Missing data and missed infections: investigating racial and ethnic disparities in SARS-CoV-2 testing and infection rates in Holyoke, Massachusetts.

Routinely collected testing data have been a vital resource for public health response during the COVID-19 pandemic and have revealed the extent to which Black and Hispanic persons have borne a disproportionate burden of SARS-CoV-2 infections and hospitalizations in the United States. However, missing race and ethnicity data and missed infections due to testing disparities limit the interpretation of testing data and obscure the true toll of the pandemic. We investigated potential bias arising from these 2 types of missing data through a case study carried out in Holyoke, Massachusetts, during the prevaccination phase of the pandemic. First, we estimated SARS-CoV-2 testing and case rates by race and ethnicity, imputing missing data using a joint modeling approach. We then investigated disparities in SARS-CoV-2 reported case rates and missed infections by comparing case rate estimates with estimates derived from a COVID-19 seroprevalence survey. Compared with the non-Hispanic White population, we found that the Hispanic population had similar testing rates (476 tested per 1000 vs 480 per 1000) but twice the case rate (8.1% vs 3.7%). We found evidence of inequitable testing, with a higher rate of missed infections in the Hispanic population than in the non-Hispanic White population (79 infections missed per 1000 vs 60 missed per 1000).

Disparities in SARS-CoV-2 Infection by Race, Ethnicity, Language, and Social Vulnerability: Evidence from a Citywide Seroprevalence Study in Massachusetts, USA.

OBJECTIVES: Uncovering and addressing disparities in infectious disease outbreaks require a rapid, methodical understanding of local epidemiology. We conducted a seroprevalence study of SARS-CoV-2 infection in Holyoke, Massachusetts, a majority Hispanic city with high levels of socio-economic disadvantage to estimate seroprevalence and identify disparities in SARS-CoV-2 infection. METHODS: We invited 2000 randomly sampled households between 11/5/2020 and 12/31/2020 to complete questionnaires and provide dried blood spots for SARS-CoV-2 antibody testing. We calculated seroprevalence based on the presence of IgG antibodies using a weighted Bayesian procedure that incorporated uncertainty in antibody test sensitivity and specificity and accounted for household clustering. RESULTS: Two hundred eighty households including 472 individuals were enrolled. Three hundred twenty-eight individuals underwent antibody testing. Citywide seroprevalence of SARS-CoV-2 IgG was 13.1% (95% CI 6.9-22.3) compared to 9.8% of the population infected based on publicly reported cases. Seroprevalence was 16.1% (95% CI 6.2-31.8) among Hispanic individuals compared to 9.4% (95% CI 4.6-16.4) among non-Hispanic white individuals. Seroprevalence was higher among Spanish-speaking households (21.9%; 95% CI 8.3-43.9) compared to English-speaking households (10.2%; 95% CI 5.2-18.0) and among individuals in high social vulnerability index (SVI) areas based on the CDC SVI (14.4%; 95% CI 7.1-25.5) compared to low SVI areas (8.2%; 95% CI 3.1-16.9). CONCLUSIONS: The SARS-CoV-2 IgG seroprevalence in a city with high levels of social vulnerability was 13.1% during the pre-vaccination period of the COVID-19 pandemic. Hispanic individuals and individuals in communities characterized by high SVI were at the highest risk of infection. Public health interventions should be designed to ensure that individuals in high social vulnerability communities have access to the tools to combat COVID-19.

Evaluation of the Access Bio CareStart rapid SARS-CoV-2 antigen test in asymptomatic individuals tested at a community mass-testing program in Western Massachusetts.

Point-of-care antigen-detecting rapid diagnostic tests (RDTs) to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) represent a scalable tool for surveillance of active SARS-CoV-2 infections in the population. Data on the performance of these tests in real-world community settings are paramount to guide their implementation to combat the COVID-19 pandemic. We evaluated the performance characteristics of the CareStart COVID-19 Antigen test (CareStart) in a community testing site in Holyoke, Massachusetts. We compared CareStart to a SARS-CoV-2 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) reference, both using anterior nasal swab samples. We calculated the sensitivity, specificity, and the expected positive and negative predictive values at different SARS-CoV-2 prevalence estimates. We performed 666 total tests on 591 unique individuals. 573 (86%) were asymptomatic. There were 52 positive tests by RT-qPCR. The sensitivity of CareStart was 49.0% (95% Confidence Interval (CI) 34.8-63.4) and specificity was 99.5% (95% CI 98.5-99.9). Among positive RT-qPCR tests, the median cycle threshold (Ct) was significantly lower in samples that tested positive on CareStart. Using a Ct ≤ 30 as a benchmark for positivity increased the sensitivity of the test to 64.9% (95% CI 47.5-79.8). Our study shows that CareStart has a high specificity and moderate sensitivity. The utility of RDTs, such as CareStart, in mass implementation should prioritize use cases in which a higher specificity is more important, such as triage tests to rule-in active infections in community surveillance programs.

Inflammation suppression prevents tumor cell proliferation in a mouse model of thyroid cancer.

The incidence of thyroid cancer, the most frequent endocrine neoplasia, is rapidly increasing. Significant progress has recently been made in the identification of genetic lesions in thyroid cancer; however, whether inflammation contributes to thyroid cancer progression remains unknown. Using a mouse model of aggressive follicular thyroid cancer (FTC; ThrbPV/PVPten+/- mice), we aimed to elucidate a cause-effect relationship at the molecular level. The ThrbPV/PVPten+/- mouse expresses a dominantly negative thyroid hormone receptor ß (denoted as PV) and a deletion of a single allele of the Pten gene. These two oncogenic signaling pathways synergistically activate PI3K-AKT signaling to drive cancer progression as in human FTC. At the age of 5-7 weeks, thyroids of ThrbPV/PVPten+/- mice exhibited extensive hyperplasia accompanied by 77.5-fold infiltration of inflammatory monocytes as compared with normal thyroids. Global gene expression profiling identified altered expression of 2387 genes, among which 1353 were upregulated and 1034 were down-regulated. Further analysis identified markedly elevated expression of inflammation mediators and cytokines such as, Csf1r, Csf1, SPP1, Aif1, IL6, Ccl9, Ccl3, Ccl12, and Ccr2 genes and decreased expression of Kit, Ephx2, Cd163, IL15, Ccl11, and Cxcl13 genes. These changes elicited the inflammatory responses in the hyperplastic thyroid of ThrbPV/PVPten+/- mice, reflecting early events in thyroid carcinogenesis. We next tested whether attenuating the inflammatory responses could mitigate thyroid cancer progression. We treated the mice with an inhibitor of colony-stimulating factor 1 receptor (CSF1R), pexidartinib (PLX-3397; PLX). CSF1R mediates the activity of the cytokine, colony stimulating factor 1 (CSF1), in the production, differentiation, and functions of monocytes and macrophages. Treatment with PLX decreased 94% and 62% of inflammatory monocytes in the thyroid and bone marrow, respectively, versus controls. Further, PLX suppressed the expression of critical cytokine and inflammation-regulating genes such as Csf1r, SPP1 (OPN), Aif1, IL6, Ccl9, Ccl3, Ccl12, and Ccr2 (25%-80%), resulting in inhibition of 89% tumor cell proliferation, evidenced by Ki-67 immunostaining. These preclinical findings suggest that inflammation occurs in the early stage of thyroid carcinogenesis and plays a critical in cancer progression. Importantly, attenuation of inflammation by inhibitors such as PLX would be beneficial in preventing thyroid cancer.

Testing Usability and Feasibility of a Mobile Educator Tool for Pediatric Diabetes Self-Management: Mixed Methods Pilot Study.

BACKGROUND: Mobile interventions hold promise as an intervention modality to engage children in improving diabetes self-management education, attitudes, and behaviors. OBJECTIVE: This pilot study aimed to explore the usability, acceptability, and feasibility of delivering a mobile diabetes educational tool to parent-child pairs in a clinical setting. METHODS: This mixed methods pilot study comprised two concurrent phases with differing study participants. Phase 1 used user testing interviews to collect qualitative data on the usability and acceptability of the tool. Phase 2 used a single-arm pre- and poststudy design to quantitatively evaluate the feasibility and preliminary efficacy of the intervention. Study participants (English-speaking families with youth aged 5-14 years with insulin-dependent diabetes) were recruited from an urban hospital in Massachusetts, United States. In phase 1, parent-child pairs were invited to complete the intervention together and participate in 90-min user testing interviews assessing the tool's usability and acceptability. Interview transcripts were analyzed using a directed content analysis approach. In phase 2, parent-child pairs were invited to complete the intervention together in the clinical setting. Measures included parental and child knowledge, attitudes, and behaviors related to diabetes management (self-report surveys) and child hemoglobin A1c levels (medical record extractions); data were collected at baseline and 1-month follow-up. Pre- and postoutcomes were compared using paired t tests and the Fisher exact test. RESULTS: A total of 11 parent-child pairs (N=22) participated in phase 1 of the study, and 10 parent-child pairs (N=20) participated in phase 2 of the study. Participants viewed the mobile educational tool as acceptable (high engagement and satisfaction with the layout, activities, and videos) and identified the areas of improvement for tool usability (duration, directions, and animation). CONCLUSIONS: The findings from this pilot study suggest that the mobile educational tool is an informative, engaging, and feasible way to deliver diabetes self-management education to parents and children in an urban hospital setting. Data will inform future iterations of this mobile diabetes educational intervention to improve usability and test intervention efficacy.

Setting global research priorities for private sector child health service delivery: Results from a CHNRI exercise.

BACKGROUND: The private health sector is an important source of sick child care, yet evidence gaps persist in best practices for integrated management of private sector child health services. Further, there is no prioritized research agenda to address these gaps. We used a Child Health and Nutrition Research Initiative (CHNRI) process to identify priority research questions in response to these evidence gaps. CHNRI is a consultative approach that entails prioritizing research questions by evaluating them against standardized criteria. METHODS: We engaged geographically and occupationally diverse experts in the private health sector and child health. Eighty-nine experts agreed to participate and provided 150 priority research questions. We consolidated submitted questions to reduce duplication into a final list of 50. We asked participants to complete an online survey to rank each question against 11 pre-determined criteria in four categories: (i) answerability, (ii) research feasibility, (iii) sustainability/equity, and (iv) importance/potential impact. Statistical data analysis was conducted in SAS 9.4 (SAS Institute Inc, Cary NC, USA). We weighted all 11 evaluation criteria equally to calculate the research priority score and average expert agreement for each question. We disaggregated results by location in high-income vs low- and middle-income countries. RESULTS: Forty-nine participants (55.1%) completed the online survey, including 33 high-income and 16 low- and middle-income country respondents. The top, prioritized research question asks whether accreditation or regulation of private clinical and non-clinical sources of care would improve integrated management of childhood illness services. Four of the top ten research priorities were related to adherence to case management protocols. Other top research priorities were related to training and supportive supervision, digital health, and infant and newborn care. Research priorities among high-income and low- and middle-income country respondents were highly correlated. CONCLUSION: To our knowledge, this is the first systematic exercise conducted to define research priorities for the management of childhood illness in the private sector. The research priorities put forth in this CHNRI exercise aim to stimulate interest from policy makers, program managers, researchers, and donors to respond to and help close evidence gaps hindering the acceleration of reductions in child mortality through private sector approaches.

CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes.

MOTIVATION: DNA copy number (CN) data are a fast-growing source of information used in basic and translational cancer research. Most CN segmentation data are presented without regard to the relationship between chromosomal regions. We offer both a toolkit to help scientists without programming experience visually explore the CN interactome and a package that constructs CN interactomes from publicly available data sets. RESULTS: The CNVScope visualization, based on a publicly available neuroblastoma CN data set, clearly displays a distinct CN interaction in the region of the MYCN, a canonical frequent amplicon target in this cancer. Exploration of the data rapidly identified cis and trans events, including a strong anticorrelation between 11q loss and17q gain with the region of 11q loss bounded by the cell cycle regulator CCND1. AVAILABILITY: The shiny application is readily available for use at http://cnvscope.nci.nih.gov/, and the package can be downloaded from CRAN (https://cran.r-project.org/package=CNVScope), where help pages and vignettes are located. A newer version is available on the GitHub site (https://github.com/jamesdalg/CNVScope/), which features an animated tutorial. The CNVScope package can be locally installed using instructions on the GitHub site for Windows and Macintosh systems. This CN analysis package also runs on a linux high-performance computing cluster, with options for multinode and multiprocessor analysis of CN variant data. The shiny application can be started using a single command (which will automatically install the public data package).

Monocyte recruitment and activated inflammation are associated with thyroid carcinogenesis in a mouse model.

Thyroid cancer is the most common endocrine malignancy. Although an association between inflammation and thyroid cancer has long been recognized, a cause-effect relationship at the molecular level has yet to be elucidated. We explored how inflammation could contribute to thyroid carcinogenesis in ThrbPV/PVPten+/- mice. The ThrbPV/PVPten+/- mouse expresses a dominantly negative thyroid hormone receptor ß (denoted as PV) and a deletion of one single allele of the Pten gene. This mutant mouse exhibits aggressive follicular thyroid cancer similarly as in patients. We found significantly increased infiltration of inflammatory monocytes in thyroid tumors of ThrbPV/PVPten+/- mice, while no apparent changes in monocyte homeostasis in the bone marrow and blood of tumor-bearing mice. Using global gene expression profiling, we found altered expression of inflammation mediators in that the expression of Ptgs1, Sphk1, OPN, Chil1, Tnfrsf18, IL6, and Ccl12 genes was significantly increased and expression of Kit, Ly96, Ephx2, CD163, IL15, and Ccr2 was significantly decreased. Subsequent validation of the gene expression by mRNA analysis prompted us to further delineate the inflammatory role of osteopontin (OPN) in thyroid carcinogenesis because of its critical role in monocyte/macrophage functions and proinflammatory responses. We found that the protein abundance of OPN and its receptor, integrin ß1, was highly increased and, concurrently, the downstream effectors AKT and NF-κB were significantly elevated to drive thyroid tumor progression of ThrbPV/PVPten+/- mice. These results demonstrated that increased inflammation driven by elevated expression of immune-related genes and cytokines promoted thyroid cancer progression. Importantly, we uncovered OPN as a novel regulator in inflammatory response during thyroid carcinogenesis. These preclinical findings suggested that OPN can be a potential target for thyroid cancer therapy via modulation of inflammatory signaling.

Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution.

BK polyomavirus (BKV) frequently causes nephropathy (BKVN) in kidney transplant recipients (KTRs). BKV has also been implicated in the etiology of bladder and kidney cancers. We characterized BKV variants from two KTRs who developed BKVN followed by renal carcinoma. Both patients showed a swarm of BKV sequence variants encoding non-silent mutations in surface loops of the viral major capsid protein. The temporal appearance and disappearance of these mutations highlights the intra-patient evolution of BKV. Some of the observed mutations conferred resistance to antibody-mediated neutralization. The mutations also modified the spectrum of receptor glycans engaged by BKV during host cell entry. Intriguingly, all observed mutations were consistent with DNA damage caused by antiviral APOBEC3 cytosine deaminases. Moreover, APOBEC3 expression was evident upon immunohistochemical analysis of renal biopsies from KTRs. These results provide a snapshot of in-host BKV evolution and suggest that APOBEC3 may drive BKV mutagenesis in vivo.

Somatic VHL Mutation in a Patient With MEN1-Associated Metastatic Pancreatic Neuroendocrine Tumor Responding to Sunitinib Treatment: A Case Report.

Multiple endocrine neoplasia type 1 (MEN1) and von Hippel-Lindau (VHL) are autosomal-dominant diseases caused by germline mutations in tumor-suppressor genes. A patient with a germline MEN1 mutation and a somatic VHL mutation in the tumor has not been reported. Herein, we report on a patient with MEN1 and a metastatic nonfunctioning pancreatic neuroendocrine tumor (PNET) with a somatic VHL mutation. This patient underwent a pancreaticoduodenectomy for a grade 2 PNET obstructing her pancreatic duct. The patient developed liver and regional lymph node metastases as well as growth of a PNET in the remnant pancreas. As part of a clinical trial for mutation-targeted therapy, a biopsy of the metastatic tumor was obtained. The clinical diagnosis, confirmed by OncoVAR-NET and molecular profiling analysis, revealed MEN1 with a germline deletion in exon 2 and a c.402 deletion C, p.Phe134LeufsX51. In addition, a somatic mutation in the VHL gene-a nonsense mutation, c.529A>T, p.Arg177Ter-was identified by hybrid capture sequencing. The mutations were confirmed by Sanger sequencing. Comparative genomic hybridization showed loss of heterozygosity in both the MEN1 and VHL genes. The patient was treated with sunitinib and had a partial response to treatment. This case illustrates not only that a second hit occurs in tumor suppressor genes but that somatic mutations are also possible in additional tumor suppressor genes. This suggests that targeted therapy selection should include analysis of somatic mutations even when the susceptibility gene is known.

Haptic fMRI: Reliability and performance of electromagnetic haptic interfaces for motion and force neuroimaging experiments.

Haptic interfaces compatible with functional magnetic resonance imaging (Haptic fMRI) promise to enable rich motor neuroscience experiments that study how humans perform complex manipulation tasks. Here, we present a large-scale study (176 scans runs, 33 scan sessions) that characterizes the reliability and performance of one such electromagnetically actuated device, Haptic fMRI Interface 3 (HFI-3). We outline engineering advances that ensured HFI-3 did not interfere with fMRI measurements. Observed fMRI temporal noise levels with HFI-3 operating were at the fMRI baseline (0.8% noise to signal). We also present results from HFI-3 experiments demonstrating that high resolution fMRI can be used to study spatio-temporal patterns of fMRI blood oxygenation dependent (BOLD) activation. These experiments include motor planning, goal-directed reaching, and visually-guided force control. Observed fMRI responses are consistent with existing literature, which supports Haptic fMRI's effectiveness at studying the brain's motor regions.

Novel near-diploid ovarian cancer cell line derived from a highly aneuploid metastatic ovarian tumor.

A new ovarian near-diploid cell line, OVDM1, was derived from a highly aneuploid serous ovarian metastatic adenocarcinoma. A metastatic tumor was obtained from a 47-year-old Ashkenazi Jewish patient three years after the first surgery removed the primary tumor, both ovaries, and the remaining reproductive organs. OVDM1 was characterized by cell morphology, genotyping, tumorigenic assay, mycoplasma testing, spectral karyotyping (SKY), and molecular profiling of the whole genome by aCGH and gene expression microarray. Targeted sequencing of a panel of cancer-related genes was also performed. Hierarchical clustering of gene expression data clearly confirmed the ovarian origin of the cell line. OVDM1 has a near-diploid karyotype with a low-level aneuploidy, but samples of the original metastatic tumor were grossly aneuploid. A number of single nucleotide variations (SNVs)/mutations were detected in OVDM1 and the metastatic tumor samples. Some of them were cancer-related according to COSMIC and HGMD databases (no founder mutations in BRCA1 and BRCA2 have been found). A large number of focal copy number alterations (FCNAs) were detected, including homozygous deletions (HDs) targeting WWOX and GATA4. Progression of OVDM1 from early to late passages was accompanied by preservation of the near-diploid status, acquisition of only few additional large chromosomal rearrangements and more than 100 new small FCNAs. Most of newly acquired FCNAs seem to be related to localized but massive DNA fragmentation (chromothripsis-like rearrangements). Newly developed near-diploid OVDM1 cell line offers an opportunity to evaluate tumorigenesis pathways/events in a minor clone of metastatic ovarian adenocarcinoma as well as mechanisms of chromothripsis.

Functional Genomic Screening Reveals Splicing of the EWS-FLI1 Fusion Transcript as a Vulnerability in Ewing Sarcoma.

Ewing sarcoma cells depend on the EWS-FLI1 fusion transcription factor for cell survival. Using an assay of EWS-FLI1 activity and genome-wide RNAi screening, we have identified proteins required for the processing of the EWS-FLI1 pre-mRNA. We show that Ewing sarcoma cells harboring a genomic breakpoint that retains exon 8 of EWSR1 require the RNA-binding protein HNRNPH1 to express in-frame EWS-FLI1. We also demonstrate the sensitivity of EWS-FLI1 fusion transcripts to the loss of function of the U2 snRNP component, SF3B1. Disrupted splicing of the EWS-FLI1 transcript alters EWS-FLI1 protein expression and EWS-FLI1-driven expression. Our results show that the processing of the EWS-FLI1 fusion RNA is a potentially targetable vulnerability in Ewing sarcoma cells.

Characterization of the metastatic phenotype of a panel of established osteosarcoma cells.

Osteosarcoma (OS) is the most common bone tumor in pediatric patients. Metastasis is a major cause of mortality and morbidity. The rarity of this disease coupled with the challenges of drug development for metastatic cancers have slowed the delivery of improvements in long-term outcomes for these patients. In this study, we collected 18 OS cell lines, confirmed their expression of bone markers and complex karyotypes, and characterized their in vivo tumorgenicity and metastatic potential. Since prior reports included conflicting descriptions of the metastatic and in vivo phenotypes of these models, there was a need for a comparative assessment of metastatic phenotypes using identical procedures in the hands of a single investigative group. We expect that this single characterization will accelerate the study of this metastatic cancer. Using these models we evaluated the expression of six previously reported metastasis-related OS genes. Ezrin was the only gene consistently differentially expressed in all the pairs of high/low metastatic OS cells. We then used a subtractive gene expression approach of the high and low human metastatic cells to identify novel genes that may be involved in OS metastasis. PHLDA1 (pleckstrin homology-like domain, family A) was identified as one of the genes more highly expressed in the high metastatic compared to low metastatic cells. Knocking down PHLDA1 with siRNA or shRNA resulted in down regulation of the activities of MAPKs (ERK1/2), c-Jun N-terminal kinases (JNK), and p38 mitogen-activated protein kinases (MAPKs). Reducing the expression of PHLDA1 also delayed OS metastasis progression in mouse xenograft models.

Mapping stiffness perception in the brain with an fMRI-compatible particle-jamming haptic interface.

We demonstrate reliable neural responses to changes in haptic stiffness perception using a functional magnetic resonance imaging (fMRI) compatible particle-jamming haptic interface. Our haptic interface consists of a silicone tactile surface whose stiffness we can control by modulating air-pressure in a sub-surface pouch of coarsely ground particles. The particles jam together as the pressure decreases, which stiffens the surface. During fMRI acquisition, subjects performed a constant probing task, which involved continuous contact between the index fingertip and the interface and rhythmic increases and decreases in fingertip force (1.6 Hz) to probe stiffness. Without notifying subjects, we randomly switched the interface's stiffness (switch time, 300-500 ms) from soft (200 N/m) to hard (1400 N/m). Our experiment design's constant motor activity and cutaneous tactile sensation helped disassociate neural activation for both from stiffness perception, which helped localized it to a narrow region in somatosensory cortex near the supra-marginal gyrus. Testing different models of neural activation, we found that assuming indepedent stiffness-change responses at both soft-hard and hard-soft transitions provides the best explanation for observed fMRI measurements (three subjects; nine four-minute scan runs each). Furthermore, we found that neural activation related to stiffness-change and absolute stiffness can be localized to adjacent but disparate anatomical locations. We also show that classical finger-tapping experiments activate a swath of cortex and are not suitable for localizing stiffness perception. Our results demonstrate that decorrelating motor and sensory neural activation is essential for characterizing somatosensory cortex, and establish particle-jamming haptics as an attractive low-cost method for fMRI experiments.

Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling.

Microarray technologies provide high-resolution maps of chromosome imbalances and epigenomic aberrations in the cancer cell genome. Such assays are often sensitive to sample DNA integrity, voiding the utility of many archival pathology specimens and necessitating the special handling of prospective clinical specimens. We have identified the remarkable preservation of higher-molecular weight DNA in archival fine-needle aspiration cytopathology specimens from patients greater than 10 years of age. We further demonstrate the outstanding technical performance of 57 fine-needle aspiration cytopathology samples for aberration detection on high-resolution comparative genomic hybridization array, DNA methylation, and single nucleotide polymorphism genotyping platforms. Forty-four of 46 malignant aspirates in this study manifested unequivocal genomic aberrations. Importantly, matched Papanicolaou and Diff-Quik fine-needle aspiration cytopathology samples showed critical differences in DNA preservation and DNA integrity. Overall, this study identifies a largely untapped reserve of human pathology specimens for molecular profiling studies, with ramifications for the prospective collection of clinical biospecimens.