BioMarin Pharmaceuticals (BMRN) - Get Report is entering a crucial two-month period in which the company's ability to internally develop new treatments for rare diseases will come under renewed investor scrutiny.

BioMarin on Wednesday will present full results from a clinical trial involving children with a type of Batten's disease, a fatal neurodegenerative disorder. If the data on BioMarin's drug are positive, the company intends to file for U.S. and European approval in the middle of the year.

Later in March, BioMarin expects to announce results from a pivotal, phase III study of a new drug for phenylketonuria. In April, the company is holding a research meeting for investors that will focus on clinical updates from two drug development programs addressing dwarfism and a gene therapy for hemophilia.

If the clinical updates on four pipeline programs go well over the next two months, BioMarin could have two new rare disease drugs on the market in 2017 with two more products, each with blockbuster sales potential, moving toward approval. Investors might finally start to forget and forgive the Food and Drug Administration drisapersen rejection debacle of January and focus on the company's future.

The company's shares are down 20% this year and 45% off their all-time peak last year.

BioMarin needs to show investors a clear path to solid profitability. Revenue grew 19% to just under $890 million in 2015 but the company is still spending a lot and losing money. In 2016, BioMarin expects revenue to top $1 billion but adjusted losses will still be in the range of $75 million to $100 million.

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BioMarin believes it can reach break-even or modest profitability in 2017 by managing expenses and achieving modest sales growth from its existing rare disease drugs. But good news from the pipeline over the next two months could have investors -- and potential acquirers -- gaining confidence in lot more growth in 2017 and beyond.

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The BioMarin drug in the spotlight Wednesday is cerliponase alfa, an enzyme replacement therapy for children with CLN2 disorder, a form of Batten's Disease caused by an inherited mutation in the CLN2 gene. The CLN2 gene directs production of an enzyme known as TPP1 needed to remove certain proteins and lipids from nerve cells. When the CLN2 gene is mutated, deficient TPP1 is unable to clear these toxic waste products from the nerve cells.

Kids with CLN2 disorder look healthy at birth but by the age of 3 start to lose the ability to speak and walk. The disease progresses fairly rapidly and most patients die at approximately at 12 years old. BioMarin believes the disease affects approximately 1,200 to 1,600 children worldwide.

Cerliponase alfa is designed to replace the defective TPP1 enzyme so that the body can remove the toxic proteins and lipids from nerve cells.

BioMarin's clinical trial enrolled 24 patients with early to moderate CLN2 disease. All the patients are treated with cerliponase alfa. The primary endpoint measures change over one year in the ability to walk and talk on a six-point scale. (Normal function is six points, with the walk/talk score dropping as patients lose function over time). 

Preliminary, six-month results from this study were announced in January 2015, showing six of nine patients with stable walk/talk scores and the remaining three patients with decreases of one point or less. A continuation of disease stabilization with more patients over one year is what the company and investors are hoping to see.

However, interpreting the cerliponase alfa study results is complicated by the lack of a control arm. The company is relying on natural history data showing CLN2 patients lose approximately one point on the walk/talk scale every six months.

Whether or not FDA will accept a single-arm study as the basis for an approval, even for a rare and fatal childhood disease, is an issue likely to cause concern for investors, especially since the same strategy has blown up in the face of Sarepta Therapeutics (SRPT) - Get Report so far.

Adam Feuerstein writes regularly for TheStreet. In keeping with company editorial policy, he doesn't own or short individual stocks, although he owns stock in TheStreet. He also doesn't invest in hedge funds or other private investment partnerships. Feuerstein appreciates your feedback; click here to send him an email.