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Cluster Report

Date: 2024-07-24 18:46:23

### Cluster 0 **Annotation:** CD8+ T cells (effector/memory subset)

Description: This cell cluster ( CD8+ T cells (effector/memory subset) ) has up-regulated genes: LDHB, LTB, CD3D, IL7R, JUNB, CD3E, RPS25, RPS12, RPS27A, RPS27, RPL31, RPS3A, RPL9, TPT1, IL32, NOSIP, TMEM66, RPS29, RPS6, RPL30 and down-regulated genes: LYZ, HLA-DRA, FTL, CD74, CST3, TYROBP, FTH1, HLA-DPB1, HLA-DRB1, HLA-DPA1, FCER1G, LGALS1, SAT1, CYBA, CTSS, HLA-DRB5, COTL1, OAZ1, S100A6, GSTP1 .

Reason: Based on the gene expression profile of this cell cluster, the annotation "CD8+ T cells (effector/memory subset)" is likely due to the following reasons:

  • Up-regulation of genes involved in immune function and activation:
    • CD3D and CD3E are part of the T-cell receptor complex, indicating T-cell activation.
    • IL7R is a cytokine receptor involved in T-cell development and activation.
    • JUNB is a transcription factor involved in T-cell activation and differentiation.
  • Down-regulation of genes involved in immune suppression or tolerance:
    • LYZ is an immunosuppressive protein, its down-regulation suggests reduced immune suppression.
    • HLA-DR and HLA-DP/B1 are major histocompatibility complex (MHC) class II molecules involved in antigen presentation. Their down-regulation may indicate reduced antigen presentation and immune tolerance.

These patterns of gene expression are consistent with an effector/memory T-cell subset, which is characterized by:

  • Activation and proliferation
  • Production of cytokines and chemokines
  • Expression of surface receptors involved in immune function (e.g., CD3D/E)
  • Reduced expression of genes involved in immune suppression or tolerance

The CD8+ annotation suggests that this cell cluster consists primarily of CD8-positive T cells, which are a subset of T cells that recognize antigens presented by MHC class I molecules.

### Cluster 1 **Annotation:** Neutrophil

Description: This cell cluster ( Neutrophil ) has up-regulated genes: S100A9, LYZ, S100A8, CST3, FTL, TYROBP, FCN1, LGALS2, FTH1, LGALS1, AIF1, TYMP, GSTP1, S100A6, CTSS, GPX1, SAT1, LST1, S100A4, S100A11 and down-regulated genes: LTB, IL32, MALAT1, PTPRCAP, RPS27A, CD3D, RPSA, RPS3A, RPL9, RPS27, CXCR4, RPL21, CD3E, RPL23A, LDHB, RPL31, RPS25, RPL3, RPS29, MYL12A .

Reason: Based on the up-regulated genes and down-regulated genes listed in the description, I can provide some insights that suggest the cell cluster is annotated as a Neutrophil.

Here are some key points that support this annotation:

  1. Up-regulation of S100 proteins: The S100 family of proteins is highly expressed in neutrophils. In particular, S100A8 and S100A9 are known to be up-regulated in neutrophils during inflammation.
  2. Expression of LYZ (Lysozyme): Lysozyme is an enzyme that breaks down bacterial cell walls, which is a key function of neutrophils.
  3. Up-regulation of CST3 (Cystatin C): Cystatin C is a cysteine protease inhibitor that is highly expressed in neutrophils and plays a role in regulating the activity of neutrophil elastase.
  4. Down-regulation of LTB (Leukotriene B4): Leukotriene B4 is a chemoattractant that recruits neutrophils to sites of inflammation. Its down-regulation suggests that the cell cluster may not be actively recruiting new neutrophils.
  5. Expression of FCN1 (Ficolin 1): Ficolin 1 is a pattern recognition receptor that recognizes bacterial carbohydrates and activates the complement system, which is important for neutrophil function.

These genes are all involved in neutrophil function, such as chemotaxis, phagocytosis, and antimicrobial defense. The down-regulation of LTB and other genes involved in neutrophil recruitment suggests that this cell cluster may be a mature, activated neutrophil population rather than a newly recruited one.

Overall, the combination of up-regulated S100 proteins, lysozyme, cystatin C, and ficolin 1, along with the down-regulation of LTB and other genes involved in neutrophil recruitment, supports the annotation of this cell cluster as a Neutrophil.

### Cluster 2 **Annotation:** Plasma cells (CD19+ CD20- CD38+)

Description: This cell cluster ( Plasma cell ) has up-regulated genes: CD74, CD79A, HLA-DRA, CD79B, HLA-DPB1, HLA-DQA1, TCL1A, HLA-DQB1, MS4A1, HLA-DRB1, HLA-DPA1, CD37, HLA-DRB5, LINC00926, HLA-DMA, HLA-DQA2, CXCR4, HLA-DMB, LAPTM5, ISG20 and down-regulated genes: LYZ, S100A4, LGALS1, S100A6, IL32, FTH1, CD3D, S100A11, ANXA1, SRGN, S100A10, GIMAP7, HCST, CD3E, COTL1, VIM, GAPDH, TMSB4X, ACTB, LDHB .

Reason: Based on the gene expression profile provided, the annotation for the cell cluster as "Plasma cells (CD19+ CD20- CD38+)" is reasonable because:

  • Up-regulation of genes involved in plasma cell differentiation and function:
    • CD74: a surface protein expressed by mature B cells and plasma cells.
    • CD79A/B: components of the B-cell receptor complex, which is also present on plasma cells.
    • HLA-DRA, -DPB1, -DQA1, -DQB1, -DRB1, -DPA1, -DRB5, and -DMA: MHC class II genes involved in antigen presentation, which is a key function of plasma cells.
    • TCL1A: a gene involved in T-cell activation, but also expressed by plasma cells.
    • MS4A1: a gene encoding a surface protein found on mature B cells and plasma cells.
  • Down-regulation of genes characteristic of other cell types:
    • LYZ (lysozyme), S100A4/A6/A10/A11, LGALS1, IL32, FTH1, CD3D/E, VIM, GAPDH, TMSB4X, ACTB, and LDHB: genes primarily expressed by cells other than plasma cells, such as neutrophils, macrophages, or lymphocytes.

The absence of CD20 (a surface protein characteristic of mature B cells) and the presence of CD38 (a surface protein involved in plasma cell differentiation) support the annotation as "Plasma cells". The expression profile is consistent with a cell cluster that has undergone plasma cell differentiation.

### Cluster 3 **Annotation:** CD8+ T cells (Tc1/Tc2)

Description: This cell cluster ( CD8+ T cells (Tc1/Tc2) ) has up-regulated genes: CCL5, GZMK, IL32, LYAR, CTSW, GZMA, IL7R, MT-ND2, JUN, MT-CYB, CD3E, IER2, ZFP36L2, CD3D, PTPRCAP, ID2, RARRES3, CST7, HCST, CD7 and down-regulated genes: LYZ, HLA-DRA, FTL, FTH1, CD74, HLA-DPA1, HLA-DPB1, CTSS, SAT1, PSAP, TMSB10, S100A11, CD37, COTL1, OAZ1, ARPC3, SRGN, NEAT1, LY6E, RPS11 .

Reason: Based on the gene expression profile provided, the annotation "CD8+ T cells (Tc1/Tc2)" is likely due to the up-regulation of genes characteristic of CD8+ T cells and the Th1/Th2 cytokine pattern.

Here are some reasons why:

  1. Cytokines: The up-regulation of IL7R, a receptor for interleukin-7 (IL-7), which is important for T cell development and activation. Additionally, the presence of JUN, a transcription factor involved in Th1 cytokine production, supports the idea that these cells are producing Th1-type cytokines.
  2. Chemokines: The up-regulation of CCL5, a chemokine involved in T cell migration and activation, is consistent with CD8+ T cell behavior.
  3. Granzymes: The presence of GZMA and GZMK, granzymes A and K, respectively, which are important for cytolytic activity and apoptosis induction, is typical of CD8+ T cells.
  4. Co-stimulatory molecules: The up-regulation of CD3E, a co-receptor involved in T cell activation, and CD7, a surface molecule involved in T cell activation and adhesion, supports the idea that these cells are activated T cells.

On the other hand, the down-regulation of genes associated with myeloid or dendritic cell function (e.g., LYZ, HLA-DR, FTL, FTH1) suggests that these cells are not myeloid or dendritic cells. The lack of up-regulation of genes characteristic of Th17 or Treg cells (e.g., RORC, FOXP3) further supports the idea that these cells are CD8+ T cells with a Th1/Th2 cytokine pattern.

In summary, the combination of gene expression patterns and functional markers suggests that this cell cluster is composed of CD8+ T cells with a Th1/Th2 cytokine profile, consistent with the annotation "CD8+ T cells (Tc1/Tc2)".

### Cluster 4 **Annotation:** Natural Killer cells (NK cells)

Description: This cell cluster ( Natural Killer cells (NK cells) ) has up-regulated genes: GNLY, NKG7, GZMB, PRF1, FGFBP2, CCL4, CST7, GZMA, CTSW, CD247, SPON2, CCL5, HOPX, IGFBP7, FCGR3A, CD7, CLIC3, PLAC8, GZMM, GZMH and down-regulated genes: LYZ, HLA-DRA, FTL, FTH1, LTB, COTL1, CD74, HLA-DPB1, VIM, HLA-DPA1, CD3D, SAT1, RPS12, RPL18A, RPL32, JUNB, RPS27, RPL13, RPS25, CTSS .

Reason: Based on the up-regulated genes and down-regulated genes listed in the description, I can provide some insights that support the annotation of this cell cluster as Natural Killer cells (NK cells).

Up-regulated genes:

  • GNLY: Glycine-rich secreted protein, also known as CD57, is a surface marker specific to NK cells.
  • NKG7: A gene involved in the activation and maturation of NK cells.
  • GZMB, PRF1, GZMA, GZMM, GZMH: These genes are involved in granule-mediated cytotoxicity, which is a characteristic feature of NK cell function.
  • CD247: The gene for CD3 epsilon chain, which is also expressed on NK cells.

Down-regulated genes:

  • LYZ: Lysozyme, an enzyme that is not typically expressed by NK cells.
  • HLA-DR, HLA-DP, HLA-DPA1, HLA-DPB1: These genes are involved in antigen presentation and are characteristic of T cells. The down-regulation of these genes suggests that the cell cluster is not a T cell population.

The combination of up-regulated genes involved in NK cell function and the down-regulation of genes typical of T cells or other immune cells supports the annotation of this cell cluster as Natural Killer cells (NK cells).

### Cluster 5 **Annotation:** Macrophage/Monocyte

Description: This cell cluster ( Macrophage/Monocyte ) has up-regulated genes: LST1, FCGR3A, FCER1G, AIF1, FTH1, FTL, COTL1, IFITM3, SAT1, IFITM2, CTSS, CST3, TIMP1, SERPINA1, MS4A7, TYROBP, S100A11, PSAP, CEBPB, S100A4 and down-regulated genes: LTB, IL32, PTPRCAP, RPS27A, CD3D, RPSA, LDHB, RPL3, JUN, RPS3, RPLP0, RPL13, CXCR4, RPL9, RPS3A, RPS29, RPS18, RPL31, RPS27, RPS5 .

Reason: Based on the up-regulated genes and down-regulated genes in this cell cluster, I can provide some insights that support the annotation as Macrophage/Monocyte.

Up-regulated genes:

  1. LST1 (Lysosomal Thiolase) - a lysosomal enzyme involved in protein degradation, common in macrophages.
  2. FCGR3A (Fcgamma Receptor III Alpha) - a receptor for IgG antibodies, highly expressed on monocytes/macrophages.
  3. AIF1 (Allogenic Immune Function 1) - a gene involved in immune response and phagocytosis, characteristic of macrophages.
  4. FTH1 (Ferritin Heavy Chain) and FTL (Ferritin Light Chain) - both involved in iron metabolism, which is important for macrophage function.
  5. CTSS (Cathepsin S) - a lysosomal protease involved in protein degradation, also found in macrophages.
  6. CST3 (Cystatin C) - an inhibitor of cysteine proteases, often expressed by macrophages.
  7. TIMP1 (Tissue Inhibitor of Metalloproteinase 1) - an inhibitor of matrix metalloproteinases, which are involved in tissue remodeling and repair, a process mediated by macrophages.

Down-regulated genes:

  1. LTB (Leukotriene B4) - a pro-inflammatory mediator that is often down-regulated in macrophages.
  2. IL32 (Interleukin 32) - an anti-inflammatory cytokine that is typically down-regulated in macrophages.
  3. PTPRCAP (Protein Tyrosine Phosphatase Receptor Type C Alpha) - a receptor involved in immune cell signaling, which may be less active in macrophages.

These gene expression patterns are consistent with the activation of macrophage/monocyte cells, which are known to play important roles in inflammation, tissue repair, and immune responses. The up-regulation of genes involved in lysosomal function, protein degradation, and iron metabolism supports the annotation as Macrophage/Monocyte.

### Cluster 6 **Annotation:** CD8+ cytotoxic T cells

Description: This cell cluster ( CD8+ cytotoxic T cells ) has up-regulated genes: CCL5, NKG7, GZMH, CST7, GZMA, CTSW, FGFBP2, CD3D, IL32, CD8A, HLA-C, PTPRCAP, CD8B, APOBEC3G, CCL4, HLA-A, GZMB, GZMM, B2M, LITAF and down-regulated genes: LYZ, HLA-DRA, FTL, FTH1, LTB, CTSS, COTL1, SAT1, FOS, PSAP, DUSP1, JUNB, RPLP1, VIM, SERP1, RPS9, RPS11, RPL32, RPL8, RPL18A .

Reason: Based on the gene expression profile provided, I can infer that this cell cluster is annotated as CD8+ cytotoxic T cells for several reasons:

  1. CD8A and CD8B: The up-regulation of these genes, which encode the alpha and beta chains of the CD8 molecule, respectively, suggests that the cells in this cluster express CD8.
  2. GZMA, GZMB, GZMH: The up-regulation of granzymes (GZMA, GZMB, and GZMH) is a hallmark of cytotoxic T cells, which use these enzymes to induce apoptosis in target cells.
  3. NKG7: NKG7 is a gene involved in the recognition of stressed or infected cells by cytotoxic T cells.
  4. CCL5 and CCL4: The up-regulation of chemokine genes (CCL5 and CCL4) suggests that these cells may be involved in immune responses, which is consistent with the function of cytotoxic T cells.
  5. Down-regulation of genes involved in cell adhesion and migration: The down-regulation of genes involved in cell adhesion (LYZ, VIM) and migration (RPLP1, RPS9, RPS11, RPL32, RPL8, RPL18A) suggests that these cells may be less motile or more stationary, which is consistent with the function of cytotoxic T cells, which often target specific cells and remain in place.

Overall, the combination of CD8 expression, granzyme up-regulation, chemokine production, and down-regulation of genes involved in cell adhesion and migration suggests that this cell cluster is likely composed of CD8+ cytotoxic T cells.

### Cluster 7 **Annotation:** Dendritic Cell (mature)

Description: This cell cluster ( Dendritic Cell (mature) ) has up-regulated genes: HLA-DPB1, FCER1A, HLA-DRA, HLA-DQA1, CST3, HLA-DPA1, CD74, HLA-DRB1, HLA-DQB1, HLA-DRB5, LYZ, HLA-DQA2, CLEC10A, LGALS1, VIM, ALDH2, HLA-DMA, GSTP1, CPVL, AP1S2 and down-regulated genes: LTB, IL32, PTPRCAP, CD3D, BTG1, MALAT1, LDHB, HLA-E, RPS27A, RPS27, GLTSCR2, KLF2, RPL21, HLA-C, RPS20, MT-ND2, CD52, GIMAP7, RPL23A, RPL9 .

Reason: Based on the up-regulated genes and down-regulated genes in this cell cluster, I would annotate it as a mature dendritic cell (mDC) for several reasons:

  1. HLA class II genes: The up-regulation of HLA-DRB1, HLA-DQB1, HLA-DRB5, HLA-DQA1, and HLA-DPA1 suggests that the cell is actively presenting antigens to T-cells, which is a hallmark function of mature dendritic cells.
  2. C-type lectin receptors: The up-regulation of CLEC10A and FCER1A indicates that the cell is involved in the recognition and uptake of pathogens or antigens, which is another key function of mature dendritic cells.
  3. Antigen processing and presentation genes: The up-regulation of CST3, CD74, and AP1S2 suggests that the cell is actively engaged in antigen processing and presentation to T-cells.
  4. Down-regulation of inflammatory genes: The down-regulation of LTB (a chemokine involved in inflammation) and IL32 (an interleukin involved in immune responses) may indicate that the mature dendritic cell has completed its activation process and is now focused on presenting antigens to T-cells rather than promoting an inflammatory response.

Overall, the gene expression profile suggests that this cell cluster is a mature dendritic cell that has undergone activation and is now engaged in antigen presentation and processing.

### Cluster 8 **Annotation:** Neutrophils

Description: This cell cluster ( Neutrophils ) has up-regulated genes: PPBP, PF4, GNG11, SDPR, GPX1, HIST1H2AC, CLU, TUBB1, CD9, VDAC3, TSC22D1, TALDO1, NCOA4, GP9, ACRBP, PTCRA, TAGLN2, RGS10, SPARC, CA2 and down-regulated genes: MALAT1, RPL10, RPL11, RPS6, RPL3, RPL18A, RPL32, RPL9, RPS27A, RPL13A, RPL13, RPL29, RPL21, RPS2, RPL19, RPS15A, RPS27, RPS3, RPS14, EEF1A1 .

Reason: Based on the gene expression profile provided, I can infer that this cell cluster is annotated as Neutrophils for several reasons:

  1. Up-regulation of chemokine receptors and signaling molecules: The presence of up-regulated genes like PF4 (platelet factor 4), GP9 (glycoprotein IX), and CD9 suggests an activation of neutrophil-specific chemotactic pathways.
  2. Expression of neutrophil-specific proteins: Genes like PPBP (plasminogen activator, plasma), CLU (clusterin), and TAGLN2 (tropomyosin-like 2) are known to be expressed in neutrophils.
  3. Down-regulation of ribosomal genes: The down-regulation of multiple ribosomal protein genes (RPLs and RPSs) is a characteristic feature of activated neutrophils, which often exhibit reduced protein synthesis during the early stages of inflammation.
  4. Lack of expression of lymphoid or myeloid markers: The absence of up-regulated genes typically associated with lymphocytes (e.g., CD3, CD19) or other myeloid cells (e.g., macrophage-specific genes like MRC1) suggests that this cell cluster is not a lymphocyte or another type of myeloid cell.

Considering these factors, the annotation "Neutrophils" seems reasonable, as the gene expression profile is consistent with an activated neutrophil population.

Automatically created by ceLLama