Single-Cell Mass Spectrometry Studies of Secondary Drug Resistance of Tumor Cells DOI

Guizhen Zhu,

Wenmei Zhang, Yaoyao Zhao

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 20, 2024

Patients with epidermal growth factor receptor mutant nonsmall cell lung cancer (NSCLC) often fail to treat gefitinib because of secondary drug resistance. The development tumor resistance is closely related variations in metabolism. Single-cell metabolomics analysis can provide unique information about Herein, we constructed a platform study the cells based on single-cell (sSRTC-scM). A gefitinib-resistant NSCLC line (PC9GR) was by increasing dose step step. metabolic profiles parental PC9 and PC9GR different levels were detected intact living-cell electrolaunching ionization mass spectrometry at level. data analyzed statistical methods such as t-SNE, variance, volcano plot, heat map, pathway analysis. Using this platform, found that fingerprints evaluate degrees. continue be altered increase We revealed 19 markers variance clarified glycerophospholipid changed significantly. In addition, levels, heterogeneity metabolism became greater number weak gradually decreased. This phenomenon utilized illustrate degrees cells. provides diagnostic for evaluating tumors gives new insight into overcoming tumors.

Language: Английский

Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective DOI Creative Commons
Boryana Petrova, Arzu Tuğçe Güler

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 22, 2024

Recent advancements in single-cell (sc) resolution analyses, particularly sc transcriptomics and proteomics, have revolutionized our ability to probe understand cellular heterogeneity. The study of metabolism through small molecules, metabolomics, provides an additional level information otherwise unattainable by or proteomics shedding light on the metabolic pathways that translate gene expression into functional outcomes. Metabolic heterogeneity, critical health disease, impacts developmental outcomes, disease progression, treatment responses. However, dedicated approaches probing metabolome not reached maturity other omics technologies. Over past decade, innovations metabolomics addressed some practical limitations, including cell isolation, signal sensitivity, throughput. To fully exploit their potential biological research, however, remaining challenges must be thoroughly addressed. Additionally, integrating with orthogonal techniques will required validate relevant results gain systems-level understanding. This perspective offers a broad-stroke overview recent mass spectrometry (MS)-based advancements, focusing ongoing from biologist's viewpoint, aimed at addressing pertinent innovative questions. we emphasize use showcase systems these sophisticated methodologies are apt explore.

Language: Английский

Citations

6
A micropeptide regulates seed desiccation DOI Creative Commons

Rong Chun Lu,

Zilin Zhang,

Songping Hu

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: March 26, 2025

Seeds serve as the major means of reproduction for most plant species and form foundation both agriculture natural ecosystems (Waterworth et al., 2024). are also key genetic resources to deal with increasing human population climate fluctuations (Leprince 2017).Seed development can be categorized into three stages: maturation, dormancy, germination (Figure 1A; Zinsmeister 2020;Powell, 2022;Nadarajan 2023;Waterworth 2024).In maturation phase, seeds acquire desiccation tolerance, followed by developmental processes that expands longevity dormancy stage. Maturation drying reduces seed moisture content 5% -15% fresh weight 2020). Dormancy under optimal conditions, such low temperature humidity, prolongs viability, while suboptimal conditions lead aging Powell 2023). Seed is modulated a complex interplay genetic, biochemical, molecular determinants intricately connected environmental signals light, temperature, nitrate availability, phytohormones including abscisic acid (ABA) gibberellin (GA) (Chahtane 2017;Matilla, 2024;Rachappanavar, 2025).The difference between dormant non-dormant could attributed number gene expression changes (Meimoun 2014), physiological, developmental, morphological features grains on spike, pericarp color, transparency, hairiness, waxiness, permeability water, α-amylase activity, concentrations growth regulators ABA GA within embryo (Sohn al. 2021). initiated water uptake (imbibition), resulting in activation multiple cellular actions, completed emergence young roots shoots 1A;Carrera-Castaño 2020;Waterworth 2024).The acquisition tolerance at late stage provides critical survival mechanism crops, enabling them adaptive adverse extreme temperatures drought 2017;Zinsmeister The majority crop plants generate classified orthodox seeds, which possess ability withstand (below 7%) harsh freezing (-10 ℃) long time (Nadarajan maize, kernel suitable mechanized harvesting from 15% -25%, however, some regions China, maize varieties have high grain harvest, ranging 30% -40% (Xiang 2012;Kebebe 2015;Dai 2017;Li 2018aLi , 2018b;;Zhou 2018). Kernel dehydration rate (KDR), defined loss two adjacent periods after pollination (Zhang 2024a), determinant quality exerts significant impact efficiency mechanical (Li 2018c).Besides, removal free leads phase transition cytoplasm mobility fluid glassy state (Buitink Leprince, 2008), metabolic quiescence increased (Zinsmeister To date, elements implicated modulation reactive oxygen (ROS) signaling, lipid peroxidation cell membrane, preservation DNA RNA integrity, methylation status, biosynthesis storage proteins (SSPs), ABA, auxin, GA, brassinosteroids (BRs) been documented crucial 2023;Pirredda 2024).Abiotic factors thermal salinity stress significantly longevity, availability emerging predominant In several quantitative trait loci (QTLs) characterized pivotal players regulation KDR 2020(Li 2021a;;Zhang 2023;Jin Collectively, higher level harvesting, preventing breakage, mildew, reducing costs associated harvest (de Jager 2004;Xiang 2015;Wang 2022;Xia Thus, comprehensive understanding mechanisms governing necessary crucial.Seed linked multitude physiological modifications, accumulation macromolecules (proteins, lipids, carbohydrates), enhanced membrane defense mechanisms, governed hormone signaling pathways ethylene (Angelovici 2010;Bewley 2013;Kijak Ratajczak, 2020;Oliver 2020;Smolikova onset occurs when enter 2017;Smolikova Numerous components Late Embryogenesis Abundant (LEA) proteins, small heat shock (sHSPs), non-reducing oligosaccharides, antioxidants, (ROS), well (GA), identified 2010;Kijak addition, many transcription ABA-INSENSITIVE 3 (ABI3), FUSCA (FUS3) LEAFY COTYLEDONS 2 (LEC2) discovered defines balance finally initiate (Smolikova However, regulatory mediated peptides remain largely elusive.Micropeptides, referred microproteins or short open reading frame (sORF)-encoded peptides, essential products derived larger polypeptide MicroRNAs (miRNAs), non-coding (lncRNA), circular (circRNA), typically an arbitrary length less than 100 -150 amino acids (Hashimoto 2008;Makarewich Olson, 2017;Sousa Farkas, 2018;Vitorino 2021;Pan 2022;Sruthi 2022;Bhar Roy, 2023;Gautam A growing evidence show roles micropeptides various but not limited (Sharma 2020;Erokhina 2021;Badola 2022), adventitious root formation (Chen 2020), nodule (Couzigou 2016), cold response anthocyanin (Vale 2024), responses cadmium arsenic stressors (Kumar 2023;Lu immunity (Zhou 2022). Recently, microRPG1 (micropeptide RPG ORF1) peptide governs (KDR) has identified, offering novel perspectives regulate micropeptide providing valuable insights future breeding cereal crops 1B; Lyu, 2024;Yu 2024).Maize (Zea mays) one important world-wide, annual global production over 1147 million tons (Yang Yan, Mechanized kernels viable solution reduce labor enhance efficiency. yet achieved China due absence appropriate corn cultivars 2018a;Wang 2018;Liu requires sufficiently (15% -25%) (Liu This poses challenge exhibit during usually 40% (Dai 2018a;Zhou Consequently, enhancing minimizing become aim modern (Sala 2006;Qu this end, prominent locus (QTL) KDR, designated Dehydration Rate 1 (qKDR1), recombinant inbred line population, originated crossbreeding lines K22 DAN340, known their variant KDRs (Pan 2016;Xiao 2016;Yu 2024).qKDR1 located chromosome 1, specifically 1417 base pair (bp) intergenic noncoding region genome (Yu Targeted deletion sequence via CRISPR-Cas9 yields varying KDRs, demonstrating 1417-bp segment qKDR1 variability, its knockout impaired KDR. investigate transient transcriptional activity assays were conducted protoplasts. findings reveal functions silencer, 369-bp repressive element. Subsequent RNA-sequencing analysis performed ascertain potential targets qKDR1, leading identification target gene, Regulated Peptide Gene (RPG). situated 10 kilobases upstream exhibits levels kernels, declines later stages maturation. where knocked out, markedly elevated. these results indicate acts repressor expression. Furthermore, public chromatin immunoprecipitation sequencing (ChIP-seq) datasets uncovered MYB-related factors, ZmMYBST1 ZmMYBR43, bind locus. Both ZmMYBR43 patterns similar RPG, they inhibit activity. Additionally, CRISPR-Cas9-generated double mutants demonstrate reduced These suggest interact downregulate expression, thereby modulating KDR.Ribosome profiling (Ribo-seq) reveals mRNA ribosome bound frames, ORF1, ORF2, ORF3. Mutations ORF1 accelerated whereas mutations other ORFs no obvious effect Overexpressing resulted decelerated decreased different environments. endogenous verified (IP) mass spectrometry (MS). encodes functional (microRPG1). ZmEIL1 ZmEIL3, downstream RNA-seq assay. ZmEIL3 upregulated downregulated overexpression lines, respectively. Consistently, contrast, application facilitates rate. Hence, microRPG1peptide represses further decelerates 1B).Although function established Arabidopsis precise warrant exploration. First, binding affinities sites elucidated. Secondly, inhibits potentially through native promoter investigation. It proposed localized plasma nucleus, cytoplasm, indicating unidentified receptors may exist recognize peptide, initiating cascades, nucleus finely tolerance. advanced CRISPR screening platform powerful methodology generating single receptor-like kinases (RLKs) simultaneously (Gaillochet 2021), will facilitate uncharacterized signal modulate it plausible effects independently any specific receptors.Additionally, interactions (Kijak necessitate scrutiny. Importantly, single-cell transcriptomic facilitated involved (Liew 2024;Yao technique unveil resolution establish unprecedented networks govern Notably, develop sustain 1A). question remains unresolved how initiates peptide. interacts yet-to-be-identified require elucidation 2020;Farrant 2022;Waterworth 2024).Despite fact exclusively found genera Zea influence Desiccation maternal array programmed suggesting process, CLAVATA3/EMBRYO SURROUNDING REGION 9 (CLE9) 2019) andCLE25/26 (Takahashi 2018;Endo Fukuda, C-TERMINALLY ENCODED PEPTIDE 5 (CEP5) (Smith RAPID ALKALINIZATION FACTOR (RALF) (Jing along droughtresponsive (Xie 2022;Ji 2025;Zhang 2025), examinations. imaging (MSI) employed elucidate spatial distribution structurally diverse hormones 2024) compounds (Garcí a-Rojas 2024;Yin 2024;Zou even (Croslow 2024;Zhang 2024b). successfully identify mammalian cells (David 2018;Bottomley MSI instrumental discovering existing knowledge underlying addition miPEPs horticultural (Ji 2025); biological uncharacterized. CRISPR-Cas system generation miPEP 2021b), Moreover, CRISPR-mediated tools, interference (CRISPRi), (CRISPRa), CRISPRoff, CROP-seq, CRISP-seq, CRISPR-based epigenetic Perturb-seq coupled transcriptomics utilized growth, agronomic traits, resolution. tools enable construction peptides.In summary, discovery contributes improvement adapt harvesting. According Worldostats (https:://worldostats.com/corn-maize-production-by-country-2025/) FAO (Food Agriculture Organization United Nations) staggering 1.16 billion tones per year. top producing countries USA (348.8 tons), (277.2 tons) Brazil (109.4 accounting half production. would lower prevent increase worldwide food supplement future. possible introduce rice, wheat millet artificially exogenous manipulate beneficial future.Identifying subsequently promote period. reduction levels.DT maintained intricate dormancy. Optimal humidity prolong favorable contribute senescence. Water imbibition triggers activities processes, culminating germination. Cutting-edge technologies rehydrate desiccation,

Language: Английский

Citations

0
Recent advances in single-cell metabolomics using mass spectrometry: emerging challenges and future perspectives DOI
Rafiqul Alam, Jung‐Hyun Lee, Dasom Shin

et al.

Applied Spectroscopy Reviews, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 37

Published: April 1, 2025

Language: Английский

Citations

0
Recent Advancements in the Characterization of D‐Amino Acid and Isoaspartate Post‐Translational Modifications DOI Creative Commons
Samuel Okyem, Jonathan V. Sweedler

Mass Spectrometry Reviews, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 18, 2024

ABSTRACT One of the great triumphs mass spectrometry‐based peptide and protein characterization is their modifications as most have a characteristic shift. What happens when modification does not change peptide? Here, several proteins that do involve shift are highlighted. Protein synthesis on ribosomes involves L‐amino acids; however, posttranslational (PTMs) can convert these acids into D‐isomers. As another example, nonenzymatic PTM aspartate leads to formation three different isomers, with isoaspartate being prevalent. Both alter yet profound impact physicochemical characteristics peptide. Several MS ion mobility techniques highlighted, other methods such chromatography, enzymatic enrichment, labeling. The challenges inherent analytical prospective developments in bioinformatics computational strategies discussed for zero‐dalton PTMs.

Language: Английский

Citations

1
Single-Cell Mass Spectrometry Studies of Secondary Drug Resistance of Tumor Cells DOI

Guizhen Zhu,

Wenmei Zhang, Yaoyao Zhao

et al.

Analytical Chemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 20, 2024

Patients with epidermal growth factor receptor mutant nonsmall cell lung cancer (NSCLC) often fail to treat gefitinib because of secondary drug resistance. The development tumor resistance is closely related variations in metabolism. Single-cell metabolomics analysis can provide unique information about Herein, we constructed a platform study the cells based on single-cell (sSRTC-scM). A gefitinib-resistant NSCLC line (PC9GR) was by increasing dose step step. metabolic profiles parental PC9 and PC9GR different levels were detected intact living-cell electrolaunching ionization mass spectrometry at level. data analyzed statistical methods such as t-SNE, variance, volcano plot, heat map, pathway analysis. Using this platform, found that fingerprints evaluate degrees. continue be altered increase We revealed 19 markers variance clarified glycerophospholipid changed significantly. In addition, levels, heterogeneity metabolism became greater number weak gradually decreased. This phenomenon utilized illustrate degrees cells. provides diagnostic for evaluating tumors gives new insight into overcoming tumors.

Language: Английский

Citations

0