NEXGEM Lab

Research

We are witnessing the beginning of a new generation of medicine. The unprecedented amount of large-scale next-generation sequencing data from patients with cancer and other diseases makes data science and artificial intelligence (AI) play a pivotal role in biomedical research. The pressing question is how to best translate the accumulated data into a more effective practice of medicine. This question forms the cornerstone of our research articles.

Highlighted

Synthetic lethality-mediated precision oncology via the tumor transcriptome
Synthetic lethality-mediated precision oncology via the tumor transcriptome
Joo Sang Lee, Nishanth Ulhas Nair, Gal Dinstag, Lesley Chapman, Youngmin Chung, ..., Mark R. Gilbert, Razelle Kurzrock, Se-Hoon Lee, Kenneth Aldape, Eytan Ruppin
Cell   ·   01 Apr 2021   ·   doi:10.1016/j.cell.2021.03.030
synthetic lethality cancer therapy precision medicine

All

2024

Accurate Spatial Gene Expression Prediction by integrating Multi-resolution features
Accurate Spatial Gene Expression Prediction by integrating Multi-resolution features
Youngmin Chung, Ji Hun Ha, Kyeong Chan Im, Joo Sang Lee
arXiv   ·   26 Apr 2024   ·   arxiv:2403.07592
A systematic analysis of the landscape of synthetic lethality-driven precision oncology
A systematic analysis of the landscape of synthetic lethality-driven precision oncology
Alejandro A. Schäffer, Youngmin Chung, Ashwin V. Kammula, Eytan Ruppin, Joo Sang Lee
Med   ·   01 Jan 2024   ·   doi:10.1016/j.medj.2023.12.009

2023

Increased interleukin-6/C-reactive protein levels are associated with the upregulation of the adenosine pathway and serve as potential markers of therapeutic resistance to immune checkpoint inhibitor-based therapies in non-small cell lung cancer
Increased interleukin-6/C-reactive protein levels are associated with the upregulation of the adenosine pathway and serve as potential markers of therapeutic resistance to immune checkpoint inhibitor-based therapies in non-small cell lung cancer
Abdul Rafeh Naqash, Justin D McCallen, Emma Mi, Sanna Iivanainen, Mona A Marie, ..., Se-Hoon Lee, Li V Yang, David J Pinato, Joo Sang Lee, Alessio Cortellini
Journal for ImmunoTherapy of Cancer   ·   01 Oct 2023   ·   doi:10.1136/jitc-2023-007310

2022

AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer
AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer
Ashish Noronha, Nishanth Belugali Nataraj, Joo Sang Lee, Benny Zhitomirsky, Yaara Oren, ..., Joan S. Brugge, Aviv Regev, Gad Getz, Eytan Ruppin, Yosef Yarden
Cancer Discovery   ·   27 Jul 2022   ·   doi:10.1158/2159-8290.CD-22-0111
Nucleoporin-93 reveals a common feature of aggressive breast cancers: robust nucleocytoplasmic transport of transcription factors
Nucleoporin-93 reveals a common feature of aggressive breast cancers: robust nucleocytoplasmic transport of transcription factors
Nishanth Belugali Nataraj, Ashish Noronha, Joo Sang Lee, Soma Ghosh, Harsha Raj Mohan Raju, ..., Aaron Ciechanover, Igor Ulitsky, Rony Seger, Eytan Ruppin, Yosef Yarden
Cell Reports   ·   01 Feb 2022   ·   doi:10.1016/j.celrep.2022.110418
Deconvolving Clinically Relevant Cellular Immune Cross-talk from Bulk Gene Expression Using CODEFACS and LIRICS Stratifies Patients with Melanoma to Anti–PD-1 Therapy
Deconvolving Clinically Relevant Cellular Immune Cross-talk from Bulk Gene Expression Using CODEFACS and LIRICS Stratifies Patients with Melanoma to Anti–PD-1 Therapy
Kun Wang, Sushant Patkar, Joo Sang Lee, E. Michael Gertz, Welles Robinson, Fiorella Schischlik, David R. Crawford, Alejandro A. Schäffer, Eytan Ruppin
Cancer Discovery   ·   04 Jan 2022   ·   doi:10.1158/2159-8290.CD-21-0887

2021

A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing
A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing
Sanju Sinha, Karina Barbosa, Kuoyuan Cheng, Mark D. M. Leiserson, Prashant Jain, ..., Ji Luo, Ze’ev A. Ronai, Joo Sang Lee, Aniruddha J. Deshpande, Eytan Ruppin
Nature Communications   ·   11 Nov 2021   ·   doi:10.1038/s41467-021-26788-6
Synthetic lethality-mediated precision oncology via the tumor transcriptome
Synthetic lethality-mediated precision oncology via the tumor transcriptome
Joo Sang Lee, Nishanth Ulhas Nair, Gal Dinstag, Lesley Chapman, Youngmin Chung, ..., Mark R. Gilbert, Razelle Kurzrock, Se-Hoon Lee, Kenneth Aldape, Eytan Ruppin
Cell   ·   01 Apr 2021   ·   doi:10.1016/j.cell.2021.03.030
synthetic lethality cancer therapy precision medicine
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma
Man Hsin Hung, Joo Sang Lee, Chi Ma, Laurence P. Diggs, Sophia Heinrich, ..., Jittiporn Chaisaingmongkol, Mathuros Ruchirawat, Eytan Ruppin, Tim F. Greten, Xin Wei Wang
Nature Communications   ·   05 Mar 2021   ·   doi:10.1038/s41467-021-21804-1

2020

Targeting purine synthesis in ASS1-expressing tumors enhances the response to immune checkpoint inhibitors
Targeting purine synthesis in ASS1-expressing tumors enhances the response to immune checkpoint inhibitors
Rom Keshet, Joo Sang Lee, Lital Adler, Muhammed Iraqi, Yarden Ariav, ..., Nir Peled, Igor Ulitsky, Angel Porgador, Eytan Ruppin, Ayelet Erez
Nature Cancer   ·   31 Aug 2020   ·   doi:10.1038/s43018-020-0106-7
Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma
Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma
Shelly Kalaora, Joo Sang Lee, Eilon Barnea, Ronen Levy, Polina Greenberg, ..., Michal Lotem, Yishai Levin, Arie Admon, Eytan Ruppin, Yardena Samuels
Nature Communications   ·   14 Feb 2020   ·   doi:10.1038/s41467-020-14639-9

2019

Translational reprogramming marks adaptation to asparagine restriction in cancer
Translational reprogramming marks adaptation to asparagine restriction in cancer
Gaurav Pathria, Joo Sang Lee, Erez Hasnis, Kristofferson Tandoc, David A. Scott, ..., Lionel Larue, Avinash D. Sahu, Ivan Topisirovic, Eytan Ruppin, Ze’ev A. Ronai
Nature Cell Biology   ·   18 Nov 2019   ·   doi:10.1038/s41556-019-0415-1
Multiomics Prediction of Response Rates to Therapies to Inhibit Programmed Cell Death 1 and Programmed Cell Death 1 Ligand 1
Multiomics Prediction of Response Rates to Therapies to Inhibit Programmed Cell Death 1 and Programmed Cell Death 1 Ligand 1
Joo Sang Lee, Eytan Ruppin
JAMA Oncology   ·   01 Nov 2019   ·   doi:10.1001/jamaoncol.2019.2311
A Platform of Synthetic Lethal Gene Interaction Networks Reveals that the GNAQ Uveal Melanoma Oncogene Controls the Hippo Pathway through FAK
A Platform of Synthetic Lethal Gene Interaction Networks Reveals that the GNAQ Uveal Melanoma Oncogene Controls the Hippo Pathway through FAK
Xiaodong Feng, Nadia Arang, Damiano Cosimo Rigiracciolo, Joo Sang Lee, Huwate Yeerna, ..., David D. Schlaepfer, Pablo Tamayo, Qianming Chen, Eytan Ruppin, J. Silvio Gutkind
Cancer Cell   ·   01 Mar 2019   ·   doi:10.1016/j.ccell.2019.01.009

2018

Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures
Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures
Joo Sang Lee, Lital Adler, Hiren Karathia, Narin Carmel, Shiran Rabinovich, ..., Arkaitz Carracedo, Yardena Samuels, Sridhar Hannenhalli, Eytan Ruppin, Ayelet Erez
Cell   ·   01 Sep 2018   ·   doi:10.1016/j.cell.2018.07.019
Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma
Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma
Noam Auslander, Gao Zhang, Joo Sang Lee, Dennie T. Frederick, Benchun Miao, ..., Ryan J. Sullivan, Genevieve Boland, Keith Flaherty, Meenhard Herlyn, Eytan Ruppin
Nature Medicine   ·   20 Aug 2018   ·   doi:10.1038/s41591-018-0157-9
Harnessing synthetic lethality to predict the response to cancer treatment
Harnessing synthetic lethality to predict the response to cancer treatment
Joo Sang Lee, Avinash Das, Livnat Jerby-Arnon, Rand Arafeh, Noam Auslander, ..., Eyal Gottlieb, Cyril H. Benes, Yardena Samuels, Emma Shanks, Eytan Ruppin
Nature Communications   ·   29 Jun 2018   ·   doi:10.1038/s41467-018-04647-1