Effect of nonsteroidal anti-inflammatory drugs (aspirin and naproxen) on inflammation-associated proteomic profiles in mouse plasma and prostate during TMPRSS2-ERG (fusion)-driven prostate carcinogenesis

Recent preclinical studies have shown that the intake of nonsteroidal anti-inflammatory drugs (NSAIDs) aspirin and naproxen could be an effective intervention strategy against TMPRSS2-ERG fusion-driven prostate tumorigenesis. Herein, as a follow-up mechanistic study, employing TMPRSS2-ERG (fusion) positive tumors and plasma from TMPRSS2-ERG. Ptenflox/flox mice, we profiled the stage specific proteomic changes (focused on inflammatory circulating and prostate tissue/tumor-specific cytokines, chemokines, and growth factors/growth signaling-associated molecules) that contribute to prostate cancer (PCa) growth and progression in the TMPRSS2-ERG fusion-driven mouse model of tumorigenesis. In addition, the association of the protective effects of NSAIDs (aspirin 1400 ppm and naproxen 400 ppm) with the modulation of these specific molecular pathways was determined. A sandwich Elisa based membrane array-proteome profiler identifying 111 distinct signaling molecules was employed. Overall, the plasma and prostate tissue sample analyses identified 54 significant and differentially expressed cytokines, chemokines, and growth factors/growth signaling-associated molecules between PCa afflicted mice (TMPRSS2-ERG. Ptenflox/flox, age-matched noncancerous controls, NSAIDs-supplemented and no-drug controls). Bioinformatic analysis of the array outcomes indicated that the protective effect of NSAIDs was associated with reduced expression of (a) tumor promoting inflammatory molecules (M-CSF, IL-33, CCL22, CCL12, CX3CL1, CHI3L1, and CD93), (b) growth factors- growth signaling-associated molecules (Chemerin, FGF acidic, Flt-3 ligand, IGFBP-5, and PEDF), and (c) tumor microenvironment/stromal remodeling proteins MMP2 and MMP9. Overall, our findings corroborate the pathological findings that protective effects of NSAIDs in TMPSS2-ERG fusion-driven prostate tumorigenesis are associated with antiproliferative and anti-inflammatory effects and possible modulation of the immune cell enriched microenvironment.

Dynamic changes in extracellular vesicle-associated miRNAs elicited by ultrasound in inflammatory bowel disease patients

Blood-based biomarkers that reliably indicate disease activity in the intestinal tract are an important unmet need in the management of patients with IBD. Extracellular vesicles (EVs) are cell-derived membranous microparticles, which reflect the cellular and functional state of their site of site of origin. As ultrasound waves may lead to molecular shifts of EV contents, we hypothesized that application of ultrasound waves on inflamed intestinal tissue in IBD may amplify the inflammation-specific molecular shifts in EVs like altered EV-miRNA expression, which in turn can be detected in the peripheral blood. 26 patients with IBD were included in the prospective clinical study. Serum samples were collected before and 30 min after diagnostic transabdominal ultrasound. Differential miRNA expression was analyzed by sequencing. Candidate inducible EV-miRNAs were functionally assessed in vitro by transfection of miRNA mimics and qPCR of predicted target genes. Serum EV-miRNA concentration at baseline correlated with disease severity, as determined by clinical activity scores and sonographic findings. Three miRNAs (miR-942-5p, mir-5588, mir-3195) were significantly induced by sonography. Among the significantly regulated EV-miRNAs, miR-942-5p was strongly induced in higher grade intestinal inflammation and correlated with clinical activity in Crohn's disease. Prediction of target regulation and transfection of miRNA mimics inferred a role of this EV-miRNA in regulating barrier function in inflammation. Induction of mir-5588 and mir-3195 did not correlate with inflammation grade. This proof-of-concept trial highlights the principle of induced molecular shifts in EVs from inflamed tissue through transabdominal ultrasound. These inducible EVs and their molecular cargo like miRNA could become novel biomarkers for intestinal inflammation in IBD.

Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in h-BRCA1

Preliminary studies have shown BRCA1 (170-1600) residues to be intrinsically disordered with unknown structural details. However, thousands of clinically reported variants have been identified in this central region of BRCA1. Therefore, we aimed to characterize h-BRCA1(260-553) to assess the structural basis for pathogenicity of two rare missense variants Ser282Leu, Gln356Arg identified from the Indian and Russian populations respectively. Small-angle X-ray scattering analysis revealed WT scores Rg -32 Å, Dmax -93 Å, and Rflex-51% which are partially disordered, whereas Ser282Leu variant displayed a higher degree of disorderedness and Gln356Arg was observed to be aggregated. WT protein also possesses an inherent propensity to undergo a disorder-to-order transition in the presence of cruciform DNA and 2,2,2-Trifluoroethanol (TFE). An increased alpha-helical pattern was observed with increasing concentration of TFE for the Gln356Arg mutant whereas Ser282Leu mutant showed significant differences only at the highest TFE concentration. Furthermore, higher thermal shift was observed for WT-DNA complex compared to the Gln356Arg and Ser282Leu protein-DNA complex. Moreover, mature amyloid-like fibrils were observed with 30 μM thioflavin T (ThT) at 37°C for Ser282Leu and Gln356Arg proteins while the WT protein exists in a protofibril state as observed by TEM. Gln356Arg formed higher-order aggregates with amyloidogenesis over time as monitored by ThT fluorescence. In addition, computational analyses confirmed larger conformational fluctuations for Ser282Leu and Gln356Arg mutants than for the WT. The global structural alterations caused by these variants provide a mechanistic approach for further classification of the variants of uncertain clinical significance in BRCA1 into amyloidogenic variants which may have a significant role in disease pathogenesis.

Mutations at proximal cysteine residues in PML impair ATO binding by destabilizing the RBCC domain

Acute promyelocytic leukemia (APL) is characterized by the fusion gene promyelocytic leukemia-retinoic acid receptor-alpha (PML-RARA) and is conventionally treated with arsenic trioxide (ATO). ATO binds directly to the RING finger, B-box, coiled-coil (RBCC) domain of PML and initiates degradation of the fusion oncoprotein PML-RARA. However, the mutational hotspot at C212-S220 disrupts ATO binding, leading to drug resistance in APL. Therefore, structural consequences of these point mutations in PML that remain uncertain require comprehensive analysis. In this study, we investigated the structure-based ensemble properties of the promyelocytic leukemia-RING-B-box-coiled-coil (PML-RBCC) domains and ATO-resistant mutations. Oligomeric studies reveal that PML-RBCC wild-type and mutants C212R, S214L, A216T, L217F, and S220G predominantly form tetramers, whereas mutants C213R, A216V, L218P, and D219H tend to form dimers. The stability of the dimeric mutants was lower, exhibiting a melting temperature (Tm) reduction of 30 °C compared with the tetrameric mutants and wild-type PML protein. Furthermore, the exposed surface of the C213R mutation rendered it more prone to protease digestion than that of the C212R mutation. The spectroscopic analysis highlighted ATO-induced structural alterations in S214L, A216V, and D219H mutants, in contrast to C213R, L217F, and L218P mutations. Moreover, the computational analysis revealed that the ATO-resistant mutations C213R, A216V, L217F, and L218P caused changes in the size, shape, and flexibility of the PML-RBCC wild-type protein. The mutations C213R, A216V, L217F, and L218P destabilize the wild-type protein structure due to the adaptation of distinct conformational changes. In addition, these mutations disrupt several hydrogen bonds, including interactions involving C212, C213, and C215, which are essential for ATO binding. The local and global structural features induced by these mutations provide mechanistic insight into ATO resistance and APL pathogenesis.

Serine metabolism is crucial for cGAS-STING signaling and viral defense control in the gut

Inflammatory bowel diseases are characterized by the chronic relapsing inflammation of the gastrointestinal tract. While the molecular causality between endoplasmic reticulum (ER) stress and intestinal inflammation is widely accepted, the metabolic consequences of chronic ER stress on the pathophysiology of IBD remain unclear. By using in vitro, in vivo models, and patient datasets, we identified a distinct polarization of the mitochondrial one-carbon metabolism and a fine-tuning of the amino acid uptake in intestinal epithelial cells tailored to support GSH and NADPH metabolism upon ER stress. This metabolic phenotype strongly correlates with IBD severity and therapy response. Mechanistically, we uncover that both chronic ER stress and serine limitation disrupt cGAS-STING signaling, impairing the epithelial response against viral and bacterial infection and fueling experimental enteritis. Consequently, the antioxidant treatment restores STING function and virus control. Collectively, our data highlight the importance of serine metabolism to allow proper cGAS-STING signaling and innate immune responses upon gut inflammation.

Unveiling the Compositional Analysis of Green Coffee Beans with and without Silver Skin

BACKGROUND

Green Coffee Bean (GCB) is covered with silver skin that is shed as a by-product of the roasting process. For the first time, a comparative study was conducted to differentiate the compositional analysis of green coffee beans with silver skin and without silver skin.

OBJECTIVE

The study aims comparatively assessing nutritional, anti-nutritional and fatty acids composition of green coffee beans with silver skin and without silver skin. The present study is also intended to find out various organic compounds of green coffee beans.

METHODS

The proximate analysis was used to study nutritional composition. Mineral analysis was assessed by atomic absorption spectroscopy. The antinutrients like phytic acid and tannin were assessed by UV-visible spectroscopy whereas volumetric and gravimetric analysis was used to determine oxalates and alkaloids. Gas chromatography and Fourier Transform Infra-Red spectroscopy were used for studying fatty acids and organic compounds, respectively.

RESULTS

Protein content was significantly (p<0.05) high in green coffee beans with silver skin, indicating 15% higher protein. Macro mineral content was also found significantly (p<0.05 and p<0.01) high in green coffee beans with silver skin, whereby 5.11% higher Phosphorus and 24.12% higher Calcium content was observed. However, iron content was 68.10% lower in green coffee beans with silver skin which might be due to its higher tannin content. Trace minerals zinc and copper were also found to contain 57.18% to 18.11% higher concentrations respectively in silver skin. Anti-nutritional analysis revealed the content of phytic acid and tannin as 161 and 77.29 mg/100g, respectively in green coffee beans with silver skin. The percentages of oxalates and alkaloids were found to be 0.64 and 14.30. These anti-nutritional compounds were significantly (p<0.05 and p<0.01) higher from green coffee beans without silver skin. Green coffee beans have been found with an utmost number of saturated fatty acids having palmitic acid as the most abundant. The unsaturated part is mainly composed of linoleic and oleic acid. Chlorogenic acid isomers and caffeine were the organic compounds detected through Fourier transform infrared spectroscopy.

CONCLUSION

These findings reveal the presence of both nutritional and anti-nutritional components in Coffee silver skin, with significantly higher levels of anti-nutritional factors in green coffee with silver skin, emphasizing the need for caution in the consumption of green coffee and utilization of coffee silver skin as a valuable bioresource.

Variant of uncertain significance Arg866Cys enhances disorderedness of h-BRCA1 (759-1064) region

High structural flexibility has been reported in the central region of BRCA1, which hinders the structural and functional evaluations of mutations identified in the domain. Additionally, the need to categorize variants of unknown significance (VUS) has increased due to the growth in the number of variants reported in clinical settings. Therefore, unraveling the disease-causing mechanism of VUS identified in different functional domains of BRCA1 is still challenging. The current study uses a multidisciplinary approach to assess the structural impact of BRCA1 Arg866Cys mutation discovered in the central domain of BRCA1. The structural alterations have been characterized using Circular-Dichroism spectroscopy, nano-DSF, and molecular-dynamics simulations. BRCA1 Arg866Cys mutant demonstrated more flexibility and lesser affinity to DNA than the wild-type protein. The BRCA1(759-1064) wild-type protein was shown to be a βII-rich protein with an induced D-O transition in the presence of DNA and 2,2,2-Trifluoroethanol (TFE). The protein's alpha-helical composition did not significantly change in the presence of TFE, besides an increase in β-turns and loops. Under Transmission Electron Microscopes (TEM), amyloid-like fibrils structure was detected for Arg866Cys mutant whereas the wild-type protein showed amorphous aggregates. An increased ThT fluorescence indicated β-rich composition and aggregation-prone behaviour for BRCA1 wild-type protein, while the fluorescence intensity was significantly quenched in the Arg866Cys mutant. Furthermore, increased conformational flexibility in the Arg866Cys variant was observed by principal component analysis. This work aims to comprehend the inherently disordered region of BRCA1 as well as the impact of missense mutations on folding patterns and binding to DNA for functional aspects.

Dexamethasone targets actin cytoskeleton signaling and inflammatory mediators to reverse sulfur mustard-induced toxicity in rabbit corneas

PURPOSE

Sulfur mustard (SM), a bi-functional alkylating agent, was used during World War I and the Iran-Iraq war. SM toxicity is ten times higher in eyes than in other tissues. Cornea is exceptionally susceptible to SM-injuries due to its anterior positioning and mucous-aqueous interphase. Ocular SM exposure induces blepharitis, photosensitivity, dry eye, epithelial defects, limbal ischemia and stem cell deficiency, and mustard gas keratopathy leading to temporary or permanent vision impairments. We demonstrated that dexamethasone (Dex) is a potent therapeutic intervention against SM-induced corneal injuries; however, its mechanism of action is not well known. Investigations employing proteomic profiling (LC-MS/MS) to understand molecular mechanisms behind SM-induced corneal injury and Dex efficacy were performed in the rabbit cornea exposed to SM and then received Dex treatment. PEAKS studio was used to extract, search, and summarize peptide identity. Ingenuity Pathway Analysis was used for pathway identification. Validation was performed using immunofluorescence. One-Way ANOVA (FDR < 0.05; p < 0.005) and Student's t-test (p < 0.05) were utilized for analyzing proteomics and IF data, respectively. Proteomic analysis revealed that SM-exposure upregulated tissue repair pathways, particularly actin cytoskeleton signaling and inflammation. Prominently dysregulated proteins included lipocalin2, coronin1A, actin-related protein2, actin-related protein2/3 complex subunit2, actin-related protein2/3 complex subunit4, cell division cycle42, ezrin, bradykinin/kininogen1, moesin, and profilin. Upregulated actin cytoskeleton signaling increases F-actin formation, dysregulating cell shape and motility. Dex reversed SM-induced increases in the aforementioned proteins levels to near control expression profiles. Dex aids corneal wound healing and improves corneal integrity via actin cytoskeletal signaling and anti-inflammatory effects following SM-induced injuries.

Routine sterile glove and instrument change at the time of abdominal wound closure to prevent surgical site infection (ChEETAh): a model-based cost-effectiveness analysis of a pragmatic, cluster-randomised trial in seven low-income and middle-income countries

BACKGROUND

Surgical site infection (SSI) is a major burden on patients and health systems. This study assessed the cost-effectiveness of routine change of sterile gloves and instruments before abdominal wall closure to prevent SSI.

METHODS

A decision-analytic model was built to estimate average costs and outcomes of changing gloves and instruments before abdominal wall closure compared with current practice. Clinical data were obtained from the ChEETAh trial, a multicentre, cluster-randomised trial in seven low-income and middle-income countries (LMICs), and costs were obtained from a study (KIWI) that assessed costs associated with SSIs in LMICs. Outcomes were measured as the percentage of surgeries resulting in SSIs. Costs were measured from a health-care provider perspective and were reported in 2021 US$. The economic analysis used a partially split single-country costing approach, with pooled outcomes data from all seven countries in the ChEETAh trial, and data for resource use and unit costs from India (KIWI); secondary analyses used resource use and costs from Mexico and Ghana (KIWI).

FINDINGS

In the base case, the average cost of the intervention was $259∙92 compared with $261∙10 for current practice (cost difference -$1∙18, 95% CI -4∙08 to 1∙33). In the intervention group, an estimated 17∙6% of patients had an SSI compared with 19∙7% of patients in the current practice group (absolute risk reduction 2∙10%, 95% CI 2∙07-2∙84). At all cost-effectiveness thresholds assumed ($0 to $14 000), the intervention had a higher likelihood of being cost-effective compared with current practice, indicating that the intervention was cost-effective. Similar results were obtained when the analysis using data from India was repeated using resource use and unit cost data from Mexico and Ghana.

INTERPRETATION

Routine sterile glove and instrument change before abdominal wall closure is effective and the costs are similar to those for current practice. Routine change of gloves and instruments before abdominal wall closure should be rolled out in LMICs.

FUNDING

National Institute for Health and Care Research (NIHR) Clinician Scientist Award, NIHR Global Health Research Unit Grant, and Mölnlycke Healthcare.

Computation-aided Design of Rod-Shaped Janus Base Nanopieces for Improved Tissue Penetration and Therapeutics Delivery

Despite the development of various drug delivery technologies, there remains a significant need for vehicles that can improve targeting and biodistribution in "hard-to-penetrate" tissues. Some solid tumors, for example, are particularly challenging to penetrate due to their dense extracellular matrix (ECM). In this study, we have formulated a new family of rod-shaped delivery vehicles named Janus base nanopieces (Rod JBNps), which are more slender than conventional spherical nanoparticles, such as lipid nanoparticles (LNPs). These JBNp nanorods are formed by bundles of DNA-inspired Janus base nanotubes (JBNts) with intercalated delivery cargoes. To develop this novel family of delivery vehicles, we employed a computation-aided design (CAD) methodology that includes molecular dynamics and response surface methodology. This approach precisely and efficiently guides experimental designs. Using an ovarian cancer model, we demonstrated that JBNps markedly improve penetration into the dense ECM of solid tumors, leading to better treatment outcomes compared to FDA-approved spherical LNP delivery. This study not only successfully developed a rod-shaped delivery vehicle for improved tissue penetration but also established a CAD methodology to effectively guide material design.

Nitrogen Mustard-Induced Ex Vivo Human Cornea Injury Model and Therapeutic Intervention by Dexamethasone

Sulfur mustard (SM), a vesicating agent first used during World War I, remains a potent threat as a chemical weapon to cause intentional/accidental chemical emergencies. Eyes are extremely susceptible to SM toxicity. Nitrogen mustard (NM), a bifunctional alkylating agent and potent analog of SM, is used in laboratories to study mustard vesicant-induced ocular toxicity. Previously, we showed that SM-/NM-induced injuries (in vivo and ex vivo rabbit corneas) are reversed upon treatment with dexamethasone (DEX), a US Food and Drug Administration-approved, steroidal anti-inflammatory drug. Here, we optimized NM injuries in ex vivo human corneas and assessed DEX efficacy. For injury optimization, one cornea (randomly selected from paired eyes) was exposed to NM: 100 nmoles for 2 hours or 4 hours, and 200 nmoles for 2 hours, and the other cornea served as a control. Injuries were assessed 24 hours post NM-exposure. NM 100 nmoles exposure for 2 hours was found to cause optimal corneal injury (epithelial thinning [∼69%]; epithelial-stromal separation [6-fold increase]). In protein arrays studies, 24 proteins displayed ≥40% change in their expression in NM exposed corneas compared with controls. DEX administration initiated 2 hours post NM exposure and every 8 hours thereafter until 24 hours post-exposure reversed NM-induced corneal epithelial-stromal separation [2-fold decrease]). Of the 24 proteins dysregulated upon NM exposure, six proteins (delta-like canonical Notch ligand 1, FGFbasic, CD54, CCL7, endostatin, receptor tyrosine-protein kinase erbB-4) associated with angiogenesis, immune/inflammatory responses, and cell differentiation/proliferation, showed significant reversal upon DEX treatment (Student's t test; P ≤ 0.05). Complementing our animal model studies, DEX was shown to mitigate vesicant-induced toxicities in ex vivo human corneas. SIGNIFICANCE STATEMENT: Nitrogen mustard (NM) exposure-induced injuries were optimized in an ex vivo human cornea culture model and studies were carried out at 24 h post 100 nmoles NM exposure. Dexamethasone (DEX) administration (started 2 h post NM exposure and every 8 h thereafter) reversed NM-induced corneal injuries. Molecular mediators of DEX action were associated with angiogenesis, immune/inflammatory responses, and cell differentiation/proliferation, indicating DEX aids wound healing via reversing vesicant-induced neovascularization (delta-like canonical Notch ligand 1 and FGF basic) and leukocyte infiltration (CD54 and CCL7).

Establishing a Dexamethasone Treatment Regimen To Alleviate Sulfur Mustard-Induced Corneal Injuries in a Rabbit Model

Sulfur mustard (SM) is an ominous chemical warfare agent. Eyes are extremely susceptible to SM toxicity; injuries include inflammation, fibrosis, neovascularization (NV), and vision impairment/blindness, depending on the exposure dosage. Effective countermeasures against ocular SM toxicity remain elusive and are warranted during conflicts/terrorist activities and accidental exposures. We previously determined that dexamethasone (DEX) effectively counters corneal nitrogen mustard toxicity and that the 2-hour postexposure therapeutic window is most beneficial. Here, the efficacy of two DEX dosing frequencies [i.e., every 8 or 12 hours (initiated, as previously established, 2 hours after exposure)] until 28 days after SM exposure was assessed. Furthermore, sustained effects of DEX treatments were observed up to day 56 after SM exposure. Corneal clinical assessments (thickness, opacity, ulceration, and NV) were performed at the day 14, 28, 42, and 56 post-SM exposure time points. Histopathological assessments of corneal injuries (corneal thickness, epithelial degradation, epithelial-stromal separation, inflammatory cell, and blood vessel counts) using H&E staining and molecular assessments (COX-2, MMP-9, VEGF, and SPARC expressions) were performed at days 28, 42, and 56 after SM exposure. Statistical significance was assessed using two-way ANOVA, with Holm-Sidak post hoc pairwise multiple comparisons; significance was established if P < 0.05 (data represented as the mean ± S.E.M.). DEX administration every 8 hours was more potent than every 12 hours in reversing ocular SM injury, with the most pronounced effects observed at days 28 and 42 after SM exposure. These comprehensive results are novel and provide a comprehensive DEX treatment regimen (therapeutic-window and dosing-frequency) for counteracting SM-induced corneal injuries. SIGNIFICANCE STATEMENT: The study aims to establish a dexamethasone (DEX) treatment regimen by comparing the efficacy of DEX administration at 12 versus 8 hours initiated 2 hours after exposure. DEX administration every 8 hours was more effective in reversing sulfur mustard (SM)-induced corneal injuries. SM injury reversal during DEX administration (initial 28 days after exposure) and sustained [further 28 days after cessation of DEX administration (i.e., up to 56 days after exposure)] effects were assessed using clinical, pathophysiological, and molecular biomarkers.

Synoptic Operative Reporting in Cervical Cancer Surgeries: Experience From a Single Oncology Center

Objective In today's era of highly methodological oncological practices in place, we have a huge database to regulate, and it is foreseeable that a humongous load of information is ahead of us that we need to organize and comprehend. With the advancement in surgical equipment and evolving procedures, we need to store the information in a transferrable, understandable, and systematic way to prevent any ebb in the future. The systematic recording of operative data is even more important for patient management, training, and research. Standardized reporting also helps surgical residents have a better understanding of all aspects of the procedure. This study aims to analyze the synoptic operative reporting in cervical cancer patients from December 2009 to February 2020 in a single tertiary care center dedicated to providing oncology services to patients. This study will analyze the understandability, volume, and ease of transference of data during the given time period. Methodology The Alberta Cancer Registry was contacted to obtain data from the synoptic operative reports. Synoptic Operative Reports of all the patients operated on cervical cancer from December 2009 to February 2020. Results The data were obtained for 574 patients. As many as 463 patients were operated on for stage 1 and 2 cervical cancers and 10 patients for advanced and recurrent cervical cancer. A total of 101 patients were operated on for high-grade cervical dysplasia (HSIL). Adenocarcinoma was the most common histology. Laparotomy was performed in 308 patients, whereas others had laparoscopic procedures. Details of the surgery from the beginning of the incision to closure were recorded. The cervical cancer template consisted of 356 questions. There were separate templates for advanced and early-stage cancer. However, even with the meticulously detailed report, an average of only eight minutes was taken by each user to complete the template. Conclusion The computerized synoptic operative report has an upper hand over the dictated documentation report along with the ease of execution without missing essential substance. Its utility as an educational tool is very promising. Therefore, we encourage other facilities, especially cancer centers, to use synoptic operative reports more extensively not only for cervical cancer surgeries but also for other ones.

Proteasome inhibition potentiates Kv1.3 potassium channel expression as therapeutic target in drug-sensitive and -resistant human melanoma cells

Primary and acquired therapy resistance is a major problem in patients with BRAF-mutant melanomas being treated with BRAF and MEK inhibitors (BRAFI, MEKi). Therefore, development of alternative therapy regimes is still required. In this regard, new drug combinations targeting different pathways to induce apoptosis could offer promising alternative approaches. Here, we investigated the combination of proteasome and Kv1.3 potassium channel inhibition on chemo-resistant, BRAF inhibitor-resistant as well as sensitive human melanoma cells. Our experiments demonstrated that all analyzed melanoma cell lines were sensitive to proteasome inhibitor treatment at concentrations that are not toxic to primary human fibroblasts. To further reduce proteasome inhibitor-associated side effects, and to foster apoptosis, potassium channels, which are other targets to induce pro-apoptotic effects in cancer cells, were blocked. In support, combined exposure of melanoma cells to proteasome and Kv1.3 channel inhibitor resulted in synergistic effects and significantly reduced cell viability. On the molecular level, enhanced apoptosis correlated with an increase of intracellular Kv1.3 channels and pro-apoptotic proteins such as Noxa and Bak and a reduction of anti-apoptotic proteins. Thus, use of combined therapeutic strategies triggering different apoptotic pathways may efficiently prevent the outgrowth of drug-resistant and -sensitive BRAF-mutant melanoma cells. In addition, this could be the basis for an alternative approach to treat other tumors expressing mutated BRAF such as non-small-cell lung cancer.

Phytochemicals as Immunomodulatory Molecules in Cancer Therapeutics

Phytochemicals are natural plant-derived products that provide significant nutrition, essential biomolecules, and flavor as part of our diet. They have long been known to confer protection against several diseases via their anti-inflammatory, immune-regulatory, anti-microbial, and several other properties. Deciphering the role of phytochemicals in the prevention, inhibition, and treatment of cancer-unrestrained cell proliferation due to the loss of tight regulation on cell growth and replication-has been the focus of recent research. Particularly, the immunomodulatory role of phytochemicals, which is pivotal in unchecked cell proliferation and metastasis, has recently been studied extensively. The immune system is a critical component of the tumor microenvironment, and it plays essential roles in both preventing and promoting oncogenesis. Immunomodulation includes stimulation, amplification, or inactivation of some stage(s) of the immune response. Phytochemicals and their products have demonstrated immune regulation, such as macrophage migration, nitric oxide synthase inhibition, lymphocyte, T-cell, and cytokine stimulation, natural killer cell augmentation, and NFκB, TNF, and apoptosis regulation. There is a dearth of extensive accounts of the immunomodulatory effects of phytochemicals in cancer; thus, we have compiled these effects with mechanistic aspects of dietary phytochemicals in cancer, highlighting promising candidates and ongoing clinical trials on immunotherapeutic strategies to mitigate oncogenesis.

Phenylarsine oxide induced corneal injury involves oxidative stress mediated unfolded protein response and ferroptotic cell death: Amelioration by NAC

Phenylarsine oxide (PAO), an analog of lewisite, is a highly toxic trivalent arsenical and a potential chemical warfare agent. PAO-induced toxicity has been studied in lung, liver, and skin tissues. Nevertheless, very few studies have been published to comprehend the impact of PAO-induced toxicity on ocular tissues, even though eyes are uniquely vulnerable to injury by vesicants. Notably, arsenical vesicants such as lewisite have been shown to cause edema of eyelids, inflammation, massive corneal necrosis, and blindness. Accordingly, human corneal epithelial cells were used to study the effects of PAO exposure. PAO (100 and 200 nM) induced significant oxidative stress in corneal epithelial cells. Simultaneous treatment with N-acetyl-l-cysteine (NAC), an FDA-approved antioxidant, reversed the PAO-induced toxicity in human corneal epithelial cells. Furthermore, oxidative stress induction by PAO was accompanied by unfolded protein response (UPR) signaling activation and ferroptotic cell death. Further, to validate the findings of our in vitro studies, we optimized injury biomarkers and developed an ex vivo rabbit corneal culture model of PAO exposure. Investigations using PAO in ex vivo rabbit corneas revealed similar results. PAO (5 or 10 μg) for 3, 5, and 10 min caused moderate to extensive corneal epithelial layer degradation and reduced the epithelial layer thickness in a concentration- and time-dependent manner. Similar to human corneal cells, injuries by PAO in ex vivo cultured rabbit corneas were also associated with elevated oxidative stress, UPR signaling, and ferroptosis induction. NAC mitigated PAO-induced corneal injuries in rabbit ex vivo cornea culture as well. The reversal of PAO toxicity upon NAC treatment observed in our studies could be attributed to its antioxidant properties. These findings suggest that PAO exposure can cause significant corneal injury and highlight the need for further mechanistic studies to better understand the pathobiology of different arsenical vesicants, including PAO and lewisite.

Metabolomics for identifying pathways involved in vesicating agent lewisite-induced corneal injury

Lewisite (LEW) is an arsenical vesicant that can be a potentially dangerous chemical warfare agent (CWA). Eyes are particularly susceptible to vesicant induced injuries and ocular LEW exposure can act swiftly, causing burning of eyes, edema, inflammation, cell death and even blindness. In our previous studies, we developed a LEW exposure-induced corneal injury model in rabbit and showed increased inflammation, neovascularization, cell death, and structural damage to rabbit corneas upon LEW exposure. In the present study, we further assessed the metabolomic changes to delineate the possible mechanisms underlying the LEW-induced corneal injuries. This information is vital and could help in the development of effective targeted therapies against ocular LEW injuries. Thus, the metabolomic changes associated with LEW exposures in rabbit corneas were assessed as a function of time, to delineate pathways from molecular perturbations at the genomic and proteomic levels. New Zealand white rabbit corneas (n = 3-6) were exposed to LEW vapor (0.2 mg/L; flow rate: 300 ml/min) for 2.5 min (short exposure; low dose) or 7.5 min (long-exposure; high dose) and then collected at 1, 3, 7, or 14 days post LEW exposure. Samples were prepared using the automated MicroLab STAR® system, and proteins precipitated to recover the chemically diverse metabolites. Metabolomic analysis was carried out by reverse phase UPLC-MS/MS and gas chromatography (GC)-MS. The data obtained were analyzed using Metabolon's software. The results showed that LEW exposures at high doses were more toxic, particularly at the day 7 post exposure time point. LEW exposure was shown to dysregulate metabolites associated with all the integral functions of the cornea and cause increased inflammation and immune response, as well as generate oxidative stress. Additionally, all important metabolic functions of the cells were also affected: lipid and nucleotide metabolism, and energetics. The high dose LEW exposures were more toxic, particularly at day 7 post LEW exposure (>10-fold increased levels of histamine, quinolinate, N-acetyl-β-alanine, GMP, and UPM). LEW exposure dysregulated integral functions of the cornea, caused inflammation and heightened immune response, and generated oxidative stress. Lipid and nucleotide metabolism, and energetics were also affected. The novel information about altered metabolic profile of rabbit cornea following LEW exposure could assist in delineating complex molecular events; thus, aid in identifying therapeutic targets to effectively ameliorate ocular trauma.

The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease

Chronic inflammatory diseases (CIDs), including inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are thought to emerge from an impaired complex network of inter- and intracellular biochemical interactions among several proteins and small chemical compounds under strong influence of genetic and environmental factors. CIDs are characterised by shared and disease-specific processes, which is reflected by partially overlapping genetic risk maps and pathogenic cells (e.g., T cells). Their pathogenesis involves a plethora of intracellular pathways. The translation of the research findings on CIDs molecular mechanisms into effective treatments is challenging and may explain the low remission rates despite modern targeted therapies. Modelling CID-related causal interactions as networks allows us to tackle the complexity at a systems level and improve our understanding of the interplay of key pathways. Here we report the construction, description, and initial applications of the SYSCID map (https://syscid.elixir-luxembourg.org/), a mechanistic causal interaction network covering the molecular crosstalk between IBD, RA and SLE. We demonstrate that the map serves as an interactive, graphical review of IBD, RA and SLE molecular mechanisms, and helps to understand the complexity of omics data. Examples of such application are illustrated using transcriptome data from time-series gene expression profiles following anti-TNF treatment and data from genome-wide associations studies that enable us to suggest potential effects to altered pathways and propose possible mechanistic biomarkers of treatment response.

Differential Effect of Non-Steroidal Anti-Inflammatory Drugs Aspirin and Naproxen against TMPRSS2-ERG (Fusion)-Driven and Non-Fusion-Driven Prostate Cancer

The consumption of the non-steroidal anti-inflammatory drug (NSAID) aspirin is associated with a significant reduction in the risk of developing TMPRSS2-ERG (fusion)-positive prostate cancer (PCa) compared to fusion-negative PCa in population-based case-control studies; however, no extensive preclinical studies have been conducted to investigate and confirm these protective benefits. Thus, the focus of this study was to determine the potential usefulness of aspirin and another NSAID, naproxen, in PCa prevention, employing preclinical models of both TMPRSS2-ERG (fusion)-driven (with conditional deletion of Pten) and non-TMPRSS2-ERG-driven (Hi-Myc+/- mice) PCa. Male mice (n = 25 mice/group) were fed aspirin- (700 and 1400 ppm) and naproxen- (200 and 400 ppm) supplemented diets from (a) 6 weeks until 32 weeks of Hi-Myc+/- mice age; and (b) 1 week until 20 weeks post-Cre induction in the fusion model. In all NSAID-fed groups, compared to no-drug controls, there was a significant decrease in higher-grade adenocarcinoma incidence in the TMPRSS2-ERG (fusion)-driven PCa model. Notably, there were no moderately differentiated (MD) adenocarcinomas in the dorsolateral prostate of naproxen groups, and its incidence also decreased by ~79-91% in the aspirin cohorts. In contrast, NSAIDs showed little protective effect against prostate tumorigenesis in Hi-Myc+/- mice, suggesting that NSAIDs exert a specific protective effect against TMPRSS2-ERG (fusion)-driven PCa.

Efficacy of a Novel Electroconductive Matrix To Treat Muscle Atrophy and Fat Accumulation in Chronic Massive Rotator Cuff Tears of the Shoulder

The high retear rate after a successful repair of the rotator cuff (RC) is a major clinical challenge. Muscle atrophy and fat accumulation of RC muscles over time adversely affect the rate of retear. Since current surgical techniques do not improve muscle degenerative conditions, new treatments are being developed to reduce muscle atrophy and fat accumulation. In the previous study, we have shown the efficacy of aligned electroconductive nanofibrous fabricated by coating poly(3,4-ethylene dioxythiophene): poly(styrenesulfonate) (PEDOT:PSS) nanoparticles onto aligned poly(ε-caprolactone) (PCL) electrospun nanofibers (PEDOT:PSS matrix) to reduce muscle atrophy in acute and subacute models of RC tears (RCTs). In this study, we further evaluated the efficacy of the PEDOT:PSS matrix to reduce muscle atrophy and fat accumulation in a rat model of chronic massive full-thickness RCTs (MRCTs). The matrices were transplanted on the myotendinous junction to the belly of the supraspinatus and infraspinatus muscles at 16 weeks after MRCTs. The biomechanics and histological assessments showed the potential of the PEDOT:PSS matrix to suppress the progression of muscle atrophy, fat accumulation, and fibrosis in both supraspinatus and infraspinatus muscles at 24 and 32 weeks after MRCTs. We also demonstrated that the PEDOT:PSS matrix implantation significantly improved the tendon morphology and tensile properties compared with current surgical techniques.

In-silico and structure-based assessment to evaluate pathogenicity of missense mutations associated with non-small cell lung cancer identified in the Eph-ephrin class of proteins

Ephs belong to the largest family of receptor tyrosine kinase and are highly conserved both sequentially and structurally. The structural organization of Eph is similar to other receptor tyrosine kinases; constituting the extracellular ligand binding domain, a fibronectin domain followed by intracellular juxtamembrane kinase, and SAM domain. Eph binds to respective ephrin ligand, through the ligand binding domain and forms a tetrameric complex to activate the kinase domain. Eph-ephrin regulates many downstream pathways that lead to physiological events such as cell migration, proliferation, and growth. Therefore, considering the importance of Eph-ephrin class of protein in tumorigenesis, 7,620 clinically reported missense mutations belonging to the class of variables of unknown significance were retrieved from cBioPortal and evaluated for pathogenicity. Thirty-two mutations predicted to be pathogenic using SIFT, Polyphen-2, PROVEAN, SNPs&GO, PMut, iSTABLE, and PremPS in-silico tools were found located either in critical functional regions or encompassing interactions at the binding interface of Eph-ephrin. However, seven were reported in nonsmall cell lung cancer (NSCLC). Considering the relevance of receptor tyrosine kinases and Eph in NSCLC, these seven mutations were assessed for change in the folding pattern using molecular dynamic simulation. Structural alterations, stability, flexibility, compactness, and solvent-exposed area was observed in EphA3 Trp790Cys, EphA7 Leu749Phe, EphB1 Gly685Cys, EphB4 Val748Ala, and Ephrin A2 Trp112Cys. Hence, it can be concluded that the evaluated mutations have potential to alter the folding pattern and thus can be further validated by in-vitro, structural and in-vivo studies for clinical management.

Structural dynamics of clinically-reported VUS in the BARD1 ARD-BRCT region to predict the molecular basis of alterations

The functional domains of BARD1, comprise the Ankyrin Repeat Domain (ARD), C-Terminal domains (BRCTs), and a linker between ARD and the BRCTs, which are known to bind to Cleavage stimulation Factor complex-subunit of 50 kDa (CstF-50). The pathogenic mutation Q564H in the BARD1 ARD-linker-BRCT region has been reported to abrogate the binding between BARD1 and CstF-50. Intermediate penetrance variants of BARD1 are associated with the occurrence of breast cancer. Therefore, seven missense variants of unknown significance (VUS), L447V, P454L, N470S, V507M, I509T, C557S, and Q564H of BARD1, reported in the ARD domain and the linker region were evaluated via molecular dynamics (MD) simulations. The mutants revealed statistically significantly different distributions of RMSD (root mean square deviation), residuewise RMSF (root mean square fluctuation), R_g (radius of gyration), SASA (solvent accessible surface area), and COM (centre of mass)-to-COM distance between the ARD and the BRCT repeat, between the wild type and each mutant. The secondary structural composition of the mutants was slightly altered relative to that of the wild type. However, the reported in-silico based prediction require further validation using in-vitro, biophysical and structure-based approachCommunicated by Ramaswamy H. Sarma.

Pregnancy, infection, and epigenetic regulation: A complex scenario

A unique immunological condition, pregnancy ensures fetus from maternal rejection, allows adequate fetal development, and protects against microorganisms. Infections during pregnancy may lead to devastating consequences for pregnant women and fetuses, resulting in the mother's death, miscarriage, premature childbirth, or neonate with congenital infection and severe diseases and defects. Epigenetic (heritable changes in gene expression) mechanisms like DNA methylation, chromatin modification, and gene expression modulation during gestation are linked with the number of defects in the fetus and adolescents. The feto-maternal crosstalk for fetal survival during the entire gestational stages are tightly regulated by various cellular pathways, including epigenetic mechanisms that respond to both internal as well outer environmental factors, which can influence the fetal development across the gestational stages. Due to the intense physiological, endocrinological, and immunological changes, pregnant women are more susceptible to bacterial, viral, parasitic, and fungal infections than the general population. Microbial infections with viruses (LCMV, SARS-CoV, MERS-CoV, and SARS-CoV-2) and bacteria (Clostridium perfringens, Coxiella burnetii, Listeria monocytogenes, Salmonella enteritidis) further increase the risk to maternal and fetal life and developmental outcome. If the infections remain untreated, the possibility of maternal and fetal death exists. This article focused on the severity and susceptibility to infections caused by Salmonella, Listeria, LCMV, and SARS-CoV-2 during pregnancy and their impact on maternal health and the fetus. How epigenetic regulation during pregnancy plays a vital role in deciding the fetus's developmental outcome under various conditions, including infection and other stress. A better understanding of the host-pathogen interaction, the characterization of the maternal immune system, and the epigenetic regulations during pregnancy may help protect the mother and fetus from infection-mediated outcomes.

Identification of New Compounds against PRRSV Infection by Directly Targeting CD163

The porcine reproductive and respiratory syndrome viruses (PRRSV) led to a global panzootic and huge economical losses to the pork industry. PRRSV targets the scavenger receptor CD163 for productive infection. However, currently no effective treatment is available to control the spread of this disease. Using bimolecular fluorescence complementation (BiFC) assays, we screened a set of small molecules potentially targeting the scavenger receptor cysteine-rich domain 5 (SRCR5) of CD163. We found that the assay examining protein-protein interactions (PPI) between PRRSV glycoprotein 4 (GP4) and the CD163-SRCR5 domain mainly identifies compounds that potently inhibit PRRSV infection, while examining the PPI between PRRSV-GP2a and the SRCR5 domain maximized the identification of positive compounds, including additional ones with various antiviral capabilities. These positive compounds significantly inhibited both types 1 and 2 PRRSV infection of porcine alveolar macrophages. We confirmed that the highly active compounds physically bind to the CD163-SRCR5 protein, with dissociation constant (KD) values ranging from 28 to 39 μM. Structure-activity-relationship (SAR) analysis revealed that although both the 3-(morpholinosulfonyl)anilino and benzenesulfonamide moieties in these compounds are critical for the potency to inhibit PRRSV infection, the morpholinosulfonyl group can be replaced by chlorine substituents without significant loss of antiviral potency. Our study established a system for throughput screening of natural or synthetic compounds highly effective on blocking of PRRSV infection and shed light on further SAR modification of these compounds. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the swine industry worldwide. Current vaccines cannot provide cross protection against different strains, and there are no effective treatments available to hamper the spread of this disease. In this study, we identified a group of new small molecules that can inhibit the PRRSV interaction with its specific receptor CD163 and dramatically block the infection of both types 1 and type 2 PRRSVs to host cells. We also demonstrated the physical association of these compounds with the SRCR5 domain of CD163. In addition, molecular docking and structure-activity relationship analyses provided new insights for the CD163/PRRSV glycoprotein interaction and further improvement of these compounds against PRRSV infection.

Strategies to minimise and monitor biases and imbalances by arm in surgical cluster randomised trials: evidence from ChEETAh, a trial in seven low- and middle-income countries

BACKGROUND

Cluster randomised controlled trials (cRCT) present challenges regarding risks of bias and chance imbalances by arm. This paper reports strategies to minimise and monitor biases and imbalances in the ChEETAh cRCT.

METHODS

ChEETAh was an international cRCT (hospitals as clusters) evaluating whether changing sterile gloves and instruments prior to abdominal wound closure reduces surgical site infection at 30 days postoperative. ChEETAh planned to recruit 12,800 consecutive patients from 64 hospitals in seven low-middle income countries. Eight strategies to minimise and monitor bias were pre-specified: (1) minimum of 4 hospitals per country; (2) pre-randomisation identification of units of exposure (operating theatres, lists, teams or sessions) within clusters; (3) minimisation of randomisation by country and hospital type; (4) site training delivered after randomisation; (5) dedicated 'warm-up week' to train teams; (6) trial specific sticker and patient register to monitor consecutive patient identification; (7) monitoring characteristics of patients and units of exposure; and (8) low-burden outcome-assessment.

RESULTS

This analysis includes 10,686 patients from 70 clusters. The results aligned to the eight strategies were (1) 6 out of 7 countries included ≥ 4 hospitals; (2) 87.1% (61/70) of hospitals maintained their planned operating theatres (82% [27/33] and 92% [34/37] in the intervention and control arms); (3) minimisation maintained balance of key factors in both arms; (4) post-randomisation training was conducted for all hospitals; (5) the 'warm-up week' was conducted at all sites, and feedback used to refine processes; (6) the sticker and trial register were maintained, with an overall inclusion of 98.1% (10,686/10,894) of eligible patients; (7) monitoring allowed swift identification of problems in patient inclusion and key patient characteristics were reported: malignancy (20.3% intervention vs 12.6% control), midline incisions (68.4% vs 58.9%) and elective surgery (52.4% vs 42.6%); and (8) 0.4% (41/9187) of patients refused consent for outcome assessment.

CONCLUSION

cRCTs in surgery have several potential sources of bias that include varying units of exposure and the need for consecutive inclusion of all eligible patients across complex settings. We report a system that monitored and minimised the risks of bias and imbalances by arm, with important lessons for future cRCTs within hospitals.

Abstract 5270: Silibinin modulates migration and survival pathways in bone marrow mast cells via RAC2: Implications in its anti-cancer activity in basal cell carcinoma growth and progression

Most of the non-melanoma skin cancers are basal cell carcinoma (BCC); thus, extensive efforts to discover chemopreventive agents against BCC are ongoing. Recently, we showed that silibinin (SB) exerts strong efficacy against ultraviolet B radiation (UVB)-induced BCC growth/progression, and mast cells (MCs) are one of the targets of its efficacy. Notably, 30 days of UVB exposure in patched (Ptch)+/- mouse model of UVB-induced BCC formation increased MC numbers by ~50% that was completely inhibited by SB. Hence, understanding pathways associated with MC regulation by SB seems valuable for its efficacy against BCC and other cancers. We generated bone marrow MCs (BMMCs) in presence of interleukin (IL)-3 and stem cell factor from C57BL/6 mice (confirmed using flow cytometry dual staining: cKit/Fc€RI). They were treated with two concentrations of SB (25 µM; SB 25 and 100 µM; SB 100) or untreated (control), and proteomics was performed (liquid chromatography mass spectrometry on Fusion Lumos mass spectrometer). Total 3575 proteins were identified and 166 were found to be statistically significant (ANOVA, Fisher’s posthoc analysis, p&lt;0.05, FDR&lt;0.01) amongst the three groups (n=4/group). Proteins with highest differential expression among the groups (greatest fold change expression; n=50), greatest contribution to the selection (variable importance; n=15), and common expression profiles in both SB 25 and SB 100 compared to control (n=21) were selected for further pathway analysis. Important nodes found for SB regulation of MCs were tumor necrosis factor, interferon-gamma, and IL-13; IL-13 also emerged as a key regulatory node in normal BMMCs. Furthermore, to determine the effect of SB in BCC associated MCs, a subset of proteins implicated with skin-associated MC activity (determined using IPA) was generated. Most important molecules implicated included IL-13 and Rac Family Small GTPase2 (RAC2; regulates all myeloid lineages). RAC2 was found to modulate the expression of mast cell protease4 (MCPT4), mast cell transcriptase1 (TPSAB1), and macrophage migration inhibition factor. RAC2 also activates MC proteases via JNK signaling cascade. Together, via the regulation of MCPT4, TPSAB1, and JNK signaling, RAC2 regulates inflammatory responses, and controls MC migration via actin cytoskeleton reorganization and lamellipodia formation. Phagosome maturation was also an important pathway implicated in our analysis; MCs lyse engulfed pathogens/debris via phagosome maturation and fusion with lysosomes. In conclusion, our findings demonstrate that SB increases RAC2 expression in BMMCs, which can regulate MC migration into the tumors and effectively increase the MC protease gene expression. Thus, SB treatment shifts BMMCs towards anti-tumorigenic pathways and RAC2 can be a novel therapeutic target in BCC and other cancers as well.

Citation Format: Neha Mishra, Sandeep Paudel, Chapla Agarwal, Rajesh Agarwal. Silibinin modulates migration and survival pathways in bone marrow mast cells via RAC2: Implications in its anti-cancer activity in basal cell carcinoma growth and progression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5270.

Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity

Several perturbations in the number of peripheral blood leukocytes, such as neutrophilia and lymphopenia associated with Coronavirus disease 2019 (COVID-19) severity, point to systemic molecular cell cycle alterations during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the landscape of cell cycle alterations in COVID-19 remains primarily unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome and transcriptome data to characterize global changes in the cell cycle signature of COVID-19 patients. We found significantly enriched cell cycle-associated gene co-expression modules and an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating the molecular data of 1469 individuals (981 SARS-CoV-2 infected patients and 488 controls [either healthy controls or individuals with other respiratory illnesses]). Among these DEPs and DEGs are several cyclins, cell division cycles, cyclin-dependent kinases, and mini-chromosome maintenance proteins. COVID-19 patients partially shared the expression pattern of some cell cycle-associated genes with other respiratory illnesses but exhibited some specific differential features. Notably, the cell cycle signature predominated in the patients' blood leukocytes (B, T, and natural killer cells) and was associated with COVID-19 severity and disease trajectories. These results provide a unique global understanding of distinct alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention.

Impact of Yoga on Immune Response with Special Reference to COVID-19: A Review of Randomized Controlled Trials

Abstract:

Like other viruses, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continuously evolves due to mutations during genome replication. These mutations lead to various new variants and may alter the pathogenicity, immune escape capacity, and re-infection risk. In addition, it is also evident that a compromised immune system increases the susceptibility and severity of the disease. Therefore, strengthening the immune system is considered to combat Covid. Yoga is an ancient practice used for strengthening the body and mind. There are abundant studies that focus on yoga's benefits for stress management; however, lesser studies observed the effects of yoga on the immune system. Therefore, the present study aims to compile randomized controlled studies on the role of yoga in immunity and COVID-19. Our finding reported moderate evidence for the benefits of yoga in the levels of inflammatory markers, such as C-reactive protein (CRP), and cytokines, such as interleukin (IL) and tumor necrosis factor-alpha (TNF-α). However, lesser shreds of evidence were observed on the effect of yoga on innate and adaptive immunity. Our finding reported a paucity of studies examining the impact of yoga on the immunity of Covid patients. Thus, its efficacy as a potential adjuvant to attenuate Covid-19 infection has yet to be proven. Further extensive studies are recommended to draw the inference on the impact of yoga on Covid-19.

Insight on Vernonia Plant for its Pharmacological Properties: A Review

Vernonia is a woody shrub of the family Asteraceae. Over 1500 species are distributed in tropical and subtropical regions of Africa and Asia. There are more than 54 species known to possess similar morphological features with the characteristic bitter taste. The pharmacological properties of different parts like seeds, leaves, and roots are well documented in folk medicine. They are rich in biologically active constituents such as alkaloids, phenolics, flavonoids, terpenoids, steroid tannins, and carotenoids having broad therapeutic activities like antiinflammatory, hypoglycemic, hyperlipidemia, antimicrobial, antitumor, antioxidative, antiproliferative, antihypertensive, hepatoprotective, etc. The present study summarizes and discusses the phytochemical profile, pharmacological properties, and toxicological effects of the Vernonia plant.

Inflammasome activation and formation of ASC specks in patients with juvenile idiopathic arthritis

Objective

The formation of large intracellular protein aggregates of the inflammasome adaptor ASC is a hallmark of inflammasome activation and characteristic of autoinflammation. Inflammasome activated cells release the highly proinflammatory cytokine IL-1β in addition to ASC specks into the extracellular space. Autoinflammatory activity has been demonstrated in systemic JIA, however minimal data exist on the role of inflammasomes in other JIA subtypes. We therefore investigated, if pyroptotic cells are present in the circulation of oligo- and poly-articular JIA.

Methods

Peripheral blood of JIA patients (n = 46) was investigated for ASC speck formation, a key step in inflammasome activation, by flow cytometry and immunofluorescence. Free ASC and proinflammatory cytokine levels were determined by ELISA and multiplex assay.

Results

Oligo-articular JIA patients showed a significantly increased proportion of ASC speck⁺ monocytes compared to poly-articular JIA patients. In serum free ASC alone is not sufficient to assess inflammasome activity and does not correlate with ASC speck⁺ monocytes. Compared to control several cytokines were significantly elevated in samples of JIA patients. JIA serum containing antinuclear antibodies, incubated with ASC specks boosts a secondary inflammation by IL-1β production in macrophages.

Conclusion

For the first time, we detect ex vivo inflammasome activation by ASC speck formation in oligo- and poly-articular JIA patients. Most notably, inflammasome activation was significantly higher in oligo- compared to poly-articular JIA patients. This data suggests that inflammasome derived autoinflammation may have a greater influence in the previously thought autoimmune oligo-articular JIA patients.

Multimodal approach to characterize the tetrameric form of human PML-RBCC domain and ATO-mediated conformational changes

RING-B box-coiled coil (RBCC) domain of promyelocytic leukemia (PML) comprises a zinc finger motif that is targeted by arsenic trioxide (ATO) to treat acute promyelocytic leukemia (APL) pathogenesis. Preliminary evidence suggests that the PML-RBCC has different functional characteristics, but no structural details have been reported despite its importance in differential expression and cell-cycle regulation. Therefore, the recombinant h-PML-RBCC protein was purified to its homogeneity, and characterized for oligomeric behaviour which indicated that RBCC domain exists as a tetramer in solution. Furthermore, nano-DSF and circular-dichroism demonstrated that the tetrameric form preserves its native conformation along with thermal stability (Tm = 83.2 °C). In-silico-based PML-RBCC structure was used to perform the molecular dynamics simulation for 300 ns in the presence of zinc atoms, which demonstrated the differential dynamic of PML-RBCC tetrameric chains. MMPBSA analysis also indicated the role of hydrophobic interactions that favours stable tetrameric structure of PML-RBCC. ATO-induced secondary and tertiary structure changes were observed in PML-RBCC using circular dichroism and fluorescence spectroscopy. Dynamic light scattering and transmission electron microscopy revealed ATO-induced higher-order oligomerization and aggregation of PML-RBCC. The unique oligomeric nature of the h-PML-RBCC protein and its interactions with ATO will help to understand the mechanism of APL pathogenesis and drug resistance.

Increased protease-activated receptor 1 autoantibodies are associated with severe COVID-19

In patients with severe #COVID19, increased levels of autoantibodies against PAR1 were found. These might serve as allosteric agonists of PAR1 on endothelial cells and platelets, and thus might contribute to the pathogenesis of microthrombosis in COVID-19. https://bit.ly/3pqM9Vv.

In Silico and Structure-Based Assessment of Similar Variants Discovered in Tandem Repeats of BRCT Domains of BRCA1 and BARD1 To Characterize the Folding Pattern

BRCA1 and BARD1 are important proteins in the homologous DNA damage repair pathways. Different genetic variants identified in these proteins have been clinically correlated with the occurrence of hereditary breast and ovarian cancer (HBOC). Variants of unknown significance (VUS) reported in the BRCT domains of BRCA1 and BARD1 substantiate the importance of BRCT domain-containing proteins for genomic integrity. To classify the pathogenicity of variants, in silico, structural and molecular dynamics (MD)-based approaches were explored. Different variants reported in the BRCT region were retrieved from cBioPortal, LOVD3, BRCA Exchange, and COSMIC databases to evaluate the pathogenicity. Multiple sequence alignment and superimposition of the structures of BRCA1 BRCT and BARD1 BRCT domains were performed to compare alterations in folding patterns. From 11 in silico predictions servers, variants reported to be pathogenic by 70% of the servers were considered for structural analysis. To our observations, four residue pairs of both the proteins were reported, harboring 11 variants, H1686Y, W1718L, P1749L, P1749S, and W1837L variants for BRCA1 BRCT and H606D, H606N, W635L, P657L, P657S, and W762F for BARD1 BRCT. MD simulations of the BRCT repeat regions of these variants and wild-type proteins were performed to evaluate the differences of folding patterns. Root mean square deviation (RMSD), R _g, solvent-accessible surface area (SASA), and root mean square fluctuation (RMSF) of variants showed slight differences in the folding patterns from the wild-type proteins. Furthermore, principal components analysis of H1686Y, P1749S, and W1718L variants of BRCA1 showed less flexibility than the wild type, whereas that of H606D, W635L, and W762F of BARD1 showed more flexibility than the wild type. Normal mode analysis of the energy minima from the simulation trajectories revealed that most of the variants do not show much differences in the flexibility compared to the wild-type proteins, except for the discrete regions in the BRCT repeats, most prominently in the 1798-1801 amino acid region of BRCA1 and at the residue 744 in BARD1.

Routine sterile glove and instrument change at the time of abdominal wound closure to prevent surgical site infection (ChEETAh): a pragmatic, cluster-randomised trial in seven low-income and middle-income countries

BACKGROUND

Surgical site infection (SSI) remains the most common complication of surgery around the world. WHO does not make recommendations for changing gloves and instruments before wound closure owing to a lack of evidence. This study aimed to test whether a routine change of gloves and instruments before wound closure reduced abdominal SSI.

METHODS

ChEETAh was a multicentre, cluster randomised trial in seven low-income and middle-income countries (Benin, Ghana, India, Mexico, Nigeria, Rwanda, South Africa). Any hospitals (clusters) doing abdominal surgery in participating countries were eligible. Clusters were randomly assigned to current practice (42) versus intervention (39; routine change of gloves and instruments before wound closure for the whole scrub team). Consecutive adults and children undergoing emergency or elective abdominal surgery (excluding caesarean section) for a clean-contaminated, contaminated, or dirty operation within each cluster were identified and included. It was not possible to mask the site investigators, nor the outcome assessors, but patients were masked to the treatment allocation. The primary outcome was SSI within 30 days after surgery (participant-level), assessed by US Centers for Disease Control and Prevention criteria and on the basis of the intention-to-treat principle. The trial has 90% power to detect a minimum reduction in the primary outcome from 16% to 12%, requiring 12 800 participants from at least 64 clusters. The trial was registered with ClinicalTrials.gov, NCT03700749.

FINDINGS

Between June 24, 2020 and March 31, 2022, 81 clusters were randomly assigned, which included a total of 13 301 consecutive patients (7157 to current practice and 6144 to intervention group). Overall, 11 825 (88·9%) of 13 301 patients were adults, 6125 (46·0%) of 13 301 underwent elective surgery, and 8086 (60·8%) of 13 301 underwent surgery that was clean-contaminated or 5215 (39·2%) of 13 301 underwent surgery that was contaminated-dirty. Glove and instrument change took place in 58 (0·8%) of 7157 patients in the current practice group and 6044 (98·3%) of 6144 patients in the intervention group. The SSI rate was 1280 (18·9%) of 6768 in the current practice group versus 931 (16·0%) of 5789 in the intervention group (adjusted risk ratio: 0·87, 95% CI 0·79-0·95; p=0·0032). There was no evidence to suggest heterogeneity of effect across any of the prespecified subgroup analyses. We did not anticipate or collect any specific data on serious adverse events.

INTERPRETATION

This trial showed a robust benefit to routinely changing gloves and instruments before abdominal wound closure. We suggest that it should be widely implemented into surgical practice around the world.

FUNDING

National Institute for Health Research (NIHR) Clinician Scientist Award, NIHR Global Health Research Unit Grant, Mölnlycke Healthcare.

Pharmacological Perspective of Green Coffee Beans and their Metabolites: A Review

Abstract:

Coffee is the most extensively consumed drink in the world. However, in the last few years, unroasted coffee seeds, popularly known as green coffee beans (GCB), attracted people due to its health properties. This review covers pharmacological efficacy, mechanism of action and bioactive components of green coffee beans. It contains a unique set of polyphenolic compounds, methylxanthines and diterpenes which are responsible for the astringency, flavour, smell and taste as well as for its health benefits. Chlorogenic acid, a polyphenolic compound, is the major bioactive compound in coffee beans which contributes most to the medicinal activities present in it. The finding reveals the effectiveness of green coffee beans in all parameters of metabolic syndrome by regulating adipokines. It prevents doxorubicin induced cardiomyocyte cell death and also has antimutagenic activity on the HeLa cell line and PA-1 cell line. Neuroprotective effect of GCB in degenerative disease was achieved by reducing neuroinflammatory markers TNF-α (tumor necrosis factor-α) and IL-1β (interleukin-1β). Along with these properties, GCB has shown some potential antimicrobial, hepatoprotective, cardioprotective and sunscreen effects, as it contains a high sun protection factor. The findings from this study conclude that green coffee beans have shown bizarrely several health benefits, but a large number of trials and intervention are required to establish its medicinal values.

Research models of sulfur mustard- and nitrogen mustard-induced ocular injuries and potential therapeutics

Sulfur mustard (SM) is a notorious, bifunctional alkylating vesicant that was first used in warfare during World War I in 1917 and since then has been deployed in numerous skirmishes with its most recent documented use being during the Middle Eastern conflicts. Apart from its use in combat and terrorist activities, continual threat of accidental exposure from old stockpiles and improperly discarded munitions is ever present, especially to the innocent and unassuming civilian populations. SM can cause devastating injuries, depending on the dosage of SM exposure, route of exposure, as well as the physiological conditions of the individuals exposed. The most common routes of exposure are ocular, dermal, and exposure to the lungs and respiratory tissues through inhalation. Eyes are the most susceptible organ to SM-induced toxicities owing to their high moisture content and rapidly dividing cells. Additionally, ocular injury causes the most expeditious disablement of individuals even upon whole-body exposures. Therefore, it is imperative to understand the mechanisms underlying SM-induced ocular toxicity and design therapeutic interventions to prevent/mitigate ocular injuries. Ocular SM exposure may cause a wide range of symptoms such as inflammation, lacrimation, itching, dryness, photophobia, edema of the cornea/sclera/retina/iris, conjunctivitis, degradation of the corneal layer, fusion of two or more ocular layers, neovascularization, fibrosis, and temporary or permanent structural damage to one or more ocular layers. These symptoms may lead to vision impairments, resulting in partial or complete blindness that may be permanent. The highly toxic and exceedingly notorious nature of SM makes it a highly regulated chemical, requiring very expensive licensing, security, and safety requirements; thus, the more easily accessible analogue, nitrogen mustard (NM) that mimics SM-induced toxicity and injuries is employed in plethora of studies conducted in different animal models and culture systems. This review provides a comprehensive account of the injuries and symptoms that occur upon ocular SM exposures in human patients as well as studies in animal (in vivo, ex vivo) and cell (in vitro) models of SM and NM ocular exposures. Special emphasis has been laid on highlighting the strengths and lacunae in the research as well as the possible unexplored avenues of mechanisms underlying mustard-induced ocular injury that can be explored in future research endeavors. Furthermore, development of therapeutic interventions and targets of interest in the ocular system exposed to SM and NM, based on studies in human patients as well as in vivo, ex vivo, and in vitro models has been discussed in great depth, providing a valuable knowledge database to delineate pathways associated with vesicant-induced toxicity, and strategies/diagnostic tools against SM-induced toxicity.

Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum

India confines more than 17% of the world’s population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes, the second most targeted group of drug targets. The sequence-level analysis identified similarities and differences among different populations based on the nsSNVs and amino acid exchange frequencies whereas a comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network was investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveals critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world and investigating its implications in the sequence, structural and pharmacogenomic landscape. The preliminary investigation reported in this paper, supporting the screening and detection of ADRs specific to the Indian population could aid in the development of techniques for pre-clinical and post-market screening of drug-related adverse events in the Indian population.

Characterization of stage-specific tumor progression in TMPRSS2-ERG (fusion)-driven and non-fusion-driven prostate cancer in GEM models

In the present study, we performed a comparative stage-specific pathological and molecular marker evaluation of TMPRSS2-ERG fusion and PTEN loss-driven (TMPRSS2-ERG. Pten^flox/flox ) versus non-fusion-driven prostate tumorigenesis (Hi-Myc) in mice. Anterior, ventral, and dorsolateral prostates were collected from mice at different ages (or time points post-Cre induction). Results indicated that growth and progression of prostatic intraepithelial lesions to adenocarcinoma stages occurred in both mice models albeit at different rates. In the TMPRSS2-ERG. Pten^flox/flox mice, the initiation of tumorigenesis was slow, but subsequent progression through different stages became increasingly faster. Adenocarcinoma stage was reached early on; however, no high-grade undifferentiated tumors were observed. Conversely, in the Hi-Myc^+/- mice, tumorigenesis initiation was rapid; however, progression through different stages was relatively slower and it took a while to reach the more aggressive phenotype stage. Nevertheless, at the advanced stages in the Hi-Myc^+/- mice, high-grade undifferentiated tumors were observed compared to the later stage tumors observed in the fusion-driven TMPRSS2-ERG. Pten^flox/flox mice. These results were corroborated by the stage specific-pattern in the molecular expression of proliferation markers (PCNA and c-Myc); androgen receptor (AR); fusion-resultant overexpression of ERG; Prostein (SLC45-A3); and angiogenesis marker (CD-31). Importantly, there was a significant increase in immune cell infiltrations, which increased with the stage of tumorigenesis, in the TMPRSS2-ERG fusion-positive tumors relative to fusion negative tumors. Together, these findings are both novel and highly significant in establishing a working preclinical model for evaluating the efficacy of interventions during different stages of tumorigenesis in TMPRSS2-ERG fusion-driven PCa.

Abstract 716: Silibinin: A novel potential therapeutic agent against UVB-induced basal cell carcinoma

Herein, we report silibinin (a natural flavonolignan from milk thistle seeds) efficacy against basal cell carcinoma (BCC), the major non-melanoma skin cancer. To determine the preventive/therapeutic activity of silibinin on the progression of UVB-induced microscopic BCC lesions to more advanced BCC, both male and female 8 weeks old Ptch1+/- mice were irradiated with 240 mJ/cm2 UVB dose 3 times/week (M, W, F) for 26 weeks, and thereafter, UVB irradiation was stopped. At this point (after initial UVB exposure for 26 weeks was stopped), these Ptch1+/- mice were randomized into 3 groups: Baseline group (mice euthanized for baseline data); Vehicle group: mice treated topically with acetone for 20 more weeks, and Silibinin group: mice treated topically with silibinin (9 mg in 200 µL acetone), once a day for five days/week for 20 more weeks i.e., till 54 weeks of mice age. Assessment of BCC and non-BCC lesion pathology was performed following β-galactosidase and H&E based histopathological analysis. Results indicated that compared to BCC-associated pathologies observed at baseline, acetone exposure for another 20 weeks resulted in a significant increase in the number (~2 folds, P&lt;0.001) and area (~3.4 folds, P&lt;0.001) covered by BCC lesions. There was also a significant increase in epidermal dysplasia, fibrosarcoma, and squamous cell carcinoma incidence. Notably, topical application of silibinin during this phase significantly decreased BCC numbers as well as area covered by BCC lesions by ~76% (P&lt;0.001) and ~88% (P&lt;0.001), respectively. This protective effect of silibinin was associated with decreased proliferation of basal cells and decreased expression of Hh signaling molecules (Smo and Gli1). To further delineate the changes associated with silibinin’ s protective effect at the transcriptomic level, RNA sequencing studies were performed in skin samples from all three groups as well as non-UVB exposed control mice. Clustering of mRNA profile by sparse Partial Least Squares - Discriminant Analysis (sPLS-DA) showed that UVB exposed tissues (not treated with silibinin) were significantly different from non-UVB controls; most notably, silibinin treatment (after UVB exposure) reversed this phenomenon and the transcriptomic profile of silibinin group was almost similar to non-UVB controls. This indicated that topical silibinin was not only able to protect against progression to advanced BCC but had the potential to even normalize the aberrant gene expression driving BCC formation. In addition, Gene ontology enrichment analysis as well as Pathway enrichment analysis of differentially expressed genes showed silibinin-associated enrichment in the calcium and CX3CR1-mediated signaling pathway, and TGF-β-mediated regulation of the extracellular matrix. Taken together, these results highlight the potential of silibinin to be an effective preventive and/or therapeutic modality against BCC growth and progression.

Citation Format: Komal Raina, Sandeep Paudel, Neha Mishra, Sushil Kumar, David J. Orlicky, Zhiying You, Rama Kant, Chapla Agarwal, Rajesh Agarwal. Silibinin: A novel potential therapeutic agent against UVB-induced basal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 716.

AB0042 OPTIMAL CONDITIONS FOR THE DETECTION OF INFLAMMASOME ACTIVATION IN CD14+ CD16- MONOCYTES FROM HUMAN BLOOD BY FLOW CYTOMETRY

Background

The inflammasome activation is linked to the aggregation of the adaptor protein ASC into a multimeric structure, known as the ASC speck. The aggregation of cytosolic ASC into ASC specks is therefore used as a readout parameter for inflammasome activity. The direct detection of ASC speck formation on a single cell basis through flow cytometry, can analyze inflammasome activated cells. This allows the investigation of inflammasome activity in a clinical setting.

Objectives

Investigating the optimal conditions for a reliable identification of inflammasome activated ASC speck positive cells ex vivo using flow cytometry.

Methods

Freshly donated blood from five different healthy donors was used for all experiments. The choice of anticoagulant, storage time and storage temperature were examined. PBMCs were isolated from blood collecting tubes with ethylenediaminetetraacetic acid (EDTA) or lithium heparin (LH). PBMCs were also isolated from LH blood stored at 4 °C, room temperature (RT), 37 °C and after different storage times. After isolation, PBMCs were fixed immediately and stained for flow cytometric analysis. ASC speck positive CD14+ CD16- monocytes and THP-1 cells can be generated through incubation with nigericin in PBS.

Results

We adapted a method for flow cytometric analysis of ASC specks, with was previously described by Sester et al. [1]. As expected, we observed ASC speck formation after inflammasome activation, in CD14+ CD16-monocytes through a decrease in ASC fluorescent pulse width and an increase in ASC fluorescent pulse area. Monocytes in PBMCs collected from tubes with EDTA compared with LH showed significantly higher numbers of unspecific ASC speck positive cells. Blood storage at RT for 24 h can lead to an unspecific ASC speck formation. Storage at 37 °C resulted in contamination of the PBMC interface with erythrocytes, while blood stored at 4 °C resulted in severe cell clumping. Since storing LH blood for 24 h at RT lead to unspecific ASC speck formation in CD14+ CD16- cells, but not monocytes from freshly isolated PBMCs, the determination of the time until unspecific ASC speck signals occur was investigated. A significant increase in ASC speck positive CD14+CD16- monocytes was detected after 4 h storage at RT compared to directly processed samples and the number of ASC speck positive monocytes further accumulated over time. The incubation with nigericin in PBS leads to a significant increase in ASC speck positive CD14+ CD16- monocytes and THP-1 cells compared to incubation in RPMI media.

Conclusion

The flow cytometric detection of ASC specks is adapted for practical clinical usability. To reduce background signals, LH- instead of EDTA blood collecting tubes are recommended. The LH blood should be processed within 2 h after blood collection and be stored at RT. To avoid nonspecific activation and formation of ASC specks, the PBMCs should be isolated directly after venipuncture and fixed immediately. It is also possible to freeze the PBMCs until further usage. However, this will cause some loss of ASC speck positive cells. With these settings, clinical samples can now be examined.

References

[1]Sester, D.P et al. A novel flow cytometric method to assess inflammasome formation. J. Immunol. 2015, 194, 455–462.

Acknowledgements

We thank all healthy donors who participated in this study. The authors thank Jana Gramenz (University Medicine Greifswald, Pediatric Rheumatology and Immunology, Greifswald, Germany) for excellent technical assistance.

Disclosure of Interests

None declared

Impact of Natural Farming Cropping System on Rural Households—Evidence From Solan District of Himachal Pradesh, India

Natural farming, popularly known as zero budget natural farming, is an innovative farming approach. It is low input based, climate resilient, and low cost farming system because all the inputs (insect repellents, fungicides, and pesticides) are made up of natural herbs and locally available inputs, thereby reducing the use of artificial fertilizers and industrial pesticides. It is becoming increasingly popular among the smallholder farmers of Himachal Pradesh. Under the natural farming system, 3 to 12 crops are cultivated together on the same area, along with leguminous crops as intercrop in order to ensure that no piece of land is wasted and utilized properly. This article focuses mainly on the different cropping systems of natural farming and comparing the economics of natural farming (NF) with conventional farming (CF) systems. Study shows that farmers adopted five major crop combinations under natural farming system, i.e., vegetables-based cropping system (e.g., tomato + beans + cucumber and cauliflower + pea + radish), vegetables-cereals-based cropping system, and other three more cropping systems discussed in this article. The results indicated that a vegetable-based cropping system has 19.68% more net return in Kharif season and 24.64% more net return in Rabi season as compared to conventional farming vegetable-based monocropping system. NF maximizes land use and reduces the chance of crop yield loss. NF has resulted in increased returns especially in the vegetable cropping system where reduction in cost was 30.73 per cent (kharif) and 11.88 per cent (rabi) across all crop combinations in comparison to CF. It is found in study that NF was cost savings from not using chemical fertilizers and pesticides, as well as higher benefit from intercrops.

Salmonella Typhimurium fepB negatively regulates C. elegans behavioral plasticity

OBJECTIVES

Dauer is an alternative developmental stage of Caenorhabditis elegans (C. elegans) that gives survival benefits under unfavorable environmental conditions. Our study aims to decipher C. elegans dauer larvae development upon Salmonella Typhimurium infection and how the bacterial gene regulating the worm's behavioural plasticity for better survival.

METHODS

Age-synchronized L4 C. elegans worms were infected with Salmonella Typhimurium 14028s (WT-STM) strain and mutant strains to check the dauer larvae development using 1% SDS. Besides, bacterial load in animals' gut, pharyngeal pumping rate and viability were checked. Worm's immune genes (e.g., ilys-3, lys-7, pmk-1, abf-2, clec-60) and dauer regulatory genes (e.g., daf-7, daf-11, daf-12, daf-16, daf-3) were checked by performing qRT-PCR under infection conditions.

RESULTS

We found that deletion of the fepB gene in S. Typhimurium strain became less pathogenic with reduced flagellar motility and biofilm-forming ability. Besides, there was decreased bacterial burden in the worm's gut with no damage to their pharynx. The fepB mutant strain was also able to enhance the immune responses for better survival of worms. Infection with mutant strain could activate dauer signaling via the TGF-β pathway leading to a significant increase in dauer formation than WT-STM infection.

CONCLUSION

Our study indicated that the bacteria act as a food source for the growth of C. elegans and development and can act as a signal that might be playing an essential role in regulating the host physiology for their survival. Such a study can help us in understanding the complex host-pathogen interaction benefiting pathogen in host dissemination.

COVID-19 Risk Stratification and Mortality Prediction in Hospitalized Indian Patients: Harnessing clinical data for public health benefits

The variability of clinical course and prognosis of COVID-19 highlights the necessity of patient sub-group risk stratification based on clinical data. In this study, clinical data from a cohort of Indian COVID-19 hospitalized patients is used to develop risk stratification and mortality prediction models. We analyzed a set of 70 clinical parameters including physiological and hematological for developing machine learning models to identify biomarkers. We also compared the Indian and Wuhan cohort, and analyzed the role of steroids. A bootstrap averaged ensemble of Bayesian networks was also learned to construct an explainable model for discovering actionable influences on mortality and days to outcome. We discovered blood parameters, diabetes, co-morbidity and SpO2 levels as important risk stratification features, whereas mortality prediction is dependent only on blood parameters. XGboost and logistic regression model yielded the best performance on risk stratification and mortality prediction, respectively (AUC score 0.83, AUC score 0.92). Blood coagulation parameters (ferritin, D-Dimer and INR), immune and inflammation parameters IL6, LDH and Neutrophil (%) are common features for both risk and mortality prediction. Compared with Wuhan patients, Indian patients with extreme blood parameters indicated higher survival rate. Analyses of medications suggest that a higher proportion of survivors and mild patients who were administered steroids had extreme neutrophil and lymphocyte percentages. The ensemble averaged Bayesian network structure revealed serum ferritin to be the most important predictor for mortality and Vitamin D to influence severity independent of days to outcome. The findings are important for effective triage during strains on healthcare infrastructure.