Table 1 Summary of colon MP populations.

From: Commensal microbiota drive the functional diversification of colon macrophages

Cluster

Top5 Cluster Gene Markers

Surface markers evaluated

mRNA for known MP genesa

Differentiation Status predicted from monocle2

Specific active regulonsb

Referencesc

1

Thbs1, Ccr2, Tgm2, Emilin2, Ifi27l2a

CD11cCD206CCR2+

Ccr2

Precursor cells (unaffected in GF mice)

Mxi1

3,4,5,6,7,8,9,23,26,29

2

Cx3cr1, Dst, H2-M2, Dnmt3a, Vcam1

n.d.d

Itgax

Transional and mature cells (increased in GF mice)

Nfic, Tcf4, Mef2a, Ddit3, Nle2l2, Mitf, Fosb

26

3

Apoe, Ms4a7, Cd63, Vcam1, Hpgds

n.d.

Itgax

Transitional cells (reduced in GF mice)

Spic, Nfic, Tcf4, Mef2a, Ddit3,Mitf, Fosb

3,4,5,6,7,8,9,10,11,12,23,26,29

4

Pgf, Mmp13, Dnase1l3, Acp5, H2-M2

CD11c+CD206intCCR2CD121b+

Itgax, Cd74, IL1r2, Cd9, Cd81

Mature cells (reduced in GF mice)

Spic, Nifc,Tcf4, Pdrm1,Crem1,Fosb, Mxi1

3,4,5,6,7,8,9,10,11,12,18,23,26,29

6

Ccl7, Ccl2, F13a1, Pf4, Cd163

CD11cCD206hiCCR2CD169+

Mrc1(hi), Cd36, CD163,F13a1

Mature cells (reduced in GF mice)

Jund, Tcd4, Nfic, Mafk, Atf4, Erg2, Mef2a

5,10,11,14,15,18,19,25,29,38,39

7

Hspa1a, Hes1, Hspa1b, Ccl4, Jun

n.d.

Itgax

Mature cells (unaffected in GF mice)

Erg1, Erg2, Jun, Irf1, Atf3, Fosb, Mef2a, Nfic

3,4,5,6,7,8,9,10,11,12,29

11

Ifit2, Ifit1, Rsad2, Isg15, Cxcl9

n.d.

 

n.d.

Stat1, Stat2, Erg2, Irf1, Irf7

 
  1. aall cells express Adgre1,Fcgr1,Cd63,Zeb2,Cd68,Cx3r1; with cluster 1 expressing less Adgre1, Cd68, Cx3cr1 (see Fig. 1c, and Supplementary Tables)
  2. bpredicted compared to all MP and DC clusters (see Fig. 5f)
  3. cprimary manuscripts describing related cell types
  4. dnot determined