Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial Dynamics and Mitochondria-Lysosome Contacts in Neurogenetic Diseases

Mitochondrial network is constantly in a dynamic and regulated balance of fusion and fission processes, which is known as mitochondrial dynamics. Mitochondria make physical contacts with almost every other membrane in the cell thus impacting cellular functions. Mutations in mitochondrial dynamics genes are known to cause neurogenetic diseases. To better understand the consequences on the cellular phenotype and pathophysiology of neurogenetic diseases associated with defective mitochondrial dynamics, we have compared the fibroblasts phenotypes of (i) patients carrying pathogenic variants in genes involved in mitochondrial dynamics such as DRP1 (also known as DNM1L), GDAP1, OPA1, and MFN2, and (ii) patients carrying mutated genes that their dysfunction affects mitochondria or induces a mitochondrial phenotype, but that are not directly involved in mitochondrial dynamic network, such as FXN (encoding frataxin, located in the mitochondrial matrix), MED13 (hyperfission phenotype), and CHKB (enlarged mitochondria phenotype). We identified mitochondrial network alterations in all patients’ fibroblasts except for CHKBQ198*/Q198*. Functionally, all fibroblasts showed mitochondrial oxidative stress, without membrane potential abnormalities. The lysosomal area and distribution were abnormal in GDAP1W67L/W67L, DRP1K75E/+, OPA1F570L/+, and FXNR165C/GAA fibroblasts. These lysosomal alterations correlated with mitochondria-lysosome membrane contact sites (MCSs) defects in GDAP1W67L/W67L exclusively. The study of mitochondrial contacts in all samples further revealed a significant decrease in MFN2R104W/+ fibroblasts. GDAP1 and MFN2 are outer mitochondrial membrane (OMM) proteins and both are related to Charcot-Marie Tooth neuropathy. Here we identified their constitutive interaction as well as MFN2 interaction with LAMP-1. Therefore MFN2 is a new mitochondria-lysosome MCSs protein. Interestingly, GDAP1W67L/W67L and MFN2R104W/+ fibroblasts carry pathogenic changes that occur in their catalytic domains thus suggesting a functional role of GDAP1 and MFN2 in mitochondria–lysosome MCSs. Finally, we observed starvation-induced autophagy alterations in DRP1K75E/+, GDAP1W67L/W67L, OPA1F570L/+, MFN2R104W/+, and CHKBQ198*/Q198* fibroblasts. These genes are related to mitochondrial membrane structure or lipid composition, which would associate the OMM with starvation-induced autophagy. In conclusion, the study of mitochondrial dynamics and mitochondria-lysosome axis in a group of patients with different neurogenetic diseases has deciphered common and unique cellular phenotypes of degrading and non-degrading pathways that shed light on pathophysiological events, new biomarkers and pharmacological targets for these disorders.
CCR6 and CXCR6 Identify the Th17 Cells With Cytotoxicity in Experimental Autoimmune Encephalomyelitis

Due to the plasticity of IL-17-producing CD4 T cells (Th17 cells), a long-standing challenge in studying Th17-driven autoimmune is the lack of specific surface marker to identify the pathogenic Th17 cells in vivo. Recently, we discovered that pathogenic CD4 T cells were CXCR6 positive in experimental autoimmune encephalomyelitis (EAE), a commonly used Th17-driven autoimmune model. Herein, we further revealed that peripheral CXCR6+CD4 T cells contain a functionally distinct subpopulation, which is CCR6 positive and enriched for conventional Th17 molecules (IL-23R and RORγt) and cytotoxic signatures. Additionally, spinal cord-infiltrating CD4 T cells were highly cytotoxic by expressing Granzyme(s) along with IFNγ and GM-CSF. Collectively, this study suggested that peripheral CCR6+CXCR6+CD4 T cells were Th17 cells with cytotoxic property in EAE model, and highlighted the cytotoxic granzymes for EAE pathology.
Glia Regulate the Development, Function, and Plasticity of the Visual System From Retina to Cortex

Visual experience is mediated through a relay of finely-tuned neural circuits extending from the retina, to retinorecipient nuclei in the midbrain and thalamus, to the cortex which work together to translate light information entering our eyes into a complex and dynamic spatio-temporal representation of the world. While the experience-dependent developmental refinement and mature function of neurons in each major stage of the vertebrate visual system have been extensively characterized, the contributions of the glial cells populating each region are comparatively understudied despite important findings demonstrating that they mediate crucial processes related to the development, function, and plasticity of the system. In this article we review the mechanisms for neuron-glia communication throughout the vertebrate visual system, as well as functional roles attributed to astrocytes and microglia in visual system development and processing. We will also discuss important aspects of glial function that remain unclear, integrating the knowns and unknowns about glia in the visual system to advance new hypotheses to guide future experimental work.
Myoclonic Epilepsy: Case Report of a Mild Phenotype in a Pediatric Patient Expanding Clinical Spectrum of KCNA2 Pathogenic Variants

We report on the rare case of a male toddler presenting with myoclonic epilepsy characterized by daily episodes of upward movements of the eyebrows, and myoclonic jerks of both head and upper limbs. In addition, the child showed speech delay, tremors, and lack of motor coordination. Next Generation Sequencing analysis (NGS) performed in trio revealed in the proband the c.889C>T de novo missense variant in the KCNA2 gene in heterozygous state. This is the first case of myoclonic epilepsy in a toddler due to a c.889C>T KCNA2 missense variant. The patient was treated with valproic acid and ethosuximide with a good clinical response. At 6 years old, follow-up revealed that the proband was seizure-free with tremors and clumsiness in movements. According to the literature, this case supports the correlation between myoclonic epilepsy and KCNA2 alterations. This evidence suggests that performing genomic testing including the KCNA2 gene in preschool patients affected by myoclonic epilepsy, especially when associated with delayed neurodevelopment. Our goal is to expand the phenotypical spectrum of this rare condition and adding clinical features following a genotype-first approach.
Diet Hierarchies Guide Temporal-Spatial Variation in Drosophila suzukii Resource Use

Among insects, female oviposition preferences are critical to understanding the evolutionary dynamics between herbivores and hosts. Previous studies have shown Drosophila resource use has a strong genetic basis, although there is evidence that preferences are adaptable given isolation from ancestral hosts. Given the high degree of adaptability and behavioral plasticity of invasive species, we were interested in the mechanisms affecting host preferences of the invasive fruit fly, Drosophila suzukii, which in recent years has developed a nearly global range infesting small fruit crops. We studied the diet hierarchies of D. suzukii using a combination of laboratory and field assays designed to assess how female oviposition host choice differs given the availability of, and experience with, different fruit and non-fruit hosts. We found that host preferences did not shift over time and flies reared on two differential isolated diets up to F5 behaved and performed similarly regardless of diet lineage. Rather, female host choice appeared guided by a fixed hierarchical system of host preferences. Raspberry was more preferred to mushroom, which was more preferred to goose manure. However, if preferred resources were absent, the use of less-preferred resources was compensatory. We suggest that among niche specialists, such as D. suzukii, these hierarchies may support a bet-hedging strategy, rather than multiple-niche polymorphism, allowing for niche separation during periods of increased competition, while maintaining more diverse, ancestral feeding behaviors when preferred resources are scarce.
Denosumab for the Treatment of Hypercalcemia in a Patient With Parathyroid Carcinoma: A Case Report

Background Refractory hypercalcemia is one of the major complications of parathyroid carcinoma. Case report An 84-year old female patient presented with an acute confusional state due to hypercalcemia. This led to the diagnosis of primary hyperparathyroidism for which she underwent surgery. The initial histological diagnosis was interpreted as atypical parathyroid adenoma; the resection was microscopically incomplete. One year later, the patient presented with elevated calcium levels up to 3.89 mmol/l. Recurrent severe hypercalcemia required multiple hospitalizations. Review of the histology slides revealed that the initially resected lesion was in fact a parathyroid carcinoma. Treatment with the calcimimetic drug cinacalcet was poorly tolerated. Repeated administration of zoledronic acid only had transient effects on calcium levels, and bisphosphonate treatment was ultimately discontinued because of chronic renal failure. The patient then received denosumab (60 or 120 mg) when needed (nine doses over twenty months), the last dose in November 2020, which led to a reduction and control of here calcium levels. Currently, at three years after initial surgery, calcium levels are stable between 2.7-2.8 mmol/l and the patient has not required hospitalization for hypercalcemia for 10 months. Discussion In case of parathyroid carcinoma, en-bloc resection is the first treatment. Denosumab has proven its efficiency in treating hypercalcemia in malignancy. Several case reports studied denosumab in hypercalcemia due to parathyroid carcinoma, and the treatment were efficient to decrease levels of calcium when repeated as needed or monthly. We report another case of refractory hypercalcemia treated with several doses of denosumab in a patient with parathyroid carcinoma.
In silico Analysis of SARS-CoV-2 ORF8-Binding Proteins Reveals the Involvement of ORF8 in Acquired-Immune and Innate-Immune Systems

SARS-CoV-2 is the causative agent of a new type of coronavirus infection, COVID-19, which has rapidly spread worldwide. The overall genome sequence homology between SARS-CoV-2 and SARS-CoV is 79%. However, the homology of the ORF8 protein between these two coronaviruses is low, at ~26%. Previously, it has been suggested that infection by the ORF8-deleted variant of SARS-CoV-2 results in less severe symptoms than in the case of wild-type SARS-CoV-2. Although we found that ORF8 is involved in the proteasome autoimmunity system, the precise role of ORF8 in infection and pathology has not been fully clarified. In this study, we determined a new network of ORF8-interacting proteins by performing in silico analysis of the binding proteins against the previously described 47 ORF8-binding proteins. We used as a dataset 431 human protein candidates from Uniprot that physically interacted with 47 ORF8-binding proteins, as identified using STRING. Homology and phylogenetic profile analyses of the protein dataset were performed on 446 eukaryotic species whose genome sequences were available in KEGG OC. Based on the phylogenetic profile results, clustering analysis was performed using Ward's method. Our phylogenetic profiling showed that the interactors of the ORF8-interacting proteins were clustered into three classes that were conserved across chordates (Class 1: 152 proteins), metazoans (Class 2: 163 proteins), and eukaryotes (Class 3: 114 proteins). Following the KEGG pathway analysis, classification of cellular localization, tissue-specific expression analysis, and a literature study on each class of the phylogenetic profiling cluster tree, we predicted that the following: protein members in Class 1 could contribute to COVID-19 pathogenesis via complement and coagulation cascades and could promote sarcoidosis; the members of Class 1 and 2, together, may contribute to the downregulation of Interferon-β; and Class 3 proteins are associated with endoplasmic reticulum stress and the degradation of human leukocyte antigen.
Two Isoforms of serpent Containing Either One or Two GATA Zinc Fingers Provide Functional Diversity During Drosophila Development

GATA transcription factors play crucial roles in various developmental processes in organisms ranging from flies to humans. In mammals, GATA factors are characterized by the presence of two highly conserved domains, the N-terminal (N-ZnF) and the C-terminal (C-ZnF) zinc fingers. The Drosophila GATA factor Serpent (Srp) is produced in different isoforms that contains either both N-ZnF and C-ZnF (SrpNC) or only the C-ZnF (SrpC). Here, we investigated the functional roles ensured by each of these isoforms during Drosophila development. Using the CRISPR/Cas9 technique, we generated new mutant fly lines deleted for one (ΔsrpNC) or the other (ΔsrpC) encoded isoform, and a third one with a single point mutation in the N-ZnF that alters its interaction with its cofactor, the Drosophila FOG homolog U-shaped (Ush). Analysis of these mutants revealed that the Srp zinc fingers are differentially required for Srp to fulfill its functions. While SrpC is essential for embryo to adult viability, SrpNC, which is the closest conserved isoform to that of vertebrates, is not. However, to ensure its specific functions in larval hematopoiesis and fertility, Srp requires the presence of both N- and C-ZnF (SrpNC) and interaction with its cofactor Ush. Our results also reveal that in vivo the presence of N-ZnF restricts rather than extends the ability of GATA factors to regulate the repertoire of C-ZnF bound target genes.
Maternal Low-Protein Diet Deregulates DNA Repair and DNA Replication Pathways in Female Offspring Mammary Gland Leading to Increased Chemically Induced Rat Carcinogenesis in Adulthood

Studies have shown that maternal malnutrition, especially a low-protein diet (LPD), plays a key role in the developmental mechanisms underlying mammary cancer programming in female offspring. However, the molecular pathways associated with this higher susceptibility are still poorly understood. Thus, this study investigated the adverse effects of gestational and lactational low protein intake on gene expression of key pathways involved in mammary tumor initiation after a single dose of N-methyl-N-nitrosourea (MNU) in female offspring rats. Pregnant Sprague–Dawley rats were fed a normal-protein diet (NPD) (17% protein) or LPD (6% protein) from gestational day 1 to postnatal day (PND) 21. After weaning (PND 21), female offspring (n = 5, each diet) were euthanized for histological analysis or received NPD (n = 56 each diet). At PND 28 or 35, female offspring received a single dose of MNU (25 mg/kg body weight) (n = 28 each diet/timepoint). After 24 h, some females (n = 10 each diet/timepoint) were euthanized for histological, immunohistochemical, and molecular analyses at PDN 29 or 36. The remaining animals (n = 18 each diet/timepoint) were euthanized when tumors reached ≥2 cm or at PND 250. Besides the mammary gland development delay observed in LPD 21 and 28 groups, the gene expression profile demonstrated that maternal LPD deregulated 21 genes related to DNA repair and DNA replication pathways in the mammary gland of LPD 35 group after MNU. We further confirmed an increased γ-H2AX (DNA damage biomarker) and in ER-α immunoreactivity in mammary epithelial cells in the LPD group at PND 36. Furthermore, these early postnatal events were followed by significantly higher mammary carcinogenesis susceptibility in offspring at adulthood. Thus, the results indicate that maternal LPD influenced the programming of chemically induced mammary carcinogenesis in female offspring through increase in DNA damage and deregulation of DNA repair and DNA replication pathways. Also, Cidea upregulation gene in the LPD 35 group may suggest that maternal LPD could deregulate genes possibly leading to increased risk of mammary cancer development and/or poor prognosis. These findings increase the body of evidence of early-transcriptional mammary gland changes influenced by maternal LPD, resulting in differential response to breast tumor initiation and susceptibility and may raise discussions about lifelong prevention of breast cancer risk.
Contextual Modulation of Feedforward Inputs to Primary Visual Cortex

Throughout the brain, parallel processing streams compose the building blocks of complex neural functions. One of the most salient models for studying the functional specialization of parallel visual streams in the primate brain is the lateral geniculate nucleus (LGN) of the dorsal thalamus, through which the parvocellular and magnocellular channels, On-center and Off-center channels, and ipsilateral and contralateral eye channels are maintained and provide the foundation for cortical processing. We examined three aspects of neural processing in these streams: (1) the relationship between extraclassical surround suppression, a widespread visual computation thought to represent a canonical neural computation, and the parallel channels of the LGN; (2) the magnitude of binocular interaction in the parallel streams; and (3) the magnitude of suppression elicited by perceptual competition (binocular rivalry) in each stream. Our results show that surround suppression is almost exclusive to Off channel cells; further, we found evidence for two different components of monocular surround suppression—an early-stage suppression exhibited by all magnocellular cells, and a late-stage suppression exhibited only by Off cells in both the parvocellular and magnocellular pathways. This finding indicates that stream-specific circuits contribute to surround suppression in the primate LGN and suggests a distinct role for suppression in the Off channel to the cortex. We also examined the responses of LGN neurons in alert macaque monkeys to determine whether neurons that supply the cortex with visual information are influenced by stimulation of both eyes. Our results demonstrate that LGN neurons are not influenced by stimulation of the non-dominant eye. This was the case when dichoptic stimuli were presented to classical receptive fields of neurons, extraclassical receptive fields of neurons, and when stimuli were appropriate to produce the perception of binocular rivalry.
Simultaneous Image Reconstruction and Element Decomposition for Iodine Contrast Agent Visualization in Multienergy Element-Resolved Cone Beam CT

Iodine contrast agent is widely used in liver cancer radiotherapy at CT simulation stage to enhance detectability of tumor. However, its application in cone beam CT (CBCT) for image guidance before treatment delivery is still limited because of poor image quality and excessive dose of contrast agent during multiple treatment fractions. We previously developed a multienergy element-resolved (MEER) CBCT framework that included x-ray projection data acquisition on a conventional CBCT platform in a kVp-switching model and a dictionary-based image reconstruction algorithm that simultaneously reconstructed x-ray attenuation images at each kilovoltage peak (kVp), an electron density image, and elemental composition images. In this study, we investigated feasibility using MEER-CBCT for low-concentration iodine contrast agent visualization. We performed simulation and experimental studies using a phantom with inserts containing water and different concentrations of iodine solution and the MEER-CBCT scan with 600 projections in a full gantry rotation, in which the kVp level sequentially changed among 80, 100, and 120 kVps. We included iodine material in the dictionary of the reconstruction algorithm. We analyzed iodine detectability as quantified by contrast-to-noise ratio (CNR) and compared results with those of CBCT images reconstructed by the standard filter back projection (FBP) method with 600 projections. MEER-CBCT achieved similar contrast enhancement as FBP method but significantly higher CNR. At 2.5% iodine solution concentration, FBP method achieved 170 HU enhancement and CNR of 2.0, considered the standard CNR for successful tumor visualization. MEER-CBCT achieved the same CNR but at ~6.3 times lower iodine concentration of 0.4%.
Case Report: Food Protein-Induced Protein Losing Enteropathy (FPIPLE) in Infancy

Food-protein induced protein-losing enteropathy (FPIPLE) is a mixed IgE and non-IgE food allergy in infants along with eosinophilic gastrointestinal (GI) diseases (EGID). It is characterized by poor weight gain, edema, due to hypoproteinemia/hypoalbuminemia by enteral loss of proteins, anemia, eosinophilia, raised fecal α1-antitrypsin (α1AT), and specific-IgE and allergy skin prick test (SPT) positive for offending foods. Here, we describe 4 cases with the same clinical pattern (edema due to hypoproteinemia/hypoalbuminemia from enteral loss of proteins, confirmed by high α1AT in the stools and no other pathological findings explaining the hypoproteinemia including normal kidney and liver function parameters), and propose the term “food-protein induced protein-losing enteropathy” (FPIPLE) to define this clinical entity. We also propose diagnostic criteria and an empirical algorithm of a practical approach to the diagnosis and management for children suspected to have FPIPLE. These infants can be managed successfully with dietary modification. In our 4 cases, initially, an empirical elimination diet was applied, comprising the foods that had benn introduced in the infant's diet during the last month and, an extensively hydrolyzed or elemental formula was given. In a second approach, after evaluation by a pediatric allergist, an allergy test-directed dietary elimination alimentation was implemented, for mother and/or infant. It has yet to be demonstrated whether patients with FPIPLE are a subset of patients with EGID, and whether early intervention modifies the natural course.
Tidal Modulation of Hydrothermal Tremor: Examples From Ischia and Campi Flegrei Volcanoes, Italy

Volcano dynamics results from an interplay between internal and external processes spanning different time scales. Unravelling how such processes interact may provide key insights into the mechanisms that may lead to the destabilization of the volcanoes and eruption, a critical information to forecast hazards. Studies dealing with tidal influence on volcanoes fall within this context, yet the cause-effect relationship between tides and eruptions is still poorly understood. In the present study, we investigate the tidal influence on two nearby volcanoes, Ischia and Campi Flegrei (Italy), characterized by intense hydrothermal activity. We analyze the seismic tremor of hydrothermal origin recorded by four seismic stations between January and June 2020 by using Singular Spectrum Analysis. We detect up to five long term tidal periodicities ranging from ∼5 to ∼29 days. The results indicate that the seismic tremor is modulated by Earth tides at both volcanoes. In addition, differences in phase and amplitude modulation between the response of both hydrothermal systems to tidal forcing reveal specific features related to the tremor source and to properties of the surrounding medium. These phenomena indicate an interplay between solid Earth and the dynamics of these two volcanoes. Similar approaches on hydrothermal systems at volcanoes would contribute to better characterize the hydrothermal circulation and their evolving conditions that may represent a precursor of a new phase of activity.