The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://medicaldecathlon.com/. In addition, both data and online evaluation are accessible via https://competitions.codalab.org/competitions/17094

A framework for modelling the biomechanical behaviour of the human liver during breathing in real time using machine learning

Progress in biomechanical modelling of human soft tissue is the basis for the development of new clinical applications capable of improving the diagnosis and treatment of some diseases (e.g. cancer), as well as the surgical planning and guidance of some interventions. The finite element method (FEM) is one of the most popular techniques used to predict the deformation of the human soft tissue due to its high accuracy. However, FEM has an associated high computational cost, which makes it difficult its integration in real-time computer-aided surgery systems. An alternative for simulating the mechanical behaviour of human organs in real time comes from the use of machine learning (ML) techniques, which are much faster than FEM. This paper assesses the feasibility of ML methods for modelling the biomechanical behaviour of the human liver during the breathing process, which is crucial for guiding surgeons during interventions where it is critical to track this deformation (e.g. some specific kind of biopsies) or for the accurate application of radiotherapy dose to liver tumours. For this purpose, different ML regression models were investigated, including three tree-based methods (decision trees, random forests and extremely randomised trees) and other two simpler regression techniques (dummy model and linear regression). In order to build and validate the ML models, a labelled data set was constructed from modelling the deformation of eight ex-vivo human livers using FEM. The best prediction performance was obtained using extremely randomised trees, with a mean error of 0.07 mm and all the samples with an error under 1 mm. The achieved results lay the foundation for the future development of some real-time software capable of simulating the human liver deformation during the breathing process during clinical interventions.This work has been funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through research projects TIN2014-52033-R and DPI2013-40859-R, both also supported by European FEDER funds. The authors acknowledge the kind collaboration of the personnel from the hospital involved in the research.Lorente, D.; Martínez-Martínez, F.; Rupérez Moreno, MJ.; Lago, MA.; Martínez-Sober, M.; Escandell-Montero, P.; Martínez-Martínez, JM.... (2017). A framework for modelling the biomechanical behaviour of the human liver during breathing in real time using machine learning. Expert Systems with Applications. 71:342-357. doi:10.1016/j.eswa.2016.11.037S3423577

The Liver Tumor Segmentation Benchmark (LiTS)

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LITS) organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2016 and International Conference On Medical Image Computing Computer Assisted Intervention (MICCAI) 2017. Twenty four valid state-of-the-art liver and liver tumor segmentation algorithms were applied to a set of 131 computed tomography (CT) volumes with different types of tumor contrast levels (hyper-/hypo-intense), abnormalities in tissues (metastasectomie) size and varying amount of lesions. The submitted algorithms have been tested on 70 undisclosed volumes. The dataset is created in collaboration with seven hospitals and research institutions and manually reviewed by independent three radiologists. We found that not a single algorithm performed best for liver and tumors. The best liver segmentation algorithm achieved a Dice score of 0.96(MICCAI) whereas for tumor segmentation the best algorithm evaluated at 0.67(ISBI) and 0.70(MICCAI). The LITS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.Comment: conferenc

Tumors induce de novo steroid biosynthesis in T cells to evade immunity

Abstract: Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes to evade anti-tumor immunity. Using a transgenic steroidogenesis-reporter mouse line we identify and characterize de novo steroidogenic immune cells, defining the global gene expression identity of these steroid-producing immune cells and gene regulatory networks by using single-cell transcriptomics. Genetic ablation of T cell steroidogenesis restricts primary tumor growth and metastatic dissemination in mouse models. Steroidogenic T cells dysregulate anti-tumor immunity, and inhibition of the steroidogenesis pathway is sufficient to restore anti-tumor immunity. This study demonstrates T cell de novo steroidogenesis as a mechanism of anti-tumor immunosuppression and a potential druggable target

Lymph node stromal cells enhance drug-resistant colon cancer cell tumor formation through SDF-1α/CXCR4 paracrine signaling

Colorectal cancer (CRC) is the third most common malignancy and the second leading cause of cancer-related deaths in America. Nearly two thirds of newly diagnosed CRC cases include lymph node (LN) involvement, and LN metastasis is one of the strongest negative prognostic factors for CRC. It is thought that CRC tumors contain a small population of drug-resistant CRC tumor-initiating cells (Co-TICs) that may be responsible for cancer recurrence. To evaluate the effects of the LN stromal cells on Co-TICs, we established a unique xenoplant model using CRC cells isolated by enzymatic digestion from consented patient specimens, HT-29 cells, HCA-7 cells, and LN stromal cell line HK cells. We found that HK cells and HK cell-conditioned media enhanced CRC tumor formation and tumor angiogenesis. Cells expressing CD133(+) and the stromal cell-derived factor 1 alpha (SDF-1 alpha) receptor CXCR4 were enriched in chemotherapeutic-resistant CRC cells. CD133(+)CXCR4(+) Co-TICs isolated from patient specimens are more tumorigenic than unsorted tumor cells. Furthermore, the inhibitors specific to HK cell-derived SDF-1 alpha reduced tumor formation and tumor angiogenesis. Our results have demonstrated a role for Co-TICs in tumor growth and defined the influence of LN stromal cells on Co-TICs. We have identified a major Co-TIC/LN microenvironment-specific mechanism for CRC resistance to chemotherapeutic agents and established experimental platforms for both in vitro and in vivo testing, indicating that SDF-1 alpha and its receptor, CXCR4, may be targets for clinical therapy