Mark A. Atkinson
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Machine learning models predict long COVID outcomes based on baseline clinical and immunologic factors Open
Machine learning models identify patients at risk for developing long COVID based on baseline clinical characteristics. These models guide early interventions, improve patient outcomes, and mitigate the long-term public health impacts of S…
View article: Evaluating COVID-19 severity prediction and immune dynamics with NULISAseq: Insights from the IMPACC study.
Evaluating COVID-19 severity prediction and immune dynamics with NULISAseq: Insights from the IMPACC study. Open
The National Institutes of Health-funded IMPACC (IMmunoPhenotyping Assessment in a COVID-19 Cohort) evaluated longitudinal clinical and immunological features of human patients hospitalized for COVID-19. This study focuses on comparing the…
View article: Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes
Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes Open
Progressive β-cell dysfunction precedes the onset of type 1 diabetes (T1D), yet the molecular mechanisms driving early T1D development remain poorly understood. Although single-cell RNA-sequencing has uncovered transcript-level changes in …
View article: Distinct metabolomic profiles and systemic lipid dysregulation in longitudinal analysis of COVID-19 disease trajectory and long COVID outcomes 2785
Distinct metabolomic profiles and systemic lipid dysregulation in longitudinal analysis of COVID-19 disease trajectory and long COVID outcomes 2785 Open
Description The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a longitudinal study of 1,132 hospitalized COVID-19 patients across the US aimed at identifying molecular signatures associated with acute disease trajectory dur…
View article: Inhibition of cell-mediated immunity in type 1 diabetes by beta cell-targeted PD-1 agonists in pancreas tissue slices
Inhibition of cell-mediated immunity in type 1 diabetes by beta cell-targeted PD-1 agonists in pancreas tissue slices Open
Tissue-targeted immunotherapies for type 1 diabetes (T1D) hold potential to protect pancreatic beta cells while minimizing systemic immunosuppression. We used a bispecific agonist called Immune Modulating Monoclonal-TCR Against Autoimmune …
View article: Circulating endothelial signatures correlate with worse outcomes in COVID-19, respiratory failure and ARDS
Circulating endothelial signatures correlate with worse outcomes in COVID-19, respiratory failure and ARDS Open
Background Elevated circulating endothelial cells (CECs), released from monolayers after insult, have been implicated in worse outcomes in ARDS and COVID-19, however there is no consensus proteomic phenotype that define CECs. We queried wh…
View article: 3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors
3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors Open
Uncovering the spatial and molecular landscape of precancerous lesions is essential for developing meaningful cancer prevention and early detection strategies. High-Grade Serous Carcinoma (HGSC), the most lethal gynecologic malignancy, oft…
View article: Whole tissue spatial cellular analysis reveals increased macrophage infiltration in pancreata of autoantibody positive donors and patients with type 1 diabetes
Whole tissue spatial cellular analysis reveals increased macrophage infiltration in pancreata of autoantibody positive donors and patients with type 1 diabetes Open
While extensive efforts have characterized lymphoid populations that contribute to pancreatic ‘insulitis’ in type 1 diabetes, significant gaps remain regarding key properties of macrophages in this inflammatory lesion. Hence, we quantified…
View article: Single-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression
Single-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression Open
Cell type–specific regulatory programs that drive type 1 diabetes (T1D) in the pancreas are poorly understood. Here, we performed single-nucleus multiomics and spatial transcriptomics in up to 32 nondiabetic (ND), autoantibody-positive (AA…
View article: A multiomics recovery factor predicts long COVID in the IMPACC study
A multiomics recovery factor predicts long COVID in the IMPACC study Open
BACKGROUNDFollowing SARS-CoV-2 infection, approximately 10%-35% of patients with COVID-19 experience long COVID (LC), in which debilitating symptoms persist for at least 3 months. Elucidating the biologic underpinnings of LC could identify…
Beta cell dysfunction occurs independently of insulitis in type 1 diabetes pathogenesis Open
The loss of insulin secretory function associated with type 1 diabetes (T1D) is attributed to the immune-mediated destruction of beta cells. Yet, at onset of T1D, patients often retain a substantial beta cell mass, and T cell infiltration …
View article: <b>The loss of insulin-positive cell clusters precedes the decrease of islet frequency and beta cell area in type 1 diabetes</b>
<b>The loss of insulin-positive cell clusters precedes the decrease of islet frequency and beta cell area in type 1 diabetes</b> Open
In type 1 diabetes, insulin deficiency results from immune-mediated destruction of beta cells. The majority of functional beta cell mass is typically lost within months to years of disease diagnosis, but the timing and nature of this loss,…
View article: <b>The loss of insulin-positive cell clusters precedes the decrease of islet frequency and beta cell area in type 1 diabetes</b>
<b>The loss of insulin-positive cell clusters precedes the decrease of islet frequency and beta cell area in type 1 diabetes</b> Open
In type 1 diabetes, insulin deficiency results from immune-mediated destruction of beta cells. The majority of functional beta cell mass is typically lost within months to years of disease diagnosis, but the timing and nature of this loss,…
View article: Report of the 2023 Mary Tyler Moore Vision Initiative Workshop
Report of the 2023 Mary Tyler Moore Vision Initiative Workshop Open
The Mary Tyler Moore Vision Initiative (MTM Vision) Diabetic Retinal Disease (DRD) Clinical Endpoints Workshop was held on November 14, 2023. More than 130 clinicians, scientists, and representatives from funding and regulatory agencies, d…
View article: Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study
Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study Open
Introduction The coronavirus disease 2019 (COVID-19) pandemic threatened public health and placed a significant burden on medical resources. The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study collected clinical, demograph…
View article: MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury
MICBG406A polymorphism reduces risk of mechanical ventilation and death during viral acute lung injury Open
MHC class I polypeptide-related sequence B (MICB) is a ligand for NKG2D. We have shown NK cells are central to lung transplant acute lung injury (ALI) via NKG2D activation, and increased MICB in bronchoalveolar lavage predicts ALI severity…
View article: Integrated histopathology of the human pancreas throughout stages of type 1 diabetes progression
Integrated histopathology of the human pancreas throughout stages of type 1 diabetes progression Open
Type 1 diabetes (T1D) is a progressive autoimmune condition that culminates in loss of insulin-producing beta cells. Pancreatic histopathology provides essential insights into disease initiation and progression yet an integrated perspectiv…
View article: 3D imaging of human pancreas suggests islet size and endocrine composition influence their loss in type 1 diabetes
3D imaging of human pancreas suggests islet size and endocrine composition influence their loss in type 1 diabetes Open
A high-definition description of pancreatic islets would prove beneficial for understanding the pathophysiology of type 1 diabetes (T1D), yet significant knowledge voids exist in terms of their size, endocrine cell composition, and number …
View article: Increased inflammation as well as decreased endoplasmic reticulum stress and translation differentiate pancreatic islets from donors with pre-symptomatic stage 1 type 1 diabetes and non-diabetic donors
Increased inflammation as well as decreased endoplasmic reticulum stress and translation differentiate pancreatic islets from donors with pre-symptomatic stage 1 type 1 diabetes and non-diabetic donors Open
The LC-MS raw datasets that support the findings of this study have been deposited in the online repository: MassIVE ( https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp ) with accession no. MSV000090212.
View article: Aberrant immune regulation and enrichment of stem-like CD8 <sup>+</sup> T cells in the pancreatic lymph node during type 1 diabetes development
Aberrant immune regulation and enrichment of stem-like CD8 <sup>+</sup> T cells in the pancreatic lymph node during type 1 diabetes development Open
Summary Effector CD8 + T cells are key cellular drivers of type 1 diabetes (T1D) pathogenesis, yet questions remain regarding the molecular defects leading to altered cytotoxicity, their signature in peripheral tissues, and their receptor …
View article: Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes
Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes Open
SUMMARY This study explores the inflammatory response observed in pancreata and pancreatic lymph node (pLN) samples obtained throughout the natural history of type 1 diabetes (T1D) including non-diabetic individuals and non-diabetic autoan…
View article: High-affinity CD16A polymorphism associated with reduced risk ofsevere COVID-19
High-affinity CD16A polymorphism associated with reduced risk ofsevere COVID-19 Open
CD16A is an activating Fc receptor on NK cells that mediates antibody-dependent cellular cytotoxicity (ADCC), a key mechanism in antiviral immunity. However, the role of NK cell-mediated ADCC in SARS-CoV-2 infection remains unclear, partic…
View article: Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset
Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset Open
Autoimmune destruction of pancreatic β cells results in type 1 diabetes (T1D), with pancreatic immune infiltrate representing a key feature in this process. However, characterization of the immunological processes occurring in human pancre…
View article: 3D imaging of human pancreas suggests islet size and endocrine composition influence their loss in type 1 diabetes
3D imaging of human pancreas suggests islet size and endocrine composition influence their loss in type 1 diabetes Open
Summary A high-definition description of pancreatic islets would prove beneficial for understanding the pathophysiology of type 1 diabetes (T1D), yet significant knowledge voids exist in terms of their size, endocrine cell composition, and…
View article: The Cardiovascular Repository for Type 1 Diabetes (CaRe-T1D): An NIDDK Initiative to Advance Understanding of Mechanisms Underlying Cardiovascular Disease in Type 1 Versus Type 2 Diabetes
The Cardiovascular Repository for Type 1 Diabetes (CaRe-T1D): An NIDDK Initiative to Advance Understanding of Mechanisms Underlying Cardiovascular Disease in Type 1 Versus Type 2 Diabetes Open
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality in individuals with diabetes. Individuals with type 1 diabetes have a two- to fourfold higher risk of CVD in comparison with the general population, driven by an ea…