scholarly journals A multiparametric approach to improve the prediction of response to immunotherapy in patients with metastatic NSCLC

2020 ◽  
Author(s):  
Marzia Del Re ◽  
Federico Cucchiara ◽  
Eleonora Rofi ◽  
Lorenzo Fontanelli ◽  
Iacopo Petrini ◽  
...  
Keyword(s):  
Mutational Load ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Synonymous Mutations ◽  
Metastatic Nsclc ◽  
Molecular Determinants ◽  
Droplet Pcr ◽  
Ifn Γ ◽  
Nsclc Patients ◽  
Next Generation Sequencing Ngs

Abstract Background It is still unclear how to combine biomarkers to identify patients who will truly benefit from anti-PD-1 agents in NSCLC. This study investigates exosomal mRNA expression of PD-L1 and IFN-γ, PD-L1 polymorphisms, tumor mutational load (TML) in circulating cell-free DNA (cfDNA) and radiomic features as possible predictive markers of response to nivolumab and pembrolizumab in metastatic NSCLC patients. Methods Patients were enrolled and blood (12 ml) was collected at baseline before receiving anti-PD-1 therapy. Exosome-derived mRNA and cfDNA were extracted to analyse PD-L1 and IFN-γ expression and tumor mutational load (TML) by digital droplet PCR (ddPCR) and next-generation sequencing (NGS), respectively. The PD-L1 single nucleotide polymorphisms (SNPs) c.-14-368 T > C and c.*395G > C, were analysed on genomic DNA by Real-Time PCR. A radiomic analysis was performed on the QUIBIM Precision® V3.0 platform. Results Thirty-eight patients were enrolled. High baseline IFN-γ was independently associated with shorter median PFS (5.6 months vs. not reached p = 0.0057), and levels of PD-L1 showed an increase at 3 months vs. baseline in patients who progressed (p = 0.01). PD-L1 baseline levels showed significant direct and inverse relationships with radiomic features. Radiomic features also inversely correlated with PD-L1 expression in tumor tissue. In subjects receiving nivolumab, median PFS was shorter in carriers of c.*395GG vs. c.*395GC/CC genotype (2.3 months vs. not reached, p = 0.041). Lastly, responders had higher non-synonymous mutations and more links between co-occurring genetic somatic mutations and ARID1A alterations as well. Conclusions A combined multiparametric approach may provide a better understanding of the molecular determinants of response to immunotherapy.

scholarly journals Repli-seq: genome-wide analysis of replication timing by next-generation sequencing

2017 ◽  
Author(s):  
Claire Marchal ◽  
Takayo Sasaki ◽  
Daniel Vera ◽  
Korey Wilson ◽  
Jiao Sima ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Replication Timing ◽  
Nucleotide Polymorphisms ◽  
Robust Methods ◽  
Next Generation ◽  
Single Nucleotide ◽  
Cellular Processes ◽  
Genome Wide ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ABSTRACTCycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early and late replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and sub-nuclear position. Moreover, RT is regulated during development and is altered in disease. Exploring mechanisms linking RT to other cellular processes in normal and diseased cells will be facilitated by rapid and robust methods with which to measure RT genome wide. Here, we describe a rapid, robust and relatively inexpensive protocol to analyze genome-wide RT by next-generation sequencing (NGS). This protocol yields highly reproducible results across laboratories and platforms. We also provide computational pipelines for analysis, parsing phased genomes using single nucleotide polymorphisms (SNP) for analyzing RT allelic asynchrony, and for direct comparison to Repli-chip data obtained by analyzing nascent DNA by microarrays.

Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function

2018 ◽  
Vol 46 (4) ◽  
pp. 937-944 ◽  
Author(s):  
Robert Rauscher ◽  
Zoya Ignatova
Keyword(s):  
Protein Folding ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Synonymous Mutations ◽  
Translation Velocity ◽  
Disease Penetrance ◽  
And Function ◽  
Related Proteins ◽  
Translational Speed ◽  
Fine Tune

Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a conserved feature of mRNA and have evolved to fine-tune protein folding, expression and function. Synonymous single-nucleotide polymorphisms (sSNPs) that alter programmed translational speed affect expression and function of the encoded protein. Synergistic advances in next-generation sequencing have led to the identification of sSNPs associated with disease penetrance. Here, we draw on studies with disease-related proteins to enhance our understanding of mechanistic contributions of sSNPs to functional alterations of the encoded protein. We emphasize the importance of identification of sSNPs along with disease-causing mutations to understand genotype–phenotype relationships.

scholarly journals Whole Genome Sequencing of Nontuberculous Mycobacterium (NTM) Isolates from Sputum and Environmental Specimens in Co-Habiting Patients with NTM Pulmonary Disease

2019 ◽  
Author(s):  
Jung-Ki Yoon ◽  
Taek Soo Kim ◽  
Jong-Il Kim ◽  
Jae-Joon Yim
Keyword(s):  
Whole Genome Sequencing ◽  
Pulmonary Disease ◽  
Genome Sequencing ◽  
Genetic Distances ◽  
Mycobacterium Abscessus ◽  
Nontuberculous Mycobacterium ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Next Generation Sequencing Ngs

Abstract Background : Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spread of Mycobacterium abscessus among patients with cystic fibrosis. Results : We investigated NTM genomes through NGS to examine transmission patterns in three pairs of co-habiting NTM-PD patients who were suspected of patient-to-patient transmission. Three pairs of patients with NTM-PD co-habiting for at least 15 years were enrolled: a mother and a daughter with M. avium PD, a couple with M. intracellulare PD, and a second couple, one of whom was infected with M. intracellulare PD and the other of whom was infected with M. abscessus subsp. massiliense PD. Whole genome sequencing was performed using NTM colonies isolated from patients and environmental specimens. Genetic distances were estimated based on single nucleotide polymorphisms (SNPs) in the NTM genomes. Comparing SNPs in the consensus regions, the minimum pairwise SNP distances of NTM isolates derived from the two pairs of patients infected with the same NTM species were over 10,000. In phylogenetic analysis, the NTM isolates from patients with M. avium PD clustered with isolates from different environmental sources. Conclusions : In conclusion, considering the genetic distances between NTM strains, the likelihood of patient-to-patient transmission in pairs of co-habiting NTM-PD patients without overt immune deficiency is minimal.

scholarly journals Relationship between interleukin-18-607C/A gene polymorphism and severity of enterovirus-71 encephalitis in Chinese children

2019 ◽  
Author(s):  
Jie Song ◽  
Yedan Liu ◽  
Zhenghai Qu ◽  
Ya Guo ◽  
Peipei Liu ◽  
...  
Keyword(s):  
Serum Concentration ◽  
Innate Immune System ◽  
Promoter Region ◽  
Enterovirus 71 ◽  
Innate Immune ◽  
Nucleotide Polymorphisms ◽  
Interleukin 18 ◽  
Single Nucleotide ◽  
Ifn Γ ◽  
Infectious Encephalitis

Abstract Background: Interleukin-18 (IL-18), a pro-inflammatory cytokine encoded by IL-18 and known as interferon (IFN)-γ inducing factor, plays an important role in the innate immune system. Single nucleotide polymorphisms (SNPs) of IL-18-607C/A have been reported to be associated with many infectious and immune-related diseases. However, there is no evidence of its association with enterovirus 71 (EV71)-infectious encephalitis. This study aimed to explore the association between the promoter region polymorphisms (-607C/A) of IL-18 and the severity of EV71 encephalitis in Chinese children.Methods: We analyzed the polymorphisms of IL-18-607C/A in 185 EV71-infected patients and 214 controls for genetic association research. Clinical features and auxiliary examination results were collected and compared in the cases. The serum concentration of IFN-γ was detected using enzyme-linked immunosorbent assays (ELISA). Results: The frequency of IL-18-607 AA genotype and allele in EV71-infected patients was significantly higher than that in the controls (32.4% vs 21.5%, P=0.042, 55.1% vs 46.0%, P=0.001). Furthermore, a difference was found in severe EV71 and mild encephalitis cases (53.0% vs 20.5%, P=0.003, 67.3% vs 50%, P=0.016). The serum concentration of IFN-γ in patients with encephalitis was much lower in AA genotypes (106.0±8.9 pg/mL) than in CA and CC genotypes (120.4±8.9 and 128.1±7.5 pg/mL, respectively, P<0.001). The duration of fever and blood glucose level was obviously higher in AA than in CA and CC genotypes.Conclusions: Children with IL-18-607AA genotype were more susceptible to developing severe EV71-associated encephalitis in this study in China.

scholarly journals Interleukin-2, Interferon-gamma Gene Polymorphisms in Recurrent Aphthous Stomatitis

2017 ◽  
Vol 118 (2-3) ◽  
pp. 81-86 ◽  
Author(s):  
Shamsolmoulouk Najafi ◽  
Hila Yousefi ◽  
Mahsa Mohammadzadeh ◽  
Alireza Zare Bidoki ◽  
Elham Farhadi ◽  
...  
Keyword(s):  
Cytokine Production ◽  
Interleukin 2 ◽  
Recurrent Aphthous Stomatitis ◽  
Allele Frequencies ◽  
Aphthous Stomatitis ◽  
Unknown Etiology ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ifn Γ

Recurrent aphthous stomatitis (RAS) is the most common oral ulcerative inflammatory disease with unknown etiology. IL-2 and IFN-γ are secreted by Th1 cells and the elevated levels of them have been reported in RAS. Single nucleotide polymorphisms (SNPs) of IL-2 and IFN-γ genes could alter the cytokine production. The aim of this study was to investigate frequencies of IL-2 and IFN-γ alleles and genotypes in a group of patients with minor-RAS (MiRAS). PCR-SSP method used to type genomic DNA of 64 Iranian patients with MiRAS for IL-2 gene (G –330 T) and (G +166 T) and IFN-γ gene at position UTR5644 (A/T). Frequency of each allele and genotype was compared with control group. IL-2 +166 G allele was significantly lower among patients which was reflected in significantly decreased of GG genotype at this position, while IL-2 +166 T allele was significantly higher among patients, IL-2 GT genotype was also significantly higher in RAS patients. No significant differences were found regarding IL-2 –330 G/T allele frequencies, while IL-2 GT genotype at this position was significantly higher among patients and IL-2 –330 TT genotype was significantly lower among RAS patients. Although no significant differences were found in IFN-γ allele frequencies at UTR5644 (A/T), AT genotype at this position was significantly overrepresented among patients compared with controls. Results of this study suggest that certain SNPs of IL-2 and IFN-γ genes have association with predisposition of individuals to RAS. More studies in different ethnic groups are needed to confirm results of this study.

scholarly journals Interferon-gamma polymorphisms and risk of iron deficiency and anaemia in Gambian children

2020 ◽  
Vol 5 ◽  
pp. 40
Author(s):  
Kelvin M. Abuga ◽  
Kirk A. Rockett ◽  
John Muthii Muriuki ◽  
Oliver Koch ◽  
Manfred Nairz ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Interferon Gamma ◽  
Iron Deficiency Anaemia ◽  
Iron Status ◽  
Health Concern ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Deficiency Anaemia ◽  
Ifn Γ

Background: Anaemia is a major public health concern especially in African children living in malaria-endemic regions. Interferon-gamma (IFN-γ) is elevated during malaria infection and is thought to influence erythropoiesis and iron status. Genetic variants in the IFN-γ gene (IFNG) are associated with increased IFN-γ production. We investigated putative functional single nucleotide polymorphisms (SNPs) and haplotypes of IFNG in relation to nutritional iron status and anaemia in Gambian children over a malaria season. Methods: We used previously available data from Gambian family trios to determine informative SNPs and then used the Agena Bioscience MassArray platform to type five SNPs from the IFNG gene in a cohort of 780 Gambian children aged 2-6 years. We also measured haemoglobin and biomarkers of iron status and inflammation at the start and end of a malaria season. Results: We identified five IFNG haplotype-tagging SNPs ( IFNG-1616 [rs2069705], IFNG+874 [rs2430561], IFNG+2200 [rs1861493], IFNG+3234 [rs2069718] and IFNG+5612 [rs2069728]). The IFNG+2200C [rs1861493] allele was associated with reduced haemoglobin concentrations (adjusted β -0.44 [95% CI -0.75, -0.12]; Bonferroni adjusted P = 0.03) and a trend towards iron deficiency compared to wild-type at the end of the malaria season in multivariable models adjusted for potential confounders. A haplotype uniquely identified by IFNG+2200C was similarly associated with reduced haemoglobin levels and trends towards iron deficiency, anaemia and iron deficiency anaemia at the end of the malaria season in models adjusted for age, sex, village, inflammation and malaria parasitaemia. Conclusion: We found limited statistical evidence linking IFNG polymorphisms with a risk of developing iron deficiency and anaemia in Gambian children. More definitive studies are needed to investigate the effects of genetically influenced IFN-γ levels on the risk of iron deficiency and anaemia in children living in malaria-endemic areas.

Sign in / Sign up

Export Citation Format

Share Document