Development of a Chemometric Platform for Mid-Infrared Fermentation Monitoring

Research Square · 2025-11-28

Abstract B035: Zebrafish modeling predicts clinical outcomes in human acute lymphoblastic leukemia

Cancer Research · 2025-09-25

Abstract The complex heterogeneity of Acute lymphoblastic leukemia (ALL) often predicts poor prognosis, high morbidity, and drug resistance. Yet, the molecular drivers that initiate aggressive ALL have yet to be fully elucidated, especially in the context of the >30 subtypes of human T- and B-ALL. Here, we used a large-scale F0 transgenic screen in zebrafish to identify synergistic combinations of 65 putative oncogenes at inducing both T- and B-cell leukemia. This approach identified a new proto-oncogene SET that collaborates with both notch1a icn and mutationally activated Interleukin 7 Receptor (IL7R) to initiate aggressive leukemia in vivo. SET is a multifunctional protein that can act as a transcriptional regulator, a histone chaperone, and an inhibitor of protein phosphatase 2A (PP2A). The high expression of SET along with mutational activation of NOTCH1 and IL7R was also found in human B- and T-ALL, supporting their oncogenic roles in leukemogenesis. Our discovery that SET is capable of independently synergizing with known drivers to initiate ALL presents a unique opportunity to explore the nature of oncogene driven ALL and define the mechanisms by which it drives transformation. We next used Non-negative Matrix Factorization to unbiasedly identify six gene programs shared across the zebrafish ALL subtypes and assessed if each was predictive of outcome in human disease. One program comprised a MYC-driven transcription signature that unexpectedly predicted good outcomes in human T-ALL patients. Additional conserved programs independently stratified patients into poor outcomes and when combined with the MYC signature profile were able to better discern disease outcomes in patients, including the aggressive ETP-like and TAL1 DP-like T-ALL. Taken together, we have uncovered new roles for SET in driving ALL initiation, uncovered unexpected high MYC expression as predictive of good outcome, and defined a new combination biomarker gene signature that predicts poor overall survival in aggressive subtypes of human T-ALL. Our zebrafish-based screening approach is a powerful tool for comparative genomic studies to identify new oncogenic drivers, vulnerability pathways, and new biomarkers of aggression in ALL. Citation Format: James R Allen, Luis Antonio Corchete Sanchez, Mohamed N Bakr, Miriam Fernández-Lajarín, Alexandra Hazelwood, Nathan Ford, Anna M Lucianò, Alexandra Veloso, Alexander D Weissman, Olivia A Strom, Esther Rheinbay, David M Langenau. Zebrafish modeling predicts clinical outcomes in human acute lymphoblastic leukemia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2):Abstract nr B035.

In Vivo Genetic Screen Identifies Chromatin Remodeling Gene SET As a Collaborating Oncogenic Driver in Initiation and Maintenance of Acute Lymphoblastic Leukemia

Blood · 2024-11-05

Innovative treatment options have greatly improved outcomes for acute lymphoblastic leukemia (ALL) patients over several decades, yet relapse and refractory disease remain a significant clinical challenge. The complex genomic heterogeneity of molecular subtypes contributes to poor prognosis, high morbidity, and recurrent drug resistance in relapse and refractory ALL patients. Identifying novel genetic interactions and molecular pathways capable of initiating ALL will help to develop new diagnostic criteria and to identify actionable drug targets. Here, we developed a novel in vivo screening method using transgenic zebrafish to unbiasedly identify collaborating oncogenic drivers that when co-expressed lead to T- and B-ALL. Our high-throughput approach allows for rapid screening of collaborating oncogenic drivers across hundreds of individual animals in a cost-effective manner. Specifically, we screened a transgene pool of 68 putative oncogenes identified from relapsed human ALL for synergies at inducing leukemia in a large-scale F0 transgenic screen. Using our approach, complex gene networks involved in cancer initiation in human patients can be rapidly interrogated and unraveled with in vivo resolution utilizing the zebrafish model. Low concentrations of transgene pools containing candidate cDNAs driven by a tissue specific immune cell promoter were co-injected into zebrafish along with a fluorescent reporter (rag2:mCherry). Animals that developed tumors express mCherry along with only 5 to 20 additional transgenes (median 15 genes), indicative of random concatemeric integration of transgenes into the genome. Using histopathologic analysis and bulk mRNA sequencing, we identified zebrafish with mCherry-labeled thymic T cell lymphomas, T-ALL, and B-ALL ((>140 animals). Analysis of transgene expression from bulk-RNA sequencing studies allowed us to nominate causative combinations of human transgenes that drive leukemia onset in the zebrafish. Most notably, we identified several unique leukemia and lymphoma transgenic zebrafish models, representing T-ALL, B-ALL, mixed-phenotype acute leukemia (MPAL), T- and B-cell lymphoma, and NK cell leukemia. Our analysis also elucidated novel synergies between the proto-oncogene SET and either activated NOTCH1 or IL7R mutations to initiate ALL. To verify nominated collaborating oncogenic drivers as causative at inducing cancer, we next performed microinjection validation studies with: 1) rag2:SET + rag2:intracellular notch1a + rag2:mCherry (n=7, mean latency 105±16 days) and 2) rag2:SET + rag2:mutationally-activated IL7R + rag2:mCherry (n=5, mean latency 120±25 days). Both combinations lead to robust ALL formation in zebrafish, validating the oncogenic role of these factors in leukemia initiation. Importantly, lymphoma and leukemia were not detected in animals injected with rag2:SET (n=19, >180 days followed), or rag2:intracellular notch1a (n=31, >180 days followed) or rag2:mutationally-activated IL7R (n=18; >180 days followed). SET is a multifunctional protein involved in transcriptional regulation and histone binding. While SET has been characterized in other cancers, we found that SET collaborates with known drivers to initiate T-ALL in vivo and is also highly expressed in a vast majority of human T-ALL. SET is a potent inhibitor of H3 acetylation, suggesting that epigenetic dysregulation has a critical role in ALL oncogenic transformation. Finally, to determine whether SET is also required for human ALL maintenance, we established doxycycline inducible shRNA human ALL lines (lentiviral pINDUCER10; PMID: 21307310). We found that induced knockdown of SET inhibited cell proliferation and viability in multiple T-ALL and B-ALL cell lines while also increasing apoptotic cell death and inhibiting cell cycle progression. Taken together, our work has identified a unique role for a SET in ALL initiation and maintenance. We have generated a robust transcriptome atlas of zebrafish lymphoid malignancies, representing novel transgenic zebrafish models of several acute lymphoblastic leukemia and lymphoma molecular subtypes. In addition, our unique screening approach can be further applied towards discovery of genetic factors capable of initiating pediatric leukemias, creating a molecular “roadmap” to leukemogenesis, and identify vulnerable pathways for clinical therapies.

Titelseiten

Archiv für Geschichte der Philosophie · 2024-03-05

Minimal Change Disease Secondary to Adalimumab

Journal of the American Society of Nephrology · 2024-10-01 · 1 citations

Introduction: Adalimumab is a fully human recombinant monoclonal antibody against TNFa. There have been case reports of patients developing proteinuria following treatment with adalimumab for rheumatoid arthritis (RA). Renal pathology demonstrating membranous glomerulopathy, pauci-immune necrotizing and crescentic glomerulonephritis have been reported. We describe a patient who developed minimal change disease as an adverse effect of treatment with the anti-TNFa adalimumab. Case Description: A 63-year-old female with seropositive RA treated with adalimumab presented to the hospital with generalized swelling. Symptoms started seven days prior to admission after she received her fifth injection of adalimumab. Generalized swelling was noted the morning after her dose. She met clinical criteria for nephrotic syndrome with nephrotic range proteinuria, hypoalbuminemia, peripheral swelling, and hyperlipidemia. Significant labs included cholesterol and triglycerides of 413mg/dL and 392mg/dL, up from 208mg/dL and 178mg/dL prior to adalimumab injection. Albumin was up from 4.1gm/dL four months prior to 1.6gm/dL on admission. 24-hour urine protein was greater than 3.9g/day. Renal biopsy was obtained which showed minimal glomerular alterations with marked effacement of foot processes ultra-structurally and negative immunofluorescence studies consistent with minimal change disease. Treatment was initiated with 1mg/kg/day of prednisone with following taper after one month. Supportive management including statins and diuretics was prescribed. With the protein to creatinine ratio decreasing to 0.106g/day and albumin improving to 4.2gm/dL on the two month follow up, steroids were discontinued. Discussion: We present a case of a rare cause of adult-onset minimal changed disease secondary to adalimumab. Patients on anti-TNF therapy should be monitored for signs of nephrotic syndrome including peripheral edema, proteinuria, and hypoalbuminemia.

Titelseiten

Archiv für Geschichte der Philosophie · 2024-06-06

Abstract A002 A transgenic zebrafish screen identifies new collaborating oncogenic drivers in acute lymphoblastic leukemia

Cancer Research · 2024-09-05

Abstract Acute lymphoblastic leukemia (ALL) is an aggressive hematological malignancy that affects thousands of pediatric and adult patients each year. A major hurdle to developing more effective treatments is a limited understanding of the genes and pathways that drive ALL malignancy, and which are required for continued tumor growth. ALL is often diagnosed with the onset of advanced symptoms, making it difficult to study the early drivers of oncogenic initiation. Identifying novel genetic interactions and pathways capable of driving ALL will help to develop new diagnostic criteria and identify actionable drug targets for clinical treatments. In addition, genetic interactions between co-expressed oncogenes and their impact on initiation, progression, and therapy resistance is difficult to study and requires the costly use of genetically engineered animal models, usually mice. Here, we report a novel screening method using transgenic zebrafish to unbiasedly identify collaborating oncogenic drivers that when co-expressed lead to T- and B-ALL. We screened a transgene pool of 68 putative oncogenes identified from human ALL for synergies in driving the initiation of leukemia using a large-scale F0 transgenic gain-of-function screen in zebrafish. We recovered zebrafish with tumors that were predominantly T- and B-ALL, but also identified several fish with thymic T cell lymphomas, muscle sarcomas, and liposarcomas, demonstrating the robust capability of our approach to discover novel oncogenic collaborations. Comparative transcriptome analysis using bulk RNA sequencing between zebrafish tumors (>150 tumors) revealed candidate transgene combinations that likely act as drivers of tumor formation in T- and B-ALL. When microinjected for validation studies, two transgene combinations: 1) rag2:SET + rag2:intracellular notch1a and 2) rag2:SET + rag2:mutationally-activated IL7R lead to robust ALL formation in zebrafish, validating the oncogenic role of these factors in leukemia initiation. SET is a multifunctional protein involved in transcriptional regulation, histone binding, and cell death. While SET has been well characterized in other cancers, we found that SET is capable of collaborating with known drivers to initiate T-ALL in vivo and highly expressed in a vast majority of human T-ALL. Our SET models also revealed an enrichment of key pathways that drive proliferation in both zebrafish and human disease. We are currently performing molecular characterization of SET in human ALL cell lines to investigate SET driven ALL growth and maintenance. In addition, our panel of unique zebrafish tumors will allow help establish new models of hematologic malignancies, launch future investigations into leukemia pathology, and identify novel targets of therapy resistance. Citation Format: James R. Allen, Luis Antonio Corchete Sanchez, Mohamed N. Bakr, Miriam Fernandez-Lajarin, Alexandra Hazelwood, Nathan Ford, Alexandra Veloso, Victoriano Mulero, Maria L. Cayuela, Esther Rheinbay, David M. Langenau. A transgenic zebrafish screen identifies new collaborating oncogenic drivers in acute lymphoblastic leukemia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr A002.

Titelseiten

Archiv für Geschichte der Philosophie · 2023

• Computer Science
• Computer Science

Titelseiten

Archiv für Geschichte der Philosophie · 2023-09-05

CASZ1 upregulates PI3K-AKT-mTOR signaling and promotes T-cell acute lymphoblastic leukemia

Haematologica · 2023-12-07 · 8 citations

CASZ1 is a conserved transcription factor involved in neural development, blood vessel assembly and heart morphogenesis. CASZ1 has been implicated in cancer, either suppressing or promoting tumor development depending on the tissue. However, the impact of CASZ1 on hematological tumors remains unknown. Here, we show that the T-cell oncogenic transcription factor TAL1 is a direct positive regulator of CASZ1, that T-cell acute lymphoblastic leukemia (T-ALL) samples at diagnosis overexpress CASZ1b isoform, and that CASZ1b expression in patient samples correlates with PI3K-AKT-mTOR signaling pathway activation. In agreement, overexpression of CASZ1b in both Ba/F3 and T-ALL cells leads to the activation of PI3K signaling pathway, which is required for CASZ1b-mediated transformation of Ba/F3 cells in vitro and malignant expansion in vivo. We further demonstrate that CASZ1b cooperates with activated NOTCH1 to promote T-ALL development in zebrafish, and that CASZ1b protects human T-ALL cells from serum deprivation and treatment with chemotherapeutic drugs. Taken together, our studies indicate that CASZ1b is a TAL1-regulated gene that promotes T-ALL development and resistance to chemotherapy.