scholarly journals Vitiligo Skin Biomarkers Associated With Favorable Therapeutic Response

2021 ◽  
Vol 12 ◽  
Author(s):  
Qianli Yang ◽  
Guohong Zhang ◽  
Mingwan Su ◽  
Gigi Leung ◽  
Harvey Lui ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Duration ◽  
Therapeutic Response ◽  
Target Lesion ◽  
Response To Therapy ◽  
Ultraviolet B ◽  
Clinical Parameters ◽  
Short Disease Duration ◽  
Tacrolimus Therapy ◽  
Active Genes

Vitiligo is an acquired depigmentation skin disease caused by immune-mediated death of melanocytes. The most common treatment for vitiligo is narrow band ultraviolet B phototherapy, which often is combined with topical therapies such as tacrolimus. However, patients’ responses to these treatments show large variations. To date, the mechanism for this heterogeneity is unknown, and there are no molecular indicators that can predict an individual patient’s response to therapy. The goal of this study is to identify clinical parameters and gene expression biomarkers associated with vitiligo response to therapy. Six patients with segmental vitiligo and 30 patients with non-segmental vitiligo underwent transcriptome sequencing of lesional and nonlesional skin at baseline before receiving combined UBUVB and tacrolimus therapy for 6 month, and were separated into good response and bad response groups based on target lesion achieving > 10% repigmentation or not. Our study revealed that treatment-responsive vitiligo lesions had significantly shorter disease duration compared with non-responsive vitiligo lesions (2.5 years vs 11.5 years, p=0.046, t-Test), while showing no significant differences in the age, gender, ethnicity, vitiligo subtype, or disease severity. Transcriptomic analyses identified a panel of 68 genes separating the good response from bad response lesions including upregulation of immune active genes, such as CXCL10, FCRL3, and TCR, Further, compared with vitiligo lesions with long disease duration, the lesions with short duration also have much higher level of expression of immune-active genes, including some (such as FCRL3 and TCR genes) that are associated with favorable therapeutic response. In conclusion, our study has identified clinical parameters such as short disease duration and a panel of immune active and other gene expression biomarkers that are associated with favorable response to immune suppressive NBUVB + tacrolimus therapy. These markers may be useful clinically for individualized therapeutic management of vitiligo patients in the future.

scholarly journals COMP-17. LARGE-SCALE TRANSCRIPTOMIC CHARACTERIZATION OF PRIMARY AND RECURRENT GLIOBLASTOMA IDENTIFIES GENE EXPRESSION SIGNATURE OF TUMOR RESPONSE TO STANDARD THERAPY

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi64-vi65
Author(s):  
Andrew Dhawan ◽  
Justin Lathia ◽  
David Peereboom ◽  
Gene Barnett ◽  
Gabrielle Yeaney ◽  
...  
Keyword(s):  
Gene Expression ◽  
Standard Therapy ◽  
Therapeutic Response ◽  
Molecular Subtype ◽  
Gene Expression Signature ◽  
Gene Signature ◽  
Response To Therapy ◽  
Computational Method ◽  
Primary Tumors ◽  
Predictive Gene

Abstract A near-universal phenomenon in glioblastoma is disease recurrence following surgical resection and chemoradiotherapy. Development of biomarkers predictive of therapeutic response to better guide care and inform future targeted therapies is crucial. In this work, a total of 84 glioblastoma surgical specimens involving 44 primary tumors and 40 matched samples at time of re-resection, were characterized utilizing RNA-sequencing. Transcriptomic analysis was carried out with the goal of identifying underlying differences between those patients with prolonged response to standard therapy and delayed time to re-resection. We examined individual gene expression, gene coexpression networks, and well-known gene pathways in this dataset that showed consistent association with time to re-resection in both primary and progressed specimens, independent of tumor molecular subtype. Leveraging this large, well-characterized dataset, and using a novel computational methodology based on a seed-gene approach, we identified a predictive gene signature for therapeutic response. Our analyses revealed a striking degree of heterogeneity among gene expression associated with response to standard therapy and time to re-resection, adding to the complexity of signature derivation. The novel signature we obtained for response showed components involving genes such as those in the IGF pathway (IGF2BP2, IGF2BP3) and PDGF-signalling pathway (MYC, FLI1, ARHGAP4, JAK3) predictive of poor response to therapy. Likewise, predictors of positive response to therapy included genes involved in the apoptosis and RAS pathways (RAB4A, CHUK) and DNA replication pathways (SSBP2). In sum, this is among the largest cohorts of well-characterized clinical tumor samples for which there is transcriptomic information from primary and re-resected samples from matched patients. Our results not only highlight an innovative computational method for gene signature derivation in the setting of significant underlying heterogeneity, but also result in a predictive gene signature, offering the potential to give therapy to those who stand to benefit most.

scholarly journals The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers

2021 ◽  
Vol 22 (10) ◽  
pp. 5322
Author(s):  
Nitika Kandhari ◽  
Calvin A. Kraupner-Taylor ◽  
Paul F. Harrison ◽  
David R. Powell ◽  
Traude H. Beilharz
Keyword(s):  
Gene Expression ◽  
Cell Transformation ◽  
Alternative Polyadenylation ◽  
Cancer Biomarkers ◽  
Bioinformatic Analysis ◽  
Alternative Transcript ◽  
Clinical Parameters ◽  
Transcript Cleavage ◽  
Cleavage And Polyadenylation ◽  
Potential Cancer

Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinformatically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could advance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.

scholarly journals Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arika Fukushima ◽  
Masahiro Sugimoto ◽  
Satoru Hiwa ◽  
Tomoyuki Hiroyasu
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Response To Therapy ◽  
Hcv Infection ◽  
Entire Treatment Period ◽  
Time Points ◽  
Time Course Data ◽  
Conventional Methods

Abstract Background Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made using time-course data on multiple biomarkers that indicate a patient’s response to therapy contribute positively to the decision-making process associated with designing effective treatment programs for various diseases. Therefore, the development of prediction methods incorporating time-course data on multiple markers is necessary. Results We proposed new methods that may be used for prediction and gene selection via time-course gene expression profiles. Our prediction method consolidated multiple probabilities calculated using gene expression profiles collected over a series of time points to predict therapy response. Using two data sets collected from patients with hepatitis C virus (HCV) infection and multiple sclerosis (MS), we performed numerical experiments that predicted response to therapy and evaluated their accuracies. Our methods were more accurate than conventional methods and successfully selected genes, the functions of which were associated with the pathology of HCV infection and MS. Conclusions The proposed method accurately predicted response to therapy using data at multiple time points. It showed higher accuracies at early time points compared to those of conventional methods. Furthermore, this method successfully selected genes that were directly associated with diseases.

scholarly journals POS0941 IN SPONDYLOARTHRITIS PATIENTS THE PRESENCE OF COMORBIDITIES IS AN INDEPENDENT PREDICTOR OF INSUFFICIENT RESPONSE TO THERAPY WITH BIOLOGIC AGENTS AND TREATMENT DISCONTINUATION

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 733.2-734
Author(s):  
I. Flouri ◽  
N. Kougkas ◽  
N. Avgustidis ◽  
A. Repa ◽  
A. Eskitzis ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Disease Duration ◽  
Cox Regression ◽  
Independent Predictor ◽  
Response To Therapy ◽  
Treatment Discontinuation ◽  
Randomized Controlled Studies ◽  
Insufficient Response ◽  
The Impact

Background:Long-term observational studies of patients under biologic disease-modifying anti-rheumatic drug (bDMARD) therapies in routine clinical practice can provide us with important data regarding patients with comorbidities, who are usually excluded from randomized controlled studies.Objectives:To study the impact of comorbidities in the outcome (response and persistence to therapy) of patients with spondyloarthritis (SpA) receiving bDMARDs in real-world clinical practice.Methods:Prospective study of all patients who start a bDMARD in a tertiary centre University Hospital after their consent. All patient comorbidities [among a list of approximately 100 pre-specified major comorbidities] are registered by treating physicians at baseline and during follow-up.Comorbidities were studied as total Comorbidities Count (CC) and rheumatic disease comorbidity index (RDCI). Statistical analyses were performed using logistic and Cox regression models, adjusting for the potential confounding of age, sex, disease duration, diagnosis (axial vs. peripheral SpA), number of previous conventional synthetic and biologic DMARDs, year of therapy start, and co-administered methotrexate and corticosteroids (yes/no). Analyses of response to therapy also included baseline BASDAI or ASDAS indices as confounding variables.Results:A total of 603 biologic treatments (1st: 298, 2nd: 157, ≥3rd: 148) were analyzed. Half (51%) of the patients were female, 413 patients had axial SpA (AxSpA) and 190 peripheral SpA (perSpA). At baseline, median (IQR) age: 48 (38-57) years, disease duration: 11 (4-19) years, CC: 2 (1-4) and RDCI: 1 (0-2). Both comorbidity indices were significantly higher in perSpA compared to AxSpA (p<0.001).At 6 months of therapy, 31% of patients with AxSpA achieved BASDAI50 and 39% had ASDAS-ESR < 2.1. Higher CC was an independent predictor of insufficient response according to BASDAI50 [OR (95%) = 0.70 (0.52-0.94), p=0.019] and higher RDCI was predicting failure to achieve ASDAS-ESR < 2.1 [OR (95%) = 0.59 (0.37-0.94), p=0.027]. Other independent predictors of non-response were age, longer disease duration and (for ASDAS-ESR<2.1) higher baseline disease activity.During 1405 patient-years of follow-up, 349 (58%) treatments were discontinued. The adjusted hazard ratio for bDMARD discontinuation within the first 2 years of treatment due to insufficient response was doubled in patients with CC ≥2 versus those with CC ≤1 [HR = 2.27 (1.14-4.53), p=0.020] or with RDCI ≥1 (vs. RDCI = 0) [HR = 2.23 (1.22-4.07), p=0.009]. Comorbidities’ indices were not significant predictors of treatment discontinuations due to adverse events.Conclusion:The presence of comorbidities in patients with SpA is an independent predictor for insufficient 6-month response to bDMARDs and resultant treatment discontinuation due to failure.Acknowledgements:This research is co-financed by Greece and the European Union (European Social Fund- ESF) through the Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project “Reinforcement of Postdoctoral Researchers - 2nd Cycle” (MIS-5033021), implemented by the State Scholarships Foundation (ΙΚΥ).Disclosure of Interests:None declared

scholarly journals FRI0224 IDENTIFICATION OF RISK AND PROGNOSTIC FACTORS FOR POLYARTERITIS NODOSA PATIENTS WITH DIGITAL GANGRENE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 695.2-695
Author(s):  
D. Xu ◽  
X. Tian ◽  
X. Zeng ◽  
F. Zhang ◽  
L. Zhao ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Prognostic Factors ◽  
Retrospective Study ◽  
Polyarteritis Nodosa ◽  
Lupus Erythematosus ◽  
Disease Duration ◽  
Response To Therapy ◽  
Smoking History ◽  
Systemic Lupus ◽  
Poor Outcomes

Background:Polyarteritis nodosa (PAN) is a segmental, necrotizing vascular disease that primarily impacts medium-sized muscle arteries. The estimated annual incidence of PAN is still lacking in China. Digital gangrene is an ischemic manifestation of the limb. However, the causes and the treatment methods vary from case to case, and the outcome is unpredictable. These features emphasize the need to identify measurable variables that accelerate digital gangrene development in PAN patients. However, little effort has been made to identify the clinical and laboratory factors that affect PAN patients with digital gangrene to anticipate their natural history and response to therapy.Objectives:Many patients with polyarteritis nodosa (PAN) complicated with digital gangrene have poor outcomes and related research information is limited. This study was carried out to identify the associated risk and prognostic factors.Methods:We conducted a retrospective study of 148 PAN patients admitted to Peking Union Medical College Hospital (PUMCH) from September 1986 to December 2018. The characteristics, therapeutic regimens, and outcome data for patients with and without gangrene were compared. The Kaplan–Meier method and Cox hazard regression model were used to evaluate the prognostic factors.Results:Forty-seven (31.8%) PAN patients had digital gangrene complications. The average age was 40.4±17.9 years and the average disease duration was 11 (4-27) months. The presence of digital gangrene was correlated with smoking history [odds ratio (OR), 4.27; 95% confidence interval (95% CI), 1.56-11.66] and eosinophil elevation (28.12; 10.30-76.8). Thirty-two (68.1%) gangrene patients received methylprednisolone pulse therapy and all of these patients were treated with cyclophosphamide. Nine patients suffered irreversible organ injury and two died. Disease duration ≥ 24 months and elevated serum C-reactive protein (CRP) were identified as hazardous factors for poor prognosis in patients with gangrene (P=0.003, HR=8.668, 95% CI 2.11, 35.55 andP=0.042, HR=27.062, 95% CI 1.13, 648.57, respectively).Conclusion:Smoking history and eosinophil elevation in PAN patients were more prone to digital gangrene and high serum CRP level predicted poor outcomes. PAN patients with smoking history and elevated eosinophils need to be seriously evaluated by clinicians. Furthermore, the CRP level should be efficiently controlled for good prognosis.References:[1]De Virgilio A, Greco A, Magliulo G, Gallo A, Ruoppolo G, Conte M, et al. Polyarteritis nodosa: A contemporary overview. Autoimmun Rev. 2016;15:564-70.[2]Pagnoux C, Seror R, Henegar C, Mahr A, Cohen P, Le Guern V, et al. Clinical features and outcomes in 348 patients with polyarteritis nodosa: a systematic retrospective study of patients diagnosed between 1963 and 2005 and entered into the French Vasculitis Study Group Database. Arthritis Rheum. 2010;62:616-26.[3]Xu D, You X, Wang Z, Zeng Q, Xu J, Jiang L, et al. Chinese Systemic Lupus Erythematosus Treatment and Research Group Registry VI: Effect of Cigarette Smoking on the Clinical Phenotype of Chinese Patients with Systemic Lupus Erythematosus. PLoS One. 2015;10:e0134451.Acknowledgments:NoDisclosure of Interests:Dong Xu: None declared, Xinping Tian: None declared, Xiaofeng Zeng Consultant of: MSD Pharmaceuticals, Fengchun Zhang: None declared, Lin Zhao: None declared, Shangzhu Zhang: None declared, Jiaxin Zhou: None declared, Jiu-liang Zhao: None declared, Xiaodan Kong: None declared

SAT0060 Best Chance of Achieving Remission in RA Patients with Very Short Disease Duration:

2014 ◽  
Vol 73 (Suppl 2) ◽  
pp. 611.1-611
Author(s):  
T. Uhlig ◽  
V. Norvang ◽  
E. Lie ◽  
E. Rødevand ◽  
K. Mikkelsen ◽  
...  
Keyword(s):  
Disease Duration ◽  
Short Disease Duration

scholarly journals Fluconazole MIC and the Fluconazole Dose/MIC Ratio Correlate with Therapeutic Response among Patients with Candidemia

2005 ◽  
Vol 49 (8) ◽  
pp. 3171-3177 ◽  
Author(s):  
Cornelius J. Clancy ◽  
Victor L. Yu ◽  
Arthur J. Morris ◽  
David R. Snydman ◽  
M. Hong Nguyen
Keyword(s):  
Therapeutic Response ◽  
Geometric Mean ◽  
Therapeutic Failure ◽  
Response To Therapy ◽  
Success Rates ◽  
Therapeutic Success ◽  
Data Set ◽  
In Vitro Susceptibility ◽  
Dose Dependent

ABSTRACT We tested 32 Candida isolates recovered in the early 1990s from the bloodstreams of patients with candidemia for in vitro susceptibility to fluconazole and determined if MIC and/or the daily dose of fluconazole/MIC ratio correlated with the response to therapy. This is a unique data set since 87.5% (28/32) of patients were treated with fluconazole doses now considered to be inadequate (≤200 mg), which contributed to high therapeutic failure rates (53% [17/32]). The geometric mean MIC and dose/MIC ratio for isolates associated with therapeutic failure (11.55 μg/ml and 14.3, respectively) differed significantly from values associated with therapeutic success (0.95 μg/ml and 219.36 [P = 0.0009 and 0.0004, respectively]). The therapeutic success rates among patients infected with susceptible (MIC ≤ 8 μg/ml), susceptible-dose dependent (S-DD) (MIC = 16 or 32 μg/ml), and resistant (MIC ≥ 64 μg/ml) isolates were 67% (14/21), 20% (1/5), and 0% (0/6), respectively. A dose/MIC ratio >50 was associated with a success rate of 74% (14/19), compared to 8% (1/13) for a dose/MIC ratio ≤50 (P = 0.0003). Our data suggest that both fluconazole MIC and dose/MIC ratio correlate with the therapeutic response to fluconazole among patients with candidemia. In clinical practice, dose/MIC ratio might prove easier to interpret than breakpoint MICs, since it quantitates the effects of increasing fluconazole doses that are alluded to in the S-DD designation.

Epigenetics In Autoimmune Disease

2018 ◽  
Author(s):  
Matlock A Jeffries
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Autoimmune Disease ◽  
Noncoding Rna ◽  
Specific Treatment ◽  
Cell Types ◽  
Response To Therapy ◽  
Human Immune System ◽  
Treatment Regimens ◽  
New Research

Autoimmunity refers to a pathologic state of immunologic dysregulation in which the human immune system turns inward, attacking healthy tissues. The key step in this process is a break of self-immune tolerance. Recent studies have implicated dysregulation of gene expression via altered epigenetic control as a key mechanism in the development and promotion of autoimmunity. Epigenetics is defined as heritable changes in gene expression as a result of modification of DNA methylation, histone side chains, and noncoding RNA. Studies examining identical twins discordant for lupus, for example, were among the first to identify alterations in DNA methylation leading to lupus. Histone side-chain changes have been studied extensively in rheumatoid arthritis (RA), and many pathogenic cell types in RA exhibit a hyperacetylation phenotype. Finally, new research in the noncoding RNA field has not only uncovered potentially targetable pathways (e.g., miR-155) but may lead to the development of new diagnostic and prognostic biomarkers, helping physicians better tailor specific treatment regimens to improve response to therapy in autoimmune disease.   This review contains 4 figures, 1 table and 47 references Key Words: autoimmunity, big data, biomarkers, computational biology, DNA methylation, epigenetics, histone acetylation, histone methylation, microRNA, noncoding RNA

scholarly journals Germline genetic polymorphisms influence tumor gene expression and immune cell infiltration

2018 ◽  
Vol 115 (50) ◽  
pp. E11701-E11710 ◽  
Author(s):  
Yoong Wearn Lim ◽  
Haiyin Chen-Harris ◽  
Oleg Mayba ◽  
Steve Lianoglou ◽  
Arthur Wuster ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cancer Immunotherapy ◽  
Genetic Variants ◽  
Immune Cell ◽  
Response To Therapy ◽  
Cell Infiltration ◽  
Cancer Type ◽  
Immune Cell Infiltration ◽  
Durable Response ◽  
The Impact

Cancer immunotherapy has emerged as an effective therapy in a variety of cancers. However, a key challenge in the field is that only a subset of patients who receive immunotherapy exhibit durable response. It has been hypothesized that host genetics influences the inherent immune profiles of patients and may underlie their differential response to immunotherapy. Herein, we systematically determined the association of common germline genetic variants with gene expression and immune cell infiltration of the tumor. We identified 64,094 expression quantitative trait loci (eQTLs) that associated with 18,210 genes (eGenes) across 24 human cancers. Overall, eGenes were enriched for their being involved in immune processes, suggesting that expression of immune genes can be shaped by hereditary genetic variants. We identified the endoplasmic reticulum aminopeptidase 2 (ERAP2) gene as a pan-cancer type eGene whose expression levels stratified overall survival in a subset of patients with bladder cancer receiving anti–PD-L1 (atezolizumab) therapy. Finally, we identified 103 gene signature QTLs (gsQTLs) that were associated with predicted immune cell abundance within the tumor microenvironment. Our findings highlight the impact of germline SNPs on cancer-immune phenotypes and response to therapy; and these analyses provide a resource for integration of germline genetics as a component of personalized cancer immunotherapy.

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