Autoimmunity Against Surfactant Protein B Is Associated with Pneumonitis During Checkpoint Blockade.

RATIONALE: Immune checkpoint inhibitor-related pneumonitis is a serious autoimmune event affecting up to 20% of patients with non-small cell lung cancer, yet the factors underpinning its development in some patients and not others are poorly understood. OBJECTIVES: To investigate the role of autoantibodies and autoreactive T cells against surfactant-related proteins in the development of pneumonitis. METHODS: The study cohort consisted of non-small cell lung cancer patients who gave blood samples before and during immune checkpoint inhibitor treatment. Serum was used for proteomics analyses and to detect autoantibodies present during pneumonitis. T cell stimulation assays and single-cell RNA sequencing were performed to investigate the specificity and functionality of peripheral autoreactive T cells. The findings were confirmed in a validation cohort comprising patients with non-small cell lung cancer and patients with melanoma. MEASUREMENTS AND MAIN RESULTS: Across both cohorts, patients who developed pneumonitis had higher pre-treatment levels of immunoglobulin G autoantibodies targeting surfactant protein-B. At the onset of pneumonitis, these patients also exhibited higher frequencies of CD4+ interferon-gamma-positive surfactant protein B-specific T cells, and expanding T cell clonotypes recognizing this protein, accompanied by a pro-inflammatory serum proteomic profile. CONCLUSIONS: Our data suggest that the co-occurrence of surfactant protein-B-specific immunoglobulin G autoantibodies and CD4+ T cells is associated with the development of pneumonitis during ICI therapy. Pre-treatment levels of these antibodies may represent a potential biomarker for elevated risk of developing pneumonitis and on-treatment levels may provide a diagnostic aid.

Integrated DNA barcoding methods to identify species in the processed fish products from Chinese market.

DNA-based methods are reliable for a precise identification of species in processed products. In this study, we assessed five typical DNA extraction methods from multiple aspects. Full-length and mini-length DNA barcoding were performed to detect the species substitution and mislabeling of 305 processed fish products from the Chinese market covering six processed fish products. The salt extraction method that exhibited the best overall performance was applied. All samples were successfully extracted; however, only 19.3 % of samples could be amplified using the full-DNA barcode primer set, and 90.2 % of samples could be amplified using the newly designed mini-DNA barcode primer sets (401 and 320 bp). Overall, the molecular identification results revealed that 36.4 % (111/305) of the samples were inconsistent with the labels, with commercial fraud observed in all six types of processed fish products. The survey findings provide technical references for effective fish authentication monitoring, offering insights into the seafood safety in markets.

Genome-wide identification and structural analysis of the BMP gene family in Triplophysa dalaica.

BACKGROUND: Bone morphogenetic proteins (BMPs) are part of the transforming growth factor beta (TGF-ß) superfamily and play crucial roles in bone development, as well as in the formation and maintenance of various organs. Triplophysa dalaica, a small loach fish that primarily inhabits relatively high elevations and cooler water bodies, was the focus of this study. Understanding the function of BMP genes during the morphogenesis of T. dalaica helps to clarify the mechanisms of its evolution and serves as a reference for the study of BMP genes in other bony fishes. The data for the T. dalaica transcriptome and genome used in this investigation were derived from the outcomes of our laboratory sequencing. RESULTS: This study identified a total of 26 BMP genes, all of which, except for BMP1, possess similar TGF-ß structural domains. We conducted an analysis of these 26 BMP genes, examining their physicochemical properties, subcellular localization, phylogenetic relationships, covariance within and among species, chromosomal localization, gene structure, conserved motifs, conserved structural domains, and expression patterns. Our findings indicated that three BMP genes were associated with unstable proteins, while 11 BMP genes were located within the extracellular matrix. Furthermore, some BMP genes were duplicated, with the majority being enriched in the GO:0008083 pathway, which is related to growth factor activity. It was hypothesized that genes within the BMP1/3/11/15 subgroup (Group I) play a significant role in the growth and development of T. dalaica. By analyzing the expression patterns of proteins in nine tissues (gonad, kidney, gill, spleen, brain, liver, fin, heart, and muscle), we found that BMP genes play diverse regulatory roles during different stages of growth and development and exhibit characteristics of division of labor. CONCLUSIONS: This study contributes to a deeper understanding of BMP gene family member expression patterns in high-altitude, high-salinity environments and provides valuable insights for future research on the BMP gene family in bony fishes.

Effect of the VR-guided grasping task on the brain functional network.

Virtual reality (VR) technology has been demonstrated to be effective in rehabilitation training with the assistance of VR games, but its impact on brain functional networks remains unclear. In this study, we used functional near-infrared spectroscopy imaging to examine the brain hemodynamic signals from 18 healthy participants during rest and grasping tasks with and without VR game intervention. We calculated and compared the graph theory-based topological properties of the brain networks using phase locking values (PLV). The results revealed significant differences in the brain network properties when VR games were introduced compared to the resting state. Specifically, for the VR-guided grasping task, the modularity of the brain network was significantly higher than the resting state, and the average clustering coefficient of the motor cortex was significantly lower compared to that of the resting state and the simple grasping task. Correlation analyses showed that a higher clustering coefficient, local efficiency, and modularity were associated with better game performance during VR game participation. This study demonstrates that a VR game task intervention can better modulate the brain functional network compared to simple grasping movements and may be more beneficial for the recovery of grasping abilities in post-stroke patients with hand paralysis.

GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases.

Knowledge bases have been instrumental in advancing biological research, facilitating pathway analysis and data visualization, which are now widely employed in the scientific community. Despite the establishment of several prominent knowledge bases focusing on signaling, metabolic networks, or both, integrating these networks into a unified topological network has proven to be challenging. The intricacy of molecular interactions and the diverse formats employed to store and display them contribute to the complexity of this task. In a prior study, we addressed this challenge by introducing a "meta-pathway" structure that integrated the advantages of the Simple Interaction Format (SIF) while accommodating reaction information. Nevertheless, the earlier Global Integrative Network (GIN) was limited to reliance on KEGG alone. Here, we present GIN version 2.0, which incorporates human molecular interaction data from ten distinct knowledge bases, including KEGG, Reactome, and HumanCyc, among others. We standardized the data structure, gene IDs, and chemical IDs, and conducted a comprehensive analysis of the consistency among the ten knowledge bases before combining all unified interactions into GINv2.0. Utilizing GINv2.0, we investigated the glycolysis process and its regulatory proteins, revealing coordinated regulations on glycolysis and autophagy, particularly under glucose starvation. The expanded scope and enhanced capabilities of GINv2.0 provide a valuable resource for comprehensive systems-level analyses in the field of biological research. GINv2.0 can be accessed at: https://github.com/BIGchix/GINv2.0 .

Correlation between preoperative peripheral blood NLR, PLR, LMR and prognosis of patients with head and neck squamous cell carcinoma.

BACKGROUND: Markers that can be used to evaluate the prognosis of patients with head and neck squamous cell carcinoma (HNSCC) remain undefined. OBJECTIVE: This study aimed to investigate the prognostic impact of preoperative neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and lymphocyte-to-monocyte ratio (LMR) in patients with HNSCC who underwent surgery-based treatment for the first time. METHODS: This retrospective study included patients HNSCC who underwent surgery-based treatment at our institution between January 2018 and December 2020. Specificity and sensitivity were analyzed using receiver operating characteristic (ROC) curves and the critical value was determined. Patients were divided into low and high groups according to NLR, PLR, and LMR the critical value. Log-rank and Cox proportional hazards models were used to evaluate the associations between preoperative NLR, PLR, LMR, and overall survival (OS). RESULTS: A total of 304 patients with HNSCC were included, of whom 190 (62.5%) and 114 (37.5%), 203 (66.8%) and 101 (33.2%), 98 (32.2%), and 206 (67.8%) cases were classified as low NLR and high NLR groups, low PLR and high PLR groups, and low LMR and high LMR groups, respectively. Univariate analysis showed that white blood cell count (WBC), neutrophil count (NEU), platelet count (PLT), NLR, pathologic N stage (pN stage), TNM stage and postoperative complications were significantly associated with OS (p < 0.05). Multivariate analysis showed that NEU, NLR, TNM stage and postoperative complications were independent negative prognostic factors for HNSCC (p < 0.05). CONCLUSION: Preoperative NLR is an independent negative prognostic factor for HNSCC. Patients with an increased NLR may have a poor OS.

Targeting AKT induced Ferroptosis through FTO/YTHDF2-dependent GPX4 m6A methylation up-regulating and degradating in colorectal cancer.

Ferroptosis is a new type of iron-dependent programmed cell death induced by lipid peroxidation. However, the underlying mechanisms and function in tumor therapy still remain undisclosed especially in post-transcription regulation. Here, we found that targeting AKT significantly induced GPX4 dependent ferroptosis and suppressed colorectal cancer growth both in vitro and in vivo. During this process, demethylase FTO was downregulated, which increased the m6A methylation level of GPX4, subsequently recognized by YTHDF2 and degraded. Prediction results showed that there are three potential methylated sites (193/647/766), and 193 site was identified as the right one, which was demethylated by FTO and read by YTHDF2. In parallel, AKT inhibition caused the accumulation of ROS which had a negative feedback on GPX4 expression. In addition, protective autophagy was initiated by MK2206 stimulation, while blocking autophagy further increased ferroptosis and markedly enhanced the anti-tumor activity of MK2206. In a word, inhibiting AKT activated ferroptosis through FTO/YTHDF2/GPX4 axis to suppress colon cancer progression, which raised FTO/GPX4 as potential biomarkers and targets in colorectal cancer therapy.

Intelligent Recognition Using Ultralight Multifunctional Nano-Layered Carbon Aerogel Sensors with Human-Like Tactile Perception.

Humans can perceive our complex world through multi-sensory fusion. Under limited visual conditions, people can sense a variety of tactile signals to identify objects accurately and rapidly. However, replicating this unique capability in robots remains a significant challenge. Here, we present a new form of ultralight multifunctional tactile nano-layered carbon aerogel sensor that provides pressure, temperature, material recognition and 3D location capabilities, which is combined with multimodal supervised learning algorithms for object recognition. The sensor exhibits human-like pressure (0.04-100 kPa) and temperature (21.5-66.2 °C) detection, millisecond response times (11 ms), a pressure sensitivity of 92.22 kPa-1 and triboelectric durability of over 6000 cycles. The devised algorithm has universality and can accommodate a range of application scenarios. The tactile system can identify common foods in a kitchen scene with 94.63% accuracy and explore the topographic and geomorphic features of a Mars scene with 100% accuracy. This sensing approach empowers robots with versatile tactile perception to advance future society toward heightened sensing, recognition and intelligence.

The prognostic role of coagulation markers in the progression and metastasis of laryngeal squamous cell carcinoma.

BACKGROUND: The application of coagulation-related markers in laryngeal squamous cell carcinoma(LSCC) remains unclear. This study explored the prognostic role of coagulation markers in the progression and metastasis of LSCC. METHODS: Coagulation markers of patients with LSCC receiving surgery in the Second Affiliated Hospital of Fujian Medical University in China, from January 2013 to May 2022 were retrospectively analyzed and compared with those of contemporary patients with benign laryngeal diseases. The relationship between clinicopathological features of LSCC and coagulation markers was analyzed with the chi-square and rank sum tests. The ROC curve analysis was utilized to evaluate the diagnostic efficacy of seven coagulation markers for LSCC and its different clinicopathological features, and to find the optimal cutoff value of each coagulation marker. RESULTS: 303 patients with LSCC and 533 patients with benign laryngeal diseases were included in the present analysis. Compared to the control group, prothrombin time (PT) (p < 0.001), activated partial thromboplastin time (APTT) (p = 0.001), and Fib (p < 0.001) in patients with LSCC were significantly higher, while mean platelet volume (MPV) (p < 0.001) was significantly shorter. Significant increases were detected in PT (Z = 14.342, p = 0.002), Fib (Z = 25.985, p < 0.001), platelet count (PC) (Z = 12.768, p = 0.005), PCT (Z = 9.178, p = 0.027), MPV (F = 2.948, p = 0.033) in T4 stage. Fib had the highest prognostic value among the seven coagulation markers in different T stages (AUC = 0.676, p < 0.001), N stages (AUC = 0.717, p < 0.001), tumor stage (AUC = 0.665, p < 0.001), differentiation degree (AUC = 0.579, p = 0.022), and neurovascular invasion (AUC = 0.651, p = 0.007). Fib (Z = 25.832, p < 0.001), PC (Z = 23.842, p < 0.001), and PCT (Z = 20.15, p < 0.001) in N1 and N3 stages were significantly higher than in N0 stage. PT (Z = 12.174, p = 0.007), Fib (Z = 23.873, p < 0.001), PC (Z = 17.785, p < 0.001), and PCT (Z = 14.693, p = 0.002) were significantly higher in stage IV than in stage I and II. APTT (Z=-1.983, p = 0.047), Fib (Z=-2.68, p = 0.007), PC (Z=-2.723, p = 0.006), and PCT (Z=-2.592, p = 0.01) increased significantly when the tumor invaded neurovascular tissue. CONCLUSIONS: Coagulation markers have the potential to act as biomarkers for predicting pathological features of LSCC. The high level of Fib was helpful for the diagnosis of LSCC and the detection of advanced LSCC. TRIAL REGISTRATION: Not applicable.

Automatic depression diagnosis through hybrid EEG and near-infrared spectroscopy features using support vector machine.

Depression is a common mental disorder that seriously affects patients' social function and daily life. Its accurate diagnosis remains a big challenge in depression treatment. In this study, we used electroencephalography (EEG) and functional near-infrared spectroscopy (fNIRS) and measured the whole brain EEG signals and forehead hemodynamic signals from 25 depression patients and 30 healthy subjects during the resting state. On one hand, we explored the EEG brain functional network properties, and found that the clustering coefficient and local efficiency of the delta and theta bands in patients were significantly higher than those in normal subjects. On the other hand, we extracted brain network properties, asymmetry, and brain oxygen entropy as alternative features, used a data-driven automated method to select features, and established a support vector machine model for automatic depression classification. The results showed the classification accuracy was 81.8% when using EEG features alone and increased to 92.7% when using hybrid EEG and fNIRS features. The brain network local efficiency in the delta band, hemispheric asymmetry in the theta band and brain oxygen sample entropy features differed significantly between the two groups (p < 0.05) and showed high depression distinguishing ability indicating that they may be effective biological markers for identifying depression. EEG, fNIRS and machine learning constitute an effective method for classifying depression at the individual level.

[Papillary carcinoma in a thyroglossal duct remnant: a case report].

This case report has described a case of papillary carcinoma of thyroglossal duct in a young male. This patient was admitted with a mass in the anterior neck for 2 years. Preoperative Bultrasonography, CT and MR showed a subcutaneous cystic mass with irregular calcification shadow in the central region of the neck without obvious enhancement. Initial diagnosis was thyroglossal duct cyst, and was excised by Sistrunk under general anesthesia. The postoperative pathological examination showed thyroglossal duct cyst combined with thyroid papillary carcinoma, which was confirmed by immunohistochemistry as thyroglossal duct papillary carcinoma.

Predicting poststroke dyskinesia with resting-state functional connectivity in the motor network.

Significance: Motor function evaluation is essential for poststroke dyskinesia rehabilitation. Neuroimaging techniques combined with machine learning help decode a patient's functional status. However, more research is needed to investigate how individual brain function information predicts the dyskinesia degree of stroke patients. Aim: We investigated stroke patients' motor network reorganization and proposed a machine learning-based method to predict the patients' motor dysfunction. Approach: Near-infrared spectroscopy (NIRS) was used to measure hemodynamic signals of the motor cortex in the resting state (RS) from 11 healthy subjects and 31 stroke patients, 15 with mild dyskinesia (Mild), and 16 with moderate-to-severe dyskinesia (MtS). The graph theory was used to analyze the motor network characteristics. Results: The small-world properties of the motor network were significantly different between groups: (1) clustering coefficient, local efficiency, and transitivity: MtS > Mild > Healthy and (2) global efficiency: MtS < Mild < Healthy. These four properties linearly correlated with patients' Fugl-Meyer Assessment scores. Using the small-world properties as features, we constructed support vector machine (SVM) models that classified the three groups of subjects with an accuracy of 85.7%. Conclusions: Our results show that NIRS, RS functional connectivity, and SVM together constitute an effective method for assessing the poststroke dyskinesia degree at the individual level.

FYN/TOPK/HSPB1 axis facilitates the proliferation and metastasis of gastric cancer.

BACKGROUND: FYN is a nonreceptor tyrosine kinase that regulates diverse pathological processes. The pro-cancer role of FYN in multiple malignancies has been elucidated. However, the mechanisms that FYN promotes gastric cancer (GC) progression remain largely unknown. METHODS: In vitro and in vivo assays were used to investigate the function of FYN. FYN, TOPK, p-TOPK expression in GC specimens were detected by immunohistochemistry. Phosphoproteomics assays identify TOPK downstream substrate molecules. The molecular mechanism was determined using COIP assays, pull-down assays, immunofluorescence co-localization assays, western blotting, 32p-labeled isotope radioautography assays, vitro kinase assays, and TOPK knockout mice. RESULTS: FYN was found to be significantly upregulated in GC tissues as well as in GC cells. Knockdown of FYN expression markedly attenuated the malignant phenotype of GC cells in vitro and in vivo. Mechanistically, we identified TOPK/PBK as a novel downstream substrate of FYN, FYN directly phosphorylates TOPK at Y272. One phosphospecific antibodies against Y272 was developed to validate the phosphorylation of TOPK by FYN. Moreover, the TOPK-272F mutation impaired the interaction between TOPK and FYN, leading to disappeared TOPK phosphorylation. Consistently, human GC tissues displayed increased p-TOPK(Y272), which correlated with poor survival. Phosphoproteomics results showed a significant downregulation of both HSPB1 and p-HSPB1(ser15) in TOPK-knockdown cells, which was confirmed by TOPK-konckout mice. CONCLUSIONS: FYN directly binds to TOPK in GC cells and phosphorylates TOPK at the Y272, which leads to proliferation and metastasis of GC. FYN-TOPK axis facilitates GC progression by phosphorylating HSPB1. Collectively, our study elucidates the pivotal role of the FYN-TOPK-HSPB1 cascade in GC.

Exploring the differences between sole silages of gramineous forages and mixed silages with forage legumes using 16S/ITS full-length sequencing.

Background/Objective: Silage characteristics of grass materials directly affect their silage qualities. To expand the source of silage raw materials and develop mixed silages underlined by exploring the positive interactions between forage grasses and legumes, three gramineous grasses, Napier grass (Pennisetum purpureum), king grass (Pennisetum sinese), and forage maize (Zea mays) were separately mixed ensiled with a combination of four forage legumes including Medicago sativa, Vicia villosa, Vicia sativa, and Trifolium repens. Methods: The chemical composition and fermentation quality of the mixed silages were analyzed and compared with those of the sole silages of these three grasses, as well as the diversity of microbial communities, through the 16S/ITS full-length sequencing. Results: The results showed that the inclusion of forage legumes could somewhat improve the fermentation quality, as indicated by significantly (p < 0.05) higher crude protein and lactic acid contents while lower neutral detergent fiber, acid detergent fiber contents and pH values, compared with the sole silages. Among the three types of mixed silages, the mixed king grass had the highest dry matter and crude protein content as well as lowest neutral detergent fiber and acid detergent fiber content. Meanwhile, the bacterial and fungal communities in the mixed silages were influenced by increased the relative abundance of lactic acid bacteria, which inhibited the proliferation of undesirable bacteria, such as Hafnia alvei, Enterobacter cloacae, and Serratia proteamaculanss. Co-occurrence networks identified 32 nodes with 164 positive and 18 negative correlations in bacteria and 80 nodes with two negative and 76 positive correlations in fungi during fermentation. Conclusion: Inclusion of forage legume to grasses can improve the fermentation quality and optimize the structure of microbial community, which appears to be a feasible strategy to enhance the forage resource utilization.

Prognostic impact of lymphovascular and perineural invasion in squamous cell carcinoma of the tongue.

This study aimed to investigate the prognostic impact of lymphovascular and perineural invasions in patients with squamous cell carcinoma of the tongue who received surgery-based treatment at our institution between January 2013 and December 2020. Patients were divided into four groups based on the presence of perineural (P-/P +) and lymphovascular invasions (V-/V +): P-V-, P-V + , P + V-, and P + V + . Log-rank and Cox proportional hazard models were used to evaluate the association between perineural /lymphovascular invasion and overall survival (OS). Altogether, 127 patients were included, and 95 (74.8%), 8 (6.3%), 18 (14.2%), and 6 (4.7%) cases were classified as P-V-, P-V + , P + V-, and P + V + , respectively. Pathologic N stage (pN stage), tumor stage, histological grade, lymphovascular invasion, perineural invasion, and postoperative radiotherapy were significantly associated with OS (p < 0.05). OS was significantly different among the four groups (p < 0.05). Significant between-group differences in OS were detected for node-positive (p < 0.05) and stage III-IV (p < 0.05) cases. OS was the worst in the P + V + group. Lymphovascular and perineural invasions are independent negative prognostic factors for squamous cell carcinoma of the tongue. Patients with lymphovascular and/or perineural invasion may have significantly poorer overall survival than those without neurovascular involvement.

Sandwich-type electrochemical immunosensing of hypopharyngeal carcinoma biomarker carcinoembryonic antigen based on N-doped hollow mesoporous nanocarbon spheres/gold hybrids as sensing platform and gold/ferrocene as signal amplifier.

In the present work, a highly sensitive sandwich-type electrochemical immunosensor of carcinoembryonic antigen (CEA) was developed by preparing N-doped hollow mesoporous nanocarbon spheres/gold hybrids (NHMN/Au) hybridsas sensing platformand Au/ferrocene (Au/Fc) as signal amplifiers. The large surface area and high conductivity as well as good biocompatibility of NHMN/Au can increase the loading of primary antibody (Ab1) and accelerate the electron transport rate of the electrode surface, while Au can carry immobilized secondary antibodies (Ab2) and Fc derivative (Fc-SH).By using Fc-SH as response probe, the experiments show that the peak current of probe could increase after occurring the specific recognition of Ab1-CEA-Ab2, thus a novel sandwich-type immunosensor of CEA was developed. Finally, the proposed method for CEA detection was applied in human serum and the obtained results are satisfactory, indicating the developed method has important clinical applications for CEA determination.

Age-related difference in muscle metabolism patterns during upper limb's encircling exercise: a near-infrared spectroscopy study.

Aging is usually accompanied by decrease in limb motor function and change in muscle metabolism patterns. However, few studies have investigated the aging effect on muscle hemodynamics of the upper extremity. This study aims to explore the aging effect on muscle metabolism patterns during upper limb's exercise. Twelve middle-aged and elderly subjects and 12 young subjects were recruited, and muscle oxygenation signals from these subjects' biceps brachii muscles were collected during active and passive upper limb's encircling exercise with near-infrared spectroscopy (NIRS). The old group showed stronger muscle hemodynamic metabolism than the young group. The multiscale fuzzy approximate entropy and multiscale transfer entropy analyses indicated higher complexity and stronger interlimb coupling of the muscle oxygenation signals for the old group. Based on the selected muscle metabolism features, the constructed support vector machine model showed a high accuracy rate for classifying the two groups of subjects: 91.6% for the passive mode and 87.5% for the active mode. Our results proved the specific muscle metabolism patterns in the upper limb's exercise for old subjects, promoting the understanding of the aging effect on muscle hemodynamics.

Integrative Analysis of Genes Involved in the Global Response to Potato Wart Formation.

Synchytrium endobioticum, the causal agent of potato wart disease, poses a major threat to commercial potato production. Understanding the roles of transcriptionally regulated genes following pathogen infection is necessary for understanding the system-level host response to pathogen. Although some understanding of defense mechanisms against S. endobioticum infection has been gained for incompatible interactions, the genes and signaling pathways involved in the compatible interaction remain unclear. Based on the collection of wart diseased tubers of a susceptible cultivar, we performed phenotypic and dual RNA-Seq analyses of wart lesions in seven stages of disease progression. We totally detected 5,052 differentially expressed genes (DEGs) by comparing the different stages of infection to uninfected controls. The tendency toward differential gene expression was active rather than suppressed under attack by the pathogen. The number of DEGs step-up along with the development of the disease and the first, third and seventh of the disease stages showed substantially increase of DEGs in comparison of the previous stage. The important functional groups identified via Gene ontology (GO) and KEGG enrichment were those responsible for plant-pathogen interaction, fatty acid elongation and phenylpropanoid biosynthesis. Gene coexpression networks, composed of 17 distinct gene modules that contained between 25 and 813 genes, revealed high interconnectivity of the induced response and led to the identification of a number of hub genes enriched at different stages of infection. These results provide a comprehensive perspective on the global response of potato to S. endobioticum infection and identify a potential transcriptional regulatory network underlying this susceptible response, which contribute to a better understanding of the potato-S. endobioticum pathosystem.

Inhibition of AKT induces p53/SIRT6/PARP1-dependent parthanatos to suppress tumor growth.

BACKGROUND: Targeting AKT suppresses tumor growth through inducing apoptosis, however, during which whether other forms of cell death occurring is poorly understood. METHODS: The effects of increasing PARP1 dependent cell death (parthanatos) induced by inhibiting AKT on cell proliferation were determined by CCK-8 assay, colony formation assay, Hoechst 33,258 staining and analysis of apoptotic cells by flow cytometry. For the detailed mechanisms during this process, Western blot analysis, qRT-PCR analysis, immunofluorescence and co-immunoprecipitation were performed. Moreover, the inhibition of tumor growth by inducing p53/SIRT6/PARP1-dependent parthanatos was further verified in the xenograft mouse model. RESULTS: For the first time, we identified that inhibiting AKT triggered parthanatos, a new form of regulated cell death, leading to colon cancer growth suppression. For the mechanism investigation, we found that after pharmacological or genetic AKT inhibition, p53 interacted with SIRT6 and PARP1 directly to activate it, and promoted the formation of PAR polymer. Subsequently, PAR polymer transported to outer membrane of mitochondria and resulted in AIF releasing and translocating to nucleus thus promoting cell death. While, blocking PARP1 activity significantly rescued colon cancer from death. Furthermore, p53 deletion or mutation eliminated PAR polymer formation, AIF translocation, and PARP1 dependent cell death, which was promoted by overexpression of SIRT6. Meanwhile, reactive oxygen species production was elevated after inhibition of AKT, which might also play a role in the occurrence of parthanatos. In addition, inhibiting AKT initiated protective autophagy simultaneously, which advanced tumor survival and growth. CONCLUSION: Our findings demonstrated that AKT inhibition induced p53-SIRT6-PARP1 complex formation and the activation of parthanatos, which can be recognized as a novel potential therapeutic strategy for cancer. Video Abstract.

Comparison of Potato Viromes Between Introduced and Indigenous Varieties.

Viral disease in potatoes has been a major problem in potato production worldwide. In addition to the potential risk of introducing new diseases in new areas, viral-disease epidemics/pandemics can be initiated by "spillover" of indigenous viruses from infected alternative hosts into introduced cultivars. To investigate the tendency of potential viral infection/resistance, we analyzed the viromes of introduced and indigenous varieties of potatoes among different tissues using RNA-seq libraries. Bioinformatics analyses revealed that potato viruses PVM, PVY, and PVS were dominant and the most frequently identified viruses infecting potato virus-free plants in the field, and showed an infection bias between introduced and indigenous cultivars. PVY and PVS were the major viruses in introduced varieties, whereas PVM showed an extraordinarily high percentage in the indigenous variety. Other three common viruses, PVH, potato mop-top virus, and potato leafroll virus were identified specifically in the indigenous variety. There was a tendency for tissue-specific infection and sequence variation in viruses: underground parts (tubers, roots) harbored more unusual viruses, and tubers harbored relatively more variation with a high frequency of single nucleotide polymorphisms than other tissues. Taken together, our study provides a comprehensive overview of the composition, distribution, and sequence variation of viruses between introduced and indigenous varieties of potatoes.