Analysis of context-specific KRAS-effector (sub)complexes in Caco-2 cells.

Ras is a key switch controlling cell behavior. In the GTP-bound form, Ras interacts with numerous effectors in a mutually exclusive manner, where individual Ras-effectors are likely part of larger cellular (sub)complexes. The molecular details of these (sub)complexes and their alteration in specific contexts are not understood. Focusing on KRAS, we performed affinity purification (AP)-mass spectrometry (MS) experiments of exogenously expressed FLAG-KRAS WT and three oncogenic mutants ("genetic contexts") in the human Caco-2 cell line, each exposed to 11 different culture media ("culture contexts") that mimic conditions relevant in the colon and colorectal cancer. We identified four effectors present in complex with KRAS in all genetic and growth contexts ("context-general effectors"). Seven effectors are found in KRAS complexes in only some contexts ("context-specific effectors"). Analyzing all interactors in complex with KRAS per condition, we find that the culture contexts had a larger impact on interaction rewiring than genetic contexts. We investigated how changes in the interactome impact functional outcomes and created a Shiny app for interactive visualization. We validated some of the functional differences in metabolism and proliferation. Finally, we used networks to evaluate how KRAS-effectors are involved in the modulation of functions by random walk analyses of effector-mediated (sub)complexes. Altogether, our work shows the impact of environmental contexts on network rewiring, which provides insights into tissue-specific signaling mechanisms. This may also explain why KRAS oncogenic mutants may be causing cancer only in specific tissues despite KRAS being expressed in most cells and tissues.

Whole-cell energy modeling reveals quantitative changes of predicted energy flows in RAS mutant cancer cell lines.

Cellular utilization of available energy flows to drive a multitude of forms of cellular "work" is a major biological constraint. Cells steer metabolism to address changing phenotypic states but little is known as to how bioenergetics couples to the richness of processes in a cell as a whole. Here, we outline a whole-cell energy framework that is informed by proteomic analysis and an energetics-based gene ontology. We separate analysis of metabolic supply and the capacity to generate high-energy phosphates from a representation of demand that is built on the relative abundance of ATPases and GTPases that deliver cellular work. We employed mouse embryonic fibroblast cell lines that express wild-type KRAS or oncogenic mutations and with distinct phenotypes. We observe shifts between energy-requiring processes. Calibrating against Seahorse analysis, we have created a whole-cell energy budget with apparent predictive power, for instance in relation to protein synthesis.

Disease-Gene Networks of Skin Pigmentation Disorders and Reconstruction of Protein-Protein Interaction Networks.

Melanin, a light and free radical absorbing pigment, is produced in melanocyte cells that are found in skin, but also in hair follicles, eyes, the inner ear, heart, brain and other organs. Melanin synthesis is the result of a complex network of signaling and metabolic reactions. It therefore comes as no surprise that mutations in many of the genes involved are associated with various types of pigmentation diseases and phenotypes ('pigmentation genes'). Here, we used bioinformatics tools to first reconstruct gene-disease/phenotype associations for all pigmentation genes. Next, we reconstructed protein-protein interaction (PPI) networks centered around pigmentation gene products ('pigmentation proteins') and supplemented the PPI networks with protein expression information obtained by mass spectrometry in a panel of melanoma cell lines (both pigment producing and non-pigment producing cells). The analysis provides a systems network representation of all genes/ proteins centered around pigmentation and melanin biosynthesis pathways ('pigmentation network map'). Our work will enable the pigmentation research community to experimentally test new hypothesis arising from the pigmentation network map and to identify new targets for drug discovery.

Dietary Arginine Supplementation during Gestation and Lactation Increases Milk Yield and Mammary Lipogenesis in Rats.

BACKGROUND: Arginine, an essential amino acid during the reproductive period, has been shown to enhance lactation performances in livestock. Whether it could help mothers with breastfeeding difficulties is not known. OBJECTIVES: This study aimed to determine whether dietary arginine supplementation would enhance milk production in rat dams nursing large 12-pup litters and, if so, what mechanisms are involved. METHODS: In 3 series of experiments, differing in dam killing timing, 59 primiparous, pregnant Sprague-Dawley rats (mean ± SD weight: 254 ± 24.7 g) were randomly assigned to receive either 1) an AIN-93G diet supplemented with l-arginine at 2.0% (ARG diet), through lactation and gestation (AGL group); 2) a control AIN-93G diet including at 3.5% an isonitrogenous mix of amino acids that are not essential for lactation (MA diet), during gestation and lactation (MA group); or 3) the MA diet during gestation and the ARG diet during lactation (AL group). Milk flow was measured using deuterated water enrichment between days 11 and 18. Plasma hormones and mammary expression of genes involved in lactation were measured using ELISA and qRT-PCR, respectively, at lactation days 12, 18, or 21 in the 3 experiments. Data were analyzed by ANOVA. RESULTS: Dam food intake, pup weight gain, milk flow normalized to dam weight, and milk fat concentration were 17%, 9%, 20%, and 20% greater in the AGL group than in the MA group, respectively (P < 0.05). Genes involved in lipogenesis and lipid regulation were overexpressed ≤2.76-fold in the mammary gland of AGL dams compared with MA dams (P < 0.05) and plasma leptin concentration was 39% higher (P = 0.008). Milk flow and composition and mammary gene expression of the AL group did not differ from those of the MA group, whereas milk fat concentration and flow were 26% and 37% lower than in the AGL group, respectively. CONCLUSIONS: Arginine supplementation during gestation and lactation enhances milk flow and mammary lipogenesis in rats nursing large litters.

Fenugreek Stimulates the Expression of Genes Involved in Milk Synthesis and Milk Flow through Modulation of Insulin/GH/IGF-1 Axis and Oxytocin Secretion.

We previously demonstrated galactagogue effect of fenugreek in a rat model of lactation challenge, foreshadowing its use in women's breastfeeding management. To assess longitudinal molecular mechanisms involved in milk synthesis/secretion in dams submitted to fenugreek supplementation, inguinal mammary, pituitary glands and plasma were isolated in forty-three rats nursing large 12 pups-litters and assigned to either a control (CTL) or a fenugreek-supplemented (FEN) diet during lactation. RT-PCR were performed at days 12 and 18 of lactation (L12 and L18) and the first day of involution (Inv1) to measure the relative expression of genes related to both milk synthesis and its regulation in the mammary gland and lactogenic hormones in the pituitary gland. Plasma hormone concentrations were measured by ELISA. FEN diet induced 2- to 3-times higher fold change in relative expression of several genes related to macronutrient synthesis (Fasn, Acaca, Fabp3, B4galt1, Lalba and Csn2) and energy metabolism (Cpt1a, Acads) and in IGF-1 receptor in mammary gland, mainly at L12. Pituitary oxytocin expression and plasma insulin concentration (+77.1%) were also significantly increased. Altogether, these findings suggest fenugreek might extend duration of peak milk synthesis through modulation of the insulin/GH/IGF-1 axis and increase milk ejection by activation of oxytocin secretion.

Impact of Fenugreek on Milk Production in Rodent Models of Lactation Challenge.

Fenugreek, a herbal remedy, has long been used as galactologue to help mothers likely to stop breastfeeding because of perceived insufficient milk production. However, few studies highlight the efficacy of fenugreek in enhancing milk production. The aims of our study were to determine whether fenugreek increased milk yield in rodent models of lactation challenge and if so, to verify the lack of adverse effects on dam and offspring metabolism. Two lactation challenges were tested: increased litter size to 12 pups in dams fed a 20% protein diet and perinatal restriction to an 8% protein diet with eight pups' litter, with or without 1 g.kg-1.day-1 dietary supplementation of fenugreek, compared to control dams fed 20% protein diet with eight pups' litters. Milk flow was measured by the deuterium oxide enrichment method, and milk composition was assessed. Lipid and glucose metabolism parameters were assessed in dam and offspring plasmas. Fenugreek increased milk production by 16% in the litter size increase challenge, resulting in an 11% increase in pup growth without deleterious effect on dam-litter metabolism. Fenugreek had no effect in the maternal protein restriction challenge. These results suggest a galactologue effect of fenugreek when mothers have no physiological difficulties in producing milk.

Use of water turnover method to measure mother's milk flow in a rat model: Application to dams receiving a low protein diet during gestation and lactation.

Assessment of milk production is of utmost relevance for pediatricians and scientists interested in early life nutrition. The weight-suckle-weight (WSW) method, which consists of weighing babies before and after they suckle their mother, uses the difference in body weight as an estimate of milk intake. However, this is prone to many sources of error. In the current study, we used for the first time the water turnover method and compartmental analysis with deuterated water (D2O) as a non-toxic tracer to quantify in vivo milk production in a rat model. We assessed the effect of a nutritional intervention presumed to affect milk production, a maternal dietary protein restriction during gestation and lactation, which results in the birth of pups with intrauterine growth restriction. The specific aim of this study was to determine milk production with the body water turnover method in rat dams receiving during gestation and lactation, either a control diet (NP) or an iso-caloric low-protein diet (LP). In NP dams, mass of dam's total body water, output flow constant from dam to litter (K21) and median milk flow, calculated between days 11 to 14 after pup birth, were 282.1 g, 0.0122 h-1 and 3.30 g/h for NP dams, respectively. Maternal dietary protein restriction (-59%) during perinatal period led to a 34% reduction in milk flow (NP versus LP). With the WSW method, milk flow varied from 1.96 g/h to 2.37 g/h between days 11 to 14 for NP dams. The main advantage of the D20 method compared to the WSW method stems from its higher precision, as attested by the narrowest range of measured values of milk flow ([2.90; 3.75] and [0.98; 6.85] g/h, respectively) for NP group. This method could be suitable for testing the effectiveness of candidate galactologue molecules presumed to enhance milk production in the lactating rat model.