Biology subjects

Jakub, J. W.

Publications and source records attributed to Jakub, J. W..

4 recordsLinked to original sources

bioRxiv2026

A Standalone PD-1 Chimeric Switch Receptor T-Cell Platform Expands the Therapeutic Window of PD-L1 Targeting in Solid Tumors

Programmed death-ligand 1 (PD-L1) is a promising therapeutic target owing to its broad expression on tumor cells and immunosuppressive myeloid cells within the tumor microenvironment (TME), providing an opportunity to target both cellular compartments. However, physiological PD-L1 expression in normal tissues poses a substantial risk of on-target/off-tumor toxicity, limiting the therapeutic window and clinical translation of PD-L1-targeted cellular therapies. Here, we developed a standalone programmed death-1 (PD-1) chimeric switch receptor (CSR) T-cell platform designed to preserve the therapeutic advantages of PD-L1 targeting while improving tumor-normal discrimination. Iterative receptor engineering, with antitumor activity and normal-cell reactivity evaluated as parallel selection criteria, identified two lead PD-1 CSR T-cell candidates. Compared with our previously developed antibody-based PD-L1 CAR T cells, the lead candidates retained potent PD-L1-specific cytotoxicity against tumor cells while exhibiting markedly reduced cytotoxicity against primary human small airway epithelial cells, astrocytes, renal epithelial cells, hepatocytes, and cardiomyocytes. They also efficiently eliminated PD-L1-positive immunosuppressive myeloid cells and mediated dual-compartment targeting of tumor and myeloid cells in three-dimensional (3D) multicellular tumor organoids. In vivo, both candidates suppressed tumor growth and prolonged survival in orthotopic breast cancer and patient-derived glioblastoma models after systemic and intracranial administration, respectively. Collectively, these findings establish PD-1 CSR T cells as a standalone therapeutic platform that expands the therapeutic window of PD-L1-targeted cellular therapy by preserving dual-compartment targeting of tumor and immunosuppressive myeloid cells while reducing normal-cell reactivity, providing a foundation for further clinical translation across solid tumors.

molecular biology↗

bioRxiv2026

Information contracts determine what inverse perturbation benchmarks measure

Inverse perturbation benchmarks rank interventions toward a desired cellular state, but high accuracy can answer a different question from biological prioritization. We present InverseBench, which makes candidate information and endpoint construction explicit, and FSTN, a linear pipeline evaluated under it. With identical inputs, candidates and validation, nested ridge reaches Spearman 0.959 for a transcriptional principal-component proxy but 0.445 for independently measured K562 growth fitness across 7,354 genes. Controlled response-entry availability across seven tasks gives heterogeneous gains, 0.442 for CD4 activation and 0.116 for external fitness. Yet predefined shortlist comparisons show no primary-cutoff penalty in K562 or a melanoma co-culture screen, and secondary cutoffs reverse the K562 ordering. FSTN's nonnegative set selector recovers 0.840 of measured two-gene constituents in three picks, against 0.771 for an unconstrained greedy. The framework separates proxy reconstruction, response-informed prioritization and unseen-intervention ranking: an endpoint-dependent accuracy gap does not by itself mean worse biological decisions.

bioinformatics↗

bioRxiv2026

The Human Male Mammary Gland has Similar Epithelial Populations to Female but Distinct Composition and Transcriptional Properties

The normal adult male breast has not been characterized at single-cell resolution, leaving the cellular basis of male breast cancer (MBC) biology undefined. Here we present an integrated single-cell RNA sequencing atlas of the adult human breast comprising 174,471 cells from 17 donors (3 male, 14 female), including 18,117 male-derived cells. This revealed that the male breast retains all three epithelial populations, basal (BC), luminal progenitor (LP), and luminal committed cells (LC), but with an increase in LC at the expense of BC and LP across all three male donors. Male LC were distinguished from female by elevated ESR1 and PGR mRNA, enrichment of RNA processing and ribosome biogenesis programs, reduced inflammatory cytokine and growth factor signaling, elevated estradiol gene set enrichment scores, and higher inferred activity of developmental patterning transcription factors. This pattern was observed across differential expression, gene ontology, ligand profiling, and regulon-based analyses, and was not restricted to sex chromosome-linked gene expression. This is consistent with the near-universal estrogen receptor (ER) positivity that characterizes MBC clinically. This atlas provides the first cellular and transcriptional reference for the normal male breast and a resource for investigating sex differences in mammary biology, germline susceptibility variant interpretation, and modeling breast malignancies.

cancer biology↗

bioRxiv2025

Proteomic analysis of exosomes from lymphatic affluents reveals their implications in developing premetastatic niche in melanoma.

Melanoma is an aggressive form of skin cancer that often spreads via lymphatic pathways to regional and distant sites. Melanoma-derived lymphatic exosomes play a crucial role in forming a tumor-supportive environment for metastasis, or premetastatic niche, within the first tumor draining lymph node, also known as the sentinel lymph node (SLN). Therefore, analyzing the proteomic content of tumor-draining lymphatic exosomes that deliver oncogenic molecules to the SLN is important in understanding the premetastatic niche. To reveal the proteomic landscape of lymphatic exosomes, we performed multidimension liquid chromatography-tandem mass spectrometry with multiplexing (18-samples) using tandem mass tag (TMT) labeling to profile the lymphatic exosomal proteomes obtained from afferent lymphatic channels leading to the SLN of patients with melanoma (n=6), control afferent lymphatic channels from prophylactic mastectomy (n=3) and non-cancer post-operative lymphatic fluid (n=9). Lymphatic fluid from postoperative lymphadenectomy drains served as another control to filter out non-melanoma alteration in lymph that may be related to the procedure of surgical resection and wound healing process. Our proteomic analysis identified 3929 proteins in the lymphatic exosomes, of which 968 were unique proteins absent from the current exosomal database. Interestingly, melanoma lymphatic exosomes possess distinctive proteomic cargo, which is significantly associated with cancer-associated and cellular structural remodeling pathways (FDR <0.05). Moreover, proinflammatory wound healing pathways are predominantly present in melanoma and postoperative lymph fluid compared to normal control afferent lymphatic channels. We identified a total of 17 uniquely modulated proteins in melanoma compared to control and postoperative lymph, which are critically involved in the process of melanoma tumorigenesis. At least ten upregulated proteins strongly correlate with each other at the gene expression levels in melanoma tumors compared to controls and may serve as a signature panel for melanoma (p = 2.13 x 10-58). In summary, this study represents the first comparative analysis of the lymphatic exosomal proteome and highlights distinct exosomal proteins that may support premetastatic niche formation in the SLN.

cancer biology↗