Yousry Esam-Eldin Abo-Amer

Background and Objectives: Endoscopic biliary plastic stenting is a safe and effective temporary therapeutic modality used in various benign biliary disorders. Long-term indwelling stents for more than one year without retrieval are termed “forgotten biliary stents”. In clinical practice, the forgotten stents are underestimated and the majority of data were obtained from case reports. The aim of this study was to determine the forgotten-biliary-plastic-stent-related complications, their management, and the patients’ clinical outcomes. Materials and Methods: This retrospective study was performed at three hospitals during the period from January 2021 to December 2023. In total, 577 patients with biliary plastic stents—inserted for a variety of benign biliary conditions—were included. They were divided into two groups, as follows: group 1 included 527 patients who had biliary stents removed within 3 months, and group 2 included 50 patients with biliary stents retrieved after one year of their deployment. The stent-related complications (e.g., acute cholangitis, stent clogging, distal stent migration, new common bile duct (CBD) stone formation, and proximal stent migration) and the endoscopic management success rate were evaluated. Results: Irretrievable CBD stones were the main indication for biliary plastic stenting in both groups. The stent-related complications, number of endoscopic sessions, and hospital admissions were significantly higher in the patients with forgotten biliary stents than those with stent removal within 3 months. All the study patients were successfully managed endoscopically with uneventful outcomes. Conclusions: Based on this retrospective study, non-adherence to the endoscopists’ instructions is the main reason for retained biliary stents for more than one year. The patients with forgotten stents had significantly higher complication rates, a higher number of endoscopic sessions, and a higher number of hospital admissions than those with stents that were retrieved in the scheduled time. All patients were managed endoscopically with a technical success rate of 100%, and with no complication-related mortality.

Background and Objectives: Functional gastric stenosis, a consequence of sleeve gastrectomy, is defined as a rotation of the gastric tube along its longitudinal axis. It is brought on by gastric twisting without the anatomical constriction of the gastric lumen. During endoscopic examination, the staple line is deviated with a clockwise rotation, and the stenosis requires additional endoscopic manipulations for its transposition. Upper gastrointestinal series show the gastric twist with an upstream dilatation of the gastric tube in some patients. Data on its management have remained scarce. The objective was to assess the efficacy and safety of endoscopic balloon dilatation in the management of functional post-sleeve gastrectomy stenosis. Patients and Methods: Twenty-two patients with functional post-primary-sleeve-gastrectomy stenosis who had an endoscopic balloon dilatation between 2017 and 2023 were included in this retrospective study. Patients with alternative treatment plans and those undergoing endoscopic dilatation for other forms of gastric stenosis were excluded. The clinical outcomes were used to evaluate the efficacy and safety of balloon dilatation in the management of functional gastric stenosis. Results: A total of 45 dilatations were performed with a 30 mm balloon in 22 patients (100%), a 35 mm balloon in 18 patients (81.82%), and a 40 mm balloon in 5 patients (22.73%). The patients’ clinical responses after the first balloon dilatation were a complete clinical response (4 patients, 18.18%), a partial clinical response (12 patients, 54.55%), and a non-response (6 patients, 27.27%). Nineteen patients (86.36%) had achieved clinical success at six months. Three patients (13.64%) who remained symptomatic even after achieving the maximal balloon dilation of 40 mm were considered failure of endoscopic dilatation, and they were referred for surgical intervention. No significant adverse events were found during or following the balloon dilatation. Conclusions: Endoscopic balloon dilatation is an effective and safe minimally invasive procedure in the management of functional post-sleeve-gastrectomy stenosis.

Background & Aims: This research aimed to determine how variations in the vitamin D receptor gene affected the response of H. pylori infections to eradication therapy. Patients and Methods: On 105 adult H. Pylori-positive patients, a prospective cohort study was carried out. PCR was used to genotype all patients’ VDR gene polymorphisms. The patients in the study received standard triple eradication medication (clarithromycin 500 mg, amoxicillin 1000 mg, and omeprazole 20 mg) twice daily for 14 days. A stool test for H. pylori Ag was conducted 4 weeks following the end of treatment. Results: In our study, the usual triple therapy’s H. pylori eradication rate was 75.2%. The successful eradication of H. pylori and VDR rs 2228570 gene polymorphisms was more prevalent in CT gene polymorphism (64.6%) compared to non-responders (19.2%), while treatment failure was more prevalent in CC gene polymorphism (73.1% in non-responders compared to responders 24.1%), which is statistically significant. In regards to the eradication of H. pylori and VDR rs7975232 gene polymorphisms, the success of eradication was more prevalent in AC gene polymorphism (54.4%) vs non-responders (30.4%), while all patients (14) with gene AA (17.7%) are responders to standard treatment, while the failure of treatment was more prevalent in CC gene polymorphism (69.2% in non-responder vs 27.8% in responders) which is statistically significant. Our findings demonstrated a strong correlation between patients’ responses to H. pylori treatment and polymorphisms in the VDR gene (ApaI and TaqI) (P 0.05). Conclusion: As far as we are aware, this is the first study to identify a potential link between the FokI and Apal VDR polymorphism and treatment response in H pylori-positive patients. To evaluate the findings, more research with larger number of patients and different population is required.

Risk of hepatitis B virus reactivation (HBVr) in patients with resolved HBV infection receiving immunosuppressive therapy has been a growing concern, particularly in the era of biological and targeted therapies. HBV monitoring versus antiviral prophylaxis against HBVr in those patients remains controversial. The aim of the study was to determine the incidence of HBVr and HBV-related hepatitis in resolved HBV patients who received immunosuppressive therapy with or without antiviral prophylaxis. This retrospective study included 64 patients with resolved HBV infection who received different regimens of immunosuppressive medications, with moderate risk of HBVr, for variable underlying diseases. Patients who had chronic HBV infection or other viral infections were excluded. Patients who received B-cell depleting therapies were ruled out. They were divided into 2 groups: group 1 included 31 patients who received immunosuppressive therapy without antiviral prophylaxis, and group 2 included 33 patients who received antiviral prophylaxis (entecavir) within 2 weeks of commencing the immunosuppressive therapy. HBVr, HBV-related hepatitis, and HBV-unrelated hepatitis were assessed along a 1-year duration. The overall HBVr incidence was 1.56% (1/64). This patient who had HBVr was seen in group 1. There were no significant differences between the 2 groups regarding the incidence of HBVr, HBV-related hepatitis, HBV-unrelated hepatitis, and immunosuppressive therapy interruption along a 1-year duration. Based on this retrospective study, close monitoring was equal to antiviral prophylaxis regarding the outcome of resolved HBV patients who received moderate risk immunosuppressive therapy. HBV treatment should commence once HBVr is confirmed.

Despite the intense research work since the beginning of the pandemic, the pathogenesis of COVID-19 is not yet clearly understood. The previous mechanism of COVID-19, based on ACE2 tropism and explained through a single receptor, is insufficient to explain the pathogenesis due to the absence of angiotensin-converting enzyme 2 (ACE2) receptors in most of the affected organs. In the current study, we used the PatchDock server to run a molecular docking study of both the gonadotropin-releasing hormone receptor (GnRHR) and G-protein-coupled-receptor (GPCR) with the SARS-CoV-2 spike protein. Molecular Dynamics (MD) simulations were run to analyze the stability of the complexes using the GROMACS package. The docking results showed a high affinity between the spike protein with the GnRHR (−1424.9 kcal/mol) and GPCR (−1451.8 kcal/mol). The results of the MD simulations revealed the significant stability of the spike protein with the GnRHR and GPCR up to 100 ns. The SARS-CoV-2 spike protein had strong binding interactions with the GPCRs and GnRHRs, which are highly expressed in the brain, endocrine organs, and olfactory neurons. This study paves the way towards understanding the complex mechanism of neuroendocrine involvement and peripheral organ involvement, may explain the changing symptoms in patients due to new variants, and may lead to the discovery of new drug targets for COVID-19. In vitro studies involving genetic engineering or gene knockdown of the GPCRs and GnRHRs are needed to further investigate the role of these receptors in COVID-19 pathogenesis.

BackgroundDespite the intense work of researchers since the beginning of the pandemic, thepathogenesis of COVID-19 is not yet clearly understood. It is known that SARS-CoV-2 causeschemosensory receptor disorders and exerts its pathogenic effects through this mechanism.The systemic and multi-organ involvement in COVID-19 suggests that the pathogeneticdisorder develops through multiple receptors and signaling pathways. The previousmechanism of COVID-19, based on ACE2 tropism and explained through a single receptor, isinsufficient to explain the pathogenesis of COVID-19 due to the absence of ACE2 receptors inmost of the affected organs. In addition, there is no satisfactory explanation for themechanism by which ACE2-free organs are affected by COVID-19. In this study, we show thatthe SARS-CoV-2 spike protein binds directly to G-protein coupled receptors using molecularinsertion and stimulation analysis. We predict that the blocking of GPCRs by spike protein maybe the reason for the emergence of various organ-specific findings, especially neuroendocrinedisorders, in COVID-19. The intense location of GPCRs in the limbic system, which is the centerof emotional activity in the brain, and the thalamus, hypothalamus, and pituitary gland, whichis the center of neuroendocrine regulation, makes us think that the neuroendocrine tatulumin COVID-19 develops through GPCRs in these regions. The SARS-CoV-2 spike protein may bindto neuroendocrine cells in the brain, olfactory cells in the nasal epithelium, and peripheralendocrine tissues via GPCRs, causing neuroendocrine, hormonal, metabolic, and psychiatricsymptoms in COVID-19, especially smell and taste disorders.MethodologyIn the current study, we used the PatchDock server to run an insertion study of both theGnRHRs and GPCRs protein and the SARS-CoV-2 Spike protein. The crystal structure of theproteins was taken from RSCP ( https://www.rcsb.org/ ) with accession numbers (PDB ID 7BR3and 6P9X, respectively. We obtained the spike crystal structure with the accession number(PDB ID: 6VYB). The proteins are downloaded in PDB format. Spike-receptor protein wasinvestigated to identify conservative residues. Analysis of the binding of Spike protein withGnRHRsand GPCRS proteins to explore Spike's ability to interact with GnRHRs and GPCRs. Abinding site providing information on binding stability MD simulation of the complex,GROMOS96 43a1 force It was performed with the GROMACS 4.5.4 package using theGROMACS package.ResultsMolecular dynamics and molecular docking analysis of the simulations showed a high affinitybetween the Spike protein and both GnRHRs and GPCRs. The results showed that the spikebinds to GnRHRs with binding energy (-1424.7 k.cal/mol) and GPCRS with binding energy (-1451.8 k.cal/mol). The results obtained confirmed that the local model binds to GPCRS withthe highest insertion score (-1451.8) compared with other GNRHRScomplexes with the lowestbinding affinity, as evidenced by the insertion score (-1424.9). These results indicate betterconjugation of GnRHRs to the binding pocket of the spike receptor in the spike protein's RDB.A comparison of the binding free energy of GPCRS with GnRHRs showed that the GnRHRsprotein was found to bind to vital residues in the RBD of the spike protein. The study ofmolecular dynamics (MD) simulations revealed significant stability of the pike protein withindividual GnRHRsand GPCRS up to 100 ns.

BackgroundMore than two years have passed since the pandemic and despite all the efforts of researchers, the pathogenesis of COVID-19 has not yet been resolved. Multisystem involvement, neuroendocrine involvement, and pathophysiological changes caused by SARS-CoV-2 in peripheral organs have been shown in many studies. However, the molecular mechanism of these pathophysiological changes caused by COVID-19 has not been elucidated. The frequent mutations of SARS-CoV-2 and the change in the interaction of the virus with host cells have further complicated the pathogenetic mechanism in COVID-19. Unfortunately, the mechanism determined at the beginning of the pandemic and based on the single receptor tropism of ACE2 was insufficient to explain the pathogenesis of COVID-19. It is known that SARS-CoV-2 causes retinoid signaling defects and chemosensory receptor disorders and exerts its pathogenic effects through these mechanisms. Multisystem involvement and different clinical presentations in COVID-19 suggest that virus-host interaction develops through multiple receptors and signaling pathways. The previous mechanism described via ACE2, based on single-receptor tropism, was insufficient to elucidate the pathogenesis of COVID-19 due to the absence of ACE2 receptors in most of the affected organs. In addition, there is no satisfactory explanation for the mechanism by which ACE2-free organs are affected in COVID-19. In this regard, we think that ACE2 is not a true binding receptor for the SARS-CoV-2 spike protein. With our recent molecular docking studies, STRA6 and its GPCRs were identified as new binding receptors of the SARS-CoV-2 spike protein. These studies have brought a multi-receptor mechanism to the pathogenesis of COVID-19. The multi-receptor mechanism clearly illuminates the complex pathogenesis of retinoid signaling disorder, systemic organ involvement, neuroendocrine involvement, loss of smell and taste, and many other peripheral symptoms and signs, which are considered an enigma in the pathogenesis of COVID-19. Therefore, we suggest retinoid signaling defect as the main pathogenetic disorder in COVID-19 and STRA6 and GPCRs as the main binding receptors of SARS-CoV-2 spike protein. This new mechanism also clarifies the changing symptoms and findings in COVID-19 with each new variant. In addition, these studies have revealed new signaling pathways and drug targets for the treatment and prophylaxis of COVID-19.

BackgroundThe COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 100 million people causing over 2.4 million deaths over the world, and it is still expanding. Although, ACE2 has been identified as the principal host cell receptor of 2019-nCoV, and it is thought to play a critical role in the virus's entrance into the cell and subsequent infection, many cells can be infected by COVID-19 while also expressing little or no ACE2. Unlike other viral infections, COVID-19 is characterized by widespread and severe systemic manifestations, immune dysregulation and multi-organ involvement. In addition, the range of serious inflammatory, neuropsychiatric and autoimmune diseases called post-COVID syndromes are now left behind as disease tables. This wide and diverse spectrum of diseases seen in COVID-19 cannot be explained by the mechanism of viral tropism mediated by ACE2 and TMPRSS2 receptors. It is possible that different receptor and signaling mechanisms that cannot be explained by the viral tropism mechanism play a role in the pathogenesis of acute systemic effects and chronic post-COVID syndromes in COVID-19. It was showed that COVID-19 infection leads to a loss of smell (anosmia) but the COVID-19 entry receptors, angiotensin-converting enzyme 2 (ACE2), is not expressed in the receptor of olfactory neurons, or its generation is limited to a minor fraction of these neurons. Moreover It was demonstrated that COVID-19 could infect lymphocyte through its ACE2 receptors, but numerous studies found that lymphocytes don't express ACE2 receptors or express it with a little, insufficient amount. It is clear from the information and findings presented and addressed in our article that COVID-19 not only binds to ACE2, but also to additional receptors, leading to more disease lethality and existence of covid-19 symptoms which remain unexplained. As a result, discovering and identifying these receptors could lead to the development of new treatments that could suppress COVID-19 and reduce its severity and pathogenicity. Herein, we insilico discovered that blocking of STRA6 by the SARS-CoV-2 spike protein could disrupt the retinoid signaling mechanism and leads to pathogenetic consequences through some other inflammatory pathways.MethodsThe STRA6 receptor protein were submitted to the server for functional interaction associated network between partners for the STRING (Research Online of Interacting Genes/Proteins Data Basis version 10.0)13 .Docking study of each Spike -ACE 2 and STRA6 receptor protein were carried out using HDOCK server (http://hdock.phys.hust.edu.cn/). The binding mode of Spike -ACE 2 and STRA6 receptor protein is retrieved form the PDB https://www.rcsb.org/ with accession number (7DMU , 5sy1)ResultsOur results showed that COVID-19 Spike protein exhibited a high binding affinity for human STRA6 and a low binding energy with it. The docking score of COVID-19 spike protein with STRA6( -354.68) kcal/mol was higher than the docking score of spike protein with ACE2 (-341.21 ) kcal/mol. Spike protein Receptor Binding Domain(RDB) of COVID-19 strongly and efficiently binds to STRA6 receptor, definitely to the RDB vital residues of RBP-binding motif located in STRA6 receptor. The docking of STRA6 target protein with spike viral protein revealed the involvement of the spike protein into the extracellular and membrane part of the STRA6 receptor and amino acids residues of STRA6 along with spike protein which make interactions and play an important role in formation of complexes. The corresponding distances about the residue contacts between proteins STRA6- Spike protein complex are documented here where the STRA6- Spike protein complexes binding site are the RDB of the CHOLESTEROL in STRA6 receptor which bind with interface residue( ARG 511A , VAL 512A THR 515A ALA 516A ASN 519A with interface residue degree (2.965 , 3.595 , 3.286 , 4.592 , and 4.235) representatively, also the ability of the spike to bind to RDB of the STRA 6 protein in the ILE 131C , MET 145C , HIS 86A with interface residue( 4.961 , 4.953 and 3.271) representatively. STRA6- Spike protein complex with PDB ID (5SY1 , 6LZG).ConclusionsSTRA6 is a critical regulator of many biological processes thorough initiating cellular retinol uptake, in different organs and tissues as in immune cells for improving the immune system homeostasis in various populations. Our docking study reveals that COVID-19 spike protein binds directly to the integral membrane receptor (STRA6) in addition to its binding sites of the cholesterol. STRA6 mediates cellular uptake of retinol (vitamin A) by recognizing a molecule of RBP-retinol to trigger release and internalization of retinol . Therefore COVID-19 may leads to downregulation of STRA6 receptor leading to inhibition the regulatory function of retinoic acid and cholesterol helping in existing symptoms and complications including lymhopenia, Nuerogical disorders, Ineffective RIG-I pathway, Interferon inhibition, Cytokine storm, Diabetes, Hormonal imbalance, Thrombosis, and Smell loss. Therefore, we believe that this novel discovery that STRA6 receptor acts as a novel binding receptor for COVID-19 could explain COVID-19 severity and its common symptoms with unknown aetiology . Moreover, retinoic acid metabolism was found to be defective in COVID-19 (cytokine storm), sepsis, ARDS and SIRS .As a result reconstitution of the retinoid signaling may prove to be a valid strategy for COVID-19 management. We suggest that Vitamin A metabolites ,especially, retinoic acid will be promising and effective treatments for COVID-19 infection and its unknown aetiology symptoms. It worth mentioning that aerosolized all- trans retinoic acid and 13 cis retinoic acid is currently under clinical investigation (ClinicalTrials.gov Identifier: NCT05002530, NCT04353180)

Patients with B-cell chronic lymphocytic leukemia (CLL) have an increased risk of severe infections due to disease- and treatment-related immunodeficiency. As a result, patients with hematologic malignancies have been given priority for primary COVID-19 vaccination. Unfortunately, many studies have suggested that patients with B-cell chronic lymphocytic leukemia (CLL) who have been fully vaccinated can develop severe and often fatal complications. Therefore, adjuvants that can induce mRNA vaccine efficacy are desperately needed for this category of patients with haematological malignancies. A recent, study by Oxford University scientists showed that leucine zipper transcription factor-like 1(LZTFL1), as a candidate causal gene and its enhancer the rs17713054 A risk allele was significantly responsible for the twofold increased risk of respiratory failure from COVID-19 associated with 3p21.31.By using sequence analysis, the risk allele generates a second CCAAT/enhancer binding protein beta (CEBPB) motif in the enhancer. Moreover, neither LZTFL1 variants found in T cells nor B cells are responsible for increasing death risk from COVID-19 infection according to oxford study. Here, we propose attestable hypothesis that trans retinoic acid could enhance the immune response in vaccinated patients with B-cell chronic lymphocytic leukemia (CLL) according to the recent findings of Oxford scientists by inducing the casual gene(LZTFL1) in CD4 T cells and inhibiting (CEBPB) motif.Conclusions Haematological malignancies (blood cancers) patients are more vulnerable to COVID-19 disuse severity and mortality. Un fortunately mRNA vaccine seem to be less effective with weak immune response and insufficient level of generated antibodies in this category of patients. Therefore we suggest all trans retinoic acid is a good candidate as mRNA COVID-19 vaccine adjuvant via inducing LZTFL1 gene in CD4Tcells and this activation could improve the immune response and increase the level of the generated antibodies. Moreover LZTFL1 gene in CD4 T cells is not associated with increasing risk of COVID-19 infection because of absence of its enhancer(The risk allele of the SNP, rs17713054 A) in immune cells according to oxford recent study. In addition to all trans retinoic acid could inhibit CCAAT/enhancer binding protein beta motif that is generated by The risk allele of the SNP, rs17713054 A

BackgroundA global pandemic of pneumonia caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in Wuhan, China, at the end of 2019. Although, the ACE2 receptor has been demonstrated to be the main entry receptor of COVID-19, but our docking analysis , predicted and discovered a novel receptor termed STRA6 that may play a critical role in the pathogenicity of COVID-19 and explain the common pre and post COVID-19 symptoms with unknown etiology. STRA6 receptor expressed in many organs and immune cells, upregulated by retinoic acid jm6 (STRA6) was the first protein to be identified in a novel category of proteins, cytokine signaling transporters, due to its ability to function as both a cell surface receptor and a membrane protein that binds to retinol binding protein facilitating cellular uptake of retinol. The primary ligand of STRA6 (vitamin/retinol) was shown to be drastically reduced during COVID-19 infection, which agrees with our findings.Methods The STRA6 receptor protein were submitted to the server for functional interaction associated network between partners for the STRING (Research Online of Interacting Genes/Proteins Data Basis version 10.0)13 .Docking study of each Spike -ACE 2 and STRA6 receptor protein were carried out using HDOCK server (http://hdock.phys.hust.edu.cn/). The binding mode of Spike -ACE 2 and STRA6 receptor protein is retrieved form the PDB https://www.rcsb.org/ with accession number (7DMU , 5sy1)ResultsSurprisingly, our molecular docking based analysis showed that spike protein Receptor Binding Domain(RDB) of COVID-19 strongly and efficiently binds to STRA6 receptor, definitely to the RDB vital residues of RBP-binding motif located in STRA6 receptor. STRA6 receptor is a membrane receptor responsible for signaling and transporting of Vitamin A(Retinol) from plasma retinol binding protein (RBP) to our cells. In an outstanding manner, COVID-19 Spike protein exhibited high docking score with human STRA6 with low binding energy . The docking score of COVID-19 spike protein was stronger than the docking score of spike protein with ACE2.The surface view of complex reveals that the binding pocket of STRA6- Spike protein and Spike ACE 2 complexes with RMSD (189.44 Å , 1.00 Å ) representatively and docking score (-341.21 ,-354.68) kcal/mol the quality of the receptor and the ligand are LGscore and MaxSub ( 2.416 , 0.147 ). The spike to bind to RDB of the STRA 6 protein in the ILE 131C , MET 145C , HIS 86A with interface residue( 4.961 , 4.953 and 3.271) representatively.In conclusionSTRA6 mutations results in a broad spectrum of complication related to malformations including congenital heart defects , anophthalmia, alveolar capillary dysplasia, diaphragmatic hernia, lung hypoplasia and mental retardation. Moreover, Retinoic acid metabolism is defective in COVID-19 (cytokine storm), sepsis, ARDS and SIRS. Therefore, we believe that this novel discovery that STRA6 receptor acts as a novel binding receptor for COVID-19 will shed new light on effective treatments against COVID-19 and may explain many pre and post-covid-91 symptoms with unknown etiology . Therefore, reconstitution of the signaling of retinoid may prove to be a valid strategy for COVID-19 management. According to our findings Vitamin A supplements and retinoic acid will be promising and effective treatments for COVID-19 infection and its unknown aetiology symptoms. it worth mentioning that aerosolized all- trans retinoic acid is currently under clinical investigation (ClinicalTrials.gov Identifier: NCT05002530)