High-Throughput Empirical and Virtual Screening To Discover Novel Inhibitors of Polyploid Giant Cancer Cells in Breast Cancer.

Therapy resistance in breast cancer is increasingly attributed to polyploid giant cancer cells (PGCCs), which arise through whole genome doubling and exhibit heightened resilience to standard treatments. Characterized by enlarged nuclei and increased DNA content, these cells tend to be dormant under therapeutic stress, driving disease relapse. Despite their critical role in resistance, strategies to effectively target PGCCs are limited, largely due to the lack of high-throughput methods for assessing their viability.

High-Throughput Empirical and Virtual Screening to Discover Novel Inhibitors of Polyploid Giant Cancer Cells in Breast Cancer.

Therapy resistance in breast cancer is increasingly attributed to polyploid giant cancer cells (PGCCs), which arise through whole-genome doubling and exhibit heightened resilience to standard treatments. Characterized by enlarged nuclei and increased DNA content, these cells tend to be dormant under therapeutic stress, driving disease relapse. Despite their critical role in resistance, strategies to effectively target PGCCs are limited, largely due to the lack of high-throughput methods for assessing their viability.

Targeting S6K/NFκB/SQSTM1/Polθ signaling to suppress radiation resistance in prostate cancer.

In this study we have identified POLθ-S6K-p62 as a novel druggable regulator of radiation response in prostate cancer. Despite significant advances in delivery, radiotherapy continues to negatively affect treatment outcomes and quality of life due to resistance and late toxic effects to the surrounding normal tissues such as bladder and rectum. It is essential to develop new and effective strategies to achieve better control of tumor.

shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning.

Advancing precision oncology requires accurate prediction of treatment response and accessible prediction models. To this end, we present shinyDeepDR, a user-friendly implementation of our innovative deep learning model, DeepDR, for predicting anti-cancer drug sensitivity. The web tool makes DeepDR more accessible to researchers without extensive programming experience.

Sex-dependent differences in the genomic profile of lingual sensory neurons in naïve and tongue-tumor bearing mice.

Mechanisms of sex-dependent orofacial pain are widely understudied. A significant gap in knowledge exists about comprehensive regulation of tissue-specific trigeminal sensory neurons in diseased state of both sexes. Using RNA sequencing of FACS sorted retro-labeled sensory neurons innervating tongue tissue, we determined changes in transcriptomic profiles in males and female mice under naïve as well as tongue-tumor bearing conditions Our data revealed the following interesting findings: (1) FACS sorting obtained higher number of neurons from female trigeminal ganglia (TG) compared to males; (2) Naïve female neurons innervating the tongue expressed immune cell markers such as Csf1R, C1qa and others, that weren't expressed in males.

DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer.

Motivation: Large-scale genetic and pharmacologic dependency maps are generated to reveal genetic vulnerabilities and drug sensitivities of cancer. However, user-friendly software is needed to systematically link such maps.

Results: Here, we present DepLink, a web server to identify genetic and pharmacologic perturbations that induce similar effects on cell viability or molecular changes.

BRCA1 deficiency in mature CD8 T lymphocytes impairs antitumor immunity.

Women with germline mutations have approximately an 80% lifetime chance of developing breast cancer. While the tumor suppressor function of BRCA1 in breast epithelium has been studied extensively, it is not clear whether deficiency in non-breast somatic cells also contribute to tumorigenesis. Here, we report that mouse knockout (KO) in mature T lymphocytes compromises host antitumor immune response to transplanted syngeneic mouse mammary tumors.

Sex-dependent Differences in the Genomic Profile of Lingual Sensory Neurons in Naïve and Tongue-Tumor Bearing Mice.

Mechanisms of sex-dependent orofacial pain are widely understudied. A significant gap in knowledge exists about comprehensive regulation of tissue-specific trigeminal sensory neurons in diseased state of both sexes. Using RNA sequencing of FACS sorted retro-labeled sensory neurons innervating tongue tissue, we determined changes in transcriptomic profiles in males and female mice under naïve as well as tongue-tumor bearing conditions Our data revealed the following interesting findings: 1) Tongue tissue of female mice was innervated with higher number of trigeminal neurons compared to males; 2) Naïve female neurons innervating the tongue exclusively expressed immune cell markers such as Csf1R, C1qa and others, that weren't expressed in males.

Comparative Transcriptome Analysis of Superficial and Deep Partial-Thickness Burn Wounds in Yorkshire vs Red Duroc Pigs.

Hypertrophic scars are a common negative outcome of deep partial-thickness (DPT) burn wounds resulting in increased dermal thickness, wound area contracture, and inflammation of the affected area. The red Duroc and Yorkshire porcine breeds are common large animal models for studying dermal wounds due to their structural similarities to human skin; however, the porcine transcriptomic profiles of dermal burn wounds and healing process are not well known. In response, a longitudinal transcriptomic comparative study was conducted comparing red Duroc and Yorkshire superficial and DPT burn wounds to their respective control uninjured tissue.

Predicting and characterizing a cancer dependency map of tumors with deep learning.

Genome-wide loss-of-function screens have revealed genes essential for cancer cell proliferation, called cancer dependencies. It remains challenging to link cancer dependencies to the molecular compositions of cancer cells or to unscreened cell lines and further to tumors. Here, we present DeepDEP, a deep learning model that predicts cancer dependencies using integrative genomic profiles.

Androgen deprivation-induced elevated nuclear SIRT1 promotes prostate tumor cell survival by reactivation of AR signaling.

The NAD-dependent deacetylase, Sirtuin 1 (SIRT1) is involved in prostate cancer pathogenesis. However, the actual contribution is unclear as some reports propose a protective role while others suggest it is harmful. We provide evidence for a contextual role for SIRT1 in prostate cancer.

Campylobacter infection promotes IFNγ-dependent intestinal pathology via ILC3 to ILC1 conversion.

Innate lymphoid cells (ILCs) are a heterogeneous family of immune regulators that protect against mucosal pathogens but can also promote intestinal pathology. Although the plasticity between ILCs populations has been described, the role of mucosal pathogens in inducing ILC conversion leading to intestinal pathology remains unclear. Here we demonstrate that IFNγ-producing ILCs are responsible for promoting intestinal pathology in a mouse model of enterocolitis caused by Campylobacter jejuni, a common human enteric pathogen.

Antibiotic Administration Routes and Oral Exposure to Antibiotic Resistant Bacteria as Key Drivers for Gut Microbiota Disruption and Resistome in Poultry.

Previous studies have identified oral administration of antibiotics and gut-impacting drugs as critical drivers for fecal antibiotic resistance (AR) and microbiome disruption in lab mice, but the practical implications of these findings have yet to be validated in hosts nurtured in conventional environment. Using ampicillin (Amp) as a way to extrapolate the general effect of antibiotics, this project examined the impact of drug administration routes on fecal microbiota and resistome using poultry raised in a teaching farm. AR genes were found to be abundant in the feces of young Leghorn chicks without previous antibiotic treatment.

An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data.

Background: Europeans and American Indians were major genetic ancestry of Hispanics in the U.S. These ancestral groups have markedly different incidence rates and outcomes in many types of cancers.

Correction to: Predicting drug response of tumors from integrated genomic profiles by deep neural networks.

Following publication of the original article [1], the authors provided an updated funding statement to the article. The updated statement is as follows.

Integrating resistance functions to predict response to induction chemotherapy in de novo acute myeloid leukemia.

Objectives: This study explored resistance functions and their interactions in de novo AML treated with the "7 + 3" induction regimen.

Methods: We analyzed RNA-sequencing profiles of whole bone marrow samples from 52 de novo AML patients who completed the "7 + 3" regimen and stratified patients into CR (n = 35) and non-CR (n = 17) groups.

Results: A systematic gene set analysis revealed significant associations between chemoresistance and mTOR (P < .

Predicting drug response of tumors from integrated genomic profiles by deep neural networks.

Background: The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent study screened for the response of a thousand human cancer cell lines to a wide collection of anti-cancer drugs and illuminated the link between cellular genotypes and vulnerability. However, due to essential differences between cell lines and tumors, to date the translation into predicting drug response in tumors remains challenging.

scdNet: a computational tool for single-cell differential network analysis.

Background: Single-cell RNA sequencing (scRNA-Seq) is an emerging technology that has revolutionized the research of the tumor heterogeneity. However, the highly sparse data matrices generated by the technology have posed an obstacle to the analysis of differential gene regulatory networks.

Results: Addressing the challenges, this study presents, as far as we know, the first bioinformatics tool for scRNA-Seq-based differential network analysis (scdNet).

An ultra low-cost smartphone device for in-situ monitoring of acute organophosphorus poisoning for agricultural workers.

In this work, we present an ultra-low-cost smartphone device for in situ quantification of OP poisoning severity. The performance of the lens-less smartphone spectrum apparatus (LeSSA) is evaluated using standard human Interleukin-6 (IL-6) immunoassay kits. Upon dose-response curve fitting, LeSSA demonstrates an accuracy of 99.

Facile continuous production of soy peptide nanogels via nanoscale flash desolvation for drug entrapment.

A facile continuous production of soy peptide nanogels was demonstrated using a multi-inlet vortex micromixer for the entrapment of active ingredients. The full flow regime in the micromixer was systematically studied to understand the flow impact on nanogel size, drug encapsulation efficiency and drug loading efficiency. Ibuprofen was chosen as a model drug to demonstrate encapsulation capability.

An ultra-low-cost smartphone octochannel spectrometer for mobile health diagnostics.

With the rapid development and proliferation of mobile devices with powerful computing power and the ability of integrating sensors into mobile devices, the potential impact of mobile health (mHealth) diagnostics on the public health is drawing researchers' attention. We developed a Smartphone Octo-channel Spectrometer (SOS) as a mHealth diagnostic tool. The SOS has nanoscale wavelength resolution, is self-illuminated from the smartphone itself, and is ultra-low cost (less than $20).

Analytical validation of an ultra low-cost mobile phone microplate reader for infectious disease testing.

Most mobile health (mHealth) diagnostic devices for laboratory tests only analyze one sample at a time, which is not suitable for large volume serology testing, especially in low-resource settings with shortage of health professionals. In this study, we developed an ultra-low-cost clinically-accurate mobile phone microplate reader (mReader), and clinically validated this optical device for 12 infectious disease tests. The mReader optically reads 96 samples on a microplate at one time.

ADAM9 promotes lung cancer progression through vascular remodeling by VEGFA, ANGPT2, and PLAT.

Lung cancer has a very high prevalence of brain metastasis, which results in a poor clinical outcome. Up-regulation of a disintegrin and metalloproteinase 9 (ADAM9) in lung cancer cells is correlated with metastasis to the brain. However, the molecular mechanism underlying this correlation remains to be elucidated.

Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer.

Background: With the advances in high-throughput gene profiling technologies, a large volume of gene interaction maps has been constructed. A higher-level layer of gene-gene interaction, namely modulate gene interaction, is composed of gene pairs of which interaction strengths are modulated by (i.e.