Refractive Errors, Retinal Findings, and Genotype of Tuberous Sclerosis Complex: A Retrospective Cohort Study.

PURPOSE: To examine the refractive errors, retinal manifestations, and genotype in tuberous sclerosis complex (TSC) patients in a Korean population. MATERIALS AND METHODS: A total of 98 patients with TSC were enrolled in Severance Hospital for a retrospective cohort study. The number of retinal astrocytic hamartoma and retinal achromic patch within a patient, as well as the size, bilaterality, and morphological type were studied. In addition, the refractive status of patients and the comorbidity of intellectual disability and epilepsy were also examined. RESULTS: Retinal astrocytic hamartoma was found in 37 patients, and bilateral invasion was observed in 20 patients (54%). TSC1 mutation was associated with myopia (p=0.01), while TSC2 mutation was associated with emmetropia (p=0.01). Retinal astrocytic hamartoma was categorized into three morphological types and examined as follows: type I (87%), type II (35%), and type III (14%). Single invasion of retinal astrocytic hamartoma was identified in 32% of the patients, and multiple invasions in 68%. The TSC1/TSC2 detection rate was 91% (41/45). Among them, TSC1 variant was detected in 23 patients (54%), whereas TSC2 variant was detected in 18 patients (40%). The results showed that TSC2 mutations are correlated with a higher rate of retinal astrocytic hamartoma involvement (all p<0.05), and multiple and bilateral involvement of retinal hamartomas (all p<0.05). However, the size of retinal astrocytic hamartomas, comorbidity of epilepsy, or intellectual disability did not show correlation with the genetic variant. CONCLUSION: TSC1 variant patients were more myopic, while TSC2 variant patients showed association with more extensive involvement of retinal astrocytic hamartoma.

Presbyopia correction using the monocular bi-aspheric ablation profile in myopic eyes.

PURPOSE: To analyze the 6-month outcomes of the treatment combination of the monocular bi-aspheric ablation profile (PresbyMAX) and contralateral aspheric monofocal laser in situ keratomileusis (LASIK) ablation profile for correction of myopia and presbyopia. SETTING: Yonsei University College of Medicine and Eyereum Eye Clinic, Seoul, South Korea. DESIGN: Retrospective case series. METHODS: This was a retrospective case review of 92 patients (184 eyes) diagnosed with myopia who underwent uneventful simultaneous bi-aspheric ablation in the nondominant eye and aspheric monofocal regular LASIK in the dominant eye to correct myopia and presbyopia between January 2017 and August 2020. Monocular and binocular uncorrected distance visual acuity (UDVA) and near visual acuity (UNVA), and corrected distance visual acuity and near visual acuity were analyzed postoperatively. RESULTS: At 6 months postoperatively, the mean UDVAs (logMAR) in the dominant and nondominant eyes were 0.01 ± 0.02 and 0.26 ± 0.15, respectively. Furthermore, all treated dominant eyes achieved 20/20 or better monocular UDVA, and 84% achieved 20/16 or better monocular UDVA. In the nondominant treated eyes, 89% achieved 20/50 or better monocular UDVA, 78% achieved 20/40 or better, and 34% achieved 20/32 or better. The binocular cumulative UDVA at 6 months postoperatively was 20/20 or better in all patients. All patients achieved J2 or better in binocular cumulative UNVA, and 83% achieved J1. CONCLUSIONS: Presbyopia correction using the combination of PresbyMAX in the near eye and aspheric monofocal regular LASIK in the distant eye is a safe and effective treatment for presbyopia in patients with myopia.

Anterior Ocular Biometrics Using Placido-scanning-slit System, Rotating Scheimpflug Tomography, and Swept-source Optical Coherence Tomography.

PURPOSE: To compare anterior biometry measurements using placido-scanning-slit topography, rotating Scheimpflug tomography, and swept-source optical coherence tomography. METHODS: A retrospective review consisted of 80 eyes of 49 participants who underwent anterior chamber depth (ACD), central corneal thickness (CCT), and keratometry examination on the same day. We used placido-scanning-slit topography (ORBscan II), rotating Scheimpflug tomography (Pentacam HR), and swept-source optical coherence tomography (CASIA SS1000). The intraclass correlation coefficients and Bland-Altman plots were used to evaluate the agreement and differences between measurements. RESULTS: The mean ACD values were 2.88 ± 0.43, 2.82 ± 0.50, and 2.68 ± 0.44 mm; and the mean CCT values were 536.96 ± 31.19, 543.79 ± 31.04, and 561.41 ± 32.60 µm; and the mean keratometry (Km) were 43.81 ± 1.69, 43.81 ± 1.77, and 44.65 ± 1.95 diopters; as measured by CASIA SS-1000, Pentacam HR, and ORBscan II, respectively. Among the three devices, ACD was deepest to shallowest in the order of CASIA SS-1000, Pentacam HR, and ORBscan II (p < 0.05). The CCT was thickest to thinnest in the order of ORBscan II, Pentacam HR, and CASIA SS-1000 (p < 0.05). No significant differences in Km values were examined between CASIA SS-1000 and Pentacam HR, whereas ORBscan II overestimated Km with a statistically significant difference compared to the other two devices. CONCLUSIONS: High level of agreement was found between CASIA SS-1000 and Pentacam HR for anterior parameters, including ACD, CCT, and Km, suggesting interchangeability. However, ORBscan II measurements differed considerably with the measurements obtained from the other two devices; therefore, it should not be used interchangeably. However, further studies with repeatability test should be considered in order to elucidate the reliability of each device.

Analysis of keratometric measurements in accordance with axial length in an aged population.

To investigate keratometric measurements according to axial length in an aged population. Patients requiring cataract surgery with keratometric measurements from four different ophthalmic devices (autorefractor/keratometer, Scheimpflug imaging, corneal topography/ray-tracing aberrometry, and partial coherence interferometry) between January 2016 and March 2021 were reviewed retrospectively. Cases for which four ophthalmic devices were deployed in the same order a day were included in this investigation. The corneal curvature of the flattest and steepest meridian, mean corneal curvature, corneal astigmatism, steepest axis location, and axial length were evaluated. In total, 250 eyes (137 patients) were included in the analysis. A negative correlation was found between mean corneal curvature and axial length, with correlation coefficients of 0.587, 0.592, 0.588, 0.591, 0.588, and 0.562 for autorefractor/keratometer, Scheimpflug imaging, corneal topography/ray-tracing aberrometry, partial coherence interferometry, total corneal refractive power of Scheimpflug imaging, and simulated keratometry of corneal topography/ray-tracing aberrometry measurements, respectively. No statistically significant differences were found for corneal astigmatism according to axial length. In axial length group of less than 26.0 mm, negative correlation was found between axial length and mean frontal corneal curvature while no correlation was found between axial length and corneal astigmatism. All four ophthalmic devices showed good inter-device reliability for mean corneal curvature but not corneal astigmatism.

Pembrolizumab-induced Stevens-Johnson Syndrome with Severe Ocular Complications.

PURPOSE: To report a unique case of Stevens-Johnson syndrome (SJS) with severe ocular complications induced by pembrolizumab, an immune checkpoint inhibitor. CASE PRESENTATION: A 64-year-old man with urothelial cancer presented with bilateral corneal epithelial defect and conjunctival pseudo-membrane formation with erythematous patches on the four extremities, abdomen, and back. He had urothelial cancer with multifocal lesions in the renal pelvis and left ureter, and para-aortic metastatic lymph nodes. Accordingly, pembrolizumab treatment was planned. Generalized skin eruption occurred 4 days after the first cycle of pembrolizumab treatment, and ocular symptoms occurred 2 weeks after the first cycle. The patient's symptoms improved after cessation of pembrolizumab treatment and administration of steroids systemically. CONCLUSIONS: Immune checkpoint inhibitors, including pembrolizumab, have been developed recently and are widely used in the treatment of various cancers. However, it should be noted that the drugs may cause adverse events such as SJS with severe ocular complications.

Accuracy of the Kane Formula for Intraocular Lens Power Calculation in Comparison with Existing Formulas: A Retrospective Review.

PURPOSE: To evaluate the accuracy of the Kane formula for intraocular lens (IOL) power calculation in comparison with existing formulas by incorporating optional variables into calculation. MATERIALS AND METHODS: This retrospective review consisted of 78 eyes of patients who had undergone uneventful phacoemulsification with intraocular implantation at Severance Hospital in Seoul, Korea between February 2020 and January 2021. The Kane formula was compared with six of the existing IOL formulas (SRK/T, Hoffer-Q, Haigis, Holladay1, Holladay2, Barrett Universal II) based on the mean absolute error (MAE), median absolute error (MedAE), and the percentages of eyes within prediction errors of ±0.25D, ±0.50D, and ±1.00D. RESULTS: The Barrett Universal II formula demonstrated the lowest MAEs (0.26±0.17D), MedAEs (0.28D), and percentage of eyes within prediction errors of ±0.25D, ± 0.50D, and ±1.00D, although there was no statistically significant difference between Barrett Universal II-SRK/T (p=0.06), and Barrett Universal II-Kane formula (p<0.51). Following the Barrett Universal II formula, the Kane formula demonstrated the second most accurate formula with MAEs (0.30±0.19D) and MedAEs (0.28D). However, no statistical difference was shown between Kane-Barrett Universal II (p=0.51) and Kane-SRK/T (p=0.14). CONCLUSION: Although slightly better refractory outcome was noted in the Barrett Universal II formula, the performance of the Kane formula in refractive prediction was comparable in IOL power calculation, marking its superiority over many conventional IOL formulas, such as HofferQ, Haigis, Holladay1, and Holladay2.

Prediction accuracy of conventional and total keratometry for intraocular lens power calculation in femtosecond laser-assisted cataract surgery.

This study evaluated the accuracy of total keratometry (TK) and standard keratometry (K) for intraocular lens (IOL) power calculation in eyes treated with femtosecond laser-assisted cataract surgery. The retrospective study included a retrospective analysis of data from 62 patients (91 eyes) who underwent uneventful femtosecond laser-assisted cataract surgery with Artis PL E (Cristalens Industrie, Lannion, France) IOL implantation by a single surgeon between May 2020 and December 2020 in Severance Hospital, Seoul, South Korea. The new IOLMaster 700 biometry device (Carl Zeiss Meditec, Jena, Germany) was used to calculate TK and K. The mean absolute error (MAE), median absolute error (MedAE), and the percentages of eyes within prediction errors of ± 0.25 D, ± 0.50 D, and ± 1.00 D were calculated for all IOL formulas (SRK/T, Hoffer-Q, Haigis, Holladay 1, Holladay 2, and Barrett Universal II). There was strong agreement between K and TK (intraclass correlation coefficient = 0.99), with a mean difference of 0.04 D. For all formulas, MAE tended to be lower for TK than for K, and relatively lower MAE and MedAE values were observed for SRK/T and Holladay 1. Furthermore, for all formulas, a greater proportion of eyes fell within ± 0.25 D of the predicted postoperative spherical equivalent range in the TK group than in the K group. However, differences in MAEs, MedAEs, and percentages of eyes within the above prediction errors were not statistically significant. In conclusion, TK and K exhibit comparable performance for refractive prediction in eyes undergoing femtosecond laser-assisted cataract surgery.

Resting-state prefrontal EEG biomarkers in correlation with MMSE scores in elderly individuals.

We investigated whether cognitive decline could be explained by resting-state electroencephalography (EEG) biomarkers measured in prefrontal regions that reflect the slowing of intrinsic EEG oscillations. In an aged population dwelling in a rural community (total = 496, males = 165, females = 331), we estimated the global cognitive decline using the Mini-Mental State Examination (MMSE) and measured resting-state EEG parameters at the prefrontal regions of Fp1 and Fp2 in an eyes-closed state. Using a tertile split method, the subjects were classified as T3 (MMSE 28-30, N = 162), T2 (MMSE 25-27, N = 179), or T1 (MMSE ≤ 24, N = 155). The EEG slowing biomarkers of the median frequency, peak frequency and alpha-to-theta ratio decreased as the MMSE scores decreased from T2 to T1 for both sexes (-5.19 ≤ t-value ≤ -3.41 for males and -7.24 ≤ t-value ≤ -4.43 for females) after adjusting for age and education level. Using a double cross-validation procedure, we developed a prediction model for the MMSE scores using the EEG slowing biomarkers and demographic covariates of sex, age and education level. The maximum intraclass correlation coefficient between the MMSE scores and model-predicted values was 0.757 with RMSE = 2.685. The resting-state EEG biomarkers showed significant changes in people with early cognitive decline and correlated well with the MMSE scores. Resting-state EEG slowing measured in the prefrontal regions may be useful for the screening and follow-up of global cognitive decline in elderly individuals.

HDAC4 promotes Pax7-dependent satellite cell activation and muscle regeneration.

During muscle regeneration, the transcription factor Pax7 stimulates the differentiation of satellite cells (SCs) toward the muscle lineage but restricts adipogenesis. Here, we identify HDAC4 as a regulator of Pax7-dependent muscle regeneration. In HDAC4-deficient SCs, the expression of Pax7 and its target genes is reduced. We identify HDAC4-regulated Lix1 as a Pax7 target gene required for SC proliferation. HDAC4 inactivation leads to defective SC proliferation, muscle regeneration, and aberrant lipid accumulation. Further, expression of the brown adipose master regulator Prdm16 and its inhibitory microRNA-133 are also deregulated. Thus, HDAC4 is a novel regulator of Pax7-dependent SC proliferation and potentially fate determination in regenerating muscle.

Evaluation of class I HDAC isoform selectivity of largazole analogues.

Largazole is a potent class I selective histone deacetylase (HDAC) inhibitor. The majority of largazole analogues to date have modified the thiazole-thiazoline and the warhead moiety. In order to elucidate class I-specific structure-activity relationships, a series of analogues with modifications in the valine or the linker region were prepared and evaluated for their class I isoform selectivity. The inhibition profile showed that the C2 position of largazole has an optimal steric requirement for efficient HDAC inhibition and that substitution of the trans-alkene in the linker with an aromatic group results in complete loss of activity. This data will aid the design of class I isoform selective HDAC inhibitors.

The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics.

Early transplant dysfunction and failure because of immunological and nonimmunological factors still presents a significant clinical problem for transplant recipients. A critical unmet need is the noninvasive detection and prediction of immune injury such that acute injury can be reversed by proactive immunosuppression titration. In this study, we used iTRAQ -based proteomic discovery and targeted ELISA validation to discover and validate candidate urine protein biomarkers from 262 renal allograft recipients with biopsy-confirmed allograft injury. Urine samples were randomly split into a training set of 108 patients and an independent validation set of 154 patients, which comprised the clinical biopsy-confirmed phenotypes of acute rejection (AR) (n = 74), stable graft (STA) (n = 74), chronic allograft injury (CAI) (n = 58), BK virus nephritis (BKVN) (n = 38), nephrotic syndrome (NS) (n = 8), and healthy, normal control (HC) (n = 10). A total of 389 proteins were measured that displayed differential abundances across urine specimens of the injury types (p < 0.05) with a significant finding that SUMO2 (small ubiquitin-related modifier 2) was identified as a "hub" protein for graft injury irrespective of causation. Sixty-nine urine proteins had differences in abundance (p < 0.01) in AR compared with stable graft, of which 12 proteins were up-regulated in AR with a mean fold increase of 2.8. Nine urine proteins were highly specific for AR because of their significant differences (p < 0.01; fold increase >1.5) from all other transplant categories (HLA class II protein HLA-DRB1, KRT14, HIST1H4B, FGG, ACTB, FGB, FGA, KRT7, DPP4). Increased levels of three of these proteins, fibrinogen beta (FGB; p = 0.04), fibrinogen gamma (FGG; p = 0.03), and HLA DRB1 (p = 0.003) were validated by ELISA in AR using an independent sample set. The fibrinogen proteins further segregated AR from BK virus nephritis (FGB p = 0.03, FGG p = 0.02), a finding that supports the utility of monitoring these urinary proteins for the specific and sensitive noninvasive diagnosis of acute renal allograft rejection.

Brief report: genome sequence and construction of an infectious cDNA clone of Ribgrass mosaic virus from Chinese cabbage in Korea.

Ribgrass mosaic virus (RMV) has severely decreased the production and lowered quality of Chinese cabbage co-infected with Turnip mosaic virus (63.4%) in Korea. The complete genome sequence of RMV isolated from Brassica rapa ssp. pekinensis was determined. The full genome consisted of 6,304 nucleotides and showed sequence identities of 91.5-94.2% with the corresponding genome of other RMV strains. Full-length cDNA of RMV-Br was amplified by RT-PCR with a 5'-end primer harboring a T7 promoter sequence and a 3'-end RMV specific primer. Subsequently, the full-length cDNA was cloned into plasmid vectors. Capped transcripts synthesized from the cDNA clone were highly infectious and caused characteristic symptoms in B. rapa ssp. pekinensis and several indicator plants, similar to wild type RMV. Since there has not been found RMV resistant Chinese cabbage yet and the virus has been prevalent already throughout the natural fields of Korea, the identification of full sequence and development of infectious clone would help developing breeding program for RMV resistant crops.

A statistical approach to peptide identification from clustered tandem mass spectrometry data.

Tandem mass spectrometry experiments generate from thousands to millions of spectra. These spectra can be used to identify the presence of proteins in biological samples. In this work, we propose a new method to identify peptides, substrings of proteins, based on clustered tandem mass spectrometry data. In contrast to previously proposed approaches, which identify one representative spectrum for each cluster using traditional database searching algorithms, our method uses all available information to score all the spectra in a cluster against candidate peptides using Bayesian model selection. We illustrate the performance of our method by applying it to seven-standard-protein mixture data.

Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics.

The Purkinje cell degeneration (pcd) mouse is a recessive model of neurodegeneration, involving cerebellum and retina. Purkinje cell death in pcd is dramatic, as >99% of Purkinje neurons are lost in 3 weeks. Loss of function of Nna1 causes pcd, and Nna1 is a highly conserved zinc carboxypeptidase. To determine the basis of pcd, we implemented a two-pronged approach, combining characterization of loss-of-function phenotypes of the Drosophila Nna1 ortholog (NnaD) with proteomics analysis of pcd mice. Reduced NnaD function yielded larval lethality, with survivors displaying phenotypes that mirror disease in pcd. Quantitative proteomics revealed expression alterations for glycolytic and oxidative phosphorylation enzymes. Nna proteins localize to mitochondria, loss of NnaD/Nna1 produces mitochondrial abnormalities, and pcd mice display altered proteolytic processing of Nna1 interacting proteins. Our studies indicate that Nna1 loss of function results in altered bioenergetics and mitochondrial dysfunction.

Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics.

BACKGROUND: Functional development of the prostate is governed by stromal mesenchyme induction and epithelial response. Stromal/epithelial signaling can be mediated through direct cell-cell contact and diffusible factors and their cell surface receptors. These inducers are likely secreted or membrane-associated extracellular proteins. Given the importance of intercellular communication, it is possible that diseases like cancer could arise from a loss of this communication. One approach to gain a molecular understanding of stromal cells is to identify, as a first step, secreted stromal signaling factors. We proposed to do this by comparative analysis between bladder and prostate. METHODS: Secreted proteins were identified from cultured normal prostate and bladder stromal mesenchyme cells by glycopeptide-capture method followed by mass spectrometry. Differences in protein abundance between prostate and bladder were quantified from calculated peptide ion current area (PICA) followed by Western validation. Functional and pathway analyses of the proteins were carried out by Gene Ontology (GO) and Teranode software. RESULTS: This analysis produced a list of 116 prostate and 84 bladder secreted glycoproteins with ProteinProphet probability scores > or =0.9. Stromal proteins upregulated in the prostate include cathepsin L, follistatin-related protein, neuroendocrine convertase, tumor necrosis factor receptor, and others that are known to be involved in signal transduction, extracellular matrix interaction, differentiation and transport. CONCLUSIONS: We have identified a number of potential proteins for stromal signaling and bladder or prostate differentiation program. The prostate stromal/epithelial signaling may be accomplished through activation of the ECM-receptor interaction, complement and coagulation cascades, focal adhesion and cell adhesion pathways.

Exploration of the normal human bronchoalveolar lavage fluid proteome.

We obtained insight into normal lung function by proteome analysis of bronchoalveolar lavage fluid (BALF) from six normal human subjects using a "Lyse-N-Go' shotgun proteomic protocol. Intra-sample variation was calculated using three different label-free methods, (i) protein sequence coverage; (ii) peptide spectral counts and (iii) peptide single-ion current areas (PICA), which generates protein expression data by summation of the area under the curve for a given peptide single-ion current trace and then adding values for all peptides from that same parent protein. PICA gave the least intra-subject variability and was used to calculate differences in protein expression between the six subjects. We observed an average threefold inter-sample variability, which affects analysis of changes in protein expression that occur in different diseases. We detected 167 unique proteins with >100 proteins detected in each of the six individual BAL samples, 42 of which were common to all six subjects. Gene ontology analysis demonstrated enrichment of several biological processes in the lung, reflecting its expected role in gas exchange and host defense as an immune organ. The same biological processes were enriched compared to either plasma or total genome proteome, suggesting an active enrichment of plasma proteins in the lung rather than passive capillary leak.

Comparison of a label-free quantitative proteomic method based on peptide ion current area to the isotope coded affinity tag method.

Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing data on each sample to be acquired independently from all other samples to which they can later be compared in silico for the purpose of measuring changes in protein expression between various biological states. We developed label free software based on direct measurement of peptide ion current area (PICA) and compared it to two other methods, a simpler label free method known as spectral counting and the isotope coded affinity tag (ICAT) method. Data analysis by these methods of a standard mixture containing proteins of known, but varying, concentrations showed that they performed similarly with a mean squared error of 0.09. Additionally, complex bacterial protein mixtures spiked with known concentrations of standard proteins were analyzed using the PICA label-free method. These results indicated that the PICA method detected all levels of standard spiked proteins at the 90% confidence level in this complex biological sample. This finding confirms that label-free methods, based on direct measurement of the area under a single ion current trace, performed as well as the standard ICAT method. Given the fact that the label-free methods provide ease in experimental design well beyond pair-wise comparison, label-free methods such as our PICA method are well suited for proteomic expression profiling of large numbers of samples as is needed in clinical analysis.

MglA regulates Francisella tularensis subsp. novicida (Francisella novicida) response to starvation and oxidative stress.

MglA is a transcriptional regulator of genes that contribute to the virulence of Francisella tularensis, a highly infectious pathogen and the causative agent of tularemia. This study used a label-free shotgun proteomics method to determine the F. tularensis subsp. novicida (F. novicida) proteins that are regulated by MglA. The differences in relative protein amounts between wild-type F. novicida and the mglA mutant were derived directly from the average peptide precursor ion intensity values measured with the mass spectrometer by using a suite of mathematical algorithms. Among the proteins whose relative amounts changed in an F. novicida mglA mutant were homologs of oxidative and general stress response proteins. The F. novicida mglA mutant exhibited decreased survival during stationary-phase growth and increased susceptibility to killing by superoxide generated by the redox-cycling agent paraquat. The F. novicida mglA mutant also showed increased survival upon exposure to hydrogen peroxide, likely due to increased amounts of the catalase KatG. Our results suggested that MglA coordinates the stress response of F. tularensis and is likely essential for bacterial survival in harsh environments.

Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry.

We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies, simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.