A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties1-3. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions-in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.

A guide to the BRAIN Initiative Cell Census Network data ecosystem

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

Integrated multimodal cell atlas of Alzheimer's disease

Alzheimer's disease (AD) is the most common cause of dementia in older adults. Neuropathological and imaging studies have demonstrated a progressive and stereotyped accumulation of protein aggregates, but the underlying molecular and cellular mechanisms driving AD progression and vulnerable cell populations affected by disease remain coarsely understood. The current study harnesses single cell and spatial genomics tools and knowledge from the BRAIN Initiative Cell Census Network to understand the impact of disease progression on middle temporal gyrus cell types. We used image-based quantitative neuropathology to place 84 donors spanning the spectrum of AD pathology along a continuous disease pseudoprogression score and multiomic technologies to profile single nuclei from each donor, mapping their transcriptomes, epigenomes, and spatial coordinates to a common cell type reference with unprecedented resolution. Temporal analysis of cell-type proportions indicated an early reduction of Somatostatin-expressing neuronal subtypes and a late decrease of supragranular intratelencephalic-projecting excitatory and Parvalbumin-expressing neurons, with increases in disease-associated microglial and astrocytic states. We found complex gene expression differences, ranging from global to cell type-specific effects. These effects showed different temporal patterns indicating diverse cellular perturbations as a function of disease progression. A subset of donors showed a particularly severe cellular and molecular phenotype, which correlated with steeper cognitive decline. We have created a freely available public resource to explore these data and to accelerate progress in AD research at SEA-AD.org.

The mannose-binding lectin (MBL2) haplotype and breast cancer: an association study in African-American and Caucasian women

Common genetic variants in cancer-related genes contribute to breast cancer. The innate immune system plays a crucial role in the immune surveillance against malignancies, thus it is plausible that genetic variations in key genes of the innate immunity such as the mannose-binding lectin (MBL), MBL2, could influence the risk for breast cancer. We investigated the association of MBL2 genotypes with breast cancer and conducted a comprehensive genotype and haplotype analysis of 26 MBL2 single nucleotide polymorphisms (SNPs) in a case-control study of breast cancer [166 African-American (AA) case patients versus 180 controls and 127 Caucasian (CAU) case patients versus 137 controls]. We observed that the A allele of the 3'-UTR SNP Ex4-1067 (NCBI SNP ID: rs10824792) was significantly associated with a decreased disease risk in AA women [odds ratio (OR) = 0.47, 95% confidence interval (CI) = 0.27-0.81]. Haplotype analysis of MBL2 showed that the frequency of the corresponding 3' haplotype TATAAC (Ex4-1483, Ex4-1067, Ex4-1047, Ex4-901, Ex4-710, 3238bp 3' STP) was lower in cases than controls among AA women (0.15 versus 0.21; P = 0.02) suggesting a protective effect after adjusting for covariates (OR = 0.51, 95% CI = 0.29-0.88, P = 0.018). In conclusion, this study presents preliminary evidence that common genetic variants in the 3'-UTR of MBL2 might influence the risk for breast cancer in AA women, probably in interaction with the 5' secretor haplotypes that are associated with high concentrations of MBL.

Associations of Classic Kaposi Sarcoma with Common Variants in Genes that Modulate Host Immunity

Classic Kaposi sarcoma (CKS) is an inflammatory-mediated neoplasm primarily caused by Kaposi sarcoma-associated herpesvirus (KSHV). Kaposi sarcoma lesions are characterized, in part, by the presence of proinflammatory cytokines and growth factors thought to regulate KSHV replication and CKS pathogenesis. Using genomic DNA extracted from 133 CKS cases and 172 KSHV-latent nuclear antigen-positive, population-based controls in Italy without HIV infection, we examined the risk of CKS associated with 28 common genetic variants in 14 immune-modulating genes. Haplotypes were estimated for IL1A, IL1B, IL4, IL8, IL8RB, IL10, IL12A, IL13, and TNF. Compared with controls, CKS risk was decreased with 1235T/-1010G-containing diplotypes of IL8RB (odds ratio, 0.49; 95% confidence interval, 0.30-0.78; P = 0.003), whereas risk was increased with diplotypes of IL13 containing the promoter region variant 98A (rs20541, alias +130; odds ratio, 1.88; 95% confidence interval, 1.15-3.08; P = 0.01) when considered in multivariate analysis. Risk estimates did not substantially vary by age, sex, incident disease, or disease burden. Our data provide preliminary evidence for variants in immune-modulating genes that could influence the risk of CKS. Among KSHV-seropositive Italians, CKS risk was associated with diplotypes of IL8RB and IL13, supporting laboratory evidence of immune-mediated pathogenesis.

SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes

The SNP500Cancer database provides sequence and genotype assay information for candidate SNPs useful in mapping complex diseases, such as cancer. The database is an integral component of the NCI Cancer Genome Anatomy Project (http://cgap.nci.nih.gov). SNP500Cancer reports sequence analysis of anonymized control DNA samples (n = 102 Coriell samples representing four self-described ethnic groups: African/African-American, Caucasian, Hispanic and Pacific Rim). The website is searchable by gene, chromosome, gene ontology pathway, dbSNP ID and SNP500Cancer SNP ID. As of October 2005, the database contains >13 400 SNPs, 9124 of which have been sequenced in the SNP500Cancer population. For each analysed SNP, gene location and >200 bp of surrounding annotated sequence (including nearby SNPs) are provided, with frequency information in total and per subpopulation as well as calculation of Hardy-Weinberg equilibrium for each subpopulation. The website provides the conditions for validated sequencing and genotyping assays, as well as genotype results for the 102 samples, in both viewable and downloadable formats. A subset of sequence validated SNPs with minor allele frequency >5% are entered into a high-throughput pipeline for genotyping analysis to determine concordance for the same 102 samples. In addition, the results of genotype analysis for select validated SNP assays (defined as 100% concordance between sequence analysis and genotype results) are posted for an additional 280 samples drawn from the Human Diversity Panel (HDP). SNP500Cancer provides an invaluable resource for investigators to select SNPs for analysis, design genotyping assays using validated sequence data, choose selected assays already validated on one or more genotyping platforms, and select reference standards for genotyping assays. The SNP500Cancer database is freely accessible via the web page at http://snp500cancer.nci.nih.gov.

Sequence analysis of the mannose-binding lectin (MBL2) gene reveals a high degree of heterozygosity with evidence of selection

Human mannose-binding protein (MBL) is a component of innate immunity. To capture the common genetic variants of MBL2, we resequenced a 10.0 kb region that includes MBL2 in 102 individuals representing four major US ethnic groups. In all, 87 polymorphic sites were observed, indicating a high level of heterozygosity (total pi=18.3 x 10(-4)). Estimates of linkage disequilibrium across MBL2 indicate that it is divided into two blocks, with a probable recombination hot spot in the 3' end. Three non-synonymous SNPs in exon 1 of the encoding MBL2 gene and three upstream SNPs form common 'secretor haplotypes' that can predict circulating levels. Common variants have been associated with increased susceptibility to infection and autoimmune diseases. The high frequencies of B, C and D alleles in certain populations suggest a possible selective advantage for heterozygosity. There is limited diversity of haplotype structure; the 'secretor haplotypes' lie on a restricted number of extended haplotypes, which could include additional linked SNPs, which might also have possible functional implications. There is evidence for gene conversion in the region between the two blocks, in the last exon. Our data should form the basis for conducting MBL2 candidate gene association studies using a locus-wide approach.

Failed or inadequate bone marrow aspiration: a fast, simple and cost-effective method to produce a cell suspension from a core biopsy specimen

Failure to aspirate bone marrow (BM) diminishes diagnostic accuracy and efficiency because BM cell suspensions are crucial for modern haematological diagnostic methods such as cytomorphology, flow cytometric immunophenotyping (FCI), cytogenetics or fluorescent in situ hybridization (FISH). We mechanically disaggregated unfixed BM core biopsies with the Dako Medimachine in 65 cases of macroscopically suspected dry taps. Cytospins, three-colour FCI and in some cases karyotyping and FISH were performed successfully. Most cytospins (34 of 50; 68.0%) were of good quality, while a further 18.0% showed moderate but still informative quality. FCI showed good quality in 36 of 60 (60.0%) cases; in 13.3% quality was moderate, but diagnostically useful results were obtained. Surprisingly, all four cases of formerly undiagnosed BM-carcinosis could be clearly detected on cytospins. Finally, five of seven (71.4%) attempts yielded analysable metaphases mostly in cases where no metaphases could be obtained from BM or peripheral blood. The described method of mechanical disaggregation of unfixed BM core biopsies compares favourably with other published approaches, allowing the application of all techniques where BM cell suspensions are needed. Thus, it can help to establish the underlying diagnosis in patients with abnormalities in peripheral blood and unsuccessful marrow aspirations.

SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes

The SNP500Cancer Database provides sequence and genotype assay information for candidate single nucleotide polymorphisms (SNPs) useful in mapping complex diseases, such as cancer. The database is an integral component of the NCI's Cancer Genome Anatomy Project. SNP500Cancer provides bi-directional sequencing information on a set of control DNA samples derived from anonymized subjects (102 Coriell samples representing four self-described ethnic groups: African/African-American, Caucasian, Hispanic and Pacific Rim). All SNPs are chosen from public databases and reports, and the choice of genes includes a bias towards non-synonymous and promoter SNPs in genes that have been implicated in one or more cancers. The web site is searchable by gene, chromosome, gene ontology pathway and by known dbSNP ID. As of July 2003, the database contains over 3400 SNPs, 2490 of which have been sequenced in the SNP500Cancer population. For each analyzed SNP, gene location and over 200 bp of surrounding annotated sequence (including nearby SNPs) are provided, with frequency information in total and per subpopulation, and calculation of Hardy-Weinberg Equilibrium (HWE) for each subpopulation. Sequence validated SNPs with minor allele frequency > 5% are entered into a high-throughput pipeline for genotyping analysis to determine concordance for the same 102 samples. The website provides the conditions for validated genotyping assays. SNP500Cancer provides an invaluable resource for investigators to select SNPs for analysis, design genotyping assays using validated sequence data, choose selected assays already validated on one or more genotyping platforms, and select reference standards for genotyping assays. The SNP500Cancer Database is freely accessible via the web page at http://snp500cancer.nci.nih.gov/.

Two cases of fibrocystic breast disease with polysomy 18 as the sole clonal cytogenetic abnormality

In the present study, we describe the occurrence of numerical alterations of chromosome 18 in two cases of benign fibrous/fibrocystic tumors of the breast, both of which were studied by conventional cytogenetic investigations and one of which was additionally tested by fluorescence in situ hybridization with the use of an alphoid centromeric probe specific for chromosome 18. Case 1 showed a tetrasomy 18 in 2 of 33 metaphases as the only clonal chromosomal aberration. Case 2 revealed both trisomy and tetrasomy 18 as clonal alterations in metaphases and interphase nuclei.

A fibroadenoma with a t(4;12) (q27;q15) affecting the HMGI-C gene, a member of the high mobility group protein gene family

An intracanalicular fibroadenoma of the breast showing a clonal chromosomal aberration t(4;12) (q27;q15) as the sole cytogenetic abnormality is described. In order to narrow down the breakpoint region on chromosome 12 on the molecular level we performed fluorescence in situ hybridization (FISH) analysis with a cosmid pool originating from a YAC-contig overspanning part of the region 12q14-15. We were able to narrow down the breakpoint to an approximately 230kb fragment belonging to the HMGI-C gene which maps within an area recently designated as MAR (Multiple Aberration Region). The chromosomal breakpoints of other frequent benign solid tumors, i.e. lipomas, uterine leiomyomas, and pleomorphic adenomas are clustered within the third intron of that gene.

Significance of clonal chromosome aberrations in breast fibroadenomas

Despite the high frequency of fibroadenomas of the breast, cytogenetic results are relatively limited. We describe our cytogenetic findings in 30 fibroadenomas. Of these, three showed clonal chromosome abnormalities, i.e., 46,XX,der(6)t(1;6)(q25;p21.3); 48,XX,del(6)(q21),r(11)(?),der(14)t(6;14)(q21;q32),+2mar; and 47,XX,+5.

Fluorescence in situ hybridization studies on breast tumor samples for distinguishing between different subsets of breast cancer

OBJECTIVES

To evaluate fluorescence in situ hybridization for distinguishing between malignant and benign breast tumors and determining genetic subgroups of breast cancers.

STUDY DESIGN

Touch preparations from 94 surgically removed breast tumors (17 benign and 77 malignant) were hybridized with a DNA probe specific for centromeric DNA sequences of chromosome 1. Twenty samples were additionally hybridized with a chromosome 9-specific probe.

RESULTS

We investigated the heterogeneity of the cell populations on the basis of the number of signals per nucleus. All benign tumors showed two signals per nucleus. In contrast, carcinomas revealed a broad spectrum of hybridization patterns. Some showed almost exclusively two signals per nucleus, and others exceeded four signals.

CONCLUSION

The hybridization patterns of individual tumors can be used for defining different subsets of breast cancer. The results may have prognostic impact, leading to "molecular-cytogenetic grading" of breast cancer.

Trisomy 8 and 18 as frequent clonal and single-cell aberrations in 185 primary breast carcinomas

For cytogenetic investigations short-term cultures of 185 breast carcinomas (135 invasive ductal, 21 invasive lobular, 12 invasive ductal with intraductal components, seven heterogeneous, six intraductal, four invasive ductal and lobular) were prepared. Cytogenetic examinations revealed clonal abnormalities in 39 cases with a predominance of simple numerical chromosome changes, i.e., trisomies of chromosomes 7, 8, and 18. One hundred forty-six tumors did not show clonal abnormalities, but single-cell aberrations other than monosomies occurred in 79 of these tumors. Compared to cells of epithelial hyperplasia of the breast, amniotic fluid cells, and cells from pleomorphic adenomas cultivated using the same medium, the frequency of single-cell trisomies was significantly higher. Trisomy 8 was not only found as a clonal aberration in 10 cases but was also the most frequent non-clonal aberration. Trisomy 7 and 18 were also frequent clonal as well as non-clonal cytogenetic deviations.

Two human breast tumors with translocations involving 12q13-15 as the sole cytogenetic abnormality

Two benign epithelial breast lesions showing clonal chromosomal alterations involving 12q13-15 are reported. As the only clonal aberration a t(12;14)(q13-14;q24) was noted in a florid epithelial hyperplasia with extended adenosis. A t(10;12)(p14-15;q13) was found in a papilloma also with areas of florid epithelial hyperplasia.

Effect of mild-to-moderate airflow limitation on exercise capacity

To determine the effect of mild-to-moderate airflow limitation on exercise tolerance and end-expiratory lung volume (EELV), we studied 9 control subjects with normal pulmonary function [forced expired volume in 1 s (FEV1) 105% pred; % of forced vital capacity expired in 1 s (FEV1/FVC%) 81] and 12 patients with mild-to-moderate airflow limitation (FEV1 72% pred; FEV1/FVC % 58) during progressive cycle ergometry. Maximal exercise capacity was reduced in patients [69% of pred maximal O2 uptake (VO2max)] compared with controls (104% pred VO2max, P less than 0.01); however, maximal expired minute ventilation-to-maximum voluntary ventilation ratio and maximal heart rate were not significantly different between controls and patients. Overall, there was a close relationship between VO2max and FEV1 (r2 = 0.62). Resting EELV was similar between controls and patients [53% of total lung capacity (TLC)], but at maximal exercise the controls decreased EELV to 45% of TLC (P less than 0.01), whereas the patients increased EELV to 58% of TLC (P less than 0.05). Overall, EELV was significantly correlated to both VO2max (r = -0.71, P less than 0.001) and FEV1 (r = -0.68, P less than 0.001). This relationship suggests a ventilatory influence on exercise capacity; however, the increased EELV and associated pleural pressures could influence cardiovascular function during exercise. We suggest that the increase in EELV should be considered a response reflective of the effect of airflow limitation on the ventilatory response to exercise.