Protein List and Enrichment Analysis of USP7-IP-MS

SRSF Family Proteins Essentiality in Tumor Cell Lines

Mutation Status of Selected Splicing Factors in T-ALL patients

KEGG Pathway Enrichment Analysis of Differential Expressed Genes Between Thymus and T-ALL

KEGG Enrichment Analysis of Differential Expressed Genes Between Thymus and T-ALL

Protein List and Enrichment Analysis of KGG-MS

Gene Ontology Analysis of Overlap Proteins from USP7-IP-MS and KGG-MS

KEGG Pathway Enrichment Analysis of Differential Expressed Genes Between CD4 T-Cells and T-ALL

Motif Analysis of Skip Exon Events in T-ALL Compared to CD3 T Cells

CRISP Screens of RNA Binding Proteins in T-ALL

Supplementary Figures S1-S15 and Legends

KEGG Enrichment Analysis of Overlapped rMATS Transcripts in CD3 T Cells vs Thymus and CD4 T Cells vs Thymus

Alternative Spliced Genes Between HR and NHR T-ALL Patients and Enrichment Analysis

A block in cellular differentiation is a hallmark of acute myeloid leukemia (AML) that promote clonal expansion and influence therapy response 1,2. It has become evidently clear that non-genetic mechanisms are critical to prevent malignant cells to resume its lineage maturation trajectory 3,4. However, there is still an incomplete understanding of gene regulatory pathways that induce differentiation arrest of leukemia cells. Here, we applied an immunophenotypic readout and positive selection CRISPR/Cas9 screens to identify suppressors of leukemia differentiation. These screens converged on ZBTB7A, a zinc finger transcription factor whose loss-of-function restricted AML maturation in the prescence of differentiation-inducing agents. Mechanstically, ZBTB7A ablation led to an elevated inflammatory state to stimulate leukemia proliferation. In addition, we found that genetic deletion of ZBTB7A and its paralog, ZBTB7B cooperatively suppresses myeloid differentiation and promotes resistance to several clinical compounds. Lastly, we identify that leukemic cells hijack multiple upstream 3'UTR processes, such as alternative polyadenylation and mRNA decay to downregulate ZBTB7A and ZBTB7B expression. Together, these data provide fundamental insight into non-genetic mechanisms that impede myeloid differentiation and mediate drug resistance.

Differential Gene Expression and Enrichment Analysis Between Control and shSRSF6-Treated JURKAT Cells

KEGG Pathway Enrichment Analysis of Differential Expressed Genes Between CD3 T-Cells and T-ALL

Supplementary Figures and Figure Legends

Author(s): Wang, Eric | Advisor(s): Oakes, Scott | Abstract: Apoptosis is a highly conserved form of programmed cell death in multicellular organisms where a cell activates caspase proteases to trigger its own demise. It has critical functions under physiological conditions in removing superfluous or damaged cells from a healthy organism. However, dysregulated apoptosis plays an important role in diseases: improper or elevated apoptosis leads to diseases of cell loss, such as diabetes or neurodegeneration, while deficiencies in apoptosis can contribute to tumor cell growth and survival.While the importance of apoptosis during late embryogenesis is well-established, its function during the earliest stages of development, namely the exit of embryonic stem cells (ESC) from the pluripotent state, is unclear. Here, I discovered that apoptosis plays a critical role in removing slow-differentiating murine ESC from the total cell population. This is initiated by p53-dependent upregulation of the Fas death receptor on straggling ESCs, which then triggers apoptosis specifically in these cells. An inability to initiate apoptosis, by transient knockdown or genetic deletion of components of this pathway, causes retention of slow-differentiating ESCs and a global delay in differentiation, both in vitro and in an in vivo teratoma model. Thus, apoptosis is crucial in promoting the efficient differentiation of ESCs.While apoptosis is important for normal development, elevated levels due to cellular stress can cause inappropriate cell loss and degeneration, leading to disease. One such example is retinitis pigmentosa, an inherited disease where rod photoreceptors are progressively lost from the neural retina, eventually leading to blindness. There is increasing evidence that accumulation of unfolded proteins within the endoplasmic reticulum (ER) of rod photoreceptors causes ER stress and subsequent cell death. Here, I utilize a novel small molecule inhibitor to show that inhibition of IRE1α, an ER transmembrane kinase/endoribonuclease that can signal both adaptation and apoptosis in response to ER stress, preserves rod photoreceptor viability and function in two rodent models of ER stress-induced photoreceptor degeneration.These findings reveal new insights into the role of apoptosis under both normal and stressed conditions, and may have implications for human diseases such as cancer and neurodegeneration.