Biology subjects

Pikarsky, E.

Publications and source records attributed to Pikarsky, E..

10 recordsLinked to original sources

bioRxiv2026

Single-section multiplexed imaging enables comprehensive lung cancer diagnosis

Accurate and timely diagnosis is essential for effective lung cancer treatment. However, contemporary workflows rely on sequential immunohistochemistry of small biopsy specimens, which can exhaust tissue, limit biomarker assessment, and delay treatment decisions. Here, we demonstrate that multiplexed imaging addresses these limitations by enabling comprehensive lung cancer diagnosis from a single tissue section. We developed and validated a clinically informed multiplexed antibody panel that integrates tumor classification, predictive biomarker assessment, and immune profiling. In diagnostic biopsies, multiplexed imaging achieved 96% concordance with standard pathology, while enabling accurate automated PD-L1 scoring and rapid detection of clinically approved and emerging actionable targets. Simultaneously measuring dozens of proteins improves standard pathology by incorporating complex multi-protein biomarkers, supporting quantitative computational analysis to streamline diagnosis, and generating spatial data for translational research. By reducing turnaround time and preserving scarce tissue, this workflow has the potential to accelerate treatment decisions, improve patient outcomes and bridge clinical care with translational discovery.

cancer biology↗

bioRxiv2026

Stage-specific metabolic rewiring coordinates nucleotide supply and demand during spermatogenesis

Male meiotic prophase I features a major transition from leptotene/zygotene to pachytene/diplotene characterized by a massive transcriptomic and proteomic shift, yet how metabolism is coordinated across this transition remains unclear. Here, using stage-resolved purification of spermatogenic cells combined with respirometry, proteomics, metabolomics, and isotope tracing, we define metabolic programs across these stages. Early prophase cells rely on glutamine and fatty acid {beta}-oxidation to sustain mitochondrial respiration while directing glucose into the pentose phosphate pathway and de novo pyrimidine synthesis. In contrast, late prophase cells utilize glucose and lactate as fuels, suppress fatty-acid oxidation, lose pentose phosphate pathway entry, and silence nucleotide biosynthesis despite a surge in nascent RNA synthesis and lower nucleotide pools. Inhibiting nucleoside uptake does not impair meiotic progression, indicating that late prophase transcription depends primarily on nucleotide pools synthesized earlier. These findings reveal a developmentally programmed separation between nucleotide production in early prophase and nucleotide use in later meiotic stages. TEASERMeiotic germ cells rewire central carbon metabolism to match stage-specific nucleotide production and RNA demand during spermatogenesis.

developmental biology↗

bioRxiv2026

Inflammatory injury drives CIN and STING loss in polyploidpancreatic acinar cells

Epidemiological studies link pancreatic inflammation to increased cancer risks with elevated levels of chromosomal instability (CIN), yet the underlying cause remains unclear. The exocrine pancreas and lactating mammary gland harbor polyploid cells to boost secretory efficiency. Using organoid and in vivo models of pancreatic injury, we show that polyploid acinar cells contribute to regeneration via acinar-to-ductal metaplasia. The metaplasia induced cell size reduction is associated with crowding and spindle misorientation, leading to mitotic errors such as lagging chromosomes, chromatin bridges, and micronuclei. Micronucleated cells are not always eliminated or arrested in the cell cycle but can continue to proliferate and expand. Polyploid cells in post-lactational mammary gland organoids equally exhibited proliferation-related CIN. Single-cell proteomics of acinar cells shows STING1 loss and increased ATR levels in polyploid cells, enabling continued proliferation. These findings uncover physiological links between polyploidy, tissue repair, and CIN, offering new insights into cancer risks after tissue remodeling.

cell biology↗

bioRxiv2025

Allosteric Ligand-Aptamer Complexes Orchestrate Supramolecular or Transient Catalytic, Transcription and Fibrinogenesis Processes

Allosteric regulation, the modulation of biological macromolecular function through binding of molecules at distant sites distinct from the active site, is a fundamental principle in biology that governs enzyme activity, signaling, and gene expression. In this work, we present allosteric ligand/aptamer complexes, coupled to biocatalytic reaction modules composed of enzymes, DNAzymes, or transcription machineries, regulating the catalytic and transient functions of these frameworks. This principle is exemplified by the assembly of ligand/aptamer subunits supramolecular complexes that allosterically stabilize the Mg{superscript 2}-dependent DNAzyme, allowing its ribonucleobase cleavage activity, promoting the formation of transcription templates that yield RNA products, and modulating the assembly of thrombin aptamer subunits that inhibit thrombin-induced coagulation. Specifically, melamine (Mel)/aptamer subunits complexes allosterically stabilize the assembly of Mg{superscript 2}-dependent DNAzyme strands for substrate cleavage, the formation of thrombin aptamer subunits that inhibit the conversion of fibrinogen to fibrin, and the stabilization of a transcription template encoding the Malachite Green (MG) RNA aptamer. Furthermore, coupling an enzyme that depletes the ligand/aptamer complex, which allosterically stabilizes the biocatalytic reaction module, demonstrates the dissipative and transient operation of the catalytic system. This concept is illustrated by the adenosine (Ade)/aptamer subunits supramolecular complex, which stabilizes thrombin aptamer subunits to inhibit thrombin-induced fibrinogenesis, and promotes the formation of an active transcription template for RNA synthesis. In the presence of adenosine deaminase (ADA), Ade is transformed into inosine, which lacks affinity for the aptamer subunits, thereby degrading the Ade/aptamer assemblies and depleting the allosteric complexes. The temporal disassembly of these allosteric stabilizing complexes leads to the transient inhibition of thrombin-induced coagulation or to the transient operation of a transcription machinery. For Table of Contents Only: O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/684577v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1a82199org.highwire.dtl.DTLVardef@135f2d1org.highwire.dtl.DTLVardef@d8b689org.highwire.dtl.DTLVardef@1b7e609_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Inducible re-epithelialization of cancer cells increases autophagy and DNA damage: implications for breast cancer dormancy

Epithelial lineage differentiation is pivotal to mammary gland development and it can pause metastasis of breast cancer (BC) by inducing tumor dormancy. To simulate this, we expressed epithelial genes in mesenchymal BC cells. Inducible expression of the epithelial OVOL genes in metastatic BC cells suppressed proliferation and migration. We found that C1ORF116, an OVOLs target, is susceptible to genetic and epigenetic aberrations in BC. It is regulated by steroids and functions as a putative autophagy receptor that inhibits antioxidants like thioredoxin. Accordingly, boosting epithelialization lowered glutathione, elevated reactive oxygen species and increased both DNA oxidation and double strand breaks. Epithelialization also associated with redistribution of NRF2 and an altered interplay among p38, ATM, and the other kinases regulating the DNA damage response. Hence, hormonal regulation of OVOLs and chronic stress might permit epithelial differentiation and retard exit from dormancy, while altering redox homeostasis and permitting DNA damage accumulation, which may awaken dormant tumors.

cancer biology↗

bioRxiv2024

Targeting primary and metastatic ovarian cancer with a peptide derived from the human NAF-1/CISD2 protein

Ovarian cancer is the most fatal cancer of female reproductive organs. Ovarian cancer is typically diagnosed at a late stage, after metastasis occurred, leading to a 5-years relative survival rate of only [~]5%. Here, we demonstrate the anti-ovarian cancer properties of a peptide derived from the human protein CISD2/NAF-1 (3D-NAF-144-67-6K). This peptide selectively permeates the plasma membrane of ovarian cancer SKOV-3 cells without affecting healthy cells. 3D-NAF-144-67-6K targets and destroys the cancer cells mitochondria which leads to cancer cell death. In vivo studies of mice carrying xenograft tumours of SKOV-3 showed that the peptide significantly decreased the overall size and growth rate of both primary and metastatic ovarian cancer tumours. We further show that 3D-NAF-144-67-6K has a broad-spectrum anticancer activity targeting leukaemia, brain, and pancreas cancer cells. Our study suggests that 3D-NAF-144-67-6K could be used, alone or in drug combinations, to treat ovarian cancer and improve patient survival.

cancer biology↗

bioRxiv2024

Immune organization in sentinel lymph nodes of melanoma patients is prognostic of distant metastases

Sentinel lymph node (sLN) biopsy is part of melanoma staging, as involved LNs indicate a higher risk of recurrence. However, how the sLN is shaped by the tumor and reciprocally affects metastatic progression is poorly understood. Here, we mapped immune organization in involved and non-involved sLNs of 69 melanoma patients using high-resolution spatial proteomics, spatial transcriptomics and deep learning, leveraging the data for prognostic evaluation. In patients with involved LNs, a robust T cell response correlated with absence of recurrence. In non-involved LNs, protection from metastases was linked to expanded sinuses colocalized with plasmablasts whereas CCR7+ cells and Tregs correlated with future development of distant metastases. We trained a model that predicts development of distant metastases with 79% and 93% AUC for non-metastatic and metastatic LNs, respectively. Our findings reveal conserved immune patterns in sLNs that prospectively identify patients at risk for metastatic disease and may aid in therapeutic decisions.

cancer biology↗

bioRxiv2022

RORc expressing immune cells support pro-tumorigenic functions of tertiary lymphoid structures

Tertiary lymphoid structures (TLSs) are formed in many cancer types and have been correlated with better prognosis and response to immunotherapy. In liver cancer, TLSs have been reported to be pro-tumorigenic as they harbor tumor progenitor cells and nurture their growth. The processes involved in TLS development and the acquisition of a pro- or anti-tumorigenic phenotype in cancer are largely unknown. RORc expressing immune cells have been previously implicated in TLS formation, however we find that they are not necessary for TLS neogenesis in the context of inflammation-associated liver cancer. On the contrary, RORc expressing cells negatively regulate TLS formation, since in their absence TLSs form in excess. CD4 cells are essential for liver TLS formation whereas B cells are required for TLS formation specifically in the absence of RORc expressing cells. Importantly, in chronically inflamed livers lacking RORc expressing cells, TLSs become anti-tumorigenic, resulting in reduced tumor load. Comparing liver pro- and anti-tumorigenic TLSs by transcriptional, proteomic and immunohistochemical analyses, revealed enrichment of exhausted CD8 cells that retained effector functions as well as germinal center B cells and plasma cells in anti-tumorigenic TLSs. Cell depletion experiments revealed a role mainly for B cells in limiting tumor development, possibly via tumor directed antibodies. Thus, RORc expressing cells negatively regulate B cell responses, and facilitate the pro-tumorigenic functions of hepatic TLSs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/498540v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@385067org.highwire.dtl.DTLVardef@126c45corg.highwire.dtl.DTLVardef@25ad06org.highwire.dtl.DTLVardef@1829326_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

2-hydroxyglutarate controls centromere and heterochromatin conformation and function in the male germline

2-hydroxyglutarate (2HG) is recognized as an epigenetic regulator in cancer and some transient biological processes. Of all organs, the testis harbors the highest baseline physiological levels of 2HG, yet its putative functions in germ cell biology are unknown. Here we show that 2HG is generated in specific stages of spermatogenesis by the testis specific lactate dehydrogenase C (LDHC), beginning at the last stages of prophase I. Unexpectedly LDHC enters nuclei and concentrates in centromeres. LDHC-generated L-2HG controls centromere condensation and pericentromeric heterochromatin organization through multiple effects including clustering of chromocenters, centromere and chromocenter condensation and expression of satellite RNAs. These effects are rapid and specific to L but not D-2HG. In vivo depletion of L-2HG causes centromere malfunction and activation of the spindle assembly checkpoint. Our findings reveal that 2HG can directly affect centromere and pericentromeric heterochromatin conformation and function and is necessary for licensing chromosome segregation.

cell biology↗

bioRxiv2021

Human nasal and lung tissues infected ex vivo with SARS-CoV-2 provide insights into differential tissue-specific and virus-specific innate immune responses in the upper and lower respiratory tract

The nasal-mucosa constitutes the primary entry site for respiratory viruses including SARS-CoV-2. While the imbalanced innate immune response of end-stage COVID-19 has been extensively studied, the earliest stages of SARS-CoV-2 infection at the mucosal entry site have remained unexplored. Here we employed SARS-CoV-2 and influenza virus infection in native multi-cell-type human nasal turbinate and lung tissues ex vivo, coupled with genome-wide transcriptional analysis, to investigate viral susceptibility and early patterns of local-mucosal innate immune response in the authentic milieu of the human respiratory tract. SARS-CoV-2 productively infected the nasal turbinate tissues, predominantly targeting respiratory epithelial cells, with rapid increase in tissue-associated viral sub-genomic mRNA, and secretion of infectious viral progeny. Importantly, SARS-CoV-2 infection triggered robust antiviral and inflammatory innate immune responses in the nasal mucosa. The upregulation of interferon stimulated genes, cytokines and chemokines, related to interferon signaling and immune-cell activation pathways, was broader than that triggered by influenza virus infection. Conversely, lung tissues exhibited a restricted innate immune response to SARS-CoV-2, with a conspicuous lack of type I and III interferon upregulation, contrasting with their vigorous innate immune response to influenza virus. Our findings reveal differential tissue-specific innate immune responses in the upper and lower respiratory tract, that are distinct to SARS-CoV-2. The studies shed light on the role of the nasal-mucosa in active viral transmission and immune defense, implying a window of opportunity for early interventions, whereas the restricted innate immune response in early-SARS-CoV-2-infected lung tissues could underlie the unique uncontrolled late-phase lung damage of advanced COVID-19. IMPORTANCEIn order to reduce the late-phase morbidity and mortality of COVID-19, there is a need to better understand and target the earliest stages of SARS-CoV-2 infection in the human respiratory tract. Here we have studied the initial steps of SARS-CoV-2 infection and the consequent innate immune responses within the natural multicellular complexity of human nasal-mucosal and lung tissues. Comparing the global innate response patterns of nasal and lung tissues, infected in parallel with SARS-CoV-2 and influenza virus, we have revealed distinct virus-host interactions in the upper and lower respiratory tract, which could determine the outcome and unique pathogenesis of SARS-CoV-2 infection. Studies in the nasal-mucosal infection model can be employed to assess the impact of viral evolutionary changes, and evaluate new therapeutic and preventive measures against SARS-CoV-2 and other human respiratory pathogens.

microbiology↗