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Article: A network map of cytoskeleton-associated protein 4 (CKAP4) mediated signaling pathway in cancer.

Suchitha, G P / Balaya, Rex Devasahayam Arokia / Raju, Rajesh / Keshava Prasad, T S / Dagamajalu, Shobha

Journal of cell communication and signaling

2023 Volume 17, Issue 3, Page(s) 1097–1104

Abstract: Cytoskeleton-associated protein 4 (CKAP4) is a non-glycosylated type II transmembrane protein that serves as a cell surface-activated receptor. It is expressed primarily in the plasma membranes of bladder epithelial cells, type II alveolar pneumocytes, ... ...

Abstract	Cytoskeleton-associated protein 4 (CKAP4) is a non-glycosylated type II transmembrane protein that serves as a cell surface-activated receptor. It is expressed primarily in the plasma membranes of bladder epithelial cells, type II alveolar pneumocytes, and vascular smooth muscle cells. CKAP4 is involved in various biological activities including cell proliferation, cell migration, keratinocyte differentiation, glycogenesis, fibrosis, thymic development, cardiogenesis, neuronal apoptosis, and cancer. CKAP4 has been described as a pro-tumor molecule that regulates the progression of various cancers, including lung cancer, breast cancer, esophageal squamous cell carcinoma, hepatocellular carcinoma, cervical cancer, oral cancer, bladder cancer, cholangiocarcinoma, pancreatic cancer, myeloma, renal cell carcinoma, melanoma, squamous cell carcinoma, colorectal cancer, and osteosarcoma. CKAP4 and its isoform bind to DKK1 or DKK3 (Dickkopf proteins) or antiproliferative factor (APF) and regulates several downstream signaling cascades. The CKAP4 complex plays a crucial role in regulating the signaling pathways including PI3K/AKT and MAPK1/3. Recently, CKAP4 has been recognized as a potential target for cancer therapy. Due to its biomedical importance, we integrated a network map of CKAP4. The available literature on CKAP4 signaling was manually curated according to the NetPath annotation criteria. The consolidated pathway map comprises 41 activation/inhibition events, 21 catalysis events, 35 molecular associations, 134 gene regulation events, 83 types of protein expression, and six protein translocation events. CKAP4 signaling pathway map data is freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5322 ). Generation of CKAP4 signaling pathway map.
Language	English
Publishing date	2023-03-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2299380-0
ISSN	1873-961X ; 1873-9601
ISSN (online)	1873-961X
ISSN	1873-9601
DOI	10.1007/s12079-023-00739-w
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Article: An assembly of TROP2-mediated signaling events.

Upadhyay, Shubham Sukerndeo / Devasahayam Arokia Balaya, Rex / Parate, Sakshi Sanjay / Dagamajalu, Shobha / Keshava Prasad, T S / Shetty, Rohan / Raju, Rajesh

Journal of cell communication and signaling

2023 Volume 17, Issue 3, Page(s) 1105–1111

Abstract: Trophoblast cell surface antigen 2 (TROP2) is a calcium-transducing transmembrane protein mainly involved in embryo development. The aberrant expression of TROP2 is observed in numerous cancers, including triple-negative breast cancer, gastric, ... ...

Abstract	Trophoblast cell surface antigen 2 (TROP2) is a calcium-transducing transmembrane protein mainly involved in embryo development. The aberrant expression of TROP2 is observed in numerous cancers, including triple-negative breast cancer, gastric, colorectal, pancreatic, squamous cell carcinoma of the oral cavity, and prostate cancers. The main signaling pathways mediated by TROP2 are calcium signaling, PI3K/AKT, JAK/STAT, MAPKs, and β-catenin signaling. However, collective information about the TROP2-mediated signaling pathway is not available for visualization or analysis. In this study, we constructed a TROP2 signaling map with respect to its role in different cancers. The data curation was done manually by following the NetPath annotation criteria. The described map consists of different molecular events, including 8 activation/inhibition, 16 enzyme catalysis, 19 gene regulations, 12 molecular associations, 39 induced-protein expressions, and 2 protein translocation. The data of the TROP2 pathway map is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5300 ). Development of TROP2 signaling pathway map.
Language	English
Publishing date	2023-04-04
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2299380-0
ISSN	1873-961X ; 1873-9601
ISSN (online)	1873-961X
ISSN	1873-9601
DOI	10.1007/s12079-023-00742-1
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Article ; Online: A signaling network map of Lipoxin (LXA4): an anti-inflammatory molecule.

Suchitha, G P / Devasahayam Arokia Balaya, Rex / Prasad, T S Keshava / Dagamajalu, Shobha

Inflammation research : official journal of the European Histamine Research Society ... [et al.

2024

Abstract: ... immune cells, including neutrophils, macrophages, and T and B cells, by promoting the clearance of apoptotic ...

Abstract	Lipoxins (LXs) are a class of endogenous bioactive lipid mediators that are involved in the regulation of inflammation. They exert immunomodulatory effects by regulating the behaviour of various immune cells, including neutrophils, macrophages, and T and B cells, by promoting the clearance of apoptotic neutrophils. This helps to dampen inflammation and promote tissue repair. LXs regulate the expression of many inflammatory genes by modulating the levels of transcription factors, such as nuclear factor κB (NF-κB), activator protein-1 (AP-1), nerve growth factor-regulated factor 1A binding protein 1 (NGF), and peroxisome proliferator activated receptor γ (PPAR-γ), which are elevated in various diseases, such as respiratory tract diseases, renal diseases, cancer, neurodegenerative diseases, and viral infections. Lipoxin-mediated signaling is involved in chronic inflammation, cancer, diabetes-associated kidney disease, lung injury, liver injury, endometriosis, respiratory tract diseases, neurodegenerative diseases, chronic cerebral hypoperfusion, and retinal degeneration. In this study, we systematically investigated the intricate network of lipoxin signaling by analyzing the relevant literature. The resulting map comprised 467 molecules categorized as activation/inhibition, enzyme catalysis, gene and protein expression, molecular associations, and translocation events. This map serves as a valuable resource for understanding the complexity of lipoxin signaling and its impact on various cellular functions.
Language	English
Publishing date	2024-04-26
Publishing country	Switzerland
Document type	Letter
ZDB-ID	1221794-3
ISSN	1420-908X ; 1023-3830
ISSN (online)	1420-908X
ISSN	1023-3830
DOI	10.1007/s00011-024-01885-6
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Article ; Online: Isolation and characterization of extracellular vesicles from Fusarium oxysporum f. sp. cubense, a banana wilt pathogen

Fernandes, Lizelle B. / D'Souza, Jacinta S. / Prasad, T.S. Keshava / Ghag, Siddhesh B.

BBA - General Subjects. 2023 July, v. 1867, no. 7 p.130382-

2023

Abstract: Fusarium wilt of banana is a destructive widespread disease caused by Fusarium oxysporum f. sp. cubense (Foc) that ravaged banana plantations globally, incurring huge economic losses. Current knowledge demonstrates the involvement of several ... ...

Abstract	Fusarium wilt of banana is a destructive widespread disease caused by Fusarium oxysporum f. sp. cubense (Foc) that ravaged banana plantations globally, incurring huge economic losses. Current knowledge demonstrates the involvement of several transcription factors, effector proteins, and small RNAs in the Foc-banana interaction. However, the precise mode of communication at the interface remains elusive. Cutting-edge research has emphasized the significance of extracellular vesicles (EVs) in trafficking the virulent factors modulating the host physiology and defence system. EVs are ubiquitous inter- and intra-cellular communicators across kingdoms. This study focuses on the isolation and characterization of Foc EVs from methods that make use of sodium acetate, polyethylene glycol, ethyl acetate, and high-speed centrifugation. Isolated EVs were microscopically visualized using Nile red staining. Further, the EVs were characterized using transmission electron microscopy, which revealed the presence of spherical, double-membrane, vesicular structures ranging in size from 50 to 200 nm (diameter). The size was also determined using the principle based on Dynamic Light Scattering. The Foc EVs contained proteins that were separated using SDS-PAGE and ranged between 10 and 315 kDa. Mass spectrometry analysis revealed the presence of EV-specific marker proteins, toxic peptides, and effectors. The Foc EVs were found to be cytotoxic, whose toxicity increased with EVs isolated from the co-culture preparation. Taken together, a better understanding of Foc EVs and their cargo will aid in deciphering the molecular crosstalk between banana and Foc.
Keywords	Fusarium oxysporum f. sp. cubense ; Panama disease ; bananas ; centrifugation ; coculture ; cytotoxicity ; ethyl acetate ; mass spectrometry ; pathogens ; peptides ; physiology ; polyacrylamide gel electrophoresis ; polyethylene glycol ; sodium acetate ; transmission electron microscopy ; virulence ; Fusarium wilt ; Banana ; Extracellular vesicles ; Proteomic analysis ; Leaf cytotoxicity assay
Language	English
Dates of publication	2023-07
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	840755-1
ISSN	0304-4165
ISSN	0304-4165
DOI	10.1016/j.bbagen.2023.130382
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Article: A network map of apelin-mediated signaling.

Dagamajalu, Shobha / Rex, D A B / Philem, Pushparani Devi / Rainey, Jan K / Keshava Prasad, T S

Journal of cell communication and signaling

2021 Volume 16, Issue 1, Page(s) 137–143

Abstract: The apelin receptor (APLNR) is a class A (rhodopsin-like) G-protein coupled receptor with a wide distribution throughout the human body. Activation of the apelin/APLNR system regulates AMPK/PI3K/AKT/mTOR and RAF/ERK1/2 mediated signaling pathways. APLNR ... ...

Abstract	The apelin receptor (APLNR) is a class A (rhodopsin-like) G-protein coupled receptor with a wide distribution throughout the human body. Activation of the apelin/APLNR system regulates AMPK/PI3K/AKT/mTOR and RAF/ERK1/2 mediated signaling pathways. APLNR activation orchestrates several downstream signaling cascades, which play diverse roles in physiological effects, including effects upon vasoconstriction, heart muscle contractility, energy metabolism regulation, and fluid homeostasis angiogenesis. We consolidated a network map of the APLNR signaling map owing to its biomedical importance. The curation of literature data pertaining to the APLNR system was performed manually by the NetPath criteria. The described apelin receptor signaling map comprises 35 activation/inhibition events, 38 catalysis events, 4 molecular associations, 62 gene regulation events, 113 protein expression types, and 4 protein translocation events. The APLNR signaling pathway map data is made freely accessible through the WikiPathways Database ( https://www.wikipathways.org/index.php/Pathway:WP5067 ).
Language	English
Publishing date	2021-04-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2299380-0
ISSN	1873-961X ; 1873-9601
ISSN (online)	1873-961X
ISSN	1873-9601
DOI	10.1007/s12079-021-00614-6
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Article: A modular map of Bradykinin-mediated inflammatory signaling network.

Rex, D A B / Deepak, K / Vaid, Neelanchal / Dagamajalu, Shobha / Kandasamy, Richard Kumaran / Flo, Trude Helen / Keshava Prasad, T S

Journal of cell communication and signaling

2021 Volume 16, Issue 2, Page(s) 301–310

Abstract: Bradykinin, a member of the kallikrein-kinin system (KKS), is associated with an inflammatory response pathway with diverse vascular permeability functions, including thrombosis and blood coagulation. In majority, bradykinin signals through Bradykinin ... ...

Abstract	Bradykinin, a member of the kallikrein-kinin system (KKS), is associated with an inflammatory response pathway with diverse vascular permeability functions, including thrombosis and blood coagulation. In majority, bradykinin signals through Bradykinin Receptor B2 (B2R). B2R is a G protein-coupled receptor (GPCR) coupled to G protein family such as Gα
Language	English
Publishing date	2021-10-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2299380-0
ISSN	1873-961X ; 1873-9601
ISSN (online)	1873-961X
ISSN	1873-9601
DOI	10.1007/s12079-021-00652-0
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Article ; Online: Isolation and characterization of extracellular vesicles from Fusarium oxysporum f. sp. cubense, a banana wilt pathogen.

Fernandes, Lizelle B / D'Souza, Jacinta S / Prasad, T S Keshava / Ghag, Siddhesh B

Biochimica et biophysica acta. General subjects

2023 Volume 1867, Issue 7, Page(s) 130382

Abstract	Fusarium wilt of banana is a destructive widespread disease caused by Fusarium oxysporum f. sp. cubense (Foc) that ravaged banana plantations globally, incurring huge economic losses. Current knowledge demonstrates the involvement of several transcription factors, effector proteins, and small RNAs in the Foc-banana interaction. However, the precise mode of communication at the interface remains elusive. Cutting-edge research has emphasized the significance of extracellular vesicles (EVs) in trafficking the virulent factors modulating the host physiology and defence system. EVs are ubiquitous inter- and intra-cellular communicators across kingdoms. This study focuses on the isolation and characterization of Foc EVs from methods that make use of sodium acetate, polyethylene glycol, ethyl acetate, and high-speed centrifugation. Isolated EVs were microscopically visualized using Nile red staining. Further, the EVs were characterized using transmission electron microscopy, which revealed the presence of spherical, double-membrane, vesicular structures ranging in size from 50 to 200 nm (diameter). The size was also determined using the principle based on Dynamic Light Scattering. The Foc EVs contained proteins that were separated using SDS-PAGE and ranged between 10 and 315 kDa. Mass spectrometry analysis revealed the presence of EV-specific marker proteins, toxic peptides, and effectors. The Foc EVs were found to be cytotoxic, whose toxicity increased with EVs isolated from the co-culture preparation. Taken together, a better understanding of Foc EVs and their cargo will aid in deciphering the molecular crosstalk between banana and Foc.
MeSH term(s)	Fusarium ; Musa ; Plant Diseases ; Transcription Factors
Chemical Substances	Transcription Factors
Language	English
Publishing date	2023-05-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	60-7
ISSN	1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1872-8006 ; 1879-2596 ; 1879-260X ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbagen.2023.130382
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Article: Phosphoproteome profiling of rice tissues provides new insights into responsive mechanisms and kinase activity upon salt stress

Arefian, Mohammad / Antil, Neelam / Najar, Mohd Altaf / Subba, Pratigya / Prasad, T.S. Keshava

Environmental and experimental botany. 2022 May 12,

2022

Abstract: Rice is a model monocot plant and a major food crop worldwide that is known as the most salt-sensitive cereal. Phosphorylation of proteins regulates the stimulus perception and triggers responses; however, remains largely unknown in crops, particularly ... ...

Abstract	Rice is a model monocot plant and a major food crop worldwide that is known as the most salt-sensitive cereal. Phosphorylation of proteins regulates the stimulus perception and triggers responses; however, remains largely unknown in crops, particularly in rice under salinity. Here, we report in-depth physiological, proteomic, and phosphoproteomic kinetics of rice shoot and root tissues in response to short-term salt stress. We identified 8,160 proteins, 5,684 phosphopeptides that assigned to 3,142 ‎phosphoproteins. In the root, hypophosphorylation of KAT1, BORs, HAKs, NHX2, and NHX8 transporters, RBOHs and nitrate reductase implied less efficiency in ion, minerals, and ROS haemostasis, thus likely resulting in membrane damages and sensitivity of rice to salinity. Predominantly, the PKA, CDK, MAPK, and PP2A families modulated plant response through interaction with densely interconnected protein modules. We identified 17 phosphomotifs reflecting the identities of the upstream kinases. Furthermore, phylogenetic mapping of 245 identified kinases together with the kinase of known target motifs and function, expanded the biological characters of kinases in rice. We also assigned target motifs for rice kinase families, including PDK1, PKA, CAMKL, CK1, CDK, GSK, and MAPK. This study expands the set of kinase substrates and their signaling networks. Our data also assigns new stress-responsive functions to a large number of novel phosphoproteins, thus will serve as a resource for further studies of salt stress signaling in plants.
Keywords	food crops ; hemostasis ; nitrate reductase ; phosphopeptides ; phosphoproteins ; phosphoproteome ; phosphorylation ; phylogeny ; plant response ; proteomics ; rice ; salinity ; salt stress
Language	English
Dates of publication	2022-0512
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	195968-2
ISSN	0098-8472
ISSN	0098-8472
DOI	10.1016/j.envexpbot.2022.104917
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Article ; Online: Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops.

Arefian, Mohammad / Bhagya, N / Prasad, T S Keshava

Biological reviews of the Cambridge Philosophical Society

2021 Volume 96, Issue 5, Page(s) 2164–2191

Abstract: Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic ... ...

Abstract	Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
MeSH term(s)	Arabidopsis ; Crops, Agricultural ; Flowers ; Humans ; Phosphorylation ; Signal Transduction
Language	English
Publishing date	2021-05-27
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1423558-4
ISSN	1469-185X ; 0006-3231 ; 1464-7931
ISSN (online)	1469-185X
ISSN	0006-3231 ; 1464-7931
DOI	10.1111/brv.12748
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Article ; Online: Discovery of Molecular Networks of Neuroprotection Conferred by Brahmi Extract in Aβ

Deolankar, Sayali Chandrashekhar / Najar, Mohd Altaf / Ramesh, Poornima / Kanichery, Anagha / Kudva, Avinash K / Raghu, Shamprasad Varija / Prasad, T S Keshava

Molecular neurobiology

2022 Volume 60, Issue 1, Page(s) 303–316

Abstract: Accumulation of ... ...

Abstract	Accumulation of Aβ
Language	English
Publishing date	2022-10-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	645020-9
ISSN	1559-1182 ; 0893-7648
ISSN (online)	1559-1182
ISSN	0893-7648
DOI	10.1007/s12035-022-03066-0
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