Laboratory of Raphael Bueno, MD

Overview

Dr. Bueno is a thoracic surgeon and a molecular biologist studying biomarkers and cancer therapeutics. He is the PI of multiple studies that focus on thoracic malignancies, with a specific interest in mesothelioma, lung cancer and esophageal cancer. One focus of his work is the development of biomarkers for diagnosis, prognosis, and treatment in mesothelioma and lung cancer. Since 1998, his team has collected large prospective clinical cohorts linked to consented well-annotated fresh, frozen, and FFPE tumor samples with germ-line DNA, serum, and plasma (over 5,000 cases). Dr. Bueno’s team has developed, optimized, and validated the gene-ratio algorithm and other diagnostic, prognostic, and predictive tests, some of which were commercialized with NCI support. His team has assembled validation sets of specimens internally and through the Alliance for Clinical Trials, which were used to validate commercial lung adenocarcinoma prognostic tests for Myriad, Novartis, and squamous cell carcinoma tests through an NCI-funded U01 mechanism. The second area of Dr. Bueno’s research is the use of next-generation sequencing (NGS) for the identification of therapeutic targets in thoracic cancers. His team was the first to report large-scale sequencing data in mesothelioma. They developed methods to identify and validate potential targets for therapy for which they are developing and testing biological drugs as well as personalized immunotherapy.  Currently, the focus of the research is on using single cell sequencing and spatial transcriptomic to define the mechanisms of cancer and response to therapies (immunotherapy, and target therapy) in lung cancer, mesothelioma and esophageal malignancies with emphasis on developing and testing therapeutic targets.

Publications

Multiomic, Histologic, and scRNA-seq Profiling of Pleural Mesothelioma Reveals Negative Prognosis Associated With a Novel Uncommitted Molecular Phenotype

David T. Severson, MD, DPhila,b Samuel Freyaldenhoven, MDa ∙ Benjamin Wadowski, MDa ∙ Yin P. Hung, MD, PhDc ∙ Travis Hughes, MD, PhDd,e,f ∙ Beow Y. Yeap, PhDg ∙ William G. Richards, PhDa ∙ Sanna Laaksonen, MD, PhDh ∙ Lucian Chirieac, MDh ∙ Matthew B. Couger, PhDa ∙ Roderick V. Jensen, PhDa ∙ Ahmed A. Sadek, MDa ∙ Ilkka Ilonen, MD, PhDa ∙ Kimberly Vermilya, MDa ∙ Simona Innocenti, BSa ∙ Stephanie L. Korle, PhDa ∙ Julianne S. Barlow, MS, CPHSa  ∙  Jamie Anderson, MSa  ∙  Jason Meyerovitz, BSa  ∙  Vivian Wang, MDa ∙ Mary N. Dao, MSa ∙ Alex K. Shalek, PhDd,e,f ∙ Assunta De Rienzo, PhDa ∙ Raphael Bueno, MD

Optimal Margin for Sublobar Resection of Invasive Lung Adenocarcinoma Presenting as Mixed Ground-Glass Nodules

Hao Li, Fatemehsadat Pezeshkian, Evert Sugarbaker, Emanuele Mazzola, Suzanne C Byrne, Fatemeh Hooshmand, Raphael Bueno, Mark M Hammer, Paula Ugalde Figueroa, Scott Swanson. Ann Thorac Surg. 2026 Mar 5:S0003-4975(26)00200-6. doi: 10.1016/j.athoracsur.2026.02.024. Online ahead of print.  PubMed

Candidate biomarkers to identify mesothelioma patients at risk of developing venous thromboembolism post-surgery

Adnan Shami-Shah, Shira Roth, Shad R Morton, Bogdan Budnik, William G Richards, Raphael Bueno, Rushdy Ahmad, David R Walt. Sci Rep. 2026 Feb 16. doi: 10.1038/s41598-026-39805-9. Online ahead of print.  PubMed

Corrigendum to 'Advances in the Basic Sciences in Thoracic Oncology in the Last 20 Years and Their Translational Impact' [Journal of Thoracic Oncology Volume 21 Issue 1 (2026) 41-76]

Michele Carbone, Christopher Amos, Richard L Attanoos, Mattia Boeri, Raphael Bueno, Paul A Bunn, Lucian R Chirieac, Benjamin Cooper, Dean Fennell, Francoise Galateau-Salle, Lydia Giannakou, Chandra V Goparaju, Raffit Hassan, Paul Hofman, Mark G Kris, Weimin Mao, Michael Minaai, Tsetsuya Mitsudomi, Thierry J Molina, Luis M Montuenga, Kazuki Nabeshima, Antonio Passaro, Solange Peters, Arun Rajan, David B Richardson, Hilary Robbins, Christian Rolfo, Charles M Rudin, Jonathan M Samet, Arnaud Scherpereel, David S Schrump, Gabriella Sozzi, Emanuela Taioli, Silvia D Visonà, Haining Yang, Yoshie Yoshikawa, An Zhao, Harvey I Pass. J Thorac Oncol. 2026 Feb 13:103576. doi: 10.1016/j.jtho.2026.103576. Online ahead of print.  PubMed

Feasibility of multimodality treatment, including pleurectomy decortication, in carefully selected patients with sarcomatoid mesothelioma

Moshe Lapidot, Emanuele Mazzola, Raphael Bueno. Transl Lung Cancer Res. 2026 Jan 31;15(1):11. doi: 10.21037/tlcr-2025-990. Epub 2026 Jan 26.  PubMed

Advances in the Basic Sciences in Thoracic Oncology in the Last 20 Years and Their Translational Impact

Michele Carbone, Christopher Amos, Richard L Attanoos, Mattia Boeri, Raphael Bueno, Paul A Bunn, Lucian R Chirieac, Benjamin Cooper, Dean Fennell, Francoise Galateau-Salle, Lydia Giannakou, Chandra V Goparaju, Raffit Hassan, Paul Hofman, Mark G Kris, Weimin Mao, Michael Minaai, Tsetsuya Mitsudomi, Thierry J Molina, Luis M Montuenga, Kazuki Nabeshima, Antonio Passaro, Solange Peters, Arun Rajan, David B Richardson, Hilary Robbins, Christian Rolfo, Charles M Rudin, Jonathan M Samet, Arnaud Scherpereel, David S Schrump, Gabriella Sozzi, Emanuela Taioli, Silvia D Visonà, Haining Yang, Yoshie Yoshikawa, An Zhao, Harvey I Pass. J Thorac Oncol. 2026 Jan;21(1):41-76. doi: 10.1016/j.jtho.2025.11.002.  PubMed

Long-term survival for preoperative versus postoperative treatment of N2 lung cancer: The importance of complete adjuvant therapy for occult N2 disease

Fatemehsadat Pezeshkian, Chandana Adhikarla, Emanuele Mazzola, Hao Li, Carla Vega, Anupama Singh, Fatemeh Hooshmand, Miles McAllister, Rafael Ribeiro Barcelos, Elias Bou Farhat, Abby A White, Matthew M Rochefort, Raphael Bueno, Desiree Steimer, Matthew J Pommerening, Paula A Ugalde Figueroa, Michael T Jaklitsch, Scott J Swanson. JTCVS Open. 2025 Sep 17;28:541-553. doi: 10.1016/j.xjon.2025.09.008. eCollection 2025 Dec.  PubMed

Real-time margin assessment for video-assisted thoracic surgery: A pilot clinical trial

Jayender Jagadeesan, Sarah Lobo, Alan Lucas, Julie Barlow, Ahmed Sadek, Zahra Sarawat Alam, Rajat Mukherjee, Eric J Schmidlin, Michael T Jaklitsch, Lynette Marie Sholl, Raphael Bueno, Scott J Swanson. JTCVS Tech. 2025 Sep 3;34:207-218. doi: 10.1016/j.xjtc.2025.08.015. eCollection 2025 Dec.  PubMed

Multiomic, Histologic, and scRNA-seq Profiling of Pleural Mesothelioma Reveals Negative Prognosis Associated With a Novel Uncommitted Molecular Phenotype

David T Severson, Samuel Freyaldenhoven, Benjamin Wadowski, Yin P Hung, Travis Hughes, Beow Y Yeap, William G Richards, Sanna Laaksonen, Lucian Chirieac, Matthew B Couger, Roderick V Jensen, Ahmed A Sadek, Ilkka Ilonen, Kimberly Vermilya, Simona Innocenti, Stephanie L Korle, Julianne S Barlow, Jamie Anderson, Jason Meyerovitz, Vivian Wang, Mary N Dao, Alex K Shalek, Assunta De Rienzo, Raphael Bueno. J Thorac Oncol. 2025 Nov 28:S1556-0864(25)02937-5. doi: 10.1016/j.jtho.2025.11.019. Online ahead of print.  PubMed

Association of hypoxemia during one-lung ventilation and postoperative complications: A retrospective cohort study

Andres Zorrilla-Vaca, Daniel A Zapata-Pena, Raphael Bueno, Michael T Jaklitsch, Sergey Karamnov, Matthew B Allen. Anaesth Crit Care Pain Med. 2025 Nov 7:101672. doi: 10.1016/j.accpm.2025.101672. Online ahead of print.  PubMed

A cellular and spatial atlas of TP53-associated tissue remodeling defines a multicellular tumor ecosystem in lung adenocarcinoma

William Zhao, Thinh T Nguyen, Atharva Bhagwat, Akhil Kumar, Bruno Giotti, Benjamin Kepecs, Jason L Weirather, Navin R Mahadevan, Asa Segerstolpe, Komal Dolasia, Jamshid Abdul-Ghafar, Naomi R Besson, Stephanie M Jones, Brian Y Soong, Chendi Li, Sebastien Vigneau, Michal Slyper, Isaac Wakiro, Mei-Ju Su, Karla Helvie, Allison Frangieh, Judit Jane-Valbuena, Orr Ashenberg, Mark Awad, Asaf Rotem, Raphael Bueno, Orit Rozenblatt-Rosen, Kathleen Pfaff, Scott Rodig, Aaron N Hata, Aviv Regev, Bruce E Johnson, Alexander M Tsankov. Nat Cancer. 2025 Nov;6(11):1857-1879. doi: 10.1038/s43018-025-01053-7. Epub 2025 Oct 7.  PubMed

Malignant Local Seeding in Procedure Tracts of Pleural Mesothelioma: Incidence and Novel Risk Factors in 308 Patients

Moshe Lapidot, Emanuele Mazzola, Raphael Bueno. Cancers (Basel). 2025 Aug 26;17(17):2786. doi: 10.3390/cancers17172786.  PubMed

Segmentectomy vs Lobectomy for Occult N1 in Non-Small Cell Lung Cancer: Is Less More?

Mohammad Abdallat, Rachel T Leo, Evert A Sugarbaker, Miles McAllister, Yue Xie, Emanuele Mazzola, Mia Silvestri, Raphael Bueno, Michael Jaklitsch, Paula Ugalde, Scott J Swanson, Daniel C Wiener. Ann Thorac Surg. 2026 Feb;121(2):290-298. doi: 10.1016/j.athoracsur.2025.07.020. Epub 2025 Aug 8.  PubMed

Why Surgery Has a Role in Pleural Mesothelioma

Raphael Bueno. Ann Thorac Surg. 2026 Mar;121(3):642-643. doi: 10.1016/j.athoracsur.2025.07.011. Epub 2025 Jul 26.  PubMed

Circulating T-cell receptor repertoire for cancer early detection

Yilong Li, Michelle Nahas, Dennis Stephens, Kate Froburg, Emma Hintz, Devin Champagne, Amaneet Lochab, Markus Brown, Jasper Braun, María Antonia Fortuño, María-Del-Mar Ocón, Andrea Pasquier, Inés Luque-Vázquez, Hita Moudgalya, Sophie Kivlehan, Iliana Gjeci, Stephanie L Korle, Arantza Campo, Maria Rodriguez, Christopher W Seder, Patrick H Lizotte, Raphael Bueno, Jeffrey A Borgia, Luis M Seijo, Luis M Montuenga, Roman Yelensky. NPJ Precis Oncol. 2025 Jul 19;9(1):245. doi: 10.1038/s41698-025-01036-y.  PubMed

Discovery of BMS-986408, a First-In-Class Dual DGKα and DGKζ Inhibitor that Unleashes PD-1 Checkpoint and CAR T-cell Immunotherapies

Michael Wichroski, Si-Qi Liu, Lauren M Zasadil, Joseph L Benci, Patrick C Gedeon, Kendall J Condon, Suhasini Joshi, Shana Posy, Patrick Carlson, Alison Maier, Jiao Shen, Rakeeb Kureshi, Yuka Amako, Tai Wang, Ryan L Powles, Yanyun Li, Tho Lai, Igor Katsyv, Hongchen Qiu, Huilin Qi, Jessica Wong, Dandan Zhao, Dana Banas, Joelle Onorato, Gregory Locke, Xueer Chen, Wen-Chi Chou, Erica Cook, Abigail E Witt, Christopher M Barbieri, Hong Zhang, Jonathan B Olsen, Alba Font Tello, Eugene Drokhlyansky, Denise C Grünenfelder, Louis Chupak, Tyler A Longmire, Jon C Jones, Travis J Hollmann, David G Kugler, John N Feder, Raphael Bueno, John Wain, Pallavur Sivakumar, Yu Liu, Stephanie K Dougan, Cloud P Paweletz, David A Barbie, Emma Lees. Cancer Immunol Res. 2025 Sep 2;13(9):1342-1362. doi: 10.1158/2326-6066.CIR-25-0156.  PubMed

A Response to the Letter to the Editor: MARS2 Perspective

Harvey I Pass, Eric Lim, Isabelle Opitz, Gavitt Woodard, Raphael Bueno, Marc de Perrot, Raja Flores, Ritu Gill, David Jablons. J Thorac Oncol. 2025 May;20(5):e60-e61. doi: 10.1016/j.jtho.2025.02.018.  PubMed

Lung cancer recurrence after neoadjuvant immunotherapy

Hao Li, Fatemehsadat Pezeshkian, Yue Xie, Emanuele Mazzola, Rafael Ribeiro Barcelos, Fatemeh Hooshmand, Tianxiao Han, Sanna Laaksonen, Lynette Sholl, Carla Vega, Elias Bou Farhat, Raphael Bueno, Paula Ugalde Figueroa, Scott Swanson. J Thorac Cardiovasc Surg. 2025 Sep;170(3):852-863.e6. doi: 10.1016/j.jtcvs.2025.04.028. Epub 2025 May 4.  PubMed

Young lung cancer patients undergoing surgery: Comparison of clinicopathological characteristics and outcomes in patients aged ≤50 years versus <50 years

Rachel T Leo, Evert A Sugarbaker, Miles McAllister, Anupama Singh, Rafael R Barcelos, Ali Basil Ali, Raphael Bueno, Michael T Jaklitsch, Paula Ugalde Figueroa, Scott J Swanson. JTCVS Open. 2024 Dec 20;24:409-422. doi: 10.1016/j.xjon.2024.12.008. eCollection 2025 Apr.  PubMed

Recurrence Patterns and Management after Pleurectomy Decortication for Pleural Mesothelioma

Juuso Paajanen, William G Richards, Yue Xie, Emanuele Mazzola, Kristina Sidopoulos, John Kuckelman, Ritu R Gill, Raphael Bueno. Ann Surg. 2025 Jan 15. doi: 10.1097/SLA.0000000000006627. Online ahead of print.  PubMed

A Perspective on the MARS2 Trial

Eric Lim, Isabelle Opitz, Gavitt Woodard, Raphael Bueno, Marc de Perrot, Raja Flores, Ritu Gill, David Jablons, Harvey Pass. J Thorac Oncol. 2025 Mar;20(3):262-272. doi: 10.1016/j.jtho.2024.12.014. Epub 2025 Jan 8.  PubMed