ALL-tRNAseq enables robust tRNA profiling in tissue samples

Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. However, it remains unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research.

Exploratory study of the subcutaneous fat gene expression profile in patients with metastatic pancreatic carcinoma treated with standard gemcitabine chemotherapy regimen

e22220

Background: Most clinical trials are designed to assess the antitumor effect of the chemoterapeutic intervention. There are few examples where the endpoint is to assess the biology of the host response to the treatment of the tumor. A large number of patients with pancreatic cancer present features of the cachexia syndrome and specially a marked weight loss. It has been postulated that a “cytokine storm” is the cause of the profound effect that this cancer has on distant tissues. This trial analyzed changes in the subcutaneous fat gene expression profile in relation with the clinical benefit variable with standard gemcitabine (G) treatment. Methods: Patients with histology confirmed advanced pancreatic cancer, adequate organ function and written informed consent. Eligible pts were intended for a subcutaneous fat biopsy pretreatment and after 7 weeks of gemcitabine 1000 mg/m2 together with response assessment. Clinical benefit (CB) (pain, analgesic consumption, Karnofsky and weight), QLQ-C30, serum cytokines and tumor markers were evaluated pretreatment, at 4 and 8 weeks. Fat gene expression profile was analyzed using Affimetrix U133Plus2.0 with the corresponding bioinformatic software. Serum cytokines where analyzed with xMAP technology with the Luminex 200 platform. Results: 16 pts [8 m, 8 f, median age 62 yrs (range 47–72)]. Median weight change -0.75 kg (range -4.5 to 2). Nine pts had pre and post treatment biopsies and 7 only pretreatment. Three pts achieved CB at 8 weeks. Objective responses: 0 CR, 0 PR, 31% SD and 68%PD. Toxicity was similar to the one reported in gemcitabine's label. It was possible to extract quality RNA for microarray from subcutaneous fat use from all samples but 1. The limited number of samples precluded to obtain genes clearly involved in cachexia, however the IL-8 expression (p0.03) was significantly correlated with CB response either to gene and serum profile. Conclusions: It is feasible to study prospectively the impact of cancer treatment on different tissue biomarkers and correlated with standard antitumor evaluation system. The reduced number of samples in this exploratory trial precludes producing significant biological conclusions.

No significant financial relationships to disclose.

A phase I study of erlotinib, bevacizumab and gemcitabine in patients with advanced pancreatic cancer

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Background: Erlotinib is an EGFR TKI active in combination with gemcitabine in p with advanced pancreatic cancer (PC). The combination of gemcitabine and bevacizumab is also active in PC. A phase I of gemcitabine, bevacizumab and erlotinib in p with unresectable locally advanced or metastatic PC is being conducted. Methods: Two cohorts of 6 patients with advanced PC have been treated either with erlotinib (150 mg/day po), bevacizumab (5 mg/Kg iv, days 1 and 15, every 28 days), and either 10 mg/m2/min infusion of gemcitabine 850 mg/m2 or 1,000 mg/m2 days 1 and 15 every 28 days. P received a maximum of 6 cycles of 28 days. Cohort 1: Daily erlotinib 150 mg po + bevacizumab 5 mg/kg iv days 1 and 15 + gemcitabine 850 mg/m2 over 10 mg/m2/min infusion days 1 and 15. Cohort 2: daily erlotinib 150 mg po + bevacizumab 5 mg/kg iv days 1 and 15 + gemcitabine 100 mg/m2 over 10 mg/m2/min infusion days 1 and 15. Results: 12 p have been included in this study (6 cohort 1 and 6 cohort 2), being evaluable for toxicity. 11 p have concluded the study and 7 have received complete treatment as per protocol. Median age 62.6 yrs (range 38–71); male/female: 5/7 (42%/58%); stage III/IV: 3/9 (25%/75%); Karnofsky index 100%/80%: 2/10. 3 of 6 p in cohort 1 developed gr. 3 asthenia (50%), 2 p gr. 3 neutropenia (33.3%), whereas 1 p had grade 3 leucopenia and gr. 3 skin rash. In cohort 2, most severe adverse events were: 1 case of grade 4 GGT elevation, 1 p gr. 3 skin rash and 1 p. experienced asthenia gr. 3. No severe hematological toxicity in cohort 2 was reported. One p of each cohort required dose reduction of erlotinib, both due to skin rash. Mild diarrhea was reported in 11 of 12 p evaluated. No dose limiting toxicities has been reported. All p were available for response: 2 p reached partial response (both included in cohort 1) and 7 showed stabilization (3 and 4 in cohorts 1 and 2, respectively). No complete responses were observed. Overall disease control index was 75%. Conclusions: The combination of gemcitabine, erlotinib and bevacizumab is well tolerated. MTD has not been reached. Encouraging clinical activity in advanced pancreatic cancer has been observed. Phase I is still ongoing. Toxicity data for all the p will be presented.

No significant financial relationships to disclose.

Rifampin does not improve the efficacy of quinolone antibacterial prophylaxis in neutropenic cancer patients: results of a randomized clinical trial

PURPOSE

To determine whether the addition of rifampin to a quinolone-based antibacterial prophylactic regimen in patients undergoing high-dose chemotherapy (HDC) with peripheral-blood stem-cell transplantation (PBSCT) decreases the incidence of neutropenia and fever, Gram-positive bacteremia, and infection-related morbidity.

PATIENTS AND METHODS

Patients with solid tumors undergoing HDC with PBSCT were randomized to receive prophylactic antibiotics with either ciprofloxacin 500 mg orally every 8 hours or the same ciprofloxacin regimen with rifampin 300 mg orally every 12 hours. Prophylaxis was started 48 hours before stem-cell reinfusion. Patients were monitored to document the occurrence of neutropenia and fever, incidence and cause of bacterial infection, time to onset and duration of fever, requirement for intravenous antimicrobials, and length of hospital admission.

RESULTS

Sixty-five patients were randomized to receive ciprofloxacin and 65 to receive ciprofloxacin plus rifampin, and from these groups, 62 and 61 were assessable, respectively. The proportion of patients who developed neutropenia and fever was 87% in the group treated with ciprofloxacin and 78% in the group treated with ciprofloxacin and rifampin (P =.25). Although there was a trend toward a reduction in the overall incidence of bacteremia (12 v 4 patients), and Gram-positive bacteremia (8 v 2 patients) with the addition of rifampin, none of these comparisons was statistically significant (P =.05 and P =.09, respectively).

CONCLUSION

The results of this study, which demonstrate that rifampin does not improve ciprofloxacin antibacterial prophylaxis in cancer patients undergoing HDC with PBSCT support but that it does increase the occurrence of undesirable side effects, do not support the routine use of rifampin in this setting.