Pathogenesis of Cardiomyopathy Caused by Variants in ALPK3, an Essential Pseudokinase in the Cardiomyocyte Nucleus and Sarcomere.

BACKGROUND: ALPK3 encodes α-kinase 3, a muscle-specific protein of unknown function. ALPK3 loss-of-function variants cause cardiomyopathy with distinctive clinical manifestations in both children and adults, but the molecular functions of ALPK3 remain poorly understood. METHODS: We explored the putative kinase activity of ALPK3 and the consequences of damaging variants using isogenic human induced pluripotent stem cell-derived cardiomyocytes, mice, and human patient tissues. RESULTS: Multiple sequence alignment of all human α-kinase domains and their orthologs revealed 4 conserved residues that were variant only in ALPK3, demonstrating evolutionary divergence of the ALPK3 α-kinase domain sequence. Phosphoproteomic evaluation of both ALPK3 kinase domain inhibition and overexpression failed to detect significant changes in catalytic activity, establishing ALPK3 as a pseudokinase. Investigations into alternative functions revealed that ALPK3 colocalized with myomesin proteins (MYOM1, MYOM2) at both the nuclear envelope and the sarcomere M-band. ALPK3 loss-of-function variants caused myomesin proteins to mislocalize and also dysregulated several additional M-band proteins involved in sarcomere protein turnover, which ultimately impaired cardiomyocyte structure and function. CONCLUSIONS: ALPK3 is an essential cardiac pseudokinase that inserts in the nuclear envelope and the sarcomere M-band. Loss of ALPK3 causes mislocalization of myomesins, critical force-buffering proteins in cardiomyocytes, and also dysregulates M-band proteins necessary for sarcomere protein turnover. We conclude that ALPK3 cardiomyopathy induces ventricular dilatation caused by insufficient myomesin-mediated force buffering and hypertrophy by impairment of sarcomere proteostasis.

Filamin C Cardiomyopathy Variants Cause Protein and Lysosome Accumulation.

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Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing.

With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis-based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10-37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population.

Myosin Sequestration Regulates Sarcomere Function, Cardiomyocyte Energetics, and Metabolism, Informing the Pathogenesis of Hypertrophic Cardiomyopathy.

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is caused by pathogenic variants in sarcomere protein genes that evoke hypercontractility, poor relaxation, and increased energy consumption by the heart and increased patient risks for arrhythmias and heart failure. Recent studies show that pathogenic missense variants in myosin, the molecular motor of the sarcomere, are clustered in residues that participate in dynamic conformational states of sarcomere proteins. We hypothesized that these conformations are essential to adapt contractile output for energy conservation and that pathophysiology of HCM results from destabilization of these conformations. METHODS: We assayed myosin ATP binding to define the proportion of myosins in the super relaxed state (SRX) conformation or the disordered relaxed state (DRX) conformation in healthy rodent and human hearts, at baseline and in response to reduced hemodynamic demands of hibernation or pathogenic HCM variants. To determine the relationships between myosin conformations, sarcomere function, and cell biology, we assessed contractility, relaxation, and cardiomyocyte morphology and metabolism, with and without an allosteric modulator of myosin ATPase activity. We then tested whether the positions of myosin variants of unknown clinical significance that were identified in patients with HCM, predicted functional consequences and associations with heart failure and arrhythmias. RESULTS: Myosins undergo physiological shifts between the SRX conformation that maximizes energy conservation and the DRX conformation that enables cross-bridge formation with greater ATP consumption. Systemic hemodynamic requirements, pharmacological modulators of myosin, and pathogenic myosin missense mutations influenced the proportions of these conformations. Hibernation increased the proportion of myosins in the SRX conformation, whereas pathogenic variants destabilized these and increased the proportion of myosins in the DRX conformation, which enhanced cardiomyocyte contractility, but impaired relaxation and evoked hypertrophic remodeling with increased energetic stress. Using structural locations to stratify variants of unknown clinical significance, we showed that the variants that destabilized myosin conformations were associated with higher rates of heart failure and arrhythmias in patients with HCM. CONCLUSIONS: Myosin conformations establish work-energy equipoise that is essential for life-long cellular homeostasis and heart function. Destabilization of myosin energy-conserving states promotes contractile abnormalities, morphological and metabolic remodeling, and adverse clinical outcomes in patients with HCM. Therapeutic restabilization corrects cellular contractile and metabolic phenotypes and may limit these adverse clinical outcomes in patients with HCM.

SarcTrack.

RATIONALE: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in combination with CRISPR/Cas9 genome editing provide unparalleled opportunities to study cardiac biology and disease. However, sarcomeres, the fundamental units of myocyte contraction, are immature and nonlinear in hiPSC-CMs, which technically challenge accurate functional interrogation of contractile parameters in beating cells. Furthermore, existing analysis methods are relatively low-throughput, indirectly assess contractility, or only assess well-aligned sarcomeres found in mature cardiac tissues. OBJECTIVE: We aimed to develop an analysis platform that directly, rapidly, and automatically tracks sarcomeres in beating cardiomyocytes. The platform should assess sarcomere content, contraction and relaxation parameters, and beat rate. METHODS AND RESULTS: We developed SarcTrack, a MatLab software that monitors fluorescently tagged sarcomeres in hiPSC-CMs. The algorithm determines sarcomere content, sarcomere length, and returns rates of sarcomere contraction and relaxation. By rapid measurement of hundreds of sarcomeres in each hiPSC-CM, SarcTrack provides large data sets for robust statistical analyses of multiple contractile parameters. We validated SarcTrack by analyzing drug-treated hiPSC-CMs, confirming the contractility effects of compounds that directly activate (CK-1827452) or inhibit (MYK-461) myosin molecules or indirectly alter contractility (verapamil and propranolol). SarcTrack analysis of hiPSC-CMs carrying a heterozygous truncation variant in the myosin-binding protein C ( MYBPC3) gene, which causes hypertrophic cardiomyopathy, recapitulated seminal disease phenotypes including cardiac hypercontractility and diminished relaxation, abnormalities that normalized with MYK-461 treatment. CONCLUSIONS: SarcTrack provides a direct and efficient method to quantitatively assess sarcomere function. By improving existing contractility analysis methods and overcoming technical challenges associated with functional evaluation of hiPSC-CMs, SarcTrack enhances translational prospects for sarcomere-regulating therapeutics and accelerates interrogation of human cardiac genetic variants.

Evaluation of diallelic STR markers with inter-population allelic database for their usefulness in paternity trios in the Central Indian population.

BACKGROUND: Most of the forensic DNA laboratories have migrated to new generation STR kits of 6 dye chemistry with more than 20 autosomal STRs. The population-specific databases of such STR markers are lacking in many regions. AIM: To evaluate the effect of the inter-population database in 100 paternity trios with no inconsistencies at 23 STRs. SUBJECTS AND METHODS: 100 paternity trios were evaluated considering inter-population allelic frequency values for calculation of Combined Paternity Index (CPI) and Probability of Paternity (POP). RESULTS: No significant variation (p < 0.05) among the allele frequencies at the interpopulation level was observed. The number of obligate alleles and the likelihood of transferring obligate alleles from the putative father showed a positive correlation (p < 0.005) with Power of Discrimination (PD), Polymorphic Information Content (PIC), Power of Exclusion (PE), Paternity Index (PI), Observed and Expected Heterozygosity (Ho and He), and a statistically significant negative correlation (p < 0.005) with Matching Probability (Pm). The average Combined Paternity Index (CPI) and Probability of Paternity (POP) did not show any statistically significant difference (p < 0.05) at the interpopulation level. CONCLUSION: The allelic database showed no effect on the CPI and POP in 100 paternity trios. This suggests no urgent need for using population-specific databases for statistical evaluation of paternity trios without inconsistencies.

Expanding the clinical and genetic spectrum of ALPK3 variants: Phenotypes identified in pediatric cardiomyopathy patients and adults with heterozygous variants.

INTRODUCTION: Biallelic damaging variants in ALPK3, encoding alpha-protein kinase 3, cause pediatric-onset cardiomyopathy with manifestations that are incompletely defined. METHODS AND RESULTS: We analyzed clinical manifestations of damaging biallelic ALPK3 variants in 19 pediatric patients, including nine previously published cases. Among these, 11 loss-of-function (LoF) variants, seven compound LoF and deleterious missense variants, and one homozygous deleterious missense variant were identified. Among 18 live-born patients, 8 exhibited neonatal dilated cardiomyopathy (44.4%; 95% CI: 21.5%-69.2%) that subsequently transitioned into ventricular hypertrophy. The majority of patients had extracardiac phenotypes, including contractures, scoliosis, cleft palate, and facial dysmorphisms. We observed no association between variant type or location, disease severity, and/or extracardiac manifestations. Myocardial histopathology showed focal cardiomyocyte hypertrophy, subendocardial fibroelastosis in patients under 4 years of age, and myofibrillar disarray in adults. Rare heterozygous ALPK3 variants were also assessed in adult-onset cardiomyopathy patients. Among 1548 Dutch patients referred for initial genetic analyses, we identified 39 individuals with rare heterozygous ALPK3 variants (2.5%; 95% CI: 1.8%-3.4%), including 26 missense and 10 LoF variants. Among 149 U.S. patients without pathogenic variants in 83 cardiomyopathy-related genes, we identified six missense and nine LoF ALPK3 variants (10.1%; 95% CI: 5.7%-16.1%). LoF ALPK3 variants were increased in comparison to matched controls (Dutch cohort, P = 1.6×10-5; U.S. cohort, P = 2.2×10-13). CONCLUSION: Biallelic damaging ALPK3 variants cause pediatric cardiomyopathy manifested by DCM transitioning to hypertrophy, often with poor contractile function. Additional extracardiac features occur in most patients, including musculoskeletal abnormalities and cleft palate. Heterozygous LoF ALPK3 variants are enriched in adults with cardiomyopathy and may contribute to their cardiomyopathy. Adults with ALPK3 LoF variants therefore warrant evaluations for cardiomyopathy.

Feedback regulation of Caulobacter crescentus holdfast synthesis by flagellum assembly via the holdfast inhibitor HfiA.

To permanently attach to surfaces, Caulobacter crescentusproduces a strong adhesive, the holdfast. The timing of holdfast synthesis is developmentally regulated by cell cycle cues. When C. crescentusis grown in a complex medium, holdfast synthesis can also be stimulated by surface sensing, in which swarmer cells rapidly synthesize holdfast in direct response to surface contact. In contrast to growth in complex medium, here we show that when cells are grown in a defined medium, surface contact does not trigger holdfast synthesis. Moreover, we show that in a defined medium, flagellum synthesis and regulation of holdfast production are linked. In these conditions, mutants lacking a flagellum attach to surfaces over time more efficiently than either wild-type strains or strains harboring a paralyzed flagellum. Enhanced adhesion in mutants lacking flagellar components is due to premature holdfast synthesis during the cell cycle and is regulated by the holdfast synthesis inhibitor HfiA. hfiA transcription is reduced in flagellar mutants and this reduction is modulated by the diguanylate cyclase developmental regulator PleD. We also show that, in contrast to previous predictions, flagella are not necessarily required for C. crescentus surface sensing in the absence of flow, and that arrest of flagellar rotation does not stimulate holdfast synthesis. Rather, our data support a model in which flagellum assembly feeds back to control holdfast synthesis via HfiA expression in a c-di-GMP-dependent manner under defined nutrient conditions.

Structure-function analysis and genetic interactions of the Luc7 subunit of the Saccharomyces cerevisiae U1 snRNP.

Luc7 is an essential 261-amino acid protein subunit of the Saccharomyces cerevisiae U1 snRNP. To establish structure-function relations for yeast Luc7, we conducted an in vivo mutational analysis entailing N- and C-terminal truncations and alanine scanning of phylogenetically conserved amino acids, including two putative zinc finger motifs, ZnF1 and ZnF2, and charged amino acids within the ZnF2 module. We identify Luc7-(31-246) as a minimal functional protein and demonstrate that whereas mutations of the CCHH ZnF2 motif are lethal, mutations of the ZnF1 CCCH motif and the charged residues of the ZnF2 modules are not. Though dispensable for vegetative growth in an otherwise wild-type background, the N-terminal 18-amino acid segment of Luc7 plays an important role in U1 snRNP function, evinced by our findings that its deletion (i) impaired the splicing of SUS1 pre-mRNA; (ii) was synthetically lethal absent other U1 snRNP constituents (Mud1, Nam8, the TMG cap, the C terminus of Snp1), absent the Mud2 subunit of the Msl5•Mud2 branchpoint binding complex, and when the m(7)G cap-binding site of Cbc2 was debilitated; and (iii) bypassed the need for the essential DEAD-box ATPase Prp28. Similar phenotypes were noted for ZnF1 mutations C45A, C53A, and C68A and ZnF2 domain mutations D214A, R215A, R216A, and D219A These findings highlight the contributions of the Luc7 N-terminal peptide, the ZnF1 motif, and the ZnF2 module in stabilizing the interactions of the U1 snRNP with the pre-mRNA 5' splice site and promoting the splicing of a yeast pre-mRNA, SUS1, that has a nonconsensus 5' splice site.

Toxicity of Bisphenol in Pregnant Females: First Review of Literature in Humans.

Bisphenol analogues are widely used in consumer products such as disposable dinnerware, canned food, personal care products, bottled beverages, and more, and dietary exposure is the main pathway. Bisphenol A is used to manufacture synthetic resins and commercial plastics in large quantities. According to epidemiological and animal studies, bisphenols disrupt the reproductive, immunological, and metabolic systems. These analogues are estrogenic like Bisphenol A, although human studies are limited. We did a thorough search of the literature on the toxicity of bisphenol on reproductive and endocrine systems in pregnancy, focusing particularly on human studies. Hence, we present a comprehensive literature review on this topic.​​​​​​​ During our literature search, three epidemiological studies and one human observational study demonstrated a substantial link between bisphenol toxicity and recurrent miscarriages.​​​​​​​ The aforementioned research shows that bisphenol may harm pregnancy and cause miscarriages. We believe this is the first literature review on the topic.

Acute Exposure to Bisphenol S Decreases In Vitro Right Atrial Contractility in Rats.

AIM/OBJECTIVE: Bisphenols are widely used in the manufacturing of polycarbonate material and epoxy resins which constitute the essential component of plastic. Bisphenol A (BPA) has been reported to produce toxicity on organs in both animal and human studies. Therefore, plastic manufacturers are replacing BPA with other analogues that are considered to be safe, and BPA-free products are now available in the market. However, some studies have reported that bisphenol-S (BPS) also possesses toxic properties. It has been reported to depress ventricular contraction as well as produce ventricular arrhythmia on acute exposure. The present study was performed to examine the effect of BPS on in vitro spontaneously-beating right atria in rats. METHODS: In the present study, in vitro spontaneous contractions of right atria obtained from adult female rats of the Wistar strain were recorded. The atria were exposed to BPS (10-6-10 mM) and its effects on atrial contractions were recorded in the form of cumulative-concentration response with and without administration of antagonists namely atropine, L-NAME, and methylene blue. RESULTS: BPS decreased the rate as well as the force of atrial contractions. The changes produced in the rate and force of atrial contractions were not attributed to ethanol, which was used to prepare BPS solutions. The decrease in right atrial contractility produced by BPS was blocked by L-NAME; however, atropine and methylene blue were not able to antagonize the effects of BPS on atria. CONCLUSIONS: The present study indicates the involvement of NO-dependent but cGMP independent pathway responsible for BPS-induced cardio-toxicity.

Optimization of a stochastic model having erratic server with immediate or delayed repair.

The thought to put forward a queuing model proposed in this work was its pertinence in everyday life wherever we can see the uses of computing and networking systems. Industrial software developers and system managers can consider the results of the model to evolve their system for better results. Here we present a novel queueing model having erratic server with delayed repair and balking. Two distinct breakdowns i.e. active and passive breakdown for the system are also considered with their respective amendments. This model is closely related with the smooth functioning of the system during some internal faults (virus attack, electricity failures etc.). The performance indicators which are utilized in enhancing the service standards are obtained using supplementary variable technique. Using ANFIS soft computing technique we have compared the analytical results with those of neuro fuzzy results. Furthermore single and bi-objective minimization problems are considered and minima is obtained using particle swarm optimization and multi objective genetic algorithm respectively. Also, the minimization problems are shown as a convex programming problem to ensure the global optimality of the result. The proposed approach makes it conceivable to accomplish a relevant harmony between operational expenses and administration quality.

USG Guided Fine Needle Aspiration Cytology along with Immunocytochemistry to Diagnose Primary Malignant Mixed Mullerian Tumors: A Three-Year Study from a Tertiary Care Center.

Aims and Objectives: To study the diagnostic utility of fine-needle aspiration cytology (FNAC) and immunocytochemistry in diagnosing primary malignant mixed Mullerian tumors (MMMT). Materials and Methods: A 3-year retrospective study carried out in a tertiary care hospital, which included all the gynecological patients who underwent USG-guided FNAC of their abdominopelvic masses. Observations and Results: Out of the 324 total cases, 05 (1.5%) were reported as primary malignant mixed Mullerian tumors. Out of these 05 cases, 03 were ovarian, 01 was uterine, and 01 involved both uterus and one-sided adnexa. The FNA smears from the masses revealed cytomorphological features of a biphasic neoplasm with elongated pleomorphic spindle cells and dispersed, focal attempted acinar pattern, thus indicating the possibility of MMMT. Immunocytochemistry was further carried out which showed both vimentin and cytokeratin positivity. The diagnosis was confirmed on subsequent biopsy and immunohistochemistry (without any histopathological-cytological discrepancy). Conclusion: Though the literature is replete in establishing a histo-pathological diagnosis of MMMT, the diagnosis on USG-guided FNAC has been rarely described. Emphasis should be made on the careful examination of small sarcomatous elements in smears. Utilization of cell block and immunocytochemistry with histopathological correlation should be done to avoid misdiagnosis.

Evaluation of immunocytochemistry on destained giemsa stained smears as an alternative to conventional technique.

Introduction: Protocol for immunocytochemical (ICC) staining in May-Grünwald Giemsa (MGG)-stained smears has been difficult to establish. It is the need of the hour to be able to use prestained slides for ICC in specific cases to deliver timely diagnoses and reduce inconvenience to patients. Aims and Objectives: To evaluate and compare the use of MGG-stained smears for the purpose of ICC, after de-staining and saline rehydration to that of routine standard ICC. Materials and Methods: A prospective study was conducted on 40 FNAC samples: 25 cases of breast disease and 15 cases of reactive lymphoid hyperplasia known to express pancytokeratin and leukocyte common antigen (LCA)/CD45, respectively. Air-dried smears of each case were stained by standard MGG stain and after the report was dispatched, one smear was selected and sent for ICC. The smears were analyzed to determine the overall result and grade each smear semi-quantitatively with respect to staining-intensity, stain-localization, staining-uniformity, counter-staining, and background-staining. Observations and Results: The proposed protocol was inferior to conventional ICC in all the parameters, more pronounced in pancytokeratin than LCA/CD45. Only 8% of air-dried smears stained for pancytokeratin showed optimal stain intensity (as opposed to 44% of wet-fixed smears), whereas only 14.3% of air-dried smears were optimally stained for LCA (as opposed to 85.7% of wet-fixed smears). Conclusion: The proposed protocol of de-stained Giemsa smears as an alternative to conventional technique for ICC was unsuccessful in giving satisfactory results.

Acinic cell carcinoma of the parotid gland with neuroendocrine differentiation.

Acinic cell carcinoma (ACC) is a malignant salivary gland tumor characterized by tumor cells displaying acinar features. Usually presenting as a slow-growing tumor, ACC, however, may show dedifferentiation to a higher grade including neuroendocrine carcinoma. In addition, ACC may rarely show focal neuroendocrine differentiation without any frank evidence of neuroendocrine carcinoma. We describe such a case of ACC of the parotid gland in a 65-year-old female, which showed neuroendocrine differentiation. The diagnostic clues, immunohistochemistry panel, and prognostic and treatment aspects are also presented.

Localized cutaneous infection caused by Scedosporium apiospermum: Report of a case diagnosed on cytology.

Scedosporium apiospermum (also known as Pseudallescheria boydii) is a ubiquitous filamentous fungus. This fungus is known as a cause of mycetoma, which may occur in a normal immune host following trauma and nonmycetoma-localized skin infections without grain production which are much rarer. However, in an immunocompromised host, S. apiospermum may cause a life-threatening infection. We describe a case of S. apiospermum infection of the left middle finger in an immunocompetent patient, which was diagnosed on cytology and later confirmed on culture.

Utility of fine needle aspiration cytology to diagnose intraoral lymphoma: 7 years study from a tertiary care center.

OBJECTIVE: Fine needle aspiration (FNA) cytology has been successfully utilized in the preoperative diagnosis of oral masses. Lymphoma involving other sites has also been diagnosed frequently on FNA. Oral cavity lymphoma (OL) is rare and is clinically indistinguishable from other lesions of the mouth. A complete excision of these may be difficult. Our experience with FNA diagnosis of 11 OLs along with histopathological correlation is reported herein in a tertiary health care setting. METHODS: In this retrospective study, clinico pathological characteristics of patients with final diagnosis of non-Hodgkin's lymphoma (NHL) were reviewed over a 7 year period. Routine cytological giemsa staining was performed in all cases along with immunocytochemistry (ICC) wherever possible. The gold standard for diagnosis of NHL was based on: (1) Histopathology and immunohistochemistry and/or (2) Flow cytometry (FC). RESULTS: A total of 11 cases were diagnosed as NHL. All showed B cell immunophenotype. Two of them were diagnosed as follicular lymphoma on histopathology. Male to female ratio was 7:4 and ranged in age from 37 to 70 years. The most common site was tonsillar fossa (N = 5), followed by hard palate (N = 3), soft palate (N = 2), and buccal mucosa (N = 1). Size ranged from 1 to 6 cm. CONCLUSIONS: Diagnosis of OLs may be hampered by its rarity and difficulties in obtaining sufficient cellularity in oral FNA but there is need for immediate and accurate diagnostic procedures, including immunohistochemical analysis to avoid delay in treatment. FNA along with ICC helps in early diagnosis of this rare entity and can also provide sample for FC.