Proteomic-miRNA Biomics Profile Reveals 2D Cultures of Human iPSC-Derived Neural Progenitor Cells More Sensitive than 3D Spheroid System Against the Experimental Exposure to Arsenic

The iPSC-derived 3D models are considered to be a connective link between 2D culture and in vivo studies. However, the sensitivity of such 3D models is yet to be established. We assessed the sensitivity of the hiPSC-derived 3D spheroids against 2D cultures of neural progenitor cells. The sub-toxic dose of Sodium Arsenite (SA) was used to investigate the alterations in miRNA-proteins in both systems. Though SA exposure induced significant alterations in the proteins in both 2D and 3D systems, these proteins were uncommon except for 20 proteins. The number and magnitude of altered proteins were higher in the 2D system compared to 3D. The association of dysregulated miRNAs with the target proteins showed their involvement primarily in mitochondrial bioenergetics, oxidative and ER stress, transcription and translation mechanism, cytostructure, etc., in both culture systems. Further, the impact of dysregulated miRNAs and associated proteins on these functions and ultrastructural changes was compared in both culture systems. The ultrastructural studies revealed a similar pattern of mitochondrial damage, while the cellular bioenergetics studies confirm a significantly higher energy failure in the 2D system than to 3D. Such a higher magnitude of changes could be correlated with a higher amount of internalization of SA in 2D cultures than in 3D spheroids. Our findings demonstrate that a 2D culture system seems better responsive than a 3D spheroid system against SA exposure.

HCMV miR-UL70-3p downregulates the rapamycin-induced autophagy by targeting the autophagy-related protein 9A (ATG9A)

Human cytomegalovirus (HCMV) is a representative β-herpesvirus that establishes persistent infections in humans, and exhibits high seropositivity rates in adults. It has co-evolved with its human host and employs various strategies to evade antiviral mechanisms by utilizing a significant portion of its genome. HCMV-encoded proteins and miRNAs have been implicated in regulating these mechanisms, enabling viral survival within the human body. During viral infections, autophagy, a conserved catabolic process essential for cellular homeostasis, acts as an antiviral defense mechanism. Multiple studies have reported that HCMV can modulate autophagy through its proteins and miRNAs, thereby influencing its survival within the host. In this study, we showed the potential involvement of HCMV miRNAs in cellular autophagy. We employed various bioinformatic tools to predict putative HCMV miRNAs that target autophagy-related genes and their corresponding cellular autophagy genes. Our results show that the 3'UTR of autophagy-related genes, including ATG9A, ATG9B, ATG16L2, SQSTM1, and EIF2AK2, harbors potential binding sites for hcmv-miR-UL70-3p. Experimental manipulation involving ectopic expression of hcmv-miR-UL70-3p demonstrated a significant reduction in rapamycin-induced autophagy, with ATG9A as its functional target. These findings establish that hcmv-miR-UL70-3p acts as an autophagy inhibitor by suppressing the expression of ATG9A.

Pesticide mediated silent neurotoxicity and its unmasking: An update on recent progress

Being human's one of the most protected organs, brain is yet most vulnerable to xenobiotics exposure. Though pesticide-mediated neurotoxicity is well-explored, the fraternity of neurotoxicologists is less focused on the phenomenon of "silent" or "clinically undetectable" neurotoxicity. Silent neurotoxicity defines continual trivial changes in the nervous system that do not manifest any overt signs of toxicity unless unmasked by any natural or experimental event. Although this perception is not novel, insufficient experimental and epidemiological evidence makes it an outlier among toxicological research. A report in 2016 highlighted the need to investigate silent neurotoxicity and its potential challenges. The limited existing experimental data unveiled the unique responsiveness of neurons following silent neurotoxicity unmasking. Concerned studies have shown that low-dose developmental exposure to pesticides sensitizes the nigrostriatal dopaminergic system towards silent neurotoxicity, making it vulnerable to advanced cumulative neurotoxicity following pesticide challenges later in life. Therefore, conducting such studies may explain the precise etiology of pesticide-induced neurological disorders in humans. With no updates on this topic since 2016, this review is an attempt to acquaint the neurotoxicologist with silent neurotoxicity as a serious threat to human health, and proof-of-concept through a narrative using relevant published data so far with future perspectives.

Proteome architecture of human-induced pluripotent stem cell-derived three-dimensional organoids as a tool for early diagnosis of neuronal disorders

BACKGROUND AND OBJECTIVES

Induced pluripotent stem cells (iPSCs) derived three-dimensional (3D) model for rare neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) is emerging as a novel alternative to human diseased tissue to explore the disease etiology and potential drug discovery. In the interest of the same, we have generated a TDP-43-mutated human iPSCs (hiPSCs) derived 3D organoid model of ALS disease. The high-resolution mass spectrometry (MS)-based proteomic approach is used to explore the differential mechanism under disease conditions and the suitability of a 3D model to study the disease.

MATERIALS AND METHODS

The hiPSCs cell line was procured from a commercial source, grown, and characterized following standard protocols. The mutation in hiPSCs was accomplished using CRISPR/Cas-9 technology and predesigned gRNA. The two groups of organoids were produced by normal and mutated hiPSCs and subjected to the whole proteomic profiling by high-resolution MS in two biological replicates with three technical replicas of each.

RESULTS

The proteomic analysis of normal and mutated organoids revealed the proteins associated with pathways of neurodegenerative disorders, proteasomes, autophagy, and hypoxia-inducible factor-1 signaling. Differential proteomic analysis revealed that the mutation in TDP-43 gene caused proteomic deregulation, which impaired protein quality mechanisms. Furthermore, this impairment may contribute to the generation of stress conditions that may ultimately lead to the development of ALS pathology.

CONCLUSION

The developed 3D model represents the majority of candidate proteins and associated biological mechanisms altered in ALS disease. The study also offers novel protein targets that may uncloud the precise disease pathological mechanism and be considered for future diagnostic and therapeutic purposes for various neurodegenerative disorders.

Hcmv-miR-UL148D regulates the staurosporine-induced apoptosis by targeting the Endoplasmic Reticulum to Nucleus signaling 1(ERN1)

The propensity of viruses to co-opt host cellular machinery by reprogramming the host’s RNA-interference machinery has been a major focus of research, however, regulation of host defense mechanisms by virus-encoded miRNA, is an additional regulatory realm gaining momentum in the arena of host-viral interactions. The Human Cytomegalovirus (HCMV) miRNAs, regulate many cellular pathways alone or in concordance with HCMV proteins, thereby paving a conducive environment for successful infection in the human host. We show that HCMV miRNA, hcmv-miR-UL148D inhibits staurosporine-induced apoptosis in HEK293T cells. We establish that ERN1 mRNA is a bonafide target of hcmv-miR-UL148D and its encoded protein IRE1α is translationally repressed by the overexpression of hcmv-miR-UL148D resulting in the attenuation of apoptosis. Unlike the host microRNA seed sequence (6–8 nucleotides), hcmv-miR-UL148D has long complementarity to 3’ UTR of ERN1 mRNA resulting in mRNA degradation. The repression of IRE1α by the hcmv-miR-UL148D further downregulates Xbp1 splicing and c-Jun N-terminal kinase phosphorylation thus regulating ER-stress and ER-stress induced apoptotic pathways. Strikingly, depletion of ERN1 attenuates staurosporine-induced apoptosis which further suggests that hcmv-miR-UL148D functions through regulation of its target ERN1. These results uncover a role for hcmv-miR-UL148D and its target ERN1 in regulating ER stress-induced apoptosis.

Ameliorative effect of fluvoxamine against colon carcinogenesis via COX-2 blockade with oxidative and metabolic stress reduction at the cellular, molecular and metabolic levels

Fluvoxamine's (FLX's) anticancer potential was investigated in pre-clinical research utilizing a DMH-induced colorectal cancer (CRC) rat model. qRT-PCR and immunoblotting validated the mechanistic investigation. The CRC condition was induced in response to COX-2 and IL-6, however, following FLX therapy, the condition returned to normal. FLX's anti-CRC potential may be attributable to COX-2 inhibition since this molecular activity was more apparent for COX-2 than IL-6. FLX repaired the altered metabolites linked to CRC rats, according to ¹H-NMR analysis. FLX was shown to be similar to 5-FU in terms of tumor protection, which may be useful in future medication development.

Human Cytomegalovirus miR-UL70-3p Downregulates the H2O2-Induced Apoptosis by Targeting the Modulator of Apoptosis-1 (MOAP1)

Human Cytomegalovirus (HCMV) is a prototypic beta herpesvirus, causing persistent infections in humans. There are medications that are used to treat the symptoms; however, there is no cure yet. Thus, understanding the molecular mechanisms of HCMV replication and its persistence may reveal new prevention strategies. HCMV evasive strategies on the antiviral responses of the human host largely rely on its significant portion of genome. Numerous studies have highlighted the importance of miRNA-mediated regulation of apoptosis, which is an innate immune mechanism that eradicates virus-infected cells. In this study, we explore the antiapoptotic role of hcmv-miR-UL70-3p in HEK293T cells. We establish that hcmv-miR-UL70-3p targets the proapoptotic gene Modulator of Apoptosis-1 (MOAP1) through interaction with its 3'UTR region of mRNA. The ectopic expression of hcmv-miR-UL70-3p mimic significantly downregulates the H₂O₂-induced apoptosis through the translational repression of MOAP1. Silencing of MOAP1 through siRNA also inhibits the H₂O₂-induced apoptosis, which further supports the hcmv-miR-UL70-3p mediated antiapoptotic effect by regulating MOAP1 expression. These results uncover a role for hcmv-miR-UL70-3p and its target MOAP1 in regulating apoptosis.

Role of HCMV miR-UL70-3p and miR-UL148D in overcoming the cellular apoptosis

The studies into the pathophysiology of viral miRNAs are still in infancy; the interspecies regulation at the miRNA level fuels the spark of the investigation into the repertoire of virus-host interactions. Reports pertaining to the viral miRNAs role in modulating/evading the host immune response are surging up; we initiated this in silico study to speculate the role of human cytomegalovirus (HCMV)-encoded miRNAs on human antiviral mechanisms such as apoptosis and autophagy. The results indicate that both the above mechanisms were targeted by the HCMV miRNAs, located in the unique long region of the HCMV genome. The proapoptotic genes MOAP1, PHAP, and ERN1 are identified to be the potential targets for the miR-UL70-3p and UL148D, respectively. The ERN1 gene plays a role in the initiation of Endoplasmic reticulum stress-induced apoptosis as well as autophagosome formation. This study shows that HCMV employs its miRNA repertoire for countering the cellular apoptosis and autophagy, particularly the mitochondrial-dependent intrinsic pathway of apoptosis. In addition, the homology studies reveal no HCMV miRNA bears sequence homology with human miRNAs.

Pattern of dyslipidemia and evaluation of non-HDL cholesterol as a marker of risk factor for cardiovascular disease in type 2 diabetes mellitus

People with type 2 Diabetes have an elevated risk for developing cardiovascular disease (CVD) for which dyslipidemia is the major contributor. Diabetic patients have characteristic pattern of dyslipidemia with decreased level of high density lipoprotein cholesterol (HDL-C) and elevated triglycerides (TG) level. However, in diabetes mellitus, low density lipoprotein cholesterol (LDL-C) which is used as one of the markers for the risk of CVD, is underestimated so in such cases the levels of non-High density lipoprotein cholesterol (non-HDL-C) can be a stronger predictor of CVD as it strongly correlates with atherogenic lipoproteins. Therefore, an attempt has been made to evaluate the level of non-HDL-C as a newer marker for the risk of cardiovascular disease and to find out the pattern of dyslipidemia in diabetes mellitus. The present study comprised of 82 type 2 Diabetic cases and 81 non-diabetic controls. Among the diabetics, the majority of the subjects (61.0%) were HDL-C dyslipidemic. However, among the controls, the maximum numbers of individuals (40.7%) were TG dyslipidemic. Diabetics have significantly elevated ratio of total cholesterol to high density lipoprotein cholesterol (TC/HDL-C) and the significant increased levels of non-high density lipoprotein cholesterol (non-HDL-C) compared to controls which can be used as markers of dyslipidemia and can also be used to predict the risk of cardiovascular disease in type 2 Diabetes Mellitus.

Serum lipid profile in patients with thyroid disorders in central Nepal

Thyroid dysfunction is a major public health problem among Nepalese population. Hence the study is aimed to find out the prevalence of thyroid dysfunction and to investigate the effect of it in serum lipids. Serum fT3, fT4, TSH, total cholesterol (TC), low density lipoprotein (LDL), high density lipoprotein (HDL) and triglycerides (TG) were measured using standardized assays. Overall thyroid dysfunction was detected in 25.7% of the study population with the higher prevalence among females. The distribution of overt hypothyroidism, subclinical hypothyroidism, overt hyperthyroidism and subclinical hyperthyroidism were 3.7%, 14.1%, 3.3% and 4.6% respectively. There was a positive association between hypothyroidism and TC>200, LDL>130 and TG>200mg/dl; 48.4% of hypothyroid patient had hypercholesterolemia and 32.3% had hypertriglyceridemia. The mean TC, LDL and TG levels were increased progressively with the increase in the serum TSH. It was noteworthy in this study that even a slight increase in serum TSH (between 6.2-10 mIU/L) showed significant increase in serum lipid level. However there was no association among patients with hyperthyroidism and control group.

Assessment of kidney stone and prevalence of its chemical compositions

Kidney stone analysis is the test done on the stone which cause problems when they block the flow of urine through or out of the kidneys. The stones cause severe pain and are also associated with morbidity and renal damage. There is also no clear understanding on the relative metabolic composition of renal calculi. Hence, the study is aimed to find out the chemical composition of it which can guide treatment and give information that may prevent more stones from forming. The study was carried out on the stones that had been sent to the department of Biochemistry (n = 99; M = 61; F = 38; Mean age: 33.6 +/- 14.4 years) Approximately 98.9% of stones were composed of oxalate, 95.9% of Calcium, 85.8% of phosphate, 62.6% of Urate, 46.4% of Ammonium and very few percentages of Carbonate.

Oxidative stress in benign prostate hyperplasia

Benign Prostate Hyperplasia (BPH) is the common health problem in ageing male. Free radicals and reactive oxygen species (ROS) are produced more with advancement of age leads to oxidative stress. This study aims to assess Malondialdehyde (MDA), the marker of lipid peroxidation and vitaminic antioxidants e.g. alpha-Tocopherol (Toc) and Ascorbate (Asc) status in plasma of BPH patients. This is a case control study conducted in Department of Biochemistry in collaboration with Dept of Surgery, BPKIHS. Forty eight (n = 48) confirmed patients of BPH and forty six (n = 46) healthy age matched controls were enrolled. Plasma MDA, Asc and alpha-Toc were estimated. Plasma MDA level showed 4.81 +/- 1.87 nmol/ml in BPH patients compared to 3.69 +/- 1.56 nmol/ml in healthy controls (p < 0.001). There were significant decrease in plasma alpha-Toc and Asc level which were 0.85 +/- 0.12 mg/dl and 0.93 +/- 0.13 mg/dl in BPH patients compared to 1.37 +/- 0.31 mg/dl and 1.44 +/- 0.38 mg/dl in healthy controls respectively. Inverse correlation of plasma MDA with a- Toc (r = -0.09) and Asc (r = -0.51) was found in BPH patients. There was mild elevation of PSA in BPH patients compared with control but was not statistically significant. Thus, our study showed the evidence of association of oxidative stress in BPH patients.

Oxidative stress in patients with benign prostate hyperplasia

Benign Prostate Hyperplasia (BPH) is a common health problem in aging male. Free radicals and Reactive Oxygen Species (ROS) are produced in overwhelming quantity with advancement of age. When in oxidative stress, these reactive species cause extensive damage to various organ in the body, may be associated with pathogenesis of BPH also. This study aimed at assessing Malondialdehyde (MDA), the marker of lipid peroxidation and anti-oxidants e.g. alpha-Tocopherol and Ascorbate status in plasma in BPH patients. Forty eight (n=48) cases of BPH and forty six (n = 46) healthy age matched controls were enrolled. Plasma MDA level showed 4.81+/-1.87 nmol/ml in cases compared to 3.69+/-1.56 nmol/ml in healthy controls (p<0.001). There were significant decrease in plasma alpha-Tocopherol and ascorbate level which were 0.85+/-0.12 mg/dl and 0.93 +/- 0.13 mg/dl in cases compared to 1.37+/-0.31 mg/dl and 1.44+/-0.38 mg/dl in healthy controls respectively. Inverse correlation of plasma MDA with alpha-Tocopherol (r = -0.09, p>0.05) and Ascorbate (r =-0.51, p=0.008) was found in BPH patients. There was mild elevation of PSA in BPH patients compared with control but was not statistically significant. Thus, our study showed the evidence of association of oxidative stress in BPH patients.