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Li W, Yu Y, Zhou G, Hu G, Li B, Ma H, Yan W, Pei H. Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity. Comput Struct Biotechnol J 2023; 21:5201-5211. [PMID: 37928948 PMCID: PMC10624585 DOI: 10.1016/j.csbj.2023.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
In the human genome, 98% of genes can be transcribed into non-coding RNAs (ncRNAs), among which lncRNAs and their encoded peptides play important roles in regulating various aspects of cellular processes and may serve as crucial factors in modulating the biological effects induced by ionizing radiation and microgravity. Unfortunately, there are few reports in space radiation biology on lncRNA-encoded peptides below 10kD due to limitations in detection techniques. To fill this gap, we integrated a variety of methods based on genomics and peptidomics, and discovered 22 lncRNA-encoded small peptides that are sensitive to space radiation and microgravity, which have never been reported before. We concurrently validated the transmembrane helix, subcellular localization, and biological function of these small peptides using bioinformatics and molecular biology techniques. More importantly, we found that these small peptides function independently of the lncRNAs that encode them. Our findings have uncovered a previously unknown human proteome encoded by 'non-coding' genes in response to space conditions and elucidated their involvement in biological processes, providing valuable strategies for individual protection mechanisms for astronauts who carry out deep space exploration missions in space radiation environments.
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Affiliation(s)
- Wanshi Li
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yongduo Yu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Guang Hu
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Center for Systems Biology, Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Bingyan Li
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Hong Ma
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Wenying Yan
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Center for Systems Biology, Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Hailong Pei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
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Fankhauser D, Alissandratos A, Liutkus M, Easton CJ. Easy Production of "Difficult Peptides" Using Cell-Free Protein Synthesis and a New Methionine Analogue as a Latent Peptide Cleavage Site. Chemistry 2021; 27:17487-17494. [PMID: 34651362 DOI: 10.1002/chem.202103161] [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: 08/31/2021] [Indexed: 11/08/2022]
Abstract
Aliphatic γ-chloro-α-amino acids incorporated in place of their canonical analogues through cell-free protein synthesis act as heat-labile linkers, offering a useful strategy for the straightforward production of target peptides as fusion proteins, from which the targets are readily released. Until now, the natural abundance of aliphatic amino acids in peptides has limited the scope of the method, as it leads to undesired cleavage sites in synthesized products, but here the authors report the development of a new cleavable chloro amino acid that incorporates in place of the relatively rare amino acid methionine, thus greatly expanding the scope of producible targets. This new strategy is employed for simplified peptide synthesis with a methionine-free fusion partner, allowing single-site incorporation of the cleavable linker for clean release and easy purification of the target peptide. Its utility is demonstrated through the straightforward preparation of two peptides reported to be challenging targets and not accessible through standard solid-phase chemical methodologies, as well as analogues.
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Affiliation(s)
- Daniel Fankhauser
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Apostolos Alissandratos
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Mantas Liutkus
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, 137 Sullivans Creek Road, Acton, ACT 2601, Australia
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4
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Łuksza M, Riaz N, Makarov V, Balachandran VP, Hellmann MD, Solovyov A, Rizvi NA, Merghoub T, Levine AJ, Chan TA, Wolchok JD, Greenbaum BD. A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy. Nature 2017; 551:517-520. [PMID: 29132144 DOI: 10.1038/nature24473] [Citation(s) in RCA: 457] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 10/09/2017] [Indexed: 12/12/2022]
Abstract
Checkpoint blockade immunotherapies enable the host immune system to recognize and destroy tumour cells. Their clinical activity has been correlated with activated T-cell recognition of neoantigens, which are tumour-specific, mutated peptides presented on the surface of cancer cells. Here we present a fitness model for tumours based on immune interactions of neoantigens that predicts response to immunotherapy. Two main factors determine neoantigen fitness: the likelihood of neoantigen presentation by the major histocompatibility complex (MHC) and subsequent recognition by T cells. We estimate these components using the relative MHC binding affinity of each neoantigen to its wild type and a nonlinear dependence on sequence similarity of neoantigens to known antigens. To describe the evolution of a heterogeneous tumour, we evaluate its fitness as a weighted effect of dominant neoantigens in the subclones of the tumour. Our model predicts survival in anti-CTLA-4-treated patients with melanoma and anti-PD-1-treated patients with lung cancer. Importantly, low-fitness neoantigens identified by our method may be leveraged for developing novel immunotherapies. By using an immune fitness model to study immunotherapy, we reveal broad similarities between the evolution of tumours and rapidly evolving pathogens.
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Affiliation(s)
- Marta Łuksza
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vladimir Makarov
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vinod P Balachandran
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Alexander Solovyov
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Naiyer A Rizvi
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Taha Merghoub
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arnold J Levine
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jedd D Wolchok
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin D Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Bohórquez HJ, Suárez CF, Patarroyo ME. Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements. Sci Rep 2017; 7:7717. [PMID: 28798365 PMCID: PMC5552740 DOI: 10.1038/s41598-017-08041-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022] Open
Abstract
Why is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn ↔ Asp, Phe ↔ Tyr, Lys ↔ Arg, Gln ↔ Glu, Ile ↔ Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation (\documentclass[12pt]{minimal}
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\begin{document}$$\overline{R}$$\end{document}R¯ = 0.85) between thirty amino acid mutability scales and the mutational inertia (IX), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions.
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Affiliation(s)
- Hugo J Bohórquez
- Bio-mathematics, Fundación Instituto de Inmunología de Colombia, FIDIC, Cra. 50 No. 26-00, Of. 102, Bogotá DC, 111321160, Cundinamarca, Colombia.
| | - Carlos F Suárez
- Bio-mathematics, Fundación Instituto de Inmunología de Colombia, FIDIC, Cra. 50 No. 26-00, Of. 102, Bogotá DC, 111321160, Cundinamarca, Colombia.,Universidad de Ciencias Aplicadas y Ambientales, UDCA, Bogotá DC, Colombia.,Universidad del Rosario, Bogotá DC, Colombia
| | - Manuel E Patarroyo
- Bio-mathematics, Fundación Instituto de Inmunología de Colombia, FIDIC, Cra. 50 No. 26-00, Of. 102, Bogotá DC, 111321160, Cundinamarca, Colombia.,Universidad Nacional de Colombia, Bogotá DC, Colombia
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