Comparative whole-genome transcriptome analysis in renal cell populations reveals high tissue specificity of MAPK/ERK targets in embryonic kidney.

BACKGROUND: MAPK/ERK signaling is a well-known mediator of extracellular stimuli controlling intracellular responses to growth factors and mechanical cues. The critical requirement of MAPK/ERK signaling for embryonic stem cell maintenance is demonstrated, but specific functions in progenitor regulation during embryonic development, and in particular kidney development remain largely unexplored. We previously demonstrated MAPK/ERK signaling as a key regulator of kidney growth through branching morphogenesis and normal nephrogenesis where it also regulates progenitor expansion. Here, we performed RNA sequencing-based whole-genome expression analysis to identify transcriptional MAPK/ERK targets in two distinct renal populations: the ureteric bud epithelium and the nephron progenitors. RESULTS: Our analysis revealed a large number (5053) of differentially expressed genes (DEGs) in nephron progenitors and significantly less (1004) in ureteric bud epithelium, reflecting likely heterogenicity of cell types. The data analysis identified high tissue-specificity, as only a fraction (362) of MAPK/ERK targets are shared between the two tissues. Tissue-specific MAPK/ERK targets participate in the regulation of mitochondrial energy metabolism in nephron progenitors, which fail to maintain normal mitochondria numbers in the MAPK/ERK-deficient tissue. In the ureteric bud epithelium, a dramatic decline in progenitor-specific gene expression was detected with a simultaneous increase in differentiation-associated genes, which was not observed in nephron progenitors. Our experiments in the genetic model of MAPK/ERK deficiency provide evidence that MAPK/ERK signaling in the ureteric bud maintains epithelial cells in an undifferentiated state. Interestingly, the transcriptional targets shared between the two tissues studied are over-represented by histone genes, suggesting that MAPK/ERK signaling regulates cell cycle progression and stem cell maintenance through chromosome condensation and nucleosome assembly. CONCLUSIONS: Using tissue-specific MAPK/ERK inactivation and RNA sequencing in combination with experimentation in embryonic kidneys, we demonstrate here that MAPK/ERK signaling maintains ureteric bud tip cells, suggesting a regulatory role in collecting duct progenitors. We additionally deliver new mechanistic information on how MAPK/ERK signaling regulates progenitor maintenance through its effects on chromatin accessibility and energy metabolism.

Plasma Proteomics Unveil Novel Immune Signatures and Biomarkers upon SARS-CoV-2 Infection.

Several elements have an impact on COVID-19, including comorbidities, age and sex. To determine the protein profile changes in peripheral blood caused by a SARS-CoV-2 infection, a proximity extension assay was used to quantify 1387 proteins in plasma samples among 28 Finnish patients with COVID-19 with and without comorbidities and their controls. Key immune signatures, including CD4 and CD28, were changed in patients with comorbidities. Importantly, several unreported elevated proteins in patients with COVID-19, such as RBP2 and BST2, which show anti-microbial activity, along with proteins involved in extracellular matrix remodeling, including MATN2 and COL6A3, were identified. RNF41 was downregulated in patients compared to healthy controls. Our study demonstrates that SARS-CoV-2 infection causes distinct plasma protein changes in the presence of comorbidities despite the interpatient heterogeneity, and several novel potential biomarkers associated with a SARS-CoV-2 infection alone and in the presence of comorbidities were identified. Protein changes linked to the generation of SARS-CoV-2-specific antibodies, long-term effects and potential association with post-COVID-19 condition were revealed. Further study to characterize the identified plasma protein changes from larger cohorts with more diverse ethnicities of patients with COVID-19 combined with functional studies will facilitate the identification of novel diagnostic, prognostic biomarkers and potential therapeutic targets for patients with COVID-19.

To assess the aggressiveness of oral squamous cell carcinoma in the young population.

Objectives: To assess the recurrence and disease-free survival in oral squamous cell carcinoma patients, and to compare them between two age groups. METHODS: Data were extracted from Patel hospital cancer registry database of patients admitted from January 1st2008 to December 31st 2018 based on retrospective diagnosed with oral squamous cell carcinoma. Patient stratified in to two groups i.e. patients with less than or more than 40 years. Various etiological factors, staging, treatment, site of the tumor and recurrence and mortality were assessed. RESULTS: Of the 450 patients, 124(27.5%) were in group A and 327(72.5%) were in group B. There were 101(81%) males in group A and 240(73.4%) males in group B. The overall mean age was 43.63±10.75 years (range: 22-70 years). The most common site of the tumour was cheek 232(51.5%). Recurrence of tumour was 45(36%) in group A and 120(37%) in group B (p=0.653). Overall mortality in group A was 67(54%) compared to 168(51%) in group B (p=0.811). CONCLUSIONS: Mortality and disease recurrence in both age groups was almost the same. Cheek was the most common site of presentation.

Risk factors associated with disease recurrence in patients with T4 staged Squamous Cell Carcinoma of the Oral Cavity treated with surgery and postoperative radiotherapy.

Objective: To determine the association of clinical and pathological parameters on recurrence of treated stage T4squamous cell carcinoma of oral cavity patients managed with surgery followed by concomitant chemo and radiation therapy. METHODS: The retrospective, cohort study was conducted at Patel Hospital, Karachi, and comprised data of patients diagnosed with oral squamous cell carcinoma and admitted between January 1, 2014, and January 30, 2019. Patients of either gender aged 20-80 years who had a minimum follow-up of one year were included. Data was collected using the Head and Neck Cancer registry form and the medical record files. The subjects were also contacted by telephone when needed. The study end-points were disease-free survival and overall survival. Data was analysed using SPSS 21. RESULTS: Out of the 83 patients, 65(78%) were male. The overall median(range) age was 46(20-80) years, and 43(52%) of them were aged 31-50 years. Overall, 15(18%) patients had positive margins and 48(58%) had proven cervical node metastasis on histopathology. Overall survival was 42.2% with the median(range) follow-up time was 14(9-21) months and 5-year disease-free survival was 45.8% with the median (range) follow-up time was 13(7-19). The factor that affected the final outcome was found to be the increasing nodal ratio (p=0.043). Conclusion: Among T4 oral squamous cell carcinoma patients treated with surgery and adjuvant therapy, the rate of disease recurrence was found to be high. Tumours with a high cervical nodal disease burden and/or margin involved were at substantially higher risk of recurrence.

Role of contrast enhanced computed tomography in assessing cervical lymph node metastases in oral cavity squamous cell carcinoma.

OBJECTIVE: To evaluate the diagnostic accuracy of contrast-enhanced computed tomography scan in detecting cervical nodal metastasis in oral cavity squamous cell carcinoma. METHODS: The retrospective cross-sectional study was conducted at Aga Khan University Hospital, Karachi, Pakistan. and comprised records from January 1, 2015, to October 31, 2016, of patients diagnosed with oral cavity squamous cell carcinoma and who underwent surgical resection of primary tumour along with neck dissection after having a contrast-enhanced computed tomography scan of head and neck. Diagnostic accuracy of the scans was calculated using final histopathology as the gold standard. All scans were reviewed by a consultant radiologist. Data was analysed using SPSS 23. RESULTS: Of the 100 patients whose records were reviewed, 70(70%) were female, 55(55%) had buccal and 32(32%) had tongue cancer.. The scans had sensitivity 83%, specificity 61.7%, positive predictive value 70.9%, negative predictive value 76.3% and overall diagnostic accuracy 73%. CONCLUSIONS: Computed tomography scan was found to be a useful tool for preoperative staging of oral cavity squamous cell carcinoma. However, due to low specificity and negative predictive value, elective neck dissection should still be done in a negative scan for cervical lymph node metastases.

Genotype-phenotype correlations in recessive titinopathies.

PURPOSE: High throughput sequencing analysis has facilitated the rapid analysis of the entire titin (TTN) coding sequence. This has resulted in the identification of a growing number of recessive titinopathy patients. The aim of this study was to (1) characterize the causative genetic variants and clinical features of the largest cohort of recessive titinopathy patients reported to date and (2) to evaluate genotype-phenotype correlations in this cohort. METHODS: We analyzed clinical and genetic data in a cohort of patients with biallelic pathogenic or likely pathogenic TTN variants. The cohort included both previously reported cases (100 patients from 81 unrelated families) and unreported cases (23 patients from 20 unrelated families). RESULTS: Overall, 132 causative variants were identified in cohort members. More than half of the cases had hypotonia at birth or muscle weakness and a delayed motor development within the first 12 months of life (congenital myopathy) with causative variants located along the entire gene. The remaining patients had a distal or proximal phenotype and a childhood or later (noncongenital) onset. All noncongenital cases had at least one pathogenic variant in one of the final three TTN exons (362-364). CONCLUSION: Our findings suggest a novel association between the location of nonsense variants and the clinical severity of the disease.

A case report of Munchausen syndrome presenting with bleeding from ear: a rare factitious disorder.

Munchausen syndrome is a rare psychiatric illness that includes mimicking a group of medical conditions, in which a person repeatedly harms him or herself or falsely misinterprets any medical condition when he or she is not actually sick, in order to achieve health care attention. Underdiagnosis of this syndrome leads to irrelevant use of medical assets. Here, we document an interesting and rare case of a young girl presented in the outpatient department of the Otolaryngology department of Patel Hospital with episodes of bleeding from her ear, which is a rare presentation of Munchausen syndrome. Her complete physical, otolar yngological, haematological and radiological examination failed to reveal any clue towards a particular diagnosis. Hence a diagnosis of Munchausen syndrome was made by exclusion of other possibilities of ear bleeding, and it was considered as a case report after taking duly signed written consent from the patient. This report will help in increasing the self-knowledge and perception of different clinical based presentations of this syndrome in medical practitioners, in order to avoid overlooking such cases. Further exploratory work is required in this regard to discover the etiology and predisposing factors and to develop new treatment strategies.

Improving Anemia in Inflammatory Bowel Disease: Impact of the Anemia Care Pathway.

BACKGROUND: Anemia is a common complication of inflammatory bowel disease (IBD). Despite existing guidelines for anemia in IBD, it is frequently under-treated and the prevalence of anemia has remained high. To address this gap, the Crohn's and Colitis Foundation developed the Anemia Care Pathway (ACP). AIMS: To implement the ACP in a managed care setting and identify where it improves practice habits and where barriers remain. METHODS: The ACP was implemented from July 2016 through June 2017 and retrospectively studied. Run charts were used to identify shifts in iron deficiency screening and treatment as well as anemia prevalence. Results were compared to those of other providers in the same center not using the ACP. RESULTS: 640 IBD encounters were studied. In the ACP clinic (n = 213), anemics received iron therapy in only 30% of encounters at baseline but improved to 80%. Concurrently, anemia prevalence decreased from 48 to 25%. Screening for iron deficiency, however, did not improve. No shifts were seen in the non-ACP clinics (n = 427) across the same period despite awareness of the ACP and other guidelines. CONCLUSIONS: Across 1 year, we observed gaps in the screening and treatment of anemia in IBD. Although screening rates did not improve, the ACP appeared to reduce missed opportunities for iron therapy by about half. Most importantly, this was associated with an overall decrease in anemia prevalence. Future refinements to the ACP should be focused on enhanced screening and follow-up.

Calcifying fibrous pseudotumour of maxilla: A rare entity mimicking malignancy: A case report.

Occurrence of inflammatory pseudotumour in head and neck region or nose and paranasal sinuses is rare. However, when they do occur, they could be quite aggressive. Etiologically, they are believed to be reactive than neoplastic, and calcification may suggest end-stage. Their clinical presentation and radiologic features may resemble a malignancy. Grossly, they are not encapsulated, but multilobulated and can be circumscribed or infiltrative. Histologically, they constitute of bland spindle cells with scant cytoplasm and occasional mitotic figures. Scattered lymphocytic and plasma cell infiltrates with abundant dense hyalinized collagenous stroma and focal small calcifications are seen. Presence of atypia, DNA aneuploidy, and abnormal p53 expression may suggest malignant potential. Though not known to metastasize, they can lead to local complications, causing destruction of bone and surrounding tissues. Management is mainly by surgical excision though adjunct corticosteroids have been advocated. We report such a rare case of calcifying fibrous pseudotumour of maxilla.

Effectiveness of plain X-ray in detection of fish and chicken bone foreign body in upper aerodigestive tract.

OBJECTIVE: To assess the use of plain film radiology in the detection of fish and chicken bones in the upper aerodigestive tract. METHODS: This retrospective chart review was conducted at the Aga Khan University Hospital, Karachi, and comprised medical charts of patients who had undergone oesophagoscopy for removal of fish and chicken bone from 1990 to 2015.SPSS 19 was used for data analysis. RESULTS: Of the 24 patients, foreign body was detected on X-ray in 7(29.2%) and through fibre optic laryngoscopy in 13(54.2%).All the patients underwent surgical intervention for removal of the foreign body. Also, 19(79.2%) patients underwent direct laryngoscopy and 5(16.7%) required oesophagoscopy. The sensitivity with X-ray was 15% and specificity was zero. The sensitivity of fibre optic laryngoscopy in comparison to intra-operative findings was 65% and the specificity was 100%. CONCLUSIONS: X-ray was not found to be an ideal modality to diagnose fish or chicken bone impaction in the upper aerodigestive tract.

Effects of bomb blast injury on the ears: The Aga Khan University Hospital experience.

OBJECTIVE: To evaluate the frequency and effects of blast-related otologic injuries. METHODS: his retrospective study was conducted at the Aga Khan University Hospital, Karachi, and comprised charts of patients who were victims of bomb explosions between January 2011 and July 2013. Frequency and percentages were reported using cross tabulation with size of bomb, distance of person from blast and the presence of victim in open or closed space. Association of associated variables were also analysed. RESULTS: Of the 100 patients, 81(81%) were men and 19(19%) were women. Besides, 68(68%) patients were aged <30 years. Also, 78(78%) subjects were exposed to < 80kg of explosives and 68(68%) were at a distance of>10m. Furthermore, 61(61%) patients were exposed to explosion in openspace. The prevalence of ear injuries was 21(21%). The odds of experiencing various symptoms of ears was high in those who were exposed to >80 kg of explosives (odds ratio: 3.38; 95% confidence interval, 1.16, 9.91). The odds of hearing loss in those who were within 10m was 8.62 (95% confidence interval: 2.72, 27.28) times than those who were >10 m from the site of explosion. CONCLUSIONS: Otologic injuries were frequently associated with large blasts.

Learning curve for the transsphenoidal endoscopic endonasal approach to pituitary tumors.

INTRODUCTION: The transsphenoidal endoscopic approach is a relatively new procedure compared to the microscopic approach in pituitary adenoma resection. The endoscopic approach has shown to significantly decrease the rate of complications, time in the operating room and hospital, and patient post-op discomfort. However, this procedure requires the surgeon to make use of different visual and tactile clues that must be developed with experience. Therefore, it is important to understand the learning curve that the surgeon must overcome to become proficient with the endoscopic approach. METHODS: Retrospective review of a single-surgeon consecutive series of 78 patients undergoing endoscopic pituitary tumor surgery from 2006 to 2012 at Rush University Medical Center has been used in this study. Patients were grouped according to an early (n = 9) and late group (n = 68) determined by a significant difference in outcomes. Our primary outcome measures were: duration of operation, CSF leak, hospital length of stay, visual field improvement, diabetes insipidus, panhypopituitarism, and subtotal resection. RESULTS: There was a significant reduction in OR time and intraoperative CSF leaks between the early and late groups. There was no difference in hospital LOS or visual field improvement between the groups. With regards to complication rates, there was no difference found for DI, panhypopituitarism, lumbar drain placement, sinusitis, or subtotal resection between the two groups. CONCLUSION: This study indicates that there may be a learning curve of approximately 9 cases before a surgical team can decrease OR times and reduce the rate of intraoperative CSF leaks for the endonasal endoscopic approach to pituitary adenoma resection.

Frequency of Sensorineural hearing loss in chronic suppurative otitis media.

Chronic suppurative otitis media (CSOM) is defined as chronic otorrhea (i.e., lasting > 6-12 weeks) through a perforated tympanic membrane. It is generally associated with some degree of conductive hearing loss. However, recurrent ear infections due to perforated eardrum result in absorption of toxins and macromolecules into the cochlea leading to sensorineural hearing loss (SNHL). We planned to determine the frequency of sensorineural hearing loss in chronic suppurative otitis media. A descriptive cross-sectional study was conducted at Aga Kgan University Hospital, Karachi, from October 2013 to March 2014. Average threshold of speech frequencies was calculated via pure tone audiogram for both diseased and normal contralateral ear.A mean of >25db in diseased ear was labelled as positive case for SNHL. SNHL was reported in 64(52%) patients and the frequency was found to increase with increasing duration. Patients with CSOM should be counselled regarding the risk of developing SNHL if left untreated.

Optimising head and neck cancer patient management: the crucial contributions of multidisciplinary tumour board decision-making.

Introduction: Squamous cell carcinoma (SCC) of the head and neck is a great burden globally, which is being tackled through treatment options of surgery, radiation therapy, chemotherapy, or a combination of these, to avoid disease-related mortality. Multidisciplinary tumour boards play a pivotal role in customising and deciding management plan based on clinical aspects. The objective of the study is to determine the concordance of opinion between the treatment plan of a primary physician and board members. Material and methods: This is a retrospective cross-sectional study that includes 137 head and neck carcinoma cases. They were discussed in the multidisciplinary tumour board meeting and were reviewed; all demographics were analysed including the tumour staging and the decisions of the primary physician was compared with those of the board. To check the concordance between primary surgeon plans or after board discussion Kappa agreement test was used. Results: Total of 137 patients were included in the study out of which 63 cases were pre-treatment and 74 cases were post-treatment, i.e., surgically treated cases, with the distribution being 46% and 54%, respectively. Most cases, totaling 120, were SCC, accounting for 80% of the total cases. Among the pre-treatment cases, T4a and N0 were the most common categories, with 29 and 40 cases, respectively. Similarly, in post-treatment cases, the majority fell into the T4a and N1 categories, with 29 and 38 cases, respectively. When comparing the primary surgeon's plan with the tumour board meeting decision, the agreement showed a value of 0.273, indicating a slight level of agreement between the two entities. Conclusion: Our data indicates that the multidisciplinary head and neck tumour board may have influenced the treatment plans of the primary surgeon, in approximately one in two patients (43.06%).

Proteomics approaches to characterize the immune responses in cancer.

Despite the dynamic development of cancer research, annually millions of people die of cancer. The human immune system is the major 'guard' against tumor development. Unfortunately, cancer cells have the ability to evade the immune system and continue to grow. The proper understanding of the intricate immune response in tumorigenesis remains the holy grail of cancer immunology and designing effective immunotherapy. To decode the immune responses in cancer, in recent years, proteomics studies have received considerable attention. Proteomics studies focus on the detection and quantification of proteins, which are the effectors of biological functions, and as such, are proven to reflect the cell state more accurately, in comparison to genomic or transcriptomic studies. In this review, we discuss the proteomics studies applied to characterize the immune responses in cancer and tumor immune microenvironment heterogeneity. Further, we describe emerging single-cell proteomics approaches that have the potential to be applied in cancer immunity studies.

Secondary Causes of Hypertriglyceridemia are Prevalent Among Patients Presenting With Hypertriglyceridemia Induced Acute Pancreatitis.

BACKGROUND: Hypertriglyceridemia induced acute pancreatitis (HIAP) is the third common cause of acute pancreatitis. HIAP can result in recurrent attacks of severe AP with significant morbidity and mortality. Hypertriglyceridemia (HTG) could be primary or secondary. Although genetic causes of HTG are well studied, the prevalence of secondary causes of HTG in patients presenting with HIAP is not well characterized. This study aimed to identify the prevalence of risk factors for secondary hypertriglyceridemia among patients presenting with HIAP in a tertiary referral center in a large metropolitan area. METHODS: This is a retrospective analysis of all patients admitted with AP from August 2012-2017. A subgroup of patients with triglycerides >880 mg/dl were included for analysis. Secondary causes of HTG were identified. Secondary analysis evaluating the severity of pancreatitis was performed. RESULTS: There were 3,746 patients admitted for AP of which 57 patients had AP and HTG. Of these 57 patients, 70.2% had history of diabetes mellitus, 26.3% had history of heavy alcohol use, 22.8% had chronic kidney disease, 47.3% with obesity, and 21.1% with metabolic syndrome. Two patients were classified as unexplained HTG. Secondary analysis showed a total of 45.6% of patients requiring ICU admission. 26.3% of patients with severe inflammatory pancreatitis and 17.5% of patients with severe necrotizing pancreatitis. CONCLUSIONS: In our cohort of HIAP, 55 out of 57 patients had secondary causes for HTG. Identifying secondary causes of HTG during acute hospitalization is important to tailor outpatient treatment in order to prevent future admissions with HIAP.

Organophosphate Poisoning: Demographics, Severity Scores and Outcomes From National Poisoning Control Centre, Karachi.

Introduction Organophosphate ingestion is the commonest cause of self-harm encountered at poison control centers in Pakistan. It usually affects a young populous. Organophosphates are found in various forms and formulations that are easily accessible to the general public. These compounds are extremely potent poisons causing rapid clinical deterioration with minimal ingestion or exposure. Signs and symptoms can range from mild or none to severe such as bradycardia, miosis, fasciculations, seizures and altered level of consciousness. Poisoning severity is measured using the Peradeniya Organophosphorus Poisoning (POP) scale. Mortality rates are relatively low for mild to moderate disease. Severe disease as calculated by the POP carries an exceptionally high mortality rate. The National Poisoning Control Centre (NPCC) at Jinnah Postgraduate Medical Centre, Karachi treats an extraordinary number of poisoning cases on a daily basis. Despite this data pertaining specifically to OP ingestion is nearly absent. There have been no studies analyzing the various aspects of organophosphate poisoning in the last 30 years to the best of our knowledge. Here, we look to rectify this. Aims To evaluate the demographics, severity scores and outcomes of organophosphate poisoning cases in the last year from the NPCC, Karachi. Methods This was a retrospective study. It was held from 1st January 2019 to 31st December 2019. All data was recorded from patients admitted to the NPCC with a proven diagnosis of organophosphate poisoning. Results Three thousand and three hundred patients were inducted into this study. Over 3/4th of the patients were teenagers or aged less than 30 years. Almost all referrals were made from within the city. Overall survival rate at 28 days was 89.45%. Most patients presented with mild to moderate disease as calculated by the POP; severe disease had a mortality rate of nearly 50%. Conclusion Organophosphates make up a significant portion of all cases of poisoning treated at the NPCC. The POP is an excellent tool to evaluate disease severity. Overall survival rates are good but mortality rate is high for severe disease even in young patients.

A rare case of three years disease free survival in a locally advanced parathyroid carcinoma successfully excised by complete surgical resection.

Parathyroid carcinoma (PC) is one of the rarest malignancies making approximately 0.005% of all cancers. It may arise sporadically or less commonly, in conjunction with genetic endocrine syndromes. Due to the rarity of the disease, no general consensus or definitive guidelines exist for its pre-operative diagnosis, management, or follow up. Surgical tumor removal is the gold standard treatment to prevent its recurrence. Parathyroid carcinoma has a high recurrence rate ranging from 40 to 60% in recent literature. We report a case of a seventy-year-old elderly female with locally advanced parathyroid carcinoma successfully surgically excised completely with a 3 year disease free survival period without adjuvant chemotherapy or radiotherapy.

Identification and Characterization of Splicing Defects by Single-Molecule Real-Time Sequencing Technology (PacBio).

Although DNA-sequencing is the most effective procedure to achieve a molecular diagnosis in genetic diseases, complementary RNA analyses are often required.Reverse-Transcription polymerase chain reaction (RT-PCR) is still a valuable option when the clinical phenotype and/or available DNA-test results address the diagnosis toward a gene of interest or when the splicing effect of a single variant needs to be assessed.We use Single-Molecule Real-Time sequencing to detect and characterize splicing defects and single nucleotide variants in well-known disease genes (DMD, NF1, TTN). After proper optimization, the procedure could be used in the diagnostic setting, simplifying the workflow of cDNA analysis.