Research laboratory of Deanna Kroetz, PhD
Pharmacogenomics and Molecular Pharmacology Laboratory

Research & Projects

Research in the Kroetz Lab is focused on pharmacogenetics and the identification of new drug targets for the treatment of renal injury. Jump below to:

Pharmacogenomics research projects

Our pharmacogenetics research uses a combination of genomic tools, including candidate gene and genome-wide association studies, exome sequencing, complex trait analyses, comparative genomics, and cell and model organism studies for identification of genetic biomarkers of drug response. The results from these human genetics studies can also direct investigations into novel strategies to prevent or treat drug-induced toxicity. Specific phenotypes being studied are:

Chemotherapy-induced sensory peripheral neuropathy

One of the most common toxicities associated with cancer chemotherapy treatment is sensory peripheral neuropathy, resulting from damage to the peripheral nerves in the hands and feet. Symptoms of peripheral neuropathy include pain, numbness, tingling, or burning in the hands and feet, loss of function of the fingers, and increased temperature sensitivity. In most cases chemotherapy-induced peripheral neuropathy is associated with a reduced quality of life. While a number of clinical factors increase a patient’s likelihood of developing this toxicity, there is increasing evidence that interindividual variation in DNA sequence also contributes to a patient’s risk. To this end, we are using genome-wide genotyping and sequencing approaches to identify genetic markers of chemotherapy-induced sensory peripheral neuropathy and to identify novel genes implicated in the mechanism of this toxicity. Functional genomic studies in neuronal cells in culture and in model organisms are used to understand the molecular basis for the involvement of specific genes and variants in this toxicity.

paclitaxel graph

A SNP in FGD4 predicts increased risk of developing paclitaxel-induced peripheral neuropathy

Genes in axon extension

Genes in axon extension and regulation pathways implicated in the heritability of paclitaxel-induced peripheral neuropathy

 

Response and toxicity to antiretroviral therapy

Morbidity and mortality have dramatically improved in HIV-positive patients since the advent of highly active antiretroviral therapy (HAART). However, toxicities associated with HAART and the lack of a complete immune reconstitution remain significant clinical problems. This is especially true in resource-limited settings where treatment is typically delayed; patients often have multiple co-morbidities and access to the newest antiretrovirals is limited. In collaboration with HIV clinical researchers at UCSF and Harvard we are studying the genetic basis for differences in immune response and toxicity in HIV-infected Ugandans, using candidate gene and genome-wide association studies and exome sequencing. Specific phenotypes of interest are NRTI-induced peripheral neuropathy, CD4 recovery, and kynurenine:tryptophan ratio. Understanding the genetic basis for drug response and toxicity can inform more appropriate clinical use of antiretrovirals in sub-Saharan Africa.

antiretrovirals africa

Bevacizumab-induced hypertension

Bevacizumab is a humanized monoclonal antibody targeting vascular endothelial growth factor A (VEGF). Despite its effectiveness as an angiogenesis inhibitor for the treatment of colorectal cancer and other tumors, bevacizumab treatment can also lead to the development of hypertension. In most patients, the blood pressure increase can be controlled with standard anti-hypertensive medications. However, 5 to 18 percent of patients undergoing bevacizumab treatment develop severe hypertension, and treatment that may otherwise be beneficial must be discontinued.

We use exome sequencing to identify rare variants associated with the most severe form of this toxicity. We also use candidate gene studies focused on the VEGF signaling pathway to identify common genetic variants that are predictive of bevacizumab-induced hypertension. Signaling from endothelial to smooth muscle cells is being studied to understand how specific genes in the VEGF pathway are involved in the development of hypertension.

bevacizumab

Functional genomics of ABC transporters

The ATP-binding cassette transporters play a critical role in the efflux of drugs, other xenobiotics, and endogenous compounds from cells. Interindividual variation in ABC transporter expression and function is associated with variation in a drug’s pharmacokinetic and pharmacodynamic properties. Our lab studies the effect of coding region variation on ABC transporter function, using cell-based assays and vesicle studies, and collaborates with computational biologists to predict the effects of genetic variation on transport function. We also combine comparative genomics with in vitro and in vivo reporter gene assays to characterize how variation in the noncoding regulatory regions influences ABC transporter transcription and expression. We are also interested in the regulation of ABC transporter expression by miRNAs and alternative splicing. Studies in healthy volunteers or patient populations can be used to validate functional variants found in vitro.

Regulation of MRP4 expression

Regulation of MRP4 expression by miRNAs

Kidney injury research projects

Renal cytochrome P450 eicosanoids

Cytochrome P450 (P450s) eicosanoids are highly produced in the kidney and are associated with numerous biological effects. We are particularly interested in the products of the CYP2C and CYP2J epoxygenases, the epoxyeicosatrienoic acids (EETs). Earlier work from our lab has demonstrated potent antihypertensive effects from inhibition of soluble epoxide hydrolase (sEH), which prevents degradation of EETs within the cell and prolongs EET effects. Our current work is focused on understanding whether sEH inhibition can be used to prevent or treat acute and chronic renal injury. Our animal and cellular studies take advantage of potent and selective sEH inhibitors and Ephx2-/- mice (which lack functional sEH).

Acute kidney injury

Inhibition of sEH is being studied in acute kidney injury models in mice, including cisplatin-induced acute kidney injury and renal ischemia-reperfusion. We have demonstrated potent effects in a model of prevention and are studying the molecular basis for these effects. We are also interested in testing whether a similar strategy can reverse toxicity after it is initiated.

Inhibition of sEH

Inhibition of sEH attenuates cisplatin-induced renal injury

p38-MAPK phosphorylation

p38-MAPK phosphorylation

 

Chronic kidney disease

The incidence of chronic kidney disease continues to increase in the United States and other Western countries largely because of the increasing incidence of diabetes. Effective treatment strategies for prevention or reversal of the fibrosis associated with chronic kidney injury is critically needed. We are testing the ability of sEH inhibition to prevent renal fibrosis in mouse models, using a similar strategy of a combination of chemical and genetic disruption of EET degradation.

EET degradation