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The plethora of biological functions that sustain life is rooted in the remarkable evolvability of proteins. An emerging view highlights the importance of a protein's initial state in dictating evolutionary success. A deeper comprehension of the mechanisms that govern the evolvability of these initial states can provide invaluable insights into protein evolution. In this review, we describe several molecular determinants of protein evolvability, unveiled by experimental evolution and ancestral sequence reconstruction studies. We further discuss how genetic variation and epistasis can promote or constrain functional innovation and suggest putative underlying mechanisms. By establishing a clear framework for these determinants, we provide potential indicators enabling the forecast of suitable evolutionary starting points and delineate molecular mechanisms in need of deeper exploration., Competing Interests: Declaration of interests The authors declare no conflicts of interest., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Background: Vasculogenic mimicry (VM), an alternative microvascular circulation independent of angiogenesis, is formed by aggressive cancer cells. Tumor-expressed B7-H3 has been reported to promote VM formation in hepatocellular carcinoma and modulate angiogenesis in breast cancer and colorectal cancer. However, its effects on VM generation and angiogenesis in non-small cell Lung cancer (NSCLC) remained to be elucidated., Methods: CRISPR/Cas9-mediated B7-H3 knockout (KO) was conducted in NSCLC A549 and H3255 cells. The expression of VM-related proteins, including vascular endothelial (VE)-cadherin and matrix metalloproteinase 14 (MMP14), and the secretion of vascular endothelial growth factor (VEGF) were measured by western blotting and chemiluminescence assay in both B7-H3 KO and mock-edited A549 and H3255 cells. To examine VM formation, a three-dimensional (3D) culture model was used for B7-H3 KO and mock A549 and H3255 cells. For in vivo analysis, xenograft mice models were established using B7-H3 KO and mock-edited A549 cells, and immunohistochemical (CD31) and histochemical (periodic acid-Schiff, PAS) double staining were performed to identify VM and endothelial vessels in tumor tissues. Finally, specific signaling inhibitors were used to analyze B7-H3-induced signaling pathway responsible for VE-cadherin and MMP14 expression and VM generation., Results: Higher expression of B7-H3 was associated with a worse prognosis and more advanced T-category in NSCLC. CRISPR/Cas9-mediated B7-H3 KO in A549 and H3255 cells led to decreased expression of VE-cadherin and MMP14; however, the secretion of VEGF by the two cell lines remained unchanged. In the 3D cell culture model, both B7-H3 KO A549 and H3255 cells showed a significant reduction in the formation of capillary-like tubular structures compared to mock-edited cells. In the in vivo xenograft model, mock-edited A549 cells formed excessive PAS +  CD31 -  VM channels, while B7-H3 KO restrained VM formation in the xenograft tumors. However, no significant differences were found in CD31 +  endothelial vessels between xenografts formed by B7-H3 KO and mock-edited A549 cells. Finally, we analyzed the signaling pathway responsible for B7-H3-induced VM formation and found that selective inhibition of the phosphoinositide 3-kinase(PI3K)/protein kinase B (AKT) hyperactivation by LY294002 was associated with decreased expression of MMP14 and VE-cadherin, and in vitro VM formation by both A549 and H3255 cells., Conclusions: Tumor-expressed B7-H3 acts via PI3K/AKT signaling pathway to promote VM formation by NSCLC cells while bears no effects on angiogenesis in NSCLC., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Automatic cell type annotation methods are increasingly used in single-cell RNA sequencing (scRNA-seq) analysis due to their fast and precise advantages. However, current methods often fail to account for the imbalance of scRNA-seq datasets and ignore information from smaller populations, leading to significant biological analysis errors. Here, we introduce scBalance, an integrated sparse neural network framework that incorporates adaptive weight sampling and dropout techniques for auto-annotation tasks. Using 20 scRNA-seq datasets with varying scales and degrees of imbalance, we demonstrate that scBalance outperforms current methods in both intra- and inter-dataset annotation tasks. Additionally, scBalance displays impressive scalability in identifying rare cell types in million-level datasets, as shown in the bronchoalveolar cell landscape. scBalance is also significantly faster than commonly used tools and comes in a user-friendly format, making it a superior tool for scRNA-seq analysis on the Python-based platform., (© 2023. The Author(s).)

Background: Chaperonin-containing tailless complex polypeptide 1 (TCP1) subunit 3 (CCT3) has tumor-promoting effects in lung adenocarcinoma (LUAD). This study aims to investigate the molecular mechanisms of CCT3 in LUAD oncogenesis., Methods: The UALCAN databases, Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) data were used to analyze CCT3 expression in LUAD. Both the Wilcoxon rank-sum test and the regression model were used to investigate the connection between clinicopathologic characteristics of LUAD patients and CCT3 expression. The prognostic value of CCT3 was determined by Cox regression models, the Kaplan-Meier method and Nomogram prediction. Next, we identified the most related genes with CCT3 via GeneMANIA and String databases, and the association between CCT3 and infiltrated immune cells using single-sample Gene Set Enrichment Analysis (ssGSEA). CCT3-related pathway enrichment analysis was investigated by GSEA. Finally, CCT3 roles in cell proliferation and apoptosis of LUAD A549 cells was verified by siRNA (small interfering RNA) mediated CCT3 knockdown., Results: CCT3 was upregulated in LUAD both in mRNA and protein levels. CCT3 overexpression was associated with clinicopathological characteristics including sex, smoking, T- and N-categories, pathological staging, and a poor prognosis of LUAD patients. GeneMANIA and String databases found a set of CCT3-related genes that are connected to the assembly and stability of proteins involved in proteostasis of cytoskeletal filaments, DNA repair and protein methylation. Furthermore, CCT3 was found to be positively correlated with the infiltrating Th2 cells (r = 0.442, p < 0.01) while negatively correlated with mast cells (r = -0.49, p < 0.01) and immature dendritic cells (iDCs, r = -0.401, p < 0.001) according to ssGSEA analyzes. The pathway analysis based on GSEA method showed that the cell cycle pathway, the protein export pathway, the proteasome pathway and the ribosome pathway are enriched in CCT3 high group, whereas the JAK/STAT pathway, B cell receptor pathway, T cell receptor pathway and toll like receptor pathway were enriched in CCT3 low group. Finally, CCT3 knockdown substantially inhibited proliferation while promoted apoptosis of A549 cells., Conclusion: Integrated analyzes identify CCT3 as a modulator to shape immunosuppressive tumor microenvironment in LUAD and therefore, a prognostic factor for LUAD., (© 2023. The Author(s).)

Peroxidase nanozyme, enabling decomposition of hydrogen peroxide (H 2 O 2 ) into highly toxic hydroxyl radical (•OH), is an emerging technology for tumor treatment. However, limited by the low H 2 O 2 level in the tumor microenvironment, the standalone peroxidase nanozyme-mediated therapy usually fails to achieve desirable therapeutic outcomes. Herein, we presented a mesoporous nanozyme that not only had peroxidase-like activity but also could deliver anticancer drug for synergistic tumor therapy. The nanozyme, that was, iron-doped mesoporous silica nanoparticle (FeMSN), was prepared by a sol-gel method and then a calcination treatment. The introduction of iron endowed FeMSN with peroxidase-like activity that could decompose H 2 O 2 into •OH under acidic condition for chemodynamic therapy of tumors. Meanwhile, the mesoporous structure enabled FeMSN to deliver anticancer drug doxorubicin (DOX) for chemotherapy and enhanced chemodynamic therapy through H 2 O 2 production, ultimately achieving synergistic effect to improve the efficacy of tumor treatment. The in-vitro and in-vivo results demonstrated that DOX-loaded FeMSN exhibited significant cancer cell-killing effect and potently inhibited tumor growth. Collectively, this study represented a paradigm for achieving efficient tumor therapy through design of peroxidase-like nanozyme with drug delivery capability, which might advance the development of nanozyme in tumor chemodynamic therapy., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Employing hypoxia-activated prodrugs is an appealing oncotherapy strategy, but limited by insufficient tumor hypoxia. Moreover, a standalone prodrug fails to treat tumors satisfactorily due to tumor complexity. Herein, a nanosystem (TPZ@FeMSN-GOX) was established for triple synergetic cancer starvation therapy, hypoxia-activated chemotherapy and chemodynamic therapy (CDT). TPZ@FeMSN-GOX was prepared by synthesizing iron-doped mesoporous silica nanoparticles (FeMSNs) followed by surface conjugation with glucose oxidase (GOX), and then loading with hypoxia-activated prodrug tirapazamine (TPZ). When TPZ@FeMSN-GOX entered the tumor cells, GOX could not only exhaust glucose to starve cancer cells and concomitantly produce H 2 O 2 , but also consume O 2 to aggravate the hypoxia environment and amplify TPZ-mediated chemotherapy. Meanwhile, the released Fe 3+ was reduced to reactive Fe 2+ by endogenous glutathione, which ultimately decomposed the produced H 2 O 2 and endogenous H 2 O 2 into highly toxic ˙OH, guaranteeing highly efficient CDT. Together, TPZ@FeMSN-GOX could effectively kill cancer cells and significantly inhibit tumor growth, providing a good paradigm for effective tumor treatment.

Oral cancer is known as one of the relatively common malignancy types worldwide. Despite the easy access of the oral cavity to examination, the invasive biopsy is still essential for final diagnosis, which requires laborious operation and complicated trained specialists. With the development of deep learning, the artificial intelligence (AI) technique is applied for oral cancer examinations and alleviates the workload of manual screening on biopsy. However, existing computer-aided oral cancer diagnostic methods focus on oral cavity environment photos and histology images, which require complicated operations for doctors and are invasive and painful for patients. As a noninvasive, real-time imaging technique, optical coherence tomography (OCT) can express sufficient identical information for oral cancer screening, but it has not been effectively explored for automatic oral cancer diagnosis. This paper proposes a novel deep learning method named Local Residual Adaptation Network (LRAN) for noninvasive oral cancer screening on OCT images, collected from 25 patients in Beijing Stomatological Hospital. Our proposed LRAN consists of a Residual Feature Representation (RFR) module and a Local Distribution Adaptation (LDA) module. Specifically, RFR firstly adopts stacked residual blocks as the backbone network to learn feature representations for training data, optimized by the Cross-Entropy loss, and then deploy Euclidean distance to measure the distribution distance between training and testing OCT images. Finally, LRAN achieves distribution-gap bridging by the LDA module, which integrates local maximum mean discrepancy constraint to estimate and minimize the distribution discrepancy between training and testing sets within the same category. We also collected an OCT-based oral cancer image dataset to evaluate the effectiveness of the proposed method, and it achieves an accuracy of 91.62%, a sensitivity of 91.66%, and a specificity of 92.58% on this self-collected dataset. Furthermore, we conduct a quantitative and qualitative analysis, and the results demonstrate LRAN model has excellent capability to solve the noninvasive oral cancer screening task., (© 2022. International Federation for Medical and Biological Engineering.)

Injuries on lower-extremity joints were caused by high impact force in parachuting landing. Knee brace was used to protect knee by restraining motion of knee. Backpack was necessary in parachuting landing and would increase lower-extremity joints injuries. This study aimed to analyze kinematics and kinetics of hip, knee and ankle for investigating multi-joint protection of knee brace for those joints in parachuting landing with backpack. Seven participants landed from 120 cm height. Kinematics and kinetics of hip, knee and ankle were analyzed. It was found that without backpack knee brace decreased angular displacements of hip (12.0%), knee (10.3%) and ankle (18.6%) on sagittal plane and angular velocities of hip (11.9%), knee (6.6%) and ankle (20.9%) on sagittal plane. With backpack, knee brace decreased angular displacement (5.5%) and angular velocity of knee (6.2%) on sagittal plane, but did not significantly influence those of hip and ankle on sagittal plane. Ground reaction force, joint moments and joint energy absorptions were not significantly influenced with knee brace. In conclusion, in parachuting landing without backpack, knee brace could provide multi-joint protection for hip, knee and ankle. In parachuting landing with backpack, knee brace could still protect knee, but could not protect hip and ankle., Competing Interests: Declaration of Competing Interest None declared., (Copyright © 2020. Published by Elsevier Ltd.)