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Niemelä S, Oksi J, Jero J, Löyttyniemi E, Rahi M, Rinne J, Posti JP, Laukka D. Glioma grade and post-neurosurgical meningitis risk. Acta Neurochir (Wien) 2024; 166:300. [PMID: 39023552 PMCID: PMC11258166 DOI: 10.1007/s00701-024-06193-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Post-neurosurgical meningitis (PNM) constitutes a grave complication associated with substantial morbidity and mortality. This study aimed to determine the risk factors predisposing patients to PNM following surgery for low- and high-grade gliomas. METHODS We conducted a retrospective analysis encompassing all patients who underwent glioma surgery involving craniotomy at Turku University Hospital, Turku, Finland, between 2011 and 2018. Inclusion criteria for PNM were defined as follows: (1) Positive cerebrospinal fluid (CSF) culture, (2) CSF leukocyte count ≥ 250 × 106/L with granulocyte percentage ≥ 50%, or (3) CSF lactate concentration ≥ 4 mmol/L, detected after glioma surgery. Glioma grades 3-4 were classified as high-grade (n = 261), while grades 1-2 were designated as low-grade (n = 84). RESULTS Among the 345 patients included in this study, PNM developed in 7% (n = 25) of cases. The median time interval between glioma surgery and diagnosis of PNM was 12 days. Positive CSF cultures were observed in 7 (28%) PNM cases, with identified pathogens encompassing Staphylococcus epidermidis (3), Staphylococcus aureus (2), Enterobacter cloacae (1), and Pseudomonas aeruginosa (1). The PNM group exhibited a higher incidence of reoperations (52% vs. 18%, p < 0.001) and revision surgery (40% vs. 6%, p < 0.001) in comparison to patients without PNM. Multivariable analysis revealed that reoperation (OR 2.63, 95% CI 1.04-6.67) and revision surgery (OR 7.08, 95% CI 2.55-19.70) were significantly associated with PNM, while glioma grade (high-grade vs. low-grade glioma, OR 0.81, 95% CI 0.30-2.22) showed no significant association. CONCLUSIONS The PNM rate following glioma surgery was 7%. Patients requiring reoperation and revision surgery were at elevated risk for PNM. Glioma grade did not exhibit a direct link with PNM; however, the presence of low-grade gliomas may indirectly heighten the PNM risk through an increased likelihood of future reoperations. These findings underscore the importance of meticulous post-operative care and infection prevention measures in glioma surgeries.
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Affiliation(s)
- Sakke Niemelä
- Department of Otorhinolaryngology, Turku University Hospital and University of Turku, Turku, Finland.
| | - Jarmo Oksi
- Department of Infectious Diseases, Turku University Hospital and University of Turku, Turku, Finland
| | - Jussi Jero
- Department of Otorhinolaryngology, Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Eliisa Löyttyniemi
- Unit of Biostatistics, University of Turku and Turku University Hospital, Turku, Finland
| | - Melissa Rahi
- Clinical Neurosciences, University of Turku, Turku, Finland
- Department of Neurosurgery, Neurocenter, Turku University Hospital, Turku, Finland
| | - Jaakko Rinne
- Clinical Neurosciences, University of Turku, Turku, Finland
- Department of Neurosurgery, Neurocenter, Turku University Hospital, Turku, Finland
| | - Jussi P Posti
- Clinical Neurosciences, University of Turku, Turku, Finland
- Department of Neurosurgery, Neurocenter, Turku University Hospital, Turku, Finland
| | - Dan Laukka
- Clinical Neurosciences, University of Turku, Turku, Finland
- Department of Neurosurgery, Neurocenter, Turku University Hospital, Turku, Finland
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2
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Stepanenko AA, Sosnovtseva AO, Valikhov MP, Chernysheva AA, Abramova OV, Naumenko VA, Chekhonin VP. The need for paradigm shift: prognostic significance and implications of standard therapy-related systemic immunosuppression in glioblastoma for immunotherapy and oncolytic virotherapy. Front Immunol 2024; 15:1326757. [PMID: 38390330 PMCID: PMC10881776 DOI: 10.3389/fimmu.2024.1326757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Despite significant advances in our knowledge regarding the genetics and molecular biology of gliomas over the past two decades and hundreds of clinical trials, no effective therapeutic approach has been identified for adult patients with newly diagnosed glioblastoma, and overall survival remains dismal. Great hopes are now placed on combination immunotherapy. In clinical trials, immunotherapeutics are generally tested after standard therapy (radiation, temozolomide, and steroid dexamethasone) or concurrently with temozolomide and/or steroids. Only a minor subset of patients with progressive/recurrent glioblastoma have benefited from immunotherapies. In this review, we comprehensively discuss standard therapy-related systemic immunosuppression and lymphopenia, their prognostic significance, and the implications for immunotherapy/oncolytic virotherapy. The effectiveness of immunotherapy and oncolytic virotherapy (viro-immunotherapy) critically depends on the activity of the host immune cells. The absolute counts, ratios, and functional states of different circulating and tumor-infiltrating immune cell subsets determine the net immune fitness of patients with cancer and may have various effects on tumor progression, therapeutic response, and survival outcomes. Although different immunosuppressive mechanisms operate in patients with glioblastoma/gliomas at presentation, the immunological competence of patients may be significantly compromised by standard therapy, exacerbating tumor-related systemic immunosuppression. Standard therapy affects diverse immune cell subsets, including dendritic, CD4+, CD8+, natural killer (NK), NKT, macrophage, neutrophil, and myeloid-derived suppressor cell (MDSC). Systemic immunosuppression and lymphopenia limit the immune system's ability to target glioblastoma. Changes in the standard therapy are required to increase the success of immunotherapies. Steroid use, high neutrophil-to-lymphocyte ratio (NLR), and low post-treatment total lymphocyte count (TLC) are significant prognostic factors for shorter survival in patients with glioblastoma in retrospective studies; however, these clinically relevant variables are rarely reported and correlated with response and survival in immunotherapy studies (e.g., immune checkpoint inhibitors, vaccines, and oncolytic viruses). Our analysis should help in the development of a more rational clinical trial design and decision-making regarding the treatment to potentially improve the efficacy of immunotherapy or oncolytic virotherapy.
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Affiliation(s)
- Aleksei A. Stepanenko
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, The Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N.I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasiia O. Sosnovtseva
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, The Ministry of Health of the Russian Federation, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marat P. Valikhov
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, The Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N.I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia A. Chernysheva
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga V. Abramova
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Victor A. Naumenko
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, The Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir P. Chekhonin
- Department of Fundamental and Applied Neurobiology, V. P. Serbsky National Medical Research Center of Psychiatry and Narcology, The Ministry of Health of the Russian Federation, Moscow, Russia
- Department of Medical Nanobiotechnology, Institute of Translational Medicine, N.I. Pirogov Russian National Research Medical University, The Ministry of Health of the Russian Federation, Moscow, Russia
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3
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Hoffmann M, Willruth LL, Dietrich A, Lee HK, Knabl L, Trummer N, Baumbach J, Furth PA, Hennighausen L, List M. Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2. Sci Rep 2024; 14:2808. [PMID: 38307916 PMCID: PMC10837437 DOI: 10.1038/s41598-024-53117-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/28/2024] [Indexed: 02/04/2024] Open
Abstract
Bulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we propose that RNA-seq should be considered a diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers insights into a patient's immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 196 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that-combined with sequence alignments and BLASTp-they could be used to classify a patient's disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.
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Affiliation(s)
- Markus Hoffmann
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, 85748, Garching, Germany.
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA.
| | - Lina-Liv Willruth
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Alexander Dietrich
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA
| | | | - Nico Trummer
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A Furth
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, 85748, Garching, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, 85748, Garching, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Markus List
- Data Science in Systems Biomedicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
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4
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Dusoswa SA, Verhoeff J, van Asten S, Lübbers J, van den Braber M, Peters S, Abeln S, Crommentuijn MH, Wesseling P, Vandertop WP, Twisk JWR, Würdinger T, Noske D, van Kooyk Y, Garcia-Vallejo JJ. The immunological landscape of peripheral blood in glioblastoma patients and immunological consequences of age and dexamethasone treatment. Front Immunol 2024; 15:1343484. [PMID: 38318180 PMCID: PMC10839779 DOI: 10.3389/fimmu.2024.1343484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Background Glioblastomas manipulate the immune system both locally and systemically, yet, glioblastoma-associated changes in peripheral blood immune composition are poorly studied. Age and dexamethasone administration in glioblastoma patients have been hypothesized to limit the effectiveness of immunotherapy, but their effects remain unclear. We compared peripheral blood immune composition in patients with different types of brain tumor to determine the influence of age, dexamethasone treatment, and tumor volume. Methods High-dimensional mass cytometry was used to characterise peripheral blood mononuclear cells of 169 patients with glioblastoma, lower grade astrocytoma, metastases and meningioma. We used blood from medically-refractory epilepsy patients and healthy controls as control groups. Immune phenotyping was performed using FlowSOM and t-SNE analysis in R followed by supervised annotation of the resulting clusters. We conducted multiple linear regression analysis between intracranial pathology and cell type abundance, corrected for clinical variables. We tested correlations between cell type abundance and survival with Cox-regression analyses. Results Glioblastoma patients had significantly fewer naive CD4+ T cells, but higher percentages of mature NK cells than controls. Decreases of naive CD8+ T cells and alternative monocytes and an increase of memory B cells in glioblastoma patients were influenced by age and dexamethasone treatment, and only memory B cells by tumor volume. Progression free survival was associated with percentages of CD4+ regulatory T cells and double negative T cells. Conclusion High-dimensional mass cytometry of peripheral blood in patients with different types of intracranial tumor provides insight into the relation between intracranial pathology and peripheral immune status. Wide immunosuppression associated with age and pre-operative dexamethasone treatment provide further evidence for their deleterious effects on treatment with immunotherapy.
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Affiliation(s)
- Sophie A. Dusoswa
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
- Department of Neurosurgery, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Jan Verhoeff
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Saskia van Asten
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Joyce Lübbers
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Marlous van den Braber
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Sophie Peters
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Sanne Abeln
- Department of Computer Science, Free University, Amsterdam, Netherlands
| | - Matheus H.W. Crommentuijn
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Pieter Wesseling
- Department of Pathology, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam and Princes Máxima Center for Pediatric Oncology, Amsterdam UMC, VU Amsterdam, Utrecht, Netherlands
| | | | - Jos W. R. Twisk
- Department of Epidemiology and Biostatistics and Biostatistics, Amsterdam Public Health Research Institute, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Thomas Würdinger
- Department of Neurosurgery, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - David Noske
- Department of Neurosurgery, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
| | - Juan J. Garcia-Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Cancer Center Amsterdam, Amsterdam UMC, VU Amsterdam, Amsterdam, Netherlands
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5
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Taylor JW, Warrier G, Hansen HM, McCoy L, Rice T, Guerra G, Francis SS, Clarke JL, Bracci PM, Hadad S, Kelsey KT, Wrensch M, Molinaro AM, Wiencke JK. Oligodendroglioma patient survival is associated with circulating B-cells and age. Neurooncol Adv 2024; 6:vdae143. [PMID: 39247497 PMCID: PMC11379917 DOI: 10.1093/noajnl/vdae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024] Open
Abstract
Background Variations in survival among patients with oligodendroglioma are unexplained by known prognostic factors. To assess the impact of peripheral immune profiles on prognosis, we applied immunomethylomics analyses-DNA methylation of archived whole blood samples, to characterize immune cells. Methods We compared the proportions of immune cells from patients with oligodendroglioma to other glioma subtypes and controls. We used recursive partitioning analysis (RPA) within the oligodendrogliomas to correlate with survival. Results Patients with oligodendrogliomas (141) were median age at diagnosis of 44 years; 57% male; 75% White; 60% prior chemotherapy; and 25% on dexamethasone at sample collection. Patients with oligodendrogliomas had immune profiles more similar to controls than other glioma subtypes, though with notably lower B-cells. RPA of patients with oligodendrogliomas delineated 2 survival groups based on an interaction between age and B-naïve cells. Patients with longer survival (median 24.2 years) were ≤42 years of age with higher B-naïve cells versus worse survival (median 16.9 years) who were ≤42 years of age with lower B-naïve cells or >42 years of age (P = .00032). Patients with worse survival also had lower CD4- and CD8-naïve T-cells. Similar immune profiles were observed in an independent cohort of oligodendroglioma patients prior to surgery. Conclusions Peripheral blood immune profiles in oligodendroglioma suggested that younger patients with lower B-naïve cells experienced shorter survival. Though our findings lack of validation cohort and use a heterogenous patient population, they suggest peripheral blood immune profiles may be prognostic for patients with glioma and warrant further investigation.
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Affiliation(s)
- Jennie W Taylor
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Geno Guerra
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jennifer L Clarke
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Sara Hadad
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Karl T Kelsey
- Departments of Epidemiology; Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Annette M Molinaro
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - John K Wiencke
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
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6
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Mistry AM. Perioperative dexamethasone in high-grade gliomas: the short-term benefits and long-term harms. Front Oncol 2023; 13:1335730. [PMID: 38162484 PMCID: PMC10755919 DOI: 10.3389/fonc.2023.1335730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Dexamethasone has been commonly given to patients with a presumed new GBM in relatively large doses (6-16 mg daily for 1-2 weeks) since the 1960s without any rigorous evidence. This treatment with dexamethasone before the diagnosis and adjuvant therapy makes GBM patients unique compared to other newly diagnosed cancer patients. While dexamethasone may be beneficial, recent studies suggest that this potent immunosuppressant with pleiotropic effects is harmful in the long term. This perspective article summarizes the disadvantages of perioperative dexamethasone from multiple facets. It concludes that these growing data mandate rigorously testing the benefits of using perioperative dexamethasone.
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Affiliation(s)
- Akshitkumar M. Mistry
- Department of Neurological Surgery, University of Louisville, Louisville, KY, United States
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7
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Hoffmann M, Willruth LL, Dietrich A, Lee HK, Knabl L, Trummer N, Baumbach J, Furth PA, Hennighausen L, List M. Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.564190. [PMID: 38076885 PMCID: PMC10705570 DOI: 10.1101/2023.11.03.564190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Bulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we argue that RNA-seq should be considered a routine diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers vital insights into a patient's immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 240 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that - combined with sequence alignments and pBLAST - they could be used to classify a patient's disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.
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Affiliation(s)
- Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Alexander Dietrich
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | | | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A. Furth
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, United States of America
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2 a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
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8
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Wang S, Zhang G, Cui Q, Yang Y, Wang D, Liu A, Xia Y, Li W, Liu Y, Yu J. The DC-T cell axis is an effective target for the treatment of non-small cell lung cancer. Immun Inflamm Dis 2023; 11:e1099. [PMID: 38018578 PMCID: PMC10681037 DOI: 10.1002/iid3.1099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023] Open
Abstract
The dendritic cell (DC)-T cell axis is a bridge that connects innate and adaptive immunities. The initial immune response against tumors is mainly induced by mature antigen-presenting DCs. Enhancing the crosstalk between DCs and T cells may be an effective approach to improve the immune response to non-small cell lung cancer (NSCLC). In this article, a review was made of the interaction between DCs and T cells in the treatment of NSCLC and how this interaction affects the treatment outcome.
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Affiliation(s)
- Shuangcui Wang
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
- National Clinical Research Center for Chinese Medicine Acupuncture and MoxibustionTianjinChina
- Graduate SchoolTianjin University of Traditional Chinese MedicineTianjinChina
| | - Guan Zhang
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
- National Clinical Research Center for Chinese Medicine Acupuncture and MoxibustionTianjinChina
- Graduate SchoolTianjin University of Traditional Chinese MedicineTianjinChina
| | - Qian Cui
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
- National Clinical Research Center for Chinese Medicine Acupuncture and MoxibustionTianjinChina
- Graduate SchoolTianjin University of Traditional Chinese MedicineTianjinChina
| | - Yanjie Yang
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
- National Clinical Research Center for Chinese Medicine Acupuncture and MoxibustionTianjinChina
- Graduate SchoolTianjin University of Traditional Chinese MedicineTianjinChina
| | - Dong Wang
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
- National Clinical Research Center for Chinese Medicine Acupuncture and MoxibustionTianjinChina
- Graduate SchoolTianjin University of Traditional Chinese MedicineTianjinChina
| | - Aqing Liu
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
- National Clinical Research Center for Chinese Medicine Acupuncture and MoxibustionTianjinChina
- Graduate SchoolTianjin University of Traditional Chinese MedicineTianjinChina
| | - Ying Xia
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
- National Clinical Research Center for Chinese Medicine Acupuncture and MoxibustionTianjinChina
- Graduate SchoolTianjin University of Traditional Chinese MedicineTianjinChina
| | - Wentao Li
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
| | - Yunhe Liu
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
| | - Jianchun Yu
- Department of OncologyFirst Teaching Hospital of Tianjin University of Traditional Chinese MedicineTianjinChina
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Kachuri L, Guerra GA, Wendt GA, Hansen HM, Molinaro AM, Bracci P, McCoy L, Rice T, Wiencke JK, Eckel-Passow JE, Jenkins RB, Wrensch M, Francis SS. Genetic predisposition to altered blood cell homeostasis is associated with glioma risk and survival. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.15.23296448. [PMID: 37905116 PMCID: PMC10614986 DOI: 10.1101/2023.10.15.23296448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Glioma is a highly fatal brain tumor comprised of molecular subtypes with distinct clinical trajectories. Observational studies have suggested that variability in immune response may play a role in glioma etiology. However, their findings have been inconsistent and susceptible to reverse causation due to treatment effects and the immunosuppressive nature of glioma. We applied genetic variants associated (p<5×10-8) with blood cell traits to a meta-analysis of 3418 glioma cases and 8156 controls. Genetically predicted increase in the platelet to lymphocyte ratio (PLR) was associated with an increased risk of glioma (odds ratio (OR)=1.25, p=0.005), especially in IDH-mutant (IDHmut OR=1.38, p=0.007) and IDHmut 1p/19q non-codeleted (IDHmut-noncodel OR=1.53, p=0.004) tumors. However, reduced glioma risk was observed for higher counts of lymphocytes (IDHmut-noncodel OR=0.70, p=0.004) and neutrophils (IDHmut OR=0.69, p=0.019; IDHmut-noncodel OR=0.60, p=0.009), which may reflect genetic predisposition to enhanced immune-surveillance. In contrast to susceptibility, there was no association with survival in IDHmut-noncodel; however, in IDHmut 1p/19q co-deleted tumors, we observed higher mortality with increasing genetically predicted counts of lymphocytes (hazard ratio (HR)=1.65, 95% CI: 1.24-2.20), neutrophils (HR=1.49, 1.13-1.97), and eosinophils (HR=1.59, 1.18-2.14). Polygenic scores for blood cell traits were also associated with tumor immune microenvironment features, with heterogeneity by IDH status observed for 17 signatures related to interferon signaling, PD-1 expression, and T-cell/Cytotoxic responses. In summary, we identified novel, immune-mediated susceptibility mechanisms for glioma with potential disease management implications.
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Affiliation(s)
- Linda Kachuri
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Geno A. Guerra
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | - George A. Wendt
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Helen M. Hansen
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Annette M. Molinaro
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | - Paige Bracci
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - John K. Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, US
| | | | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
| | - Stephen S. Francis
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, US
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