Suppression of BRCA1 sensitizes cells to proteasome inhibitors

BRCA1 is a multifunctional protein best known for its role in DNA repair and association with breast and ovarian cancers. To uncover novel biologically significant molecular functions of BRCA1, we tested a panel of 198 approved and experimental drugs to inhibit growth of MDA-MB-231 breast cancer cells depleted for BRCA1 by siRNA. 26S proteasome inhibitors bortezomib and carfilzomib emerged as a new class of selective BRCA1-targeting agents. The effect was confirmed in HeLa and U2OS cancer cell lines using two independent siRNAs, and in mouse embryonic stem (ES) cells with inducible deletion of Brca1. Bortezomib treatment did not cause any increase in nuclear foci containing phosphorylated histone H2AX, and knockdown of BRCA2 did not entail sensitivity to bortezomib, suggesting that the DNA repair function of BRCA1 may not be directly involved. We found that a toxic effect of bortezomib on BRCA1-depleted cells is mostly due to deregulated cell cycle checkpoints mediated by RB1-E2F pathway and 53BP1. Similar to BRCA1, depletion of RB1 also conferred sensitivity to bortezomib, whereas suppression of E2F1 or 53BP1 together with BRCA1 reduced induction of apoptosis after bortezomib treatment. A gene expression microarray study identified additional genes activated by bortezomib treatment only in the context of inactivation of BRCA1 including a critical involvement of the ERN1-mediated unfolded protein response. Our data indicate that BRCA1 has a novel molecular function affecting cell cycle checkpoints in a manner dependent on the 26S proteasome activity.BRCA1 is an important tumor suppressor gene whose germ-line or somatic inactivation is implicated in a significant number of breast and ovarian cancers.¹ Human BRCA1 encodes an 1863 amino-acid-long protein with a RING-finger domain at the N terminus and two BRCT domains located at the C terminus.^{2, 3} BRCT domains mediate interaction with phosphorylated proteins such as Abraxas, BACH1, CtIP and others involved in sensing DNA damage and assembly of the BRCA1-associated genome surveillance complex at sites of DNA breaks.⁴ The RING domain constitutively interacts with the BRCA1-associated RING domain protein (BARD1), forming a heterodimer having an E3 ubiquitin ligase activity.⁵ Ubiquitination of target proteins, including cell cycle or DNA repair-regulating proteins (e.g. CtIP (RBBP8), nucleophosmin (NPM1, B23), claspin (CLSPN) and others), occurs either at Lys48 residue of the ubiquitin leading to the 26S proteasome-mediated degradation of target proteins or at Lys6 or Lys63 having a trafficking and signaling role.⁶ A serine cluster coiled-coil domain spanning amino acids 1280–1524 contains multiple phosphorylation sites for ATM and ATR kinases activated by DNA damage.⁷ The same region also binds PALB2 protein linking BRCA1 to another major breast cancer predisposition gene BRCA2.⁸The most prominent function of BRCA1 is associated with its role in repair of DNA damage, particularly of double-stranded DNA breaks (DSBs), one of the most severe types of DNA lesions.⁹ BRCA1 is recruited to sites of DNA damage via a series of phosphorylation and ubiquitination events, where it serves as a binding scaffold for other DNA repair proteins,^{10, 11} ubiquitinates claspin, cyclin B and CDC25C, triggering cell cycle arrest to allow time for repair,¹² and facilitates BRCA2-mediated loading of RAD51 recombinase to enable the homologous recombination (HR) mechanism of DNA repair.⁹ In addition, BRCA1 may contribute to maintaining genome integrity by stabilizing the heterochromatin structure via ubiquitination of histone H2A.¹³ BRCA1 is also required for centrosome-dependent and -independent mitotic spindle formation, providing another route, by which loss of BRCA1 could promote chromosome instability and tumor formation.^{14, 15}Such a critical role of BRCA1 in DNA repair is exploited therapeutically. DNA-damaging agents, particularly DNA-crosslinking agents such as platinum-containing drugs, or ionizing radiation lead to the accumulation of DNA breaks requiring HR for repair and, therefore, are particularly toxic to BRCA1-deficient tumor cells.¹⁶ Pharmacological inhibitors of poly-(ADP-ribose) polymerases (PARPs) selectively kill BRCA1-deficient cells owing to defective HR, functioning as a back-up repair mechanism in the absence of the PARP-mediated repair of single-stranded DNA breaks.¹⁷ However, multiple mechanisms allow BRCA1-deficient cells to develop resistance to these drugs including elevated expression of the efflux transporters pumping the drugs out of the cell, secondary mutations restoring a functional BRCA1 protein and loss of 53BP1 protein, which counteracts BRCA1 and HR by blocking resection of DNA ends around the breaks (see Lord and Ashworth¹⁸ for the latest review). Therefore, additional efforts to identify small-molecule agents especially targeting BRCA1 functions unrelated to its DNA repair function are warranted.Here we performed a high-throughput chemical screen of BRCA1-depleted MDA-MB-231 cells using a collection of 198 US Food and Drug Administration (FDA)-approved and experimental drugs. We found that 26S proteasome inhibitors were more toxic to BRCA1 knockdown than control cells. Response of BRCA1-deficient cells to bortezomib involved deregulation of the RB1-mediated cell cycle checkpoint, activation of a noncanonical ERN1-mediated unfolded protein response and 53BP1-related G2/M cell cycle arrest. Our results reveal novel aspects of BRCA1 function unrelated to DNA repair.     

The role of tubulin in the mitochondrial metabolism and arrangement in muscle cells

Tubulin, a well-known component of the microtubule in the cytoskeleton, has an important role in the transport and positioning of mitochondria in a cell type dependent manner. This review describes different functional interactions of tubulin with cellular protein complexes and its functional interaction with the mitochondrial outer membrane. Tubulin is present in oxidative as well as glycolytic type muscle cells, but the kinetics of the in vivo regulation of mitochondrial respiration in these muscle types is drastically different. The interaction between VDAC and tubulin is probably influenced by such factors as isoformic patterns of VDAC and tubulin, post-translational modifications of tubulin and phosphorylation of VDAC. Important factor of the selective permeability of VDAC is the mitochondrial creatine kinase pathway which is present in oxidative cells, but is inactive or missing in glycolytic muscle and cancer cells. As the tubulin-VDAC interaction reduces the permeability of the channel by adenine nucleotides, energy transfer can then take place effectively only through the mitochondrial creatine kinase/phosphocreatine pathway. Therefore, closure of VDAC by tubulin may be one of the reasons of apoptosis in cells without the creatine kinase pathway. An important question in tubulin regulated interactions is whether other proteins are interacting with tubulin. The functional interaction may be direct, through other proteins like plectins, or influenced by simultaneous interaction of other complexes with VDAC.     

New mechanisms of biological effects of electromagnetic fields

The production of ATP in mitochondria depends on the magnesium nuclear spin and magnetic moment of a Mg2+ ion in creatine kinase and ATPase. This suggests that enzymatic synthesis of ATP is an ion-radical process and thus depends on the external magnetic field (magnetobiology originates from this fact) and microwave fields, which control the spin states of ion-radical pairs and affect the ATP synthesis. The chemical mechanism of ATP synthesis and the origin of biological effects of electromagnetic (microwave) fields are discussed.     

The Activity of the Peroxidase System in the Course of Stress-Induced CAM Development

The activity of the peroxidase system in Mesembryanthemum crystallinum L. plants in relation to the shift from C₃ to CAM photosynthesis was studied. In detached leaves of the fourth and fifth stories treated with NaCl (0.3 M), a rapid (after 30 min) transient induction of the ionically bound peroxidase (the first maximum) was observed followed by a second weak increase in the enzyme activity (90 min after salt treatment). In the leaves of intact plants, which received a longer treatment with NaCl, a two-phase change in the enzyme activity was also observed. It was most pronounced at the early stages of the NaCl-induced plant shift from C₃ to CAM photosynthesis. In this case, in both detached and intact leaves of juvenile plants, the activity of soluble peroxidase was at a low steady-state level. The situation changed dramatically when M. crystallinum plants transitioned to the reproductive developmental phase and photosynthesis switched from C₃ to CAM. The time dependence of the activities of both peroxidase types, the soluble ones in particular, was characterized by marked diurnal oscillations (light–dark), which coincided with the fluctuations of the total titratable acidity. In this case, the activity of the soluble enzyme was several orders of magnitude higher than the activity of the ionically bound peroxidase, even though the optimum pH for both isoforms was similar (pH 5.0). Three acid isoforms of soluble peroxidases, which operated more actively when the cytoplasm had a higher acidity, were distinguished by isoelectrofocusing. Their activity increased under salinity. Alkaline and neutral components were predominant in more than 30 molecular forms of the soluble peroxidase detected. We concluded that the operation of the peroxidase system changed substantially when plants shifted from the juvenile to the reproductive state and switched from C₃ to CAM photosynthesis: the activity of stress-induced ionically bound peroxidase was drastically inhibited with a concurrent increase in the activity of soluble peroxidase and a change in the spectrum of its molecular forms.     

On Bacterial Origin of Mitochondria in Eukaryotes in the Light of Current Ideas of Evolution of the Organic World

The hypothesis of bacterial origin of mitochondria, which existed until the end of the 20th century, has been confirmed on the basis of the current concepts of organic world evolution in the open sea hydrosphere and original data on the entry of bacteria (prokaryotes) in the cells of eukaryotes and their transformation into the mitochondrial mechanism of aerobic energy metabolism. This hypothesis can now be considered as a factually substantiated theory. The process of endocytosis of bacteria in the tissues of eukaryotes, which began at the onset of transition of the anaerobic state of open sea hydrosphere and land atmosphere (Early Proterozoic), is considered as the beginning of symbiotic mode of life of organisms of the Proterozoic and Postproterozoic organic world.     

Boundary of the adiabatic motion of a charged particle in a dipole magnetic field

The motion of a charged particle in a dipole magnetic field is considered using a quasi-adiabatic model in which the particle guiding center trajectory is approximated by the central trajectory, i.e., a trajectory that passes through the center of the dipole. A study is made of the breakdown of adiabaticity in the particle motion as the adiabaticity parameter χ (the ratio of the Larmor radius to the radius of the magnetic field line curvature in the equatorial plane) increases. Initially, for χ?0.01, the magnetic moment μ of a charged particle undergoes reversible fluctuations, which can be eliminated by subtracting the particle drift velocity. For χ?0.1, the magnetic moment μ undergoes irreversible fluctuations, which grow exponentially with χ. Numerical integration of the equations of motion shows that, during the motion of a particle from the equatorial plane to the mirror point and back to the equator in a coordinate system related to the central trajectory, the analogue of the magnetic moment μ is conserved. In the equatorial plane, this analogue undergoes a jump. The long-term particle dynamics is described in a discrete manner, by approximating the Poincaré mapping. The existence of the regions of steady and stochastic particle motion is established, and the boundary between these regions is determined. The position of this boundary depends not only on the adiabaticity parameter χ but also on the pitch angle. The calculated boundary is found to agree well with that obtained previously by using the model of a resonant interaction between particle oscillations associated with different degrees of freedom.     

Identification of common oncogenic and early developmental pathways in the ovarian carcinomas controlling by distinct prognostically significant microRNA subsets

Background

High-grade serous ovarian carcinoma (HG-SOC) is the dominant tumor histologic type in epithelial ovarian cancers, exhibiting highly aberrant microRNA expression profiles and diverse pathways that collectively determine the disease aggressiveness and clinical outcomes. However, the functional relationships between microRNAs, the common pathways controlled by the microRNAs and their prognostic and therapeutic significance remain poorly understood.

Methods

We investigated the gene expression patterns of microRNAs in the tumors of 582 HG-SOC patients to identify prognosis signatures and pathways controlled by tumor miRNAs. We developed a variable selection and prognostic method, which performs a robust selection of small-sized subsets of the predictive features (e.g., expressed microRNAs) that collectively serves as the biomarkers of cancer risk and progression stratification system, interconnecting these features with common cancer-related pathways.

Results

Across different cohorts, our meta-analysis revealed two robust and unbiased miRNA-based prognostic classifiers. Each classifier reproducibly discriminates HG-SOC patients into high-confidence low-, intermediate- or high-prognostic risk subgroups with essentially different 5-year overall survival rates of 51.6-85%, 20-38.1%, and 0-10%, respectively. Significant correlations of the risk subgroup’s stratification with chemotherapy treatment response were observed. We predicted specific target genes involved in nine cancer-related and two oocyte maturation pathways (neurotrophin and progesterone-mediated oocyte maturation), where each gene can be controlled by more than one miRNA species of the distinct miRNA HG-SOC prognostic classifiers.

Conclusions

We identified robust and reproducible miRNA-based prognostic subsets of the of HG-SOC classifiers. The miRNAs of these classifiers could control nine oncogenic and two developmental pathways, highlighting common underlying pathologic mechanisms and perspective targets for the further development of a personalized prognosis assay(s) and the development of miRNA-interconnected pathway-centric and multi-agent therapeutic intervention.

     

Ecology of Arctic cod <Emphasis Type="Italic">Boreogadus saida</Emphasis> (Gadiformes,Gadidae) and its fishery potential in Kara Sea

According to the bottom trawl-survey data, 97% of the ichthyomass in the southwestern region of the Kara Sea are composed of the Arctic cod Boreogadus saida; its stock is significantly higher than the previously registered resources. The Arctic cod is most unevenly distributed across the water area and capable to form the high-density aggregations, which can be caught by the targeted trawls. A wide range of the age composition (0+?6+), the size-age composition, and the growth rates of the Arctic cod in the trawl catches in the Kara Sea, which are different from those in the fish in the adjacent Barents Sea, can indicate their assignment of the Arctic cod in these seas to different populations.     

The Morphology and Microscopic Anatomy of the Deep-Sea Echiurid <Emphasis Type="Italic">Protobonellia zenkevitchi</Emphasis> Murina, 1976

Echiurida is a small group of marine benthic invertebrates that burrow in sediments and live a hidden lifestyle. Investigation of the morphology and anatomical features of various organ systems allows better understanding of the biology of these enigmatic animals, many of which are deep-sea species. The morphology and microscopic anatomy of the deep-sea echiurid Protobonellia zenkevitchi Murina, 1976 have been studied using the light microscopy and histology methods. The body of P. zenkevitchi is divided into a proboscis and trunk. The ciliary grooves and large vacuolated cells in the connective tissue of the distal part of the proboscis suggest a specific position of the proboscis on the sediment surface and a mechanism for sorting food particles. It has been shown for the first time that the coelom is not subdivided into compartments. In the digestive tract, an unusual part of the midgut has been found that was previously unknown in echiurids; it probably performs the function of food storage. This part contributes to thorough food digestion, which is important in the oligotrophic conditions of greater depths. The circulatory system of P. zenkevitchi lacks the neuro-intestinal and ring blood vessels. The oocyte storage chamber of the gonoduct has a pore, which apparently connects its cavity with the trunk coelom, but lacks a specialized and well-expressed part, the androecium. A comparative analysis of the microscopic anatomy shows that many organ systems (muscular, coelomic, circulatory, excretory, and reproductive) in P. zenkevitchi have a simpler organization compared to those in other echiurids. This can probably be explained by the small body size of P. zenkevitchi and the great depths of its habitat. At the same time, P. zenkevitchi possesses some unique anatomical characteristics related to the features of the biology of this deep-sea species.     

The Raman Spectroscopy,XRD, SEM,and AFM Study of Arabinogalactan Sulfates Obtained Using Sulfamic Acid

The structure of sodium salts of arabinogalactan (AG) sulfates obtained by sulfating AG of larch wood with a sulfamic acid–urea mixture in 1,4-dioxane was studied by the methods of Raman spectroscopy, X-ray diffraction (XRD) phase analysis, scanning electron microscopy (SEM), and atomic force microscopy (AFM). The introduction of sulfate groups into the structure of arabinogalactan was confirmed by the appearance in the Raman spectra of new absorption bands related to the deformation vibrations δ (SO₃) at 420 cm^–1 and δ (О=S=O) at 588 cm^–1, stretching vibrations ν (C–O–S) at 822 cm^–1, symmetrical stretching vibrations ν_s (O=S=O) at 1076 cm^–1, and asymmetric stretching vibrations of ν_as (O=S=O) at 1269 cm^–1. According to the XRD data, the amorphization of arabinogalactan structure occurs during the sulfation process. The SEM method revealed a significant difference in the morphology of the sulfated and starting arabinogalactan. The starting AG consists of particles of predominantly globular shape with a size of 10 to 90 μm; arabinogalactan sulfates, of particles of various shapes with sizes of 1–8 μm. According to the AFM, the surface of sulfated arabinogalactan film consists of rather homogeneous spherical particles about 70 nm in size. The root-mean-square value of the surface roughness is 33 nm. The surface of sulfated AG film does not contain impurities.