An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release.

ABTRACT: Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays.

FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.

Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.

FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.

Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from the existing dataset, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues-of-origin directly from plasma whole-genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow-coverage WGS and whole-genome bisulfite sequencing (WGBS) data.

Results of Leveraging Pharmaceutical Patient Assistance Programs to Expand Access to High Cost Medications in a Student-Run Free Clinic.

High costs make many medications inaccessible to patients in the United States. Uninsured and underinsured patients are disproportionately affected. Pharmaceutical companies offer patient assistance programs (PAPs) to lower the cost-sharing burden of expensive prescription medications for uninsured patients. PAPs are used by various clinics, particularly oncology clinics and those caring for underserved communities, to expand patients' access to medications. Prior studies describing the implementation of PAPs in student-run free clinics have demonstrated cost-savings during the first few years of using PAPs. However, there is a lack of data regarding the efficacy and cost savings of longitudinal use of PAPs across several years. This study describes the growth of PAP use at a student-run free clinic in Nashville, Tennessee over ten years, demonstrating that PAPs can be used reliably and sustainably to expand patients' access to expensive medications. From 2012 to 2021, we increased the number of medications available through PAPs from 8 to 59 and the number of patient enrollments from 20 to 232. In 2021, our PAP enrollments demonstrated potential cost savings of over $1.2 million. Strategies, limitations, and future directions of PAP use are also discussed, highlighting that PAPs can be a powerful tool for free clinics in serving underserved communities.

Counternarratives: An Antiracist Approach in Social Work Education, Practice, and Research.

Given renewed attention to racial equity in the social work profession, the authors suggest the use of counternarratives, an established tool of critical race theory, as an accessible method to challenge racism and examine privilege in social work education, practice, and research. Counternarratives use the technique of storytelling to elevate the lived experiences of marginalized individuals and communities and invite the listener into critical reflection about dominant, privileged discourses. The ultimate goal of counternarratives is the achievement of racial equity. The authors provide context about how counternarratives can align with social work education, practice, and research, and then use specific, illustrative examples from their own work to bring this method and its application to life. The authors also share their own processes of reflection and dialogue across disciplines and social locations in the use of counternarratives. The reflections of an experienced social justice educator provide additional insights on the use of counternarratives in the field of social work.

A Letter to Your Care Providers: Implementation and Analysis of a Letter-based Advance Care Planning Initiative for Gynecologic Oncology Patients.

To determine the impact of a letter-based advance care planning (ACP) healthcare improvement (HI) initiative on rates of ACP conversations and documentation among gynecologic oncology (GO) inpatients. An HI initiative was implemented from January to December 2020 to improve ACP documentation among GO inpatients. Patients admitted to the GO service were given ACP packets with a letter-based ACP worksheet. GO inpatients who were interested in learning more about ACP were visited by medical students trained to lead ACP conversations. ACP documentation rates in the EMR (electronic medical record) pre- and post-intervention were evaluated. Descriptive statistics were calculated. Associations between sociodemographic characteristics and ACP documentation were analyzed using logistic regression. There were 172 patients admitted in 2019 (pre-implementation cohort). Of these, 45/172 patients (26%) had an advance directive (AD) documented in their electronic medical record (EMR). Following the implementation of the ACP HI in 2020, 55/168 patients (33%) had an AD documented in their EMR. This was a 7% absolute increase and 27% relative increase from pre-intervention AD documentation rates. Increasing age was associated with an increased likelihood of having an AD in the chart (p = 0.004). Married women were less likely to have an AD in their chart (p = 0.05). An HI utilizing a letter-based ACP packet given to GO inpatients improved AD documentation in the EMR. This HI offers a unique method for introducing ACP to patients. More work is needed to improve the occurrence and documentation of ACP conversations.

CHIP Happens: Clonal Hematopoiesis of Indeterminate Potential and Its Relationship to Solid Tumors.

Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by the expansion of hematopoietic cells harboring leukemia-associated somatic mutations in otherwise healthy people and occurs in at least 10% of adults over 70. It is well established that people with CHIP have increased rates of hematologic malignancy, increased risk of cardiovascular disease, and worse all-cause mortality compared with those without CHIP. Despite recent advancements in understanding CHIP as it relates to these known outcomes, much remains to be learned about the development and role of CHIP in other disease states. Emerging research has identified high rates of CHIP in patients with solid tumors, driven in part by oncologic therapy, and revealed associations between CHIP and differential outcomes in both solid tumors and other diseases. Recent studies have demonstrated that CHIP can contribute to dysregulated inflammatory signaling in multiple contexts, underscoring the importance of interrogating how CHIP might alter tumor immunology. Here, we review the role of CHIP mutations in clonal expansion of hematopoietic cells, explore the relationship between CHIP and solid tumors, and discuss the potential roles of CHIP in inflammation and solid tumor biology.

Zooming into the COVID Era Together.

The pre-clinical medical school curriculum provides students with extraordinary experiences in preparation to become physicians. However, it was not originally designed to be delivered remotely. The COVID-19 pandemic promptly threw the medical education process into unforeseen circumstances. A model of student-faculty collaboration created to address new challenges and implement practical solutions rapidly is presented. This model was used effectively to respond to pre-clinical educational interruptions that were imposed by the COVID-19 pandemic and maintain high-quality training. Our experience provides valuable insights and lessons learned that can be applied to the ongoing pandemic response and to future educational challenges.

Recognizing the emergency department's role in oncologic care: a review of the literature on unplanned acute care.

Background: The global prevalence of cancer is rapidly increasing and will increase the acute care needs of patients with cancer, including emergency department (ED) care. Patients with cancer present to the ED across the cancer care continuum from diagnosis through treatment, survivorship, and end-of-life. This article describes the characteristics and determinants of ED visits, as well as challenges in the effort to define preventable ED visits in this population. Findings: The most recent population-based estimates suggest 4% of all ED visits are cancer-related and roughly two thirds of these ED visits result in hospitalization-a 4-fold higher ED hospitalization rate than the general population. Approximately 44% of cancer patients visit the ED within 1 year of diagnosis, and more often have repeat ED visits within a short time frame, though there is substantial variability across cancer types. Similar patterns of cancer-related ED use are observed internationally across a range of different national payment and health system settings. ED use for patients with cancer likely reflects a complex interaction of individual and contextual factors-including provider behavior, health system characteristics, and health policies-that warrants greater attention in the literature. Conclusions: Given the amount and complexity of cancer care delivered in the emergency setting, future research is recommended to examine specific symptoms associated with cancer-related ED visits, the contextual determinants of ED use, and definitions of preventable ED use specific to patients with cancer.

Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth.

Assaying for large numbers of low-frequency mutations requires sequencing at extremely high depth and accuracy. Increasing sequencing depth aids the detection of low-frequency mutations yet limits the number of loci that can be simultaneously probed. Here we report a method for the accurate tracking of thousands of distinct mutations that requires substantially fewer reads per locus than conventional hybrid-capture duplex sequencing. The method, which we named MAESTRO (for minor-allele-enriched sequencing through recognition oligonucleotides), combines massively parallel mutation enrichment with duplex sequencing to track up to 10,000 low-frequency mutations, with up to 100-fold fewer reads per locus. We show that MAESTRO can be used to test for chimaerism by tracking donor-exclusive single-nucleotide polymorphisms in sheared genomic DNA from human cell lines, to validate whole-exome sequencing and whole-genome sequencing for the detection of mutations in breast-tumour samples from 16 patients, and to monitor the patients for minimal residual disease via the analysis of cell-free DNA from liquid biopsies. MAESTRO improves the breadth, depth, accuracy and efficiency of mutation testing by sequencing.

Hierarchical tumor heterogeneity mediated by cell contact between distinct genetic subclones.

Intratumor heterogeneity is an important mediator of poor outcomes in many cancers, including breast cancer. Genetic subclones frequently contribute to this heterogeneity; however, their growth dynamics and interactions remain poorly understood. PIK3CA and HER2 alterations are known to coexist in breast and other cancers. Herein, we present data that describe the ability of oncogenic PIK3CA mutant cells to induce the proliferation of quiescent HER2 mutant cells through a cell contact-mediated mechanism. Interestingly, the HER2 cells proliferated to become the major subclone over PIK3CA counterparts both in vitro and in vivo. Furthermore, this phenotype was observed in both hormone receptor-positive and -negative cell lines, and was dependent on the expression of fibronectin from mutant PIK3CA cells. Analysis of human tumors demonstrated similar HER2:PIK3CA clonal dynamics and fibronectin expression. Our study provides insight into nonrandom subclonal architecture of heterogenous tumors, which may aid the understanding of tumor evolution and inform future strategies for personalized medicine.

Nurse-Led Telephonic Symptom Support for Patients Receiving Chemotherapy.

PROBLEM STATEMENT: The use of evidence-informed symptom guides has not been widely adopted in telephonic support. DESIGN: This is a descriptive study of nurse-led support using evidence-based symptom guides during telephone outreach. DATA SOURCES: Documentation quantified telephone encounters by frequency, length, and type of patient-reported symptoms. Nurse interviews examined perceptions of their role and the use of symptom guides. ANALYSIS: Quantitative data were summarized using univariate descriptive statistics, and interviews were analyzed using directed descriptive content analysis. FINDINGS: Symptom guides were viewed as trusted evidence-based resources, suitable to address common treatment-related symptoms. A threshold effect was a reported barrier of the guides, such that the benefit diminished over time for managing recurring symptoms. IMPLICATIONS FOR PRACTICE: Telephone outreach using evidence-based symptom guides can contribute to early symptom identification while engaging patients in decision making. Understanding nurse activities aids in developing an economical and high-quality model for symptom support, as well as in encouraging nurses to practice at the highest level of preparation.

The Personal Health Network Mobile App for Chemotherapy Care Coordination: Qualitative Evaluation of a Randomized Clinical Trial.

BACKGROUND: Cancer care coordination addresses the fragmented and inefficient care of individuals with complex care needs. The complexity of care coordination can be aided by innovative technology. Few examples of information technology-enabled care coordination exist beyond the conventional telephone follow-up. For this study, we implemented a custom-designed app, the Personal Health Network (PHN)-a Health Insurance Portability and Accountability Act-compliant social network built around a patient to enable patient-centered health and health care activities in collaboration with clinicians, care team members, caregivers, and others designated by the patient. The app facilitates a care coordination intervention for patients undergoing chemotherapy. OBJECTIVE: This study aimed to understand patient experiences with PHN technology and assess their perspectives on the usability and usefulness of PHNs with care coordination during chemotherapy. METHODS: A two-arm randomized clinical trial was conducted to compare the PHN and care coordination with care coordination alone over a 6-month period beginning with the initiation of chemotherapy. A semistructured interview guide was constructed based on a theoretical framework of technology acceptance addressing usefulness, usability, and the context of use of the technology within the participant's life and health care setting. All participants in the intervention arm were interviewed on completion of the study. Interviews were recorded and transcribed verbatim. A summative thematic analysis was completed for the transcribed interviews. Features of the app were also evaluated. RESULTS: A total of 27 interviews were completed. The resulting themes included the care coordinator as a partner in care, learning while sick, comparison of other technology to make sense of the PHN, communication, learning, usability, and usefulness. Users expressed that the nurse care coordinators were beneficial to them because they helped them stay connected to the care team and answered their questions. They shared that the mobile app gave them access to the health information they were seeking. Users expressed that the mobile app would be more useful if it was fully integrated with the electronic health record. CONCLUSIONS: The findings highlight the value of care coordination from the perspectives of cancer patients undergoing chemotherapy and the important role of technology, such as the PHN, in enhancing this process by facilitating better communication and access to information regarding their illness.

Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer.

PURPOSE: Existing cell-free DNA (cfDNA) methods lack the sensitivity needed for detecting minimal residual disease (MRD) following therapy. We developed a test for tracking hundreds of patient-specific mutations to detect MRD with a 1,000-fold lower error rate than conventional sequencing. EXPERIMENTAL DESIGN: We compared the sensitivity of our approach to digital droplet PCR (ddPCR) in a dilution series, then retrospectively identified two cohorts of patients who had undergone prospective plasma sampling and clinical data collection: 16 patients with ER+/HER2- metastatic breast cancer (MBC) sampled within 6 months following metastatic diagnosis and 142 patients with stage 0 to III breast cancer who received curative-intent treatment with most sampled at surgery and 1 year postoperative. We performed whole-exome sequencing of tumors and designed individualized MRD tests, which we applied to serial cfDNA samples. RESULTS: Our approach was 100-fold more sensitive than ddPCR when tracking 488 mutations, but most patients had fewer identifiable tumor mutations to track in cfDNA (median = 57; range = 2-346). Clinical sensitivity was 81% (n = 13/16) in newly diagnosed MBC, 23% (n = 7/30) at postoperative and 19% (n = 6/32) at 1 year in early-stage disease, and highest in patients with the most tumor mutations available to track. MRD detection at 1 year was strongly associated with distant recurrence [HR = 20.8; 95% confidence interval, 7.3-58.9]. Median lead time from first positive sample to recurrence was 18.9 months (range = 3.4-39.2 months). CONCLUSIONS: Tracking large numbers of individualized tumor mutations in cfDNA can improve MRD detection, but its sensitivity is driven by the number of tumor mutations available to track.

Social Determinants of Health: Underreported Heterogeneity in Systematic Reviews of Caregiver Interventions.

BACKGROUND AND OBJECTIVES: Although most people have some experience as caregivers, the nature and context of care are highly variable. Caregiving, socioeconomic factors, and health are all interrelated. For these reasons, caregiver interventions must consider these factors. This review examines the degree to which caregiver intervention research has reported and considered social determinants of health. RESEARCH DESIGN AND METHODS: We examined published systematic reviews and meta-analyses of interventions for older adults with age-related chronic conditions using the PRISMA and AMSTAR 2 checklists. From 2,707 papers meeting search criteria, we identified 197 potentially relevant systematic reviews, and selected 33 for the final analysis. RESULTS: We found scant information on the inclusion of social determinants; the papers lacked specificity regarding race/ethnicity, gender, sexual identity, socioeconomic status, and geographic location. The majority of studies focused on dementia, with other conditions common in later life vastly underrepresented. DISCUSSION AND IMPLICATIONS: Significant gaps in evidence persist, particularly for interventions targeting diverse conditions and populations. To advance health equity and improve the effectiveness of interventions, research should address caregiver heterogeneity and improve assessment, support, and instruction for diverse populations. Research must identify aspects of heterogeneity that matter in intervention design, while recognizing opportunities for common elements and strategies.

Fear of cancer recurrence and associations with mental health status and individual characteristics among cancer survivors: Findings from a nationally representative sample.

Purpose: To describe the prevalence of fear of cancer recurrence (FCR) and test its associations with validated mental health status measures.Design: Cross-sectional survey using the Medical Expenditure Panel Survey Experiences with Cancer Survivorship Supplement.Sample: Post-treatment cancer survivors (n = 1032).Methods: Survey-weighted U.S. population-based estimates describe the prevalence of sociodemographic, health and mental health characteristics of cancer survivors by their level of FCR. Multinomial logistic regression was used to test associations of validated measures of mental health status and individual characteristics on levels of FCR in unadjusted models and those controlling for sociodemographic and health characteristics.Findings: Overall, 34.3% of cancer survivors reported no FCR, 54.4% reported low FCR, and 11.3% reported high FCR. Cancer survivors were at increased risk of reporting high FCR relative to no FCR if they had a low 12-item Short Form Health Survey Mental Component Summary score (≤48) compared to high scores (odds ratio = 2.88; 95% confidence interval = 1.57, 5.29). Reporting depressive symptoms or psychological distress did not significantly increase the risk of reporting high or low FCR relative to no FCR.Conclusions: To our knowledge, this study is the first to provide U.S. population-based estimates of associations between FCR and individual and health characteristics.Implications for Psychosocial Providers or Policy: Our results provide valuable information about which survivors are most at-risk for FCR. Future research is needed to more clearly differentiate FCR from other constructs.

Relationships Between Fear of Cancer Recurrence and Lifestyle Factors Among Cancer Survivors.

We examine the relationships between fear of cancer recurrence (FCR), physical activity, smoking status, and engagement in healthier habits in a US population-based sample of post-treatment cancer survivors. We used data from the 2011 Medical Expenditure Panel Survey (MEPS) Experience with Cancer Survivorship Supplement. Multivariable logistic regression was used to test the relationship of FCR to physical activity, smoking status, and engagement in healthier habits. In all analyses, MEPS survey weights were applied to account for the survey design. Compared with those reporting no FCR, survivors reporting high FCR had significantly lower odds of reporting that they were not currently smokers (odds ratio [OR] = 0.46; 95% CI 0.24, 0.91) and those with any level of FCR had significantly higher odds of reporting healthier habits since diagnosis relative to those with no FCR (low FCR OR = 1.97; 95% CI 1.36, 2.85; high FCR OR = 2.40; 95% CI 1.33, 4.32). FCR was not associated with the odds of reporting physical activity. Findings from this large population-based survey suggest that some of survivors' lifestyle factors may be related to their level of FCR. Understanding the effects of FCR on lifestyle factors may help survivors, survivorship care providers, and policy makers better understand important differences among cancer survivors and personalize interventions in clinical care.

Unmet Needs for Information and Support Among Military Caregivers.

INTRODUCTION: In the United States, there are 5.5 million military caregivers, defined as family members, friends, or other acquaintances who provide essential care and support to current or former military service members. This study describes the prevalence and predictors of unmet information and support needs in this unique group of caregivers. Until recently, little research has focused on military caregivers. In 2014, a comprehensive RAND report underscored the specific challenges experienced by military caregivers including greater physical, financial, and emotional strain when compared with civilian caregivers. Of note, compared to civilian caregivers, military caregivers provide care and support for care recipients who are more likely to have complex illness. While this recent research improved our understanding of the increased burden associated with military caregiving, it also identified gaps for future work, including the need for additional studies to better understand unmet information and support needs to inform future interventions. The current study was designed to address this gap. MATERIALS AND METHODS: We examined data collected in the Caregiving in the U.S. Survey, a cross-sectional online survey fielded in 2014, by the National Alliance for Caregiving and the American Association of Retired Persons (AARP) for primary caregivers who had been in the role for at least six months. Four outcomes representing unmet caregiver needs were examined measuring caregiver report of needing more help or information to: (1) keep the care recipient safe at home; (2) manage challenging behaviors such as wandering; (3) manage their own emotional and physical stress; and (4) make end-of-life decisions. Survey-weighted logistic regression was used to test associations between military caregiver status (military/civilian) and unmet needs while controlling for key socio-demographic, caregiving and care recipient health variables, with nationally generalizable results. RESULTS: Compared to their civilian counterparts, military caregivers had significantly higher odds of reporting need for information or support to make end-of-life decisions (OR = 2.22; 95% CI: 1.24, 3.97; p = 0.01) and marginally higher odds of reporting need for more information or support to manage physical and emotional stress (OR = 1.64; 95% CI: 0.93, 2.88; p = 0.08). In contrast, military caregivers had significantly lower odds of reporting need for more information or support to keep the care recipient safe compared to civilian caregivers (OR = 0.54; 95% CI: 0.30, 0.95; p = 0.03). Reports of unmet needs related to managing challenging behaviors were similar between military and civilian caregivers. CONCLUSIONS: Needs for information and support differ for civilian and military caregivers and may reflect direct or indirect impacts on caregivers arising from differences in TRICARE and Veterans Affairs health insurance coverage and related benefits, services and systems or access to resources that address the unique needs of military populations. Future research is needed to better understand the unique concerns of military caregivers and inform interventions that support end-of-life care decision-making for military service members and their caregivers.

Tumor fraction in cell-free DNA as a biomarker in prostate cancer.

BACKGROUND: Tumor content in circulating cell-free DNA (cfDNA) is a promising biomarker, but longitudinal dynamics of tumor-derived and non-tumor-derived cfDNA through multiple courses of therapy have not been well described. METHODS: CfDNA from 663 plasma samples from 140 patients with castration-resistant prostate cancer (CRPC) was subject to sparse whole genome sequencing. Tumor fraction (TFx) estimated using the computational tool ichorCNA was correlated with clinical features and responses to therapy. RESULTS: TFx associated with the number of bone metastases (median TFx = 0.014 with no bone metastases, 0.047 with 1-3 bone metastases, 0.190 for 4+ bone metastases; P < 0.0001) and with visceral metastases (P < 0.0001). In multivariable analysis, TFx remained associated with metastasis location (P = 0.042); TFx was positively correlated with alkaline phosphatase (P = 0.0227) and negatively correlated with hemoglobin (Hgb) (P < 0.001), but it was not correlated with prostate specific antigen (PSA) (P = 0.75). Tumor-derived and non-tumor-derived cfDNA track together and do not increase with generalized tissue damage from chemotherapy or radiation at the time scales examined. All new treatments that led to ≥30% PSA decline at 6 weeks were associated with TFx decline when baseline TFx was >7%; however, TFx in patients being subsequently maintained on secondary hormonal therapy was quite dynamic. CONCLUSION: TFx correlates with clinical features associated with overall survival in CRPC, and TFx decline is a promising biomarker for initial therapeutic response. TRIAL REGISTRATION: Dana-Farber/Harvard Cancer Center (DF/HCC) protocol no. 18-135. FUNDING: Wong Family Award in Translational Oncology, Dana Farber Cancer Institute Medical Oncology grant, Gerstner Family Foundation, Janssen Pharmaceuticals Inc., and Koch Institute Support (core) grant P30-CA14051 from the National Cancer Institute (NCI).