Figure 1

<p>Expression of UGT1A isoforms among multiple human tissue samples. For each functional UGT1A isoform (A through I), an example for the PCR gels for expression in multiple human tissues together with molecular weight markers is shown.</p

Cis eQTL analysis of SLC2A2 in human liver tissue

A three-stage genome wide association study (GWAS) reports the finding of the C-allele of rs8192675 in the intron of SLC2A2, which encodes the facilitated glucose transporter GLUT2, was associated with a 0.17% (p=6.6x10^-14) greater metformin induced HbA1c reduction in 10,577 participants of European ancestry (doi:10.1038/ng.3632).  The SNP, rs8192675 is the top cis-eQTL for SLC2A2 in 1,226 human liver samples, suggesting a key role for hepatic GLUT2 in regulation of metformin action. Here, we deposit the SLC2A2 transcript levels (see Supplemental Table A) in 583 human liver samples and their genotypes within the SLC2A2 region (see Supplemental Table B). The data here are referred to as data set 4 in the published GWAS (doi:10.1038/ng.3632)

Genetic Diversity of the KIR/HLA System and Outcome of Patients with Metastatic Colorectal Cancer Treated with Chemotherapy

<div><p>Objective</p><p>To explore genes of the killer-cell immunoglobulin-like receptor (KIR) and of the HLA ligand and their relationship with the outcome of metastatic colorectal cancer (mCRC) patients treated with first-line 5-fluorouracil, leucovorin, and irinotecan (FOLFIRI).</p><p>Methods</p><p>A total of 224 mCRC patients were screened for KIR/HLA typing. The determination of the KIR/HLA combinations was based upon the gene content and variants. Genetic associations with complete response (CR), time to progression (TTP) and overall survival (OS) were evaluated by calculating odds and hazard ratios. Multivariate modeling with prognostic covariates was also performed.</p><p>Results</p><p>For CR, the presence of KIR2DL5A, 2DS5, 2DS1, 3DS1, and KIR3DS1/HLA-Bw4-I80 was associated with increased CR rates, with median ORs ranging from 2.1 to 4.3, while the absence of KIR2DS4 and 3DL1 was associated with increased CR rates (OR 3.1). After univariate analysis, patients that underwent resective surgery of tumor, absence of KIR2DS5, and presence of KIR3DL1/HLA-Bw4-I80 showed a significant better OS (HR 1.5 to 2.8). Multivariate analysis identified as parameters independently related to OS the type of treatment (surgery; HR 2.0) and KIR3DL1/HLA-Bw4-I80 genotype (HR for T-I80 2.7 and for no functional KIR/HLA interaction 1.8). For TTP, no association with KIR/HLA genes was observed.</p><p>Conclusion</p><p>This study, for the first time, evidences that the genotyping for KIR-HLA pairs are found predictive markers associated with complete response and improves overall survival prediction of FOLFIRI treatment response in metastatic colorectal cancer. These results suggest a role of the KIR/HLA system in patient outcome, and guide new research on the immunogenetics of mCRC through mechanistic studies and clinical validation.</p></div

Association between KIR/HLA and complete response (CR) rate.

<p>CR: complete response; PR: partial response; SD: stable disease; PD: progressive disease. + and − refer to presence and absence of a gene (respectively).</p

Characteristics of the mCRC patients treated with FOLFIRI.

<p><b>$ Radical surgery:</b> Surgical resection of locally recurrent cancer.</p

Kaplan-Meier survival curves (truncated at 80months) A) Kaplan-Meier plots of OS stratified by radical surgery Yes and No refer to presence or absence of radical surgery, respectively.

<p><b>B) Kaplan-Meier plots of the association between KIR2DS5 and OS.</b> OS curves of patients with KIR2DS5 (solid black line), or without the gene (−, red dashed line). The implication of this result could not be further investigated as the ligand of KIR2DS5 has not been identified yet. <b>C) Kaplan-Meier plots of the association between KIR3DL1/HLA-B and OS.</b> OS curves of patients with KIR3DL1/HLA-Bw4-I80 (solid black line), KIR3DL1/HLA-Bw4-T80 (dashed red line), or without either one (−/−, green dashed line). <b>D) Kaplan-Meier plots of the association between a combination of surgery, KIR2DS5 and KIR3DL1/HLA and OS.</b> Yes and No refer to presence or absence of radical surgery, respectively. − refers to the absence of the gene. Kaplan-Meier method, and log-rank were used to test the differences between subgroups. 0.95 LCL and 0.95 UCL; lower and upper 95th percentile, respectively; CI (95%); 95% confidence interval.</p

Presence of KIR3DS1/HLA-Bw4-I80 genotype associated with CR, improves the survival of patients stratified on combination of genes and surgical treatment.

<p>OS Kaplan-Meier survival curves (truncated at 80months) of patients stratified on patients with the identified better (A factors) and worse (B factors) prognostic combination of genes and surgical treatment.</p

Association between the number of activating KIR (aKIR) genes and complete response (CR) rate.

<p>The KIR gene analysis shows a trend (chi squared test for trend, p<0.001) between an increasing number of aKIR genes (KIR2DS3 and KIR2DS5; ligand unknown) or aKIR/HLA-ligand (KIR2DS1/HLA-C2, KIR2DS2/HLA-C1, KIR2DS4full/HLA-Cw*04, KIR3DS1/HLA-Bw4) and the rate of CR.</p

KIR3D and HLA-B ligands and their association with the CR rate.

<p>The NK effector functions are determined by the cumulative signal generated via the ligation of activating and inhibitory NK cell receptors with their putative HLA ligand on target cells. Activating (KIR3DS1) and inhibitory (KIR3DL1) receptors are genes of a same locus and have similar HLA-B ligand specificity with thus a possible balancing role in the NK response. The KIR3D receptor can recognize the HLA-B molecules carrying the Bw4 common epitope (Bw4-I80 and Bw4-T80 variants), but not the Bw6 motif. The figure shows a greater frequency of patients with CR in patients carrying KIR3Ds with the Bw4-I80 ligand (10%) than in patients with Bw4-T80 (0%) or Bw6/6 (4%). Among the HLA-Bw4-I80 ligand, the presence of the KIR3DS1 gene is associated with a trend towards improved CR rate (Chi square test for trend, p 0.016). + and – indicate presence or absence of the gene, respectively.</p

Genomic Characterization of Metformin Hepatic Response

<div><p>Metformin is used as a first-line therapy for type 2 diabetes (T2D) and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK) inhibitor (allowing to identify AMPK-independent pathways). We identified thousands of metformin responsive AMPK-dependent and AMPK-independent differentially expressed genes and regulatory elements. We functionally validated several elements for metformin-induced promoter and enhancer activity. These include an enhancer in an ataxia telangiectasia mutated (<i>ATM</i>) intron that has SNPs in linkage disequilibrium with a metformin treatment response GWAS lead SNP (rs11212617) that showed increased enhancer activity for the associated haplotype. Expression quantitative trait locus (eQTL) liver analysis and CRISPR activation suggest that this enhancer could be regulating <i>ATM</i>, which has a known role in AMPK activation, and potentially also <i>EXPH5</i> and <i>DDX10</i>, its neighboring genes. Using ChIP-seq and siRNA knockdown, we further show that activating transcription factor 3 (<i>ATF3</i>), our top metformin upregulated AMPK-dependent gene, could have an important role in gluconeogenesis repression. Our findings provide a genome-wide representation of metformin hepatic response, highlight important sequences that could be associated with interindividual variability in glycemic response to metformin and identify novel T2D treatment candidates.</p></div