Velociraptor: Cross-Platform Quantitative Search Using Hallmark Cell Features.

A key challenge for single cell discovery analysis is to identify new cell types, describe them quantitatively, and seek these novel cells in new studies often using a different platform. Over the last decade, tools were developed to address identification and quantitative description of cells in human tissues and tumors. However, automated validation of populations at the single cell level has struggled due to the cytometry field's reliance on hierarchical, ordered use of features and on platform-specific rules for data processing and analysis. Here we present Velociraptor, a workflow that implements Marker Enrichment Modeling in three cross-platform modules: 1) identification of cells specific to disease states, 2) description of hallmark features for each cell and population, and 3) searching for cells matching one or more hallmark feature sets in a new dataset. A key advance is that Velociraptor registers cells between datasets, including between flow cytometry and quantitative imaging using different, overlapping feature sets. Four datasets were used to challenge Velociraptor and reveal new biological insights. Working at the individual sample level, Velociraptor tracked the abundance of clinically significant glioblastoma brain tumor cell subsets and characterized the cells that predominate in recurrent tumors as a close match for rare, negative prognostic cells originally observed in matched pre-treatment tumors. In patients with inborn errors of immunity, Velociraptor identified genotype-specific cells associated with GATA2 haploinsufficiency. Finally, in cross-platform analysis of immune cells in multiplex imaging of breast cancer, Velociraptor sought and correctly identified memory T cell subsets in tumors. Different phenotypic descriptions generated by algorithms or humans were shown to be effective as search inputs, indicating that cell identity need not be described in terms of per-feature cutoffs or strict hierarchical analyses. Velociraptor thus identifies cells based on hallmark feature sets, such as protein expression signatures, and works effectively with data from multiple sources, including suspension flow cytometry, imaging, and search text based on known or theoretical cell features.

Curative Therapies for Sickle Cell Disease.

Sickle cell disease (SCD) is an autosomal recessive hemoglobinopathy that affects individuals worldwide. The mutation in the beta-globin gene leads to abnormal hemoglobin production, sickle hemoglobin, which polymerizes under stress leading to, among other end-organ manifestations, chronic hemolytic anemia, debilitating vaso-occlusive crises, and stroke. Unfortunately, chronic stress on end-organs impacts the life expectancy of patients with SCD, which in the United States averages 43 years, approximately 36 years less than people without the disease. Here, we review the progress made in curative interventions for those with SCD, namely allogeneic hematopoietic cell transplantation and gene therapy. These interventions continue to evolve as we better understand SCD pathophysiology, use new graft-versus-host disease prophylaxis regimens, expand stem cell donor options, and understand the genetic control of hemoglobin production. Although significant progress has been made, many gaps remain in the successful implementation of these interventions globally and for all patients. [Pediatr Ann. 2024;53(2):e56-e61.].

Approach to Diagnosing Inborn Errors of Immunity.

Inborn errors of immunity are now understood to encompass manifold features including but not limited to immunodeficiency, autoimmunity, autoinflammation, atopy, bone marrow defects, and/or increased malignancy risk. As such, it is essential to maintain a high index of suspicion, as these disorders are not limited to specific demographics such as children or those with recurrent infections. Clinical presentations and standard immunophenotyping are informative for suggesting potential underlying etiologies, but integration of data from multimodal approaches including genomics is often required to achieve diagnosis.

Systems Immunology Analyses of STAT1 Gain-of-Function Immune Phenotypes Reveal Heterogeneous Response to IL-6 and Broad Immunometabolic Roles for STAT1.

Patients with STAT1 gain-of-function (GOF) pathogenic variants have enhanced or prolonged STAT1 phosphorylation following cytokine stimulation and exhibit increased yet heterogeneous susceptibility to infections, autoimmunity, and cancer. Although disease phenotypes are diverse and other genetic factors contribute, how STAT1 GOF affects cytokine sensitivity and cell biology remains poorly defined. In this study, we analyzed the immune and immunometabolic profiles of two patients with known pathogenic heterozygous STAT1 GOF mutation variants. A systems immunology approach of peripheral blood cells from these patients revealed major changes in multiple immune cell compartments relative to healthy adult and pediatric donors. Although many phenotypes of STAT1 GOF donors were shared, including increased Th1 cells but decreased class-switched B cells and plasmacytoid dendritic cell populations, others were heterogeneous. Mechanistically, hypersensitivity for cytokine-induced STAT1 phosphorylation in memory T cell populations was particularly evident in response to IL-6 in one STAT1 GOF patient. Immune cell metabolism directly influences cell function, and the STAT1 GOF patients shared an immunometabolic phenotype of heightened glucose transporter 1 (GLUT1) and carnitine palmitoyl transferase 1A (CPT1a) expression across multiple immune cell lineages. Interestingly, the metabolic phenotypes of the pediatric STAT1 GOF donors more closely resembled or exceeded those of healthy adult than healthy age-similar pediatric donors, which had low expression of these metabolic markers. These results define new features of STAT1 GOF patients, including a differential hypersensitivity for IL-6 and a shared increase in markers of metabolism in many immune cell types that suggests a role for STAT1 in metabolic regulation of immunity.

Outcomes of pediatric patients with therapy-related myeloid neoplasms.

Long-term outcomes after allogeneic hematopoietic cell transplantation (HCT) for therapy-related myeloid neoplasms (tMNs) are dismal. There are few multicenter studies defining prognostic factors in pediatric patients with tMNs. We have accumulated the largest cohort of pediatric patients who have undergone HCT for a tMN to perform a multivariate analysis defining factors predictive of long-term survival. Sixty-eight percent of the 401 patients underwent HCT using a myeloablative conditioning (MAC) regimen, but there were no statistically significant differences in the overall survival (OS), event-free survival (EFS), or cumulative incidence of relapse and non-relapse mortality based on the conditioning intensity. Among the recipients of MAC regimens, 38.4% of deaths were from treatment-related causes, especially acute graft versus host disease (GVHD) and end-organ failure, as compared to only 20.9% of deaths in the reduced-intensity conditioning (RIC) cohort. Exposure to total body irradiation (TBI) during conditioning and experiencing grade III/IV acute GVHD was associated with worse OS. In addition, a diagnosis of therapy-related myelodysplastic syndrome and having a structurally complex karyotype at tMN diagnosis were associated with worse EFS. Reduced-toxicity (but not reduced-intensity) regimens might help to decrease relapse while limiting mortality associated with TBI-based HCT conditioning in pediatric patients with tMNs.

The role of biomarkers in risk stratification, treatment and outcome in acute GVHD.

PURPOSE OF REVIEW: Graft-versus-host disease (GVHD) following hematopoietic cell transplant (HCT) has a significant impact on morbidity and mortality among recipients. Predicting the long-term outcomes at the time of diagnosis of GVHD or even after response to up-front therapy can be challenging and only has modest accuracy. With biomarkers available to help guide decision-making, the landscape of GVHD is evolving. RECENT FINDINGS: Several acute GVHD biomarkers have been identified, with some better able to categorize patients based on their GVHD severity and potential for refractory disease than standard clinical staging or response criteria. SUMMARY: Biomarkers are now being incorporated into the clinical trial design for both high and low-risk GVHD. These findings will likely impact how clinical care is delivered in the future as improved risk stratification has the potential to improve outcomes by providing individualized treatment plans for affected patients.

Immunodeficiency and bone marrow failure with mosaic and germline TLR8 gain of function.

Inborn errors of immunity (IEI) are a genetically heterogeneous group of disorders with a broad clinical spectrum. Identification of molecular and functional bases of these disorders is important for diagnosis, treatment, and an understanding of the human immune response. We identified 6 unrelated males with neutropenia, infections, lymphoproliferation, humoral immune defects, and in some cases bone marrow failure associated with 3 different variants in the X-linked gene TLR8, encoding the endosomal Toll-like receptor 8 (TLR8). Interestingly, 5 patients had somatic variants in TLR8 with <30% mosaicism, suggesting a dominant mechanism responsible for the clinical phenotype. Mosaicism was also detected in skin-derived fibroblasts in 3 patients, demonstrating that mutations were not limited to the hematopoietic compartment. All patients had refractory chronic neutropenia, and 3 patients underwent allogeneic hematopoietic cell transplantation. All variants conferred gain of function to TLR8 protein, and immune phenotyping demonstrated a proinflammatory phenotype with activated T cells and elevated serum cytokines associated with impaired B-cell maturation. Differentiation of myeloid cells from patient-derived induced pluripotent stem cells demonstrated increased responsiveness to TLR8. Together, these findings demonstrate that gain-of-function variants in TLR8 lead to a novel childhood-onset IEI with lymphoproliferation, neutropenia, infectious susceptibility, B- and T-cell defects, and in some cases, bone marrow failure. Somatic mosaicism is a prominent molecular mechanism of this new disease.

BCR-ABL1-like B-Lymphoblastic Leukemia/Lymphoma with FOXP1-ABL1 Rearrangement: Comprehensive Laboratory Identification Allowing Tyrosine Kinase Inhibitor Use.

B-lymphoblastic leukemia/lymphoma (B-ALL) is the most common type of childhood cancer; it also occurs in teenagers and adults, in whom the prognosis is generally less favorable. Therapeutic and molecular advances have substantially improved the treatment for subtypes of B-ALL, such that subclassification by cytogenetic and molecular alterations is critical for risk stratification and management. Novel rearrangements involving ABL1, JAK2, EPO, and other kinases have been identified that may respond to inhibition akin to BCR-ABL1. This diverse group of leukemias has been recognized as a provisional entity in the 2016 revision of the World Health Organization (WHO) Classification of the Hematopoietic Neoplasms as B-lymphoblastic leukemia/lymphoma, BCR-ABL1-like (Ph-like B-ALL). Herein, we present cytogenetic and molecular analysis of a case of B-ALL in a 16-year-old Caucasian boy with t(3;9) FOXP1-ABL1 rearrangement and concurrent loss of IKZF1, CDKN2A, and RB1 gene loci, meeting WHO criteria for Ph-like ALL. This case highlights diagnostic, prognostic, and therapeutic considerations of this recently recognized entity.

Biological Drivers of Wilms Tumor Prognosis and Treatment.

Prior to the 1950s, survival from Wilms tumor (WT) was less than 10%. Today, a child diagnosed with WT has a greater than 90% chance of survival. These gains in survival rates from WT are attributed largely to improvements in multimodal therapy: Enhanced surgical techniques leading to decreased operative mortality, optimization of more effective chemotherapy regimens (specifically, dactinomycin and vincristine), and inclusion of radiation therapy in treatment protocols. More recent improvements in survival, however, can be attributed to a growing understanding of the molecular landscape of Wilms tumor. Particularly, identification of biologic markers portending poor prognosis has facilitated risk stratification to tailor therapy that achieves the best possible outcome with the least possible toxicity. The aim of this review is to (1) outline the specific biologic markers that have been associated with prognosis in WT and (2) provide an overview of the current use of biologic and other factors to stratify risk and assign treatment accordingly.

Text Messaging and Mobile Phone Apps as Interventions to Improve Adherence in Adolescents With Chronic Health Conditions: A Systematic Review.

BACKGROUND: The number of adolescents with chronic health conditions (CHCs) continues to increase. Medication nonadherence is a global challenge among adolescents across chronic conditions and is associated with poor health outcomes. While there has been growing interest in the use of mHealth technology to improve medication adherence among adolescents with CHCs, particularly text messaging and mobile phone apps, there has been no prior systematic review of their efficacy. OBJECTIVE: The purpose of this review was to systematically evaluate the most recent evidence for the efficacy of text messaging and mobile phone apps as interventions to promote medication adherence among adolescents with CHCs. METHODS: PubMed, Embase, CENTRAL, PsycINFO, Web of Science, Google Scholar, and additional databases were searched from 1995 until November 2015. An additional hand search of related themes in the Journal of Medical Internet Research was also conducted. The Preferred Reporting Results of Systematic Reviews and Meta-Analyses guidelines were followed. Two reviewers independently screened titles/abstracts, assessed full-text articles, extracted data from included articles, and assessed their quality using Grades of Recommendation, Assessment, Development, and Evaluation criteria. Included studies were described in original research articles that targeted adherence in adolescents with CHCs (12-24 years-old). RESULTS: Of the 1423 records examined, 15 met predefined criteria: text messaging (n=12) and mobile phone apps (n=3). Most studies were performed in the United States (11/15, 73%), were randomized-controlled trials (8/15, 53%), had a sample size <50 (11/15, 73%), and included adherence self-report and/or biomarkers (9/15, 60%). Only four studies were designed based on a theoretical framework. Approaches for text messaging and mobile phone app interventions varied across studies. Seven articles (7/15, 47%) reported significant improvement in adherence with moderate to large standardized mean differences. Most of the included studies were of low or moderate quality. Studies varied in sample size, methods of adherence assessment, and definition of adherence, which prohibited performing a meta-analysis. CONCLUSIONS: The use of text messaging and mobile phone app interventions to improve medication adherence among adolescents with CHCs has shown promising feasibility and acceptability, and there is modest evidence to support the efficacy of these interventions. Further evaluation of short- and long-term efficacy and cost-effectiveness of these interventions is warranted given the early and evolving state of the science.