Organelle stress and alterations in interorganelle crosstalk during liver fibrosis.

The synchronous functioning and quality control of organelles ensure cell survival and function and are essential for maintaining homeostasis. Prolonged exposure to stressors (viruses, bacteria, parasitic infections, alcohol, drugs) or genetic mutations often disrupt the functional integrity of organelles which plays a critical role in the initiation and progression of several diseases including chronic liver diseases. One of the most important pathologic consequences of chronic liver diseases is liver fibrosis, characterized by tissue scarring due to the progressive accumulation of extracellular matrix components. Left untreated, fibrosis may advance to life-threatening complications such as cirrhosis, hepatic decompensation, and HCC, which collectively accounts for ∼1 million deaths per year worldwide. Owing to the lack of treatment options that can regress or reverse cirrhosis, liver transplantation is currently the only available treatment for end-stage liver disease. However, the limited supply of usable donor organs, adverse effects of lifelong immunosuppressive regimes, and financial considerations pose major challenges and limit its application. Hence, effective therapeutic strategies are urgently needed. An improved understanding of the organelle-level regulation of fibrosis can help devise effective antifibrotic therapies focused on reducing organelle stress, limiting organelle damage, improving interorganelle crosstalk, and restoring organelle homeostasis; and could be a potential clinical option to avoid transplantation. This review provides a timely update on the recent findings and mechanisms covering organelle-specific dysfunctions in liver fibrosis, highlights how correction of organelle functions opens new treatment avenues and discusses the potential challenges to clinical application.

The Emerging Role of Raman Spectroscopy as an Omics Approach for Metabolic Profiling and Biomarker Detection toward Precision Medicine.

Omics technologies have rapidly evolved with the unprecedented potential to shape precision medicine. Novel omics approaches are imperative toallow rapid and accurate data collection and integration with clinical information and enable a new era of healthcare. In this comprehensive review, we highlight the utility of Raman spectroscopy (RS) as an emerging omics technology for clinically relevant applications using clinically significant samples and models. We discuss the use of RS both as a label-free approach for probing the intrinsic metabolites of biological materials, and as a labeled approach where signal from Raman reporters conjugated to nanoparticles (NPs) serve as an indirect measure for tracking protein biomarkers in vivo and for high throughout proteomics. We summarize the use of machine learning algorithms for processing RS data to allow accurate detection and evaluation of treatment response specifically focusing on cancer, cardiac, gastrointestinal, and neurodegenerative diseases. We also highlight the integration of RS with established omics approaches for holistic diagnostic information. Further, we elaborate on metal-free NPs that leverage the biological Raman-silent region overcoming the challenges of traditional metal NPs. We conclude the review with an outlook on future directions that will ultimately allow the adaptation of RS as a clinical approach and revolutionize precision medicine.

Metabolic Response to Small Molecule Therapy in Colorectal Cancer Tracked with Raman Spectroscopy and Metabolomics.

Despite numerous screening tools for colorectal cancer (CRC), 25 % of patients are diagnosed with advanced disease. Novel diagnostic technologies that are early, accurate, and rapid are imperative to assess the therapeutic efficacy of clinical drugs and identify new biomarkers of treatment response. Here Raman spectroscopy (RS) was used to track metabolic reprogramming in KRAS-mutant HCT116 and SW837 cells, and KRAS wild-type CC cells. RS combined with multivariate analysis methods distinguished nonresponsive, partially responsive, and responsive cells treated with cetuximab, a monoclonal antibody for EGFR inhibition, sotorasib, a clinically approved KRAS inhibitor, and various doses of trametinib, an inhibitor of the MAPK pathway. Cells treated with a combination of subtoxic doses of trametinib and BKM120, an inhibitor of the PI3K pathway, showed a synergistic response between the two pathways. Using a supervised machine learning regression model, we established a scoring methodology trained to a priori predict therapeutic response to new treatment combinations. RS metabolites were verified with mass spectrometry, and enrichment pathways were identified, including amino acid, purine, and nicotinate and nicotinamide metabolism that differentiated monotherapy from combination therapy. Our approach may ultimately be applicable to patient-derived primary cells and cultures of patient tumors to predict effective drugs for individualized care.

Monitoring Metabolic Changes in Response to Chemotherapies in Cancer with Raman Spectroscopy and Metabolomics.

Resistance to clinical therapies remains a major barrier in cancer management. There is a critical need for rapid and highly sensitive diagnostic tools that enable early prediction of treatment response to allow accurate clinical decisions. Here, Raman spectroscopy was employed to monitor changes in key metabolites as early predictors of response in KRAS-mutant colorectal cancer (CRC) cells, HCT116, treated with chemotherapies. We show at the single cell level that HCT116 is resistant to cetuximab (CTX), the first-line treatment in CRC, but this resistance can be overcome with pre-sensitization of cells with oxaliplatin (OX). In combination treatment of CTX + OX, sequential delivery of OX followed by CTX rather than simultaneous administration of drugs was observed to be critical for effective therapy. Our results demonstrated that metabolic changes are well aligned to cellular mechanical changes where Young's modulus decreased after effective treatment, indicating that both changes in mechanical properties and metabolism in cells are likely responsible for cancer proliferation. Raman findings were verified with mass spectrometry (MS) metabolomics, and both platforms showed changes in lipids, nucleic acids, and amino acids as predictors of resistance/response. Finally, key metabolic pathways enriched were identified when cells are resistant to CTX but downregulated with effective treatment. This study highlights that drug-induced metabolic changes both at the single cell level (Raman) and ensemble level (MS) have the potential to identify mechanisms of response to clinical cancer therapies.

Recent Trends in the Preparation of Nano-Starch Particles.

Starch is affected by several limitations, e.g., retro-gradation, high viscosity even at low concentrations, handling issues, poor freeze-thaw stability, low process tolerance, and gel opacity. In this context, physical, chemical, and enzymatic methods have been investigated for addressing such limitations or adding new attributes. Thus, the creation of biomaterial-based nanoparticles has sparked curiosity. Because of that, single nucleotide polymorphisms are gaining a lot of interest in food packaging technology. This is due to their ability to increase the mechanical and water vapor resistance of the matrix, as well as hide its re-crystallization during storage in high-humidity atmospheres and enhance the mechanical properties of films when binding in paper machines and paper coating. In medicine, single nucleotide polymorphisms (SNPs) are suitable as carriers in the field of drug delivery for immobilized bioactive or therapeutic agents, as well as wastewater treatments as an alternative to expensive activated carbons. Starch nanoparticle preparations can be performed by hydrolysis via acid hydrolysis of the amorphous part of a starch molecule, the use of enzymes such as pullulanase or isoamylase, or a combination of two regeneration and mechanical treatments with the employment of extrusion, irradiation, ultrasound, or precipitation. The possibility of obtaining cheap and easy-to-use methods for starch and starch derivative nanoparticles is of fundamental importance. Nano-precipitation and ultra-sonication are rather simple and reliable methods for nanoparticle production. The process involves the addition of a diluted starch solution into a non-solvent, and ultra-sonication aims to reduce the size by breaking the covalent bonds in polymeric material due to intense shear forces or mechanical effects associated with the collapsing of micro-bubbles by sound waves. The current study focuses on starch nanoparticle manufacturing, characterization, and emerging applications.

Effects of noninherited ancestral genotypes on offspring phenotypes†.

It is well established that environmental exposures can modify the profile of heritable factors in an individual's germ cells, ultimately affecting the inheritance of phenotypes in descendants. Similar to exposures, an ancestor's genotype can also affect the inheritance of phenotypes across generations, sometimes in offspring who do not inherit the genetic aberration. This can occur via a variety of prenatal, in utero, or postnatal mechanisms. In this review, we discuss the evidence for this process in mammals, with a focus on examples that are potentially mediated through the germline, while also considering alternate routes of inheritance. Noninherited ancestral genotypes may influence descendant's disease risk to a much greater extent than currently appreciated, and focused evaluation of this phenomenon may reveal novel mechanisms of inheritance.

Molecular characterization of exons 6, 8 and 9 of ABCB4 gene in children with Progressive Familial Intrahepatic Cholestasis type 3.

AIM OF WORK: To estimate the frequency of mutations involving exons 6, 8 and 9 of Adenosine triphosphate-binding cassette, subfamily B, member 4 (ABCB4) gene among children with progressive intrahepatic cholestasis with high γ-GT activity (PFIC3). SUBJECTS AND METHODS: Cross sectional study was conducted on 30 children with PFIC3. Genotyping was performed by sequencing analysis of exons 6, 8 and exon 9 of ABCB4 gene. RESULTS: Heterozygous synonymous polymorphic variant was detected in exon 6 (rs 1202283) and in exon 8 (rs 2109505). No mutations in studied exons were detected. CONCLUSION: Exons 6, 8 and 9 mutations of ABCB4 gene are not common among Egyptian children with PFIC3.

The relation between autophagy modulation by intermittent fasting and aquaporin 2 expression in experimentally induced diabetic nephropathy in albino rat.

Polyuria is an early sign of diabetic nephropathy (DN) that produces dehydration in diabetic patients. This could be caused by alteration of renal aquaporin 2 (AQP2) expression. This study aimed to describe the relation between autophagy modulation via intermittent fasting (IF) and renal AQP2 expression and polyuria in case of DN. We divided the rats into control, DN and IF groups. After 2 and 4 weeks of diabetes induction, blood glucose (BG), serum creatinine (Scr), urine volume, and 24 hours urine protein (UP) were examined. Diabetic nephropathy histopathological index (DNHI) was calculated to evaluate histopathological changes. Immunohistochemistry and real-time PCR were performed to measure the levels of AQP2 and the autophagy marker; LC3 in kidney tissue. DNHI was correlated to the PCR and immunoexpression of AQP2 and LC3. Intermittent fasting significantly decreased the BG, Scr, urine volume, 24 hours UP, and DNHI as compared diabetes. Diabetes significantly elevated the immunoreactivity and mRNA expression levels of AQP2 and LC3 as compared to the control. However, the IF decreased AQP2 and stimulated autophagy in cyclic fashion. Our data revealed significant positive correlations between AQP2 and LC3 at the level of immunoexpression and mRNA at 2nd weeks. Taken together, these data showed that autophagy stimulation didn't regulate AQP2 expression in case of diabetic nephropathy, however IF decreased polyuria through improvement of glycemic state.

Mesenteric Parametrial Fat Pad Surgery for in vivo Implantation of Hepatocytes in Nude Mice.

Cell-based liver therapies utilizing functionally stabilized engineered hepatic tissue hold promise in improving host liver functions and are emerging as a potential alternative to whole-organ transplantation. Owing to the ability to accommodate a large ex vivo engineered hepatocyte mass and dense vascularization, the mesenteric parametrial fat pad in female nude mice forms an ideal anatomic microenvironment for ectopic hepatocyte transplantation. However, the lack of any reported protocol detailing the presurgical preparation and construction of the engineered hepatic hydrogel, fat pad surgery, and postsurgical care and bioluminescence imaging to confirm in vivo hepatocyte implantation makes it challenging to reliably perform and test engraftment and integration with the host. In this report, we provide a step-by-step protocol for in vivo hepatocyte implantation, including preparation of hepatic tissue for implantation, the surgery process, and bioluminescence imaging to assess survival of functional hepatocytes. This will be a valuable protocol for researchers in the fields of tissue engineering, transplantation, and regenerative medicine. Key features • Primary human hepatocytes transduced ex vivo with a lentiviral vector carrying firefly luciferase are surgically implanted onto the fat pad. • Bioluminescence helps monitor survival of transplanted hepatic tissue over time. • Applicable for assessment of graft survival, graft-host integration, and liver regeneration.

Khdc3 Regulates Metabolism Across Generations in a DNA-Independent Manner.

Genetic variants can alter the profile of heritable molecules such as small RNAs in sperm and oocytes, and in this manner ancestral genetic variants can have a significant effect on offspring phenotypes even if they are not themselves inherited. Here we show that wild type female mice descended from ancestors with a mutation in the mammalian germ cell gene Khdc3 have hepatic metabolic defects that persist over multiple generations. We find that genetically wild type females descended from Khdc3 mutants have transcriptional dysregulation of critical hepatic metabolic genes, which persist over multiple generations and pass through both female and male lineages. This was associated with dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with mutational ancestry. The oocytes of Khdc3-null females, as well as their wild type descendants, had dysregulation of multiple small RNAs, suggesting that these epigenetic changes in the gametes transmit the phenotype between generations. Our results demonstrate that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes, potentially indefinitely.

Cisplatin-Induced Metabolic Responses Measured with Raman Spectroscopy in Cancer Cells, Spheroids, and Canine-Derived Organoids.

Ex vivo assessment of drug response with conventional cell viability assays remains the standard practice for guiding initial therapeutic choices. However, such ensemble approaches fail to capture heterogeneities in treatment response and cannot identify early markers of response. Here, we leverage Raman spectroscopy (RS) as an accurate, low-cost, extraction-free, and label-free approach to track metabolic changes in cancer cells, spheroids, and organoids in response to cisplatin treatment. We identified 12 statistically significant metabolites in cells and 19 metabolites in spheroids and organoids as a function of depth. We show that the cisplatin treatment of 4T1 cells and spheroids results in a shift in metabolite levels; metabolites including nucleic acids such as DNA, 783 cm-1 with p = 0.00021 for cells; p = 0.02173 for spheroids, major amino acids such as threonine, 1338 cm-1 with p = 0.00045 for cells; p = 0.01022 for spheroids, proteins such as amide III, 1248 cm-1 with p = 0.00606 for cells; p = 0.00511 for spheroids serve as early predictors of response. Our RS findings were also applicable to canine-derived organoids, showing spatial variations in metabolic changes as a function of organoid depth in response to cisplatin. Further, the metabolic pathways such as tricarboxylic acid (TCA)/citric acid cycle and glyoxylate and dicarboxylate metabolism that drive drug response showed significant differences based on organoid depth, replicating the heterogeneous treatment response seen in solid tumors where there is a difference from the periphery to the tumor core. Our study showcases the versatility of RS as a predictive tool for treatment response applicable from cells to organotypic cultures, that has the potential to decrease animal burden and readout time for preclinical drug efficacy.

Liver-specific Mettl14 deletion induces nuclear heterotypia and dysregulates RNA export machinery.

Modification of RNA with N6-methyladenosine (m6A) has gained attention in recent years as a general mechanism of gene regulation. In the liver, m6A, along with its associated machinery, has been studied as a potential biomarker of disease and cancer, with impacts on metabolism, cell cycle regulation, and pro-cancer state signaling. However these observational data have yet to be causally examined in vivo. For example, neither perturbation of the key m6A writers Mettl3 and Mettl14, nor the m6A readers Ythdf1 and Ythdf2 have been thoroughly mechanistically characterized in vivo as they have been in vitro. To understand the functions of these machineries, we developed mouse models and found that deleting Mettl14 led to progressive liver injury characterized by nuclear heterotypia, with changes in mRNA splicing, processing and export leading to increases in mRNA surveillance and recycling.

Dual-Reporter System for Real-Time Monitoring of SARS-CoV-2 Main Protease Activity in Live Cells Enables Identification of an Allosteric Inhibition Path.

The SARS-CoV-2 pandemic is an ongoing threat to global health, and the continuing emergence of contagious variants highlights the urgent need for additional antiviral therapy to attenuate COVID-19 disease. The SARS-CoV-2 main protease (3CLpro) presents an attractive target for such therapy due to its high sequence conservation and key role in the viral life cycle. In this study, we designed a fluorescent-luminescent cell-based reporter for the detection and quantification of 3CLpro intracellular activity. Employing this platform, we examined the efficiency of known protease inhibitors against 3CLpro and further identified potent inhibitors through high-throughput chemical screening. Computational analysis confirmed a direct interaction of the lead compounds with the protease catalytic site and identified a prototype for efficient allosteric inhibition. These developments address a pressing need for a convenient sensor and specific targets for both virus detection and rapid discovery of potential inhibitors.

Characterization of Biofilm Producer Nanobacteria Isolated from Kidney Stones of Some Egyptian Patients.

<b>Background and Objective:</b> Nanobacteria (NB) appear to contribute to many calcifying diseases including kidney stones which represent a common problem with inadequate prevention exist. NB framing itself with a mineral coat that assists as a primary defence shield against the immune system, antibiotics. This study aims to collect and detect nanobes from different kidney stones from patients with active urolithiasis then investigated the anti-nano-bacterial activity of some antibiotics alone or in combination with extracts of irradiated herbs of certain medicinal plants which will represent a new approach to therapy for patients with kidney stones. <b>Materials and Methods:</b> Total of 32 nanobes were isolated from 54 kidney stones. Fourier Transforms Infrared Spectroscopy (FTIR) revealed that calcium and phosphate are the main components of stones. Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray spectroscopy (EDX) and Transmission Electron Microscope (TEM), showed that nanobes were Gram-ve cocci with size ranged from (375:600 nm). The biofilm production ability of nanobes was estimated qualitatively and quantitatively. <b>Results:</b> The results revealed that all were strong biofilm producers. Further, the antibiotic susceptibility test indicates their resistance towards most of the tested antibiotics. Molecular identification of the strong biofilm producer isolates by ribosomal ribonucleic acid (rRNA) revealed that it is indicated by 85.37% to <i>Bartonella apis</i> strain PEB0122. <b>Conclusion:</b> The findings of the current study evidenced that combination treatment between Doxycycline (DO) and water extract of khella exhibited a significant reduction in biofilm formation ability of the strongest producers nanobes. Therefore, this treatment can play a role in enhancing public health, especially with patients who suffer from recurrent kidney stone formation.

Comparing polarized Raman spectroscopy and birefringence as probes of molecular scale alignment in 3D printed thermoplastics.

Polymer chain orientation is crucial to understanding the polymer dynamics at interfaces formed during thermoplastic material extrusion additive manufacturing. The flow field and rapid cooling produced during material extrusion can result in chains which are oriented and stretched, which has implications for interdiffusion and crystallization. Polarized Raman spectroscopy offers a non-destructive and surface sensitive method to quantify chain orientation. To study orientation and alignment of chains in 3D printed polycarbonate filaments, we used a combination of polarized Raman spectroscopy and birefringence (Δn) measurements. By changing the orientation of the sample with respect to polarization of incident radiation, we probe changes in the ratio between orientation-dependent vibration modes and orientation-independent modes. We used principal component analysis (PCA) and partial least squares (PLS) regression to develop correlations for birefringence and Raman measurements in samples that were pulled at different draw ratios (DRs). PCA was used to differentiate between orientation-dependent and orientation-independent modes, while PLS regression was used to calculate birefringence from Raman measurements of 3D printed samples. Birefringence measurements were compared to the polycarbonate intrinsic birefringence of 0.2, to estimate the degree of orientation. We find that measured values of birefringence underestimate orientation compared to Raman measurements.

Evidence for a quantum dipole liquid state in an organic quasi-two-dimensional material.

Mott insulators are commonly pictured with electrons localized on lattice sites, with their low-energy degrees of freedom involving spins only. Here, we observe emergent charge degrees of freedom in a molecule-based Mott insulator κ-(BEDT-TTF)2Hg(SCN)2Br, resulting in a quantum dipole liquid state. Electrons localized on molecular dimer lattice sites form electric dipoles that do not order at low temperatures and fluctuate with frequency detected experimentally in our Raman spectroscopy experiments. The heat capacity and Raman scattering response are consistent with a scenario in which the composite spin and electric dipole degrees of freedom remain fluctuating down to the lowest measured temperatures.

The prevalence of iron deficiency anemia in a Saudi University female students.

The study aims to determine the prevalence of anemia in apparently healthy university female students. This study was conducted in 2007-2008 at Taibah University and a total of 268 female students participated in this research. In order to assess iron deficiency and iron deficiency anemia, the venous blood samples were collected from consecutive female students at the medical center of Taibah University excluding those already on iron supplementation for iron-deficiency anemia. One hundred and seventy-one (64%) students were found to be anemic. The overall prevalence of mild (10-11 g/dL), moderate (7-10 g/dL), and severe (Hb <7 g/dL) anemia was 45%, 49%, and 6%, respectively. Out of the anemic students, 81% showed microcytic (MCV <80 fL) and 1.6% had macrocytic (MCV >96 fL) variety. The results of this study warrant further evidence-based surveys on a larger scale to validate these findings and eventually set a stage to develop well-organized educational and nutritional programs to safeguard and improve the nation's health. The high prevalence of iron deficiency anemia in the present study might be related to life style of female students as well as to their dietary habits. It is recommended that female students never skip breakfast as it is essential for their cognitive functions and physical activities.