Faculty Profile
Preethi Gunaratne
Moores Professor
Department of Biology and Biochemistry
Research Division: Biochemistry (Primary)
Office: Science & Engineering Research Center, 4028
Contact: phgunaratne@uh.edu - 713-743-2686
Education: Ph.D, Cornell University
Dr. Preethi Gunaratne’s current research interests are focused on discovering immunogenic neoantigens from chimeric RNAs to develop peptide and mRNA vaccines for the treatment & prevention of cancer. To achieve this goal, her lab has established a high-throughput genomics platform that combines the latest Next-Generation Sequencing applications (WGS, WES, RNAseq), Single Cell Sequencing (scRNA-seq) and bioinformatics pipelines to extract chimeric RNAs and matching TCRs (Cytotoxic T-Cell Receptors) to design tumor vaccines for peptide & mRNA-mediated T-cell activation and immunotherapies targeting cancer cells. Discordant paired end reads that are discarded are rescued and screened for high-confidence junction crossing reads to discover fusion junctions that if translated can generate tumor-specific neoantigens. Candidate peptides are filtered through the MHCnuggets pipeline (Karchin et al.) that predicts the binding affinity of peptides to class I and class II Major Histocompatibility Complex (MHC) molecules. Immunogenic neopeptides identified are validated through Western Blots and ELISpot. Ongoing projects focus on actionable fusions for breast, lung and colon cancer from clinically relevant patient-derived xenograft (XPDX) models. This work is a collaboration with XenoSTART, a non-clinical oncology contract research organization. To rapidly translate the findings into clinical practice a provisional patent UHID-2021-002-Winstead Ref. No. 23853-P162WO has been filed.
A second pipeline developed by Gunaratne (leader of the microRNA & Non-Coding RNA groups for NCI/NHGRI-The Cancer Genome Atlas (TCGA), NHGRI-Zebrafinch and NHGRI-Marmoset Genome Sequencing Consortia) & collaborators for ‘Lineage Tracing’ of small numbers of metastatic cancer stem cells to the primary sites of origin has been used in the last decade (2008-2019) to make significant contributions to the Pan Cancer Atlas. As Director, UH-Sequencing & Gene Editing Core, Dr. Gunaratne has established a student run operation that serves both academic & commercial users including XenoSTART, Chevron, Shell Oil etc.
More recently, the ‘Lineage Tracing’ application has been adapted to build a Reservoir & Drainage Diagnostic (RDD) application for landing & fracking wells in the optimal zones of production from tight oil and liquids-rich gas shales. GeOME Analytics a UH-start-up has established a field-tested platform that extracts and integrates personalized DNA biomarkers from multiple pads to provide metrics for upstream asset development. GeOME uses RDD for monitoring oil fields during the full production cycle to predict drainage heights, % contribution and well-to-well and pad-to-pad communication. Dr. Gunaratne is the co-founder, president, CEO and CSO of GeOME.
Honors & Awards
2014 McNair Foundation Award
2012 McNair Foundation Award
2011 Virginia & L. E. Simmons Family Foundation Award (joint award with Jason Shohet and Xiabo Zhou)
2011 Cullen Foundation Award
2010 Baylor Partnership Fund Raising Featured Beneficiary Award (joint award with Matthew Anderson and Martin Matzuk)
2004-2006 Moran Foundation Award (joint award with Dolores Lopez Terrada)
1989 Leukemia Research Foundation Fellowship Award
1988 Northwestern Memorial Galter Fellowship Award
1986 Amoco Research Award, Chicago
Organizations, Outreach, Boards, Memberships
Co-Founder/Chief Scientific Officer – NEXTmiRNA Technologies
National Consortia
- NCI – TCGA PanCancer Consortium – 2016-2019
- Leader Long non-coding RNA Group
- NCI/NHGRI –The Cancer Genome Atlas (TCGA) Consortium 2009-present
- Leader microRNA Analysis Groups – Ovarian, Colorectal, Kidney cancers
- NHGRI – Marmoset Genome Consortium – 2010-2013
- Leader microRNA Analysis Group
- NHGRI – Zebrafinch Genome Consortium 2009
- Leader microRNA Analysis Group
- NIDDK – Stem Cell Genome Anatomy Project (SCGAP) Consortium 2003-2005
- NHGRI/NCI – Mammalian Gene Collection (MGC) Consortium 2002-2005
- Leader Baylor Human Genome Sequencing Center-Gene sequencing Group
- Led Baylor Team to make the largest single contribution to the NCI- Mammalian Gene Collection in Phase I
- NHGRI – The International Human Genome Project Consortium 1999-2003
- Human Chromosomes 3, 12 and X
Editorial Boards
2011-2019 Review Editor, Frontiers in Non-coding RNA Journal
Manuscript Review
Nature Reviews, Nature Protocols, Proc. Natl. Acad. Sci. (PNAS), Molecular Cell, Genome Research, Cancer Research, Clinical Cancer Research, Oncotarget, Nucleic Acids Research, PLoS ONE, BMC Genomics, BMC Bioinformatics, Briefings in Bioinformatics, British Journal of Cancer, Genome Biology, Molecular Carcinogenesis, Molecular Cancer Therapeutics, Frontiers in Non- coding RNA, Genomics, Genome Medicine, Gene Expression Patterns (GEP), Elsevier, Cell Research, Toxicology & Applied Pharmacology (TAAP), Journal of Theoretical Biology, Pancreas Journal
A.12. Expert Peer Reviewer – Grants & Programs
- 2020-2023 - KTH (Royal Institute of Technology in Stockholm), Sweden RAE-2020-2023
- 2020-2022 - Research Foundation Flanders (FWO), Belgium
- 2020-2021 - Department of Defense (DOD) – Peer Reviewed Medical Research Program (PRMRP)
- 2015, 2021 - Swiss National Science Foundation (SNF)
- 2017-2021 - Florida Department of Health (F-DOH)
- 2020 - Department of Defense (DOD)
Peer Reviewed Medical Research Program (PRMRP) COVID-T-2 - 2020 - Department of Defense (DOD)
Breast Cancer Research Program – Nanotechnology Panel (BCRP-NT) - 2017-2019 - Pennsylvania Department of Health (PA-DOH)
- 2017-2018 - Expert Peer Review U.S. FDA Research Program
- 2016 - NCI-2016/05 ZCA1 SRB-J (M2) R–Special Emphasis Panel/Scientific Review Group
Provocative Question 6, “What are the underlying molecular mechanisms that are responsible for the functional differences between benign proliferative diseases and premalignant states” - 2015 - NCI-ZCA1 SRB-J (M2) S–Special Emphasis Panel/Scientific Review Group Pennsylvania Department of Health (PA DOH) Scientific Review Group
- 2011/2012 - NIH-ZRG1GGG-H30S–Special Emphasis Panel/Scientific Review Group
NIH-ZRG1 GGG-H31S – High-end Instrumentation Grants
NHMRC-National Health and Medical Research Council- Australia - 2012 - Duncan Family Institute (DFI) Seed Funding Research Program
- 2011 - Czech Science Foundation
- 2011 - Netherlands-Research Foundation Flanders (FWO)
- 2010 - NIH–CNIHR–AdHoc
Cancer Research UK - 2009-2010 - US-Israel Binational Science Foundation
- 2010 - Israel Science Foundation
Patents - Inventor/Co-Inventor
- Provisional Application: UH ID No. 2021-002|Attorney Docket No. 23853-P162V1 Discovery and use of immunogenic peptides for the treatment and prevention of cancers
- Provisional Application: UH ID No. 2021-002|Attorney Docket No. 2019-058 (T-11416-
P)
Systems and methods for analytic mapping of the metageomic and hydrocarbon footprints of geologic subzones - U.S. Patent Appl. No. 13/136,498; PCT patent # PCT/US2011/001356
Interior Functionalized Hyperbranched Dendron-Conjugated Nanoparticles and uses Thereof - U.S. Patent Appl. No. 13/319,446. CLFR.P0342US miRNA Expression in Allergic Disease
- U.S. Patent Appl. No. 13/437,128; PCT patent PCT/US2012/31809 microRNA-29a,b,c as a sensitizing agent for chemotherapy
- Issued: U.S. Patent Appl. No. 13/437,251; PCT patent PCT/US2012/31822 microRNA-130a,b as a tumor suppressor of cancer
- Issued: U.S. Patent Appl. No. 13/453,553; PCT patent PCT/US2012/34655 microRNA-140-5p as a tumor suppressor of cancer
- U.S. Patent Appl. No. 13/501,806; PCT patent PCT/US2012/34655 microRNA miRNA-31 as a therapeutic approach for the treatment of cancer
- BLG# 11-052: MicroRNAs sensitize ovarian cancers to platinum chemotherapy
- Provisional patent application for UHID-2021-002-Immunogenic Peptides for the
Treatment and Prevention of Cancer-Winstead Ref. No. 23853-P162V1 - UHID 2020-060; Appl No. 63/063,815; A Dual Viral Infection|Host Response detection Test Kit: Winstead Ref. 23853-P161V1
- UHID 2329-51 (2019-058) Systems and Methods for Analytic Mapping of the Metageomic and Hydrocarbon Footprints of Geologic Subzones. Chevron Corporation.
New Company Formation
- 2019: Co-Founder, CEO and CSO, GeOME Analytics
- 2014: Founder and Chief Scientific Officer (CSO) NEXTmiRNA Technologies (http://www.nextmirna.com/)
B.2. Trainees
Faculty
- 2019-2022: Kimberly Holloway, Ph.D. (UH-Sequencing Core – Project Manager)
- Associate Director, Translational Oncology, Iterion Therapeutics
- 2019-2021: Jignesh Chandana, M.S. (UH-Sequencing Core - Automation/Clinical Sequencing Specialist)
- Lead Lab Automation Developer-Invitae
- 2016–2018: Sujash Chaterjee, Ph.D. (Research Assistant Professor)
- Lead-Product Marketing and Commercialization, Genomics, NA at QIAGEN
- Global Cancer Research Lead, Illumina
- 2017: Navin Rustagi, Ph.D. (Research Assistant Professor)
- Data Scientist at McKinsey & Company
- 2015–2016: Utpal Pandya, Ph.D. (Research Assistant Professor)
- 2011–2013: Weiming Xiao, Ph.D. (Research Assistant Professor)
- Co-founder and Chief Scientist at Shenzhen Lucky Source Investment Management Corporation.
Postdoctoral
- 2022-Present: Partha Bhagavatula, Ph.D. (UH-Sequencing Core, Senior Data Analytst)
- 2013–2018: Yinghong Pan, Ph.D. (Research Associate)
- Project Manager, Genome Center, University of Pittsburgh Medical College (UPMC)
- Sr. Application Scientist at PerkinElmer, Inc.
- 2009–2013: Lalithya Jayarathne, Ph.D. (Research Associate)
- 2007: Rafal Drabek, Ph.D. (Postdoctoral Fellow)
Graduate Students
- 2020-Present: Micah Castillo, Ph.D. Candidate, Biochemistry
- 2019-Present: Sakuni Rankothgedera, Ph.D. Candidate, Biochemistry
- 2021-Present: Aaranya Kandasamy, Ph.D. Candidate, Biochemistry
- 2021-Present: Shiyanth Thevasagayampillai, Ph.D. Candidate, Biochemistry
- 2021-Present: Dilshan Adhikari, Ph.D. Candidate, Biochemistry
- 2016–2020: Asha Palat: Ph.D. Candidate, Molecular & Cellular Biology
- McCammon Fellowship 2019
- Technical Support Scientist, Novogene America
- Post Doctoral Fellow, UH-Sequencing Core, Houston, TX
- Brandon Mistretta, Ph.D. Candidate, Biochemistry
- McCammon Fellowship 2020
- Field Application Scientist, 10X Genomics
- 2016–2019: Jason Hoggard, Ph.D. Candidate, Biochemistry
- McCammon Fellowship, 2018
- Post Doctoral Fellow, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Postdoctoral Research Fellow, Division of Congenital Heart Surgery, Texas Children’s Hospital, Houston, TX
- 2012–2017: Ian Wilson. M.Sc. Candidate, Biochemistry
- M.Sc. (2020)
- Sagar Patil: Ph.D. Candidate, Biochemistry
- Harwood Fellowship 2016
- Postdoctoral Fellow, Columbia University, New York, NY
- Lead Researcher at St. Jude Children's Research Hospital
- Project Manager, GlaxoSmithKline (GSK) -Philadelphia
- 2012–2017: Johnson Hoang: Ph.D Candidate, Biochemistry
- Ph.D., SCYM (ASCP),
- 2009–2014: Anadulce Hernandez-Herrera, Ph.D. Biochemistry (Contactyn-Fellowship)
- Lester and Sue Smith Breast Center, Biobank Research Coordinator,
- Baylor College of Medicine – 2017
- Clinical Trials Team, UCSF, San Francisco, CA; Breast Center
- 2008–2012: Rajib Ghosh, Ph.D. Molecular & Cellular Biology
- Post Doctoral Fellow – Johns Hopkins University, MD
- Research Assistant Professor, University of West Virginia, VA
- Senior Scientist at Abcam
- Principal Scientist, Bristol Myers Squibb
- 2007–2011: Jayantha Tennakoon, Ph.D. Molecular & Cellular Biology
- Healthcare Consulting Firm, Chicago, IL
- 2007–2011: Ashley Benham-Duret, Ph.D. Biochemistry
- Post Doctoral Fellow – Texas Heart Institute, Houston
- Senior Scientist, 10X Genomics
- Sales Executive II
- 2007–2008: Arash Naghavi-M.SC., Molecular & Cellular Biology
- MD program UTMB, Radiology Fellow-Moffit Cancer Center, Radiation Oncologist, FL