The Vector

Volume 11, Issue 6: June 2022


Editorial Team

Edith Pfister, PhD – Editor, The Vector
Karen Bulaklak, PhD – Associate Editor, The Vector
Jon Brudvig, PhD – Junior Editor, The Vector

Inside This Issue

Leadership Message
Breaking Through
From Molecular Therapy
Society News
Career Center
Public Policy
Industry News

Leadership Message


Watch #ASGCT22 Sessions On Demand Through June 19

Hello, ASGCT Members! 

I hope you’re all doing well. For those of you who don’t know me, my name is Hans-Peter Kiem, and I’m incredibly grateful to serve as ASGCT president for the upcoming year! I’m a professor of medicine and pathology at the University of Washington and the director of the stem cell and gene therapy program, as well as the Stephanus Family Endowed Chair for Cell and Gene Therapy, at the Fred Hutchinson Cancer Center. At ASGCT, I’ve been a Member for over 20 years and have served on more than a handful of committees. I’m looking forward to meeting and working with many of you over the next year to implement new ASGCT initiatives and programs. 

I’m sure I’m not the only one still thinking about all the phenomenal research and the insightful discussions from last month’s Annual Meeting. After two years of online events, it was such a joy to be together again in person. I’m proud to report that our first meeting in a convention center was our largest yet with more than 7,500 attendees! Please remember that you can watch most of the sessions on demand through June 19 on the virtual meeting platform, and you can still register through that date as well. Thank you to everyone who made this meeting such a huge success! 

Finally, we are officially into award season at ASGCT! This year, ASGCT Members can apply through August 1 for more than $1 million in funded awards. We’re offering $100,000 each to six Members working toward career independence in the field through our Career Development Awards (CDA) program, and the Cystic Fibrosis Foundation will support three more $100,000 CDA awards. We’re also offering three Diversity, Equity, & Inclusion Award (DEI) opportunities for Members who are part of underrepresented populations or are researching conditions that disproportionately affect minority populations. If you know anyone who you think might be interested in these opportunities, please pass this information along and make sure they are a Member of ASGCT

Thank you for giving me the opportunity to serve as president this year, and I’m excited to work with many of you soon.
 

Sincerely,
 

Hans-Peter Kiem, MD, PhD 
ASGCT President 

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Breaking Through


Deepm5C: A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy

Hasan MM, Tsukiyama S, Cho JY, Kurata H, Alam MA, Liu X, Manavalan B, Deng H

DOI: https://doi.org/10.1016/j.ymthe.2022.05.001

Summary by Edith Pfister, PhD

RNA modifications can affect RNAs' localization, accessibility, stability, or structure. Researchers have identified hundreds of RNA modifications; 5-methylcytosine (m5C) is a common RNA modification found in a variety of types of RNA, including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), messenger RNAs (mRNAs), and non-coding RNAs (ncRNAs). The m5C modification is dynamically regulated, and in mRNA, m5C modification can influence RNA stability, expression, and protein synthesis. Several antibody-based methods for transcriptome-wide mapping of m5C sites exist*, however computational prediction methods have largely been optimized to detect human m5C sites and are less advanced. In a paper in Molecular Therapy, Hasan et al. have developed and validated a deep learning-based method for predicting m5C sites.

Deep learning is a type of unsupervised machine learning; the learning process involves extracting features from a training dataset by iterating over levels of increasing abstraction, much as children do when learning language. This process allows the program to learn the important features that define a true m5C from a biological dataset. A variety of variables can influence the accuracy of the resulting predictor, including how the data is encoded and exactly what type of model is used. The authors tested four methods of encoding and eight different models. To go a step further, they combined the best single models using a method called stacking. The stacking algorithm involves learning how best to combine and harness predictions from multiple models. The authors show that this method outperforms any of their single models and several established algorithms. This method represents an improvement over existing predictors and can likely be used to examine other types of modifications.

* Xue, C., Zhao, Y. & Li, L. Advances in RNA cytosine-5 methylation: Detection, regulatory mechanisms, biological functions and links to cancer. Biomarker Research vol. 8 (2020).

From Molecular Therapy


Now open: Search for Molecular Therapy—Oncolytics editor-in-chief: ASGCT has opened its search for the next editorial leader of MTO as the inaugural editor-in-chief Dr. Yuman Fong’s term ends Dec. 31, 2022. MTO is an online, open-access journal focusing on the development and clinical testing of viral, cellular, and other biological therapies targeting cancer. Its 2020 impact factor is 7.200.

Applications must include a letter of intent detailing relevant experience and vision for the journal as well as a current C.V. Interested ASGCT members may submit inquiries to ASGCT CEO David Barrett.

Latest MT issues: Check out the most recent issues of these Molecular Therapy family journals:

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Society News


Associate Members: Become the Next Junior Editor of The Vector

All Associate Members are invited to apply for this one-year position on The Vector, ASGCT's monthly member newsletter. Each month on a rotating basis, the Junior Editor is responsible for summarizing a Molecular Therapy article or compiling a list of industry news articles. The Junior Editor will then ascend through the editorial team succession in the following years. Interested? Send your CV and a 500-word summary of this article to drose@asgct.org by July 6.

Apply for Career Development & DEI Awards by Aug. 1

This year, ASGCT Members can apply for funded awards totaling more than $1 million. ASGCT Members working toward independence in their gene and cell therapy careers are eligible for one of nine $100,000 Career Development Awards. Three more Members from underrepresented minority populations or groups in the scientific workforce, or those conducting research for conditions disproportionately affecting minorities, can apply for Diversity, Equity, and Inclusion Awards.

June 19 is the Final Day to Watch #ASGCT22 Sessions

We hope your experience at the 25th Annual Meeting was packed with new ideas, insights, and connections to help you advance your research and excel in your career. Catch up on any sessions you missed or want to rewatch through June 19 on the virtual platform. Know someone who couldn't attend? Register through that date for on-demand access.

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Career Center


Are you looking for a job in the field of gene and cell therapy? Check out the new ASGCT Career Center for great opportunities with industry, government, and academic organizations. Sign up to receive alerts for open jobs in your area.

If you're from a recruiting institution, advertise in the Featured Jobs section to target the 4,000+ audience of The Vector.

Featured Jobs

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Public Policy


Highlights from the Annual Meeting 

Newborn Screening Workshop & Podcast on System Modernization 

Speakers during the Pre-meeting Workshop Newborn Screening: Toward a System That Keeps Pace with Gene Therapy Advances debated challenges and solutions to the current newborn screening (NBS) system, given the anticipated wave of innovative therapy approvals. They discussed a host of issues surrounding the RUSP and NBS process, and emphasized the need for modernization. Specific topics included hastening state uptake of newly approved conditions, addressing the challenges of data collection via NBS pilot programs, and evaluating emerging screening and clinical programs.  

ASGCT has been active in the NBS space since the Society’s current strategic plan took effect in 2020. The Policy and Advocacy team recently sat down with the Newborn Screening Translational Research Network to discuss some of the same issues raised in the NBS workshop. ASGCT’s Senior Manager of Government Affairs, Christina Mayer, details how gene therapy advocates can work to advance the newborn screening system in this podcast episode

Peter Marks, Ana Hidalgo-Simon Pose Solutions to Development Challenges 

On the second day of the Annual Meeting, audience members stepped up to the mic to ask high-level EMA and FDA regulators about regulatory barriers to gene and cell therapy development. Manufacturing challenges took center stage as Drs. Peter Marks and Ana Hidalgo-Simon outlined the need for platform approaches and global harmonization. For regulators specifically, one of these challenges has been changing or inconsistent manufacturing approaches throughout a product lifecycle, making comparability difficult at different stages in development.  

Marks and Hidalgo-Simon also shared their thoughts on potential solutions to some of these barriers. Both regulators supported a gene therapy “playbook” approach to standardize early and late-stage manufacturing across products. Marks pointed to the Bespoke Gene Therapy Consortium, of which ASGCT is a member, as an example of the NIH’s commitment to the future of platform technologies.  

In addition, audience members asked several questions about the accelerated approval pathway and its applications to gene therapies. The discussion between regulators pivoted to the use and importance of surrogate endpoints, urging early communication with FDA and EMA around the use of endpoints and their evidence of clinical benefit. Marks specifically addressed the communication concerns over OTAT staffing as the number of submitted INDs is expected to increase. 

Assessing Ethical Considerations on CGT for Human Enhancement 

Speakers during The Ethical Gray Zone? Perspectives on the Development and Governance of Gene and Cell Therapies for Human Enhancement considered a range of questions in the public and professional policy discussions of human genetic modification. Such discussions have traditionally drawn a line at going beyond the treatment of serious disease to attempt to improve on normal human traits within particular social contexts. Recent waves of reports addressing human genome editing concur with that context, even while they acknowledge the theoretical difficulties of defining the “treatment vs. enhancement” line clearly in specific cases. This symposium dived into the myriad considerations that the public dialogue on this issue must address, with the goal of supporting a responsible framework for this research frontier. Case studies in this session provided insight into cultural considerations and the role of governance, and offered a survey of the path leading to human enhancement. Registered attendees can watch the full session on demand to help answer some of these pervasive ethical questions for the field and to better understand the broader context of the “enhancement” debate around gene editing and new gene therapy applications. 

Registered attendees can watch all sessions on demand through June 19. Not yet registered? Register here for access to Annual Meeting content. 

Industry News


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2022

ASGCT Policy Summit

September 26-27, 2022

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