Spatiotemporal Omics-Refining the landscape of precision medicine

Abstract

Current streamline of precision medicine uses histomorphological and molecular information to indicate individual phenotypes and genotypes to achieve optimal outcome of treatment. The knowledge of detected mutations and alteration can hardly describe molecular interaction and biological process which can finally be manifested as a disease. With molecular diagnosis revising the modalities of disease, there is a trend in precision medicine to apply multi-omic and multi-dimensional information to decode tumors, regarding heterogeneity, pathogenesis, prognosis, etc. Emerging state-of-art spatiotemporal omics provides a novel vision for in discovering clinicopathogenesis associated findings, some of which show a promising potential to be translated to facilitate clinical practice. Here, we summarize the available spatiotemporal omic technologies and algorithms, highlight the novel scientific findings and explore potential applications in the clinical scenario. Spatiotemporal omics present the ability to provide impetus to rewrite clinical pathology and to answer outstanding clinical questions. This review emphasizes the novel vision of spatiotemporal omics to refine the landscape of precision medicine in the clinic.

StereoSiTE: A framework to spatially and quantitatively profile the cellular neighborhood organized iTME

“…In current on-going studies, our group has been further proving the molecular mechanism of neutrophils regulating tumoral cells in CN6 with wet experimental evidence. Spatial multi-omic techniques promises new modalities to obtain spatially informed omic data (8). Comparing to other omic methods, spatial transcriptomic technologies can generate high-throughput data at resolution of subcellular level (18).…”

“…Spatially organized iTME and its disorganized manner can be manifested as pathological disease. Therefore, to decode spatial signature of iTME is crucial to find the clinicopathological association for understanding mechanism(8). Alterations in tissue organization and cellular morphology set up the foundation of diagnosis of cancer, and provide gold criteria in pathology(26).…”

“…It indicates the irreplaceable role of spatial information in understanding the initial and process of cancer. Pathological structures like invasive front, buddings and Tertiary Lymphoid Structures (TLSs) have been studied or used in pathology to indicate risk of metastasis, relapse and survival(8). Ji et al(12) reported that tumor-specific keratinocytes (TSKs) at leading edges of squamous cell cancer associated to tumorigenesis.…”

“…Spatial multi-omic techniques promises new modalities to obtain spatially informed omic data (8). Comparing to other omic methods, spatial transcriptomic technologies can generate high-throughput data at resolution of subcellular level(18).…”

“…Unfortunately, trade-off between "-omics" tools generated comprehensive molecular measurement and "-targeted" tools conferred low-throughput but highly resolved cellular investigation in situ is a long-lasting debate, which, thereby, hinders our understanding in biology (7). However, this historical conundrum is being up to termination under the recent development of spatial transcriptomic (ST) technologies (8). The recent developments in the spatial transcriptome (ST) provide opportunities to better elucidate physiological and pathological progress covering cell-type definition (9)(10)(11), cellular interaction (7,12), molecular signaling (13,14), and hence facilitated us to spatially map the microenvironment landscape.…”