Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests.

The effects of mutations in continuously emerging variants of SARS-CoV-2 are a major concern for the performance of rapid antigen tests. To evaluate the impact of mutations on 17 antibodies used in 11 commercially available antigen tests with emergency use authorization, we measured antibody binding for all possible Nucleocapsid point mutations using a mammalian surface-display platform and deep mutational scanning. The results provide a complete map of the antibodies' epitopes and their susceptibility to mutational escape. Our data predict no vulnerabilities for detection of mutations found in variants of concern. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutational profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system.

DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins.

Tandem zinc finger (ZF) proteins are the largest and most rapidly diverging family of DNA-binding transcription regulators in mammals. ZFP568 represses a transcript of placental-specific insulin like growth factor 2 (Igf2-P0) in mice. ZFP568 binds a 24-base pair sequence-specific element upstream of Igf2-P0 via the eleven-ZF array. Both DNA and protein conformations deviate from the conventional one finger-three bases recognition, with individual ZFs contacting 2, 3, or 4 bases and recognizing thymine on the opposite strand. These interactions arise from a shortened minor groove caused by an AT-rich stretch, suggesting adaptability of ZF arrays to sequence variations. Despite conservation in mammals, mutations at Igf2 and ZFP568 reduce their binding affinity in chimpanzee and humans. Our studies provide important insights into the evolutionary and structural dynamics of ZF-DNA interactions that play a key role in mammalian development and evolution.

Structural basis for human PRDM9 action at recombination hot spots.

The multidomain zinc finger (ZnF) protein PRDM9 (PRD1-BF1-RIZ1 homologous domain-containing 9) is thought to influence the locations of recombination hot spots during meiosis by sequence-specific DNA binding and trimethylation of histone H3 Lys4. The most common variant of human PRDM9, allele A (hPRDM9A), recognizes the consensus sequence 5'-NCCNCCNTNNCCNCN-3'. We cocrystallized ZnF8-12 of hPRDM9A with an oligonucleotide representing a known hot spot sequence and report the structure here. ZnF12 was not visible, but ZnF8-11, like other ZnF arrays, follows the right-handed twist of the DNA, with the α helices occupying the major groove. Each α helix makes hydrogen-bond (H-bond) contacts with up to four adjacent bases, most of which are purines of the complementary DNA strand. The consensus C:G base pairs H-bond with conserved His or Arg residues in ZnF8, ZnF9, and ZnF11, and the consensus T:A base pair H-bonds with an Asn that replaces His in ZnF10. Most of the variable base pairs (N) also engage in H bonds with the protein. These interactions appear to compensate to some extent for changes from the consensus sequence, implying an adaptability of PRDM9 to sequence variations. We investigated the binding of various alleles of hPRDM9 to different hot spot sequences. Allele C was found to bind a C-specific hot spot with higher affinity than allele A bound A-specific hot spots, perhaps explaining why the former is dominant in A/C heterozygotes. Allele L13 displayed higher affinity for several A-specific sequences, allele L9/L24 displayed lower affinity, and allele L20 displayed an altered sequence preference. These differences can be rationalized structurally and might contribute to the variation observed in the locations and activities of meiotic recombination hot spots.

Characterization of SETD3 methyltransferase-mediated protein methionine methylation.

Most characterized protein methylation events encompass arginine and lysine N-methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these instances, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain-containing 3 (SETD3) is a protein (i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S-methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr312 and Trp273, as well as the hydrocarbon side chain of Ile310 Our results suggest that placing methionine properly in the active site-within close proximity to and in line with the incoming methyl group of SAM-would allow some SET domain proteins to selectively methylate methionine in proteins.

Development of a new class of liver receptor homolog-1 (LRH-1) agonists by photoredox conjugate addition.

LRH-1 is a nuclear receptor that regulates lipid metabolism and homeostasis, making it an attractive target for the treatment of diabetes and non-alcoholic fatty liver disease. Building on recent structural information about ligand binding from our labs, we have designed a series of new LRH-1 agonists that further engage LRH-1 through added polar interactions. While the current synthetic approach to this scaffold has, in large part, allowed for decoration of the agonist core, significant variation of the bridgehead substituent is mechanistically precluded. We have developed a new synthetic approach to overcome this limitation, identified that bridgehead substitution is necessary for LRH-1 activation, and described an alternative class of bridgehead substituents for effective LRH-1 agonist development. We determined the crystal structure of LRH-1 bound to a bridgehead-modified compound, revealing a promising opportunity to target novel regions of the ligand binding pocket to alter LRH-1 target gene expression.

Clinical presentation and outcome of retinoblastoma based on age at presentation: a review of 1450 children.

PURPOSE: To compare the clinical presentation and outcomes of retinoblastoma (RB) based on age at presentation. METHODS: Retrospective comparative study of 1940 eyes of 1450 children with RB. RESULTS: Presentation of RB with enlarged eyeball and eyelid swelling (2% and < 1% in ≤ 1 year, 4% and 2% in > 1-2 years, 7% and 2% in > 2-3 years, and 12% and 4% in > 3 years; p < 0.0001 and p = 0.05, respectively) is more common with increasing age. Based on the 8th edition of American Joint Committee Classification, T1 is more common in children younger than 1 year (27%), while T4 is more common in children > 3 years of age (20%) (p < 0.0001). Kaplan-Meier (KM) estimate at 1 and 5 years for globe salvage was 64% and 58% in children ≤ 1 year of age versus 30% and 20% in children > 3 years, respectively [Hazard ratio (HR) = 2.48; p < 0.0001], and KM estimate at 1 and 5 years for life salvage was 99% and 97% in children ≤ 1 year of age versus 89% and 78% in children older than 3 years, respectively (HR = 7.65; p < 0.0001). CONCLUSION: Uncommon clinical features of RB including enlarged eyeball and eyelid swelling are more common with increasing age. Younger age at presentation with RB is associated with better prognosis including higher chances of life and globe salvage.

ROUTINE FUNDUS SCREENING OF FAMILIES OF CHILDREN WITH RETINOBLASTOMA: A Prospective Study of 131 Consecutive Families.

PURPOSE: To discuss the importance of routine ophthalmic examination of parents and siblings of retinoblastoma (RB) patients. METHODS: Prospective nonrandomized observational/interventional case series of consecutive families of 131 RB patients. RESULTS: Routine ophthalmic examination of families (parents and siblings) of 131 consecutive newly diagnosed RB patients, including 262 parents and 23 siblings, revealed spontaneously regressed RB in at least 1 parent of 10 (8%) patients and active RB in at least 1 sibling of 3 (2%) patients. Of the 10 parents with spontaneously regressed RB, the lesions were unilateral (n = 7) or bilateral (n = 3). The regression patterns (n = 13) were comparable with postirradiation regression patterns Type 1 (n = 3), Type 2 (n = 2), Type 3 (n = 2), and Type 4 (n = 3), and spontaneous phthisis bulbi (n = 3). Fundus screening of siblings revealed active RB in at least 1 sibling of 3 (2%) patients. Of these 3 siblings, 2 had unilateral and 1 had bilateral disease. The mean age at detection of RB was 15 months (median, 6 months; range, 2-36 months). The disease was unilateral in 2 and bilateral in 1 patient. Based on International Classification of Intraocular Retinoblastoma, the tumors (n = 4) were classified as Group A (n = 2) and Group B (n = 2). CONCLUSION: Routine fundus screening of siblings allows for early detection of RB in otherwise asymptomatic children. Detection of spontaneously regressed RB in parents may act as a surrogate marker for germline RB1 mutation and is helpful in genetic counseling.

RETINOBLASTOMA IN INDIA: Clinical Presentation and Outcome in 1,457 Patients (2,074 Eyes).

PURPOSE: To study the clinical presentation, treatment, and outcome of patients with retinoblastoma (RB) in India. METHODS: Retrospective study of 1,457 patients with RB (2,074 eyes). RESULTS: The mean age at presentation of RB was 29 months (median, 24 months; range, <1-370 months). There were 812 (56%) men and 645 (44%) women with unilateral presentation of RB in 57% (n = 834) and bilateral in 43% (n = 623). Familial RB was present in 4% (n = 55). The most common presenting complaints included leukocoria (n = 1,100; 75%), proptosis (n = 91; 6%), strabismus (n = 77; 5%), and red eye (n = 68; 5%). Most (n = 1,889; 91%) tumors were intraocular in location, and 185 (n = 185; 9%) had extraocular tumor extension at presentation. The most common modalities of primary treatment-included systemic chemotherapy (n = 1,171; 60%) and enucleation (n = 674; 35%). At a mean follow-up period of 44 months (median, 30 months; range, 3-234 months), 92% (n = 1,206) were alive, and 108 (8%) patients died because of RB. Based on Kaplan-Meier analysis, the survival at 1, 3, 5, and 10 years was 94%, 91%, 90%, and 89%, respectively. CONCLUSION: The most common presenting signs of RB in Asian Indian population are leukocoria and proptosis. With appropriate treatment, the survival rate is favorable at 92%.

Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence.

PRDM9 is the only mammalian gene that has been associated with speciation. The PR/SET domain 9 (PRDM9) protein is a major determinant of meiotic recombination hot spots and acts through sequence-specific DNA binding via its C2H2 zinc finger (ZF) tandem array, which is highly polymorphic within and between species. The most common human variant, PRDM9 allele A (PRDM9a), contains 13 fingers (ZF1-13). Allele C (PRDM9c) is the second-most common among African populations and differs from PRDM9a by an arginine-to-serine change (R764S) in ZF9 and by replacement of ZF11 with two other fingers, yielding 14 fingers in PRDM9c. Here we co-crystallized the six-finger fragment ZF8-13 of PRDM9c, in complex with an oligonucleotide representing a known PRDM9c-specific hot spot sequence, and compared the structure with that of a characterized PRDM9a-specific complex. There are three major differences. First, Ser764 in ZF9 allows PRDM9c to accommodate a variable base, whereas PRDM9a Arg764 recognizes a conserved guanine. Second, the two-finger expansion of ZF11 allows PRDM9c to recognize three-base-pair-longer sequences. A tryptophan in the additional ZF interacts with a conserved thymine methyl group. Third, an Arg-Asp dipeptide immediately preceding the ZF helix, conserved in two PRDM9a fingers and three PRDM9c fingers, permits adaptability to variations from a C:G base pair (G-Arg interaction) to a G:C base pair (C-Asp interaction). This Arg-Asp conformational switch allows identical ZF modules to recognize different sequences. Our findings illuminate the molecular mechanisms for flexible and conserved binding of human PRDM9 alleles to their cognate DNA sequences.

Automethylation activities within the mixed lineage leukemia-1 (MLL1) core complex reveal evidence supporting a "two-active site" model for multiple histone H3 lysine 4 methylation.

The mixed lineage leukemia-1 (MLL1) core complex predominantly catalyzes mono- and dimethylation of histone H3 at lysine 4 (H3K4) and is frequently altered in aggressive acute leukemias. The molecular mechanisms that account for conversion of mono- to dimethyl H3K4 (H3K4me1,2) are not well understood. In this investigation, we report that the suppressor of variegation, enhancer of zeste, trithorax (SET) domains from human MLL1 and Drosophila Trithorax undergo robust intramolecular automethylation reactions at an evolutionarily conserved cysteine residue in the active site, which is inhibited by unmodified histone H3. The location of the automethylation in the SET-I subdomain indicates that the MLL1 SET domain possesses significantly more conformational plasticity in solution than suggested by its crystal structure. We also report that MLL1 methylates Ash2L in the absence of histone H3, but only when assembled within a complex with WDR5 and RbBP5, suggesting a restraint for the architectural arrangement of subunits within the complex. Using MLL1 and Ash2L automethylation reactions as probes for histone binding, we observed that both automethylation reactions are significantly inhibited by stoichiometric amounts of unmethylated histone H3, but not by histones previously mono-, di-, or trimethylated at H3K4. These results suggest that the H3K4me1 intermediate does not significantly bind to the MLL1 SET domain during the dimethylation reaction. Consistent with this hypothesis, we demonstrate that the MLL1 core complex assembled with a catalytically inactive SET domain variant preferentially catalyzes H3K4 dimethylation using the H3K4me1 substrate. Taken together, these results are consistent with a "two-active site" model for multiple H3K4 methylation by the MLL1 core complex.

Role of IgG avidity in eyes with active Toxoplasma retinochoroiditis.

PURPOSE: To study the role of Toxoplasma IgG avidity in evaluating the stage of systemic infection during manifestation as toxoplasma retinochoroiditis and its clinical implications in eastern India. METHODS: Retrospective chart review of Toxoplasma retinochoroiditis cases with Toxoplasma serology for IgG, IgM, and IgG avidity. RESULTS: Included in this study were 17 eyes of 17 patients who had active retinitis located in the macula (14), mid-periphery (2), or periphery (1). They were either primary lesions (12) or reactivations (5). All the cases had Toxoplasma IgG positive; one case had IgM positivity, while all the cases had high IgG avidity values. IgG avidity had a positive correlation with the duration of symptoms. CONCLUSION: We observed high IgG avidity values in active retinochoroiditis in both primary ocular Toxoplasmosis and reactivation subgroups. These results indicate a late ocular manifestation after initial systemic infection with a possible incubation period ranging from 5 weeks to 5 months.

Macular Punctate Lesions Presenting as a Primary Manifestation of Ocular Toxoplasmosis.

PURPOSE: To study clinical features and outcomes of primary ocular Toxoplasmosis (OT) cases presenting as macular punctate lesions. METHODS: Retrospective review of three cases of OT with positive Toxoplasma serology. RESULTS: We describe three cases presenting as primary OT with no evidence of old retinochoroidal scar in either eye. All the cases had multiple foveal or extrafoveal, punctate, inner/outer, or combined lesions at macula with minimal vitreous reaction. During the first/primary episode, all the lesions resolved with 1. retinal atrophy, thinning (n = 1) or 2. Progressed to limited full-thickness retinitis lesions (n = 2). Recurrence as typical retinochoroiditis was seen in one eye. More than four-fold IgG positivity was seen in all cases while IgM positivity was seen in two cases. CONCLUSIONS: Macular punctate lesions (inner/outer/combination) can be the primary manifestation of ocular toxoplasmosis in the absence of old retinochoroiditis scars in either eye.

Anterior Non-Necrotizing Scleritis with Active Uveitis in Cases of Ocular Syphilis.

PURPOSE: To study clinical characteristics and management outcomes of cases of ocular syphilis co-presenting with scleritis and active uveitis. METHODS: A retrospective analysis of cases diagnosed with ocular syphilis between January 2020 and December 2023 was conducted at a tertiary eye care centre. Clinical records, investigations, and outcomes were reviewed to identify cases with scleritis with active uveitis. Demographic data, clinical features, treatment modalities, and resolution patterns were analyzed. RESULTS: Among the 135 eyes of 95 cases of ocular syphilis studied, scleritis with uveitis was observed in 3.70% of eyes (five eyes). All cases with scleritis and uveitis were unilateral and male, with ages ranging from 32 to 61 years. Concurrent features included placoid chorioretinitis, retinal vasculitis, and anterior uveitis. Misdiagnosis with subsequent oral steroid therapy precipitated scleritis as an exacerbation in two cases. Three cases, which were previously undiagnosed, were found to be HIV-positive. Scleritis manifested as anterior, non-necrotizing inflammation, often accompanied by chemosis, and responded rapidly to antibiotic and non-steroidal anti-inflammatory therapy. Scleritis resolution preceded that of chorioretinitis and retinal vasculitis. CONCLUSIONS: Non-necrotizing anterior scleritis with chemosis can be a rare presentation of active syphilitic uveitis. Large placoid chorioretinitis lesions, preceding inadvertent oral steroid and/or undiagnosed HIV status were the possible risk factors for the development of concurrent scleritis.

Structural basis for WDR5 interaction (Win) motif recognition in human SET1 family histone methyltransferases.

Translocations and amplifications of the mixed lineage leukemia-1 (MLL1) gene are associated with aggressive myeloid and lymphocytic leukemias in humans. MLL1 is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, which are required for transcription of genes involved in hematopoiesis and development. MLL1 associates with a subcomplex containing WDR5, RbBP5, Ash2L, and DPY-30 (WRAD), which together form the MLL1 core complex that is required for sequential mono- and dimethylation of H3K4. We previously demonstrated that WDR5 binds the conserved WDR5 interaction (Win) motif of MLL1 in vitro, an interaction that is required for the H3K4 dimethylation activity of the MLL1 core complex. In this investigation, we demonstrate that arginine 3765 of the MLL1 Win motif is required to co-immunoprecipitate WRAD from mammalian cells, suggesting that the WDR5-Win motif interaction is important for the assembly of the MLL1 core complex in vivo. We also demonstrate that peptides that mimic SET1 family Win motif sequences inhibit H3K4 dimethylation by the MLL1 core complex with varying degrees of efficiency. To understand the structural basis for these differences, we determined structures of WDR5 bound to six different naturally occurring Win motif sequences at resolutions ranging from 1.9 to 1.2 Å. Our results reveal that binding energy differences result from interactions between non-conserved residues C-terminal to the Win motif and to a lesser extent from subtle variation of residues within the Win motif. These results highlight a new class of methylation inhibitors that may be useful for the treatment of MLL1-related malignancies.

A comparative randomized controlled study of modified 4 in 1 block versus IPACK plus adductor canal block for post-operative analgesia in total knee arthroplasty.

Background and Aims: Postoperative analgesia for Total Knee Arthroplasty (TKA) is paramount for early mobilisation and rehabilitation. The newer motor sparing peripheral nerve blocks for analgesia for TKA are 4 in 1 block, modified 4 in 1 block, infiltration between popliteal artery and capsule of the knee (IPACK) block along with adductor canal block (ACB). We hypothesised that Modified 4 in 1 block is as efficient as the already proven technique of combined IPACK and ACB in providing post-operative analgesia to the patients of TKA. Methods: Seventy patients fulfilling the inclusion criteria posted for TKA surgery were randomised into two groups: Modified 4 in 1 block group (Group - M) and combined IPACK + ACB group (Group - I). After thorough preoperative evaluation and with mimimum standard monitoring the patients received sub-arachnoid block followed by the desired peripheral nerve block as per the group. After the surgery the visual analog scale (VAS) pain score was compared at 3, 6, 12, 24 hours postoperatively and tabulated. Results: The mean pain scores between both the groups was comparable at 3 hours, 6 hours and 24 hours. But at 12 hours after the surgery, VAS was less in Group-M in comparison to Group-I, Haemodynamic parameters were comparable between both the groups. None of the patients in both the groups showed any complications like muscle weakness in the post-operative period. Conclusion: Modified 4 in 1 block is a new and novel technique for the TKA surgeries and is comparable with already established combined IPACK+ACB technique for providing adequate postoperative analgesia after TKA.

Beaded Pearls Appearance in Syphilitic Chorioretinitis.

PURPOSE: To report an atypical case of bilateral syphilitic chorioretinitis. METHODS: A case report. RESULTS: A young male presented with bilateral pigmentary retinal changes along with multifocal chorioretinal lesions along the blood vessels giving a "beaded pearl" appearance. He was a hitherto undiagnosed case of human immunodeficiency virus infection and was diagnosed to have syphilis. He had a favourable visual and anatomical outcome following treatment. CONCLUSION: Multifocal chorioretinal lesions along blood vessels forming a "beaded pearls" appearance can be a rare and unique presentation of syphilis.