The deep learning framework iCanTCR enables early cancer detection using the T cell receptor repertoire in peripheral blood.

T cells recognize tumor antigens and initiate an anti-cancer immune response in the very early stages of tumor development, and the antigen specificity of T cells is determined by the T cell receptor (TCR). Therefore, monitoring changes in the TCR repertoire in peripheral blood may offer a strategy to detect various cancers at a relatively early stages. Here, we developed the deep learning framework iCanTCR to identify cancer patients based on the TCR repertoire. The iCanTCR framework uses TCRß sequences from an individual as an input and outputs the predicted cancer probability. The model was trained on over 2000 publicly available TCR repertoires from eleven types of cancer and healthy controls. Analysis of several additional publicly available datasets validated the ability of iCanTCR to distinguish cancer patients from non-cancer individuals and demonstrated the capability of iCanTCR for the accurate classification of multiple cancers. Importantly, iCanTCR precisely identified individuals with early-stage cancer with an area under the curve (AUC) of 86%. Altogether, this work provides a liquid biopsy approach to capture immune signals from peripheral blood for non-invasive cancer diagnosis.

The first 3D-bioprinted personalized active bone to repair bone defects: A case report.

The repair and reconstruction of bone defects are still major problems to be solved in the field of orthopedics. Meanwhile, 3D-bioprinted active bone implants may provide a new and effective solution. In this case, we used bioink prepared from the patient's autologous platelet-rich plasma (PRP) combined with polycaprolactone/ß-tricalcium phosphate (PCL/ß-TCP) composite scaffold material to print personalized PCL/ß-TCP/PRP active scaffolds layer by layer through 3D bioprinting technology. The scaffold was then applied in the patient to repair and reconstruct bone defect after tibial tumor resection. Compared with traditional bone implant materials, 3D-bioprinted personalized active bone will have significant clinical application prospects due to its advantages of biological activity, osteoinductivity, and personalized design.

Comprehensive Analysis of Regulatory Networks of m6A Regulators and Reveals Prognosis Biomarkers in Sarcoma.

Sarcomas are rare malignant tumors that may arise from anywhere of the body, such as bone, adipose, muscle and vascular. However, the conventional pathogenesis of sarcomas has not been found. Therefore, there is an urgent need to identify novel therapeutic strategies and improve prognosis effects for sarcomas. Methylation of N6 adenosine (m6A) regulation is a novel proposed regulatory pattern that works in post-transcription level, which was also the most widely distributed methylation modification in eukaryotic mRNA. Growing evidences have demonstrated that m6A modification played an indispensable role in tumorigenesis. Here, we integrated multi-omics data including genetic alterations, gene expression and epigenomics regulation to systematically analysis the regulatory atlas of 21 m6A regulators in sarcoma. Firstly, we investigated the genetic alterations of m6A regulators and found that ~44% TCGA sarcoma patients have genetic mutations. We also investigated the basic annotation of 21 regulators, such as expression correlation and PPI interactions. Then we identified the upstream and downstream regulatory networks of between transcription factors (TFs)/non-coding RNAs and m6A regulators in sarcoma based on motif analysis and gene expression. These results implied that m6A regulator mediated regulatory axes could be used as prognostic biomarkers in sarcoma. Knockdown experiment results revealed that m6A regulators, YTHDF2 and HNRNPA2B1 participated in the cancer cell invasion and metastasis. Moreover, we also found that the expression levels of m6A regulators were related to immune cell infiltration of sarcoma patients.

Integrated Analysis of the Transcriptome Profile Reveals the Potential Roles Played by Long Noncoding RNAs in Immunotherapy for Sarcoma.

BACKGROUND: Long-term survival is still low for high-risk patients with soft tissue sarcoma treated with standard management options, including surgery, radiation, and chemotherapy. Immunotherapy is a promising new potential treatment paradigm. However, the application of immune checkpoint inhibitors for the treatment of patients with sarcoma did not yield promising results in a clinical trial. Therefore, there is a considerable need to identify factors that may lead to immune checkpoint inhibitor resistance. METHODS: In this study, we performed a bioinformatic analysis of The Cancer Genome Atlas (TCGA) to detect key long noncoding RNAs (lncRNAs) that were correlated with immune checkpoint inhibitory molecules in sarcoma. The expression levels of these lncRNAs and their correlation with patient prognosis were explored. The upstream long noncoding RNAs were also examined via 450K array data from the TCGA. The potential roles of these lncRNAs were further examined via KEGG and GO analysis using DAVID online software. Finally, the relationship between these lncRNAs and immune cell infiltration in tumors and their effect on immune checkpoint inhibitors were further explored. RESULTS: We identified lncRNAs correlated with tumor cell immune evasion in sarcoma. The expression of these lncRNAs was upregulated and correlated with worse prognosis in sarcoma and other human cancer types. Moreover, low DNA methylation occupation of these lncRNA loci was detected. Negative correlations between DNA methylation and lncRNA expression were also found in sarcoma and other human cancer types. KEGG and GO analyses indicated that these lncRNAs correlated with immune evasion and negative regulation of the immune response in sarcoma. Finally, high expression of these lncRNAs correlated with more suppressive immune cell infiltration and reduced sensitivity to immune checkpoint inhibitors in sarcoma and other human cancer types. CONCLUSION: Our results suggest that long noncoding RNAs confer immune checkpoint inhibitor resistance in human cancer. Further characterization of these lncRNAs may help to elucidate the mechanisms underlying immune checkpoint inhibitor resistance and uncover a novel therapeutic intervention point for immunotherapy.

Contribution of epicardial and abdominopelvic visceral adipose tissues in Chinese adults with impaired glucose regulation and diabetes.

AIMS: To quantify epicardial adipose tissue (EAT) and visceral adipose tissue (VAT) in Chinese adults with impaired glucose regulation (IGR) or diabetes and compare the contributions of EAT and VAT to the occurrence of IGR and diabetes with those of traditional obesity indices. METHODS: Cardiac and abdominopelvic noncontrast computed tomographic images of 668 individuals were used to measure EAT and VAT volume. Multivariable logistic regression and area under the receiver operating characteristic (ROC) curve were used to illustrate the contributions of these tissues. RESULTS: Patients with IGR or diabetes had larger EAT and VAT volumes than did the controls, and the VAT volume was significantly different between the IGR and diabetic groups. In multivariable models, higher EAT or VAT volume was positively associated with the presence of IGR and diabetes. After adjusting further for body mass index (BMI) and waist-to-hip ratio (WHR), a higher EAT volume was still positively associated with IGR (odds ratio (OR) = 1.46; 95% confidence interval (CI), 1.04-2.03), and a higher VAT volume was positively associated with IGR (OR = 1.86; 95% CI, 1.15-3.02) and diabetes (OR = 1.86; 95% CI, 1.16-2.99). The areas under the curve (AUCs) of the association of EAT (AUC = 0.751; 95% CI, 0.712-0.789) and VAT (AUC = 0.752; 95% CI, 0.713-0.792) with dysglycemia (IGR + diabetes) were significantly larger than those of the traditional obesity indices (all P < 0.05). CONCLUSIONS: High EAT or VAT volume is positively associated with IGR and diabetes in Chinese adults. With a given WHR and BMI, such an association still exists to some extent. The correlation may be stronger than those of the traditional obesity indices.

Modulation of autophagy in human diseases strategies to foster strengths and circumvent weaknesses.

Autophagy is central to the maintenance of intracellular homeostasis across species. Accordingly, autophagy disorders are linked to a variety of diseases from the embryonic stage until death, and the role of autophagy as a therapeutic target has been widely recognized. However, autophagy-associated therapy for human diseases is still in its infancy and is supported by limited evidence. In this review, we summarize the landscape of autophagy-associated diseases and current autophagy modulators. Furthermore, we investigate the existing autophagy-associated clinical trials, analyze the obstacles that limit their progress, offer tactics that may allow barriers to be overcome along the way and then discuss the therapeutic potential of autophagy modulators in clinical applications.

Landscape of tumor suppressor long noncoding RNAs in breast cancer.

BACKGROUND: The landscape and biological functions of tumor suppressor long noncoding RNAs in breast cancer are still unknown. METHODS: Data from whole transcriptome sequencing of 33 breast specimens in the Harbin Medical University Cancer Center cohort and The Cancer Genome Atlas was applied to identify and validate the landscape of tumor suppressor long noncoding RNAs, which was further validated by The Cancer Genome Atlas pancancer data including 33 cancer types and 12,839 patients. Next, the expression model, prognostic roles, potential biological functions and epigenetic regulation of tumor suppressor long noncoding RNAs were investigated and validated in the breast cancer and pancancer cohorts. Finally, EPB41L4A-AS2 was selected to validate our novel finding, and the tumor suppressive roles of EPB41L4A-AS2 in breast cancer were examined. RESULTS: We identified and validated the landscape of tumor suppressor long noncoding RNAs in breast cancer. The expression of the identified long noncoding RNAs was downregulated in cancer tissue samples compared with normal tissue samples, and these long noncoding RNAs correlated with a favorable prognosis in breast cancer patients and the patients in the pancancer cohort. Multiple carcinogenesis-associated biological functions were predicted to be regulated negatively by these long noncoding RNAs. Moreover, these long noncoding RNAs were transcriptionally regulated by epigenetic modification, including DNA methylation and histone methylation modification. Finally, EPB41L4A-AS2 inhibited breast cancer cell proliferation, migration and invasion and induced cell apoptosis in vitro. Mechanistically, EPB41L4A-AS2, acting at least in part as a tumor suppressor, upregulated tumor suppressor gene expression. Moreover, ZNF217 recruited EZH2 to the EPB41L4A-AS2 locus and suppressed the expression of EPB41L4A-AS2 by epigenetically increasing H3K27me3 enrichment. CONCLUSIONS: This work enlarges the functional landscape of known long noncoding RNAs in human cancer and provides novel insights into the suppressive roles of these long noncoding RNAs.

Upregulation of DLEU1 expression by epigenetic modification promotes tumorigenesis in human cancer.

The function of DLEU1 in human cancer is largely unknown. The Cancer Genome Atlas data were applied to identify the landscape of differential genes between tumor tissues and normal tissues, which was further validated by our cohort data and pan-cancer data including 33 cancer types with 11,060 patients. Next, DLEU1 was selected to validate the novel finding and result showed that it promoted tumorigenesis in vitro and in vivo. Mechanistically, DLEU1 promotes SRP4 expression via increasing H3K27ac enrichment to SRP4 locus epigenetically. Moreover, epigenetic modification leads to upregulation of DLEU1 expression via decreased DNA methylation and increased H3K27ac and H3K4me3 histone modification in its locus. Finally, high expression of DLEU1 correlates with worse prognosis not only in specific cancer type patients but also in patients in the pan-cancer cohort. In summary, the work broadens the function landscape of known long noncoding RNAs in human cancer and provides novel insights into their roles in tumorigenesis.