Docsity
Docsity

Prepare for your exams
Prepare for your exams

Study with the several resources on Docsity


Earn points to download
Earn points to download

Earn points by helping other students or get them with a premium plan


Guidelines and tips
Guidelines and tips

molecular cellar biology primary infection of B-cells, transcription, EBV, molecules, dna,, Study notes of Molecular biology

molecular cellar biology primary infection of B-cells, transcription, EBV, molecules, dna, etc.

Typology: Study notes

2023/2024

Uploaded on 06/21/2025

sabina-veysalova
sabina-veysalova 🇺🇸

1 document

1 / 7

Toggle sidebar

This page cannot be seen from the preview

Don't miss anything!

bg1
BIOL 374: Molecular Biology Lab
Lab 10: The impact of primary EBV infection on primary B cellular transcriptomes
BIOL 374 Molecular Bio Lab 10: EBV primary infection & the host transcriptome page 1 Dr. Vanderlaan | Dr. Gacura
BACKGROUND:
Viral encephalitis
Viral encephalitis is an inflammation of the brain caused by viral infection, leading to swelling, neuronal damage, and
potentially life-threatening complications (1). In neonates, it is particularly dangerous because their immune systems are
immature, making them less able to control viral spread (1). Additionally, their blood-brain barrier is more permeable,
allowing viruses easier access to the central nervous system, which can result in seizures, developmental delays, or death
if not promptly treated. In pediatric cases, infectious viral agents are recognized contributors not only to viral encephalitis
but also to a range of clinical symptoms that can mimic signs of child neglect, such as failure-to-thrive (FTT), involuntary
convulsions, and seizures (1). These viruses include several herpesviruses, notably herpes simplex virus-1 (HSV-1) and HSV-
2, varicella-zoster virus (VZV or chickenpox), human herpesvirus 4 (HHV-4 or Epstein-Barr virus or EBV), human
herpesvirus 5 (HHV-5 or cytomegalovirus or CMV), and human herpesvirus 6 (HHV-6 or roseolovirus) (1).
Human oncoviruses
Human oncoviruses are viruses known to contribute to the development of cancer through chronic infection, immune
evasion, and disruption of normal cellular control mechanisms (Figure 10-1) (2,3). For instance, Epstein-Barr virus (EBV)
is a herpesvirus linked to several lymphomas, including Burkitt lymphoma and Hodgkin lymphoma, as well as
nasopharyngeal carcinoma (411). Hepatitis B virus (HBV) and Hepatitis C virus (HCV) both cause chronic liver infections
that can progress to cirrhosis and hepatocellular carcinoma (2,3). Human herpesvirus 8 (HHV-8) is associated with Kaposi’s
sarcoma, particularly in immunocompromised individuals (2,3). Human papillomavirus (HPV), especially high-risk types
like HPV-16 and HPV-18, is a major cause of cervical, anal, and oropharyngeal cancers through the action of viral oncogenes
that inactivate tumor suppressor proteins (2,3). Human T-lymphotropic virus type 1 (HTLV-1) causes adult T-cell
leukemia/lymphoma by integrating into host DNA and promoting uncontrolled T-cell proliferation (2,3). Lastly, Merkel cell
polyomavirus (MCPyV) has been implicated in the development of Merkel cell carcinoma, a rare but aggressive skin cancer,
particularly in the elderly and immunosuppressed (2,3). Oncoviruses leverage multi-hit models of oncogenic
transformation in target cells (Figure 10-2) (2,3,12).
Figure 10-1. The human oncovirus landscape.
pf3
pf4
pf5

Partial preview of the text

Download molecular cellar biology primary infection of B-cells, transcription, EBV, molecules, dna, and more Study notes Molecular biology in PDF only on Docsity!

Lab 10 : The impact of primary EBV infection on primary B cellular transcriptomes

BACKGROUND:

Viral encephalitis Viral encephalitis is an inflammation of the brain caused by viral infection, leading to swelling, neuronal damage, and potentially life-threatening complications (1). In neonates, it is particularly dangerous because their immune systems are immature, making them less able to control viral spread (1). Additionally, their blood-brain barrier is more permeable, allowing viruses easier access to the central nervous system, which can result in seizures, developmental delays, or death if not promptly treated. In pediatric cases, infectious viral agents are recognized contributors not only to viral encephalitis but also to a range of clinical symptoms that can mimic signs of child neglect, such as failure-to-thrive (FTT), involuntary convulsions, and seizures (1). These viruses include several herpesviruses, notably herpes simplex virus-1 (HSV-1) and HSV- 2, varicella-zoster virus (VZV or chickenpox), human herpesvirus 4 ( HHV- 4 or Epstein-Barr virus or EBV ), human herpesvirus 5 (HHV-5 or cytomegalovirus or CMV), and human herpesvirus 6 (HHV-6 or roseolovirus) (1). Human oncoviruses Human oncoviruses are viruses known to contribute to the development of cancer through chronic infection, immune evasion, and disruption of normal cellular control mechanisms ( Figure 10- 1 ) (2,3). For instance, Epstein-Barr virus ( EBV ) is a herpesvirus linked to several lymphomas, including Burkitt lymphoma and Hodgkin lymphoma, as well as nasopharyngeal carcinoma (4–11). Hepatitis B virus (HBV) and Hepatitis C virus (HCV) both cause chronic liver infections that can progress to cirrhosis and hepatocellular carcinoma (2,3). Human herpesvirus 8 (HHV-8) is associated with Kaposi’s sarcoma, particularly in immunocompromised individuals (2,3). Human papillomavirus (HPV), especially high-risk types like HPV-16 and HPV-18, is a major cause of cervical, anal, and oropharyngeal cancers through the action of viral oncogenes that inactivate tumor suppressor proteins (2,3). Human T-lymphotropic virus type 1 (HTLV-1) causes adult T-cell leukemia/lymphoma by integrating into host DNA and promoting uncontrolled T-cell proliferation (2,3). Lastly, Merkel cell polyomavirus (MCPyV) has been implicated in the development of Merkel cell carcinoma, a rare but aggressive skin cancer, particularly in the elderly and immunosuppressed (2,3). Oncoviruses leverage multi-hit models of oncogenic transformation in target cells (Figure 10-2) (2,3,12). Figure 10- 1. The human oncovirus landscape.

Lab 10 : The impact of primary EBV infection on primary B cellular transcriptomes

Figure 10- 2. The human oncovirus role in the multi-hit model of oncogenic transformation. While HTLV-1 must fully integrate into the host genome, some oncoviruses like EBV (HHV-4) and KSHV (HHV-8) form an episome which is a circular viral genome that associates with the host genome using viral proteins like ENBA or LANA, respectively. Viruses that utilize episomes during latency are not fully integrated but rather associate with the host genome. EBV Lifecycle Overview The Epstein-Barr virus (EBV) lifecycle is characterized by distinct phases: primary infection , latency , and lytic reactivation (13–17). EBV persists in the host via dynamic shifts in viral tropism and a gene expression pattern to support its complex viral lifecycle (13–17). Viral tropism refers to the preferred host cell target for a virus at a specified point across its viral lifecycle (13–17).

  • Primary infection : Broad tropism (epithelial cells + naïve B cells); expression of EBNA, LMP-1, LMP-2 in proliferating B cell blasts.
  • Latency : Narrow tropism (resting memory B cells); LMP- 2 is a key marker; minimal viral gene expression for immune evasion.
  • Lytic reactivation : Renewed epithelial tropism; full viral replication and virion release. The interplay of latency and lytic cycles, along with shifting tropism, enables EBV to persist and evade immunity (13–17). A lifelong reservoir of EBV can then potentiate oncogenesis in some cases (2–11). EBV: Primary Infection EBV typically enters the host through the oropharyngeal epithelium and initially infects epithelial cells and naïve B cells in the tonsils (13–17). This marks the start of the primary infection, often asymptomatic in children but potentially causing infectious mononucleosis in adolescents and adults (18,19). During this stage, EBV exhibits broad tropism, targeting both epithelial cells and B cells, including the resting B cells localized to the mucosal-associated lymphatic tissue (MALT) ( Figure 10 - 3 ) (13–17). In B cells, EBV drives polyclonal B cell activation and proliferation, aided by the expression of several viral latency genes, such as EBNA and LMP-1, and LMP- 2 (13–17). EBNA (Epstein-Barr nuclear antigen) is essential for initiating and maintaining B cell transformation (13–17). LMP-1 (Latent Membrane Protein 1) functions as a viral mimic of CD40, promoting B cell activation, survival, and proliferation (13–17). LMP-2 (Latent Membrane Protein 2) mimics B cell receptor signaling, allowing infected cells to resist apoptosis and external activation cues (13–17). These viral gene products (i.e., EBNA , LMP- 1 , and LMP- 2 ) are thus characteristic molecular hallmarks of EBV-infected B cell blasts seen during primary infection, especially in lymphoid tissues (13–17).

Lab 10 : The impact of primary EBV infection on primary B cellular transcriptomes

25). Lytic reactivation of EBV includes the full complement of lytic gene expression, leading to viral DNA replication, production of new virions, and cell lysis ( Figure 10- 3 ) (23–25). This facilitates viral shedding in saliva, promoting transmission to new hosts. Reactivation is particularly significant in immunocompromised individuals, where uncontrolled lytic replication can lead to tissue damage and increase the risk of EBV-associated cancers (23–25). The goal of today’s lab is to examine the extent by which primary infection stages of EBV upon host resting B-cells might misregulate the expression of genetic loci that have critical roles in normal mitochondrial function (26–31). This is especially important since pediatric cases of viral encephalitis exhibit seizures and epilepsy which is a shared clinical manifestation for of mitochondrial disease patients afflicted by POLG lesions, especially for alleles that disrupt the POLG CTD that contains the polymerase’s active site (1,18,19,32–38). In such cases, EBV-induced haploinsufficiency at the POLG locus of a pediatric POLG heterozygote may result in an amplification of clinical manifestations and pose very serious risk to the patient (1,18,19,32–38). Today, we will re-analyze a public-domain RNA-seq dataset involving EBV infection of primary resting B cells:

  • Identify a precise GEO containing the transcriptomes of EBV-exposed B-cells
  • Prepare a suitable read counts and experimental design file for iDEP
  • Extract meaningful iDEP digestions to arrive at DEG lists as well as GSEA (gene-set enrichment analyses)

DATABASES & PORTALS:

  • NCBI GEO – NCBI GEO (Gene Expression Omnibus) is a public functional genomics data repository that stores high- throughput gene expression and other functional genomics data (39–42).
  • iDEP – Interactive Differential Expression and Pathway analysis (iDEP) is an online tool designed for analyzing gene expression data. It allows users to perform differential expression analysis, pathway analysis, and visualizations of genomic data with an easy-to-use interface (43,44).

MATERIALS:

  • Internet connection

GUI PROTOCOL:

All activities in Lab 10 can be done in any browser inside or outside of the IHACK high-performance cluster (HPC), Gannon University’s supercomputer. I have tested everything in a Windows environment running Google Chrome browsers. Please keep in mind that the Microsoft Edge and the MacOS Safari browsers do not always work for all tasks. For a more hands-on, guided tutorial of how to use iDEP, please refer to the Lab 09 exercise.

  1. Navigate to NCBI GEO and search for the following GEO: GSE125974.
  2. Locate the PMID (PubMed ID) which is the publication accession that accompanied the GSE125974.
  3. Download the Wang et al ., 2019 article. Look it over to get a better idea underling the researchers’ experiment. a. What is their negative control group? ___________________________________________ b. What was their manipulation? ___________________________________________ c. What was their endpoint (i.e., their target dataset)? ___________________________________________
  4. Navigate to iDEP 2.0 and access the uniformly-processed reads for GSE125974. a. Download the gene-level read counts. b. Create a revised gene-level read counts file (CSV) and also an experimental design file (CSV).

Lab 10 : The impact of primary EBV infection on primary B cellular transcriptomes

c. Make sure to use short, simple names. d. When pruning the Wang et al., 2019 GSE125974 dataset, keep only the 0 days and 2 days treatments. e. You should end with only 6 final columns where each column represents a treatment group replicate.

  1. Upload both CSV files to iDEP.
  2. Perform iDEP analyses as discussed in Lab 09, capturing the various analytical datapoints as graphs or dataframes.
  3. I recommend creating the following subfolders to store all captured datapoints:
  4. There are two main goals of your analysis: DEGs + GSEAs
  5. Your DEG goal is to locate genes that might be simultanously 1) in the MitoCarta database as well as 2) exhibit statistically-significant differentially-expressed gene (DEG) patterns when comparing control resting B-cells to those of B-cells exposed to EBV during primary infection stages.
  6. You GSEA goal is to locate pathways in which your DEG list might intersect with in terms of biological mitochondrial activities. Please refer Lab 06 Molecular Epistasis of POLG to get a perspective of some underlying pathways that require normal host mitochondrial function.
  7. The table below are some useful targets for your GSEA journey. In addition, try to capture more GSEA endpoints. Pathway Database Specific GO term page Rationale Curated.MSigDB Zhan Multiple Myeloma Oncogenic transformation GO Molecular Function GO: 0043139 5’ to 3 ’ mtDNA helicase mtDNA replisome (Twinkle helicase) GO: 0017108 5’ FEN activity mtDNA replisome (Flap Endonuclease) GO Biological Processes GO: 006189 de novo IMP biosynthesis Purine anabolism GO: 0044208 de novo AMP biosynthesis Purine anabolism GO: 0097293 XMP biosynthesis Purine anabolism GO Cellular Component GO: 0042719 mito TIM TOM Mitochondrial transporter system Curated.Reactome hsa8956320 Nucleotide biosynthesis Purinosome hsa176974 Unwind DNA Nuclear replisome (oncogenic transformation) hsa69478 G2M DNA replication checkpts Mitotic checkpoints hsa69109 lead strand synth Nuclear replisome (oncogenic transformation) hsa69091 pol switching Nuclear replisome (oncogenic transformation) hsa8983711 OAS AVR Host IFN antiviral (AVS) responses hsa69166 removal of flap intermediate Replisomes, RNA primer removal & processing
  8. For GSEA involving KEGG, I recommend capturing these three KEGG GO terms and mapp to KEGG pathways. Pathway Database Specific GO term page Rationale KEGG hsa00020 TCA Kreb’s Cycle KEGG hsa00860 Porphyrin metabolism Heme biosynthesis KEGG hsa03030 DNA replication Nuclear DNA replisome
  9. Try to see if you can also locate additional KEGG pathways involved in mitochondrial function!

Lab 10 : The impact of primary EBV infection on primary B cellular transcriptomes

  1. Miller G. The Switch between Latency and Replication of Epstein-Barr Virus. Journal of Infectious Diseases. 1990 May 1;161(5):833–44.
  2. Murata T, Sugimoto A, Inagaki T, Yanagi Y, Watanabe T, Sato Y, et al. Molecular Basis of Epstein–Barr Virus Latency Establishment and Lytic Reactivation. Viruses. 2021 Nov 23;13(12):2344.
  3. Wiedmer A, Wang P, Zhou J, Rennekamp AJ, Tiranti V, Zeviani M, et al. Epstein-Barr Virus Immediate-Early Protein Zta Co-Opts Mitochondrial Single-Stranded DNA Binding Protein To Promote Viral and Inhibit Mitochondrial DNA Replication. J Virol. 2008 May;82(9):4647–55.
  4. Vernon SD, Whistler T, Cameron B, Hickie IB, Reeves WC, Lloyd A. Preliminary evidence of mitochondrial dysfunction associated with post-infective fatigue after acute infection with Epstein Barr Virus. BMC Infect Dis. 2006 Dec;6(1):15.
  5. Saneto RP. Epilepsy and Mitochondrial Dysfunction: A Single Center’s Experience. Journal of Inborn Errors of Metabolism and Screening. 2017 Jan;5:232640981773301.
  6. Ohta A, Nishiyama Y. Mitochondria and viruses. Mitochondrion. 2011 Jan;11(1):1–12.
  7. LaJeunesse DR, Brooks K, Adamson AL. Epstein–Barr virus immediate-early proteins BZLF1 and BRLF1 alter mitochondrial morphology during lytic replication. Biochemical and Biophysical Research Communications. 2005 Jul;333(2):438–42.
  8. D’Agostino DM, Bernardi P, Chieco‐Bianchi L, Ciminale V. Mitochondria as Functional Targets of Proteins Coded by Human Tumor Viruses. In: Advances in Cancer Research [Internet]. Elsevier; 2005 [cited 2025 Apr 7]. p. 87–142. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0065230X
  9. Dagan R, Shahak E. Prolonged meningoencephalitis due to Epstein-Barr virus with favorable outcome in a young infant. Infection. 1993;21(6):400–2.
  10. Russell J. Status Epilepticus and Epstein-Barr Virus Encephalopathy: Diagnosis by Modern Serologic Techniques. Arch Neurol. 1985 Aug 1;42(8):789.
  11. Nichols L, Thompson M, Bentz GL. Comparison of clinical characteristics of a patient with Epstein–Barr virus‐associated seizure and patients with COVID‐19‐associated seizure. Journal of Medical Virology. 2021 Dec;93(12):6442–3.
  12. Bassan H, Bloch AM, Mesterman R, Assia A, Harel S, Fattal-Valevski A. Myoclonic Seizures as a Main Manifestation of Epstein- Barr Virus Infection. J Child Neurol. 2002 Jun;17(6):446–7.
  13. Basel D. Mitochondrial DNA Depletion Syndromes. Clinics in Perinatology. 2020 Mar;47(1):123–41.
  14. Cohen B, Chinnery P, Copeland W. POLG-Related Disorders. In: Adam MP, Feldman J, Mirzaa GM, Wallace SE, Amemiya A, editors. GeneReviews [Internet]. Seattle, Washington: University of Washington-Seattle; 2024. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26471/
  15. Rahman S, Copeland WC. POLG-related disorders and their neurological manifestations. Nat Rev Neurol. 2019 Jan;15(1):40–52.
  16. Barrett T. NCBI GEO: mining millions of expression profiles--database and tools. Nucleic Acids Research. 2004 Dec 17;33(Database issue):D562–6.
  17. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, et al. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Research. 2009 Jan 1;37(Database):D885–90.
  18. Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Research. 2012 Nov 26;41(D1):D991–5.
  19. Clough E, Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, et al. NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update. Nucleic Acids Research. 2024 Jan 5;52(D1):D138–44.
  20. Ge X. iDEP Web Application for RNA-Seq Data Analysis. In: Picardi E, editor. RNA Bioinformatics [Internet]. New York, NY: Springer US; 2021 [cited 2025 Apr 3]. p. 417–43. (Methods in Molecular Biology; vol. 2284). Available from: https://link.springer.com/10.1007/978- 1 - 0716 - 1307 - 8_
  21. Ge SX, Son EW, Yao R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics. 2018 Dec;19(1):534.