Details for: LYSMD2

Gene ID: 256586

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: LYSMD2

Ensembl ID: ENSG00000140280

Description: LysM domain containing 2

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • central memory CD4-positive, alpha-beta T cell CL0000904
    CSI 10.74
    rCSI 6.34%
    PRS 88.53
  • lung neuroendocrine cell CL1000223
    CSI 8.87
    rCSI 13.12%
    PRS 77.3
  • mature B cell CL0000785
    CSI 8.38
    rCSI 7.28%
    PRS 82.88
  • vascular associated smooth muscle cell CL0000359
    CSI 7.91
    rCSI 25.65%
    PRS 71.39
  • pancreatic D cell CL0000173
    CSI 6.76
    rCSI 6.65%
    PRS 75.24
  • pro-B cell CL0000826
    CSI 6.67
    rCSI 5.52%
    PRS 74.93
  • type B pancreatic cell CL0000169
    CSI 6.03
    rCSI 13.35%
    PRS 71.43
  • type L enteroendocrine cell CL0002279
    CSI 5.99
    rCSI 11.25%
    PRS 82.99
  • CD8-positive, alpha-beta memory T cell, CD45RO-positive CL0001203
    CSI 5.95
    rCSI 7.2%
    PRS 55.32
  • granulocyte monocyte progenitor cell CL0000557
    CSI 5.57
    rCSI 4.82%
    PRS 77.31
  • common dendritic progenitor CL0001029
    CSI 5.5
    rCSI 6.91%
    PRS 82.31
  • unswitched memory B cell CL0000970
    CSI 5.29
    rCSI 4.45%
    PRS 87.13
  • activated CD8-positive, alpha-beta T cell, human CL0001049
    CSI 5.23
    rCSI 8.94%
    PRS 87.38
  • plasmacytoid dendritic cell, human CL0001058
    CSI 5.03
    rCSI 3.51%
    PRS 75.7
  • effector memory CD4-positive, alpha-beta T cell CL0000905
    CSI 4.69
    rCSI 6.39%
    PRS 92.01
  • hematopoietic stem cell CL0000037
    CSI 4.59
    rCSI 3.05%
    PRS 75.35
  • Langerhans cell CL0000453
    CSI 4.51
    rCSI 6.89%
    PRS 85.86
  • CD4-positive, alpha-beta thymocyte CL0000810
    CSI 4.42
    rCSI 3.54%
    PRS 88.85
  • perivascular cell CL4033054
    CSI 4.38
    rCSI 5.99%
    PRS 77.97
  • astrocyte of the cerebral cortex CL0002605
    CSI 4.34
    rCSI 9.74%
    PRS 54.38
  • effector CD8-positive, alpha-beta T cell CL0001050
    CSI 4.33
    rCSI 3.29%
    PRS 85.27
  • pancreatic PP cell CL0002275
    CSI 4.27
    rCSI 17%
    PRS 82.23
  • CD4-positive, alpha-beta cytotoxic T cell CL0000934
    CSI 4.17
    rCSI 5.73%
    PRS 89.56
  • immature B cell CL0000816
    CSI 4.14
    rCSI 3.08%
    PRS 84.68
  • alternatively activated macrophage CL0000890
    CSI 4.01
    rCSI 5.04%
    PRS 83.27
  • plasmablast CL0000980
    CSI 3.96
    rCSI 3.12%
    PRS 78.97
  • retina horizontal cell CL0000745
    CSI 3.87
    rCSI 5.91%
    PRS 69.13
  • enteroendocrine cell of small intestine CL0009006
    CSI 3.73
    rCSI 8.22%
    PRS 82.75
  • T-helper 17 cell CL0000899
    CSI 3.65
    rCSI 2.9%
    PRS 90.95
  • central memory CD8-positive, alpha-beta T cell CL0000907
    CSI 3.61
    rCSI 2.43%
    PRS 85.75
  • intestinal tuft cell CL0019032
    CSI 3.6
    rCSI 5.5%
    PRS 76.84
  • rod bipolar cell CL0000751
    CSI 3.46
    rCSI 6.21%
    PRS 65.69
  • double negative thymocyte CL0002489
    CSI 3.31
    rCSI 2.3%
    PRS 83.94
  • double-positive, alpha-beta thymocyte CL0000809
    CSI 3.26
    rCSI 3.33%
    PRS 83.55
  • effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL0001062
    CSI 3.12
    rCSI 15.64%
    PRS 84.86
  • activated CD4-positive, alpha-beta T cell CL0000896
    CSI 3.09
    rCSI 2.86%
    PRS 88.78
  • class switched memory B cell CL0000972
    CSI 2.92
    rCSI 2.18%
    PRS 86.57
  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.78
    rCSI 3.32%
    PRS 53.65
  • CD14-positive, CD16-positive monocyte CL0002397
    CSI 2.59
    rCSI 3.4%
    PRS 84.63
  • epithelial cell of lower respiratory tract CL0002632
    CSI 2.49
    rCSI 1.93%
    PRS 75.98
  • ciliated columnar cell of tracheobronchial tree CL0002145
    CSI 2.48
    rCSI 5.66%
    PRS 67.41
  • ciliated cell CL0000064
    CSI 2.48
    rCSI 4.02%
    PRS 68.19
  • pulmonary capillary endothelial cell CL4028001
    CSI 2.47
    rCSI 4.72%
    PRS 84.18
  • mature alpha-beta T cell CL0000791
    CSI 2.43
    rCSI 8.81%
    PRS 89.3
  • pancreatic A cell CL0000171
    CSI 2.43
    rCSI 2.55%
    PRS 75.97
  • effector CD4-positive, alpha-beta T cell CL0001044
    CSI 2.39
    rCSI 6.86%
    PRS 90.29
  • ON-bipolar cell CL0000749
    CSI 2.36
    rCSI 3.51%
    PRS 73.1
  • hematopoietic precursor cell CL0008001
    CSI 2.34
    rCSI 2.4%
    PRS 86.27
  • T follicular helper cell CL0002038
    CSI 2.3
    rCSI 1.72%
    PRS 86.3
  • enteroendocrine cell CL0000164
    CSI 2.27
    rCSI 3.1%
    PRS 73.3
  • CD4-positive helper T cell CL0000492
    CSI 2.27
    rCSI 1.71%
    PRS 85.56
  • myeloid leukocyte CL0000766
    CSI 2.26
    rCSI 2.08%
    PRS 74.21
  • activated CD8-positive, alpha-beta T cell CL0000906
    CSI 2.19
    rCSI 2.15%
    PRS 88.64
  • elicited macrophage CL0000861
    CSI 2.17
    rCSI 1.99%
    PRS 81.49
  • activated type II NK T cell CL0000931
    CSI 2.09
    rCSI 2.35%
    PRS 87.09
  • lung ciliated cell CL1000271
    CSI 2.08
    rCSI 2.41%
    PRS 63.83
  • megakaryocyte-erythroid progenitor cell CL0000050
    CSI 2.04
    rCSI 1.85%
    PRS 69.98
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 2.04
    rCSI 6.38%
    PRS 58.07
  • CD14-low, CD16-positive monocyte CL0002396
    CSI 2
    rCSI 1.54%
    PRS 74.64
  • common myeloid progenitor CL0000049
    CSI 1.97
    rCSI 1.6%
    PRS 74.68
  • intermediate monocyte CL0002393
    CSI 1.93
    rCSI 2.91%
    PRS 77.85
  • pulmonary artery endothelial cell CL1001568
    CSI 1.88
    rCSI 2.56%
    PRS 82.36
  • common lymphoid progenitor CL0000051
    CSI 1.87
    rCSI 2.5%
    PRS 89.32
  • cerebral cortex neuron CL0010012
    CSI 1.87
    rCSI 7.61%
    PRS 65.13
  • lung macrophage CL1001603
    CSI 1.77
    rCSI 3.95%
    PRS 80.54
  • CD8-positive, alpha-beta thymocyte CL0000811
    CSI 1.69
    rCSI 2.63%
    PRS 91.62
  • CD1c-positive myeloid dendritic cell CL0002399
    CSI 1.67
    rCSI 2.02%
    PRS 81.26
  • germinal center B cell CL0000844
    CSI 1.66
    rCSI 4.94%
    PRS 85.1
  • basal cell of prostate epithelium CL0002341
    CSI 1.63
    rCSI 4.73%
    PRS 81.49
  • ciliated epithelial cell CL0000067
    CSI 1.63
    rCSI 1.43%
    PRS 60.88
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 1.57
    rCSI 1.95%
    PRS 51.8
  • mononuclear phagocyte CL0000113
    CSI 1.56
    rCSI 3.44%
    PRS 76.77
  • group 3 innate lymphoid cell CL0001071
    CSI 1.54
    rCSI 1.16%
    PRS 78.48
  • basal cell CL0000646
    CSI 1.45
    rCSI 1.94%
    PRS 72.05
  • club cell CL0000158
    CSI 1.42
    rCSI 2.09%
    PRS 67.48
  • peripheral nervous system neuron CL2000032
    CSI 1.38
    rCSI 1.88%
    PRS 63.79
  • duct epithelial cell CL0000068
    CSI 1.32
    rCSI 1.94%
    PRS 77.55
  • microcirculation associated smooth muscle cell CL0008035
    CSI 1.24
    rCSI 3.59%
    PRS 72.99
  • CD8-positive, CD28-negative, alpha-beta regulatory T cell CL0000920
    CSI 1.19
    rCSI 2.38%
    PRS 86.52
  • alveolar macrophage CL0000583
    CSI 1.17
    rCSI 1.93%
    PRS 77.6
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 1.08
    rCSI 6.34%
    PRS 54.78
  • hematopoietic multipotent progenitor cell CL0000837
    CSI 1.05
    rCSI 2.52%
    PRS 87.3
  • dendritic cell, human CL0001056
    CSI 0.93
    rCSI 1.43%
    PRS 81.86
  • intraepithelial lymphocyte CL0002496
    CSI 0.91
    rCSI 2.49%
    PRS 93.1
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 0.91
    rCSI 1.53%
    PRS 53.8
  • late pro-B cell CL0002048
    CSI 0.71
    rCSI 1.77%
    PRS 89.87
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 0.67
    rCSI 2.41%
    PRS 51.87
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 0.63
    rCSI 1.54%
    PRS 52.05
  • enteroendocrine cell of colon CL0009042
    CSI 0.57
    rCSI 2.65%
    PRS 84.63
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 0.54
    rCSI 2.03%
    PRS 54.27
  • myeloid lineage restricted progenitor cell CL0000839
    CSI 0.51
    rCSI 2.65%
    PRS 90
  • P/D1 enteroendocrine cell CL0002268
    CSI 0.5
    rCSI 2.73%
    PRS 83.22
  • L6b glutamatergic cortical neuron CL4023038
    CSI 0.5
    rCSI 1.56%
    PRS 55.59
  • type EC enteroendocrine cell CL0000577
    CSI 0.49
    rCSI 1.73%
    PRS 78.57
  • CD14-positive, CD16-negative classical monocyte CL0002057
    CSI 0.39
    rCSI 2.36%
    PRS 86.88
  • cytotoxic T cell CL0000910
    CSI 0.19
    rCSI 1.11%
    PRS 79.04

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

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Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [LYSMD2](/details-gene/256586), or LysM domain containing 2, is a protein-coding gene located on chromosome 15q21.2. The protein contains a LysM domain, which suggests a potential role in binding carbohydrates such as peptidoglycans, a common component of bacterial cell walls. Functionally, it is annotated with a role in protein binding ([GO:0005515](https://www.ebi.ac.uk/QuickGO/term/GO:0005515)). **Overall**, expression data reveals a broad but distinct significance profile for [LYSMD2](/details-gene/256586). It is a highly significant gene in various adaptive immune cells, including [central memory CD4-positive, alpha-beta T cell](/details-cell/CL0000904) and [mature B cell](/details-cell/CL0000785). Concurrently, it shows prominent significance in several non-hematopoietic cell types such as [lung neuroendocrine cell](/details-cell/CL1000223) and [vascular associated smooth muscle cell](/details-cell/CL0000359), suggesting a pleiotropic function that spans both immunological surveillance and tissue-specific cellular processes. ## Cellular Roles and Expression Landscape The expression landscape of [LYSMD2](/details-gene/256586) is characterized by its significant presence in diverse and functionally distinct cell populations. **Overall**, the gene is most significant in cell types central to the adaptive immune system. It ranks highest in [central memory CD4-positive, alpha-beta T cell](/details-cell/CL0000904) (CSI: 10.74), followed by other key lymphocyte populations like [mature B cell](/details-cell/CL0000785) (CSI: 8.38), [CD8-positive, alpha-beta memory T cell, CD45RO-positive](/details-cell/CL0001203) (CSI: 5.95), and progenitor cells such as [pro-B cell](/details-cell/CL0000826) (CSI: 6.67). Its relevance extends to innate immunity, with significant scores in [granulocyte monocyte progenitor cell](/details-cell/CL0000557) and [plasmacytoid dendritic cell, human](/details-cell/CL0001058), suggesting a broad role across hematopoietic lineages. Intriguingly, [LYSMD2](/details-gene/256586) also demonstrates high significance in several non-immune cell types. It is the second-most significant marker in [lung neuroendocrine cell](/details-cell/CL1000223) (CSI: 8.87) and is also prominent in [vascular associated smooth muscle cell](/details-cell/CL0000359) (CSI: 7.91). Furthermore, it shows notable significance in endocrine cells of the pancreas, including [pancreatic D cell](/details-cell/CL0000173) and [type B pancreatic cell](/details-cell/CL0000169). This dual-expression profile in both immune and specialized structural/endocrine cells suggests that [LYSMD2](/details-gene/256586) may have context-dependent functions, possibly related to environmental sensing, cell-cell communication, or tissue homeostasis in these varied microenvironments. ## Pathways and Molecular Function The functional annotation of [LYSMD2](/details-gene/256586) is currently sparse, with its primary molecular function described as protein binding ([GO:0005515](https://www.ebi.ac.uk/QuickGO/term/GO:0005515)). The most significant functional clue comes from its name, indicating the presence of a Lysin Motif (LysM) domain. LysM domains are evolutionarily conserved carbohydrate-binding modules known to recognize peptidoglycans from bacterial cell walls and chitin from fungi. This structural feature strongly implies a role for [LYSMD2](/details-gene/256586) in host-microbe interactions. Consistent with this hypothesis, its high expression in a wide range of immune cells, from progenitors to mature T and B cells, suggests it may act as a pattern recognition receptor or a co-receptor involved in sensing microbial components and initiating or modulating immune responses. Several large-scale phosphoproteomic studies have identified LYSMD2 in analyses of T cell signaling and cancer cells ([Link](https://doi.org/10.1126/scisignal.2000007), [Link](https://doi.org/10.1021/pr300630k)), which is consistent with its protein-binding function and may indicate that its activity is regulated by phosphorylation during cellular signaling events. ## Research Directions The diverse expression pattern of [LYSMD2](/details-gene/256586) in both immune and non-immune cells, combined with its putative function as a carbohydrate-binding protein, opens up several avenues for future investigation. **Proposed Hypotheses:** 1. Given its LysM domain and high significance in lymphocytes like [central memory CD4-positive, alpha-beta T cell](/details-cell/CL0000904), [LYSMD2](/details-gene/256586) may function as a co-receptor on the cell surface that modulates T cell or B cell activation in response to bacterial or fungal-derived ligands, thereby fine-tuning the adaptive immune response during infection. 2. The high significance of [LYSMD2](/details-gene/256586) in specialized cells like [lung neuroendocrine cell](/details-cell/CL1000223) and [vascular associated smooth muscle cell](/details-cell/CL0000359) suggests a non-immunological role. In these contexts, it might be involved in sensing the local microbiome or binding endogenous glycans to mediate cell adhesion, tissue repair, or specialized secretory functions. **Experimental Approach:** To test the first hypothesis regarding its role in T cell modulation, a CRISPR-Cas9 knockout of [LYSMD2](/details-gene/256586) could be generated in a human T cell line (e.g., Jurkat) or in primary human CD4+ T cells. The wild-type and knockout cells could then be co-stimulated through the T cell receptor (TCR) in the presence or absence of LysM-domain ligands like peptidoglycan. The impact on T cell activation could be assessed by measuring key downstream readouts such as IL-2 production (ELISA), proliferation (CFSE dilution assay), and the phosphorylation status of key signaling intermediates (e.g., LCK, ZAP70) via Western blot or phosphoproteomics. This would clarify whether [LYSMD2](/details-gene/256586) is necessary for integrating microbial signals with TCR-mediated activation. **Therapeutic Potential:** The therapeutic potential of [LYSMD2](/details-gene/256586) is currently speculative and depends heavily on its precise function and subcellular localization. If it is a cell-surface receptor that amplifies inflammatory responses in T cells during autoimmune disease or sepsis, it could represent a viable target for inhibitory monoclonal antibodies. Conversely, if its function is to enhance pathogen clearance, agonistic molecules could be developed to boost immunity. However, its broad expression across multiple essential cell types, including pancreatic and vascular cells, presents a significant challenge, as systemic targeting could lead to undesirable off-target effects. A therapeutic strategy would likely require cell-type-specific delivery or targeting of a disease-specific conformation or interaction.

Genular Protein ID: 4238504432

Symbol: LYSM2_HUMAN

Name: LysM and putative peptidoglycan-binding domain-containing protein 2

UniProtKB Accession Codes:

Q8IV50 Q5CZ88 Q8WTV3

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CDD 1 CTD 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 4 Ensembl 3 ExpressionAtlas 1 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MANE-Select 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PROSITE 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 2 Pumba 1 RNAct 1 RefSeq 3 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 15592455

Title: Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.

PubMed ID: 15592455

DOI: 10.1038/nbt1046

PubMed ID: 19690332

Title: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.

PubMed ID: 19690332

DOI: 10.1126/scisignal.2000007

PubMed ID: 20068231

Title: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

PubMed ID: 20068231

DOI: 10.1126/scisignal.2000475

PubMed ID: 22814378

Title: N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

PubMed ID: 22814378

DOI: 10.1073/pnas.1210303109

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

PubMed ID: 24275569

Title: An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.

PubMed ID: 24275569

DOI: 10.1016/j.jprot.2013.11.014

Sequence Information:

  • Length: 215
  • Mass: 23463
  • Checksum: A87E666478E903AC
  • Sequence:
    • MADSSPALSL REGGPRAPRP SAPSPPPRSR SGSESEEAEL SLSLARTKTR SYGSTASVRA 
PLGAGVIERH VEHRVRAGDT LQGIALKYGV TMEQIKRANK LFTNDCIFLK KTLNIPVISE 
KPLLFNGLNS IDSPENETAD NSFSQEEEPV VAGEDLPPPS PQESDVQPVQ PEEVSARDFL 
QRLDLQIKLS TQAAKKLKEE SRDEESPYAT SLYHS