Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse

Ramalho, Rodrigo F.; Li, Sujun; Radivojac, Predrag; Hahn, Matthew W.

doi:10.1109/tcbb.2015.2480068

Cited by 4 publications

(7 citation statements)

References 34 publications

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“…Papaleo et al [27] used dynamic cross correlation matrix to find the correlated motions between domains of a peptidase. Ralaho et al [28] performed experiments on different organs of humans and mouse, and they were able to show that both out frame and in frame transcript can be used to regulate protein activity or localization. Song and Yan [29] proposed a method composed of autoregressive models and hidden Markov models to detect the hidden periodicities and solenoid recognition in a protein sequence.…”

Section: Prior Workmentioning

confidence: 99%

Parametric Models for Understanding Atomic Trajectories in Different Domains of Lung Cancer Causing Protein

et al. 2019

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Non-small cell lung cancer (NSCLC) is a major cause of death worldwide. About 80% to 85% of lung cancer cases are NSCLC. It is well known that mutation of the epidermal growth factor (EGFR) may lead to the NSCLC. The first generation drugs are effective initially, but almost all patients develop drug resistance after about a year due to a secondary mutation. The computational methods are an efficient tool for investigating drug resistance, design, and discovery. Moreover, molecular dynamics (MD) simulation enables us to study and analyze the behavior of proteins and molecules at the atomic level. MD simulations offer extraordinary insight about biomolecules and are a valuable tool for computer aided drug discovery. Earlier studies on EGFR only focused on the kinase domain. Because EGFR is a multi-domain protein, mutations in the kinase domain may affect the function in other domains. Therefore, it is important to investigate the complete structure of the EGFR and its mutants. In this paper, we first generate the complete structure of the EGFR and perform MD simulation for the wildtype EGFR, EGFR with L858R mutation and EGFR with L858R and T790M mutation. We divide the complete structure of the EGFR and its mutants into 8 domains according to the reference crystal structure. We then consider atom trajectories as time series signals and estimate the power spectral densities using the auto-regressive integrated (ARI) model, which shows interesting insight. Dynamic time warping is used to analyze the similarity between each domain of the structures. Interesting patterns are observed which may be useful for investigating drug resistance and design. Furthermore, Pearson correlation coefficient, peaks, and widths of the power spectral density are calculated for each domain. The simulation results provide useful insight about conformation dynamics of the EGFR, such as atom motion and protein stability. The domains are less correlated in L858R type and even weaker when the second mutation occurs. The warping patterns are changed due to mutation and the movement of atoms is distorted. Hence, it is difficult for a drug to bind to the protein. These findings will be useful in understanding the characteristics of the EGFR and for computer aided drug design process for the NSCLC patients. INDEX TERMS Autoregressive integrated model, drug resistance, dynamic time warping, epidermal growth factor receptor, molecular dynamics, non-small cell lung cancer.

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Section: Prior Workmentioning

confidence: 99%

Parametric Models for Understanding Atomic Trajectories in Different Domains of Lung Cancer Causing Protein

et al. 2019

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“…Of these, 12 were exon-skipping events. In a later study, Ramalho et al [13] also searched public mass-spectrometry data for evidence of alternative proteins. In this work, hundreds of exon-skipping events, previously found by RNA-Seq, were used in the creation of a customized mRNA sequence database.…”

Section: Evidences For Translation Of Human Alternatively Spliced Tramentioning

confidence: 99%

“…Several of the exon-skipping events detected at the protein level by Ramalho et al 2015 had been previously detected at the transcript level by distinct methods and authors and eight events (in the following genes: IMMT [26], COL6A3 [20], FN1 [21], TSC2 [27], CLIP170 [28], THYN1 [29], Junctin [30], Ktn1 [31]) had been previously detected not only by the recent high-throughput RNA sequencing but also by exon-array, quantitative real-time RT-PCR, and Southern and Northern Blot assays. Some of theses exon-skipping events were described as tissue-specific and/or associated with tumor tissues.…”

Section: Evidences For Translation Of Human Alternatively Spliced Tramentioning

confidence: 99%

“…Thus, in comparison with the transcriptome, the known proteome diversity is still scarce and the assumption of a single reference protein for each gene is currently under challenge. Interestingly, among the increasing number of experimentally detected cases of alternative proteins [11][12][13], many were discovered in cancer tissues or cell lines [14] highlighting their relevance for the cancer research.…”

Section: Introductionmentioning

confidence: 99%

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Increasing evidence for the presence of alternative proteins in human tissues and cell lines

Ramalho

Carraro

2017

Appl Cancer Res

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Recent findings coming from human proteome research employing mass-spectrometry and ribosomal profiling methods have provided evidence for the translation of non-annotated coding sequence (CDSs) into alternative proteins (APs). The presence of APs in many human tissues and cell lines may become an important issue in genome sciences, especially in cancer genomics where the frequency of alternative proteins seems to be 10-fold higher than normal tissues. Finding new proteins can impact medical research by filling gaps in known molecular pathways or revealing new molecular markers and therapeutic targets. Among the cellular processes possibly involved in protein diversity, alternative splicing (AS) is the most cited, and it consists of an often-regulated mechanism that generates different mRNAs from the same gene, contributing to the functional diversity of mammalian cells. In the past, evidence for AS from multi-exon genes have come mainly from expression sequence tag (EST) data; only recently has mass-spectrometry (MS) been used to investigate the translation of alternative transcripts. Exploration of human MS data has detected tens to hundreds of alternative proteins in normal tissues, and thousands in cancer cell lines, suggesting that alternative proteins may have an important role in cancer. Analysis of MS data has revealed a vastly diverse AP repertoire, with some of this diversity being exclusively detected in cancer cells. Proteomic characterization of 20 breast cancer cell lines revealed a surprising 1,860 protein variants resulting from AS. Among these, 4 AP are clearly involved in cancer. A truncated variant of the NF-kB p65 subunit, a truncated form of the focal adhesion kinase PTK2 and two CD47 transmembrane receptor protein variants. Until now, little is known about the functional differences between these variants. Another cellular mechanism that possibly creates protein diversity is the alternative usage of translation initiation site (TIS). Detection of TIS is made possible by the Ribosome Profiling (RP) method. The principle of this technique is to capture mRNA translation by freezing the actively translating ribosomes onto transcripts, and then separating them by ultracentrifugation. Recently, RP was applied to mouse embryonic fibroblast cells and human HEK293 cells. The results revealed that the majority of mRNAs contain more than one translation initiation site (TIS), with more than 50% of the detected TISs mapping to alternative ORFs. In this review, we present a list of human alternative proteins validated by small and large-scale experimental methods. We also highlight that APs are probably not a secondary product of inaccurate splicing or translational process and most likely play an important role in the tumorigenic process. Thus, APs constitutes a promising research line for basic and clinical aspects of cancer.

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“…Shotgun methods have played an important role in this field, although technical and statistical limitations still prevent complete coverage of identified protein sequences in a single experiment. This shortcoming compromises our ability to detect many biologically important events such as alternatively spliced products or post-translational modifications …”

Section: Introductionmentioning

confidence: 99%

Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics

Dabir

Misal

et al. 2016

J. Proteome Res.

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Peptide amidination labeling using S-methyl thioacetimidate (SMTA) is investigated in an attempt to increase the number and types of peptides that can be detected in a bottom-up proteomics experiment. This derivatization method affects the basicity of lysine residues, and is shown here to significantly impact the idiosyncracies of peptide fragmentation and peptide detectability. The unique and highly reproducible fragmentation properties of SMTA-labeled peptides, such as the strong propensity for forming b1 fragment ions, can be further exploited to modify the scoring of peptide-spectrum pairs and improve peptide identification. To this end, we have developed a supervised post-processing algorithm to exploit these characteristics of peptides labeled by SMTA. Our experiments show that, although the overall number of identifications are similar, the SMTA modification enabled the detection of 16-26% peptides not previously observed in comparable CID/HCD tandem mass spectrometry experiments without SMTA labeling.

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Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse

Cited by 4 publications

References 34 publications

Parametric Models for Understanding Atomic Trajectories in Different Domains of Lung Cancer Causing Protein

Parametric Models for Understanding Atomic Trajectories in Different Domains of Lung Cancer Causing Protein

Increasing evidence for the presence of alternative proteins in human tissues and cell lines

Impact of Amidination on Peptide Fragmentation and Identification in Shotgun Proteomics

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