Drug screening on digital microfluidics for cancer precision medicine.

Drug screening based on in-vitro primary tumor cell culture has demonstrated potential in personalized cancer diagnosis. However, the limited number of tumor cells, especially from patients with early stage cancer, has hindered the widespread application of this technique. Hence, we developed a digital microfluidic system for drug screening using primary tumor cells and established a working protocol for precision medicine. Smart control logic was developed to increase the throughput of the system and decrease its footprint to parallelly screen three drugs on a 4 × 4 cm2 chip in a device measuring 23 × 16 × 3.5 cm3. We validated this method in an MDA-MB-231 breast cancer xenograft mouse model and liver cancer specimens from patients, demonstrating tumor suppression in mice/patients treated with drugs that were screened to be effective on individual primary tumor cells. Mice treated with drugs screened on-chip as ineffective exhibited similar results to those in the control groups. The effective drug identified through on-chip screening demonstrated consistency with the absence of mutations in their related genes determined via exome sequencing of individual tumors, further validating this protocol. Therefore, this technique and system may promote advances in precision medicine for cancer treatment and, eventually, for any disease.

Using oral bioaccessibility measurements to refine risk assessment of potentially toxic elements in topsoils across an urban area.

Elevated concentrations of As, Cr, Cu, Ni, Pb, V and Zn in topsoils in Belfast, Northern Ireland have been found to exceed assessment criteria in the city and therefore may pose a risk to human health. Most generic assessment criteria (GAC) for potentially toxic elements (PTEs) in soils assume PTEs are 100% bioavailable to humans. Here we use in-vitro oral bioaccessibility testing using the Unified BARGE method (UBM) to measure what proportion of soil contamination dissolves in the digestive tract and therefore is available for absorption by the body. This study considers how PTE bioaccessibility in soils varies spatially across urban areas and refines human health risk assessment for these PTEs using site specific oral bioaccessibility results to present the first regional assessment of risk that incorporates bioaccessibility testing. A total of 103 urban soil samples were selected for UBM testing. Results showed low bioaccessible fraction (BAF) for the PTEs from geogenic sources: Cr (0.45-5.9%), Ni (1.1-46.3%) and V (2.2-23.9%). Higher BAF values were registered for PTEs from anthropogenic sources: As (8.0-86.9%), Cu (3.4-67.8%), Pb (9.1-106.2%) and Zn (2.4-77.5%). Graphs of bioaccessibility adjusted assessment criteria (BAAC) were derived for each urban land use type and PTE. These provide a visual representation of the significance of oral bioaccessibility when deriving BAAC and how this is affected by 1) dominant exposure pathways for each land use and 2) relative harm posed from exposure to PTEs via each pathway, allowing oral bioaccessibility research to be targeted to contaminants and pathways that most significantly impact risk assessment. Pb was the most widespread contaminant with 16.5% of sites exceeding the Pb GAC. Applying BAAC did not significantly change risk evaluation for these samples as many had Pb BAF>50%. In contrast, all samples that exceeded the As GAC were found to no longer exceed a minimal level of risk when oral bioaccessibility was considered. Oral bioaccessibility testing resulted in a 45% reduction in the number of sites identified as posing a potential risk to human health.

Distinguishing Gastric/Esophageal Adenocarcinoma from Pancreatic Adenocarcinoma Using Methylation-Based Droplet Digital PCR.

The goal of this study was to develop a methylation-based droplet digital PCR to separate 2 cancer classes that do not have sensitive and specific immunohistochemical stains: gastric/esophageal and pancreatic adenocarcinomas. The assay used methylation-independent primers and methylation-dependent probes to assess a single differentially methylated CpG site; analyses of array data from The Cancer Genome Atlas network showed that high methylation at the cg06118999 probe supports the presence of cells originating from the stomach or esophagus (eg, as in gastric metastasis), whereas low methylation suggests that these cells are rare to absent (eg, pancreatic metastasis). On validation using formalin-fixed paraffin-embedded primary and metastatic samples from our institution, methylation-based droplet digital PCR targeting the corresponding CpG dinucleotide generated evaluable data for 60 of the 62 samples (97%) and correctly classified 50 of the 60 evaluable cases (83.3%), mostly adenocarcinomas from the stomach or pancreas. This ddPCR was created to be easy-to-interpret, rapid, inexpensive, and compatible with existing platforms at many clinical laboratories. We suggest that similarly accessible PCRs could be developed for other differentials in pathology that do not have sensitive and specific immunohistochemical stains.

Definition of a new blood cell count score for early survival prediction for non-small cell lung cancer patients treated with atezolizumab: Integrated analysis of four multicenter clinical trials.

Importance: Blood cell count test (BCT) is a robust method that provides direct quantification of various types of immune cells to reveal the immune landscape to predict atezolizumab treatment outcomes for clinicians to decide the next phase of treatment. Objective: This study aims to define a new BCTscore model to predict atezolizumab treatment benefits in non-small lung cell cancer (NSCLC) patients. Design Setting and Participants: This study analyzed four international, multicenter clinical trials (OAK, BIRCH, POPLAR, and FIR trials) to conduct post-hoc analyses of NSCLC patients undergoing atezolizumab (anti-PD-L1) single-agent treatment (n = 1,479) or docetaxel single-agent treatment (n = 707). BCT was conducted at three time points: pre-treatment (T1), the first day of treatment cycle 3 (T2), and first day of treatment cycle 5 (T3). Univariate and multivariate Cox regression analyses were conducted to identify early BCT biomarkers to predict atezolizumab treatment outcomes in NSCLC patients. Main Outcomes and Measures: Overall survival (OS) was used as the primary end point, whereas progression-free survival (PFS) according to Response Evaluation Criteria in Solid Tumors (RECIST), clinical benefit (CB), and objective response rate (ORR) were used as secondary end points. Results: The BCT biomarkers of neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) at time point T3 and neutrophil-to-monocyte ratio (NMR) at time point T2 with absolute cutoff values of NLR_T3 = 5, PLR_T3 = 180, and NMR_T2 = 6 were identified as strong predictive biomarkers for atezolizumab (Ate)-treated NSCLC patients in comparison with docetaxel (Dtx)-treated patients regarding OS (BCTscore low risk: HR Ate vs. Dtx = 1.54 (95% CI: 1.04-2.27), P = 0.031; high risk: HR Ate vs. Dtx = 0.84 (95% CI: 0.62-1.12), P = 0.235). The identified BCTscore model showed better OS AUC in the OAK (AUC12month = 0.696), BIRCH (AUC12month = 0.672) and POPLAR+FIR studies (AUC12month = 0.727) than that of each of the three single BCT biomarkers. Conclusion and Relevance: The BCTscore model is a valid predictive and prognostic biomarker for early survival prediction in atezolizumab-treated NSCLC patients.

Adaptation of diabetes prevention program for Chinese Americans - a qualitative study.

BACKGROUND: Studies have demonstrated that a culturally and linguistically tailored Diabetes Prevention Program (DPP) can be effective in reducing diabetes risk in Chinese Americans. The purpose of this study was to explore the cultural and linguistic acceptability of the Centers for Disease Control and Prevention's Prevent T2 curriculum in an online format in the Chinese American community in New York City (NYC). METHODS: Three focus groups among a total of 24 Chinese Americans with prediabetes and one community advisory board (CAB) meeting with 10 key stakeholders with expertise in diabetes care and lifestyle interventions were conducted. Each focus group lasted approximately 1 to 1.5 h. All groups were moderated by a bilingual moderator in Chinese. The sessions were audiotaped, transcribed and translated to English for analysis. Using Atlas.ti software and open coding techniques, two researchers analyzed transcripts for thematic analysis. RESULTS: Five key themes were identified: barriers to behavioral changes, feedback on curriculum content and suggestions, web-based intervention acceptability, web-based intervention feasibility, and web-based intervention implementation and modifications. Participants with prediabetes were found to have high acceptability of web-based DPP interventions. Suggestions for the curriculum included incorporating Chinese American cultural foods and replacing photos of non-Asians with photos of Asians. Barriers included lack of access to the internet, different learning styles and low technology self-efficacy for older adults. CONCLUSION: Although the acceptability of web-based DPP in the Chinese American community in NYC is high, our focus group findings indicated that the major concern is lack of internet access and technical support. Providing support, such as creating an orientation manual for easy online program access for future participants, is important.

Elucidation of the Application of Blood Test Biomarkers to Predict Immune-Related Adverse Events in Atezolizumab-Treated NSCLC Patients Using Machine Learning Methods.

Background: Development of severe immune-related adverse events (irAEs) is a major predicament to stop treatment with immune checkpoint inhibitors, even though tumor progression is suppressed. However, no effective early phase biomarker has been established to predict irAE until now. Method: This study retrospectively used the data of four international, multi-center clinical trials to investigate the application of blood test biomarkers to predict irAEs in atezolizumab-treated advanced non-small cell lung cancer (NSCLC) patients. Seven machine learning methods were exploited to dissect the importance score of 21 blood test biomarkers after 1,000 simulations by the training cohort consisting of 80%, 70%, and 60% of the combined cohort with 1,320 eligible patients. Results: XGBoost and LASSO exhibited the best performance in this study with relatively higher consistency between the training and test cohorts. The best area under the curve (AUC) was obtained by a 10-biomarker panel using the XGBoost method for the 8:2 training:test cohort ratio (training cohort AUC = 0.692, test cohort AUC = 0.681). This panel could be further narrowed down to a three-biomarker panel consisting of C-reactive protein (CRP), platelet-to-lymphocyte ratio (PLR), and thyroid-stimulating hormone (TSH) with a small median AUC difference using the XGBoost method [for the 8:2 training:test cohort ratio, training cohort AUC difference = -0.035 (p < 0.0001), and test cohort AUC difference = 0.001 (p=0.965)]. Conclusion: Blood test biomarkers currently do not have sufficient predictive power to predict irAE development in atezolizumab-treated advanced NSCLC patients. Nevertheless, biomarkers related to adaptive immunity and liver or thyroid dysfunction warrant further investigation.

Learning the Language of Medical Device Innovation: A Longitudinal Interdisciplinary Elective for Medical Students.

PROBLEM: Physicians are playing a growing role as clinician-innovators. Academic physicians are well positioned to contribute to the medical device innovation process, yet few medical school curricula provide students opportunities to learn the conceptual framework for clinical needs finding, needs screening, concept generation and iterative prototyping, and intellectual property management. This framework supports innovation and encourages the development of valuable interdisciplinary communication skills and collaborative learning strategies. APPROACH: Our university offers a novel 3-year-long medical student Longitudinal Interdisciplinary Elective in Biodesign (MSLIEB) that teaches medical device innovation in 4 stages: (1) seminars and small-group work, (2) shared clinical experiences for needs finding, (3) concept generation and product development by serving as consultants for biomedical engineering capstone projects, and (4) reflection and mentorship. The MSLIEB objectives are to: create a longitudinal interdisciplinary peer mentorship relationship between undergraduate biomedical engineering students and medical students, and encourage codevelopment of professional identities in relation to medical device innovation. OUTCOMES: The MSLIEB enrolled 5 entering cohorts from 2017 to 2021 with a total of 37 medical student participants. The first full entering cohort of 12 medical students produced 8 mentored biomedical engineering capstone projects, 7 of which were based on clinical needs statements derived from earlier in the elective. Medical student participants have coauthored poster and oral presentations; contributed to projects that won WolfieTank, a university-wide competition modeled after the television show Shark Tank; and participated in the filing of provisional patents. Students reflecting on the course reported a change in their attitude towards existing medical problems, felt better-equipped to collaboratively design solutions for clinical needs, and considered a potential career path in device design. NEXT STEPS: The MSLIEB will be scaled up by recruiting additional faculty, broadening clinical opportunities to include the outpatient setting, and increasing medical student access to rapid prototyping equipment.

Assessment of chimeric antigen receptor T cytotoxicity by droplet microfluidics in vitro.

Chimeric antigen receptor T (CAR-T) cells are cytotoxic T cells engineered to specifically kill cancer cells expressing specific target receptor(s). Prior CAR-T efficacy tests include CAR expression analysis by qPCR or ELISA, in vitro measurement of interferon-γ (IFNγ) or interleukin-2 (IL-2), and xenograft models. However, the in vitro measurements did not reflect CAR-T cytotoxicity, whereas xenograft models are low throughput and costly. Here, we presented a robust in vitro droplet microfluidic assay for CAR-T cytotoxicity assessment. This method not only enabled assessment of CAR-T cytotoxic activity under different fluid viscosity conditions, but also facilitated measurement of CAR-T expansion and dissection of mechanism of action via phenotype analysis in vitro. Furthermore, our data suggested that label-free cytotoxicity analysis is feasible by acquiring data before and after treatment. Hence, this study presented a novel in vitro method for assessment of cellular cytotoxicity that could potentially be applied to any cytotoxicity experiment with varying solvent composition.

Comparison of influenza surveillance systems in Australia, China, Malaysia and expert recommendations for influenza control.

BACKGROUND: The Western Pacific Region (WPR) is exposed each year to seasonal influenza and is often the source of new influenza virus variants and novel pathogen emergence. National influenza surveillance systems play a critical role in detecting emerging viruses, monitoring influenza epidemics, improving public disease awareness and promoting pandemic preparedness, but vary widely across WPR countries. The aim of this study is to improve existing influenza surveillance systems by systematically comparing selected WPR influenza surveillance systems. METHODS: Three national influenza surveillance systems with different levels of development (Australia, China and Malaysia) were compared and their adherence to World Health Organization (WHO) guidance was evaluated using a structured framework previously tested in several European countries consisting of seven surveillance sub-systems, 19 comparable outcomes and five evaluation criteria. Based on the results, experts from the Asia-Pacific Alliance for the Control of Influenza (APACI) issued recommendations for the improvement of existing surveillance systems. RESULTS: Australia demonstrated the broadest scope of influenza surveillance followed by China and Malaysia. In Australia, surveillance tools covered all sub-systems. In China, surveillance did not cover non-medically attended respiratory events, primary care consultations, and excess mortality modelling. In Malaysia, surveillance consisted of primary care and hospital sentinel schemes. There were disparities between the countries across the 5 evaluation criteria, particularly regarding data granularity from health authorities, information on data representativeness, and data communication, especially the absence of publicly available influenza epidemiological reports in Malaysia. This dual approach describing the scope of surveillance and evaluating the adherence to WHO guidance enabled APACI experts to make a number of recommendations for each country that included but were not limited to introducing new surveillance tools, broadening the use of specific existing surveillance tools, collecting and sharing data on virus characteristics, developing immunization status registries, and improving public health communication. CONCLUSIONS: Influenza monitoring in Australia, China, and Malaysia could benefit from the expansion of existing surveillance sentinel schemes, the broadened use of laboratory confirmation and the introduction of excess-mortality modelling. The results from the evaluation can be used as a basis to support expert recommendations and to enhance influenza surveillance capabilities.

Molecular landscape and subtype-specific therapeutic response of nasopharyngeal carcinoma revealed by integrative pharmacogenomics.

Nasopharyngeal carcinoma (NPC) is a malignant head and neck cancer type with high morbidity in Southeast Asia, however the pathogenic mechanism of this disease is poorly understood. Using integrative pharmacogenomics, we find that NPC subtypes maintain distinct molecular features, drug responsiveness, and graded radiation sensitivity. The epithelial carcinoma (EC) subtype is characterized by activations of microtubule polymerization and defective mitotic spindle checkpoint related genes, whereas sarcomatoid carcinoma (SC) and mixed sarcomatoid-epithelial carcinoma (MSEC) subtypes exhibit enriched epithelial-mesenchymal transition (EMT) and invasion promoting genes, which are well correlated with their morphological features. Furthermore, patient-derived organoid (PDO)-based drug test identifies potential subtype-specific treatment regimens, in that SC and MSEC subtypes are sensitive to microtubule inhibitors, whereas EC subtype is more responsive to EGFR inhibitors, which is synergistically enhanced by combining with radiotherapy. Through combinational chemoradiotherapy (CRT) screening, effective CRT regimens are also suggested for patients showing less sensitivity to radiation. Altogether, our study provides an example of applying integrative pharmacogenomics to establish a personalized precision oncology for NPC subtype-guided therapies.

Cisplatin prevents breast cancer metastasis through blocking early EMT and retards cancer growth together with paclitaxel.

Cancer growth is usually accompanied by metastasis which kills most cancer patients. Here we aim to study the effect of cisplatin at different doses on breast cancer growth and metastasis. Methods: We used cisplatin to treat breast cancer cells, then detected the migration of cells and the changes of epithelial-mesenchymal transition (EMT) markers by migration assay, Western blot, and immunofluorescent staining. Next, we analyzed the changes of RNA expression of genes by RNA-seq and confirmed the binding of activating transcription factor 3 (ATF3) to cytoskeleton related genes by ChIP-seq. Thereafter, we combined cisplatin and paclitaxel in a neoadjuvant setting to treat xenograft mouse models. Furthermore, we analyzed the association of disease prognosis with cytoskeletal genes and ATF3 by clinical data analysis. Results: When administered at a higher dose (6 mg/kg), cisplatin inhibits both cancer growth and metastasis, yet with strong side effects, whereas a lower dose (2 mg/kg) cisplatin blocks cancer metastasis without obvious killing effects. Cisplatin inhibits cancer metastasis through blocking early steps of EMT. It antagonizes transforming growth factor beta (TGFß) signaling through suppressing transcription of many genes involved in cytoskeleton reorganization and filopodia formation which occur early in EMT and are responsible for cancer metastasis. Mechanistically, TGFß and fibronectin-1 (FN1) constitute a positive reciprocal regulation loop that is critical for activating TGFß/SMAD3 signaling, which is repressed by cisplatin induced expression of ATF3. Furthermore, neoadjuvant administration of cisplatin at 2 mg/kg in conjunction with paclitaxel inhibits cancer growth and blocks metastasis without causing obvious side effects by inhibiting colonization of cancer cells in the target organs. Conclusion: Thus, cisplatin prevents breast cancer metastasis through blocking early EMT, and the combination of cisplatin and paclitaxel represents a promising therapy for killing breast cancer and blocking tumor metastasis.

Targeting NF-κB Signaling for Multiple Myeloma.

Multiple myeloma (MM) is the second most common hematologic malignancy in the world. Even though survival rates have significantly risen over the past years, MM remains incurable, and is also far from reaching the point of being managed as a chronic disease. This paper reviews the evolution of MM therapies, focusing on anti-MM drugs that target the molecular mechanisms of nuclear factor kappa B (NF-κB) signaling. We also provide our perspectives on contemporary research findings and insights for future drug development.

Genome-wide piggyBac transposon-based mutagenesis and quantitative insertion-site analysis in haploid Candida species.

Invasive fungal infections caused by Candida species are life threatening with high mortality, posing a severe public health threat. New technologies for rapid, genome-wide identification of virulence genes and therapeutic targets are urgently needed. Our recent engineering of a piggyBac (PB) transposon-mediated mutagenesis system in haploid Candida albicans provides a powerful discovery tool, which we anticipate should be adaptable to other haploid Candida species. In this protocol, we use haploid C. albicans as an example to present an improved version of the mutagenesis system and provide a detailed description of the protocol for constructing high-quality mutant libraries. We also describe a method for quantitative PB insertion site sequencing, PBISeq. The PBISeq library preparation procedure exploits tagmentation to quickly and efficiently construct sequencing libraries. Finally, we present a pipeline to analyze PB insertion sites in a de novo assembled genome of our engineered haploid C. albicans strain. The entire protocol takes ~7 d from transposition induction to having a final library ready for sequencing. This protocol is highly efficient and less labor intensive than alternative approaches and significantly accelerates genetic studies of Candida.

A Comparison of Computerized Versus Pen-and-Paper Cognitive Tests for Monitoring Electroconvulsive Therapy-Related Cognitive Side Effects.

OBJECTIVE: Cognitive side effects are a common unintended outcome of electroconvulsive therapy (ECT). Routine cognitive assessment is important for monitoring patient outcomes, although it can pose challenges in busy clinical settings. Computerized cognitive testing has advantages that can facilitate routine monitoring. This study explored the construct and criterion validity of computerized cognitive testing compared with standard pen-and-paper tests for monitoring cognition in ECT patients. METHODS: The study included 24 participants with major depression who received an acute course of ECT. Cognition was assessed at pretreatment and at posttreatment with 3 computerized tests from the CogState battery (International Shopping List task, One-Card Learning, and One-Back Task) and 3 conceptually matched pen-and-paper-administered neuropsychological tests. RESULTS: At pretreatment, only performance on the computer-administered test of verbal anterograde memory (International Shopping List task) was significantly correlated with the analogous pen-and-paper measure, whereas the other computerized tests were not. Of the computerized measures, only the International Shopping List task showed significant changes from pretreatment to posttreatment (P < 0.01, Cohen d > 1.0). In contrast, all the pen-and-paper-administered tests showed significant changes from pretreatment to posttreatment (P < 0.01, Cohen d range, 0.8-1.2). Pretreatment to posttreatment cognitive changes on the computerized measures were not correlated with changes on the pen-and-paper-administered tests. CONCLUSION: Construct and criterion validity and tolerability varied between the computerized measures. The results highlighted potentially important issues related to the interpretation and utility of computerized tests in this patient population.

A digital microfluidic system with 3D microstructures for single-cell culture.

Despite the precise controllability of droplet samples in digital microfluidic (DMF) systems, their capability in isolating single cells for long-time culture is still limited: typically, only a few cells can be captured on an electrode. Although fabricating small-sized hydrophilic micropatches on an electrode aids single-cell capture, the actuation voltage for droplet transportation has to be significantly raised, resulting in a shorter lifetime for the DMF chip and a larger risk of damaging the cells. In this work, a DMF system with 3D microstructures engineered on-chip is proposed to form semi-closed micro-wells for efficient single-cell isolation and long-time culture. Our optimum results showed that approximately 20% of the micro-wells over a 30 × 30 array were occupied by isolated single cells. In addition, low-evaporation-temperature oil and surfactant aided the system in achieving a low droplet actuation voltage of 36V, which was 4 times lower than the typical 150 V, minimizing the potential damage to the cells in the droplets and to the DMF chip. To exemplify the technological advances, drug sensitivity tests were run in our DMF system to investigate the cell response of breast cancer cells (MDA-MB-231) and breast normal cells (MCF-10A) to a widely used chemotherapeutic drug, Cisplatin (Cis). The results on-chip were consistent with those screened in conventional 96-well plates. This novel, simple and robust single-cell trapping method has great potential in biological research at the single cell level.

A Novel and Robust Single-cell Trapping Method on Digital Microfluidics.

Due to cell heterogeneity, the differences among individual cells are averaged out in bulk analysis methods, especially in the analysis of primary tumor biopsy samples from patients. To deeply understand the cell-to-cell variation in a primary tumor, single-cell culture and analysis with limited amount of cells are in high demand. Microfluidics has been an optimum platform to address the issue given its small reaction volume requirements. Digital microfluidics, which utilizes an electric signal to manipulate individual droplets has shown promise in cell-culture with easy controls. In this work, we realize single cell trapping on digital microfluidic platform by fabricating 3D microstructures on-chip to form semi-closed micro-wells. With this design, 20% of 30 x 30 array can be occupied by isolated single cells. We also use a low evaporation silicon oil and a fluorinated surfactant to lower the droplet actuation voltage and prevent the drop from evaporation, while allowing cell respiration during the long term of culture (24 h). The main steps for single cell trapping on digital microfluidics, as illustrated in this protocol, include 3D microstructures design, 3D microstructures construction on chip and oil film with surfactant for single cell trapping on chip.

Author Correction: Drug screening of cancer cell lines and human primary tumors using droplet microfluidics.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Genome-wide germline correlates of the epigenetic landscape of prostate cancer.

Oncogenesis is driven by germline, environmental and stochastic factors. It is unknown how these interact to produce the molecular phenotypes of tumors. We therefore quantified the influence of germline polymorphisms on the somatic epigenome of 589 localized prostate tumors. Predisposition risk loci influence a tumor's epigenome, uncovering a mechanism for cancer susceptibility. We identified and validated 1,178 loci associated with altered methylation in tumoral but not nonmalignant tissue. These tumor methylation quantitative trait loci influence chromatin structure, as well as RNA and protein abundance. One prominent tumor methylation quantitative trait locus is associated with AKT1 expression and is predictive of relapse after definitive local therapy in both discovery and validation cohorts. These data reveal intricate crosstalk between the germ line and the epigenome of primary tumors, which may help identify germline biomarkers of aggressive disease to aid patient triage and optimize the use of more invasive or expensive diagnostic assays.

Comparative toxicoproteogenomics of mouse and rat liver identifies TCDD-resistance genes.

The aryl hydrocarbon receptor (AHR) mediates many toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, the AHR alone does not explain the widely different outcomes among organisms. To identify the other factors involved, we evaluated three transgenic mouse lines, each expressing a different rat AHR isoform (rWT, DEL, and INS) providing widely different resistance to TCDD toxicity, as well as C57BL/6 and DBA/2 mice which exhibit a ~ tenfold divergence in TCDD sensitivity (exposures of 5-1000 µg/kg TCDD). We supplement these with whole-genome sequencing, together with transcriptomic and proteomic analyses of the corresponding rat models, Long-Evans (L-E) and Han/Wistar (H/W) rats (having a ~ 1000-fold difference in their TCDD sensitivities; 100 µg/kg TCDD), to identify genes associated with TCDD-response phenotypes. Overall, we identified up to 50% of genes with altered mRNA abundance following TCDD exposure are associated with a single AHR isoform (33.8%, 11.7%, 5.2% and 0.3% of 3076 genes altered unique to rWT, DEL, C57BL/6 and INS respectively following 1000 µg/kg TCDD). Hepatic Pxdc1 was significantly repressed in all three TCDD-sensitive animal models (C57BL/6 and rWT mice, and L-E rat) after TCDD exposure. Three genes, including Cxxc5, Sugp1 and Hgfac, demonstrated different AHRE-1 (full) motif occurrences within their promoter regions between rat strains, as well as different patterns of mRNA abundance. Several hepatic proteins showed parallel up- or downward alterations with their RNAs, with three genes (SNRK, IGTP and IMPA2) showing consistent, strain-dependent changes. These data show the value of integrating genomic, transcriptomic and proteomic evidence across multi-species models in toxicologic studies.