January Newsletter
Dear MDS Center Community,
Happy New Year!
Please see below for our January news and announcements.
Please direct any questions to fs291@cumc.columbia.edu
---------------------------------------------------------------------------------------------------
MDS Center Programs
E.P. Evans MDS Center Hematological Malignancies Seminar Series:
Wednesday, January 10 ,2024
12:00 PM to 1:00 PM
ICRC first floor auditorium
Rudd Delwel, PhD
Department of Hematology
Erasmus University Cancer Center, The Netherlands.
Title: “The Evil side of gene regulation in acute myeloid leukemia”
Hosted By: Aaron Viny MD
E.P. Evans MDS Center Special Seminar:
Wednesday, January 17 ,2024
12:00 PM to 1:00 PM
ICRC first floor auditorium
Christin Zhang, PhD
Department of Medicine in the division of Oncology
Washington University School of Medicine
Title: TBD
Hosted By: Stavroula Kousteni PhD
MDS Faculty Meeting & Seminar:
Tuesday, January 9 ,2024
12:00PM to 1:30PM
Black Building, Conference Room 1418
Speaker: Dr. Raul Rabadan
Title: “Language models of regulation for cancer genetics”
Abstract: “Foundation models have demonstrated significant potential for integrating vast amounts of data and exerting considerable impact across various scientific domains. In this talk, we explore their applicability to cancer biology. Initially, we introduce the Evolutionary and Structure (ES) score, which builds upon protein language models and AlphaFold. The ES score amalgamates evolutionary data with protein structure prediction to prioritize functional regions in proteins. This approach is empirically validated within the context of relapsed pediatric leukemias. Simultaneously, we present GET, a foundation model trained on chromatin accessibility data spanning 235 human cell types. GET excels at predicting gene expression in previously unseen cell types and identifies both universal and cell-specific transcription factor interaction networks. Noteworthy applications encompass the discovery of distant regulatory regions in fetal erythroblasts and the elucidation of the regulatory impact of germline coding mutations in lymphoma-associated transcription factors such as PAX5. Collectively, these computational methodologies exemplify how foundation models can facilitate the study of biological data, yielding functionally relevant insights.”
MDS Member Anoucements
New Publications from Center Members: (Some are preprint)
Liu Y, Jin Y, Azizi E, Blumberg AJ. Cellstitch:
3D cellular anisotropic image segmentation via optimal transport.
BMC Bioinformatics. 2023 Dec 15;24(1):480. doi: 10.1186/s12859-023-05608-2. PMID: 38102537; PMCID: PMC10724925.
Leeman-Neill RJ, Song D, Bizarro J, Wacheul L, Rothschild G, Singh S, Yang Y, Sarode AY, Gollapalli K, Wu L, Zhang W, Chen Y, Lauring MC, Whisenant DE, Bhavsar S, Lim J, Swerdlow SH, Bhagat G, Zhao Q, Berchowitz LE, Lafontaine DLJ, Wang J, Basu U.
Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression.
Nat Genet. 2023 Dec;55(12):2160-2174. doi: 10.1038/s41588-023-01561-1. Epub 2023 Dec 4. PMID: 38049665; PMCID: PMC10703697.
Brown JR, Eichhorst B, Hillmen P, Jurczak W, Kaźmierczak M, Lamanna N, O'Brien SM, Tam CS, Qiu L, Zhou K, Simkovic M, Mayer J, Gillespie-Twardy A, Ferrajoli A, Ganly PS, Weinkove R, Grosicki S, Mital A, Robak T, Osterborg A, Yimer HA, Salmi T, Wang MD, Fu L, Li J, Wu K, Cohen A, Shadman M.
Plain language summary of zanubrutinib or ibrutinib in chronic lymphocytic leukemia that is resistant to treatment or has come back after treatment.
Future Oncol. 2023 Dec 13. doi: 10.2217/fon-2023-0849. Epub ahead of print. PMID: 38088119.
Martinez AL, Shannon MJ, Sloan T, Mace EM.
CD56/NCAM mediates cell migration of human NK cells by promoting integrin-mediated adhesion turnover.
bioRxiv [Preprint]. 2023 Nov 22:2023.11.21.567714. doi: 10.1101/2023.11.21.567714. PMID: 38045340; PMCID: PMC10690223.
Shannon MJ, Eisman SE, Lowe AR, Sloan T, Mace EM.
cellPLATO: an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data.
bioRxiv [Preprint]. 2023 Nov 5:2023.10.28.564355. doi: 10.1101/2023.10.28.564355. PMID: 37961659; PMCID: PMC10634992.
Seo S, Patil SL, Ahn YO, Armetta J, Hegewisch-Solloa E, Castillo M, Guilz NC, Patel A, Corneo B, Borowiak M, Gunaratne P, Mace EM.
iPSC-based modeling of helicase deficiency reveals impaired cell proliferation and increased apoptosis after NK cell lineage commitment.
bioRxiv [Preprint]. 2023 Sep 25:2023.09.25.559149. doi: 10.1101/2023.09.25.559149. PMID: 37808662; PMCID: PMC10557596.
Zhang J, Xie J, Huang J, Liu X, Xu R, Tholen J, Galej WP, Tong L, Manley JL, Liu Z.
Characterization of the SF3B1-SUGP1 interface reveals how numerous cancer mutations cause mRNA missplicing.
Genes Dev. 2023 Dec 26;37(21-24):968-983. doi: 10.1101/gad.351154.123. PMID: 37977822.
Lydeard JR, Lin MI, Ge HG, Halfond A, Wang S, Jones MB, Etchin J, Angelini G, Xavier-Ferrucio J, Lisle J, Salvadore K, Keschner Y, Mager H, Scherer J, Hu J, Mukherjee S, Chakraborty T.
Development of a gene edited next-generation hematopoietic cell transplant to enable acute myeloid leukemia treatment by solving off-tumor toxicity.
Mol Ther Methods Clin Dev. 2023 Oct 13;31:101135. doi: 10.1016/j.omtm.2023.101135. Erratum in: Mol Ther Methods Clin Dev. 2023 Nov 30;31:101167. PMID: 38027064; PMCID: PMC10643325.
Looney M, Conrad C, Magnen M, Tsui J, Wismer H, Naser M, Venkataramani U, Samad B, Cleary S, Qiu L, Tian J, De Giovanni M, Mende N, Passegue E, Laurenti E, Combes A.
Functional haematopoietic progenitor cells in the adult human lung.
Res Sq [Preprint]. 2023 Nov 28:rs.3.rs-3576483. doi: 10.21203/rs.3.rs-3576483/v1. PMID: 38077002; PMCID: PMC10705601.
LaMarche NM, Hegde S, Park MD, Maier BB, Troncoso L, Le Berichel J, Hamon P, Belabed M, Mattiuz R, Hennequin C, Chin T, Reid AM, Reyes-Torres I, Nemeth E, Zhang R, Olson OC, Doroshow DB, Rohs NC, Gomez JE, Veluswamy R, Hall N, Venturini N, Ginhoux F, Liu Z, Buckup M, Figueiredo I, Roudko V, Miyake K, Karasuyama H, Gonzalez-Kozlova E, Gnjatic S, Passegué E, Kim-Schulze S, Brown BD, Hirsch FR, Kim BS, Marron TU, Merad M.
An IL-4 signalling axis in bone marrow drives pro-tumorigenic myelopoiesis.
Nature. 2023 Dec 6. doi: 10.1038/s41586-023-06797-9. Epub ahead of print. PMID: 38057662.
Su J, Reynier JB, Fu X, Zhong G, Jiang J, Escalante RS, Wang Y, Aparicio L, Izar B, Knowles DA, Rabadan R. Smoother:
a unified and modular framework for incorporating structural dependency in spatial omics data.
Genome Biol. 2023 Dec 18;24(1):291. doi: 10.1186/s13059-023-03138-x. PMID: 38110959; PMCID: PMC10726548.
Postler TS, Wang A, Brundu FG, Wang P, Wu Z, Butler KE, Grinberg-Bleyer Y, Krishnareddy S, Lagana SM, Saqi A, Oeckinghaus A, Rabadan R, Ghosh S.
A pan-cancer analysis implicates human NKIRAS1 as a tumor-suppressor gene.
Proc Natl Acad Sci U S A. 2023 Nov 14;120(46):e2312595120. doi: 10.1073/pnas.2312595120. Epub 2023 Nov 6. PMID: 37931099; PMCID: PMC10655574.
Rajbhandari N, Hamilton M, Quintero CM, Ferguson LP, Fox R, Schürch CM, Wang J, Nakamura M, Lytle NK, McDermott M, Diaz E, Pettit H, Kritzik M, Han H, Cridebring D, Wen KW, Tsai S, Goggins MG, Lowy AM, Wechsler-Reya RJ, Von Hoff DD, Newman AM, Reya T.
Single-cell mapping identifies MSI+ cells as a common origin for diverse subtypes of pancreatic cancer.
Cancer Cell. 2023 Nov 13;41(11):1989-2005.e9. doi: 10.1016/j.ccell.2023.09.008. Epub 2023 Oct 5. PMID: 37802055.
Bae SY, Chen Y, Chen H, Kumar D, Karaiskos S, Xu J, Lu C, Viny AD, Giancotti FG.
Noncanonical Activity of Med4 as a Gatekeeper of Metastasis through Epigenetic Control of Integrin Signaling.
bioRxiv [Preprint]. 2023 Nov 19:2023.11.18.566087. doi: 10.1101/2023.11.18.566087. PMID: 38014033; PMCID: PMC10680920.
Li Y, Shah RB, Sarti S, Belcher AL, Lee BJ, Gorbatenko A, Nemati F, Yu H, Stanley Z, Rahman M, Shao Z, Silva JM, Zha S, Sidi S.
A noncanonical IRAK4-IRAK1 pathway counters DNA damage-induced apoptosis independently of TLR/IL-1R signaling.
Sci Signal. 2023 Dec 19;16(816):eadh3449. doi: 10.1126/scisignal.adh3449. Epub 2023 Dec 19. PMID: 38113335.
Wu-Baer F, Wong M, Tschoe L, Lin CS, Jiang W, Zha S, Baer R.
ATM/ATR Phosphorylation of CtIP on Its Conserved Sae2-like Domain Is Required for Genotoxin-Induced DNA Resection but Dispensable for Animal Development.
Cells. 2023 Dec 4;12(23):2762. doi: 10.3390/cells12232762. PMID: 38067190; PMCID: PMC10706839.
------------------------------------------------------------------------------------------------------------
Other Events
IICD Seminar Series: Fabian Theis, Helmholtz Munich
January 10th- 2:00 to 3:00 PM
IICD welcomes Fabian Theis, PhD, Director of the Computational Health Center, Director of the Institute for Computational Biology, Helmholtz Munich, Technical University of Munich. Seminar hosted by Elham Azizi, PhD. The seminar will take place virtually. If you wish to attend the seminar, please register using the following link: https://columbiauniversity.zoom.us/meeting/register/tJUtdOisqTMpHdddW9wtLHsLyAbe7wX3daTW
Title: Generative AI for Modeling Single-Cell State and Response
HICCC Cancer Cell Metabolism and Institute of Human Nutrition Joint Seminar
Wednesday, January 10, 2024
Thales Papagiannakopoulos, PhD
Associate Professor, Department of Pathology at NYU
Grossman School of Medicine
Title: Dissecting tumorigenesis in genetic subsets of lung cancer
Monthly Columbia Trainee Community Cancer Research Conference
Thursday, January 11, 2024 | 4:00 PM - 5:00 PM
CSCI Work-in-Progress Presentation
Thursday, January 11, 2024 | 11:30 AM - 12:30 PM
Hammer Health Sciences Room 401
Jane Xu (Viny Lab): “
Title: Stag2 loss remodels Npm1c mutant hematopoietic stem and progenitors”
State of the Science Summit: Leukemia/Lymphoma
January 16th | 6:00 PM to 9:00 PM ET
OncLive® State of the Science Summit™ (SOSS) are in-person meetings designed for academic & community-based physicians and health care professionals that provide education on the science driving updates in cancer management and the associated clinical benefits for patients. SOSS attendees will improve their knowledge of novel treatment approaches and reinforce their confidence in applying state-of-the-art treatment strategies.
Registration for this Summit is complimentary.
Topic:
Treatment of Patients with Myelofibrosis
Emerging Treatment Standards for MDS
Use of BTK Inhibitors in MCL and CLL
Bispecific Antibodies in DLBCL
Live Q&A
HICCC Seminar Series: Research-in-Progress
Wed, January 17, 2024 | 4:00 PM - 5:00 PM
Ricardo Cruz-Acuña, Ph.D.
Assistant Professor of Cancer Engineering
College of Dental Medicine & Herbert Irving Comprehensive Cancer Center
Program: Tumor Biology and Microenvironment Program
Title: The role of matrix stiffness in esophageal cancer: mechanism to translational therapeutics
CSCI Seminar Series | Julie B. Sneddon, PhD
Thursday, January 18, 2024 | 11:30 AM - 12:30 PM
Hammer Health Sciences Room 401
Title: “Harnessing Insights about Human Development to Improve Cell Replacement Therapy for Diabetes”
Dr. Sneddon’s research focuses on the niche in pancreatic development and Type I Diabetes. Her research group employs the tools of stem cell biology, developmental biology, genomics, and tissue engineering. Dr. Sneddon’s laboratory studies the underlying biology of the cellular microenvironment, including the cellular diversity and lineage relationships of the non-epithelial compartment of the pancreas in the context of organogenesis, adult organ function, and disease. The hope is that a deeper understanding of the identity and biology of non-epithelial “niche” cell types within the pancreas will enable a more directed and efficient attempt at replacing lost cell and organ function via regenerative medicine. – Claudia Doege, PhD
HICCC Seminar Series: Interdisciplinary Research
January 31st- 4:00 to 5:00 PM
Elisa Konofagou, PhD
Robert and Margaret Hariri Professor of Biomedical Engineering and Professor of Radiology (Physics),
Julia McGuinness, MD
Assistant Professor of Medicine at the Columbia University Medical Center
Title: Harmonic Motion Imaging for monitoring of chemotherapeutic response and HIFU ablation
Description: Ultrasound has been known to cause effects in tissues for more than a century. Yet, only now are we starting to see the wide range of benefits that it can have to cancer treatment. In this talk, I will first discuss the different effects that ultrasound waves can cause in cancerous tissues. I will then introduce the therapeutic effects that focused ultrasound can have in the treatment of breast cancer as a noninvasive ablative therapy. Finally, I will describe the reversible effects that ultrasound in conjunction with microbubbles can have on brain tumors and especially pediatric glioma for the enhancement of local drug delivery and efficacy.
Via Zoom Meeting ID: 999 0430 6839 PW: seminar