FISH analysis reveals CDKN2A and IFNA14 co-deletion is heterogeneous and is a prominent feature of glioblastoma.

Deletion of CDKN2A occurs in 50% of glioblastomas (GBM), and IFNA locus deletion in 25%. These genes reside closely on chromosome 9. We investigated whether CDKN2A and IFNA were co-deleted within the same heterogeneous tumour and their prognostic implications. We assessed CDKN2A and IFNA14 deletions in 45 glioma samples using an in-house three-colour FISH probe. We examined the correlation between p16INK4a protein expression (via IHC) and CDKN2A deletion along with the impact of these genomic events on patient survival. FISH analyses demonstrated that grades II and III had either wildtype (wt) or amplified CDKN2A/IFNA14, whilst 44% of GBMs harboured homozygous deletions of both genes. Cores with CDKN2A homozygous deletion (n = 11) were negative for p16INK4a. Twenty p16INK4a positive samples lacked CDKN2A deletion with some of cells showing negative p16INK4a. There was heterogeneity in IFNA14/CDKN2A ploidy within each GBM. Survival analyses of primary GBMs suggested a positive association between increased p16INK4a and longer survival; this persisted when considering CDKN2A/IFNA14 status. Furthermore, wt (intact) CDKN2A/IFNA14 were found to be associated with longer survival in recurrent GBMs. Our data suggest that co-deletion of CDKN2A/IFNA14 in GBM negatively correlates with survival and CDKN2A-wt status correlated with longer survival, and with second surgery, itself a marker for improved patient outcomes.

Palliative care delivery in India during COVID-19 pandemic: role of faith-based hospitals - a qualitative study.

OBJECTIVES: The COVID-19 pandemic challenged palliative care (PC) services globally. We studied the ways healthcare professionals (HCPs) working in faith-based hospitals (FBHs) experienced and adapted care through the pandemic, and how this impacted patients with PC needs. METHODS: In-depth interviews were conducted with HCPs from FBHs serving rural and urban population across India. Thematic analysis was conducted. RESULTS: A total of 10 in-depth interviews were conducted during the COVID-19 pandemic, first wave (4), second wave (4) and between them (2). HCPs described fear and stigma in the community early in the pandemic. Migrant workers struggled, many local health services closed and cancer care was severely affected. Access and availability of healthcare services was better during the second wave. During both waves, FBHs provided care for non-COVID patients, earning community appreciation. For HCPs, the first wave entailed preparation and training; the second wave was frightening with scarcity of hospital beds, oxygen and many deaths. Eight of the 10 FBHs provided COVID-19 care. PC teams adapted services providing teleconsultations, triaging home visits, delivering medications, food at home, doing online teaching for adolescents, raising funds. Strengths of FBHs were dedicated teamwork, staff care, quick response and adaptations to community needs, building on established community relationship. CONCLUSION: FBHs remained open and continued providing consistent, good quality, person-centred care during the pandemic. Challenges were overcome innovatively using novel approaches, often achieving good outcomes despite limited resources. By defining and redefining quality using a PC lens, FBHs strengthened patient care services.

Identification of novel interferon responsive protein partners of human leukocyte antigen A (HLA-A) using cross-linking mass spectrometry (CLMS) approach.

The interferon signalling system elicits a robust cytokine response against a wide range of environmental pathogenic and internal pathological signals, leading to induction of a subset of interferon-induced proteins. We applied DSS (disuccinimidyl suberate) mediated cross-linking mass spectrometry (CLMS) to capture novel protein-protein interactions within the realm of interferon induced proteins. In addition to the expected interferon-induced proteins, we identified novel inter- and intra-molecular cross-linked adducts for the canonical interferon induced proteins, such as MX1, USP18, OAS3, and STAT1. We focused on orthogonal validation of a cohort of novel interferon-induced protein networks formed by the HLA-A protein (H2BFS-HLA-A-HMGA1) using co-immunoprecipitation assay, and further investigated them by molecular dynamics simulation. Conformational dynamics of the simulated protein complexes revealed several interaction sites that mirrored the interactions identified in the CLMS findings. Together, we showcase a proof-of-principle CLMS study to identify novel interferon-induced signaling complexes and anticipate broader use of CLMS to identify novel protein interaction dynamics within the tumour microenvironment.

'COVID-19 and palliative medicine: faith-based hospitals in India'.

OBJECTIVES: Faith-based organisations (FBOs) in India provide health services particularly to marginalised communities. We studied their preparedness and delivery of palliative care during COVID-19 as part of a mixed-method study. We present the results of an online questionnaire. METHODS: All FBOs providing palliative care in India were invited to complete an online questionnaire. Descriptive analysis was undertaken. RESULTS: Response rate was 46/64 (72%); 44 provided palliative care; 30/44 (68%) were in rural or semiurban areas with 10-2700 beds. Fifty-two per cent (23/44) had dedicated palliative care teams and 30/44 (68%) provided it as part of general services; 17/44 (39%) provided both. 29/44 (66%) provided palliative care for cancer patients; 17/44 (34%) reported that this was more than half their workload.The pandemic led to reduced clinical work: hospital 36/44 (82%) and community 40/44 (91%); with reduction in hospital income for 41/44 (93%). 18/44 (44%) were designated government COVID-19 centres; 11/40 (32%) had admitted between 1 and 2230 COVID-19 patients.COVID-19 brought challenges: 14/44 (32%) lacked personal protective equipment; 21/44 (48%) had reduced hospital supplies and 19/44 (43%) lacked key medications including morphine. 29/44 (66%) reported reduction in palliative care work; 7/44 (16%) had stopped altogether. Twenty-three per cent (10/44) reported redeployment of palliative care teams to other work. For those providing, palliative care 32/37 (86%) was principally for non-COVID patients; 13/37 (35%) cared for COVID-19 patients. Service adaptations included: teleconsultation, triaged home visits, medication delivery at home and food supply. CONCLUSIONS: FBOs in India providing palliative care had continued to do so despite multiple challenges. Services were adapted to enable ongoing patient care. Further research is exploring the effects of COVID-19 in greater depth.

MicroPOTS Analysis of Barrett's Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress.

Moving from macroscale preparative systems in proteomics to micro- and nanotechnologies offers researchers the ability to deeply profile smaller numbers of cells that are more likely to be encountered in clinical settings. Herein a recently developed microscale proteomic method, microdroplet processing in one pot for trace samples (microPOTS), was employed to identify proteomic changes in ∼200 Barrett's esophageal cells following physiologic and radiation stress exposure. From this small population of cells, microPOTS confidently identified >1500 protein groups, and achieved a high reproducibility with a Pearson's correlation coefficient value of R > 0.9 and over 50% protein overlap from replicates. A Barrett's cell line model treated with either lithocholic acid (LCA) or X-ray had 21 (e.g., ASNS, RALY, FAM120A, UBE2M, IDH1, ESD) and 32 (e.g., GLUL, CALU, SH3BGRL3, S100A9, FKBP3, AGR2) overexpressed proteins, respectively, compared to the untreated set. These results demonstrate the ability of microPOTS to routinely identify and quantify differentially expressed proteins from limited numbers of cells.

Ileal Perforation and Enteric Fever: Implications for Burden of Disease Estimation.

BACKGROUND: Ileal perforation occurs in about 1% of enteric fevers as a complication, with a case fatality risk (CFR) of 20%-30% in the early 1990s that decreased to 15.4% in 2011 in South East Asia. We report nontraumatic ileal perforations and its associated CFR from a 2-year prospective enteric fever surveillance across India. METHODS: The Surveillance for Enteric Fever in India (SEFI) project established a multitiered surveillance system for enteric fever between December 2017 and March 2020. Nontraumatic ileal perforations were surveilled at 8 tertiary care and 6 secondary care hospitals and classified according to etiology. RESULTS: Of the 158 nontraumatic ileal perforation cases identified,126 were consented and enrolled. Enteric fever (34.7%), tuberculosis (19.0%), malignancy (5.8%), and perforation of Meckel diverticulum (4.9%) were the common etiology. In those with enteric fever ileal perforation, the CFR was 7.1%. CONCLUSIONS: Enteric fever remains the most common cause of nontraumatic ileal perforation in India, followed by tuberculosis. Better modalities of establishing etiology are required to classify the illness, and frame management guidelines and preventive measures. CFR data are critical for comprehensive disease burden estimation and policymaking.

The effects of p53 gene inactivation on mutant proteome expression in a human melanoma cell model.

BACKGROUND: The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potential mutated proteins and any one output fails to cover completely a specific landscape. METHODS: An isogenic melanoma cell with a p53-null genotype was created by CRISPR/CAS9 system to determine how p53 gene inactivation affects mutant proteome expression. A mutant peptide reference database was developed by comparing two distinct DNA and RNA variant detection platforms using these isogenic cells. Chemically fractionated tryptic peptides from lysates were processed using a TripleTOF 5600+ mass spectrometer and their spectra were identified against this mutant reference database. RESULTS: Approximately 190 mutated peptides were enriched in wt-p53 cells, 187 mutant peptides were enriched in p53-null cells, with an overlap of 147 mutated peptides. STRING analysis highlighted that the wt-p53 cell line was enriched for mutant protein pathways such as CDC5L and POLR1B, whilst the p53-null cell line was enriched for mutated proteins comprising EGF/YES, Ubiquitination, and RPL26/5 nodes. CONCLUSION: Our study produces a well annotated p53-dependent and p53-independent mutant proteome of a common melanoma cell line model. Coupled to the application of an integrated DNA and RNA variant detection platform (CLCbio) and software for identification of proteins (ProteinPilot), this pipeline can be used to detect high confident mutant proteins in cells. GENERAL SIGNIFICANCE: This pipeline forms a blueprint for identifying mutated proteins in diseased cell systems.

A High Malaria Prevalence Identified by PCR among Patients with Acute Undifferentiated Fever in India.

BACKGROUND: Approximately one million malaria cases were reported in India in 2015, based on microscopy. This study aims to assess the malaria prevalence among hospitalised fever patients in India identified by PCR, and to evaluate the performance of routine diagnostic methods. METHODS: During June 2011-December 2012, patients admitted with acute undifferentiated fever to seven secondary level community hospitals in Assam (Tezpur), Bihar (Raxaul), Chhattisgarh (Mungeli), Maharashtra (Ratnagiri), Andhra Pradesh (Anantapur) and Tamil Nadu (Oddanchatram and Ambur) were included. The malaria prevalence was assessed by polymerase chain reaction (PCR), routine microscopy, and a rapid diagnostic test (RDT) with PCR as a reference method. RESULTS: The malaria prevalence by PCR was 19% (268/1412) ranging from 6% (Oddanchatram, South India) to 35% (Ratnagiri, West India). Among malaria positive patients P. falciparum single infection was detected in 46%, while 38% had P. vivax, 11% mixed infections with P. falciparum and P. vivax, and 5% P. malariae. Compared to PCR, microscopy had sensitivity of 29% and specificity of 98%, while the RDT had sensitivity of 24% and specificity of 99%. CONCLUSIONS: High malaria prevalence was identified by PCR in this cohort. Routine diagnostic methods had low sensitivity compared to PCR. The results suggest that malaria is underdiagnosed in rural India. However, low parasitaemia controlled by immunity may constitute a proportion of PCR positive cases, which calls for awareness of the fact that other pathogens could be responsible for the febrile disease in submicroscopic malaria.

PMA-SiO2 catalyzed synthesis of indolo[2,3-c]quinolines as potent anti cancer agents.

PMA-SiO2 catalyzed Pictet-Spengler reaction of aryl amine linked to C-3 of the indole and the aryl aldehydes was achieved. In the series of the synthesized compounds, 6b, 10b and 12b were found to be cytotoxic against prostate, lung, breast and cervical cancer cell lines selectively with no significant effect on the growth of the control fibroblast cell line NIH3T3. Further determining their cytotoxic potential we found that 10b and 12b show cell cycle arrest in DU145 prostate cancer cells indicating a role in cell cycle progression. Both the molecules showed effect on decreased phosphorylation of NF-κB on serine 536 residue which is strongly implicated in many different types of cancers. Taken together, the series of indoloquinolines elicit potent anti-cancer potential providing a mean for developing novel indoloquinoline based anti-cancer agents.

Convenient one-pot synthesis, anti-mycobacterial and anticancer activities of novel benzoxepinoisoxazolones and pyrazolones.

Series of new benzoxepinoisoxazolones 4a-d and pyrazolones 6a-t were prepared by the cyclocondensation of substituted (E)-ethyl 3-oxo-2,3-dihydrobenzo[b]oxepine-4-carboxylates 3a-d with hydroxylamine hydrochloride and phenylhydrazine hydrochlorides 5a-k. Synthesized compounds were screened for their in vitro anti-mycobacterial activity and anticancer activity. Ten compounds displayed good anti-mycobacterial activity, among these; compound 4d and 6b found to be potent when compared to standard drug isoniazid. Eleven compounds displayed good anticancer activity and compounds 4b-d displayed equipotent activity on HeLa cell lines when compared to standard drug doxorubicin. Activation of caspase-3 and caspase-9 has been measured for compounds 4b-d on HeLa cell lines (apoptosis). This is the first report assigning in vitro anti-mycobacterial, anticancer and structure-activity relationship for this new class of benzoxepinoisoxazolones and pyrazolones.

5-epi-Torrubiellutin C shows antiproliferative activity on DU145 prostate cancer cells through inactivation of the AKT/mTOR pathway.

Cell-based assays for evaluation of the anticancer potential of a focused small molecule library have identified a few potential hit molecules. Among the hits identified, Torrubiellutins (3a) showed good anticancer potential across the cells used in screening assays. Torrubiellutins are isolated from fungal insects Torrubiella luteorostrata and diverse pharmacological effects for these have been reported. However, it is not known as to how Torrubiellutins act through signaling pathways inhibiting the growth of eukaryotic cells. The current study aimed to determine the anticancer potential of Torrubiellutins by defining the molecular mechanism of cytotoxicity using DU145 cells. The results showed that the inhibition of prostate cancer cell growth by 3a was associated with inhibition of anchorage-independent growth, cell migration, and, to a small extent, apoptosis-mediated cell death by caspase activation. The growth-inhibitory effects of 3a are supported by inactivation of prosurvival pathways. Immunoblot analysis showed that the treatment of DU145 cells with 3a resulted in specific downregulation of AKT/mammalian target of rapamycin (mTOR) and its downstream effector proteins p70S6K, GSK3ß, and STAT3. On the basis of these findings, we propose that the changes observed in the AKT/mTOR signaling axis are new targets of 3a that are involved in its inhibitory activity on the proliferation of prostate cancer cells, suggesting its potential for further investigation as a promising anticancer agent.

Awareness and attitude toward diabetes in the rural population of Arunachal Pradesh, Northeast India.

BACKGROUND: India has the largest number of patients with diabetes in the world, accounting for more than 50 million subjects. There are limited studies on diabetes awareness, attitude, and prevalence in rural communities, especially in the northeastern part of India. MATERIALS AND METHODS: A community-based survey using the STEPS questionnaire with recording of blood pressure, fasting blood glucose, postprandial blood glucose, waist circumference, and height was conducted among the residents of Kameng district of Arunachal Pradesh. A door-to-door survey was conducted in each village, and members above the age of 25 years from each household were considered eligible to participate. RESULTS AND CONCLUSION: The awareness of diabetes in the study population was found to be as low as 21%. Majority of subjects (58%) had a normal BMI and adequate physical activity (88%). The prevalence of smoking (72%) and alcohol consumption (49%) was found to be very high amongst the study population. Blood glucose screening revealed that 13% had impaired fasting glucose and 6% had impaired glucose tolerance.