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.

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<0.05, FDR<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.

Muscle degeneration in chronic massive rotator cuff tears of the shoulder: Addressing the real problem using a graphene matrix

Massive rotator cuff tears (MRCTs) of the shoulder cause disability and pain among the adult population. In chronic injuries, the tendon retraction and subsequently the loss of mechanical load lead to muscle atrophy, fat accumulation, and fibrosis formation over time. The intrinsic repair mechanism of muscle and the successful repair of the torn tendon cannot reverse the muscle degeneration following MRCTs. To address these limitations, we developed an electroconductive matrix by incorporating graphene nanoplatelets (GnPs) into aligned poly(l-lactic acid) (PLLA) nanofibers. This study aimed to understand 1) the effects of GnP matrices on muscle regeneration and inhibition of fat formation in vitro and 2) the ability of GnP matrices to reverse muscle degenerative changes in vivo following an MRCT. The GnP matrix significantly increased myotube formation, which can be attributed to enhanced intracellular calcium ions in myoblasts. Moreover, the GnP matrix suppressed adipogenesis in adipose-derived stem cells. These results supported the clinical effects of the GnP matrix on reducing fat accumulation and muscle atrophy. The histological evaluation showed the potential of the GnP matrix to reverse muscle atrophy, fat accumulation, and fibrosis in both supraspinatus and infraspinatus muscles at 24 and 32 wk after the chronic MRCTs of the rat shoulder. The pathological evaluation of internal organs confirmed the long-term biocompatibility of the GnP matrix. We found that reversing muscle degenerative changes improved the morphology and tensile properties of the tendon compared with current surgical techniques. The long-term biocompatibility and the ability of the GnP matrix to treat muscle degeneration are promising for the realization of MRCT healing and regeneration.

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<0.001) and area (~3.4 folds, P<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<0.001) and ~88% (P<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.