Integrated analysis of multimodal single-cell data.

The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.

Bradysia (Sciara) coprophila larvae up-regulate DNA repair pathways and down-regulate developmental regulators in response to ionizing radiation.

The level of resistance to radiation and the developmental and molecular responses can vary between species, and even between developmental stages of one species. For flies (order: Diptera), prior studies concluded that the fungus gnat Bradysia (Sciara) coprophila (sub-order: Nematocera) is more resistant to irradiation-induced mutations that cause visible phenotypes than the fruit fly Drosophila melanogaster (sub-order: Brachycera). Therefore, we characterized the effects of and level of resistance to ionizing radiation on B. coprophila throughout its life cycle. Our data show that B. coprophila embryos are highly sensitive to even low doses of gamma-irradiation, whereas late-stage larvae can tolerate up to 80 Gy (compared to 40 Gy for D. melanogaster) and still retain their ability to develop to adulthood, though with a developmental delay. To survey the genes involved in the early transcriptional response to irradiation of B. coprophila larvae, we compared larval RNA-seq profiles with and without radiation treatment. The up-regulated genes were enriched for DNA damage response genes, including those involved in DNA repair, cell cycle arrest, and apoptosis, whereas the down-regulated genes were enriched for developmental regulators, consistent with the developmental delay of irradiated larvae. Interestingly, members of the PARP and AGO families were highly up-regulated in the B. coprophila radiation response. We compared the transcriptome responses in B. coprophila to the transcriptome responses in D. melanogaster from 3 previous studies: whereas pathway responses are highly conserved, specific gene responses are less so. Our study lays the groundwork for future work on the radiation responses in Diptera.

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cells. We introduce an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. Our approach outperforms existing strategies and can resolve cell types and subtle cell state differences.

Medroxyprogesterone Acetate in Gender-Affirming Therapy for Transwomen: Results From a Retrospective Study.

CONTEXT: Medroxyprogesterone acetate (MPA) is a widely used progestin in feminizing hormone therapy. However, the side effects and hormonal changes elicited by this drug have never been investigated in the transgender population. OBJECTIVE: We evaluated the incidence of self-reported effects among transwomen using MPA and this drug's impact on hormonal and metabolic parameters. DESIGN, SETTING, AND PARTICIPANTS: We retrospectively collected data from 290 follow-up visits (FUVs) of transwomen treated at Rhode Island Hospital from January 2011 to July 2018 (mean duration of therapy 3.4 ± 1.7 years). FUVs followed regimens of estradiol (E) and spironolactone, with MPA (n = 102) or without MPA (n = 188). MAIN OUTCOME MEASURES: We assessed the incidence of self-reported effects after MPA treatment. We also compared blood levels of E, testosterone, and various laboratory parameters between MPA and non-MPA groups. RESULTS: Mean weighted E level was 211 ± 57 pg/mL after MPA treatment and 210 ± 31 pg/mL otherwise; this difference was nonsignificant [t(274) = 0.143, P = 0.886]. Mean weighted testosterone level was 79 ± 18 ng/dL after MPA treatment and 215 ± 29 ng/dL otherwise; testosterone levels were significantly lower in the MPA group [t(122) = 32.4, P < 0.001]. There were minimal changes in other laboratory parameters. Of 39 patients receiving MPA, 26 reported improved breast development and 11 reported decreased facial hair. Five patients experienced mood swings on MPA. CONCLUSIONS: In our cohort of transwomen, we found minimal side effects, unchanged E levels, and a decline in testosterone associated with MPA, outcomes consistent with feminization. Prospective studies are needed to confirm our findings.