Tehran University of Medical Sciences

Science Communicator Platform

Stay connected! Follow us on X network (Twitter):
Share this content! On (X network) By
Whole-Transcriptome Sequencing–Based Profiling of the Cutaneous Virome in Patients With Secondary Immunodeficiency Publisher



Youssefian L1, 2 ; Saeidian AH2, 3 ; Saffarian Z4, 5 ; Ariamanesh M6 ; Abdollahimajd F7 ; Molkara S8 ; Shahididadras M7 ; Diab R7 ; Vahidnezhad F9 ; Zeinali S10 ; Beziat V11, 12, 13 ; Jouanguy E11, 12, 13 ; Casanova JL11, 12, 13, 14, 15 ; Uitto J16 Show All Authors
Authors
  1. Youssefian L1, 2
  2. Saeidian AH2, 3
  3. Saffarian Z4, 5
  4. Ariamanesh M6
  5. Abdollahimajd F7
  6. Molkara S8
  7. Shahididadras M7
  8. Diab R7
  9. Vahidnezhad F9
  10. Zeinali S10
  11. Beziat V11, 12, 13
  12. Jouanguy E11, 12, 13
  13. Casanova JL11, 12, 13, 14, 15
  14. Uitto J16
  15. Vahidnezhad H2, 17, 18, 19
Show Affiliations
Authors Affiliations
  1. 1. Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, United States
  2. 2. Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
  3. 3. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
  4. 4. Imam Khomeini Hospital, Tehran University of Medical Science, Tehran, Iran
  5. 5. Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
  6. 6. Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
  7. 7. Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
  8. 8. Department of Dermatology, Gonabad University of Medical Sciences, Gonabad, Iran
  9. 9. UCSC Silicon Valley Extension, University of California, Santa Cruz, CA, United States
  10. 10. Kawsar Human Genetics Research Center, Tehran, Iran
  11. 11. St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, United States
  12. 12. Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm, Necker Hospital for Sick Children, Paris, U1163, France
  13. 13. Imagine Institute, Paris University, Paris, France
  14. 14. Howard Hughes Medical Institute, New York, NY, United States
  15. 15. Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
  16. 16. Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
  17. 17. Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
  18. 18. Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, United States
  19. 19. Department of Dermatology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, United States

Source: JID Innovations Published:2024


Abstract

Most viral infections can be self-limited, with no requirement for medical intervention. However, the same viruses can cause severe diseases in patients with compromised immunity due to single-gene diseases, acquired immune deficiency syndrome, or hematologic malignancies or those receiving immunosuppressive drugs. Occasionally, these immunocompromised patients harbor >1 infectious agent, requiring several concomitant diagnostic tests. We have developed, to our knowledge, a previously unreported whole-transcriptome sequencing–based pipeline that allows virome profiling, quantitation, and expression pattern analysis of 926 distinct viruses by sequencing of RNA isolated from a single lesional skin biopsy. This pipeline can also explore host genetics if there is a Mendelian predisposition to infection. We applied this pipeline to 6 Iranian patients with viral-induced skin lesions associated with immune deficiency secondary to HIV, human T-lymphotropic virus 1, chronic lymphocytic leukemia, and post transplant immunosuppression. In 5 cases, definitive human papillomavirus infections were identified, some caused by multiple viral types. In addition to human papillomavirus, coinfection with other viruses (Merkle cell polyomavirus, cytomegalovirus, and human herpesvirus 4) was detected in some lesions. In 1 case, whole-transcriptome sequencing validated the clinical diagnosis of adult T-cell leukemia/lymphoma in a patient with an initial diagnosis of mycosis fungoides/Sezary syndrome. These findings attest to the power of whole-transcriptome sequencing in profiling the cutaneous virome in the context of compromised immunity. © 2024 The Authors
Related Docs
View other Related Docs
1. Recalcitrant Cutaneous Warts in a Family With Inherited Icos Deficiency, Journal of Investigative Dermatology (2022)
2. Whole Transcriptome-Based Skin Virome Profiling in Typical Epidermodysplasia Verruciformis Reveals Α-, Β-, and Γ-Hpv Infections, JCI Insight (2023)
3. Whole-Transcriptome Sequencing–Based Concomitant Detection of Viral and Human Genetic Determinants of Cutaneous Lesions, JCI Insight (2022)
4. Flt3l Governs the Development of Partially Overlapping Hematopoietic Lineages in Humans and Mice, Cell (2024)
5. A Pleiotropic Recurrent Dominant Itpr3 Variant Causes a Complex Multisystemic Disease, Science Advances (2024)
6. Clinicogenetic Characterisation of Slc29a3-Related Syndromes: A Case Series, Tracing Ancestral Variants and Molecular Dynamics Simulation, Journal of Medical Genetics (2025)
7. The Immunopathological Landscape of Human Pre-Tcra Deficiency: From Rare to Common Variants, Science (2024)
8. The Human Cib1-Ever1-Ever2 Complex Governs Keratinocyte-Intrinsic Immunity to Β-Papillomaviruses, Journal of Experimental Medicine (2018)
Experts (# of related papers)
View all Related Experts
Hamid Reza Mahmoodi (6)
Nima Parvaneh (5)
Other Related Docs
9. Updates of Cancer Hallmarks in Patients With Inborn Errors of Immunity, Current Opinion in Allergy and Clinical Immunology (2022)
10. Biallelic Krt5 Mutations in Autosomal Recessive Epidermolysis Bullosa Simplex, Including a Complete Human Keratin 5 “Knock-Out”, Matrix Biology (2019)
11. Dna Repair-Related Heritable Photosensitivity Syndromes: Mutation Landscape in a Multiethnic Cohort of 17 Multigenerational Families With High Degree of Consanguinity, DNA Repair (2024)
12. Human Mcts1-Dependent Translation of Jak2 Is Essential for Ifn-Γ Immunity to Mycobacteria, Cell (2023)
13. Decreased Expression of Hsa-Mir-142-3P and Hsa-Mir-155-5P in Common Variable Immunodeficiency and Involvement of Their Target Genes and Biological Pathways, Allergologia et Immunopathologia (2025)
14. Identification of a Novel Missense C.386G > a Variant in a Boy With the Pomgnt1-Related Muscular Dystrophy-Dystroglycanopathy, Acta Neurologica Belgica (2021)
15. Epilepsia Partialis Continua a Clinical Feature of a Missense Variant in the Adck3 Gene and Poor Response to Therapy, Journal of Molecular Neuroscience (2022)
16. 3D Hydrogel-Based Microcapsules As an in Vitro Model to Study Tumorigenicity, Cell Migration and Drug Resistance, Acta Biomaterialia (2022)
17. Kindler Epidermolysis Bullosa-Like Skin Phenotype and Downregulated Basement Membrane Zone Gene Expression in Poikiloderma With Neutropenia and a Homozygous Usb1 Mutation, Matrix Biology (2021)
18. X-Linked Recessive Tlr7 Deficiency in ~1% of Men Under 60 Years Old With Life-Threatening Covid-19, Science Immunology (2021)
19. Recalcitrant Warts, Epidermodysplasia Verruciformis, and the Tree-Man Syndrome: Phenotypic Spectrum of Cutaneous Human Papillomavirus Infections at the Intersection of Genetic Variability of Viral and Human Genomes, Journal of Investigative Dermatology (2022)
20. Mutation Update: The Spectra of Plec Sequence Variants and Related Plectinopathies, Human Mutation (2022)
21. Prdm12 Is Transcriptionally Active and Required for Nociceptor Function Throughout Life, Frontiers in Molecular Neuroscience (2021)
22. Broadening the Phenotype and Genotype Spectrum of Glycogen Storage Disease by Unraveling Novel Variants in an Iranian Patient Cohort, Biochemical Genetics (2024)
23. Tuberculosis and Impaired Il-23–Dependent Ifn- Immunity in Humans Homozygous for a Common Tyk2 Missense Variant, Science Immunology (2018)
24. Inherited Human Itk Deficiency Impairs Ifn-Γ Immunity and Underlies Tuberculosis, Journal of Experimental Medicine (2023)
25. Genomic Resources for Wild Populations of the House Mouse, Mus Musculus and Its Close Relative Mus Spretus, Scientific Data (2016)
26. Losartan Treatment Improves Recessive Dystrophic Epidermolysis Bullosa: A Case Series, Dermatologic Therapy (2022)
27. Germline Biallelic Mutation Affecting the Transcription Factor Helios Causes Pleiotropic Defects of Immunity, Science Immunology (2021)
28. Novel Digital Anomalies, Hippocampal Atrophy, and Mutations Expand the Genotypic and Phenotypic Spectra of Cnksr2 in the Houge Type of X-Linked Syndromic Intellectual Development Disorder (Mrxshg), American Journal of Medical Genetics, Part A (2025)