Background:The 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. Methods:Anti-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. Findings:MPNSTs 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. Interpretation:Plasma 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. Funding:This 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 Context:Evidence before this study: For 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 study: Studies 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 evidence: The 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.

Circulating tumor cells (CTCs) face challenges to their survival, including mechanical and oxidative stresses that are different from cancer cells in solid primary and metastatic tumors. The impact of adaptations to the fluid microenvironment of the circulation on the outcome of the metastatic cascade is not well understood. Here, we find that cancer cells exposed to brief pulses of high-level fluid shear stress (FSS) exhibit enhanced invasiveness and anchorage-independent proliferation in vitro and enhanced metastatic colonization/tumor formation in vivo. Cancer cells exposed to FSS rapidly alter their metabolism in a manner that promotes survival by providing energy for cytoskeletal remodeling and contractility as well as reducing equivalents to counter oxidative stress associated with cell detachment. Thus, exposure to FSS may provide CTCs with an unexpected survival benefit that promotes metastatic colonization.

Background: Malignant peripheral nerve sheath tumors (MPNSTs) are deadly sarcomas that arise from Schwann cells and lack effective therapies. RABL6A is an oncogenic Rab-like GTPase whose expression is associated with worse survival in many human cancers. It is required for human MPNST cell survival, and its expression is dramatically increased in patient MPNSTs compared to benign precursor lesions. Methods: To model elevated expression of RABL6A in vivo, we developed transgenic mice expressing Cre-inducible Rabl6a. These Rabl6a-tg mice express the murine Rabl6a cDNA with a 5' hemagglutinin [HA] epitope sequence downstream of a CMV enhancer and separated by a lox-stop-lox cassette. Double transgenic DhhCre; Rabl6a-tg mice were generated to achieve Schwann-cell specific Cre expression from the Desert hedgehog (Dhh) promoter. De novo MPNSTs were induced by CRISPR editing of Nf1, Ink4a, and Arf genes in the mouse sciatic nerve. Results: Cre-dependent expression of transgenic Rabl6a was verified at the mRNA and protein levels in Cre-positive mouse embryo fibroblasts and tissues. Increased Rabl6a expression in DhhCre; Rabl6a-tg mice had no effect on de novo MPNST initiation but significantly accelerated tumor progression relative to DhhCre control mice. The Rabl6a phenotype was associated with increased tumor angiogenesis but not proliferation. Interestingly, many MPNSTs in the DhhCre background exhibited varying levels of rhabdomyoblastic (RMB) features. That immature muscle cell phenotype is a hallmark of malignant Triton tumors, a rare histological variant of human MPNSTs associated with worse outcomes. Conclusions: These data provide direct evidence that Rabl6a is a functional driver of MPNSTs while establishing Rabl6a-tg mice as a suitable model for investigating Rabl6a's role in other lethal RABL6A-high tumors.

Sarcomas are a heterogeneous group of cancers with few shared therapeutic targets. We show that PI3K signaling is frequently activated in sarcomas due to PTEN loss (in 30%-60%), representing a common therapeutic target. The PI3K pathway has lacked a downstream oncogenic transcription factor. We show TAZ and YAP are transcriptional coactivators regulated by PI3K and drive a transcriptome necessary for tumor growth in a PI3K-driven sarcoma mouse model. This PI3K/ TAZ/YAP axis exists in parallel to the known PI3K/AKT/mTORC1 axis, providing a rationale for combination therapy targeting the TAZ/YAP-TEAD interaction and mTORC1. Combination therapy using IK-930 (TEAD inhibitor) and everolimus (mTORC1 inhibitor) synergistically diminished proliferation and anchorage-independent growth of PI3K-activated sarcoma cell lines at low, physiologically achievable doses. Furthermore, this combination therapy showed a synergistic effect in vivo, suggesting that an integrated view of PI3K and Hippo signaling can be leveraged therapeutically in PI3K-activated sarcomas.

Abstract Most heritable risk for orofacial clefts (OFC) remains unassigned to specific genes or loci. IRF6 and GRHL3 , two established OFC risk genes, encode transcription factors (TFs) essential for the differentiation of the periderm, a transient embryonic tissue required for secondary palate fusion. To identify novel risk candidates, we modeled the zebrafish periderm transcriptional regulatory network (TRN). Using single-cell multiome sequencing (RNA-seq and ATAC-seq) from shield-stage embryos, we inferred TF-to-target gene connections by integrating correlated gene expression with TF binding site predictions within chromatin elements open in periderm cells. We generated sets of gold-standard edges by conducting RNA-seq on TF-depleted embryos and ChIP-seq/CUT&RUN on wild-type embryos and used them to benchmark model performance. Within the top-performing model, zebrafish periderm modules are strongly preserved in human embryonic periderm and orthologs of human OFC-associated genes have higher centrality and edge-sum scores than non-associated genes. Functional validation confirmed the network’s predictive power: depleting high-centrality TFs, including grhl1 , klf6a , tead3b , and klf17 , disrupted periderm differentiation in sensitized embryos. Moreover, analysis of whole-genome sequencing data from 2,415 OFC trios identified 15 individuals with rare or de novo GRHL1 variants, four of which introduced premature stop codons. This study establishes GRHL1 as a novel OFC risk gene and highlights the power of cross-species gene regulatory network analysis to prioritize candidates for rare variants in complex structural birth defects.

Correlation among the observations in high-dimensional regression modeling can be a major source of confounding. We present a new open-source package, plmmr, to implement penalized linear mixed models in R. This R package estimates correlation among observations in high-dimensional data and uses those estimates to improve prediction with the best linear unbiased predictor. The package uses memory mapping so that genome-scale data can be analyzed on ordinary machines even if the size of data exceeds random-access memory. We present here the methods, workflow, and file-backing approach upon which plmmr is built, and we demonstrate its computational capabilities with two examples from real genome-wide association studies data.

Adults with Down syndrome (DS) are two times more likely to be diagnosed with chronic heart failure post-anthracycline chemotherapy compared to age and sex-matched adults without DS. They have an elevated lifetime risk of cardiovascular diseases, increasing their likelihood of anthracycline-induced chronic cardiovascular toxicity. We investigated the chronic effects of daunorubicin on the cardiovascular system of the adult Ts65Dn mouse model of DS compared to wild type euploid mice (WT). WT and Ts65Dn mice received two doses of 2mg/kg or 4mg/kg of daunorubicin or saline and were monitored for up to 117 days. Cardiac and vascular function were evaluated using left ventricular catheterization, histology, pulse wave velocity, and cardiac troponin tests. Survival significantly decreased in the Ts65Dn 4mg/kg group compared to saline controls (p<0.001). Further experiments were carried out with the saline and 2mg/kg groups, which exhibited lower mortality, more consistent with chronic toxicity. Body weight (p=0.001), end-diastolic pressure (p=0.016), and left ventricular mass (p=0.021) decreased in treated mice. The effect of treatment differed significantly between strains for ejection fraction (p=0.029). Pulse wave velocity increased over time (p<0.001). A significant interaction between treatment and strain was observed for collagen in both the left ventricles and thoracic aorta (p=0.002 and p<0.001, respectively). There was a strain difference for cardiac troponin I, indicating an increase in Ts65Dn mice (p=0.020). Daunorubicin treatment results in a distinct cardiovascular remodeling phenotype in Ts65Dn mice. More mechanistic studies are warranted to outline the pathophysiology of anthracycline cardiovascular toxicity in DS.

BACKGROUND:The role of intratumoural plasma cells in immune checkpoint blockade (ICB) therapy has never been tested although their presence is linked with improved response and survival in people with cancer. Malignant peripheral nerve sheath tumours (MPNSTs) are deadly sarcomas with minimal responsiveness to ICB therapies. Strikingly, drugs inhibiting cyclin-dependent kinases 4/6 (CDK4/6) and MEK sensitise de novo MPNSTs to immunotherapy targeting programmed death-ligand 1 (PD-L1), which correlates with increased intratumoural plasma cells. Here, we tested if plasma cells mediate MPNST response to anti-PD-L1 therapy and how they modulate tumour immune responsiveness to CDK4/6-MEK inhibition. METHODS:Anti-tumour 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 immune cell analyses. FINDINGS:Plasma cell-deficient MPNSTs failed to respond to anti-PD-L1 monotherapy and were no longer sensitised by CDK4/6-MEK inhibition to immunotherapy. Following kinase inhibitor treatment, plasma cells were necessary for a pro-inflammatory response marked by increased tumour infiltration and activation of natural killer (NK) and CD8+ T cells, major histocompatibility class I antigen presentation, and decreased M2 macrophages. By comparison, elevated CD4+ T cell and B cell infiltration dominated the plasma cell knockout phenotype. INTERPRETATION:Plasma cells favourably remodel the tumour immune environment for anti-tumour immunity and are critical for successful ICB therapy in MPNSTs. These findings may inform ICB treatment strategies and patient stratification for therapy of many tumour types. FUNDING:This research was supported by University of Iowa Sarcoma Research Program awards, the Gilbert Family Foundation, and NIH grants T34-GM141143, T32-GM067795, F31-CA281312, P30-CA086862, and R01-NS119322.

Nonsyndromic cleft lip (nsCL) exhibits a non-random laterality pattern, with left-sided clefts occurring approximately twice as frequently as right-sided clefts. The molecular mechanisms underlying this laterality bias remain poorly understood. We performed whole-genome sequencing and methylation profiling on a family comprising monozygotic twins with mirror-image nsCL, their affected mother, and unaffected father and brother. We conducted three independent replications via (1) publicly available whole genome data; (2) genome-wide methylation analysis in 38 individuals with unilateral cleft; and (3) validation of methylation results in the top 3 candidate genes in 385 unrelated individuals with unilateral clefts (DNA from blood or saliva). We identified a variant in FGF20 (p.Ile79Val) shared by the twins and their mother. We observed laterality and severity-associated methylation differences in three main genes. ARID5B showed higher methylation in left clefts (saliva, p=0.001; blood, p=0.032). ZFP57 demonstrated a strong cleft-extent effect, with cleft lip and palate (CLP) showing markedly higher methylation than cleft lip only (CL) (LCLP vs. RCL padj=0.0004; LCLP vs. LCL padj = 0.019). HOOK2 displayed a cross-tissue cleft-extent effect in the opposite direction - CLP subtypes were hypomethylated relative to CL-only subtypes in blood (p<0.0001) and saliva p=0.0008). This study provides evidence that DNA methylation patterns plays a role in both the laterality and severity of cleft lip. ARID5B provides a consistent laterality signal across tissues, while ZFP57 and HOOK2 track palatal involvement independently of side. Together, these findings suggest that epigenetic variation acts downstream of genetic predisposition to shape cleft phenotypes.

Supplementary Figure S8. Additional MPNST analyses for CDK4/6-MEK inhibition plus anti-PD-L1 therapy study.

Supplementary Figure S3. Tumor growth kinetics of individual de novo MPNSTs during therapy

Supplementary Table S4. Primers for qRT-PCR analyses

Objective Oculoauriculovertebral spectrum (OAVS) encompasses abnormalities on derivatives from the first and second pharyngeal arches including macrostomia, hemifacial microsomia, micrognathia, preauricular tags, ocular, and vertebral anomalies. We present genetic findings on a 3-generation family affected with macrostomia, preauricular tags and ptosis following an autosomal dominant pattern. Design We generated whole-genome sequencing data for the proband, affected father, and unaffected paternal grandmother followed by Sanger sequencing on 23 family members for the top candidate gene mutations. We performed parent and sibling-based transmission disequilibrium tests (TDTs) and burden analysis via a penalized linear mixed model, for segregation and mutation burden, respectively. Next, via bioinformatic tools we predicted protein function, mutation pathogenicity, and pathway enrichment to investigate the biological relevance of mutations identified. Results Rare missense mutations in SIX1, KDR/VEGFR2, and PDGFRA showed the best segregation with the OAVS phenotypes in this family. When considering any of the 3 OAVS phenotypes as an outcome, SIX1 had the strongest associations in parent-TDTs and sib-TDTs ( P = 0.025, P = 0.052) (unadjusted P-values). Burden analysis identified SIX1 (RC = 0.87) and PDGFRA (RC = 0.98) strongly associated with OAVS severity. Using phenotype-specific outcomes, sib-TDTs identified SIX1 with uni- or bilateral ptosis ( P = 0.049) and ear tags ( P = 0.01), and PDGFRA and KDR/VEGFR2 with ear tags (both P < 0.01). Conclusion SIX1, PDGFRA, and KDR/VEGFR2 are strongly associated to OAVS phenotypes. SIX1 has been previously associated with OAVS ear malformations and is co-expressed with EYA1 during ear development. Efforts to strengthen the genotype-phenotype co-relation underlying the OAVS are key to discover etiology, family counseling, and prevention.

Supplementary Table S2. Antibodies and dyes used for immunophenotyping by flow cytometry.

Supplementary Figure S2. Dual CDK4/6-MEK inhibition synergistically suppresses the growth of some, but not all, MPNST PDXs in immune deficient mice

In mammals, odors are encoded by a combinatorial code determined by the pattern of responses across hundreds of odorant receptors expressed monogenically and monoallelically in olfactory sensory neurons. The compositions of these receptor response patterns are largely unknown and overlap between them has yet to be explored. Activity-dependent reporter gene expression in freely behaving S100a5-tauGFP mice allowed capture of activated olfactory sensory neurons and identified 168 receptors responsive to moderate concentrations of 1 or more of 12 aliphatic (5 to 8 carbons) ketones, alcohols, and carboxylic acids. These 12 response patterns are remarkably different, with only 19% of the receptors responding to more than 1 of these odorants. This distinctiveness corresponds with the ease of discrimination of these odorants and may help maintain perceptual constancy in the face of response pattern variability, such as across odorant concentrations. This set of 168 receptors is not specific to aliphatic odorants but instead has 16% overlap with the receptors responsive to 7 odors tested previously in vivo, consistent with a receptor repertoire evolved to produce combinatorial codes. Aliphatic odorant response pattern similarity depends more upon odorant functional group than carbon chain length but the impact of chain length increases with the number of carbons. The response patterns to these aliphatic odorants are mostly composed of unrelated receptors, except some patterns contain minor subsets of closely related receptors. These findings argue that the major selective forces driving OR evolution are expansion of the odorant receptor gene family and the production of distinct response patterns.

Supplementary Figure S7. Analyses of p-RB1, Ki67, and PD-L1 in combination therapy-sensitive and - resistant MPNSTs and PD-L1 in NF1 patient tumors.

Supplementary Figure S5. Evaluation of differentially expressed genes (DEGs) and tumor infiltrating immune cells (plasma cells and B cells) in drug-treated de novo MPNSTs.

Supplementary Table S3. Cluster of differentiation (CD) markers used to delineate immune cell populations after gating on CD45+ live cells.

Supplementary Table S5. Abbreviated list of top kinase inhibitory compounds predicted to be effective against MPNSTs from C-Map analyses of the MPNST transcriptome from NF1 patients.