Differential prognosis of single and multiple TP53 abnormalities in high-count MBL and untreated CLL

TP53 aberrations, including mutations and deletion of 17p13, are important adverse prognostic markers in chronic lymphocytic leukemia (CLL) but are less studied in high count monoclonal B-cell lymphocytosis (HCMBL), an asymptomatic pre-malignant stage of CLL. Here we estimated the prevalence and impact of TP53 aberrations in 1,230 newly diagnosed treatment-naïve individuals (849 CLL, 381 HCMBL). We defined TP53 state as: wild-type (no TP53 mutations and normal 17p), single-hit (del(17p) or one TP53 mutation), or multi-hit (TP53 mutation and del(17p), TP53 mutation and loss of heterozygosity, or multiple TP53 mutations). Cox regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for time to first treatment and overall survival by TP53 state. We found 64 (7.5%) CLL patients and 17 (4.5%) HCMBL individuals had TP53 mutations with variant allele fraction >10%. Del(17p) was present in 58 (6.8%) of CLL and 11 (2.9%) of HCMBL cases. Most individuals had wild-type (N=1,128, 91.7%) TP53 state, followed by multi-hit (N=55, 4.5%) and then single-hit (N=47, 3.8%) TP53 state. The risk of shorter time to therapy and death increased with the number of TP53 abnormalities. Compared to wild-type patients, multi-hit patients had 3-fold and single-hit patients had 1.5-fold increased risk of requiring therapy. Multi-hit patients also had 2.9-fold increased risk of death compared to wild-type. These results remained stable after accounting for other known poor prognostic factors. Both TP53 mutations and del(17p) may provide important prognostic information for HCMBL and CLL that would be missed if only one were measured.

Integrated analysis of next generation sequencing minimal residual disease (MRD) and PET scan in transplant eligible myeloma patients

Minimal residual disease (MRD) assays allow response assessment in patients with multiple myeloma (MM), and negativity is associated with improved survival outcomes. The role of highly sensitive next generation sequencing (NGS) MRD in combination with functional imaging remains to be validated. We performed a retrospective analysis on MM patients who underwent frontline autologous stem cell transplant (ASCT). Patients were evaluated at day 100 post-ASCT with NGS-MRD and positron emission tomography (PET-CT). Patients with ≥ 2 MRD measurements were included in a secondary analysis for sequential measurements. 186 patients were included. At day 100, 45 (24.2%) patients achieved MRD negativity at a sensitivity threshold of 10-6. MRD negativity was the most predictive factor for longer time to next treatment (TTNT). Negativity rates did not differ according to MM subtype, R-ISS Stage nor cytogenetic risk. PET-CT and MRD had poor agreement, with high rates of PET-CT negativity in MRD-positive patients. Patients with sustained MRD negativity had longer TTNT, regardless of baseline risk characteristics. Our results show that the ability to measure deeper and sustainable responses distinguishes patients with better outcomes. Achieving MRD negativity was the strongest prognostic marker and could help guide therapy-related decisions and serve as a response marker for clinical trials.

Response to COVID-19 vaccination post CAR T therapy in patients with non-Hodgkin lymphoma and multiple myeloma

COVID-19 adversely affects individuals with cancer. Several studies have found that seroconversion rates among patients with hematologic malignancies are suboptimal when compared to patients without cancer. Patients with non-Hodgkin lymphoma (NHL) and multiple myeloma (MM) are immunocompromised due to impaired humoral and cellular immunity in addition to prescribed immunosuppressive therapy. Chimeric antigen receptor T-cell (CAR T) therapy is now widely used for NHL and MM, but little is known about seroconversion rates after COVID-19 vaccination among these populations. We evaluated SARS-CoV-2 spike-binding IgG antibody levels following COVID-19 vaccination among NHL and MM CAR T therapy recipients. Out of 104 CAR T infusions, 19 patients developed known COVID-19 infection post-CAR T. We tested 17 patients that received CAR T for antibody spike titers post COVID-19 vaccination, only 29 % (n = 5) were able to mount a clinically relevant antibody response (>250 IU/mL).

Bone marrow oxalosis with pancytopenia in a patient with short bowel syndrome: Report of a case and review of the literature

Systemic oxalosis is a condition in which calcium oxalate crystals deposit into various bodily tissues. Although this may occur as the result of a rare primary syndrome in which an error of glyoxylate metabolism causes an overproduction of oxalate, it is more often seen as a secondary process characterized by increased enteric oxalate absorption. Here, we describe a patient with short bowel syndrome on long-term parenteral nutrition support who developed a unique manifestation of systemic oxalosis, leading to deposition of oxalate crystals within the bone marrow contributing to pancytopenia. In this report, in addition to reviewing the literature on this presumably rare manifestation of oxalosis, we also discuss its pathogenesis in the setting of short bowel syndrome and its management, including prevention.

Abstract 3352: Identifying copy number variations in chronic lymphocytic leukemia using targeted next generation sequencing

Chronic lymphocytic leukemia (CLL) is characterized by multiple copy number abnormalities (CNVs) with prognostic value. Identifying these structural variations is central to defining CLL pathogenesis, risk stratification, and therapeutic approaches. Fluorescence in situ hybridization (FISH) is the clinical gold standard in detecting prognostic CNVs in CLL. However, next-generation sequencing (NGS) techniques have become more readily available for clinical genomic applications and can also be used to identify CNVs. Here we present bioinformatic methods to accurately identify CNVs in CLL using NGS data.

We used the CNV-calling algorithm PatternCNV to detect clinically relevant CNVs: deletion 17p13 [del(17p)], deletion 11q23 [del(11q)], deletion 13q14 [del(13q)], and trisomy 12. PatternCNV was run on 2274 samples (1500 somatic and 774 germline samples) from six different sequencing batches, screened using a targeted sequencing panel that covers all exons of 59 recurrently CLL mutated genes and additional amplicons covering the minimal affected regions of relevant CNVs. To correct for potential batch effects, PatternCNV was initially run to quantify exon coverage behavior without the chromosomes containing recurrent CNV events, 11, 12, 13, and 17. Principal component analyses and correlation matrices were analyzed, grouping the samples into four distinct clusters that contain similar exon coverage patterns. Samples in each of the four clusters were then independently re-run through PatternCNV using all chromosomes. Visual analysis of CNV plots revealed a bias in normalization. To correct this, the log2ratios were corrected to center the log ratio on the median coverage. Sample noisiness was calculated from the difference in the median absolute deviation (DiffMAD) and samples with a DiffMAD score greater than 0.3 were excluded. All CNV analyses were blinded to clinical FISH results.

The effectiveness of our CNV calling was evaluated in 522 CLL patients who had FISH conducted within three months of the sample date. We excluded samples with low tumor metrics identified by FISH (less than 20% of cells with either del(17p), del(11q), trisomy 12 or del(13q)). When we compared our CNV analyses with the FISH data, we found high concordance 99.6% for del(17p), 97.5% for del(11p), 99.1% for trisomy 12, and 93.7% for del(13q). N=46 total discordant pairs were identified, with the highest discordance for del(13q), N=28, followed by del(11q), N=12.

These novel bioinformatic methods allow for accurate detection of CNVs across NGS sequencing batches. The high concordance in detecting CNVs between targeted NGS and the gold standard of FISH, suggest NGS is an accurate tool for calling CNVs in CLL. Further, NGS can infer clinically relevant CNVs in genomic locations not targeted by FISH.

Citation Format: Chantal E. McCabe, Erik Jessen, Daniel R. O'Brien, Julia E. Wiedmeier-Nutor, Susan L. Slager, Esteban Braggio. Identifying copy number variations in chronic lymphocytic leukemia using targeted next generation sequencing [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 3352.

Outcomes of COVID-19 in Patients With Cancer: A Closer Look at Pre-Emptive Routine Screening Strategies

PURPOSE

The benefit of routine pre-emptive screening for severe acute respiratory syndrome coronavirus 2 infections in patients with cancer before cancer-directed therapies is unclear. Herein, we characterize the outcomes of a cohort of patients with cancer who were diagnosed with COVID-19 by routine screening (RS) in comparison with those diagnosed on the basis of clinical suspicion or exposure history (nonroutine screening [NRS]).

METHODS

A multisite prospective observational study was conducted at three major and five satellite campuses of the Mayo Clinic Cancer Center between March 18 and July 31, 2020. The primary outcome was COVID-19-related hospital admission. Secondary outcomes included intensive care unit admissions and all-cause mortality.

RESULTS

Five thousand four hundred fifty-two patients underwent RS in the outpatient setting only, and 44 (0.81%) were diagnosed with COVID-19. RS detected 19 additional patients from the scheduled inpatient admissions for surgical or interventional procedures or inpatient chemotherapy. One hundred sixty-one patients were diagnosed with COVID-19 on the basis of NRS. COVID-19-related hospitalization rate (17.5% v 26.7%; P = .14), intensive care unit admission (1.6% v 5.6%; P = .19), and mortality (4.8% v 3.7%; P = .72) were not significantly different between the RS and NRS groups. In the multivariable analysis, age ≥ 60 years (odds ratio, 4.4; P = .023) and an absolute lymphocyte count ≤ 1.4 × 10⁹/L (odds ratio, 9.2; P = .002) were independent predictors of COVID-19-related hospital admission.

CONCLUSION

The COVID-19 positivity rate was low on the basis of RS. Comparing the hospital admission and mortality outcomes with the NRS cohort, there were no significant differences. The value of routine pre-emptive screening of asymptomatic patients with cancer for COVID-19 remains low.