In-silico evaluation of the T-cell based immune response against SARS-CoV-2 omicron variants.

During of COVID-19 pandemic, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has continuously evolved, resulting in the emergence of several new variants of concerns (VOCs) with numerous mutations. These VOCs dominate in various regions due to increased transmissibility and antibody evasion, potentially reducing vaccine effectiveness. Nonetheless, it remains uncertain whether the recent SARS-CoV-2 VOCs have the ability to circumvent the T cell immunity elicited by either COVID-19 vaccination or natural infection. To address this, we conducted in-silico analysis to examine the impact of VOC-specific mutations at the epitope level and T cell cross-reactivity with the ancestral SARS-CoV-2. According to the in-silico investigation, T cell responses triggered by immunization or prior infections still recognize the variants in spite of mutations. These variants are expected to either maintain their dominant epitope HLA patterns or bind with new HLAs, unlike the epitopes of the ancestral strain. Our findings indicate that a significant proportion of immuno-dominant CD8 + and CD4 + epitopes are conserved across all the variants, implying that existing vaccines might maintain efficacy against new variations. However, further in-vitro and in-vivo studies are needed to validate the in-silico results and fully elucidate immune sensitivities to VOCs.

Phytochemicals of Different Medicinal Herbs as Potential Inhibitors Against Dengue Serotype 2 Virus: A Computational Approach.

Dengue is one of the major mosquito-borne infectious diseases of the present century, reported to affect about 100-400 million people globally. The lack of effective therapeutic options has inspired several in vitro and in silico studies for the search of antivirals. Our previous study revealed the anti-dengue activity of different plant extracts from Plumeria alba, Bacopa monnieri, Vitex negundo, and Ancistrocladus heyneanus. Therefore, the current in silico study was designed to identify the phytochemicals present in the aforementioned plants, which are possibly responsible for the anti-dengue activity. Different plant databases as well as relevant literature were explored to find out the major compounds present in the above-stated plants followed by screening of the retrieved phytochemicals for the assessment of their binding affinity against different dengue viral proteins via molecular docking. The best poses of protein-ligand complexes obtained after molecular docking were selected for the calculation of binding free energy via MM-GBSA method. Based on the highest docking score and binding energy, six complexes were considered for further analysis. To analyze the stability of the complex, 100 ns molecular dynamics (MD) simulations were carried out using Desmond module in the Schrodinger suite. The MD simulation analysis showed that four compounds viz. liriodendrin, bacopaside VII, isoorientin, and cynaroside exhibited stability with viral targets including the RdRp, NS3 helicase, and E protein indicating their potential as novel anti-dengue antivirals.

Metagenomic Analysis of Viromes of Aedes Mosquitoes across India.

Metagenomic analysis of Aedes aegypti and Ae. albopictus mosquitoes from diverse geographical regions of India revealed the presence of several insect viruses of human interest. Most abundant reads found in Ae. aegypti mosquitoes were of Phasi Charoen-like virus (PCLV), Choristoneura fumiferana granulovirus (CfGV), Cell fusing agent virus (CFAV), and Wenzhou sobemo-like virus 4 (WSLV4), whereas WSLV4 and CfGV constituted the highest percentage of reads in Ae. albopictus viromes. Other reads that were of low percentage included Hubei mosquito virus 2 (HMV2), Porcine astrovirus 4 (PAstV4), and Wild Boar astrovirus (WBAstV). PCLV and CFAV, which were found to be abundant in Ae. aegypti viromes were absent in Ae. albopictus viromes. Among the viromes analyzed, Ae. aegypti sampled from Pune showed the highest percentage (79.82%) of viral reads, while Ae. aegypti mosquitoes sampled from Dibrugarh showed the lowest percentage (3.47%). Shamonda orthobunyavirus (SHAV), African swine fever virus (ASFV), Aroa virus (AROAV), and Ilheus virus (ILHV), having the potential to infect vertebrates, including humans, were also detected in both mosquito species, albeit with low read numbers. Reads of gemykibivirus, avian retrovirus, bacteriophages, herpesviruses, and viruses infecting protozoans, algae, etc., were also detected in the mosquitoes. A high percentage of reads in the Ae. albopictus mosquito samples belonged to unclassified viruses and warrant further investigation. The data generated in the present work may not only lead to studies to explain the influence of these viruses on the replication and transmission of viruses of clinical importance but also to find applications as biocontrol agents against pathogenic viruses.

Tumour-infiltrating lymphocyte subsets and their individual prognostic impact in oral squamous cell carcinoma.

AIMS: Current understanding of oral squamous cell carcinoma (OSCC) is incomplete with regard to prognostic factors that lead to the considerable heterogeneity in treatment response and patient outcomes. We aimed to evaluate the impact of individual tumour-infiltrating lymphocyte (TIL) subsets on prognosis as a possible rationale for this, in a retrospective observational study. METHODS: Immunohistochemistry was performed to quantitatively assess cell densities of CD3+, CD20+, CD4+, CD8+ and FOXP3+TIL subsets in 50 surgically treated OSCC cases. Results were correlated with disease-free survival (DFS) and overall survival (OS). Receiver operating characteristic curve analysis and Youden index were applied to determine prognostically significant cut-off values. RESULTS: Mean counts for CD3+, CD4+, CD8+, CD20+ and FOXP3+TILs were 243, 52, 132, 53 and 116 cells per high power field, respectively. High CD8+ and low FOXP3+TIL counts, and high ratio of CD8:FOXP3 were significantly associated with longer DFS and OS, as well as with improved tumour-host interface parameters. CONCLUSIONS: Host immune response and its interaction with cancer cells have a significant impact on OSCC outcomes, with some TIL subsets being more clinically relevant than others. High cytotoxic T-cell (CD8) and low Treg (FOXP3) counts, and high cytotoxic T-cell to Treg (CD8:FOXP3) ratio are significantly associated with favourable prognosis. These results may serve as a leading point in identifying novel therapeutic agents that can redesign the tumour immune microenvironment by reducing infiltrating FOXP3-lymphocytes, and modifying their signalling pathways.

Cytological diagnosis of olfactory neuroblastoma at metastatic sites, with emphasis on role of insulinoma-associated protein 1 immunocytochemistry.

BACKGROUND: Olfactory neuroblastoma (ONB) is a rare neuroectodermal tumor with a propensity for lymph node and distant metastases in a proportion of cases, presenting opportunities for cytological diagnosis. Insulinoma-associated protein 1 (INSM1) is a recently identified marker of neuroendocrine differentiation with higher sensitivity and specificity than traditional neuroendocrine immunostains used in diagnosis of ONB. METHODS: Archival aspirates diagnosed as metastatic ONB were retrieved and reviewed for described characteristics of ONB. Spare direct smears with sufficient cellular material from each case were selected, if available, and immunocytochemistry for INSM1 was performed on the destained alcohol-fixed smears. INSM1 was also performed on non-neuroendocrine malignant round cell tumors (MRCT). RESULTS: Seven fine needle aspirates (FNA) from five patients were identified, all of which showed a small round cell tumor with fine to coarse granular chromatin. Most cases had moderate to high cellularity, comprised of loosely cohesive clusters and dispersed cells. While two-cell pattern, nuclear streaking and moulding were frequent, background neuropil, fibrillary cytoplasm, and rosettes were uncommon. INSM1 immunostaining performed on spare direct smears showed strong positivity in 30%-100% of tumor cells (mean: 62%) in all aspirates tested (100%). In comparison with other immunostains, INSM1 showed more robust staining, and was easier to interpret. All non-neuroendocrine MRCTs were negative for INSM1. CONCLUSION: Metatstatic ONB can resemble other small round cell tumors, as all the diagnostic features of ONB may not be readily evident. INSM1 immunocytochemistry has high sensitivity and specificity and can reliably be used as a single marker to support the cytomorphology for a confirmatory diagnosis of ONB, even on direct smears if a cell block is not available.

Immunohistochemical Analysis of the Expression of Cytokeratins in Acquired Cholesteatoma and Its Clinico-Radiological Correlation.

BACKGROUND AND OBJECTIVES: Cholesteatomatous chronic otitis media acquires epithelial proliferation and differentiation characteristics, which render it able to erode the underlying bone and cause complications. We attempt to characterize the cholesteatoma epithelium by observing the expression of cytokeratins (such as 34ße12, CK17, and CK13) and Ki67 among patients with cholesteatoma with different aggressiveness as compared to disease-free controls. Subjects and. METHODS: In this prospective study (2017-2021), we enrolled all consenting consecutive patients with cholesteatomatous chronic otitis media. They were staged in accordance with the staging guidelines of the European Academy of Otology and Neurotology and the Japanese Otological Society. Bony external auditory canal (EAC) skin specimens of the patients undergoing tympanoplasty were chosen as controls. We did an immunohistochemical analysis of the cholesteatoma specimens and normal bony EAC controls by observing the expression of 34ße12, CK17, CK13, and Ki67 across the layers of the epithelium. Fisher's exact test and chi-square test were used to evaluate any statistical significance between the cases and the controls, and the subgroups were made based on the clinical stage. RESULTS: An increased expression of CK17 (p<0.001), CK13 (p<0.03), and Ki67 (p<0.001) was observed in cholesteatoma specimens when compared to normal bony EAC controls. Also, there was a loss of expression of 34ße12 in a subset of cholesteatoma specimens, all of which showed full-thickness expression of CK13. There was no difference in the expression of cytokeratin among specimens from patients belonging to different subgroups based on clinical stage, age, sex, duration of ear symptoms, or type of hearing loss (conductive vs. sensorineural). CONCLUSIONS: The majority of cholesteatoma specimens significantly overexpressed CK17, CK13, and Ki67 when compared to normal bony EAC skin controls, while a subset showed loss of expression of 34ße12, which provides some insight into its pathogenesis.

Exploring the structural aspects and therapeutic perspectives of cyanobacterial phycobiliproteins.

Phycobiliproteins (PBPs) of cyanobacteria and algae possess unique light harvesting capacity which expand the photosynthetically active region (PAR) and allow them to thrive in extreme niches where higher plants cannot. PBPs of cyanobacteria/algae vary in abundance, types, amino acid composition and in structure as a function of species and the habitat that they grow in. In the present review, the key aspects of structure, stability, and spectral properties of PBPs, and their correlation with ecological niche of cyanobacteria are discussed. Besides their role in light-harvesting, PBPs possess antioxidant, anti-aging, neuroprotective, hepatoprotective and anti-inflammatory properties, which can be used in therapeutics. Recent developments in therapeutic applications of PBPs are reviewed with special focus on 'route of PBPs administration' and 'therapeutic potential of PBP-derived peptide and chromophores'.

Metastases to the Parotid Gland: Study from a Tertiary Care Centre.

BACKGROUND: Metastases account for 6-25% of parotid tumors, often presenting dilemmas in their diagnosis. METHODS: Parotid metastases diagnosed on histology/cytology were retrieved. MUC2, MUC5AC, androgen receptor immunohistochemistry was performed in select cases. RESULTS: Fifty-one samples were identified from 42 patients, including 14 aspirates, 7 biopsies and 30 parotidectomies. Previous history was available in 17 cases, 13 parotidectomies accompanied excision of the primary, and relevant clinical data was unavailable for 12 patients. Majority (81%) had head and neck primaries; eye and ocular adnexa were the commonest subsite (52.4%), and sebaceous carcinoma the commonest histology (33%). When history was unavailable, most metastases were initially diagnosed as poorly differentiated carcinoma/malignant tumor, or mucoepidermoid carcinoma on cytology. CONCLUSIONS: Intraparotid metastases encompass a wide spectrum, often mimicking primary salivary gland neoplasms, particularly on limited samples. Metastases should be considered when histological/cytological features are unusual; detailed clinical information and ancillary techniques aid in arriving at an accurate diagnosis.

In vivo lentiviral vector gene therapy to cure hereditary tyrosinemia type 1 and prevent development of precancerous and cancerous lesions.

Conventional therapy for hereditary tyrosinemia type-1 (HT1) with 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC) delays and in some cases fails to prevent disease progression to liver fibrosis, liver failure, and activation of tumorigenic pathways. Here we demonstrate cure of HT1 by direct, in vivo administration of a therapeutic lentiviral vector targeting the expression of a human fumarylacetoacetate hydrolase (FAH) transgene in the porcine model of HT1. This therapy is well tolerated and provides stable long-term expression of FAH in pigs with HT1. Genomic integration displays a benign profile, with subsequent fibrosis and tumorigenicity gene expression patterns similar to wild-type animals as compared to NTBC-treated or diseased untreated animals. Indeed, the phenotypic and genomic data following in vivo lentiviral vector administration demonstrate comparative superiority over other therapies including ex vivo cell therapy and therefore support clinical application of this approach.

Ocular non-teratoid medulloepithelioma with teratoid metastases in ipsilateral intraparotid lymph nodes.

PURPOSE: To describe a rare presentation of a case of intraocular non-teratoid medulloepithelioma with teratoid metastases in ipsilateral intraparotid lymph nodes. CASE DESCRIPTION: A 9-year-old male child with previous history of ciliary body non-teratoid medulloepithelioma presented with a swelling in the right pre-auricular region for 1 month. Magnetic resonance imaging and positron emission tomography-computed tomography showed a right intraparotid mass with enlarged ipsilateral cervical lymph nodes. A core biopsy was taken from the lesion, which on microscopy showed a tumor composed of small round cells arranged in cords, tubules lined by multilayered cells, and in cribriform pattern. These cells were embedded in a hypocellular, loose myxoid matrix. Based on the histopathological characteristics and previous history, a diagnosis of medulloepithelioma metastastic to ipsilateral parotid gland was made. The patient underwent right total conservative parotidectomy and bilateral neck dissection. Histopathological examination revealed metastatic medulloepithelioma in five out of eight intraparotid lymph nodes, with extranodal extension into the adjacent parotid parenchyma. Foci of hyaline cartilage were identified within the tumor, leading to a diagnosis of metastatic teratoid medulloepithelioma. CONCLUSION: Intraparotid lymph node metastases from intraocular medulloepithelioma is a rare possibility and we recommend that the parotid should be evaluated in cases of intraocular medulloepithelioma at initial presentation as well as during the follow-up period. Also, metastasis should be considered in all pediatric patients with solitary mass lesions showing unconventional histology for a primary parotid neoplasm.