The use of next-generation sequencing technologies has enabled the rapid identification of non-synonymous somatic mutations in cancer cells. Neoantigens are mutated peptides derived from somatic ...mutations not present in normal tissues that may result in the presentation of tumour-specific peptides capable of eliciting antitumour T-cell responses. Personalised neoantigen-based cancer vaccines and adoptive T-cell therapies have been shown to prime host immunity against tumour cells and are under clinical trial development. However, the optimisation and standardisation of neoantigen identification, as well as its delivery as immunotherapy are needed to increase tumour-specific T-cell responses and, thus, the clinical efficacy of current cancer immunotherapies.
In this recommendation article, launched by the European Society for Medical Oncology (ESMO), we outline and discuss the available framework for neoantigen prediction and present a systematic review of the current scientific evidence.
A number of computational pipelines for neoantigen prediction are available. Most of them provide peptide major histocompatibility complex (MHC) binding affinity predictions, but more recent approaches incorporate additional features like variant allele fraction, gene expression, and clonality of mutations. Neoantigens can be predicted in all cancer types with high and low tumour mutation burden, in part by exploiting tumour-specific aberrations derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other tumour-specific processes that could yield more potently immunogenic tumour neoantigens. Ongoing clinical trials will highlight those cancer types and combinations of immune therapies that would derive the most benefit from neoantigen-based immunotherapies.
Improved identification, selection and prioritisation of tumour-specific neoantigens are needed to increase the scope of benefit from cancer vaccines and adoptive T-cell therapies. Novel pipelines are being developed to resolve the challenges posed by high-throughput sequencing and to predict immunogenic neoantigens.
•Next-generation sequencing technologies have provided the means to directly identify somatic gene mutations in tumours.•Neoantigens are tumour-specific mutated peptides capable of inducing antitumour immune responses.•The discovery of immunogenic neoantigens is instrumental for the pursuit of cancer vaccines and adoptive T-cell therapy.•Refining computational workflows towards the optimal identification of immunogenic neoepitopes is needed.
Background:
Rheumatoid Arthritis (RA) is a systemic autoimmune disease, associated with hiperproduction of autoantibodies (AAb), in which the most specific are the AAb against citrullinated peptides ...(ACPA). RA is influenced by genetic factors, specifically, there is a strong genetic association with the shared epitope (SE), a five amino acid sequence motif in positions 70–74 of HLA-DRβ1 chains encoded by HLA-DRB1 alleles: QKRAA, QRRAA and RRRAA.
The present study aims to analyze whether SE-peptides (SE-p) can be a target of the autoimmune response in RA.
Objectives:
To analyze the presence of AAb against the unmodified (
Un
) SE-p, citrullinated (
Cit
) SE-p and carbamylated (
Car
) SE-p.
Methods:
Sera from consecutive 117 RA patients and 21 psoriasic arthritis (PsA) from our outpatient clinic were collected by venopunture. Also 138 sera from blood donors were obtained as healthy controls (HC). All participants signed the informed consent.
We perfomed a homemade ELISA test using a sequence of 15 aminoacid peptides from positions 65-79 of HLA-DRB1 containing the 3 different SE sequences, in the
Un
,
Cit
and
Ca
r SE-p, synthesized in a linear and cycled form. We established a 90% of specificity using a ROC curve obtained from HC and PsA for each ELISA test.
HLA-DRB1 polymorphism was performed using a HLA-DRB1 sequence specific oligonucleotide typing kit (Lifecodes) in 95 RA and in 15 PsA.
ACPA and RF were determined with commercial assays (Inova Diagnostics and Binding Site, respectively).
Results:
The overall sensitivity of the different SE-p AAb tests ranged from 5.1-21.4%.
RRRAA SE polymorphism was associated with AAb against cycled CitCitCitAA SE-p (p=0.025), QKRAA polymorphism was almost significantly associated with AAb against cycled QKCitAA SE-p (p=0.067), whereas there was no association between QRRAA polymorphism and AAb against cycled QCitCitAA SE-p (p=0.690). On the other hand, there was no association between SE polymorphisms and AAb to any other peptide used in the ELISA test.
Significant differences were observed in the presence of AAb against lineal RRRAA, lineal CitCitCitAA and cycled CitCitCitAA SE-p when comparing RA vs. HC patients (p=0.022, 0.044, 0.022, respectively). Moreover, there also were significant differences in the presence of AAb against cycled CitCitCitAA SE-p between RA and PsA patients (sensitivity 21.4%, specificity 100%; p=0.014).
It must be highlighted that cycled CitCitCitAA SE-p AAb were detected in 20.0% of RA patient sera that were negative for RF and ACPA.
There was no association between RF or ACPA with the presence of any SE-p AAb.
Conclusion:
RA patients have autoantibodies against the Shared Epitope (SE). The cycled CitCitCitAA SE peptide (SE-p) shows the best performance among all the peptides tested and could identify patients seronegative for ACPA and RF, both analyzed by commercial assays.
Additional studies must be performed to verify the diagnostic and utility of these new autoantibodies against SE-p in RA.
Acknowledgements:
This work was granted by the 2018 call of the “Fundación Española de Reumatologia” and the 2017 call grant “Fundació Parc Taulí”.
Disclosure of Interests:
None declared
Summary
This investigation was conducted to assess the baseline level of sperm DNA fragmentation (SDF) in a cohort of patients presenting chromosomal rearrangements (nine reciprocal translocations ...and two inversions). In a separate experiment, a dynamic analysis to calculate the rate of SDF (rSDF), after a varying period of sperm storage (0 h, 1 h, 4 h, 8 h and 24 h) at 37 °C, was performed. Results were compared with eight fertile donors. Different experimental approaches to assess SDF, such as terminal transferase dUTP nick‐end labelling (TUNEL), sperm chromatin structure assay (SCSA) and sperm chromatin dispersion test (SCDt), were used. No differences for the baseline level of SDF were found. Carriers of reorganized genomes showed statistically higher levels of SDF than did control donors (p = 0.025 for TUNEL; p = 0.022 for SCSA; p = 0.014 for SCDt). However, 54.5% (6/11) of the patients presented values similar to those of control donors. There was no significant difference in rSDF (p = 0.34). Nevertheless, the results suggest that a high variability for SDF and rSDF exists in these patients. Routine analysis of SDF and rSDF should be considered in patients presenting rearranged genomes to determine fertility status for assisted reproductive techniques (ART) purposes.
Background. It has been suggested that routine CD4 cell count monitoring in human immunodeficiency virus (HIV)–monoinfected patients with suppressed viral loads and CD4 cell counts >300 cell/μL could ...be reduced to annual. HIV/hepatitis C virus (HCV) coinfection is frequent, but evidence supporting similar reductions in CD4 cell count monitoring is lacking for this population. We determined whether CD4 cell count monitoring could be reduced in monoinfected and coinfected patients by estimating the probability of maintaining CD4 cell counts ≥200 cells/μL during continuous HIV suppression. Methods. The PISCIS Cohort study included data from 14 539 patients aged ≥16 years from 10 hospitals in Catalonia and 2 in the Balearic Islands (Spain) since January 1998. All patients who had at least one period of 6 months of continuous HIV suppression were included in this analysis. Cumulative probabilities with 95% confidence intervals were calculated using the Kaplan–Meier estimator stratified by the initial CD4 cell count at the period of continuous suppression initiation. Results. A total of 8695 patients were included. CD4 cell counts fell to <200 cells/μL in 7.4% patients, and the proportion was lower in patients with an initial count >350 cells/μL (1.8%) and higher in those with an initial count of 200–249 cells/μL (23.1%). CD4 cell counts fell to <200 cells/μL in 5.7% of monoinfected and 11.1% of coinfected patients. Of monoinfected patients with an initial CD4 cell count of 300–349 cells/μL, 95.6% maintained counts ≥200 cells/μL. In the coinfected group with the same initial count, this rate was lower, but 97.6% of coinfected patients with initial counts >350 cells/μL maintained counts ≥200 cells/μL. Conclusions. From our data, it can be inferred that CD4 cell count monitoring can be safely performed annually in HIV-monoinfected patients with CD4 cell counts >300 cells/μL and HIV/HCV-coinfected patients with counts >350 cells/μL.
Malnutrition and sarcopenia may last beyond hospital discharge, especially in patients admitted to intensive care units (ICU), having a negative impact on patient recovery and leading to disability, ...poor quality of life, and additional morbidity. No prior evidence is available for post-ICU management and follow-up of coronavirus disease 2019 (COVID-19) patients and their long-term evolution. This study reports on the one-year-long evolution of a cohort of COVID-19 survivors after ICU discharge, in terms of nutritional and functional status as well as health-related quality of life (HRQoL).
A multicenter, ambispective, observational cohort study (NUTRICOVID study) was conducted in 16 public hospitals located in the Community of Madrid with COVID-19 survivors who were admitted to ICU during the first outbreak. Retrospective and prospective data were collected from hospital admission to one year after discharge. At hospital discharge and at 3, 6 and 12 months post-discharge, the following outcomes were recorded: weight, risk of malnutrition (MUST) and sarcopenia (SARC-F), medical nutrition therapy (MNT), functional status (Barthel index), and HRQoL (EQ-5D-5L).
A total of 199 patients (70.4% male, mean age SD of 60.7 10.1) were included in the study. At hospital discharge, mean weight loss was 16.4% (8.0%), whereas most patients gained weight after discharge with an increase of 16.5% (14.0%) at 12 months. The proportion of patients at high risk of malnutrition decreased from 83.2% at hospital discharge to 2.1% at 12 months. The proportion at risk of sarcopenia decreased from 86.9% at hospital discharge to 13.4% at 12 months. At hospital discharge, 69 patients received MNT by means of oral nutritional supplements (ONS) while two patients required enteral nutrition (EN). At 12 months, only 12 patients continued taking ONS, with no patients taking EN. Regarding functional status, 72.9% of patients were moderately or severely dependent at hospital discharge, whereas 87.2% showed low dependency or independency after 12 months. The EQ-VAS values increased from hospital discharge (39 21.2) to 6 months post-discharge and remained steady up to 12 months (72.7 19.0). The mean health value improved from hospital discharge (0.25 0.41) to 6 months post-discharge (0.80 0.24) and was maintained thereafter.
Patients’ nutritional and functional impairment at hospital discharge was high, with high dependency status and low HRQoL; however, their situation improved progressively during the 12 months following hospital discharge. Nevertheless, there is a need to define early strategies to optimize the nutritional and functional recovery of COVID-19 patients.
This study using the Catalan PISCIS cohort explores risk factors of migrants’ late presentation and the impact of late presentation on their health outcomes. We analyse 9590 new HIV diagnoses ...enrolled in the cohort between 2004 and 2016. Univariate and multivariate logistic regression models are used to identify risk factors associated with late presentation among migrants, giving crude and adjusted odds ratios and their 95% confidence intervals. Cox regression models are estimated to identify risk factors associated with AIDS/death, and crude and adjusted hazard ratios and 95% confidence intervals are reported. Late presentation is higher in migrants than non-migrants. Among migrants, region of origin is associated with late presentation and AIDS/death during follow-up. The results highlight persisting inequalities in HIV diagnosis and care among migrants in Catalonia. Targeted interventions addressed to specific subgroups in the migrant population are needed.
Although several reports on male infertility suggest a relationship between chromosome 9 polymorphisms and infertility, the effects on the phenotype have not been extensively reported. In this study, ...an infertile patient was found to carry a 9qh+++ chromosome. The flow cytometric TUNEL assay and SCD test have been applied to characterize sperm DNA integrity. In order to assess its meiotic behaviour, synapsis, recombination, and aneuploidy, analyses have been also performed. Sperm DNA fragmentation (SDF) was 77.81% and 87% for the TUNEL and SCD tests, respectively. Ninety-two percent of pachytene cells analyzed showed meiotic abnormalities. The mean number of MLH1 foci per pachytene in the control group was higher (49) than the mean found in the 9qh+++ patient (38) (P<.0001). In spermatozoa, significant increases of disomy rates were observed for chromosome 18 and for the sex chromosomes (P<.0001). These disturbances could be present in other male carriers of a less marked 9qh+.
Background: Thrombocytopenia is a common haematological abnormality and no simple diagnostic test is available to diagnose thrombocytopenia pathogenesis. Aim: To evaluate sensitivity and specificity ...of reticulated platelets (RP) as a diagnostic test for thrombocytopenia with increased thrombopoietic activity. Design: Prospective observational study in thrombocytopenic patients. Methods: A direct, whole-blood, dual-labelling flow cytometric method was used. Direct, whole-blood double coverage was achieved using a monoclonal anti-glycoprotein (GP)-III antibody (CD61 PerCP®) for platelet identification and thiazole orange (Retic-count®) as platelet mARN stain. Results: RP were measured in 101 thrombocytopenic patients and 104 non-thrombocytopenic controls. The mean RP percentage in 60 thrombocytopenic patients with no increased thrombopoietic activity was 7.5% (CI for 95%: 5.2–9.7) and RP absolute number was 3.2 × 109/l (CI for 95%: 2.1–4.3). The mean RP percentage in 41 thrombocytopenic patients with increased thrombopoietic activity was 30.3% (CI for 95%: 25.1–35.5) and RP absolute number was 6.2 (CI for 95%: 4.8–7.7). The RP percentage cut-off for a diagnosis of thrombocytopenia with increased thrombopoietic activity was 11% sensitivity 93%, specificity 85%, positive predictive value (PPV) 83%, negative predictive value (NPV) 95%. Conclusions: RP measurement by flow cytometry, directly from whole-blood, is a useful screening test to differentiate between thrombocytopenia with high or low thrombopoietic activity. A RP percentage in excess of 11%, has a high sensitivity and good specificity for a diagnosis of thrombocytopenia with increased thrombopoietic activity.
Omalizumab is an effective drug for allergic asthma. The purpose of this study was to evaluate the effectiveness and tolerance of this drug in non-allergic GINA step V asthma patients. This study was ...single-centre, prospective, open-label, observational, naturalistic. Non-allergic asthma patients requiring a mean dose of oral prednisolone of at least 5 mg/day during greater than or equal to 1 year or an accumulated oral corticosteroid dose/year greater than or equal to 1500 mg were enrolled. At entry and the end of the 12-month follow-up we measured blood eosinophilia and IgE concentration; at every monthly visit a forced spirometry and exhaled fraction of nitric oxide (NO) were carried out. The subjects were seven adult patients (5 female), age range 37-63 years, with the following mean values: IgE: 226.7+/-176 IU/mL; FVC 74+/-18 percent; FEV1 57+/-11 percent; NO: 21.2+/-7 ppb. The study was approved by the IRB of the hospital. One patient decided to stop treatment after 12 weeks and was excluded from the evaluation. We did not observe changes in eosinophil count, spirometry or NO values. Three patients considered responders did not need prednisolone during the follow-up. The mean daily dose of prednisolone fell from 6.6+/-8.1 mg/day at entry to 1.5+/-2.3 mg/day (p less than 0.16) at the end of follow-up. The mean monthly accumulated dose fell from 92+/-112 to 12+/-26 mg/month (p=0.26). Total blood IgE increased 1.93-fold. Side effects were only local: treatment tolerance was excellent; three out of six patients seemed to slightly benefit from anti-IgE treatment; to date there is no evidence strong enough to systematically prescribe omalizumab in non-allergic asthma patients.
Interplay between chromatin-associated complexes and modifications critically contribute to the partitioning of epigenome into stable and functionally distinct domains. Yet there is a lack of ...systematic identification of chromatin crosstalk mechanisms, limiting our understanding of the dynamic transition between chromatin states during development and disease. Here we perform co-dependency mapping of genes using CRISPR-Cas9-mediated fitness screens in pan-cancer cell lines to quantify gene-gene functional relationships. We identify 145 co-dependency modules and further define the molecular context underlying the essentiality of these modules by incorporating mutational, epigenome, gene expression and drug sensitivity profiles of cell lines. These analyses assign new protein complex composition and function, and predict new functional interactions, including an unexpected co-dependency between two transcriptionally counteracting chromatin complexes - polycomb repressive complex 2 (PRC2) and MLL-MEN1 complex. We show that PRC2-mediated H3K27 tri-methylation regulates the genome-wide distribution of MLL1 and MEN1. In lymphoma cells with EZH2 gain-of-function mutations, the re-localization of MLL-MEN1 complex drives oncogenic gene expression and results in a hypersensitivity to pharmacologic inhibition of MEN1. Together, our findings provide a resource for discovery of trans-regulatory interactions as mechanisms of chromatin regulation and potential targets of synthetic lethality.
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