We began our group during the 2022 Hack4NF event hosted by Children's Tumor Foundation.  By this time, DMV Petri Dish grew to involve both bioscientists and data professionals. We brought together 15 science and tech professionals to work towards producing proposed solutions to help the Children's Tumor Foundation make progress towards finding solutions to help advance the research in Neurofibromatosis forward. 

At the end of the hackathon, we were declared winners of the hackathon and were given a small monetary reward and extended mentorship support to help support our research. After a year of work, we published a paper that can be found at the bottom of this page in the "key paper to read deeper" section.

Today, we continue our work for a variety of reasons as stated on the home page.

Neurofibromatosis is a genetic disorder that causes tumors to form throughout the body. It is progressive and is one of the most common genetic diseases in the United States. Although neurofibromatosis is not a cancer, some forms of NF can be associated with certain malignancies. Neurofibromas and schwannomas are two common tumor types that can result from neurofibromatosis.

Neurofibromatosis encompasses three distinct disorders: neurofibromatosis type 1 (NF1), neurofibromatosis type 2 (NF2) and schwannomatosis. Each type is characterized by tumors along the peripheral nerves, and symptoms that are different for each disorder.

• Neurofibromas, most often seen in patients with NF1, appear as multiple, rubbery lumps on or under the skin. They may be painful or itchy, but many do not cause any other symptoms.

• Vestibular schwannomas are most common in patients with NF2. These tumors affect the nerves of the inner ear and disrupt hearing and balance.

• Schwannomatosis is associated with painful tumors called schwannomas that can cause pain, tingling and weakness.

Treatments are available to manage neurofibromatosis symptoms, but a cure is not available.

Sources:

https://www.hopkinsmedicine.org/health/conditions-and-diseases/neurofibromatosis

https://nfnetwork.org/understand-nf/what-is-nf/

Meetings

Our meetings are publicly posted on meetup.com and syndicated across two different meetup groups to bring awareness to bioscientists and data professionals. 

Links

Petri Dish Bio: https://www.meetup.com/petri-dish-bio/

MoCo Makers: https://www.meetup.com/mocomakers/

Workspace

We use slack as our central workspace for communication throughout the weeks and between meetings. Please send your email to matt@mocomakers.com to get access to the slack workspace.

Getting Started With Our Group

1. Simply attend our weekly Computational Biology meetings on meetup. We post them on DMV Petri Dish – https://www.meetup.com/petri-dish-bio/ – and MoCo Makers – https://www.meetup.com/mocomakers/

2. Read our paper – https://pubmed.ncbi.nlm.nih.gov/38136356/

3. Watch our ‘onboarding’ videos. This really is the BEST way to get spun up with what we are working on. They are quite long, but will save the organizer a ton of time – as we will have to restate common questions. See these videos below.

Video 1: NF1 Biology and Foundation

Drug Responses in Plexiform Neurofibroma Type I (PNF1) Cell Lines Using High-Throughput Data and Combined Effectiveness and Potency (Written by us)

Link: https://pubmed.ncbi.nlm.nih.gov/38136356/

Downloadable File: https://www.mdpi.com/2072-6694/15/24/5811/pdf?version=1702528450

Summary

• This paper outlines the need for additional drugs for Plexiform Neurofiromatosis 1

• This paper establishes the development of a score characterizing the effect of a compound on a single cell line, S = log[EFF/AC50], and (b) a relative score, ΔS, characterizing the relative difference between a reference (e.g., non-tumor) and test (tumor) cell line. 

• ΔS was applied to data from high-throughput screening (HTS) of a drug panel tested on NF1-/- tumor cells, using immortalized non-tumor NF1+/- cells as a reference.

•  We identified drugs with sensitivity, targeting expected pathways, such as MAPK-ERK and PI3K-AKT, as well as serotonin-related targets, among others. The ΔS technique used here, in tandem with a supplemental ΔS web tool, simplifies HTS analysis and may provide a springboard for further investigations into drug response in NF1-related cancers. The tool may also prove useful for drug development in a variety of other cancers.

Drug Response Evaluation for NF1 Tumors using HIgh Throughput Screening Analysis

These videos are knowledge transfer on specific or advanced topics. Feel free to get to these in over time in the future.

Please share your questions in Slack.

Past Videos

• Intro to Neo4J - https://www.youtube.com/watch?v=qKNo_8aw3Xw

• Knowledge Graph Workstream Discussion - https://www.youtube.com/watch?v=dHn9NuYiv_I

• K-Means Clustering and Biomedical Data from STRING and STITCH - https://www.youtube.com/watch?v=p8MTd3Ynby8

• K Means Clustering - Concepts and Python Code - https://www.youtube.com/watch?v=GNJqHVb5Gc4 (recommend closed captions)