Causal effects of diabetic retinopathy on depression, anxiety and bipolar disorder in the European population: a Mendelian randomization study

PURPOSE

To verify the causal effects of diabetic retinopathy (DR) on depression, anxiety and bipolar disorder (BD).

METHODS

Mendelian randomization (MR) analysis was performed to identify the causal relationships between DR and depression or anxiety or BD via using DR-related GWAS data (14,584 cases and 176,010 controls), depression-related GWAS data (59,851 cases and 113,154 controls), anxiety-related GWAS data (7016 cases and 14,745 controls) and BD-related GWAS data (41,917 cases and 371,549 controls). The inverse-variance weighted (IVW) model was adopted to estimate the causal relationship. The outcome was expressed as odds ratio (OR) with 95% confidence intervals (CI).

RESULTS

The MR analysis results presented that DR was causally associated with a significantly increased risk of BD in the European population (IVW, OR = 1.06, 95%CI [1.03, 1.08], P = 2.44 × 10-6), while DR was unable to causally influence the risk of depression (IVW, OR = 1.01, 95%CI [0.99, 1.04], P = 0.32) and anxiety (IVW, OR = 0.97, 95%CI [0.89, 1.06], P = 0.48) in the European population. Subgroup analysis based on BD identified DR causally increased the risk of bipolar I disorder (BD I) but not bipolar II disorder (BD II). Sensitivity analysis results did not show any pleiotropy and heterogeneity in both groups of analyses, indicating that the results were stable and reliable.

CONCLUSIONS

The results of the current MR analysis indicated a causal relationship between DR and BD in the European population, while there was no causal connection between DR and depression or anxiety. However, further research is needed to confirm these conclusions.

[Effectiveness analysis of hybrid endoscopic submucosal dissection in patients with colorectal epithelium-derived tumors]

Objective: To compare the clinical benefits of classic endoscopic submucosal dissection (ESD) and hybrid ESD for the treatment of colorectal epithelium-derived tumors. Methods: The current investigation was a retrospective multicenter study of 418 patients who underwent ESD between January 2015 and April 2021 at Beijing Jishuitan Hospital. The patients were assigned to one of two groups based on the surgical procedure they underwent; a classic ESD group or a hybrid ESD group. The primary outcome was the rate of en bloc resection and complete resection. SPSS 26.0 was used for statistical analysis. Homogeneity of variance was assessed via Cochran's test. Normally distributed data with homogeneity of variance were analyzed via the t-test for independent samples. Non-normally distributed data and data with unequal variance were analyzed via the Kruskal-Wallis non-parametric test. Categorical data were analyzed via the Chi-square test or Fisher's exact test. Multivariable assessment was performed via logistic regression analysis. Results: The en bloc resection rates [89.4% (84/94) vs. 87.0% (194/223), χ2=0.34, P=0.558] and complete resection rates [85.1% (80/94) vs. 82.1% (183/223), χ2=0.33, P=0.510] were similar. Compared with classic ESD, procedures were shorter in the hybrid ESD group [22(7, 213) vs. 47(12, 680) min, Z=0.23, P<0.001], dissection was completed more rapidly [0.14(0.02, 0.32) vs. 0.10(0.02, 0.41) cm2/min, Z=0.08, P<0.001], and there was a higher rate of perforation (9.6% vs. 2.2%, χ2=2.67, P=0.006). Laterally spreading tumor granular type nodular mixed, non-granular type pseudo-depressed, flat-elevated type (odds ratio 2.826, P=0.012), and tumor location (odds ratio 6.970, P=0.005) were independently associated with complete resection in the hybrid ESD group. Conclusion: Classic ESD and hybrid ESD had similar en bloc and complete resection rates for colorectal epithelium-derived tumors, but hybrid ESD had shorter operation times. With respect to hybrid ESD, factors associated with failure of complete resection included lesion type and crossing tissue boundaries.

Dissecting cellular states of infiltrating microenvironment cells in melanoma by integrating single-cell and bulk transcriptome analysis

BACKGROUND

Cellular states of different immune cells can affect the activity of the whole immune microenvironment.

METHODS

Here, leveraging reference profiles of microenvironment cell states that were constructed based on single-cell RNA-seq data of melanoma, we dissected the composition of microenvironment cell states across 463 skin cutaneous melanoma (SKCM) bulk samples through CIBERSORT-based deconvolution of gene expression profiles and revealed high heterogeneity of their distribution. Correspondence analysis on the estimated cellular fractions of melanoma bulk samples was performed to identify immune phenotypes. Based on the publicly available clinical survival and therapy data, we analyzed the relationship between immune phenotypes and clinical outcomes of melanoma.

RESULTS

By analysis of the relationships among those cell states, we further identified three distinct tumor microenvironment immune phenotypes: "immune hot/active", "immune cold-suppressive" and "immune cold-exhausted". They were characterized by markedly different patterns of cell states: most notably the CD8 T Cytotoxic state, CD8 T Mixed state, B non-regulatory state and cancer-associated fibroblasts (CAFs), depicting distinct types of antitumor immune response (or immune activity). These phenotypes had prognostic significance for progression-free survival and implications in response to immune therapy in an independent cohort of anti-PD1 treated melanoma patients.

CONCLUSIONS

The proposed strategy of leveraging single-cell data to dissect the composition of microenvironment cell states in individual bulk tumors can also extend to other cancer types, and our results highlight the importance of microenvironment cell states for the understanding of tumor immunity.

Identifying the personalized driver gene sets maximally contributing to abnormality of transcriptome phenotype in glioblastoma multiforme individuals

High heterogeneity in genome and phenotype of cancer populations made it difficult to apply population-based common driver genes to the diagnosis and treatment of cancer individuals. Characterizing and identifying the personalized driver mechanism for glioblastoma multiforme (GBM) individuals were pivotal for the realization of precision medicine. We proposed an integrative method to identify the personalized driver gene sets by integrating the profiles of gene expression and genetic alterations in cancer individuals. This method coupled genetic algorithm and random walk to identify the optimal gene sets that could explain abnormality of transcriptome phenotype to the maximum extent. The personalized driver gene sets were identified for 99 GBM individuals using our method. We found that genomic alterations in between one and seven driver genes could maximally and cumulatively explain the dysfunction of cancer hallmarks across GBM individuals. The driver gene sets were distinct even in GBM individuals with significantly similar transcriptomic phenotypes. Our method identified MCM4 with rare genetic alterations as previously unknown oncogenic genes, the high expression of which were significantly associated with poor GBM prognosis. The functional experiments confirmed that knockdown of MCM4 could significantly inhibit proliferation, invasion, migration, and clone formation of the GBM cell lines U251 and U118MG, and overexpression of MCM4 significantly promoted the proliferation, invasion, migration, and clone formation of the GBM cell line U87MG. Our method could dissect the personalized driver genetic alteration sets that are pivotal for developing targeted therapy strategies and precision medicine. Our method could be extended to identify key drivers from other levels and could be applied to more cancer types.

A 2-Stage Root Analog Implant with Compact Structure, Uniform Roughness, and High Accuracy

Immediate implant placement has the advantages of shortening the operation time, reducing the treatment cycle and cost. At present, this technology has been used widely, but the indications of immediate implantation are still limited. Here, a novel type of root analog implant (RAI) was manufactured by selective laser melting technology to address the limitation. Under optimized condition, RAIs were printed with the internal density of 99.73% and the uniform surface roughness of 11 μm (Sa). Besides, the deviation between RAI specimen and design models is controlled within 0.15 mm after optimizing scanning parameters. The substrate printed could promote human bone marrow stromal cell proliferation, spreading, and osteogenic differentiation. The bone-implant contact (BIC, 75% ± 7%) and bone volume/total volume (BV/TV, 74% ± 7%) of RAIs were significantly higher than that of conventional implants (BIC, 66% ± 5%; BV/TV, 62% ± 5%) in in vivo experiments. Further, customized abutments were designed for the RAIs, improving the masticatory ability of the beagle dogs after crown restoration. This study aims to design a personalized 2-stage RAI with compact structure and uniform roughness, in order to achieve better fracture resistance, initial osseointegration efficiency, and dispersed stress in immediate implantation. It provides a certain guiding value for standardizing the manufacture and clinical application of RAI in immediate implantation.

Revealing the functions of clonal driver gene mutations in patients based on evolutionary dependencies

The clonal mutations in driver genes enable cells to gradually acquire growth advantage in tumor development. Therefore, revealing the functions of clonal driver gene mutations is important. Here, we proposed the method FCMP that considered evolutionary dependencies to analyze the functions of clonal driver gene mutations in a single patient. Applying our method to five cancer types from The Cancer Genome Atlas, we identified specific functions and common functions of clonal driver gene mutations. We found that the clonal driver gene mutations in the same patient played multiple functions. We also found that clonal mutations in the same driver gene performed different functions in different patients. These findings suggested that the clonal driver gene mutations showed strong tumor heterogeneity. In the pan-cancer analysis, the immune-related functions for clonal driver gene mutations were shared by multiple cancer types. In addition, clonal mutations in some driver genes predicted the survival of patients in cancers.

[Mechanism of nerve growth factor promotes angiogenesis and skeletal muscle fiber remodeling in a mouse hindlimb ischemic model]

Objective: To explore the mechanism of nerve growth factor (NGF) in the skeletal muscle fiber remodeling in ischemic limbs during therapeutic angiogenesis. Methods: Eighteen female mice with SPF grade, 6 weeks old and 25-30 g weighed were randomly allocated to sham-operated group (n=6), blank control group (n=6) and NGF gene transfection group (n=6). The left hindlimb ischemia models were established by ligating the femoral artery in blank control group and NGF gene transfection group. Seven days after the operation, mice in the three groups were separately injected with normal saline, empty plasmids, and NGF plasmids. Gastrocnemius of left hindlimbs was harvested after the blood perfusion assessment of the ischemic limb on the 21st postoperative day. The gastrocnemius muscle specimens were stained with HE, CD31 and proliferating cell nuclear antigen (PCNA) immunohistochemistry staining, the mRNA expressions of myosin heavy chain-Ⅰ(MHC-Ⅰ), MHC-Ⅱa and MHC-Ⅱb were measured by real-time PCR, and the protein level of NGF and peroxisome proliferator-activated receptors-β/δ (PPAR β/δ) were detected by Western blot. The expression of cytochrome C oxidase (COX), isocitrate dehydrogenase (IDH) and adenosine triphosphate (ATP) were examined by enzyme-linked immunosorbent assay (ELISA). Results: On the 21st day after operation, the blood perfusion of the ischemic limb in NGF gene transfection group was (195.70±9.99)PU, which was lower than that in sham-operated group (312.15±17.32)PU (P=0.001), while it was higher than that in blank control group (82.11±8.55)PU (P=0.001). The degree of muscle atrophy in the NGF gene transfection group was lower than that in the blank control group. The capillary density of NGF gene transfection group (0.34±0.05) was higher than that of sham-operated group (0.11±0.03) and blank control group (0.27±0.04) (P<0.05). The endothelial cell proliferation index in NGF gene transfection group (0.39±0.19) was significantly higher than that in sham-operated group (0.18±0.01) and blank control group (0.25±0.14) (P<0.05). The expression of NGF, PPAR β/δ, COX, IDH, ATP, and MHC-Ⅰ mRNA in NGF gene transfection group were significantly higher than those in sham-operated group and blank control group (P<0.05). Conclusions: NGF gene transfection can promote angiogenesis in the ischemic limbs of mice, increase the blood perfusion, and thus induce the remodeling of skeletal muscle fibers to type Ⅰ. This process may be related to NGF-induced PPAR β/δ expression and promote the cellular aerobic metabolism in skeletal muscle.

Decoding the associations between cell functional states in head and neck cancer based on single-cell transcriptome

OBJECTIVES

Systematically identifying cancer cell functional states, especially their associations, is key to understanding the pathogenesis of cancers.

MATERIALS AND METHODS

Here, we systematically identified six cancer-related states, including epithelial-mesenchymal transition (EMT), immune response, epithelial differentiation, stress, G1/S and G2/M phases, in head and neck squamous cell carcinoma (HNSCC) based on single-cell RNA-sequencing (scRNA-seq).

RESULTS AND CONCLUSION

We defined the association patterns between these functional states and found the patterns were correlated with the state activity. Particularly, immune response and EMT were negatively, positively, or non-significantly correlated in samples with the highest immune response activity, the lowest activity of the two states, or with the highest EMT activity, respectively. Combining scRNA-seq data of immune cells and four independent HNSCC cohorts, we found the negative relationship between EMT and immune response was correlated with an activated immune microenvironment and a longer survival, while the non-significant relationship was correlated with an immunosuppressed microenvironment and a poor prognosis. Collectively, our results provide insight into the association patterns between functional states in HNSCC, and may facilitate the elucidation of the interactions between cancer cells and immune system during cancer progression.

MSX1 Drives Tooth Morphogenesis Through Controlling Wnt Signaling Activity

Tooth agenesis is a common structural birth defect in humans that results from failure of morphogenesis during early tooth development. The homeobox transcription factor Msx1 and the canonical Wnt signaling pathway are essential for "bud to cap" morphogenesis and are causal factors for tooth agenesis. Our recent study suggested that Msx1 regulates Wnt signaling during early tooth development by suppressing the expression of Dkk2 and Sfrp2 in the tooth bud mesenchyme, and it demonstrated partial rescue of Msx1-deficient molar teeth by a combination of DKK inhibition and genetic inactivation of SFRPs. In this study, we found that Sostdc1/Wise, another secreted Wnt antagonist, is involved in regulating the odontogenic pathway downstream of Msx1. Whereas Sostdc1 expression in the developing tooth germ was not increased in Msx1-/- embryos, genetic inactivation of Sostdc1 rescued maxillary molar, but not mandibular molar, morphogenesis in Msx1-/- mice with full penetrance. Since the Msx1-/-;Sostdc1-/- embryos exhibited ectopic Dkk2 expression in the developing dental mesenchyme, similar to Msx1-/- embryos, we generated and analyzed tooth development in Msx1-/-;Dkk2-/- double and Msx1-/-;Dkk2-/-;Sostdc1-/- triple mutant mice. The Msx1-/-;Dkk2-/- double mutants showed rescued maxillary molar morphogenesis at high penetrance, with a small percentage also exhibiting mandibular molars that transitioned to the cap stage. Furthermore, tooth development was rescued in the maxillary and mandibular molars, with full penetrance, in the Msx1-/-;Dkk2-/-;Sostdc1-/- mice. Together, these data reveal 1) that a key role of Msx1 in driving tooth development through the bud-to-cap transition is to control the expression of Dkk2 and 2) that modulation of Wnt signaling activity by Dkk2 and Sostdc1 plays a crucial role in the Msx1-dependent odontogenic pathway during early tooth morphogenesis.

Systematic investigation of the prognostic impact of clonal status of somatic mutations across multiple cancer types

Tumors are genetically heterogeneous and many mutations are actually present in subclonal populations. The clonal status of mutations is valuable for accurate prognosis, clinical management. The aim of this study was to identify the clonal status of somatic mutations and systematically evaluate their prognostic values across various cancer types. We totally identified 227 clonal and 432 subclonal mutations contributed to prognosis and demonstrated the importance of clonal status in improving mutation-related clinical guidance. We further developed a customized multi-step approach to identify gene-specific prognostic patterns of clonal status at pan-cancer level and found some cancer-specific prognostic patterns. The 'subclonal-dependent risk' subpattern was one of the most common subpatterns, it usually accompanied by high genomic in-stability and high extent of intra-tumor heterogeneity and could be used to improve the accuracy of prognostic analysis. Our results revealed the importance of clonal status, especially subclonal mutation in clinical survival.

Revealing the contribution of somatic gene mutations to shaping tumor immune microenvironment

Interaction between tumor cells and immune cells determined highly heterogeneous microenvironments across patients, leading to substantial variation in clinical benefits from immunotherapy. Somatic gene mutations were found not only to elicit adaptive immunity but also to influence the composition of tumor immune microenvironment and various processes of antitumor immunity. However, due to an incomplete view of associations between gene mutations and immunophenotypes, how tumor cells shape the immune microenvironment and further determine the clinical benefit of immunotherapy is still unclear. To address this, we proposed a computational approach, inference of mutation effect on immunophenotype by integrated gene set enrichment analysis (MEIGSEA), for tracing back the genomic factor responsible for differences in immunophenotypes. MEIGSEA was demonstrated to accurately identify the previous confirmed immune-associated gene mutations, and systematic evaluation in simulation data further supported its performance. We used MEIGSEA to investigate the influence of driver gene mutations on the infiltration of 22 immune cell types across 19 cancers from The Cancer Genome Atlas. The top associated gene mutations with infiltration of CD8 T cells, such as CASP8, KRAS and EGFR, also showed extensive impact on other immune components; meanwhile, immune effector cells shared critical gene mutations that collaboratively contribute to shaping distinct tumor immune microenvironment. Furthermore, we highlighted the predictive capacity of gene mutations that are positively associated with CD8 T cells for the clinical benefit of immunotherapy. Taken together, we present a computational framework to help illustrate the potential of somatic gene mutations in shaping the tumor immune microenvironment.

Effects of nitrogen supply rate on photosynthesis, nitrogen uptake and growth of seedlings in a Eucalyptus/Dalbergia odorifera intercropping system

The introduction of N₂ -fixing species into a Eucalyptus plantation resulted in a successful planting system. It is essential to understand the contribution of nitrogen (N) competition and photosynthetic efficiency to plant dry matter yield to shed more light on the growth mechanism of the Eucalyptus/legume system. We compared N competition, photosynthesis and dry matter yield of Eucalyptus urophylla × E. grandis and the N₂ -fixing tree species Dalbergia odorifera in intercropping and monoculture systems under different N levels. The photosynthesis of E. urophylla × E. grandis was improved, while that of D. odorifera was inhibited in the intercropping system. Intercropped E. urophylla × E. grandis increased the N utilization and the dry matter yield by 6.57-48.46% and 7.59-97.26%, and decreased those of D. odorifera by 10.21-30.33% and 0.48-13.19%, respectively. Furthermore, N application enhanced the competitive ability of E. urophylla × E. grandis relative to D. odorifera and changed the N contents and chlorophyll synthesis to optimize the photosynthetic structure of both species. Our results reveal Eucalyptus for photosynthesis, N absorption and increasing the growth benefit from the introduction of N₂ -fixing species, which hence can be considered to be an effective sustainable management option of Eucalyptus plantations.

Analysis of Mutations and Dysregulated Pathways Unravels Carcinogenic Effect and Clinical Actionability of Mutational Processes

Somatic mutations accumulate over time in cancer cells as a consequence of mutational processes. However, the role of mutational processes in carcinogenesis remains poorly understood. Here, we infer the causal relationship between mutational processes and somatic mutations in 5,828 samples spanning 34 cancer subtypes. We found most mutational processes cause abundant recurrent mutations in cancer genes, while exceptionally ultraviolet exposure and altered activity of the error-prone polymerase bring a large number of recurrent non-driver mutations. Furthermore, some mutations are specifically induced by a certain mutational process, such as IDH1 p.R132H which is mainly caused by spontaneous deamination of 5-methylcytosine. At the pathway level, clock-like mutational processes extensively trigger mutations to dysregulate cancer signal transduction pathways. In addition, APOBEC mutational process destroys DNA double-strand break repair pathway, and bladder cancer patients with high APOBEC activity, though with homologous recombination proficient, show a significantly longer overall survival with platinum regimens. These findings help to understand how mutational processes act on the genome to promote carcinogenesis, and further, presents novel insights for cancer prevention and treatment, as our results showing, APOBEC mutagenesis and HRD synergistically contributed to the clinical benefits of platinum-based treatment.

CT texture analysis-based nomogram for the preoperative prediction of visceral pleural invasion in cT1N0M0 lung adenocarcinoma: an external validation cohort study

AIM

To develop a nomogram based on computed tomography (CT) texture analysis for the preoperative prediction of visceral pleural invasion in patients with cT1N0M0 lung adenocarcinoma.

MATERIALS AND METHODS

A dataset of chest CT containing lung nodules was collected from two institutions, and all surgically resected nodules were classified pathologically based on the presence of visceral pleural invasion. Each nodule on the CT image was segmented automatically by artificial-intelligence software and its CT texture features were extracted. The dataset was divided into training and external validation cohorts according to the institution, and a nomogram for predicting visceral pleural invasion was developed and validated.

RESULTS

Of a total of 313 patients enrolled from two independent institutions, 63 were diagnosed with visceral pleural invasion. Three-dimensional (3D) CT long diameter, skewness, and sphericity, and chronic obstructive pulmonary disease were identified as independent predictors for visceral pleural invasion by multivariable logistic regression. The nomogram based on multivariable logistic regression showed great discriminative ability, as indicated by a C-index of 0.890 (95% confidence interval [CI]: 0.867-0.914) and 0.864 (95% CI: 0.817-0.911) for the training and external validation cohorts, respectively. Additionally, calibration of the nomogram revealed good predictive ability, as indicated by the Brier score (0.108 and 0.100 for the training and external validation cohorts, respectively).

CONCLUSIONS

A nomogram was developed that could compute the probability of visceral pleural invasion in patients with cT1N0M0 lung adenocarcinoma with good calibration and discrimination. The nomogram has potential as a reliable tool for clinical evaluation and decision-making.

Stoichioproteomics study of differentially expressed proteins and pathways in head and neck cancer

Hypoxia is a prominent feature of head and neck cancer. However, the oxygen element characteristics of proteins and how they adapt to hypoxia microenvironments of head and neck cancer are still unknown. Human genome sequences and proteins expressed data of head and neck cancer were retrieved from pathology atlas of Human Protein Atlas project. Then compared the oxygen and carbon element contents between proteomes of head and neck cancer and normal oral mucosa-squamous epithelial cells, genome locations, pathways, and functional dissection associated with head and neck cancer were also studied. A total of 902 differentially expressed proteins were observed where the average oxygen content is higher than that of the lowly expressed proteins in head and neck cancer proteins. Further, the average oxygen content of the up regulated proteins was 2.54% higher than other. None of their coding genes were distributed on the Y chromosome. The up regulated proteins were enriched in endocytosis, apoptosis and regulation of actin cytoskeleton. The increased oxygen contents of the highly expressed and the up regulated proteins might be caused by frequent activity of cytoskeleton and adapted to the rapid growth and fast division of the head and neck cancer cells. The oxygen usage bias and key proteins may help us to understand the mechanisms behind head and neck cancer in targeted therapy, which lays a foundation for the application of stoichioproteomics in targeted therapy and provides promise for potential treatments for head and neck cancer.

Models for Predicting Sentinel and Non-sentinel Lymph Nodes Based on Pre-operative Ultrasonic Breast Imaging to Optimize Axillary Strategies

Axillary strategy decisions have become more complex and controversial in considering minimally traumatic therapy instead of sentinel lymph node biopsy, axillary lymph node dissection or regional nodal irradiation for people with breast cancer. The purpose of this study was to noninvasively predict sentinel lymph node (SLN) and non-sentinel lymph node (NSLN) status based on pre-operative sonographic and clinicopathologic features to determine optimal decisions regarding axillary therapy. In total, 701 patients with breast cancer from two independent centers were retrospectively analyzed. The SLN model (SLNM) for predicting SLN status and the NSLN model (NSLNM) for predicting NSLN status were trained based on a training set using the random-forest algorithm, and their performance was validated using an independent external test set. A receiver operating characteristic curve was drawn to obtain the area under the curve, which was used to assess performance. The area under the curve for the SLNM in the training and test, respectively, was 94.2% and 83.0%, and for the NSLNM, 99.5% and 92.7%. The SLNM and NSLNM accurately predicted that 61.46% (319/519) and 17.53% (91/519), respectively, of our participants were non-metastatic. The overall benefit of the three models was 78.99% in our participants. The two models for predicting SLN and NSLN status showed excellent application potential in optimizing axillary strategies.

Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis

Background

Glioblastoma multiforme (GBM) is a highly, malignant tumor of the primary central nervous system. Patients diagnosed with this type of tumor have a poor prognosis. Lymphocyte activation plays important roles in the development of cancers and its therapeutic treatments.

Objective

We sought to identify an efficient lymphocyte activation-associated gene signature that could predict the progression and prognosis of GBM.

Methods

We used univariate Cox proportional hazards regression and stepwise regression algorithm to develop a lymphocyte activation-associated gene signature in the training dataset (TCGA, n = 525). Then, the signature was validated in two datasets, including GSE16011 (n = 150) and GSE13041 (n = 191) using the Kaplan Meier method. Univariate and multivariate Cox proportional hazards regression models were used to adjust for clinicopathological factors.

Results

We identified a lymphocyte activation-associated gene signature (TCF3, IGFBP2, TYRO3 and NOD2) in the training dataset and classified the patients into high-risk and low-risk groups with significant differences in overall survival (median survival 15.33 months vs 12.57 months, HR = 1.55, 95% CI [1.28-1.87], log-rank test P < 0.001). This signature showed similar prognostic values in the other two datasets. Further, univariate and multivariate Cox proportional hazards regression models analysis indicated that the signature was an independent prognostic factor for GBM patients. Moreover, we determined that there were differences in lymphocyte activity between the high- and low-risk groups of GBM patients among all datasets. Furthermore, the lymphocyte activation-associated gene signature could significantly predict the survival of patients with certain features, including IDH-wildtype patients and patients undergoing radiotherapy. In addition, the signature may also improve the prognostic power of age.

Conclusions

In summary, our results suggested that the lymphocyte activation-associated gene signature is a promising factor for the survival of patients, which is helpful for the prognosis of GBM patients.

[Long-term therapeutic effects and liver fibrosis changes with direct-antiviral therapy in HIV/HCV co-infected patients]

Objective: To investigate the long-term characteristic changes of virus, immune status, and liver fibrosis markers in human immunodeficiency virus (HIV)/hepatitis C virus (HCV) co-infected patients after receiving direct-antiviral agents (DAAs). Methods: HIV/HCV co-infected patients who visited the Guangzhou Eighth People's Hospital, Guangzhou Medical University from May 2014 to December 2019 were selected as the research subjects. The changes of virological response rate, peripheral blood CD4(+)T lymphocyte level and serological markers of liver fibrosis (APRI score and FIB-4 index) were observed during 144 weeks of follow-up course after the end of DAAs treatment. Kruskal-Wallis test was used for statistical approach. Results: A total of 103 cases were included in the study. There were 87 males (87.5%), with a median age of 44 years. Sustained virological response rate at 12 weeks (SVR12) after DAAs treatment was 97.6%, and the SVR during the entire follow-up period was at least 95.9%. Compared with baseline, CD4(+)T lymphocyte count were significantly increased equally at 12 weeks (Z = -2.283, P = 0.022), 24 weeks (Z = -3.538, P < 0.001), 48 weeks (Z = -3.297, P = 0.001), 96 weeks (Z = -3.562, P < 0.001), and 144 weeks (Z = -2.842, P = 0.004). APRI score (Z = -6.394, P < 0.001) and FIB-4 index (Z = -2.528, P = 0.011) were significantly lower than baseline at week 4 of DAAs treatment, and thereafter remained at a low level, without further declination. Conclusion: HIV/HCV co-infected patients can maintain high SVR for a long time, acquire good immune reconstitution, and significantly improve liver fibrosis after DAAs treatment.

COSMOS next generation - A public knowledge base leveraging chemical and biological data to support the regulatory assessment of chemicals

The COSMOS Database (DB) was originally established to provide reliable data for cosmetics-related chemicals within the COSMOS Project funded as part of the SEURAT-1 Research Initiative. The database has subsequently been maintained and developed further into COSMOS Next Generation (NG), a combination of database and in silico tools, essential components of a knowledge base. COSMOS DB provided a cosmetics inventory as well as other regulatory inventories, accompanied by assessment results and in vitro and in vivo toxicity data. In addition to data content curation, much effort was dedicated to data governance - data authorisation, characterisation of quality, documentation of meta information, and control of data use. Through this effort, COSMOS DB was able to merge and fuse data of various types from different sources. Building on the previous effort, the COSMOS Minimum Inclusion (MINIS) criteria for a toxicity database were further expanded to quantify the reliability of studies. COSMOS NG features multiple fingerprints for analysing structure similarity, and new tools to calculate molecular properties and screen chemicals with endpoint-related public profilers, such as DNA and protein binders, liver alerts and genotoxic alerts. The publicly available COSMOS NG enables users to compile information and execute analyses such as category formation and read-across. This paper provides a step-by-step guided workflow for a simple read-across case, starting from a target structure and culminating in an estimation of a NOAEL confidence interval. Given its strong technical foundation, inclusion of quality-reviewed data, and provision of tools designed to facilitate communication between users, COSMOS NG is a first step towards building a toxicological knowledge hub leveraging many public data systems for chemical safety evaluation. We continue to monitor the feedback from the user community at support@mn-am.com.

Identifying Key Somatic Copy Number Alterations Driving Dysregulation of Cancer Hallmarks in Lower-Grade Glioma

Somatic copy-number alterations (SCNAs) are major contributors to cancer development that are pervasive and highly heterogeneous in human cancers. However, the driver roles of SCNAs in cancer are insufficiently characterized. We combined network propagation and linear regression models to design an integrative strategy to identify driver SCNAs and dissect the functional roles of SCNAs by integrating profiles of copy number and gene expression in lower-grade glioma (LGG). We applied our strategy to 511 LGG patients and identified 98 driver genes that dysregulated 29 cancer hallmark signatures, forming 143 active gene-hallmark pairs. We found that these active gene-hallmark pairs could stratify LGG patients into four subtypes with significantly different survival times. The two new subtypes with similar poorest prognoses were driven by two different gene sets (one including EGFR, CDKN2A, CDKN2B, INFA8, and INFA5, and the other including CDK4, AVIL, and DTX3), respectively. The SCNAs of the two gene sets could disorder the same cancer hallmark signature in a mutually exclusive manner (including E2F_TARGETS and G2M_CHECKPOINT). Compared with previous methods, our strategy could not only capture the known cancer genes and directly dissect the functional roles of their SCNAs in LGG, but also discover the functions of new driver genes in LGG, such as IFNA5, IFNA8, and DTX3. Additionally, our method can be applied to a variety of cancer types to explore the pathogenesis of driver SCNAs and improve the treatment and diagnosis of cancer.

Transcriptomic heterogeneity of driver gene mutations reveals novel mutual exclusivity and improves exploration of functional associations

Background

Lung adenocarcinoma (LUAD), as the most common subtype of lung cancer, is the leading cause of cancer deaths in the world. The accumulation of driver gene mutations enables cancer cells to gradually acquire growth advantage. Therefore, it is important to understand the functions and interactions of driver gene mutations in cancer progression.

Methods

We obtained gene mutation data and gene expression profile of 506 LUAD tumors from The Cancer Genome Atlas (TCGA). The subtypes of tumors with driver gene mutations were identified by consensus cluster analysis.

Results

We found 21 significantly mutually exclusive pairs consisting of 20 genes among 506 LUAD patients. Because of the increased transcriptomic heterogeneity of mutations, we identified subtypes among tumors with non‐silent mutations in driver genes. There were 494 mutually exclusive pairs found among driver gene mutations within different subtypes. Furthermore, we identified functions of mutually exclusive pairs based on the hypothesis of functional redundancy of mutual exclusivity. These mutually exclusive pairs were significantly enriched in nuclear division and humoral immune response, which played crucial roles in cancer initiation and progression. We also found 79 mutually exclusive triples among subtypes of tumors with driver gene mutations, which were key roles in cell motility and cellular chemical homeostasis. In addition, two mutually exclusive triples and one mutually exclusive triple were associated with the overall survival and disease‐specific survival of LUAD patients, respectively.

Conclusions

We revealed novel mutual exclusivity and generated a comprehensive functional landscape of driver gene mutations, which could offer a new perspective to understand the mechanisms of cancer development and identify potential biomarkers for LUAD therapy.

Nomograms for Predicting Axillary Lymph Node Status Reconciled With Preoperative Breast Ultrasound Images

Introduction

The axillary lymph node (ALN) status of breast cancer patients is an important prognostic indicator. The use of primary breast mass features for the prediction of ALN status is rare. Two nomograms based on preoperative ultrasound (US) images of breast tumors and ALNs were developed for the prediction of ALN status.

Methods

A total of 743 breast cancer cases collected from 2016 to 2019 at the Second Affiliated Hospital of Harbin Medical University were randomly divided into a training set (n = 523) and a test set (n = 220). A primary tumor feature model (PTFM) and ALN feature model (ALNFM) were separately generated based on tumor features alone, and a combination of features was used for the prediction of ALN status. Logistic regression analysis was used to construct the nomograms. A receiver operating characteristic curve was plotted to obtain the area under the curve (AUC) to evaluate accuracy, and bias-corrected AUC values and calibration curves were obtained by bootstrap resampling for internal and external verification. Decision curve analysis was applied to assess the clinical utility of the models.

Results

The AUCs of the PTFM were 0.69 and 0.67 for the training and test sets, respectively, and the bias-corrected AUCs of the PTFM were 0.67 and 0.67, respectively. Moreover, the AUCs of the ALNFM were 0.86 and 0.84, respectively, and the bias-corrected AUCs were 0.85 and 0.81, respectively. Compared with the PTFM, the ALNFM showed significantly improved prediction accuracy (p < 0.001). Both the calibration and decision curves of the ALNFM nomogram indicated greater accuracy and clinical practicality. When the US tumor size was ≤21.5 mm, the Spe was 0.96 and 0.92 in the training and test sets, respectively. When the US tumor size was greater than 21.5 mm, the Sen was 0.85 in the training set and 0.87 in the test set. Our further research showed that when the US tumor size was larger than 35 mm, the Sen was 0.90 in the training set and 0.93 in the test set.

Conclusion

The ALNFM could effectively predict ALN status based on US images especially for different US tumor size.

Krüppel-like factor 6 promotes odontoblastic differentiation through regulating the expression of dentine sialophosphoprotein and dentine matrix protein 1 genes

AIM

To investigate the potential role of Krüppel-like factor 6 (KLF6) in the odontoblastic differentiation of immortalized dental papilla mesenchymal cells (iMDP-3) cells.

METHODOLOGY

Alizarin Red S (ARS) and Alkaline phosphatase (ALP) staining was used to examine the mineralization effect of iMDP-3 cells after odontoblastic induction. Real-time PCR and Western blotting were employed to analyse dentine sialophosphoprotein (DSPP), dentine matrix protein 1 (DMP1), RUNX family transcription factor 2 (RUNX2), ALP and KLF6 expression during this process. Co-expression of the KLF6 with DMP1, DSPP and RUNX2 was detected by double immunofluorescence staining to explore their local relationship in the cell. To further investigate KLF6 functions, Klf6 gain- and loss-of-function assays followed by ARS and ALP stainings, real-time PCR and Western blotting were performed using Klf6-overexpression plasmids and Klf6 siRNA to investigate whether changes in Klf6 expression affect the odontoblastic differentiation of iMDP-3 cells. Dual-luciferase reporter assays were used to elucidate the mechanistic regulation of Dspp and Dmp1 expression by Klf6. Means were compared using the unpaired t-test and Kruskal-Wallis one-way anova with P < 0.05 and P < 0.01 defined as statistical significance levels.

RESULTS

The expression levels of Klf6 (P < 0.01), Dspp (P < 0.05), Dmp1 (P < 0.01), Runx2 (P < 0.01) and Alp (P < 0.01) were significantly elevated during odontoblastic differentiation of iMDP-3 cells. KLF6 was co-localized with DSPP, DMP1 and RUNX2 in the cytoplasm and nucleus of iMDP-3 cells. Overexpression of Klf6 promoted the odontoblastic differentiation of iMDP-3, whereas the inhibition of Klf6 prevented this procession. Dual-luciferase assays revealed that Klf6 upregulates Dspp and Dmp1 transcription in iMDP-3 cells during odontoblastic differentiation.

CONCLUSION

Klf6 promoted odontoblastic differentiation by targeting the transcription promoter of Dmp1 and Dspp. This study may offer novel insights into strategies for treating injuries to dental pulp tissue.

Dissecting the Invasion-Associated Long Non-coding RNAs Using Single-Cell RNA-Seq Data of Glioblastoma

Glioblastoma (GBM) is characterized by rapid and lethal infiltration of brain tissue, which is the primary cause of treatment failure and deaths for GBM. Therefore, understanding the molecular mechanisms of tumor cell invasion is crucial for the treatment of GBM. In this study, we dissected the single-cell RNA-seq data of 3345 cells from four patients and identified dysregulated genes including long non-coding RNAs (lncRNAs), which were involved in the development and progression of GBM. Based on co-expression network analysis, we identified a module (M1) that significantly overlapped with the largest number of dysregulated genes and was confirmed to be associated with GBM invasion by integrating EMT signature, experiment-validated invasive marker and pseudotime trajectory analysis. Further, we denoted invasion-associated lncRNAs which showed significant correlations with M1 and revealed their gradually increased expression levels along the tumor cell invasion trajectory, such as VIM-AS1, WWTR1-AS1, and NEAT1. We also observed the contribution of higher expression of these lncRNAs to poorer survival of GBM patients. These results were mostly recaptured in another validation data of 7930 single cells from 28 GBM patients. Our findings identified lncRNAs that played critical roles in regulating or controlling cell invasion and migration of GBM and provided new insights into the molecular mechanisms underlying GBM invasion as well as potential targets for the treatment of GBM.

Opsin 5 is a key regulator of ultraviolet radiation-induced melanogenesis in human epidermal melanocytes

Background

Human skin, which is constantly exposed to solar ultraviolet radiation (UVR), has a unique ability to respond by increasing its pigmentation in a protective process driven by melanogenesis in human epidermal melanocytes (HEMs). However, the molecular mechanisms used by HEMs to detect and respond to UVR remain unclear.

Objectives

To investigate the function and potential mechanism of opsin 5 (OPN5), a photoreceptor responsive to UVR wavelengths, in melanogenesis in HEMs.

Methods

Melanin content in HEMs was determined using the NaOH method, and activity of tyrosinase (TYR) (a key enzyme in melanin synthesis) was determined by the l‐DOPA method. OPN5 expression in UVR‐treated vs. untreated HEMs and explant tissues was detected by reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR), Western blotting and immunofluorescence. Short interfering RNA‐mediated OPN5 knockdown and a lentivirus OPN5 overexpression model were used to examine their respective effects on TYR, tyrosinase‐related protein 1 (TRP1), TRP2 and microphthalmia‐associated transcription factor (MITF) expression, under UVR. Changes in expression of TYR, TRP1 and TRP2 caused by changes in OPN5 expression level were detected by RT‐qPCR and Western blot. Furthermore, changes in signalling pathway proteins were assayed.

Results

We found that OPN5 is the key sensor in HEMs responsible for UVR‐induced melanogenesis. OPN5‐induced melanogenesis required Ca²⁺‐dependent G protein‐coupled receptor‐ and protein kinase C signal transduction, thus contributing to the UVR‐induced MITF response to mediate downstream cellular effects, and providing evidence of OPN5 function in mammalian phototransduction. Remarkably, OPN5 activation was necessary for UVR‐induced increase in cellular melanin and has an inherent function in melanocyte melanogenesis.

Conclusions

Our results provide insight into the molecular mechanisms of UVR sensing and phototransduction in melanocytes, and may reveal molecular targets for preventing pigmentation or pigment diseases.

What is already known about this topic?

Ultraviolet radiation (UVR) induces a protective response to DNA damage mediated by melanin synthesis in human epidermal melanocytes (HEMs).

Tyrosinase (TYR), with tyrosinase‐related proteins (TRP1, TRP2), are the key enzymes for melanin synthesis.

Microphthalmia‐associated transcription factor regulates key genes for melanocyte development and differentiation, and can stimulate melanogenesis by activating transcription of TYR and other pigmentation genes, including TRP1.

Opsin 5 (OPN5) is known to function as a photoreceptor responsive to wavelengths in the near UV spectrum.

What does this study add?

UVR induces melanogenesis in HEMs via OPN5.

OPN5 regulates expression of TYR, TRP1 and TRP2 through the calcium‐dependent G protein‐coupled and protein kinase C signalling pathways.

OPN5 has an inherent role in HEMs in mediating melanogenesis.

What is the translational message?

OPN5 was discovered as a key sensor for UVR‐induced melanogenesis in human skin melanocytes.

It could be a target for early treatment of pigmentation or pigment diseases, to provide a more personalized and economically feasible method.

Linked Comment: L.V.M. de Assis and A.M. de Lauro Castrucci. Br J Dermatol 2021; 185:249–250.

Plain language summary available online

Breast cancer prognosis signature: linking risk stratification to disease subtypes

Breast cancer is a very complex and heterogeneous disease with variable molecular mechanisms of carcinogenesis and clinical behaviors. The identification of prognostic risk factors may enable effective diagnosis and treatment of breast cancer. In particular, numerous gene-expression-based prognostic signatures were developed and some of them have already been applied into clinical trials and practice. In this study, we summarized several representative gene-expression-based signatures with significant prognostic value and separately assessed their ability of prognosis prediction in their originally targeted populations of breast cancer. Notably, many of the collected signatures were originally designed to predict the outcomes of estrogen receptor positive (ER+) patients or the whole breast cancer cohort; there are no typical signatures used for the prognostic prediction in a specific population of patients with the intrinsic subtype. We thus attempted to identify subtype-specific prognostic signatures via a computational framework for analyzing multi-omics profiles and patient survival. For both the discovery and an independent data set, we confirmed that subtype-specific signature is a strong and significant independent prognostic factor in the corresponding cohort. These results indicate that the subtype-specific prognostic signature has a much higher resolution in the risk stratification, which may lead to improved therapies and precision medicine for patients with breast cancer.

Identification of a Six-lncRNA Signature With Prognostic Value for Breast Cancer Patients

Breast cancer (BRCA) is the most common cancer and a major cause of death in women. Long non-coding RNAs (lncRNAs) are emerging as key regulators and have been implicated in carcinogenesis and prognosis. In this study, we aimed to develop a lncRNA signature of BRCA patients to improve risk stratification. In the training cohort (GSE21653, n = 232), 17 lncRNAs were identified by univariate Cox proportional hazards regression, which were significantly associated with patients’ survival. The least absolute shrinkage and selection operator-penalized Cox proportional hazards regression analysis was used to identify a six-lncRNA signature. According to the median of the signature risk score, patients were divided into a high-risk group and a low-risk group with significant disease-free survival differences in the training cohort. A similar phenomenon was observed in validation cohorts (GSE42568, n = 101; GSE20711, n = 87). The six-lncRNA signature remained as independent prognostic factors after adjusting for clinical factors in these two cohorts. Furthermore, this signature significantly predicted the survival of grade III patients and estrogen receptor-positive patients. Furthermore, in another cohort (GSE19615, n = 115), the low-risk patients that were treated with tamoxifen therapy had longer disease-free survival than those who underwent no therapy. Overall, the six-lncRNA signature can be a potential prognostic tool used to predict disease-free survival of patients and to predict the benefits of tamoxifen treatment in BRCA, which will be helpful in guiding individualized treatments for BRCA patients.

Transcriptome analysis reveals a reprogramming energy metabolism-related signature to improve prognosis in colon cancer

Although much progress has been made to improve treatment, colon cancer remains a leading cause of cancer death worldwide. Metabolic reprogramming is a significant ability of cancer cells to ensure the necessary energy supply in uncontrolled proliferation. Since reprogramming energy metabolism has emerged as a new hallmark of cancer cells, accumulating evidences have suggested that metabolism-related genes may serve as key regulators of tumorigenesis and potential biomarkers. In this study, we analyzed a set of reprogramming energy metabolism-related genes by transcriptome analysis in colon cancer and revealed a five-gene signature that could significantly predict the overall survival. The reprogramming energy metabolism-related signature could distinguish patients into high-risk and low-risk groups with significantly different survival times (P = 0.0011; HR = 1.92; 95% CI [1.29–2.87]). Its prognostic value was confirmed in another two independent colon cancer cohorts (P = 5.2e–04; HR = 2.09, 95%; CI [1.37–3.2] for GSE17538 and P = 3.8e−04; HR = 2.08, 95% CI [1.37–3.16] for GSE41258). By multivariable analysis, we found that the signature was independent of clinicopathological features. Its power in promoting risk stratification of the current clinical stage was then evaluated by stratified analysis. Moreover, the signature could improve the power of the TNM stage for the prediction of overall survival and could be used in patients who received adjuvant chemotherapy. Overall, our results demonstrated the important role of the reprogramming energy metabolism-related signature in promoting stratification of high-risk patients, which could be diagnostic of adjuvant therapy benefit.

Measurement of the Spectral Shape of the β-Decay of ^{137}Xe to the Ground State of ^{137}Cs in EXO-200 and Comparison with Theory

We report on a comparison between the theoretically predicted and experimentally measured spectra of the first-forbidden nonunique β-decay transition ^{137}Xe(7/2^{-})→^{137}Cs(7/2^{+}). The experimental data were acquired by the EXO-200 experiment during a deployment of an AmBe neutron source. The ultralow background environment of EXO-200, together with dedicated source deployment and analysis procedures, allowed for collection of a pure sample of the decays, with an estimated signal to background ratio of more than 99 to 1 in the energy range from 1075 to 4175 keV. In addition to providing a rare and accurate measurement of the first-forbidden nonunique β-decay shape, this work constitutes a novel test of the calculated electron spectral shapes in the context of the reactor antineutrino anomaly and spectral bump.

CellMarker: a manually curated resource of cell markers in human and mouse

One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up new ways to track this question by revealing substantial cell markers for distinguishing different cell types in tissues. Here, we developed the CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/ or http://bio-bigdata.hrbmu.edu.cn/CellMarker/), aiming to provide a comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. By manually curating over 100 000 published papers, 4124 entries including the cell marker information, tissue type, cell type, cancer information and source, were recorded. At last, 13 605 cell markers of 467 cell types in 158 human tissues/sub-tissues and 9148 cell makers of 389 cell types in 81 mouse tissues/sub-tissues were collected and deposited in CellMarker. CellMarker provides a user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Furthermore, a summarized marker prevalence in each cell type is graphically and intuitively presented through a vivid statistical graph. We believe that CellMarker is a comprehensive and valuable resource for cell researches in precisely identifying and characterizing cells, especially at the single-cell level.

Genome-wide Identification of Foxf2 Target Genes in Palate Development

Cleft palate is among the most common structural birth defects in humans. Previous studies have shown that mutations in FOXF2 are associated with cleft palate in humans and mice and that Foxf2 acts in a Shh-Foxf-Fgf18-Shh molecular network controlling palatal shelf growth. In this study, we combined RNA-seq and ChIP-seq approaches to identify direct transcriptional target genes mediating Foxf2 function in palate development in mice. Of 155 genes that exhibited Foxf2-dependent expression in the developing palatal mesenchyme, 88 contained or were located next to Foxf2-binding sites. Through in situ hybridization analyses, we demonstrate that expression of many of these target genes, including multiple genes encoding transcription factors and several encoding extracellular matrix-modifying proteins, were specifically upregulated in the posterior region of palatal shelves in Foxf2^-/- mouse embryos. Foxf2 occupancy at many of these putative target loci, including Fgf18, in the developing palatal tissues was verified by ChIP-polymerase chain reaction analyses. One of the Foxf2 target genes, Chst2, encodes a carbohydrate sulfotransferase integral to glycosaminoglycan sulfation. Correlating with ectopic Chst2 expression, Foxf2^-/- embryos a exhibited region-specific increase in sulfated keratan sulfate and a concomitant reduction in chondroitin sulfate accumulation in the posterior palatal mesenchyme. However, expression of the core protein of versican, a major chondroitin sulfate proteoglycan important in palatal shelf morphogenesis, was increased, whereas expression of collagen I was reduced in the corresponding region of the palatal mesenchyme. These results indicate that, in addition to regulating palatal shelf growth through the Fgf18-Shh signaling network, Foxf2 controls palatal shelf morphogenesis through regulating expression of multiple transcription factors as well as through directly controlling the synthesis and processing of extracellular matrix components in the palatal mesenchyme. Our ChIP-seq and RNA-seq data sets provide an excellent resource for comprehensive understanding of the molecular network controlling palate development.

Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids

Engineered organoids by sequential introduction of key mutations could help modeling the dynamic cancer progression. However, it remains difficult to determine gene paths which were sufficient to capture cancer behaviors and to broadly explain cancer mechanisms. Here, as a case study of colorectal cancer (CRC), functional and dynamic characterizations of five types of engineered organoids with different mutation combinations of five driver genes (APC, SMAD4, KRAS, TP53, and PIK3CA) showed that sequential introductions of all five driver mutations could induce enhanced activation of more hallmark signatures, tending to cancer. Comparative analysis of engineered organoids and corresponding CRC tissues revealed sequential introduction of key mutations could continually shorten the biological distance from engineered organoids to CRC tissues. Nevertheless, there still existed substantial biological gaps between the engineered organoid even with five key mutations and CRC samples. Thus, we proposed an integrative strategy to prioritize gene cascading paths for shrinking biological gaps between engineered organoids and CRC tissues. Our results not only recapitulated the well-known adenoma–carcinoma sequence model (e.g., AKST-organoid with driver mutations in APC, KRAS, SMAD4, and TP53), but also provided potential paths for delineating alternative pathogenesis underlying CRC populations (e.g., A-organoid with APC mutation). Our strategy also can be applied to both organoids with more mutations and other cancers, which can improve and innovate mechanism across cancer patients for drug design and cancer therapy.

Requirement of Hyaluronan Synthase-2 in Craniofacial and Palate Development

Cleft palate is a common major birth defect resulting from disruption of palatal shelf growth, elevation, or fusion during fetal palatogenesis. Whereas the molecular mechanism controlling palatal shelf elevation is not well understood, a prevailing hypothesis is that region-specific accumulation of hyaluronan, a predominant extracellular glycosaminoglycan in developing palatal mesenchyme, plays a major role in palatal shelf elevation. However, direct genetic evidence for a requirement of hyaluronan in palate development is still lacking. In this study, we show that Has2, 1 of 3 hyaluronan synthases in mammals, plays a major role in hyaluronan synthesis in the neural crest-derived craniofacial mesenchyme during palatogenesis in mice. We analyzed developmental defects caused by tissue-specific inactivation of Has2 throughout the cranial neural crest lineage or specifically in developing palatal or mandibular mesenchyme, respectively, using Wnt1-Cre, Osr2-Cre, and Hand2-Cre transgenic mice. Inactivation of Has2 either throughout the neural crest lineage or specifically in the developing palatal mesenchyme caused reduced palatal shelf size and increased palatal mesenchyme cell density prior to the time of normal palatal shelf elevation. Whereas both Has2f/f;Wnt1-Cre and Has2f/f;Osr2-Cre mutant mice exhibit cleft palate at complete penetrance, the Has2f/f; Wnt1-Cre fetuses showed dramatically reduced mandible size and complete failure of palatal shelf elevation, whereas Has2f/f;Osr2-Cre fetuses had normal mandibles and delayed palatal shelf elevation. All Has2f/f;Hand2-Cre pups showed reduced mandible size and about 50% of them had cleft palate with disruption of palatal shelf elevation. Results from explant culture assays indicate that disruption of palatal shelf elevation in Has2f/f;Hand2-Cre mutant fetuses resulted from physical obstruction by the malformed mandible and tongue. Together, these data indicate that hyaluronan plays a crucial intrinsic role in palatal shelf expansion and timely reorientation to the horizontal position above the tongue as well as an important role in mandibular morphogenesis that secondarily affects palatal shelf elevation.

Opsin 3 is a key regulator of ultraviolet A-induced photoageing in human dermal fibroblast cells

Background

Chronic exposure to ultraviolet (UV) radiation (mainly UVA) induces a sustained increase of matrix metalloproteinases (MMPs), especially MMP1, MMP2, MMP3 and MMP9 in human skin fibroblasts. MMPs can lead to the degradation of fibrous connective tissue, which is the main cause of skin photoageing. The molecular mechanisms through which fibroblasts sense UVA and trigger the cell signalling pathways involved in the upregulation of MMPs have not been well elucidated.

Objectives

Here, we investigated the function and potential mechanisms of photoageing of opsin (OPN)3 in normal human dermal fibroblasts (NHDFs).

Methods

Real‐time polymerase chain reaction and Western blot analysis were used to analyse the expression levels of OPN3 in NHDFs and photoageing models. Subsequently, NHDFs transfected with OPN3 inhibitors and indicators related to photoageing before and after UVA irradiation included expression levels of MMP1, MMP2, MMP3 and MMP9, and signalling pathway protein molecules were examined.

Results

We provide evidence that OPN3 initiates UVA phototransduction in NHDFs. OPN3 triggers phosphorylation of activator protein 1 and ultimately upregulates MMP1, MMP2, MMP3 and MMP9 in NHDFs through activating Ca²⁺/calmodulin‐dependent protein kinase II, cyclic adenosine monophosphate response element‐binding protein, extracellular signal‐regulated kinase, c‐JUN N‐terminal kinase and p38. Here, we demonstrate for the first time that OPN3 is the key sensor responsible for upregulating MMP1, MMP2, MMP3 and MMP9 in NHDFs following UVA exposure via the calcium‐dependent G protein‐coupled signalling pathway.

Conclusions

Our studies provide insights into the understanding of the molecular mechanisms through which human skin cells respond to UVA radiation and may reveal molecular targets for skin photoageing prevention or clinical management.

What's already known about this topic?

Photoaged fibroblasts accumulate with long‐term ultraviolet (UV) exposure.

Matrix metalloproteinases (MMPs) play an important role in the pathogenesis of photoageing.

MMP1, MMP2, MMP3 and MMP9 are responsible for the destruction of fibroblast collagen in severely photodamaged skin.

Opsins (OPNs) are light‐sensitive members of the superfamily of heptahelical G protein‐coupled receptors, a family of cell surface receptors that are activated by a variety of stimuli and mediate signalling across membranes.

What does this study add?

OPN3 is highly expressed in fibroblasts and responds to UVA irradiation.

OPN3 regulates the expression of MMP1, MMP2, MMP3 and MMP9 via the calcium‐dependent G protein‐coupled signalling pathway.

OPN3 is a light‐sensitive sensor that plays an important role in photoageing of the skin.

Linked Comment: Julie Thornton. Br J Dermatol 2020; 182:1086–1087.

Plain language summary available online

Search for Neutrinoless Double-β Decay with the Complete EXO-200 Dataset

A search for neutrinoless double-β decay (0νββ) in ^{136}Xe is performed with the full EXO-200 dataset using a deep neural network to discriminate between 0νββ and background events. Relative to previous analyses, the signal detection efficiency has been raised from 80.8% to 96.4±3.0%, and the energy resolution of the detector at the Q value of ^{136}Xe 0νββ has been improved from σ/E=1.23% to 1.15±0.02% with the upgraded detector. Accounting for the new data, the median 90% confidence level 0νββ half-life sensitivity for this analysis is 5.0×10^{25}  yr with a total ^{136}Xe exposure of 234.1 kg yr. No statistically significant evidence for 0νββ is observed, leading to a lower limit on the 0νββ half-life of 3.5×10^{25}  yr at the 90% confidence level.

Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines

Epigenetic modifications play critical roles in modulating gene expression, yet their roles in regulatory networks in human cell lines remain poorly characterized. We integrated multiomics data to construct directed regulatory networks with nodes and edges labeled with chromatin states in human cell lines. We observed extensive association of diverse chromatin states and network motifs. The gene expression analysis showed that diverse chromatin states of coherent type-1 feedforward loop (C1-FFL) and incoherent type-1 feedforward loops (I1-FFL) contributed to the dynamic expression patterns of targets. Notably, diverse chromatin state compositions could help C1- or I1-FFL to control a large number of distinct biological functions in human cell lines, such as four different types of chromatin state compositions cooperating with K562-associated C1-FFLs controlling “regulation of cytokinesis,” “G1/S transition of mitotic cell cycle,” “DNA recombination,” and “telomere maintenance,” respectively. Remarkably, we identified six chromatin state-marked C1-FFL instances (HCFC1-NFYA-ABL1, THAP1-USF1-BRCA2, ZNF263-USF1-UBA52, MYC-ATF1-UBA52, ELK1-EGR1-CCT4, and YY1-EGR1-INO80C) could act as prognostic biomarkers of acute myelogenous leukemia though influencing cancer-related biological functions, such as cell proliferation, telomere maintenance, and DNA recombination. Our results will provide novel insight for better understanding of chromatin state-mediated gene regulation and facilitate the identification of novel diagnostic and therapeutic biomarkers of human cancers.

Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements

Over the past decade, thousands of long noncoding RNAs (lncRNAs) have been identified, many of which play crucial roles in normal physiology and human disease. LncRNAs can interact with chromatin and then recruit protein complexes to remodel chromatin states, thus regulating gene expression. However, how lncRNA-chromatin interactions contribute to their biological functions is largely unknown. Here, we collected and constructed an atlas of 188,647 lncRNA-chromatin interactions in human and mouse. All lncRNAs showed diverse epigenetic modification patterns at their binding sites, especially the marks of enhancer activity. Functional analysis of lncRNA target genes further revealed that lncRNAs could exert their functions by binding to both promoter and distal regulatory elements, especially the distal regulatory elements. Intriguingly, many important pathways were observed to be widely regulated by lncRNAs through distal binding. For example, NEAT1, a cancer lncRNA, controls 13.3% of genes in the PI3K-AKT signaling pathway by interacting with distal regulatory elements. In addition, "two-gene" signatures composed of a lncRNA and its distal target genes, such as HOTAIR-CRIM1, provided significant clinical benefits relative to the lncRNA alone. In summary, our findings underscored that lncRNA-distal interactions were essential for lncRNA functions, which would provide new clues to understand the molecular mechanisms of lncRNAs in complex disease.

DiseaseEnhancer: a resource of human disease-associated enhancer catalog

Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribution to disease progression. To facilitate better usage of published data and exploring enhancer deregulation in various human diseases, we created DiseaseEnhancer (http://biocc.hrbmu.edu.cn/DiseaseEnhancer/), a manually curated database for disease-associated enhancers. As of July 2017, DiseaseEnhancer includes 847 disease-associated enhancers in 143 human diseases. Database features include basic enhancer information (i.e. genomic location and target genes); disease types; associated variants on the enhancer and their mediated phenotypes (i.e. gain/loss of enhancer and the alterations of transcription factor bindings). We also include a feature on our website to export any query results into a file and download the full database. DiseaseEnhancer provides a promising avenue for researchers to facilitate the understanding of enhancer deregulation in disease pathogenesis, and identify new biomarkers for disease diagnosis and therapy.

Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability

Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial cancer pathways. Recently, there is considerable evidence showing that, mutual exclusivity reflects alternative functions in tumor initiation and progression, or suggests adverse effects of their concurrence. Given its importance, numerous computational approaches have been proposed to study mutual exclusivity using genomic profiles alone, or by integrating networks and phenotypes. Some of them have been routinely used to explore genetic associations, which lead to a deeper understanding of carcinogenic mechanisms and reveals unexpected tumor vulnerabilities. Here, we present an overview of mutual exclusivity from the perspective of cancer genome. We describe the common hypothesis underlying mutual exclusivity, summarize the strategies for the identification of significant mutually exclusive patterns, compare the performance of representative algorithms from simulated data sets and discuss their common confounders.

Association between phosphodiesterase type 5 inhibitors use and risk of melanoma: a meta-analysis

This meta-analysis aimed to clarify the actual association between the phosphodiesterase type 5 inhibitors (PDE5-Is) use and the risk of melanoma in erectile dysfunction (ED) patients. A systematic literature search was conducted in online databases in October, 2016 to identify studies focusing on the association between PDE5-Is use and the risk of melanoma. Summarized multivariate adjusted risk ratios (RRs) and 95% confidence intervals (CIs) were calculated to assess the strength of associations. A total of six clinical trials containing more than one million participants were included. ED patients  using PDE5-Is shared a significant high risk of melanoma (RR=1.12, 95% CI=1.03-1.21, p=0.006). Positive associations were observed in all kinds of prescriptions: single prescription (RR=1.20, 95% CI=1.06-1.35, p=0.003), medium number of prescription (RR=1.15, 95% CI=1.01-1.30, p=0.03), and high number of prescription (RR=1.18, 95% CI=1.05-1.34, P=0.006). Additionally, PDE5-Is were also found to be significantly associated with increased risk of basal cell carcinoma (RR=1.14, 95% CI=1.09-1.19, p<0.00001). Our study indicates that PDE5-Is use could significantly increase the risk of melanoma and basal cell carcinoma. However, the risk of melanoma did not rise significantly with the increased number of prescriptions. Consequently, owing to the lack of information about other potential synergistic factors, it is difficult for us to make a solid conclusion that application of PDE5-Is is the direct cause of increased risk of melanoma. Their relationship needs to be validated by further evidences.

[Discussion on optimal duration of pegylated interferon α combined with ribavirin for chronic hepatitis C in HIV-infected patients]

Objective: To investigate the optimal duration of pegylated-alpha interferon (Peg-INFα) combined with ribavirin (RBV) in treating chronic hepatitis C infection in human immunodeficiency virus (HIV)-infected patients. Methods: A multicenter prospective study was conducted. The study subjects were divided into two groups; HIV/HCV co-infections (Group A, n = 158) and control with HCV-monoinfections (Group B, n = 60). All recruited patients received standard Peg-INFα plus RBV therapy. Group A was divided into 3 subgroups according to CD4(+) cell counts: A1 subgroup, 79 cases, CD4(+) counts > 350 cells /μl, who received anti-HCV before combination antiretroviral therapy(cART); A2 subgroup, 45 cases, CD4(+) counts between 200 and 350 cells/μl, who did not start anti-HCV until they could tolerate cART well; A3 subgroup, 34 cases, CD4(+) counts < 200 cells /μl, cART was administered first, and anti-HCV therapy was started when CD4(+) counts > 200 cells/μl. The anti-HCV efficacy of two groups and 3 subgroups were compared. Statistical analysis for normal distribution and homogeneity of variance data was calculated by t-test and the counting data was analyzed by χ (2) test. The Mann-Whitney U test was used for non-normal data. A one-way analysis of variance (ANOVA) was used for the comparison of multiple groups, followed by SNK method. Multiple independent samples were used for non-parametric tests. Results: There was no significant difference in age and baseline HCV RNA levels between groups and subgroups (P > 0.05). By an intent-to-treat (ITT) analysis, in Group A, the ratio of complete early virological response (cEVR) rate was 75.3% (119/158), the ratio of end of treatment virological response (eTVR) rate was 68.4% (108/158), and the ratio of sustained virological response (SVR) rate was 48.7% (77/158); in Group B, the ratio of cEVR rate was 93.3% (56/60), the ratio of eTVR rate was 90.0% (54/60), and the ratio of SVR rate was 71.7% (43/60); The therapeutic index of Group A were lower than those of Group B (P≤0.05). By per-protocol (PP) analysis, the ratio of cEVR rate in Group A [75.2% (88/112)] was still lower than that in Group B [93.3% (56/60)], but no significant differences were found in the ratio of eTVR rate and SVR rate between 2 groups (P > 0.05). Comparing the efficacy of subgroups (A1, A2 and A3) by ITT analysis, the ratios of cEVR rate were respectively 78.5% (62/79), 75.6% (34/45) and 67.6% (23/34); the ratios of eTVR rate were respectively 68.4%(54/79), 80.0%(36/45)and 52.9%(18/34); and the ratios of SVR rate were respectively 41.8%(33/79), 64.4%(29/45)and 44.1%(15/34). The ratio of eTVR in subgroup A2 was obviously higher than that in subgroup A3 and the ratio of SVR in subgroup A2 was statistically higher than that of subgroup A1(P≤0.05). However, by PP analysis, no significant differences of the therapeutic indexes were found among the respective subgroups (P > 0.05). Conclusion: HIV-HCV co-infected patients would have better anti-HCV efficacy with Peg-INFα-2a plus RBV than HCV- monoinfected patients. The best time for initiating anti-HCV therapy in HIV-HCV co-infected patients is when CD4(+) counts 200 cells/ μl.