Browsing by Author "Bakoyannis, Giorgos"
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Item An activated Th17-prone T cell subset involved in chronic graft-versus-host disease sensitive to pharmacological inhibition(American Society for Clinical Investigation, 2017-06-15) Forcade, Edouard; Paz, Katelyn; Flynn, Ryan; Griesenauer, Brad; Amet, Tohti; Li, Wei; Liu, Liangyi; Bakoyannis, Giorgos; Jiang, Di; Chu, Hong Wei; Lobera, Mercedes; Yang, Jianfei; Wilkes, David S.; Du, Jing; Gartlan, Kate; Hill, Geoffrey R.; MacDonald, Kelli P.A.; Espada, Eduardo L.; Blanco, Patrick; Serody, Jonathan S.; Koreth, John; Cutler, Corey S.; Antin, Joseph H.; Soiffer, Robert J.; Ritz, Jerome; Paczesny, Sophie; Blazar, Bruce R.; Pediatrics, School of MedicineChronic graft-versus-host disease (cGvHD) remains a major complication of allogeneic stem cell transplantation requiring novel therapies. CD146 and CCR5 are expressed by activated T cells and associated with increased T cell migration capacity and Th17 polarization. We performed a multiparametric flow cytometry analysis in a cohort of 40 HSCT patients together with a cGvHD murine model to understand the role of CD146-expressing subsets. We observed an increased frequency of CD146+ CD4 T cells in the 20 patients with active cGvHD with enhanced RORγt expression. This Th17-prone subset was enriched for cells coexpressing CD146 and CCR5 that harbor mixed Th1/Th17 features and were more frequent in cGvHD patients. Utilizing a murine cGvHD model with bronchiolitis obliterans (BO), we observed that donor T cells from CD146-deficient mice versus those from WT mice caused significantly reduced pulmonary cGvHD. Reduced cGvHD was not the result of failed germinal center B cell or T follicular helper cell generation. Instead, CD146-deficient T cells had significantly lower pulmonary macrophage infiltration and T cell CCR5, IL-17, and IFN-γ coexpression, suggesting defective pulmonary end-organ effector mechanisms. We, thus, evaluated the effect of TMP778, a small-molecule RORγt activity inhibitor. TMP778 markedly alleviated cGvHD in murine models similarly to agents targeting the Th17 pathway, such as STAT3 inhibitor or IL-17-blocking antibody. Our data suggest CD146-expressing T cells as a cGvHD biomarker and suggest that targeting the Th17 pathway may represent a promising therapy for cGvHD.Item An Analysis of Survival Data when Hazards are not Proportional: Application to a Cancer Treatment Study(2021-12) White, John Benjamin; Yiannoutsos, Constantin; Bakoyannis, Giorgos; Fadel, WilliamThe crossing of Kaplan-Meier survival curves presents a challenge when conducting survival analysis studies, making it unclear whether any of the study groups involved present any significant difference in survival. An approach involving the determination of maximum vertical distance between the curves is considered here as a method to assess whether a survival advantage exists between different groups of patients. The method is illustrated on a dataset containing survival times of patients treated with two cancer treatment regimes, one involving treatment by chemotherapy alone, and the other by treatment with both chemotherapy and radiotherapy.Item Antigen-specific T cell responses correlate with decreased occurrence of acute GVHD in a multicenter contemporary cohort(Springer Nature, 2022) Cruz, Conrad Russell Y.; Bo, Na; Bakoyannis, Giorgos; Wright, Kaylor E.; Chorvinsky, Elizabeth A.; Powell, Allison; Bollard, Catherine M.; Jacobsohn, David; Cooke, Kenneth R.; Duncan, Christine; Krance, Robert M.; Carpenter, Paul A.; Rowan, Courtney M.; Paczesny, Sophie; Biostatistics and Health Data Science, Richard M. Fairbanks School of Public HealthItem Bayesian Adaptive Dose-Finding Clinical Trial Designs with Late-Onset Outcomes(2021-07) Zhang, Yifei; Zhang, Yong; Song, Yiqing; Liu, Hao; Bakoyannis, GiorgosThe late-onset outcome issue is common in early phase dose- nding clinical trials. This problem becomes more intractable in phase I/II clinical trials because both toxicity and e cacy responses are subject to the late-onset outcome issue. The existing methods applying for the phase I trials cannot be used directly for the phase I/II trial due to a lack of capability to model the joint toxicity{e cacy distribution. We propose a conditional weighted likelihood (CWL) method to circumvent this issue. The key idea of the CWL method is to decompose the joint probability into the product of marginal and conditional probabilities and then weight each probability based on each patient's actual follow-up time. We further extend the proposed method to handle more complex situations where the late-onset outcomes are competing risks or semicompeting risks outcomes. We treat the late-onset competing risks/semi-competing risks outcomes as missing data and develop a series of Bayesian data-augmentation methods to e ciently impute the missing data and draw the posterior samples of the parameters of interest. We also propose adaptive dose- nding algorithms to allocate patients and identify the optimal biological dose during the trial. Simulation studies show that the proposed methods yield desirable operating characteristics and outperform the existing methods.Item Building Prediction Models for Dementia: The Need to Account for Interval Censoring and the Competing Risk of Death(2019-08) Marchetti, Arika L.; Bakoyannis, Giorgos; Li, Xiaochun; Gao, Sujuan; Yiannoutsos, ConstantinContext. Prediction models for dementia are crucial for informing clinical decision making in older adults. Previous models have used genotype and age to obtain risk scores to determine risk of Alzheimer’s Disease, one of the most common forms of dementia (Desikan et al., 2017). However, previous prediction models do not account for the fact that the time to dementia onset is unknown, lying between the last negative and the first positive dementia diagnosis time (interval censoring). Instead, these models use time to diagnosis, which is greater than or equal to the true dementia onset time. Furthermore, these models do not account for the competing risk of death which is quite frequent among elder adults. Objectives. To develop a prediction model for dementia that accounts for interval censoring and the competing risk of death. To compare the predictions from this model with the predictions from a naïve analysis that ignores interval censoring and the competing risk of death. Methods. We apply the semiparametric sieve maximum likelihood (SML) approach to simultaneously model the cumulative incidence function (CIF) of dementia and death while accounting for interval censoring (Bakoyannis, Yu, & Yiannoutsos, 2017). The SML is implemented using the R package intccr. The CIF curves of dementia are compared for the SML and the naïve approach using a dataset from the Indianapolis Ibadan Dementia Project. Results. The CIF from the SML and the naïve approach illustrated that for healthier individuals at baseline, the naïve approach underestimated the incidence of dementia compared to the SML, as a result of interval censoring. Individuals with a poorer health condition at baseline have a CIF that appears to be overestimated in the naïve approach. This is due to older individuals with poor health conditions having an elevated risk of death. Conclusions. The SML method that accounts for the competing risk of death along with interval censoring should be used for fitting prediction/prognostic models of dementia to inform clinical decision making in older adults. Without controlling for the competing risk of death and interval censoring, the current models can provide invalid predictions of the CIF of dementia.Item Comparison of nonlinear curves and surfaces(Elsevier, 2020-10) Zhao, Shi; Bakoyannis, Giorgos; Lourens, Spencer; Tu, Wanzhu; Biostatistics, School of Public HealthEstimation of nonlinear curves and surfaces has long been the focus of semiparametric and nonparametric regression analysis. What has been less studied is the comparison of nonlinear functions. In lower-dimensional situations, inference typically involves comparisons of curves and surfaces. The existing comparative procedures are subject to various limitations, and few computational tools have been made available for off-the-shelf use. To address these limitations, two modified testing procedures for nonlinear curve and surface comparisons are proposed. The proposed computational tools are implemented in an R package, with a syntax similar to that of the commonly used model fitting packages. An R Shiny application is provided with an interactive interface for analysts who do not use R. The new tests are consistent against fixed alternative hypotheses. Theoretical details are presented in an appendix. Operating characteristics of the proposed tests are assessed against the existing methods. Applications of the methods are illustrated through real data examples.Item Confirmatory factor analysis of the Insomnia Severity Index (ISI) and invariance across race: a pooled analysis of MsFLASH data(Wolters Kluwer, 2019-08-01) Otte, Julie L.; Bakoyannis, Giorgos; Rand, Kevin L.; Ensrud, Kristine E.; Guthrie, Katherine A.; Joffe, Hadine; McCurry, Susan M.; Newton, Kathrine M.; Carpenter, Janet S.; School of NursingObjective: Women's sleep at menopause is widely reported to be problematic. The Insomnia Severity Index is a commonly used tool for quantifying sleep problems in clinical and research settings, but psychometric properties in menopausal women have not been reported. Our study aim was to examine the factor structure of the Insomnia Severity Index in a large and diverse sample of midlife women with hot flashes. Methods: Baseline data were from 899 women enrolled in one of the three clinical trials using similar entry criteria conducted by the Menopause Strategies Finding Lasting Answers to Symptoms and Health (MsFLASH) research network. We conducted confirmatory factor analyses for the total sample and within strata defined by race/ethnicity (Black and White women). Results: The Insomnia Severity Index had two factors in the total sample. The 2-factor structure was consistent across Black and White women, with the exception of one item “Difficulty falling asleep”. Conclusions: The Insomnia Severity Index in midlife women with hot flashes is composed of two factors that capture dimensions of the insomnia severity and daytime impact. The instrument is a psychometrically sound scale appropriate for use in research and clinical practice to capture the severity and daytime impact of insomnia symptoms in diverse samples of midlife women with hot flashes. An abbreviated screening of two items could be considered to determine if further evaluation is needed of sleep complaints.Item Contemporary Outcomes of Distal Lower Extremity Bypass for Chronic Limb Threatening Ischemia and a Model Based Comparison with Non-surgical Therapies(2021-03) Leckie, Katherin; Bakoyannis, Giorgos; Yiannoutsos, Constantin; Murphy, MichaelObjective: Gold standard therapy for chronic limb threatening ischemia (CLTI) is revascularization but in patients in whom below-the-knee bypass is indicated autologous vein conduit may not be available. Contemporary outcomes of distal bypass with suboptimal conduits have not been well described and recent advances in non-surgical therapies raise the question of whether in some cases there is evidence that these should be considered. Methods: Data was obtained from the Vascular Quality Initiative (VQI) registry as well as from a multi-center, randomized clinical trial of cell therapy. Incidence of major amputation after distal bypass was estimated for the VQI cohort by conduit type using non-parametric survival analysis with death as a competing risk. A cox proportional hazards model was then fit to the pooled data in a stepwise fashion with death as a competing risk, including evaluations for appropriate transformation, time dependency and interactions for each included covariate, and hazard ratios were estimated for the risk of major amputation by treatment. Results: At 365 days, the estimated cumulative incidence of major amputation with death as a competing risk is 25% after distal bypass with non-autologous biologic conduit (0.2499, 95% CI 0.2242 - 0.2785), 13% for prosthetic (0.1276, 95% CI 0.1172 - 0.1389) and 9% for GSV (0.0900, 95% CI 0.0848 - 0.0956). The cox proportional hazards model found a significant interaction between age and treatment. Compared to bypass with non-autogenous biologic, the hazard ratios for bypass with GSV were 0.41 (p<0.0001), 0.41 (p<0.0001), 0.42 (p<0.0001) and 0.42 (p<0.0001) respectively at ages 55, 60, 65 and 70 and for bypass with prosthetic were 0.68 (p=0.0043), 0.67 (p=0.0004), 0.65 (p<0.0001) and 0.64 (p<0.0001) respectively and for autologous cell therapy 0.22 (p=0.0005), 0.34 (p=0.0011), 0.52 (p=0.0196) and 0.76 (p=0.3677) respectively. No significant differences were found between best medical management and distal bypass with non-autologous biologic. Conclusion: The risk of major amputation after distal bypass is lowest in patients with GSV conduit and highest following bypass with non-autologous biologic. Using a semi-parametric model, cell therapy was estimated to significantly decrease the risk of amputation compared to distal bypass with non-autologous biologic conduit in younger patients.Item COVID-19 Diagnosis and Risk of Death Among Adults With Cancer in Indiana: Retrospective Cohort Study(JMIR Publications, 2022-10-06) Valvi, Nimish; Patel, Hetvee; Bakoyannis, Giorgos; Haggstrom, David A.; Mohanty, Sanjay; Dixon, Brian E.; Surgery, School of MedicineBackground: Prior studies, generally conducted at single centers with small sample sizes, found that individuals with cancer experience more severe outcomes due to COVID-19, caused by SARS-CoV-2 infection. Although early examinations revealed greater risk of severe outcomes for patients with cancer, the magnitude of the increased risk remains unclear. Furthermore, prior studies were not typically performed using population-level data, especially those in the United States. Given robust prevention measures (eg, vaccines) are available for populations, examining the increased risk of patients with cancer due to SARS-CoV-2 infection using robust population-level analyses of electronic medical records is warranted. Objective: The aim of this paper is to evaluate the association between SARS-CoV-2 infection and all-cause mortality among recently diagnosed adults with cancer. Methods: We conducted a retrospective cohort study of newly diagnosed adults with cancer between January 1, 2019, and December 31, 2020, using electronic health records linked to a statewide SARS-CoV-2 testing database. The primary outcome was all-cause mortality. We used the Kaplan-Meier estimator to estimate survival during the COVID-19 period (January 15, 2020, to December 31, 2020). We further modeled SARS-CoV-2 infection as a time-dependent exposure (immortal time bias) in a multivariable Cox proportional hazards model adjusting for clinical and demographic variables to estimate the hazard ratios (HRs) among newly diagnosed adults with cancer. Sensitivity analyses were conducted using the above methods among individuals with cancer-staging information. Results: During the study period, 41,924 adults were identified with newly diagnosed cancer, of which 2894 (6.9%) tested positive for SARS-CoV-2. The population consisted of White (n=32,867, 78.4%), Black (n=2671, 6.4%), Hispanic (n=832, 2.0%), and other (n=5554, 13.2%) racial backgrounds, with both male (n=21,354, 50.9%) and female (n=20,570, 49.1%) individuals. In the COVID-19 period analysis, after adjusting for age, sex, race or ethnicity, comorbidities, cancer type, and region, the risk of death increased by 91% (adjusted HR 1.91; 95% CI 1.76-2.09) compared to the pre-COVID-19 period (January 1, 2019, to January 14, 2020) after adjusting for other covariates. In the adjusted time-dependent analysis, SARS-CoV-2 infection was associated with an increase in all-cause mortality (adjusted HR 6.91; 95% CI 6.06-7.89). Mortality increased 2.5 times among adults aged 65 years and older (adjusted HR 2.74; 95% CI 2.26-3.31) compared to adults 18-44 years old, among male (adjusted HR 1.23; 95% CI 1.14-1.32) compared to female individuals, and those with ≥2 chronic conditions (adjusted HR 2.12; 95% CI 1.94-2.31) compared to those with no comorbidities. Risk of mortality was 9% higher in the rural population (adjusted HR 1.09; 95% CI 1.01-1.18) compared to adult urban residents. Conclusions: The findings highlight increased risk of death is associated with SARS-CoV-2 infection among patients with a recent diagnosis of cancer. Elevated risk underscores the importance of adhering to social distancing, mask adherence, vaccination, and regular testing among the adult cancer population.Item Development and Testing of the Dysmenorrhea Symptom Interference (DSI) Scale(2020-07-17) Chen, Chen X.; Murphy, Tabitha; Ofner, Susan; Yahng, Lilian; Krombach, Peter; LaPradd, Michelle; Bakoyannis, Giorgos; Carpenter, Janet S.; School of NursingDysmenorrhea affects most reproductive-age women and increases the risk of future pain. To evaluate dysmenorrhea interventions, validated outcome measures are needed. In this two-phase study, we developed and tested the dysmenorrhea symptom interference scale. During the scale-development phase (n = 30), we created a nine-item scale based on qualitative data from cognitive interviews. During the scale-testing phase (n = 686), we evaluated reliability, validity, and responsiveness to change. The scale measures how dysmenorrhea symptoms interfere with physical, mental, and social activities. Internal consistency was strong with Cronbach's α > 0.9. Test-retest reliability was acceptable (r = 0.8). The scale showed satisfactory content validity, construct validity (supported by confirmatory factor analysis), concurrent validity, and responsiveness to change. The minimally important difference was 0.3 points on a scale with a possible total score ranging from 1 to 5. This new psychometrically sound scale can be used in research and clinical practice to facilitate the measurement and management of dysmenorrhea.