Scientific Papers

For more papers, visit a faculty member's page from the listing on Whitehead Faculty and access the PubMed link.

Mitochondrial metabolism promotes adaptation to proteotoxic stress.

Nat Chem Biol. 2019 May 27. doi: 10.1038/s41589-019-0291-9.

Tsvetkov, P.*, Detappe, A., Cai, K., Keys, H.R.*, Brune, Z.*, Ying, W., Thiru, P.*, Reidy, M., Kugener, G., Rossen, J., Kocak, M., Kory, N.*, Tsherniak, A., Santagata, S., Whitesell, L.*, Ghobrial, I.M., Markley, J.L., Lindquist, S.*, and Golub, T.R.

The mechanisms by which cells adapt to proteotoxic stress are largely unknown, but are key to understanding how tumor cells, particularly in vivo, are largely resistant to proteasome inhibitors. Analysis of cancer cell lines, mouse xenografts and patient-derived tumor samples all showed an association between mitochondrial metabolism and proteasome inhibitor sensitivity. When cells were forced to use oxidative phosphorylation rather than glycolysis, they became proteasome-inhibitor resistant. This mitochondrial state, however, creates a unique vulnerability: sensitivity to the small molecule compound elesclomol. Genome-wide CRISPR-Cas9 screening showed that a single gene, encoding the mitochondrial reductase FDX1, could rescue elesclomol-induced cell death. Enzymatic function and nuclear-magnetic-resonance-based analyses further showed that FDX1 is the direct target of elesclomol, which promotes a unique form of copper-dependent cell death. These studies explain a fundamental mechanism by which cells adapt to proteotoxic stress and suggest strategies to mitigate proteasome inhibitor resistance.


Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program.

Proc Natl Acad Sci U S A. 2019 May 21;116(21):10382-10391. doi: 10.1073/pnas.1804013116. 

Kikani, C.K., Wu, X., Fogarty, S., Kang, S.A.W.*, Dephoure, N., Gygi, S.P., Sabatini, D.M.*, and Rutter, J.

During skeletal muscle regeneration, muscle stem cells (MuSCs) respond to multiple signaling inputs that converge onto mammalian target of rapamycin complex 1 (mTORC1) signaling pathways. mTOR function is essential for establishment of the differentiation-committed progenitors (early stage of differentiation, marked by the induction of myogenin expression), myotube fusion, and, ultimately, hypertrophy (later stage of differentiation). While a major mTORC1 substrate, p70S6K, is required for myotube fusion and hypertrophy, an mTORC1 effector for the induction of myogenin expression remains unclear. Here, we identified Per-Arnt-Sim domain kinase (PASK) as a downstream phosphorylation target of mTORC1 in MuSCs during differentiation. We have recently shown that the PASK phosphorylates Wdr5 to stimulate MuSC differentiation by epigenetically activating the myogenin promoter. We show that phosphorylation of PASK by mTORC1 is required for the activation of myogenin transcription, exit from self-renewal, and induction of the myogenesis program. Our studies reveal that mTORC1-PASK signaling is required for the rise of myogenin- positive committed myoblasts (early stage of myogenesis), whereas mTORC1-S6K signaling is required for myoblast fusion (later stage of myogenesis). Thus, our discoveries allow molecular dissection of mTOR functions during different stages of the myogenesis program driven by two different substrates.


Bacteroides-derived sphingolipids are critical for maintaining intestinal homeostasis and symbiosis.

Cell Host Microbe. 2019 May 8;25(5):668-680.e7. doi: 10.1016/j.chom.2019.04.002.

Brown, E.M., Ke, X., Hitchcock, D., Jeanfavre, S., Avila-Pacheco, J., Nakata, T., Arthur, T.D., Fornelos, N., Heim, C., Franzosa, E.A., Watson, N.*, Huttenhower, C., Haiser, H.J., Dillow, G., Graham, D.B., Finlay, B.B., Kostic, A.D., Porter, J.A., Vlamakis, H., Clish, C.B., and Xavier, R.J.

Sphingolipids are structural membrane components and important eukaryotic signaling molecules. Sphingolipids regulate inflammation and immunity and were recently identified as the most differentially abundant metabolite in stool from inflammatory bowel disease (IBD) patients. Commensal bacteria from the Bacteroidetes phylum also produce sphingolipids, but the impact of these metabolites on host pathways is largely uncharacterized. To determine whether bacterial sphingolipids modulate intestinal health, we colonized germ-free mice with a sphingolipid- deficient Bacteroides thetaiotaomicron strain. A lack of Bacteroides- derived sphingolipids resulted in intestinal inflammation and altered host ceramide pools in mice. Using lipidomic analysis, we described a sphingolipid biosynthesis pathway and revealed a variety of Bacteroides- derived sphingolipids including ceramide phosphoinositol and deoxy- sphingolipids. Annotating Bacteroides sphingolipids in an IBD metabolomic dataset revealed lower abundances in IBD and negative correlations with inflammation and host sphingolipid production. These data highlight the role of bacterial sphingolipids in maintaining homeostasis and symbiosis in the gut.


Distinct transcriptional regulation of Nanos2 in the germ line and soma by the Wnt and delta/notch pathways.

Dev Biol. 2019 May 7. pii: S0012-1606(19)30203-9. doi: 10.1016/j.ydbio.2019.04.010. 

Oulhen, N., Swartz, S.Z.*, Wang, L., Wikramanayake, A., and Wessel, G.M.

Specification of the primordial germ cells (PGCs) is essential for sexually reproducing animals. Although the mechanisms of PGC specification are diverse between organisms, the RNA binding protein Nanos is consistently required in the germ line in all species tested. How Nanos is selectively expressed in the germ line, however, remains largely elusive. We report that in sea urchin embryos, the early expression of Nanos2 in the PGCs requires the maternal Wnt pathway. During gastrulation, however, Nanos2 expression expands into adjacent somatic mesodermal cells and this secondary Nanos expression instead requires Delta/Notch signaling through the forkhead family member FoxY. Each of these transcriptional regulators were tested by chromatin immunoprecipitation analysis and found to directly interact with a DNA locus upstream of Nanos2. Given the conserved importance of Nanos in germ line specification, and the derived character of the micromeres and small micromeres in the sea urchin, we propose that the ancestral mechanism of Nanos2 expression in echinoderms was by induction in mesodermal cells during gastrulation. 


Paternally acting canonical RNA-directed DNA methylation pathway genes sensitize Arabidopsis endosperm to paternal genome dosage.

Plant Cell. 2019 May 7. pii: tpc.00047.2019. doi: 10.1105/tpc.19.00047.

Satyaki, P.R.V.*, and Gehring, M.*

Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic excess frequently results in extensive endosperm proliferation without cellularization and seed abortion. We previously showed that loss of the RNA Pol IV gene nrpd1 in tetraploid fathers represses seed abortion in paternal excess crosses. Here we show genetically that RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is sufficient to determine the viability of paternal excess seeds. We compared transcriptomes, DNA methylation, and small RNAs from endosperm of balanced crosses (diploid x diploid) and lethal (diploid x tetraploid) and viable paternal excess (diploid x tetraploid nrpd1). Endosperm from both lethal and viable paternal excess seeds share widespread transcriptional and DNA methylation changes at genes and TEs. Interploidy seed abortion is thus unlikely to be caused by either transposable element or imprinted gene mis-regulation, and its repression by loss of paternal RdDM is associated with only modest gene expression changes. Finally, using allele-specific transcription data, we present evidence for a transcriptional buffering system that increases expression of maternal alleles and represses paternal alleles in response to excess paternal genomic dosage. These findings prompt reconsideration of models for dosage sensitivity in endosperm.


EMT and cancer: More than meets the eye.

Dev Cell. 2019 May 6;49(3):313-316. doi: 10.1016/j.devcel.2019.04.026.

Derynck, R., and Weinberg, R.A.*

Epithelial cells acquire mesenchymal characteristics during development, wound healing and inflammation, and in cancer and fibrosis. With increasing appreciation of different roles of epithelial-mesenchymal transition (EMT), we address the question of how to define and recognize EMT processes and discuss their properties in cancer progression.


Hominoid-specific transposable elements and KZFPs facilitate human embryonic genome activation and control transcription in naive human ESCs.

Cell Stem Cell. 2019 May 2;24(5):724-735.e5. doi: 10.1016/j.stem.2019.03.012.

Pontis, J., Planet, E., Offner, S., Turelli, P., Duc, J., Coudray, A., Theunissen, T.W.*, Jaenisch, R.*, and Trono, D.

Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Kruppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation.


A giant leap for womankind.

Nat Med. 2019 May;25(5):704-707. doi: 10.1038/s41591-019-0446-y. 

Valantine, H., Travis, E., El-Adhami, W., Vernos, I., Mosqueda, L., Wayne, E., Kearns-Zimmerman, F., Bonefont, L., Visweswariah, S.S., Akande-Sholabi, W., and Polka, J.*

We asked 11 thought leaders on how they would advise the research community to make real progress in the next 25 years to address gender inequality in medical research. They offer concrete ideas for change.


WWOX somatic ablation in skeletal muscles alters glucose metabolism. 

Mol Metab. 2019 Apr;22:132-140. doi: 10.1016/j.molmet.2019.01.010.

Abu-Remaileh, M., Abu-Remaileh, M.*, Akkawi, R., Knani, I., Udi, S., Pacold, M.E., Tam, J., and Aqeilan, R.I.

OBJECTIVE: WWOX, a well-established tumor suppressor, is frequently lost in cancer and plays important roles in DNA damage response and cellular metabolism. METHODS: We re-analyzed several genome-wide association studies (GWAS) using the Type 2 Diabetes Knowledge Portal website to uncover WWOX's association with metabolic syndrome (MetS). Using several engineered mouse models, we studied the effect of somatic WWOX loss on glucose homeostasis. RESULTS: Several WWOX variants were found to be strongly associated with MetS disorders. In mouse models, somatic ablation of Wwox in skeletal muscle (Wwox(DeltaSKM)) results in weight gain, glucose intolerance, and insulin resistance. Furthermore, Wwox(DeltaSKM) mice display reduced amounts of slow-twitch fibers, decreased mitochondrial quantity and activity, and lower glucose oxidation levels. Mechanistically, we found that WWOX physically interacts with the cellular energy sensor AMP-activated protein kinase (AMPK) and that its loss is associated with impaired activation of AMPK, and with significant accumulation of the hypoxia inducible factor 1 alpha (HIF1alpha) in SKM. CONCLUSIONS: Our studies uncover an unforeseen role of the tumor suppressor WWOX in whole-body glucose homeostasis and highlight the intimate relationship between cancer progression and metabolic disorders, particularly obesity and type-2 diabetes. SUBJECT AREAS: Genetics, Metabolic Syndrome, Diabetes.


The reference genome sequence of Scutellaria baicalensis provides insights into the evolution of wogonin biosynthesis.

Mol Plant. 2019 Apr 15. pii: S1674-2052(19)30131-5. doi: 10.1016/j.molp.2019.04.002.

Zhao, Q., Yang, J., Cui, M.Y., Liu, J., Fang, Y., Yan, M., Qiu, W., Shang, H., Xu, Z., Yidiresi, R., Weng, J.K.*, Pluskal, T.*, Vigouroux, M., Steuernagel, B., Wei, Y., Yang, L., Hu, Y., Chen, X.Y., and Martin, C.

Molecular plant Scutellaria baicalensis Georgi is important in Chinese Traditional Medicine where preparations of dried roots, 'Huang Qin', are used for liver and lung complaints including complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14 Mb genome has been assembled into 9 pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence to those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed how the specialised metabolic pathway for the synthesis of 4'deoxyflavone bioactives evolved in the genus, Scutellaria. We found that the gene encoding a specific cinnamate CoA ligase likely obtained its new function following recent mutations, and four genes encoding enzymes in the 4'deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification and point mutations coupled to gene neo- and sub-functionalizations were involved in the evolution of 4'deoxyflavone synthesis in the genus, Scutellaria. The reference genome of S. baicalensis will facilitate the development of improved assemblies of genome sequences for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in members of the mint family, Lamiaceae, but also would facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants.


*Author affiliated with Whitehead Institute for Biomedical Research

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