The Department of Pathology’s Research Service Core laboratories provide expert faculty leadership and innovative instrumentation, technologies and specialized services, to a large number of our UCLA biomedical researchers. Our Cores provide a number of services essential for modern research, including whole genome sequencing, state-of-the-art digital imaging/automated imaging analysis, biobanking, chemistry, hematology, coagulation and endocrine testing for clinical trial work and immune assessment services for clinical trials. I will be highlighting below updates for The Technology Center for Genomics & Bioinformatics (TCGB) and The Translational Pathology Core Laboratory (TPCL).

TECHNOLOGY CENTER FOR GENOMICS & BIOINFORMATICS (TCGB) UPDATE

• In 2023, the TCGB introduced 4 new technologies, 11 new services and offered 23 seminars & trainings in high-throughput sequencing, single cell multiomics and spatial genomics:
  • Novaseq X plus
  • DNBseq T7
  • BD Rhapsody HT Express
  • CosMx SM

• The TCGB provides multi-dimensional support resulted in substantial scientific, financial and intellectual impact. In the past 5 years, the TCGB contributed to UCLA Jonsson Comprehensive Cancer Center (JCCC) accomplishments:
  • 166 publications
  • 193 awarded grants totaling ~$277M
  • 21 patent applications

• The TCGB will continuously make impactful contributions to UCLA investigators’ research by developing advanced technologies, services and solutions. In 2024, the TCGB will launch:
  • Stereoseq spatial technology & services for whole genome multiomics analysis at a single cell resolution
  • Multiomics dataset integration and analysis
  • Monthly office hours for Q&A and consultation

THE TCGB TEAM

Top Row: Andrew Rao, YooJin Lee, Lynda Jauregui, Reyna Mathai, JaeMo Kim, Gexin Zhao, Yu-Chyuan Trent Su

Middle Row: Varuzhan Balasanyan, Jo Bodhaine, Lilly Boiton, Melody Wu, Mark I. Duhon, Jahan R. Bruce

Bottom Row: Toni Mckenzie-Mendiola, Denise Llera, Lea DeMarco, Xinmin Li, Hyun-Ju Lim, Catherine Sutarjo, Chao Niu

TRANSLATIONAL PATHOLOGY CORE LABORATORY (TPCL) UPDATE

The Translational Pathology Core Laboratory (TPCL), a UCLA Jonsson Comprehensive Cancer Center (JCCC) Shared Resource since 1998, provides pathology services critical for basic, translational, clinical, and population cancer research. TPCL provides a College of American Pathologists accredited human tissue biobank, histology (animal/human; frozen/formalin-fixed paraffin embedded), laser capture microdissection, immunohistochemistry, and in-situ hybridization services (established/new antibody optimization), and pathology consultation services. TPCL connects cancer researchers with subspecialty pathologists and was an early adopter of digital pathology, assisting with custom digital image analysis algorithms for complex evaluations of tissue sections.

TPCL provides essential services including the utilization of spatial transcriptomics (see figure). TPCL adapted the spatial gene expression platform Visium (10X Genomics along with supporting the GeoMx (Nanostring) platform (with TCGB). TPCL has also expanded processes to identify and retrieve remnant biofluids with increased customized clinical variables, expanded research blood draw order capabilities within routine clinical lab orders, and added biofluid acquisition, processing, and storage.

SPATIAL TRANSCRIPTOMICS (VISIUM, 10X GENOMICS) MAPPING HUMAN HEMATOPOIETIC STEM CELLS FROM HEMOGENIC ENDOTHELIUM TO BIRTH

Spatial transcriptomics (Visium) Performed at TPCL in collaboration with Pathology’s Technology Center for Genomics & Bioinformatics (TCGB) demonstrated, for the first time generation of hematopoetic stem cells (HSC)s from hemogenic endothelial cells (highlighted by SPINK2) in the aorta of 5 week old embryos.

METHYLOME SEQUENCING OF CELL-FREE DNA FOR CANCER SCREENING FROM PATIENT PLASMA DR. JASMINE ZHOU’S LABORATORY

TPCL provided colon, liver, lung and stomach cancer specimens for assay development. Blood samples were also provided. This allowed for the development of a highly sensitive early cancer screen by Dr. Jasmine Zhou and her team.

Assay demonstrates high sensitivity for carcinoma, including early stage.

ADDITIONAL UPDATES

Exciting future TPCL directions to support and benefit JCCC research include:

1. Automated IF/combined IF/RNA-ISH staining and expansion of RNA (F)ISH services to include miRNA detection;
2. Increased clinical variable searches for remnant biofluids; 
3. Facilitated use of research blood draw requests by non-clinicians;
4. Expansion of clinical annotations of biorepository management system to include synoptic reports;
5. Upgrade and expansion of image analysis software (Visiopharm);
6. Expansion of GSR collaboration to include CosMx (Nanostring) and Stereo-seq platforms; and
7.  Adding a dedicated staff member to assist with consenting/procurement for special JCCC supported studies

TPCL TEAM

Top Row: Sam French, Sepehr Hamidi, Joseph Bautista

Middle Row: Rick Huang, Roxana Gonzalez, Jo Anne Olivas, Clara Magyar

Bottom Row: Yunfeng Li, Ko Kiehle, Kim Flores, Chris Creencia, Kody Lopez Devoux (not pictured)

Congratulations to Dr. Lily Zhang, Dr. Wayne Grody, and collaborators on receiving a $4.6M grant from National Cancer Institute to develop & improve liquid biopsy technologies for the early detection of lung cancer — the leading cause of cancer death in both men & women in the U.S.

Congratulations to Dr. Elaine Reed and Dr. Enrique Rozengurt on receiving a new $3.6 million dollar grant from the National Institute Allergy and Infectious Diseases (NIAID). The grant focuses on signaling pathways that mediate transplant rejection focusing on endothelial cells.

In a study conducted by Dr. Helen Lavretsky regarding the effect of Tai Chi on inflammation during depression, the Immune Assessment Core & Dr. Monica Cappelletti performed immunological measurements.

UCLA Pathology’s Clinical Microbiology Fellowship Program has been reaccredited! Congratulations to our Microbiology team for their continued support of education & excellence.

Congratulations to Microbiology Fellows Dr. JR Caldera and Dr. Hannah Gray, along with Dr. Omai Garner and Dr. Shaun Yang on their recent article "FDA trial regulation of laboratory developed tests (LDTs): An academic medical center's experience with Mpox in-house testing."

The wonderful staff at our Ackerman Blood & Platelet Center make donating easy & enjoyable. Please consider donating!

Congratulations to Dr. Harry Vinters and collaborators on their article "Structure-based design of nanobodies that inhibit seeding of Alzheimer's patient-extracted tau fibrils."

Congratulations to Dr. Nicole Valenzuela and collaborators on their articles "The Transplant Bellwether: Endothelial Cells in Antibody-Mediated Rejection" in the Journal of Immunology, "Personalizing kidney transplant donor-specific antibody surveillance: The devil is in the details" in the American Journal of Transplantation, and "New insights into maladaptive vascular responses to donor specific HLA antibodies in organ transplantation" in Frontiers.

Is a faint line on a COVID-19 test actually positive? Dr. Garner explains at-home COVID-19 test results via Today.

Thank you to everyone who participated in the 2023 UCLA Health Heart & Stroke Walk! Our department was in the Top 10 Fundraising Teams with $4,632.70 raised! A special thank you to Nathan Okawa for being our department coach!

Pictured from left to right: Jowin Rioveros, Nathan Okawa, Stan Cabotaje, & Marivic Visico

It gives us great pleasure to announce the appointment of Crystal Le as Director of the Santa Monica Clinical Laboratory effective October 23, 2023. 

Crystal began her UCLA career in 2013 as the Sr. CLS Specialist for Hematology / Coagulation at the Santa Monica Hospital. In 2017, she was promoted to Sr. CLS Supervisor of the analytical area at the Santa Monica Lab. Crystal subsequently accepted the position of Sr. CLS Specialist - Quality, Safety, and Education at the Regulatory Affairs office in February 2021. Her most recent position was as Clinical Laboratory Manager at the City of Hope Orange County Lennar Foundation Cancer Center. In this role, Crystal successfully established a new clinical laboratory that passed state inspection, obtained state licensure, and opened for patient testing within seven months of implementation; within six months of opening, the lab received CAP and Joint Commission accreditation. She also brought up Point-of-Care testing, supported validation of the automation line, assisted with implementation of lab-collaborated bone marrow collection in Radiology, and oversaw daily operations of the anatomic pathology lab for a period.

Crystal obtained her M.S. in Healthcare Administration in 2013 and comes to us with over 16 years of CLS experience in high volume facilities. During her career, she has trained employees in technical and non-technical areas, standardized the competency assessment process for CLS staff, and was integral in maintaining continuous readiness for CAP, Joint Commission, and state inspections. Crystal has provided both supervisory and technical support for multiple validations and implementations of new tests, procedures, software, and instruments. She additionally has extensive experience in emergency preparedness, laboratory safety, education, budget forecasting, and executing vendor service agreements.

Please join us in congratulating Crystal on her new appointment and return to Santa Monica!