Ling Cai Lab

Welcome to the Dr. Ling Cai Lab!

Research Interests

Bioinformatics, data integration

Cancer metabolism

Inborn errors of metabolism

Lung neoplasm

Latest Publications

A complete publication list can be found here.

MORE PUBLICATIONS

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.
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.

publisher's website

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

publisher's website

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

Cai L, DeBerardinis RJ, Xiao G, Minna JD, Xie Y.
iScience. 2023 Jun 16;26(6):106983. doi: 10.1016/j.isci.2023.106983. eCollection 2023 Jun 16. PubMed PMID: 37378310; PubMed Central PMCID: PMC10291506.

publisher's website

Research Interests

Development of bioinformatics methodology, database, and web tools

My work is primarily focused on the development of computational methods and user-friendly informatics tools to exploit publicly available cancer datasets. Examples from previous work includes the creation of a web portal for co-expression analysis with denoised gene expression data, the establishment of a comprehensive lung cancer patient database housing clinical and gene expression data for over 6,700 patients, the design of a web application to assess functional data consistency for cancer cell lines, and a web tool for co-mutation analysis with AACR Project GENIE data.

Publications

Cai L, Li Q, Du Y, Yun J, Xie Y, DeBerardinis RJ, Xiao G. Genomic regression analysis of coordinated expression. Nat Commun. 2017 Dec 19;8(1):2187. doi: 10.1038/s41467-017-02181-0. PubMed PMID: 29259170; PubMed Central PMCID: PMC5736603.

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. LCE: an open web portal to explore gene expression and clinical associations in lung cancer. Oncogene. 2019 Apr;38(14):2551-2564. doi: 10.1038/s41388-018-0588-2. Epub 2018 Dec 7. PubMed PMID: 30532070; PubMed Central PMCID: PMC6477796.

Cai L, Liu H, Minna JD, DeBerardinis RJ, Xiao G, Xie Y#. Assessing Consistency Across Functional Screening Datasets in Cancer Cells. Bioinformatics. 2021 Jun 3;. doi: 10.1093/bioinformatics/btab423. [Epub ahead of print] PubMed PMID: 34081116; PubMed Central PMCID: PMC8652113. #, co-corresponding author

Cai L, DeBerardinis RJ, Xiao G, Minna JD, Xie Y#. A Pan-Cancer Assessment of RB1/TP53 Co-Mutations. Cancers (Basel). 2022 Aug 30;14(17). doi: 10.3390/cancers14174199. PubMed PMID: 36077736; PubMed Central PMCID: PMC9454436. #, co-corresponding author
Small cell lung cancer (SCLC) research

In collaboration with Dr. Adi Gazdaar, we studied the molecular changes during the neuroendocrine (NE) transdifferentiation of classic SCLC to variant SCLC. We discovered that cell-autonomous immune gene repression is released during this transition, a pattern also seen in pulmonary neuroendocrine cells. To facilitate further exploration, I’ve developed the SCLC Neuroendocrine Transdifferentiation Explorer, a web application that enables users to investigate transcriptomic changes associated with NE transdifferentiation in patient and preclinical model SCLC and neuroblastoma datasets. Additionally, I’ve drawn parallels between SCLC and neuroblastoma, another NE neoplasm, identifying numerous similarities in the molecular and functional changes associated with NE transdifferentiation. Lastly, I’ve devised a generalized method to compute NE scores, opening avenues for investigating NE transdifferentiation across a wider range of cancer types.

Publications

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. #, co-corresponding author

Cai L, DeBerardinis RJ, Xie Y, Minna JD, Xiao G. A comparative study of neuroendocrine heterogeneity in SCLC and NBL. Mol Cancer Res. 2023 May 12;MCR-23-0002. doi: 10.1158/1541-7786.MCR-23-0002 #, co-corresponding author

Cai L, DeBerardinis RJ, Xiao G, Minna JD, Xie Y. Dissecting Molecular, Pathological, and Clinical Features Associated with Tumor Neural/Neuroendocrine Heterogeneity. iScience. 2023 May 28;26(6):106983. doi: 10.1016/j.isci.2023.106983. eCollection 2023 Jun 16. #, co-corresponding author

Cai L, Sondhi V, Zhu M, Akbay E, DeBerardinis RJ, Xie Y, Minna JD, Xiao G, Gazdar A. The small cell lung cancer neuroendocrine transdifferentiation explorer. bioRxiv. [Preprint]. August 01, 2022 [cited 2023 Jan 19]. Available from: https://doi.org/10.1101/2022.08.01.502252 #, co-corresponding author
Non-small cell lung cancer (NSCLC) research

In my research, I have effectively utilized my expertise in Non-Small Cell Lung Cancer (NSCLC) data mining to generate valuable insights across multiple projects. I have developed the Lung Cancer Explorer database, a comprehensive resource that has enabled me to conduct systematic analyses investigating the relationship between tumor and normal gene expression differences and their associations with prognosis. A notable outcome of this work was the identification of KYNU as a functionally significant prognostic factor in KEAP1/STK11 co-mutated lung adenocarcinoma, discovered through a meta-analysis of bimodally-distributed prognostic genes. Furthermore, my expertise has been instrumental in supporting numerous lung cancer research collaborators in their respective projects, demonstrating the broad applicability and impact of my work.

Publications

Cai L, Luo D, Yao B, Yang DM, Lin S, Girard L, DeBerardinis RJ, Minna JD, Xie Y, Xiao G. Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of FAM83A and FAM83B. Cancers (Basel). 2019 Jun 25;11(6). doi: 10.3390/cancers11060886. PubMed PMID: 31242643; PubMed Central PMCID: PMC6627508.

Cai L, Rogers T, Li H, Kim J, Xie Y, Xiao G, Minna JD, DeBerardinis RJ. KYNU expression is a prognostic factor in KEAP1/STK11 co-mutated lung adenocarcinoma. [Conference Proceeding] American Association for Cancer Research Annual Meeting; 2021 April 11.

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.

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.
Analysis of metabolic profiling data in cancer and inborn errors of metabolism

Through a long-term collaboration with Dr. Ralph DeBerardinis, an expert in cancer metabolism research, I have developed expertise in processing and integrative analysis of data from metabolic profiling (such as metabolomics and metabolic tracing experiments). I have applied these skills to characterize the molecular mechanism of metabolic reprogramming in lung cancer. My colleagues and I investigate the association between metabolic phenotypes and orthogonal datasets that include mutations, gene expression, protein expression, therapeutic sensitivity, and imaging data. Many critical findings have been experimentally validated and mechanistically studied.

Publications

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. Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells. Mol 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. *, co-first author

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.

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

Publications

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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

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.

Opportunities

Bioinformatics Postdoc

A postdoctoral fellow position in bioinformatics is now available in the laboratories of Dr. Ling Cai at the Quantitative Biomedical Research Center in the Peter O’Donnell School of Public Health and Dr. Ralph DeBerardinis at Children’s Research Institute at UT Southwestern Medical Center at UT Southwestern Medical Center at Dallas, to study cancer and metabolism with computational approaches.

The training activities for this position will focus on advancing key aspects of our funded research, including the harmonization and integration of large-scale molecular datasets, pathology image analysis, and spatial transcriptomics. Candidates will gain expertise in the development and application of novel bioinformatics tools and workflows tailored for cross-model comparisons and fidelity assessments between preclinical models and human tumors. This position offers the opportunity to lead projects involving integrative analysis of metabolomics and multi-omics data, particularly in the context of lung cancer and genetic diseases.

We are seeking highly motivated individuals with exceptional analytical and problem-solving skills. The postdoc will play a pivotal role in analyzing high-dimensional datasets, developing computational pipelines, and contributing to the construction of a comprehensive web-based platform for lung cancer research. Additionally, the candidate will support the development of data-driven approaches to study tumor microenvironment heterogeneity and its metabolic implications, thereby addressing critical gaps in preclinical model fidelity and translational research.

Candidates with a Ph.D. in biostatistics, epidemiology, computational biology, bioinformatics, or biology with advanced data analysis skills are encouraged to apply.

Information on our postdoctoral training program, benefits, and a virtual tour can be found HERE.

Interested individuals should send a CV, statement of interests, and a list of three references to:

Ling Cai
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Dallas, TX 75390-8821
Ling.Cai@UTSouthwestern.edu
Cai Lab
Ralph DeBerardinis Lab

About PI

Ling Cai

Assistant Professor, Quantitative Biomedical Research Center, UT Southwestern Medical Center

Ling.Cai@UTSouthwestern.edu

5323 Harry Hines Blvd. Dallas, TX 75390

Download CV

Biography

Dr. Ling Cai is an Assistant Professor in the Peter O’Donnell School of Public Health, the Children’s Research Institute, and a member of the Quantitative Biomedical Research Center (QBRC) and the Harold C. Simmons Cancer Center at UT Southwestern Medical Center (UTSW).

During her Ph.D. training in the Mechanism of Disease Track of the Integrative Biology Graduate Program at UTSW, she received comprehensive training in basic science, with a particular focus on cellular metabolism and disease mechanisms. This foundation has been instrumental in her research on understanding the intricate molecular mechanisms and metabolic pathways implicated in cancer development and progression. Her postdoctoral work focused on the integrated analysis of high-dimensional datasets from cancer metabolism research and developed various bioinformatics tools and databases for lung cancer research.

In her role as an Assistant Professor, Dr. Cai continues to delve into cancer metabolism and inborn errors of metabolism. Her research endeavors are centered around understanding the complex nature of tumors and the role of metabolic pathways in cancer and metabolic diseases. She is also actively involved in the creation and upkeep of data management and analysis systems specifically designed for lung cancer research.

Positions and Scientific Appointments

present 2022

Assistant Professor
Peter O’Donnell Jr. School of Public Health, Children’s Research Institute, UT Southwestern Medical Center
2022 2019

Assistant Professor
Department of Population and Data Sciences, Children’s Research Institute, UT Southwestern Medical Center
2019 2016

Data Scientist
Children’s Research Institute, Quantitative Biomedical Research Center, UT Southwestern Medical Center
2016 2014

Postdoctoral Fellow
Children’s Research Institute, Quantitative Biomedical Research Center, UT Southwestern Medical Center
2014 2013

Research associate
Children’s Research Institute, Quantitative Biomedical Research Center, UT Southwestern Medical Center
2013 2008

Graduate student
Integrative Biology Program, Mechanisms of Disease and Translational Science (MoDTS) Graduate Track, UT Southwestern Medical Center

Education

2016 2014

Post-doc, Bioinformatics, Cancer Metabolism
UT Southwestern Medical Center, USA
2013 2008

Ph.D., Integrative Biology, Mechanism of Disease
UT Southwestern Medical Center, USA
2005 2008

B.Sc., Biochemistry
The Hong Kong University of Science and Technology, Hong Kong

Honors

2021

Career Enhancement Program (CEP) award for the Lung Cancer SPORE development program
2015

American Association for Cancer Research Basic Research Fellowship
2010

Sara and Frank McKnight Fellowship
2008

Academic Achievement Medal of the Hong Kong University of Science and Technology
2008

Chiap Hua Cheng's Foundation Scholarship

Ling Cai Lab

Research Interests

Latest Publications

Comprehensive isotopomer analysis of glutamate and aspartate in small tissue samples

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

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

Research Interests

Development of bioinformatics methodology, database, and web tools

Small cell lung cancer (SCLC) research

Non-small cell lung cancer (NSCLC) research

Analysis of metabolic profiling data in cancer and inborn errors of metabolism

Publications

Members

Jeanette Burns

Bo Yao

Ying Gao

Opportunities

About PI

Ling Cai

Biography

Positions and Scientific Appointments

Education

Honors