Mapping genetic interactions in the SLC Transporter Superfamily.
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ABSTRACT:
PROVIDER: PRJNA1124096 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29419600_1.fastq.gz | Fastqsanger.gz | |||
| SRR29419600_2.fastq.gz | Fastqsanger.gz | |||
| SRR29419700.fastq.gz | Fastqsanger.gz | |||
| SRR29419800.fastq.gz | Fastqsanger.gz | |||
| SRR29419601_1.fastq.gz | Fastqsanger.gz |
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Project description:Transporters mediate and control the flux of molecules across compartmental membranes. The human genome encodes 1500 genes with transport functions, of which the solute carriers (SLCs) form the largest superfamily with more than 450 members. Over 250 different SLCs are expressed in a typical human cell, many exhibiting overlapping expression patterns and substrate specificities. The collective role of these often seemingly redundant transporters in defining cellular outcomes, such as cell survival, remains unclear. Here, we performed pooled combinatorial KO screens to identify genetic interactions between 258 expressed SLCs, and between a subset of SLCs and selected metabolic enzymes under different growth conditions using both CRISPR-Cas12a and -Cas9 double knockout systems in the colorectal carcinoma cell line HCT116.
2024-06-19 | GSE269905 | GEO
Project description:The human solute carrier (SLC) superfamily of transporters is comprised of over 400 membrane-bound proteins, and plays essential roles in a multitude of physiological and pharmacological processes. In addition, perturbation of SLC transporter function underlies numerous human diseases, which renders SLC transporters attractive drug targets. Common genetic polymorphisms in SLC genes have been associated with inter-individual differences in drug efficacy and toxicity. However, despite their tremendous clinical relevance, epidemiological data of these variants are mostly derived from heterogeneous cohorts of small sample size and the genetic SLC landscape beyond these common variants has not been comprehensively assessed. In this study, we analyzed Next-Generation Sequencing data from 141,456 individuals from seven major human populations to evaluate genetic variability, its functional consequences, and ethnogeographic patterns across the entire SLC superfamily of transporters. Importantly, of the 204,287 exonic single-nucleotide variants (SNVs) which we identified, 99.8% were present in less than 1% of analyzed alleles. Comprehensive computational analyses using 13 partially orthogonal algorithms that predict the functional impact of genetic variations based on sequence information, evolutionary conservation, structural considerations, and functional genomics data revealed that each individual genome harbors 29.7 variants with putative functional effects, of which rare variants account for 18%. Inter-ethnic variability was found to be extensive, and 83% of deleterious SLC variants were only identified in a single population. Interestingly, population-specific carrier frequencies of loss-of-function variants in SLC genes associated with recessive Mendelian disease recapitulated the ethnogeographic variation of the corresponding disorders, including cystinuria in Jewish individuals, type II citrullinemia in East Asians, and lysinuric protein intolerance in Finns, thus providing a powerful resource for clinical geneticists to inform about population-specific prevalence and allelic composition of Mendelian SLC diseases. In summary, we present the most comprehensive data set of SLC variability published to date, which can provide insights into inter-individual differences in SLC transporter function and guide the optimization of population-specific genotyping strategies in the bourgeoning fields of personalized medicine and precision public health.
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Project description:Objectives: The aim of this study was to investigate the prognostic significance of thirteen anticancer drug-relevant solute carrier transporters (SLCs) in pancreatic cancer in the context of clinical-pathological characteristics and the KRAS mutation status of tumors. Methods: Tumors and non-neoplastic pancreatic tissues were obtained from 32 histologically verified patients with pancreatic ductal adenocarcinoma. The transcript profile of SLCs was assessed using quantitative real-time PCR. KRAS mutations in exon 2 were assessed by high resolution melting analysis and confirmed by sequencing. Results: SLC22A3 was upregulated and SLC22A1, SLC22A2, SLC22A11, SLC28A1, SLC28A3 and SLC29A1 were downregulated when compared with non-neoplastic pancreatic tissues. Moreover, significantly lower levels of SLC22A1, SLC22A11 and SLC29A1 were found in tumors with angioinvasion. There was also a significantly higher transcript level of SLC28A1 in tumors with regional lymph nodes affected by metastasis. The study found that a high expression of SLC22A1 or SLC28A1was significantly associated with poor overall survival in unselected patients. In contrast, a high expression of SLC22A3 or SLC29A3 was significantly associated with longer overall survival in patients treated with nucleoside analogs. Finally, SLC levels were not found to be associated with KRAS mutation status in exon 2. Conclusions: This study identified a number of associations of SLCs with prognosis of pancreatic cancer patients. Transcript levels of thirteen anticancer drug-relevant solute carrier transporters (SLCs) were determined by qPCR in pancreatic ductal adenocarcinomas and non-neoplastic tissue samples from 32 pancreatic cancer patients. MRPL19, ELF1 and POLR2A were used as reference genes for data normalization.
2013-06-30 | E-GEOD-47368 | biostudies-arrayexpress
Project description:<p>Solute carrier (SLC) transporters control fluxes of nutrients and metabolites across membranes and thereby represent a critical interface between the microenvironment and cellular and subcellular metabolism. Because of substantial functional overlap, the interplay and relative contributions of SLCs in response to environmental stresses remain poorly elucidated. To infer functional relationships between SLCs and metabolites, we developed a strategy to identify SLCs able to sustain cell viability and proliferation under growth-limiting concentrations of essential nutrients. One-by-one depletion of 13 amino acids required for cell proliferation enabled gain-of-function genetic screens using a SLC-focused CRISPR/Cas9–based transcriptional activation approach to uncover transporters relieving cells from growth-limiting metabolic bottlenecks. Among the transporters identified, we characterized the cationic amino acid transporter SLC7A3 as a gene that, when up-regulated, overcame low availability of arginine and lysine by increasing their uptake, whereas SLC7A5 was able to sustain cellular fitness upon deprivation of several neutral amino acids. Moreover, we identified metabolic compensation mediated by the glutamate/aspartate transporters SLC1A2 and SLC1A3 under glutamine-limiting conditions. Overall, this gain-of-function approach using human cells uncovered functional transporter-nutrient relationships and revealed that transport activity up-regulation may be sufficient to overcome environmental metabolic restrictions.</p>
2022-09-20 | MTBLS4268 | MetaboLights
Project description:Objectives: The aim of this study was to investigate the prognostic significance of thirteen anticancer drug-relevant solute carrier transporters (SLCs) in pancreatic cancer in the context of clinical-pathological characteristics and the KRAS mutation status of tumors. Methods: Tumors and non-neoplastic pancreatic tissues were obtained from 32 histologically verified patients with pancreatic ductal adenocarcinoma. The transcript profile of SLCs was assessed using quantitative real-time PCR. KRAS mutations in exon 2 were assessed by high resolution melting analysis and confirmed by sequencing. Results: SLC22A3 was upregulated and SLC22A1, SLC22A2, SLC22A11, SLC28A1, SLC28A3 and SLC29A1 were downregulated when compared with non-neoplastic pancreatic tissues. Moreover, significantly lower levels of SLC22A1, SLC22A11 and SLC29A1 were found in tumors with angioinvasion. There was also a significantly higher transcript level of SLC28A1 in tumors with regional lymph nodes affected by metastasis. The study found that a high expression of SLC22A1 or SLC28A1was significantly associated with poor overall survival in unselected patients. In contrast, a high expression of SLC22A3 or SLC29A3 was significantly associated with longer overall survival in patients treated with nucleoside analogs. Finally, SLC levels were not found to be associated with KRAS mutation status in exon 2. Conclusions: This study identified a number of associations of SLCs with prognosis of pancreatic cancer patients.
2013-06-30 | GSE47368 | GEO
Project description:Both present hemagglutinins and anti HLA antibodies bind to vascular endothelial cells in kidney transplantation, however in some patients this antibody-endothelial interaction is not associated with obvious tissue injury. Mechanisms of this phenomenon called accommodation remain poorly understood. Illumina Human HT-12 v4 Expression BeadChips whole renal transcriptome was evaluated in 3-months protocol biopsies with isolated C4d staining in otherwise stable ABO incompatible and HLA incompatible DSA positive kidney grafts (n=18) as well as in C4d negative HLA compatible grafts with normal histological findings (n=8). Top differently regulated genes were further validated using RT-qPCR at the independent patient cohort (n=24). GO terms with the highest fold enrichment revealed by gene annotation analysis of deregulated genes between ABOi and HLAi groups were represented by cadmium ion binding (p<0.01), apical plasma membrane (p<0.01) and anion transmembrane transporter activity (p<0.05). Majority of deregulated genes between both groups belongs to metallothioneins (MT) and solute carrier family (Slc) genes. The decreased expression of 5 Slc family genes (SLC4A1; SLC4A9; SLC17A3; SLC12A3; SLC30A2) and 3 metallothioneins of class1 (MT1F, MT1G and MT1X) in ABOi compared to HLAi group was verified by RT-qPCR. The most deregulated genes in C4d negative compared with C4d positive cohorts were those included in GO term “mitochondrion” which suggests the activation of metabolism in complement activation. In conclusion, hemagglutinin- and anti-HLA antibody-endothelial interactions and complement activation lead to different regulation of metallothioneins and distinct solute carrier family genes, which suggests its specific role in the accommodation phenomenon.
2018-01-19 | GSE109346 | GEO
Project description:The low permeability and high selectivity of the blood vessels of the brain and central nervous system (CNS) characterize the blood-brain barrier (BBB). Tight junctions, a lack of fenestrations, and low rates of transcytosis in the endothelial cells of the vasculature prevent passive diffusion of most molecules other than water, gases and some lipid soluble molecules (Obermeier, Daneman, & Ransohoff, 2013). Any additional nutrients must be transported across the barrier with the help of transporter proteins. Two protein families account for most transporters. ABC transporters use ATP to power primary-active transport to move molecules across the BBB against an electrochemical gradient, frequently excluding drugs from entering the brain. Some SLC transporters facilitate transport of solutes along an electrochemical gradient, while others permit secondary-active transport by coupling the flow of a solute traveling down the electrochemical gradient to power another solute against its electrochemical gradient. Brain microvessel endothelial cells (BMEC) from human cerebral cortex were enriched through a homogenization and centrifugation procedure. Two BMEC and two tissue were sequenced with paired-end reads on a SOLiD 5500 Wildfire. Raw data was aligned using LifeScope Genomic Analysis, gene expression determined through Cufflinks, and splice junctions identified by aligning to a custom database of known to known and known to novel junctions. We found numerous examples of transporters with enriched expression in the isolated BMECs compared to whole brain tissue. In total, 131 transporter genes or pseudogenes (109 SLC, 22 ABC) are enriched at least 1.25 fold in BMEC enriched samples, and 57 of these are enriched over 2-fold (50 SLC, 7 ABC). Thirteen genes were found to have at least twice as many counts in BMEC enriched samples than in whole tissue for at least one alternative splice junction. Inversely, 23 genes were found to have at least one alternative splice junction with half as many counts in BMEC enriched samples than in whole tissue.
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Project description:On a daily basis, we turnover billions of apoptotic cells that are removed by professional and non-professional phagocytes1-10. While characterizing the transcriptional program of phagocytes, we discovered a novel solute carrier family (SLC) gene signature (33 SLC members) that is specifically modified during engulfment of apoptotic cells (efferocytosis) but not during antibody-mediated phagocytosis. When we assessed the functional relevance of these SLCs, we noted robust induction of an aerobic glycolysis program in engulfing phagocytes, initiated by SLC2A1-mediated glucose uptake, and suppression of oxidative phosphorylation program. Interestingly, the different steps of phagocytosis10,11, i.e. smell (‘find-me’ signals / sensing factors released by apoptotic cells), taste (phagocyte- apoptotic cell contact), and ingestion (corpse internalization), activated different molecules to promote this glycolytic process. Further, lactate, a natural by-product of aerobic glycolysis12,13, was released from engulfing phagocytes via SLC16A1, an SLC member activated after corpse uptake. While glycolysis within phagocytes contributed to actin polymerization and the continued uptake of corpses, the lactate released via SLC16A1 influenced the establishment of an anti-inflammatory environment. Collectively, these data reveal a novel SLC program activated during efferocytosis, identify a previously unknown reliance on aerobic glycolysis during apoptotic cell uptake, and that glycolytic byproducts of efferocytosis can also influence other cells in the microenvironment.
2018-11-30 | GSE119273 | GEO