From genes to modules, from cells to ecosystems

Abstract

Twenty years ago, molecular biology transitioned from predominantly studying genes as isolated elements to viewing them as part of complex modules, giving rise to the field of systems biology. This transition was made possible by technological advances that allowed to simultaneously measure the expression levels of thousands of genes in a single experiment and drove a shift toward analyses identifying gene sets, modules, and pathways involved in a biological process of interest. Today we are excitingly facing a similar turning point in cell biology, where single‐cell technologies have enabled us to approach cells as cellular modules.

Lack of TGFβ signaling competency predicts immune poor cancer conversion to immune rich and response to checkpoint blockade

“…Although the mechanisms mediating suppression of NK cell axis are not yet fully known, the data reported here highlight the necessity of NK cell mediated immune cell infiltration to convert high βAlt, immune poor to tumors responsive to ICB. Because the immune system is a distributed organ that has a limited repertoire of mechanisms to suppress cancer, research in cancer immunity is moving away from tissue-of-origin specificity towards tissue-agnostic ecosystems and processes 48,49 . Here our analysis was aided by the immune archetype paradigm based on the immunoprofiling initiative that conducted a holistic survey across cancers 30 .…”

“…Because the immune system is a distributed organ that has a limited repertoire of mechanisms to suppress cancer, research in cancer immunity is moving away from tissue-of-origin specificity towards tissue-agnostic ecosystems and processes 48, 49 . Here our analysis was aided by the immune archetype paradigm based on the immunoprofiling initiative that conducted a holistic survey across cancers 30 .…”

“…CC-BY-NC 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made towards tissue-agnostic ecosystems and processes 48,49 . Here our analysis was aided by the immune archetype paradigm based on the immunoprofiling initiative that conducted a holistic survey across cancers 30 .…”

“…The goal of personalized medicine is to determine which patients will benefit most from a therapeutic regimen. Because the immune system is a distributed organ that has a regulated repertoire of mechanisms to suppress cancer, research in cancer immunity is moving away from tissue-of-origin specificity towards tissue-agnostic ecosystems and processes 48, 49 . The more nuanced classification of cancer by immune archetypes is a significant advancement that will enhance patient outcomes by enabling the selection of optimal therapeutic strategies.…”

Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma

“…Future methods should further explore integration of immune features into interpretable networks so we can derive knowledge from the intersection of features. 70 …”