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Article ; Online: Multiomics data analysis workflow to assess severity in longitudinal plasma samples of COVID-19 patients

Sakshi Rajoria / Mehar Un Nissa / Kruthi Suvarna / Harsh Khatri / Sanjeeva Srivastava

Data in Brief, Vol 46, Iss , Pp 108765- (2023)

2023

Abstract: ... to the related full-length article (Suvarna et al., 2021). ...

Abstract	Elucidation of molecular markers related to the mounted immune response is crucial for understanding the disease pathogenesis. In this article, we present the mass-spectrometry-based metabolomic and proteomic data of blood plasma of COVID-19 patients collected at two-time points, which showed a transition from non-severe to severe conditions during these time points. Metabolites were extracted and subjected to mass spectrometric analysis using the Q-Exactive mass spectrometer. For proteomic analysis, depleted plasma samples were tryptic digested and subjected to mass spectrometry analysis. The expression of a few significant proteins was also validated by employing the targeted proteomic approach of multiple reaction monitoring (MRM). Integrative pathway analysis was performed with the significant proteins to obtain biological insights into disease severity. For discussion and more information on the dataset creation, please refer to the related full-length article (Suvarna et al., 2021).
Keywords	Proteomics ; Metabolomics ; Mass spectrometry ; Workflow ; Longitudinal ; Plasma ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multiomics data analysis workflow to assess severity in longitudinal plasma samples of COVID-19 patients.

Rajoria, Sakshi / Nissa, Mehar Un / Suvarna, Kruthi / Khatri, Harsh / Srivastava, Sanjeeva

Data in brief

2022 Volume 46, Page(s) 108765

Abstract: ... to the related full-length article (Suvarna et al., 2021). ...

Abstract	Elucidation of molecular markers related to the mounted immune response is crucial for understanding the disease pathogenesis. In this article, we present the mass-spectrometry-based metabolomic and proteomic data of blood plasma of COVID-19 patients collected at two-time points, which showed a transition from non-severe to severe conditions during these time points. Metabolites were extracted and subjected to mass spectrometric analysis using the Q-Exactive mass spectrometer. For proteomic analysis, depleted plasma samples were tryptic digested and subjected to mass spectrometry analysis. The expression of a few significant proteins was also validated by employing the targeted proteomic approach of multiple reaction monitoring (MRM). Integrative pathway analysis was performed with the significant proteins to obtain biological insights into disease severity. For discussion and more information on the dataset creation, please refer to the related full-length article (Suvarna et al., 2021).
Language	English
Publishing date	2022-11-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2022.108765
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Article ; Online: Measurement of ATPase Activity of Valosin-containing Protein/p97.

Suvarna, Kruthi / Honda, Kaori / Muroi, Makoto / Kondoh, Yasumitsu / Osada, Hiroyuki / Watanabe, Nobumoto

Bio-protocol

2020 Volume 10, Issue 3, Page(s) e3516

Abstract: Valosin-containing protein (VCP; also known as p97) is a type II ATPase regulating several cellular processes. Using proteomic techniques, we identified a chemical compound that binds to the D1 ATPase domain of VCP. The protocol described here was to ... ...

Abstract	Valosin-containing protein (VCP; also known as p97) is a type II ATPase regulating several cellular processes. Using proteomic techniques, we identified a chemical compound that binds to the D1 ATPase domain of VCP. The protocol described here was to study the effect of the compound on ATPase activity
Language	English
Publishing date	2020-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.3516
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Article ; Online: Identification of Target Protein for Bio-active Small Molecule Using Photo-cross Linked Beads and MALDI-TOF Mass Spectrometry.

Suvarna, Kruthi / Honda, Kaori / Muroi, Makoto / Kondoh, Yasumitsu / Watanabe, Nobumoto / Osada, Hiroyuki

Bio-protocol

2020 Volume 10, Issue 3, Page(s) e3517

Abstract: Development of methods for protein identification is one of the important aspects of proteomics. Here, we report a protocol for the preparation of compound conjugated beads by photo-crosslinking, affinity purification, gel electrophoresis, and highly ... ...

Abstract	Development of methods for protein identification is one of the important aspects of proteomics. Here, we report a protocol for the preparation of compound conjugated beads by photo-crosslinking, affinity purification, gel electrophoresis, and highly sensitive mass spectrometric assay for drug-target identification. Although there are several other methods used for drug-target identification, such as biochemical fractionation or radioactive ligand binding assay, affinity purification is widely used for its straight-forward and easy approach. To identify the target protein of an inhibitor of cancer cell-accelerated fibroblast migration, we prepared the inhibitor-conjugated beads by photo-crosslinking. Proteins were pulled down from cell lysates by the compound beads and separated by SDS-PAGE, and a specifically pulled down protein was cut out, trypsin-digested, analyzed using matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF-MS) and identified by peptide mass fingerprinting (PMF) method. Since the photo-crosslinking enables the immobilization of ligands on an affinity matrix in a functional group-independent manner, we do not have to determine the functional group of the compound to conjugate the matrix. In addition, as compared to other MS techniques such as electrospray ionization, MALDI offers a less complex sample preparation procedure and higher sensitivity, and thus is better suited for the rapid identification of proteins isolated by gel electrophoresis.
Language	English
Publishing date	2020-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.3517
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Article: Proteomic Investigation of COVID-19 Severity During the Tsunamic Second Wave in Mumbai.

Rajoria, Sakshi / Nair, Divya / Suvarna, Kruthi / Pai, Medha Gayathri J / Salkar, Akanksha / Palanivel, Viswanthram / Verma, Ayushi / Barpanda, Abhilash / Awasthi, Gaurav / Doshi, Hastyn / Dhara, Vivek / Burli, Ananya / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

Advances in experimental medicine and biology

2023 Volume 1412, Page(s) 175–195

Abstract: Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second ... ...

Abstract	Maharashtra was severely affected during the noxious second wave of COVID-19, with the highest number of cases recorded across India. The emergence of new symptoms and dysregulation of multiple organs resulted in high disease severity during the second wave which led to increased difficulties in understanding the molecular mechanisms behind the disease pathology. Exploring the underlying factors can help to relieve the burden on the medical communities to some extent by prioritizing the patients and, at the same time, opening avenues for improved treatments. In the current study, we have performed a mass-spectrometry-based proteomic analysis to investigate the disease pathology using nasopharyngeal swab samples collected from the COVID-19 patients in the Mumbai region of Maharashtra over the period of March-June 2021, the peak of the second wave. A total of 59 patients, including 32 non-severe and 27 severe cases, were considered for this proteomic study. We identified 23 differentially regulated proteins in severe patients as a host response to infection. In addition to the previously identified innate mechanisms of neutrophil and platelet degranulation, this study revealed significant alterations of anti-microbial peptide pathways in severe conditions, illustrating its role in the severity of the infectious strain of COVID-19 during the second wave. Furthermore, myeloperoxidase, cathepsin G, and profilin-1 were identified as potential therapeutic targets of the FDA-approved drugs dabrafenib, ZINC4097343, and ritonavir. This study has enlightened the role of the anti-microbial peptide pathway associated with the second wave in India and proposed its importance in potential therapeutics for COVID-19.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Proteomics/methods ; India/epidemiology ; Ritonavir
Chemical Substances	Ritonavir (O3J8G9O825)
Language	English
Publishing date	2023-06-28
Publishing country	United States
Document type	Journal Article
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-031-28012-2_9
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Article ; Online: Downregulation of METTL6 mitigates cell progression, migration, invasion and adhesion in hepatocellular carcinoma by inhibiting cell adhesion molecules.

Bolatkan, Amina / Asada, Ken / Kaneko, Syuzo / Suvarna, Kruthi / Ikawa, Noriko / Machino, Hidenori / Komatsu, Masaaki / Shiina, Shuichiro / Hamamoto, Ryuji

International journal of oncology

2021 Volume 60, Issue 1

Abstract: RNA modifications have attracted increasing interest in recent years because they have been frequently implicated in various human diseases, including cancer, highlighting the importance of dynamic post‑transcriptional modifications. Methyltransferase‑ ... ...

Abstract	RNA modifications have attracted increasing interest in recent years because they have been frequently implicated in various human diseases, including cancer, highlighting the importance of dynamic post‑transcriptional modifications. Methyltransferase‑like 6 (METTL6) is a member of the RNA methyltransferase family that has been identified in many cancers; however, little is known about its specific role or mechanism of action. In the present study, we aimed to study the expression levels and functional role of METTL6 in hepatocellular carcinoma (HCC), and further investigate the relevant pathways. To this end, we systematically conducted bioinformatics analysis of METTL6 in HCC using gene expression data and clinical information from a publicly available dataset. The mRNA expression levels of
MeSH term(s)	Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/physiopathology ; Cell Adhesion Molecules/adverse effects ; Cell Adhesion Molecules/therapeutic use ; Cell Line ; Cell Movement/genetics ; Cell Movement/physiology ; Cell Proliferation/genetics ; Cell Proliferation/physiology ; Down-Regulation/genetics ; Humans ; Liver Neoplasms/genetics ; Liver Neoplasms/physiopathology ; tRNA Methyltransferases/adverse effects ; tRNA Methyltransferases/metabolism
Chemical Substances	Cell Adhesion Molecules ; METTL6 protein, human (EC 2.1.1.-) ; tRNA Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2021-12-16
Publishing country	Greece
Document type	Journal Article
ZDB-ID	1154403-x
ISSN	1791-2423 ; 1019-6439
ISSN (online)	1791-2423
ISSN	1019-6439
DOI	10.3892/ijo.2021.5294
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Article ; Online: Identification of a small-molecule ligand of β-arrestin1 as an inhibitor of stromal fibroblast cell migration accelerated by cancer cells.

Suvarna, Kruthi / Honda, Kaori / Kondoh, Yasumitsu / Osada, Hiroyuki / Watanabe, Nobumoto

Cancer medicine

2018 Volume 7, Issue 3, Page(s) 883–893

Abstract: Stromal fibroblasts, which occupy a major portion of the tumor microenvironment, play an important role in cancer metastasis. Thus, targeting of these fibroblasts activated by cancer cells (carcinoma-associated fibroblasts; CAFs) might aid in the ... ...

Abstract	Stromal fibroblasts, which occupy a major portion of the tumor microenvironment, play an important role in cancer metastasis. Thus, targeting of these fibroblasts activated by cancer cells (carcinoma-associated fibroblasts; CAFs) might aid in the improved treatment of cancer metastasis. NIH3T3 fibroblasts cocultured with MCF7 cells displayed enhanced migration compared to NIH3T3 fibroblasts cultured alone. We used this system to identify the small-molecule inhibitors responsible for their enhanced migration, a characteristic of CAFs. We selected β-arrestin1, which showed high expression in cocultured cells, as a molecular target for such inhibitors. Cofilin, a protein downstream of β-arrestin1, is activated/dephosphorylated in this condition. The small-molecule ligands of β-arrestin1 obtained by chemical array were then examined using a wound healing coculture assay. RKN5755 was identified as a selective inhibitor of activated fibroblasts. RKN5755 inhibited the enhanced migration of fibroblasts cocultured with cancer cells by binding to β-arrestin1 and interfering with β-arrestin1-mediated cofilin signaling pathways. Therefore, these results demonstrate the role of β-arrestin1 in the activation of fibroblasts and inhibiting this protein by small molecule inhibitor might be a potential therapeutic target for the stromal fibroblast activation (cancer-stroma interaction).
MeSH term(s)	Animals ; Cell Line, Tumor ; Cell Movement ; Cell Proliferation ; Fibroblasts/metabolism ; Humans ; Ligands ; Mice ; Neoplasms/genetics ; Neoplasms/metabolism ; Stromal Cells/metabolism ; Tumor Microenvironment ; beta-Arrestin 1/metabolism
Chemical Substances	Ligands ; beta-Arrestin 1
Language	English
Publishing date	2018-01-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2045-7634
ISSN (online)	2045-7634
DOI	10.1002/cam4.1339
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Article ; Online: A small-molecule ligand of valosin-containing protein/p97 inhibits cancer cell-accelerated fibroblast migration.

Suvarna, Kruthi / Honda, Kaori / Muroi, Makoto / Kondoh, Yasumitsu / Osada, Hiroyuki / Watanabe, Nobumoto

The Journal of biological chemistry

2019 Volume 294, Issue 9, Page(s) 2988–2996

Abstract: Carcinoma-associated fibroblasts are fibroblasts activated by surrounding cancer cells. Carcinoma-associated fibroblasts exhibit enhanced cell migration, which plays an important role in cancer metastasis. Previously, we demonstrated enhanced migration ... ...

Abstract	Carcinoma-associated fibroblasts are fibroblasts activated by surrounding cancer cells. Carcinoma-associated fibroblasts exhibit enhanced cell migration, which plays an important role in cancer metastasis. Previously, we demonstrated enhanced migration of NIH3T3 fibroblasts when they were cultured in the presence of MCF7 breast cancer cells. Human fibroblasts displayed a similar phenomenon even when they were co-cultured with cancer cells other than MCF7 cells. In this study, we screened ∼16,000 compounds from the RIKEN Natural Products Depository chemical library for inhibitors of enhanced NIH3T3 cell migration in the presence of MCF7. We identified NPD8733 as an inhibitor of cancer cell-enhanced fibroblast migration. This inhibition was observed not only in a wound-healing co-culture assay but also in a Transwell migration assay. Using NPD8733 and a structurally similar but inactive derivative, NPD8126, on immobilized beads, we found that NPD8733, but not NPD8126, specifically binds to valosin-containing protein (VCP)/p97, a member of the ATPase-associated with diverse cellular activities (AAA+) protein family. Using VCP truncation variants, we found that NPD8733 binds to the D1 domain of VCP. Because VCP's D1 domain is important for its function, we concluded that NPD8733 may act on VCP by binding to this domain. siRNA-mediated silencing of VCP in NIH3T3 fibroblasts, but not in MCF7 cells, reduced the migration of the co-cultured NIH3T3 fibroblasts. These results indicate that MCF7 activates the migration of NIH3T3 cells through VCP and that NPD8733 binds VCP and thereby inhibits its activity.
MeSH term(s)	Animals ; Cell Movement/drug effects ; Coculture Techniques ; Drug Evaluation, Preclinical ; Fibroblasts/cytology ; Fibroblasts/drug effects ; Humans ; Ligands ; MCF-7 Cells ; Mice ; NIH 3T3 Cells ; Protein Domains ; Small Molecule Libraries/metabolism ; Small Molecule Libraries/pharmacology ; Valosin Containing Protein/chemistry ; Valosin Containing Protein/metabolism
Chemical Substances	Ligands ; Small Molecule Libraries ; Valosin Containing Protein (EC 3.6.4.6)
Language	English
Publishing date	2019-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA118.004741
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Article ; Online: A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients.

Suvarna, Kruthi / Salkar, Akanksha / Palanivel, Viswanthram / Bankar, Renuka / Banerjee, Nirjhar / Gayathri J Pai, Medha / Srivastava, Alisha / Singh, Avinash / Khatri, Harsh / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

Journal of proteome research

2021 Volume 20, Issue 10, Page(s) 4667–4680

Abstract: Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific ... ...

Abstract	Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific molecular signatures associated with the elevated immune response are yet to be elucidated. We performed a mass-spectrometry-based proteomic and metabolomic analysis of COVID-19 plasma samples collected at two time points. Using Orbitrap Fusion LC-MS/MS-based label-free proteomic analysis, we identified around 10 significant proteins, 32 significant peptides, and 5 metabolites that were dysregulated at the severe time points. Few of these proteins identified by quantitative proteomics were validated using the multiple reaction monitoring (MRM) assay. Integrated pathway analysis using distinct proteomic and metabolomic signatures revealed alterations in complement and coagulation cascade, platelet aggregation, myeloid leukocyte activation pathway, and arginine metabolism. Further, we highlight the role of leukocyte activation and arginine metabolism in COVID-19 pathogenesis and targeting these pathways for COVID-19 therapeutics.
MeSH term(s)	COVID-19 ; Chromatography, Liquid ; Humans ; Leukocytes ; Longitudinal Studies ; Proteomics ; SARS-CoV-2 ; Tandem Mass Spectrometry
Language	English
Publishing date	2021-08-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00215
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Article ; Online: Proteomic investigation reveals dominant alterations of neutrophil degranulation and mRNA translation pathways in patients with COVID-19.

Bankar, Renuka / Suvarna, Kruthi / Ghantasala, Saicharan / Banerjee, Arghya / Biswas, Deeptarup / Choudhury, Manisha / Palanivel, Viswanthram / Salkar, Akanksha / Verma, Ayushi / Singh, Avinash / Mukherjee, Amrita / Pai, Medha Gayathri J / Roy, Jyotirmoy / Srivastava, Alisha / Badaya, Apoorva / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

iScience

2021 Volume 24, Issue 3, Page(s) 102135

Abstract: The altered molecular proteins and pathways in response to COVID-19 infection are still unclear. Here, we performed a comprehensive proteomics-based investigation of nasopharyngeal swab samples from patients with COVID-19 to study the host response by ... ...

Abstract	The altered molecular proteins and pathways in response to COVID-19 infection are still unclear. Here, we performed a comprehensive proteomics-based investigation of nasopharyngeal swab samples from patients with COVID-19 to study the host response by employing simple extraction strategies. Few of the host proteins such as interleukin-6, L-lactate dehydrogenase, C-reactive protein, Ferritin, and aspartate aminotransferase were found to be upregulated only in COVID-19-positive patients using targeted multiple reaction monitoring studies. The most important pathways identified by enrichment analysis were neutrophil degranulation, interleukin-12 signaling pathways, and mRNA translation of proteins thus providing the detailed investigation of host response in COVID-19 infection. Thus, we conclude that mass spectrometry-detected host proteins have a potential for disease severity progression; however, suitable validation strategies should be deployed for the clinical translation. Furthermore, the
Language	English
Publishing date	2021-02-04
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2021.102135
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