Biomarkers Of Immune Response Research Articles

Clinical Detection of Peripheral Blood Natural Killer Cell Activity

Natural Killer (NK) cells are specific immune cells in human immune system. They have a quick effect and can exert a cytotoxic function without prior sensitization, and they show great application potential in cell-based immunotherapy, anti-infection in vivo. NK cell activity in peripheral blood can be used as one of the biomarkers of immune function response. It has a great positive guiding significance for the clinical prognosis of tumor patients, the prevention of cancer and anti-aging. The clinical detection strategies of NK cell activity in circulation mainly grouped into five types: methyl thiazolyl tetrazolium colorimetric, lactate dehydrogenase release, radionuclide labeling, flow cytometry and NK Vue cytokine release method. It has played an important role in different stages of clinical application development. This paper will make a comparative review of the above-mentioned detection strategies for the NK cell activity.

Thyroid function abnormality induced by PD-1 inhibitors have a positive impact on survival in patients with non-small cell lung cancer

BackgroundThyroid function abnormality (TFA) is a common immune-related adverse event (irAEs), but the association between it and the efficacy of programmed cell death protein 1 (PD-1) inhibitor in advanced non-small cell lung cancer (NSCLC) is finitely understood. Materials and MethodsWe conducted a single center, retrospective study of advanced NSCLC patients who were treated with PD-1 inhibitors between 10 October 2016 and 1 April 2020. TFA was characterized as new onset subclinical hypothyroidism, overt hypothyroidism, subclinical hyperthyroidism and overt hyperthyroidism. Frequency of development of TFA-irAEs, and its relationship with overall survival (OS) and progression free survival (PFS) were evaluated. ResultsIn our study, 191 patients were treated with PD-1 inhibitors. Among them, forty patients (20.9%) developed TFA, of whom 10 (5.2%) presented with subclinical hypothyroidism, 15 (7.9%) with overt hypothyroidism, 6 (3.1%) with subclinical hyperthyroidism and 9 (4.7%) with overt hyperthyroidism. Survival analysis showed that the OS (16.8 months vs. 11.1 months, p < 0.001) and PFS (10.4 months vs. 5.5 months, p < 0.001) were significantly longer in patients with TFA-irAEs than in those without TFA-irAEs. In subgroup analysis of hypothyroidism and hyperthyroidism groups, similar trends were also obtained for both OS and PFS. After adjusting for potential confounding variables, patients with TFA-irAEs had a lower mortality risk (HR 0.334, 95%CI 0.196–0.571) than those without TFA-irAEs. ConclusionsTFA-irAEs is associated with enhanced PD-1 inhibitor efficacy in advanced NSCLC patients and it may be a biomarker for antitumor immune response.

Change Point Inference in the Presence of Missing Covariates for Principal Surrogate Evaluation in Vaccine Trials.

We consider the use of threshold-based regression models for evaluating immune response biomarkers as principal surrogate markers of a vaccine's protective effect. Threshold-based regression models, which allow the relationship between a clinical outcome and a covariate to change dramatically across a threshold value in the covariate, have been studied by various authors under fully observed data. Limited research, however, has examined these models in the presence of missing covariates, such as the counterfactual potential immune responses of a participant in the placebo arm of a standard vaccine trial had s/he been assigned to the vaccine arm instead. Based on a hinge model for a threshold effect of the principal surrogate on vaccine efficacy, we develop a regression methodology that consists of two components: (1) The estimated likelihood method is employed to handle missing potential outcomes, and (2) a penalty is imposed on the estimated likelihood to ensure satisfactory finite sample performance. We develop a method that allows joint estimation of all model parameters as well as a two-step method that separates the estimation of the threshold parameter from the rest of the parameters. Stable iterative algorithms are developed to implement the two methods and the asymptotic properties of the proposed estimators are established. In simulation studies, the proposed estimators are shown to have satisfactory finite sample performance. The proposed methods are applied to analyze a real dataset collected from dengue vaccine efficacy trials to predict how vaccine efficacy varies with an individual's potential immune response if receiving vaccine.

Functional biomarker signatures of circulating T-cells and its association with distinct clinical status of leprosy patients and their respective household contacts

BackgroundLeprosy is a chronic infectious disease classified into two subgroups for therapeutic purposes: paucibacillary (PB) and multibacillary (MB), closely related to the host immune responses. In this context it is noteworthy looking for immunological biomarkers applicable as complementary diagnostic tools as well as a laboratorial strategy to follow-up leprosy household contacts.MethodsThe cross-sectional study enrolled 49 participants, including 19 patients and 30 healthy controls. Peripheral blood mononuclear cells (PBMC) were isolated and incubated in the presence of Mycobacterium leprae bacilli. The cells were prepared for surface (CD4+ and CD8+) and intracytoplasmic cytokine staining (IFN-γ, IL-4 and IL-10). Multiple comparisons amongst groups were carried out by ANOVA, Kruskal–Wallis, Student T or Mann–Whitney test. Comparative analysis of categorical variables was performed by Chi-square. Functional biomarker signature analysis was conducted using the global median values for each biomarker index as the cut-off edge to identify the proportion of subjects with high biomarker levels.ResultsThe cytokine signature analysis demonstrated that leprosy patients presented a polyfunctional profile of T-cells subsets, with increased frequency of IFN-γ+ T-cell subsets along with IL-10+ and IL-4+ from CD4+ T-cells, as compared to health Controls (Venn diagram report). Moreover, statistical analysis was carried out using parametric or non-parametric variance analysis followed by pairwise multiple comparisons, according to the data normality distribution. L(PB) displayed a polyfunctional profile characterized by enhanced percentage of IFN-γ+, IL-10+ and IL-4+ produced by most T-cell subsets, as compared to L(MB) that presented a more restricted cytokine functional profile mediated by IL-10+ and IL-4+ T-cells with minor contribution of IFN-γ produced by CD4+ T-cells. Noteworthy was that HHC(MB) exhibited enhanced frequency of IFN-γ+ T-cells, contrasting with HHC(PB) that presented a cytokine profile limited to IL-10 and IL-4.ConclusionsOur data demonstrated that L(PB) displayed enhanced percentage of IFN-γ+, IL-10+ and IL-4+ as compared to L(MB) that presented functional profile mediated by IL-10+ and IL-4+ T-cells and HHC(MB) exhibited enhanced frequency of IFN-γ+ T-cells, contrasting with HHC(PB). Together, our findings provide additional immunological features associated with leprosy and household contacts. These data provide evidence that biomarkers of immune response can be useful complementary diagnostic/prognostic tools as well as insights that household contacts should be monitored to access putative subclinical infection.

(Invited) Development of the Hydrogel-Based Biosensors for Non-Invasive Perspiration Analysis

Non-invasive diagnostic sensors for biomarkers are generally required as an alternative to blood-based diagnoses for the next generation of advanced healthcare. Sweat is one of the promising bodily fluids that are non-invasively accessible source of biomarkers. However, it is difficult to collect small amount of sweat from human skin surface in a periodic or continuous manner. Whereas wearable-type of tattoo- and microfluidics-based biosensors have enabled in-situ and real-time sampling and monitoring of sweat biomarkers, it has been necessary to induce continuous perspiration under special conditions such as with exercise, in a high-temperature environment, or with the use of cholinergic agonist-assisted perspiration. These circumstances are not practical in the application of sweat sensors for daily health diagnostics. In this presentation, we show our new perspiration sensor, a hydrogel-based touch sensor pad for the non-invasive extraction and detection of sweat components. The sensor was composed of the printed electrochemical biosensing working and planar liquid-junction Ag/AgCl reference electrodes fully covered with an agarose hydrogel including a sweat-extraction solution, Phosphate Buffer Saline (PBS). We found that biocompatible PBS with physiological osmotic pressure was suitable to continuous extraction of sweat. In this study, an enzyme-based L-lactate sensor was fabricated as a model because L-lactate is included in sweat in relatively high concentrations. L-lactate was oxidized by Lactate oxidase (LOx) to generate hydrogen peroxide, which oxidize reduced form of prussian blue (PB) immobilized on the working electrode surface. The LOx / PB-modified electrode was fabricated by screen-printing of a carbon-graphite ink including PB on an Au electrode, followed by drop-casting of a mixture of LOx with chitosan as a matrix to immobilize LOx on the electrode. The structure of the screen-printed planar liquid-junction Ag/AgCl reference electrode was composed of a silver-lead pattern, Ag/AgCl active layer, internal electrolyte layer, polyurethane-based liquid junction, and insulation layer on a substrate. Then, a silicone rubber sheet with a 6 mm diameter through-hole was attached to the electrode film as to expose the active area of working and reference electrodes to the through-hole. A low melting point agarose prepolymer solution in PBS was drop-deposited onto the through-hole in the silicone sheet, and incubated at room temperature to induce gelation. We measured the potentiometric response of the sensor electrodes when the ball of the subject’s forefinger contacted the agarose gel surface. After 20 s of time lag for diffusion of extracted L-lactate in the gel, the potential difference started to increase, followed by approaching steady-state. This result suggested successful extraction and detection of sweat L-lactate using this device. Without LOx, no potentiometric response was observed upon touching the gel with the subject’s forefinger, suggesting that the extracted sweat compounds except for L-lactate did not affect the sensor response. This new type of touch sensor pad integrated with biosensors will enable non-invasive and daily periodic monitoring of sweat biomarkers without harsh exercise-, environmental temperature control, and cholinergic agonist-assisted perspiration. In a future study, we will apply the present sensor to the other sweat analytes such as D-glucose (diabetes biomarker), electrolytes (heat stroke biomarker), ammonium ion (anaerobic exercise biomarker), and some cytokines (immune response biomarker) to evaluate the sensor characteristics in more detail.

Analysis in epithelial ovarian cancer identifies KANSL1 as a biomarker and target gene for immune response and HDAC inhibition

ObjectiveThere is an immunoreactive subtype of ovarian cancer with a favorable prognosis, but the majority of ovarian cancers have limited immune reactivity. The reason for this is poorly understood. This study aimed to approach this question by identifying prognostically relevant genes whose prognostic mRNA expression levels correlated with a genomic event. MethodsExpression microarray and 5-year survival data on 170 ovarian tumors and aCGH data on 45 ovarian cancer cell lines were used to identify amplified/deleted genes associated with prognosis. Three immune-response genes were identified mapping to epigenetically modified chromosome 6p21.3. Genes were searched for roles in epigenetic modification, identifying KANSL1. Genome-wide association studies were searched to identify genetic variants in KANSL1 associated with altered immune profile. Sensitivity to HDAC inhibition in cell lines with KANSL1 amplification/rearrangement was studied. ResultsExpression of 196 genes was statistically significantly associated with survival, and expression levels correlated with copy number variations for 82 of them. Among these, 3 immune-response genes (HCP5, PSMB8, PSMB9) clustered together at epigenetically modified chromosome 6p21.3 and their expression was inversely correlated to epigenetic modification gene KANSL1. KANSL1 is amplified/rearranged in ovarian cancer, associated with lymphocyte profile, a biomarker for response to HDAC inhibition, and may drive expression of immune-response genes. ConclusionThis study identifies 82 genes with prognostic relevance and genomic alteration in ovarian cancer. Among these, immune-response genes have correlated expression which is associated with 5-year survival. KANSL1 may be a master gene altering immune-response gene expression at 6p21.3 and drive response to HDAC inhibitors. Future research should investigate KANSL1 and determine whether targeting it alters the immune profile of ovarian cancer and improves survival, HDAC inhibition, and/or immunotherapy response.

SERUM ACUTE-PHASE PROTEINS IN BOTTLENOSE DOLPHINS (TURSIOPS TRUNCATUS) AND CORRELATION WITH COMMONLY UTILIZED INFLAMMATORY INDICES.

Acute-phase proteins (APP) are the foundation to the innate immune response and valuable biomarkers that increase with inflammation, infection, neoplasia, stress, and trauma.2,4,16 Little is known about the acute-phase response in cetaceans and if these proteins can be used for health monitoring in individuals and free-ranging populations. The purpose of this study was to characterize serum concentrations of haptoglobin (Hp) and serum amyloid A (SAA), as well as electrophoretic profiles of common bottlenose dolphins (Tursiops truncatus) in free-ranging (n = 33) and professional care (n = 27) settings. Results were correlated to commonly utilized inflammatory indices including erythrocyte sedimentation rate (ESR), fibrinogen, total white blood cell count (WBC), and absolute neutrophil count. SAA levels, measured with a dolphin-specific enzyme linked immunosorbent assay (ELISA), were significantly higher (P = 0.05) in free-ranging dolphins (mean = 4.26; SE = 1.12) when compared with those under professional care (mean = 1.82; SE = 0.45). For dolphins under professional care, a statistically significant correlation was identified between ESR and Hp (P < 0.001; r = 0.69), ESR and SAA (P < 0.001; r = 0.67), fibrinogen and Hp (P = 0.001; r = 0.58), and fibrinogen and SAA (P = 0.002; r = 0.56). In addition, there was a significant correlation between WBC and SAA (P = 0.01; r = 0.38) and absolute neutrophil count and SAA (P = 0.04; r = 0.32). There were no significant correlations between study variables observed in free-ranging dolphins. The variable correlation of APPs with commonly utilized inflammatory indices demonstrates that these proteins are independent measures of inflammation with unique sensitivity, specificity, and timeline of expression. The results of this study contribute to improved health monitoring of dolphins and have the potential to assist in identification of compromised health.

Curcumin Treatment Identifies Therapeutic Targets within Biomarkers of Liver Colonization by Highly Invasive Mesothelioma Cells-Potential Links with Sarcomas.

Simple SummaryAggressive sarcomatoid tumors designed in inbred strains of immunocompetent rats represent useful tools for both the identification of biomarkers of invasiveness and evaluation of innovative therapies. Our aim was to investigate the molecular determinants of liver colonization and potential common biomarkers of sarcomas and sarcomatoid tumors, using the most invasive (M5-T1) of our four experimental models of peritoneal sarcomatoid malignant mesothelioma in the F344 rat. Using an advanced and robust technique of quantitative proteomics and a bank of paraffin-embedded tumor and tissue samples, we analyzed changes in the proteotype patterns of the liver from normal rats, adjacent non-tumorous liver from untreated tumor-bearing rats, and liver from tumor-bearing rats positively responding to repeated administrations of curcumin given intraperitoneally. The identification of proteome alterations accounting for the antitumor effects of curcumin and changes in the liver microenvironment, which favored the induction of an immune response, could be useful to the research community.Investigations of liver metastatic colonization suggest that the microenvironment is preordained to be intrinsically hospitable to the invasive cancer cells. To identify molecular determinants of that organotropism and potential therapeutic targets, we conducted proteomic analyses of the liver in an aggressive model of sarcomatoid peritoneal mesothelioma (M5-T1). The quantitative changes between SWATH-MS (sequential window acquisition of all theoretical fragmentation spectra) proteotype patterns of the liver from normal rats (G1), adjacent non-tumorous liver from untreated tumor-bearing rats (G2), and liver from curcumin-treated rats without hepatic metastases (G3) were compared. The results identified 12 biomarkers of raised immune response against M5-T1 cells in G3 and 179 liver biomarker changes in (G2 vs. G1) and (G3 vs. G2) but not in (G3 vs. G1). Cross-comparing these 179 candidates with proteins showing abundance changes related to increasing invasiveness in four different rat mesothelioma tumor models identified seven biomarkers specific to the M5-T1 tumor. Finally, analysis of correlations between these seven biomarkers, purine nucleoside phosphorylase being the main biomarker of immune response, and the 179 previously identified proteins revealed a network orchestrating liver colonization and treatment efficacy. These results highlight the links between potential targets, raising interesting prospects for optimizing therapies against highly invasive cancer cells exhibiting a sarcomatoid phenotype and sarcoma cells.

Azacitidine (AZA) with Nivolumab (Nivo), and AZA with Nivo + Ipilimumab (Ipi) in Relapsed/Refractory (R/R) Acute Myeloid Leukemia: Clinical and Immune Biomarkers of Response

Azacitidine (AZA) with Nivolumab (Nivo), and AZA with Nivo + Ipilimumab (Ipi) in Relapsed/Refractory (R/R) Acute Myeloid Leukemia: Clinical and Immune Biomarkers of Response

A Phase 2 Trial of Daratumumab and Pembrolizumab in Refractory Multiple Myeloma

A Phase 2 Trial of Daratumumab and Pembrolizumab in Refractory Multiple Myeloma

Immune checkpoint blockade and biomarkers of clinical response in non-small cell lung cancer.

Immunotherapy with PD‐1 and PD‐L1 inhibitors has revolutionized the treatment for patients with NSCLC the last years with increased overall survival and in particular increased number of long‐time survivors in patients with metastatic disease. It is now a treatment of choice for patients with distant metastases (stage IV) and in conjunction with chemoradiotherapy for patients with limited spread confined to the chest (stage III). PD‐1 inhibition has been proven to be superior to standard chemotherapy, both as a single treatment and when combined with either chemotherapy or CTLA‐4 inhibition. Despite the success of immunotherapy, the majority of patients do not respond or relapse within a short time frame. Biomarkers that would help to properly select patients with a high likelihood of clinical response to PD‐1 and PD‐L1 inhibitors are scarce and far from optimal, and only one (PD‐L1 expression) has reached clinical practice. Thus for immunotherapy to be effective, the discovery and validation of additional biomarkers is critical for patient selection and prediction of clinical response. In this mini‐review, we give an overview of current clinical management of NSCLC including treatment landscape with regard to immunotherapy, as well as discuss the current genetic and immune cell biomarker studies and their potential for introduction into clinical practice.

Differences in biomarkers of inflammation and immune responses in chronic smokers and moist snuff users

BackgroundCigarette smoking is a major risk factor for cancer and other diseases. While smoking induces chronic inflammation and aberrant immune responses, the effects of smokeless tobacco products (STPs) on immune responses is less clear. Here we evaluated markers related to immune regulation in smokers (SMK), moist snuff consumers (MSC) and non-tobacco consumers (NTC) to better understand the effects of chronic tobacco use. Materials and methodsSeveral markers associated with immune regulation were measured in peripheral blood mononuclear cells (PBMCs) from SMK (n = 40), MSC (n = 40), and NTC (n = 40) by flow cytometry. ResultsRelative to NTC, seven markers were significantly suppressed in SMK, whereas in MSC, only one marker was significantly suppressed. In a logistic regression model, markers including granzyme B+ lymphocytes, perforin+ lymphocytes, granzyme B+ CD8+T cells, and KLRB1+ CD8+ T cells remained as statistically significant predictors for classifying the three cohorts. Further, cell-surface receptor signaling pathways and cell–cell signaling processes were downregulated in SMK relative to MSC; chemotaxis and LPS-mediated signaling pathways, were upregulated in SMK compared to MSC. A network of the tested markers was constructed to visualize the immunosuppression in SMK relative to MSC. ConclusionMoist snuff consumption is associated with significantly fewer perturbations in inflammation and immune function biomarkers relative to smoking. ImpactThis work identifies several key immunological biomarkers that differentiate the effects of chronic smoking from the use of moist snuff. Additionally, a molecular basis for aberrant immune responses that could render smokers more susceptible for infections and cancer is provided.

All in the Levels-Programmed Death-Ligand 1 Expression as a Biomarker for Immune Checkpoint Inhibitor Response in Patients with Gastrointestinal Cancer.

Immune checkpoint inhibitors (ICIs) benefit patients with rare subsets of gastrointestinal (GI) cancer. Significant interest exists to identify predictive biomarkers that may increase the applicability of ICI therapy for these patients. Programmed death ligand 1 (PD-L1) is one such candidate; however, this biomarker has well-chronicled limitations. Combined positive score (CPS) ≥1 is the minimum PD-L1 expression threshold necessary for patients with gastric or gastroesophageal junction (GEJ) cancer to qualify for treatment with pembrolizumab; however, studies suggest that patients with higher CPS scores may derive greater benefit. We present the cases of two patients, both with low tumor mutational burden, microsatellite stable, and CPS ≥70 GI tumors (cholangiocarcinoma and GEJ cancer), who have achieved excellent tumor control with pembrolizumab. We postulate that, by testing for CPS in all patients with GI cancer and identifying a CPS threshold predictive of ICI response, PD-L1 expression could identify the patiets with GI cancer, in tissue agnostic fashion, who could benefit from ICI therapy.

The Tumor and Host Immune Signature, and the Gut Microbiota as Predictive Biomarkers for Immune Checkpoint Inhibitor Response in Melanoma Patients.

There are various melanoma treatment strategies that are based on immunological responses, among which immune checkpoint inhibitors (ICI) are relatively novel form. Nowadays, anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and anti-programmed death-1 (PD-1) antibodies represent a standard treatment for metastatic melanoma. Although there are remarkable curative effects in responders to ICI therapy, up to 70% of melanoma patients show resistance to this treatment. This low response rate is caused by innate as well as acquired resistance, and some aspects of treatment resistance are still unknown. Growing evidence shows that gut microbiota and bacterial metabolites, such as short-chain fatty acids (SCFAs), affect the efficacy of immunotherapy. Various bacterial species have been indicated as potential biomarkers of anti-PD-1 or anti-CTLA-4 therapy efficacy in melanoma, next to biomarkers related to molecular and genetic tumor characteristics or the host immunological response, which are detected in patients’ blood. Here, we review the current status of biomarkers of response to ICI melanoma therapies, their pre-treatment predictive values, and their utility as on-treatment monitoring tools in order to select a relevant personalized therapy on the basis of probability of the best clinical outcome.

Prolonged infection triggered by dormant Mycobacterium tuberculosis: Immune and inflammatory responses in lungs of genetically susceptible and resistant mice.

We developed an approach for substantial attenuation of Mycobacterium tuberculosis by prolonged culturing under gradually acidifying conditions. Bacteria subjected to acidification lost the capacity to form colonies on solid media, but readily resuscitated their growth in the murine host, providing a useful model to study in vivo development of infection mimicking latent and reactivation tuberculosis (TB) in humans. Here we characterize biomarkers of lung pathology and immune responses triggered by such attenuated bacteria in genetically TB-susceptible and resistant mice. In susceptible I/St mice, CFU counts in lungs and spleens were ~1.5-log higher than in resistant B6 mice, accompanied by diffuse pneumonia and excessive lung infiltration with highly activated CD44+CD62L- T-lymphocytes resulting in death between months 7–9 post challenge. B6 mice were characterized by development of local inflammatory foci, higher production of pro-inflammatory IL-6 and IL-11 cytokines and a more balanced T-cell activation in their lungs. CFU counts remained stable in B6 mice during the whole 18-mo observation period, and all mice survived. Thus, we established a mouse model of fatal reactivation TB vs. indefinite mycobacterial possession after identical challenge and characterized the features of immune responses in the lung tissue underlining these polar phenotypes.

Microplastics, microfibres and nanoplastics cause variable sub-lethal responses in mussels (Mytilus spp.)

We compare the toxicity of microplastics, microfibres and nanoplastics on mussels. Mussels (Mytilus spp.) were exposed to 500 ng mL-1 of 20 μm polystyrene microplastics, 10 × 30 μm polyamide microfibres or 50 nm polystyrene nanoplastics for 24 h or 7 days. Biomarkers of immune response, oxidative stress response, lysosomal destabilisation and genotoxic damage were measured in haemolymph, digestive gland and gills. Microplastics and microfibres were observed in the digestive glands, with significantly higher plastic concentrations after 7-days exposure (ANOVA, P < 0.05). Nanoplastics had a significant effect on hyalinocyte-granulocyte ratios (ANOVA, P < 0.05), indicative of a heightened immune response. SOD activity was significantly increased followed 24 h exposure to plastics (two-way ANOVA, P < 0.05), but returned to normal levels after 7-days exposure. No evidence of lysosomal destabilisation or genotoxic damage was observed from any form of plastic. The study highlights how particle size is a key factor in plastic particulate toxicity.

Abstract 4980: T-cell receptor clonotyping and immune infiltrate quantification with whole transcriptome RNA-seq from FFPE

Abstract Background: Even within patients with high tumor mutational burden (TMB) and/or PD-L1 expression, objective response rates to checkpoint therapies remain below 50% (e.g. Checkmate 227). Identifying predictive biomarkers for immune checkpoint inhibition therapy is an active area of research. Tumor infiltrating lymphocytes (TILs) show potential as a predictive biomarker for immune-oncology therapies. Rearrangement of the T-cell receptor (TCR) complementarity-determining region 3 (CDR3) serves as a marker for T-cell clones, and can be detected by RNA-seq of the region. The standard mechanism of tissue storage, formalin fixation and paraffin embedding (FFPE), degrades nucleic acids and makes sequencing more challenging. We present detection of TCR CDR3 of TILs from FFPE RNA-seq as a potential biomarker. Methods: FFPE Tumors from 65 head and neck squamous cell cancer (HNSCC), 233 colorectal carcinoma (CRC), and 217 non-small cell lung cancer (NSCLC) patients were profiled using deep full-transcriptome RNA-seq. Patients were assigned a TCR score by first aligning RNA-seq reads to TCRα and TCRβ CDR3 sequences, then counting overall CDR3 read support. Gene expression profiles were also used to predict consensus molecular subtype (CMS) and estimate immune cell abundance. To assess tumor sample purity, deep whole genome (N=244) or whole exome (N=271) DNA sequencing was performed on both tumor and normal blood samples from each patient. TMB was calculated directly by counting somatic non-synonymous exonic mutations. Results: Immune populations revealed high correlation (Pearson's r = .84, p = 3.6e-169) between TCR CDR3 counts and independent gene expression-based estimates of T-cell activity. Using the CMS of colon cancer samples, we found that CMS2 patients had a significantly lower average number of reads aligned to CDR3 (46.5 vs 91.6, p = 1.5e-7) which agrees with previous reports of low immune activity in that subtype. We compared CDR3 read count against TMB and found significant correlation (Spearman's rho = 0.34, p = 0.0048) in head and neck tumors where the median TMB was 98, but no association in lung or colon tumors where TMB is higher (median TMB 169 and 132 respectively). Finally, tumor purity estimated via DNA-seq was anti-correlated with CDR3 read count (Spearman's ρ = -0.39, p = 3.3e-21). Conclusions: TCR CDR3 read support from bulk RNA-seq on 515 solid tumor FFPE samples provides a related but distinct measure of T-cell infiltration to gene expression-based estimates. TMB and TCR support are generally independent biomarkers, especially in those tissues with higher average mutation rate. TCR support has potential to complement TMB as a predictive biomarker of immune checkpoint therapy response. Citation Format: Andrew J. Sedgewick, Jacob J. Adashek, Christopher W. Szeto, Charles J. Vaske, Philippe E. Spiess, Stephen C. Benz. T-cell receptor clonotyping and immune infiltrate quantification with whole transcriptome RNA-seq from FFPE [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4980.

A Multiple N-Glucosylated Peptide Epitope Efficiently Detecting Antibodies in Multiple Sclerosis.

Diagnostics of Multiple Sclerosis (MS) are essentially based on the gold standard magnetic resonance imaging. Few alternative simple assays are available to follow up disease activity. Considering that the disease can remain elusive for years, identification of antibodies fluctuating in biological fluids as relevant biomarkers of immune response is a challenge. In previous studies, we reported that anti-N-glucosylated (N-Glc) peptide antibodies that can be easily detected in Solid-Phase Enzyme-Linked ImmunoSorbent Assays (SP-ELISA) on MS patients’ sera preferentially recognize hyperglucosylated adhesin of non-typeable Haemophilus Influenzae. Since multivalency can be useful for diagnostic purposes to allow an efficient coating in ELISA, we report herein the development of a collection of Multiple N-glucosylated Peptide Epitopes (N-Glc MEPs) to detect anti-N-Glc antibodies in MS. To this aim, a series of N-Glc peptide antigens to be represented in the N-GlcMEPs were tested in competitive ELISA. We confirmed that the epitope recognized by antibodies shall contain at least 5-mer sequences including the fundamental N-Glc moiety. Using a 4-branched dendrimeric lysine scaffold, we selected the N-Glc MEP 24, carrying the minimal epitope Asn(Glc) anchored to a polyethylene glycol-based spacer (PEG) containing a 19-atoms chain, as an efficient multivalent probe to reveal specific and high affinity anti-N-Glc antibodies in MS.

Neuroinflammation PET Imaging: Current Opinion and Future Directions.

Neuroinflammation is a key pathologic hallmark of numerous neurologic diseases, however, its exact role in vivo is yet to be fully understood. PET imaging enables investigation, quantification, and tracking of different neuroinflammation biomarkers in living subjects longitudinally. One such biomarker that has been imaged extensively using PET is translocator protein 18 kDa (TSPO). Although imaging TSPO has yielded valuable clinical data linking neuroinflammation to various neurodegenerative diseases, considerable limitations of TSPO PET have prompted identification of other more cell-specific and functionally relevant biomarkers. This review analyzes the clinical potential of available and emerging PET biomarkers of innate and adaptive immune responses, with mention of exciting future directions for the field.

SEPSIS project: a protocol for studying biomarkers of neonatal sepsis and immune responses of infants in a malaria-endemic region.

IntroductionNeonatal sepsis outreaches all causes of neonatal mortality worldwide and remains a major societal burden in low and middle income countries. In addition to limited resources, endemic morbidities, such as malaria and prematurity, predispose neonates and infants to invasive infection by altering neonatal immune response to pathogens. Nevertheless, thoughtful epidemiological, diagnostic and immunological evaluation of neonatal sepsis and the impact of gestational malaria have never been performed.Methods and analysisA prospective longitudinal multicentre follow-up of 580 infants from birth to 3 months of age in urban and suburban Benin will be performed. At delivery, and every other week, all children will be examined and clinically evaluated for occurrence of sepsis. At delivery, cord blood systematic analysis of selected plasma and transcriptomic biomarkers (procalcitonin, interleukin (IL)-6, IL-10, IP10, CD74 and CX3CR1) associated with sepsis pathophysiology will be evaluated in all live births as well as during the follow-up, and when sepsis will be suspected. In addition, whole blood response to selected innate stimuli and extensive peripheral blood mononuclear cells phenotypic characterisation will be performed. Reference intervals specific to sub-Saharan neonates will be determined from this cohort and biomarkers performances for neonatal sepsis diagnosis and prognosis tested.Ethics and disseminationEthical approval has been obtained from the Comité d’Ethique de la Recherche – Institut des Sciences Biomédicales Appliquées (CER-ISBA 85 - 5 April 2016, extended on 3 February 2017). Results will be disseminated through international presentations at scientific meetings and publications in peer-reviewed journals.Trial registration numberClinicalTrials.gov registration number: NCT03780712.