@article{MTMT:34461310,
	title = {Survival Outcomes, Digital TILs, and On-treatment PET/CT During Neoadjuvant Therapy for HER2-positive Breast Cancer: Results from the Randomized PREDIX HER2 Trial},
	url = {https://m2.mtmt.hu/api/publication/34461310},
	author = {Matikas, Alexios and Johansson, Hemming and Gryback, Per and Bjohle, Judith and Ács, Balázs and Boyaci, Ceren and Lekberg, Tobias and Fredholm, Hanna and Elinder, Ellinor and Margolin, Sara and Isaksson-Friman, Erika and Bosch, Ana and Lindman, Henrik and Adra, Jamila and Andersson, Anne and Agartz, Susanne and Hellstrom, Mats and Zerdes, Ioannis and Hartman, Johan and Bergh, Jonas and Hatschek, Thomas and Foukakis, Theodoros},
	doi = {10.1158/1078-0432.CCR-22-2829},
	journal-iso = {CLIN CANCER RES},
	journal = {CLINICAL CANCER RESEARCH},
	volume = {29},
	unique-id = {34461310},
	issn = {1078-0432},
	abstract = {Purpose: PREDIX HER2 is a randomized Phase II trial that compared neoadjuvant docetaxel, trastuzumab, and pertuzumab (THP) with trastuzumab emtansine (T-DM1) for HER2-positive breast cancer. Rates of pathologic complete response (pCR) did not differ between the two groups. Here, we present the survival out-comes from PREDIX HER2 and investigate metabolic response and tumor-infiltrating lymphocytes (TIL) as prognostic factors.Patients and Methods: In total, 202 patients with HER2-positive breast cancer were enrolled and 197 patients received six cycles of either THP or T-DM1. Secondary endpoints included event-free survival (EFS), recurrence-free survival (RFS), and overall survival (OS). Assessment with PET/CT was performed at baseline, after two and six treatment cycles. TILs were assessed manually at baseline biopsies, while image-based evaluation of TILs [digital TILs (DTIL)] was performed in digitized full-face sections.Results: After a median follow-up of 5.21 years, there was no difference between the two treatment groups in terms of EFS [HR = 1.26; 95% confidence interval (CI), 0.54-2.91], RFS (HR = 0.69; 95% CI, 0.24-1.93), or OS (HR = 0.52; 95% CI, 0.09-2.82). Higher SUVmax at cycle 2 (C2) predicted lower pCR (ORadj = 0.65; 95% CI, 0.48-0.87; P = 0.005) and worse EFS (HRadj = 1.27; 95% CI, 1.12-1.4 1; P < 0.001). Baseline TILs and DTILs provided additional prognostic information to clinical parameters and C2 SUVmax.Conclusions: Long-term outcomes following neoadjuvant T-DM1 were similar to neoadjuvant THP. SUVmax after two cycles of neoadjuvant therapy for HER2-positive breast cancer may be an independent predictor of both short-and long-term outcomes. Combined assessment with TILs may facilitate early selection of poor responders for alternative treatment strategies.},
	year = {2023},
	eissn = {1557-3265},
	pages = {532-540},
	orcid-numbers = {Matikas, Alexios/0000-0002-4122-9624; Ács, Balázs/0000-0002-0972-4633; Boyaci, Ceren/0000-0001-5598-0243; Elinder, Ellinor/0000-0001-8596-5327; Hartman, Johan/0000-0002-6500-8527}
}

@article{MTMT:33490607,
	title = {External Quality Assessment 2.0: The Importance of a Standardized Implementation of TILs for Daily and Trial Practices},
	url = {https://m2.mtmt.hu/api/publication/33490607},
	author = {Nauwelaers, Inne and Laudus, Nele and Peeters, Dieter and Ács, Balázs and Denkert, Carsten and Michiels, Stefan and Horlings, Hugo and Siziopikou, Kalliopi P. and Ely, Scott and Zardavas, Dimitrios and Mustimbo, Roberts and Bartlett, John and Floris, Giuseppe and Hartman, Johan and van Deurzen, Carolien H. M. and Ceusters, Dorien and Dequeker, Els and Salgado, Roberto},
	doi = {10.3390/cancers14153762},
	journal-iso = {CANCERS},
	journal = {CANCERS},
	volume = {14},
	unique-id = {33490607},
	abstract = {Simple Summary New assays are developed regularly to improve health care for patients. It is important to ensure that assays are performed correctly. Therefore, it is advised to participate in training and proficiency (competence assessment) programs. Tumor infiltrating lymphocytes (TILs) might improve the estimates of response to therapy and prognosis. Herewith, we propose a new training and proficiency program in which each pathologist can train and test themselves regarding TILs (and PDL1) scoring.},
	year = {2022},
	eissn = {2072-6694},
	orcid-numbers = {Nauwelaers, Inne/0000-0003-3577-6776; Laudus, Nele/0000-0001-6876-3475; Ács, Balázs/0000-0002-0972-4633; Michiels, Stefan/0000-0002-6963-2968; Hartman, Johan/0000-0002-6500-8527; Ceusters, Dorien/0000-0002-2436-0284}
}

@article{MTMT:33443345,
	title = {Objective assessment of tumor infiltrating lymphocytes as a prognostic marker in melanoma using machine learning algorithms},
	url = {https://m2.mtmt.hu/api/publication/33443345},
	author = {Aung, Thazin Nwe and Sha, Saba and Wilmott, James S. and Nourmohammadi, Saeed and Vathiotis, Ioannis and Gavrielatou, Niki and Fernandez, Aileen and Yaghoobi, Vesal and Sinnberg, Tobias and Amaral, Teresa and Ikenberg, Kristian and Khosrotehrani, Kiarash and Osman, Iman and Ács, Balázs and Bai, Yalai and Martinez-Morilla, Sandra and Mouta, Myrto and Thompson, John F. and Scolyer, Richard A. and Rimm, David L.},
	doi = {10.1016/j.ebiom2202.104143},
	journal-iso = {EBIOMEDICINE},
	journal = {EBIOMEDICINE},
	volume = {82},
	unique-id = {33443345},
	issn = {2352-3964},
	abstract = {Background The prognostic value of tumor-infiltrating lymphocytes (TILs) assessed by machine learning algorithms in melanoma patients has been previously demonstrated but has not been widely adopted in the clinic. We evaluated the prognostic value of objective automated electronic TILs (eTILs) quantification to define a subset of melanoma patients with a low risk of relapse after surgical treatment. Methods We analyzed data for 785 patients from 5 independent cohorts from multiple institutions to validate our previous finding that automated TIL score is prognostic in clinically-localized primary melanoma patients. Using serial tissue sections of the Yale TMA-76 melanoma cohort, both immunofluorescence and Hematoxylin-and-Eosin (H & E) staining were performed to understand the molecular characteristics of each TIL phenotype and their associations with survival outcomes. Findings Five previously-described TIL variables were each significantly associated with overall survival (p < 0.0001). Assessing the receiver operating characteristic (ROC) curves by comparing the clinical impact of two models sug-gests that etTILs (electronic total TILs) (AUC: 0.793, specificity: 0.627, sensitivity: 0.938) outperformed eTILs (AUC: 0.77, specificity: 0.51, sensitivity: 0.938). We also found that the specific molecular subtype of cells representing TILs includes predominantly cells that are CD3+ and CD8+ or CD4+ T cells. Interpretation eTIL% and etTILs scores are robust prognostic markers in patients with primary melanoma and may identify a subgroup of stage II patients at high risk of recurrence who may benefit from adjuvant therapy. We also show the molecular correlates behind these scores. Our data support the need for prospective testing of this algorithm in a clinical trial. Copyright (C) 2022 The Author(s). Published by Elsevier B.V.},
	keywords = {Prognostic marker; Digital image analysis; Tumor-infiltrating lymphocytes (TILs); EARLY-STAGE MELANOMA; Machine learning cell segmentation algorithm},
	year = {2022},
	eissn = {2352-3964},
	orcid-numbers = {Ács, Balázs/0000-0002-0972-4633}
}

@article{MTMT:32757782,
	title = {Deconstructing Immune Cell Infiltration in Human Colorectal Cancer: A Systematic Spatiotemporal Evaluation},
	url = {https://m2.mtmt.hu/api/publication/32757782},
	author = {Ágoston, Emese Irma and Ács, Balázs and Herold, Zoltán and Fekete, Krisztina and Kulka, Janina and Nagy, Ákos and Mühl, Dorottya and Mohácsi, Réka and Dank, Magdolna and Garay, Tamás and Harsányi, László and Győrffy, Balázs and Szász, Attila Marcell},
	doi = {10.3390/genes13040589},
	journal-iso = {GENES-BASEL},
	journal = {GENES},
	volume = {13},
	unique-id = {32757782},
	issn = {2073-4425},
	year = {2022},
	eissn = {2073-4425},
	orcid-numbers = {Ágoston, Emese Irma/0000-0001-9290-9630; Ács, Balázs/0000-0002-0972-4633; Herold, Zoltán/0000-0001-5990-4889; Kulka, Janina/0000-0001-6498-5943; Mühl, Dorottya/0000-0001-7565-8462; Mohácsi, Réka/0000-0002-6982-6893; Dank, Magdolna/0000-0002-4442-8733; Garay, Tamás/0000-0003-0329-9207; Harsányi, László/0000-0003-2657-0039; Győrffy, Balázs/0000-0002-5772-3766; Szász, Attila Marcell/0000-0003-2739-4196}
}

@article{MTMT:33459722,
	title = {What do we still need to learn on digitally assessed biomarkers?},
	url = {https://m2.mtmt.hu/api/publication/33459722},
	author = {Ács, Balázs and Salgado, Roberto and Hartman, Johan},
	doi = {10.1016/j.ebiom.2021.103520},
	journal-iso = {EBIOMEDICINE},
	journal = {EBIOMEDICINE},
	volume = {70},
	unique-id = {33459722},
	issn = {2352-3964},
	year = {2021},
	eissn = {2352-3964},
	orcid-numbers = {Ács, Balázs/0000-0002-0972-4633}
}

@article{MTMT:33459703,
	title = {Independent Clinical Validation of the Automated Ki67 Scoring Guideline from the International Ki67 in Breast Cancer Working Group},
	url = {https://m2.mtmt.hu/api/publication/33459703},
	author = {Boyaci, Ceren and Sun, Wenwen and Robertson, Stephanie and Ács, Balázs and Hartman, Johan},
	doi = {10.3390/biom11111612},
	journal-iso = {BIOMOLECULES},
	journal = {BIOMOLECULES},
	volume = {11},
	unique-id = {33459703},
	issn = {2218-273X},
	abstract = {Ki67 is an important biomarker with prognostic and potential predictive value in breast cancer. However, the lack of standardization hinders its clinical applicability. In this study, we aimed to investigate the reproducibility among pathologists following the guidelines of the International Ki67 in Breast Cancer Working Group (IKWG) for Ki67 scoring and to evaluate the prognostic potential of this platform in an independent cohort. Four algorithms were independently built by four pathologists based on our study cohort using an open-source digital image analysis (DIA) platform (QuPath) following the detailed guideline of the IKWG. The algorithms were applied on an ER+ breast cancer study cohort of 157 patients with 15 years of follow-up. The reference Ki67 score was obtained by a DIA algorithm trained on a subset of the study cohort. Intraclass correlation coefficient (ICC) was used to measure reproducibility. High interobserver reliability was reached with an ICC of 0.938 (CI: 0.920-0.952) among the algorithms and the reference standard. Comparing each machine-read score against relapse-free survival, the hazard ratios were similar (2.593-4.165) and showed independent prognostic potential (p & LE; 0.018, for all comparisons). In conclusion, we demonstrate high reproducibility and independent prognostic potential using the IKWG DIA instructions to score Ki67 in breast cancer. A prospective study is needed to assess the clinical utility of the IKWG DIA Ki67 instructions.},
	keywords = {VALIDATION; reproducibility; breast cancer; KI67; Digital image analysis; QuPath},
	year = {2021},
	eissn = {2218-273X},
	orcid-numbers = {Boyaci, Ceren/0000-0001-5598-0243; Robertson, Stephanie/0000-0002-9843-3028; Ács, Balázs/0000-0002-0972-4633; Hartman, Johan/0000-0002-6500-8527}
}

@article{MTMT:33033281,
	title = {Assessment of Ki67 in Breast Cancer: Updated Recommendations From the International Ki67 in Breast Cancer Working Group},
	url = {https://m2.mtmt.hu/api/publication/33033281},
	author = {Nielsen, Torsten O. and Leung, Samuel C. Y. and Rimm, David L. and Dodson, Andrew and Ács, Balázs and Badve, Sunil and Denkert, Carsten and Ellis, Matthew J. and Fineberg, Susan and Flowers, Margaret and Kreipe, Hans H. and Laenkholm, Anne-Vibeke and Pan, Hongchao and Penault-Llorca, Friderique M. and Polley, Mei-Yin and Salgado, Roberto and Smith, Ian E. and Sugie, Tomoharu and Bartlett, John M. S. and McShane, Lisa M. and Dowsett, Mitch and Hayes, Daniel F.},
	doi = {10.1093/jnci/djaa201},
	journal-iso = {JNCI-J NATL CANCER I},
	journal = {JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE},
	volume = {113},
	unique-id = {33033281},
	issn = {0027-8874},
	abstract = {Ki67 immunohistochemistry (IHC), commonly used as a proliferation marker in breast cancer, has limited value for treatment decisions due to questionable analytical validity. The International Ki67 in Breast Cancer Working Group (IKWG) consensus meeting, held in October 2019, assessed the current evidence for Ki67 IHC analytical validity and clinical utility in breast cancer, including the series of scoring studies the IKWG conducted on centrally stained tissues. Consensus observations and recommendations are: 1) as for estrogen receptor and HER2 testing, preanalytical handling considerations are critical; 2) a standardized visual scoring method has been established and is recommended for adoption; 3) participation in and evaluation of quality assurance and quality control programs is recommended to maintain analytical validity; and 4) the IKWG accepted that Ki67 IHC as a prognostic marker in breast cancer has clinical validity but concluded that clinical utility is evident only for prognosis estimation in anatomically favorable estrogen receptor-positive and HER2-negative patients to identify those who do not need adjuvant chemotherapy. In this T1-2, N0-1 patient group, the IKWG consensus is that Ki675% or less, or 30% or more, can be used to estimate prognosis. In conclusion, analytical validity of Ki67 IHC can be reached with careful attention to preanalytical issues and calibrated standardized visual scoring. Currently, clinical utility of Ki67 IHC in breast cancer care remains limited to prognosis assessment in stage I or II breast cancer. Further development of automated scoring might help to overcome some current limitations.},
	keywords = {labeling index; ESTROGEN-RECEPTOR; PROGNOSTIC VALUE; ENDOCRINE THERAPY; CLINICAL-PRACTICE GUIDELINES; AMERICAN-SOCIETY; Adjuvant systemic therapy; PATIENT-LEVEL METAANALYSIS; STANDARDIZED SCORING PROTOCOL},
	year = {2021},
	eissn = {1460-2105},
	pages = {808-819},
	orcid-numbers = {Nielsen, Torsten O./0000-0003-3769-2517; Rimm, David L./0000-0001-5820-4397; Dodson, Andrew/0000-0002-7443-2362; Ács, Balázs/0000-0002-0972-4633; Badve, Sunil/0000-0001-8861-9980; Ellis, Matthew J./0000-0002-8467-8534; Fineberg, Susan/0000-0002-4769-7875; Laenkholm, Anne-Vibeke/0000-0003-2166-8686}
}

@article{MTMT:32507032,
	title = {In Situ Hybridization of PRRSV-1 Combined with Digital Image Analysis in Lung Tissues of Pigs Challenged with PRRSV-1},
	url = {https://m2.mtmt.hu/api/publication/32507032},
	author = {Dénes, Lilla and Horváth, Dávid Géza and Duran, O and Ratkhjen, PH and Kraft, C and Ács, Balázs and Szász, Attila Marcell and Rumenapf, T and Papp, Márton and Ladinig, A and Balka, Gyula},
	doi = {10.3390/vetsci8100235},
	journal-iso = {VET SCI},
	journal = {VETERINARY SCIENCES},
	volume = {8},
	unique-id = {32507032},
	issn = {2306-7381},
	abstract = {Betaarterivirus suid 1 and 2 are the causative agents of porcine reproductive and respiratory syndrome (PRRS), which is one of the most significant diseases of the swine industry, causing significant economic losses in the main pig producing countries. Here, we report the development of a novel, RNA-based in situ hybridization technique (RNAscope) to detect PRRS virus (PRRSV) RNA in lung tissues of experimentally infected animals. The technique was applied to lung tissues of 20 piglets, which had been inoculated with a wild-type, highly pathogenic PRRSV-1 strain. To determine the RNAscope's applicability as a semi-quantitative method, we analysed the association between the proportion of the virus-infected cells measured with an image analysis software (QuPath) and the outcome of the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) tests performed in parallel. The results of the quantitative approach of these two molecular biological methods show significant association (pseudo R-2 = 0.3894, p = 0.004). This is the first time RNAscope assay has been implemented for the detection of PRRSV-1 in experimental animals.},
	keywords = {Pathogenesis; In Situ Hybridization; IMPACT; porcine reproductive and respiratory syndrome virus; qRT-PCR; RNAscope; QuPath; RESPIRATORY-SYNDROME-VIRUS; FIXED TISSUES},
	year = {2021},
	orcid-numbers = {Ács, Balázs/0000-0002-0972-4633; Szász, Attila Marcell/0000-0003-2739-4196; Papp, Márton/0000-0003-4975-253X}
}

@article{MTMT:32344609,
	title = {Automated digital TIL analysis (ADTA) adds prognostic value to standard assessment of depth and ulceration in primary melanoma},
	url = {https://m2.mtmt.hu/api/publication/32344609},
	author = {Moore, Michael R. and Friesner, Isabel D. and Rizk, Emanuelle M. and Fullerton, Benjamin T. and Mondal, Manas and Trager, Megan H. and Mendelson, Karen and Chikeka, Ijeuru and Kurc, Tahsin and Gupta, Rajarsi and Rohr, Bethany R. and Robinson, Eric J. and Ács, Balázs and Chang, Rui and Kluger, Harriet and Taback, Bret and Geskin, Larisa J. and Horst, Basil and Gardner, Kevin and Niedt, George and Celebi, Julide T. and Gartrell-Corrado, Robyn D. and Messina, Jane and Ferringer, Tammie and Rimm, David L. and Saltz, Joel and Wang, Jing and Vanguri, Rami and Saenger, Yvonne M.},
	doi = {10.1038/s41598-021-82305-1},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {11},
	unique-id = {32344609},
	issn = {2045-2322},
	abstract = {Accurate prognostic biomarkers in early-stage melanoma are urgently needed to stratify patients for clinical trials of adjuvant therapy. We applied a previously developed open source deep learning algorithm to detect tumor-infiltrating lymphocytes (TILs) in hematoxylin and eosin (H&E) images of early-stage melanomas. We tested whether automated digital (TIL) analysis (ADTA) improved accuracy of prediction of disease specific survival (DSS) based on current pathology standards. ADTA was applied to a training cohort (n=80) and a cutoff value was defined based on a Receiver Operating Curve. ADTA was then applied to a validation cohort (n=145) and the previously determined cutoff value was used to stratify high and low risk patients, as demonstrated by Kaplan-Meier analysis (p <= 0.001). Multivariable Cox proportional hazards analysis was performed using ADTA, depth, and ulceration as co-variables and showed that ADTA contributed to DSS prediction (HR: 4.18, CI 1.51-11.58, p=0.006). ADTA provides an effective and attainable assessment of TILs and should be further evaluated in larger studies for inclusion in staging algorithms.},
	year = {2021},
	eissn = {2045-2322},
	orcid-numbers = {Ács, Balázs/0000-0002-0972-4633; Wang, Jing/0000-0003-1580-1356}
}

@article{MTMT:32341736,
	title = {A new tool for technical standardization of the Ki67 immunohistochemical assay},
	url = {https://m2.mtmt.hu/api/publication/32341736},
	author = {Aung, Thazin Nwe and Ács, Balázs and Warrell, Jonathan and Bai, Yalai and Gaule, Patricia and Martinez-Morilla, Sandra and Vathiotis, Ioannis and Shafi, Saba and Moutafi, Myrto and Gerstein, Mark and Freiberg, Benjamin and Fulton, Regan and Rimm, David L.},
	doi = {10.1038/s41379-021-00745-6},
	journal-iso = {MODERN PATHOL},
	journal = {MODERN PATHOLOGY},
	volume = {34},
	unique-id = {32341736},
	issn = {0893-3952},
	abstract = {Ki67, a nuclear proliferation-related protein, is heavily used in anatomic pathology but has not become a companion diagnostic or a standard-of-care biomarker due to analytic variability in both assay protocols and interpretation. The International Ki67 Working Group in breast cancer has published and has ongoing efforts in the standardization of the interpretation of Ki67, but they have not yet assessed technical issues of assay production representing multiple sources of variation, including antibody clones, antibody formats, staining platforms, and operators. The goal of this work is to address these issues with a new standardization tool. We have developed a cell line microarray system in which mixes of human Karpas 299 or Jurkat cells (Ki67(+)) with Sf9 (Spodoptera frugiperda) (Ki67(-)) cells are present in incremental standardized ratios. To validate the tool, six different antibodies, including both ready-to-use and concentrate formats from six vendors, were used to measure Ki67 proliferation indices using IHC protocols for manual (bench-top) and automated platforms. The assays were performed by three different laboratories at Yale and analyzed using two image analysis software packages, including QuPath and Visiopharm. Results showed statistically significant differences in Ki67 reactivity between each antibody clone. However, subsets of Ki67 assays using three clones performed in three different labs show no significant differences. This work shows the need for analytic standardization of the Ki67 assay and provides a new tool to do so. We show here how a cell line standardization system can be used to normalize the staining variability in proliferation indices between different antibody clones in a triple negative breast cancer cohort. We believe that this cell line standardization array has the potential to improve reproducibility among Ki67 assays and laboratories, which is critical for establishing Ki67 as a standard-of-care assay.},
	year = {2021},
	eissn = {1530-0285},
	pages = {1261-1270},
	orcid-numbers = {Ács, Balázs/0000-0002-0972-4633; Moutafi, Myrto/0000-0002-9314-3187}
}