Novel PPFIA1-ALK, ALK-C2orf91(intergenic) double-fusion responded well to alectinib in an advanced lung adenocarcinoma patient: a case report

Non-small cell lung cancers (NSCLCs) with anaplastic lymphoma kinase (ALK)-rearrangement have favorable responses to ALK inhibitors. However, ALK fusion mutations harbored approximately 90 distinct fusion partners. Patients with different ALK fusions might respond distinctly to different-generation ALK inhibitors. In this case report, we identified a novel non-reciprocal ALK fusion, ALK-C2orf91(intergenic) (A19: intergenic) and PPFIA1-ALK (P2:A20), by next-generation DNA sequencing in an advanced lung adenocarcinoma patient. After 2 months of alectinib, the targeted lung lesion regressed significantly, and evaluation of therapeutic efficiency indicated partial response. To date, the patient had achieved 12 months of progression-free survival from alectinib treatment. Our study extended the spectrum of ALK fusion partners in ALK-positive NSCLC, and we reported a new ALK fusion, PPFIA1-ALK and ALK-C2orf91(intergenic), and its sensitivity to alectinib firstly in lung cancer. We believe that this case report has an important clinical reference.


Introduction
ALK gene rearrangement is one of the most important driver mutations in non-small cell lung cancer (NSCLC) occurring in 3%-7% of the cases (1).Echinoderm microtubuleassociated protein-like 4 (EML4)-ALK is the most common fusion variant, accounting for over 80% of fusion partners.With the increasing coverage of next-generation DNA sequencing, more than 90 rare ALK fusion subtypes have been discovered in NSCLC, such as kinesin family member 5B (KIF5B)-ALK and striatin gene (STRN)-ALK (2).Firstto third-generation anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs), including crizotinib, alectinib, and ceritinib, have brought outstanding efficacy and tolerability to patients (3)(4)(5).However, for the newly discovered fusion variants, especially those EML4-ALK fusion mutations, it is necessary to evaluate the clinical effectiveness of ALK-TKI in the first line or even the posterior line, and it is helpful to infer possible new therapeutic measures in the face of diverse rare fusion targets.Here, an advanced lung adenocarcinoma patient with PPFIA1-ALK and ALK-C2orf91(intergenic) double-fusion variants is sensitive to first-line alectinib.

Case presentation
A 46-year-old non-smoking Chinese man, without a family history of genetic disease, presented to another hospital in June 2022, with a cough for over 1 month and shortness of breath for approximately 10 days.A computed tomography (CT) scan revealed hydropneumothorax, compression atelectasis (approximately 80% collapse) and tumor mass of the right lung, and multiple nodules in the left lung (Figure 1A).He received pleural space drainage, and malignant cells were found in the pleural effusion.Then, he visited our hospital for further treatment.The pathologic results of ultrasound-guided percutaneous lung biopsy showed infiltrating growth of the allotypic glandular duct (Figure 2A), and the lesions tend to be pulmonary adenocarcinoma, with strongly positive expression for thyroid CK7, TTF-1, and Napsin A and negative for CK5/6, P40, and P60 as assayed by immunohistochemical staining.Bone scan, brain CT scan, and ultrasonography of the abdominal system, urinary system, and cardiovascular system identified no evidence of metastatic disease.Consequently, the patient was diagnosed with right lung adenocarcinoma with pleural metastasis (cT4N0M1a, stage IVa).To identify targetable mutations, the tumor biopsy specimen was sequenced by capture-based next-generation DNA sequencing with a panel containing 73 cancer-related genes ( (6) gene list is shown in Supplementary Table 1, Beijing Geneplus Technology Co., Ltd.).The mean effective depth of coverage of the sequence was 2,032×.Non-reciprocal ALK fusion PPFIA1-ALK (P2: A20) (abundance, 10%) and ALK-C2orf91 (A19, intergenic) (abundance, 13%) was identified in tissue (Figure 3).No other gene mutation was detected.Immunohistochemistry staining revealed that the tumor had positive expression for ALK with the Ventana D5F3 (Figure 2B).Therefore, based on guidelines and clinical studies, combined with the patient's wishes, he received alectinib (600 mg twice daily) as first-line therapy on July 15, 2022.
After 2 months of alectinib therapy, a follow-up CT scan found the right lung tumor remarkably reduced, thus achieving a partial response based on Response Evaluation Criteria in Solid Tumors [RECIST] version 1.1 (Figure 1B).Follow-up CT scans at 9 months and 12 months showed reduced stable disease (Figures 1C, D).At the cutoff date of this study, the patient had been receiving alectinib for 12 months with no complaints of discomfort and no adverse effects.

Discussion
In summary, this is the first case to describe a novel PPFIA1-ALK and ALK-C2orf91 (intergenic) double-fusion lung adenocarcinoma patient who is sensitive to alectinib.Multiple ALK types have been reported in NSCLC patients, among which different fusion partners and different breakpoint variants may affect the response to ALK-TKIs (7,8).Previous reports described that HIP1-ALK (H21:A20) and HIP1-ALK (H30:A20) responded well to crizotinib (9, 10), while HIP1-ALK (H19:A20) showed resistance to crizotinib with progression of pleural effusion (8).Therefore, determining the efficacy of different ALK fusions to different ALK inhibitors is vital for personalized therapeutic decision-making.
As far as we know, PPFIA1-ALK fusion has not been reported in lung cancer before.PPFIA1 is a putative invasion suppressor gene located in the 11q13 region, while ALK is located in the short arm of chromosome 2. Amplification and overexpression of PPFIA1 were reported to be associated with poor prognosis in breast cancer (11).In the current case, exon 2 of the PPFIA1 gene rearranged with exon 20 of the ALK gene to form a new fusion gene, PPFIA1-ALK.
Although there is no direct evidence to support PPFIA1-ALK as a driver mutation, considering that PPFIA1 has been reported to be highly expressed in lung tissues (12), there is a possibility that PPFIA1-ALK rearrangement is a driver mutation.
According to the global ALEX study, alectinib showed superior progression-free survival (PFS) versus crizotinib in untreated EML4-ALK fusion NSCLC, irrespective of the EML4-ALK variant (13).For patients with 3′-ALK fusion, the retention of 5′-ALK fusion was defined as non-reciprocal fusion, which was predictive for worse PFS at first-line crizotinib (14).Therefore, ALK-C2orf91 (A19: intergenic) as 5′-ALK and PPFIA1-ALK (P2:A20) as 3′-ALK in our case were defined together as a non-reciprocal ALK fusion.Zeng reported an NSCLC patient with non-reciprocal ALK fusion after resistance to first-line gefitinib who responded to alectinib and had a PFS of more than 26 months.Similar to the previous report, the patient in the present case was also sensitive to alectinib and had been receiving alectinib for 12 months.

Conclusions
In summary, this case presented a rare novel non-reciprocal PPFIA1-ALK and ALK-C2orf91 (intergenic) double-fusion sensitive to first-line alectinib.

FIGURE 1
FIGURE 1 Dynamic imaging of lung lesions at different stages of treatment.(A) Lung lesions at diagnosis.(B) After targeted therapy with alectinib for 2 months, the right lung tumor was significantly reduced, resulting in partial response (PR).(C) After targeted therapy with alectinib for 9 months, the tumor in the right lung continued to shrink.(D) After targeted therapy with alectinib for 12 months, the right lung tumor tends to be stable.

3
FIGURE 3 Identification of PPFIA1-ALK and ALK-C2orf91(intergenic) double-fusion variants by next-generation sequencing.(A) Sequencing reads of PPFIA1-ALK were visualized by the Integrative Genomics Viewer (IGV).(B) The schematic structure of the genomic DNA sequence shows the PPFIA1-ALK fusion points.(C) Sequencing reads of ALK-C2orf91(intergenic) were visualized by the IGV.(D) The schematic structure of the genomic DNA sequence shows the ALK-C2orf91(intergenic) fusion points.