Isotope Effect and Heavy-Light-Heavy Reactivity Oscillation in the Cl + CHD3/CHT3 Reaction.

Previous experiments and theories have shown the existence of heavy-light-heavy (HLH) reactivity oscillation in the Cl + CH4 reaction and anticipated that similar oscillations should exist in many HLH reactions involving polyatomic reagents. However, the total reaction probabilities for the Cl + CHD3 → HCl + CD3 reaction exhibit only a step-like feature, and the total reaction probabilities for Cl + CHT3 → HCl + CT3 do not show any structure at all. Here, we report seven-dimensional state-to-state quantum dynamics studies for this reaction on the FI-NN PES, and we demonstrate that HLH reactivity oscillations also exist in these two reactions, manifesting as peaks in the reaction probabilities for low product rotational states. These oscillations, however, are obscured in the total reaction probability because of the higher excitation of j ≥ 2 product rotational states. Furthermore, the isotope replacement of nonreactive hydrogen with deuterium and tritium significantly enhances reactivity at collision energies above 0.112 eV, indicating an inverse secondary isotope effect on the probabilities, which is proved to be also caused by HLH mass combination. We also demonstrate that the highly rotational excitation of CHD3 substantially enhances reactivity and the HLH oscillations, similar to HLH triatomic reactions. These observations are completely different from those in the H + CHD3 reaction, which is also a late-barrier reaction. Therefore, the HLH mass combination is very important, which affects not only the reactivity oscillation but also the amplitude and product rotational state distribution and makes the initial rotation excitation play a pivotal role in the reaction.

An efficient and universal parallel algorithm for high-dimensional quantum dynamics in poly-atomic reactions.

This study presents a parallel algorithm for high-dimensional quantum dynamics simulations in poly atomic reactions, integrating distributed- and shared-memory models. The distributions of the wave function and potential energy matrix across message passing interface processes are based on bundled radial and angular dimensions, with implementations featuring either two- or one-sided communication schemes. Using realistic parameters for the H + NH3 reaction, performance assessment reveals linear scalability, exceeding 90% efficiency with up to 600 processors. In addition, owing to the universal and concise structure, the algorithm demonstrates remarkable extensibility to diverse reaction systems, as demonstrated by successes with six-atom and four-atom reactions. This work establishes a robust foundation for high-dimensional dynamics studies, showcasing the algorithm's efficiency, scalability, and adaptability. The algorithm's potential as a valuable tool for unraveling quantum dynamics complexities is underscored, paving the way for future advancements in the field.

Observation of geometric phase effect through backward angular oscillations in the H + HD → H2 + D reaction.

Quantum interference between reaction pathways around a conical intersection (CI) is an ultrasensitive probe of detailed chemical reaction dynamics. Yet, for the hydrogen exchange reaction, the difference between contributions of the two reaction pathways increases substantially as the energy decreases, making the experimental observation of interference features at low energy exceedingly challenging. We report in this paper a combined experimental and theoretical study on the H + HD → H2 + D reaction at the collision energy of 1.72 eV. Although the roaming insertion pathway constitutes only a small fraction (0.088%) of the overall contribution, angular oscillatory patterns arising from the interference of reaction pathways were clearly observed in the backward scattering direction, providing direct evidence of the geometric phase effect at an energy of 0.81 eV below the CI. Furthermore, theoretical analysis reveals that the backward interference patterns are mainly contributed by two distinct groups of partial waves (J ~ 10 and J ~ 19). The well-separated partial waves and the geometric phase collectively influence the quantum reaction dynamics.

Disruption of mitochondrial energy metabolism is a putative pathogenesis of Diamond-Blackfan anemia.

Energy metabolism in the context of erythropoiesis and related diseases remains largely unexplored. Here, we developed a primary cell model by differentiating hematopoietic stem progenitor cells toward the erythroid lineage and suppressing the mitochondrial oxidative phosphorylation (OXPHOS) pathway. OXPHOS suppression led to differentiation failure of erythroid progenitors and defects in ribosome biogenesis. Ran GTPase-activating protein 1 (RanGAP1) was identified as a target of mitochondrial OXPHOS for ribosomal defects during erythropoiesis. Overexpression of RanGAP1 largely alleviated erythroid defects resulting from OXPHOS suppression. Coenzyme Q10, an activator of OXPHOS, largely rescued erythroid defects and increased RanGAP1 expression. Patients with Diamond-Blackfan anemia (DBA) exhibited OXPHOS suppression and a concomitant suppression of ribosome biogenesis. RNA-seq analysis implied that the substantial mutation (approximately 10%) in OXPHOS genes accounts for OXPHOS suppression in these patients. Conclusively, OXPHOS disruption and the associated disruptive mitochondrial energy metabolism are linked to the pathogenesis of DBA.

SET domain containing 2 promotes megakaryocyte polyploidization and platelet generation through methylation of α-tubulin.

BACKGROUND: Megakaryocytes (MKs) are polyploid cells responsible for producing ∼1011 platelets daily in humans. Unraveling the mechanisms regulating megakaryopoiesis holds the promise for the production of clinical-grade platelets from stem cells, overcoming significant current limitations in platelet transfusion medicine. Previous work identified that loss of the epigenetic regulator SET domain containing 2 (SETD2) was associated with an increased platelet count in mice. However, the role of SETD2 in megakaryopoiesis remains unknown. OBJECTIVES: Here, we examined how SETD2 regulated MK development and platelet production using complementary murine and human systems. METHODS: We manipulated the expression of SETD2 in multiple in vitro and ex vivo models to assess the ploidy of MKs and the function of platelets. RESULTS: The genetic ablation of Setd2 increased the number of high-ploidy bone marrow MKs. Peripheral platelet counts in Setd2 knockout mice were significantly increased ∼2-fold, and platelets exhibited normal size, morphology, and function. By knocking down and overexpressing SETD2 in ex vivo human cell systems, we demonstrated that SETD2 negatively regulated MK polyploidization by controlling methylation of α-tubulin, microtubule polymerization, and MK nuclear division. Small-molecule inactivation of SETD2 significantly increased the production of high-ploidy MKs and platelets from human-induced pluripotent stem cells and cord blood CD34+ cells. CONCLUSION: These findings identify a previously unrecognized role for SETD2 in regulating megakaryopoiesis and highlight the potential of targeting SETD2 to increase platelet production from human cells for transfusion practices.

Decoding human in vitro terminal erythropoiesis originating from umbilical cord blood mononuclear cells and pluripotent stem cells.

Ex vivo red blood cell (RBC) production generates unsatisfactory erythroid cells. A deep exploration into terminally differentiated cells is required to understand the impairments for RBC generation and the underlying mechanisms. Here, we mapped an atlas of terminally differentiated cells from umbilical cord blood mononuclear cells (UCBMN) and pluripotent stem cells (PSC) and observed their dynamic regulation of erythropoiesis at single-cell resolution. Interestingly, we detected a few progenitor cells and non-erythroid cells from both origins. In PSC-derived erythropoiesis (PSCE), the expression of haemoglobin switch regulators (BCL11A and ZBTB7A) were significantly absent, which could be the restraint for its adult globin expression. We also found that PSCE were less active in stress erythropoiesis than in UCBMN-derived erythropoiesis (UCBE), and explored an agonist of stress erythropoiesis gene, TRIB3, could enhance the expression of adult globin in PSCE. Compared with UCBE, there was a lower expression of epigenetic-related proteins (e.g., CASPASE 3 and UBE2O) and transcription factors (e.g., FOXO3 and TAL1) in PSCE, which might restrict PSCE's enucleation. Moreover, we characterized a subpopulation with high proliferation capacity marked by CD99high in colony-forming unit-erythroid cells. Inhibition of CD99 reduced the proliferation of PSC-derived cells and facilitated erythroid maturation. Furthermore, CD99-CD99 mediated the interaction between macrophages and erythroid cells, illustrating a mechanism by which macrophages participate in erythropoiesis. This study provided a reference for improving ex vivo RBC generation.

A panel sequencing dataset of peripheral blood gene variations in pan-cancer.

Circulating cell-free DNA (cfDNA) in the peripheral blood is a promising biomarker for cancer diagnosis and prognosis. Somatic mutations identified in cancers have been used to detect therapeutic targets for clinical transformation and individualize drug selection, while germline variants can predict a patient's risk of developing cancer and drug sensitivity. However, no platform has been developed to analyze, calculate, integrate, and friendly visualize these pan-cancer cfDNA mutations deeply. In this work, we performed panel sequencing encompassing 1,115 cancer-related genes across 16,659 cancer patients, spanning 27 cancer types. We detected 496 germline variants in leukocytes and 11,232 somatic mutations in the cfDNA of all patients. CPGV (Cancer Peripheral blood Gene Variations), a database constructed from this dataset, is the first pan-cancer cfDNA database that encompasses somatic mutations, germline variants, and further comparative analyses of mutations across different cancer types. It bears great promise to serve as a valuable resource for cancer research.

Combined JAK inhibition and PD-1 immunotherapy for non-small cell lung cancer patients.

Persistent inflammation driven by cytokines such as type-one interferon (IFN-I) can cause immunosuppression. We show that administration of the Janus kinase 1 (JAK1) inhibitor itacitinib after anti-PD-1 (programmed cell death protein 1) immunotherapy improves immune function and antitumor responses in mice and results in high response rates (67%) in a phase 2 clinical trial for metastatic non-small cell lung cancer. Patients who failed to respond to initial anti-PD-1 immunotherapy but responded after addition of itacitinib had multiple features of poor immune function to anti-PD-1 alone that improved after JAK inhibition. Itacitinib promoted CD8 T cell plasticity and therapeutic responses of exhausted and effector memory-like T cell clonotypes. Patients with persistent inflammation refractory to itacitinib showed progressive CD8 T cell terminal differentiation and progressive disease. Thus, JAK inhibition may improve the efficacy of anti-PD-1 immunotherapy by pivoting T cell differentiation dynamics.