Structure, function and regulation of the vacuolar (H+)-ATPase

Specific expression profiles of lncRNAs in cis-regulatory responses to gill in Litopenaeus vannamei under high alkalinity

As a pivotal regulatory molecule, long non-coding RNA (lncRNA) can coordinate the network regulation of transcription and post-transcriptional processes. However, little is known about their cis-regulatory contributions in gene expression of crustaceans under alkalinity stress. In this study, the purpose was to explore the potential role of lncRNA in gill of Pacific white shrimp (Litopenaeus vannamei) under different alkalinity stress (C: 50 mg/L and T: 350 mg/L). We found 5034 high confidence lncRNAs in gills. Among them, 82 differentially expressed lncRNA (DELs) in C and T groups may affect gill stress by regulating gene expression in cis- or trans- mode at transcriptional level. The cis-functions DELs were enriched in several pathways, including Glutathione metabolism, Peroxisome and Lysosome. The trans-functions DELs were enriched in Toll-like receptor signaling pathway, Peroxisome and Lysosome. We also obtained 12 DELs-mRNA pairs consisting of 6 DELs and 11 mRNAs, and DELs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner. In addition, we found that two hub genes, ARSB and gba-3, were significantly enriched in Lysosome. In the silencing experiment, XR_003476973.1 and MSTRG.20723.1 were found to regulate the Lysosomal pathway under alkalinity stress through cis-acting. Under alkalinity stress, physiological parameters related to homeostasis regulation, immune response and lysosomal hydrolysis changed significantly. These results provide new insights into the mechanism of lncRNA in shrimp gills under alkaline stress, and also offer valuable perspectives into the implications of gill regulation for crustaceans in saline-alkaline water.

Drosophila aux orchestrates the phosphorylation-dependent assembly of the lysosomal V-ATPase in glia and contributes to SNCA/α-synuclein degradation

Glia contribute to the neuropathology of Parkinson disease (PD), but how they react opposingly to be beneficial or detrimental under pathological conditions, like promoting or eliminating SNCA/α-syn (synuclein alpha) inclusions, remains elusive. Here we present evidence that aux (auxilin), the Drosophila homolog of the PD risk factor GAK (cyclin G associated kinase), regulates the lysosomal degradation of SNCA/α-syn in glia. Lack of glial GAK/aux increases the lysosome number and size, regulates lysosomal acidification and hydrolase activity, and ultimately blocks the degradation of substrates including SNCA/α-syn. Whereas SNCA/α-syn accumulates prominently in lysosomes devoid of glial aux, levels of injected SNCA/α-syn preformed fibrils are further enhanced in the absence of microglial GAK. Mechanistically, aux mediates phosphorylation at the serine 543 of Vha44, the V1 C subunit of the vacuolar-type H+-translocating ATPase (V-ATPase), and regulates its assembly to control proper acidification of the lysosomal milieu. Expression of Vha44, but not the Vha44 variant lacking S543 phosphorylation, restores lysosome acidity, locomotor deficits, and DA neurodegeneration upon glial aux depletion, linking this pathway to PD. Our findings identify a phosphorylation-dependent switch controlling V-ATPase assembly for lysosomal SNCA/α-syn degradation in glia. Targeting the clearance of glial SNCA/α-syn inclusions via this lysosomal pathway could potentially be a therapeutic approach to ameliorate the disease progression in PD.Abbreviation: aux: auxilin; GAK: cyclin G associated kinase; LTG: LysoTracker Green; LTR: LysoTracker Red; MR: Magic Red; PD: Parkinson disease; SNCA/a-syn: synuclein alpha; V-ATPase: vacuolar-type H+-translocating ATPase.

Pitolisant alleviates brain network dysfunction and cognitive deficits in a mouse model of Alzheimer's disease

Histamine H3 receptor (H3R) antagonists regulate histamine release that modulates neuronal activity and cognitive function. Although H3R is elevated in Alzheimer's disease (AD) patients, whether H3R antagonists can rescue AD-associated neural impairments and cognitive deficits remains unknown. Pitolisant is a clinically approved H3R antagonist/inverse agonist that treats narcolepsy. Here, we find that pitolisant reverses AD-like pathophysiology and cognitive impairments in an AD mouse model. Behavioral assays and in vivo wide-field Ca2+ imaging revealed that recognition memory, learning flexibility, and slow-wave impairment were all improved following the 15-day pitolisant treatment. Improved recognition memory was tightly correlated with slow-wave coherence, suggesting slow waves serve as a biomarker for treatment response and for AD drug screening. Furthermore, pitolisant reduced amyloid-β deposition and dystrophic neurites surrounding plaques, and enhanced neuronal lysosomal activity, inhibiting which blocked cognitive and slow-wave restoration. Our findings identify pitolisant as a potential therapeutic agent for AD treatments.

Alkaline Adjuvant Regulates Proteolytic Activity of Macrophages for Antigen Cross-Presentation and Potentiates Radioimmunotherapy

Failures of radiotherapy (RT) in adaptive antitumor immunomodulation often associate with recruited tissue-repairing macrophages. Although training these macrophages to phagocytose post-RT cancer cells reverses their protumoral performance, engulfed tumor antigens are severely underrated. In fact, regulating the processing and presentation of tumor antigens, a key determinant of tumor immunogenicity, can fundamentally affect adaptive immune responses. Here it is reported that a simple Alum-like adjuvant (MgAl-based hydrotalcite, bLDH) improves radioimmunotherapy via inducing antigen cross-presentation by macrophages, independent of phenotypes. It is identified that cytidine monophosphate guanosine oligodeoxynucleotide engenders macrophages to phagocytose irradiated cancer cells. However, as semiprofessional antigen-presenting cells, macrophages possess powerful proteolytic function that is detrimental to antigen presentation. The administration of alkaline bLDH intriguingly relieves the activity of phagolysosomal proteases with acidic pH optima by preventing phagosomal acidification resulting from the vacuolar-type ATPase proton pump. The adjuvant-modulated phagolysosomes thus limit antigen degradation and enhance tumor antigen cross-presentation over tenfold. To examine from an in vivo breast tumor model, trained macrophages successfully cross-prime antigen-specific CD8+ T cells and curb RT-associated metastasis. The findings propose to pay close attention to the effect of adjuvants on precision immunotherapy and highlight the positive contribution of cross-presenting macrophages in radioimmunotherapy.

Newly developed mRNA vaccines induce immune responses in Litopenaeus vannamei shrimps during primary vaccination

White spot syndrome virus (WSSV) causes highly destructive infection in crustacean aquaculture, often resulting in 100% mortality within a week. However, there is lack of studies addressing the safety issues of WSSV vaccines in shrimps. In this study, WSSV VP28 mRNA vaccines were developed using codon deoptimization approach. These vaccines were administered to Litopenaeus vannamei shrimps at various dosages to access their safety and the shrimps' immune responses using quantification PCR (qPCR). The findings of this study indicate that the expression level of codon deoptimized VP28 mRNA vaccines are lower compared to the wild type VP28 vaccines, as observed through a comparison of bioinformatic predictions and experimental results. Additionally, the total haemocyte count (THC) in shrimps injected with codon deoptimized VP28 vaccine was higher than those injected with wild type VP28 vaccines. Furthermore, the expression of immune-related genes differed between codon deoptimized and wild type VP28 vaccines. In summary, the results suggest that 0.01 μg codon deoptimized VP28-D1 mRNA vaccine is the most promising WSSV mRNA vaccine, displaying low pathogenicity and expression in shrimps. To the best of our knowledge, this research represents the first attempt to attenuate WSSV using codon deoptimization method and development of a potential mRNA vaccine for shrimp purpose. The study addresses an important gap in shrimp vaccine research, offering potential solutions for WSSV control in shrimps.

Nematodes exposed to furfural acetone exhibit a species-specific vacuolar H+-ATPase response

Furfural acetone (FAc) is widely used as an additive by the food industry, as well as an intermediate in several fine chemical industries. Its nematicidal activity against the free-living model organism Caenorhabditis elegans and the parasitic nematode Meloidogyne incognita are well known, but its molecular mechanism of action remains unclear. To deep this subject, we performed 48-h lethal tests on eight nematode species, encompassing free-living, plant-parasitic, and animal-parasitic nematodes. Our results revealed that FAc possesses broad-spectrum nematicidal activity, with potent effects against parasitic nematodes such as Strongyloides stercoralis and M. incognita. In contrast, it exhibited weak activity against the free-living nematode C. elegans, suggesting its potential as a selective nematicide. Our investigation unveiled that FAc binds to the vacuolar H+-ATPase subunits VHA-12 and VHA-13, accelerating intestinal cell necrosis and leading to the death of C. elegans. It is the first discovery that VHA-12 and VHA-13 can serve as target proteins for triggering nematode cell necrosis. The interaction results indicated that FAc targets proteins VHA-12 and VHA-13 of different nematodes and confers broad-spectrum nematicidal activity. And the Spearman analysis results illustrated that the differential nematicidal activity of FAc against various nematodes is attributed to variations in the sequence and structure of the receptor proteins VHA-12 and VHA-13 among different nematode species. Our results illuminate the molecular mechanism underlying the differential toxicity of FAc to different nematodes, and provide valuable data for the comprehensive risk assessment of FAc release into the environment.

Thermophysical Insights into the Anti-Inflammatory Potential of Magnetic Fields

Background: Inflammation is caused by an excess of Sodium ions inside the cell. This generates a variation in the cell's membrane electric potential, becoming a steady state from a thermodynamic viewpoint. Methods: This paper introduces a thermodynamic approach to inflammation based on the fundamental role of the electric potential of the cell membrane, introducing an analysis of the effect of heat transfer related to the inflammation condition. Results: The direct proportionality between the reduction in temperature and the increase of Na+ outflow may ameliorate the inflammation cascade. Conclusions: Based on these ion fluxes, we suggest the consideration of a 'companion' electromagnetic therapeutic wave concept in support of the present anti-inflammatory treatment.

High-Affinity Plasma Membrane Ca2+ Channel Cch1 Modulates Adaptation to Sodium Dodecyl Sulfate-Triggered Rise in Cytosolic Ca2+ Concentration in Ogataea parapolymorpha

The cytosolic calcium concentration ([Ca2+]cyt) in yeast cells is maintained at a low level via the action of different transporters sequestrating these cations in the vacuole. Among them, the vacuolar Ca2+ ATPase Pmc1 crucially contributes to this process. Its inactivation in Ogataea yeasts was shown to cause sodium dodecyl sulfate (SDS) hypersensitivity that can be alleviated by the inactivation of the plasma membrane high-affinity Ca2+ channel Cch1. Here, we show that SDS at low concentrations induces a rapid influx of external Ca2+ into cells, while the plasma membrane remains impermeable for propidium iodide. The inactivation of Pmc1 disturbs efficient adaptation to this activity of SDS. The inactivation of Cch1 partially restores the ability of pmc1 mutant cells to cope with an increased [Ca2+]cyt that correlates with the suppression of SDS hypersensitivity. At the same time, Cch1 is unlikely to be directly involved in SDS-induced Ca2+ influx, since its inactivation does not decrease the amplitude of the rapid [Ca2+]cyt elevation in the pmc1-Δ mutant. The obtained data suggest that the effects of CCH1 inactivation on SDS sensitivity and coping with increased [Ca2+]cyt are related to an additional Cch1 function beyond its direct involvement in Ca2+ transport.

Multiple cell-death patterns predict the prognosis and drug sensitivity of melanoma patients

Background

Melanoma, a malignant tumor of the skin, presents challenges in its treatment process involving modalities such as surgery, chemotherapy, and targeted therapy. However, there is a need for an ideal model to assess prognosis and drug sensitivity. Programmed cell death (PCD) modes play a crucial role in tumor progression and has the potential to serve as prognostic and drug sensitivity indicators for melanoma.

Methods

We analyzed 13 PCD modes including apoptosis, necroptosis, ferroptosis, pyroptosis, netotic cell death, entotic cell death, lysosome-dependent cell death, parthanatos, autophagy-dependent cell death, oxeiptosis, disulfidptosis, and alkaliptosis. These modes were used to construct a model that incorporated genes related to these 13 PCD modes to establish a cell death index (CDI) to conduct prognosis analysis. Transcriptomic, genomic, and clinical data were collected from cohorts including TCGA-SKCM, GSE19234, and GSE65904 to validate this model.

Results

A CDI consisting of ten gene signatures was established using machine learning algorithms and divided into two groups based on CDI values. The high CDI group exhibited relatively lower numbers of immune-infiltrating cells and showed resistance to commonly used drugs such as docetaxel and axitinib. Our validation results demonstrated good discrimination in PCA analysis between CDI groups, and melanoma patients with higher CDI values had worse postoperative prognoses (all p < 0.01).

Conclusion

The CDI model, incorporating multiple PCD modes, accurately predicts the clinical prognosis and drug sensitivity of melanoma patients.

Membrane phospholipids activate the inflammatory response in macrophages by various mechanisms

Exosomes, which are small membrane-encapsulated particles derived from all cell types, are emerging as important mechanisms for intercellular communication. In addition, exosomes are currently envisioned as potential carriers for the delivery of drugs to target tissues. The natural population of exosomes is very variable due to the limited amount of cargo components present in these small vesicles. Consequently, common components of exosomes may play a role in their function. We have proposed that membrane phospholipids could be a common denominator in the effect of exosomes on cellular functions. In this regard, we have previously shown that liposomes made of phosphatidylcholine (PC) or phosphatidylserine (PS) induced a robust alteration of macrophage (Mϕ) gene expression. We herewith report that these two phospholipids modulate gene expression in Mϕs by different mechanisms. PS alters cellular responses by the interaction with surface receptors, particularly CD36. In contrast, PC is captured by a receptor-independent process and likely triggers an activity within endocytic vesicles. Despite this difference in the capture mechanisms, both lipids mounted similar gene expression responses. This investigation suggests that multiple mechanisms mediated by membrane phospholipids could be participating in the alteration of cellular functions by exosomes.

Comparative spatial proteomics of Plasmodium-infected erythrocytes

Plasmodium parasites contribute to one of the highest global infectious disease burdens. To achieve this success, the parasite has evolved a range of specialized subcellular compartments to extensively remodel the host cell for its survival. The information to fully understand these compartments is likely hidden in the so far poorly characterized Plasmodium species spatial proteome. To address this question, we determined the steady-state subcellular location of more than 12,000 parasite proteins across five different species by extensive subcellular fractionation of erythrocytes infected by Plasmodium falciparum, Plasmodium knowlesi, Plasmodium yoelii, Plasmodium berghei, and Plasmodium chabaudi. This comparison of the pan-species spatial proteomes and their expression patterns indicates increasing species-specific proteins associated with the more external compartments, supporting host adaptations and post-transcriptional regulation. The spatial proteome offers comprehensive insight into the different human, simian, and rodent Plasmodium species, establishing a powerful resource for understanding species-specific host adaptation processes in the parasite.

VPS8D, a CORVET subunit, is required to maintain the contractile vacuole complex in Tetrahymena thermophila

Contractile vacuole complexes (CVCs) are complex osmoregulatory organelles, with vesicular (bladder) and tubular (spongiome) subcompartments. The mechanisms that underlie their formation and maintenance within the eukaryotic endomembrane network are poorly understood. In the Ciliate Tetrahymena thermophila, six differentiated CORVETs (class C core vacuole/endosome tethering complexes), with Vps8 subunits designated A-F, are likely to direct endosomal trafficking. Vps8Dp localizes to both bladder and spongiome. We show by inducible knockdown that VPS8D is essential to CVC organization and function. VPS8D knockdown increased susceptibility to osmotic shock, tolerated in the wildtype but triggering irreversible lethal swelling in the mutant. The knockdown rapidly triggered contraction of the spongiome and lengthened the period of the bladder contractile cycle. More prolonged knockdown resulted in disassembly of both the spongiome and bladder, and dispersal of proteins associated with those compartments. In stressed cells where the normally singular bladder is replaced by numerous vesicles bearing bladder markers, Vps8Dp concentrated conspicuously at long-lived inter-vesicle contact sites, consistent with tethering activity. Similarly, Vps8Dp in cell-free preparations accumulated at junctions formed after vacuoles came into close contact. Also consistent with roles for Vps8Dp in tethering and/or fusion were the emergence in knockdown cells of multiple vacuole-related structures, replacing the single bladder.

Yeast Deletomics to Uncover Gadolinium Toxicity Targets and Resistance Mechanisms

Among the rare earth elements (REEs), a crucial group of metals for high-technologies. Gadolinium (Gd) is the only REE intentionally injected to human patients. The use of Gd-based contrasting agents for magnetic resonance imaging (MRI) is the primary route for Gd direct exposure and accumulation in humans. Consequently, aquatic environments are increasingly exposed to Gd due to its excretion through the urinary tract of patients following an MRI examination. The increasing number of reports mentioning Gd toxicity, notably originating from medical applications of Gd, necessitates an improved risk-benefit assessment of Gd utilizations. To go beyond toxicological studies, unravelling the mechanistic impact of Gd on humans and the ecosystem requires the use of genome-wide approaches. We used functional deletomics, a robust method relying on the screening of a knock-out mutant library of Saccharomyces cerevisiae exposed to toxic concentrations of Gd. The analysis of Gd-resistant and -sensitive mutants highlighted the cell wall, endosomes and the vacuolar compartment as cellular hotspots involved in the Gd response. Furthermore, we identified endocytosis and vesicular trafficking pathways (ESCRT) as well as sphingolipids homeostasis as playing pivotal roles mediating Gd toxicity. Finally, tens of yeast genes with human orthologs linked to renal dysfunction were identified as Gd-responsive. Therefore, the molecular and cellular pathways involved in Gd toxicity and detoxification uncovered in this study underline the pleotropic consequences of the increasing exposure to this strategic metal.

α-Hemolysin promotes uropathogenic E. coli persistence in Bladder epithelial cells Via abrogating bacteria-harboring lysosome acidification

There is a growing consensus that a significant proportion of recurrent urinary tract infections are linked to the persistence of uropathogens within the urinary tract and their re-emergence upon the conclusion of antibiotic treatment. Studies in mice and human have revealed that uropathogenic Escherichia coli (UPEC) can persist in bladder epithelial cells (BECs) even after the apparent resolution of the infection. Here, we found that, following the entry of UPEC into RAB27b+ fusiform vesicles in BECs, some bacteria escaped into the cytoplasmic compartment via a mechanism involving hemolysin A (HlyA). However, these UPEC were immediately recaptured within LC3A/B+ autophagosomes that matured into LAMP1+ autolysosomes. Thereafter, HlyA+ UPEC-containing lysosomes failed to acidify, which is an essential step for bacterial elimination. This lack of acidification was related to the inability of bacteria-harboring compartments to recruit V-ATPase proton pumps, which was attributed to the defragmentation of cytosolic microtubules by HlyA. The persistence of UPEC within LAMP1+ compartments in BECs appears to be directly linked to HlyA. Thus, through intravesicular instillation of microtubule stabilizer, this host defense response can be co-opted to reduce intracellular bacterial burden following UTIs in the bladder potentially preventing recurrence.

The endo-lysosomal system in Parkinson's disease: expanding the horizon

Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, and its prevalence is increasing with age. A wealth of genetic evidence indicates that the endo-lysosomal system is a major pathway driving PD pathogenesis with a growing number of genes encoding endo-lysosomal proteins identified as risk factors for PD, making it a promising target for therapeutic intervention. However, detailed knowledge and understanding of the molecular mechanisms linking these genes to the disease are available for only a handful of them (e.g. LRRK2, GBA1, VPS35). Taking on the challenge of studying poorly characterized genes and proteins can be daunting, due to the limited availability of tools and knowledge from previous literature. This review aims at providing a valuable source of molecular and cellular insights into the biology of lesser-studied PD-linked endo-lysosomal genes, to help and encourage researchers in filling the knowledge gap around these less popular genetic players. Specific endo-lysosomal pathways discussed range from endocytosis, sorting, and vesicular trafficking to the regulation of membrane lipids of these membrane-bound organelles and the specific enzymatic activities they contain. We also provide perspectives on future challenges that the community needs to tackle and propose approaches to move forward in our understanding of these poorly studied endo-lysosomal genes. This will help harness their potential in designing innovative and efficient treatments to ultimately re-establish neuronal homeostasis in PD but also other diseases involving endo-lysosomal dysfunction.

Clathrin-dependent endocytosis plays a critical role in larval and pupal development, and female oocyte production in the red flour beetle (Tribolium castaneum)

BACKGROUND

Clathrin-dependent endocytosis is a vesicular transport process by which cells take macromolecules from the extracellular space to the intracellular space. It plays important roles in various cellular functions, but its biological significance in insect development and reproduction has not been well studied.

RESULTS

We characterized and functionally analyzed four major clathrin-dependent endocytic pathway genes (TcChc, TcAP50, TcVhaSFD, TcRab7) in Tribolium castaneum. RNA interference (RNAi) by injecting double-stranded RNA (dsRNA) targeting each gene at three doses (50, 100, or 200 ng per insect) in 20-day-old larvae led to 100% larval mortality. When the expressions of TcChc, TcVhaSFD, and TcRab7 were suppressed by injecting their respective dsRNAs at each dose in 1-day-old pupae, the adults that emerged from the dsRNA-injected pupae were deformed, with the absence of wing development. The deformed adults died within 2 days after eclosion. When the expression of TcAP50 was suppressed by injecting its dsRNA into 1-day-old pupae, although no apparent deformed adults were observed, all the adults died within 35 days after eclosion. In addition, when the expressions of TcChc and TcVhaSFD were suppressed by injecting their respective dsRNAs at a reduced dose (10 ng per insect) in 5-day-old pupae, the ovarian development and oocyte production in the resultant females were completely inhibited.

CONCLUSION

Our results indicate that clathrin-dependent endocytosis is essential for insect development and reproduction. The results from this study can help researchers identify potential molecular targets for developing novel strategies for insect pest management. © 2023 Society of Chemical Industry.

Osteoclast rich osteopetrosis due to defects in the TCIRG1 gene

Discovery that mutations in TCIRG1 (also known as Atp6i) gene are responsible for most instances of autosomal recessive osteopetrosis (ARO) heralded a new era for comprehension and treatment of this phenotypically heterogeneous rare bone disease. TCIRG1 encodes the a3 subunit, an essential isoform of the vacuolar ATPase proton pump involved in acidification of the osteoclast resorption lacuna and in secretory lysosome trafficking. TCIRG1 defects lead to inefficient bone resorption by nonfunctional osteoclasts seen in abundance on bone marrow biopsy, delineating this ARO as 'osteoclast-rich'. Presentation is usually in early childhood and features of extramedullary haematopoiesis (hepatosplenomegaly, anaemia, thrombocytopenia) due to bone marrow fibrosis, and cranial nerve impingement (blindness in particular). Impaired dietary calcium uptake due to high pH causes the co-occurrence of rickets, described as "osteopetrorickets". Osteoclast dysfunction leads to early death if untreated, and allogeneic haematopoietic stem cell transplantation is currently the treatment of choice. Studies of patients as well as of mouse models carrying spontaneous (the oc/oc mouse) or targeted disruption of Atp6i (TCIRG1) gene have been instrumental providing insight into disease pathogenesis and development of novel cellular therapies that exploit gene correction.

Subunit C of V-ATPase-VmaC Is Required for Hyphal Growth and Conidiation in A. fumigatus by Affecting Vacuolar Calcium Homeostasis and Cell Wall Integration

Aspergillus fumigatus is a widespread airborne fungal pathogen in humans. However, the functional genes in A. fumigatus that may contribute to its pathogenesis have not yet been fully identified. Vacuolar H+-ATPase is universal in eukaryotic organisms but exhibits specific roles in various species. Here, we identified VmaC as a putative subunit of vacuolar H+-ATPase in A. fumigatus that is widely conserved through evolution. The C-terminal hydrophobic domain of VmaC plays a critical role in its vacuolar localization and growth and conidiation. Deletion or turn-off of VmaC encoding gene-AfvmaC expression is not lethal but leads to a very sick and tiny colony phenotype, which is different from that of yeast with conditional ScvmaC defects. Furthermore, we found that AfvmaC not only participates in maintaining calcium homeostasis and vacuolar acidity but is also involved in cell wall integration pathway regulation, highlighting the importance of the vacuole as a storage organelle associated with many aspects of cellular homeostasis. This study indicates that fungal VmaC is relatively conserved. When compared to that in model yeasts, VmaC in A. fumigatus is required for hyphal growth and conidiation, suggesting that specific motifs in VmaC might be functioned in Aspergilli.

Leveraging diverse cell-death patterns to predict the prognosis and drug sensitivity of triple-negative breast cancer patients after surgery

BACKGROUND

Postoperative progression and chemotherapy resistance is the major cause of treatment failure in patients with triple-negative breast cancer (TNBC). Currently, there is a lack of an ideal predictive model for the progression and drug sensitivity of postoperative TNBC patients. Diverse programmed cell death (PCD) patterns play an important role in tumor progression, which has the potential to be a prognostic and drug sensitivity indicator for TNBC after surgery.

MATERIALS AND METHODS

Twelve PCD patterns (apoptosis, necroptosis, pyroptosis, ferroptosis, cuproptosis, entotic cell death, netotic cell death, parthanatos, lysosome-dependent cell death, autophagy-dependent cell death, alkaliptosis, and oxeiptosis) were analyzed for model construction. Bulk transcriptome, single-cell transcriptome, genomics, and clinical information were collected from TCGA-BRCA, METABRIC, GSE58812, GSE21653, GSE176078, GSE75688, and KM-plotter cohorts to validate the model.

RESULTS

The machine learning algorithm established a cell death index (CDI) with a 12-gene signature. Validated in five independent datasets, TNBC patients with high CDI had a worse prognosis after surgery. Two molecular subtypes of TNBC with distinct vital biological processes were identified by an unsupervised clustering model. A nomogram with high predictive performance was constructed by incorporating CDI with clinical features. Furthermore, CDI was associated with immune checkpoint genes and key tumor microenvironment components by integrated analysis of bulk and single-cell transcriptome. TNBC patients with high CDI are resistant to standard adjuvant chemotherapy regimens (docetaxel, oxaliplatin, etc.); however, they might be sensitive to palbociclib (an FDA-approved drug for luminal breast cancer).

CONCLUSION

Generally, we established a novel CDI model by comprehensively analyzing diverse cell death patterns, which can accurately predict clinical prognosis and drug sensitivity of TNBC after surgery. A user-friendly website was created to facilitate the application of this prediction model (https://tnbc.shinyapps.io/CDI_Model/).

The vacuole shapes the nucleus and the ribosomal DNA loop during mitotic delays

Chromosome structuring and condensation is one of the main features of mitosis. Here, Matos-Perdomo et al show how the nuclear envelope reshapes around the vacuole to give rise to the outstanding ribosomal DNA loop in budding yeast.

The ribosomal DNA (rDNA) array of Saccharomyces cerevisiae has served as a model to address chromosome organization. In cells arrested before anaphase (mid-M), the rDNA acquires a highly structured chromosomal organization referred to as the rDNA loop, whose length can double the cell diameter. Previous works established that complexes such as condensin and cohesin are essential to attain this structure. Here, we report that the rDNA loop adopts distinct presentations that arise as spatial adaptations to changes in the nuclear morphology triggered during mid-M arrests. Interestingly, the formation of the rDNA loop results in the appearance of a space under the loop (SUL) which is devoid of nuclear components yet colocalizes with the vacuole. We show that the rDNA-associated nuclear envelope (NE) often reshapes into a ladle to accommodate the vacuole in the SUL, with the nucleus becoming bilobed and doughnut-shaped. Finally, we demonstrate that the formation of the rDNA loop and the SUL require TORC1, membrane synthesis and functional vacuoles, yet is independent of nucleus–vacuole junctions and rDNA-NE tethering.

Adipocytes control food intake and weight regain via Vacuolar-type H+ ATPase

Energy metabolism becomes dysregulated in individuals with obesity and many of these changes persist after weight loss and likely play a role in weight regain. In these studies, we use a mouse model of diet-induced obesity and weight loss to study the transcriptional memory of obesity. We found that the 'metabolic memory' of obesity is predominantly localized in adipocytes. Utilizing a C. elegans-based food intake assay, we identify 'metabolic memory' genes that play a role in food intake regulation. We show that expression of ATP6v0a1, a subunit of V-ATPase, is significantly induced in both obese mouse and human adipocytes that persists after weight loss. C. elegans mutants deficient in Atp6v0A1/unc32 eat less than WT controls. Adipocyte-specific Atp6v0a1 knockout mice have reduced food intake and gain less weight in response to HFD. Pharmacological disruption of V-ATPase assembly leads to decreased food intake and less weight re-gain. In summary, using a series of genetic tools from invertebrates to vertebrates, we identify ATP6v0a1 as a regulator of peripheral metabolic memory, providing a potential target for regulation of food intake, weight loss maintenance and the treatment of obesity.

Targeting Membrane Trafficking as a Strategy for Cancer Treatment

Membrane trafficking is emerging as an attractive therapeutic strategy for cancer. Recent reports have found a connection between Wnt signaling, receptor-mediated endocytosis, V-ATPase, lysosomal activity, and macropinocytosis through the canonical Wnt pathway. In macropinocytic cells, a massive internalization of the plasma membrane can lead to the loss of cell-surface cadherins, integrins, and other antigens that mediate cell–cell adhesion, favoring an invasive phenotype. V-ATPase is a key regulator in maintaining proper membrane trafficking, homeostasis, and the earliest developmental decisions in the Xenopus vertebrate development model system. Here, we review how the interference of membrane trafficking with membrane trafficking inhibitors might be clinically relevant in humans.

Overexpression of V-ATPase B2 attenuates lung injury/fibrosis by stabilizing lysosomal membrane permeabilization and increasing collagen degradation

Excessive oxidative stress causes lysosomal membrane permeabilization (LMP), which leads to cell death. Vacuolar ATPase (V-ATPase) is the enzyme responsible for pumping H⁺ into the cytosol and thus maintaining intracellular pH. Previously, we reported that V-ATPase B2 subunit expression is upregulated in the TiO₂-exposed lung epithelium. We investigated the role of the lysosomal V-ATPase B2 subunit in oxidative stress-induced alveolar epithelial cell death and in an experimental lung injury/fibrosis model. Overexpression of V-ATPase B2 increased lysosomal pH and lysosomal activities in the cells. In the presence of H₂O₂, overexpression of V-ATPase B2 increased survival, and silencing of V-ATPase B2 dramatically increased cell death. Overexpression of V-ATPase B2 diminished H₂O₂-triggered LMP, as evidenced by a reduction in acridine orange staining and leakage of cathepsin D from the lysosome to the cytoplasm. In addition, V-ATPase B2-overexpressing macrophages exhibited significantly enhanced uptake and degradation of collagen. V-ATPase B2-overexpressing transgenic mice showed significant inhibition of the bleomycin-induced increases in lung inflammation and fibrosis. We conclude that V-ATPase B2 is critical for maintaining lysosomal activities against excessive oxidative stress by stabilizing LMP. Our findings reveal a previously unknown role of this V-ATPase subunit in a lung injury and fibrosis model.

An enzyme involved in maintaining the correct pH inside the lysosome, an organelle involved in disposal of cellular waste, also plays a critical role in preventing lung injury. Using human lung cells and mouse models of lung fibrosis, a team led by Sung Woo Park from Soonchunhyang University Bucheon Hospital, South Korea, showed that a overexpression of subunit of the vacuolar ATPase enzyme B2, which pumps protons into cellular compartments to create more acidic environments, helps to boost lysosomal activities that lead to prevent oxidative stress-induced cell death and alleviate experimental lung injury/fibrosis. In addition, V-ATPase B2 overexpressed macrophages increased collagen uptake and degradation activities. The findings point to the vacuolar ATPase, and its B2 subunit in particular, as a promising drug target for future treatments of pulmonary fibrosis.

Coordinated glucose-induced Ca2+ and pH responses in yeast Saccharomyces cerevisiae

Ca²⁺ and pH homeostasis are closely intertwined and this interrelationship is crucial in the cells' ability to adapt to varying environmental conditions. To further understand this Ca²⁺-pH link, cytosolic Ca²⁺ was monitored using the aequorin-based bioluminescent assay in parallel with fluorescence reporter-based assays to monitor plasma membrane potentials and intracellular (cytosolic and vacuolar) pH in yeast Saccharomyces cerevisiae. At external pH 5, starved yeast cells displayed depolarized membrane potentials and responded to glucose re-addition with small Ca²⁺ transients accompanied by cytosolic alkalinization and profound vacuolar acidification. In contrast, starved cells at external pH 7 were hyperpolarized and glucose re-addition induced large Ca²⁺ transients and vacuolar alkalinization. In external Ca²⁺-free medium, glucose-induced pH responses were not affected but Ca²⁺ transients were abolished, indicating that the intracellular [Ca²⁺] increase was not prerequisite for activation of the two primary proton pumps, being Pma1 at the plasma membrane and the vacuolar and Golgi localized V-ATPases. A reduction in Pma1 expression resulted in membrane depolarization and reduced Ca²⁺ transients, indicating that the membrane hyperpolarization generated by Pma1 activation governed the Ca²⁺ influx that is associated with glucose-induced Ca²⁺ transients. Loss of V-ATPase activity through concanamycin A inhibition did not alter glucose-induced cytosolic pH responses but affected vacuolar pH changes and Ca²⁺ transients, indicating that the V-ATPase established vacuolar proton gradient is substantial for organelle H⁺/Ca²⁺ exchange. Finally, a systematic analysis of yeast deletion strains allowed us to reveal an essential role for both the vacuolar H⁺/Ca²⁺ exchanger Vcx1 and the Golgi exchanger Gdt1 in the dissipation of intracellular Ca²⁺.

A capsule-associated gene of Cryptococcus neoformans, CAP64, is involved in pH homeostasis

The CAP64 gene is known to be involved in capsule formation in the basidiomycete yeast Cryptococcus neoformans. A null mutant of CAP64, Δcap64, lacks a capsule around the cell wall and its acidic organelles are not stained with quinacrine. In order to clarify whether the Cap64 protein indeed maintains vacuole or vesicle acidification, so that the vesicle containing the capsule polysaccharide or DBB substrate are transported to the cell membrane side, the relationship between CAP64 and intracellular transport genes and between CAP64 and enzyme-secretion activity were analysed. Laccase activity was higher in the Δcap64 strain than in the wild-type strain, and the transcriptional levels of SAV1 and VPH1 were also higher in the Δcap64 strain than in the wild-type strain. The intracellular localization of the Cap64 protein was analysed by overexpressing an mCherry-tagged Cap64 and observing its fluorescence. The Cap64 protein was accumulated within cells in a patch-like manner. The quinacrine-stained cells were observed to analyse the acidified cell compartments; quinacrine was found to be accumulated in a patch-like manner, with the patches overlapping the fluorescence of CAP64-mCherry fusion protein. Quinacrine was thus accumulated in a patch-like fashion in the cells, and the mCherry-tagged Cap64 protein position was consistent with the position of quinacrine accumulation in cells. These results suggest that CAP64 might be involved in intracellular acidification and vesicle secretion via exocytosis.

Intracellular pH regulation and the acid delusion

The hydrogen ion concentration ([H+]) in intracellular cytoplasmic fluid (ICF) must be maintained in a narrow range in all species for normal protein functions. Thus, mechanisms regulating ICF are of fundamental biological importance. Studies on the regulation of ICF [H+] have been hampered by use of pH notation, failure to consider the roles played by differences in the concentration of strong ions (strong ion difference, SID), the conservation of mass, the principle of electrical neutrality, and that [H+] and bicarbonate ions [HCO3-] are dependent variables. This argument is based on the late Peter Stewart's physical-chemical analysis of [H+] regulation reported in this journal nearly forty years ago (Stewart. 1983. Can. J. Physiol. Pharmacol. 61: 1444-1461. Doi:10.1139/y83-207). We start by outlining the principles of Stewart's analysis and then provide a general understanding of its significance for regulation of ICF [H+]. The system may initially appear complex, but it becomes evident that changes in SID dominate regulation of [H+]. The primary strong ions are Na+, K+, and Cl-, and a few organic strong anions. The second independent variable, partial pressure of carbon dioxide (PCO2), can easily be assessed. The third independent variable, the activity of intracellular weak acids ([Atot]), is much more complex but largely plays a modifying role. Attention to these principles will potentially provide new insights into ICF pH regulation.

Nanoalgosomes: Introducing extracellular vesicles produced by microalgae

Cellular, inter-organismal and cross kingdom communication via extracellular vesicles (EVs) is intensively studied in basic science with high expectation for a large variety of bio-technological applications. EVs intrinsically possess many attributes of a drug delivery vehicle. Beyond the implications for basic cell biology, academic and industrial interests in EVs have increased in the last few years. Microalgae constitute sustainable and renewable sources of bioactive compounds with a range of sectoral applications, including the formulation of health supplements, cosmetic products and food ingredients. Here we describe a newly discovered subtype of EVs derived from microalgae, which we named nanoalgosomes. We isolated these extracellular nano-objects from cultures of microalgal strains, including the marine photosynthetic chlorophyte Tetraselmis chuii, using differential ultracentrifugation or tangential flow fractionation and focusing on the nanosized small EVs (sEVs). We explore different biochemical and physical properties and we show that nanoalgosomes are efficiently taken up by mammalian cell lines, confirming the cross kingdom communication potential of EVs. This is the first detailed description of such membranous nanovesicles from microalgae. With respect to EVs isolated from other organisms, nanoalgosomes present several advantages in that microalgae are a renewable and sustainable natural source, which could easily be scalable in terms of nanoalgosome production.

Inhibiting ATP6V0D2 Aggravates Liver Ischemia-Reperfusion Injury by Promoting NLRP3 Activation via Impairing Autophagic Flux Independent of Notch1/Hes1

At present, liver ischemia-reperfusion (IR) injury is still a great challenge for clinical liver partial resection and liver transplantation. The innate immunity regulated by liver macrophages orchestrates the cascade of IR inflammation and acts as a bridge. As a specific macrophage subunit of vacuolar ATPase, ATP6V0D2 (V-ATPase D2 subunit) has been shown to promote the formation of autophagolysosome in vitro. Our research fills a gap which has existed in the study of inflammatory stress about the V-ATPase subunit ATP6V0D2 in liver macrophages. We first found that the expression of specific ATP6V0D2 in liver macrophages was upregulated with the induction of inflammatory cascade after liver IR surgery, and knockdown of ATP6V0D2 resulted in increased secretion of proinflammatory factors and chemokines, which enhanced activation of NLRP3 and aggravation of liver injury. Further studies found that the exacerbated activation of NLRP3 was related to the autophagic flux regulated by ATP6V0D2. Knocking down ATP6V0D2 impaired the formation of autophagolysosome and aggravated liver IR injury through nonspecific V-ATPase activation independent of V-ATPase-Notchl-Hesl signal axis. In general, we illustrated that the expression of ATP6V0D2 in liver macrophages was upregulated after liver IR, and by gradually promoting the formation of autophagolysosomes to increase autophagy flux to limit the activation of liver inflammation, this regulation is independent of the Notch1-Hes1 signal axis.

Biofuels from Micro-Organisms: Thermodynamic Considerations on the Role of Electrochemical Potential on Micro-Organisms Growth

Biofuels from micro-organisms represents a possible response to the carbon dioxide mitigation. One open problem is to improve their productivity, in terms of biofuels production. To do so, an improvement of the present model of growth and production is required. However, this implies an understanding of the growth spontaneous conditions of the bacteria. In this paper, a thermodynamic approach is developed in order to highlight the fundamental role of the electrochemical potential in bacteria proliferation. Temperature effect on the biosystem behaviour has been pointed out. The results link together the electrochemical potential, the membrane electric potential, the pH gradient through the membrane, and the temperature, with the result of improving the thermodynamic approaches, usually introduced in this topic of research.

Expression analysis of DIO2, EYA3, KISS1 and GPR54 genes in year-round estrous and seasonally estrous rams

The expression characteristics of the hypothalamic-pituitary-gonadal (HPG) axis-related candidate genes, DIO2, EYA3, KISS1 and GPR54, were analyzed in year-round estrous rams (small-tail Han sheep, STH) and seasonally estrous rams (Sunite sheep, SNT) using qPCR. The results were as follows: DIO2 was mainly expressed in pituitary, and KISS1 was specifically expressed in hypothalamus in the two groups. However, EYA3 and GPR54 were widely expressed in the cerebrum, cerebellum, hypothalamus, pituitary, testis, epididymis, vas deferens and adrenal gland tissues in both breeds, with significant differences in the cerebellum, hypothalamus, pituitary, testis and vas deferens tissues. We speculated that DIO2 and KISS1 may have positive roles in different regions in ram year-round estrus. Moreover, the expression patterns of EYA3 and GPR54 suggested that they may regulate the estrous mode of ram via testis and vas deferens. This is the first study to systematically analyze the expression patterns of HPG axis-related genes in rams.

Rab11B participates in erythrocyte storage lesion of under-collected whole blood

BACKGROUND AND OBJECTIVES

The storage lesion of the red blood cell affects the life span of RBC and the quality of blood component. The elucidation of this mechanism is helpful to reduce the storage damage of RBC and improve the efficacy and safety of blood transfusion. The aim of this study was to discover the potential molecular mechanism of erythrocyte storage lesion with Under-collected whole blood (UC-WB) model.

METHODS

The label-free MS/MS quantitative method was used to identify the differential proteins of erythrocyte membrane proteins and the difference of Rab11B, V-ATPase and plasma GDI2 protein expression were further verified by western blot at the end of blood storage.

RESULTS

A total of 12 Rab proteins and 3 interacting effector proteins were identified among the membrane protein of normal WB and UC-WB, including 5 differential Rab proteins and 2 interacting effector proteins. Compared with normal WB, the expression of membrane Rab11B protein and ATP6V1B1/2 subunit of V-ATPases protein as well as the plasma GDI2 protein of UC-WB increased at the end of storage period.

CONCLUSION

Rab protein might be related to RBC storage lesions, Rab11B participates in the RBC storage lesion through Rab11B/V-ATPases pathways.

Sympathetic and Sensory-Motor Nerves in Peripheral Small Arteries

Small arteries, which play important roles in controlling blood flow, blood pressure, and capillary pressure, are under nervous influence. Their innervation is predominantly sympathetic and sensory motor in nature, and while some arteries are densely innervated, others are only sparsely so. Innervation of small arteries is a key mechanism in regulating vascular resistance. In the second half of the previous century, the physiology and pharmacology of this innervation were very actively investigated. In the past 10-20 yr, the activity in this field was more limited. With this review we highlight what has been learned during recent years with respect to development of small arteries and their innervation, some aspects of excitation-release coupling, interaction between sympathetic and sensory-motor nerves, cross talk between endothelium and vascular nerves, and some aspects of their role in vascular inflammation and hypertension. We also highlight what remains to be investigated to further increase our understanding of this fundamental aspect of vascular physiology.

Comparative Ubiquitome Analysis under Heat Stress Reveals Diverse Functions of Ubiquitination in Saccharina japonica

Ubiquitination is a major post-translational modification involved in nearly all aspects of eukaryotic biology. Previous RNA-Seq studies showed that ubiquitination plays essential roles in the heat tolerance of Saccharina japonica, but to date, large-scale profiling of the ubiquitome in S. japonica has not been reported. To better understand the regulatory roles of ubiquitination in heat responses of S. japonica, we investigated its ubiquitome under normal and heat stress by the combination of affinity enrichment and high-resolution liquid chromatography-tandem mass spectroscopy analysis. Altogether, 3305 lysine ubiquitination sites in 1562 protein groups were identified. After normalization, 152 lysine ubiquitination sites in 106 proteins were significantly upregulated and 208 lysine ubiquitination sites in 131 proteins were significantly downregulated in response to heat stress. Protein annotation and functional analysis suggested that ubiquitination modulates a variety of essential cellular and physiological processes, including but not limited to the ubiquitin-26S proteasome system, ribosome, carbohydrate metabolism, and oxidative phosphorylation. Our results provide a global view of the heat response ubiquitome in S. japonica, and could facilitate future studies on the physiological roles of these ubiquitination-related proteins.

Non-Equilibrium Thermodynamic Approach to Ca2+-Fluxes in Cancer

Living systems waste heat in their environment. This is the measurable effect of the irreversibility of the biophysical and biochemical processes fundamental to their life. Non-equilibrium thermodynamics allows us to analyse the ion fluxes through the cell membrane, and to relate them to the membrane electric potential, in order to link this to the biochemical and biophysical behaviour of the living cells. This is particularly interesting in relation to cancer, because it could represent a new viewpoint, in order to develop new possible anticancer therapies, based on the thermoelectric behaviour of cancer itself. Here, we use a new approach, recently introduced in thermodynamics, in order to develop the analysis of the ion fluxes, and to point out consequences related to the membrane electric potential, from a thermodynamic viewpoint. We show how any increase in the cell temperature could generate a decrease in the membrane electric potential, with a direct relation between cancer and inflammation. Moreover, a thermal threshold, for the cell membrane electric potential gradient, has been obtained, and related to the mitotic activity. Finally, we obtained the external surface growth of the cancer results related (i) to the Ca2+-fluxes, (ii) to the temperature difference between the the system and its environment, and (iii) to the chemical potential of the ion species.

The Synaptic Vesicle Cycle Revisited: New Insights into the Modes and Mechanisms

Neurotransmission is sustained by endocytosis and refilling of synaptic vesicles (SVs) locally within the presynapse. Until recently, a consensus formed that after exocytosis, SVs are recovered by either fusion pore closure (kiss-and-run) or clathrin-mediated endocytosis directly from the plasma membrane. However, recent data have revealed that SV formation is more complex than previously envisaged. For example, two additional recycling pathways have been discovered, ultrafast endocytosis and activity-dependent bulk endocytosis, in which SVs are regenerated from the internalized membrane and synaptic endosomes. Furthermore, these diverse modes of endocytosis appear to influence both the molecular composition and subsequent physiological role of individual SVs. In addition, previously unknown complexity in SV refilling and reclustering has been revealed. This review presents a modern view of the SV life cycle and discusses how neuronal subtype, physiological temperature, and individual activity patterns can recruit different endocytic modes to generate new SVs and sculpt subsequent presynaptic performance.

A new pH sensor localized in the Golgi apparatus of Saccharomyces cerevisiae reveals unexpected roles of Vph1p and Stv1p isoforms

The gradual acidification of the secretory pathway is conserved and extremely important for eukaryotic cells, but until now there was no pH sensor available to monitor the pH of the early Golgi apparatus in Saccharomyces cerevisiae. Therefore, we developed a pHluorin-based sensor for in vivo measurements in the lumen of the Golgi. By using this new tool we show that the cis- and medial-Golgi pH is equal to 6.6–6.7 in wild type cells during exponential phase. As expected, V-ATPase inactivation results in a near neutral Golgi pH. We also uncover that surprisingly Vph1p isoform of the V-ATPase is prevalent to Stv1p for Golgi acidification. Additionally, we observe that during changes of the cytosolic pH, the Golgi pH is kept relatively stable, mainly thanks to the V-ATPase. Eventually, this new probe will allow to better understand the mechanisms involved in the acidification and the pH control within the secretory pathway.

The Morphology of Cross-Beaks and BMP4 Gene Expression in Huiyang Bearded Chickens

Simple Summary

Recently, the emergence of cross-beaks has been reported in several domestic chickens. Despite several candidate genes, bone morphogenetic protein 4 (BMP4) has been suggested as responsible for chicken cross-beaks. The subtypes of the morphology term, etiopathogenesis, and the relationship of the candidate BMP4 gene to cross-beaks are not yet known. The objective of this study was to describe the subtypes of cross-beaks by left or right and upper and lower jaw bones and to figure out the relationship between BMP4 and the development of craniofacial bones in Huiyang bearded chickens.

Abstract

Bird beaks are important for biological purposes such as food intake, removing parasites, and defining phenotypic attributes. Cross-beaks are a threat to poultry health and are harmful to productivity, wasting some units in the poultry industry. However, there is still limited research on subtypes of cross-beaks and the genetic basis of cross-beaks as well. Here, we described the subtypes of cross-beaks in terms of left or right and upper or lower jaw bones. We evaluated the impact of cross-beaks on craniofacial bones and figured out the relationship between bone morphogenetic protein 4 (BMP4) and the development of craniofacial bones in Huiyang bearded chickens. We identified five typical subtypes of cross-beaks by morphological assessment and X-ray scanning. We found that cross-beaks caused certain changes in the facial bone morphology, including changes to the length and width of the bone around the ocular area (p < 0.05). The relative expressions of BMP4 in lacrimal, mandible, premaxilla, frontal, and parietal bones were significantly higher in the severe cross-beak group, followed by that of the medium cross-beak group, weak cross-beak group, and control group (p < 0.05). Overall, we constructed a generally applicable method to classify cross-beaks in term of the angle. The skeleton around the ocular area was affected by the cross-beak. The expression levels of BMP4 in craniofacial bones may provide insight to potential role of BMP4 in the development of cross-beaks.

Distal renal tubular acidosis: genetic causes and management

BACKGROUND

Distal renal tubular acidosis (dRTA) is a kidney tubulopathy that causes a state of normal anion gap metabolic acidosis due to impairment of urine acidification. This review aims to summarize the etiology, pathophysiology, clinical findings, diagnosis and therapeutic approach of dRTA, with emphasis on genetic causes of dRTA.

DATA SOURCES

Literature reviews and original research articles from databases, including PubMed and Google Scholar. Manual searching was performed to identify additional studies about dRTA.

RESULTS

dRTA is characterized as the dysfunction of the distal urinary acidification, leading to metabolic acidosis. In pediatric patients, the most frequent etiology of dRTA is the genetic alteration of genes responsible for the codification of distal tubule channels, whereas, in adult patients, dRTA is more commonly secondary to autoimmune diseases, use of medications and uropathies. Patients with dRTA exhibit failure to thrive and important laboratory alterations, which are used to define the diagnosis. The oral alkali and potassium supplementation can correct the biochemical defects, improve clinical manifestations and avoid nephrolithiasis and nephrocalcinosis.

CONCLUSIONS

dRTA is a multifactorial disease leading to several clinical manifestations. Clinical and laboratory alterations can be corrected by alkali replacement therapy.

Immunomic Identification of Malaria Antigens Associated With Protection in Mice

Efforts to develop vaccines against malaria represent a major research target. The observations that 1) sterile protection can be obtained when the host is exposed to live parasites and 2) the immunity against blood stage parasite is principally mediated by protective antibodies suggest that a protective vaccine is feasible. However, only a small number of proteins have been investigated so far and most of the Plasmodium proteome has yet to be explored. To date, only few immunodominant antigens have emerged for testing in clinical trials but no formulation has led to substantial protection in humans. The nature of parasite molecules associated with protection remains elusive. Here, immunomic screening of mice immune sera with different protection efficiencies against the whole parasite proteome allowed us to identify a large repertoire of antigens validated by screening a library expressing antigens. The calculation of weighted scores reflecting the likelihood of protection of each antigen using five predictive criteria derived from immunomic and proteomic data sets, highlighted a priority list of protective antigens. Altogether, the approach sheds light on conserved antigens across Plasmodium that are amenable to targeting by the host immune system upon merozoite invasion and blood stage development. Most of these antigens have preliminary protection data but have not been widely considered as candidate for vaccine trials, opening new perspectives that overcome the limited choice of immunodominant, poorly protective vaccines currently being the focus of malaria vaccine researches.

Temporal proteomics of Arabidopsis plasma membrane during cold- and de-acclimation

Freezing stress is one of the most important limiting factors of plant survival. Plants have developed a freezing adaptation mechanism upon sensing low temperatures (cold acclimation). Compositional changes in the plasma membrane, one of the initial sites of freezing injury, is prerequisite of achieving cold acclimation and have been investigated in several plant species. Conversely, the cold dehardening process at elevated temperatures (de-acclimation) has not yet been fully characterized and few studies have addressed the importance of the plasma membrane in the de-acclimation process. In the present study, we conducted shotgun proteomics with label-free semiquantification on plasma membrane fractions of Arabidopsis leaves during cold acclimation and de-acclimation. We consequently obtained a list of 873 proteins with significantly changed proteins in response to the two processes. Although the cold-acclimation-responsive proteins were globally returned to non-acclimated levels by de-acclimation, several representative cold-acclimation-responsive proteins tended to remain at higher abundance during de-acclimation process. Taken together, our results suggest plants deharden right after cold acclimation to restart growth and development but some cold-acclimation-induced changes of the plasma membrane may be maintained under de-acclimation to cope with the threat of sudden freezing during de-acclimation process. SIGNIFICANCE: Plant freezing tolerance can be enhanced by low temperature treatment (cold acclimation), while elevated temperatures right after cold acclimation can result in the dehardening of freezing tolerance (de-acclimation). However, the de-acclimation process, particularly its relevance to the plasma membrane as the primary site of freezing injury, has not been elucidated. In the present study, a comprehensive proteomic analysis of the plasma membrane during cold acclimation and de-acclimation was carried out as a first step to elucidating how plants respond to rising temperatures. Cold acclimation induced a number of proteomic changes as reported in previous studies, but most proteins, in general, immediately returned to NA levels during de-acclimation treatment for two days. However, the abundances of stress-related proteins (e.g. LTI29, COR78 and TIL) decreased slower than other functional proteins during de-acclimation. Therefore, plants harden during cold acclimation by aborting growth and development and accumulating stress-responsive proteins but seem to deharden quickly under subsequent elevated temperature to resume these processes while guarding against the threat of sudden temperature drops.

Symbiont photosynthesis in giant clams is promoted by V-type H+-ATPase from host cells

Giant clams (genus Tridacna) are the largest living bivalves and, like reef-building corals, host symbiotic dinoflagellate algae (Symbiodinium) that significantly contribute to their energy budget. In turn, Symbiodinium rely on the host to supply inorganic carbon (C_i) for photosynthesis. In corals, host 'proton pump' vacuolar-type H⁺-ATPase (VHA) is part of a carbon-concentrating mechanism (CCM) that promotes Symbiodinium photosynthesis. Here, we report that VHA in the small giant clam (Tridacna maxima) similarly promotes Symbiodinium photosynthesis. VHA was abundantly expressed in the apical membrane of epithelial cells of T. maxima's siphonal mantle tubule system, which harbors Symbiodinium Furthermore, application of the highly specific pharmacological VHA inhibitors bafilomycin A1 and concanamycin A significantly reduced photosynthetic O₂ production by ∼40%. Together with our observation that exposure to light increased holobiont aerobic metabolism ∼5-fold, and earlier estimates that translocated fixed carbon exceeds metabolic demand, we conclude that VHA activity in the siphonal mantle confers strong energetic benefits to the host clam through increased supply of C_i to algal symbionts and subsequent photosynthetic activity. The convergent role of VHA in promoting Symbiodinium photosynthesis in the giant clam siphonal mantle tubule system and coral symbiosome suggests that VHA-driven CCM is a common exaptation in marine photosymbioses that deserves further investigation in other taxa.

Host-directed combinatorial RNAi improves inhibition of diverse strains of influenza A virus in human respiratory epithelial cells

Influenza A virus infections are important causes of morbidity and mortality worldwide, and currently available prevention and treatment methods are suboptimal. In recent years, genome-wide investigations have revealed numerous host factors that are required for influenza to successfully complete its life cycle. However, only a select, small number of influenza strains were evaluated using this platform, and there was considerable variation in the genes identified across different investigations. In an effort to develop a universally efficacious therapeutic strategy with limited potential for the emergence of resistance, this study was performed to investigate the effect of combinatorial RNA interference (RNAi) on inhibiting the replication of diverse influenza A virus subtypes and strains. Candidate genes were selected for targeting based on the results of multiple previous independent genome-wide studies. The effect of single and combinatorial RNAi on the replication of 12 diverse influenza A viruses, including three strains isolated from birds and one strain isolated from seals, was then evaluated in primary normal human bronchial epithelial cells. After excluding overly toxic siRNA, two siRNA combinations were identified that reduced mean viral replication by greater than 79 percent in all mammalian strains, and greater than 68 percent in all avian strains. Host-directed combinatorial RNAi effectively prevents growth of a broad range of influenza virus strains in vitro, and is a potential therapeutic candidate for further development and future in vivo studies.

Proteomic analysis of watery saliva secreted by white-backed planthopper, Sogatella furcifera

The white-backed planthopper, Sogatella furcifera, is a phloem sap feeder that secretes watery and gelling saliva during feeding. In this study, we identified the major proteins in watery saliva of S. furcifera by shotgun LC-MS/MS analysis combined with transcriptomic analysis. A total of 161 proteins were identified, which were divided into 8 function categories, including enzymes, transporter, calcium ion binding protein, salivary sheath protein, cytoskeleton protein, DNA-, RNA-, and protein-binding or regulating proteins, other non-enzyme proteins and unknown proteins. Gene expression pattern of 11 secretory proteins were analyzed by real time quantitative-PCR. We detected the mucin-like protein, which had a unique expression level in salivary gland, most likely to be a candidate effector involved in regulation of plant defense. This study identified the watery saliva component of S. furcifera and it provided a list of proteins which may play a role in interaction between S. furcifera and rice.

A mouse model of autism implicates endosome pH in the regulation of presynaptic calcium entry

Psychoactive compounds such as chloroquine and amphetamine act by dissipating the pH gradient across intracellular membranes, but the physiological mechanisms that normally regulate organelle pH remain poorly understood. Interestingly, recent human genetic studies have implicated the endosomal Na⁺/H⁺ exchanger NHE9 in both autism spectrum disorders (ASD) and attention deficit hyperactivity disorder (ADHD). Plasma membrane NHEs regulate cytosolic pH, but the role of intracellular isoforms has remained unclear. We now find that inactivation of NHE9 in mice reproduces behavioral features of ASD including impaired social interaction, repetitive behaviors, and altered sensory processing. Physiological characterization reveals hyperacidic endosomes, a cell-autonomous defect in glutamate receptor expression and impaired neurotransmitter release due to a defect in presynaptic Ca²⁺ entry. Acute inhibition of synaptic vesicle acidification rescues release but without affecting the primary defect due to loss of NHE9.

The Na⁺/H⁺ exchanger NHE9 is proposed to regulate the H⁺ electrochemical gradient across endosomal membranes. Here, the authors find that NHE9 knockout mice show autism spectrum disorder-like behaviors and disrupted synaptic vesicle exocytosis due to impaired presynaptic calcium entry.

Changes in V-ATPase subunits of human urinary exosomes reflect the renal response to acute acid/alkali loading and the defects in distal renal tubular acidosis

In the kidney, final urinary acidification is achieved by V-ATPases expressed in type A intercalated cells. The B1 subunit of the V-ATPase is required for maximal urinary acidification, while the role of the homologous B2 subunit is less clear. Here we examined the effect of acute acid/alkali loading in humans on B1 and B2 subunit abundance in urinary exosomes in normal individuals and of acid loading in patients with distal renal tubular acidosis (dRTA). Specificities of B1 and B2 subunit antibodies were verified by yeast heterologously expressing human B1 and B2 subunits, and murine wild-type and B1-deleted kidney lysates. Acute ammonium chloride loading elicited systemic acidemia, a drop in urinary pH, and increased urinary ammonium excretion. Nadir urinary pH was achieved at four to five hours, and exosomal B1 abundance was significantly increased at two through six hours after ammonium chloride loading. After acute equimolar sodium bicarbonate loading, blood and urinary pH rose rapidly, with a concomitant reduction of exosomal B1 abundance within two hours, which remained lower throughout the test. In contrast, no change in exosomal B2 abundance was found following acid or alkali loading. In patients with inherited or acquired distal RTA, the urinary B1 subunit was extremely low or undetectable and did not respond to acid loading in urine, whereas no change in B2 subunit was found. Thus, both B1 and B2 subunits of the V-ATPase are detectable in human urinary exosomes, and acid and alkali loading or distal RTA cause changes in the B1 but not B2 subunit abundance in urinary exosomes.

Differential proteome profiling in the hippocampus of amnesic mice

Amnesia or memory loss is associated with brain aging and several neurodegenerative pathologies including Alzheimer's disease (AD). This can be induced by a cholinergic antagonist scopolamine but the underlying molecular mechanism is poorly understood. This study of proteome profiling in the hippocampus could provide conceptual insights into the molecular mechanisms involved in amnesia. To reveal this, mice were administered scopolamine to induce amnesia and memory impairment was validated by novel object recognition test. Using two-dimensional gel electrophoresis coupled with MALDI-MS/MS, we have analyzed the hippocampal proteome and identified 18 proteins which were differentially expressed. Out of these proteins, 11 were downregulated and 7 were upregulated in scopolamine-treated mice as compared to control. In silico analysis showed that the majority of identified proteins are involved in metabolism, catalytic activity, and cytoskeleton architectural functions. STRING interaction network analysis revealed that majority of identified proteins exhibit common association with Actg1 cytoskeleton and Vdac1 energy transporter protein. Furthermore, interaction map analysis showed that Fascin1 and Coronin 1b individually interact with Actg1 and regulate the actin filament dynamics. Vdac1 was significantly downregulated in amnesic mice and showed interaction with other proteins in interaction network. Therefore, we silenced Vdac1 in the hippocampus of normal young mice and found similar impairment in recognition memory of Vdac1 silenced and scopolamine-treated mice. Thus, these findings suggest that Vdac1-mediated disruption of energy metabolism and cytoskeleton architecture might be involved in scopolamine-induced amnesia.

Proton electrochemical gradient: Driving and regulating neurotransmitter uptake

Accumulation of neurotransmitters in the lumen of synaptic vesicles (SVs) relies on the activity of the vacuolar-type H⁺ -ATPase. This pump drives protons into the lumen, generating a proton electrochemical gradient (Δμ_H+ ) across the membrane. Recent work has demonstrated that the balance between the chemical (ΔpH) and electrical (ΔΨ) components of Δμ_H+ is regulated differently by some distinct vesicle types. As different neurotransmitter transporters use ΔpH and ΔΨ with different relative efficiencies, regulation of this gradient balance has the potential to influence neurotransmitter uptake. Nevertheless, the underlying mechanisms responsible for this regulation remain poorly understood. In this review, we provide an overview of current neurotransmitter uptake models, with a particular emphasis on the distinct roles of the electrical and chemical gradients and current hypotheses for regulatory mechanisms.