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Ampliseq results for the enrolled patients (n = 21)

Purpose:To assess the antitumor activity and safety of tipifarnib, a highly potent and selective farnesyltransferase inhibitor, we performed a phase II clinical trial in patients with advanced and refractory urothelial carcinoma harboring missense HRAS mutations.Patients and Methods:A total of 245 adult patients with previously treated, advanced urothelial carcinoma entered the molecular screening program including HRAS. Those with missense HRAS mutations or STK11:rs2075606 received oral tipifarnib 900 mg twice daily on days 1–7 and 15–21 of 28-day treatment cycles. The primary endpoint was progression-free survival at 6 months (PFS6).Results:We identified 16 (7%) missense HRAS mutations (G13R, 7; Q61R, 4; G12S, 3; G12C, 2) and 104 (46%) STK11:rs2075606 carriers. In 21 patients enrolled in the study, 14 and 7 patients had missense HRAS mutations and STK11:rs2075606, respectively. The most frequently observed adverse events included fatigue (86%) and hematologic toxicities. With a median follow-up of 28 months, 4 patients (19%) reached PFS6: 3 had missense HRAS mutations and one patient, enrolled as an STK11 carrier, had HRAS frameshift insertions at H27fs and H28fs rendering a nonsense HRAS mutation. The overall response rate by intent-to-treat analysis was 24% (4 missense and one nonsense frameshift HRAS mutation); no response was observed in patients with urothelial carcinoma with wild-type HRAS tumors. Five responses were observed in 12 evaluable patients of 15 with tumors carrying HRAS mutations.Conclusions:Oral tipifarnib resulted in a manageable safety profile and encouraging antitumor efficacy against treatment-refractory urothelial carcinoma containing HRAS mutations.

Comparison of the somatic mutational landscape in our patient population with The Cancer Genome Atlas (TCGA) data

Supplementary Figure Legends

Heatmap showing genomic biomarkers found in all genetically screened patients (n = 224)

We conducted a phase I clinical trial of H3B-8800, an oral small molecule that binds Splicing Factor 3B1 (SF3B1), in patients with MDS, CMML, or AML. Among 84 enrolled patients (42 MDS, 4 CMML and 38 AML), 62 were red blood cell (RBC) transfusion dependent at study entry. Dose escalation cohorts examined two once-daily dosing regimens: schedule I (5 days on/9 days off, range of doses studied 1–40 mg, n = 65) and schedule II (21 days on/7 days off, 7–20 mg, n = 19); 27 patients received treatment for ≥180 days. The most common treatment-related, treatment-emergent adverse events included diarrhea, nausea, fatigue, and vomiting. No complete or partial responses meeting IWG criteria were observed; however, RBC transfusion free intervals >56 days were observed in nine patients who were transfusion dependent at study entry (15%). Of 15 MDS patients with missense SF3B1 mutations, five experienced RBC transfusion independence (TI). Elevated pre-treatment expression of aberrant transcripts of Transmembrane Protein 14C (TMEM14C), an SF3B1 splicing target encoding a mitochondrial porphyrin transporter, was observed in MDS patients experiencing RBC TI. In summary, H3B-8800 treatment was associated with mostly low-grade TAEs and induced RBC TI in a biomarker-defined subset of MDS.

Purpose:To assess the antitumor activity and safety of tipifarnib, a highly potent and selective farnesyltransferase inhibitor, we performed a phase II clinical trial in patients with advanced and refractory urothelial carcinoma harboring missense HRAS mutations.Patients and Methods:A total of 245 adult patients with previously treated, advanced urothelial carcinoma entered the molecular screening program including HRAS. Those with missense HRAS mutations or STK11:rs2075606 received oral tipifarnib 900 mg twice daily on days 1–7 and 15–21 of 28-day treatment cycles. The primary endpoint was progression-free survival at 6 months (PFS6).Results:We identified 16 (7%) missense HRAS mutations (G13R, 7; Q61R, 4; G12S, 3; G12C, 2) and 104 (46%) STK11:rs2075606 carriers. In 21 patients enrolled in the study, 14 and 7 patients had missense HRAS mutations and STK11:rs2075606, respectively. The most frequently observed adverse events included fatigue (86%) and hematologic toxicities. With a median follow-up of 28 months, 4 patients (19%) reached PFS6: 3 had missense HRAS mutations and one patient, enrolled as an STK11 carrier, had HRAS frameshift insertions at H27fs and H28fs rendering a nonsense HRAS mutation. The overall response rate by intent-to-treat analysis was 24% (4 missense and one nonsense frameshift HRAS mutation); no response was observed in patients with urothelial carcinoma with wild-type HRAS tumors. Five responses were observed in 12 evaluable patients of 15 with tumors carrying HRAS mutations.Conclusions:Oral tipifarnib resulted in a manageable safety profile and encouraging antitumor efficacy against treatment-refractory urothelial carcinoma containing HRAS mutations.

Mutations in theWe enrolled 30 patients with R/M HNSCC in a single-arm, open-label phase II trial of tipifarnib for mOf the 22 patients with HNSCC with high VAF, 20 were evaluable for response at the time of data cutoff. Objective response rate for evaluable patients with high-VAF HNSCC was 55% (95% CI, 31.5 to 76.9). Median progression-free survival on tipifarnib was 5.6 months (95% CI, 3.6 to 16.4) versus 3.6 months (95% CI, 1.3 to 5.2) on last prior therapy. Median overall survival was 15.4 months (95% CI, 7.0 to 29.7). The most frequent treatment-emergent adverse events among the 30 patients with HNSCC were anemia (37%) and lymphopenia (13%).Tipifarnib demonstrated encouraging efficacy in patients with R/M HNSCC with

Key Points Gene expression and mutational analysis confirm the differences among the 3 peripheral TCL subclasses: AITL, PTCL-NOS, and PTCL-TFH.The expression of a gene set, including B-cell genes, is an IPI-independent prognostic factor for AITL cases., Visual Abstract, Peripheral T-cell lymphoma (PTCL) is a clinically aggressive disease, with a poor response to therapy and a low overall survival rate of approximately 30% after 5 years. We have analyzed a series of 105 cases with a diagnosis of PTCL using a customized NanoString platform (NanoString Technologies, Seattle, WA) that includes 208 genes associated with T-cell differentiation, oncogenes and tumor suppressor genes, deregulated pathways, and stromal cell subpopulations. A comparative analysis of the various histological types of PTCL (angioimmunoblastic T-cell lymphoma [AITL]; PTCL with T follicular helper [TFH] phenotype; PTCL not otherwise specified [NOS]) showed that specific sets of genes were associated with each of the diagnoses. These included TFH markers, cytotoxic markers, and genes whose expression was a surrogate for specific cellular subpopulations, including follicular dendritic cells, mast cells, and genes belonging to precise survival (NF-κB) and other pathways. Furthermore, the mutational profile was analyzed using a custom panel that targeted 62 genes in 76 cases distributed in AITL, PTCL-TFH, and PTCL-NOS. The main differences among the 3 nodal PTCL classes involved the RHOAG17V mutations (P < .0001), which were approximately twice as frequent in AITL (34.09%) as in PTCL-TFH (16.66%) cases but were not detected in PTCL-NOS. A multivariate analysis identified gene sets that allowed the series of cases to be stratified into different risk groups. This study supports and validates the current division of PTCL into these 3 categories, identifies sets of markers that can be used for a more precise diagnosis, and recognizes the expression of B-cell genes as an IPI-independent prognostic factor for AITL.

Background Real-world data (RWD) has been increasingly used in drug development. A reliable evaluation of efficacy for current treatments is challenging with very limited publication data of clinical trials available. The RWD provides a unique value and an alternative way to achieve such goal. Use data from metastatic Breast Cancer (mBC) patients in the real world clinical practice, we examine the treatment patterns and durations of different endocrine monotherapies in various clinical settings. Methods We obtained Flatiron Health subject-level mBC data set which consists a group of 20645 mBC patients. The analysis set consisted of subjects who were ER+/Her2-/(PgR+ or PgR-), received at least one prior line of CDK4/6 inhibitor (mono or combo) and one prior line of endocrine therapy (mono or combo) in the mBC settings, and had an ECOG performance score Result Out of all subjects in the mBC RWD database, 263 subjects met the inclusion criteria and were included in the analysis set. Among all 263 ER+/Her2- subjects, the median TTD of endocrine monotherapies was 3.0 months (95% CI: 2.8-3.7 months, N=263) in all subjects, 3.7 months (95% CI: 3.0-4.3 months, N=186) in PgR+ group and 2.1 months (95% CI: 1.9-2.9 months, N=77) in PgR- group. Among 186 ER+/PgR+/Her2- subjects, 1) the median TTD of endocrine monotherapies was 3.3 months (95% CI: 2.8-4.6 months, N=153) in ECOG=3 prior treatment lines group. Conclusion By investigating the RWD, we observed that the PgR status is prognostic in post CDK setting: endocrine monotherapies in PgR+ group has longer TTD compared to PgR- group in ER+/Her2- mBC subjects. By further looking into ER+/PgR+/Her2- subjects, we observed different treatment durations of endocrine therapies in various clinical scenarios, which may provide a helpful understanding of the mBC monotherapy treatments. Citation Format: Tenghui Chen, Zhaojie Zhang, Lei Gao, Catherine Scholz, Antonio Gualberto, Lihua Yu, Kun Yu. Using real-world data to evaluate the performance of endocrine therapies in ER+/Her2- metastatic breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5247.

To assess the antitumor activity and safety of tipifarnib, a highly potent and selective farnesyltransferase inhibitor, we performed a phase II clinical trial in patients with advanced and refractory urothelial carcinoma harboring missenseA total of 245 adult patients with previously treated, advanced urothelial carcinoma entered the molecular screening program includingWe identified 16 (7%) missenseOral tipifarnib resulted in a manageable safety profile and encouraging antitumor efficacy against treatment-refractory urothelial carcinoma containing

Patients diagnosed with T-cell leukemias and T-cell lymphomas (TCLs) still have a poor prognosis and an inadequate response to current therapies, highlighting the need for targeted treatments. We have analyzed the potential therapeutic value of the farnesyltransferase inhibitor, tipifarnib, in 25 TCL cell lines through the identification of genomic and/or immunohistochemical markers of tipifarnib sensitivity. More than half of the cell lines (60%) were considered to be sensitive. Tipifarnib reduced cell viability in these T-cell leukemia and TCL cell lines, induced apoptosis and modified the cell cycle. A mutational study showed TP53, NOTCH1 and DNMT3 to be mutated in 84.6%, 69.2% and 30.0% of sensitive cell lines, and in 62.5%, 0% and 0% of resistant cell lines, respectively. An immunohistochemistry study showed that p-ERK and RelB were associated as potential biomarkers of tipifarnib sensitivity and resistance, respectively. Data from RNA-seq show that tipifarnib at IC50 after 72 h downregulated a great variety of pathways, including those controlling cell cycle, metabolism, and ribosomal and mitochondrial activity. This study establishes tipifarnib as a potential therapeutic option in T-cell leukemia and TCL. The mutational state of NOTCH1, p-ERK and RelB could serve as potential biomarkers of tipifarnib sensitivity and resistance. Acknowledgements: We thank Phil Mason for his help in correcting the English and Helena Pisonero (IDIVAL) for technical assistance in the lab. The research was supported by grants from the Instituto de Salud Carlos III, from the Ministerio de Economía, Industria y Competitividad [SAF2013-47416-R, CIBERONC-ISCIII, ISCIII-MINECO-AES-FEDER (Plan Estatal I + D + I 2013–2016)}. The AECC PROYE18054PIRI, CAM B2017/BMD-3778, PIC97/2017_FJD, PIE15/0081 and PIE16/01294; Asociación Española Contra el Cáncer (AECC), Comunidad Autónoma de Madrid and Instituto Formación e Investigación, Hospital Universitario Marqués de Valdecilla (IDIVAL): NVAL16/18. A E-C is funded by ISCIII /MINECO (PT17/0009/0019) and co-funded by FEDER.

Background: Admixture of archaic (Neandertal and Denisova) and ancestral genes enhanced natural immunity during out of Africa migrations and modulates modern susceptibility to autoimmunity and cancer. We investigated a series of functional interactions between archaic and ancestral STING1 and TLR genes to identify vulnerabilities that could be addressed by STING agonist therapy. Methods: Gene variants from 10,389 cancer patients (pts) were obtained from TCGA. Archaic sequences were accessed using UCSD genome browser 410. Linkage disequilibrium was investigated using LDlink v5.0. Patient 1 was treated within NCT04144140. Results: STING1 variants were overrepresented in gastroesophageal cancer pts. V48V (rs7447927-C>G) with GWAS of lower rate of Asian esophageal cancer was in linkage disequilibrium with the reference alleles of the partially active HAQ and REF variants, and with rs13153461, present in Neandertal sequences. STING1 rs7447927-G was also associated with HLA A*24:02 (p Citation Format: Antonio Gualberto, Tenghui Chen, Catherine Scholz, Jason Luke. Neandertal introgressions contribute to upper aero-digestive tract tumor patient survival and identify patients who may benefit from STING agonist treatment [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P110.

The prognosis of acute myeloid leukemia (AML) remains poor in part due to the leukemic bone marrow microenvironment. Our lab has found that CXCL12, a chemokine abundant within the leukemic bone marrow microenvironment, induces apoptosis of AML cells expressing CXCR4, the receptor for CXCL12. However, this CXCL12/CXCR4-induced apoptosis is inhibited by differentiating osteoblasts, which protect AML cells from apoptosis in the bone marrow. Tipifarnib is a farnesyltransferase inhibitor shown to increase progression-free survival in AML patients that express high levels of CXCL12. Here, we report that tipifarnib inhibits the CXCL12/CXCR4-directed migration of AML cells via an ERK independent pathway. Furthermore, tipifarnib enhances CXCL12/CXCR4-mediated AML cell apoptosis via a mechanism that alters expression of apoptosis-regulating proteins. In addition, tipifarnib disrupts AML protection by osteoblasts, increasing AML cell apoptosis. Tipifarnib inhibits the osteoblast-mediated protection of AML cells via disrupting COL1A1 and TNAP, proteins essential for extracellular matrix production. In conclusion, tipifarnib alters the bone marrow microenvironment which is predicted to enhance eradication of AML via inhibiting CXCL12/CXCR4 directed cellular migration of AML cells, reducing the protective effects of differentiating osteoblasts by disrupting matrix protection proteins, and increasing CXCL12/CXCR4-mediated apoptosis.

Vedolizumab, a humanized monoclonal antibody against the α4β7 integrin, is indicated for treatment of moderately to severely active ulcerative colitis or Crohn’s disease. In this placebo-controlled, double-blind, randomized, single ascending-dose study, the pharmacokinetics, pharmacodynamics, safety, and tolerability of vedolizumab were evaluated in healthy volunteers. Forty-nine participants (in five cohorts) were randomly assigned in a 4:1 ratio to receive a single intravenous infusion of either vedolizumab (0.2, 0.5, 2.0, 6.0, or 10.0 mg/kg) or placebo. Blood samples were collected for measurement of vedolizumab serum concentrations and α4β7 saturation on peripheral blood lymphocytes by vedolizumab. Pharmacokinetic parameters were computed using a non-compartmental approach. Adverse events were monitored. Vedolizumab maximum observed serum concentration (C max) demonstrated dose proportionality over the dose range tested. Greater than dose-proportional increases in area under the serum concentration–time curve from time 0 to infinity (AUC0–inf) and shorter terminal elimination half-life (t 1/2) were observed from 0.2 to 2.0 mg/kg, suggestive of nonlinear pharmacokinetics at lower doses. At doses higher than 2.0 mg/kg, these parameters increased dose proportionally. Saturation of α4β7 was at or near maximal levels (>90 %) at all doses and time points when vedolizumab was measurable in serum. A total of 21 of 39 (54 %) vedolizumab-treated participants were anti-drug antibody (ADA) positive, and 11 (28 %) were persistently ADA positive. Overall, no adverse event signals, including serious infections or malignancies, were apparent. Vedolizumab exhibited target-mediated disposition, characterized by a rapid, saturable, nonlinear elimination process at low concentrations and a slower linear elimination process at higher concentrations. Nearly complete α4β7 saturation was observed at all doses. A single intravenous infusion of vedolizumab was well tolerated by healthy volunteers.

Background Vedolizumab, a gut-selective, anti-inflammatory monoclonal antibody, has shown preliminary efficacy in ulcerative colitis (UC) and Crohn's disease (CD). We report long-term experience with vedolizumab for active UC and CD. Methods After a placebo-controlled study, 38 patients with UC were randomized to a loading regimen of vedolizumab 2, 6, or 10 mg/kg on days 1, 15, and 43, followed by maintenance dosing every 8 weeks. Thirty-four vedolizumab-naive patients (15 UC; 19 CD) were randomized to vedolizumab 2, 6, or 10 mg/kg on the same schedule. Rollover patients were treated up to 630 days and treatment-naive patients were treated up to 547 days. Results Seventy-two patients were dosed; 52 (72%) completed the study. In exploratory analyses, 28 of 72 (39%; UC: 21 of 53, CD: 7 of 19) achieved clinical response and 42 of 72 (58.3%; UC: 38 of 53, CD: 4 of 19) achieved clinical remission. Mean partial Mayo scores declined from baseline through day 155 in both treatment-naive patients with UC (5.4 to 1.7, respectively) and rollover patients with UC (2.3 to 1.4, respectively), leveling off thereafter. Mean Crohn's Disease Activity Index scores decreased from 295 (baseline) to 238 at day 43, continued to trend downward through day 155, and remained below baseline through day 491. Mean Inflammatory Bowel Disease Questionnaire scores increased in all treatment groups. No deaths or systemic opportunistic infections were reported. Conclusion Vedolizumab every 8 weeks for up to 78 weeks had an adverse event profile similar to that previously observed. Mean disease activity indices (partial Mayo score and Crohn's Disease Activity Index score) improved with all 3 doses investigated.

Background: Vedolizumab is a gut-selective biologic that has shown efficacy in ulcerative colitis (UC) and Crohn's disease (CD). We studied the pharmacokinetics, pharmacodynamics, safety, tolerability, and efficacy of a new formulation of vedolizumab produced by an improved manufacturing process. Methods: UC patients were randomized to receive vedolizumab (2, 6, or 10 mg/kg) or placebo on days 1, 15, 29, and 85. Safety, pharmacokinetics, pharmacodynamics, and immunogenicity evaluations were performed at multiple timepoints through day 253. Partial Mayo Scores and fecal calprotectin levels were used to assess efficacy. Results: In all, 46 patients (9 placebo, 37 vedolizumab) received at least one dose of study medication. The vedolizumab serum concentration declined monoexponentially until concentrations reached 1–10 μg/mL, and then fell nonlinearly. Vedolizumab maximum serum concentration (Cmax) and area under the curve (AUC) increased approximately proportionally as a function of dose. Vedolizumab maximally saturated α4β7 receptors on peripheral serum lymphocytes at all measurable serum concentrations. Vedolizumab was well tolerated, with no deaths and no adverse events leading to discontinuation. At every assessment from day 29 through day 253, over 50% of vedolizumab-treated patients were in clinical response, while placebo response rates generally ranged between 22% and 33%. Vedolizumab treatment reduced fecal calprotectin levels compared with placebo. Conclusions: Vedolizumab demonstrated dose-proportional pharmacokinetics and maximally saturated α4β7 receptors over the tested dose range. Multiple dosing up to 10 mg/kg was well tolerated. Over the course of follow-up a greater proportion of patients treated with vedolizumab were in clinical response than those who were assigned to placebo. (Inflamm Bowel Dis 2012)

TPS2618 Background: Tipifarnib is a potent and highly selective inhibitor of farnesyltransferase (FT). FT catalyzes the post-translational attachment of farnesyl groups to signaling proteins that are requisite for localization to the inner cell membrane. While all RAS isoforms (KRAS/NRAS/HRAS) are FT substrates, only HRAS is exclusively dependent upon farnesylation for membrane localization and signaling activation, making HRAS mutant tumors uniquely susceptible to tipifarnib mediated inhibition of FT. Tipifarnib has demonstrated robust activity in HRAS mutant head and neck squamous cell carcinoma (HNSCC) and HRAS mutant squamous non-small cell lung cancer (NSCLC) patient derived xenograft (PDX) models resistant to standard therapies. Methods: This is a multi-institutional, open-label Phase II trial evaluating the efficacy and safety of tipifarnib for pts with HRAS mutant solid tumors. Pts must have either unresectable, locally advanced or metastatic non-hematological malignancies that harbor a missense HRAS mutation. The primary endpoint of the study is overall response rate. Secondary endpoints include safety and tolerability, PFS, duration of response. Two cohorts (N = 18 each) are enrolling, each being evaluated with a Simon two-stage design. Cohort 1 is for patients with malignant thyroid tumors of any histology. Cohort 2 was originally designated for pts with any other solid tumor. The prespecified activity goal for the first stage of accrual in Cohort 2 was met. Based on data observed in the first stage of this group, enrollment to the second stage of Cohort 2 has been limited to HRAS mutant HNSCC since August 2016. Enrolled patients are treated with tipifarnib 900 mg administered orally twice daily on days 1-7 and 15-21 of 28-day treatment cycles until progression of disease or unacceptable toxicity. Clinical trial information: NCT02383927.

Purpose: To evaluate the toxicity profile, pharmacologic, and biological properties of 3-pyridylmethyl N-{4-[(2-aminophenyl)carbamoyl]benzyl}carbamate (MS-275), a histone deacetylase inhibitor, when administered orally on three different dosing schedules. Experimental Design: Patients with advanced solid malignancies and lymphomas were treated on three dose schedules: once every other week, twice weekly for 3 weeks every 28 days, and once weekly for 3 weeks every 28 days. First-cycle plasma pharmacokinetics and peripheral blood mononuclear cell histone acetylation were determined. Results: Twenty-seven patients received ≥149 courses of treatment. Hypophosphatemia and asthenia were dose limiting on the weekly and twice-weekly dosing schedules; there was no dose-limiting toxicity on the every other week schedule. Pharmacokinetic variables revealed dose-dependent and dose-proportional increases. Two of 27 patients showed partial remissions, including one patient with metastatic melanoma who had a partial response and has remained on study for >5 years. Six patients showed prolonged disease stabilization. Levels of histone H3 and H4 acetylation in peripheral blood mononuclear cells increased qualitatively but with a high degree of interpatient variation. Conclusions: MS-275 is well tolerated at doses up to 6 mg/m2 every other week or 4 mg/m2 weekly for 3 weeks followed by 1 week of rest and results in biologically relevant plasma concentrations and antitumor activity. Twice-weekly dosing was not tolerable due to asthenia, and further evaluation of this schedule was halted. The recommended dose for further disease-focused studies is 4 mg/m2 given weekly for 3 weeks every 28 days or 2 to 6 mg/m2 given once every other week.