Quantification of Structural Heterogeneity Using Fractal Analysis of Contrast-Enhanced CT Image to Predict Survival in Gastric Cancer Patients

Predicting lymphovascular invasion in N0 stage non-small cell lung cancer: A nomogram based on Dual-energy CT imaging and clinical findings

PURPOSE

To construct a nomogram for predicting lymphovascular invasion (LVI) in N0 stage non-small cell lung cancer (NSCLC) using dual-energy computed tomography (DECT) findings combined with clinical findings.

METHODS

We retrospectively recruited 135 patients with N0 stage NSCLC from two hospitals underwent DECT before surgery and were divided into development cohort (n = 107) and validation cohort (n = 28). The clinical findings (baseline characteristics, biochemical markers, serum tumor markers and Immunohistochemical markers), DECT-derived parameters (iodine concentration [IC], effective atomic number [Eff-Z] and normalized iodine concentration [NIC], iodine enhancement [IE] and NIC ratio [NICr]) and Fractal dimension (FD) were collected and measured. A nomogram was constructed using significant findings to predict LVI in N0 stage NSCLC and was externally validated.

RESULTS

Multivariable analysis revealed that lymphocyte count (LYMPH, odds ratio [OR]: 3.71, P=0.014), IC in arterial phase (ICa, OR: 1.25, P=0.021), NIC in venous phase (NICv, OR: 587.12, P=0.009) and FD (OR: 0.01, P=0.033) were independent significant factors for predicting LVI in N0 stage NSCLC, and were used to construct a nomogram. The nomogram exhibited robust predictive capabilities in both the development and validation cohort, with AUCs of 0.819 (95 % CI: 72.6-90.4) and 0.844 (95 % CI: 68.2-95.8), respectively. The calibration plots showed excellent agreement between the predicted probabilities and the actual rates of positive LVI, on external validation.

CONCLUSIONS

Combination of clinical and DECT imaging findings could aid in predicting LVI in N0 stage NSCLC using significant findings of LYMPH, ICa, NICv and FD.

An image analysis approach to characterize micronuclei differences in different subtypes of breast cancer

BACKGROUND

Micronuclei (MN) have been used as screening, diagnostic and prognostic markers in multiple cancer types, including breast cancer (BC). However, the question that the MN present in all subtypes of BC are similar or different remains unanswered. We thus hypothesized that MN present in different subtypes of BC may differ in their contents which may be visible as differences in their morphologic and morphometric features. This study was thus carried out with the aim to identify the differences between MN morphometry, complexity, and texture in different subtypes of BC, such as estrogen and progesterone receptor-positive (ER+/PR+; MCF-7, T-47D), human epidermal growth factor receptor-positive (Her2 +;SKBR3) and triple-negative BC (TNBC; MDA-MB-231, MDA-MB-468) cell lines (CLs) by ImageJ software.

METHODS

For analysis of MN dimensions, MN irregularity, and texture, we used morphometry and two mathematical computer-assisted algorithms, i.e., fractal dimension (FD) and grey level co-occurrence matrix (GLCM) of ImageJ software.

RESULTS

MN area and perimeter values showed differences in the size of MN in different subtypes of BC, with the largest MN in TNBC CLs. GLCM parameters (entropy, angular second moment, inverse difference moment, contrast, and correlation) showed highly heterogenous texture in case of TNBC MN as compared to the others. FD analysis also revealed more complexity and irregularity in MN found in TNBC cells.

CONCLUSION

The study for the first time showed morphometric, architectural and texture related differences amongst MN present in different subtypes of BC. The above may reflect differences in their composition and contents. Further, these differences may point towards the distinct mechanisms involved in the formation of MN in different subtypes of BC that need to be explored further.

Lower fractional dimension in Alzheimer's disease correlates with reduced locus coeruleus signal intensity

This study aimed to determine the pattern of fractional dimension (FD) in Alzheimer's disease (AD) patients, and investigate the relationship between FD and the locus coeruleus (LC) signal intensity.A total of 27 patients with AD and 25 healthy controls (HC) were collected to estimate the pattern of fractional dimension (FD) and cortical thickness (CT) using the Computational Anatomy Toolbox (CAT12), and statistically analyze between groups on a vertex level using statistical parametric mapping 12. In addition, they were examined by neuromelanin sensitive MRI(NM-MRI) technique to calculate the locus coeruleus signal contrast ratios (LC-CRs). Additionally, correlations between the pattern of FD and LC-CRs were further examined.Compared to HC, AD patients showed widespread lower CT and FD Furthermore, significant positive correlation was found between local fractional dimension (LFD) of the left rostral middle frontal cortex and LC-CRs. Results suggest lower cortical LFD is associated with LCCRs that may reflect a reduction due to broader neurodegenerative processes. This finding may highlight the potential utility for advanced measures of cortical complexity in assessing brain health and early identification of neurodegenerative processes.

Fractal nature of human gastrointestinal system: Exploring a new era

The morphological complexity of cells and tissues, whether normal or pathological, is characterized by two primary attributes: Irregularity and self-similarity across different scales. When an object exhibits self-similarity, its shape remains unchanged as the scales of measurement vary because any part of it resembles the whole. On the other hand, the size and geometric characteristics of an irregular object vary as the resolution increases, revealing more intricate details. Despite numerous attempts, a reliable and accurate method for quantifying the morphological features of gastrointestinal organs, tissues, cells, their dynamic changes, and pathological disorders has not yet been established. However, fractal geometry, which studies shapes and patterns that exhibit self-similarity, holds promise in providing a quantitative measure of the irregularly shaped morphologies and their underlying self-similar temporal behaviors. In this context, we explore the fractal nature of the gastrointestinal system and the potential of fractal geometry as a robust descriptor of its complex forms and functions. Additionally, we examine the practical applications of fractal geometry in clinical gastroenterology and hepatology practice.

SurvivalCNN: A deep learning-based method for gastric cancer survival prediction using radiological imaging data and clinicopathological variables

Radiological images have shown promising effects in patient prognostication. Deep learning provides a powerful approach for in-depth analysis of imaging data and integration of multi-modal data for modeling. In this work, we propose SurvivalCNN, a deep learning structure for cancer patient survival prediction using CT imaging data and non-imaging clinical data. In SurvivalCNN, a supervised convolutional neural network is designed to extract volumetric image features, and radiomics features are also integrated to provide potentially different imaging information. Within SurvivalCNN, a novel multi-thread multi-layer perceptron module, namely, SurvivalMLP, is proposed to perform survival prediction from censored survival data. We evaluate the proposed SurvivalCNN framework on a large clinical dataset of 1061 gastric cancer patients for both overall survival (OS) and progression-free survival (PFS) prediction. We compare SurvivalCNN to three different modeling methods and examine the effects of various sets of data/features when used individually or in combination. With five-fold cross validation, our experimental results show that SurvivalCNN achieves averaged concordance index 0.849 and 0.783 for predicting OS and PFS, respectively, outperforming the compared state-of-the-art methods and the clinical model. After future validation, the proposed SurvivalCNN model may serve as a clinical tool to improve gastric cancer patient survival estimation and prognosis analysis.

Fractal dimension of the brain in neurodegenerative disease and dementia: A systematic review

Sensitive and specific antemortem biomarkers of neurodegenerative disease and dementia are crucial to the pursuit of effective treatments, required both to reliably identify disease and to track its progression. Atrophy is the structural magnetic resonance imaging (MRI) hallmark of neurodegeneration. However in most cases it likely indicates a relatively advanced stage of disease less susceptible to treatment as some disease processes begin decades prior to clinical onset. Among emerging metrics that characterise brain shape rather than volume, fractal dimension (FD) quantifies shape complexity. FD has been applied in diverse fields of science to measure subtle changes in elaborate structures. We review its application thus far to structural MRI of the brain in neurodegenerative disease and dementia. We identified studies involving subjects who met criteria for mild cognitive impairment, Alzheimer's Disease, Vascular Dementia, Lewy Body Dementia, Frontotemporal Dementia, Amyotrophic Lateral Sclerosis, Parkinson's Disease, Huntington's Disease, Multiple Systems Atrophy, Spinocerebellar Ataxia and Multiple Sclerosis. The early literature suggests that neurodegenerative disease processes are usually associated with a decline in FD of the brain. The literature includes examples of disease-related change in FD occurring independently of atrophy, which if substantiated would represent a valuable advantage over other structural imaging metrics. However, it is likely to be non-specific and to exhibit complex spatial and temporal patterns. A more harmonious methodological approach across a larger number of studies as well as careful attention to technical factors associated with image processing and FD measurement will help to better elucidate the metric's utility.

The seen and the unseen: Molecular classification and image based-analysis of gastrointestinal cancers

Gastrointestinal cancers account for 22.5% of cancer related deaths worldwide and represent circa 20% of all cancers. In the last decades, we have witnessed a shift from histology-based to molecular-based classifications using genomic, epigenomic, and transcriptomic data. The molecular based classification revealed new prognostic markers and may aid the therapy selection. Because of the high-costs to perform a molecular classification, in recent years immunohistochemistry-based surrogate classification were developed which permit the stratification of patients, and in parallel multiple groups developed hematoxylin and eosin whole slide image analysis for sub-classifying these entities. Hence, we are witnessing a return to an image-based classification with the purpose to infer hidden information from routine histology images that would permit to detect the patients that respond to specific therapies and would be able to predict their outcome. In this review paper, we will discuss the current histological, molecular, and immunohistochemical classifications of the most common gastrointestinal cancers, gastric adenocarcinoma, and colorectal adenocarcinoma, and will present key aspects for developing a new artificial intelligence aided image-based classification of these malignancies.

Quantification of tumor heterogeneity: from data acquisition to metric generation

Tumors are unique and complex ecosystems, in which heterogeneous cell subpopulations with variable molecular profiles, aggressiveness, and proliferation potential coexist and interact. Understanding how heterogeneity influences tumor progression has important clinical implications for improving diagnosis, prognosis, and treatment response prediction. Several recent innovations in data acquisition methods and computational metrics have enabled the quantification of spatiotemporal heterogeneity across different scales of tumor organization. Here, we summarize the most promising efforts from a common experimental and computational perspective, discussing their advantages, shortcomings, and challenges. With personalized medicine entering a new era of unprecedented opportunities, our vision is that of future workflows integrating across modalities, scales, and dimensions to capture intricate aspects of the tumor ecosystem and to open new avenues for improved patient care.

Computed tomography-derived biomarker for predicting the treatment response to neoadjuvant chemoradiotherapy of rectal cancer

BACKGROUND

Malignant tumor essentially implies structural heterogeneity. Analysis of medical imaging can quantify this structural heterogeneity, which can be a new biomarker. This study aimed to evaluate the usefulness of texture analysis of computed tomography (CT) imaging as a biomarker for predicting the therapeutic response of neoadjuvant chemoradiotherapy (nCRT) for locally advanced rectal cancer.

METHODS

We enrolled 76 patients with rectal cancer who underwent curative surgery after nCRT. Texture analyses (Fractal analysis and Histogram analysis) were applied to contrast-enhanced CT images, and fractal dimension (FD), skewness, and kurtosis of the tumor were calculated. These CT-derived parameters were compared with the therapeutic response and prognosis.

RESULTS

Forty-six of 76 patients were diagnosed as clinical responders after nCRT. Kurtosis was significantly higher in the responders group than in the non-responders group (4.17 ± 4.16 vs. 2.62 ± 3.19, p = 0.04). Nine of 76 patients were diagnosed with pathological complete response (pCR) after surgery. FD of the pCR group was significantly lower than that of the non-pCR group (0.90 ± 0.12 vs. 1.01 ± 0.12, p = 0.009). The area under the receiver-operating characteristics curve of tumor FD for predicting pCR was 0.77, and the optimal cut-off value was 0.84 (accuracy; 93.4%). Furthermore, patients with lower FD tumors tended to show better relapse-free survival and disease-specific survival than those with higher FD tumors (5-year, 80.8 vs. 66.6%, 94.4 vs. 80.2%, respectively), although it was not statistically significant (p = 0.14, 0.11).

CONCLUSIONS

CT-derived texture parameters could be potential biomarkers for predicting the therapeutic response of rectal cancer.

Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging

Motivation

Tumour heterogeneity is being increasingly recognized as an important characteristic of cancer and as a determinant of prognosis and treatment outcome. Emerging spatial transcriptomics data hold the potential to further our understanding of tumour heterogeneity and its implications. However, existing statistical tools are not sufficiently powerful to capture heterogeneity in the complex setting of spatial molecular biology.

Results

We provide a statistical solution, the HeTerogeneity Average index (HTA), specifically designed to handle the multivariate nature of spatial transcriptomics. We prove that HTA has an approximately normal distribution, therefore lending itself to efficient statistical assessment and inference. We first demonstrate that HTA accurately reflects the level of heterogeneity in simulated data. We then use HTA to analyze heterogeneity in two cancer spatial transcriptomics datasets: spatial RNA sequencing by 10x Genomics and spatial transcriptomics inferred from H&E. Finally, we demonstrate that HTA also applies to 3D spatial data using brain MRI. In spatial RNA sequencing, we use a known combination of molecular traits to assert that HTA aligns with the expected outcome for this combination. We also show that HTA captures immune-cell infiltration at multiple resolutions. In digital pathology, we show how HTA can be used in survival analysis and demonstrate that high levels of heterogeneity may be linked to poor survival. In brain MRI, we show that HTA differentiates between normal ageing, Alzheimer’s disease and two tumours. HTA also extends beyond molecular biology and medical imaging, and can be applied to many domains, including GIS.

Availability and implementation

Python package and source code are available at: https://github.com/alonalj/hta.

Supplementary information

Supplementary data are available at Bioinformatics online.

Endoscopic Ultrasound vs. Computed Tomography for Gastric Cancer Staging: A Network Meta-Analysis

Gastric cancer preoperative staging is of outmost importance to assure proper management of the disease. Providing a relevant clinical stage relies on different imaging methods such as computed tomography (CT) or endoscopic ultrasound (EUS). We aimed to perform a network meta-analysis for gastric cancer clinical stage diagnostic tests, thus comparing the diagnostic accuracy of EUS vs. multidetector CT (MDCT) and EUS vs. EUS + MDCT. We plotted study estimates of pooled sensitivity and specificity on forest plots and summary receiver operating characteristic space to explore between-study variation in the performance of EUS, MDCT and EUS + MDCT for T1–T4, N0–N3, M0–M1 when data were available. Exploratory analyses were undertaken in RevMan 5. We included twelve studies with 2047 patients. Our results suggest that EUS was superior to MDCT in preoperative T1 and N staging. MDCT is more specific for the M stage but no significant difference in sensitivity was obtained. When comparing EUS vs. EUS + MDCT for T1 both sensitivity and specificity were not relevant. No significant differences were observed in T2–T4 stages. Even though EUS helped differentiate between the presence of invaded nodules, N stages should be carefully assessed by both methods since there is not sufficient data.