SPRY4-IT1

Summary

SPRY4-IT1 (SPRY4 intronic transcript 1, HGNC:42394) is a long non-coding RNA gene on chromosome 5q31.3.

This gene produces a non-coding RNA that is upregulated in several different tumors, including melanoma and breast and prostate cancer cells. This transcript may mediate cell growth, proliferation, and apoptosis. It regulates levels of lipin 2, and therefore may be involved in lipid biosynthesis. The primary transcript is cleaved to release a mature product that localizes to the cytoplasm (PMID:25344859). The full length structure of the primary and cleaved transcripts is unclear, and it is possible that the primary transcript is a splice variant of SPRY4 (sprouty RTK signaling antagonist 4).

Source: NCBI Gene 100642175 — RefSeq curated summary.

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:42394
Approved symbol	SPRY4-IT1
Name	SPRY4 intronic transcript 1
Location	5q31.3
Locus type	RNA, long non-coding
Status	Approved
Aliases	SPRIGHTLY
OMIM	617617
Entrez	100642175
RNAcentral	URS0000812019 — lncRNA, 703 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Top tissues by expression

0 total, by Bgee expression score (0-100, higher = more expressed):

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 40)

• Higher expression of SPRY4-IT1 may have an important role in the molecular etiology of human melanoma. (PMID:21558391)
• The up-regulation of SPRY4-IT1 plays an important role in clear cell renal cell carcinoma progression. (PMID:25337221)
• Our data suggest that SPRY4-IT1 plays a critical role in GC tumorigenesis and may represent a novel prognostic marker and potential therapeutic target in patients with Gastric cancer. (PMID:25835973)
• Low expression of SPRY4-IT1 is involved in progression and metastasis of gastric cancer. (PMID:26238992)
• SPRY4-IT1 was up-regulated in human glioma tissues and cell lines. Knockdown of SPRY4-IT1 could inhibit glioma cell growth and migration. Moreover, knockdown of SPRY4-IT1 could inhibit epithelial-mesenchymal transition (EMT) phenotype in glioma cells. (PMID:26464658)
• findings highlight a novel role for SPRY4-IT1 in controlling the intestinal epithelial barrier and define a mechanism by which SPRY4-IT1 modulates tight junction (TJ)proteins expression by altering the stability and translation of TJ mRNAs. (PMID:26680741)
• SPRIGHTLY regulates cell proliferation and anchorage-independent colony formation in primary human melanocytes (PMID:26829028)
• our study indicates that SPRY4-IT1 promotes proliferation and migration of esophageal squamous cell carcinoma (ESCC) cells and is a potential oncogene of ESCC (PMID:26883252)
• Results suggest that lncRNA SPRY4-IT1 might be considered as a novel oncogene involved in ESCC progression. (PMID:27250657)
• SPRY4-IT1 plays a critical role in HCC tumorigenesis. (PMID:27278245)
• High SPRY4-IT1 expression is associated with colorectal cancer metastasis. (PMID:27391336)
• In vitro function assays demonstrated that SPRY4-IT1 cause promotion of cell viability in ESCC cells. Authors further verified that SPRY4-IT1 could also activate the expression of ZNF703 in ESCC cells, which might contribute to the role of SPRY4-IT1 in ESCC cells. (PMID:27453415)
• results highlight the roles of SPRY4-IT1 in causing trophoblast cell dysfunction by acting through the Wnt/beta-catenin pathway, and consequently in impairing spiral artery remodelling. (PMID:27853262)
• Long non-coding RNA SPRY4-IT1 promotes tumor cell proliferation and invasion by activating EZH2 in hepatocellular carcinoma and epigenetically repressing E-cadherin expression. (PMID:27899259)
• these researches indicated that SPRY4-IT1 is highly expressed in GBC. SPRY4-IT1 promotes the growth and migration of GBC cells, suggesting that SPRY4-IT1 may be an important contributor to GBC development. (PMID:27902971)
• LncRNA SPRY4-IT1 can serve as a new molecular marker for cancer metastasis and prognosis (PMID:28054316)
• SPRY4-IT1 might be associated with tumorigenesis and progression of colorectal cancer. (PMID:28099409)
• SPRY4-IT1 may be considered as a new predictor in the clinical prognosis of ovarian cancer patients. (PMID:28129625)
• the meta-analysis results suggested that increased expression level of SPRY4-IT1 was positively associated with unfavorable prognosis and advanced features of cancers in cancer patients but not in patients with NSCLC. (PMID:28410241)
• Significantly decreases SPRIGHTLY lncRNA levels. (PMID:28508063)
• In this review, we have focused on the characteristics of SPRY4-IT1 and illustrated the biological function and mechanism of SPRY4-IT1 in cancer development. (PMID:28651500)
• overexpression of SPRY4-IT1 increased E-cadherin and decreased N-cadherin and vimentin protein levels, indicating that SPRY4-IT1 may regulate ovarian cancer cell metastasis through the inhibition of epithelial-mesenchymal transition. (PMID:28691641)
• The bioinformatics prediction revealed putative miR-101-3p binding sites within SPRY4-IT1 transcripts. Above all, knockdown of SPRY4-IT1 could represent a rational therapeutic strategy for colorectal carcinoma. (PMID:28720069)
• Increased expression level of SPRY4-IT1 correlated with lymph node metastasis in Digestive System Malignancies. (PMID:28965279)
• meta-analysis of value as prognostic biomarker of survival in cancer (PMID:29145271)
• High SPRY4-IT1 expression is associated with development of hepatic cellular carcinoma. (PMID:29214989)
• The findings indicate that SPRY4 and SPRY4-IT1 may act as oncogenes in testicular germ cell tumors via activation of the PI3K/Akt signaling pathway. (PMID:29410498)
• Long non-coding RNA SPRY4-IT1 promotes cell proliferation and invasion by regulation of Cdc20 in pancreatic cancer cells (PMID:29489909)
• Results demonstrated that SPRY4-IT1 was abnormally upregulated in pancreatic ductal adenocarcinoma (PDAC ) tissues and cell lines. Tumor stage and differentiation grade was closely correlated with SPRY4-IT1 expression. Additionally, decreased SPRY4-IT1 contributed to tumor suppressive effect through attenuating cell growth, clonogenic ability and facilitating apoptosis via Bcl-2/caspase-3 pathway in PDAC. (PMID:29551494)
• SPRY4-IT1 is upregulated in human CCA tissues and cells, and its overexpression may be an unfavorable prognostic factor for patients with CCA. (PMID:29642935)
• We aimed to explore the biological activity of lncRNA SPRY4-IT1 in breast cancer cells and whether N-terminal polypeptide derived from viral macrophage inflammatory protein II (NT21MP) could exert its anti-tumor effect by regulating lncRNA SPRY4-IT1 and its target gene SKA2 (PMID:30104400)
• Findings indicate that the SPYR4-IT1/miR-101-3p/zinc finger E-box binding homeobox 1 protein (ZEB1) axis contributes to cervical cancer (CC) migration and invasion, which may provide novel insights into the function of lncRNA-driven tumorigenesis of CC. (PMID:31092700)
• Clinical significance of SPRY4-IT1 in efficacy and survival prediction in breast cancer patients undergoing neoadjuvant chemotherapy. (PMID:31638266)
• LncRNA SPRY4-IT1 regulates breast cancer cell stemness through competitively binding miR-6882-3p with TCF7L2. (PMID:31736268)
• LncRNA SPRY4IT1 promotes progression of osteosarcoma by regulating ZEB1 and ZEB2 expression through sponging of miR101 activity. (PMID:31746422)
• Long noncoding RNA SPRY4-IT1 promotes proliferation and metastasis of hepatocellular carcinoma via mediating TNF signaling pathway. (PMID:31943198)
• Deregulation of long noncoding RNAs ANCR, TINCR, HOTTIP and SPRY4-IT1 in plasma of systemic sclerosis patients: SPRY4-IT1 as a novel biomarker of scleroderma and its subtypes. (PMID:32442909)
• Expression profiling revealed up-regulation of three lncRNAs in breast cancer samples. (PMID:32976818)
• Prognostic Value of Long Noncoding RNA SPRY4-IT1 on Survival Outcomes in Human Carcinomas: A Systematic Review and Meta-Analysis with TCGA Database. (PMID:33204703)
• Identification and biological analysis of LncSPRY4-IT1-targeted functional proteins in photoaging skin. (PMID:34081809)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (0):

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000900820 (5:142318492 AAAAAAAAG>A), RS1001152851 (5:142318211 G>A), RS1001438706 (5:142317874 G>A,C), RS1001533779 (5:142319201 G>A), RS1001649910 (5:142319558 G>A), RS1001870858 (5:142317387 C>T), RS1001985447 (5:142317697 T>A,C), RS1002755484 (5:142319028 T>C), RS1004130956 (5:142318122 T>C), RS1008236108 (5:142318347 A>G,T), RS1008350721 (5:142318766 C>T), RS1009650743 (5:142318180 A>G), RS1009660245 (5:142318500 GA>G), RS1009794771 (5:142317764 A>G), RS1013425042 (5:142317427 G>A)

Disease associations

OMIM: gene MIM:617617 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	increases expression	1
monomethylarsonous acid	decreases expression	1
Smoke	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.