Biology subjects

Knight, B.

Publications and source records attributed to Knight, B..

8 recordsLinked to original sources

bioRxiv2026

Sustained interferon exposure creates a hyper-metastatic subset of melanoma cells

We generated interferon signaling reporters in human and mouse melanoma cells and observed heterogeneity in interferon responses among cells in the same tumors. This was marked by inflamed regions within primary tumors that contained increased numbers of interferon-expressing macrophages/monocytes and elevated type I interferon signaling in melanoma cells. Melanoma cells that expressed GFP-Interferon stimulated gene 15 (ISG15) or GFP-Interferon-induced protein with tetraticopeptide repeats 3 (IFIT3) fusion reporters exhibited a profoundly increased ability to form metastatic tumors as compared to GFP-ISG15- melanoma cells from the same tumors, particularly when transplanted into immunocompetent mice. The increased metastatic potential of GFP-ISG15+ cells was driven partly by increased CD47 expression, which protected metastasizing cells from phagocytosis by macrophages. Macrophages are thus a double-edged sword, inhibiting the development of metastatic disease by phagocytosing disseminated melanoma cells, but promoting the emergence of a hyper-metastatic subpopulation of cells in inflamed regions of primary tumors as a consequence of sustained interferon production. One sentence summarySustained interferon exposure within inflamed regions of primary tumors dramatically increases the metastatic potential of a subpopulation of melanoma cells, partly by promoting CD47 expression, which protects against phagocytosis by macrophages.

cancer biology↗

bioRxiv2026

Automated morphometry and weight prediction of juvenile Chinook Salmon leveraging open-source deep learning models

Minimizing handling of threatened and endangered fish has become increasingly important as populations have dwindled. To minimize handling in morphometric measurements, the HandsFreeFishing program has been developed for juvenile Chinook Salmon (Oncorhynchus tshawytscha). By segmenting a 2D image many morphometric measurements are able to be estimated; from these measurements a weight prediction model is built based on fish whose ground truthed weights were measured using a digital scale. While many segmentation methods may be used, here Metas Segment Anything model (SAM) is employed to produce segmentation masks of raw images. This model is open-source and easily used on any image (of any size) with good performance. In the proposed framework, the user supplies a bounding box around a target fish along with minimal orientation data (left or right facing, upside down or right-side up); the rest of the segmentation, feature extraction, and final weight prediction is completely automated. A main goal of the segmentation is to estimate the surface area of the side profile of the fish. Then, assuming an ellipsoidal shape, this surface area can be related to the volume of the fish, which is directly proportional to the weight. Even on a relatively small dataset of 149 images (fork length 27-90mm) our results confirm the predictive qualities of the morphometric features measured. The model achieved weight prediction with a mean absolute error of 0.16 g with a mean absolute percentage error of 12%, and an r-squared value of 0.99, on fish ranging from 0.31g - 7.74g. The raw images come from a variety of fish viewers, the design of which is relatively inexpensive and reproducible, and, in conjunction with the HandsFreeFishing program, allows for minimal handling compared to traditional length and weight measurement methods.

ecology↗

bioRxiv2023

Identification of arginine-vasopressin receptor 1a (Avpr1a/AVPR1A) as a novel candidate gene for chronic visceral pain.

Chronic abdominal pain in the absence of ongoing disease is the hallmark of disorders of gut-brain interaction (DGBIs), including irritable bowel syndrome (IBS). While the etiology of DGBIs remains poorly understood, there is evidence that both genetic and environmental factors play a role. In this study, we report the identification and validation of Avpr1a as a novel candidate gene for visceral hypersensitivity (VH), a primary peripheral mechanism underlying abdominal pain in DGBI/IBS. Comparing two C57BL/6 (BL/6) substrains (C57BL/6NTac and C57BL/6J) revealed differential susceptibility to the development of chronic VH following intrarectal zymosan (ZYM) instillation, a validated preclinical model for post-inflammatory IBS. Using whole genome sequencing, we identified a SNP differentiating the two strains in the 5 intergenic region upstream of Avpr1a, encoding the protein arginine-vasopressin receptor 1A (AVPR1A). We used behavioral, histological, and molecular approaches to identify distal colon- specific gene expression differences and neuronal hyperresponsiveness covarying with Avpr1a genotype and VH susceptibility. While the two BL/6 substrains did not differ across other gastrointestinal (GI) phenotypes (e.g., GI motility), VH-susceptible BL/6NTac mice had higher colonic Avpr1a mRNA and protein expression. Moreover, neurons of the enteric nervous system were hyperresponsive to the AVPR1A agonist AVP, suggesting a role for enteric neurons in the pathology underlying VH. These results parallel our findings that patients colonic Avpr1a mRNA expression was higher in patients with higher pain ratings. Taken together, these findings implicate differential regulation of Avpr1a as a novel mechanism of VH-susceptibility as well as a potential therapeutic target specific to VH. SummaryA combination of approaches, from genomic analysis to functional analyses, confirm Avpr1a as a high priority candidate gene for visceral pain.

genetics↗

bioRxiv2023

Periostin facilitates ovarian cancer recurrence by enhancing cancer stemness

Ovarian cancer (OC) is the deadliest reproductive system cancer. Its high lethality is due to the high recurrence rate and the development of chemotherapeutic resistance, which requires synergy between cancer cells and non-cancerous cells of the tumor microenvironment (TME). Analysis of gene expression microarray data from paired primary and recurrent OC tissues revealed significantly elevated expression of the gene encoding periostin (POSTN) in recurrent OC compared to matched primary tumors (p=0.014). Finding POSTN primarily localized to the TME, we investigated the role of TME POSTN in OC cell viability, migration/invasion, and chemosensitivity. Conditioned media with high levels of POSTN (CMPOSTNhigh) was generated using POSTN-transfected fibroblastic preadipocyte 3T3-L1 cells. CMPOSTNhigh-cultured OC cells exhibited faster migration, more invasiveness (p=0.006), and more chemoresistance (p<0.05) compared to OC cells cultured with control medium (CMCTL). Furthermore, CMPOSTNhigh-cultured HEYA8 cells demonstrated increased resistance to paxlitaxel-induced apoptosis. Multiple OC cell lines (HEYA8, CAOV2, and SKOV3) cultured with CMPOSTNhighshowed increases in stem cell side population relative to CMCTL-cultured cells. POSTN-transfected 3T3-L1 cells exhibited more intracellular and extracellular lipids, and this was linked to increased cancer cell expression of the oncogene fatty acid synthetase (FASN). Additionally, POSTN functions in the TME were linked to Akt pathway activities. In a xenograft mouse model of OC, the mean tumor volume in mice injected with CMPOSTNhigh-grown OC cells was larger than that in mice injected with CMCTL-grown OC cells (p=0.0023). Altogether, higher POSTN expression is present in recurrent OC and promotes a more aggressive and chemoresistant oncogenic phenotype in vitro. Within cancer TME fibroblasts, POSTN can stimulate lipid production and is associated with increased OC stem cell side population, consistent with its known role in maintaining stemness. Our results bolster the need for further study of POSTN as a potential therapeutic target in treatment and potential prevention of recurrent ovarian cancer. Author SummaryOvarian cancer has a high rate of recurrent disease that is often resistant to chemotherapy. Comparing primary and recurrent ovarian cancer tumors, we found that the gene POSTN, which encodes the protein periostin, is more highly expressed in recurrent tumors, and more highly expressed in the tumor microenvironment, outside of the cancer cells. We transfected cells with vectors encoding POSTN or with blank vectors to generate conditioned media with high POSTN or control media. Ovarian cancer cells cultured in the POSTN-high conditioned media showed faster wound healing, more invasiveness, and more resistance to apoptosis caused by chemotherapeutic agents, and increased stemness, an important trait in cancer cells, especially recurrent cells. POSTN-transfected cells showed higher expression of the enzyme fatty acid synthase and higher concentrations of lipids, indicating that POSTN may play a role in increasing the energy available to cancer cells. The Akt pathway, often activated in ovarian cancer growth, was activated more in cells cultured in the POSTN-high environment. Finally, we injected immunocompromised mice with ovarian cancer cells that were grown in either the POSTN-high media or the control media, and the average tumor size was higher in mice injected with the cells that were grown in the POSTN-high media.

cancer biology↗

bioRxiv2023

Unlocking de novo antibody design with generative artificial intelligence

Generative AI has the potential to redefine the process of therapeutic antibody discovery. In this report, we describe and validate deep generative models for the de novo design of antibodies against human epidermal growth factor receptor (HER2) without additional optimization. The models enabled an efficient workflow that combined in silico design methods with high-throughput experimental techniques to rapidly identify binders from a library of [~]106 heavy chain complementarity-determining region (HCDR) variants. We demonstrated that the workflow achieves binding rates of 10.6% for HCDR3 and 1.8% for HCDR123 designs and is statistically superior to baselines. We further characterized 421 diverse binders using surface plasmon resonance (SPR), finding 71 with low nanomolar affinity similar to the therapeutic anti-HER2 antibody trastuzumab. A selected subset of 11 diverse high-affinity binders were functionally equivalent or superior to trastuzumab, with most demonstrating suitable developability features. We designed one binder with [~]3x higher cell-based potency compared to trastuzumab and another with improved cross-species reactivity1. Our generative AI approach unlocks an accelerated path to designing therapeutic antibodies against diverse targets.

synthetic biology↗

bioRxiv2021

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

evolutionary biology↗

bioRxiv2019

Major surgery induces acute changes in DNA methylation associated with activation of the immune response.

BackgroundSurgery is an invasive procedure evoking acute inflammatory and immune responses that are believed to mediate risk for postoperative complications including cognitive dysfunction and delirium. Although the specific mechanisms driving these responses have not been well-characterized, they are hypothesized to involve the epigenetic regulation of gene expression. We quantified genome-wide levels of DNA methylation in purified peripheral blood mononuclear cells (PBMCs) longitudinally collected from 55 elderly patients undergoing three types of major surgery (elective colorectal and hip replacement surgery, and emergency hip fracture surgery), comparing samples collected at baseline to those collected immediately post-operatively and at discharge from hospital.\n\nResultsMajor surgery was associated with acute changes in DNA methylation at sites annotated to immune system genes, paralleling changes in serum-levels of markers including C-reactive protein (CRP) and Interleukin 6 (IL-6) measured in the same individuals. Although many of the observed changes in DNA methylation are consistent across the three types of surgery, there is notable heterogeneity between surgery types at certain loci. The acute changes in DNA methylation induced by surgery are relatively stable in the postoperative period, generally persisting until discharge from hospital.\n\nConclusionsOur results highlight the dramatic alterations in gene regulation induced by invasive surgery, primarily reflecting upregulation of the immune system in response to trauma, wound healing and anaesthesia.

genomics↗

bioRxiv2019

Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer

Prostate is the most frequent cancer in men. Prostate cancer progression is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription by stimulating androgen receptor (AR) activity, yet also control pre-mRNA splicing through less clear mechanisms. Here we find androgens regulate splicing through AR-mediated transcriptional control of the epithelial-specific splicing regulator ESRP2. Both ESRP2 and its close paralog ESRP1 are highly expressed in primary prostate cancer. Androgen stimulation induces splicing switches in many endogenous ESRP2-controlled mRNA isoforms, including a key splicing switch in the metastatic regulator FLNB which is associated with disease relapse. ESRP2 expression in clinical prostate cancer is repressed by ADT, which may thus inadvertently dampen epithelial splice programmes. Supporting this, FLNB splicing was reciprocally switched by the AR antagonist bicalutamide (Casodex(R)). Our data reveal a new mechanism of splicing control in prostate cancer with important implications for metastatic disease progression.\n\nKey pointsO_LITranscriptional regulation of ESRP2 by the androgen receptor controls splice isoform patterns in prostate cancer cells.\nC_LIO_LISplicing switches regulated by the androgen-ESRP2 axis include a splice isoform in the FLNB gene that is a known metastatic driver.\nC_LIO_LIBoth ESRP1 and ESRP2 are highly expressed in prostate cancer tissue.\nC_LIO_LIEctopic expression of ESRP1 and 2 inhibits prostate cancer cell growth.\nC_LIO_LIBy repressing ESRP2 expression androgen deprivation therapy (ADT) may dampen epithelial splicing programmes to inadvertently prime disease progression towards metastasis.\nC_LI

molecular biology↗