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Tag: Transcription Factors

  • Research identifies how leukemia develops resistance to first line treatments

    Research identifies how leukemia develops resistance to first line treatments

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    Relapses in a common form of leukemia may be preventable following new research which has identified how the cancer develops resistance to first line treatments.

    New research published in iScience by researchers from the University of Birmingham, the Institute of Cancer Research (ICR), Newcastle University, the Princess Maxima Centre of Pediatric oncology and the University of Virginia identified changes in a mutated form of acute myeloid leukemia (AML) samples from patients who relapsed after receiving FLT3 inhibitor treatment.

    The team found that the resistant cancer had up-regulated multiple other signalling pathways to overcome the drug’s action, and that the genetic change was able to be replicated in lab tests.

    These experiments revealed that by targeting RAS family proteins, using a small molecule inhibitor developed from a chemical library screen using the paratope of an inhibitory intracellular antibody by Terry Rabbitts’ team at the Weatherall Institute of Molecular Medicine University of Oxford and the ICR, increased signalling no longer rescued the cells from cell death.

    The team identified that the transcription factors AP-1 and RUNX1 were at the heart of mediating drug resistance. The two factors cooperate and bind to their target genes together, but only in the presence of growth factor signalling. The drugs targeting FLT3 rewire the cell, resulting in the upregulation of other signalling pathway associated genes, which then restored AP-1 and RUNX1 binding. Drugging RAS, which is a key component in multiple signalling pathways, prevented this restoration of RUNX1 binding, and therefore signalling from growth factors no longer rescued the cancer cells from death.

    Professor Constanze Bonifer from the Institute of Cancer and Genomic Sciences at the University of Birmingham, who has just taken up a position at the University of Melbourne, and is one of the senior authors of the paper said:

    “The pharmaceutical industry had high hopes that drugs targeting aberrant growth factor receptors such as the FLT3-ITD would prevent people from relapse. However, cancer cells are smart, and rewire their growth control machinery to use other growth factors present in the body. Targeting RAS family members prevents the cancer from rewiring and using different signalling pathways to escape cell death.”

    Targeting RAS blocks rewiring

    The small molecule inhibitors used to target RAS in this study were developed using intracellular antibody technology. This technology involves screening a large number of antibody fragments to identify those which bind to the target protein in cells and prevent their protein-protein interactions. Small molecule inhibitors are can be screened from chemical libraries that interact with the parts of the target protein where these antibody fragments bind (the paratope). Due to the unparalleled natural specificity of these antibody fragments, this technology (called Antibody derived or Abd technology) can be used to target difficult to drug proteins and identify new parts of the protein which can be targeted to prevent protein-protein interactions.

    Professor Terry Rabbitts from the Institute of Cancer Research who developed these drugs said:

    “The strength of the Antibody-derived technology approach is that intracellular antibodies can selected to essentially any protein. In turn, their specific binding sites can be employed to select chemical compounds for drug discovery against hard to drug proteins. Mutant RAS was considered undruggable, but the Abd technology facilitated the development of the RAS-binding compounds used in the current study of cancer cell re-wiring. Abd technology will allow development of a new generation of drugs to hard-to-drug and intrinsically disordered proteins.“

    AML with a FLT3-ITD mutation occurs in nearly 30% of all patients and is a highly aggressive disease with a poor prognosis. This genetic change causes the expression of a mutant growth factor receptor which is always active and therefore cancer cells expressing it grow uncontrollably. While inhibitors which specifically target the FLT3 protein are now in use in the clinic, patients treated with these inhibitors frequently relapse.

    This work was funded by Leukaemia Research UK, the Medical Research Council, Blood Cancer Research UK, the Royal Society, the Wellcome and Cancer Research UK. The first author, Daniel Coleman is a John Goldman Fellow of Leukaemia UK.

    Source:

    Journal reference:

    Daniel J.L., et al. (2024). Pharmacological inhibition of RAS overcomes FLT3 inhibitor resistance in FLT3-ITD+ AML through AP-1 and RUNX1. iScience. doi.org/10.1016/j.isci.2024.109576.

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  • Scientists uncover four proteins that govern the identity of anaplastic large cell lymphoma

    Scientists uncover four proteins that govern the identity of anaplastic large cell lymphoma

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    A collaboration between scientists from St. Jude Children’s Research Hospital and Dana-Farber Cancer Institute uncovered four proteins that govern the identity of anaplastic large cell lymphoma (ALCL), an aggressive form of cancer. These proteins comprise a core regulatory circuit (CRC) that surprisingly incorporates a dysregulated signaling protein. Establishing the CRC for this lymphoma gives researchers insight into potential vulnerabilities that may be future therapeutic targets. The findings were published today in Cell Reports Medicine.

    “Mutations in signaling pathways have long been known to drive oncogenic transformation and tumor progression,” said senior co-corresponding author Mark Zimmerman, PhD, currently of Foghorn Therapeutics, previously of Dana-Farber Cancer Institute and Boston Children’s Hospital. “Our new results show a mechanistic link in this aggressive T-cell lymphoma between aberrant signaling pathway activation and the dysregulated gene expression that is a hallmark of these tumor cells.”

    ALCL patient tumors and models showed significant dysregulation of a protein called signal transducer and activator of transcription 3 (STAT3). STAT3 is a signaling protein that integrates information from other proteins, acting as a transcription factor (a protein involved in regulating the copying of genetic information from DNA into messenger RNA). 

    We have found how dysregulation of the signaling protein STAT3 is central to enforcing ALCL cancer identity. A healthy cell has a ‘Board of Directors’ made up of a few dominant regulators, and STAT3 gets ‘promoted’ from a division chief to a full board member with all the rights and powers that grants.”


    Brian J. Abraham, PhD, co-corresponding author, St. Jude Department of Computational Biology

    Among the genes it controls, STAT3 increases expression of the protein MYC, which is well-known to be associated with cancers. Nearly every ALCL cell line tested showed either a mutation in STAT3 or in a protein that signals to STAT3, causing it always to be always “on” and directing gene expression, promoting perpetual cell growth through its targets.

    The findings have implications for treatment because drugs that target the STAT family of proteins and other proteins that signal through STAT3 already exist.

    Finding a core regulatory circuit for all ALCL subtypes

    “Transcription factors and proteins that regulate the oncogenic gene expression programs are emerging as some of the most direct and effective targets for cancer therapy,” said first author Nicole Prutsch, PhD, Dana-Farber Cancer Institute and Boston Children’s Hospital. “STAT3 was already a recognized transcriptional activator in ALCL, but our research has identified a core transcriptional regulatory circuit hijacked by STAT3 to drive genes essential for ALCL cell growth.”

    STAT3 hijacks three transcription factors that comprise the CRC: BATF3, IRF4 and IKZF1. All were expressed at high levels in ALCL cells, although they lacked any cancer-causing mutations. They were also identified as potential vulnerabilities in the DepMap Consortium gene knockout studies. When the scientists lowered the expression of any of these proteins, it significantly reduced cancer cell growth, demonstrating the centrality of the CRC.

    “This is the first core regulatory circuit, to our knowledge, identified for ALCL,” Abraham said. Of the two major known molecular ALCL subtypes, anaplastic lymphoma kinase (ALK)-positive has an 80% survival rate, while ALK-negative has a 48% survival rate. Contrary to these differences, the researchers found both types relied on the same CRC.

    “ALCL represents a diverse group of T-cell lymphomas with distinct clinical behaviors,” Prutsch said. “While ALK-positive cases respond well to ALK inhibitors, ALK-negative ALCL is highly aggressive and possesses limited targeted therapy options, highlighting the critical need for new treatment strategies.”

    To understand the difference between the subtypes and find potential vulnerabilities, the researchers mapped special complexes of DNA and proteins called super-enhancers. These clusters of transcription-regulating elements are known to influence gene expression tightly. In cancers, super-enhancers can play a role in maintaining the cancer’s identity as a malignancy. 

    The scientists found that super-enhancers that differed among ALCLs converged to highlight the same CRC across ALCL tumors and models.

    “The core regulatory circuit appears to be common across what have historically been treated as distinct diseases,” Abraham said. “Regardless of if an ALCL cell is ALK-positive or ALK-negative, it relies on the expression and the positive feedback provided by this circuit to stay ALCL.”

    Potential vulnerabilities highlight treatment opportunities

    Understanding the central role of the CRC in this cancer has implications for treatment. Drugs that target the STAT family of proteins and other proteins that signal through STAT3 already exist -; but they have seen limited success, particularly in ALK-negative disease. Knowledge of the CRC and its interaction with STAT3 may allow for developing novel therapeutics and combination strategies.

    “Our findings reveal a significant relationship between the core regulatory circuit members and STAT3,” Prutsch said, “This emphasizes the potential for therapies leveraging these connections and offers attractive options for developing new treatments in ALK-negative ALCL.”

    The same methods used in the study may also provide a path to understanding and searching for vulnerabilities in other malignancies without a clear driver mutation.

    “Our discovery indicates that exploiting the interconnectedness between signaling and transcriptional dependencies is a rational approach to developing new treatment strategies across a broad range of cancers,” Zimmerman said.

    Authors and funding

    The study’s other authors are Shuning He, Alla Berezovskaya, and Kimberly Stegmaier, Dana-Farber Cancer Institute and Boston Children’s Hospital; Neekesh Dharia, Genentech; Jamie Matthews, Lucy Hare, and Suzanne Turner, University of Cambridge, Addenbrooke’s Hospital; Lukas Kenner, Masaryk University; Olaf Merkel, Medical University of Vienna; and Adam Durbin, and Kelsey Maher, St. Jude.

    The study was supported by grants from the National Institutes of Health (R35CA210064, R35CA210030 and K08CA245251), Lymphoma Research Foundation, Julia’s Legacy of Hope St. Baldrick’s Foundation Fellowship, National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102), European Union – Next Generation, Cancer Research UK Cambridge Centre (CTRQQR-2021\100012), Alex’s Lemonade Stand Foundation, Charles A. King Trust, Claudia Adams Barr Foundation and ALSAC, the fundraising and awareness organization of St. Jude.

    Source:

    St. Jude Children’s Research Hospital

    Journal reference:

    Prutsch, N., et al. (2024) STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma. Cell Reports Medicine. doi.org/10.1016/j.xcrm.2024.101472.

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  • New method simplifies production of limb progenitor cells from fibroblasts

    New method simplifies production of limb progenitor cells from fibroblasts

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    In a collaborative study, researchers from Kyushu University and Harvard Medical School have identified proteins that can turn or “reprogram” fibroblasts -; the most commonly found cells in skin and connective tissue -; into cells with similar properties to limb progenitor cells. Publishing in Developmental Cell, the researchers’ findings have enhanced our understanding of limb development and have set the stage for regenerative therapy in the future.

    Globally, close to 60 million people are living with limb loss. Amputations can result from various medical conditions such as tumors, infections, and birth defects, or due to trauma from industrial accidents, traffic accidents, and natural disasters such as earthquakes. People with limb injuries often rely on synthetic materials and metal prostheses, but many researchers are studying the process of limb development, with the aim of bringing regenerative therapy, or natural tissue replacement, one step closer as a potential treatment.

    “During limb development in the embryo, limb progenitor cells in the limb bud give rise to most of the different limb tissues, such as bone, muscle, cartilage and tendon. It’s therefore important to establish an easy and accessible way of making these cells,” explains Dr. Yuji Atsuta, lead researcher who began tackling this project at Harvard Medical School and continues it as a lecturer at Kyushu University’s Graduate School of Sciences.

    Currently, a common way to obtain limb progenitor cells is directly from embryos, which, in the case of human embryos, raises ethical concerns. Alternatively, they can be made using induced pluripotent stem cells -; adult cells which are reprogrammed into an embryonic-like state, and which can later be coaxed into specific tissue types. The new method developed by Atsuta and colleagues, which directly reprograms fibroblast cells into limb progenitor cells and bypasses induced pluripotent stem cells, simplifies the process and reduces costs. It also mitigates the concern of cells turning cancerous, which often occurs with induced pluripotent stem cells.

    In the initial phase of the study, the researchers looked at what genes were expressed in the early limb buds in mice and chicken embryos. Almost all cells in the body, including fibroblasts and limb progenitor cells, contain identical genomic DNA, but the different properties and functions of each cell type emerge during development due to changes in gene expression (in other words, which genes are active, and which proteins are produced by the cell). One way that gene expression is controlled in cells is by specific proteins, called transcription factors.

    The research group identified 18 genes, mostly transcription factors, that are more highly expressed in the early limb bud compared to other tissues. They cultured fibroblasts from mouse embryos and introduced these 18 genes into the fibroblasts using viral vectors so that the cells produced these 18 protein factors. They found that the modified fibroblasts took on the properties and showed similar gene expression to naturally-occurring limb progenitor cells found in limb buds. 

    Next, over a series of experiments, the researchers narrowed down their selection and determined that only three protein factors were essential to reprogram mouse fibroblasts into limb progenitor-like cells: Prdm16, Zbtb16, and Lin28a. A fourth protein, Lin41, helped the cultured limb progenitor cells grow and multiply more rapidly.

    The researchers not only confirmed that the reprogrammed limb progenitor cells had similar gene expression to natural limb progenitor cells, but also had similar ability.

    These reprogrammed cells are not only molecular mimics; we have confirmed their potential to develop into specialized limb tissues, both in laboratory dishes (in vitro) and also in living organisms (in vivo). Testing in vivo was particularly challenging, as we had to transplant the reprogrammed mouse cells into the limb buds of chicken embryos.”

    Dr. Yuji Atsuta, lead researcher

    In these experiments, the researchers used lentiviruses, which insert genes directly into the infected cells’ genome, raising the risk that the cells can become cancer. Instead, the team is considering other safer vectors, such as adeno-associated viruses or plasmids, which deliver genes to the cells without inserting genes into the genome.

    Atsuta’s lab group is now trying to apply this method to human cells, for future therapeutic applications, and also to snakes, whose ancestors had limbs that were subsequently lost during evolution.

    “Interestingly, the reprogrammed limb progenitor cells generated limb bud-like organoids, so it seems possible to generate limb tissues in species that no longer possess them. The study of limbless snakes can uncover new pathways and knowledge in developmental biology.“

    Source:

    Journal reference:

    Atsuta, Y., et al. (2024). Direct reprogramming of non-limb fibroblasts to cells with properties of limb progenitors. Developmental Cell. doi.org/10.1016/j.devcel.2023.12.010.

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  • Targeting gene-fibroblast interaction offers hope for treatment-resistant colon cancer

    Targeting gene-fibroblast interaction offers hope for treatment-resistant colon cancer

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    A new research paper was published in Aging (listed by MEDLINE/PubMed as “Aging (Albany NY)” and “Aging-US” by Web of Science) Volume 16, Issue 2, entitled, “PROX1 interaction with α-SMA-rich cancer-associated fibroblasts facilitates colorectal cancer progression and correlates with poor clinical outcomes and therapeutic resistance.”

    The tumor microenvironment (TME) plays a vital role in tumor progression through intricate molecular interactions. Cancer-associated fibroblasts (CAFs), notably those expressing alpha-smooth muscle actin (α-SMA) or myofibroblasts, are instrumental in this context and correlate with unfavorable outcomes in colorectal cancer (CRC). While several transcription factors influence TME, the exact regulator causing CAF dysregulation in CRC remains elusive. Prospero Homeobox 1 (PROX1) stands out, as its inhibition reduces α-SMA-rich CAF activity. However, the therapeutic role of PROX1 is debated due to inconsistent study findings.

    In this new study, researchers Shiue-Wei Lai, Yi-Chiao Cheng, Kee-Thai Kiu, Min-Hsuan Yen, Ying-Wei Chen, Vijesh Kumar Yadav, Chi-Tai Yeh, Kuang-Tai Kuo, and Tung-Cheng Chang from Taipei’s National Defense Medical Center, Taipei Medical University, Taipei Medical University Shuang-Ho Hospital, and National Taitung University used the ULCAN portal and noted an elevated PROX1 level in advanced colon adenocarcinoma, linking to a poor prognosis. Their assays determined the impact of PROX1 overexpression on CRC cell properties, while co-culture experiments spotlighted the PROX1-CAF relationship. Molecular expressions were validated by qRT-PCR and Western blots, with in vivo studies further solidifying the observations.

    “Our study emphasized the connection between PROX1 and α-SMA in CAFs.”

    Elevated PROX1 in CRC samples correlated with increased α-SMA in tumors. PROX1 modulation influenced the behavior of specific CRC cells, with its overexpression fostering invasiveness. Kaplan-Meier evaluations demonstrated a link between PROX1 or α-SMA and survival outcomes. Consequently, PROX1, alone or with α-SMA, emerges as a CRC prognostic marker. Co-culture and animal experiments further highlighted this relationship.

    PROX1 appears crucial in modulating CRC behavior and therapeutic resistance within the TME by influencing CAFs, signifying the combined PROX1/α-SMA gene as a potential CRC prognostic marker. The concept of developing inhibitors targeting this gene set emerges as a prospective therapeutic strategy. However, this study is bound by limitations, including potential challenges in clinical translation, a focused exploration on PROX1/α-SMA potentially overlooking other significant molecular contributors, and the preliminary nature of the inhibitor development proposition.

    “As we advance in this field, the development and clinical validation of small-molecule inhibitors targeting PROX1/α-SMA become imperative, paving the way to refine and optimize CRC therapeutic interventions.”

    Source:

    Journal reference:

    Lai, S.-W., et al. (2024). PROX1 interaction with α-SMA-rich cancer-associated fibroblasts facilitates colorectal cancer progression and correlates with poor clinical outcomes and therapeutic resistance. Aging. doi.org/10.18632/aging.205447.

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  • Scientists decode how tiny mutations can derail development

    Scientists decode how tiny mutations can derail development

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    Our genomes provide the instructions for proper growth and development. Millions of genomic switches, known as enhancers, control the location and timing of gene expression, which in turn ensures the correct proteins are made in the right cells at the right time throughout our lives. New research from University of California San Diego Assistant Professor Emma Farley’s lab shows how we can now predict which single base-pair changes to the DNA within our genomes will alter these instructions and disrupt development, causing extra digits and hearts.

    We now have genome sequences for over half a million people and counting. These genomes hold the key to how each of us comes to be and the promise of attaining precision medicine tailored to an individual’s own genetic makeup. Yet we cannot take full advantage of these datasets since we don’t understand a critical aspect of the genome: enhancers, which act as switches to control when and where our genes are expressed as proteins. Most genetic variants or mutations that cause disease lie within these enhancers. A central challenge has been to determine which sequence changes within enhancers matter and which do not. Thus far, pinpointing such causal enhancer variants has been akin to searching for a needle in a haystack.

    Publishing in the journal Nature, the Farley lab has addressed this challenge by achieving the ability to predict which changes to enhancers would cause changes in gene expression across thousands of enhancers and cell types. This ability to predict causal enhancer variants is rooted in a deep understanding of how enhancers function. The researchers showed that enhancers activate gene expression by binding proteins known as transcription factors very weakly. Adhering to this rule ensures enhancers activate gene expression, and thus protein production, at the right level, place and time. The Farley lab found that single-letter changes to our genome that strengthen the interaction of an enhancer with a transcription factor cause enhancers to switch on gene expression inappropriately and make proteins at the wrong level, time and/or place. Therefore, these single-letter changes to the enhancer DNA within our genome have dramatic effects on the genetic instructions, leading to extra fingers in mice and humans.

    The Farley lab identified three human families in which such mutations cause extra fingers and was able to predict which mutations would lead to even more fingers and more severe limb defects. Their ability to predict which enhancer variants will alter genomic instructions is not limited to limbs and generalizes to thousands of enhancers across cell types and species. In a complementary study published in Developmental Cell, the Farley lab showed that within marine animals known as sea squirts, single-letter changes that make heart enhancers stronger led to the development of a second beating heart.

    Pinpointing enhancer variants that alter the instructions for development encoded in a genome is key for seizing the full potential of genomic data for improving human health and obtaining the goals of precision medicine. Across thousands of enhancers, the Farley lab found that searching for DNA base-pair changes that make enhancers stronger enabled (up to) a seven-fold increase in their ability to find causal enhancer variants.

    Our study illustrates a key vulnerability in our genomes: single base-pair changes that make transcription factors bind to an enhancer even slightly stronger can cause developmental defects. Taking advantage of this knowledge will allow us to better predict which enhancer variants underlie disease in order to harness the full potential of our genomes for better human health.”


    Emma Farley, Faculty Member, Departments of Medicine (School of Medicine) and Molecular Biology (School of Biological Sciences), University of California San Diego 

    Farley is a recipient of the New Innovator Award and National Science Foundation CAREER Award, which funded this work. For the Nature paper, the first authors of this work are two UC San Diego graduate students, Fabian Lim (Biological Sciences) and Joe Solvason (Bioinformatics and Systems Biology), and postdoctoral scholar Genevieve Ryan. They were supported by Farley lab members: Sophia Le, Granton Jindal, Paige Steffen and Simran Jandu.

    The Developmental Cell paper was authored by postdoc Granton Jindal, graduate students Alexis Bantle (Biological Sciences) and Joe Solvason (Bioinformatics and Systems Biology), Jessica Grudzien, Agnieszka D’Antonio-Chronowska, Fabian Lim, Sophia Le, Benjamin Song, Michelle Ragsac, Adam Klie, Reid Larsen Kelly Frazer and Emma Farley.

    The research was funded by National Institutes of Health (DP2HG010013, T32HL007444, T32GM127235, T32GM133351, T32GM008666 and U01HL107442), National Science Foundation (2239957, CMMI1728497), American Heart Association (18POST34030077), UC San Diego Chancellor’s Research Excellence Scholars Program and California Institute for Regenerative Medicine (CIRM GC1R-06673-B).

    Source:

    University of California – San Diego

    Journal reference:

    Lim, F., et al. (2024). Affinity-optimizing enhancer variants disrupt development. Nature. doi.org/10.1038/s41586-023-06922-8.

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  • Study shines light on the role of transcription factors during early embryonic development

    Study shines light on the role of transcription factors during early embryonic development

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    New international research shines a light on the role of transcription factors during early embryonic development. Transcription factors are proteins that are critical for gene regulation. The study unveiled over a thousand protein-protein interactions, particularly spotlighting the previously underappreciated paired-like homeobox (PRDL) family of transcription factors that are active only in early embryonic stages.

    The research is published in EMBO Reports.

    New findings are key to understanding embryonic genome activation (EGA), a vital process in early development. The research paves the way for new investigations into early embryogenesis at the molecular level, with the potential to advance treatments for developmental disorders and enhance regenerative medicine.

    The study also recasts homeobox gene TPRX2 that encodes DNA-binding proteins. TPRX2 is thought to be inactive as a pseudogene, as an essential transcriptional activator in these initial phases of development.

    The research gained deeper insights into the genomic binding patterns

    The study also gained deeper insights into the genomic binding patterns of these transcription factors. The study revealed crucial aspects of how these proteins interact with the genome, playing a pivotal role in chromatin modification and epigenetic regulation during early embryonic development.
    Beyond enhancing our fundamental comprehension of human biology, this study paves the way for investigating developmental diseases.

    We’ve constructed a comprehensive map of crucial protein interactions, marking a significant advancement in developmental biology and medicine. Knowing the key regulators and their association with each other’s and with DNA paves way on understanding the critical early steps of human development. Still, comprehensive understanding of these processes will require further extensive research.”

    Dr. Markku Varjosalo, University of Helsinki

    The study was led by Dr. Markku Varjosalo, with key contributions from international experts Professors Juha Kere and Gong-Hong Wei.

    Source:

    Helsingin yliopisto (University of Helsinki)

    Journal reference:

    Gawriyski, L., et al. (2024). Interaction network of human early embryonic transcription factors. EMBO Reports. doi.org/10.1038/s44319-024-00074-0.

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