Human d-3-phosphoglycerate dehydrogenase (PHGDH), the first enzyme in the serine biosynthetic pathway, is genomically amplified in tumors including breast cancer and melanoma. In PHGDH-amplified cancer cells, knockdown of PHGDH is not fully rescued by exogenous serine, suggesting possible additional growth-promoting roles for the enzyme. Here we show that, in addition to catalyzing oxidation of 3-phosphoglycerate, PHGDH catalyzes NADH-dependent reduction of α-ketoglutarate (AKG) to the oncometabolite d-2-hydroxyglutarate (d-2HG). Knockdown of PHGDH decreased cellular 2HG by approximately 50% in the PHGDH-amplified breast cancer cell lines MDA-MB-468 (normal concentration 93 μM) and BT-20 (normal concentration 35 μM) and overexpression of PHGDH increased cellular 2HG by over 2-fold in non-PHGDH-amplified MDA-MB-231 breast cancer cells, which normally display very low PHGDH expression. The reduced 2HG level in PHGDH knockdown cell lines can be rescued by PHGDH re-expression, but not by a catalytically inactive PHGDH mutant. The initial connection between cancer and d-2HG involved production of high levels of d-2HG by mutant isocitrate dehydrogenase. More recently, however, elevated d-2HG has been observed in breast cancer tumors without isocitrate dehydrogenase mutation. Our results suggest that PHGDH is one source of this d-2HG.
Humand-3-phosphoglycerate dehydrogenase (PHGDH), the first enzyme in the serine biosynthetic pathway, is genomically amplified in tumors including breast cancer and melanoma. In PHGDH-amplified cancer cells, knockdown of PHGDH is not fully rescued by exogenous serine, suggesting possible additional growth-promoting roles for the enzyme. Here we show that, in addition to catalyzing oxidation of 3-phosphoglycerate, PHGDH catalyzes NADH-dependent reduction of α-ketoglutarate (AKG) to the oncometabolite d-2-hydroxyglutarate (d-2HG). Knockdown of PHGDH decreased cellular 2HG by approximately 50% in the PHGDH-amplified breast cancer cell lines MDA-MB-468 (normal concentration 93 μM) and BT-20 (normal concentration 35 μM) and overexpression of PHGDH increased cellular 2HG by over 2-fold in non-PHGDH-amplified MDA-MB-231breast cancer cells, which normally display very low PHGDH expression. The reduced 2HG level in PHGDH knockdown cell lines can be rescued by PHGDH re-expression, but not by a catalytically inactive PHGDH mutant. The initial connection between cancer and d-2HG involved production of high levels of d-2HG by mutant isocitrate dehydrogenase. More recently, however, elevated d-2HG has been observed in breast cancer tumors without isocitrate dehydrogenase mutation. Our results suggest that PHGDH is one source of this d-2HG.
Cancer genome analysis
has identified a variety of alterations
that affect metabolic enzymes, including point mutations in the gene
encoding the TCA-cycle enzyme isocitrate dehydrogenase (IDH)[1−3] and amplifications of the gene encoding the serine pathway enzyme
phosphoglycerate dehydrogenase (PHGDH).[4,5] Active site
IDH1 and IDH2 mutations are associated with brain cancer and acute
myeloid leukemia,[1−3] with the mutant enzyme producing the metabolic error
product d-2HG.[6,7]d-2HG is a competitive
inhibitor of AKG-dependent enzymes, including DNA and histone demethylases[8−11] and is sufficient to promote leukemic transformation, while l-2HG is not able to induce such transformation.[12] More recently, elevated d-2HG has been
found in humanbreast cancers with wild type IDH.[13]The committed enzyme of serine biosynthesis, phosphoglycerate
dehydrogenase
(PHGDH), is involved in a genomic region of copy number gain found
across humancancers, and amplifications involving PHGDH occur with highest frequency in subsets of breast cancers and melanomas.
When not genomically amplified, PHGDH is often overexpressed.[4,5,14] PHDGH catalyzes the first reaction
of de novo serine biosynthesis, producing 3-phosphohydroxypyruvate
by NAD+-coupled oxidation of 3-phosphoglycerate (3PG).
The PHGDH reaction is reversible and, under standard conditions, thermodynamically
favors the direction from 3-phosphohydroxypyruvate to 3PG. In cells
engaged in serine synthesis, the reaction is driven toward 3-phosphohydroxypyruvate
due to its consumption by downstream pathway steps.Genomic
amplification of PHGDH enables cells to
grow in serine free media.[5] Suppression
of PHGDH inhibits growth of PHGDH-amplified cells
both in vitro and in vivo.[4,5] However, the mechanism by which PHGDH amplification
supports cancer growth is not yet fully understood. The simplest hypothesis
is that it increases de novo serine synthesis. Serine
is an important building block of proteins and lipid head groups,
and a major feedstock for one-carbon metabolism, with both glycine
and folate species derived from serine.[14,15] Serine demand,
however, does not completely explain PHGDH dependence, at least in vitro where a standard tissue culture medium contains
copious serine and glycine. Even in PHGDH-amplified
cell lines, e.g., the breast cancer cell lines MDA-MB-468, less than
20% of serine is generated from de novo synthesis
in standard tissue culture conditions.[16] Consistent with this, PHGDH knockdown does not significantly reduce
the intracellular concentration of serine, and the growth inhibition
caused by PHGDH knockdown cannot be rescued by the addition of exogenous
serine or serine ester.[5]This led
us to explore the possibility that PHGDH has an additional
enzymatic activity beyond 3PG/3-phosphohydroxypyruvate oxidation/reduction.
PHGDH belongs to the d-isomer-specific 2-hydroxyacid dehydrogenase
family. The thermodynamically favored PHGDH substrate, 3-phosphohydroxypyruvate,
is structurally similar to the more abundant metabolite AKG. Here,
we show that PHGDH also catalyzes the reduction of AKG to d-2HG. Thus, PHGDH can also produce d-2HG. Such production
could contribute to elevated d-2HG observed in breast cancers
without IDH mutations.
Result and Discussion
Promiscuity of Human PHGDH
The favored PHGDH substrate,
3-phosphohydroxypyruvate, is structurally similar to other central
metabolites, including pyruvate (lacks the phosphate of 3-phosphohydroxypyruvate),
oxaloacetate (OAA, substitutes phosphate with carboxylic acid), and
AKG (substitutes phosphate with acetate; Figure 1A). Previous studies have shown that the E. coli homologue of PHGDH, SerA, produces d-2HG from AKG.[17] RatPHGDH, however, was found to lack such activity,[18] leading to the assumption that mammalianPHGDH
does not produce d- or l-2HG, without the human
enzyme being tested. We examined whether recombinant purified humanPHGDH (one version His-tagged and another version Streptavidin-tagged)
catalyzes the NADH-driven reduction of pyruvate, OAA, or AKG. At pH
7.6 and 37 °C, NADH oxidation was observed in the presence of
OAA or AKG, but not pyruvate (Figure 1B). Minimal
activity was observed with NADPH in place of NADH. Analysis by LC-MS
revealed that the reaction produces malate and 2HG, respectively,
and each of the two different tagged versions of PHGDH were able to
generate these products (Figure 1C). To confirm
the observed activities are indeed due to humanPHGDH, rather than
from a contaminating activity resulting from the purification process,
the same reaction was run with PHGDH replaced by an unrelated enzyme
(humangalactokinase), which was expressed and purified in an identical
manner as the His-tagged PHGDH. No malate or 2HG was produced from
OAA or AKG using this negative control enzyme (Figure 1C). While slow NADH oxidation was observed with the control
enzyme (consistent with the generally labile nature of NADH), this
rate of spontaneous NADH oxidation was much smaller than that observed
in the presence of PHGDH (Supplementary Figure
1; all data in the main text are corrected for this background
rate). These results demonstrate that OAA and AKG reduction activity
is specifically due to PHGDH. Consistent with these findings, throughout
the PHGDH reaction time course, 2HG and NAD+ were produced
stoichiometrically (Figure 1D).
Figure 1
Human PHGDH catalyzes
NADH-driven reduction of OAA and AKG into
malate and d-2HG. (A) Structures of the primary PHGDH substrate/product
(box) and various possible alternative endogenous substrates/products.
(B) PHGDH-catalyzed NADH-driven reduction of OAA and AKG but not pyruvate.
A total of 5 mM of each α-ketoacid was incubated with 0.5 mM
NADH and PHGDH (red) or no enzyme control (blue). The reaction was
monitored by a decrease in NADH absorbance. For AKG reduction, activity
with NADPH was also tested (PHGDH, green; no enzyme control, purple).
(C) LC-MS analysis of the AKG reduction product 2HG (left) and the
OAA reduction product malate (right). His-tagged PHGDH or strep-tagged
PHGDH was incubated with 0.5 mM NADH and 5 mM α-keoglutarate
or OAA. The assays included two negative controls: incubation of the
same amount of PHGDH without substrate or incubation of the same substrates
with human galactokinase (expressed and purified as for His-PHGDH).
(D) PHGDH-catalyzed AKG reduction produces NAD+ and 2HG
stoichiometrically. (E) PHGDH produces the d- enantiomer
of 2HG. GC-MS traces for the l-2HG standard, d-2HG
standard, the product of PHGDH-driven AKG reduction, and a mixture
of the l- and d-2HG standards. (F) PHGDH oxidizes d-2HG but not l-2HG. PHGDH was incubated with 1 mM
NAD+ and 10 mM l-2HG or d-2HG. NADH production,
monitored by changes in absorbance at 340 nm, is shown on top, and
AKG production analyzed by LC-MS is shown on the bottom.
HumanPHGDH catalyzes
NADH-driven reduction of OAA and AKG into
malate and d-2HG. (A) Structures of the primary PHGDH substrate/product
(box) and various possible alternative endogenous substrates/products.
(B) PHGDH-catalyzed NADH-driven reduction of OAA and AKG but not pyruvate.
A total of 5 mM of each α-ketoacid was incubated with 0.5 mM
NADH and PHGDH (red) or no enzyme control (blue). The reaction was
monitored by a decrease in NADH absorbance. For AKG reduction, activity
with NADPH was also tested (PHGDH, green; no enzyme control, purple).
(C) LC-MS analysis of the AKG reduction product 2HG (left) and the
OAA reduction product malate (right). His-tagged PHGDH or strep-tagged
PHGDH was incubated with 0.5 mM NADH and 5 mM α-keoglutarate
or OAA. The assays included two negative controls: incubation of the
same amount of PHGDH without substrate or incubation of the same substrates
with humangalactokinase (expressed and purified as for His-PHGDH).
(D) PHGDH-catalyzed AKG reduction produces NAD+ and 2HG
stoichiometrically. (E) PHGDH produces the d- enantiomer
of 2HG. GC-MS traces for the l-2HG standard, d-2HG
standard, the product of PHGDH-driven AKG reduction, and a mixture
of the l- and d-2HG standards. (F) PHGDH oxidizes d-2HG but not l-2HG. PHGDH was incubated with 1 mM
NAD+ and 10 mM l-2HG or d-2HG. NADH production,
monitored by changes in absorbance at 340 nm, is shown on top, and
AKG production analyzed by LC-MS is shown on the bottom.Because the LC-MS method does not distinguish l-2HG and d-2HG, we also analyzed the reaction mixture
by GC-MS following
a two step derivatization previously demonstrated to separate the
two enantiomers,[19] with the PHGDH-derived
2HG coeluting with the d-2HG but not l-2HG standard
(Figure 1E). The reverse reaction was observed
when d-2HG (but not the corresponding l-enantiomer)
was mixed with NAD+ and PHGDH (Figure 1F). Thus, in addition to catalyzing 3PG oxidation, humanPHGDH
is capable of catalyzing the NADH-driven reduction of OAA into malate,
and more importantly AKG into d-2HG.
Kinetics of AKG Reduction
Relative to 3PG Oxidation
To test how these additional activities
compare to 3PG oxidation,
we measured the kinetic parameters for PHGDH-catalyzed 3PG oxidation,
OAA reduction, and AKG reduction (Table 1)
by varying concentration of one substrate in the presence of saturating
concentrations of the other substrate. The results were fitted to
Michaelis–Menten kinetics (Supplementary
Figure 2). The enzyme has similar kcat for 3PG oxidation and OAA or AKG reduction, with OAA reduction slightly
faster than 3PG oxidation. Among these substrates, the highest affinity
binder was 3PG (Km = 260 μM), consistent
with its being the primary physiological substrate. OAA and AKG both
bound similarly, with 20–40-fold higher km than 3PG. NAD(H) binding was high affinity in all cases (Km ≤ 25 μM). The kinetics of NAD+ reduction with malate or 2HG were substantially slower and
thus not quantified.
Table 1
Michaelis–Menten
Parameters
of the Different Reactions Catalyzed by PHGDH, Compared to Intracellular
Concentrations of the Corresponding Substrates and Products in Different
Cell Lines
3-phosphoglycerate
→ 3-phosphohydroxypyravate
oxaloacetate
→ malate
α-ketoglutarate
→ 2-hydroxyglutarate
Kcat (1/min)
4.5 ± 0.6
Kcat (1/min)
10.6 ± 1.6
Kcat (1/min)
4.7 ± 0.9
Km, 3-phosphoglycerate
(mM)
0.26 ± 0.034
Km, oxaloacetate (mM)
6.5 ± 1.3
Km, α-ketoglutarate (mM)
10.1 ±
1.8
[3-phosphoglycerate]
(mM)
MDA-MB-468
0.18 ± 0.01
[oxaloacetate]
(mM)
MDA-MB-468
not detectable
[α-ketoglutarate] (mM)
MDA-MB-468
0.55 ± 0.02
BT20
0.11 ± 0.01
BT20
not detectable
BT20
0.47 ± 0.02
[3-phosphohydroxypyruvate]
(mM)
MDA-MB-468
not detectable
[malate] (mM)
MDA-MB-468
3.3 ± 0.08
[2-hydroxyglutarate] (mM)
MDA-MB-468
0. 093 ± 0.009
BT20
not detectable
BT20
0.99 ± 0.07
BT20
0.035 ± 0.002
Km, NAD+ (mM)
0.022 ±
0.003
Km, NADH (mM)
0.004 + 0.001
Km, NADH (mM)
0.004 ± 0.001
[NAD+] (mM)
MDA-MB-468
0.99 ± 0.01
[NADH]
(mM)
MDA-MB-468
0.37 ± 0.02
[NADH] (mM)
MDA-MB-468
0.37 ± 0.02
BT20
0.77 ± 0.02
BT20
0.186 ± 0.001
BT20
0.186 ± 0.001
[NADH] (mM)
MDA-MB-468
0.37 ± 0.02
[NAD+] (mM)
MDA-MB-468
0.99 ± 0.01
[NAD+] (mM)
MDA-MB-468
0.99 ± 0.01
BT20
0.186 ± 0.001
BT20
0.77 ± 0.02
BT20
0.77 ± 0.02
To put the
enzyme kinetic parameters into a physiological context,
we determined the absolute intracellular concentrations of the relevant
substrates (Table 1). In MDA-MB-468 cells,
NAD+ and NADH were both >300 μM, and thus saturating
in all cases. Among the other substrates, the most abundant was AKG
(550 μM), which was ∼3 fold higher than 3PG. 3-Phosphohydroxypyruvate
and OAA, consistent with prior literature, were not detectable. Isotopic
labeling experiments showed that the pathways producing these two
compounds are active; the absence of a measurable signal by LC-MS
indicates that their intracellular concentrations fall below the limit
of detection (LOD). For OAA, the LOD is 60 μM; for 3-phosphohydroxypyruvate,
the LOD cannot be directly determined due to the lack of a commercially
available standard but is likely in the vicinity of 10 μM based
on the structurally similar compound 3PG. Thus, the likely main physiological
reactions are 3PG oxidation to 3-phosphohydroxypyruvate and AKG reduction
to 2HG, with the competition with other potential in vitro substrates likely minor. 3PG and AKG compete for one binding site
on PHGDH, and NAD+ and NADH for another. We therefore plugged
the observed values into a Michaelis–Menten-type equation that
approximates competition for these two active sites, e.g., for the
3PG oxidation reaction:The results predicted cellular 2HG production
fluxes in MDA-MB-468 and BT-20, respectively, as 17% and 15% of the
3PG oxidation (i.e., serine biosynthetic flux).
Contribution
of PHGDH to the Cellular 2HG Pool
To test
whether the production of 2HG by PHGDH is significant in the cell,
we knocked down PHGDH using shRNA in MDA-MB-468 and BT-20, two breast
cancer lines with genomically amplified PHGDH (successful knockdown
of PHGDH was obtained for two shRNA sequences in MDA-MB-468 and one
in BT-20). We then analyzed metabolites in control and knockdown cell
lines (Figure 2A). Consistent with effective
knockdown of PHGDH, a large decrease in the unique serine biosynthetic
pathway intermediate, 3-phosphoserine, was observed in MDA-MB-468
cells. (3-Phosphoserine was below our limit of detection in BT-20
cells.) In addition to 3-phosphoserine, 2HG levels were decreased
by both shRNA knockdowns in the MDA-MB-468 cells, and 2HG was also
decreased in the BT-20 cells (Figure 2A,B).
Because the 2HG levels in the cell extract were too low to quantitate
by GC-MS, especially given background signals from other cellular
metabolites, we could not determine stereospecificity and instead
report total levels as measured by LC-MS. Serine and malate concentrations
were not significantly affected by PHGDH knockdown, and there was
a minimal effect on AKG (Figure 2), which can
be produced when glutamate transaminates the PHGDH product 3-phosphohydroxypyruvate.[4,5] Thus, in these cell lines and culture conditions, PHGDH influences
2HG levels the most of any metabolite that was consistently measured.
Figure 2
PHGDH
knockdown in MDA-MB-468 and BT-20 cells depletes 2HG. (A)
Validation of PHGDH knockdown by western (top) and heat map of metabolite
levels revealing depletion of 2HG and 3-phosphoserine (bottom). Metabolite
levels were averaged and normalized to cell number/volume (which were
equivalent as cell size did not change with PHGDH knockdown), then
normalized to shNT of the corresponding cell line. Results are log2
transformed and clustered. (B) Relative concentrations of key metabolites
in two PHGDH-amplified breast cancer cell lines with shPHGDH or control
knockdown.
PHGDH
knockdown in MDA-MB-468 and BT-20 cells depletes 2HG. (A)
Validation of PHGDH knockdown by western (top) and heat map of metabolite
levels revealing depletion of 2HG and 3-phosphoserine (bottom). Metabolite
levels were averaged and normalized to cell number/volume (which were
equivalent as cell size did not change with PHGDH knockdown), then
normalized to shNT of the corresponding cell line. Results are log2
transformed and clustered. (B) Relative concentrations of key metabolites
in two PHGDH-amplified breast cancer cell lines with shPHGDH or control
knockdown.To determine if the impact of
PHGDH on intracellular 2HG is dependent
on its catalytic activity, wildtype protein or a catalytically inactive
mutant (R236E) of PHGDH was overexpressed in a non-PHGDH-amplified
breast cancer cell line, MDA-MB-231. PHGDH expression in these cells
increases the intracellular 2HG level by over 2-fold, while overexpression
of catalytic dead enzymes does not cause a change in 2HG level; similar,
but less profound, changes were also observed in αAKG levels
in these cells (Figure 3A). We further re-expressed
shRNA-resistant PHGDH or its catalytic dead mutant in control and
PHGDH knockdown MDA-MB-468 cells. Re-expression of wild-type PHGDH,
but not R263E mutant, rescues the 2HG level in shPHGDH knockdown cells.
Additionally, overexpression of wild type, but not R263E, PHGDH increases
the 2HG level in cells without PHGDH knockdown (shGFP). No significant
changes were observed in the intracellular AKG level in these cells
(Figure 3B). Collectively, these data suggest
that PHGDH controls the intracellular 2HG concentration by directly
catalyzing 2HG synthesis.
Figure 3
Dependence of cellular 2HG concentration on
PHGDH catalytic activity.
(A) Relative concentrations of 2-HG and AKG in the non-PHGDH-amplified
breast cancer cell line, MDA-MB-231, transfected with control vector,
PHGDH, or catalytically inactive PHGDH (R236E). PHGDH expression by
western is shown on the bottom. (B) Relative concentrations of 2-HG
and AKG in MDA-MB-468 cells, with or without PHGDH knockdown, with
catalytically active or inactive PHGDH re-expression. PHGDH expression
by western is shown on the bottom. Mean ± SD, N = 3.
Dependence of cellular 2HG concentration on
PHGDH catalytic activity.
(A) Relative concentrations of 2-HG and AKG in the non-PHGDH-amplified
breast cancer cell line, MDA-MB-231, transfected with control vector,
PHGDH, or catalytically inactive PHGDH (R236E). PHGDH expression by
western is shown on the bottom. (B) Relative concentrations of 2-HG
and AKG in MDA-MB-468 cells, with or without PHGDH knockdown, with
catalytically active or inactive PHGDH re-expression. PHGDH expression
by western is shown on the bottom. Mean ± SD, N = 3.
Discussion Regarding Biological
Significance
2HG impacts
protein and DNA covalent modification, including methylation, by competitive
inhibition of AKG-dependent dioxygenase enzymes. l-2HG is
an error product of malate dehydrogenase and can accumulate to toxic
levels in individuals deficient in l-2HG-dehydrogenase activity.[20]d-2HG is produced in large amounts
by IDH active site mutants found in glioma and acute myeloid leukemia
(AML). Unlike l-2HG, d-2HG is sufficient to induce
leukemic transformation.[9] Here, we demonstrate
that another cancer-associated core metabolic enzyme, PHGDH, also
produces d-2HG, albeit at lower levels than those observed
in IDH mutant cancers.An important question is whether the
concentrations of d-2HG produced by PHGDH are biologically
significant. PHGDH knockdown reduces the total cellular 2HG concentration
by about 50% in the tested cell lines; since the measured cellular
2HG is the sum of the d- and l-stereoisomers, the
effect on d-2HG is presumably larger. In another cancer cell
line with wild-type IDH, HCC70, we observed higher concentrations
of 2HG that were not reduced by PHGDH knockdown, suggesting that other
enzymes can produce significant amounts of 2HG (J.F. and X.T., unpublished
results). Previously, millimolar concentrations of d-2HG
have been shown to directly impact demethylase activity in
vitro.[8,10] Lower concentrations, however,
may inhibit certain enzymes or otherwise impact cellular state. For
instance, d-2HG has been shown to inhibit histone demethylase
JMJD2A and JMJD2C at an IC50 of 24 μM and 79 μM.[11]A recent study found that 2HG accumulates
in a subset of breast
cancers, and this accumulation is associated with poor prognosis.
In breast cancer, PHGDH amplification and overexpression
occurs frequently. Interestingly, 2HG accumulation was found to be
associated with the activity of the oncogene Myc,[13] which positively regulates expression of a large number
of genes including PHGDH.In addition to previously proposed
mechanisms by which PHGDH amplification could promote
tumor growth, including
supplying serine for protein synthesis and one carbon metabolism,
promoting TCA cycle anapleurosis,[5] and
nonenzymatic functions including FOXM1 binding,[21] our results raise the possibility that PHGDH amplification could potentially influence cell physiology by overproduction
of the oncometabolite d-2HG. Further work is required to
elucidate the functional significance of PHGDH’s multiple activities
in different physiological and pathological settings.
Methods
Enzyme
Activity
To test the activity of human phosphoglycerate
dehydrogenase (PHGDH) on its natural substrate, 3-phosphoglycerate,
and the potential alternative substrates pyruvate, AKG and OAA, two
types of recombinant humanPHGDH, were used: His-tagged PHGDH (BPS
Biosciences) and Streptavidin-tagged PHGDH (a gift from Dr. Olszewski).
Similar AKG and OAA reduction activities were found in both preparations
of the enzyme. The kinetic parameters were measured using the His-tagged
enzyme in 200 mM Tris buffer (pH = 7.6) at 37 °C. All substrates
were purchased from Sigma. The reaction rate was monitored as NADH
production or consumption, measured by absorbance at 340 nm using
a plate reader (BioTek, Synergy HT). To test the 3PG oxidation reaction,
200 mM of hydrazine was added to the buffer to drive the reaction
forward. Kinetic parameters were measured by varying concentration
of the substrate of interest, with saturating concentration of the
other substrate. To control for non-PHGDH dependent background NADH
oxidation, reactions were also run substituting PHGDH with humangalactokinase,
which was expressed and purified with the same protocol as PHGDH,
as a control. When measuring the kinetic parameters the galactokinase
data were subtracted from the observed PHGDH raw data. All kinetic
parameters were fit to the Michaelis–Menten equation by nonlinear
least-squares fitting (MATLAB). The products of PHGDH acting on alternative
substrates were analyzed by GC-MS or LC-MS. For MS-based analysis,
reactions were quenched with four volumes of methanol and centrifuged
to remove protein. Supernatant was further diluted or derivatized
before MS-based measurement.
Separation of l- and d-2-Hydroxyglutarate
To determine the chirality of 2-hydroxyglutarate (2HG), samples
were derivatized according to a protocol modified from a previous
report.[19] Samples were dried down under
a N2 flow, then resuspended in (R)-2-butanol with 1 M HCl
and heated for 2 h at 100 °C. The product was dried down under
a nitrogen gas flow and resuspended in 1:1 pyridine/acetic anhydride
and heated for 0.5 h at 100 °C. Standards of l- and d-2-hydroxyglutarate and all reagents were purchased from Sigma.After drying the final product, samples were dissolved in chloroform
and analyzed by an Aglient 7890A GC system with Aux EPC column (30
m × 0.25 mm, 0.25 um film thickness) coupled with a TOF mass
spectrometer in negative mode. The temperature gradient used in this
analysis was 100 °C for 3 min, 4 °C per min from 100 to
230 °C, 15 °C per min from 230 to 300 °C, and 300 °C
for 5 min.
Cell Lines and Culture Conditions
Two PHGDH-amplified breast cancer cell lines, MDA-MB-468
and BT-20, and a
non-PHGDH-amplified breast cancer cell line, MDA-MB-231, were purchased
from ATCC. All cell lines were grown in Dulbecco’s modified
eagle media (DMEM) without pyruvate (CELLGRO), supplemented with 10%
dialyzed fetal bovine serum (Invitrogen) in a 5% CO2 incubator
at 37 °C. Growth medium was replaced every 2 days.
PHGDH Knockdown
Knockdowns were performed by infection
with lentivirus expressing the PHGDH shRNA (#1, TRCN0000233031; #2,
TRCN0000028532, Sigma) and puromycin selection. To obtain the shRNA-expressing
virus, shRNA vectors (Sigma-Aldrich) were cotransfected with lentivirus
packaging plasmids into HEK293FT cells using the X-tremeGENE HP DNA
transfection reagent (Roche, Catlog # 6366236001). Viral supernatants
were collected every 24 h for 3 days. Target cells were infected by
a viral supernatant (diluted 1:1 with fresh DMEM). Such treatment
was repeated three times, followed by selection with 2 μg/mL
puromycin initiated at day 4 and allowed to proceed for 2–3
days. Thereafter, cells were maintained in DMEM with 2 μg/mL
puromycin. Knockdown was verified by Western blot using anti-PHGDH
antibody (Sigma).Overexpression was performed by retroviral
infection with the following vectors: (1) pLHCX empty vector, (2)
PHGDH cDNA coloned into pLHCX with HindIII and ClaI sites with a Kozak sequence, (3) enzymatically dead
PHGDHR236E. Mutation of the analogous residue in the E. coli protein destroys enzyme function.[22] The
mutated site is underlined in the following sequence: tggtgaactgtgccgagggagggatcgtgga. Both PHGDH-containing constructs also
included mutations, cccaaagggaccatccaagttatcacacagggaacatccc,
designed to confer resistance to the shRNA targeting sequence cttagcaaagaggagctgata.
The PHGDH expressing virus was obtained by cotransfecting the overexpression
vectors with retrovirus packing plasmids into HEK293T cells using
the X-tremeGENE DNA transfection reagent. Target cells were infected
every day by virus containing media (with 8 μg/mL Polybrene)
which were collected every 24 h for 3 days. Infected cells were selected
by 200 μg/mL and 700 μg/mL hygromycin for MDA-MB-468 and
MDA-MB-231 cells, respectively. The overexpression cells were then
infected by lentiviral shRNA vector.
Measurement of Intracellular
Metabolite Concentrations
To measure the effect of PHGDH
knockdown on intracellular metabolites
levels, cells were harvested at ∼80% confluency. Fresh medium
was replaced 2 h before metabolome harvesting. Metabolism was quenched
and metabolites extracted by aspirating media and immediately adding
−80 °C 80:20 methanol/water (v/v). Supernatants from two
rounds of methanol/water extraction were combined, dried under a nitrogen
gas flow, and resuspended in HPLC water for analysis.The LC-MS
method involved reversed-phase ion-pairing chromatography coupled
by negative mode electrospray ionization to a stand-alone orbitrap
mass spectrometer (Thermo Scientific) scanning from m/z 85–1000 at 1 Hz at 100 000 resolution
with LC separation on a Synergy Hydro-RP column (100 mm × 2 mm,
2.5 μm particle size, Phenomenex, Torrance, CA) using a gradient
of solvent A (97:3 H2O/MeOH with 10 mM tributylamine and
15 mM acetic acid) and solvent B (100% MeOH).[23−25] Data were analyzed
using the MAVEN software suite.[26] Absolute
concentrations were quantified by feeding cells U–13C-glucose and U–13C-glutamine to label intracellular
metabolites and comparing the signal of isotope-labeled intracellular
compound to signal of unlabeled internal standard as described previously.[27]
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