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1.
Clin Cancer Res ; 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38980919

ABSTRACT

PURPOSE: Interleukin-2 and -12 cytokines have potent anti-cancer activity, but suffer a narrow therapeutic window due to off-tumor immune cell activation. Engineering cytokines with the ability to bind and associate with tumor collagen after intratumoral injection potentiated response without toxicity in mice, and was previously safe in pet dogs with sarcoma. Here we sought to test the efficacy of this approach with in dogs with advanced melanoma. EXPERIMENTAL DESIGN: This study examined fifteen client-owned dogs with histologically- or cytologically-confirmed malignant melanoma who received a single 9 Gray fraction of radiation therapy, followed by six cycles of combined collagen-anchored IL-2 and IL-12 therapy Q2W. Cytokine dosing followed a 3+3 dose escalation design, with the initial cytokine dose chosen from prior evaluation in canine sarcomas. No exclusion criteria for tumor stage or metastatic burden, age, weight, or neuter status were applied for this trial. RESULTS: Median survival regardless of tumor stage or dose level was 256 days and 10/13 (76.9%) dogs that completed treatment had CT-measured tumor regression at the treated lesion. In dogs with metastatic disease, 8/13 (61.5%) dogs had partial responses across their combined lesions, evidence of locoregional response. Profiling by Nanostring of treatment-resistant dogs revealed that B2m loss was predictive of poor response to this therapy. CONCLUSIONS: Collectively, these results confirm the ability of locally administered tumor-anchored cytokines to potentiate responses at regional disease sites when combined with radiation. This evidence supports the clinical translation of this approach and highlights the utility of comparative investigation in canine cancers.

2.
Acta Neuropathol ; 148(1): 3, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38980423

ABSTRACT

This study investigates various pathological tau isoforms in the retina of individuals with early and advanced Alzheimer's disease (AD), exploring their connection with disease status. Retinal cross-sections from predefined superior-temporal and inferior-temporal subregions and corresponding brains from neuropathologically confirmed AD patients with a clinical diagnosis of either mild cognitive impairment (MCI) or dementia (n = 45) were compared with retinas from age- and sex-matched individuals with normal cognition (n = 30) and non-AD dementia (n = 4). Retinal tau isoforms, including tau tangles, paired helical filament of tau (PHF-tau), oligomeric-tau (Oligo-tau), hyperphosphorylated-tau (p-tau), and citrullinated-tau (Cit-tau), were stereologically analyzed by immunohistochemistry and Nanostring GeoMx digital spatial profiling, and correlated with clinical and neuropathological outcomes. Our data indicated significant increases in various AD-related pretangle tau isoforms, especially p-tau (AT8, 2.9-fold, pS396-tau, 2.6-fold), Cit-tau at arginine residue 209 (CitR209-tau; 4.1-fold), and Oligo-tau (T22+, 9.2-fold), as well as pretangle and mature tau tangle forms like MC-1-positive (1.8-fold) and PHF-tau (2.3-fold), in AD compared to control retinas. MCI retinas also exhibited substantial increases in Oligo-tau (5.2-fold), CitR209-tau (3.5-fold), and pS396-tau (2.2-fold). Nanostring GeoMx analysis confirmed elevated retinal p-tau at epitopes: Ser214 (2.3-fold), Ser396 (2.6-fold), Ser404 (2.4-fold), and Thr231 (1.8-fold), particularly in MCI patients. Strong associations were found between retinal tau isoforms versus brain pathology and cognitive status: a) retinal Oligo-tau vs. Braak stage, neurofibrillary tangles (NFTs), and CDR cognitive scores (ρ = 0.63-0.71), b) retinal PHF-tau vs. neuropil threads (NTs) and ABC scores (ρ = 0.69-0.71), and c) retinal pS396-tau vs. NTs, NFTs, and ABC scores (ρ = 0.67-0.74). Notably, retinal Oligo-tau strongly correlated with retinal Aß42 and arterial Aß40 forms (r = 0.76-0.86). Overall, this study identifies and quantifies diverse retinal tau isoforms in MCI and AD patients, underscoring their link to brain pathology and cognition. These findings advocate for further exploration of retinal tauopathy biomarkers to facilitate AD detection and monitoring via noninvasive retinal imaging.


Subject(s)
Alzheimer Disease , Protein Isoforms , Retina , tau Proteins , Humans , tau Proteins/metabolism , Male , Female , Aged , Alzheimer Disease/pathology , Alzheimer Disease/metabolism , Retina/pathology , Retina/metabolism , Aged, 80 and over , Cognitive Dysfunction/pathology , Cognitive Dysfunction/metabolism , Middle Aged , Neurofibrillary Tangles/pathology , Neurofibrillary Tangles/metabolism , Brain/pathology , Brain/metabolism
3.
Am J Hum Biol ; : e24126, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38957054

ABSTRACT

Organ weights are a possible diagnostic or pathophysiological clue to distinguishing sudden infant death syndrome (SIDS) cases from other infant deaths but suffer from major confounding. Using autopsy data from the Chicago Infant Mortality Study, a majority African-American case-control study of deceased infants under 1 year conducted 1993-96, we assessed differences in the weights of brain, thymus, kidneys, lungs, liver, spleen, total body, and four length anthropometry measures in SIDS-diagnosed infants compared to controls. Using exact and coarsened matching, we ran Bayesian linear models with these anthropometry outcomes and repeated the analyses substituting the corresponding fitted allometrically-scaled organ weight indices to account for body size. After detailed analysis and adjustment for potential confounders, we found that matched SIDS infants were generally bigger than controls, with higher mean brain, liver, spleen, thymus, lung, and total body weights, and higher mean head and chest circumference, crown-heel, crown-rump lengths. SIDS infants also had higher mean thymus, liver, spleen, lung and total body weight indices. The association with thymus weight was proportionately greater in magnitude than any other outcome measure and independent of body size. The results of these more detailed analyses are consistent with recent findings from other studies with differing racial compositions, and substantially confirm the primary organ sites for more detailed mechanistic research into the biological dysregulation contributing to underlying pathophysiology of SIDS.

4.
Bull Math Biol ; 86(8): 104, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38980556

ABSTRACT

Atherosclerotic plaques are fatty deposits that form in the walls of major arteries and are one of the major causes of heart attacks and strokes. Macrophages are the main immune cells in plaques and macrophage dynamics influence whether plaques grow or regress. Macrophage proliferation is a key process in atherosclerosis, particularly in the development of mid-stage plaques, but very few mathematical models include proliferation. In this paper we reframe the lipid-structured model of Ford et al. (J Theor Biol 479:48-63, 2019. https://doi.org/10.1016/j.jtbi.2019.07.003 ) to account for macrophage proliferation. Proliferation is modelled as a non-local decrease in the lipid structural variable. Steady state analysis indicates that proliferation assists in reducing eventual necrotic core lipid content and spreads the lipid load of the macrophage population amongst the cells. The contribution of plaque macrophages from proliferation relative to recruitment from the bloodstream is also examined. The model suggests that a more proliferative plaque differs from an equivalent (defined as having the same lipid content and cell numbers) recruitment-dominant plaque in the way lipid is distributed amongst the macrophages. The macrophage lipid distribution of an equivalent proliferation-dominant plaque is less skewed and exhibits a local maximum near the endogenous lipid content.


Subject(s)
Atherosclerosis , Cell Proliferation , Lipid Metabolism , Macrophages , Mathematical Concepts , Models, Cardiovascular , Plaque, Atherosclerotic , Macrophages/pathology , Macrophages/metabolism , Atherosclerosis/pathology , Atherosclerosis/metabolism , Plaque, Atherosclerotic/pathology , Humans , Animals , Computer Simulation , Lipids
5.
Proc Natl Acad Sci U S A ; 121(29): e2401420121, 2024 Jul 16.
Article in English | MEDLINE | ID: mdl-38995966

ABSTRACT

Cerebral (Aß) plaque and (pTau) tangle deposition are hallmarks of Alzheimer's disease (AD), yet are insufficient to confer complete AD-like neurodegeneration experimentally. Factors acting upstream of Aß/pTau in AD remain unknown, but their identification could enable earlier diagnosis and more effective treatments. T cell abnormalities are emerging AD hallmarks, and CD8 T cells were recently found to mediate neurodegeneration downstream of tangle deposition in hereditary neurodegeneration models. The precise impact of T cells downstream of Aß/pTau, however, appears to vary depending on the animal model. Our prior work suggested that antigen-specific memory CD8 T ("hiT") cells act upstream of Aß/pTau after brain injury. Here, we examine whether hiT cells influence sporadic AD-like pathophysiology upstream of Aß/pTau. Examining neuropathology, gene expression, and behavior in our hiT mouse model we show that CD8 T cells induce plaque and tangle-like deposition, modulate AD-related genes, and ultimately result in progressive neurodegeneration with both gross and fine features of sporadic human AD. T cells required Perforin to initiate this pathophysiology, and IFNγ for most gene expression changes and progression to more widespread neurodegenerative disease. Analogous antigen-specific memory CD8 T cells were significantly elevated in the brains of human AD patients, and their loss from blood corresponded to sporadic AD and related cognitive decline better than plasma pTau-217, a promising AD biomarker candidate. We identify an age-related factor acting upstream of Aß/pTau to initiate AD-like pathophysiology, the mechanisms promoting its pathogenicity, and its relevance to human sporadic AD.


Subject(s)
Alzheimer Disease , CD8-Positive T-Lymphocytes , Disease Models, Animal , Alzheimer Disease/immunology , Alzheimer Disease/pathology , Alzheimer Disease/genetics , Animals , CD8-Positive T-Lymphocytes/immunology , Mice , Humans , Plaque, Amyloid/pathology , Plaque, Amyloid/immunology , Amyloid beta-Peptides/metabolism , Mice, Transgenic , Brain/pathology , Brain/immunology , Male , Interferon-gamma/metabolism , Interferon-gamma/immunology , Aging/immunology , Immunologic Memory , Memory T Cells/immunology , Perforin/metabolism , Perforin/genetics , Female
6.
Nat Commun ; 15(1): 5837, 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38992034

ABSTRACT

To inform clinical trial design and real-world precision pediatric oncology practice, we classified diagnoses, assessed the landscape of mutations, and identified genomic variants matching trials in a large unselected institutional cohort of solid tumors patients sequenced at Dana-Farber / Boston Children's Cancer and Blood Disorders Center. Tumors were sequenced with OncoPanel, a targeted next-generation DNA sequencing panel. Diagnoses were classified according to the International Classification of Diseases for Oncology (ICD-O-3.2). Over 6.5 years, 888 pediatric cancer patients with 95 distinct diagnoses had successful tumor sequencing. Overall, 33% (n = 289/888) of patients had at least 1 variant matching a precision oncology trial protocol, and 14% (41/289) were treated with molecularly targeted therapy. This study highlights opportunities to use genomic data from hospital-based sequencing performed either for research or clinical care to inform ongoing and future precision oncology clinical trials. Furthermore, the study results emphasize the importance of data sharing to define the genomic landscape and targeted treatment opportunities for the large group of rare pediatric cancers we encounter in clinical practice.


Subject(s)
High-Throughput Nucleotide Sequencing , Information Dissemination , Neoplasms , Precision Medicine , Humans , Neoplasms/genetics , Neoplasms/drug therapy , Child , Precision Medicine/methods , Male , Child, Preschool , Female , High-Throughput Nucleotide Sequencing/methods , Adolescent , Infant , Mutation , Clinical Trials as Topic , Molecular Targeted Therapy/methods , Genomics/methods , Infant, Newborn
7.
Ethn Health ; : 1-18, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38937933

ABSTRACT

Dementia can be overwhelming to families and their caregivers. Informal caregiving is a widespread mode of providing dementia care in African American communities, yet impact of caregiving on informal or family caregivers in African American communities is burdensome. This study aimed to describe the lived experiences of informal caregivers of African American People Living with Dementia (PLWD) to understand their perceptions of dementia and dementia care, caregiver support needs, and service needs. Interpretive phenomenological qualitative inquiry guided this study to understand caregivers' experiences and needs. Ten family caregivers of African American PLWD in the community participated in this study. Data were collected through in-depth interviews and a diary study approach to document and interpret caregivers' experiences. The data analysis was based on procedures of content analysis. Four major themes emerged from the in-depth interviews: caregiver burden, familism, lack of information and community-based resources, and desire and need for culturally appropriate community-based resources. Triangulated diary entry data complemented the in-depth interviews with similar themes. This study highlights how African American informal caregivers of PLWD face various caregiving needs and challenges in dementia care including lack of culturally appropriate community resources and information. The study illustrates that African American cultural beliefs of familism are significant aspects of their caregiving experience and their coping strategies. These study results provide a useful foundation for various stakeholders to develop culturally targeted interventions and programs to support African American informal caregivers and their family members with dementia.

8.
Acta Neuropathol Commun ; 12(1): 109, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38943220

ABSTRACT

The relationship between amyloidosis and vasculature in cognitive impairment and Alzheimer's disease (AD) pathogenesis is increasingly acknowledged. We conducted a quantitative and topographic assessment of retinal perivascular amyloid plaque (AP) distribution in individuals with both normal and impaired cognition. Using a retrospective dataset of scanning laser ophthalmoscopy fluorescence images from twenty-eight subjects with varying cognitive states, we developed a novel image processing method to examine retinal peri-arteriolar and peri-venular curcumin-positive AP burden. We further correlated retinal perivascular amyloidosis with neuroimaging measures and neurocognitive scores. Our study unveiled that peri-arteriolar AP counts surpassed peri-venular counts throughout the entire cohort (P < 0.0001), irrespective of the primary, secondary, or tertiary vascular branch location, with a notable increase among cognitively impaired individuals. Moreover, secondary branch peri-venular AP count was elevated in the cognitively impaired (P < 0.01). Significantly, peri-venular AP count, particularly in secondary and tertiary venules, exhibited a strong correlation with clinical dementia rating, Montreal cognitive assessment score, hippocampal volume, and white matter hyperintensity count. In conclusion, our exploratory analysis detected greater peri-arteriolar versus peri-venular amyloidosis and a marked elevation of amyloid deposition in secondary branch peri-venular regions among cognitively impaired subjects. These findings underscore the potential feasibility of retinal perivascular amyloid imaging in predicting cognitive decline and AD progression. Larger longitudinal studies encompassing diverse populations and AD-biomarker confirmation are warranted to delineate the temporal-spatial dynamics of retinal perivascular amyloid deposition in cognitive impairment and the AD continuum.


Subject(s)
Amyloidosis , Atrophy , Cognitive Dysfunction , Hippocampus , Humans , Male , Female , Aged , Cognitive Dysfunction/pathology , Cognitive Dysfunction/diagnostic imaging , Hippocampus/pathology , Hippocampus/diagnostic imaging , Atrophy/pathology , Amyloidosis/pathology , Amyloidosis/diagnostic imaging , Aged, 80 and over , Retrospective Studies , Middle Aged , Plaque, Amyloid/pathology , Plaque, Amyloid/diagnostic imaging , Retinal Diseases/pathology , Retinal Diseases/diagnostic imaging , Retinal Vessels/pathology , Retinal Vessels/diagnostic imaging , Ophthalmoscopy/methods
9.
Stem Cells Dev ; 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38877807

ABSTRACT

Prolonged tissue ischemia and inflammation lead to organ deterioration and are often accompanied by microvasculature rarefaction, fibrosis, and elevated systemic Activin A (ActA), the level of which frequently correlates with disease severity. Mesenchymal stromal cells are prevalent in the perivascular niche and are likely involved in tissue homeostasis and pathology. This study investigated the effects of inflammatory cells on modulation of phenotype of adipose mesenchymal stromal cells (ASC) and the role of ActA in this process. Peripheral blood mononuclear cells were activated with lipopolysaccharide (activated peripheral blood mononuclear cells [aPBMC]) and presented to ASC. Expression of smooth muscle/myofibroblast markers, ActA, transforming growth factors beta 1-3 (TGFß1-3), and connective tissue growth factor (CTGF) was assessed in ASC. Silencing approaches were used to dissect the signaling cascade of aPBMC-induced acquisition of myofibroblast phenotype by ASC. ASC cocultured with aPBMC or exposed to the secretome of aPBMC upregulated smooth muscle cell markers alpha smooth muscle actin (αSMA), SM22α, and Calponin I; increased contractility; and initiated expression of ActA. Interleukin (IL)-1ß was sufficient to replicate this response, whereas blocking IL-1ß eliminated aPBMC effects. ASC-derived ActA stimulated CTGF and αSMA expression in ASC; the latter independent of CTGF. Induction of αSMA in ASC by IL-1ß or ActA-enriched media relied on extracellular enzymatic activity. ActA upregulated mRNA levels of several extracellular matrix proteins in ASC, albeit to a lesser degree than TGFß1, and marginally increased cell contractility. In conclusion, the study suggests that aPBMC induce myofibroblast phenotype with weak fibrotic activity in perivascular progenitors, such as ASC, through the IL-1ß-ActA signaling axis, which also promotes CTGF secretion, and these effects require ActA extracellular enzymatic processing.

10.
Cureus ; 16(5): e59478, 2024 May.
Article in English | MEDLINE | ID: mdl-38826995

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections to date and has led to a worldwide pandemic. Most patients had a complete recovery from the acute infection, however, a large number of the affected individuals experienced symptoms that persisted more than 3 months after diagnosis. These symptoms most commonly include fatigue, memory difficulties, brain fog, dyspnea, cough, and other less common ones such as headache, chest pain, paresthesias, mood changes, muscle pain, and weakness, skin rashes, and cardiac, endocrine, renal and hepatic manifestations. The treatment of this syndrome remains challenging. A multidisciplinary approach to address combinations of symptoms affecting multiple organ systems has been widely adopted. This narrative review aims to bridge the gap surrounding the broad treatment approaches by providing an overview of multidisciplinary management strategies for the most common long COVID conditions.

11.
Breast Cancer Res ; 26(1): 97, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38858721

ABSTRACT

BACKGROUND: Tumor immune infiltration and peripheral blood immune signatures have prognostic and predictive value in breast cancer. Whether distinct peripheral blood immune phenotypes are associated with response to neoadjuvant chemotherapy (NAC) remains understudied. METHODS: Peripheral blood mononuclear cells from 126 breast cancer patients enrolled in a prospective clinical trial (NCT02022202) were analyzed using Cytometry by time-of-flight with a panel of 29 immune cell surface protein markers. Kruskal-Wallis tests or Wilcoxon rank-sum tests were used to evaluate differences in immune cell subpopulations according to breast cancer subtype and response to NAC. RESULTS: There were 122 evaluable samples: 47 (38.5%) from patients with hormone receptor-positive, 39 (32%) triple-negative (TNBC), and 36 (29.5%) HER2-positive breast cancer. The relative abundances of pre-treatment peripheral blood T, B, myeloid, NK, and unclassified cells did not differ according to breast cancer subtype. In TNBC, higher pre-treatment myeloid cells were associated with lower pathologic complete response (pCR) rates. In hormone receptor-positive breast cancer, lower pre-treatment CD8 + naïve and CD4 + effector memory cells re-expressing CD45RA (TEMRA) T cells were associated with more extensive residual disease after NAC. In HER2 + breast cancer, the peripheral blood immune phenotype did not differ according to NAC response. CONCLUSIONS: Pre-treatment peripheral blood immune cell populations (myeloid in TNBC; CD8 + naïve T cells and CD4 + TEMRA cells in luminal breast cancer) were associated with response to NAC in early-stage TNBC and hormone receptor-positive breast cancers, but not in HER2 + breast cancer. TRIAL REGISTRATION: NCT02022202 . Registered 20 December 2013.


Subject(s)
Breast Neoplasms , Immunophenotyping , Neoadjuvant Therapy , Humans , Female , Neoadjuvant Therapy/methods , Middle Aged , Breast Neoplasms/drug therapy , Breast Neoplasms/immunology , Breast Neoplasms/blood , Breast Neoplasms/pathology , Adult , Aged , Receptor, ErbB-2/metabolism , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Leukocytes, Mononuclear/metabolism , Biomarkers, Tumor/blood , Prognosis , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/immunology , Triple Negative Breast Neoplasms/blood , Triple Negative Breast Neoplasms/pathology , Prospective Studies , Treatment Outcome , Chemotherapy, Adjuvant/methods
12.
Prog Retin Eye Res ; 101: 101273, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38759947

ABSTRACT

The retina is an emerging CNS target for potential noninvasive diagnosis and tracking of Alzheimer's disease (AD). Studies have identified the pathological hallmarks of AD, including amyloid ß-protein (Aß) deposits and abnormal tau protein isoforms, in the retinas of AD patients and animal models. Moreover, structural and functional vascular abnormalities such as reduced blood flow, vascular Aß deposition, and blood-retinal barrier damage, along with inflammation and neurodegeneration, have been described in retinas of patients with mild cognitive impairment and AD dementia. Histological, biochemical, and clinical studies have demonstrated that the nature and severity of AD pathologies in the retina and brain correspond. Proteomics analysis revealed a similar pattern of dysregulated proteins and biological pathways in the retina and brain of AD patients, with enhanced inflammatory and neurodegenerative processes, impaired oxidative-phosphorylation, and mitochondrial dysfunction. Notably, investigational imaging technologies can now detect AD-specific amyloid deposits, as well as vasculopathy and neurodegeneration in the retina of living AD patients, suggesting alterations at different disease stages and links to brain pathology. Current and exploratory ophthalmic imaging modalities, such as optical coherence tomography (OCT), OCT-angiography, confocal scanning laser ophthalmoscopy, and hyperspectral imaging, may offer promise in the clinical assessment of AD. However, further research is needed to deepen our understanding of AD's impact on the retina and its progression. To advance this field, future studies require replication in larger and diverse cohorts with confirmed AD biomarkers and standardized retinal imaging techniques. This will validate potential retinal biomarkers for AD, aiding in early screening and monitoring.


Subject(s)
Alzheimer Disease , Retina , Retinal Diseases , Alzheimer Disease/physiopathology , Humans , Retinal Diseases/physiopathology , Retinal Diseases/diagnosis , Retina/physiopathology , Animals , Tomography, Optical Coherence/methods , Amyloid beta-Peptides/metabolism , Retinal Vessels/physiopathology , Retinal Vessels/diagnostic imaging
13.
bioRxiv ; 2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38712225

ABSTRACT

Cell density, the ratio of cell mass to volume, is an indicator of molecular crowding and therefore a fundamental determinant of cell state and function. However, existing density measurements lack the precision or throughput to quantify subtle differences in cell states, particularly in primary samples. Here we present an approach for measuring the density of 30,000 single cells per hour with a precision of 0.03% (0.0003 g/mL) by integrating fluorescence exclusion microscopy with a suspended microchannel resonator. Applying this approach to human lymphocytes, we discovered that cell density and its variation decrease as cells transition from quiescence to a proliferative state, suggesting that the level of molecular crowding decreases and becomes more regulated upon entry into the cell cycle. Using a pancreatic cancer patient-derived xenograft model, we found that the ex vivo density response of primary tumor cells to drug treatment can predict in vivo tumor growth response. Our method reveals unexpected behavior in molecular crowding during cell state transitions and suggests density as a new biomarker for functional precision medicine.

14.
J Immunother Cancer ; 12(5)2024 May 15.
Article in English | MEDLINE | ID: mdl-38754917

ABSTRACT

BACKGROUND: Cancer neoantigens arise from protein-altering somatic mutations in tumor and rank among the most promising next-generation immuno-oncology agents when used in combination with immune checkpoint inhibitors. We previously developed a computational framework, REAL-neo, for identification, quality control, and prioritization of both class-I and class-II human leucocyte antigen (HLA)-presented neoantigens resulting from somatic single-nucleotide mutations, small insertions and deletions, and gene fusions. In this study, we developed a new module, SPLICE-neo, to identify neoantigens from aberrant RNA transcripts from two distinct sources: (1) DNA mutations within splice sites and (2) de novo RNA aberrant splicings. METHODS: First, SPLICE-neo was used to profile all DNA splice-site mutations in 11,892 tumors from The Cancer Genome Atlas (TCGA) and identified 11 profiles of splicing donor or acceptor site gains or losses. Transcript isoforms resulting from the top seven most frequent profiles were computed using novel logic models. Second, SPLICE-neo identified de novo RNA splicing events using RNA sequencing reads mapped to novel exon junctions from either single, double, or multiple exon-skipping events. The aberrant transcripts from both sources were then ranked based on isoform expression levels and z-scores assuming that individual aberrant splicing events are rare. Finally, top-ranked novel isoforms were translated into protein, and the resulting neoepitopes were evaluated for neoantigen potential using REAL-neo. The top splicing neoantigen candidates binding to HLA-A*02:01 were validated using in vitro T2 binding assays. RESULTS: We identified abundant splicing neoantigens in four representative TCGA cancers: BRCA, LUAD, LUSC, and LIHC. In addition to their substantial contribution to neoantigen load, several splicing neoantigens were potent tumor antigens with stronger bindings to HLA compared with the positive control of antigens from influenza virus. CONCLUSIONS: SPLICE-neo is the first tool to comprehensively identify and prioritize splicing neoantigens from both DNA splice-site mutations and de novo RNA aberrant splicings. There are two major advances of SPLICE-neo. First, we developed novel logic models that assemble and prioritize full-length aberrant transcripts from DNA splice-site mutations. Second, SPLICE-neo can identify exon-skipping events involving more than two exons, which account for a quarter to one-third of all skipping events.


Subject(s)
Antigens, Neoplasm , Neoplasms , RNA Splicing , Humans , Antigens, Neoplasm/immunology , Antigens, Neoplasm/genetics , Neoplasms/immunology , Neoplasms/genetics
15.
bioRxiv ; 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38645018

ABSTRACT

Over-activation of the epidermal growth factor receptor (EGFR) is a hallmark of glioblastoma. However, EGFR-targeted therapies have led to minimal clinical response. While delivery of EGFR inhibitors (EGFRis) to the brain constitutes a major challenge, how additional drug-specific features alter efficacy remains poorly understood. We apply highly multiplex single-cell chemical genomics to define the molecular response of glioblastoma to EGFRis. Using a deep generative framework, we identify shared and drug-specific transcriptional programs that group EGFRis into distinct molecular classes. We identify programs that differ by the chemical properties of EGFRis, including induction of adaptive transcription and modulation of immunogenic gene expression. Finally, we demonstrate that pro-immunogenic expression changes associated with a subset of tyrphostin family EGFRis increase the ability of T-cells to target glioblastoma cells.

16.
Res Sq ; 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38645250

ABSTRACT

In this study, we tested a novel approach of "repurposing" a biomarker typically associated with breast cancer for use in melanoma. HER2/neu is a well characterized biomarker in breast cancer for which effective anti-HER2/neu therapies are readily available. We constructed a lentivirus encoding c-erb-B2 (the animal homolog to HER2/neu). This was used to transfect B16 melanoma in vitro for use in an orthotopic preclinical mouse model, which resulted in expression of c-erb-B2 as a neoantigen target for anti-c-erb-B2 monoclonal antibody (7.16.4). The c-erb-B2-expressing melanoma was designated B16/neu. 7.16.4 produced statistically significant in vivo anti-tumor responses against B16/neu. This effect was mediated by NK-cell antibody-dependent cell-mediated cytotoxicity. To further model human melanoma (which expresses <5% HER2/neu), our c-erb-B2 encoding lentivirus was used to inoculate naïve (wild-type) B16 tumors in vivo, resulting in successful c-erb-B2 expression. When combined with 7.16.4, anti-tumor responses were again demonstrated where approximately 40% of mice treated with c-erb-B2 lentivirus and 7.16.4 achieved complete clinical response and long-term survival. For the first time, we demonstrated a novel strategy to repurpose c-erb-B2 as a neoantigen target for melanoma. Our findings are particularly significant in the contemporary setting where newer anti-HER2/neu antibody-drug candidates have shown increased efficacy.

17.
Chem Res Toxicol ; 37(5): 791-803, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38652897

ABSTRACT

Burn pits are a method of open-air waste management that was common during military operations in Iraq, Afghanistan, and other regions in Southwest Asia. Veterans returning from deployment have reported respiratory symptoms, potentially from exposure to burn pit smoke, yet comprehensive assessment of such exposure on pulmonary health is lacking. We have previously shown that exposure to condensates from burn pit smoke emissions causes inflammation and cytotoxicity in mice. In this study, we explored the effects of burn pit smoke condensates on human airway epithelial cells (HAECs) to understand their impact on cellular targets in the human lung. HAECs were cultured at the air-liquid interface (ALI) and exposed to burn pit waste smoke condensates (plywood, cardboard, plastic, mixed, and mixed with diesel) generated under smoldering and flaming conditions. Cytotoxicity was evaluated by measuring transepithelial electrical resistance (TEER) and lactate dehydrogenase (LDH) release; toxicity scores (TSs) were quantified for each exposure. Pro-inflammatory cytokine release and modulation of gene expression were examined for cardboard and plastic condensate exposures. Burn pit smoke condensates generated under flaming conditions affected cell viability, with flaming mixed waste and plywood exhibiting the highest toxicity scores. Cardboard and plastic smoke condensates modulated cytokine secretion, with GM-CSF and IL-1ß altered in more than one exposure group. Gene expression of detoxifying enzymes (ALDH1A3, ALDH3A1, CYP1A1, CYP1B1, NQO1, etc.), mucins (MUC5AC, MUC5B), and cytokines was affected by several smoke condensates. Particularly, expression of IL6 was elevated following exposure to all burn pit smoke condensates, and polycyclic aromatic hydrocarbon acenaphthene was positively associated with the IL-6 level in the basolateral media of HAECs. These observations demonstrate that exposure to smoke condensates of materials present in burn pits adversely affects HAECs and that aberrant cytokine secretion and altered gene expression profiles following burn pit material smoke exposure could contribute to the development of airway disease.


Subject(s)
Epithelial Cells , Smoke , Humans , Smoke/adverse effects , Epithelial Cells/drug effects , Epithelial Cells/metabolism , Cells, Cultured , Cell Survival/drug effects , Cytokines/metabolism , Cell Line , Open Waste Burning
18.
J Sch Health ; 94(8): 768-776, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38637288

ABSTRACT

BACKGROUND: School Resource Officer (SRO) programs do not reduce school violence and increase school discipline. We describe the use of a culturally responsive framework to form a school community collaborative among students, parents, staff, administrators, and law enforcement to reform an SRO program, promote school safety, and reduce punitive measures. METHODS: Members of a participating school district, a local county, and a university collaborated. Adapting an identified culturally responsive model, a racially/ethnically diverse school community co-developed and implemented a School Community Collaborative (SCC) to address a school safety priority (SRO program reform). The main outcomes were SCC model development and implementation, policy change, and school community feedback. RESULTS: Sixteen community members participated in the 5-week SCC with students, staff, law enforcement, and parents. The SCC revised the district's SRO memorandum of understanding (MOU) with law enforcement. Participants reported favorable feedback, and 89% reported the inclusion of diverse voices. CONCLUSIONS: Co-development and implementation of an SCC process with schools were feasible. School SCC participated in a community-engaged evaluation and revision of an MOU.


Subject(s)
Schools , Humans , Schools/organization & administration , Safety , Law Enforcement , Cooperative Behavior , Students , Community-Institutional Relations , Violence/prevention & control , Program Development , Child , Male , Female , Community Participation/methods
19.
Cancer Cell ; 42(5): 904-914.e9, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38579724

ABSTRACT

A subset of patients with IDH-mutant glioma respond to inhibitors of mutant IDH (IDHi), yet the molecular underpinnings of such responses are not understood. Here, we profiled by single-cell or single-nucleus RNA-sequencing three IDH-mutant oligodendrogliomas from patients who derived clinical benefit from IDHi. Importantly, the tissues were sampled on-drug, four weeks from treatment initiation. We further integrate our findings with analysis of single-cell and bulk transcriptomes from independent cohorts and experimental models. We find that IDHi treatment induces a robust differentiation toward the astrocytic lineage, accompanied by a depletion of stem-like cells and a reduction of cell proliferation. Furthermore, mutations in NOTCH1 are associated with decreased astrocytic differentiation and may limit the response to IDHi. Our study highlights the differentiating potential of IDHi on the cellular hierarchies that drive oligodendrogliomas and suggests a genetic modifier that may improve patient stratification.


Subject(s)
Brain Neoplasms , Cell Differentiation , Isocitrate Dehydrogenase , Mutation , Oligodendroglioma , Oligodendroglioma/genetics , Oligodendroglioma/pathology , Oligodendroglioma/drug therapy , Isocitrate Dehydrogenase/genetics , Isocitrate Dehydrogenase/antagonists & inhibitors , Humans , Cell Differentiation/drug effects , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Brain Neoplasms/drug therapy , Cell Lineage/drug effects , Receptor, Notch1/genetics , Receptor, Notch1/metabolism , Cell Proliferation/drug effects , Animals , Astrocytes/metabolism , Astrocytes/drug effects , Astrocytes/pathology , Mice , Single-Cell Analysis/methods
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