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Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteomic analysis overtop the existing data-dependent acquisition (DDA)-MS-based proteomic analysis to enable deep proteome coverage and precise relative quantitative analysis in single-shot liquid chromatography (LC)-MS/MS. However, DIA-MS-based proteomic analysis has not yet been optimized in terms of system robustness and throughput, particularly for its practical applications. We established a single-shot LC-MS/MS system with an MS measurement time of 90 min for a highly sensitive and deep proteomic analysis by optimizing the conditions of DIA and nanoLC. We identified 7020 and 4068 proteins from 200 ng and 10 ng, respectively, of tryptic floating human embryonic kidney cells 293 (HEK293F) cell digest by performing the constructed LC-MS method with a protein sequence database search. The numbers of identified proteins from 200 ng and 10 ng of tryptic HEK293F increased to 8509 and 5706, respectively, by searching the chromatogram library created by gas-phase fractionated DIA. Moreover, DIA protein quantification was highly reproducible, with median coefficients of variation of 4.3% in eight replicate analyses. We could demonstrate the power of this system by applying the proteomic analysis to detect subtle changes in protein profiles between cerebrums in germ-free and specific pathogen-free mice, which successfully showed that >40 proteins were differentially produced between the cerebrums in the presence or absence of bacteria.

Intestinal colonization by bacteria of oral origin has been correlated with several negative health outcomes, including inflammatory bowel disease. However, a causal role of oral bacteria ectopically colonizing the intestine remains unclear. Using gnotobiotic techniques, we show that strains of Klebsiella spp. isolated from the salivary microbiota are strong inducers of T helper 1 (TH1) cells when they colonize in the gut. These Klebsiella strains are resistant to multiple antibiotics, tend to colonize when the intestinal microbiota is dysbiotic, and elicit a severe gut inflammation in the context of a genetically susceptible host. Our findings suggest that the oral cavity may serve as a reservoir for potential intestinal pathobionts that can exacerbate intestinal disease.

Purpose Our aim was to compare postoperative outcomes of laparoscopic and open appendectomies for acute appendicitis in children under the circumstance of widespread use of laparoscopic surgery. Method This study included data on laparoscopic and open appendectomies in children with acute appendicitis from the National Clinical Database, which is a Japanese nationwide surgical database, in 2015. The occurrence rates of complications within 30 days after the surgery and postoperative hospital stay were compared by univariate and multivariate analyses. p  < 0.05 was considered statistically significant. Results This study included 4489 appendectomies, of which 3166 surgeries (70.5%) were performed laparoscopically. Appendectomy was performed for complicated and uncomplicated appendicitis in 1765 (39.3%) and 2724 cases (60.7%), respectively. Postoperative complications within 30 days were observed in 246 operations (5.5%). Organ-space surgical site infection (SSI), deep wound SSIs, and superficial wound SSIs were observed in 2.3%, 1.0%, and 2.4% of operations, respectively. On multivariate analysis, the incidence of postoperative complications (odds ratio 1.21, 95% CI 0.90–1.64, p  = 0.207) and the length of hospital stay (median 4 days in both groups, p  = 0.835) were not significantly different between patients who underwent laparoscopic or open appendectomy. Subgroup analysis in complicated and uncomplicated appendicitis cases also demonstrated no significant differences in the incidence of postoperative complications between those who underwent laparoscopic or open appendectomy. Conclusion This study suggested that the occurrence of postoperative complication and the length of hospital stay in pediatric patients who underwent laparoscopic appendectomy are similar with those in pediatric patients who underwent open appendectomy for acute appendicitis.

Increased levels of proteases, such as trypsin, in the distal intestine have been implicated in intestinal pathological conditions 1 – 3 . However, the players and mechanisms that underlie protease regulation in the intestinal lumen have remained unclear. Here we show that Paraprevotella strains isolated from the faecal microbiome of healthy human donors are potent trypsin-degrading commensals. Mechanistically, Paraprevotella recruit trypsin to the bacterial surface through type IX secretion system-dependent polysaccharide-anchoring proteins to promote trypsin autolysis. Paraprevotella colonization protects IgA from trypsin degradation and enhances the effectiveness of oral vaccines against Citrobacter rodentium . Moreover, Paraprevotella colonization inhibits lethal infection with murine hepatitis virus-2, a mouse coronavirus that is dependent on trypsin and trypsin-like proteases for entry into host cells 4 , 5 . Consistently, carriage of putative genes involved in trypsin degradation in the gut microbiome was associated with reduced severity of diarrhoea in patients with SARS-CoV-2 infection. Thus, trypsin-degrading commensal colonization may contribute to the maintenance of intestinal homeostasis and protection from pathogen infection. Colonization of trypsin-degrading commensal bacteria may contribute to the maintenance of intestinal homeostasis and protection against pathogen infection in humans and mice.

PurposeThis study aimed to investigate the optimal indication and availability of prophylactic innominate artery transection (PIAT).MethodsWe retrospectively analyzed the medical records of the patients with neurological or neuromuscular disorders (NMDs) who underwent PIAT. Meanwhile, we originally defined the tracheal flatting ratio (TFR) and mediastinum–thoracic anteroposterior ratio (MTR) from preoperative chest computed tomography imaging and compared these parameters between non-PIAT and PIAT group.ResultsThere were 13 patients who underwent PIAT. The median age was 22 years. PIAT was planned before in one, simultaneously in five, and after tracheostomy or laryngotracheal separation in seven patients. Image evaluations of the brain to assess circle of Willis were performed in all patients. Appropriate skin incisions with sternotomy to expose the innominate artery were made in four patients. All patients are still alive except one late death without any association with PIAT. No neurological complications occurred in any patients. As significant differences (p < 0.01) between two groups were observed for TFR and MTR, objective validity of the indication of PIAT was found.ConclusionsPIAT is safe and tolerable in case of innominate artery compression of the trachea with NMDs. TFR and MTR are useful objective indexes to judge the indication of PIAT.

Meconium, a non-invasive biomaterial reflecting prenatal substance accumulation, could provide valuable insights into neonatal health. However, the comprehensive protein profile of meconium across gestational ages remains unclear. Here, we conducted an extensive proteomic analysis of first meconium from 259 newborns across varied gestational ages to delineate protein composition and elucidate its relevance to neonatal diseases. The first meconium samples were collected, with the majority obtained before feeding, and the mean time for the first meconium passage from the anus was 11.9 ± 9.47 h. Our analysis revealed 5370 host-derived meconium proteins, which varied depending on sex and gestational age. Specifically, meconium from preterm infants exhibited elevated concentrations of proteins associated with the extracellular matrix. Additionally, the protein profiles of meconium also exhibited unique variations depending on both specific diseases, including gastrointestinal diseases, congenital heart diseases, and maternal conditions. Furthermore, we developed a machine learning model to predict gestational ages using meconium proteins. Our model suggests that newborns with gastrointestinal diseases and congenital heart diseases may have immature gastrointestinal systems. These findings highlight the intricate relationship between clinical parameters and meconium protein composition, offering potential for a novel approach to assess neonatal gastrointestinal health. Meconium, a non-invasive biomaterial reflecting prenatal substance accumulation, holds promise for offering valuable insights into neonatal health. Here, the authors perform an extensive proteomic analysis of meconium samples collected from 259 newborns spanning various gestational ages.

Multiple epiphyseal dysplasia (MED) is a congenital disease causing epiphyseal dysplasia in long bones. Herein, we report a case of a middle-aged man with bilateral knee joint locking symptoms who was diagnosed with multiple epiphyseal dysplasia caused by Matrilin-3 (MATN3) pathogenic variants and was successfully treated with arthroscopic loose body removal. A 48-year-old man has had bilateral knee pain since his twenties and underwent loose body removal of both knees in his thirties. He visited our hospital for worsening locking symptoms in both knees. Twenty years ago, his son had been diagnosed with suspected multiple epiphyseal dysplasia. Genetic and imaging testing confirmed his diagnosis of multiple epiphyseal dysplasia due to Matrilin-3 pathogenic variants. Arthroscopic loose body removal was performed, and the locking symptoms disappeared after surgery. Arthroscopic loose body removal was effective for the locking symptoms in a mild adult case of multiple epiphyseal dysplasias caused by Matrilin-3 pathogenic variants.

Background/Objectives: To elucidate the differential transcriptional and intercellular signaling features of tumor components across various cancers, we conducted a comparative analysis using single-cell RNA sequencing (scRNA-seq). This technology enables detailed characterization of tumor ecosystems and may explain variations in tumor behavior among distinct cancer types. Methods: We analyzed publicly available scRNA-seq datasets (GEO) from seven cancer types—pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC), esophageal squamous cell carcinoma (ESCC), breast cancer (BC), thyroid cancer (TC), gastric cancer (GC), and colorectal cancer (CRC)—to define their unique molecular characteristics and intercellular interactions. Results: PDAC displayed a distinct tumor microenvironment (TME) dominated by myeloid cells (~42%), including abundant CXCR1/CXCR2-expressing tumor-associated neutrophils (TANs) that preferentially interacted with immune rather than cancer cells. The competitive receptor ACKR1 was minimally expressed on endothelial cells, consistent with PDAC hypo-vascularity. In HCC, tumor cells lacked EPCAM and expressed complement and stem cell markers; cancer-associated fibroblasts (CAFs) were scarce, and stellate cells expressed the pericyte marker RGS5. CAFs were abundant in ESCC and BC, with IGF1/2 expression, while in GC, these markers were uniquely found in plasma cells. Since BC and GC subtypes exhibit distinct TME patterns, it is necessary to perform subtype-specific analyses for these cancers. TC showed high expression of tumor-suppressor genes, including HOPX, in tumor cells. Differential interactions and the presence of “dominant signaling cell populations “ with dominant outgoing signals may underlie the heterogeneity in tumor aggressiveness across these cancers. Conclusions: Comparative scRNA-seq analysis of multiple cancers reveals distinct tumor phenotypes and cell–cell communication patterns, offering insights into the molecular architecture of human solid tumors.

The gut microbiome is highly variable among individuals, largely due to differences in host lifestyle and physiology. However, little is known about the underlying processes or rules that shape the complex microbial community. In this paper, we show that the cumulative relative abundance distribution (CRAD) of microbial species can be approximated by a power law function, and found that the power exponent of CRADs generated from 16S rRNA gene and metagenomic data for normal gut microbiomes of humans and mice was similar consistently with ∼0.9. A similarly robust power exponent was observed in CRADs of gut microbiomes during dietary interventions and several diseases. However, the power exponent was found to be ∼0.6 in CRADs from gut microbiomes characterized by lower species richness, such as those of human infants and the small intestine of mice. In addition, the CRAD of gut microbiomes of mice treated with antibiotics differed slightly from those of infants and the small intestines of mice. Based on these observations, in addition to data on the spatial distribution of microbes in the digestive tract, we developed a 3-dimensional mathematical model of microbial proliferation that reproduced the experimentally observed CRAD patterns. Our model indicated that the CRAD may be determined by the ratio of emerging to pre-existing species during non-uniform spatially competitive proliferation, independent of species composition.