Katherine Alexander
Assistant Professor
Cancer Center Member
Ph.D., Cornell University, 2016
B.A., Carleton College, 2010
kalexander@cshl.edu | 516-367-8864
Faculty ProfileYour genetic material, the DNA, is housed in a small compartment within your cells, called the cell nucleus. While famous as the cell’s DNA container, the nucleus is not just DNA. It also contains non-DNA substructures that intermingle with DNA. We study how DNA interfaces with these substructures and why this organization is important.
Our research centers on the fundamental mechanisms of gene regulation as mediated by nuclear speckles. Nuclear speckles are a prominent gene-activating substructure defined by specific protein markers and present within nuclei of cells throughout our bodies. While these structures have been long observed, their role in the central dogma of biology and importance across dynamic biological processes remain enigmatic. The Alexander Lab aims to build textbook models for nuclear-speckle-based gene regulation.
We are currently focused on two major levels of gene regulation by nuclear speckles: 1) regulation of what DNA is positioned next to speckles – this is mediated by DNA-binding transcription factors and 2) regulation of speckle state, which varies in two major ways in human cancer, correlating with survival and drug responsiveness. We seek to apply these paradigms to normal and pathogenic processes, uncovering the overarching functions of speckle-based gene regulation and using this information to improve disease outcomes and patient quality-of-life.
A speckle of hope for cancer patients
January 2, 2025
Research from new CSHL Assistant Professor Katherine Alexander suggests that nuclear speckles could influence kidney cancer patient outcomes.
CSHL’s oldest haunts
October 31, 2024
These buildings have weathered oceans of time to be here. Pull back the veil and cross over into CSHL’s storied past for a closer look.
Katherine Alexander joins CSHL cancer faculty
August 5, 2024
Her team will explore mysterious cellular structures known as nuclear speckles and their role in diseases such as cancer.
All Publications
Nuclear speckles regulate functional programs in cancer
2 Jan 2025 | Nature Cell Biology
Alexander, Katherine; Yu, Ruofan; Skuli, Nicolas; Coffey, Nathan; Nguyen, Son; Faunce, Christine; Huang, Hua; Dardani, Ian; Good, Austin; Lim, Joan; Li, Catherine; Biddle, Nicholas; Joyce, Eric; Raj, Arjun; Lee, Daniel; Keith, Brian; Simon, M; Berger, Shelley;
Post-transcriptional splicing can occur in a slow-moving zone around the gene
5 Apr 2024 | eLife | 12
Coté, Allison; O'Farrell, Aoife; Dardani, Ian; Dunagin, Margaret; Coté, Chris; Wan, Yihan; Bayatpour, Sareh; Drexler, Heather; Alexander, Katherine; Chen, Fei; Wassie, Asmamaw; Patel, Rohan; Pham, Kenneth; Boyden, Edward; Berger, Shelly; Phillips-Cremins, Jennifer; Churchman, L; Raj, Arjun;
Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer
16 Sep 2023 | bioRxiv
Alexander, Katherine; Yu, Ruofan; Skuli, Nicolas; Coffey, Nathan; Nguyen, Son; Faunce, Christine; Huang, Hua; Dardani, Ian; Good, Austin; Lim, Joan; Li, Catherine; Biddle, Nicholas; Joyce, Eric; Raj, Arjun; Lee, Daniel; Keith, Brian; Simon, M; Berger, Shelley;
CTCF/cohesin organize the ground state of chromatin-nuclear speckle association
22 Jul 2023 | bioRxiv
Yu, Ruofan; Roseman, Shelby; Siegenfeld, Allison; Nguyen, Son; Joyce, Eric; Liau, Brian; Krantz, Ian; Alexander, Katherine; Berger, Shelley;
TOX2 coordinates with TET2 to positively regulate central memory differentiation in human CAR T cells
21 Jul 2023 | Science Advances | 9(29)
Collins, Sierra; Alexander, Katherine; Lundh, Stefan; Dimitri, Alexander; Zhang, Zhen; Good, Charly; Fraietta, Joseph; Berger, Shelley;
Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer
2 Jun 2022 | Cancer Discovery | 12(6):1462-1481
Rajurkar, Mihir; Parikh, Aparna; Solovyov, Alexander; You, Eunae; Kulkarni, Anupriya; Chu, Chong; Xu, Katherine; Jaicks, Christopher; Taylor, Martin; Wu, Connie; Alexander, Katherine; Good, Charly; Szabolcs, Annamaria; Gerstberger, Stefanie; Tran, Antuan; Xu, Nova; Ebright, Richard; Van Seventer, Emily; Vo, Kevin; Tai, Eric; Lu, Chenyue; Joseph-Chazan, Jasmin; Raabe, Michael; Nieman, Linda; Desai, Niyati; Arora, Kshitij; Ligorio, Matteo; Thapar, Vishal; Cohen, Limor; Garden, Padric; Senussi, Yasmeen; Zheng, Hui; Allen, Jill; Blaszkowsky, Lawrence; Clark, Jeffrey; Goyal, Lipika; Wo, Jennifer; Ryan, David; Corcoran, Ryan; Deshpande, Vikram; Rivera, Miguel; Aryee, Martin; Hong, Theodore; Berger, Shelley; Walt, David; Burns, Kathleen; Park, Peter; Greenbaum, Benjamin; Ting, David;
An NK-like CAR T cell transition in CAR T cell dysfunction
Dec 2021 | Cell | 184(25):6081-6100.e26
Good, Charly; Aznar, M; Kuramitsu, Shunichiro; Samareh, Parisa; Agarwal, Sangya; Donahue, Greg; Ishiyama, Kenichi; Wellhausen, Nils; Rennels, Austin; Ma, Yujie; Tian, Lifeng; Guedan, Sonia; Alexander, Katherine; Zhang, Zhen; Rommel, Philipp; Singh, Nathan; Glastad, Karl; Richardson, Max; Watanabe, Keisuke; Tanyi, Janos; O’Hara, Mark; Ruella, Marco; Lacey, Simon; Moon, Edmund; Schuster, Stephen; Albelda, Steven; Lanier, Lewis; Young, Regina; Berger, Shelley; June, Carl;
p53 mediates target gene association with nuclear speckles for amplified RNA expression
15 Apr 2021 | Molecular Cell | 81(8):1666-1681.e6
Alexander, Katherine; Coté, Allison; Nguyen, Son; Zhang, Liguo; Gholamalamdari, Omid; Agudelo-Garcia, Paula; Lin-Shiao, Enrique; Tanim, K; Lim, Joan; Biddle, Nicolas; Dunagin, Margaret; Good, Charly; Mendoza, Mariel; Little, Shawn; Belmont, Andrew; Joyce, Eric; Raj, Arjun; Berger, Shelley;
TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion
17 Jun 2019 | Nature | 571(7764):211-218
Khan, Omar; Giles, Josephine; McDonald, Sierra; Manne, Sasikanth; Ngiow, Shin; Patel, Kunal; Werner, Michael; Huang, Alexander; Alexander, Katherine; Wu, Jennifer; Attanasio, John; Yan, Patrick; George, Sangeeth; Bengsch, Bertram; Staupe, Ryan; Donahue, Greg; Xu, Wei; Amaravadi, Ravi; Xu, Xiaowei; Karakousis, Giorgos; Mitchell, Tara; Schuchter, Lynn; Kaye, Jonathan; Berger, Shelley; Wherry, E;
p63 establishes epithelial enhancers at critical craniofacial development genes
3 May 2019 | Science Advances | 5(5)
Lin-Shiao, Enrique; Lan, Yemin; Welzenbach, Julia; Alexander, Katherine; Zhang, Zhen; Knapp, Michael; Mangold, Elisabeth; Sammons, Morgan; Ludwig, Kerstin; Berger, Shelley;