Translational and structural vaccinomics approach to design a multi-epitope vaccine against NOL4 autologous antigen of small cell lung cancer.

Small cell lung cancer (SCLC) is one of the most common cancers and it is the sixth common cause for cancer-related deaths. The high plasticity and metastasis have been a major challenge for humanity to treat the disease. Hence, a vaccine for SCLC has become an urgent need of the hour due to public health concern. Implementation of immunoinformatics technique is one of the best way to find a suitable vaccine candidate. Immunoinformatics tools can be used to overcome the limitations and difficulties of traditional vaccinological techniques. Multi-epitope cancer vaccines have become a next-generation technique in vaccinology which can be used to stimulate more potent immune response against a particular antigen by eliminating undesirable molecules. In this study, we used multiple computational and immunoinformatics approach to design a novel multi-epitope vaccine for small cell lung cancer. Nucleolar protein 4 (NOL4) is an autologous cancer-testis antigen overexpressed in SCLC cells. Seventy-five percent humoral immunity have been identified for this particular antigen. In this study, we mapped immunogenic cytotoxic T lymphocyte, helper T lymphocyte, and interferon-gamma epitopes present in NOL4 antigen and designed a multi-epitope-based vaccine using the predicted epitopes. The designed vaccine was antigenic, non-allergenic, and non-toxic with 100% applicability on human population. The chimeric vaccine construct showed stable and significant interaction with endosomal and plasmalemmal toll-like receptors in molecular docking and protein-peptide interaction analysis, thus assuring a strong potent immune response against the vaccine upon administration. Therefore, these preliminary results can be used to carry out further experimental investigations.

Anti-biofilm activity of caffeine against uropathogenic E. coli is mediated by curli biogenesis.

Biofilms are assemblages of sessile microorganisms that form an extracellular matrix around themselves and mediate attachment to surfaces. The major component of the extracellular matrix of Uropathogenic E. coli and other Enterobacteriaceae are curli fibers, making biofilms robust and resistant to antimicrobials. It is therefore imperative to screen antibiofilm compounds that can impair biofilm formation. In the present study, we investigated the curli-dependent antibiofilm activity of caffeine against UPEC strain CFT073 and commensal strain E. coli K-12MG1655.Caffeine significantly reduced the biofilm formation of both UPEC and E. coli K-12 by 86.58% and 91.80% respectively at 48 mM caffeine as determined by Crystal Violet assay. These results were further confirmed by fluorescence microscopy and Scanning Electron Microscope (SEM). Caffeine significantly reduced the cytotoxicity and survivability of UPEC. Molecular docking analysis revealed a strong interaction between caffeine and curli regulator protein (Csg D) of E. coli. The qRT-PCR data also showed significant downregulation in the expression of CsgBA and the CsgDEFG operon at both 24 mM and 48 mM caffeine. The findings revealed that caffeine could inhibit E. coli biofilm formation by regulating curli assembly and thus may be used as an alternative therapeutic strategy for the treatment of chronic E. coli biofilm-related infections.

Machine learning based predictive model and systems-level network of host-microbe interactions in post-COVID-19 mucormycosis.

Mucormycosis, a rare infection is caused by fungi Mucorales. The affiliation of mucormycosis with Coronavirus disease (COVID-19) is a rising issue of concern in India. There have been numerous case reports of association of rhino-cerebral-orbital, angioinvasive, pulmonary, respiratory and gastrointestinal tract related mucormycosis in patients with history of COVID-19. The immune dysregulation, preposterous use of steroids, interleukin-6-directed therapies and mechanical ventilation in COVID-19 immunocompromised individuals hypothesizes and predisposes to advancement of mucormycosis. The gaps in mode of presentation, disease course, diagnosis and treatment of post-COVID-19 mucormycosis requires critical analysis in order to control its morbidity and incidence and for prevention and management of opportunistic infections in COVID-19 patients. Our study performs machine learning, systems biology and bioinformatics analysis of post-COVID-19 mucormycosis in India incorporating multitudinous techniques. Text mining identifies candidate characteristics of post-COVID-19 mucormycosis cases including city, gender, age, symptoms, clinical parameters, microorganisms and treatment. The characteristics are incorporated in a machine learning based disease model resulting in predictive potentiality of characteristics of post-COVID-19 mucormycosis. The characteristics are used to create a host-microbe interaction disease network comprising of interactions between microorganism, host-microbe proteins, non-specific markers, symptoms and drugs resulting in candidate molecules. R1A (Replicase polyprotein 1a) and RPS6 (Ribosomal Protein S6) are yielded as potential drug target and biomarker respectively via potentiality analysis and expression in patients. The potential risk factors, drug target and biomarker can serve as prognostic, early diagnostic and therapeutic molecules in post-COVID-19 mucormycosis requiring further experimental validation and analysis on post-COVID-19 mucormycosis cases.

Targeting of Uropathogenic Escherichia coli papG gene using CRISPR-dot nanocomplex reduced virulence of UPEC.

Urinary tract infections (UTI) are the most common infectious diseases in the world. It is becoming increasingly tough to treat because of emergence of antibiotic resistance. So, there is an exigency to develop novel anti-virulence therapeutics to combat multi-drug resistance pathogenic strains. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) discovery has revolutionized the gene editing technology for targeted approach. The greatest obstacle for CRISPR/Cas9 is cargo delivery systems and both viral and plasmid methods have disadvantages. Here, we report a highly efficient novel CRISPR based gene editing strategy, CRISPR-dots for targeting virulence factor Fimbrial Adhesion (papG gene), the bacterial adhesion molecule. Carbon quantum dots (CQD) were used as a delivery vehicle for Cas9 and gRNA into CFT073, a UPEC strain. CQDs were covalently conjugated to cas9 and papG-targeted guide RNA (gRNA) forming a nanocomplex CRISPR-dots (Cri-dots) as confirmed by DLS and transmission electron microscopy. Cri-dots-papG significantly targeted papG as demonstrated by decrease in the expression of papG.Further papG deficient UPEC had significantly reduced adherence ability and biofilm forming ability as demonstrated by fluorescence microscopy and scanning electron microscopy. Also, papG deficient UPEC had reduced virulence as shown by significantly increased survival of Caenorhabditis elegans (C. elegans) worms compared to UPEC. Our findings suggest that targeting of papG gene using Cri-dots nanocomplexes significantly reduced the pathogenicity of UPEC. Thus, Cri-dots nanocomplex offer a novel anti-bacterial strategy against multi-drug resistant UPEC.

In-silico study of peptide-protein interaction of antimicrobial peptides potentially targeting SARS and SARS-CoV-2 nucleocapsid protein.

This study is an attempt to find a suitable therapy using antimicrobial peptides (AMPs) by identifying peptide-protein interaction of AMPs and nucleocapsid protein of SARS and SARS-CoV- 2. The AMPs were shortlisted from the APD3 database (Antimicrobial peptide database) based on various physicochemical parameters. The binding efficacy of AMPs was measured using the lowest energy score of the docked complexes with 10 selected AMPs. For SARS-CoV, AP00180 showed the best pose with a binding affinity value of - 6.4 kcal/mol. Prominent hydrogen bonding interactions were observed between Lys85 (nucleocapsid receptor) and Arg13 (antimicrobial peptide ligand) having the least intermolecular distance of 1.759 Å. For SARS-CoV-2, AP00549 was docked with a binding affinity value of - 3.4 kcal/mol and Arg119 and Glu14 of receptor nucleocapsid protein and ligand AMP having the least intermolecular distance of 2.104 The dynamic simulation was performed at 50 ns to check the stability of the final docked complexes, one with each protein. The two best AMPs were AP00180 (Human Defensin-5) for SARS and AP00549 (Plectasin) for SARS-CoV-2. From positive results of dynamic simulation and previously known knowledge that some AMPs interact with the nucleocapsid of coronaviruses, these AMPs might be used as a potential therapeutic agent for the treatment regime of SARS-CoV-2 and SARS infection. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40203-021-00103-z.

Leukemia associated RUNX1T1 gene reduced proliferation and invasiveness of glioblastoma cells.

RUNX1T1 has been found to be mutated in different cancers such as prostate, lung, colon, and breast cancer. A recent computational study involving the TCGA database of glioma patients found RUNX1T1 as one of the downregulated driver genes associated with poor overall survival of glioma patients. Hypoxia-inducible factor 1α (HIF1α) is upregulated in glioma and has been associated with the severity and drug resistance of glioma. Previously, we have shown that RUNX1T3 degrades HIF1α affecting the proliferation of leukemia cells. We hypothesize that RUNX1T1 might be associated with the growth and development of glioma through the regulation of HIF1α. We have evaluated the expression level of RUNX1T1 at different stages of glioma and the effect of RUNX1T1 on the proliferation and invasiveness of glioblastoma cells in vitro. We further looked at the effect of RUNX1T1 on the expression and stability of HIF1α in vitro. Expression of RUNX1T1 was significantly downregulated, both at RNA and protein levels in glioma samples as studied by quantitative real-time polymerase chain reaction and immunohistochemistry. While expression of HIF1α was higher in glioma tissues compared with its level in the normal brain. In vitro studies demonstrated that RUNX1T1 interacted with HIF1α and recruited HIF1α modification factor such as PHD2 and GSK3ß causing hydroxylation of HIF1α following ubiquitination by FBW7. RUNX1T1 led to the degradation of HIF1α and decreased proliferation/invasiveness of glioblastoma cell lines. Further, RUNX1T1 increased the effectiveness of temozolomide (TMZ), a conventional glioma drug toward glioblastoma cell lines. This study indicates that downregulation of RUNX1T1 might play an important role in the severity and development of glioma.

Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach.

Reactive Arthritis (ReA), a rare seronegative inflammatory arthritis, lacks exquisite classification under rheumatic autoimmunity. ReA is solely established using differential clinical diagnosis of the patient cohorts, where pathogenic triggers linked to enteric and urogenital microorganisms e.g. Salmonella, Shigella, Yersinia, Campylobacter, Chlamydia have been reported. Inflammatory Bowel Disease (IBD), an idiopathic enteric disorder co-evolved and attuned to present gut microbiome dysbiosis, can be correlated to the genesis of enteropathic arthropathies like ReA. Gut microbes symbolically modulate immune system homeostasis and are elementary for varied disease patterns in autoimmune disorders. The gut-microbiota axis structured on the core host-microbe interactions execute an imperative role in discerning the etiopathogenesis of ReA and IBD. This study predicts the molecular signatures for ReA with co-evolved IBD through the enveloped host-microbe interactions and microbe-microbe 'interspecies communication', using synonymous gene expression data for selective microbes. We have utilized a combinatorial approach that have concomitant in-silico work-pipeline and experimental validation to corroborate the findings. In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. Cross validation of the target/s or biomarker/s was done by targeted gene expression analysis following a non-probabilistic convenience sampling. Studies were performed to substantiate the host-microbe disease network consisting of protein-marker-symptom/disease-pathway-drug associations resulting in possible identification of vital drug targets, biomarkers, pathways and inhibitors for IBD and ReA.Our study identified Na(+)/H(+) anti-porter (NHAA) and Kynureninase (KYNU) to be robust early and essential host-microbe interacting targets for IBD co-evolved ReA. Other vital host-microbe interacting genes, proteins, pathways and drugs include Adenosine Deaminase (ADA), Superoxide Dismutase 2 (SOD2), Catalase (CAT), Angiotensin I Converting Enzyme (ACE), carbon metabolism (folate biosynthesis) and methotrexate. These can serve as potential prognostic/theranostic biomarkers and signatures that can be extrapolated to stratify ReA and related autoimmunity patient cohorts for further pilot studies.

In silico screening of potential lead compounds against 3-oxo-5-alpha-steroid 4-dehydrogenase 2 for treating prostate cancer.

Increased levels of androgen dihydrotestosterone is responsible for the development of prostate cancer in humans. The formation of dihydrotestosterone from testosterone is catalysed by an intracellular enzyme 3-oxo-5-alpha-steroid 4-dehydrogenase 2, which is found to be the most promising target for the treatment of prostate cancer. In this study, the identification of a therapeutic inhibitor of 3-oxo-5-alpha-steroid 4-dehydrogenase 2 using in silico approach has been done to treat prostate cancer. ZINC biogenic compounds (Zbc) database was used for docking and virtual screening against the predicted structure. The MD simulation of the docked complex was done to ensure the ligand interaction with 3-oxo-5-alpha-steroid 4-dehydrogenase 2 for 100 ns. The validation results of the established 3D structure strongly favoured the acceptance reliability of the predicted model. Zbc was screened against 3-oxo-5-alpha-steroid 4-dehydrogenase 2 and ZINC00277963 was selected as the lead with significant docking pose with docking score of -9.961 kcal/mole and having -63.182 kcal/mol binding affinity. The protein-ligand complex system remained stable throughout the MD run and seven stable hydrogen bonds were observed. Our study proposes a lead compound that could be validated by in vitro experimental method(s), suggesting its ability to function as a prospective therapeutic drug against prostate cancer.

Development and Implementation of Maternity Dashboard in Regional Hospital for Quality Improvement at Ground Level: A Pilot Study.

OBJECTIVES: We sought to develop and implement a Maternity Dashboard to improve the quality of health care at the ground level. METHODS: We conducted a prospective, descriptive cross-sectional study, involving patients with high-risk pregnancies who had been referred to Nizwa Hospital, Oman. The selection of quality indicators was based on the prototype of clinical outcomes from the Royal College of Obstetricians and Gynecologists. The Maternity Dashboard team adapted local parameters and used preselected general parameters, based on clinical observations, to develop the dashboard. RESULTS: The issues posing a threat to Nizwa Hospital in becoming a world-class healthcare facility were: overbooked outpatient department, insufficient staff, and more junior doctors compared to senior doctors and consultants. Additionally, being pioneers, naturally, the dashboard development team faced difficulties while handling adverse situations. More time, guidance, and standardization of quality indicators are desirable. CONCLUSIONS: Following the approval for a Maternity Dashboard in Nizwa Hospital, the data compiled in an Excel sheet are transmitted manually every month for display on the dashboard in the delivery suite. It is intended to make data collected and dissemination completely automated in the future with the help of the Al-Shifa Healthcare Information System. Expansion of the idea of a Maternity Dashboard to other hospitals and specialties at the regional and tertiary level of the health care system in Oman and a comparison of the standard of health care provided between hospitals based on similar quality indicators would be the next milestone.

Association of Inflammatory Bowel Disease with Arthritis: Evidence from In Silico Gene Expression Patterns and Network Topological Analysis.

Inflammatory bowel disease (IBD) is an idiopathic prolonged ailment accountable for inflammatory conditions of the intestine. Moreover, arthritis is responsible for joints' stiffness and painful inflammation. IBD shows certain articular extra-intestinal manifestations associating IBD with arthritis. IBD associated arthritis is found to be linked with ankylosing spondylitis (AS). The present study insights for the potential and putative drug targets and biomarkers of IBD associated with arthritis using in silico approaches. Microarray data analysis of datasets involving IBD affected and AS affected vs controls were done to explore the differentially expressed genes (DEGs). In majority of the datasets, the common DEGs found were sterile alpha motif domain containing 9 like (SAMD9L), inhibin beta A subunit (INHBA), transmembrane protein 45A (TMEM45A) and transmembrane and tetratricopeptide repeat containing 1 (TMTC1). The common functions and pathways found between the DEGs were control of macromolecule metabolism process, control of metabolic process, control of primary metabolic process, and control of protein metabolic process, cell differentiation, organ development, single-organism development process, multicellular organism development process, development of system, single-multicellular organism development process, developmental process, development of anatomical structure, multicellular organismal development process, control of biological process, cell proliferation, hematopoietic progenitor cell differentiation and immune system process. TMTC1 and INBHA were found to be more biologically significant genes according to the topological properties of the network. This study also suggests that TMTC1, INBHA, TMEM45A and SAMD9L DEGs and their accompanying pathways might have the potential to be exploited as drug targets and biomarkers in the diagnosis and/or treatment of IBD linked arthritis and warrants for further experimental validation.

A study of post-caesarean section wound infections in a regional referral hospital, oman.

OBJECTIVES: The aim of this study was to determine the incidence of surgical site infections (SSI) in patients undergoing a Caesarean section (CS) and to identify risk factors, common bacterial pathogens and antibiotic sensitivity. SSI significantly affect the patient's quality of life by increasing morbidity and extending hospital stays. METHODS: A retrospective cross-sectional study was conducted in Nizwa Hospital, Oman, to determine the incidence of post-Caesarean (PCS) SSI from 2001 to 2012. This was followed by a case-control study of 211 PCS cases with SSI. Controls (220) were randomly selected cases, at the same hospital in the same time period, who had undergone CS without any SSI. Data was collected on CS type, risk factors, demographic profile, type of organism, drug sensitivity and date of infection. RESULTS: The total number of PCS wound infections was 211 (2.66%). There was a four-fold higher incidence of premature rupture of the membranes (37, 17.53%) and a three-fold higher incidence of diabetes (32, 15.16%) in the PCS cases compared with controls. The most common organisms responsible for SSI were Staphylococcus aureus (66, 31.27%) and the Gram-negative Escherichia coli group (40, 18.95%). The most sensitive antibiotics were aminoglycoside and cephalosporin. Polymicrobial infections were noted in 42 (19.90%), while 47 (22.27%) yielded no growth. A high incidence of associated risk factors like obesity, hypertension, anaemia and wound haematoma was noted. CONCLUSION: Measures are recommended to reduce the incidence of SSI, including the implementation of infection prevention practices and the administration of antibiotic prophylaxis with rigorous surgical techniques.

Methotrexate treatment of ectopic pregnancy: experience at nizwa hospital with literature review.

OBJECTIVES: Ectopic pregnancy occurs when the embryo fails to implant within the uterine cavity. Methotrexate, a folic acid antagonist has been widely used to treat ectopic pregnancy. The aim of this study is to determine the efficacy of methotrexate treatment for ectopic pregnancies in our settings which will in-turn help us reduce maternal mortality and morbidity. METHODS: This was a retrospective review of 60 cases of ectopic pregnancy treated with single dose methotrexate in Nizwa hospital, Oman. Demographic data, clinical presentation, treatment progress, outcome, side effects and future fertility follow up were analysed using a computer database. Selection criteria included hemodynamically stable women with ß-hcg level of ≤5000 mIU/ml, adnexal mass ≤4 cm, absent cardiac activity and hemoperitoneum less than 100 ml. Human chorionic gonadotrophin (hcg) assay and clinical presentation were used to determine cases which warranted surgical intervention. RESULTS: The success rate of single dose methotrexate therapy in our study was 65% (n=39) and 35% (n=21) required surgical intervention compared to reported success rate of 67-100% published in various studies. Careful selection of cases and confining strictly to the criteria improved the success rate from 40% to 60% in five and half years of the study. The mean average time of resolution of ectopic pregnancy was 32 days for a single dose and 58 days for repeat second or third doses. Eight cases of pregnancy of unknown location were treated successfully with Methotrexate. No major side effects were noted. A successful fertility outcome of 30% in the first year followed by 13.3% in the subsequent second year with a secondary infertility rate of 11.6% was observed in this study. CONCLUSION: Methotrexate treatment of ectopic pregnancies is safe and effective with no major side effects. Intramuscular methotrexate has the advantage of tubal conservation and saves patients from requiring surgery. It is easier to administer than intraoperative route, which is by laparoscopy and needs expertise. Our study showed single dose methotrexate to be an effective treatment option for selected patients with unruptured tubal ectopic pregnancy.

Genome subtraction for novel target definition in Salmonella typhi.

Large genomic sequencing projects of pathogens as well as human genome leads to immense genomic and proteomic data which would be very beneficial for the novel target identification in pathogens. Subtractive genomic approach is one of the most useful strategies helpful in identification of potential targets. The approach works by subtracting the genes or proteins homologous to both host and the pathogen and identify those set of gene or proteins which are essential for the pathogen and are exclusively present in the pathogen. Subtractive genomic approach is employed to identify novel target in salmonella typhi. The pathogen has 4718 proteins out of which 300 are found to be essential (" indispensable to support cellular life") in the pathogen with no human homolog. Metabolic pathway analyses of these 300 essential proteins revealed that 149 proteins are exclusively involved in several metabolic pathway of S. typhi. 8 metabolic pathways are found to be present exclusively in the pathogen comprising of 27 enzymes unique to the pathogen. Thus, these 27 proteins may serve as prospective drug targets. Sub-cellular localization prediction of the 300 essential proteins was done which reveals that 11 proteins lie on the outer membrane of the pathogen which could be probable vaccine candidates.