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Single-cell metabolomics hits its stride


An array of new techniques allow researchers to catalog the chemical contents of a single cell, or even a single
organelle.

Caroline Seydel

S
tudying genomics reveals what a cell
is capable of; transcriptomics gives
a view of what the cell is planning
to do. To find out what the cell is actually
doing, however, requires proteomics and
metabolomics.
“Metabolomics is very important,”
says computational biologist Theodore
Alexandrov of the European Molecular
Biology Laboratory (EMBL). “It is the
youngest of the omics, but it provides the
readout which is closest to the phenotype.”
Taking a census of metabolites gives
the best view of what chemical processes
are taking place in a given cell. Two
genetically identical cells can have widely
different chemical metabolomes. The cell
and the extracellular environment interact
dynamically via a variety of molecules,
including metabolites. The food we eat
can change the cell’s metabolome. Cancer Single-cell metabolomics combined with spatial analysis can help uncover how diseases progress.
cells are well known to fill the tumor This image combines light microscopy images of hepatocytes and single-cell intensities of a fatty acid,
microenvironment with chemicals that detected using SpaceM, shown in the jet color map. Using SpaceM, the team observed changes in
befuddle the immune system, spur the fatty acid metabolism associated with non-alcoholic fatty liver disease. Credit: Theodore Alexandrov,
growth of new blood vessels and launch Luca Rappez
metastases. In the brain, cells send signals
using neurotransmitters, which can then
alter the activity of nearby cells.
“Single-cell metabolomics is remarkably Alisdair Fernie, who studies metabolism the same. But the metabolome won’t just sit
helpful,” says Anne Le, who studies cancer in plant cells at the Max Planck Institute of there waiting for you.”
metabolism at Johns Hopkins University. Molecular Plant Physiology. “There’s a lack Sample preparation is key to getting
“Within the tumor of a single patient, of absolute knowledge on that, even with an accurate snapshot of the metabolome.
you can see subpopulations and you can very precise weighing.” Different mass spectrometry setups
determine which cells do what.” Additionally, to understand how are compatible with different methods
To advance single-cell metabolomics, heterogeneous populations of cells interact, for quenching metabolism, Le says.
researchers have needed to address several it’s important to analyze cells in their native Snap-freezing with liquid nitrogen is a
key challenges. The metabolome changes context, accurately matching up metabolome common method, as is the addition of
rapidly, meaning that even collecting a data with the physical characteristics and organic solvents. Using a solvent can
sample to analyze can alter the metabolome neighborhood of the cell it came from. also help with metabolite extraction. For
from its native state. Metabolites can vary example, she points out, acetonitrile is
wildly in their abundances in a single cell, An immense and moving target used for both quenching and extraction for
and the tiny quantities present require high All of these challenges make characterizing matrix-assisted laser desorption/ionization
sensitivity to detect. Unlike the genome and quantifying the cell’s chemical contents mass spectrometry (MALDI–MS).
and transcriptome, which consist of just a seem impossibly complex. For one thing, Hua Tian of Pennsylvania State
few different nucleotide bases, metabolites the metabolome is far more dynamic than University, who developed a method called
come in all shapes and sizes. When dealing the genome or even the transcriptome. high-energy gas cluster ion beam–secondary
with large biomolecules, it can be tricky to “If you check someone’s genes, for example, ion mass spectrometry (GCIB–SIMS)1,
distinguish between isomers, even with the you’d find that person is one-quarter prepares her samples using frozen hydration.
aid of software. “If you look at very complex French and three-quarters Vietnamese,” “Frozen hydration is really important,” she
secondary metabolites which have many, explains Le. “The way you take the sample says. “It freezes the biological system in
many molecules, the number of possible won’t change that result. If you leave the space and time and provides a snapshot
structural configurations that can have the sample at room temperature and come of the near-nature state of the biological
same atomic mass becomes huge,” explains back in five days, the genome will still be system.” Freeze-drying or chemical fixation
1452 Nature Methods | VOL 18 | December 2021 | 1452–1456 | www.nature.com/naturemethods
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allow some metabolites to diffuse away, she book,” a zygote’s DNA doesn’t change as it
says, losing a bit of biological information. reproduces and differentiates. Throughout
Another key difference between the stages of development, the genome stays
genomics and metabolomics is complexity. essentially the same, and the changes are
Although a few tricky regions of the genome driven by the metabolome.
remained difficult to sequence, nearly all of Peter Nemes and his team at the University
it can be sequenced and annotated. Not so of Maryland, College Park, have honed a
for the metabolome: metabolites come in all method to analyze metabolites from a single
different shapes and sizes, and they number cell of a frog embryo. During embryonic
in the millions. Of these, typically about development, the cells divide rapidly, going
5% can be definitively identified from mass from one very large cell to two smaller ones
spectrometry data. and so on, doubling in number and halving
“Metabolite identification is one of the in size roughly every quarter of an hour.
foundational problems in metabolomics,” “Studying single-cell metabolomics in such
says Alexandrov. To help tease concrete spatially and temporally developing samples is
information out of the jumble of peaks a real methodological challenge,” Nemes says.
Using a specially microfabricated capillary, the
in the spectra, Alexandrov’s team created First, while the embryo is in the
Nemes lab can aspirate a sample from a single cell
METASPACE, an algorithm for metabolite four-cell stage, Nemes and his team use
of the eight-cell Xenopus laevis embryo. Additional
identification and an open-platform light microscopy to identify the left-dorsal
samples can be taken for proteomic analysis, and
knowledge base for people to share their and left-ventral cells. Using precision
the embryo continues developing normally.
imaging mass spectrometry data2. microcapillaries that they fabricate in-house,
Credit: Peter Nemes
“This was transformational for us, and they aspirate a sample of the contents of
now it’s also used by about 100 labs around a single cell. Capillary electrophoresis
the world,” Alexandrov says. Instead of separates the metabolites, and is followed by
spending years becoming proficient in electrospray ionization and high-resolution operational conditions to most efficiently
interpreting mass spectra, he says, a biologist mass spectrometry to identify and quantify convert the molecules to ions,” Nemes says.
can learn to use METASPACE in a much the molecules. Importantly, this procedure, “And we developed custom-built software to
shorter time, allowing them to make sense called sampling, doesn’t harm the embryo’s extract the very small peak intensities.”
of the spectra they collect. “The software is ability to develop into a normal tadpole3. Commercial software, he explains,
pretty user friendly, and within 2 months “We can remove the capillary and within assumes that the metabolites have been
they are producing good molecular data, a few minutes the cell heals its membrane,” separated using chromatography, which
focusing on improving and interpreting the Nemes says. “After the first sampling, produces wider peaks than capillary
molecular content of the data without the we can come back for a second sampling electrophoresis. “We got these large
need to manually browse through myriads or even a third.” amounts of data, but we couldn’t analyze
of spectral peaks corresponding to unknown Because the capillary extraction does less them,” Nemes says. “If we used popular,
molecules,” Alexandrov says. damage than traditional dissection methods, commercially available software packages,
Additionally, “there’s a lack of linearity the cell is less stressed. “This is cool because we’d get thousands of false positives. It was a
between the number of substrates and you’re much closer to measuring the real huge dataset that was just noise.”
number of products,” explains Fernie. metabolome of the cell than in a cell that The team collaborated with Chen Zeng at
Transcriptomics and proteomics methods has undergone oxidative stress,” Nemes the George Washington University to create
might reveal that a cell produces a explains. The ability to re-sample the same their own analysis software, which they called
particular enzyme, and that generates a cell also allows the researchers to combine Trace. “We trained an artificial neural network
reasonable expectation that the cell also metabolomics with proteomics within a live, that could recognize the trace sensitive signals
contains the molecules acted on by the developing embryo. Any changes in anatomy in our dataset,” Nemes says. “This worked
enzyme. But those molecules may form or behavior as the tadpole develops can then extremely well. 95% of the signals that we find
intermediates or get sucked into side be correlated with changes in the proteome with the Trace software are true signals.”
reactions, generating unpredictable new and metabolome. Using their method, Nemes’s lab
products. “There’s also a very small minority Achieving sufficient sensitivity posed documented the differences in metabolite
of non-enzyme-catalyzed reactions, another challenge. “Unlike single-cell composition among the cells in the eight-cell
spontaneous reactions, and these are transcriptomics, where you can amplify the frog embryo. They have shown that
difficult to predict,” Fernie says. entire transcriptome, you cannot do that at metabolites drive the differentiation of the
Though metabolomics may fall short of the level of the metabolome,” Nemes says. stem cells into organ-specific lineages, and
measuring the full and complete chemical “There’s no technology available where we that altering the metabolites in a cell can
contents of the cell, new techniques can amplify millionfold copy numbers of all change that cell’s fate4.
that increase throughput and sensitivity the metabolites in the cell. The entire field of “We’ve discovered novel molecules that
are yielding a wealth of new biological single-cell metabolomics comes down are able to alter this stem cell trajectory,”
information. to sensitivity.” Nemes says. “We can actually reprogram
Nemes’s method heightens sensitivity in a an epidermally fated cell to become neural
Demystifying differentiation few ways. First, the capillary electrophoresis tissue and vice versa by doing single-cell
The great miracle of vertebrate life is how efficiently separates the sample molecules, metabolomics.”
a single cell, the zygote, contains all the producing crisp, sharply defined peaks.
information needed to generate dozens of Then, the team perfected the ionization Spatial relations
different specialized cell types. Though the step. “We build these ion sources ourselves, Detecting the metabolomes of individual
genome is often considered “life’s instruction because we know how to find the proper cells while preserving the spatial

Nature Methods | VOL 18 | December 2021 | 1452–1456 | www.nature.com/naturemethods 1453


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relationships between them adds yet microenvironment has very special chemical
another layer of information. Because a and physical properties,” he says. “You have
cell’s native environment can have a strong a gradient in oxygen, you have a gradient
impact on its biochemistry, researchers are in metabolic waste like lactate.” These
working on methods to compare single-cell chemicals have an effect on the different
metabolomics data among members of cells populating the microenvironment,
a population. including the vast array of immune cells
The Alexandrov lab is developing swarming the cancer. “One of the key
methods to collect and interpret data from applications of single-cell metabolomics
commercially available instrumentation. will be immunometabolism,” Alexandrov
MALDI-imaging mass spectrometry is says. “If we know the metabolism in every
one of the most popular techniques for cell, if we know how cancer cells adapt their
single-cell metabolic analysis. For MALDI, metabolism, then we can potentially help the
the samples to be analyzed are mixed with a immune cells to adapt their metabolism to
matrix, then irradiated by a UV laser beam. be more functional in this environment.”
The beam desorbs and ionizes the analytes, “It’s really important to understand the
sending them into the mass spectrometer. metabolic states of the different cells in the
With its minimal sample preparation and content of tissue without dissociation,” says
high throughput, MALDI–MS is well suited Tian. “This is the new frontier of biological
to analyzing large populations of cells, analysis. It will help understand why some
and has been used successfully to reveal immune cells can penetrate into the tumor
heterogeneity among clonal populations of microenvironment and some not.”
single-celled organisms and to discover rare Tian works with GCIB–SIMS, a method
cell subtypes in tissue samples. that preserves the spatial relationships
MALDI-imaging mass spectrometry between the cells without requiring special
measures mass spectra at different points preparation. GCIB–SIMS bombards the cell
on a tissue section or glass slide containing with an energetic beam of ions, dislodging
plated cells, allowing researchers to create ions that fly off and are collected in a mass
a spatial map of metabolites. However, spectrometer. The technique combines the
assigning metabolite intensities to single chemical specificity of mass spectrometry
cells is challenging. “The spatial resolution with imaging resolution approaching 1
of MALDI imaging is pretty close, but not as micron, small enough to image a single
good as microscopy,” Alexandrov says. “Our cell. Using gas cluster ion beams causes
pixel size is close to one cell.” The same breast cancer section, imaged first less damage to biological specimens than
To address this, Alexandrov and graduate with (H2O)n-GCIB-SIMS to detect lipids and using monoatomic ion beams, because the
student Luca Rappez developed SpaceM, metabolites and then with C60-SIMS (carbon beam’s energy is divided among thousands
a method that integrates MALDI imaging cluster SIMS) to detect the lanthanide-tagged of gas molecules. It also results in less
with light microscopy and digital image antibodies used as cell type markers. This method fragmentation and can be used to detect
processing to precisely match up the mass allows the researchers to precisely localize larger-mass biomolecules.
spectrometry data with the cells they different cell types in the tumor microenvironment In collaboration with Sadia Sheraz
came from5. and compare their metabolomes. Credit: Hua Tian and John Vickerman at the University of
The MALDI laser creates visible burn Manchester, Tian has developed a new
marks in the matrix, and this is the key SIMS protocol using water cluster ion
to SpaceM. Before performing MALDI single slide. In collaboration with Mathias beams, which is pushing the sensitivity
imaging, the researchers use microscopy Heikenwälder’s team at the German Cancer limits even further. “The water cluster
to capture the cells’ relative positions, their Research Center, experts in inflammation, ion beam is probably the most effective
fluorescence phenotype and any other the researchers used SpaceM to analyze desorption source I have ever seen,” says
pertinent information. After metabolite data the lipid composition of human cultured Tian. “Particularly running it with our newly
is collected using MALDI imaging, a second liver cells, an in vitro model of two lipid constructed ion gun, operating at high
microscope image is taken that shows the metabolic disorders, nonalcoholic fatty voltage to focus the beam. We have a cooling
positions of the burn marks. These marks liver disease (NAFLD) and nonalcoholic pad through the beam column that will also
provide a visual cue indicating which cells steatohepatitis (NASH). SpaceM revealed focus the lens, and we can focus this beam
the metabolite data was collected from. that a large subpopulation of NAFLD down to 1 micron.”
The tricky part is lining up the before and cells, around a quarter of them, showed Tian analyzed breast cancer tissue
after images with subcellular precision. “To accumulation of lipid droplets and neutral samples with multimodal SIMS imaging,
do this, Luca used fiducials, or some features lipids, consistent with the metabolic state combining the water cluster ion beam
that you can see in both images,” Alexandrov associated with the diseases. Then, after with one that uses carbon clusters. The
says. They create these fiducials by making they induced NASH with an inflammatory water cluster beam detects the metabolites
marks with a black Sharpie pen around cytokine, around 93% of the cells adopted without damaging the samples, allowing
the edge of the slide. “The key to achieving this metabolic profile. a second pass. The cells are stained with
subcellular precision was to automatically This ability to detect the metabolic lanthanide-labeled antibodies specific to
recognize these fiducials, thousands of them.” heterogeneity of individual cells in a protein markers identifying the cell types,
SpaceM also provides high throughput, population could also have applications for and these are detected using the carbon
as thousands of cells can be imaged in a cancer, Alexandrov points out. “The tumor cluster beam. The antibody panel targets

1454 Nature Methods | VOL 18 | December 2021 | 1452–1456 | www.nature.com/naturemethods


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T cells, B cells, macrophages and tumor Neural cells package chemical points out, so cataloguing the distribution
epithelial cells, as well as chromatin and messenger molecules, such as hormones of hormones and other signaling molecules
extracellular matrix proteins. and neurotransmitters, into lipid-lined sacs within cells could help identify when things
“With these two sets of images, we can called dense-core vesicles or electron-lucent go awry. “You first have to have a good way
integrate the lipids, metabolites and proteins vesicles. Sweedler and his colleagues set of measuring something before you know its
in single cells,” Tian says. “We see some out to adapt MALDI–MS to analyze these exact impact on disease,” Sweedler says.
interesting phenomena that are in some individual vesicles6.
ways consistent with previous bulk analysis, “We’ve been doing single-cell peptidomics Inside the trash compactor
but some are not. Moreover, we provide a for 20 years,” Sweedler says. “This paper Although vesicles enable communication
more comprehensive visualization of the takes it to the next step and demonstrates between cells, lysosomes could be what
tumor microenvironment.” For instance, that we could make measurements on an keeps our bodies young. Most eukaryotic
tumor epithelial cells had an enhanced object smaller than a single cell. A cell cells contain lysosomes, membrane-bound
antioxidant pathway, whereas rapidly contains lots of vesicles that eventually organelles full of digestive enzymes to
dividing cells had high levels of gangliosides. fuse with the membrane and release their break down cellular proteins or destroy
This multimodal approach opens the contents. Our goal both was to push the bacteria and viruses. They also have
door to much richer investigations into technology forward and to ask the question, very active metabolism. “Lysosomes are
the interactions between cancer cells and How heterogeneous [are these vesicles]?” essential for maintaining energy and
immune cells, as well as cell–cell interactions The researchers scatter thousands of metabolic homeostasis, signal transduction,
in other systems. Still, a cell isn’t just a organelles across a microscope slide with and recovery of damaged proteins and
homogeneous sac of chemicals, evenly enough space between them that the laser organelles,” explains Wei Xiong, of the
distributed throughout. Some researchers will hit only one item at a time. Next, University of Science and Technology of
are looking even closer, at individual they image the slide and its objects with China, in Hefei.
organelles, again using MALDI–MS, a microscope. Then, a machine-learning Lysosomes play a role in cellular
nanospray ionization mass spectrometry system classifies the images, identifying the senescence as well as cancer, and
and GCIB–SIMS to come at the problem in coordinates of the objects most likely to understanding the metabolic processes
different ways. be dense-core vesicles. These locations are taking place inside could unlock new
used to guide the mass spectrometer information about how to slow down aging
Smaller and smaller laser to target only those objects. or about new drug targets for tumors. But
“How do you identify what a cell type Automating this process, Sweedler says, lysosomes are highly heterogeneous: a single
is?” asks Jonathan Sweedler, who studies enables the method to capture thousands cell may contain hundreds, all differing in
analytical neurochemistry at the University of spectra in a single slide. size, density and enzymatic composition.
of Illinois. Early microscopists named “The hardest part, which makes sense, Although researchers have identified a few
different brain cells based on their shape, was adapting our single-cell approaches to different types of lysosomes, “so far, there
or how they looked under the microscope. much smaller organelles. You have to find is no satisfying classification method for
Astrocytes, pyramidal cells, chandelier the objects when they’re below a micron in lysosomes,” Xiong says. “Considering their
cells—these names are evocative but size,” Sweedler says. “That took a surprising enormous heterogeneity in physiological
reveal little about the cells’ function. As amount of time.” and pathological processes, the development
neuroscientists developed methods for To develop the technique, Sweedler’s of single-lysosome technology is a
measuring biochemicals in the brain, lab used cells from the sea slug, Aplysia prerequisite for fully understanding the
cells became defined by the chemicals californica, because their organelles are fairly features of different types of lysosomes.”
they release: cells could be dopaminergic, large, around 0.5–2 microns in diameter. Now, Xiong and colleagues have created
serotonergic, GABAergic. But these They identified three distinct populations a single-lysosome mass spectrometry
designations don’t entirely overlap with the of dense-core vesicles that contain distinct, (SLMS) platform that combines
morphological categories. though overlapping, distributions of lysosomal patch-clamp recording with
“If you have an astrocyte that’s next peptide hormones. induced nanoelectrospray ionization
to neurons using glutamate or GABA as The ability to peek inside a vesicle mass spectrometry7. This allows the
a neurotransmitter, it will have more of can improve our understanding of simultaneous detection of the lysosome’s
the proteins required for taking them up diseases involving cell-to-cell signaling. electrophysiological properties and its
and processing them,” Sweedler explains. Hormones and neurotransmitters play a metabolome.
“If you have an astrocyte in another area role in physiological functions as diverse as Based on their metabolite content,
of the brain that’s near dopamine- or circadian rhythms, maintenance of water– the lysosomes could be classified into
serotonin-releasing neurons, and it has to sodium balance and social bonding. five subtypes. Two of these subtypes
deal with those molecules, it would have “There are cases where you can have corresponded to previously postulated
different transporters and enzymes. Do these a single prohormone, and you can cleave lysosome types, autolysosomes and
differences mean it’s a different cell type?” and package some of the peptides that are endolysosomes, and the other three are
The same cell can change its metabolite produced from one side of a furin site novel. “We surprisingly found that there
lineup if it’s moved to a different area, versus the other into different vesicles,” was a striking one-to-one correspondence
so Sweedler is less interested in cell type Sweedler says. “Does that imply that the between the five subpopulations of
designation than cell state. “Transcriptomics same cell could release different peptide lysosomes from completely different cell
gives you the potential of the cell, what hormones depending on how you stimulated types,” Xiong says.
building blocks it could make,” he says. it? These types of fundamental questions The SLMS method also successfully
“Proteomics tells you the building blocks it aren’t known.” detected a significant drop in amino
did make. The state it’s in is reflected in its Changes in the specific hormones acids, saccharides and their derivatives,
metabolome.” released by cells can change behaviors, he suggesting that as the cell ages, lysosomes

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become less efficient at breaking down the mitochondria rather than diffused cool stuff, but the associated costs make it
large biomolecules. Similarly, when they throughout the cell. very hard to apply them in a clinical setting.”
tested cancer cells, the researchers found Indeed, that is what they found. “We For example, Alexandrov envisions a
that certain metabolites increased and used the GCIB–SIMS to localize the personalized medicine approach for cancer
some decreased in the different types of intermediates,” Tian says. GCIB-SIMS using metabolomics on organoids grown
lysosomes. provided a high-resolution map of the from patients’ tumor samples. Instead of
“More and more evidence shows that cell, made up of voxels 1 micron by 1 treating the patient with a drug and waiting
senescence and cancer are closely related micron in size—small enough to capture a to see whether the cancer responds, multiple
to lysosomes and their internal metabolic purinosome. They found direct evidence drugs could be tested simultaneously on
processes,” Xiong says. By studying for metabolic channeling within the organoids. Single-cell metabolomics could
metabolic function changes in different purine-synthesizing enzyme complex and then reveal how tumor cells responded to
types of lysosomes during aging or cancer, for the association with mitochondria. each drug. “If we can measure this, then
he says, it may be possible to develop new They discovered discrete pockets of high we can select the therapy that restores the
anti-aging or anti-cancer drugs. concentration of the intermediate metabolite healthy state of cells in the best way, and
AICAR, as well as other telltale interme­ we can recommend it for the treatment,”
Whence biosynthesis diates of the purine biosynthesis process8. Alexandrov says.
Spatially resolved metabolomics can “This really opens a new opportunity “The real advantage is these techniques
also provide evidence for how a cell is for in situ single-cell metabolomics,” are opening up the possibility of looking
conducting its chemical business, such as Tian says. “It could assist the discovery at what cells actually do in nature and
biosynthesis. When cells divide, they need of therapeutically important metabolic not what their capacity is in an artificial
a way to make their own building materials. vulnerabilities for cancer treatment.” system,” says Fernie. “That’s the power of
De novo purine synthesis is the process by the approach.” ❐
which cells make more purine nucleotides Toward the clinic
from scratch. This method is favored by As techniques for single-cell metabolomics Caroline Seydel ✉
cancer cells and other fast-proliferating cells, continue to proliferate and improve, it’s Los Angeles, CA, USA.
whereas normal cells tend to recycle their easy to imagine a metabolomics revolution ✉e-mail: caroline.seydel@gmail.com
purines through a salvage pathway. taking the baton from the earlier omics and
Working with Stephen Benkovic, finally bringing the potential of personalized Published online: 3 December 2021
who studies enzyme complex assembly medicine to fruition. Metabolomics poses https://doi.org/10.1038/s41592-021-01333-x
and kinetics at Penn State, Tian used more up-front challenges than genomics or
References
GCIB–SIMS to look for “purinosomes,” transcriptomics, but as researchers start to 1. Tian, H. et al. Anal. Chem. 93, 8143–8151 (2021).
biosynthetic hotspots in the cell that would overcome those challenges, the benefits of 2. Alexandrov, T. et al. Preprint at bioRxiv https://doi.
prove the hypothesis of enzyme clusters, metabolomics become more prominent. org/10.1101/539478 (2019).
3. Lombard-Banek, C. et al. Angew. Chem. Intl. Edn. 60, 2–9 (2021).
or the so-called “metabolon.” Purine “Metabolomics, which is based on mass 4. Onjiko, R. et al. Genesis 59, e23418 (2021).
biosynthesis draws on input metabolites spectrometry, is the cheapest and fastest of 5. Rappez, L. et al. Nat. Methods 18, 799–805 (2021).
from the mitochondria, and the researchers the omics,” says Alexandrov. “Sequencing, 6. Castro, D. C., Xie, Y. R., Rubakhin, S. S., Romanova, E. V. &
Sweedler, J. V. Nat. Methods 18, 1233–1238 (2021).
hypothesized that the intermediates and end by comparison, is very expensive. Single-cell 7. Zhu, H. et al. Nat. Methods 18, 788–798 (2021).
products of de novo purine biosynthesis genomics revelations are grand and 8. Pareek, V., Tian, H., Winograd, N. & Benkovic, S. J. Science 368,
would be localized in confined spots near transformational, they show a lot of really 283–290 (2020).

1456 Nature Methods | VOL 18 | December 2021 | 1452–1456 | www.nature.com/naturemethods

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