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Article ; Online: Identification of glucose-independent and reversible metabolic pathways associated with anti-proliferative effect of metformin in liver cancer cells.

Islam, Sk Ramiz / Manna, Soumen Kanti

Metabolomics : Official journal of the Metabolomic Society

2024 Volume 20, Issue 2, Page(s) 29

Abstract: Introduction: Despite the ability of cancer cells to survive glucose deprivation, most studies on anti-cancer effect of metformin explored its impact on glucose metabolism. No study ever examined whether its anti-cancer effect is reversible. Existing ... ...

Abstract	Introduction: Despite the ability of cancer cells to survive glucose deprivation, most studies on anti-cancer effect of metformin explored its impact on glucose metabolism. No study ever examined whether its anti-cancer effect is reversible. Existing evidences warrant understanding of glucose-independent non-cytotoxic anti-proliferative effect of metformin to rationalize its role in liver cancer. Objectives: Characterization of glucose-independent anti-proliferative metabolic effects of metformin as well as analysis of their reversibility in liver cancer cells. Methodology: The dose-dependent effects of metformin on HepG2 cells were examined in presence and absence of glucose. The longitudinal evolution of metabolome was analyzed along with gene and protein expression as well as their correlations with and reversibility of cellular phenotype and metabolic signatures. Results: Metformin concentrations up to 2.5 mM were found to be anti-proliferative irrespective of presence of glucose without significant increase in cytotoxicity. Apart from mitochondrial impairment, derangement of fatty acid desaturation, one-carbon, glutathione, and polyamine metabolism were associated with metformin treatment irrespective of glucose supplementation. Depletion of pantothenic acid, downregulation of essential amino acid uptake and metabolism alongside purine salvage were identified as novel glucose-independent effects of metformin. These were significantly correlated with cMyc expression and reduction in proliferation. Rescue experiments established reversibility upon metformin withdrawal and tight association between proliferation, metabotype, and cMyc expression. Conclusions: The derangement of multiple glucose-independent metabolic pathways, which are often upregulated in therapy-resistant cancer, and concomitant cMyc downregulation coordinately contribute to the anti-proliferative effect of metformin in liver cancer cells. These are reversible and may influence its therapeutic utility.
MeSH term(s)	Humans ; Metformin/pharmacology ; Metformin/therapeutic use ; Glucose/metabolism ; Hypoglycemic Agents/pharmacology ; Metabolomics ; Metabolic Networks and Pathways ; Cell Line, Tumor ; Liver Neoplasms/drug therapy
Chemical Substances	Metformin (9100L32L2N) ; Glucose (IY9XDZ35W2) ; Hypoglycemic Agents
Language	English
Publishing date	2024-02-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2250617-2
ISSN	1573-3890 ; 1573-3882
ISSN (online)	1573-3890
ISSN	1573-3882
DOI	10.1007/s11306-024-02096-0
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Article ; Online: Protocol for analyzing energy metabolic pathway dependency in human liver cancer cell lines.

Islam, Sk Ramiz / Maity, Sebabrata / Chakrabarti, Oishee / Manna, Soumen Kanti

STAR protocols

2024 Volume 5, Issue 2, Page(s) 102964

Abstract: Cellular energy metabolism analysis is complex, expensive, and indirect. We present a protocol to analyze relative contribution of metabolic pathways to ATP production by directly measuring ATP levels. We describe steps for cell counting and seeding in ... ...

Abstract	Cellular energy metabolism analysis is complex, expensive, and indirect. We present a protocol to analyze relative contribution of metabolic pathways to ATP production by directly measuring ATP levels. We describe steps for cell counting and seeding in 96-well plate, treating with metformin, and systematic inhibition with metabolic inhibitors. We then detail procedures for a viability and ATP assay and calculating energy metabolism dependency. This high-throughput and accessible protocol works with any cell line and allows for flexible perturbation studies.
Language	English
Publishing date	2024-03-18
Publishing country	United States
Document type	Journal Article
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2024.102964
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Article ; Online: Lipidomic Analysis of Cancer Cell and Tumor Tissues.

Islam, Sk Ramiz / Manna, Soumen Kanti

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1928, Page(s) 175–204

Abstract: Due to their role in cellular structure, energetics, and signaling, characterization of changes in cellular and extracellular lipid composition is of key importance to understand cancer biology. In addition, several mass spectrometry-based profiling as ... ...

Abstract	Due to their role in cellular structure, energetics, and signaling, characterization of changes in cellular and extracellular lipid composition is of key importance to understand cancer biology. In addition, several mass spectrometry-based profiling as well as imaging studies have indicated that lipid molecules may be useful to augment existing biochemical and histopathological methods for diagnosis, staging, and prognosis of cancer. Therefore, analysis of lipidomic changes associated with cancer cells and tumor tissues can be useful for both fundamental and translational studies. Here, we provide a high-throughput single-extraction-based method that can be used for simultaneous lipidomic and metabolomic analysis of cancer cells or healthy or tumor tissue samples. In this chapter, a modified Bligh-Dyer method is described for extraction of lipids followed by analysis of fatty acid composition by gas chromatography-mass spectrometry (GC-MS) or untargeted lipidomics using electrospray ionization mass spectrometry (ESIMS) coupled with reverse-phase (RP) ultraperformance liquid chromatography (UPLC) followed by multivariate data analysis to identify features of interest.
MeSH term(s)	Cell Line ; Chromatography, High Pressure Liquid ; Chromatography, Reverse-Phase ; Databases, Factual ; Fatty Acids/metabolism ; Gas Chromatography-Mass Spectrometry ; Humans ; Lipid Metabolism ; Lipids/chemistry ; Lipids/isolation & purification ; Metabolome ; Metabolomics/methods ; Neoplasms/metabolism ; Solvents ; Spectrometry, Mass, Electrospray Ionization
Chemical Substances	Fatty Acids ; Lipids ; Solvents
Language	English
Publishing date	2019-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9027-6_11
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mass Spectrometry-Based Profiling of Metabolites in Human Biofluids.

Chakraborty, Tanushree / Manna, Soumen Kanti

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1928, Page(s) 205–234

Abstract: Cancer poses a daunting challenge to researchers and clinicians alike. Early diagnosis, accurate prognosis, and prediction of therapeutic response remain elusive in most types of cancer. In addition, lacunae in our understanding of cancer biology ... ...

Abstract	Cancer poses a daunting challenge to researchers and clinicians alike. Early diagnosis, accurate prognosis, and prediction of therapeutic response remain elusive in most types of cancer. In addition, lacunae in our understanding of cancer biology continue to hinder advancement of therapeutic strategies. Metabolic reprogramming has been identified as integral to pathogenesis and progression of the disease. Consequently, analysis of biofluid metabolome has emerged as a promising approach to further our understanding of disease biology as well as to identify cancer biomarkers. However, unbiased identification of robust and meaningful differences in metabolic signatures remains a non-trivial task. This chapter describes a generalized strategy for global metabolic profiling of human biofluids using ultra-performance liquid chromatography (UPLC) and mass spectrometry, which together offer a sensitive, high-throughput, and versatile platform. A step-by-step protocol for performing untargeted metabolic profiling of urine and serum (or plasma), using hydrophilic interaction liquid chromatography (HILIC) or reverse-phase (RP) chromatography coupled with electrospray ionization mass spectrometry (ESI-MS) to multivariate data analysis and identification of metabolites of interest has been detailed.
MeSH term(s)	Body Fluids/metabolism ; Chromatography, Liquid ; Chromatography, Reverse-Phase ; Data Analysis ; Data Mining ; Databases, Factual ; Humans ; Magnetic Resonance Spectroscopy ; Mass Spectrometry/methods ; Metabolome ; Metabolomics/methods ; Software ; Solvents ; Spectrometry, Mass, Electrospray Ionization ; Web Browser
Chemical Substances	Solvents
Language	English
Publishing date	2019-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9027-6_12
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Assessment of Metabolic Signature for Cancer Diagnosis Using Desorption Electrospray Ionization Mass Spectrometric Imaging.

Banerjee, Shibdas / Manna, Soumen Kanti

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1928, Page(s) 275–297

Abstract: Metabolic reprogramming is a hallmark of tumor development. A technique that can map this complex biochemical shift by taking a snapshot of various metabolites in a tissue specimen (biopsy) is of high utility in the context of cancer diagnosis. ... ...

Abstract	Metabolic reprogramming is a hallmark of tumor development. A technique that can map this complex biochemical shift by taking a snapshot of various metabolites in a tissue specimen (biopsy) is of high utility in the context of cancer diagnosis. Desorption electrospray ionization mass spectrometric imaging (DESI-MSI) is such a powerful and emerging analytical technique to simultaneously visualize the distributions of hundreds of metabolites, lipids, and other small molecules in the biological tissue. In DESI-MSI, a fine spray of high-velocity charged microdroplets rapidly extracts molecular species from the tissue surface and subsequently transfers them to the mass spectrometer, while the sample is continuously moved in two dimensions under the impinging spray of microdroplets. This allows a detailed multiplex molecular mapping of the tissue. DESI-MSI enables simultaneous examination of hundreds of putative metabolic biomarkers, an approach that lends much more predictive power than simply evaluating one or a few candidate biomarkers. The speed, versatility, lack of complicated sample preparation, and operation at ambient conditions make DESI-MSI extremely promising as a rapid diagnostic and prognostic tool.
MeSH term(s)	Biopsy ; Data Analysis ; Databases, Factual ; Humans ; Immunohistochemistry ; Liquid Biopsy ; Metabolome ; Metabolomics/methods ; Neoplasms/diagnosis ; Neoplasms/metabolism ; Software ; Spectrometry, Mass, Electrospray Ionization/methods
Language	English
Publishing date	2019-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9027-6_15
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effect of short-term use of FFP2 (N95) masks on the salivary metabolome of young healthy volunteers: a pilot study.

Islam, Sk Ramiz / Prusty, Debasish / Maiti, Subhadip / Dutta, Raju / Chattopadhyay, Partha / Manna, Soumen Kanti

Molecular omics

2023 Volume 19, Issue 5, Page(s) 383–394

Abstract: The use of face masks has become an integral part of public life in the post-pandemic era. However, the understanding of the effect of wearing masks on physiology remains incomplete and is required for informing public health policies. For the first time, ...

Abstract	The use of face masks has become an integral part of public life in the post-pandemic era. However, the understanding of the effect of wearing masks on physiology remains incomplete and is required for informing public health policies. For the first time, we report the effects of wearing FFP2 masks on the metabolic composition of saliva, a proximal matrix to breath, along with cardiopulmonary parameters. Un-induced saliva was collected from young (31.2 ± 6.3 years) healthy volunteers (
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Masks ; Pilot Projects ; Metabolome
Language	English
Publishing date	2023-06-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/d2mo00232a
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Article ; Online: Structural basis of fitness of emerging SARS-COV-2 variants and considerations for screening, testing and surveillance strategy to contain their threat.

Islam, Sk Ramiz / Prusty, Debasish / Manna, Soumen Kanti

medRxiv

Abstract: While emergence of new SAS-COV-2 variants is posing grave challenge to efforts to deal with the COVID-19 pandemic, the structural and molecular basis of their fitness remain poorly understood. We performed in silico analysis of structures of two most ... ...

Abstract	While emergence of new SAS-COV-2 variants is posing grave challenge to efforts to deal with the COVID-19 pandemic, the structural and molecular basis of their fitness remain poorly understood. We performed in silico analysis of structures of two most frequent SARS-COV-2 mutations, namely, N501Y and E484K, to identify plausible basis of their fitness over the original strain. The analysis suggested that the N501Y mutation is associated with strengthening of intra- as well as intermolecular H-bond in the hACE2 receptor-spike protein complex, which could result in increased affinity and, therefore, higher infectivity. While E484K mutation did not seem to directly affect the binding with hACE2 receptor, it disrupted H-bonding and salt-bridge interaction associated with binding with neutralizing antibody, which could affect chance of re-infection, disease outcome. Survey of several other mutations showing reduction in antibody-mediated neutralization also revealed that similar disruption of H-bonding or salt-bridge or Van der Waals interaction might explain their phenotype. Analysis of GESS database indicated that N501Y, EK484 as well as these other mutations existed since March-April, 2020, might have evolved independently across the world and may keep accumulating, which could affect efficacy of vaccination and antibody-based therapies. Our analysis also indicated that these may spread in spite of current travel restrictions focused on few countries and evolve indigenously warranting intensification of surveillance for emerging mutations among all travellers as well as people in their dwelling zones. Meta-analysis of existing literature showed that repeat testing of travellers, contacts and others under scrutiny 7-11 days after the initial RT-PCR test may significantly help to contain the spread of emerging variants by catching false negative results. In addition, existing evidence calls for development of strain-specific tests, escalated sequencing and broadening the scope of surveillance including in hospitals and animal farms to contain the threat of emerging variants.
Keywords	covid19
Language	English
Publishing date	2021-01-31
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.01.28.21250666
Database	COVID19

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Article ; Online: Thiourea mediated ROS-metabolites reprogramming restores root system architecture under arsenic stress in rice.

Ghate, Tejashree / Soneji, Kanchan / Barvkar, Vitthal / Ramakrishnan, Padma / Prusty, Debasish / Islam, Sk Ramiz / Manna, Soumen Kanti / Srivastava, Ashish Kumar

Journal of hazardous materials

2022 Volume 435, Page(s) 129020

Abstract: Arsenic (As) is a ubiquitous carcinogenic metalloid that enters into human food chain, through rice consumption. To unravel the conundrum of oxidative vs. reductive stress, the differential root-system architecture (RSA) was studied under As (a ROS ... ...

Abstract	Arsenic (As) is a ubiquitous carcinogenic metalloid that enters into human food chain, through rice consumption. To unravel the conundrum of oxidative vs. reductive stress, the differential root-system architecture (RSA) was studied under As (a ROS producer) and thiourea (TU; a ROS scavenger) alone treatments, which indicated 0.80- and 0.74-fold reduction in the number of lateral roots (NLR), respectively compared with those of control. In case of As+TU treatment, NLR was increased by 4.35-fold compared with those of As-stress, which coincided with partial restoration of redox-status and auxin transport towards the root-tip. The expression levels of 16 ROS related genes, including RBOHC, UPB-1 C, SHR1, PUCHI, were quantified which provided the molecular fingerprint, in accordance with endogenous ROS signature. LC-MS based untargeted and targeted metabolomics data revealed that As-induced oxidative stress was metabolically more challenging than TU alone-induced reductive stress. Cis/trans-ferruloyl putrescine and γ-glutamyl leucine were identified as novel As-responsive metabolites whose levels were decreased and increased, respectively under As+TU than As-treated roots. In addition, the overall amino acid accumulation was increased in As+TU than As-treated roots, indicating the improved nutritional availability. Thus, the study revealed dynamic interplay between "ROS-metabolites-RSA", to the broader context of TU-mediated amelioration of As-stress in rice.
MeSH term(s)	Arsenic/metabolism ; Arsenic/toxicity ; Humans ; Oryza/genetics ; Oryza/metabolism ; Plant Roots/metabolism ; Reactive Oxygen Species/metabolism ; Thiourea/metabolism ; Thiourea/pharmacology
Chemical Substances	Reactive Oxygen Species ; Thiourea (GYV9AM2QAG) ; Arsenic (N712M78A8G)
Language	English
Publishing date	2022-04-27
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2022.129020
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission

Laha, Sayantan / Chakraborty, Joyeeta / Das, Shantanab / Manna, Soumen Kanti / Biswas, Sampa / Chatterjee, Raghunath

Infection, genetics, and evolution. 2020 Nov., v. 85

2020

Abstract: The recent pandemic of SARS-CoV-2 infection has affected more than 3.0 million people worldwide with more than 200 thousand reported deaths. The SARS-CoV-2 genome has the capability of gaining rapid mutations as the virus spreads. Whole-genome sequencing ...

Abstract	The recent pandemic of SARS-CoV-2 infection has affected more than 3.0 million people worldwide with more than 200 thousand reported deaths. The SARS-CoV-2 genome has the capability of gaining rapid mutations as the virus spreads. Whole-genome sequencing data offers a wide range of opportunities to study mutation dynamics. The advantage of an increasing amount of whole-genome sequence data of SARS-CoV-2 intrigued us to explore the mutation profile across the genome, to check the genome diversity, and to investigate the implications of those mutations in protein stability and viral transmission. We have identified frequently mutated residues by aligning ~660 SARS-CoV-2 genomes and validated in 10,000 datasets available in GISAID Nextstrain. We further evaluated the potential of these frequently mutated residues in protein structure stability of spike glycoprotein and their possible functional consequences in other proteins. Among the 11 genes, surface glycoprotein, nucleocapsid, ORF1ab, and ORF8 showed frequent mutations, while envelop, membrane, ORF6, ORF7a and ORF7b showed conservation in terms of amino acid substitutions. Combined analysis with the frequently mutated residues identified 20 viral variants, among which 12 specific combinations comprised more than 97% of the isolates considered for the analysis. Some of the mutations across different proteins showed co-occurrences, suggesting their structural and/or functional interaction among different SARS-COV-2 proteins, and their involvement in adaptability and viral transmission. Analysis of protein structure stability of surface glycoprotein mutants indicated the viability of specific variants and are more prone to be temporally and spatially distributed across the globe. A similar empirical analysis of other proteins indicated the existence of important functional implications of several variants. Identification of frequently mutated variants among COVID-19 patients might be useful for better clinical management, contact tracing, and containment of the disease.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; data collection ; empirical research ; evolution ; glycoproteins ; infection ; nucleocapsid ; pandemic ; people ; protein structure ; viability ; virus transmission ; viruses
Language	English
Dates of publication	2020-11
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2037068-4
ISSN	1567-1348
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104445
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 5645: Show issues

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Article: Thiourea mediated ROS-metabolites reprogramming restores root system architecture under arsenic stress in rice

Ghate, Tejashree / Soneji, Kanchan / Barvkar, Vitthal / Ramakrishnan, Padma / Prusty, Debasish / Islam, Sk Ramiz / Manna, Soumen Kanti / Srivastava, Ashish Kumar

Journal of hazardous materials. 2022 Aug. 05, v. 435

2022

Abstract	Arsenic (As) is a ubiquitous carcinogenic metalloid that enters into human food chain, through rice consumption. To unravel the conundrum of oxidative vs. reductive stress, the differential root-system architecture (RSA) was studied under As (a ROS producer) and thiourea (TU; a ROS scavenger) alone treatments, which indicated 0.80- and 0.74-fold reduction in the number of lateral roots (NLR), respectively compared with those of control. In case of As+TU treatment, NLR was increased by 4.35-fold compared with those of As-stress, which coincided with partial restoration of redox-status and auxin transport towards the root-tip. The expression levels of 16 ROS related genes, including RBOHC, UPB-1 C, SHR1, PUCHI, were quantified which provided the molecular fingerprint, in accordance with endogenous ROS signature. LC-MS based untargeted and targeted metabolomics data revealed that As-induced oxidative stress was metabolically more challenging than TU alone-induced reductive stress. Cis/trans-ferruloyl putrescine and γ-glutamyl leucine were identified as novel As-responsive metabolites whose levels were decreased and increased, respectively under As+TU than As-treated roots. In addition, the overall amino acid accumulation was increased in As+TU than As-treated roots, indicating the improved nutritional availability. Thus, the study revealed dynamic interplay between “ROS-metabolites-RSA”, to the broader context of TU-mediated amelioration of As-stress in rice.
Keywords	arsenic ; auxins ; carcinogenicity ; human food chain ; leucine ; metabolites ; metabolomics ; oxidative stress ; putrescine ; rice ; root systems ; root tips ; thiourea
Language	English
Dates of publication	2022-0805
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2022.129020
Database	NAL-Catalogue (AGRICOLA)

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