A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

Here, we present FissionNet, a proteome-wide binary protein interactome for S. pombe, comprising 2,278 high-quality interactions, of which ∼ 50% were previously not reported in any species. FissionNet unravels previously unreported interactions implicated in processes such as gene silencing and pre-mRNA splicing. We developed a rigorous network comparison framework that accounts for assay sensitivity and specificity, revealing extensive species-specific network rewiring between fission yeast, budding yeast, and human. Surprisingly, although genes are better conserved between the yeasts, S. pombe interactions are significantly better conserved in human than in S. cerevisiae. Our framework also reveals that different modes of gene duplication influence the extent to which paralogous proteins are functionally repurposed. Finally, cross-species interactome mapping demonstrates that coevolution of interacting proteins is remarkably prevalent, a result with important implications for studying human disease in model organisms. Overall, FissionNet is a valuable resource for understanding protein functions and their evolution.

A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice.

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.

Genomic landscape of young ATLL patients identifies frequent targetable CD28 fusions.

Adult T-cell leukemia/lymphoma (ATLL) in Japan presents at a median age of 70 years and only 5% of patients are <50 years of age. We conducted RNA and targeted DNA sequencing of 8 ATLLs from Japanese patients <50 years of age and identified 3 (37.5%) with both CTLA4-CD28 and inducible costimulator (ICOS)-CD28 fusions. Mutations of PLCG1, PRKCB, and STAT3, which were frequent in other ATLL-sequencing studies, were not identified. Differential expression analysis identified the negative checkpoint molecule LAG3 as the most downregulated gene among cases with the fusions. Immunohistochemistry demonstrated expression of CD80 and CD86, the ligands for CTLA4 and CD28, on ATLL cells and tumor-associated macrophages, respectively. Expression of CTLA4-CD28 in Ba/F3 cells conferred cytokine-independent growth when cocultured with Raji cells that express CD80 and CD86. Growth was associated with recruitment of the p85 subunit of phosphatidylinositol 3-kinase to CTLA4-CD28 and phosphorylation of AKT and extracellular signal-regulated kinase. A CTLA4-blocking antibody reduced cytokine-independent growth in a dose-dependent manner. Together, these results suggest that young Japanese ATLL cases have a unique biology dependent on cell-nonautonomous interactions that drive CD28 signaling. Assessment for CD28 fusions and treatment with CTLA4 blockade should be considered in younger patients with relapsed/refractory ATLL.

Experimental and theoretical studies on the effect of the oxo group in 1,4-benzodiazepines.

Two families of regioisomeric 1,4-benzodiazepines, 4-benzyl-3H-benzo[e][1,4]diazepin-5-ones and 4-benzoyl-4,5-dihydro-3H-benzo[e][1,4]diazepines, have been synthesized through a similar Ugi/reduction cyclization sequence. Their conformation and stability depend on the position of the tautomeric imine/enamine equilibrium present in the diazepine nucleus, which in turn depends on the relative position of the carbonyl group adjacent to the nitrogen at the 4-position in the benzodiazepine system. Moreover, the electrophilic center on the imine tautomer is essential for the antitumor activity of some benzodiazepines as a DNA binding position. The mechanism of tautomerization in the presence or absence of the oxo group has been studied computationally using DFT methods (B3LYP/6-31G** level).

Electric Field Effects on Curved Graphene Quantum Dots.

The recent and continuous research on graphene-based systems has opened their usage to a wide range of applications due to their exotic properties. In this paper, we have studied the effects of an electric field on curved graphene nanoflakes, employing the Density Functional Theory. Both mechanical and electronic analyses of the system have been made through its curvature energy, dipolar moment, and quantum regeneration times, with the intensity and direction of a perpendicular electric field and flake curvature as parameters. A stabilisation of non-planar geometries has been observed, as well as opposite behaviours for both classical and revival times with respect to the direction of the external field. Our results show that it is possible to modify regeneration times using curvature and electric fields at the same time. This fine control in regeneration times could allow for the study of new phenomena on graphene.

Quantum Revivals in Curved Graphene Nanoflakes.

Graphene nanostructures have attracted a lot of attention in recent years due to their unconventional properties. We have employed Density Functional Theory to study the mechanical and electronic properties of curved graphene nanoflakes. We explore hexagonal flakes relaxed with different boundary conditions: (i) all atoms on a perfect spherical sector, (ii) only border atoms forced to be on the spherical sector, and (iii) only vertex atoms forced to be on the spherical sector. For each case, we have analysed the behaviour of curvature energy and of quantum regeneration times (classical and revival) as the spherical sector radius changes. Revival time presents in one case a divergence usually associated with a phase transition, probably caused by the pseudomagnetic field created by the curvature. This could be the first case of a phase transition in graphene nanostructures without the presence of external electric or magnetic fields.

Gaussian Curvature Effects on Graphene Quantum Dots.

In the last few years, much attention has been paid to the exotic properties that graphene nanostructures exhibit, especially those emerging upon deforming the material. Here we present a study of the mechanical and electronic properties of bent hexagonal graphene quantum dots employing density functional theory. We explore three different kinds of surfaces with Gaussian curvature exhibiting different shapes-spherical, cylindrical, and one-sheet hyperboloid-used to bend the material, and several boundary conditions regarding what atoms are forced to lay on the chosen surface. In each case, we study the curvature energy and two quantum regeneration times (classic and revival) for different values of the curvature radius. A strong correlation between Gaussian curvature and these regeneration times is found, and a special divergence is observed for the revival time for the hyperboloid case, probably related to the pseudo-magnetic field generated by this curvature being capable of causing a phase transition.

Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models.

T- and NK-cell lymphomas (TCL) are a heterogenous group of lymphoid malignancies with poor prognosis. In contrast to B-cell and myeloid malignancies, there are few preclinical models of TCLs, which has hampered the development of effective therapeutics. Here we establish and characterize preclinical models of TCL. We identify multiple vulnerabilities that are targetable with currently available agents (e.g., inhibitors of JAK2 or IKZF1) and demonstrate proof-of-principle for biomarker-driven therapies using patient-derived xenografts (PDXs). We show that MDM2 and MDMX are targetable vulnerabilities within TP53-wild-type TCLs. ALRN-6924, a stapled peptide that blocks interactions between p53 and both MDM2 and MDMX has potent in vitro activity and superior in vivo activity across 8 different PDX models compared to the standard-of-care agent romidepsin. ALRN-6924 induced a complete remission in a patient with TP53-wild-type angioimmunoblastic T-cell lymphoma, demonstrating the potential for rapid translation of discoveries from subtype-specific preclinical models.

Drug sensitivity of single cancer cells is predicted by changes in mass accumulation rate.

Assays that can determine the response of tumor cells to cancer therapeutics could greatly aid the selection of drug regimens for individual patients. However, the utility of current functional assays is limited, and predictive genetic biomarkers are available for only a small fraction of cancer therapies. We found that the single-cell mass accumulation rate (MAR), profiled over many hours with a suspended microchannel resonator, accurately defined the drug sensitivity or resistance of glioblastoma and B-cell acute lymphocytic leukemia cells. MAR revealed heterogeneity in drug sensitivity not only between different tumors, but also within individual tumors and tumor-derived cell lines. MAR measurement predicted drug response using samples as small as 25 µl of peripheral blood while maintaining cell viability and compatibility with downstream characterization. MAR measurement is a promising approach for directly assaying single-cell therapeutic responses and for identifying cellular subpopulations with phenotypic resistance in heterogeneous tumors.

Exploring mechanisms of human disease through structurally resolved protein interactome networks.

The study of the molecular basis of human disease has gained increasing attention over the past decade. With significant improvements in sequencing efficiency and throughput, a wealth of genotypic data has become available. However the translation of this information into concrete advances in diagnostic and clinical setups has proved far more challenging. Two major reasons for this are the lack of functional annotation for genomic variants and the complex nature of genotype-to-phenotype relationships. One fundamental approach to bypass these issues is to examine the effects of genetic variation at the level of proteins as they are directly involved in carrying out biological functions. Within the cell, proteins function by interacting with other proteins as a part of an underlying interactome network. This network can be determined using interactome mapping - a combination of high-throughput experimental toolkits and curation from small-scale studies. Integrating structural information from co-crystals with the network allows generation of a structurally resolved network. Within the context of this network, the structural principles of disease mutations can be examined and used to generate reliable mechanistic hypotheses regarding disease pathogenesis.

Wavepacket revivals in monolayer and bilayer graphene rings.

We have studied the existence of quantum revivals in graphene quantum rings within a simplified model. The time evolution of a Gaussian-populated wavepacket shows revivals in monolayer and bilayer graphene rings. We have also studied this behavior for quantum rings in a perpendicular magnetic field. We have found that revival time is an observable that shows different values for monolayer and bilayer graphene quantum rings. In addition, the revival time shows valley degeneracy breaking.

Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways.

The fission yeast Schizosaccharomyces pombe has more metazoan-like features than the budding yeast Saccharomyces cerevisiae, yet it has similarly facile genetics. We present a large-scale verified binary protein-protein interactome network, "StressNet," based on high-throughput yeast two-hybrid screens of interacting proteins classified as part of stress response and signal transduction pathways in S. pombe. We performed systematic, cross-species interactome mapping using StressNet and a protein interactome network of orthologous proteins in S. cerevisiae. With cross-species comparative network studies, we detected a previously unidentified component (Snr1) of the S. pombe mitogen-activated protein kinase Sty1 pathway. Coimmunoprecipitation experiments showed that Snr1 interacted with Sty1 and that deletion of snr1 increased the sensitivity of S. pombe cells to stress. Comparison of StressNet with the interactome network of orthologous proteins in S. cerevisiae showed that most of the interactions among these stress response and signaling proteins are not conserved between species but are "rewired"; orthologous proteins have different binding partners in both species. In particular, transient interactions connecting proteins in different functional modules were more likely to be rewired than conserved. By directly testing interactions between proteins in one yeast species and their corresponding binding partners in the other yeast species with yeast two-hybrid assays, we found that about half of the interactions that are traditionally considered "conserved" form modified interaction interfaces that may potentially accommodate novel functions.