Biallelic loss-of-function variants of SLC12A9 cause lysosome dysfunction and a syndromic neurodevelopmental disorder

PURPOSE

Pathogenic variants of FIG4 generate enlarged lysosomes and neurological and developmental disorders. To identify additional genes regulating lysosomal volume, we carried out a genome-wide activation screen to detect suppression of enlarged lysosomes in FIG4-/- cells.

METHODS

The CRISPR-a gene activation screen utilized sgRNAs from the promoters of protein-coding genes. Fluorescence-activated cell sorting separated cells with correction of the enlarged lysosomes from uncorrected cells. Patient variants of SLC12A9 were identified by exome or genome sequencing and studied by segregation analysis and clinical characterization.

RESULTS

Overexpression of SLC12A9, a solute co-transporter, corrected lysosomal swelling in FIG4-/- cells. SLC12A9 (NP_064631.2) colocalized with LAMP2 at the lysosome membrane. Biallelic variants of SLC12A9 were identified in 3 unrelated probands with neurodevelopmental disorders. Common features included intellectual disability, skeletal and brain structural abnormalities, congenital heart defects, and hypopigmented hair. Patient 1 was homozygous for nonsense variant p.(Arg615∗), patient 2 was compound heterozygous for p.(Ser109Lysfs∗20) and a large deletion, and proband 3 was compound heterozygous for p.(Glu290Glyfs∗36) and p.(Asn552Lys). Fibroblasts from proband 1 contained enlarged lysosomes that were corrected by wild-type SLC12A9 cDNA. Patient variant p.(Asn552Lys) failed to correct the lysosomal defect.

CONCLUSION

Impaired function of SLC12A9 results in enlarged lysosomes and a recessive disorder with a recognizable neurodevelopmental phenotype.

Clinical value of SLC12A9 for diagnosis and prognosis in colorectal cancer

OBJECTIVE

The goal of the study is to assess the clinical value and the potential mechanism of SLC12A9 combing transcriptome and single cell sequencing data.

METHODS

In this study, the expression level and the receiver operating characteristic curve analysis of SLC12A9 in CRC and normal tissue were analyzed in multiple data cohort. The standardized mean difference (SMD) calculation and the summary receiver operating characteristic (SROC) analysis were performed further to detect its diagnostic ability and expression level. KM survival analysis was performed to assess the prognosis value of SLC12A9. The expression level of SLC12A9 in different clinical characteristics was analyzed to explore the clinical value. Single cell data was studied to reveal the potential mechanism of SLC12A9. The correlation analysis of immunoinfiltration was performed to detect the potential immune cell related to SLC12A9. The nomogram was drawn to assess the probable mortality rate of CRC patient.

RESULTS

We found that SLC12A9 was significantly up-regulated with the moderate diagnostic value in CRC. Patients with overexpressed SLC12A9 had a worse prognosis. SLC12A9 was related to Age, Pathologic N stage, Pathologic M stage, Lymphatic invasion and Pathologic stage (p < 0.05). The 1, 3 and 5-year survival rates of patient named TCGA-G4-6309 are 0.959, 0.897 and 0.827. PCR also showed that SLC12A9 was overexpressed in CRC comparing with normal tissue.

CONCLUSION

In conclusion, our study comprehensively analyzed the clinical value of SLC12A9 and its potential mechanism, as well as immune cell infiltration, which may accelerate the diagnosis and improve the prognosis of CRC.