Computational Characterization of Undifferentially Expressed Genes with Altered Transcription Regulation in Lung Cancer

A transcriptome profiles the expression levels of genes in cells and has accumulated a huge amount of public data. Most of the existing biomarker-related studies investigated the differential expression of individual transcriptomic features under the assumption of inter-feature independence. Many transcriptomic features without differential expression were ignored from the biomarker lists. This study proposed a computational analysis protocol (mqTrans) to analyze transcriptomes from the view of high-dimensional inter-feature correlations. The mqTrans protocol trained a regression model to predict the expression of an mRNA feature from those of the transcription factors (TFs). The difference between the predicted and real expression of an mRNA feature in a query sample was defined as the mqTrans feature. The new mqTrans view facilitated the detection of thirteen transcriptomic features with differentially expressed mqTrans features, but without differential expression in the original transcriptomic values in three independent datasets of lung cancer. These features were called dark biomarkers because they would have been ignored in a conventional differential analysis. The detailed discussion of one dark biomarker, GBP5, and additional validation experiments suggested that the overlapping long non-coding RNAs might have contributed to this interesting phenomenon. In summary, this study aimed to find undifferentially expressed genes with significantly changed mqTrans values in lung cancer. These genes were usually ignored in most biomarker detection studies of undifferential expression. However, their differentially expressed mqTrans values in three independent datasets suggested their strong associations with lung cancer.

Lipid-anchored proteasomes control membrane protein homeostasis

Protein degradation in eukaryotic cells is mainly carried out by the 26S proteasome, a macromolecular complex not only present in the cytosol and nucleus but also associated with various membranes. How proteasomes are anchored to the membrane and the biological meaning thereof have been largely unknown in higher organisms. Here, we show that N-myristoylation of the Rpt2 subunit is a general mechanism for proteasome-membrane interaction. Loss of this modification in the Rpt2-G2A mutant cells leads to profound changes in the membrane-associated proteome, perturbs the endomembrane system, and undermines critical cellular processes such as cell adhesion, endoplasmic reticulum-associated degradation and membrane protein trafficking. Rpt2G2A/G2A homozygous mutation is embryonic lethal in mice and is sufficient to abolish tumor growth in a nude mice xenograft model. These findings have defined an evolutionarily conserved mechanism for maintaining membrane protein homeostasis and underscored the significance of compartmentalized protein degradation by myristoyl-anchored proteasomes in health and disease.

Carcass traits, proximate composition, amino acid and fatty acid profiles, and mineral contents of meat from Cherry Valley, Chinese crested, and crossbred ducks

Duck meat is known for its taste and high nutritive value. To preserve local genetic diversity while maintaining commercial viability, we obtained a crossbreed (CB) between high-performing Cherry Valley (CV) and traditional Chinese crested (CC) ducks. We compared carcass traits and meat quality characteristics of CB and parental breeds. Meat from the above ducks at their respective marketable ages was evaluated for proximate composition, amino acid and fatty acid profiles, and selected mineral content. The live weights, carcass weights, and breast muscle percentage of CB were higher than CC but lower than CV; the leg muscle of CB was lower than CV and CC. CB had higher intramuscular fat content than CV; its collagen content was lower than CC but higher than CV in breast and thigh muscles. Additionally, the saturated fatty acid content of CB muscle was lower than CV and higher than CC. CB contained more monounsaturated fatty acids than CV and CC. Zn content was higher in CB breast than CV and CC. CB, obtained by crossing CV and CC, has partial advantages over both the breeds suggesting that these characteristics aligned with standards to breed ducks with high-quality meat.

Iodixanol-associated acute kidney injury and prognosis in patients undergoing elective percutaneous coronary intervention: a prospective, multi-center study

OBJECTIVE

To evaluate iodixanol-associated acute kidney injury (AKI) and prognosis in patients undergoing elective percutaneous coronary intervention (PCI).

METHODS

Patients undergoing elective PCI and iodixanol administration were prospectively enrolled in 8 centers between May 2020 and November 2021. The primary endpoint was AKI, defined as an increase in SCr of ≥ 0.3 mg/dL (26.4 μmol/L) or relative elevation ≥ 50% from baseline in the 48-72 h after PCI. Prognosis evaluations included the major adverse renal and cardiovascular events (MARCE): all-cause mortality, new-onset renal replacement therapy (NRRT), non-fatal myocardial infarction, and non-fatal stroke. AKI predictors were identified using multivariable logistic regression and associations between AKI and outcomes were examined using Cox regression.

RESULTS

A total of 3630 patients were included in the final analysis and 2.9% of patients (107/3,630) suffered AKI. Among them, 95.3% (102/107) of AKI were stage 1, and 4.6% (5/107) of stage 2. The multivariable analysis indicated that age over 75-year-old, diabetes, NT-pro-BNP > 300 pg/mL, hemoglobin < 110 g/L, eGFR < 60 mL/min/1.73m2, and diuretics were independently associated with AKI (p < 0.05). After a median follow-up of 13 months, MARCE occurred in 3.6% (131/3630) of the study population, and their incidence was higher in AKI (9.4%, 10/107) vs. non-AKI patients (3.4%, 121/3,523). However, after multivariable adjustment, there was no statistically significant association between AKI and MARCE (p = 0.382).

CONCLUSIONS

In patients undergoing elective PCI, cases of iodixanol-associated AKI were mostly mild and, after multivariable adjustment, held no statistically significant association with MARCE on mid-term follow-up.

CLINICAL RELEVANCE STATEMENT

The incidence of iodixanol-associated AKI was low and mainly limited to mild renal impairment in patients undergoing elective PCI. Physicians should provide adequate contrast for coronary artery evaluation and, at the same time, minimize the contrast volume.

KEY POINTS

• The incidence of iodixanol-associated acute kidney injury was low and mostly limited to mild renal impairment. • Iodixanol administration had no statistically significant impact on the major adverse renal and cardiovascular events in patients undergoing elective percutaneous coronary intervention.

Inhibition of Integrin αvβ3-FAK-MAPK signaling constrains the invasion of T-ALL cells

The role of adhesion receptor integrin αvβ3 in T-ALL was unclear. Firstly, we performed quantitative real-time PCR to assess medullary expression of integrin β3(ITGB3) in T-ALL patients and high ITGB3 expression was relevant with the central nervous system leukemia(CNSL) incidence. Decreasing of cell invasion was observed in Jurkat and Molt4 treated with integrin αvβ3 specific antibody and inhibitor as well as cells with ITGB3 interference. Further, phosphorylation of FAK, cRAF, MEK and ERK decreased in cells with integrin αvβ3 inhibition or interference. Invasion decreased in T-ALL cells treated with FAK and ERK inhibitors. In conclusion, inhibition of integrin αvβ3 signals significantly limits the cell invasion of T-ALL cells.

Study on Immunoregulatory Effects of Fucoidan from Sargassum graminifolium In Vivo and Immunoactivation Activity of Its Fecal Fermentation Products Using Co-Culture Model

Fucoidan, brown seaweed-derived dietary fibers (DFs), can be considered a promising candidate for modulating immune responses. Due to its structural complexity and diversity, it is unclear whether Sargassum graminifolium fucoidans (SGFs) also show marvelous immunoregulatory effects. In the present study, two fractions, SGF-1 and SGF-2, were purified from SGFs by DEAE-Sepharose Fast Flow and Sephacryl S-400 HR column chromatography. We investigated the in vivo immune regulatory activity of SGF-2 and explored the immune activation of SGF-2 fecal fermentation products with in vitro fecal fermentation combined with a Caco-2/RAW264.7 co-culture system. In vivo results exhibited that SGF-2 could elevate the thymus/spleen indices, CD8+ splenic T lymphocyte subpopulations, and CD4+ Foxp3+ splenic Tregs. The 16S high-throughput sequencing results showed that SGF-2 administration significantly increased the relative abundance of Lactobacillus, Alloprevotella, Ruminococcus, and Akkermansia. In addition, it was found that SGF-2 fermented by feces could significantly improve the phagocytosis, NO, and cytokine (TNF-α, IL-6, and IL-10) production of macrophages in the co-culture system. These results indicated that SGFs have the potential to modulate immunity and promote health by affecting the gut microbiota.

Proximity Labeling Expansion Microscopy (PL-ExM) resolves structure of the interactome

Elucidating the spatial relationships within the protein interactome is pivotal to understanding the organization and regulation of protein-protein interactions. However, capturing the 3D architecture of the interactome presents a dual challenge: precise interactome labeling and super-resolution imaging. To bridge this gap, we present the Proximity Labeling Expansion Microscopy (PL-ExM). This innovation combines proximity labeling (PL) to spatially biotinylate interacting proteins with expansion microscopy (ExM) to increase imaging resolution by physically enlarging cells. PL-ExM unveils intricate details of the 3D interactome's spatial layout in cells using standard microscopes, including confocal and Airyscan. Multiplexing PL-ExM imaging was achieved by pairing the PL with immunofluorescence staining. These multicolor images directly visualize how interactome structures position specific proteins in the protein-protein interaction network. Furthermore, PL-ExM stands out as an assessment method to gauge the labeling radius and efficiency of different PL techniques. The accuracy of PL-ExM is validated by our proteomic results from PL mass spectrometry. Thus, PL-ExM is an accessible solution for 3D mapping of the interactome structure and an accurate tool to access PL quality.

Transcriptomic Analysis of the Reduction in Seed Oil Content through Increased Nitrogen Application Rate in Rapeseed (Brassica napus L.)

Nitrogen is essential for improving the seed oil yield of rapeseed (Brassica napus L.). However, the molecular mechanism by which increased nitrogen rates impact seed oil content is largely unknown. Therefore, a field experiment was conducted to determine how three nitrogen application rates (120, 240, and 360 kg ha-1) regulated seed oil content via transcriptomic analysis. The results showed that the seed yield and the protein and total N contents increased from N1 to N3, with average increases of 57.2%, 16.9%, and 79.5%, respectively. However, the seed oil content significantly decreased from N1 to N3, with an average decrease of 8.6%. These results were repeated over a number of years. The quantity of oil protein bodies observed under a transmission electron microscope was in accordance with the ultimate seed oil and protein contents. As the nitrogen application rate increased, a substantial number of genes involved in the photosynthesis, glycolysis, and phenylpropanoid biosynthesis pathways were up-regulated, as were TF families, such as AP2/ERF, MYB, and NAC. The newly identified genes were mainly involved in carbohydrate, lipid, and amino acid metabolism. Metabolic flux analysis showed that most of the genes involved in glycolysis and fatty acid biosynthesis had higher transcript levels in the early development stages. Our results provide new insights into the molecular regulation of rapeseed seed oil content through increased nitrogen application rates.

Genotype 4 HEV infection triggers the initiation and development of acute pancreatitis

The role of HEV infection in AP remains unclear. 1000 patients with AP and 1000 HCs were enrolled, and pancreatitis was evaluated in HEV-infected rhesus macaques. The positive rates of anti-HEV IgG, IgM, and HEV RNA in the AP patients were significantly higher than HCs. With the increase in the severity of AP, the percentage of HEV infection increased. AP patients were divided into AP- and AP + AHE groups. The percentage of severe AP in the AP + AHE group was significantly higher than in the AP- group. HEV infection was one of the main independent risk factors and had high predictive power for AP outcomes. A high level of HEV titer would prolong the recovery time and increase the risk of recurrent AP. Moreover, AP + AHE patients receiving conservative treatment showed a better prognosis. Furthermore, HEV can replicate in the pancreas of rhesus macaques. The pancreatic islet structure was damaged, the tissue was loose after 272 dpi, and a large amount of hyperemia appeared after 770 dpi. HEV infection also caused a large number of inflammatory cells in the pancreas. The pancreas and liver had a comparable viral load. HEV infection affects AP's occurrence, development, and prognosis.

Structural surfaceomics reveals an AML-specific conformation of integrin β2 as a CAR T cellular therapy target

Safely expanding indications for cellular therapies has been challenging given a lack of highly cancer-specific surface markers. Here we explore the hypothesis that tumor cells express cancer-specific surface protein conformations that are invisible to standard target discovery pipelines evaluating gene or protein expression, and these conformations can be identified and immunotherapeutically targeted. We term this strategy integrating cross-linking mass spectrometry with glycoprotein surface capture 'structural surfaceomics'. As a proof of principle, we apply this technology to acute myeloid leukemia (AML), a hematologic malignancy with dismal outcomes and no known optimal immunotherapy target. We identify the activated conformation of integrin β2 as a structurally defined, widely expressed AML-specific target. We develop and characterize recombinant antibodies to this protein conformation and show that chimeric antigen receptor T cells eliminate AML cells and patient-derived xenografts without notable toxicity toward normal hematopoietic cells. Our findings validate an AML conformation-specific target antigen and demonstrate a tool kit for applying these strategies more broadly.

How Antioxidants, Osmoregulation, Genes and Metabolites Regulate the Late Seeding Tolerance of Rapeseeds (Brassica napus L.) during Wintering

Rapeseed seeding dates are largely delayed under the rice-rape rotation system, but how rapeseeds adapt to the delayed environment remains unclear. Here, five seeding dates (20 October, 30 October, 10 November, 20 November and 30 November, T1 to T5) were set and the dynamic differences between two late-seeding-tolerant (LST) and two late-seeding-sensitive (LSS) rapeseed cultivars were investigated in a field experiment. The growth was significantly repressed and the foldchange (LST/LSS) of yield increased from 1.50-T1 to 2.64-T5 with the delay in seeding. Both LST cultivars showed higher plant coverage than the LSS cultivars according to visible/hyperspectral imaging and the vegetation index acquired from an unmanned aerial vehicle. Fluorescence imaging, DAB and NBT staining showed that the LSS cultivars suffered more stress damage than the LST cultivars. Antioxidant enzymes (SOD, POD, CAT, APX) and osmoregulation substances (proline, soluble sugar, soluble protein) were decreased with the delay in seeding, while the LST cultivar levels were higher than those of the LSS cultivars. A comparative analysis of transcriptomes and metabolomes showed that 55 pathways involving 123 differentially expressed genes (DEGs) and 107 differentially accumulated metabolites (DAMs) participated in late seeding tolerance regulation, while 39 pathways involving 60 DEGs and 68 DAMs were related to sensitivity. Levanbiose, α-isopropylmalate, s-ribosyl-L-homocysteine, lauroyl-CoA and argino-succinate were differentially accumulated in both cultivars, while genes including isocitrate dehydrogenase, pyruvate kinase, phosphoenolpyruvate carboxykinase and newgene_7532 were also largely regulated. This study revealed the dynamic regulation mechanisms of rapeseeds on late seeding conditions, which showed considerable potential for the genetic improvement of rapeseed.

[Characteristics and impact factors of SARS-CoV-2 infection in adult patients with relapsed/refractory B-cell non-Hodgkin lymphoma receiving chimeric antigen receptor T-cell therapy]

Objective: To explore the clinical characteristics and treatment of COVID-19 infection in patients with relapsed/refractory B-cell non-Hodgkin lymphoma before and after receiving chimeric antigen receptor T-cell therapy, and study the influencing factors of severe COVID-19 infection in these patients. Methods: The data of 59 patients with relapsed/refractory B-cell non-Hodgkin lymphoma who received chimeric antigen receptor T-cell therapy at the Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology and Department of Hematology, the Second Affiliated Hospital, College of Medicine, Zhejiang University between December 2017 and February 2023, and who were infected with novel coronavirus between December 2022 and February 2023 were retrospectively studied. Patients were divided into light, medium, severe, and critical groups, and the differences between the groups were analyzed using the chi-square test. A univariate logistic regression model was used to evaluate the contribution of each variable and its relationship with severe infection. The chi-square and Fisher's exact tests were used to analyze the differences between the B-cell aplasia and B-cell recovery (BCR) groups. Results: Of the 59 pre- and post-infusion infections, 39 (66.1%) led to mild COVID-19, 9 (15.3%) resulted in moderate COVID-19, 10 (16.9%) resulted in severe COVID-19, and 1 (1.7%) led to critical COVID-19. Moroever, age greater than 55 years, having received autologous hematopoietic stem cell transplantation, progressive disease status, and B-cell aplasia at the time of diagnosis of COVID-19 infection are factors affecting severe infection. Patients with B-cell aplasia had a more severe infection with COVID-19 (P<0.001), a longer duration (P=0.015), a longer antiviral therapy course (P<0.001), and a higher hospitalization rate (P<0.001) than the BCR group. Conclusion: Active prevention and treatment of COVID-19 infection remains a crucial issue requiring urgent attention in managing patients with relapsed/refractory B-cell non-Hodgkin lymphoma treated with chimeric antigen receptor T-cell therapy.

The optimal time restricted eating interventions for blood pressure, weight, fat mass, glucose, and lipids: A meta-analyses and systematic review

BACKGROUND

No previous systematic review or meta-analysis has evaluated the effect of optimal time-restricted eating (TRE) interventions on cardiovascular (CVD) risk factors. This meta-analysis aimed to illustrate the effect of a suitable TRE on CVD risk factors.

METHODS

A systematic review was performed to identify trials reporting the effects of TRE, relative to non-diet controls, on CVD risk factors in humans. A random-effects model was used to evaluate the effect sizes, and the results are expressed as the mean difference (MD) and 95% confidence intervals (CIs). Subgroup analyses were performed to examine the influence of the study population, age, duration of intervention, and baseline mean BMI on the CVD indexes.

RESULTS

TRE intervention significantly reduced systolic pressure (SBP) (MD: -3.45 mmHg; 95%CI:(-6.20,-0.71) mmHg; P = 0.01), body weight (MD: -1.63 Kg; 95%CI:(-2.09,-1.17) Kg; P<0.001), body mass index (BMI) (MD: -0.47 Kg/m2; 95% CI: (-0.72, -0.22) Kg/m2; P<0.001), and fat mass (MD: -0.98 Kg; 95% CI: (-1.51,-0.44) Kg; P<0.001), and reduced blood glucose levels. Based on the results of subgroup analysis, this meta-analysis identified the optimal TRE for BP (with a 6 h feeding window, last eating time point at 6-8 PM, and male participants with obesity and aged ≥ 45 years), obesity (with a 6 h feeding window, last eating time point at 6-8 PM, and female participants aged ≥ 45 years), lipids (with an 8 h feeding window, last eating time point at 6-8 PM, and male participants aged < 45 years), and glucose (with a 10-12 h feeding window, last eating time point before 6 PM, and female participants aged < 45years).

CONCLUSIONS

Relative to a non-diet control, TRE is effective for the improvement of CVD risks. Moreover, individual TRE interventions should be developed for different populations to achieve the most effective health improvement for CVD risk factors.

Unveiling poly(rC)-binding protein 2 as the target protein for curcusone C against prostate cancer: mechanism validation through click chemistry-activity based proteomics profiling approach

BACKGROUND

Prostate cancer is a disease that seriously troubles men. However, there are some inevitable limitations in interventional therapy for prostate cancer patients at present, most of which are caused by low selectivity and high toxic side effects due to unclear drug targets. In this study, we identified the target protein of Curcusone C with anti-prostate cancer potential activity and verified its target and mechanism of action.

METHODS

Click chemistry-activity based proteomics profiling (CC-ABPP) method was used to find target protein of Curcusone C against prostate cancer. Competitive CC-ABPP, drug affinity responsive target stability (DARTS) and surface plasmon resonance (SPR) methods were used to verifying the target protein. Moreover, potential mechanism was validated by western blot in vitro and by hematoxylin-eosin (HE) staining, detection of apoptosis in tumor tissue (TUNEL), and immunohistochemical (IHC) in vivo.

RESULTS

We found that poly(rC)-binding protein 2 (PCBP2) was the target protein of Curcusone C. In addition, Curcusone C might disrupt the Bax/Bcl-2 balance in PC-3 cells by inhibiting the expression of the target protein PCBP2, thereby inducing mitochondrial damage and activation of the mitochondrial apoptosis pathway, and ultimately inducing apoptosis of prostate cancer cells.

CONCLUSIONS

Curcusone C is a potential compound with anti-prostate cancer activity, and this effect occurs by targeting the PCBP2 protein, which in turn may affect the TGF/Smad signaling pathway and Bax/Bcl-2 balance. Our results laid a material and theoretical foundation for Curcusone C, to be widely used in anti-prostate cancer.

Nanometer flat blazed x-ray gratings using ion beam figure correction

With the development of nanometer accuracy stitching interferometry, ion beam figuring (IBF) of x-ray mirrors can now be achieved with unprecedented performance. However, the process of producing x-ray diffraction gratings on these surfaces may degrade the figure quality due to process errors introduced during the ruling of the grating grooves. To address this challenge, we have investigated the post-production correction of gratings using IBF, where stitching interferometry is used to provide in-process feedback. A concern with ion beam correction in this case is that ions will induce enough surface mobility of atoms to cause smoothing of the grating structure and degradation of diffraction efficiency. In this study we found however that it is possible to achieve a nanometer-level planarity of the global grating surface with IBF, while preserving the grating structure. The preservation was so good, that we could not detect a change in the diffraction efficiency after ion beam correction. This is of major importance in achieving ultra-high spectral resolution, and the preservation of brightness for coherent x-ray beams.

Exosomes-mediated transfer of LINC00691 regulates the formation of CAFs and promotes the progression of gastric cancer

OBJECTIVE

Gastric cancer (GC) is one of the malignant tumors with the highest mortality worldwide. Our previous studies have revealed that LINC00691 is up-regulated in serum of GC patients as a novel potential biomarker for GC diagnosis and prognosis. However, the roles of serum exosomal LINC00691 in GC has not been clarified. This study aimed to find the expression pattern of serum exosomal LINC00691 in GC patients and the correlation between the level of serum exosomal LINC00691 and the pathology of gastric cancer patients.

METHODS

We collected the serum of 94 GC patients before surgery and extracted exosomes to detect the expression level of exosomal LINC00691, with 21 healthy volunteers and 17 patients with benign gastric diseases as controls. Surgical GC tissues and paired healthy tissues were collected to culture primary cancer-associated fibroblasts (CAFs) and normal fibroblasts (NFs). We then treated NFs with LINC00691-rich GC cell culture supernatant or exosomes and detected the activation markers and biological functions of the fibroblasts.

RESULTS

The results of real-time qPCR indicated that the serum exosomal LINC00691 of GC patients was significantly higher than that of healthy subjects and patients with benign gastric diseases, and was associated with the clinicopathology of GC patients. More interestingly, when the NFs were treated with GC exosomes, the level of LINC00691 was significantly increased, the cell proliferation and migration were noticeably enhanced, and the ability to accelerate GC cell proliferation and invasion was promoted, which means that the induced fibroblasts gained the properties of CAFs. In addition, we found that knockdown of LINC00691 and the use of the JAK2/STAT3 signaling pathway inhibitor ruxolitinib effectively deprived exosome-containing GC cell supernatants of the effects on NFs.

CONCLUSION

Our study suggested that exosomal LINC00691 promoted NFs to gained the properties of CAFs depending on JAK2/STAT3 signaling pathway as a potential diagnostic biomarker for GC.

Associations of Dietary Anthocyanidins Intake with Bone Health in Children: A Cross-Sectional Study

PURPOSE

Bone health and body composition share several common mechanisms like oxidative stress and inflammation. Anthocyanins have antioxidant and anti-inflammatory properties. We have reported that anthocyanins are associated with better body composition in children, but the associations with bone health have not been elucidated. We aimed to explore the association of anthocyanins with bone mineral content (BMC) and bone mineral density (BMD) at multiple sites in children.

METHODS

In this cross-sectional study, 452 Chinese children aged 6-9 years were recruited. A validated 79-item food frequency questionnaire was used to collect dietary information. BMC and BMD at multiple sites (whole body; whole body excluding head, WBEH; limbs; arms; legs) were measured by dual-energy X-ray.

RESULTS

Higher dietary intake of total anthocyanidins (per one standard deviation increase) was associated with a 1.28-13.6 g (1.31-1.60%, compared to median) higher BMC at all sites and a 3.61-6.96 mg (0.65-0.90%) higher BMD at the whole body, WBEH, and arm sites after controlling for a number of possible covariates. The results were similar and more pronounced for cyanidin, but not for delphinidin and peonidin. Higher dietary intake of cyanidin (per one standard deviation increase) was associated with a 1.33-15.4 g (1.48-1.68%) higher BMC at all sites and a 4.15-7.77 mg (0.66-1.00%) higher BMD at all sites except the legs. No statistically significant associations with BMC or BMD were found for dietary intake of delphinidin and peonidin.

CONCLUSIONS

Higher dietary intake of total anthocyanidins and cyanidins were associated with higher BMC and BMD in Chinese children.

Potential Predictive Value of Intravoxel Incoherent Motion Magnetic Resonance for Xerostomia of Nasopharyngeal Carcinoma

PURPOSE/OBJECTIVE(S)

Xerostomia, caused by radiation-induced parotid damage, is the most commonly reported complications of radiotherapy (RT) to nasopharyngeal carcinoma (NPC). This study aimed to evaluate the value of IVIM MR in monitoring radiation parotid gland damage and predicting the risk of xerostomia.

MATERIALS/METHODS

A total of 54 patients were enrolled and underwent IVIM MR scans at before RT, after the fifth fraction, halfway through the course of RT, and at the end of radiotherapy. The parameters of IVIM MR include pseudo-diffusion coefficient (D*), perfusion fraction (f), and pure diffusion coefficient (D). The degree of xerostomia in NPC patients was assessed before each MR examination using the acute radiation morbidity scoring criteria proposed by the Radiation Therapy Oncology Group (RTOG). Concurrently, the time when the patient first reported suffering from xerostomia was recorded. The IVIM parameters trend throughout the RT, and the relationships between IVIM parameters and xerostomia, were analyzed.

RESULTS

All of the IVIM parameters increased from pre-RT to post-RT significantly (all p < 0.001). The increase rate of D from pre-RT to halfway through the RT was 32.61%, which was significantly higher than 15.64% from halfway to post-RT (p<0.001), indicating that cell necrosis in the first half of treatment is significantly higher than that in the second half. Both D* and F had significantly increased from pre-RT to halfway through the radiotherapy (p<0.001), with an increase rate of 19.58% and 29.38%, respectively. However, no significant increase was observed from Halfway to post-RT (p>0.05), with an increase rate of 4.10% and 8.30%, respectively. This may be due to radiation-induced vasculitic dilation that is significant in the first half of the radiotherapy but plateaus in the second half. Pre-D (OR = 23.85; 95% CI = 2.39, 237.82; p = .007) and pre-D* (OR = 0.75; 95% CI = 0.63, 0.91; p = 0.003) are independent influencing factors for xerostomia at 3 months after the completion of RT. D and F were significantly higher after the fifth fraction compared with Pre-RT (both p<0.05), respectively increased 31.25% and 25.16%. D* increase by 15% (p = 0.081). IVIM scans can assess parotid gland damage early. And the average time of parotid damage underwent IVIM scan was 5.99 ± 0.84 (day), much earlier than 11.84 ± 2.74 (day) according to RTOG.

CONCLUSION

Our study indicates that IVIM MR can dynamically monitor radiotherapy-induced parotid gland damage, and much earlier and objectively than RTOG.

The Epidemiology of Tinea Capitis in Guangxi Province, China

The aim of this study was to analyze the epidemiological characteristics and pathogen spectrum of tinea capitis in Guangxi, southern China. A multicenter prospective descriptive study was conducted in 8 hospitals across Guangxi. From January 2019 to July 2022, one hundred seventy-one (171) patients diagnosed with tinea capitis were included. Demographic data, risk factors, and fungal data were collected. If necessary, species were further identified by morphological or molecular sequencing in the central laboratory. Of the 171 cases of tinea capitis, 74.3% occurred in patients aged 2-8 years. Children with tinea capitis were mainly boys (59.6%) and were more likely than adults to have a history of animal contact (44.2% vs. 33.3%) and zoophilic dermatophyte infection (76.9% vs. 46.7%, P = 0.008). The adults were mainly female (53%) and were more likely than children to have a history of infection with anthropophilic organisms (53.3% vs. 18.9%). The causative agents of tinea capitis in Guangxi were diverse, and the most common pathogen was Microsporum canis (M. cani, n = 98, 62%), followed by Trichophyton mentagrophytes (T. mentagrophytes n = 18, 11.4%) and Trichophyton tonsurans (T. tonsurans n = 12, 7.6%). In addition, tinea capitis caused by Nannizzia incurvata (N. incurvata) and Trichophyton verrucosum (T. verrucosum) was detected in the study. Notably, the proportion of patients with kerion in the study was 41.5% (n = 71), and most of those patients were children (n = 68), especially neglected children living in the rural mountainous areas of Guangxi, where they were unable to receive timely diagnosis and appropriate treatment. In conclusion, the causative agents of tinea capitis in Guangxi, South China, are diverse, and the incidence of kerion is high, indicating that diagnosis and treatment modalities in the region remain grossly inadequate. Clinicians and policy-makers should collaborate to adopt public health strategies to control the disease.

New advances in cross-linking mass spectrometry toward structural systems biology

Elucidating protein-protein interaction (PPI) networks and their structural features within cells is central to understanding fundamental biology and associations of cell phenotypes with human pathologies. Owing to technological advancements during the last decade, cross-linking mass spectrometry (XL-MS) has become an enabling technology for delineating interaction landscapes of proteomes as they exist in living systems. XL-MS is unique due to its capability to simultaneously capture PPIs from native environments and uncover interaction contacts though identification of cross-linked peptides, thereby permitting the determination of both identity and connectivity of PPIs in cells. In combination with high resolution structural tools such as cryo-electron microscopy and AI-assisted prediction, XL-MS has contributed significantly to elucidating architectures of large protein assemblies. This review highlights the latest developments in XL-MS technologies and their applications in proteome-wide analysis to advance structural systems biology.

Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system

Among CRISPR-Cas genome editing systems, Streptococcus pyogenes Cas9 (SpCas9), sourced from a human pathogen, is the most widely used. Here, through in silico data mining, we have established an efficient plant genome engineering system using CRISPR-Cas9 from probiotic Lactobacillus rhamnosus. We have confirmed the predicted 5'-NGAAA-3' PAM via a bacterial PAM depletion assay and showcased its exceptional editing efficiency in rice, wheat, tomato, and Larix cells, surpassing LbCas12a, SpCas9-NG, and SpRY when targeting the identical sequences. In stable rice lines, LrCas9 facilitates multiplexed gene knockout through coding sequence editing and achieves gene knockdown via targeted promoter deletion, demonstrating high specificity. We have also developed LrCas9-derived cytosine and adenine base editors, expanding base editing capabilities. Finally, by harnessing LrCas9's A/T-rich PAM targeting preference, we have created efficient CRISPR interference and activation systems in plants. Together, our work establishes CRISPR-LrCas9 as an efficient and user-friendly genome engineering tool for diverse applications in crops and beyond.

Reconstructing the cytokine view for the multi-view prediction of COVID-19 mortality

BACKGROUND

Coronavirus disease 2019 (COVID-19) is a rapidly developing and sometimes lethal pulmonary disease. Accurately predicting COVID-19 mortality will facilitate optimal patient treatment and medical resource deployment, but the clinical practice still needs to address it. Both complete blood counts and cytokine levels were observed to be modified by COVID-19 infection. This study aimed to use inexpensive and easily accessible complete blood counts to build an accurate COVID-19 mortality prediction model. The cytokine fluctuations reflect the inflammatory storm induced by COVID-19, but their levels are not as commonly accessible as complete blood counts. Therefore, this study explored the possibility of predicting cytokine levels based on complete blood counts.

METHODS

We used complete blood counts to predict cytokine levels. The predictive model includes an autoencoder, principal component analysis, and linear regression models. We used classifiers such as support vector machine and feature selection models such as adaptive boost to predict the mortality of COVID-19 patients.

RESULTS

Complete blood counts and original cytokine levels reached the COVID-19 mortality classification area under the curve (AUC) values of 0.9678 and 0.9111, respectively, and the cytokine levels predicted by the feature set alone reached the classification AUC value of 0.9844. The predicted cytokine levels were more significantly associated with COVID-19 mortality than the original values.

CONCLUSIONS

Integrating the predicted cytokine levels and complete blood counts improved a COVID-19 mortality prediction model using complete blood counts only. Both the cytokine level prediction models and the COVID-19 mortality prediction models are publicly available at http://www.healthinformaticslab.org/supp/resources.php .

[Impact of different diagnostic criteria for assessing mild micro-hepatic encephalopathy in liver cirrhosis: an analysis based on a prospective, multicenter, real-world study]

Objective: To compare the differences in the prevalence of mild micro-hepatic encephalopathy (MHE) among patients with cirrhosis by using the psychometric hepatic encephalopathy score (PHES) and the Stroop smartphone application (Encephal App) test. Methods: This prospective, multi-center, real-world study was initiated by the National Clinical Medical Research Center for Infectious Diseases and the Portal Hypertension Alliance and registered with International ClinicalTrials.gov (NCT05140837). 354 cases of cirrhosis were enrolled in 19 hospitals across the country. PHES (including digital connection tests A and B, digital symbol tests, trajectory drawing tests, and serial management tests) and the Stroop test were conducted in all of them. PHES was differentiated using standard diagnostic criteria established by the two studies in China and South Korea. The Stroop test was evaluated based on the criteria of the research and development team. The impact of different diagnostic standards or methods on the incidence of MHE in patients with cirrhosis was analyzed. Data between groups were differentiated using the t-test, Mann-Whitney U test, and χ (2) test. A kappa test was used to compare the consistency between groups. Results: After PHES, the prevalence of MHE among 354 cases of cirrhosis was 78.53% and 15.25%, respectively, based on Chinese research standards and Korean research normal value standards. However, the prevalence of MHE was 56.78% based on the Stroop test, and the differences in pairwise comparisons among the three groups were statistically significant (kappa = -0.064, P < 0.001). Stratified analysis revealed that the MHE prevalence in three groups of patients with Child-Pugh classes A, B, and C was 74.14%, 83.33%, and 88.24%, respectively, according to the normal value standards of Chinese researchers, while the MHE prevalence rates in three groups of patients with Child-Pugh classes A, B, and C were 8.29%, 23.53%, and 38.24%, respectively, according to the normal value standards of Korean researchers. Furthermore, the prevalence rates of MHE in the three groups of patients with Child-Pugh grades A, B, and C were 52.68%, 58.82%, and 73.53%, respectively, according to the Stroop test standard. However, among the results of each diagnostic standard, the prevalence of MHE showed an increasing trend with an increasing Child-Pugh grade. Further comparison demonstrated that the scores obtained by the number connection test A and the number symbol test were consistent according to the normal value standards of the two studies in China and South Korea (Z = -0.982, -1.702; P = 0.326, 0.089), while the other three sub-tests had significant differences (P < 0.001). Conclusion: The prevalence rate of MHE in the cirrhotic population is high, but the prevalence of MHE obtained by using different diagnostic criteria or methods varies greatly. Therefore, in line with the current changes in demographics and disease spectrum, it is necessary to enroll a larger sample size of a healthy population as a control. Moreover, the establishment of more reliable diagnostic scoring criteria will serve as a basis for obtaining accurate MHE incidence and formulating diagnosis and treatment strategies in cirrhotic populations.

Multi-task prediction-based graph contrastive learning for inferring the relationship among lncRNAs, miRNAs and diseases

MOTIVATION

Identifying the relationships among long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and diseases is highly valuable for diagnosing, preventing, treating and prognosing diseases. The development of effective computational prediction methods can reduce experimental costs. While numerous methods have been proposed, they often to treat the prediction of lncRNA-disease associations (LDAs), miRNA-disease associations (MDAs) and lncRNA-miRNA interactions (LMIs) as separate task. Models capable of predicting all three relationships simultaneously remain relatively scarce. Our aim is to perform multi-task predictions, which not only construct a unified framework, but also facilitate mutual complementarity of information among lncRNAs, miRNAs and diseases.

RESULTS

In this work, we propose a novel unsupervised embedding method called graph contrastive learning for multi-task prediction (GCLMTP). Our approach aims to predict LDAs, MDAs and LMIs by simultaneously extracting embedding representations of lncRNAs, miRNAs and diseases. To achieve this, we first construct a triple-layer lncRNA-miRNA-disease heterogeneous graph (LMDHG) that integrates the complex relationships between these entities based on their similarities and correlations. Next, we employ an unsupervised embedding model based on graph contrastive learning to extract potential topological feature of lncRNAs, miRNAs and diseases from the LMDHG. The graph contrastive learning leverages graph convolutional network architectures to maximize the mutual information between patch representations and corresponding high-level summaries of the LMDHG. Subsequently, for the three prediction tasks, multiple classifiers are explored to predict LDA, MDA and LMI scores. Comprehensive experiments are conducted on two datasets (from older and newer versions of the database, respectively). The results show that GCLMTP outperforms other state-of-the-art methods for the disease-related lncRNA and miRNA prediction tasks. Additionally, case studies on two datasets further demonstrate the ability of GCLMTP to accurately discover new associations. To ensure reproducibility of this work, we have made the datasets and source code publicly available at https://github.com/sheng-n/GCLMTP.

ILC1-derived IFN-γ regulates macrophage activation in colon cancer

BACKGROUND

Tumor-associated macrophages (TAMs) are an important subset of innate immune cells in the tumor microenvironment, and they are pivotal regulators of tumor-promoting inflammation and tumor progression. Evidence has proven that TAM numbers are substantially increased in cancers, and most of these TAMs are polarized toward the alternatively activated M2 phenotype; Thus, these TAMs strongly promote the progression of cancer diseases. Type 1 innate lymphocytes (ILC1s) are present in high numbers in intestinal tissues and are characterized by the expression of the transcription factor T-bet and the secretion of interferon (IFN)-γ, which can promote macrophages to polarize toward the classically activated antitumor M1 phenotype. However, the relationship between these two cell subsets in colon cancer remains unclear.

METHODS

Flow cytometry was used to determine the percentages of M1-like macrophages, M2-like macrophages and ILC1s in colon cancer tissues and paracancerous healthy colon tissues in the AOM/DSS-induced mouse model of colon cancer. Furthermore, ILC1s were isolated and bone marrow-derived macrophages were generated to analyze the crosstalk that occurred between these cells when cocultured in vitro. Moreover, ILC1s were adoptively transferred or inhibited in vivo to explore the effects of ILC1s on tumor-infiltrating macrophages and tumor growth.

RESULTS

We found that the percentages of M1-like macrophages and ILC1s were decreased in colon cancer tissues, and these populations were positively correlated. ILC1s promoted the polarization of macrophages toward the classically activated M1-like phenotype in vitro, and this effect could be blocked by an anti-IFN-γ antibody. The in vivo results showed that the administration of the Group 1 innate lymphocyte-blocking anti-NK1.1 antibody decreased the number of M1-like macrophages in the tumor tissues of MC38 tumor-bearing mice and promoted tumor growth, and adoptive transfer of ILC1s inhibited tumors and increased the percentage of M1-like macrophages in MC38 tumor-bearing mice.

CONCLUSIONS

Our studies preliminarily prove for the first time that ILC1s promote the activation of M1-like macrophages by secreting IFN-γ and inhibit the progression of colon cancer, which may provide insight into immunotherapeutic approaches for colon cancer.

The Hippo pathway noncanonically drives autophagy and cell survival in response to energy stress

The Hippo pathway is known for its crucial involvement in development, regeneration, organ size control, and cancer. While energy stress is known to activate the Hippo pathway and inhibit its effector YAP, the precise role of the Hippo pathway in energy stress response remains unclear. Here, we report a YAP-independent function of the Hippo pathway in facilitating autophagy and cell survival in response to energy stress, a process mediated by its upstream components MAP4K2 and STRIPAK. Mechanistically, energy stress disrupts the MAP4K2-STRIPAK association, leading to the activation of MAP4K2. Subsequently, MAP4K2 phosphorylates ATG8-family member LC3, thereby facilitating autophagic flux. MAP4K2 is highly expressed in head and neck cancer, and its mediated autophagy is required for head and neck tumor growth in mice. Altogether, our study unveils a noncanonical role of the Hippo pathway in energy stress response, shedding light on this key growth-related pathway in tissue homeostasis and cancer.

A Survey of Computational Methods and Databases for lncRNA-MiRNA Interaction Prediction

Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are two prevalent non-coding RNAs in current research. They play critical regulatory roles in the life processes of animals and plants. Studies have shown that lncRNAs can interact with miRNAs to participate in post-transcriptional regulatory processes, mainly involved in regulating cancer development, metastatic progression, and drug resistance. Additionally, these interactions have significant effects on plant growth, development, and responses to biotic and abiotic stresses. Deciphering the potential relationships between lncRNAs and miRNAs may provide new insights into our understanding of the biological functions of lncRNAs and miRNAs, and the pathogenesis of complex diseases. In contrast, gathering information on lncRNA-miRNA interactions (LMIs) through biological experiments is expensive and time-consuming. With the accumulation of multi-omics data, computational models are extremely attractive in systematically exploring potential LMIs. To the best of our knowledge, this is the first comprehensive review of computational methods for identifying LMIs. Specifically, we first summarized the available public databases for predicting animal and plant LMIs. Second, we comprehensively reviewed the computational methods for predicting LMIs and classified them into two categories, including network-based methods and sequence-based methods. Third, we analyzed the standard evaluation methods and metrics used in LMI prediction. Finally, we pointed out some problems in the current study and discuss future research directions. Relevant databases and the latest advances in LMI prediction are summarized in a GitHub repository https://github.com/sheng-n/lncRNA-miRNA-interaction-methods, and we'll keep it updated.

Thioredoxin-interacting protein-activated intracellular potassium deprivation mediates the anti-tumour effect of a novel histone acetylation inhibitor HL23, a fangchinoline derivative, in human hepatocellular carcinoma

INTRODUCTION

Hyperactivated histone deacetylases (HDACs) act as epigenetic repressors on gene transcription and are frequently observed in human hepatocellular carcinoma (HCC). Although multiple pharmacological HDAC inhibitors (HDACis) have been developed, none is available in human HCC.

OBJECTIVES

To investigate the pharmacological effects of a fangchinoline derivative HL23, as a novel HDACi and its molecular mechanisms through TXNIP-mediated potassium deprivation in HCC.

METHODS

Both in vitro assays and orthotopic HCC mouse models were used to investigate the effects of HL23 in this study. The inhibitory activity of HL23 on HDACs was evaluated by in silico studies and cellular assays. Chromatin immunoprecipitation (ChIP) was conducted to confirm the regulation of HL23 on acetylation mark at TXNIP promoter. Genome-wide transcriptome analysis together with bioinformatic analysis were conducted to identify the regulatory mechanisms of HL23. The clinical significance of TXNIP and HDACs was evaluated by analysing publicly available database.

RESULTS

HL23 exerted compatible HDACs inhibition potency as Vorinostat (SAHA) while had superior anti-HCC effects than SAHA and sorafenib. Both in vitro and in vivo studies showed HL23 significantly suppressed HCC progression and metastasis. HL23 significantly upregulated TXNIP expression via regulating acetylation mark (H3K9ac) at TXNIP promoter. TXNIP was responsible for anti-HCC activity of HL23 through mediating potassium channel activity. HDAC1 was predicted to be the target of HL23 and HDAC1lowTXNIPhigh could jointly predict promising survival outcome of patients with HCC. Combination treatment with HL23 and sorafenib could significantly enhance sorafenib efficacy.

CONCLUSION

Our study identified HL23 as a novel HDACi through enhancing acetylation at TXNIP promoter to trigger TXNIP-dependent potassium deprivation and enhance sorafenib efficacy in HCC treatment.

Analysis of the value of echocardiographic parameters in the early diagnosis of preterm infants with bronchopulmonary dysplasia

OBJECTIVE

The objective of this study was to investigate the role of echocardiographic parameters in diagnosing bronchopulmonary dysplasia (BPD) in preterm infants.

PATIENTS AND METHODS

Ninety preterm infants with a gestational age of less than 32 weeks and a weight less than 1.5 kg, admitted to the neonatal intensive care unit of the hospital between January 2020 and January 2021, were selected for the study. The study subjects were divided into two groups: a BPD group (54 cases, observation group) and a non-BPD group (36 cases, control group). The correlation between tricuspid regurgitation (TR) velocity and BPD was investigated by detecting the cardiac function of preterm infants in both groups using a color Doppler ultrasound diagnostic instrument and analyzing the cardiac ultrasound results. The early prediction efficiency of TR velocity (m/s) for BPD was evaluated using the receiver operator characteristic (ROC) curve.

RESULTS

The incidence of patent ductus arteriosus (PDA) and pulmonary hypertension (PH) in the observation group was significantly higher than that in the control group. The levels of left ventricular ejection fraction (LVEF) and left ventricular shorting fraction (LVFS) were significantly lower than those in the control group (p < 0.05). The incidence of patent foramen ovale (PFO), atrial septal defect (ASD), and ventricular septal defect (VSD) in the observation group were not significantly different from the control group (p > 0.05). The proportion of tricuspid regurgitation in the observation group was significantly higher than that in the control group, and the TR velocity was significantly higher than that in the control group. The Spearman correlation analysis showed that TR velocity (m/s) was positively correlated to BPD severity (r = 0.379, p < 0.05). The area under the curve (AUC) for predicting BPD with TR velocity was 0.735. The sensitivity and specificity were 88.0% and 62.6%, respectively, when the TR velocity was 1.45 m/s.

CONCLUSIONS

Echocardiography is useful for understanding the degree of impaired cardiac function in preterm infants and for early detection of PH, which may reduce the mortality rate to a certain extent. The risk of BPD is significantly increased when TR velocity is higher than 1.45 m/s.

Real-World Impact of Prophylactic Growth Factor Use on Timing of Febrile Neutropenia and Infection After High-Risk Chemotherapy

BACKGROUND

Prophylactic growth-factor therapy with granulocyte colony-stimulating factor (G-CSF) reduces the risk of febrile neutropenia (FN) in patients with breast cancer initiating myelosuppressive chemotherapy. However, little is known about the protective benefit early in the chemotherapy cycle.

METHODS

To assess the relationship between G-CSF prophylaxis and incidence of FN/infection in week 1 versus beyond week 1 of the first chemotherapy cycle, a retrospective study was conducted using Medicare claims from 2005 through 2020 among patients with breast cancer initiating high-risk chemotherapy. Two cohorts were compared based on G-CSF prophylaxis within 3 days following chemotherapy initiation. The primary outcome was FN or infection, defined as hospitalization with neutropenia, fever, or infection diagnosis. Secondary outcomes were a stricter definition of FN and infection-related hospitalization. Unadjusted and regression-adjusted proportions of patients experiencing each outcome during week 1 versus beyond week 1 of the first chemotherapy cycle were compared.

RESULTS

Of 78,810 patients meeting all inclusion criteria (>98% female; mean age, 69 years), 79% initiated TC (docetaxel/cyclophosphamide), 14% TCH (docetaxel/carboplatin/trastuzumab), and 7% TAC (docetaxel/doxorubicin/cyclophosphamide). Among patients receiving G-CSF (74%), incidence of first-cycle FN/infection was lower compared with patients not receiving G-CSF (overall, 6% vs 13%; TAC, 12% vs 19%; TC, 6% vs 12%; TCH, 5% vs 15%). However, patients who received G-CSF were generally more likely to experience FN/infection in week 1 (adjusted odds ratio [aOR], 1.24 for all; 1.73 for TAC; 1.35 for TC; and 0.76 for TCH). Results were similar for strictly defined FN (overall aOR, 1.29 for week 1 and 0.12 for beyond week 1) and infection-related hospitalization (overall aOR, 1.33 for week 1 and 0.27 for beyond week 1).

CONCLUSIONS

Overall, the rates of chemotherapy-related FN and infection in week 1 of the first chemotherapy cycle are similar for patients receiving and not receiving G-CSF, suggesting continued risk in week 1 despite prophylactic G-CSF.

The associations between hematological parameters and the incidence of prehypertension and hypertension in children and adolescents: a prospective cohort study

Uncontrolled pediatric hypertension may increase the risk of hypertension in adulthood. Several studies have reported an association between hematological parameters and blood pressure (BP) levels. However, epidemiologic evidence of this association in children and adolescents remains scarce. This study aims to explore the associations between hematological parameters and the incidence of prehypertension and hypertension in children and adolescents. This longitudinal study was conducted with 1368 participants aged 6-8 years from baseline visit to follow-up visit. Compared with participants from the normal blood pressure (BP) group, participants from the elevated BP group had significantly higher baseline red blood cell (RBC) counts, hemoglobin (Hb) counts and hematocrit (Hct) levels (all P < 0.001). A multilevel linear mixed model was conducted to analyze the relationship between hematological parameters and BP levels. The results suggested that SBP, DBP and MAP increased significantly with a quartile increase of levels of hematological parameters (all P < 0.05). Furthermore, a multilevel mixed logistic regression model was used to analyze the risk of per interquartile range increase in hematological parameters on the incidence of prehypertension and hypertension. The risk of prehypertension and hypertension incidence increased by (1.34 (95%CIs: 1.20, 1.50)), (1.38 (95%CIs: 1.24,1.54)), (1.33 (95%CIs: 1.19,1.50)), (1.14 (95%CIs: 1.03,1.26)) fold with a one-quartile increase in levels of RBC, Hb, Hct and Fe, respectively (all P < 0.05). This longitudinal study showed that hematological parameters were positively associated with BP levels in healthy children and adolescents, which excluded the effect of antihypertensive drugs on BP levels that often appeared in adults.

OCMR: A comprehensive framework for optical chemical molecular recognition

Artificial intelligence (AI) has achieved significant progress in the field of drug discovery. AI-based tools have been used in all aspects of drug discovery, including chemical structure recognition. We propose a chemical structure recognition framework, Optical Chemical Molecular Recognition (OCMR), to improve the data extraction capability in practical scenarios compared with the rule-based and end-to-end deep learning models. The proposed OCMR framework enhances the recognition performances via the integration of local information in the topology of molecular graphs. OCMR handles complex tasks like non-canonical drawing and atomic group abbreviation and substantially improves the current state-of-the-art results on multiple public benchmark datasets and one internally curated dataset.

Unravelling the Link between Psychological Distress and Liver Disease: Insights from an Anxiety-like Rat Model and Metabolomics Analysis

Psychological distress is associated with an increase in liver disease mortality. This association highlights the close relationship between psychological and physical health. The underlying mechanism of this association needs to be elucidated. In this study, a rat model of anxiety was developed via compound stress. Changes in the HPA axis and inflammatory factors in the brains of the rats were evaluated for behavioral tests and liver function, respectively. The liver metabolic profiles of the rats were characterized through liquid chromatography-mass spectrometry (LC-MS). Differential metabolites were screened based on the conditions of p < 0.05 and VIP > 1. A pathway enrichment analysis was performed on the metabolomics data using the Ingenuity Pathway Analysis (IPA). Immunofluorescence (IF), immunohistochemistry (IHC), and Western blotting assays were performed to examine the expression of the screened target epidermal growth factor receptor (EGFR) and to elucidate the pathway associated with the mechanism. The results showed the impairment of liver function among the rats in an anxiety-like state. Additionally, 61 differential metabolites in the control and anxiety groups were screened using metabolomics (p < 0.05, VIP > 1). The results of the IPA analysis showed that the key target was EGFR. We also found that an anxiety-like state in rats may cause liver injury through the EFGR/PI3K/AKT/NF-κB pathway, which can lead to the production of inflammatory factors in the liver. Our results revealed a mechanism by which anxiety-like behavior leads to liver damage in rats. The findings of this study provided new insights into the deleterious effects of psychological problems on physical health.

Molecular mechanism for activation of the 26S proteasome by ZFAND5

Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated proteins can increase, we studied mouse ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5's AN1 Zn-finger domain interacts with the Rpt5 ATPase and its C terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Upon proteasome binding, ZFAND5 widens the entrance of the substrate translocation channel, yet it associates only transiently with the proteasome. Dissociation of ZFAND5 then stimulates opening of the 20S proteasome gate. Using single-molecule microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.

HLA-DQ and alcohol in the pathogenesis of irritable bowel syndrome in college students: a case-control study

Some researchers have shown that genetics contribute to the incidence of IBS. However, no research has focused on the interaction between HLA-DQ and living habits in the pathogenesis of IBS. The present study explored the risk factors for IBS in college students of Guangxi Han nationality and explored the interaction between HLA-DQ and living habits on the pathogenesis of IBS. Univariate and multivariate analyses were used to determine the risk factors for IBS. Logistic interaction analysis and the Excel table made by Andersson were used to explore the interaction between genes and living habits in the context of IBS. We found that low expression of HLA-DQ2 and DQ8 were associated with the pathogenesis of IBS, while mild to moderate alcohol consumption was associated with the occurrence of IBS symptoms. Only the HLA-DQ8 gene and alcohol consumption had additive interactions in the context of the occurrence of IBS. In other words, for college students of Guangxi Han nationality, HLA-DQ2 and HLA-DQ8 might be protective against IBS, while alcohol consumption might be an independent risk factor. There was an additive interaction between HLA-DQ8 and alcohol consumption in the occurrence of IBS.

[Association between volatile organic compounds and mortality risk of stroke]

Objective: To investigate the effect of volatile organic compounds (VOCs) exposure in the atmosphere on the risk of daily death from stroke in Guangzhou. Methods: Daily average concentrations of twelve atmospheric VOCs, meteorological factors, and daily deaths for stroke and its subtypes (including ischemic and hemorrhagic stroke) in Guangzhou from 2020 to 2021 were collected. The time-series Poisson generalized additive model was established to analyze the relationship between daily average concentrations of atmospheric VOCs and daily mortality from a stroke on different lag days. The season, gender, and age group further performed stratification analysis. Results: Toluene and n-pentane were associated with a higher mortality risk from stroke and its subtypes. For each interquartile range (IQR) increment in toluene concentration at lag0- 1 days, the RRs for mortality from stroke and hemorrhagic stroke were 1.060 (95%CI: 1.036-1.085) and 1.071 (95%CI: 1.030-1.113), respectively. For each IQR increment in n-pentane concentration, the RR for mortality from ischemic stroke was 1.064 (95%CI: 1.030-1.099). The effect estimates of VOCs may be higher during the cold season and among women and people aged ≥75 years. For each IQR increment in toluene concentration, the RRs for mortality risk of stroke in the cold season and women were 1.099 (95%CI: 1.056-1.143) and 1.085 (95%CI: 1.050-1.120), respectively. For n-pentane, the RR for death risk of stroke in people aged ≥75 years old was 1.072 (95%CI: 1.036-1.109). Results of sensitivity analysis showed that the effect estimates fluctuated less when PM2.5 and O3 were separately introduced for the two-pollutant model, as well as changing the degrees of freedom for covariates. Conclusions: This study suggests that VOCs may be an independent risk factor for daily mortality from stroke. Moreover, Toluene presented the most significant health impact.

Mapping Pregnancy-dependent Sulfhydrome Unfolds Diverse Functions of Protein Sulfhydration in Human Uterine Artery

Uterine artery (UA) hydrogen sulfide (H2S) production is augmented in pregnancy and, on stimulation by systemic/local vasodilators, contributes to pregnancy-dependent uterine vasodilation; however, how H2S exploits this role is largely unknown. S-sulfhydration converts free thiols to persulfides at reactive cysteine(s) on targeted proteins to affect the entire proteome posttranslationally, representing the main route for H2S to elicit its function. Here, we used Tag-Switch to quantify changes in sulfhydrated (SSH-) proteins (ie, sulfhydrome) in H2S-treated nonpregnant and pregnant human UA. We further used the low-pH quantitative thiol reactivity profiling platform by which paired sulfhydromes were subjected to liquid chromatography tandem mass spectrometry-based peptide sequencing to generate site (cysteine)-specific pregnancy-dependent H2S-responsive human UA sulfhydrome. Total levels of sulfhydrated proteins were significantly greater in pregnant vs nonpregnant human UA and further stimulated by treatment with sodium hydrosulfide. We identified a total of 360 and 1671 SSH-peptides from 480 and 1186 SSH-proteins in untreated and sodium hydrosulfide-treated human UA, respectively. Bioinformatics analyses identified pregnancy-dependent H2S-responsive human UA SSH peptides/proteins, which were categorized to various molecular functions, pathways, and biological processes, especially vascular smooth muscle contraction/relaxation. Pregnancy-dependent changes in these proteins were rectified by immunoblotting of the Tag-Switch labeled SSH proteins. Low-pH quantitative thiol reactivity profiling failed to identify low abundance SSH proteins such as KATP channels in human UA; however, immunoblotting of Tag-Switch-labeled SSH proteins identified pregnancy-dependent upregulation of SSH-KATP channels without altering their total proteins. Thus, comprehensive analyses of human UA sulfhydromes influenced by endogenous and exogenous H2S inform novel roles of protein sulfhydration in uterine hemodynamics regulation.

Programmed cell death of periodontal ligament cells

The periodontal ligament is a crucial tissue that provides support to the periodontium. Situated between the alveolar bone and the tooth root, it consists primarily of fibroblasts, cementoblasts, osteoblasts, osteoclasts, periodontal ligament stem cells (PDLSCs), and epithelial cell rests of Malassez. Fibroblasts, cementoblasts, osteoblasts, and osteoclasts are functionally differentiated cells, whereas PDLSCs are undifferentiated mesenchymal stem cells. The dynamic development of these cells is intricately linked to periodontal changes and homeostasis. Notably, the regulation of programmed cell death facilitates the clearance of necrotic tissue and plays a pivotal role in immune response. However, it also potentially contributes to the loss of periodontal supporting tissues and root resorption. These findings have significant implications for understanding the occurrence and progression of periodontitis, as well as the mechanisms underlying orthodontic root resorption. Further, the regulation of periodontal ligament cell (PDLC) death is influenced by both systemic and local factors. This comprehensive review focuses on recent studies reporting the mechanisms of PDLC death and related factors.

Effect of ubiquinol on cardiorespiratory fitness during high-altitude acclimatization and de-acclimatization in healthy adults: the Shigatse CARdiorespiratory fitness study design

Cardiorespiratory function influences exercise capacity and is an important determinant of high-altitude adaptation. Some studies have investigated the characteristics of changes in cardiorespiratory fitness during high-altitude acclimatization. However, studies on changes in cardiorespiratory fitness during high-altitude de-acclimatization are still lacking and have not yet been elucidated. Furthermore, few drugs have been studied to improve cardiorespiratory function during both processes. The Shigatse CARdiorespiratory Fitness (SCARF) study is a single-center, randomized, double-blind, placebo-control clinical trial to explore the effects of ubiquinol on cardiorespiratory fitness during high-altitude acclimatization and de-acclimatization in healthy adults. Participants will be randomly assigned 1:1 to ubiquinol 200 mg daily or a placebo for 14 days before departure until the end of data collection after return in 7 days. Cardiorespiratory fitness is the primary outcome, while acute mountain sickness and high-altitude de-acclimatization symptoms are secondary endpoints. In addition, laboratory measurements, including routine blood tests and serological measurements, will be performed. To the best of our knowledge, the SCARF study will be the first to reveal the changes in the cardiorespiratory fitness characteristics during high-altitude acclimatization and de-acclimatization. Furthermore, the results of this study will contribute to exploring whether ubiquinol supplementation could be beneficial for endurance exercise capacity at different altitudes and help improve adaptation to acute hypoxia and de-acclimatization. Clinical Trial Registration: This study has been registered in the Chinese Clinical Trial Register (www.chictr.org.cn) as ChiCTR2200059900 and ChiCTR2200066328.

Progress of PD-1/PD-L1 signaling in immune response to liver transplantation for hepatocellular carcinoma

Primary liver cancer is one of the most common malignant tumors in China. The vast majority of primary liver cancer are hepatocellular carcinoma. Due to its high incidence and mortality from HCC, HCC has always been a feared type of cancer. Liver transplantation, as one of the important means to treat advanced liver cancer, has brought new hope to patients. However, as patients have been in a state of immunosuppression after liver transplantation, these patients face new problems of HCC recurrence and metastasis. A increasing number of studies have proved that blocking the PD-1/PD-L1 signaling pathway and restoring the immune killing inhibition of T cells can produce better therapeutic effects on tumors and chronic infectious diseases. As a promising treatment in the field of tumor immunotherapy, PD-1/PD-L1 inhibitors have achieved important results in liver cancer patients, but their application in liver transplantation patients is still highly controversial. This paper will introduce the mechanism of action of PD-1/PD-L1 signaling pathway and the current basic and clinical studies of PD-1/PD-L1 signaling pathway associated with immune response in HCC transplantation.

Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis

Survival analysis is critical to cancer prognosis estimation. High-throughput technologies facilitate the increase in the dimension of genic features, but the number of clinical samples in cohorts is relatively small due to various reasons, including difficulties in participant recruitment and high data-generation costs. Transcriptome is one of the most abundantly available OMIC (referring to the high-throughput data, including genomic, transcriptomic, proteomic and epigenomic) data types. This study introduced a multitask graph attention network (GAT) framework DQSurv for the survival analysis task. We first used a large dataset of healthy tissue samples to pretrain the GAT-based HealthModel for the quantitative measurement of the gene regulatory relations. The multitask survival analysis framework DQSurv used the idea of transfer learning to initiate the GAT model with the pretrained HealthModel and further fine-tuned this model using two tasks i.e. the main task of survival analysis and the auxiliary task of gene expression prediction. This refined GAT was denoted as DiseaseModel. We fused the original transcriptomic features with the difference vector between the latent features encoded by the HealthModel and DiseaseModel for the final task of survival analysis. The proposed DQSurv model stably outperformed the existing models for the survival analysis of 10 benchmark cancer types and an independent dataset. The ablation study also supported the necessity of the main modules. We released the codes and the pretrained HealthModel to facilitate the feature encodings and survival analysis of transcriptome-based future studies, especially on small datasets. The model and the code are available at http://www.healthinformaticslab.org/supp/.

Effects of atorvastatin in suppressing pulmonary vascular remodeling in rats with chronic obstructive pulmonary disease

OBJECTIVE

To investigate the effects of atorvastatin calcium on pulmonary vascular remodeling, the authors explored the regulatory mechanism of Histone Deacetylation Enzyme-2 (HDAC2) in rats with Chronic Obstructive Pulmonary Disease (COPD), and provided a new direction for drug treatment in the progression of vascular remodeling.

METHODS

Eighteen female SD rats were randomly divided into control (Group S1), COPD (Group S2), and atorvastatin calcium + COPD (Group S3) groups. A COPD rat model was established by passive smoking and intratracheal injection of Lipopolysaccharide (LPS). Haematoxylin and eosin staining and Victoria Blue + Van Gibson staining were used to observe pathological changes in the lung tissue. The pulmonary vascular inflammation score was calculated, and the degree of pulmonary vascular remodeling was evaluated. The ratio of Muscular Arteries in lung tissue (MA%), the ratio of the vessel Wall Area to the vessel total area (WA%), and the ratio of the vessel Wall Thickness to the vascular outer diameter (WT%) were measured using imaging software. The expression of HDAC2 was measured using western blotting, ELISA (Enzyme-Linked Immunosorbent Assay), and qPCR (Real-time PCR).

RESULTS

Compared with the control group, the degree of pulmonary vascular inflammation and pulmonary vascular remodeling increased in rats with COPD. The WT%, WA%, and lung inflammation scores increased significantly; the expression of HDAC2 and HDAC2mRNA in the serum and lung tissue decreased, and the level of Vascular Endothelial Growth Factor (VEGF) in the lung tissues increased (p < 0.05). Compared with the COPD group, the lung tissues from rats in the atorvastatin group had fewer inflammatory cells, and the vascular pathological changes were significantly relieved. The WT%, WA%, and lung inflammation scores decreased significantly; the expression of HDAC2 and HDAC2mRNA in the serum and lung tissues increased, and the level of VEGF in the lung tissues decreased (p < 0.05).

CONCLUSION

The present study revealed that atorvastatin calcium could regulate the contents and expression of HDAC2 in serum and lung tissues and inhibit the production of VEGF, thereby regulating pulmonary vascular remodeling in a rat model with COPD.

Adolescent exposure to low-dose THC disrupts energy balance and adipose organ homeostasis in adulthood

One of cannabis' most iconic effects is the stimulation of hedonic high-calorie eating-the "munchies"-yet habitual cannabis users are, on average, leaner than non-users. We asked whether this phenotype might result from lasting changes in energy balance established during adolescence, when use of the drug often begins. We found that daily low-dose administration of cannabis' intoxicating constituent, Δ9-tetrahydrocannabinol (THC), to adolescent male mice causes an adult metabolic phenotype characterized by reduced fat mass, increased lean mass and utilization of fat as fuel, partial resistance to diet-induced obesity and dyslipidemia, enhanced thermogenesis, and impaired cold- and β-adrenergic receptor-stimulated lipolysis. Further analyses revealed that this phenotype is associated with molecular anomalies in the adipose organ, including ectopic overexpression of muscle-associated proteins and heightened anabolic processing. Thus, adolescent exposure to THC may promote an enduring "pseudo-lean" state that superficially resembles healthy leanness but might in fact be rooted in adipose organ dysfunction.

The novel compound heterozygous variants identified in a Chinese family with glucose phosphate isomerase deficiency and pathogenicity analysis

BACKGROUND AND AIMS

Glucose phosphate isomerase (GPI) deficiency is an extremely rare autosomal recessive disorder caused by mutations in the GPI gene. In this research, the proband displaying typical manifestations of haemolytic anaemia and his family members were recruited to analyse the pathogenicity of the detected variants.

METHODS

Peripheral blood samples were collected from the family members and genomic DNA was extracted and targeted for capture and sequencing. The effect of the candidate pathogenic variants on splicing was further investigated using the minigene splicing system. The computer simulation was also used for further analysis of the detected data.

RESULTS

The proband carried the compound heterozygous variants c.633 + 3 A > G and c.295G > T in the GPI gene, which have never been reported before. In the genealogy, co-segregation of the mutant genotype with the phenotype was established. The minigene study showed that intronic mutations resulted in abnormal pre-mRNA splicing. Specifically, the two aberrant transcripts: r.546_633del and r.633 + 1_633 + 2insGT were transcribed by the minigene plasmid expressing the c.633 + 3 A > G variant. The missense mutation c.295G > T in exon 3 resulted in altering glycine at codon 87 to cysteine which was predicted to be pathogenic in an in silico analysis. Deeper analyses revealed that the Gly87Cys missense mutation led to steric hindrance. Compared to the wild-type, the mutation G87C led to a significant increase in intermolecular forces.

CONCLUSION

Overall, the novel compound heterozygous variants in the GPI gene contributed to the etiology of the disease. Genetic testing can assist in the diagnosis. The novel gene variants identified in the present study has further expanded the mutational spectrum of GPI deficiency, which can better guide family counselling.

Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing

In Trypanosoma brucei, the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.