Automated tumor immunophenotyping predicts clinical benefit from anti-PD-L1 immunotherapy.

CD8+ T cell anti‐PD‐L1 immunotherapy artificial intelligence immunophenotype non‐small cell lung cancer panCK/CD8 immunohistochemistry survival analysis triple‐negative breast cancer

Journal

The Journal of pathology
ISSN: 1096-9896
Titre abrégé: J Pathol
Pays: England
ID NLM: 0204634

Informations de publication

Date de publication:
25 Mar 2024
Historique:
revised: 22 12 2023
received: 01 07 2023
accepted: 14 02 2024
medline: 25 3 2024
pubmed: 25 3 2024
entrez: 25 3 2024
Statut: aheadofprint

Résumé

Cancer immunotherapy has transformed the clinical approach to patients with malignancies, as profound benefits can be seen in a subset of patients. To identify this subset, biomarker analyses increasingly focus on phenotypic and functional evaluation of the tumor microenvironment to determine if density, spatial distribution, and cellular composition of immune cell infiltrates can provide prognostic and/or predictive information. Attempts have been made to develop standardized methods to evaluate immune infiltrates in the routine assessment of certain tumor types; however, broad adoption of this approach in clinical decision-making is still missing. We developed approaches to categorize solid tumors into 'desert', 'excluded', and 'inflamed' types according to the spatial distribution of CD8+ immune effector cells to determine the prognostic and/or predictive implications of such labels. To overcome the limitations of this subjective approach, we incrementally developed four automated analysis pipelines of increasing granularity and complexity for density and pattern assessment of immune effector cells. We show that categorization based on 'manual' observation is predictive for clinical benefit from anti-programmed death ligand 1 therapy in two large cohorts of patients with non-small cell lung cancer or triple-negative breast cancer. For the automated analysis we demonstrate that a combined approach outperforms individual pipelines and successfully relates spatial features to pathologist-based readouts and the patient's response to therapy. Our findings suggest that tumor immunophenotype generated by automated analysis pipelines should be evaluated further as potential predictive biomarkers for cancer immunotherapy. © 2024 The Pathological Society of Great Britain and Ireland.

Identifiants

pubmed: 38525811
doi: 10.1002/path.6274
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Genentech, Inc.

Informations de copyright

© 2024 The Pathological Society of Great Britain and Ireland.

Références

Korman AJ, Garrett‐Thomson SC, Lonberg N. The foundations of immune checkpoint blockade and the ipilimumab approval decennial. Nat Rev Drug Discov 2021; 7: 509–528.
Robert C. A decade of immune‐checkpoint inhibitors in cancer therapy. Nat Commun 2020; 11: 3801.
Marin‐Acevedo JA, Kimbrough EO, Lou Y. Next generation of immune checkpoint inhibitors and beyond. J Hematol Oncol 2021; 14: 45.
Labrijn AF, Janmaat ML, Reichert JM, et al. Bispecific antibodies: a mechanistic review of the pipeline. Nat Rev Drug Discov 2019; 18: 585–608.
Bagchi S, Yuan R, Engleman EG. Immune checkpoint inhibitors for the treatment of cancer: clinical impact and mechanisms of response and resistance. Annu Rev Pathol 2020; 16: 223–249.
Taube JM, Klein A, Brahmer JR, et al. Association of PD‐1, PD‐1 ligands, and other features of the tumor immune microenvironment with response to anti‐PD‐1 therapy. Clin Cancer Res 2014; 20: 5064–5074.
Tsao MS, Kerr KM, Kockx M, et al. PD‐L1 immunohistochemistry comparability study in real‐life clinical samples: results of blueprint phase 2 project. J Thorac Oncol 2018; 13: 1302–1311.
Rimm DL, Han G, Taube JM, et al. A prospective, multi‐institutional, pathologist‐based assessment of 4 immunohistochemistry assays for PD‐L1 expression in non‐small cell lung cancer. JAMA Oncol 2017; 3: 1051.
Doroshow DB, Bhalla S, Beasley MB, et al. PD‐L1 as a biomarker of response to immune‐checkpoint inhibitors. Nat Rev Clin Oncol 2021; 18: 345–362.
Kefford R, Ribas A, Hamid O, et al. Clinical efficacy and correlation with tumor PD‐L1 expression in patients (pts) with melanoma (MEL) treated with the anti‐PD‐1 monoclonal antibody MK‐3475. J Clin Oncol 2014; 32(Number 15–Suppl): Abstract 3005.
Kockx MM, McCleland M, Koeppen H. Microenvironmental regulation of tumour immunity and response to immunotherapy. J Pathol 2021; 254: 374–383.
Bai R, Lv Z, Xu D, et al. Predictive biomarkers for cancer immunotherapy with immune checkpoint inhibitors. Biomark Res 2020; 8: 34.
Li N, Hou X, Huang S, et al. Biomarkers related to immune checkpoint inhibitors therapy. Biomed Pharmacother 2022; 147: 112470.
Johnson SK, Kerr KM, Chapman AD, et al. Immune cell infiltrates and prognosis in primary carcinoma of the lung. Lung Cancer 2000; 27: 27–35.
Galon J, Costes A, Sanchez‐Cabo F, et al. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 2006; 313: 1960–1964.
Galon J, Angell HK, Bedognetti D, et al. The continuum of cancer immunosurveillance: prognostic, predictive, and mechanistic signatures. Immunity 2013; 39: 11–26.
Pagès F, Mlecnik B, Marliot F, et al. International validation of the consensus immunoscore for the classification of colon cancer: a prognostic and accuracy study. Lancet 2018; 391: 2128–2139.
Savas P, Salgado R, Denkert C, et al. Clinical relevance of host immunity in breast cancer: from TILs to the clinic. Nat Rev Clin Oncol 2016; 13: 228–241.
Bairi KE, Haynes HR, Blackley E, et al. The tale of TILs in breast cancer: a report from The International Immuno‐Oncology Biomarker Working Group. NPJ Breast Cancer 2021; 7: 150.
Hendry S, Salgado R, Gevaert T, et al. Assessing tumor‐infiltrating lymphocytes in solid tumors. Adv Anat Pathol 2017; 24: 311–335.
Fuchs TL, Sioson L, Sheen A, et al. Assessment of tumor‐infiltrating lymphocytes using international TILs working group (ITWG) system is a strong predictor of overall survival in colorectal carcinoma: a study of 1034 patients. Am J Surg Pathology 2020; 44: 536–544.
de Jong VMT, Wang Y, ter Hoeve ND, et al. Prognostic value of stromal tumor‐infiltrating lymphocytes in young, node‐negative, triple‐negative breast cancer patients who did not receive (neo)adjuvant systemic therapy. J Clin Oncol 2022; 40: 2361–2374.
Kos Z, Roblin E, Kim RS, et al. Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer. NPJ Breast Cancer 2020; 6: 17.
Amgad M, Stovgaard ES, Balslev E, et al. Report on computational assessment of tumor infiltrating lymphocytes from the international immuno‐oncology biomarker working group. NPJ Breast Cancer 2020; 6: 16.
de Ruiter EJ, de Roest RH, Brakenhoff RH, et al. Digital pathology‐aided assessment of tumor‐infiltrating T lymphocytes in advanced stage, HPV‐negative head and neck tumors. Cancer Immunol Immunother 2020; 69: 581–591.
Sun P, He J, Chao X, et al. A computational tumor‐infiltrating lymphocyte assessment method comparable with visual reporting guidelines for triple‐negative breast cancer. EBioMedicine 2021; 70: 103492.
Albusayli R, Graham JD, Pathmanathan N, et al. Artificial intelligence‐based digital scores of stromal tumour‐infiltrating lymphocytes and tumour‐associated stroma predict disease‐specific survival in triple‐negative breast cancer. J Pathol 2023; 260: 32–42.
Acs B, Salgado R, Hartman J. What do we still need to learn on digitally assessed biomarkers? EBioMedicine 2021; 70: 103520.
Szabo PM, Lee G, Ely S, et al. CD8+ T cells in tumor parenchyma and stroma by image analysis (IA) and gene expression profiling (GEP): potential biomarkers for immuno‐oncology (I‐O) therapy. J Clin Oncol 2019; 37(Number 15_Suppl): Abstract 2594.
Lee G, Desai K, Tang H, et al. 387 the utility of AI‐powered spatial classification of intratumoral CD8+ immune‐cell distribution in predicting overall survival in patients with melanoma as part of the checkMate 067 clinical trial. J Immunother Cancer 2021; 9(Suppl 2): Abstract 387.
Fehrenbacher L, Spira A, Ballinger M, et al. Atezolizumab versus docetaxel for patients with previously treated non‐small‐cell lung cancer (POPLAR): a multicentre, open‐label, phase 2 randomised controlled trial. Lancet 2016; 387: 1837–1846.
Rittmeyer A, Barlesi F, Waterkamp D, et al. Atezolizumab versus docetaxel in patients with previously treated non‐small‐cell lung cancer (OAK): a phase 3, open‐label, multicentre randomised controlled trial. Lancet 2016; 389: 255–265.
Schmid P, Adams S, Rugo HS, et al. Atezolizumab and nab‐paclitaxel in advanced triple‐negative breast cancer. New Engl J Med 2018; 379: 2108–2121.
Vennapusa B, Baker B, Kowanetz M, et al. Development of a PD‐L1 complementary diagnostic immunohistochemistry assay (SP142) for atezolizumab. Appl Immunohistochem Mol Morphol 2019; 27: 92–100.
Breiman L. Random forests. Machine Learning 2001; 45: 5–32.
Chien L‐C, Li X, Staudt A. Physical inactivity displays a mediator role in the association of diabetes and poverty: a spatiotemporal analysis. Geospatial Health 2016; 12: 528.
Li X, Staudt A, Chien L‐C. Identifying counties vulnerable to diabetes from obesity prevalence in the United States: a spatiotemporal analysis. Geospatial Health 2015; 11: 439.
Li X, Gaire F, Jansen G, et al. Spatial‐statistics‐based modeling for predicting treatment response in non‐small cell lung cancer (NSCLC) patients using H&E pathology images. Ann Oncol 2020; 31(Suppl 4): Abstract 1382P, S879.
Nawaz S, Heindl A, Koelble K, et al. Beyond immune density: critical role of spatial heterogeneity in estrogen receptor‐negative breast cancer. Modern Pathol 2015; 28: 766–777.
Rempala GA, Seweryn M. Methods for diversity and overlap analysis in T‐cell receptor populations. J Math Biol 2013; 67: 1339–1368.
Lee S‐I. Developing a bivariate spatial association measure: an integration of Pearson's r and Moran's I. J Geogr Syst 2001; 3: 369–385.
Geary RC. The contiguity ratio and statistical mapping. Incorporated Statistician 1954; 5: 115–145.
Anselin L. Local indicators of spatial association—LISA. Geogr Anal 1995; 27: 93–115.
Karrer TM, Garmhausen M, Li X, et al. Combining hematoxylin and eosin (H&E) stained images and RNA sequencing (RNA‐seq) data to predict overall survival (OS) in patients with non‐small cell lung cancer (NSCLC). J Clin Oncol 2021; 39(Number 15–Suppl): Abstract 1547.
Hussein SE, Chen P, Medeiros LJ, et al. Artificial intelligence strategy integrating morphologic and architectural biomarkers provides robust diagnostic accuracy for disease progression in chronic lymphocytic leukemia. J Pathol 2022; 256: 4–14.
Allam M, Hu T, Lee J, et al. Spatially variant immune infiltration scoring in human cancer tissues. NPJ Precis Oncol 2022; 6: 60.
Elomaa H, Ahtiainen M, Väyrynen SA, et al. Prognostic significance of spatial and density analysis of T lymphocytes in colorectal cancer. Br J Cancer 2022; 127: 514–523.
Angell HK, Bruni D, Barrett JC, et al. The immunoscore: colon cancer and beyond. Clin Cancer Res 2020; 26: 332–339.
Chen DS, Mellman I. Elements of cancer immunity and the cancer‐immune set point. Nature 2017; 541: 321–330.
Park S, Ock C‐Y, Kim H, et al. Artificial intelligence‐powered spatial analysis of tumor‐infiltrating lymphocytes as complementary biomarker for immune checkpoint inhibition in non‐small‐cell lung cancer. J Clin Oncol 2022; 40: 1916–1928.
Backman M, Fleur LL, Kurppa P, et al. Infiltration of NK and plasma cells is associated with a distinct immune subset in non‐small cell lung cancer. J Pathol 2021; 255: 243–256.
Ilse M, Tomczak JM, Welling M. Attention‐based deep multiple instance learning. arXiv 2018. [Not peer reviewed].
Cardoso MJ, Li W, Brown R, et al. MONAI: an open‐source framework for deep learning in healthcare. arXiv 2022. [Not peer reviewed].
Tumeh PC, Harview CL, Yearley JH, et al. PD‐1 blockade induces responses by inhibiting adaptive immune resistance. Nature 2014; 515: 568–571.
Westergaard MCW, Milne K, Pedersen M, et al. Changes in the tumor immune microenvironment during disease progression in patients with ovarian cancer. Cancers (Basel) 2020; 12: 3828.
Yang J, Zhang Q, Wang J, et al. Dynamic profiling of immune microenvironment during pancreatic cancer development suggests early intervention and combination strategy of immunotherapy. EBioMedicine 2022; 78: 103958.
Murciano‐Goroff YR, Warner AB, Wolchok JD. The future of cancer immunotherapy: microenvironment‐targeting combinations. Cell Res 2020; 30: 507–519.
de Ruijter LK, van de Donk PP, Hooiveld‐Noeken JS, et al. Whole‐body CD8+ T cell visualization before and during cancer immunotherapy: a phase 1/2 trial. Nat Med 2022; 28: 2601.

Auteurs

Xiao Li (X)

Genentech, South San Francisco, CA, USA.

Jeffrey Eastham (J)

Genentech, South San Francisco, CA, USA.

Jennifer M Giltnane (JM)

Genentech, South San Francisco, CA, USA.

Wei Zou (W)

Genentech, South San Francisco, CA, USA.

Andries Zijlstra (A)

Genentech, South San Francisco, CA, USA.

Evgeniy Tabatsky (E)

Genentech, South San Francisco, CA, USA.

Romain Banchereau (R)

Genentech, South San Francisco, CA, USA.

Ching-Wei Chang (CW)

Genentech, South San Francisco, CA, USA.

Barzin Y Nabet (BY)

Genentech, South San Francisco, CA, USA.

Namrata S Patil (NS)

Genentech, South San Francisco, CA, USA.

Luciana Molinero (L)

Genentech, South San Francisco, CA, USA.

Steve Chui (S)

Genentech, South San Francisco, CA, USA.

Maureen Harryman (M)

Genentech, South San Francisco, CA, USA.

Shari Lau (S)

Genentech, South San Francisco, CA, USA.

Linda Rangell (L)

Genentech, South San Francisco, CA, USA.

Mark Kockx (M)

CellCarta, Antwerp, Belgium.

Darya Orlova (D)

Genentech, South San Francisco, CA, USA.

Hartmut Koeppen (H)

Genentech, South San Francisco, CA, USA.

Classifications MeSH