An in-silico approach to predict and exploit synthetic lethality in cancer metabolism

Synthetic lethality is a promising concept in cancer research, potentially opening new possibilities for the development of more effective and selective treatments. Here, we present a computational method to predict and exploit synthetic lethality in cancer metabolism. Our approach relies on the concept of genetic minimal cut sets and gene expression data, demonstrating a superior performance to previous approaches predicting metabolic vulnerabilities in cancer. Our genetic minimal cut set computational framework is applied to evaluate the lethality of ribonucleotide reductase catalytic subunit M1 (RRM1) inhibition in multiple myeloma. We present a computational and experimental study of the effect of RRM1 inhibition in four multiple myeloma cell lines. In addition, using publicly available genome-scale loss-of-function screens, a possible mechanism by which the inhibition of RRM1 is effective in cancer is established. Overall, our approach shows promising results and lays the foundation to build a novel family of algorithms to target metabolism in cancer.

Exploiting synthetic lethality is a promising approach for cancer therapy. Here, the authors present an approach to identifying such interactions by finding genetic minimal cut sets (gMCSs) that block cancer proliferation, and apply it to study the lethality of RRM1 inhibition in multiple myeloma.

Chiral Spin-Orbital Liquids with Nodal Lines

Strongly correlated materials with strong spin-orbit coupling hold promise for realizing topological phases with fractionalized excitations. Here, we propose a chiral spin-orbital liquid as a stable phase of a realistic model for heavy-element double perovskites. This spin liquid state has Majorana fermion excitations with a gapless spectrum characterized by nodal lines along the edges of the Brillouin zone. We show that the nodal lines are topological defects of a non-Abelian Berry connection and that the system exhibits dispersing surface states. We discuss some experimental signatures of this state and compare them with properties of the spin liquid candidate Ba_{2}YMoO_{6}.

Comparison of Hydrolyzed Protein Baits and Various Grape Juice Products as Attractants for Anastrepha Fruit Flies (Diptera: Tephritidae)

Mexican fruit flies, Anastrepha ludens (Loew; Diptera: Tephritidae), have traditionally been trapped in citrus orchards in Mexico using protein hydrolysates as bait. Recently, CeraTrap(®), an enzymatic hydrolyzed protein, has emerged as an effective lure for monitoring A. ludens at the orchard level and is currently being used by growers in the region of Veracruz. Several studies have revealed that grape juice is highly attractive to A. ludens, and recent work supports its potential use for regulation purposes. In our study, the attraction of A. ludens to different grape products was evaluated in citrus orchards and in comparison to other Anastrepha species in an area composed of mango and chicozapote orchards. Attraction to grape lures was compared with CeraTrap and the standard protein Captor +borax trap. In general, CeraTrap was more attractive than different commercial grape products in several experiments. Only Jumex, a commercial grape juice, did not differ significantly from CeraTrap in the capture of A. ludens males and females in a citrus crop. However, several drawbacks were detected when using Jumex grape juice: 1) higher tendency to capture males, 2) less selectivity against non-targeted insects, 3) higher capture of beneficial lacewings, and iv) the need to re-bait weekly owing to lower stability. In the area containing mango and chicozapote, CeraTrap was more attractive than Captor + borax for Anastrepha obliqua and Anastrepha serpentina, followed by grape juice products, which were the least attractive for these fruit fly species.

Emergent SU(3) Symmetry in Random Spin-1 Chains

We show that generic SU(2)-invariant random spin-1 chains have phases with an emergent SU(3) symmetry. We map out the full zero-temperature phase diagram and identify two different phases: (i) a conventional random-singlet phase (RSP) of strongly bound spin pairs [SU(3) "mesons"] and (ii) an unconventional RSP of bound SU(3) "baryons," which are formed, in the great majority, by spin trios located at random positions. The emergent SU(3) symmetry dictates that susceptibilities and correlation functions of both dipolar and quadrupolar spin operators have the same asymptotic behavior.

Economic and Highly Effective Trap-Lure Combination to Monitor the Mexican Fruit Fly (Diptera: Tephritidae) at the Orchard Level

Monitoring population levels of the Mexican fruit fly, Anastrepha ludens (Loew) (Diptera: Tephritidae), at the orchard level prior and during the fruit ripening period can result in significant savings in the costs of managing this pestiferous insect. Unfortunately, to date, no highly effective and economically viable trap is available to growers. To move toward this goal, trap-lure combinations were evaluated in trials performed in citrus orchards in Veracruz, Mexico. CeraTrap, an enzymatic hydrolyzed protein from pig intestinal mucose, was 3.6 times more attractive to A. ludens than the most commonly used bait of Captor (hydrolyzed protein and borax) when using Multilure traps. When several commercial traps were evaluated, the efficacy of a simple and inexpensive transparent polyethylene (PET) bottle with 10-mm lateral holes was similar to that of the costly Multilure trap when baited with CeraTrap and significantly more effective than a Multilure trap baited with Captor. PET bottles filled with Cera Trap, rebaited at 8-wk intervals, and tested in trials encompassing 72 ha of citrus groves, were significantly more effective than Multilure traps baited with Captor that need to be serviced weekly. In addition to this relevant finding, CeraTrap baited traps detected A. ludens at lower population densities and attracted a significantly higher number of flies at all densities when compared with Captor-baited traps. We conclude that CeraTrap represents a cost-effective and highly efficient bait that will enable us to pursue the goal of developing economic thresholds, a badly needed management tool for A. ludens.

Improving health behaviours of Latina mothers of youths and adults with intellectual and developmental disabilities

BACKGROUND

Latina mothers who care for children with intellectual and developmental disabilities (IDD) over the lifespan struggle to take care of their own health needs in the context of their caregiving experience. Services are typically aimed at the persons with IDD and not their family caregivers. Yet, attending to family caregiver needs may contribute to better long-term care of persons with IDD who remain at home. To address this unmet need, we developed a culturally sensitive health education intervention for Latina mothers who care for youth and adults with IDD. The aim of the intervention is to improve maternal health-related self-efficacy and health behaviours, and to reduce stress.

METHOD

A randomised control design was employed to determine preliminary efficacy of the intervention. Paired sample t-tests were conducted to examine within-group changes from baseline to 3-month post-test. Repeated-measures analysis of covariance was used to examine the group-by-time interaction effects.

RESULTS

Intervention participants showed greater increases between pre- and post-test in health-related self-efficacy; self-care, nutrition and overall health behaviours. Both groups reported decreases in depressive symptoms and caregiver burden.

CONCLUSIONS

While additional research is needed to determine long-term effects and to replicate findings, our results suggest that this culturally sensitive health intervention is a promising way to increase health behaviours which may lead to overall good health for Latina mothers who care for children with IDD across the lifespan.

Non-Gaussian spatial correlations dramatically weaken localization

We perform variational studies of the interaction-localization problem to describe the interaction-induced renormalizations of the effective (screened) random potential seen by quasiparticles. Here we present results of careful finite-size scaling studies for the conductance of disordered Hubbard chains at half-filling and zero temperature. While our results indicate that quasiparticle wave functions remain exponentially localized even in the presence of moderate to strong repulsive interactions, we show that interactions produce a strong decrease of the characteristic conductance scale g^{*} signaling the crossover to strong localization. This effect, which cannot be captured by a simple renormalization of the disorder strength, instead reflects a peculiar non-Gaussian form of the spatial correlations of the screened disordered potential, a hitherto neglected mechanism to dramatically reduce the impact of Anderson localization (interference) effects.

HIF-1 promotes the expression of its α-subunit via an epigenetically regulated transactivation loop

A HIF-1 protein–protein interaction inhibitor is used to establish the presence of a HIF-1α transactivation loop in hypoxia.

Irrelevant and independent natural extension for sets of desirable gambles

The results in this paper add useful tools to the theory of sets of desirable gambles, a growing toolbox for reasoning with partial probability assessments. We investigate how to combine a number of marginal coherent sets of desirable gambles into a joint set using the properties of epistemic irrelevance and independence. We provide formulas for the smallest such joint, called their independent natural extension, and study its main properties. The independent natural extension of maximal coherent sets of desirable gambles allows us to define the strong product of sets of desirable gambles. Finally, we explore an easy way to generalise these results to also apply for the conditional versions of epistemic irrelevance and independence. Having such a set of tools that are easily implemented in computer programs is clearly beneficial to fields, like AI, with a clear interest in coherent reasoning under uncertainty using general and robust uncertainty models that require no full specification.

The effects of weekly augmentation therapy in patients with PiZZ α1-antitrypsin deficiency

Background

The major concept behind augmentation therapy with human α₁-antitrypsin (AAT) is to raise the levels of AAT in patients with protease inhibitor phenotype ZZ (Glu342Lys)-inherited AAT deficiency and to protect lung tissues from proteolysis and progression of emphysema.

Objective

To evaluate the short-term effects of augmentation therapy (Prolastin^®) on plasma levels of AAT, C-reactive protein, and chemokines/cytokines.

Materials and methods

Serum and exhaled breath condensate were collected from individuals with protease inhibitor phenotype ZZ AAT deficiency-related emphysema (n = 12) on the first, third, and seventh day after the infusion of intravenous Prolastin. Concentrations of total and polymeric AAT, interleukin-8 (IL-8), monocyte chemotactic protein-1, IL-6, tumor necrosis factor-α, vascular endothelial growth factor, and C-reactive protein were determined. Blood neutrophils and primary epithelial cells were also exposed to Prolastin (1 mg/mL).

Results

There were significant fluctuations in serum (but not in exhaled breath condensate) levels of AAT polymers, IL-8, monocyte chemotactic protein-1, IL-6, tumor necrosis factor-α, and vascular endothelial growth factor within a week of augmentation therapy. In general, augmented individuals had higher AAT and lower serum levels of IL-8 than nonaugmented subjects. Prolastin added for 3 hours to neutrophils from protease inhibitor phenotype ZZ individuals in vitro reduced IL-8 release but showed no effect on cytokine/chemokine release from human bronchial epithelial cells.

Conclusion

Within a week, augmentation with Prolastin induced fluctuations in serum levels of AAT polymers and cytokine/chemokines but specifically lowered IL-8 levels. It remains to be determined whether these effects are related to the Prolastin preparation per se or to the therapeutic efficacy of augmentation with AAT.

Preclinical activity of LBH589 alone or in combination with chemotherapy in a xenogeneic mouse model of human acute lymphoblastic leukemia

Histone deacetylases (HDACs) have been identified as therapeutic targets due to their regulatory function in chromatin structure and organization. Here, we analyzed the therapeutic effect of LBH589, a class I-II HDAC inhibitor, in acute lymphoblastic leukemia (ALL). In vitro, LBH589 induced dose-dependent antiproliferative and apoptotic effects, which were associated with increased H3 and H4 histone acetylation. Intravenous administration of LBH589 in immunodeficient BALB/c-RAG2(-/-)γc(-/-) mice in which human-derived T and B-ALL cell lines were injected induced a significant reduction in tumor growth. Using primary ALL cells, a xenograft model of human leukemia in BALB/c-RAG2(-/-)γc(-/-) mice was established, allowing continuous passages of transplanted cells to several mouse generations. Treatment of mice engrafted with T or B-ALL cells with LBH589 induced an in vivo increase in the acetylation of H3 and H4, which was accompanied with prolonged survival of LBH589-treated mice in comparison with those receiving vincristine and dexamethasone. Notably, the therapeutic efficacy of LBH589 was significantly enhanced in combination with vincristine and dexamethasone. Our results show the therapeutic activity of LBH589 in combination with standard chemotherapy in pre-clinical models of ALL and suggest that this combination may be of clinical value in the treatment of patients with ALL.

ANCA-associated vasculitis is linked to carriage of the Z allele of α₁ antitrypsin and its polymers

BACKGROUND

Small studies have linked α1 antitrypsin (α1AT) deficiency to patients with antineutrophil cytoplasmic antibodies (ANCA)-associated vasculitis (AAV).

OBJECTIVE

To test the validity and the mechanism of this association between α1AT and AAV.

METHODS

The distribution of α1AT deficiency alleles Z and S was compared between 856 White Europeans with AAV and 1505 geographic and ethnically matched healthy controls. Genotyping was performed by allelic discrimination assay.

RESULTS

were compared between cases and controls using χ(2) tests. The serum and renal biopsies for α1AT polymers were compared using the polymer-specific 2C1 antibody. The role of α1AT polymers in promoting inflammation was investigated by examining their ability to prime neutrophils for ANCA activation as assessed by CD62L shedding, superoxide production and myeloperoxidase degranulation. Results The Z but not the S allele was over-represented in the patients compared with controls (HR=2.25, 95% CI 1.60 to 3.19). Higher concentrations of polymers of α1AT were detected in serum from patients carrying the Z allele than in those not carrying the Z allele (median (IQR) 1.40 (0.91-3.32) mg/dl vs 0.17 (0.06-0.28) mg/dl, p<0.001); polymers of α1AT were also seen in the renal biopsy of a patient with vasculitic glomerulonephritis. Polymers of α1AT primed neutrophils with CD62L shedding and increased superoxide production following ANCA activation. Carriage of the Z allele was not associated with disease severity, survival or relapse.

CONCLUSIONS

The Z but not the S deficiency allele is associated with AAV. Polymers of α1AT are present in the serum and glomeruli of at least some patients with the Z allele, which may promote inflammation through priming of neutrophils.