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Abstract Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.

Abstract Background Myelodysplastic neoplasms (MDS) are myeloid neoplasms characterized by disordered differentiation of hematopoietic stem cells and a predisposition to acute myeloid leukemia (AML). The underline pathogenesis remains unclear. Methods In this study, the trajectory of differentiation and mechanisms of leukemic transformation were explored through bioinformatics analysis of single-cell RNA-Seq data from hematopoietic stem and progenitor cells (HSPCs) in MDS patients. Results Among the HSPC clusters, the proportion of common myeloid progenitor (CMP) was the main cell cluster in the patients with excess blasts (EB)/ secondary AML. Cell cycle analysis indicated the CMP of MDS patients were in an active proliferative state. The genes involved in the cell proliferation, such as MAML3 and PLCB1, were up-regulated in MDS CMP. Further validation analysis indicated that the expression levels of MAML3 and PLCB1 in patients with MDS-EB were significantly higher than those without EB. Patients with high expression of PLCB1 had a higher risk of transformation to AML. PLCB1 inhibitor can suppress proliferation, induce cell cycle arrest, and activate apoptosis of leukemic cells in vitro. Conclusion This study revealed the transcriptomic change of HSPCs in MDS patients along the pseudotime and indicated that PLCB1 plays a key role in the transformation of MDS into leukemia.

Abstract Accumulating evidence has implicated impaired extracellular matrix (ECM) clearance as a key factor in fibrotic disease. Despite decades of research elucidating the effectors of ECM clearance, relatively little is understood regarding the upstream regulation of this process. Collagen is the most abundant constituent of normal and fibrotic ECM in mammalian tissues. Its catabolism occurs through extracellular proteolysis and cell-mediated uptake of collagen fragments for intracellular degradation. Given the paucity of information regarding the regulation of this latter process, here we execute unbiased genome-wide screens to understand the molecular underpinnings of cell-mediated collagen clearance. Using this approach, we discover a mechanism through which collagen biosynthesis is sensed by cells internally and directly regulates clearance of extracellular collagen. The sensing mechanism appears to be dependent on endoplasmic reticulum-resident protein SEL1L and occurs via a noncanonical function of this protein. This pathway functions as a homeostatic negative feedback loop that limits collagen accumulation in tissues. In human fibrotic lung disease, the induction of this collagen clearance pathway by collagen synthesis is impaired, thereby contributing to the pathological accumulation of collagen in lung tissue. Thus, we describe cell-autonomous, rheostatic collagen clearance as an important pathway of tissue homeostasis.

Abstract The SEL1L-HRD1 protein complex represents the most conserved branch of endoplasmic reticulum (ER)-associated degradation (ERAD). Despite recent advances in both mouse models and humans, in vivo evidence for the importance of SEL1L in the ERAD complex formation and its (patho-)physiological relevance in mammals remains limited. Here we report that SEL1L variant p.Ser658Pro (SEL1L S658P ) is a pathogenic hypomorphic mutation, causing partial embryonic lethality, developmental delay, and early-onset cerebellar ataxia in homozygous mice carrying the bi-allelic variant. Biochemical analyses reveal that SEL1L S658P variant not only reduces the protein stability of SEL1L, but attenuates the SEL1L-HRD1 interaction, likely via electrostatic repulsion between SEL1L F668 and HRD1 Y30 residues. Proteomic screens of SEL1L and HRD1 interactomes reveal that SEL1L-HRD1 interaction is a prerequisite for the formation of a functional HRD1 ERAD complex, as SEL1L is required for the recruitment of E2 enzyme UBE2J1 as well as DERLIN to HRD1. These data not only establish the disease relevance of SEL1L-HRD1 ERAD, but also provide additional insight into the formation of a functional HRD1 ERAD complex.

Pancreatic cancer is difficult to diagnose early and progresses rapidly. Researchers have found that a cytokine called Interleukin-6 (IL-6) is involved in the entire course of pancreatic cancer, promoting its occurrence and development. From the earliest stages of pancreatic intraepithelial neoplasia to the invasion and metastasis of pancreatic cancer cells and the appearance of tumor cachexia, IL-6 drives oncogenic signal transduction pathways and immune escape that accelerate disease progression. IL-6 is considered a biomarker for pancreatic cancer diagnosis and prognosis, as well as a potential target for treatment. IL-6 antibodies are currently being explored as a hot topic in oncology. This article aims to systematically explain how IL-6 induces the deterioration of normal pancreatic cells, with the goal of finding a breakthrough in pancreatic cancer diagnosis and treatment.

ERCC2 plays a pivotal role in DNA damage repair, however, its specific function in cancer remains elusive. In this study, we made a significant breakthrough by discovering a substantial upregulation of ERCC2 expression in glioblastoma (GBM) tumor tissue. Moreover, elevated levels of ERCC2 expression were closely associated with poor prognosis. Further investigation into the effects of ERCC2 on GBM revealed that suppressing its expression significantly inhibited malignant growth and migration of GBM cells, while overexpression of ERCC2 promoted tumor cell growth. Through mechanistic studies, we elucidated that inhibiting ERCC2 led to cell cycle arrest in the G0/G1 phase by blocking the CDK2/CDK4/CDK6/Cyclin D1/Cyclin D3 pathway. Notably, we also discovered a direct link between ERCC2 and CDK4, a critical protein in cell cycle regulation. Additionally, we explored the potential of TRAIL, a low-toxicity death ligand cytokine with anticancer properties. Despite the typical resistance of GBM cells to TRAIL, tumor cells undergoing cell cycle arrest exhibited significantly enhanced sensitivity to TRAIL. Therefore, we devised a combination strategy, employing TRAIL with the nanoparticle DMC-siERCC2, which effectively suppressed the GBM cell proliferation and induced apoptosis. In summary, our study suggests that targeting ERCC2 holds promise as a therapeutic approach to GBM treatment.

Abstract Endoplasmic reticulum-associated degradation (ERAD) plays indispensable roles in many physiological processes; however, the nature of endogenous substrates remains largely elusive. Here we report a proteomics strategy based on the intrinsic property of the SEL1L-HRD1 ERAD complex to identify endogenous ERAD substrates both in vitro and in vivo. Following stringent filtering using a machine learning algorithm, over 100 high-confidence potential substrates are identified in human HEK293T and mouse brown adipose tissue, among which ~88% are cell type-specific. One of the top shared hits is the catalytic subunit of the glycosylphosphatidylinositol (GPI)-transamidase complex, PIGK. Indeed, SEL1L-HRD1 ERAD attenuates the biogenesis of GPI-anchored proteins by specifically targeting PIGK for proteasomal degradation. Lastly, several PIGK disease variants in inherited GPI deficiency disorders are also SEL1L-HRD1 ERAD substrates. This study provides a platform and resources for future effort to identify proteome-wide endogenous substrates in vivo, and implicates SEL1L-HRD1 ERAD in many cellular processes including the biogenesis of GPI-anchored proteins.

Purpose This study evaluated the value of contrast-enhanced ultrasonography (CEUS) in the ultrasound-guided microwave ablation (MWA) treatment of symptomatic focal uterine adenomyosis. Methods This retrospective study was conducted between March 2020 and January 2023, enrolling 52 patients with symptomatic focal uterine adenomyosis who had undergone MWA. All patients were examined with CEUS before and after MWA. The non-perfused volume (NPV) was compared between CEUS and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) following ablation. Therapeutic efficacy and safety were evaluated at 3-, 6-, and 12-month follow-ups. Additionally, this study explored the correlations between pre-treatment CEUS features and a volume reduction ratio indicating sufficient ablation, defined as 50% or more at the 3-month follow-up. Results No significant differences in NPV were noted between CEUS and DCE-MRI immediately after MWA and during follow-up (all P>0.05). At the 3-month follow-up, the median VRRs for the uterus and adenomyosis were 33.2% and 63.9%, respectively. Sufficient ablation was achieved in 69.2% (36/52) of adenomyosis cases, while partial ablation was observed in the remaining 30.8% (16/52). The identification of non-enhancing areas on pre-treatment CEUS was associated with sufficient ablation (P=0.016). At the 12-month follow-up, significant decreases were observed in both the uterine and adenomyosis volumes (all P

CBM well pattern optimization design and deployment is a key part of CBM development plan formulation. Reasonable well pattern deployment can not only optimize CBM production, but also reduce CBM development costs and improve economic benefits. In response to this problem, taking Daning block in the Ordos Basin as the research object, the coal seam conditions and coal reservoir characteristics in the study area were systematically analyzed, and the suitable well type and well pattern orientation for CBM development were determined. The results show that the No.5 coal seam of Shanxi Formation in the Daning block has the characteristics of large thickness, simple structure, high gas content and low permeability. The well type of CBM development should be mainly directional wells, supplemented by horizontal wells, with the corresponding well pattern for large-scale development, and the well pattern orientation is NE66°; using the CBM productivity numerical simulation software COMET3, the current use of the Daning block is analyzed. The productivity was predicted based on the well pattern and well spacing, and the productivity under the open scheme of different well pattern and well spacing was simulated and evaluated. Numerical simulation results show that the CBM recovery rate is only 19.03% after 3086 d of well pattern and well spacing used in the current CBM development in the Daning block, indicating a low degree of CBM resource production. When the well spacing is 300 m×80 m and 400 m×100 m (that is, the well spacing ratio is 4∶1), the cumulative gas production of a single well in the five-spot well pattern is the largest. That is, when the well row spacing ratio is 3∶1), the cumulative gas production of a single well in the rectangular well pattern is the largest. Therefore, it is considered that the five-point well pattern should be selected when setting the well row spacing ratio of 4∶1 in the Daning block, and the 3∶1 Rectangular well pattern should be selected for the well spacing ratio of 1. After the well pattern and well spacing are optimized, the CBM recovery rate reaches 44.18% and 36.85% respectively, and the CBM resource production degree is greatly improved.

Abstract Aim The gut microbiota has been reported to be associated with acute graft‐versus‐host disease (aGvHD) in hematopoietic stem cell transplantation (HSCT). Dynamic surveillance of the microbiota is required to understand the detailed pathogenesis involved in the process of aGvHD. Methods Fecal samples were collected prospectively at four timepoints, including pre‐HSCT (T1), graft infusion (T2), neutrophil engraftment (T3), and 30 days after transplantation (T4). Fecal samples were profiled by 16S ribosomal RNA gene sequencing to assess the microbiota composition. Results From the T1 to T4 timepoint, the diversity of the gut microbiota decreased, and the dominant species also changed, with a decrease in the obligate anaerobic bacteria and a shift toward a “pathogenic community”. Compared with non‐aGvHD patients, aGvHD patients had a lower abundance of Roseburia at T1 and a higher abundance of Acinetobacter johnsonii at T2. Furthermore, Acinetobacter johnsonii was negatively correlated with the secretion of IL‐4 and TNF‐α. At T3, Rothia mucilaginos was demonstrated to be linked with a decreased risk of aGvHD, which was accompanied by decreased secretion of IL‐8. At T4, higher abundances of Lactobacillus paracasei and Acinetobacter johnsonii were identified to be related with aGvHD. Lactobacillus paracasei was associated with the downregulation of IL‐10, and Acinetobacter johnsonii was associated with the downregulation of IL‐2 and TNF‐α. Conclusions Dynamic changes in gut microbiota composition and related cytokines were found to be related to aGvHD, including pathogenic or protective changes. These findings suggested that manipulation of gut microbiota at different timepoints might be a promising avenue for preventing or treating this common complication.

Abstract Background The orthopedic treatment of the stiff clubfoot is challenging for clinicians, and the purpose of this study was to explore the preliminary findings of 3D printing-assisted patient-specific instrument (PSI) osteotomy guide for use in the orthopedic treatment of the stiff clubfoot. Material and methods There were 20 patients (25 feet) with stiff clubfoot admitted from December 2018 to June 2022, including 13 males (16 feet) and 7 females (9 feet), aged 24–52 years, mean 40.15 years; 8 left feet, 7 right feet, 5 bipedal. All patients underwent triple arthrodesis and were divided into 10 cases (12 feet) in the PSI group (n = 12) and 10 cases (13 feet) in the conventional surgery group (n = 13) according to the surgical approach. The duration of surgery and the number of radiation exposures were recorded in all cases, and the American Orthopedic Foot and Ankle Society (AOFAS), and International Congenital Clubfoot Study Group (ICFSG) scoring systems were applied postoperatively to assess the effect of corrective treatment. All measurement data were expressed as mean ± standard deviation, and differences between groups were determined by Student’s t test. All count data between the two groups were compared using the chi-square test or Fisher’s exact test analysis. Results All 20 patients (25 feet) were followed up for 1 year. No major complications related to osteotomy, such as overcorrection, incomplete correction, or bone nonunion, were observed in the PSI and conventional surgery groups at the final follow-up, and the PSI group had the advantage of shorter operative time (P 0.05) and ICFSG score (P > 0.05) at the last follow-up were not statistically significant in both groups, but the excellent rate at the last follow-up was 91.7% in the PSI group which was significantly higher than that of the conventional surgery group at 76.9%. Conclusions The utilization of 3D printing-assisted PSI osteotomy guide in orthopedic surgery for stiff clubfoot offers a safe and effective surgical tool for triple joint fusion treatment. This technology simplifies surgical procedures, minimizes intraoperative radiation exposures, reduces surgical time, and enables precise and personalized treatment.

Objective To explore the pathogenic genes in a Chinese family affected by nonsyndromic tooth agenesis so as to study the pathogenesis of oligodontia. Methods Hospital ethical approval and informed consent of the patients and family members were obtained. Clinical data of the proband and close family members were collected, peripheral venous blood was collected, and DNA was extracted. Gene sequencing was performed through whole-exome sequencing, and then the screened pathogenic genes were verified by Sanger sequencing. The three-dimensional structure of the mutant proteins was analyzed and compared with the wild-type using bioinformatics tools. Results The two patients with congenital majority tooth loss in this family were cousins, and there were no other patients with congenital majority tooth loss in the family. Besides congenital multiple tooth loss, the two patients had no obvious hair abnormalities, finger/toe abnormalities, sweating abnormalities or other abnormal manifestations of ectodermal tissue. We found a mutant gene that in this family by carrying out gene sequencing of the patients and their close family members. A novel EDA (ectodysplasin A) missense mutation c.983C>T (p. Pro328Leu) was identified, which changed the encoded amino acid from proline (Pro) to leucine (Leu). Analysis of the mutation site showed that the site was highly conserved, and three-dimensional structure modeling also found that it changed the structure of EDA. Conclusion A novel EDA missense variant (c.983C>T, p.Pro328Leu) was first identified in a Chinese family with nonsyndromic tooth agenesis, extending the mutation spectrum of the EDA gene.

Summary: Pancreatic cancer is highly lethal with limited effective treatments. This study explores the therapeutic effects of eupalinolide B (EB) from Eupatorium lindleyanum DC on pancreatic cancer cells. Through cellular functional assays, we observed that EB effectively inhibits cell viability, proliferation, migration, and invasion. In a xenograft mouse model, EB treatment resulted in reduced pancreatic cancer tumor growth and decreased expression of Ki-67. Mechanistically, EB induces apoptosis, elevates reactive oxygen species (ROS) levels, and disrupts copper homeostasis. RNA sequencing (RNA-seq) and gene set enrichment analysis (GSEA) identified copper ion binding pathways and potential involvement in cuproptosis. Furthermore, EB enhances the cytotoxic effects of elesclomol (ES), increasing ROS levels in a copper-dependent manner and exhibiting synergistic cytotoxicity. These findings suggest that EB, either alone or in combination with ES, represents a promising strategy for targeting metal ion dysregulation and inducing potential cuproptosis in pancreatic cancer, offering a potential improvement in therapeutic outcomes.

BackgroundPulmonary sarcomatoid carcinoma (PSC) is a rare highly aggressive and poorly differentiated non-small cell carcinoma, and little is known about the information on the usefulness of 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT). We investigated the clinical and 18F-FDG PET/CT features of PSC.MethodsWe retrospectively analyzed 25 consecutive PSC patients who had undergone 18F-FDG PET/CT. Demographic data, PET/CT findings before treatment, pathological features, and prognosis in these patients were investigated to define correlates between maximal standard uptake value (SUVmax) and clinicopathological parameters.ResultsFrom March 2017 to January 2023, twenty-five eligible patients with PSC were identified. There were 23 (92%) men, aged 68.5 ± 8.5 (range 56-90) years. Eighteen (72%) patients had a frequent smoking history. The mean size of PSCs was 59.3 ± 18.6 (range 29-97) mm, and 23 (92%) PSCs were Stage IV tumors. 20 (80%) lesions were located in the upper lung and 19 (76%) cases belonged to the peripheral type. Necrotic foci appeared in 21(84%) tumors. 11 (44%) PSCs invaded the pleura. All PSCs were FDG avid, and the mean of SUVmax was 11.8 ± 5.3 (range 4.8-25.5). Metastases were found on PET/CT in 24(96%) patients. The SUVmax of the lesions ≥ 5cm was higher than that of the lesions < 5cm (p=0.004), and the SUVmax of lesions with TTF-1 expression was higher than those of lesions without TTF-1 expression (p=0.009). All of the 25 primary lesions were considered malignant and confirmative, probable, and possible diagnosis of PSC was made in 2 (8%), 4 (16%), and 5(20%) patients, respectively on PET/CT. PSC was not considered in 14 (56%) patients, in PET/CT. The survival of patients with surgery didn’t demonstrate a significantly good prognosis as compared with those without surgery (p=0.675).ConclusionAll PSCs had obvious FDG avidity. Although imaging diagnosis is still difficult, combined clinical and imaging features more than 40% of primary lesions were considered for the possibility of PSC in our group. Early histopathological diagnosis is necessary to help develop a reasonable regimen.

Abstract Background Supramalleolar osteotomy (SMOT) has emerged as a valuable treatment for ankle varus deformity; however, there are fewer reports of treatment outcomes in adolescents. The purpose of this study was to investigate the radiologic and clinical outcomes of SMOT for the treatment of traumatic ankle joint varus deformity (TAVD) in adolescents. Methods We reviewed 32 adolescent cases who underwent SMOT between February 2017 and February 2022 for TAVD. Radiologic assessment included tibial anterior surface angle (TAS), talar tilt angle (TT), and tibial lateral surface angle (TLS) preoperatively and at 3 months and 12 months postoperatively, and clinical assessment was performed using American Orthopaedic Foot and Ankle Society (AOFAS) scores, Visual Analogue Scale (VAS) scores, and ankle dorsiflexion–plantarflexion ROM including preoperative and 6 months postoperative and 12 months postoperative. Results All 32 patients were followed up completely with a mean follow-up of (20.3 ± 3.2) months. From the radiologic outcomes, the mean preoperative TAS improved from 61.53 ± 3.74 to 88 ± 1.72 at 12 months postoperatively, the mean preoperative TT decreased from 2.25 ± 1.32 to 0.5 ± 0.57 at 12 months postoperatively, the mean preoperative TLS improved from 76.72 ± 0.21 to 79.34 ± 1.52 at 12 months postoperatively, the differences between the above preoperative and 12 months postoperative radiologic outcomes were statistically significant (p

Abstract Background Anthropogenic activities are causing unprecedented loss of genetic diversity in many species. However, the effects on genetic diversity from large-scale grafting onto wild plants of crop species are largely undetermined. Iron walnut (Juglans sigillata Dode) is a deciduous nut tree crop endemic to southwestern China with a long history of cultivation. Due to the rapid expansion of the walnut industry, many natural populations are now being replaced by cultivars grafted onto wild rootstocks. However, little is known about the potential genetic consequences of such action on natural populations. Results We sampled the scion and the rootstock from each of 149 grafted individuals within nine wild populations of J. sigillata from Yunnan Province which is the center of walnut diversity and cultivation in China, and examined their genetic diversity and population structure using 31 microsatellite loci. Scions had lower genetic diversity than rootstocks, and this pattern was repeated in seven of the nine examined populations. Among those seven populations, AMOVA and clustering analyses showed a clear genetic separation between all rootstocks and all scions. However, the two remaining populations, both from northern Yunnan, showed genetic similarity between scions and rootstocks, possibly indicating that wild populations here are derived from feralized local cultivars. Moreover, our data indicated probable crop-to-wild gene flow between scions and rootstocks, across all populations. Conclusions Our results indicate that large-scale grafting has been causing genetic diversity erosion and genetic structure breakdown in the wild material of J. sigillata within Yunnan. To mitigate these effects, we caution against the overuse of grafting in wild populations of iron walnut and other crop species and recommend the preservation of natural genotypes through in situ and ex situ conservation.