A Comprehensive Study of the Effects by Sequence Truncation within Inverted Terminal Repeats (ITRs) on the Productivity, Genome Packaging, and Potency of AAV Vectors.

One of the primary challenges in working with adeno-associated virus (AAV) lies in the inherent instability of its inverted terminal repeats (ITRs), which play vital roles in AAV replication, encapsidation, and genome integration. ITRs contain a high GC content and palindromic structure, which occasionally results in truncations and mutations during plasmid amplification in bacterial cells. However, there is no thorough study on how these alterations in ITRs impact the ultimate AAV vector characteristics. To close this gap, we designed ITRs with common variations, including a single B, C, or D region deletion at one end, and dual deletions at both ends of the vector genome. These engineered ITR-carrying plasmids were utilized to generate AAV vectors in HEK293 cells. The crude and purified AAV samples were collected and analyzed for yield, capsid DNA-filled percentage, potency, and ITR integrity. The results show that a single deletion had minor impact on AAV productivity, packaging efficiency, and in vivo potency. However, deletions on both ends, except A, showed significant negative effects on the above characteristics. Our work revealed the role of ITR regions, A, B, C, and D for AAV production and DNA replication, and proposes a new strategy for the quality control of ITR-bearing plasmids and final AAV products.

Structural Mechanism and Inhibitors Targeting EGFR Exon 20 Insertion (Ex20ins) Mutations.

Epidermal growth factor receptor (EGFR) targeted therapy is one of the most important and effective strategies to combat EGFR mutant nonsmall-cell lung cancer (NSCLC). However, a substantial number of patients bearing EGFR exon 20 insertion (Ex20ins) mutations respond poorly to common EGFR targeted therapies. This clinical need remained unmet until recently, when the EGFR Ex20ins mutation inhibitor mobocertinib was approved by the FDA. Despite this progress, the structural mechanisms of EGFR Ex20ins mutation resistance and characterization of inhibitor binding modes have not been systematically summarized. Herein, we analyze the structural mechanisms for ligand binding and resistance and summarize recent developments for the reported inhibitors of EGFR Ex20ins mutations. Furthermore, this Perspective aims to provide insights for the design of the next generation of EGFR Ex20ins inhibitors.

Targeting Vascular Smooth Muscle Cell Senescence: A Novel Strategy for Vascular Diseases.

Vascular diseases are a major threat to human health, characterized by high rates of morbidity, mortality, and disability. VSMC senescence contributes to dramatic changes in vascular morphology, structure, and function. A growing number of studies suggest that VSMC senescence is an important pathophysiological mechanism for the development of vascular diseases, including pulmonary hypertension, atherosclerosis, aneurysm, and hypertension. This review summarizes the important role of VSMC senescence and senescence-associated secretory phenotype (SASP) secreted by senescent VSMCs in the pathophysiological process of vascular diseases. Meanwhile, it concludes the progress of antisenescence therapy targeting VSMC senescence or SASP, which provides new strategies for the prevention and treatment of vascular diseases.

[Effects of different types of exercise on contractile properties and expressions of MuRF1, PGC-1α /FNDC5 in soleus muscle of unloaded rats].

Objective: To investigate the effects of aerobic versus resistance exercise on soleus muscle contractile properties and the expressions of MuRF1, PGC-1α and FNDC5 in amyotrophic rats after unloading, and the possible molecular biological mechanisms. Methods: Male Wistar rats were randomly divided into recovery group (CT), aerobic exercise group (A), resistance exercise group (R) and control group (C), with 6 rats in each group. The control group did not receive any treatment. The other three groups underwent tail suspension for 2 weeks, and then the recovery group recovered quietly. The aerobic group and the resistance group underwent a 2-week exercise intervention. Exercise plan: the aerobic group rats were treated with treadmill speed corresponding to 65% maximum oxygen uptake (VO2max), 60 min/d, 5 d/w; the rats in the resistance group were allowed to climb the ladder with 65% of the maximum voluntary weight-bearing (MVCC) for 3 times, with a total of 5 sets. Each time had a rest of 1 min, with an interval of 2 min among sets, and 5 d/w. Fasting for 24 hours after the last exercise, the soleus muscle samples were collected to observe the histological changes, test the contractility, and detect MuRF1 and PGC-1α and FNDC5 expressions. Results: compared with the control group, the body weight, soleus muscle wet weight, average cross-sectional area of muscle fibers and muscle contractility of the recovery group were decreased significantly(P<0.01), and the expression of MuRF1 was increased significantly(P<0.01). Compared with the recovery group, the body weight, wet weight of soleus muscle, the average cross-sectional area of muscle fiber and muscle contractility of rats in aerobic group and resistance group were increased (P<0.01), the expression of PGC-1α/FNDC5 was increased (P<0.01) and the expression of MuRF1 was decreased significantly (P<0.01). Compared with the aerobic group, the expression of PGC-1α in soleus muscle of rats in the resistance group was increased (P<0.05), while the expression of MuRF1 was decreased (P<0.05). Conclusion: Aerobic and resistance exercise can significantly improve muscle contractility, upregulate the expression of PGC-1α/FNDC5, and inhibit the expression of MuRF1, indicating that the molecular mechanisms of aerobic and resistance exercise to improve unloaded muscular atrophy may be related to PGC-1α and MuRF1.

A Transfer Learning Approach for Malignant Prostate Lesion Detection on Multiparametric MRI.

PURPOSE: In prostate focal therapy, it is important to accurately localize malignant lesions in order to increase biological effect of the tumor region while achieving a reduction in dose to noncancerous tissue. In this work, we proposed a transfer learning-based deep learning approach, for classification of prostate lesions in multiparametric magnetic resonance imaging images. METHODS: Magnetic resonance imaging images were preprocessed to remove bias artifact and normalize the data. Two state-of-the-art deep convolutional neural network models, InceptionV3 and VGG-16, were pretrained on ImageNet data set and retuned on the multiparametric magnetic resonance imaging data set. As lesion appearances differ by the prostate zone that it resides in, separate models were trained. Ensembling was performed on each prostate zone to improve area under the curve. In addition, the predictions from lesions on each prostate zone were scaled separately to increase the area under the curve for all lesions combined. RESULTS: The models were tuned to produce the highest area under the curve on validation data set. When it was applied to the unseen test data set, the transferred InceptionV3 model achieved an area under the curve of 0.81 and the transferred VGG-16 model achieved an area under the curve of 0.83. This was the third best score among the 72 methods from 33 participating groups in ProstateX competition. CONCLUSION: The transfer learning approach is a promising method for prostate cancer detection on multiparametric magnetic resonance imaging images. Features learned from ImageNet data set can be useful for medical images.

Screening epitopes on systemic lupus erythematosus autoantigens with a peptide array.

Systemic lupus erythematosus (SLE) is a common autoimmune disease. Many autoantibodies are closely associated with SLE. However, the specific epitopes recognized and bound by these autoantibodies are still unclear. This study screened the binding epitopes of SLE-related autoantibodies using a high-throughput screening method. Epitope prediction on 12 SLE-related autoantigens was performed using the Immune Epitope Database and Analysis Resource (IEDB) software. The predicted epitopes were synthesized into peptides and developed into a peptide array. Serum IgG from 50 SLE patients and 25 healthy controls was detected using the peptide array. The results were then validated using an enzyme-linked immunosorbent assay (ELISA). The diagnostic efficiency of each epitope was analyzed using a ROC curve. Seventy-three potential epitopes were screened for using the IEDB software after the epitopes on the 12 SLE-related autoantigens were analyzed. Peptide array screening revealed that the levels of the autoantibodies recognized and bound by 4 peptide antigens were significantly upregulated in the serum of SLE patients (P < 0.05). The ELISA results showed that the 4 antigens with significantly increased serum autoantibodies levels in SLE patients were acidic ribosomal phosphoprotein (P0)-4, acidic ribosomal phosphoprotein (P0)-11, DNA topoisomerase 1 (full length)-1, and U1-SnRNP 68/70 KDa-1 (P < 0.05), and the areas under the ROC curve for diagnosing SLE on the basis of these peptides were 0.91, 0.90, 0.93, and 0.91, respectively. Many autoantibodies specifically expressed in the serum of patients with SLE can be detected by specific peptide fragments and may be used as markers in clinical auxiliary diagnoses.

Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats.

BACKGROUND: Plastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path undertaken by different plant species during evolution. To identify molecular signatures of positive selection associated to adaptation to contrasting ecological niches, we sequenced with Solexa technology the plastomes of two congeneric Brassicaceae species with different habitat preference, Cardamine resedifolia and Cardamine impatiens. RESULTS: Following in-depth characterization of plastome organization, repeat patterns and gene space, the comparison of the newly sequenced plastomes between each other and with 15 fully sequenced Brassicaceae plastomes publically available in GenBank uncovered dynamic variation of the IR boundaries in the Cardamine lineage. We further detected signatures of positive selection in ten of the 75 protein-coding genes of the examined plastomes, identifying a range of chloroplast functions putatively involved in adaptive processes within the family. For instance, the three residues found to be under positive selection in RUBISCO could possibly be involved in the modulation of RUBISCO aggregation/activation and enzymatic specificty in Brassicaceae. In addition, our results points to differential evolutionary rates in Cardamine plastomes. CONCLUSIONS: Overall our results support the existence of wider signatures of positive selection in the plastome of C. resedifolia, possibly as a consequence of adaptation to high altitude environments. We further provide a first characterization of the selective patterns shaping the Brassicaceae plastomes, which could help elucidate the driving forces underlying adaptation and evolution in this important plant family.

Lipoprotein lipase, tissue expression and effects on genes related to fatty acid synthesis in goat mammary epithelial cells.

Lipoprotein lipase (LPL) serves as a central factor in hydrolysis of triacylglycerol and uptake of free fatty acids from the plasma. However, there are limited data concerning the action of LPL on the regulation of milk fat synthesis in goat mammary gland. In this investigation, we describe the cloning and sequencing of the LPL gene from Xinong Saanen dairy goat mammary gland, along with a study of its phylogenetic relationships. Sequence analysis showed that goat LPL shares similarities with other species including sheep, bovine, human and mouse. LPL mRNA expression in various tissues determined by RT-qPCR revealed the highest expression in white adipose tissue, with lower expression in heart, lung, spleen, rumen, small intestine, mammary gland, and kidney. Expression was almost undetectable in liver and muscle. The expression profiles of LPL gene in mammary gland at early, peak, mid, late lactation, and the dry period were also measured. Compared with the dry period, LPL mRNA expression was markedly greater at early lactation. However, compared with early lactation, the expression was lower at peak lactation and mid lactation. Despite those differences, LPL mRNA expression was still greater at peak, mid, and late lactation compared with the dry period. Using goat mammary epithelial cells (GMEC), the in vitro knockdown of LPL via shRNA or with Orlistat resulted in a similar degree of down-regulation of LPL (respectively). Furthermore, knockdown of LPL was associated with reduced mRNA expression of SREBF1, FASN, LIPE and PPARG but greater expression of FFAR3. There was no effect on ACACA expression. Orlistat decreased expression of LIPE, FASN, ACACA, and PPARG, and increased FFAR3 and SREBF1 expression. The pattern of LPL expression was similar to the changes in milk fat percentage in lactating goats. Taken together, results suggest that LPL may play a crucial role in fatty acid synthesis.