Elucidating the chemical structure of native 1-deoxysphingosine

Article abstract of DOI:10.1194/jlr.M067033

The 1-deoxysphingolipids (1-deoxySLs) are formed by an alternate substrate usage of the enzyme, serine-palmitoyltransferase, and are devoid of the C1-OH-group present in canonical sphingolipids. Pathologically elevated 1-deoxySL levels are associated with the rare inherited neuropathy, HSAN1, and diabetes type 2 and might contribute to β cell failure and the diabetic sensory neuropathy. In analogy to canonical sphingolipids, it was assumed that 1-deoxySLs also bear a (4E) double bond, which is normally introduced by sphingolipid delta(4)-desaturase 1. This, however, was never confirmed. We therefore supplemented HEK293 cells with isotope-labeled D₃-1-deoxysphinganine and compared the downstream formed D3-1-deoxysphingosine (1-deoxySO) to a commercial synthetic SPH m18:1(4E)(3OH) standard. Both compounds showed the same m/z, but differed in their RPLC retention time and atmospheric pressure chemical ionization in-source fragmentation, suggesting that the two compounds are structural isomers. Using dimethyl disulfide derivatization followed by MS² as well as differential-mobility spectrometry combined with ozone-induced dissociation MS, we identified the carbon-carbon double bond in native 1-deoxySO to be located at the (Δ14) position. Comparing the chromatographic behavior of native 1-deoxySO to chemically synthesized SPH m18:1(14Z) and (14E) stereoisomers assigned the native compound to be SPH m18:1(14Z). This indicates that 1-deoxySLs are metabolized differently than canonical sphingolipids.

Full text of DOI:10.1194/jlr.M067033

Elucidating the chemical structure of native 1-deoxysphingosine
Regula Steiner1*, Essa Mostafa2*, Alaa Othman1,$, Christoph Arenz3, Alan T. Maccarone4, Berwyck L.
J.Poad5, Stephen J. Blanksby5, Arnold von Eckardstein1 and Thorsten Hornemann1#
Affiliations
1.
2.
3.
4.
5.
Institute of Clinical Chemistry, University and University Hospital of Zurich, Raemistrasse 100,
CH-8091 Zurich, Switzerland
Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin,
Germany and Institute for Chemistry Suez Canal University, Egypt
Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin,
Germany
Mass Spectrometry User Resource and Research Facility, School of Chemistry, University of
Wollongong, NSW 2522, Australia
Central Analytical Research Facility, Institute for Future Environments, Queensland University
of Technology, QLD 4001, Australia
* both authors contributed equally to this work
$ current address: Center of Brain Behaviour and Metabolism(CBBM) Institute of Experimental and
Clinical Pharmacology and Toxicology University of Lübeck Ratzeburger Allee 160, 23562 Lübeck
# corresponding author:
Thorsten Hornemann
Institute of Clinical Chemistry
University and University Hospital of Zurich,
Raemistrasse 100,
CH-8091 Zurich
Switzerland
1

Abstract
1-Deoxysphingolipids (1-deoxySL) are formed by an alternate substrate usage of the enzyme serine-
palmitoyltransferase and devoid of the C1-OH-group present in canonical sphingolipids (SL).
Pathologically elevated 1-deoxySL levels are associated with the rare inherited neuropathy HSAN1
and diabetes type 2 (T2DM) and might contribute to beta cell failure and the diabetic sensory
neuropathy. In analogy to canonical SL it was assumed that also 1-deoxySL bear a (4E) double bond
which is normally introduced by sphingolipid delta(4)-desaturase 1 (DES1). This, however, was never
confirmed. We therefore supplemented HEK293 cells with isotope labeled D3-1-deoxy-sphinganine
(1-deoxySA) and compared the downstream formed D3-1-deoxy-sphingosine (1-deoxySO) to a
commercial synthetic SPH m18:1(4E)(3OH) standard. Both compounds showed the same mass-to-
charge ratio (m/z) but differed in their RPLC retention time and APCI in-source fragmentation,
suggesting that the two compounds are structural isomers. Using dimethyl disulfide (DMDS)
derivatization followed by MS2 as well as differential mobility spectrometry combined with ozon-
induced dissociation mass spectrometry, we identified the carbon-carbon DB in native 1-deoxySO to
be located at (Δ14) position. Comparing the chromatographic behavior of native 1-deoxySO to
chemically synthesized SPH m18:1(14Z) and (14E) stereoisomers assigned the native compound to be
SPH m18:1(14Z). This indicates that 1-deoxySL are metabolized differently than canonical
sphingolipids.
2

Keywords:
deoxysphingolipids, 1-deoxysphingosine, double bond position, dimethyl disulfide adducts, mass
spectrometry, differential mobility spectrometry, ozone-induced dissociation, structural isomers
3

Introduction
Sphingolipids are typically formed by the condensation of serine and palmitoyl-CoA, a reaction
catalyzed by the serine-palmitoyltransferase (SPT) enzyme. Besides these canonical substrates SPT
can use other acyl-CoA’s but also alanine or glycine as substrate which then forms a category of
atypical 1-deoxysphingolipids (1-deoxySL) which lack the C1-OH group of canonical sphingolipids
(1, 2).
Several missense mutations in SPT which are associated with the rare inherited neuropathy HSAN1,
induce a permanent shift in the substrate specificity of the enzyme resulting in increased 1-deoxySL
formation. HSAN1 is a rare autosomal and dominantly inherited axonopathy and clinically
characterized by a progressive loss of pain and temperature sensation often accompanied by
neuropathic pain attacks and skin ulcers (3). 1-DeoxySL are toxic to primary sensory neurons in
culture and lead to neurite retraction and the disruption of the neuronal cytoskeleton structure in a dose
dependent manner (3, 4). They also interfere with the survival and insulin secretory capacity of
pancreatic beta cells and 1-deoxySL plasma levels have been found to be prospective biomarkers for
the risk to develop T2DM (5-7).
The 1-deoxy-sphinganine (1-deoxySA) which is formed by SPT can be converted to 1-deoxy-
ceramides (1-deoxyCer) but not to complex sphingolipids because of the missing 1-OH group. During
catabolism 1-deoxyCer is degraded by ceramidase to form 1-deoxysphingosine (1-deoxySO) but not
phosphorylated to form the catabolic intermediate sphingosine-1-P (S1P). This prevents its cleavage to
hexadecenal by S1P-lyase meaning that 1-deoxySL cannot be degraded by the canonical catabolic
pathway (2). Apart from that, it was assumed that 1-deoxySA is metabolized by the same set of
enzymes as canonical sphingoid bases and that 1-deoxySO like SO bears a (4E) double bond which is
introduced by the sphingolipid delta(4)-desaturase 1 (DES1).
However, we observed that natively formed 1-deoxySO showed a different RPLC retention time than
a synthetic SPH m18:1(4E)(3OH) standard, though the m/z was identical for both compounds. This
suggested that native 1-deoxySO and the synthetic SPH m18:1(4E)(3OH) are structural isomers
probably differing in position and / or configuration of the carbon-carbon double bond. To further
4

elucidate this difference we used a set of tandem mass spectrometry methods in combination with total
synthesis to elucidate the real double bond position and configuration of native 1-deoxySO.
5

Materials and Methods
Unless stated differently all solvents and reagents were purchased from Sigma-Aldrich Chemie GmbH
(Buchs, Switzerland) excluding methanol, which was purchased from Honeywell specialty chemicals
Seelze GmBH, Germany.
Cell extract
HEK293 cells were fed with 1 µM deuterium labelled D3-1-deoxysphinganine (Avanti Polar Lipids,
Alabaster, AL) or with the unlabeled 1-deoxysphinganine (Avanti Polar Lipids, Alabaster, AL). Cells
were harvested after 24 h and the whole sphingolipid extract was hydrolyzed to get the free sphingoid
bases as described previously with some modifications (7, 8). The cell pellet was dissolved in 100 µL
of PBS. 500 µL methanol including D7-sphingosine and D7-sphinganine (Avanti Polar Lipids,
Alabaster, AL) as the internal standards were added. Lipids were extracted for one hour under constant
agitation at 37°C. Samples were centrifuged to pellet precipitated proteins and the supernatant
transferred into a new tube. Lipids were hydrolyzed by adding 75 μL of methanolic HCl (1 N HCl and
10 M H2O in methanol) and incubated for 16 h at 65°C. HCl was neutralized by adding 100 μL of
KOH (10M). Then 625μL chloroform was added followed by 100 μL 2N ammonium hydroxide and
0.5 mL alkaline water to complete phase separation. The sample was vortexed, centrifuged at 16,000 g
for 5 min, the upper phase discarded and the lower (organic) phase washed 3 times with alkaline
water. The organic phase was finally dried under N2 and stored at −20oC until analysis.
Throughout this paper we refer to the extracted 1-deoxySO as native.
LC-MS Method
A commercial 1-deoxySO standard (SPH m18:1(4E)(3OH)) was purchased from Avanti Polar Lipids
Inc. (Alabaster, AL). SPH m18:1(14Z)(3OH) was synthesized according to the method described
below. The SPH m18:1(E)(3OH) standards (5E, 8E, 12E, 13E, 14E) were synthesized based on an
unpublished method that will be issued elsewhere i. An LC-MS method described previously (8), was
used to compare retention times and in source fragmentation. Sphingoid bases were separated by
RPLC on a C18-column (Uptispere 120 Å, 5 μm, 125 × 2 mm; Interchim, Montluçon, France) and
i Manuscript in preparation
6

analyzed on a TSQ Quantum Ultra or a Q Exactive (Thermo, Reinach, BL, Switzerland) using an
atmospheric pressure chemical ionization (APCI) interface. Mobile phases consisted of A: ultra-pure
H2O / MeOH 1/1 v/v with 2.6mM ammonium acetate and B: MeOH. Gradient was set from 50% B to
100% B within 25 min followed by 5 min 100% B and 5 min of equilibration with a flow rate of 0.3
ml/min. For mass spectral detection, the following parameters were set on the APCI source: discharge
current of 4 µA, vaporizer temperature of 450°C, sheath gas pressure 20 AU, aux gas 5 AU and
capillary temperature of 200°C.
DMDS adduct analysis
Dimethyl disulfide (DMDS, 100 L) and 20 L of I2 (in diethyl ether, 60 mg/mL) was added to whole
cell extracts or 15 nmol SPH m18:1(4E)(3OH) standard. Samples were agitated for 16 h in an
Eppendorf Thermo Shaker at 1400 rpm and 35°C. The reaction was quenched with 100 L of 5%
aqueous Na2S2O3, extracted with 200 L of hexane and dried under N2. Samples were dissolved in 200
L isopropanol for further analysis according to the method of Dunkelblum et al (9). The sample was
directly injected into the MS at a flowrate of 10 µL/min. The [M + H]+ ion of the DMDS adduct of 1-
deoxySO was generated by electrospray ionization (ESI) on a Thermo Fisher Scientific Q-Exactive
and both collision-induced dissociation and high-resolution accurate mass analysis were performed.
For detection, the following parameters were set on the ESI source: spray voltage of 4.2 kV, vaporizer
temperature of 30°C, sheath gas pressure 5 AU, aux gas 0 AU, capillary temperature of 320°C and for
fragmentation in-source collision-induced dissociation (CID) was performed at 30 eV and higher-
energy collision induced dissociation (HCD) of the ion at m/z 378.3 was performed with setting of 25.
Differential Mobility Spectrometry combined with Ozone-Induced Dissociation
A SelexIONTM differential mobility spectrometer (DMS) was employed with a QTRAP®5500 triple
quadrupole ion-trap mass spectrometer (SCIEX, Ontario, Canada). The instrument has been modified
for ozone-induced dissociation (OzID) as previously described (10). Solutions for analysis were
prepared in LC-grade methanol (VWR Scientific, Murrarie, QLD, Australia) with 5 mM UPLC-grade
ammonium acetate (Sigma Aldrich, St. Louis, MO); SPH standard concentrations were 0.05 M.
Sample solutions were subjected to ESI in a TurboVTM (SCIEX) and passed through the mobility
7

spectrometer. Compensation voltage (CV) applied across the electrodes was scanned while the
separation voltage (SV) was held constant at 4100 V. Ionograms were obtained from scanning CV and
represent the sum of five mass spectra at each voltage point and have been smoothed using PeakView®
(SCIEX). The ESI source and DMS cell temperatures were 100 and 150°C, respectively; the ESI
voltage was set to 5500 V. Nitrogen was set to 20 psi for each of the following: resolving gas in the
DMS cell, the nebulizing ESI gas, and the MS curtain gas. Ions exiting the DMS cell into the mass
spectrometer were mass selected in first quadrupole prior to isolation in the collision cell with ozone
present. Ozone was produced by an external generator (Titan, Absolute Ozone, Alberta, Canada)
operating at 220 g/Nm3 (10.3% v/v ozone in oxygen) from which a small portion was mixed into the
nitrogen collision gas input to the mass spectrometer through a variable leak valve (Nenion, Lustenau,
Austria). The isolation time for ionized lipids in the collision cell was optimized between 100 ms and
15 s depending on the ozone-reactivity of a given ionized lipid (11, 12). Following ozonolysis, ions
were transferred to the third quadrupole region where mass analysis was performed using a trap-scan
at 1000 Th/s. OzID spectra obtained at discrete CV values were averaged between 2 to 5 mins.
Synthesis of 1-deoxysphingosine (SPH m18:1(14Z)(3OH) or (2S,3R,14Z)-2-aminooctadec-14-en-
3-ol)
Eleven intermediate compounds en route to the target SPH m18:1 (14Z)(3OH) were synthesized as
described in the supplementary info. A stirred solution of compound 11 (57 mg, 3 mmol) in 1,4-
dioxane (1 mL) at 0°C was treated with a solution of 4M HCl-dioxane (2 mL) over a period of 10 min.
The resulting reaction mixture was allowed to stir for 1 h at the same conditions, gradually warmed to
ambient temperature, and followed by TLC analysis. After being stirred for additional 2 h (as
monitored by TLC, Pet. ether/EtOAc 4:1; Rf(adduct)= 0.5; Rf(product)=0.0; visualized with KMnO4
solution), the reaction mixture was concentrated under reduced pressure. The resultant residue was
dissolved in with CH2Cl2 (50 mL) and sequentially washed with saturated NaHCO3 solution (40 mL),
water (30 mL), and brine solution (40 mL). The organic layer was subsequently dried over anhydrous
Na2SO4, filtered and concentrated in vacuo to afford a pale yellow oily residue. Flash column
chromatography of the obtained crude amine over silica gel using ethylacetate and isopropanol as
8

eluents (from 0-10% isopropanol in ethylacetate) provided the final compound 12 as colorless oil.
Yield: 32 mg (71%). Rf: 0.32 (EtOAc/iso-propanol 4:1, visualized with 1.3% ninhydrine). 1H NMR
(500 MHz, MeOD) δ 5.35 (ddd, J = 5.9, 3.6, 2.8 Hz, 2H), 3.70 (ddd, J = 8.1, 5.3, 3.0 Hz, 1H), 3.26
(qd, J = 6.7, 3.1 Hz, 1H), 2.07 – 1.98 (m, 4H), 1.52 (dt, J = 10.3, 8.2 Hz, 1H), 1.47 – 1.41 (m, 2H),
1.41 – 1.28 (m, 18H), 1.21 (d, J = 6.8 Hz, 3H), 0.91 (t, J = 7.4 Hz, 3H).13C NMR (126 MHz, MeOD) δ
131.05, 130.65, 71.71, 52.61, 34.02, 30.86, 30.75, 30.73, 30.69, 30.65, 30.35, 30.31, 28.15, 27.00,
23.98, 14.16, 12.08. HRMS (ESI+) m/z calcd for C18H38NO [M + H]+ 284.2953; found 284.2959.
9

Results
1-deoxySO is a downstream metabolite of 1-deoxySA
HEK293 cells were cultured in the presence of deuterium labeled D3-1-deoxySA or unlabeled 1-
deoxySA. Cells were harvested after 24 h and the profile of the extracted sphingoid bases analyzed by
RPLC-MS. We observed the appearance of [M + H]+ ions with m/z 284.3 (unlabeled 1-deoxySO) and
of m/z 287.3 (labeled D3-1-deoxySO) which both eluted at the same time from the LC column (Figure
1A), indicating that 1-deoxySO is a product formed downstream of 1-deoxySA (labeled and
unlabeled).
Comparison of synthetic SPH m18:1(4E) and native 1-deoxySO
Retention time and APCI in-source fragmentation was compared between native 1-deoxySO and a
commercially available synthetic SPH m18:1(4E)(3OH) standard. The native 1-deoxySO eluted from
the C18 column after 12.70 min whereas the synthetic SPH m18:1(4E)(3OH) eluted after 14.77 min
(Figure 1A). [M + H]+ ions formed by APCI showed in-source fragmentation and a significant water
loss for the SPH m18:1(4E)(3OH) standard which was considerably less pronounced for the native 1-
deoxySO (Figure 1B). As both molecules showed identical m/z using high-resolution accurate mass
spectrometry (HRAMS, < 2ppm for [M + H]+ and [M + H - H2O]+ ) the observed deviations in
retention time and in-source fragmentation suggested that native 1-deoxySO and the synthetic
SPH m18:1(4E)(3OH) were structural isomers.
Dimethyl disulfide (DMDS) derivatization
As the synthetic SPH m18:1(4E)(3OH) and the native 1-deoxySO showed different RPLC properties
we aimed to elucidate the carbon-carbon double bond position of native 1-deoxySO by derivatization
with dimethyl disulfide (DMDS). The DMDS adducts of 1-deoxySO were analyzed by HRAMS using
direct injection and ESI ionization. The [M + H]+ ions from the DMDS adducts of 1-deoxySO were
selected at m/z 378.3 and subjected to collision-induced dissociation. The CID spectrum showed four
abundant but non-specific product ions at m/z 330.3 [M + H - CH3SH]+, 312.3 [M+H - CH3SH -
H2O]+, 282.3 [M + H -2CH3SH]+ and 264.3 [M + H - 2CH3SH - 2H2O]+ corresponding to the neutral
loss of methane thiols and water as indicated (Figure 2).
10

Importantly, two less abundant but structurally diagnostic product ions were observed at m/z 274.2 (A)
and 103.1 (B). These product ions were formed by a cleavage of the carbon-carbon bond between the
two methyl sulfide moieties. The mass distribution of the two fragments indicated a double bond in
(Δ14)-position for native 1-deoxySO. Product ions indicating a fragmentation at the (Δ4)-position (m/z
243.2 and 134.1) were not detected.
Differential-mobility spectrometry (DMS) combined with Ozone-Induced Dissociation
DMS has previously been deployed successfully for lipid isomer separation prior to mass
spectrometric analysis (10, 13). Here it was combined with OzID which exploits the reaction between
mass-selected lipid ions and gaseous ozone inside a mass spectrometer to drive fragmentation
diagnostic of the position(s) of carbon-carbon double bonds (12, 14). In these experiments the D3-
labeled hydrolyzed extract from HEK cells was spiked with a 1:1 mixture of the unlabeled commercial
SPH m18:1(4E)(3OH) and synthesized SPH m18:1(14E)(3OH) structural isomers and the mixture
subjected to electrospray ionization. Figure 3A shows DMDS ionograms obtained for m/z 284 (black
trace) and 287 (red trace) corresponding in mass to the [M + H]+ ions expected from unlabeled and
labeled 1-deoxySO, receptively. The black trace shows peaks corresponding to at least two chemically
distinct ion populations of m/z 284 (i.e., isobars): one with a maximum CV at around 17 V and another
peaking at 20 V. Isobars carrying m/z 284 in this mixture should be dominated by the protonated forms
of the synthetic SPH m18:1(4E)(3OH) and SPH m18:1(14E)(3OH) isomers. The red trace,
corresponding to isobars of m/z 287 (Figure 3A), showed an analogous pair of peaks at CV 17 and 20
V. These signals could be assigned to [M + H]+ ions arising from native forms of 1-deoxySO present
in the cell extract. To interrogate the structure of the ions responsible for each of the two peaks in the
ionogram, OzID spectra were acquired for m/z 284 and 287 ions using fixed CV settings of 17 V and
20 V. Figure 3B shows product ions arising from the synthetic lipids (at m/z 284) in black and the
corresponding D3-labeled native lipid (at m/z 287) in red. Both spectra revealed product ions arising
from neutral loss of 40 and 24 Da characteristic of ozonolysis of a carbon-carbon double bond at the
(Δ14)-position on the sphingoid backbone (15) (see Supplementary Figure 1A and Supplementary
Table 1). Conversely, in the OzID spectra obtained at a CV of 20 V (Figure 3C) these product ions
11

were absent, while fragments arising from oxidative cleavage of a (Δ4)-double bond (neutral losses of
180 and 164) were observed at m/z 104 and 120 for the unlabeled standard (see Supplementary Figure
1B and supplementary Table 1). Of this pair of ions, the aldehyde is mass-shifted and appears as
expected at m/z 107 for the D3-isotopologue while the m/z 123 is absent in this spectrum: possibly due
to the lower abundance of the CV = 20 V feature in the native extract. Interestingly, an abundant water
loss was observed in the spectra in Figure 3C, which is much diminished in the spectra in Figure 3B
providing further evidence of the structural difference between the two lipids.
DMS-OzID analysis was also performed on non-hydrolyzed lipid extract from HEK cells. Four 1-
deoxyceramide species could be detected as [M + H]+ ions consistent with the assignments: Cer
m18:1/16:0, Cer m18:1/18:0, Cer m18:1/22:0 and Cer m18:1/24:1. As before, the OzID spectra
showed a neutral loss of 40 Da as a characteristic signature for 1-deoxySO with a carbon-carbon
double bond at the (Δ14)-position (Figure 4). These data support the presence of the (Δ14) carbon-
carbon double bond in both 1-deoxyceramide and the 1-deoxySO and exclude the possibility that the
observed (Δ14) desaturation is formed as an artifact of the hydrolysis reaction.
Synthesis of deoxy-Sphingosine standards
Although the previous analysis confirmed the (Δ14) carbon-carbon double bond in native 1-deoxySO
they did not unambiguously assign the stereochemistry of the bond. To further confirm the position
and configuration of the double bond a number of 1-deoxySO analogues with different double bond
positions and confirmations (5E, 8E, 12E, 13E, 14E and 14Z) were synthesized. Here we focus on the
synthesis of the SPH m18:1(14Z)(3OH) as details on the synthesis of the other derivatives will be
published elsewherei. The synthesis of SPH m18:1(14Z)(3OH) 12 commenced from commercially
available 1,10-decandilol (Scheme 1). Treatment of 1,10-decanediol with dihydropyran in the presence
of a catalytic amount of p-toluenesulfonic acid (PTSA) afforded the mono-THP ether 3 in moderate
yield. Subsequent conversion of mono-hydroxyl compound 3 to the corresponding bromo derivative 4
was accomplished through treatment of 3 with tetrabromomethane (CBr4) and triphenyl phosphine
(PPh3) to provide compound 4. With intermediate 4 in hand, the coupling with lithiated 1-pentyne was
i Manuscript in preparation
12

performed following a previously described protocol (16) with some modifications (see supporting
information Table 1for details). Thus, tert-butyllithium was added to 1-pentyne at -78°C, and the in
situ generated 1-lithio-1-pentyne was sequentially reacted with DMPU and bromo substrate 4 to afford
compound 5 in a satisfactory yield. Subsequent stereoselective hydrogenation of alkyne 5 was
accomplished with Lindlar catalyst after optimization of reaction conditions to afford the desired Z-
configuration of the alkene 6 as a sole isomer (see supporting information Table 2 for more details). It
is noteworthy, that initial attempts to furnish alkene 6 led to a product that was contaminated (10-15%)
1
with inseparable by-products. Careful analysis of H-NMR spectra of the crude mixture identified
these by-products as the E-configured alkene and the over reduced-product 1-bromopentadecane.
Cleavage of the THP-protecting group in 6 under acid-catalyzed ethanol treatment proceeded
smoothly to provide the hydroxyl alkene 7 which was subsequently subjected to Appel reaction with
CBr4/PPh3 to furnish the Z-bromo-alkene 8.
Next, the obtained bromo-alkenyl chain 8 was converted into the corresponding Grignard reagent 9
and subsequently coupled to the Weinreb amide 2 (prepared from L-alanine in two steps, see the
supporting information for details). Toward this end, Weinreb amide 2 was reacted with 0.9 equivalent
of methylmagnesium bromide (as sacrificial base), followed by addition the Grignard reagent 9 to
afford ketone 10 in 78% isolated yield. The subsequent diastereoselective reduction of the carbonyl
group in 10 with lithium tri-(tert-butoxy)-aluminum hydride (TBLAH) (1.7 equiv.) in absolut ethanol
at -78°C was accomplished without reduction of the double bond to furnish the desired anti-amino
alcohol 11 as a mere stereoisomer. Acidic hydrolysis of the tert-butyl carbamate protecting group of
11 with 4M HCl-dioxane solution yieled the corresponding hydrochloric salt of
SPH m18:1(14Z)(3OH) (.HCl). The desired product 12 was finally obtained after neutralization
workup in 71% yield.
Retention-time correlation of native lipids with synthetic standards
The RPLC retention times of the synthetic SPH m18:1(E)(3OH) standards with double bonds in
positions 5E, 8E, 12E and14E, were compared. We observed an inverse logarithmic correlation
(R2=0.96) between retention times and the double bond position (Figure 5A). The more the DB was
13

positioned towards the omega end the earlier the molecule eluted from the column. The closest match
in retention time between native 1-deoxySO and the synthetic standards was seen again for
SPH m18:1(14E)(3OH) although the elution time between the two compounds still differed by about
30 seconds (Figure 5B).
To further elucidate the DB configuration, we compared the retention times of native 1-deoxySO with
the synthetic standard in (14Z) configuration (Figure 5B and supplementary Figure 3). The
SPH m18:1(14Z) eluted at 13.0 min and was therefore coinciding with the elution time of native 1-
doxySO. From these results we conclude that native 1-deoxySO bears a (14Z) double bond.
14

Discussion
1-deoxySO is an atypical sphingolipid, lacking the 1-hydroxylgroup of canonical sphingosine. It is a
downstream metabolite of 1-deoxySA which is formed by SPT due to its alternative activity with
alanine. Because of the missing C1-hydroxyl group, 1-deoxySO cannot be phosphorylated to
sphingosine 1-phosphate and therefore also not degraded by S1P-lyase (2).
Pathologically elevated 1-deoxySL play an important role in the inherited neuropathy HSAN I but
were also found in other conditions like the metabolic syndrome and type 2 diabetes (3, 7). However,
the metabolism of 1-deoxySLs and their molecular structures have not been investigated in detail yet.
Comparing native 1-deoxySO to a synthetic SPH m18:1(4E) standard by RPLC we observed a
significant deviation in retention time although m/z was identical for both molecules. Analyzing the
DMDS derivatized adducts of native 1-deoxySO by MS2 revealed two specific fragments which
indicated the double bond position at (Δ14) and therefore distinct to that of the canonical (Δ4)-
position. The (Δ14)-position was further confirmed using differential mobility spectrometry combined
with ozone-induced dissociation. Comparing retention times of native 1-deoxySO to a set of synthetic
SPH m18:1 standards finally confirmed a (14Z) DB in native 1-deoxySO.
During the sphingolipid de-novo synthesis, the sphingolipid delta(4)-desaturase 1 (DES1) normally
introduces a (4E) double bond into the sphingoid base backbone of dihydro-ceramide to form
ceramide. The observation that native 1-deoxySO bears a (14Z) instead of (4E) DB, indicates that the
metabolism of 1-deoxySL deviates from that of canonical sphingolipids. Interestingly, sphingadiene
(SAdiene) a poly unsaturated downstream product of sphingosine (17) has double bonds at both, (4E)
and (14Z) positions (Figure 5C). The presence of a (14Z) double bond in both, SAdiene and native 1-
deoxySO suggests that both metabolites are substrates of the same desaturase although the responsible
enzyme is unknown so far (18). The fact that exogenously added D3-lableled 1-deoxySA is converted
to D3-labeled 1-deoxySO also showed that the double bond is introduced downstream of 1-deoxySA
and not formed by an SPT mediated incorporation of an unsaturated acyl-CoA. Interestingly, 1-
deoxymethylsphingosine (1-deoxymethSO), the corresponding downstream product of 1-
deoxymethylsphinganine which is formed by the condensation with glycine, seems to contain a (3E)
15

DB. The m/z as well as RPLC retention time of native 1-deoxymethSO matched that of an synthetic
m17:1 (3E)(2OH) standard (supplementary Figure 4). As 1-deoxymethSO contains only 17 carbons
this equals the (4E) DB position of canonical SL.
In conclusion we provide strong evidences from multiple, orthogonal analytical techniques to
unambiguously assign native 1-deoxySO as it is formed in HEK293 cells to be a SPH
m18:1(14Z)(3OH) structure. This furthermore implies that 1-deoxy-ceramides are metabolized distinct
from canonical sphingolipids. However, more detailed studies are needed to further investigate the
enzymatic pathways and metabolic steps involved in the conversion of these lipids.
Acknowledgments:
RS, AO, AVE and TH want to thank the following funding sources for support: The 7th Framework
Program of the European Commission (“RESOLVE”, Project number 305707), the Swiss National
Foundation SNF (Project 31003A_153390/1); the Hurka Foundation, the Novartis Foundation and the
Rare Disease Initiative Zurich (“radiz”, Clinical Research Priority Program for Rare Diseases,
University of Zurich). SJB and ATM would like to thank Assoc. Prof. Todd W. Mitchell for insightful
discussion regarding the DMS-OzID experiments. SJB is supported by project funding through the
Australian Research Councilvia the Discovery and Linkage programs (DP150101715and
LP110200648;the latter is an industry partnership with SCIEX, Ontario, Canada).
16

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Figure 1: (A) Difference RPLC retention time of synthetic SPH m18:1(4E)(3OH) and native 1-
deoxySO extracted from HEK293 cells treated with 1-deoxySA or D3-1-deoxySA. (B) APCI in-source
fragmentation of a synthetic SPH m18:1(4E)(3OH) standard, native 1-deoxySO and D3-1-deoxySO:
the precursor [M + H]+ ion (m/z of 284) is identical for SPH m18:1(4E)(3OH) and native 1-deoxySO.
However, synthetic SPH m18:1(4E)(3OH) formed an abundant [M + H - H2O]+ product ion (m/z 266)
which was formed much less from native 1-deoxySO and D3-1-deoxySO at identical conditions. MS
spectra were recorded on a triple quad MS (TSQ Quantum Ultra) with APCI ionisation.
Figure 2: (A) Hydrolyzed lipid extract from HEK293 cells was subjected to DMDS derivatization and
analyzed on a high-resolution accurate mass spectrometer using ESI ionization and direct injection.
The [M + H]+ ion formed from DMDS adduct of native 1-deoxySO (m/z of 378.2857) was in
+
excellent agreement (< 1 ppm) with the calculated mass of 378.2859 (C20H44NOS2 ). The precursor
ion was selected for collision-induced dissociation yielding to the spectrum shown. Product ions A
(m/z 274) and B (m/z 103) are indicated in the spectrum and are diagnostic for a fragmentation at
(Δ14) position. (B) Spektrum from SPH m18:1(4E)(3OH) showing product ion B (m/z 243). (C)
Spektrum from SPH m18:1(14Z)(3OH) showing product ions A (m/z 274) and B (m/z 103). Putative
structures for the diagnostic product ions are shown as insets in the spectra.
Figure 3: ESI(+) was undertaken on a mixture of D3-labeled hydrolyzed HEK cell lipid extracts
spiked with unlabeled synthetic standards SPH m18:1(4E)(3OH) and SPH m18:1(14E)(3OH). (A)
Ionograms showing separation in voltage space of the [M + H]+ ions formed from the two lipid
isomers. Each of the synthetic lipids spiked into the extract produced a peak in the black trace (m/z
284) and similar features were observed for the labeled HEK293 extract shown in the red trace (m/z
287). (B) OzID spectra obtained for synthetic standard (black spectrum) and the D3-labelled extract
(red spectrum) corresponding to the first feature in the ionogram (i.e., CV = 17 V ozone reaction time
of 100 ms). (C) OzID spectra obtained for synthetic standard (black spectrum) and the D3-labelled
extract (red spectrum) corresponding to the second feature in the ionogram (i.e., CV = 20 V ozone
reaction time of 15 s). OzID product ions characteristic of the locations of the carbon-carbon double
bonds are indicated by closed circles and enable assignment of the position of unsaturation to (B) (Δ
14) - position and (C) (Δ4) - position.
18

Figure 4: ESI(+)-OzID spectra obtained for m/z values corresponding to deoxyceramides present in
an non-hydrolyzed HEK cell lipid extract. All spectra show a product ion at m/z 266, which is
consistent with the collision-induced dehydration of the backbone followed by cleavage of the amide
bond to liberate the acyl chain. Product ions arising from a characteristic neutral loss of 40 Da from
the [M+H]+ or [M+H-H2O]+ are marked with circles and are consistent with an n-4 double bond (i.e.,
a Δ14 double bond in the SPH m18:1 backbone). Product ions arising from a characteristic neutral loss
of 110 Da from the [M+H]+ or [M+H-H2O]+ are marked with squares and are consistent with the
presence of an n-9 double bond (e.g., 24:1 Δ15 acyl chain). These spectra are consistent with the
deoxyceramides (a) Cer m18:1(Δ14)/16:0, (b) Cer m18:1(Δ14)/18:0, (c) Cer m18:1(Δ14)/22:0, (d) Cer
m18:1(Δ14)/24:1(Δ15). (See also supplementary Figure 2 and supplementary table 1). Product ions
marked with an asterisk (*) showed different mobility characteristics to the OzID peaks and likely
arise from isobaric interference.
Figure 5: (A) RPLC retention times for a set of synthetic SPH m18:1 standards having double bonds
in positions (4E), (5E), (8E), (12E) and (14E). The position of the double bond within the alkyl chain
showed a logarithmic correlation to the retention times (B) Comparing the retention times of native 1-
deoxySO to the synthetic standards SPH m18:1 (14Z) and SPH m18:1 (14E) identified native 1-
deoxySO as SPH m18:1 (14Z) ( **** p< 0.0001). (C) Comparison of the chemical structures of 1-
deoxySO and Sphingadiene
Scheme 1: Synthesis of the 14Z-deoxy-sphingosine analogue. Reagents and conditions: a) DHP,
PTSA (cat.), THF:DCM, 0°C-rt, 12 h. b) CBr4, PPh3, DCM, 0°C-rt, 4 h. c) (i) 1-Pentyne, tert-BuLi,
toluene, -78°C, 1 h, and then (ii) DMPU, 4, THF, -78°C-rt, 7 h d) H2, EDA, Lindlar catalyst, 5% DMF
in EtOAc, 0°C, 6 h. e) PPTS (cat.), EtOH, 62°C, 2 h. f) (i) Mg, 1,2-DBE (drops), Et2O, reflux, 2 h, and
then (ii) 2, MeMgBr, DCM:Et2O; reflux, 2 h. g) TBLAH, EtOH, -78°C, 1 h h) 4M HCl-Dioxane, 0°C,
3 h.
19

Figure 1
20

Figure 2
21

Figure 3
22

Figure 4
23

Figure 5
24

Scheme 1
25