Phase I Study of Bortezomib, Fludarabine, and Melphalan, with or without Total Marrow Irradiation as Conditioning for Allogeneic Hematopoietic Stem Cell Transplantation in Patients with High-Risk or Relapsed/Refractory Multiple Myeloma

PURPOSE/OBJECTIVE(S)

Though outcomes of patients with multiple myeloma (MM) have improved, cure remains elusive. Allogeneic hematopoietic stem cell transplantation (allo-sCT) is associated with a lower relapse rate, but its role is hindered due to toxicities. We hypothesized that targeted total body irradiation in the form of total marrow irradiation (TMI) could safely facilitate allo-SCT via an improved toxicity profile. Therefore, we conducted a phase I study to investigate the safety and feasibility of a bortezomib (BTZ), fludarabine (FLU), and melphalan (MEL), with or without TMI, prior to allo-SCT for patients with high-risk (HR) or relapsed/refractory (R/R) MM.

MATERIALS/METHODS

Between 2012 and 2018 this study enrolled patients with HR or R/R MM on one of two strata, each comprising BTZ dose-escalation cohorts. Patients aged 18-60 with no prior radiation (RT) received TMI at 900 cGy (in 6 fractions delivered twice-daily), FLU, and MEL conditioning, with BTZ added in the second cohort (stratum I). Patients aged 18-70 with prior RT received FLU, MEL, and BTZ, without TMI (stratum II). The primary endpoint was feasibility of escalating doses of BTZ, with or without TMI, defined using a 3+3 design. Dose-limiting toxicity (DLT) was defined as any Grade 3+ Bearman toxicity or prolonged CTCAE v4.0 Grade 4+ neutropenia. Secondary endpoints included treatment response, time to neutrophil and platelet engraftment, incidence of acute (a) and chronic (c) graft-versus-host disease (GVHD), progression-free-survival (PFS), and overall survival (OS).

RESULTS

Eight patients were enrolled on stratum I. One of three patients in the first cohort of stratum I experienced DLT, which led to expansion to three more patients with no DLT. Cohort 2 enrolled only 2 patients due to low accrual, with BTZ added at 0.5 mg/m2; neither experienced DLT. Nine patients were enrolled on stratum II. Three patients were enrolled on cohort 1 (BTZ 0.5 mg/m2) and none experienced DLT. Three were enrolled on cohort 2 (bortezomib 0.7 mg/m2), and one experienced DLT. Therefore, the cohort expanded to three more patients. One more patient experienced DLT and 0.5 mg/m2 was considered the maximum tolerated dose. There were no primary or secondary graft failures. Complete response was achieved in 7 and 4 patients in strata I and II, respectively. Median follow-up for all patients was 30.7 months (mos) and was 99.8 mos for surviving patients. Median overall survival (OS) on strata I and II were 44.5 mos and 21.6 mos, respectively. Median PFS on strata I and II were 18.1 mos and 8.9 mos, respectively. In strata I, 5 patients developed Grade 2+ aGVHD and 8 developed extensive cGVHD. In strata II, 4 patients developed Grade 2+ aGVHD and 6 developed extensive cGVHD.

CONCLUSION

The TMI 900 cGy, FLU, and MEL conditioning regimen is considered safe as conditioning for allo-SCT and may warrant further investigation due to favorable response rates and survival; the conditioning regimen of FLU, MEL, and BTZ (0.7 mg/m2) is associated with unacceptable toxicities.

Characterization of Non-Small-Cell Lung Cancers With MET Exon 14 Skipping Alterations Detected in Tissue or Liquid: Clinicogenomics and Real-World Treatment Patterns

PURPOSE

MET exon 14 (METex14) skipping alterations are oncogenic drivers in non–small-cell lung cancer (NSCLC). We present a comprehensive overview of METex14 samples from 1,592 patients with NSCLC, associated clinicogenomic characteristics, potential mechanisms of acquired resistance, treatment patterns, and outcomes to MET inhibitors.

METHODS

Hybrid capture–based comprehensive genomic profiling (CGP) was performed on samples from 69,219 patients with NSCLC. For treatment patterns and outcomes analysis, patients with advanced METex14-altered NSCLC were selected from the Flatiron Health-Foundation Medicine clinicogenomic database, a nationwide deidentified electronic health record–derived database linked to Foundation Medicine CGP for patients treated between January 2011 and March 2020.

RESULTS

A total of 1,592 patients with NSCLC (2.3%) were identified with 1,599 METex14 alterations spanning multiple functional sites (1,458 of 60,244 tissue samples and 134 of 8,975 liquid samples). Low tumor mutational burden and high programmed death ligand 1 expression were enriched in METex14-altered samples. MDM2, CDK4, and MET coamplifications and TP53 mutations were present in 34%, 19%, 11%, and 42% of tissue samples, respectively. Comparing tissue and liquid cohorts, coalteration frequency and acquired resistance mechanisms, including multiple MET mutations, EGFR, ERBB2, KRAS, and PI3K pathway alterations, were generally similar. Positive percent agreement with the tissue was 100% for METex14 pairs collected within 1 year (n = 7). Treatment patterns showed increasing adoption of MET inhibitors in METex14-altered NSCLC after receipt of CGP results; the real-world response rate to MET inhibitors was 45%, and time to treatment discontinuation was 4.4 months.

CONCLUSION

Diverse METex14 alterations were present in 2%-3% of NSCLC cases. Tissue and liquid comparisons showed high concordance and similar coalteration profiles. Characterizing common co-occurring alterations and immunotherapy biomarkers, including those present before or acquired after treatment, may be critical for predicting responses to MET inhibitors and informing rational combination strategies.

Targetable BRAF and RAF1 Alterations in Advanced Pediatric Cancers

RAF family protein kinases signal through the MAPK pathway to orchestrate cellular proliferation, survival, and transformation. Identifying BRAF alterations in pediatric cancers is critically important as therapeutic agents targeting BRAF or MEK may be incorporated into the clinical management of these patients. In this study, we performed comprehensive genomic profiling on 3,633 pediatric cancer samples and identified a cohort of 221 (6.1%) cases with known or novel alterations in BRAF or RAF1 detected in extracranial solid tumors, brain tumors, or hematological malignancies. Eighty percent (176/221) of these tumors had a known-activating short variant (98, 55.7%), fusion (72, 40.9%), or insertion/deletion (6, 3.4%). Among BRAF altered cancers, the most common tumor types were brain tumors (74.4%), solid tumors (10.8%), hematological malignancies (9.1%), sarcomas (3.4%), and extracranial embryonal tumors (2.3%). RAF1 fusions containing intact RAF1 kinase domain (encoded by exons 10-17) were identified in seven tumors, including two novel fusions TMF1-RAF1 and SOX6-RAF1. Additionally, we highlight a subset of patients with brain tumor with positive clinical response to BRAF inhibitors, demonstrating the rationale for incorporating precision medicine into pediatric oncology. IMPLICATIONS FOR PRACTICE: Precision medicine has not yet gained a strong foothold in pediatric cancers. This study describes the landscape of BRAF and RAF1 genomic alterations across a diverse spectrum of pediatric cancers, primarily brain tumors, but also encompassing melanoma, sarcoma, several types of hematologic malignancy, and others. Given the availability of multiple U.S. Food and Drug Administration-approved BRAF inhibitors, identification of these alterations may assist with treatment decision making, as described here in three cases of pediatric cancer.

Characterization of Clinical Cases of Malignant PEComa via Comprehensive Genomic Profiling of DNA and RNA

PURPOSE

Perivascular epithelioid cell tumor (PEComa) is a rare mesenchymal soft tissue neoplasm often linked to mTOR pathway activation via TSC2 mutation. We analyzed a series of 31 consecutive metastatic PEComa (mPEComa) cases using a combined DNA/RNA hybrid capture-based comprehensive genomic profiling (CGP) assay to assess the genomic landscape of mPEComa.

PATIENTS AND METHODS

Formalin-fixed, paraffin-embedded (FFPE) blocks or slides were obtained from tumors from 31 unique patients with mPEC-oma. DNA and RNA were extracted and CGP was performed on 405 genes using a targeted next-generation sequencing (NGS) assay in a CLIA-certified lab.

RESULTS

All cases had locally advanced or metastatic disease, and 58% of patients were female with a median age of 50 years (range 8-76), and 17 and 14 specimens were from primary and metastatic sites, respectively. One hundred genomic alterations were identified in the cohort, with an average of 3.2 genomic alterations/case including alterations in TSC2 32.3% of cases (10), TSC1 9.6% (3), TFE3 16.1% (5, all fusions), and folliculin (FLCN) 6.4% (2), with all occurring in mutually exclusive fashion. Of TSC2 mutant cases, 70% had biallelic inactivation of this locus, as were 100% of TSC1 mutant cases. Two TSC1/2 wildtype cases harbored truncating mutations in FLCN, both of which were under LOH. Five TFE3 fusion cases were identified including the novel 5' fusion partner ZC3H4.

CONCLUSIONS

We describe for the first time mPEComa cases with FLCN mutations under LOH, further characterizing dysregulation of the mTOR pathway as a unifying theme in mPEC-oma. Cumulatively, we demonstrate the feasibility and potential utility of segregating mPEComa by TSC, TFE3, and FLCN status via CGP in clinical care.

Patients with NSCLCs Harboring Internal Inversions or Deletion Rearrangements of the ALK Gene Have Durable Responses to ALK Kinase Inhibitors

Background

ALK fusions are targetable drivers in non-small-cell lung cancer (NSCLC). However, patients with NSCLC harboring ALK rearrangements without a fusion partner identified in DNA have also been shown to respond to ALK inhibitors. We aimed to characterize complex ALK variants that may predict sensitivity to multiple approved ALK inhibitors.

Methods

Comprehensive genomic profiling (CGP) of DNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue or blood-based circulating tumor DNA was performed for 39,159 NSCLC patients during routine clinical care. For a subset of cases, RNA sequencing was performed, and prior ALK test results and clinical treatment information were collected from treating physicians.

Results

We queried the Foundation Medicine NSCLC database and identified ALK internal inversions, as well as internal deletions, as the sole ALK rearrangements in 6 (0.02%) and 3 (0.01%) of cases, respectively. In cases with ALK internal inversions, RNA testing identified an EML4-ALK fusion in 2/2 cases evaluated, and 3/3 patients treated with ALK inhibitors had durable responses. A single patient with an ALK internal deletion and clinical data available responded to multiple ALK inhibitors. RNA data available for a subset of non-NSCLC cases suggest that ALK internal deletions removing a portion of the N-terminus are drivers themselves and do not result in ALK fusions. Fluorescence in situ hybridization (FISH) results were inconsistent for both classes of DNA events.

Conclusion

Rare internal inversions of ALK appear to be indicative of ALK fusions, which can be detected in RNA, and response to ALK inhibitors in patients with NSCLC. In contrast, ALK internal deletions are not associated with ALK fusions in RNA but likely represent targetable drivers themselves. These data suggest that CGP of DNA should be supplemented with immunohistochemistry or RNA-based testing to further resolve these events and match patients to effective therapies.

Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer

Background

Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer.

Patients and methods

To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots.

Results

We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations.

Conclusions

Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.

Novel PDGFRB rearrangement in multifocal infantile myofibromatosis is tumorigenic and sensitive to imatinib

Infantile myofibromatosis (IM) is an aggressive neoplasm composed of myofibroblast-like cells in children. Although typically localized, it can also present as multifocal disease, which represents a challenge for effective treatment. IM has previously been linked to activating somatic and germline point mutations in the PDGFRβ tyrosine kinase encoded by the PDGFRB gene. Clinical panel-based targeted tumor sequencing of a tumor from a newborn with multifocal IM revealed a novel PDGFRB rearrangement, which was reported as being of unclear significance. Additional sequencing of cDNA from tumor and germline DNA confirmed a complex somatic/mosaic PDGFRB rearrangement with an apparent partial tandem duplication disrupting the juxtamembrane domain. Ectopic expression of cDNA encoding the mutant form of PDGFRB markedly enhanced cell proliferation of mouse embryo fibroblasts (MEFs) compared to wild-type PDGFRB and conferred tumor-forming capacity on nontumorigenic 10T1/2 fibroblasts. The mutated protein enhanced MAPK activation and retained sensitivity to the PDGFRβ inhibitor imatinib. Our findings reveal a new mechanism by which PDGFRB can be activated in IM, suggest that therapy with tyrosine kinase inhibitors including imatinib may be beneficial, and raise the possibility that this receptor tyrosine kinase might be altered in a similar fashion in additional cases that would similarly present annotation challenges in clinical DNA sequencing analysis pipelines.

Abstract P1-17-10: The impact of age and adjuvant chemotherapy modifications on disease-free and overall survival among African American women with breast cancer

Background: During chemotherapy for breast cancer, African American women receive less relative dose intensity with more dose reductions and early chemotherapy cessation compared to Caucasian women. Other research has found that older breast cancer patients are most at risk for treatment modifications; however, it is unclear if this remains true for African American patients. Furthermore, the clinical implications of treatment modifications and delays on survival is uncertain, particularly in African American patients.

Purpose: The purpose of this study was to investigate whether age (diagnosis <55 vs. diagnosis ≥55) was a moderator for the association between treatment modifications (dose held, dose delayed, and early cessation) and overall survival (OS) and disease-free survival (DFS) in African American women with breast cancer.

Methods: A retrospective cohort study of early stage African American breast cancer patients treated with adjuvant chemotherapy was employed. Dose held, dose delayed and early cessation were examined as dichotomous variables: any adjustment to the initially prescribed treatment plan was considered a modification. Medical record data extraction was utilized to gather this information. The sample was divided into two groups: those diagnosed <55 years of age and those diagnosed ≥55 years of age. A Cox's proportional hazards regression model was used to examine the interaction between age group and treatment modifications for OS and DFS, while controlling for stage and ER and HER2 status.

Results: In the study of 115 participants, 58 (50.4%) were diagnosed before the age of 55, and 57 (49.6%) were diagnosed age 55 or older. Across the entire sample, 43 (37.4%) patients experienced a treatment modification. There were no significant differences in the proportions of treatment modifications between the two age groups. We found no interaction between age group and treatment modifications for OS. However, there was a significant interaction between age group and held dose for DFS (p=0.045). Specifically, those diagnosed at 55 years of age and older, who had doses of chemotherapy held, experienced worse DFS compared to those who did not (hazard ratio (HR)=3.390, 95% CI (1.013,11.34)). In contrast, there was no difference in DFS between those who did and did not have doses held in patients diagnosed below 55 years of age (HR=0.563, 95%CI (0.159, 1.986)).

Conclusions: African American women receiving adjuvant chemotherapy for treatment of early stage breast cancer have high levels of treatment modifications across all age groups. However, held doses of chemotherapy in older African American patients were associated with worse DFS. Further research is needed to elucidate the clinical implications of adjuvant chemotherapy treatment modifications, particularly in African American patients, and the subgroups of patients who are at greatest risk.

Citation Format: Nugent BD, Ren D, Bender C, Rosenzweig M. The impact of age and adjuvant chemotherapy modifications on disease-free and overall survival among African American women with breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-17-10.

Abstract P2-08-48: Features associated with long-term survival in metastatic breast cancer

Background: 5-10% of women with metastatic breast cancer (MBC) survive ≥5 years. Predictors of long-term survival are not clearly elucidated. We used data from 122 long-term MBC survivors (≥5-year survival from date of MBC diagnosis) and 191 short-term MBC survivors (≤2-year survival from date from MBC diagnosis) to identify clinico-pathologic and socioeconomic features associated with MBC survival.

Methods: Women initially diagnosed with breast cancer (BC) in or after 1999, and diagnosed with MBC at Magee Women's Cancer Program of UPMC were included (N=313). Data abstracted from medical records included: stage at initial BC diagnosis, body mass index (BMI), Charlson Comorbidity Index (CCI), age, menopausal status at initial BC diagnosis, tumor receptor status at initial BC diagnosis, site of initial metastases, time to recurrence between initial diagnosis and MBC, household income, race, employment status, and partner status. Differences between groups were assessed using t-tests and Chi-square or Fisher's exact tests. Odds ratios (OR) and 95% confidence intervals (CI) were calculated using multivariate logistic regression models.

Results: Long-term survivors were significantly (P<0.05) younger, had more ER positive, PR positive, and Her2 positive disease, lower CCI, more often premenopausal at initial diagnosis, lower rates of visceral metastases, higher household income, and more often partnered than short-term survivors. The association of premenopausal status at initial diagnosis with long-term survival remained significant after adjustment for stage at initial diagnosis, tumor receptor status, and CCI (OR: 1.96, 95% CI 1.02- 3.79). Long-term term survivors were also significantly more often diagnosed with de novo MBC compared to short-term survivors. The association of de novo MBC with long-term survival remained significant after adjustment for age, tumor receptor status, and CCI (OR: 3.0, 95% CI 1.6-5.4). Time to recurrence between initial diagnosis and MBC, BMI, race, and employment status were not associated with survival.

Conclusions: Diagnosis of de novo MBC, ER-, PR- and/or Her2-positive primary tumor, lower rates of visceral metastases, higher household income, younger age, lower CCI, premenopausal status, and having a partner are associated with long-term survival after diagnosis of MBC. This is one of the first studies to show a survival benefit in MBC for patients with de novo MBC, premenopausal status at initial diagnosis, positive partner status, and higher household income.

Citation Format: Klar NJ, Rosenzweig M, Diergaarde B, Brufsky A. Features associated with long-term survival in metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-08-48.

BRAF in Lung Cancers: Analysis of Patient Cases Reveals Recurrent BRAF Mutations, Fusions, Kinase Duplications, and Concurrent Alterations

Purpose

Dabrafenib and trametinib are approved for the management of advanced non-small-cell lung cancers (NSCLCs) that harbor BRAF V600E mutations. Small series and pan-cancer analyses have identified non-V600 alterations as therapeutic targets. We sought to examine a large genomic data set to comprehensively characterize non-V600 BRAF alterations in lung cancer.

Patients and Methods

A total of 23,396 patients with lung cancer provided data to assay with comprehensive genomic profiling. Data were reviewed for predicted pathogenic BRAF base substitutions, short insertions and deletions, copy number changes, and rearrangements.

Results

Adenocarcinomas represented 65% of the occurrences; NSCLC not otherwise specified (NOS), 15%; squamous cell carcinoma, 12%; and small-cell lung carcinoma, 5%. BRAF was altered in 4.5% (1,048 of 23,396) of all tumors; 37.4% (n = 397) were BRAF V600E, 38% were BRAF non-V600E activating mutations, and 18% were BRAF inactivating. Rearrangements were observed at a frequency of 4.3% and consisted of N-terminal deletions (NTDs; 0.75%), kinase domain duplications (KDDs; 0.75%), and BRAF fusions (2.8%). The fusions involved three recurrent fusion partners: ARMC10, DOCK4, and TRIM24. BRAF V600E was associated with co-occurrence of SETD2 alterations, but other BRAF alterations were not and were instead associated with CDKN2A, TP53, and STK11 alterations (P < .05). Potential mechanisms of acquired resistance to BRAF V600E inhibition are demonstrated.

Conclusion

This series characterized the frequent occurrence (4.4%) of BRAF alterations in lung cancers. Recurrent BRAF alterations in NSCLC adenocarcinoma are comparable to the frequency of other NSCLC oncogenic drivers, such as ALK, and exceed that of ROS1 or RET. This work supports a broad profiling approach in lung cancers and suggests that non-V600E BRAF alterations represent a subgroup of lung cancers in which targeted therapy should be considered.

Identification of NTRK fusions in pediatric mesenchymal tumors

BACKGROUND

NTRK fusions are known oncogenic drivers and have recently been effectively targeted by investigational agents in adults. We sought to assess the frequency of NTRK fusions in a large series of pediatric and adolescent patients with advanced cancers.

PROCEDURE

Genomic profiles from 2,031 advanced cancers from patients less than 21 years old who were assayed with comprehensive genomic profiling were reviewed to identify NTRK fusions.

RESULTS

Total of nine cases (0.44%) harbored NTRK fusions, including novel partners. Four of these cases were in children less than 2 years old for which infantile fibrosarcoma was considered as a diagnosis, and two harbored the canonical ETV6-NTRK3. The remaining cases carried other diagnoses, at least one that carried the diagnosis of inflammatory myofibroblastic tumor.

CONCLUSIONS

NTRK fusions occur in a subset of young patients with mesenchymal or sarcoma-like tumors at a low frequency, and are eminently druggable targets via either investigational agents or approved drugs.

Abstract 1118: Activation of MET via diverse exon 14 skipping mutations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors

Amplification and point mutation in MET are well-characterized oncogenic drivers that confer susceptibility to MET inhibitors, such as crizotinib, particularly in non-small cell lung cancer. Splice site alterations at exon 14 of the MET (METex14) gene result in exon skipping and MET activation through loss of a DpYR motif (Y1003) that recruits the ubiquitin ligase CBL, targeting MET for degradation. METex14 skipping mutations have primarily been detected in lung adenocarcinoma, occurring in ∼3% of cases, but also in neuroblastoma and gastric cancer cell lines. 17 distinct variants have been characterized, however, their full diversity and prevalence across tumor types is unknown. Most importantly, it is unknown whether these mutations confer clinical susceptibility to targeted therapy with multiple MET inhibitors.

We report here analysis of 29,714 cancer genomes to identify 168 harboring METex14 splicing mutations, including 101 distinct genomic variants. They are detected most frequently in lung adenocarcinoma (3.1%, 104/3360), but also in other lung neoplasms (2.0%, 40/2022), brain glioma (0.5%, 6/1312), tumors of unknown primary origin (0.4%, 11/2516), and other tumor types (0.03% 7/20504). Lung malignancies with these mutations do not have other characteristic driver mutations, and have a distinct profile of co-occurring mutations, supporting the role of METex14 skipping as the primary drivers of oncogenesis in these specimens. Most importantly, patients with tumors harboring these mutations demonstrate durable response to anti-MET targeted therapy, in several tumor types.

These data demonstrate that METex14 splicing mutations define a distinct class of tumors that are responsive to targeted therapy. The diversity of these variants indicates that diagnostic testing via massively parallel sequencing is necessary for detection in a clinical setting. The data also suggest that thousands of cancer genome profiles will be required to discover non-coding cancer drivers with degenerate genomic signatures.

Citation Format: Garrett M. Frampton, Siraj Ali, Juliann Chmielecki, Mark Rosenzweig, Timothy Brennan, Zachary Chalmers, Julia Elvin, Alex Fichtenholtz, Kyle Gowan, Joel Greenbowe, Adrienne Johnson, Lily Khaira, Doron Lipson, Caitlin McMahon, Steven Roels, Roman Yelensky, Deborah Morosini, Philip Stephens, Vincent Miller. Activation of MET via diverse exon 14 skipping mutations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1118. doi:10.1158/1538-7445.AM2015-1118

Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors

Focal amplification and activating point mutation of the MET gene are well-characterized oncogenic drivers that confer susceptibility to targeted MET inhibitors. Recurrent somatic splice site alterations at MET exon 14 (METex14) that result in exon skipping and MET activation have been characterized, but their full diversity and prevalence across tumor types are unknown. Here, we report analysis of tumor genomic profiles from 38,028 patients to identify 221 cases with METex14 mutations (0.6%), including 126 distinct sequence variants. METex14 mutations are detected most frequently in lung adenocarcinoma (3%), but also frequently in other lung neoplasms (2.3%), brain glioma (0.4%), and tumors of unknown primary origin (0.4%). Further in vitro studies demonstrate sensitivity to MET inhibitors in cells harboring METex14 alterations. We also report three new patient cases with METex14 alterations in lung or histiocytic sarcoma tumors that showed durable response to two different MET-targeted therapies. The diversity of METex14 mutations indicates that diagnostic testing via comprehensive genomic profiling is necessary for detection in a clinical setting.

SIGNIFICANCE

Here we report the identification of diverse exon 14 splice site alterations in MET that result in constitutive activity of this receptor and oncogenic transformation in vitro. Patients whose tumors harbored these alterations derived meaningful clinical benefit from MET inhibitors. Collectively, these data support the role of METex14 alterations as drivers of tumorigenesis, and identify a unique subset of patients likely to derive benefit from MET inhibitors.

TrpA1 regulates thermal nociception in Drosophila

Pain is a significant medical concern and represents a major unmet clinical need. The ability to perceive and react to tissue-damaging stimuli is essential in order to maintain bodily integrity in the face of environmental danger. To prevent damage the systems that detect noxious stimuli are therefore under strict evolutionary pressure. We developed a high-throughput behavioral method to identify genes contributing to thermal nociception in the fruit fly and have reported a large-scale screen that identified the Ca²⁺ channel straightjacket (stj) as a conserved regulator of thermal nociception. Here we present the minimal anatomical and neuronal requirements for Drosophila to avoid noxious heat in our novel behavioral paradigm. Bioinformatics analysis of our whole genome data set revealed 23 genes implicated in Ca²⁺ signaling that are required for noxious heat avoidance. One of these genes, the conserved thermoreceptor TrpA1, was confirmed as a bona fide “pain” gene in both adult and larval fly nociception paradigms. The nociceptive function of TrpA1 required expression within the Drosophila nervous system, specifically within nociceptive multi-dendritic (MD) sensory neurons. Therefore, our analysis identifies the channel TRPA1 as a conserved regulator of nociception.

A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene

Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing.

Long-term treatment with intravenous bisphosphonates in metastatic breast cancer (MBC)

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Background: Intravenous bisphosphonates (IV BPs) are safe and effective in reducing skeletal related events in MBC. The effects of IV BPs after 24 months of therapy are unknown. The incidence of osteonecrosis of the jaw (ONJ) and renal insufficiency (RI) among women with MBC receiving >= 24 months of IV BPs is also poorly defined. We studied the long term effect of IV BPs in a cohort of women with MBC. Methods: We maintain an ongoing prospective database of >600 women with MBC diagnosed and treated at our institution from January 1999. A long-term cohort (LTC) of 159 women with metastatic breast cancer to bone treated for >= 24 months with pamidronate (n = 9), zoledronic acid (n = 110), or both (n = 40) was identified. A control cohort (CC) of 62 women with MBC to bone treated with IV BPs for 12–23 months was also identified. RI was defined as an increase in serum creatinine (scr) of > 0.5 mg/dl or an absolute level of scr >1.5mg/dl; ONJ was diagnosed by dental consultation. Results: Median follow-up of the LTC was 39 months (range 24–99) months. Median overall survival in this cohort was 43 months (range 24–114). The vast majority of women in the LTC (140/159, 88.1%) continued to receive IV BPs at standard dose every 3–4 weeks. The incidence of ONJ in the LTC was 6/159 (3.8%), after a mean 42.2 treatment cycles, with a median time to ONJ of 44 months. Three of six patients with ONJ (50%) underwent surgical resection, and 3/6 (50%) were managed conservatively, and 3/6 (50%) resumed IV BPs after a mean 12 month hold. The incidence of RI (all pts had baseline scr < 1.4 mg/dl) in the LTC was 19/159 (11.9%), occurring after a mean 43.4 treatment cycles, with a median time to RI of 43 months. Eleven of 19 patients (57.9%) recovered to baseline scr and 7/19 (36.7%) patients showed partial recovery. Seventeen of 19 patients (89.4%) were able to resume therapy after temporary discontinuation, decreasing the dose, or increasing the interval of the IV BP. Incidence of ONJ in the CC was 1/62 (1.6%) and RI in the CC was 6/62 (9.7%). Conclusions: Long term (>=24 month) IV BP use in MBC is well tolerated and safe, with relatively low incidence of ONJ and RI. Most patients were able to resume IV BP therapy after a therapy hold without further complication.

No significant financial relationships to disclose.

Febrile reactions occurring with second cycle of high-dose melphalan and SCT in patients with AL amyloidosis: a 'melphalan recall' reaction

Aggressive treatment with high-dose i.v. melphalan followed by auto-SCT (HDM/SCT) is effective in inducing hematological and clinical remissions, and in extending survival in AL amyloidosis. Tandem cycles of HDM/SCT have been shown to increase hematologic complete response rates in patients with AL amyloidosis. Between April 1994 and July 2008, 57 patients with AL amyloidosis at the Boston University Medical Center were treated with a second cycle of HDM/SCT after failing to achieve a complete response after a first transplantation. A total of 11 of 57 patients (19%) treated with tandem transplantation developed high fever 12-24 h after melphalan administration. The average peak temperature was 39.1 degrees C. Other clinical features include hypotension, acute renal failure and skin rash. No infectious etiology was identified. One of the patients had serum available for measurement of cytokines before, during and after the febrile reaction. The concentration of several pro-inflammatory cytokines, including IL-6 and TNFalpha, increased significantly, showing a clear physiological response correlating with the clinical findings. We conclude that an unusual cytokine-mediated febrile reaction can occur in patients with AL amyloidosis exposed to a second cycle of high-dose melphalan, which we have termed a 'melphalan recall' reaction.

An internal thermal sensor controlling temperature preference in Drosophila

Animals from flies to humans are able to distinguish subtle gradations in temperature and show strong temperature preferences. Animals move to environments of optimal temperature and some manipulate the temperature of their surroundings, as humans do using clothing and shelter. Despite the ubiquitous influence of environmental temperature on animal behaviour, the neural circuits and strategies through which animals select a preferred temperature remain largely unknown. Here we identify a small set of warmth-activated anterior cell (AC) neurons located in the Drosophila brain, the function of which is critical for preferred temperature selection. AC neuron activation occurs just above the fly's preferred temperature and depends on dTrpA1, an ion channel that functions as a molecular sensor of warmth. Flies that selectively express dTrpA1 in the AC neurons select normal temperatures, whereas flies in which dTrpA1 function is reduced or eliminated choose warmer temperatures. This internal warmth-sensing pathway promotes avoidance of slightly elevated temperatures and acts together with a distinct pathway for cold avoidance to set the fly's preferred temperature. Thus, flies select a preferred temperature by using a thermal sensing pathway tuned to trigger avoidance of temperatures that deviate even slightly from the preferred temperature. This provides a potentially general strategy for robustly selecting a narrow temperature range optimal for survival.

Women with Her2 unamplified but chromosome 17 hyperploid metatstatic breast cancer (MBC) respond to traztuzumab

21051

Background: Guidelines for the interpretation of Her2 testing by FISH in determining therapy for Her2 positive metatstatic breast cancer generally suggest that only women with Her2 to chromosome 17 (CEP 17) amplification ratios of greater than 2.0 will benefit from traztuzumab. However, hyperploidy of chromosome 17 may lead to increased Her2 copy number despite a normal HER2/CEP 17 ratio, which may also predict response. We sought to examine hyperploid frequency in a well defined Her2 positive MBC population. We also sought to determine the time to progression (TTP) on first chemotherapy for MBC in such women, as well as their overall survival (OS) with MBC. Methods: A tissue mircoarray (TMA) with 3-fold redundancy was constructed using 0.6mm cores from primary or metatstatic paraffin embedded tumor from 124 cases which were Her2 2+ or 3+ by IHC, or amplified by FISH, on pathology report. Four micron thick TMA sections were used for HER2 IHC and HER2 FISH analysis. HER2/CEP 17 ratios of 2.0 or more was considered as amplification. If the tumor was 2+ or 3+ by IHC, greater than or equal to 3 signals for chromosome 17 were seen in a majority of cell nuclei, and the HER2/CEP17 ratio was less than 2.0, the tumor was considered hyperploid Her2 FISH negative. Results: Tissue blocks from 52 tumors delivered clearly interpretable amplification for Her2 by FISH. An additional 10 tumors (8%) were hyperploid, IHC positive (2+ or 3+), and FISH negative. Median survival (Kaplan-Meier) was 39 months (95% CI, 21–62) for women with hyperploid FISH negative tumors and 41 months (95% CI, 25–53) for women with FISH positive tumors (p=0.63, NS, Wilcoxon). Median time to progression (Kaplan-Meier) on first therapy for metastatic disease was 14 months (95% CI, 8–20) for hyperploid FISH negative tumors and 15 months (95% CI, 12–18) for women with FISH positive tumors (p=0.41, NS, Wilcoxon). Conclusions: In this analysis, women with hyperploid Her2 FISH negative IHC positive tumors had similar TTP and OS as women with Her2 FISH positive tumors. These women, although Her2 FISH negative, appeared to respond well to traztuzumab. These provocative results should be repeated on larger data sets.

No significant financial relationships to disclose.

Topoisomerase II-alpha (TOP2A) gene co-amplification does not predict response to therapy and survival in Her-2 neu positive metastatic breast cancer

21108

Background: Preliminary data from a phase III trial of adjuvant traztuzumab (BCIRG, SABCS 2005, abstract 1045) suggested that co-amplification of the genes for HER2 and topisomerase II alpha (TOP2A) on chromosome 17 resulted in improved disease free survival with chemotherapy regimens containing both and anthracycline and traztuzumab. We sought to determine if co-amplification of HER2 and TOP2A was a predictor of response and benefit (or lack thereof) to herceptin containing chemotherapy in the metastatic setting, since few women receive both therapies concurrently for MBC. Methods: A tissue mircoarray (TMA) with 3-fold redundancy was constructed using 0.6mm cores from primary or metatstatic paraffin embedded tumor from 124 cases from Magee-Women's Hospital which were Her2 2+ or 3+ by IHC, or amplified by FISH, on pathology report. Four micron thick TMA sections were used for HER2 immunohistochemical (CB11 monoclonal antibody, Ventana Medical Systems, Tucson, AZ) and HER2 and TOP2A FISH analysis (HER2/CEP 17 and TOP2A/CEP 17 dual color probes from Vysis Inc. Downers Grove, IL). HER2 (or TOP2A) gene to chromosome 17 ratios of 2.0 or more was considered as amplification. Results: Tissue blocks from 52 tumors delivered clearly interpretable amplification for Her2 by FISH on reanalysis. The remaining 72 tumors are undergoing further reanalysis. Of the 52 tumors with Her2 amplification, 15 (29%) had co- amplification of TOP2A. Median survival was 44 months (95% CI, 31–69) for women with TOP2A coamplified tumors and 35 months (95% CI, 29- 63) for women with non-coamplified tumors (p=0.448, NS). Median time to progression on first therapy was 17 months (95% CI, 14–20) for women with TOP2A coamplified tumors and 15 months (95% CI, 12–17) for women with non-coamplified tumors (p=0.939, NS) Conclusions: In this analysis, TOP2A and HER2 gene co-amplification did not correlate with worse TTP on first metatstatic therapy or worse OS from metatstatic disease.

No significant financial relationships to disclose.

Clinical and molecular characteristics of patients with non-amyloid light chain deposition disorders, and outcome following treatment with high-dose melphalan and autologous stem cell transplantation

Light chain deposition disease (LCDD) is caused by a clonal plasma cell disorder in which fragments of monoclonal immunoglobulin light chains form non-fibrillary deposits in various tissues resulting in organ dysfunction. Crystal storing histiocytosis (CSH) is another light chain deposition disorder in which monoclonal light chains form intracytoplasmic crystals. Both are uncommon diseases for which there is limited treatment experience. Between 2003 and 2005, five patients with LCDD and one with CSH were treated at Boston University Medical Center with high-dose melphalan and autologous peripheral blood stem cell transplantation (HDM/SCT). Five of the six patients had predominantly renal involvement, and one patient with LCDD had biopsy-proven deposits in the myocardium. Molecular characterization revealed that the pathologic light chains were kappa in four of the six patients, and sequence analysis revealed unusual germline donor genes and high rates of amino-acid substitutions. One light chain sequence encoded a new potential N-linked glycosylation site, and another showed evidence of antigen selection. All patients are alive and five of the six patients are in complete hematologic remission at a median follow-up of 12 months (range 4-29 months) after HDM/SCT. In our experience, HDM/SCT is a feasible and effective treatment approach for these disorders.

A phase II trial of lenalidomide for patients with AL amyloidosis

7524

Introduction: A phase II trial was designed to evaluate the toxicity and response rate of lenalidomide (Revlimid, CC-5013), alone and in combination with dexamethasone in patients with AL amyloidosis. Patients with this plasma cell disorder have organ dysfunction that makes them more susceptible to drug toxicity. Methods: Planned enrollment, 35 patients. Regimen: 3 cycles of lenalidomide at 25 mg/d for 21d, with dexamethasone 10 mg bid for 4 days, 3 times a month, every other month, for those patients not responding to lenalidomide alone. Toxicity and responses were evaluated after 1, 3, 6, 9, and 12 months of treatment. Hematologic responses were based upon qualitative and quantitative measures of clonal plasma cell disease. Organ responses were scored according to published criteria. Results: 24 patients have been enrolled to date, age range is 47–76, M:F 18:6, κ:λ 7:17. Organ involvement: 75% renal, 38% cardiac, 18% hepatic or gastrointestinal, 17% neuropathy, 13% soft tissue or lymph node. 22 had been treated previously, and 12 had undergone treatment with HDM/SCT. After none of the first 6 patients tolerated 3 treatment cycles at 25 mg/day, the starting dose was reduced to 15 mg/day. A total of 112 cycles have been administered (1–14 cycles per patient). 2 patients were removed from study because of rashes; one because of gout and severe fatigue; one by choice; and one patient died in the first treatment cycle, apparently due to complications of the underlying disease. Grade 3 toxicities observed included fatigue (33%), hypoalbuminemia (29%), worsening performance status (29%), neutropenia (21%), rash (21%), dizziness (13%), gout (13%), dyspnea (8%), muscle weakness (8%), and pneumonia (8%). One patient (4%) had a DVT on lenalidomide and dexamethasone. 8 out of 13 have had a measureable hematologic response, of which 3 were complete or near complete. 8 patients had elevated free light chains (FLC) with a skewed κ:λ ratio, and 4 of these had ≥50% reduction in FLC level. 4 of 14 patients with proteinuria improved. Conclusion: Lenalidomide is reasonably well-tolerated in patients with AL amyloidosis, and alone or in combination with dexamethasone, can induce excellent hematologic responses and improvement in organ disease.

No significant financial relationships to disclose.

Symptom distress, quality of life and challenges of illness according to race and income in women with metastatic breast cancer

8609

Background: Response to a diagnosis of metastatic breast cancer (MBC) may vary according to race and income. The aims of this study were: 1) to identify quality of life, symptom distress and challenges of illness during MBC treatment and 2) to determine if these variables differ according to race and income. Methods: The study was a 2×2 prospective design conducted at an urban breast cancer center. Women with MBC were categorized into four groups based on race and income: white low (WL), white high (WH), African American high (AAH) and African American low (AAL). Instruments were 1) Symptom Distress Scale (SDS), (higher scores /worse distress) 2) Functional Assessment of Cancer Therapy (FACT), (higher scores/better QOL) and a 3) semi structured interview assessing patient perspectives of MBC. Interview analysis utilized grounded theory. Results: Preliminary results are for 51 women. Mean age was 58.2 years, with mean 24 months since MBC diagnosis. Quantitative data indicated worse quality of life in AA than white women. (P=0.06), with AALI women exhibiting worse symptom distress (P=0.03) as compared to white women. Qualitative data (n=48) corroborated quantitative data. The most prevalent themes among all sociodemographic groups were of hope (33/48 - 69%), faith (28/48 - 58%) and progressive loss (29/48, 60%). Each racial/economic delineation expressed unique themes: AALI talked about physical (7/7,100%)and social distress (6/7, 86%) as well as uncertainty regarding “whether treatment was worth it” (6/7 - 86%). WLI women verbalized an overall optimism, describing themselves as “lucky” (6/14 - 43%), with minimization of symptoms (10/14 - 71%). WHI women articulated a sense of betrayal at their progressive illness (9/20 - 45%) and fear of physical and economic dependence. Conclusion: Race and economic delineation brings unique symptom experience, quality of life and patient perspective to the metastatic breast cancer experience. These findings will advise tailored intervention.

[Table: see text]

No significant financial relationships to disclose.

The Drosophila ortholog of vertebrate TRPA1 regulates thermotaxis

Thermotaxis is important for animal survival, but the molecular identities of temperature sensors controlling this behavior have not been determined. We demonstrate dTRPA1, a heat-activated Transient Receptor Potential (TRP) family ion channel, is essential for thermotaxis in Drosophila. dTrpA1 knockdown eliminates avoidance of elevated temperatures along a thermal gradient. We observe dTRPA1 expression in cells without previously ascribed roles in thermosensation and implicate dTRPA1-expressing neurons in mediating thermotaxis. Our data suggest that thermotaxis relies upon neurons and molecules distinct from those required for high-temperature nociception. We propose dTRPA1 may control thermotaxis by sensing environmental temperature.

Expansion of HPCs from cord blood in a novel 3D matrix

BACKGROUND

An optimal system for the expansion of pluripotent HPCs would ideally eliminate the use of cytokines and animal-derived serum. We have shown previously that a 3D, tantalum-coated porous biomaterial (Cytomatrix) supports the maintenance and expansion of human BM HPCs in the absence of cytokines.

METHODS

Umbilical cord blood (UCB) derived HPC were cultured in the Cytomatrix in the absence of exogenous cytokines. Phenotype was determined using FACS. Colony-forming units (CFU) activity was evaluated. Engraftment capacity was evaluated by transplanting the expanded cells into non-obese diabetic (NOD)/SCID mice.

RESULTS

We describe the expansion of HPCs from UCB using the Cytomatrix system. When UCB-derived CD34(+) cells were cultured in the Cytomatrix system for 2 weeks we observed an increase in the number of nucleated cells (3-fold) and CFU (2.6-fold). The number of CD45(+) and CD34(+) cells both increased three-fold. Trends demonstrated an increase in the frequency of CD34(+)C38(-) cells, and an increase in both CD34(+)C33(+) cells and CD34(+)C61(+) cells. No expansion of T or B lymphocytes was observed. When expanded UCB cells from the Cytomatrix were injected into sub-lethally irradiated NOD/SCID mice, human cells were detected in the murine peripheral blood and BM 6 weeks post-transplantation.

DISCUSSION

This unique approach to the expansion of UCB cells in a serum-free, cytokine-free environment may provide expansion of HPCs with multi-lineage engraftment capability that could be used clinically.

Axon targeting meets protein trafficking: Comm takes Robo to the cleaners

Axon guidance at the Drosophila midline relies on dynamic regulation of the guidance receptor Robo by its negative regulator Comm. Recent findings demonstrate that Comm collaborates with the ubiquitin-protein ligase DNedd4 to inhibit Robo signaling by promoting the sorting of Robo into the endocytic pathway.

T-cell differentiation of human and non-human primate CD34+ hematopoietic progenitor cells using porcine thymic stroma

Transplantation of swine thymic tissue has been proposed as an approach to reconstitute the immune system of HIV-infected individuals. This is an attractive strategy because miniature swine are readily available as donors and porcine tissue is resistant to infection with HIV-1. Demonstration that porcine thymus tissue supports primate T-cell differentiation is critical to the ultimate utility of this approach. Using a thymic stroma culture system we have previously described [Rosenzweig M, Marks DF, Zhu H et al. In vitro T lymphopoiesis of human and rhesus CD34+ progenitor cells. Blood 1996; 87: 4040], we demonstrate that porcine thymus tissue is able to promote the in vitro T-lymphocyte differentiation of both human and non-human primate hematopoietic progenitor cells. CD34+ hematopoietic progenitors differentiated into both double positive (CD4+CD8+) and single positive thymocytes expressing CD4 or CD8 alone. A polyclonal T-cell repertoire was evident. In addition, the T cells responded appropriately to mitogen and were permissive to infection with simian immunodeficiency virus (SIV). These data demonstrate the ability of porcine thymus to support T-cell differentiation of both human and non-human hematopoietic progenitor cells and support in vivo studies of transplantation of swine thymic tissue as a strategy for immune reconstitution in AIDS.

Induction of cytotoxic T lymphocyte and antibody responses to enhanced green fluorescent protein following transplantation of transduced CD34(+) hematopoietic cells

Genetic modification of hematopoietic stem cells often results in the expression of foreign proteins in pluripotent progenitor cells and their progeny. However, the potential for products of foreign genes introduced into hematopoietic stem cells to induce host immune responses is not well understood. Gene marking and induction of immune responses to enhanced green fluorescent protein (eGFP) were examined in rhesus macaques that underwent nonmyeloablative irradiation followed by infusions of CD34(+) bone marrow cells transduced with a retroviral vector expressing eGFP. CD34(+) cells were obtained from untreated animals or from animals treated with recombinant human granulocyte colony-stimulating factor (G-CSF) alone or G-CSF and recombinant human stem cell factor. Levels of eGFP-expressing cells detected by flow cytometry peaked at 0.1% to 0.5% of all leukocytes 1 to 4 weeks after transplantation. Proviral DNA was detected in 0% to 17% of bone marrow--derived colony-forming units at periods of 5 to 18 weeks after transplantation. However, 5 of 6 animals studied demonstrated a vigorous eGFP-specific cytotoxic T lymphocyte (CTL) response that was associated with a loss of genetically modified cells in peripheral blood, as demonstrated by both flow cytometry and polymerase chain reaction. The eGFP-specific CTL responses were MHC-restricted, mediated by CD8(+) lymphocytes, and directed against multiple epitopes. eGFP-specific CTLs were able to efficiently lyse autologous CD34(+) cells expressing eGFP. Antibody responses to eGFP were detected in 3 of 6 animals. These data document the potential for foreign proteins expressed in CD34(+) hematopoietic cells and their progeny to induce antibody and CTL responses in the setting of a clinically applicable transplantation protocol. (Blood. 2001;97:1951-1959)

Cytokine-augmented culture of haematopoietic progenitor cells in a novel three-dimensional cell growth matrix

Studies aimed at the in vitro expansion of haematopoietic progenitor cells (HPCs) have suffered from the conflict of increasing cell numbers while maintaining long-term repopulating ability. We have developed a long-term bone marrow bioreactor culture system resembling the marrow-microenvironment that cultures HPCs in an inert, three-dimensional, porous biomatrix termed Cellfoam. Previous studies have shown that the short-term culture of CD34(+)cells in Cellfoam improved the maintenance and multipotency of haematopoietic stem cells compared to cells cultured on plastic dishes. In this study, we examined the effects of low concentrations of cytokines including stem cell factor (SCF), IL-3, and Flk-2/Flt-3 ligand, on the maintenance, preservation and multipotency of CD34(+) cells cultured for 3 or 6 weeks in Cellfoam. Analysis of cell yields using flow cytometry showed that in SCF and Flk-2/Flt-3 ligand-supplemented cultures as well as cytokine-free cultures, a higher number of CD45(+)34(+) and CD45(+)34(+)38(-) cells is observed in Cellfoam cultures as compared to plastic cultures. The function of cultured cells was evaluated in colony-forming assays. The data demonstrate that Cellfoam cultures supplemented with SCF and Flk-2/Flt-3 ligand resulted in a higher output of colony activity compared to plastic cultures. Analysis of CAFC (29 days) activity also demonstrated that primitive progenitors were maintained to a greater extent in Cellfoam cultures containing either no cytokines or low concentrations of early-acting cytokines. These data suggest that culture of HPCs in three-dimensional bioreactors such as Cellfoam for extended periods may benefit from the addition of low levels of early-acting cytokines, including SCF and Flk-2/Flt-3 ligand, resulting in high yields of cells that are enriched for multipotent haematopoietic progenitors. These findings demonstrate that a three-dimensional matrix promotes the survival of primitive HPCs in culture and may modulate the in vitro effects of cytokines.