Information Flow and Genetics

TWiM #212: A Coronavirus Outbreak and IRF4 Deficiency in Whipple’s Disease

Podcast and Annotation Information
  • Annotation by Nidhi Athreya, Bernie Cueto, Connor Dechiro, Claire Min, and Maggie Schlarman
  • Podcast audio by TWiM: Listen to TWiM #212 Podcast
  • Podcast transcript by Otter.ai and edited by Grace Helle and Harshita Sharma: Access Podcast Transcripts
  • Papers Discussed:
    • Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, et al. 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet. 395(10223): 497–506. doi:10.1016/S0140-6736(20)30183-5.
    • Guérin A, Kerner G, Marr N, Markle JG, Fenollar F, Wong N, Boughorbel S, Avery DT, Ma CS, Bougarn S, Bouaziz M, Béziat V, Della Mina E, Oleaga-Quintas C, Lazarov T, Worley L, Nguyen T, Patin E, Deswarte C, Martinez-Barricarte R, Boucherit S, Ayral X, Edouard S, Boisson-Dupuis S, Rattina V, Bigio B, Vogt G, Geissmann F, Quintana-Murci L, Chaussabel D, Tangye SG, Raoult D, Abel L, Bustamante J, Casanova JL. 2018. IRF4 haploinsufficiency in a family with Whipple’s disease. eLife. 7:e32340. doi:10.7554/eLife.32340.

1. Paper Abstracts

1.1. Snippet paper; discussion starts at 3:15 minutes

The Most Interesting Things (according to students)

  • Since the virus’ genome had been sequenced, PCR primers could be used to confirm infection in patients presenting symptoms.
  • The technique of viral genome sequencing is fascinating. It is amazing that scientists can use genome sequencing to find the exact sequence of the virus’ genome and trace it to very similar viruses. This shows how important recent biological advances allow us to combat diseases.

The abstract cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.2.

1.2. Main paper; discussion starts at 26:09 minutes

The Most Interesting Things (according to students)

  • The discussion of Whipple’s disease and Johne’s disease and how they are both linked to Actinomycetes bacteria was quite interesting. Looking at the presence of IRF4 mutations in cows and their inbred nature, as well as the fact that there are many similarities between the two diseases, allows for interesting comparisons to be drawn between humans and other animals.
  • The fact that almost everyone has this bacterial species in their guts, so much that they call it one of our commensal bacteria, is frightening; especially because there are many things that are unknown as of now. If an individual were to constantly have a mutating the IRF4 gene, they would experience the disease.

“Most humans are exposed to Tropheryma whipplei (Tw). Whipple’s disease (WD) strikes only a small minority of individuals infected with Tw (<0.01%), whereas asymptomatic chronic carriage is more common (<25%). We studied a multiplex kindred, containing four WD patients and five healthy Tw chronic carriers. We hypothesized that WD displays autosomal dominant (AD) inheritance, with age-dependent incomplete penetrance. We identified a single very rare non-synonymous mutation in the four patients: the private R98W variant of IRF4, a transcription factor involved in immunity. The five Tw carriers were younger, and also heterozygous for R98W. We found that R98W was loss-of-function, modified the transcriptome of heterozygous leukocytes following Tw stimulation, and was not dominant-negative. We also found that only six of the other 153 known non-synonymous IRF4 variants were loss-of-function. Finally, we found that IRF4 had evolved under purifying selection. AD IRF4 deficiency can underlie WD by haploinsufficiency, with age-dependent incomplete penetrance.” (Guérin et al 2018, no changes)

2. Vision and Change Core Concepts and 2024 ASM Fundamental Statements

Snippet Main
Vision and Change Topics
  • Information Flow and Genetics (V&C_IFG)
  • Impact of Microorganisms (V&C_IM)
  • Information Flow and Genetics (V&C_IFG)
  • Evolution (V&C_E)
ASM Fundamental Statements
  • Fundamental Statement 19 (ASM_19): Non-cellular infectious agents, such as viruses, prions, viroids, and satellites, are dependent on host cell processes in order to replicate.
  • Fundamental Statement 28 (ASM_28): A minority of microbes are pathogens that can cause diseases and harm host organisms, society, and ecosystems.
  • Fundamental Statement 2 (ASM_2): The diversity of microbes has arisen because of processes that include horizontal gene transfer, mutation, reassortment, recombination, and natural selection in varying ecological niches favor the growth and survival of certain variants.
  • Fundamental Statement 16 (ASM_16): Genetic variation can influence microbial structures and their functions.

3.  Potential Learning Objectives for the Podcast

The student will be able to: Paper1 Order2
  • Define the symptoms of the 2019 coronavirus disease.
  • Identify the origin and genetic characteristics of the 2019 coronavirus,
  • Recall how asymptomatic carriers and incubation periods each play a role in viral transmission, specifically with the 2019 coronavirus.
 S L
  • Hypothesize the relationship of hypothetical viruses based on genetic similarity.
 S H
  • Describe the key symptoms associated with Whipple’s disease.
  • Define the concept of haploinsufficiency.
  • Identify the function of the IRF4 protein.
 M L
  • Predict whether a person is more or less likely to acquire Whipple’s disease based their IRF4 protein’s defect.
 M H

1 Papers: Snippet (S) or Main (M)

2 Learning Objectives: Lower Order or Higher Order (H)

4. Techniques Described (with Time Stamps)

Here is a link to a bio-dictionary that has many, but not all definitions if you need a definition: Explore Biology Bio-Dictionary

4.1. Snippet Paper

  • Genome Sequencing (3:15–6:14): This is a process that allows scientists to identify the sequence of bases in DNA or RNA, providing a comprehensive map of an organism’s genetic makeup.
  • Antiviral Drug Testing of Remdesivir (12:10–13:03): This test evaluates the efficacy and safety of potential antiviral medications. This process typically involves in vitro assays to assess a drug’s ability to inhibit viral replication and cell death, as well as in vivo studies in animal models. In this study, a clinical trial was initiated to test Remdesivir, to assess its effectiveness against the coronavirus.

4.2. Main Paper

  • Tissue Culture (28:01–28:15): This is a technique that many research labs use to isolate and grow cells to study them in detail. The researchers in this study identified a bacterial species called Tropheryma whipplei through cell culture.

5. Connections to General Microbiology Processes/Concepts (with Time Stamps)

5.1. Snippet Paper

  • Viral Structure (9:12–10:50): Coronavirus is a positive-stranded RNA virus. This means that the virus itself can act as a messenger RNA and use the host machinery to replicate into more negative sense RNA and the spike protein.

5.2. Main Paper

  • Transcriptome (28:01): A complete set of RNA transcripts produced by the genome of an organism at a given time or in a specific cell type.
  • Gram-positive Bacteria (28:01- 28:46): These bacteria have a cell wall composed of a thick peptidoglycan layer and only one plasma membrane. Elio Schaechter explained that the bacteria Tropheryma whipplei that causes Whipple’s disease is a gram-positive species and a member of Actinomyces.
  • Haploinsufficiency (32:40–34:27): Individuals that are heterozygous and have one copy of the mutated DNA have the disease because having both “good” or functional copies are required for a normal phenotype, here for enough transcription. Even though there is one allele that produces normal versions of the protein, such as for Whipple’s disease, the patient has disease with just one mutant allele.

6. Podcast Questions

  1. Genetic analysis revealed that the 2019 coronavirus is most closely related to which of the following?
    1. The original SARS-CoV virus that was isolated in 2003
    2. An avian influenza virus from 2017, but remains unknown
    3. A bat coronavirus from a cave 1,000 miles from Wuhan
    4. A swine influenza virus detected in rural China in 2009
  2. According to the discussion of early COVID-19 cases in Wuhan, which of the following groups of symptoms were most commonly observed in patients?
    1. Sore throat, rash, itchiness
    2. Fever, dry cough, fatigue
    3. Runny nose, rash, hair loss
    4. Vomiting, diarrhea, nausea
  3. What role did asymptomatic and/or presymptomatic individuals likely play in the transmission of the 2019 coronavirus?
    1. Neither individuals played a significant role in viral transmission.
    2. Presymptomatic individuals allowed spread due to viral expulsion.
    3. Both believed their symptoms were associated with another illness.
    4. Both likely contributed to community spread due to viral shedding.
  4. Genetic similarity value (0-100%) is shown in the table for four hypothetical viruses (1-4). Based on the discussion about virus relatedness and genetic identity, which hypothetical viruses would you predict are most closely related to each other? What is your evidence?
Virus 1 Virus 2 Virus 3 Virus 4
Virus 1 100% 85% 56% 22%
Virus 2 85% 100% 92% 35%
Virus 3 56% 92% 100% 39%
Virus 4 22% 35% 39% 100%
    1. Virus 2 and 3 are most closely related because they are 92% genetically identical.
    2. Virus 1 and 4 are most closely related because they are 35% genetically identical.
    3. Virus 1 and 2 are most closely related because they are 100% genetically identical.
    4. There is not enough information/evidence given to tell relatedness from these data.

5. Which of the following symptoms are most closely associated with Whipple’s disease?

    1. Severe skin blistering and bowel irritation
    2. Respiratory distress and periodic high fever
    3. Malabsorption and other systemic issues
    4. Body hair loss and visual disturbances

6. Haploinsufficiency in diploid organisms such as humans or mice is when _______ .

    1. both copies of a gene are deleted or inactivated in an individual.
    2. one copy of a gene is deleted or inactivated in an individual.
    3. an embryo is produced using only one parent’s complete genome.
    4. a pathogen becomes contagious only after environmental stress.

7. In which broad biological process/pathway does the IRF4 protein function?

    1. Adaptive immunity
    2. Cell growth and repair
    3. Membrane transport
    4. Innate immunity

8. The podcasters discuss a model for how the IRF4 R98W defect causes disease susceptibility in the family.  They suggest that when there is too little binding of the defective IRF4 protein to its regulatory regions, too little transcription of specific genes occurs and this results in susceptibility.  If this model were true, what would you predict for a mutant IRF4 that has too much binding? Pick all that apply.

    1. The mutation would not cause Whipple’s disease, but possibly some other genetic disease.
    2. The mutation would cause the person to be susceptible to nearly all infectious diseases.
    3. The mutation would cause a general immune system failure and disturb the gut microbiome.
    4. The mutation would lead to an overactive immune response causing autoimmune disease.

7. Figure Reading Exercises

The following are two figure reading exercises, one from the snippet paper (Figure 1) and one from the main paper (Figure 1).

7.1. First Figure Reading Exercise

7.1.1. Learning Objectives

Students will be able to:

  • Identify key features in a timeline bar chart.
  • Analyze patient data to make conclusions about the age range most affected and most severely affected in the early part of the pandemic.
Experimental Background (Huang et al., Figure 1)

In late 2019, the pandemic virus SARS-Cov2, which causes COVID-19, was just being identified.  It was originally called the 2019 novel coronavirus or 2019-nCoV.  Huang et al. (2020) investigated the relationship of age and disease severity for the novel coronavirus by looking at hospital admission type (panel A) and also the timeline for symptom onset for patients who had or had not visited the Huanan Seafood Market (Panel B).

7.1.2. Questions

  1. When was the Huanan Seafood Market closed?
    1. December 30, 2019
    2. December 31, 2019
    3. January 1, 2020
    4. January 2, 2020
  2. Around what percentage of patients were exposed to the Huanan Seafood Market?
    1. ~25%
    2. ~40%
    3. ~66%
    4. ~90%
  3. What age group had the least number of hospitalized patients from Coronavirus infection in these data?
    1. <18
    2. 18–24
    3. 25–49
    4. 50–64
    5. >65
  4. Which age range shows the largest relative disease severity? What is your evidence?
    1. 18-24; the disease is lethal and were not admitted.
    2. 25-49; they have the largest hospital admissions.
    3. 50-64; they have a high ratio of ICU admissions.
    4. >65; while smaller, they have 50% ICU admissions.

7.2. Second Figure Reading Exercise

7.2.1. Learning Objectives

Students will be able to:

  • Identify key features on a schematic diagram.
  • Interpret electropherograms of DNA sequence information.
  • Predict the functional effects of specific base/amino acid mutations based on a protein domain schematic.
  • Predict the IRF4 DNA sequence electropherogram results for a person who is more or less likely to acquire Whipple’s disease.
Experimental Background (Guérin et al., Figure 1BC)

Most people have been exposed to the bacterium Tropheryma whipplei, but only a small fraction of these people develop an autosomal dominant genetic disease called Whipple’s disease. This rare event highlights that the disease requires both genetic and environmental events. To gain a better understanding of the genetic components of this disease, Guérin et al. (2018) identified a family with four patients.  They sequenced the genomes of the patients and an unrelated control to identify DNA changes specific to the patients.  Genomic sequence of the IRF4 gene region of patients (panel C; P1-P4) and the unrelated control (panel C; C) are displayed as electropherograms.  The mutation location and effect at the protein level were mapped to the IRF protein structure and functional domains (panel B), which are noted in the figure legend.

Protein schematic and 5 electropherogramsshowing showing DNA sequences.
Figure 1. “Autosomal dominant IRF4 deficiency…. (B) Schematic representation of the IRF4 protein, showing the DNA-binding domain (DBD), P-rich domain, activation domain, α-helical domain, Q-rich domain, IRF association domain (IAD), and auto-inhibitory domain. The R98W substitution is indicated in red. (C) Electropherogram of IRF4 genomic DNA sequences from a healthy unrelated control (C) and the patients (P1, P2, P3, P4). The R98W IRF4 mutation leads to the replacement of an arginine with a tryptophan residue in position 98 (exon 3, c.292 C > T). The corresponding amino acids are represented above each electropherogram….” (Guérin et al. 2018, cropped to panels B-C)

 

7.2.2. Questions

  1. The IRF4 R98W mutation results in which amino acid change?
    1. Arginine to Tryptophan at position 98
    2. Tryptophan to Arginine at position 98
    3. Asparagine to Tryptophan at position 98
    4. Arginine to Tryptophan at position 99
  2. What are the bases of the DNA sequence (5’ to 3’; left to right) for this electropherogram if the fluorescent tags for each base are: Black = Guanine; Green = Adenine; Red = Thymine; Blue = Cytosine?

Electropherogram with black, green, red, black, blue, red, black, black, blue, blue, blue, and black spikes.

    1. 5’- CGGGCCAGCATC–3’
    2. 5’–GCCCGGTCGTAG–3’
    3. 5’- CTACGACCGGGC–3’
    4. 5’- GATGCTGGCCCG–3’

Source of electropherogram: Whiteley MH. 2014. Allelic variation in the canine Cox-2 promoter causes hypermethylation of the canine Cox-2 promoter in clinical cases of renal dysplasia. Clin Epigenetics. 6(1):7. doi: 10.1186/1868-7083-6-7.; CC BY 2.0 Figure 3 cropped to a portion of panel A.

  1. Control and patient sequencing electropherograms are displayed in panel C. What genotype and electropherogram results would you expect to find for a fifth patient with Whipple’s Disease
    1. A C/C genotype with a single high peak for C at base 98.
    2. A C/T genotype with a peak for both C and T at base 98.
    3. A C/T genotype with a peak for both C and T at base 292.
    4. A C/C genotype with a single high peak for C at  base 292.
  2. Given the schematic of the IRF4 protein domains (panel B) and where the R98W mutation occurs, why is this mutation likely so significant?
    1. It is found in the DNA-binding domain, so it likely degrades the genomic DNA using its endonuclease activity.
    2. It is found in the DNA-binding domain, so it likely impacts the protein’s ability to regulate transcription.
    3. It is found in the activation domain, so it likely results in uncontrolled transcription for all the promoters it binds.
    4. It is found in the autoinhibitory domain so this change likely affects protein folding and causes denaturation.

8. Paper Information and Licensing

8.1. Snippet paper

  • Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, et al. 2020. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet. 395(10223): 497–506. doi:10.1016/S0140-6736(20)30183-5.
  • The abstract cannot be copied due to licensing restrictions: see the article’s copyright information. Please see the article at the journal’s web page and/or PubMed.

8.2. Main paper

  • Guérin A, Kerner G, Marr N, Markle JG, Fenollar F, Wong N, Boughorbel S, Avery DT, Ma CS, Bougarn S, Bouaziz M, Béziat V, Della Mina E, Oleaga-Quintas C, Lazarov T, Worley L, Nguyen T, Patin E, Deswarte C, Martinez-Barricarte R, Boucherit S, Ayral X, Edouard S, Boisson-Dupuis S, Rattina V, Bigio B, Vogt G, Geissmann F, Quintana-Murci L, Chaussabel D, Tangye SG, Raoult D, Abel L, Bustamante J, Casanova JL. 2018. IRF4 haploinsufficiency in a family with Whipple’s disease. eLife. 7:e32340. https://elifesciences.org/articles/32340 
  • This article is licensed for Creative Commons use using CC BY 4.0, which allows re-use and adaptation with proper attribution and notation of any changes. See https://elifesciences.org/articles/32340#copyright. 

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Podcast Annotation and Resources in Microbiology Copyright © 2025 by Rebecca Seipelt-Thiemann; Nancy Boury; Gwendowlyn S. Knapp; Amaya Garcia Costas; and Patrick Armstrong is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

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