Heterogeneity and subtypes of CD4+ regulatory T cells: implications for tumor therapy

In the conventional view, CD4+ regulatory T cell (Treg) represents a subset of lymphocytes that involve the perception and negative regulation of the immune response. CD4+Treg plays an important role in the maintenance of immune homeostasis and immune tolerance. However, recent studies have revealed that CD4+Treg do not suppress the immune response in some diseases, but promote inflammatory injury or inhibit tissue remodeling, suggesting the functional heterogeneity of CD4+Treg. Their involvement in tumor pathogenesis is more complex than previously understood. This article reviews the relevant research on the heterogeneity of CD4+Treg, subtype classification, and their relationship with tumor therapy.

A Machine-Learning Tool Concurrently Models Single Omics and Phenome Data for Functional Subtyping and Personalized Cancer Medicine

One of the major challenges in defining clinically-relevant and less heterogeneous tumor subtypes is assigning biological and/or clinical interpretations to etiological (intrinsic) subtypes. Conventional clustering/subtyping approaches often fail to define such subtypes, as they involve several discrete steps. Here we demonstrate a unique machine-learning method, phenotype mapping (PhenMap), which jointly integrates single omics data with phenotypic information using three published breast cancer datasets (n = 2045). The PhenMap framework uses a modified factor analysis method that is governed by a key assumption that, features from different omics data types are correlated due to specific "hidden/mapping" variables (context-specific mapping variables (CMV)). These variables can be simultaneously modeled with phenotypic data as covariates to yield functional subtypes and their associated features (e.g., genes) and phenotypes. In one example, we demonstrate the identification and validation of six novel "functional" (discrete) subtypes with differential responses to a cyclin-dependent kinase (CDK)4/6 inhibitor and etoposide by jointly integrating transcriptome profiles with four different drug response data from 37 breast cancer cell lines. These robust subtypes are also present in patient breast tumors with different prognosis. In another example, we modeled patient gene expression profiles and clinical covariates together to identify continuous subtypes with clinical/biological implications. Overall, this genome-phenome machine-learning integration tool, PhenMap identifies functional and phenotype-integrated discrete or continuous subtypes with clinical translational potential.

Robust mixture modeling reveals category-free selectivity in reward region neuronal ensembles

Classification of neurons into clusters based on their response properties is an important tool for gaining insight into neural computations. However, it remains unclear to what extent neurons fall naturally into discrete functional categories. We developed a Bayesian method that models the tuning properties of neural populations as a mixture of multiple types of task-relevant response patterns. We applied this method to data from several cortical and striatal regions in economic choice tasks. In all cases, neurons fell into only two clusters: one multiple-selectivity cluster containing all cells driven by task variables of interest and another of no selectivity for those variables. The single cluster of task-sensitive cells argues against robust categorical tuning in these areas. The no-selectivity cluster was unanticipated and raises important questions about what distinguishes these neurons and what role they play. Moreover, the ability to formally identify these nonselective cells allows for more accurate measurement of ensemble effects by excluding or appropriately down-weighting them in analysis. Our findings provide a valuable tool for analysis of neural data, challenge simple categorization schemes previously proposed for these regions, and place useful constraints on neurocomputational models of economic choice and control. NEW & NOTEWORTHY We present a Bayesian method for formally detecting whether a population of neurons can be naturally classified into clusters based on their response tuning properties. We then examine several data sets of reward system neurons for variables and find in all cases that neurons can be classified into only two categories: a functional class and a non-task-driven class. These results provide important constraints for neural models of the reward system.