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BSCD Summer Undergraduate Research Fellowship in Pathophysiology, Biology, and Bioenergetics of Renal Diseases - 2021

Summer Undergraduate Research Fellowship in Pathophysiology, Biology, and Bioenergetics of Renal Diseases

Please bear in mind that while BSCD Summer Fellowships are currently scheduled to proceed these opportunities may have to be modified or cancelled if the situation warrants. 

We are launching an interdisciplinary summer research program in Pathophysiology, Biology, and Bioenergetics of Renal Diseases. We will be sponsoring six undergraduate fellows to take part in three projects (two students per project and the projects are described below). The Fellowship covers a $5000 stipend for the summer research period.
Summer Research Program Description:
This proposal is a Department of Medicine, Nephrology Section multi-investigator effort of three federally funded research labs who work closely in related fields of interest. With a focus on two common kidney disorders, autosomal dominant polycystic kidney disease (ADPKD) (Drs Chapman, Chen and Muir) and nephrolithiasis (Drs Coe, Worcester, Hassan, Ko, Zisman and Prochaska), students will learn about intestinal and renal regulation of urinary oxalate excretion, metabolomic features of bioenergetics regulation of the kidney, mechanisms of urinary acidification and the impact of the microbiome on a number of these measurements. These programs will provide students an introduction to the field of renal physiology and cell biology in the context of common renal medical disorders. Our curriculum will include weekly meetings with all students present together, with the expectation of a presentation of their ongoing work with their faculty mentors. This seminar will be led by the Chief of Nephrology, Dr. Arlene Chapman, and Dr. Hatim Hassan. Each student will briefly discuss the overall progress of his/her particular lab as well present his/her own summer project. This will be followed by an open discussion where all of the students can discuss the presented data and give questions and answers. This program will be more of a small group tutorial with the opportunity for group mentoring. This will give the students the opportunity to present their work to each other on weekly basis. Additional programmatic ideas for this cohort include the following: 1) Participation in the summer TREKS Nephrology Modules, under the direction of Dr. Ben Ko, which is held for one week each summer with students from throughout North America participating. 2) Attending weekly conferences within the section of nephrology typically held on Thursdays and Fridays. 3) Attending individual lab meetings held weekly or twice weekly by each of the research programs outlined in the application and will also include daily lab work when lab meetings are not being held. 4) shadowing expert clinicians in their weekly clinics on Tuesdays and Wednesdays (Drs. Zisman, Prochaska, and Chapman) to observe patients with underlying kidney problems associated with the research studies in their respective labs. 5) Observation of human subject research on the Clinical Research Center which is a research-only inpatient and outpatient ward studying detailed phenotypes of ADPKD and nephrolithiasis study participants. This is expected to be a wonderful opportunity for this summer cohort. Overall, it is expected that the students in this program will be deeply immersed in their projects during the summer and as time permits throughout the rest of the academic year.
1. Required skills:
- Excellent written, verbal communications and analytical skills
- Ability to work as a team member
- Ability to manage time efficiently, multi-task and prioritize
- Self-directed and able to work without supervision
- Proficient computer skills, including Microsoft Office Suite
2. Required Materials
- Resume or CV
- Cover Letter/Statement of Interest
Application Expiration Date:
Applications must be submitted by April 9, 2021.
Interviews may be requested.

Please Note: If you are applying to multiple BSCD Fellowship Grants, please fill out the following BSCD Preference Form -

Description of Projects:
Project # 1:
Title: Targeting Amino Acid Metabolic Crossroads in ADPKD
Mentors: Arlene Chapman, MD, Alex Muir, PhD, Peili Chen, PhD, Departments of Medicine and Molecular Biology. Drs. Chapman, Muir and Chen will be available and committed to fully mentor the students, including guidance about overall career development. 
Project description
Autosomal dominant polycystic kidney disease (ADPKD), the most common hereditary kidney disease, is caused by mutations in the PKD1 or PKD2 gene which encode polycystin-1 and polycystin-2 transmembrane heterodimer proteins. Multiple signaling pathways are affected by mutated polycystin1 and polycystin 2, including primary ciliary signaling and Ca2+/cAMP cascade that contribute to the abnormal proliferation of epithelial cells and cyst formation in ADPKD. Initiated in early childhood, progression of renal cysts gradually damages kidney structure and function, eventually leading to renal failure typically in the 5 to 6th decade of life. Despite promising results from recent studies and trials, therapies that cure or slow the progression of disease are limited. The slow progressive nature of ADPKD make it difficult to diagnose and treat at early stage as the estimated glomerular filtration rate (eGFR) is normal for decades. Height corrected total kidney volume (htTKV), an accurate and reproducible FDA approved imaging prognostic biomarker can increase several-fold prior to loss of kidney function and represents cyst burden and epithelial proliferation. However, measurement cyst burden through HtTKV using magnetic resonance imaging (MRI) is only useful in the setting of macroscopic cysts which have been developing for decades. Candidate biomarkers have been evaluated in urine and plasma from ADPKD patients including neutrophil gelatinase-associated lipocalin (NGAL), monocyte chemotactic protein (MCP)1 and CD14, as well as non-targetted profiling of urinary proteome and miRNAs however their contribution to understanding the progression of ADPKD or strength as a biomarker are not additive to htTKV.
Increasing understanding of the signaling and pathological derangements characteristic of ADPKD has revealed marked similarities to those of cancers at the cellular and molecular level. ADPKD shares most of cancer hallmarks including sustained proliferative signaling, evasion of growth suppressors, induction of angiogenesis, deregulation of cellular energetics, tumor-promoting inflammation, genomic instability and mutation and abnormally reprogrammed metabolism. Metabolic reprogramming provides energy and substrates that is necessary to support tumor growth, survival, immune evasion, and metastasis. Recent studies in PKD1 cells demonstrate a Warburg-like effect as observed in cancer cells, which when inhibited results in inhibited cell proliferation and decreased cyst growth and TKV. This metabolic change is also observed in cystic epithelia in ADPKD patient kidneys, indicating altered bioenergetics and adaptation supporting a proliferative cystic phenotype in ADPKD.
We have demonstrated comprehensive abnormalities in multiple amino acid concentrations and metabolic pathways in our studies in urine and plasma in ADPKD patients with normal kidney function, particularly the histidine pathway. Furthermore, levels of histidine metabolites correlate with cyst burden (htTKV) and kidney function (eGFR). In ADPKD cyst fluids, concentrations of all amino acids, except for Glutamine and Proline, are elevated compared to those in plasma and urine, suggesting that active accumulation of amino acids on the apical surface of cystic epithelia occur. Pharmacologically targeting histidine metabolism at histidine decarboxylase or histidine ammino-lysase affects cystic cell proliferation but not healthy non-cystic human epithelia, indicating a possible therapeutic role in the treatment of this disorder. 
Specific Aims
To determine the effects of loss of the PKD1 or PKD2 genes on amino acid (specifically histidine) metabolism, transport and flux.
Approach and Methods
1. To investigate histidine homeostasis by evaluation of histidine transporters in small intestinal epithelia, hepatocyte and renal cystic (PKD1 or PKD2 mutations) compared to normal non-cystic epithelia. Expression and function of histidine transporters will be studied in tissues and specific cell types including resident macrophages, fibroblasts, cystic and non-cystic epithelial cells harvested from genetically modified mice using immunostaining and affinity assays.
2. To characterize histidine and its metabolic flux into different pathways in PKD1 and PKD2 knockdown cells established by siRNA using stable isotopic 13C-histidine.
3. To define difference in energy production from histidine in PKD1/PKD2 cells compared to normal non-cystic controls under controlled environmental conditions including cell starvation and hypoxia.
Project # 2:
Title: Oxalobacter formigenes-derived peptides impacting Hyperoxalemia, Hyperoxaluria, and related Kidney Stones
Mentor: Hatim Hassan, MD, PhD, John Alverdy, MD, and Matthew Tirrell, Departments of Medicine and Surgery and Institute of Molecular Engineering. Drs. Hassan, Alverdy, and Tirrell will be available and committed to fully mentor the students, including guidance about overall career development. 
Project Description:
Kidney stones (KS) affect ~1 in 5 men and ~1 in 11 women, are costly (>$10B annually), and are associated with CKD and ESRD. High recurrence rates (50% in 5 years and up to 80% in 10 years), indicate that current interventions are inadequate and alternative therapies are needed. Most KS are composed of calcium oxalate and very small increases in urine oxalate concentration increase the risk for stone formation. Lower urinary CaOx supersaturation definitively reduces KS formation. Currently, no FDA approved drugs reduce urinary oxalate excretion. The gut bacterium Oxalobacter formigenes (Of) induces colonic oxalate secretion and reduces urinary oxalate excretion via an unknown secretagogue. Given the difficulties with recolonization, Of alone is not therapeutically feasible and underscores the need to identify the secretagogue that induces colonic oxalate secretion. To this end, we have identified Of-derived factors secreted in its culture conditioned medium (CM) that significantly stimulate (>2.8-fold) oxalate transport by human intestinal Caco2-BBE (C2) cells through PKA activation and stimulation of the oxalate transporters SLC26A6 (A6) and SLC26A2 (A2). In vivo, rectal administration of Of CM reduced urinary oxalate excretion > 32.5% in hyperoxaluric mice, and stimulated colonic oxalate secretion >42%, reflecting the potential therapeutic impact of these factors. We identified a family of a signaling protein as the major Of-derived factors. These proteins closely recapitulate the effects of the Of-derived factors and similarly stimulate (1.4-2.4-fold) oxalate transport by C2 cells. We also identified 35-amino acid peptides (P7-10) within one protein that significantly stimulate (1.5-fold individually and >2.4-fold by P8+9) oxalate transport by C2 cells. Importantly, P8+9 peptides significantly stimulated oxalate transport by HUMAN sigmoid colon (1.8-fold), distal colon (1.7-fold), and ileum (2-fold) organoids (ex vivo intestinal epithelia models fully mimicking the in vivo physiological responses), confirming that P8+9 peptides work in human tissues and that they will likely stimulate oxalate secretion in human colonic and ileal epithelia in vivo. Identification and characterization of the active motifs responsible for colonic oxalate transport can ultimately be translated into an effective novel therapeutic targeting the reduction of plasma and urine oxalate levels. I founded a startup company (Oxalo Therapeutics) to help with developing these peptides into a peptide-based therapeutic and obtained an NIH fast-track STTR grant to optimize our lead peptides through structural modifications (some of which had already being completed). We also obtained phase I NSF STTR grant to develop an innovative drug delivery system consisting of peptide-loaded hydrogel nanoparticles (PLHN) as a vehicle to deliver novel peptides to the intestinal epithelium. Once delivered, the nanoparticles will adhere to the intestinal mucosa and slowly release the peptides, stimulating intestinal oxalate secretion, thereby lowering plasma and urine oxalate and hence preventing KS formation. Such delivery will enable P8+9 peptides to immediately act on the intestinal epithelium to induce oxalate secretion, before being degraded by proteolytic enzymes, mimicking of behavior. In collaboration with Dr. Matthew Tirrell, we are also developing P8 and P9 peptide amphiphiles (peptide-based micellar constructs which can be an effective carrier vehicle for therapeutic drugs) for in vivo testing. 
Specific Aims:
1. Evaluate whether the optimized P8+9 peptides, P8+9 PLHN, and P8+9 peptide amphiphiles (administered rectally as enemas) will reduce plasma and urinary oxalate levels in hyperoxalemic and hyperoxaluric mice.
2. Develop enteric coated capsules containing the optimized P8+9 peptides, P8+9 PLHN, and/or P8+9 peptide amphiphiles for oral administration and evaluate their therapeutic potential in the above mice. 
3. Identify the shortest functional P8 and P9 peptides subdomains by deleting specific amino acid residues.
4. Identify and characterize the involved cell surface receptors in C2 cells.
5. Characterize the involved signaling pathways in C2 cells.
Approach and Methods:
Following collection of baseline urine, blood, and fecal samples (for oxalate measurements), hyperoxalemic and hyperoxaluric mice will be given the optimized P8+9 peptides, P8+9 PLHN, P8+9 peptide amphiphiles, or vehicle twice daily for 3-4 weeks via intrarectal administration. At the end of treatment periods, urine, blood, and fecal samples will be collected for oxalate measurements and intestinal tissues (ileum, cecum, proximal, and distal colon) will be isolated and mounted in Ussing chambers to assess whether any observed reduction in plasma and urinary oxalate levels is due to enhanced intestinal oxalate secretion. Seeing enhanced secretion, the expression of the oxalate transporters A1, A2, A3, and A6 in intestinal tissues will be assessed using qpcr, immnunocytochemistry, and immunoblotting. The capsules will be given by oral gavage (twice daily) for 3-4 weeks and similar studies will be done as described above. The effects of truncated and full-length P8 and P9 on oxalate transport by C2 cells will be compared to identify the shortest functional P8 and P9 peptides subdomains.
Project # 3:
Title: Diet Acid-Base Balance in Patients with Calcium Kidney Stone Disease
Mentors: Fredric Coe, MD, Elaine Worcester, MD, Ben Ko, MD, Anna Zisman, MD, Megan Prochaska, MD. Department of Medicine. Drs. Coe, Worcester, Ko, Zisman and Prochaska will be available and committed to fully mentor the students, including guidance about overall career development.
Project Description
Diet sodium and acid intake strongly affect mineral metabolism and risk for kidney stone formation. Acid loads raise urine calcium losses, saturating urine with stone forming calcium salts, and foster bone mineral loss. The effects are most severe in those people with inherited hypercalciuria, a polygenic trait that makes calcium balance and urine calcium loss abnormally responsive to both salt and acid load. We have found that patients who make calcium phosphate stones, and women who make calcium oxalate stones, have abnormalities of acid-base status, compared to same-sex normal subjects. We have also discovered differences in acid-base handling that involve both gastrointestinal system and kidney in normal men and women. Funded by an NIH Program Project grant (Worcester, PI) the group presently studies effects of varying diet sodium and alkali supplementation on renal calcium handling in the University of Chicago Clinical Research Center.
A full understanding of acid-base balance requires a complete accounting for all renal acid excretion, which is not obtainable from standard urine measurements. In order to better understand the abnormalities we have seen in various types of stone formers, as well as the differences in acid-base handling between normal men and women, we have added novel measurements of urine anion excretion that are the effectors of acid production from diet. We are studying these anions in response to altered diet sodium and alkali, in both types of calcium stone formers and normal subjects. To complement our new measurements, we plan metabolomic measurements of urine anion patterns in collaboration with Dr. Arlene Chapman’s group.
Our previous work has shown differences in segmental renal tubule handling of sodium and calcium between normal subjects and stone formers, which foster loss of calcium in the urine. As there is no appropriate animal model of human stone formation, it has been difficult to examine the possible differences in renal tubule transporter abundance or function that may create the altered mineral handling. Dr. Ko has recently applied the techniques of urine exosome analysis to characterize how nutrient ingestion alters renal transporters, by measuring the levels of transporters of interest in urine exosomes during nutrient challenges. 
Specific Aims
  1. Identify and quantify the differences in renal tubule sodium and calcium handling between calcium stone formers and normal subjects under conditions of high and low salt intake, with or without alkali.
  2. Quantify the differences in renal tubule transporter abundance between calcium stone formers and normals under conditions of high and low salt intake, with or without alkali.
  3. Quantify the differences in acid-base handling between normal subjects and calcium stone formers using standard measurements of acid excretion and titration of urine organic anions.
Approach and Methods
  1. Calculate proximal and distal nephron sodium and calcium reabsorption using endogenous lithium clearance in normal men and women and in men and women with calcium oxalate or calcium phosphate stones on each of 4 diets. Diets will be low sodium or high sodium, with 20 meq potassium citrate daily or placebo, in random order.
  2. Measure urine exosome levels of NHE3, SLC26A6, claudin 2, NKCC2, Claudin 14, NCC, TRPV5 and prostasin in patients in aim 1.
  3. Measure urine markers of acid and alkali balance and urine organic anions by titration, in stone formers and normal subjects, and calculate acid balance.
Names, qualifications and delineation of roles of proposal leaders:
1. Arlene Chapman, MD, Professor of Medicine, Chief of Nephrology
Directs the ADPKD center of excellence, with NIH funding for over 18 years in the study of ADPKD. She has over 2200 ADPKD patients in her program where students will learn about the clinical manifestations of the disease and apply them to the proposed laboratory experiments. She will lead the conceptual development of projects with the investigative team along where the students will participate.
2. Peili Chen, PhD, Research Associate: Cell and Molecular biologist, working with genetic murine and cultured cell models of PKD, experienced in cell metabolism and mitochondrial homeostasis in hypoxic and normoxic conditions, and will mentor studies in cell proliferation, bioenergetics, metabolomics, PKD mouse models, tissue harvesting, and amino acid transporter immunohistochemistry and HPLC analyses.
3. Alex Muir PhD, Ben May Department of Cancer Research, trained investigator in Krebs cycle intermediates, mitochondrial function, bioenergetics and amino acid transport and cellular uptake, will be responsible for providing mentorship in nutrient studies, histidine uptake, krebs cycle intermediates as they relate to reduction in polycystin levels.
4. Hatim Hassan, MD, PhD, Associate Professor of Medicine: A well trained investigator in epithelial transport (with specific expertise in gastrointestinal oxalate transport and its relevance to overall oxalate homeostasis), cell signaling, biochemistry, and molecular biology. He will lead the conceptual development of projects with the investigative team along where the students will participate.
5. John Alverdy, MD, Sarah and Harold Lincoln Thompson Professor of Surgery and Executive Vice-Chair of the department of surgery at UOC. Dr. Alverdy is the director of the Center for Surgical Infection Research at UOC that studies the microbial pathogenesis of infections that develop following surgery including sepsis, wound infection, and anastomotic leak. He has been funded by the NIH for this work since 1999. He will provide mentorship in studies related to the in vivo administration of peptide-loaded hydrogel nanoparticles.
6. Matthew Tirrell, PhD, dean of the Pritzker School of Molecular Engineering at UOC. He is a pioneering researcher in the fields of biomolecular engineering and nanotechnology, with expertise in peptide-based micellar constructs (amphiphiles) where the dense presentation of a functional peptide at the micelle surface improves the interaction of nanomaterials with cells. He will provide mentorship in studies related to the development of P8 and P9 peptide amphiphiles.
7. Fred Coe, MD, Professor of Medicine and Physiology. The founder of the Kidney Stone Program at UCM, with over 40 years of continuous NIH funding for the study of the pathophysiology of kidney stones. He will mentor the students in the performance and analysis of studies of acid-base handling in normal subjects and kidney stone patients, including laboratory measurements, data management, analysis and the implications for altered physiology.
8. Elaine Worcester, MD, Professor of Medicine, is an NIH-funded clinical investigator leading studies of altered renal mineral handling in patients with kidney stones and normal subjects and will mentor the students in the design, performance and analysis of human studies, and the ethical implications of human research.
9. Ben Ko, MD, Associate Professor of Medicine, has expertise in isolation of urine exosomes and their use to understand alterations of renal tubule specific transport activity in humans under varying dietary conditions. He will provide mentorship in the relevant laboratory techniques and their interpretation as part of studies of human renal mineral handling in health and disease.
10. Anna Zisman, MD, Associate Professor of Medicine, is a funded investigator with active clinical and research interests in kidney stones and chronic renal disease. She has been recognized for her excellence in teaching and clinical care with several awards, and is the director of the Nephrology Fellowship Program.
11. Megan Prochaska, MD, MPH, Instructor of Medicine, is a young investigator with clinical and research focus in kidney stones. She has a background in epidemiology, and is now studying the effects of the microbiome on risks for kidney stone disease.