Descemet stripping endothelial keratoplasty versus penetrating keratoplasty in bullous keratopathy: A 2-year analysis of graft survival and outcomes in a tertiary eye centre in Kuala Lumpur

INTRODUCTION

This study aims to compare the 2-year graft survival and outcomes of descemet stripping endothelial keratoplasty (DSEK) and penetrating keratoplasty (PK) for the treatment of bullous keratopathy (BK) among multiethnic Malaysia populations treated at a Tertiary Eye Centre in Kuala Lumpur, Malaysia.

MATERIALS AND METHODS

This was a retrospective study of BK or Fuchs endothelial dystrophy (FED) patients who underwent DSEK or PK from 2015 to 2019 in Kuala Lumpur Hospital with a minimal post-operative follow-up of 2 years. Outcome measures included best-corrected visual acuity (BCVA), graft survival and complications. A total of 26 DSEK cases and 32 PK cases were included.

RESULTS

At 2 years, graft survival rates were quite similar in two groups (DSEK 80.8% vs PK 75%, p=0.765). The mean follow-up period was 35.2 months in DSEK and 31.4 months for PK (p=0.465). The cumulative survival rates were slightly higher in the DSEK group (DSEK 73.1% vs PK 53.1%, p=0.119), but the result was not statistically significant. Postoperative complications were associated with higher graft failure in both groups (p=0.019). DSEK group has better post-operative BCVA (LogMAR DSEK 0.42 vs PK 0.83, p=0.003).

CONCLUSION

Similar graft survival rates were observed with both corneal transplant techniques for 2 years among Malaysian patients with BK. Post-operative complications can cause a higher risk of graft failure. DSEK produced better post-operative BCVA compared to PK.

Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.

Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes

Many antibacterial drugs have multiple mechanisms of resistance, which are often represented simultaneously by a mixture of resistance mutations (some more frequent than others) in a clinical population. This presents a challenge for Genome-Wide Association Studies (GWAS) methods, making it difficult to detect less prevalent resistance mechanisms purely through (weak) statistical associations. Homoplasy, or the occurrence of multiple independent mutations at the same site, is often observed with drug resistance mutations and can be a strong indicator of positive selection. However, traditional GWAS methods, such as those based on allele counting or linear regression, are not designed to take homoplasy into account. In this article, we present a new method, called ECAT (for Evolutionary Cluster-based Association Test), that extends traditional regression-based GWAS methods with the ability to take advantage of homoplasy. This is achieved through a preprocessing step which identifies hypervariable regions in the genome exhibiting statistically significant clusters of distinct evolutionary changes, to which association testing by a linear mixed model (LMM) is applied using GEMMA (a well-established LMM-based GWAS tool). Thus, the approach can be viewed as extending GEMMA from the usual site- or gene-level analysis to focusing on clustered regions of mutations. This approach was evaluated on a large collection of more than 600 clinical isolates of multidrug-resistant (MDR) Mycobacterium tuberculosis from Lima, Peru. We show that ECAT does a better job of detecting known resistance mutations for several antitubercular drugs (including less prevalent mutations with weaker associations), compared with (site- or gene-based) GEMMA, as representative of existing GWAS methods. The power of the multiphase approach in ECAT comes from focusing association testing on the hypervariable regions of the genome, which reduces complexity in the model and increases statistical power.

[Prospective association between early adiposity rebound and adolescent development in girls]

Objective: To determine possible relations between early adiposity rebound and adolescent development. Methods: Prospective children cohort from 2 kindergartens selected through clustering convenience sampling method in Anhui Province was established since Sep. 2010. Participants were classified as Cohort 1 (2010), Cohort 2 (2011) and Cohort 3 (2012) according to the recruiting year. Till Sep. 2015, a toal of 802 girls were included in this study, and received follow-up till primary school. During kindergarten period, physical examination was carried out every 3 months, 8 times in total. In primary school, physical examination was carried out annually; till Sep.2015, the cohort 1, 2, 3 took physical examination for 12, 11, 10 times, respectively. Information on household economic status and child physical activity was acquired through parents questionnaire survey, and breast development were assessed through visual inspection and palpation. Adiposity rebound was determined according to Rolland-Cachera's method for each girl. Differences between early adiposity rebound and normal adiposity rebound groups were compared by using t test and χ(2) test. Multivariate regression analysis was applied to explore the association between early adiposity rebound and breast development. Results: The average age of participants was (8.90±0.87) years old and the BMI was (17.48±2.70) kg/m(2). The average age at adiposity rebound was (6.16±0.90) years old and the BMI was (15.33±1.82) kg/m(2). Premature breast development was found significantly higher in girls in early adiposity rebound group (27.8%, 54/802) than it in normal adiposity rebound group (13.7%) (P<0.001). After current adiposity, age, household economic status, childhood physical activity adjusted, the OR of premature beast development in early adiposity rebound group was 2.41(95%CI: 1.41-4.12). Conclusion: Early adiposity rebound increases the risk of premature puberty in girls.

A statistical method to identify recombination in bacterial genomes based on SNP incompatibility

BACKGROUND

Phylogeny estimation for bacteria is likely to reflect their true evolutionary histories only if they are highly clonal. However, recombination events could occur during evolution for some species. The reconstruction of phylogenetic trees from an alignment without considering recombination could be misleading, since the relationships among strains in some parts of the genome might be different than in others. Using a single, global tree can create the appearance of homoplasy in recombined regions. Hence, the identification of recombination breakpoints is essential to better understand the evolutionary relationships of isolates among a bacterial population.

RESULTS

Previously, we have developed a method (called ACR) to detect potential breakpoints in an alignment by evaluating compatibility of polymorphic sites in a sliding window. To assess the statistical significance of candidate breakpoints, we propose an extension of the algorithm (ptACR) that applies a permutation test to generate a null distribution for comparing the average local compatibility. The performance of ptACR is evaluated on both simulated and empirical datasets. ptACR is shown to have similar sensitivity (true positive rate) but a lower false positive rate and higher F1 score compared to basic ACR. When used to analyze a collection of clinical isolates of Staphylococcus aureus, ptACR finds clear evidence of recombination events in this bacterial pathogen, and is able to identify statistically significant boundaries of chromosomal regions with distinct phylogenies.

CONCLUSIONS

ptACR is an accurate and efficient method for identifying genomic regions affected by recombination in bacterial genomes.

A comprehensive characterization of PncA polymorphisms that confer resistance to pyrazinamide

Tuberculosis chemotherapy is dependent on the use of the antibiotic pyrazinamide, which is being threatened by emerging drug resistance. Resistance is mediated through mutations in the bacterial gene pncA. Methods for testing pyrazinamide susceptibility are difficult and rarely performed, and this means that the full spectrum of pncA alleles that confer clinical resistance to pyrazinamide is unknown. Here, we performed in vitro saturating mutagenesis of pncA to generate a comprehensive library of PncA polymorphisms resultant from a single-nucleotide polymorphism. We then screened it for pyrazinamide resistance both in vitro and in an infected animal model. We identify over 300 resistance-conferring substitutions. Strikingly, these mutations map throughout the PncA structure and result in either loss of enzymatic activity and/or decrease in protein abundance. Our comprehensive mutational and screening approach should stand as a paradigm for determining resistance mutations and their mechanisms of action.The antibiotic pyrazinamide is central to tuberculosis treatment regimens, globally. Despite its efficacy, resistance to the drug is increasing. Here, Eric Rubin and colleagues characterise the genetic basis of pyrazinamide resistance.

iGC-an integrated analysis package of gene expression and copy number alteration

BACKGROUND

With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual.

RESULTS

We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance.

CONCLUSION

The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .

Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes

BACKGROUND

Gene regulation is dynamic across cellular conditions and disease subtypes. From the aspect of regulation under modulation, regulation strength between a pair of genes can be modulated by (dependent on) expression abundance of another gene (modulator gene). Previous studies have demonstrated the involvement of genes modulated by single modulator genes in cancers, including breast cancer. However, analysis of multi-modulator co-modulation that can further delineate the landscape of complex gene regulation is, to our knowledge, unexplored previously. In the present study we aim to explore the joint effects of multiple modulator genes in modulating global gene regulation and dissect the biological functions in breast cancer.

RESULTS

To carry out the analysis, we proposed the Covariability-based Multiple Regression (CoMRe) method. The method is mainly built on a multiple regression model that takes expression levels of multiple modulators as inputs and regulation strength between genes as output. Pairs of genes were divided into groups based on their co-modulation patterns. Analyzing gene expression profiles from 286 breast cancer patients, CoMRe investigated ten candidate modulator genes that interacted and jointly determined global gene regulation. Among the candidate modulators, ESR1, ERBB2, and ADAM12 were found modulating the most numbers of gene pairs. The largest group of gene pairs was composed of ones that were modulated by merely ESR1. Functional annotation revealed that the group was significantly related to tumorigenesis and estrogen signaling in breast cancer. ESR1-ERBB2 co-modulation was the largest group modulated by more than one modulators. Similarly, the group was functionally associated with hormone stimulus, suggesting that functions of the two modulators are performed, at least partially, through modulation. The findings were validated in majorities of patients (> 99%) of two independent breast cancer datasets.

CONCLUSIONS

We have showed CoMRe is a robust method to discover critical modulators in gene regulatory networks, and it is capable of achieving reproducible and biologically meaningful results. Our data reveal that gene regulatory networks modulated by single modulator or co-modulated by multiple modulators play important roles in breast cancer. Findings of this report illuminate complex and dynamic gene regulation under modulation and its involvement in breast cancer.

Sulfasalazine suppresses drug resistance and invasiveness of lung adenocarcinoma cells expressing AXL

Metastasis and drug resistance are the major causes of mortality in patients with non-small cell lung cancer (NSCLC). Several receptor tyrosine kinases (RTKs), including AXL, are involved in the progression of NSCLC. The AXL/MER/SKY subfamily is involved in cell adhesion, motility, angiogenesis, and signal transduction and may play a significant role in the invasiveness of cancer cells. Notably, no specific inhibitors of AXL have been described. A series of CL1 sublines with progressive invasiveness established from a patient with NSCLC has been identified that positively correlates with AXL expression and resistance to chemotherapeutic drugs. The ectopic overexpression of AXL results in elevated cell invasiveness and drug resistance. Nuclear factor-kappaB (NF-kappaB) signaling activity is associated with AXL expression and may play an important role in the enhancement of invasiveness and doxorubicin resistance, as shown by using the NF-kappaB inhibitor, sulfasalazine, and IkappaB dominant-negative transfectants. In the current study, sulfasalazine exerted a synergistic anticancer effect with doxorubicin and suppressed cancer cell invasiveness in parallel in CL1 sublines and various AXL-expressing cancer cell lines. Phosphorylation of AXL and other RTKs (ErbB2 and epidermal growth factor receptor) was abolished by sulfasalazine within 15 min, suggesting that the inhibition of NF-kappaB and the kinase activity of RTKs are involved in the pharmacologic effects of sulfasalazine. Our study suggests that AXL is involved in NSCLC metastasis and drug resistance and may therefore provide a molecular basis for RTK-targeted therapy using sulfasalazine to enhance the efficacy of chemotherapy in NSCLC.

Amebic liver abscess and human immunodeficiency virus infection: a report of three cases

Invasive amebiasis rarely occurs in homosexual men and human immunodeficiency virus (HIV)-infected individuals and has not been regarded as a beacon for concomitant HIV infection. We encountered a bisexual man with a protracted course of amebic liver abscess and amebic colitis. In the presence of fever, generalized lymphadenopathy, and elevated serum aminotransferase levels, HIV infection was suspected and then confirmed by a de novo seroconversion of HIV antibody. Subsequently, we noted two consecutive patients with amebic liver abscess, also later found to be infected with HIV. The ameba obtained from these three cases was identified as Entamoeba histolytica by amplification of 16S ribosomal RNA by polymerase chain reaction and direct sequencing. This observation suggests that amebic liver abscess and colitis can be presentations for HIV infection in the Far East. Thus, the local patients with invasive amebiasis, especially those with a protracted course or with risk factors of HIV infection, should be tested for HIV.

Long-term follow-up of interferon alfa treatment in Chinese patients with chronic hepatitis B infection: The effect on hepatitis B e antigen seroconversion and the development of cirrhosis-related complications

The long-term effect of interferon alfa (IFN-alpha) in Chinese patients with chronic hepatitis B infection is unknown. A total of 411 chronic hepatitis B patients (208 treated with IFN-alpha and 203 as control) were followed up for hepatitis B serology and the development of hepatoma and other cirrhosis-related complications. The hepatitis B e antigen (HBeAg) seroconversion rate in the IFN-alpha-treated group, though significantly greater at 6 and 24 months, was comparable with the control group on subsequent follow-up, irrespective of pretreatment alanine transaminase (ALT) levels. HBeAg seroreversion rate was higher in the IFN-alpha group compared with the control group (21.1% vs. 2.2%; P =.001). Loss of hepatitis B surface antigen (HBsAg) occurred in 2.4% of the IFN-alpha-treated patients and 0.49% of the control patients (P = NS). Around 90% of the anti-HBe-positive patients in both groups were still hepatitis B virus (HBV)-DNA-positive by polymerase chain reaction (PCR) assay. Two patients suffered from hepatic reactivation during the course of treatment. Nine (4.3%) patients in the IFN-alpha group and 2 (1.0%) in the control group developed complications of cirrhosis and hepatoma (P =.062). In Chinese HBsAg carriers, IFN-alpha was of no long-term benefit in inducing HBeAg seroconversion or in the prevention of hepatoma and other cirrhosis-related complications.

Timing and necessity of endoscopy in AIDS patients with dysphagia or odynophagia

BACKGROUND/AIMS

Dysphagia and odynophagia are common problems with significant morbidity in acquired immunodeficiency syndrome (AIDS) patients. Endoscopy in AIDS patients with esophageal symptoms is valuable for diagnosis, but the timing and necessity of routine endoscopy remains controversial.

METHODOLOGY

We retrospectively studied 40 AIDS patients undergoing upper gastrointestinal endoscopy. Among them, 25 patients were enroled with dysphagia and/or odynophagia and were put on empirical fluconazole treatment before endoscopic evaluation.

RESULTS

Fourteen (56%) of 25 patients improved after fluconazole treatment, while 11 patients had persistent symptoms. Among the 14 patients with symptomatic improvement, 7 were found to have esophageal candidiasis which improved after continuation of fluconazole for 1-2 more weeks. The other 7 patients had a normal endoscopic appearance. In contrast, among 11 patients with persistent symptoms, there were 3 patients with azole-resistant candidiasis, 3 with cytomegalovirus esophagitis, 1 with herpes simplex virus esophagitis with candidiasis, 1 with Kaposi's sarcoma, and 3 with idiopathic esophageal ulcer. They were successfully treated with Amphotericin B, Ganciclovir, Acyclovior, and oral steroids, except for the patient with Kaposi's sarcoma.

CONCLUSIONS

Routine endoscopy may not necessarily be indicated in every AIDS patient with dysphagia or odynophagia. Empirical fluconazole treatment can improve symptoms in 50% of patients. It is only indicated when patients have persistent symptoms after empirical treatment. With endoscopic examination, etiologic agents other than common candidiasis can be determined and the patients can thus be put on specific treatment.