Investigating esophageal sarcomatoid carcinoma and its comparison with esophageal squamous cell carcinoma on clinicopathological characteristics, prognosis, and radiomics features: a retrospective study.

Introduction: Esophageal sarcomatoid carcinoma (ESC) is a rare pathological subtype of esophageal carcinomas, wherein its epithelial component typically demonstrates squamous cell carcinoma (SCC). However, the clinicopathological features and prognosis of ESC remain unclear, alongside its unique aspects compared to esophageal SCC (ESCC). Methods: Between January 2008 and December 2018, we retrospectively reviewed 67 ESC patients treated at West China Hospital. Among them, 51 patients with resected ESC were matched with 98 resected ESCC patients over the same period using propensity score matching at 1:2. The survival time and radiomics features of the two groups were compared. Results: A total of 59 patients with resected ESC and eight patients with non-resected ESC were enrolled. Progression-free survival (PFS) and overall survival (OS) were significantly different in patients with different TNM stages (p < 0.001). A multivariate analysis showed that length of tumor was an independent factor for OS in resetable ESC (p = 0.041). Among matched ESC and ESCC patients, OS was significantly longer for patients with ESC than those with ESCC (5-year OS, 61.1% vs. 43.6%; HR 0.59, 95% CI 0.35-0.96; p = 0.032). A Rad-score for discriminating ESC from ESCC containing two CT-derived radiomics features was developed [area under the curve: 0.823 (95% CI 0.732-0.913) in the training cohort and 0.828 (95% CI 0.636-1.000) in the validation cohort, respectively]. Conclusions: ESC has a better prognosis when compared with ESCC. By developing a radiomics prediction model, we provide reliability and convenience for the differential diagnosis of ESC from ESCC.

Contribution of crosstalk of mesothelial and tumoral epithelial cells in pleural metastasis of lung cancer.

Background: Tumor metastasis commonly affects pleura in advanced lung cancer and results in malignant pleural effusion (MPE). MPE is related to poor prognosis, but without systematic investigation on different cell types and their crosstalk at single cell resolution. Methods: We conducted single-cell RNA-sequencing (scRNA-seq) of lung cancer patients with pleural effusion. Next, our data were integrated with 5 datasets derived from individuals under normal, non-malignant disease and lung carcinomatous conditions. Mesothelial cells were re-clustered and their interactions with epithelial cells were comprehensively analyzed. Taking advantage of inferred ligand-receptor pairs, a prediction model of prognosis was constructed. The co-culture of mesothelial cells and malignant epithelial cells in vitro and RNA-seq was performed. Epidermal growth factor receptor (EGFR) antagonist cetuximab was utilized to prevent the lung cancer cells' invasiveness. Spatial distribution of cells in lung adenocarcinoma patients' samples were also analyzed to validate our findings. Results: The most distinctive transcriptome profiles between tumor and control were revealed in mesothelial cells, which is the predominate cell type of pleura. Five subtypes were divided, including one predominately identified in MPE which was characterized by enriched cancer-related pathways (e.g., cell migration) along evolutionary trajectory from normal mesothelial cells. Cancer-associated mesothelial cells (CAMCs) exhibited varied interactions with different subtypes of malignant epithelial cells, and multiple ligands/receptors exhibited significant correlation with poor prognosis. Experimentally, mesothelial cells can increase the migration ability of lung cancer cells through co-culturing. EGFR was the only affected gene in cancer cells that exhibited interaction with mesothelial cells and was associated with poor prognosis. Using EGFR antagonist cetuximab prevented the lung cancer cells' increased invasiveness caused by mesothelial cells. Moreover, epithelial mitogen (EPGN)-EGFR interaction was supported through spatial distribution analysis, revealing the significant proximity between EPGN+ mesothelial cells and EGFR+ epithelial cells. Conclusions: Our findings highlighted the important role of mesothelial cells and their interactions with cancer cells in pleural metastasis of lung cancer, providing potential targets for treatment.

MHBase: A comprehensive database of short microhaplotypes for advancing forensic genetic analysis.

Microhaplotypes (MHs) were first recommended by Prof. Kidd for use in forensics because they can improve human identification, kinship analysis, mixture deconvolution, and ancestry prediction. Since their introduction, extensive research has demonstrated the advantages of MHs in forensic applications and provided useful data for different populations. Currently, two databases, ALFRED (ALlele FREquency Database) and MicroHapDB (MicroHaplotype DataBase), house the published MH information and population data. We previously constructed a single nucleotide polymorphism SNP-SNP MH database (D-SNPsDB) of MHs within 50 bp on the whole human genome for 26 populations integrating basic data such as physical genome positions, mapping of variant identifiers (rsIDs), allele frequencies, and basic variant information. Building upon the previous research, we further selected MHs containing at least two variants (SNPs and/or insertions/deletions [InDels]) within a short DNA fragment (≤ 50 bp) in 26 populations based on the 1000 Genomes Project dataset (Phase 3) to construct a more comprehensive database. Subsequently, we established a user-friendly website that allows users to search the MH database (MHBase) based on their research objectives and study population to find suitable loci and provides other functions such as querying reported loci, performing online calculations using the PHASE software, and calculating ancestral-related parameters. The loci in the database are classified as SNP-based MHs, which include only SNPs, and InDel-including MHs, which contain at least one InDel. Here, we provide a detailed overview of the MHBase and an analysis of shared loci at the global and continental levels, ancestral markers, the genetic distance within loci, and mapping with the genome annotation file. The website is an accessible and useful tool for researchers engaged in marker discovery, population studies, assay development, and panel design.

Diversity of extracellular HSP70 in cancer: advancing from a molecular biomarker to a novel therapeutic target.

Heat shock protein 70 (HSP70) is a highly conserved protein functioning as a "molecular chaperone", which is integral to protein folding and maturation. In addition to its high expression within cells upon stressful challenges, HSP70 can be translocated to the cell membrane or released from cells in free form or within extracellular vesicles (EVs). Such trafficking of HSP70 is also present in cancer cells, as HSP70 is overexpressed in various types of patient samples across a range of common malignancies, signifying that extracellular HSP70 (eHSP70) can serve as a tumor biomarker. eHSP70 is involved in a broad range of cancer-related events, including cell proliferation and apoptosis, extracellular matrix (ECM) remodeling, epithelial-mesenchymal transition (EMT), angiogenesis, and immune response. eHSP70 can also induce cancer cell resistance to various treatments, such as chemotherapy, radiotherapy, and anti-programmed death-1 (PD-1) immunotherapy. Though the role of eHSP70 in tumors is contradictory, characterized by both pro-tumor and anti-tumor effects, eHSP70 serves as a promising target in cancer treatment. In this review, we comprehensively summarized the current knowledge about the role of eHSP70 in cancer progression and treatment resistance and discussed the feasibility of eHSP70 as a cancer biomarker and therapeutic target.

Potential Benefits of Green Tea in Prostate Cancer Prevention and Treatment: A Comprehensive Review.

Prostate cancer is a prevalent and debilitating disease that necessitates effective prevention and treatment strategies. Green tea, a well-known beverage derived from the Camellia sinensis plant, contains bioactive compounds with potential health benefits, including catechins and polyphenols. This comprehensive review aims to explore the potential benefits of green tea in prostate cancer prevention and treatment by examining existing literature. Green tea possesses antioxidant, anti-inflammatory, and anti-carcinogenic properties attributed to its catechins, particularly epigallocatechin gallate. Epidemiological studies have reported an inverse association between green tea consumption and prostate cancer risk, with potential protection against aggressive forms of the disease. Laboratory studies demonstrate that green tea components inhibit tumor growth, induce apoptosis, and modulate signaling pathways critical to prostate cancer development and progression. Clinical trials and human studies further support the potential benefits of green tea. Green tea consumption has been found to be associated with a reduction in prostate-specific antigen levels, tumor markers, and played a potential role in slowing disease progression. However, challenges remain, including optimal dosage determination, formulation standardization, and conducting large-scale, long-term clinical trials. The review suggests future research should focus on combinatorial approaches with conventional therapies and personalized medicine strategies to identify patient subgroups most likely to benefit from green tea interventions.

Nomogram for predicting pathologic complete response to neoadjuvant chemoradiotherapy in patients with esophageal squamous cell carcinoma.

PURPOSE: A pathologic complete response (pCR) to neoadjuvant chemoradiotherapy (nCRT) is seen in up to 40% of the patients with esophageal squamous cell carcinoma (ESCC). No nomogram has been constructed for the prediction of pCR for patients whose primary chemotherapy was a taxane-based regimen. The aim is to identify characteristics associated with a pCR through analyzing multiple pre- and post-nCRT variables and to develop a nomogram for the prediction of pCR for these patients by integrating clinicopathological characteristics and hematological biomarkers. MATERIALS AND METHODS: We analyzed 293 patients with ESCC who underwent nCRT followed by esophagectomy. Clinicopathological factors, hematological parameters before nCRT, and hematotoxicity during nCRT were collected. Univariate and multivariate logistic regression analyses were performed to identify predictive factors for pCR. A nomogram model was built and evaluated for both discrimination and calibration. RESULTS: After surgery, 37.88% of the study patients achieved pCR. Six variables were included in the nomogram: sex, cN stage, chemotherapy regimen, duration of nCRT, pre-nCRT neutrophil-to-lymphocyte ratio (NLR), and pre-nCRT platelet-to-lymphocyte ratio (PLR). The nomogram indicated good accuracy and consistency in predicting pCR, with a C-index of 0.743 (95% confidence interval: 0.686, 0.800) and a p value of 0.600 (>0.05) in the Hosmer-Lemeshow goodness-of-fit test. CONCLUSIONS: Female, earlier cN stage, duration of nCRT (< 62 days), chemotherapy regimen of taxane plus platinum, pre-nCRT NLR (≥2.199), and pre-nCRT PLR (≥99.302) were significantly associated with a higher pCR in ESCC patients whose primary chemotherapy was a taxane-based regimen for nCRT. A nomogram was developed and internally validated, showing good accuracy and consistency.

Immune checkpoint inhibitor-associated cardiovascular toxicities: A review.

Immune checkpoint inhibitors (ICIs) have revolutionary effects on therapeutic strategies for multiple malignancies. Their efficacy depends on their ability to reactivate the host immune system to fight cancer cells. However, adverse reactions to ICIs are common and involve several organs, limiting their use in clinical practice. Although the incidence of cardiovascular toxicity is relatively low, it is associated with serious consequences and high mortality rates. The primary cardiovascular toxicities include myocarditis, pericarditis, Takotsubo syndrome, arrhythmia, vasculitis, acute coronary syndrome, and venous thromboembolism. Currently, the mechanism underlying ICI-associated cardiovascular toxicity remains unclear and underexplored. The diagnosis and monitoring of ICI-associated cardiovascular toxicities mainly include the following indicators: symptoms, signs, laboratory examination, electrocardiography, imaging, and pathology. Treatments are based on the grade of cardiovascular toxicity and mainly include drug withdrawal, corticosteroid therapy, immunosuppressants, and conventional cardiac treatment. This review focuses on the incidence, underlying mechanisms, clinical manifestations, diagnoses, and treatment strategies.

Efficacy and safety of anlotinib combined with the STUPP regimen in patients with newly diagnosed glioblastoma: a multicenter, single-arm, phase II trial.

OBJECTIVE: Glioblastomas are highly vascularized malignant tumors. We determined the efficacy and safety of the anti-angiogenic multi-kinase inhibitor, anlotinib, for a newly diagnosed glioblastoma. METHODS: This multicenter, single-arm trial (NCT04119674) enrolled 33 treatment-naïve patients with histologically proven glioblastomas between March 2019 and November 2020. Patients underwent treatment with the standard STUPP regimen [fractionated focal irradiation in daily fractions of 1.8-2 Gy given 5 d/w × 6 w (total = 54-60 Gy)] or radiotherapy plus continuous daily temozolomide (TMZ) (75 mg/m2 of body surface area/d, 7 d/w from the first to the last day of radiotherapy), followed by 6 cycles of adjuvant TMZ (150-200 mg/m2 × 5 d during each 28-d cycle) plus anlotinib (8 mg/d on d 1-14 of each 3-w cycle for 2 cycles during concomitant chemoradiotherapy, 8 maximal cycles as adjuvant therapy, followed by maintenance at 8 mg/d. The primary endpoint was progression-free survival (PFS). Secondary endpoints included overall survival (OS) and adverse events (AEs). RESULTS: Thirty-three patients received the planned treatment. The median PFS was 10.9 months (95% CI, 9.9-18.7 months) and the 12-month PFS rate was 48.5%. The median OS was 17.4 months (95% CI, 14.5-21.1 months) and the 12-month OS rate was 81.8%. The most common AEs included hypertriglyceridemia [58% (n = 19)], hypoalbuminemia [46% (n = 15)], and hypercholesterolemia [46% (n = 15)] during concurrent chemoradiotherapy and leukopenia [73% (n = 24)], hypertriglyceridemia [67% (n = 22)], and neutropenia [52% (n = 17)] during adjuvant therapy. Five patients discontinued treatment due to AEs. HEG1 (HR, 5.6; 95% CI, 1.3-23.7; P = 0.021) and RP1L1 alterations (HR, 11.1; 95% CI, 2.2-57.2; P = 0.004) were associated with a significantly shorter PFS. CONCLUSIONS: Anlotinib plus the STUPP regimen has promising anti-tumor activity against glioblastoma and manageable toxicity. HEG1 and RP1L1 alterations might be novel predictive biomarkers of the response to anlotinib.

Recurrence timing and patterns incorporating lymph node status after neoadjuvant chemoradiotherapy plus esophagectomy for esophageal squamous cell carcinoma.

Purpose: About 40% of esophageal squamous cell carcinoma (ESCC) patients experienced recurrence after neoadjuvant chemoradiotherapy (nCRT) plus esophagectomy. While limited information was available on recurrence risk stratification in ESCC after neoadjuvant treatment. Our previous study showed ypN status was a reliable tool to differentiate and predict the prognosis in the recurrent population. Here, we evaluated recurrence timing and patterns in ESCC patients, taking into consideration lymph node status after nCRT. Materials and methods: A total of 309 ESCC patients treated with nCRT plus esophagectomy between 2018 and 2021 were enrolled in this observational cohort study. Lymph node status was recorded by the pathologist according to the surgical specimens. We retrospectively investigated the timing and patterns of recurrence and the prognoses in ESCC patients, taking into consideration lymph node status after nCRT. Results: After nCRT plus surgery in ESCC patients, lymph node metastasis was associated with unfavorable clinicopathological factors and high risks of recurrence. In the recurrent subgroup, ypN+ patients experienced earlier recurrence, especially for locoregional recurrence within the first year. Moreover, ypN+ patients had poorer prognosis. However, the recurrence patterns in the ypN- and ypN+ groups were similar. Besides, there were no significant differences in surgery to recurrence, recurrence to death, or overall survival among patients with locoregional or distant recurrence for overall patients and within ypN- or ypN+ groups. Conclusions: Lymph node metastasis was correlated with unfavorable clinicopathological factors and high risks of recurrence. Despite a similar recurrence pattern in the recurrent subgroup between the ypN- and ypN+ groups, ypN+ patients exhibited earlier recurrence and a worse prognosis.

Optimizing Analytical Thresholds for Low-Template DNA Analysis: Insights from Multi-Laboratory Negative Controls.

When analyzing challenging samples, such as low-template DNA, analysts aim to maximize information while minimizing noise, often by adjusting the analytical threshold (AT) for optimal results. A potential approach involves calculating the AT based on the baseline signal distribution in electrophoresis results. This study investigates the impact of reagent kits, testing quarters, environmental conditions, and amplification cycles on baseline signals using historical records and experimental data on low-template DNA. Variations in these aspects contribute to differences in baseline signal patterns. Analysts should remain vigilant regarding routine instrument maintenance and reagent replacement, as these may affect baseline signals. Prompt analysis of baseline status and tailored adjustments to ATs under specific laboratory conditions are advised. A comparative analysis of published methods for calculating the optimal AT from a negative signal distribution highlighted the efficiency of utilizing baseline signals to enhance forensic genetic analysis, with the exception of extremely low-template samples and high-amplification cycles. Moreover, a user-friendly program for real-time analysis was developed, enabling prompt adjustments to ATs based on negative control profiles. In conclusion, this study provides insights into baseline signals, aiming to enhance genetic analysis accuracy across diverse laboratories. Practical recommendations are offered for optimizing ATs in forensic DNA analysis.

Causal effect of atrial fibrillation on pulmonary embolism: a mendelian randomization study.

Atrial fibrillation (AF) can increase thrombosis, especially arterial thrombosis, and some studies show that AF patients have a higher risk of developing pulmonary embolism (PE). The objective of our study is to investigate whether there is a direct causal effect of AF on PE. A two-sample Mendelian randomization (MR) approach was utilized to determine whether there is a causal relationship between AF and PE. European population-based consortia provided statistical data on the associations between Single Nucleotide Polymorphisms (SNPs) and relevant traits. The AF dataset was obtained from genome-wide association studies (GWAS) comprising 60,620 cases and 970,216 controls, while a GWAS of 1846 cases and 461,164 controls identified genetic variations associated with PE. Estimation of the causal effect was mainly performed using the random effects inverse-variance weighted method (IVW). Additionally, other tests such as MR-Egger intercept, MR-PRESSO, Cochran's Q test, "Leave-one-out," and funnel plots were conducted to assess the extent of pleiotropy and heterogeneity. Using 70 SNPs, there was no evidence to suggest an association between genetically predicted AF and risk of PE with multiplicative random-effects IVW MR analysis (odds ratio = 1.0003, 95% confidence interval: 0.9998-1.0008, P = 0.20). A null association was also observed in other methods. MR-Egger regression and MR-PRESSO respectively showed no evidence of directional (intercept, - 2.25; P = 0.94) and horizontal(P-value in the global heterogeneity test = 0.99) pleiotropic effect across the genetic variants. No substantial evidence was found to support the causal role of AF in the development of PE.

Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing.

Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300 bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37 × 10-73 and 1-1.19 × 10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.

Assessment of ForenSeq mtDNA Whole Genome Kit for forensic application.

Mitochondrial DNA (mtDNA) is an indispensable genetic marker in forensic genetics. The emergence and development of massively parallel sequencing (MPS) makes it possible to obtain complete mitochondrial genome sequences more quickly and accurately. The study evaluated the advantages and limitations of the ForenSeq mtDNA Whole Genome Kit in the practical application of forensic genetics by detecting human genomic DNA standards and thirty-three case samples. We used control DNA with different amount to determine sensitivity of the assay. Even when the input DNA is as low as 2.5 pg, most of the mitochondrial genome sequences could still be covered. For the detection of buccal swabs and aged case samples (bloodstains, bones, teeth), most samples could achieve complete coverage of mitochondrial genome. However, when ancient samples and hair samples without hair follicles were sequenced by the kit, it failed to obtain sequence information. In general, the ForenSeq mtDNA Whole Genome Kit has certain applicability to forensic low template and degradation samples, and these results provide the data basis for subsequent forensic applications of the assay. The overall detection process and subsequent analysis are easy to standardize, and it has certain application potential in forensic cases.

A Random Forest Model for Post-Treatment Survival Prediction in Patients with Non-Squamous Cell Carcinoma of the Head and Neck.

BACKGROUND: Compared to squamous cell carcinoma, head and neck non-squamous cell carcinoma (HNnSCC) is rarer. Integrated survival prediction tools are lacking. METHODS: 4458 patients of HNnSCC were collected from the SEER database. The endpoints were overall survivals (OSs) and disease-specific survivals (DSSs) of 3 and 5 years. Cases were stratified-randomly divided into the train & validation (70%) and test cohorts (30%). Tenfold cross validation was used in establishment of the model. The performance was evaluated with the test cohort by the receiver operating characteristic, calibration, and decision curves. RESULTS: The prognostic factors found with multivariate analyses were used to establish the prediction model. The area under the curve (AUC) is 0.866 (95%CI: 0.844-0.888) for 3-year OS, 0.862 (95%CI: 0.842-0.882) for 5-year OS, 0.902 (95%CI: 0.888-0.916) for 3-year DSS, and 0.903 (95%CI: 0.881-0.925) for 5-year DSS. The net benefit of this model is greater than that of the traditional prediction methods. Among predictors, pathology, involved cervical nodes level, and tumor size are found contributing the most variance to the prediction. The model was then deployed online for easy use. CONCLUSIONS: The present study incorporated the clinical, pathological, and therapeutic features comprehensively and established a clinically effective survival prediction model for post-treatment HNnSCC patients.

A meta-analysis evaluating efficacy and safety of colchicine for prevention of major cardiovascular events in patients with coronary artery disease.

BACKGROUND: Inflammatory plays a key role in the development of coronary artery disease (CAD). Colchicine as an anti-inflammatory treatment for CAD has attracted much attention, its efficacy and safety are controversial and deserved further exploration. METHODS AND RESULTS: To evaluate the efficacy and safety of colchicine for patients with CAD, relevant randomized controlled trials (RCTs) were identified by searching several databases including PubMed, Web of Science, and EMBASE from January 1992 to May 2022. Fourteen eligible trials of colchicine therapy include populations with chronic coronary syndrome (CCS) (N = 2), acute coronary syndrome (ACS) (N = 5), and percutaneous coronary intervention (PCI) or coronary artery bypass grafting (CABG) (N = 7), and involve a total of 13,235 patients which include 6654 subjects in colchicine group and 6581 subjects in the respective control arms. The outcome was reported as odds ratio (OR) and 95% confidence interval (CI), as the relative measure of association. Overall, the incidences of major adverse cardiovascular events (MACEs) (OR 0.65; 95% CI 0.54-0.77, p < 0.01), new ACS (OR 0.68; 95% CI 0.57-0.81, p < 0.01), coronary revascularization (OR 0.65; 95% CI 0.53-0.78, p < 0.01), and stroke (OR 0.51; 95% CI 0.32-0.82, p < 0.01), were lower in the colchicine group than in the placebo arm. We did not find a significant reduction in the incidence of atrial fibrillation (OR 0.84; 95% CI 0.68-1.04, p = 0.11), all-cause mortality (OR 1.06; 95% CI 0.83-1.35, p = 0.83), cardiovascular mortality (OR 0.77; 95% CI 0.52-1.15, p = 0.21). However, we found that colchicine did increase non-cardiovascular mortality (OR 1.44; 95% CI 1.04-2.01, p = 0.03). Although the incidence of gastrointestinal events in the colchicine treatment group was higher than that in the placebo arms (OR 2.08; 95% CI 1.39-3.12, p < 0.01), the symptoms disappeared rapidly after drug withdrawal and could be tolerated by most patients. Colchicine did not increase the incidence of infections (OR 1.42; 95% CI 0.82-2.46, p = 0.22), pneumonia (OR 1.55; 95% CI 0.58-4.18, p = 0.39), cancers (OR 0.98; 95% CI 0.79-1.22, p = 0.88), bleeding (OR 1.14; 95% CI 0.41-3.14, p = 0.80). CONCLUSIONS: Colchicine is an effective, relatively safe drug that could be considered for the treatment of CAD. However, we need to pay attention to the increasing occurrence of non-cardiovascular mortality and infection especially pneumonia possibly caused by colchicine. Efficacy and safety of colchicine for patients with CAD. CAD coronary artery disease; RCTs randomized controlled trials; OR odds ratio; MACEs major adverse cardiovascular events; ACS acute coronary syndrome; NNT number needed to treat; NNH number needed to harm.

Development of specific and rapid detection of human DNA by recombinase polymerase amplification assay for forensic analysis.

The determination of human-derived samples is very important in forensic investigations and case investigation in order to determine vital information on the suspect and the case. In this study, we established a recombinase polymerase amplification (RPA) assay for rapid identification of human-derived components. The sensitivity of the assay was 0.003125 ng, with excellent species specificity, and human-derived DNA could be detected in the presence of non-human-derived components at a ratio of 1:1000. Moreover, the RPA assay had a strong tolerance to inhibitors, in the presence of 800 ng/µL humic acid, 400 ng/µL tannic acid, and 8000 ng/µL collagen. In forensic investigation, common body fluids (blood, saliva, semen, vaginal secretions) are all applicable, and the presence of DNA can be detected from samples after simple alkaline lysis, which greatly shortens the detection time. Four simulation and case samples (aged bones, aged bloodstains, hair, touch DNA) were also successfully applied. The above research results show that the RPA assay constructed in this study can be fully applied to forensic medicine to provide high sensitivity and applicability detection methods.

Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing.

In recent years, microhaplotypes (MHs) have become a research hotspot within the field of forensic genetics. Traditional MHs contain only SNPs that are closely linked within short fragments. Herein, we broaden the concept of general MHs to include short InDels. Complex kinship identification plays an important role in disaster victim identification and criminal investigations. For distant relatives (e.g., 3rd-degree), many genetic markers are required to enhance power of kinship testing. We performed genome-wide screening for new MH markers composed of two or more variants (InDel or SNP) within 220 bp based on the Chinese Southern Han from the 1000 Genomes Project. An NGS-based 67plex MH panel (Panel B) was successfully developed, and 124 unrelated individual samples were sequenced to obtain population genetic data, including alleles and allele frequencies. Of the 67 genetic markers, 65 MHs were, as far as we know, newly discovered, and 32 MHs had effective number of allele (Ae) values greater than 5.0. The average Ae and heterozygosity of the panel were 5.34 and 0.7352, respectively. Next, 53 MHs from a previous study were collected as Panel A (average Ae of 7.43), and Panel C with 87 MHs (average Ae of 7.02) was formed by combining Panels A and B. We investigated the utility of these three panels in kinship analysis (parent-child, full siblings, 2nd-degree, 3rd-degree, 4th-degree, and 5th-degree relatives), with Panel C exhibiting better performance than the two other panels. Panel C was able to separate parent-child, full-sibling, and 2nd-degree relative duos from unrelated controls in real pedigree data, with a small false testing level (FTL) of 0.11% in simulated 2nd-degree duos. For more distant relationships, the FTL was much higher: 8.99% for 3rd-degree, 35.46% for 4th-degree, and 61.55% for 5th-degree. When a carefully chosen extra relative was known, this may enhance the testing power for distant kinship analysis. Two twins from the Q family (2-5 and 2-7) and W family (3-18 and 3-19) shared the same genotypes in all tested MHs, which led to the incorrect conclusion that an uncle-nephew duo was classified as a parent-child duo. In addition, Panel C showed great capacity for excluding close relatives (2nd-degree and 3rd-degree relatives) during paternity tests. Among 18,246 real and 10,000 simulated unrelated pairs, none were misinterpreted as a relative within 2nd-degree at a log10(LR) cutoff of 4. The panels presented herein could provide supplementary power for the analysis of complex kinship.

A novel metabolic-related gene signature for predicting clinical prognosis and immune microenvironment in head and neck squamous cell carcinoma.

OBJECTIVES: Metabolic reprogramming is not only an essential hallmark in the progression of head and neck squamous cell carcinoma (HNSCC), but also an important regulator of cancer cell adaptation to tumor microenvironment (TME). However, the potential mechanism of metabolic reprogramming in TME of HNSCC is still unknown. METHODS: The head and neck squamous cell carcinoma with survival information were obtained the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The metabolic-related genes were identified by differential analysis and survival analysis. Univariate and multivariate Cox regression analyses were applied to determine an overall estimate of metabolic-related risk signature and related clinical parameters. The sensitivity and specificity of the risk signature were evaluated by time-dependent receiver operation characteristic (ROC) curves. TME immune cell infiltration mediated by metabolic-related genes was explored by gene set enrichment analysis (GSEA) and correlation analysis. RESULTS: Seven metabolic-related genes (SMS, MTHFD2, HPRT1, DNMT1, PYGL, ADA, and P4HA1) were identified to develop a metabolic-related risk signature. The low-risk group had a better overall survival compared to that of the high-risk group in the TCGA and GSE65858 cohorts. The AUCs for 1-, 3-, and 5-year overall survival were 0.646 vs. 0.673, 0.694 vs. 0.639, and 0.673 vs. 0.573, respectively. The AUC vale of risk score was 0.727 vs. 0.673. The low-risk group was associated with immune cell infiltration in the TME. CONCLUSIONS: The metabolic-related risk signature were constructed and validated, which could involve in regulating the immune cell infiltration in the TME and act as an independent biomarker that predicted the prognosis of HNSCC.

An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis.

Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11-81 bp and 123-198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93-100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels.