Spatially Resolved Metabolomics：Progress and Challenges

doi:10.13560/j.cnki.biotech.bull.1985.2020-1374

Abstract

Abstract:

Spatially resolved metabolomics is developed by integrating mass spectrometry imaging（MSI）and metabolomics methods for accurate determination of types,contents,and spatial differentiation of endogenous and exogenous metabolites within plant and animal tissues. Benefiting from the unique features of label-free and non-specific detections,as well as high sensitivity,high chemical coverage,and simultaneous detection of elements and molecules,MSI has gained an increasing attention as a powerful tool in spatial and temporal visualization of various metabolites,peptides,and proteins. Herein,we introduce the current research status of metabolomics and MSI techniques,then focus on the emerging applications of spatially resolved metabolomics in plant and animal tissues,as well as at the single cell levels,and finally prospect the current bottlenecks and future developing trends in spatially resolved metabolomics. As an emerging molecular imaging-based omics technique,spatially resolved metabolomics is featured for its label-free and visualized detection of absorption,distribution,metabolism,and excretion of exogenous drugs in animal tissues,and provides insights into the biosynthesis,transport pathways,and accumulation of various metabolites in plant tissues. This technique facilitates further applications in the discovery of targeted drugs,understanding of pathological mechanisms,and a spatial metabolic network closely related to the growth and development of plants and animals.

Key words: mass spectrometry imaging, metabolomics, spatially resolved, visualized detection, metabolic products

YIN Zhi-bin, HUANG Wen-jie, WU Xin-zhou, YAN Shi-juan. Spatially Resolved Metabolomics：Progress and Challenges[J]. Biotechnology Bulletin, 2021, 37(1): 32-51.

Figures/Tables 4

References 124

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Year	Species	Lateral resolution	Imaging techniques	Nos. of metabolites	Imaging analytes	Involved pathway	Ref.
Animal Tissue Imaging
2019	Prostate cancer tissue	150 μm	DESI	25	Phospholipids,fatty acids,and organic acids	Fatty acid and lipid biosynthesis	[64]
2019	Whole-body rat tissue sections	500 μm	AFADESI	17	Epimeric drugs,neurotransmitters（GABA,glutamic acid,and glutamine）	Metabolic pathway of drugs	[65]
2019	Esophageal squamous cell carcinoma tissue	200 μm	AFADESI	27	Amino acids,pyrimidines,fatty acids,saccharides,phospholipids,and organic acids	Proline/fatty acid/ polyamine biosynthesis,and glutamine/uridine/ histidine metabolism	[15]
2020	Breast cancer tissue	100 μm	MALDI	24	Carnitines and long-chain acylcarnitines	Carnitine system-mediated fatty acid β-oxidation pathway	[62]
2020	Rat kidney tissue	200 μm	AFADESI	38	Aristolochic acid I,amino acids,lipids,inosine,adenosine triphosphate,and carnitine	Arginine-creatinine metabolic pathway,urea cycle,and serine biosynthesis	[64]
Plant Tissue Imaging
2008	Arabidopsis thaliana leaves	200 μm	MALDI	3	Glucosinolates	Location of glucosinolates within a leaf regarding plant defenses	[79]
2012	Gossypium hirsutum seed	50 μm	MALDI	69	TAGs,PAs,PEs,PCs,β-sitosterol,and polyphenolic gossypol	Location of TAGs and PCs in cotton embryos	[13]
2014	Accent grape berry surface	20 μm	LA-ESI,MALDI,and ESI-MS	41	Amino acids,carbohydrates,and anthocyanins	Location of carbohydrates and anthocyanins in berry surface	[66]
2014	Glycyrrhiza glabra L.	10-30 μm	MALDI	24	Flavonoids,flavonoid glycosides,and saponins	Biosynthetic pathway of flavonoids and saponins	[67]
2015	Brassica napus	10 μm	MALDI	93	Sinapines,methyl sinapates,cyclic spermidine conjugates,triacylglycerols,and PCs	Translocation of metabolite in matureation and early germination stages	[68]
2015	H. perforatum and H. olympicum	10-15 μm	MALDI	11	Naphthodianthrone and flavonoids	Biosynthetic pathway and storage location of hypericin and emodin	[72]
2016	Paeonia lactiflora	10 μm	MALDI	33	Amino acids,carbohydrates,lipids,and monoterpenes	Biosynthetic pathway of gallotannins and monoterpene glucosides	[71]
2017	Brassica napus	40 μm	MALDI	27	PCs and TAGs	Lipid synthesis in oil seeds	[73]
2018	Ginkgo biloba L.	50 μm	MALDI	69	Flavonoids,organic acids,saccharides,phospholipids,chlorophylls,and ginkgolides	Biosynthesis pathways of ginkgo metabolites	[69]
2018	Solanum lycopersicum root	60 μm	MALDI	35	Peptides,proteins,and secondary metabolites	Location of secondary metabolites,peptides,and proteins in plant tissues	[78]
2019	Emiliania huxleyi	100 μm	MALDI	24	Chlorophyll,vGSLs,BLL,DGCC,PDPT,and PC	Host-virus interactions and their metabolic landscape	[77]
2020	Solanum lycopersicum root	50 μm	MALDI	9	Acylsucrose,steroidal glycoalkaloids,lignans,hydroxycinnamic acids,and organic acids	Location of systemically induced root exudation of metabolites（SIREM）	[76]
2020	Solanum lycopersicum	65 μm	MALDI	23	Steroidal glycoalkaloids（e.g.,α-tomatine,（dehydro-）α-tomatine,and dehydrotomatine）and anthocyanins	Trace the steroidal glycoalkaloids pathway in tomato fruit for gene function verification	[75]
2020	Camellia sinensis	1.7 mm	LC-MS/MS	56	Catechins,alkaloids,theanine,theaflavins,flavone,amino acids,and phenolic acids	Metabolite changes of tea plant response to the wounding	[70]
Single-Cell Imaging
2012	HeLa cells	7 μm	MALDI	22	DIOC₆ and phospholipids	Location of DIOC₆ and phospholipids within a single cell	[86]
2016	Catharanthus Roseus cells	20 μm	MALDI and Live single-cell MS	12	TIA including catharanthine,ajmalicine,and strictosidine	Synthetic pathway and accumulation location of TIA	[16]
2017	P. caudatum and Rotifera cells	1.4 μm	MALDI	19	DAGs,PCs,phosphatidylserines,monoglycerides,ceramides,and small peptides	Subcellular imaging of lipid,metabolite,and peptide within a single cell	[87]
2019	HeLa cells	250 nm	NDPI	6	Proflavine and its metabolites,methylthioninium chloride	Subcellular imaging of proflavine and its metabolites within a single cell	[88]
2020	HeLa cells	250 nm	NDPI	3	Proflavine,ethacridine,and potential metabolites	Spatial differentiation of proflavine and ethacridine within a single cell	[89]
2020	HeLa cells	250 nm	NDPI	10	AgNPs and AuNPs	Location of AuNPs and AgNPs within a single cell	[90]
2020	HeLa cells	300 nm	NLP-based LDI	6	Acriflavine,azure B,folate acid,daunorubicin,SPIONs	Dynamic process of anticancer drug molecules release from nanoparticle carriers in lysosomes and entering the nucleus finally leading to apoptosis of cancer cells	[91]
2020	HeLa cells	1 μm	SIMS	24	AICAR,phospholipids	De novo purine biosynthesis by purinosome	[92]
2020	Epithelial cells,sulfur-oxidizing and methane-oxidizing bacterium	3 μm	MALDI and FISH microscopy	2 506	Carotenoids,phospholipids,TAGs,phosphoethanolamine ceramide,fatty acids	Host-microbe symbioses and their metabolic interactions	[93]

Year	Species	Lateral resolution	Imaging techniques	Nos. of metabolites	Imaging analytes	Involved pathway	Ref.
Animal Tissue Imaging
2019	Prostate cancer tissue	150 μm	DESI	25	Phospholipids,fatty acids,and organic acids	Fatty acid and lipid biosynthesis	[64]
2019	Whole-body rat tissue sections	500 μm	AFADESI	17	Epimeric drugs,neurotransmitters（GABA,glutamic acid,and glutamine）	Metabolic pathway of drugs	[65]
2019	Esophageal squamous cell carcinoma tissue	200 μm	AFADESI	27	Amino acids,pyrimidines,fatty acids,saccharides,phospholipids,and organic acids	Proline/fatty acid/ polyamine biosynthesis,and glutamine/uridine/ histidine metabolism	[15]
2020	Breast cancer tissue	100 μm	MALDI	24	Carnitines and long-chain acylcarnitines	Carnitine system-mediated fatty acid β-oxidation pathway	[62]
2020	Rat kidney tissue	200 μm	AFADESI	38	Aristolochic acid I,amino acids,lipids,inosine,adenosine triphosphate,and carnitine	Arginine-creatinine metabolic pathway,urea cycle,and serine biosynthesis	[64]
Plant Tissue Imaging
2008	Arabidopsis thaliana leaves	200 μm	MALDI	3	Glucosinolates	Location of glucosinolates within a leaf regarding plant defenses	[79]
2012	Gossypium hirsutum seed	50 μm	MALDI	69	TAGs,PAs,PEs,PCs,β-sitosterol,and polyphenolic gossypol	Location of TAGs and PCs in cotton embryos	[13]
2014	Accent grape berry surface	20 μm	LA-ESI,MALDI,and ESI-MS	41	Amino acids,carbohydrates,and anthocyanins	Location of carbohydrates and anthocyanins in berry surface	[66]
2014	Glycyrrhiza glabra L.	10-30 μm	MALDI	24	Flavonoids,flavonoid glycosides,and saponins	Biosynthetic pathway of flavonoids and saponins	[67]
2015	Brassica napus	10 μm	MALDI	93	Sinapines,methyl sinapates,cyclic spermidine conjugates,triacylglycerols,and PCs	Translocation of metabolite in matureation and early germination stages	[68]
2015	H. perforatum and H. olympicum	10-15 μm	MALDI	11	Naphthodianthrone and flavonoids	Biosynthetic pathway and storage location of hypericin and emodin	[72]
2016	Paeonia lactiflora	10 μm	MALDI	33	Amino acids,carbohydrates,lipids,and monoterpenes	Biosynthetic pathway of gallotannins and monoterpene glucosides	[71]
2017	Brassica napus	40 μm	MALDI	27	PCs and TAGs	Lipid synthesis in oil seeds	[73]
2018	Ginkgo biloba L.	50 μm	MALDI	69	Flavonoids,organic acids,saccharides,phospholipids,chlorophylls,and ginkgolides	Biosynthesis pathways of ginkgo metabolites	[69]
2018	Solanum lycopersicum root	60 μm	MALDI	35	Peptides,proteins,and secondary metabolites	Location of secondary metabolites,peptides,and proteins in plant tissues	[78]
2019	Emiliania huxleyi	100 μm	MALDI	24	Chlorophyll,vGSLs,BLL,DGCC,PDPT,and PC	Host-virus interactions and their metabolic landscape	[77]
2020	Solanum lycopersicum root	50 μm	MALDI	9	Acylsucrose,steroidal glycoalkaloids,lignans,hydroxycinnamic acids,and organic acids	Location of systemically induced root exudation of metabolites（SIREM）	[76]
2020	Solanum lycopersicum	65 μm	MALDI	23	Steroidal glycoalkaloids（e.g.,α-tomatine,（dehydro-）α-tomatine,and dehydrotomatine）and anthocyanins	Trace the steroidal glycoalkaloids pathway in tomato fruit for gene function verification	[75]
2020	Camellia sinensis	1.7 mm	LC-MS/MS	56	Catechins,alkaloids,theanine,theaflavins,flavone,amino acids,and phenolic acids	Metabolite changes of tea plant response to the wounding	[70]
Single-Cell Imaging
2012	HeLa cells	7 μm	MALDI	22	DIOC₆ and phospholipids	Location of DIOC₆ and phospholipids within a single cell	[86]
2016	Catharanthus Roseus cells	20 μm	MALDI and Live single-cell MS	12	TIA including catharanthine,ajmalicine,and strictosidine	Synthetic pathway and accumulation location of TIA	[16]
2017	P. caudatum and Rotifera cells	1.4 μm	MALDI	19	DAGs,PCs,phosphatidylserines,monoglycerides,ceramides,and small peptides	Subcellular imaging of lipid,metabolite,and peptide within a single cell	[87]
2019	HeLa cells	250 nm	NDPI	6	Proflavine and its metabolites,methylthioninium chloride	Subcellular imaging of proflavine and its metabolites within a single cell	[88]
2020	HeLa cells	250 nm	NDPI	3	Proflavine,ethacridine,and potential metabolites	Spatial differentiation of proflavine and ethacridine within a single cell	[89]
2020	HeLa cells	250 nm	NDPI	10	AgNPs and AuNPs	Location of AuNPs and AgNPs within a single cell	[90]
2020	HeLa cells	300 nm	NLP-based LDI	6	Acriflavine,azure B,folate acid,daunorubicin,SPIONs	Dynamic process of anticancer drug molecules release from nanoparticle carriers in lysosomes and entering the nucleus finally leading to apoptosis of cancer cells	[91]
2020	HeLa cells	1 μm	SIMS	24	AICAR,phospholipids	De novo purine biosynthesis by purinosome	[92]
2020	Epithelial cells,sulfur-oxidizing and methane-oxidizing bacterium	3 μm	MALDI and FISH microscopy	2 506	Carotenoids,phospholipids,TAGs,phosphoethanolamine ceramide,fatty acids	Host-microbe symbioses and their metabolic interactions	[93]

Ionization technique	Probe	Environment	Lateral resolution		Requirements	LOD	Detected molecular species
Ionization technique	Probe	Environment	Typical	Optimal	Requirements	LOD	Detected molecular species
Dynamic SIMS	High-energy ion beams	High vacuum	0.05-1 μm	30 nm	Slicing,dehydrated,no matrix needed	pmol-fmol	Elements
Static SIMS	Low-energy ion beams	High vacuum	0.1-1 μm	100 nm	Slicing,dehydrated,no matrix needed	pmol-fmol	Elements,metabolite fragments,drug fragments,and lipid fragments
MALDI	UV laser	High vacuum,low vacuum,or AP	10-100 μm	1.7 μm	Slicing,dehydrated,and homogeneous matrix coating	fmol-amol	Metabolites（e.g.,amino acids,alkaloids,glycosides,phenolics,fatty acids,and glycerides）,drugs,lipids,peptides,and proteins
LDI	UV laser	High vacuum,low vacuum,or AP	10-100 μm	350 nm	Slicing,dehydrated,no matrix coating	fmol-amol	Metabolites（e.g.,terpenoids,alkaloids,saccharides,glycerides）,drugs,and lipids
DESI	Charged spray	AP	~ 200 μm	12 μm	No particular sample preparation needed,tissue imprinting if necessary	fmol	Metabolites（e.g.,amino acids,terpenoids,alkaloids,glycosides,and glycerides）,drugs,lipids,and small peptides
LA-ESI	IR laser and charged spray	AP	200-300 μm	30 μm	No particular sample preparation needed but require water content in sample	pmol-fmol	Metabolites（e.g.,amino acids,alkaloids,glycosides,and glycerides）,drugs,and lipids,and small peptides

Ionization technique	Probe	Environment	Lateral resolution		Requirements	LOD	Detected molecular species
Ionization technique	Probe	Environment	Typical	Optimal	Requirements	LOD	Detected molecular species
Dynamic SIMS	High-energy ion beams	High vacuum	0.05-1 μm	30 nm	Slicing,dehydrated,no matrix needed	pmol-fmol	Elements
Static SIMS	Low-energy ion beams	High vacuum	0.1-1 μm	100 nm	Slicing,dehydrated,no matrix needed	pmol-fmol	Elements,metabolite fragments,drug fragments,and lipid fragments
MALDI	UV laser	High vacuum,low vacuum,or AP	10-100 μm	1.7 μm	Slicing,dehydrated,and homogeneous matrix coating	fmol-amol	Metabolites（e.g.,amino acids,alkaloids,glycosides,phenolics,fatty acids,and glycerides）,drugs,lipids,peptides,and proteins
LDI	UV laser	High vacuum,low vacuum,or AP	10-100 μm	350 nm	Slicing,dehydrated,no matrix coating	fmol-amol	Metabolites（e.g.,terpenoids,alkaloids,saccharides,glycerides）,drugs,and lipids
DESI	Charged spray	AP	~ 200 μm	12 μm	No particular sample preparation needed,tissue imprinting if necessary	fmol	Metabolites（e.g.,amino acids,terpenoids,alkaloids,glycosides,and glycerides）,drugs,lipids,and small peptides
LA-ESI	IR laser and charged spray	AP	200-300 μm	30 μm	No particular sample preparation needed but require water content in sample	pmol-fmol	Metabolites（e.g.,amino acids,alkaloids,glycosides,and glycerides）,drugs,and lipids,and small peptides