Ethylene is the key phytohormone to enhance arsenic resistance in Arabidopsis thaliana.

The toxic metalloid arsenic is prevalent in the environment and poses a threat to nearly all organisms. However, the mechanism by which phytohormones modulate arsenic resistance is not well-understood. Therefore, we analyzed multiple phytohormones based on the results of transcriptome sequencing, content changes, and related mutant growth under arsenic stress. We found that ethylene was the key phytohormone in Arabidopsis thaliana response to arsenic. Further investigation showed the ethylene-overproducing mutant eto1-1 generated less malondialdehyde (MDA), H2O2, and O2•- under arsenic stress compared to wild-type, while the ethylene-insensitive mutant ein2-5 displayed opposite patterns. Compared to wild-type, eto1-1 accumulated a smaller amount of arsenic and a larger amount of non-protein thiols. Additionally, the immediate ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), enhanced resistance to arsenic in wide-type, but not in mutants with impaired detoxification capability (i.e., cad1-3, pad2-1, abcc1abcc2), which confirmed that ethylene regulated arsenic detoxification by enhancing arsenic chelation. ACC also upregulated the expression of gene(s) involved in arsenic detoxification, among which ABCC2 was directly transcriptionally activated by the ethylene master transcription factor ethylene-insensitive 3 (EIN3). Overall, our study shows that ethylene is the key phytohormone to enhance arsenic resistance by reducing arsenic accumulation and promoting arsenic detoxification at both physiological and molecular levels.

Dynamic changes and correlation analysis of microorganisms and flavonoids/ amino acids during white tea storage.

White tea stored for various times have different flavors. However, the mechanism of flavor conversion remains elusive. Flavonoids and amino acids are two typical flavor components in tea. Herein, the contents of 46 flavonoids and 40 amino acids were measured in white tea (Shoumei) stored for 1, 3, 5 and 7 years, respectively. L-tryptophan, L-ornithine and L-theanine contribute to the refreshing taste of Shoumei 1 and 3. Quercetin, rutin and hesperidin contribute to aging charm and grain aroma of Shoumei 5 and 7. 306 bacterial OTUs and 268 fungal OTUs core microbiota existed in all samples. Interestingly, white teas contained higher richness of fungi than bacteria. The correlation analysis showed that the cooperation with bacteria and fungi may result in the flavonoids and amino acids composition changes in white teas during storage. Overall, this study provides new insights into flavor conversion of white tea during storage.

Molecular Mechanisms of Chlorophyll Deficiency in Ilex × attenuata 'Sunny Foster' Mutant.

Ilex × attenuata 'Sunny Foster' represents a yellow leaf mutant originating from I. × attenuata 'Foster#2', a popular ornamental woody cultivar. However, the molecular mechanisms underlying this leaf color mutation remain unclear. Using a comprehensive approach encompassing cytological, physiological, and transcriptomic methodologies, notable distinctions were discerned between the mutant specimen and its wild type. The mutant phenotype displayed aberrant chloroplast morphology, diminished chlorophyll content, heightened carotenoid/chlorophyll ratios, and a decelerated rate of plant development. Transcriptome analysis identified differentially expressed genes (DEGs) related to chlorophyll metabolism, carotenoid biosynthesis and photosynthesis. The up-regulation of CHLD and CHLI subunits leads to decreased magnesium chelatase activity, while the up-regulation of COX10 increases heme biosynthesis-both impair chlorophyll synthesis. Conversely, the down-regulation of HEMD hindered chlorophyll synthesis, and the up-regulation of SGR enhanced chlorophyll degradation, resulting in reduced chlorophyll content. Additionally, genes linked to carotenoid biosynthesis, flavonoid metabolism, and photosynthesis were significantly down-regulated. We also identified 311 putative differentially expressed transcription factors, including bHLHs and GLKs. These findings shed light on the molecular mechanisms underlying leaf color mutation in I. × attenuata 'Sunny Foster' and provide a substantial gene reservoir for enhancing leaf color through breeding techniques.

Co-applied biochar and PGPB promote maize growth and reduce CO2 emission by modifying microbial communities in coal mining degraded soils.

Coal mining is one of the human activities that has the greatest impact on the global carbon (C) cycle and biodiversity. Biochar and plant growth-promoting bacteria (PGPB) have been both used to improve coal mining degraded soils; however, it is uncertain whether the effects of biochar application on soil respiration and microbial communities are influenced by the presence or absence of PGPB and soil nitrogen (N) level in coal mining degraded soils. A pot experiment was carried out to examine whether the effects of biochar addition (0, 1, 2 and 4% of soil mass) on soil properties, soil respiration, maize growth, and microbial communities were altered by the presence or absence of PGPB (i.e. Sphingobium yanoikuyae BJ1) (0, 200 mL suspension (2 × 106 colony forming unit (CFU) mL-1)) and two soil N levels (N0 and N1 at 0 and 0.2 g kg-1 urea- N, respectively). The results showed the presence of BJ1 enhanced the maize biomass relative to the absence of BJ1, particularly in N1 soils, which was related to the discovery of Lysobacter and Nocardioides that favor plant growth in N1 soils. This indicates a conversion in soil microbial communities to beneficial ones. The application of biochar at a rate of 1% decreased the cumulative CO2 regardless of the presence or absence of BJ1; BJ1 increased the ß-glucosidase (BG) activities, and BG activities were also positively correlated with RB41 strain with high C turnover in N1 soils, which indicates that the presence of BJ1 improves the C utilization rates of RB41, decreasing soil C mineralization. Our results highlight that biochar addition provided environmental benefits in degraded coal mining soils, and the direction and magnitude of these effects are highly dependent on the presence of PGPB and the soil N level.

A prognostic metabolism-related gene signature associated with the tumor immune microenvironment in neuroblastoma.

Neuroblastoma (NB) is the most prevalent malignant solid tumor in children. Tumor metabolism, including lipid, amino acid, and glucose metabolism, is intricately linked to the genesis and progression of tumors. This study aimed to establish a prognostic gene signature for NB patients, based on metabolism-related genes, and to investigate a treatment approach that could enhance the survival rate of high-risk NB patients. From the NB dataset GSE49710, we identified metabolism-related gene markers utilizing the "limma" R package and univariate Cox analysis combined with least absolute shrinkage and selection operator (LASSO) regression analysis. We explored the correlation between these gene markers and the overall survival of NB patients. Gene set enrichment analysis (GSEA) and single-sample GSEA algorithms were used to assess the differences in metabolism and immune status. Furthermore, we examined the association between metabolic subgroups and drug responsiveness. Concurrently, data downloaded from TARGET and MTAB were used for external verification. Using multicolor immunofluorescence and immunohistochemistry, we investigated the relationship between the lipid metabolism-related gene ELOVL6 with both the International Neuroblastoma Staging System classification of NB and survival rate. Finally, we explored the effect of high ELOVL6 expression on the immune microenvironment in NB using flow cytometry. We identified an eight-gene signature comprising metabolism-related genes in NB: ELOVL6, OSBPL9, RPL27A, HSD17B3, ACHE, AKR1C1, PIK3R1, and EPHX2. This panel effectively predicted disease-free survival, and was validated using an internal dataset from GSE49710 and two external datasets from the TARGET and MTAB databases. Moreover, our findings confirmed that ELOVL6 fosters an immunosuppressive microenvironment and contributes to the malignant progression in NB. The eight-gene signature is significant in predicting the prognosis of NB, effectively classifying patients into high- and low-risk groups. This classification may guide the development of innovative treatment strategies for these patients. Notably, the signature gene ELOVL6 markedly encourages an immunosuppressive microenvironment and malignant progression in NB.

Prognostic significance of grade of malignancy based on histopathological differentiation and Ki-67 in pancreatic ductal adenocarcinoma.

OBJECTIVE: Tumor cell malignancy is indicated by histopathological differentiation and cell proliferation. Ki-67, an indicator of cellular proliferation, has been used for tumor grading and classification in breast cancer and neuroendocrine tumors. However, its prognostic significance in pancreatic ductal adenocarcinoma (PDAC) remains uncertain. METHODS: Patients who underwent radical pancreatectomy for PDAC were retrospectively enrolled, and relevant prognostic factors were examined. Grade of malignancy (GOM), a novel index based on histopathological differentiation and Ki-67, is proposed, and its clinical significance was evaluated. RESULTS: The optimal threshold for Ki-67 was determined to be 30%. Patients with a Ki-67 expression level > 30% rather than ≤ 30% had significantly shorter 5-year overall survival (OS) and recurrence-free survival (RFS). In multivariate analysis, both histopathological differentiation and Ki-67 were identified as independent prognostic factors for OS and RFS. The GOM was used to independently stratify OS and RFS into 3 tiers, regardless of TNM stage and other established prognostic factors. The tumor-node-metastasis-GOM stage was used to stratify survival into 5 distinct tiers, and surpassed the predictive performance of TNM stage for OS and RFS. CONCLUSIONS: Ki-67 is a valuable prognostic indicator for PDAC. Inclusion of the GOM in the TNM staging system may potentially enhance prognostic accuracy for PDAC.

A low-cost, portable, dual-function readout device for amplification-based point-of-need diagnostics.

IMPORTANCE: The first critical step in timely disease management is rapid disease identification, which is ideally on-site detection. Of all the technologies available for disease identification, nucleic acid amplification-based diagnostics are often used due to their specificity, sensitivity, adaptability, and speed. However, the modules to interpret amplification results rapidly, reliably, and easily in resource-limited settings at point-of-need (PON) are in high demand. Therefore, we developed a portable, low-cost, and easy-to-perform device that can be used for amplification readout at PON to enable rapid yet reliable disease identification by users with minimal training.

A novel clinical model for risk prediction and stratification of new-onset diabetes mellitus after distal pancreatectomy.

Background: The incidence of new-onset diabetes mellitus (NODM) after distal pancreatectomy (DP) remains high. Few studies have focused on NODM in patients with pancreatic benign or low-grade malignant lesions (PBLML). This study aimed to develop and validate an effective clinical model for risk prediction and stratification of NODM after DP in patients with PBLML. Methods: A follow-up survey was conducted to investigate NODM in patients without preoperative DM who underwent DP. Four hundred and forty-eight patients from Peking Union Medical College Hospital (PUMCH) and 178 from Guangdong Provincial People's Hospital (GDPH) met the inclusion criteria. They constituted the training cohort and the validation cohort, respectively. Univariate and multivariate Cox regression, as well as least absolute shrinkage and selection operator (LASSO) analyses, were used to identify the independent risk factors. The nomogram was constructed and verified. Concordance index (C-index), receiver operating characteristic (ROC) curve, calibration curves, and decision curve analysis (DCA) were applied to assess its predictive performance and clinical utility. Accordingly, the optimal cut-off point was determined by maximally selected rank statistics method, and the cumulative risk curves for the high- and low-risk populations were plotted to evaluate the discrimination ability of the nomogram. Results: The median follow-up duration was 42.8 months in the PUMCH cohort and 42.9 months in the GDPH cohort. The postoperative cumulative 5-year incidences of DM were 29.1% and 22.1%, respectively. Age, body mass index (BMI), length of pancreatic resection, intraoperative blood loss, and concomitant splenectomy were significant risk factors. The nomogram demonstrated significant predictive utility for post-pancreatectomy DM. The C-indexes of the nomogram were 0.739 and 0.719 in the training and validation cohorts, respectively. ROC curves demonstrated the predictive accuracy of the nomogram, and the calibration curves revealed that prediction results were in general agreement with the actual results. The considerable clinical applicability of the nomogram was certified by DCA. The optimal cut-off point for risk prediction value was 2.88, and the cumulative risk curves of each cohort showed significant differences between the high- and low-risk groups. Conclusions: The nomogram could predict and identify the NODM risk population, and provide guidance to physicians in monitoring and controlling blood glucose levels in PBLML patients after DP.

Elevated carbon dioxide concentrations increase the risk of Cd exposure in rice.

Since the Industrial Revolution, crops have been exposed to various changes in the environment, including elevated atmospheric carbon dioxide (CO2) concentration and cadmium (Cd) pollution in soil. However, information about how combined changes affect crop is limited. Here, we have investigated the changes of japonica and indica rice subspecies seedlings under elevated CO2 level (1200 ppm) and Cd exposure (5 µM Cd) conditions compared with ambient CO2 level (400 ppm) and without Cd exposure in CO2 growth chambers with hydroponic experiment. The results showed that elevated CO2 levels significantly promoted seedling growth and rescued the growth inhibition under Cd stress. However, the elevated CO2 levels led to a significant increase in the shoot Cd accumulation of the two rice subspecies. Especially, the increase of shoot Cd accumulation in indica rice was more than 50% compared with control. Further investigation revealed that the decreases in the photosynthetic pigments and photosynthetic rates caused by Cd were attenuated by the elevated CO2 levels. In addition, elevated CO2 levels increased the non-enzymatic antioxidants and significantly enhanced the ascorbate peroxidase (APX) and glutathione reductase (GR) activities, alleviating the lipid peroxidation and reactive oxygen species (ROS) accumulation induced by Cd. Overall, the research revealed how rice responded to the elevated CO2 levels and Cd exposure, which can help modify agricultural practices to ensure food security and food safety in a future high-CO2 world.

Effects of co-applied biochar and plant growth-promoting bacteria on soil carbon mineralization and nutrient availability under two nitrogen addition rates.

In the background of climate warming, the demand for improving soil quality and carbon (C) sequestration is increasing. The application of biochar to soil has been considered as a method for mitigating climate change and enhancing soil fertility. However, it is uncertain whether the effects of biochar application on C-mineralization and N transformation are influenced by the presence or absence of plant growth-promoting bacteria (PGPB) and soil nitrogen (N) level. An incubation study was conducted to investigate whether the effects of biochar application (0 %, 1 %, 2 % and 4 % of soil mass) on soil respiration, N status, and microbial attributes were altered by the presence or absence of PGPB (i.e., Sphingobium yanoikuyae BJ1) under two soil N levels (N0 and N1 soils as created by the addition of 0 and 0.2 g kg-1 urea- N, respectively). The results showed that biochar, BJ1 strain and their interactive effects on cumulative CO2 emissions were not significant in N0 soils, while the effects of biochar on the cumulative CO2 emissions were dependent on the presence or absence of BJ1 in N1 soils. In N1 soils, applying biochar at 2 % and 4 % increased the cumulative CO2 emissions by 141.0 % and 166.9 %, respectively, when BJ1 was absent. However, applying biochar did not affect CO2 emissions when BJ1 was present. In addition, the presence of BJ1 generally increased ammonium contents in N0 soils, but decreased nitrate contents in N1 soils relative to the absence of BJ1, which indicates that the combination of biochar and BJ1 is beneficial to play the N fixation function of BJ1 in N0 soils. Our results highlight that biochar addition influences not only soil C mineralization but also soil available N, and the direction and magnitude of these effects are highly dependent on the presence of PGPB and the soil N level.

Changing the diagnostic paradigm for sugarcane: development of a mill-based diagnostic for ratoon stunting disease in crude cane juice.

The availability of efficient diagnostic methods is crucial to monitor the incidence of crop diseases and implement effective management strategies. One of the most important elements in diagnostics, especially in large acreage crops, is the sampling strategy as hundreds of thousands of individual plants can grow in a single farm, making it difficult to assess disease incidence in field surveys. This problem is compounded when there are no external disease symptoms, as in the case for the ratoon stunting disease (RSD) in sugarcane. We have developed an alternative approach of disease surveillance by using the crude cane juice expressed at the sugar factory (mill). For this purpose, we optimized DNA extraction and amplification conditions for the bacterium Leifsonia xyli subsp xyli, the causal agent of RSD. The use of nucleic acid dipsticks and LAMP isothermal amplification allows to perform the assays at the mills, even in the absence of molecular biology laboratories. Our method has been validated using the qPCR industry standard and shows higher sensitivity. This approach circumvents sampling limitations, providing RSD incidence evaluation on commercial crops and facilitating disease mapping across growing regions. There is also potential is to extend the technology to other sugarcane diseases as well as other processed crops.

A new staging system for postoperative prognostication in pancreatic ductal adenocarcinoma.

The current TNM staging system for pancreatic ductal adenocarcinoma (PDAC) has revised the definitions of T and N categories as well as stage groups. However, studies validating these modifications have yielded inconsistent results. The existing TNM staging system in prognostic prediction remains unsatisfactory. The prognosis of PDAC is closely associated with pathological and biological factors. Herein, we propose a new staging system incorporating distant metastasis, postoperative serum levels of CA19-9 and CEA, tumor size, lymph node metastasis, lymphovascular involvement, and perineural invasion to enhance the accuracy of prognosis assessment. The proposed staging system exhibited a strong correlation with both overall survival and recurrence-free survival, effectively stratifying survival into five distinct tiers. Additionally, it had favorable discrimination and calibration. Thus, the proposed staging system demonstrates superior prognostic performance compared to the TNM staging system, and can serve as a valuable complementary tool to address the limitations of TNM staging in prognostication.

Laboratory scoring system to predict hepatic indocyanine green clearance ability during fluorescence imaging-guided laparoscopic hepatectomy.

BACKGROUND: Indocyanine green (ICG) fluorescence played an important role in tumor localization and margin delineation in hepatobiliary surgery. However, the preoperative regimen of ICG administration was still controversial. Factors associated with tumor fluorescence staining effect were unclear. AIM: To investigate the preoperative laboratory indexes corelated with ICG fluorescence staining effect and establish a novel laboratory scoring system to screen specifical patients who need ICG dose adjustment. METHODS: To investigate the predictive indicators of ICG fluorescence characteristics in patients undergoing laparoscopic hepatectomy from January 2018 to January 2021 were included. Blood laboratory tests were completed within 1 wk before surgery. All patients received 5 mg ICG injection 24 h before surgery for preliminary tumor imaging. ImageJ software was used to measure the fluorescence intensity values of regions of interest. Correlation analysis was used to identify risk factors. A laboratory risk model was established to identify individuals at high risk for high liver background fluorescence. RESULTS: There were 110 patients who were enrolled in this study from January 2019 to January 2021. The mean values of fluorescence intensity of liver background (FI-LB), fluorescence intensity of gallbladder, and fluorescence intensity of target area were 18.87 ± 17.06, 54.84 ± 33.29, and 68.56 ± 36.11, respectively. The receiver operating characteristic (ROC) curve showed that FI-LB was a good indicator for liver clearance ability [area under the ROC curve (AUC) = 0.984]. Correlation analysis found pre-operative aspartate aminotransferase, alanine aminotransferase, gamma-glutamyl transpeptidase, adenosine deaminase, and lactate dehydrogenase were positively associated with FI-LB and red blood cell, cholinesterase, and were negatively associated with FI-LB. Total laboratory risk score (TLRS) was calculated according to ROC curve (AUC = 0.848, sensitivity = 0.773, specificity = 0.885). When TLRS was greater than 6.5, the liver clearance ability of ICG was considered as poor. CONCLUSION: Preoperative laboratory blood indicators can predict hepatic ICG clearance ability. Surgeons can adjust the dose and timing of ICG preoperatively to achieve better liver fluorescent staining.

Functional Characterization of Lycopene ß- and ε-Cyclases from a Lutein-Enriched Green Microalga Chlorella sorokiniana FZU60.

Lutein is a high-value carotenoid with many human health benefits. Lycopene ß- and ε-cyclases (LCYB and LCYE, respectively) catalyze the cyclization of lycopene into distinct downstream branches, one of which is the lutein biosynthesis pathway, via α-carotene. Hence, LCYB and LCYE are key enzymes in lutein biosynthesis. In this study, the coding genes of two lycopene cyclases (CsLCYB and CsLCYE) of a lutein-enriched marine green microalga, Chlorella sorokiniana FZU60, were isolated and identified. A sequence analysis and computational modeling of CsLCYB and CsLCYE were performed using bioinformatics to identify the key structural domains. Further, a phylogenetic analysis revealed that CsLCYB and CsLCYE were homogeneous to the proteins of other green microalgae. Subcellular localization tests in Nicotiana benthamiana showed that CsLCYB and CsLCYE localized in chloroplasts. A pigment complementation assay in Escherichia coli revealed that CsLCYB could efficiently ß-cyclize both ends of lycopene to produce ß-carotene. On the other hand, CsLCYE possessed a strong ε-monocyclase activity for the production of δ-carotene and a weak ε-bicyclic activity for the production of ε-carotene. In addition, CsLCYE was able to catalyze lycopene into ß-monocyclic γ-carotene and ultimately produced α-carotene with a ß-ring and an ε-ring via γ-carotene or δ-carotene. Moreover, the co-expression of CsLCYB and CsLCYE in E. coli revealed that α-carotene was a major product, which might lead to the production of a high level of lutein in C. sorokiniana FZU60. The findings provide a theoretical foundation for performing metabolic engineering to improve lutein biosynthesis and accumulation in C. sorokiniana FZU60.

Survival outcomes of neoadjuvant therapy followed by radical resection versus upfront surgery for stage I-III pancreatic ductal adenocarcinoma: a retrospective cohort study.

BACKGROUND: Neoadjuvant therapy remains controversial in treating resectable pancreatic ductal adenocarcinoma (PDAC) patients. This study aims to assess the impact of neoadjuvant therapy on survival in patients with PDAC according to their clinical stage. METHODS: Patients with resected clinical Stage I-III PDAC from 2010 to 2019 were identified in the surveillance, epidemiology, and end results database. A propensity score matching method was utilized within each stage to reduce potential selection bias between patients who underwent neoadjuvant chemotherapy followed by surgery and patients who underwent upfront surgery. An overall survival (OS) analysis was performed using the Kaplan-Meier method and a multivariate Cox proportional hazards model. RESULTS: A total of 13 674 patients were included in the study. The majority of the patients ( N =10 715, 78.4%) underwent upfront surgery. Patients receiving neoadjuvant therapy followed by surgery had significantly longer OS than those with upfront surgery. Subgroup analysis revealed that the neoadjuvant chemoradiotherapy group's OS is comparable to neoadjuvant chemotherapy. In clinical Stage IA PDAC, there was no difference in survival between the neoadjuvant treatment and upfront surgery groups before or after matching. In stage IB-III patients, neoadjuvant therapy followed by surgery improved OS before and after matching compared to upfront surgery. The results revealed the same OS benefits using the multivariate Cox proportional hazards model. CONCLUSION: Neoadjuvant therapy followed by surgery could improve OS over upfront surgery in Stage IB-III PDAC but did not provide a significant survival advantage in Stage IA PDAC.

Effect of Drying Kinetics, Volatile Components, Flavor Changes and Final Quality Attributes of Moslae herba during the Hot Air Thin-Layer Drying Process.

Moslae herba is considered to be a functional food ingredient or nutraceutical due to its rich bioactive components. The present research was carried out to investigate the effects of different temperatures (40 °C, 50 °C and 60 °C) on the drying characteristics, textural properties, bioactive compounds, flavor changes and final quality attributes of Moslae herba during the hot air-drying process. The results showed that the Midilli model could effectively simulate the drying process of Moslae herba. The effective moisture diffusivity ranged from 3.14 × 10-5 m2/s to 7.39 × 10-5 m2/s, and the activation energy was estimated to be 37.29 kJ/mol. Additionally, scanning electron microscopy (SEM) images of Moslae herba samples showed the shrinkage of the underlying epidermal layers and glandular trichomes. In total, 23 volatile compounds were detected in Moslae herba. Among them, the content of thymol increased from 28.29% in fresh samples to 56.75%, 55.86% and 55.62% in samples dried at temperatures of 40 °C, 50 °C and 60 °C, respectively, while the other two components, p-cymene and γ-terpinene, decreased with an increase in the temperature. Furthermore, both radar fingerprinting and principal component analysis (PCA) of the electronic nose (E-nose) showed that the flavor substances significantly altered during the drying process. Eventually, drying Moslae herba at 60 °C positively affected the retention of total phenolics, total flavonoids and the antioxidant capacity as compared with drying at 40 °C and 50 °C. The overall results elucidated that drying Moslae herba at the temperature of 60 °C efficiently enhanced the final quality by significantly reducing the drying time and maintaining the bioactive compounds.

Quantitative annotations of T-Cell repertoire specificity.

The specificity of a T-cell receptor (TCR) repertoire determines personalized immune capacity. Existing methods have modeled the qualitative aspects of TCR specificity, while the quantitative aspects remained unaddressed. We developed a package, TCRanno, to quantify the specificity of TCR repertoires. We created deep-learning-based, epitope-aware vector embeddings to infer individual TCR specificity. Then we aggregated clonotype frequencies of TCRs to obtain a quantitative profile of repertoire specificity at epitope, antigen and organism levels. Applying TCRanno to 4195 TCR repertoires revealed quantitative changes in repertoire specificity upon infections, autoimmunity and cancers. Specifically, TCRanno found cytomegalovirus-specific TCRs in seronegative healthy individuals, supporting the possibility of abortive infections. TCRanno discovered age-accumulated fraction of severe acute respiratory syndrome coronavirus 2 specific TCRs in pre-pandemic samples, which may explain the aggressive symptoms and age-related severity of coronavirus disease 2019. TCRanno also identified the encounter of Hepatitis B antigens as a potential trigger of systemic lupus erythematosus. TCRanno annotations showed capability in distinguishing TCR repertoires of healthy and cancers including melanoma, lung and breast cancers. TCRanno also demonstrated usefulness to single-cell TCRseq+gene expression data analyses by isolating T-cells with the specificity of interest.

Peripheral Th and NK cells are associated with response to lenvatinib plus PD-1 inhibitor in unresectable hepatocellular carcinoma.

The value of peripheral blood lymphocyte subpopulations in predicting responses to lenvatinib combination with programmed death-1 (PD-1) inhibitors in unresectable hepatocellular carcinoma (HCC) was investigated. Fifteen patients received objective responses (OR) and sixteen patients had non-objective responses (NOR) were analyzed. The counts of peripheral blood lymphocyte subpopulations from patients were measured before treatment, second (at week 3), and third doses (at week 6) of the PD-1 inhibitor administration, and correlated with responses. Helper T (Th) cells and natural killers (NK) cells were more abundant in the OR group and found to be important predictors of OR in a stepwise multivariate logistic regression analysis. These cutoff values of Th and NK cells could help to distinguish OR from NOR cases accurately and provide clinical benefits.

The characteristics of Laennec's capsule around the hepatic veins: A histological study based on 71 liver surgical specimens.

Background: Laennec's capsule is a fibrous membrane attached to the surface of the liver, which is independent of the hepatic veins. However, the presence of Laennec's capsule surrounding the peripheral hepatic veins is controversial. This study aims to describe the characteristic of Laennec's capsule around the hepatic veins at all levels. Methods: Seventy-one hepatic surgical specimens were collected along the cross and longitudinal sections of the hepatic vein. Tissue sections of 3-4 mm were cut and stained with hematoxylin and eosin (H&E), resorcinol-fuchsin (R&F), and Victoria blue (V&B). Elastic fibers were observed around the hepatic veins. They were measured using K-Viewer software. Results: Morphologically, we observed a thin, dense fibrous layer (so-called Laennec's capsule) around the hepatic veins at all levels, which was different from the thick elastic fibers of the hepatic vein wall. Therefore, there was a potential gap between Laennec's capsule and the hepatic veins. Laennec's capsule was visualized significantly better with R&F and V&B staining compared to H&E staining. The thickness of Laennec's capsule around the main, first, and secondary branches of the hepatic vein were 79.86 ± 24.20 µm, 48.41 ± 18.25 µm, and 23.56 ± 10.03 µm in the R&F staining, and 80.15 ± 21.85 µm, 49.46 ± 17.52 µm, and 25.05 ± 11.03 µm in the V&B staining, respectively. They were significantly different from each other (P < .001). Conclusion: The hepatic veins were surrounded by Laennec's capsule at all levels, including the peripheral hepatic veins. However, it is thinner along the vein branches. The gap between the Laennec's capsule and hepatic veins shows potential supplemental value for liver surgery.

Construction and validation of chemoresistance-associated tumor- infiltrating exhausted-like CD8+ T cell signature in breast cancer: cr-TILCD8TSig.

Background: Accumulating evidence has revealed that CD8+ T cell exhaustion (Tex) results in worse immunotherapy outcomes. However, the molecular functions and mechanisms of action of Tex in chemoresistance needed to be elucidated. Methods: The populations of tumor-infiltrating CD8+ T cells (TILCD8Ts) in chemoresistant and chemosensitive groups of the GSE25066 dataset were calculated using CIBERSORT. Differentially expressed genes (DEGs) between TILCD8Ts and other immune cells were explored by integrating 16 immune cell datasets downloaded from the gene expression omnibus (GEO) database. Gene ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, univariate and multivariate Cox regression, and least absolute shrinkage and selection operator (LASSO) regression of TILCD8T-specific upregulated genes were used to construct a chemoresistant TILCD8T signature (cr-TILCD8TSig). Clinical prognostic data, genomic alterations, chemotherapy response, and immunotherapy response were compared between the different cr-TILCD8TSig subgroups in the GSE25066 and the cancer genome atlas breast cancer (TCGA-BRCA) cohorts. Results: A cr-TILCD8TSig with exhausted features was identified, consisting of seven genes (TCF7, RARRES3, ARL4C, ITK, CDH3, GZMB, and KLRD1), which were identified from 104 TILCD8Ts-specific DEGs. Our results showed that compared to the cr-TILCD8TSig-low subgroup, the -high subgroup had a poorer distant relapse-free survival (DRFS) in the GSE25066 cohort and worse progression-free survival (PFS) in the TCGA-BRCA cohort. Univariate and multivariate Cox regression analyses also demonstrated that cr-TILCD8TSig was an independent prognostic factor in the two independent cohorts. Furthermore, cr-TILCD8TSig-low patients benefited more from chemotherapy and immunotherapy than cr-TILCD8TSig-high patients. Besides, we found cell transmembrane signal transduction and the ECM may provide the molecular basis for resistance to antitumor agents in the cr-TILCD8Sig-high subgroup. For genomic alterations, we revealed that mutations in PIK3CA, DMD, and APOB were more common in the cr-TILCD8Sig-high subgroup than in the cr-TILCD8Sig-low subgroup. A nomogram was finally constructed with good discrimination and calibration. Conclusions: cr-TILCD8TSig is a useful tool to independently predict prognosis, chemotherapy response, and immunotherapy outcomes in patients with breast cancer.