Tsyn-Seq: a T-cell Synapse-Based Antigen Identification Platform.

Tools for genome-wide rapid identification of peptide-major histocompatibility complex targets of T-cell receptors (TCR) are not yet universally available. We present a new antigen screening method, the T-synapse (Tsyn) reporter system, which includes antigen-presenting cells (APC) with a Fas-inducible NF-κB reporter and T cells with a nuclear factor of activated T cells (NFAT) reporter. To functionally screen for target antigens from a cDNA library, productively interacting T cell-APC aggregates were detected by dual-reporter activity and enriched by flow sorting followed by antigen identification quantified by deep sequencing (Tsyn-seq). When applied to a previously characterized TCR specific for the E7 antigen derived from human papillomavirus type 16 (HPV16), Tsyn-seq successfully enriched the correct cognate antigen from a cDNA library derived from an HPV16-positive cervical cancer cell line. Tsyn-seq provides a method for rapidly identifying antigens recognized by TCRs of interest from a tumor cDNA library. See related Spotlight by Makani and Joglekar, p. 515.

Effect of ultrasound-guided stellate ganglion block on inflammatory cytokines and postoperative recovery after partial hepatectomy: a randomised clinical trial.

BACKGROUND: Stellate ganglion block (SGB) has been shown to reduce perioperative complications in various surgeries. Because laparoscopic techniques and instruments have advanced during the past two decades, laparoscopic liver resection is being increasingly adopted worldwide. Lesser blood loss, fewer postoperative complications, and shorter postoperative hospital stays are the advantages of laparoscopic liver resection, as compared to conventional open surgery. There is an urgent need for an effective intervention to reduce perioperative complications and accelerate postoperative recovery. This study investigated the effect of ultrasound-guided SGB on enhanced recovery after laparoscopic partial hepatectomy. METHODS: We compared patients who received SGB with 0.5% ropivacaine (group S) with those who received SGB with 0.9% saline (group N). A total of 58 patients with partial hepatectomy were enrolled (30 S) and (28 N). Before induction of anesthesia, SGB was performed with 0.5% ropivacaine in group S and 0.9% saline in group N. MAIN OUTCOME: Comparison of serum inflammatory cytokines concentration at each time point. RESULTS: Main outcome: When comparing IL-6 and IL-10 concentrations among groups, group S showed less variation over time compared to group N. For comparison between groups, the serum IL-6 concentration in group S was lower than that in group N at 6 and 24 h after operation (P < 0.01), and there was a significant linear relationship between serum IL-6 concentration at 24 h after operation and hospitalization situation. CONCLUSIONS: Ultrasound-guided SGB can stabilize perioperative inflammatory cytokines plays a positive role in the enhanced recovery of patients after laparoscopic partial hepatectomy. The serum IL-6 level within 24 h after surgery may be used as a predictor of hospitalization. TRIAL REGISTRATION: The study was registered at the ClinicalTrials.gov (Registration date: 13/09/2021; Trial ID: NCT05042583).

Oblique lateral interbody fusion with internal fixations in the treatment for cross-segment degenerative lumbar spine disease (L2-3 and L4-5) finite element analysis.

Multi-segmental lumbar degenerative disease, including intersegmental disc degeneration, is found in clinical practice. Controversy still exists regarding the treatment for cross-segment degeneration. Oblique Lateral Interbody Fusion (OLIF) with several internal fixations was used to treat cross-segment lumbar degenerative disease. A whole lumbar spine model was extracted from CT images of the whole lumbar spine of patients with lumbar degeneration. The L2-3 and L4-5 intervertebral spaces were fused with OLIF using modeling software, the Pedicle screws were performed on L2-3 and L4-5, and different internal fixations were performed on L3-4 in Finite Element (FE) software. Among the six 10 Nm moments of different directions, the L3-4 no surgery (NS) group had the relatively largest Range of Motion (ROM) in the whole lumbar spine, while the L2-5 Long segmental fixation (LSF)group had the smallest ROM and the other groups had similar ROM. The ROM in the L1-2 and L5-S1 was relatively close in the six group models, and the articular cartilage stress and disc stress on the L1-2 and L5-S1 were relatively close. In contrast, the L3-4 ROM differed relatively greatly, with the LSF ROM the smallest and the NS ROM the largest, and the L3-4 Coflex (Coflex) group more active than the L3-4 Bacfuse (Bacfuse) group and the L3-4 translaminar facet screw fixation (TFSF) group. The stress on the articular cartilage and disc at L3-4 was relatively greater in the NS disc and articular cartilage, and greater in the Coflex group than in the Bacfuse and TFSF groups, with the greatest stress on the internal fixation in the TFSF group, followed by the Coflex group, and relatively similar stress in the Bacfuse, LSF, and NS groups. In the TFSF group, the stress on the internal fixation was greater than the yield strength among different directional moments of 10 Nm, which means it is unsuitable to be an internal fixation. The LSF group had the greatest overall ROM, which may lead to postoperative low back discomfort. The NS group has the greatest overall ROM, but its increased stress on the L3-4 disc and articular cartilage may lead to accelerated degeneration of the L3-4 disc and articular cartilage. The Coflex and Bacfuse groups had a reduced L3-4 ROM but a greater stress on disc compared to the LSF group, which may lead to disc degeneration in the long term. However, their stress on the articular cartilage was relatively low. Coflex and Bacfuse can still be considered better surgical options.

Brown Sequard syndrome in a patient with Klippel-Feil syndrome following minor trauma: a case report and literature review.

BACKGROUND: There are some cases of Klippel-Feil syndrome with spinal cord injury in clinical work. However, there is no literature report on Brown-Sequard syndrome after trauma. We report a case of Brown-Sequard syndrome following minor trauma in a patient with KFS type III. Her Brown-Sequard syndrome is caused by Klippel-Feil syndrome. CASE PRESENTATION: We found a 38-year-old female patient with KFS in our clinical work. She was unconscious on the spot following a minor traumatic episode. After treatment, her whole body was numb and limb activity was limited. Half an hour later, she felt numb and weak in the right limb and weak in the left limb. She had no previous hypertension, diabetes, or coronary heart disease. After one-month treatment of medication, hyperbaric oxygen, rehabilitation, and acupuncture in our hospital, her muscle strength partially recovered, but the treatment effect was still not satisfactory. Then, she underwent surgical treatment and postoperative comprehensive treatment, and rehabilitation training. She was able to take care of herself with assistance, and her condition improved from grade B to grade D according to the ASIA (ASIA Impairment Scale) classification. CONCLUSION: KFS, also known as short neck deformity, is a kind of congenital deformity characterized by impaired formation and faulty segmentation of the cervical spine, often associated with abnormalities of other organs. The cervical deformity in patients with KFS can alter the overall mechanical activity of the spine, as well as the compensatory properties of the spine for decelerating and rotatory forces, thus increasing the chance of spinal cord injury (SCI) following trauma. Many mechanisms can make patients more susceptible to injury. Increased range of motion of the segment adjacent to the fused vertebral body may lead to slippage of the adjacent vertebral body and altered disc stress, as well as cervical instability. SCI can result in complete or incomplete impairment of motor, sensory and autonomic nervous functions below the level of lesion. This woman presented with symptoms of BSS, a rare neurological disorder with incomplete SCI. Judging from the woman's symptoms, we concluded that previously she had KFS, which resulted in SCI without fracture and dislocation following minor trauma, with partial BSS. After the comprehensive treatment of surgery, hyperbaric oxygen, rehabilitation therapy, and neurotrophic drugs, two years later, we found her symptoms significantly improved, with ASIA Impairment Scale from grade B to grade D, and her ability to perform activities of daily living with aids.

A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes.

MOTIVATION: Multilevel molecular profiling of tumors and the integrative analysis with clinical outcomes have enabled a deeper characterization of cancer treatment. Mediation analysis has emerged as a promising statistical tool to identify and quantify the intermediate mechanisms by which a gene affects an outcome. However, existing methods lack a unified approach to handle various types of outcome variables, making them unsuitable for high-throughput molecular profiling data with highly interconnected variables. RESULTS: We develop a general mediation analysis framework for proteogenomic data that include multiple exposures, multivariate mediators on various scales of effects as appropriate for continuous, binary and survival outcomes. Our estimation method avoids imposing constraints on model parameters such as the rare disease assumption, while accommodating multiple exposures and high-dimensional mediators. We compare our approach to other methods in extensive simulation studies at a range of sample sizes, disease prevalence and number of false mediators. Using kidney renal clear cell carcinoma proteogenomic data, we identify genes that are mediated by proteins and the underlying mechanisms on various survival outcomes that capture short- and long-term disease-specific clinical characteristics. AVAILABILITY AND IMPLEMENTATION: Software is made available in an R package (https://github.com/longjp/mediateR). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effects of different depth of anesthesia on perioperative inflammatory reaction and hospital outcomes in elderly patients undergoing laparoscopic radical gastrectomy.

BACKGROUND: To investigate the effect of different depth of anesthesia on inflammatory factors and hospital outcomes in elderly patients undergoing laparoscopic radical gastrectomy for gastric cancer, in order to select an appropriate depth of anesthesia to improve the prognosis of patients undergoing surgery and improve the quality of life of patients. METHODS: A total of 80 elderly patients aged 65 and above who underwent laparoscopic radical gastrectomy in our hospital were by convenience sampling and randomly divided into two groups : 55 groups ( group H ) and 45 groups ( group L ), 40 cases in each group. The depth of anesthesia was maintained using a closed-loop target-controlled infusion system: the EEG bispectral index was set to 55 in the H group and 45 in the L group. Venous blood samples were collected 2 h (T2), 24 h (T3) and 72 h (T4) after the start of surgery. The intraoperative dosage of propofol and remifentanil, operation duration, postoperative PACU stay time, intraoperative consciousness occurrence, postoperative hospital stay and postoperative pulmonary inflammatory events were recorded. RESULTS: The patient characteristic of the two groups had no statistical difference and were comparable (P > 0.05). The intraoperative dosage of propofol in group H was lower than that in group L (P < 0.05). Compared with the L group, the plasma IL-6 and IL-10 concentrations in the H group were significantly increased at T2 (P < 0.05), and the plasma IL-10 concentration was significantly increased at T4 (P < 0.05). The plasma concentrations of IL-6 and IL-10 were higher in both groups at T2, T3 and T4 than at T1, while at T4, the concentration of TNF-α in group H was higher than at T1 (P < 0.05). CONCLUSION: When the BIS value of the depth of anesthesia is 45, the perioperative release of inflammatory factors in elderly patients with laparoscopic radical gastrectomy for gastric cancer is less than BIS 55, and does not affect the prognosis.

CombPDX: a unified statistical framework for evaluating drug synergism in patient-derived xenografts.

Anticancer combination therapy has been developed to increase efficacy by enhancing synergy. Patient-derived xenografts (PDXs) have emerged as reliable preclinical models to develop effective treatments in translational cancer research. However, most PDX combination study designs focus on single dose levels, and dose-response surface models are not appropriate for testing synergism. We propose a comprehensive statistical framework to assess joint action of drug combinations from PDX tumor growth curve data. We provide various metrics and robust statistical inference procedures that locally (at a fixed time) and globally (across time) access combination effects under classical drug interaction models. Integrating genomic and pharmacological profiles in non-small-cell lung cancer (NSCLC), we have shown the utilities of combPDX in discovering effective therapeutic combinations and relevant biological mechanisms. We provide an interactive web server, combPDX ( https://licaih.shinyapps.io/CombPDX/ ), to analyze PDX tumor growth curve data and perform power analyses.

eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects.

Using information from allele-specific gene expression (ASE) can improve the power to map gene expression quantitative trait loci (eQTLs). However, such practice has been limited, partly due to computational challenges and lack of clarification on the size of power gain or new findings besides improved power. We have developed geoP, a computationally efficient method to estimate permutation p-values, which makes it computationally feasible to perform eQTL mapping with ASE counts for large cohorts. We have applied geoP to map eQTLs in 28 human tissues using the data from the Genotype-Tissue Expression (GTEx) project. We demonstrate that using ASE data not only substantially improve the power to detect eQTLs, but also allow us to quantify individual-specific genetic effects, which can be used to study the variation of eQTL effect sizes with respect to other covariates. We also compared two popular methods for eQTL mapping with ASE: TReCASE and RASQUAL. TReCASE is ten times or more faster than RASQUAL and it provides more robust type I error control.

A Statistical Method for Association Analysis of Cell Type Compositions.

Gene expression data are often collected from tissue samples that are composed of multiple cell types. Studies of cell type composition based on gene expression data from tissue samples have recently attracted increasing research interest and led to new method development for cell type composition estimation. This new information on cell type composition can be associated with individual characteristics (e.g., genetic variants) or clinical outcomes (e.g., survival time). Such association analysis can be conducted for each cell type separately followed by multiple testing correction. An alternative approach is to evaluate this association using the composition of all the cell types, thus aggregating association signals across cell types. A key challenge of this approach is to account for the dependence across cell types. We propose a new method to quantify the distances between cell types while accounting for their dependencies, and use this information for association analysis. We demonstrate our method in two applied examples: to assess the association between immune cell type composition in tumor samples of colorectal cancer patients versus survival time and SNP genotypes. We found immune cell composition has prognostic value, and our distance metric leads to more accurate survival time prediction than other distance metrics that ignore cell type dependencies. In addition, survival time-associated SNPs are enriched among the SNPs associated with immune cell composition.

A Mixed-Effects Model for Powerful Association Tests in Integrative Functional Genomics.

Genome-wide association studies (GWASs) have successfully identified thousands of genetic variants for many complex diseases; however, these variants explain only a small fraction of the heritability. Recently, genetic association studies that leverage external transcriptome data have received much attention and shown promise for discovering novel variants. One such approach, PrediXcan, is to use predicted gene expression through genetic regulation. However, there are limitations in this approach. The predicted gene expression may be biased, resulting from regularized regression applied to moderately sample-sized reference studies. Further, some variants can individually influence disease risk through alternative functional mechanisms besides expression. Thus, testing only the association of predicted gene expression as proposed in PrediXcan will potentially lose power. To tackle these challenges, we consider a unified mixed effects model that formulates the association of intermediate phenotypes such as imputed gene expression through fixed effects, while allowing residual effects of individual variants to be random. We consider a set-based score testing framework, MiST (mixed effects score test), and propose two data-driven combination approaches to jointly test for the fixed and random effects. We establish the asymptotic distributions, which enable rapid calculation of p values for genome-wide analyses, and provide p values for fixed and random effects separately to enhance interpretability over GWASs. Extensive simulations demonstrate that our approaches are more powerful than existing ones. We apply our approach to a large-scale GWAS of colorectal cancer and identify two genes, POU5F1B and ATF1, which would have otherwise been missed by PrediXcan, after adjusting for all known loci.