Deposition of onco-histone H3.3-G34W leads to DNA repair deficiency and activates cGAS/STING-mediated immune responses

Mutations in histone H3.3-encoding genes causing mutant histone tails are associated with specific cancers such as pediatric glioblastomas (H3.3-G34R/V) and giant cell tumor of the bone (H3.3-G34W). The mechanisms by which these mutations promote malignancy are not completely understood. Here we show that cells expressing H3.3-G34W exhibit DNA double-strand breaks (DSBs) repair defects and increased cellular sensitivity to ionizing radiation (IR). Mechanistically, H3.3-G34W can be deposited to damaged chromatin, but in contrast to wild-type H3.3, does not interact with non-homologous end-joining (NHEJ) key effectors KU70/80 and XRCC4 leading to NHEJ deficiency. Together with defective cell cycle checkpoints reported previously, this DNA repair deficiency in H3.3-G34W cells led to accumulation of micronuclei and cytosolic DNA following IR, which subsequently led to activation of the cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) pathway, thereby inducing release of immune-stimulatory cytokines. These findings suggest a potential for radiotherapy for tumors expressing H3.3-G34W, which can be further improved by combination with STING agonists to induce immune-mediated therapeutic efficacy.

Two-way pharmacodynamic modeling of drug combinations and its application to pairs of repurposed Ebola and SARS-CoV-2 agents

Existing pharmacodynamic (PD) mathematical models for drug combinations discriminate antagonistic, additive, multiplicative, and synergistic effects, but fail to consider how concentration-dependent drug interaction effects may vary across an entire dose-response matrix. We developed a two-way pharmacodynamic (TWPD) model to capture the PD of two-drug combinations. TWPD captures interactions between upstream and downstream drugs that act on different stages of viral replication, by quantifying upstream drug efficacy and concentration-dependent effects on downstream drug pharmacodynamic parameters. We applied TWPD to previously published in vitro drug matrixes for repurposed potential anti-Ebola and anti-SARS-CoV-2 drug pairs. Depending on the drug pairing, the model recapitulated combined efficacies as or more accurately than existing models and can be used to infer efficacy at untested drug concentrations. TWPD fits the data slightly better in one direction for all drug pairs, meaning that we can tentatively infer the upstream drug. Based on its high accuracy, TWPD could be used in concert with PK models to estimate the therapeutic effects of drug pairs in vivo.

DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts

Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription. Here, we use deep RNA sequencing from cancer cell lines treated with DNA methyltransferase inhibitor (DNMTi) and/or Histone deacetylase inhibitor (HDACi), to assemble a de novo transcriptome and identify several thousand ERV-derived, treatment-induced novel polyadenylated transcripts (TINPATs). Using immunopeptidomics, we demonstrate the human leukocyte antigen (HLA) presentation of 45 spectra-validated treatment-induced neopeptides (t-neopeptides) arising from TINPATs. We illustrate the potential of the identified t-neopeptides to elicit a T-cell response to effectively target cancer cells. We further verify the presence of t-neopeptides in AML patient samples after in vivo treatment with the DNMT inhibitor Decitabine. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies.

'PartBreCon' study. A UK multicentre retrospective cohort study to assess outcomes following PARTial BREast reCONstruction with chest wall perforator flaps

BACKGROUND

Partial breast reconstruction with a pedicled chest wall perforator flap (CWPF) enables breast conservation in a higher tumour: breast volume ratio scenario. Since there is limited evidence, this retrospective cohort study aimed to ascertain immediate (30-days) and medium-term (follow-up duration) surgical outcomes.

METHODS

STROBE-compliant protocol ascertained CWPF outcomes between March 2011-March 2021. UK centres known to perform CWPF were invited to participate if they performed at least 10 cases. Data were retrospectively collected, including patient demographics, tumour and treatment characteristics, and surgical and oncological outcomes. Statistical analysis (R™) included multivariable logistic regression and sensitivity analysis.

RESULTS

Across 15 centres, 507 patients with median age (54 years, IQR; 48-62), body mass index (25.4 kg/m2, IQR; 22.5-29), tumour size (26 mm, IQR; 18-35), and specimen weight (62 g, IQR; 40-92) had following flap types: LiCAP (54.1%, n = 273), MiCAP/AiCAP (19.6%, n = 99), LiCAP + LTAP (19.8%, n = 100) and TDAP (2.2%, n = 11). 30-days complication rates were in 12%: haematoma (4.3%, n = 22), wound infection (4.3%, n = 22), delayed wound healing (2.8%, n = 14) and flap loss (0.6%, n = 3; 1 full) leading to readmissions (2.6%, n = 13) and re-operations (2.6%, n = 13). Positive margins (n = 88, 17.7%) led to 15.9% (n = 79) re-excisions, including 7.5% (n = 37) at the planned 2nd of 2-stage surgery and 1.8% (n = 9) mastectomy. At median 23 months (IQR; 11-39) follow-up, there were 1.2% (n = 6) symmetrisations; recurrences: local (1%), regional/nodal (0.6%) and distant (3.2%).

CONCLUSIONS

This large multicentre cohort study demonstrates acceptable complication and margin re-excision rates. CWPF extends the range of breast conservation techniques. Further studies are required for long-term oncological outcomes.

Harnessing the MYB-dependent TAL1 5'super-enhancer for targeted therapy in T-ALL

The acquisition of genetic abnormalities engendering oncogene dysregulation underpins cancer development. Certain proto-oncogenes possess several dysregulation mechanisms, yet how each mechanism impacts clinical outcome is unclear. Using T-cell acute lymphoblastic leukemia (T-ALL) as an example, we show that patients harboring 5'super-enhancer (5'SE) mutations of the TAL1 oncogene identifies a specific patient subgroup with poor prognosis irrespective of the level of oncogene dysregulation. Remarkably, the MYB dependent oncogenic 5'SE can be targeted using Mebendazole to induce MYB protein degradation and T-ALL cell death. Of note Mebendazole treatment demonstrated efficacy in vivo in T-ALL preclinical models. Our work provides proof of concept that within a specific oncogene driven cancer, the mechanism of oncogene dysregulation rather than the oncogene itself can identify clinically distinct patient subgroups and pave the way for future super-enhancer targeting therapy.

TAL1 activation in T-Cell acute lymphoblastic leukemia: A novel oncogenic 3' neoenhancer

T-cell acute lymphocytic leukemia protein 1 (TAL1) is one of the most frequently deregulated oncogenes in T-cell acute lymphoblastic leukemia (T-ALL). Its deregulation can occur through diverse in cis-alterations, including SIL-TAL1 microdeletions, translocations with Tcell Receptor (TCR) loci and, more recently described upstream intergenic non-coding mutations. These mutations consist of recurrent focal microinsertions that create an oncogenic neo-enhancer accompanied with activating epigenetic marks. This observation laid the groundwork for an innovative paradigm, the activation of proto-oncogenes via genomic alterations of non-coding intergenic regions. However, for the majority of TAL1 expressing (TAL1+) T-ALLs, the deregulation mechanism remains "unresolved". We took advantage of H3K27ac and H3K4me3 ChIP-seq data of eight T-ALLs, including five TAL1+ cases and identified a putative novel oncogenic neo-enhancer downstream of TAL1 in an "unresolved" monoallelic TAL1+ case. A rare but recurrent somatic heterozygous microinsertion within this region creates a de novo binding site for MYB transcription factor (TF). Here, we demonstrate that this mutation leads to increased enhancer activity, gain of active epigenetic marks and TAL1 activation via recruitment of MYB. These results highlight the diversity of non-coding mutations that can drive oncogene activation.

Validity of CHA2DS2-VASc score in patients with malignancies

Introduction

Anticoagulation for patients with atrial fibrillation/flutter (AF) after risk stratification based on CHA2DS2-VASc score (congestive heart failure, hypertension, age group, Diabetes Mellitus, prior stroke, transient ischemic attack or thromboembolism, prior heart attack, peripheral artery disease or aortic plaque and patient's gender) has been the gold standard practice to prevent cerebrovascular accidents (CVA).

Purpose

Since patients with malignancies are at increased risk of thrombophilia, we tried to study if cancer patients with atrial fibrillation are at increased risk for CVA beyond what should be expected based on their comorbidities.

Methods

We used the Nationwide Readmissions Database (NRD) database for the years 2016–2019. First, we extracted all cases with a diagnosis of atrial fibrillation/flutter. Exclusion criteria included patients younger than 18-year-old. We studied the comorbidities and calculated CHA2DS2-VASc score. Then, we compared the risk for admission with an acute CVA in patients with and without any diagnosis of malignancies (solid cancer, leukemia, lymphoma or metastatic disease). Patients with carcinoma in situ were considered non-cancer patients. Corrected logistic regression and Chi-square tests using survey procedures in SAS 8.1 were applied to accommodate for complex sampling (Rao-Scott design).

Results

We identified 1,748,619 weighted admissions with AF equally distributed across the years. 5% were patients with malignancies. The mean age was 74-year-old for cancer patients and 71-year-old for non-cancer patients with quite equal gender distribution (43–49% were female). Patients with a diagnosis of cancer has high inpatient mortality (13%). Every additional point in CHA2DS2-VASc score was associated with increased odds of admission with CVA. Having a diagnosis of cancer was not associated with increased odds of admission with CVA (odd ratio for 95% confidence interval 1.0 [0.95–1.1]). Patients with history of VTE (assuming they are on anticoagulation) or who are on chronic anticoagulation have lower risk of admission with acute CVA if they have AF.

Conclusions

Although malignancies is associated with hypercoagulable status including higher risk for stroke, deep venous thrombosis and pulmonary embolism, our cross-sectional study indicates that CHA2DS2-VASc score is still a reliable tool for risk stratification in patients with atrial fibrillation. More longitudinal studies are needed.

Funding Acknowledgement

Type of funding sources: None.

Modeling explains prolonged SARS-CoV-2 nasal shedding relative to lung shedding in remdesivir treated rhesus macaques

In clinical trials, remdesivir decreased recovery time in hospitalized patients with SARS- CoV-2 and prevented hospitalization when given early during infection, despite not reducing nasal viral loads. In rhesus macaques, early remdesivir prevented pneumonia and lowered lung viral loads, but viral loads increased in nasal passages after five days. We developed mathematical models to explain these results. Our model raises the hypotheses that: 1) in contrast to nasal passages viral load monotonically decreases in lungs during therapy because of infection-dependent generation of refractory cells, 2) slight reduction in lung viral loads with an imperfect agent may result in a substantial decrease in lung damage, and 3) increases in nasal viral load may occur due to a blunting of peak viral load which decreases the intensity of the innate immune response. We demonstrate that a higher potency drug could lower viral loads in nasal passages and lung.

Multi-scale modelling reveals that early super-spreader events are a likely contributor to novel variant predominance

The emergence of new SARS-CoV-2 variants of concern (VOC) has hampered international efforts to contain the COVID-19 pandemic. VOCs have been characterized to varying degrees by higher transmissibility, worse infection outcomes and evasion of vaccine and infection-induced immunologic memory. VOCs are hypothesized to have originated from animal reservoirs, communities in regions with low surveillance and/or single individuals with poor immunologic control of the virus. Yet, the factors dictating which variants ultimately predominate remain incompletely characterized. Here we present a multi-scale model of SARS-CoV-2 dynamics that describes population spread through individuals whose viral loads and numbers of contacts (drawn from an over-dispersed distribution) are both time-varying. This framework allows us to explore how super-spreader events (SSE) (defined as greater than five secondary infections per day) contribute to variant emergence. We find stochasticity remains a powerful determinant of predominance. Variants that predominate are more likely to be associated with higher infectiousness, an SSE early after variant emergence and ongoing decline of the current dominant variant. Additionally, our simulations reveal that most new highly infectious variants that infect one or a few individuals do not achieve permanence in the population. Consequently, interventions that reduce super-spreading may delay or mitigate emergence of VOCs.

INFLUENCE OF THE DURATION OF DIABETES AND VIBRATION PERCEPTION THRESHOLD ON THE SEVERITY OF ERECTILE DYSFUNCTION IN PATIENTS WITH TYPE 2 DIABETES MELLITUS

BACKGROUND

Erectile dysfunction(ED) in men is a frequent under-reported complication of diabetes mellitus, which is becoming significant health problem worldwide.

AIMS

The study aims to determine the prevalence and risk factors for development of ED in North Indian patients with type 2 diabetes mellitus.

METHODS

We used international index of erectile function (IIEF-5) for the assessment of ED in 796 patients with type 2 diabetes mellitus. We recorded the age, duration of diabetes, glycemic status, body mass index, diabetes medications, microvascular and macrovascular complications.

RESULTS

The mean age of patients in the study was 49.38 ± 9.52 years. The prevalence of ED in patients with type 2 diabetes mellitus was 79.4%. Logistic regression analysis revealed that age, body mass index, glycemic control, insulin therapy, retinopathy and nephropathy was not significantly associated with erectile dysfunction in patients with type 2 diabetes mellitus. Duration of diabetes (OR = 1.054, 95% CI 1.007 to 1.102, P=0.023) and vibration perception threshold (OR = 1.071, 95% CI 1.042 to 1.102, P=0.000) were identified as key risk factors for development of ED.

CONCLUSION

Duration of diabetes and peripheral neuropathy emerged as significant risk factors for development of severe erectile dysfunction.

Modeling-Based Response-Guided DAA Therapy for Chronic Hepatitis C to Identify Individuals for Shortening Treatment Duration

Shortening duration of direct-acting antiviral therapy for chronic hepatitis C could provide cost savings, reduce medication exposure, and foster adherence and treatment completion in special populations. The current analysis indicates that measuring hepatitis C virus at baseline and on days 7 and 14 of therapy can identify patients for shortening therapy duration.

Antiretroviral therapy for HIV and intrahepatic hepatitis C virus replication

OBJECTIVE

HIV alters host responses to hepatitis C virus (HCV). However, the impact of antiretroviral therapy (ART) on HCV is rarely understood in relevant tissues and never before within individual hepatocytes.

DESIGN

HIV and HCV kinetics were studied before and after ART initiation among 19 HIV/HCV co-infected persons. From five persons with the largest decline in plasma HCV RNA, liver tissues collected before and during ART, when plasma HIV RNA was undetectable, were studied.

METHODS

We used single-cell laser capture microdissection and quantitative PCR to assess intrahepatic HCV. Immunohistochemistry was performed to characterize intrahepatic immune cell populations.

RESULTS

Plasma HCV RNA declined by 0.81 (0.52-1.60) log10 IU/ml from a median (range) 7.26 (6.05-7.29) log10 IU/ml and correlated with proportions of HCV-infected hepatocytes (r = 0.89, P = 2 × 10-5), which declined from median (range) of 37% (6-49%) to 23% (0.5-52%) after plasma HIV clearance. Median (range) HCV RNA abundance within cells was unchanged in four of five participants. Liver T-cell abundance unexpectedly decreased, whereas natural killer (NK) and NK T-cell infiltration increased, correlating with changes in proportions of HCV-infected hepatocytes (r = -0.82 and r = -0.73, respectively). Hepatocyte expression of HLA-E, an NK cell restriction marker, correlated with proportions of HCV-infected hepatocytes (r = 0.79).

CONCLUSION

These are the first data to show that ART control of HIV reduces the intrahepatic burden of HCV. Furthermore, our data suggest that HIV affects the pathogenesis of HCV infection by an NK/NK T-cell-mediated mechanism that may involve HLA-E and can be rescued, at least in part, by ART.

An evaluation of remineralised MIH using CPP-ACP and fluoride varnish: An in-situ and in-vitro study

BACKGROUND

Molar incisor hypomineralization (MIH) affected teeth have enamel with altered mineral content like decreased calcium and phosphorus and increased carbon content leading to porous enamel and subsequent post-eruptive breakdown.

AIM

An in situ study was conducted to evaluate and compare the effects of a Casein Phosphopeptide-Amorphous Calcium Phosphate (CPP-ACP)-based cream and fluoride varnish on the remineralization of MIH affected teeth.

METHODS

Enamel slabs were prepared from MIH affected teeth that had been extracted for various reasons and inserted in appliances of 30 participants who were undergoing interceptive orthodontic therapy. They were randomly divided into two groups using block randomization technique: Group A-daily single application of CPP-ACP cream (n = 15); Group B-professional application of fluoride varnishes every 3 months (n = 15). After 6 months of regular wear of the appliance, the enamel slabs were placed under Field Emission Scanning Microscope (FESEM) and Energy-Dispersive Spectroscopy (EDS) for evaluation of ultra structure and mineral content, respectively.

RESULTS

A significant increase in calcium and phosphorus content, and a decrease in carbon content was observed within the 6 months period, suggesting remineralization in both the groups. On comparing the Ca:P and Ca:C ratios, a significant increase in the Ca:C ratio was evident in the two groups. No significant difference was seen in the Ca:P ratio in the CPP-ACP group at six months. The inter-group comparison did not reveal any significant difference between the two groups either at baseline or at 6 months post-intervention.

CONCLUSION

Remineralization can be achieved in MIH affected teeth with the use of remineralizing agents.

Full coverage crowns for rehabilitation of MIH affected molars: 24 month randomized clinical trial

BACKGROUND

Teeth affected with severe molar incisor hypomineralization (MIH) require extensive restorations, which do not last for a long time and often require treatment in the form of onlays or full coverage restorations.

AIM

To evaluate and compare the clinical performance of zirconia, lithium disilicate, and cast metal crowns as full-coverage restorations on MIH-affected first permanent molars (FPMs).

METHODS

60 MIH affected FPMs requiring full-coverage crowns were identified in children aged 8-15 years and were randomly allocated to the three treatment groups according to the type of full coverage restoration received using block randomization technique. After an adequate removal of the MIH defect and restoration with composite resin, the tooth preparation was done followed by fabrication of crown and its cementation using resin cement. The intergroup comparison was done on the basis of USPHS criteria, gingival, plaque scores, patient and parents acceptance through a visual analog scale to decipher their clinical performance at 6, 12, 24 months.

RESULTS

After 24 months, the crowns showed similar clinical success in terms of the criterias used to compare their clinical performance. The retention, marginal adaptation, relief from hypersensitivity, proximal contact, gingival health with no statistically significant difference among the three groups.

CONCLUSION

Based on the observations, Lithium disilicate, Zirconia and full cast metal crowns showed similar clinical success in rehabilitation of First permanent molars with severe MIH over 24 months of evaluation. The clinical success is not influenced by the material of the restoration. However, prospective studies with a longer follow-up are required to reach a more definitive conclusion.

Label-free quantitative proteomics reveals molecular correlates of altered biomechanical properties in molar incisor hypomineralization (MIH): an in vitro study

PURPOSE

Molar-incisor hypomineralization (MIH) is a qualitative developmental defect of enamel that affects first permanent molars with or without affecting permanent incisors. We aimed to carry out a quantitative proteomics-based study to compare and evaluate proteins in sound and MIH-affected enamel.

MATERIALS AND METHODS

Ten blocks each of the MIH-affected enamel and sound enamel were processed and prepared for LC-MS/MS analysis. Label-free quantitation was carried out to evaluate the differentially expressed proteins in the two groups of samples.

RESULTS

A significant increase in the number of proteins in MIH-affected enamel (50.3 ± 29.6) was observed compared to the sound enamel (21.4 ± 3.2). While proteins like collagens, α1-anti-trypsin, kallikrein-4 (KLK4), matrix metalloprotease-20 (MMP-20), alpha-2-macroglobulin, and alpha-2-HS-glycoprotein were upregulated in sound enamel, there was over-expression of albumin, calcium-binding proteins, anti-thrombin III, and dentin sialophosphoprotein (DSPP), along with proteins implicated in stress response and inflammatory processes in MIH.

CONCLUSION

We propose that altered biomechanical properties of the enamel in MIH samples arise due to (i) down-regulation of proteins contributing to collagen biosynthesis and fibril formation; (ii) an overall imbalance in required levels of proteases (KLK4 and MMP-20) and anti-proteases (anti-thrombin-III which inhibits KLK-4), essential for optimal mineralization; (iii) very low levels of alpha-2-macroglobulin with important consequences in enamel mineralization and amelogenesis; and (iv) increased albumin in MIH, preventing proper growth of hydroxyapatite crystals. Increased inflammatory component was also seen in MIH; however, whether inflammation is a cause or consequence of the poor mineralization process needs to be assessed.

Estimation of the in vivo neutralization potency of eCD4Ig and conditions for AAV-mediated production for SHIV long-term remission

The engineered protein eCD4Ig has emerged as a promising approach to achieve HIV remission in the absence of antiviral therapy. eCD4Ig neutralizes nearly all HIV-1 isolates and induces antibody-dependent cell-mediated cytotoxicity (ADCC) in vitro. To characterize the in vivo antiviral neutralization and possible ADCC effects of eCD4Ig, we fit mathematical models to eCD4Ig, anti–eCD4Ig-drug antibody (ADA), and viral load kinetics from healthy and simian-human immunodeficiency virus AD8 (SHIV-AD8) infected nonhuman primates that were treated with single or sequentially dosed eCD4Ig passive administrations. Our model predicts that eCD4Ig transiently decreases SHIV viral loads due to neutralization only with an in vivo IC₅₀ of ~25 μg/ml but with limited effect due to ADA. Simulations suggest that endogenous, continuous expression of eCD4Ig at levels greater than 10⁵ μg/day, as is possible with Adeno-associated virus (AAV) vector-based production, could overcome the diminishing effects of ADA and allow for long-term remission of SHIV viremia in nonhuman primates.

Machine learning for mathematical models of HCV kinetics during antiviral therapy

Mathematical models for hepatitis C virus (HCV) dynamics have provided a means for evaluating the antiviral effectiveness of therapy and estimating treatment outcomes such as the time to cure. Recently, a mathematical modeling approach was used in the first proof-of-concept clinical trial assessing in real-time the utility of response-guided therapy with direct-acting antivirals (DAAs) in chronic HCV-infected patients. Several retrospective studies have shown that mathematical modeling of viral kinetics predicts time to cure of less than 12 weeks in the majority of individuals treated with sofosbuvir-based as well as other DAA regimens. A database of these studies was built, and machine learning methods were evaluated for their ability to estimate the time to cure for each patient to facilitate real-time modeling studies. Data from these studies exploring mathematical modeling of HCV kinetics under DAAs in 266 chronic HCV-infected patients were gathered. Different learning methods were applied and trained on part of the dataset ('train' set), to predict time to cure on the untrained part ('test' set). Our results show that this machine learning approach provides a means for establishing an accurate time to cure prediction that will support the implementation of individualized treatment.

Challenges and Road Map towards Starting a New COVID Hospital

Background and Aim:

With advent of the Coronavirus Disease 2019 (covid-19) pandemic, need for a dedicated government hospital was felt. Following directions after a cabinet decision, a dedicated Covid hospital was made functional within a month in Central district of Delhi. This manuscript briefs the journey and challenges experienced during this mission.

Method:

As per decision of the state health ministry, bed allocation was planned along with provision for diagnosis, treatment and prevention of Covid -19. Various trainings were simultaneously conducted, licences were obtained and manpower and material were arranged starting with procurement to service provision and waste management.

Result:

Concerted efforts resulted in initiation of clinical and diagnostic services within one month of initiation of teamwork. Government supported in all the licencing requirements and material management. The hospital became functional during the first wave; and by the start of second wave, 20-bedded fully equipped Intensive Care Unit (ICU) was ready with pressure swing adsorber (PSA) oxygen generator in premises.

Conclusion:

A well-coordinated action in the right direction with administrative support can help in achieving difficult targets. Opening a new hospital amidst lockdown and resource constraints in an emergency situation was a rewarding achievement.

Salivary parameters and their correlation with neutrophil counts in children with acute lymphoblastic leukemia

BACKGROUND

Chemotherapy for Acute Lymphoblastic Leukemia (ALL) is known to render children immuno-deficient. A concomitant suppression of local defence mechanisms, such as saliva may further aggravate the adverse consequences of chemotherapy. The present study was conducted to evaluate alterations in salivary flow rate, pH and buffering capacity and to correlate these parameters with Absolute Neutrophil Counts (ANC).

METHODS

A cohort of 43 patients, aged 3-12 years were evaluated for the aforementioned parameters at baseline, post-induction and post-consolidation phases. Salivary collection was done and ANC was measured from routine haematological reports.

RESULTS

A decrease in the salivary parameters was observed at the end of Induction phase as compared to baseline, with a statistically significant decrease in unstimulated salivary flow rates (p < 0.01). Statistically significant positive correlations were found between ANC and salivary flow rate (p = 0.005), pH (p < 0.00) and buffering capacity (p < 0.00). On testing the significance of these correlations, all the values for these parameters were found to be statistically significant.

CONCLUSION

Salivary parameters showed derangements over the phases of chemotherapy, with maximum decrease at the end of induction phase. The positive correlations of salivary parameters with ANC of the subjects may be considered indicative of a concomitant immunological compromise in these children.

ID3 promotes homologous recombination via non-transcriptional and transcriptional mechanisms and its loss confers sensitivity to PARP inhibition

The inhibitor of DNA-binding 3 (ID3) is a transcriptional regulator that limits interaction of basic helix-loop-helix transcription factors with their target DNA sequences. We previously reported that ID3 loss is associated with mutational signatures linked to DNA repair defects. Here we demonstrate that ID3 exhibits a dual role to promote DNA double-strand break (DSB) repair, particularly homologous recombination (HR). ID3 interacts with the MRN complex and RECQL helicase to activate DSB repair and it facilitates RAD51 loading and downstream steps of HR. In addition, ID3 promotes the expression of HR genes in response to ionizing radiation by regulating both chromatin accessibility and activity of the transcription factor E2F1. Consistently, analyses of TCGA cancer patient data demonstrate that low ID3 expression is associated with impaired HR. The loss of ID3 leads to sensitivity of tumor cells to PARP inhibition, offering new therapeutic opportunities in ID3-deficient tumors.

1191 The Use of CT Urography to Diagnose Upper Tract Urothelial Carcinomas (UTUC); Managing Surgical Resources During The COVID-19 Pandemic

Introduction

Upper tract urothelial carcinomas (UTUC) account for 5-10% of urothelial malignancies. Rapid diagnosis is essential as 60% are invasive at diagnosis and confer poor prognoses. European Association of Urology (EAU) guidelines recommend CT urography (CTU) for initial diagnosis and staging of UTUCs. Diagnostic ureteroscopy (URS) is used second line where diagnosis is unclear. The COVID-19 pandemic has limited theatre access and may delay diagnosis of suspected UTUC. Our aim was to evaluate specific CTU findings in predicting UTUC to aid prompt diagnosis and risk stratification in a tertiary centre.

Method

A retrospective analysis was performed on 122 patients who underwent CTU with diagnostic URS over two years from 2018-2019 for possible UTUC. Data including demographics, imaging and histology were collected from our electronic database.

Results

57 patients had confirmed UTUC, all had CT changes. CTU had an overall positive predictive value (PPV) of 45%. CT findings were divided into: hydronephrosis; filling defect/lesion; urothelial thickening; normal; or other. The PPV was highest for filling defects/lesions at 60%, hydronephrosis was 38%, urothelial thickening was 30%, and other was 33%. Of those with high-grade histology, 61% had evidence of filling defects/lesions and 24% had hydronephrosis.

Conclusions

A specific CTU finding of filling defect/lesion in combination with cytology can aid diagnosis and risk stratification of UTUC. This may enable us to reduce use of diagnostic URS, as well as associated risks of intravesical seeding, necessary in the COVID-19 pandemic. With other CTU findings of hydronephrosis or urothelial thickening, a diagnostic URS may be required.

1054 A Simple Intervention to Minimise the Incidence of The Forgotten Ureteric Stent: Updating the Surgical Discharge Summary

Introduction

Ureteric stents are routinely used in ureteric obstruction, however, have considerable morbidity with major complications, such as encrustation, obstruction, urosepsis, and renal failure if left in situ for longer than six months. Despite an electronic stent register, there are still multiple emergency admissions of complications from forgotten stents, as well as those presenting with significant stent symptoms. Often stents are inserted as an emergency procedure with minimal information given on their discharge summary. A discharge template was therefore introduced that could also serve as a patient information leaflet to help minimise the incidence of forgotten stents.

Method

A discharge template was designed based off the trust-endorsed and British Association of Urological Surgeons (BAUS) patient leaflet and distributed amongst the juniors. A total of 28 patients were interviewed via telephone questionnaires – 21 randomly selected pre-intervention and 7 post-intervention from a one-month scale either side of the intervention. The template included: information on stents, common stent symptoms, indications to seek healthcare advice, and contact details to use in the event they are lost to follow-up.

Results

Patients aware that stents should be changed within six months went from 52% to 100%. Awareness of stent symptoms and red-flag symptoms went from 52% to 91%, and 57% to 100% respectively. Those who felt they had sufficient information on the discharge letter to understand their stent increased from 52 to 89%.

Conclusions

Significant improvement in patient understanding of stents and therefore hopefully in appropriate health-seeking behaviour, patient rapport, safety, and improvement in stents removed within target.

Mathematical Modeling of Vaccines That Prevent SARS-CoV-2 Transmission

SARS-CoV-2 vaccine clinical trials assess efficacy against disease (VEDIS), the ability to block symptomatic COVID-19. They only partially discriminate whether VEDIS is mediated by preventing infection completely, which is defined as detection of virus in the airways (VESUSC), or by preventing symptoms despite infection (VESYMP). Vaccine efficacy against transmissibility given infection (VEINF), the decrease in secondary transmissions from infected vaccine recipients, is also not measured. Using mathematical modeling of data from King County Washington, we demonstrate that if the Moderna (mRNA-1273QS) and Pfizer-BioNTech (BNT162b2) vaccines, which demonstrated VEDIS > 90% in clinical trials, mediate VEDIS by VESUSC, then a limited fourth epidemic wave of infections with the highly infectious B.1.1.7 variant would have been predicted in spring 2021 assuming rapid vaccine roll out. If high VEDIS is explained by VESYMP, then high VEINF would have also been necessary to limit the extent of this fourth wave. Vaccines which completely protect against infection or secondary transmission also substantially lower the number of people who must be vaccinated before the herd immunity threshold is reached. The limited extent of the fourth wave suggests that the vaccines have either high VESUSC or both high VESYMP and high VEINF against B.1.1.7. Finally, using a separate intra-host mathematical model of viral kinetics, we demonstrate that a 0.6 log vaccine-mediated reduction in average peak viral load might be sufficient to achieve 50% VEINF, which suggests that human challenge studies with a relatively low number of infected participants could be employed to estimate all three vaccine efficacy metrics.

Reducing mortality in mucormycosis of the head and neck in diabetic patients: A CARE case series

INTRODUCTION

Rhinocerebral mucormycosis is extremely fatal, with mortality rates ranging from 85-93% despite the best treatment in immunocompromised patients. We emphasize the importance of early diagnosis, repeated debridement, and aggressive antifungal treatment to reduce mortality.

CASE SUMMARY

We report six cases (five male and one female), with a mean age of 51 years who were diagnosed to have mucormycosis from 2017 to 2019. All patients were diabetic. Intracranial involvement and orbital involvement were found in four cases. Facial nerve palsy was seen in two cases, one without any apparent otological involvement. Aggressive serial debridement and amphotericin B was started. Posaconazole was added subsequently to the treatment in two cases. One patient succumbed to the disease five months after discharge. The other five patients are on regular follow-up for a mean duration of 14 months at the end of which two had residual disease which was under control.

DISCUSSION

Repeated surgical debridement with an early aggressive and combination antifungal therapy can result in good outcomes even in advanced mucormycosis. Concurrent management of the underlying pathology, monitoring of liver and kidney functions, and therapeutic drug monitoring are useful to ensure smooth and effective treatment.

Dilemma of diagnosing thoracic sarcoidosis in tuberculosis endemic regions: An imaging-based approach. Part 1

Sarcoidosis is a multi-systemic disorder of unknown etiology, although commonly believed to be immune-mediated. Histologically, it is characterized by noncaseating granuloma which contrasts against the caseating granuloma seen in tuberculosis (TB), an infectious disease that closely mimics sarcoidosis, both clinically as well as radiologically. In TB-endemic regions, the overlapping clinico-radiological manifestations create significant diagnostic dilemma, especially since the management options are markedly different in the two entities. Part 1 of this review aims to summarize the clinical, laboratory, and imaging features of sarcoidosis, encompassing both typical and atypical manifestations, in an attempt to distinguish between the two disease entities.

Dilemma of diagnosing thoracic sarcoidosis in tuberculosis-endemic regions: An imaging-based approach. Part 2

The second part of the review discusses the role of different existing imaging modalities in the evaluation of thoracic sarcoidosis, including chest radiograph, computed tomography, magnetic resonance imaging, endobronchial ultrasound, and positron emission tomography. While summarizing the advantages and pitfalls of each imaging modality, the authors propose imaging recommendations and an algorithm to be followed in the evaluation of clinically suspected case of sarcoidosis in tuberculosis-endemic regions.

Radiology of anal and lower rectal cancers

Lower rectal and anal cancers are distinct from neoplasms involving rest of the rectum. These are relatively difficult to manage owing to important relationships with the sphincter muscles. Involvement of the latter portends a poorer prognosis and increased chance of recurrence. Lymphatic drainage of these tumours is into the systemic circulation and the exact set of lymph nodes involved depends on the precise location of the tumour. The role of imaging includes assessment of local invasion, infiltration of adjacent pelvic organs, assessment of locoregional lymphatic spread and metastasis, post-chemoradiation restaging as well as post-treatment surveillance.

Modeling reveals no direct role of the extent of HBV DNA integrations on the outcome of infection

Hepatitis B virus (HBV) with its high prevalence and death toll is one of the most important infectious diseases to study. Yet, there is very little progress in the development of within-host models for HBV, which has subsequently hindered our understanding of this virus. The uncertainty around the proliferation of infected hepatocytes has been studied but never in association with other important biological continuous events such as integrations and superinfections. This is despite the fact that these processes affect the diversity and composition of infected cell population in the liver and an improved understanding of the cellular composition will undoubtedly assist in strategizing against this viral infection. Here, we developed novel mathematical models that incorporate these key biological processes and analyzed them both analytically and numerically. Unaffected by the extent of integrated DNA (IDNA), the outcome of HBV infection was primarily dictated by the balance between processes generating and killing infected hepatocytes containing covalent closed circular DNA (cccDNA). The superinfection was found to be a key process in the spread of HBV infection as its exclusion could not reproduce experimentally observed composition of infected hepatocytes at peak of acute HBV infection, a stage where our model predicts that infected hepatocytes most likely carry both cccDNA and IDNA. Our analysis further suggested the existence of some form of selective advantage of infected hepatocytes containing only IDNA to explain the viral dynamics observed during antiviral treatment and the transition from peak to acute infection. Finally, the fine line between liver destruction and resolution of acute HBV infection was found to be highly influenced by the fate of cccDNA during cellular proliferation.

Screening for second malignancies in mycosis fungoides: non-Hodgkin lymphoma, Hodgkin lymphoma, lung cancer, bladder cancer and melanoma

BACKGROUND

Patients with mycosis fungoides (MF) are at increased risk of developing non-Hodgkin lymphoma (NHL), Hodgkin lymphoma (HL), lung cancer, bladder cancer and melanoma. The characteristics of patients developing these malignancies have not been specifically delineated. In addition, there are no established guidelines for screening MF patients for second malignancies.

MATERIALS/METHODS

We identified 742 patients with MF who developed second malignancies in the Surveillance Epidemiology and End Result-18 database.

RESULTS

The majority of second malignancy patients were white and male, mean age 55-67 years at diagnosis of MF, and mean age 61-72 years at diagnosis of second malignancy. The majority of patients diagnosed with second malignancies had early stage MF. MF patients with NHL, lung cancer, and bladder cancer tended to be diagnosed at earlier stages of the second malignancy than patients without MF and demonstrated better 5-year overall survival. There was no improvement in stage at diagnosis or survival for MF patients who were diagnosed with melanoma compared to patients without MF.

CONCLUSIONS

Improvements in survival in MF/NHL, MF/lung cancer and MF/bladder cancer patients may reflect differences in disease biology secondary to having MF or the importance of increased contact with the healthcare system. MF/melanoma data suggest that patients require regular pigmented-lesion-focused skin examinations. Tools for screening include regular lymph node examinations, pigmented-lesion-focused examinations and detailed review of systems questions. Smoking cessation counseling is key intervention in this population, as is ensuring that all age- and sex-specific cancer screenings are up-to-date (e.g. lung cancer screening, mammography, and colonoscopy). The utility of regular imaging for second malignancy screening and lab testing such as routine urinalysis requires additional study and expert consensus.

Endogenously Produced SARS-CoV-2 Specific IgG Antibodies May Have a Limited Impact on Clearing Nasal Shedding of Virus during Primary Infection in Humans

While SARS-CoV-2 specific neutralizing antibodies have been developed for therapeutic purposes, the specific viral triggers that drive the generation of SARS-CoV-2 specific IgG and IgM antibodies remain only partially characterized. Moreover, it is unknown whether endogenously derived antibodies drive viral clearance that might result in mitigation of clinical severity during natural infection. We developed a series of non-linear mathematical models to investigate whether SARS-CoV-2 viral and antibody kinetics are coupled or governed by separate processes. Patients with severe disease had a higher production rate of IgG but not IgM antibodies. Maximal levels of both isotypes were governed by their production rate rather than different saturation levels between people. Our results suggest that an exponential surge in IgG levels occurs approximately 5-10 days after symptom onset with no requirement for continual antigenic stimulation. SARS-CoV-2 specific IgG antibodies appear to have limited to no effect on viral dynamics but may enhance viral clearance late during primary infection resulting from the binding effect of antibody to virus, rather than neutralization. In conclusion, SARS-CoV-2 specific IgG antibodies may play only a limited role in clearing infection from the nasal passages despite providing long-term immunity against infection following vaccination or prior infection.

Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events

SARS-CoV-2 is difficult to contain because many transmissions occur during pre-symptomatic infection. Unlike influenza, most SARS-CoV-2-infected people do not transmit while a small percentage infect large numbers of people. We designed mathematical models which link observed viral loads with epidemiologic features of each virus, including distribution of transmissions attributed to each infected person and duration between symptom onset in the transmitter and secondarily infected person. We identify that people infected with SARS-CoV-2 or influenza can be highly contagious for less than 1 day, congruent with peak viral load. SARS-CoV-2 super-spreader events occur when an infected person is shedding at a very high viral load and has a high number of exposed contacts. The higher predisposition of SARS-CoV-2 toward super-spreading events cannot be attributed to additional weeks of shedding relative to influenza. Rather, a person infected with SARS-CoV-2 exposes more people within equivalent physical contact networks, likely due to aerosolization.

HIV influences clustering and intracellular replication of hepatitis C virus

HCV and HIV coinfection is common and HIV leads to increased HCV viraemia and accelerated disease progression. However, the biological basis of this interaction remains poorly understood and little is known about the impact of HIV on HCV replication at the cellular level. We analysed HCV RNA, based on single-cell laser-capture microdissection, in liver biopsies from monoinfected (n = 4) and HCV/HIV-coinfected (n = 5) participants. HCV RNA was assayed in 3200 hepatocytes with information of spatial position. We compared HCV RNA levels and clustering properties of infection between mono- and coinfected participants, and developed a mathematical model of infection. Although the median plasma HCV RNA level and the fraction of infected cells were comparable in monoinfected (7.0 log₁₀ IU/mL and ~ 30%) and coinfected (7.3 log₁₀ IU/mL and ~ 40%) participants, the median HCV RNA per infected hepatocyte in monoinfected (2.8IU) was significantly lower than in coinfected (8.2IU) participants (p = .03). Clustering of infected cells was more prominent in monoinfected participants (91% of samples) than in coinfected participants (~48%), p = .0045, suggesting that spatial spread may be influenced by HIV coinfection. Interestingly, when clustering does occur, the size of clusters is similar in both types of infection. A mathematical model of infection suggested that HIV allows higher intracellular accumulation of HCV RNA by impeding the export of HCV RNA. Our observations show that HIV coinfection impacts intracellular accumulation of HCV RNA and the clustering of HCV-infected cells, but to a less extent the fraction of HCV-infected cells.

Successful Salvage of a Mangled Injury of the Ankle in a Young Male

Introduction

The salvage of a mangled limb is quite challenging, but can be rewarding especially for younger individuals.

Case Report

We present a case of mangled injury of the ankles in a young male, which was salvaged successfully, using Orthopaedic and Plastic Surgery procedures.

Conclusion

The GHSS is helpful for decision-making and to predict the ultimate outcome of the open injuries. Younger patients with intact vascularity of the limb should be considered for limb salvage with a multidisciplinary stepwise approach.

Suppression of hepatitis B virus through therapeutic activation of RIG-I and IRF3 signaling in hepatocytes

Hepatitis B virus (HBV) mediates persistent infection, chronic hepatitis, and liver disease. HBV covalently closed circular (ccc)DNA is central to viral persistence such that its elimination is considered the cornerstone for HBV cure. Inefficient detection by pathogen recognition receptors (PRRs) in the infected hepatocyte facilitates HBV persistence via avoidance of innate immune activation and interferon regulatory factor (IRF)3 induction of antiviral gene expression. We evaluated a small molecule compound, F7, and 5′-triphosphate-poly-U/UC pathogen-associated-molecular-pattern (PAMP) RNA agonists of RIG-I, a PRR that signals innate immunity, for ability to suppress cccDNA. F7 and poly-U/UC PAMP treatment of HBV-infected cells induced RIG-I signaling of IRF3 activation to induce antiviral genes for suppression of cccDNA formation and accelerated decay of established cccDNA, and were additive to the actions of entecavir. Our study shows that activation of the RIG-I pathway and IRF3 to induce innate immune actions offers therapeutic benefit toward elimination of cccDNA.

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Hepatocyte treatment of RIG-I agonists induces IRF3 and antiviral gene expression

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RIG-I agonists direct a block to cccDNA formation in early HBV infection

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Administration of RIG-I agonists imparts cccDNA decay

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Nucleoside analogs with RIG-I agonist is synergistic to block cccDNA formation

Machine learning predicts live-birth occurrence before in-vitro fertilization treatment

In-vitro fertilization (IVF) is a popular method of resolving complications such as endometriosis, poor egg quality, a genetic disease of mother or father, problems with ovulation, antibody problems that harm sperm or eggs, the inability of sperm to penetrate or survive in the cervical mucus and low sperm counts, resulting human infertility. Nevertheless, IVF does not guarantee success in the fertilization. Choosing IVF is burdensome for the reason of high cost and uncertainty in the result. As the complications and fertilization factors are numerous in the IVF process, it is a cumbersome task for fertility doctors to give an accurate prediction of a successful birth. Artificial Intelligence (AI) has been employed in this study for predicting the live-birth occurrence. This work mainly focuses on making predictions of live-birth occurrence when an embryo forms from a couple and not a donor. Here, we compare various AI algorithms, including both classical Machine Learning, deep learning architecture, and an ensemble of algorithms on the publicly available dataset provided by Human Fertilisation and Embryology Authority (HFEA). Insights on data and metrics such as confusion matrices, F1-score, precision, recall, receiver operating characteristic (ROC) curves are demonstrated in the subsequent sections. The training process has two settings Without feature selection and With feature selection to train classifier models. Machine Learning, Deep learning, ensemble models classification paradigms have been trained in both settings. The Random Forest model achieves the highest F1-score of 76.49% in without feature selection setting. For the same model, the precision, recall, and area under the ROC Curve (ROC AUC) scores are 77%, 76%, and 84.60%, respectively. The success of the pregnancy depends on both male and female traits and living conditions. This study predicts a successful pregnancy through the clinically relevant parameters in In-vitro fertilization. Thus artificial intelligence plays a promising role in decision making process to support the diagnosis, prognosis, treatment etc.