High-throughput quantitative binding analysis of DNA aptamers using exonucleases.

Aptamers are nucleic acid bioreceptors that have been used in various applications including medical diagnostics and as therapeutic agents. Identifying the most optimal aptamer for a particular application is very challenging. Here, we for the first time have developed a high-throughput method for accurately quantifying aptamer binding affinity, specificity, and cross-reactivity via the kinetics of aptamer digestion by exonucleases. We demonstrate the utility of this approach by isolating a set of new aptamers for fentanyl and its analogs, and then characterizing the binding properties of 655 aptamer-ligand pairs using our exonuclease digestion assay and validating the results with gold-standard methodologies. These data were used to select optimal aptamers for the development of new sensors that detect fentanyl and its analogs in different analytical contexts. Our approach dramatically accelerates the aptamer characterization process and streamlines sensor development, and if coupled with robotics, could enable high-throughput quantitative analysis of thousands of aptamer-ligand pairs.

Comparison of Aptamer Signaling Mechanisms Reveals Disparities in Sensor Response and Strategies to Eliminate False Signals.

Aptamers are nucleic acid-based affinity reagents that have been incorporated into a variety of molecular sensor formats. However, many aptamer sensors exhibit insufficient sensitivity and specificity for real-world applications, and although considerable effort has been dedicated to improving sensitivity, sensor specificity has remained largely neglected and understudied. In this work, we have developed a series of sensors using aptamers for the small-molecule drugs flunixin, fentanyl, and furanyl fentanyl and compare their performance─in particular, focusing on their specificity. Contrary to expectations, we observe that sensors using the same aptamer operating under the same physicochemical conditions produce divergent responses to interferents depending on their signal transduction mechanism. For instance, aptamer beacon sensors are susceptible to false-positives from interferents that weakly associate with DNA, while strand-displacement sensors suffer from false-negatives due to interferent-associated signal suppression when both the target and interferent are present. Biophysical analyses suggest that these effects arise from aptamer-interferent interactions that are either nonspecific or induce aptamer conformational changes that are distinct from those induced by true target-binding events. We also demonstrate strategies for improving the sensitivity and specificity of aptamer sensors with the development of a "hybrid beacon," wherein the incorporation of a complementary DNA competitor into an aptamer beacon selectively hinders interferent─but not target─binding and signaling, while simultaneously overcoming signal suppression by interferents. Our results highlight the need for systematic and thorough testing of aptamer sensor response and new aptamer selection methods that optimize specificity more effectively than traditional counter-SELEX.

Cancer incidence in immunocompromised patients: a single-center cohort study.

BACKGROUND: Diminished immune defense plays an important role in cancer development. Cancer risk in immunocompromised patients may differ. Identifying individuals with elevated cancer risk can inform strategies for routine cancer screening. This study aimed to understand and compare cancer incidence and risk in three patient groups: recipients of solid organ transplant (SOT) or hematopoietic stem cell transplant (HSCT); diagnosis of primary or secondary immunodeficiency disorder (PID/SID); and recipients of tumor necrosis factor inhibitor (TNF-i) therapy. METHODS: This retrospective cohort study used the University of Utah Health System database and Huntsman Cancer Institute tumor registry. Patients aged ≥18 years with SOT/HSCT, PID/SID or ≥ 3 months of TNF-i therapy were included. The date of transplant, diagnosis of PID/SID, or 1st TNF-i medication order date was defined as the index date. We calculated cumulative cancer incidence by Kaplan-Meier method. A Cox-proportional hazard regression model with a stepwise variable selection process was used to identify independent risk factors associated with the time to onset of a new primary cancer. RESULTS: In total, 13,887 patients were included which comprised of 2982 (21%) SOT/HSCT, 7542 (54%) PID/SID and 3363 (24%) patients receiving TNF-i. The mean (SD) age ranged from 46.8 (15) years - 50.4 (18.2) years. The proportion of white patients ranged from 72.3-84.8%. The estimated cumulative cancer incidence was 11.5% in the SOT/HSCT cohort, 14.3% in the PID/SID cohort, and 8.8% in the TNF-i cohort. The multivariable model adjusted for age, benign in-situ disease, Charlson Comorbidity Index, hypertension/cardiovascular disease/end stage renal disease, gender, race/ethnicity, and renal cyst as significant risk factors. The adjusted hazard ratios for cancer development in SOT/HSCT and PID/SID cohorts compared to the TNF-i cohort over the full follow-up period were 1.57 (95% CI: 1.16-2.13) and 2.14 (95% CI: 1.65-2.77), respectively. CONCLUSION: A significantly increased risk of cancer was observed in PID/SID patients and SOT/HSCT patients compared to TNF-i patients. Age ≥ 50 years, male gender, and clinical comorbidities were additional factors impacting cancer risk. PID/SID and SOT/HSCT patients may benefit from more intensive cancer screening.

Caregiver survey in glioblastoma focused on cognitive dysfunction: development and results from a multicenter study.

Aim: To develop a cognitive dysfunction (CD) focused questionnaire to evaluate caregiver burden in glioblastoma. Materials & methods: The survey was developed from stakeholder consultations and a pilot study, and disseminated at eight US academic cancer centers. Caregivers self-reported caring for an adult with glioblastoma and CD. Results: The 89-item survey covered demographics, CD symptoms and caregiver burden domains. Among 185 caregivers, most were white, educated females and reported memory problems as the most common CD symptom. An exposure-effect was observed, with increase in number of CD symptoms significantly associated with greater caregiver burden. Conclusion: This questionnaire could guide caregiver interventions and be adapted for use longitudinally, in community cancer settings, and in patients with brain metastases.

Glioblastoma (GBM) is a very aggressive brain cancer. People who have GBM have trouble remembering things and are unable to do things they used to do. These changes can be very hard. Researchers are trying to better understand what it is like for people who take care of people with GBM (or caregivers). In this study, researchers created a new survey for caregivers. The survey included questions about what caregivers see happening in their loved one with GBM. Caregivers said that memory problems were common. Also, when the patient had more problems the caregiver had a harder time, too. Researchers hope to improve the survey and use it in the future for more studies.

Caregiver burden by treatment and clinical characteristics of patients with glioblastoma.

BACKGROUND: Glioblastoma is an incurable disease with a poor prognosis. For caregivers of people with glioblastoma, the burden of care can be high. Patients often present with different clinical characteristics, which may impact caregiver burden in different ways. This study aimed to evaluate associations between patient clinical characteristics and caregiver burden/quality of life (QoL). METHODS: Caregiver-patient dyads were enrolled at 7 academic cancer centers in the United States. Eligible caregiver participants were self-reported as the primary caregiver of an adult living with glioblastoma and completed a caregiver burden survey. Eligible patients were age ≥ 18 years at glioblastoma diagnosis and alive when their respective caregiver entered the study, with the presence of cognitive dysfunction confirmed by the caregiver. Data were analyzed with descriptive statistics and multivariable analyses. RESULTS: The final cohort included 167 dyads. Poor patient performance status resulted in patient difficulty with mental tasks, more caregiving tasks, and increased caregiving time. Language problems were reported in patients with left-sided lesions. Patient confusion was negatively associated with all caregiver domains: emotional health, social health, general health, ability to work, confidence in finances, and overall QoL. Better caregiver QoL was observed in patients with frontal lobe lesions versus non-frontal lobe lesions. CONCLUSION: This study reinforced that patient performance status is a critical clinical factor that significantly affects caregiver burden, caregiving tasks, and caregiver time. Additionally, patient confusion affects multiple facets of caregiver burden/QoL. These results could be used to support guided intervention for caregiver support, customized to the patient experience.

Malnutrition as a potential predictor of mortality in chronic kidney disease patients on dialysis: A systematic review and meta-analysis.

BACKGROUND & AIMS: Malnutrition, a significant problem in patients with chronic kidney disease (CKD), is linked to lower health-related quality of life, longer and more frequent hospital admissions, worse functional capacity, and higher levels of morbidity. However, the extent of its impact on mortality is poorly elucidated. This systematic review and meta-analysis aimed to investigate the impact of malnutrition on mortality among CKD patients on dialysis. METHODS: This meta-analysis was designed and performed in accordance with the PRISMA guidelines (CRD42023394584). A systematic electronic literature search was conducted in PubMed, ScienceDirect, and Embase to identify relevant cohort studies. The studies that reported nutritional status and its impact on mortality in patients were considered for analysis. The generic inverse variance method was used to pool the hazard ratio effect estimates by employing a random effects model. The Newcastle-Ottawa scale was used for the quality assessment. The statistical analysis was performed by utilizing RevMan and CMA 2.0. RESULTS: A total of 29 studies that comprised 11,063 patients on dialysis whose nutritional status was evaluated were eligible for quantitative analysis. Based on a comparison between the "malnutrition" category and the reference "normal nutrition status" category, the results showed that the overall pooled hazard risk (HR) for mortality was (HR 1.49, 95% CI: 1.36-1.64, p < 0.0001). According to the subgroup analysis, the hemodialysis subgroup had greater mortality hazards (HR 1.53; 95% CI 1.38-1.70, p < 0.0001), compared to the peritoneal dialysis subgroup (HR 1.26; 95% CI 1.15-1.37, p < 0.00001). Additionally, the overall incidence of mortality was explored but the authors were unable to combine the results due to limitations with the data. CONCLUSION: The findings conclude that malnutrition is a strong predictor of mortality among patients on dialysis, with the hemodialysis subgroup having a higher mortality hazard compared to the peritoneal dialysis subgroup. The results of this study will advocate for early nutritional evaluation and timely dietary interventions to halt the progression of CKD and death.

Clinical characteristics and treatment patterns of patients with NTRK fusion-positive solid tumors: A multisite cohort study at US academic cancer centers.

BACKGROUND: Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are rare oncogenic drivers prevalent in 0.3% of solid tumors. They are most common in salivary gland cancer (2.6%), thyroid cancer (1.6%), and soft-tissue sarcoma (1.5%). Currently, there are 2 US Food and Drug Administration-approved targeted therapies for NTRK gene fusions: larotrectinib, approved in 2018, and entrectinib, approved in 2019. To date, the real-world uptake of tyrosine receptor kinase inhibitor (TRKi) use for NTRK-positive solid tumors in academic cancer centers remains largely unknown. OBJECTIVE: To describe the demographics, clinical and genomic characteristics, and testing and treatment patterns of patients with NTRK-positive solid tumors treated at US academic cancer centers. METHODS: This was a retrospective chart review study conducted in academic cancer centers in the United States. All patients diagnosed with an NTRK fusion-positive (NTRK1, NTRK2, NTRK3) solid tumor (any stage) and who received cancer treatment at participating sites between January 1, 2012, and July 1, 2023, were included in this study. Patient demographics, clinical characteristics, genomic characteristics, NTRK testing data, and treatment patterns were collected from electronic medical records and analyzed using descriptive statistics as appropriate. RESULTS: In total, 6 centers contributed data for 55 patients with NTRK-positive tumors. The mean age was 49.3 (SD = 20.5) years, 51% patients were female, and the majority were White (78%). The median duration of time from cancer diagnosis to NTRK testing was 85 days (IQR = 44-978). At the time of NTRK testing, 64% of patients had stage IV disease, compared with 33% at cancer diagnosis. Prevalent cancer types in the overall cohort included head and neck (15%), thyroid (15%), brain (13%), lung (13%), and colorectal (11%). NTRK1 fusions were most common (45%), followed by NTRK3 (40%) and NTRK2 (15%). Across all lines of therapy, 51% of patients (n = 28) received a TRKi. Among TRKi-treated patients, 71% had stage IV disease at TRKi initiation. The median time from positive NTRK test to initiation of TRKi was 48 days (IQR = 9-207). TRKis were commonly given as first-line (30%) or second-line (48%) therapies. Median duration of therapy was 610 (IQR = 182-764) days for TRKi use and 207.5 (IQR = 42-539) days for all other first-line therapies. CONCLUSIONS: This study reports on contemporary real-world NTRK testing patterns and use of TRKis in solid tumors, including time between NTRK testing and initiation of TRKi therapy and duration of TRKi therapy.

Suite of Aptamer-Based Sensors for the Detection of Fentanyl and Its Analogues.

Fentanyl and its analogues are potent synthetic opioids that are commonly abused and are currently the number one cause of drug overdose death in the United States. The ability to detect fentanyl with simple, rapid, and low-cost tools is crucial for forensics, medical care, and public safety. Conventional on-site testing options for fentanyl detection─including chemical spot tests, lateral-flow immunoassays, and portable Raman spectrometers─each have their own unique flaws that limit their analytical utility. Here, we have developed a series of new aptamer-based assays and sensors that can detect fentanyl as well as several of its analogues in a reliable, accurate, rapid, and economic manner. These include colorimetric, fluorescent, and electrochemical sensors, which can detect and quantify minute quantities of fentanyl and many of its analogues with no response to other illicit drugs, cutting agents, or adulterants─even in interferent-ridden binary mixtures containing as little as 1% fentanyl. Given the high performance of these novel analytical tools, we foresee the potential for routine use by medical and law enforcement personnel as well as the general public to aid in rapid and accurate fentanyl identification.

Patient Perspectives on the Use of Digital Technology to Help Manage Cystic Fibrosis.

Background: Digital health technologies (DHTs) have shown potential to improve health outcomes through improved medication adherence in different disease states. Cystic fibrosis (CF) requires care coordination across pharmacies, patients, and providers. DHTs can potentially support patients, providers, and pharmacists in diseases like CF, where high medication burden can negatively impact patient quality of life and outcomes. Methods: In this prospective cohort study, a CF-specific mobile application (Phlo) was distributed to adults with CF who received care at the University of Utah Cystic Fibrosis Center, used an iPhone, and filled prescriptions through the University of Utah Specialty Pharmacy services. Participants were asked to use Phlo for 90 days with an optional 90-day extension period. Participants completed four surveys at baseline and after 90 days. Changes in patient-reported outcomes, adherence, clinical outcomes, and healthcare resource utilization from baseline to 90 days were tracked. Results: Phlo allowed users to track daily regimen activities, contact their care team, receive medication delivery reminders, and share progress with their healthcare team. A web-based dashboard allowed the care team to review reported performance scores from the app. Most patients (67%) said the app improved confidence in and motivation for continuing their regimen. The most important reported benefit of Phlo was having a single location to manage their whole routine. Conclusions: Phlo is a mobile health technology designed to help patients with CF manage their treatment regimen and improve patient-provider communication.

The implementation of value-based frameworks, clinical care pathways, and alternative payment models for cancer care in the United States.

BACKGROUND: Cancer treatment is a significant driver of rising health care costs in the United States, where the annual cost of cancer care is estimated to reach $246 billion in 2030. As a result, cancer centers are considering moving away from fee-for-service models and transitioning to value-based care models, including value-based frameworks (VBFs), clinical care pathways (CCPs), and alternative payment models (APMs). OBJECTIVE: To assess the barriers and motivations for using value-based care models from the perspectives of physicians and quality officers (QOs) at US cancer centers. METHODS: Sites were recruited from cancer centers in the Midwest, Northeast, South, and West regions in a 15/15/20/10 relative distribution. Cancer centers were identified based on prior research relationships and known participation in the Oncology Care Model or other APMs. Based on a literature search, multiple choice and open-ended questions were developed for the survey. A link to the survey was emailed to hematologists/oncologists and QOs at academic and community cancer centers from August to November 2020. Results were summarized using descriptive statistics. RESULTS: A total of 136 sites were contacted; 28 (21%) centers returned completed surveys, which were included in the final analysis. 45 surveys (23 from community centers, 22 from academic centers) were completed: 59% (26/44), 76% (34/45), and 67% (30/45) of physicians/QOs respondents had used or implemented a VBF, CCP, and APM, respectively. The top motivator for VBF use was "producing real-world data for providers, payers, and patients" (50% [13/26]). Among those not using CCPs, the most common barrier was a "lack of consensus on pathway choices" (64% [7/11]). For APMs, the most common difficulty was that "innovations in health care services and therapies must be adopted at the site's own financial risk" (27% [8/30]). CONCLUSIONS: The ability to measure improvements in cancer health outcomes was a large motivator for implementing value-based models. However, heterogeneity in practice size, limited resources, and potential increase in costs were possible barriers to implementation. Payers need to be willing to negotiate with cancer centers and providers to implement the payment model that will most benefit patients. The future integration of VBFs, CCPs, and APMs will depend on reducing the complexity and burden of implementation. DISCLOSURES :Dr Panchal was affiliated with the University of Utah at the time this study was conducted and discloses current employment with ZS. Dr McBride discloses employment with Bristol Myers Squibb. Dr Huggar and Dr Copher report employment, stock, and other ownership interests in Bristol Myers Squibb. The other authors have no competing interests to disclose. This study was funded by an unrestricted research grant from Bristol Myers Squibb to the University of Utah.

Applying diagnosis support systems in electronic health records to identify wild-type transthyretin amyloid cardiomyopathy risk.

Aim: Wild-type transthyretin amyloid cardiomyopathy (ATTRwt-CM) is frequently misdiagnosed, and delayed diagnosis is associated with substantial morbidity and mortality. At three large academic medical centers, combinations of phenotypic features were implemented in electronic health record (EHR) systems to identify patients with heart failure at risk for ATTRwt-CM. Methods: Phenotypes/phenotype combinations were selected based on strength of correlation with ATTRwt-CM versus non-amyloid heart failure; different clinical decision support and reporting approaches and data sources were evaluated on Cerner and Epic EHR platforms. Results: Multiple approaches/sources showed potential usefulness for incorporating predictive analytics into the EHR to identify at-risk patients. Conclusion: These preliminary findings may guide other medical centers in building and implementing similar systems to improve recognition of ATTRwt-CM in patients with heart failure.

Real-world survival analysis by tumor mutational burden in non-small cell lung cancer: a multisite U.S. study.

BACKGROUND: Tumor mutational burden (TMB) is a potential biomarker to predict tumor response to immuno-oncology agents in patients with metastatic non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: A multi-site cohort study evaluated patients diagnosed with stage IV NSCLC between 2012 and 2019 who had received comprehensive genomic profiling (CGP) and any NSCLC-related treatment at 9 U.S. cancer centers. Baseline characteristics and clinical outcomes were compared between patients with TMB <10 and TMB ≥10. RESULTS: Among the 667 patients with CGP results, most patients received CGP from Foundation Medicine (64%) or Caris (20%). Patients with TMB ≥10 (vs. TMB <10) were associated with a positive smoking history. TMB was associated with ALK (p = 0.01), EGFR (p < 0.01), and TP53 (p < 0.05) alterations. TMB >10 showed a significant association towards longer overall survival (OS) (HR: 0.43, 95% CI: 0.21-0.88, p = 0.02) and progression-free survival (PFS) (HR: 0.43, 95% CI: 0.21-0.85, p = 0.02) in patients treated with first-line immunotherapy and tested by Foundation Medicine or Caris at treatment initiation. CONCLUSIONS: TMB levels greater than or equal to 10 mut/Mb, when tested by Foundation Medicine or Caris at treatment initiation, were significantly associated with improved OS and PFS among patients treated with first-line immunotherapy-containing regimens. Additional prospective research is warranted to validate this biomarker along with PD-L1 expression.

Tumor mutational burden in lung cancer: a systematic literature review.

Purpose: To assess the association of tumor mutational burden (TMB) with clinical outcomes, other biomarkers and patient/disease characteristics in patients receiving therapy for lung cancer. Results: In total, 4,303 publications were identified; 81 publications were included. The majority of publications assessing clinical efficacy of immunotherapy reported an association with high TMB, particularly when assessing progression-free survival and objective response rate. High TMB was consistently associated with TP53 alterations, and negatively associated with EGFR mutations. High TMB was also associated with smoking, squamous cell non-small cell lung carcinoma, and being male. Methods: A systematic literature review based upon an a priori protocol was conducted following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Cochrane methodologies. Searches were conducted in EMBASE, SCOPUS, Ovid MEDLINE®, and Emcare (from January 2012 until April 2018) and in two clinical trial registries. Conference abstracts were identified in EMBASE, and in targeted searches of recent major conference proceedings (from January 2016 until April 2018). Publications reporting data in patients receiving therapy for lung cancer that reported TMB and its association with clinical efficacy, or with other biomarkers or patient/disease characteristics, were included. Results are presented descriptively. Conclusion: This systematic literature review identified several clinical outcomes, biomarkers, and patient/disease characteristics associated with high TMB, and highlights the need for standardized definitions and testing practices. Further studies using standardized methodology are required to inform treatment decisions.

Clinical and economic analysis of patients with acute myeloid leukemia by FLT3 status and midostaurin use at a Comprehensive Cancer Center.

INTRODUCTION: Identification of cytogenetic and molecular abnormalities has become vital for the appropriate treatment of acute myeloid leukemia (AML). One of the most common molecular alterations in AML is the constitutive activation by internal tandem duplication of FMS-like tyrosine kinase 3 (FLT3). METHODS: This observational, retrospective, cohort study at the Huntsman Cancer Institute (HCI) had two time periods: 1) a historical pre-midostaurin time period which consisted of the FLT3 mutated (FLT3m) and FLT3 wild type (FLT3wt) cohorts from January 1, 2007, to December 31, 2016, and 2) a post-midostaurin cohort which consisted of the FLT3 mutated midostaurin-user cohort (early mido) from May 01, 2017 to December 31, 2018. RESULTS: In total, 39 patients were included in the FLT3m cohort, 61 in the FLT3wt cohort, and seven in the early mido cohort. FLT3m patients spent fewer days in the hospital during the first consolidation regimen and received fewer consolidation cycles compared to FLT3wt patients. Overall survival (OS) was similar between FLT3m and FLT3wt patients. For patients without hematopoietic stem cell transplant, OS was significantly shorter for FLT3m patients compared to FLT3wt patients. Mean AML related inpatient charges and physician charges for FLT3m patients were significantly higher than FLT3wt patients. CONCLUSION: The FLT3 mutation is historically associated with a shorter time to transplant and increased total health care charges. More information is needed to evaluate the real-world treatment strategies for FLT3-mutated patients in the presence of FLT3 inhibitors and the impact of these treatment strategies on clinical and economic outcomes.