Genome sequencing of Pakistani families with male infertility identifies deleterious genotypes in SPAG6, CCDC9, TKTL1, TUBA3C, and M1AP.

BACKGROUND: There are likely to be hundreds of monogenic forms of human male infertility. Whole genome sequencing (WGS) is the most efficient way to make progress in mapping the causative genetic variants, and ultimately improve clinical management of the disease in each patient. Recruitment of consanguineous families is an effective approach to ascertain the genetic forms of many diseases. OBJECTIVES: To apply WGS to large consanguineous families with likely hereditary male infertility and identify potential genetic cases. MATERIALS AND METHODS: We recruited seven large families with clinically diagnosed male infertility from rural Pakistan, including five with a history of consanguinity. We generated WGS data on 26 individuals (3-5 per family) and analyzed the resulting data with a computational pipeline to identify potentially causal single nucleotide variants, indels, and copy number variants. RESULTS: We identified plausible genetic causes in five of the seven families, including a homozygous 10 kb deletion of exon 2 in a well-established male infertility gene (M1AP), and biallelic missense substitutions (SPAG6, CCDC9, TUBA3C) and an in-frame hemizygous deletion (TKTL1) in genes with emerging relevance. DISCUSSION AND CONCLUSION: The rate of genetic findings using the current approach (71%) was much higher than what we recently achieved using whole-exome sequencing (WES) of unrelated singleton cases (20%). Furthermore, we identified a pathogenic single-exon deletion in M1AP that would be undetectable by WES. Screening more families with WGS, especially in underrepresented populations, will further reveal the types of variants underlying male infertility and accelerate the use of genetics in the patient management.

Distinct regulatory functions and biological roles of lncRNA splice variants.

Alternative splicing (AS) of RNA molecules is a key contributor to transcriptome diversity. In humans, 90%-95% of multi-exon genes produce alternatively spliced RNA transcripts. Therefore, every single gene has the opportunity of producing multiple splice variants, including long non-coding RNA (lncRNA) genes that undergo RNA maturation steps such as conventional and alternative splicing. Emerging evidence suggests significant roles for these lncRNA splice variants in many aspects of cell biology. Differential changes in expression of specific lncRNA splice variants have also been associated with many diseases including cancer. This review covers the current knowledge on this emerging topic of investigation. We provide exclusive insights on the AS landscape of lncRNAs and also describe at the molecular level the functional relevance of lncRNA splice variants, i.e., RNA-based differential functions, production of micropeptides, and generation of circular RNAs. Finally, we discuss exciting perspectives for this emerging field and outline the work required to further develop research endeavors in this field.

Clinical implications of lncRNA LINC-PINT in cancer.

Long noncoding RNAs (lncRNAs) possess the potential for therapeutic targeting to treat many disorders, including cancers. Several RNA-based therapeutics (ASOs and small interfering RNAs) have gained FDA approval over the past decade. And with their potent effects, lncRNA-based therapeutics are of emerging significance. One important lncRNA target is LINC-PINT, with its universalized functions and relationship with the famous tumor suppressor gene TP53. Establishing clinical relevance, much like p53, the tumor suppressor activity of LINC-PINT is implicated in cancer progression. Moreover, several molecular targets of LINC-PINT are directly or indirectly used in routine clinical practice. We further associate LINC-PINT with immune responses in colon adenocarcinoma, proposing the potential utility of LINC-PINT as a novel biomarker of immune checkpoint inhibitors. Collectively, current evidence suggests LINC-PINT can be considered for use as a diagnostic/prognostic marker for cancer and several other diseases.

Functional Characterization of a Phf8 Processed Pseudogene in the Mouse Genome.

Most pseudogenes are generated when an RNA transcript is reverse-transcribed and integrated into the genome at a new location. Pseudogenes are often considered as an imperfect and silent copy of a functional gene because of the accumulation of numerous mutations in their sequence. Here we report the presence of Pfh8-ps, a Phf8 retrotransposed pseudogene in the mouse genome, which has no disruptions in its coding sequence. We show that this pseudogene is mainly transcribed in testis and can produce a PHF8-PS protein in vivo. As the PHF8-PS protein has a well-conserved JmjC domain, we characterized its enzymatic activity and show that PHF8-PS does not have the intrinsic capability to demethylate H3K9me2 in vitro compared to the parental PHF8 protein. Surprisingly, PHF8-PS does not localize in the nucleus like PHF8, but rather is mostly located at the cytoplasm. Finally, our proteomic analysis of PHF8-PS-associated proteins revealed that PHF8-PS interacts not only with mitochondrial proteins, but also with prefoldin subunits (PFDN proteins) that deliver unfolded proteins to the cytosolic chaperonin complex implicated in the folding of cytosolic proteins. Together, our findings highlighted PHF8-PS as a new pseudogene-derived protein with distinct molecular functions from PHF8.

Stub1 maintains proteostasis of master transcription factors in embryonic stem cells.

The pluripotency and differentiation states of embryonic stem cells (ESCs) are regulated by a set of core transcription factors, primarily Sox2, Oct4, and Nanog. Although their transcriptional regulation has been studied extensively, the contribution of posttranslational modifications in Sox2, Oct4, and Nanog are poorly understood. Here, using a CRISPR-Cas9 knockout library screen in murine ESCs, we identify the E3 ubiquitin ligase Stub1 as a negative regulator of pluripotency. Manipulation of Stub1 expression in murine ESCs shows that ectopic Stub1 expression significantly reduces the protein half-life of Sox2, Oct4, and Nanog. Mechanistic investigations reveal Stub1 catalyzes the polyubiquitination and 26S proteasomal degradation of Sox2 and Nanog through K48-linked ubiquitin chains and Oct4 via K63 linkage. Stub1 deficiency positively enhances somatic cell reprogramming and delays differentiation, whereas its enforced expression triggers ESC differentiation. The discovery of Stub1 as an integral pluripotency regulator strengthens our understanding of ESC regulation beyond conventional transcriptional control mechanisms.

PINTology: A short history of the lncRNA LINC-PINT in different diseases.

LINC-PINT is a p53-induced long intergenic noncoding transcript that plays a crucial role in many diseases, especially cancer. This long noncoding RNA (lncRNA) gene produces in total 102 (LNCipedia) alternatively spliced variants (LINC-PINT:1 to LINC-PINT:102). The functions of known variants include RNA transcripts, host transcripts for circular RNA (circRNA) generation and as sources for the translation of short peptides. In most human tumors, LINC-PINT is down-regulated where it serves as a tumor suppressor. However, the diversity of its functions in other maladies signifies its general clinical importance. Current LINC-PINT molecular functions include RNA-protein interactions, miRNA sponging and epigenetic modulation with these mechanisms operating in different cellular contexts to exert effects on biological processes ranging from DNA damage responses, cell cycle and growth arrest, senescence, cell migration and invasion, and apoptosis. Genetic polymorphisms in LINC-PINT have also been functionally associated with cancer and other pathologies including the autoimmune diseases pemphigus foliaceus and arthritis. Hence, LINC-PINT shows great potential as a clinical biomarker, especially for the diagnosis and prognosis of cancer. In this review, we explore the current knowledge highlighting the distinctive molecular functions of LINC-PINT in specific cancers and other disease states. This article is categorized under: RNA in Disease and Development > RNA in Disease.

Numerical Investigation of Darcy-Forchheimer Hybrid Nanofluid Flow with Energy Transfer over a Spinning Fluctuating Disk under the Influence of Chemical Reaction and Heat Source.

The present computational model is built to analyze the energy and mass transition rate through a copper and cobalt ferrite water-based hybrid nanofluid (hnf) flow caused by the fluctuating wavy spinning disk. Cobalt ferrite (CoFe2O4) and copper (Cu) nanoparticles (nps) are incredibly renowned in engineering and technological research due to their vast potential applications in nano/microscale structures, devices, materials, and systems related to micro- and nanotechnology. The flow mechanism has been formulated in the form of a nonlinear set of PDEs. That set of PDEs has been further reduced to the system of ODEs through resemblance replacements and computationally solved through the parametric continuation method. The outcomes are verified with the Matlab program bvp4c, for accuracy purposes. The statistical outputs and graphical evaluation of physical factors versus velocity, energy, and mass outlines are given through tables and figures. The configuration of a circulating disk affects the energy transformation and velocity distribution desirably. In comparison to a uniform interface, the uneven spinning surface augments energy communication by up to 15%. The addition of nanostructured materials (cobalt ferrite and copper) dramatically improves the solvent physiochemical characteristics. Furthermore, the upward and downward oscillation of the rotating disc also enhances the velocity and energy distribution.

COVID-19 Delta Variant-of-Concern: A Real Concern for Pregnant Women With Gestational Diabetes Mellitus.

The emergence of the COVID-19 Delta variant-of-concern (VOC), a novel variant of SARS-CoV-2, has threatened the total health systems throughout the world. This highly contagious strain is spreading at a higher exponential rate than any other variants of COVID-19 by infecting and subsequently killing hundreds of thousands of people globally. Among the most sensitive groups, pregnant women are at high risk of increased hospitalization, pneumonia, respiratory support, and admission to intensive care units during the Delta period. Pregnant people with gestational diabetes mellitus (GDM) are at increased chances of Delta VOC infection. GDM patients are nine and three times more likely to be infected by Delta VOC than those pregnant patients suffering from diabetes and cardiovascular diseases and hypertension, respectively. Additionally, they are more vulnerable to Delta VOC infection than wild-type and Alpha COVID-19 VOC ones. Thus, this review critically sheds light on the current scenario of the vulnerability of pregnant mothers, especially those with GDM, to Delta VOC infection.

lncRNA TRMP-S directs dual mechanisms to regulate p27-mediated cellular senescence.

Long noncoding RNAs (lncRNAs) undergo extensive alternative splicing, but little is known about isoform functions. A prior investigation of lncRNA RP11-369C8.1 reported that its splice variant TRMP suppressed p27 translation through PTBP1. Here we characterize a second major splice variant, TRMP-S (short variant), whose enforced loss promotes cancer cell-cycle arrest and p27-dependent entry into cellular senescence. Remarkably, despite sharing a single common exon with TRMP, TRMP-S restrains p27 expression through distinct mechanisms. First, TRMP-S stabilizes UHRF1 protein levels, an epigenetic inhibitor of p27, by promoting interactions between UHRF1 and its deubiquitinating enzyme USP7. Alternatively, binding interactions between TRMP-S and FUBP3 prevent p53 mRNA interactions with RPL26 ribosomal protein, the latter essential for promoting p53 translation with ensuing suppression of p53 translation limiting p27 expression. Significantly, as TRMP-S is itself transactivated by p53, this identifies negative feedback regulation between p53 and TRMP-S. Different splicing variants of the RP11-369C8.1 gene thereby exert distinct roles that converge on the homeostatic control of p27 expression, providing an important precedent for understanding the actions of alternatively spliced lncRNAs.

Aftermath of traumatic tympanic membrane perforation: Our findings at a tertiary care hospital in Pakistan.

OBJECTIVES: To determine the outcome of traumatic tympanic membrane perforation in a teaching hospital at Peshawar, Pakistan. METHODS: This prospective observational study was performed in the Department of ENT and Head and Neck Surgery, MTI/LRH, Peshawar, Pakistan from January 2016 to December 2019 after approved from Institutional Research and Ethical Board. All consented patients fulfilling inclusion criteria were enrolled. Sample size was calculated 114 using online sample size calculator (OpenEpi). Every patient was evaluated properly, subsequently otoscopy and PTA was performed. Required information was recorded and analyzed using SPSS (version 25). RESULTS: Out of 114 patients 81 (71.1%) were males and 33(28.9%) were female with male: female ratio of 2.5:1. Patient's age ranged from 6- 55 years with mean ± SD age of 26.41 ± 9.7 years. Majority of Patients, 46.5%( 53) were in 2nd decade. Amongst the causes slap outnumbered (80, 70.2%), and left ear was involved predominately (67, 58.7%) affecting mainly anterio-inferior quadrant (50, 43.9%). Small size perforation was most common finding (64, 56.1%). Majority of patients (72, 63.2%) presented in a week time and single perforation was the commonest (107, 93.%). Most of traumatic TM perforation got healed spontaneously (97, 85.1%). CONCLUSION: It is concluded that spontaneous healing of traumatic membrane perforation occurs in more than 90% cases provided the ear is kept dry and not accompanied by unfavorable conditions.

Exploring the Alternative Splicing of Long Noncoding RNAs.

Like protein-coding genes, long noncoding RNA (lncRNA) genes are composed of introns and exons. After their transcription, lncRNAs are subject to constitutive and/or alternative splicing. Here, we describe the current knowledge on lncRNA splice variants and their functional implications in cell biology.

TP53LNC-DB, the database of lncRNAs in the p53 signalling network.

The TP53 gene product, p53, is a pleiotropic transcription factor induced by stress, which functions to promote cell cycle arrest, apoptosis and senescence. Genome-wide profiling has revealed an extensive system of long noncoding RNAs (lncRNAs) that is integral to the p53 signalling network. As a research tool, we implemented a public access database called TP53LNC-DB that annotates currently available information relating lncRNAs to p53 signalling in humans.

Tumor-suppressive or tumor-supportive: For p53, that is the question.

We have recently reported a TP53 (known as p53) regulated long noncoding RNA named TRINGS (Tp53-regulated inhibitor of necrosis under glucose starvation). With the aid of TRINGS, p53 was shown to prevent cancer cells against necroptosis under glucose starvation. Our findings suggest that p53 may act as an oncogenic player in metabolic reprogramming.

A Novel Sex Chromosome Mosaicism 45,X/45,Y/46,XY/46,YY/47,XYY Causing Ambiguous Genitalia.

Sex chromosomal mosaicism has been considered as a major cause of human sexual differentiation disorders, like partial virilization and ambiguous genitalia. 45,X/46,XX, 45,X/46,XY and 46,XY/47,XXY are three most common sex chromosome mosaics associated with human ambiguous genitalia. Here, we report the case of a 3-year-old boy with ambiguous genitalia, bilateral cryptorchidism, and with an inguinal hernia. G banded cytological karyotyping and FISH analyses revealed that the patient has extremely rare and novel sex chromosome mosaic 45,X/45,Y/46,XY/46,YY/47,XYY karyotype. These cells exist in different percentages, important for phenotypic appearance of the patient. This is a first report of an unusual mosaic karyotype causing ambiguous genitalia.

The p53-inducible long noncoding RNA TRINGS protects cancer cells from necrosis under glucose starvation.

The tumor suppressor p53 is activated in response to cellular stress to prevent malignant transformation. However, several recent studies have shown that p53 can play protective roles in tumor cell survival under adversity. Whether p53-regulated long noncoding RNAs are involved in this process remains to be fully understood. Here, we show that under glucose starvation condition, p53 directly upregulates a novel lncRNA named TRINGS (Tp53-regulated inhibitor of necrosis under glucose starvation) in human tumor cells. TRINGS binds to STRAP and inhibits STRAP-GSK3ß-NF-κB necrotic signaling to protect tumor cells from cell death. Interestingly, TRINGS appears to respond to glucose starvation specifically, as it is not activated by serum, serine, or glutamine deprivation. Collectively, our findings reveal that p53-induced lncRNA TRINGS controls the necrotic pathway and contributes to the survival of cancer cells harboring wild-type p53 under glucose stress.

Whole Exome Sequencing Identifies a Novel Mutation in the PITX3 Gene, Causing Autosomal Dominant Congenital Cataracts in a Chinese Family.

BACKGROUND: Congenital cataract is the cloudiness of the eye's natural lens and is a primary cause of congenital vision loss. It accounts for almost 10% of childhood vision loss worldwide. METHODS: A four generation Chinese family having seven affected individuals was recruited for the current study. Exome sequencing was performed to identify the genetic cause of congenital cataract. RESULTS: Analysis of data identified a novel frameshift mutation, c.608delC (p.A203fs), in the PITX3 gene. This mutation was only observed in the affected individuals while the unaffected members of the family as well as 100 ethnically matched normal controls did not contain this deletion. CONCLUSION: These findings suggest that p.A203fs is the cause of cataracts in the recruited family. This information would be further helpful in the genetic diagnosis of cataract and in the genetic counseling of similar patients.

Antioxidant and catalytic applications of silver nanoparticles using Dimocarpus longan seed extract as a reducing and stabilizing agent.

In this study, a simple and environmental friendly method was developed for the synthesis of silver nanoparticles (Ag-NPs) using Dimocarpus longan seed extract as a source of reducing and stabilizing agent. The appearance of a surface plasmon resonance peak at 432nm confirmed the synthesis of silver nanoparticles (UV-visible spectroscopy). The biosynthesized Ag-NPs were face centered cubic structures (XRD) with an approximate particle size of 40nm (TEM). Optimization study revealed that 10mL of plant extract (2mM AgNO3) at 180min of incubation resulted the optimum product synthesis. Poly-phenolic compounds were majorly involved in the reduction of silver ions into Ag-NPs (FT-IR). The catalytic activities of Ag-NPs were assessed against the photo-catalytic degradation of methylene blue and chemo catalytic reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP). The results indicated that the prepared Ag-NPs have strong chemo catalytic activity with a complete reduction of 4-NP to 4-AP within 10min. Similarly, Ag-NPs displayed higher photo-catalytic activity (K=0.12) as compared to commercial Ag-NPs (K=0.003). In addition, the silver nanoparticles exhibited a promising antioxidant activity in scavenging DPPH radicals. The findings of this study conclude that the biosynthesized Ag-NPs are promising agent possessing strong catalytic and reducing properties.

Pattern of firearm injuries in head and neck regions at a tertiary care hospital.

OBJECTIVE: To determine the characteristics of firearm injuries on head and neck in patients presenting to the Ear Nose and Throat Department of a tertiary care hospital. METHODS: This prospective, cross-sectional study was conducted at the Lady Reading Hospital, Peshawar, from June 2014 to May 2015, and comprised victims of firearm injuries. They were subjected to a thorough examination of the wounds specifically and the rest of the Ear, Nose and Throat, Head and Neck regions generally. Data was collected on a proforma. SPSS 16 was used for data analysis. RESULTS: Out of the 56 patients, 49(87.5%) were men. The overall mean age was 28.68±1.63 years (range: 6-80 years. Besides, 33(58.9%) patients were in the age range 20-40 years followed by 18(32.1%) below 20 years. Overall, 27(48.2%) patients were jobless and 24(42.9%) had education below grade ten. Pistol was the most commonly-used weapon in 28(50%).Hospital stay was 2-10 days with a mean of 4.37±1.74 days. Single-entry wound on the neck was common 21(37.5%), predominantly on the right side 24(42.9%), while there were 33(58.9%) single-exit wounds, affecting neck in 18(32.1%) cases and on the left side in 19(33.9%). CONCLUSIONS: Firearm injuries were common among young men who were illiterate and poor socioeconomically. Homicidal injuries mostly occurred during the daytime. Pistol was the most commonly-used weapon, while wounds on the neck were more common.

LncReg: a reference resource for lncRNA-associated regulatory networks.

Long non-coding RNAs (lncRNAs) are critical in the regulation of various biological processes. In recent years, plethora of lncRNAs have been identified in mammalian genomes through different approaches, and the researchers are constantly reporting the regulatory roles of these lncRNAs, which leads to complexity of literature about particular lncRNAs. Therefore, for the convenience of the researchers, we collected regulatory relationships of the lncRNAs and built a database called 'LncReg'. This database is developed by collecting 1081 validated lncRNA-associated regulatory entries, including 258 non-redundant lncRNAs and 571 non-redundant genes. With regulatory relationships information, LncReg can provide overall perspectives of regulatory networks of lncRNAs and comprehensive data for bioinformatics research, which is useful for understanding the functional roles of lncRNAs. Database URL: http://bioinformatics.ustc.edu.cn/lncreg/.

SLC26A4 mutations in patients with moderate to severe hearing loss.

Mutations in SLC26A4 cause either syndromic or nonsyndromic hearing loss. We identified a link between hearing loss and DFNB4 in 3 of the 50 families participating in this study. Sequencing analysis revealed two SLC26A4 mutations, p.V239D and p.S57X, in affected members of the 3 families. These mutations have been previously reported in deaf individuals from the subcontinent, all of whom manifested profound deafness. The patients investigated in our study exhibited moderate to severe hearing loss. Our results show that inactivating SLC26A4 mutations that cause profound deafness can also be involved in the etiology of moderate to severe hearing loss. The type of mutation cannot predict the severity of the hearing loss in all cases, and there may be additional epistatic interactions that could modify the phenotype.