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Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism


Mass spectrometry with stable isotope labels has been seminal in discovering the dynamic state of living matter1,2, but is limited to bulk tissues or cells. We developed multi-isotope imaging mass spectrometry (MIMS) that allowed us to view and measure stable isotope incorporation with submicrometre resolution3,4. Here we apply MIMS to diverse organisms, including Drosophila, mice and humans. We test the ‘immortal strand hypothesis’, which predicts that during asymmetric stem cell division chromosomes containing older template DNA are segregated to the daughter destined to remain a stem cell, thus insuring lifetime genetic stability. After labelling mice with 15N-thymidine from gestation until post-natal week 8, we find no 15N label retention by dividing small intestinal crypt cells after a four-week chase. In adult mice administered 15N-thymidine pulse-chase, we find that proliferating crypt cells dilute the 15N label, consistent with random strand segregation. We demonstrate the broad utility of MIMS with proof-of-principle studies of lipid turnover in Drosophila and translation to the human haematopoietic system. These studies show that MIMS provides high-resolution quantification of stable isotope labels that cannot be obtained using other techniques and that is broadly applicable to biological and medical research.

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Figure 1: MIMS quantification of stable isotope-labelled thymidine incorporation by dividing cells.
Figure 2: No label-retaining stem cells in the small intestinal crypt.
Figure 3: Label-dilution in adult mice indicates random segregation of DNA strands.
Figure 4: Extending MIMS to Drosophila and human metabolism.

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We thank A. Mudge, M. Raff and A. Aperia for critical reading of the manuscript; M. Raff for numerous enlightening discussions; T. Bloom for her strong support at the origin of MIMS development; M. Wang for MIMS analysis; J. Poczatek and Z. Kaufman for MIMS analysis software development; L. Trakimas, C. MacGillivray, S. Clark and E. Hurst for histology; W. Wang for statistics advice. We thank Cambridge Isotope Laboratories for their generous gift of thymidine (15N2, 96–98%). M.L.S. is funded by the American Heart Association and Future Leaders in Cardiovascular Medicine. A.P.G. is funded by the Medical Research Council (U117584237). R.T.L. is funded by the National Institutes of Health (AG032977) and a grant from the Harvard Stem Cell Institute. C.P.L. is funded by the National Institutes of Health (EB001974, AG034641), the Ellison Medical Foundation and the Human Frontier Science Program.

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Authors and Affiliations



M.L.S. designed the experiments to study the ‘immortal strand hypothesis’ in the small intestine with input from C.P.L.; M.L.S. performed in vivo mouse experiments with help from S.E.S.; A.P.B. and A.P.G. designed and performed the Drosophila experiments. M.L.S. designed the human experiment with input from R.T.L. and T.S.P.; M.L.S. and T.S.P. conducted the human protocol. S.E.S. was involved in study design. M.L.S. analysed the data with C.P.L. input. C.G. operated the instrument and assisted with analysis of Drosophila lipid droplets. M.L.S. and C.P.L. wrote the manuscript; A.P.B. and A.P.G. contributed the section on Drosophila. R.T.L. was involved in study design and provided critical feedback at all junctures. C.P.L. conceived of the general application of MIMS to metabolism, cell turnover and human experimentation. C.P.L. designed and performed in vitro experiments.

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Correspondence to Claude P. Lechene.

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The authors declare no competing financial interests.

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Steinhauser, M., Bailey, A., Senyo, S. et al. Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism. Nature 481, 516–519 (2012).

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