Biology subjects

Sinclair, N.

Publications and source records attributed to Sinclair, N..

5 recordsLinked to original sources

bioRxiv2026

Spatial/molecular heterogeneity and treatment response in HER2+ early breast cancer: Translational analyses from the DAPHNe trial

Given the heterogeneity of HER2-positive breast cancer, reliable biomarkers to guide treatment are needed. We conducted multi-platform biomarker analyses of baseline tumor tissue from the DAPHNe trial of neoadjuvant paclitaxel/trastuzumab/pertuzumab (THP) for HER2-positive early breast cancer to characterize inter- and intra-tumor heterogeneity and to identify molecular predictors of response. A total of 98 patients with stage II-III HER2-positive breast cancer received neoadjuvant THP followed by surgery. Gene expression profiling, spatial protein profiling, and single-cell imaging (cyclic immunofluorescence) were performed on pre-treatment biopsies and a subset of residual disease specimens. Pathologic response was assessed using the residual cancer burden (RCB) score. Among HER2-positive patients included in the biomarker analysis, 34% of patients had node-positive breast cancer, and 66% had hormone receptor (HR)-positive tumors. HR-positive and HR-negative tumors differed significantly across gene expression, protein expression, and single-cell profiling. High ERBB2 gene signature, p53 gene signature, and HER2 protein expression predicted favorable response (RCB 0/1), while ESR1/PGR gene, estrogen receptor (ER) signaling gene signature, and ER alpha protein expression were associated with unfavorable response (RCB 2/3). Single-cell spatial analysis revealed that cancer cells clustered by shared HER2, ER, and PR expression, suggesting local expansion of phenotypically distinct subpopulations. ER-positive cancer cells were associated with lower HLA-A and PD-L1 expression, suggesting a less immunologically active tumor cell state. Baseline HER2 and ER expression are key predictors of response to neoadjuvant HER2-targeted therapy. Single-cell spatial profiling highlights intra-tumoral heterogeneity and suggests ER-driven immune exclusion as a potential mechanism of resistance.

cancer biology↗

bioRxiv2026

Cell painting with amphiphile-protein conjugate vaccines drives B cell activation and germinal center priming to enhance humoral immunity

Most licensed vaccines against infectious diseases mediate protection by priming B cells and humoral immune responses, where efficacy largely relies on activation of germinal centers (GCs) in lymphoid tissues that serve as the training ground for a high-affinity antibody response. While subunit vaccines offer safety advantages, they tend to be poorly immunogenic with weak and short-lived antibody responses, presenting a need for engineering strategies that enhance immunogenicity. Amphiphile-protein vaccines, consisting of protein antigens modified with an albumin-binding lipid tail via a polyethylene glycol (PEG) linker, hitchhike on albumin following subcutaneous injection to enhance lymphatic trafficking and antigen-specific immune activation. Amph-vaccines also demonstrate an ability to insert their lipid tail into cell membranes, effectively 'painting' cells with multivalent antigen. We hypothesized that cell painting may play a role in driving humoral immunity by sustaining antigen persistence in lymph nodes and generating multivalent antigen presentation for B cell activation. Here, we investigated how amph-vaccine molecular properties (antigen MW and PEG linker length) influenced conformational behaviors (micelle formation, albumin hitchhiking, and membrane insertion) along with the resulting humoral immune response. Using HIV env proteins as model antigens (eOD monomer and MD39 trimer), we investigated cell membrane insertion and B cell activation via calcium flux assay in vitro, followed by lymphatic trafficking and immunogenicity studies in vivo. Our results demonstrate that amphiphile conjugation is an effective strategy for enhancing humoral immunogenicity of both monomer and trimer protein antigens, where cell painting plays a significant role in driving B cell, GC, and humoral immune activation.

bioengineering↗

bioRxiv2025

Targeting non-canonical NF-κB signalling in CYLD cutaneous syndrome by selective inhibition of IκB kinase alpha.

CYLD cutaneous syndrome (CCS) skin tumors develop from puberty onwards, can number in the hundreds and progressively grow over time. CCS patients lack medical therapies and require repeated surgery to control tumor burden. CYLD loss of heterozygosity (LOH) drives tumor growth, and CCS tumors have previously been shown to demonstrate increased canonical NF-{kappa}B and Wnt signalling. Here, we demonstrate evidence of non-canonical NF-{kappa}B signalling in CCS tumor keratinocytes, with increased p100 to p52 processing and RelB protein expression compared to normal skin. Utilizing complementary transcriptomics and proteomics on patient derived CCS tumor cell fractions, we identify I{kappa}B kinase alpha (IKK) as a candidate target in the non-canonical NF-{kappa}B signalling pathway. A novel, highly selective, IKK inhibitor (SU1644) used in patient derived CCS tumor spheroid cultures demonstrated that IKK inhibition reduced tumor spheroid viability. These data provide the pre-clinical rationale for the assessment of topical IKK inhibitors as a novel preventative treatment for CCS. TeaserTopical IKK inhibition emerges as a potential therapy for CYLD cutaneous syndrome by targeting non-canonical NF-{kappa}B signalling Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/635629v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@829218org.highwire.dtl.DTLVardef@459f5dorg.highwire.dtl.DTLVardef@e198f6org.highwire.dtl.DTLVardef@1015685_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Native Adiponectin Plays a Role in the Adipocyte Mediated Conversion of Fibroblasts to Myofibroblasts

Adipocytes regulate tissues through production of adipokines that can act both locally and systemically. Adipocytes also have been found to play a critical role in regulating the healing process. To better understand this role, we developed a 3D human adipocyte spheroid system that has an adipokine profile similar to in vivo adipose tissues. Previously, we found that conditioned medium from these spheroids induces human dermal fibroblast conversion into highly contractile, collagen producing myofibroblasts through a transforming growth factor beta-1 (TGF-{beta}1) independent pathway. Here, we sought to identify how mature adipocytes signal to dermal fibroblasts through adipokines to induce myofibroblast conversion. By using molecular weight fractionation, heat inactivation, and lipid depletion, we determined mature adipocytes secrete a factor that is 30-100 kDa, heat labile, and lipid associated that induces myofibroblast conversion. We also show that depletion of the adipokine adiponectin, which fits those physiochemical parameters, eliminates the ability of adipocyte conditioned media to induce fibroblast to myofibroblast conversion. Interestingly, native adiponectin secreted by cultured adipocytes consistently elicited a stronger level of -SMA expression than exogenously added adiponectin. Thus, adiponectin secreted by mature adipocytes induces fibroblast to myofibroblast conversion and may lead to a phenotype of myofibroblasts distinct from TGF-{beta}1 induced myofibroblasts.

bioengineering↗

bioRxiv2019

Epigenetic dysregulation underpins tumorigenesis in a cutaneous tumor syndrome.

Patients with CYLD cutaneous syndrome (CCS; syn. Brooke-Spiegler syndrome) carry germline mutations in the tumor suppressor CYLD and develop multiple skin tumors with diverse histophenotypes 1,2. We comprehensively profiled the genomic landscape of 42 benign and malignant tumors across 13 individuals from four multigenerational families. Novel driver mutations were found in epigenetic modifiers DNMT3A and BCOR in 29% of benign tumors. Multi-level and microdissected sampling strikingly reveal that many clones with different DNMT3A mutations exist in these benign tumors, suggesting that intra-tumor heterogeneity is common. Integrated genomic and methylation profiling suggest that mutated DNMT3A drives tumorigenesis mechanistically through Wnt/{beta}-catenin pathway signaling. Phylogenetic and mutational signature analyses confirm the phenomenon of benign pulmonary metastases from primary skin lesions. In malignant tumors, additional epigenetic modifiers MBD4, CREBBP, KDM6A and EP300 were mutated. We thus present epigenetic dysregulation as a driver in CCS tumorigenesis and propose this may account for the diverse histophenotypic patterns despite the paucity of mutations seen. These findings add novel dimensions to existing paradigms of cutaneous tumorigenesis and metastasis.

cancer biology↗