Person: Stegmaier, Kimberly
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Publication Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 lysine 27 trimethylation
(2014) Lane, Andrew; Chapuy, Bjoern; Lin, Charles Y.; Tivey, Trevor; Li, Hubo; Townsend, Elizabeth C.; van Bodegom, Diederik; Day, Tovah; Wu, Shuo-Chieh; Liu, Huiyun; Yoda, Akinori; Alexe, Gabriela; Schinzel, Anna; Sullivan, Timothy J.; Malinge, Sébastien; Taylor, Jordan E.; Stegmaier, Kimberly; Jaffe, Jacob D.; Bustin, Michael; te Kronnie, Geertruy; Izraeli, Shai; Harris, Marian; Stevenson, Kristen E.; Neuberg, Donna; Silverman, Lewis; Sallan, Stephen; Bradner, James E; Hahn, William; Crispino, John D.; Pellman, David; Weinstock, DavidDown syndrome confers a 20-fold increased risk of B cell acute lymphoblastic leukemia (B-ALL)1 and polysomy 21 is the most frequent somatic aneuploidy amongst all B-ALLs2. Yet, the mechanistic links between chr.21 triplication and B-ALL remain undefined. Here we show that germline triplication of only 31 genes orthologous to human chr.21q22 confers murine progenitor B cell self-renewal in vitro, maturation defects in vivo, and B-ALL with either BCR-ABL or CRLF2 with activated JAK2. Chr.21q22 triplication suppresses H3K27me3 in progenitor B cells and B-ALLs, and “bivalent” genes with both H3K27me3 and H3K4me3 at their promoters in wild-type progenitor B cells are preferentially overexpressed in triplicated cells. Strikingly, human B-ALLs with polysomy 21 are distinguished by their overexpression of genes marked with H3K27me3 in multiple cell types. Finally, overexpression of HMGN1, a nucleosome remodeling protein encoded on chr.21q223–5, suppresses H3K27me3 and promotes both B cell proliferation in vitro and B-ALL in vivo.
Publication Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells
(2017) Meyers, Robin M.; Bryan, Jordan G.; McFarland, James M.; Weir, Barbara A.; Sizemore, Ann E.; Xu, Han; Dharia, Neekesh; Montgomery, Phillip G.; Cowley, Glenn S.; Pantel, Sasha; Goodale, Amy; Lee, Yenarae; Ali, Levi D.; Jiang, Guozhi; Lubonja, Rakela; Harrington, William F.; Strickland, Matthew; Wu, Ting; Hawes, Derek; Zhivich, Victor A.; Wyatt, Meghan R.; Kalani, Zohra; Chang, Jaime J.; Okamoto, Michael; Stegmaier, Kimberly; Golub, Todd; Boehm, Jesse S.; Vazquez, Francisca; Root, David E.; Hahn, William; Tsherniak, AviadThe CRISPR-Cas9 system has revolutionized gene editing both on single genes and in multiplexed loss-of-function screens, enabling precise genome-scale identification of genes essential to proliferation and survival of cancer cells1,2. However, previous studies reported that a gene-independent anti-proliferative effect of Cas9-mediated DNA cleavage confounds such measurement of genetic dependency, leading to false positive results in copy number amplified regions3,4. We developed CERES, a computational method to estimate gene dependency levels from CRISPR-Cas9 essentiality screens while accounting for the copy-number-specific effect. As part of our efforts to define a cancer dependency map, we performed genome-scale CRISPR-Cas9 essentiality screens across 342 cancer cell lines and applied CERES to this dataset. We found that CERES reduced false positive results and estimated sgRNA activity for both this dataset and previously published screens performed with different sgRNA libraries. Here, we demonstrate the utility of this collection of screens, upon CERES correction, in revealing cancer-type-specific vulnerabilities.