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1.
Adv Radiat Oncol ; 9(10): 101583, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39258143

RESUMEN

Purpose: External beam radiation therapy (EBRT) is a critical component of breast cancer (BC) therapy. Given the improvement in technology in the contemporary era, we hypothesized that there is no difference in the development of or worsening of existing coronary artery disease (CAD) in patients with BC receiving left versus right-sided radiation. Methods and Materials: For the meta-analysis portion of our study, we searched PubMed, Web of Science, and Scopus and included studies from January 1999 to September 2022. CAD was identified using a homogenous metric across multiple studies included. We computed the risk ratio (RR) for included studies using a random effects model. For the institutional cohort portion of our study, we selected high cardiovascular-risk patients who received diagnoses of BC between 2010 and 2022 if they met our inclusion criteria. We performed a Cox proportional hazards model with stepwise adjustment. Results: A pooled random effects model with 9 studies showed that patients with left-sided BC receiving EBRT had a 10% increased risk of CAD when compared with patients with right-sided BC receiving EBRT (RR, 1.10; 95% CI, 1.02-1.18; P = .01). However, subgroup analysis of 6 studies that included patients diagnosed after 1980 did not show a significant difference in CAD based on BC laterality (RR, 1.07; 95% CI, 0.95-1.20; P = .27). For the institutional cohort portion of the study, we found that patients with left-sided BC who received EBRT did not have a significantly higher risk of CAD when compared with their right-sided counterparts (hazard ratios [HR], 0.73; 95% CI, 0.34-1.54; P = .402). Conclusions: Our study suggests a historical trend of increased CAD in BC patients receiving left-sided EBRT. Data from patients diagnosed after 2010 in our institutional cohort did not show a significant difference, emphasizing that modern EBRT regimens are safe, and laterality of BC does not affect CAD outcomes in the short term after a BC diagnosis.

2.
Sci Rep ; 14(1): 17602, 2024 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-39080402

RESUMEN

Geographic atrophy (GA) is an advanced form of dry age-related macular degeneration (AMD) that leads to progressive and irreversible vision loss. Identifying patients with greatest risk of GA progression is important for targeted utilization of emerging therapies. This study aimed to comprehensively evaluate the role of shape-based fractal dimension features ( F fd ) of sub-retinal pigment epithelium (sub-RPE) compartment and texture-based radiomics features ( F t ) of Ellipsoid Zone (EZ)-RPE and sub-RPE compartments for risk stratification for subfoveal GA (sfGA) progression. This was a retrospective study of 137 dry AMD subjects with a 5-year follow-up. Based on sfGA status at year 5, eyes were categorized as Progressors and Non-progressors. A total of 15 shape-based F fd of sub-RPE surface and 494 F t from each of sub-RPE and EZ-RPE compartments were extracted from baseline spectral domain-optical coherence tomography scans. The top nine features were identified from F fd and F t feature pool separately using minimum Redundancy maximum Relevance feature selection and used to train a Random Forest (RF) classifier independently using three-fold cross validation on the training set ( S t , N = 90) to distinguish between sfGA Progressors and Non-progressors. Combined F fd and F t was also evaluated in predicting risk of sfGA progression. The RF classifier yielded AUC of 0.85, 0.79 and 0.89 on independent test set ( S v , N = 47) using F fd , F t , and their combination, respectively. Using combined F fd and F t , the improvement in AUC was statistically significant on S v with p-values of 0.032 and 0.04 compared to using only F fd and only F t , respectively. Combined F fd and F t appears to identify high-risk patients. Our results show that FD and texture features could be potentially used for predicting risk of sfGA progression and future therapeutic response.


Asunto(s)
Progresión de la Enfermedad , Atrofia Geográfica , Epitelio Pigmentado de la Retina , Tomografía de Coherencia Óptica , Humanos , Tomografía de Coherencia Óptica/métodos , Atrofia Geográfica/diagnóstico por imagen , Atrofia Geográfica/patología , Femenino , Masculino , Anciano , Estudios Retrospectivos , Epitelio Pigmentado de la Retina/diagnóstico por imagen , Epitelio Pigmentado de la Retina/patología , Fóvea Central/diagnóstico por imagen , Fóvea Central/patología , Persona de Mediana Edad , Anciano de 80 o más Años , Degeneración Macular/diagnóstico por imagen , Degeneración Macular/patología
3.
Heliyon ; 10(13): e32232, 2024 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-39035512

RESUMEN

Background and objective: Intravitreal injection of anti-VEGF agents is the first-line treatment for patients with neovascular-age related macular degeneration (nAMD). One unique serious adverse event that may be associated with these agents is intraocular inflammation (IOI). The main purpose of this analysis was to evaluate the potential presence of texture-based radiomics features characterizing heterogeneity within the vitreous compartment of spectral domain optical coherence tomography (SD-OCT) images that may precede or develop in association with IOI and might serve as OCT biomarkers for IOI. Methods: This is a post-hoc analysis of a subset of cases (N = 67) involving IOI, endophthalmitis, and/or retinal vascular occlusion in the phase 3 HAWK trial. These were investigator determined diagnoses that were also confirmed by the safety review committee. Intraocular inflammation was any signs of inflammation within the eye, endophthalmitis was inflammation associated with presumed infection, and retinal vascular occlusions consisted of intraocular inflammation with concurrent vascular occlusions/vasculitis. Out of 67 eyes, 34 belonged to the Safety group with an IOI event and 33 were propensity-matched Controls. A total of 481 texture-based radiomics features were extracted from the vitreous compartment of the SD-OCT scans at pre-IOI time point (i.e., much earlier than the actual event). Most discriminating five features, selected by the Wilcoxon Rank Sum feature selection were evaluated using Random Forest (RF) classifier on the training set ( S t r , N = 47) to differentiate between the two patient groups. Classifier performance was subsequently validated on the independent test set ( S t , N = 20). Additionally, the classifier performance in discriminating the Control and Safety group was also validated on S t at the IOI event timepoint. Results: The RF classifier yielded area under the Receiver Operating Characteristics curve (AUC) of 0.76 and 0.81 on S t using texture-based radiomics features at pre-IOI and event time-point, respectively. Conclusions: In this analysis, the presence of a pre-IOI safety signal was detected in the form of textural heterogeneity within the vitreous compartment even prior to the actual event being identified by the investigator. This finding may help the clinicians to assess for underlying posterior inflammation.

4.
Lancet Digit Health ; 6(8): e562-e569, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38987116

RESUMEN

BACKGROUND: The density of tumour-infiltrating lymphocytes (TILs) could be prognostic in ductal carcinoma in situ (DCIS). However, manual TIL quantification is time-consuming and suffers from interobserver and intraobserver variability. In this study, we developed a TIL-based computational pathology biomarker and evaluated its association with the risk of recurrence and benefit of adjuvant treatment in a clinical trial cohort. METHODS: In this retrospective cohort study, a computational pathology pipeline was developed to generate a TIL-based biomarker (CPath TIL categories). Subsequently, the signature underwent a masked independent validation on H&E-stained whole-section images of 755 patients with DCIS from the UK/ANZ DCIS randomised controlled trial. Specifically, continuous biomarker CPath TIL score was calculated as the average TIL density in the DCIS microenvironment and dichotomised into binary biomarker CPath TIL categories (CPath TIL-high vs CPath TIL-low) using the median value as a cutoff. The primary outcome was ipsilateral breast event (IBE; either recurrence of DCIS [DCIS-IBE] or invasive progression [I-IBE]). The Cox proportional hazards model was used to estimate the hazard ratio (HR). FINDINGS: CPath TIL-score was evaluable in 718 (95%) of 755 patients (151 IBEs). Patients with CPath TIL-high DCIS had a greater risk of IBE than those with CPath TIL-low DCIS (HR 2·10 [95% CI 1·39-3·18]; p=0·0004). The risk of I-IBE was greater in patients with CPath TIL-high DCIS than those with CPath TIL-low DCIS (3·09 [1·56-6·14]; p=0·0013), and the risk of DCIS-IBE was non-significantly higher in those with CPath TIL-high DCIS (1·61 [0·95-2·72]; p=0·077). A significant interaction (pinteraction=0·025) between CPath TIL categories and radiotherapy was observed with a greater magnitude of radiotherapy benefit in preventing IBE in CPath TIL-high DCIS (0·32 [0·19-0·54]) than CPath TIL-low DCIS (0·40 [0·20-0·81]). INTERPRETATION: High TIL density is associated with higher recurrence risk-particularly of invasive recurrence-and greater radiotherapy benefit in patients with DCIS. Our TIL-based computational pathology signature has a prognostic and predictive role in DCIS. FUNDING: National Cancer Institute under award number U01CA269181, Cancer Research UK (C569/A12061; C569/A16891), and the Breast Cancer Research Foundation, New York (NY, USA).


Asunto(s)
Neoplasias de la Mama , Carcinoma Intraductal no Infiltrante , Linfocitos Infiltrantes de Tumor , Humanos , Femenino , Carcinoma Intraductal no Infiltrante/patología , Neoplasias de la Mama/patología , Estudios Retrospectivos , Pronóstico , Persona de Mediana Edad , Recurrencia Local de Neoplasia , Biomarcadores de Tumor , Reino Unido , Anciano , Adulto
5.
medRxiv ; 2024 Jul 21.
Artículo en Inglés | MEDLINE | ID: mdl-39072032

RESUMEN

Background: Visual scoring of tubular damage has limitations in capturing the full spectrum of structural changes and prognostic potential. We investigate if computationally quantified tubular features can enhance prognostication and reveal spatial relationships with interstitial fibrosis. Methods: Deep-learning and image-processing-based segmentations were employed in N=254/266 PAS-WSIs from the NEPTUNE/CureGN datasets (135/153 focal segmental glomerulosclerosis and 119/113 minimal change disease) for: cortex, tubular lumen (TL), epithelium (TE), nuclei (TN), and basement membrane (TBM). N=104 pathomic features were extracted from these segmented tubular substructures and summarized at the patient level using summary statistics. The tubular features were quantified across the biopsy and in manually segmented regions of mature interstitial fibrosis and tubular atrophy (IFTA), pre-IFTA and non-IFTA in the NEPTUNE dataset. Minimum Redundancy Maximum Relevance was used in the NEPTUNE dataset to select features most associated with disease progression and proteinuria remission. Ridge-penalized Cox models evaluated their predictive discrimination compared to clinical/demographic data and visual-assessment. Models were evaluated in the CureGN dataset. Results: N=9 features were predictive of disease progression and/or proteinuria remission. Models with tubular features had high prognostic accuracy in both NEPTUNE and CureGN datasets and increased prognostic accuracy for both outcomes (5.6%-7.7% and 1.6%-4.6% increase for disease progression and proteinuria remission, respectively) compared to conventional parameters alone in the NEPTUNE dataset. TBM thickness/area and TE simplification progressively increased from non- to pre- and mature IFTA. Conclusions: Previously under-recognized, quantifiable, and clinically relevant tubular features in the kidney parenchyma can enhance understanding of mechanisms of disease progression and risk stratification.

6.
Npj Imaging ; 2(1): 15, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38962496

RESUMEN

Batch effects (BEs) refer to systematic technical differences in data collection unrelated to biological variations whose noise is shown to negatively impact machine learning (ML) model generalizability. Here we release CohortFinder (http://cohortfinder.com), an open-source tool aimed at mitigating BEs via data-driven cohort partitioning. We demonstrate CohortFinder improves ML model performance in downstream digital pathology and medical image processing tasks. CohortFinder is freely available for download at cohortfinder.com.

7.
Heliyon ; 10(13): e33618, 2024 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-39035539

RESUMEN

Background: The changes in the tumor microenvironment of high-grade serous ovarian carcinomas following neoadjuvant chemotherapy are a complex area of study. Previous research underscores the importance of investigating the immune and collagen components within the tumor microenvironment for prognostic implications. Methods: In this study, we utilized computational pathology techniques with Hematoxylin and Eosin-stained images to quantitatively characterize the immune and collagen architecture within the tumor microenvironment of patients with high-grade serous ovarian carcinoma. Results: Our analysis of 12 pre- and post-neoadjuvant chemotherapy images revealed an increase in immune infiltrate, primarily within the epithelial region. Additionally, post-neoadjuvant chemotherapy images exhibited chaotic collagen architecture compared to pre-neoadjuvant chemotherapy images. Importantly, features extracted from post-neoadjuvant chemotherapy images showed associations with overall survival, potentially aiding in the selection of patients for immunotherapy trials. Conclusions: These findings offer critical insights into the changes in the tumor microenvironment of high-grade serous ovarian carcinomas following neoadjuvant chemotherapy and their potential implications for clinical outcomes.

8.
Nat Rev Clin Oncol ; 21(8): 628-637, 2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38849530

RESUMEN

Artificial intelligence (AI) stands at the threshold of revolutionizing clinical oncology, with considerable potential to improve early cancer detection and risk assessment, and to enable more accurate personalized treatment recommendations. However, a notable imbalance exists in the distribution of the benefits of AI, which disproportionately favour those living in specific geographical locations and in specific populations. In this Perspective, we discuss the need to foster the development of equitable AI tools that are both accurate in and accessible to a diverse range of patient populations, including those in low-income to middle-income countries. We also discuss some of the challenges and potential solutions in attaining equitable AI, including addressing the historically limited representation of diverse populations in existing clinical datasets and the use of inadequate clinical validation methods. Additionally, we focus on extant sources of inequity including the type of model approach (such as deep learning, and feature engineering-based methods), the implications of dataset curation strategies, the need for rigorous validation across a variety of populations and settings, and the risk of introducing contextual bias that comes with developing tools predominantly in high-income countries.


Asunto(s)
Inteligencia Artificial , Oncología Médica , Neoplasias , Humanos , Neoplasias/terapia , Países en Desarrollo
9.
NPJ Digit Med ; 7(1): 164, 2024 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-38902336

RESUMEN

The discovery of patterns associated with diagnosis, prognosis, and therapy response in digital pathology images often requires intractable labeling of large quantities of histological objects. Here we release an open-source labeling tool, PatchSorter, which integrates deep learning with an intuitive web interface. Using >100,000 objects, we demonstrate a >7x improvement in labels per second over unaided labeling, with minimal impact on labeling accuracy, thus enabling high-throughput labeling of large datasets.

10.
Comput Biol Med ; 177: 108643, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38815485

RESUMEN

Severe COVID-19 can lead to extensive lung disease causing lung architectural distortion. In this study we employed machine learning and statistical atlas-based approaches to explore possible changes in lung shape among COVID-19 patients and evaluated whether the extent of these changes was associated with COVID-19 severity. On a large multi-institutional dataset (N = 3443), three different populations were defined; a) healthy (no COVID-19), b) mild COVID-19 (no ventilator required), c) severe COVID-19 (ventilator required), and the presence of lung shape differences between them were explored using baseline chest CT. Significant lung shape differences were observed along mediastinal surfaces of the lungs across all severity of COVID-19 disease. Additionally, differences were seen on basal surfaces of the lung when compared between healthy and severe COVID-19 patients. Finally, an AI model (a 3D residual convolutional network) characterizing these shape differences coupled with lung infiltrates (ground-glass opacities and consolidation regions) was found to be associated with COVID-19 severity.


Asunto(s)
COVID-19 , Aprendizaje Profundo , Pulmón , SARS-CoV-2 , Índice de Severidad de la Enfermedad , Tomografía Computarizada por Rayos X , Humanos , COVID-19/diagnóstico por imagen , Pulmón/diagnóstico por imagen , Masculino , Femenino , Estudios Retrospectivos , Persona de Mediana Edad , Anciano , Adulto
12.
Res Sq ; 2024 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-38798599

RESUMEN

Both overt and indolent inflammatory insults in heart transplantation can accelerate pathologic cardiac remodeling, but there are few tools for monitoring the speed and severity of remodeling over time. To address this need, we developed an automated computational pathology system to measure pathologic remodeling in transplant biopsy samples in a large, retrospective cohort of n=2167 digitized heart transplant biopsy slides. Biopsy images were analyzed to identify the pathologic stromal changes associated with future allograft loss or advanced allograft vasculopathy. Biopsy images were then analyzed to assess which historical allo-inflammatory events drive progression of these pathologic stromal changes over time in serial biopsy samples. The top-5 features of pathologic stromal remodeling most strongly associated with adverse outcomes were also strongly associated with histories of both overt and indolent inflammatory events. Our findings identify previously unappreciated subgroups of higher- and lower-risk transplant patients, and highlight the translational potential of digital pathology analysis.

13.
Heliyon ; 10(8): e29602, 2024 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-38665576

RESUMEN

Objectives: To evaluate the added benefit of integrating features from pre-treatment MRI (radiomics) and digitized post-surgical pathology slides (pathomics) in prostate cancer (PCa) patients for prognosticating outcomes post radical-prostatectomy (RP) including a) rising prostate specific antigen (PSA), and b) extraprostatic-extension (EPE). Methods: Multi-institutional data (N = 58) of PCa patients who underwent pre-treatment 3-T MRI prior to RP were included in this retrospective study. Radiomic and pathomic features were extracted from PCa regions on MRI and RP specimens delineated by expert clinicians. On training set (D1, N = 44), Cox Proportional-Hazards models MR, MP and MRaP were trained using radiomics, pathomics, and their combination, respectively, to prognosticate rising PSA (PSA > 0.03 ng/mL). Top features from MRaP were used to train a model to predict EPE on D1 and test on external dataset (D2, N = 14). C-index, Kalplan-Meier curves were used for survival analysis, and area under ROC (AUC) was used for EPE. MRaP was compared with the existing post-treatment risk-calculator, CAPRA (MC). Results: Patients had median follow-up of 34 months. MRaP (c-index = 0.685 ± 0.05) significantly outperformed MR (c-index = 0.646 ± 0.05), MP (c-index = 0.631 ± 0.06) and MC (c-index = 0.601 ± 0.071) (p < 0.0001). Cross-validated Kaplan-Meier curves showed significant separation among risk groups for rising PSA for MRaP (p < 0.005, Hazard Ratio (HR) = 11.36) as compared to MR (p = 0.64, HR = 1.33), MP (p = 0.19, HR = 2.82) and MC (p = 0.10, HR = 3.05). Integrated radio-pathomic model MRaP (AUC = 0.80) outperformed MR (AUC = 0.57) and MP (AUC = 0.76) in predicting EPE on external-data (D2). Conclusions: Results from this preliminary study suggest that a combination of radiomic and pathomic features can better predict post-surgical outcomes (rising PSA and EPE) compared to either of them individually as well as extant prognostic nomogram (CAPRA).

14.
NPJ Precis Oncol ; 8(1): 80, 2024 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-38553633

RESUMEN

This review delves into the most recent advancements in applying artificial intelligence (AI) within neuro-oncology, specifically emphasizing work on gliomas, a class of brain tumors that represent a significant global health issue. AI has brought transformative innovations to brain tumor management, utilizing imaging, histopathological, and genomic tools for efficient detection, categorization, outcome prediction, and treatment planning. Assessing its influence across all facets of malignant brain tumor management- diagnosis, prognosis, and therapy- AI models outperform human evaluations in terms of accuracy and specificity. Their ability to discern molecular aspects from imaging may reduce reliance on invasive diagnostics and may accelerate the time to molecular diagnoses. The review covers AI techniques, from classical machine learning to deep learning, highlighting current applications and challenges. Promising directions for future research include multimodal data integration, generative AI, large medical language models, precise tumor delineation and characterization, and addressing racial and gender disparities. Adaptive personalized treatment strategies are also emphasized for optimizing clinical outcomes. Ethical, legal, and social implications are discussed, advocating for transparency and fairness in AI integration for neuro-oncology and providing a holistic understanding of its transformative impact on patient care.

15.
Cell Rep Med ; 5(3): 101447, 2024 Mar 19.
Artículo en Inglés | MEDLINE | ID: mdl-38442713

RESUMEN

There is an unmet clinical need for a non-invasive and cost-effective test for oral squamous cell carcinoma (OSCC) that informs clinicians when a biopsy is warranted. Human beta-defensin 3 (hBD-3), an epithelial cell-derived anti-microbial peptide, is pro-tumorigenic and overexpressed in early-stage OSCC compared to hBD-2. We validate this expression dichotomy in carcinoma in situ and OSCC lesions using immunofluorescence microscopy and flow cytometry. The proportion of hBD-3/hBD-2 levels in non-invasively collected lesional cells compared to contralateral normal cells, obtained by ELISA, generates the beta-defensin index (BDI). Proof-of-principle and blinded discovery studies demonstrate that BDI discriminates OSCC from benign lesions. A multi-center validation study shows sensitivity and specificity values of 98.2% (95% confidence interval [CI] 90.3-99.9) and 82.6% (95% CI 68.6-92.2), respectively. A proof-of-principle study shows that BDI is adaptable to a point-of-care assay using microfluidics. We propose that BDI may fulfill a major unmet need in low-socioeconomic countries where pathology services are lacking.


Asunto(s)
Carcinoma de Células Escamosas , Neoplasias de Cabeza y Cuello , Neoplasias de la Boca , beta-Defensinas , Humanos , Neoplasias de la Boca/diagnóstico , Neoplasias de la Boca/patología , beta-Defensinas/análisis , beta-Defensinas/metabolismo , Carcinoma de Células Escamosas/diagnóstico , Carcinoma de Células Escamosas/patología , Biomarcadores , Carcinoma de Células Escamosas de Cabeza y Cuello
16.
Circ Heart Fail ; 17(2): e010950, 2024 02.
Artículo en Inglés | MEDLINE | ID: mdl-38348670

RESUMEN

BACKGROUND: Cardiac allograft rejection is the leading cause of early graft failure and is a major focus of postheart transplant patient care. While histological grading of endomyocardial biopsy samples remains the diagnostic standard for acute rejection, this standard has limited diagnostic accuracy. Discordance between biopsy rejection grade and patient clinical trajectory frequently leads to both overtreatment of indolent processes and delayed treatment of aggressive ones, spurring the need to investigate the adequacy of the current histological criteria for assessing clinically important rejection outcomes. METHODS: N=2900 endomyocardial biopsy images were assigned a rejection grade label (high versus low grade) and a clinical trajectory label (evident versus silent rejection). Using an image analysis approach, n=370 quantitative morphology features describing the lymphocytes and stroma were extracted from each slide. Two models were constructed to compare the subset of features associated with rejection grades versus those associated with clinical trajectories. A proof-of-principle machine learning pipeline-the cardiac allograft rejection evaluator-was then developed to test the feasibility of identifying the clinical severity of a rejection event. RESULTS: The histopathologic findings associated with conventional rejection grades differ substantially from those associated with clinically evident allograft injury. Quantitative assessment of a small set of well-defined morphological features can be leveraged to more accurately reflect the severity of rejection compared with that achieved by the International Society of Heart and Lung Transplantation grades. CONCLUSIONS: Conventional endomyocardial samples contain morphological information that enables accurate identification of clinically evident rejection events, and this information is incompletely captured by the current, guideline-endorsed, rejection grading criteria.


Asunto(s)
Insuficiencia Cardíaca , Trasplante de Corazón , Humanos , Miocardio/patología , Trasplante de Corazón/efectos adversos , Insuficiencia Cardíaca/patología , Corazón , Aloinjertos , Rechazo de Injerto/diagnóstico , Biopsia
17.
Commun Med (Lond) ; 4(1): 2, 2024 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-38172536

RESUMEN

BACKGROUND: The role of immune cells in collagen degradation within the tumor microenvironment (TME) is unclear. Immune cells, particularly tumor-infiltrating lymphocytes (TILs), are known to alter the extracellular matrix, affecting cancer progression and patient survival. However, the quantitative evaluation of the immune modulatory impact on collagen architecture within the TME remains limited. METHODS: We introduce CollaTIL, a computational pathology method that quantitatively characterizes the immune-collagen relationship within the TME of gynecologic cancers, including high-grade serous ovarian (HGSOC), cervical squamous cell carcinoma (CSCC), and endometrial carcinomas. CollaTIL aims to investigate immune modulatory impact on collagen architecture within the TME, aiming to uncover the interplay between the immune system and tumor progression. RESULTS: We observe that an increased immune infiltrate is associated with chaotic collagen architecture and higher entropy, while immune sparse TME exhibits ordered collagen and lower entropy. Importantly, CollaTIL-associated features that stratify disease risk are linked with gene signatures corresponding to TCA-Cycle in CSCC, and amino acid metabolism, and macrophages in HGSOC. CONCLUSIONS: CollaTIL uncovers a relationship between immune infiltration and collagen structure in the TME of gynecologic cancers. Integrating CollaTIL with genomic analysis offers promising opportunities for future therapeutic strategies and enhanced prognostic assessments in gynecologic oncology.


The role of cells that are part of our immune system in altering the structure of the protein collagen within cancers is not fully understood, particularly within cancers that affect women such as ovarian, cervical and uterine cancers. Here, we developed a computer-based method called CollaTIL to explore how immune cells influence collagen in these tumors and affect their growth. We found that a higher presence of immune cells leads to less organized collagen in the tumor. Conversely, when there are fewer immune cells, the collagen tends to be more structured. Additionally, CollaTIL identifies patterns that predict patient outcomes in these cancers. These findings not only enhance our understanding of tumor biology but also may be useful in helping clinicians to predict which patients are at risk of their disease progressing.

18.
Comput Methods Programs Biomed ; 244: 107990, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38194767

RESUMEN

BACKGROUND: Radiomics is a method within medical image analysis that involves the extraction of quantitative data from radiologic scans, often in conjunction with machine learning algorithms to phenotype disease appearance, prognosticate disease outcome, and predict treatment response. However, variance in CT scanner acquisition parameters, such as convolution kernels or pixel spacing, can impact radiomics texture feature values. PURPOSE: The extent to which the parameters influence radiomics features continues to be an active area of investigation. In this study, we describe a novel approach, Acquisition Impact on Radiomics Estimation (AcquIRE), to rank the impact of CT acquisition parameters on radiomic texture features. METHODS: In this work, we used three chest CT imaging datasets (n = 749 patients) from nine sites comprising: i) lung granulomas and adenocarcinomas (D1) (10 and 52 patients, respectively); ii) minimal and frank invasive adenocarcinoma (D2) (74 and 145 patients); and iii) early-stage NSCLC patients (D3) (315 patients). Datasets D2 and D3 were collected from four sites each, and D1 from a single site. For each patient, 744 texture features and nine acquisition parameters were extracted and utilized to evaluate which parameters impact radiomic features the most. The AcquIRE method establishes a relative assessment between acquisition parameters and radiomic texture featuresa through the creation of a classification model, which is then utilized to assess the rank of the acquisition parameters. RESULTS: Across the use cases, CT software version and convolution kernel parameters were found to have the most variance. In D1, it was observed that the Haralick texture feature family was the least affected by variations in acquisition parameters, while the Gabor feature family was the most impacted. However, in datasets D2 and D3, the Gabor features were found to be the least affected. Our findings suggest that the impact on radiomic parameters is as much a function of the problem in question as it is acquisition parameters. CONCLUSIONS: The software version and convolution kernel parameters impacted the radiomics feature the most.


Asunto(s)
Adenocarcinoma , Carcinoma de Pulmón de Células no Pequeñas , Neoplasias Pulmonares , Humanos , Estudios Retrospectivos , Radiómica , Tomografía Computarizada por Rayos X/métodos , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico por imagen , Adenocarcinoma/diagnóstico por imagen , Neoplasias Pulmonares/diagnóstico por imagen , Neoplasias Pulmonares/patología
20.
Transl Vis Sci Technol ; 13(1): 29, 2024 01 02.
Artículo en Inglés | MEDLINE | ID: mdl-38289610

RESUMEN

Purpose: The goal of this study was to evaluate the role of texture-based baseline radiomic features (Fr) and dynamic radiomics alterations (delta, FΔr) within multiple targeted compartments on optical coherence tomography (OCT) scans to predict response to anti-vascular endothelial growth factor (VEGF) therapy in neovascular age-related macular degeneration (nAMD). Methods: HAWK is a phase 3 clinical trial data set of active nAMD patients (N = 1082) comparing brolucizumab and aflibercept. This analysis included patients receiving 6 mg brolucizumab or 2 mg aflibercept and categorized as complete responders (n = 280) and incomplete responders (n = 239) based on whether or not the eyes achieved/maintained fluid resolution on OCT. A total of 481 Fr were extracted from each of the fluid, subretinal hyperreflective material (SHRM), retinal tissue, and sub-retinal pigment epithelium (RPE) compartments. Most discriminating eight baseline features, selected by the minimum redundancy, maximum relevance feature selection, were evaluated using a quadratic discriminant analysis (QDA) classifier on the training set (Str, n = 363) to differentiate between the two patient groups. Classifier performance was subsequently validated on independent test set (St, n = 156). Results: In total, 519 participants were included in this analysis from the HAWK phase 3 study. There were 280 complete responders and 219 incomplete responders. Compartmental analysis of radiomics featured identified the sub-RPE and SHRM compartments as the most distinguishing between the two response groups. The QDA classifier yielded areas under the curve of 0.78, 0.79, and 0.84, respectively, using Fr, FΔr, and combined Fr, FΔr, and Fc on St. Conclusions: Utilizing compartmental static and dynamic radiomics features, unique differences were identified between eyes that respond differently to anti-VEGF therapy in a large phase 3 trial that may provide important predictive value. Translational Relevance: Imaging biomarkers, such as radiomics features identified in this analysis, for predicting treatment response are needed to enhanced precision medicine in the management of nAMD.


Asunto(s)
Inhibidores de la Angiogénesis , Tomografía de Coherencia Óptica , Degeneración Macular Húmeda , Humanos , Inhibidores de la Angiogénesis/uso terapéutico , Radiómica , Epitelio Pigmentado de la Retina , Factor A de Crecimiento Endotelial Vascular/antagonistas & inhibidores , Agudeza Visual , Degeneración Macular Húmeda/diagnóstico por imagen , Degeneración Macular Húmeda/tratamiento farmacológico
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