It is not yet known whether DNA methylation levels can be used to accurately predict age across a broad spectrum of human tissues and cell types, nor whether the resulting age prediction is a biologically meaningful measure. I developed a multi-tissue predictor of age that allows one to estimate the DNA methylation age of most tissues and cell types. The predictor, which is freely available, was developed using 8,000 samples from 82 Illumina DNA methylation array datasets, encompassing 51 healthy tissues and cell types. I found that DNA methylation age has the following properties: first, it is close to zero for embryonic and induced pluripotent stem cells; second, it correlates with cell passage number; third, it gives rise to a highly heritable measure of age acceleration; and, fourth, it is applicable to chimpanzee tissues. Analysis of 6,000 cancer samples from 32 datasets showed that all of the considered 20 cancer types exhibit significant age acceleration, with an average of 36 years. Low age-acceleration of cancer tissue is associated with a high number of somatic mutations and TP53 mutations, while mutations in steroid receptors greatly accelerate DNA methylation age in breast cancer. Finally, I characterize the 353 CpG sites that together form an aging clock in terms of chromatin states and tissue variance. I propose that DNA methylation age measures the cumulative effect of an epigenetic maintenance system. This novel epigenetic clock can be used to address a host of questions in developmental biology, cancer and aging research.

/pdf/dna-methylation-age-of-human-tissues-and-cell-types-528gzlrlkl.pdf

DNA methylation age of human tissues and cell types

AACR Centennial Conference: Translational Cancer Medicine-- Nov 4-8, 2007; Singapore

PL02-05 

All cancers are due to abnormalities in DNA. The availability of the human genome sequence has led to the proposal that resequencing of cancer genomes will reveal the full complement of somatic mutations and hence all the cancer genes. To explore the nature of the information that will be derived from cancer genome sequencing we have sequenced the coding exons of the family of 518 protein kinases, ~1.3Mb DNA per cancer sample, in 210 cancers of diverse histological types. Despite the screen being directed toward the coding regions of a gene family that has previously been strongly implicated in oncogenesis, the results indicate that the majority of somatic mutations detected are “passengers”. There is considerable variation in the number and pattern of these mutations between individual cancers, indicating substantial diversity of processes of molecular evolution between cancers. The imprints of exogenous mutagenic exposures, mutagenic treatment regimes and DNA repair defects can all be seen in the distinctive mutational signatures of individual cancers. This systematic mutation screen and others have previously yielded a number of cancer genes that are frequently mutated in one or more cancer types and which are now anticancer drug targets (for example BRAF , PIK3CA , and EGFR ). However, detailed analyses of the data from our screen additionally suggest that there exist a large number of additional “driver” mutations which are distributed across a substantial number of genes. It therefore appears that cells may be able to utilise mutations in a large repertoire of potential cancer genes to acquire the neoplastic phenotype. However, many of these genes are employed only infrequently. These findings may have implications for future anticancer drug development.

Patterns of Somatic Mutation in Human Cancer Genomes

WHO laboratory manual for the examination and processing of human semen

Numerous reports have recently focused on various aspects of adverse trends in male reproductive health, such as the rising incidence of testicular cancer; low and probably declining semen quality; high and possibly increasing frequencies of undescended testis and hypospadias; and an apparently growing demand for assisted reproduction. Due to specialization in medicine and different ages at presentation of symptoms, reproductive problems used to be analysed separately by various professional groups, e.g. paediatric endocrinologists, urologists, andrologists and oncologists. This article summarizes existing evidence supporting a new concept that poor semen quality, testis cancer, undescended testis and hypospadias are symptoms of one underlying entity, the testicular dysgenesis syndrome (TDS), which may be increasingly common due to adverse environmental influences. Experimental and epidemiological studies suggest that TDS is a result of disruption of embryonal programming and gonadal development during fetal life. Therefore, we recommend that future epidemiological studies on trends in male reproductive health should not focus on one symptom only, but be more comprehensive and take all aspects of TDS into account. Otherwise, important biological information may be lost.

Testicular dysgenesis syndrome ; an increasingly common developmental disorder with environmental aspects

Human mitochondrial DNA is widely used as tool in many fields including evolutionary anthropology and population history, medical genetics, genetic genealogy, and forensic science. Many applications require detailed knowledge about the phylogenetic relationship of mtDNA variants. Although the phylogenetic resolution of global human mtDNA diversity has greatly improved as a result of increasing sequencing efforts of complete mtDNA genomes, an updated overall mtDNA tree is currently not available. In order to facilitate a better use of known mtDNA variation, we have constructed an updated comprehensive phylogeny of global human mtDNA variation, based on both coding- and control region mutations. This complete mtDNA tree includes previously published as well as newly identified haplogroups, is easily navigable, will be continuously and regularly updated in the future, and is online available at http://www.phylotree.org. © 2008 Wiley-Liss, Inc.

/pdf/updated-comprehensive-phylogenetic-tree-of-global-human-448qrnrzdo.pdf

Updated Comprehensive Phylogenetic Tree of Global Human Mitochondrial DNA Variation

In memoriam: Paolo Sassone-Corsi.

Infertility affects around 15% of couples globally with half of the cases due to a male factor. Despite this high incidence, the molecular and cellular mechanisms regulating (dys)function of human spermatogenesis remain poorly understood leading to just 30% of the infertile men receiving a causal diagnosis. The remaining 70% receive collectively descriptivediagnoseslargelybasedontheirsemenandhormoneanaly-ses. One example are men diagnosed with cryptozoospermia (Crypto). A common feature of these patients is that spermatozoa can only be foundinthesedimentofsemenaftercentrifugation,butthesepatients are otherwise extremely heterogeneous with regard to hormonal and histological parameters. To assess if there are sub-groups among the cryptozoospermicpatientcohort,weperformedclusteranalysisbased on semen, histological, and endocrine parameters of 132 Crypto and 160Controlpatients(obstructiveazoospermia).Interestingly,theclus-tering resulted in two Crypto groups largely based on their testicular architecture. In group 1, most seminiferous tubules contained sperma-tocytes as the most advanced germ cell type. In contrast, the prevalent tubular phenotypes in group 2 were Sertoli cell only (SCO) tubules and tubular shadows. We therefore termed group 1 meiotic arrest-like (MAL) and group 2 SCO-like (SCOL) Crypto. It is of note though, that about 10% of the seminiferous tubules still displayed full spermatogenesis in both groups, which is in accordance with the presence of sperm in the ejaculate and with similar sperm retrieval rates after testicularsurgeryinbothgroups.Toidentifypotentiallydistinctmolec-ular and cellular alterations between the two groups we performed single cell RNA sequencing (scRNA-seq) on four controls, two MAL and six SCOL Crypto samples, followed by histological analyses (13 samples per group). Interestingly, we identified shared alterations on the spermatogonial stem cell (SSC) compartment ABSTRACT their active ligands could be essential to chemical sperm-oocyte com-munication and their alteration could represent a cause of human infertility.AmongORs,OR51E2isexpressedontheextracellularmem-brane of the flagella, mid-piece and, with less extent, on the acrosomal cap of spermatozoa. OR51E2 has been demonstrated to bind volatile short-chain fatty acids (SCFAs) as specific ligands. SCFAs, such as propionate (PA) and acetate (AA), metabolic byproducts of anaer-obic bacterial fermentation, could be the key players in a complex interplay between microbiota and human reproduction, through spermatozoa chemotaxis. Spermatozoa chemotaxis is mostly dependent on intracellular calcium release and ERK phosphorylation (pERK). ORs seem to be among the involved receptors activating this signaling pathway. In our study, immunofluorescence analysis revealed that OR51E2 is present in the midpiece and neck of non-treated sperm cells. After an exposition of 5 mM of PA for 10 minutes, we found an enrich-ment of OR staining in the acrosomal compartments, that reached an average of 40% indicating that propionate is able to mediate OR51E2 acrosomal relocalization. pERK accumulation and calcium influx in a dose and time-dependent manner was found. This suggests that this ligand-receptor binding could be involved in the sperm migratory response. To address if propionate-mediated sperm activation depends on the bindingtoOR51E2,seminalfluidwaspretreatedwiththespecificanti-body against OR51E2. The pERK increase was impaired in the seminal fluid pre-incubated with α -OR51E2 antibody. We wondered if the PA dependent sperm activation through OR51E2 acrosomal clusterization could be involved in sperm chemotaxis. To address this question, a modified direct swim-up assay was performed. and AA or not the seminal and methods: Our cohort consists of 840 unselected, non-vasectomized, azoospermic men consecutively collected during 25 years (1997-2022) in the Western of Denmark. At least two ejac-ulates without sperm in raw as well as in the pellet after centrifugation, required have the diagnosis: azoospermia. Our routine examination program included history taking, physical examination including genital examination and ultrasonography and blood sampling. Hormone analyses included follicular stimulating hormone (FSH), luteinizing hormone (LH), testosterone, prolactin and thyroid stimulating hormone (TSH), inhibin-B, and anti-Müllerian hormone (AMH). ABSTRACT Results: Sertoli and germ cell impairment is not hormonally detected before Tanner stage 4, as reflected by normal inhibin B values until stage 3 and the fall in the inhibin B/FSH ratio during Tanner stage 4; the testosterone/LH ratio peaks during Tanner stage 3 and drops significantly in stage 5( p < 0.001), when Leydig cell deterioration begins. Impaired testosterone secretion is not an evident feature of KS boys during puberty, as reflected by the normal onset and progression of puberty observed in our KS cohort. The testicular echotexture reflects this progressive hormonal dysfunction, as it worsens during the transition age. FSH and LH have a primary role in testicular echotexture changes and chronic LH stimulation exacerbates these changes, causing the onset of Leydig cell micronodules. In childhood, testicularvolumeincreasesuptoanaveragebilateraltesticularvolume of 7.7 ml (IQR 5.3-10.6) in Tanner stage 4, with subsequent degeneration and atrophy leading to an average adult volume of 4.6 ml (IQR 3.3-6.5). Conclusions: Thefindingsfromthislargeprospectivestudyofasizable patientpopulationcontributetoourunderstandingoftheonsetoftes-ticular dysfunction in KS, underlining the importance of testicular US in infancy and childhood, as well as in puberty and adolescents, for the optimal care of KS patients. ABSTRACT Methods: A prospective, cross-sectional, observational study was carried out. CHH patients were subdivided into 2 subgroups according to the timing of treatment start (testosterone replacement therapy [TRT] or gonadotropins): CHH1) CHH patients who started treatment late after 18 years; CHH2) CHH patients who started treatment on time before 18. All KS patients did not start TRT before 18 since KS do not usually delay puberty. The following anthropometric measurements werecollectedbyusingadigitalscaleandstadiometer(Secagmbh&co): height, weight, sitting height, total arm span. Legs length was obtained by subtracting sitting height from stature; U/L was calculated dividing sitting height for legs length. Results: A total of 70 CHH and 45 KS age-matched patients were enrolled (mean age 33.7 ± 13.7 and 35.3 ± 13.7 years, respectively). CHH1 showed a longer arm span compared to CHH2( p = 0.001) and KS ( p = 0.003), and a shorter sitting height compared to KS ( p = 0.008). On the contrary, leg’s length was shorter in CHH2 compared to CHH1( p < 0.001) and KS ( p = 0.011). Accordingly, U/L and upper-to-height ratios were lower in CHH1 compared to CHH2( p < 0.001) and KS ( p = 0.001). Furthermore, the arm span-to-heightratiowashigherinCHH1comparedtoCHH2( p < 0.001)andKS ( p = 0.008). Conclusions: Under the same definition of eunuchoid body proportions, the traditional hallmark of male hypogonadism, more fine differences are observed comparing adult CHH to KS patients. CHH patients who delayed treatment showed longer arms length and lower U/L in comparison to CHH patients receiving treatment on time at pubertal age and KS. This suggests a different mechanism involved in the eunuchoid skeleton development between CHH and KS con-firming a major role for estrogen/androgen deficiency in the former (leading to disproportional growth of both legs and arms due to delay in epiphyseal closure that could benefit from on time replacement treatment) and a possible role of genetic supernumerary X in the lat-ter, displaying a disproportional growth only at the legs site since infancy. ABSTRACT a significant risk of infertility. However, there is currently no robust method for assessing the quality of collected testicular tissue, which could lead to be better patient selection for fertility preservation pro-grams. The goal of this study was to develop an in vitro approach for assessing the quality of prepubertal testicular tissue using somatic cell functionality. Testicular samples were collected from 64 prepubertal patients (aged 0.8 to 15.7 years) and separated into four study groups: non-treated, chemotherapy with or without alkylating drugs, and sickle cell disease (SCD) patients treated with hydroxyurea. In air-liquid interface culture conditions, testicular tissue samples were cultured for 21 days. Following tissue culture, in vitro testosterone released by Leydig cells, as well as anti-Müllerian hormone (AMH) and inhibin B secreted by Sertoli cells, were measured by ELISA in media collected after 7, 14, and 21 days. Preliminary results were based on 18 patient samples (1.6 to 13.1 years of age). AMH production was significantly diminished in SCD samples compared with testicular samples not exposed to chemotherapy. When compared to non-treated samples, samples exposed to alkylating agents had a declining production of AMH after 21 days. Testosterone secretion was comparable in non-treated and treated (with or without alkylating agents) testicular samples, but it was reduced in SCD samples over culture when compared to samples from the other three study groups. Compared to non-treated samples, inhibin B secretion was reduced in SCD and chemotherapy-treated samples. Altogether, we propose that in vitro secretion of AMH, inhibin B and testosterone in explant tissue cultures, combined with germ cell counts at the time of biopsy which have been described in previous studies, could be used as a quality indicator for testicular tissue taken for fertility preservation. OC12 Infertile men with unknown etiology show alterations in the abundance of specific protamine proteoforms related to sperm chromatin packaging and age ABSTRACT Some of the cancer treatments and genetic syndromes, such as Klinefelter Syndr

Oral Communications

Associazione tra varicocele, eiaculazione precoce e sintomi di prostatite: possibili meccanismi

D. T. Carrell, M. Simoni, C. Krausz and G. L. Gerton Departments of Surgery (Urology) and Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA, Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy, Sexual Medicine and Andrology Unit, Department of Clinical and Experimental Biosciences ‘Mario Serio’, University of Florence, Florence, Italy, and Department of Obstetrics and Gynecology, Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

https://onlinelibrary.wiley.com/doi/pdf/10.1111/andr.12708

Advancing the cause of improved male reproductive health.

Assisted reproductive technologies are common, and successful, therapies to treat infertility. However, challenges in improving the success of assisted reproductive technology, broadening the availability and applicability of the technologies, and minimizing complications and risks continue to confront the field. The science of genetics, including epigenetics and affiliated branches, is undergoing an explosion in the development of new technologies and knowledge. These advances can and will improve and alter the practice of assisted reproductive technology.

Symposium: Genetic and epigenetic aspects of assisted reproductive technologies Introduction: Application of genetic advances to assisted reproduction technologies

Csilla Krausz

Papers

In memoriam: Paolo Sassone-Corsi.

Oral Communications

Associazione tra varicocele, eiaculazione precoce e sintomi di prostatite: possibili meccanismi

Advancing the cause of improved male reproductive health.

Symposium: Genetic and epigenetic aspects of assisted reproductive technologies Introduction: Application of genetic advances to assisted reproduction technologies