Identification of Tumor Specific Neoantigens and Their Implications in Dendritic Cell Immunotherapy Using Liquid Biopsy Results: Findings from an Observational Cohort Study

Liquid biopsies can be a rapid, cost-effective and noninvasive alternative to tumor biopsies for detecting genetic mutations in somatic tumors. Genetic profiling of liquid biopsies can also be used to identify novel antigens for targeted therapy, provide updated information on disease prognosis and evaluate treatment efficacy. In this study, we aimed to examine mutations that could be identified in liquid biopsy and their potential implications for personalized dendritic cell immunotherapy using these antigens. We analyzed the genomic profiles of 99 blood samples from 85 patients with 22 different types of cancer using two commercially available liquid biopsy tests before the patients underwent standard cancer treatment and dendritic cell immunotherapy. Nonsynonymous mutations were detected in more than 90% of the samples, with an average frequency of 3.6 mutations per sample. The tumor mutations were specific to each patient, as approximately 94.7% of the mutations were so unique that there was almost no duplication among the patients. Clonal evolution was observed in two patients just before or after chemotherapy, radiotherapy and immunotherapy. These findings indicate that liquid biopsy can be a potential surrogate for tumor-specific antigen-based immunotherapy and the importance of tailoring immunotherapy in accordance with the liquid biopsy result in each treatment stage.

CS-1 Cerebellar liponeurocytoma; Report of two cases with detailed metabolic, immunohistochemical, and genetic evaluations

Cerebellar liponeurocytoma (cLNC), World Health Organization grade II neoplasm, is a rare brain tumor characterized by advanced neuronal/neurocytic differentiation and focal lipid accumulation in neuroepithelial tumor cells. However, the expression and genetic profiling of cLNC, as well as metabolic imaging characteristics, have been poorly studied. Two patients with lower vermian tumors were operated on with telovelar approach. Moderate methionine uptake in positron emission tomography was observed in both cases. Histologically, the tumor was composed of small, uniform cells with round nuclei in a sheet-like fashion. Vacuolate cells with displacement of nuclei suggested the lipid accumulation, which was further supported by immunohistochemical staining of S-100. Although the extent of lipidization was relatively low compared with the reported cLNC cases, the immunohistochemical findings confirmed the diagnosis of cLNC. Next-generation sequencing of tumoral DNA in one case detected a splice site mutation of the ATRX gene, which is the first observation in the literature. Neither chemotherapy nor radiotherapy were administered postoperatively in both cases. In one case with spinal dissemination, residual tumor demonstrated progression 7 months after the resection. Long term follow-up data of cLNC cases with detailed expression and genetic profiles are essential for precise diagnosis and better understanding of the oncogenic pathway as well as the natural history of cLNC.

Imaging of peripheral vascular malformations — current concepts and future perspectives

Vascular Malformations belong to the spectrum of orphan diseases and can involve all segments of the vascular tree: arteries, capillaries, and veins, and similarly the lymphatic vasculature. The classification according to the International Society for the Study of Vascular Anomalies (ISSVA) is of major importance to guide proper treatment. Imaging plays a crucial role to classify vascular malformations according to their dominant vessel type, anatomical extension, and flow pattern. Several imaging concepts including color-coded Duplex ultrasound/contrast-enhanced ultrasound (CDUS/CEUS), 4D computed tomography angiography (CTA), magnetic resonance imaging (MRI) including dynamic contrast-enhanced MR-angiography (DCE-MRA), and conventional arterial and venous angiography are established in the current clinical routine. Besides the very heterogenous phenotypes of vascular malformations, molecular and genetic profiling has recently offered an advanced understanding of the pathogenesis and progression of these lesions. As distinct molecular subtypes may be suitable for targeted therapies, capturing certain patterns by means of molecular imaging could enhance non-invasive diagnostics of vascular malformations. This review provides an overview of subtype-specific imaging and established imaging modalities, as well as future perspectives of novel functional and molecular imaging approaches. We highlight recent pioneering imaging studies including thermography, positron emission tomography (PET), and multispectral optoacoustic tomography (MSOT), which have successfully targeted specific biomarkers of vascular malformations.

Genetic Profiling of Sida rhombifolia Originated from Several Indonesian Ethnicities Based on Sequence-Related Amplified Polymorphism Markers

Sida rhombifolia is one of wild flowering plants that grows easily in many habitats with moderate humidity, with some usefulness in traditional medicine. Genetic characterization of Sida rhombifolia accessions originated from 12 ethnicities of Indonesia was analyzed based on Sequence-Related Amplified Polymorphism (SRAP) Markers. The genomic DNA were extracted from leaf samples and then were characterized by using the SRAP marker system according to Li and Quiros (2001). Nine pairs of SRAP primer resulted high polymorphic bands and were used in the genetic profiling. The data analysis was performed using GenAlEx to calculate genetic distance, Principal coordinate analysis, and Analysis of Molecular Variance (AMOVA), also using POPGENE to assess genetic diversity (Hs and Ht) and Nm to predict gene flow among populations. The coordinate analysis showed that the accessions originated from ethnicities along Wallacean line tend to differ genetically from most other locations. However, the results of analysis of molecular variance suggested that there were only slight differences (0.1%) found between ethnicities, while most genetic variances (99.9%) were found mostly among accessions within populations. The results suggested that there was an extensive genetic flow and plant spreading among Sida rhombifolia plant populations, resulting more homogenous genetic characters among most populations, while high diversity within population. The calculation of the number of migration (Nm = 1.7341) confirmed that the high rate of gene flow had occurred between populations.

A functional artificial neural network for noninvasive pretreatment evaluation of glioblastoma patients

Background Pretreatment assessments for glioblastoma (GBM) patients, especially elderly or frail patients, are critical for treatment planning. However, genetic profiling with intracranial biopsy carries a significant risk of permanent morbidity. We previously demonstrated that the CUL2 gene, encoding the scaffold cullin2 protein in the cullin2-RING E3 ligase (CRL2), can predict GBM radiosensitivity and prognosis. CUL2 expression levels are closely regulated with its copy number variations (CNVs). This study aims to develop artificial neural networks (ANNs) for pretreatment evaluation of GBM patients with inputs obtainable without intracranial surgical biopsies. Methods Public datasets including Ivy-GAP, The Cancer Genome Atlas Glioblastoma (TCGA-GBM), the Chinese Glioma Genome Atlas (CGGA) were used for training and testing of the ANNs. T1 images from corresponding cases were studied using automated segmentation for features of heterogeneity and tumor edge contouring. A ratio comparing the surface area of tumor borders vs. the total volume (SvV) was derived from the DICOM-SEG conversions of segmented tumors. The edges of these borders were detected using the canny edge detector. Packages including Keras, Pytorch, and TensorFlow were tested to build the ANNs. A 4-layered ANN (8-8-8-2) with a binary output was built with optimal performance after extensive testing. Results The 4-layered deep learning ANN can identify a GBM patient’s overall survival (OS) cohort with 80-85% accuracy. The ANN requires 4 inputs, including CUL2 copy number, patients’ age at GBM diagnosis, Karnofsky Performance Scale (KPS), and SvV ratio. Conclusion Quantifiable image features can significantly improve the ability of ANNs to identify a GBM patients’ survival cohort. Features such as clinical measures, genetic data, and image data, can be integrated into a single ANN for GBM pretreatment evaluation.

Immunotherapy for gastric cancer: a 2021 update

Gastric cancer, the fifth most frequent cancer and the fourth leading cause of cancer deaths, accounts for a devastating death rate worldwide. Since the majority of patients with gastric cancer are diagnosed at advanced stages, they are not suitable for surgery and present with locally advanced or metastatic disease. Recent advances in immunotherapy have elicited a considerable amount of attention as viable therapeutic options for several cancer types. This work presents a summary of the currently ongoing clinical trials and critically addresses the efficacy of a large spectrum of immunotherapy approaches in the general population for gastric cancer as well as in relation to tumor genetic profiling.

Identification of Tumor Specific Neoantigens and Their Implications in Dendritic Cell Immunotherapy Using Liquid Biopsy Results: Findings from an Observational Cohort Study

Liquid biopsies can be a rapid, cost-effective and noninvasive alternative to tumor biopsies for detecting genetic mutations in somatic tumors. Genetic profiling of liquid biopsies can also be used to identify novel antigens for targeted therapy, provide updated information on disease prognosis and evaluate treatment efficacy. In this study, we aimed to examine mutations that could be identified in liquid biopsy and their potential implications for personalized dendritic cell immunotherapy using neoantigens. We analyzed the genomic profiles of 99 blood samples from 85 patients with 22 different types of cancer using two commercially available liquid biopsy tests before the patients underwent standard cancer treatment and dendritic cell immunotherapy. Nonsynonymous mutations were detected in more than 90% of the samples, with an average frequency of 3.6 mutations per sample. The tumor mutations were specific to each patient, as approximately 94.7% of the mutations were so unique that there was almost no duplication among the patients. Clonal evolution was observed in two patients just before or after chemotherapy, radiotherapy and immunotherapy. These findings indicate that liquid biopsy can be a potential surrogate for neoantigen-based immunotherapy and the importance of tailoring neoantigen-based immunotherapy in accordance with the liquid biopsy result in each treatment stage.

Effect of the Lymphocyte Activation Gene 3 Polymorphism rs951818 on Mortality and Disease Progression in Patients with Sepsis—A Prospective Genetic Association Study

(1) Background: Sepsis is a leading cause of death and a global public health problem. Accordingly, deciphering the underlying molecular mechanisms of this disease and the determinants of its morbidity and mortality is pivotal. This study examined the effect of the rs951818 SNP of the negative costimulatory lymphocyte-activation gene 3 (LAG-3) on sepsis mortality and disease severity. (2) Methods: 707 consecutive patients with sepsis were prospectively enrolled into the present study from three surgical ICUs at University Medical Center Goettingen. Both 28- and 90-day mortality were analyzed as the primary outcome, while parameters of disease severity served as secondary endpoints. (3) Results: In the Kaplan–Meier analysis LAG-3 rs951818 AA-homozygote patients showed a significantly lower 28-day mortality (17.3%) compared to carriers of the C-allele (23.7%, p = 0.0476). In addition, these patients more often received invasive mechanical ventilation (96%) during the course of disease than C-allele carriers (92%, p = 0.0466). (4) Conclusions: Genetic profiling of LAG-3 genetic variants alone or in combination with other genetic biomarkers may represent a promising approach for risk stratification of patients with sepsis. Patient-individual therapeutic targeting of immune checkpoints, such as LAG-3, may be a future component of sepsis therapy. Further detailed investigations in clinically relevant sepsis models are necessary.