Cancer and Genomic Dark Matter
Forum Chairs
Forum Description
Transposable elements (TEs) make up 50% of the human genome but are referred to as "genomic dark matter" or "junk DNA" and often ignored in genomic medicine - both because they have been presumed to be unimportant and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human transposable elements and their role in cancer has never been greater, and methods enabling its study are maturing at a fast pace.
Transposable elements directly contribute to cancer through both genetic and epigenetic mechanisms. De novo transposon insertions are known to disrupt important genes and gene regulatory elements and result in tumorigenesis. Epigenetically reactivated transposable elements can become cryptic promoters and enhancers and lead to abnormal gene activities including up-regulating oncogenes. These recent mounting evidences request a full understanding of the contribution of transposable elements to cancer.
On the other hand, transposable elements are a double-edged sword. Recent discoveries reveal that epigenetically reactivated transposable elements can produce cancer specific products including immunogenic antigens and double stranded RNAs, which result in an innate immune response. These findings together with rapid development of immunotherapies open new avenues for cancer treatment.
Forum Summary
The Forbeck Foundation hosted an in-person meeting at the beautiful Asilomar Conference Grounds in Pacific Grove, California. Attendees discussed the emerging views on the role of non-coding genome in cancer, especially the role of transposable elements (TEs). It was the first Forbeck Forum to discuss topics in this specific area and one of the first in-person meetings for many attendees after the long COVID-19 hiatus. The meeting was chaired by Ting Wang, PhD (Washington University School of Medicine) and Kathleen Burns, MD/PhD (Dana Farber Cancer Institute). The meeting attendance included four Forbeck Scholars: Carlos Mendez-Dorantes, PhD; Aguirre De Cubas, PhD; Charles Ishak, PhD; and Zuzana Tothova, MD/PhD, among the 19 speakers. Also attending was Forbeck Foundation Scientific Advisory Board member, Dr. Kimryn Rathmell, MD, PhD (Vanderbilt University).
The Forum was divided into 4 sections, structured to (1) define the relationship between transposable elements and the cancer genome; (2) define the relationship between transposable elements and the cancer epigenome; (3) evaluate the implication of transposable elements in cancer therapy; (4) explore the role of transposable elements in cancer evolution.
Throughout the meeting investigators outlined recent progresses and challenges in the field to understand the “genomic dark matter” in cancer, and rigorously discussed and debated key questions, including: 1) Are changes in TE expression in cancers epiphenomenal or contributory? 2) What are the mechanisms underlying cell autonomous effects of TE expression? 3) How might TE expression impact recognition of tumors by the immune system? 4) How can we best model alterations in TE expression in experimental systems? 5) What types of therapeutics might target TE biology? The presentations and discussions highlighted how TEs directly contribute to cancer through both genetic and epigenetic mechanisms, and how their unique biology shapes the cancer genome and epigenome, and presents unorthodox opportunities to diagnose and treat many types of cancers.
Forum attendees acknowledged the difficulties associated with the study of the contribution of transposable elements in cancer, both conceptually and technically. The lack of appropriate cancer models to study transposable elements, and difficulty in mapping the repetitive genome are two examples of these challenges. Technological improvements, especially third generation sequencing, will likely provide new and innovative ways to investigate transposable elements in cancer.
All the talks and discussions inspired continued discussions among participants beyond the two-day meeting. Everyone enjoyed seeing their colleagues and discussing science in a relaxed and stimulating environment. These interactions also fueled new collaboration. Several meeting participants (Kathy Burns, Ting Wang, Guillaume Bourque, Daniel DeCarvalho, Kate Chiappinelli, Zuzana Tothova) submitted a Mark Foundation Endeavor project as a result of the follow up discussions.
Venue & Travel Information
800 Asilomar Avenue
Pacific Grove, CA 93950
Travel Forms
Travel forms are due 30 days prior to the start of the meeting to allow enough time to plan transportation.
To help reduce transportation costs, the Foundation tries to group travelers on shuttle vans rather than providing transportation for single travelers. The times below are not exclusive but represent times that we hope to have shuttles leave the airport.
The Monterey Regional Airport (MRY) is the preferred airport as it is only 20 minutes from the meeting location.
- Arrivals to MRY - Thursday around 1 PM, 3 PM and 5 PM
- Departures from the meeting venue - Sunday around 8 AM, 10 AM, and 12 PM
San Francisco International Airport (SFO) is 2 hours from the meeting location without traffic. The Foundation tries to prioritize International Flights and situations where flying into SFO is significantly cheaper than connecting to MRY. The times below are for guidance only, and depending on the volume of travelers, we may add an additional shuttle to and from the airport.
- Arrivals to SFO - Thursday around 3 PM
- Departures from the meeting venue - Sunday around 10 AM
Travel Policy
Please familiarize yourself with our policies and procedures for travel. We truly appreciate you taking the time to participate in this meeting. As you make your plans, please remember that we are a nonprofit organization dependent on donations and volunteers. We do NOT pay for upgrades, change fees, incurred costs resulting from a flight change, transportation to or from your local (home side) airport, meals or other incidentals.
- Travel Confirmation will be sent out within 1 week of the meeting. This will include a hotel confirmation number, if there is one, and airport transfer details. We have to wait until we receive almost everyone’s travel to book airport transfer. Due to frequent airline changes, we wait until the week of the meeting to send this out.
- Airport transfer is provided by Foundation staff, volunteers or arranged shuttle at specific times. If you opt to utilize Foundation airport transportation on your travel form, please be patient in receiving this information. We will send it to the week of the meeting.
- Speaker agenda is not sent out prior to the meeting. It will be provided upon arrival in the meeting packet. We do not tell people when they are speaking because we expect everyone to attend all sessions. Sessions are all day Friday and Saturday.
- REMINDER: We do not reimburse for home side airport transfer or incidentals while traveling. We will not honor miscellaneous receipts sent for these expenses.
- Spouses are welcome to come with you at their own cost but are not allowed to attend the meeting. Please no children.
What the Foundation Pays
Accommodations and meals are provided by the foundation during the meeting. Airfare will be covered only if booked through our travel agent. The Foundation will also cover airport transportation on the meeting side at the designated shuttle times. You can select not to utilize Foundation arranged transportation at your own expense when completing the travel form. Once your travel form is received your accommodations and airport transfer will be confirmed. Please let us know of any food allergies or other information we should be aware of on the travel forms.
- If you would like your airfare covered by the Foundation, you must book with our travel agent. Note we do not cover upgrades, changes, late bookings, etc.
- Flights must be booked at least 30 days prior to the meeting to confirm your accommodations and airport transfer.
- As a nonprofit we utilize volunteers and other methods to maximize our efforts (or our donor support) when making accommodations and arranging ground transportation. Ground transportation will be provided upon your arrival either by a foundation volunteer or arranged shuttle. You will be provided airport transportation information the week of the meeting. We do not reimburse for home side airport transfer or incidentals while traveling.
Abstracts
Abstracts are due 30 days prior to the start of the meeting to allow enough time to prepare the meeting book.
The abstracts should be only one or two paragraphs outlining the theme of your presentation and should reflect the objective and spirit of the meeting (see above). Abstracts will be circulated about one week before the meeting. The meeting organizer will start requesting them a month before the meeting.
Meeting Structure
The meeting structure has been developed over years of experience.
- Participants have approximately 45 minutes, depending on the number of participants, for their presentation and discussion. The presentation is meant as a conversation start and should last about twenty minutes briefly covering background information and areas that are new or need further input. This should be structured in such a way as to lead to a lively discussion. Participants are encouraged to interrupt to ask questions or start discussions.
- A MAXIMUM of 5 slide equivalents per presentation is allowed (Power point slides should not contain more than one graph or gel per slide and no more than 5 bullet points to stress the points being made by the presenter.) We appreciate cooperation with the spirit of this guideline. Handouts are welcome but should be distributed before sessions.
- Everyone is expected to actively participate in every session and discussions.
- The time spent at the meeting is relatively short, so please be familiar with papers received prior to the meeting.
- It is very important that you commit to all sessions of the 2 days of meetings.
Forbeck Scholars Participation
Scholars are selected for each Forbeck Forum. These are outstanding junior clinical or post-doctoral fellows selected based on the quality and relevance of science.
- Scholars present for 30-45 minutes, depending on the number of participants
- The same presentation rules apply for scholars
- After the Forum you are selected to attend, you will attend three years of Scholar Retreats held in Lake Geneva, WI. If you attend a Fall Forum, you will attend the Spring Retreat. If you attend a Spring Forum you will attend a Fall Retreat.
- Scholars are selected by the Foundation Scientific Advisory Board and peer reviewers selected from past Forbeck Scholars.
General Program
The outline below illustrates a typical program schedule. You will receive a complete schedule, including speaking times, the Thursday the meeting starts.
Frequently Asked Questions
Below are some of our most Frequently Asked Questions. If you have something new to ask, please feel free to contact us.
- Travel Confirmation will be sent out within 1 week of the meeting. This will include a hotel confirmation number, if there is one, and airport transfer details. We have to wait until we receive almost everyone’s travel to book airport transfer. Due to frequent airline changes, we wait until the week of the meeting to send this out.
- Airport transfer is provided by Foundation staff, volunteers or arranged shuttle at specific times. If you opt to utilize Foundation airport transportation on your travel form, please be patient in receiving this information. We will send it to the week of the meeting.
- Speaker agenda is not sent out prior to the meeting. It will be provided upon arrival in the meeting packet. We do not tell people when they are speaking because we expect everyone to attend all sessions. Sessions are all day Friday and Saturday.
- Frequently airport transfer is provided by volunteers. Please be patient on receiving this information. Airport transfer will be sent out prior to arrival.
- REMINDER: We do not reimburse for home side airport transfer or incidentals while traveling. We will not honor miscellaneous receipts sent for these expenses.