Postdoctoral Fellow - Immunology

A postdoctoral fellow position is currently available in the lab of Dr. Kristen Pauken in the Department of Immunology at UT MD Anderson Cancer Center. Harnessing the immune system using immune checkpoint inhibitors to treat cancer has revolutionized clinical cancer care, demonstrating remarkable efficacy in diverse cancer types. Despite the clinical successes, overall response rates for most cancers remain below 50%, highlighting the need to better understand immunological drivers of response and resistance to improve outcomes. Moreover, a subset of patients develops autoimmune-like immune-related adverse events, which has limited the utility of this approach. The inability to push the reset button on autoreactive immune responses is becoming a rate limiting step in the effective application of immunotherapy for the treatment of cancer and continues to hamper our ability to treat autoimmunity. Many combination therapies designed to improve efficacy also worsen the rate and severity of the associated toxicities. The central mission of the Pauken laboratory is to expand the reach of checkpoint-based immunotherapy by tackling issues related to both efficacy and safety with the long term goal of developing ways to dissociate the protective effects of immunotherapy from the toxicities.

In the open postdoctoral fellow position, the Pauken laboratory is specifically recruiting applicants with extensive computational expertise to drive single cell transcriptomic and spatial transcriptomic projects forward in the laboratory. In this position, applicants will be expected to lead projects both in the tumor microenvironment as well as in inflamed lesional tissues that develop as a side effect of checkpoint immunotherapy. Additionally, a major focus on the Pauken laboratory is understanding the ontogeny of protective vs. pathogenic immune responses in cancer patients, which will involve analyses of peripheral tissues (e.g., peripheral blood, lymph nodes) and application of tools including single cell sequencing of the T cell receptor (TCR) to track clonally related populations between tissues. The major goal of this position is to leverage both human and mouse transcriptomic datasets to identify key barriers to success in terms of anti-tumor immune responses as well as identify key differences between the immune responses driving anti-tumor immunity and pathogenic immune-related adverse events so that the field can get better at improving efficacy without worsening the toxicities.

In joining the Pauken laboratory, applicants can expect a fast paced, cutting-edge research environment, highly supportive mentor, and a supportive and collaborative research environment. Successful applicants will be expected to lead computational projects as the first author, prepare and submit manuscripts, attend conferences and present work in progress, and participate in regular laboratory meetings. Applicants will be expected to lead independent projects as well as work collaboratively as a team with other members of the Pauken laboratory and collaborators with the Pauken laboratory.

All duties and responsibilities are carried out in compliance with institutional policies, ethical research standards, and applicable federal and state regulations

LEARNING OBJECTIVES
1.) Take overall responsibility for and drive the proposed projects, focusing on identifying key barriers to success in terms of anti-tumor immune responses as well as identifying key differences between the immune responses driving anti-tumor immunity vs. pathogenic immune-related adverse events. This entails designing and planning key analyses/experiments, troubleshooting, creative problem solving, and taking the initiative to seek out new avenues of inquiry, including collaborations.
2.) Apply single cell transcriptomic data to identify immunological mechanisms driving response, resistance, and toxicities following checkpoint immunotherapy in both human and mouse datasets. This includes the analysis pipeline from raw sequencing data to dataset integration, clustering, pathway analysis, differential gene expression analysis, and other algorithms as the project requires.
3.) Determine how peripheral immune responses differ from intratumoral or intralesional immune responses and determine how peripheral immune populations contribute to protective anti-tumor immunity and immune-related adverse events.
4.) Determine how combination therapies can be leveraged to either overcome resistance to checkpoint immunotherapy in cancer or dampen toxicities that raise following cancer immunotherapy.
5.) Take the lead in writing up manuscripts and abstracts on the research with supervision from the PI. May also be asked to assist in the preparation of grant proposals or other literature, such as review articles.
6.) Engage in collaborative, cross-disciplinary research with access to state-of-the-art facilities and tools.
7.) Acquire professional development and expertise in single-cell sequencing, spatial sequencing/imaging approaches, cellular immunology, and translational research planning and strategy.

ELIGIBILITY REQUIREMENTS
• A Ph.D. or equivalent in the fields of Immunology, Cancer Biology, Cell Biology, Systems Biology, Bioinformatics, or Computational Biology is required.
• Prior experience with high-dimensional single cell RNA sequencing data analysis and data visualization software is a must. Additionally, experience with other types of single cell sequencing data (e.g., T cell receptor sequencing, CITE seq, ATAC seq) and/or spatial transcriptomics is preferred.
• A track record of scientific productivity, as evidenced by peer-reviewed publications is a must. Candidates must have demonstrated proficiency in scientific writing through at least one lead-authorship manuscript during the Ph.D. (or equivalent) thesis work.
• Good communication with the supervisor and colleagues is a must. Excellent organizational skills of both experimental notes, data, and physical reagents are also a must.

POSITION INFORMATION
Offsite work arrangements are subject to approval and may be modified or revoked at any time based on business needs, performance considerations, or regulatory requirements.

This position may be responsible for maintaining the security and integrity of critical infrastructure, as defined in Section 113.001(2) of the Texas Business and Commerce Code and therefore may require routine reviews and screening. The ability to satisfy and maintain all requirements necessary to ensure the continued security and integrity of such infrastructure is a condition of hire and continued employment.

It is the policy of The University of Texas MD Anderson Cancer Center to provide equal employment opportunity without regard to race, color, religion, age, national origin, sex, gender, sexual orientation, gender identity/expression, disability, protected veteran status, genetic information, or any other basis protected by institutional policy or by federal, state or local laws unless such distinction is required by law.