for the identification the true biological signals from single-cell RNA sequencing (scRNA-seq) data. Current methods do not sensitively identify both heterotypic and homotypic doublets and/or multiplets. Here, we describe a machine learning approach for doublet/multiplet detection utilizing VDJ-seq and/or CITE-seq data to predict their presence based on transcriptional features associated with identified hybrid droplets. This approach highlights the utility of leveraging multi-omic single-cell information for the generation of high-quality datasets. Our method has high sensitivity and specificity in inflammatory-cell-dominant scRNA-seq samples, thus presenting a powerful approach to ensuring high-quality scRNA-seq data.
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Affiliation(s)
- Bo Sun
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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Del Favero G, Bonifacio A, Rowland TJ, Gao S, Song K, Sergo V, Adler ED, Mestroni L, Sbaizero O, Taylor MRG. Danon Disease-Associated LAMP-2 Deficiency Drives Metabolic Signature Indicative of Mitochondrial Aging and Fibrosis in Cardiac Tissue and hiPSC-Derived Cardiomyocytes. J Clin Med 2020; 9:E2457. [PMID: 32751926 DOI: 10.3390/jcm9082457] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Danon disease is a severe X-linked disorder caused by deficiency of the lysosome-associated membrane protein-2 (LAMP-2). Clinical manifestations are phenotypically diverse and consist of hypertrophic and dilated cardiomyopathies, skeletal myopathy, retinopathy, and intellectual dysfunction. Here, we investigated the metabolic landscape of Danon disease by applying a multi-omics approach and combined structural and functional readouts provided by Raman and atomic force microscopy. Using these tools, Danon patient-derived cardiac tissue, primary fibroblasts, and human induced pluripotent stem cells differentiated into cardiomyocytes (hiPSC-CMs) were analyzed. Metabolic profiling indicated LAMP-2 deficiency promoted a switch toward glycolysis accompanied by rerouting of tryptophan metabolism. Cardiomyocytes' energetic balance and NAD+/NADH ratio appeared to be maintained despite mitochondrial aging. In turn, metabolic adaption was accompanied by a senescence-associated signature. Similarly, Danon fibroblasts appeared more stress prone and less biomechanically compliant. Overall, shaping of both morphology and metabolism contributed to the loss of cardiac biomechanical competence that characterizes the clinical progression of Danon disease.
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Qu N, Shi X, Zhao JJ, Guan H, Zhang TT, Wen SS, Liao T, Hu JQ, Liu WY, Wang YL, Huang S, Shi RL, Wang Y, Ji QH. Genomic and Transcriptomic Characterization of Sporadic Medullary Thyroid Carcinoma. Thyroid 2020; 30:1025-1036. [PMID: 32031055 DOI: 10.1089/thy.2019.0531] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background: Sporadic medullary thyroid carcinoma (MTC) is a relatively uncommon neuroendocrine malignancy and the molecular tumorigenesis of its sporadic type (sMTC) is only partially understood. In this study, we performed a study focusing on the genomic and transcriptomic characterization of sMTC. Methods: Twenty-nine sMTC patients were included. Whole-exome sequencing (WES) was carried out in 18 patients, including both tumor samples and matched noncancerous tissues. Whole transcriptome sequencing (RNA-Seq) was performed in all 29 tumors. WES, RNA-Seq, and copy number alteration (CNA) data were analyzed. A Cell Counting Kit-8 (CCK-8) assay was used to evaluate cell proliferation. Results: Among the somatic mutations, RET was the only recurrently cancer-related mutated gene (5/18, 27.8%). In the germline, FAT1 and FAT4, two members of the FAT gene family, were identified as the two most common mutated genes. CNA analysis found that FAT1 and FAT4, both located on chromosome 4q, were also two of the genes most commonly affected by somatic chromosomal deletions (4/18, 22.2%). Using TT and MZ-CRC-1 cell lines, the CCK-8 assay showed that FAT1 and FAT4 knockdown could promote MTC cell proliferation. Based on the gene expression profile, patients were clustered into two molecular subtypes: the mesenchymal-like subtype is characterized by epithelial-mesenchymal transition, while the proliferative-like subtype is associated with enrichment of cell cycle pathways. Most events of structural recurrence (80%) occurred in the proliferative-like subtype. Conclusion: In addition to RET, these findings demonstrate that FAT1/FAT4 genomic alterations appear to be frequent in sMTC. Two molecular subtypes of sMTC with distinct biological behavior could be identified. However, these results need to be validated by larger samples and more comprehensive experiments in the future, especially for the frequency and function of FAT1/FAT4 germline variants.
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Affiliation(s)
- Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing-Jing Zhao
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Haixia Guan
- Department of Endocrinology and Metabolism, The First Hospital of China Medical University, China Medical University, Shenyang, P.R. China
| | - Ting-Ting Zhang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi-Shuai Wen
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tian Liao
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia-Qian Hu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei-Yan Liu
- Department of General Surgery, Minhang Hospital; Fudan University, Shanghai, P.R. China
| | - Yu-Long Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Rong-Liang Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qing-Hai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Abstract
Immunotherapy with checkpoint blockers (ICBs), aimed at unleashing the immune response toward tumor cells, has shown a great improvement in overall patient survival compared to standard therapy, but only in a subset of patients. While a number of recent studies have significantly improved our understanding of mechanisms playing an important role in the tumor microenvironment (TME), we still have an incomplete view of how the TME works as a whole. This hampers our ability to effectively predict the large heterogeneity of patients' response to ICBs. Systems approaches could overcome this limitation by adopting a holistic perspective to analyze the complexity of tumors. In this Mini Review, we focus on how an integrative view of the increasingly available multi-omics experimental data and computational approaches enables the definition of new systems-based predictive biomarkers. In particular, we will focus on three facets of the TME toward the definition of new systems biomarkers. First, we will review how different types of immune cells influence the efficacy of ICBs, not only in terms of their quantification, but also considering their localization and functional state. Second, we will focus on how different cells in the TME interact, analyzing how inter- and intra-cellular networks play an important role in shaping the immune response and are responsible for resistance to immunotherapy. Finally, we will describe the potential of looking at these networks as dynamic systems and how mathematical models can be used to study the rewiring of the complex interactions taking place in the TME.
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Affiliation(s)
- Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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Finotello F, Eduati F. Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology. Front Oncol 2018; 8:430. [PMID: 30345255 PMCID: PMC6182075 DOI: 10.3389/fonc.2018.00430] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/13/2018] [Indexed: 12/20/2022] Open
Abstract
The tumor microenvironment (TME) is a multifaceted ecosystem characterized by profound cellular heterogeneity, dynamicity, and complex intercellular cross-talk. The striking responses obtained with immune checkpoint blockers, i.e., antibodies targeting immune-cell regulators to boost antitumor immunity, have demonstrated the enormous potential of anticancer treatments that target TME components other than tumor cells. However, as checkpoint blockade is currently beneficial only to a limited fraction of patients, there is an urgent need to understand the mechanisms orchestrating the immune response in the TME to guide the rational design of more effective anticancer therapies. In this Mini Review, we give an overview of the methodologies that allow studying the heterogeneity of the TME from multi-omics data generated from bulk samples, single cells, or images of tumor-tissue slides. These include approaches for the characterization of the different cell phenotypes and for the reconstruction of their spatial organization and inter-cellular cross-talk. We discuss how this broader vision of the cellular heterogeneity and plasticity of tumors, which is emerging thanks to these methodologies, offers the opportunity to rationally design precision immuno-oncology treatments. These developments are fundamental to overcome the current limitations of targeted agents and checkpoint blockers and to bring long-term clinical benefits to a larger fraction of cancer patients.
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Affiliation(s)
- Francesca Finotello
- Biocenter, Division for Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
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12
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Feo F, Pascale RM. Multifocal hepatocellular carcinoma: intrahepatic metastasis or multicentric carcinogenesis? Ann Transl Med 2015; 3:4. [PMID: 25705636 DOI: 10.3978/j.issn.2305-5839.2014.12.08] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/08/2014] [Indexed: 12/28/2022]
Abstract
Multifocal Hepatocellular carcinoma (HCC) may be multiple HCCs of multicentric origin (MO) or intrahepatic metastases (IM) arising from a primary HCC. Numerous attempts to differentiate the two types of multifocal HCC have been made including the valuation of the clinicopathologic characteristics of MO and IM patients and the recurrence time, loss-of-heterozygosity analysis of specific DNA microsatellite loci to distinguish multiclonal MO from IM of monoclonal origin, and the research of diagnostic and progression markers through genomic and proteomic analyses. These approaches, however, have been unsatisfactory hitherto. Recently, a multi-omic analysis of HBV-related multifocal HCCs, including intergraded genomics and transcriptomics, was performed and the results, validated by a cohort of 174 HCC patients, were correlated with HCC clinicopathological data. The two multifocal HCC types were effectively discerned by multi-omics profiling that could predict HCC clonality and aggressiveness. Further, the dual-specificity protein kinase TTK was recognized as a prognostic marker for HCC. Multi-omics strategy potentially opens new perspectives for the diagnosis, prognosis and personalized treatment of multi-focal HCC. Further work aimed at extending this strategy to HCC with other etiology, simplifying the analysis, and reducing its costs is necessary for its routine clinical application.
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Affiliation(s)
- Francesco Feo
- Department of Clinical and Experimental Medicine, Division of Experimental Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Rosa M Pascale
- Department of Clinical and Experimental Medicine, Division of Experimental Pathology and Oncology, University of Sassari, Sassari, Italy
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