Ling Cai Lab

Research Interests

Development of Bioinformatics Methods, Databases, and Web Tools

Our lab develops scalable and user-friendly computational tools to support research. We build informatics platforms that enable researchers to navigate, analyze, and interpret complex omics datasets across human and preclinical models.

Projects and tools include:

• Lung Cancer Autochthonous Model Gene Expression Database (LCAMGDB): A web app for transcriptomic data from over 1,300 samples across > 50 labs, enabling cross-model comparisons.

- https://lccl.shinyapps.io/LCAMGDB/
- Cai et al., Cancer Res 2025 (PMID: 40298430)

• Lung Cancer Explorer (LCE): An open web portal for survival and co-expression analysis across > 6,700 lung cancer patients in 56 studies.

- https://lce.biohpc.swmed.edu/
- Cai et al., Oncogene 2019 (PMID: 30532070)
- Cai et al., Cancers 2019 (PMID: 31242643)

• Functional Data Consistency Explorer (FDCE): A web app evaluating consistency across drug and CRISPR/RNAi screens.

- https://lccl.shinyapps.io/FDCE/
- Cai et al., Oncogene 2019 (PMID: 30532070)
- Cai et al., Cancers 2019 (PMID: 31242643)

• CoMut: A co-mutation analysis tool using AACR Project GENIE pan-cancer patient data.

- http://lccl.shinyapps.io/comut/
- Cai et al., Cancers 2022 (PMID: 36077736)

• NEcalc: A web tool for developing a generalized neuroendocrine (NE) score for classifying tumors with NE features.

- https://lccl.shinyapps.io/NEcalc/
- Cai et al., iScience 2023 (PMID: 37378310)

• Genomic Regression Analysis of Co-Expression (GRACE): A web app facilitating co-expression analysis using denoised TCGA RNA-seq data (adjusted for DNA copy number).

- https://grace.biohpc.swmed.edu/
- Cai et al., Nat Commun 2017 (PMID: 29259170)

• Gazdar Neuroendocrine Transdifferentiation Explorer (GSNE): A web tool for small cell lung cancer and neuroblastoma transcriptomic comparisons in patient and preclinical model datasets.

- https://lccl.shinyapps.io/GSNE/
- Cai et al. (https://doi.org/10.1101/2022.08.01.502252)

Under development (feedback and data contribution welcomed):

• Lung Cancer Cell Line Explorer (LCCL): A web tool to explorer multi-omics lung cancer cell line data.

- https://lccl.shinyapps.io/LCCL/

• Lung Model Pathology Viewer (LUMP): An access-controlled pathology image archive of in vivo lung cancer preclinical model pathology images.

- https://datacommons.swmed.edu/cce/lump_viewer
Cancer Metabolism and Multi-Omics Integration

We investigates metabolic heterogeneity and genotype-specific programs in cancer and rare disease. In collaboration with the DeBerardinis lab(https://cri.utsw.edu/faculty/ralph-deberardinis/), we integrate metabolomics, isotope tracing, transcriptomics, and imaging to uncover key metabolic dependencies, identify biomarkers of tumor aggressiveness, and support translational tool development.

Selected publication:

Lung Cancer

• Cai L, Hammond NG, Tasdogan A, Alsamraae M, Yang C, Cameron RB, Quan P, Solmonson A, Gu W, Pachnis P, Kaur M, Chang BK, Zhou Q, Hensley CT, Do QN, Martins Nascentes Melo L, Ubellacker JM, Kaushik A, Clare MG, Alcazar IN, Kurylowicz K, Marcuccilli JD, Allies G, Kutritz A, Klode J, Ramesh V, Rogers TJ, Rao AD, Crentsil HE, Li H, Brister F, McDaniel P, Xu X, Evers BM, Zacharias LG, Sudderth J, Xu J, Mathews TP, Oliver D, Minna JD, Waters J, Morrison SJ, Kernstine KH, Faubert B, DeBerardinis RJ. High Glucose Contribution to the TCA Cycle Is a Feature of Aggressive Non-Small Cell Lung Cancer in Patients. Cancer Discov. 2025 Apr 2;15(4):702-716. doi: 10.1158/2159-8290.CD-23-1319. PubMed PMID: 39960461; PubMed Central PMCID: PMC11962397.

• Huang F, Huffman KE, Wang Z, Wang X, Li K, Cai F, Yang C, Cai L, Shih TS, Zacharias LG, Chung A, Yang Q, Chalishazar MD, Ireland AS, Stewart CA, Cargill K, Girard L, Liu Y, Ni M, Xu J, Wu X, Zhu H, Drapkin B, Byers LA, Oliver TG, Gazdar AF, Minna JD, DeBerardinis RJ. Guanosine triphosphate links MYC-dependent metabolic and ribosome programs in small-cell lung cancer. J Clin Invest. 2021 Jan 4;131(1). doi: 10.1172/JCI139929. PubMed PMID: 33079728; PubMed Central PMCID: PMC7773395.

• Kim J, Lee HM, Cai F, Ko B, Yang C, Lieu EL, Muhammad N, Rhyne S, Li K, Haloul M, Gu W, Faubert B, Kaushik AK, Cai L, Kasiri S, Marriam U, Nham K, Girard L, Wang H, Sun X, Kim J, Minna JD, Unsal-Kacmaz K, DeBerardinis RJ. The hexosamine biosynthesis pathway is a targetable liability in KRAS/LKB1 mutant lung cancer. Nat Metab. 2020 Dec;2(12):1401-1412. doi: 10.1038/s42255-020-00316-0. Epub 2020 Nov 30. PubMed PMID: 33257855; PubMed Central PMCID: PMC7744327.

• Faubert B, Li KY, Cai L, Hensley CT, Kim J, Zacharias LG, Yang C, Do QN, Doucette S, Burguete D, Li H, Huet G, Yuan Q, Wigal T, Butt Y, Ni M, Torrealba J, Oliver D, Lenkinski RE, Malloy CR, Wachsmann JW, Young JD, Kernstine K, DeBerardinis RJ. Lactate Metabolism in Human Lung Tumors. Cell. 2017 Oct 5;171(2):358-371.e9. doi: 10.1016/j.cell.2017.09.019. PubMed PMID: 28985563; PubMed Central PMCID: PMC5684706.

• Kim J, Hu Z, Cai L, Li K, Choi E, Faubert B, Bezwada D, Rodriguez-Canales J, Villalobos P, Lin YF, Ni M, Huffman KE, Girard L, Byers LA, Unsal-Kacmaz K, Peña CG, Heymach JV, Wauters E, Vansteenkiste J, Castrillon DH, Chen BPC, Wistuba I, Lambrechts D, Xu J, Minna JD, DeBerardinis RJ. CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells. Nature. 2017 Jun 1;546(7656):168-172. doi: 10.1038/nature22359. Epub 2017 May 24. PubMed PMID: 28538732; PubMed Central PMCID: PMC5472349.

Kidney Cancer

• Bezwada D, Perelli L, Lesner NP, Cai L, Brooks B, Wu Z, Vu HS, Sondhi V, Cassidy DL, Kasitinon S, Kelekar S, Cai F, Aurora AB, Patrick M, Leach A, Ghandour R, Zhang Y, Do D, McDaniel P, Sudderth J, Dumesnil D, House S, Rosales T, Poole AM, Lotan Y, Woldu S, Bagrodia A, Meng X, Cadeddu JA, Mishra P, Garcia-Bermudez J, Pedrosa I, Kapur P, Courtney KD, Malloy CR, Genovese G, Margulis V, DeBerardinis RJ. Mitochondrial complex I promotes kidney cancer metastasis. Nature. 2024 Sep;633(8031):923-931. doi: 10.1038/s41586-024-07812-3. Epub 2024 Aug 14. PubMed PMID: 39143213; PubMed Central PMCID: PMC11424252.

• Zhang Y, Udayakumar D, Cai L, Hu Z, Kapur P, Kho EY, Pavía-Jiménez A, Fulkerson M, de Leon AD, Yuan Q, Dimitrov IE, Yokoo T, Ye J, Mitsche MA, Kim H, McDonald JG, Xi Y, Madhuranthakam AJ, Dwivedi DK, Lenkinski RE, Cadeddu JA, Margulis V, Brugarolas J, DeBerardinis RJ, Pedrosa I. Addressing metabolic heterogeneity in clear cell renal cell carcinoma with quantitative Dixon MRI. JCI Insight. 2017 Aug 3;2(15). doi: 10.1172/jci.insight.94278. eCollection 2017 Aug 3. PubMed PMID: 28768909; PubMed Central PMCID: PMC5543910.

Tool Development

• Cai L, Vu HS, Gu W, Chen H, Franklin J, Haidar LA, Wu Z, Pan C, Cai F, Nguyen P, Ko B, Yang C, Zacharias LG, Sudderth J, Montgomery S, Uhles C, Fisher H, Hudnall J, Hornbuckle C, Quinn C, Michel D, Umaña L, Scheuerle A, McNutt MC, Gotway GK, Afroze B, Ni M, DeBerardinis R. An interactive web application for exploring human plasma and fibroblast metabolomics data from patients with inborn errors of metabolism. bioRxiv. 2023 Dec 12;. doi: 10.1101/2023.12.11.571124. PubMed PMID: 38168314; PubMed Central PMCID: PMC10760037.

• Cai F, Bezwada D, Cai L, Mahar R, Wu Z, Chang MC, Pachnis P, Yang C, Kelekar S, Gu W, Brooks B, Ko B, Vu HS, Mathews TP, Zacharias LG, Martin-Sandoval M, Do D, Oaxaca KC, Jin ES, Margulis V, Malloy CR, Merritt ME, DeBerardinis RJ. Comprehensive isotopomer analysis of glutamate and aspartate in small tissue samples. Cell Metab. 2023 Oct 3;35(10):1830-1843.e5. doi: 10.1016/j.cmet.2023.07.013. Epub 2023 Aug 22. PubMed PMID: 37611583; PubMed Central PMCID: PMC10732579.
Small Cell Lung Cancer (SCLC) and Neuroendocrine Plasticity

In collaboration with SCLC investigators, we explored neuroendocrine (NE) transdifferentiation and its implications for immune evasion and molecular reclassification. Our work revealed parallels between SCLC and neuroblastoma, informed NE scoring systems, and helped reclassify YAP1⁺ SCLC lines as SMARCA4-deficient malignancies.

Selected publication:

• Cai L, Liu H, Huang F, Fujimoto J, Girard L, Chen J, Li Y, Zhang YA, Deb D, Stastny V, Pozo K, Kuo CS, Jia G, Yang C, Zou W, Alomar A, Huffman K, Papari-Zareei M, Yang L, Drapkin B, Akbay EA, Shames DS, Wistuba II, Wang T, Johnson JE, Xiao G, DeBerardinis RJ, Minna JD, Xie Y, Gazdar AF. Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. Commun Biol. 2021 Mar 9;4(1):314. doi: 10.1038/s42003-021-01842-7. PubMed PMID: 33750914; PubMed Central PMCID: PMC7943563.

• Cai L, DeBerardinis RJ, Xie Y, Minna JD, Xiao G. A Comparative Study of Neuroendocrine Heterogeneity in Small Cell Lung Cancer and Neuroblastoma. Mol Cancer Res. 2023 Aug 1;21(8):795-807. doi: 10.1158/1541-7786.MCR-23-0002. PubMed PMID: 37255415; PubMed Central PMCID: PMC10390888.

• Ng J, Cai L, Girard L, Prall OWJ, Rajan N, Khoo C, Batrouney A, Byrne DJ, Boyd DK, Kersbergen AJ, Christie M, Minna JD, Burr ML, Sutherland KD. Molecular and Pathologic Characterization of YAP1-Expressing Small Cell Lung Cancer Cell Lines Leads to Reclassification as SMARCA4-Deficient Malignancies. Clin Cancer Res. 2024 May 1;30(9):1846-1858. doi: 10.1158/1078-0432.CCR-23-2360. PubMed PMID: 38180245; PubMed Central PMCID: PMC11061608.
Non-Small Cell Lung Cancer (NSCLC) Data Mining

We have leveraged public and institutional NSCLC datasets to generate integrative analyses and provide insights for collaborating investigators.

Selected publication:

• Cai L, Xiao G, Gerber D, D Minna J, Xie Y. Lung Cancer Computational Biology and Resources. Cold Spring Harb Perspect Med. 2022 Feb 1;12(2). doi: 10.1101/cshperspect.a038273. Review. PubMed PMID: 34751162; PubMed Central PMCID: PMC8805643.

• Chiang JC, Shang Z, Rosales T, Cai L, Chen WM, Cai F, Vu H, Minna JD, Ni M, Davis AJ, Timmerman RD, DeBerardinis RJ, Zhang Y. Lipoylation inhibition enhances radiation control of lung cancer by suppressing homologous recombination DNA damage repair. Sci Adv. 2025 Mar 14;11(11):eadt1241. doi: 10.1126/sciadv.adt1241. Epub 2025 Mar 12. PubMed PMID: 40073141; PubMed Central PMCID: PMC11900879.

• Lee HM, Muhammad N, Lieu EL, Cai F, Mu J, Ha YS, Cao G, Suchors C, Joves K, Chronis C, Li K, Ducker GS, Olszewski K, Cai L, Allison DB, Bachert SE, Ewing WR, Wong H, Seo H, Kim IY, Faubert B, Kim J, Kim J. Concurrent loss of LKB1 and KEAP1 enhances SHMT-mediated antioxidant defence in KRAS-mutant lung cancer. Nat Metab. 2024 Jul;6(7):1310-1328. doi: 10.1038/s42255-024-01066-z. Epub 2024 Jun 14. PubMed PMID: 38877143; PubMed Central PMCID: PMC11809267.

• Park JV, Chandra R, Cai L, Ganguly D, Li H, Toombs JE, Girard L, Brekken RA, Minna JD. Tumor Cells Modulate Macrophage Phenotype in a Novel In Vitro Co-Culture Model of the NSCLC Tumor Microenvironment. J Thorac Oncol. 2022 Oct;17(10):1178-1191. doi: 10.1016/j.jtho.2022.06.011. Epub 2022 Jul 5. PubMed PMID: 35798240; PubMed Central PMCID: PMC9529910.

• Wang S, Rong R, Yang DM, Fujimoto J, Bishop JA, Yan S, Cai L, Behrens C, Berry LD, Wilhelm C, Aisner D, Sholl L, Johnson BE, Kwiatkowski DJ, Wistuba II, Bunn PA Jr, Minna J, Xiao G, Kris MG, Xie Y. Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer. J Clin Invest. 2023 Jan 17;133(2). doi: 10.1172/JCI160330. PubMed PMID: 36647832; PubMed Central PMCID: PMC9843059.

• Ci B, Yang DM, Cai L, Yang L, Girard L, Fujimoto J, Wistuba II, Xie Y, Minna JD, Travis W, Xiao G. Molecular differences across invasive lung adenocarcinoma morphological subgroups. Transl Lung Cancer Res. 2020 Aug;9(4):1029-1040. doi: 10.21037/tlcr-19-321. PubMed PMID: 32953482; PubMed Central PMCID: PMC7481608.

• Wang S, Chen A, Yang L, Cai L, Xie Y, Fujimoto J, Gazdar A, Xiao G. Comprehensive analysis of lung cancer pathology images to discover tumor shape and boundary features that predict survival outcome. Sci Rep. 2018 Jul 10;8(1):10393. doi: 10.1038/s41598-018-27707-4. PubMed PMID: 29991684; PubMed Central PMCID: PMC6039531.

Publications

Filter by year:

The Lung Cancer Autochthonous Model Gene Expression Database Enables Cross-Study Comparisons of the Transcriptomic Landscapes Across Mouse Models

Ling Cai, Fangjiang Wu, Qinbo Zhou, Ying Gao, Bo Yao, Ralph J. DeBerardinis, George K. Acquaah-Mensah, Vassilis Aidinis, Jennifer E. Beane, Shyam Biswal, Ting Chen, Carla P. Concepcion-Crisol, Barbara M. Grüner, Deshui Jia, Robert A. Jones, Jonathan M. Kurie, Min Gyu Lee, Per Lindahl, Yonathan Lissanu, Corina Lorz, David MacPherson, Rosanna Martinelli, Pawel K. Mazur, Sarah A. Mazzilli, Shinji Mii, Herwig P. Moll, Roger A. Moorehead, Edward E. Morrisey, Sheng Rong Ng, Matthew G. Oser, Arun R. Pandiri, Charles A. Powell, Giorgio Ramadori, Mirentxu Santos, Eric L. Snyder, Rocio Sotillo, Kang-Yi Su, Tetsuro Taki, Kekoa Taparra, Phuoc T. Tran, Yifeng Xia, J. Edward van Veen, Monte M. Winslow, Guanghua Xiao, Charles M. Rudin, Trudy G. Oliver, Yang Xie, John D. Minna

Apr. 2025Cancer Research, OF1-OF15

High Glucose Contribution to the TCA Cycle Is a Feature of Aggressive Non–Small Cell Lung Cancer in Patients

Ling Cai, Nia G Hammond, Alpaslan Tasdogan, Massar Alsamraae, Chendong Yang, Robert B Cameron, Peiran Quan, Ashley Solmonson, Wen Gu, Panayotis Pachnis, Mayher Kaur, Brianna K Chang, Qin Zhou, Christopher T Hensley, Quyen N Do, Luiza Martins Nascentes Melo, Jessalyn M Ubellacker, Akash Kaushik, Maia G Clare, Isabel N Alcazar, Katarzyna Kurylowicz, Joseph D Marcuccilli, Gabriele Allies, Andrea Kutritz, Joachim Klode, Vijayashree Ramesh, Thomas J Rogers, Aparna D Rao, Hannah E Crentsil, Hong Li, Fang Brister, Phyllis McDaniel, Xiaohong Xu, Bret M Evers, Lauren G Zacharias, Jessica Sudderth, Jian Xu, Thomas P Mathews, Dwight Oliver, John D Minna, John Waters, Sean J Morrison, Kemp H Kernstine, Brandon Faubert, Ralph J DeBerardinis

Apr. 2025Cancer discovery 15 (4), 702-716

Lipoylation inhibition enhances radiation control of lung cancer by suppressing homologous recombination DNA damage repair

Jui-Chung Chiang, Zengfu Shang, Tracy Rosales, Ling Cai, Wei-Min Chen, Feng Cai, Hieu Vu, John D Minna, Min Ni, Anthony J Davis, Robert D Timmerman, Ralph J DeBerardinis, Yuanyuan Zhang

Mar. 2025Science Advances 11 (11), eadt1241

Metabolic profiles of cutaneous lupus have abnormalities in the nicotinamide adenine dinucleotide pathway

Laila F Abbas, Grant Barber, Grace Lu, Bahir Chamseddin, Hieu Vu, Ling Cai, Divya Srivastava, Rajiv L Nijhawan, Richard C Wang, Benjamin F Chong

Jan. 2025Lupus Science & Medicine 12 (1)

Navigating electronic health record accuracy by examination of sex incongruent conditions

L Cai, RJ DeBerardinis, X Zhan, G Xiao, Y Xie

Dec. 2024Journal of the American Medical Informatics Association 31 (12), 2849-2856

Mitochondrial complex I promotes kidney cancer metastasis

Bezwada, D., Perelli, L., Lesner, N.P., Cai, L. et al.

Sep. 2024Nature 633, 923–931 (2024). https://doi.org/10.1038/s41586-024-07812-3

Navigating electronic health record accuracy by examination of sex incongruent conditions

Ling Cai, Ralph J DeBerardinis, Xiaowei Zhan, Guanghua Xiao, Yang Xie

Sep. 2024Journal of the American Medical Informatics Association, 2024;, ocae236, https://doi.org/10.1093/jamia/ocae236

Evaluation of the clinical, biochemical, and molecular spectrum of Cobalamin C (CblC) defect in 33 patients from Pakistan

Sibtain Ahmed, Ling Cai, Fizza Akbar, Ayra Siddiqui, Ralph J DeBerardinis, Min Ni, Hieu Vu, Bushra Afroze

Aug. 2024Scandinavian Journal of Clinical and Laboratory Investigation, 84(6), 391–397.

635 Intraoperative 13C-glucose tracing and metabolomics of patient melanoma tumors reveal metabolic features associated with aggressive melanomas

JG Gill, A Rao, R Walsdorf, M Snyman, S Wix, A Brown, G Gard, J Kim, J Santos Patricio, L Zacharias, A Solmonson, B Tillman, R Sharma, T Vandergriff, T Mathews, L Cai, R DeBerardinis

Aug. 2024Journal of Investigative Dermatology, 144(8), S110.

Concurrent loss of LKB1 and KEAP1 enhances SHMT-mediated antioxidant defence in KRAS-mutant lung cancer

Lee, H.M., Muhammad, N., Lieu, E.L. et al.

June 2024Nat Metab 6, 1310–1328 (2024).

Electron transport chain inhibition increases cellular dependence on purine transport and salvage

Zheng Wu, Divya Bezwada, Feng Cai, Robert C Harris, Bookyung Ko, Varun Sondhi, Chunxiao Pan, Hieu S Vu, Phong T Nguyen, Brandon Faubert, Ling Cai, Hongli Chen, Misty Martin-Sandoval, Duyen Do, Wen Gu, Yuanyuan Zhang, Yuannyu Zhang, Bailey Brooks, Sherwin Kelekar, Lauren G Zacharias, K Celeste Oaxaca, Joao S Patricio, Thomas P Mathews, Javier Garcia-Bermudez, Min Ni, Ralph J DeBerardinis

June 2024Cell Metabolism, Volume 36, Issue 7, 1504 - 1520.e9

Molecular and pathologic characterization of YAP1-expressing small cell lung cancer cell lines leads to reclassification as SMARCA4-deficient malignancies

Jin Ng, Ling Cai, Luc Girard, Owen W.J. Prall, Neeha Rajan, Christine Khoo, Ahida Batrouney, David J. Byrne, Danielle K. Boyd, Ariena J. Kersbergen, Michael Christie, John D. Minna, Marian L. Burr, Kate D. Sutherland

May 2024Clin Cancer Res 1 May 2024; 30 (9): 1846–1858.

Induced degradation of lineage-specific oncoproteins drives the therapeutic vulnerability of small cell lung cancer to PARP inhibitors

Chiho Kim, Xu-Dong Wang, Zhengshuai Liu, Jianwei Hao, Shuai Wang, Peng Li, Zhenzhen Zi, Qing Ding, Seoyeon Jang, Jiwoong Kim, Yikai Luo, Kenneth E Huffman, Shreoshi Pal Choudhuri, Sofia Del Rio, Ling Cai, Han Liang, Benjamin J Drapkin, John D Minna, Yonghao Yu

Jan. 2024Sci. Adv.10,eadh2579(2024).

EP07. 01-16 The Relationship of FDG PET-SUVm and Glucose Metabolism and Contribution to Early-Stage Non-Small Cell Lung Cancer Survival

K Kernstine, BM Faubert, QN Do, TJ Rogers, CT Hensley, L Cai, JR Torrealba, DH Oliver, A Kandathil, RE Lenkinski, CR Malloy, JK Waters, SI Reznik, ME Jessen, RJ Deberardinis

Nov. 2023Journal of Thoracic Oncology, Volume 18, Issue 11, S514 - S515

Comprehensive isotopomer analysis of glutamate and aspartate in small tissue samples

Cai F, Bezwada D, Cai L, Mahar R, Wu Z, Chang MC, Pachnis P, Yang C, Kelekar S, Gu W, Brooks B, Ko B, Vu HS, Mathews TP, Zacharias LG, Martin-Sandoval M, Do D, Oaxaca KC, Jin ES, Margulis V, Malloy CR, Merritt ME, DeBerardinis RJ.

Oct. 2023Cell Metab. 2023 Oct 3;35(10):1830-1843.e5. doi: 10.1016/j.cmet.2023.07.013. Epub 2023 Aug 22. PubMed PMID: 37611583.

Silencing of GRHL2 induces epithelial‑to‑mesenchymal transition in lung cancer cell lines with different effects on proliferation and clonogenic growth

Kawabe N, Matsuoka K, Komeda K, Muraki N, Takaba M, Togami Y, Ito Y, Yamada M, Sunaga N, Girard L, Minna JD, Cai L, Xie Y, Tanaka I, Morise M, Sato M.

Sep. 2023Oncol Lett. 2023 Sep;26(3):391. doi: 10.3892/ol.2023.13977. eCollection 2023 Sep. PubMed PMID: 37600329; PubMed Central PMCID: PMC10433723.

Dissecting molecular, pathological, and clinical features associated with tumor neural/neuroendocrine heterogeneity

Cai L, DeBerardinis RJ, Xiao G, Minna JD, Xie Y.

Jun. 2023iScience. 2023 Jun 16;26(6):106983. doi: 10.1016/j.isci.2023.106983. eCollection 2023 Jun 16. PubMed PMID: 37378310; PubMed Central PMCID: PMC10291506.

A comparative study of neuroendocrine heterogeneity in small cell lung cancer and neuroblastoma

Cai L, DeBerardinis RJ, Xie Y, Minna JD, Xiao G.

May. 2023Mol Cancer Res. 2023 May 12;. doi: 10.1158/1541-7786.MCR-23-0002. [Epub ahead of print] PubMed PMID: 37171983.

Electron transport chain inhibition increases cellular dependence on purine transport and salvage

Wu Z, Bezwada D, Harris RC, Pan C, Nguyen PT, Faubert B, Cai L, Cai F, Vu HS, Chen H, Sandoval MM, Do D, Gu W, Zhang Y, Ko B, Brooks B, Kelekar S, Zhang Y, Zacharias LG, Oaxaca KC, Mathews TP, Garcia-Bermudez J, Ni M, DeBerardinis RJ.

May. 2023bioRxiv. 2023 May 11;. doi: 10.1101/2023.05.11.540429. PubMed PMID: 37214913; PubMed Central PMCID: PMC10197673.

Mitochondrial metabolism in primary and metastatic human kidney cancers

Bezwada D, Lesner NP, Brooks B, Vu HS, Wu Z, Cai L, Kasitinon S, Kelekar S, Cai F, Aurora AB, Patrick M, Leach A, Ghandour R, Zhang Y, Do D, Sudderth J, Dumesnil D, House S, Rosales T, Poole AM, Lotan Y, Woldu S, Bagrodia A, Meng X, Cadeddu JA, Mishra P, Pedrosa I, Kapur P, Courtney KD, Malloy CR, Margulis V, DeBerardinis RJ.

Feb. 2023bioRxiv. 2023 Feb 7;. doi: 10.1101/2023.02.06.527285. PubMed PMID: 36798172; PubMed Central PMCID: PMC9934542.

Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer

Wang S, Rong R, Yang DM, Fujimoto J, Bishop JA, Yan S, Cai L, Behrens C, Berry LD, Wilhelm C, Aisner D, Sholl L, Johnson BE, Kwiatkowski DJ, Wistuba II, Bunn PA Jr, Minna J, Xiao G, Kris MG, Xie Y.

Jan. 2023J Clin Invest. 2023 Jan 17;133(2). doi: 10.1172/JCI160330. PubMed PMID: 36647832; PubMed Central PMCID: PMC9843059.

Tumor Cells Modulate Macrophage Phenotype in a Novel In Vitro Co-Culture Model of the NSCLC Tumor Microenvironment

Park JV, Chandra R, Cai L, Ganguly D, Li H, Toombs JE, Girard L, Brekken RA, Minna JD.

Oct. 2022J Thorac Oncol. 2022 Oct;17(10):1178-1191. doi: 10.1016/j.jtho.2022.06.011. Epub 2022 Jul 5. PubMed PMID: 35798240; PubMed Central PMCID: PMC9529910.

A Pan-Cancer Assessment of RB1/ TP53 Co-Mutations

Cai L, DeBerardinis RJ, Xiao G, Minna JD, Xie Y.

Aug. 2022Cancers (Basel). 2022 Aug 30;14(17). doi: 10.3390/cancers14174199. PubMed PMID: 36077736; PubMed Central PMCID: PMC9454436.

Compartmentalized metabolism supports midgestation mammalian development

Solmonson A, Faubert B, Gu W, Rao A, Cowdin MA, Menendez-Montes I, Kelekar S, Rogers TJ, Pan C, Guevara G, Tarangelo A, Zacharias LG, Martin-Sandoval MS, Do D, Pachnis P, Dumesnil D, Mathews TP, Tasdogan A, Pham A, Cai L, Zhao Z, Ni M, Cleaver O, Sadek HA, Morrison SJ, DeBerardinis RJ.

Apr. 202Nature. 2022 Apr;604(7905):349-353. doi: 10.1038/s41586-022-04557-9. Epub 2022 Apr 6. PubMed PMID: 35388219; PubMed Central PMCID: PMC9007737.

Lung Cancer Computational Biology and Resources

Cai L, Xiao G, Gerber D, D Minna J, Xie Y.

Feb. 2022Cold Spring Harb Perspect Med. 2022 Feb 1;12(2). doi: 10.1101/cshperspect.a038273. Review. PubMed PMID: 34751162; PubMed Central PMCID: PMC8805643.

Assessing consistency across functional screening datasets in cancer cells

Cai L, Liu H, Minna JD, DeBerardinis RJ, Xiao G, Xie Y.

Dec. 2021Bioinformatics. 2021 Dec 7;37(23):4540-4547. doi: 10.1093/bioinformatics/btab423. PubMed PMID: 34081116; PubMed Central PMCID: PMC8652113.

Modular gene analysis reveals distinct molecular signatures for subsets of patients with cutaneous lupus erythematosus

Zhu JL, Tran LT, Smith M, Zheng F, Cai L, James JA, Guthridge JM, Chong BF.

Sep. 2021Br J Dermatol. 2021 Sep;185(3):563-572. doi: 10.1111/bjd.19800. Epub 2021 Mar 3. PubMed PMID: 33400293; PubMed Central PMCID: PMC8255330.

Metabolic impact of pathogenic variants in the mitochondrial glutamyl-tRNA synthetase EARS2

Ni M, Black LF, Pan C, Vu H, Pei J, Ko B, Cai L, Solmonson A, Yang C, Nugent KM, Grishin NV, Xing C, Roeder E, DeBerardinis RJ.

Jul. 2021J Inherit Metab Dis. 2021 Jul;44(4):949-960. doi: 10.1002/jimd.12387. Epub 2021 Apr 27. PubMed PMID: 33855712; PubMed Central PMCID: PMC9219168.

A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental anomalies and epilepsy

Ni M, Afroze B, Xing C, Pan C, Shao Y, Cai L, Cantarel BL, Pei J, Grishin NV, Hewson S, Knight D, Mahida S, Michel D, Tarnopolsky M, Poduri A, Rotenberg A, Sondheimer N, DeBerardinis RJ.

May. 2021Genet Med. 2021 May;23(5):900-908. doi: 10.1038/s41436-020-01071-z. Epub 2021 Jan 20. PubMed PMID: 33473208; PubMed Central PMCID: PMC8105169.

Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer

Cai L, Liu H, Huang F, Fujimoto J, Girard L, Chen J, Li Y, Zhang YA, Deb D, Stastny V, Pozo K, Kuo CS, Jia G, Yang C, Zou W, Alomar A, Huffman K, Papari-Zareei M, Yang L, Drapkin B, Akbay EA, Shames DS, Wistuba II, Wang T, Johnson JE, Xiao G, DeBerardinis RJ, Minna JD, Xie Y, Gazdar AF.

Mar. 2021Commun Biol. 2021 Mar 9;4(1):314. doi: 10.1038/s42003-021-01842-7. PubMed PMID: 33750914; PubMed Central PMCID: PMC7943563.

Guanosine triphosphate links MYC-dependent metabolic and ribosome programs in small-cell lung cancer

Huang F, Huffman KE, Wang Z, Wang X, Li K, Cai F, Yang C, Cai L, Shih TS, Zacharias LG, Chung A, Yang Q, Chalishazar MD, Ireland AS, Stewart CA, Cargill K, Girard L, Liu Y, Ni M, Xu J, Wu X, Zhu H, Drapkin B, Byers LA, Oliver TG, Gazdar AF, Minna JD, DeBerardinis RJ.

Jan. 2021J Clin Invest. 2021 Jan 4;131(1). doi: 10.1172/JCI139929. PubMed PMID: 33079728; PubMed Central PMCID: PMC7773395.

KYNU expression is a prognostic factor in KEAP1/STK11 co-mutated lung adenocarcinoma

Cai L, Rogers T, Li H, Kim J, Xie Y, Xiao G, Minna JD, DeBerardinis RJ.

Apr. 2021American Association for Cancer Research Annual Meeting; 2021 April 11.

The hexosamine biosynthesis pathway is a targetable liability in KRAS/LKB1 mutant lung cancer

Kim J, Lee HM, Cai F, Ko B, Yang C, Lieu EL, Muhammad N, Rhyne S, Li K, Haloul M, Gu W, Faubert B, Kaushik AK, Cai L, Kasiri S, Marriam U, Nham K, Girard L, Wang H, Sun X, Kim J, Minna JD, Unsal-Kacmaz K, DeBerardinis RJ.

Nov. 2020Nat Metab. 2020 Dec;2(12):1401-1412. doi: 10.1038/s42255-020-00316-0. Epub 2020 Nov 30. PubMed PMID: 33257855; PubMed Central PMCID: PMC7744327.

Molecular differences across invasive lung adenocarcinoma morphological subgroups

Ci B, Yang DM, Cai L, Yang L, Girard L, Fujimoto J, Wistuba II, Xie Y, Minna JD, Travis W, Xiao G.

Aug. 2020Transl Lung Cancer Res. 2020 Aug;9(4):1029-1040. doi: 10.21037/tlcr-19-321. PubMed PMID: 32953482; PubMed Central PMCID: PMC7481608.

Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer

Wang S, Rong R, Yang DM, Fujimoto J, Yan S, Cai L, Yang L, Luo D, Behrens C, Parra ER, Yao B, Xu L, Wang T, Zhan X, Wistuba II, Minna J, Xie Y, Xiao G.

May. 2020Cancer Res. 2020 May 15;80(10):2056-2066. doi: 10.1158/0008-5472.CAN-19-1629. Epub 2020 Jan 8. PubMed PMID: 31915129; PubMed Central PMCID: PMC7919065.

Does Tumor FDG-PET Avidity Represent Enhanced Glycolytic Metabolism in Non-Small Cell Lung Cancer?

Kernstine KH, Faubert B, Do QN, Rogers TJ, Hensley CT, Cai L, Torrealba J, Oliver D, Wachsmann JW, Lenkinski RE, Malloy CR, Deberardinis RJ.

Apr. 2020Ann Thorac Surg. 2020 Apr;109(4):1019-1025. doi: 10.1016/j.athoracsur.2019.10.061. Epub 2019 Dec 14. PubMed PMID: 31846640; PubMed Central PMCID: PMC7370816.

Dysfunctional adaptive immune response in adolescents and young adults with suicide behavior

Jha MK, Cai L, Minhajuddin A, Fatt CC, Furman JL, Gadad BS, Mason BL, Greer TL, Hughes JL, Xiao G, Emslie G, Kennard B, Mayes T, Trivedi MH.

Jan. 2020Psychoneuroendocrinology. 2020 Jan;111:104487. doi: 10.1016/j.psyneuen.2019.104487. Epub 2019 Oct 25. PubMed PMID: 31756521.

Chen PH, Cai L, Huffman K, Yang C, Kim J, Faubert B, Boroughs L, Ko B, Sudderth J, McMillan EA, Girard L, Chen D, Peyton M, Shields MD, Yao B, Shames DS, Kim HS, Timmons B, Sekine I, Britt R, Weber S, Byers LA, Heymach JV, Chen J, White MA, Minna JD, Xiao G, DeBerardinis RJ.

Dec. 2019Mol Cell. 2019 Dec 5;76(5):838-851.e5. doi: 10.1016/j.molcel.2019.08.028. Epub 2019 Sep 26. PubMed PMID: 31564558; PubMed Central PMCID: PMC6898782.

Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of FAM83A and FAM83B

Cai L, Luo D, Yao B, Yang DM, Lin S, Girard L, DeBerardinis RJ, Minna JD, Xie Y, Xiao G.

Jun. 2019Cancers (Basel). 2019 Jun 25;11(6). doi: 10.3390/cancers11060886. PubMed PMID: 31242643; PubMed Central PMCID: PMC6627508.

Functional Assessment of Lipoyltransferase-1 Deficiency in Cells, Mice, and Humans

Ni M, Solmonson A, Pan C, Yang C, Li D, Notzon A, Cai L, Guevara G, Zacharias LG, Faubert B, Vu HS, Jiang L, Ko B, Morales NM, Pei J, Vale G, Rakheja D, Grishin NV, McDonald JG, Gotway GK, McNutt MC, Pascual JM, DeBerardinis RJ.

Apr. 2019Cell Rep. 2019 Apr 30;27(5):1376-1386.e6. doi: 10.1016/j.celrep.2019.04.005. PubMed PMID: 31042466; PubMed Central PMCID: PMC7351313.

LCE: an open web portal to explore gene expression and clinical associations in lung cancer

Cai L, Lin S, Girard L, Zhou Y, Yang L, Ci B, Zhou Q, Luo D, Yao B, Tang H, Allen J, Huffman K, Gazdar A, Heymach J, Wistuba I, Xiao G, Minna J, Xie Y.

Apr. 2019Oncogene. 2019 Apr;38(14):2551-2564. doi: 10.1038/s41388-018-0588-2. Epub 2018 Dec 7. PubMed PMID: 30532070; PubMed Central PMCID: PMC6477796.

ACSS2 promotes systemic fat storage and utilization through selective regulation of genes involved in lipid metabolism

Huang Z, Zhang M, Plec AA, Estill SJ, Cai L, Repa JJ, McKnight SL, Tu BP.

Oct. 2018Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):E9499-E9506. doi: 10.1073/pnas.1806635115. Epub 2018 Sep 18. PubMed PMID: 30228117; PubMed Central PMCID: PMC6176566.

Inosine Monophosphate Dehydrogenase Dependence in a Subset of Small Cell Lung Cancers

Huang F, Ni M, Chalishazar MD, Huffman KE, Kim J, Cai L, Shi X, Cai F, Zacharias LG, Ireland AS, Li K, Gu W, Kaushik AK, Liu X, Gazdar AF, Oliver TG, Minna JD, Hu Z, DeBerardinis RJ.

Sep. 2018Cell Metab. 2018 Sep 4;28(3):369-382.e5. doi: 10.1016/j.cmet.2018.06.005. Epub 2018 Jun 28. PubMed PMID: 30043754; PubMed Central PMCID: PMC6125205.

Comprehensive analysis of lung cancer pathology images to discover tumor shape and boundary features that predict survival outcome

Wang S, Chen A, Yang L, Cai L, Xie Y, Fujimoto J, Gazdar A, Xiao G.

Jul. 2018Sci Rep. 2018 Jul 10;8(1):10393. doi: 10.1038/s41598-018-27707-4. PubMed PMID: 29991684; PubMed Central PMCID: PMC6039531.

TNF-driven adaptive response mediates resistance to EGFR inhibition in lung cancer

Gong K, Guo G, Gerber DE, Gao B, Peyton M, Huang C, Minna JD, Hatanpaa KJ, Kernstine K, Cai L, Xie Y, Zhu H, Fattah FJ, Zhang S, Takahashi M, Mukherjee B, Burma S, Dowell J, Dao K, Papadimitrakopoulou VA, Olivas V, Bivona TG, Zhao D, Habib AA.

Jun. 2018J Clin Invest. 2018 Jun 1;128(6):2500-2518. doi: 10.1172/JCI96148. Epub 2018 May 7. PubMed PMID: 29613856; PubMed Central PMCID: PMC5983340.

A two-stage approach of gene network analysis for high-dimensional heterogeneous data

Lee S, Liang F, Cai L, Xiao G.

Apr. 2018Biostatistics. 2018 Apr 1;19(2):216-232. doi: 10.1093/biostatistics/kxx033. PubMed PMID: 29036516; PubMed Central PMCID: PMC5862270.

Genomic regression analysis of coordinated expression

Cai L, Li Q, Du Y, Yun J, Xie Y, DeBerardinis RJ, Xiao G.

Dec. 2017Nat Commun. 2017 Dec 19;8(1):2187. doi: 10.1038/s41467-017-02181-0. PubMed PMID: 29259170; PubMed Central PMCID: PMC5736603.

Lactate Metabolism in Human Lung Tumors

Faubert B, Li KY, Cai L, Hensley CT, Kim J, Zacharias LG, Yang C, Do QN, Doucette S, Burguete D, Li H, Huet G, Yuan Q, Wigal T, Butt Y, Ni M, Torrealba J, Oliver D, Lenkinski RE, Malloy CR, Wachsmann JW, Young JD, Kernstine K, DeBerardinis RJ.

Oct. 2017Cell. 2017 Oct 5;171(2):358-371.e9. doi: 10.1016/j.cell.2017.09.019. PubMed PMID: 28985563; PubMed Central PMCID: PMC5684706.

Addressing metabolic heterogeneity in clear cell renal cell carcinoma with quantitative Dixon MRI

Zhang Y, Udayakumar D, Cai L, Hu Z, Kapur P, Kho EY, Pavía-Jiménez A, Fulkerson M, de Leon AD, Yuan Q, Dimitrov IE, Yokoo T, Ye J, Mitsche MA, Kim H, McDonald JG, Xi Y, Madhuranthakam AJ, Dwivedi DK, Lenkinski RE, Cadeddu JA, Margulis V, Brugarolas J, DeBerardinis RJ, Pedrosa I.

Aug. 2017JCI Insight. 2017 Aug 3;2(15). doi: 10.1172/jci.insight.94278. eCollection 2017 Aug 3. PubMed PMID: 28768909; PubMed Central PMCID: PMC5543910.

CPS1 maintains pyrimidine pools and DNA synthesis in KRAS/LKB1-mutant lung cancer cells

Kim J, Hu Z, Cai L, Li K, Choi E, Faubert B, Bezwada D, Rodriguez-Canales J, Villalobos P, Lin YF, Ni M, Huffman KE, Girard L, Byers LA, Unsal-Kacmaz K, Peña CG, Heymach JV, Wauters E, Vansteenkiste J, Castrillon DH, Chen BPC, Wistuba I, Lambrechts D, Xu J, Minna JD, DeBerardinis RJ.

Jun. 2017Nature. 2017 Jun 1;546(7656):168-172. doi: 10.1038/nature22359. Epub 2017 May 24. PubMed PMID: 28538732; PubMed Central PMCID: PMC5472349.

Integrative Analysis of Gene Networks and Their Application to Lung Adenocarcinoma Studies

Lee S, Liang F, Cai L, Xiao G.

Feb. 2017Cancer Inform. 2017;16:1176935117690778. doi: 10.1177/1176935117690778. eCollection 2017. PubMed PMID: 28469387; PubMed Central PMCID: PMC5392014.

Dietary control of chromatin

Huang Z, Cai L, Tu BP.

Jun. 2015Curr Opin Cell Biol. 2015 Jun;34:69-74. doi: 10.1016/j.ceb.2015.05.004. Epub 2015 Jun 19. Review. PubMed PMID: 26094239; PubMed Central PMCID: PMC4597913.

Acetate dependence of tumors

Comerford SA, Huang Z, Du X, Wang Y, Cai L, Witkiewicz AK, Walters H, Tantawy MN, Fu A, Manning HC, Horton JD, Hammer RE, McKnight SL, Tu BP.

Dec. 2014Cell. 2014 Dec 18;159(7):1591-602. doi: 10.1016/j.cell.2014.11.020. PubMed PMID: 25525877; PubMed Central PMCID: PMC4272450.

High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

Kuang Z, Cai L, Zhang X, Ji H, Tu BP, Boeke JD.

Oct. 2014Nat Struct Mol Biol. 2014 Oct;21(10):854-63. doi: 10.1038/nsmb.2881. Epub 2014 Aug 31. PubMed PMID: 25173176; PubMed Central PMCID: PMC4190017.

Integration of multiple nutrient cues and regulation of lifespan by ribosomal transcription factor Ifh1

Cai L, McCormick MA, Kennedy BK, Tu BP.

Sep. 2013Cell Rep. 2013 Sep 26;4(6):1063-71. doi: 10.1016/j.celrep.2013.08.016. Epub 2013 Sep 12. PubMed PMID: 24035395; PubMed Central PMCID: PMC3792855.

Analysis of tumor metabolism reveals mitochondrial glucose oxidation in genetically diverse human glioblastomas in the mouse brain in vivo

Marin-Valencia I, Yang C, Mashimo T, Cho S, Baek H, Yang XL, Rajagopalan KN, Maddie M, Vemireddy V, Zhao Z, Cai L, Good L, Tu BP, Hatanpaa KJ, Mickey BE, Matés JM, Pascual JM, Maher EA, Malloy CR, Deberardinis RJ, Bachoo RM.

Jun. 2012Cell Metab. 2012 Jun 6;15(6):827-37. doi: 10.1016/j.cmet.2012.05.001. PubMed PMID: 22682223; PubMed Central PMCID: PMC3372870.

Driving the cell cycle through metabolism

Cai L, Tu BP.

May. 2012Annu Rev Cell Dev Biol. 2012;28:59-87. doi: 10.1146/annurev-cellbio-092910-154010. Epub 2012 May 11. Review. PubMed PMID: 22578140; NIHMSID:NIHMS387911.

Inhibition of pyrimidine synthesis reverses viral virulence factor-mediated block of mRNA nuclear export

Zhang L, Das P, Schmolke M, Manicassamy B, Wang Y, Deng X, Cai L, Tu BP, Forst CV, Roth MG, Levy DE, García-Sastre A, de Brabander J, Phillips MA, Fontoura BM.

Feb. 2012J Cell Biol. 2012 Feb 6;196(3):315-26. doi: 10.1083/jcb.201107058. PubMed PMID: 22312003; PubMed Central PMCID: PMC3275370.

Acetyl-CoA drives the transcriptional growth program in yeast

Cai L, Tu BP.

Sep. 2011Cell Cycle. 2011 Sep 15;10(18):3045-6. doi: 10.4161/cc.10.18.17000. Epub 2011 Sep 15. PubMed PMID: 21869612; PubMed Central PMCID: PMC3218616.

On acetyl-CoA as a gauge of cellular metabolic state

Cai L, Tu BP.

May. 2011Cold Spring Harb Symp Quant Biol. 2011;76:195-202. doi: 10.1101/sqb.2011.76.010769. Epub 2011 Sep 6. Review. PubMed PMID: 21900151; NIHMSID:NIHMS387904.

Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes

Cai L, Sutter BM, Li B, Tu BP.

May. 2011Mol Cell. 2011 May 20;42(4):426-37. doi: 10.1016/j.molcel.2011.05.004. PubMed PMID: 21596309; PubMed Central PMCID: PMC3109073.

Ling Cai Lab

Research Interests

Latest Publications

The Lung Cancer Autochthonous Model Gene Expression Database Enables Cross-Study Comparisons of the Transcriptomic Landscapes Across Mouse Models

High Glucose Contribution to the TCA Cycle Is a Feature of Aggressive Non–Small Cell Lung Cancer in Patients

Lipoylation inhibition enhances radiation control of lung cancer by suppressing homologous recombination DNA damage repair

Research Interests

Development of Bioinformatics Methods, Databases, and Web Tools

Cancer Metabolism and Multi-Omics Integration

Small Cell Lung Cancer (SCLC) and Neuroendocrine Plasticity

Non-Small Cell Lung Cancer (NSCLC) Data Mining

Publications

Members

Jeanette Burns

Bo Yao

Qinbo Zhou

Reza Mousavi Jafarabad

Alumni

Ying Gao

Collaboration

About PI

Ling Cai

Biography

Positions and Scientific Appointments

Education

Honors