Biology subjects

Lingo, J. J.

Publications and source records attributed to Lingo, J. J..

4 recordsLinked to original sources

bioRxiv2026

Perturb-seq resolves physiologic programs and bidirectional regulation of non-canonical NF-κB signaling in epidermal organoids

Regulated keratinocyte differentiation is required for formation of the stratified epidermis and a functional barrier. Understanding genetic drivers of keratinocyte differentiation is crucial for understanding several skin diseases. Perturb-seq is a single-cell CRISPR screen that measures transcriptomic responses to perturbations. To date, Perturb-seq experiments have principally focused on 2-dimensional cell culture models lacking hallmarks of skin development - physiological desmosome formation and barrier function. Here, we leverage Perturb-seq in an epidermal organoid model that recapitulates physiologically relevant differentiation programs. We demonstrate that our perturbations significantly impact diverse differentiation programs and reveal bidirectional function of non-canonical NF-{kappa}B signaling in late keratinocyte differentiation.

genomics↗

bioRxiv2026

Intratumoral plasma cells are required for activation of CD8+ T cells and success of immune checkpoint blockade therapy in de novo MPNSTs

BackgroundThe role of intratumoral plasma cells in immune checkpoint blockade (ICB) therapy has never been tested although their presence is linked with improved patient response and survival. Malignant peripheral nerve sheath tumors (MPNSTs) are deadly sarcomas with minimal responsiveness to ICB therapies. Strikingly, drugs inhibiting cyclin-dependent kinases 4/6 (CDK4/6) and MEK sensitize de novo MPNSTs to immunotherapy targeting programmed death-ligand 1 (PD-L1), which correlates with increased intratumoral plasma cells. Here, we tested if plasma cells mediate the MPNST response to anti-PD-L1 therapy. MethodsAnti-tumor activity of PD-L1 inhibition, with or without CDK4/6-MEK inhibition, was measured in de novo MPNSTs within wild-type versus plasma cell-deficient mice. Plasma cell-dependent effects of CDK4/6-MEK inhibition on priming the MPNST immune environment were determined by single cell transcriptomics and immunostaining. FindingsMPNSTs lacking plasma cells failed to respond to anti-PD-L1 monotherapy and were no longer sensitized to immunotherapy by CDK4/6-MEK inhibition. Plasma cell-deficient MPNSTs exposed to CDK4/6-MEK inhibitors had impaired antigen presentation on major histocompatibility class I (MHC-I) and decreased CD8+ T cell infiltration and activation. Complementary analyses of human sarcomas showed increased intratumoral plasma cell signatures prognose better patient survival. InterpretationPlasma cells favorably remodel the tumor immune environment by increasing CD8+ T cell infiltration and are critical for successful ICB therapy in MPNSTs. This work may help inform ICB treatment strategies and cancer patient stratification for many different tumor types. FundingThis research was supported by University of Iowa Sarcoma Research Program awards and NIH grants T34-GM141143, T32-GM067795, F31-CA281312, P30-CA086862, and R01-NS119322. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSFor many types of cancer, intratumoral plasma cells have been correlated with better patient survival and improved response to immune checkpoint blockade (ICB) therapies. However, the biology underlying those associations is not understood and no study has examined the requirement of plasma cells in immunotherapy response. Compelling data in malignant peripheral nerve sheath tumors (MPNSTs) showed that dual kinase inhibition of oncogenic CDK4/6 and MEK induced intratumoral plasma cell accumulation and sensitized tumors to ICB therapy. While CDK4/6-MEK inhibition is known to enhance antitumor immunity in other tumor types by CD8+ T cells or natural killer (NK) cells, a role for plasma cells has never been explored. Added value of this studyStudies were performed in MPNSTs, an under-researched cancer that normally responds poorly to ICB monotherapies. This is the first investigation to show that intratumoral plasma cells are essential for successful ICB therapy and they support anti-tumor immunity by promoting a pro-inflammatory, CD8+ T cell state involving MHC-I antigen presentation. Findings provide new insight into immunomodulatory effects of CDK4/6-MEK inhibitor therapies, revealing plasma cells are needed for those drugs to activate CD8+ T cell mediated antitumor immunity. Implications of all the available evidenceThe fundamental advance in understanding how plasma cells promote successful ICB immunotherapy is likely applicable to other solid tumors and may guide novel therapeutic strategies in which plasma cell-inducing agents are combined with ICB antibodies. Moreover, an increased presence of intratumoral plasma cells in tumor specimens may streamline clinical decisions regarding which patients are most likely to benefit from ICB therapy.

cancer biology↗

bioRxiv2026

Proteomics and single-cell transcriptomics identify LRP1 as a diagnostic biomarker for atypical fibroxanthoma and pleomorphic dermal sarcoma.

Atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS) are cutaneous neoplasms that fall along a spectrum. PDS is more aggressive than AFX with higher rates of local and distant metastases. Diagnostic biomarkers for AFX and PDS are lacking and therefore these tumors are diagnosed only after excluding other dermal spindle cell neoplasms, including cutaneous leiomyosarcoma (cLMS), spindle cell melanoma (SCM), and sarcomatoid squamous cell carcinoma (sSCC). To identify clinically valuable biomarkers, we contrast the tumors within the diagnostic differential using single-cell RNA sequencing and bulk proteomic data. Gene Ontology (GO) analysis of transcripts and proteins enriched in AFX/PDS identified multiple shared pathways associated with cell adherence and the extracellular matrix. We identify that LRP1, LTBP2, and NAV1 are all enriched in AFX/PDS over other tumors in the differential at both the level of mRNA and protein. IHC reveals that LRP1 is 90% sensitive and 73% specific for AFX/PDS in a cohort of AFX, PDS, cLMS, SCM, and sSCC. This outperforms published data for CD10, which is currently used clinically (sensitivity 83.5% and specificity 50%). When used in conjunction with LTBP2, specificity for AFX/PDS within the differential rises from 73% to 93%. These findings suggest that LRP1, particularly if evaluated in conjunction with existing stains, can improve diagnostic accuracy for AFX and PDS.

cancer biology↗

bioRxiv2021

Oncogenic RABL6A promotes NF1-associated MPNST progression in vivo

BackgroundMalignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that display complex molecular and genetic alterations. Powerful tumor suppressors CDKN2A and TP53 are commonly disrupted in these lesions along with NF1, a gene that encodes a negative regulator of Ras. Many additional factors have been implicated in MPNST pathogenesis. A greater understanding of critical drivers of the disease is needed to guide more informed targeted therapies for patients. RABL6A is a newly identified driver of MPNST cell survival and proliferation whose in vivo role in the disease is unknown. MethodsUsing CRISPR-Cas9 targeting of Nf1+Cdkn2a or Nf1+Tp53 in the sciatic nerve to form de novo MPNSTs, we investigated the biological significance of RABL6A in MPNST development. Molecular evaluation of terminal tumors (western blot, qRT-PCR, immunohistochemistry) yielded several insights. ResultsMice lacking Rabl6 displayed slower tumor growth and extended survival relative to wildtype animals in both genetic contexts. YAP oncogenic activity was selectively downregulated in RABL6A-null, Nf1+Cdkn2a lesions but not in RABL6A-null, Nf1+Tp53 tumors. Regardless of genetic context, loss of RABL6A caused upregulation of the CDK inhibitor, p27 in tumors. Paradoxically, both models displayed elevated Myc protein expression and Ki67 staining in terminal tumors lacking RABL6A. ConclusionsThese findings demonstrate RABL6A is required for optimal tumor progression of NF1 mutant MPNSTs in vivo in both Cdkn2a and p53 inactivated settings. However, sustained RABL6A loss may provide selective pressure for molecular alterations, such as Myc upregulation, that ultimately promote an unwanted, hyper-proliferative tumor phenotype akin to drug resistant lesions. Importance of the StudyMPNSTs are aggressive, deadly, and challenging to treat tumors due to location around nerves and high mutational burden. Many factors implicated in MPNST genesis have yet to be fully tested for biological significance in disease formation. We establish a critical physiological role for a new oncoprotein, RABL6A, in promoting NF1-associated MPNST progression. We identify novel RABL6A-regulated pathways that likely contribute to tumor growth, specifically YAP and Myc signaling, and found that sustained RABL6A loss eventually yields more proliferative tumors. We liken RABL6A deficient tumors to those being treated with therapies targeting RABL6A effectors, such as CDKs. Therefore, those lesions should provide a powerful platform to uncover key mediators of drug resistance. Our data suggest oncogenic YAP and Myc could be such mediators of resistance. This study provides a novel system to examine one of the most pressing clinical challenges, drug resistant tumor growth and relapse, in cancer therapy.

cancer biology↗