Author

Andrea Borghese Apolo

National Institutes of HealthORCID 0000-0001-9409-1836Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Organism:human· 4 Assay:bulk RNA-seq· 3 Approach:statistical model· 3 Research Focus:drug response / drug discovery· 2 Approach:experimental assay· 2 Research Focus:benchmarking· 1 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell signaling & trafficking· 1

Frequent Co-Authors

Eytan RuppiniD· 3 shared Abbas Yousefi-Rad· 2 shared Alejandro A. SchäfferiD· 2 shared Danh-Tai HoangiD· 2 shared Kenneth AldapeiD· 2 shared Tiangen ChangiD· 2 shared Ze’ev A. RonaiiD· 2 shared Abdul Rouf BandayiD· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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3 shared papersCancer Biology

Eytan RuppinORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

APOBEC3-driven neoantigen-rich cancers co-opt 1q23.3 amplification for tumor-intrinsic immune cloaking

Dhanusha Yesudhas, Bilal A. Lone, Ecem Ünal, Arup Chakraborty, Ayşe Gökçe Keşküş, Jaimie Ryou, KM Butler, Tania Colon Aquino, Abbas Yousefi-Rad, Weiming Yang, Lisa M. Miller Jenkins, Raju R. Chelluri, Elias B. A. Chandran, Vladimir Valera Romero, Salah Boudjadi, , Abdul Rouf Banday

The paper identifies a tumor-intrinsic immune-cloaking mechanism in neoantigen-rich cancers driven by APOBEC3 mutagenesis and 1q23.3 amplification, showing NECTIN4's role in suppressing immune responses.

bioRxiv · Jul 4, 2026 · PreprintCancer Biology

Pan-cancer prediction of tumor immune activation and response to immune checkpoint blockade from tumor transcriptomics and histopathology

Sumit Mukherjee, Sumeet Patiyal, Lipika R. Pal, Keluo Yao, Tiangen Chang, Sumona Biswas, Saugato Rahman Dhruba, Amos Stemmer, Arashdeep Singh, Abbas Yousefi-Rad, Tien-Hua Chen, Binbin Wang, Denis Marino, Wonwoo Shon, Yuan Yuan, , Eytan Ruppin

This paper introduces TIME_ACT, a transcriptomic signature predicting immune checkpoint blockade response across cancers, validated using histopathology and multiple cohorts.

bioRxiv · Jun 27, 2025 · PreprintCancer Biology

Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities

Parth Anil Desai, Nobuyuki Takahashi, Rajesh Kumar, Samantha Nichols, Justin Malin, Allison L. Hunt, Christopher William Schultz, Yingying Cao, Desiree Tillo, Darryl Nousome, Lakshya Chauhan, Linda C. Sciuto, Kimberly Rae Jordan, Vinodh N. Rajapakse, Mayank Tandon, , Anish Thomas

This study maps the SCLC tumor microenvironment and identifies cancer-associated fibroblasts as key drivers of neuroendocrine state plasticity and poor prognosis.

Cell Reports Medicine · Jun 1, 2024Peer-reviewedCancer Biology

Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome

Gal Dinstag, Eldad David Shulman, Efrat Elis, Doreen S. Ben-Zvi, Omer Tirosh, Eden Maimon, Isaac Meilijson, Emmanuel Elalouf, Boris Temkin, Philipp Vitkovsky, Eyal Schiff, Danh-Tai Hoang, Sanju Sinha, Nishanth Ulhas Nair, Joo Sang Lee, , Ranit Aharonov

ENLIGHT predicts patient response to targeted and immunotherapies using tumor transcriptomes without prior treatment response data, showing better accuracy than existing transcriptomics-based signatures.

Med · Dec 12, 2022Peer-reviewedBioinformatics