Retinoblastoma Treatment: Past, Present and Future

A blog post that I wrote for the Canadian Retinoblastoma blog. See below for link to original article.

As a 35-year-old patient who was treated for retinoblastoma that many years ago, I am curious how retinoblastoma treatment has changed over the years? I had bilateral retinoblastoma, and one of my eyes was removed; in the other, I had xenon arc (an older type of laser) therapy and cryotherapy. At that time, external beam radiation and radioactive patches were also common retinoblastoma treatments. I know that these therapies have been fine-tuned since then, but I don’t know much more than that. To answer my questions, I sat down with Dr. Brenda Gallie to talk about how care has changed over the years, and what future directions may look like.

Me: How has the field of retinoblastoma changed over the last 30 or so years?

Dr. Gallie: The field of retinoblastoma has changed a lot. Now it is totally feasible for all 8000 children who have retinoblastoma in the world to live, and DePICT is one of the tools at the center of this possibility. Retinoblastoma could be a zero-death cancer in the next ten years. DePICT is a digital tool where all patient information, including all treatments, can be archived, and patients have the ability to access it. DePICT also provides tremendous opportunity for research, as it will preserve a lot of information that is lost in the current patient record system.

Major developments in retinoblastoma treatment include intra-arterial chemotherapy (chemotherapy delivered to the eye via ophthalmic artery) and intra-vitreal chemotherapy (injection of chemotherapy into the eye) in 2010 and 2011, as well as removal of the tumor and vitreous from inside the eye (2017). These new therapies are changing how eyes are treated, and the DePICTRB database will allow clinicians and researchers to assess if the treatments are better or worse, how they are better, and for which patients they are appropriate.

In addition, a new staging system for retinoblastoma (TNMH stage vs the Murphree A-E classification) was developed from outcome data on 1,728 eyes in 13 countries, to help all doctors ‘speak the same language’ about retinoblastoma and compare patients across centres.

A child now diagnosed with:

1. T3 eye: eye must come out

2. T1a eye: treat with laser, cryotherapy

3. T1b eye: treat with chemotherapy then laser, cryotherapy

4. T2a eye (retinal detachment with no seeding): treat with chemotherapy then laser, cryotherapy

5. T2b eye (any subretinal or vitreous seeding): treat first with chemotherapy, then injection of chemotherapy directly into the vitreous, and the new idea to surgically remove the tumor in some eyes when other treatments fail. We think that vitreous seeds may be easier to treat than subretinal seeds, and we will know once we have complete data in the DePICTRB

Intra-arterial chemotherapy in particular has swept the world without evidence of outcomes. It definitely has an important role, and we look forward to full data on the outcomes of all children who receive intra-arterial chemotherapy, so we can know which children it serves well and which children do better with systemic chemotherapy.

Me: How much involvement do patients usually have in treatment decisions for their kids?

Dr. Gallie: Each treatment is a discussion, and every treatment is agreed to by the parents of patients. What clinicians need to do better is showing the parents the outcomes of each choice, for example how far to go to save a blind and dangerous eye.

Me: Where is the best place for patients and families to go to get information about treatment?

Dr. Gallie: World Eye Cancer Hope, which can be found here: https://wechope.org.

As a patient, I feel invested in the implementation of DePICT, Dr. Gallie’s passion project, perhaps for the same reasons as she is. I was treated 35 years ago, and since then I have moved many times, with my family, to go away to school, and now for work. Over all those moves, so much information about my treatment has been lost – well, it could be found, but it is locked in clinic basements in files, and nobody wants to go look for it. All I have is a series of letters. DePICT will allow for continuity of care, and for data about treatment and follow up to be retained so easily. As a patient, I also value the possibility that it will allow easy discussion among physicians about treatment in cases where collaboration on care would be beneficial. And lastly, as a patient, I think it would be beneficial for researchers to have comprehensive data for retrospective studies. For example, Dr. Gallie spoke of how intra-arterial chemotherapy has swept the world as a treatment without evidence that it is better. DePICT can provide the data to test that. Other examples of retrospective studies are: a lot is not yet understood about why second cancers arise, whether there may be particular RB1 mutations that predispose to second cancers, or what types of consequences arise from specific treatments. DePICT holds promise to facilitate all of this.

A link to the original publication of this article can be found here

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Posted in Retinoblastoma | Tagged , ,

Disability accommodation in academia – what can be expected?

A blog post that I wrote for the Quebec Center for Biodiversity Science’s Le Beagle. See below for a link to the post on Le Beagle.

The self-serving question that I would like an answer to is: “what should disability accommodation encompass in academia”? Or, for me more specifically, how can the added time that my visual impairment takes be accommodated – the time that it takes to figure out which accommodations might be best, the time to implement and trouble-shoot those accommodations, and the time to accommodate the fact that I read more slowly due to being visually impaired? These questions surrounding added time nag at me most days as I chip away at my postdoc, trying to get old PhD papers out while simultaneously producing new work and aiming to get that out as quickly as possible, because in this line of work, papers are currency. I am a postdoc at Concordia University in Montreal working on conservation genomics of fishes, and I would really like to be able to continue in science. I worry though about my ability to perform as quickly as is needed to be competitive.

To my knowledge there are no answers to my questions. There is no answer to just how much time the added tasks of sorting out my accommodations take, or how much more slowly I read (making there no absolute number that I can give HR professionals and the like). There is also no answer to how postdocs or new professors should be accommodated by universities – myself and a group of others tried to put together national postdoc accommodation guidelines, but the project failed after our first rejection and we had no more time to invest in it.

There are many accommodations available throughout the educational pathway, all the way from elementary to graduate school, and I used many of these. There are also many resources for accommodation in the workplace. A quick google search for “accommodating disability in the workplace” brings up a host of hits. And there are many people who have disabilities that graduate with PhDs. A relatively recent study by the National Science Foundation shows that hundreds of people who have disabilities graduate with PhDs, and are employed (although these numbers are fewer than those who do not have disabilities). Papers are being written about how to make scientific information accessible, and a book has been written about how to create a culture of accessibility in the sciences.

And yet, I never disclose my disability when I am applying for a postdoc or job for fear of discrimination (a well documented trend, see here), and after graduate school, no grant that I have applied for has provided any space for me to discuss any challenges that I have that may reduce my output. There are several visually impaired scientists in North America (see here for most of them, and I know of a few others), and several of these individuals shared my sentiments. Each have some sort of solution (e.g., extended time to get tenure, needing to read much less once established in the field). However, I found no well-established solutions. I believe that with increased attention to disability and diversity in STEM, the types of questions for which I am searching solutions will be more and more common. In addition, my questions are not only relevant to science, as can be seen in this excellent article written by a CBC staffer who is visually impaired. If you, the reader, have suggestions, I would be glad to receive them.


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Ella Bowles at Meshik Lake, Aniakchak National Monument, AK. One of many PhD field sites. Ella Bowles is a postdoc at Concordia, working with Dylan Fraser and the Cree Nation of Mistissini on community-based fisheries monitoring. She is interested in conservation, and has worked primarily with fish and in the north. Ella did her PhD (evolutionary genomics) with Sean Rogers at the University of Calgary, and her MSc (molecular ecology) with Andrew Trites and Trish Schulte at UBC. Find out more about her work and interests hereellabowlesphd.wordpress.com.

 

Link to original article here

Posted in Visual Impairment in Science | 1 Comment

STEM SIGHTS: The Concordian who investigates species conservation with the Cree community

An article about my current fisheries monitoring work with the Cree Nation of Mistissini and Niskamoon Corporation.
Postdoctoral researcher Ella Bowles brings genomics to a collaborative fishery project
Posted on September 19, 2017
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By: Kenneth Gibson
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Mistassini Lake
, a remote place about 800 kilometers north of Montreal, is sometimes referred to as “fly-in” country by those who visit it for the fishing tourism that has boomed there in the last 15 years.

For centuries, the Cree Nation of Mistissini has harvested the lake’s fish populations for subsistence, and they currently manage its fishing tourism. The community is keenly interested in the conservation of these fisheries.

Ella Bowles, a postdoctoral researcher working with Dylan Fraser’s lab in the Department of Biology at Concordia, studies conservation genomics in fish. Her research seeks to understand how harvesting fish impacts these populations on a genetic level, which in turn would help to inform sustainable harvesting practices.

A statistically significant reduction in both the length and mass of walleye populations living in Mistassini Lake occurred during the rise of the fishing tourism industry in the region. Bowles’ postdoctoral work is determining whether there has been an associated reduction in genetic diversity among these populations.

She is using knowledge gleaned from her research to collaborate with the Cree Nation of Mistissini in its goal of resource conservation. Integrating scientific information with traditional ecological knowledge (TEK), she hopes to facilitate a comprehensive, community-based approach to population management.


‘The goal is to ensure the fish stocks are available for generations to come’


How does this specific image (top) relate to your research at Concordia? 

In this photo, I am extracting DNA that I will later sequence to generate thousands of single nucleotide polymorphisms (SNPs).

An SNP is a unit of information that I use to make inferences about the fish populations I am studying. I can determine things like how many populations or genetically distinct groups there are and whether populations have evolved and changed over time.

I can also see what parts of the genome might be driving that change, whether populations may be under selection within the genome, ​how much interbreeding is occurring between populations and — depending on the type of fish I am investigating and how much we know about them — information as precise as a fish’s river of origin.

What is the hoped-for result of your project?

To arrive at a clear understanding as to whether or not there have been any changes over time in the populations of a number of fish species that are both harvested for subsistence and fished recreationally in Mistassini Lake. Last year I worked only on walleye, but in the coming two years I’ll also be working on lake trout, brook trout and northern pike. ​

What impact could you see it having on people’s lives?

All of the work that we are doing on this project is either for, or in collaboration with, the Cree Nation of Mistissini. They use this information to guide the management and harvesting of certain fish species within Mistassini Lake. This is with the intention of maintaining stocks to ensure that the resource is available for generations to come.

What are some of the major challenges you face in your research?

A major challenge for my work is how rapidly the methodology changes, both in the molecular lab and at the analysis stage. For example, when I began grad school 10 years ago, most labs used between one and two dozen microsatellite markers. These are the locations in an organism’s genome that provide information about evolutionary processes that shaped their geographic distribution.

Now, the norm is to use thousands of markers distributed throughout a given genome. This means that biologists have to rely increasingly on computer programming to navigate the data. The software used for this kind of analysis is always changing, so it is an added difficulty to be constantly learning new programs, both in terms of publishing before work becomes dated and the amount of information you must retain.

What are some of the key areas where your work could be applied?

It applies directly to resource conservation. My particular research project is important to the Cree Nation of Mistissini but more broadly I am using both scientific knowledge and TEK to study the fish species in the area. The use of interdisciplinary methods for resource conservation is growing, but much more is needed.

My methods and the way that I interpret and apply the results may therefore be able to serve as a blueprint for others who would like to use TEK to complement their scientific methods, such as wildlife managers.

What person, experience or moment in time first inspired you to study this subject and get involved in the field?

I have been interested in environmental issues since I was very young, perhaps influenced by my “concerned citizen” parents. But also, my bachelor of science degree at the University of British Columbia used an evolutionary framework, which I particularly enjoyed.

During and after my undergraduate education I was also involved in molecular cancer research. I really enjoyed this work and it introduced me to the power of molecular biology as a tool.

While taking a biology of marine fishes course at the Bamfield Marine Sciences Centre, I became enchanted with the biodiversity of fish. I was simultaneously shocked by the state and trajectory of our fisheries and struck by the understanding that molecular tools could bring to these problems. That was really the start of my current path.

How can interested STEM students get involved in this line of research? What advice would you give them?

Volunteer! The best advice that I have for students is to read about some of the researchers at their institution (or other institutions) and contact them about opportunities to volunteer or work in their labs. Paid work is ideal, of course, but any contact with research will give you a feel for whether you like it or not and what kind of work you enjoy most.

What do you like best about being at Concordia?

There are two things that make being at Concordia truly great.

First, my supervisor and lab are a wealth of knowledge, often about things that are relatively new to me and complementary to my work. My colleagues are quite generous with their time as well, which has resulted in productive collaborations.

Second, I am grateful to have full access to the GradProSkills workshops as a postdoc. I have taken several courses, including on grammar, project management, literature review and French conversation. They have all been excellent, both in content and presentation.

Are there any partners, agencies or other funding/support attached to your research?

Yes! I am grateful to have recently been awarded a Mitacs Elevate fellowship. This is a collaborative project between Concordia, Mitacs and Niskamoon Corporation, who are funding a majority of the work. Niskamoon is a not-for-profit agency that facilitates work between the Cree people and Hydro-Quebec.

They support multiple environmental and cultural projects that encourage sustainable resource use and autonomy for the Cree people. My work helps with all of those things, so it fit nicely within their mandate. Being able to engage in on-the-ground conservation through this fellowship is the realization of my dream.

Original publication can be found here

 

Posted in Conservation, life history, genomics and traditional ecological knowledge, Research

Visually impaired biology graduate leaves lasting impression

A piece written on my PhD, published in UToday at the U of Calgary

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Ella Bowles is one of only a handful of legally blind students in Canada to earn a science PhD
November 8, 2016

Ready to sample stickleback in Meshik Lake, Aniakchak National Preserve, Alaska. Photo courtesy Ella Bowles

Ready to sample stickleback in Meshik Lake, Aniakchak National Preserve, Alaska. Photo courtesy Ella Bowles

For the last six years, you could find new PhD graduate Ella Bowles plumbing the icy depths of lakes in Alaska’s grizzly-dense Katmai National Park, mapping fish genetics in the lab, and persuasively advocating for reasonable accommodations for students like her with disabilities.

The one place the legally blind and very determined Bowles seems never to have been is on the path of least resistance.

Bowles — who was diagnosed with retinoblastoma as a child — is one of only a handful of Canadians with a visual impairment ever to have earned a PhD in science. “I know of one applied molecular oncology graduate, a physics graduate, and someone in actuarial sciences,” Bowles says. “But, yes, it’s very unusual.”

It’s rare, because it’s tough. It’s hard enough to earn a PhD, but to overcome the challenges of a visual impairment takes incredible dedication, time, and some additional resources. “It’s really difficult. In fact there were several times I just really wanted to quit,” Bowles says.

Instead, she recruited a support team drawn together by her positive outlook and clarity of purpose. Among others, that team included her adviser Sean Rogers, an associate professor in biological sciences; Lawrence Harder, PhD committee member; Lisa Young, dean and vice-provost of Graduate Studies; and Student Accessibility Services.

Rewriting the rules

Bowles knew she’d need some specialized equipment like magnifying lamps, a monitor, and some software to read PDF files. The trick was to find the funding.

Not content to find one-off solutions that merely met her own needs — which would have been relatively straight forward — Bowles set about addressing the system of accommodations for all graduate students so that others could benefit down the road.

“There was no real precedent, and it took 19 months going around in circles and circles and circles,” Bowles says. Once she brought her requests forward to Young, Bowles says everything fell in to place.

“To graduate from a program after six years and be filled with gratitude is a win-win, and definitely a credit to Dr. Young, to Sean, and to everyone at the University of Calgary who stood behind me,” Bowles says.

Accustomed to rationalizing the extra time and money it can require to accommodate students with disabilities, Bowles’ response is: why not? “Most accommodations don’t cost a lot of money,” she says. “Give us the equivalent of a pen, a desk and a computer, and we can be equally capable. Why not let people with a disability reach their potential, and along the way create contributing members of society?”

Flying in for fish field work

An NSERC recipient and a Garfield Weston Doctoral award winner, Bowles’ PhD research involved studying the distribution of threespine stickleback fish in Katmai National Park in Alaska to learn more about adaptation in aquatic environments using conservation genetics.

The fact that Bowles headed out to the field clearly impresses those she worked most closely with.

“You might think someone facing vision issues like Ella’s would choose to do a lab study,” says Harder, professor in the Department of Biology. “Instead, she goes out and collects fish in Alaska! Not for the faint of heart, even if you’re fully visually capable.”

The field work meant hiring a part-time assistant and taking float planes to relatively remote locations over three summers. It meant venturing into grizzly country. And it even resulted in Bowles learning how to shoot a gun — though she wasn’t allowed to use it.

“Ella is the kind of ecologist we hope we are training here: one that can go out in the field, and also come back in the lab,” Rogers says. “The challenge from my perspective, as her supervisor, was to figure out how to accommodate Ella and at the same time ensure she remains competitive with others in her field. And I think we’ve accomplished that.”

Now a postdoc at Concordia, Bowles is continuing to blaze a trail and apply her knowledge.

As Rogers says: “That’s Ella. She’ll make a difference wherever she goes.”

Advice to students

Cultivate your network: Sounds cheesy, Bowles says, but it’s true. It’s the friendships and support system that will allow you to do meaningful, enjoyable work into the future.

Use the time in graduate school to develop the skills that are critical long term. For example, Bowles says bioinformatics is critical in her work, skills that would be hard to develop after graduate school.

It’s never too early to think about the kind of work you want eventually to do: having a long term goal helps keep you motivated day-to-day in your PhD program.

The original piece can be found here.

Posted in Visual Impairment in Science

Moving on, I’m now a Post-Doc at Concordia University in Montreal

IMG_9082 (1)

Me, with PhD advisor Sean Rogers, after my defense on April 15, 2016

A quick post to say that I have moved on! I defended my PhD on April 15 (hooray) and started a Post-Doc in Dylan Fraser’s lab at Concordia in June. Holy smokes that was a fast-turn-around. I have spent the last few months finishing projects, archiving samples and wrapping up in Calgary, and then moving and starting a new position here in Montreal. I’m both excited and nervous about the next steps! Mostly, I’m excited that my work here at Concordia will be an application of what I have done before. I will be genomics and evolutionary biology to conservation questions. More on all of this to come.

Posted in Conservation, genomics, life history and traditional ecological knowledge, Conservation, life history, genomics and traditional ecological knowledge, Research

Why I’m here, my story

Over the years, many people have asked me how I got here –that is, to my PhD, and I have wondered the same about others. So, I thought I would share my story, in the off chance that any of you are interested.

As you probably already know, I’m currently a PhD candidate in Biological Sciences at the University of Calgary. But what you may not know is that I’m also visually impaired, and because of this am involved in advocacy work for university students with disabilities and surrounding visual impairment and science.

My path to pursue academic research actually began with my advocacy work as a visually-impaired undergraduate science student at University of British Columbia, and because of my participation in the retinoblastoma community (retinoblastoma is the disease of the eye that I was diagnosed with as a baby). I was asked to give the keynote address at a National Retinoblastoma Society meeting, where I spoke with Dr. Brenda Gallie, a world renowned researcher in the field. I asked her if I could do summer work in her lab; I spent two summers and a fall in Toronto working at the University Health Network/University of Toronto. Her acceptance of my request changed the direction of my life. With employment in her lab my foray into molecular biology and a career in research began.

I had a long-standing interest in environmental biology, and my undergraduate had been largely focused on evolution and ecology. Between summers in Toronto, while back at UBC, I wanted to explore these interests in a more comprehensive way, and took an intensive Biology of Fishes field course at the Bamfield Marine Science Centre. While I was there, I read an paper on collapsing fisheries stocks that shifted my interest in research to the environment, but that also made me realize how I could use molecular biology as a powerful tool to address environmental concerns.

Since then, the time between then and now has been a matter of developing skills that would allow me to bridge molecular and environmental biology. This began with an internship working on a salmon enhancement research project at the Alaska SeaLife Center in Seward, Alaska, work at the Vancouver Aquarium, my MSc in molecular ecology at UBC, and finally my PhD here at the University of Calgary. And that is where I am at today.

Although my work and interests in Biology have changed over the years, advocacy has been a constant throughout my journey. You can read about some of this on the “visual impairment and science” page of this site.

Posted in Research, Visual Impairment in Science | 1 Comment

My field work, a brief tour in pictures

During the first three years of my PhD, I had the privilege of spending anywhere from six to thirteen weeks of a summer in Alaska conducting the field work for my project. I’m stuyding the impacts of migration on divergence of the Threespine stickleback (Gasterosteus aculeatus). To do this I collaborated with the US National Park Service, and am very lucky that I stumbled on the opportunity to work with them. The following pictures show some of my journey to find and study the stickleback.

This is a map of Katmai National Park and Preserve, where I spent most of my time.

Katmai National Park and Preserve

Katmai National Park and Preserve

We packed up to load the plane.

Stevi and Ella in King Salmon, heading down to the dock to load the plane. 2011.

Stevi and Ella in King Salmon, heading down to the dock to load the plane, 2011.

The plane that took us to most of my sites.

In the slip on the Naknek River, at King Salmon, Alaska

In the slip on the Naknek River, at King Salmon, Alaska.

We sampled fish using minnow traps and seines in many places.

Some of the 2010 field crew at JoJo lakes, Alaska. Bob, Matthew and Kyle.

Some of the 2010 field crew at JoJo Lake, Scott, Matthew and Kyle.

Inspecting our catch for kokanee, stickleback and any other critters. Matthew, Scott, Me, Bob, Kyle. 2010.

Inspecting our catch for Kokanee, stickleback and any other critters. Matthew, Scott, Bob, Kyle and me, 2010. Photo: Rowan Barrett.

Traps at JoJo Lake

Traps at JoJo Lake.

The stickleback can be plentiful.

The stickleback can be plentiful.

And then we processed our samples.

Sampling fish next to JoJo Lake in Katmai National Park, Alaska

Fin-clipping and preserving fish next to JoJo Lake, 2012.

Most of our pictures were taken when the weather was perfect, but the bulk of the days it wasn’t. With very patchy radio contact, we waited for our flight for 8 hours one day in the rain and the wind.

Perhaps four hours into our wait...Nonvianuk Lake, 2011.

Perhaps four hours into our wait. Nonvianuk Lake, 2011.

Katmai is known for it's bugs.

Katmai is known for its bugs.

Just emphasizing that point a little further.

Just emphasizing that point further.

But, I can’t complain, we got to see some pretty amazing places.

Tundra, King Salmon, Alaska.

Tundra, King Salmon, Alaska.

Valley of 10 000 smokes, the valley of ash created in the wait of Novarupta.

Valley of 10 000 smokes, the valley of ash created in the wake of Novarupta.

From the ridge between two lakes, looking down at JoJo Lake. Kyle and me. 2011.

From the ridge between two lakes, looking down at JoJo Lake. Kyle and me, 2011.

Naknek Lake, from Dumpling mountain. 2011

Naknek Lake, from Dumpling mountain, 2011.

Bay of Islands, Naknek Lake. 2012.

Bay of Islands, Naknek Lake, 2012.

Fure's cabin. The trapper who settled here over 100 yrs ago. Where people stay at the Bay of Islands.

Fure’s cabin, where people stay at the Bay of Islands. Fure was the trapper who settled and built this special cabin there over 100 yrs ago.

Our small camp on an island in in the eastern part of Kukaklek Lake in the north of the park. 2012.

Our small camp on an island in the eastern part of Kukaklek Lake in the north of the park, 2012.

Swikshak, on the Pacific coast. 2012.

Swikshak, on Shelikoff strait, Pacific coast, 2012.

Swikshak, along the Pacific Coast, across from Kodiak Island.

Swikshak, 2012.

Meshik Lake, Aniakchak National Monument, about half-way down the Alaska peninsula.

Meshik Lake, Aniakchak National Monument, about half-way down the Alaska peninsula, 2012.

And we got to see spectacular flora and fauna.

Threespine stickleback, Lake Camp, Naknek Lake, 2011.

Threespine stickleback, Lake Camp, Naknek Lake, 2011.

Bob, an infamous fisherman, with his beloved King Salmon.

Bob, a famous fisherman, with his beloved King Salmon, 2011.

At Brooks falls

At Brooks falls, 2010.

bear meets moose

bear meets moose, 2011.

pretty

pretty

more pretty

more pretty

and some more....

and some more….

King Salmon, our base, is a fishing community. The population swells in the summer with salmon fisheries.

Cannery lodging.

Cannery lodging.

And I am learning, ever so slowly, how to fish.

My first silver (Coho) salmon. 2012.

My first silver (Coho) salmon, 2012.

I am one very lucky student!

Posted in Processes that shape biodiversity, Research