Kidney stone matrix proteins glue kidney stone crystals together to make the stones we encounter and treat. Some of the matrix proteins control whether kidney stone crystals form at all, and the rates that they can grow at. Some call these ‘inhibitors’ or ‘promoters of kidney stones, although their exact role in kidney stone formation remains uncertain to today. Many matrix proteins belong to the immune system, or the inflammatory response.

Our Lack of Knowledge

When I joined this field in 1969 we already knew that stones contained an obvious organic component. In my aging and well thumbed ‘Proceedings of the Renal Stone Symposium’ held at Leeds, April 1968 (J A Churchill Ltd, publishers, Standard Book Number 7000 1421 7) Professor WIlliam Boyce wrote a wonderful review of stone architecture that focused on matrix. In it, he set the case forward in a ringing affirmation: ‘The best reason to consider calculous matrix is because it is there. In every human urinary concretion the matrix is present from centre to surface.’

Limitations of Analytical Methods

The sheer analytics styme us. No techniques until now have permitted resolution of matrix into its molecular components. In 2014 I reviewed what I found concerning the proteome of stones, and that review lies below the present lead article by Witzmann. His work uses the most modern techniques and is a great advance over what has been.

Witzmann et al. 

The Main Results

Using the methods detailed in the paper, we identified a total of 1,059 unique proteins in two human calcium oxalate kidney stones.

Sheer prolixity, for want of a better word, of nature makes it hard to understand what these proteins do. Probably many are irrelevant to stone formation and simply ride along with the crystals or even other proteins doing no useful work at all. But many are calcium binding and therefore could alter crystal dynamics.

As a group the proteins in these two stones are known to have roles in the immune response system, inflammation, injury and tissue repair which raises the question of whether or not stones cause injury or inflammation or simply that these proteins, fitted to respond to invaders whose walls are generally highly charged are themselves anionic and prone to attach to crystals.

If you want to peruse the entirety here is our spreadsheet. There is also one with the paper itself.

Comments By Frank WItzmann

A New Method

Because our label-free quantitative mass spectrometry (LFQMS) platform has performed well in the past, we used it to extract protein from kidney stone powder and identify and quantify as many proteins as possible. Since previous attempts seemed inadequate for technical reasons, we thought our more comprehensive analysis might give us unique insights into stone formation.

We have quantified 1,059 unique proteins in the organic matrices of two CaOx stones. They corroborate and expand on previous observations of the kidney stone matrix protein composition. As well, they reveal a more complex matrix proteome than previously reported for human kidney stones of any type. But do we have new testable hypotheses concerning how the matrix predisposes to stones?

Does it Matter?

The simple comparison of two CaOx stones may not be enough to answer that question. The two differ markedly. Only one contains neutrophil-associated proteins like calgranulin C, azurocidin, cathelicidin antimicrobial peptide, defensin 4, beta-defensin 1, neutrophil elastase, gelatinase-associated lipocalin, and lysozyme C. Only the other contains kidney proteins like biglycan, dermicidin, destrin, napsin-A, osteoclast-stimulating factor 1, tight junction protein ZO-2, and uroplakin-3a.

Do proteins like these point to unique stone formation mechanisms?

Despite the limitations of our initial proteomic analysis, we believe our approach will enable us to analyse and compare comprehensive protein profiles in small stone specimens from individual patients. We have already studies kidney stone samples from male and female cohorts with CaOx and CaP (brushite) stones. We will share our conclusions here after the CaOx – CaP comparison is published.

The papers below are ones I reviewed over a year ago and remain of interest.

 Canales et al

Canales acanales papernd his colleagues extracted the organic material from seven pure COM stones and found 68 proteins. Of these the authors considered as previously unidentified in stone matrix. Myeloperoxidase chain A (MPO-A), α defensin, and the the calgranulins (there are 3 found so far in stones) may be part of the immediate immune response. In addition they found three cell injury proteins, one stress response protein, an array of plasma proteins such as albumin, hemoglobin and transferrin, carbonic anhydrase, and a mixture of proteins that include osteopontin. Finally they found cell adhesion, membrane transport, biogenesis, cell signalling and coagulation proteins. They found Tamm Horsfall protein as most of us would expect.

Merchant et al

Merchant and colleaguesLederer header did much the same kind of work. From stones of 5 people not otherwise described they identified 58 proteins, of which 11 were high abundance and 10 of these present in all three analyses of the extracts from stones. Of these, all but 1 had been previously been identified as binding to CaOx or HA surfaces. Four proteins were prevalent and high abundance on the basis of normalized abundance computation: calgranulins A and B, apolipoprotein A-1, and THP. Using ingenuity analysis, 3 principle pathways were identified: tumorigenesis, immune, and inflammation. The top canonical pathway was acute phase response signaling. The serious weakness of this work is in the stones: unknown crystals.

Okumura et al

Okumura et al obtained stones from 9 patients otherwise unidentified. All were predominant CaOx by FTIR. Because they found very heterogeneous electrophoretic mobilities of certain matrix proteins, such as THP, they decided to do in solution protease digestion followed by proteomic analysis. This differs from most other studies which did peptide digestion and analysis from bands of gels.

All of the stones hOkumura paperad some osteopontin, prothrombin F1 fragments, THP, calgranulins A, B and C, myeloperoxidase, and albumin (See Featured figure at the top of this post). What is striking is the variation of protein abundances among the stones. The PTF1 fragment abundance varied over 10 fold; for THP variations were slighter. Calgranulins A and B were almost inverse to PTF1 but ran together.

This variability itself suggests profitable research. Some of the variability surely arises from heredity. It may cause part of the well known heritability of stones themselves. Possibly variability reflects the effects of stones or of the tissue injuries from procedures used to treat stones.


I redacted this article from a longer review you can reach through this link. Although I made no effort to pretty it up, you may enjoy it. If I have missed important references, perhaps yours, please let me know.

Some questions

We know more and more about the molecules. But we have almost no knowledge about how it all works. Are these stone matrix molecules simply surface active components of urine that adsorb to crystals as they form? Do they affect how crystals form, and become part of stones? Do they bind crystals together to make clinically important stone mass? Being in immune and inflammatory pathways, are some of the molecules a response to stones: does having stones set the stage for more stones by altering the urine proteome?

We have far better tools than in 1969. Do we have new testable hypotheses concerning how the matrix predisposes to stones?


  1. Kimberly

    My 79 year old mother has passed several large Matrix kidney zones. I had her save the stones to show the specialist. He said he had never seen anything like it in his 27 years of practice. He sent them off to be test so we now know they are Matrix. Mom had Scan with contrast for bladder and kidney and two stones were sited; one in both ureters. Scoping procedure to the bladder was done as it was completely clear. Due to the radiology report findings of Matrix and blood, the doc wants to scope to the kidney to see what is causing these stones. From your research and experience, will you speculate what they could possibly find? I’m not sure it is absolutely necessary at the his time. Please advise ASAP.
    Thank you in advance,

    • Fredric Coe, MD

      Hi Kimberly, You are the second person this month reporting matrix stones. Radiology cannot diagnose such stones, only stone analysis, so I presume stones have been so analysed. If not, if this is just radiology, I would not rely on it. If you have the stones, get them analysed – they may contain some crystals that are organizing the protein into these stones. Regards, Fred Coe

  2. Rae Dalton

    Dr Coe, I have MSK and have had many episodes with kidney stones since age 15. I am 68 now. I need spinal fusion for scoliosis and have been taking Forteo for 3 1/2 mos. Anout 2 wks ago I began having flank pain and as of an ultrasound two days ago, I have clusters of new stones in both kineys. My spine surgery requires my bone density to be improved to assure fusion. Is there anything I can do to prevent making more stones in the future, and should I d/c the Forteo? Thanks for any advice you can provide.

    • Fredric Coe, MD

      Hi Rae, Forteo is parathyroid hormone that can increase urine calcium and foster stones. You need it for your bones. Very low sodium diet would help lower urine calcium, and if combined with high fluids might stave off more. Ask your treating physician. Finally a low dose of thiazide – like agents like chlorthalidone 12.5 mg every other day – if combined with low sodium diet could lower urine sodium even more. Regards, Fred Coe

  3. Steven

    I have been passing little red crystals in the urine, I feel them in the uriter when passing. I had them sent to a lab at N.S Manhassett Hospital. They came back as not stones, but rather protein blood mix. What are they From? And is there anything I can do to prevent them in the future?
    Thank you

    • Fredric Coe, MD

      Hi Steven, These may indeed be blood clots. You need evaluation for this by a urologist who can find the source of the blood and fix things for you. Prevention is to find the cause and get rid of it. Do not omit to get a full evaluation for this from your physicians. Regards, Fred Coe

  4. Mandy Alderink

    HI Dr. Coe,

    I’m gathering all of my info, so for my next appointment I can be more prepared. Right now I’m doing my 24 hour urine test, just got my blood work done which came back normal and got a KUB. I had a CT scan back in Nov. 2016, and I have 26 STONES!!! I’m only 39 years old and a female. Three years ago was the first time I discovered I had kidney stones. 17 in my left kidney and 9 in my right, right now. I asked what the stones are called and they’re called Carbonite Apatite stones. Is there another name for my kidney stones??? I can’t find a lot of info on my stones on the Internet. I take Urocit K but not all of the time because it gives me heartburn. Is there anything you recommend I ask in my next appointment? I’m really stressed with the amount of stones I have and just don’t want to keep going through this if I’m doing something myself to cause these. Thank you for your time. P.S. not sure if it matters, but I had four kids in the past eight years. My last baby exactly a year ago.

  5. Dawn Marie

    6 weeks ago I had scope with lithotripsy done, 4 weeks later pain arrived and I was back in ER. 2 weeks after I had another lithotripsy. Is this common for reoccurring stone patients? And can lithotripsies cause damage when having done so often?

    • Fredric Coe, MD

      Hi Dawn and thanks for the interesting question. If by lithotripsy you mean external shock wave lithotripsy 3 in 6 weeks seems frequent enough you would certainly want to stop these stones from forming. The first event however sounds like endoscopy with laser lithotripsy, which is altogether different. In general, modern urologists are very well informed about the risks and benefits of their surgical modalities and the AUA has published some excellent guidelines for them to assist in thinking about which ones are best. Your problem sounds like frequent stones that need prevention treatment, so procedures will stop being an issue. I would certainly focus my attention on prevention, and hope you can obtain it as soon as possible. As for shock wave lithotripsy and renal damage, it is not a dramatic risk thus far in your case, at least that is how things seem from a distance, but I am sure you and your doctors will be a lot happier when stone recurrence is ended by effective medical prevention. Regards, Fred Coe

      • Dawn Marie

        Thank you for your reply Dr Coe. I have been battling these stones for almost 20years, but seems for frequent the last few years. Dr Patel has referred me to you. As soon as I complete my tests, I will be making the appointment. I look forward to the prevention process. Light at the end of the tunnel.
        Again, thank you for your time in replying.

        • Fredric Coe, MD

          Dear Marie, I am happy to be of help. Since Dr. Patel referred you here, I will be pleased to see you and do what I can for stone prevention. Fred Coe

  6. iswinar

    what is the best method to remove kidney stone?

    • Fredric Coe, MD

      There is no best method, because best is related to the kind of stone and the person being treated. Perhaps one might say a single stone in the renal pelvis might be ideal for shock wave lithotripsy, but even here: How big is it? Is there a chance it is uric acid? Are there any complicating issues that make shock waves undesirable. Would flexible ureteroscopy with laser disruption be better for any reason? Surgeons exert considerable judgement in choosing how to remove a stone and I would always be guided by that judgment. When two approaches are deemed more or less the same, patients can choose. Regards, Fred Coe


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