Purvi Patel

Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection

Adaptive changes in the genome of a locally predominant clinical isolate of the multidrug-resistant Klebsiella pneumoniae ST258 (KP35) were identified and help to explain the selection of this strain as a successful pulmonary pathogen. The acquisition of 4 new ortholog groups, including an arginine transporter, enabled KP35 to outcompete related ST258 strains lacking these genes. KP35 infection elicited a monocytic response, dominated by Ly6Chi monocytic myeloid-derived suppressor cells that lacked phagocytic capabilities, expressed IL-10, arginase, and antiinflammatory surface markers. In comparison with other K. pneumoniae strains, KP35 induced global changes in the phagocytic response identified with proteomics, including evasion of Ca2+ and calpain activation necessary for phagocytic killing, confirmed in functional studies with neutrophils. This comprehensive analysis of an ST258 K. pneumoniae isolate reveals ongoing genetic adaptation to host microenvironments and innate immune clearance mechanisms that complements its repertoire of antimicrobial resistance genes and facilitates persistence in the lung.

Identifying Predictors of Taxane-Induced Peripheral Neuropathy Using Mass Spectrometry-Based Proteomics Technology

Major advances in early detection and therapy have significantly increased the survival of breast cancer patients. Unfortunately, most cancer therapies are known to carry a substantial risk of adverse long-term treatment-related effects. Little is known about patient susceptibility to severe side effects after chemotherapy. Chemotherapy-induced peripheral neuropathy (CIPN) is a common side effect of taxanes. Recent advances in genome-wide genotyping and sequencing technologies have supported the discoveries of a number of pharmacogenetic markers that predict response to chemotherapy. However, effectively implementing these pharmacogenetic markers in the clinic remains a major challenge. On the other hand, recent advances in proteomic technologies incorporating mass spectrometry (MS) for biomarker discovery show great promise to provide clinically relevant protein biomarkers. In this study, we evaluated the association between protein content in serum exosomes and severity of CIPN. Women with early stage breast cancer receiving adjuvant taxane chemotherapy were assessed with the FACT-Ntx score and serum was collected before and after the taxane treatment. Based on the change in FACT-Ntx score from baseline to 12 month follow-up, we separated patients into two groups: those who had no change (Group 1, N = 9) and those who had a ≥20% worsening (Group 1, N = 8). MS-based proteomics technology was used to identify proteins present in serum exosomes to determine potential biomarkers. Mann–Whitney–Wilcoxon analysis was applied and maximum FDR was controlled at 20%. From the serum exosomes derived from this cohort, we identified over 700 proteins known to be in different subcellular locations and have different functions. Statistical analysis revealed a 12-protein signature that resulted in a distinct separation between baseline serum samples of both groups (q<0.2) suggesting that the baseline samples can predict subsequent neurotoxicity. These toxicity-associated biomarkers can be further validated in larger retrospective cohorts for their utility in identifying patients at high risk for CIPN.

Candidate protein markers for radiation biodosimetry in the hematopoietically humanized mouse model

After a radiological incident, there is an urgent need for fast and reliable bioassays to identify radiation-exposed individuals within the first week post exposure. This study aimed to identify candidate radiation-responsive protein biomarkers in human lymphocytes in vivo using humanized NOD scid gamma (Hu-NSG) mouse model. Three days after X-irradiation (0–2 Gy, 88 cGy/min), human CD45+ lymphocytes were collected from the Hu-NSG mouse spleen and quantitative changes in the proteome of the human lymphocytes were analysed by mass spectrometry. Forty-six proteins were differentially expressed in response to radiation exposure. FDXR, BAX, DDB2 and ACTN1 proteins were shown to have dose-dependent response with a fold change greater than 2. When these proteins were used to estimate radiation dose by linear regression, the combination of FDXR, ACTN1 and DDB2 showed the lowest mean absolute errors (≤0.13 Gy) and highest coefficients of determination (R2 = 0.96). Biomarker validation studies were performed in human lymphocytes 3 days after irradiation in vivo and in vitro. In conclusion, this is the first study to identify radiation-induced human protein signatures in vivo using the humanized mouse model and develop a protein panel which could be used for the rapid assessment of absorbed dose 3 days after radiation exposure.

Proteomics Analysis of Circulating Serum Exosomes

Proteomics characterization of biofluids, such as urine and plasma, has been explored for the discovery of predictive, prognostic, and mechanistic biomarkers of diseases and tissue injury. Here we describe comprehensive characterization of protein cargos from cell-derived secreted vesicles (extracellular vesicles or exosome) for biomarker discovery using the mass spectrometry-based technology.

Abstract PR13: Using a hypoxia-induced CSC tumor initiation model to improve predictive potential for patients with metastatic breast cancer

About 10-20% of breast cancers are found to be triple-negative. TNBCs have a relapse pattern that is very different from hormone-positive breast cancers: the risk of relapse is much higher for the first 3-5 years but drops substantially below that of hormone-positive breast cancers after that. Therefore, preventing tumor recurrence and metastasis in high-risk TNBC patients within 3-5 years of diagnosis will dramatically improve the long-term survival of these patients. Currently, most of preclinical animal models have limited predictive clinical potential for advanced metastatic diseases. One possible explanation is that most of the pre-clinical studies focus on the therapeutic benefit of eradicating bulk tumor cells. Using a stem-like subpopulation from triple negative breast cancer (TNBC) cell lines enriched by exposing the cells to cycles of hypoxia and reoxygenation, we showed that mammary tumors initiated from this subpopulation have a high recurrence rate (100%) after the taxol treatment compared to no recurrence from taxol treated tumors initiated from the bulk cancer cells. Our model mimics the progression of recurrence-prone breast tumors with a period of dormancy before the recurrence of local and distal tumors. Molecular analysis of the treatment naive and recurrent tumors revealed increased expression of chemoresistance-associated miRNAs in the recurred xenograft tumors. In addition, we identified new markers in the recurred xenograft tumors that are also increased in drug resistant human breast tumors compared to the treatment naive breast tumors. Ultimately, we propose that cancer stem cell based tumor model can be used to improve the predictive potential of pre-clinical models for patients with metastatic breast tumors. This abstract is also presented as Poster A12. Citation Format: Purvi Patel, Yupo Ma, Haiyan Zhai, Jingfeng Ju, Emily Chen. Using a hypoxia-induced CSC tumor initiation model to improve predictive potential for patients with metastatic breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr PR13.