New Preprints: Using multiomics to study the role of ASXL1 in Bohring Optiz Syndrome and AML

We just published two new preprints— the hard work of Isabella Lin, MSTP student in her PhD 3 year in the lab! These are a long term projects we have exploring the gene regulatory role of ASXL1 in patient-derived cells. here we identify how ASXL1 mutations change the epigenetic landscape and activate Wnt signaling pathtways in differentiated cells. Specifically we highlight both canonical signaling pathways and non-canoncial planar cell polarity pathways are affected by BOS. For the full preprint see here:

Truncating ASXL1 mutations in Bohring-Opitz Syndrome dysregulate canonical and non-canonical Wnt Signaling

We also explored whether the same observations in patient germline syndomes with ASXL1 mutations affect the same pathways in Acute myeloid leukemia with ASXL1 mutations.

ASXL1 mutations that cause Bohring Opitz Syndrome (BOS) or acute myeloid leukemia share epigenomic and transcriptomic signatures

Congrats to Isabella Cardenas for her CARE Fellowship Program acceptance!

Isabella Cardenas, an undergraduate research volunteer, has been named a CARE Fellow for the 22-23’ academic year. The CARE Fellowship Program funds sophomores in research at UCLA and provides professional development on research writing and presentations. As a CARE fellow in the Arboleda Lab, Isabella will continue working with PhD student, Aileen Nava, on KAT6 loss-of-function and gain-of-function experiments in human stem cells."

Genetics and Genomics Graduate Student, Leroy Bondhus publishes his first Paper!

Leroy Bondhus, PhD student along with two UCLA undergraduate students: Yenifer Hernandez and Roshni Varma, published a paper in Briefings in Bioinformatics this week: Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity

The spatial and temporal domain of a gene's expression can range from ubiquitous to highly specific. Quantifying the degree to which this expression is unique to a specific tissue or developmental timepoint can provide insight into the etiology of genetic diseases. However, quantifying specificity remains challenging as measures of specificity are sensitive to similarity between samples in the sample set. For example, in the Gene-Tissue Expression project (GTEx), brain subregions are overrepresented at 13 of 54 (24%) unique tissues sampled. In this dataset, existing specificity measures have a decreased ability to identify genes specific to the brain relative to other organs. To solve this problem, we leverage sample similarity information to weight samples such that overrepresented tissues do not have an outsized effect on specificity estimates. We test this reweighting procedure on 4 measures of specificity, Z-score, Tau, Tsi and Gini, in the GTEx data and in single cell datasets for zebrafish and mouse. For all of these measures, incorporating sample similarity information to weight samples results in greater stability of sets of genes called as specific and decreases the overall variance in the change of specificity estimates as sample sets become more unbalanced. Furthermore, the genes with the largest improvement in their specificity estimate's stability are those with functions related to the overrepresented sample types. Our results demonstrate that incorporating similarity information improves specificity estimates' stability to the choice of the sample set used to define the transcriptome, providing more robust and reproducible measures of specificity for downstream analyses.

Congratulations to Sarah Spendlove on her First, First Author paper as a graduate Student!

link to PDF

Sarah’s paper explore the role of common genetic variation in the rare, pediatric phenotype of congenital heart disease. Her work shows that common genetic varients that influence more common traits like heart-valve disease can account for ~ 2 % of the genetic variance of these disorders. This work is among the first papers that look at the role of polygenic risk scores on the severity of congenital phenotypes! Congrats Sarah!

Applying to Graduate School and PhD programs?

We will be accepting rotation students for the 2021 and 2022 years!

For PhD-programs in the biosciences, please apply through the Graduate Program in Biosciences (GPB) https://bioscience.ucla.edu/; Valerie Arboleda is a member of the Home Areas of : Genetics and Genomics, Gene Regulation Epigenomics and Transcriptomics (GREaT), and Bioinformatics!

Interested in an MD-PhD dual degree program? Consider https://mstp.healthsciences.ucla.edu/ . Its an amazing program that continues to evolve and consistently improve!

Swab-Seq: Development of a high-throughput platform for massively scaled up SARS-CoV-2 testing and Sequencing

Our work on a novel, sequencing-based diagnostic platform for COVID-19 is out in Nature Biomedical Engineering, click here for full paper!

Here we describe SwabSeq— our efforts to circumvent the supply chain disruptions with nasal swabs and use untapped sequencing capacity for widespread screening of individuals for COVID19. Together with a team from the Departments of Human Genetics and Computational Medicine , we have developed and deployed scalable testing that was used throughout the winter surge in Southern California and has performed over 150,000 tests since starting testing 7 months ago.

Today, our test is used for widespread asymptomatic screening across the UCLA campus and other southern California sites.

I’m incredibly proud of our team for developing and deploying the assay! It was a lot of work, but 100% worth it. Stay safe out there— from what we are seeing— the delta variant is definitely spreading.

Contact us: 

David Geffen School of  Medicine, UCLA
Department of Pathology and Laboratory Medicine
615 Charles E. Young Drive South
lab: BSRB 346
Los Angeles, CA 90095
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Join Us

We are looking for highly motivated and enthusiastic postdocs, graduate students, and undergraduates. Please see our Opportunities page or contact Valerie by email if you are interested in joining the lab.