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Ariffin N, Newman DW, Nelson MG, O’cualain R, Hubbard SJ. Proteogenomic Gene Structure Validation in the Pineapple Genome. J Proteome Res 2024; 23:1583-1592. [PMID: 38651221 PMCID: PMC11077482 DOI: 10.1021/acs.jproteome.3c00675] [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: 10/13/2023] [Revised: 03/15/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
MD2 pineapple (Ananas comosus) is the second most important tropical crop that preserves crassulacean acid metabolism (CAM), which has high water-use efficiency and is fast becoming the most consumed fresh fruit worldwide. Despite the significance of environmental efficiency and popularity, until very recently, its genome sequence has not been determined and a high-quality annotated proteome has not been available. Here, we have undertaken a pilot proteogenomic study, analyzing the proteome of MD2 pineapple leaves using liquid chromatography-mass spectrometry (LC-MS/MS), which validates 1781 predicted proteins in the annotated F153 (V3) genome. In addition, a further 603 peptide identifications are found that map exclusively to an independent MD2 transcriptome-derived database but are not found in the standard F153 (V3) annotated proteome. Peptide identifications derived from these MD2 transcripts are also cross-referenced to a more recent and complete MD2 genome annotation, resulting in 402 nonoverlapping peptides, which in turn support 30 high-quality gene candidates novel to both pineapple genomes. Many of the validated F153 (V3) genes are also supported by an independent proteomics data set collected for an ornamental pineapple variety. The contigs and peptides have been mapped to the current F153 genome build and are available as bed files to display a custom gene track on the Ensembl Plants region viewer. These analyses add to the knowledge of experimentally validated pineapple genes and demonstrate the utility of transcript-derived proteomics to discover both novel genes and genetic structure in a plant genome, adding value to its annotation.
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Affiliation(s)
- Norazrin Ariffin
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
- Department
of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Selangor Darul Ehsan, Malaysia
| | - David Wells Newman
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Michael G. Nelson
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Ronan O’cualain
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
| | - Simon J. Hubbard
- School
of Biological Sciences, Faculty of Biology Medicine and Health, MAHSC, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
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2
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Wang C, Shi Z, Huang Q, Liu R, Su D, Chang L, Xiao C, Fan X. Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development. PLoS Biol 2024; 22:e3002505. [PMID: 38363809 PMCID: PMC10903961 DOI: 10.1371/journal.pbio.3002505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 02/29/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
Alternative splicing is an essential regulatory mechanism for development and pathogenesis. Through alternative splicing one gene can encode multiple isoforms and be translated into proteins with different functions. Therefore, this diversity is an important dimension to understand the molecular mechanism governing embryo development. Isoform expression in preimplantation embryos has been extensively investigated, leading to the discovery of new isoforms. However, the dynamics of isoform switching of different types of transcripts throughout the development remains unexplored. Here, using single-cell direct isoform sequencing in over 100 single blastomeres from the mouse oocyte to blastocyst stage, we quantified isoform expression and found that 3-prime partial transcripts lacking stop codons are highly accumulated in oocytes and zygotes. These transcripts are not transcription by-products and might play a role in maternal to zygote transition (MZT) process. Long-read sequencing also enabled us to determine the expression of transposable elements (TEs) at specific loci. In this way, we identified 3,894 TE loci that exhibited dynamic changes along the preimplantation development, likely regulating the expression of adjacent genes. Our work provides novel insights into the transcriptional regulation of early embryo development.
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Affiliation(s)
- Chaoyang Wang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingpei Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Rong Liu
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Dan Su
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Lei Chang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaoying Fan
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
- The Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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3
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Cervantes-Gracia K, Chahwan R, Husi H. Integrative OMICS Data-Driven Procedure Using a Derivatized Meta-Analysis Approach. Front Genet 2022; 13:828786. [PMID: 35186042 PMCID: PMC8855827 DOI: 10.3389/fgene.2022.828786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
The wealth of high-throughput data has opened up new opportunities to analyze and describe biological processes at higher resolution, ultimately leading to a significant acceleration of scientific output using high-throughput data from the different omics layers and the generation of databases to store and report raw datasets. The great variability among the techniques and the heterogeneous methodologies used to produce this data have placed meta-analysis methods as one of the approaches of choice to correlate the resultant large-scale datasets from different research groups. Through multi-study meta-analyses, it is possible to generate results with greater statistical power compared to individual analyses. Gene signatures, biomarkers and pathways that provide new insights of a phenotype of interest have been identified by the analysis of large-scale datasets in several fields of science. However, despite all the efforts, a standardized regulation to report large-scale data and to identify the molecular targets and signaling networks is still lacking. Integrative analyses have also been introduced as complementation and augmentation for meta-analysis methodologies to generate novel hypotheses. Currently, there is no universal method established and the different methods available follow different purposes. Herein we describe a new unifying, scalable and straightforward methodology to meta-analyze different omics outputs, but also to integrate the significant outcomes into novel pathways describing biological processes of interest. The significance of using proper molecular identifiers is highlighted as well as the potential to further correlate molecules from different regulatory levels. To show the methodology’s potential, a set of transcriptomic datasets are meta-analyzed as an example.
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Affiliation(s)
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
- *Correspondence: Richard Chahwan, ; Holger Husi,
| | - Holger Husi
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
- Division of Biomedical Sciences, Centre for Health Science, University of the Highlands and Islands, Inverness, United Kingdom
- *Correspondence: Richard Chahwan, ; Holger Husi,
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4
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Dunstan RW, Salte KM, Todorović V, Lowe M, Wetter JB, Harms PW, Burney RE, Scott VE, Smith KM, Rosenblum MD, Gudjonsson JE, Honore P. Histologic progression of acne inversa/hidradenitis suppurativa: Implications for future investigations and therapeutic intervention. Exp Dermatol 2021; 30:820-830. [PMID: 33377546 PMCID: PMC8247901 DOI: 10.1111/exd.14273] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/03/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Since first recognized in 1839, the pathogenesis of acne inversa (AI) has undergone repeated revisions. Although there is agreement that AI involves occlusion of hair follicles with subsequent inflammation and the formation of tracts, the histologic progression of this disease still requires refinement. The objective of this study was to examine the histologic progression of AI based on the examination of a large cohort of punch biopsies and excisional samples that were examined first by hematoxylin and eosin staining. The most informative of these samples were step‐sectioned and stained by immunohistochemistry for epithelial and inflammatory markers. Based on this examination, the following observations were made: 1) AI arises from the epithelium of the infundibulum of terminal and vellus hairs; 2) These form cysts and epithelial tendrils that extend into soft tissue; 3) Immunohistochemical staining demonstrates the epithelium of AI is disordered with infundibular and isthmic differentiation and de novo expression of stem cell markers; 4) The inflammatory response in AI is heterogeneous and largely due to cyst rupture. The conclusions of this investigation were that AI is an epithelial‐driven disease caused by infiltrative, cyst forming tendrils and most of the inflammation is due to cyst rupture and release of cornified debris and bacteria. Cyst rupture often occurs below the depths of punch biopsy samples indicating their use for analysis may give an incomplete picture of the disease. Finally, our data suggest that unless therapies inhibit tendril development, it is unlikely they will cause prolonged treatment‐induced remission in AI.
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Affiliation(s)
| | | | | | - Margaret Lowe
- Department of Dermatology, University of California, San Francisco, CA, USA
| | | | - Paul W Harms
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Richard E Burney
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
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Gadaleta E, Fourgoux P, Pirró S, Thorn GJ, Nelan R, Ironside A, Rajeeve V, Cutillas PR, Lobley AE, Wang J, Gea E, Ross-Adams H, Bessant C, Lemoine NR, Jones LJ, Chelala C. Characterization of four subtypes in morphologically normal tissue excised proximal and distal to breast cancer. NPJ Breast Cancer 2020; 6:38. [PMID: 32885042 PMCID: PMC7442642 DOI: 10.1038/s41523-020-00182-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/06/2020] [Indexed: 01/20/2023] Open
Abstract
Widespread mammographic screening programs and improved self-monitoring allow for breast cancer to be detected earlier than ever before. Breast-conserving surgery is a successful treatment for select women. However, up to 40% of women develop local recurrence after surgery despite apparently tumor-free margins. This suggests that morphologically normal breast may harbor early alterations that contribute to increased risk of cancer recurrence. We conducted a comprehensive transcriptomic and proteomic analysis to characterize 57 fresh-frozen tissues from breast cancers and matched histologically normal tissues resected proximal to (<2 cm) and distant from (5-10 cm) the primary tumor, using tissues from cosmetic reduction mammoplasties as baseline. Four distinct transcriptomic subtypes are identified within matched normal tissues: metabolic; immune; matrisome/epithelial-mesenchymal transition, and non-coding enriched. Key components of the subtypes are supported by proteomic and tissue composition analyses. We find that the metabolic subtype is associated with poor prognosis (p < 0.001, HR6.1). Examination of genes representing the metabolic signature identifies several genes able to prognosticate outcome from histologically normal tissues. A subset of these have been reported for their predictive ability in cancer but, to the best of our knowledge, these have not been reported altered in matched normal tissues. This study takes an important first step toward characterizing matched normal tissues resected at pre-defined margins from the primary tumor. Unlocking the predictive potential of unexcised tissue could prove key to driving the realization of personalized medicine for breast cancer patients, allowing for more biologically-driven analyses of tissue margins than morphology alone.
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Affiliation(s)
- Emanuela Gadaleta
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Pauline Fourgoux
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
| | - Stefano Pirró
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Graeme J. Thorn
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Rachel Nelan
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Alastair Ironside
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Vinothini Rajeeve
- Center for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Pedro R. Cutillas
- Center for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Anna E. Lobley
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Jun Wang
- Center for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Esteban Gea
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | - Helen Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Conrad Bessant
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | - Nicholas R. Lemoine
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Louise J. Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ UK
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, EC1M 6BQ UK
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Ramesh P, Nagarajan V, Khanchandani V, Desai VK, Niranjan V. Proteomic variations of esophageal squamous cell carcinoma revealed by combining RNA-seq proteogenomics and G-PTM search strategy. Heliyon 2020; 6:e04813. [PMID: 32913912 PMCID: PMC7472856 DOI: 10.1016/j.heliyon.2020.e04813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/10/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cancer that arises from epithelial cells of the esophagus is called esophagus squamous cell carcinoma (ESCC) and is mostly observed in developing nations. Evaluation of cancer genomes and its regulation into proteins plays a predominant role in understanding the cancer progressions. Mass-spectrometry-based proteomics is a consequential tool to estimate proteomic variation and posttranslational modifications (PTMs) from standard protein databases. Post-translational modifications play a crucial role in protein folding and PTMs can be accounted for as a biological signal to interpret the structural changes and transition order of proteins. Functional validation of cancer-related mutations can explain the effects of mutations on genes and the identification of Oncogenes and tumor suppressor genes. Therefore, we present a study on protein variations to interpret the structural changes and transition order of proteins in ESCC carcinogenesis. METHODOLOGY We are using a bottom-up proteomics approach with Galaxy-P framework and RNA sequence data analysis to generate the sample-specific databases containing details of RNA splicing and variant peptides. Once the database generated with information on variable modification, only the curated PTMs at specific positions are considered to perform spectral matching. Proteogenomics mapping was performed to identify protein variations in ESCC. RESULTS RNA-sequence proteogenomics with G-PTM (Global Post-Translational Modification) searching strategy has revealed proteomic events including several peptides that contain single amino acid variations, novel splice junction peptides and posttranslationally modified peptides. Proteogenomic mapping exhibited the splice junction peptides mapped predominantly for Malic enzyme exon type (ME-3) and MCM7 protein-coding genes that promote cancer progression, found to be exhibited in ESCC samples. Approximately 25 ± types of PTM modifications were recorded, and Protein Phosphorylation was largely noted. CONCLUSION ESCC cancer prognosis at the molecular level enables a better understanding of cancer carcinogenesis and protein modifications can be used as potential biomarkers.
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Affiliation(s)
- Pooja Ramesh
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | | | - Vartika Khanchandani
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | - Vasanth Kumar Desai
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bangalore, Karnataka, India
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