The modification of acidification

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In Parkinson’s research, a great deal of the attention is focused on a handful of proteins that are associated with Parkinson’s. The majority of this knowledge has come from the discovery of genetic variations being apparent in some member of the PD community.

The proteins (and biological pathways) underlying these genetic variations include alpha synuclein, LRRK2, PARKIN and GBA – all of which have been discussed on this website. But scientists have identified over 80 different regions of DNA that are associated with Parkinson’s and only recently have some of the proteins associated with these other regions of DNA been investigated.

One of these proteins is particularly interesting. It’s called TMEM175. And recently published research has provided new insights into this protein.

In today’s post, we will look at what is known about TMEM175 and discuss how biotech companies are therapeutically modulating it as a potential novel treatment for Parkinson’s.

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Source: Sciencetrends

Lysosomes are a key component of the waste disposal/recycling system of our cells.

They are small bags that are full of digestive enzymes that help to break down material inside of cells. Sometimes that material is newly imported from outside of the cell, while other times it may be old proteins that need to be disposed of.

Lysosomes provide the digestive enzymes for the job of breaking down the material.
Lysosomes

How lysosomes work. Source: Prezi

We haver discussed lysosomes in previous posts in more depth (Click here to read that SoPD post) – but understand that they are an absolutely critical component of normal biological function inside of cells.

Got it. What do they have to do with Parkinson’s?

Well, increasingly it is becoming apparent that lysosomes may be playing an influential role in the underlying biology of many cases of Parkinson’s.

This statement is largely based on the observation that a number of the genetic risk factors that increase the risk of developing Parkinson’s are associated with proteins involved in normal lysosomal function.

In fact, a report published in 2017 found that the many people with Parkinson’s also have a genetic risk factor for other lysosome-related medical conditions.

This is the report here:

Title: Excessive burden of lysosomal storage disorder gene variants in Parkinson’s disease.
Authors: Robak LA, Jansen IE, van Rooij J, Uitterlinden AG, Kraaij R, Jankovic J; International Parkinson’s Disease Genomics Consortium (IPDGC), Heutink P, Shulman JM; IPDGC Consortium members; International Parkinson’s Disease Genomics Consortium (IPDGC).
Journal: Brain. 2017, 140(12): 3191–3203.
PMID: 29140481              (This report is OPEN ACCESS if you would like to read it)

In this study, the researchers focused their analysis on not on genetic risk factors for Parkinson’s, but rather they went looking for genetic risk factors associated with 54 different lysosomal disorders. And there are many types of lysosomal conditions – click here for a list. The investigators screened the DNA collected from 1156 individuals with Parkinson’s and 1679 unaffected “control” participants.

The researchers found that over half (56%) of the Parkinson’s cases they analysed had at least one genetic risk factor for another lysosomal condition (and 21% had more than one). And this result was consistent across two other independent cohorts (cohort 1. containing 436 PD cases and 169 controls, and cohort 2. containing an additional 6713 PD cases and 5964 controls).

The researchers concluded that multiple genetic hits may act in combination to reduce overall lysosomal function, which in turn could enhance Parkinson’s susceptibility (perhaps by reducing the clearance of waste proteins in cells).

If lysosomes are just small bags of enzymes, why are so many genetic risk factors associated with them?

My description of them as “small bags of enzymes” is rather a gross simplification.

There are many facets to lysosomes that need to be carefully regulated by cells. For example, the right level of acidity is required inside lysosomes in order for them to do their job, and this is controlled by numerous factors.

One of those factors is a protein called TMEM175.

What does TMEM175 do?

Several years ago, a group of researchers published this study:

Title: TMEM175 Is an Organelle K(+) Channel Regulating Lysosomal Function.
Authors: Cang C, Aranda K, Seo YJ, Gasnier B, Ren D.
Journal: Cell. 2015 Aug 27;162(5):1101-12.
PMID: 26317472                    (This report is OPEN ACCESS if you would like to read it)

In this study, the investigators discovered a major potassium-selective channel, which is made up of a protein called TMEM175, which at the time was a protein of unknown function.

What is a potassium-selective channel?

Potassium channels are tetrameric (meaning 4 components are involved) membrane-spanning (meaning that they interact with both the inside and outside world of the cell) proteins that provide a selective conduit for the flow of potassium across cell membranes. And potassium is one of those essential elements for life – regulating heartbeats, proper functioning of muscles and nerves, and it is vital for synthesizing protein and metabolizing carbohydrates.

Source: Moleculardevices

So TMEM175 is one of the components making a potassium channel?

Exactly. And in this study, the investigators found that it was located in the membrane of lysosomes:

Source: Cell

By disrupting and manipulating TMEM175, the researchers discovered that this protein plays an important role in potassium flow in lysosomes, and contributes significantly to levels of acidity inside of lysosomes. They reported that lysosomes lacking TMEM175 exhibit no potassium flow and displayed marked instability in their acidity.

This discovery was particularly interesting for the Parkinson’s research community because the year before this study was published, another report indicated that genetic variations in and around the TMEM175 gene (the section of DNA that provides the instructions for making TMEM175 protein) are a risk factor for developing Parkinson’s.

This is the report in question:

Title: Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson’s disease.
Authors: Nalls MA, Pankratz N, Lill CM, Do CB,…(there are a lot of researchers were in the list of authors)…, Gasser T, Bertram L, Eriksson N, Foroud T, Singleton AB.
Journal: Nat Genet. 2014 Sep;46(9):989-93.
PMID: 25064009                   (This report is OPEN ACCESS if you would like to read it)

In this report, it was discovered that there was a highly significant genetic risk factor for Parkinson’s on chromosome 4. The region in question covers several genes (including TMEM175 – see blue arrow in image below).

The location of TMEM175 (blue arrow). Source: PMC

And this finding was supported by a second large genetics study published a few years later (Click here to read that second study). The two genetics studies found that the region of DNA where TMEM175 sits contains the third most significant association with Parkinson’s.

Interesting. What do we know about the biological function of TMEM175 and how it relates to Parkinson’s?

In 2017, an independent group of researchers published one of the first report really exploring the function of TMEM175 in the context of Parkinson’s:

Title: TMEM175 deficiency impairs lysosomal and mitochondrial function and increases α-synuclein aggregation.
Authors: Jinn S, Drolet RE, Cramer PE, Wong AH, Toolan DM, Gretzula CA, Voleti B, Vassileva G, Disa J, Tadin-Strapps M, Stone DJ.
Journal: Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2389-2394.
PMID: 28193887                  (This report is OPEN ACCESS if you would like to read it)

In this study, the investigators reported that eliminating (or reducing) TMEM175 protein in cells disrupted lysosomal function. This effect resulted in increased neuronal vulnerability to stressors, such as the aggregated form of Parkinson’s-associated alpha synuclein protein (Click here to read a previous SoPD post about this).

Their findings suggested not only that loss of TMEM175 screwed up the ability of cells to dispose of waste, but that this also made the cells more sensitive to stress.

These same researchers published a second report in 2019 that expanded on these results:

Title: Functionalization of the TMEM175 p.M393T variant as a risk factor for Parkinson disease.
Authors: Jinn S, Blauwendraat C, Toolan D, Gretzula CA, Drolet RE, Smith S, Nalls MA, Marcus J, Singleton AB, Stone DJ.
Journal: Hum Mol Genet. 2019 Oct 1;28(19):3244-3254.
PMID: 31261387                 (This report is OPEN ACCESS if you would like to read it)

In this study, the researchers dug deeper into the genetics TMEM175 and identified one genetic variant (called p.M393T) in the TMEM175 gene, which was 20 orders of magnitude more significantly associated with Parkinson’s than any other variant in the area.

The investigators then explored this particular genetic variant in models of Parkinson’s and found that while increasing levels of normal TMEM175 protein was able to reduce levels of alpha synuclein aggregation (via normal lysosomal activity), increasing levels of TMEM175 protein carrying the p.M393T variant resulted in no change in alpha synuclein aggregation.

Cells that produced the TMEM175 protein carrying the p.M393T variant were found to have reduced regulation of lysosomal acidity and reduced lysosomal activity. And these findings were supported by another publication from a separate group of researchers:

Title: Genetic, Structural, and Functional Evidence Link TMEM175 to Synucleinopathies.
Authors: Krohn L, Öztürk TN, Vanderperre B, Ouled Amar Bencheikh B, Ruskey JA, Laurent SB, Spiegelman D, Postuma RB, Arnulf I, Hu MTM, Dauvilliers Y, Högl B, Stefani A, Monaca CC, Plazzi G, Antelmi E, Ferini-Strambi L, Heidbreder A, Rudakou U, Cochen De Cock V, Young P, Wolf P, Oliva P, Zhang XK, Greenbaum L, Liong C, Gagnon JF, Desautels A, Hassin-Baer S, Montplaisir JY, Dupré N, Rouleau GA, Fon EA, Trempe JF, Lamoureux G, Alcalay RN, Gan-Or Z.
Journal: Ann Neurol. 2020 Jan;87(1):139-153.
PMID: 31658403

In this study the researchers identified two genetic variations in the TMEM175 gene that were associated with Parkinson’s: the p.M393T variation mentioned above, but also p.Q65P. Interestingly, p.M393T was also found to be associated with REM sleep behaviour disorder – a prodromal condition for PD.

When the investigators explored the function of the M393T variation, they found that it was associated with reduced GCase activity (the lysosomal enzyme that is affected in GBA-associated Parkinson’s – click here to read a previous SoPD post about this).

All of this research suggested that TMEM175 may be an important player in the biology underlying some cases of Parkinson’s. And very recently published research provides further support to this idea.

This report was published this month:

Title: Parkinson’s disease-risk protein TMEM175 is a proton-activated proton channel in lysosomes.
Authors: Hu M, Li P, Wang C, Feng X, Geng Q, Chen W, Marthi M, Zhang W, Gao C, Reid W, Swanson J, Du W, Hume RI, Xu H.
Journal: Cell. 2022 Jun 23;185(13):2292-2308.e20.
PMID: 35750034

In this study, the researchers found that at normal lysosomal acidity (pH 4.5–5.0), TMEM175 was significantly more permeable to protons than to potassium. Optimal acidity is maintained by a very dynamic equilibrium between proton inflow and outflow across the lysosomal membrane. Reducing TMEM175 in cells resulted in lysosomal hyper-acidification and dysfunction (basically the waste disposal system stopped breaking down waste). In mice with no TMEM175, the investigators observed the aggregation of α-synuclein in the brain, as well as lysosomal over-acidification and impaired lysosomal activity in neurons. 

The researchers also discovered that TMEM175 was activated by an endogenous polyunsaturated fatty acid (arachidonic acid) and two other synthetic chemicals, and by treating cells with these molecules, there was an increase in steady-state acidity which improved lysosomal function. These new discoveries led the investigators to propose that TMEM175 could be an interesting target for therapeutic intervention in Parkinson’s.

Source: Cell

Are any biotech companies exploring TMEM175 for Parkinson’s?

Yes.

Despite the research on TMEM175 only being 4-5 years old, there is already a biotech company called Caraway Therapeutics going after this area therapeutically.

Originally called Rheostat Therapeutics, this company focused on improving lysosomal function. Caraway has multiple active programs working on small molecules targeting cellular waste disposal, but their most advanced drug is targeting TMEM175.

In late 2020, Caraway Therapeutics announced that they had received a research grant from the Michael J Fox Foundation to further develop their TMEM175-activators (Source), so Parkinson’s is an area of interest for the company.

And in the middle of the COVID pandemic, in July 2021, Caraway announced that it had initiated an exclusive collaboration with the pharmaceutical company AbbVie to develop and commercialise the small molecule therapeutics that Caraway has been developing around TMEM175 (Click here to read more about this).

It is also interesting to note that most of the researchers listed as authors on the Jinn et al (2017) and Jinn et al (2019) studies mentioned above are employees of the pharmaceutical company Merck.

A large company like Merck would certainly have the resources and expertise to conduct the large screening experiments required to identify potential TMEM175-activators for Parkinson’s.

And given that Parkinson’s may not be the only condition that TMEM175-activators could be useful for, one would think that Merck would certainly be interested.

What do you mean?

TMEM175 appears to be involved with other conditions as well as Parkinson’s.

For example, last year an interesting report was published highlighting TMEM175 in the context of Lewy body dementia.

Here is the report here:

Title: Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture.
Authors: Chia R, Sabir MS, Bandres-Ciga S, Saez-Atienzar S,… (there is a VERY long list of authors in this study – to save space, I’m cutting a few out)…., Chiò A, Ross OA, Gibbs JR, Dalgard CL, Traynor BJ, Scholz SW.
Journal: Nature Genetics 2021 Feb 15. Online ahead of print.
PMID: 33589841              (A preprint manuscript of this report was made OPEN ACCESS if you would like to read it)

In this study, the researchers were interested in determining the genetic risk factors of Lewy body dementia, with the goal of better understanding the underlying biology of the condition.

They collected DNA sequencing data from 2,591 individuals with Lewy body dementia and 4,027 unaffected control cases. There analysis found 5 genetic regions where variations were associated with increased risk of Lewy body dementia.

Those 5 regions were GBA, BIN1, SNCA-AS1, APOE, and….. drum roll please, TMEM175.

Source: BioRxiv

The investigators highlight TMEM175 in the discussion of their report, noting that the “identification of TMEM175 underscores the role of lysosomal dysfunction in the pathogenesis of Lewy body diseases“.

Many of the reports highlighted in today’s post have pointed towards TMEM175 as a “targetable mechanism”. Hopefully we’ll see more research on this protein in the near future.

So what does it all mean?

Since the genetic sequencing revolution of the 1990s/2000s, we have become aware of at least 80 genetic regions associated with an increased risk of developing Parkinson’s. Most of these have only been discovered in the last 10 years and scientists have been madly trying to decipher the biological pathways related to these risk factors to gain potential insights into what could be happening in Parkinson’s.

Here at the SoPD HQ, we have been concerned for some time that too much focus in Parkinson’s research is centered on the “usual suspects” (alpha synuclein, LRRK2, GBA1, etc). Thus, we are always interested to learn about novel therapeutics being developed around new aspects of Parkinson’s-associated biology.

There is so much research going on with targeting alpha synuclein, LRRK2 and GBA1 that one could easily be left wondering if there were no other options. It is exciting to see a better understanding of the biology associated with other Parkinson’s-related proteins.

 

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2 thoughts on “The modification of acidification

  1. Through research like that focused on TMEM175, we are learning more and more about factors that can help to bring Parkinson’s on, and which thus are associated with it. And learning about these factors that are associated with disease initiation of course could shed light upon the overall mechanisms that maintain the illness and further its progression.

    But Parkinson’s is a disorder that is perpetuated by a number of interacting underlying factors. And once the syndrome has set in, correcting even 100 percent of the factors that *caused* it to occur may not prevent the illness from continuing, because other things will have happened in the course of disease progression that lock in the disease process in ways that cannot be undone by modifying its initiating factors alone.

    And unfortunately, one gets the sense that this research is keening toward the development of products for treating Parkinson’s that work on these individual factors, and not toward gaining an overall understanding of the illness, let alone toward treating the illness in ways that actually halt or reverse progression and have visible effects upon symptoms.

    So who is currently working on collecting all of this knowledge about individual factors and then forming an overall model of the illness that can be used to devise integrated treatment programs to be used by clinicians with the goal of slowing or halting progression? I am afraid that the answer is currently “nobody.” There is a lot of potentially useful information being generated, and this site is one of the few places where the patient population can become aware of it, but if it does not lead to monetization through new drug sales, I’m afraid it will be largely overlooked as irrelevant.

    So I suspect that we will one day see reports that claim efficacy for Parkinson’s of a TMEM175 activator drug by showing that TMEM175 has been increased, without any clear evidence of slower progression or improved function. Thus, a measurement thought to be *associated* with the illness is “improved,” and this is self-servingly interpreted as helpful in treating the disease. We saw this happen recently with aducanumab, which provably reduces the amyloid protein associated with Alzheimer’s, but is not provably effective for overall progression of that illness.

    I fear that the extreme orientation of research toward product development has focused that research myopically on one particular factor or another, and has defined the efficacy of treatments in ways other than their overall benefit to the patient.

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  2. I agree with this comment – very little in research and development in PD will really turn out to impact the course of the disease, and especially have a meaningful benefit in the near term on unmet symptom burden – just as in AD, FTD and every other neurodegenerative disease.
    I don’t however feel the mistake is that there is a focus on a ‘product’, just that the products being pursued almost all fail to identify what is causally associated with brain vulnerability, fail to appreciate the complexity of the brain, and are too obsessed that monogenic ‘factors’ (that are often unique to such smaller populations within many of these diseases), or deficiencies unique to single cell types. All are examples of extreme wishful thinking.
    Nature didn’t conveniently sprinkle lots of SNPs across the genome with associated arrows with footnote: ‘look here for drug targets’, and many of medicines best targets have no genetic precedent and were arrived at via serendipity coupled with an understanding of physiology, pathobiology and complex organ system biology. PD, AD, FTD etc are the result of complex, heterocellular, organ dysfunction, and only with an eye on heterocellularity will medicines arrive that can slow deterioration and offer near term benefit.
    One correction for Simon – the ‘Merck’ logo you used in this article is that of the German company Merck KGAa, based in Darmstadt, and not the same as the Merck based in US (also MSD in Rest of World), where the work mentioned in some of the cited papers was conducted.

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