TISIDB

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Basic function annotation. > Subcellular Location, Domain and Function > Gene Ontology > KEGG and Reactome Pathway

> Subcellular Location, Domain and Function [ TOP ]
Subcellular Location	Cytoplasm. Nucleus. Cytoplasm, P-body. Cell junction, adherens junction. Cell junction, focal adhesion. Note=Shuttles between cytoplasm and nucleus but is localized predominantly to the cytoplasm. Found in the nucleus but not nucleoli. Colocalizes with VCL in the focal adhesions. Down-regulation and/or elimination of its expression from the nucleus of neoplastic cells correlates strongly with poor patient prognosis and aggressive forms of breast carcinoma. Conversely, strong nuclear localization correlates with low-tumor grade and better patient prognosis.
Domain	PF00412 LIM domain
Function	Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation.

> Gene Ontology [ TOP ]
Biological Process	GO:0001503 ossification GO:0001649 osteoblast differentiation GO:0001666 response to hypoxia GO:0002076 osteoblast development GO:0006417 regulation of translation GO:0008360 regulation of cell shape GO:0010608 posttranscriptional regulation of gene expression GO:0016055 Wnt signaling pathway GO:0016441 posttranscriptional gene silencing GO:0016458 gene silencing GO:0017148 negative regulation of translation GO:0022604 regulation of cell morphogenesis GO:0022613 ribonucleoprotein complex biogenesis GO:0022618 ribonucleoprotein complex assembly GO:0030111 regulation of Wnt signaling pathway GO:0030178 negative regulation of Wnt signaling pathway GO:0030278 regulation of ossification GO:0030279 negative regulation of ossification GO:0031047 gene silencing by RNA GO:0033962 cytoplasmic mRNA processing body assembly GO:0034248 regulation of cellular amide metabolic process GO:0034249 negative regulation of cellular amide metabolic process GO:0035194 posttranscriptional gene silencing by RNA GO:0035195 gene silencing by miRNA GO:0035329 hippo signaling GO:0035330 regulation of hippo signaling GO:0035331 negative regulation of hippo signaling GO:0036293 response to decreased oxygen levels GO:0040029 regulation of gene expression, epigenetic GO:0045667 regulation of osteoblast differentiation GO:0045668 negative regulation of osteoblast differentiation GO:0060070 canonical Wnt signaling pathway GO:0060147 regulation of posttranscriptional gene silencing GO:0060148 positive regulation of posttranscriptional gene silencing GO:0060828 regulation of canonical Wnt signaling pathway GO:0060964 regulation of gene silencing by miRNA GO:0060966 regulation of gene silencing by RNA GO:0060968 regulation of gene silencing GO:0070482 response to oxygen levels GO:0071826 ribonucleoprotein complex subunit organization GO:0090090 negative regulation of canonical Wnt signaling pathway GO:0198738 cell-cell signaling by wnt GO:1902532 negative regulation of intracellular signal transduction GO:2000637 positive regulation of gene silencing by miRNA
Molecular Function	GO:0003714 transcription corepressor activity
Cellular Component	GO:0000932 cytoplasmic mRNA processing body GO:0005667 transcription factor complex GO:0005924 cell-substrate adherens junction GO:0005925 focal adhesion GO:0016442 RISC complex GO:0030055 cell-substrate junction GO:0031332 RNAi effector complex GO:0035770 ribonucleoprotein granule GO:0036464 cytoplasmic ribonucleoprotein granule

> KEGG and Reactome Pathway [ TOP ]
KEGG	hsa04390 Hippo signaling pathway
Reactome	R-HSA-2262749: Cellular response to hypoxia R-HSA-2262752: Cellular responses to stress R-HSA-1234176: Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha R-HSA-1234174: Regulation of Hypoxia-inducible Factor (HIF) by oxygen

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between LIMD1 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.

> Text Mining [ TOP ]
There is no record.

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.

> High-throughput Screening

[ TOP ]

Statistical results of LIMD1 in screening data sets for detecting immune reponses.

PMID	Screening System	Cancer Type	Cell Line	Data Set	Statistical Results	Relation to immunity
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	Second most enriched score: 0.64	Sensitive to T cell-mediated killing
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets. > Expression difference between responders and non-responders > Mutation difference between responders and non-responders

> Expression difference between responders and non-responders

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Points in the above scatter plot represent the expression difference of LIMD1 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	Log2 (Fold Change)	P value
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	-0.686	0.082
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.219	0.865
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	-1.355	0.2
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.301	0.34
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0.426	0.849
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.14	0.959
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.049	0.889
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	0.336	0.826
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	-0.44	0.789
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.087	0.922
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	0.683	0.566
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	0.04	0.642

> Mutation difference between responders and non-responders

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Points in the above scatter plot represent the mutation difference of LIMD1 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/Res	% Mut/NRes	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	0	1.4	-1.4	1
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	0	1.7	-1.7	1
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	4.8	0	4.8	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	7.7	0	7.7	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0	0	0	1
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0	0	0	1
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	0	0	0	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	0	0	0	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	7.7	-7.7	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	8.3	-8.3	1

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of LIMD1. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.

> Lymphocyte [ TOP ]

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of LIMD1. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by LIMD1. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of LIMD1. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene. > Chemokine > Receptor

> Chemokine [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of LIMD1 expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between LIMD1 and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	LIMD1
Name	LIM domains containing 1
Aliases	LIM domain-containing protein 1
Chromosomal Location	3p21.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting LIMD1 collected from DrugBank database.

> Drugs from DrugBank database [ TOP ]
There is no record.

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