This document summarizes a journal club presentation discussing a research article published in The Journal of Cell Discovery. The presentation provides an overview of the journal and article, including critiques of the title, abstract, introduction, methods, results, discussion, and references. The key findings of the article are that single-cell RNA sequencing of COVID-19 patient samples revealed upregulation of myeloid-derived suppressor cells and macrophages, along with disturbances in T-cell populations. However, the small sample size and lack of explanation of specific mechanisms were identified as limitations.

2. JOURNAL CLUB
Medical Biochemistry and Molecular Biology
Department
(PhD Program)
Presented by
Haytham Khalid
Mohammed Esawie
16/12/2020

3. Talk Outlines
Why this journal and article?
Introduction critique
Methods critique
Discussion critique
Results critique
References critique
Title & abstract critique

4. The Journal of Cell Discovery
It is a Specialized journal in our field of
research.
It is a peer- reviewed journal.
A recognized journal publisher : Springer.
Thomson Reuters journal 2 year impact
factor 2019 is 6.255.

5. • Discusses a very recent and urgent
problem(Covid 19 complications).
• Illuminating a hotspot research point
(mechanism that leads to immune
dysfunction in severe coronavirus disease).
• Highlighting an interesting technique (RNA
sequencing).
• Recent (published October 2020).
Why this article ?

6. Title critique
Interesting
catch
Title contains
vague word
(peripheral) ?
Reflects
content of
the paper
Average
length
Contains
abbreviations
Doesn’t mention
study group

7. Authors
Most of
them have
publications
related to
the paper
points.

8. keywords
No keywords included
in this article

9. Abstract critique
• Precise and to
the point
• No unexplained
abbreviations
• Explains the
strategy and
policy of the
article
• The mentioned
results are
present in the
article later

10. Abstract critique
No mention of number
of included patients
Not enough data of the
included methods, a lot
of uninterpreted
abbreviations

11. introduction critique
Clearly explains the studied
disease problem and the
problem in understanding the
underlying molecular
pathology

12. Clearly summarized the
research methodology,
avoided unknown
abbreviations
In my opinion the
introduction needed
more comprehensive
illustration of the
immune mechanisms
involved in COVID-19
infection

13. Methods critique
Ethical approval was
considered and mentioned

14. Comprehensive and
detailed explanation of
the cell isolation
techniques

15. Detailed explanation of
the bioinformatic
validation of RNA-seq
results

16. No mention of treatment plan of these patients, were the
samples taken before or after treatment? If taken before
what about after treatment samples?
Small number of patients included,
also no detailed explanation of the
selection criteria (explained in
chinese)
No mention of
infection control
procedures in
taking the samples
No CAT number of
used kits

17. Some unexplained
abbreviations

18. Single-Cell RNA-seq library prep

19. Results critique
• Background
• The differential immune responses with SARS-
Cov2
• Critical appraisal

20. Background

22. • The genes for CELLULAR IDENTITY
Vs.
The genes for NORMAL CELLULAR FUNCTION
• Cellular heterogeneity between nearby cells in
differentiation
e.g.: CD4+ and CD8+

23. The differential immune responses
with SARS-Cov2

24. Myeloid Derived Suppressive Cells
(MDSCs)
• Dominant in peripheral Blood
• Identity Receptor: CD14+ / HLA-DR-/lo ????

26. Myeloid Derived Suppressive Cells
(MDSCs)
• Pathways down-regulated:
- Type 1 INF (inspite of Interferon Stimulating
Genes (ISGs) upregulation)
- MHC2 receptors
• Associated with:
- High scores : IL-6, CRP and Neu/ Lym ratio
- Small amounts: CD3+, CD4+ and CD8+

27. Macrophages
• Dominant in BALF
• Identity Receptor: CD14+, CD68+ and FCGR3A

28. • Pathways up-regulated:
- Response to hypoxia and high temperatures
- Chemokines for neutrophils chemotaxis e.g.
CCL2, CCL3 …
• Pathways down-regulated:
- Apoptosis?????
- Ag Presentation

29. T-Cell Landscape Disturbances
• CD4+ and CD8+ are affected (but CD8+ is more
down)
• Other distributed T-Cells: Treg-CTLA4, Cycling
T-Cells
THE CELLULAR CONVERSION BETWEEN CD4+ and
Treg-CTLA4, Cycling T-Cells > BETWEEN CD4+
and CD8+

30. T-Cell Landscape Disturbances
On Transcriptomic Analysis 
No Cell Exhausion or Apoptosis intiation
So, COULD NOT be a reason to explain T-Cell
mass loss

31. Critical Appraisal

32. Causality in check!!
• The study doesn’t
provide explanations
• Case Control Study!
• Other recent studies
report the genes:
IFNAR2, TYK2, OAS1,
DPP9 and CCR2 –
partially explain the
progress from mild to
severe

33. Repetition of data, Distracting Syntax

34. Repetition of data, Distracting Syntax

35. Figures don’t stand on its own

36. Distracting Syntax and Figures

37. However,
• The rest was enough explanatory
• Statistical analysis was well performed
(explained in the methods)
• Answer How? And Why? Questions

38. • Answering the main question of the study?
Introduction Discussion
Discussion critique

39. • They should’ve started with:

40. • Another major finding:

41. • Consistency in the shadow of literature:

42. • Big Finish

43. They didn’t clarify limitations
• More of a description than of defining specific
mechanisms
• Small size of sample??
Is this really a limitation??

44. References critique
All references are very
recent and serving the
research points