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  • Alex Cloherty

Recycling HIV

Updated: Mar 3, 2021

Da da da daaaaaaa! Hear Ye, Hear Ye! I can finally tell you the details about what I've been working on in the lab for the last 3 years… Because my work has been published.

I started this project in January 2018, as I wrote about here, so it's been a long time in the making. Last week, on February 26, 2021, our manuscript entitled, "Autophagy-enhancing drugs limit mucosal HIV-1 acquisition and suppress viral replication ex vivo" was published in a peer-reviewed scientific journal.

Yes, I know, it's a long title. Let's unpack it.

We'll start with that first phrase: "Autophagy enhancing drugs". To understand what that means, first you have to know what autophagy is. Well, autophagy is my favourite cellular pathway. I'm a bit of a hippie at heart, so I try to live by a phrase that my Mum often used as I was growing up: "Use it up, wear it out, make it do, or do without". It makes me happy to know that my cells are doing the same: via the pathway of autophagy.

As I've written about before, autophagy is the recycling pathway of the cell. It is an ongoing process, always in motion. Autophagy starts with the formation of structures inside your cells, which can enclose not only worn out proteins from your own cell, but also dangerous microbial invaders that have entered the cell and must be dealt with. These balloon-like structures are called autophagosomes, and they don't stop at enclosing the worn out cellular proteins or microbial invaders. After enveloping their cargo, autophagosomes acidify, which basically digests everything inside, like a stomach digesting food.

The research focus of the group that I am part of at the Amsterdam UMC focuses on the role of autophagy in immunity. All of us within the group look at different aspects of this larger umbrella topic, and for the few last years I have been focusing specifically on how we can turn up the dial on autophagy, in order to super-drive the digestion of dangerous viral invaders.

One way that we can boost autophagy is via drug treatment. There are many existing drugs that modulate the autophagy pathway, so we picked out a dozen or so of those options that were already approved by the US Food & Drug Administration (FDA) for treating conditions like epilepsy and cancer. Why did we do that? If drugs are FDA-approved, it means that they have already been determined to be safe for use in humans. Thereby, although we planned to repurpose these autophagy-enhancing drugs for use in viral infections, we already knew that those drugs were considered safe for medical use. So, in other words, if we found that these drugs could be repurposed as antivirals, we would also already know that they could be safely used by humans at proper dosages, and that the time necessary to actually move from our antiviral research in the lab to real use of the drugs in medicine would be reduced - because the long-term trials to assess safety of the drugs in humans have already been done.

So, that covers the first phrase: Autophagy-enhancing drugs. Let's jump to that Latin phrase at the end of the title, "Autophagy-enhancing drugs limit mucosal HIV-1 acquisition and suppress viral replication ex vivo", now.

"Ex vivo" literally means "out of the living" in Latin. In biology, we take this to refer to experiments that use tissue taken out from an organism, and in which we try to mimic the environment that that tissue would have "in vivo" (in the living, i.e. when that tissue was still part of the whole organism) as closely as possible. In my case, our ex vivo model involved human skin.

We are lucky enough to have excess skin after cosmetic surgery donated to the hospital. This really means that we get sort of chunks of skin that would otherwise simply be thrown away. Without this donated skin, our experiments would have to be done in much less life-like conditions. It is also a possibility to do experiments this way, but it leaves questions like, "Is this really how it works in a human?" Using donated skin gives us much more confidence that what we are finding is real - that what we see is really how things work in the natural world. It's kind of like building a model of a skyscraper with lego, versus building a model of a skyscraper with miniaturized building materials. Neither is the real deal skyscraper, but the latter (i.e. the donated skin) is much more realistic.

Also, if you're wondering, "Why skin?" the cells in skin are remarkably similar to cells in genital and intestinal tissues - which are major points of entry into the human body for HIV, either through sexual contact or mother-to-child transmission via breastfeeding - which makes it all the more realistic. We also make use of genital and intestinal tissues, but as you might imagine, those are donated less often and in smaller quantities. So we work with what we've got.

Now we get to the complicated middle bit of the title. "Autophagy-enhancing drugs limit mucosal HIV-1 acquisition and suppress viral replication ex vivo". To explain to you what that means, I want to tell you exactly what I did in the lab. Here's a picture of it:

First, once I had these slabs of excess skin, I punched biopsies in it using a specialized instrument co-developed by my supervisor, Carla Ribeiro. This punch-biopsy instrument cuts short cylinders of tissue that we can more easily work with. From there, I "cultured" the skin biopsies, or in other words, gave them everything they needed to stay alive for a week or so. In concrete terms, I put the skin biopsies in a 24-well plate, which is basically 24 mini-petri dishes all stuck together, and "fed" them with a liquid designed to supply the skin with all of the nutrients necessary for its short-term survival. From there, I could run tests on the skin with different autophagy-enhancing drugs. Put simply, I would either treat the skin first with drugs, and then infect with HIV (a prophylactic model, to mimic preventative treatment) or first infect the skin with HIV, and then treat with drugs (a therapeutic model, mimicking post-infection treatment). Then, after waiting a bit to give the virus enough time to infect the skin cells, I would simply check how many cells were infected.

To make a long story short, I found that yes, indeed, these autophagy-enhancing drugs were able to both prevent HIV-1 infection of the skin cells in the pre-infection treatment model, and put the brakes on ongoing HIV-1 infection in the post-infection treatment model. And, although the cells in skin are remarkably similar to cells in normal tissues where HIV-1 gains access to human bodies (e.g. genital and intestinal tissues) as I mentioned above, we also checked if indeed these drugs were effective in vaginal and intestinal cells. And yep, they were.

Why is this important? Well, although we often think of HIV-1 as a pandemic of the 80s, it is still a major issue today. Every single day, 4600 people are newly infected with HIV, and there are 38 million people living with the virus. Currently, we have no cure for it, and prophylaxis isn't always available or effective for everybody. So, adding extra weapons to our armoury in defense against HIV is definitely a socially, as well as scientifically, relevant question. What is particularly cool about our manuscript, is that we not only show that repurposing clinically-approved autophagy drugs is a relevant strategy for combating HIV, but by developing this skin model for screening potential antiviral drugs, we have laid out an experimental procedure to test additional drugs against not only HIV, but also other viruses. And that is precisely what we're on to next. Stay tuned to see future research out of our lab that identifies new antivirals!

Until next time,

Stay safe and stay hopeful!

~ Alex

Some acknowledgements:

  1. Science is teamwork. The whole author list on this paper is: Alexandra P M Cloherty, Nienke H van Teijlingen, Tracy-Jane T H D Eisden, John L van Hamme, Anusca G Rader, Teunis B H Geijtenbeek, Renée R C E Schreurs, Carla M S Ribeiro

  2. Diagram created with

68 views2 comments


Mar 06, 2021

Congratulations Alex! Your work sounds fascinating and very stimulating,

(if a little complex!). Most people have little idea about the real practice of bio-medicine, thanks for helping pull back the curtain. Cheers, michael.

Alex Cloherty
Alex Cloherty
Mar 08, 2021
Replying to

Thank you Michael! I hope it was still understandable! Cheers, Alex

Can't get enough? I can fix that.
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