Scientific Papers

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

The molecular basis for centromere identity and function.

Nat Rev Mol Cell Biol. 2015 Nov 25.

McKinley, K.L.*, and Cheeseman, I.M.*

The centromere is the region of the chromosome that directs its segregation in mitosis and meiosis. Although the functional importance of the centromere has been appreciated for more than 130 years, elucidating the molecular features and properties that enable centromeres to orchestrate chromosome segregation is an ongoing challenge. Most eukaryotic centromeres are defined epigenetically and require the presence of nucleosomes containing the histone H3 variant centromere protein A (CENP-A; also known as CENH3). Ongoing work is providing important molecular insights into the central requirements for centromere identity and propagation, and the mechanisms by which centromeres recruit kinetochores to connect to spindle microtubules.


Combined loss of Tet1 and Tet2 promotes B cell, but not myeloid malignancies, in mice.

Cell Rep. 2015 Nov 24;13(8):1692-704.

Zhao, Z., Chen, L., Dawlaty, M.M.*, Pan, F., Weeks, O., Zhou, Y., Cao, Z., Shi, H., Wang, J., Lin, L., Chen, S., Yuan, W., Qin, Z., Ni, H., Nimer, S.D., Yang, F.C., Jaenisch, R.*, Jin, P., and Xu, M.

Cell reportsTET1/2/3 are methylcytosine dioxygenases that regulate cytosine hydroxymethylation. Tet1/2 are abundantly expressed in HSC/HPCs and are implicated in hematological malignancies. Tet2 deletion in mice causes myeloid malignancies, while Tet1-null mice develop B cell lymphoma after an extended period of latency. Interestingly, TET1/2 are often concomitantly downregulated in acute B-lymphocytic leukemia. Here, we investigated the overlapping and non-redundant functions of Tet1/2 using Tet1/2 double-knockout (DKO) mice. DKO and Tet2-/- HSC/HPCs show overlapping and unique 5hmC and 5mC profiles. DKO mice exhibit strikingly decreased incidence and delayed onset of myeloid malignancies in comparison to Tet2-/- mice and in contrast develop lethal B cell malignancies. Transcriptome analysis of DKO tumors reveals expression changes in many genes dysregulated in human B cell malignancies, including LMO2, BCL6, and MYC. These results highlight the critical roles of TET1/2 individually and together in the pathogenesis of hematological malignancies.


Tet1 and Tet2 protect DNA methylation canyons against hypermethylation.

Mol Cell Biol. 2015 Nov 23.

Wiehle, L., Raddatz, G., Musch, T., Dawlaty, M.M.*, Jaenisch, R.*, Lyko, F., and Breiling, A.

DNA methylation is a dynamic epigenetic modification with an important role in cell fate specification and reprogramming. The Ten eleven translocation family of enzymes converts 5-methylcytosine to 5-hydroxymethylcytosine which promotes passive DNA demethylation and functions as intermediate in an active DNA demethylation process. Tet1/Tet2 double-knockout mice are characterized by developmental defects and epigenetic instability, suggesting a requirement for Tet-mediated DNA demethylation for the proper regulation of gene expression during differentiation. Here we used whole-genome bisulfite and transcriptome sequencing to characterize the underlying mechanisms. Our results uncover the hypermethylation of DNA methylation canyons as the genomic key feature of Tet1/Tet2 double-knockout mouse embryonic fibroblasts. Canyon hypermethylation coincided with disturbed regulation of associated genes, suggesting a mechanistic explanation for the observed Tet-dependent differentiation defects. Based on these results we propose an important regulatory role of Tet-dependent DNA demethylation for the maintenance of DNA methylation canyons, which prevents invasive DNA methylation and allows functional regulation of canyon associated genes.


Transcription factor trapping by RNA in gene regulatory elements.

Science. 2015 Nov 20;350(6263):978-81.

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.


Creating patient-specific neural cells for the in vitro study of brain disorders.

Stem Cell Reports. 2015 Nov 20.

Brennand, K.J., Marchetto, M.C., Benvenisty, N., Brustle, O., Ebert, A., Izpisua Belmonte, J.C., Kaykas, A., Lancaster, M.A., Livesey, F.J., McConnell, M.J., McKay, R.D., Morrow, E.M., Muotri, A.R., Panchision, D.M., Rubin, L.L., Sawa, A., Soldner, F.*, Song, H., Studer, L., Temple, S., Vaccarino. F.M., Wu, J., Vanderhaeghen, P., Gage, F.H., and Jaenisch, R.*

As a group, we met to discuss the current challenges for creating meaningful patient-specific in vitro models to study brain disorders. Although the convergence of findings between laboratories and patient cohorts provided us confidence and optimism that hiPSC-based platforms will inform future drug discovery efforts, a number of critical technical challenges remain. This opinion piece outlines our collective views on the current state of hiPSC-based disease modeling and discusses what we see to be the critical objectives that must be addressed collectively as a field.


Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway.

Science. 2015 Nov 19.

Saxton, R.A.*, Knockenhauer, K.E., Wolfson, R.L.*, Chantranupong, L.*, Pacold, M.E.*, Wang, T.*, Schwartz, T.U., and Sabatini, D.M.*

Eukaryotic cells coordinate growth with the availability of nutrients through mTOR complex 1 (mTORC1), a master growth regulator. Leucine is of particular importance and activates mTORC1 via the Rag GTPases and their regulators GATOR1 and GATOR2. Sestrin2 interacts with GATOR2 and is a leucine sensor. We present the 2.7-A crystal structure of Sestrin2 in complex with leucine. Leucine binds through a single pocket that coordinates its charged functional groups and confers specificity for the hydrophobic side chain. A loop encloses leucine and forms a lid-latch mechanism required for binding. A structure-guided mutation in Sestrin2 that decreases its affinity for leucine leads to a concomitant increase in the leucine concentration required for mTORC1 activation in cells. These results provide a structural mechanism of amino acid sensing by the mTORC1 pathway.


Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism.

Nature. 2015 Nov 11.

Oldridge, D.A., Wood, A.C., Weichert-Leahey, N., Crimmins, I., Sussman, R., Winter, C., McDaniel, L.D., Diamond, M., Hart, L.S., Zhu, S., Durbin, A.D., Abraham, B.J.*, Anders, L.*, Tian, L., Zhang, S., Wei, J.S., Khan, J., Bramlett, K., Rahman, N., Capasso, M., Iolascon, A., Gerhard, D.S., Guidry Auvil, J.M., Young, R.A.*, Hakonarson, H., Diskin, S.J., Thomas Look, A., and Maris, J.M.

Neuroblastoma is a paediatric malignancy that typically arises in early childhood, and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumours with excellent outcomes to widely metastatic disease in which long-term survival is approximately 40% despite intensive therapy. A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumour cells. Here we investigate the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation and transcription factor binding sites. We show that SNP rs2168101 G>T is the most highly associated variant (combined P = 7.47 x 10-29, odds ratio 0.65, 95% confidence interval 0.60-0.70), and resides in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumour formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P = 0.028) in neuroblastoma primary tumours, and ablates GATA3 binding (P < 0.0001). We demonstrate allelic imbalance favouring the G-containing strand in tumours heterozygous for this SNP, as demonstrated both by RNA sequencing (P < 0.0001) and reporter assays (P = 0.002). These findings indicate that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumour cells.


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.


A systematic approach to identify candidate transcription factors that control cell identity.

Stem Cell Reports. 2015 Oct 23.

D'Alessio, A.C.*, Fan, Z.P.*, Wert, K.J.*, Baranov, P., Cohen, M.A.*, Saini, J.S., Cohick, E.*, Charniga, C., Dadon, D.*, Hannett, N.M.*, Young, M.J., Temple, S., Jaenisch, R.*, Lee, T.I.*, and Young, R.A.*

Hundreds of transcription factors (TFs) are expressed in each cell type, but cell identity can be induced through the activity of just a small number of core TFs. Systematic identification of these core TFs for a wide variety of cell types is currently lacking and would establish a foundation for understanding the transcriptional control of cell identity in development, disease, and cell-based therapy. Here, we describe a computational approach that generates an atlas of candidate core TFs for a broad spectrum of human cells. The potential impact of the atlas was demonstrated via cellular reprogramming efforts where candidate core TFs proved capable of converting human fibroblasts to retinal pigment epithelial-like cells. These results suggest that candidate core TFs from the atlas will prove a useful starting point for studying transcriptional control of cell identity and reprogramming in many human cell types.


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. 


*Author affiliated with Whitehead Institute for Biomedical Research

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