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Zhou W, Cuomo ASE, Xue A, Kanai M, Chau G, Krishna C, Xavier RJ, MacArthur DG, Powell JE, Daly MJ, Neale BM. Efficient and accurate mixed model association tool for single-cell eQTL analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307317. [PMID: 38798318 PMCID: PMC11118640 DOI: 10.1101/2024.05.15.24307317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Understanding the genetic basis of gene expression can help us understand the molecular underpinnings of human traits and disease. Expression quantitative trait locus (eQTL) mapping can help in studying this relationship but have been shown to be very cell-type specific, motivating the use of single-cell RNA sequencing and single-cell eQTLs to obtain a more granular view of genetic regulation. Current methods for single-cell eQTL mapping either rely on the "pseudobulk" approach and traditional pipelines for bulk transcriptomics or do not scale well to large datasets. Here, we propose SAIGE-QTL, a robust and scalable tool that can directly map eQTLs using single-cell profiles without needing aggregation at the pseudobulk level. Additionally, SAIGE-QTL allows for testing the effects of less frequent/rare genetic variation through set-based tests, which is traditionally excluded from eQTL mapping studies. We evaluate the performance of SAIGE-QTL on both real and simulated data and demonstrate the improved power for eQTL mapping over existing pipelines.
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Hao Y, Gu Z, Yu Z, Schomann T, Sayedipour S, Aguilar JC, ten Dijke P, Cruz LJ. Photodynamic Therapy in Combination with the Hepatitis B Core Virus-like Particles (HBc VLPs) to Prime Anticancer Immunity for Colorectal Cancer Treatment. Cancers (Basel) 2022; 14:cancers14112724. [PMID: 35681703 PMCID: PMC9179923 DOI: 10.3390/cancers14112724] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Photodynamic therapy (PDT) by means of a photosensitizer is a clinically used therapeutic treatment in a variety of cancers. To further improve the anti-cancer efficiency of PDT, combination therapy with immune agents is a promising option. In this study, we used a viral vaccine as the immune therapeutic partner for PDT. We studied the biological properties of single and combined modalities. Our research suggests that combination therapy enhances innate and humoral immunity, improved survival, and generated a long-term memory capacity in the MC-38 murine colorectal tumor model to prevent a recurrence. Abstract Photodynamic therapy (PDT), which combines light and oxygen with a photosensitizer to induce reactive oxygen species (ROS)-mediated killing of primary tumor cells, benefits from non-invasive properties and its negligible toxicity to surrounding healthy tissues. In this study, we have shown that the second-generation photosensitizer FOSCAN can be internalized by tumor cells and effectively induce tumor cell death when exposed to laser irradiation in vitro. In addition, these dying tumor cells can be phagocytosed by dendritic cells and lead to their activation and maturation as assessed by in vitro co-culture models. While PDT induces immunogenic tumor cell apoptosis, its application for the treatment of tumors located in deep tissues and advanced malignancies has been limited. In this study, we demonstrate that hepatitis B core virus-like particles (HBc VLPs) can serve as a vaccine to enhance PDT-induced anti-cancer immunity by priming humoral immune responses and inducing CD8+ T cell responses. The combination of PDT and HBc VLPs increased the survival rate of MC-38 tumor-bearing mice to 55%, compared to 33% in PDT alone and no tumor-free mice in vaccine alone. Moreover, the combination effectively prevented tumor recurrence in vivo through enhanced immune memory T cells after therapy. Therefore, as both are clinically approved techniques, this combination provides a promising strategy for cancer therapy.
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Affiliation(s)
- Yang Hao
- Translational Nanobiomaterials and Imaging (TNI) Group, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Y.H.); (Z.G.); (Z.Y.); (T.S.); (S.S.)
| | - Zili Gu
- Translational Nanobiomaterials and Imaging (TNI) Group, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Y.H.); (Z.G.); (Z.Y.); (T.S.); (S.S.)
| | - Zhenfeng Yu
- Translational Nanobiomaterials and Imaging (TNI) Group, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Y.H.); (Z.G.); (Z.Y.); (T.S.); (S.S.)
| | - Timo Schomann
- Translational Nanobiomaterials and Imaging (TNI) Group, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Y.H.); (Z.G.); (Z.Y.); (T.S.); (S.S.)
- Percuros B.V., Zernikedreef 8, 2333 CL Leiden, The Netherlands
| | - Sana Sayedipour
- Translational Nanobiomaterials and Imaging (TNI) Group, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Y.H.); (Z.G.); (Z.Y.); (T.S.); (S.S.)
| | - Julio C. Aguilar
- Center for Genetic Engineering and Biotechnology, CIGB, Havana 10600, Cuba;
| | - Peter ten Dijke
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands
- Correspondence: (P.t.D.); (L.J.C.); Tel.: +31-71-526-9271 (P.t.D.); +31-71-5265764 (L.J.C.)
| | - Luis J. Cruz
- Translational Nanobiomaterials and Imaging (TNI) Group, Department of Radiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Y.H.); (Z.G.); (Z.Y.); (T.S.); (S.S.)
- Correspondence: (P.t.D.); (L.J.C.); Tel.: +31-71-526-9271 (P.t.D.); +31-71-5265764 (L.J.C.)
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Pucino V, Turner JD, Nayar S, Kollert F, Rauz S, Richards A, Higham J, Poveda-Gallego A, Bowman SJ, Barone F, Fisher BA. Sjögren's and non-Sjögren's sicca share a similar symptom burden but with a distinct symptom-associated proteomic signature. RMD Open 2022; 8:e002119. [PMID: 35589331 PMCID: PMC9121491 DOI: 10.1136/rmdopen-2021-002119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/07/2022] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES Given the similarity in symptoms between primary Sjogren's syndrome (SjS) and non-SjS sicca syndrome (sicca), we sought to characterise clinical and proteomic predictors of symptoms in both groups in order to better understand disease mechanisms and help guide development of immunomodulatory treatments. These have not, to date, unequivocally improved symptoms in SjS clinical trials. METHODS Serum proteomics was performed using O-link inflammation and cardiovascular II panels. SjS (n=53) fulfilled 2016 ACR/European Alliance of Associations for Rheumatology (EULAR) criteria whereas sicca (n=60) were anti-Ro negative, displayed objective or subjective dryness, and either had a negative salivary gland biopsy or, in the absence of a biopsy, it was considered that a biopsy result would not change classification status. Linear regression analysis was performed to identify the key predictors of symptoms. Cluster analysis was completed using protein expression values. RESULTS EULAR-Sjögren's-Syndrome-Patient-Reported-Index (ESSPRI), EuroQoL-5 Dimension utility values, and anxiety and depression did not differ between SjS and sicca. Correlations between body mass index (BMI) and ESSPRI were found in sicca and to a lesser extent in SjS. Twenty proteins positively associated with symptoms in sicca but none in SjS. We identified two proteomically defined subgroups in sicca and two in SjS that differed in symptom burden. Within hierarchical clustering of the SjS and sicca pool, the highest symptom burden groups were the least distinct. Levels of adrenomedullin (ADM), soluble CD40 (CD40) and spondin 2 (SPON2) together explained 51% of symptom variability in sicca. ADM was strongly correlated with ESSPRI (spearman's r=0.62; p<0.0001), even in a multivariate model corrected for BMI, age, objective dryness, depression and anxiety scores. CONCLUSIONS Obesity-related metabolic factors may regulate symptoms in sicca. Further work should explore non-inflammatory drivers of high symptom burden in SjS to improve clinical trial outcomes.
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Affiliation(s)
- Valentina Pucino
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre and Department of Rheumatology, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
| | - Jason D Turner
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Saba Nayar
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Florian Kollert
- Department of Rheumatology and Immunology, Inselspital University Hospital Bern, Bern, Switzerland
| | - Saaeha Rauz
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Academic Unit of Ophthalmology, Birmingham and Midland Eye Centre, Birmingham, UK
| | - Andrea Richards
- Department of Oral Medicine, Birmingham Dental Hospital, Birmingham, UK
| | - Jon Higham
- Department of Oral Medicine, Birmingham Dental Hospital, Birmingham, UK
| | - Ana Poveda-Gallego
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Oral Medicine, Birmingham Dental Hospital, Birmingham, UK
| | - Simon J Bowman
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre and Department of Rheumatology, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
| | - Francesca Barone
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Candel Therapeutics, Boston, Massachusetts, USA
| | - Benjamin A Fisher
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre and Department of Rheumatology, University Hospitals Birmingham NHS Foundation Trust, University of Birmingham, Birmingham, UK
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Fadul CE, Mao-Draayer Y, Ryan KA, Noelle RJ, Wishart HA, Channon JY, Kasper IR, Oliver B, Mielcarz DW, Kasper LH. Safety and Immune Effects of Blocking CD40 Ligand in Multiple Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2021; 8:e1096. [PMID: 34654708 PMCID: PMC8527364 DOI: 10.1212/nxi.0000000000001096] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/11/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVES Costimulation by CD40 and its ligand CD40L (CD154) is important for the functional differentiation of T cells. Preclinical studies have recognized the importance of this costimulatory interaction in the pathogenesis of experimental models of multiple sclerosis (MS). To determine safety, pharmacokinetics, and immune effect of a humanized monoclonal antibody (mAb) against CD40 ligand (toralizumab/IDEC-131) in patients with relapsing-remitting MS (RRMS). METHODS This single-institution open-label dose-escalation study (phase I) enrolled 12 patients with RRMS to receive 4 doses of 1, 5, 10, or 15 mg/kg of humanized αCD40L (toralizumab) IV infusion every other week. Patients were followed up to 18 weeks, annually, and finally at 5 years. In addition to safety and pharmacokinetics, other secondary and exploratory measurements are immune effects, clinical, MRI, laboratory, and neuropsychological evaluations. RESULTS Fifteen adverse events, all of mild to moderate severity, were considered to be of possible or of unknown relationship to treatment. No serious adverse events, including thromboembolic events, occurred during the 18-week defined study period. Annual and long-term follow-up at 5 years revealed no delayed toxicity. Pharmacokinetics were nonlinear between the 5 and 10 mg/kg dose groups. The serum half-life of toralizumab was consistent between the dose groups with a mean of 15.3 days (SD = 1.9). Flow cytometry revealed no depletion of lymphocyte subsets. An increase in the CD25+/CD3+ and CD25+/CD4+ ratio and a shift toward an anti-inflammatory cytokine response were seen after treatment. DISCUSSION Our study suggests that blocking CD40L is safe and well tolerated in patients with RRMS while increasing CD25 + T cells and anti-inflammatory cytokine profile. These findings support further studies to assess the efficacy of blocking CD40L as a potential treatment of RRMS. CLASSIFICATION OF EVIDENCE This study provides Class IV evidence on the safety, pharmacokinetics, and immune effects of an mAb to CD40L in patients with RRMS.
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MESH Headings
- Adult
- Antibodies, Blocking/administration & dosage
- Antibodies, Blocking/adverse effects
- Antibodies, Blocking/pharmacology
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/pharmacokinetics
- Antibodies, Monoclonal, Humanized/pharmacology
- CD40 Ligand
- Female
- Follow-Up Studies
- Humans
- Immunologic Factors/administration & dosage
- Immunologic Factors/adverse effects
- Immunologic Factors/pharmacokinetics
- Immunologic Factors/pharmacology
- Male
- Middle Aged
- Multiple Sclerosis, Relapsing-Remitting/drug therapy
- Multiple Sclerosis, Relapsing-Remitting/immunology
- Outcome Assessment, Health Care
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Affiliation(s)
| | | | - Kathleen A. Ryan
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
| | - Randolph J. Noelle
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
| | - Heather A. Wishart
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
| | - Jacqueline Y. Channon
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
| | - Isaac R. Kasper
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
| | - Brant Oliver
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
| | - Daniel W. Mielcarz
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
| | - Lloyd H. Kasper
- From the Department of Neurology (C.E.F.), University of Virginia School of Medicine, Charlottesville; Department of Medicine, Microbiology/Immunology and Psychiatry (K.A.R., R.J.N., H.A.W., J.Y.C., J.R.K., B.O., D.W.M., L.H.K.), Dartmouth Medical School, Lebanon, NH; and Department of Neurology (Y.M.-D.), Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor
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Shibru B, Fey K, Fricke S, Blaudszun AR, Fürst F, Weise M, Seiffert S, Weyh MK, Köhl U, Sack U, Boldt A. Detection of Immune Checkpoint Receptors - A Current Challenge in Clinical Flow Cytometry. Front Immunol 2021; 12:694055. [PMID: 34276685 PMCID: PMC8281132 DOI: 10.3389/fimmu.2021.694055] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Immunological therapy principles are increasingly determining modern medicine. They are used to treat diseases of the immune system, for tumors, but also for infections, neurological diseases, and many others. Most of these therapies base on antibodies, but small molecules, soluble receptors or cells and modified cells are also used. The development of immune checkpoint inhibitors is amazingly fast. T-cell directed antibody therapies against PD-1 or CTLA-4 are already firmly established in the clinic. Further targets are constantly being added and it is becoming increasingly clear that their expression is not only relevant on T cells. Furthermore, we do not yet have any experience with the long-term systemic effects of the treatment. Flow cytometry can be used for diagnosis, monitoring, and detection of side effects. In this review, we focus on checkpoint molecules as target molecules and functional markers of cells of the innate and acquired immune system. However, for most of the interesting and potentially relevant parameters, there are still no test kits suitable for routine use. Here we give an overview of the detection of checkpoint molecules on immune cells in the peripheral blood and show examples of a possible design of antibody panels.
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Affiliation(s)
- Benjamin Shibru
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Katharina Fey
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Stephan Fricke
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | | | - Friederike Fürst
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Max Weise
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Sabine Seiffert
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Maria Katharina Weyh
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Institute for Cellular Therapeutics, Hannover Medical School, Hannover, Germany
| | - Ulrich Sack
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Andreas Boldt
- Institute of Clinical Immunology, Medical Faculty, University of Leipzig, Leipzig, Germany
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