A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death.

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions as a critical stress sentinel that coordinates cell survival, inflammation, and immunogenic cell death (ICD). Although the catalytic function of RIPK1 is required to trigger cell death, its non-catalytic scaffold function mediates strong pro-survival signaling. Accordingly, cancer cells can hijack RIPK1 to block necroptosis and evade immune detection. We generated a small-molecule proteolysis-targeting chimera (PROTAC) that selectively degraded human and murine RIPK1. PROTAC-mediated depletion of RIPK1 deregulated TNFR1 and TLR3/4 signaling hubs, accentuating the output of NF-κB, MAPK, and IFN signaling. Additionally, RIPK1 degradation simultaneously promoted RIPK3 activation and necroptosis induction. We further demonstrated that RIPK1 degradation enhanced the immunostimulatory effects of radio- and immunotherapy by sensitizing cancer cells to treatment-induced TNF and interferons. This promoted ICD, antitumor immunity, and durable treatment responses. Consequently, targeting RIPK1 by PROTACs emerges as a promising approach to overcome radio- or immunotherapy resistance and enhance anticancer therapies.

Targeting TRIM37-driven centrosome dysfunction in 17q23-amplified breast cancer.

Genomic instability is a hallmark of cancer, and has a central role in the initiation and development of breast cancer1,2. The success of poly-ADP ribose polymerase inhibitors in the treatment of breast cancers that are deficient in homologous recombination exemplifies the utility of synthetically lethal genetic interactions in the treatment of breast cancers that are driven by genomic instability3. Given that defects in homologous recombination are present in only a subset of breast cancers, there is a need to identify additional driver mechanisms for genomic instability and targeted strategies to exploit these defects in the treatment of cancer. Here we show that centrosome depletion induces synthetic lethality in cancer cells that contain the 17q23 amplicon, a recurrent copy number aberration that defines about 9% of all primary breast cancer tumours and is associated with high levels of genomic instability4-6. Specifically, inhibition of polo-like kinase 4 (PLK4) using small molecules leads to centrosome depletion, which triggers mitotic catastrophe in cells that exhibit amplicon-directed overexpression of TRIM37. To explain this effect, we identify TRIM37 as a negative regulator of centrosomal pericentriolar material. In 17q23-amplified cells that lack centrosomes, increased levels of TRIM37 block the formation of foci that comprise pericentriolar material-these foci are structures with a microtubule-nucleating capacity that are required for successful cell division in the absence of centrosomes. Finally, we find that the overexpression of TRIM37 causes genomic instability by delaying centrosome maturation and separation at mitotic entry, and thereby increases the frequency of mitotic errors. Collectively, these findings highlight TRIM37-dependent genomic instability as a putative driver event in 17q23-amplified breast cancer and provide a rationale for the use of centrosome-targeting therapeutic agents in treating these cancers.

A prosurvival DNA damage-induced cytoplasmic interferon response is mediated by end resection factors and is limited by Trex1.

Radiotherapy and chemotherapy are effective treatment methods for many types of cancer, but resistance is common. Recent findings indicate that antiviral type I interferon (IFN) signaling is induced by these treatments. However, the underlying mechanisms still need to be elucidated. Expression of a set of IFN-stimulated genes comprises an IFN-related DNA damage resistance signature (IRDS), which correlates strongly with resistance to radiotherapy and chemotherapy across different tumors. Classically, during viral infection, the presence of foreign DNA in the cytoplasm of host cells can initiate type I IFN signaling. Here, we demonstrate that DNA-damaging modalities used during cancer therapy lead to the release of ssDNA fragments from the cell nucleus into the cytosol, engaging this innate immune response. We found that the factors that control DNA end resection during double-strand break repair, including the Bloom syndrome (BLM) helicase and exonuclease 1 (EXO1), play a major role in generating these DNA fragments and that the cytoplasmic 3'-5' exonuclease Trex1 is required for their degradation. Analysis of mRNA expression profiles in breast tumors demonstrates that those with lower Trex1 and higher BLM and EXO1 expression levels are associated with poor prognosis. Targeting BLM and EXO1 could therefore represent a novel approach for circumventing the IRDS produced in response to cancer therapeutics.

Pathway-based signatures predict patient outcome, chemotherapy benefit and synthetic lethal dependencies in invasive lobular breast cancer.

BACKGROUND: Invasive Lobular Carcinoma (ILC) is a morphologically distinct breast cancer subtype that represents up to 15% of all breast cancers. Compared to Invasive Breast Carcinoma of No Special Type (IBC-NST), ILCs exhibit poorer long-term outcome and a unique pattern of metastasis. Despite these differences, the systematic discovery of robust prognostic biomarkers and therapeutically actionable molecular pathways in ILC remains limited. METHODS: Pathway-centric multivariable models using statistical machine learning were developed and tested in seven retrospective clinico-genomic cohorts (n = 996). Further external validation was performed using a new RNA-Seq clinical cohort of aggressive ILCs (n = 48). RESULTS AND CONCLUSIONS: mRNA dysregulation scores of 25 pathways were strongly prognostic in ILC (FDR-adjusted P < 0.05). Of these, three pathways including Cell-cell communication, Innate immune system and Smooth muscle contraction were also independent predictors of chemotherapy response. To aggregate these findings, a multivariable machine learning predictor called PSILC was developed and successfully validated for predicting overall and metastasis-free survival in ILC. Integration of PSILC with CRISPR-Cas9 screening data from breast cancer cell lines revealed 16 candidate therapeutic targets that were synthetic lethal with high-risk ILCs. This study provides interpretable prognostic and predictive biomarkers of ILC which could serve as the starting points for targeted drug discovery for this disease.

Serotype and genomic diversity of dengue virus during the 2023 outbreak in Pakistan reveals the circulation of genotype III of DENV-1 and cosmopolitan genotype of DENV-2.

Dengue, a mosquito-borne viral disease, poses a significant public health challenge in Pakistan, with a significant outbreak in 2023, prompting our investigation into the serotype and genomic diversity of the dengue virus (DENV). NS-1 positive blood samples from 153 patients were referred to the National Institute of Health, Pakistan, between July and October 2023. Among these, 98 (64.1%) tested positive using multiplex real-time PCR, with higher prevalence among males (65.8%) and individuals aged 31-40. Serotyping revealed DENV-1 as the predominant serotype (84.7%), followed by DENV-2 (15.3%). Whole-genome sequencing of 18 samples (DENV-1 = 17, DENV-2 = 01) showed that DENV-1 (genotype III) samples were closely related (>99%) to Pakistan outbreak samples (2022), and approx. > 98% with USA (2022), Singapore and China (2016), Bangladesh (2017), and Pakistan (2019). The DENV-2 sequence (cosmopolitan genotype; clade IVA) shared genetic similarity with Pakistan outbreak sequences (2022), approx. > 99% with China and Singapore (2018-2019) and showed divergence from Pakistan sequences (2008-2013). No coinfection with dengue serotypes or other viruses were observed. Comparisons with previous DENV-1 sequences highlighted genetic variations affecting viral replication efficiency (NS2B:K55R) and infectivity (E:M272T). These findings contribute to dengue epidemiology understanding and underscore the importance of ongoing genomic surveillance for future outbreak responses in Pakistan.

Genomic characterization of human respiratory syncytial virus circulating in Islamabad, Pakistan, during an outbreak in 2022-2023.

In this study, conducted at the National Institute of Health, Islamabad, during an outbreak of human respiratory syncytial virus (hRSV) from December 2022 to January 2023, the first whole-genome sequences of hRSV isolates from Islamabad, Pakistan, were determined. Out of 10 positive samples, five were sequenced, revealing the presence of two genotypes: RSV-A (GA2.3.5, ON1 strain) and RSV-B (GB5.0.5.a, BA-10 strain). A rare non-synonymous substitution (E232G) in G the protein and N276S in the F protein were found in RSV-A. In RSV-B, the unique mutations K191R, Q209R, and I206M were found in the F protein. These mutations could potentially influence vaccine efficacy and viral pathogenicity. This research underscores the importance of genomic surveillance for understanding RSV diversity and guiding public health responses in Pakistan.

Implications of tumour heterogeneity on cancer evolution and therapy resistance: lessons from breast cancer.

Tumour heterogeneity is pervasive amongst many cancers and leads to disease progression, and therapy resistance. In this review, using breast cancer as an exemplar, we focus on the recent advances in understanding the interplay between tumour cells and their microenvironment using single cell sequencing and digital spatial profiling technologies. Further, we discuss the utility of lineage tracing methodologies in pre-clinical models of breast cancer, and how these are being used to unravel new therapeutic vulnerabilities and reveal biomarkers of breast cancer progression. © 2023 The Pathological Society of Great Britain and Ireland.

Shifting perspectives in coronary involvement of polyarteritis nodosa: case of 3-vessel occlusion treated with 4-vessel CABG and review of literature.

BACKGROUND: Polyarteritis Nodosa (PAN) is a systemic vasculitis (SV) historically thought to spare the coronary arteries. Coronary angiography and contemporary imaging reveal coronary stenosis and dilation, which are associated with significant morbidity and mortality. Coronary arteries in PAN are burdened with accelerated atherosclerosis from generalized inflammation adding to an inherent arteritic process. Traditional atherosclerotic risk factors fail to approximate risk. Few reports document coronary pathology and optimal therapy has been guarded. METHODS: Database publication query of English literature from 1990-2022. RESULTS: Severity of coronary involvement eludes laboratory monitoring, but coronary disease associates with several clinical symptoms. Framingham risk factors inadequately approximate disease burden. Separating atherosclerosis from arteritis requires advanced angiographic methods. Therapy includes anticoagulation, immunosuppression and revascularization. PCI has been the mainstay, though stenting is confounded by vagarious alteration in luminal diameter and reports of neointimization soon after placement. CONCLUSIONS: When graft selection avoids the vascular territory of SV's, CABG offers definitive therapy. We have contributed report of a novel CABG configuration in addition to reviewing, updating and discussing the literature. Accumulating evidence suggests discrete clinical symptoms warrant suspicion for coronary involvement.

Large Language Models for Intraoperative Decision Support in Plastic Surgery: A Comparison between ChatGPT-4 and Gemini.

Background and Objectives: Large language models (LLMs) are emerging as valuable tools in plastic surgery, potentially reducing surgeons' cognitive loads and improving patients' outcomes. This study aimed to assess and compare the current state of the two most common and readily available LLMs, Open AI's ChatGPT-4 and Google's Gemini Pro (1.0 Pro), in providing intraoperative decision support in plastic and reconstructive surgery procedures. Materials and Methods: We presented each LLM with 32 independent intraoperative scenarios spanning 5 procedures. We utilized a 5-point and a 3-point Likert scale for medical accuracy and relevance, respectively. We determined the readability of the responses using the Flesch-Kincaid Grade Level (FKGL) and Flesch Reading Ease (FRE) score. Additionally, we measured the models' response time. We compared the performance using the Mann-Whitney U test and Student's t-test. Results: ChatGPT-4 significantly outperformed Gemini in providing accurate (3.59 ± 0.84 vs. 3.13 ± 0.83, p-value = 0.022) and relevant (2.28 ± 0.77 vs. 1.88 ± 0.83, p-value = 0.032) responses. Alternatively, Gemini provided more concise and readable responses, with an average FKGL (12.80 ± 1.56) significantly lower than ChatGPT-4's (15.00 ± 1.89) (p < 0.0001). However, there was no difference in the FRE scores (p = 0.174). Moreover, Gemini's average response time was significantly faster (8.15 ± 1.42 s) than ChatGPT'-4's (13.70 ± 2.87 s) (p < 0.0001). Conclusions: Although ChatGPT-4 provided more accurate and relevant responses, both models demonstrated potential as intraoperative tools. Nevertheless, their performance inconsistency across the different procedures underscores the need for further training and optimization to ensure their reliability as intraoperative decision-support tools.

First report of coinfection and whole-genome sequencing of norovirus and sapovirus in an acute gastroenteritis patient from Pakistan.

Acute gastroenteritis is one of the most common diseases in infants and children in developing countries including Pakistan. In Pakistan, rotavirus (RVA) is known to contribute significantly to pediatric diarrheal illness, but the contribution of other viruses is still unclear. In the current study we have identified a case of mixed infection of norovirus (NoV) and sapovirus (SaV) in a 2-year-old child with acute gastroenteritis. The sample was initially processed for the detection of group A RVA through ELISA followed by NoV using RT-PCR assay. The sample tested positive for NoV RNA and was later subjected to whole-genome sequencing using meta-genome approach on Miseq (Illumina) platform. Sequencing results revealed GII.15 genotype of NoV that clustered with viruses from China and USA from 2017 to 2021. We also retrieved the complete genome of SaV (GI.1 genotype) from the same sample and phylogenetic analysis showed clustering with strains reported from Japan, South Korea, US, and Taiwan during 2012-2016. This is the first report from Pakistan that confirms coinfection of NoV and SaV and elucidates their whole genomes. We recommend initiation of NoV and SaV surveillance program to ascertain disease burden and explore genetic diversity, especially as RVA vaccines have been included in national immunization program.

Whole-genome sequencing of Crimean-Congo hemorrhagic fever virus circulating in Pakistan during 2022.

Pakistan is an endemic country for Crimean-Congo hemorrhagic fever (CCHF) and its Balochistan province is considered a hotspot region for circulation of the virus whereas sporadic cases have been reported from other parts of the country. Our study aims to investigate the genomic diversity of the CCHF virus circulating in Punjab and Khyber Pakhtunkhwa provinces of Pakistan. Between April to September 2022, 46 samples from suspected CCHF patients were tested, with 6 (13%) showing positive RT-PCR results. Among the positive cases, all were male, aged 14-48 years among which 4 were butchers. Three CCHF patients succumbed to the disease. The complete S-M-L-gene fragments of 4 positive samples were sequenced. The S and L segments belonged to the Asia-1 clade and clustered with regional strains from Iran, India, and Afghanistan. One M segment sequence grouped into Africa-2 along with those reported from India during 2016-2019. We report the detection of a reassorted virus (NIH-PAK-CCHF-03|2022) having Asia-1-Africa-2-Asia-1 (S-M-L) segment pattern for the first time from Pakistan. Mutational analysis showed M segments harboring eight mutations (T55A, S80P, T110I, T185A, T189A, A212T, and N239I/T) in the mucin-like domain, five mutations (D250N, T333S, I375V, M401I, A433T), four mutations (N545D, Y657F, K688R, and I824V) in GP38-domain, and three mutations (T1418N, A1431V, and G1449S) in Gc-domain. These findings highlight the significance of whole-genome sequencing of indigenous strains for a better understanding of the CCHFV evolution in Pakistan.

Genomic characterization of the first mpox and varicella-zoster co-infection in Pakistan (2023) through next-generation sequencing.

The global mpox outbreak spanning 2022-2023 has affected numerous countries worldwide. In this study, we present the first report on the detection, whole-genome sequence, and coinfection of the mpox virus and varicella zoster virus (VZV) from Pakistan. During April-May 2023, samples from 20 suspected cases of mpox were tested at the National Institutes of Health, Islamabad among which 4 tested positive. All four cases had a travel history of Saudi Arabia. All the suspected samples were processed by using a Zymo research kit for DNA extraction, followed by qRT-PCR amplification by using a DaAn Gene detection kit for the mpox virus. Further, two of the positive samples with a low Ct value (<20) were subjected to whole-genome sequencing using a metagenomic approach on the iSeq (Illumina) platform. The sequencing results revealed Clade IIb and genotype A.2.1 of MPXV, which clustered with viruses from Slovenia and the UK in July and June 2022, respectively. Our analysis identified two novel nonsynonymous substitutions in mpox virus, namely V98I in OPG046 and P600S in OPG109. Furthermore, we successfully retrieved the complete genome of VZV from the same sample, belonging to Clade 5. This study represents the first positive case of MPXV in Pakistan and the coinfection of mpox and VZV by using a metagenome approach providing insights into their complete genomes. Our results highlight the importance of surveillance at the point of entries, strengthening lab capacities including next-generation sequencing, and using differential diagnosis for timely and accurate detection of mpox cases.

The Association of Mental Illness With Outcomes of Emergency Surgery for Bowel Obstruction.

INTRODUCTION: Bowel obstruction is one of the most common surgical emergencies. The management of SBO is variable and influenced by numerous confounding factors. Recent studies have identified mental health as a health disparity that affects surgical outcomes. We aim to assess whether mental illness is a health disparity and its association with postoperative complications and secondary outcomes for bowel obstruction in Emergency General Surgery (EGS). METHODS: This was a retrospective study utilizing the National Inpatient Sample. Individuals aged 18-64 who underwent emergency adehesiolysis or bowel resection from 2015 to 2017 were identified. Postoperative complications, in-hospital mortality, length of stay, and total cost for surgical patients with and without mental illness were recorded. Univariate and multivariate analyses were used to evaluate the association between mental health and bowel obstruction. RESULTS: 20,574 patients who underwent surgery for bowel obstruction were identified. 3756 of these patients had mental illness and 16,998 patients did not. Patients with mental illness did not have significantly worse outcomes compared to patients without mental illness. Among 3576 patients with mental illness, sex, race, patient location, insurance, location/teaching status of hospital, hospital control and procedure type were significant predictors of prolonged length of stay, higher cost, and increased postoperative complications. CONCLUSIONS: Mental health does not appear to be a health disparity in outcomes for bowel obstruction procedures. However, the intersection of mental health with race and insurance status predicts worse outcomes. This essential area should be further explored to determine how marginalized populations are affected in emergency surgical care.

The Mediating Effect of Operative Approach on Racial Disparities in Bariatric Surgery Complications.

INTRODUCTION: A laparoscopic approach to bariatric surgeries confers a favorable side-effect profile as compared to an open approach. However, literature regarding the independent association of race with access to and postoperative outcomes in laparoscopic Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (GS) is scarce. MATERIALS AND METHODS: All RYGB and GS cases recorded in American College of Surgeons National Quality Improvement Program data from 2012 to 2020 were subjected to propensity score matching to assess the independent association between Black self-identified race on access to a laparoscopic approach and postoperative complications. Finally, a series of logistic regressions enabled evaluation of the mediating effect of operative approach on racial disparities in postoperative complications. RESULTS: 55,846 cases of RYGB and 94,209 cases of GS were identified. Following propensity score matching, logistic regression identified Black race as an independent predictor of open approach to RYGB (P < 0.001) and GS (P = 0.019). Black patients had increased incidence of any, minor and severe postoperative complications and unplanned readmissions in both RYGB (P < 0.001, P < 0.001, P = 0.0412, and P < 0.001, respectively) and GS (P < 0.001, P < 0.001, P = 0.0037, and P < 0.001, respectively). Open approach to RYGB was identified as a partial mediator of the independent association between Black race and any complication, minor complications, and unplanned readmission. CONCLUSIONS: This methodology identified racial disparities in complications following RYGB and GS. Interestingly, reduced access to a laparoscopic approach mediated racial disparities in complications following RYGB but not GS. Further research might elucidate upstream determinants of health that catalyze these disparities.

Bioevaluation of synthetic pyridones as dual inhibitors of α-amylase and α-glucosidase enzymes and potential antioxidants.

Herein, a library of novel pyridone derivatives 1-34 was designed, synthesized, and evaluated for α-amylase and α-glucosidase inhibitory as well as antioxidant activities. Pyridone derivatives 1-34 were synthesized via a one-pot multi-component reaction of variously substituted aromatic aldehydes, acetophenone, ethyl cyanoacetate, and ammonium acetate in absolute ethanol. Synthetic compounds 1-34 were structurally characterized by different spectroscopic techniques. Most of the tested compounds showed more promising inhibition potential than the standard acarbose (IC50 = 14.87 ± 0.16 µM) but compounds 13 and 12 were found to be the most potent compounds with IC50 values of 9.20 ± 0.14 µM and 3.05 ± 0.18 µM against α-amylase and α-glucosidase enzymes, respectively. Compounds 1-34 also displayed moderate antioxidant potential in the range of IC50 = 96.50 ± 0.45 to 189.98 ± 1.00 µM in comparison to the control butylated hydroxytoluene (BHT) (IC50 = 66.50 ± 0.36 µM), in DPPH radical scavenging activities. Additionally, all synthetic derivatives were subjected to a molecular docking study to investigate the interaction details of compounds 1-34 (ligands) with the active site of enzymes (receptors). These results indicate that the newly synthesized pyridone class may serve as promising lead candidates for controlling diabetes mellitus and as antioxidants.

An Improved Multimodal Biometric Identification System Employing Score-Level Fuzzification of Finger Texture and Finger Vein Biometrics.

This research work focuses on a Near-Infra-Red (NIR) finger-images-based multimodal biometric system based on Finger Texture and Finger Vein biometrics. The individual results of the biometric characteristics are fused using a fuzzy system, and the final identification result is achieved. Experiments are performed for three different databases, i.e., the Near-Infra-Red Hand Images (NIRHI), Hong Kong Polytechnic University (HKPU) and University of Twente Finger Vein Pattern (UTFVP) databases. First, the Finger Texture biometric employs an efficient texture feature extracting algorithm, i.e., Linear Binary Pattern. Then, the classification is performed using Support Vector Machine, a proven machine learning classification algorithm. Second, the transfer learning of pre-trained convolutional neural networks (CNNs) is performed for the Finger Vein biometric, employing two approaches. The three selected CNNs are AlexNet, VGG16 and VGG19. In Approach 1, before feeding the images for the training of the CNN, the necessary preprocessing of NIR images is performed. In Approach 2, before the pre-processing step, image intensity optimization is also employed to regularize the image intensity. NIRHI outperforms HKPU and UTFVP for both of the modalities of focus, in a unimodal setup as well as in a multimodal one. The proposed multimodal biometric system demonstrates a better overall identification accuracy of 99.62% in comparison with 99.51% and 99.50% reported in the recent state-of-the-art systems.

Assessing the knowledge, attitude, and practice measures against tuberculosis in patients in ambulatory department facilities in Pakistan: a cross-sectional analysis.

Tuberculosis (TB), at present, is the leading infectious etiology of death globally. In Pakistan, there are approximately 510,000 new cases annually, with more than 15,000 of them developing into drug-resistant TB, making the nation the fifth-leading country in TB prevalence in the world. Due to the ongoing COVID-19 pandemic, the focus has drifted away from TB screening, diagnostic and health awareness campaigns, and therapeutic measures endangering knowledge, attitude, and practices (KAP) towards TB in our population. We conducted a cross-sectional descriptive study in Pakistan to assess the KAP of Pakistani residents attending the adult outpatient departments of public hospitals for any health-related concerns. Our sample size was 856 participants, with a median age of 22 years. Occupation-wise, those who were employed had better knowledge of TB than those who were unemployed [odds ratio (OR): 1.011; 95% confidence interval (CI): 1.005-1.8005]. No differences were observed in TB knowledge between those adherents to common preventive practices versus those not adherent (OR: 0.875; 95% CI: 0.757-1.403). More than 90% of participants agreed that TB is dangerous for the community, and the majority opted against stigmatizing TB patients (79.1%). People who could read and write were 3.5 times more likely to have a good attitude towards TB compared to those who could not (OR: 3.596; 95% CI: 1.821-70.230; p=0.037). Similarly, employed subjects had better attitudes compared to unemployed ones (OR: 1.125; 95% CI: 0.498-1.852; p=0.024) and those with better knowledge of TB had a better attitude grade (OR: 1.749; 95% CI: 0.832-12.350; p=0.020). Age, occupation, and educational status were statistically significant among the two groups (p=0.038, p=0.023, p=0.000). Literate subjects had three times better practice towards TB than illiterate subjects (OR: 3.081; 95% CI: 1.869-4.164; p=0.000). Future education and awareness programs should target specific groups, such as the unemployed and illiterate, with practice-focused approaches. Our study outcomes can enable the concerned officials and authorities to take appropriate evidence-based steps to direct the efforts efficiently to curtail the burden of TB in Pakistan and to limit its progression, which could potentially lead our nation to become a multi drug-resistant TB endemic territory.

Functional annotation of breast cancer risk loci: current progress and future directions.

Genome-wide association studies coupled with large-scale replication and fine-scale mapping studies have identified more than 150 genomic regions that are associated with breast cancer risk. Here, we review efforts to translate these findings into a greater understanding of disease mechanism. Our review comes in the context of a recently published fine-scale mapping analysis of these regions, which reported 352 independent signals and a total of 13,367 credible causal variants. The vast majority of credible causal variants map to noncoding DNA, implicating regulation of gene expression as the mechanism by which functional variants influence risk. Accordingly, we review methods for defining candidate-regulatory sequences, methods for identifying putative target genes and methods for linking candidate-regulatory sequences to putative target genes. We provide a summary of available data resources and identify gaps in these resources. We conclude that while much work has been done, there is still much to do. There are, however, grounds for optimism; combining statistical data from fine-scale mapping with functional data that are more representative of the normal "at risk" breast, generated using new technologies, should lead to a greater understanding of the mechanisms that influence an individual woman's risk of breast cancer.

Genomic diversity of SARS-CoV-2 in Pakistan during the fourth wave of pandemic.

The emergence of different variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in upsurges of coronavirus disease 2019 (COVID-19) cases around the globe. Pakistan faced the fourth wave of COVID-19 from July to August 2021 with 314,786 cases. To understand the genomic diversity of circulating SARS-CoV-2 strains during the fourth wave of the pandemic in Pakistan, this study was conducted. The samples from 140 COVID-19-positive patients were subjected to whole-genome sequencing using the iSeq Sequencer by Illumina. The results showed that 97% (n = 136) of isolates belonged to the delta variant while three isolates belonged to alpha and only one isolate belonged to the beta variant. Among delta variant cases, 20.5% (n = 28) isolates were showing B.1.617.2 while 23.5% (n = 25), 17.59% (n = 19), 14.81% (n = 16), and 13.89% (n = 15) of isolates were showing AY.108, AY.43 AY.127, and AY.125 lineages, respectively. Islamabad was found to be the most affected city with 65% (n = 89) of delta variant cases, followed by Karachi (17%, n = 23), and Rawalpindi (10%, n = 14). Apart from the characteristic spike mutations (T19R, L452R, T478K, P681R, and D950N) of the delta variant, the sublineages exhibited other spike mutations as E156del, G142D, T95I, A222V, G446V, K529N, N532S, Q613H, and V483A. The phylogenetic analysis revealed the introductions from Singapore, the United Kingdom, and Germany. This study highlights the circulation of delta variants (B.1.617.2 and sublineages) during the fourth wave of pandemic in Pakistan.

Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan.

SARS-CoV-2 variants of concern (VOCs) have emerged worldwide and gained significant importance due to their high transmissibility and global spread, thus meriting close monitoring. In Pakistan, limited information is available on circulation of these variants as the alpha variant has been reported the main circulating lineage. The current study was designed to detect and explore the genomic diversity of SARS-CoV-2 lineages circulating during the third wave of the pandemic in the indigenous population. From May 01 to June 09, 2021, a total of 16 689 samples were tested using TaqPath™ COVID-19 kit for the presence of SARS-CoV-2. Overall, 2562 samples (15.4%) were COVID-19 positive. Out of these positive samples, 2124 (12.7%) did not show the spike gene amplification (spike gene target failure ([SGTF]), whereas 438 (2.6%) showed spike gene amplification (non-SGTF). A subset (n = 58/438) of non-SGTF samples were randomly selected for whole-genome sequencing. Among VOCs, 45% (n = 26/58) were delta, 46% (n = 27/58) were beta, and one was gamma variant. The delta variant cases were reported mainly from Islamabad (n = 15; 58%) followed by Rawalpindi and Azad Kashmir (n = 1; 4% each). Beta variant cases originated mainly from Karachi (n = 8; 30%) and Islamabad (n = 11; 41%) and the gamma variant case was reported in a traveler from Italy. The delta, beta, and gamma variants possessed lineage-specific spike mutations. Notably, two rare mutations (E484Q and L5F) were found in the delta variant. Furthermore, in the beta variant, two significant rare non-synonymous spike mutations (A879S and K444R) were also reported. High prevalence of beta and delta variants in local population may increase the number of cases in the near future and provides an early warning to national health authorities to take timely decisions and devise suitable interventions to contain a possible fourth wave.