Intramolecular i-Motif Structures of Telomeric DNA

Abstract The i-motif is an intercalated structure formed by association in a head to tail orientation of two parallel duplexes whose strands are held together by hemiprotonated C·C(+) pairs. The i-motif may be formed by a single strand containing four cytidine repeats, by association of two strands containing two cytidine repeats or by four strands containing a single cytidine stretch. The repeated C-rich sequences of centromeric and telomeric regions can potentially fold into an intramolecular i-motif. We have investigated by NMR spectroscopy the structure of d(CCCTA(2)CCCTA(2)CCCTA(2)CCCT), a fragment of the vertebrate telomere. It includes an i-motif core of six intercalated C·C(+) pairs. At one end (the "top"), the central TA(2) linker loops across one of the narrow grooves, and the core is extended by base stacking in the loop. At the bottom, where the two other TA(2) linkers loop across the wide grooves, the NMR spectra reveal motions in the microsecond to millisecond scale. The pseudo-symmetry of the structure, which results in degenerate spectra and poor resolution, was broken by appropriate substitution of T by U and of C by 5-methylcytidine (5mC). This allowed us to solve the structure of d(CCCTA(2)5mCCCTA(2)CCCUA(2)CCCT). The motion is restricted to a flip of A18 around the glycosidic bond. Returning to the pseudo-symmetrical sequence, we find that each of the bottom loops switches between the structures of the first and third loops of the non-symmetrical sequence. We also analyzed the effects of the loop sequence and of the length of the C-stretches on the topology and stability of the intramolecular i-motif structure.

Patient preferences for chemoradiation-related side effects

e20604

Background: Patients (pts) undergoing chemoradiation (CRT) face intense treatment (tx) schedules and adverse tx- related side-effects (SEs). We conducted this study to determine whether pts’ preferences (PREFs) for CRT-related SEs changed over tx duration. Methods: We used the visual analog scale (VAS) and modified time trade-off (TTO) to assess PREFs of newly diagnosed pts with gynecologic (GYN) and gastrointestinal (GI) cancers scheduled to receive CRT. Pts evaluated 16 SE health state scenarios during interviews conducted at 3 points in time: T1=prior to starting CRT; T2=2–3 weeks after starting CRT; and T3=4–6 weeks after completing CRT. Using the VAS, pts ranked SEs on a scale of 0=worst to 100=best. The TTO asked pts whether they would accept a hypothetical tx for a specified time with the SE in question or a tx for a shorter length of time that involved a worse SE profile. PREF scores were converted to 0.0=least preferred to 1.0=most preferred. Mann-Whitney and Kruskal-Wallis tests were used to analyze data. P- values were adjusted for multiple comparisons. Results: PREFs were collected from 93 pts (GYN=43; GI=50). 46/93 pts were female (3 women were GI pts). Median age was 53.7 yrs. Pts received a median of 5 chemo cycles (31/50 GI and all GYN pts received platinum) and 5.4 wks of external beam radiation. Median time between T1-T2 was 2.6 wks and T2-T3 was 9.1 wks. TTO PREFs were stable over time regardless of disease group or tx regimen. VAS scores for 7 SEs worsened significantly after initiation of CRT and remained low despite completion of CRT ( table ). Pts gave low baseline PREF scores for diarrhea, fatigue, and loss of appetite; these did not change significantly over time. Conclusions: Pts receiving CRT were willing to accept tx of longer duration with less severe SEs instead of shorter tx with more severe SEs. Relative to other SEs, pts rated GI-associated SEs lower after initiation of CRT. Ratings remained low 4–6 weeks after tx completion. Further studies are needed to determine whether pts’ experiences with and perceptions of SEs influence tx compliance.

[Table: see text]

[Table: see text]

A phase II study of IMGN242 (huC242-DM4) in patients with CanAg-positive gastric or gastroesophageal (GE) junction cancer

e15625

Background: IMGN242 is a conjugate of the cytotoxic maytansinoid DM4 and the monoclonal antibody huC242, which binds to CanAg. In a Phase I study, the maximum tolerated dose for IMGN242 was determined to be 168 mg/m2, with ocular changes the primary dose-limiting toxicity. This Phase II study was initiated to assess IMGN242 for the treatment of gastric cancer. Methods: In this open-label, multi-center study, IMGN242 is given as a single IV infusion every three weeks to patients with CanAg-expressing metastatic or locally-advanced gastric or GE junction cancer. Patients must have been treated with at least one prior therapy to qualify for enrollment. The study has a 2-step design: If ≥1 objective response is achieved among the first 23 patients (Step 1), a total of 39 response-evaluable patients will be enrolled (Step 2). Results: Overall, 9 patients have received IMGN242. The first 6 were treated with 168 mg/m2, and 1 of these patients showed a marked biologic response by the FDG-PET scan in Cycle 1 followed by an unconfirmed partial response based on CT scan in Cycle 2. However, 3 of these 6 patients developed ocular toxicities assessed to be study drug related. Only patients with low plasma CanAg levels (<1000 U/ml) developed ocular toxicities, and clinical pharmacokinetic and pharmacodynamic (PK/PD) analyses revealed that plasma CanAg affects study drug exposures. The study was amended to differentiate the IMGN242 doses (126 mg/m2 or 168 mg/m2) administered based on the patient's plasma CanAg levels (< or >1000 U/mL). To date, 3 patients have received IMGN242 with this dosing strategy and no ocular toxicities have been reported. Conclusions: IMGN242 showed preliminary evidence of activity in this patient population. A novel Phase II dosing strategy is being used that should enhance tolerability. Patient enrollment is ongoing and updated results will be reported.

[Table: see text]

First-in-human phase-I pharmacokinetic trial of NS-9, a liposomal poly(I):poly(C), in patients with liver metastases from various primary cancers

13016

Background: NS-9 is a complex of poly-inosinate [poly(I)] and poly-cytidylate [poly(C)] in a cationic liposome and is active in vitro and in vivo. Objectives: to determine the tolerability, safety, and maximal tolerated dose (MTD), and pharmacokinetics of NS-9 by 1 hr IV infusion, given daily x5 q 28 days. Methods: A phase I dose escalation study was undertaken in patients with liver metastases from solid tumors. Eligible patients were adults with ECOG PS 0–1 and no recent chemotherapy (≥ 4 wks prior). Dose cohorts studied were 0.1, 0.15, 0.2, 0.3 and 0.4mg/m2. Results: 18 patients were enrolled (13M:5F) median age 58 (range 21 to 77 yrs). Tumor types included neuroendocrine (8), and ocular melanoma (1), gastric (1), GE junction (1), esophageal (2), and colorectal (5) carcinomas. Two of three patients treated at the first dose level (0.4 mg/m2) had grade 3/4 reversible lipase elevation with or without acute pancreatitis, a dose limiting toxicity (DLT). De-escalation to doses ranging from 0.1 to 0.2 mg/m2/day was with no DLT. At 0.3 mg/m2 two of three patients treated had a DLT (neutropenia and thrombocytopenia). The MTD was determined at 0.2 mg/m2. Common toxicities included pyrexia, chills, nausea, fatigue, abdominal pain, myalgia, anorexia, sweating, neutropenia, thrombocytopenia, and elevated glucose, amylase, and LFTs. Pharmacokinetics showed rapid elimination (T1/2 ranged from 2.4 to 5.0 hours) without accumulation after multiple doses. 1 patient (esophageal Ca) had a PR in the target lesions in the liver. Conclusions: The MTD is 0.2 mg/m2/day with a hint of antitumor activity. NS-9 should be pursued in phase-II studies.

No significant financial relationships to disclose.

Phase II study of RAD001 (everolimus) and depot octreotide (Sandostatin LAR) in patients with advanced low grade neuroendocrine carcinoma (LGNET)

4042

Background: Effective systemic therapy for advanced LGNET is lacking. Patients with mutation in TSC2, an endogenous inhibitor of mTOR develop LGNET. mTOR also mediate signaling downstream of IGF1 and VEGF, pathways important in LGNET. RAD001 inhibits the serine-threonine kinase activity of mTOR. Octreotide may have cytostatic activity and has been described to inhibit VEGF and IGF1 production in solid tumors. Methods: Treatment consisted of depot octreotide 30 mg IM q28 days, and RAD001 5 or 10 mg po daily. Response evaluation is performed every 12 weeks. Results: 32 patients (18 carcinoids, 13 islet cell) were enrolled between 2/05 - 1/06. 20 had prior octreotide. 27 patients have completed 12 weeks of therapy at the 5 mg dose level and undergone response evaluation. By RECIST criteria, response rate was 15%. There were 4 PR, 19 SD (including 4 patients having 18–28% reduction), 4 PD. PR occurred in 2 carcinoids, and 2 islet cell. PFS rate at week 24 was 71%. Of 21 patients with radiological progression prior to study entry, 17 have completed 12 weeks of therapy. Among these, there were 3 PR, 10 SD, 4 PD. Of 18 patients with elevated chromogranin A at baseline, 9 (50%) patients had > 50% reduction. Treatment is generally well tolerated. The most common toxicity is mild aphthous ulceration. CTC G3/4 toxicity include: anemia (1), thrombocytopenia (1), leukopenia (1), fatigue (3), aphthous ulcer (2), diarrhea (2), hypoglycemia (2), pain (2), rash (2), hyperglycemia (1), edema (1), nausea (1). Conclusions: RAD001 5 mg po daily is well tolerated in combination with Depot Octreotide. Anti-tumor activity has been observed. An additional cohort will be treated at RAD001 10 mg daily dose. Optional blood draws and tumor biopsies will be performed to help assess biomarkers that may predict benefit.

No significant financial relationships to disclose.

Association of VEGF expression with poor prognosis among patients with low-grade neuroendocrine carcinoma

4091

Background: Low-grade neuroendocrine carcinomas (LGNET) can arise from neuroendocrine cells throughout the body and have a wide range of aggressiveness. Reliable predictive and prognostic markers of outcome are lacking. Angiogenesis is critical for metastasis and tumor growth beyond a small tumor size and VEGF is a powerful mediator of tumor angiogenesis. Methods: LGNET tissue from 50 patients (24 with local-regional disease, 26 with metastasis) who underwent tumor resection at the University of Texas M.D. Anderson Cancer Center was evaluated for expression VEGF by immunohistochemistry. Chi-square and Fisher’s exact test were used to test the association between study parameters. Kaplan-Meier analysis was used to assess the affect of study parameters on progression free survival (PFS). Results: Strong, weak, and negative VEGF expression was observed in 32%, 54%, and 14% of cases respectively. Larger tumor size was observed among patients with strong VEGF expression. Mean tumor sizes in patients with strong, weak and negative VEGF were 4.8, 2.8, and 2.9 cm. Compared to the group with negative VEGF expression, VEGF (weak/strong) expression was associated with metastasis (14% v 58%; P = .045). The median PFS durations of patients with strong and weak VEGF expression were 29 months and 81 months respectively. With a median follow-up duration of 50 months, the median PFS duration for the group with negative VEGF expression has not been reached. Compared by log rank test VEGF expression was associated with poor PFS (P = .022). Conclusions: This study suggests that tissue VEGF expression is associated with aggressive tumor growth and metastasis among patients with LGNET. VEGF expression may serve as a useful prognostic marker following tumor resection.

No significant financial relationships to disclose.

Phase I/II trial of capecitabine (C), dacarbazine (D) and imatinib (I) (CDI) for patients (pts) metastatic medullary thyroid carcinomas (MTC)

13048

Background: MTC is a rare tumor that responds poorly to conventional chemotherapy. 5-FU and D are frequently used, with an expected response rate of around 15%. MTC is often associated with multiple endocrine neoplasia type 2, an autosomal dominant syndrome caused by a mutation in the RET proto-oncogene which encodes RET, a tyrosine kinase receptor. I is a tyrosine kinase inhibitor with activity against c-Kit, PDGF and possibly RET, and we postulated that its addition to chemotherapy would increase its efficacy against this disease. Methods: We designed a phase I/II trial combining escalating doses of oral C, IV D and oral I. Pts with any advanced solid tumors were eligible for the phase I part of the trial. Results: 13 pts were entered and 12 were eligible (7 MTC, 2 adrenocortical, 1 islet-cell, 1 insular thyroid and 1 small cell). 4 pts did not complete one cycle (1 pt withdrew after 5 days and 2 pts progressed in less than 10 days and were replaced for toxicity analysis, 1 had a DLT and is included). 3 patients were entered in dose level 1, without DLT. 2 out of 6 pts developed DLT at the second dose level (1 G 3 fatigue and 1 G3 hypokalemia). Three additional pts are being entered on dose level 1. The first one had PD after 7 days and is being replaced. For the 11 pts who were evaluable, best response was 3 SD (range 3 to 9 + months) and 8 PD. Conclusions: The combination of CDI is feasible but has resulted in an unexpected pattern of toxicity in this patient population, with fatigue and hypokalemia as the DLT. No significant diarrhea or hand-foot syndrome was seen. Only G1 and 2 fluid retention and neutropenia have been encountered. Only minor reduction in tumor size has been seen among these heavily pretreated pts. Once the phase I is complete, the trial will continue in a phase II setting for untreated MTC pts.

[Table: see text]

[Table: see text]

Extended safety and efficacy data on S-1 plus cisplatin in patients with advanced gastric carcinoma in a multi-center phase II study

4083

Background: We obtained additional phase II safety and efficacy data in a multi-center setting on an active regimen of S-1 plus cisplatin; the experimental arm of the global phase III First-Line Advanced Gastric cancer Study (FLAGS). Methods: Eligible patients had untreated advanced gastric cancer (AGC), histologic proof, KPS ≥70%, adequate organ function, and gave written consent. Patients received S-1 (25mg/m2 p.o. bid on days 1–21) plus cisplatin (75mg/m2 i.v. on day 1) every 28 days. All reported confirmed overall response rate (C-ORR), response durations, and time-to-progression (TTP) are externally reviewed. Results: All 72 patients were assessed for safety and 64 for efficacy. The median age was 56 years and median KPS was 90%. Median no. of cycles was 4. C-ORR was 50% (95% CI, 37%-63%). Median duration of response is >6 months. At 6 months, only 35% of patients have had cancer progression. Median survival (n=72) is 10.5 months (95% CI, 9.3 to NR). At least one SAE occurred in 43% of patients. The frequent grade 3 or 4 adverse events (occurring in >10% of patients) included: fatigue/asthenia (26%), vomiting (21%), nausea (18%), diarrhea (17%), neutropenia (18%), anorexia (11%), and dehydration (11%). Febrile neutropenia (1.4%) and grade 4 diarrhea (1.4%) were rare. Conclusions: These extended data confirm that S-1 plus cisplatin has a very desirable safety profile and impressive efficacy data in AGC. FLAGS will complete accrual of >700 patients by March of 2007. (Supported by Taiho Pharma-USA).

[Table: see text]

Through-bond correlation of sugar and base protons in unlabeled nucleic acids

This work presents two methods for through-bond correlation between sugar and base protons in view of model-independent assignment in unlabeled or slightly enriched nucleic acids. Each method uses a combination of multiple-bond and one-bond heteronuclear J-couplings to the aromatic carbon C6 for pyrimidines ((3)J(H1',C6) and (1)J(H6,C6)) or C8 for purines ((3)J(H1',C8) and (1)J(H8,C8)). The techniques are demonstrated in the duplex [d(CGCGAATTCGCG)](2) and the dimeric G-quadruplex [d(GGGTTCAGG)](2) at natural abundance.

Mylotarg (gemtuzumab ozogamicin) therapy is associated with hepatic venoocclusive disease in patients who have not received stem cell transplantation

BACKGROUND

Mylotarg (Wyeth-Ayerst Laboratories, St. Davids, PA) is the brand name for a calicheamicin-conjugated humanized anti-CD33 monoclonal antibody (gemtuzumab ozogamicin, CMA-676) and has been approved recently for the treatment of a subset of elderly patients who have relapsed acute myeloid leukemia (AML). Mylotarg is associated with an incidence of approximately 20% Grade 3 or 4 hyperbilirubinemia and liver transaminitis in this patient population. Hepatic venoocclusive disease (VOD) has been reported in patients who have undergone stem cell transplantation (SCT) after Mylotarg therapy. Outside of the SCT setting, VOD has been associated very rarely with cytotoxic therapy.

METHODS

The authors assessed the incidence of VOD in 119 patients who were receiving Mylotarg-containing non-SCT regimens. VOD was diagnosed through the use of standard Seattle and Baltimore criteria.

RESULTS

A cohort of 119 (61 previously untreated, 58 with relapsed disease) patients with AML (92 patients), advanced myelodysplastic syndrome (25 patients), or chronic myeloid leukemia in blast phase (2 patients), received Mylotarg-based regimens. Fourteen (12%) developed VOD. The diagnosis of VOD was supported by histology in 2 patients and radiologic studies in a further 10 patients. Five (36%) of 14 patients with VOD had received no prior antileukemic cytotoxic therapy, including 2 patients who received single-agent Mylotarg therapy.

CONCLUSIONS

Mylotarg was shown to be associated with the development of potentially fatal VOD in patients with leukemia who had not received SCT. VOD occurred when Mylotarg was used either as a single agent or when it was given with other cytotoxic agents. VOD occurred in Mylotarg-treated patients who had received no prior cytotoxic therapy. The current study concluded that risk factors for VOD should be assessed when considering Mylotarg therapy, and that attempts to avoid and treat VOD are warranted in patients who receive Mylotarg therapy.

The solution structure and internal motions of a fragment of the cytidine-rich strand of the human telomere

We present the solution structure of d(CCCTA2CCCTA2CCCTA2CCCT), a fragment of the vertebrate telomere which folds intramolecularly. The four cytidine stretches form an i-motif which includes six intercalated C.C+ pairs and terminates with the cytidines at the 5' extremity of each stretch. Above, the second TA2 linker loops across one of the narrow grooves, while at the bottom, the first and third linkers loop across the wide grooves. At 30 degrees C, the spectra of the first and third linkers are quasi-degenerate. Severe broadening at lower temperature indicates that this results from motional averaging between at least two structures of each bottom loop, and makes it impossible to solve the configuration of the bottom loops directly, in contrast to the rest of the structure. We therefore turned to the modified sequence d(CCCTA(2)5MCCCTA2CCCUA2CCCT) in which the two base substitutions (underlined) break the quasi-symmetry between linkers 1 and 3. The three loops follow approximately the hairpin "second pattern" of Hilbers. In the first loop, T4 is in the syn orientation, whereas its analog in the third loop, U16, oriented anti, is in a central location, where it interacts with bases of both loops, thus contributing to their tight association. The only motion is a syn/anti flip of A18 in the third loop. Returning to the telomere fragment, we show that each of the bottom loops switches between the structures identified in the first and third loops of the modified structure. The motions are concerted, and the resulting configurations of the bottom loop cluster present a bulge to either right (T4 syn) or left (T16 syn).

Long-range imino proton-13C J-couplings and the through-bond correlation of imino and non-exchangeable protons in unlabeled DNA

Thanks to rather large (5-9 Hz) long-range imino proton-13C J-couplings, heteronuclear correlation experiments in H2O provide unambiguous assignment of imino protons by intranucleotide through-bond connectivities to guanosine H8 and thymidine CH3 protons, or sequence-specific assignment of non-exchangeable protons when the imino protons are identified independently. This method is demonstrated in the Dickerson dodecamer [d(CGCGAATTCGCG)]2 and in a human telomeric fragment of 22 nucleotides.

Determination of the residence time of water molecules hydrating B'- DNA and B-DNA, by one-dimensional zero-enhancement nuclear Overhauser effect spectroscopy

The residence time of water in the minor groove of the d(CGCGAATTCGCG) duplex has been determined by a recent measurement combining nuclear Overhauser enhancements (NOE, ROE) and 17O relaxation dispersion. The time is in the range of nanoseconds, so that it may be measured by a rather simple method proposed here, namely the choice of conditions such that the NOE between the observed DNA proton and a nearby water proton is zero. This condition is realized when the residence time of the water molecule is 0.178 times the nuclear magnetic resonance period (e.g. 0.297 ns at 600 MHz). It may be achieved by varying the magnetic field and/or the temperature. The zero-NOE measurement may be performed by one-dimensional NMR, and has therefore good sensitivity. We have developed excitation sequences which suppress two spurious contributions to the NOE: from neighboring exchangeable protons and from H3' protons whose chemical shift is close to that of water. The method is applied here to the comparison of residence times of water next to B-DNA and next to B'-DNA, the latter corresponding to better stacked, propeller-twisted base-pairs and a correspondingly narrower minor groove. In the minor groove of [d(CGCGAATTCGCG)]2, a B'-DNA duplex, the residence time of the water molecule next to H2 of adenine(6) (underlined), is 0.6 ns at 10 degreesC, in good agreement with the value obtained previously. The residence time is slightly but distinctly shorter for the water next to A5, suggesting non-cooperative departure of these two molecules which are presumed to be part of the hydration spine. Near A5 and A4 of [d(AAAAATTTTT)]2, another B'-DNA duplex, the residence times are approximately twice as long, but the activation enthalpies are about the same, ca. 38 kJ/mol. The residence time in the minor groove of the regular B-DNA sequence d(CGCGATCGCG) was 0.3 ns at 10 degreesC, shorter than in the case of the B'-DNA sequences by factors of 2 and 4, respectively. The temperature dependence is less, with an activation enthalpy of 27 kJ/mol. The major groove residence times are comparable for the three sequences, and a few times shorter than those of minor groove water. A value of 0.36 ns, or even more in case of rotation of water, is obtained around -8 degreesC. The most striking aspect of these results is the relatively small difference in the residence times of reputedly fast and slow-exchanging water molecules bound to DNA in biological conditions. This suggests that the spine of hydration is perhaps not a major stabilizer of the B'-DNA structure as compared with B-DNA.

Following G-quartet formation by UV-spectroscopy

Oligodeoxynucleotides which include stretches of guanines form a well-known tetrameric structure. We show that the recording of reversible absorbance changes at 295 nm allows to precisely monitor intramolecular guanine (G)-quartet formation and dissociation. Accurate Tm and thermodynamic values could be easily extracted from the data, whereas classical recordings at 260 nm led to a much larger uncertainty and in extreme cases, to completely inaccurate measurements. This inverted denaturation profile was observed for all G-quartet-forming oligonucleotides studied so far. This technique is very useful in all cases where intramolecular or intermolecular quadruplex formation is suspected.

Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability

BACKGROUND

Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif.

RESULTS

NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*.

CONCLUSIONS

Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize into an i-motif. The change of folding topology resulting from the substitution of a single nucleoside emphasizes the influence of the loop residues on the i-motif structure formed by two folded strands.