Biology subjects

Harris, C. C.

Publications and source records attributed to Harris, C. C..

14 recordsLinked to original sources

bioRxiv2026

Spin-Dependent Extracellular Respiration

Biological energy conversion relies on highly efficient electron transfer. The chirality induced spin selectivity (CISS) effect, which couples electron spin to momentum in chiral molecules, is hypothesized to promote this efficiency. While observed in isolated biomolecules, the physiological relevance of CISS during active cellular metabolism remains unknown. Here, we demonstrate that CISS influences extracellular electron transfer in living Geobacter sulfurreducens biofilms. Cultivation on ferromagnetic electrodes yields a significant asymmetry in respiratory current between opposite substrate spin states. Furthermore, in situ magnetization reversal induces reversible changes in respiratory flux. These results provide the first in vivo demonstration that spin selectivity directly impacts respiration. By revealing a quantum feature of extracellular respiration, our findings offer a strategy to exploit the spin degree of freedom in bioelectronics.

biophysics↗

bioRxiv2026

The senescence-inhibitory p53 isoform Δ133p53α represses the proinflammatory chemokine CXCL10 in progeria model mice and naturally aged mice

Aims{Delta}133p53 is a naturally occurring isoform of the human p53 protein that inhibits p53-mediated cellular senescence. We previously reported that transgenic expression of this senescence-inhibitory p53 isoform counteracts aging-associated pathological changes in progeria model mice (heterozygous LmnaG609G/+). The anti-aging effect of {Delta}133p53 was attributed in part to reduced levels of the proinflammatory cytokine IL-6. This study aims to comprehensively profile {Delta}133p53-induced changes in cytokines and chemokines. MethodsA Luminex-based multiplex quantitative assay was performed using mouse serum samples from transgenic {Delta}133p53-expressing LmnaG609G/+ mice and non-expressing controls. Quantitative RT-PCR and RNA in situ hybridization assays were used to assess Cxcl10 expression in mouse tissues. In addition, gene expression datasets from human tissues were analyzed. ResultsWe confirmed {Delta}133p53-mediated repression of serum IL-6 levels. We also found that {Delta}133p53 reduced serum levels of CXCL1, IL-1, and CXCL10. We further characterized CXCL10, which has not previously been associated with progeria in mice or humans. Consistent with reduced serum CXCL10 levels, both young (15-week-old) and old (10-month-old) {Delta}133p53-expressing LmnaG609G/+ mice showed reduced Cxcl10 expression in the liver, spleen, and brain, major organs that produce CXCL10, compared with age-matched non-expressing controls. In naturally aged wild-type mice (2 years old), transgenic {Delta}133p53 expression also significantly repressed Cxcl10 expression in the spleen and brain. An inverse association between CXCL10 and {Delta}133p53 levels was observed in human spleen tissues, suggesting physiological relevance to human aging. ConclusionCXCL10, a proinflammatory chemokine elevated in both accelerated and natural aging, is a potential target of the anti-inflammatory activity of {Delta}133p53.

physiology↗

bioRxiv2026

Senescence-inhibitory Δ133p53α counteracts accelerated ageing and mortality

Research on progeria not only contributes to treatments for the disease but also enhances our understanding of physiological ageing1. Mouse models of progeria recapitulate pathological ageing phenotypes seen in patients, including cardiovascular defects, increased cellular senescence, systemic inflammation, DNA damage accumulation, and shortened lifespan2. In cultured cells from Hutchinson-Gilford progeria syndrome (HGPS) patients, the human p53 isoform {Delta}133p53 was previously shown to inhibit p53-mediated cellular senescence, proinflammatory IL-6 production, and DNA damage accumulation, and to extend cellular replicative lifespan3. Here we show that, in a heterozygous HGPS mouse model4, transgenic expression of {Delta}133p53 reproduces these in vitro-observed effects across multiple organs in vivo and extends median lifespan by 11% (387 versus 349 days, P = 0.0379). In the aorta and skin, {Delta}133p53 abrogates progeria-characteristic pathological changes and preserves tissue integrity. Our data further suggest that {Delta}133p53 may promote a broad spectrum of ageing-counteracting mechanisms, including bone homeostasis, metabolic fitness, antioxidant defense, youthful epigenome, and tissue stemness. Together with the anti-inflammatory and tissue-preserving effects of {Delta}133p53 in naturally aged mice and its age-associated downregulation in human tissues, this study suggests that {Delta}133p53-based therapeutic strategies may be applicable not only to HGPS but also as broader interventions for preventing or delaying ageing.

physiology↗

bioRxiv2025

Pharmacologic activation of Δ133p53α reduces cellular senescence in progeria patients-derived cells

BackgroundPatients with Hutchinson-Gilford progeria syndrome (HGPS) show accelerated aging phenotypes and have shortened lifespan, with implications in physiological aging processes as well. While therapeutic approaches targeting the disease-causing abnormal protein, progerin, have been developed, further efforts to explore mechanistically distinct and complementary strategies are still critical to better treatment regimens. We previously showed that lentiviral vector-driven expression of {Delta}133p53, a natural inhibitory isoform of p53, rescued HGPS patients-derived fibroblasts from early entry into cellular senescence, which is a downstream event of progerin-induced DNA damage. We also performed a quantitative high-throughput screen (qHTS) of approved drug and investigational agent libraries, leading to the identification of celastrol and AZD1981 as compounds that upregulate {Delta}133p53 protein levels. MethodsTo investigate whether celastrol and ADZ1981 upregulate endogenous {Delta}133p53 in HGPS-derived fibroblasts and reduce their senescence-associated phenotypes, we performed western blot assays ({Delta}133p53, progerin, and p21WAF1, which mediates p53-induced senescence and is inhibited by {Delta}133p53), senescence-associated {beta}-galactosidase (SA-{beta}-gal) staining, enzyme-linked immunosorbent assay (IL-6, which is a proinflammatory cytokine secreted from senescent cells), and qRT-PCR assays (p21WAF1 and IL-6). ResultsTreatment with celastrol (0.1 {micro}M for 24 h) or AZD1981 (10 {micro}M for 24 h) reproducibly increased {Delta}133p53 expression and decreased p21WAF1 expression in two strains of fibroblasts derived from HGPS patients. These compounds reduced the percentage of SA-{beta}-gal-positive senescent cells and the secretion of IL-6 into culture medium in both of these fibroblast strains, irrespective of their different basal levels of senescence and IL-6 secretion. These compounds had no effect on the level of progerin. ConclusionCelastrol and ADZ1981 upregulate endogenous {Delta}133p53 and, reproducing the effects of its vector-driven expression, inhibit cellular senescence and IL-6 secretion in HGPS-derived fibroblasts. Their progerin-independent action suggests that they may synergize with currently available progerin-targeting therapies. This study also warrants further investigation of these compounds for potential applications in other diseases and conditions in which {Delta}133p53-regulated senescence plays a role.

cell biology↗

bioRxiv2025

SRSF3 knockdown-induced cellular senescence as a possible therapeutic strategy for non-small cell lung cancer

Tyrosine kinase (TK) inhibitors improve clinical outcomes in non-small cell lung cancer (NSCLC) with targetable mutations. However, such NSCLC cases only consist of about 50% in the western populations. This study, for the first time in NSCLC cells including those without a targetable TK mutation, explores a tumor-suppressive activity of siRNA knockdown of a splicing factor SRSF3, which was reportedly effective in other cancer cell types. The knockdown of SRSF3 increased cellular senescence, indicated by senescence-associated {beta}-galactosidase activity and reduced cell proliferation, in all NSCLC cell lines examined, including A549 (no TK mutation; TP53 wild-type), NCI-H1975 (EGFR L858R/T790M; TP53 R273H mutant), NCI-H322 (no TK mutation; TP53 R248L mutant) and NCI-H596 (no TK mutation; TP53 G245C mutant). An increase in apoptotic cleavage of caspase-3 and poly(ADP-ribose) polymerase was also observed in A549 cells. p53{beta}, a tumor-suppressive p53 isoform generated via alternative mRNA splicing, was upregulated by SRSF3 knockdown, as previously reported in normal fibroblasts. However, neither cellular senescence nor apoptosis was increased by overexpression of p53{beta}, suggesting no or minimum contribution of this p53 isoform to the tumor-suppressive activity of SRSF3 knockdown in NSCLC cells. Our gene expression assay indicated that the SRSF3 knockdown-induced senescence in NSCLC cells may be mediated by downregulation of TOP2A, UBE2C or ASPM, which are known to be oncogenic and are associated with poor patient prognosis. We also generated SRSF3 siRNA-encapsulating lipid nanoparticles as a future therapeutic tool. This study suggests a therapeutic strategy for NSCLC irrespective of the mutation status of TP53 and TK-encoding genes. SummaryKnockdown of a splicing factor SRSF3 increases cellular senescence in NSCLC cells including those with no targetable mutation of tyrosine kinases and thus may represent a novel therapeutic strategy for a hard-to-treat group of NSCLC.

cancer biology↗

bioRxiv2024

Federated deep learning enables cancer subtyping by proteomics

Artificial intelligence applications in biomedicine face major challenges from data privacy requirements. To address this issue for clinically annotated tissue proteomic data, we developed a Federated Deep Learning (FDL) approach (ProCanFDL), training local models on simulated sites containing data from a pan-cancer cohort (n=1,260) and 29 cohorts held behind private firewalls (n=6,265), representing 19,930 replicate data-independent acquisition mass spectrometry (DIA-MS) runs. Local parameter updates were aggregated to build the global model, achieving a 43% performance gain on the hold-out test set (n=625) in 14 cancer subtyping tasks compared to local models, and matching centralized model performance. The approachs generalizability was demonstrated by retraining the global model with data from two external DIA-MS cohorts (n=55) and eight acquired by tandem mass tag (TMT) proteomics (n=832). ProCanFDL presents a solution for internationally collaborative machine learning initiatives using proteomic data, e.g., for discovering predictive biomarkers or treatment targets, while maintaining data privacy. Statement of SignificanceA federated deep learning approach applied to human proteomic data, acquired using two distinct proteomic technologies from 40 tumor cohorts from eight countries, enabled accurate cancer histopathological subtyping while preserving data privacy. This approach will enable privacy-compliant development of large-scale proteomic AI models, including foundation models, across institutions globally.

cancer biology↗

bioRxiv2023

Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue

Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and Barretts esophagus (BE) is a strong risk factor along with smoking. Smoking is well-known to induce microbial dysbiosis and we asked if BE and esophageal microbiomes had shared microbial alterations that could provide novel biomarkers. We extracted DNA from BE tissues (n=5) and tumors of 158 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNAseq (n = 173) and WGS (n = 139) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alternations that allow disease progression in esophageal cancer.

cancer biology↗

bioRxiv2022

Acidovorax temperans polarizes T17 cells and skews neutrophil maturation to promote lung adenocarcinoma development

Dysbiosis, or changes within the microbiome, is a common feature of solid tumors, however whether this dysbiosis directly contributes to tumor development is largely unknown. We previously characterized the lung cancer microbiome and identified Acidovorax temperans as enriched in tumors. In this study, we instilled A. temperans in an animal model driven by mutant Kras and Tp53 alleles. This revealed A. temperans accelerates tumor development and burden through infiltration of proinflammatory cells. Neutrophils exposed to A. temperans displayed a mature, pro-tumorigenic genotype with increased cytokine signaling, with a global shift away from IL-1{beta} signaling. Neutrophil to monocyte and macrophage signaling upregulated MHC II to activate CD4+ T cells which polarized to an IL-17A+ phenotype detectable in CD4+ and {gamma}{delta} populations. T17 cells shared a common gene expression program predictive of poor survival in human LUAD. These data indicate dysbiosis promotes tumor growth by modulating inflammation.

cancer biology↗

bioRxiv2022

Matrin3 regulates cell proliferation and spindle dynamics by regulating CDC14B alternative splicing

Matrin3 is an RNA-binding protein that affects diverse RNA-related processes, including mRNA splicing. While Matrin3 has been intensively studied in neurodegenerative diseases, its function in cancer remains unclear. Here, we discovered Matrin3-mediated regulation of mitotic spindle dynamics in colorectal cancer (CRC) cells. We identified bound and regulated Matrin3-target RNAs transcriptome-wide in CRC cells and found that Matrin3 broadly modulates mRNA splicing patterns. Among the top Matrin3 targets, we focused on CDC14B and found that Matrin3 loss increased inclusion of an exon containing a premature termination codon into the CDC14B transcript and simultaneous down-regulation of the standard CDC14B transcript. Selective knockdown of the CDC14B standard transcript phenocopied Matrin3 knockdown and exhibited reduced proliferation and defects in mitotic spindle formation, suggesting that CDC14B is a key downstream effector of Matrin3. Collectively, these data reveal an important role for the Matrin3/CDC14B axis in control of CRC cell proliferation and mitotic spindle formation.

molecular biology↗

bioRxiv2021

Δ133p53α Protects Human Astrocytes from Amyloid-Beta Induced Senescence and Neurotoxicity

Cellular senescence is an important contributor to aging and age-related diseases such as Alzheimers disease (AD). Senescent cells are characterized by a durable cell proliferation arrest and the acquisition of a proinflammatory senescence-associated secretory phenotype (SASP), which participates in the progression of neurodegenerative disorders. Clearance of senescent glial cells in an AD mouse model prevented cognitive decline suggesting pharmacological agents targeting cellular senescence might provide novel therapeutic approaches for AD. {Delta}133p53, a natural protein isoform of p53, was previously shown to be a negative regulator of cellular senescence in primary human astrocyte, with clinical implications from its diminished expression in brain tissues from AD patients. Here we show that treatment of proliferating human astrocytes with amyloid-beta oligomers (A{beta}), an endogenous pathogenic agent of AD, results in reduced expression of {Delta}133p53, as well as induces the cells to become senescent and express proinflammatory SASP cytokines such as IL-6, IL-1{beta} and TNF. Our data suggest that A{beta}-induced astrocyte cellular senescence is associated with accelerated DNA damage, and upregulation of full-length p53 and its senescence-inducing target gene p21WAF1. We also show that exogenously enhanced expression of {Delta}133p53 rescues human astrocytes from A{beta}-induced cellular senescence and SASP through both protection from DNA damage and dominantnegative inhibition of full-length p53, leading to inhibition of A{beta}-induced, astrocyte-mediated neurotoxicity. The results presented here demonstrate that {Delta}133p53 manipulation could modulate cellular senescence in the context of AD, possibly opening new therapeutic avenues. HIGHLIGHTSO_LIA{beta} diminishes the expression of the p53 isoform {Delta}133p53, and induces cellular senescence, SASP, and DNA damage in human astrocytes. C_LIO_LI{Delta}133p53 protects human astrocytes from A{beta}-induced DNA damage and cellular senescence. C_LIO_LI{Delta}133p53 prevents astrocyte-mediated neurotoxicity to neuro-progenitor cells. C_LI

neuroscience↗

bioRxiv2020

Anatomic position determines oncogenic specificity in melanoma

Oncogenic alterations to DNA are not transforming in all cellular contexts1,2. This may be due to pre-existing transcriptional programs in the cell of origin. Here, we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet, or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma but CRKL amplifications in acral melanoma. We modeled these changes in transgenic zebrafish models and found that CRKL-driven tumors predominantly formed in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin/limb melanocytes, compared to body melanocytes, revealed a positional identity gene program typified by posterior HOX13 genes. This positional gene program synergized with CRKL to drive tumors at acral sites. Abrogation of this CRKL-driven program eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.

cancer biology↗

bioRxiv2019

Functional Genomic Complexity Defines Intratumor Heterogeneity and Tumor Aggressiveness in Liver Cancer

BackgroundChronic inflammation and chromosome aneuploidy are major traits of primary liver cancer (PLC), which represent the second most common cause of cancer related death worldwide. Increased cancer fitness and aggressiveness of PLC may be achieved by enhancing tumoral genomic complexity that alters tumor biology.\n\nMethodHere, we developed a scoring method, namely functional genomic complexity (FGC), to determine the degree of molecular heterogeneity among 580 liver tumors with diverse ethnicities and etiologies by assessing integrated genomic and transcriptomic data.\n\nResultsWe found that tumors with higher FGC scores are associated with chromosome instability and TP53 mutations, and a worse prognosis, while tumors with lower FGC scores have elevated infiltrating lymphocytes and a better prognosis. These results indicate that FGC scores may serve as a surrogate to define genomic heterogeneity of PLC linked to chromosomal instability and evasion of immune surveillance.\n\nConclusionOur findings demonstrate an ability to define genomic heterogeneity and corresponding tumor biology of liver cancer based only on bulk genomic and transcriptomic data. Our data also provide a rationale for applying this approach to survey liver tumor immunity and to stratify patients for immune-based therapy.\n\nSTATEMENT OF SIGNIFICANCEGenomic heterogeneity contributes to therapeutic failure and poor outcome in patients with liver cancer and poses a challenge in defining targeted therapy. Our findings demonstrate an ability to define genomic heterogeneity and corresponding tumor biology of liver cancer based only on bulk genomic and transcriptomic data. Our data also provide a rationale for applying this approach to survey liver tumor immunity and to stratify patients for immune-based therapy. \\body

genomics↗

bioRxiv2018

Cross-cancer pleiotropic associations with lung cancer risk in African Americans

BackgroundIdentifying genetic variants with pleiotropic associations across multiple cancers can reveal shared biologic pathways. Prior pleiotropic studies have primarily focused on European descent individuals. Yet population-specific genetic variation can occur and potential pleiotropic associations among diverse racial/ethnic populations could be missed. We examined cross-cancer pleiotropic associations with lung cancer risk in African Americans.\n\nMethodsWe conducted a pleiotropic analysis among 1,410 African American lung cancer cases and 2,843 controls. We examined 36,958 variants previously associated (or in linkage disequilibrium) with cancer in prior genome-wide association studies. Logistic regression analyses were conducted, adjusting for age, sex, global ancestry, study site, and smoking status.\n\nResultsWe identified three novel genomic regions significantly associated (FDR-corrected p-value < 0.10) with lung cancer risk (rs336958 on 5q14.3, rs7186207 on 16q22.2, and rs11658063 on 17q12). On chromosome16q22.2, rs7186207 was significantly associated with increased risk (OR=1.24, 95% CI: 1.12-1.38) and functional annotation using GTEx showed rs7186207 modifies DHODH gene expression. The risk allele at rs336958 on 5q14.3 was associated with reduced lung cancer risk (OR=0.68, 95% CI: 0.56-0.82), while the risk allele at rs11658063 on 17q12 was associated with increased risk (OR=1.24, 95% CI: 1.11-1.39).\n\nConclusionWe identified novel associations on chromosomes 5q14.3, 16q22.2, and 17q12, which contain HNF1B, DHODH, and HAPLN1 genes, respectively. SNPs within these regions have been previously associated with multiple cancers. This is the first study to examine cross-cancer pleiotropic associations for lung cancer in African Americans.\n\nImpactOur findings demonstrate novel cross-cancer pleiotropic associations with lung cancer risk in African Americans.

genetics↗

bioRxiv2018

Microbiome-TP53 Gene Interaction in Human Lung Cancer

BackgroundLung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesized that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from controls (n=33) and cancer cases (n=143), we conducted 16S rRNA bacterial gene sequencing, with RNA-seq data from lung cancer cases in The Cancer Genome Atlas (n=1112) serving as the validation cohort.\n\nResultsOverall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma (SCC) specifically, a separate group of taxa were identified, in which Acidovorax was enriched in smokers (P =0.0013). Acidovorax temporans was identified by fluorescent in situ hybridization within tumor sections, and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibited higher abundance among the subset of SCC cases with TP53 mutations, an association not seen in adenocarcinomas (AD).\n\nConclusionsThe results of this comprehensive study show both a microbiome-gene and microbiome-exposure interactions in SCC lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can damage epithelial function, have a unique bacterial consortia which is higher in relative abundance in smoking-associated SCC. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.

cancer biology↗