Modeling Heterogeneity of Triple-Negative Breast Cancer Uncovers a Novel Combinatorial Treatment Overcoming Primary Drug Resistance

Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype characterized by a remarkable molecular heterogeneity. Currently, there are no effective druggable targets and advanced preclinical models of the human disease. Here, a unique mouse model (MMTV-R26Met mice) of mammary tumors driven by a subtle increase in the expression of the wild-type MET receptor is generated. MMTV-R26Met mice develop spontaneous, exclusive TNBC tumors, recapitulating primary resistance to treatment of patients. Proteomic profiling of MMTV-R26Met tumors and machine learning approach show that the model faithfully recapitulates intertumoral heterogeneity of human TNBC. Further signaling network analysis highlights potential druggable targets, of which cotargeting of WEE1 and BCL-XL synergistically kills TNBC cells and efficiently induces tumor regression. Mechanistically, BCL-XL inhibition exacerbates the dependency of TNBC cells on WEE1 function, leading to Histone H3 and phosphoS33RPA32 upregulation, RRM2 downregulation, cell cycle perturbation, mitotic catastrophe, and apoptosis. This study introduces a unique, powerful mouse model for studying TNBC formation and evolution, its heterogeneity, and for identifying efficient therapeutic targets.

Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics

Genetically modified genomes are often used today in many areas of fundamental and applied research. In many studies, coding or noncoding regions are modified in order to change protein sequences or gene expression levels. Modifying one or several nucleotides in a genome can also lead to unexpected changes in the epigenetic regulation of genes. When designing a synthetic genome with many mutations, it would thus be very informative to be able to predict the effect of these mutations on chromatin. We develop here a deep learning approach that quantifies the effect of every possible single mutation on nucleosome positions on the full Saccharomyces cerevisiae genome. This type of annotation track can be used when designing a modified S. cerevisiae genome. We further highlight how this track can provide new insights on the sequence-dependent mechanisms that drive nucleosomes' positions in vivo.

In Situ and Step-Heating 40Ar/39Ar Dating of White Mica in Low-Temperature Shear Zones (Tenda Massif, Alpine Corsica, France)

In order to clarify the link between 40Ar/39Ar record in white mica and deformation, we performed in situ and bulkwise 40Ar/39Ar dating over the East Tenda Shear Zone (Tenda massif, Alpine Corsica). White micas from 11 samples were selected and extensively analyzed using in situ techniques across nested scales of strain-intensity gradients developed at the expense of a late-Variscan protolith. 40Ar/39Ar systematics are unaffected by inherited Ar and directly linked to deformation with little or no Ar lattice (volume) diffusion. Extensive sampling allows constraining the end of deformation related to burial and exhumation, respectively, at ~34 and ~22 Ma, bracketing the duration of regional extensional shear to ~12 Myr. Results also highlight a regional strain localization toward the upper contact of the unit with smaller-scale localization in specific lithologies, notably meta-aplites. Second-order complications exist, such as local ill-defined correlations between ages and finite-strain microstructures. Thus, the use of a strain gradient as a proxy for strain localization in time is regionally valid but sometimes locally too complex to track or resolve strain partitioning/localization trends at the meter (outcrop) scale and below. Age mixing and incomplete isotopic homogenization by dissolution/precipitation are identified as the main causes of local discrepancies that complicate the link between age and microstructure and the derivation of strain localization rates. Tracking temporal trends in shear distribution across regional-scale deformation gradients in such settings is possible but requires a multi-scale approach as implemented here to reveal younging patterns associated to strain localization.

Multinuclear PtII Complexes: Why Three is Better Than Two to Enhance Photophysical Properties

The self-assembly of platinum complexes is a well-documented process that leads to interesting changes of the photophysical and electrochemical behavior as well as to a change in reactivity of the complexes. However, it is still not clear how many metal units must interact in order to achieve the desired properties of a large assembly. This work aimed to clarify the role of the number of interacting PtII units leading to an enhancement of the spectroscopic properties and how to address inter- versus intramolecular processes. Therefore, a series of neutral multinuclear PtII complexes were synthesized and characterized, and their photophysical properties at different concentration were studied. Going from the monomer to dimers, the growth of a new emission band and the enhancement of the emission properties were observed. Upon increasing the platinum units up to three, the monomeric blue emission could not be detected anymore and a concentration independent bright-yellow/orange emission, due to the establishment of intramolecular metallophilic interactions, was observed.

The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions

Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TRs). However, how recruitment of a myriad of TRs is orchestrated at cis-regulatory modules (CRMs) to account for coregulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRMs involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic, and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRMs), which consist of subsets of preferentially and coordinately corecruited TRs, assemble into hierarchical combinations at hepatic CRMs. Different combinations of TRMs add to a core TRM, broadly found across the whole landscape of CRMs, to discriminate promoters from enhancers. These combinations also specify distinct sets of CRM differentially organized along the genome and involved in regulation of either housekeeping/cellular maintenance genes or liver-specific functions. In addition to these TRMs which we define as obligatory, we show that facultative TRMs, such as one comprising core circadian TRs, are further recruited to selective subsets of CRMs to modulate their activities. TRMs transcend TR classification into ubiquitous versus liver-identity factors, as well as TR grouping into functional families. Hence, hierarchical superimpositions of obligatory and facultative TRMs bring about independent transcriptional regulatory inputs defining different sets of CRMs with logical connection to regulation of specific gene sets and biological pathways. Altogether, our study reveals novel principles of concerted transcriptional regulation by multiple TRs at CRMs.