Scientific Papers

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

Activator-inhibitor coupling between Rho signalling and actin assembly makes the cell cortex an excitable medium.

Nat Cell Biol. 2015 Nov;17(11):1471-83.

Bement, W.M., Leda, M., Moe, A.M., Kita, A.M., Larson, M.E., Golding, A.E., Pfeuti, C., Su, K.C.*, Miller, A.L., Goryachev, A.B., and von Dassow, G.

Animal cell cytokinesis results from patterned activation of the small GTPase Rho, which directs assembly of actomyosin in the equatorial cortex. Cytokinesis is restricted to a portion of the cell cycle following anaphase onset in which the cortex is responsive to signals from the spindle. We show that shortly after anaphase onset oocytes and embryonic cells of frogs and echinoderms exhibit cortical waves of Rho activity and F-actin polymerization. The waves are modulated by cyclin-dependent kinase 1 (Cdk1) activity and require the Rho GEF (guanine nucleotide exchange factor), Ect2. Surprisingly, during wave propagation, although Rho activity elicits F-actin assembly, F-actin subsequently inactivates Rho. Experimental and modelling results show that waves represent excitable dynamics of a reaction-diffusion system with Rho as the activator and F-actin the inhibitor. We propose that cortical excitability explains fundamental features of cytokinesis including its cell cycle regulation.


Transcription factor trapping by RNA in gene regulatory elements.

Science. 2015 Oct 29.

Sigova, A.A.*, Abraham, B.J.*, Ji, X.*, Molinie, B., Hannett, N.M.*, Guo, Y.E.*, Jangi, M., Giallourakis, C.C., Sharp, P.A., and Young, R.A.*

Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription. RNA is transcribed from both of these DNA elements, and some DNA-binding TFs bind RNA. Hence, RNA transcribed from regulatory elements may contribute to stable TF occupancy at these sites. We show that the ubiquitously expressed TF YY1 binds to both gene regulatory elements and also to their associated RNA species genome-wide. Reduced transcription of regulatory elements diminishes YY1 occupancy whereas artificial tethering of RNA enhances YY1 occupancy at these elements. We propose that RNA makes a modest but important contribution to the maintenance of certain TFs at gene regulatory elements and suggest that transcription of regulatory elements produces a positive feedback loop that contributes to the stability of gene expression programs.


Tumor cell-derived periostin regulates cytokines that maintain breast cancer stem cells.

Mol Cancer Res. 2015 Oct 27.

Lambert, A.W.*, Wong, C.K., Ozturk, S., Papageorgis, P., Raghunathan, R., Alekseyev, Y., Gower, A.C., Reinhard, B.M., Abdolmaleky, H.M., and Thiagalingam, S.

Basal-like breast cancer (BLBC) is an aggressive subtype of breast cancer which is often enriched with cancer stem cells (CSCs), but the underlying molecular basis for this connection remains elusive. We hypothesized that BLBC cells are able to establish a niche permissive to the maintenance of CSCs and found that tumor cell-derived periostin (POSTN), a component of the extracellular matrix, as well as a corresponding cognate receptor, integrin alphavbeta3, are highly expressed in a subset of BLBC cell lines as well as in cancer stem cell-enriched populations. Furthermore, we demonstrated that an intact periostin-integrin beta3 signaling axis is required for the maintenance of breast CSCs. POSTN activates the ERK signaling pathway and regulates NF-kappaB-mediated transcription of key cytokines, namely IL6 and IL8, which in turn control downstream activation of STAT3. In summary, these findings suggest that BLBC cells have an innate ability to establish a microenvironmental niche supportive of CSCs. IMPLICATIONS: The findings reported here indicate that POSTN produced by CSCs acts to reinforce the stem cell state through the activation of integrin receptors and the production of key cytokines.


Germinal center selection and the antibody response to influenza.

Cell. 2015 Oct 22;163(3):545-8.

Victora, G.D.*, and Wilson, P.C.

In this Minireview, we discuss basic aspects of germinal center biology in the context of immunity to influenza infection and speculate on how the simultaneous evolutionary races of virus and antibody may impact our efforts to design a universal influenza vaccine.


Sensitivity-enhanced NMR reveals alterations in protein structure by cellular milieus. 
Cell. 2015 Oct 22;163(3):620-8.

Frederick, K.K.*, Michaelis, V.K., Corzilius, B., Ong, T.C., Jacavone, A.C., Griffin, R.G., and Lindquist, S.*

Biological processes occur in complex environments containing myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can dramatically enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and enable structural studies in biologically complex environments. Here, we applied DNP NMR to investigate the structure of a protein containing both an environmentally sensitive folding pathway and an intrinsically disordered region, the yeast prion protein Sup35. We added an exogenously prepared isotopically labeled protein to deuterated lysates, rendering the biological environment "invisible" and enabling highly efficient polarization transfer for DNP. In this environment, structural changes occurred in a region known to influence biological activity but intrinsically disordered in purified samples. Thus, DNP makes structural studies of proteins at endogenous levels in biological contexts possible, and such contexts can influence protein structure.


Graphene oxide nanosheets modified with single-domain antibodies for rapid and efficient capture of cells.

Chemistry. 2015 Oct 16.

Chen, G.Y.*, Li, Z.*, Theile, C.S.*, Bardhan, N.M., Kumar, P.V., Duarte, J.N.*, Maruyama, T.*, Rashidfarrokh, A.*, Belcher, A.M., and Ploegh, H.L.*

Peripheral blood can provide valuable information on an individual's immune status. Cell-based assays typically target leukocytes and their products. Characterization of leukocytes from whole blood requires their separation from the far more numerous red blood cells. Current methods to classify leukocytes, such as recovery on antibody-coated beads or fluorescence-activated cell sorting require long sample preparation times and relatively large sample volumes. A simple method that enables the characterization of cells from a small peripheral whole blood sample could overcome limitations of current analytical techniques. We describe the development of a simple graphene oxide surface coated with single-domain antibody fragments. This format allows quick and efficient capture of distinct WBC subpopulations from small samples (approximately 30 muL) of whole blood in a geometry that does not require any specialized equipment such as cell sorters or microfluidic devices.


Identification and characterization of essential genes in the human genome.

Science. 2015 Oct 15.

Wang, T.*, Birsoy, K.*, Hughes, N.W., Krupczak, K.M.*, Post, Y.*, Wei, J.J.*, Lander, E.S., and Sabatini, D.M.*

Large-scale genetic analysis of lethal phenotypes has elucidated the molecular underpinnings of many biological processes. Using the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) system, we constructed a genome-wide single-guide RNA (sgRNA) library to screen for genes required for proliferation and survival in a human cancer cell line. Our screen revealed the set of cell-essential genes, which was validated by an orthogonal gene-trap-based screen and comparison with yeast gene knockouts. This set is enriched for genes that encode components of fundamental pathways, are expressed at high levels, and contain few inactivating polymorphisms in the human population. We also uncovered a large group of uncharacterized genes involved in RNA processing, a number of whose products localize to the nucleolus. Lastly, screens in additional cell lines showed a high degree of overlap in gene essentiality, but also revealed differences specific to each cell line and cancer type that reflect the developmental origin, oncogenic drivers, paralogous gene expression pattern, and chromosomal structure of each line. These results demonstrate the power of CRISPR-based screens and suggest a general strategy for identifying liabilities in cancer cells.


Sestrin2 is a leucine sensor for the mTORC1 pathway.

Science. 2015 Oct 8.

Wolfson, R.L.*, Chantranupong, L.*, Saxton, R.A.*, Shen, K.*, Scaria, S.M.*, Cantor, J.R.*, and Sabatini, D.M.*

Leucine is a proteogenic amino acid that also regulates many aspects of mammalian physiology, in large part by activating the mTOR complex 1 (mTORC1) protein kinase, a master growth controller. Amino acids signal to mTORC1 through the Rag guanosine triphosphatases (GTPases). Several factors regulate the Rags, including GATOR1, a GTPase-activating protein (GAP); GATOR2, a positive regulator of unknown function; and Sestrin2, a GATOR2-interacting protein that inhibits mTORC1 signaling. We find that leucine, but not arginine, disrupts the Sestrin2-GATOR2 interaction by binding to Sestrin2 with a dissociation constant of 20 muM, which is the leucine concentration that half-maximally activates mTORC1. The leucine-binding capacity of Sestrin2 is required for leucine to activate mTORC1 in cells. These results indicate that Sestrin2 is a leucine sensor for the mTORC1 pathway.


Affinity inequality among serum antibodies that originate in lymphoid germinal centers.

PLoS One. 2015 Oct 7;10(10):e0139222.

Kang, M., Eisen, T.J., Eisen, E.A.*, Chakraborty, A.K., and Eisen, H.N.

Upon natural infection with pathogens or vaccination, antibodies are produced by a process called affinity maturation. As affinity maturation ensues, average affinity values between an antibody and ligand increase with time. Purified antibodies isolated from serum are invariably heterogeneous with respect to their affinity for the ligands they bind, whether macromolecular antigens or haptens (low molecular weight approximations of epitopes on antigens). However, less is known about how the extent of this heterogeneity evolves with time during affinity maturation. To shed light on this issue, we have taken advantage of previously published data from Eisen and Siskind (1964). Using the ratio of the strongest to the weakest binding subsets as a metric of heterogeneity (or affinity inequality), we analyzed antibodies isolated from individual serum samples. The ratios were initially as high as 50-fold, and decreased over a few weeks after a single injection of small antigen doses to around unity. This decrease in the effective heterogeneity of antibody affinities with time is consistent with Darwinian evolution in the strong selection limit. By contrast, neither the average affinity nor the heterogeneity evolves much with time for high doses of antigen, as competition between clones of the same affinity is minimal.


The biology and evolution of mammalian Y chromosomes.

Annu Rev Genet. 2015 Oct 6.

Hughes, J.F.*, and Page, D.C.*

Mammals have the oldest sex chromosome system known: the mammalian X and Y chromosomes evolved from ordinary autosomes beginning at least 180 million years ago. Despite their shared ancestry, mammalian Y chromosomes display enormous variation among species in size, gene content, and structural complexity. Several unique features of the Y chromosome-its lack of a homologous partner for crossing over, its functional specialization for spermatogenesis, and its high degree of sequence amplification-contribute to this extreme variation. However, amid this evolutionary turmoil many commonalities have been revealed that have contributed to our understanding of the selective pressures driving the evolution and biology of the Y chromosome. Two biological themes have defined Y-chromosome research over the past six decades: testis determination and spermatogenesis. A third biological theme begins to emerge from recent insights into the Y chromosome's roles beyond the reproductive tract-a theme that promises to broaden the reach of Y-chromosome research by shedding light on fundamental sex differences in human health and disease.


*Author affiliated with Whitehead Institute for Biomedical Research

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