Primitive neuroectodermal tumor of the kidney: a rare case

Background

Primitive neuroectodermal tumor commonly occurs in bones and is equivalent to Ewing’s sarcoma. Very few cases have been reported in the literature and they had a very different presentation and very aggressive behavior.

Case presentation

We present a case of a young 23-year-old male who presented with complaints of pain in left lumbar region of abdomen since 8 months and hematuria off and on. CT scan of the abdomen was done which revealed a large heterogeneously enhancing mass lesion in the left lumbar region arising from the superior and mid-pole of left kidney showing multiple non-enhancing necrotic areas. A diagnosis of left renal cell carcinoma was kept. Through the transperitoneal approach, the left kidney was approached and a left radical nephrectomy was done. The histopathology report revealed the tumor cells to be positive for CD99 and focally positive for Vimentin and negative for cytokeratin thereby making a diagnosis of primary neuroectodermal tumor (PNET).

Conclusions

Renal PNET is a rare renal malignancy that should be kept in the differential diagnosis of a renal SOL especially when it is a presenting feature in adolescent and young adult. It has a very aggressive course and multimodal therapy has to be considered in its treatment

ADULT-ONSET CYSTIC HYGROMA IN AXILLA: A RARE CASE REPORT FROM INDIA AND LITERATURE REVIEW

Background. Cystic hygroma (CH), occurs in 1/6000 live births and in 90% of cases develops in age less than 2 years old. They are mainly located in cervicofacial region. Adult-onset CH is very rare. Objective. The aim of this study is to review literature to discuss the clinical presentation, diagnosis, and treatment of CH in adults through a case report of unilocular CH in the axillary region in an adult male from India. Methods. A first case report of unilocular CH in axillary region in an adult male from India is being investigated. Results. Here we report a case of unilocular CH in the axillary region in a 49-year-old male with a 14x16x8 cm cystic swelling in left axilla with a history of aspiration failure. Contrast-enhanced MRI (CEMRI) showed well-defined thin walled, unilocular cystic lesion which appeared hyperintense on T2 & STIR and hypointense on T1W1 and showed thin peripheral rim of enhancement on post contrast images. The patient underwent surgical excision and the diagnosis of a pathological CH was established. His postoperative recovery was uneventful and had no evidence of recurrence. Conclusion. Due to rarity of adult-onset unilocular CH in axilla, its evaluation for prompt diagnosis and definitive treatment to prevent recurrence and complications is urgent. Furthermore, this is the first reported case from India which has been successfully managed at a peripheral hospital in Northeast-India and our report of this case contributes to the evidences supporting the role of CH in a differential diagnosis for masses in the adult axilla, especially in acute phase with no predisposing factors.

Artemisinin Binds and Inhibits the Activity of Plasmodium falciparum Ddi1, a Retroviral Aspartyl Protease

Reduced sensitivity of the human malaria parasite, Plasmodium falciparum, to Artemisinin and its derivatives (ARTs) threatens the global efforts towards eliminating malaria. ARTs have been shown to cause ubiquitous cellular and genetic insults, which results in the activation of the unfolded protein response (UPR) pathways. The UPR restores protein homeostasis, which otherwise would be toxic to cellular survival. Here, we interrogated the role of DNA-damage inducible protein 1 (PfDdi1), a unique proteasome-interacting retropepsin in mediating the actions of the ARTs. We demonstrate that PfDdi1 is an active A₂ family protease that hydrolyzes ubiquitinated proteasome substrates. Treatment of P. falciparum parasites with ARTs leads to the accumulation of ubiquitinated proteins in the parasites and blocks the destruction of ubiquitinated proteins by inhibiting the PfDdi1 protease activity. Besides, whereas the PfDdi1 is predominantly localized in the cytoplasm, exposure of the parasites to ARTs leads to DNA fragmentation and increased recruitment of the PfDdi1 into the nucleus. Furthermore, we show that Ddi1 knock-out Saccharomycescerevisiae cells are more susceptible to ARTs and the PfDdI1 protein robustly restores the corresponding functions in the knock-out cells. Together, these results show that ARTs act in multiple ways; by inducing DNA and protein damage and might be impairing the damage recovery by inhibiting the activity of PfDdi1, an essential ubiquitin-proteasome retropepsin.

Plasmodium falciparum metacaspase-2 capture its natural substrate in a non-canonical way

Programmed cell death (PCD) is a multi-step process initiated by a set of proteases, which interacts and cleaves diverse proteins, thus modulating their biochemical and cellular functions. In metazoans, PCD is mediated by proteolytic enzymes called caspases, which triggered cell death by proteolysis of human Tudor staphylococcus nuclease (TSN). Non-metazoans lack a close homologue of caspases but possess an ancestral family of cysteine proteases termed ‘metacaspases’. Studies supported that metacaspases are involved in PCD, but their natural substrates remain unknown. In this study, we performed the Plasmodium falciparum TSN (PfTSN) cleavage assay using wild and selected mutants of P. falciparum metacaspases-2 (PfMCA-2) in vitro and in vivo. Interestingly, PfMCA-2, cleaved a phylogenetically conserved protein, PfTSN at multiple sites. Deletion or substitution mutation in key interacting residues at the active site, Cys157 and His205 of PfMCA-2, impaired its enzymatic activity with the artificial substrate, z-GRR-AMC. However, the mutant Tyr224A did not affect the activity with z-GRR-AMC but abolished the cleavage of PfTSN. These results indicated that the catalytic dyad, Cys157 and His205 of PfMCA-2 was essential for its enzymatic activity with an artificial substrate, whereas Tyr224 and Cys157 residues were responsible for its interaction with the natural substrate and subsequent degradation of PfTSN. Our results suggested that MCA-2 interacts with TSN substrate in a non-canonical way using non-conserved or conformationally available residues for its binding and cleavage. In future, it would be interesting to explore how this interaction leads to the execution of PCD in the Plasmodium.

Atomic Resolution Homology Models and Molecular Dynamics Simulations of Plasmodium falciparum Tubulins

Microtubules are tubulin polymers present in the eukaryotic cytoskeleton essential for structural stability and cell division that are also roadways for intracellular transport of vesicles and organelles. In the human malaria parasite Plasmodium falciparum, apart from providing structural stability and cell division, microtubules also facilitate important biological activities crucial for parasite survival in hosts, such as egression and motility. Hence, parasite structures and processes involving microtubules are among the most important drug targets for discovering much-needed novel Plasmodium inhibitors. The current study aims to construct reliable and high-quality 3D models of α-, β-, and γ-tubulins using various modeling techniques. We identified a common binding pocket specific to Plasmodium α-, β-, and γ-tubulins. Molecular dynamics simulations confirmed the stability of the Plasmodium tubulin 3D structures. The models generated in the present study may be used for protein-protein and protein-drug interaction investigations targeted toward designing malaria parasite tubulin-specific inhibitors.

Thermal desorption effects on fragment ion production from multi-photon ionized uridine and selected analogues

Experiments on neutral gas-phase nucleosides are often complicated by thermal lability. Previous mass spectrometry studies of nucleosides have identified enhanced relative production of nucleobase ions (e.g. uracil⁺ from uridine) as a function of desorption temperature to be the critical indicator of thermal decomposition. On this basis, the present multi-photon ionization (MPI) experiments demonstrate that laser-based thermal desorption is effective for producing uridine, 5-methyluridine, and 2′-deoxyuridine targets without thermal decomposition. Our experiments also revealed one notable thermal dependence: the relative production of the sugar ion C₅H₉O₄⁺ from intact uridine increased substantially with the desorption laser power and this only occurred at MPI wavelengths below 250 nm (full range studied 222–265 nm). We argue that this effect can only be rationalized plausibly in terms of changing populations of different isomers, tautomers, or conformers in the target as a function of the thermal desorption conditions. Furthermore, the wavelength threshold behavior of this thermally-sensitive MPI channel indicates a critical dependence on neutral excited state dynamics between the absorption of the first and second photons. The experimental results are complemented by density functional theory (DFT) optimizations of the lowest-energy structure of uridine and two further conformers distinguished by different orientations of the hydroxymethyl group on the sugar part of the molecule. The energies of the transitions states between these three conformers are low compared with the energy required for decomposition.

This work reveals the first experimental evidence supporting isomer-dependence in the radiation response of a nucleoside.

A Plasmodium falciparum protein tyrosine phosphatase inhibitor identified from the ChEMBL-NTD database blocks parasite growth

Post‐translational modifications, especially reversible phosphorylation, are among the most common mechanisms that regulate protein function and biological processes in Plasmodium species. Of the Plasmodium phosphatases, phosphatase of regenerating liver (PfPRL) is secreted and is an essential phosphatase. Here, we expressed PfPRL in a heterologous expression system, and then purified and characterized its phosphatase activity. We found that Novartis_003209, a previously identified inhibitor, inhibited the PfPRL phosphatase activity of recombinant PfPRL and blocked in vitro parasite growth in a dose‐dependent manner. Further, in silico docking analysis of Novartis_003209 with all four P. falciparum tyrosine phosphatases (PTP) demonstrated that Novartis_003209 is a Plasmodium PTP inhibitor. Overall, our results identify a scaffold as a potential starting point to design a PTP‐specific inhibitor.

“Clots and Failures” A Case of COVID-19 Causing STEMI and Persistent Cardiogenic Shock Ultimately Requiring LVAD

Introduction

We present a case of COVID-19 causing hypercoagulability and inflammatory stress leading to STEMI in a patient who went on to develop persistent cardiogenic shock requiring LVA) implantation.

Case Report

57-year-old lady developed COVID-19 infection in May 2020. In June 2020, she presented with chest pain, was noted to have STEMI on EKG, complicated by cardiac arrest with ROSC in 14 minutes. She was in cardiogenic shock as well and was started on veno-arterial ECMO. She underwent left anterior descending artery stent placement. Further hospitalization was complicated by persistent cardiogenic shock and complete heart block and underwent pacemaker and cardiac-defibrillator implantation. She developed pulmonary edema, acute kidney injury requiring hemodialysis, shock liver, and persistent cardiogenic shock. She was weaned off VA-ECMO after 4 days but continued to have severely reduced cardiac function. RHC revealed severe volume overload, pulmonary venous hypertension, low cardiac output, and right heart dysfunction. Echo showed severe LV dysfunction with an EF of 15%. A femoral intra-aortic balloon pump(IABP) was placed on July 7, 2020. An attempt was made to wean her off of IABP on July 10^th,however, it was unsuccessful and she was transitioned to axillary intra-aortic balloon pump. She remained IABP dependent thereafter and on July 15th, given persistent cardiogenic shock, decision was made to pursue advanced heart failure therapies. After multi-disciplinary discussion, the decision to pursue LVAD implantation was made. She underwent a successful LVAD implantation on July 20^th . She failed an extubation trial and underwent tracheostomy on July 23^rd . Post LVAD, she developed atrial fibrillation and was started on digoxin and amiodarone. Her symptoms improved and she was subsequently discharged to rehabilitation in late August on amiodarone, digoxin, metoprolol, prasugrel, warfarin, spironolactone and lisinopril. The detailed timeline is shown in figure 1.

Summary

Hypercoagulability and severe inflammatory stress leading to life-threatening illness is a significant complication of COVID-19 infection. A low threshold for suspecting and treating hypercoagulability and inflammatory induced myocardial ischemia and injury and cardiogenic shock is a reasonable strategy to decrease acute as well as chronic morbidity and mortality.

ECMO for Critically Ill COVID-19 with ARDS: A Case Series

Introduction

Veno-venous extracorporeal membrane oxygenation (VV-ECMO) as bridge to recovery in critically ill COVID-19 continues to be commonly utilized strategy in cases with persistent respiratory failure refractory to traditional ventilation support

Case Report

We report 5 cases of severe acute respiratory syndrome coronavirus-2 infection (SARS-CoV-2) who were treated with ECMO (Table 1). All 5 cases presented with fever, cough and shortness of breath and a positive nasopharyngeal swab for SARS-CoV-2 on admission. Case 1, 2, 3 and 5 patients were hypoxemic with saturation less than 90% on admission and decompensated rapidly, whereas Case 4 decompensated after day 14. Mechanical ventilation failed to provide adequate oxygenation in all 5 cases; case 2,3 and 5 were started on recruitment measures with proning while it was not possible for case 1 owing to morbid obesity. Proning was not possible in the case 4 as patient became severely hypoxemic while patient was undergoing mechanical thrombectomy. The case 1-4 remained on ECMO for 19, 17, 17 and 2 days respectively. All except case 2 had improvement in APACHEII and SOFA score after ECMO initiation. All 5 patients had elevated inflammatory markers of serum ferritin, D-dimer, Lactate dehydrogenase (LDH), C-reactive protein (CRP) which trended down after a few days of ECMO initiation All 5 patients received high dose steroids during their stay in the ICU. Case 4 and 5 passed away after compassionate extubation. Case 1-3 had prolonged hospital course with complication of hospital acquired pneumonia requiring multiple courses of broad-spectrum antibiotics.

Summary

Our observational report of 5 patients reports the use of ECMO in critically ill SARS-CoV-2 with ARDS and difficult to maintain saturation despite mechanical ventilation and proning with recovery for 3 patients. However, given the lack of ECMO centers; this is not a readily available option. Further studies are warranted to investigate the role of ECMO in SARRS-CoV-2 and careful identification of appropriate candidates.

Plasmodium DEH is ER-localized and crucial for oocyst mitotic division during malaria transmission

Cells use fatty acids (FAs) for membrane biosynthesis, energy storage, and the generation of signaling molecules. 3-hydroxyacyl-CoA dehydratase-DEH-is a key component of very long chain fatty acid synthesis. Here, we further characterized in-depth the location and function of DEH, applying in silico analysis, live cell imaging, reverse genetics, and ultrastructure analysis using the mouse malaria model Plasmodium berghei DEH is evolutionarily conserved across eukaryotes, with a single DEH in Plasmodium spp. and up to three orthologs in the other eukaryotes studied. DEH-GFP live-cell imaging showed strong GFP fluorescence throughout the life-cycle, with areas of localized expression in the cytoplasm and a circular ring pattern around the nucleus that colocalized with ER markers. Δdeh mutants showed a small but significant reduction in oocyst size compared with WT controls from day 10 postinfection onwards, and endomitotic cell division and sporogony were completely ablated, blocking parasite transmission from mosquito to vertebrate host. Ultrastructure analysis confirmed degeneration of Δdeh oocysts, and a complete lack of sporozoite budding. Overall, DEH is evolutionarily conserved, localizes to the ER, and plays a crucial role in sporogony.

SARS-CoV-2 and Plasmodium falciparum common immunodominant regions may explain low COVID-19 incidence in the malaria-endemic belt

Coronavirus disease 2019 (COVID-19) has caused significant morbidity and mortality and new cases are on the rise globally, yet malaria-endemic areas report statistically significant lower incidences. We identified potential shared targets for an immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by immune determinants' shared identities with P. falciparum using the Immune Epitope Database and Analysis Resource Immune 9.0 browser tool. Probable cross-reactivity is suggested through HLA-A∗02:01 and subsequent CD8+ T-cell activation. The apparent immunodominant epitope conservation between SARS-CoV-2 (N and open reading frame (ORF) 1ab) and P. falciparum thrombospondin-related anonymous protein (TRAP) may underlie the low COVID-19 incidence in the malaria-endemic zone by providing immunity against virus infection to those previously infected with Plasmodium. Additionally, we hypothesize that the shared epitopes which lie within antigens that aid in the establishment of the P. falciparum erythrocyte invasion may be an alternative route for SARS-CoV-2 via the erythrocyte CD147 receptor, although this remains to be proven.

Simple And Cost-Effective Classics Are Back- Revisiting The Role Of Urine Microscopic Analysis For Assessing Severity Of Renal Involvement In Lupus Nephritis

Casestudy

Urinalysis is important to assess disease activity in Lupus nephritis (LN). Hematuria, pyuria, cellular/granular casts and proteinuria are scored separately for assessing renal activity in SLEDAI. However, pyuria is not specific, and could indicate infection. We studied the correlation of microscopic urinalysis and degree of lymphocyturia with histological ISN/RPS 2018 class of LN.

Methods

Pre-biopsy urine was collected in 76 LN patients. The urine sediment was analyzed using light and phase- contrast microscope. Smear stained with supravital stain Sternheimer Malbin, was assessed semi-quantitatively for lymphocytes (per HPF). Renal biopsy was classified into proliferative (Class III/IV ± V)[N=64] and non-proliferative LN (Class I, II, V, VI) [N=12].

Results

48 patients had active urinary sediment. Cellular and/or granular casts were identified only in proliferativeLN (n=15/64; 23.4%). Hematuria (Range 0-65/HPF) was seen in 45 patients. Dysmorphic RBCs were identified in proliferative (n=17/41; mean 9.9 RBCs/HPF) and were absent in non-proliferative LN (mean 1.4 RBCs/HPF). 20 of the 34 patients with pyuria showed predominant lymphocytes. Lymphocyturia (Range 0-20/HPF) was significantly higher in proliferative LN (Mean 4.6/HPF) as compared to non-proliferative LN (Mean 1.5/HPF). Degree of pyuria or proteinuria had no correlation with biopsy class or activity. Lymphocyturia and hematuria showed correlation with biopsy activity index (r=0.30 and 0.39; p<0.05 and <0.001 respectively). A cut-off of average 6 RBCs/HPF or 5 lymphocytes/HPF could correctly identify proliferative LN with 100% specificity (p<0.001; AUC 0.72 and 0.74 respectively, combined AUC 0.81) and sensitivity of 0.42 and 0.36 respectively.

Conclusion

Although renal biopsy is the gold standard for assessment of renal lesions in LN, urine lymphocytes ≥5 and RBCs ≥6/HPF have a high specificity to differentiate proliferative and non-proliferative LN. This may be especially important in patients having comorbidities contraindicating a renal biopsy. Defining urine sediments using lymphocytes can increase the specificity of clinical activity indices.

Ligand-based pharmacophore modeling of TNF-α to design novel inhibitors using virtual screening and molecular dynamics

Tumor necrosis factor-α (TNF-α) is one of the promising targets for treating inflammatory (Crohn disease, psoriasis, psoriatic arthritis, rheumatoid arthritis) and various other diseases. Commercially available TNF-α inhibitors are associated with several risks and limitations. In the present study, we have identified small TNF-α inhibitors using in silico approaches, namely pharmacophore modeling, virtual screening, molecular docking, molecular dynamics simulation and free binding energy calculations. The study yielded better and potent hits that bind to TNF-α with significant affinity. The best pharmacophore model generated using LigandScout has an efficient hit rate and Area Under the operating Curve. High throughput virtual screening of SPECS database molecules against crystal structure of TNF-α protein, coupled with physicochemical filtration, PAINS test. Virtual hit compounds used for molecular docking enabled the identification of 20 compounds with better binding energies when compared with previously known TNF-α inhibitors. MD simulation analysis on 20 virtual identified hits showed that ligand binding with TNF-α protein is stable and protein-ligand conformation remains unchanged. Further, 16 compounds passed ADMET analysis suggesting these identified hit compounds are suitable for designing a future class of potent TNF-α inhibitors.Communicated by Ramaswamy H. Sarma.

Real-time dynamics of Plasmodium NDC80 reveals unusual modes of chromosome segregation during parasite proliferation

Eukaryotic cell proliferation requires chromosome replication and precise segregation to ensure daughter cells have identical genomic copies. Species of the genus Plasmodium, the causative agents of malaria, display remarkable aspects of nuclear division throughout their life cycle to meet some peculiar and unique challenges to DNA replication and chromosome segregation. The parasite undergoes atypical endomitosis and endoreduplication with an intact nuclear membrane and intranuclear mitotic spindle. To understand these diverse modes of Plasmodium cell division, we have studied the behaviour and composition of the outer kinetochore NDC80 complex, a key part of the mitotic apparatus that attaches the centromere of chromosomes to microtubules of the mitotic spindle. Using NDC80-GFP live-cell imaging in Plasmodium berghei, we observe dynamic spatiotemporal changes during proliferation, including highly unusual kinetochore arrangements during sexual stages. We identify a very divergent candidate for the SPC24 subunit of the NDC80 complex, previously thought to be missing in Plasmodium, which completes a canonical, albeit unusual, NDC80 complex structure. Altogether, our studies reveal the kinetochore to be an ideal tool to investigate the non-canonical modes of chromosome segregation and cell division in Plasmodium.

A divergent cyclin/cyclin-dependent kinase complex controls the atypical replication of a malaria parasite during gametogony and transmission

Cell cycle transitions are generally triggered by variation in the activity of cyclin-dependent kinases (CDKs) bound to cyclins. Malaria-causing parasites have a life cycle with unique cell-division cycles, and a repertoire of divergent CDKs and cyclins of poorly understood function and interdependency. We show that Plasmodium berghei CDK-related kinase 5 (CRK5), is a critical regulator of atypical mitosis in the gametogony and is required for mosquito transmission. It phosphorylates canonical CDK motifs of components in the pre-replicative complex and is essential for DNA replication. During a replicative cycle, CRK5 stably interacts with a single Plasmodium-specific cyclin (SOC2), although we obtained no evidence of SOC2 cycling by transcription, translation or degradation. Our results provide evidence that during Plasmodium male gametogony, this divergent cyclin/CDK pair fills the functional space of other eukaryotic cell-cycle kinases controlling DNA replication.

Plasmodium Condensin Core Subunits SMC2/SMC4 Mediate Atypical Mitosis and Are Essential for Parasite Proliferation and Transmission

Condensin is a multi-subunit protein complex regulating chromosome condensation and segregation during cell division. In Plasmodium spp., the causative agent of malaria, cell division is atypical and the role of condensin is unclear. Here we examine the role of SMC2 and SMC4, the core subunits of condensin, during endomitosis in schizogony and endoreduplication in male gametogenesis. During early schizogony, SMC2/SMC4 localize to a distinct focus, identified as the centromeres by NDC80 fluorescence and chromatin immunoprecipitation sequencing (ChIP-seq) analyses, but do not form condensin I or II complexes. In mature schizonts and during male gametogenesis, there is a diffuse SMC2/SMC4 distribution on chromosomes and in the nucleus, and both condensin I and condensin II complexes form at these stages. Knockdown of smc2 and smc4 gene expression reveals essential roles in parasite proliferation and transmission. The condensin core subunits (SMC2/SMC4) form different complexes and may have distinct functions at various stages of the parasite life cycle.

Ultrasound is a reliable and faster tool for confirmation of endotracheal intubation compared to chest auscultation and capnography when performed by novice anaesthesia residents - A prospective controlled clinical trial

Background

Anesthesia trainee may initially take longer time to intubate and unintentionally place the endotracheal tube (ETT) in the esophagus. The present study determined if ultrasound is the fastest method of confirmation of correct placement of ETT compared to capnography, and chest auscultation in trainees.

Methods

First year anesthesia residents performed intubation in 120 patients recruited after ethical clearance and informed consent. Time to visualize flutter in trachea, double trachea sign, time to appearance of first and sixth capnography, and time to execute chest auscultation was noted.

Results

Ultrasonography was statistically fastest method to determine endotracheal intubation (36.50 ± 15.14 seconds) vs unilateral chest auscultation (50.29 ± 15.50 seconds) vs bilateral chest auscultation (51.90 ± 15.98 seconds) vs capnography first waveform (53.57 ± 15.97 seconds) vs capnography sixth waveform (61.67 ± 15.88 seconds).

Conclusion

When teaching endotracheal intubation to novice anesthesia residents using conventional direct laryngoscopy, ultrasonography is the fastest method to confirm correct ETT placement compared to capnograph and chest auscultation. Mentor can guide trainee to direct ETT towards trachea and can promptly detect esophageal intubation by double trachea sign.