Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.

DNA N6-adenine methylation (6mA) has recently been described in diverse eukaryotes, spanning unicellular organisms to metazoa. Here, we report a DNA 6mA methyltransferase complex in ciliates, termed MTA1c. It consists of two MT-A70 proteins and two homeobox-like DNA-binding proteins and specifically methylates dsDNA. Disruption of the catalytic subunit, MTA1, in the ciliate Oxytricha leads to genome-wide loss of 6mA and abolishment of the consensus ApT dimethylated motif. Mutants fail to complete the sexual cycle, which normally coincides with peak MTA1 expression. We investigate the impact of 6mA on nucleosome occupancy in vitro by reconstructing complete, full-length Oxytricha chromosomes harboring 6mA in native or ectopic positions. We show that 6mA directly disfavors nucleosomes in vitro in a local, quantitative manner, independent of DNA sequence. Furthermore, the chromatin remodeler ACF can overcome this effect. Our study identifies a diverged DNA N6-adenine methyltransferase and defines the role of 6mA in chromatin organization.

OPTN/SRTR 2022 Annual Data Report: Heart.

The number of heart transplants in the United States has continued to increase. Since 2011, pediatric heart transplants have increased 31.7% to 494 and adult heart transplants have increased 85.8% to 3,668 in 2022. The numbers of new candidates for pediatric and adult heart transplants have also increased, with 703 new pediatric candidates and 4,446 new adult candidates in 2022. Adult heart transplant rates continue to rise, peaking at 122.5 transplants per 100 patient-years in 2022; however, the pediatric heart transplant rate decreased to its lowest rate in the past decade, 104.2 transplants per 100 patient-years, a decrease of 13.9% from 121 transplants per 100 patient-years in 2011. Despite this, pretransplant mortality among pediatric candidates has decreased by 52.2%, from 20.8 deaths per 100 patient-years in 2011 to 10.0 deaths per 100 patient-years in 2022, but remains excessive for candidates younger than 1 year at 25.7 deaths per 100 patient-years. Among adult candidates, pretransplant mortality declined from 15 deaths per 100 patient-years in 2011 to 8.7 deaths per 100 patient-years in 2022. Since 2011, posttransplant mortality has been stable to slightly better; among recipients who underwent transplant in 2015-2017, the 1-, 3-, and 5-year pediatric survival rates were 93.7%, 89.2%, and 85.0%, respectively, and the adult survival rates were 91.3%, 85.7%, and 80.4%. Donor trends have been favorable, with an increase in the numbers of hearts recovered and growing numbers of hearts procured after circulatory death.

OPTN/SRTR 2022 Annual Data Report: COVID-19.

This chapter updates the COVID-19 chapter from the 2021 Annual Data Report with trends through November 12, 2022, and introduces trends in recovery and use of organs from donors with a positive COVID-19 test. Posttransplant mortality and graft failure, which remained a concern in all organs at the last report due to the Omicron variant wave, have returned to lower levels in the most recent available data through November 2022. Use of organs from donors with a positive COVID-19 test has grown, particularly after the first year of the pandemic. Mortality due to COVID-19 should continue to be monitored, but most other measures have sustained their recovery and may now be responding more to changes in policy than to ongoing concerns with COVID-19.

OPTN/SRTR 2021 Annual Data Report: COVID-19.

This chapter updates the COVID-19 chapter from the 2020 Annual Data Report with trends through February 12, 2022, and introduces trends in COVID-19-specific cause of death on the waiting list and posttransplant. Transplant rates remain at or above prepandemic levels for all organs, indicating a sustained transplantation system recovery following the initial 3-month disruption due to the onset of the pandemic. Posttransplant mortality and graft failure remain a concern in all organs, with rates surging corresponding to waves of the pandemic. Waitlist mortality due to COVID-19 is also a concern, particularly among kidney candidates. While the recovery of the transplantation system has been sustained in the second year of the pandemic, ongoing efforts should focus on reducing posttransplant and waitlist mortality due to COVID-19, and graft failure.

OPTN/SRTR 2021 Annual Data Report: Heart.

The past 5 years have posed challenges to the field of heart transplantation. The 2018 heart allocation policy revision was accompanied by anticipated practice adjustments and increased use of short-term circulatory support, changes that may ultimately serve to advance the field. The COVID-19 pandemic also had an impact on heart transplantation. While the number of heart transplants in the United States continued to increase, the number of new candidates decreased slightly during the pandemic. There were slightly more deaths following removal from the waiting list for reasons other than transplant during 2020, and a decline in transplants among candidates listed as status 1, 2, or 3 compared with the other statuses. Heart transplant rates decreased among pediatric candidates, most notably among those younger than 1 year. Despite this, pretransplant mortality has declined for both pediatric and adult candidates, particularly candidates younger than 1 year. Transplant rates have increased in adults. The prevalence of ventricular assist device use has increased among pediatric heart transplant recipients, while the prevalence of short-term mechanical circulatory support, particularly intra-aortic balloon pump and extracorporeal membrane oxygenation, has increased among adult recipients.

Stem cell donor HLA typing improves CPRA in kidney allocation.

The Organ Procurement and Transplantation Network (OPTN) Kidney Allocation System provides a priority to sensitized candidates based on the calculated panel reactive antibody (CPRA) value. The human leukocyte antigen (HLA) haplotype reference panel used for calculation of the CPRA by the United Network for Organ Sharing (UNOS), the OPTN contractor, has limitations. We derived a novel panel from the National Marrow Donor Program HLA haplotype data set and compared the accuracy of CPRA values generated with this panel (NMDP-CPRA) to those generated from the UNOS panel (UNOS-CPRA), using predicted and actual deceased donor kidney offers for a cohort of 24 282 candidates. The overall accuracy for kidney offers was similar using NMDP-CPRA and UNOS-CPRA. Accuracy was slightly higher for NMDP-CPRA than UNOS-CPRA for candidates in several highly sensitized CPRA categories, with deviations in linkage disequilibrium for Caucasians and the smaller size of the UNOS panel as contributing factors. HLA data derived from stem cell donors yields CPRA values that are comparable to those derived from deceased kidney donors while improving upon several problems with the current reference panel. Consideration should be given to using stem cell donors as the reference panel for calculation of CPRA to improve equity in kidney transplant allocation.

A change of heart: Preliminary results of the US 2018 adult heart allocation revision.

In 2018, the Organ Procurement and Transplantation Network (OPTN) modified adult heart allocation to better stratify candidates and provide broader access to the most medically urgent candidates. We analyzed OPTN data that included waiting list and transplant characteristics, geographical distribution, and early outcomes 1 year before (pre: October 18, 2017-October 17, 2018) and following (post: October 18, 2018-October 17, 2019) implementation. The number of adult heart transplants increased from 2954 pre- to 3032 postimplementation. Seventy-eight percent of transplants in the post era were for the most medically urgent (statuses 1-3) compared to 68% for status 1A in the pre era. The median distance between the donor hospital and transplant center increased from 83 to 216 nautical miles, with an increase in total ischemic time from 3 to 3.4 hours (all P < .001). Waiting list mortality was not different across eras (14.8 vs 14.9 deaths per 100 patient-years pre vs post respectively). Posttransplant patient survival was not different, 93.6% pre and 92.8% post. There is early evidence that the heart allocation policy has enhanced stratification of candidates by their medical urgency and broader distribution for the most medically urgent candidates with minimal impact on overall waiting list mortality and posttransplant outcomes.

Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms.

BACKGROUND: Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even "third generation" sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. RESULTS: We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. CONCLUSIONS: This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation.

Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development.

The ciliate Oxytricha trifallax maintains two genomes: a germline genome that is active only during sexual conjugation and a transcriptionally active, somatic genome that derives from the germline via extensive sequence reduction and rearrangement. Previously, we found that long noncoding (lnc) RNA "templates"-telomere-containing, RNA-cached copies of mature chromosomes-provide the information to program the rearrangement process. Here we used a modified RNA-seq approach to conduct the first genome-wide search for endogenous, telomere-to-telomere RNA transcripts. We find that during development, Oxytricha produces long noncoding RNA copies for over 10,000 of its 16,000 somatic chromosomes, consistent with a model in which Oxytricha transmits an RNA-cached copy of its somatic genome to the sexual progeny. Both the primary sequence and expression profile of a somatic chromosome influence the temporal distribution and abundance of individual template RNAs. This suggests that Oxytricha may undergo multiple rounds of DNA rearrangement during development. These observations implicate a complex set of thousands of long RNA molecules in the wiring and maintenance of a highly elaborate somatic genome architecture.

: a database of ciliate genome rearrangements.

Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor segments in the MIC genome rearranges to form transcriptionally active genes in the mature MAC genome, making these ciliates model organisms to study the process of somatic genome rearrangement. Similar broad scale, somatic rearrangement events occur in many eukaryotic cells and tumors. The (http://oxytricha.princeton.edu/mds_ies_db) is a database of genome recombination and rearrangement annotations, and it provides tools for visualization and comparative analysis of precursor and product genomes. The database currently contains annotations for two completely sequenced ciliate genomes: Oxytricha trifallax and Tetrahymena thermophila.

A national assessment of one-year heart outcomes after the 2018 adult heart allocation change.

PURPOSE: On 10/18/2018 the Organ Procurement and Transplantation Network (OPTN) implemented modifications to adult heart allocation to better stratify the most medically urgent candidates by WL mortality. This paper reviews two years of post-policy monitoring with focus on post-transplant outcomes, especially for recipients with MCSDs. METHODS: Cohorts of WL additions and recipients pre (10/18/16-10/17/18) and post (10/18/18-10/17/20) policy implementation were compared using the OPTN database. Competing risks analyses of waitlist mortality and Kaplan-Meier one-year post-transplant survival were performed by medical urgency statuses and policy era. Similar analyses were performed for subsets of candidates and recipients on devices. RESULTS: Pre-implementation status 1A candidates had the highest cumulative incidence of removal from the waitlist due to death or too sick to transplant and the highest cumulative incidence of transplant, followed by statuses 1B and 2. Median time to transplant decreased from 226 to 85 days for those transplanted. There was no difference in one-year patient survival (pre=91.3% [90.2, 92.4]; post=91.8% [90.8, 92.9]; p=0.44) overall, or for recipients transplanted with an LVAD (pre=91.7% [90.1, 93.2]; post=91.4% [89.7, 93.2]; p=0.85) or IABP (pre=91.7% [88.1, 95.4]; post=92.1% [90.1, 94.0]; p=0.92). CONCLUSION: The policy improved stratification of the most medically urgent candidates according to risk of death on the WL with decreased median wait times, higher transplant rates and no observed adverse effect on 1-year patient survival. No adverse effects for candidates listed or transplanted on IABP, ECMO, or LVAD were observed.

HLA Homozygosity and Likelihood of Sensitization in Kidney Transplant Candidates.

Background: Homozygosity for HLAs has been associated with adverse outcomes after viral infection as well as pregnancy-induced HLA sensitization. We sought to assess the relationship between HLA locus homozygosity and the level of HLA antibody sensitization. Methods: We measured sensitization using the calculated panel reactive antibody value for a large cohort of 147 461 patients added to the US OPTN/United Network for Organ Sharing kidney transplant waitlist between December 2014 and December 2019. We used multinomial logistic modeling to compare 62 510 sensitized patients to 84 955 unsensitized controls. Results: We found that the number of homozygous HLA loci was strongly associated with the level of sensitization. Within mildly, highly, or extremely sensitized candidates, women displayed a higher relative abundance of HLA homozygosity at multiple HLA loci as compared with men, with attenuation of this effect in Black candidates. In a multivariable logistic model, the number of homozygous HLA loci interacted with female sex but not with other factors associated with sensitization, including recipient ethnicity and a history of prior kidney transplant. Conclusions: This study shows that HLA homozygosity is an innate genetic factor that affects the likelihood of HLA sensitization. Further research is needed to identify the immunologic mechanisms that underlie this observation.

The International Thoracic Organ Transplant Registry of the International Society for Heart and Lung Transplantation: Thirty-eighth adult lung transplantation report - 2021; Focus on recipient characteristics.

For over 30 years, the International Society for Heart and Lung Transplantation (ISHLT) International Thoracic Organ Transplant (TTX) Registry has gathered data regarding transplant procedures, donor and recipient characteristics, and outcomes from a global community of transplant centers. Almost 70,000 adult lung transplant procedures have been reported to the Registry since its inception, each one providing an opportunity for a recipient with end-stage lung disease to regain quality of life and longevity. With each year's report, we provide more detailed analyses on a particular focus theme important to recipient outcomes. Since 2013, these have been donor and recipient age; retransplantation; early graft failure; indication for transplant; allograft ischemic time; multiorgan transplantation; and donor and recipient size matching.1-7 In response to a changing regulatory environment, the ISHLT TTX Registry is undergoing an update in data acquisition, and the patient cohort examined in this report is therefore derived from the same data source or datasets as that examined in the 2019 annual reports.2,8-10 We refer the reader to the 2019 and prior reports for a detailed description of the baseline characteristics of the cohort, and additional core analyses not directly related to the focus explored in this year's report. To complement the 2020 report which focussed on donor characteristics, the goal of this year's report was to focus entirely on changes in recipient factors over the past 3 decades and to identify important recipient characteristics and transplant processes that may influence post-transplant outcomes. Due to small numbers, heart-lung transplant recipient characteristics and transplant outcomes have not been included. This 38th annual adult lung transplant report is hence based on data submitted to the ISHLT TTX Registry on 67,493 adult recipients of deceased recipient transplants between January 1, 1992 and June 30, 2018.

Cocaine use in organ donors and long-term outcome after heart transplantation: An International Society for Heart and Lung Transplantation registry analysis.

BACKGROUND: Cardiac allografts from donors with a history of cocaine use (DHCU) are often discarded owing to concerns regarding organ quality. We investigated long-term outcomes of de novo adult heart transplantation (HTx) using DHCU. METHODS: Using the International Society for Heart and Lung Transplantation Thoracic Organ Transplant Registry, we identified 24,430 adult recipients of primary, deceased donor, heart-alone transplants between January 1, 2000, and June 30, 2013. Transplants were categorized on the basis of DHCU. Survival rates were compared using Kaplan-Meier curves and log-rank tests. RESULTS: A total of 3,246 (13.3%) HTx were performed using DHCU during the study period. Of these, 1,477 (45.5%) were classified as current users. Organs from DHCU were transplanted at a later sequence number (data from a sub-group of patients transplanted in the United States) than those from the non-cocaine use group (mean sequence number 16.1 ± 55.6 vs 11.5 ± 38.2; p < 0.001), suggesting higher decline rates by centers. Kaplan-Meier estimates of survival were not different between groups (p = 0.16), with post-transplant survival rates at 1, 5, and 10 years of 88.1%, 75.8%, and 58.5%, respectively, in the non-cocaine use group and 90.0%, 76.7%, and 59.7%, respectively, in the DHCU group. On multivariate analysis, DHCU were not associated with mortality (hazard ratio [HR]: 0.94; 95% CI: 0.88-1.00; p = 0.050), cardiac allograft vasculopathy (HR: 1.02; 95% CI: 0.94-1.11; p = 0.56), or allograft rejection (HR: 0.98; 95% CI: 0.92-1.05; p = 0.61). CONCLUSIONS: Our findings demonstrate that adult HTx performed using DHCU is not associated with an adverse impact on long-term clinical outcomes. These findings should spur efforts to reduce discard rates of organs from DHCU.

A simple electronic tool for assessing amino acid sequence polymorphisms within exon-2 of HLA-DPB1 alleles.

In November 2014, the OPTN/UNOS Board of Directors mandated that HLA-DPB1 typing be performed for all deceased donors. Currently, there are over 1,000 known HLA DPB1 alleles, yet fewer than 30 are represented on commonly used single antigen bead (SAB) solid phase antibody assays. Moreover, the official World Health Organization (WHO) nomenclature for the DPB1 locus does not permit assessment of structural relationships between alleles based on their names. Thus, for donor DPB1 alleles lacking a corresponding SAB, determining the compatibility between a donor-recipient pair when the recipient possesses DPB1 antibodies currently requires the use of manual sequence alignments. Multiple studies have reported that DPB1 alleles can be classified into serological-defined categories based on shared protein sequence motifs residing in distinct hypervariable regions. To date, six such motifs have been recognized. To address this problem, we developed a computer-assisted tool to compare donor and recipient DPB1 allele sequences, specifically those defined by DPB1 hypervariable region motifs located in exon 2 (http://dpreport.hlatools.org). This tool quickly identifies mismatched DPB1 motifs, and easily permits the identification of motif-based donor-specific antibodies (DSA) to DPB1.