Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data.

Single cell genomics has revolutionized our ability to map immune heterogeneity and responses. With the influx of large-scale data sets from diverse modalities, the resolution achieved has supported the long-held notion that immune cells are naturally organized into hierarchical relationships, characterized at multiple levels. Such a multigranular structure corresponds to key geometric and topological features. Given that differences between an effective and ineffective immunological response may not be found at one level, there is vested interest in characterizing and predicting outcomes from such features. In this review, we highlight single cell methods and principles for learning geometric and topological properties of data at multiple scales, discussing their contributions to immunology. Ultimately, multiscale approaches go beyond classical clustering, revealing a more comprehensive picture of cellular heterogeneity.

PD-1 maintains CD8 T cell tolerance towards cutaneous neoantigens.

The peripheral T cell repertoire of healthy individuals contains self-reactive T cells1,2. Checkpoint receptors such as PD-1 are thought to enable the induction of peripheral tolerance by deletion or anergy of self-reactive CD8 T cells3-10. However, this model is challenged by the high frequency of immune-related adverse events in patients with cancer who have been treated with checkpoint inhibitors11. Here we developed a mouse model in which skin-specific expression of T cell antigens in the epidermis caused local infiltration of antigen-specific CD8 T cells with an effector gene-expression profile. In this setting, PD-1 enabled the maintenance of skin tolerance by preventing tissue-infiltrating antigen-specific effector CD8 T cells from (1) acquiring a fully functional, pathogenic differentiation state, (2) secreting significant amounts of effector molecules, and (3) gaining access to epidermal antigen-expressing cells. In the absence of PD-1, epidermal antigen-expressing cells were eliminated by antigen-specific CD8 T cells, resulting in local pathology. Transcriptomic analysis of skin biopsies from two patients with cutaneous lichenoid immune-related adverse events showed the presence of clonally expanded effector CD8 T cells in both lesional and non-lesional skin. Thus, our data support a model of peripheral T cell tolerance in which PD-1 allows antigen-specific effector CD8 T cells to co-exist with antigen-expressing cells in tissues without immunopathology.

Single-cell multi-modal GAN reveals spatial patterns in single-cell data from triple-negative breast cancer.

Exciting advances in technologies to measure biological systems are currently at the forefront of research. The ability to gather data along an increasing number of omic dimensions has created a need for tools to analyze all of this information together, rather than siloing each technology into separate analysis pipelines. To advance this goal, we introduce a framework called the single-cell multi-modal generative adversarial network (scMMGAN) that integrates data from multiple modalities into a unified representation in the ambient data space for downstream analysis using a combination of adversarial learning and data geometry techniques. The framework's key improvement is an additional diffusion geometry loss with a new kernel that constrains the otherwise over-parameterized GAN. We demonstrate scMMGAN's ability to produce more meaningful alignments than alternative methods on a wide variety of data modalities and that its output can be used to draw conclusions from real-world biological experimental data.

Analysis of Oral Leukoplakia and Tobacco-Related Habits in Population of Chengalpattu District- An Institution-Based Retrospective Study.

Objective The study aimed to evaluate the prevalence of oral leukoplakia and to assess the risk of developing oral leukoplakia in patients with tobacco-related habits among the populations of Chengalpattu district, Tamil Nadu, India.  Materials and Methods Incidence and prevalence of oral leukoplakia differ among different populations in India due to cultural and demographic diversities. The results obtained from this study can be used as a reference in future research and policy-making for tobacco control. Data for this study were manually ascertained from the Department of Oral Pathology and Microbiology, SRM Kattankulathur Dental College and Hospital, SRM Institute of Science and Technology, Potheri, Chengalpet district, Tamil Nadu, India. The medical records of the patients diagnosed with the abnormalities and diseases of the oral mucosa, especially the white lesions of the oral cavity, between January 2011- March 2021 (10 years). The basic inclusion criteria for this study were to include the histopathology reports of the white lesions with no malignant changes during clinical diagnosis. The data was analyzed based on age, gender, tobacco-related habits, and histopathological diagnosis. The exclusion criteria for the study were the cases reported as carcinoma, patients associated with syndromes, biopsies outside the mentioned period, and those patients with incomplete clinical or histopathological details. Results Among 141 white lesions, about 85 cases [60.2%] were confirmed as oral leukoplakia, of which the study population had 55 (64.7%) males and 30 (35.3%) females. The age group which was commonly seen was 41-60 years. About 80% of the population with oral leukoplakia had the habit of tobacco consumption. The use of tobacco products was seen more commonly in the male population than the female, and consumption of tobacco and alcohol was seen in 6% of the population. In our study, we found the study population had the habit of using smokeless tobacco rather than smoking cigarettes and bidis. About 20% of the population diagnosed with leukoplakia did not have any habits. The most commonly affected site was buccal mucosa (67%), followed by the tongue (12%). Conclusion Our study shows a statistical association between oral leukoplakia and tobacco product consumption among the population of Chengalpattu district. The oral health care providers must take utmost care and vigilance to diagnose the lesion at its earliest stage and give appropriate treatment modalities and effective tobacco interventions.

A reservoir of stem-like CD8+ T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response.

"Stem-like" TCF1+ CD8+ T (TSL) cells are necessary for long-term maintenance of T cell responses and the efficacy of immunotherapy, but, as tumors contain signals that should drive T cell terminal differentiation, how these cells are maintained in tumors remains unclear. In this study, we found that a small number of TCF1+ tumor-specific CD8+ T cells were present in lung tumors throughout their development. Yet, most intratumoral T cells differentiated as tumors progressed, corresponding with an immunologic shift in the tumor microenvironment (TME) from "hot" (T cell inflamed) to "cold" (non­T cell inflamed). By contrast, most tumor-specific CD8+ T cells in tumor-draining lymph nodes (dLNs) had functions and gene expression signatures similar to TSL from chronic lymphocytic choriomeningitis virus infection, and this population was stable over time despite the changes in the TME. dLN T cells were the developmental precursors of, and were clonally related to, their more differentiated intratumoral counterparts. Our data support the hypothesis that dLN T cells are the developmental precursors of the TCF1+ T cells in tumors that are maintained by continuous migration. Last, CD8+ T cells similar to TSL were also present in LNs from patients with lung adenocarcinoma, suggesting that a similar model may be relevant in human disease. Thus, we propose that the dLN TSL reservoir has a critical function in sustaining antitumor T cells during tumor development and in protecting them from the terminal differentiation that occurs in the TME.

Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.

Toxoplasma gondii is a useful model for intracellular parasitism given its ease of culture in the laboratory and genomic resources. However, as for many other eukaryotes, the T. gondii genome contains hundreds of sequence gaps owing to repetitive and/or unclonable sequences that disrupt the assembly process. Here, we use the Oxford Nanopore Minion platform to generate near-complete de novo genome assemblies for multiple strains of T. gondii and its near relative, N. caninum We significantly improved T. gondii genome contiguity (average N50 of ∼6.6 Mb) and added ∼2 Mb of newly assembled sequence. For all of the T. gondii strains that we sequenced (RH, ME49, CTG, II×III progeny clones CL13, S27, S21, S26, and D3X1), the largest contig ranged in size between 11.9 and 12.1 Mb in size, which is larger than any previously reported T. gondii chromosome, and found to be due to a consistent fusion of Chromosomes VIIb and VIII. These data were validated by mapping existing T. gondii ME49 Hi-C data to our assembly, providing parallel lines of evidence that the T. gondii karyotype consists of 13, rather than 14, chromosomes. By using this technology, we also resolved hundreds of tandem repeats of varying lengths, including in well-known host-targeting effector loci like rhoptry protein 5 (ROP5) and ROP38 Finally, when we compared T. gondii with N. caninum, we found that although the 13-chromosome karyotype was conserved, extensive, previously unappreciated chromosome-scale rearrangements had occurred in T. gondii and N. caninum since their most recent common ancestry.

Twitter-based analysis reveals differential COVID-19 concerns across areas with socioeconomic disparities.

OBJECTIVE: We sought to understand spatial-temporal factors and socioeconomic disparities that shaped U.S. residents' response to COVID-19 as it emerged. METHODS: We mined coronavirus-related tweets from January 23rd to March 25th, 2020. We classified tweets by the socioeconomic status of the county from which they originated with the Area Deprivation Index (ADI). We applied topic modeling to identify and monitor topics of concern over time. We investigated how topics varied by ADI and between hotspots and non-hotspots. RESULTS: We identified 45 topics in 269,556 unique tweets. Topics shifted from early-outbreak-related content in January, to the presidential election and governmental response in February, to lifestyle impacts in March. High-resourced areas (low ADI) were concerned with stocks and social distancing, while under-resourced areas shared negative expression and discussion of the CARES Act relief package. These differences were consistent within hotspots, with increased discussion regarding employment in high ADI hotspots. DISCUSSION: Topic modeling captures major concerns on Twitter in the early months of COVID-19. Our study extends previous Twitter-based research as it assesses how topics differ based on a marker of socioeconomic status. Comparisons between low and high-resourced areas indicate more focus on personal economic hardship in less-resourced communities and less focus on general public health messaging. CONCLUSION: Real-time social media analysis of community-based pandemic responses can uncover differential conversations correlating to local impact and income, education, and housing disparities. In future public health crises, such insights can inform messaging campaigns, which should partly focus on the interests of those most disproportionately impacted.

Comparative 3D genome organization in apicomplexan parasites.

The positioning of chromosomes in the nucleus of a eukaryotic cell is highly organized and has a complex and dynamic relationship with gene expression. In the human malaria parasite Plasmodium falciparum, the clustering of a family of virulence genes correlates with their coordinated silencing and has a strong influence on the overall organization of the genome. To identify conserved and species-specific principles of genome organization, we performed Hi-C experiments and generated 3D genome models for five Plasmodium species and two related apicomplexan parasites. Plasmodium species mainly showed clustering of centromeres, telomeres, and virulence genes. In P. falciparum, the heterochromatic virulence gene cluster had a strong repressive effect on the surrounding nuclear space, while this was less pronounced in Plasmodium vivax and Plasmodium berghei, and absent in Plasmodium yoelii In Plasmodium knowlesi, telomeres and virulence genes were more dispersed throughout the nucleus, but its 3D genome showed a strong correlation with gene expression. The Babesia microti genome showed a classical Rabl organization with colocalization of subtelomeric virulence genes, while the Toxoplasma gondii genome was dominated by clustering of the centromeres and lacked virulence gene clustering. Collectively, our results demonstrate that spatial genome organization in most Plasmodium species is constrained by the colocalization of virulence genes. P. falciparum and P. knowlesi, the only two Plasmodium species with gene families involved in antigenic variation, are unique in the effect of these genes on chromosome folding, indicating a potential link between genome organization and gene expression in more virulent pathogens.