https://cdr.lib.unc.edu/downloads/db78tf26w

The Molecular Taxonomy of Primary Prostate Cancer

There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part of The Cancer Genome Atlas (TCGA), we present a comprehensive molecular analysis of 333 primary prostate carcinomas. Our results revealed a molecular taxonomy in which 74% of these tumors fell into one of seven subtypes defined by specific gene fusions (ERG, ETV1/4, and FLI1) or mutations (SPOP, FOXA1, and IDH1). Epigenetic profiles showed substantial heterogeneity, including an IDH1 mutant subset with a methylator phenotype. Androgen receptor (AR) activity varied widely and in a subtype-specific manner, with SPOP and FOXA1 mutant tumors having the highest levels of AR-induced transcripts. 25% of the prostate cancers had a presumed actionable lesion in the PI3K or MAPK signaling pathways, and DNA repair genes were inactivated in 19%. Our analysis reveals molecular heterogeneity among primary prostate cancers, as well as potentially actionable molecular defects.

Here we conducted a large-scale genetic association analysis of educational attainment in a sample of approximately 1.1 million individuals and identify 1,271 independent genome-wide-significant SNPs. For the SNPs taken together, we found evidence of heterogeneous effects across environments. The SNPs implicate genes involved in brain-development processes and neuron-to-neuron communication. In a separate analysis of the X chromosome, we identify 10 independent genome-wide-significant SNPs and estimate a SNP heritability of around 0.3% in both men and women, consistent with partial dosage compensation. A joint (multi-phenotype) analysis of educational attainment and three related cognitive phenotypes generates polygenic scores that explain 11-13% of the variance in educational attainment and 7-10% of the variance in cognitive performance. This prediction accuracy substantially increases the utility of polygenic scores as tools in research.

/pdf/gene-discovery-and-polygenic-prediction-from-a-genome-wide-28jxdgwqo5.pdf

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. Here we describe quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers, of which 77 provided high-quality data. Integrated analyses provided insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. Interrogation of the 5q trans-effects against the Library of Integrated Network-based Cellular Signatures, connected loss of CETN3 and SKP1 to elevated expression of epidermal growth factor receptor (EGFR), and SKP1 loss also to increased SRC tyrosine kinase. Global proteomic data confirmed a stromal-enriched group of proteins in addition to basal and luminal clusters, and pathway analysis of the phosphoproteome identified a G-protein-coupled receptor cluster that was not readily identified at the mRNA level. In addition to ERBB2, other amplicon-associated highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates the functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets.

https://dash.harvard.edu/bitstream/handle/1/29626102/5102256.pdf?sequence=1

Proteogenomics connects somatic mutations to signalling in breast cancer

Cyclin-dependent kinases (Cdks) are serine/threonine kinases and their catalytic activities are modulated by interactions with cyclins and Cdk inhibitors (CKIs). Close cooperation between this trio is necessary for ensuring orderly progression through the cell cycle. In addition to their well-established function in cell cycle control, it is becoming increasingly apparent that mammalian Cdks, cyclins and CKIs play indispensable roles in processes such as transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions and spermatogenesis. Even more remarkably, they can accomplish some of these tasks individually, without the need for Cdk/cyclin complex formation or kinase activity. In this Review, we discuss the latest revelations about Cdks, cyclins and CKIs with the goal of showcasing their functional diversity beyond cell cycle regulation and their impact on development and disease in mammals.

Cdks, cyclins and CKIs: roles beyond cell cycle regulation

Various cyclin-dependent kinase (Cdk) complexes have been implicated in the regulation of transcription. In this study, we identified a 70-kDa Cyclin K (CycK) that binds Cdk12 and Cdk13 to form two different complexes (CycK/Cdk12 or CycK/Cdk13) in human cells. The CycK/Cdk12 complex regulates phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and expression of a small subset of human genes, as revealed in expression microarrays. Depletion of CycK/Cdk12 results in decreased expression of predominantly long genes with high numbers of exons. The most prominent group of down-regulated genes are the DNA damage response genes, including the critical regulators of genomic stability: BRCA1 (breast and ovarian cancer type 1 susceptibility protein 1), ATR (ataxia telangiectasia and Rad3-related), FANCI, and FANCD2. We show that CycK/Cdk12, rather than CycK/Cdk13, is necessary for their expression. Nuclear run-on assays and chromatin immunoprecipitations with RNA polymerase II on the BRCA1 and FANCI genes suggest a transcriptional defect in the absence of CycK/Cdk12. Consistent with these findings, cells without CycK/Cdk12 induce spontaneous DNA damage and are sensitive to a variety of DNA damage agents. We conclude that through regulation of expression of DNA damage response genes, CycK/Cdk12 protects cells from genomic instability. The essential role of CycK for organisms in vivo is further supported by the result that genetic inactivation of CycK in mice causes early embryonic lethality.

/pdf/the-cyclin-k-cdk12-complex-maintains-genomic-stability-via-4874j4l9lp.pdf

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

Among genetic factors implicated in autoimmunity, the autoimmune regulator (AIRE) is an important transcriptional activator that mediates central tolerance in the thymus. Loss-of-function mutations in the human Aire gene lead to the development of autoimmune polyendocrinopathy syndrome type 1 (APECED), which is manifested by the destruction of mostly endocrine glands (31). AIRE is expressed mainly in the thymus but is also present in low levels in lymph nodes, spleen, and fetal liver (16, 31). In the thymus, its expression is restricted to a subpopulation of medullary thymic epithelial cells (mTECs) (16). Indeed, mTECs express ectopically a number of tissue-restricted antigens (9, 19), which is abolished in AIRE−/− mice (4). This absence leads to a defect in negative selection of autoreactive T cells in the thymus (3, 26) and autoimmunity in the periphery, which is manifested by the infiltration of autoreactive T cells in many tissues and the expression of autoantibodies in the periphery (4, 40).

AIRE is a 55-kDa nuclear protein. It has several functional domains, such as the N-terminal homogenously staining region, a functional bipartite nuclear localization signal, a putative DNA-binding SAND (Sp100, AIRE, NucP41/75, and DEAF-1) domain (5, 10), two plant homeodomain (PHD)-type Zn2+ fingers separated by a proline-rich region, and four LXXLL nuclear receptor motifs (1, 15). When fused to a heterologous DNA-binding domain, AIRE can activate transcription in transient-expression assays (37). Because it binds preferentially to GG repeats and AT-rich sequences (24, 39), its interactions with DNA could be rather promiscuous (reviewed in references 28 and 36). The first PHD may also function as an E3 ubiquitin ligase (47). Finally, analyses of AIRE−/− mice revealed that mouse insulin 2 (Ins2), salivary protein 1 (Spt1), casein α, and several hundred other genes are regulated by AIRE (4). Interestingly, some of these genes are localized in chromosomal clusters (9, 19).

Eukaryotic transcription starts with the recruitment of RNA polymerase II (RNAPII) to start sites of transcription. This process requires DNA-bound activators, general transcription factors, chromatin remodeling machinery, and RNAPII. This recruitment leads to the formation of the preinitiation complex (PIC) (reviewed in reference 30). At this stage, transcription is initiated but further elongation is blocked by the negative transcription elongation factor (N-TEF), which contains the DRB sensitivity-inducing factor and the negative elongation factor (reviewed in reference 35). To enable efficient elongation and cotranscriptional processing of primary transcripts, positive transcription elongation factor b (P-TEFb) must be recruited to the PIC. It counteracts N-TEF and prepares RNAPII for elongation. P-TEFb is a heterodimer of a C-type cyclin (CycT1, CycT2, or CycK) and cyclin-dependent kinase 9 (Cdk9). P-TEFb phosphorylates N-TEF and the C-terminal domain of RNAPII, and this change enables RNAPII to transition from abortive to productive elongation. In cells, P-TEFb is found in two molecular complexes. In the small complex, the catalytically active P-TEFb associates with activators and RNAPII. In the catalytically inactive large complex, P-TEFb binds 7SK snRNA and hexamethylene bis-acetamide inducible protein 1 (HEXIM1) (reviewed in reference 35). Thus, HEXIM1 is a specific inhibitor of P-TEFb.

Transcriptional activators can be divided into three groups: type I (e.g., Sp1 and CTF), which stimulate initiation; type IIA (e.g., Tat from human immunodeficiency virus), which stimulate predominantly elongation; and type IIB (VP16, class II transactivator [CIITA], and NF-κB, among others), which stimulate both initiation and elongation of transcription (6). Moreover, type I and type IIA activators can synergize with one another but not with type IIB activators. Synergy occurs from concerted actions of factors stimulating two different steps in transcription: initiation and elongation (6). In this study, we wanted to determine how AIRE regulates transcription in mTECs.

AIRE recruits P-TEFb for transcriptional elongation of target genes in medullary thymic epithelial cells.

The cyclin-dependent kinases (Cdks) regulate many cellular processes, including the cell cycle, neuronal development, transcription, and posttranscriptional processing. To perform their functions, Cdks bind to specific cyclin subunits to form a functional and active cyclin/Cdk complex. This review is focused on Cyclin K, which was originally considered an alternative subunit of Cdk9, and on its newly identified partners, Cdk12 and Cdk13. We briefly summarize research devoted to each of these proteins. We also discuss the proteins' functions in the regulation of gene expression via the phosphorylation of serine 2 in the C-terminal domain of RNA polymerase II, contributions to the maintenance of genome stability, and roles in the onset of human disease and embryo development.

/pdf/cyclin-k-goes-with-cdk12-and-cdk13-2899ugg2ww.pdf

Cyclin K goes with Cdk12 and Cdk13

Innate and adaptive immunity are connected via antigen processing and presentation (APP), which results in the presentation of antigenic peptides to T cells in the complex with the major histocompatibility (MHC) determinants. MHC class II (MHC II) determinants present antigens to CD4+ T cells, which are the main regulators of the immune response. Their genes are transcribed from compact promoters that form first the MHC II enhanceosome, which contains DNA-bound activators and then the MHC II transcriptosome with the addition of the class II transactivator (CIITA). CIITA is the master regulator of MHC II transcription. It is expressed constitutively in dendritic cells (DC) and mature B cells and is inducible in most other cell types. Three isoforms of CIITA exist, depending on cell type and inducing signals. CIITA is regulated at the levels of transcription and post-translational modifications, which are still not very clear. Inappropriate immune responses are found in several diseases, including cancer and autoimmunity. Since CIITA regulates the expression of MHC II genes, it is involved directly in the regulation of the immune response. The knowledge of CIITA will facilitate the manipulation of the immune response and might contribute to the treatment of these diseases.

Expression of MHC II genes

Regulation of gene expression is essential to all aspects of physiological processes in single-cell as well as multicellular organisms. It gives ultimately cells the ability to efficiently respond to extra- and intracellular stimuli participating in cell cycle, growth, differentiation and survival. Regulation of gene expression is executed primarily at the level of transcription of specific mRNAs by RNA polymerase II (RNAPII), typically in several distinct phases. Among them, transcription elongation is positively regulated by the positive transcription elongation factor b (P-TEFb), consisting of CDK9 and cyclin T1, T2 or K. P-TEFb enables transition from abortive to productive transcription elongation by phosphorylating carboxyl-terminal domain (CTD) in RNAPII and negative transcription elongation factors. Over the years, we have learned a great deal about molecular composition of P-TEFb complexes, their assembly and their role in transcription of specific genes, but function of P-TEFb in other physiological processes was not apparent until just recently. In light of emerging discoveries connecting P-TEFb to regulation of cell cycle, development and several diseases, I would like to discuss these observations as well as future perspectives.

/pdf/p-tefb-the-final-frontier-zq94k2tyvu.pdf

Jiri Kohoutek

Papers

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

AIRE recruits P-TEFb for transcriptional elongation of target genes in medullary thymic epithelial cells.

Cyclin K goes with Cdk12 and Cdk13

Expression of MHC II genes

P-TEFb- the final frontier