Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT.

Identifying cell types and states remains a time-consuming and error-prone challenge for spatial biology. While deep learning is increasingly used, it is difficult to generalize due to variability at the level of cells, neighborhoods, and niches in health and disease. To address this, we developed TACIT, an unsupervised algorithm for cell annotation using predefined signatures that operates without training data, using unbiased thresholding to distinguish positive cells from background, focusing on relevant markers to identify ambiguous cells in multiomic assays. Using five datasets (5,000,000-cells; 51-cell types) from three niches (brain, intestine, gland), TACIT outperformed existing unsupervised methods in accuracy and scalability. Integration of TACIT-identified cell with a novel Shiny app revealed new phenotypes in two inflammatory gland diseases. Finally, using combined spatial transcriptomics and proteomics, we discover under- and overrepresented immune cell types and states in regions of interest, suggesting multimodality is essential for translating spatial biology to clinical applications.

Social Determinants of Health and Informed Consent Comprehension for Pediatric Cancer Clinical Trials.

Importance: Ensuring valid informed consent (IC) prior to enrollment in clinical trials is a fundamental ethical right. Objective: To assess whether social determinants of health (SDOH) and related sociocontextual factors are associated with parental IC comprehension in therapeutic childhood cancer clinical trials. Design, Setting, and Participants: This cross-sectional study prospectively enrolled 223 parents of children with newly diagnosed cancer at Rady Children's Hospital San Diego, a large quaternary academic center in California, from October 1, 2014, to March 31, 2021. Linear mixed effects models were used to assess whether IC comprehension overall and by domain (purpose, procedures, and randomization; risks and benefits; alternatives; and voluntariness) were associated with SDOH and sociocontextual factors. Data were analyzed from January 1, 2022, to July 31, 2023. Exposures: Informed consent for a therapeutic childhood cancer clinical trial. Main Outcomes and Measures: The primary outcome of interest was IC comprehension and its associations with SDOH (marital status, language, educational attainment, employment, insurance type, socioeconomic status, and health literacy) and sociocontextual factors (ethnicity, satisfaction with informed consent, and cancer type). Results: Of 223 parents, 172 (77.1%) were aged 18 to 44 years, 111 (49.8%) were Hispanic, 152 (68.2%) were women, and 163 (73.1%) were married. In terms of race, 2 (0.9%) were American Indian or Alaska Native, 22 (9.9%) were Asian or Pacific Islander, 8 (3.6%) were Black, 149 (66.8%) were White, and 42 (18.8%) were more than 1 race. In multivariable linear mixed-effects analyses, limited vs adequate health literacy was associated with lower comprehension of informed consent overall (mean [SD], 68.28 [11.81] vs 79.24 [11.77]; ß estimate, -9.02 [95% CI, -12.0 to -6.07]; P < .001) and with lower comprehension of the purpose, procedures, and randomization (mean [SD], 65.00 [12.64] vs 76.14 [11.53]; ß estimate, -7.87 [95% CI, -10.9 to -4.85]; P < .001); risks and benefits (mean [SD], 62.84 [20.24] vs 73.14 [20.86]; ß estimate, -10.1 [95% CI, -15.6 to -4.59]; P < .001); alternatives (mean [SD], 54.27 [43.18] vs 82.98 [34.24]; ß estimate, -14.3 [95% CI, -26.1 to -2.62]; P .02); and voluntariness (mean [SD], 76.52 [24.33] vs 95.39 [13.89]; ß estimate, -9.14 [95% CI, -14.9 to -3.44]; P = .002) domains. Use of Spanish vs English language for medical communication was associated with lower comprehension overall (mean [SD], 66.45 [12.32] vs 77.25 [12.18]; ß estimate, -5.30 [95% CI, -9.27 to -1.34]; P = .01) and with lower comprehension of the purpose, procedures, and randomization (mean [SD], 63.33 [11.98] vs 74.07 [12.52]; ß estimate, -4.33 [95% CI, -8.43 to -0.23]; P = .04) and voluntariness (mean [SD], 70.83 [24.02] vs 92.54 [17.27]; ß estimate, -9.69 [95% CI, -16.8 to -2.56]; P = .009) domains. Conclusions and Relevance: In this cross-sectional study including parents of children with newly diagnosed cancer who provided IC for their child's participation in a therapeutic clinical trial, limited health literacy and use of Spanish language for medical communication were associated with lower comprehension of IC. These findings suggest that, in this setting, parents with limited health literacy or those who use Spanish language for medical communication may not fully comprehend IC and therefore may not make truly informed decisions. These findings support the investigation of interventions, across pediatric disciplines, tailored to the participant's language and health literacy level to improve IC comprehension, particularly in racial and ethnic minority populations.

Assessment of Factors Associated With Parental Perceptions of Voluntary Decisions About Child Participation in Leukemia Clinical Trials.

Importance: Obtaining voluntary informed consent prior to enrollment in clinical trials is a fundamental ethical requirement. Objective: To assess whether health literacy, contextual factors, or sociodemographic characteristics are associated with perception of voluntariness among parents who had consented for their child's participation in a leukemia therapeutic clinical trial. Design, Setting, and Participants: This cross-sectional study prospectively enrolled 97 parents of children diagnosed as having leukemia at Rady Children's Hospital San Diego, a large tertiary academic center in California, from 2014 to 2017. Health literacy, contextual factors (acculturation, decisional regret, and satisfaction with informed consent), sociodemographic characteristics, and perception of voluntariness after consenting for a therapeutic clinical trial were measured. Univariable and multivariable regression were used to determine significant associations. The analyses for the present study were conducted from May 2019 to May 2020. Exposures: Informed consent for a therapeutic leukemia clinical trial. Main Outcomes and Measures: The primary outcome of interest was perception of voluntariness and its associations with health literacy and other contextual factors (acculturation, decisional regret, and satisfaction with informed consent) and sociodemographic characteristics, including age, race/ethnicity, parental language, educational level, insurance type, marital status, and socioeconomic status. Results: Of 97 parents included, the majority were women (65 [67%]), married (71 [73%]), and of self-reported Hispanic ethnicity (50 [52%]). Lower perception of voluntariness was significantly associated with lower health literacy (r = 0.30; 95% CI, 0.11-0.47; P = .004), Spanish language (x̅ = -4.50, P = .05), lower acculturation if of Hispanic ethnicity (r = 0.30; 95% CI, 0.02-0.54; P = .05), greater decisional regret (r = -0.54; 95% CI, -0.67 to -0.38; P < .001), and lower satisfaction with informed consent (r = 0.39; 95% CI, 0.21-0.54; P < .001) in univariable analysis. Lower health literacy remained significantly associated with lower perception of voluntariness in multivariable analysis after adjustment for contextual factors and sociodemographic characteristics (ß = 4.06; 95% CI, 1.60-6.53; P = .001). Lower health literacy was significantly associated with Hispanic ethnicity (mean, 4.16; 95% CI, 3.75-4.57; P < .001), Spanish language spoken at home (mean, 3.17; 95% CI, 1.94-4.40; P < .001), high school or less educational level (mean, 3.41; 95% CI, 2.83-3.99; P < .001), public insurance (mean, 4.00; 95% CI, 3.55-4.45; P < .001), and unmarried status (mean, 3.71; 95% CI, 2.91-4.51; P = .03). Conclusions and Relevance: Among parents of children with newly diagnosed leukemia who had consented for their child's participation in a therapeutic clinical trial, lower perception of voluntariness was significantly associated with lower health literacy. These results suggest that parents with low health literacy may perceive external influences in their decision for their child's participation in clinical trials. This finding highlights the potential role of recruitment interventions tailored to the participant's health literacy level to improve voluntary informed consent in underserved populations.

Improving Pediatric Neuro-Oncology Survival Disparities in the United States-Mexico Border Region: A Cross-Border Initiative Between San Diego, California, and Tijuana, Mexico.

PURPOSE: Treatment of children with CNS tumors (CNSTs) demands a complex, interdisciplinary approach that is rarely available in low- and middle-income countries. We established the Cross-Border Neuro-Oncology Program (CBNP) between Rady Children's Hospital, San Diego (RCHSD), and Hospital General, Tijuana (HGT), Mexico, to provide access to neuro-oncology care, including neurosurgic services, for children with CNSTs diagnosed at HGT. Our purpose was to assess the feasibility of the CBNP across the United States-Mexico border and improve survival for children with CNSTs at HGT by implementing the CBNP. PATIENTS AND METHODS: We prospectively assessed clinicopathologic profiles, the extent of resection, progression-free survival, and overall survival (OS) in children with CNSTs at HGT from 2010 to 2017. RESULTS: Sixty patients with CNSTs participated in the CBNP during the study period. The most common diagnoses were low-grade glioma (24.5%) and medulloblastoma (22.4%). Of patients who were eligible for surgery, 49 underwent resection at RCHSD and returned to HGT for collaborative management. Gross total resection was achieved in 78% of cases at RCHSD compared with 0% at HGT (P < .001) and was a predictor of 5-year OS (hazard ratio, 0.250; 95% CI, 0.067 to 0.934; P = .024). Five-year OS improved from 0% before 2010 to 52% in 2017. CONCLUSION: The CBNP facilitated access to complex neuro-oncology care for underserved children in Mexico through binational exchanges of resources and expertise. Survival for patients in the CBNP dramatically improved. Gross total resection at RCHSD was associated with higher OS, highlighting the critical role of experienced neurosurgeons in the treatment of CNSTs. The CBNP model offers an attractive alternative for children with CNSTs in low- and middle-income countries who require complex neuro-oncology care, particularly those in close proximity to institutions in high-income countries with extensive neuro-oncology expertise.