AFF4 globally affects the release of paused RNA polymerase II in HEL cells

P-TEFb, a heterodimer of the kinase CDK9 and Cyclin T1, is a critical regulator of promoter-proximal pause release of Pol II in metazoans. It is capable of forming three larger complexes, including the super elongation complex (SEC), the BRD4/P-TEFb complex and the 7SK snRNP. In the SEC or the BRD4/P-TEFb complex, P-TEFb is enzymatically active, while in the 7SK snRNP, its activity is inhibited. The SEC consists of AFF1 or 4, ENL or AF9, ELL1, 2 or 3 and EAF1 or 2 in addition to P-TEFb, the only subunit with catalytic activity, and the noncatalytic subunits have been found to be able to regulate pause release through P-TEFb. We and others recently found that AFF1, ENL and AF9 are capable of regulating transcriptional initiation, but it is unknown yet whether AFF4 is also capable of doing so. With respect to the gene regulation selectivity of the SEC and the BRD4/P-TEFb complex, one recent study showed that in human DLD-1 cells, the SEC only regulates pause release of heat shock (HS) genes, whereas the BRD4/P-TEFb complex regulates pause release of the rest of the genes. However, it is unclear whether those mechanisms are general. In this study for the purpose of further understanding the role of AFF4 in transcriptional regulation, we found that AFF4 knockdown by RNA interference in human HEL cells decreased not only cellular level but also global chromatin occupancy of CTD serine 2 phosphorylated Pol II. Direct target genes of AFF4 were identified by RNA-seq and CUT&Tag. Notably, we found by ChIP-seq and PRO-seq that AFF4 loss also increased promoter-proximal pause of Pol II on several hundred HS and thousands of non-HS genes. Mechanistically, AFF4 promotes pause release likely by facilitating the binding of P-TEFb to Pol II. These results suggest that extent of the impact of AFF4 on pause release is likely to be context-dependent or cell-type dependent.

[Evaluation of two biomechanical stiffness indexes in the diagnosis of eratoconus and their changes after corneal collagen cross-linking surgery]

Objective: To evaluate the diagnostic efficacy of stress-strain index (SSI) for different stages or degrees of keratoconus and changes of SSI and stiffness parameter A1 (SPA1) after corneal collagen cross-linking (CXL) surgery. Methods: Cross-sectional study and retrospective case series study. Ninety-four patients (113 eyes) diagnosed as clinical keratoconus (CKC) in Qingdao Eye Hospital from July 2019 to August 2021 were enrolled in the CKC group, including 69 males and 25 females, aged (20.82±4.53) years, and further divided into subgroups of mild (35 patients, 36 eyes), moderate (36 patients, 40 eyes) and severe (33 patients, 37 eyes) CKC. Fifty-six unaffected eyes of monocular keratoconus patients were enrolled in the subclinical keratoconus (SKC) group. Ninety-one healthy subjects (91 eyes) were recruited as the control group. All subjects were examined by Pentacam topography and Corvis ST measurements to obtain mean keratometry, maximal keratometry, deformation amplitude (DA) ratio at 2 mm, integrated radius (IR), Ambrósio's relational thickness to the horizontal profile, corneal central thickness, SPA1 and SSI for comparison. Forty-eight CKC patients (65 eyes) underwent CXL surgery, and the above parameters were recorded before and 3, 6 and 12 months after operation. Data were analyzed by the ANOVA test, Kruskal-Wallis H test, paired sample test, receiver operating characteristic curves and Pearson correlation. Results: The value of SPA1 in the SKC group accounted for 85.53% (87.92±12.38 vs. 102.79±11.74; t=-6.614, P<0.001) compared with the control group, but the value of SSI had no difference in the two groups (t=0.105, P=0.916). The value of SPA1 in the CKC group accounted for 52.87% (54.35±14.70 vs. 102.79±11.74; t=25.985, P<0.001) compared with the control group. The value of SSI in the CKC group accounted for 67.96% (0.70±0.14 vs. 1.03±0.14; t=-15.305, P<0.001) compared with the control group. The more severe the disease was, the smaller the SPA1 and SSI values were 64.27±12.12, 55.22±12.23, 43.75±12.33; 0.78±0.14, 0.71±0.11, 0.61±0.09, and there were significant statistical differences among groups (mild vs. moderate, mild vs. severe, moderate vs. severe; SPA1: t=3.257, -7.249, -4.159; all P<0.001. SSI: t=2.383, 5.065, 2.798; P=0.018,<0.001,=0.006). Receiver operating characteristic analysis showed that SPA1 had good diagnostic efficiency for subclinical patients [area under curve (AUC)=0.802], while the SSI had no diagnostic value (P=0.802). SPA1 had better diagnostic efficiency than the SSI for keratoconus in different stages, especially in the mild CKC and SKC groups (AUC: 0.914 vs. 0.847). The SSI had a significant positive correlation with SPA1 and a significant negative correlation with DA ratio and IR in the control, SKC and CKC groups (r=0.278, 0.368, 0.550; r=-0.346, -0.462, -0.547; r=-0.612, -0.591, -0.718; P<0.01). For patients who received CXL, maximal keratometry decreased significantly at 6 and 12 months postoperatively (t=4.029, 3.633; all P<0.001), whereas SPA1 increased significantly (t=-3.960, -4.500; all P<0.001). However, the SSI only increased significantly at 3 months (t=-2.577, P=0.012) and returned to the preoperative level at 6 and 12 months postoperatively, with no statistical difference compared with the preoperative level (t=-0.544, -0.257; P=0.589, 0.798). Conclusions: While there was no significant change in the SSI of SKC, the SSI of CKC decreased, and the more severe the disease was, the smaller the value was. The SSI was significantly and consistently correlated with DA ratio, IR and SPA1. The SSI compared with SPA1 had a lower degree of identification in different stages and degrees of keratoconus. The consistency of SPA1 with clinical effects after CXL surgery was higher than that of the SSI parameter.

[Characteristics of corneal topography in parents of keratoconus patients]

Objective: To investigate the corneal topographic characteristics of the parents of patients with keratoconus (KC) and the correlation with their offspring. Methods: Case-control study. Twenty-six patients (49 eyes) with KC, who were 15 males and 11 females, and (18.83±2.74) years old, 48 parents (96 eyes) of patients with KC, who were 23 males and 25 females, and (44.14±1.70) years old, and 44 controls (88 eyes), who were 22 males and 22 females, and (42.81±4.03) years old, were enrolled in Qingdao Eye Hospital. The indexes in the Belin/Ambrósio Enhanced Ectasia Display were acquired with Pentacam topography. The basic indicators were flat K/steep K/maximum K (Kmax) curvature and astigmatism, thinnest pachymetry (TP), and front/back elevation (Ef/Eb); the Belin indexes included deviation of normality of the front/back elevation (Df/Db), deviation of average pachymetry progression/normality of corneal thinnest point/normality of relational thickness (Dp/Dt/Da), overall deviation of normality (Do), minimum/maximum/average pachymetric progression indices (PPImin/PPImax/PPIave), and Ambrósio's average and maximum relational thickness indices (ARTave/ARTmax). All parameters in the groups of parents and controls were compared by Mann-Whitney U test. The ROC curve was used to analyze the differential value of each abnormal index. In addition, the ratio of abnormal indicators in the Belin/Ambrósio Enhanced Ectasia Display was statistically analyzed. Partial correlation analysis was used to find the correlation between the parameters of KC patients and their parents, and binary logistics regression analysis was used to predict the prevalence in children through the parental indicators. Results: Clinical KC was diagnosed in 1 of the 48 parents (2.08%) of patients with KC. There was no statistically significant difference in anterior surface parameters such as K1, K2, Kmax, astigmatism and Ef, but differences in the thickness [522.00 (493.00, 542.75) μm versus 540.00 (523.25, 559.50) μm] and posterior surface elevation value [8.00 (4.00, 11.00) μm versus 5.00 (3.00, 8.00) μm] were statistically significant. Except for Df, the other Belin/Ambrósio indicators such as Do (Z=-4.551, P=0.000), PPImax (Z=-3.959, P=0.000) and ARTave (Z=-4.792, P=0.000) indicated significant difference. The ROC curve analyses showed ARTave had the greatest value in the identification of KC patients (AUC=0.705), PPImax had the best sensitivity (0.845), and Eb had the best specificity (0.837). The ratio of suspicious indicators between the parents' group and the control group was 1.5∶1, and the ratio of pathological indicators was 3∶1. There was a correlation in multiple parameters between KC patients and their parents (all P>0.05). Do/Eb/TP indices of mothers and Do/Kmax indices of fathers were the major influence factors for the disease in the offspring, with a diagnosis rate of 85.6%. Conclusions: The corneal topographic map of the parents of patients with KC showed that the index of the anterior surface was normal, but the thickness was thinner and the posterior surface was higher. According to Belin's analysis, all indicators except Df were abnormal. Moreover, the ratio of suspected and pathological indicators increased. These data suggested that the corneal topography of parents of patients with KC had features of subclinical KC. Compared with the traditional index, ARTave was of the highest value in the identification of subclinical KC. There was a strong correlation between parents of patients with KC and offspring. The Do and Kmax indices of paternal parents and the Do, Eb and TP indices of maternal parents were good predictors of children's disease. (Chin J Ophthalmol, 2020, 56:456-464).

[The changes in corneal transparency after orthokeratology with juvenile myopia]

Objective: To evaluate the changes of corneal transparency undergoing overnight orthokeratology treatment. Methods: Prospective cohort study. Right eyes of juvenile myopic patients fitted with Ortho-K CL at Qingdao Eye Hospital were enrolled. Corneal optical density values were measured by the Pentacam Scheimpflug system before orthokeratology and at 1 day, 1 week, and 1, 3, 6, and 12 months after wearing. Four concentric radial zones centered on the apex of the cornea (≤2 mm, >2 mm and ≤6 mm, >6 mm and ≤10 mm, and>10 mm and ≤12 mm diameter) were applied. Anterior layer (anterior 120 μm), central layer, and posterior layer (posterior 60 μm) were defined according to corneal depth. The data analysis were used One-Way Repeated Measures ANOVA and LSD test. Results: Forty patients (40 eyes) with myopia (24 male and 16 female, age 10.76±1.74 years) were in enrolled. Corneal optical density value was 13.18±0.23 before orthokeratology, then showed a decreasing trend at the early stage, but there was no statistical difference (within 3months: t=-1.594, -1.472, 0.064, 1.971; P>0.05). The value increased significantly and reached the peak (15.31±0.23, t=7.613, P<0.01) at 6-month, and was still maintained in a high value at 1-year (15.15±0.24, t=7.227, P<0.01). Anterior, central, and posterior layer of corneal optical density values had a downward trend at early stage, and increased significantly in 6-and 12-month (anterior layer t=7.143, 6.177, central layer t=7.508, 6.563, posterior layer t=6.722, 8.533;P<0.01). Only the values decreased significantly in posterior layer at 1-week (baseline 10.21±0.14 vs. 1-week 9.91±0.14, t=-2.348, P=0.024). The corneal optical density value of ≤2 mm diameter began to increase significantly at 1-month (baseline 12.88±0.14 vs. 1-month 13.31±0.19, t=2.158, P=0.037),>2 mm and ≤6 mm diameter at 3-month (baseline 11.71±0.13 vs. 3-month 12.50±0.19, t=3.213, P=0.003), and>6 mm and ≤10 mm diameter at 6-month (baseline 11.40±0.30 vs. 6-month 13.70±0.33, t=7.635, P=0.000). The high values lasted for 1 year at this three areas. However, >10 mm and ≤12 mm diameter had no obvious change in optical density (F=1.668, P>0.05). In addition, the significant reduction of optical density values at early stage were mainly concentrated in the posterior layer of the cornea and the>6 mm and ≤10 mm diameter. Conclusions: Orthokeratology transiently increases corneal transparency of the posterior layer and the>6 mm and ≤10 mm diameter at early stage. However, long-term wearing can cause a decrease of transparency within a 10 mm diameter range. The corneal transparency changes first at the center of the optical zone, then gradually expanding to the periphery, and the anterior, central and posterior layers of cornea are all affected. We speculate orthokeratology affect the corneal oxygen supply and compress cornea mechanically, that leads to corneal stromal remodeling. (Chin J Ophthalmol, 2019, 55:435-441).