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Abstract Background The prognosis nutritional index (PNI) and the systemic inflammatory immunological index (SII) are characteristic indicators of the nutritional state and the systemic inflammatory response, respectively. However, there is an unknown combined effect of these indicators in the clinic. Therefore, the practicality of using the SII-PNI score to predict prognosis and tumor response of locally advanced gastric cancer (LAGC) following chemotherapy was the main focus of this investigation. Methods We retrospectively analyzed 181 patients with LAGC who underwent curative resection after neoadjuvant chemotherapy in a prospective study (NCT01516944). We divided these patients into tumour regression grade(TRG) 3 and non-TRG3 groups based on tumor response (AJCC/CAP guidelines). The SII and PNI were assessed and confirmed the cut-off values before treatment. The SII-PNI values varied from 0 to 2, with 2 being the high SII (≥ 471.5) as well as low PNI (≤ 48.6), a high SII or low PNI is represented by a 1 and neither is represented by a 0, respectively. Results 51 and 130 samples had TRG3 and non-TRG3 tumor responses respectively. Patients with TRG3 had substantially higher SII-PNI scores than those without TRG3 (p

Abstract Background This study aimed to develop a novel six-gene expression biomarker panel to enhance the early detection and risk stratification of peritoneal recurrence and micrometastasis in locally advanced gastric cancer (LAGC). Methods We used genome-wide transcriptome profiling and rigorous bioinformatics to identify a six-gene expression biomarker panel. This panel was validated across multiple clinical cohorts using both tissue and liquid biopsy samples to predict peritoneal recurrence and micrometastasis in patients with LAGC. Results Through genome-wide expression profiling, we identified six mRNAs and developed a risk prediction model using 196 samples from a surgical specimen training cohort. This model, incorporating a 6-mRNA panel with clinical features, demonstrated high predictive accuracy for peritoneal recurrence in gastric cancer patients, with an AUC of 0.966 (95% CI: 0.944–0.988). Transitioning from invasive surgical or endoscopic biopsy to noninvasive liquid biopsy, the model retained its predictive efficacy (AUC = 0.963; 95% CI: 0.926–1.000). Additionally, the 6-mRNA panel effectively differentiated patients with or without peritoneal metastasis in 95 peripheral blood specimens (AUC = 0.970; 95% CI: 0.936–1.000) and identified peritoneal micrometastases with a high efficiency (AUC = 0.941; 95% CI: 0.874–1.000). Conclusions Our study provides a novel gene expression biomarker panel that significantly enhances early detection of peritoneal recurrence and micrometastasis in patients with LAGC. The RSA model's predictive capability offers a promising tool for tailored treatment strategies, underscoring the importance of integrating molecular biomarkers with clinical parameters in precision oncology.

Abstract Background China has thousands years of goat breeding and abundant goat genetic resources. Additionally, the Hainan black goat is one of the high-quality local goat breeds in China. In order to conserve the germplasm resources of the Hainan black goat, facilitate its genetic improvement and further protect the genetic diversity of goats, it is urgent to develop a single nucleotide polymorphism (SNP) chip for Hainan black goat. Results In this study, we aimed to design a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets (cGPS). A total of 45,588 candidate SNP sites were obtained, 10,677 of which representative SNP sites were selected to design probes, which finally covered 9,993 intervals and formed a 10K cGPS liquid chip for Hainan black goat. To verify the 10K cGPS liquid chip, some southern Chinese goat breeds and a sheep breed with similar phenotype to the Hainan black goat were selected. A total of 104 samples were used to verify the clustering ability of the 10K cGPS liquid chip for Hainan black goat. The results showed that the detection rate of sites was 97.34% -99.93%. 84.5% of SNP sites were polymorphic. The heterozygosity rate was 3.08%-36.80%. The depth of more than 99.4% sites was above 10X. The repetition rate was 99.66%-99.82%. The average consistency between cGPS liquid chip results and resequencing results was 85.58%. In addition, the phylogenetic tree clustering analysis verified that the SNP sites on the chip had better clustering ability. Conclusion These results indicate that we have successfully realized the development and verification of the 10K cGPS liquid chip for Hainan black goat, which provides a useful tool for the genome analysis of Hainan black goat. Moreover, the 10K cGPS liquid chip is conducive to the research and protection of Hainan black goat germplasm resources and lays a solid foundation for its subsequent breeding work.

Abstract Background People living with HIV (PLHIV) on effective antiretroviral therapy are living near-normal lives. Although they are less susceptible to AIDS-related complications, they remain highly vulnerable to non-communicable diseases. In this exploratory study of older PLHIV (OPLHIV) in Eswatini, we investigated whether epigenetic aging (i.e., the residual between regressing epigenetic age on chronological age) was associated with HIV-related parameters, and whether lifestyle factors modified these relationships. We calculated epigenetic aging focusing on the Horvath, Hannum, PhenoAge and GrimAge epigenetic clocks, and a pace of biological aging biomarker (DunedinPACE) among 44 OPLHIV in Eswatini. Results Age at HIV diagnosis was associated with Hannum epigenetic age acceleration (EAA) (β-coefficient [95% Confidence Interval]; 0.53 [0.05, 1.00], p = 0.03) and longer duration since HIV diagnosis was associated with slower Hannum EAA (− 0.53 [− 1.00, − 0.05], p = 0.03). The average daily dietary intake of fruits and vegetables was associated with DunedinPACE (0.12 [0.03, 0.22], p = 0.01). The associations of Hannum EAA with the age at HIV diagnosis and duration of time since HIV diagnosis were attenuated when the average daily intake of fruits and vegetables or physical activity were included in our models. Diet and self-perceived quality of life measures modified the relationship between CD4+ T cell counts at participant enrollment and Hannum EAA. Conclusions Epigenetic age is more advanced in OPLHIV in Eswatini in those diagnosed with HIV at an older age and slowed in those who have lived for a longer time with diagnosed HIV. Lifestyle and quality of life factors may differentially affect epigenetic aging in OPLHIV. To our knowledge, this is the first study to assess epigenetic aging in OPLHIV in Eswatini and one of the few in sub-Saharan Africa.

Abstract Neutrophil extracellular traps (NETs) have garnered attention for their dual role in host defense and tumor promotion. With their involvement documented across a spectrum of tumors, their influence on the progression of cholangiocarcinoma (CCA) is of paramount interest. We employed immunohistochemistry and immunofluorescence to detect NET deposition in CCA tissues. Through in vitro and in vivo investigation, including CCA organoid and transposon-based models in PAD4 KO mice, we explored the effects of NETs on cell proliferation and metastasis. Molecular insights were gained through RNA sequencing, enzyme linked immunosorbent assay, and chromatin immunoprecipitation. Elevated intratumoral NET deposition within CCA tissues was associated with poor survival. The influence of NETs on CCA proliferation, migration and invasion was primarily mediated by NET-DNA. RNA sequencing unveiled the activation of the NFκB signaling pathway due to NET-DNA stimulation. NET-DNA pull-down assay coupled with mass spectrometry revealed the interaction between NET-DNA and αV integrin (ITGAV), culmination in the activation of the NFκB pathway. Furthermore, NET-DNA directly upregulated the expression of VEGF-A in cancer cells. The study unequivocally establishes NETs as facilitators of CCA progression, orchestrating proliferation, metastasis, and angiogenesis through ITGAV/NFκB pathway activation. This novel insight positions NETs as prospective therapeutic targets for managing CCA patients. By implementing a variety of methodologies and drawing intricate connections between NETs, DNA interactions, and signaling pathways, this research expands our comprehension of the complex interplay between the immune system and cancer progression, offering promising avenues for intervention.

Abstract Background Alport syndrome (AS; OMIM#308,940) is a hereditary kidney disease that progresses over time and is distinguished by hearing loss and ocular irregularities. The syndrome has three subtypes, namely X-linked (XL; OMIM#301,050), autosomal recessive (AR; OMIM#203,780), and autosomal dominant (AD; OMIM#104,200), which are categorized based on their respective modes of inheritance. XLAS is attributed to a pathogenic variant in the COL4A5 (OMIM*303,630) gene, which encodes the α5(IV) chain of type IV collagen (Col-IV). In contrast, ADAS and ARAS are the result of variants in the COL4A3 (OMIM*120,070) and COL4A4 (OMIM*120,131) genes, which encode the α3(IV) and α4(IV) chains of Col-IV, respectively. Typically, the diagnosis of AS necessitates hereditary or pathological assessments. The determination of splicing variants as pathogenic or non-pathogenic based on gene sequencing outcomes is challenging. Methods In this study, we conducted exome sequencing and Sanger sequencing on two unrelated Chinese patients with AS. We identified a deletion variant c.4414delG in the COL4A5 gene and a splicing variant c.4298-20T > A in the same gene. In order to ascertain the impact of c.4298-20T > A on the synthesis of COL4A5 mRNA, we performed experiments involving minigene splicing. Additionally, we predicted the ability of these two variants to affect triple helix formation of α345(IV) using molecular dynamics methods. Results The c.4414delG deletion variant caused a change in the genetic code of the COL4A5 gene. Specifically, it caused a shift in codon 1472 from encoding aspartate to encoding methionine. This shift resulted in a change of 75 amino acids in the protein sequence, ultimately leading to an early stop codon. This premature stop codon caused the production of a truncated α5(IV) chain with a predicted protein effect of p.D1472Mfs. The mRNA of the COL4A5 gene experienced intron 46 retention due to the splicing variant c.4298-20T > A, leading to the inclusion of six additional amino acids between amino acids 1432 and 1433 of the α5(IV) chain. This variant is predicted to have a protein effect of p.(P1432_G1433insDYFVEI). The impact of two variants, c.4414delG and c.4298-20T > A, on the aggregation region for α3(IV), α4(IV), and α5(IV) trimerisation were studied using molecular dynamics simulations. Results showed that the deletion variant c.4414delG had a significantly stronger disruption on NC1, compared to the splicing variant c.4298-20T > A. This difference in impact is consistent with the varying clinical phenotypes observed in the two patients. Based on the American College of Medical Genetics and Genomics (ACMG) classification criteria and guidelines for genetic variants, the deletion variant c.4414delG was rated as pathogenic while the splicing variant c.4298-20T > A was rated as likely-pathogenic. Conclusion Our study has identified two novel pathogenic loci, the deletion variant c.4414delG and the splicing variant c.4298-20T > A, associated with XLAS. This finding expands the genetic spectrum of XLAS. We suggest that molecular dynamics can effectively model the effect of genetic variation on α345(IV) trimerization, which may offer valuable insights into the mechanisms of XLAS pathogenesis.

Abstract Background Previous studies have confirmed that preoperative nutritional-inflammatory indicators can predict prognosis in various malignancies. However, to the best of our knowledge, no study has investigated the assessment of systemic inflammatory immunity index (SII) combined with prognostic nutritional index (PNI) scores to predict prognosis after neoadjuvant treatment with imatinib in locally advanced gastrointestinal stromal tumours (LA-GIST). The aim of this study was to evaluate the predictive value of pretreatment SII-PNI scores in predicting recurrence after neoadjuvant therapy with imatinib in patients with LA-GIST. Methods We retrospectively analyzed 57 patients with LA-GIST who received imatinib neoadjuvant from January 2013 to March 2019. Patients were divided into recurrence and non-recurrence groups according to their follow-up status, and SII and PNI cut-offs were calculated by receiver operating characteristic. The SII-PNI score ranged from 0 to 2 and were categorized into the following: score of 2, high SII (≥ 544.6) and low PNI (≤ 47.2); score of 1, either high SII (≥ 544.6) or low PNI (≤ 47.2); score of 0, no high SII (≥ 544.6) nor low PNI (≤ 47.2). Results All patients received imatinib neoadjuvant therapy for a median treatment period of 8.5 months (ranging from 3.2 to 12.6 months), with 8 patients (14.04%) and 49 patients (85.96%) developing recurrence and non-recurrence, respectively. Patients with a high SII-PNI score had a significantly worse recurrence-free survival time than those with a low SII-PNI score (P = 0.022, 0.046), and had a poorer pathological response (P = 0.014). Multivariate analysis demonstrated that the SII-PNI score was an independent prognostic factor for prediction of recurrence-free survival (P = 0.002). Conclusion The pre-treatment SII-PNI score can be used to predict the efficacy after neoadjuvant treatment with imatinib in patients with LA-GIST, which may be a promising predictor of recurrence-free survival time for patients.

Abstract Background High myopia-related complications have become a major cause of irreversible vision loss. Evaluating the association between potential factors and high myopia can provide insights into pathophysiologic mechanisms and further intervention targets for myopia progression. Method Participants aged 12–25 years from National Health and Nutrition Examination Survey 2001–2006 were selected for the analysis. Myopia was defined as spherical equivalent (sum of spherical error and half of the cylindrical error) of any eyes ≤-0.5 diopters. High myopia was defined as the spherical equivalent of any eye ≤ − 5.00 diopters. Essential variables were selected by Random Forest algorithm and verified by multivariable logistic regression. Results A total of 7,033 participants and 74 potential factors, including demographic (4 factors), physical examination (6 factors), nutritional and serological (45 factors), immunological (9 variables), and past medical history factors (10 factors), were included into the analysis. Random Forest algorithm found that several anthropometric, nutritional, and serological factors were associated with high myopia. Combined with multivariable logistic regression, high levels of serum vitamin A was significantly associated with an increased prevalence of high myopia (adjusted odd ratio = 1.46 for 1 µmol/L increment, 95% confidence interval [CI] 1.01–2.10). Furthermore, we found that neither C-reactive protein nor asthma increased the risk and severity of myopia. Conclusion High levels of serum vitamin A was seemingly associated with an increased prevalence of high myopia. This borderline significant association should be interpreted with caution because the potential increased type I error after the multiple testing. It still needs further investigation regarding the mechanism underlying this association. Neither C-reactive protein nor asthma increased the risk and severity of myopia.

Abstract Pancreatic cancer is the most lethal type of malignancy and is characterized by high invasiveness without severe symptoms. It is difficult to detect PC at an early stage because of the low diagnostic accuracy of existing routine methods, such as abdominal ultrasound, CT, MRI, and endoscopic ultrasound (EUS). Therefore, it is of value to develop new diagnostic techniques for early detection with high accuracy. In this review, we aim to highlight research progress on novel biomarkers, artificial intelligence, and nanomaterial applications on the diagnostic accuracy of pancreatic cancer.

Abstract Objective To compare the outcomes of open reduction and hook plate fixation (ORHPF) and modified TightRope loop plate fixation (MTRLPF) in the treatment of Rockwood type III acromioclavicular joint dislocation. Methods This was a retrospective study. Data on 71 patients with Rockwood type III acromioclavicular joint dislocation who underwent either ORHPF (n = 39) or MTRLPF (n = 32) between January 2016 and October 2019 were extracted and analyzed. Baseline data at injury were compared to evaluate the balance. The disabilities of the arm, shoulder, and hand (DASH) score, Constant-Murley score and visual analog scores (VAS) score at 1 month, 3 months, 6 months and 12 months after operation were compared; further, at 12 months coracoclavicular distance and related complications were evaluated and compared. Results Both groups did not differ for any baseline data. At 1 and 3 months after operation, MTRLPF group exhibited a significantly better performance than the ORHPF group in VAS (1 month: 2.4 ± 1.8 vs 3.0 ± 1.7; 3 months: 1.2 ± 1.4 vs 1.8 ± 1.6), Constant-Murley (1 month: 75.2 ± 11.2 vs 63.8 ± 13.7; 3 months: 81.4 ± 9.8 vs 75.8 ± 10.6), DASH (1 month: 33.6 ± 6.8 vs 40.6 ± 6.1; 3 months: 21.2 ± 7.4 vs 25.6 ± 6.6). At 6 months, only Constant-Murley remained marginally significant (p = 0.048). At 12 months, no statistical difference was observed for any outcome variable (all P > 0.05 for VAS, Constant-Murley and DASH), coracoclavicular distance (12.7 ± 1.6 mm vs 12.2 ± 1.6 mm; P = 0.374), or overall complication rate (P = 0.763). Conclusions For Rockwood type III acromioclavicular joint dislocation, both methods can achieve satisfactory 1-year results, but modified minimally invasive TightRope treatment is more advantageous in early functional recovery at 1 and 3-month follow-ups.

Abstract Background This study was done to observe the incidence of Osteo-line on the femur neck and to explore the clinical application of Osteo-line in osteotomy. Methods Eighty-nine adult femur specimens were selected to observe the incidence of Osteo-line on the femur neck. From August 2015 to January 2019, a total of 278 patients who completed unilateral hip arthroplasty at the Third Hospital of Hebei Medical University were retrospectively included. Patients who accepted osteotomy via Osteo-line on the femur neck were defined as the experimental group (n = 139), and patients who accepted osteotomy via traditional method (The femoral distance 1.5 cm above the trochanter was retained for osteotomy by visual inspection.) were defined as the control group (n = 139). According to the postoperative pelvic X-ray, Photoshop was used to evaluate the leg length discrepancy (LLD) by the CFR-T-LT method. Results Among the 89 specimens, the incidence of anterior Osteo-line was 75.28%, and the incidence of posterior Osteo-line was 100%. According to the clinical application results, the incidence of anterior Osteo-line on the femur neck was 80%, and the incidence of posterior Osteo-line was 100%. The Osteo-line was clearer than those on the femoral specimens. Twenty-six cases had LLD greater than 1 cm (9.29%), including 2 cases in the experimental group and 24 cases in the control group. The average postoperative LLD in the experimental group (0.19 ± 0.38 mm) was significantly shorter than in the control group (0.54 ± 0.51 mm)(P = 0.005). Conclusion The incidence of Osteo-line on the femur neck was high, and patients who accepted osteotomy via Osteo-line on the femur neck can achieve shorter postoperative LLD than the control group.

Abstract Background Several studies have suggested that global DNA methylation in circulating white blood cells (WBC) is associated with breast cancer risk. Methods To address conflicting results and concerns that the findings for WBC DNA methylation in some prior studies may reflect disease effects, we evaluated the relationship between global levels of WBC DNA methylation in white blood cells and breast cancer risk in a case-control study nested within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO) cohort. A total of 428 invasive breast cancer cases and 419 controls, frequency matched on age at entry (55–59, 60–64, 65–69, ≥70 years), year of entry (on/before September 30, 1997, on/after October 1, 1997) and period of DNA extraction (previously extracted, newly extracted) were included. The ratio of 5-methyl-2’ deoxycytidine [5-mdC] to 2’-deoxyguanine [dG], assuming [dG] = [5-mdC] + [2’-deoxycytidine [dC]] (%5-mdC), was determined by liquid chromatography-electrospray ionization-tandem mass spectrometry, an especially accurate method for assessing total genomic DNA methylation. Results Odds ratio (OR) estimates and 95% confidence intervals (CI) for breast cancer risk adjusted for age at entry, year of entry, and period of DNA extraction, were 1.0 (referent), 0.89 (95% CI, 0.6–1.3), 0.88 (95% CI, 0.6–1.3), and 0.84 (95% CI, 0.6–1.2) for women in the highest compared to lowest quartile levels of %5md-C (p for trend = .39). Effects did not meaningfully vary by time elapsed from WBC collection to diagnosis. Discussion These results do not support the hypothesis that global DNA hypomethylation in WBC DNA is associated with increased breast cancer risk prior to the appearance of clinical disease.