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.

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.

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.

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.

Beyond ray optics absorption of light in CsPbBr3perovskite nanowire arrays studied experimentally and with wave optics modelling.

We study experimentally and with wave optics modelling the absorption of light in CsPbBr3perovskite nanowire arrays fabricated into periodic pores of an anodized aluminum oxide matrix, for nanowire diameters from 30 to 360 nm. First, we find that all the light that couples into the array can be absorbed by the nanowires at sufficient nanowire length. This behavior is in strong contrast to the expectation from a ray-optics description of light where, for normally incident light, only the rays that hit the cross-section of the nanowires can be absorbed. In that case, the absorption in the sample would be limited to the area fill factor of nanowires in the hexagonal array, which ranges from 13% to 58% for the samples that we study. Second, we find that the absorption saturates already at a nanowire length of 1000-2000 nm, making these perovskite nanowires promising for absorption-based applications such as solar cells and photodetectors. The absorption shows a strong diameter dependence, but for all diameters the transmission is less than 24% already at a nanowire length of 500 nm. For some diameters, the absorption exceeds that of a calculated thin film with 100% coverage. Our analysis indicates that the strong absorption in these nanowires originates from light-trapping induced by the out-of-plane disorder due to random axial position of each nanowire within its pore in the matrix.

Nanoscale X-ray Imaging of Composition and Ferroelastic Domains in Heterostructured Perovskite Nanowires: Implications for Optoelectronic Devices.

Metal halide perovskites (MHPs) have garnered significant interest as promising candidates for nanoscale optoelectronic applications due to their excellent optical properties. Axially heterostructured CsPbBr3-CsPb(Br(1-x)Clx)3 nanowires can be produced by localized anion exchange of pregrown CsPbBr3 nanowires. However, characterizing such heterostructures with sufficient strain and real space resolution is challenging. Here, we use nanofocused scanning X-ray diffraction (XRD) and X-ray fluorescence (XRF) with a 60 nm beam to investigate a heterostructured MHP nanowire as well as a reference CsPbBr3 nanowire. The nano-XRD approach gives spatially resolved maps of composition, lattice spacing, and lattice tilt. Both the reference and exchanged nanowire show signs of diverse types of ferroelastic domains, as revealed by the tilt maps. The chlorinated segment shows an average Cl composition of x = 66 and x = 70% as measured by XRD and XRF, respectively. The XRD measurements give a much more consistent result than the XRF ones. These findings are consistent with photoluminescence measurements, showing x = 73%. The nominally unexchanged segment also has a small concentration of Cl, as observed with all three methods, which we attribute to diffusion after processing. These results highlight the need to prevent such unwanted processes in order to fabricate optoelectronic devices based on MHP heterostructures.

[miR-497 inhibits the growth and metastasis of SGC-7901 human gastric cancer anoikis resistant cells via blocking Wnt/ß-catenin signaling pathway].

Objective To investigate the effects of microRNA497 (miR-497) on the metastasis of gastric cancer and its possible molecular mechanism. Methods SGC-7901 gastric cancer parent cells were cultured in an ultra-low adhesion environment, and the anoikis resistance model of SGC-7901 cells was created after re-adhesion. Clone formation assay, flow cytometry, TranswellTM test and scratch healing test were used to detect the differences of biological behavior compared with their parent cells. Fluorescence quantitative PCR was performed to detect the expression of miR-497. Western blot analysis was used to detect the changes of key proteins of Wnt/ß-catenin signaling pathway and epithelial mesenchymal transformation (EMT) related proteins such as vimentin and E-cadherin. Parent cells and anoikis resistant SGC-7901 cells were transfected with miR-497 inhibitor or miR-497 mimic, and CCK-8 assay was used to detect the proliferation activity. TranswellTM invasion assay was performed to detect the invasion ability of cells. TranswellTM migration test and scratch healing assay was used to determine the migration ability. Western blot analysis was used to detect the expressions of Wnt1, ß-catenin, vimentin and E-cadherin. By transfecting miR-497 mimic into the anoikis resistance SGC-7901 cells and inoculating them subcutaneously in nude mice, the changes in the volume and mass of tumor tissues were measured and recorded. Western blot analysis was used to determine the expressions of Wnt1, ß-catenin, vimentin and E-cadherin of tumor tissues. Results Compared with the parent cells, the anoikis resistance SGC-7901 gastric cancer cells had faster proliferation rate, stronger colony formation, lower apoptosis rate, stronger invasion and migration ability. The expression of miR-497 was significantly decreased. After down-regulation of miR-497, the proliferation ability, invasion and migration ability were significantly enhanced. The expressions of Wnt1, ß-catenin and vimentin increased significantly, while E-cadherin decreased notably. The results of up-regulation miR-497 were the opposite. The tumor growth rate, tumor volume and mass of miR-497 overexpression group were significantly lower than those of control group. The expressions of Wnt1, ß-catenin and vimentin decreased significantly, while the expression of E-cadherin increased significantly. Conclusion The expression of miR-497 is low in the anoikis resistance SGC-7901 cells. miR-497 can inhibit the growth and metastasis of gastric cancer cells by blocking Wnt/ß-catenin signaling pathway and EMT.

Signal recovery in single cell batch integration.

Data integration to align cells across batches has become a cornerstone of single cell data analysis, critically affecting downstream results. Yet, how much biological signal is erased during integration? Currently, there are no guidelines for when the biological differences between samples are separable from batch effects, and thus, data integration usually involve a lot of guesswork: Cells across batches should be aligned to be "appropriately" mixed, while preserving "main cell type clusters". We show evidence that current paradigms for single cell data integration are unnecessarily aggressive, removing biologically meaningful variation. To remedy this, we present a novel statistical model and computationally scalable algorithm, CellANOVA, to recover biological signal that is lost during single cell data integration. CellANOVA utilizes a "pool-of-controls" design concept, applicable across diverse settings, to separate unwanted variation from biological variation of interest. When applied with existing integration methods, CellANOVA allows the recovery of subtle biological signals and corrects, to a large extent, the data distortion introduced by integration. Further, CellANOVA explicitly estimates cell- and gene-specific batch effect terms which can be used to identify the cell types and pathways exhibiting the largest batch variations, providing clarity as to which biological signals can be recovered. These concepts are illustrated on studies of diverse designs, where the biological signals that are recovered by CellANOVA are shown to be validated by orthogonal assays. In particular, we show that CellANOVA is effective in the challenging case of single-cell and single-nuclei data integration, where the recovered biological signals are replicated in an independent study.

FIPRESCI: droplet microfluidics based combinatorial indexing for massive-scale 5'-end single-cell RNA sequencing.

Single-cell RNA sequencing methods focusing on the 5'-end of transcripts can reveal promoter and enhancer activity and efficiently profile immune receptor repertoire. However, ultra-high-throughput 5'-end single-cell RNA sequencing methods have not been described. We introduce FIPRESCI, 5'-end single-cell combinatorial indexing RNA-Seq, enabling massive sample multiplexing and increasing the throughput of the droplet microfluidics system by over tenfold. We demonstrate FIPRESCI enables the generation of approximately 100,000 single-cell transcriptomes from E10.5 whole mouse embryos in a single-channel experiment, and simultaneous identification of subpopulation differences and T cell receptor signatures of peripheral blood T cells from 12 cancer patients.

Proteomic Profiling of Colorectal Adenomas Identifies a Predictive Risk Signature for Development of Metachronous Advanced Colorectal Neoplasia.

BACKGROUND & AIMS: Colonic adenomatous polyps, or adenomas, are frequent precancerous lesions and the origin of most cases of colorectal adenocarcinoma. However, we know from epidemiologic studies that although most colorectal cancers (CRCs) originate from adenomas, only a small fraction of adenomas (3%-5%) ever progress to cancer. At present, there are no molecular markers to guide follow-up surveillance programs. METHODS: We profiled, by mass spectrometry-based proteomics combined with machine learning analysis, a selected cohort of formalin-fixed, paraffin-embedded high-grade (HG) adenomas with long clinical follow-up, collected as part of the Danish national screening program. We grouped subjects in the cohort according to their subsequent history of findings: a nonmetachronous advanced neoplasia group (G0), with no new HG adenomas or CRCs up to 10 years after polypectomy, and a metachronous advanced neoplasia group (G1) where individuals developed a new HG adenoma or CRC within 5 years of diagnosis. RESULTS: We generated a proteome dataset from 98 selected HG adenoma samples, including 20 technical replicates, of which 45 samples belonged to the nonmetachronous advanced neoplasia group and 53 to the metachronous advanced neoplasia group. The clear distinction of these 2 groups seen in a uniform manifold approximation and projection plot indicated that the information contained within the abundance of the ∼5000 proteins was sufficient to predict the future occurrence of HG adenomas or development of CRC. CONCLUSIONS: We performed an in-depth analysis of quantitative proteomic data from 98 resected adenoma samples using various novel algorithms and statistical packages and found that their proteome can predict development of metachronous advanced lesions and progression several years in advance.

Stereodynamical control of the H + HD → H2 + D reaction through HD reagent alignment.

Prealigning nonpolar reacting molecules leads to large stereodynamical effects because of their weak steering interaction en route to the reaction barrier. However, experimental limitations in preparing aligned molecules efficiently have hindered the investigation of steric effects in bimolecular reactions involving hydrogen. Here, we report a high-resolution crossed-beam study of the reaction H + HD(v = 1, j = 2) → H2(v', j') + D at collision energies of 0.50, 1.20, and 2.07 electron volts in which the vibrationally excited hydrogen deuteride (HD) molecules were prepared in two collision configurations, with their bond preferentially aligned parallel and perpendicular to the relative velocity of collision partners. Notable stereodynamical effects in differential cross sections were observed. Quantum dynamics calculations revealed that strong constructive interference in the perpendicular configuration plays an important role in the stereodynamical effects observed.

Proteome expression profiling of red blood cells during the tumorigenesis of hepatocellular carcinoma.

The early diagnosis of hepatocellular carcinoma (HCC) has not been clinically elucidated, leading to an increased mortality rate in patients with HCC. HCC is a systemic disease related to disorders of blood homeostasis, and the association between red blood cells (RBCs) and HCC tumorigenesis remains elusive. We performed data-independent acquisition proteomic analyses of 72 clinical RBC samples, including HCC (n = 30), liver cirrhosis (LC, n = 17), and healthy controls (n = 25), and characterized the clinical relevance of RBCs and tumorigenesis in HCC. We observed dynamic changes in RBCs during HCC tumorigenesis, and our findings indicate that, based on the protein expression profiles of RBCs, LC is a developmental stage closely approaching HCC. The expression of hemoglobin (HbA and HbF) in peripheral blood dynamically changed during HCC tumorigenesis, suggesting that immature erythroid cells exist in peripheral blood of HCC patients and that erythropoiesis is influenced by the onset of LC. We also identified the disrupted autophagy pathway in RBCs at the onset of LC, which persisted during HCC tumorigenesis. The oxytocin and GnRH pathways were disrupted and first identified during the development of LC into HCC. Significantly differentially expressed SMIM1, ANXA7, HBA1, and HBE1 during tumorigenesis were verified as promising biomarkers for the early diagnosis of HCC using parallel reaction monitoring technology. This study may enhance the understanding of HCC tumorigenesis from a different point of view and aid the early diagnosis of HCC.

ANTXR1 Regulates Erythroid Cell Proliferation and Differentiation through wnt/ß-Catenin Signaling Pathway In Vitro and in Hematopoietic Stem Cell.

Erythropoiesis is a highly complex and sophisticated multistage process regulated by many transcription factors, as well as noncoding RNAs. Anthrax toxin receptor 1 (ANTXR1) is a type I transmembrane protein that binds the anthrax toxin ligands and mediates the entry of its toxic part into cells. It also functions as a receptor for the Protective antigen (PA) of anthrax toxin, and mediates the entry of Edema factor (EF) and Lethal factor (LF) into the cytoplasm of target cells and exerts their toxicity. Previous research has shown that ANTXR1 inhibits the expression of γ-globin during the differentiation of erythroid cells. However, the effect on erythropoiesis from a cellular perspective has not been fully determined. This study examined the role of ANTXR1 on erythropoiesis using K562 and HUDEP-2 cell lines as well as cord blood CD34+ cells. Our study has shown that overexpression of ANTXR1 can positively regulate erythrocyte proliferation, as well as inhibit GATA1 and ALAS2 expression, differentiation, and apoptosis in K562 cells and hematopoietic stem cells. ANTXR1 knockdown inhibited proliferation, promoted GATA1 and ALAS2 expression, accelerated erythrocyte differentiation and apoptosis, and promoted erythrocyte maturation. Our study also showed that ANTXR1 may regulate the proliferation and differentiation of hematopoietic cells, though the Wnt/ß-catenin pathway, which may help to establish a possible therapeutic target for the treatment of blood disorders.

Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions.

The epigenetic control of gene expression is highly cell-type and context specific. Yet, despite its complexity, gene regulatory logic can be broken down into modular components consisting of a transcription factor (TF) activating or repressing the target gene expression through its binding to a cis-regulatory region. We propose a nonparametric approach, TRIPOD, to detect and characterize the three-way relationships between a TF, its target gene, and the accessibility of the TF's binding site using single-cell RNA and ATAC multiomic data. We apply TRIPOD to interrogate the cell-type-specific regulatory logic in peripheral blood mononuclear cells and contrast our results to detections from enhancer databases, cis-eQTL studies, ChIP-seq experiments, and TF knockdown/knockout studies. We then apply TRIPOD to mouse embryonic brain data and identify regulatory relationships, validated by ChIP-seq and PLAC-seq. Finally, we demonstrate TRIPOD on the SHARE-seq data of differentiating mouse hair follicle cells and identify lineage-specific regulation supported by histone marks and super-enhancer annotations. A record of this paper's transparent peer review process is included in the supplemental information.

Transmembrane Protein ANTXR1 Regulates γ-Globin Expression by Targeting the Wnt/ß-Catenin Signaling Pathway.

Reactivation of fetal hemoglobin (HbF, α2γ2) alleviates clinical symptoms in patients with ß-thalassemia and sickle cell disease, although the regulatory mechanisms of γ-globin expression have not yet been fully elucidated. Recent studies found that interfering with the expression of the membrane protein ANTXR1 gene upregulated γ-globin levels. However, the exact mechanism by which ANTXR1 regulates γ-globin levels remains unclear. Our study showed that overexpression and knockdown of ANTXR1 in K562, cord blood CD34+, and HUDEP-2 cells decreased and increased γ-globin expression, respectively. ANTXR1 regulates the reactivation of fetal hemoglobin (HbF, α2γ2) in K562, cord blood CD34+, and adult peripheral blood CD34+ cells through interaction with LRP6 to promote the nuclear entry of ß-catenin and activate the Wnt/ß-catenin signaling pathway. The overexpression or knockdown of ANTXR1 on γ-globin and Wnt/ß-catenin signaling in K562 cells was reversed by the inhibitor XAV939 and the activator LiCl, respectively, where XAV939 inhibits the transcription of ß-catenin in the Wnt pathway, but LiCl inhibits GSK3-ß. We also showed that the binding ability of the rank4 site in the transcriptional regulatory region of the SOX6 gene to c-Jun was significantly increased after overexpression of ANTXR1 in K562 cells. SOX6 protein expression was increased significantly after overexpression of the c-Jun gene, indicating that the transcription factor c-Jun initiated the transcription of SOX6, thereby silencing γ-globin. Our findings may provide a new intervention target for the treatment of ß-hemoglobinopathies.

The Thyroid Condition and Residual Clinical Signs in 31 Existing Endemic Neurological Cretins After 42 Years of Iodine Supplementation in China.

Backgroud: Endemic cretinism is the most severe manifestation among the iodine deficiency-related disorders. The clinical status of the cretins may be modified subsequently by the duration and severity of the disease. We aimed to reassess the clinical status and thyroid function of 31 surviving "neurological cretins" after 42 years of iodine supplementation in a historically severely iodine deficiency area of China. Methods: It was a cross-sectional study in design and we investigated all 31 surviving neurological cretins and 85 controls. A detailed neurological examination was conducted on each patients. All the participants were given a questionnaire and underwent B-mode ultrasonography of the thyroid. The serum levels of thyroid hormones, thyroid antibodies, serum iodine concentration (SIC) and urine iodine concentration (UIC) were measured. Results: The neurological cretins had shorter stature than that of the control. Neurological damage is still present in patients with cretinism. The prevalence of subclinical hypothyroidism and thyroid nodule in the cretins was significantly higher (χ2 =4.766, P=0.029 and χ2 =17.077, P<0.0001, respectively) compared with the control. After adjusting for confounding factors, endemic neurocretinism was found to be an independent risk factor for subclinical hypothyroidism (OR=4.412; 95% CI: 1.358-14.334; P=0.014) and thyroid nodule (OR=6.433; 95% CI: 2.323-17.816; P<0.0001). Conclusions: Iodine supplementation after birth does not reverse the neurological damage that results from maternal/foetal hypothyroidism in utero and is subsequently manifested as neurological cretinism. There is a cross-sectional association between endemic neurocretinism and subclinical hypothyroidism and thyroid nodule.

Mapping the single-cell landscape of acral melanoma and analysis of the molecular regulatory network of the tumor microenvironments.

Acral melanoma (AM) exhibits a high incidence in Asian patients with melanoma, and it is not well treated with immunotherapy. However, little attention has been paid to the characteristics of the immune microenvironment in AM. Therefore, in this study, we collected clinical samples from Chinese patients with AM and conducted single-cell RNA sequencing to analyze the heterogeneity of its tumor microenvironments (TMEs) and the molecular regulatory network. Our analysis revealed that genes, such as TWIST1, EREG, TNFRSF9, and CTGF could drive the deregulation of various TME components. The molecular interaction relationships between TME cells, such as MIF-CD44 and TNFSF9-TNFRSF9, might be an attractive target for developing novel immunotherapeutic agents.

Acral melanoma is a type of cancer that affects the hands and feet. It tends to form on the palms, soles, and under the nails. It is rare in people of European descent, but in Asian populations it makes up more than half of all melanoma cases. Unlike other types of skin cancer, it does not respond well to immunotherapy, but scientists did not understand why. Historically, cancer research has focused on the genetics of whole tumors. But cancer is complicated. Malignant cells recruit other cells to help them survive and grow, and to protect them from attacks by the immune system. Together, they create their own ecosystem, called the tumor microenvironment. The exact makeup of the tumor microenvironment differs depending on the type of cancer and on the genetics of the individual. Investigating the cells that 'support' the tumor could help to explain how acral melanoma develops and why it does not respond to treatment. To address these questions, He et al. collected samples from six patients with acral melanoma and examined the genes used by more than 60,000 individual cells. This revealed nine different types of cells in the tumor microenvironment. Most were cancer cells, but there were also immune cells, blood vessel cells, skin cells, and a type of cell that makes connective tissue. He et al. also identified four genes that most likely shape the tumor microenvironment, and two gene pairs that may control some of the interactions between the cells. Investigating these early findings in more detail could open new treatment avenues for acral melanoma. The number of samples in this study was small, but it provides a starting point for future investigation. With more data, researchers could start to develop treatments that target the unique tumor microenvironment of this type of cancer.