Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers

Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.

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Global analysis of protein lysine 2-hydroxyisobutyrylation (Khib) profiles in Chinese herb rhubarb (Dahuang)

BMC Genomics ◽

10.1186/s12864-021-07847-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Tong Qi ◽

Jinping Li ◽

Huifang Wang ◽

Xiaofan Han ◽

Junrong Li ◽

...

Keyword(s):

Amino Acid ◽

Global Analysis ◽

Chinese Herb ◽

Side Chain ◽

Sequence Motif ◽

Cellular Processes ◽

Amino Acid Sequence Motif ◽

Wide Range ◽

Modified Peptides ◽

Modified Proteins

Abstract Background Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered protein posttranslational modification (PTM) and is involved in the broad-spectrum regulation of cellular processes that are found in both prokaryotic and eukaryotic cells, including in plants. The Chinese herb rhubarb (Dahuang) is one of the most widely used traditional Chinese medicines in clinical applications. To better understand the physiological activities and mechanism of treating diseases with the herb, it is necessary to conduct intensive research on rhubarb. However, Khib modification has not been reported thus far in rhubarb. Results In this study, we performed the first global analysis of Khib-modified proteins in rhubarb by using sensitive affinity enrichment combined with high-accuracy HPLC-MS/MS tandem spectrometry. A total of 4333 overlapping Khib modification peptides matched on 1525 Khib-containing proteins were identified in three independent tests. Bioinformatics analysis showed that these Khib-containing proteins are involved in a wide range of cellular processes, particularly in protein biosynthesis and central carbon metabolism and are distributed mainly in chloroplasts, cytoplasm, nucleus and mitochondria. In addition, the amino acid sequence motif analysis showed that a negatively charged side chain residue (E), a positively charged residue (K), and an uncharged residue with the smallest side chain (G) were strongly preferred around the Khib site, and a total of 13 Khib modification motifs were identified. These identified motifs can be classified into three motif patterns, and some motif patterns are unique to rhubarb and have not been identified in other plants to date. Conclusions A total of 4333 Khib-modified peptides on 1525 proteins were identified. The Khib-modified proteins are mainly distributed in the chloroplast, cytoplasm, nucleus and mitochondria, and involved in a wide range of cellular processes. Moreover, three types of amino acid sequence motif patterns, including EKhib/KhibE, GKhib and k.kkk….Khib….kkkkk, were extracted from a total of 13 Khib-modified peptides. This study provides comprehensive Khib-proteome resource of rhubarb. The findings from the study contribute to a better understanding of the physiological roles of Khib modification, and the Khib proteome data will facilitate further investigations of the roles and mechanisms of Khib modification in rhubarb.

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Effect of Dasatinib on Genes Related to Mitotic Catastrophe Pathway in Chronic Myeloid Leukemia Cells

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520620666201106085929 ◽

2020 ◽

Vol 20 ◽

Author(s):

Sezgi Kipcak ◽

Buket Ozel ◽

Cigir B. Avci ◽

Leila S. Takanlou ◽

Maryam S. Takanlou ◽

...

Keyword(s):

Chronic Myeloid Leukemia ◽

Myeloid Leukemia ◽

Kinase Inhibitors ◽

Fusion Gene ◽

Philadelphia Chromosome ◽

K562 Cells ◽

Mitotic Catastrophe ◽

Control Group ◽

Cancer Therapies ◽

Apoptosis Pathways

Background: Chronic myeloid leukemia (CML), is characterized by a reciprocal translocation t(9;22) and forms the BCR/ABL1 fusion gene, which is called the Philadelphia chromosome. The therapeutic targets for CML patients which are mediated with BCR/ABL1 oncogenic are tyrosine kinase inhibitors such as imatinib, dasatinib, and nilotinib. The latter two of which have been approved for the treatment of imatinib-resistant or intolerance CML patients. Mitotic catastrophe (MC) is one of the non-apoptotic mechanisms which frequently initiated in types of cancer cells in response to anti-cancer therapies; pharmacological inhibitors of G2 checkpoint members or genetic suppression of PLK1, PLK2, ATR, ATM, CHK1, and CHK2 can trigger DNA-damage-stimulated mitotic catastrophe. PLK1, AURKA/B anomalously expressed in CML cells, that phosphorylation and activation of PLK1 occur by AURKB at centromeres and kinetochores. Objective: The purpose of this study was to investigate the effect of dasatinib on the expression of genes in MC and apoptosis pathways in K562 cells. Methods: Total RNA was isolated from K-562 cells treated with the IC50 value of dasatinib and untreated cells as a control group. The expression of MC and apoptosis-related genes were analyzed by the qRT-PCR system. Results: The array-data demonstrated that dasatinib-treated K562 cells significantly caused the decrease of several genes (AURKA, AURKB, PLK, CHEK1, MYC, XPC, BCL2, and XRCC2). Conclusion: The evidence supply a basis to support clinical researches for the suppression of oncogenes such as PLKs with AURKs in the treatment of types of cancer especially chronic myeloid leukemia.

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Kinase Inhibitors Targeting Anti-angiogenesis as Anti-cancer Therapies

Current Angiogenesis ◽

10.2174/2211552811201040335 ◽

2012 ◽

Vol 1 (4) ◽

pp. 335-346 ◽

Cited By ~ 1

Author(s):

Jing Liu ◽

Feiyang Liu ◽

David L. Waller ◽

Junfeng Wang ◽

Qingsong Liu

Keyword(s):

Kinase Inhibitors ◽

Cancer Therapies ◽

Anti Cancer

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Adiponectin and its receptors in patients with cardiovascular disease

European Journal of Preventive Cardiology ◽

10.1093/eurjpc/zwab061.238 ◽

2021 ◽

Vol 28 (Supplement_1) ◽

Author(s):

E Belik ◽

OV Gruzdeva ◽

YUA Dyleva ◽

EG Uchasova ◽

MYU Sinitsky ◽

...

Keyword(s):

Heart Defects ◽

Post Translational Modification ◽

Fat Depots ◽

Funding Sources ◽

Adiponectin Mrna ◽

Fat Stores ◽

Group 2 ◽

High Level ◽

Group 1

Abstract Funding Acknowledgements Type of funding sources: None. Aim to determine the features of adiponectin expression, secretion of adiponectin and its receptors in local fat depots in CVD. Materials and methods The study included 90 patients with СAD (Group 1) and 60 patients with heart defects (Group 2). Adipocytes were isolated from samples of subcutaneous (SAT), epicardial (EAT) and perivascular (PVAT) adipose tissue obtained during CABG or heart valve replacement. The expression of adiponectin was determined by qPCR using TaqManTM Gene Expression Assays (Applied Biosystems, USA) in the ViiA 7 Real-Time PCR System (Applied Biosystems, USA), the levels of expression products was determined using enzyme immunoassay (Bender MedSystems GmbH, Vienna, Austria). The data were analyzed using the statistical software Statistica 9.0. Results EAT adipocytes were characterized by the lowest adiponectin expression relative to adipocytes of other localization both in Group 1 and Group 2. In patients Group 1 adiponectin expression in EAT was reduced relative in SAT and PVAT (by 1.2 and 1.5 times). In Group 2, the adiponectin mRNA in the EAT was lower than in the SAT and PVAT (1.4 and 1.5 times). The expression of adiponectin in EAT in Group 2 exceeded the same indicator in Group 1 by 1.2 times. The maximum expression of adiponectin was observed in the PVAT culture in patients of both groups. For Group 2, this indicator exceeded the values of Group 1 by 1.2 times. The content of adiponectin in the culture EAT was lower than in the SAT, both in Group 1 and Group 2 (by 1.3 and 1.13 times). The level of this indicator in Group 2 was 1.4 times higher than in Group 1. PVAT adipocytes of patients with CAD were characterized by the lowest level of adiponectin secretion in comparison with adipocytes of other localization. The adiponectin level in the PVAT of Group 2 exceeded that of fat stores of other localization and in Group 1 patients by 1.8 times. There were no statistically significant differences in the expression and concentration of adiponectin in the culture of adipocytes of the SAT between the groups of patients. In Group 1, the lowest level of AdipoR1 was found in the adipocyte culture of the PVAT. Noteworthy is the decrease in the level of AdipoR1 in Group 1 compared to the level of Group 2, observed in the SAT and PVAT: 1.3 and 1.5 times. There were no significant differences in the concentration of the AdipoR1 in the EAT, as well as AdipoR2 in all types of AT between the groups of patients. Conclusion: in CVD the EAT is characterized by minimal expression and secretion of adiponectin, regardless of nosology. In CAD despite the high level of expression of adiponectin, the adipocytes of the PVAT were found to have the lowest content in comparison with adipocytes of other localization. Dysregulation of the adiponectin/AdipoR axis is observed in PVAT, which may be due to low expression of adiponectin receptors and long-term processes of its post-translational modification and oligomerization in CAD.

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RegulatING chromatin regulators: post-translational modification of the ING family of epigenetic regulators

Biochemical Journal ◽

10.1042/bj20121632 ◽

2013 ◽

Vol 450 (3) ◽

pp. 433-442 ◽

Cited By ~ 8

Author(s):

Shankha Satpathy ◽

Arash Nabbi ◽

Karl Riabowol

Keyword(s):

Biological Significance ◽

Type Ii ◽

Post Translational Modification ◽

Post Translational Modifications ◽

Chromatin Regulators ◽

Cancer Types ◽

Splicing Isoforms ◽

Enrichment Techniques ◽

Affect Cell Growth

The five human ING genes encode at least 15 splicing isoforms, most of which affect cell growth, differentiation and apoptosis through their ability to alter gene expression by epigenetic mechanisms. Since their discovery in 1996, ING proteins have been classified as type II tumour suppressors on the basis of reports describing their down-regulation and mislocalization in a variety of cancer types. In addition to their regulation by transcriptional mechanisms, understanding the range of PTMs (post-translational modifications) of INGs is important in understanding how ING functions are fine-tuned in the physiological setting and how they add to the repertoire of activities affected by the INGs. In the present paper we review the different PTMs that have been reported to occur on INGs. We discuss the PTMs that modulate ING function under normal conditions and in response to a variety of stresses. We also describe the ING PTMs that have been identified by several unbiased MS-based PTM enrichment techniques and subsequent proteomic analysis. Among the ING PTMs identified to date, a subset has been characterized for their biological significance and have been shown to affect processes including subcellular localization, interaction with enzymatic complexes and ING protein half-life. The present review aims to highlight the emerging role of PTMs in regulating ING function and to suggest additional pathways and functions where PTMs may effect ING function.

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Semisynthetic triazoles as an approach in the discovery of Novel Lead Compounds

Current Organic Chemistry ◽

10.2174/1385272825666210126100227 ◽

2021 ◽

Vol 25 ◽

Author(s):

Pedro Alves Bezerra Morais ◽

Carla Santana Francisco ◽

Heberth de Paula ◽

Rayssa Ribeiro ◽

Mariana Alves Eloy ◽

...

Keyword(s):

Natural Products ◽

Medicinal Chemistry ◽

Chemical Space ◽

Biological Activities ◽

Post Translational Modification ◽

Cellular Processes ◽

Modern Drug ◽

New Chemical Entities ◽

Almost All ◽

The 19Th Century

: Historically, the medicinal chemistry is concerned with the approach of organic chemistry to new drug synthesis. Considering the fruitful collections of new molecular entities, the dedicated efforts for medicinal chemistry are rewarding. Planning and search of new and applicable pharmacologic therapies involve the altruistic nature of the scientists. Since the 19th century, notoriously the application of isolated and characterized plant-derived compounds in modern drug discovery and in various stages of clinical development highlight its viability and significance. Natural products influence a broad range of biological processes, covering transcription, translation, and post-translational modification and being effective modulators of almost all basic cellular processes. The research of new chemical entities through “click chemistry” continuously opens up a map for the remarkable exploration of chemical space in towards leading natural products optimization by structure-activity relationship. Finally, here in this review, we expect to gather a broad knowledge involving triazolic natural products derivatives, synthetic routes, structures, and their biological activities.

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NAD+Metabolism in Aging and Cancer

Annual Review of Cancer Biology ◽

10.1146/annurev-cancerbio-030518-055905 ◽

2019 ◽

Vol 3 (1) ◽

pp. 105-130 ◽

Cited By ~ 14

Author(s):

Tyler G. Demarest ◽

Mansi Babbar ◽

Mustafa N. Okur ◽

Xiuli Dan ◽

Deborah L. Croteau ◽

...

Keyword(s):

Molecular Mechanisms ◽

Therapeutic Potential ◽

Redox Homeostasis ◽

Accelerated Aging ◽

Cancer Therapies ◽

Nad Metabolism ◽

Cellular Processes ◽

Cancer Pathogenesis ◽

Nicotinamide Mononucleotide ◽

Age Related

Aging is a major risk factor for many types of cancer, and the molecular mechanisms implicated in aging, progeria syndromes, and cancer pathogenesis display considerable similarities. Maintaining redox homeostasis, efficient signal transduction, and mitochondrial metabolism is essential for genome integrity and for preventing progression to cellular senescence or tumorigenesis. NAD+is a central signaling molecule involved in these and other cellular processes implicated in age-related diseases and cancer. Growing evidence implicates NAD+decline as a major feature of accelerated aging progeria syndromes and normal aging. Administration of NAD+precursors such as nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) offer promising therapeutic strategies to improve health, progeria comorbidities, and cancer therapies. This review summarizes insights from the study of aging and progeria syndromes and discusses the implications and therapeutic potential of the underlying molecular mechanisms involved in aging and how they may contribute to tumorigenesis.

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The split protein phosphatase system

Biochemical Journal ◽

10.1042/bcj20170726 ◽

2018 ◽

Vol 475 (23) ◽

pp. 3707-3723 ◽

Cited By ~ 9

Author(s):

Anne Bertolotti

Keyword(s):

Protein Phosphatase ◽

Catalytic Subunit ◽

Regulatory Subunit ◽

Post Translational Modification ◽

Antagonistic Action ◽

Cellular Processes ◽

Depth Study ◽

Split Protein ◽

Phosphatase System ◽

Physiological Substrates

Reversible phosphorylation of proteins is a post-translational modification that regulates all aspect of life through the antagonistic action of kinases and phosphatases. Protein kinases are well characterized, but protein phosphatases have been relatively neglected. Protein phosphatase 1 (PP1) catalyzes the dephosphorylation of a major fraction of phospho-serines and phospho-threonines in cells and thereby controls a broad range of cellular processes. In this review, I will discuss how phosphatases were discovered, how the view that they were unselective emerged and how recent findings have revealed their exquisite selectivity. Unlike kinases, PP1 phosphatases are obligatory heteromers composed of a catalytic subunit bound to one (or two) non-catalytic subunit(s). Based on an in-depth study of two holophosphatases, I propose the following: selective dephosphorylation depends on the assembly of two components, the catalytic subunit and the non-catalytic subunit, which serves as a high-affinity substrate receptor. Because functional complementation of the two modules is required to produce a selective holophosphatase, one can consider that they are split enzymes. The non-catalytic subunit was often referred to as a regulatory subunit, but it is, in fact, an essential component of the holoenzyme. In this model, a phosphatase and its array of mostly orphan substrate receptors constitute the split protein phosphatase system. The set of potentially generalizable principles outlined in this review may facilitate the study of these poorly understood enzymes and the identification of their physiological substrates.

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Patient-derived models of acquired resistance can identify effective drug combinations for cancer

Science ◽

10.1126/science.1254721 ◽

2014 ◽

Vol 346 (6216) ◽

pp. 1480-1486 ◽

Cited By ~ 418

Author(s):

Adam S. Crystal ◽

Alice T. Shaw ◽

Lecia V. Sequist ◽

Luc Friboulet ◽

Matthew J. Niederst ◽

...

Keyword(s):

Growth Factor ◽

Kinase Inhibitors ◽

Acquired Resistance ◽

Growth Factor Receptor ◽

Drug Combinations ◽

Effective Drug ◽

Cancer Therapies ◽

Lung Cancer Patients ◽

Anaplastic Lymphoma ◽

Culture Models

Targeted cancer therapies have produced substantial clinical responses, but most tumors develop resistance to these drugs. Here, we describe a pharmacogenomic platform that facilitates rapid discovery of drug combinations that can overcome resistance. We established cell culture models derived from biopsy samples of lung cancer patients whose disease had progressed while on treatment with epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors and then subjected these cells to genetic analyses and a pharmacological screen. Multiple effective drug combinations were identified. For example, the combination of ALK and MAPK kinase (MEK) inhibitors was active in an ALK-positive resistant tumor that had developed a MAP2K1 activating mutation, and the combination of EGFR and fibroblast growth factor receptor (FGFR) inhibitors was active in an EGFR mutant resistant cancer with a mutation in FGFR3. Combined ALK and SRC (pp60c-src) inhibition was effective in several ALK-driven patient-derived models, a result not predicted by genetic analysis alone. With further refinements, this strategy could help direct therapeutic choices for individual patients.

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Functional analysis of the SUMOylation pathway in Drosophila

Biochemical Society Transactions ◽

10.1042/bst0360868 ◽

2008 ◽

Vol 36 (5) ◽

pp. 868-873 ◽

Cited By ~ 31

Author(s):

Ana Talamillo ◽

Jonatan Sánchez ◽

Rosa Barrio

Keyword(s):

Functional Analysis ◽

Fine Tuning ◽

Model Systems ◽

Post Translational Modification ◽

Reversible Process ◽

Cellular Processes ◽

Tuning Mechanism ◽

Sumo Conjugation

SUMOylation, a reversible process used as a ‘fine-tuning’ mechanism to regulate the role of multiple proteins, is conserved throughout evolution. This post-translational modification affects several cellular processes by the modulation of subcellular localization, activity or stability of a variety of substrates. A growing number of proteins have been identified as targets for SUMOylation, although, for many of them, the role of SUMO conjugation on their function is unknown. The use of model systems might facilitate the study of SUMOylation implications in vivo. In the present paper, we have compiled what is known about SUMOylation in Drosophila melanogaster, where the use of genetics provides new insights on SUMOylation's biological roles.

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