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Claes J, Agten A, Blázquez-Moreno A, Crabbe M, Tuefferd M, Goehlmann H, Geys H, Peng CY, Neyens T, Faes C. The influence of resolution on the predictive power of spatial heterogeneity measures as biomarkers of liver fibrosis. Comput Biol Med 2024; 171:108231. [PMID: 38422965 DOI: 10.1016/j.compbiomed.2024.108231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/23/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Spatial heterogeneity of cells in liver biopsies can be used as biomarker for disease severity of patients. This heterogeneity can be quantified by non-parametric statistics of point pattern data, which make use of an aggregation of the point locations. The method and scale of aggregation are usually chosen ad hoc, despite values of the aforementioned statistics being heavily dependent on them. Moreover, in the context of measuring heterogeneity, increasing spatial resolution will not endlessly provide more accuracy. The question then becomes how changes in resolution influence heterogeneity indicators, and subsequently how they influence their predictive abilities. In this paper, cell level data of liver biopsy tissue taken from chronic Hepatitis B patients is used to analyze this issue. Firstly, Morisita-Horn indices, Shannon indices and Getis-Ord statistics were evaluated as heterogeneity indicators of different types of cells, using multiple resolutions. Secondly, the effect of resolution on the predictive performance of the indices in an ordinal regression model was investigated, as well as their importance in the model. A simulation study was subsequently performed to validate the aforementioned methods. In general, for specific heterogeneity indicators, a downward trend in predictive performance could be observed. While for local measures of heterogeneity a smaller grid-size is outperforming, global measures have a better performance with medium-sized grids. In addition, the use of both local and global measures of heterogeneity is recommended to improve the predictive performance.
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Affiliation(s)
- Jari Claes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium.
| | - Annelies Agten
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium
| | - Alfonso Blázquez-Moreno
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Marjolein Crabbe
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Marianne Tuefferd
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Hinrich Goehlmann
- Translational Biomarkers, Infectious Diseases, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Helena Geys
- Discovery Statistics, Global Development, Janssen Research and Development, Turnhoutseweg 30, Beerse, 2340, Belgium
| | | | - Thomas Neyens
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium; L-BioStat, KU Leuven, Kapucijnenvoer 35, Leuven, 3000, Belgium
| | - Christel Faes
- Data Science Institute, UHasselt - Hasselt University, Agoralaan 1, Diepenbeek, 3590, Belgium
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Yousef A, Ghobrial L, Diamandis EP. Tumor heterogeneity: how could we use it to achieve better clinical outcomes? Diagnosis (Berl) 2024; 11:25-30. [PMID: 37817292 DOI: 10.1515/dx-2023-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/17/2023] [Indexed: 10/12/2023]
Abstract
Differences in tumors related to location, tissue type, and histological subtype have been well documented for decades. Tumors are also molecularly very diverse. In this short review we describe the current classification schemes for tumor heterogeneity. We enlist the various drivers of tumor heterogeneity generation and comment on their clinical significance. New molecular techniques promise to assess tumor heterogeneity at affordable cost, so that these techniques can soon enter the clinic. While tumor heterogeneity currently represents a major unfavorable barrier in the field of oncology, it may also be a key in revolutionizing cancer diagnosis and treatment. Information regarding tumor heterogeneity has the potential to provide more thorough prognostic information, guide more efficacious combination treatment regimens, and lead to the development of novel therapeutic strategies and identification of new targets. For these gains to be realized, assessment of tumor heterogeneity needs to be incorporated into current diagnostic protocols but standardized and reproducible assessment methods are required. Fortunately, when these advances are realized, tumor heterogeneity has the potential to improve clinical outcomes.
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Affiliation(s)
| | - Lucianna Ghobrial
- School of Medicine, and Department of Public Health, King's College London, London, UK
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Azzalini E, Stanta G, Canzonieri V, Bonin S. Overview of Tumor Heterogeneity in High-Grade Serous Ovarian Cancers. Int J Mol Sci 2023; 24:15077. [PMID: 37894756 PMCID: PMC10606847 DOI: 10.3390/ijms242015077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Ovarian cancers encompass a group of neoplasms originating from germinal tissues and exhibiting distinct clinical, pathological, and molecular features. Among these, epithelial ovarian cancers (EOCs) are the most prevalent, comprising five distinct tumor histotypes. Notably, high-grade serous ovarian cancers (HGSOCs) represent the majority, accounting for over 70% of EOC cases. Due to their silent and asymptomatic behavior, HGSOCs are generally diagnosed in advanced stages with an evolved and complex genomic state, characterized by high intratumor heterogeneity (ITH) due to chromosomal instability that distinguishes HGSOCs. Histologically, these cancers exhibit significant morphological diversity both within and between tumors. The histologic patterns associated with solid, endometrioid, and transitional (SET) and classic subtypes of HGSOCs offer prognostic insights and may indicate specific molecular profiles. The evolution of HGSOC from primary to metastasis is typically characterized by clonal ITH, involving shared or divergent mutations in neoplastic sub-clones within primary and metastatic sites. Disease progression and therapy resistance are also influenced by non-clonal ITH, related to interactions with the tumor microenvironment and further genomic changes. Notably, significant alterations occur in nonmalignant cells, including cancer-associated fibroblast and immune cells, during tumor progression. This review provides an overview of the complex nature of HGSOC, encompassing its various aspects of intratumor heterogeneity, histological patterns, and its dynamic evolution during progression and therapy resistance.
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Affiliation(s)
- Eros Azzalini
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
| | - Giorgio Stanta
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
| | - Vincenzo Canzonieri
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
- Pathology Unit, Centro di Riferimento Oncologico (CRO) IRCCS, Aviano-National Cancer Institute, 33081 Pordenone, Italy
| | - Serena Bonin
- Department of Medical Sciences (DSM), University of Trieste, 34149 Trieste, Italy; (E.A.); (G.S.); (V.C.)
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Azzalini E, Tierno D, Bartoletti M, Barbazza R, Giorda G, Puglisi F, Cecere SC, Losito NS, Russo D, Stanta G, Canzonieri V, Bonin S. AKT Isoforms Interplay in High-Grade Serous Ovarian Cancer Prognosis and Characterization. Cancers (Basel) 2022; 14:cancers14020304. [PMID: 35053468 PMCID: PMC8773580 DOI: 10.3390/cancers14020304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 01/10/2023] Open
Abstract
Simple Summary New therapeutical strategies are needed to improve survival in high-grade serous ovarian cancer (HGSOC) patients. AKT inhibitors are promising agents able to act in synergy with PARP inhibitors and platinum-based therapies, but the subset of patients who could benefit from this approach is still unclear. We analyzed AKT isoforms expression in a retrospective cohort and we identified four AKT expression groups related to patients’ survival, tumor morphology and the BRCA status that could help in stratifying patients for future clinical trials. Abstract High-grade serous ovarian cancer (HGSOC) is among the deadliest gynecological malignancies. The acquired resistance to platinum-based therapies and the intrinsic heterogeneity of the disease contribute to the low survival rate. To improve patients’ outcomes, new combinatorial approaches able to target different tumor vulnerabilities and enhance the efficacy of the current therapies are required. AKT inhibitors are promising antineoplastic agents able to act in synergy with PARP inhibitors, but the spectrum of patients who can benefit from this combination is unclear, since the role of the three different isoforms of AKT is still unknown. Here, we study the expression of AKT isoforms on a retrospective cohort of archive tissue by RT-droplet digital PCR (ddPCR) analyzing their association with the clinicopathological features of patients. Based on AKT1/AKT2 and AKT1/AKT3 ratios, we define four AKT classes which were related to patients’ survival, tumor morphology and BRCA1 expression. Moreover, our results show that high AKT3 expression levels were frequently associated with tumors having classic features, a low number of mitoses and the presence of psammoma bodies. Overall, our study obtains new insights on AKT isoforms and their associations with the clinicopathological features of HGSOC patients. These evidences could help to better define the subsets of patients who can benefit from AKT and PARP inhibitors therapy in future clinical trials.
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Affiliation(s)
- Eros Azzalini
- Department of Medical Sciences (DSM), University of Trieste, 34147 Trieste, Italy; (E.A.); (D.T.); (R.B.); (G.S.)
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Domenico Tierno
- Department of Medical Sciences (DSM), University of Trieste, 34147 Trieste, Italy; (E.A.); (D.T.); (R.B.); (G.S.)
| | - Michele Bartoletti
- Unit of Medical Oncology and Cancer Prevention, Department of Medical Oncology, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy; (M.B.); (F.P.)
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Renzo Barbazza
- Department of Medical Sciences (DSM), University of Trieste, 34147 Trieste, Italy; (E.A.); (D.T.); (R.B.); (G.S.)
| | - Giorgio Giorda
- Unit of Gynecologic Oncology Surgery, IRCCS CRO Aviano, National Cancer Institute, 33081 Aviano, Italy;
| | - Fabio Puglisi
- Unit of Medical Oncology and Cancer Prevention, Department of Medical Oncology, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy; (M.B.); (F.P.)
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
| | - Sabrina Chiara Cecere
- Istituto Nazionale Tumori IRCCS—Fondazione G. Pascale, 80131 Napoli, Italy; (S.C.C.); (N.S.L.); (D.R.)
| | - Nunzia Simona Losito
- Istituto Nazionale Tumori IRCCS—Fondazione G. Pascale, 80131 Napoli, Italy; (S.C.C.); (N.S.L.); (D.R.)
| | - Daniela Russo
- Istituto Nazionale Tumori IRCCS—Fondazione G. Pascale, 80131 Napoli, Italy; (S.C.C.); (N.S.L.); (D.R.)
| | - Giorgio Stanta
- Department of Medical Sciences (DSM), University of Trieste, 34147 Trieste, Italy; (E.A.); (D.T.); (R.B.); (G.S.)
| | - Vincenzo Canzonieri
- Department of Medical Sciences (DSM), University of Trieste, 34147 Trieste, Italy; (E.A.); (D.T.); (R.B.); (G.S.)
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
- Correspondence: (V.C.); (S.B.); Tel.: +39−0434−659−618 (V.C.); +39−040−399−3266 (S.B.)
| | - Serena Bonin
- Department of Medical Sciences (DSM), University of Trieste, 34147 Trieste, Italy; (E.A.); (D.T.); (R.B.); (G.S.)
- Correspondence: (V.C.); (S.B.); Tel.: +39−0434−659−618 (V.C.); +39−040−399−3266 (S.B.)
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