Biology subjects

Rosen, N.

Publications and source records attributed to Rosen, N..

11 recordsLinked to original sources

bioRxiv2026

Coexistent PTEN and PIK3CA alterations hyperactivate mTORC1 signaling in endometrial cancers and cause their selective sensitivity to mTORC1 inhibition

In approximately half of endometrial carcinoma (EC), PTEN loss-of-function and activating PI3K mutants coexist. Unlike cells with either single mutation, PTEN/PIK3CA coexistent alterations result in elevated membrane phosphatidylinositol (3,4,5)-trisphosphate (PIP3) levels and mTORC1 hyperactivation, rendering PI3K or AKT inhibition ineffective in blocking mTORC1 activity and tumor growth. The bi-steric mTORC1 kinase inhibitor, RMC-6272, suppresses mTORC1 activity and cell growth by reducing protein translation and cell cycle progression. In vivo, RMC-6272, but not PI3K inhibitors, effectively suppressed mTORC1 and growth of EC PDXs with coexistent PTEN/PIK3CA lesions. These findings are consistent with a phase I trial of bi-steric mTORC1 inhibitor RMC-5552, showing anti-tumor activity in patients with EC. PDXs with KRAS co-mutations regrew after RMC-6272 treatment, which was prevented by the addition of the RAS(ON) multi-selective inhibitor RMC-7977. Overall, these data suggest that mTORC1 hyperactivation drives ECs with coexistent PTEN/PIK3CA mutations, explain the limited antitumor activity of PI3K and AKT inhibitors, and support clinical evaluation of mTORC1 inhibitors as potential therapy for EC. SignificanceWe have found the mechanistic consequences of PTEN/PIK3CA co-alterations in endometrial tumors and that these mutations result in a profound hyperactivation of mTORC1 signaling. Single mutant tumors are sensitive to PI3K inhibition but those with both mutations are insensitive to PI3K or AKT inhibition but are exquisitely dependent on mTORC1 kinase. This provides strong preclinical rationale for targeting mTORC1, alone or combined with RAS inhibition (in RAS co-mutant tumors), as an effective therapeutic strategy.

cancer biology↗

bioRxiv2025

Reduced CSF1R expression in myeloid cells has limited impact on chronic lymphocytic leukemia progression

Targeting the colony-stimulating factor 1 receptor (CSF1R) to remove tumor-associated macrophages is being explored as cancer therapy. This strategy may be relevant for chronic lymphocytic leukemia (CLL), which strongly depends on support from myeloid cells. However, it is unclear how CSF1R expression affects the CLL microenvironment and leukemic progression. To examine this question, we created CLL mice with Csf1r haploinsufficiency to investigate changes in myeloid cells, Csf1r expression, and leukemia progression. Reducing Csf1r expression on circulating monocytes did not change the overall numbers of monocytes or macrophages in blood and lymphoid tissues. Mice with lower Csf1r levels had less leukemia during early disease, but this effect faded with disease progression, and their overall survival was similar to controls. Furthermore, reduced Csf1r expression on macrophages did not affect the survival or migration of patient-derived CLL cells. In summary, our results show that while the CSF1R pathway is important for maintaining the myeloid cells that support CLL, simply reducing CSF1R expression has only a limited effect on disease progression. Attempts to target the CSF1R for leukemic therapy might benefit from a stronger depletion of macrophages or the combination with other agents.

cancer biology↗

bioRxiv2025

Diet induced insulin resistance is due to induction of PTEN expression

Insulin resistance is a condition associated with obesity, type 2 diabetes(T2D), hyperinsulinemia, hyperglycemia and defined by reduced sensitivity to insulin signaling. Molecular causes and early signaling events underlying insulin resistance are not well understood. Here we show that insulin activation of PI3K/AKT/mTOR signaling in insulin target tissues, causes mTORC1 induction of PTEN translation, a negative regulator of PI3K signaling. We hypothesized that insulin resistance is due to insulin dependent induction of PTEN that prevents further increases in PI3K signaling. In a diet induced animal model of obesity and insulin resistance, we show that PTEN levels are increased in fat, muscle, and liver. Hyperinsulinemia and PTEN induction are followed by hyperglycemia, severe glucose intolerance, and hepatic steatosis. In response to chronic hyperinsulinemia, PTEN remains increased, while AKT activity is induced transiently before settling down to a PTEN-high and AKT-low state in the tissues, predicted by computational modeling of the PTEN-AKT feedback loop. Treatment with PTEN and mTORC1 inhibitors prevent and reverse the effect of PTEN induction, rescue insulin resistance and increase PI3K/AKT signaling. Thus, we show that PTEN induction by increased insulin levels elevates feedback inhibition of the pathway causing insulin resistance, its associated phenotypes, and is a potential therapeutic target.

cell biology↗

bioRxiv2025

Systemic MIF facilitates chronic lymphocytic leukemia development independent of its cellular source

Macrophage migration inhibitory factor (MIF) is broadly produced by various cell types, particularly immune cells, and functions as a key modulator of innate and adaptive immunity. Increasing evidence has linked MIF to the pathogenesis of both solid tumors and hematologic malignancies, including chronic lymphocytic leukemia (CLL). We previously showed that the global deletion of Mif in the TCL1 transgenic mouse model for CLL significantly delayed disease development leading to longer overall survival of the knockout mice. In this study, we demonstrated that adaptive transfer of murine CLL cells failed to establish disease in Mif-deficient recipients due to impaired homing of leukemic cells into the spleens, indicating that host-derived Mif is essential for leukemic infiltration and expansion. To identify the most relevant source of Mif in CLL, we generated two CLL mouse strains with B-lymphoid- or myeloid-lineage-specific Mif deletion. In contrast to the global Mif knockout, neither conditional Mif knockout significantly altered CLL progression, illustrating that the cellular source of Mif is less critical than its systemic presence in the tissue environment. Taken together, these in vivo findings indicate that MIF plays a relevant role in CLL pathogenesis, acting independently of its specific cellular origin. HighlightsO_LICLL cells failed to establish disease in Mif-deficient hosts due to impaired tissue homing C_LIO_LIConditional deletion of Mif in B lymphoid- or myeloid cells did not significantly impact CLL progression in vivo C_LIO_LISystemic MIF is critical for CLL pathogenesis, independent of its cellular source C_LI

cancer biology↗

bioRxiv2025

Paired primary-metastasis patient-derived organoids and mouse models identify phenotypic evolution and druggable dependencies of peritoneal metastasis from appendiceal cancer

Peritoneal carcinomatosis is a common yet deadly manifestation of gastrointestinal cancers, with few effective treatments. To identify targetable determinants of peritoneal metastasis, we focused on appendiceal adenocarcinoma (AC), a gastrointestinal cancer that metastasizes almost exclusively to the peritoneum. Current treatments are extrapolated from colorectal cancer (CRC), yet AC has distinct genomic alterations, mucinous morphology and peritoneum restricted metastatic pattern. Further, no stable preclinical models of AC exist, limiting drug discovery and representing an unmet clinical need. We establish a first-in-class stable biobank of 16 long-term cultured AC patient-derived organoids (PDOs), including 3 matched, simultaneously resected primary AC-peritoneal carcinomatosis (AC-PC) pairs. By enriching for cancer cells, AC PDOs enable accurate genomic characterization relative to paucicellular AC tissue. We establish an organoid orthotopic intraperitoneal xenograft model that recapitulates diffuse peritoneal carcinomatosis and show that PC-organoids retain increased metastatic capacity, decreased growth factor dependency and sensitivity to standard of care chemotherapy relative to matched primary AC organoids. Single cell profiling of AC-PC pairs reveals dedifferentiation from mucinous differentiated states in primary AC into intestinal stem cell and fetal progenitor states in AC-PC, with upregulation of oncogenic signaling pathways. Through hypothesis-driven drug testing, we identify KRASMULTI-ON inhibitor RMC-7977 and Wnt-targeting tyrosine kinase inhibitor WNTinib as novel, clinically actionable strategies to target AC-PC more effectively.

cancer biology↗

bioRxiv2024

RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions

Identifying evolutionary changes in DNA methylation bears a huge potential for unraveling adaptations that have occurred in modern humans. Over the past decade, computational methods to reconstruct DNA methylation patterns from ancient DNA sequences have been developed, allowing for the exploration of DNA methylation changes during the past hundreds of thousands of years of human evolution. Here, we introduce a new version of RoAM (Reconstruction of Ancient Methylation), a flexible tool that allows for the reconstruction of ancient methylomes, as well as the identification of differentially methylated regions between ancient populations. RoAM incorporates a series of filtering and quality control steps, resulting in highly reliable DNA methylation maps that exhibit similar characteristics to modern maps. To showcase RoAMs capabilities, we used it to compare ancient methylation patterns between pre- and post-Neolithic revolution samples from the Balkans. Differentially methylated regions separating these populations are shown to be associated with genes related to regulation of sugar metabolism. Notably, we provide evidence for overexpression of the gene PTPRN2 in post-Neolithic revolution samples. PTPRN2 is a key regulator of insulin secretion, and our finding is compatible with hypoinsulinism in pre-Neolithic revolution hunter-gatherers. Additionally, we observe methylation changes in the genes EIF2AK4 and SLC2A5, which provide further evidence to metabolic adaptations to a changing diet during the Neolithic transition. RoAM offers powerful algorithms that position it as a key asset for researchers seeking to identify evolutionary regulatory changes through the lens of paleoepigenetics.

evolutionary biology↗

bioRxiv2024

eIF4A controls translation of estrogen receptor alpha and is a therapeutic target in advanced breast cancer

The majority of human breast cancers are dependent on hormone-stimulated estrogen receptor alpha (ER) and are sensitive to its inhibition. Treatment resistance arises in most advanced cancers due to genetic alterations that promote ligand independent activation of ER itself or ER target genes. Whereas re-targeting of the ER ligand binding domain (LBD) with newer ER antagonists can work in some cases, these drugs are largely ineffective in many genetic backgrounds including ER fusions that lose the LBD or in cancers that hyperactivate ER targets. By identifying the mechanism of ER translation, we herein present an alternative strategy to target ER and difficult to treat ER variants. We find that ER translation is cap-independent and mTOR inhibitor insensitive, but dependent on 5 UTR elements and sensitive to pharmacologic inhibition of the translation initiation factor eIF4A, an mRNA helicase. EIF4A inhibition rapidly reduces expression of ER and short-lived targets of ER such as cyclin D1 and other components of the cyclin D-CDK complex in breast cancer cells. These effects translate into suppression of growth of a variety of ligand-independent breast cancer models including those driven by ER fusion proteins that lack the ligand binding site. The efficacy of eIF4A inhibition is enhanced when it is combined with fulvestrant--an ER degrader. Concomitant inhibition of ER synthesis and induction of its degradation causes synergistic and durable inhibition of ER expression and tumor growth. The clinical importance of these findings is confirmed by results of an early clinical trial (NCT04092673) of the selective eIF4A inhibitor zotatifin in patients with estrogen receptor positive metastatic breast cancer. Multiple clinical responses have been observed on combination therapy including durable regressions. These data suggest that eIF4A inhibition could be a useful new strategy for treating advanced ER+ breast cancer.

cancer biology↗

bioRxiv2023

ERK Activation by BRAFV600E suppresses mesenchymal migration and tumorigenesis by inhibiting RAC1.

BRAFV600E mutation occurs in 46% of melanomas and drives high levels of ERK activity and ERK-dependent proliferation. However, BRAFV600E is insufficient to drive melanoma in GEMM models, and 82% of human benign nevi harbor BRAFV600E mutations. We show here that BRAFV600E inhibits mesenchymal migration by causing feedback inhibition of RAC1 activity. ERK pathway inhibition induces RAC1 activation and restores migration and invasion. In cells with BRAFV600E, mutant RAC1, overexpression of PREX1, PREX2, or PTEN inactivation restore RAC1 activity and cell motility. Together, these lesions occur in 48% of BRAFV600E melanomas. Thus, although BRAFV600E activation of ERK deregulates cell proliferation, it prevents full malignant transformation by causing feedback inhibition of cell migration. Secondary mutations are, therefore, required for tumorigenesis. One mechanism underlying tumor evolution may be the selection of lesions that rescue the deleterious effects of oncogenic drivers. Statement of significanceBRAFV600E activation of ERK causes feedback inhibition of cell migration and invasion and thus blocks tumorigenesis. Secondary genetic lesions are required to rescue these processes and enable tumor development. Thus, oncogenic feedback can shape the details of tumor progression and, in doing so, selects for new mutations that may be therapeutic targets.

cancer biology↗

bioRxiv2020

Anatomic position determines oncogenic specificity in melanoma

Oncogenic alterations to DNA are not transforming in all cellular contexts1,2. This may be due to pre-existing transcriptional programs in the cell of origin. Here, we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet, or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL-driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes, compared to body melanocytes, revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL-driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.

cancer biology↗

bioRxiv2020

Mutant-selective Degradation by BRAF-targeting PROTACs

Over 300 BRAF missense mutations have been identified in patients, yet currently approved drugs target V600 mutants alone. Moreover, acquired resistance inevitably emerges, primarily due to RAF lesions that prevent inhibition of BRAF V600 with current treatments. Therefore, there is a need for new therapies that target other mechanisms of activated BRAF. In this study, we use the Proteolysis Targeting Chimera (PROTAC) technology, which promotes ubiquitination and degradation of neo-substrates, to address the limitations of BRAF inhibitor-based therapies. Using vemurafenib-based PROTACs, we successfully achieve sub-nanomolar degradation of all classes of BRAF mutants, but spare degradation of WT RAF family members. Our lead PROTAC outperforms vemurafenib in inhibiting cancer cell growth and shows in vivo efficacy in a Class 2 BRAF xenograft model. Mechanistic studies reveal that BRAFWT is spared due to weak ternary complex formation in cells owing to its quiescent inactivated conformation, and activation of BRAFWT sensitizes it to degradation. This study highlights the degree of selectivity achievable using degradation-based therapies by targeting mutant BRAF-driven cancers while sparing BRAFWT and thus expanding the therapeutic window using a new anti-tumor drug modality.

cancer biology↗

bioRxiv2020

Anti-tumor effects of an Id antagonist with no acquired resistance

Id proteins are helix-loop-helix (HLH) transcriptional regulators frequently overexpressed in cancer. Id proteins inhibit basic HLH transcription factors through protein-protein interactions, often inhibiting differentiation and sustaining proliferation. We recently identified a small-molecule, AGX51, which targets Id proteins for degradation and impairs ocular neovascularization in mouse models. Here we show that AGX51 treatment of cancer cell lines impaired cell growth and viability that results from a dramatic increase in ROS production upon Id degradation. In mouse models, AGX51 treatment suppressed breast cancer colonization in the lung, regressed the growth of paclitaxel-resistant breast tumors when combined with paclitaxel and reduced tumor burden in a model of sporadic colorectal neoplasia. Furthermore, in cells and mice, we failed to observe acquired resistance to AGX51 likely the result of the immutability of the binding pocket and efficient degradation of the Id proteins. Thus, AGX51 is a first-in-class compound that antagonizes Id proteins, shows strong anti-tumor effects and may be further developed for the management of multiple cancers.

cancer biology↗