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Northwestern University Feinberg School of Medicine
Thomas Lab

Publications

Featured Publications

Learn more about the work we do in the Thomas Laboratory through a curated list of publications.

  1. Schroeder BA, Mohindroo C, Meinhardt AL, Takahashi N, Zhang Y, Lee MJ, Sahoo S, Donahue RN, Kumar R, Nirula M, Yang Y, Rastogi S, Sato N, Lee S, Tsai YT, Zhang S, Kaz S, Hu Y, Desai P, Nichols S, Sciuto L, Pinkiert D, Chrisafis G, Greenberg M, Biery DN, Al-Marayati R, Yang HH, Lee MP, Schultz CW, Meskini RE, Atkinson D, Fousek K, Gulley JL, Schlom J, Sato M, Shrestha RL, Sharma AK, Jolly MK, Palena C, Wakefield LM, Thomas A. Blockade of Tumor-Intrinsic TGF-β Signaling Drives Hyperprogression in Small Cell Lung Cancer. Cancer Discovery. 2026, April 22. doi: 10.1158/2159-8290.CD-25-1454.
  2. Desai P, Takahashi N, Kumar R, Nichols S, Malin J, Hunt A, Schultz C, Cao Y, Tillo D, Nousome D, Chauhan L, Sciuto L, Jordan K, Rajapakse V, Tandon M, Lissa D, Zhang Y, Kumar S, Pongor L, Singh A, Schroder B, Sharma AK, Chang T, Vilimas R, Pinkiert D, Graham C, Butcher D, Warner A, Sebastian R, Mahon M, Baker K, Cheng J, Berger A, Lake R, Abel M, Krishnamurthy M, Chrisafis G, Fitzgerald P, Nirula M, Goyal S, Atkinson D, Bateman NW, Abulez T, Nair G, Apolo A, Guha U, Karim B, El Meskini R, Ohler ZW, Jolly MK, Schaffer A, Ruppin E, Kleiner D, Miettinen M, Brown GT, Hewitt S, Conrads T, Thomas A. Microenvironment Shapes Small-Cell Lung Cancer Neuroendocrine States and Presents Therapeutic Opportunities. Cell Reports Medicine. 2024. doi: 10.1016/j.xcrm.2024.101610.
  3. Krishnamurthy M, Dhall A, Schultz CW, Baird MA, Desai P, Odell J, Sahoo S, Takahashi N, Nirula M, Zhuang S, Huang Y, Schroeder B, Zhang Y, Thomas MS, Redon C, Robinson C, Thang L, Ileva L, Patel NL, Kalen JD, Varlet AA, Zuela-Sopilniak N, Jha A, Wangsa D, Butcher D, Morgan T, Afzal AN, Chari R, Baktiar K, Kumar S, Pongor L, Difilippantonio S, Aladjem MI, Pommier Y, Jolly MK, Lammerding J, Sharma AK, Thomas A. Metastatic Organotropism in Small Cell Lung Cancer. bioRxiv. 2024.
  4. Pongor LS, Schultz CW, Rinaldi L, Wangsa D, Redon CE, Takahashi N, Fialkoff G, Desai P, Zhang Y, Burkett S, Hermoni N, Vilk J, Gutin J, Gergely R, Zhao Y, Nichols S, Vilimas R, Sciuto L, Graham C, Caravaca JM, Turan S, Tsai-Wei S, Rajapakse VN, Kumar R, Upadhyay D, Kumar S, Kim YS, Roper N, Tran B, Hewitt SM, Kleiner DE, Aladjem MI, Friedman N, Hager GL, Pommier Y, Ried T, Thomas A. Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes. Cancer Discovery. 2023,
    Apr 3;13(4):928-949. doi: 10.1158/2159-8290.CD-22-0796.
  5. Roper N, Velez MJ, Chiappori A, Kim YS, Wei JS, Sindiri S, Takahashi N, Mulford D, Kumar S, Ylaya K, Trindade C, Manukyan I, Brown AL, Trepel JB, Lee JM, Hewitt S, Khan J, Thomas A. Notch Signaling and Efficacy of PD-1/PD-L1 Blockade in Relapsed Small Cell Lung Cancer. Nature Communications. 2021, Jun 23;12(1):3880. doi: 10.1038/s41467-021-24164-y.
  6. Thomas A, Takahashi N, Rajapakse VN, Zhang X, Sun Y, Ceribelli M, Wilson KM, Zhang Y, Beck E, Sciuto L, Nichols S, Elenbaas B, Puc J, Dahmen H, Zimmermann A, Varonin J, Schultz CW, Kim S, Shimellis H, Desai P, Klumpp-Thomas C, Chen L, Travers J, McKnight C, Michael S, Itkin Z, Lee S, Yuno A, Lee MJ, Redon CE, Kindrick JD, Peer CJ, Wei JS, Aladjem MI, Figg WD, Steinberg SM, Trepel JB, Zenke FT, Pommier Y, Khan J, Thomas CJ. Therapeutic Targeting of ATR Yields Durable Regressions in Small Cell Lung Cancers with High Replication Stress. Cancer Cell. 2021, Apr 12;39(4):566-579.e7. doi: 10.1016/j.ccell.2021.02.014.

All Recent Publications

  1. Mohindroo C, Takahashi N, Nichols S, Pinkiert D, Thomas A  Phase II Study of Olaparib Plus Durvalumab in EGFR-Mutant NSCLC Transformed to Small Cell Lung Cancer.  Oncologist  2026 Aug 14;. pii:oyag328
  2. Schroeder BA, Mohindroo C, Meinhardt AL, Takahashi N, Zhang Y, Lee MJ, Sahoo S, Donahue RN, Kumar R, Nirula M  et al.  Blockade of Tumor-Intrinsic TGFβ Signaling Drives Hyperprogression in Small Cell Lung Cancer.  Cancer Discov  2026 Aug 03;16(8):1529-1549. doi:10.1158/2159-8290.CD-25-1454
  3. Ghaemi B, Olkowski CP, Basuli F, Shi J, Lang L, Thomas A, Choyke PL, Jacobson O  SEZ6-Targeted PET Imaging and Alpha-Particle Radioimmunotherapy is Effective for Detection and Treatment of Small Cell Lung Cancer.  Cancer Res  2026 Jul 29;. doi:10.1158/0008-5472.CAN-25-5938
  4. Ty S, Haque F, Desai P, Takahashi N, Chaudhary U, Choyke PL, Thomas A, Türkbey B, Harmon SA  Automated detection and characterization of small cell lung cancer liver metastasis on computed tomography.  Diagn Interv Radiol  2026 Jul 01;32(4):382-390. doi:10.4274/dir.2025.253310
  5. Ghafoor A, Zhu L, Weaver Ohler Z, El Meskini R, Ying H, Atkinson D, Day A, Pate N, Bassel L, Wang W  et al.  HDAC inhibition unlocks tumor plasticity and enhances immunotherapy response in Myc-driven small cell lung cancer.  Mol Cancer Ther  2026 May 01;. doi:10.1158/1535-7163.MCT-25-1077
  6. Parmar K, Surolia I, Thomas A  Reframing small cell lung cancer: therapeutic lessons from hematologic malignancies.  Front Oncol  2026;16:1821271. pii:1821271
  7. Vashista S, Meena RK, Kulkarni P, Salgia R, Thomas A, Jolly MK  Bidirectional coupling among EMT, AXL-RB1 signaling and lineage switch drives resistance to osimertinib and worse clinical outcomes in NSCLC.  bioRxiv  2026 Apr 24;. pii:2026.04.21.719547
  8. Li C, Yin J, Abel ML, Vargas Solivan DS, Bhadresha K, Kartal S, Nichols S, Parmar K, Twohig J, Truong TM  et al.  Integrative molecular analyses of lineage identity and morphology in aggressive variant prostate cancer.  NPJ Precis Oncol  2026 Apr 09;10(1). pii:208
  9. Mohindroo C, Thomas A  Incidence, Mortality, and Federal Research Funding by Cancer Type in the US.  JAMA Netw Open  2026 Apr 01;9(4):e267837. pii:e267837
  10. Thomas A, Mohindroo C, Huang Y, Sage J, Massagué J  Metastasis as a Multiorgan Disease: Toward Organ-Informed Precision Oncology.  Cancer Discov  2026 Apr 01;16(4):656-659. doi:10.1158/2159-8290.CD-25-2052
  11. Kirk NA, Ng J, Ly KL, Choi M, Ban YH, Dzhivhuho GA, Jang J, Ko KP, Kareta MS, Park JI  et al.  SMARCA4 Loss Promotes Late-Stage Tumor Progression in Nonneuroendocrine Small Cell Lung Cancer.  Mol Cancer Res  2026 Mar 03;24(3):169-178. doi:10.1158/1541-7786.MCR-25-0592
  12. Waddle SD, Thomas A, Campbell BT, Betz ME, Johnson JK, Royan R, Ellyin A, Jang A, Crandall ML, Stey AM  Exploratory qualitative study of firearm storage practices among surgeons in the USA: contexts and motivations.  Inj Prev  2026 Jan 20;32(1):82-89. doi:10.1136/ip-2023-045205
  13. Li C, Yin J, Abel ML, Solivan DSV, Bhadresha K, Kartal S, Nichols S, Parmar K, Twohig J, Truong TM  et al.  Molecular decoupling of lineage identity and morphology in aggressive variant prostate cancer.  medRxiv  2026 Jan 09;. pii:2026.01.07.26343520
  14. Navarro A, Thomas A, Cheng Y, Chen Y, Reguart N, Yoshida T, Cousin S, Dong X, Yamamoto N, Cappuzzo F  et al.  A phase II, multicenter, open-label, single-arm study of berzosertib plus topotecan in patients with relapsed platinum-resistant small-cell lung cancer (DDRiver SCLC 250).  ESMO Open  2026 Jan;11(1):105918. pii:105918
  15. Liskovykh M, Kochanova NY, Chiang CY, Dhall A, Aksenova V, Chen YC, Reinhold WC, Dasso M, Thomas A, Cheng KC  et al.  A genome-wide RNAi screen for novel CIN genes using human artificial chromosome.  PNAS Nexus  2025 Dec;4(12):pgaf345. pii:pgaf345
  16. Jung H, Lee Y, Yu D, Jeon Y, Kang H, Um D, Seo M, Park D, Kim J, Lee SJ  et al.  Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition.  bioRxiv  2025 Nov 25;. pii:2025.11.23.690049
  17. Ireland AS, Xie DA, Hawgood SB, Barbier MW, Zuo LY, Hanna BE, Lucas-Randolph S, Tyson DR, Witt BL, Govindan R  et al.  Basal cell of origin resolves neuroendocrine-tuft lineage plasticity in cancer.  Nature  2025 Nov;647(8088):257-267. doi:10.1038/s41586-025-09503-z
  18. Schultz CW, Saha S, Dhall A, Zhang Y, Desai P, Pongor LS, Scheiblin DA, Magidson V, Shuklah RP, Sebastian R  et al.  Lamin A/C loss promotes R-loop-mediated genomic instability and poor survival in small-cell lung cancer.  Proc Natl Acad Sci U S A  2025 Oct 28;122(43):e2503387122. pii:e2503387122
  19. Thomas A, Takahashi N, Oplustil O'Connor L, Redon CE, Mohindroo C, Sciuto L, Pongor L, Schmidt KT, Steinberg SM, Aladjem MI  et al.  Tumor-targeted top1 inhibitor delivery with optimized parp inhibition in advanced solid tumors: a phase i trial of gapped scheduling.  Nat Commun  2025 Oct 27;16(1):9457. pii:9457
  20. Mascaux C, Sen T, Sanchez-Cespedes M, Ortiz-Cuaran S, Bossé Y, Dammeijer F, Cavic M, Barr MP, Arulananda S, Armisen R  et al.  Advances in Lung Cancer Basic and Translational Research in 2025 - Overview and Perspectives Focusing on NSCLC.  J Thorac Oncol  2025 Oct;20(10):1369-1391. doi:10.1016/j.jtho.2025.05.024
  21. Fazal A, Harker EJ, Neelam V, Olson SM, Rolfes MA, Reinhart K, Kniss K, Frutos A, Leonard J, Reed C  et al.  Pediatric Influenza-Associated Encephalopathy and Acute Necrotizing Encephalopathy - United States, 2024-25 Influenza Season.  MMWR Morb Mortal Wkly Rep  2025 Sep 25;74(36):556-564. doi:10.15585/mmwr.mm7436a1
  22. van Marcke C, Pogoda K, Fenton H, Vallet M, Plavc G, Borges M, Yousuf H, Dumas E, Berliere M, Ciliberto G  et al.  Association between neoadjuvant paclitaxel dose intensity and outcomes in early triple-negative and HER2-positive breast cancer: a real-world data analysis.  ESMO Real World Data Digit Oncol  2025 Sep;9:100158. pii:100158
  23. Kosaraju NS, Choudhury T, Stoner L, Thomas AL, White KE, Andrews MR, Lawrence BI, Ormiston CK, Mason L, Shiels MS  et al.  Severe housing cost burden and premature cardiovascular mortality.  Am J Prev Cardiol  2025 Sep;23:101021. pii:101021
  24. Simon NI, Kydd AR, Akbulut D, Takeda D, Del Rivero J, Merino M, Redd B, Lindenberg L, Mena E, Chandran E  et al.  Small cell carcinoma of the bladder: Review of pathogenesis, presentation, and management.  Bladder Cancer  2025;11(3):23523735251370956. pii:23523735251370956
  25. Ghafoor A, Zhu L, Ohler ZW, Meskini RE, Atkinson D, Day A, Bassel L, Wang W, Ying H, Calvo KR  et al.  HDAC inhibition unlocks tumor plasticity and enhances immunotherapy response in Myc-Driven Small Cell Lung Cancer.  bioRxiv  2025 Aug 09;. pii:2025.08.06.668958
  26. Rastogi S, Sato N, Lee S, Lee MJ, McKinney Y, Lindenberg L, Mena E, Thomas A, Shrestha RL, Choyke PL  Circulating Tumor Cells Are Detectable and Independent of PSA and PSMA-PET Metrics in Localized High-Risk and Biochemically Recurrent Prostate Cancer.  medRxiv  2025 Jul 15;. pii:2025.07.09.25331014
  27. Waddle SD, Reyes AM, Thomas A, Betz ME, Johnson JK, Royan R, Ellyin A, Jang A, Crandall M, Stey AM  et al.  The intersection between firearm injury prevention and surgical practice: A qualitative study.  J Trauma Acute Care Surg  2025 Jul 01;99(1):79-88. doi:10.1097/TA.0000000000004612
  28. Nemes K, Fűr GM, Benő A, Schultz CW, Topolcsányi P, Magó É, Desai P, Takahashi N, Aladjem MI, Reinhold W  et al.  SurvSig: Harnessing gene expression signatures to uncover heterogeneity in lung neuroendocrine neoplasms.  Comput Struct Biotechnol J  2025;27:2574-2583. doi:10.1016/j.csbj.2025.06.010
  29. Thomas A, Mohindroo C, Giaccone G  Advancing therapeutics in small-cell lung cancer.  Nat Cancer  2025 Jun;6(6):938-953. doi:10.1038/s43018-025-00996-1
  30. Kirk NA, Ng J, Ly KL, Ban YH, Dzhivhuho G, Jang J, Ko KP, Kareta MS, Park JI, Karnezis AN  et al.  SMARCA4 is essential for early-stage tumor development but its loss promotes late-stage cancer progression in small-cell lung cancer.  bioRxiv  2025 May 24;. pii:2025.05.21.655382
  31. Schultz CW, Saha S, Dhall A, Zhang Y, Desai P, Pongor LS, Scheiblin DA, Magidson V, Sun Y, Redon C  et al.  Lamin A/C Deficiency Drives Genomic Instability and Poor Survival in Small-Cell Lung Cancer through Increased R-loop Accumulation.  bioRxiv  2025 May 03;. pii:2025.04.29.651052
  32. Ghoshal D, Petersen I, Ringquist R, Kramer L, Bhatia E, Hu T, Richard A, Park R, Corbin J, Agarwal S  et al.  Multi-niche human bone marrow on-a-chip for studying the interactions of adoptive CAR-T cell therapies with multiple myeloma.  Biomaterials  2025 May;316:123016. doi:10.1016/j.biomaterials.2024.123016
  33. Thomas AL, Kulchar RJ, Stephens ES, Mason L, Jackson SS, Harris AR, Ewing AP, Shiels MS, Pichardo CM, McGee-Avila JK  et al.  County socioeconomic status and premature mortality from cancer in the United States.  Cancer Epidemiol  2025 Apr;95:102747. doi:10.1016/j.canep.2025.102747
  34. Takahashi N, Pongor L, Agrawal SP, Shtumpf M, Gurjar A, Rajapakse VN, Shafiei A, Schultz CW, Kim S, Roame D  et al.  Genomic alterations and transcriptional phenotypes in circulating free DNA and matched metastatic tumor.  Genome Med  2025 Feb 25;17(1):15. pii:15
  35. Zbukvic I, Fisher E, Stainton A, Bryce S, Kartal D, Kunin M, Nicholas J, Hamilton C, Smith D, Murphy M  et al.  Exploring the Implementation of Cognitive Screening in First-Episode Psychosis Settings: The CogScreen Implementation Study.  Early Interv Psychiatry  2025 Feb;19(2):e70004. pii:e70004
  36. Krishnamurthy M, Dhall A, Sahoo S, Schultz CW, Baird MA, Desai P, Odell J, Takahashi N, Nirula M, Zhuang S  et al.  Metastatic organotropism in small cell lung cancer.  bioRxiv  2025 Jan 24;. pii:2024.10.07.617066
  37. Stainton A, Bryce S, Rattray A, Pert A, Zbukvic I, Fisher E, Anderson D, Bowden SC, Chakma S, Cheng N  et al.  Validating cognitive screening in young people with first-episode psychosis: The CogScreen protocol.  Early Interv Psychiatry  2025 Jan;19(1):e13558. pii:e13558
  38. Sabapathypillai S, Miller VJ, Shakoor A, Palestine AG, Thorne JE, Goldstein DA, Gaudio PA, Goldberg N, Vitale A, Schlaen A  et al.  Optic Disc Edema Is an Under-Recognized Feature of Birdshot Chorioretinitis.  J Neuroophthalmol  2024 Dec 01;44(4):545-551. doi:10.1097/WNO.0000000000002085
  39. Dastoor JD, Thomas A, Slocum JD, Regan S, Stone L, Richardson JB, Mason M, Johnson JK, Lin K, Stey A  Investigating the 2016 surge in firearm violence in Illinois, USA, through community-based organisations: a qualitative study.  Inj Prev  2024 Nov 21;30(6):503-508. doi:10.1136/ip-2023-045075
  40. Nasca B, Reddy S, Furmanchuk A, Lundberg A, Kong N, Andrei AC, Theros J, Thomas A, Ingram M, Sanchez J  et al.  Hospital variation in adoption of balanced transfusion practices among injured patients requiring blood transfusions.  Surgery  2024 Oct;176(4):1273-1280. doi:10.1016/j.surg.2024.06.037
  41. Taniguchi H, Chakraborty S, Takahashi N, Banerjee A, Caeser R, Zhan YA, Tischfield SE, Chow A, Nguyen EM, Villalonga ÁQ  et al.  ATR inhibition activates cancer cell cGAS/STING-interferon signaling and promotes antitumor immunity in small-cell lung cancer.  Sci Adv  2024 Sep 27;10(39):eado4618. pii:eado4618
  42. Sonkin D, Thomas A, Teicher BA  Cancer treatments: Past, present, and future.  Cancer Genet  2024 Aug;286-287:18-24. doi:10.1016/j.cancergen.2024.06.002
  43. Desai P, Takahashi N, Kumar R, Nichols S, Malin J, Hunt A, Schultz C, Cao Y, Tillo D, Nousome D  et al.  Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities.  Cell Rep Med  2024 Jun 18;5(6):101610. pii:101610
  44. Takahashi N, Pongor L, Agrawal SP, Shtumpf M, Rajapakse VN, Shafiei A, Schultz CW, Kim S, Roame D, Carter P  et al.  Genomic alterations and transcriptional phenotypes in circulating tumor DNA and matched metastatic tumor.  bioRxiv  2024 Jun 03;. pii:2024.06.02.597054
  45. Hiatt JB, Doebley AL, Arnold HU, Adil M, Sandborg H, Persse TW, Ko M, Wu F, Quintanal Villalonga A, Santana-Davila R  et al.  Molecular phenotyping of small cell lung cancer using targeted cfDNA profiling of transcriptional regulatory regions.  Sci Adv  2024 Apr 12;10(15):eadk2082. pii:eadk2082
  46. Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E  et al.  CDK-independent role of D-type cyclins in regulating DNA mismatch repair.  Mol Cell  2024 Apr 04;84(7):1224-1242.e13. doi:10.1016/j.molcel.2024.02.010
  47. Ormiston CK, Lawrence WR, Sulley S, Shiels MS, Haozous EA, Pichardo CM, Stephens ES, Thomas AL, Adzrago D, Williams DR  et al.  Trends in Adolescent Suicide by Method in the US, 1999-2020.  JAMA Netw Open  2024 Mar 04;7(3):e244427. pii:e244427
  48. Schultz CW, Zhang Y, Elmeskini R, Zimmermann A, Fu H, Murai Y, Wangsa D, Kumar S, Takahashi N, Atkinson D  et al.  Author Correction: ATR inhibition augments the efficacy of lurbinectedin in small-cell lung cancer.  EMBO Mol Med  2024 Mar;16(3):664. doi:10.1038/s44321-024-00029-x
  49. Rona G, Miwatani-Minter B, Zhang Q, Goldberg HV, Kerzhnerman MA, Howard JB, Simoneschi D, Lane E, Hobbs JW, Sassani E  et al.  D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability.  bioRxiv  2024 Jan 13;. pii:2024.01.12.575420
  50. Sharma H, Parekh S, Pujari P, Shewale S, Desai S, Bhatla N, Joshi S, Pimple S, Kawade A, Balasubramani L  et al.  Immunogenicity and safety of a new quadrivalent HPV vaccine in girls and boys aged 9-14 years versus an established quadrivalent HPV vaccine in women aged 15-26 years in India: a randomised, active-controlled, multicentre, phase 2/3 trial.  Lancet Oncol  2023 Dec;24(12):1321-1333. doi:10.1016/S1470-2045(23)00480-1