Wu, F. et al. A new coronavirus associated with human respiratory disease in China. Nature 579 (7798), 265–269 (2020).
Organization, W. H. Coronavirus disease (COVID-19) pandemic 2024.
Papadopoulou, G. et al. Molecular and clinical prognostic biomarkers of COVID-19 severity and persistence. Pathogens 11(3). (2022).
Lee, Y. et al. Variants affecting exon skipping contribute to complex traits. PLoS Genet. 8 (10), e1002998 (2012).
Wang, Y. et al. Mechanism of alternative splicing and its regulation (Review). Biomed. Rep. 3 (2), 152–158 (2015).
Sakabe, N. J. & de Souza, S. J. Sequence features responsible for intron retention in human. BMC Genom. 8 (1), 59 (2007).
Jin, Y., Dong, H., Shi, Y. & Bian, L. Mutually exclusive alternative splicing of pre-mRNAs. Wiley Interdiscip Rev. RNA 9 (3), e1468 (2018).
Nakanishi, T. et al. Alternative splicing in lung influences COVID-19 severity and respiratory diseases. Nat. Commun. 14 (1), 6198 (2023).
Lam, S. D., Babu, M. M., Lees, J. & Orengo, C. A. Biological impact of mutually exclusive exon switching. PLoS Comput. Biol. 17 (3), e1008708 (2021).
Wang, C. et al. Abnormal global alternative RNA splicing in COVID-19 patients. PLoS Genet. 18 (4), e1010137 (2022).
Chen, Y. et al. CASA: a comprehensive database resource for the COVID-19 alternative splicing atlas. J. Transl Med. 20 (1), 473 (2022).
de Prisco, N. et al. Alternative polyadenylation alters protein dosage by switching between intronic and 3’UTR sites. Sci. Adv. 9 (7), eade4814 (2023).
Guo, S. & Lin, S. mRNA alternative polyadenylation (APA) in regulation of gene expression and diseases. Genes Dis. 10 (1), 165–174 (2023).
Sommerkamp, P. et al. Differential alternative polyadenylation landscapes mediate hematopoietic stem cell activation and regulate glutamine metabolism. Cell. Stem Cell. 26 (5), 722–38e7 (2020).
Zhang, Y. et al. Alternative polyadenylation: methods, mechanism, function, and role in cancer. J. Exp. Clin. Cancer Res. 40 (1), 51 (2021).
Fu, Y. et al. Differential genome-wide profiling of tandem 3’ UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res. 21 (5), 741–747 (2011).
Chen, W. et al. Alternative polyadenylation: methods, findings, and impacts. Genomics Proteom. Bioinf. 15 (5), 287–300 (2017).
An, S. et al. Genome-Wide profiling reveals alternative polyadenylation of innate Immune-Related mRNA in patients with COVID-19. Front. Immunol. 12, 756288 (2021).
Brunet-Ratnasingham, E. et al. Integrated Immunovirological profiling validates plasma SARS-CoV-2 RNA as an early predictor of COVID-19 mortality. Sci. Adv. 7 (48), eabj5629 (2021).
Farahani, M. et al. Molecular pathways involved in COVID-19 and potential pathway-based therapeutic targets. Biomed. Pharmacother. 145, 112420 (2022).
Cecilia, L-M. et al. Transcriptomic clustering of critically ill COVID-19 patients. Eur. Respir. J. 2200592. (2022).
Deb, P. et al. Association of HLA gene polymorphism with susceptibility, severity, and mortality of COVID-19: A systematic review. HLA 99 (4), 281–312 (2022).
Augusto, D. G. & Hollenbach, J. A. HLA variation and antigen presentation in COVID-19 and SARS-CoV-2 infection. Curr. Opin. Immunol. 76, 102178 (2022).
Augusto, D. G. et al. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 620 (7972), 128–136 (2023).
Tremblay, K. et al. The Biobanque Québécoise de La COVID-19 (BQC19)—A cohort to prospectively study the clinical and biological determinants of COVID-19 clinical trajectories. PLOS ONE 16 (5), e0245031 (2021).
Greenspan, N. S. & Cavacini, L. A. 15 – Immunoglobulin function. In: (eds Rich, R. R., Fleisher, T. A., Shearer, W. T., Schroeder, H. W., Frew, A. J. & Weyand, C. M.) Clinical Immunology (Fifth Edition). London: Elsevier; p. (2019). 223 – 33.e1.
Khalid, Z. et al. Identification of novel therapeutic candidates against SARS-CoV-2 infections: an application of RNA sequencing toward mRNA based nanotherapeutics. Front. Microbiol. 13, 901848 (2022).
Gudowska-Sawczuk, M. & Mroczko, B. Free light chains Κ and Λ as new biomarkers of selected diseases. Int. J. Mol. Sci. 24(11). (2023).
Townsend, C. L. et al. Significant differences in physicochemical properties of human Immunoglobulin kappa and lambda CDR3 regions. Front. Immunol. 7, 388 (2016).
Małecka-Giełdowska, M., Fołta, M., Wiśniewska, A., Czyżewska, E. & Ciepiela, O. Cell population data and serum polyclonal Immunoglobulin free light chains in the assessment of COVID-19 severity. Viruses 13 (7), 1381 (2021).
Porcu, M. et al. Mutation of the receptor tyrosine phosphatase PTPRC (CD45) in T-cell acute lymphoblastic leukemia. Blood 119 (19), 4476–4479 (2012).
Ambreen K, José VP, Sadaf N. RGS3 and IL1RAPL1missense variants implicate defective neurotransmission in early-onset inherited schizophrenias.Journal of Psychiatry and Neuroscience. 2022;47(6):E379.
Coperchini, F., Chiovato, L., Croce, L., Magri, F. & Rotondi, M. The cytokine storm in COVID-19: an overview of the involvement of the chemokine/chemokine-receptor system. Cytokine Growth Factor. Rev. 53, 25–32 (2020).
Hsu, R-J. et al. The role of cytokines and chemokines in severe acute respiratory syndrome coronavirus 2 infections. Front. Immunol. 13. (2022).
Hosseini, E., Minagar, A., Ghasemzadeh, M., Arabkhazaeli, A. & Ghasemzadeh, A. HLA-E*01:01 + HLA-E*01:01 genotype confers less susceptibility to COVID-19, while HLA-E*01:03 + HLA-E*01:03 genotype is associated with more severe disease. Hum. Immunol. 84 (4), 263–271 (2023).
Vastrad, B., Vastrad, C. & Tengli, A. Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. Gene Rep. 21, 100956 (2020).
Zheng, W. et al. Host factor interaction networks identified by integrative bioinformatics analysis reveals therapeutic implications in COPD patients with COVID-19. Front. Pharmacol. 12, 718874 (2021).
Todorovic-Rakovic, N. & Whitfield, J. R. Between Immunomodulation and immunotolerance: the role of IFNgamma in SARS-CoV-2 disease. Cytokine 146, 155637 (2021).
Yonekura, S. & Ueda, K. EVI2B is a new prognostic biomarker in metastatic melanoma with IFNgamma associated immune infiltration. Cancers (Basel) 13(16). (2021).
Pohl, M., Bortfeldt, R. H., Grützmann, K. & Schuster, S. Alternative splicing of mutually exclusive exons—A review. Biosystems 114 (1), 31–38 (2013).
Sun, J. et al. Computational methods to study human transcript variants in COVID-19 infected lung cancer cells. Int. J. Mol. Sci. 22, 18 (2021).
He, D. et al. Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma. Allergy Asthma Clin. Immunol. 15, 67 (2019).
Aktas Samur, A. et al. In-depth analysis of alternative splicing landscape in multiple myeloma and potential role of dysregulated splicing factors. Blood Cancer J. 12 (12), 171 (2022).
Chen, X. et al. A novel genetic variant potentially altering the expression of MANBA in the cerebellum associated with attention deficit hyperactivity disorder in Han Chinese children. World J. Biol. Psychiatry 23 (7), 548–559 (2022).
Kushary, S. T. et al. ZTTK syndrome: clinical and molecular findings of 15 cases and a review of the literature. Am. J. Med. Genet. Part. A 185 (12), 3740–3753 (2021).
Glinton, K. E. et al. Phenotypic expansion of the BPTF-related neurodevelopmental disorder with dysmorphic facies and distal limb anomalies. Am. J. Med. Genet. Part. A 185 (5), 1366–1378 (2021).
Xu, E., Xie, Y. & Al-Aly, Z. Long-term neurologic outcomes of COVID-19. Nat. Med. 28 (11), 2406–2415 (2022).
Li, C., Liu, J., Lin, J. & Shang, H. COVID-19 and risk of neurodegenerative disorders: A Mendelian randomization study. Translational Psychiatry. 12 (1), 283 (2022).
Kiltschewskij, D. J., Harrison, P. F., Fitzsimmons, C., Beilharz Traude, H. & Cairns Murray, J. Extension of mRNA poly(A) Tails and 3′utrs during neuronal differentiation exhibits variable association with post-transcriptional dynamics. Nucleic Acids Res. 51 (15), 8181–8198 (2023).
Jia, X. et al. The role of alternative polyadenylation in the antiviral innate immune response. Nat. Commun. 8, 14605 (2017).
Li, M-T. et al. Negative regulation of RIG-I-Mediated innate antiviral signaling by SEC14L1. J. Virol. 87 (18), 10037–10046 (2013).
Matsumiya, T. & Stafforini, D. M. Function and regulation of retinoic acid-inducible gene-I. Crit. Rev. Immunol. 30 (6), 489–513 (2010).
Yamada, T. et al. RIG-I triggers a signaling-abortive anti-SARS-CoV-2 defense in human lung cells. Nat. Immunol. 22 (7), 820–828 (2021).
Wen, W. et al. Immune cell profiling of COVID-19 patients in the recovery stageby single-cell sequencing. Cell. Discovery 6 (1), 31 (2020).
Pike, K. A. & Tremblay, M. L. Protein tyrosine phosphatases: regulators of CD4 T cells in inflammatory bowel disease. Front. Immunol. 9, 2504 (2018).
Ganne, A. et al. In Silico analysis of TUBA4A mutations in amyotrophic lateral sclerosis to define mechanisms of microtubule disintegration. Sci. Rep. 13 (1), 2096 (2023).
Castrogiovanni, P. et al. Brain CHID1 expression correlates with NRGN and CALB1 in healthy subjects and AD patients. Cells [Internet] 10(4). (2021).
Muramatsu, T. Basigin (CD147), a multifunctional transmembrane glycoprotein with various binding partners. J. Biochem. 159 (5), 481–490 (2016).
Ghavampour, S., Lange, C., Bottino, C. & Gerke, V. Transcriptional profiling of human monocytes identifies the inhibitory receptor CD300a as regulator of transendothelial migration. PLOS ONE 8 (9), e73981 (2013).
Zhang, Q. & Jiu, Y. The regulation of host cytoskeleton during SARS-CoV-2 infection in the nervous system. Brain Sci. Adv. 9 (1), 43–52 (2023).
Pillai, J. A. et al. Highly elevated cerebrospinal fluid total Tau level reflects higher likelihood of Non-Amnestic subtype of Alzheimer’s disease. J. Alzheimers Dis. 70 (4), 1051–1058 (2019).
Frontera, J. A. et al. Comparison of serum neurodegenerative biomarkers among hospitalized COVID-19 patients versus non-COVID subjects with normal cognition, mild cognitive impairment, or Alzheimer’s dementia. Alzheimer’s Dement. 18 (5), 899–910 (2022).
Kloc, M., Uosef, A., Wosik, J., Kubiak, J. Z. & Ghobrial, R. M. Virus interactions with the actin cytoskeleton-what we know and do not know about SARS-CoV-2. Arch. Virol. 167 (3), 737–749 (2022).
Aminpour, M., Hameroff, S., Tuszynski, J. A. & How COVID-19 hijacks the cytoskeleton: therapeutic implications. Life (Basel) 12(6). (2022).
Wang, Y. et al. Identification of GGT5 as a novel prognostic biomarker for gastric cancer and its correlation with immune cell infiltration. Front. Genet. 13. (2022).
Liu, J. et al. The clinical implication of gamma-glutamyl transpeptidase in COVID-19. Liver Res. 5 (4), 209–216 (2021).
Yuan, C. et al. The role of cell death in SARS-CoV-2 infection. Signal. Transduct. Target. Therapy. 8 (1), 357 (2023).
Ghosh S, Dellibovi-Ragheb TA, Kerviel A, Pak E, Qiu Q, Fisher M, et al. β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway. Cell 183(6):1520-35.e14 (2020).
Jevtic, S. D. & Nazy, I. The COVID complex: A review of platelet activation and immune complexes in COVID-19. Front. Immunol. 13. (2022).
Fenizia, S., Gaggini, M. & Vassalle, C. The Sphingolipid-Signaling pathway as a modulator of infection by SARS-CoV-2. Curr. Issues Mol. Biol. 45 (10), 7956–7973 (2023).
Ciechanover, A., Orian, A. & Schwartz, A. L. Ubiquitin-mediated proteolysis: biological regulation via destruction. BioEssays 22 (5), 442–451 (2000).
Taheri, G. & Habibi, M. Comprehensive analysis of pathways in coronavirus 2019 (COVID-19) using an unsupervised machine learning method. Appl. Soft Comput. 128, 109510 (2022).
Carreto-Binaghi, L. E. et al. Reduced IL-8 secretion by NOD-like and Toll-like receptors in blood cells from COVID-19 patients. Biomedicines 11(4). (2023).
Choudhary, S., Sharma, K. & Silakari, O. The interplay between inflammatory pathways and COVID-19: A critical review on pathogenesis and therapeutic options. Microb. Pathog. 150, 104673 (2021).
Mancilla-Ceballos, R., Milne, K. M., Guenette, J. A. & Cortes-Telles, A. Inflammation associated with lung function abnormalities in COVID-19 survivors. BMC Pulm Med. 23 (1), 235 (2023).
Brunet-Ratnasingham, E. et al. Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity. Nat. Commun. 15 (1), 4177 (2024).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34 (17), i884–i90 (2018).
Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37 (8), 907–915 (2019).
Liao, Y., Smyth, G. K. & Shi, W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30 (7), 923–930 (2014).
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11 (10), R106 (2010).
Shen, S. et al. rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proceedings of the National Academy of Sciences. 111(51):E5593-E601. (2014).
Shen, S. et al. MATS: a bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res. 40 (8), e61–e (2012).
Xia, Z. et al. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types. Nat. Commun. 5 (1), 5274 (2014).
Orenbuch, R. et al. ArcasHLA: high-resolution HLA typing from RNAseq. Bioinformatics 36 (1), 33–40 (2020).
Kishore, A. & Petrek, M. Next-Generation sequencing based HLA typing: Deciphering Immunogenetic aspects of sarcoidosis. Front. Genet. 9. (2018).
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34 (5), 525–527 (2016).
Robinson, J. et al. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res. 43 (D1), D423–D31 (2015).
Ge, S. X., Jung, D. & Yao, R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 36 (8), 2628–2629 (2020).
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44 (D1), D457–D462 (2016).
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28 (1), 27–30 (2000).
