Analyzing Gene Expression in Cartilage Cells for the Treatment of Osteoarthritis by Isita Tripathi

 (Image – Mosby’s Medical Dictionary, 9th edition.)

As a high school student, my preconceptions were that lab work only involved the wet-lab responsibilities of pipetting, centrifuging, and cell culture. But with hands-on lab experience, I soon realized that there is so much more that goes into a biological research project in order to make it both effective and applicable. With the intersection of biology, statistics, and computer science, the possibilities have expanded to include precise processing of information, changing the way in which we look at the human body and revolutionizing the field. Realizing that we are on the precipice of the new era of “big data,” I immersed myself in gene expression analysis as part of the biomedical research I undertook in the Lab of Orthopaedic Surgery at Stanford; I am eager to share my findings.

Almost 10% of the American population is plagued by osteoarthritis, the most common chronic degenerative condition affecting the joints.

In osteoarthritis, the cartilage that normally surrounds the ends of bones breaks down, creating increased friction between the bones in a joint, and resulting in swelling and extreme pain during movement. The problem remains that once osteoarthritis commences, the cartilage continues degenerating and inflammatory processes further damage the existing cartilage.

Unlike our skin, cartilage does not naturally regenerate and repair itself, making osteoarthritis a downward spiral of pain if left untreated. That is why an increasingly popular target of research is stem cell cartilage repair. While one option is to take neonatal chondrocytes (cartilage cells) and place them into the adult body, this form of stem cell cultivation is often considered unethical. However, if researchers can create induced pluripotent stem cells (iPSCs) and provide them with the proper transcriptional factors, cell culture, etc. to differentiate into chondrocytes in vitro, then these cells should be able to replenish the supply of damaged cartilage cells in vivo, acting as neonatal cartilage cells. Although many labs have established this procedure, nobody has perfected it to the point where the iPSCs would have sustained success in the body. The only way to do so is to gain more knowledge on exactly what makes each type of chondrocyte different from one another, and then study these variances to discover methods for improving existing forms of treatment.

With my project at Stanford, I was able to take a step towards answering this fundamental question. During the 10 weeks of my internship, I conducted a data analysis project on the microarray data from an ongoing project on chondrocyte differentiation at the lab. The goal was to denote significant differences and patterns in gene expression across neonatal, normal adult, iPSC, and osteoarthritic chondrocytes.

My first challenge was learning to use advanced gene expression softwares that I had never encountered before, such as dChip and MetaCore. And through this process, I realized there was so much more about the project that I had yet to learn, so I read as many articles as possible, scrounging for information that could help me tackle this process further.

After mastering the programs, I began making excel sheets that compared the data from different chondrocytes based off of fold change (a comparative measure) and probe set values (microarray data indicating levels of gene expression in a cell). Then, I created lists that denoted which genes were most heavily expressed in one chondrocyte, but under expressed in the other. Entering this information into a pathway analysis, I was able to visualize which kinds of genes made two chondrocytes different. To my surprise, I found that the difference between osteoarthritic and normal adult chondrocytes was that the cartilage cells plagued with osteoarthritis were actually expressing many of the genes that neonatal chondrocytes expressed. And through digging into this information, I landed on the very core problem of osteoarthritis: the remodeling of the extracellular matrix.

Essentially, each chondrocyte is in its own microenvironment that facilitates cell signaling and proper nourishment of the cells. As the cartilage begins to degenerate, inflammatory processes are a signal to the cell that something is wrong. In order to combat this issue, the chondrocyte begins changing the components of its extracellular matrix, the barrier that separates the cell from the outside environment. However, this changes the microenvironment within the cell, exacerbating the condition instead of helping. Perhaps suppressing the expression of some of the key genes involved in ECM remodeling, such as MMP2, would allow the cell to revert back to its original microenvironment, and even “reverse” osteoarthritis.

Although I thought I had found something original, my mentor informed me that this has been a target of research for quite some time–but nobody has been able to control or change ECM remodeling effectively. Still, I refused to be discouraged. With some more digging, I found that one of the genes highly expressed in osteoarthritic chondrocytes was a gene that was supposed to be suppressed completely 6 weeks after birth. And the only information about this gene is that it codes for opioid receptors, which manage pain perception in the brain.

Many studies had published this up-regulation of the “PENK” gene, yet none had actually explored its potential. But maybe the key was not reversing ECM remodeling or even trying to replenish damaged cartilage. I figured that the first step was to control pain and the progression of remodeling. After compiling all of the information I could find on PENK, I suggested that its high expression levels could be utilized as an internal mechanism for pain relief in osteoarthritic patients if the gene was expressed in the iPSC chondrocytes. Or maybe removing this gene would help cease ECM remodeling, prohibiting further cartilage degeneration.

While I had initially set out to make a revolutionary discovery in the field of osteoarthritis, I instead generated new ideas on how to tackle the problem, becoming proficient in terms and ideas that had never existed until the beginning of my summer. As I approach the next four years, I hope to continue my work on osteoarthritis and develop projects that can morph my the research proposals I made using microarray data into positive action.

But one of the most important things I learned throughout last summer was that past the contentment associated with making concrete discoveries, research provides the opportunity to expand the creative capacity of our minds, pushing us to think and plan in novel ways. Even after finding information there is always more to uncover, because regardless of your level of education or social status, research thrives on one leveling commonality. Everyone must keep exploring; there is always more to find.

Isita Tripathi is a senior at a Bay Area High School. She worked as a student intern in the Lab of Orthopaedic Surgery at Stanford, where she has cultivated her passion for medical research. In addition to pursuing a career as a surgeon, Isita aspires to continue performing her flute and learning Spanish during her college years.

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A For-Profit for Nonprofits: Can It Work? By Evelyn Horng

Evelyn Horng picI have always been interested in social causes.  In college, I majored in public policy, and I interned one summer for a nonprofit that organizes done-in-a-day projects for busy people who can’t commit to long term volunteer opportunities.  I also volunteered quite a bit myself – helping to build homes for low income people, pulling out non-native vegetation (aka weeding!), sorting food at a food bank.….

My senior year in college, the obvious set in.  You just don’t make as much money working in nonprofit as you do in the for-profit world.  I envisioned the kind of life I wanted for myself, and the type of funds that would be needed to support it.  And while I never imagined a lavish lifestyle, I just didn’t want to struggle to buy a home in Silicon Valley, or worry about covering all my expenses.

So I entered the corporate world, doing a two-year stint in strategy consulting and then moving on to high tech product management, and climbing the professional ladder.  By the time the kids came around, I started re-thinking how I wanted to spend my time.  I wasn’t quite satisfied in my last job, and I was looking for more….

More personal fulfillment,
More flexible work situation,
More control over what I was doing….

So a co-worker and I started a company called Roonga (  Its original goal was to encourage people to share things with their friends and trusted groups.  In doing so, we’d encourage reuse, reduce waste, and help our communities be more sustainable.  But smaller trusted circles made it harder to get rid of things you no longer need, and people didn’t always have the things that you need in these tighter networks.  So recently, we’ve redirected Roonga to work with nonprofits, providing a platform for nonprofits to communicate in-kind needs and building an audience of followers specifically interested in hearing about these.

With the latest turn that Roonga has taken, I feel like I’ve come full circle back to where I started.  We are working with nonprofits to improve the efficiency of their in-kind donations, and to support their causes by opening up their audience.  In the process, I am learning a lot about the local causes in Silicon Valley, and I am having a great time doing this!

However, it remains to be seen whether we can build a successful for-profit company working with nonprofits.  Roonga is a for-profit company – we like the potential of allowing employees to benefit from the company’s success, and we feel it is important to reward talent at competitive for-profit rates.  And for me, I like the self-fulfillment of working for a nonprofit cause, while also still retaining the for-profit mindset.  I’d like to think that we can take the best of both worlds and meld them into Roonga – but we are only at the beginning of our journey and still have a long way to go…..  The future is ahead of us, and we’ll have to see where we end up.

In the meantime, take a look at our nonprofit beta, follow one of our local nonprofits (, and let me know what you think!  Email me at with any thoughts, suggestions, or feedback.

ABOUT THE AUTHOR:  Evelyn Horng is the co-founder of Roonga, a Silicon Valley startup.  She was previously VP, Product Management, at MLSListings, Inc., and held other product management positions in various high tech companies.  She has a B.A. in Public Policy from Stanford University.  She spends most of her spare time trying to keep up with her two young sons.

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