In Vivo Evidence for Serine Biosynthesis-Defined Sensitivity of Lung Metastasis, but Not of Primary Breast Tumors, to mTORC1 Inhibition.

In tumors, nutrient availability and metabolism are known to be important modulators of growth signaling. However, it remains elusive whether cancer cells that are growing out in the metastatic niche rely on the same nutrients and metabolic pathways to activate growth signaling as cancer cells within the primary tumor. We discovered that breast-cancer-derived lung metastases, but not the corresponding primary breast tumors, use the serine biosynthesis pathway to support mTORC1 growth signaling. Mechanistically, pyruvate uptake through Mct2 supported mTORC1 signaling by fueling serine biosynthesis-derived α-ketoglutarate production in breast-cancer-derived lung metastases. Consequently, expression of the serine biosynthesis enzyme PHGDH was required for sensitivity to the mTORC1 inhibitor rapamycin in breast-cancer-derived lung tumors, but not in primary breast tumors. In summary, we provide in vivo evidence that the metabolic and nutrient requirements to activate growth signaling differ between the lung metastatic niche and the primary breast cancer site.

PHGDH heterogeneity potentiates cancer cell dissemination and metastasis.

Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs1. Genetic, transcriptional and translational heterogeneity contributes to this dynamic process2,3. Metabolic heterogeneity has also been observed4, yet its role in cancer progression is less explored. Here we find that the loss of phosphoglycerate dehydrogenase (PHGDH) potentiates metastatic dissemination. Specifically, we find that heterogeneous or low PHGDH expression in primary tumours of patients with breast cancer is associated with decreased metastasis-free survival time. In mice, circulating tumour cells and early metastatic lesions are enriched with Phgdhlow cancer cells, and silencing Phgdh in primary tumours increases metastasis formation. Mechanistically, Phgdh interacts with the glycolytic enzyme phosphofructokinase, and the loss of this interaction activates the hexosamine-sialic acid pathway, which provides precursors for protein glycosylation. As a consequence, aberrant protein glycosylation occurs, including increased sialylation of integrin αvß3, which potentiates cell migration and invasion. Inhibition of sialylation counteracts the metastatic ability of Phgdhlow cancer cells. In conclusion, although the catalytic activity of PHGDH supports cancer cell proliferation, low PHGDH protein expression non-catalytically potentiates cancer dissemination and metastasis formation. Thus, the presence of PHDGH heterogeneity in primary tumours could be considered a sign of tumour aggressiveness.

Frizzled2 receives WntA signaling during butterfly wing pattern formation.

Butterfly color patterns provide visible and biodiverse phenotypic readouts of the patterning processes. Although the secreted ligand WntA has been shown to instruct the color pattern formation in butterflies, its mode of reception remains elusive. Butterfly genomes encode four homologs of the Frizzled-family of Wnt receptors. Here, we show that CRISPR mosaic knockouts of frizzled2 (fz2) phenocopy the color pattern effects of WntA loss of function in multiple nymphalids. Whereas WntA mosaic clones result in intermediate patterns of reduced size, fz2 clones are cell-autonomous, consistent with a morphogen function. Shifts in expression of WntA and fz2 in WntA crispant pupae show that they are under positive and negative feedback, respectively. Fz1 is required for Wnt-independent planar cell polarity in the wing epithelium. Fz3 and Fz4 show phenotypes consistent with Wnt competitive-antagonist functions in vein formation (Fz3 and Fz4), wing margin specification (Fz3), and color patterning in the Discalis and Marginal Band Systems (Fz4). Overall, these data show that the WntA/Frizzled2 morphogen-receptor pair forms a signaling axis that instructs butterfly color patterning and shed light on the functional diversity of insect Frizzled receptors.

BNIP3 promotes HIF-1α-driven melanoma growth by curbing intracellular iron homeostasis.

BNIP3 is a mitophagy receptor with context-dependent roles in cancer, but whether and how it modulates melanoma growth in vivo remains unknown. Here, we found that elevated BNIP3 levels correlated with poorer melanoma patient's survival and depletion of BNIP3 in B16-F10 melanoma cells compromised tumor growth in vivo. BNIP3 depletion halted mitophagy and enforced a PHD2-mediated downregulation of HIF-1α and its glycolytic program both in vitro and in vivo. Mechanistically, we found that BNIP3-deprived melanoma cells displayed increased intracellular iron levels caused by heightened NCOA4-mediated ferritinophagy, which fostered PHD2-mediated HIF-1α destabilization. These effects were not phenocopied by ATG5 or NIX silencing. Restoring HIF-1α levels in BNIP3-depleted melanoma cells rescued their metabolic phenotype and tumor growth in vivo, but did not affect NCOA4 turnover, underscoring that these BNIP3 effects are not secondary to HIF-1α. These results unravel an unexpected role of BNIP3 as upstream regulator of the pro-tumorigenic HIF-1α glycolytic program in melanoma cells.

Breast cancer cells rely on environmental pyruvate to shape the metastatic niche.

The extracellular matrix is a major component of the local environment-that is, the niche-that determines cell behaviour1. During metastatic growth, cancer cells shape the extracellular matrix of the metastatic niche by hydroxylating collagen to promote their own metastatic growth2,3. However, only particular nutrients might support the ability of cancer cells to hydroxylate collagen, because nutrients dictate which enzymatic reactions are active in cancer cells4,5. Here we show that breast cancer cells rely on the nutrient pyruvate to drive collagen-based remodelling of the extracellular matrix in the lung metastatic niche. Specifically, we discovered that pyruvate uptake induces the production of α-ketoglutarate. This metabolite in turn activates collagen hydroxylation by increasing the activity of the enzyme collagen prolyl-4-hydroxylase (P4HA). Inhibition of pyruvate metabolism was sufficient to impair collagen hydroxylation and consequently the growth of breast-cancer-derived lung metastases in different mouse models. In summary, we provide a mechanistic understanding of the link between collagen remodelling and the nutrient environment in the metastatic niche.

Evidence for an alternative fatty acid desaturation pathway increasing cancer plasticity.

Most tumours have an aberrantly activated lipid metabolism1,2 that enables them to synthesize, elongate and desaturate fatty acids to support proliferation. However, only particular subsets of cancer cells are sensitive to approaches that target fatty acid metabolism and, in particular, fatty acid desaturation3. This suggests that many cancer cells contain an unexplored plasticity in their fatty acid metabolism. Here we show that some cancer cells can exploit an alternative fatty acid desaturation pathway. We identify various cancer cell lines, mouse hepatocellular carcinomas, and primary human liver and lung carcinomas that desaturate palmitate to the unusual fatty acid sapienate to support membrane biosynthesis during proliferation. Accordingly, we found that sapienate biosynthesis enables cancer cells to bypass the known fatty acid desaturation pathway that is dependent on stearoyl-CoA desaturase. Thus, only by targeting both desaturation pathways is the in vitro and in vivo proliferation of cancer cells that synthesize sapienate impaired. Our discovery explains metabolic plasticity in fatty acid desaturation and constitutes an unexplored metabolic rewiring in cancers.

Molecular monitoring of viral infections in immunocompromised patients in a large university hospital in Italy: reflections after thirteen years of real-life activity.

PURPOSE: This study aimed to investigate the prevalence and viral reactivations of clinical interest in the immunocompromised patient with particular focus on hematologic and solid organ transplant recipients. METHODS: Molecular screening data of CMV, EBV, JCV and BKV from 2011 to 2023 were analyzed. This extensive time span allowed the access to more than 100,000 samples from over 20,000 patients treated at Policlinico Umberto I. It was possible to temporally investigate patient attendance patterns, average age distribution, seasonality of infections, and positivity rates of the analyzed viruses. RESULTS: Between 2019 and 2022 a significant reduction in organ transplants performed and in the positive molecular detection of EBV, JCV and BKV was observed. Additionally, there has been a noteworthy decrease in CMV reactivations, with a reduction of up to 50% starting in 2019. A remarkable reduction of 39% in the rate of CMV viral reactivation has been also achieved in SOT between 2016 and 2023. CONCLUSION: The years following 2019 were profoundly impacted by the COVID-19 pandemic era. This period resulted in a substantial reduction in healthcare services and hospital visits. Furthermore, the introduction of the drug Letermovir in Italy in 2019 demonstrated remarkable efficacy, evidenced by a reduction in CMV reactivations. Additionally, the adoption of a novel clinical approach centered on personalized therapy facilitated improved management of immunocompromised patients.

Neural divergence and hybrid disruption between ecologically isolated Heliconius butterflies.

The importance of behavioral evolution during speciation is well established, but we know little about how this is manifest in sensory and neural systems. A handful of studies have linked specific neural changes to divergence in host or mate preferences associated with speciation. However, the degree to which brains are adapted to local environmental conditions, and whether this contributes to reproductive isolation between close relatives that have diverged in ecology, remains unknown. Here, we examine divergence in brain morphology and neural gene expression between closely related, but ecologically distinct, Heliconius butterflies. Despite ongoing gene flow, sympatric species pairs within the melpomene-cydno complex are consistently separated across a gradient of open to closed forest and decreasing light intensity. By generating quantitative neuroanatomical data for 107 butterflies, we show that Heliconius melpomene and Heliconius cydno clades have substantial shifts in brain morphology across their geographic range, with divergent structures clustered in the visual system. These neuroanatomical differences are mirrored by extensive divergence in neural gene expression. Differences in both neural morphology and gene expression are heritable, exceed expected rates of neutral divergence, and result in intermediate traits in first-generation hybrid offspring. Strong evidence of divergent selection implies local adaptation to distinct selective optima in each parental microhabitat, suggesting the intermediate traits of hybrids are poorly matched to either condition. Neural traits may therefore contribute to coincident barriers to gene flow, thereby helping to facilitate speciation.

Soft tissue reconstruction of the trunk with pedicled perforator and musculocutaneous flaps: A single-center comparative retrospective study.

BACKGROUND: Soft tissue trunk reconstruction is often challenging. Although free microvascular flaps are a feasible option in case of extensive defects involving deep structures, pedicled flaps represent a good alternative, especially if harvested and dissected with a "microsurgical" approach. The aim of this study is to evaluate the feasibility of trunk reconstruction with the use of pedicled flaps, according to the application of our reconstructive algorithm, and to compare it to other reconstructive methods. PATIENTS AND METHODS: From January 2017 to December 2021, we retrospectively analyzed patients who underwent soft tissue reconstruction of the trunk with pedicled flaps at the authors' institution. Patient's demographic, clinical and surgical characteristics and postoperative complications were recorded and analyzed by descriptive statistics. A comparative analysis was made between the study group and two other groups who underwent reconstruction of trunk defects with free flaps and skin grafts, respectively, at the authors' institution. RESULTS: Forty-seven patients were included in the study. Patients' age ranged between 36 and 82 years (mean: 57.8 years). Twenty-eight patients were male, while 19 patients were female. In 76.6% of patients (36 out of 47), reconstructive procedures were performed to repair defects resulting from cancer resection. Reconstruction of superficial defects was always achieved with perforator flaps (n = 25). In case of full-thickness defects, reconstruction was carried out with musculocutaneous flaps (n = 22); latissimus dorsi and vastus lateralis were the most used flaps for chest and abdominal wall reconstruction, respectively. In our series, we observed only one case of total flap loss requiring re-operation under general anesthesia. Minor complications occurred in 8.5% of cases (4 out of 47 patients). We observed two cases of partial flap necrosis and two cases of wound dehiscence. In the skin grafts group (n = 53), the mean age was 54.5 years (range 39-85) and 56% of patients were male (n = 30). In 66% of cases (n = 30) the defect resulted from oncological resection. The overall complication rate was 18.8% (n = 10). In the free flaps group (n = 10), the mean age was 49.0 years (range 29-77) and 60% of patients (n = 6) were male. In 70% of cases (n = 7) the defect was caused by oncological resection. Complications occurred in two patients (20%). No statistically significant differences were found in terms of overall complication rate between the study group and the two comparative groups (p = .48). A significant correlation was found between the reconstructive method and the type and size of the defect, with reconstruction through free flaps being associated with larger (344.0 vs. 220.4 cm2 ) (p = .04) and full-thickness defects (80.0% vs. 46.8%) (p < .01) if compared to pedicled flaps. CONCLUSIONS: In the new era of microsurgery, pedicled flaps represent a valid alternative to free flaps for the majority of soft tissue defects of the trunk. In our series, no statistically significant differences in terms of complications were found between reconstructions of similar defects achieved with pedicled and free flaps, and free flap use was limited to extensive full-thickness defects. In addition, the rate of postoperative complications with pedicled flaps found in our cohort was lower than the rate reported in the literature.

Latissimus Dorsi Flap and Thoracodorsal Artery Perforator Flap with Immediate Fat Transfer (LIFT and TIFT): A Retrospective Study about Total Breast Reconstruction in High-Risk Patients.

INTRODUCTION: Microsurgical breast reconstruction has become popular over the past twenty years and allows a tailor-tuck approach to each patient. However, smoking or coagulation disorders may switch surgeon's choice towards alternative options. When facing these risk factors, we performed pedicled latissimus dorsi (LD) flap and thoracodorsal artery perforator (TDAP) flap reconstruction with immediate fat transfer (LIFT and TIFT), achieving satisfactory surgical outcomes. Hence, we aim to present our seven-years case-series and discuss our decisional algorithm. MATERIALS AND METHODS: Thirty smoker women and seven women affected by coagulation disorder (n = 37) respectively had LIFT and TIFT surgery and were retrospectively evaluated. Patients' demographics and outcomes were recorded and compared. RESULTS: LIFT patients received higher volumes of immediate fat grafting compared to TIFT patients (p < 0.05), which required additional lipofilling to provide adequate volume amount, since the TDAP flap was not immediately grafted. However, the additional lipofilling procedures and fat volume were similar (p > 0.05). Flap survival reached 100%, and flap necrosis or loss did not occur. Few minor complications were evidenced in the LIFT group only (p > 0.05). CONCLUSION: Based on our experience, we support the reliability of pedicled LD and TDAP flaps with immediate fat transfer in breast reconstruction as valuable alternative to microsurgery in smokers (LIFT) and patients with coagulation disorders (TIFT). However, the results of our study are not conclusive since still must be clarified the role of the smoking and coagulation disorders in microsurgery and the real benefit of a non-microsurgical procedure. LEVEL OF EVIDENCE IV: Opinions of respected authorities, based on clinical experience, descriptive studies, or reports of expert committees. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Link Prediction with Continuous-Time Classical and Quantum Walks.

Protein-protein interaction (PPI) networks consist of the physical and/or functional interactions between the proteins of an organism, and they form the basis for the field of network medicine. Since the biophysical and high-throughput methods used to form PPI networks are expensive, time-consuming, and often contain inaccuracies, the resulting networks are usually incomplete. In order to infer missing interactions in these networks, we propose a novel class of link prediction methods based on continuous-time classical and quantum walks. In the case of quantum walks, we examine the usage of both the network adjacency and Laplacian matrices for specifying the walk dynamics. We define a score function based on the corresponding transition probabilities and perform tests on six real-world PPI datasets. Our results show that continuous-time classical random walks and quantum walks using the network adjacency matrix can successfully predict missing protein-protein interactions, with performance rivalling the state-of-the-art.

Emergent entanglement structures and self-similarity in quantum spin chains.

We introduce an experimentally accessible network representation for many-body quantum states based on entanglement between all pairs of its constituents. We illustrate the power of this representation by applying it to a paradigmatic spin chain model, the XX model, and showing that it brings to light new phenomena. The analysis of these entanglement networks reveals that the gradual establishment of quasi-long range order is accompanied by a symmetry regarding single-spin concurrence distributions, as well as by instabilities in the network topology. Moreover, we identify the existence of emergent entanglement structures, spatially localized communities enforced by the global symmetry of the system that can be revealed by model-agnostic community detection algorithms. The network representation further unveils the existence of structural classes and a cyclic self-similarity in the state, which we conjecture to be intimately linked to the community structure. Our results demonstrate that the use of tools and concepts from complex network theory enables the discovery, understanding and description of new physical phenomena even in models studied for decades. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Identification of Characteristic Points in Multivariate Physiological Signals by Sensor Fusion and Multi-Task Deep Networks.

Identification of characteristic points in physiological signals, such as the peak of the R wave in the electrocardiogram and the peak of the systolic wave of the photopletismogram, is a fundamental step for the quantification of clinical parameters, such as the pulse transit time. In this work, we presented a novel neural architecture, called eMTUnet, to automate point identification in multivariate signals acquired with a chest-worn device. The eMTUnet consists of a single deep network capable of performing three tasks simultaneously: (i) localization in time of characteristic points (labeling task), (ii) evaluation of the quality of signals (classification task); (iii) estimation of the reliability of classification (reliability task). Preliminary results in overnight monitoring showcased the ability to detect characteristic points in the four signals with a recall index of about 1.00, 0.90, 0.90, and 0.80, respectively. The accuracy of the signal quality classification was about 0.90, on average over four different classes. The average confidence of the correctly classified signals, against the misclassifications, was 0.93 vs. 0.52, proving the worthiness of the confidence index, which may better qualify the point identification. From the achieved outcomes, we point out that high-quality segmentation and classification are both ensured, which brings the use of a multi-modal framework, composed of wearable sensors and artificial intelligence, incrementally closer to clinical translation.

Convolutional Neural Networks Cascade for Automatic Pupil and Iris Detection in Ocular Proton Therapy.

Eye tracking techniques based on deep learning are rapidly spreading in a wide variety of application fields. With this study, we want to exploit the potentiality of eye tracking techniques in ocular proton therapy (OPT) applications. We implemented a fully automatic approach based on two-stage convolutional neural networks (CNNs): the first stage roughly identifies the eye position and the second one performs a fine iris and pupil detection. We selected 707 video frames recorded during clinical operations during OPT treatments performed at our institute. 650 frames were used for training and 57 for a blind test. The estimations of iris and pupil were evaluated against the manual labelled contours delineated by a clinical operator. For iris and pupil predictions, Dice coefficient (median = 0.94 and 0.97), Szymkiewicz-Simpson coefficient (median = 0.97 and 0.98), Intersection over Union coefficient (median = 0.88 and 0.94) and Hausdorff distance (median = 11.6 and 5.0 (pixels)) were quantified. Iris and pupil regions were found to be comparable to the manually labelled ground truths. Our proposed framework could provide an automatic approach to quantitatively evaluating pupil and iris misalignments, and it could be used as an additional support tool for clinical activity, without impacting in any way with the consolidated routine.

Noisy Quantum Metrology Enhanced by Continuous Nondemolition Measurement.

We show that continuous quantum nondemolition (QND) measurement of an atomic ensemble is able to improve the precision of frequency estimation even in the presence of independent dephasing acting on each atom. We numerically simulate the dynamics of an ensemble with up to N=150 atoms initially prepared in a (classical) spin coherent state, and we show that, thanks to the spin squeezing dynamically generated by the measurement, the information obtainable from the continuous photocurrent scales superclassically with respect to the number of atoms N. We provide evidence that such superclassical scaling holds for different values of dephasing and monitoring efficiency. We moreover calculate the extra information obtainable via a final strong measurement on the conditional states generated during the dynamics and show that the corresponding ultimate limit is nearly achieved via a projective measurement of the spin-squeezed collective spin operator. We also briefly discuss the difference between our protocol and standard estimation schemes, where the state preparation time is neglected.

Large Polarons as Key Quasiparticles in SrTiO_{3} and SrTiO_{3}-Based Heterostructures.

Despite its simple structure and low degree of electronic correlation, SrTiO_{3} (STO) features collective phenomena linked to charge transport and, ultimately, superconductivity, that are not yet fully explained. Thus, a better insight into the nature of the quasiparticles shaping the electronic and conduction properties of STO is needed. We studied the low-energy excitations of bulk STO and of the LaAlO_{3}/SrTiO_{3} two-dimensional electron gas (2DEG) by Ti L_{3} edge resonant inelastic x-ray scattering. In all samples, we find the hallmark of polarons in the form of intense dd+phonon excitations, and a decrease of the LO3-mode electron-phonon coupling when going from insulating to highly conducting STO single crystals and heterostructures. Both results are attributed to the dynamic screening of the large polaron self-induced polarization, showing that the low-temperature physics of STO and STO-based 2DEGs is dominated by large polaron quasiparticles.

Viruses of protozoan parasites and viral therapy: Is the time now right?

Infections caused by protozoan parasites burden the world with huge costs in terms of human and animal health. Most parasitic diseases caused by protozoans are neglected, particularly those associated with poverty and tropical countries, but the paucity of drug treatments and vaccines combined with increasing problems of drug resistance are becoming major concerns for their control and eradication. In this climate, the discovery/repurposing of new drugs and increasing effort in vaccine development should be supplemented with an exploration of new alternative/synergic treatment strategies. Viruses, either native or engineered, have been employed successfully as highly effective and selective therapeutic approaches to treat cancer (oncolytic viruses) and antibiotic-resistant bacterial diseases (phage therapy). Increasing evidence is accumulating that many protozoan, but also helminth, parasites harbour a range of different classes of viruses that are mostly absent from humans. Although some of these viruses appear to have no effect on their parasite hosts, others either have a clear direct negative impact on the parasite or may, in fact, contribute to the virulence of parasites for humans. This review will focus mainly on the viruses identified in protozoan parasites that are of medical importance. Inspired and informed by the experience gained from the application of oncolytic virus- and phage-therapy, rationally-driven strategies to employ these viruses successfully against parasitic diseases will be presented and discussed in the light of the current knowledge of the virus biology and the complex interplay between the viruses, the parasite hosts and the human host. We also highlight knowledge gaps that should be addressed to advance the potential of virotherapy against parasitic diseases.

Type I interferons induced by endogenous or exogenous viral infections promote metastasis and relapse of leishmaniasis.

The presence of the endogenous Leishmania RNA virus 1 (LRV1) replicating stably within some parasite species has been associated with the development of more severe forms of leishmaniasis and relapses after drug treatment in humans. Here, we show that the disease-exacerbatory role of LRV1 relies on type I IFN (type I IFNs) production by macrophages and signaling in vivo. Moreover, infecting mice with the LRV1-cured Leishmania guyanensis (LgyLRV1- ) strain of parasites followed by type I IFN treatment increased lesion size and parasite burden, quantitatively reproducing the LRV1-bearing (LgyLRV1+ ) infection phenotype. This finding suggested the possibility that exogenous viral infections could likewise increase pathogenicity, which was tested by coinfecting mice with L. guyanensis and lymphocytic choriomeningitis virus (LCMV), or the sand fly-transmitted arbovirus Toscana virus (TOSV). The type I IFN antiviral response increased the pathology of L. guyanensis infection, accompanied by down-regulation of the IFN-γ receptor normally required for antileishmanial control. Further, LCMV coinfection of IFN-γ-deficient mice promoted parasite dissemination to secondary sites, reproducing the LgyLRV1+ metastatic phenotype. Remarkably, LCMV coinfection of mice that had healed from L. guyanensis infection induced reactivation of disease pathology, overriding the protective adaptive immune response. Our findings establish that type I IFN-dependent responses, arising from endogenous viral elements (dsRNA/LRV1), or exogenous coinfection with IFN-inducing viruses, are able to synergize with New World Leishmania parasites in both primary and relapse infections. Thus, viral infections likely represent a significant risk factor along with parasite and host factors, thereby contributing to the pathological spectrum of human leishmaniasis.

Revisiting the developmental and cellular role of the pigmentation gene yellow in Drosophila using a tagged allele.

Pigmentation is a diverse and ecologically relevant trait in insects. Pigment formation has been studied extensively at the genetic and biochemical levels. The temporality of pigment formation during animal development, however, is more elusive. Here, we examine this temporality, focusing on yellow, a gene involved in the formation of black melanin. We generated a protein-tagged yellow allele in the fruit fly Drosophila melanogaster, which allowed us to precisely describe Yellow expression pattern at the tissue and cellular levels throughout development. We found Yellow expressed in the pupal epidermis in patterns prefiguring black pigmentation. We also found Yellow expressed in a few central neurons from the second larval instar to adult stages, including a subset of neurons adjacent to the clock neurons marked by the gene Pdf. We then specifically examined the dynamics of Yellow expression domain and subcellular localization in relationship to pigment formation. In particular, we showed how a late step of re-internalization is regulated by the large low-density lipoprotein receptor-related protein Megalin. Finally we suggest a new function for Yellow in the establishment of sharp pigmentation pattern boundaries, whereby this protein may assume a structural role, anchoring pigment deposits or pigmentation enzymes in the cuticle.