Identification of ancestral gnathostome Gli3 enhancers with activity in mammals.

Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15-21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. These results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.

In-silico Evaluation of Novel Honokiol Derivatives against Breast Cancer Target Protein LKB1.

BACKGROUND: Breast cancer is characterized by uncontrolled cell growth in the breast tissue and is a leading cause of death globally. Cytotoxic effects and reduced efficacy of currently used therapeutics insist to look for new chemo-preventive strategies against breast cancer. LKB1 gene has recently been categorized as a tumor suppressor gene where its inactivation can cause sporadic carcinomas in various tissues. Mutations in the highly conserved LKB1 catalytic domain lead to the loss of function and subsequently elevated expression of pluripotency factors in breast cancer. OBJECTIVE: The utilization of drug-likeness filters and molecular simulation has helped evaluate the pharmacological activity and binding abilities of selected drug candidates to the target proteins in many cancer studies. METHODS: The current in silico study provides a pharmacoinformatic approach to decipher the potential of novel honokiol derivatives as therapeutic agents against breast cancer. AutoDock Vina was used for molecular docking of the molecules. A 100 nano second (ns) molecular dynamics simulation of the lowest energy posture of 3'-formylhonokiol- LKB1, resulting from docking studies, was carried out using the AMBER 18. RESULTS: Among the three honokiol derivatives, ligand-protein binding energy of 3' formylhonokiol with LKB1 protein was found to be the highest via molecular docking. Moreover, the stability and compactness inferred for 3'- formylhonokiol with LKB1 are suggestive of 3' formylhonokiol being an effective activator of LKB1 via simulation studies. CONCLUSION: It was further established that 3'- formylhonokiol displays an excellent profile of distribution, metabolism, and absorption, indicating it is an anticipated future drug candidate.

Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions.

BACKGROUND: Human accelerated regions (HARs) are short conserved genomic sequences that have acquired significantly more nucleotide substitutions than expected in the human lineage after divergence from chimpanzees. The fast evolution of HARs may reflect their roles in the origin of human-specific traits. A recent study has reported positively-selected single nucleotide variants (SNVs) within brain-exclusive human accelerated enhancers (BE-HAEs) hs1210 (forebrain), hs563 (hindbrain) and hs304 (midbrain/forebrain). By including data from archaic hominins, these SNVs were shown to be Homo sapiens-specific, residing within transcriptional factors binding sites (TFBSs) for SOX2 (hs1210), RUNX1/3 (hs563), and FOS/JUND (hs304). Although these findings suggest that the predicted modifications in TFBSs may have some role in present-day brain structure, work is required to verify the extent to which these changes translate into functional variation. RESULTS: To start to fill this gap, we investigate the SOX2 SNV, with both forebrain expression and strong signal of positive selection in humans. We demonstrate that the HMG box of SOX2 binds in vitro with Homo sapiens-specific derived A-allele and ancestral T-allele carrying DNA sites in BE-HAE hs1210. Molecular docking and simulation analysis indicated highly favourable binding of HMG box with derived A-allele containing DNA site when compared to site carrying ancestral T-allele. CONCLUSION: These results suggest that adoptive changes in TF affinity within BE-HAE hs1210 and other HAR enhancers in the evolutionary history of Homo sapiens might. have brought about changes in gene expression patterns and have functional consequences on forebrain formation and evolution. METHODS: The present study employ electrophoretic mobility shift assays (EMSA) and molecular docking and molecular dynamics simulations approaches.

COVID-19 in cancer patients with diabetes in Pakistan: Clinical features and management.

Background: Diabetes and cancer are the leading causes of mortality all over the world. Infectious diseases are more common and/or life-threatening in patients with diabetes. Cancer patients with diabetes are individuals that are more susceptible to the current COVID-19 pandemic. We investigated the clinical features of survivor and non-survivor COVID-19-infected cancer patients with diabetes. Patients and Methods: We did a retrospective study of 43 diabetic cancer patients with PCR-confirmed COVID-19 infection from Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan between March 03, 2020, and May 18, 2021. These patients either were discharged from the hospital or had died by Jun 16, 2021. Clinicopathological and radiological features were compared between survivors and non-survivors by fisher's exact test and chi-square test. Results: Forty-three diabetic cancer patients with SARS-CoV-2 infection were enrolled and the majority were males 26 (60.5%). The overall mean age was 61.67 ± 11.80. 39 (90.7%) had solid tumors and 3 (7.0%) had hematological malignancies. Fever (74.4%) and dyspnea (58.1%) were the most common symptoms. Complications were reported in 36 (83.7%) patients; during the course of the disease. Additionally, all the deceased patients (n=15) had acquired the complications. 11 (25.6%) patients were admitted to an intensive care unit (ICU). Furthermore, 29 (67.4%) out of 43 patients showed abnormal features in the radiological findings. We found significantly elevated levels of C-reactive protein (P=0.005), serum lactate (P=0.01), albumin (P=0.02), alkaline phosphate (P=0.03), and neutrophil count (P=0.04) in the non-survivors as compared to the survivors. Conclusion: Cancer patients with diabetes are a vulnerable population in the current pandemic. Identifying how diabetes in cancer patients affects the severity of SARS-CoV-2 infection is crucial for the clinical management of these patients. Rigorous scrutiny of clinicopathological features of COVID-19 infected cancer patients with diabetes especially values of C-reactive protein, lactate, albumin, alkaline phosphate, neutrophils, and regular monitoring of blood glucose levels may play a critical role in the outcome of the disease.

Pan-Genome-Assisted Computational Design of a Multi-Epitopes-Based Vaccine Candidate against Helicobacter cinaedi.

Helicobacter cinaedi is a Gram-negative bacterium from the family Helicobacteraceae and genus Helicobacter. The pathogen is a causative agent of gastroenteritis, cellulitis, and bacteremia. The increasing antibiotic resistance pattern of the pathogen prompts the efforts to develop a vaccine to prevent dissemination of the bacteria and stop the spread of antibiotic resistance (AR) determinants. Herein, a pan-genome analysis of the pathogen strains was performed to shed light on its core genome and its exploration for potential vaccine targets. In total, four vaccine candidates (TonB dependent receptor, flagellar hook protein FlgE, Hcp family type VI secretion system effector, flagellar motor protein MotB) were identified as promising vaccine candidates and subsequently subjected to an epitopes' mapping phase. These vaccine candidates are part of the pathogen core genome: they are essential, localized at the pathogen surface, and are antigenic. Immunoinformatics was further applied on the selected vaccine proteins to predict potential antigenic, non-allergic, non-toxic, virulent, and DRB*0101 epitopes. The selected epitopes were then fused using linkers to structure a multi-epitopes' vaccine construct. Molecular docking simulations were conducted to determine a designed vaccine binding stability with TLR5 innate immune receptor. Further, binding free energy by MMGB/PBSA and WaterSwap was employed to examine atomic level interaction energies. The designed vaccine also stimulated strong humoral and cellular immune responses as well as interferon and cytokines' production. In a nutshell, the designed vaccine is promising in terms of immune responses' stimulation and could be an ideal candidate for experimental analysis due to favorable physicochemical properties.

An Evolutionary Insight Into the Heterogeneous Severity Pattern of the SARS-CoV-2 Infection.

The ongoing pandemic of COVID-19 has elaborated an idiosyncratic pattern of SARS-CoV-2-induced symptoms in the human host. Some populations have succumbed to the SARS-CoV-2 infection in large numbers during this pandemic, whereas others have shown a resilient side by manifesting only milder or no symptoms at all. This observation has relayed the onus of the heterogeneous pattern of SARS-CoV-2-induced critical illness among different populations to the host genetic factors. Here, the evolutionary route was explored and three genetic loci, i.e., rs10735079, rs2109069, and rs2236757, associated with COVID-19 were analyzed. Among the three, the risk allele A at genetic locus rs2236757 residing in the IFNAR2 gene was observed to have undergone recent positive selection in the African population.

Encapsulated peritoneal sclerosis.

Encapsulating peritoneal sclerosis (EPS) also known as abdominal cacoon is a rare cause of acute or subacute small bowel obstruction. It is characterized by total or partial encasement of the small bowel within a thick fibrocollagenous membrane which may be formed in response to prolonged, repetitive, and severe insult to the peritoneal mesothelium. This is frequently seen in the setting of peritoneal dialysis. However other causes may include chronic inflammation. We present a case of EPS in a male with infrequent abdominal pain, nausea and fever.

Anterior Abdominal Wall Synovial Sarcoma: A Rare Presentation.

Abdominal wall sarcoma belongs to a heterogeneous group of uncommon malignant neoplastic conditions with differentiated morphological patterns and originating from mesenchymal tissues. Soft tissue sarcomas predominantly involve the lower and upper limbs and retroperitoneum. We present a case of a 30-year-old patient, complaining of swelling in the left flank whose magnetic resonance imaging (MRI) revealed a solid tumour on the abdominal wall of the flank and biopsy turned out to be synovial sarcoma.

Molecular signatures of selection on the human GLI3 associated central nervous system specific enhancers.

The zinc finger-containing transcription factor Gli3 is a key mediator of Hedgehog (Hh) signaling pathway. In vertebrates, Gli3 has widespread expression pattern during early embryonic development. Along the anteroposterior axes of the central nervous system (CNS), dorsoventral neural pattern elaboration is achieved through Hh mediated spatio-temporal deployment of Gli3 transcripts. Previously, we and others uncovered a set of enhancers that mediate many of the known aspects of Gli3 expression during neurogenesis. However, the potential role of Gli3 associated enhancers in trait evolution has not yet received any significant attention. Here, we investigate the evolutionary patterns of Gli3 associated CNS-specific enhancers that have been reported so far. A subset of these enhancers has undergone an accelerated rate of molecular evolution in the human lineage in comparison to other primates/mammals. These fast-evolving enhancers have acquired human-specific changes in transcription factor binding sites (TFBSs). These human-unique changes within subset of Gli3 associated CNS-specific enhancers were further validated as single nucleotide polymorphisms through 1000 Genome Project Phase 3 data. This work not only infers the molecular evolutionary patterns of Gli3 associated enhancers but also provides clues for putative genetic basis of the population-specificity of gene expression regulation.

Suprasellar Meningiomas: An Experience of Four Cases With Brief Review of Literature.

Suprasellar meningiomas make a relevant differential when it comes to sellar/suprasellar masses. The most common pathology in this location is pituitary adenomas. It is imperative to differentiate the two entities based on imaging as the clinical picture, and sometimes the biochemical profile can show significant overlap. It is also essential for the neurosurgeons to have a preoperative diagnosis as the behavior of both tumors is different. This piece will give a pictorial review of the imaging features of suprasellar meningiomas, in patients who presented to us with sellar/suprasellar masses. The aim is to help the radiologists as well as fellow clinicians to diagnose this entity with confidence based on imaging.

Sarcomatoid Carcinoma of the Maxilla: A Diagnostic Dilemma.

Sarcomatoid malignant neoplasm, are extremely rare and aggressive head and neck tumours characterized by twin microscopic differentiation of epithelial cell and mesenchymal cell tumours. The clinical and histopathologic features make it difficult to distinguish sarcomatoid cancer from epithelioid sarcoma; creating a challenge for the pathologist to arrive at a diagnosis. Squamous cell carcinoma is the second most common head and neck malignancy; of which only 3% show features similar to sarcomatoid cancer. We present a case of sarcomatoid carcinoma of the maxilla. This has previously only been documented in a few case reports.

Breast Imaging Chameleon: Pseudoangiomatous Stromal Hyperplasia Presenting as Breast Malignancy.

Pseudoangiomatous stromal hyperplasia (PASH) is a benign mesenchymal proliferative lesion of the breast, often an incidental finding on breast biopsy specimens and rarely presents as a palpable lump. The case being reported is interesting as a lactating female presented with gross left breast enlargement due to a huge firm mass with skin thickening and palpable left axillary lymph nodes. A provisional diagnosis of left breast malignancy was made and the patient extensively worked up with ultrasound, CT scan, bone scan and core biopsy. The histopathology, however, revealed PASH of the breast. There was no invasive or in situ malignancy. The patient was successfully managed conservatively.

Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook.

In recent years, the number of human long noncoding RNAs (lncRNAs) that have been identified has increased exponentially. However, these lncRNAs are poorly annotated compared to protein-coding genes, posing great challenges for a better understanding of their functional significance and elucidating their complex functioning molecular mechanisms. Here we employ both community and expert curation to yield a comprehensive collection of human lncRNAs and their annotations. Specifically, LncRNAWiki (http://lncrna.big.ac.cn/index.php/Main_Page) uses a wiki-based community curation model, thus showing great promise in dealing with the flood of biological knowledge, while LncBook (http://bigd.big.ac.cn/lncbook) is an expert curation-based database that provides a complement to LncRNAWiki. LncBook features a comprehensive collection of human lncRNAs and a systematic curation of lncRNAs by multi-omics data integration, functional annotation, and disease association. These protocols provide step-by-step instructions on how to browse and search a specific lncRNA and how to obtain a range of related information including expression, methylation, variation, function, and disease association. © 2019 by John Wiley & Sons, Inc.

Cholecystocolonic Fistula.

Cholecystocolonic fistula (CCF) is a rare complication of gallstone disease with a variable clinical presentation. It is difficult to diagnose CCF pre-operatively despite modern diagnostic and imaging modalities as they are often asymptomatic or incidentally discovered, often peri-operatively. However, management of this uncommon yet important finding is not very well described in the literature. The most common fistula is the cholecystoduodenal fistula, followed by the cholecystocolonic fistula; the cholecystogastric fistula is reportedly the least commonly reported. We report our experience with three cases of cholecystocolonic fistula discovered on imaging which were subsequently confirmed through surgery.

Torsion of Wandering Spleen with Infarction.

Wandering spleen is a rare entity that results from the absence or maldevelopment of the ligaments that support the spleen in its normal location. As a result, the spleen is hypermobile and may be predisposed to hilar torsion and subsequent infarction, making it a potentially fatal abdominal emergency. We present a case of a 36-year-old Afghan female who presented with an acute abdomen, and was radiologically and surgically confirmed to have a wandering spleen with torsion and complete infarction. Knowledge of this condition and its radiological findings can play a crucial role in making a correct and timely diagnosis.

A Variant of Crossed Pulmonary Arteries in Association with Coarctation of Aorta.

Crossed or "crisscross" pulmonary arteries (CPA) are a result of an anomalous origin and course of both the pulmonary arteries from the main pulmonary trunk in which the left pulmonary artery (PA) ostium usually lies directly superior and to the right PA ostium after which they cross each other and supply their respective lungs. This condition is usually associated with conotruncal malformations and genetic syndromes. We describe a case report of an infant, suspected to have Down syndrome, who was diagnosed with CPA and coarctation of aorta on computed tomography (CT) angiography. Our case is unusual because in our patient the right PA ostium was superior and to the left of the left PA suggesting a variant of CPA that has not been documented before. Three-dimensional (3D) CT reconstruction has shown to improve the understanding of this anomaly and its unique 3D display of various angles may enhance anatomical comprehension of such complex cases.