An unmet clinical need in solid tumor cancers is the ability to harness the intrinsic spatial information in primary tumors that can be exploited to optimize prognostics, diagnostics and therapeutic strategies for precision medicine. Here, we develop a transformational spatial analytics computational and systems biology platform (SpAn) that predicts clinical outcomes and captures emergent spatial biology that can potentially inform therapeutic strategies. We apply SpAn to primary tumor tissue samples from a cohort of 432 chemo-naïve colorectal cancer (CRC) patients iteratively labeled with a highly multiplexed (hyperplexed) panel of 55 fluorescently tagged antibodies. We show that SpAn predicts the 5-year risk of CRC recurrence with a mean AUROC of 88.5% (SE of 0.1%), significantly better than current state-of-the-art methods. Additionally, SpAn infers the emergent network biology of tumor microenvironment spatial domains revealing a spatially-mediated role of CRC consensus molecular subtype features with the potential to inform precision medicine.

SUMMARY Tumors are dynamic ecosystems comprising localized niches (microdomains), possessing distinct compositions and spatial configurations of cancer and non-cancer cell populations. Microdomain-specific network signaling coevolves with a continuum of cell states and functional plasticity associated with disease progression and therapeutic responses. We present LEAPH, an unsupervised machine learning algorithm for identifying cell phenotypes, which applies recursive steps of probabilistic clustering and spatial regularization to derive functional phenotypes (FPs) along a continuum. Combining LEAPH with pointwise mutual information and network biology analyses enables the discovery of outcome-associated microdomains visualized as distinct spatial configurations of heterogeneous FPs. Utilization of an immunofluorescence-based (51 biomarkers) image dataset of colorectal carcinoma primary tumors (n = 213) revealed microdomain-specific network dysregulation supporting cancer stem cell maintenance and immunosuppression that associated selectively with the recurrence phenotype. LEAPH enables an explainable artificial intelligence platform providing insights into pathophysiological mechanisms and novel drug targets to inform personalized therapeutic strategies.

LEAPH is an unsupervised machine learning algorithm for characterizing in situ phenotypic heterogeneity in tissue samples. LEAPH builds a phenotypic hierarchy of cell types, cell states and their spatial configurations. The recursive modeling steps involve determining cell types with low-ranked mixtures of factor analyzers and optimizing cell states with spatial regularization. We applied LEAPH to hyperplexed (51 biomarkers) immunofluorescence images of colorectal carcinoma primary tumors (N=213). LEAPH, combined with pointwise mutual information (PMI), enables the discovery of phenotypically distinct microdomains, composed of spatially configured computational phenotypes. LEAPH identified a subset of microdomains whose network biology is consistent with a tumor mediated immunosuppression program driven by cancer stem cells through an enhanced Wnt signaling pathway. The LEAPH framework, when combined with microdomain discovery and microdomain-specific network biology, has the potential to provide insights into pathophysiological mechanisms, identify novel drug targets and inform therapeutic strategies for individual patients.

An unmet clinical need in solid tumor cancers is the ability to harness the intrinsic spatial information in primary tumors that can be exploited to optimize prognostics, diagnostics and therapeutic strategies for precision medicine. We have developed a transformational spatial analytics (SpAn) computational and systems biology platform that predicts clinical outcomes and captures emergent spatial biology that can potentially inform therapeutic strategies. Here we apply SpAn to primary tumor tissue samples from a cohort of 432 chemo-naïve colorectal cancer (CRC) patients iteratively labeled with a highly multiplexed (hyperplexed) panel of fifty-five fluorescently tagged antibodies. SpAn predicted the 5-year risk of CRC recurrence with a mean area under the ROC curve of 88.5% (SE of 0.1%), significantly better than current state-of-the-art methods. SpAn also inferred the emergent network biology of the tumor spatial domains revealing a synergistic role of known features from CRC consensus molecular subtypes that will enhance precision medicine. MainColorectal Cancer (CRC) is the second most common type of cancer and the third leading cause of cancer-related deaths worldwide. 1 This multi-factorial disease like other carcinomas, develops and progresses through the selection of epithelial clones with the potential to confer malignant phenotypes in the context of a reciprocally coevolving tumor microenvironment (TME) comprising immune and stromal cells. 2-4 CRC patients are staged using the well-established tumor-nodemetastases (TNM) classification. 5,6 However, there is significant variability in patient outcomes within each stage. For example, CRC will recur in up to 30% of Stage II patients despite complete tumor resection, no residual tumor burden and no signs of metastasis. 7 In contrast, more advanced CRC has been known to show stability or indeed even to spontaneously regress. 7,8 The intrinsic plasticity of the TME underlying this variability in outcome is controlled by complex network biology emerging from the spatial organization of diverse cell types within the TME and their heterogeneous states of activation. 3,[9][10][11] The important role of the TME in CRC progression and recurrence has recently been highlighted by the identification of four consensus molecular subtypes (CMS) 12,13 , functional studies defining the critical role of stromal cells in determining overall survival, 14 and the development of Immunoscore® 14 which quantifies tumorinfiltrating T-lymphocytes in different regions of the tumor and associates their infiltration with CRC recurrence. 15,16 However the TME can be further harnessed to significantly improve CRC prognosis through the identification of biomarkers mechanistically linked to disease progression and the development of novel therapeutic strategies.Deeper understanding of the TME may arise from imaging methods capable of labeling > 7 cellular and tissue components in the same sample (hyperplexed 17 (HxIF) fluorescence and other imaging modalities). [17][18][19][20][21] To...

A generic model of automatic gain control (AGC) is proposed as a general framework for multidimensional automatic contrast sensitivity adjustment in vision, as well as in other sensory modalities. We show that a generic feedback AGC mechanism, incorporating a nonlinear synaptic interaction into the feedback loop of a neural network, can enhance and emphasize important image attributes, such as curvature, size, depth, convexity/concavity and more, similar to its role in the adjustment of photoreceptors and retinal network sensitivity over the extremely high dynamic range of environmental light intensities, while enhancing the contrast. We further propose that visual illusions, well established by psychophysical experiments, are a by-product of the multidimensional AGC. This hypothesis is supported by simulations implementing AGC, which reproduce psychophysical data regarding size contrast effects known as the Ebbinghaus illusion, and depth contrast effects. Processing of curvature by an AGC network illustrates that it is an important mechanism of image structure pre-emphasis, which thereby enhances saliency. It is argued that the generic neural network of AGC constitutes a universal, parsimonious, unified mechanism of neurobiological automatic contrast sensitivity control. This mechanism/model can account for a wide range of physiological and psychophysical phenomena, such as visual illusions and contour completion, in cases of occlusion, by a basic neural network. Likewise, and as important, biologically motivated AGC provides attractive new means for the development of intelligent computer vision systems.