Faculty Bibliography

RIP1 regulates cell death and inflammation and is believed to play an important role in contributing to a variety of human pathologies, including immune-mediated inflammatory diseases and cancer. While small-molecule inhibitors of RIP1 kinase have been advanced to the clinic for inflammatory diseases and CNS indications, RIP1 inhibitors for oncology indications have yet to be described. Herein we report on the discovery and profile of GSK3145095 (compound 6). Compound 6 potently binds to RIP1 with exquisite kinase specificity and has excellent activity in blocking RIP1 kinase-dependent cellular responses. Highlighting its potential as a novel cancer therapy, the inhibitor was also able to promote a tumor suppressive T cell phenotype in pancreatic adenocarcinoma organ cultures. Compound 6 is currently in phase 1 clinical studies for pancreatic adenocarcinoma and other selected solid tumors.

Protein prenylation is believed to be catalyzed by three heterodimeric enzymes: FTase, GGTase1 and GGTase2. Here we report the identification of a previously unknown human prenyltransferase complex consisting of an orphan prenyltransferase α-subunit, PTAR1, and the catalytic β-subunit of GGTase2, RabGGTB. This enzyme, which we named GGTase3, geranylgeranylates FBXL2 to allow its localization at cell membranes, where this ubiquitin ligase mediates the polyubiquitylation of membrane-anchored proteins. In cells, FBXL2 is specifically recognized by GGTase3 despite having a typical carboxy-terminal CaaX prenylation motif that is predicted to be recognized by GGTase1. Our crystal structure analysis of the full-length GGTase3-FBXL2-SKP1 complex reveals an extensive multivalent interface specifically formed between the leucine-rich repeat domain of FBXL2 and PTAR1, which unmasks the structural basis of the substrate-enzyme specificity. By uncovering a missing prenyltransferase and its unique mode of substrate recognition, our findings call for a revision of the 'prenylation code'.

INTRODUCTION/BACKGROUND:Rapid diagnosis of drug resistant tuberculosis is required for better patient management and treatment outcome. Whole-genome sequencing (WGS) can detect single nucleotide polymorphisms (SNPs) and deletions/insertions which are responsible for mostMycobacterium tuberculosis drug resistance. WGS is being performed at scale in high-income countries but there are still limited reports of its use in India. METHOD/METHODS:In this study, 33 clinicalM. tuberculosis isolates were taken from Mycobacterial repository in Chandigarh and were whole-genome sequenced. Phenotypic drug susceptibility testing was performed according to WHO recommendations. Four were considered culture contaminated. RESULTS:Among the other 29 isolates, 21(72.4%) were multi-drug resistance (MDR-TB) and one was extensively-drug resistant (XDR-TB). The most common mutations observed for isoniazid, rifampicin, ofloxacin and kanamycin werekatG_S315 T, rpoB_S450 L, gyrA_A90 V and rrs_A1401 G respectively. The isolates belonged to lineage 2 and 3, with most MDR-TB among lineage 2 isolates. CONCLUSION/CONCLUSIONS:Whole-Genome Sequencing ofMycobacterium tuberculosis offers the detection of drug resistance to all drugs in a single test and also provides insight into the evolution and drug-resistant tuberculosis.

Background and Aims: Endoscopic Ultrasound (EUS)guided fine needle aspiration (FNA)is the best tool available for the diagnosis and risk stratification of pancreatic cystic lesions (PCLs). However, due to lack of standardization in diagnostic criteria and surgical pathology reference standard in most patients, Interobserver agreement (IOA)between Endosonographers has been inconsistent in published literature. We aimed to assess 1)IOA among Endosonographers utilizing: clinical, imaging and biochemical and tumour marker data in a sequential multi-step process; and 2)Impact of standardized diagnostic criteria.
Method(s): Consecutive patients with EUS-FNA results of PCLs were included as part of a recently concluded multicenter, single-blinded randomized controlled trial to assess the utility of various needle sizes in aspiration of PCLs. All imaging, EUS and FNA results (cytology + tumour markers)of PCLs were reviewed by a consensus board of two expert Endosonographers (ES1 and ES2)blinded to the clinical diagnosis rendered at each participating site. Using the diagnostic criteria (Image 1), ES1 and ES2 independently classified the PCL after each step of a structured 3-tier process: Step 1- Clinical presentation + cross-sectional and EUS imaging; Step 2- Aspirate Characteristics (colour + viscosity); and Step 3- CEA + Cytology results. In 65/249 (26%)patients, surgical resection was done and histology results served as the final standard diagnosis (Dx). For the remaining patients, a final Dx was made by incorporating decisions of both ES1 and ES2. IOA was determined using Cohen's kappa (k). We also assessed the aggregate impact of each step on progression towards the final histology diagnosis (in 65 patients)using a pre/post-test McNemar Bowker analysis. To maintain the simplicity of comparisons, the final Dx was categorized as Mucinous (IPMN+Mucinous)or Non-mucinous (Pseudocyst+Serous+Undetermined).
Result(s): A total of 249 PCLs were assessed by ES1 and ES2 independently at each step. Percentage agreement between both after Step-1, 2 and 3 was 96.4%, 95.2% and 94.8% with a k of 0.933, 0.910, and 0.912 respectively (Image 1). The final Dx for those 65 patients showed: 29 had IPMN, 12 Mucinous, 3 Serous, 10 Pseudocyst and 11 Undetermined PCLs. For both experts, there was a statistically significant change in diagnosis from Step-3 (after incorporation of FNA data)to final Dx (all p-values<0.05; Table 1). We did not observe the same trend from Step 1 to 2.
Conclusion(s): IOA between expert Endosonographers for classification of PCLs was almost perfect (k>0.80). We believe this is mainly a result of the application of standardized criteria for each classification. FNA plays an important role in the diagnosis of PCLs as reflected by increased accuracy that is closer to final Dx after the availability of FNA-derived data (cytopathology + tumour markers). [Figure presented][Figure presented]
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Imiquimod is a topical toll-like-receptor-7 agonist currently used for treating basal cell carcinoma. Recently, imiquimod has demonstrated tumor regression in melanoma and breast cancer skin metastases. However, the molecular perturbations induced by imiquimod in breast cancer metastases have not been previously characterized. Here, we describe transcriptomic profiles associated with responsiveness to imiquimod in breast cancer skin metastases. Baseline and post-treatment tumor samples from patients treated with imiquimod in a clinical trial were profiled using Nanostring technology. Through an integrative analytic pipeline, we showed that tumors from patients who achieved a durable clinical response displayed a permissive microenvironment, substantiated by the upregulation of transcripts encoding for molecules involved in leukocyte adhesion and migration, cytotoxic functions, and antigen presentation. In responding patients, Imiquimod triggered a strong T-helper-1 (Th-1)/cytotoxic immune response, characterized by the coordinated upregulation of Th-1 chemokines, migration of Th-1 and cytotoxic T cells into the tumor, and activation of immune-effector functions, ultimately mediating tumor destruction. In conclusion, we have shown that topical imiquimod can induce a robust immune response in breast cancer metastases, and this response is more likely to occur in tumors with a pre-activated microenvironment. In this setting, imiquimod could be utilized in combination with other targeted immunotherapies to increase therapeutic efficacy.

Although bacterial dysbiosis has been previously associated with carcinogenesis and HIV infection, the impact of the virome and these disease states has been less well studied. In this review, we will summarize what is known about the interplay between both the bacterial and the viral components of the microbiome on cancer and HIV pathogenesis. Bacterial dysbiosis has been associated with carcinogenesis such as colorectal cancer (CRC), hepatocellular carcinoma (HCC), lung cancer, breast cancer, and gastric cancer. The dysbiotic pathogenesis may be species-based or community-based and can have varying mechanisms of carcinogenesis. The human virome was also associated with certain cancers. Viruses, such as cytomegalovirus (CMV), Human herpesvirus 8 (HHV-8), human papilloma virus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), and Epstein-Barr virus (EBV), all had associations with cancers. It was also reported that an altered bacteriophage community may lead to carcinogenesis by allowing opportunistic, oncogenic bacteria to proliferate in a gastrointestinal biofilm. This mechanism shows the importance of analyzing the bacteriome and the virome concurrently as their interactions can provide insight into new mechanisms in the pathogenesis of not only cancer, but other diseases as well. The enteric bacteriome was shown to be distinctly altered in immunocompromised HIV-infected individuals, and highly active antiretroviral therapy (HAART) was shown to at least partially reverse the alterations that HIV causes in the bacteriome. Studies have shown that the progression to HIV is associated with changes in the plasma concentration of commensal viruses. HIV also acts synergistically with multiple other viruses, such as HPV, EBV, varicella zoster virus (VZV), and HHV-8. Although it has been shown that HIV infection leads to enteric virome expansion in humans, most of the research on HIV's effect on the virome was conducted in non-human primates, and there is a lack of research on the effect of HAART on the virome. Virome-wide analysis is necessary for identifying novel viral etiologies. There is currently a wealth of information on the bacteriome and its associations with cancer and HIV, but more research should be conducted on the virome's associations and reaction to HAART as well as the bacteriome-virome interactions that may play a major role in pathogenesis and recovery.

We used the whole-cell current clamp technique to examine the response of our in-house hiPSC-CMs to the 28 CiPA-selected compounds, aiming to compare field potential via MEA from core-sites and action potential via current clamp measurement. Our blinded study showed that all seven high-risk test compounds, including bepridil, caused early afterdepolarizations (EADs) at mid-high and/or high concentration(s). All hERG channel blockers in the mid-risk category prolonged APD30 and APD90 at mid-high, and then led to EADs at their respective high concentrations; while chlorpromazine, clarithromycin and risperidone showed little effects. In addition, ranolazine was the only low-risk test compound to prolong APD30 and APD90 at mid-high, and then produce EADs at high concentration. In conclusion, our results generally agreed with data from all core-sites of the CiPA consortium using the MEA method. Moreover, our assay can successfully detect pro-arrhythmic risk of drug candidates such as bepridil with superior sensitivity.

Well-known causes of zinc deficiency, also referred to as acrodermatitis enteropathica (AE), include defects in intestinal zinc transporters and inadequate intake, but a rare cause of acquired zinc deficiency discussed here is an iatrogenic nutritional deficiency caused by parenteral nutrition administered without trace elements. While zinc-depleted parenteral nutrition causing dermatosis of acquired zinc deficiency was first reported in the 1990s, it is now again relevant due to a national vitamin and trace element shortage. A high index of suspicion may be necessary to diagnose zinc deficiency, particularly because early clinical findings are nonspecific. We present this case of acquired zinc deficiency in a patient admitted to a pediatric intensive care unit for respiratory distress and atypical pneumonia, who subsequently developed a severe bullous eruption due to iatrogenic zinc deficiency but was treated effectively with enteral and parenteral zinc supplementation, allowing for rapid re-epithelialization of previously denuded skin.

Mitochondria contain their own genomes that, unlike nuclear genomes, are inherited only in the maternal line. Owing to a high mutation rate and low levels of recombination of mitrochondrial DNA (mtDNA), special selection mechanisms exist in the female germline to prevent the accumulation of deleterious mutations^1-5. However, the molecular mechanisms that underpin selection are poorly understood⁶. Here we visualize germline selection in Drosophila using an allele-specific fluorescent in situ-hybridization approach to distinguish wild-type from mutant mtDNA. Selection first manifests in the early stages of Drosophila oogenesis, triggered by reduction of the pro-fusion protein Mitofusin. This leads to the physical separation of mitochondrial genomes into different mitochondrial fragments, which prevents the mixing of genomes and their products and thereby reduces complementation. Once fragmented, mitochondria that contain mutant genomes are less able to produce ATP, which marks them for selection through a process that requires the mitophagy proteins Atg1 and BNIP3. A reduction in Atg1 or BNIP3 decreases the amount of wild-type mtDNA, which suggests a link between mitochondrial turnover and mtDNA replication. Fragmentation is not only necessary for selection in germline tissues, but is also sufficient to induce selection in somatic tissues in which selection is normally absent. We postulate that there is a generalizable mechanism for selection against deleterious mtDNA mutations, which may enable the development of strategies for the treatment of mtDNA disorders.

The current model of polarized plasma membrane protein sorting in epithelial cells has been largely generated on the basis of experiments characterizing the polarized distribution of a relatively small number of overexpressed model proteins under various experimental conditions. Thus, the possibility exists that alternative roles of various types of sorting machinery may have been underestimated or missed. Here, we utilize domain-selective surface biotinylation combined with stable isotope labeling with amino acids in cell culture (SILAC) and mass spectrometry to quantitatively define large populations of apical and basolateral surface proteins in Madin-Darby canine kidney (MDCK) cells. We identified 313 plasma membrane proteins, of which 38% were apical, 51% were basolateral, and 11% were nonpolar. Silencing of clathrin adaptor proteins (AP) AP-1A, AP-1B, or both caused redistribution of basolateral proteins as expected but also, of a large population of apical proteins. Consistent with their previously reported ability to compensate for one another, the strongest loss of polarity was observed when we silenced AP-1A and AP-1B simultaneously. We found stronger evidence of compensation in the apical pathway compared with the basolateral pathway. Surprisingly, we also found subgroups of proteins that were affected after silencing just one adaptor, indicating previously unrecognized independent roles for AP-1A and AP-1B. While AP-1B silencing mainly affected basolateral polarity, AP-1A silencing seemed to cause comparable loss of apical and basolateral polarity. Our results uncover previously overlooked roles of AP-1 in polarized distribution of apical and basolateral proteins and introduce surface proteomics as a method to examine mechanisms of polarization with a depth not possible until now.