Improved analysis of kidney cancer

August 11, 2017, Lund University

Every year, just over 1000 people are diagnosed with kidney cancer in Sweden. The three most common variants are clear cell, papillary and chromophobe renal cancer. Researchers compare the gene expression in tumour cells from a kidney cancer patient with cells from healthy tissue to figure out in which part of the kidney the cancer began and what went wrong in these cells. Now, a research team at Lund University in Sweden has discovered that in the Cancer Genome Atlas database, the gene expression in reference samples from normal tissue varies, depending on where in the kidney the samples happen to have been taken. The analyses can be improved by clarifying which samples correspond to the correct tissue. The study has now been published in Cell Reports.

The part of the which purifies the blood and generates urine is called the nephron and functions as a kind of tubing system. Each kidney contains around a million nephrons which collectively filter 180 litres of primary urine (waste products, water and salts) every day. This results in 1.5 litres of concentrated liquid, which is excreted through urination.

"Everything is very specifically regulated and the cells have different and hence properties depending on their location in the tubing.", explains Håkan Axelson, research team leader and professor of molecular biology.

When a tumour biopsy is taken from a patient and compared with healthy kidney tissue, it serves to map how the various are expressed so as to clarify what has gone wrong in the tumour cells. The Cancer Genome Atlas – an international database containing almost 1000 samples from kidney tumours and healthy tissue – is a tool in this process.

"But when our research team studied the samples from the database, we noticed a great range of gene expressions between normal tissue samples. It emerged that the samples in the Cancer Genome Atlas were taken at different depths in the kidney and therefore contain different types of cells, which means that their gene expressions also vary", says Håkan Axelson.

Unreliable and sometimes completely incorrect comparison

The normal reference samples thus contain various types of cells depending on where in the kidney they happen to have been taken. Since the Atlas does not state the location in the kidney the reference sample was collected, the comparison risks being unreliable and sometimes completely incorrect.

"Since the gene expression in the cells varies depending on their location, it is important that the normal samples contained in the database should also be taken from the location corresponding to that of the patient's tumour", says David Lindgren, who is the lead author of the study.

As an example, it was previously suspected that clear cell tumours occur in the first part of the nephron, but if these are compared with a normal sample taken deeper inside the nephron, the cells will not correspond to the tumour . The gene is thereby different. Although each patient is unique, the various types of tumours have different specific genetic changes which occur as a consequence of properties in the cell in which the tumour originated.

"It is extremely important to know what characterises the in which the tumour occurs. Through better understanding of this interaction, we can increase our understanding of the course of the disease, which could be significant for diagnostics and, in the longer term, also for the choice of treatment", concludes Håkan Axelson.

Explore further: Study discovers proteins which suppress the growth of breast cancer tumors

More information: David Lindgren et al. Cell-Type-Specific Gene Programs of the Normal Human Nephron Define Kidney Cancer Subtypes, Cell Reports (2017). DOI: 10.1016/j.celrep.2017.07.043

Related Stories

Study discovers proteins which suppress the growth of breast cancer tumors

June 12, 2017
Researchers at the University of Birmingham have found that a type of protein could hold the secret to suppressing the growth of breast cancer tumours.

Kidney tumors have a mind of their own

November 21, 2012
New research has found there are several different ways that kidney tumours can achieve the same result – namely, grow.

New genetic cause of childhood cancer found

May 30, 2017
Scientists have identified a genetic mutation that causes a childhood kidney cancer called Wilms' tumour.

A 'key' to metastasis formation

July 13, 2016
Researchers at Hokkaido University in Japan have demonstrated that a molecule called biglycan plays an intrinsic role in attracting tumour cells toward the inner wall of tumour blood vessels.

Tumor-trained T cells go on patrol

May 15, 2017
'Tumour-trained' immune cells - which have the potential to kill cancer cells - have been seen moving from one tumour to another for the first time. The new findings, which were uncovered by scientists at Australia's Garvan ...

Highly prevalent gene variants in minority populations cause kidney disease

March 1, 2017
African Americans have a heightened risk of developing chronic and end-stage kidney disease. This association has been attributed to two common genetic variants - named G1 and G2—in APOL1, a gene that codes for a human-specific ...

Recommended for you

Scientists block the siren call of two aggressive cancers

January 23, 2018
Aggressive cancers like glioblastoma and metastatic breast cancer have in common a siren call that beckons the bone marrow to send along whatever the tumors need to survive and thrive.

Boosting cancer therapy with cross-dressed immune cells

January 22, 2018
Researchers at EPFL have created artificial molecules that can help the immune system to recognize and attack cancer tumors. The study is published in Nature Methods.

Workouts may boost life span after breast cancer

January 22, 2018
(HealthDay)—Longer survival after breast cancer may be as simple as staying fit, new research shows.

Cancer patients who tell their life story find more peace, less depression

January 22, 2018
Fifteen years ago, University of Wisconsin–Madison researcher Meg Wise began interviewing cancer patients nearing the end of life about how they were living with their diagnosis. She was surprised to find that many asked ...

Single blood test screens for eight cancer types

January 18, 2018
Johns Hopkins Kimmel Cancer Center researchers developed a single blood test that screens for eight common cancer types and helps identify the location of the cancer.

Researchers find a way to 'starve' cancer

January 18, 2018
Researchers at Vanderbilt University Medical Center (VUMC) have demonstrated for the first time that it is possible to starve a tumor and stop its growth with a newly discovered small compound that blocks uptake of the vital ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.