Accuracy of 14 intraocular lens power calculation formulas in extremely long eyes.

PURPOSE: To compare the accuracy of 14 formulas in calculating intraocular lens (IOL) power in extremely long eyes with axial length (AL) over 30.0 mm. METHODS: In this retrospective study, 211 eyes (211 patients) with ALs > 30.0 mm were successfully treated with cataract surgery without complications. Ocular biometric parameters were obtained from IOLMaster 700. Fourteen formulas were evaluated using the optimized A constants: Barrett Universal II (BUII), Kane, Emmetropia Verifying Optical (EVO) 2.0, PEARL-DGS, T2, SRK/T, Holladay 1, Holladay 2, Haigis and Wang-Koch AL adjusted formulas (SRK/Tmodified-W/K, Holladay 1modified-W/K, Holladay 1NP-modified-W/K, Holladay 2modified-W/K, Holladay 2NP-modified-W/K). The mean prediction error (PE) and standard deviation (SD), mean absolute errors (MAE), median absolute errors (MedAE), and the percentage of prediction errors (PEs) within ± 0.25 D, ± 0.50 D, ± 1.00 D were analyzed. RESULTS: The Kane formula had the smallest MAE (0.43 D) and MedAE (0.34 D). The highest percentage of PE within ± 0.25 D was for EVO 2.0 (37.91%) and the Holladay 1NP-modified-W/K formulas (37.91%). The Kane formula had the highest percentage of PEs in the range of ± 0.50, ± 0.75, ± 1.00, and ± 2.00 D. There was no significant difference in PEs within ± 0.25, ± 0.50 ± 0.75 and ± 1.00 D between BUII, Kane, EVO 2.0 and Wang-Koch AL adjusted formulas (P > .05) by using Cochran's Q test. The Holladay 2modified-W/K formula has the lowest percentage of hyperopic outcomes (29.38%). CONCLUSIONS: The BUII, Kane, EVO 2.0 and Wang-Koch AL adjusted formulas have comparable accuracy for IOL power calculation in eyes with ALs > 30.0 mm.

Syk-dependent homologous recombination activation promotes cancer resistance to DNA targeted therapy.

Enhanced DNA repair is an important mechanism of inherent and acquired resistance to DNA targeted therapies, including poly ADP ribose polymerase (PARP) inhibition. Spleen associated tyrosine kinase (Syk) is a non-receptor tyrosine kinase acknowledged for its regulatory roles in immune cell function, cell adhesion, and vascular development. This study presents evidence indicating that Syk expression in high-grade serous ovarian cancer and triple-negative breast cancers promotes DNA double-strand break resection, homologous recombination (HR), and subsequent therapeutic resistance. Our investigations reveal that Syk is activated by ATM following DNA damage and is recruited to DNA double-strand breaks by NBS1. Once localized to the break site, Syk phosphorylates CtIP, a pivotal mediator of resection and HR, at Thr-847 to promote repair activity, particularly in Syk-expressing cancer cells. Inhibition of Syk or its genetic deletion impedes CtIP Thr-847 phosphorylation and overcomes the resistant phenotype. Collectively, our findings suggest a model wherein Syk fosters therapeutic resistance by promoting DNA resection and HR through a hitherto uncharacterized ATM-Syk-CtIP pathway. Moreover, Syk emerges as a promising tumor-specific target to sensitize Syk-expressing tumors to PARP inhibitors, radiation and other DNA-targeted therapies.

Comparison of short-term clinical outcomes of a diffractive trifocal intraocular lens with phacoemulsification and femtosecond laser assisted cataract surgery.

PURPOSE: To evaluate short-term visual and refractive outcomes after implantation of a diffractive trifocal intraocular lens (IOL) in cataract patients with phacoemulsification (PHACO) and femtosecond laser assisted cataract surgery (FLACS). SETTING: Department of Ophthalmology, Shanghai Aier Eye Hospital, China. DESIGN: A retrospective, observational study. METHODS: Patients who underwent cataract surgery combined with Acrysoft IQ PanOptix trifocal IOL implantation were enrolled and divided into three groups: PHACO group, LAstig-FLACS group (astigmatism less then 1D) and HAstig-FLACS group (astigmatism more than 1D). Logarithm of the minimum angle of resolution (logMAR) visual acuity of uncorrected distance (UDVA), intermediate (UIVA), near visual (UNVA), defocus curve, surgically induced astigmatism (SIA) were evaluated in 1 months postoperatively and wavefront aberrations were evaluated in 6 months. RESULTS: 101 eyes of 60 patients were included with 31 eyes in PHACO group, 45 eyes in LAstig-FLACS group and 25 eyes in HAstig-FLACS group. Significant difference was found of internal Strehl Ratio (SR) between PHACO and LAstig-FLACS group (P = 0.026). In PHACO group, 79.31%, 86.21%, 72.41% of eyes gain visual acuity LogMAR 0.1 or more in UDVA, UIVA and UNVA, while 83.72%, 93.02%, 93.02% of those in LAstig-FLACS group and 92.00%, 84.00%, 76.00% in HAstig-FLACS group. CONCLUSIONS: Panoptix diffractive trifocal IOL provides satisfied visual outcome in no matter FLACS or PHACO. Besides, trifocal IOL implantation via FLACS can provide a better accumulative visual acuity outcome at all distance than PHACO in 1 month. Femtosecond laser assisted limbal relaxing incisions (FLLRIs) is an excellent way to reduce a patient's corneal astigmatism.

Improving the accuracy of the SRK/T formula in Chinese with implanting less than 10 D IOL calculated by the SRK/T formula: the SRK/T-Li formula.

PURPOSE: To explore the accuracy of the improved SRK/T-Li formula in eyes following implantation of intraocular lens (IOL) of less than 10 D as calculated by using the SRK/T formula in Chinese. METHODS: A total of 489 eyes from 489 patients with cataracts were included in this study. These patients were divided into a training set (271 patients) and a testing set (218 patients). The IOL power calculated by using SRK/T was less than 10 D. We evaluated the accuracy of the modified SRK/T-Li formula (P = PSRK/T × 0.8 + 2 (P = implanted IOL power; PSRK/T = IOL power calculated by SRK/T)). We evaluated the mean absolute error (MAE), percentage of prediction error (PE) within ± 0.25, ± 0.50, and ± 1.00 D, and the percentage of postoperative hyperopia. RESULTS: The MAE values in order of lowest to highest were as follows: 0.412 D (SRK/T-Li), 0.414 D (Barrett Universal II, (BUII)), 0.814 D (SRK/T), and 1.039 D (Holladay 1). The percentage of PE within ± 0.25 D, ± 0.50 D, and ± 1.00 D was 38.99%, 69.27% and 92.66% (BUII), 40.83%, 69.27% and 94.04% (SRK/T-Li), 20.64%, 41.28% and 71.56% (SRK/T), and 7.34%, 16.51% and 53.21% (Holladay 1), respectively. SRK/T-Li had the smallest postoperative hyperopic shift. CONCLUSIONS: For Chinese patients with an IOL power of less than 10 D as calculated by using the SRK/T, the SRK/T-Li has good accuracy and is the best choice to reduce postoperative hyperopic shift.

Comparison of visual performance with iTrace analyzer following femtosecond laser-assisted cataract surgery with bilateral implantation of two different trifocal intraocular lenses.

AIM: To compare the postoperative binocular visual performance with an iTrace analyzer following femtosecond laser-assisted cataract surgery (FLACS) combined with bilateral implantation of two different types of diffractive trifocal intraocular lenses (IOL). METHODS: During this retrospective observational study, patients who received bilateral FLACS combined with implantation of two different types of diffractive trifocal IOLs were evaluated. According to the IOLs' different types and design, the patients were divided into AT LISA tri839MP group (tri839 group) and AcrySof PanOptix TFNT00 group (TFNT group). Study parameters included preoperative and postoperative uncorrected distance visual acuity (UDVA) at 5 m, uncorrected near visual acuity (UNVA) at 30 cm and 40 cm, uncorrected intermediate visual acuity (UIVA) at 60 cm and 80 cm, postoperative refractive status, objective visual qualities and total high order aberrations (HOAs) postoperatively. The postoperative complications were also recorded. RESULTS: Totally 56 eyes of 28 patients (tri839 group, n=26; TFNT group, n=30) were included. Preoperative baseline characteristics between groups were not statistically significantly different. UDVA was not significantly different between groups except for 1wk follow-up due to the postoperative corneal edema. TFNT group showed statistically significant better UNIA at 60 cm than tri839 group at the 1wk (0.05±0.19 vs 0.15±0.10 logMAR, P=0.013), 1mo (0.05±0.12 vs 0.15±0.09 logMAR, P=0.001) and 3mo (0.04±0.12 vs 0.15±0.11 logMAR, P=0.001) follow-up, while tri839 group showed statistically significant better UNIA at 80 cm than TFNT group at the 1d (0.14±0.15 vs 0.20±0.14 logMAR, P=0.041) and 1mo (0.09±0.07 vs 0.14±0.10 logMAR, P=0.042) follow-up. Postoperative refractive status showed stable at every visit. Modulated transfer function (MTF) values and strehl ratio (SR) values were improved and HOAs were lower significantly after surgery. CONCLUSION: FLACS with bilateral implantations of both tri839 and TFNT00 can achieve satisfactory natural whole-course vision, high postoperative refractive stability and good visual quality but without significantly difference. iTrace aberration instrument can accurately evaluate the visual quality under different status.

Syk-dependent alternative homologous recombination activation promotes cancer resistance to DNA targeted therapy.

Enhanced DNA repair is an important mechanism of inherent and acquired resistance to DNA targeted therapies, including poly ADP ribose polymerase inhibition. Spleen associated tyrosine kinase (Syk) is a non-receptor tyrosine kinase known to regulate immune cell function, cell adhesion, and vascular development. Here, we report that Syk can be expressed in high grade serous ovarian cancer and triple negative breast cancers and promotes DNA double strand break resection, homologous recombination (HR) and therapeutic resistance. We found that Syk is activated by ATM following DNA damage and is recruited to DNA double strand breaks by NBS1. Once at the break site, Syk phosphorylates CtIP, a key mediator of resection and HR, at Thr-847 to promote repair activity, specifically in Syk expressing cancer cells. Syk inhibition or genetic deletion abolished CtIP Thr-847 phosphorylation and overcame the resistant phenotype. Collectively, our findings suggest that Syk drives therapeutic resistance by promoting DNA resection and HR through a novel ATM-Syk-CtIP pathway, and that Syk is a new tumor-specific target to sensitize Syk-expressing tumors to PARPi and other DNA targeted therapy.

A ribosomal gene panel predicting a novel synthetic lethality in non-BRCAness tumors.

Poly (ADP-ribose) polymerase (PARP) inhibitors are one of the most exciting classes of targeted therapy agents for cancers with homologous recombination (HR) deficiency. However, many patients without apparent HR defects also respond well to PARP inhibitors/cisplatin. The biomarker responsible for this mechanism remains unclear. Here, we identified a set of ribosomal genes that predict response to PARP inhibitors/cisplatin in HR-proficient patients. PARP inhibitor/cisplatin selectively eliminates cells with high expression of the eight genes in the identified panel via DNA damage (ATM) signaling-induced pro-apoptotic ribosomal stress, which along with ATM signaling-induced pro-survival HR repair constitutes a new model to balance the cell fate in response to DNA damage. Therefore, the combined examination of the gene panel along with HR status would allow for more precise predictions of clinical response to PARP inhibitor/cisplatin. The gene panel as an independent biomarker was validated by multiple published clinical datasets, as well as by an ovarian cancer organoids library we established. More importantly, its predictive value was further verified in a cohort of PARP inhibitor-treated ovarian cancer patients with both RNA-seq and WGS data. Furthermore, we identified several marketed drugs capable of upregulating the expression of the genes in the panel without causing HR deficiency in PARP inhibitor/cisplatin-resistant cell lines. These drugs enhance PARP inhibitor/cisplatin sensitivity in both intrinsically resistant organoids and cell lines with acquired resistance. Together, our study identifies a marker gene panel for HR-proficient patients and reveals a broader application of PARP inhibitor/cisplatin in cancer therapy.

SLFN5-mediated chromatin dynamics sculpt higher-order DNA repair topology.

Repair of DNA double-strand breaks (DSBs) elicits three-dimensional (3D) chromatin topological changes. A recent finding reveals that 53BP1 assembles into a 3D chromatin topology pattern around DSBs. How this formation of a higher-order structure is configured and regulated remains enigmatic. Here, we report that SLFN5 is a critical factor for 53BP1 topological arrangement at DSBs. Using super-resolution imaging, we find that SLFN5 binds to 53BP1 chromatin domains to assemble a higher-order microdomain architecture by driving damaged chromatin dynamics at both DSBs and deprotected telomeres. Mechanistically, we propose that 53BP1 topology is shaped by two processes: (1) chromatin mobility driven by the SLFN5-LINC-microtubule axis and (2) the assembly of 53BP1 oligomers mediated by SLFN5. In mammals, SLFN5 deficiency disrupts the DSB repair topology and impairs non-homologous end joining, telomere fusions, class switch recombination, and sensitivity to poly (ADP-ribose) polymerase inhibitor. We establish a molecular mechanism that shapes higher-order chromatin topologies to safeguard genomic stability.

SUMOylation of HNRNPA2B1 modulates RPA dynamics during unperturbed replication and genotoxic stress responses.

Replication protein A (RPA) is a major regulator of eukaryotic DNA metabolism involved in multiple essential cellular processes. Maintaining appropriate RPA dynamics is crucial for cells to prevent RPA exhaustion, which can lead to replication fork breakage and replication catastrophe. However, how cells regulate RPA availability during unperturbed replication and in response to stress has not been well elucidated. Here, we show that HNRNPA2B1SUMO functions as an endogenous inhibitor of RPA during normal replication. HNRNPA2B1SUMO associates with RPA through recognizing the SUMO-interacting motif (SIM) of RPA to inhibit RPA accumulation at replication forks and impede local ATR activation. Declining HNRNPA2SUMO induced by DNA damage will release nuclear soluble RPA to localize to chromatin and enable ATR activation. Furthermore, we characterize that HNRNPA2B1 hinders homologous recombination (HR) repair via limiting RPA availability, thus conferring sensitivity to PARP inhibitors. These findings establish HNRNPA2B1 as a critical player in RPA-dependent surveillance networks.

METTL16 antagonizes MRE11-mediated DNA end resection and confers synthetic lethality to PARP inhibition in pancreatic ductal adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers. Characterization of genetic alterations will improve our understanding and therapies for this disease. Here, we report that PDAC with elevated expression of METTL16, one of the 'writers' of RNA N6-methyladenosine modification, may benefit from poly-(ADP-ribose)-polymerase inhibitor (PARPi) treatment. Mechanistically, METTL16 interacts with MRE11 through RNA and this interaction inhibits MRE11's exonuclease activity in a methyltransferase-independent manner, thereby repressing DNA end resection. Upon DNA damage, ATM phosphorylates METTL16 resulting in a conformational change and autoinhibition of its RNA binding. This dissociates the METTL16-RNA-MRE11 complex and releases inhibition of MRE11. Concordantly, PDAC cells with high METTL16 expression show increased sensitivity to PARPi, especially when combined with gemcitabine. Thus, our findings reveal a role for METTL16 in homologous recombination repair and suggest that a combination of PARPi with gemcitabine could be an effective treatment strategy for PDAC with elevated METTL16 expression.

Engineering of reaction specificity, enantioselectivity, and catalytic activity of nitrilase for highly efficient synthesis of pregabalin precursor.

Simultaneous evolution of multiple enzyme properties remains challenging in protein engineering. A chimeric nitrilase (BaNITM0 ) with high activity towards isobutylsuccinonitrile (IBSN) was previously constructed for biosynthesis of pregabalin precursor (S)-3-cyano-5-methylhexanoic acid ((S)-CMHA). However, BaNITM0 also catalyzed the hydration of IBSN to produce by-product (S)-3-cyano-5-methylhexanoic amide. To obtain industrial nitrilase with vintage performance, we carried out engineering of BaNITM0 for simultaneous evolution of reaction specificity, enantioselectivity, and catalytic activity. The best variant V82L/M127I/C237S (BaNITM2 ) displayed higher enantioselectivity (E = 515), increased enzyme activity (5.4-fold) and reduced amide formation (from 15.8% to 1.9%) compared with BaNITM0 . Structure analysis and molecular dynamics simulations indicated that mutation M127I and C237S restricted the movement of E66 in the catalytic triad, resulting in decreased amide formation. Mutation V82L was incorporated to induce the reconstruction of the substrate binding region in the enzyme catalytic pocket, engendering the improvement of stereoselectivity. Enantio- and regio-selective hydrolysis of 150 g/L IBSN using 1.5 g/L Escherichia coli cells harboring BaNITM2 as biocatalyst afforded (S)-CMHA with >99.0% ee and 45.9% conversion, which highlighted the robustness of BaNITM2 for efficient manufacturing of pregabalin.

Constitutive expression of nitrilase from Rhodococcus zopfii for efficient biosynthesis of 2-chloronicotinic acid.

2-chloronicotinic acid (2-CA) is a key precursor for the synthesis of a series of pesticides and pharmaceuticals. Nitrilase-catalyzed bioprocess is a promising method for 2-CA production from 2-chloronicotinonitrile (2-CN). In this study, a mutant of nitrilase from Rhodococcus zopfii (RzNIT/W167G) was constitutively overexpressed with Escherichia coli as host, which exhibited a onefold increase in enzymatic activity compared with inducible expression. Biosynthesis of 2-CA using whole cells harboring nitrilase as biocatalysts were investigated and 318.5 mM 2-CA was produced, which was the highest level for 2-CA production catalyzed by nitrilase to date. 2-CA was recovered from the reaction mixture through a simple acidification step with a recovery yield of 90%. This study developed an efficient bioprocess for 2-CA with great potential for industrial application. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03119-0.

Rational Regulation of Reaction Specificity of Nitrilase for Efficient Biosynthesis of 2-Chloronicotinic Acid through a Single Site Mutation.

Nitrilase-catalyzed hydrolysis of 2-chloronicotinonitrile (2-CN) is a promising approach for the efficient synthesis of 2-chloronicotinic acid (2-CA). The development of nitrilase with ideal catalytic properties is crucial for the biosynthetic route with industrial potential. Herein, a nitrilase from Rhodococcus zopfii (RzNIT), which showed much higher hydration activity than hydrolysis activity, was designed for efficient hydrolysis of 2-CN. Two residues (N165 and W167) significantly affecting the reaction specificity were precisely identified. By tuning these two residues, a single mutation of W167G with abolished hydration activity and 20-fold improved hydrolysis activity was obtained. Molecular dynamics simulation and molecular docking revealed that the mutation generated a larger binding pocket, causing the substrate 2-CN to bind more deeply in the pocket and form a delocalized π bond between the residues W190 and Y196, which reduced the negative influence of steric hindrance and electron effect caused by chlorine substituent. With mutant W167G as biocatalyst, 100 mM 2-CN was exclusively converted into 2-CA within 16 h. The study provides useful guidance in nitrilase engineering for simultaneous improvement of reaction specificity and catalytic activity, which are highly desirable in value-added carboxylic acids production from nitriles hydrolysis. IMPORTANCE 2-CA is an important building block for agrochemicals and pharmaceuticals with a rapid increase in demand in recent years. It is currently manufactured from 3-cyanopyridine by chemical methods. However, during the final step of 2-CN hydrolysis under high temperature and strong alkaline conditions, the byproduct 2-CM was generated except for the target product, leading to low yield and tedious separation steps. Nitrilase-mediated hydrolysis is regarded as a promising alternative for 2-CA production, which proceeded under mild conditions. Nevertheless, nitrilase capable of efficient hydrolysis of 2-CN has not been reported because the enzymes showed either extremely low activity or surprisingly high hydration activity toward 2-CN. Herein, the reaction specificity of RzNIT was precisely tuned through a single site mutation. The mutant exhibited remarkably enhanced hydrolysis activity without the formation of byproducts, providing a robust biocatalyst for 2-CA biosynthesis with industrial potential.

[Development and practice of national first-class undergraduate course "bioengineering equipment"].

As a strategic emerging industry of China, the biotechnology industry develops rapidly in recent years, which significantly increased the demand for creative and capable talents. As a core curriculum of bioengineering specialty, biotechnology equipment plays an important role in fostering such talents. To address the problems in biotechnology equipment course teaching such as limited equipment availability, limited engineering practice, and lack of learning motivations, curriculum reform and optimization were performed based on curriculum resource development, virtual reality-physical combined engineering training, and boosting learning motivations. The optimized teaching contents focus on fostering morality, intelligence, and creative practice abilities by connecting new requirements of social development, introducing new progress in biotechnology research, as well as new practices in research and development (R & D). Measures such as teaching methods innovation, assessment and evaluation methods optimization, cutting-edge R & D progress, diverse resources integration, and online-offline combined teaching, were developed to boost the learning motivation and foster the innovation competence of students. By above exploration and practice, the practice and innovation competence of students were significantly enhanced.

Analysis of the effects of different nitrogen sources and calcium on the production of amphotericin by Streptomyces nodosus based on comparative transcriptome.

Streptomyces nodosus is known as the main manufacturer of amphotericin B (AmB), which is an effective antifungal drug. It is verified that the optimization of fermentation conditions and key growth factors have a great impact on the yield of AmB. The AmB production of S. nodosus in cotton-seed meal (CM) medium was 1.6 times than that of beef-paste medium. The transcriptome analysis was used to analyze the effects of different nitrogen media and calcium on S. nodosus. Related genes of the EMP and TCA pathways, such as phosphofructokinase, pyruvate dehydrogenase, and citrate synthase, were upregulated in CM medium. The expression level of the PKS modules of the amphotericin synthesis gene cluster in beef-paste medium was higher. Other functional genes, such as amphGH and amphRIV, have the advantage of expressing in CM medium. Ca2+ promoted the upregulation of genes in metabolic pathways such as EMP pathway (pyruvate dehydrogenase), TCA pathway (citrate synthase), and amphotericin synthesis genes (PKS modules). The expression of WhiB family genes SNOD_RS 13310 and SNOD_RS 17625 was positively correlated with Ca2+ concentration. In addition, in the presence of calcium, the expression level of Sec transport system genes of S. nodosus was lower.

Enhancing the production of amphotericin B by Strepyomyces nodosus in a 50-ton bioreactor based on comparative genomic analysis.

Amphotericin, as an important macrolide antibiotic, is synthesized by Streptomyces nodosus. A high-yield S. nodosus ZJB2016050 was obtained by mutagenesis in our lab with the advantages of high yield, short fermentation cycle and few by-products, which was more suitable for industrial production. The fermentation differences in 50-tons bioreactor between S. nodosus ATCC14899 and S. nodosus ZJB2016050 were compared. The amphotericin B (AmB) yield of S. nodosus ZJB2016050 was 9.73 mg/g at 96 h, which was 30% higher than that of S. nodosus ATCC14899. The by-product amphotericin A (AmA) production of S. nodosus ZJB2016050 was 78% lower than that of S. nodosus ATCC14899. By performing whole-genome sequencing of S. nodosus ZJB2016050 and comparative genome analysis with the wild-type S. nodosus ATCC14899, it was found that the two strains have high synteny, but each has a special gene fragment. The genes functions of fragment were identified in the amino acid transport and metabolism, carbohydrate metabolism and lipid transport and metabolism. The gene functions of SNP (single nucleotide polymorphism) genes were identified in amino acid transport and metabolism, carbohydrate metabolism, coenzyme metabolism and secondary metabolites biosynthesis. The difference in signal-regulation and transcription may be the main reason for the differences between these two strains. Three GntR family egulatory factors of S. nodosus ATCC14899 may reduce the synthesis of amphotericin. Based on the analysis of comparative genomes, the effects of corn oil in S. nodosus ATCC14899 and S. nodosus ZJB2016050 were also compared. The results showed that corn oil can promote the fermentation of S. nodosus ZJB2016050. The S. nodosus ZJB2016050 may degrade fatty acids faster, and the degraded acyl-coenzyme can be used to synthesize amphotericin. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02844-2.

Reciprocal regulation of RIG-I and XRCC4 connects DNA repair with RIG-I immune signaling.

The RNA-sensing pathway contributes to type I interferon (IFN) production induced by DNA damaging agents. However, the potential involvement of RNA sensors in DNA repair is unknown. Here, we found that retinoic acid-inducible gene I (RIG-I), a key cytosolic RNA sensor that recognizes RNA virus and initiates the MAVS-IRF3-type I IFN signaling cascade, is recruited to double-stranded breaks (DSBs) and suppresses non-homologous end joining (NHEJ). Mechanistically, RIG-I interacts with XRCC4, and the RIG-I/XRCC4 interaction impedes the formation of XRCC4/LIG4/XLF complex at DSBs. High expression of RIG-I compromises DNA repair and sensitizes cancer cells to irradiation treatment. In contrast, depletion of RIG-I renders cells resistant to irradiation in vitro and in vivo. In addition, this mechanism suggests a protective role of RIG-I in hindering retrovirus integration into the host genome by suppressing the NHEJ pathway. Reciprocally, XRCC4, while suppressed for its DNA repair function, has a critical role in RIG-I immune signaling through RIG-I interaction. XRCC4 promotes RIG-I signaling by enhancing oligomerization and ubiquitination of RIG-I, thereby suppressing RNA virus replication in host cells. In vivo, silencing XRCC4 in mouse lung promotes influenza virus replication in mice and these mice display faster body weight loss, poorer survival, and a greater degree of lung injury caused by influenza virus infection. This reciprocal regulation of RIG-I and XRCC4 reveals a new function of RIG-I in suppressing DNA repair and virus integration into the host genome, and meanwhile endues XRCC4 with a crucial role in potentiating innate immune response, thereby helping host to prevail in the battle against virus.

LRRK2 inhibition potentiates PARP inhibitor cytotoxicity through inhibiting homologous recombination-mediated DNA double strand break repair.

PARP inhibitors induce DNA lesions, the repair of which are highly dependent on homologous recombination (HR), and preferentially kill HR- deficient cancers. However, cancer cells have developed several mechanisms to transform HR and confer drug resistance to PARP inhibition. Therefore, there is a great clinical interest in exploring new therapies that induce HR deficiency (HRD), thereby sensitizing cancer cells to PARP inhibitors. Here, we found that GSK2578215A, a high-selective and effective leucine-rich repeat kinase 2 (LRRK2) inhibitor, or LRRK2 depletion suppresses HR preventing the recruitment of RAD51 to DNA damage sites through disruption of the interaction of RAD51 and BRCA2. Moreover, LRRK2 inhibition or depletion increases the susceptibility of ovarian cancer cells to Olaparib in vitro and in vivo. In clinical specimens, LRRK2 high expression is high related with advanced clinical characteristics and poor survival of ovarian cancer patients. All these findings indicate ovarian cancers expressing high levels of LRRK2 are more resistant to treatment potentially through promoting HR. Furthermore, combination treatment with an LRRK2 and PARP inhibitor may be a novel strategy to improve the effectiveness of LRRK2 expression ovarian cancers.

USP13 regulates the replication stress response by deubiquitinating TopBP1.

The DNA replication stress-induced checkpoint activated through the TopBP1-ATR axis is important for maintaining genomic stability. However, the regulation of TopBP1 in DNA-damage responses remains unclear. In this study, we identify the deubiquitinating enzyme (DUB) USP13 as an important regulator of TopBP1. Mechanistically, USP13 binds to TopBP1 and stabilizes TopBP1 by deubiquitination. Depletion of USP13 impedes ATR activation and hypersensitizes cells to replication stress-inducing agents. Furthermore, high USP13 expression enhances the replication stress response, promotes cancer cell chemoresistance, and is correlated with poor prognosis of cancer patients. Overall, these findings suggest that USP13 is a novel deubiquitinating enzyme for TopBP1 and coordinates the replication stress response.

Discovery and validation of hsa_circ_0001953 as a potential biomarker for proliferative diabetic retinopathy in human blood.

PURPOSE: This study aimed to determine whether circular RNAs (circRNAs) in whole blood could be served as novel non-invasive biomarkers for proliferative diabetic retinopathy (PDR). METHODS: This retrospective cross-sectional study comprised 34 healthy participants, 34 PDR patients and 34 non-proliferative DR (NPDR) patients. High-throughput whole transcriptome sequencing was performed to explore the expression profile of circRNAs in the whole blood, and the candidate circRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Receiver operating characteristic (ROC) analysis evaluated the ability of these candidate circRNAs in discriminating PDR patients from NPDR patients and healthy subjects. Finally, the networks of circRNA-miRNA-mRNA based on the candidate circRNAs were constructed. RESULTS: Using sequencing and qRT-PCR, hsa_circ_0001953 was found to be elevated in PDR patients in contrast with the other two groups. Statistical analysis showed that the expression levels of hsa_circ_0001953 in PDR patients were positively related to the duration of diabetes and HbAc1. Receiver operating characteristic (ROC) curve analysis revealed that hsa_circ_0001953 was associated with a high diagnostic accuracy in discriminating PDR patients from NPDR patients and healthy controls, resulting in an area under the curve (AUC) of 0.87 and 0.92, respectively. The circRNA-miRNA-target gene networks for hsa_circ_0001953 showed that hsa_circ_0001953 could interact with dozens of miRNAs and some targeted mRNAs have been potentially involved in the pathogenesis of diabetes. CONCLUSION: The present findings indicate that hsa_circ_0001953 in the whole blood may serve as a novel diagnostic biomarker and potential therapeutic target for PDR.