Comprehensive analysis and experimental verification of the mechanism of action of T cell-mediated tumor-killing related genes in Colon adenocarcinoma

BACKGROUND

Colorectal cancer (CRC) is a prevalent malignancy of the digestive tract. A new prognostic scoring model for colon adenocarcinoma (COAD) is developed in this study based on the genes involved in tumor cell-mediated killing of T cells (GSTTKs), accurately stratifying COAD patients, thus improving the current status of personalized treatment.

METHOD

The GEO and TCGA databases served as the sources of the data for the COAD cohort. This study identified GSTTKs-related genes in COAD through single-factor Cox analysis. These genes were used to categorize COAD patients into several subtypes via unsupervised clustering analysis. The biological pathways and tumor microenvironments of different subgroups were compared. We performed intersection analysis between different subtypes to obtain intersection genes. Single-factor Cox regression analysis and Lasso-Cox analysis were conducted to establish clinical prognostic models. Two methods are used to assess the accuracy of model predictions: ROC and Kaplan-Meier analysis. Next, the prediction model was further validated in the validation cohort. Differential immune cell infiltration between various risk categories was identified via single sample gene set enrichment analysis (ssGSEA). The COAD model's gene expression was validated via single-cell data analysis and experiments.

RESULT

We established two distinct GSTTKs-related subtypes. Biological processes and immune cell tumor invasion differed significantly between various subtypes. Clinical prognostic models were created using five GSTTKs-related genes. The model's risk score independently served as a prognostic factor. COAD patients were classified as low- or high-risk depending on their risk scores. Patients in the low-risk category recorded a greater chance of surviving. The outcomes from the validation cohort match those from the training set. Risk scores and several tumor-infiltrating immune cells were strongly correlated, according to ssGSEA. Single-cell data illustrated that the model's genes were linked to several immune cells. The experimental results demonstrated a significant increase in the expression of HOXC6 in colon cancer tissue.

CONCLUSION

Our research findings established a new gene signature for COAD. This gene signature helps to accurately stratify the risk of COAD patients and improve the current status of individualized care.

Identification and analysis of prognostic metabolic characteristics in colon adenocarcinoma

Colon adenocarcinoma (COAD) is a highly lethal gastrointestinal malignancy. The five-year survival rate of metastatic colorectal cancer remains low, at 14 percent. Numerous publications have suggested a role for peroxisome proliferator-activated receptors (PPARs) in malignancy. Recent studies have shown that PPARs, as nuclear transcription factors, may serve as potential targets for the treatment of metabolic syndrome tumors and their associated complications. However, the molecular mechanism has not been thoroughly investigated. Hence, in order to enhance the prediction of personalized medicine for PPAR-associated modulators in malignancy treatment, a timely review becomes essential. Utilizing TCGA-COAD expression profile data and patient overall survival (OS) information, this study systematically conducted investigations to identify and develop Hub stem cell-related diagnostic and prognostic identification models, aiming to enhance the multi-gene markers for COAD. Utilizing the differential expression profiles of stem cell-related genes, an 11-gene (SLC27A4, CPT1C, CPT1B, CPT2, CYP4A11, FABP3, FABP7, AQP7, MMP1, ACOX1, ANGPTL4) diagnostic and prognostic model was developed. This model demonstrated precise diagnostic and prognostic capabilities and holds the potential to characterize the clinicopathologic features of COAD. Univariate and multivariate Cox proportional hazards regression analyses were conducted to ascertain the independent factors influencing OS outcomes in COAD. The results revealed that CPT1B, SLC27A4, and FABP3 were identified as independent risk prognostic factors for OS in COAD, whereas ACOX1 and CPT2 served as independent protective prognostic factors. The hub genes associated with PPARs were identified through the differential expression of contrast agent COAD and normal tissues. Finally, the investigation of variations in immune infiltration and the analysis of relevant biological pathways validate the prognostic significance of the independent post-factors within this molecular model. This research aims to provide references for comprehending the mechanism of post-transcriptional regulation of COAD and molecular therapy.

Identification of biomarkers of renal ischemia-reperfusion injury by bioinformatics analysis and single-cell sequencing analysis combined with in vivo validation

BACKGROUND

Renal ischemia-reperfusion injury (IRI) is a serious clinical complication of kidney injury. This research dealt with investigating the hub genes and pathways associated with renal IRI.

METHODS

The transcriptome expression dataset of mouse renal ischemia samples (GSE39548) was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were filtered by R software for key genes utilized for gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene enrichment analysis (GSEA). The gene co-expression network was developed by WGCNA analysis to screen important modules. Hub genes from the intersection of DEGs and WGCNA were subjected to protein-protein interaction (PPI) network. The biomarkers obtained by SVM-REF and LASSO algorithm were validated by other datasets and subjected to GSEA analysis. The expression of biomarkers in renal IRI was detected by qRT-PCR and subjected to single-cell analysis.

RESULTS

A total of 157 DEGs were discovered. Biological function analysis depicted that the DEGs were primarily involved in cytokine-cytokine receptor interaction, as well as the signaling pathways IL-17, MAPK, and TNF. The intersection of DEGs and the genes obtained by WGCNA analysis yielded 149 hubs genes. Based on SVM-REF and LASSO algorithm, cyp1a1 and pdk4 were determined as potential biomarkers in individuals with renal ischemia and showed good diagnostic value. qRT-PCR results depicted that cyp1a1 and pdk4 were significantly up-regulated in renal ischemia mice (P < 0.05). Finally, the single-cell analysis identified the expression of Cyp1a1 and Pdk4 in mice kidney tissue.

CONCLUSION

cyp1a1 and pdk4 were identified to play important roles in renal IRI. This research provides a new perspective and basis for studying the pathogenesis of renal IRI and developing new treatments.

The reinfection threshold, revisited

One mode by which infection-derived immunity fails is when recovery leads to a reduced but nonzero risk of reinfection. This type of partial protection is called leaky immunity with the degree of leakiness quantified by the relative probability a previously infected individual will get infected upon exposure compared to a naively susceptible individual. Previous authors have defined the reinfection threshold, which occurs when the basic reproduction number equals the inverse of the leakiness, however, there has been some debate about whether or not this is a real threshold. Here we show how the reinfection threshold relates to two important occurrences: (1) the point at which the endemic equilibrium changes from being a stable spiral to a stable node, and (2) the point at which the rate of change of the prevalence increases the most relative to leakiness. When the recovery period is short relative to the average lifetime then both occurrences are close to the reinfection threshold. We show how these results are related to the reinfection threshold found in other models of imperfect immunity. To further demonstrate the significance of this threshold in modeling, we conducted a simulation study to evaluate some of the consequences the reinfection threshold might have in parameter estimation and modeling. Using specific parameter values chosen to reflect an acute infection, we found that the basic reproduction number values larger than that of the reinfection threshold value were less identifiable than those below the threshold.

Evaluation of the Efficiency of TIMP-2 as a Biomarker for Acute Kidney Injury in Sepsis

The aim of this study was to evaluate the biomarker potential of TIMP-2 in septic-induced acute kidney injury (AKI). Healthy male rats (n=56, age 8-10 weeks, body weight 250-300 g) were randomized into 3 groups: controls (intact rats, n=6), sham-operated (SO, n=24), and sepsis model (cecum ligation and perforation, CLP, n=24). Thirty minutes before and 6, 12, 24, and 48 h after surgery, blood samples were collected to measure serum creatinine, blood urea nitrogen (BUN), and TIMP-2 and the kidneys were isolated for histopathological analysis and Western blotting. The key sepsis-related genes were screened through bioinformatics analysis. In 24 and 48 h after surgery, 2 rats in the SO group reached the diagnostic criteria of AKI (increased levels of serum creatinine and BUN). In the CLP group, serum creatinine in 6 h after the surgery was slightly higher than 30 min before the surgery, but this change did not meet the diagnostic criteria for AKI. In the CLP group, BUN was normal 6 h after the surgery, but increased after 12 h. In more than 50% rats of the CLP group, serum creatinine and BUN significantly increased 12 h after operation, so this can be diagnosed as AKI. In rats of the CLP group, plasma TIMP-2 was elevated 6 h after surgery and increased with time, suggesting that plasma TIMP-2 can be used as an early marker of AKI. Histological examination of the kidneys in this group revealed destruction of the renal tubular structure, swelling of renal tubular epithelium, the disappearance of brush edge and collapse of necrotic epithelial cells, etc., and the degree of damage increased with time. Immunohistochemistry showed that TIMP-2 was expressed in rats of the CLP group at all terms of the experiment. The expression of TIMP-2 and pyroptosis-related proteins (NLRP3, IL-1β, caspase-1, and GSDMD) in the CLP group was higher than in the SO group (p<0.05) and increased with time, suggesting that pyroptosis is involved in AKI. Thus, plasma TIMP-2 is sensitive indicator for the early detection of kidney injury and can be used as an early biomarker of AKI.

Dual-mode optical thermometer based on fluorescence intensity ratio of Eu3+/Mn4+ co-doping zinc titanate phosphors

Zinc titanate phosphors containing Eu³⁺/ Mn⁴⁺ as active ions were synthesized by using the solid-state method. XRD patterns of the powders confirmed that the samples were a mixture of cubic Zn₂TiO₄ and hexagonal ZnTiO₃ phases. The luminous intensity of ZTO: Eu³⁺phosphors and ZTO: Mn⁴⁺ phosphors both increased with the increase of doping concentration, reaching the maximum at 2 mol% Eu³⁺ and 0.3 mol% Mn⁴⁺, respectively. In the photoluminescence spectra of ZTO: Eu³⁺(2 mol%) phosphors with different Mn⁴⁺ doping amounts excited at 465 nm, the emission spectra revealed the characteristic peaks of Eu³⁺ with low Mn⁴⁺ content, and with the Mn⁴⁺ content increasing, the emission spectra contained both Mn⁴⁺ and Eu³⁺ luminescence peaks. In the variable temperature spectra, the relative sensitivity of the samples was improved with the concentration of Mn⁴⁺ increasing and achieved the maximum value of 3.2 %/K.

Effect of continuous aerobic exercise on endothelial function: A systematic review and meta-analysis of randomized controlled trials

Background: Current research suggests that continuous aerobic exercise can be effective in improving vascular endothelial function, while the effect between different intensities and durations of exercise is unclear. The aim of this study was to explore the effect of different durations and intensities of aerobic exercise on vascular endothelial function in different populations. Methods: Searches were performed in PubMed, Web of Science, and EBSCO databases. We included studies that satisfied the following criteria: 1) randomized controlled trials (RCTs); 2) including both an intervention and control group; 3) using flow-mediated dilation (FMD) as the outcome measure; and 4) testing FMD on the brachial artery. Results: From 3,368 search records initially identified, 41 studies were eligible for meta-analysis. There was a significant effect of continuous aerobic exercise on improving flow-mediated dilation (FMD) [weighted mean difference (WMD), 2.55, (95% CI, 1.93-3.16), p < 0.001]. Specifically, moderate-intensity [2.92 (2.02-3.825), p < 0.001] and vigorous-intensity exercise [2.58 (1.64-3.53), p < 0.001] significantly increased FMD. In addition, a longer duration [<12 weeks, 2.25 (1.54-2.95), p < 0.001; ≥12 weeks, 2.74 (1.95-3.54), p < 0.001], an older age [age <45, 2.09 (0.78-3.40), p = 0.002; 45 ≤ age <60, 2.25 (1.49-3.01), p < 0.001; age ≥60, 2.62 (1.31-3.94), p < 0.001], a larger basal body mass index (BMI) [20 < BMI < 25, 1.43 (0.98-1.88), p < 0.001; 25 ≤ BMI < 30, 2.49 (1.07-3.90), p < 0.001; BMI ≥ 30, 3.05 (1.69-4.42), p < 0.001], and a worse basal FMD [FMD < 4, 2.71 (0.92-4.49), p = 0.003; 4 ≤ FMD < 7, 2.63 (2.03-3.23), p < 0.001] were associated with larger improvements in FMD. Conclusion: Continuous aerobic exercise, especially moderate-intensity and vigorous-intensity aerobic exercise, contributed to improving FMD. The effect of continuous aerobic exercise on improving FMD was associated with duration and participant's characteristics. Specifically, a longer duration, an older age, a larger basal BMI, and a worse basal FMD contributed to more significant improvements in FMD. Systematic Review Registration: [https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=341442], identifier [CRD42022341442].

Virtual versus jaw simulation in inlay preparation preclinical teaching: a randomised controlled trial

BACKGROUND

To investigate the effect of virtual simulation systems on the teaching of inlay experiments and to guide the experimental teaching of tooth preparation.

METHODS

Participants in their second semester of the junior year were selected to carry out the unified teaching and evaluation of dental preparation theory. The age varied from 18 to 22 years (19.96 ± 0.70) and the participants were randomly divided into four groups (n = 19) with a similar male-to-female ratio following CONSORT guidelines, including a jaw simulation model training group (Group J), a virtual simulation system training group (Group V), a jaw model training first followed by a virtual system training group (Group J-V), and a virtual system followed by a jaw model training group (Group V-J). The inlay tooth preparation assessment was performed on the extracted teeth. The data were analysed according to the assessment scores by a senior clinician. The subjective feelings of the students towards the system were evaluated using questionnaires.

RESULTS

The second theoretical scores of Group V-J (63.5 ± 2.89) and Group J-V (60.5 ± 3.25) were higher than those of Group V (57.5 ± 3.13) and Group J (58.0 ± 3.67). The experimental scores of Groups J-V and V-J (62.79 ± 2.84; 64.00 ± 2.85) were higher than those of Groups V and J (56.05 ± 3.39; 55.74 ± 2.53). The questionnaire survey illustrated that most students preferred the digital virtual simulation system (perfect assessment: 91.3%, accuracy: 82.6%, satisfaction: 52.2%).

CONCLUSION

Virtual simulation training can facilitate the teaching effect of tooth preparation in inlay experiments, and the teaching mode of Group V-J was the best. Therefore, this teaching mode is to be popularised.

Synergistic Radiosensitization Mediated by Chemodynamic Therapy via a Novel Biodegradable Peroxidases Mimicking Nanohybrid

Purpose

Reactive oxygen species (ROS) are practically essential in radiotherapy to damage cancer cells; however, they are always inadequate for some malignant entities. Here, we designed a biodegradable mesoporous silica decorated with hemin and glucose oxidase (GOD@Hemin-MSN) to generate a chemodynamic therapy in order to enhance the killing capacity of radiotherapy.

Methods

Mesoporous silica, as an outstanding drug carrier, can deliver hemin and glucose oxidase to the tumor site. With high level of metabolism activity, cancer cells are abundant in glucose, which can be oxidized into H₂O₂ by glucose oxidase (GOD) on site. The generated H₂O₂ is subsequently converted into intracellular ROS, especially hydroxyl radical within the tumor microenvironment, by hemin, which has mimetic peroxidase properties. By this means, the ROS can be supplemented or enriched to facilitate the killing of tumor cells.

Results

The chemodynamic therapy induced by GOD@Hemin-MSN produced quantities of ROS, which compensated for their inadequacy as a result of radiotherapy, and exhibited remarkable antitumor efficacy, with a tumor inhibition rate of 91.5% in A549 tumor-bearing mice.

Conclusion

This work has validated GOD@Hemin-MSN as a radiosensitizer in chemodynamic therapy, which showed biocompatibility and potential for translational application.

Mathematical model and experiment analysis of pressure fluctuation inside dual-stack drainage system in residential buildings

The final velocity was put forward to study the water flow characteristics inside the building drainage system; however, it is more suitable for low-rise and multi-storey buildings, not for high-rise buildings. This study revealed the drainage transient characteristics of a double stack drainage system in high-rise residential buildings. Based on the final velocity, the air-water interaction mechanism and two-phase flow conditions in high-rise residential drainage stacks were discussed. An influence model of drainage system flow rate on pressure fluctuation under the change of state parameters such as ventilation rate, pipe wall roughness and building height was established. The pressure limit and flow rate data were obtained through full-scale experiments. The pressure limit and flow rate model were simplified to P_n = A ċ Q² + B ċ Q^1:81 + C. After the data were verified, the fitting coefficients A, B and C were linear to the floor height.

Camptothecin Delivery via Tumor-Derived Exosome for Radiosensitization by Cell Cycle Regulation on Patient-Derived Xenograft Mice

Purpose: While radiotherapy remains the leading clinical treatment for many tumors, its efficacy can be significantly hampered by the insensitivity of cells in the S phase of the cell cycle to such irradiation.

Methods: Here, we designed a highly targeted drug delivery platform in which exosomes were loaded with the FDA-approved anti-tumor drug camptothecin (CPT) which is capable of regulating cell cycle. The utilized exosomes were isolated from patient tumors, enabling the personalized treatment of individuals to ensure better therapeutic outcomes.

Results: This exosome-mediated delivery strategy was exhibited robust targeted to patient-derived tumor cells in vitro and in established patient-derived xenograft models. By delivering CPT to tumor cells, this nanoplatform was able to decrease cell cycle arrest in the S phase, increasing the frequency of cells in the G1 and G2/M phases such that they were more radiosensitive.

Conclusion: This therapeutic approach was able to substantially enhance the sensitivity of patient-derived tumors to ionizing radiation, thereby improving the overall efficacy of radiotherapy without the need for a higher radiation dose.

Genetic Epidemiology of Medication Safety and Efficacy Related Variants in the Central Han Chinese Population With Whole Genome Sequencing

Medication safety and efficacy-related pharmacogenomic research play a critical role in precision medicine. This study comprehensively analyzed the pharmacogenomic profiles of the central Han Chinese population in the context of medication safety and efficacy and compared them with other global populations. The ultimate goal is to improve medical treatment guidelines. We performed whole-genome sequencing in 487 Han Chinese individuals and investigated the allele frequencies of pharmacogenetic variants in 1,731 drug response-related genes. We identified 2,139 (81.18%) previously reported variants in our population with annotations in the PharmGKB database. The allele frequencies of these 2,139 clinical-related variants were similar to those in other East Asian populations but different from those in other global populations. We predicted the functional effects of nonsynonymous variants in the 1,731 pharmacogenes and identified 1,281 novel and 4,442 previously reported deleterious variants. Of the 1,281 novel deleterious variants, five are common variants with an allele frequency >5%, and the rest are rare variants with an allele frequency <5%. Of the 4,442 known deleterious variants, the allele frequencies were found to differ from those in other populations, of which 146 are common variants. In addition, we found many variants in non-coding regions, the functions of which require further investigation. This study compiled a large amount of data on pharmacogenomic variants in the central Han Chinese population. At the same time, it provides insight into the role of pharmacogenomic variants in clinical medication safety and efficacy.

Mn2+ ions substitution inducing improvement of optical performances in ZnAl2O4: Cr3+ phosphors: Energy transfer and ratiometric optical thermometry

Zn_1-xMn_xAl₂O₄:0.1 mol% Cr³⁺ (0.04≤x≤0.16) phosphors with single spinel phase were synthesized by using sol-gel method and the structure, optical and temperature sensing performances were reported herein. The results of X-ray photoelectron spectra indicate that the inversion defects related to octahedral Zn are reduced and the crystal field surrounding Al changes with Mn²⁺ doping in ZnAl₂O₄ lattices. Mn²⁺/Cr³⁺ co-doped ZnAl₂O₄ nanophosphors reveal a green emission band assigned to Mn²⁺ and a series of red emission peaks assigned to Cr³⁺, respectively. With the concentration of Mn²⁺ increasing, the intensity of zero phonon line (R line) assigned to Cr³⁺ increases, reaching the maximum at the optimal Mn²⁺ concentration of x=0.14. The energy transfer from Mn²⁺ to Cr³⁺ is confirmed with the energy transfer efficiency of 83%. The separation between ²E(e_g) and ²E(t_g) of Cr³⁺ is enlarged due to Mn²⁺ dopants giving rise to a change of crystal field. The luminous intensity ratio between two separated emission peaks at 685 nm (R₃) and 689 nm (R₂) reveals an obvious temperature dependence. The relative sensitivity changes from 3.7 %K^-1 to 0.25 %K^-1 with the temperature increasing from 80 K to 310 K, which is much larger than that of ZnAl₂O₄:Cr³⁺ nanophosphors without Mn²⁺, indicating its good application prospect in optical thermometry.

Changes in bone mineral density in Down syndrome individuals: a systematic review and meta-analysis

Data evaluating changes in bone mineral density (BMD) in Down syndrome (DS) individuals remains controversial. Therefore, we conducted a systematic review and meta-analysis to better understand associations between BMD and DS. A systematic literature search of PubMed, EMBASE, Web of Science, and the Cochrane Library up until 1st January 2021 was conducted. We used the keywords "bone mineral density" and "Down Syndrome." Fifteen studies were included. Overall, our results showed a significant decrease in BMD of total body (TB BMD) [MD =  - 0.18; 95% CI (- 0.23 and - 0.12), P < 0.00001, I2 = 89%], total hip (TH BMD) [MD =  - 0.12; 95% CI (- 0.15 and - 0.10), P < 0.00001, I2 = 0%], lumbar spine (LS BMD) [MD =  - 0.12; 95% CI (- 0.14 and - 0.09), P < 0.00001, I2 = 18%], and femoral neck (FN BMD) [MD =  - 0.08; 95% CI (- 0.10 and - 0.06), P < 0.00001, I2 = 0%] in DS individuals when compared with controls. Moreover, the volumetric BMD of lumbar spine (LS vBMD) [MD =  - 0.01; 95% CI (- 0.02 and - 0.01), P = 0.0004, I2 = 19%] also showed a decreasing tendency while the volumetric BMD of the femoral neck (FN vBMD) [MD = 0.01; 95% CI (0.00 and 0.02), P = 0.02, I2 = 0%] was elevated in DS individuals versus controls. These findings demonstrated that individuals with DS had a decreased total and regional (TH, LS, and FN) BMD when compared with the general population. Additionally, when BMD was adjusted for skeletal volume, LS vBMD was also lower, while FN vBMD was elevated in DS individuals versus controls.

NTRK3-rearranged thyroid carcinoma, clinical and pathologic features

Introduction/Objective

NTRK3 gene encodes a transmembrane protein receptor of the tropomyosin receptor kinase (Trk) family. Gene fusions involving NTRK3 result in a constitutive activation or overexpression of Trk receptor, potentially leading to oncogenesis. NTRK targeted therapies show a promising activity in varied cancer types with NTRK fusions. The aim of this case review is to describe the clinical and pathologic findings of thyroid neoplasm with NTRK3 gene fusions.

Methods/Case Report

The cytology fine needle aspiration (FNA), molecular testing results and pathology of surgical resections are reviewed in 220 cases of total and hemithyroidectomy from January 2018 to May 2021.

Results (if a Case Study enter NA)

Three cases with NTRK3 gene fusions are identified by Thyroseq or Afirma GSC from FNA of thyroid nodules with later surgical intervention. No other mutations or gene fusions were identified. Each case had total thyroidectomy. Case 1 is a 41-year-old female with FNA diagnosis of suspicious for papillary thyroid carcinoma (PTC) and ETV6/NTRK3 fusion found by Afirma GSC. Pathology diagnosis is PTC classic type, two tumor nodules 1.1cm and 1.0cm, lymphovascular invasion not identified, three lymph nodes not involved by tumor and pathologic stage pT1b(m) pN0. Case 2 is a 49-year-old female with FNA diagnosis of atypia of undetermined significance and ETV6/NTRK3 fusion detected by Thyroseq. Pathology diagnosis is infiltrative PTC follicular variant, 2.0cm, angioinvasion present, no lymph nodes submitted and pathologic stage pT1b(m) pNX. Case 3 is a 28-year-old female with FNA diagnosis of suspicious for follicular derived neoplasm and NTRK3/RBPMS fusion is detected by Afirma GSC. Pathology diagnosis is infiltrative PTC follicular variant, 1.5cm, 9 of 11 lymph nodes positive for metastatic carcinoma and pathologic stage pT1b pN1b.

Conclusion

Thyroid neoplasm with NTRK3-rearrangement is rare. Cases 1 and 2 with common ETV6-NTRK3 fusion show PTC classic type and infiltrative PTC follicular variant with angioinvasion. Case 3 with less common NTRK3/RBPMS fusion shows infiltrative PTC follicular variant and significant lymph node involvement. Our limited cases of NTRK3-rearranged thyroid carcinoma demonstrate infiltrative growth, diverse phenotypes, one case with angioinvasion and no lymph nodes submitted and one case with multiple lymph node metastasis. This suggests aggressive behavior of thyroid cancer with NTRK3 gene fusion and patients may benefit from targeted NTRK therapy.

Clinicopathologic features of thyroid neoplasm with THADA-IGF2BP3 fusion

Introduction/Objective

Thyroid adenoma-associated (THADA)-IGF2BP3 fusions is related to strong overexpression of insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) mRNA and protein, increased IGF2 translation and IGF1 receptor signaling via PI3K and MAPK pathways. THADA-IGF2BP3 have been identified as an oncogenic event in thyroid neoplasms, but the clinicopathologic features have not been greatly evaluated. The purpose of this cases review is to describe the clinical and pathologic findings of thyroid nodules with THADA-IGF2BP3 fusion on molecular testing.

Methods/Case Report

Surgical Pathology 220 cases of total and hemithyroidectomy from January 2018 to December 2019 were reviewed for cytology fine needle aspiration (FNA), molecular testing results and surgical resection pathology.

Results (if a Case Study enter NA)

Three cases of THADA-IGF2BP3 fusion identified by Thyroseq testing from FNA of thyroid nodules with all diagnosed as atypia of undetermined significance, Bethesda category 3. No other mutations or gene fusions are identified. Successive surgical interventions are performed. Case 1 is a 49-year-old female right hemithyroidectomy with pathologic diagnosis of papillary thyroid carcinoma (PTC) follicular variant with tumor capsular invasion and no lymphvascular invasion. The tumor is 2cm, two lymph nodes evaluated are not involved by tumor and pathological stage is pT1b pN0. Case 2 is a 71-year-old female total thyroidectomy and the pathologic diagnosis is PTC follicular variant with tumor capsular invasion and no lymphvascular invasion. The tumor is 2cm, one lymph node evaluated is not involved by tumor and pathologic stage is pT1b pN0. Case 3 is a 76-year-old male left hemithyroidectomy and pathologic diagnosis is PTC follicular variant with tumor capsular invasion and no lymphvascular invasion. The tumor is 2cm, two lymph nodes evaluated are not involved by tumor and pathologic stage is pT1b pN0.

Conclusion

THADA-GF2BP3 fusion is uncommon in thyroid neoplasms and only three cases are detected in 220 cases evaluated. The three cases of thyroid nodules are all diagnosed as AUS by FNA, and all are diagnosed as PTC follicular variant with capsular invasion upon resection without lymphvascular invasion or lymph node involvement. THADA-F2BP3 fusion is associated with thyroid carcinoma, with low-risk non-aggressive behavior, conservative surgery appears necessary and lobectomy is likely adequate.

Pleural Metastasis of High-Grade Endometrial Stromal Sarcoma With YWHAE Gene (17p13.3) Rearrangement, A Rare Case Report

Introduction/Objective

Endometrial stromal sarcoma (ESS), a rare malignant neoplasm of endometrial stroma, accounts for less than 1% of all uterine tumors. High grade ESS (HGESS) is aggressive and commonly relapses even after surgical and neoadjuvant therapy. Abdominal and pelvic regions are common sites of metastasis, however, distant metastases to the liver, lung, vertebrae, and brain have been reported.

Methods/Case Report

We encountered a 49-year-old female who presented with shortness of breath, found to have a left pleural effusion and multiple pleural masses. She initially presented three years ago with heavy irregular menses and left pelvic pain for one year. D&C revealed prominent small spindle cells for which a stromal nodule and low-grade or malignant process was probable. CT scan showed an enlarged uterus. Hysterectomy with bilateral salpingo- oophorectomy, bilateral pelvic and para-aortic lymph node dissection, and partial omentectomy were performed. The uterus revealed an intramural 7 cm mass with a serpiginous growth pattern and lymphovascular invasion. Tumor cells were plump to spindled with areas of high cellularity, rounded nuclei, increased atypia and mitosis. Atypical areas were positive for cyclin D1, focally positive for CD10, and negative for ER, PR, SMA, desmin, AE1/3 and CAM5.2. FISH studies showed rearrangement of YWHAE gene (17p13.3) and no rearrangement of JAZF1 or PHF1 gene regions. Findings supported the diagnosis of HGESS. The patient received post-operative chemotherapy. Biopsy of the current pleural lesion revealed a nonspecific malignant spindle cell neoplasm positive for BCL1, CD56, CD117, CD99, TLE1 and INI1, while negative for AE1/3, CAM5.2, EMA, ER, PR, CK5/6, calretinin, SMA, desmin and S100. The CD10 stain was inconclusive. FISH studies showed rearrangement of YWHAE gene (17p13.3) and no rearrangement involving JAZF1 or PHF1 gene regions. No rearrangement of the SS18 gene region was observed and synovial sarcoma was excluded. Overall findings support the diagnosis of metastatic HGESS.

Results (if a Case Study enter NA)

NA

Conclusion

HGESS, a rare tumor with a nonspecific immunostain profile, has the ability to metastasize to rare body sites, such as the pleura in our case. Display of spindle cell morphology is a nonspecific finding that raises broad differential diagnoses. In women, with or without a history of uterine neoplasm, HGESS is a clinically worthwhile diagnosis to be mindful of.

SCAMP4 is a novel prognostic marker and correlated with the tumor progression and immune infiltration in glioma

BACKGROUND

Glioma is the most prevalent brain tumor with high mortality and morbidity and the prognosis of patients remains very poor. Glioma therapy is largely limited by the extraordinary invasive capability in glioma and the lack of valuable biomarkers of LGG and GBM. So it is urgent and important for us to identify valuable biomarkers to treat glioma patients. SCAMP4 (Secretory Carrier-Associated Membrane Protein 4) has not been reported to be linked to cancer prognostic or any treatments.

METHODS

We analyzed the role of SCAMP4 in LGG and GBM via the publicly available CGGA (The Chinese Glioma Atlas) and TCGA (The Cancer Genome Atlas) databases. The correlations between SCAMP4 and the immune cells were analyzed by applying CIBERSORT and TIMER, while R was utilized in the analysis of the statistical data.

RESULTS

Our results indicated that SCAMP4 which is correlated to age, stage, grade and tumor status and may be a promising independent prognostic factor in LGG and GBM. Meanwhile, the expression of SCAMP4 is closely associated with some tumor-infiltrating immune cells such as Monocytes, NK cells activated, Macrophages, Mast cells resting and so on. Furthermore, during the in-depth analysis of the integrated correlations, we also find that isocitrate dehydrogenase 1 (IDH1) and SCAMP4 shared similar prognostic values.

CONCLUSIONS

Together with all these findings, the identification of SCAMP4 as a new biomarker could elucidate how the immune microenvironment influence the glioma development. With further analysis, SCAMP4 may be a predictor for glioma prognosis.

The low expression of NUP62CL indicates good prognosis and high level of immune infiltration in lung adenocarcinoma

A primary factor in tumor morbidity and mortality, lung adenocarcinoma (LUAD) is known to be a major subtype of lung cancer, having the lowest survival rate among all other cancers. Using The Cancer Genome Atlas (TCGA) database the relationship between the immune infiltrate and the NUP62CL was explored and the value of the NUP62CL expression in the prognosis and diagnosis LUAD was examined. Using the logistic regression and the Wilcoxon signed‐rank test the relationship between the NUP62CL and the clinico‐pathological features was analyzed. There was a significant correlation between the clinical stage (p = 0.005), the N (p = 0.004), and the decreased expression of NUP62CL. The prognosis of LUAD with high NUP62CL expression was revealed to be worse than that with low NUP62CL expression (p < 0.001) by the Kaplan‐Meier survival analysis. The potentiality of NUP62CL to be a significant factor of prognosis for LUAD was indicated by the analyses of the multivariate and the univariate Cox regression models. In LUAD, the crucial role of recombination and maintenance of telomere as a significant pathway for NUP62CL was suggested by the Gene Set Enrichment Analysis (GSEA). To analyze the correlation between the genes and the tumor infiltrating immune cells the CIBERSORT was used. Moreover the positive correlation with the NUP62CL expression in LUAD of the infiltration level of the tumor infiltrating B lymphocytes and memory CD4+ T cells was exhibited by CIBERSORT. Therefore, NUP62CL may be a new valuable prognostic indicator for LUAD.

Development of a Prognostic Model for Ovarian Cancer Patients Based on Novel Immune Microenvironment Related Genes

Ovarian cancer (OV) has become the most lethal gynecological cancer. However, its treatment methods and staging system are far from ideal. In the present study, taking the advantage of large-scale public cohorts, we extracted a list of immune-related prognostic genes that differentially expressed in tumor and normal ovarian tissues. Importantly, an individualized immune-related gene based prognostic model (IPM) for OV patients were developed. Furthermore, we validated our IPM in Gene Expression Omnibus (GEO) repository and compared the immune landscape and pathways between high-risk and low-risk groups. The results of our study can serve as an important model to identify the immune subset of patients and has potential for use in immune therapeutic selection and patient management.

Accuracy of prenatal ultrasound screening to identify fetuses infected by cytomegalovirus which will develop severe long-term sequelae

OBJECTIVES

To compare the ability of detailed routine ultrasound examination, performed without knowledge of maternal serology and fetal status, with that of targeted prenatal imaging performed in prenatal diagnostic units in cases of known fetal infection to identify cytomegalovirus (CMV)-infected fetuses that will develop long-term sequelae.

METHODS

All prenatal imaging reports were collected for 255 children with congenital CMV in a registered cohort between 2013 and 2017 (NCT01923636). All women had undergone detailed routine fetal ultrasound examination at 20-24 and 30-34 weeks as part of routine antenatal care. All cases of known fetal CMV infection had also undergone targeted prenatal ultrasound examination. Postnatal structured follow-up for up to 48 months of age involved clinical, audiological and neurological assessment, including Brunet-Lezine scoring. Long-term sequelae (> 12 months) were considered to be mild in cases with isolated unilateral hearing loss and/or vestibular disorders, and severe in cases with bilateral hearing loss and/or neurological sequelae. All imaging reports were analyzed retrospectively with the knowledge of congenital CMV infection, searching for reference to findings that were, or could have been, related to fetal infection. Findings were analyzed in relation to whether the cases were diagnosed with CMV in utero or only postnatally.

RESULTS

There were 237 children with complete follow-up data (> 12 months), for a median of 24 (range, 12-48) months. Of these, 30% (71/237) were diagnosed with CMV prenatally and 70% (166/237) were diagnosed within 3 weeks after birth. 72.5% (29/40) of children with long-term sequelae, including 74% (14/19) with severe long-term sequelae, were not identified in the prenatal period. Among those diagnosed prenatally, the sensitivity of prenatal imaging for predicting long-term sequelae and severe long-term sequelae was 91% and 100%, respectively, while, in the group diagnosed only postnatally, non-specific infection-related ultrasound findings had been reported without raising suspicion in 48% of cases with long-term sequelae and 64% of those with severe long-term sequelae.

CONCLUSIONS

Routine detailed ultrasound examination in pregnancy is not an appropriate screening tool for congenital CMV infection that leads to long-term sequelae, in contrast with the high performance of targeted prenatal imaging in known cases of fetal infection. The non-specific nature of ultrasound features of CMV and their evolution, and a lack of awareness of caregivers about congenital CMV, are likely explanations. Awareness of the sonologist regarding congenital CMV and knowledge of the maternal serological status in the first trimester seem key to the performance of prenatal ultrasound. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.

Development and Validation of a Clinical Prognostic Model Based on Immune-Related Genes Expressed in Clear Cell Renal Cell Carcinoma

Background: Clear cell renal cell carcinoma (ccRCC) is the most frequent and terminal subtype of RCC. Reliable markers associated with the immune response are not available to predict the prognosis of patients with ccRCC. We exploited the extensive number of ccRCC samples from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) repository to perform a comprehensive analysis of immune-related genes (IRGs). Methods: Based on TCGA data, we incorporated IRGs and their expression profiles of 72 normal and 539 ccRCC samples. Univariate Cox analysis was used to evaluate the relationship between overall survival (OS) and IRGs expression. The Lasso Cox regression model identified prognostic genes used to establish a clinical immune prognostic model. The TF-IRG network was used to study the potential molecular mechanisms of action and properties of ccRCC-specific IRGs. Multivariate Cox analysis established a clinical prognostic model of IRGs. Results: We found a significant correlation among 15 differentially expressed IRGs with the OS of patients with ccRCC. Gene function enrichment analysis showed that these IRGs are significantly associated with response to receptor ligand activity. Lasso Cox regression analysis identified 10 genes with the greatest prognostic value. A clinical prognostic model based on six IRGs, which performed well for predicting prognosis, revealed significant associations of patients' survival with age, sex, stage, tumor, node, and metastasis. Moreover, these findings reflect the infiltration of tumors by various immune cells. Conclusion: We identified six clinically significant IRGs and incorporated them into a clinical prognostic model with great significance for monitoring and predicting prognosis of ccRCC.

miR-29a is a potential protective factor for fibrogenesis in gluteal muscle contracture

Circulating miRNAs have been proposed as the effective diagnostic biomarkers for muscular fibrosis-associated diseases. However, circulating biomarkers for early diagnosis of contracture muscles are limited in gluteal muscle contracture (GMC) patients. Here we sought to explore the abnormally expressed miRNAs in plasma and contraction bands of GMC patients. The results showed miR-29a-3p expression in plasma and contraction bands tissue was significantly reduced in GMC patients compared with normal control. Cell viability and levels of proliferation-associated protein cyclin D1 and cyclin-dependent-kinase 2 (CDK2) were powerfully inhibited by miR-29a mimics and enhanced by miR-29a inhibitor compared with negative control. Furthermore, miR-29a mimics effectively impeded, while miR-29a inhibitor enhanced the expression of collagen I and collagen III, followed by the secretion of transforming growth factor beta1 (TGF-beta1), TGF-beta3 and connective tissue growth factor (CTGF) in primary human contraction bands (CB) fibroblasts. The miR-29a-3p negatively regulated the expression of TGF-beta1 through binding to the 3´ UTR region of SERPINH1 (encoding heat shock protein HSP47), but had no effect on Smad2 activity. The miR-29a-3p was inversely correlated with HSP47 in contraction bands tissue from GMC patients. Collectively, miR-29a was notably depressed and regulated cell viability and fibrosis by directly targeting HSP47 in GMC, which suggest that circulating miR-29a might be a potential biomarker for early diagnosis and provides a novel therapeutic target for GMC.

SYT16 is a prognostic biomarker and correlated with immune infiltrates in glioma: A study based on TCGA data

BACKGROUND

Glioma is the most lethal primary brain tumor. Lower-grade glioma (LGG) is the crucial pathological type of Glioma. Immune-infiltration of the tumor microenvironment positively associated with overall survival in LGG. SYT16 is a gene has not been reported in cancer. We assess the role of SYT16 in LGG, via the publicly available TCGA database.

METHODS

Gene Expression Profiling Interactive Analysis (GEPIA) was used to analyze the expression of SYT16 in LGG. We evaluated the influence of SYT16 on survival of LGG patients by survival module. Then, datasets of LGG were downloaded from TCGA. The correlations between the clinical information and SYT16 expression were analyzed using logistic regression. Univariable survival and Multivariate Cox analysis was used to compare several clinical characteristics with survival. we also explore the correlation between SYT16 and cancer immune infiltrates using CIBERSORT and correlation module of GEPIA. Gene set enrichment analysis (GSEA) was performed using the TCGA dataset. In addition, we use TIMER to explore the collection of SYT16 Expression and Immune Infiltration Level in LGG and to explore cumulative survival in LGG.

RESULTS

The univariate analysis using logistic regression, indicated that increased SYT16 expression significantly correlated with the tumor grade. Moreover, multivariate analysis revealed that the up-regulated SYT16 expression is an independent prognostic factor for good prognosis. Specifically, SYT16 expression level has significant negative correlations with infiltrating levels of B cell, CD4+ T cells, Macrophages, Neutrophils and DCs in LGG. In addition, GSEA identified ingle organism behavior, gated channel activity, cognition, transporter complex and ligand gated channel activity  in Gene Ontology (GO) were differentially enriched in the high SYT16 expression phenotype pathway. Neuroactive ligand receptor interaction, calcium signaling pathway, long term potentiation, type II diabetes mellitus and long term depression were identified as differentially enriched  pathway in Kyoto Encyclopedia of Genes and Genomes (KEGG).

CONCLUSION

SYT16 is a Prognostic Biomarker and Correlated with Immune Infiltrates in LGG.

Low expression of RGL4 is associated with a poor prognosis and immune infiltration in lung adenocarcinoma patients

Lung adenocarcinoma (LUAD) is a frequently diagnosed histologic subtype with increasing morbidity and mortality. RalGDS-Like 4 (RGL4) has not been reported to be associated with cancer risk, prognosis, immunotherapy or any other treatments. We perform a bioinformatics analysis on data downloaded from the Cancer Genome Atlas (TCGA)-LUAD, and we find that low expression of RGL4 is accompanied by worse outcomes and prognosis in LUAD patients. As a promising predictor, the potential influence and mechanisms of RGL4 on overall survival are worth exploring. Moreover, RGL4 expression is significantly associated with a variety of tumor-infiltrating immune cells (TIICs), particularly memory B cells, CD8⁺T cells and neutrophils. Subsequently, we evaluated the most notable KEGG pathways, including glycolysis gluconeogenesis, the P53 signaling pathway, RNA degradation, and the B cell receptor signaling pathway, among others. Our findings provide evidence that the decreased expression of RGL4 is significantly associated with poor prognosis and immune cell infiltration in patients with LUAD and highlight the use of RGL4 as a novel predictive biomarker for the prognosis of LUAD and other cancers. RGL4 may also be used in combination with immune checkpoints to identify the benefits of immunotherapy. Subjects: Bioinformatics, Genomics, Oncology, Thoracic surgery.

HER2 exon 20 insertions in non-small-cell lung cancer are sensitive to the irreversible pan-HER receptor tyrosine kinase inhibitor pyrotinib

BACKGROUND

Effective targeted therapy for non-small-cell lung cancer (NSCLC) patients with human epidermal growth factor receptor 2 (HER2) mutations remains an unmet need. This study investigated the antitumor effect of an irreversible pan-HER receptor tyrosine kinase inhibitor, pyrotinib.

PATIENTS AND METHODS

Using patient-derived organoids and xenografts established from an HER2-A775_G776YVMA-inserted advanced lung adenocarcinoma patient sample, we investigated the antitumor activity of pyrotinib. Preliminary safety and efficacy of pyrotinib in 15 HER2-mutant NSCLC patients in a phase II clinical trial are also presented.

RESULTS

Pyrotinib showed significant growth inhibition of organoids relative to afatinib in vitro (P = 0.0038). In the PDX model, pyrotinib showed a superior antitumor effect than afatinib (P = 0.0471) and T-DM1 (P = 0.0138). Mice treated with pyrotinib displayed significant tumor burden reduction (mean tumor volume, -52.2%). In contrast, afatinib (25.4%) and T-DM1 (10.9%) showed no obvious reduction. Moreover, pyrotinib showed a robust ability to inhibit pHER2, pERK and pAkt. In the phase II cohort of 15 patients with HER2-mutant NSCLC, pyrotinib 400 mg resulted in a objective response rate of 53.3% and a median progression-free survival of 6.4 months.

CONCLUSION

Pyrotinib showed activity against NSCLC with HER2 exon 20 mutations in both patient-derived organoids and a PDX model. In the clinical trial, pyrotinib showed promising efficacy.

CLINICAL TRIAL REGISTRATION

NCT02535507.

Prognostic biomarker MITD1 and its correlation with immune infiltrates in hepatocellular carcinoma (HCC)

BACKGROUND

Hepatocellular carcinoma (HCC) is globally recognized as one of the most frequently occurring primary malignant liver tumors, making the identification of HCC biomarkers critically important. The protein MITD1 (Microtubule Interacting and Trafficking Domain containing 1) has been shown to interact with ESCRT-III and participates in cytokinesis, the last step in cell division. This is the first investigation into the expression of MITD1 and its prognostic value, potential biological functions and effects on the immune system in HCC patients.

METHODS

The gene expression and clinicopathology analysis, enrichment analysis and immune infiltration analysis are based on data obtained from The Cancer Genome Atlas (TCGA), with additional bioinformatics analyses performed. The statistical analysis was conducted in R and immune responses of MITD1 expression in HCC were analyzed using TIMER and CIBERSORT. In addition, GEPIA, K-M survival analysis and data from the HPA were used to validate the outcomes.

RESULTS

Our results highlighted that MITD1 plays a key role as an independent prognostic factor in patients with HCC. MITD1 expression was associated with age, grade, stage and tumor status. GSEA revealed that MITD1 is closely correlated with cell cycle control via the NOTCH signaling pathway. CIBERSORT analysis revealed that the amount of NK cells decreased when MITD1 expression was high.

CONCLUSIONS

The identification of MITD1 as a new biomarker for HCC could help elucidate how changes in cytokinesis and the immune environment promote liver cancer development. With further analysis, MITD1 may be able to serve as a predictor for human HCC prognosis.

Reduced GRAMD1C expression correlates to poor prognosis and immune infiltrates in kidney renal clear cell carcinoma

There has been an increase in the mortality rate and morbidity of kidney cancer (KC) with kidney renal clear cell carcinoma (KIRC) being the most common subtype of KC. GRAMD1C (GRAM Domain Containing 1C) has not been reported to relate to prognosis and immunotherapy in any cancers. Using bioinformatics methods, we judged the prognostic value of GRAMD1C expression in KIRC and investigated the underlying mechanisms of GRAMD1C affecting the overall survival of KIRC based on data downloaded from The Cancer Genome Atlas (TCGA). The outcome revealed that reduced GRAMD1C expression could be a promising predicting factor of poor prognosis in kidney renal clear cell carcinoma. Meanwhile, GRAMDIC expression was significantly correlated to several tumor-infiltrating immune cells (TIICs), particularly the regulatory T cells (Tregs). Furthermore, GRAMD1C was most significantly associated with the mTOR signaling pathway, RNA degradation, WNT signaling pathway, toll pathway and AKT pathway in KIRC. Thus, GRAMD1C has the potential to become a novel predictor to evaluate prognosis and immune infiltration for KIRC patients.

Increased expression of TTC21A in lung adenocarcinoma infers favorable prognosis and high immune infiltrating level

BACKGROUND

Lung adenocarcinoma (LUAD) is a crucial pathological type of lung cancer. Immune-infiltration of the tumor microenvironment positively associated with overall survival in LUAD. TTC21A is a gene has not reported in cancer, and the mechanism behind it is still unclear. Our study assesses TTC21A role in LUAD, via TCGA data.

METHODS

GEPIA was utilized to analyze the expression of TTC21A in LUAD. We evaluated the influence of TTC21A on survival of LUAD patients by survival module. Then, data sets of LUAD were downloaded from TCGA. The correlations between clinical information and TTC21A expression were analyzed using logistic regression. Clinicopathologic characteristics associated with overall survival in TCGA patients using Cox regression. In addition, we explored the correlation between TTC21A and cancer immune infiltrates using CIBERSORT and "Correlation" module of GEPIA.

RESULTS

The univariate analysis using logistic regression, wherein TTC21A expression served as a categorical dependent variable (with a median expression value of 2.5), indicated that increased TTC21A expression is significantly correlated with pathological stage, tumor status and lymph nodes. Moreover, multivariate analysis revealed that the up-regulated TTC21A expression, negative results of pathological stage and distant metastasis are independent prognostic factors for good prognosis. Specifically, a positive correlation between increased TTC21A expression and immune infiltrating level of B cells, Neutrophils, Mast cells and T cells was established using CIBERSORT analysis. Furthermore, we confirmed it in "correlation" module of GEPIA.

CONCLUSION

Together with all these findings, increased TTC21A expression correlates with favorable prognosis and increased proportion of immune cells, such as B cells, Neutrophils, Mast cells and T cells in LUAD. These conclusions indicate that TTC21A could serve as a potential biomarker to assess prognosis and immune infiltration level in LUAD.