DNA mismatch and damage patterns revealed by single-molecule sequencing.

Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other diseases1,2. Most mutations begin as nucleotide mismatches or damage in one of the two strands of the DNA before becoming double-strand mutations if unrepaired or misrepaired3,4. However, current DNA-sequencing technologies cannot accurately resolve these initial single-strand events. Here we develop a single-molecule, long-read sequencing method (Hairpin Duplex Enhanced Fidelity sequencing (HiDEF-seq)) that achieves single-molecule fidelity for base substitutions when present in either one or both DNA strands. HiDEF-seq also detects cytosine deamination-a common type of DNA damage-with single-molecule fidelity. We profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes, and derive from them single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumours deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples that are deficient in only polymerase proofreading. We also define a single-strand damage signature for APOBEC3A. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. As double-strand DNA mutations are only the end point of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable studies of how mutations arise in a variety of contexts, especially in cancer and ageing.

Effects of virtual reality erotica on ejaculate quality of sperm donors: a balanced and randomized controlled cross-over within-subjects trial.

BACKGROUND: Previous research has shown that the type and duration of erotic material that men have access to during masturbation can influence semen parameters. To our knowledge, the use of virtual reality (VR) headsets to present erotica has not previously been studied. We reasoned that, because VR can provide a more immersive experience to the user, semen parameters of masturbatory ejaculates may be altered. METHODS: This study had a balanced and randomized controlled cross-over within-subjects design. 504 ejaculates were collected from 63 sperm donors at 4 locations in Denmark. During masturbation each donor was instructed to observe erotic material either on a touch screen monitor or using a VR headset. The order of each pair of within-subject treatments was randomized by the throw of a dice. Anonymized data were analysed with linear mixed and piecewise structural equation models. RESULTS: Both abstinence period and VR-use influenced the total number of motile spermatozoa ejaculated. For short abstinence periods, VR-use increased the number of motile sperm in the ejaculate. However, the difference between VR and non-VR ejaculates decreased as abstinence period increased such that there was no difference at the mean abstinence period of 58 h. For longer abstinence periods, total motile sperm counts were lower, on average, when men used VR compared to those that did not. CONCLUSION: The use of VR headsets to view erotica had a strong positive effect on the number of motile sperm in an ejaculate when the donor's abstinence time was short (< 24 h). VR-use could improve the ejaculate quality of men who are asked to provide samples after a short period of abstinence, such as men in infertile partnerships producing samples for ART or cancer patients depositing sperm before treatment. TRIAL REGISTRATION: Trial retrospectively registered on 13 July 2022 at ClinicalTrials.gov. Identifier: NCT05457764.

Investigation of motivations for depositing sperm during the COVID-19 pandemic.

People are becoming parents later in life and with increased parental age adverse reproductive outcomes are increased. Cryopreservation of gametes enables men and women to protect, prolong and seemingly preserve their fertility. Social freezing is an increasingly popular way of cryopreservation. During the COVID-19 pandemic, the gamete bank Cryos International experienced an increased influx of men wanting to deposit their sperm. A questionnaire-based study was initiated to investigate their motivations for doing so. The results showed that the men chose to deposit mainly due to medical indications (e.g. cancer and sex change), and that the COVID-19 pandemic had no significant influence on the reason for banking their sperm. Investigations into the altruistic reasons for depositing sperm (i.e. caring for reproductive masculinity) could shed new light onto the sparsely studied topic of male reproductive journeys.

Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing.

Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other genetic diseases1-4. Almost all of these mosaic mutations begin as nucleotide mismatches or damage in only one of the two strands of the DNA prior to becoming double-strand mutations if unrepaired or misrepaired5. However, current DNA sequencing technologies cannot resolve these initial single-strand events. Here, we developed a single-molecule, long-read sequencing method that achieves single-molecule fidelity for single-base substitutions when present in either one or both strands of the DNA. It also detects single-strand cytosine deamination events, a common type of DNA damage. We profiled 110 samples from diverse tissues, including from individuals with cancer-predisposition syndromes, and define the first single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumors deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples deficient in only polymerase proofreading. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. Since the double-strand DNA mutations interrogated by prior studies are only the endpoint of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable new studies of how mutations arise in a variety of contexts, especially in cancer and aging.