Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer.

Breast cancers (BRCA) exhibit substantial transcriptional heterogeneity, posing a significant clinical challenge. The global transcriptional changes in a disease context, however, are likely mediated by few key genes which reflect disease etiology better than the differentially expressed genes (DEGs). We apply our network-based tool PathExt to 1,059 BRCA tumors across 4 subtypes to identify key mediator genes in each subtype. Compared to conventional differential expression analysis, PathExt-identified genes exhibit greater concordance across tumors, revealing shared and subtype-specific biological processes; better recapitulate BRCA-associated genes in multiple benchmarks, and are more essential in BRCA subtype-specific cell lines. Single-cell transcriptomic analysis reveals a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target key genes potentially mediating drug resistance.

Phage-inclusive profiling of human gut microbiomes with Phanta.

Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer.

Breast cancers exhibit substantial transcriptional heterogeneity, posing a significant challenge to the prediction of treatment response and prognostication of outcomes. Especially, translation of TNBC subtypes to the clinic remains a work in progress, in part because of a lack of clear transcriptional signatures distinguishing the subtypes. Our recent network-based approach, PathExt, demonstrates that global transcriptional changes in a disease context are likely mediated by a small number of key genes, and these mediators may better reflect functional or translationally relevant heterogeneity. We apply PathExt to 1059 BRCA tumors and 112 healthy control samples across 4 subtypes to identify frequent, key-mediator genes in each BRCA subtype. Compared to conventional differential expression analysis, PathExt-identified genes (1) exhibit greater concordance across tumors, revealing shared as well as BRCA subtype-specific biological processes, (2) better recapitulate BRCA-associated genes in multiple benchmarks, and (3) exhibit greater dependency scores in BRCA subtype-specific cancer cell lines. Single cell transcriptomes of BRCA subtype tumors reveal a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified TNBC subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target top novel genes potentially mediating drug resistance. Overall, PathExt applied to breast cancer refines previous views of gene expression heterogeneity and identifies potential mediators of TNBC subtypes, including potential therapeutic targets.

How Should US Health Care Lead Global Change in Plastic Waste Disposal?

Disposal of health care waste is one of the biggest threats to global sustainable health care. Current practices of dumping domestic and international health care waste into the earth's terra firma and oceans also undermine global health equity by adversely affecting the health of vulnerable communities. While the United Kingdom works toward circular health care economy streams that produce minimal waste, the United States continues to amplify downstream environmental and health effects of health care organizational waste management decisions. This article suggests how to reframe social and ethical responsibility for health care waste production and management by assigning strict accountability to health care organizational leaders, incentivizing circular supply chain implementation and maintenance, and encouraging strong collaborations across medical, plastic, and waste industries.

Tipping Cancer Cells Over the Edge: The Context-Dependent Cost of High Ploidy.

Tetraploidy is an aneuploidy-permissive condition that can fuel tumorgenesis. The tip-over hypothesis of cytotoxic therapy sensitivity proposes that therapy is effective if it pushes a cell's aneuploidy above a viable tipping point. But elevated aneuploidy alone may not account for this tipping point. Tissue microenvironments that lack sufficient resources to support tetraploid cells can explain the fitness cost of aneuploidy. Raw materials needed to generate deoxynucleotides, the building blocks of DNA, are candidate rate-limiting factors for the evolution of high-ploidy cancer cells. Understanding the resource cost of high ploidy is key to uncover its therapeutic vulnerabilities across tissue sites with versatile energy supplies.

COVID-19 Solutions Are Climate Solutions: Lessons From Reusable Gowns.

The COVID-19 pandemic has laid bare the inadequacy of the U.S. healthcare system to deliver timely and resilient care. According to the American Hospital Association, the pandemic has created a $202 billion loss across the healthcare industry, forcing health care systems to lay off workers and making hospitals scramble to minimize supply chain costs. However, as the demand for personal protective equipment (PPE) grows, hospitals have sacrificed sustainable solutions for disposable options that, although convenient, will exacerbate supply strains, financial burden, and waste. We advocate for reusable gowns as a means to lower health care costs, address climate change, and improve resilience while preserving the safety of health care workers. Reusable gowns' polyester material provides comparable capacity to reduce microbial cross-transmission and liquid penetration. In addition, previous hospitals have reported a 50% cost reduction in gown expenditures after adopting reusable gowns; given the current 2000% price increase in isolation gowns during COVID-19, reusable gown use will build both healthcare resilience and security from price fluctuations. Finally, with the United States' medical waste stream worsening, reusable isolation gowns show promising reductions in energy and water use, solid waste, and carbon footprint. The gowns are shown to withstand laundering 75-100 times in contrast to the single-use disposable gown. The circumstances of the pandemic forewarn the need to shift our single-use PPE practices to standardized reusable applications. Ultimately, sustainable forms of protective equipment can help us prepare for future crises that challenge the resilience of the healthcare system.