Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer.

Breast cancers (BRCA) exhibit substantial transcriptional heterogeneity, posing a significant clinical challenge. The global transcriptional changes in a disease context, however, are likely mediated by few key genes which reflect disease etiology better than the differentially expressed genes (DEGs). We apply our network-based tool PathExt to 1,059 BRCA tumors across 4 subtypes to identify key mediator genes in each subtype. Compared to conventional differential expression analysis, PathExt-identified genes exhibit greater concordance across tumors, revealing shared and subtype-specific biological processes; better recapitulate BRCA-associated genes in multiple benchmarks, and are more essential in BRCA subtype-specific cell lines. Single-cell transcriptomic analysis reveals a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target key genes potentially mediating drug resistance.

Separate gut-brain circuits for fat and sugar reinforcement combine to promote overeating.

Food is a powerful natural reinforcer that guides feeding decisions. The vagus nerve conveys internal sensory information from the gut to the brain about nutritional value; however, the cellular and molecular basis of macronutrient-specific reward circuits is poorly understood. Here, we monitor in vivo calcium dynamics to provide direct evidence of independent vagal sensing pathways for the detection of dietary fats and sugars. Using activity-dependent genetic capture of vagal neurons activated in response to gut infusions of nutrients, we demonstrate the existence of separate gut-brain circuits for fat and sugar sensing that are necessary and sufficient for nutrient-specific reinforcement. Even when controlling for calories, combined activation of fat and sugar circuits increases nigrostriatal dopamine release and overeating compared with fat or sugar alone. This work provides new insights into the complex sensory circuitry that mediates motivated behavior and suggests that a subconscious internal drive to consume obesogenic diets (e.g., those high in both fat and sugar) may impede conscious dieting efforts.

Phase 1/2 Study of the Timing and Efficacy of 3 mg Peg-GCSF in Neo/Adjuvant Dose Dense Breast Cancer Treatment Protocols.

Amol PatelBackground Peg-GCSF has similar efficacy at a dose of 60 µg/kg and 100 µg/kg. The conventional 6 mg SC dose was based on the maximum tolerable dose. In Japan, 3.6 mg dose was approved on the basis of dose finding studies. Peg-GCSF is an integral part of dose-dense chemotherapy protocols. Dose finding and scheduling study of peg-GCSF have not been conducted in Indian patients. Materials and Methods We conducted two-center phase 1/2 clinical study addressing the timing and efficacy of peg-GCSF in Indian breast cancer patients (CTRI no: 2021/07/034751). Three groups of timing administration were studied, namely 1, 6, and 24 hours post chemotherapy. The phase 2 part was the expansion of the best timing group. The primary objective was dose density, which was defined as receiving chemotherapy on < 3 days of scheduled date. Adriamycin/epirubicin cyclophosphamide (AC/EC) was administered q2 weeks. The total leucocyte (TLC) and absolute neutrophil (ANC) kinetics were studied. Other outcomes were incidence of grade 4 neutropenia, febrile neutropenia (FN), and requirement of additional doses of G-CSF. Bone pain, fever, and myalgia were studied for adverse effects. Results From November 20 to December 21, 36 patients were enrolled. Patient characteristics are depicted in Table 1. Initially, three patients received the peg-GCSF in each timing group. One patient in each 1-hour and 6 hours needed G-CSF support for maintaining the dose density. The 24-hour group was carried to phase 2 part. Dose density was maintained in 97% of patients. None of the patient in 24-hour group had FN. Also, 4/30 patients had grade 4 neutropenia and required an additional dose of GCSF. Grade 3 or 4 bone pain was not noticed by any of the patients. During the first cycle, the mean ANC (cells/µL) was 5284, 20704, 3010, 6954 on D0, D + 3, D + 7, and D + 13, respectively (Fig. 1A-TLC and 1B-ANC). The mean ANC (cells/µL) rise on D + 3 in cycles 1, 2, 3, 4 was 23810, 29209, 32428,22455, respectively. Conclusion Dose density of AC/EC breast cancer protocol is maintained with peg-GCSF 3 mg. Post chemotherapy 24-hour timing of peg-GCSF administration remains as the standard. A phase 3 trial of 6 mg versus 3 mg is warranted.

Separate orexigenic hippocampal ensembles shape dietary choice by enhancing contextual memory and motivation.

The hippocampus (HPC), traditionally known for its role in learning and memory, has emerged as a controller of food intake. While prior studies primarily associated the HPC with food intake inhibition, recent research suggests a critical role in appetitive processes. We hypothesized that orexigenic HPC neurons differentially respond to fats and/or sugars, potent natural reinforcers that contribute to obesity development. Results uncover previously-unrecognized, spatially-distinct neuronal ensembles within the dorsal HPC (dHPC) that are responsive to separate nutrient signals originating from the gut. Using activity-dependent genetic capture of nutrient-responsive HPC neurons, we demonstrate a causal role of both populations in promoting nutrient-specific preference through different mechanisms. Sugar-responsive neurons encode an appetitive spatial memory engram for meal location, whereas fat-responsive neurons selectively enhance the preference and motivation for fat intake. Collectively, these findings uncover a neural basis for the exquisite specificity in processing macronutrient signals from a meal that shape dietary choices.

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer.

Breast cancers exhibit substantial transcriptional heterogeneity, posing a significant challenge to the prediction of treatment response and prognostication of outcomes. Especially, translation of TNBC subtypes to the clinic remains a work in progress, in part because of a lack of clear transcriptional signatures distinguishing the subtypes. Our recent network-based approach, PathExt, demonstrates that global transcriptional changes in a disease context are likely mediated by a small number of key genes, and these mediators may better reflect functional or translationally relevant heterogeneity. We apply PathExt to 1059 BRCA tumors and 112 healthy control samples across 4 subtypes to identify frequent, key-mediator genes in each BRCA subtype. Compared to conventional differential expression analysis, PathExt-identified genes (1) exhibit greater concordance across tumors, revealing shared as well as BRCA subtype-specific biological processes, (2) better recapitulate BRCA-associated genes in multiple benchmarks, and (3) exhibit greater dependency scores in BRCA subtype-specific cancer cell lines. Single cell transcriptomes of BRCA subtype tumors reveal a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified TNBC subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target top novel genes potentially mediating drug resistance. Overall, PathExt applied to breast cancer refines previous views of gene expression heterogeneity and identifies potential mediators of TNBC subtypes, including potential therapeutic targets.

Non-Nutritive Sweetened Beverages Impair Therapeutic Benefits of Metformin in Prediabetic Diet-Induced Obese Mice.

Metformin, a frontline therapy for type 2 diabetes and related metabolic diseases, results in variable outcomes. This study aimed to investigate whether sweetened beverages (caloric or non-caloric) affect the therapeutic benefits of metformin on glucose, food intake, and weight loss in diet-induced obesity. Mice were given a high-fat diet and sweetened water for 8 weeks to induce obesity and glucose intolerance. Then, mice were randomized to receive metformin in either water, high-fructose corn syrup (HFCS), or the non-nutritive sweetener saccharin for 6 weeks. After 6 weeks of metformin treatment, all groups had improved glucose tolerance compared to pretreatment. However, saccharin resulted in worse glucose tolerance and weight gain outcomes than the water or HFCS groups and correlated with lower plasma growth differentiation factor 15 levels. In conclusion, reducing non-nutritive sweetener consumption during metformin therapy is recommended to avoid impairing the therapeutic effects of metformin on body weight and glucose homeostasis.

Effect of extrusion processing on techno-functional properties, textural properties, antioxidant activities, in vitro nutrient digestibility and glycemic index of sorghum-chickpea-based extruded snacks.

Physico-chemical, textural, functional, and nutritional properties of the twin screw extruded whole sorghum-chickpea (8:2) snacks was investigated using in vitro procedures. The extruded snacks were analyzed for the effect of variations in extruded conditions on their properties: barrel BT (BT) (130-170°C) and feed moisture (FM) (14%-18%), keeping screw speed constant (400 rpm). The results revealed that specific mechanical energy (SME) decreased (74.4-60.0) in response to rise in both BT and FM, whereas expansion ratio (ER) had shown an alternative relation as it decreased with elevated FM (2.17 at 14%, 130°C to 2.14 at 16%, 130°C) and increased with BT (1.75 at 18%, 130°C to 2.48 at 18%, 170°C). The values of WAI and WSI improved with the surge in BT, which was associated with enhanced disruption of starch granules at higher BT. Raise in FM incremented the total phenolic content (TPC) and hence the antioxidant activity (AA) (FRAP and DPPH) along with the hardness of snacks. As per in vitro starch digestibility is concerned, slowly digestible starch (SDS) content as well as glycemic index (51-53) of the extrudates depressed with increasing BT and FM. Also, lower BT and FM improved the functional properties such as expansion ratio, in-vitro protein digestibility, and overall acceptability of the snacks. A positive correlation was seen among SME and hardness of the snacks, WSI and ER, TPC and AA, SDS and Exp-GI, color and OA, texture and OA.

Asymmetric control of food intake by left and right vagal sensory neurons.

We investigated the lateralization of gut-innervating vagal sensory neurons and their roles in feeding behavior. Using genetic, anatomical, and behavioral analyses, we discovered a subset of highly lateralized vagal sensory neurons with distinct sensory responses to intestinal stimuli. Our results demonstrated that left vagal sensory neurons (LNG) are crucial for distension-induced satiety, while right vagal sensory neurons (RNG) mediate preference for nutritive foods. Furthermore, these lateralized neurons engage different central circuits, with LNG neurons recruiting brain regions associated with energy balance and RNG neurons activating areas related to salience, memory, and reward. Altogether, our findings unveil the diverse roles of asymmetrical gut-vagal-brain circuits in feeding behavior, offering new insights for potential therapeutic interventions targeting vagal nerve stimulation in metabolic and neuropsychiatric diseases.

A genetic variant of fatty acid amide hydrolase (FAAH) exacerbates hormone-mediated orexigenic feeding in mice.

Fatty acid amide hydrolase (FAAH) degrades the endocannabinoid anandamide. A polymorphism in FAAH (FAAH C385A) reduces FAAH expression, increases anandamide levels, and increases the risk of obesity. Nevertheless, some studies have found no association between FAAH C385A and obesity. We investigated whether the environmental context governs the impact of FAAH C385A on metabolic outcomes. Using a C385A knock-in mouse model, we found that FAAH A/A mice are more susceptible to glucocorticoid-induced hyperphagia, weight gain, and activation of hypothalamic AMP-activated protein kinase (AMPK). AMPK inhibition occluded the amplified hyperphagic response to glucocorticoids in FAAH A/A mice. FAAH knockdown exclusively in agouti-related protein (AgRP) neurons mimicked the exaggerated feeding response of FAAH A/A mice to glucocorticoids. FAAH A/A mice likewise presented exaggerated orexigenic responses to ghrelin, while FAAH knockdown in AgRP neurons blunted leptin anorectic responses. Together, the FAAH A/A genotype amplifies orexigenic responses and decreases anorexigenic responses, providing a putative mechanism explaining the diverging human findings.

Ball-milling: A sustainable and green approach for starch modification.

Ball-milling is a low-cost and green technology that offers mechanical actions (shear, friction, collision, and impact) to modify and reduce starch to nanoscale size. It is one of the physical modification techniques used to reduce the relative crystallinity and improve the digestibility of starch to their better utility. Ball-milling alters surface morphology, improving the overall surface area and texture of starch granules. This approach also can improve functional properties, including swelling, solubility, and water solubility, with increased energy supplied. Further, the increased surface area of starch particles and subsequent increase in active sites enhance chemical reactions and alteration in structural transformations and physical and chemical properties. This review is about current information on the impact of ball-milling on the compositions, fine structures, morphological, thermal, and rheological characteristics of starch granules. Furthermore, ball-milling is an efficient approach for the development of high-quality starches for applications in the food and non-food industries. There is also an attempt to compare ball-milled starches from various botanical sources.

Beetroot as a novel ingredient for its versatile food applications.

Beta vulgaris, also known as Beetroot, is a member of a family of Chenopodiaceae and is widely used as a natural food colorant. It gets its distinctive color due to nitrogen-containing water-soluble pigments betalains. Beetroot is an exquisite cradle of nutrients, including proteins, sucrose, carbohydrates, vitamins (B complex and vitamin C), minerals, fiber. They also contain an appreciable amount of phenolic compounds and antioxidants such as coumarins, carotenoids, sesquiterpenoids, triterpenes, flavonoids (astragalin, tiliroside, rhamnocitrin, kaempferol, rhamnetin). Recent studies evidenced that beetroot consumption had favorable physiological benefits, leading to improved cardiovascular diseases, hypertension, diabetes, cancer, hepatic steatosis, liver damage, etc. This review gives insights into developing beetroot as a potential and novel ingredient for versatile food applications and the latest research conducted worldwide. The phytochemical diversity of beetroot makes them potential sources of nutraceutical compounds from which functional foods can be obtained. The article aimed to comprehensively collate some of the vital information published on beetroot incurred in the agri-food sector and a comprehensive review detailing the potentiality of tapping bioactive compounds in the entire agriculture-based food sector.

Physical, morphological and storage stability of clove oil nanoemulsion based delivery system.

Clove oil based Nanoemulsions (NE) were prepared ultrasonically using Tween 80 and soy lecithin as synthetic and natural surfactants, respectively. The developed NEs were characterized for various parameters (particle size, polydispersity index, zeta potential, morphology, viscosity, colour, turbidity and pH) and the comparative effect of both the surfactants at variable levels (oil:tween 80-1:1, 1:2, 1:3 and 1:4 and oil: soy lecithin- 1:1, 1:1.5 and 1:2) was assessed. It was found that the type of surfactant and oil to surfactant ratio significantly affected particle size and stability of NEs. The NE prepared using tween 80 @1:3 had smallest average droplet diameter (40.9 nm). The formulated NEs were stored at 25 °C and 4 °C and analyzed for turbidity, pH and phase separation up to 90 days. Results revealed that the type and concentration of the surfactant significantly influenced the particle size and stability of NEs. NEs prepared using tween 80 were found to be more viscous than those prepared with soy lecithin. The prepared clove oil NEs have important implication to be used as a natural delivery system to increase the shelf life of food products.

Broad misappropriation of developmental splicing profile by cancer in multiple organs.

Oncogenesis mimics key aspects of embryonic development. However, the underlying mechanisms are incompletely understood. Here, we demonstrate that the splicing events specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. Such events are associated with key oncogenic processes and predict proliferation rates in cancer cell lines as well as patient survival. Such events preferentially target nitrosylation and transmembrane-region domains, whose coordinated splicing in multiple genes respectively affect intracellular transport and N-linked glycosylation. We infer critical splicing factors potentially regulating embryonic splicing events and show that such factors are potential oncogenic drivers and are upregulated specifically in malignant cells. Multiple complementary analyses point to MYC and FOXM1 as potential transcriptional regulators of critical splicing factors in brain and liver. Our study provides a comprehensive demonstration of a splicing-mediated link between development and cancer, and suggest anti-cancer targets including splicing events, and their upstream splicing and transcriptional regulators.

Modulation in Techno-Functional, Textural Properties, In Vitro Starch Digestibility and Macromolecular-Structural Interactions of Pasta with Potato (Solanum tuberosum L.).

The replacement of semolina with potato flour (PF) and potato mash (PM) at different levels was assessed for its effects on pasta quality. The results showed that the addition of PF and PM increased the pasting viscosity of the blends; in addition, PF enhanced the functional properties, while PM reduced them. The minimum cooking time decreased with PF and PM, while the PF pasta exhibited a higher cooking loss (5.02 to 10.44%) than the PM pasta, which exhibited a lower cooking loss. The pasta with PF and PM showed an increase in the total phenolic and flavonoid content, with reduced in vitro digestibility as confirmed by Fourier transform infrared spectroscopy. The PF pasta exhibited lower lightness and higher yellowness than the PM pasta, and its firmness and toughness also modulated owing to the complex interaction between potato starches and the gluten protein matrix, as evident from scanning electron microscopy. Sensory data revealed that pasta containing 30% PF and 16% PM was highly acceptable.

MPYS Modulates Fatty Acid Metabolism and Immune Tolerance at Homeostasis Independent of Type I IFNs.

MPYS/STING (stimulator of IFN genes) senses cyclic dinucleotides (CDNs), generates type I IFNs, and plays a critical role in infection, inflammation, and cancer. In this study, analyzing genotype and haplotype data from the 1000 Genomes Project, we found that the R71H-G230A-R293Q (HAQ) MPYS allele frequency increased 57-fold in East Asians compared with sub-Saharan Africans. Meanwhile, the G230A-R293Q (AQ) allele frequency decreased by 98% in East Asians compared with sub-Saharan Africans. We propose that the HAQ and AQ alleles underwent a natural selection during the out-of-Africa migration. We used mouse models of HAQ and AQ to investigate the underlying mechanism. We found that the mice carrying the AQ allele, which disappeared in East Asians, had normal CDN-type I IFN responses. Adult AQ mice, however, had less fat mass than did HAQ or wild-type mice on a chow diet. AQ epididymal adipose tissue had increased regulatory T cells and M2 macrophages with protein expression associated with enhanced fatty acid oxidation. Conditional knockout mice and adoptive cell transfer indicate a macrophage and regulatory T cell-intrinsic role of MPYS in fatty acid metabolism. Mechanistically, AQ/IFNAR1-/- mice had a similar lean phenotype as for the AQ mice. MPYS intrinsic tryptophan fluorescence revealed that the R71H change increased MPYS hydrophilicity. Lastly, we found that the second transmembrane (TM) and the TM2-TM3 linker region of MPYS interact with activated fatty acid, fatty acyl-CoA. In summary, studying the evolution of the human MPYS gene revealed an MPYS function in modulating fatty acid metabolism that may be critical during the out-of-Africa migration.

Splicing of branchpoint-distant exons is promoted by Cactin, Tls1 and the ubiquitin-fold-activated Sde2.

Intron diversity facilitates regulated gene expression and alternative splicing. Spliceosomes excise introns after recognizing their splicing signals: the 5'-splice site (5'ss), branchpoint (BP) and 3'-splice site (3'ss). The latter two signals are recognized by U2 small nuclear ribonucleoprotein (snRNP) and its accessory factors (U2AFs), but longer spacings between them result in weaker splicing. Here, we show that excision of introns with a BP-distant 3'ss (e.g. rap1 intron 2) requires the ubiquitin-fold-activated splicing regulator Sde2 in Schizosaccharomyces pombe. By monitoring splicing-specific ura4 reporters in a collection of S. pombe mutants, Cay1 and Tls1 were identified as additional regulators of this process. The role of Sde2, Cay1 and Tls1 was further confirmed by increasing BP-3'ss spacings in a canonical tho5 intron. We also examined BP-distant exons spliced independently of these factors and observed that RNA secondary structures possibly bridged the gap between the two signals. These proteins may guide the 3'ss towards the spliceosome's catalytic centre by folding the RNA between the BP and 3'ss. Orthologues of Sde2, Cay1 and Tls1, although missing in the intron-poor Saccharomyces cerevisiae, are present in intron-rich eukaryotes, including humans. This type of intron-specific pre-mRNA splicing appears to have evolved for regulated gene expression and alternative splicing of key heterochromatin factors.

Neural Pathway for Gut Feelings: Vagal Interoceptive Feedback From the Gastrointestinal Tract Is a Critical Modulator of Anxiety-like Behavior.

BACKGROUND: Anxiety disorders are associated with an altered perception of the body's internal state. Therefore, understanding the neuronal basis of interoception can foster novel anxiety therapies. In rodents, the feeding status bidirectionally modulates anxiety-like behavior but how the sensing of gastrointestinal state affects anxiety remains unclear. METHODS: We combined chemogenetics, neuropharmacology, and behavioral approaches in male and female rats to test whether vagal afferents terminating in the gastrointestinal tract mediate feeding-induced tuning of anxiety. Using saporin-based lesions and transcriptomics, we investigated the chronic impact of this gut-brain circuit on anxiety-like behavior. RESULTS: Both feeding and selective chemogenetic activation of gut-innervating vagal afferents increased anxiety-like behavior. Conversely, chemogenetic inhibition blocked the increase in anxiety-like behavior induced by feeding. Using a selective saporin-based lesion, we demonstrate that the loss of gut-innervating vagal afferent signaling chronically reduces anxiety-like behavior in male rats but not in female rats. We next identify a vagal circuit that connects the gut to the central nucleus of the amygdala, using anterograde transsynaptic tracing from the nodose ganglia. Lesion of this gut-brain vagal circuit modulated the central amygdala transcriptome in both sexes but selectively affected a network of GABA (gamma-aminobutyric acid)-related genes only in males, suggesting a potentiation of inhibitory control. Blocking GABAergic signaling in the central amygdala re-established normal anxiety levels in male rats. CONCLUSIONS: Vagal sensory signals from the gastrointestinal tract are critical for baseline and feeding-induced tuning of anxiety via the central amygdala in rats. Our results suggest vagal gut-brain signaling as a target to normalize interoception in anxiety disorders.

Effect of extrusion processing on techno-functional, textural and bioactive properties of whole-grain corn flour-based breakfast cereals sweetened with honey.

The present study investigated the effect of honey and extrusion processing parameters on techno-functional and bioactive properties of whole-grain corn flour breakfast cereals. The central composite rotatable design (CCRD) was used to plan the experiments using feed moisture (FM), extrusion temperature (ET), and honey level as process variables and sectional expansion ratio (SER), bulk density (BD), water absorption index (WAI), water solubility index (WSI), and textural hardness as response variables. The feed containing honey and whole-grain corn flour was extruded through a twin-screw extruder according to CCRD. The data were fit to the appropriate regression models based on model significance and insignificant lack of fit. The selected experiments from CCRD were considered for studying the bioactive properties, and the effect of ET and honey level on bioactive properties was determined. The results of the study indicated that FM and honey adversely affected the SER, BD, and textural hardness, while ET augmented these properties of breakfast cereals. The WAI decreased with an increase in honey level and ET during extrusion. The incremental addition of honey in the mix as well extrusion at elevated temperature led to higher WSI. The whole-grain corn flour added with 10.22% honey and extruded at 16.06% FM, and 138.07°C ET produced optimum quality breakfast cereals with 0.70 desirability. The total phenolic content of breakfast cereals decreased, and antioxidant activity and hydroxymethylfurfural content increased upon extrusion at the higher temperatures. Honey addition lowers the loss of phenolic content during extrusion and improves the antioxidant activity of breakfast cereals.

Quality changes in fish sausages supplemented with pangas protein isolates as affected by frozen storage and casing material.

Influence of pangas protein isolates (10PI) and casing material on frozen storage (-18 °C) characteristics of pangas mince sausages was studied for a period of three months along with control sausages (CO). The expressible fluid content of sausage emulsion increased as storage progressed to 3 months, reaching 31.32 and 17.57 g 100 g-1 for control and 10% PI emulsions, respectively. Water holding capacity and cooking yield values showed a gradual and significant (p < 0.05) reduction with progress in the storage time. The G' and G″ values decreased during storage, indicating the change in protein structure and gelling ability. Sausages packed in LDPE casings had higher oxidation and bacterial counts than sausages packed in cellulose casings. Irrespective of the casing material and protein isolates, the sensory scores varied non-significantly in all the sausages during the initial storage phase. After three months, sausages from COCL and 10PICL were still acceptable with sensory scores of 5.6 and 5.8, respectively, indicating better quality of sausages stuffed into cellulose casings than LDPE casings. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-021-05222-1.