Investigation of the Pulmonary Artery Hypertension Using an Ad Hoc OpenFOAM CFD Solver

Cardiovascular diseases are a group of disorders that affect the heart and blood vessels, representing a leading cause of death worldwide. With the help of computational fluid dynamics, it is possible to study the hemodynamics of the pulmonary arteries in detail and simulate various physiological conditions, thus offering numerous advantages over invasive analyses in the phases of diagnosis and surgical planning. Specifically, the aim of this study is the fluid dynamic analysis of the pulmonary artery, comparing the characteristics of the blood flow in a healthy subject with that of a patient affected by pulmonary arterial hypertension. We performed CFD simulations with the OpenFOAM C++ library using a purposely developed solver that features the Windkessel model as a pressure boundary condition. This methodology, scarcely applied in the past for this problem, allows for a proficient analysis and the detailed quantification of the most important fluid-dynamic parameters (flow velocity, pressure distribution, and wall shear stress (WSS)) with improved accuracy and resolution when compared with classical simulation and diagnostic techniques. We verified the validity of the adopted methodology in reproducing the blood flow by relying on experimental data. A detailed comparative analysis highlights the differences between healthy and pathological cases in hemodynamic terms. The outcomes of this work contribute to enlarging the knowledge of the blood flow characteristics in the human pulmonary artery, revealing substantial differences between the two clinical scenarios investigated and highlighting how arterial hypertension drastically changes the blood flow. The analysis of the data confirmed the importance of CFD as a supportive tool in understanding, diagnosing, and monitoring the pathophysiological mechanisms underlying cardiovascular diseases, proving to be a powerful means for personalizing surgical treatments

Diverse modes of binding in structures of Leishmania major N-myristoyltransferase with selective inhibitors

The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT) has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic -carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed

Coordinating cell cycle-regulated histone gene expression through assembly and function of the Histone Locus Body

Metazoan replication-dependent (RD) histone genes encode the only known cellular mRNAs that are not polyadenylated. These mRNAs end instead in a conserved stem-loop, which is formed by an endonucleolytic cleavage of the pre-mRNA. The genes for all 5 histone proteins are clustered in all metazoans and coordinately regulated with high levels of expression during S phase. Production of histone mRNAs occurs in a nuclear body called the Histone Locus Body (HLB), a subdomain of the nucleus defined by a concentration of factors necessary for histone gene transcription and pre-mRNA processing. These factors include the scaffolding protein NPAT, essential for histone gene transcription, and FLASH and U7 snRNP, both essential for histone pre-mRNA processing. Histone gene expression is activated by Cyclin E/Cdk2-mediated phosphorylation of NPAT at the G1-S transition. The concentration of factors within the HLB couples transcription with pre-mRNA processing, enhancing the efficiency of histone mRNA biosynthesis

Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression

Histone locus bodies (HLBs) are biomolecular condensates that assemble at replication-dependent (RD) histone genes in animal cells. These genes produce unique mRNAs that are not polyadenylated and instead end in a conserved 3' stem loop critical for coordinated production of histone proteins during S phase of the cell cycle. Several evolutionarily conserved factors necessary for synthesis of RD histone mRNAs concentrate only in the HLB. Moreover, because HLBs are present throughout the cell cycle even though RD histone genes are only expressed during S phase, changes in HLB composition during cell cycle progression drive much of the cell cycle regulation of RD histone gene expression. Thus, HLBs provide a powerful opportunity to determine the cause-and-effect relationships between nuclear body formation and cell cycle regulated gene expression. In this review, we focus on progress during the last five years that has advanced our understanding of HLB biology

Coordinating transcription and replication to mitigate their conflicts in early Drosophila embryos.

Collisions between transcribing RNA polymerases and DNA replication forks are disruptive. The threat of collisions is particularly acute during the rapid early embryonic cell cycles of Drosophila when S phase occupies the entirety of interphase. We hypothesize that collision-avoidance mechanisms safeguard this early transcription. Real-time imaging of endogenously tagged RNA polymerase II (RNAPII) and a reporter for nascent transcripts in unperturbed embryos shows clustering of RNAPII at around 2 min after mitotic exit, followed by progressive dispersal as associated nascent transcripts accumulate later in interphase. Abrupt inhibition of various steps in DNA replication, including origin licensing, origin firing, and polymerization, suppresses post-mitotic RNAPII clustering and transcription in nuclear cycles. We propose that replication dependency defers the onset of transcription so that RNAPII transcribes behind advancing replication forks. The resulting orderly progression can explain how early embryos circumvent transcription-replication conflicts to express essential developmental genes

Developing S-phase control

The duration of S phase in early embryos is often short, and then increases as development proceeds because of the appearance of late-replicating regions of the genome. In the April 1, 2012, issue of Genes & Development, Farrell and colleagues (pp. 714–725) demonstrate that the down-regulation of cyclin-dependent kinase 1 (Cdk1) activity triggers the onset of late-replicating DNA and an increase in S-phase length in Drosophila embryos, revealing an unexpected role for Cdk1 in replication control during development

Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila

The methylation state of lysine 20 on histone H4 (H4K20) has been linked to chromatin compaction, transcription, DNA repair and DNA replication. Monomethylation of H4K20 (H4K20me1) is mediated by the cell cycle-regulated histone methyltransferase PR-Set7. PR-Set7 depletion in mammalian cells results in defective S phase progression and the accumulation of DNA damage, which has been partially attributed to defects in origin selection and activation. However, these studies were limited to only a handful of mammalian origins, and it remains unclear how PR-Set7 and H4K20 methylation impact the replication program on a genomic scale. We employed genetic, cytological, and genomic approaches to better understand the role of PR-Set7 and H4K20 methylation in regulating DNA replication and genome stability in Drosophila cells. We find that deregulation of H4K20 methylation had no impact on origin activation throughout the genome. Instead, depletion of PR-Set7 and loss of H4K20me1 results in the accumulation of DNA damage and an ATR-dependent cell cycle arrest. Coincident with the ATR-dependent cell cycle arrest, we find increased DNA damage that is specifically limited to late replicating regions of the Drosophila genome, suggesting that PR-Set7-mediated monomethylation of H4K20 is critical for maintaining the genomic integrity of late replicating domains

Tumor Heterogeneity and Plasticity in Small Cell Lung Cancer

Gina N Duronio, Julien Sage Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USACorrespondence: Julien Sage, 265 Campus Drive, Lokey SIM1 G2078, Stanford University, Stanford, CA, 94305, USA, Email [email protected]: The heterogeneous nature of cell populations in human tumors is a major contributor to tumor evolution, including and perhaps most importantly in response to treatment. Here, we review current knowledge on tumor heterogeneity and cell state plasticity in small cell lung cancer (SCLC), a fast growing and highly metastatic form of lung cancer which develops rapid resistance to therapy. There is a pressing need to expand treatment options for patients with SCLC, which requires a better understanding of the mechanisms by which this disease is able to rapidly grow and evolve in response to therapy. Our current understanding points to epigenetic rather than genetic factors in defining major aspects of inter- and intra-tumoral heterogeneity in SCLC. SCLC is overall considered to be a neuroendocrine (NE) cancer type but SCLC tumors harbor a wide diversity of cancer cell states, including both NE and non-neuroendocrine (non-NE) states, defined by their mutually exclusive expression of a set of transcription factors such as ASCL1, NEUROD1, and POU2F3. The immune microenvironments of SCLC tumors also contain a great deal of heterogeneity. Here, we discuss the different SCLC cell states associated with their defining transcription factors, as well as the epigenetic mechanisms regulating the ability of SCLC cells to switch from one state to another. We further discuss how the composition of SCLC tumors and the surrounding immune cells may affect the response to chemotherapy and immunotherapy. Being able to control plasticity and heterogeneity in SCLC may in the future offer unique opportunities to improve treatment efficacy in this recalcitrant cancer.Keywords: tumor heterogeneity, plasticity, SCLC, neuroendocrin