MiR-223-3p promotes genomic stability of hematopoietic progenitors after radiation

When hematopoietic cells are overwhelmed with ionizing radiation (IR) DNA damage, the alternative non-homologous end-joining (aNHEJ) repair pathway is activated to repair stressed replication forks. While aNHEJ can rescue cells overwhelmed with DNA damage, it can also mediate chromosomal deletions and fusions, which can cause mis-segregation in mitosis and resultant aneuploidy. We previously reported that a hematopoietic microRNA, miR-223-3p, normally represses aNHEJ. We found that miR-223-/- mice have increased survival of hematopoietic stem and progenitor cells (HSPCs) after sublethal IR. However, this came at the cost of significantly more genomic aberrancies, with miR-223-/- hematopoietic progenitors having increased metaphase aberrancies, including chromothripsis, and increased sequence abnormalities, especially deletions, which is consistent with aNHEJ. These data imply that when an HSPC is faced with substantial DNA damage, it may trade genomic damage for its own survival by choosing the aNHEJ repair pathway, and this choice is regulated in part by miR-223-3p.

TATDN2 resolution of R-loops is required for survival of BRCA1-mutant cancer cells

BRCA1-deficient cells have increased IRE1 RNase, which degrades multiple microRNAs. Reconstituting expression of one of these, miR-4638-5p, resulted in synthetic lethality in BRCA1-deficient cancer cells. We found that miR-4638-5p represses expression of TATDN2, a poorly characterized member of the TATD nuclease family. We discovered that human TATDN2 has RNA 3' exonuclease and endonuclease activity on double-stranded hairpin RNA structures. Given the cleavage of hairpin RNA by TATDN2, and that BRCA1-deficient cells have difficulty resolving R-loops, we tested whether TATDN2 could resolve R-loops. Using in vitro biochemical reconstitution assays, we found TATDN2 bound to R-loops and degraded the RNA strand but not DNA of multiple forms of R-loops in vitro in a Mg2+-dependent manner. Mutations in amino acids E593 and E705 predicted by Alphafold-2 to chelate an essential Mg2+ cation completely abrogated this R-loop resolution activity. Depleting TATDN2 increased cellular R-loops, DNA damage and chromosomal instability. Loss of TATDN2 resulted in poor replication fork progression in the presence of increased R-loops. Significantly, we found that TATDN2 is essential for survival of BRCA1-deficient cancer cells, but much less so for cognate BRCA1-repleted cancer cells. Thus, we propose that TATDN2 is a novel target for therapy of BRCA1-deficient cancers.

PINE-TREE enables highly efficient genetic modification of human cell lines

Prime editing technologies enable precise genome editing without the caveats of CRISPR nuclease-based methods. Nonetheless, current approaches to identify and isolate prime-edited cell populations are inefficient. Here, we established a fluorescence-based system, prime-induced nucleotide engineering using a transient reporter for editing enrichment (PINE-TREE), for real-time enrichment of prime-edited cell populations. We demonstrated the broad utility of PINE-TREE for highly efficient introduction of substitutions, insertions, and deletions at various genomic loci. Finally, we employ PINE-TREE to rapidly and efficiently generate clonal isogenic human pluripotent stem cell lines, a cell type recalcitrant to genome editing.

Prescribing patterns for paediatric hyperopia among paediatric eye care providers

PURPOSE

To survey paediatric eye care providers to identify current patterns of prescribing for hyperopia.

METHODS

Paediatric eye care providers were invited, via email, to participate in a survey to evaluate current age-based refractive error prescribing practices. Questions were designed to determine which factors may influence the survey participant's prescribing pattern (e.g., patient's age, magnitude of hyperopia, patient's symptoms, heterophoria and stereopsis) and if the providers were to prescribe, how much hyperopic correction would they prescribe (e.g., full or partial prescription). The response distributions by profession (optometry and ophthalmology) were compared using the Kolmogorov-Smirnov cumulative distribution function test.

RESULTS

Responses were submitted by 738 participants regarding how they prescribe for their hyperopic patients. Most providers within each profession considered similar clinical factors when prescribing. The percentages of optometrists and ophthalmologists who reported considering the factor often differed significantly. Factors considered similarly by both optometrists and ophthalmologists were the presence of symptoms (98.0%, p = 0.14), presence of astigmatism and/or anisometropia (97.5%, p = 0.06) and the possibility of teasing (8.3%, p = 0.49). A wide range of prescribing was observed within each profession, with some providers reporting that they would prescribe for low levels of hyperopia while others reported that they would never prescribe. When prescribing for bilateral hyperopia in children with age-normal visual acuity and no manifest deviation or symptoms, the threshold for prescribing decreased with age for both professions, with ophthalmologists typically prescribing 1.5-2 D less than optometrists. The threshold for prescribing also decreased for both optometrists and ophthalmologists when children had associated clinical factors (e.g., esophoria or reduced near visual function). Optometrists and ophthalmologists most commonly prescribed based on cycloplegic refraction, although optometrists most commonly prescribed based on both the manifest and cycloplegic refraction for children ≥7 years.

CONCLUSION

Prescribing patterns for paediatric hyperopia vary significantly among eye care providers.

EEPD1 promotes repair of oxidatively-stressed replication forks

Unrepaired oxidatively-stressed replication forks can lead to chromosomal instability and neoplastic transformation or cell death. To meet these challenges cells have evolved a robust mechanism to repair oxidative genomic DNA damage through the base excision repair (BER) pathway, but less is known about repair of oxidative damage at replication forks. We found that depletion or genetic deletion of EEPD1 decreases clonogenic cell survival after oxidative DNA damage. We demonstrate that EEPD1 is recruited to replication forks stressed by oxidative damage induced by H2O2 and that EEPD1 promotes replication fork repair and restart and decreases chromosomal abnormalities after such damage. EEPD1 binds to abasic DNA structures and promotes resolution of genomic abasic sites after oxidative stress. We further observed that restoration of expression of EEPD1 via expression vector transfection restores cell survival and suppresses chromosomal abnormalities induced by oxidative stress in EEPD1-depleted cells. Consistent with this, we found that EEPD1 preserves replication fork integrity by preventing oxidatively-stressed unrepaired fork fusion, thereby decreasing chromosome instability and mitotic abnormalities. Our results indicate a novel role for EEPD1 in replication fork preservation and maintenance of chromosomal stability during oxidative stress.

A novel synergistic effect of TiO2 and ZnO incorporation in PES-based thin-film nanocomposite nanofiltration membrane for treatment of textile wastewater

A novel synergistic effect of TiO₂ and ZnO incorporation in the PES-based thin-film nanocomposite nanofiltration membranes was developed for the treatment of common effluent treatment plant (CETP) textile wastewater. PES@TiO₂ membranes were developed by phase inversion via the immersion precipitation method followed by the addition of zinc oxide nanoparticles prepared by the rapid microwave-assisted hydrothermal process via interfacial polymerization. p-Phenylenediamine was used as a monomer for the IP process that was coated on the PES@TiO₂ support layer. Various techniques have been applied to characterize the developed thin-film nanocomposite membranes such as Fourier transform infrared (FTIR) microscopy, field emission scanning electron microscopy (FESEM), X-ray powder diffraction (XRD), and contact angle measurement to examine the presence of vibrational modes, surface morphology, the crystal structure of nanoparticles, and hydrophilicity of the membrane, respectively. Membrane properties include porosity, salt rejection, mean pore radius, pure water flux, and industrial effluent rejection efficiency that were studied. The thin-film nanocomposite membrane T5-PES@TiO₂(2%)-ZnO(0.3%) was prepared with a combination of 17 wt% PES, 78 wt% DMF, 3 wt% PVP K30, 2% TiO₂, 2.5 wt% PPD, 0.3 wt% ZnO, and 1.0 wt% TMC that exhibited high water permeability, porosity, higher industrial effluent rejection, and salt rejection efficiency compared to the neat PES membrane.

A microcarrier-based protocol for scalable generation and purification of human induced pluripotent stem cell-derived neurons and astrocytes

Here, we describe a protocol for a microcarrier (MC)-based, large-scale generation and cryopreservation of human-induced pluripotent stem cell (hiPSC)-derived neurons and astrocytes. We also detail steps to isolate these populations with a high degree of purity. Finally, we describe how to cryopreserve these cell types while maintaining high levels of viability and preserving cellular function post-thaw. For complete details on the use and execution of this protocol, please refer to Brookhouser et al. (2021).

In-plane current induced nonlinear magnetoelectric effects in single crystal films of barium hexaferrite

This report is on the observation and analysis of nonlinear magnetoelectric effects (NLME) for in-plane currents perpendicularly to the hexagonal axis in single crystals and liquid phase epitaxy grown thin films of barium hexaferrite. Measurements involved tuning of ferromagnetic resonance (FMR) at 56–58 GHz in the multidomain and single domain states in the ferrite by applying a current. Data on the shift in the resonance frequency with input electric power was utilized to estimate the variations in the magnetic parameter that showed a linear dependence on the input electric power. The NLME tensor coefficients were determined form the estimated changes in the magnetization and uniaxial anisotropy field. The estimated NLME coefficients for in-plane currents are shown to be much higher than for currents flowing along the hexagonal axis. Although the frequency shift of FMR was higher for the single domain resonance, the multi-domain configuration is preferable for device applications since it eliminates the need for a large bias magnetic field. Thus, multidomain resonance with current in the basal plane is favorable for use in electrically tunable miniature, ferrite microwave signal processing devices requiring low operating power.

The Emergence of Model Systems to Investigate the Link Between Traumatic Brain Injury and Alzheimer’s Disease

Numerous epidemiological studies have demonstrated that individuals who have sustained a traumatic brain injury (TBI) have an elevated risk for developing Alzheimer’s disease and Alzheimer’s-related dementias (AD/ADRD). Despite these connections, the underlying mechanisms by which TBI induces AD-related pathology, neuronal dysfunction, and cognitive decline have yet to be elucidated. In this review, we will discuss the various in vivo and in vitro models that are being employed to provide more definite mechanistic relationships between TBI-induced mechanical injury and AD-related phenotypes. In particular, we will highlight the strengths and weaknesses of each of these model systems as it relates to advancing the understanding of the mechanisms that lead to TBI-induced AD onset and progression as well as providing platforms to evaluate potential therapies. Finally, we will discuss how emerging methods including the use of human induced pluripotent stem cell (hiPSC)-derived cultures and genome engineering technologies can be employed to generate better models of TBI-induced AD.

Prevalence of depression and anxiety among drug resistant tuberculosis: A study in North India

BACKGROUND

Drug Resistant Tuberculosis (DR-TB) is an emergent issue in the recent decades. Multidrug resistant (MDR-TB) and Extensive drug resistant (XDR-TB) tuberculosis are the common type of DR-TB. Psychological issues like depression and anxiety are common among the chronic illnesses like tuberculosis. This study aimed at estimating the prevalence of depression and anxiety among these patients.

METHODS

Our study is conducted in a tertiary care teaching hospital in North India. This study aimed at identifying the prevalence of depression and anxiety among the drug resistant tuberculosis patients attending DOTS clinic. The depression and anxiety were screened using PHQ-9 and HAM-A inventories. Binomial and multinomial regression analysis were done to identifying the predictors of depression and anxiety.

RESULTS

The prevalence rate of depression in MDR-TB and XDR-TB is 68% and 78% respectively. The prevalence of anxiety is 54% in MDR-TB and 66% in XDR-TB respectively in our study. Duration of illness and literacy were the significant predictors of depression and anxiety.

CONCLUSION

Patients with DR-TB faces huge psychological burden and this study highlighted the toll of depression and anxiety among them. Adequate screening, identification and treatment for these disorders among DR-TB patients at their earlier treatment stage helps in improving the adherence to treatment and functionality.

APOE2 mitigates disease-related phenotypes in an isogenic hiPSC-based model of Alzheimer's disease

Genome-wide association studies (GWAS) have identified polymorphism in the Apolipoprotein E gene (APOE) to be the most prominent risk factor for Alzheimer's disease (AD). Compared to individuals homozygous for the APOE3 variant, individuals with the APOE4 variant have a significantly elevated risk of AD. On the other hand, longitudinal studies have shown that the presence of the APOE2 variant reduces the lifetime risk of developing AD by 40 percent. While there has been significant research that has identified the risk-inducing effects of APOE4, the underlying mechanisms by which APOE2 influences AD onset and progression have not been extensively explored. In this study, we utilize an isogenic human induced pluripotent stem cell (hiPSC)-based system to demonstrate that conversion of APOE3 to APOE2 greatly reduced the production of amyloid-beta (Aβ) peptides in hiPSC-derived neural cultures. Mechanistically, analysis of pure populations of neurons and astrocytes derived from these neural cultures revealed that mitigating effects of APOE2 are mediated by cell autonomous and non-autonomous effects. In particular, we demonstrated the reduction in Aβ is potentially driven by a mechanism related to non-amyloidogenic processing of amyloid precursor protein (APP), suggesting a gain of the protective function of the APOE2 variant. Together, this study provides insights into the risk-modifying effects associated with the APOE2 allele and establishes a platform to probe the mechanisms by which APOE2 enhances neuroprotection against AD.

A humanized monoclonal antibody against the endothelial chemokine CCL21 for the diagnosis and treatment of inflammatory bowel disease

Chemokines are small proteins that promote leukocyte migration during development, infection, and inflammation. We and others isolated the unique chemokine CCL21, a potent chemo-attractant for naïve T-cells, naïve B-cells, and immature dendritic cells. CCL21 has a 37 amino acid carboxy terminal extension that is distinct from the rest of the chemokine family, which is thought to anchor it to venule endothelium where the amino terminus can interact with its cognate receptor, CCR7. We and others have reported that venule endothelium expressing CCL21 plays a crucial role in attracting naïve immune cells to sites of antigen presentation. In this study we generated a series of monoclonal antibodies to the amino terminus of CCL21 in an attempt to generate an antibody that blocked the interaction of CCL21 with its receptor CCR7. We found one humanized clone that blocked naïve T-cell migration towards CCL21, while memory effector T-cells were less affected. Using this monoclonal antibody, we also demonstrated that CCL21 is expressed in the mucosal venule endothelium of the large majority of inflammatory bowel diseases (IBD), including Crohn's disease, ulcerative colitis, and also in celiac disease. This expression correlated with active IBD in 5 of 6 cases, whereas none of 6 normal bowel biopsies had CCL21 expression. This study raises the possibility that this monoclonal antibody could be used to diagnose initial or recurrent of IBD. Significantly, this antibody could also be used for therapeutic intervention in IBD by selectively interfering with recruitment of naïve immune effector cells to sites of antigen presentation, without harming overall memory immunity.

Influence of monomers involved in the fabrication of a novel PES based nanofiltration thin-film composite membrane and its performance in the treatment of common effluent (CETP) textile industrial wastewater

OBJECTIVE

In this article, monomers (tannic acid (TA) and m- phenylenediamine (MPD)) were used in the fabrication of a novel PES based thin-film composite nanofiltration (TFC-NF) membrane for the treatment of a common effluent treatment plant (CETP) of textile industrial wastewater.

MEMBRANE SYNTHESIS

PES support sheets and TFC layers were fabricated via non-solvent induced phase inversion and in-situ interfacial polymerization (IP) process. The ultra-thin active layer was synthesized via the IP process with monomers such as tannic acid (TA) and m- phenylenediamine (MPD). T and M series membranes correspond to (PES/x wt% TA, x = 2, 4, 6) as T1, T2, T3 -TA and (PES/x wt% MPD, x = 2, 4, 6) as M1, M2, M3-MPD respectively. M0 corresponds to PES which is the virgin membrane.

RESULTS

The chemical structure, surface morphology, surface roughness and surface properties were explored using fourier transform infrared (FTIR) spectroscopy, field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM) and contact angle, respectively. The filtration performance of the thin-film composite nanofiltration (TFC-NF) membranes was investigated by various properties like pure water flux, salt rejection, porosity, mean pore radius and antifouling analysis.

CONCLUSION

T1-TA membrane showed better water permeability, high salt rejection and better industrial effluent rejection with 94.4% of TDS that are suitable for industrial reuse and agricultural irrigation. Moreover, for T1-TA membrane, the water flux, porosity, mean pore radius, salt rejection, surface roughness and contact angle of 43.5lm^- 2 h ^- 1, 47.1%, 16.7nm, 72.7%, 11.7nm and 41.48°was achieved respectively that was found to be higher than that of all the other fabricated membranes. Further, the rejection efficiency rate of textile effluent characteristics such as pH, turbidity, TDS, alkalinity, total hardness, BOD and COD were also achieved with maximum deduction in the T1-TA TFC-NF membrane compared to the M0-Virgin PES membrane. From the results, it can be confirmed that the T1-TA membrane significantly reduced the alkalinity, total hardness, BOD and COD rejections of 78%, 77.3%, 58.5% and 67.5% respectively, present in the effluent. Water flux recovery ratio (FRR) was improved from 74.6% for M0-Virgin PES membrane to 94.8% for T1-TA membrane. The modified TFC-NF membranes especially T1-TA, had better anti-fouling property and excellent hydrophilicity than the unmodified M0-Virgin PES membrane.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-021-00624-x.

Nonlinear magnetoelectric effects in Al-substituted strontium hexaferrite

This report is on the observation and theory of electric field E induced non-linear magnetoelectric (NLME) effects in single crystal platelets of ferrimagnetic M-type strontium aluminum hexagonal ferrite. Using microwave measurement techniques, it was found that a DC electric field along the hexagonal c-axis results in significant changes in the saturation magnetization and uniaxial magneto-crystalline anisotropy field and these changes are proportional to the square of the applied static electric field. The NLME effects were present with or without an external bias magnetic field. The E-induced variation in magnetic order parameters is attributed to weakening of magnetic exchange and spin-orbit interactions since conduction electrons in the ferrite are effectively excluded from both interactions while being in transit from one Fe ion to another. We present a phenomenological theory which considers magneto-bielectric effects characterized by a quadratic term in electric field E in the free energy density. The coefficients for the NLME coupling terms have been calculated from experimental data and they do show variations with the Al substitution level and the largest rates of change of the saturation magnetization and anisotropy constant change with the applied power were observed for x = 0.4. It was also clear from the study that strength of the NLME effect does not depend on the amount Al substitution, but critically depends on the electrical conductivity of the sample with the highest NLME coefficients estimated for the sample with the highest conductivity. Results of this work are of importance for a new family of electric field tunable, miniature, high frequency ferrite devices.

Hyperlipidemia impairs uterine β-adrenergic signaling by reducing cAMP in late pregnant rats

The aim of the present study was to reveal the effect of hyperlipidemia on β2- and β3-adrenergic signaling in late pregnant rat uterus. Hyperlipidemia was induced in female Wistar rats by feeding a high-fat high-cholesterol diet for 8 weeks before and after mating upto the 21st day of gestation. The effect of hyperlipidemia on β-adrenergic signaling was studied with the help of tension experiments, real-time PCR and cAMP ELISA in 21-day pregnant rat uterus. In tension experiments, hyperlipidemia neither altered the spontaneous contractility nor the oxytocin-induced contractions. However, it decreased the -logEC50 values of β2-adrenoceptor agonist, salbutamol and β3-adrenoceptor agonist, BRL37344. It also decreased the efficacy of adenylyl cyclase activator, forskolin. Further, there was a significant decrease in salbutamol and BRL37344-stimulated cAMP content in uterine tissues. However, there was no alteration in mRNA expressions of β2-adrenoceptor (Adrb2), β3-adrenoceptor (Adrb3) and Gs protein (Gnas) though there was a significant increase in the mRNA expression of Gi protein (Gnai). In conclusion, reduced cAMP content after beta-adrenergic receptor stimulation, which correlates with an increase in Gnai mRNA, may explain the mechanism of the impairment of uterine β-adrenergic signaling in hyperlipidemic pregnant rats. The clinical implication of the present study may relate to reduced myometrial relaxant response to β-adrenergic agonists in high fat-induced uterine dysfunction.

Leptin receptor stimulation in late pregnant mouse uterine tissue inhibits spontaneous contractions by increasing NO and cGMP

The adipokine, leptin exerts inhibitory effect on both spontaneous and oxytocin-induced contractions in myometrium. However, the mechanisms involved in leptin-induced effect are not clear. In the present study, we studied the altered characteristics of uterine contractions in the presence of leptin and the possible mechanisms of its effect in late pregnant (18.5 day) mouse uterus. We conducted functional, biochemical and molecular biology studies to demonstrate the mechanism of leptin-induced response. Leptin exerted an inhibitory response (E_max 40.5 ± 3.99%) on basal uterine contractions. The extent of inhibition was less than that obtained with known uterine relaxants, salbutamol (E_max103 ± 8.66%) and BRL-37344 (E_max 84.79 ± 8.12%). Leptin-induced uterine response was inhibited by leptin receptor antagonist SHLA and JAK-STAT pathway inhibitor, AG-490. The relaxant response was also subdued by NO-cGMP-PK-G pathway blockers L-NAME, 1400W, ODQ and KT-5823. Further, leptin enhanced the levels of NO and cGMP in uterine tissues. Also, SHLA, AG-490 and a combination of 1400 W and L-NAME prevented leptin-induced increase in NO. Similar effect was observed on cGMP levels in presence of leptin and SHLA. However, leptin did not influence CaCl₂-induced response in potassium-depolarized tissues. We also detected leptin receptor protein in late pregnant mouse uterus located in endometrial luminal epithelium and myometrial layers. Real-time PCR studies revealed significantly higher expression of short forms of the receptor (ObRa and ObRc) in comparison to the long form (ObRb). In conclusion, the results of the present study suggest that leptin inhibits mouse uterine contraction by stimulating short forms of the leptin receptors and activating NO pathway in a JAK-STAT-dependent manner.

A Defined and Scalable Peptide-Based Platform for the Generation of Human Pluripotent Stem Cell-Derived Astrocytes

Astrocytes comprise the most abundant cell type in the central nervous system (CNS) and play critical roles in maintaining neural tissue homeostasis. In addition, astrocyte dysfunction and death has been implicated in numerous neurological disorders such as multiple sclerosis, Alzheimer’s disease, amyotrophic lateral sclerosis (ALS), and Parkinson’s disease (PD). As such, there is much interest in using human pluripotent stem cell (hPSC)-derived astrocytes for drug screening, disease modeling, and regenerative medicine applications. However, current protocols for generation of astrocytes from hPSCs are limited by the use of undefined xenogeneic components and two-dimensional (2D) culture surfaces, which limits their downstream applications where large-quantities of cells generated under defined conditions are required. Here, we report the use of a completely synthetic, peptide-based substrate that allows for the differentiation of highly pure populations of astrocytes from several independent hPSC lines, including those derived from patients with neurodegenerative disease. This substrate, which we demonstrate is compatible with both conventional 2D culture formats and scalable microcarrier (MC)-based technologies, leads to the generation of cells that express high levels of canonical astrocytic markers as well as display properties characteristic of functionally mature cells including production of apolipoprotein E (ApoE), responsiveness to inflammatory stimuli, ability to take up amyloid-β (Aβ), and appearance of robust calcium transients. Finally, we show that these astrocytes can be cryopreserved without any loss of functionality. In the future, we anticipate that these methods will enable the development of bioprocesses for the production of hPSC-derived astrocytes needed for biomedical research and clinical applications.

1,4-Bis(4-methoxyphenyl)naphthalene

The title naphthalene derivative, C24H20O2, features 4-methyoxy-substituted benzene rings in the 1 and 4 positions of the naphthalene ring system. There are two crystallographically independent molecules (A and B) in asymmetric unit. The independent molecules have very similar conformations in which the naphthalene ring systems are only slightly bent, exhibiting dihedral angles between the constituent benzene rings of 3.76 (15) and 3.39 (15)° for A and B, respectively. The pendent 4-methyoxybenzene rings are splayed out of the plane through the naphthalene ring system to which they are connected [range of dihedral angles = 59.63 (13) to 67.09 (13)°]. In the crystal, the molecular packing is consolidated by intermolecular C—H...π interactions, leading to supramolecular chains along the b axis. The chains assemble without directional interactions between them.

The splicing component ISY1 regulates APE1 in base excision repair

The integrity of cellular genome is continuously challenged by endogenous and exogenous DNA damaging agents. If DNA damage is not removed in a timely fashion the replisome may stall at DNA lesions, causing fork collapse and genetic instability. Base excision DNA repair (BER) is the most important pathway for the removal of oxidized or mono-alkylated DNA. While the main components of the BER pathway are well defined, its regulatory mechanism is not yet understood. We report here that the splicing factor ISY1 enhances apurinic/apyrimidinic endonuclease 1 (APE1) activity, the multifunctional enzyme in BER, by promoting its 5'-3' endonuclease activity. ISY1 expression is induced by oxidative damage, which would provide an immediate up-regulation of APE1 activity in vivo and enhance BER of oxidized bases. We further found that APE1 and ISY1 interact, and ISY1 enhances the ability of APE1 to recognize abasic sites in DNA. Using purified recombinant proteins, we reconstituted BER and demonstrated that ISY1 markedly promoted APE1 activity in both the short- and long-patch BER pathways. Our study identified ISY1 as a regulator of the BER pathway, which would be of physiological relevance where suboptimal levels of APE1 are present. The interaction of ISY1 and APE1 also establishes a connection between DNA damage repair and pre-mRNA splicing.

5,13-Bis(4-methoxyphenyl)dinaphtho[2,3-b:2′,3′-d]thiophene S,S-dioxide dichloromethane hemisolvate

The title compound, C34H24O4S·0.5CH2Cl2, crystallizes with two independent molecules and one dichloromethane solvent molecule in the asymmetric unit. The crystal packing is consolidated by C—H...O hydrogen bonds.

Resident memory CD8+ T cells within cancer islands mediate survival in breast cancer patients

CD8+ tumor-infiltrating lymphocytes (TILs) correlate with relapse-free survival (RFS) in most cancer types, including breast cancer. However, subset composition, functional status, and spatial location of CD8+ TILs in relation to RFS in human breast tumors remain unclear. Spatial tissue analysis via quantitative immunofluorescence showed that infiltration of CD8+ T cells into cancer islands was more significantly associated with RFS than CD8+ T cell infiltration into either tumor stroma or total tumor. Localization into cancer islands within tumors is mediated by expression of the integrin CD103, which is a marker for tissue-resident memory T cells (TRMs). Analysis of fresh tumor samples revealed that CD8+ TRMs are functionally similar to other CD8+ TILs, suggesting that the basis of their protective effect is their spatial distribution rather than functional differences. Indeed, CD103+ TRMs, as compared with CD103-CD8+ TILs, are enriched within cancer islands, and CD8+ TRM proximity to cancer cells drives the association of CD8+ TIL densities with RFS. Together, these findings reveal the importance of cancer island-localized CD8+ TRMs in surveillance of the breast tumor microenvironment and as a critical determinant of RFS in patients with breast cancer.

Validity of the Spot Vision Screener in detecting vision disorders in children 6 months to 36 months of age

PURPOSE

To evaluate the Spot Vision Screener in detecting targeted vision disorders compared to cycloplegic retinoscopy in children <3 years of age.

METHODS

Children, ages 6 months to 36 months underwent vision screening using the Spot Vision Screener. Results were compared to results of comprehensive eye examinations. Validity of the Spot was evaluated by calculating the area under the curve (AUC); the receiver operating characteristics (ROC) were used to determine optimal sensitivity and specificity for detection of targeted vision disorders.

RESULTS

A total of 249 children were included. The AUC for detecting targeted vision disorders as defined by the study specific criteria using the Spot was 0.790. Compared to cycloplegic retinoscopy, the Spot underestimated hyperopia by 1.02 D (95% CI, 0.86-1.17 D). For hyperopia ≥4.5 D spherical equivalent (n = 10), the mean difference between the Spot and cycloplegic retinoscopy was 3.46 D (95% CI, 1.95-4.98 D). In contrast, the Spot overestimated astigmatism compared to cycloplegic retinoscopy (-1.00 D vs -0.48 D; P < 0.001) by -0.52 D (95% CI, 0.43-0.62 D).

CONCLUSIONS

The Spot Vision Screener showed good overall validity in detecting targeted vision disorders. It was within 0.5 D and 1 D of cycloplegic retinoscopy with regard to low hyperopia and astigmatism. Higher hyperopic spherical equivalent refractive errors showed larger differences in mean values between the Spot and cycloplegic retinoscopy.

MiR223-3p promotes synthetic lethality in BRCA1-deficient cancers

Defects in DNA repair give rise to genomic instability, leading to neoplasia. Cancer cells defective in one DNA repair pathway can become reliant on remaining repair pathways for survival and proliferation. This attribute of cancer cells can be exploited therapeutically, by inhibiting the remaining repair pathway, a process termed synthetic lethality. This process underlies the mechanism of the Poly-ADP ribose polymerase-1 (PARP1) inhibitors in clinical use, which target BRCA1 deficient cancers, which is indispensable for homologous recombination (HR) DNA repair. HR is the major repair pathway for stressed replication forks, but when BRCA1 is deficient, stressed forks are repaired by back-up pathways such as alternative nonhomologous end-joining (aNHEJ). Unlike HR, aNHEJ is nonconservative, and can mediate chromosomal translocations. In this study we have found that miR223-3p decreases expression of PARP1, CtIP, and Pso4, each of which are aNHEJ components. In most cells, high levels of microRNA (miR) 223-3p repress aNHEJ, decreasing the risk of chromosomal translocations. Deletion of the miR223 locus in mice increases PARP1 levels in hematopoietic cells and enhances their risk of unprovoked chromosomal translocations. We also discovered that cancer cells deficient in BRCA1 or its obligate partner BRCA1-Associated Protein-1 (BAP1) routinely repress miR223-3p to permit repair of stressed replication forks via aNHEJ. Reconstituting the expression of miR223-3p in BRCA1- and BAP1-deficient cancer cells results in reduced repair of stressed replication forks and synthetic lethality. Thus, miR223-3p is a negative regulator of the aNHEJ DNA repair and represents a therapeutic pathway for BRCA1- or BAP1-deficient cancers.

Abstract 1758: Splicing component ISY1 interacts with APE1 and regulates base excision repair

Cellular genome is continuously challenged by endogenous and exogenous DNA damaging agents. In the genome, base modifications are the most common form of DNA damage. Base excision DNA repair (BER) is the most important pathway for the removal of oxidized or alkylated DNA. If these base modifications continue to persist, the replisome may stall at DNA lesions, causing the replication fork to collapse, leading to genetic instability. While the main components of the BER pathway are well defined, its regulatory mechanism remains poorly understood. We report here that apurinic/apyrimidinic endonuclease 1 (APE1), a multifunctional protein interacts with the pre-mRNA splicing factor ISY1. However, this interaction is independent of DNA or RNA based upon our pull-down experimental results. ISY1 expression is induced by oxidative or DNA alkylation damage, which would then provide an immediate up-regulation of APE1 activity in vivo and enhanced BER of oxidized bases. This was supported from our results of in vitro reconstituted experiment suggesting that ISY1 can stimulate 5’-3’ endonuclease 1 activity of APE1 in both the short- and long-patch BER pathways and increase its binding to AP site DNA. The interaction between ISY1 and APE1 also establishes a connection between DNA damage repair and pre-mRNA splicing. Based upon these results, we propose that ISY1 is an important regulator of BER and enhances the ability of APE1 to efficiently recognize abasic sites in DNA. Role of ISY1 becomes important in aging tissues where decreased APE1 activity results in the accumulation of oxidative genomic damages. Therefore, ISY1 may work as an anti-aging factor. Induction of ISY1 in malignancies could constitute a mechanism to avoid apoptotic death after treatment with alkylating agents.

Citation Format: Aruna Jaiswal, Elizabeth Williamson, Bhavita Patel, Gayathri Srinivasan, Kimi Kong, Carrie Lomelino, Satya Narayan, Robert Hromas. Splicing component ISY1 interacts with APE1 and regulates base excision repair [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1758.

2-Amino-6-chloropyridine–glutaric acid (1/1)

In the title 1:1 co-crystal [systematic name: 6-chloropyridin-2-amine–pentanedioic acid (1/1)], C5H5ClN2·C5H8O4, the pyridine ring is essentially planar, with a maximum deviation of 0.003 (1) Å. The base and acid molecules are linked via N—H...O and O—H...N hydrogen bonds, while inversion-related acid molecules are linked via pairs of O—H...O hydrogen bonds. These interactions together with a C—H...O hydrogen bond connect the two components, forming (001) sheets.

2-Amino-6-chloropyridinium 3-carboxy-4-hydroxybenzenesulfonate

In the 3-carboxy-4-hydroxybenzenesulfonate anion of the title salt, C5H6ClN2 +·C7H5O6S−, an intramolecular O—H...O hydrogen bond with an S(6) ring motif is observed. In the crystal, the anions are linked into a chain structure running along [1\overline{1}0] via an O—H...O hydrogen bond formed between the carboxy and sulfonate groups. The 2-amino-6-chloropyridinium cations bridge the anion chains via N—H...O and C—H...O hydrogen bonds, forming a sheet parallel to the ab plane. In the sheet, a C—H...Cl interaction between the cations is also observed.

An integrated biomanufacturing platform for the large-scale expansion and neuronal differentiation of human pluripotent stem cell-derived neural progenitor cells

Human pluripotent stem cell derived neural progenitor cells (hNPCs) have the unique properties of long-term in vitro expansion as well as differentiation into the various neurons and supporting cell types of the central nervous system (CNS). Because of these characteristics, hNPCs have tremendous potential in the modeling and treatment of various CNS diseases and disorders. However, expansion and neuronal differentiation of hNPCs in quantities necessary for these applications is not possible with current two dimensional (2-D) approaches. Here, we used a fully defined peptide substrate as the basis for a microcarrier (MC)-based suspension culture system. Several independently derived hNPC lines were cultured on MCs for multiple passages as well as efficiently differentiated to neurons. Finally, this MC-based system was used in conjunction with a low shear rotating wall vessel (RWV) bioreactor for the integrated, large-scale expansion and neuronal differentiation of hNPCs. Overall, this fully defined and scalable biomanufacturing system will facilitate the generation of hNPCs and their neuronal derivatives in quantities necessary for basic and translational applications.

STATEMENT OF SIGNIFICANCE

In this work, we developed a microcarrier (MC)-based culture system that allows for the expansion and neuronal differentiation of human pluripotent stem cell-derived neural progenitor cells (hNPCs) under defined conditions. In turn, this MC approach was implemented in a rotating wall vessel (RWV) bioreactor for the large-scale expansion and neuronal differentiation of hNPCs. This work is of significance as it overcomes current limitations of conventional two dimensional (2-D) culture systems to enable the generation of hNPCs and their neuronal derivatives in quantities required for downstream applications in disease modeling, drug screening, and regenerative medicine.

<b>Water striders, the genus Cylindrostethus Mayr (Insecta: Heteroptera: Gerridae) from India with a new record</b>

The genus Cylindrostethus Mayr, 1865 from India is studied.  Prior to this study C. productus (Spinola, 1837) and C. scrutator (Kirkaldy, 1899) of Cylindrostethus were known from India.  The record of C. scrutator (Kirkaldy, 1899) from India is doubtful.  Study of gerrid specimens from Andaman Islands revealed one more additional species, C. costalis costalis Schmidt, 1915 new to Indian fauna.  So, presently two species of this genus are known from India namely C. costalis costalis and C. productus, both belonging to the C. costalis species group (Polhemus 1994).  A detailed study has been made of the male and female genitalia of Cylindrostethus known from India.  

Modeling flow and transport in fracture networks using graphs

Fractures form the main pathways for flow in the subsurface within low-permeability rock. For this reason, accurately predicting flow and transport in fractured systems is vital for improving the performance of subsurface applications. Fracture sizes in these systems can range from millimeters to kilometers. Although modeling flow and transport using the discrete fracture network (DFN) approach is known to be more accurate due to incorporation of the detailed fracture network structure over continuum-based methods, capturing the flow and transport in such a wide range of scales is still computationally intractable. Furthermore, if one has to quantify uncertainty, hundreds of realizations of these DFN models have to be run. To reduce the computational burden, we solve flow and transport on a graph representation of a DFN. We study the accuracy of the graph approach by comparing breakthrough times and tracer particle statistical data between the graph-based and the high-fidelity DFN approaches, for fracture networks with varying number of fractures and degree of heterogeneity. Due to our recent developments in capabilities to perform DFN high-fidelity simulations on fracture networks with large number of fractures, we are in a unique position to perform such a comparison. We show that the graph approach shows a consistent bias with up to an order of magnitude slower breakthrough when compared to the DFN approach. We show that this is due to graph algorithm's underprediction of the pressure gradients across intersections on a given fracture, leading to slower tracer particle speeds between intersections and longer travel times. We present a bias correction methodology to the graph algorithm that reduces the discrepancy between the DFN and graph predictions. We show that with this bias correction, the graph algorithm predictions significantly improve and the results are very accurate. The good accuracy and the low computational cost, with O(10^{4}) times lower times than the DFN, makes the graph algorithm an ideal technique to incorporate in uncertainty quantification methods.

How many patients self-medicate with St John's wort?

Aims and Method

St John's wort is popularly taken as a herbal remedy, but it interacts with prescribed drugs. The aim of this survey was to estimate the prevalence of patients self-medicating with St John's wort. All new referrals to a community mental health team over 5 months were asked about any use of St John's wort.

Results

Fifteen patients, of 101, had taken St John's wort at some time and of those seven were currently taking it. Patients who used St John's wort tended to be younger and female. Only nine of the 15 patients took it for depressive symptoms and none had received medical advice. One patient was taking an interacting medication.

Clinical Implications

A significant number of patients are taking St John's wort. In order to prevent drug interactions, doctors should ask all patients whether they use it, especially young women who may be on the contraceptive pill. Patients need better education about its risks and benefits and it should be taken with medical advice.

Abstract A35: Precision targeting of Homologous Recombination-deficient cancers using microRNA synthetic lethality

Introduction: Because cancer often occurs from defects in DNA repair, cancer cells become addicted to the remaining repair pathways for survival and proliferation. This addiction of cancer cells to residual DNA repair pathways can be exploited therapeutically by inhibiting the residual repair pathway, which is termed synthetic lethality. An example for this is using PARP1 inhibitors as drugs that target cancer cells with an inherited deficiency in BRCA1 or 2. Indeed, PARP1 inhibitors are now being tested as a new treatment option for many other malignancies. In addition to BRCA1/2-deficient malignancies, we here show another type of malignancy, BAP1 mutant mesothelioma, which can be targeted by synthetic lethality. Similar to BRCA1/2, BAP1 is an HR component and these cells rely on other DNA repair pathways for survival. We report here a type of PARP1 regulation, with an endogenous microRNA, that may be subverted for therapy of HR-deficient malignancies. MicroRNAs (miRNA) are small (~22 nucleotides) non-coding RNAs that regulate gene expression by binding to the 3'UTR of mRNA with complete/partial complementarity. MiR223-3p targets the 3'UTR of PARP1 mRNA, and thereby abrogates PARP1 protein levels.

Hypothesis: We hypothesize that miR223-3p can be used to induce synthetic lethality in BRCA1/2 and BAP1 deficient malignancies by targeting the destruction of PARP1. By exploiting the addiction of HR-deficient malignancies to other DNA repair pathways, miR223-3p can be used as a therapeutic for such cancers.

Methods: By using colony formation assay, we found that the BRCA1/2 and BAP1 mutant cells can be killed by miR223-3p. We will assess the efficiency of HR and other DNA repair pathways in these cancer cells to study the molecular mechanisms of toxicity in these cells induced by miR223-3p. We will also modify the nucleotide sequence of miR223-3p to enhance PARP1 inhibition. Finally, we will package miR223-3p in either liposomes or exosomes to deliver to BRCA1/2 and BAP1 deficient malignancies in vivo.

Results: Using the 3 UTR of PARP1 driving a luciferase promoter, we demonstrated that miR223-3p over-expression could reduce luciferase expression from this reporter construct indicating that PARP1 mRNA is a direct target of miR223-3p. BAP1 deficient MPMs and BRCA1/2 mutant malignancies are addicted to other DNA repair pathways for survival and these cancers are effectively targeted by miR223-3p mediated destruction of PARP1. We found that the BAP1 and BRCA1/2 deficient cancer cells have repressed levels of miR223-3p since they cannot tolerate repressed PARP1 levels in cells. When miR223-3p is restored in these cells, they showed decreased active replication forks and deficient fork restart due to destruction of PARP1. We also found that miR223-3p is 120 fold more effective in killing HR deficient malignancies than olaparib, an FDA approved PARP1 inhibitor for BRCA1/2 deficient ovarian cancer.

Conclusions: Packaging miR223-3p in a nanoparticle can be a potential therapeutic for HR-deficient malignancies and it can confer less risk of toxicity to normal cells since this microRNA is naturally present in mammalian cells.

Citation Format: Gayathri Srinivasan, Elizabeth Williamson, Robert Hromas. Precision targeting of Homologous Recombination-deficient cancers using microRNA synthetic lethality [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A35.

Measurement Techniques of the Magneto-Electric Coupling in Multiferroics

The current surge of interest in multiferroic materials demands specialized measurement techniques to support multiferroics research. In this review article we detail well-established measurement techniques of the magneto-electric coupling coefficient in multiferroic materials, together with newly proposed ones. This work is intended to serve as a reference document for anyone willing to develop experimental measurement techniques of multiferroic materials.

Synthetic lethality in malignant pleural mesothelioma with PARP1 inhibition

Malignant pleural mesotheliomas (MPM) are most often surgically unresectable, and they respond poorly to current chemotherapy and radiation therapy. Between 23 and 64% of malignant pleural mesothelioma have somatic inactivating mutations in the BAP1 gene. BAP1 is a homologous recombination (HR) DNA repair component found in the BRCA1/BARD1 complex. Similar to BRCA1/2 deficient cancers, mutation in the BAP1 gene leads to a deficient HR pathway and increases the reliance on other DNA repair pathways. We hypothesized that BAP1-mutant MPM would require PARP1 for survival, similar to the BRCA1/2 mutant breast and ovarian cancers. Therefore, we used the clinical PARP1 inhibitors niraparib and olaparib to assess whether they could induce synthetic lethality in MPM. Surprisingly, we found that all MPM cell lines examined, regardless of BAP1 status, were addicted to PARP1-mediated DNA repair for survival. We found that niraparib and olaparib exposure markedly decreased clonal survival in multiple MPM cell lines, with and without BAP1 mutations. This clonal cell death may be due to the extensive replication fork collapse and genomic instability that PARP1 inhibition induces in MPM cells. The requirement of MPM cells for PARP1 suggests that they may generally arise from defects in HR DNA repair. More importantly, these data demonstrate that the PARP1 inhibitors could be effective in the treatment of MPM, for which little effective therapy exists.

Abstract 1420: The endonuclease Metnase promotes base excision repair of Clustered abasic DNA lesions

Metnase, a human SET-transposase fusion protein contains two functional domains: a SET domain and transposase domain. Transposase domain exhibit strand transfer and end joining activity while set domain is responsible for histone lysine methyltransferase activity (KMT). Metnase also increases the efficiency of double strand break repair by non-homologous end joining (NHEJ); however, its role in the excision of clustered DNA damage remains to be investigated. We hypothesize that 5’-3’ endonuclease activity of metnase could possibly substitute for APE1 in BER and serve as an alternative initiator of BER in tumor cells lacking APE1. In the present study, we examined in vitro endonuclease activity of Metnase using abasic site containing artificial DNA, and describe its activity in BER. Its unique 5’ endonuclease activity was selective only for abasic lesions, but not other base modifications such as 8-oxoguanine, uracil, hypoxanthine or xanthenes. Metnase specifically initiates removal of reduced abasic lesions from DNA, and allows completion of short-patch or long-patch BER. APE1 has difficulty cleaving 5’ of clustered abasic lesions. This endonuclease that promotes BER in clustered oxidative DNA damage is not known. Metnase also cleaves multiple abasic lesions (clustered DNA damage) and facilitates the repair of DNA if the multiple DNA damages are 3 or more nucleotides apart on the opposing strands. However, repair of multiple DNA damages remains inefficient if these are in close proximity of each other (&lt; 3nt apart on the opposing strands) and results in DNA double strand break (DSB). These results suggest that Metnase can promote BER of oxidative nucleotides, where APE1 is unable to function.

Citation Format: Aruna S. Jaiswal, Elizabeth A. Williamson, Bhavita Patel, Gayathri Srinivasan, Satya Narayan, Robert A. Hromas. The endonuclease Metnase promotes base excision repair of Clustered abasic DNA lesions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1420. doi:10.1158/1538-7445.AM2017-1420

CD8+ tissue resident memory T cells are associated with good prognosis in breast cancer patients

CD8+ Tumor Infiltrating Lymphocytes (TILs) have been shown to correlate with patient prognosis in breast cancer. Recently, resident memory T cells (TRM) have been established as a potent functional subset of memory T cells that exist in peripheral tissue without recirculation. We assayed CD8+ T cells from fresh breast tumors to phenotype memory T cells and found them to be almost exclusively made up of effector memory T cells. Further profiling by examining expression of CD103 and CD69 showed that on average 40% of CD8+ TILs are composed of TRM. Functional analysis of these T cells showed robust production of IFNγ and TNFα by these TRMs suggesting that despite existence in the tumor microenvironment TRMs maintain functional potency. To examine if CD8+ TRM have prognostic value in breast cancer patients, we examined a set of primary tumors from ‘good’ and ‘bad’ outcome patients, which we defined as having a relapse in more than 5 years after diagnosis or in less than 3 years after diagnosis respectively. In good outcome patients TRMs represented 60% of CD8+ T cells found in cancer islands, while only 20% of such in bad outcome patients. Similarly, CD8+ TRMs were observed in higher numbers in both the cancer islands and stroma of good outcome patient tumors in comparison to bad outcome patient tumors. This observed significance was greater than that found for CD8+ T cells in general, highlighting the importance of TRM in affecting patient outcome. Finally we showed that TRMs also exist in non-cancerous breast tissue and are found within the mammary ducts associated with epithelial cells perhaps in surveillance of potential pathogens. We suggest that TRMs are a potential vaccine target for preventing recurrence and metastasis in cancer patients.

Human brain metastatic stroma attracts breast cancer cells via chemokines CXCL16 and CXCL12

The tumor microenvironment is composed of heterogeneous populations of cells, including cancer, immune, and stromal cells. Progression of tumor growth and initiation of metastasis is critically dependent on the reciprocal interactions between cancer cells and stroma. Through RNA-Seq and protein analyses, we found that cancer-associated fibroblasts derived from human breast cancer brain metastasis express significantly higher levels of chemokines CXCL12 and CXCL16 than fibroblasts from primary breast tumors or normal breast. To further understand the interplay between cancer cells and cancer-associated fibroblasts from each site, we developed three-dimensional organoids composed of patient-derived primary or brain metastasis cancer cells with matching cancer-associated fibroblasts. Three-dimensional CAF aggregates generated from brain metastasis promote migration of cancer cells more effectively than cancer-associated fibroblast aggregates derived from primary tumor or normal breast stromal cells. Treatment with a CXCR4 antagonist and/or CXCL16 neutralizing antibody, alone or in combination, significantly inhibited migration of cancer cells to brain metastatic cancer-associated fibroblast aggregates. These results demonstrate that human brain metastasis cancer-associated fibroblasts potently attract breast cancer cells via chemokines CXCL12 and CXCL16, and blocking CXCR6-CXCL16/CXCR4-CXCL12 receptor–ligand interactions may be an effective therapy for preventing breast cancer brain metastasis.

Breast cancer metastases to the brain secrete signaling molecules that promote additional cancer cells to migrate there. Peter P. Lee and colleagues from the City of Hope in Duarte, California, USA, analyzed protein and gene expression levels in brain metastases, and showed that it is the stromal cells (support cells such as fibroblasts), rather than the cancer cells themselves, that are the source of these homing signals. When compared against stromal cells derived from primary breast tumors or healthy breast tissue, they found that the stromal cells that had lodged themselves in the brain expressed the highest levels of CXCL12 and CXCL16, two chemokines involved in cell movement. Using three-dimensional aggregates, the researchers showed that these metastatic stromal cells promoted cancer cells migration more potently than stromal cells from primary tumors or normal breast tissues. Blocking the chemokine activity or that of its receptor impaired cancer cell movement, suggesting a possible therapeutic strategy for preventing brain metastasis in patients with breast cancer. These results highlight the importance of the tumor microenvironment and stromal cells in the metastasis process of breast cancer.

Endonuclease EEPD1 Is a Gatekeeper for Repair of Stressed Replication Forks

Replication is not as continuous as once thought, with DNA damage frequently stalling replication forks. Aberrant repair of stressed replication forks can result in cell death or genome instability and resulting transformation to malignancy. Stressed replication forks are most commonly repaired via homologous recombination (HR), which begins with 5′ end resection, mediated by exonuclease complexes, one of which contains Exo1. However, Exo1 requires free 5′-DNA ends upon which to act, and these are not commonly present in non-reversed stalled replication forks. To generate a free 5′ end, stalled replication forks must therefore be cleaved. Although several candidate endonucleases have been implicated in cleavage of stalled replication forks to permit end resection, the identity of such an endonuclease remains elusive. Here we show that the 5′-endonuclease EEPD1 cleaves replication forks at the junction between the lagging parental strand and the unreplicated DNA parental double strands. This cleavage creates the structure that Exo1 requires for 5′ end resection and HR initiation. We observed that EEPD1 and Exo1 interact constitutively, and Exo1 repairs stalled replication forks poorly without EEPD1. Thus, EEPD1 performs a gatekeeper function for replication fork repair by mediating the fork cleavage that permits initiation of HR-mediated repair and restart of stressed forks.

High glucose variability is associated with poor neurodevelopmental outcomes in neonatal hypoxic ischemic encephalopathy

BACKGROUND

In neonatal hypoxic ischemic encephalopathy (HIE), hypo- and hyperglycemia have been associated with poor outcomes. However, glucose variability has not been reported in this population.

OBJECTIVE

To examine the association between serum glucose variability within the first 24 hours and two-year neurodevelopmental outcomes in neonates cooled for HIE.

STUDY DESIGN

In this retrospective cohort study, glucose, clinical and demographic data were documented from 23 term newborns treated with whole body therapeutic hypothermia. Severe neurodevelopmental outcomes from planned two-year assessments were defined as the presence of any one of the following: Gross Motor Function Classification System levels 3 to 5, Bayley III Motor Standard Score <70, Bayley III Language Score <70 and Bayley III Cognitive Standard Score <70.

RESULTS

The neurodevelopmental outcomes from 8 of 23 patients were considered severe, and this group demonstrated a significant increase of mean absolute glucose (MAG) change (-0.28 to -0.03, 95% CI, p = 0.032). There were no significant differences between outcome groups with regards to number of patients with hyperglycemic means, one or multiple hypo- or hyperglycemic measurement(s). There were also no differences between both groups with mean glucose, although mean glucose standard deviation was approaching significance.

CONCLUSIONS

Poor neurodevelopmental outcomes in whole body cooled HIE neonates are significantly associated with MAG changes. This information may be relevant for prognostication and potential management strategies.

On the distribution of Aeshna petalura Martin, 1908 (Odonata: Anisoptera: Aeshnidae) in the Indian subcontinent

Aeshna petalura Martin, is documented for the first time from the high ranges of the eastern Himalaya (above 4,000m) and also a new record from the Tawang Region of Arunachal Pradesh, India.  The description of the species along with a distribution range map is also provided.  The type locality and distribution within India is also discussed. 

EEPD1 Rescues Stressed Replication Forks and Maintains Genome Stability by Promoting End Resection and Homologous Recombination Repair

Replication fork stalling and collapse is a major source of genome instability leading to neoplastic transformation or cell death. Such stressed replication forks can be conservatively repaired and restarted using homologous recombination (HR) or non-conservatively repaired using micro-homology mediated end joining (MMEJ). HR repair of stressed forks is initiated by 5’ end resection near the fork junction, which permits 3’ single strand invasion of a homologous template for fork restart. This 5’ end resection also prevents classical non-homologous end-joining (cNHEJ), a competing pathway for DNA double-strand break (DSB) repair. Unopposed NHEJ can cause genome instability during replication stress by abnormally fusing free double strand ends that occur as unstable replication fork repair intermediates. We show here that the previously uncharacterized Exonuclease/Endonuclease/Phosphatase Domain-1 (EEPD1) protein is required for initiating repair and restart of stalled forks. EEPD1 is recruited to stalled forks, enhances 5’ DNA end resection, and promotes restart of stalled forks. Interestingly, EEPD1 directs DSB repair away from cNHEJ, and also away from MMEJ, which requires limited end resection for initiation. EEPD1 is also required for proper ATR and CHK1 phosphorylation, and formation of gamma-H2AX, RAD51 and phospho-RPA32 foci. Consistent with a direct role in stalled replication fork cleavage, EEPD1 is a 5’ overhang nuclease in an obligate complex with the end resection nuclease Exo1 and BLM. EEPD1 depletion causes nuclear and cytogenetic defects, which are made worse by replication stress. Depleting 53BP1, which slows cNHEJ, fully rescues the nuclear and cytogenetic abnormalities seen with EEPD1 depletion. These data demonstrate that genome stability during replication stress is maintained by EEPD1, which initiates HR and inhibits cNHEJ and MMEJ.

The cell itself damages its own DNA throughout the cell cycle as a result of oxidative metabolism, and this damage creates barriers for replication fork progression. Thus, DNA replication is not a smooth and continuous process, but rather one of stalls and restarts. Therefore, proper replication fork restart is crucial to maintain the integrity of the cell’s genome, and preventing its own death or immortalization. To restart after stalling, the replication fork subverts a DNA repair pathway termed homologous recombination. Using any other pathway for fork repair will result in an unstable genome. How the homologous recombination repair pathway is initiated at the replication fork is not well defined. In this study we demonstrate the previously uncharacterized EEPD1 protein is a novel gatekeeper for the initiation of this fork repair pathway. EEPD1 promotes 5’ end resection, the initial step of homologous recombination, which also prevents alternative fork repair pathways that lead to unstable chromosomes. Thus, EEPD1 protects the integrity of the cell genome by promoting the safe homologous recombination fork repair pathway.