Optimal Irreversible Electroporation Combined with Nano-Enabled Immunomodulatory to Boost Systemic Antitumor Immunity.

In this work, we proposed nµPEF, a novel pulse configuration combining nanosecond and microsecond pulses (nµPEF), to enhance tumor ablation in irreversible electroporation (IRE) for oncological therapy. nµPEF demonstrated improved efficacy in inducing immunogenic cell death, positioning it as a potential candidate for next-generation ablative therapy. However, the immune response elicited by nµPEF alone was insufficient to effectively suppress distant tumors. To address this limitation, we developed PPR@CM-PD1, a genetically engineered nanovesicle. PPR@CM-PD1 employed a polyethylene glycol-polylactic acid-glycolic acid (PEG-PLGA) nanoparticle encapsulating the immune adjuvant imiquimod and coated with a genetically engineered cell membrane expressing programmed cell death protein 1 (PD1). This design allowed PPR@CM-PD1 to target both the innate immune system through toll-like receptor 7 (TLR7) agonism and the adaptive immune system through programmed cell death protein 1/programmed cell death-ligand 1 (PD1/PDL1) checkpoint blockade. In turn, nµPEF facilitated intratumoral infiltration of PPR@CM-PD1 by modulating the tumor stroma. The combination of nµPEF and PPR@CM-PD1 generated a potent and systemic antitumor immune response, resulting in remarkable suppression of both nµPEF-treated and untreated distant tumors (abscopal effects). This interdisciplinary approach presents a promising perspective for oncotherapy and holds great potential for future clinical applications.

STING Agonist-Loaded Nanoparticles Promotes Positive Regulation of Type I Interferon-Dependent Radioimmunotherapy in Rectal Cancer.

Hypoxia-associated radioresistance in rectal cancer (RC) has severely hampered the response to radioimmunotherapy (iRT), necessitating innovative strategies to enhance RC radiosensitivity and improve iRT efficacy. Here, a catalytic radiosensitizer, DMPtNPS, and a STING agonist, cGAMP, are integrated to overcome RC radioresistance and enhance iRT. DMPtNPS promotes efficient X-ray energy transfer to generate reactive oxygen species, while alleviating hypoxia within tumors, thereby increasing radiosensitivity. Mechanistically, the transcriptomic and immunoassay analysis reveal that the combination of DMPtNPS and RT provokes bidirectional regulatory effects on the immune response, which may potentially reduce the antitumor efficacy. To mitigate this, cGAMP is loaded into DMPtNPS to reverse the negative impact of DMPtNPS and RT on the tumor immune microenvironment (TiME) through the type I interferon-dependent pathway, which promotes cancer immunotherapy. In a bilateral tumor model, the combination treatment of RT, DMPtNPS@cGAMP, and αPD-1 demonstrates a durable complete response at the primary site and enhanced abscopal effect at the distant site. This study highlights the critical role of incorporating catalytic radiosensitizers and STING agonists into the iRT approach for RC.

Superantigen-fused T cell engagers for tumor antigen-mediated robust T cell activation and tumor cell killing.

Inadequate T cell activation has severely limited the success of T cell engager (TCE) therapy, especially in solid tumors. Enhancing T cell activity while maintaining the tumor specificity of TCEs is the key to improving their clinical efficacy. However, currently, there needs to be more effective strategies in clinical practice. Here, we design novel superantigen-fused TCEs that display robust tumor antigen-mediated T cell activation effects. These innovative drugs are not only armed with the powerful T cell activation ability of superantigens but also retain the dependence of TCEs on tumor antigens, realizing the ingenious combination of the advantages of two existing drugs. Superantigen-fused TCEs have been preliminarily proven to have good (>30-fold more potent) and specific (>25-fold more potent) antitumor activity in vitro and in vivo. Surprisingly, they can also induce the activation of T cell chemotaxis signals, which may promote T cell infiltration and further provide an additional guarantee for improving TCE efficacy in solid tumors. Overall, this proof-of-concept provides a potential strategy for improving the clinical efficacy of TCEs.

A case report and literature review on a rare subtype of triple-negative breast cancer in children.

BACKGROUND: Triple-negative breast cancer (TNBC) is a type of breast tumor with a poor prognosis because it lacks or expresses low levels of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2). TNBC is more common in middle-aged and older women, and cases of TNBC in children are rarely reported. This is the only case of childhood SBC in our hospital in more than 70 years, and the disease is extremely rare internationally. We analyzed and studied the disease and TNBC from both clinical and pathological aspects and found that SBC is very different from TNBC. CASE PRESENTATION: We report a case of secretory breast cancer (SBC), a subtype of TNBC, in an 8-year-old girl from our institution. The child presented with a single mass in the left breast only, with no skin rupture and no enlargement of the surrounding lymph nodes. The child underwent two surgeries and was followed up for one year with a good prognosis. CONCLUSIONS: SBC is highly prevalent among the multiple pathological types of pediatric breast cancer. Almost all pediatric SBC patients are characterized by the ETV6-NTRK3 fusion gene, which has a good prognosis and a 10-year survival rate of more than 90% when compared with other TNBC subtypes. According to the patient, we performed local mass resection and a postoperative pathological diagnosis of SBC (a subtype of BL-TNBC). The TNBC case had a good prognosis and differed from basal TNBC in several aspects, including clinical presentation, treatment, and prognosis. It is necessary to exclude SBC from BL-type TNBC, enhance understanding of the disease, and individualize the treatment plan, so as to avoid medical errors.

Early outcomes of the "Chimney" commando procedure in the small aortic and mitral annuli.

Background: Commando procedure, the surgical replacement of the mitral and aortic valves combined with reconstruction of the fibrosa fibrous body, is a technical challenge in patients with small aortic and mitral annuli. In this study, we evaluated the safety and early outcomes of the "Chimney" modality of the Commando procedure, in patients with small aortic and mitral annuli, after prior valve surgery, using a self-assembled valved conduit. Methods: From April 2021 to April 2022, 30 consecutive cases of the "Chimney" Commando procedure, with a self-assembled valved conduit and other combined cardiac procedures, were fully performed for re-operative patients with small aortic roots. Data were obtained through a medical record review, at the Asian Heart Hospital in Wuhan, China. Results: The patient's mean age was 52.7 ± 13.53 years, with 93.3% females. All patients had a previous heart valve surgery, 90% of which had double valve replacement (DVR). Hospital death occurred in 3.3% (n = 1) of the patients, due to malignant arrhythmias and multiorgan failure. Postoperative echocardiogram exams showed that the sizes of the aortic and mitral valve prostheses were 24.23 ± 1.60 mm and 28.33 ± 1.21 mm, respectively. All patients had intact intervalvular fibrosa (IVF) repair and no patient had any aberration in the left heart chamber communication. With the exception of one postoperative sick sinus syndrome and one re-sternotomy for bleeding, there were no significant postoperative complications, such as mortality, renal failure requiring ongoing dialysis, or mediastinitis. Echocardiography exams in the sixth postoperative month showed that the mean gradients of the aortic and mitral valves were 16.26 ± 6.44 mmHg and 11.24 ± 4.90 mmHg, respectively. Conclusions: In comparison with the standard Commando operation, the early outcomes and safety of the "Chimney" Commando procedure proved to be a feasible therapeutic option for patients with small aortic and mitral annuli, after prior valve operations. This approach enables the enlargement of the aortic and mitral annuli and the implantation of the necessary valve prosthesis.

DeepTAP: An RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens.

The transport of peptides from the cytoplasm to the endoplasmic reticulum (ER) by transporters associated with antigen processing (TAP) is a critical step in the intracellular presentation of cytotoxic T lymphocyte (CTL) epitopes. The development and application of computational methods, especially deep learning methods and new neural network strategies that can automatically learn feature representations with limited knowledge, provide an opportunity to develop fast and efficient methods to identify TAP-binding peptides. Herein, this study presents a comprehensive analysis of TAP-binding peptide sequences to derive TAP-binding motifs and preferences for N-terminal and C-terminal amino acids. A novel recurrent neural network (RNN)-based method called DeepTAP, using bidirectional gated recurrent unit (BiGRU), was developed for the accurate prediction of TAP-binding peptides. Our results demonstrated that DeepTAP achieves an optimal balance between prediction precision and false positives, outperforming other baseline models. Furthermore, DeepTAP significantly improves the prediction accuracy of high-confidence neoantigens, especially the top-ranked ones, making it a valuable tool for researchers studying antigen presentation processes and T-cell epitope screening. DeepTAP is freely available at https://github.com/zjupgx/deeptap and https://pgx.zju.edu.cn/deeptap.

TSNAD and TSNAdb: The Useful Toolkit for Clinical Application of Tumor-Specific Neoantigens.

Tumor-specific neoantigens play important roles in tumor immunotherapy. How to predict neoantigens accurately and efficiently has attracted much attention. TSNAD is the first one-stop neoantigen prediction tool from next-generation sequencing data, and TSNAdb provides both predicted and validated neoantigens based on pan-cancer immunogenomics analyses. In this chapter, we describe the usage of TSNAD and TSNAdb for the clinical application of neoantigens. The latest version of TSNAD is available at https://pgx.zju.edu.cn/tsnad , and the latest version of TSNAdb is available at https://pgx.zju.edu.cn/tsnadb .

TSNAdb v2.0: The Updated Version of Tumor-specific Neoantigen Database.

In recent years, neoantigens have been recognized as ideal targets for tumor immunotherapy. With the development of neoantigen-based tumor immunotherapy, comprehensive neoantigen databases are urgently needed to meet the growing demand for clinical studies. We have built the tumor-specific neoantigen database (TSNAdb) previously, which has attracted much attention. In this study, we provide TSNAdb v2.0, an updated version of the TSNAdb. TSNAdb v2.0 offers several new features, including (1) adopting more stringent criteria for neoantigen identification, (2) providing predicted neoantigens derived from three types of somatic mutations, and (3) collecting experimentally validated neoantigens and dividing them according to the experimental level. TSNAdb v2.0 is freely available at https://pgx.zju.edu.cn/tsnadb/.

TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection.

TSNAD is a one-stop software solution for predicting neoantigens from the whole genome/exome sequencing data of tumor-normal pairs. Here we present TSNAD v2.0 which provides several new features such as the function of RNA-Seq analysis including gene expression and gene fusion analysis, the support of different versions of the reference genome. Most importantly, we replace the NetMHCpan with DeepHLApan we developed previously, which considers both the binding between peptide and major histocompatibility complex (MHC) and the immunogenicity of the presented peptide-MHC complex (pMHC). TSNAD v2.0 achieves good performamce on a standard dataset. For better usage, we provide the Docker version and the web service of TSNAD v2.0. The source code of TSNAD v2.0 is freely available at https://github.com/jiujiezz/tsnad. And the web service of TSNAD v2.0 is available at http://biopharm.zju.edu.cn/tsnad/.

CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model.

Current cancer genomics databases have accumulated millions of somatic mutations that remain to be further explored. Due to the over-excess mutations unrelated to cancer, the great challenge is to identify somatic mutations that are cancer-driven. Under the notion that carcinogenesis is a form of somatic-cell evolution, we developed a two-component mixture model: while the ground component corresponds to passenger mutations, the rapidly evolving component corresponds to driver mutations. Then, we implemented an empirical Bayesian procedure to calculate the posterior probability of a site being cancer-driven. Based on these, we developed a software CanDriS (Cancer Driver Sites) to profile the potential cancer-driving sites for thousands of tumor samples from the Cancer Genome Atlas and International Cancer Genome Consortium across tumor types and pan-cancer level. As a result, we identified that approximately 1% of the sites have posterior probabilities larger than 0.90 and listed potential cancer-wide and cancer-specific driver mutations. By comprehensively profiling all potential cancer-driving sites, CanDriS greatly enhances our ability to refine our knowledge of the genetic basis of cancer and might guide clinical medication in the upcoming era of precision medicine. The results were displayed in a database CandrisDB (http://biopharm.zju.edu.cn/candrisdb/).

Shared neoantigens: ideal targets for off-the-shelf cancer immunotherapy.

Neoantigen, as an important member of tumor-specific antigens, has attracted a great deal of attention as a target for immunotherapy. Neoantigens are potential targets for personalized vaccines and adoptive cell transfer therapies. However, most of the neoantigen-targeted immunotherapies in the process are customized and costly. So, we are inclined to find shared neoantigens suitable for more patients. With the help of existing neoantigen prediction algorithms, we found that the most frequent shared neoantigens occurred in more than 1% of patients for 17 tumor types and the ten most frequent shared neoantigens covered approximately 50% of pancreatic cancer patients, providing a potential list of targets for off-the-shelf immunotherapy.

Anti-tumor immune response varies among individuals: A gene expression profiling of mouse melanoma.

Melanoma is amongst the most aggressive malignant tumors. The purpose of this study is to detect the tumor microenvironment systematically using multi-omics analyses and to propose strategies for precision medicine. Multiple factors of tumor microenvironment contribute to the drug resistance and immune surveillance failure. Here we analyzed genome mutations and characterized the immune state of tumor microenvironments in mouse melanoma by whole exome sequencing (WES) and RNA sequencing (RNA-Seq) approaches. Somatic mutation analysis revealed 35.1% novel mutations in mouse tumors when compared with B16F10 cell line, provided a basis for multi-site sequencing for accurate neoantigen selection. Mutation cluster, gene expression comparison, and gene ontology (GO) analyses by R packages proved DNA repair damage, inflammation, slower cell division, and metabolic change in tumor microenvironment. Further analyses of T-cell receptor (TCR) sequences, immune signaling pathway activation, tumor infiltrated immune cells and chemokine expression revealed extensive difference of antitumor immune response among individuals. Our study revealed the characteristics of tumor microenvironment with mouse melanoma model, suggested the need of comprehensive genome mutations and personal immune state analyses for cancer precision medicine.

DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity.

Neoantigens play important roles in cancer immunotherapy. Current methods used for neoantigen prediction focus on the binding between human leukocyte antigens (HLAs) and peptides, which is insufficient for high-confidence neoantigen prediction. In this study, we apply deep learning techniques to predict neoantigens considering both the possibility of HLA-peptide binding (binding model) and the potential immunogenicity (immunogenicity model) of the peptide-HLA complex (pHLA). The binding model achieves comparable performance with other well-acknowledged tools on the latest Immune Epitope Database (IEDB) benchmark datasets and an independent mass spectrometry (MS) dataset. The immunogenicity model could significantly improve the prediction precision of neoantigens. The further application of our method to the mutations with pre-existing T-cell responses indicating its feasibility in clinical application. DeepHLApan is freely available at https://github.com/jiujiezz/deephlapan and http://biopharm.zju.edu.cn/deephlapan.

Neoantigens Derived from Recurrently Mutated Genes as Potential Immunotherapy Targets for Gastric Cancer.

Neoantigens are optimal tumor-specific targets for T-cell based immunotherapy, especially for patients with "undruggable" mutated driver genes. T-cell immunotherapy can be a "universal" treatment for HLA genotype patients sharing same oncogenic mutations. To identify potential neoantigens for therapy in gastric cancer, 32 gastric cancer patients were enrolled in our study. Whole exome sequencing data from these patients was processed by TSNAD software to detect cancer somatic mutations and predict neoantigens. The somatic mutations between different patients suggested a high interpatient heterogeneity. C>A and C>T substitutions are common, suggesting an active nucleotide excision repair. The number of predicted neoantigens was significantly higher in patients at stage T1a compared to in patients at T2 or T4b. Six genes (PIK3CA, FAT4, BRCA2, GNAQ, LRP1B, and PREX2) were found as recurrently mutated driver genes in our study. Combining with highly frequent HLA alleles, several neoantigens derived from six recurrently mutated genes were considered as potential targets for further immunotherapy.

TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis.

Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients, which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.

Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis.

Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN /CS ) and normal populations (pN /pS ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels. Both the relaxation of purifying selection on passenger mutations and the positive selection of driver mutations may contribute to the increased CN /CS values of human genes in cancer genomes compared with the pN /pS values in human populations. The CN /CS values also contribute to the improved classification of cancer genes and a better understanding of the onco-functionalization of cancer genes during oncogenesis. The use of our computational pipeline to identify cancer-specific positively and negatively selected genes may provide useful information for understanding the evolution of cancers and identifying possible targets for therapeutic intervention.

TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection.

Tumour antigens have attracted much attention because of their importance to cancer diagnosis, prognosis and targeted therapy. With the development of cancer genomics, the identification of tumour-specific neoantigens became possible, which is a crucial step for cancer immunotherapy. In this study, we developed software called the tumour-specific neoantigen detector for detecting cancer somatic mutations following the best practices of the genome analysis toolkit and predicting potential tumour-specific neoantigens, which could be either extracellular mutations of membrane proteins or mutated peptides presented by class I major histocompatibility complex molecules. This pipeline was beneficial to the biologist with little programmatic background. We also applied the software to the somatic mutations from the International Cancer Genome Consortium database to predict numerous potential tumour-specific neoantigens. This software is freely available from https://github.com/jiujiezz/tsnad.

Association Between Cardiovascular Risk Factors and Serum Thyrotropin Concentration Among Healthy Chinese Subjects and Subjects with Unsuspected Subclinical Hypothyroidism.

BACKGROUND: Even within the reference range, thyrotropin (TSH) levels were found to be positively associated with the risk of cardiovascular disease (CVD). However, the underlying mechanism of TSH remains ambiguous. This study investigated the association of TSH with cardiovascular risk factors among healthy Chinese subjects and subjects with unsuspected subclinical hypothyroidism (SCH). METHODS: A total of 741 subjects were included in this cross-sectional study. The subjects were grouped into four, including tertile groups for the TSH reference range and an SCH group based on the TSH level. All the participants underwent physical examination and fasting blood analyses to determine the levels of TSH, free thyroxine, free triiodothyronine, plasma glucose, triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), apolipoprotein A1, apolipoprotein B (ApoB), lipoprotein(a), homocysteine (Hcy), and high sensitivity C-reactive protein (hs-CRP). RESULTS: The TSH subgroups exhibited a significant increasing trend in terms of LDL-C, ApoB, and Hcy levels (p = 0.01, p < 0.01, and p = 0.01, respectively), whereas the HDL-C levels exhibited a decreasing trend (p = 0.03). After adjusting for gender, age, and smoking status, the TSH levels were found to be positively correlated with body mass index, waist circumference, diastolic blood pressure (DBP), and TG, TC, LDL-C, ApoB, Hcy, and hs-CRP levels (p < 0.05 for all), but negatively correlated with the HDL-C levels (p < 0.01). Multiple linear regression analysis showed that the TSH levels were independently positively associated with the female gender (ß = 0.21, p < 0.01), DBP (ß = 0.14, ß = 0.01), and Hcy levels (ß = 0.10, p = 0.01), and negatively associated with the HDL-C (ß = -0.11, p = 0.01) and FT4 levels (ß = -0.15, p < 0.01). CONCLUSIONS: The TSH levels were independently associated with several cardiovascular risk factors in an apparently healthy Chinese population, and thus may increase the risk of CVD.

Familial Cushing syndrome due to thymic carcinoids in a multiple endocrine neoplasia type 1 kindred.

The objective of this study is to present a familial Cushing syndrome (CS) caused by multiple endocrine neoplasia type 1 (MEN-1)-associated thymic carcinoid. Immunohistochemistry, gene sequencing, loss of heterozygosity analysis, and Western blot were used to determine the expression of ACTH in MEN-1-related thymic tumors, MEN1 gene mutation, the pattern and extent of allelic deletion, and the expression of Menin in MEN-1-associated tumors, respectively. Tumor cells from thymus ectopic-secreted ACTH. A deletion involving the MEN1 gene locus was confirmed. The expression of Menin in MEN-1-associated tumors declined. To conclude, we presented an unusual kindred of MEN-1, which pointed out the significance of making screening of MEN-1 for both male and female patients with CS and thymic carcinoid.

Hormones other than aldosterone may contribute to hypertension in 3 different subtypes of primary aldosteronism.

Blood pressure (BP) level is similar in patients with 3 subtypes of primary aldosteronism (PA), even though aldosterone levels may vary. Glucocorticoids and adrenomedullary hormones may be influenced and may contribute to hypertension in PA. The authors' objective was to investigate the influence of PA on adrenal gland secretion and the roles of these hormones in hypertension. Patients diagnosed with PA (229 cases) were enrolled and classified into 3 subgroups: aldosterone-producing adenoma (APA), unilateral nodular adrenal hyperplasia (UNAH), and idiopathic hyperaldosteronism (IHA). Patients with essential hypertension served as the control group (100 cases). Concentration of the above hormones was measured and compared between groups. Level of plasma adrenocorticotrophic hormone (ACTH) in patients with APA was significantly lower than that in patients with IHA (P<.001) and UNAH (P<0.5). The 24-hour urinary free cortisol and adrenomedullary hormone levels were highest in patients with IHA, lower in patients with APA, and lowest in patients with UNAH. Systolic BP level was positively correlated with 8 am plasma cortisol level (r=0.142, P=.039) and plasma ACTH level (r=0.383, P=.016). Cortisol and adrenomedullary hormones were different between PA subtypes and they might involve regulation of BP in those patients.