Distinct Repertoires Research Articles

Conserved and divergent expression dynamics during early patterning of the telencephalon in mouse and chick embryos

The mammalian and the avian telencephalon are nearly indistinguishable at early embryonic vesicle stages but differ substantially in form and function at their adult stage. We sequenced and analyzed RNA populations present in mouse and chick during the early stages of embryonic telencephalon to understand conserved and lineage-specific developmental differences. We found approximately 3000 genes that orchestrate telencephalon development. Many chromatin-associated epigenetic and transcription regulators show high expression in both species and some show species-specific expression dynamics. Interestingly, previous studies associated them to autism, intellectual disabilities, and mental retardation supporting a causal link between their impaired functions during telencephalon development and brain dysfunction. Strikingly, the conserved up-regulated genes were differentially enriched in ontologies related to development or functions of the adult brain. Moreover, a differential enrichment of distinct repertoires of transcription factor binding motifs in their upstream promoter regions suggest a species-specific regulation of the various gene groups identified. Overall, our results reveal that the ontogenetic divergences between the mouse and chick telencephalon result from subtle differences in the regulation of common patterning signaling cascades and regulatory networks unique to each species at their very early stages of development.

Relationship to Place for Older Adults in a New York City Neighborhood Undergoing Gentrification: A Discourse Analysis

While many older adults live in neighborhoods undergoing gentrification, research rarely explores their narratives about the gentrification process and their relationships with gentrifiers. This study uses discourse analysis of ethnographic data in Queens, NY, to identify repertoires in older adults’ narratives about the meaning of place and gentrification. Five distinct repertoires emerged: (1) gentrification brings a discussion of losses; (2) talk of the insider versus outsider claim to space; (3) social connectivity phrased as a strength during gentrification; (4) statements about adaptation strategies used to buffer change; and (5) language about neighborhood change as good—even during gentrification. These repertoires show older residents seek to understand and validate their role in a changing place. Their individual dialogues echo discussions and power differentials in their larger social worlds. Older persons’ repertoires illustrate the struggle to contextualize gentrification and not simply homogenize the process or create only limited, stereotypical insider–outsider arguments.

The architecture of the IgG anti-carbohydrate repertoire in primary antibody deficiencies

AbstractImmune system failure in primary antibody deficiencies (PADs) has been linked to recurrent infections, autoimmunity, and cancer, yet clinical judgment is often based on the reactivity to a restricted panel of antigens. Previously, we demonstrated that the human repertoire of carbohydrate-specific immunoglobulin G (IgG) exhibits modular organization related to glycan epitope structure. The current study compares the glycan-specific IgG repertoires between different PAD entities. Distinct repertoire profiles with extensive qualitative glycan-recognition defects were observed, which are characterized by the common loss of Galα and GalNAc reactivity and disease-specific recognition of microbial antigens, self-antigens, and tumor-associated carbohydrate antigens. Antibody repertoire analysis may provide a useful tool to elucidate the degree and the clinical implications of immune system failure in individual patients.

MiRNAs in Extracellular Vesicles from iPS-Derived Cardiac Progenitor Cells Effectively Reduce Fibrosis and Promote Angiogenesis in Infarcted Heart.

Cardiac stem cell therapy offers the potential to ameliorate postinfarction remodeling and development of heart failure but requires optimization of cell-based approaches. Cardiac progenitor cells (CPCs) induction by ISX-9, a small molecule possessing antioxidant, prosurvival, and regenerative properties, represents an attractive potential approach for cell-based cardiac regenerative therapy. Here, we report that extracellular vesicles (EV) secreted by ISX-9-induced CPCs (EV-CPCISX-9) faithfully recapitulate the beneficial effects of their parent CPCs with regard to postinfarction remodeling. These EV contain a distinct repertoire of biologically active miRNAs that promoted angiogenesis and proliferation of cardiomyocytes while ameliorating fibrosis in the infarcted heart. Amongst the highly enriched miRNAs, miR-373 was strongly antifibrotic, targeting 2 key fibrogenic genes, GDF-11 and ROCK-2. miR-373 mimic itself was highly efficacious in preventing scar formation in the infarcted myocardium. Together, these novel findings have important implications with regard to prevention of postinfarction remodeling.

Categorization of Mouse Ultrasonic Vocalizations Using Machine Learning Techniques

A study of the ultrasonic vocalizations of several adult male BALB/c mice in the presence of a female, is undertaken in this study. A total of 179 distinct ultrasonic syllables referred to as “phonemes” are isolated, and in the resulting dataset, k-means and agglomerative clustering algorithms are implemented to group the ultrasonic vocalizations into clusters based on features extracted from their pitch contours. In order to find the optimal number of clusters, the elbow method was used, and nine distinct categories were obtained. Results when the k-means method was applied are presented through a matching matrix, while clustering results when the agglomerative technique was applied are presented as a dendrogram. The results of both methods are in line with the manual annotations made by the authors, as well as with the ones presented in the literature. The two methods of unsupervised analysis applied on 14 element feature vectors provide evidence that vocalizations can be grouped into nine clusters, which translates into the claim that there is a distinct repertoire of “syllables” or “phonemes”.

Wastewater as a Probable Environmental Reservoir of Extended-Spectrum-β-Lactamase Genes: Detection of Chimeric β-Lactamases CTX-M-64 and CTX-M-123.

The presence of antimicrobial-resistant bacteria and resistance genes in aquatic environments is a serious public health concern. This study focused on Escherichia coli possessing blaCTX-M genes in wastewater inflows. Twelve crude inflow water samples from wastewater treatment plant (WWTP) A and two samples each from three other WWTPs were collected in 2017 and 2018. A total of 73 E. coli isolates with 31 different sequence types (STs) harboring distinctive blaCTX-M gene repertoires were detected. In WWTP A influents, blaCTX-M-14 (14 isolates) was dominant, followed by blaCTX-M-15 (12 isolates) and blaCTX-M-27 (10 isolates). The chimeric blaCTX-M-64 and blaCTX-M-123 genes were each identified in one of the E. coli isolates from the same WWTP A inflow port. The blaCTX-M-27 gene was associated with five of seven B2-ST131 isolates, including three isolates of the B2-O25b-ST131-H30R/non-Rx lineage. One of the remaining two isolates belonged to the B2-O25b-ST131-H30R/Rx lineage harboring the blaCTX-M-15 gene. As for the B2-O25b-ST131-H30R/non-Rx lineage, two isolates with blaCTX-M-27 were recovered from each of the WWTP B and D influents, and one isolate with blaCTX-M-174 was also recovered from WWTP B influent. Whole-genome sequencing of chimeric blaCTX-M-harboring E. coli isolates revealed that the blaCTX-M-64 gene was integrated into the chromosome of ST10 E. coli B22 via ISEcp1-mediated transposition of a 9,467-bp sequence. The blaCTX-M-123-carrying IncI1 plasmid pB64 was 109,169 bp in length with pST108. The overall findings suggest that wastewater may act as a probable reservoir of clinically significant clonal lineages mediating antimicrobial resistance genes and chimeric genes that have not yet been identified from human isolates of domestic origin in Japan.IMPORTANCE Global spread of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a critical concern in both clinical and community settings. This dominance of CTX-M-type ESBL producers may be largely due to the successful international spread of epidemic clones, as represented by the extraintestinal pathogenic Escherichia coli (ExPEC) ST131. Our findings highlight the worrisome presence of diverse E. coli clones associated with humans, including ExPEC lineages harboring the most common blaCTX-M variants in untreated wastewater samples. Moreover, the chimeric genes blaCTX-M-64 and blaCTX-M-123, which have not yet been identified from human isolates of domestic origin in Japan, were identified. Exposure to untreated wastewater through combined sewer overflow caused by heavy rains derived from abnormal weather change could pose a risk for human health due to ingesting those antimicrobial-resistant bacteria.

Divergent chemosensory gene expression accompanies ecological specialisation of pea aphid morphs

1. Chemosensation is fundamental to the adaptation of insects to their environments. It is used in multiple ecological contexts such as host selection, mate selection, conspecific communication, and predator defence simultaneously. Therefore, understanding the molecular genetic mechanisms underlying specific chemosensory adaptations is important.2. Here a unique study system is used that provides a means to focus on separate aspects of chemosensory specialisation. Pea aphids (Acyrthosiphon pisum) produce different morphs such as winged asexual females, wingless asexual females, sexual females, winged males, and wingless males during their annual life cycle. These morphs have the same or similar genotypes but distinct ecologies and chemosensory repertoires.3. It is hypothesised that divergent chemosensory gene expression underlies ecological and thus chemosensory specialisation. RNA‐Seq data were used to compare chemosensory gene expression levels of five pea aphid morphs. The study focused on 113 genes belonging to six chemosensory gene families (odorant‐binding proteins, chemosensory proteins, odorant receptors, gustatory receptors, ionotropic receptors, and sensory neuron membrane proteins).4. Gene expression analysis revealed that 85% of the chemosensory genes displayed significant differential expression among the five morphs. By performing pairwise morph comparisons, candidate chemosensory genes associated with the distinct chemosensory repertoires of the morphs were identified. Extensive phenotypic plasticity was also found in the expression of chemosensory genes. These results provide insights into the transcriptional variation in chemosensory genes underlying chemosensory and ecological specialisation of distinct morphs.

Sociosexual behavioral patterns involving nulliparous female orangutans (Pongo sp.) reflect unique challenges during the adolescent period.

The primate adolescent period is characterized by a series of changes in physiology, behavior, and social relationships. Orangutans have the slowest life history and the longest period of dependency of all primates. As members of a semisolitary species with high levels of sexual coercion, adolescent female orangutans face a unique combination of challenges when achieving independence from their mother. This study examined the mating behavior of adolescent female orangutans and compared it with that of adult females to assess whether mating behavior reflects distinct strategies at these different points in the life cycle. Data were collected in Gunung Palung National Park on the island of Borneo over 20 years. Mating events from adolescent (n = 19) and adult females (n = 26) were scored and compared. Adolescent female mating events had significantly higher mating scores (indicating more proceptivity) than those of adult females (β = 1.948, p = .001). Adolescent females also engaged in elaborate sociosexual interactions with different flanged males, behaviors that were never observed during mating events of adult females. These interactions involved characteristic behavior on the part of both the adolescent females and the flanged males. Given these findings and the documentation of similar accounts of adolescent female-flanged male mating from the island of Sumatra, we propose that adolescent female orangutans display distinctive behavioral repertoires throughout the genus Pongo which serves to overcome male ambivalence toward nulliparous females, establish familiarity, and evaluate coercive tendencies in flanged males. We suggest that these behavioral patterns are an integral part of female social development in a female philopatric, but highly dispersed species where consistent social support is absent after ranging independence is achieved.

Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.

MotivationBreast cancer consists of multiple distinct tumor subtypes, and results from epigenetic and genetic aberrations that give rise to distinct transcriptional profiles. Despite previous efforts to understand transcriptional deregulation through transcription factor networks, the transcriptional mechanisms leading to subtypes of the disease remain poorly understood.ResultsWe used a sophisticated computational search of thousands of expression datasets to define extended signatures of distinct breast cancer subtypes. Using ENCODE ChIP-seq data of surrogate cell lines and motif analysis we observed that these subtypes are determined by a distinct repertoire of lineage-specific transcription factors. Furthermore, specific pattern and abundance of copy number and DNA methylation changes at these TFs and targets, compared to other genes and to normal cells were observed. Overall, distinct transcriptional profiles are linked to genetic and epigenetic alterations at lineage-specific transcriptional regulators in breast cancer subtypes.Availability and implementationThe analysis code and data are deposited at https://bitbucket.org/qzhu/breast.cancer.tf/.Supplementary information Supplementary data are available at Bioinformatics online.

Innate αβ T Cells Mediate Antitumor Immunity by Orchestrating Immunogenic Macrophage Programming.

Unconventional T-lymphocyte populations are emerging as important regulators of tumor immunity. Despite this, the role of TCRαβ+CD4-CD8-NK1.1- innate αβ T cells (iαβT) in pancreatic ductal adenocarcinoma (PDA) has not been explored. We found that iαβTs represent ∼10% of T lymphocytes infiltrating PDA in mice and humans. Intratumoral iαβTs express a distinct T-cell receptor repertoire and profoundly immunogenic phenotype compared with their peripheral counterparts and conventional lymphocytes. iαβTs comprised ∼75% of the total intratumoral IL17+ cells. Moreover, iαβT-cell adoptive transfer is protective in both murine models of PDA and human organotypic systems. We show that iαβT cells induce a CCR5-dependent immunogenic macrophage reprogramming, thereby enabling marked CD4+ and CD8+ T-cell expansion/activation and tumor protection. Collectively, iαβTs govern fundamental intratumoral cross-talk between innate and adaptive immune populations and are attractive therapeutic targets. SIGNIFICANCE: We found that iαβTs are a profoundly activated T-cell subset in PDA that slow tumor growth in murine and human models of disease. iαβTs induce a CCR5-dependent immunogenic tumor-associated macrophage program, T-cell activation and expansion, and should be considered as novel targets for immunotherapy.See related commentary by Banerjee et al., p. 1164.This article is highlighted in the In This Issue feature, p. 1143.

Patterns of antibody responses to nonviral cancer antigens in head and neck squamous cell carcinoma patients differ by human papillomavirus status.

There have been hints that nonviral cancer antigens are differentially expressed in human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC). Antibody responses (AR) to cancer antigens may be used to indirectly determine cancer antigen expression in the tumor using a noninvasive and tissue-saving liquid biopsy. Here, we set out to characterize AR to a panel of nonviral cancer antigens in HPV-positive and HPV-negative HNSCC patients. A fluorescent microbead multiplex serology to 29 cancer antigens (16 cancer-testis antigens, 5 cancer-retina antigens and 8 oncogenes) and 29 HPV-antigens was performed in 382 HNSCC patients from five independent cohorts (153 HPV-positive and 209 HPV-negative). AR to any of the cancer antigens were found in 272/382 patients (72%). The ten most frequent AR were CT47, cTAGE5a, c-myc, LAGE-1, MAGE-A1, -A3, -A4, NY-ESO-1, SpanX-a1 and p53. AR to MAGE-A3, MAGE-A9 and p53 were found at significantly different prevalences by HPV status. An analysis of AR mean fluorescent intensity values uncovered remarkably different AR clusters by HPV status. To identify optimal antigen selections covering a maximum of patients with ≤10 AR, multiobjective optimization revealed distinct antigen selections by HPV status. We identified that AR to nonviral antigens differ by HPV status indicating differential antigen expression. Multiplex serology may be used to characterize antigen expression using serum or plasma as a tissue-sparing liquid biopsy. Cancer antigen panels should address the distinct antigen repertoire of HPV-positive and HPV-negative HNSCC.

Clonal replacement of tumor-specific T cells following PD-1 blockade.

Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of cancer patients1. However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor infiltrating T cells (TILs) or on recruitment of novel T cells remains unclear2–4. Here, we performed paired single-cell RNA (scRNA) and T cell receptor (TCR)- sequencing on 79,046 cells from site-matched tumors from patients with basal cell carcinoma (BCC) or squamous cell carcinoma (SCC) pre- and post-anti-PD-1 therapy. Tracking TCR clones and transcriptional phenotypes revealed a coupling of tumor-recognition, clonal expansion, and T cell dysfunction marked by clonal expansions of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, this expansion did not derive from pre-existing TIL clones; rather, it was comprised of novel clonotypes not previously observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+ T cells and evident in BCC and SCC patients. These results demonstrate that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.

Distinct immunoglobulin heavy chain variable region gene repertoire and lower frequency of del(11q) in Taiwanese patients with chronic lymphocytic leukaemia.

SummaryChronic lymphocytic leukaemia (CLL) is the most common leukaemia in Western countries but very rare in Asia. Peripheral blood or bone marrow mononuclear cells obtained at initial diagnosis from 194 patients with CLL were analysed to determine the ethnic difference in genetic abnormalities. Mutated IGHV was detected in 71·2% of Taiwanese CLL and IGHV3‐23 was the most frequently used gene. Stereotyped BCR was present in 18·3% with subset 8 being the most frequent. All cases with subset 8 belonged to IGHV 4‐39 and were exclusively associated with un‐mutated IGHV and poor outcome. Mutation frequencies of SF3B1 (9·7%), NOTCH1 (8·6%), BIRC3 (1·1%), ATM (16·9%) or TP53 (8·1%), and frequencies of cytogenetic abnormalities including trisomy 12 (18·6%), del(17p) (10·4%), del(13q) (43·7%) and IGH translocation (10·1%) were comparable to those reported from Western countries, except del(11q) (6·9%) which was lower in our patients. Patients with un‐mutated IGHV, subset 8, disrupted TP53, trisomy 12, and SF3B1 mutations had a worse outcome compared to patients without these mutations. In conclusion, IGHV3‐23 usage, stereotyped subset 8 and lower frequency of del(11q) show an ethnicity‐dependent association in Taiwanese CLL patients.

Public relations channel “repertoires”: Exploring patterns of channel use in practice

While public relations practitioners may use any number of channels to accomplish organizational objectives, research has focused on the use of single communication channels in isolation from other available channels. The purpose of this exploratory study is to identify the common combinations of channels or “channel repertoires” that practitioners use to reach their publics. Analyses of survey data (N = 504) of practitioners from five countries revealed four distinct patterns or repertoires of channels. The results also indicated that many public relations functions predict the use of certain repertoires, and explained which functions of public relations use more channels than others. The findings have implications for theory building, practice, and pedagogy on planning and engagement with publics.

Identification of exhausted CD8+ T cells in low tumor mutation burden breast cancer patients

Abstract Tumor immunogenicity is generally thought to be correlated with increased tumor mutation burden and the resulting neoantigen driven T cell reactivity to cancer cells. This immunogenicity results in the formation of tumor specific, but exhausted tumor infiltrating CD8+ T cells (TILex). Breast cancer tumors, which are predominantly low mutation burden, are widely viewed as non-immunogenic. Here we demonstrate that subsets of both triple negative and estrogen receptor positive breast cancer patients have primary tumors heavily infiltrated by tumor specific CD8+ TILex. CD8+ TILex in breast cancer patients were demonstrated to coexpress PD-1 and CD39 and showed a significant reduction of IFNγ, TNFα, and IL-2 production capacity. Like melanoma and colorectal CD8+ TILex, CD8+ TILex human breast tumors had increased expression of CD103, CD38, and TIM-3 in addition to loss of KLRG1 and CD127 expression. Similarly, melanoma, colorectal, and breast tumor CD8+ TILex shared transcriptional signatures identified by single cell sequencing. T cell receptor sequencing revealed a distinct repertoire of CD8+ TILex as compared to other CD8+ TILs from the same tumors, suggesting them to be a unique population in response to tumor antigen. Finally, we demonstrated that increased levels of CD8+ TILex in human breast tumors are not associated with higher levels of tumor mutation burden, as assessed by a tumor mutation load oncogene panel. This work suggests that a subset of breast cancer patients have inflamed, tumors associated with the presence of exhausted CD8+ T cells and that these patients may benefit from immunotherapeutic interventions.

Explaining the uncertainty: understanding small-scale farmers\u2019 cultural beliefs and reasoning of drought causes in Gaza Province, Southern Mozambique

This paper explores small-scale farmers’ cultural beliefs about the causes of drought events and the reasoning behind their beliefs. Cultural beliefs vary across countries, regions, communities, and social groups; this paper takes the case of farmers from Gaza Province in southern Mozambique as its focus. Findings show that the farmers have a limited knowledge and understanding of the scientific explanation about drought. Thus, farmers’ beliefs about the causes of drought are strongly based on the indigenous (the power of spirits) and Christian philosophies that attribute drought to supernatural forces, such as ancestors or God, and as a punishment for (some unknown) wrongdoings. Farmers have a distinct and under-explored repertoire of possible wrongdoings to justify the punishments driven by those cultural beliefs. Some of their reasoning is static, while some is mutable, and is based on their observation and perception of the negative, unexpected, or harmful recent or current events which happen in their surrounding environment, and which they believe could be avoided or prevented. Farmers’ beliefs about drought causes, and their underlying reasoning for those beliefs, are what will primarily influence their perception of their own capacity to adapt, their motivation to respond, and their behavioral responses. Yet, their social groups exert a great influence on their choices of response. The paper concludes that more context-specific investigations into the socio-psychological nature of farmers’ beliefs are required prior to interventions in order to better help farmers to respond to future drought risks.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

The role of intestinal Prevotella species in human health is controversial, with both positive and negative associations. Strain-level diversity may contribute to discrepancies in genus and species associations with health and disease. We dissected the gut metagenomes of Italians with varying dietary habits, investigating the presence of distinct Prevotella copri strains. Fiber-rich diets were linked to P.copri types with enhanced potential for carbohydrate catabolism. P.copri strains associated with an omnivore diet had ahigher prevalence of the leuB gene-involved in branched-chain amino acid biosynthesis-a risk factor for glucose intolerance and type 2 diabetes. These P.copri pangenomes were compared to existing cohorts, providing evidence of distinct gene repertoires characterizing different P.copri populations, with drug metabolism and complex carbohydrate degradation significantly associated with Western and non-Western individuals, respectively. Strain-level P.copri diversity in gut microbiomes is affected by diet and should be considered when examining host-microbe associations.

In vitro-generated MART-1-specific CD8 T cells display a broader T-cell receptor repertoire than exvivo naïve and tumor-infiltrating lymphocytes.

The differentiation of human hematopoietic stem cells into CD8 T cells can be achieved invitro with the OP9-DL4 system. We considered that in the absence of medullary thymic epithelial cells, which serve to restrict the breath of the T-cell receptor (TCR) repertoire by expressing tissue-restricted antigens, a distinct repertoire would be generated invitro. To test this notion, we compared the TCR-Vα/Vβ (TRAV/TRBV) gene usage of major histocompatibility complex-restricted antigen (MART-1)-specific T cells generated invitro to that from exvivo naïve T cells and tumor-infiltrating lymphocytes (TILs) using high-throughput DNA sequencing. In contrast to naïve T cells and TILs, which showed the expected narrow TRAV repertoire, invitro-generated MART-1-specific T cells used almost all TRAV gene families and displayed unique CDR3 lengths. Our work demonstrates that the OP9-DL4 system supports the creation of a broad antigen-specific TCR repertoire, suggesting that T cells generated invitro may undergo a different set of selection events that otherwise constrains the TCR repertoire of thymus-derived T cells.

Memory CD4+ T cells are generated in the human fetal intestine.

The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+ T cells reside in the fetal intestine. Here we combined functional assays with mass cytometry, single-cell RNA-sequencing and high-throughput T cell antigen receptor (TCR) sequencing to characterize the CD4+ T cell compartment in the human fetal intestine. We identified 22 CD4+ T cell clusters, including naive-like, regulatory-like and memory-like subpopulations, which were confirmed and further characterized at the transcriptional level. Memory-like CD4+ T cells had high expression of Ki-67, indicative of cell division, and CD5, a surrogate marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway analysis revealed a differentiation trajectory associated with cellular activation and proinflammatory effector functions, and TCR repertoire analysis indicated clonal expansions, distinct repertoire characteristics and interconnections between subpopulations of memory-like CD4+ T cells. Imaging-mass cytometry indicated that memory-like CD4+ T cells colocalized with antigen-presenting cells. Collectively, these results provide evidence for the generation of memory-like CD4+ T cells in the human fetal intestine that is consistent with exposure to foreign antigens.