Progressive Loss of Function in a Limb Enhancer during Snake Evolution.

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.

The little skate genome and the evolutionary emergence of wing-like fins.

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

Pathogenic Aß production by heterozygous PSEN1 mutations is intrinsic to the mutant protein and not mediated by conformational hindrance of wild-type PSEN1.

Presenilin-1 (PSEN1) is the catalytic subunit of the intramembrane protease γ-secretase and undergoes endoproteolysis during its maturation. Heterozygous mutations in the PSEN1 gene cause early-onset familial Alzheimer's disease (eFAD) and increase the proportion of longer aggregation-prone amyloid-ß peptides (Aß42 and/or Aß43). Previous studies had suggested that PSEN1 mutants might act in a dominant-negative fashion by functional impediment of wild-type PSEN1, but the exact mechanism by which PSEN1 mutants promote pathogenic Aß production remains controversial. Using dual recombinase-mediated cassette exchange (dRMCE), here we generated a panel of isogenic embryonic and neural stem cell lines with heterozygous, endogenous expression of PSEN1 mutations. When catalytically inactive PSEN1 was expressed alongside the wild-type protein, we found the mutant accumulated as a full-length protein, indicating that endoproteolytic cleavage occurred strictly as an intramolecular event. Heterozygous expression of eFAD-causing PSEN1 mutants increased the Aß42/Aß40 ratio. In contrast, catalytically inactive PSEN1 mutants were still incorporated into the γ-secretase complex but failed to change the Aß42/Aß40 ratio. Finally, interaction and enzyme activity assays demonstrated the binding of mutant PSEN1 to other γ-secretase subunits, but no interaction between mutant and wild-type PSEN1 was observed. These results establish that pathogenic Aß production is an intrinsic property of PSEN1 mutants and strongly argue against a dominant-negative effect in which PSEN1 mutants would compromise the catalytic activity of wild-type PSEN1 through conformational effects.

The cellular landscape of the endochondral bone during the transition to extrauterine life.

The cellular complexity of the endochondral bone underlies its essential and pleiotropic roles during organismal life. While the adult bone has received significant attention, we still lack a deep understanding of the perinatal bone cellulome. Here, we have profiled the full composition of the murine endochondral bone at the single-cell level during the transition from fetal to newborn life and in comparison with the adult tissue, with particular emphasis on the mesenchymal compartment. The perinatal bone contains different fibroblastic clusters with blastema-like characteristics in organizing and supporting skeletogenesis, angiogenesis and hematopoiesis. Our data also suggest dynamic inter- and intra-compartment interactions, as well as a bone marrow milieu that seems prone to anti-inflammation, which we hypothesize is necessary to ensure the proper program of lymphopoiesis and the establishment of central and peripheral tolerance in early life. Our study provides an integrative roadmap for the future design of genetic and cellular functional assays to validate cellular interactions and lineage relationships within the perinatal bone.

Enhancer redundancy provides phenotypic robustness in mammalian development.

Distant-acting tissue-specific enhancers, which regulate gene expression, vastly outnumber protein-coding genes in mammalian genomes, but the functional importance of this regulatory complexity remains unclear. Here we show that the pervasive presence of multiple enhancers with similar activities near the same gene confers phenotypic robustness to loss-of-function mutations in individual enhancers. We used genome editing to create 23 mouse deletion lines and inter-crosses, including both single and combinatorial enhancer deletions at seven distinct loci required for limb development. Unexpectedly, none of the ten deletions of individual enhancers caused noticeable changes in limb morphology. By contrast, the removal of pairs of limb enhancers near the same gene resulted in discernible phenotypes, indicating that enhancers function redundantly in establishing normal morphology. In a genetic background sensitized by reduced baseline expression of the target gene, even single enhancer deletions caused limb abnormalities, suggesting that functional redundancy is conferred by additive effects of enhancers on gene expression levels. A genome-wide analysis integrating epigenomic and transcriptomic data from 29 developmental mouse tissues revealed that mammalian genes are very commonly associated with multiple enhancers that have similar spatiotemporal activity. Systematic exploration of three representative developmental structures (limb, brain and heart) uncovered more than one thousand cases in which five or more enhancers with redundant activity patterns were found near the same gene. Together, our data indicate that enhancer redundancy is a remarkably widespread feature of mammalian genomes that provides an effective regulatory buffer to prevent deleterious phenotypic consequences upon the loss of individual enhancers.

The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits.

One of the central problems of vertebrate evolution is understanding the relationship among the distal portions of fins and limbs. Lacking comparable morphological markers of these regions in fish and tetrapods, these relationships have remained uncertain for the past century and a half. Here we show that Gli3 functions in controlling the proliferative expansion of distal progenitors are shared among dorsal and paired fins as well as tetrapod limbs. Mutant knockout gli3 fins in medaka (Oryzias latipes) form multiple radials and rays, in a pattern reminiscent of the polydactyly observed in Gli3-null mutant mice. In limbs, Gli3 controls both anterior-posterior patterning and cell proliferation, two processes that can be genetically uncoupled. In situ hybridization, quantification of proliferation markers, and analysis of regulatory regions reveal that in paired and dorsal fins, gli3 plays a main role in controlling proliferation but not in patterning. Moreover, gli3 down-regulation in shh mutant fins rescues fin loss in a manner similar to how Gli3 deficiency restores digits in the limbs of Shh mutant mouse embryos. We hypothesize that the Gli3/Shh gene pathway preceded the origin of paired appendages and was originally involved in modulating cell proliferation. Accordingly, the distal regions of dorsal fins, paired fins, and limbs retain a deep regulatory and functional homology that predates the origin of paired appendages.

Rapid or Immediate ART, HIV Stigma, Medical Mistrust, and Retention in Care: An Exploratory Mixed Methods Pilot Study.

Rapid or immediate antiretroviral therapy (iART) after HIV diagnosis improves linkage to care and time to viral suppression. However, iART may affect or be affected by HIV-related stigma and medical mistrust. In this mixed-methods pilot study, we examined the bi-directional role of HIV stigma, medical mistrust, and visit adherence (VA) in the context of iART in a diverse, newly diagnosed patient population. Participants were recruited from an HIV clinic in New York City and we utilized a convergent parallel design integrating quantitative data from demographic surveys, the HIV Stigma Survey (HIVSS), the Medical Mistrust Index (MMI) and electronic medical records, and qualitative data from in-depth interviews. Among the sample (N = 30), 26% (N = 8) initiated ART same-day or within 3 days, while the majority (N = 17) initiated between 4 and 30 days, and 17% (N = 5) initiated ART > 30 days. The median (range) age was 35, and most were English-speaking, Black or Hispanic men and identified as gay. Time to ART initiation was associated with time to linkage to care and time to viral suppression. Day 0-3 group's major theme was iART as stigma prevention, and they had the highest mean HIVSS, lowest MMI score, and a visit adherence of 0.86. Day 4-30 group's major theme was alleviation of internalized stigma, and they had the lowest mean HIVSS score, and highest visit adherence of 0.91. Day > 30 group's major theme was exacerbation of perceived or anticipated stigma, had the highest MMI score and a visit adherence of 0.85. iART implementation requires equitable strategies that address HIV-stigma and mistrust.

Transgender Women's Experiences Using SMARTtest, a Smartphone Application to Facilitate Self- and Partner-HIV/Syphilis Testing Using the INSTI Multiplex.

We present experiences of transgender women (TW) who have sex with men with SMARTtest, a smartphone app to accompany the INSTI Multiplex®, a one-minute, dual blood-based HIV/syphilis rapid test. TW participants (N = 11) received 10 INSTI Multiplex® tests to take home for self- and/or partner-testing and installed the SMARTtest app on their phones. The SMARTtest app aimed to support INSTI Multiplex users in correctly performing the test, interpreting the results, and connecting with care following a positive HIV or syphilis screening. After 3 months, users completed in-depth interviews on their experiences. A total of 9 TW used SMARTtest with partners. App feedback was positive, but refining is necessary. Specifically, TW reported that SMARTtest is easy to use and convenient; instructions on how to use the INSTI Multiplex presented on the app were helpful to complete procedures correctly; the most frequently used feature on SMARTtest was the information on clinics that offered confirmatory testing; and participants and their partners were not concerned about app privacy but reported that this could change if INSTI Multiplex detected an HIV-positive result. Further, participants provided recommendations on how to improve SMARTtest, and changes were mostly related to features, content, functionality, navigation, and overall "look" of the app. SMARTtest is promising to facilitate INSTI Multiplex® use in TW. User feedback should be integrated in future versions.

Infrequent STI Testing in New York City Among High Risk Sexual and Gender Minority Individuals Interested In Self- and Partner-Testing.

Testing for sexually transmitted infections (STIs) remains low among sexual and gender minority populations. We assessed STI testing history using a retrospective survey among 129 HIV-negative cisgender men who have sex with men (cMSM) and transgender women who have sex with men (tWSM) who were at high risk for STI acquisition. All participants were enrolled in a parent study on self- and partner-testing for HIV and syphilis, and reported condomless anal intercourse with multiple partners during the prior 3 months. We additionally used bivariate tests to evaluate participants' STI testing by their history of using pre-exposure prophylaxis (PrEP). One-in-seven respondents (n = 18) reported having never tested for an STI, one-quarter (n = 33) had not tested in the past year, and two-thirds (n = 83) had never used PrEP. PrEP-naïve respondents were less likely to report recent STI testing (47% vs. 85%). "Routine doctor's visit" was the most prevalent reason for testing, but was less common among PrEP-naïve respondents (83% vs. 100%). Testing was remarkably low given the sample's high risk of HIV and STI infection. Findings suggest that STI testing is more frequent among those who have ever used PrEP, but the risk of selection bias warrants evaluation in a larger probability sample.

Experiences of Transgender Women Who Used a Dual HIV/Syphilis Rapid Self-test to Screen Themselves and Potential Sexual Partners (the SMARTtest Study).

HIV/syphilis self- and partner-testing may be especially appropriate for transgender women, since they shoulder a disproportionate burden of HIV, other STIs (e.g., syphilis), and report high levels of medical mistrust. The SMARTest study enrolled N = 50 sexual and gender minority individuals. The present analysis aims to understand the experiences (via in-depth interviews) of a subset of n = 11 transgender women who used INSTI Multiplex®, a combination HIV/syphilis rapid self-test, on themselves and potential sex partners. Participants reported that many partners were willing to test, and reported no testing-related violence. Most participants completed tests successfully, though gaining comfort with blood collection took time. There were no HIV-positive tests in this study; one participant and two partners reported a positive syphilis screening. All sought care. Our sample was small and results should be interpreted with caution, but indicate potential future directions for conducting research on self- and partner-testing among transgender women.

Negotiating Use of a Blood-Based, Dual HIV and Syphilis Test with Potential Sexual Partners Among a Sample of Cisgender Men and Transgender Women Who Have Sex with Men in New York City.

Cisgender men who have sex with men (cMSM) and transgender women (TGW) are disproportionally burdened by HIV. Among these populations, HIV partner-testing is a highly acceptable harm reduction tool. Particularly, cMSM and TGW report a stronger preference for blood-based tests that include assays for multiple STIs. However, no existing research has explored how these populations negotiate blood-based testing with sexual partners. In the SMARTtest study, 48 sexually active cMSM and TGW took home dual, blood-based HIV/Syphilis kits for self- and partner-testing. After 3 months, they completed a follow-up assessment and in-depth interviews about their experiences initiating testing. Of the 42 responding participants, 27 (64%) reported that it had been "fairly" or "very easy" to raise the idea of testing with partners. Participants predominantly employed partner-conscious communication strategies, including framing the testing proposal as a mandatory, non-personal component of their participation in a research study, gradually incorporating testing mentions into discussions about sexual health, and using the kits to facilitate joint testing. Yet, 21 (44%) participants reported having sex with at least one partner they did not ask to test. Concern regarding partner reactions emerged as a significant barrier to discussing test use; similarly, many partners were averse to taking a blood-based test in the context of a casual sexual encounter. Nonetheless, these findings suggest that dual, blood-based HIV/STI rapid tests may represent acceptable harm reduction tools among similar populations of cMSM and TGW, particularly if future partner-testing research is broadened to consider key couples' dynamics that may impact test usage.

Experiences Receiving HIV-Positive Results by Phone: Acceptability and Implications for Clinical and Behavioral Research.

Improving HIV testing rates and increasing early detection among men who have sex with men (MSM) are critical strategies for enhancing overall health and decreasing HIV transmission. Remote testing and phone delivery of HIV test results may reduce barriers such as geographic isolation or HIV-related stigma. In 2018-19, 50 MSM completed qualitative interviews about their experience receiving a positive HIV test result via phone through their participation in a research study that included remote HIV testing. Interview topics included the acceptability of, and concerns about, phone delivery of HIV results, as well as suggestions for improvement. Interviews were transcribed, coded, and analysed using an inductive thematic approach. Overall, participants reported high acceptability of phone delivery of HIV-positive results. Participants praised the support and information provided by study staff. Benefits identified included increased convenience compared to in-person medical visits, allowing participants to emotionally process their test results privately, as well as receiving the results from supportive and responsive staff members. A few participants indicated drawbacks to phone-based HIV test result delivery, such as logistical concerns about receiving a phone call during the day (e.g., while at work), reduced confidentiality, and the lack of in-person emotional support. Overall, participants described phone delivery of positive HIV-results as acceptable. At-home testing with phone delivery has the potential to increase HIV testing access, especially to geographically isolated or medically underserved patients.

Transgender Women's Barriers, Facilitators, and Preferences on Tailored Injection Delivery Strategies to Administer Long-Acting Injectable Cabotegravir (CAB-LA) for HIV Pre-exposure Prophylaxis (PrEP).

Long-acting injectable cabotegravir (CAB-LA) is in advanced stages of clinical trials. Under the standard protocol, CAB-LA is injected into the gluteal muscle by a healthcare provider every eight weeks. To explore transgender women's barriers and facilitators to tailored delivery strategies-including self-injection and injection in "drop-in" centers-we completed in-depth interviews with N = 15 transgender women in New York City. Participants endorsed the alternative delivery methods and the corresponding features we proposed, and expressed likes and dislikes about each. These fell into the following categories: competence (e.g., the person delivering CAB-LA must have skills to do so), convenience (e.g., CAB-LA must be easy to obtain), and privacy or fear of judgement (e.g., participants did not want to feel judged for using CAB-LA by providers or other service consumers). Findings suggest the need to offer CAB-LA to transgender women through multiple delivery protocols.

SMARTtest: A Smartphone App to Facilitate HIV and Syphilis Self- and Partner-Testing, Interpretation of Results, and Linkage to Care.

Acceptability of rapid HIV self-testing is high but potential users remain concerned about correct use, interpretation of test results, and linkage to care. This article describes user preferences for a smartphone app to mitigate these challenges and how these were integrated into the SMARTtest app to support self- and partner-testing using the INSTI Multiplex®. Sixty men and transgender women who have sex with men self-tested for HIV and syphilis while guided by a prototype app that provided a video, pictorial step-by-step instructions, and sample test results presented textually ("positive," "negative"). Subsequently, participants provided feedback on revisions and additional app content. Participants recommended offering different user modes (self, partner, both), and retaining the video, step-by-step instructions, and textual test results. They strongly favored the ability to save and send test results to sexual partners or providers. These features were integrated into the SMARTtest app to facilitate HIV/syphilis self- and partner-testing, HIV/syphilis status awareness and disclosure, and linkage to care.

Substance Use and Testing Sexual Partners Using HIV Self-tests.

HIV self-tests (HIVST) provide the possibility of testing partners prior to sexual activity. This study examines the role of substance use among men who have sex with men (n = 123) and transgender women (n = 13) who were provided HIVST to use with potential sex partners. Several reported avoiding/delaying alcohol (44%) or drug use (27%) because they intended to use HIVST. Those who used HIVST with alcohol (37%) or drugs (24%) did not differ from those who did not on number of partners asked, proportion who agreed, or intentions to use HIVST. A minority reported problems caused by substances. Ten did not ask someone to test because they were too drunk/high. Fourteen said it was fairly or very hard to use HIVST when under the influence. Eleven reported substances caused problems when discussing or administering HIVST, but only two of those felt the problems were major.

Then We Looked at His Results: Men Who Have Sex With Men from New York City and Puerto Rico Report Their Sexual Partner's Reactions to Receiving Reactive HIV Self-Test Results.

Secondary distribution of HIV self-tests to sexual partners is acceptable but concerns remain about reactions if a partner tests HIV-positive. We report on 14 participants whose sexual partners tested HIV-positive during the "I'll Show You Mine" Study, a randomized controlled trial (N = 272) of HIV self- and partner-testing among men who have sex with men (MSM) and transgender women (TGW). All 14 were MSM and racial/ethnic minorities, mean age was 36.6 years; 86% were gay-identified. Twenty-four partners tested positive; about half were new partners. Six participants had multiple partners test positive. During in-depth interviews with 10 of these participants, they reported their partners' reactions ranged from tearful and worried among those whose result was unexpected, to resignation among those who suspected a positive result, to nonchalance among partners who participants concluded knew of their HIV infection. After testing, some HIV-positive partners disclosed prior knowledge of their status. No partner reacted violently. Participants typically comforted their partners and encouraged confirmatory testing. Four participants had anal intercourse with partners who tested positive. Participants and partners were able to effectively handle situations in which the partner tested HIV-positive.

Use of Rapid HIV Self-Test to Screen Potential Sexual Partners: Results of the ISUM Study.

ISUM ("I'll show you mine") was a randomized controlled trial in which 272 transgender women and men who have sex with men in New York, NY (NYC) and San Juan, Puerto Rico (SJU) were assigned to an intervention group (n = 136), in which they had access to free HIV self-testing (ST) kits, or to a control group (n = 136). The trial aimed to determine whether the intervention group would use ST to screen sexual partners and have fewer condomless anal intercourse (CAI) occasions with serodiscordant or unknown status partners than the control group. The intervention group had on average 10 (32%) fewer CAI occasions; though clinically relevant, this difference fell short of statistical significance (p = .08). In NYC (n = 166) intervention participants had significantly fewer CAI occasions, whereas in SJU (n = 106) they reported non-significantly more CAI occasions. Two devastating hurricanes hit SJU during the study and may have impacted results in unmeasured ways.

Using an HIV Self-test Kit to Test a Partner: Attitudes and Preferences Among High-Risk Populations.

For those most at risk of contracting HIV, new strategies for preventing transmission and increasing testing are needed. As part of a multi-site, randomized, controlled trial, we explored attitudes and preferences among 272 HIV-negative men who have sex with men and HIV-negative transgender women using an HIV self-testing (HIVST) kit to test partners. Less than one quarter had previously self-tested with HIVST kits (21.7%) and few had partner-tested (4.8%). Most preferred gum swab (96%) over fingerprick tests (69%), but would prefer a blood test if it gave results for other sexually transmitted infections (STIs) (86%). Five percent reported difficulties performing the test, four percent with storage, and 26% with portability. Ninety-three percent reported likelihood of using HIVST to test partners in future, but only 3% were willing to pay the current price. Efforts to improve HIVST uptake should focus on incorporating testing for other STIs, reducing test kit size, and reducing cost.

RESUMEN: Se necesitan nuevas estrategias para prevenir la transmisión del VIH e incrementar el testeo para aquellos con mayor riesgo al contagio. Como parte de un ensayo controlado aleatorio (ECA) multicentrico, exploramos las actitudes y preferencias entre 272 hombres VIH-negativos que tienen sexo con hombres y mujeres transgenero VIH-negativos que utilizaron kits del auto-test para el VIH (HIVST) para testear a sus parejas. Menos de una cuarta parte de los participantes había utilizado HIVST para auto-testearse (21.7%), y solo pocos para testear a sus parejas (4.8%) antes del comienzo del estudio. El hisopo bucal fue preferido (96%) sobre una prueba con un pinchazo de sangre (69%) por la mayoría de los participantes pero estos preferirían la prueba de sangre si puedieran obtener resultados para otras enfermedades de transmisión sexual (ETS) (86%). Cinco por ciento reportó problemas con el uso de la prueba, 4% con el almacenamiento, y el 26% con la portabilidad. Noventa y tres por ciento reportó que utilizarían HIVST para testear a sus parejas en el futuro, pero solo 3% estaba dispuesto a pagar el precio actual. Los futuros esfuerzos para mejorar la adopción del HIVST deberían enfocarse en incorporar otras pruebas de ETS, en reducir el tamaño del kit y en reducir los costos.

Transgender Women's Experiences Using a Home HIV-Testing Kit for Partner-Testing.

HIV partner-testing (PT) may represent a unique and empowering HIV prevention strategy for groups that face structural and institutional barriers to HIV testing and care, including transgender women. We report on in-depth interviews (IDIs) with N = 10 transgender women who used HIV self-test kits for three months to screen potential sexual partners in a randomized controlled trial (iSUM; "I'll Show You Mine") that took place in New York City and San Juan, Puerto Rico. Participants were assigned to intervention (supplied with 10 self-test kits immediately) or control groups (received 6 test kits after 3 months). We conducted IDIs with the first N = 10 transgender women to enroll in the intervention group after three months in the study (after participants used kits with partners) to understand their experiences. Themes discussed in IDIs included: partners' reaction to HIV testing, participants' reactions to partners' test results or refusal to test, partners' own reaction to their test results, and decision-making around test use. Data were independently analyzed by two coders. Overwhelmingly, participants' experiences with PT was positive. Participants reported kits were convenient and acceptable to most partners. Transgender women felt that PT could pose additional risk for them; one woman experienced violence related to kit use. Furthermore, the availability of kits appeared to encourage participants and their partners to think about their HIV status and, in some cases, modify sexual behavior. Work suggests that HIV PT could be a viable risk-reduction strategy for transgender women.

Information and Motivation Predict HIV-Serostatus Among a Population of High-Risk Men and Transgender Women Who Have Sex with Men.

Two constructs from the information-motivation-behavioral skills model were used to predict HIV-serostatus among a sample of men and transgender women who have sex with men. Hypotheses were that lower levels of HIV knowledge and lower levels of motivation to remain HIV-negative would be associated with an increased likelihood of receiving a positive HIV test result at a study eligibility-screening session. Results of a backwards stepwise logistic regression analysis demonstrated that lower levels of HIV knowledge, lower levels of motivation to remain HIV-negative, lower levels of education, and identifying as Hispanic/Latinx were associated with greater odds of receiving a positive HIV test result. These findings are consistent with the broader HIV-prevention literature that demonstrates that information and motivation are fundamental determinants of HIV preventive behavior. This work has implications for informing the development and improvement of HIV-prevention interventions.