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Abstract Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA molecule hybridizes with the DNA template strand. This study investigated the role of RAD52, a known DNA repair factor, in preventing collisions by directing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Furthermore, RAD52’s ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide evidence of an increased mutational burden from double-strand breaks at conserved R-loop sites in human tumor samples, which is increased in tumors with low RAD52 expression. In summary, this study underscores the importance of RAD52 in orchestrating the balance between replication and transcription processes to prevent collisions and maintain genome stability.

Abstract Background Pathogenic BRCA1 or BRCA2 germline mutations contribute to hereditary breast, ovarian, prostate, and pancreatic cancer. Paradoxically, bi-allelic inactivation of BRCA1 or BRCA2 (bBRCA1/2) is embryonically lethal and decreases cellular proliferation. The compensatory mechanisms that facilitate oncogenesis in bBRCA1/2 tumors remain unclear. Methods We identified recurrent genetic alterations enriched in human bBRCA1/2 tumors and experimentally validated if these improved proliferation in cellular models. We analyzed mutations and copy number alterations (CNAs) in bBRCA1/2 breast and ovarian cancer from the TCGA and ICGC. We used Fisher’s exact test to identify CNAs enriched in bBRCA1/2 tumors compared to control tumors that lacked evidence of homologous recombination deficiency. Genes located in CNA regions enriched in bBRCA1/2 tumors were further screened by gene expression and their effects on proliferation in genome-wide CRISPR/Cas9 screens. A set of candidate genes was functionally validated with in vitro clonogenic survival and functional assays to validate their influence on proliferation in the setting of bBRCA1/2 mutations. Results We found that bBRCA1/2 tumors harbor recurrent large-scale genomic deletions significantly more frequently than histologically matched controls (n = 238 cytobands in breast and ovarian cancers). Within the deleted regions, we identified 277 BRCA1-related genes and 218 BRCA2-related genes that had reduced expression and increased proliferation in bBRCA1/2 but not in wild-type cells in genome-wide CRISPR screens. In vitro validation of 20 candidate genes with clonogenic proliferation assays validated 9 genes, including RIC8A and ATMIN (ATM-Interacting protein). We identified loss of RIC8A, which occurs frequently in both bBRCA1/2 tumors and is synthetically viable with loss of both BRCA1 and BRCA2. Furthermore, we found that metastatic homologous recombination deficient cancers acquire loss-of-function mutations in RIC8A. Lastly, we identified that RIC8A does not rescue homologous recombination deficiency but may influence mitosis in bBRCA1/2 tumors, potentially leading to increased micronuclei formation. Conclusions This study provides a means to solve the tumor suppressor paradox by identifying synthetic viability interactions and causal driver genes affected by large-scale CNAs in human cancers.

Abstract Melanoma response to immune-modulating therapy remains incompletely characterized at the molecular level. In this study, we assess melanoma immunotherapy response using a multi-scale network approach to identify gene modules with coordinated gene expression in response to treatment. Using gene expression data of melanoma before and after treatment with nivolumab, we modeled gene expression changes in a correlation network and measured a key network geometric property, dynamic Ollivier-Ricci curvature, to distinguish critical edges within the network and reveal multi-scale treatment-response gene communities. Analysis identified six distinct gene modules corresponding to sets of genes interacting in response to immunotherapy. One module alone, overlapping with the nuclear factor kappa-B pathway (NFkB), was associated with improved patient survival and a positive clinical response to immunotherapy. This analysis demonstrates the usefulness of dynamic Ollivier-Ricci curvature as a general method for identifying information-sharing gene modules in cancer.

ABSTRACT Background: Myocardial infarction remains a leading cause of global morbidity and mortality. One major risk factor for atherosclerosis and MI is smoking, a highly prevalent habit in South Asian adolescents and healthcare professionals; particularly in Pakistan. This study was conducted to compare clinical presentation and outcome of myocardial infarction (MI) in smokers and non-smokers. Methodology: This study included a total of 100 patients who presented to a tertiary care centre for cardiac patients in Karachi. Patients between 18-65 years presenting with MI were included in the study (N=100). They were divided into two groups, based on smoking status. The smoking group included patients who had smoked for 10 years or more. Patients who had smoked for less than 10 years or had quit less than 5 years back were excluded from both samples. Informed consent was taken from each participant. Results: This study observed that 46% of the non-smokers as compared to 8% smokers present with chest pain (p = 0.001). Arrhythmia was seen in 20% of the smokers compared to 4% of the non-smokers (p = 0.001). Acute heart failure was seen in 24% smokers and only 4% non-smokers (p = 0.004). Of the smoking group, 32% of the patients expired despite treatment as compared to 6% of smokers (p = 0.001). Conclusions: Specific symptoms of myocardial infarction are more commonly seen in non-smokers, aiding early diagnosis and consequently leading to a good prognosis. Alternatively, fatal complications and death rate is a more likely outcome in smokers.

Human papilloma virus (HPV)-related oncogenesis in head and neck cancer establishes a local microenvironment rich with immune cells, however the composition of the microenvironment in recurrent disease following definitive treatment is poorly understood. Here, we investigate the composition and spatial relationships between tumor and immune cells in recurrent head and neck cancer following curative intent chemoradiotherapy. Multiplexed immunofluorescence with 12 unique markers, through two multiplex immunofluorescent panels, was performed to evaluate 27 tumor samples including 18 pre-treatment primary and 9 paired recurrent tumors. Tumor and immune cell populations were phenotyped and quantified using a previously validated semi-automated digital pathology platform for cell segmentation. Spatial analysis was conducted by evaluating immune cells within the tumor, peri-tumoral stroma, and distant stroma. Initial tumors in patients with subsequent recurrence were found to be enriched in tumor associated macrophages and displayed an immune excluded spatial distribution. Recurrent tumors after chemoradiation were hypo-inflamed, with a statistically significant reduction in the recently identified stem-like TCF1+ CD8 T-cells, which normally function to maintain HPV-specific immune responses in the setting of chronic antigen exposure. Our findings indicate that the tumor microenvironment of recurrent HPV-related head and neck cancers displays a reduction in stem-like T cells, consistent with an immune microenvironment with a reduced ability to mount T-cell-driven anti-tumor immune responses.

BACKGROUND Recurrent and/or metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) is generally an incurable disease, with patients experiencing median survival of under 10 months and significant morbidity. While immune checkpoint blockade (ICB) drugs are effective in approximately 20% of patients, the remaining experience limited clinical benefit and are exposed to potential adverse effects and financial costs. Clinically approved biomarkers, such as tumor mutational burden (TMB), have a modest predictive value in HNSCC.METHODS We analyzed clinical and genomic features, generated using whole-exome sequencing, in 133 ICB-treated patients with R/M HNSCC, of whom 69 had virus-associated and 64 had non-virus-associated tumors.RESULTS Hierarchical clustering of genomic data revealed 6 molecular subtypes characterized by a wide range of objective response rates and survival after ICB therapy. The prognostic importance of these 6 subtypes was validated in an external cohort. A random forest-based predictive model, using several clinical and genomic features, predicted progression-free survival (PFS), overall survival (OS), and response with greater accuracy than did a model based on TMB alone. Recursive partitioning analysis identified 3 features (systemic inflammatory response index, TMB, and smoking signature) that classified patients into risk groups with accurate discrimination of PFS and OS.CONCLUSION These findings shed light on the immunogenomic characteristics of HNSCC tumors that drive differential responses to ICB and identify a clinical-genomic classifier that outperformed the current clinically approved biomarker of TMB. This validated predictive tool may help with clinical risk stratification in patients with R/M HNSCC for whom ICB is being considered.FUNDING Fundación Alfonso Martín Escudero, NIH R01 DE027738, US Department of Defense CA210784, The Geoffrey Beene Cancer Research Center, The MSKCC Population Science Research Program, the Jayme Flowers Fund, the Sebastian Nativo Fund, and the NIH/NCI Cancer Center Support Grant P30 CA008748.

Abstract Pathogenic germline mutations in the RAD51 paralog genes RAD51C and RAD51D, are known to confer susceptibility to ovarian and triple-negative breast cancer. Here, we investigated whether germline loss-of-function variants affecting another RAD51 paralog gene, RAD51B, are also associated with breast and ovarian cancer. Among 3422 consecutively accrued breast and ovarian cancer patients consented to tumor/germline sequencing, the observed carrier frequency of loss-of-function germline RAD51B variants was significantly higher than control cases from the gnomAD population database (0.26% vs 0.09%), with an odds ratio of 2.69 (95% CI: 1.4–5.3). Furthermore, we demonstrate that tumors harboring biallelic RAD51B alteration are deficient in homologous recombination DNA repair deficiency (HRD), as evidenced by analysis of sequencing data and in vitro functional assays. Our findings suggest that RAD51B should be considered as an addition to clinical germline testing panels for breast and ovarian cancer susceptibility.

Background Merkel cell carcinoma (MCC) often responds to PD-1 pathway blockade, regardless of tumor-viral status (~80% of cases driven by the Merkel cell polyomavirus (MCPyV)). Prior studies have characterized tumor-specific T cell responses to MCPyV, which have typically been CD8, but little is known about the T cell response to UV-induced neoantigens.Methods A patient in her mid-50s with virus-negative (VN) MCC developed large liver metastases after a brief initial response to chemotherapy. She received anti-PD-L1 (avelumab) and had a partial response within 4 weeks. Whole exome sequencing (WES) was performed to determine potential neoantigen peptides. Characterization of peripheral blood neoantigen T cell responses was evaluated via interferon-gamma (IFNγ) ELISpot, flow cytometry and single-cell RNA sequencing. Tumor-resident T cells were characterized by multiplexed immunohistochemistry.Results WES identified 1027 tumor-specific somatic mutations, similar to the published average of 1121 for VN-MCCs. Peptide prediction with a binding cut-off of ≤100 nM resulted in 77 peptides that were synthesized for T cell assays. Although peptides were predicted based on class I HLAs, we identified circulating CD4 T cells targeting 5 of 77 neoantigens. In contrast, no neoantigen-specific CD8 T cell responses were detected. Neoantigen-specific CD4 T cells were undetectable in blood before anti-PD-L1 therapy but became readily detectible shortly after starting therapy. T cells produced robust IFNγ when stimulated by neoantigen (mutant) peptides but not by the normal (wild-type) peptides. Single cell RNAseq showed neoantigen-reactive T cells expressed the Th1-associated transcription factor (T-bet) and associated cytokines. These CD4 T cells did not significantly exhibit cytotoxicity or non-Th1 markers. Within the pretreatment tumor, resident CD4 T cells were also Th1-skewed and expressed T-bet.Conclusions We identified and characterized tumor-specific Th1-skewed CD4 T cells targeting multiple neoantigens in a patient who experienced a profound and durable partial response to anti-PD-L1 therapy. To our knowledge, this is the first report of neoantigen-specific T cell responses in MCC. Although CD4 and CD8 T cells recognizing viral tumor antigens are often detectible in virus-positive MCC, only CD4 T cells recognizing neoantigens were detected in this patient. These findings suggest that CD4 T cells can play an important role in the response to anti-PD-(L)1 therapy.

Abstract Inherited mutations in BRCA1, BRCA2, and PALB2 cause a high risk of breast cancer. Here, we conducted parallel conditional knockout (CKO) of Brca1, Palb2, and Brca2, individually and in combination, along with one copy of Trp53, in the mammary gland of nulliparous female mice. We observed a functional equivalence of the three genes in their basic tumor-suppressive activity, a linear epistasis of Palb2 and Brca2, but complementary roles of Brca1 and Palb2 in mammary tumor suppression, as combined ablation of either Palb2 or Brca2 with Brca1 led to delayed tumor formation. Whole-exome sequencing (WES) revealed both similarities and differences between Brca1 and Palb2 or Brca2 null tumors. Analyses of mouse mammary glands and cultured human cells showed that combined loss of BRCA1 and PALB2 led to high levels of reactive oxygen species (ROS) and increased apoptosis, implicating oxidative stress in the delayed tumor development in Brca1;Palb2 double CKO mice. The functional complementarity between BRCA1 and PALB2/BRCA2 and the role of ROS in tumorigenesis require further investigation.

Abstract Metaplastic breast cancers (MBCs) are characterized by complex genomes, which seem to vary according to their histologic subtype. TERT promoter hotspot mutations and gene amplification are rare in common forms of breast cancer, but present in a subset of phyllodes tumors. Here, we sought to determine the frequency of genetic alterations affecting TERT in a cohort of 60 MBCs with distinct predominant metaplastic components (squamous, 23%; spindle, 27%; osseous, 8%; chondroid, 42%), and to compare the repertoire of genetic alterations of MBCs according to the presence of TERT promoter hotspot mutations or gene amplification. Forty-four MBCs were subjected to: whole-exome sequencing (WES; n = 27) or targeted sequencing of 341-468 cancer-related genes (n = 17); 16 MBCs were subjected to Sanger sequencing of the TERT promoter, TP53 and selected exons of PIK3CA, HRAS, and BRAF. TERT promoter hotspot mutations (n = 9) and TERT gene amplification (n = 1) were found in 10 of the 60 MBCs analyzed, respectively. These TERT alterations were less frequently found in MBCs with predominant chondroid differentiation than in other MBC subtypes (p = 0.01, Fisher’s exact test) and were mutually exclusive with TP53 mutations (p

There is an unmet clinical need for simple, accessible biomarkers to select patients who are more likely to respond to immune checkpoint therapy. Here the authors show that a lower neutrophil-to-lymphocyte ratio is associated with better overall and progressive-free survival, as well as higher rate of response, in a multi-cancer cohort of patients treated with immune checkpoint inhibitors.

Purpose: Recurrent head and neck cancers are associated with significant morbidity and mortality. Outcomes of multiple courses of radiation have not yet been described. Methods and Materials: A single institution database was queried to retrospectively review treatment plans and select patients who underwent ≥ 3 courses of radiation to the head and neck region. Results: Thirty-three patients were found to have ≥ 3 courses of radiation with overlapping fields. Median local recurrence free survival after last course of reirradiation was 9.1 months and median overall survival was 10 months. Grade 3 and above toxicities were reported in 15 patients (45%). Grade 4 and above toxicities were reported in seven patients (21%). There was no grade 5 toxicity. 20 patients (61%) underwent subsequent therapies following completion of repeat reirradiation. Conclusions: Repeat reirradiation to the head and neck region is feasible and carries significant risks that are most appropriately managed with a multi-disciplinary team and must be balanced against the potential for local control and opportunities for emerging systemic therapies.

Purpose: To demonstrate temporal lobe necrosis (TLN) rate and clinical/dose-volume factors associated with TLN in radiation-naïve patients with head and neck cancer treated with proton therapy where the field of radiation involved the skull base. Materials and Methods: Medical records and dosimetric data for radiation-naïve patients with head and neck cancer receiving proton therapy to the skull base were retrospectively reviewed. Patients with < 3 months of follow-up, receiving < 45GyRBE or nonconventional fractionation, and/or no follow-up magnetic resonance imaging (MRI) were excluded. TLN was determined using MRI and graded using Common Terminology Criteria for Adverse Events (CTCAE) v5.0. Clinical (gender, age, comorbidities, concurrentchemotherapy, smoking, radiation techniques) and dose-volume parameters were analyzed for TLN correlation. The receiver operating characteristic curve and area under the curve (AUC) were performed to determine the cutoff points of significant dose-volume parameters. Results: Between 2013 and 2019, 234 patients were included. The median follow-up time was 22.5 months (range =3.2–69.3). Overall TLN rates of any grade, ≥ grade 2, and ≥ grade 3 were 5.6% (N =13), 2.1%, and 0.9%, respectively. The estimated 2-year TLN rate was 4.6%, and the 2-year rate of any brain necrosis was 6.8%. The median time to TLN was 20.9 months from proton completion. Absolute volume receiving 40, 50, 60, and 70 GyRBE (absolute volume [aV]); mean and maximum dose received by the temporallobe; and dose to the 0.5, 1, and 2 cm3 volume receiving the maximum dose (D0.5cm3, D1cm3, and D2cm3, respectively) of the temporal lobe were associated with greater TLN risk while clinical parameters showed no correlation. Among volume parameters, aV50 gave maximum AUC (0.921), and D2cm3 gave the highest AUC (0.935) among dose parameters. The 11-cm3 cutoff value for aV50 and 62 GyRBE for D2cm3 showed maximum specificity and sensitivity. Conclusion: The estimated 2-year TLN rate was 4.6% with a low rate of toxicities ≥grade 3; aV50 ≤11 cm3, D2cm3 ≤62 GyRBE and other cutoff values are suggested as constraints in proton therapy planning to minimize the risk of any grade TLN. Patients whose temporal lobe(s) unavoidably receive higher doses than these thresholds should be carefully followed with MRI after proton therapy.

Purpose: Radiation treatment plans undergo peer review during chart rounds, but changes to treatment volumes would require replanning. Our group implemented weekly head and neck cancer “volume rounds” to peer review all target volumes for head and neck cancer before radiation therapy (RT) planning and chart rounds. Methods and Materials: We analyzed modifications made to planning target volumes (PTVs) at volume rounds for consecutive nonproton head and neck cancer cases from May 2020 to May 2021. Nine head and neck radiation oncologists participated in weekly volume rounds during this time. Recommendations were categorized as no changes, minor changes, major changes, additional workup (eg, biopsy or imaging), and consultation or tumor board discussion needed before the start of RT. Minor changes to PTVs generally did not require a second review before treatment planning while major changes did. Results: PTVs for 511 cases involving 432 patients underwent peer review and 298 (58.3%) of these cases did not require any modifications before treatment planning. Minor and major changes were recommended in 75 (14.7%) and 86 (16.8%) cases, respectively. Forty-five (8.8%) cases were recommended to have additional workup and 23 (4.5%) required additional consultation with nonradiation surgeons or medical oncologists. Of the 45 cases that were recommended for additional workup, 40 underwent biopsy or imaging. Positive findings on imaging or biopsy occurred in 13 patients, leading to a significant change in management, including 4 patients who underwent additional surgery after positive findings before the start of RT. Conclusions: Prospective peer review during head and neck cancer volume rounds led to frequent minor and major alterations to PTVs. Significant changes in the overall treatment plan, such as additional surgery before start of RT, occurred in a minority of patients.

Genome wide association studies (GWAS) of human diseases have generally identified many loci associated with risk with relatively small effect sizes. The omnigenic model attempts to explain this observation by suggesting that diseases can be thought of as networks, where genes with direct involvement in disease-relevant biological pathways are named 'core genes', while peripheral genes influence disease risk via their interactions or regulatory effects on core genes. Here, we demonstrate a method for identifying candidate core genes solely from genes in or near disease-associated SNPs (GWAS hits) in conjunction with protein-protein interaction network data. Applied to 1,381 GWAS studies from 5 ancestries, we identify a total of 1,865 candidate core genes in 343 GWAS studies. Our analysis identifies several well-known disease-related genes that are not identified by GWAS, including BRCA1 in Breast Cancer, Amyloid Precursor Protein (APP) in Alzheimer's Disease, INS in A1C measurement and Type 2 Diabetes, and PCSK9 in LDL cholesterol, amongst others. Notably candidate core genes are preferentially enriched for disease relevance over GWAS hits and are enriched for both Clinvar pathogenic variants and known drug targets-consistent with the predictions of the omnigenic model. We subsequently use parent term annotations provided by the GWAS catalog, to merge related GWAS studies and identify candidate core genes in over-arching disease processes such as cancer-where we identify 109 candidate core genes.

Purpose: Deficiencies in DNA damage repair (DDR) and response represent a common alteration in tumors, and exploitation of this feature using therapeutics has become more prominent. Methods and materials: Recent work has highlighted the important interaction between DDR defects, as well as DDR targeting agents such as radiation and the immunogenicity of the tumor. This relationship emphasizes the potential for combination therapeutics with immune checkpoint inhibitors (ICI). Somatic mutations and DDR defects are some of the strongest predictors of response to ICI. Results: This review highlights the interplay among DDR pathways, ionizing radiation, and ICI efficacy. The mechanisms of radiation immunogenicity, including the cytosolic DNA sensing cGAS/STING pathways, are also described. Conclusions: A greater mechanistic understanding of the complex interaction between the DNA damage response and the immune system will expand the therapeutic potential of immunotherapy for patients with advanced cancer.

Targeting DNA repair-deficient tumors is one of the most promising therapeutic strategies in cancer research; however, accurately predicting which tumors will respond can be a challenge. Here the authors present a review of the current state of knowledge in DNA repair deficiency across human cancers.

ABSTRACT OBJECTIVE: To evaluate the frequency and factors associated with smoking among female university students in Pakistan. METHODS: This cross-sectional survey was conducted in 4 cities (Karachi, Hyderabad, Multan and Lahore) of Pakistan. A total of 689 female students from 18 universities (including medical, engineering & social sciences universities) filled the questionnaire through convenient sampling method. Data analysis was done on SPSS 22. Binary logistic regression, with 95% confidence interval (CI) was used to determine the factors associated with smoking. RESULTS: Mean age at initiation of smoking was 16.65±2.46 years. Total frequency of smoking was 7.4% (n=51/689). Out of 51 students involved in smoking, 25 (49%) used shisha, 7 (13.7%) used Cigarette and 19 (37%) used both modes of smoking. Students who consider smoking necessary for Social gathering are 5 times more prone to smoke. Strong relationship between advertisement on Social media and smoking was found (p

Germline mutations in homologous recombination (HR) DNA repair genes are linked to breast and ovarian cancer. Here, the authors show that mutually exclusive bi-allelic inactivation of HR genes are present in other cancer types and associated with genomic features of HR deficiency, expanding the potential use of HR-directed therapies.

Myoepithelial carcinoma (MECA) is a rare aggressive salivary gland cancer. Here, the authors analyze the genomic landscape of MECA and identify a high prevalence of oncogenic gene fusions, primarily PLAG1 fusions, highlighting TGFBR3-PLAG1 as a potential hallmark of MECA.

Abstract Background Pakistan is classified as one of the high multi-drug resistant tuberculosis (MDR-TB) burden countries. A poorly regulated private sector, over-prescription of antibiotics and self-medication has led to augmented rates of drug-resistance in the country. Pakistan’s first national anti-tuberculosis drug resistance survey identified high prevalence of fluoroquinolone resistance among MDR-TB patients. Further institutional evidence of fluoroquinolone drug-resistance can support re-evaluation of treatment regimens as well as invigorate efforts to control antibiotic resistance in the country. Findings In this study, data for drug-susceptibility testing (DST) was retrospectively analyzed for a total of 133 patients receiving MDR-TB treatment at the Chest Department of Jinnah Postgraduate Medical Center, Karachi, Pakistan. Frequency analyses for resistance patterns was carried out and association of fluoroquinolone (ofloxacin) resistance with demographics and past TB treatment category were assessed. Within first-line drugs, resistance to isoniazid was detected in 97.7% of cases, followed by rifampicin (96.9%), pyrazinamide (86.4%), ethambutol (69.2%) and streptomycin (64.6%). Within second-line drugs, ofloxacin resistance was detected in 34.6% of cases. Resistance to ethionamide and amikacin was 2.3% and 1.6%, respectively. Combined resistance of oflaxacin and isoniazid was detected in 33.9% of cases. Age, gender and past TB treatment category were not significantly associated with resistance to ofloxacin. Conclusion Fluoroquinolone resistance was observed in an alarmingly high proportion of MDR-TB cases. Our results suggest caution in their use for empirical management of MDR-TB cases and recommended treatment regimens for MDR-TB may require re-evaluation. Greater engagement of private providers and stringent pharmacy regulations are urgently required.

Background: The phenomenon of smoking among schoolchildren has been observed to stem from lenient attitudes of teachers towards smoking. Smoking, a health hazard, proven over years of research, leads to increase in morbidity and mortality rates. This study determined the role of school policies and teacher attitudes towards the perception and adoption of smoking habits by students of private and public schools. Method: This was a cross-sectional study in which 632 school personnel in various private and public schools of South Karachi filled a questionnaire. Informed consent was obtained from all participants; ethical approval for this study was obtained from the Ethical Review Committee of JPMC before the study was conducted. Data was collected via survey forms after consent from individuals. Statistical analysis was done using SPSS v.17. Results: The prevalence of teacher smoking within school premises was found to be 8.8% and 5.9% in private and public sectors, respectively. A significant difference was found between the school policies enforced in private and government schools against personnel found smoking (p=0.00016). Even though private school personnel smoked more in school premises than government but 32.6% of private school teachers felt responsible for teaching about health compared to only 21.5% public school teachers (p=0.0072). Conclusion: There is a pressing need for awareness and education of teachers regarding their attitude towards smoking on school grounds and its significant link with students adopting smoking. Other exposures and risk factors influencing student tobacco usage needs to be studied in more depth.

Pulmonary alveolar microlithiasis is a rare disease with an almost unheard of pathogenesis. With very few cases to document worldwide, predominantly being discovered in Turkey, Italy, and America, it has been nearly impossible to determine a concrete etiology. However, one standout biochemical finding most cases of PAM have in common is a mutation in the SLC34A2 gene coding for the sodium-phosphate cotransporter found in Type II alveolar cells. This cotransporter is responsible for maintaining equilibrium of phosphorus which is a vital component of surfactant. Diagnostic exploration is achieved via radiological imaging, bronchoalveolar lavage and above all, transbronchial lung biopsy. However, in this particular case, due to the patient’s hypoxic condition, Technetium 99m diphosphonate scanning was employed in place of the biopsy. A non-invasive procedure, technetium 99m can detect extensive pulmonary uptake, hereby diagnosing the patient and protect against the physical damage and accompanying side effects inflicted upon the patient by various invasive procedures. In future, to avoid wastage of resources, the use of technetium 99m diphosphonate scanning should be more prevalent in the diagnosis process of PAM.

Fusion of two teeth is rare developmental disorder which is encountered by a clinician. It is commonly reported in deciduous dentition. The fused crown appears broader and usually an esthetic concern. This condition usually reveals a decreased teeth count. Unilateral occurrence of fusion in permanent mandibular anterior teeth is a rare phenomenon. Hence this case report is presented.

Background: A lung abscess is characterized by a necrotic lesion with marked cavitation and exudate within the lung parenchyma. The objective of this study was to identify the most common causative agent of lung abscess within our target population. Methods: Retrospective data from two consecutive years was obtained from the pulmonology department at Jinnah Postgraduate Medical Centre, one of Pakistan’s largest public hospitals. A total of 41 cases of lung abscess were identified on the bases of clinical, radiological and microbiological evidence. These cases were then analysed to establish a link between the incidence of abscess and key factors such as the most common causative organism, the correlation of age and gender and the location within the lung parenchyma. Results: Sputum for routine culture and sensitivity (C/S) showed Pseudomonas Aeruginosa (29.3%) as the most common causative organism. Correlation between abscess and risk factors such as history of smoking (65.9%), poor oral hygiene (56.1%), diabetes (43.9%) and alcoholism (14.6%) have been discussed and compared to previous publications. The frequency of common symptoms such as productive cough (90.2%), fever (82.9%) hemoptysis (58.5%) and clubbing of fingers (46.3%) have been analysed and a contrast is drawn in some instances between our obtained values and pre-existing data. The most common site of involvement is the lower lobe of the right lung (51.2%). Conclusion: Pseudomonas Aeruginosa was found to be the most common causative bacteria within the population for lung abscess while smoking was shown to be the most common risk factor.

Background and purpose: In this study we investigated the ability of textures from T1-weighted MRI scans post-contrast (T1wpost) to identify the critical muscle(s) for radiation-induced trismus. Materials and methods: The study included ten cases (Trismus: ≥Grade 1), and ten age-sex-tumor-location-and-stage-matched controls treated with intensity-modulated radiotherapy to 70 Gy@2.12 Gy in 2005–2009. Trismus status and T1wPost were conducted within one year post-radiotherapy. For the masseter, lateral and medial pterygoids, and temporalis (M/LP/MP/T), 24 textures were extracted (Grey Level Co-Occurrence (GLCM), Histogram, and Shape). Univariate logistic regression with Bootstrapping (1000 populations) was applied to compare the muscle mean dose (Dmean) and textures between cases and controls (ipsilateral muscles); candidate predictors were suggested by an average p ≤ 0.20 across all Bootstrap populations. Results: Dmean to M/LP/MP (p = 0.03/0.14/0.09), one MP/T (p = 0.12/0.17), and three M (p = 0.14–0.19) textures were candidate predictors. Three of these textures were GLCM- and two Histogram textures with the former being generally higher and the latter lower for cases compared to controls. The Dmean to M and MP, and Haralick Correlation (GLCM) of MP presented with the best discriminative ability (area under the receiver-operating characteristic curve: 0.85, 0.77, and 0.78), and the correlation between Dmean and this texture was weak (Spearman’s rank correlation coefficient: 0.26–0.27). Conclusions: Our exploratory study points towards an interplay between the dose to the masseter, and the medial pterygoid together with the local relationship between the mean MRI intensity relative to its variance of the medial pterygoid for radiation-induced trismus. This opens up for exploration of this interplay within the radiation-induced trismus etiology in the larger multi-institutional setting. Keywords: Head and neck cancer, Radiotherapy, Trismus, Quantitative image, Texture, Radiomics

Objective: To determine frequency of factors leading to poor outcome of non-invasive positive pressure ventilation in acute exacerbation of chronic obstructive pulmonary disease. Methods: This cross sectional study was conducted at our center between May 2012 and November 2012. A total of 195 diagnosed patients of acute exacerbation of chronic obstructive pulmonary disease meeting the inclusion criteria were selected from the ER department. At the time of admission age was inquired BP, respiratory rate and oxygen saturation will be noted and pedal edema was assessed and investigations were sent for pH assessment. Noninvasive positive pressure ventilation (NIPPV) using BiPAP was applied in spontaneous mode by the help of oronasal mask. Presence of respiratory rate (less than 12/min), systolic blood pressure 140 bpm was taken as poor outcome. Results: The average age of the cases was 61.9±9.3 years with male to female ratio being 1.5:1. NIPPV was successful in 151 (77.4%) cases and 44 (22.6%) cases were underwent endotracheal intubation. About 38 (44.7%) of patients with oxygen saturation (82%–86%) had poor prognosis. A total of 40 (55.6%) of patients with pH range 7.20–7.26, required endotracheal intubation, 43 (66.2%) with pedal edema underwent endotracheal intubation. While 29 (24.16%) patients of age >60 years needed endotracheal intubation. Conclusions: In this study, NIPPV was successful in 77.4% cases and 22.6% cases were underwent endotracheal intubation. Pedal edema was the most common factor leading to poor outcomes while age >60 years was the least common factor, 66.2% and 24.2% respectively.

Background: To determine the diagnostic yield of closed percutaneous pleural biopsy using Abrams needle and obtaining specific diagnosis in cases of exudative pleural effusion. Material & Methods: This observational study was undertaken during March 2015 to September 2015 in the Department of Thoracic Medicine Jinnah Post Graduate Medical Center Karachi. All patients with pleural effusion who were admitted and fulfilling the inclusion criteria were included in the study .Percutaneous pleural biopsy using Abrams needle was performed in all patients, the samples were sent for histopathology. The data was entered in a pre-designed performa. Results: A total of 60 patients participated in the study. The male to female ratio was 1.6:1. Average age of patients was 42.8 years. Data revealed that yield of pleural biopsy using Abrams needle was 70%. Specific diagnosis through Abram’s biopsy have shown 21 (35%) cases of tuberculosis, 16 (26.7%) cases of adenocarcinoma, 4 (6.7%) cases of chronic non specific inflammation, one (1.7%) case of lymphoma and 18 (30%) cases could not be reached for any diagnosis. Conclusion: Due to availability of newer techniques and image guided biopsies, closed needle biopsy procedures are becoming less common in developed countries. However, in a set up like Pakistan, due to the higher cost and lack of availability of newer techniques, closed biopsy procedures remain the standard of management for the diagnosis of pleural effusions.

Objective: To evaluate risk factors for multidrug-resistant tuberculosis (MDR-TB) in an urban setting of Pakistan. Design and methods: In this multicenter case–control study, patients aged 15 years old or older with sputum culture and sensitivity (C/S) diagnosed with pulmonary MDR-TB were defined as cases, whereas patients aged 15 years old or older with sputum C/S diagnosed and susceptible to pulmonary TB were regarded as controls. Fifty cases and 75 controls were enrolled from three tertiary-care hospitals in Karachi. Results: Multivariable logistic regression models showed that cases were more likely to have had a TB patient in the house prior to the diagnosis of MDR-TB (adjusted odds ratio [ORadj]=3.1, 95% confidence interval [CI]: 1.2, 8.3) or had a history of prior TB treatment (ORadj = 4.2, 95% CI: 1.1, 15.4). Furthermore, cases compared with controls tended to be male (ORadj = 3.6, 95% CI: 1.4, 9.7), 15–25 years of age (ORadj = 3.7, 95% CI: 1.2, 11.3), of Sindhi ethnicity (adjusted OR=9.1, 95% CI: 1.9, 43.4) or with low educational attainment (ORadj OR=5.5, 95% CI: 1.7–17.6, for no formal schooling; ORadj = 3.8, 95% CI: 1.1–14.1, 1 for 1–5 school years). Conclusions: A TB patient in the house or a history of prior TB treatment was strongly associated with MDR-TB in this study. Furthermore, younger age, male gender, Sindhi ethnicity and poor educational attainment entailed a high risk for MDR-TB. Targeted educational intervention for patients and their contacts may minimize the noncompliance with prescribed TB treatment and lessen MDR-TB magnitude in settings like Karachi.

Mutations, deletions, and changes in copy number of mitochondrial DNA (mtDNA), are observed throughout cancers. Here, we survey mtDNA copy number variation across 22 tumor types profiled by The Cancer Genome Atlas project. We observe a tendency for some cancers, especially of the bladder, breast, and kidney, to be depleted of mtDNA, relative to matched normal tissue. Analysis of genetic context reveals an association between incidence of several somatic alterations, including IDH1 mutations in gliomas, and mtDNA content. In some but not all cancer types, mtDNA content is correlated with the expression of respiratory genes, and anti-correlated to the expression of immune response and cell-cycle genes. In tandem with immunohistochemical evidence, we find that some tumors may compensate for mtDNA depletion to sustain levels of respiratory proteins. Our results highlight the extent of mtDNA copy number variation in tumors and point to related therapeutic opportunities.

Background Measuring eCo is rapid, non-invasive and inexpensive tool and correlate correctly with carboxyhemoglobin levels in blood. The aim of this study was to evaluate and compare the increase in end tidal carbon monoxide (eCO) levels in exhaled breath of passive smokers and healthy smokers after cigarette and shisha smoking. Methods In a cross sectional study eCO levels were measured in 70 subjects (24 cigarette smokers, 20 shisha smoker, 26 passive smokers) by use of portable device. Smokers were asked to smoke shisha for 30 mins in shisha cafe or to smoke 5 cigarettes in 30 mins in a restaurant. eCo levels were measured at baseline (30 mins), 35 mins, 60 mins and 90 mins in all groups after entry to the venue. The baseline mean eCO level among cigarette smokers was 3.5 +/- 0.6 ppm (part per million), passive cigarette smokers 3.7+/-1.0 ppm, shisha smokers 27.7+/-4.9 ppm and passive shisha smokers 18.3+/-8.4 ppm .The mean increase in eCO after 90 min among smokers was 9.4+/-4.6 (p

Introduction: Chronic obstructive pulmonary disease in non-smokers has been an important concern in past decade. We studied the risk factors responsible for more severe Chronic obstructive pulmonary disease. Identifying them would help to work against progression to more severe disease as well as prevention. Methods: A prospective cross sectional study was done in outpatient clinic of Jinnah postgraduate medical center from December 2010 to December 2011. All patients fulfilling the criteria for Chronic obstructive pulmonary disease were taken in study. Patients with less than five pack years smoking with other risk factors for Chronic obstructive pulmonary disease were evaluated. Results: Out of total 90 patients, 74 (82.2%) had mild chronic obstructive pulmonary disease and 16 (17.7%) had moderate to severe chronic obstructive pulmonary disease. Patients with single biomass exposure were found to have mild chronic obstructive pulmonary disease except those having mosquito coil exposure. Patients with mosquito coil and wood smoke exposure were observed to have moderate to severe chronic obstructive pulmonary disease (p-value 0.009). Conclusions: Wood smokewith mosquito coil smoke exposure is responsible for more severe chronic obstructive pulmonary disease. _______________________________________________________________________________________ Keywords: biomass; chronic obstructive pulmonary disease; non-smoker; tuberculosis.

Introduction: Chronic obstructive pulmonary disease in non-smokers has been an important concern in past decade. We studied the risk factors responsible for more severe Chronic obstructive pulmonary disease. Identifying them would help to work against progression to more severe disease as well as prevention. Methods: A prospective cross sectional study was done in outpatient clinic of Jinnah postgraduate medical center from December 2010 to December 2011. All patients fulfilling the criteria for Chronic obstructive pulmonary disease were taken in study. Patients with less than five pack years smoking with other risk factors for Chronic obstructive pulmonary disease were evaluated. Results: Out of total 90 patients, 74 (82.2%) had mild chronic obstructive pulmonary disease and 16 (17.7%) had moderate to severe chronic obstructive pulmonary disease. Patients with single biomass exposure were found to have mild chronic obstructive pulmonary disease except those having mosquito coil exposure. Patients with mosquito coil and wood smoke exposure were observed to have moderate to severe chronic obstructive pulmonary disease (p-value 0.009). Conclusions: Wood smokewith mosquito coil smoke exposure is responsible for more severe chronic obstructive pulmonary disease. _______________________________________________________________________________________ Keywords: biomass; chronic obstructive pulmonary disease; non-smoker; tuberculosis.