Scientific Papers

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

Molecular movement in the Arabidopsis thaliana female gametophyte.

Plant Reprod. 2017 Jul 10. doi: 10.1007/s00497-017-0304-3.

Erdmann, R.M.*, Hoffmann, A., Walter, H.K., Wagenknecht, H.A., Gross-Hardt, R., and Gehring, M.*

Cellular decisions can be influenced by information communicated from neighboring cells. Communication can occur via signaling or through the direct transfer of molecules. Movement of RNAs and proteins has frequently been observed among symplastically connected plant cells. In flowering plants, the female gametes, the egg cell and central cell, are closely apposed within the female gametophyte. Here we investigated the ability of fluorescently labeled dyes and small RNAs to move from the Arabidopsis thaliana central cell to the egg apparatus following microinjection. These results define a size limit of at least 20 kDa for symplastic movement between the two gametes, somewhat larger than that previously observed in Torenia fournieri. Our results indicate that symplastic connectivity in Arabidopsis thaliana changes after fertilization and suggest that prior to fertilization mechanisms are in place to facilitate small RNA movement from the central cell to the egg cell and synergids.

Upholding a role for EMT in breast cancer metastasis.

Nature. 2017 Jul 5;547(7661):E1-E3.

Ye, X.*, Brabletz, T., Kang, Y., Longmore, G.D., Nieto, M.A., Stanger, B.Z., Yang, J., and Weinberg, R.A.*

Upholding a role for EMT in pancreatic cancer metastasis. 

Nature. 2017 Jul 5;547(7661):E7-E8.

Aiello, N.M., Brabletz, T., Kang, Y., Nieto, M.A., Weinberg, R.A.*, and Stanger, B.Z. 


Predicting the response to CTLA-4 blockade by longitudinal noninvasive monitoring of CD8 T cells.

J Exp Med. 2017 Jun 30.

Rashidian, M.*, Ingram, J.R.*, Dougan, M.*, Dongre, A.*, Whang, K.A.*, LeGall, C.*, Cragnolini, J.J., Bierie, B.*, Gostissa, M., Gorman, J., Grotenbreg, G.M., Bhan, A., Weinberg, R.A.*, and Ploegh, H.L.*

Immunotherapy using checkpoint-blocking antibodies against targets such as CTLA-4 and PD-1 can cure melanoma and non-small cell lung cancer in a subset of patients. The presence of CD8 T cells in the tumor correlates with improved survival. We show that immuno-positron emission tomography (immuno-PET) can visualize tumors by detecting infiltrating lymphocytes and, through longitudinal observation of individual animals, distinguish responding tumors from those that do not respond to therapy. We used 89Zr-labeled PEGylated single-domain antibody fragments (VHHs) specific for CD8 to track the presence of intratumoral CD8+ T cells in the immunotherapy-susceptible B16 melanoma model in response to checkpoint blockade. A 89Zr-labeled PEGylated anti-CD8 VHH detected thymus and secondary lymphoid structures as well as intratumoral CD8 T cells. Animals that responded to CTLA-4 therapy showed a homogeneous distribution of the anti-CD8 PET signal throughout the tumor, whereas more heterogeneous infiltration of CD8 T cells correlated with faster tumor growth and worse responses. To support the validity of these observations, we used two different transplantable breast cancer models, yielding results that conformed with predictions based on the antimelanoma response. It may thus be possible to use immuno-PET and monitor antitumor immune responses as a prognostic tool to predict patient responses to checkpoint therapies. 

Non-model model organisms.

BMC Biol. 2017 Jun 29;15(1):55.

Russell, J.J., Theriot, J.A., Sood, P., Marshall, W.F., Landweber, L.F., Fritz-Laylin, L., Polka, J.K.*, Oliferenko, S., Gerbich, T., Gladfelter, A., Umen, J., Bezanilla, M., Lancaster, M.A., He, S., Gibson, M.C., Goldstein, B., Tanaka, E.M., Hu, C.K., and Brunet, A.

Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.


The long noncoding RNA Wisper controls cardiac fibrosis and remodeling.

Sci Transl Med. 2017 Jun 21;9(395).

Micheletti, R., Plaisance, I., Abraham, B.J.*, Sarre, A., Ting, C.C., Alexanian, M., Maric, D., Maison, D., Nemir, M., Young, R.A.*, Schroen, B., González, A., Ounzain, S., and Pedrazzini, T.

Long noncoding RNAs (lncRNAs) are emerging as powerful regulators of cardiac development and disease. However, our understanding of the importance of these molecules in cardiac fibrosis is limited. Using an integrated genomic screen, we identified Wisper (Wisp2 super-enhancer-associated RNA) as a cardiac fibroblast-enriched lncRNA that regulates cardiac fibrosis after injury. Wisper expression was correlated with cardiac fibrosis both in a murine model of myocardial infarction (MI) and in heart tissue from human patients suffering from aortic stenosis. Loss-of-function approaches in vitro using modified antisense oligonucleotides (ASOs) demonstrated that Wisper is a specific regulator of cardiac fibroblast proliferation, migration, and survival. Accordingly, ASO-mediated silencing of Wisper in vivo attenuated MI-induced fibrosis and cardiac dysfunction. Functionally, Wisper regulates cardiac fibroblast gene expression programs critical for cell identity, extracellular matrix deposition, proliferation, and survival. In addition, its association with TIA1-related protein allows it to control the expression of a profibrotic form of lysyl hydroxylase 2, implicated in collagen cross-linking and stabilization of the matrix. Together, our findings identify Wisper as a cardiac fibroblast-enriched super-enhancer-associated lncRNA that represents an attractive therapeutic target to reduce the pathological development of cardiac fibrosis in response to MI and prevent adverse remodeling in the damaged heart.

The super-enhancer-derived alncRNA-EC7/bloodlinc potentiates red blood cell development in trans.

Cell Rep. 2017 Jun 20;19(12):2503-2514. 

Alvarez-Dominguez, J.R.*, Knoll, M.*, Gromatzky, A.A.*, and Lodish, H.F.*

Enhancer-derived RNAs are thought to act locally by contributing to their parent enhancer function. Whether large domains of clustered enhancers (super-enhancers) also produce cis-acting RNAs, however, remains unclear. Unlike typical enhancers, super-enhancers form large spans of robustly transcribed chromatin, amassing capped and polyadenylated RNAs that are sufficiently abundant to sustain trans functions. Here, we show that one such RNA, alncRNA-EC7/Bloodlinc, is transcribed from a super-enhancer of the erythroid membrane transporter SLC4A1/BAND3 but diffuses beyond this site. Bloodlinc localizes to trans-chromosomal loci encoding critical regulators and effectors of terminal erythropoiesis and directly binds chromatin-organizing and transcription factors, including the chromatin attachment factor HNRNPU. Inhibiting Bloodlinc or Hnrnpu compromises the terminal erythropoiesis gene program, blocking red cell production, whereas expressing Bloodlinc ectopically stimulates this program and can promote erythroblast proliferation and enucleation in the absence of differentiation stimuli. Thus, Bloodlinc is a trans-acting super-enhancer RNA that potentiates red blood cell development.

Germinal center selection and affinity maturation require dynamic regulation of mTORC1 kinase.

Immunity. 2017 Jun 20;46(6):1045-1058.e6.

Ersching, J.*, Efeyan, A.*, Mesin, L.*, Jacobsen, J.T.*, Pasqual, G.*, Grabiner, B.C.*, Dominguez-Sola, D., Sabatini, D.M.*, and Victora, G.D.*

During antibody affinity maturation, germinal center (GC) B cells cycle between affinity-driven selection in the light zone (LZ) and proliferation and somatic hypermutation in the dark zone (DZ). Although selection of GC B cells is triggered by antigen-dependent signals delivered in the LZ, DZ proliferation occurs in the absence of such signals. We show that positive selection triggered by T cell help activates the mechanistic target of rapamycin complex 1 (mTORC1), which promotes the anabolic program that supports DZ proliferation. Blocking mTORC1 prior to growth prevented clonal expansion, whereas blockade after cells reached peak size had little to no effect. Conversely, constitutively active mTORC1 led to DZ enrichment but loss of competitiveness and impaired affinity maturation. Thus, mTORC1 activation is required for fueling B cells prior to DZ proliferation rather than for allowing cell-cycle progression itself and must be regulated dynamically during cyclic re-entry to ensure efficient affinity-based selection


Centromeres are maintained by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome transition.

Nat Commun. 2017 Jun 9;8:15775. 

Guo, L.Y., Allu, P.K., Zandarashvili, L., McKinley, K.L.*, Sekulic, N., Dawicki-McKenna, J.M., Fachinetti, D., Logsdon, G.A., Jamiolkowski, R.M., Cleveland, D.W., Cheeseman, I.M.*, and Black, B.E.

Maintaining centromere identity relies upon the persistence of the epigenetic mark provided by the histone H3 variant, centromere protein A (CENP-A), but the molecular mechanisms that underlie its remarkable stability remain unclear. Here, we define the contributions of each of the three candidate CENP-A nucleosome-binding domains (two on CENP-C and one on CENP-N) to CENP-A stability using gene replacement and rapid protein degradation. Surprisingly, the most conserved domain, the CENP-C motif, is dispensable. Instead, the stability is conferred by the unfolded central domain of CENP-C and the folded N-terminal domain of CENP-N that becomes rigidified 1,000-fold upon crossbridging CENP-A and its adjacent nucleosomal DNA. Disrupting the 'arginine anchor' on CENP-C for the nucleosomal acidic patch disrupts the CENP-A nucleosome structural transition and removes CENP-A nucleosomes from centromeres. CENP-A nucleosome retention at centromeres requires a core centromeric nucleosome complex where CENP-C clamps down a stable nucleosome conformation and CENP-N fastens CENP-A to the DNA.

3D primary culture model to study human mammary development.

Methods Mol Biol. 2017;1612:139-147.

Miller, D.H.*, Sokol, E.S.*, and Gupta, P.B.*

We present a protocol for expanding human mammary tissues from primary patient-derived cells in three-dimensional (3D) cultures. The primary epithelial cells are seeded into 3D hydrogels with defined components, which include both proteins and carbohydrates present in mammary tissue. Over a span of 10-14 days, the seeded cells form mammary tissues with complex ductal-lobular topologies and include luminal and basal cells in the correct orientation, together with cells that stain positively for stem cell markers. In addition to recapitulating key architectural features of human mammary tissue, the expanded tissues also respond to lactogenic hormones including estrogen, progesterone, and prolactin. We anticipate that these cultures will prove useful for studies of mammary development and breast cancer.


*Author affiliated with Whitehead Institute for Biomedical Research

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